Multiple sequence alignment - TraesCS2B01G205400

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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 TraesCS2B01G205400 chr2B 100.000 2607 0 0 1 2607 184660116 184662722 0.000000e+00 4815.0
1 TraesCS2B01G205400 chr2B 92.328 378 29 0 2230 2607 183212359 183211982 2.950000e-149 538.0
2 TraesCS2B01G205400 chr2B 82.274 299 31 11 1214 1497 183262935 183262644 3.350000e-59 239.0
3 TraesCS2B01G205400 chr2D 86.603 2187 160 53 11 2120 131160927 131163057 0.000000e+00 2292.0
4 TraesCS2B01G205400 chr2D 85.443 790 60 24 1845 2607 129838470 129837709 0.000000e+00 771.0
5 TraesCS2B01G205400 chr2D 95.630 389 17 0 2219 2607 131163112 131163500 2.200000e-175 625.0
6 TraesCS2B01G205400 chr2D 92.857 378 27 0 2230 2607 129942192 129941815 1.360000e-152 549.0
7 TraesCS2B01G205400 chr2D 81.387 274 25 11 934 1207 129945692 129945445 1.580000e-47 200.0
8 TraesCS2B01G205400 chr2D 93.103 58 2 2 800 856 129839733 129839677 1.660000e-12 84.2
9 TraesCS2B01G205400 chr2A 87.758 727 48 19 918 1644 137256243 137256928 0.000000e+00 811.0
10 TraesCS2B01G205400 chr2A 93.282 387 26 0 2221 2607 137259521 137259907 2.910000e-159 571.0
11 TraesCS2B01G205400 chr2A 83.698 411 51 8 474 878 137255847 137256247 8.810000e-100 374.0
12 TraesCS2B01G205400 chr2A 86.325 234 23 4 1742 1972 137259080 137259307 2.000000e-61 246.0
13 TraesCS2B01G205400 chr2A 81.293 294 35 10 10 301 137242350 137242625 1.210000e-53 220.0
14 TraesCS2B01G205400 chr2A 90.351 114 9 1 1645 1756 137257292 137257405 5.810000e-32 148.0
15 TraesCS2B01G205400 chrUn 87.734 481 39 8 1001 1462 17475990 17475511 6.350000e-151 544.0
16 TraesCS2B01G205400 chrUn 85.019 267 40 0 280 546 130419354 130419620 3.310000e-69 272.0
17 TraesCS2B01G205400 chr5D 81.278 673 90 15 60 710 298936196 298936854 1.790000e-141 512.0
18 TraesCS2B01G205400 chr3B 82.447 564 78 8 35 585 812501426 812500871 8.440000e-130 473.0
19 TraesCS2B01G205400 chr5B 82.011 567 79 12 152 707 402748551 402747997 6.570000e-126 460.0
20 TraesCS2B01G205400 chr4B 78.797 665 99 22 11 649 613381820 613381172 2.420000e-110 409.0


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 TraesCS2B01G205400 chr2B 184660116 184662722 2606 False 4815.0 4815 100.0000 1 2607 1 chr2B.!!$F1 2606
1 TraesCS2B01G205400 chr2D 131160927 131163500 2573 False 1458.5 2292 91.1165 11 2607 2 chr2D.!!$F1 2596
2 TraesCS2B01G205400 chr2D 129837709 129839733 2024 True 427.6 771 89.2730 800 2607 2 chr2D.!!$R1 1807
3 TraesCS2B01G205400 chr2D 129941815 129945692 3877 True 374.5 549 87.1220 934 2607 2 chr2D.!!$R2 1673
4 TraesCS2B01G205400 chr2A 137255847 137259907 4060 False 430.0 811 88.2828 474 2607 5 chr2A.!!$F2 2133
5 TraesCS2B01G205400 chr5D 298936196 298936854 658 False 512.0 512 81.2780 60 710 1 chr5D.!!$F1 650
6 TraesCS2B01G205400 chr3B 812500871 812501426 555 True 473.0 473 82.4470 35 585 1 chr3B.!!$R1 550
7 TraesCS2B01G205400 chr5B 402747997 402748551 554 True 460.0 460 82.0110 152 707 1 chr5B.!!$R1 555
8 TraesCS2B01G205400 chr4B 613381172 613381820 648 True 409.0 409 78.7970 11 649 1 chr4B.!!$R1 638

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
20 21 0.241213 CAGCTTCTTGTCTCGACGGA 59.759 55.0 0.0 0.0 0.0 4.69 F
1003 1093 0.108138 GCACCCGACAGCTAACATCT 60.108 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1210 1306 0.454600 GTAATCGTCCTCAGGCGACA 59.545 55.0 11.74 1.91 40.03 4.35 R
2576 5996 0.551396 TCATCTCCTCGGACCTGCTA 59.449 55.0 0.00 0.00 0.00 3.49 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
18 19 2.066000 GCAGCTTCTTGTCTCGACG 58.934 57.895 0.00 0.00 0.00 5.12
19 20 1.347817 GCAGCTTCTTGTCTCGACGG 61.348 60.000 0.00 0.00 0.00 4.79
20 21 0.241213 CAGCTTCTTGTCTCGACGGA 59.759 55.000 0.00 0.00 0.00 4.69
21 22 1.135257 CAGCTTCTTGTCTCGACGGAT 60.135 52.381 0.00 0.00 0.00 4.18
54 55 3.499406 TGGCTCCATCTTGGCAGT 58.501 55.556 0.00 0.00 37.47 4.40
116 127 1.358046 GCCGTCGGCGAGTATAGTT 59.642 57.895 22.50 0.00 39.62 2.24
139 156 1.111277 GGAGTGGTGCTGTTTTTGGT 58.889 50.000 0.00 0.00 0.00 3.67
156 173 3.588906 TGGTGACGACAGCGACGT 61.589 61.111 12.10 5.69 46.03 4.34
176 193 3.556213 CGTATCCAAGAATAATGCCCGGA 60.556 47.826 0.73 0.00 0.00 5.14
269 288 3.731089 TGGTCGACGGTTTTAGATGTTT 58.269 40.909 9.92 0.00 0.00 2.83
272 291 3.742369 GTCGACGGTTTTAGATGTTTGGA 59.258 43.478 0.00 0.00 0.00 3.53
278 297 3.561503 GTTTTAGATGTTTGGACGGTGC 58.438 45.455 0.00 0.00 0.00 5.01
281 300 0.981183 AGATGTTTGGACGGTGCCTA 59.019 50.000 0.00 0.00 0.00 3.93
341 361 0.247460 GGTTCCAGATTTGGGCTTGC 59.753 55.000 1.81 0.00 45.10 4.01
357 377 0.248012 TTGCGGATTGAAGGCGACTA 59.752 50.000 0.00 0.00 42.68 2.59
360 380 1.261619 GCGGATTGAAGGCGACTAATG 59.738 52.381 0.00 0.00 42.68 1.90
413 449 1.457643 ATGGCTCCGGGATTCGAGA 60.458 57.895 0.00 0.00 42.43 4.04
524 560 3.557264 GGTTGTGGTTCTCCTTCGAATCT 60.557 47.826 0.00 0.00 34.23 2.40
562 598 2.349817 GGCGACGGATATTGCAGAATTG 60.350 50.000 0.00 0.00 0.00 2.32
563 599 2.349817 GCGACGGATATTGCAGAATTGG 60.350 50.000 0.00 0.00 0.00 3.16
580 616 6.921857 CAGAATTGGCTAATGATTCCAATGTC 59.078 38.462 10.73 10.21 46.55 3.06
620 668 5.812127 GCAAATTTCTGAGGACACTTGTTTT 59.188 36.000 0.00 0.00 0.00 2.43
632 680 4.237018 ACACTTGTTTTCCCTCTACCCTA 58.763 43.478 0.00 0.00 0.00 3.53
634 682 3.260128 ACTTGTTTTCCCTCTACCCTACG 59.740 47.826 0.00 0.00 0.00 3.51
652 701 1.153901 GGGTCGATTTCGCGTCTGA 60.154 57.895 5.77 0.00 39.60 3.27
672 724 7.286508 GTCTGAGCGTTGTATTCATCATATTG 58.713 38.462 0.00 0.00 0.00 1.90
690 744 6.374053 TCATATTGGTGATCAATGAAACGTGT 59.626 34.615 0.23 0.00 45.00 4.49
691 745 3.894782 TGGTGATCAATGAAACGTGTG 57.105 42.857 0.00 0.00 0.00 3.82
692 746 3.471680 TGGTGATCAATGAAACGTGTGA 58.528 40.909 0.00 0.00 0.00 3.58
693 747 4.071423 TGGTGATCAATGAAACGTGTGAT 58.929 39.130 0.00 0.00 33.45 3.06
695 749 5.703130 TGGTGATCAATGAAACGTGTGATTA 59.297 36.000 0.00 0.00 30.94 1.75
697 751 6.021596 GTGATCAATGAAACGTGTGATTACC 58.978 40.000 0.00 0.00 33.29 2.85
698 752 5.123186 TGATCAATGAAACGTGTGATTACCC 59.877 40.000 0.00 0.00 30.94 3.69
699 753 4.647611 TCAATGAAACGTGTGATTACCCT 58.352 39.130 0.00 0.00 0.00 4.34
700 754 5.795972 TCAATGAAACGTGTGATTACCCTA 58.204 37.500 0.00 0.00 0.00 3.53
701 755 5.872617 TCAATGAAACGTGTGATTACCCTAG 59.127 40.000 0.00 0.00 0.00 3.02
762 820 1.569493 CGCGTTCACCAAACCTGAG 59.431 57.895 0.00 0.00 34.11 3.35
766 824 1.541233 CGTTCACCAAACCTGAGCTCT 60.541 52.381 16.19 0.00 34.11 4.09
787 845 0.388006 GGCGGATTTCCAACCAAACG 60.388 55.000 0.00 0.00 33.34 3.60
788 846 0.312729 GCGGATTTCCAACCAAACGT 59.687 50.000 0.00 0.00 35.14 3.99
789 847 1.928595 GCGGATTTCCAACCAAACGTG 60.929 52.381 0.00 0.00 35.14 4.49
790 848 1.604755 CGGATTTCCAACCAAACGTGA 59.395 47.619 0.00 0.00 35.14 4.35
791 849 2.350388 CGGATTTCCAACCAAACGTGAG 60.350 50.000 0.00 0.00 35.14 3.51
792 850 2.607038 GGATTTCCAACCAAACGTGAGC 60.607 50.000 0.00 0.00 35.64 4.26
793 851 1.757682 TTTCCAACCAAACGTGAGCT 58.242 45.000 0.00 0.00 0.00 4.09
795 853 0.468226 TCCAACCAAACGTGAGCTCT 59.532 50.000 16.19 0.00 0.00 4.09
797 855 0.508641 CAACCAAACGTGAGCTCTCG 59.491 55.000 30.58 30.58 38.62 4.04
859 920 0.962356 CAGGCAGATCACCAACCCAC 60.962 60.000 7.47 0.00 0.00 4.61
860 921 2.040544 GGCAGATCACCAACCCACG 61.041 63.158 0.00 0.00 0.00 4.94
862 923 1.676968 CAGATCACCAACCCACGGA 59.323 57.895 0.00 0.00 0.00 4.69
864 925 1.078426 GATCACCAACCCACGGAGG 60.078 63.158 0.00 0.00 37.03 4.30
869 930 4.722700 CAACCCACGGAGGCCCTG 62.723 72.222 0.00 0.00 35.39 4.45
888 949 4.003788 CCGCCGCCCATACCCTAG 62.004 72.222 0.00 0.00 0.00 3.02
889 950 2.915659 CGCCGCCCATACCCTAGA 60.916 66.667 0.00 0.00 0.00 2.43
890 951 2.504274 CGCCGCCCATACCCTAGAA 61.504 63.158 0.00 0.00 0.00 2.10
891 952 1.371558 GCCGCCCATACCCTAGAAG 59.628 63.158 0.00 0.00 0.00 2.85
892 953 1.408453 GCCGCCCATACCCTAGAAGT 61.408 60.000 0.00 0.00 0.00 3.01
893 954 2.005370 CCGCCCATACCCTAGAAGTA 57.995 55.000 0.00 0.00 0.00 2.24
894 955 1.893801 CCGCCCATACCCTAGAAGTAG 59.106 57.143 0.00 0.00 0.00 2.57
895 956 2.490351 CCGCCCATACCCTAGAAGTAGA 60.490 54.545 0.00 0.00 0.00 2.59
896 957 3.228453 CGCCCATACCCTAGAAGTAGAA 58.772 50.000 0.00 0.00 0.00 2.10
897 958 3.640029 CGCCCATACCCTAGAAGTAGAAA 59.360 47.826 0.00 0.00 0.00 2.52
898 959 4.501058 CGCCCATACCCTAGAAGTAGAAAC 60.501 50.000 0.00 0.00 0.00 2.78
899 960 4.407945 GCCCATACCCTAGAAGTAGAAACA 59.592 45.833 0.00 0.00 0.00 2.83
900 961 5.684291 GCCCATACCCTAGAAGTAGAAACAC 60.684 48.000 0.00 0.00 0.00 3.32
901 962 5.424252 CCCATACCCTAGAAGTAGAAACACA 59.576 44.000 0.00 0.00 0.00 3.72
902 963 6.338937 CCATACCCTAGAAGTAGAAACACAC 58.661 44.000 0.00 0.00 0.00 3.82
903 964 6.154706 CCATACCCTAGAAGTAGAAACACACT 59.845 42.308 0.00 0.00 0.00 3.55
904 965 7.310485 CCATACCCTAGAAGTAGAAACACACTT 60.310 40.741 0.00 0.00 37.69 3.16
905 966 5.855045 ACCCTAGAAGTAGAAACACACTTG 58.145 41.667 0.00 0.00 35.17 3.16
906 967 5.365895 ACCCTAGAAGTAGAAACACACTTGT 59.634 40.000 0.00 0.00 35.17 3.16
988 1078 4.899687 TACGATCGAGCGCGCACC 62.900 66.667 35.10 22.85 37.46 5.01
1003 1093 0.108138 GCACCCGACAGCTAACATCT 60.108 55.000 0.00 0.00 0.00 2.90
1117 1207 1.442688 CGCTTCTTTTCTTGGCCGC 60.443 57.895 0.00 0.00 0.00 6.53
1186 1282 4.803426 GACGGCGCCTGAGGACAG 62.803 72.222 26.68 8.67 43.12 3.51
1232 1328 1.672854 CGCCTGAGGACGATTACCCA 61.673 60.000 0.65 0.00 0.00 4.51
1344 1449 1.963464 TACGATTCCCGGGTTCAGCC 61.963 60.000 22.86 4.25 43.93 4.85
1349 1454 3.330720 CCCGGGTTCAGCCTTCCT 61.331 66.667 14.18 0.00 37.43 3.36
1351 1456 2.045926 CGGGTTCAGCCTTCCTGG 60.046 66.667 0.00 0.00 42.05 4.45
1353 1458 2.356667 GGTTCAGCCTTCCTGGGG 59.643 66.667 0.00 0.00 42.05 4.96
1411 1520 1.078759 GCCGTGACATGAACTCGGAG 61.079 60.000 27.39 2.83 43.88 4.63
1450 1559 2.358615 GTGTGCCGTCCATGCTCA 60.359 61.111 0.00 0.00 0.00 4.26
1455 1564 1.026182 TGCCGTCCATGCTCATTGTC 61.026 55.000 0.00 0.00 0.00 3.18
1562 1703 8.450964 CGATAAAAATCCTGTGATACAGTGTTT 58.549 33.333 0.00 0.00 44.50 2.83
1604 1745 8.217111 ACTTTTGGATTTACACCCATTGAAATT 58.783 29.630 0.00 0.00 31.66 1.82
1605 1746 9.717942 CTTTTGGATTTACACCCATTGAAATTA 57.282 29.630 0.00 0.00 31.66 1.40
1657 2162 6.127535 ACTGACATGCAATATTTTTCAGGGAG 60.128 38.462 8.49 2.44 34.55 4.30
1761 4752 4.447054 CGCATGAACCAGAAGATCAGATAC 59.553 45.833 0.00 0.00 0.00 2.24
1765 4756 6.857437 TGAACCAGAAGATCAGATACTGAA 57.143 37.500 5.57 0.00 44.04 3.02
1772 4763 7.432059 CAGAAGATCAGATACTGAACATGCTA 58.568 38.462 5.57 0.00 44.04 3.49
1805 5147 7.686438 ATCTCACATATTTACAAGCACAACA 57.314 32.000 0.00 0.00 0.00 3.33
1823 5165 3.667497 ACAGAAAGCTGAATCGAGTCA 57.333 42.857 15.60 15.60 45.17 3.41
1824 5166 3.995199 ACAGAAAGCTGAATCGAGTCAA 58.005 40.909 17.16 1.13 45.17 3.18
1825 5167 4.573900 ACAGAAAGCTGAATCGAGTCAAT 58.426 39.130 17.16 5.74 45.17 2.57
1862 5205 2.541178 CGTAGTTCGGTACAGCCTGATC 60.541 54.545 0.00 0.00 35.71 2.92
1898 5273 3.650281 TGCCTAGATTTCCATCTTGCA 57.350 42.857 0.00 5.48 40.82 4.08
1914 5291 6.403527 CCATCTTGCAATTGAGATAAACGACA 60.404 38.462 10.34 0.00 31.64 4.35
1937 5317 8.311650 ACAAAGATGAAGCGATATATTGTACC 57.688 34.615 1.88 0.00 0.00 3.34
1939 5319 8.939929 CAAAGATGAAGCGATATATTGTACCAT 58.060 33.333 1.88 3.18 0.00 3.55
1972 5353 2.012673 CAGAGCTCAGTATTTGTGCCC 58.987 52.381 17.77 0.00 45.19 5.36
1974 5355 0.034089 AGCTCAGTATTTGTGCCCCC 60.034 55.000 0.00 0.00 45.19 5.40
1975 5356 0.034089 GCTCAGTATTTGTGCCCCCT 60.034 55.000 0.00 0.00 39.73 4.79
1979 5360 1.080638 AGTATTTGTGCCCCCTTGGA 58.919 50.000 0.00 0.00 35.39 3.53
1980 5361 1.645919 AGTATTTGTGCCCCCTTGGAT 59.354 47.619 0.00 0.00 35.39 3.41
1982 5363 3.467103 AGTATTTGTGCCCCCTTGGATAT 59.533 43.478 0.00 0.00 35.39 1.63
1983 5364 2.157640 TTTGTGCCCCCTTGGATATG 57.842 50.000 0.00 0.00 35.39 1.78
1984 5365 0.396974 TTGTGCCCCCTTGGATATGC 60.397 55.000 0.00 0.00 35.39 3.14
1985 5366 1.229927 GTGCCCCCTTGGATATGCA 59.770 57.895 0.00 0.00 35.39 3.96
1987 5368 1.075374 GTGCCCCCTTGGATATGCATA 59.925 52.381 9.27 9.27 35.39 3.14
2014 5423 1.424493 AATCGCTAGCGCTTGCACTC 61.424 55.000 35.95 13.28 42.66 3.51
2015 5424 2.290122 ATCGCTAGCGCTTGCACTCT 62.290 55.000 35.95 18.44 42.66 3.24
2036 5445 0.035915 TGCAGTAATGGGTTAGCGCA 60.036 50.000 11.47 0.00 41.83 6.09
2125 5537 7.264221 AGCCGCAAAATCATTTCACATTTATA 58.736 30.769 0.00 0.00 0.00 0.98
2126 5538 7.927629 AGCCGCAAAATCATTTCACATTTATAT 59.072 29.630 0.00 0.00 0.00 0.86
2177 5592 5.252969 TCCATTTGTCAAGCATAGCAATC 57.747 39.130 0.00 0.00 0.00 2.67
2178 5593 4.705991 TCCATTTGTCAAGCATAGCAATCA 59.294 37.500 0.00 0.00 0.00 2.57
2183 5598 3.506844 TGTCAAGCATAGCAATCAAGCAA 59.493 39.130 0.00 0.00 36.85 3.91
2207 5622 3.236632 GCGATTTGCCAGGAAGAAATT 57.763 42.857 0.00 0.00 37.76 1.82
2209 5624 4.743493 GCGATTTGCCAGGAAGAAATTAA 58.257 39.130 0.00 0.00 37.76 1.40
2210 5625 5.351458 GCGATTTGCCAGGAAGAAATTAAT 58.649 37.500 0.00 0.00 37.76 1.40
2215 5630 8.829373 ATTTGCCAGGAAGAAATTAATAGAGT 57.171 30.769 0.00 0.00 0.00 3.24
2217 5632 7.865706 TGCCAGGAAGAAATTAATAGAGTTC 57.134 36.000 0.00 0.00 0.00 3.01
2576 5996 0.178990 GCAGGAAACCCCACTTGTCT 60.179 55.000 0.00 0.00 37.41 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.241213 TCCGTCGAGACAAGAAGCTG 59.759 55.000 4.02 0.00 0.00 4.24
2 3 1.178276 ATCCGTCGAGACAAGAAGCT 58.822 50.000 4.02 0.00 0.00 3.74
3 4 2.846039 TATCCGTCGAGACAAGAAGC 57.154 50.000 4.02 0.00 0.00 3.86
4 5 4.358494 ACTTATCCGTCGAGACAAGAAG 57.642 45.455 8.21 6.32 0.00 2.85
5 6 4.778534 AACTTATCCGTCGAGACAAGAA 57.221 40.909 8.21 0.00 0.00 2.52
8 9 3.367703 GGGAAACTTATCCGTCGAGACAA 60.368 47.826 4.02 0.00 40.62 3.18
9 10 2.165030 GGGAAACTTATCCGTCGAGACA 59.835 50.000 4.02 0.00 40.62 3.41
10 11 2.480932 GGGGAAACTTATCCGTCGAGAC 60.481 54.545 0.00 0.00 40.62 3.36
12 13 1.479323 TGGGGAAACTTATCCGTCGAG 59.521 52.381 0.00 0.00 40.62 4.04
13 14 1.479323 CTGGGGAAACTTATCCGTCGA 59.521 52.381 0.00 0.00 40.62 4.20
14 15 1.472728 CCTGGGGAAACTTATCCGTCG 60.473 57.143 0.00 0.00 40.62 5.12
15 16 1.746171 GCCTGGGGAAACTTATCCGTC 60.746 57.143 0.00 0.00 40.62 4.79
16 17 0.255033 GCCTGGGGAAACTTATCCGT 59.745 55.000 0.00 0.00 40.62 4.69
17 18 0.465642 GGCCTGGGGAAACTTATCCG 60.466 60.000 0.00 0.00 40.62 4.18
18 19 0.927029 AGGCCTGGGGAAACTTATCC 59.073 55.000 3.11 0.00 38.86 2.59
19 20 1.410224 CCAGGCCTGGGGAAACTTATC 60.410 57.143 40.24 0.00 46.81 1.75
20 21 0.631212 CCAGGCCTGGGGAAACTTAT 59.369 55.000 40.24 0.00 46.81 1.73
21 22 2.083715 CCAGGCCTGGGGAAACTTA 58.916 57.895 40.24 0.00 46.81 2.24
54 55 0.531090 CGACACCACCGGAAAAGACA 60.531 55.000 9.46 0.00 0.00 3.41
116 127 1.846007 AAAACAGCACCACTCCACAA 58.154 45.000 0.00 0.00 0.00 3.33
139 156 1.579964 ATACGTCGCTGTCGTCACCA 61.580 55.000 0.00 0.00 41.72 4.17
156 173 3.650942 AGTCCGGGCATTATTCTTGGATA 59.349 43.478 9.71 0.00 0.00 2.59
176 193 4.816984 ATCGAGACGGGCCGGAGT 62.817 66.667 31.78 14.22 0.00 3.85
269 288 1.128200 ATAATGCTAGGCACCGTCCA 58.872 50.000 0.00 0.00 43.04 4.02
272 291 0.180171 TGCATAATGCTAGGCACCGT 59.820 50.000 0.00 0.00 45.31 4.83
278 297 3.185188 GTGACATCGTGCATAATGCTAGG 59.815 47.826 10.28 0.00 45.31 3.02
281 300 1.942657 GGTGACATCGTGCATAATGCT 59.057 47.619 10.28 0.49 45.31 3.79
291 310 4.388499 GCCCACCGGTGACATCGT 62.388 66.667 36.07 0.00 0.00 3.73
341 361 2.285220 CACATTAGTCGCCTTCAATCCG 59.715 50.000 0.00 0.00 0.00 4.18
357 377 0.981183 TCGAGGCCAAGTACCACATT 59.019 50.000 5.01 0.00 0.00 2.71
360 380 1.445582 CGTCGAGGCCAAGTACCAC 60.446 63.158 5.01 0.00 0.00 4.16
426 462 4.736896 GGCGTGTCGACCAGGGAC 62.737 72.222 14.12 2.78 34.99 4.46
472 508 3.565516 CGTTGTGAGTCGATGAAGAAGA 58.434 45.455 0.00 0.00 0.00 2.87
524 560 1.017177 GCCACCGCTGAATGTCGTTA 61.017 55.000 0.00 0.00 0.00 3.18
632 680 2.505557 GACGCGAAATCGACCCGT 60.506 61.111 15.93 6.83 43.02 5.28
634 682 1.140407 CTCAGACGCGAAATCGACCC 61.140 60.000 15.93 0.00 43.02 4.46
649 698 6.203530 ACCAATATGATGAATACAACGCTCAG 59.796 38.462 0.00 0.00 0.00 3.35
652 701 6.054941 TCACCAATATGATGAATACAACGCT 58.945 36.000 0.00 0.00 0.00 5.07
672 724 4.685169 ATCACACGTTTCATTGATCACC 57.315 40.909 0.00 0.00 0.00 4.02
735 793 1.007849 GGTGAACGCGCCAAACATT 60.008 52.632 5.73 0.00 44.29 2.71
736 794 2.642700 GGTGAACGCGCCAAACAT 59.357 55.556 5.73 0.00 44.29 2.71
762 820 1.449601 TTGGAAATCCGCCGAGAGC 60.450 57.895 0.00 0.00 39.43 4.09
766 824 0.537600 TTTGGTTGGAAATCCGCCGA 60.538 50.000 7.92 4.25 39.43 5.54
771 829 2.607038 GCTCACGTTTGGTTGGAAATCC 60.607 50.000 0.00 0.00 0.00 3.01
792 850 2.358737 AGGTTTTGGCGGCGAGAG 60.359 61.111 12.98 0.00 0.00 3.20
793 851 2.358247 GAGGTTTTGGCGGCGAGA 60.358 61.111 12.98 0.00 0.00 4.04
871 932 4.003788 CTAGGGTATGGGCGGCGG 62.004 72.222 9.78 0.00 0.00 6.13
872 933 2.436087 CTTCTAGGGTATGGGCGGCG 62.436 65.000 0.51 0.51 0.00 6.46
873 934 1.371558 CTTCTAGGGTATGGGCGGC 59.628 63.158 0.00 0.00 0.00 6.53
874 935 1.893801 CTACTTCTAGGGTATGGGCGG 59.106 57.143 0.00 0.00 0.00 6.13
875 936 2.872732 TCTACTTCTAGGGTATGGGCG 58.127 52.381 0.00 0.00 0.00 6.13
876 937 4.407945 TGTTTCTACTTCTAGGGTATGGGC 59.592 45.833 0.00 0.00 0.00 5.36
877 938 5.424252 TGTGTTTCTACTTCTAGGGTATGGG 59.576 44.000 0.00 0.00 0.00 4.00
878 939 6.154706 AGTGTGTTTCTACTTCTAGGGTATGG 59.845 42.308 0.00 0.00 0.00 2.74
879 940 7.171630 AGTGTGTTTCTACTTCTAGGGTATG 57.828 40.000 0.00 0.00 0.00 2.39
880 941 7.234988 ACAAGTGTGTTTCTACTTCTAGGGTAT 59.765 37.037 0.00 0.00 35.08 2.73
881 942 6.552350 ACAAGTGTGTTTCTACTTCTAGGGTA 59.448 38.462 0.00 0.00 35.08 3.69
882 943 5.365895 ACAAGTGTGTTTCTACTTCTAGGGT 59.634 40.000 0.00 0.00 35.08 4.34
883 944 5.696724 CACAAGTGTGTTTCTACTTCTAGGG 59.303 44.000 3.17 0.00 40.96 3.53
884 945 6.513180 TCACAAGTGTGTTTCTACTTCTAGG 58.487 40.000 11.06 0.00 45.76 3.02
885 946 8.420374 TTTCACAAGTGTGTTTCTACTTCTAG 57.580 34.615 11.06 0.00 45.76 2.43
886 947 8.780846 TTTTCACAAGTGTGTTTCTACTTCTA 57.219 30.769 11.06 0.00 45.76 2.10
887 948 7.606456 TCTTTTCACAAGTGTGTTTCTACTTCT 59.394 33.333 11.06 0.00 45.76 2.85
888 949 7.748847 TCTTTTCACAAGTGTGTTTCTACTTC 58.251 34.615 11.06 0.00 45.76 3.01
889 950 7.681939 TCTTTTCACAAGTGTGTTTCTACTT 57.318 32.000 11.06 0.00 45.76 2.24
890 951 7.681939 TTCTTTTCACAAGTGTGTTTCTACT 57.318 32.000 11.06 0.00 45.76 2.57
891 952 8.736751 TTTTCTTTTCACAAGTGTGTTTCTAC 57.263 30.769 11.06 0.00 45.76 2.59
892 953 8.026607 CCTTTTCTTTTCACAAGTGTGTTTCTA 58.973 33.333 11.06 0.00 45.76 2.10
893 954 6.868339 CCTTTTCTTTTCACAAGTGTGTTTCT 59.132 34.615 11.06 0.00 45.76 2.52
894 955 6.401047 GCCTTTTCTTTTCACAAGTGTGTTTC 60.401 38.462 11.06 0.00 45.76 2.78
895 956 5.408299 GCCTTTTCTTTTCACAAGTGTGTTT 59.592 36.000 11.06 0.00 45.76 2.83
896 957 4.929211 GCCTTTTCTTTTCACAAGTGTGTT 59.071 37.500 11.06 0.00 45.76 3.32
897 958 4.494484 GCCTTTTCTTTTCACAAGTGTGT 58.506 39.130 11.06 0.00 45.76 3.72
898 959 3.547468 CGCCTTTTCTTTTCACAAGTGTG 59.453 43.478 5.02 5.02 46.91 3.82
899 960 3.769536 CGCCTTTTCTTTTCACAAGTGT 58.230 40.909 0.00 0.00 0.00 3.55
900 961 2.535574 GCGCCTTTTCTTTTCACAAGTG 59.464 45.455 0.00 0.00 0.00 3.16
901 962 2.794631 CGCGCCTTTTCTTTTCACAAGT 60.795 45.455 0.00 0.00 0.00 3.16
902 963 1.780860 CGCGCCTTTTCTTTTCACAAG 59.219 47.619 0.00 0.00 0.00 3.16
903 964 1.535015 CCGCGCCTTTTCTTTTCACAA 60.535 47.619 0.00 0.00 0.00 3.33
904 965 0.030101 CCGCGCCTTTTCTTTTCACA 59.970 50.000 0.00 0.00 0.00 3.58
905 966 0.030235 ACCGCGCCTTTTCTTTTCAC 59.970 50.000 0.00 0.00 0.00 3.18
906 967 0.030101 CACCGCGCCTTTTCTTTTCA 59.970 50.000 0.00 0.00 0.00 2.69
907 968 1.275471 GCACCGCGCCTTTTCTTTTC 61.275 55.000 0.00 0.00 32.94 2.29
908 969 1.299850 GCACCGCGCCTTTTCTTTT 60.300 52.632 0.00 0.00 32.94 2.27
909 970 2.335011 GCACCGCGCCTTTTCTTT 59.665 55.556 0.00 0.00 32.94 2.52
988 1078 3.119291 GTGATGAGATGTTAGCTGTCGG 58.881 50.000 0.00 0.00 0.00 4.79
992 1082 5.259832 TCTCTGTGATGAGATGTTAGCTG 57.740 43.478 0.00 0.00 38.08 4.24
1003 1093 1.483827 GTGGGCTGATCTCTGTGATGA 59.516 52.381 0.00 0.00 35.14 2.92
1210 1306 0.454600 GTAATCGTCCTCAGGCGACA 59.545 55.000 11.74 1.91 40.03 4.35
1364 1469 0.881600 TTGATCATGGCTCATCGGCG 60.882 55.000 0.00 0.00 42.02 6.46
1411 1520 2.159226 ACTGTCTCCGGAAATGATCGAC 60.159 50.000 5.23 8.25 0.00 4.20
1450 1559 3.243501 ACACCACAACGTACGTAGACAAT 60.244 43.478 23.12 0.97 0.00 2.71
1455 1564 0.780002 GCACACCACAACGTACGTAG 59.220 55.000 23.12 14.28 0.00 3.51
1604 1745 6.405538 TGTCATGTGTGAGACTTGCATATTA 58.594 36.000 0.00 0.00 34.36 0.98
1605 1746 5.247862 TGTCATGTGTGAGACTTGCATATT 58.752 37.500 0.00 0.00 34.36 1.28
1606 1747 4.835678 TGTCATGTGTGAGACTTGCATAT 58.164 39.130 0.00 0.00 34.36 1.78
1607 1748 4.270245 TGTCATGTGTGAGACTTGCATA 57.730 40.909 0.00 0.00 34.36 3.14
1657 2162 3.255642 ACATCAAAGTTGGCATGGTGTAC 59.744 43.478 2.99 0.00 36.68 2.90
1782 4773 6.934083 TCTGTTGTGCTTGTAAATATGTGAGA 59.066 34.615 0.00 0.00 0.00 3.27
1805 5147 4.825422 TGATTGACTCGATTCAGCTTTCT 58.175 39.130 5.56 0.00 0.00 2.52
1823 5165 7.435488 CGAACTACGAACATTATCTCCTTGATT 59.565 37.037 0.00 0.00 45.77 2.57
1824 5166 6.918569 CGAACTACGAACATTATCTCCTTGAT 59.081 38.462 0.00 0.00 45.77 2.57
1825 5167 6.263344 CGAACTACGAACATTATCTCCTTGA 58.737 40.000 0.00 0.00 45.77 3.02
1898 5273 7.965107 GCTTCATCTTTGTCGTTTATCTCAATT 59.035 33.333 0.00 0.00 0.00 2.32
1937 5317 6.820656 ACTGAGCTCTGTTTATTAACCAGATG 59.179 38.462 19.51 1.67 33.15 2.90
1939 5319 6.360370 ACTGAGCTCTGTTTATTAACCAGA 57.640 37.500 19.51 3.95 33.15 3.86
1952 5333 2.012673 GGGCACAAATACTGAGCTCTG 58.987 52.381 18.15 18.15 38.93 3.35
1972 5353 3.890756 TGCTTGTTATGCATATCCAAGGG 59.109 43.478 29.31 17.32 35.31 3.95
1974 5355 6.361481 CGATTTGCTTGTTATGCATATCCAAG 59.639 38.462 26.85 26.85 42.04 3.61
1975 5356 6.207928 CGATTTGCTTGTTATGCATATCCAA 58.792 36.000 7.36 12.21 42.04 3.53
2014 5423 2.477863 GCGCTAACCCATTACTGCAAAG 60.478 50.000 0.00 0.00 0.00 2.77
2015 5424 1.470890 GCGCTAACCCATTACTGCAAA 59.529 47.619 0.00 0.00 0.00 3.68
2036 5445 1.676916 CGATGTGCATCCAAGGTGTCT 60.677 52.381 6.60 0.00 34.40 3.41
2072 5481 7.602265 CCTTGTTTGATTTATTTTAGGTGTGGG 59.398 37.037 0.00 0.00 0.00 4.61
2125 5537 8.423906 ACTATCCGATTATCAAGTTAGTCCAT 57.576 34.615 0.00 0.00 0.00 3.41
2126 5538 7.834881 ACTATCCGATTATCAAGTTAGTCCA 57.165 36.000 0.00 0.00 0.00 4.02
2148 5560 7.093814 TGCTATGCTTGACAAATGGAAATTACT 60.094 33.333 0.00 0.00 0.00 2.24
2177 5592 2.375981 GCAAATCGCCCATTGCTTG 58.624 52.632 7.52 0.00 46.42 4.01
2178 5593 4.917474 GCAAATCGCCCATTGCTT 57.083 50.000 7.52 0.00 46.42 3.91
2209 5624 9.515226 GGTACAGATCAGATTAGAGAACTCTAT 57.485 37.037 11.57 3.76 41.37 1.98
2210 5625 8.719596 AGGTACAGATCAGATTAGAGAACTCTA 58.280 37.037 7.37 7.37 40.93 2.43
2215 5630 5.893824 TGCAGGTACAGATCAGATTAGAGAA 59.106 40.000 0.00 0.00 0.00 2.87
2217 5632 5.781210 TGCAGGTACAGATCAGATTAGAG 57.219 43.478 0.00 0.00 0.00 2.43
2576 5996 0.551396 TCATCTCCTCGGACCTGCTA 59.449 55.000 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.