Multiple sequence alignment - TraesCS1A01G054200

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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 TraesCS1A01G054200 chr1A 100.000 2793 0 0 1 2793 35579497 35576705 0.000000e+00 5158.0
1 TraesCS1A01G054200 chr1A 89.965 1734 158 10 844 2574 35485993 35487713 0.000000e+00 2224.0
2 TraesCS1A01G054200 chr1A 87.039 1844 171 30 866 2687 35536206 35538003 0.000000e+00 2019.0
3 TraesCS1A01G054200 chr1A 88.840 1577 168 4 1000 2574 35525793 35527363 0.000000e+00 1930.0
4 TraesCS1A01G054200 chr1A 86.139 606 64 12 125 718 35514441 35515038 1.090000e-178 636.0
5 TraesCS1A01G054200 chr1A 87.211 563 55 9 121 673 35535343 35535898 2.360000e-175 625.0
6 TraesCS1A01G054200 chr1A 81.831 710 73 32 121 788 35484912 35485607 1.890000e-151 545.0
7 TraesCS1A01G054200 chr1D 91.854 1731 133 6 849 2574 36315606 36317333 0.000000e+00 2409.0
8 TraesCS1A01G054200 chr1D 90.495 1536 127 13 121 1646 36363882 36362356 0.000000e+00 2010.0
9 TraesCS1A01G054200 chr1D 93.845 1121 65 3 1675 2791 36362365 36361245 0.000000e+00 1685.0
10 TraesCS1A01G054200 chr1D 89.078 293 25 4 341 629 36314955 36315244 9.510000e-95 357.0
11 TraesCS1A01G054200 chr1D 100.000 31 0 0 95 125 180780026 180780056 1.080000e-04 58.4
12 TraesCS1A01G054200 chr1B 86.921 1858 182 30 246 2062 55976421 55978258 0.000000e+00 2028.0
13 TraesCS1A01G054200 chr1B 93.688 1204 75 1 859 2062 56140945 56139743 0.000000e+00 1801.0
14 TraesCS1A01G054200 chr1B 86.707 1640 183 21 846 2465 56016955 56018579 0.000000e+00 1788.0
15 TraesCS1A01G054200 chr1B 89.871 1244 122 2 820 2062 55998277 55999517 0.000000e+00 1596.0
16 TraesCS1A01G054200 chr1B 93.352 707 44 2 2089 2793 56139746 56139041 0.000000e+00 1042.0
17 TraesCS1A01G054200 chr1B 93.760 641 36 3 95 734 56141897 56141260 0.000000e+00 959.0
18 TraesCS1A01G054200 chr1B 92.324 482 35 2 2089 2568 55978255 55978736 0.000000e+00 684.0
19 TraesCS1A01G054200 chr1B 91.701 482 38 2 2089 2568 55999514 55999995 0.000000e+00 667.0
20 TraesCS1A01G054200 chr1B 87.935 489 47 9 246 733 56016177 56016654 1.450000e-157 566.0
21 TraesCS1A01G054200 chr1B 85.930 398 44 8 340 736 55997579 55997965 5.570000e-112 414.0
22 TraesCS1A01G054200 chr1B 89.916 119 8 4 2678 2793 188913780 188913663 1.730000e-32 150.0
23 TraesCS1A01G054200 chrUn 100.000 98 0 0 1 98 384318797 384318894 6.150000e-42 182.0
24 TraesCS1A01G054200 chr4A 100.000 98 0 0 1 98 240382435 240382338 6.150000e-42 182.0
25 TraesCS1A01G054200 chr4A 93.519 108 7 0 2684 2791 47750345 47750238 8.010000e-36 161.0
26 TraesCS1A01G054200 chr6B 99.010 101 0 1 1 100 29476788 29476888 2.210000e-41 180.0
27 TraesCS1A01G054200 chr6B 94.643 112 4 2 1 112 577285863 577285972 3.700000e-39 172.0
28 TraesCS1A01G054200 chr6B 95.413 109 1 3 1 109 79869921 79870025 1.330000e-38 171.0
29 TraesCS1A01G054200 chr5A 98.039 102 2 0 1 102 215053817 215053716 7.950000e-41 178.0
30 TraesCS1A01G054200 chr5A 94.737 114 2 4 1 114 215591636 215591527 1.030000e-39 174.0
31 TraesCS1A01G054200 chr5A 92.308 117 7 2 1 116 130102378 130102263 6.190000e-37 165.0
32 TraesCS1A01G054200 chr3A 97.030 101 3 0 1 101 266730288 266730388 1.330000e-38 171.0
33 TraesCS1A01G054200 chr6D 94.175 103 5 1 2689 2791 431160670 431160771 3.720000e-34 156.0
34 TraesCS1A01G054200 chr5D 93.333 105 7 0 2689 2793 412100099 412100203 3.720000e-34 156.0
35 TraesCS1A01G054200 chr4D 92.593 108 8 0 2684 2791 416061557 416061664 3.720000e-34 156.0
36 TraesCS1A01G054200 chr4D 100.000 31 0 0 95 125 225373788 225373818 1.080000e-04 58.4
37 TraesCS1A01G054200 chr2A 91.818 110 9 0 2682 2791 2784818 2784709 1.340000e-33 154.0
38 TraesCS1A01G054200 chr7B 88.525 122 14 0 2670 2791 431659080 431659201 6.230000e-32 148.0
39 TraesCS1A01G054200 chr7D 88.889 45 1 3 95 139 202952159 202952119 5.000000e-03 52.8


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 TraesCS1A01G054200 chr1A 35576705 35579497 2792 True 5158.000000 5158 100.000000 1 2793 1 chr1A.!!$R1 2792
1 TraesCS1A01G054200 chr1A 35525793 35527363 1570 False 1930.000000 1930 88.840000 1000 2574 1 chr1A.!!$F2 1574
2 TraesCS1A01G054200 chr1A 35484912 35487713 2801 False 1384.500000 2224 85.898000 121 2574 2 chr1A.!!$F3 2453
3 TraesCS1A01G054200 chr1A 35535343 35538003 2660 False 1322.000000 2019 87.125000 121 2687 2 chr1A.!!$F4 2566
4 TraesCS1A01G054200 chr1A 35514441 35515038 597 False 636.000000 636 86.139000 125 718 1 chr1A.!!$F1 593
5 TraesCS1A01G054200 chr1D 36361245 36363882 2637 True 1847.500000 2010 92.170000 121 2791 2 chr1D.!!$R1 2670
6 TraesCS1A01G054200 chr1D 36314955 36317333 2378 False 1383.000000 2409 90.466000 341 2574 2 chr1D.!!$F2 2233
7 TraesCS1A01G054200 chr1B 55976421 55978736 2315 False 1356.000000 2028 89.622500 246 2568 2 chr1B.!!$F1 2322
8 TraesCS1A01G054200 chr1B 56139041 56141897 2856 True 1267.333333 1801 93.600000 95 2793 3 chr1B.!!$R2 2698
9 TraesCS1A01G054200 chr1B 56016177 56018579 2402 False 1177.000000 1788 87.321000 246 2465 2 chr1B.!!$F3 2219
10 TraesCS1A01G054200 chr1B 55997579 55999995 2416 False 892.333333 1596 89.167333 340 2568 3 chr1B.!!$F2 2228

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
93 94 0.394488 TTCTGCAACGTTCCCCAACA 60.394 50.0 0.0 0.0 32.14 3.33 F
1012 1447 0.608130 CCCAGTCATGGTGAACTCGA 59.392 55.0 0.0 0.0 46.10 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1696 0.460459 GGCGAAGTTGTAGCCTCTCC 60.46 60.0 6.41 0.0 46.83 3.71 R
2270 2764 0.660488 TACAACGCAACCAAGCAGTG 59.34 50.0 0.00 0.0 0.00 3.66 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 2.993937 ACTCTCTCCCTAGACTCGTTG 58.006 52.381 0.00 0.00 0.00 4.10
21 22 1.673920 CTCTCTCCCTAGACTCGTTGC 59.326 57.143 0.00 0.00 0.00 4.17
22 23 1.282447 TCTCTCCCTAGACTCGTTGCT 59.718 52.381 0.00 0.00 0.00 3.91
23 24 2.096248 CTCTCCCTAGACTCGTTGCTT 58.904 52.381 0.00 0.00 0.00 3.91
24 25 3.054582 TCTCTCCCTAGACTCGTTGCTTA 60.055 47.826 0.00 0.00 0.00 3.09
25 26 3.280295 TCTCCCTAGACTCGTTGCTTAG 58.720 50.000 0.00 0.00 0.00 2.18
26 27 3.054582 TCTCCCTAGACTCGTTGCTTAGA 60.055 47.826 0.00 0.00 0.00 2.10
27 28 3.886505 CTCCCTAGACTCGTTGCTTAGAT 59.113 47.826 0.00 0.00 0.00 1.98
28 29 3.632604 TCCCTAGACTCGTTGCTTAGATG 59.367 47.826 0.00 0.00 0.00 2.90
29 30 3.632604 CCCTAGACTCGTTGCTTAGATGA 59.367 47.826 0.00 0.00 0.00 2.92
30 31 4.098044 CCCTAGACTCGTTGCTTAGATGAA 59.902 45.833 0.00 0.00 0.00 2.57
31 32 5.038033 CCTAGACTCGTTGCTTAGATGAAC 58.962 45.833 0.00 0.00 0.00 3.18
32 33 4.792521 AGACTCGTTGCTTAGATGAACT 57.207 40.909 0.00 0.00 0.00 3.01
33 34 4.739195 AGACTCGTTGCTTAGATGAACTC 58.261 43.478 0.00 0.00 0.00 3.01
34 35 4.218635 AGACTCGTTGCTTAGATGAACTCA 59.781 41.667 0.00 0.00 0.00 3.41
35 36 5.078411 ACTCGTTGCTTAGATGAACTCAT 57.922 39.130 0.00 0.00 39.70 2.90
36 37 6.095580 AGACTCGTTGCTTAGATGAACTCATA 59.904 38.462 0.00 0.00 36.57 2.15
37 38 6.269315 ACTCGTTGCTTAGATGAACTCATAG 58.731 40.000 0.00 0.00 36.57 2.23
38 39 6.095580 ACTCGTTGCTTAGATGAACTCATAGA 59.904 38.462 0.00 0.00 36.57 1.98
39 40 7.043961 TCGTTGCTTAGATGAACTCATAGAT 57.956 36.000 0.00 0.00 36.57 1.98
40 41 6.920210 TCGTTGCTTAGATGAACTCATAGATG 59.080 38.462 0.00 0.00 36.57 2.90
41 42 6.145209 CGTTGCTTAGATGAACTCATAGATGG 59.855 42.308 0.00 0.00 36.57 3.51
42 43 6.983906 TGCTTAGATGAACTCATAGATGGA 57.016 37.500 0.00 0.00 36.57 3.41
43 44 7.550597 TGCTTAGATGAACTCATAGATGGAT 57.449 36.000 0.00 0.00 36.57 3.41
44 45 7.609960 TGCTTAGATGAACTCATAGATGGATC 58.390 38.462 0.00 0.00 36.57 3.36
45 46 7.454066 TGCTTAGATGAACTCATAGATGGATCT 59.546 37.037 0.00 0.00 40.86 2.75
46 47 8.313292 GCTTAGATGAACTCATAGATGGATCTT 58.687 37.037 0.00 0.00 38.32 2.40
47 48 9.642327 CTTAGATGAACTCATAGATGGATCTTG 57.358 37.037 0.00 0.00 38.32 3.02
48 49 7.006865 AGATGAACTCATAGATGGATCTTGG 57.993 40.000 0.00 0.00 38.32 3.61
49 50 6.558014 AGATGAACTCATAGATGGATCTTGGT 59.442 38.462 0.00 0.00 38.32 3.67
50 51 5.922053 TGAACTCATAGATGGATCTTGGTG 58.078 41.667 0.00 0.00 38.32 4.17
51 52 5.662657 TGAACTCATAGATGGATCTTGGTGA 59.337 40.000 0.00 0.00 38.32 4.02
52 53 6.156775 TGAACTCATAGATGGATCTTGGTGAA 59.843 38.462 0.00 0.00 38.32 3.18
53 54 6.566079 ACTCATAGATGGATCTTGGTGAAA 57.434 37.500 0.00 0.00 38.32 2.69
54 55 6.352516 ACTCATAGATGGATCTTGGTGAAAC 58.647 40.000 0.00 0.00 38.32 2.78
84 85 8.888716 AGGAAAAATTTTAATTTTCTGCAACGT 58.111 25.926 12.19 0.00 45.16 3.99
85 86 9.497030 GGAAAAATTTTAATTTTCTGCAACGTT 57.503 25.926 12.19 0.00 45.16 3.99
87 88 9.497030 AAAAATTTTAATTTTCTGCAACGTTCC 57.503 25.926 12.19 0.00 45.16 3.62
88 89 6.779115 ATTTTAATTTTCTGCAACGTTCCC 57.221 33.333 0.00 0.00 0.00 3.97
89 90 2.812358 AATTTTCTGCAACGTTCCCC 57.188 45.000 0.00 0.00 0.00 4.81
90 91 1.698506 ATTTTCTGCAACGTTCCCCA 58.301 45.000 0.00 0.00 0.00 4.96
91 92 1.475403 TTTTCTGCAACGTTCCCCAA 58.525 45.000 0.00 0.00 0.00 4.12
92 93 0.741915 TTTCTGCAACGTTCCCCAAC 59.258 50.000 0.00 0.00 0.00 3.77
93 94 0.394488 TTCTGCAACGTTCCCCAACA 60.394 50.000 0.00 0.00 32.14 3.33
200 202 3.407967 GGCGAGGGGTGGATTGGA 61.408 66.667 0.00 0.00 0.00 3.53
220 222 3.213506 GAATTTTTGGGCAGCAACCTTT 58.786 40.909 0.00 0.00 0.00 3.11
305 320 2.128771 TTTGGGCAGCTATTGGAGAC 57.871 50.000 0.00 0.00 0.00 3.36
311 327 3.267483 GGCAGCTATTGGAGACGTTTTA 58.733 45.455 0.00 0.00 0.00 1.52
316 332 3.625764 GCTATTGGAGACGTTTTATGGCA 59.374 43.478 0.00 0.00 0.00 4.92
417 436 2.091541 ACATGCATGGTTTTAGGTCGG 58.908 47.619 29.41 0.88 0.00 4.79
534 561 8.681486 TTATAGGATCATTCAACATGAAGGTG 57.319 34.615 0.00 0.00 40.05 4.00
775 870 7.265599 TCATTGTACCCTCTCCTAAATTCAA 57.734 36.000 0.00 0.00 0.00 2.69
783 878 4.806247 CCTCTCCTAAATTCAAGCGTACAG 59.194 45.833 0.00 0.00 0.00 2.74
834 1147 8.756486 TCATCAATGACACATCCATCTATTTT 57.244 30.769 0.00 0.00 0.00 1.82
837 1151 7.118060 TCAATGACACATCCATCTATTTTCCA 58.882 34.615 0.00 0.00 0.00 3.53
1012 1447 0.608130 CCCAGTCATGGTGAACTCGA 59.392 55.000 0.00 0.00 46.10 4.04
1117 1552 3.403057 CAACACCGTCGAGTGCCG 61.403 66.667 12.07 0.00 41.67 5.69
1125 1560 2.670592 TCGAGTGCCGAACGAGGA 60.671 61.111 0.00 0.00 45.43 3.71
1164 1600 2.551413 AATGCTCAAGCCCTGGGGT 61.551 57.895 12.68 12.68 41.18 4.95
1200 1636 1.964373 GTGCGTTCCCATCAACCGT 60.964 57.895 0.00 0.00 0.00 4.83
1226 1662 2.886730 GAAACCATCGCCCCGGACAT 62.887 60.000 0.73 0.00 0.00 3.06
1236 1672 3.970332 CCGGACATGGGATCCTCA 58.030 61.111 12.58 8.57 33.70 3.86
1260 1696 3.744942 CGAATCAGCAATATGAGGTCAGG 59.255 47.826 0.00 0.00 31.44 3.86
1272 1708 0.413832 AGGTCAGGGAGAGGCTACAA 59.586 55.000 0.00 0.00 0.00 2.41
1360 1796 2.584608 CCGAGGCGGTTTCTCCAT 59.415 61.111 0.00 0.00 42.73 3.41
1361 1797 1.815421 CCGAGGCGGTTTCTCCATG 60.815 63.158 0.00 0.00 42.73 3.66
1363 1799 1.299976 GAGGCGGTTTCTCCATGGT 59.700 57.895 12.58 0.00 35.57 3.55
1371 1807 3.255642 CGGTTTCTCCATGGTTGTTGAAT 59.744 43.478 12.58 0.00 35.57 2.57
1374 1810 2.170166 TCTCCATGGTTGTTGAATGCC 58.830 47.619 12.58 0.00 0.00 4.40
1376 1812 0.975135 CCATGGTTGTTGAATGCCCA 59.025 50.000 2.57 0.00 0.00 5.36
1546 1982 5.523588 AGGAGATTGAGGAAGACATCTACA 58.476 41.667 0.00 0.00 0.00 2.74
1623 2059 3.599730 AAGCAGATCGATGTGAGTTCA 57.400 42.857 25.37 0.00 0.00 3.18
1624 2060 3.815856 AGCAGATCGATGTGAGTTCAT 57.184 42.857 25.37 1.51 0.00 2.57
1634 2079 1.421268 TGTGAGTTCATGTGCCTCCTT 59.579 47.619 0.00 0.00 0.00 3.36
1665 2110 0.621609 CCGACCCCCTTACATTCCAA 59.378 55.000 0.00 0.00 0.00 3.53
1779 2227 2.682494 GGAGTCCTACCGGGTGCA 60.682 66.667 10.66 0.00 36.25 4.57
1846 2294 5.906073 ACAGTAAGCAAGCAAAGTGAATTT 58.094 33.333 8.03 0.00 0.00 1.82
1912 2360 8.498054 AGCTACATAATCCATCGATTAATTGG 57.502 34.615 0.00 0.00 42.76 3.16
1983 2431 3.748048 TGTAAGCAGCAAGTGATGACTTC 59.252 43.478 0.00 0.00 40.68 3.01
2057 2505 4.430137 CACTAGTGGTGCTTCGTTACTA 57.570 45.455 15.49 0.00 39.22 1.82
2080 2528 5.114764 TGGTATCATCAGCAATTGGAAGA 57.885 39.130 7.72 0.00 0.00 2.87
2081 2529 5.698104 TGGTATCATCAGCAATTGGAAGAT 58.302 37.500 7.72 7.48 0.00 2.40
2168 2657 5.041287 AGTACATTCGTTCACATACATCCG 58.959 41.667 0.00 0.00 0.00 4.18
2260 2754 3.485463 TTGCTAGCTAACTGTTGTGGT 57.515 42.857 17.23 4.52 0.00 4.16
2270 2764 1.789078 CTGTTGTGGTGAGTGCCAGC 61.789 60.000 0.00 0.00 39.53 4.85
2420 2914 4.208686 GGCGTGTCTAGGAGGCCG 62.209 72.222 0.00 0.00 33.58 6.13
2476 2970 1.852965 CCCTTGGTGGTCCCTATCATT 59.147 52.381 0.00 0.00 0.00 2.57
2510 3004 3.810896 GGGTTTCATGACGCCGCC 61.811 66.667 0.00 0.00 0.00 6.13
2528 3022 1.472026 GCCCGGTTCATACGCTTTCTA 60.472 52.381 0.00 0.00 0.00 2.10
2601 3095 0.881796 GTTGGCAGTGGCTAGGAAAC 59.118 55.000 18.53 9.47 40.87 2.78
2705 3202 7.298854 GTGAAATTCTCCTTCCGTTCTTAAAG 58.701 38.462 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.942306 GCAACGAGTCTAGGGAGAGAGT 60.942 54.545 0.00 0.00 30.20 3.24
1 2 1.673920 GCAACGAGTCTAGGGAGAGAG 59.326 57.143 0.00 0.00 30.20 3.20
2 3 1.282447 AGCAACGAGTCTAGGGAGAGA 59.718 52.381 0.00 0.00 30.20 3.10
3 4 1.757682 AGCAACGAGTCTAGGGAGAG 58.242 55.000 0.00 0.00 30.20 3.20
4 5 2.217510 AAGCAACGAGTCTAGGGAGA 57.782 50.000 0.00 0.00 0.00 3.71
5 6 3.280295 TCTAAGCAACGAGTCTAGGGAG 58.720 50.000 0.00 0.00 0.00 4.30
6 7 3.361281 TCTAAGCAACGAGTCTAGGGA 57.639 47.619 0.00 0.00 0.00 4.20
7 8 3.632604 TCATCTAAGCAACGAGTCTAGGG 59.367 47.826 0.00 0.00 0.00 3.53
8 9 4.902443 TCATCTAAGCAACGAGTCTAGG 57.098 45.455 0.00 0.00 0.00 3.02
9 10 5.885881 AGTTCATCTAAGCAACGAGTCTAG 58.114 41.667 0.00 0.00 0.00 2.43
10 11 5.414765 TGAGTTCATCTAAGCAACGAGTCTA 59.585 40.000 0.00 0.00 0.00 2.59
11 12 4.218635 TGAGTTCATCTAAGCAACGAGTCT 59.781 41.667 0.00 0.00 0.00 3.24
12 13 4.486090 TGAGTTCATCTAAGCAACGAGTC 58.514 43.478 0.00 0.00 0.00 3.36
13 14 4.521130 TGAGTTCATCTAAGCAACGAGT 57.479 40.909 0.00 0.00 0.00 4.18
14 15 6.499172 TCTATGAGTTCATCTAAGCAACGAG 58.501 40.000 0.00 0.00 37.76 4.18
15 16 6.451064 TCTATGAGTTCATCTAAGCAACGA 57.549 37.500 0.00 0.00 37.76 3.85
16 17 6.145209 CCATCTATGAGTTCATCTAAGCAACG 59.855 42.308 0.00 0.00 37.76 4.10
17 18 7.212976 TCCATCTATGAGTTCATCTAAGCAAC 58.787 38.462 0.00 0.00 37.76 4.17
18 19 7.365497 TCCATCTATGAGTTCATCTAAGCAA 57.635 36.000 0.00 0.00 37.76 3.91
19 20 6.983906 TCCATCTATGAGTTCATCTAAGCA 57.016 37.500 0.00 0.00 37.76 3.91
20 21 7.839907 AGATCCATCTATGAGTTCATCTAAGC 58.160 38.462 0.00 0.00 37.76 3.09
21 22 9.642327 CAAGATCCATCTATGAGTTCATCTAAG 57.358 37.037 0.00 0.00 35.76 2.18
22 23 8.591940 CCAAGATCCATCTATGAGTTCATCTAA 58.408 37.037 0.00 0.00 35.76 2.10
23 24 7.732140 ACCAAGATCCATCTATGAGTTCATCTA 59.268 37.037 0.00 0.00 35.76 1.98
24 25 6.558014 ACCAAGATCCATCTATGAGTTCATCT 59.442 38.462 0.00 0.00 35.76 2.90
25 26 6.649973 CACCAAGATCCATCTATGAGTTCATC 59.350 42.308 0.00 0.00 35.76 2.92
26 27 6.328410 TCACCAAGATCCATCTATGAGTTCAT 59.672 38.462 0.00 0.00 35.76 2.57
27 28 5.662657 TCACCAAGATCCATCTATGAGTTCA 59.337 40.000 0.00 0.00 35.76 3.18
28 29 6.166984 TCACCAAGATCCATCTATGAGTTC 57.833 41.667 0.00 0.00 35.76 3.01
29 30 6.566079 TTCACCAAGATCCATCTATGAGTT 57.434 37.500 0.00 0.00 35.76 3.01
30 31 6.352516 GTTTCACCAAGATCCATCTATGAGT 58.647 40.000 0.00 0.00 35.76 3.41
31 32 5.762218 GGTTTCACCAAGATCCATCTATGAG 59.238 44.000 0.00 0.00 38.42 2.90
32 33 5.684704 GGTTTCACCAAGATCCATCTATGA 58.315 41.667 0.00 0.00 38.42 2.15
33 34 4.512944 CGGTTTCACCAAGATCCATCTATG 59.487 45.833 0.00 0.00 38.47 2.23
34 35 4.164221 ACGGTTTCACCAAGATCCATCTAT 59.836 41.667 0.00 0.00 38.47 1.98
35 36 3.517901 ACGGTTTCACCAAGATCCATCTA 59.482 43.478 0.00 0.00 38.47 1.98
36 37 2.305927 ACGGTTTCACCAAGATCCATCT 59.694 45.455 0.00 0.00 38.47 2.90
37 38 2.711542 ACGGTTTCACCAAGATCCATC 58.288 47.619 0.00 0.00 38.47 3.51
38 39 2.879103 ACGGTTTCACCAAGATCCAT 57.121 45.000 0.00 0.00 38.47 3.41
39 40 2.027561 CCTACGGTTTCACCAAGATCCA 60.028 50.000 0.00 0.00 38.47 3.41
40 41 2.235402 TCCTACGGTTTCACCAAGATCC 59.765 50.000 0.00 0.00 38.47 3.36
41 42 3.604875 TCCTACGGTTTCACCAAGATC 57.395 47.619 0.00 0.00 38.47 2.75
42 43 4.360951 TTTCCTACGGTTTCACCAAGAT 57.639 40.909 0.00 0.00 38.47 2.40
43 44 3.842007 TTTCCTACGGTTTCACCAAGA 57.158 42.857 0.00 0.00 38.47 3.02
44 45 4.904253 TTTTTCCTACGGTTTCACCAAG 57.096 40.909 0.00 0.00 38.47 3.61
45 46 5.855740 AATTTTTCCTACGGTTTCACCAA 57.144 34.783 0.00 0.00 38.47 3.67
46 47 5.855740 AAATTTTTCCTACGGTTTCACCA 57.144 34.783 0.00 0.00 38.47 4.17
47 48 8.821147 ATTAAAATTTTTCCTACGGTTTCACC 57.179 30.769 9.06 0.00 34.05 4.02
53 54 8.984764 GCAGAAAATTAAAATTTTTCCTACGGT 58.015 29.630 9.06 0.00 45.70 4.83
54 55 8.983724 TGCAGAAAATTAAAATTTTTCCTACGG 58.016 29.630 9.06 4.45 45.70 4.02
58 59 8.888716 ACGTTGCAGAAAATTAAAATTTTTCCT 58.111 25.926 9.06 5.83 45.70 3.36
59 60 9.497030 AACGTTGCAGAAAATTAAAATTTTTCC 57.503 25.926 9.06 3.98 45.70 3.13
61 62 9.497030 GGAACGTTGCAGAAAATTAAAATTTTT 57.503 25.926 15.52 0.00 45.70 1.94
63 64 7.254966 GGGGAACGTTGCAGAAAATTAAAATTT 60.255 33.333 21.74 0.00 40.15 1.82
64 65 6.203915 GGGGAACGTTGCAGAAAATTAAAATT 59.796 34.615 21.74 0.00 0.00 1.82
65 66 5.699001 GGGGAACGTTGCAGAAAATTAAAAT 59.301 36.000 21.74 0.00 0.00 1.82
66 67 5.051153 GGGGAACGTTGCAGAAAATTAAAA 58.949 37.500 21.74 0.00 0.00 1.52
67 68 4.099573 TGGGGAACGTTGCAGAAAATTAAA 59.900 37.500 21.74 0.00 0.00 1.52
68 69 3.637229 TGGGGAACGTTGCAGAAAATTAA 59.363 39.130 21.74 0.00 0.00 1.40
69 70 3.223435 TGGGGAACGTTGCAGAAAATTA 58.777 40.909 21.74 0.00 0.00 1.40
70 71 2.035632 TGGGGAACGTTGCAGAAAATT 58.964 42.857 21.74 0.00 0.00 1.82
71 72 1.698506 TGGGGAACGTTGCAGAAAAT 58.301 45.000 21.74 0.00 0.00 1.82
72 73 1.135333 GTTGGGGAACGTTGCAGAAAA 59.865 47.619 21.74 6.84 0.00 2.29
73 74 0.741915 GTTGGGGAACGTTGCAGAAA 59.258 50.000 21.74 9.26 0.00 2.52
74 75 0.394488 TGTTGGGGAACGTTGCAGAA 60.394 50.000 21.74 10.10 0.00 3.02
75 76 1.098712 GTGTTGGGGAACGTTGCAGA 61.099 55.000 21.74 3.97 0.00 4.26
76 77 1.358759 GTGTTGGGGAACGTTGCAG 59.641 57.895 21.74 0.00 0.00 4.41
77 78 2.473760 CGTGTTGGGGAACGTTGCA 61.474 57.895 21.74 0.00 35.13 4.08
78 79 2.330041 CGTGTTGGGGAACGTTGC 59.670 61.111 11.85 11.85 35.13 4.17
79 80 2.330041 GCGTGTTGGGGAACGTTG 59.670 61.111 5.00 0.00 41.76 4.10
80 81 3.273834 CGCGTGTTGGGGAACGTT 61.274 61.111 0.00 0.00 41.76 3.99
81 82 2.641439 TAACGCGTGTTGGGGAACGT 62.641 55.000 24.00 0.00 41.76 3.99
82 83 1.893168 CTAACGCGTGTTGGGGAACG 61.893 60.000 24.00 0.00 39.12 3.95
83 84 1.864176 CTAACGCGTGTTGGGGAAC 59.136 57.895 24.00 0.00 39.12 3.62
84 85 1.962306 GCTAACGCGTGTTGGGGAA 60.962 57.895 24.00 2.77 39.12 3.97
85 86 2.357760 GCTAACGCGTGTTGGGGA 60.358 61.111 24.00 3.16 39.12 4.81
86 87 2.666862 TGCTAACGCGTGTTGGGG 60.667 61.111 24.00 14.20 39.12 4.96
87 88 2.860293 CTGCTAACGCGTGTTGGG 59.140 61.111 24.00 16.49 39.12 4.12
88 89 1.911293 ATGCTGCTAACGCGTGTTGG 61.911 55.000 24.00 21.71 39.12 3.77
89 90 0.519175 GATGCTGCTAACGCGTGTTG 60.519 55.000 24.00 14.39 39.12 3.33
90 91 1.635663 GGATGCTGCTAACGCGTGTT 61.636 55.000 14.98 19.53 42.19 3.32
91 92 2.100631 GGATGCTGCTAACGCGTGT 61.101 57.895 14.98 5.77 39.65 4.49
92 93 1.811266 AGGATGCTGCTAACGCGTG 60.811 57.895 14.98 1.19 39.65 5.34
93 94 1.811266 CAGGATGCTGCTAACGCGT 60.811 57.895 5.58 5.58 39.65 6.01
133 134 1.604593 AGCCAAATCTGTTGCCGCT 60.605 52.632 0.00 0.00 0.00 5.52
200 202 2.950975 CAAAGGTTGCTGCCCAAAAATT 59.049 40.909 0.00 0.00 34.68 1.82
417 436 6.215845 AGACATGTTTTGGTAGTCAAATTGC 58.784 36.000 0.00 0.00 43.95 3.56
534 561 4.888038 TGCAATGCTGATCTACACATTC 57.112 40.909 6.82 0.00 32.42 2.67
626 653 6.642733 TGAATTTCTCCCTCTAGACCATTT 57.357 37.500 0.00 0.00 0.00 2.32
764 850 4.171005 CGTCTGTACGCTTGAATTTAGGA 58.829 43.478 0.00 0.00 43.12 2.94
812 910 7.118060 TGGAAAATAGATGGATGTGTCATTGA 58.882 34.615 0.00 0.00 0.00 2.57
873 1298 0.177604 AGATACGACGAGGACGAGGT 59.822 55.000 0.00 0.00 42.66 3.85
998 1433 0.526211 CTCCGTCGAGTTCACCATGA 59.474 55.000 0.00 0.00 0.00 3.07
1063 1498 4.798682 ACCACCCGCCTCCCTAGG 62.799 72.222 0.06 0.06 46.76 3.02
1117 1552 1.646189 GACATCAGCCTTCCTCGTTC 58.354 55.000 0.00 0.00 0.00 3.95
1119 1554 1.513158 CGACATCAGCCTTCCTCGT 59.487 57.895 0.00 0.00 0.00 4.18
1125 1560 2.437359 GGCAGCGACATCAGCCTT 60.437 61.111 0.00 0.00 43.70 4.35
1226 1662 1.345741 GCTGATTCGATGAGGATCCCA 59.654 52.381 8.55 6.76 0.00 4.37
1236 1672 5.219343 TGACCTCATATTGCTGATTCGAT 57.781 39.130 0.00 0.00 0.00 3.59
1260 1696 0.460459 GGCGAAGTTGTAGCCTCTCC 60.460 60.000 6.41 0.00 46.83 3.71
1360 1796 1.118356 GGGTGGGCATTCAACAACCA 61.118 55.000 0.00 0.00 41.61 3.67
1361 1797 0.831711 AGGGTGGGCATTCAACAACC 60.832 55.000 0.00 0.00 42.31 3.77
1363 1799 0.831288 CCAGGGTGGGCATTCAACAA 60.831 55.000 0.00 0.00 32.67 2.83
1391 1827 0.607489 GGATGGCATAGCAAGGCGAT 60.607 55.000 0.00 0.00 33.31 4.58
1447 1883 4.400109 TCGCTCGCGCTCGAAAGT 62.400 61.111 17.52 0.00 44.98 2.66
1486 1922 2.614057 CGGAGAATTGCGGCTTCTTTAT 59.386 45.455 0.00 0.00 33.18 1.40
1493 1929 0.464036 TGATACGGAGAATTGCGGCT 59.536 50.000 0.00 0.00 43.03 5.52
1623 2059 1.000396 GGGAGCAAAGGAGGCACAT 60.000 57.895 0.00 0.00 0.00 3.21
1624 2060 2.129555 GAGGGAGCAAAGGAGGCACA 62.130 60.000 0.00 0.00 0.00 4.57
1779 2227 1.194781 ACAGGGTCAGCGATTGTCCT 61.195 55.000 0.00 0.00 35.59 3.85
1846 2294 2.076100 GAATGTGAACTGTGATCCGCA 58.924 47.619 0.00 0.00 0.00 5.69
1912 2360 6.320164 ACATACCAACTCTGACTCTATCTGAC 59.680 42.308 0.00 0.00 32.32 3.51
2047 2495 6.447162 TGCTGATGATACCATAGTAACGAAG 58.553 40.000 0.00 0.00 32.09 3.79
2057 2505 5.698104 TCTTCCAATTGCTGATGATACCAT 58.302 37.500 0.00 0.00 35.29 3.55
2080 2528 8.044309 TGCAATTACTAGTACACCACATTACAT 58.956 33.333 0.91 0.00 0.00 2.29
2081 2529 7.387643 TGCAATTACTAGTACACCACATTACA 58.612 34.615 0.91 0.00 0.00 2.41
2109 2558 8.508883 AACATACTAACTCGAGTATCAAGAGT 57.491 34.615 20.39 16.13 46.01 3.24
2118 2567 5.618056 TCAACGAACATACTAACTCGAGT 57.382 39.130 13.58 13.58 35.34 4.18
2168 2657 7.721286 AGTACTAGCATTGAGATTGCAATAC 57.279 36.000 12.97 10.28 42.62 1.89
2270 2764 0.660488 TACAACGCAACCAAGCAGTG 59.340 50.000 0.00 0.00 0.00 3.66
2420 2914 4.537135 TGTCATTCAACTACCTCACTCC 57.463 45.455 0.00 0.00 0.00 3.85
2476 2970 1.617018 CCCTCGGATGCTCCAAGACA 61.617 60.000 3.57 0.00 35.91 3.41
2491 2985 2.750888 GCGGCGTCATGAAACCCTC 61.751 63.158 9.37 0.00 0.00 4.30
2510 3004 2.159142 ACCTAGAAAGCGTATGAACCGG 60.159 50.000 0.00 0.00 0.00 5.28
2528 3022 3.252284 CCAGCCCCACTCACACCT 61.252 66.667 0.00 0.00 0.00 4.00
2591 3085 1.066358 AGCAGTAACCGTTTCCTAGCC 60.066 52.381 0.00 0.00 0.00 3.93
2601 3095 3.188786 GCGGCTCAGCAGTAACCG 61.189 66.667 0.00 0.00 46.50 4.44
2678 3175 3.006537 AGAACGGAAGGAGAATTTCACGA 59.993 43.478 0.00 0.00 0.00 4.35
2679 3176 3.326747 AGAACGGAAGGAGAATTTCACG 58.673 45.455 0.00 0.00 0.00 4.35
2687 3184 7.177921 TGACTTATCTTTAAGAACGGAAGGAGA 59.822 37.037 0.00 0.00 38.56 3.71
2743 3240 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86


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

AutoCloner maintained by Alex Coulton.