Multiple sequence alignment - TraesCS7A01G025000

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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 TraesCS7A01G025000 chr7A 100.000 2597 0 0 1 2597 9755977 9758573 0.000000e+00 4796.0
1 TraesCS7A01G025000 chr7A 98.000 50 1 0 2060 2109 9757980 9758029 1.280000e-13 87.9
2 TraesCS7A01G025000 chr7A 98.000 50 1 0 2004 2053 9758036 9758085 1.280000e-13 87.9
3 TraesCS7A01G025000 chr4A 87.334 1658 103 38 1 1602 728085942 728084336 0.000000e+00 1799.0
4 TraesCS7A01G025000 chr4A 93.284 268 12 4 1652 1916 728084242 728083978 8.710000e-105 390.0
5 TraesCS7A01G025000 chr4A 92.350 183 13 1 2063 2244 728083779 728083597 2.560000e-65 259.0
6 TraesCS7A01G025000 chr4A 91.367 139 12 0 1915 2053 728083871 728083733 9.490000e-45 191.0
7 TraesCS7A01G025000 chr7D 86.713 1016 70 27 738 1708 10716868 10717863 0.000000e+00 1068.0
8 TraesCS7A01G025000 chr7D 90.824 643 25 14 1 632 10716166 10716785 0.000000e+00 830.0
9 TraesCS7A01G025000 chr7D 87.590 556 43 18 1365 1919 10719092 10719622 2.840000e-174 621.0
10 TraesCS7A01G025000 chr7D 92.793 333 21 2 2268 2597 10722077 10722409 1.810000e-131 479.0
11 TraesCS7A01G025000 chr7D 93.220 118 7 1 2149 2265 10721776 10721893 3.440000e-39 172.0
12 TraesCS7A01G025000 chr7D 91.589 107 9 0 2063 2169 10719819 10719925 5.790000e-32 148.0
13 TraesCS7A01G025000 chr2B 90.850 153 13 1 135 286 510167747 510167595 1.220000e-48 204.0


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 TraesCS7A01G025000 chr7A 9755977 9758573 2596 False 1657.266667 4796 98.666667 1 2597 3 chr7A.!!$F1 2596
1 TraesCS7A01G025000 chr4A 728083597 728085942 2345 True 659.750000 1799 91.083750 1 2244 4 chr4A.!!$R1 2243
2 TraesCS7A01G025000 chr7D 10716166 10722409 6243 False 553.000000 1068 90.454833 1 2597 6 chr7D.!!$F1 2596

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
952 1043 0.030369 CCCCACGTACGAGCTCATAC 59.97 60.0 24.41 12.52 0.0 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 5862 0.103026 TGATCCTTGGCGTCGATGAG 59.897 55.0 9.31 0.0 0.0 2.9 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
57 58 1.440850 TCGTGTACTGCGTACGTGC 60.441 57.895 17.90 0.93 41.41 5.34
75 76 4.241555 GCGCGATCCCTGGTCCAT 62.242 66.667 12.10 0.00 0.00 3.41
76 77 2.029666 CGCGATCCCTGGTCCATC 59.970 66.667 0.00 0.00 0.00 3.51
90 106 0.323087 TCCATCCGTCGACTCCTGAA 60.323 55.000 14.70 0.00 0.00 3.02
323 344 1.883275 CGCCATTAAACTGAACCCACA 59.117 47.619 0.00 0.00 0.00 4.17
325 346 2.029380 GCCATTAAACTGAACCCACACC 60.029 50.000 0.00 0.00 0.00 4.16
363 384 4.454504 ACACTGTTGTTTTTCGTCAGAGTT 59.545 37.500 0.00 0.00 28.43 3.01
365 386 4.693566 ACTGTTGTTTTTCGTCAGAGTTCA 59.306 37.500 0.00 0.00 0.00 3.18
366 387 5.163854 ACTGTTGTTTTTCGTCAGAGTTCAG 60.164 40.000 0.00 0.00 0.00 3.02
367 388 4.693566 TGTTGTTTTTCGTCAGAGTTCAGT 59.306 37.500 0.00 0.00 0.00 3.41
368 389 4.857871 TGTTTTTCGTCAGAGTTCAGTG 57.142 40.909 0.00 0.00 0.00 3.66
369 390 3.621268 TGTTTTTCGTCAGAGTTCAGTGG 59.379 43.478 0.00 0.00 0.00 4.00
370 391 3.536956 TTTTCGTCAGAGTTCAGTGGT 57.463 42.857 0.00 0.00 0.00 4.16
371 392 2.795175 TTCGTCAGAGTTCAGTGGTC 57.205 50.000 0.00 0.00 0.00 4.02
372 393 1.982660 TCGTCAGAGTTCAGTGGTCT 58.017 50.000 0.00 0.00 0.00 3.85
373 394 3.136009 TCGTCAGAGTTCAGTGGTCTA 57.864 47.619 0.00 0.00 0.00 2.59
374 395 3.483421 TCGTCAGAGTTCAGTGGTCTAA 58.517 45.455 0.00 0.00 0.00 2.10
375 396 3.887110 TCGTCAGAGTTCAGTGGTCTAAA 59.113 43.478 0.00 0.00 0.00 1.85
404 425 2.896044 AGACAGTGAGCTCATTCAGTGA 59.104 45.455 21.47 0.00 46.67 3.41
469 490 4.394712 CTGGGGTCGGTGCTGGTC 62.395 72.222 0.00 0.00 0.00 4.02
611 632 0.536260 GCAGCAGGAGAGAGTGTGAT 59.464 55.000 0.00 0.00 0.00 3.06
612 633 1.471327 GCAGCAGGAGAGAGTGTGATC 60.471 57.143 0.00 0.00 0.00 2.92
614 635 0.463620 GCAGGAGAGAGTGTGATCCC 59.536 60.000 0.00 0.00 31.86 3.85
640 661 2.487934 GAAGTCTGAACTGCAGCAAGA 58.512 47.619 15.27 11.50 44.52 3.02
732 755 4.632538 CGTAGGAAATTTGGATGGGAAC 57.367 45.455 0.00 0.00 0.00 3.62
777 819 1.489649 AGATGCTCTGGTGAAGATGGG 59.510 52.381 0.00 0.00 33.29 4.00
800 842 6.429385 GGGGATGAACTATGAGATGTTGATTC 59.571 42.308 0.00 0.00 0.00 2.52
831 873 9.494271 TGTCACTCAAATCCATCTATAATTAGC 57.506 33.333 0.00 0.00 0.00 3.09
832 874 8.940952 GTCACTCAAATCCATCTATAATTAGCC 58.059 37.037 0.00 0.00 0.00 3.93
874 932 2.618241 TCATGTCCGAATTAGCAATGGC 59.382 45.455 0.00 0.00 41.61 4.40
924 1014 2.547855 CCTGTGTCGTCCTTCATTGACA 60.548 50.000 0.00 0.00 38.91 3.58
952 1043 0.030369 CCCCACGTACGAGCTCATAC 59.970 60.000 24.41 12.52 0.00 2.39
960 1054 6.304922 CCACGTACGAGCTCATACATAAATAC 59.695 42.308 24.41 4.10 0.00 1.89
966 1060 5.063944 CGAGCTCATACATAAATACCCATGC 59.936 44.000 15.40 0.00 0.00 4.06
978 1072 3.293714 CCATGCCGCACAACCACA 61.294 61.111 0.00 0.00 0.00 4.17
985 1079 1.227527 CGCACAACCACACTCCTGA 60.228 57.895 0.00 0.00 0.00 3.86
1007 1101 0.244994 GATCGAGGTAGCATGGCGAT 59.755 55.000 10.31 10.31 43.48 4.58
1046 1140 4.697756 CACCACGTCCATGGCGGT 62.698 66.667 25.35 17.56 44.33 5.68
1210 1313 3.011885 CCTCCCTCTCCTCCGACT 58.988 66.667 0.00 0.00 0.00 4.18
1212 1315 1.152839 CTCCCTCTCCTCCGACTCC 60.153 68.421 0.00 0.00 0.00 3.85
1603 3261 4.796231 GCATCGCCTGACCGTCGT 62.796 66.667 0.00 0.00 0.00 4.34
1604 3262 2.579787 CATCGCCTGACCGTCGTC 60.580 66.667 0.00 0.00 39.66 4.20
1605 3263 4.175489 ATCGCCTGACCGTCGTCG 62.175 66.667 0.00 0.00 42.37 5.12
1617 3275 4.847516 TCGTCGATCGGCCGCTTG 62.848 66.667 23.51 16.26 40.32 4.01
1643 3302 3.250323 CGAGACATGCGTGCTCGG 61.250 66.667 29.29 18.26 42.67 4.63
1752 3460 7.881643 TTGGTATGTGCAATGTTTTTACATC 57.118 32.000 0.00 0.00 34.22 3.06
1758 3466 3.005261 TGCAATGTTTTTACATCCAGCGT 59.995 39.130 0.00 0.00 0.00 5.07
1812 3520 2.486472 AGCCATGTGGTCTTCAAGAG 57.514 50.000 0.35 0.00 37.57 2.85
1853 3561 4.113354 CAACTAGCGAATCTAAGACACCC 58.887 47.826 0.00 0.00 0.00 4.61
1896 3604 8.106348 GTCTTACATTATCTCGTACAAAAACGG 58.894 37.037 0.00 0.00 43.05 4.44
1930 3747 1.241990 CCGAGGAAGAGGACACGTGA 61.242 60.000 25.01 0.00 0.00 4.35
1944 3761 4.913126 GTGAAGGGCCACGAGTAG 57.087 61.111 6.18 0.00 0.00 2.57
1945 3762 1.448013 GTGAAGGGCCACGAGTAGC 60.448 63.158 6.18 0.00 0.00 3.58
1947 3764 1.153549 GAAGGGCCACGAGTAGCAG 60.154 63.158 6.18 0.00 0.00 4.24
1948 3765 2.579684 GAAGGGCCACGAGTAGCAGG 62.580 65.000 6.18 0.00 0.00 4.85
1957 3776 0.531532 CGAGTAGCAGGCATTGGGAG 60.532 60.000 0.00 0.00 0.00 4.30
2026 3845 2.857186 TCAAGCAGAACATGTAGCCA 57.143 45.000 0.00 0.00 0.00 4.75
2027 3846 3.138884 TCAAGCAGAACATGTAGCCAA 57.861 42.857 0.00 0.00 0.00 4.52
2028 3847 3.485394 TCAAGCAGAACATGTAGCCAAA 58.515 40.909 0.00 0.00 0.00 3.28
2029 3848 3.253188 TCAAGCAGAACATGTAGCCAAAC 59.747 43.478 0.00 0.00 0.00 2.93
2030 3849 2.862541 AGCAGAACATGTAGCCAAACA 58.137 42.857 0.00 0.00 0.00 2.83
2031 3850 2.554032 AGCAGAACATGTAGCCAAACAC 59.446 45.455 0.00 0.00 30.75 3.32
2032 3851 2.351738 GCAGAACATGTAGCCAAACACC 60.352 50.000 0.00 0.00 30.75 4.16
2033 3852 2.095768 CAGAACATGTAGCCAAACACCG 60.096 50.000 0.00 0.00 30.75 4.94
2034 3853 1.199097 GAACATGTAGCCAAACACCGG 59.801 52.381 0.00 0.00 30.75 5.28
2035 3854 0.109723 ACATGTAGCCAAACACCGGT 59.890 50.000 0.00 0.00 30.75 5.28
2036 3855 1.348366 ACATGTAGCCAAACACCGGTA 59.652 47.619 6.87 0.00 30.75 4.02
2037 3856 2.224572 ACATGTAGCCAAACACCGGTAA 60.225 45.455 6.87 0.00 30.75 2.85
2038 3857 2.863132 TGTAGCCAAACACCGGTAAT 57.137 45.000 6.87 0.00 0.00 1.89
2039 3858 2.428491 TGTAGCCAAACACCGGTAATG 58.572 47.619 6.87 6.62 0.00 1.90
2040 3859 2.038689 TGTAGCCAAACACCGGTAATGA 59.961 45.455 6.87 0.00 0.00 2.57
2041 3860 2.279935 AGCCAAACACCGGTAATGAA 57.720 45.000 6.87 0.00 0.00 2.57
2042 3861 2.159382 AGCCAAACACCGGTAATGAAG 58.841 47.619 6.87 0.00 0.00 3.02
2043 3862 2.156098 GCCAAACACCGGTAATGAAGA 58.844 47.619 6.87 0.00 0.00 2.87
2044 3863 2.095415 GCCAAACACCGGTAATGAAGAC 60.095 50.000 6.87 0.00 0.00 3.01
2045 3864 2.158841 CCAAACACCGGTAATGAAGACG 59.841 50.000 6.87 0.00 0.00 4.18
2046 3865 3.061322 CAAACACCGGTAATGAAGACGA 58.939 45.455 6.87 0.00 0.00 4.20
2047 3866 3.604875 AACACCGGTAATGAAGACGAT 57.395 42.857 6.87 0.00 0.00 3.73
2048 3867 2.888594 ACACCGGTAATGAAGACGATG 58.111 47.619 6.87 0.00 0.00 3.84
2049 3868 2.494471 ACACCGGTAATGAAGACGATGA 59.506 45.455 6.87 0.00 0.00 2.92
2050 3869 2.858344 CACCGGTAATGAAGACGATGAC 59.142 50.000 6.87 0.00 0.00 3.06
2051 3870 2.159142 ACCGGTAATGAAGACGATGACC 60.159 50.000 4.49 0.00 0.00 4.02
2052 3871 2.159156 CCGGTAATGAAGACGATGACCA 60.159 50.000 0.00 0.00 0.00 4.02
2053 3872 3.492656 CCGGTAATGAAGACGATGACCAT 60.493 47.826 0.00 0.00 0.00 3.55
2054 3873 4.119862 CGGTAATGAAGACGATGACCATT 58.880 43.478 0.00 0.00 0.00 3.16
2055 3874 4.025730 CGGTAATGAAGACGATGACCATTG 60.026 45.833 0.00 0.00 0.00 2.82
2056 3875 4.876107 GGTAATGAAGACGATGACCATTGT 59.124 41.667 2.68 2.68 38.11 2.71
2060 3879 2.006772 GACGATGACCATTGTCGGC 58.993 57.895 12.96 0.00 44.86 5.54
2061 3880 0.460284 GACGATGACCATTGTCGGCT 60.460 55.000 12.96 0.00 44.86 5.52
2062 3881 0.821517 ACGATGACCATTGTCGGCTA 59.178 50.000 0.00 0.00 44.86 3.93
2063 3882 1.412710 ACGATGACCATTGTCGGCTAT 59.587 47.619 0.00 0.00 44.86 2.97
2064 3883 2.061773 CGATGACCATTGTCGGCTATC 58.938 52.381 0.00 0.00 44.86 2.08
2065 3884 2.545742 CGATGACCATTGTCGGCTATCA 60.546 50.000 0.00 0.00 44.86 2.15
2066 3885 3.466836 GATGACCATTGTCGGCTATCAA 58.533 45.455 0.00 0.00 44.86 2.57
2067 3886 2.905075 TGACCATTGTCGGCTATCAAG 58.095 47.619 0.00 0.00 44.86 3.02
2068 3887 3.000067 TGACCATTGTCGGCTATCAAGC 61.000 50.000 0.00 0.00 44.86 4.01
2069 3888 5.500621 TGACCATTGTCGGCTATCAAGCA 62.501 47.826 0.00 0.00 45.44 3.91
2082 3901 2.857186 TCAAGCAGAACATGTAGCCA 57.143 45.000 0.00 0.00 0.00 4.75
2083 3902 3.138884 TCAAGCAGAACATGTAGCCAA 57.861 42.857 0.00 0.00 0.00 4.52
2171 5862 5.982516 CCTCTTGAGACACATGATTAGTAGC 59.017 44.000 0.00 0.00 33.35 3.58
2198 5889 4.021456 TCGACGCCAAGGATCATGTATAAT 60.021 41.667 0.00 0.00 0.00 1.28
2200 5891 5.516696 CGACGCCAAGGATCATGTATAATAG 59.483 44.000 0.00 0.00 0.00 1.73
2234 5925 1.499007 GGAATAAGCCCCTTGGATGGA 59.501 52.381 0.00 0.00 0.00 3.41
2235 5926 2.110721 GGAATAAGCCCCTTGGATGGAT 59.889 50.000 0.00 0.00 0.00 3.41
2255 5946 1.267121 TGTGACCTCCCTGTAGAAGC 58.733 55.000 0.00 0.00 0.00 3.86
2265 5956 2.550855 CCCTGTAGAAGCTGAAGCAACA 60.551 50.000 4.90 2.91 45.16 3.33
2288 6160 6.040166 ACATCAAAAGTGAAGCACAAGATCTT 59.960 34.615 0.88 0.88 37.30 2.40
2291 6163 6.263842 TCAAAAGTGAAGCACAAGATCTTCAT 59.736 34.615 4.57 0.00 46.86 2.57
2334 6206 3.669939 AGGTTGGATGGGGATAAACTG 57.330 47.619 0.00 0.00 0.00 3.16
2359 6234 5.458451 AGGAGATTAAGGGAAAGGGAAAG 57.542 43.478 0.00 0.00 0.00 2.62
2367 6242 1.532604 GGAAAGGGAAAGGGGCAACG 61.533 60.000 0.00 0.00 37.60 4.10
2397 6272 1.630878 GATCCCAGTCACAACCCTTCT 59.369 52.381 0.00 0.00 0.00 2.85
2402 6277 2.289694 CCAGTCACAACCCTTCTTCGAT 60.290 50.000 0.00 0.00 0.00 3.59
2409 6284 0.984230 ACCCTTCTTCGATGGCTTGA 59.016 50.000 0.00 0.00 0.00 3.02
2439 6314 2.247358 GGTGCCAAGAATCAAAAGGGA 58.753 47.619 0.00 0.00 0.00 4.20
2448 6323 7.500141 CCAAGAATCAAAAGGGAAGAAAAAGA 58.500 34.615 0.00 0.00 0.00 2.52
2450 6325 7.055667 AGAATCAAAAGGGAAGAAAAAGACC 57.944 36.000 0.00 0.00 0.00 3.85
2467 6342 1.829222 GACCGGGAAATCACTAGGTGA 59.171 52.381 6.32 2.80 46.90 4.02
2482 6357 4.963628 ACTAGGTGAGAAGGGAGGTTATTC 59.036 45.833 0.00 0.00 0.00 1.75
2521 6396 1.710013 GAATCGAGCCAAAGTCGTCA 58.290 50.000 0.00 0.00 38.60 4.35
2550 6425 0.663153 GCCACGACAAAGAACAAGCT 59.337 50.000 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.427753 GGATGGACCAGGGATCGC 59.572 66.667 0.00 0.54 38.79 4.58
63 64 2.134287 CGACGGATGGACCAGGGAT 61.134 63.158 0.00 0.00 38.90 3.85
66 67 2.005960 GAGTCGACGGATGGACCAGG 62.006 65.000 10.46 0.00 38.90 4.45
67 68 1.433879 GAGTCGACGGATGGACCAG 59.566 63.158 10.46 0.00 38.90 4.00
69 70 1.753463 AGGAGTCGACGGATGGACC 60.753 63.158 10.46 6.49 34.24 4.46
70 71 1.030488 TCAGGAGTCGACGGATGGAC 61.030 60.000 10.46 0.00 33.94 4.02
71 72 0.323087 TTCAGGAGTCGACGGATGGA 60.323 55.000 10.46 1.75 0.00 3.41
72 73 0.101399 CTTCAGGAGTCGACGGATGG 59.899 60.000 10.46 0.41 0.00 3.51
75 76 1.835494 AATCTTCAGGAGTCGACGGA 58.165 50.000 10.46 4.08 0.00 4.69
76 77 3.777465 TTAATCTTCAGGAGTCGACGG 57.223 47.619 10.46 1.54 0.00 4.79
90 106 9.595823 CCAATCAAAATCTTGCATCTTTAATCT 57.404 29.630 0.00 0.00 32.14 2.40
163 184 3.390521 TCAGCAGCAGGTACCCGG 61.391 66.667 8.74 2.04 0.00 5.73
209 230 2.436646 CTGAAGGCGGCGGTGAAT 60.437 61.111 9.78 0.00 0.00 2.57
299 320 1.471287 GGTTCAGTTTAATGGCGGACC 59.529 52.381 0.00 0.00 0.00 4.46
323 344 0.399949 TGTTCAGAGAGTGGGTGGGT 60.400 55.000 0.00 0.00 0.00 4.51
325 346 1.051812 AGTGTTCAGAGAGTGGGTGG 58.948 55.000 0.00 0.00 0.00 4.61
363 384 3.578282 TCTGATGCAGTTTAGACCACTGA 59.422 43.478 4.23 0.00 43.90 3.41
365 386 3.324846 TGTCTGATGCAGTTTAGACCACT 59.675 43.478 15.43 0.00 38.96 4.00
366 387 3.664107 TGTCTGATGCAGTTTAGACCAC 58.336 45.455 15.43 0.00 38.96 4.16
367 388 3.324846 ACTGTCTGATGCAGTTTAGACCA 59.675 43.478 15.43 6.97 43.87 4.02
368 389 3.681897 CACTGTCTGATGCAGTTTAGACC 59.318 47.826 15.43 3.91 43.87 3.85
369 390 4.560128 TCACTGTCTGATGCAGTTTAGAC 58.440 43.478 12.72 12.72 43.87 2.59
370 391 4.814147 CTCACTGTCTGATGCAGTTTAGA 58.186 43.478 0.00 0.00 43.87 2.10
371 392 3.370366 GCTCACTGTCTGATGCAGTTTAG 59.630 47.826 0.00 2.12 43.87 1.85
372 393 3.007290 AGCTCACTGTCTGATGCAGTTTA 59.993 43.478 0.00 0.00 43.87 2.01
373 394 2.149578 GCTCACTGTCTGATGCAGTTT 58.850 47.619 0.00 0.00 43.87 2.66
374 395 1.347050 AGCTCACTGTCTGATGCAGTT 59.653 47.619 0.00 0.00 43.87 3.16
375 396 0.975135 AGCTCACTGTCTGATGCAGT 59.025 50.000 0.00 0.00 46.86 4.40
404 425 5.351458 TCATCAGATCAATCGACAATTCGT 58.649 37.500 0.00 0.00 46.01 3.85
469 490 1.467678 CGAGGTAGAGGCCCAGGATG 61.468 65.000 0.00 0.00 0.00 3.51
545 566 1.898154 CTACCTCCACCGTCTTGGG 59.102 63.158 0.00 0.00 44.64 4.12
547 568 0.108615 CTGCTACCTCCACCGTCTTG 60.109 60.000 0.00 0.00 0.00 3.02
611 632 0.316204 GTTCAGACTTCGGTTCGGGA 59.684 55.000 0.00 0.00 0.00 5.14
612 633 0.317479 AGTTCAGACTTCGGTTCGGG 59.683 55.000 0.00 0.00 29.87 5.14
614 635 0.784778 GCAGTTCAGACTTCGGTTCG 59.215 55.000 0.00 0.00 32.54 3.95
640 661 7.199766 TCTAGTTCAAAATTTCAAATGCGTGT 58.800 30.769 0.00 0.00 0.00 4.49
697 720 3.423539 TCCTACGGTACAGTACAGTGT 57.576 47.619 22.52 14.65 37.64 3.55
728 751 4.756642 TCATGTCAAGATCACAACTGTTCC 59.243 41.667 0.00 0.00 0.00 3.62
732 755 5.120363 CACTCTCATGTCAAGATCACAACTG 59.880 44.000 0.00 0.00 0.00 3.16
777 819 8.504815 CATGAATCAACATCTCATAGTTCATCC 58.495 37.037 0.00 0.00 34.03 3.51
800 842 4.267536 AGATGGATTTGAGTGACACCATG 58.732 43.478 0.84 0.00 34.46 3.66
831 873 1.004277 GAACGACACAGAGTGAGCGG 61.004 60.000 16.39 2.72 38.39 5.52
832 874 1.330779 CGAACGACACAGAGTGAGCG 61.331 60.000 3.88 9.35 39.28 5.03
874 932 2.507944 CCCCAAGCCGGAGATCAG 59.492 66.667 5.05 0.00 36.56 2.90
875 933 3.797353 GCCCCAAGCCGGAGATCA 61.797 66.667 5.05 0.00 36.56 2.92
916 1006 0.984230 GGGTGAGGGTCTGTCAATGA 59.016 55.000 0.00 0.00 0.00 2.57
924 1014 1.608627 GTACGTGGGGTGAGGGTCT 60.609 63.158 0.00 0.00 0.00 3.85
952 1043 1.952990 TGTGCGGCATGGGTATTTATG 59.047 47.619 5.72 0.00 0.00 1.90
960 1054 4.054825 GTGGTTGTGCGGCATGGG 62.055 66.667 5.72 0.00 0.00 4.00
966 1060 2.111043 AGGAGTGTGGTTGTGCGG 59.889 61.111 0.00 0.00 0.00 5.69
978 1072 2.290464 CTACCTCGATCGTTCAGGAGT 58.710 52.381 23.80 8.54 0.00 3.85
985 1079 0.249489 GCCATGCTACCTCGATCGTT 60.249 55.000 15.94 3.47 0.00 3.85
1617 3275 3.490759 CATGTCTCGCACGTGCCC 61.491 66.667 33.23 19.02 35.18 5.36
1643 3302 6.011277 CGTTTTTATTTACCACTACGTCAGC 58.989 40.000 0.00 0.00 0.00 4.26
1696 3401 2.816087 GCAGCCATGTTGAAAGAAGAGA 59.184 45.455 0.00 0.00 0.00 3.10
1702 3407 4.707030 TCTTATGCAGCCATGTTGAAAG 57.293 40.909 0.00 0.00 32.85 2.62
1752 3460 3.242413 CGTCTTCCATTGATAAACGCTGG 60.242 47.826 0.00 0.00 0.00 4.85
1758 3466 5.789521 TCACACTCGTCTTCCATTGATAAA 58.210 37.500 0.00 0.00 0.00 1.40
1812 3520 7.008447 GCTAGTTGTACGGATCATATCGATTTC 59.992 40.741 1.71 0.00 33.17 2.17
1896 3604 4.585955 TCCTCGGTCTCATAATGTAAGC 57.414 45.455 0.00 0.00 0.00 3.09
1930 3747 2.660064 CCTGCTACTCGTGGCCCTT 61.660 63.158 0.00 0.00 36.12 3.95
1943 3760 2.274760 GCTCTCCCAATGCCTGCT 59.725 61.111 0.00 0.00 0.00 4.24
1944 3761 2.832201 GGCTCTCCCAATGCCTGC 60.832 66.667 0.00 0.00 43.05 4.85
1945 3762 2.335092 ATCGGCTCTCCCAATGCCTG 62.335 60.000 0.00 0.00 44.09 4.85
1947 3764 1.599240 GATCGGCTCTCCCAATGCC 60.599 63.158 0.00 0.00 42.94 4.40
1948 3765 1.958205 CGATCGGCTCTCCCAATGC 60.958 63.158 7.38 0.00 0.00 3.56
1957 3776 4.560856 AGCAGCGTCGATCGGCTC 62.561 66.667 18.81 10.31 40.26 4.70
2005 3824 4.486125 TGGCTACATGTTCTGCTTGATA 57.514 40.909 2.30 0.00 0.00 2.15
2026 3845 3.389925 TCGTCTTCATTACCGGTGTTT 57.610 42.857 19.93 0.00 0.00 2.83
2027 3846 3.056393 TCATCGTCTTCATTACCGGTGTT 60.056 43.478 19.93 0.24 33.39 3.32
2028 3847 2.494471 TCATCGTCTTCATTACCGGTGT 59.506 45.455 19.93 2.23 33.39 4.16
2029 3848 2.858344 GTCATCGTCTTCATTACCGGTG 59.142 50.000 19.93 0.00 32.92 4.94
2030 3849 2.159142 GGTCATCGTCTTCATTACCGGT 60.159 50.000 13.98 13.98 0.00 5.28
2031 3850 2.159156 TGGTCATCGTCTTCATTACCGG 60.159 50.000 0.00 0.00 0.00 5.28
2032 3851 3.159353 TGGTCATCGTCTTCATTACCG 57.841 47.619 0.00 0.00 0.00 4.02
2033 3852 4.876107 ACAATGGTCATCGTCTTCATTACC 59.124 41.667 0.00 0.00 0.00 2.85
2034 3853 5.276395 CGACAATGGTCATCGTCTTCATTAC 60.276 44.000 0.13 0.00 44.54 1.89
2035 3854 4.803613 CGACAATGGTCATCGTCTTCATTA 59.196 41.667 0.13 0.00 44.54 1.90
2036 3855 3.618594 CGACAATGGTCATCGTCTTCATT 59.381 43.478 0.13 0.00 44.54 2.57
2037 3856 3.190079 CGACAATGGTCATCGTCTTCAT 58.810 45.455 0.13 0.00 44.54 2.57
2038 3857 2.606108 CGACAATGGTCATCGTCTTCA 58.394 47.619 0.13 0.00 44.54 3.02
2039 3858 1.927174 CCGACAATGGTCATCGTCTTC 59.073 52.381 0.13 0.00 44.54 2.87
2040 3859 2.007049 GCCGACAATGGTCATCGTCTT 61.007 52.381 0.13 0.00 44.54 3.01
2041 3860 0.460284 GCCGACAATGGTCATCGTCT 60.460 55.000 0.13 0.00 44.54 4.18
2042 3861 0.460284 AGCCGACAATGGTCATCGTC 60.460 55.000 0.13 0.00 44.54 4.20
2043 3862 0.821517 TAGCCGACAATGGTCATCGT 59.178 50.000 0.13 0.00 44.54 3.73
2044 3863 2.061773 GATAGCCGACAATGGTCATCG 58.938 52.381 0.13 0.00 44.54 3.84
2045 3864 3.111853 TGATAGCCGACAATGGTCATC 57.888 47.619 0.13 0.00 44.54 2.92
2046 3865 3.470709 CTTGATAGCCGACAATGGTCAT 58.529 45.455 0.13 0.00 44.54 3.06
2047 3866 2.905075 CTTGATAGCCGACAATGGTCA 58.095 47.619 0.13 0.00 44.54 4.02
2048 3867 1.599542 GCTTGATAGCCGACAATGGTC 59.400 52.381 0.00 0.00 41.74 4.02
2049 3868 1.668419 GCTTGATAGCCGACAATGGT 58.332 50.000 0.00 0.00 41.74 3.55
2060 3879 4.445453 TGGCTACATGTTCTGCTTGATAG 58.555 43.478 2.30 0.00 0.00 2.08
2061 3880 4.486125 TGGCTACATGTTCTGCTTGATA 57.514 40.909 2.30 0.00 0.00 2.15
2062 3881 3.354948 TGGCTACATGTTCTGCTTGAT 57.645 42.857 2.30 0.00 0.00 2.57
2063 3882 2.857186 TGGCTACATGTTCTGCTTGA 57.143 45.000 2.30 0.00 0.00 3.02
2064 3883 3.004629 TGTTTGGCTACATGTTCTGCTTG 59.995 43.478 2.30 0.00 0.00 4.01
2065 3884 3.004734 GTGTTTGGCTACATGTTCTGCTT 59.995 43.478 2.30 0.00 0.00 3.91
2066 3885 2.554032 GTGTTTGGCTACATGTTCTGCT 59.446 45.455 2.30 0.00 0.00 4.24
2067 3886 2.351738 GGTGTTTGGCTACATGTTCTGC 60.352 50.000 2.30 6.65 0.00 4.26
2068 3887 2.095768 CGGTGTTTGGCTACATGTTCTG 60.096 50.000 2.30 0.00 0.00 3.02
2069 3888 2.151202 CGGTGTTTGGCTACATGTTCT 58.849 47.619 2.30 0.00 0.00 3.01
2070 3889 1.199097 CCGGTGTTTGGCTACATGTTC 59.801 52.381 2.30 0.00 0.00 3.18
2071 3890 1.243902 CCGGTGTTTGGCTACATGTT 58.756 50.000 2.30 0.00 0.00 2.71
2072 3891 0.109723 ACCGGTGTTTGGCTACATGT 59.890 50.000 6.12 2.69 0.00 3.21
2073 3892 2.102070 TACCGGTGTTTGGCTACATG 57.898 50.000 19.93 0.00 0.00 3.21
2074 3893 2.863132 TTACCGGTGTTTGGCTACAT 57.137 45.000 19.93 0.00 0.00 2.29
2075 3894 2.038689 TCATTACCGGTGTTTGGCTACA 59.961 45.455 19.93 0.00 0.00 2.74
2076 3895 2.702261 TCATTACCGGTGTTTGGCTAC 58.298 47.619 19.93 0.00 0.00 3.58
2077 3896 3.008157 TCTTCATTACCGGTGTTTGGCTA 59.992 43.478 19.93 0.00 0.00 3.93
2078 3897 2.159382 CTTCATTACCGGTGTTTGGCT 58.841 47.619 19.93 0.00 0.00 4.75
2079 3898 2.156098 TCTTCATTACCGGTGTTTGGC 58.844 47.619 19.93 0.00 0.00 4.52
2080 3899 4.006989 TCATCTTCATTACCGGTGTTTGG 58.993 43.478 19.93 2.03 0.00 3.28
2081 3900 5.353956 TCATCATCTTCATTACCGGTGTTTG 59.646 40.000 19.93 12.05 0.00 2.93
2082 3901 5.354234 GTCATCATCTTCATTACCGGTGTTT 59.646 40.000 19.93 0.00 0.00 2.83
2083 3902 4.876107 GTCATCATCTTCATTACCGGTGTT 59.124 41.667 19.93 0.24 0.00 3.32
2171 5862 0.103026 TGATCCTTGGCGTCGATGAG 59.897 55.000 9.31 0.00 0.00 2.90
2198 5889 1.329913 TTCCTCTCTGGCGCATGCTA 61.330 55.000 17.13 0.86 42.25 3.49
2200 5891 0.250038 TATTCCTCTCTGGCGCATGC 60.250 55.000 10.83 7.91 41.71 4.06
2234 5925 2.237392 GCTTCTACAGGGAGGTCACAAT 59.763 50.000 0.00 0.00 0.00 2.71
2235 5926 1.623811 GCTTCTACAGGGAGGTCACAA 59.376 52.381 0.00 0.00 0.00 3.33
2255 5946 4.443394 GCTTCACTTTTGATGTTGCTTCAG 59.557 41.667 0.00 0.00 31.01 3.02
2265 5956 6.263842 TGAAGATCTTGTGCTTCACTTTTGAT 59.736 34.615 14.00 0.00 43.88 2.57
2291 6163 9.753674 ACCTATGGAGATACAAAAATCTTTTCA 57.246 29.630 0.00 0.00 36.33 2.69
2316 6188 3.382083 ACCAGTTTATCCCCATCCAAC 57.618 47.619 0.00 0.00 0.00 3.77
2318 6190 3.053077 CCTACCAGTTTATCCCCATCCA 58.947 50.000 0.00 0.00 0.00 3.41
2334 6206 4.304659 TCCCTTTCCCTTAATCTCCTACC 58.695 47.826 0.00 0.00 0.00 3.18
2359 6234 3.915536 GATCTTACTAGATCGTTGCCCC 58.084 50.000 0.00 0.00 45.33 5.80
2385 6260 1.610624 GCCATCGAAGAAGGGTTGTGA 60.611 52.381 0.00 0.00 46.84 3.58
2397 6272 0.605319 GGTGGTGTCAAGCCATCGAA 60.605 55.000 0.00 0.00 38.40 3.71
2402 6277 1.228521 CCATGGTGGTGTCAAGCCA 60.229 57.895 2.57 0.00 31.35 4.75
2439 6314 4.470602 AGTGATTTCCCGGTCTTTTTCTT 58.529 39.130 0.00 0.00 0.00 2.52
2448 6323 1.831736 CTCACCTAGTGATTTCCCGGT 59.168 52.381 0.00 0.00 41.94 5.28
2450 6325 3.430929 CCTTCTCACCTAGTGATTTCCCG 60.431 52.174 0.00 0.00 41.94 5.14
2467 6342 2.507471 CCTGCTGAATAACCTCCCTTCT 59.493 50.000 0.00 0.00 0.00 2.85
2482 6357 0.392336 GTCCTAGAGATGCCCTGCTG 59.608 60.000 0.00 0.00 0.00 4.41
2521 6396 2.035237 TTGTCGTGGCCTTCCTCGTT 62.035 55.000 3.32 0.00 46.27 3.85
2527 6402 1.305201 TGTTCTTTGTCGTGGCCTTC 58.695 50.000 3.32 0.00 0.00 3.46
2550 6425 0.404426 TCCTCTCTTGGTCGTCCTCA 59.596 55.000 0.00 0.00 34.23 3.86


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

AutoCloner maintained by Alex Coulton.