Multiple sequence alignment - TraesCS3A01G009500

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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 TraesCS3A01G009500 chr3A 100.000 2525 0 0 1 2525 8594889 8597413 0.000000e+00 4663.0
1 TraesCS3A01G009500 chr3A 95.511 1849 58 15 102 1938 8904346 8902511 0.000000e+00 2931.0
2 TraesCS3A01G009500 chr3A 96.438 393 6 1 971 1355 8904743 8904351 2.120000e-180 641.0
3 TraesCS3A01G009500 chr3A 94.180 189 3 1 971 1151 8905483 8905295 5.320000e-72 281.0
4 TraesCS3A01G009500 chr3B 90.877 1414 67 20 522 1915 5587875 5589246 0.000000e+00 1840.0
5 TraesCS3A01G009500 chr3B 78.747 367 36 24 1828 2174 5585722 5586066 9.150000e-50 207.0
6 TraesCS3A01G009500 chr3B 100.000 28 0 0 380 407 671023579 671023606 5.000000e-03 52.8
7 TraesCS3A01G009500 chr7A 83.947 679 74 25 1828 2485 409263315 409263979 3.570000e-173 617.0
8 TraesCS3A01G009500 chr7D 83.053 714 83 27 1828 2518 12904907 12905605 4.620000e-172 614.0
9 TraesCS3A01G009500 chr2A 77.445 634 125 14 1035 1660 702243110 702242487 1.850000e-96 363.0
10 TraesCS3A01G009500 chr2D 76.637 672 132 17 990 1657 560561849 560562499 5.170000e-92 348.0
11 TraesCS3A01G009500 chr4A 96.970 33 0 1 375 407 626036336 626036305 1.000000e-03 54.7
12 TraesCS3A01G009500 chr5A 100.000 28 0 0 380 407 14224264 14224237 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 TraesCS3A01G009500 chr3A 8594889 8597413 2524 False 4663.000000 4663 100.000000 1 2525 1 chr3A.!!$F1 2524
1 TraesCS3A01G009500 chr3A 8902511 8905483 2972 True 1284.333333 2931 95.376333 102 1938 3 chr3A.!!$R1 1836
2 TraesCS3A01G009500 chr3B 5585722 5589246 3524 False 1023.500000 1840 84.812000 522 2174 2 chr3B.!!$F2 1652
3 TraesCS3A01G009500 chr7A 409263315 409263979 664 False 617.000000 617 83.947000 1828 2485 1 chr7A.!!$F1 657
4 TraesCS3A01G009500 chr7D 12904907 12905605 698 False 614.000000 614 83.053000 1828 2518 1 chr7D.!!$F1 690
5 TraesCS3A01G009500 chr2A 702242487 702243110 623 True 363.000000 363 77.445000 1035 1660 1 chr2A.!!$R1 625
6 TraesCS3A01G009500 chr2D 560561849 560562499 650 False 348.000000 348 76.637000 990 1657 1 chr2D.!!$F1 667

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
82 83 0.457851 CTTCTCTACCACGAGCTGGG 59.542 60.0 0.0 0.0 45.78 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 3772 0.177604 CCATCACCTCTGAGACCAGC 59.822 60.0 6.17 0.0 40.2 4.85 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
25 26 6.524101 TTAAGCGGGCTTCATTTTTCTAAT 57.476 33.333 9.52 0.00 37.47 1.73
27 28 3.131046 AGCGGGCTTCATTTTTCTAATGG 59.869 43.478 0.00 0.00 0.00 3.16
28 29 3.130340 GCGGGCTTCATTTTTCTAATGGA 59.870 43.478 0.00 0.00 0.00 3.41
30 31 4.440112 CGGGCTTCATTTTTCTAATGGACC 60.440 45.833 0.00 0.00 0.00 4.46
31 32 4.141937 GGGCTTCATTTTTCTAATGGACCC 60.142 45.833 0.00 0.00 31.95 4.46
33 34 4.672409 CTTCATTTTTCTAATGGACCCGC 58.328 43.478 0.00 0.00 0.00 6.13
35 36 4.340617 TCATTTTTCTAATGGACCCGCTT 58.659 39.130 0.00 0.00 0.00 4.68
37 38 3.713826 TTTTCTAATGGACCCGCTTCT 57.286 42.857 0.00 0.00 0.00 2.85
40 41 2.467880 TCTAATGGACCCGCTTCTTCT 58.532 47.619 0.00 0.00 0.00 2.85
42 43 2.586648 AATGGACCCGCTTCTTCTTT 57.413 45.000 0.00 0.00 0.00 2.52
43 44 2.586648 ATGGACCCGCTTCTTCTTTT 57.413 45.000 0.00 0.00 0.00 2.27
44 45 2.358322 TGGACCCGCTTCTTCTTTTT 57.642 45.000 0.00 0.00 0.00 1.94
61 62 3.810310 TTTTTGAGTTGTTCGGCCATT 57.190 38.095 2.24 0.00 0.00 3.16
70 71 3.973206 TGTTCGGCCATTTCTTCTCTA 57.027 42.857 2.24 0.00 0.00 2.43
72 73 2.937149 GTTCGGCCATTTCTTCTCTACC 59.063 50.000 2.24 0.00 0.00 3.18
73 74 2.184533 TCGGCCATTTCTTCTCTACCA 58.815 47.619 2.24 0.00 0.00 3.25
75 76 2.280628 GGCCATTTCTTCTCTACCACG 58.719 52.381 0.00 0.00 0.00 4.94
76 77 2.093658 GGCCATTTCTTCTCTACCACGA 60.094 50.000 0.00 0.00 0.00 4.35
80 81 3.577649 TTTCTTCTCTACCACGAGCTG 57.422 47.619 0.00 0.00 0.00 4.24
82 83 0.457851 CTTCTCTACCACGAGCTGGG 59.542 60.000 0.00 0.00 45.78 4.45
85 86 1.608717 CTCTACCACGAGCTGGGCTT 61.609 60.000 0.00 0.00 45.78 4.35
86 87 1.153549 CTACCACGAGCTGGGCTTC 60.154 63.158 0.00 0.00 45.78 3.86
87 88 2.890847 CTACCACGAGCTGGGCTTCG 62.891 65.000 0.00 0.00 45.78 3.79
88 89 4.379243 CCACGAGCTGGGCTTCGT 62.379 66.667 0.00 9.73 39.88 3.85
89 90 2.357517 CACGAGCTGGGCTTCGTT 60.358 61.111 0.00 0.63 39.88 3.85
90 91 1.961277 CACGAGCTGGGCTTCGTTT 60.961 57.895 0.00 0.00 39.88 3.60
92 93 1.961277 CGAGCTGGGCTTCGTTTGT 60.961 57.895 0.00 0.00 39.88 2.83
94 95 0.603975 GAGCTGGGCTTCGTTTGTCT 60.604 55.000 0.00 0.00 39.88 3.41
97 98 1.593196 CTGGGCTTCGTTTGTCTCAA 58.407 50.000 0.00 0.00 0.00 3.02
98 99 1.946768 CTGGGCTTCGTTTGTCTCAAA 59.053 47.619 0.00 0.00 0.00 2.69
128 1167 5.350504 AAGACAGAGAGAGAGAGAGAGAG 57.649 47.826 0.00 0.00 0.00 3.20
129 1168 4.614475 AGACAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
130 1169 4.648762 AGACAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
455 1494 7.556635 TCATCGGATTCTCTACTCTACTTTTGA 59.443 37.037 0.00 0.00 0.00 2.69
530 2163 7.924103 TGCGCATATAATTCCTATATACGTG 57.076 36.000 5.66 0.00 40.03 4.49
855 2500 4.588106 TCAATGCTCACCTTTTTCAATGGA 59.412 37.500 0.00 0.00 0.00 3.41
1076 2731 1.142748 CCAGCGCTTCCACTCTAGG 59.857 63.158 7.50 0.00 0.00 3.02
1134 2789 5.302059 GGACATCTCCTACAACTACTGCATA 59.698 44.000 0.00 0.00 33.07 3.14
1575 3236 6.392625 CTGGCTAACAGTTCTAGCTATACA 57.607 41.667 7.79 0.00 42.42 2.29
1576 3237 6.145338 TGGCTAACAGTTCTAGCTATACAC 57.855 41.667 7.79 0.00 41.32 2.90
1662 3331 2.147958 TGCAAGTACGTTTGGATGGAC 58.852 47.619 0.00 0.00 0.00 4.02
1718 3389 7.510549 TGCAGGGCTTATAGTATTGATTTTC 57.489 36.000 0.00 0.00 0.00 2.29
1719 3390 7.290061 TGCAGGGCTTATAGTATTGATTTTCT 58.710 34.615 0.00 0.00 0.00 2.52
1741 3419 5.191124 TCTTGGAATAAAAGTACTCCCTCCC 59.809 44.000 0.00 0.00 0.00 4.30
1742 3420 4.706616 TGGAATAAAAGTACTCCCTCCCT 58.293 43.478 0.00 0.00 0.00 4.20
1743 3421 4.720273 TGGAATAAAAGTACTCCCTCCCTC 59.280 45.833 0.00 0.00 0.00 4.30
1744 3422 4.969999 GGAATAAAAGTACTCCCTCCCTCT 59.030 45.833 0.00 0.00 0.00 3.69
1745 3423 5.163290 GGAATAAAAGTACTCCCTCCCTCTG 60.163 48.000 0.00 0.00 0.00 3.35
1746 3424 3.277416 AAAAGTACTCCCTCCCTCTGT 57.723 47.619 0.00 0.00 0.00 3.41
1747 3425 2.535836 AAGTACTCCCTCCCTCTGTC 57.464 55.000 0.00 0.00 0.00 3.51
1748 3426 0.632294 AGTACTCCCTCCCTCTGTCC 59.368 60.000 0.00 0.00 0.00 4.02
1749 3427 0.397394 GTACTCCCTCCCTCTGTCCC 60.397 65.000 0.00 0.00 0.00 4.46
1750 3428 1.591280 TACTCCCTCCCTCTGTCCCC 61.591 65.000 0.00 0.00 0.00 4.81
1820 3498 1.745232 TGTCCCATGTAATGTTCGGC 58.255 50.000 0.00 0.00 44.81 5.54
1867 3548 7.440556 CAGTATGGTGAAGACTATTCTGAATGG 59.559 40.741 13.01 12.29 39.41 3.16
1928 3611 4.033932 CCATCGAATTTCGTCAGCACATAA 59.966 41.667 17.61 0.00 41.35 1.90
1938 3621 5.664457 TCGTCAGCACATAAGAATCTTGAT 58.336 37.500 5.64 0.00 0.00 2.57
1945 3642 7.220300 CAGCACATAAGAATCTTGATTTTGCTC 59.780 37.037 5.64 0.00 33.27 4.26
1998 3695 5.183713 CAGGGTTGATGAAAGAACATGCTTA 59.816 40.000 0.00 0.00 0.00 3.09
2002 3699 6.583806 GGTTGATGAAAGAACATGCTTAAGTG 59.416 38.462 4.02 0.00 0.00 3.16
2003 3700 7.362662 GTTGATGAAAGAACATGCTTAAGTGA 58.637 34.615 4.02 0.00 0.00 3.41
2024 3722 7.163441 AGTGAATTTGGCAATAGCAGATTTTT 58.837 30.769 0.00 0.00 44.61 1.94
2046 3744 1.228644 TGCAGAGTGGGCAAAGCAT 60.229 52.632 0.00 0.00 38.54 3.79
2047 3745 1.214589 GCAGAGTGGGCAAAGCATG 59.785 57.895 0.00 0.00 0.00 4.06
2061 3759 3.533606 AAGCATGGCAGAGTAGTGTAG 57.466 47.619 0.00 0.00 0.00 2.74
2073 3771 5.361285 CAGAGTAGTGTAGCTGGACCTTAAT 59.639 44.000 0.00 0.00 0.00 1.40
2074 3772 5.361285 AGAGTAGTGTAGCTGGACCTTAATG 59.639 44.000 0.00 0.00 0.00 1.90
2086 3784 3.791245 GACCTTAATGCTGGTCTCAGAG 58.209 50.000 5.05 0.00 46.65 3.35
2093 3791 0.177604 GCTGGTCTCAGAGGTGATGG 59.822 60.000 0.00 0.00 43.49 3.51
2099 3797 3.964031 GGTCTCAGAGGTGATGGTAGAAT 59.036 47.826 0.00 0.00 30.18 2.40
2113 3811 7.660617 GTGATGGTAGAATGTCTCATCATCATT 59.339 37.037 10.90 0.00 38.86 2.57
2148 3846 5.928839 GCTTTGTAGTCTTCAGAGTGATTCA 59.071 40.000 0.05 0.00 0.00 2.57
2151 3849 5.080337 TGTAGTCTTCAGAGTGATTCACCT 58.920 41.667 13.14 7.46 34.49 4.00
2199 3897 4.701765 TGTTTTCCCCATTTGATTGTGTG 58.298 39.130 0.00 0.00 0.00 3.82
2201 3899 5.071519 TGTTTTCCCCATTTGATTGTGTGAT 59.928 36.000 0.00 0.00 0.00 3.06
2236 3934 6.810911 TCTTTATGTCAGGATTCTAGACAGC 58.189 40.000 14.01 0.00 44.51 4.40
2238 3936 7.780271 TCTTTATGTCAGGATTCTAGACAGCTA 59.220 37.037 14.01 4.27 44.51 3.32
2241 3939 5.204292 TGTCAGGATTCTAGACAGCTATGT 58.796 41.667 0.00 0.00 44.31 2.29
2274 3973 6.088016 TGTTCTTTTCTGGTGGAAATGATG 57.912 37.500 7.26 0.00 43.10 3.07
2284 3983 7.292319 TCTGGTGGAAATGATGATCAACATAT 58.708 34.615 17.73 6.81 39.56 1.78
2290 3989 7.933033 TGGAAATGATGATCAACATATCGAAGA 59.067 33.333 17.73 0.00 39.59 2.87
2291 3990 8.226448 GGAAATGATGATCAACATATCGAAGAC 58.774 37.037 17.73 5.05 38.44 3.01
2298 3997 7.496747 TGATCAACATATCGAAGACCATGTAA 58.503 34.615 0.00 0.00 42.40 2.41
2307 4006 5.670485 TCGAAGACCATGTAATTGTGCTAT 58.330 37.500 0.00 0.00 0.00 2.97
2312 4011 5.104360 AGACCATGTAATTGTGCTATCAGGT 60.104 40.000 0.00 0.00 0.00 4.00
2326 4025 4.511826 GCTATCAGGTATGTTAAGGTGCAC 59.488 45.833 8.80 8.80 0.00 4.57
2327 4026 2.967362 TCAGGTATGTTAAGGTGCACG 58.033 47.619 11.45 0.00 0.00 5.34
2339 4038 1.276421 AGGTGCACGCTTACTGAAGAT 59.724 47.619 11.45 0.00 34.25 2.40
2343 4042 2.736721 TGCACGCTTACTGAAGATCAAC 59.263 45.455 0.00 0.00 34.25 3.18
2346 4045 2.996621 ACGCTTACTGAAGATCAACAGC 59.003 45.455 15.69 5.49 37.61 4.40
2354 4053 2.490509 TGAAGATCAACAGCAGCATTGG 59.509 45.455 9.02 0.00 0.00 3.16
2378 4077 7.392113 TGGAAGAAGAGTAAACTGTGTTTTCAA 59.608 33.333 0.94 0.00 0.00 2.69
2408 4109 2.349438 GCATGTTGTAACTGTGGTGTCG 60.349 50.000 0.00 0.00 0.00 4.35
2409 4110 1.942677 TGTTGTAACTGTGGTGTCGG 58.057 50.000 0.00 0.00 0.00 4.79
2411 4112 2.282407 GTTGTAACTGTGGTGTCGGTT 58.718 47.619 0.00 0.00 39.73 4.44
2415 4116 1.375551 AACTGTGGTGTCGGTTGAAC 58.624 50.000 0.00 0.00 35.85 3.18
2417 4118 1.134220 ACTGTGGTGTCGGTTGAACAT 60.134 47.619 0.00 0.00 0.00 2.71
2418 4119 1.946768 CTGTGGTGTCGGTTGAACATT 59.053 47.619 0.00 0.00 0.00 2.71
2422 4123 2.124122 GGTGTCGGTTGAACATTTTGC 58.876 47.619 0.00 0.00 0.00 3.68
2426 4127 4.026886 GTGTCGGTTGAACATTTTGCTTTC 60.027 41.667 0.00 0.00 0.00 2.62
2427 4128 4.109050 GTCGGTTGAACATTTTGCTTTCA 58.891 39.130 0.00 0.00 0.00 2.69
2440 4141 7.657354 ACATTTTGCTTTCAGGGTATTTTTCTC 59.343 33.333 0.00 0.00 0.00 2.87
2453 4154 8.589701 GGGTATTTTTCTCCCTTTCAATAGAA 57.410 34.615 0.00 0.00 38.29 2.10
2458 4159 9.764363 ATTTTTCTCCCTTTCAATAGAAAACAC 57.236 29.630 8.23 0.00 43.76 3.32
2459 4160 8.533569 TTTTCTCCCTTTCAATAGAAAACACT 57.466 30.769 0.00 0.00 42.78 3.55
2460 4161 7.510549 TTCTCCCTTTCAATAGAAAACACTG 57.489 36.000 0.00 0.00 42.78 3.66
2463 4164 7.559897 TCTCCCTTTCAATAGAAAACACTGTTT 59.440 33.333 1.00 1.00 42.78 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.809673 AGAAAAATGAAGCCCGCTTAAAG 58.190 39.130 1.05 0.00 36.26 1.85
2 3 5.968528 TTAGAAAAATGAAGCCCGCTTAA 57.031 34.783 1.05 0.00 36.26 1.85
3 4 5.163561 CCATTAGAAAAATGAAGCCCGCTTA 60.164 40.000 1.05 0.00 36.26 3.09
5 6 3.131046 CCATTAGAAAAATGAAGCCCGCT 59.869 43.478 0.00 0.00 0.00 5.52
6 7 3.130340 TCCATTAGAAAAATGAAGCCCGC 59.870 43.478 0.00 0.00 0.00 6.13
7 8 4.440112 GGTCCATTAGAAAAATGAAGCCCG 60.440 45.833 0.00 0.00 0.00 6.13
8 9 4.141937 GGGTCCATTAGAAAAATGAAGCCC 60.142 45.833 0.00 4.51 0.00 5.19
9 10 4.440112 CGGGTCCATTAGAAAAATGAAGCC 60.440 45.833 0.00 0.00 0.00 4.35
10 11 4.672409 CGGGTCCATTAGAAAAATGAAGC 58.328 43.478 0.00 0.00 0.00 3.86
11 12 4.399303 AGCGGGTCCATTAGAAAAATGAAG 59.601 41.667 0.00 0.00 0.00 3.02
12 13 4.340617 AGCGGGTCCATTAGAAAAATGAA 58.659 39.130 0.00 0.00 0.00 2.57
18 19 3.263425 AGAAGAAGCGGGTCCATTAGAAA 59.737 43.478 0.00 0.00 0.00 2.52
20 21 2.467880 AGAAGAAGCGGGTCCATTAGA 58.532 47.619 0.00 0.00 0.00 2.10
21 22 2.990066 AGAAGAAGCGGGTCCATTAG 57.010 50.000 0.00 0.00 0.00 1.73
25 26 2.358322 AAAAAGAAGAAGCGGGTCCA 57.642 45.000 0.00 0.00 0.00 4.02
42 43 3.383185 AGAAATGGCCGAACAACTCAAAA 59.617 39.130 0.00 0.00 0.00 2.44
43 44 2.955660 AGAAATGGCCGAACAACTCAAA 59.044 40.909 0.00 0.00 0.00 2.69
44 45 2.582052 AGAAATGGCCGAACAACTCAA 58.418 42.857 0.00 0.00 0.00 3.02
46 47 2.814336 AGAAGAAATGGCCGAACAACTC 59.186 45.455 0.00 0.00 0.00 3.01
47 48 2.814336 GAGAAGAAATGGCCGAACAACT 59.186 45.455 0.00 0.00 0.00 3.16
48 49 2.814336 AGAGAAGAAATGGCCGAACAAC 59.186 45.455 0.00 0.00 0.00 3.32
50 51 2.859165 AGAGAAGAAATGGCCGAACA 57.141 45.000 0.00 0.00 0.00 3.18
51 52 2.937149 GGTAGAGAAGAAATGGCCGAAC 59.063 50.000 0.00 0.00 0.00 3.95
52 53 2.569853 TGGTAGAGAAGAAATGGCCGAA 59.430 45.455 0.00 0.00 0.00 4.30
53 54 2.093658 GTGGTAGAGAAGAAATGGCCGA 60.094 50.000 0.00 0.00 0.00 5.54
54 55 2.280628 GTGGTAGAGAAGAAATGGCCG 58.719 52.381 0.00 0.00 0.00 6.13
58 59 3.862267 CAGCTCGTGGTAGAGAAGAAATG 59.138 47.826 0.00 0.00 40.57 2.32
59 60 3.118956 CCAGCTCGTGGTAGAGAAGAAAT 60.119 47.826 0.00 0.00 42.17 2.17
60 61 2.231478 CCAGCTCGTGGTAGAGAAGAAA 59.769 50.000 0.00 0.00 42.17 2.52
61 62 1.819288 CCAGCTCGTGGTAGAGAAGAA 59.181 52.381 0.00 0.00 42.17 2.52
70 71 4.379243 CGAAGCCCAGCTCGTGGT 62.379 66.667 0.00 0.00 46.37 4.16
72 73 1.961277 AAACGAAGCCCAGCTCGTG 60.961 57.895 12.44 0.00 40.22 4.35
73 74 1.961277 CAAACGAAGCCCAGCTCGT 60.961 57.895 7.82 7.82 41.31 4.18
75 76 0.603975 AGACAAACGAAGCCCAGCTC 60.604 55.000 0.00 0.00 38.25 4.09
76 77 0.603975 GAGACAAACGAAGCCCAGCT 60.604 55.000 0.00 0.00 42.56 4.24
80 81 3.430333 TTTTTGAGACAAACGAAGCCC 57.570 42.857 0.00 0.00 0.00 5.19
103 104 6.542821 TCTCTCTCTCTCTCTCTGTCTTTTT 58.457 40.000 0.00 0.00 0.00 1.94
105 106 5.485353 TCTCTCTCTCTCTCTCTCTGTCTTT 59.515 44.000 0.00 0.00 0.00 2.52
128 1167 4.553323 TCTAGTTACAAACACGAAGCCTC 58.447 43.478 0.00 0.00 0.00 4.70
129 1168 4.557205 CTCTAGTTACAAACACGAAGCCT 58.443 43.478 0.00 0.00 0.00 4.58
130 1169 3.123116 GCTCTAGTTACAAACACGAAGCC 59.877 47.826 0.00 0.00 0.00 4.35
455 1494 1.549203 GGAAGCCAACATGGTGTCAT 58.451 50.000 10.47 0.00 40.46 3.06
530 2163 0.109597 CCAGAAGCCAACATGAACGC 60.110 55.000 0.00 0.00 0.00 4.84
855 2500 5.867330 TCTTGGGCAATCAATTCAACAAAT 58.133 33.333 0.00 0.00 0.00 2.32
1076 2731 0.512952 GACGGACTTGCATGTGTCAC 59.487 55.000 10.37 0.00 35.11 3.67
1134 2789 2.365293 GTTGTTGGCCTGGAAGAACAAT 59.635 45.455 16.95 0.00 39.39 2.71
1353 3008 3.674997 GTCCTGCAAATTACCTGACTCA 58.325 45.455 0.00 0.00 0.00 3.41
1697 3368 8.502738 TCCAAGAAAATCAATACTATAAGCCCT 58.497 33.333 0.00 0.00 0.00 5.19
1718 3389 5.191921 AGGGAGGGAGTACTTTTATTCCAAG 59.808 44.000 0.00 0.00 36.09 3.61
1719 3390 5.105853 AGGGAGGGAGTACTTTTATTCCAA 58.894 41.667 0.00 0.00 36.09 3.53
1745 3423 1.098712 TGCGCCGATTAAATGGGGAC 61.099 55.000 4.18 8.42 40.41 4.46
1746 3424 1.098712 GTGCGCCGATTAAATGGGGA 61.099 55.000 4.18 0.00 40.41 4.81
1747 3425 1.358759 GTGCGCCGATTAAATGGGG 59.641 57.895 4.18 8.52 40.88 4.96
1748 3426 0.453793 TTGTGCGCCGATTAAATGGG 59.546 50.000 4.18 0.00 0.00 4.00
1749 3427 2.490328 ATTGTGCGCCGATTAAATGG 57.510 45.000 4.18 0.00 0.00 3.16
1750 3428 3.541903 GCAAATTGTGCGCCGATTAAATG 60.542 43.478 4.18 5.03 45.10 2.32
1867 3548 3.216800 TCCTTCCAGCATATGCATTGAC 58.783 45.455 28.62 0.00 45.16 3.18
1928 3611 5.649831 GGTACCAGAGCAAAATCAAGATTCT 59.350 40.000 7.15 0.00 0.00 2.40
1998 3695 5.927281 ATCTGCTATTGCCAAATTCACTT 57.073 34.783 0.00 0.00 38.71 3.16
2002 3699 9.154847 ACTTAAAAATCTGCTATTGCCAAATTC 57.845 29.630 0.00 0.00 38.71 2.17
2003 3700 8.938906 CACTTAAAAATCTGCTATTGCCAAATT 58.061 29.630 0.00 0.00 38.71 1.82
2024 3722 1.896220 CTTTGCCCACTCTGCACTTA 58.104 50.000 0.00 0.00 38.72 2.24
2046 3744 1.186200 CCAGCTACACTACTCTGCCA 58.814 55.000 0.00 0.00 0.00 4.92
2047 3745 1.135333 GTCCAGCTACACTACTCTGCC 59.865 57.143 0.00 0.00 0.00 4.85
2049 3747 2.729194 AGGTCCAGCTACACTACTCTG 58.271 52.381 0.00 0.00 0.00 3.35
2050 3748 3.459710 AAGGTCCAGCTACACTACTCT 57.540 47.619 0.00 0.00 0.00 3.24
2051 3749 5.593010 CATTAAGGTCCAGCTACACTACTC 58.407 45.833 0.00 0.00 0.00 2.59
2052 3750 4.141914 GCATTAAGGTCCAGCTACACTACT 60.142 45.833 0.00 0.00 0.00 2.57
2053 3751 4.120589 GCATTAAGGTCCAGCTACACTAC 58.879 47.826 0.00 0.00 0.00 2.73
2054 3752 4.030913 AGCATTAAGGTCCAGCTACACTA 58.969 43.478 0.00 0.00 33.06 2.74
2061 3759 1.383523 GACCAGCATTAAGGTCCAGC 58.616 55.000 0.00 0.00 46.79 4.85
2073 3771 0.900421 CATCACCTCTGAGACCAGCA 59.100 55.000 6.17 0.00 40.20 4.41
2074 3772 0.177604 CCATCACCTCTGAGACCAGC 59.822 60.000 6.17 0.00 40.20 4.85
2086 3784 5.282055 TGATGAGACATTCTACCATCACC 57.718 43.478 0.00 0.00 34.68 4.02
2124 3822 5.928839 TGAATCACTCTGAAGACTACAAAGC 59.071 40.000 0.00 0.00 0.00 3.51
2127 3825 5.540337 AGGTGAATCACTCTGAAGACTACAA 59.460 40.000 13.53 0.00 34.40 2.41
2137 3835 2.028294 ACAGCAGAGGTGAATCACTCTG 60.028 50.000 24.93 24.93 39.82 3.35
2138 3836 2.255406 ACAGCAGAGGTGAATCACTCT 58.745 47.619 13.53 10.74 34.87 3.24
2148 3846 6.294473 CCTATATCATCAAAACAGCAGAGGT 58.706 40.000 0.00 0.00 0.00 3.85
2151 3849 5.683681 TGCCTATATCATCAAAACAGCAGA 58.316 37.500 0.00 0.00 0.00 4.26
2181 3879 5.777223 TGTAATCACACAATCAAATGGGGAA 59.223 36.000 0.00 0.00 0.00 3.97
2183 3881 5.657826 TGTAATCACACAATCAAATGGGG 57.342 39.130 0.00 0.00 0.00 4.96
2213 3911 6.815089 AGCTGTCTAGAATCCTGACATAAAG 58.185 40.000 0.00 0.00 39.55 1.85
2236 3934 9.778993 CAGAAAAGAACAATTACCATGACATAG 57.221 33.333 0.00 0.00 0.00 2.23
2238 3936 7.233348 ACCAGAAAAGAACAATTACCATGACAT 59.767 33.333 0.00 0.00 0.00 3.06
2241 3939 6.015519 CCACCAGAAAAGAACAATTACCATGA 60.016 38.462 0.00 0.00 0.00 3.07
2242 3940 6.015519 TCCACCAGAAAAGAACAATTACCATG 60.016 38.462 0.00 0.00 0.00 3.66
2245 3943 6.399639 TTCCACCAGAAAAGAACAATTACC 57.600 37.500 0.00 0.00 0.00 2.85
2274 3973 7.946655 TTACATGGTCTTCGATATGTTGATC 57.053 36.000 0.00 0.00 35.55 2.92
2284 3983 3.937814 AGCACAATTACATGGTCTTCGA 58.062 40.909 0.00 0.00 0.00 3.71
2290 3989 5.116084 ACCTGATAGCACAATTACATGGT 57.884 39.130 0.00 0.00 0.00 3.55
2291 3990 6.712095 ACATACCTGATAGCACAATTACATGG 59.288 38.462 0.00 0.00 0.00 3.66
2298 3997 6.767902 CACCTTAACATACCTGATAGCACAAT 59.232 38.462 0.00 0.00 0.00 2.71
2307 4006 2.933492 GCGTGCACCTTAACATACCTGA 60.933 50.000 12.15 0.00 0.00 3.86
2312 4011 3.930229 CAGTAAGCGTGCACCTTAACATA 59.070 43.478 21.75 6.44 0.00 2.29
2326 4025 2.995939 TGCTGTTGATCTTCAGTAAGCG 59.004 45.455 15.27 0.00 33.43 4.68
2327 4026 3.181512 GCTGCTGTTGATCTTCAGTAAGC 60.182 47.826 19.51 19.51 36.85 3.09
2339 4038 2.275134 TCTTCCAATGCTGCTGTTGA 57.725 45.000 16.24 0.38 0.00 3.18
2343 4042 2.434428 ACTCTTCTTCCAATGCTGCTG 58.566 47.619 0.00 0.00 0.00 4.41
2346 4045 5.471456 ACAGTTTACTCTTCTTCCAATGCTG 59.529 40.000 0.00 0.00 0.00 4.41
2354 4053 9.788960 AATTGAAAACACAGTTTACTCTTCTTC 57.211 29.630 0.00 0.00 0.00 2.87
2408 4109 3.809279 CCCTGAAAGCAAAATGTTCAACC 59.191 43.478 0.00 0.00 31.21 3.77
2409 4110 4.441792 ACCCTGAAAGCAAAATGTTCAAC 58.558 39.130 0.00 0.00 31.21 3.18
2411 4112 6.418057 AATACCCTGAAAGCAAAATGTTCA 57.582 33.333 0.00 0.00 0.00 3.18
2415 4116 7.118245 GGAGAAAAATACCCTGAAAGCAAAATG 59.882 37.037 0.00 0.00 0.00 2.32
2417 4118 6.463755 GGGAGAAAAATACCCTGAAAGCAAAA 60.464 38.462 0.00 0.00 40.39 2.44
2418 4119 5.011635 GGGAGAAAAATACCCTGAAAGCAAA 59.988 40.000 0.00 0.00 40.39 3.68
2440 4141 8.716646 AAAAACAGTGTTTTCTATTGAAAGGG 57.283 30.769 29.13 0.00 42.34 3.95


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

AutoCloner maintained by Alex Coulton.