Multiple sequence alignment - TraesCS1A01G418800

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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 TraesCS1A01G418800 chr1A 100.000 2738 0 0 1 2738 575871791 575874528 0.000000e+00 5057
1 TraesCS1A01G418800 chr1D 92.727 935 55 5 1193 2119 479596770 479597699 0.000000e+00 1338
2 TraesCS1A01G418800 chr1D 92.895 563 32 5 36 596 479595590 479596146 0.000000e+00 811
3 TraesCS1A01G418800 chr1D 90.017 591 32 11 622 1191 479596133 479596717 0.000000e+00 739
4 TraesCS1A01G418800 chr2A 97.424 621 15 1 2118 2738 104997973 104997354 0.000000e+00 1057
5 TraesCS1A01G418800 chr2A 96.457 621 22 0 2118 2738 98603030 98602410 0.000000e+00 1026
6 TraesCS1A01G418800 chr2A 95.032 624 23 5 2118 2738 17213178 17213796 0.000000e+00 974
7 TraesCS1A01G418800 chr4A 96.613 620 21 0 2119 2738 641519222 641518603 0.000000e+00 1029
8 TraesCS1A01G418800 chr4A 82.742 423 58 9 1700 2118 646311167 646311578 2.000000e-96 363
9 TraesCS1A01G418800 chr5D 95.813 621 23 2 2119 2738 515096299 515096917 0.000000e+00 1000
10 TraesCS1A01G418800 chr5D 84.841 409 50 8 1709 2113 11211378 11210978 4.250000e-108 401
11 TraesCS1A01G418800 chr7D 95.330 621 26 2 2119 2738 636818043 636817425 0.000000e+00 983
12 TraesCS1A01G418800 chr7D 84.524 420 48 8 1708 2110 388999208 388998789 1.530000e-107 399
13 TraesCS1A01G418800 chr3D 95.185 623 27 2 2117 2738 569837308 569837928 0.000000e+00 981
14 TraesCS1A01G418800 chr3D 89.024 410 42 3 1704 2113 393010451 393010045 3.150000e-139 505
15 TraesCS1A01G418800 chr6B 94.847 621 29 2 2118 2738 55691817 55691200 0.000000e+00 966
16 TraesCS1A01G418800 chr6D 94.847 621 27 3 2119 2736 6359950 6360568 0.000000e+00 965
17 TraesCS1A01G418800 chr1B 94.118 595 25 6 1 594 667823555 667824140 0.000000e+00 896
18 TraesCS1A01G418800 chr1B 89.060 585 47 6 622 1191 667824129 667824711 0.000000e+00 710
19 TraesCS1A01G418800 chr1B 86.200 529 46 12 1193 1703 667824765 667825284 5.150000e-152 547
20 TraesCS1A01G418800 chr3A 89.583 336 33 2 1780 2115 512580206 512579873 2.520000e-115 425
21 TraesCS1A01G418800 chr7A 83.571 420 51 8 1708 2110 439634967 439634549 7.160000e-101 377
22 TraesCS1A01G418800 chr3B 84.478 393 48 8 1710 2102 704295540 704295161 2.570000e-100 375
23 TraesCS1A01G418800 chr7B 83.255 424 50 10 1706 2110 384202897 384202476 1.200000e-98 370


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 TraesCS1A01G418800 chr1A 575871791 575874528 2737 False 5057.000000 5057 100.000000 1 2738 1 chr1A.!!$F1 2737
1 TraesCS1A01G418800 chr1D 479595590 479597699 2109 False 962.666667 1338 91.879667 36 2119 3 chr1D.!!$F1 2083
2 TraesCS1A01G418800 chr2A 104997354 104997973 619 True 1057.000000 1057 97.424000 2118 2738 1 chr2A.!!$R2 620
3 TraesCS1A01G418800 chr2A 98602410 98603030 620 True 1026.000000 1026 96.457000 2118 2738 1 chr2A.!!$R1 620
4 TraesCS1A01G418800 chr2A 17213178 17213796 618 False 974.000000 974 95.032000 2118 2738 1 chr2A.!!$F1 620
5 TraesCS1A01G418800 chr4A 641518603 641519222 619 True 1029.000000 1029 96.613000 2119 2738 1 chr4A.!!$R1 619
6 TraesCS1A01G418800 chr5D 515096299 515096917 618 False 1000.000000 1000 95.813000 2119 2738 1 chr5D.!!$F1 619
7 TraesCS1A01G418800 chr7D 636817425 636818043 618 True 983.000000 983 95.330000 2119 2738 1 chr7D.!!$R2 619
8 TraesCS1A01G418800 chr3D 569837308 569837928 620 False 981.000000 981 95.185000 2117 2738 1 chr3D.!!$F1 621
9 TraesCS1A01G418800 chr6B 55691200 55691817 617 True 966.000000 966 94.847000 2118 2738 1 chr6B.!!$R1 620
10 TraesCS1A01G418800 chr6D 6359950 6360568 618 False 965.000000 965 94.847000 2119 2736 1 chr6D.!!$F1 617
11 TraesCS1A01G418800 chr1B 667823555 667825284 1729 False 717.666667 896 89.792667 1 1703 3 chr1B.!!$F1 1702

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
957 965 0.038067 TGAACTTGCATGCATGTGCC 60.038 50.0 32.44 26.49 44.43 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2067 0.179073 CTCAACCTCCACTATGGCCG 60.179 60.0 0.0 0.0 37.47 6.13 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
83 84 5.528690 TGCTAATGAAATGAGACCAGCATAC 59.471 40.000 0.00 0.00 33.15 2.39
86 87 4.142609 TGAAATGAGACCAGCATACCTC 57.857 45.455 0.00 0.00 0.00 3.85
115 116 2.231964 ACACGTGGCTAATTTCTACGGA 59.768 45.455 21.57 0.00 38.92 4.69
120 121 4.189231 GTGGCTAATTTCTACGGACATGT 58.811 43.478 0.00 0.00 0.00 3.21
131 132 0.390603 CGGACATGTTTACCCGCTGA 60.391 55.000 10.37 0.00 35.29 4.26
132 133 1.816074 GGACATGTTTACCCGCTGAA 58.184 50.000 0.00 0.00 0.00 3.02
304 305 4.772886 AGTTAGGGCCTAAGGTACAATG 57.227 45.455 26.03 0.00 0.00 2.82
406 408 4.753186 TGAACTCTCTTCCTCCTTAACCT 58.247 43.478 0.00 0.00 0.00 3.50
445 447 2.027745 TCTCACACTTGCTCATCCTTCC 60.028 50.000 0.00 0.00 0.00 3.46
586 588 0.994263 GCCGCAATGTGATTTTCTGC 59.006 50.000 0.00 0.00 0.00 4.26
587 589 1.403249 GCCGCAATGTGATTTTCTGCT 60.403 47.619 0.00 0.00 0.00 4.24
588 590 2.523015 CCGCAATGTGATTTTCTGCTC 58.477 47.619 0.00 0.00 0.00 4.26
589 591 2.163010 CCGCAATGTGATTTTCTGCTCT 59.837 45.455 0.00 0.00 0.00 4.09
590 592 3.423571 CGCAATGTGATTTTCTGCTCTC 58.576 45.455 0.00 0.00 0.00 3.20
591 593 3.126514 CGCAATGTGATTTTCTGCTCTCT 59.873 43.478 0.00 0.00 0.00 3.10
592 594 4.660105 GCAATGTGATTTTCTGCTCTCTC 58.340 43.478 0.00 0.00 0.00 3.20
593 595 4.395542 GCAATGTGATTTTCTGCTCTCTCT 59.604 41.667 0.00 0.00 0.00 3.10
594 596 5.447548 GCAATGTGATTTTCTGCTCTCTCTC 60.448 44.000 0.00 0.00 0.00 3.20
595 597 5.680594 ATGTGATTTTCTGCTCTCTCTCT 57.319 39.130 0.00 0.00 0.00 3.10
596 598 5.070770 TGTGATTTTCTGCTCTCTCTCTC 57.929 43.478 0.00 0.00 0.00 3.20
597 599 4.771577 TGTGATTTTCTGCTCTCTCTCTCT 59.228 41.667 0.00 0.00 0.00 3.10
598 600 5.105797 TGTGATTTTCTGCTCTCTCTCTCTC 60.106 44.000 0.00 0.00 0.00 3.20
599 601 5.126061 GTGATTTTCTGCTCTCTCTCTCTCT 59.874 44.000 0.00 0.00 0.00 3.10
600 602 5.357878 TGATTTTCTGCTCTCTCTCTCTCTC 59.642 44.000 0.00 0.00 0.00 3.20
601 603 4.574674 TTTCTGCTCTCTCTCTCTCTCT 57.425 45.455 0.00 0.00 0.00 3.10
602 604 3.827008 TCTGCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
603 605 3.378512 TCTGCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
604 606 3.386078 TCTGCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
605 607 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
606 608 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
607 609 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
608 610 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
609 611 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
610 612 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
611 613 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
612 614 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
613 615 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
614 616 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
615 617 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
616 618 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
617 619 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
618 620 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
619 621 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
620 622 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
621 623 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
622 624 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
623 625 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
639 641 6.640518 TCTCTCTCTCTCTCTCTCTTTGTAC 58.359 44.000 0.00 0.00 0.00 2.90
747 753 5.883115 TGAACCAGACAGACAATGTTGTAAA 59.117 36.000 0.00 0.00 44.17 2.01
757 763 6.918022 CAGACAATGTTGTAAAAAGGGAGTTC 59.082 38.462 0.00 0.00 42.43 3.01
762 768 3.457610 TGTAAAAAGGGAGTTCGACGT 57.542 42.857 0.00 0.00 0.00 4.34
765 771 4.278170 TGTAAAAAGGGAGTTCGACGTAGA 59.722 41.667 0.00 0.00 0.00 2.59
864 870 2.037847 GGGAGTGCCATGCCCTTT 59.962 61.111 0.00 0.00 38.85 3.11
893 900 5.903810 AGTCTAACACGAAAAGTTGAGAGT 58.096 37.500 0.00 0.00 0.00 3.24
897 904 4.386867 ACACGAAAAGTTGAGAGTGAGA 57.613 40.909 0.00 0.00 34.16 3.27
941 949 5.000591 TCAAATTCTAACAGCATCGGTGAA 58.999 37.500 0.00 0.00 34.87 3.18
954 962 0.241749 CGGTGAACTTGCATGCATGT 59.758 50.000 28.16 28.16 36.13 3.21
955 963 1.705256 GGTGAACTTGCATGCATGTG 58.295 50.000 32.44 22.22 35.06 3.21
957 965 0.038067 TGAACTTGCATGCATGTGCC 60.038 50.000 32.44 26.49 44.43 5.01
958 966 1.074319 GAACTTGCATGCATGTGCCG 61.074 55.000 32.44 15.24 44.43 5.69
986 1008 5.957771 TCTATAAATAGGGCATAGCTGGG 57.042 43.478 0.00 0.00 0.00 4.45
1002 1024 2.822215 GGGACGCTATCTTCCCAGA 58.178 57.895 3.33 0.00 46.94 3.86
1030 1052 1.536766 TGCAAAGCTCCATCGAACTTG 59.463 47.619 0.00 0.00 0.00 3.16
1061 1083 3.094572 AGCATAGAAATGGCTGCAAAGT 58.905 40.909 0.50 0.00 37.09 2.66
1062 1084 4.272489 AGCATAGAAATGGCTGCAAAGTA 58.728 39.130 0.50 0.00 37.09 2.24
1078 1100 0.984995 AGTACCCACTTCTCCTTGGC 59.015 55.000 0.00 0.00 0.00 4.52
1122 1144 1.381191 TCTCCCAGGATGTAGCGCA 60.381 57.895 11.47 0.00 0.00 6.09
1128 1150 0.812811 CAGGATGTAGCGCATGCAGT 60.813 55.000 19.57 6.24 46.68 4.40
1136 1158 1.153449 GCGCATGCAGTAGGTGGTA 60.153 57.895 19.57 0.00 42.15 3.25
1169 1191 4.911514 ACCGCAAAACTGTTAAGAACAT 57.088 36.364 0.00 0.00 41.26 2.71
1176 1198 7.193595 GCAAAACTGTTAAGAACATGTAGTGT 58.806 34.615 0.00 0.00 44.84 3.55
1191 1213 8.615878 ACATGTAGTGTTGCTAGTTAATTGAA 57.384 30.769 0.00 0.00 38.01 2.69
1220 1294 9.632638 ATTGAATAGGACATATTGCTAAGTTGT 57.367 29.630 0.00 0.00 34.10 3.32
1243 1317 1.094073 CAGCCTGCAGGTGCTATGTC 61.094 60.000 32.81 14.22 42.66 3.06
1251 1325 5.185828 CCTGCAGGTGCTATGTCTATATGTA 59.814 44.000 25.53 0.00 42.66 2.29
1293 1369 1.739466 TCCATGCAGAAGAAACGATGC 59.261 47.619 0.00 0.00 39.14 3.91
1334 1410 1.673767 ATAGTGGATATGGGCCTGGG 58.326 55.000 4.53 0.00 0.00 4.45
1339 1415 1.677552 GATATGGGCCTGGGTACGG 59.322 63.158 4.53 0.00 0.00 4.02
1411 1493 1.443407 GCAGCGGCTATCCTTGAGA 59.557 57.895 0.26 0.00 36.96 3.27
1420 1502 5.064452 GCGGCTATCCTTGAGATGAATATTG 59.936 44.000 0.00 0.00 36.33 1.90
1438 1520 2.519780 TGGGGTGGCGGTCAAAAC 60.520 61.111 0.00 0.00 0.00 2.43
1443 1525 2.124653 TGGCGGTCAAAACGGTGT 60.125 55.556 0.00 0.00 0.00 4.16
1444 1526 2.181521 TGGCGGTCAAAACGGTGTC 61.182 57.895 0.00 0.00 0.00 3.67
1526 1608 3.128068 TCATCTGCTCGAGCGTTTACTTA 59.872 43.478 30.75 11.10 45.83 2.24
1536 1618 3.094572 AGCGTTTACTTACTAGCAGGGA 58.905 45.455 0.00 0.00 0.00 4.20
1604 1689 4.888038 TGCATGACATATGCTGACTTTC 57.112 40.909 12.45 0.00 44.79 2.62
1719 1816 9.708092 CTATACTAGTTTAGGGCATTTCTAACC 57.292 37.037 11.39 0.00 0.00 2.85
1763 1860 6.596888 GGAATATCCGGCCTAATAAACCTTAC 59.403 42.308 0.00 0.00 0.00 2.34
1804 1901 2.180432 AGTTTTGGTCGGTTCTAGCC 57.820 50.000 0.00 0.00 0.00 3.93
1823 1920 1.544982 CCGATCCCCTAGACTTAGCGA 60.545 57.143 0.00 0.00 0.00 4.93
1868 1965 6.924111 ACATTCAATTTAGCTTCAACCGAAT 58.076 32.000 0.00 0.00 0.00 3.34
1872 1969 7.636259 TCAATTTAGCTTCAACCGAATTTTG 57.364 32.000 0.00 0.00 0.00 2.44
1995 2092 3.209410 CATAGTGGAGGTTGAGCCAATC 58.791 50.000 0.00 0.00 40.61 2.67
1996 2093 0.329596 AGTGGAGGTTGAGCCAATCC 59.670 55.000 0.00 0.00 40.61 3.01
2032 2129 3.708210 TCGGTGAGACATGGGTCC 58.292 61.111 0.00 0.00 45.48 4.46
2058 2155 0.523072 GTGCCATCGTCATTGCAGTT 59.477 50.000 0.00 0.00 31.46 3.16
2089 2186 2.338620 CGCCACTCCTTGACGTCA 59.661 61.111 15.76 15.76 0.00 4.35
2287 2387 6.231211 ACTACCAGATTACAAAGTTGACCAG 58.769 40.000 0.00 0.00 0.00 4.00
2298 2398 1.528076 TTGACCAGGCACGCAACAT 60.528 52.632 0.00 0.00 0.00 2.71
2410 2512 8.491950 GTTGAGATTGTTCTTGAACTCTTCTAC 58.508 37.037 13.65 9.41 30.30 2.59
2420 2522 0.037232 ACTCTTCTACCTTGCGCCAC 60.037 55.000 4.18 0.00 0.00 5.01
2561 2663 5.163713 GGTTCTAGCATGAAACACTGGATTC 60.164 44.000 0.00 0.00 34.08 2.52
2602 2704 3.571828 CCAATGTTATCACACCACAACCA 59.428 43.478 0.00 0.00 35.03 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 4.996976 CACGTGTGGAAGGAGAGG 57.003 61.111 7.58 0.00 0.00 3.69
142 143 1.774110 TTTTCAGGCTTTCTGGTGCA 58.226 45.000 0.00 0.00 43.53 4.57
170 171 9.066892 ACATGGGTACTAGCATATTATTTTGTG 57.933 33.333 0.00 0.00 0.00 3.33
171 172 9.284968 GACATGGGTACTAGCATATTATTTTGT 57.715 33.333 0.00 0.00 0.00 2.83
172 173 9.283768 TGACATGGGTACTAGCATATTATTTTG 57.716 33.333 0.00 0.00 0.00 2.44
173 174 9.284968 GTGACATGGGTACTAGCATATTATTTT 57.715 33.333 0.00 0.00 0.00 1.82
174 175 8.660435 AGTGACATGGGTACTAGCATATTATTT 58.340 33.333 0.00 0.00 0.00 1.40
176 177 7.676043 AGAGTGACATGGGTACTAGCATATTAT 59.324 37.037 0.00 0.00 0.00 1.28
177 178 7.010771 AGAGTGACATGGGTACTAGCATATTA 58.989 38.462 0.00 0.00 0.00 0.98
238 239 4.081087 GTCTGGCTTAGATGGTTAGGTTCA 60.081 45.833 0.00 0.00 37.83 3.18
281 282 4.831674 TTGTACCTTAGGCCCTAACTTC 57.168 45.455 0.00 0.00 0.00 3.01
304 305 6.903883 TTGATTTAGGCGTTCATTCTCTAC 57.096 37.500 0.00 0.00 0.00 2.59
406 408 2.244117 GAGAGCCAAGCCGGTGATGA 62.244 60.000 1.90 0.00 36.97 2.92
445 447 2.084546 CTAGGACTTCGGGGCTTTTTG 58.915 52.381 0.00 0.00 0.00 2.44
536 538 7.333528 TGAGTTCAGCACTAGTTTTTCAAAT 57.666 32.000 0.00 0.00 35.01 2.32
586 588 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
587 589 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
588 590 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
589 591 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
590 592 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
591 593 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
592 594 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
593 595 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
594 596 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
595 597 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
596 598 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
597 599 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
598 600 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
599 601 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
600 602 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
601 603 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
602 604 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
603 605 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
604 606 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
605 607 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
606 608 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
607 609 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
608 610 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
609 611 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
610 612 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
611 613 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
612 614 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
613 615 5.485353 ACAAAGAGAGAGAGAGAGAGAGAGA 59.515 44.000 0.00 0.00 0.00 3.10
614 616 5.738909 ACAAAGAGAGAGAGAGAGAGAGAG 58.261 45.833 0.00 0.00 0.00 3.20
615 617 5.762179 ACAAAGAGAGAGAGAGAGAGAGA 57.238 43.478 0.00 0.00 0.00 3.10
616 618 6.313905 GTGTACAAAGAGAGAGAGAGAGAGAG 59.686 46.154 0.00 0.00 0.00 3.20
617 619 6.170506 GTGTACAAAGAGAGAGAGAGAGAGA 58.829 44.000 0.00 0.00 0.00 3.10
618 620 5.937540 TGTGTACAAAGAGAGAGAGAGAGAG 59.062 44.000 0.00 0.00 0.00 3.20
619 621 5.870706 TGTGTACAAAGAGAGAGAGAGAGA 58.129 41.667 0.00 0.00 0.00 3.10
620 622 6.757897 ATGTGTACAAAGAGAGAGAGAGAG 57.242 41.667 0.00 0.00 0.00 3.20
621 623 7.531857 AAATGTGTACAAAGAGAGAGAGAGA 57.468 36.000 0.00 0.00 0.00 3.10
622 624 9.868277 ATTAAATGTGTACAAAGAGAGAGAGAG 57.132 33.333 0.00 0.00 0.00 3.20
724 726 6.371809 TTTACAACATTGTCTGTCTGGTTC 57.628 37.500 0.00 0.00 42.35 3.62
747 753 1.201880 GCTCTACGTCGAACTCCCTTT 59.798 52.381 0.00 0.00 0.00 3.11
806 812 2.024655 ACCTGTGACGGAGGTTATAGGA 60.025 50.000 8.42 0.00 41.69 2.94
864 870 5.796424 ACTTTTCGTGTTAGACTTCCCTA 57.204 39.130 0.00 0.00 0.00 3.53
893 900 2.025981 AGCAGGGTATTTGTGCATCTCA 60.026 45.455 0.00 0.00 39.80 3.27
897 904 1.340017 ACGAGCAGGGTATTTGTGCAT 60.340 47.619 0.00 0.00 39.80 3.96
907 915 2.568623 AGAATTTGAACGAGCAGGGT 57.431 45.000 0.00 0.00 0.00 4.34
954 962 2.304761 CCTATTTATAGAAGGGCCGGCA 59.695 50.000 30.85 6.55 32.05 5.69
955 963 2.355818 CCCTATTTATAGAAGGGCCGGC 60.356 54.545 21.18 21.18 43.47 6.13
986 1008 2.961526 TTGTCTGGGAAGATAGCGTC 57.038 50.000 0.00 0.00 0.00 5.19
1030 1052 7.137426 CAGCCATTTCTATGCTTCTTGATAAC 58.863 38.462 0.00 0.00 0.00 1.89
1061 1083 0.834687 ACGCCAAGGAGAAGTGGGTA 60.835 55.000 0.00 0.00 35.28 3.69
1062 1084 2.113243 GACGCCAAGGAGAAGTGGGT 62.113 60.000 0.00 0.00 35.28 4.51
1078 1100 0.591741 GGAGAGCGACCAATACGACG 60.592 60.000 0.00 0.00 0.00 5.12
1122 1144 3.016736 GTTTGCATACCACCTACTGCAT 58.983 45.455 0.00 0.00 43.51 3.96
1128 1150 4.442332 CGGTATCAGTTTGCATACCACCTA 60.442 45.833 11.47 0.00 43.40 3.08
1136 1158 3.255642 AGTTTTGCGGTATCAGTTTGCAT 59.744 39.130 0.00 0.00 35.20 3.96
1200 1274 7.505258 TGCATACAACTTAGCAATATGTCCTA 58.495 34.615 0.00 0.00 33.48 2.94
1211 1285 1.064654 GCAGGCTGCATACAACTTAGC 59.935 52.381 33.33 1.28 44.26 3.09
1293 1369 3.414700 GTCTGGACGTTGCGCAGG 61.415 66.667 11.31 9.80 0.00 4.85
1303 1379 2.062971 TCCACTATACCCGTCTGGAC 57.937 55.000 0.00 0.00 37.49 4.02
1317 1393 0.270699 TACCCAGGCCCATATCCACT 59.729 55.000 0.00 0.00 0.00 4.00
1334 1410 1.153958 GTCGTAGCCACCACCGTAC 60.154 63.158 0.00 0.00 0.00 3.67
1339 1415 0.584876 GTTGTTGTCGTAGCCACCAC 59.415 55.000 0.00 0.00 0.00 4.16
1411 1493 1.691196 CGCCACCCCACAATATTCAT 58.309 50.000 0.00 0.00 0.00 2.57
1420 1502 2.519780 TTTTGACCGCCACCCCAC 60.520 61.111 0.00 0.00 0.00 4.61
1526 1608 4.924625 ACTATCATATCGTCCCTGCTAGT 58.075 43.478 0.00 0.00 0.00 2.57
1536 1618 5.568685 AGCTCGCAATACTATCATATCGT 57.431 39.130 0.00 0.00 0.00 3.73
1604 1689 2.989909 TGACTGTTGCCACCATATCTG 58.010 47.619 0.00 0.00 0.00 2.90
1627 1722 9.625747 ATGGATATGTGTTCAAATACATGTACA 57.374 29.630 7.96 13.78 43.06 2.90
1782 1879 4.067192 GGCTAGAACCGACCAAAACTTAA 58.933 43.478 0.00 0.00 0.00 1.85
1804 1901 1.893544 TCGCTAAGTCTAGGGGATCG 58.106 55.000 0.00 0.00 38.36 3.69
1808 1905 6.110707 TGTTTTATTTCGCTAAGTCTAGGGG 58.889 40.000 0.00 0.00 38.36 4.79
1845 1942 7.816945 AATTCGGTTGAAGCTAAATTGAATG 57.183 32.000 0.00 0.00 37.57 2.67
1890 1987 4.748102 TCGGTTGTCAAGACTATGTTGAAC 59.252 41.667 1.53 0.00 35.71 3.18
1970 2067 0.179073 CTCAACCTCCACTATGGCCG 60.179 60.000 0.00 0.00 37.47 6.13
1995 2092 1.144936 GATGGCCTGTCGAGGAAGG 59.855 63.158 3.32 4.67 42.93 3.46
1996 2093 1.227089 CGATGGCCTGTCGAGGAAG 60.227 63.158 21.60 0.00 42.93 3.46
2089 2186 3.009714 GGCGGGGAGGAGGAGTTT 61.010 66.667 0.00 0.00 0.00 2.66
2287 2387 1.438651 TACTCTTGATGTTGCGTGCC 58.561 50.000 0.00 0.00 0.00 5.01
2410 2512 2.823829 GCCTTATCGTGGCGCAAGG 61.824 63.158 15.59 15.59 41.03 3.61
2420 2522 5.817816 AGATGGTTTCACTAAAGCCTTATCG 59.182 40.000 0.00 0.00 41.42 2.92
2561 2663 4.550577 TGGTGCAACATATTTATCAGCG 57.449 40.909 0.00 0.00 39.98 5.18
2602 2704 4.697352 GTGTTAATCACTCTCCTGTTGCAT 59.303 41.667 0.00 0.00 43.13 3.96
2632 2734 7.671819 TGATATGGGTTCAAACCTTGTTGAATA 59.328 33.333 11.52 0.00 46.31 1.75


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

AutoCloner maintained by Alex Coulton.