Multiple sequence alignment - TraesCS2A01G575800

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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 TraesCS2A01G575800 chr2A 100.000 3077 0 0 1 3077 770130602 770133678 0.000000e+00 5683.0
1 TraesCS2A01G575800 chr2A 95.582 679 20 7 62 738 52583281 52582611 0.000000e+00 1079.0
2 TraesCS2A01G575800 chr2A 71.351 733 185 22 2040 2760 544279948 544280667 1.900000e-37 167.0
3 TraesCS2A01G575800 chr2A 100.000 36 0 0 737 772 719293382 719293347 1.980000e-07 67.6
4 TraesCS2A01G575800 chr5B 91.261 2300 187 8 786 3077 543287165 543289458 0.000000e+00 3121.0
5 TraesCS2A01G575800 chr4D 88.724 2288 250 7 788 3072 54061107 54063389 0.000000e+00 2789.0
6 TraesCS2A01G575800 chr4D 96.613 679 13 5 62 738 170151851 170151181 0.000000e+00 1118.0
7 TraesCS2A01G575800 chr7D 87.951 2299 258 8 786 3075 76326265 76323977 0.000000e+00 2693.0
8 TraesCS2A01G575800 chr7D 95.742 681 20 4 59 738 423402181 423401509 0.000000e+00 1088.0
9 TraesCS2A01G575800 chr7D 87.637 364 43 1 65 426 59876284 59876647 3.670000e-114 422.0
10 TraesCS2A01G575800 chr5D 86.672 2296 295 7 776 3069 539853897 539856183 0.000000e+00 2534.0
11 TraesCS2A01G575800 chr3A 87.306 2001 234 16 786 2780 730877140 730875154 0.000000e+00 2270.0
12 TraesCS2A01G575800 chr2B 95.131 1335 58 3 1744 3077 22595023 22593695 0.000000e+00 2098.0
13 TraesCS2A01G575800 chr7A 93.702 1302 79 3 786 2085 110828248 110826948 0.000000e+00 1947.0
14 TraesCS2A01G575800 chr3B 84.164 1907 298 4 1174 3077 47802519 47804424 0.000000e+00 1845.0
15 TraesCS2A01G575800 chr3B 84.119 1908 298 5 1174 3077 47734968 47736874 0.000000e+00 1840.0
16 TraesCS2A01G575800 chr3B 83.604 1909 294 14 1174 3077 48071963 48073857 0.000000e+00 1773.0
17 TraesCS2A01G575800 chr3B 96.146 934 29 3 2144 3077 581643716 581642790 0.000000e+00 1519.0
18 TraesCS2A01G575800 chr7B 90.389 1311 117 6 786 2093 504472265 504470961 0.000000e+00 1714.0
19 TraesCS2A01G575800 chr7B 95.852 675 19 4 65 738 677306051 677306717 0.000000e+00 1083.0
20 TraesCS2A01G575800 chr7B 84.991 553 62 13 61 606 193347185 193347723 2.700000e-150 542.0
21 TraesCS2A01G575800 chr6A 97.626 674 10 3 65 738 594340149 594339482 0.000000e+00 1151.0
22 TraesCS2A01G575800 chr1D 96.884 674 13 3 65 738 92095576 92096241 0.000000e+00 1122.0
23 TraesCS2A01G575800 chr2D 96.444 675 15 4 65 738 529654644 529653978 0.000000e+00 1105.0
24 TraesCS2A01G575800 chr2D 90.769 65 3 2 1 65 644839438 644839499 1.970000e-12 84.2


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 TraesCS2A01G575800 chr2A 770130602 770133678 3076 False 5683 5683 100.000 1 3077 1 chr2A.!!$F2 3076
1 TraesCS2A01G575800 chr2A 52582611 52583281 670 True 1079 1079 95.582 62 738 1 chr2A.!!$R1 676
2 TraesCS2A01G575800 chr5B 543287165 543289458 2293 False 3121 3121 91.261 786 3077 1 chr5B.!!$F1 2291
3 TraesCS2A01G575800 chr4D 54061107 54063389 2282 False 2789 2789 88.724 788 3072 1 chr4D.!!$F1 2284
4 TraesCS2A01G575800 chr4D 170151181 170151851 670 True 1118 1118 96.613 62 738 1 chr4D.!!$R1 676
5 TraesCS2A01G575800 chr7D 76323977 76326265 2288 True 2693 2693 87.951 786 3075 1 chr7D.!!$R1 2289
6 TraesCS2A01G575800 chr7D 423401509 423402181 672 True 1088 1088 95.742 59 738 1 chr7D.!!$R2 679
7 TraesCS2A01G575800 chr5D 539853897 539856183 2286 False 2534 2534 86.672 776 3069 1 chr5D.!!$F1 2293
8 TraesCS2A01G575800 chr3A 730875154 730877140 1986 True 2270 2270 87.306 786 2780 1 chr3A.!!$R1 1994
9 TraesCS2A01G575800 chr2B 22593695 22595023 1328 True 2098 2098 95.131 1744 3077 1 chr2B.!!$R1 1333
10 TraesCS2A01G575800 chr7A 110826948 110828248 1300 True 1947 1947 93.702 786 2085 1 chr7A.!!$R1 1299
11 TraesCS2A01G575800 chr3B 47802519 47804424 1905 False 1845 1845 84.164 1174 3077 1 chr3B.!!$F2 1903
12 TraesCS2A01G575800 chr3B 47734968 47736874 1906 False 1840 1840 84.119 1174 3077 1 chr3B.!!$F1 1903
13 TraesCS2A01G575800 chr3B 48071963 48073857 1894 False 1773 1773 83.604 1174 3077 1 chr3B.!!$F3 1903
14 TraesCS2A01G575800 chr3B 581642790 581643716 926 True 1519 1519 96.146 2144 3077 1 chr3B.!!$R1 933
15 TraesCS2A01G575800 chr7B 504470961 504472265 1304 True 1714 1714 90.389 786 2093 1 chr7B.!!$R1 1307
16 TraesCS2A01G575800 chr7B 677306051 677306717 666 False 1083 1083 95.852 65 738 1 chr7B.!!$F2 673
17 TraesCS2A01G575800 chr7B 193347185 193347723 538 False 542 542 84.991 61 606 1 chr7B.!!$F1 545
18 TraesCS2A01G575800 chr6A 594339482 594340149 667 True 1151 1151 97.626 65 738 1 chr6A.!!$R1 673
19 TraesCS2A01G575800 chr1D 92095576 92096241 665 False 1122 1122 96.884 65 738 1 chr1D.!!$F1 673
20 TraesCS2A01G575800 chr2D 529653978 529654644 666 True 1105 1105 96.444 65 738 1 chr2D.!!$R1 673

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
742 750 0.620556 ACGGATGAAAGAGGCCATGT 59.379 50.0 5.01 0.0 0.0 3.21 F
1499 1514 0.327924 AGGGTTCGGCATGATGTTCA 59.672 50.0 0.00 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1594 0.173029 CCACACACACTGCAAAAGCA 59.827 50.0 0.00 0.0 0.0 3.91 R
2561 2591 0.675633 GCATGCCAACAAACAGTCCT 59.324 50.0 6.36 0.0 0.0 3.85 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
21 22 4.329462 GCTAGACAGGTAGATCCCTTTG 57.671 50.000 0.00 0.00 36.75 2.77
22 23 3.493524 GCTAGACAGGTAGATCCCTTTGC 60.494 52.174 0.00 0.00 36.75 3.68
23 24 2.839228 AGACAGGTAGATCCCTTTGCT 58.161 47.619 0.00 0.00 36.75 3.91
24 25 3.185455 AGACAGGTAGATCCCTTTGCTT 58.815 45.455 0.00 0.00 36.75 3.91
25 26 3.054802 AGACAGGTAGATCCCTTTGCTTG 60.055 47.826 0.00 0.00 36.75 4.01
26 27 2.019984 CAGGTAGATCCCTTTGCTTGC 58.980 52.381 0.00 0.00 36.75 4.01
27 28 1.918957 AGGTAGATCCCTTTGCTTGCT 59.081 47.619 0.00 0.00 36.75 3.91
28 29 2.310052 AGGTAGATCCCTTTGCTTGCTT 59.690 45.455 0.00 0.00 36.75 3.91
29 30 3.523564 AGGTAGATCCCTTTGCTTGCTTA 59.476 43.478 0.00 0.00 36.75 3.09
30 31 4.018415 AGGTAGATCCCTTTGCTTGCTTAA 60.018 41.667 0.00 0.00 36.75 1.85
31 32 4.705023 GGTAGATCCCTTTGCTTGCTTAAA 59.295 41.667 0.00 0.00 0.00 1.52
32 33 5.163612 GGTAGATCCCTTTGCTTGCTTAAAG 60.164 44.000 0.00 0.00 39.07 1.85
33 34 4.666512 AGATCCCTTTGCTTGCTTAAAGA 58.333 39.130 6.90 0.00 38.24 2.52
34 35 5.079643 AGATCCCTTTGCTTGCTTAAAGAA 58.920 37.500 6.90 0.00 38.24 2.52
35 36 5.539955 AGATCCCTTTGCTTGCTTAAAGAAA 59.460 36.000 6.90 0.00 38.24 2.52
36 37 5.606348 TCCCTTTGCTTGCTTAAAGAAAA 57.394 34.783 6.90 0.00 40.55 2.29
43 44 6.588348 TGCTTGCTTAAAGAAAAGAAAAGC 57.412 33.333 13.28 13.28 42.32 3.51
48 49 7.003939 TGCTTAAAGAAAAGAAAAGCAAAGC 57.996 32.000 5.64 0.00 46.84 3.51
49 50 6.593382 TGCTTAAAGAAAAGAAAAGCAAAGCA 59.407 30.769 5.64 0.00 46.84 3.91
50 51 7.118971 TGCTTAAAGAAAAGAAAAGCAAAGCAA 59.881 29.630 5.64 0.00 46.84 3.91
51 52 7.962373 GCTTAAAGAAAAGAAAAGCAAAGCAAA 59.038 29.630 0.00 0.00 41.65 3.68
52 53 9.481800 CTTAAAGAAAAGAAAAGCAAAGCAAAG 57.518 29.630 0.00 0.00 0.00 2.77
53 54 5.475273 AGAAAAGAAAAGCAAAGCAAAGC 57.525 34.783 0.00 0.00 0.00 3.51
54 55 4.937015 AGAAAAGAAAAGCAAAGCAAAGCA 59.063 33.333 0.00 0.00 0.00 3.91
55 56 4.870221 AAAGAAAAGCAAAGCAAAGCAG 57.130 36.364 0.00 0.00 0.00 4.24
56 57 3.531934 AGAAAAGCAAAGCAAAGCAGT 57.468 38.095 0.00 0.00 0.00 4.40
57 58 4.654091 AGAAAAGCAAAGCAAAGCAGTA 57.346 36.364 0.00 0.00 0.00 2.74
58 59 4.614946 AGAAAAGCAAAGCAAAGCAGTAG 58.385 39.130 0.00 0.00 0.00 2.57
59 60 2.428888 AAGCAAAGCAAAGCAGTAGC 57.571 45.000 0.00 0.00 42.56 3.58
60 61 1.321474 AGCAAAGCAAAGCAGTAGCA 58.679 45.000 0.00 0.00 45.49 3.49
61 62 1.268899 AGCAAAGCAAAGCAGTAGCAG 59.731 47.619 0.00 0.00 45.49 4.24
62 63 1.694639 CAAAGCAAAGCAGTAGCAGC 58.305 50.000 0.00 0.00 45.49 5.25
63 64 1.001048 CAAAGCAAAGCAGTAGCAGCA 60.001 47.619 0.00 0.00 45.49 4.41
191 193 9.011095 AGCCTCCTTAACAATTTTAGTAAGTTC 57.989 33.333 0.00 0.00 0.00 3.01
449 452 8.682936 ACAGATACAAGATAATTTGGATCACC 57.317 34.615 12.15 0.00 46.43 4.02
602 610 8.046708 AGTGTGATATGTTAACCTGCTAATTCA 58.953 33.333 2.48 0.00 0.00 2.57
738 746 1.672881 CAATCACGGATGAAAGAGGCC 59.327 52.381 0.00 0.00 38.69 5.19
739 747 0.911769 ATCACGGATGAAAGAGGCCA 59.088 50.000 5.01 0.00 38.69 5.36
740 748 0.911769 TCACGGATGAAAGAGGCCAT 59.088 50.000 5.01 0.00 0.00 4.40
741 749 1.019673 CACGGATGAAAGAGGCCATG 58.980 55.000 5.01 0.00 0.00 3.66
742 750 0.620556 ACGGATGAAAGAGGCCATGT 59.379 50.000 5.01 0.00 0.00 3.21
743 751 1.303309 CGGATGAAAGAGGCCATGTC 58.697 55.000 5.01 0.00 0.00 3.06
744 752 1.134280 CGGATGAAAGAGGCCATGTCT 60.134 52.381 5.01 0.00 0.00 3.41
745 753 2.570135 GGATGAAAGAGGCCATGTCTC 58.430 52.381 5.01 5.46 34.04 3.36
746 754 2.092753 GGATGAAAGAGGCCATGTCTCA 60.093 50.000 5.01 0.71 36.65 3.27
747 755 3.614092 GATGAAAGAGGCCATGTCTCAA 58.386 45.455 5.01 0.00 36.65 3.02
748 756 3.507162 TGAAAGAGGCCATGTCTCAAA 57.493 42.857 5.01 0.00 36.65 2.69
749 757 3.149196 TGAAAGAGGCCATGTCTCAAAC 58.851 45.455 5.01 6.46 36.65 2.93
750 758 3.181440 TGAAAGAGGCCATGTCTCAAACT 60.181 43.478 5.01 0.00 36.65 2.66
751 759 3.515602 AAGAGGCCATGTCTCAAACTT 57.484 42.857 5.01 0.00 36.65 2.66
752 760 2.787994 AGAGGCCATGTCTCAAACTTG 58.212 47.619 5.01 0.00 36.65 3.16
753 761 2.107204 AGAGGCCATGTCTCAAACTTGT 59.893 45.455 5.01 0.00 36.65 3.16
754 762 3.327757 AGAGGCCATGTCTCAAACTTGTA 59.672 43.478 5.01 0.00 36.65 2.41
755 763 4.072131 GAGGCCATGTCTCAAACTTGTAA 58.928 43.478 5.01 0.00 34.02 2.41
756 764 3.821033 AGGCCATGTCTCAAACTTGTAAC 59.179 43.478 5.01 0.00 32.49 2.50
757 765 3.821033 GGCCATGTCTCAAACTTGTAACT 59.179 43.478 0.00 0.00 32.49 2.24
758 766 4.320494 GGCCATGTCTCAAACTTGTAACTG 60.320 45.833 0.00 0.00 32.49 3.16
759 767 4.787598 CCATGTCTCAAACTTGTAACTGC 58.212 43.478 0.00 0.00 32.49 4.40
760 768 4.320494 CCATGTCTCAAACTTGTAACTGCC 60.320 45.833 0.00 0.00 32.49 4.85
761 769 4.150897 TGTCTCAAACTTGTAACTGCCT 57.849 40.909 0.00 0.00 0.00 4.75
762 770 4.523083 TGTCTCAAACTTGTAACTGCCTT 58.477 39.130 0.00 0.00 0.00 4.35
763 771 4.574828 TGTCTCAAACTTGTAACTGCCTTC 59.425 41.667 0.00 0.00 0.00 3.46
764 772 4.816925 GTCTCAAACTTGTAACTGCCTTCT 59.183 41.667 0.00 0.00 0.00 2.85
765 773 5.050023 GTCTCAAACTTGTAACTGCCTTCTC 60.050 44.000 0.00 0.00 0.00 2.87
766 774 5.036117 TCAAACTTGTAACTGCCTTCTCT 57.964 39.130 0.00 0.00 0.00 3.10
767 775 5.437060 TCAAACTTGTAACTGCCTTCTCTT 58.563 37.500 0.00 0.00 0.00 2.85
768 776 5.296780 TCAAACTTGTAACTGCCTTCTCTTG 59.703 40.000 0.00 0.00 0.00 3.02
769 777 3.744660 ACTTGTAACTGCCTTCTCTTGG 58.255 45.455 0.00 0.00 0.00 3.61
770 778 3.391296 ACTTGTAACTGCCTTCTCTTGGA 59.609 43.478 0.00 0.00 0.00 3.53
771 779 3.685139 TGTAACTGCCTTCTCTTGGAG 57.315 47.619 0.00 0.00 0.00 3.86
772 780 3.239449 TGTAACTGCCTTCTCTTGGAGA 58.761 45.455 0.00 0.00 36.86 3.71
773 781 3.646162 TGTAACTGCCTTCTCTTGGAGAA 59.354 43.478 9.24 9.24 45.01 2.87
774 782 3.864789 AACTGCCTTCTCTTGGAGAAA 57.135 42.857 10.55 0.00 46.18 2.52
775 783 4.379302 AACTGCCTTCTCTTGGAGAAAT 57.621 40.909 10.55 0.00 46.18 2.17
776 784 5.505181 AACTGCCTTCTCTTGGAGAAATA 57.495 39.130 10.55 1.34 46.18 1.40
777 785 5.707066 ACTGCCTTCTCTTGGAGAAATAT 57.293 39.130 10.55 0.00 46.18 1.28
778 786 5.435291 ACTGCCTTCTCTTGGAGAAATATG 58.565 41.667 10.55 5.45 46.18 1.78
779 787 5.045286 ACTGCCTTCTCTTGGAGAAATATGT 60.045 40.000 10.55 5.93 46.18 2.29
780 788 5.431765 TGCCTTCTCTTGGAGAAATATGTC 58.568 41.667 10.55 0.00 46.18 3.06
781 789 5.190528 TGCCTTCTCTTGGAGAAATATGTCT 59.809 40.000 10.55 0.00 46.18 3.41
782 790 5.526846 GCCTTCTCTTGGAGAAATATGTCTG 59.473 44.000 0.00 0.00 46.18 3.51
783 791 6.648192 CCTTCTCTTGGAGAAATATGTCTGT 58.352 40.000 0.00 0.00 46.18 3.41
784 792 7.633772 GCCTTCTCTTGGAGAAATATGTCTGTA 60.634 40.741 0.00 0.00 46.18 2.74
848 861 0.831307 GTCACCCCTGAGTATCCCAC 59.169 60.000 0.00 0.00 0.00 4.61
894 907 1.141881 GCTCTCTCGATCGGCCAAA 59.858 57.895 16.41 0.00 0.00 3.28
993 1007 2.739132 GGAACGTCGGACCTTGGT 59.261 61.111 1.91 0.00 0.00 3.67
1248 1262 1.946984 TGGGAGACTGGGAACGTATT 58.053 50.000 0.00 0.00 0.00 1.89
1249 1263 1.553248 TGGGAGACTGGGAACGTATTG 59.447 52.381 0.00 0.00 0.00 1.90
1259 1273 2.477863 GGGAACGTATTGTGCATCAAGC 60.478 50.000 0.00 0.00 45.96 4.01
1499 1514 0.327924 AGGGTTCGGCATGATGTTCA 59.672 50.000 0.00 0.00 0.00 3.18
1502 1517 1.164411 GTTCGGCATGATGTTCACCA 58.836 50.000 0.00 0.00 0.00 4.17
1579 1594 1.076332 GCGTTACGAGAAACTGGCAT 58.924 50.000 9.62 0.00 0.00 4.40
1584 1599 1.609208 ACGAGAAACTGGCATGCTTT 58.391 45.000 18.92 10.48 0.00 3.51
1626 1641 3.489355 TGGTCATGATTGCAAAGAGTGT 58.511 40.909 1.71 0.00 0.00 3.55
1788 1803 1.966451 GCCGGGAAAGACAGTGGTG 60.966 63.158 2.18 0.00 0.00 4.17
1794 1813 0.472471 GAAAGACAGTGGTGGACCCA 59.528 55.000 0.00 0.00 42.51 4.51
1865 1884 0.540454 CAAGGAGATCCAGCAGCTCA 59.460 55.000 0.92 0.00 38.89 4.26
1980 1999 2.187946 GCACATGCCTCGCCTACT 59.812 61.111 0.00 0.00 34.31 2.57
2096 2115 5.957771 TGAATATCCTAGCTTGGAACTGT 57.042 39.130 20.95 7.11 39.85 3.55
2307 2336 2.265367 TGGGATGAGAAGTTGCAGGTA 58.735 47.619 0.00 0.00 0.00 3.08
2381 2410 7.099120 GTGGCAAATGATAAAAGTTGGAGAAT 58.901 34.615 0.00 0.00 0.00 2.40
2474 2503 2.267351 TTTCGTCGGAGCCGTGGTA 61.267 57.895 8.96 0.00 40.74 3.25
2545 2575 2.780595 GCCCAGCGCTCTGAAAATA 58.219 52.632 7.13 0.00 42.95 1.40
2551 2581 3.873361 CCAGCGCTCTGAAAATAAGATGA 59.127 43.478 7.13 0.00 42.95 2.92
2561 2591 9.618890 CTCTGAAAATAAGATGAGGTTATTCCA 57.381 33.333 0.00 0.00 39.02 3.53
2603 2633 4.524053 GAATTATGGGACCTCGGTTTCTT 58.476 43.478 0.00 0.00 0.00 2.52
2650 2681 1.556911 GGCAGATTGGAGAGAGGAACA 59.443 52.381 0.00 0.00 0.00 3.18
2675 2706 0.102481 GTTCGCCTTGATCGAGCCTA 59.898 55.000 4.21 0.00 37.26 3.93
2754 2785 2.046292 TCATGTTCTGACCACTGTCCA 58.954 47.619 0.00 0.00 41.01 4.02
2807 2838 1.003646 AGGACTACAGCCTCTCCTCA 58.996 55.000 0.00 0.00 0.00 3.86
2828 2859 6.806668 TCAGTATGAGATTATGTGGGAACA 57.193 37.500 0.00 0.00 42.56 3.18
3072 3103 1.279152 CTCAACTCGATGAGCTGCTG 58.721 55.000 7.01 0.00 40.31 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.619074 GCAAGCAAAGGGATCTACCTGT 60.619 50.000 0.00 0.00 40.87 4.00
6 7 2.019984 GCAAGCAAAGGGATCTACCTG 58.980 52.381 0.00 0.00 40.87 4.00
7 8 1.918957 AGCAAGCAAAGGGATCTACCT 59.081 47.619 0.00 0.00 44.56 3.08
8 9 2.426842 AGCAAGCAAAGGGATCTACC 57.573 50.000 0.00 0.00 38.08 3.18
9 10 5.648092 TCTTTAAGCAAGCAAAGGGATCTAC 59.352 40.000 0.00 0.00 33.48 2.59
11 12 4.666512 TCTTTAAGCAAGCAAAGGGATCT 58.333 39.130 0.00 0.00 33.48 2.75
12 13 5.391312 TTCTTTAAGCAAGCAAAGGGATC 57.609 39.130 5.41 0.00 33.48 3.36
13 14 5.806654 TTTCTTTAAGCAAGCAAAGGGAT 57.193 34.783 5.41 0.00 33.48 3.85
14 15 5.362430 TCTTTTCTTTAAGCAAGCAAAGGGA 59.638 36.000 7.29 0.00 42.72 4.20
15 16 5.600696 TCTTTTCTTTAAGCAAGCAAAGGG 58.399 37.500 7.29 0.00 42.72 3.95
16 17 7.538303 TTTCTTTTCTTTAAGCAAGCAAAGG 57.462 32.000 7.29 0.00 42.72 3.11
17 18 7.637519 GCTTTTCTTTTCTTTAAGCAAGCAAAG 59.362 33.333 16.45 16.45 43.41 2.77
18 19 7.118971 TGCTTTTCTTTTCTTTAAGCAAGCAAA 59.881 29.630 14.84 0.00 45.66 3.68
19 20 6.593382 TGCTTTTCTTTTCTTTAAGCAAGCAA 59.407 30.769 14.84 5.24 45.66 3.91
20 21 6.105333 TGCTTTTCTTTTCTTTAAGCAAGCA 58.895 32.000 13.91 13.91 45.66 3.91
21 22 6.588348 TGCTTTTCTTTTCTTTAAGCAAGC 57.412 33.333 0.00 0.00 45.66 4.01
24 25 6.593382 TGCTTTGCTTTTCTTTTCTTTAAGCA 59.407 30.769 0.00 0.00 46.60 3.91
25 26 7.003939 TGCTTTGCTTTTCTTTTCTTTAAGC 57.996 32.000 0.00 0.00 41.10 3.09
26 27 9.481800 CTTTGCTTTGCTTTTCTTTTCTTTAAG 57.518 29.630 0.00 0.00 0.00 1.85
27 28 7.962373 GCTTTGCTTTGCTTTTCTTTTCTTTAA 59.038 29.630 0.00 0.00 0.00 1.52
28 29 7.118971 TGCTTTGCTTTGCTTTTCTTTTCTTTA 59.881 29.630 0.00 0.00 0.00 1.85
29 30 6.072563 TGCTTTGCTTTGCTTTTCTTTTCTTT 60.073 30.769 0.00 0.00 0.00 2.52
30 31 5.412286 TGCTTTGCTTTGCTTTTCTTTTCTT 59.588 32.000 0.00 0.00 0.00 2.52
31 32 4.937015 TGCTTTGCTTTGCTTTTCTTTTCT 59.063 33.333 0.00 0.00 0.00 2.52
32 33 5.163824 ACTGCTTTGCTTTGCTTTTCTTTTC 60.164 36.000 0.00 0.00 0.00 2.29
33 34 4.696877 ACTGCTTTGCTTTGCTTTTCTTTT 59.303 33.333 0.00 0.00 0.00 2.27
34 35 4.256110 ACTGCTTTGCTTTGCTTTTCTTT 58.744 34.783 0.00 0.00 0.00 2.52
35 36 3.865446 ACTGCTTTGCTTTGCTTTTCTT 58.135 36.364 0.00 0.00 0.00 2.52
36 37 3.531934 ACTGCTTTGCTTTGCTTTTCT 57.468 38.095 0.00 0.00 0.00 2.52
37 38 3.183172 GCTACTGCTTTGCTTTGCTTTTC 59.817 43.478 0.00 0.00 36.03 2.29
38 39 3.126073 GCTACTGCTTTGCTTTGCTTTT 58.874 40.909 0.00 0.00 36.03 2.27
39 40 2.101249 TGCTACTGCTTTGCTTTGCTTT 59.899 40.909 0.00 0.00 40.48 3.51
40 41 1.682854 TGCTACTGCTTTGCTTTGCTT 59.317 42.857 0.00 0.00 40.48 3.91
41 42 1.268899 CTGCTACTGCTTTGCTTTGCT 59.731 47.619 0.00 0.00 40.48 3.91
42 43 1.694639 CTGCTACTGCTTTGCTTTGC 58.305 50.000 0.00 0.00 40.48 3.68
43 44 1.001048 TGCTGCTACTGCTTTGCTTTG 60.001 47.619 0.00 0.00 40.48 2.77
44 45 1.268899 CTGCTGCTACTGCTTTGCTTT 59.731 47.619 0.00 0.00 40.48 3.51
45 46 0.879765 CTGCTGCTACTGCTTTGCTT 59.120 50.000 0.00 0.00 40.48 3.91
46 47 0.959372 CCTGCTGCTACTGCTTTGCT 60.959 55.000 0.00 0.00 40.48 3.91
47 48 1.505353 CCTGCTGCTACTGCTTTGC 59.495 57.895 0.00 0.00 40.48 3.68
48 49 1.930908 GCCCTGCTGCTACTGCTTTG 61.931 60.000 0.00 0.00 40.48 2.77
49 50 1.676967 GCCCTGCTGCTACTGCTTT 60.677 57.895 0.00 0.00 40.48 3.51
50 51 2.045536 GCCCTGCTGCTACTGCTT 60.046 61.111 0.00 0.00 40.48 3.91
51 52 4.463879 CGCCCTGCTGCTACTGCT 62.464 66.667 0.00 0.00 40.48 4.24
53 54 3.729965 CTCCGCCCTGCTGCTACTG 62.730 68.421 0.00 0.00 0.00 2.74
54 55 3.465403 CTCCGCCCTGCTGCTACT 61.465 66.667 0.00 0.00 0.00 2.57
120 122 7.870509 TGCTCTCTGTAATTATCTTTTGCAT 57.129 32.000 0.00 0.00 0.00 3.96
191 193 2.253392 GCTGGTTGCTTCGAATTCTG 57.747 50.000 0.00 0.00 38.95 3.02
535 542 8.316946 ACTCTCATCTCATATCAGTGTTGAAAA 58.683 33.333 0.00 0.00 36.78 2.29
550 558 7.345691 ACTAATCTCTCTCAACTCTCATCTCA 58.654 38.462 0.00 0.00 0.00 3.27
602 610 8.856153 ACTACTCACTATCTGATTCATACGAT 57.144 34.615 0.00 0.00 0.00 3.73
687 695 2.967615 GGGATTAGACGCGGCTGC 60.968 66.667 28.40 14.05 37.91 5.25
738 746 4.516698 AGGCAGTTACAAGTTTGAGACATG 59.483 41.667 0.00 0.00 33.31 3.21
739 747 4.718961 AGGCAGTTACAAGTTTGAGACAT 58.281 39.130 0.00 0.00 0.00 3.06
740 748 4.150897 AGGCAGTTACAAGTTTGAGACA 57.849 40.909 0.00 0.00 0.00 3.41
741 749 4.816925 AGAAGGCAGTTACAAGTTTGAGAC 59.183 41.667 0.00 0.00 0.00 3.36
742 750 5.036117 AGAAGGCAGTTACAAGTTTGAGA 57.964 39.130 0.00 0.00 0.00 3.27
743 751 5.059833 AGAGAAGGCAGTTACAAGTTTGAG 58.940 41.667 0.00 0.00 0.00 3.02
744 752 5.036117 AGAGAAGGCAGTTACAAGTTTGA 57.964 39.130 0.00 0.00 0.00 2.69
745 753 5.506317 CCAAGAGAAGGCAGTTACAAGTTTG 60.506 44.000 0.00 0.00 0.00 2.93
746 754 4.580580 CCAAGAGAAGGCAGTTACAAGTTT 59.419 41.667 0.00 0.00 0.00 2.66
747 755 4.137543 CCAAGAGAAGGCAGTTACAAGTT 58.862 43.478 0.00 0.00 0.00 2.66
748 756 3.391296 TCCAAGAGAAGGCAGTTACAAGT 59.609 43.478 0.00 0.00 0.00 3.16
749 757 3.999663 CTCCAAGAGAAGGCAGTTACAAG 59.000 47.826 0.00 0.00 0.00 3.16
750 758 3.646162 TCTCCAAGAGAAGGCAGTTACAA 59.354 43.478 0.00 0.00 35.59 2.41
751 759 3.239449 TCTCCAAGAGAAGGCAGTTACA 58.761 45.455 0.00 0.00 35.59 2.41
752 760 3.963428 TCTCCAAGAGAAGGCAGTTAC 57.037 47.619 0.00 0.00 35.59 2.50
761 769 8.424918 GGATACAGACATATTTCTCCAAGAGAA 58.575 37.037 2.94 2.94 45.45 2.87
762 770 7.015682 GGGATACAGACATATTTCTCCAAGAGA 59.984 40.741 0.00 0.00 35.77 3.10
763 771 7.158021 GGGATACAGACATATTTCTCCAAGAG 58.842 42.308 0.00 0.00 39.74 2.85
764 772 6.043243 GGGGATACAGACATATTTCTCCAAGA 59.957 42.308 0.00 0.00 39.74 3.02
765 773 6.043706 AGGGGATACAGACATATTTCTCCAAG 59.956 42.308 0.00 0.00 39.74 3.61
766 774 5.911178 AGGGGATACAGACATATTTCTCCAA 59.089 40.000 0.00 0.00 39.74 3.53
767 775 5.476983 AGGGGATACAGACATATTTCTCCA 58.523 41.667 0.00 0.00 39.74 3.86
768 776 5.336849 CGAGGGGATACAGACATATTTCTCC 60.337 48.000 0.00 0.00 39.74 3.71
769 777 5.715070 CGAGGGGATACAGACATATTTCTC 58.285 45.833 0.00 0.00 39.74 2.87
770 778 4.021016 GCGAGGGGATACAGACATATTTCT 60.021 45.833 0.00 0.00 39.74 2.52
771 779 4.246458 GCGAGGGGATACAGACATATTTC 58.754 47.826 0.00 0.00 39.74 2.17
772 780 3.306088 CGCGAGGGGATACAGACATATTT 60.306 47.826 0.00 0.00 39.74 1.40
773 781 2.231478 CGCGAGGGGATACAGACATATT 59.769 50.000 0.00 0.00 39.74 1.28
774 782 1.819288 CGCGAGGGGATACAGACATAT 59.181 52.381 0.00 0.00 39.74 1.78
775 783 1.244816 CGCGAGGGGATACAGACATA 58.755 55.000 0.00 0.00 39.74 2.29
776 784 2.041976 CGCGAGGGGATACAGACAT 58.958 57.895 0.00 0.00 39.74 3.06
777 785 2.782222 GCGCGAGGGGATACAGACA 61.782 63.158 12.10 0.00 39.74 3.41
778 786 2.027751 GCGCGAGGGGATACAGAC 59.972 66.667 12.10 0.00 39.74 3.51
779 787 2.016393 CTTGCGCGAGGGGATACAGA 62.016 60.000 17.45 0.00 39.74 3.41
780 788 1.592669 CTTGCGCGAGGGGATACAG 60.593 63.158 17.45 0.00 39.74 2.74
781 789 2.499205 CTTGCGCGAGGGGATACA 59.501 61.111 17.45 0.00 39.74 2.29
782 790 2.280186 CCTTGCGCGAGGGGATAC 60.280 66.667 32.89 0.00 32.94 2.24
783 791 4.235762 GCCTTGCGCGAGGGGATA 62.236 66.667 38.52 0.00 37.29 2.59
832 843 1.004361 GGGTGGGATACTCAGGGGT 59.996 63.158 0.00 0.00 0.00 4.95
848 861 1.979693 GGAGGGAGATCGATCGGGG 60.980 68.421 19.33 0.00 0.00 5.73
917 931 2.202932 CGGGAGGCTCCATCGTTG 60.203 66.667 33.27 12.45 38.64 4.10
982 996 2.617788 CCATGAAATCACCAAGGTCCGA 60.618 50.000 0.00 0.00 0.00 4.55
993 1007 5.009911 CAGGTTGAGTTGTTCCATGAAATCA 59.990 40.000 0.00 0.00 0.00 2.57
1140 1154 1.764571 AAGCCGCCCGCATATCCTTA 61.765 55.000 0.00 0.00 41.38 2.69
1248 1262 2.628696 CCAAGGCGCTTGATGCACA 61.629 57.895 17.53 0.00 43.42 4.57
1249 1263 2.180017 CCAAGGCGCTTGATGCAC 59.820 61.111 17.53 0.00 43.42 4.57
1319 1334 2.065799 ACACCATGGGAACTTCCTCTT 58.934 47.619 18.09 0.00 36.57 2.85
1499 1514 0.846693 AAACTTGGTGAGAGGCTGGT 59.153 50.000 0.00 0.00 0.00 4.00
1502 1517 1.490490 TGACAAACTTGGTGAGAGGCT 59.510 47.619 0.00 0.00 0.00 4.58
1579 1594 0.173029 CCACACACACTGCAAAAGCA 59.827 50.000 0.00 0.00 0.00 3.91
1584 1599 1.823470 GAGCCCACACACACTGCAA 60.823 57.895 0.00 0.00 0.00 4.08
1626 1641 1.638679 CCTCATGCACCCCTGATCCA 61.639 60.000 0.00 0.00 0.00 3.41
1724 1739 4.744570 CGTATGTTGCTTCTGACTCCTTA 58.255 43.478 0.00 0.00 0.00 2.69
1788 1803 2.565841 GTATCAAGCATGTCTGGGTCC 58.434 52.381 0.00 0.00 0.00 4.46
1794 1813 2.430694 TGTAGCCGTATCAAGCATGTCT 59.569 45.455 0.00 0.00 0.00 3.41
1865 1884 3.251484 TCCTCCATGGAGAGTCTTTTGT 58.749 45.455 38.37 0.00 44.53 2.83
1980 1999 2.690497 CCTCTTACTGCTAGCACTGCTA 59.310 50.000 14.93 10.39 40.44 3.49
2307 2336 1.238439 CACAAGAATCCAGCACCGTT 58.762 50.000 0.00 0.00 0.00 4.44
2381 2410 3.395639 GGTTCACCATAGACAAACGTCA 58.604 45.455 0.00 0.00 34.22 4.35
2474 2503 5.308825 CCTCATTAAAGTCTCCACACACTT 58.691 41.667 0.00 0.00 34.16 3.16
2545 2575 4.785376 ACAGTCCTGGAATAACCTCATCTT 59.215 41.667 0.00 0.00 39.86 2.40
2551 2581 4.724279 ACAAACAGTCCTGGAATAACCT 57.276 40.909 0.00 0.00 39.86 3.50
2561 2591 0.675633 GCATGCCAACAAACAGTCCT 59.324 50.000 6.36 0.00 0.00 3.85
2675 2706 2.366837 TCCACCCCTCATCCGCAT 60.367 61.111 0.00 0.00 0.00 4.73
2807 2838 5.428457 TGGTGTTCCCACATAATCTCATACT 59.572 40.000 0.00 0.00 43.71 2.12
2828 2859 4.619227 CTGACAACGCCGGGTGGT 62.619 66.667 12.97 1.27 34.70 4.16


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

AutoCloner maintained by Alex Coulton.