Multiple sequence alignment - TraesCS4A01G381100

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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 TraesCS4A01G381100 chr4A 100.000 2604 0 0 1 2604 658824356 658826959 0.000000e+00 4809.0
1 TraesCS4A01G381100 chr4A 86.405 1883 208 24 10 1879 657500996 657499149 0.000000e+00 2015.0
2 TraesCS4A01G381100 chr4A 91.022 401 24 6 2063 2458 657499293 657498900 4.930000e-147 531.0
3 TraesCS4A01G381100 chr4A 97.895 95 1 1 2505 2599 657498900 657498807 2.070000e-36 163.0
4 TraesCS4A01G381100 chr7D 89.461 2078 165 22 1 2058 45514328 45512285 0.000000e+00 2575.0
5 TraesCS4A01G381100 chr7D 94.318 88 5 0 2118 2205 45512277 45512190 4.520000e-28 135.0
6 TraesCS4A01G381100 chr7D 79.310 145 16 9 2464 2603 45511729 45511594 3.570000e-14 89.8
7 TraesCS4A01G381100 chr7A 87.889 1544 156 21 97 1626 47574357 47572831 0.000000e+00 1786.0
8 TraesCS4A01G381100 chr7A 87.500 1544 162 21 97 1626 47608775 47607249 0.000000e+00 1753.0
9 TraesCS4A01G381100 chr7A 87.435 1544 163 21 97 1626 47588499 47586973 0.000000e+00 1748.0
10 TraesCS4A01G381100 chr7A 86.111 180 9 7 2210 2388 47572319 47572155 2.060000e-41 180.0
11 TraesCS4A01G381100 chr7A 86.111 180 9 7 2210 2388 47586453 47586289 2.060000e-41 180.0
12 TraesCS4A01G381100 chr7A 85.000 180 11 7 2210 2388 47606739 47606575 4.460000e-38 169.0
13 TraesCS4A01G381100 chr7A 88.393 112 7 4 2094 2205 47572639 47572534 2.100000e-26 130.0
14 TraesCS4A01G381100 chr7A 88.393 112 7 4 2094 2205 47586772 47586667 2.100000e-26 130.0
15 TraesCS4A01G381100 chr7A 88.393 112 7 4 2094 2205 47607057 47606952 2.100000e-26 130.0
16 TraesCS4A01G381100 chr7A 78.173 197 20 16 2430 2603 47606435 47606239 1.270000e-18 104.0
17 TraesCS4A01G381100 chr7A 77.665 197 21 16 2430 2603 47572015 47571819 5.930000e-17 99.0
18 TraesCS4A01G381100 chr7A 77.665 197 21 16 2430 2603 47586149 47585953 5.930000e-17 99.0
19 TraesCS4A01G381100 chrUn 87.630 1544 160 21 97 1626 264365969 264364443 0.000000e+00 1764.0
20 TraesCS4A01G381100 chrUn 87.630 1544 160 21 97 1626 317692231 317693757 0.000000e+00 1764.0
21 TraesCS4A01G381100 chrUn 87.807 1140 125 9 97 1230 399199835 399200966 0.000000e+00 1323.0
22 TraesCS4A01G381100 chrUn 86.169 629 80 5 97 723 370957105 370957728 0.000000e+00 673.0
23 TraesCS4A01G381100 chrUn 92.025 326 23 3 1302 1626 362060464 362060787 3.050000e-124 455.0
24 TraesCS4A01G381100 chrUn 92.025 326 23 3 1302 1626 414618909 414619232 3.050000e-124 455.0
25 TraesCS4A01G381100 chrUn 86.111 180 9 7 2210 2388 317694277 317694441 2.060000e-41 180.0
26 TraesCS4A01G381100 chrUn 85.000 180 11 7 2210 2388 362061296 362061460 4.460000e-38 169.0
27 TraesCS4A01G381100 chrUn 85.000 180 11 7 2210 2388 414619742 414619906 4.460000e-38 169.0
28 TraesCS4A01G381100 chrUn 88.393 112 7 4 2094 2205 317693958 317694063 2.100000e-26 130.0
29 TraesCS4A01G381100 chrUn 88.393 112 7 4 2094 2205 414619424 414619529 2.100000e-26 130.0
30 TraesCS4A01G381100 chrUn 87.500 112 8 4 2094 2205 362060979 362061084 9.780000e-25 124.0
31 TraesCS4A01G381100 chrUn 77.665 197 21 16 2430 2603 317694581 317694777 5.930000e-17 99.0
32 TraesCS4A01G381100 chrUn 77.665 197 21 16 2430 2603 362061600 362061796 5.930000e-17 99.0


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 TraesCS4A01G381100 chr4A 658824356 658826959 2603 False 4809.000000 4809 100.000000 1 2604 1 chr4A.!!$F1 2603
1 TraesCS4A01G381100 chr4A 657498807 657500996 2189 True 903.000000 2015 91.774000 10 2599 3 chr4A.!!$R1 2589
2 TraesCS4A01G381100 chr7D 45511594 45514328 2734 True 933.266667 2575 87.696333 1 2603 3 chr7D.!!$R1 2602
3 TraesCS4A01G381100 chr7A 47571819 47574357 2538 True 548.750000 1786 85.014500 97 2603 4 chr7A.!!$R1 2506
4 TraesCS4A01G381100 chr7A 47585953 47588499 2546 True 539.250000 1748 84.901000 97 2603 4 chr7A.!!$R2 2506
5 TraesCS4A01G381100 chr7A 47606239 47608775 2536 True 539.000000 1753 84.766500 97 2603 4 chr7A.!!$R3 2506
6 TraesCS4A01G381100 chrUn 264364443 264365969 1526 True 1764.000000 1764 87.630000 97 1626 1 chrUn.!!$R1 1529
7 TraesCS4A01G381100 chrUn 399199835 399200966 1131 False 1323.000000 1323 87.807000 97 1230 1 chrUn.!!$F2 1133
8 TraesCS4A01G381100 chrUn 370957105 370957728 623 False 673.000000 673 86.169000 97 723 1 chrUn.!!$F1 626
9 TraesCS4A01G381100 chrUn 317692231 317694777 2546 False 543.250000 1764 84.949750 97 2603 4 chrUn.!!$F3 2506
10 TraesCS4A01G381100 chrUn 414618909 414619906 997 False 251.333333 455 88.472667 1302 2388 3 chrUn.!!$F5 1086
11 TraesCS4A01G381100 chrUn 362060464 362061796 1332 False 211.750000 455 85.547500 1302 2603 4 chrUn.!!$F4 1301

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
552 553 0.681175 GCACAGGGCTGATTGGTTTT 59.319 50.0 0.0 0.0 40.25 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2595 0.036388 TGCTAGGAAGGAAACCAGCG 60.036 55.0 0.0 0.0 35.75 5.18 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
33 34 3.272574 TGGAGAATGCAGAATCTGGAC 57.727 47.619 12.66 0.00 34.07 4.02
50 51 2.291346 TGGACTCCCTCGATCTACACAA 60.291 50.000 0.00 0.00 0.00 3.33
56 57 5.067936 ACTCCCTCGATCTACACAATAACTG 59.932 44.000 0.00 0.00 0.00 3.16
60 61 6.202937 CCTCGATCTACACAATAACTGTCTC 58.797 44.000 0.00 0.00 35.47 3.36
63 64 6.038382 TCGATCTACACAATAACTGTCTCTCC 59.962 42.308 0.00 0.00 35.47 3.71
89 90 3.589988 GCATACCAGATGATTCCCGTAG 58.410 50.000 0.00 0.00 0.00 3.51
113 114 4.003648 CTCCACAATCTGTCCCAACTTAC 58.996 47.826 0.00 0.00 0.00 2.34
141 142 8.867097 ACCTTAGATTTGTCTTCTAACACACTA 58.133 33.333 0.00 0.00 33.34 2.74
187 188 2.158769 TGGCGAATGCAGAATATGGAGT 60.159 45.455 0.00 0.00 45.35 3.85
188 189 2.481952 GGCGAATGCAGAATATGGAGTC 59.518 50.000 0.00 0.00 45.35 3.36
192 193 2.988010 TGCAGAATATGGAGTCGCTT 57.012 45.000 0.00 0.00 0.00 4.68
198 199 4.685165 CAGAATATGGAGTCGCTTGATCTG 59.315 45.833 0.00 0.00 0.00 2.90
214 215 6.536582 GCTTGATCTGCACAATAACTCTCTAA 59.463 38.462 6.44 0.00 0.00 2.10
252 253 8.896744 CCATATGATTTCTGTAAGCTCAAGAAA 58.103 33.333 16.33 16.33 33.78 2.52
262 263 1.771255 AGCTCAAGAAACTGTCCTGGT 59.229 47.619 0.00 0.00 0.00 4.00
274 275 6.783708 AACTGTCCTGGTTTTTATTGAACA 57.216 33.333 0.00 0.00 0.00 3.18
338 339 6.359480 GTTACAATTAACCTCCATCTTCCG 57.641 41.667 0.00 0.00 32.71 4.30
354 355 2.604046 TCCGCCTCAATTTCTCTAGC 57.396 50.000 0.00 0.00 0.00 3.42
463 464 3.223674 ACCACTTTGGAAACCTACCTG 57.776 47.619 0.00 0.00 40.96 4.00
491 492 4.696877 CACCAGATTGCACTTGAAGATGTA 59.303 41.667 0.00 0.00 0.00 2.29
496 497 7.254692 CCAGATTGCACTTGAAGATGTATGTAG 60.255 40.741 0.00 0.00 0.00 2.74
499 500 5.419542 TGCACTTGAAGATGTATGTAGTCC 58.580 41.667 0.00 0.00 0.00 3.85
501 502 5.751028 GCACTTGAAGATGTATGTAGTCCTC 59.249 44.000 0.00 0.00 0.00 3.71
505 506 5.766590 TGAAGATGTATGTAGTCCTCCTCA 58.233 41.667 0.00 0.00 0.00 3.86
509 510 2.965831 TGTATGTAGTCCTCCTCATGGC 59.034 50.000 0.00 0.00 0.00 4.40
552 553 0.681175 GCACAGGGCTGATTGGTTTT 59.319 50.000 0.00 0.00 40.25 2.43
575 576 9.912634 TTTTACTAAGATCAAGGCATTTTTCTG 57.087 29.630 0.00 0.00 0.00 3.02
576 577 8.635765 TTACTAAGATCAAGGCATTTTTCTGT 57.364 30.769 0.00 0.00 0.00 3.41
580 581 7.765695 AAGATCAAGGCATTTTTCTGTAAGA 57.234 32.000 0.00 0.00 44.68 2.10
650 651 8.080417 CCAAGCTATTGATTATGACATTCAAGG 58.920 37.037 8.21 5.50 38.83 3.61
655 656 7.591421 ATTGATTATGACATTCAAGGCATCA 57.409 32.000 8.21 0.00 33.26 3.07
696 697 4.988598 CTTGTCGGCAGCGGTGGT 62.989 66.667 17.54 0.00 0.00 4.16
727 728 4.130118 GGTGTATAAGATCTGCCTTGGTG 58.870 47.826 0.00 0.00 0.00 4.17
729 730 5.455326 GGTGTATAAGATCTGCCTTGGTGAT 60.455 44.000 0.00 0.00 0.00 3.06
730 731 5.468072 GTGTATAAGATCTGCCTTGGTGATG 59.532 44.000 0.00 0.00 0.00 3.07
736 737 2.942804 TCTGCCTTGGTGATGAAAACA 58.057 42.857 0.00 0.00 0.00 2.83
771 772 5.415415 CTGTCAAGCAAATATGGAGTAGC 57.585 43.478 0.00 0.00 0.00 3.58
852 856 3.507162 TCCATCCGACATGCCAATATT 57.493 42.857 0.00 0.00 0.00 1.28
873 877 5.782893 TTGTAAAGTTGCTTGGCTACATT 57.217 34.783 6.83 3.97 36.81 2.71
915 919 6.096141 AGCTCCTCATATACGAATACATGGAG 59.904 42.308 0.00 0.00 35.58 3.86
937 941 2.116238 ACGGTAGCCTGTATGAATGGT 58.884 47.619 0.00 0.00 0.00 3.55
1047 1054 1.176527 GGCTGTGTTACATGCACCAT 58.823 50.000 13.27 0.00 36.11 3.55
1123 1130 3.688673 GGATCTTCAGTTCAGAGCAAAGG 59.311 47.826 0.00 0.00 0.00 3.11
1150 1157 3.680620 TTTGGCCTAGCTCGCGCAT 62.681 57.895 8.75 0.00 39.10 4.73
1227 1234 7.232941 GGATACATAGCTCCAGGTAAGAACTTA 59.767 40.741 0.00 0.00 0.00 2.24
1230 1237 4.810191 AGCTCCAGGTAAGAACTTAGTG 57.190 45.455 0.00 0.00 0.00 2.74
1259 1273 6.546772 ACTTTGGTTATTTTGAACTCGGGTAA 59.453 34.615 0.00 0.00 0.00 2.85
1283 1297 5.991328 ATAACTGTGTGACAAGTGACTTG 57.009 39.130 22.73 22.73 45.85 3.16
1475 1497 9.064706 ACATCCATTTGACAAATCTGATAGATC 57.935 33.333 10.52 0.00 32.89 2.75
1503 1525 1.448119 CGAGATCCAGCCTACTCGCA 61.448 60.000 0.00 0.00 43.71 5.10
1668 1690 3.609103 CCAGAAGGTCGTCAAAAGTTG 57.391 47.619 0.00 0.00 0.00 3.16
1672 1694 3.442273 AGAAGGTCGTCAAAAGTTGCAAA 59.558 39.130 0.00 0.00 0.00 3.68
1678 1700 3.687212 TCGTCAAAAGTTGCAAAGAGACA 59.313 39.130 0.00 0.00 0.00 3.41
1680 1702 3.786048 GTCAAAAGTTGCAAAGAGACACG 59.214 43.478 0.00 0.00 0.00 4.49
1686 1708 1.082496 GCAAAGAGACACGCACTGC 60.082 57.895 0.00 0.00 0.00 4.40
1706 1728 6.741358 CACTGCGGTTTTATTCTTACTAAAGC 59.259 38.462 0.00 0.00 32.36 3.51
1728 1750 7.440523 AGCTAGTTTGTCTAAATGAAACTGG 57.559 36.000 0.00 0.00 39.62 4.00
1735 1757 3.127030 GTCTAAATGAAACTGGAAGGGCG 59.873 47.826 0.00 0.00 39.30 6.13
1740 1762 1.228154 AAACTGGAAGGGCGACACC 60.228 57.895 0.00 0.00 39.30 4.16
1823 1845 2.228138 CAGCATGTTTTGTGGCTGTT 57.772 45.000 0.00 0.00 46.47 3.16
1830 1852 3.030291 TGTTTTGTGGCTGTTGATCCTT 58.970 40.909 0.00 0.00 0.00 3.36
1838 1860 5.362430 TGTGGCTGTTGATCCTTTTTACTTT 59.638 36.000 0.00 0.00 0.00 2.66
1839 1861 5.691754 GTGGCTGTTGATCCTTTTTACTTTG 59.308 40.000 0.00 0.00 0.00 2.77
1840 1862 5.221422 TGGCTGTTGATCCTTTTTACTTTGG 60.221 40.000 0.00 0.00 0.00 3.28
1860 1882 6.648879 TTGGGATTCAGTTTAAAGTCAAGG 57.351 37.500 0.00 0.00 0.00 3.61
1875 1897 5.652994 AGTCAAGGACTGAACAGAGTATC 57.347 43.478 8.87 0.00 41.76 2.24
1878 1900 3.367646 AGGACTGAACAGAGTATCGGA 57.632 47.619 8.87 0.00 42.67 4.55
1886 1908 6.812160 ACTGAACAGAGTATCGGAATAAACAC 59.188 38.462 8.87 0.00 42.67 3.32
1892 1914 5.895534 AGAGTATCGGAATAAACACCTGGTA 59.104 40.000 0.00 0.00 42.67 3.25
1898 1929 4.076394 GGAATAAACACCTGGTACTGCAA 58.924 43.478 0.00 0.00 0.00 4.08
1921 1952 1.202290 CCTGCAACGCTGAAAAACACT 60.202 47.619 0.00 0.00 0.00 3.55
1922 1953 2.032799 CCTGCAACGCTGAAAAACACTA 59.967 45.455 0.00 0.00 0.00 2.74
1954 1988 1.839994 TCCTAAGCCATCTGAACCAGG 59.160 52.381 0.00 0.00 31.51 4.45
1979 2013 3.251004 GTCGCCAAAAGTTTCAGAGACAT 59.749 43.478 13.35 0.00 0.00 3.06
2001 2035 4.823157 TGCCGTGCTGTTATTCTTACTAA 58.177 39.130 0.00 0.00 0.00 2.24
2058 2101 6.366877 ACGACACACGCAGTAGTTTTTATTAT 59.633 34.615 0.00 0.00 41.61 1.28
2059 2102 6.676995 CGACACACGCAGTAGTTTTTATTATG 59.323 38.462 0.00 0.00 41.61 1.90
2061 2104 6.128117 ACACACGCAGTAGTTTTTATTATGGG 60.128 38.462 0.00 0.00 41.61 4.00
2062 2105 5.163693 ACACGCAGTAGTTTTTATTATGGGC 60.164 40.000 0.00 0.00 41.61 5.36
2064 2107 5.163693 ACGCAGTAGTTTTTATTATGGGCAC 60.164 40.000 0.00 0.00 41.94 5.01
2065 2108 5.163703 CGCAGTAGTTTTTATTATGGGCACA 60.164 40.000 0.00 0.00 0.00 4.57
2066 2109 6.033966 GCAGTAGTTTTTATTATGGGCACAC 58.966 40.000 0.00 0.00 0.00 3.82
2067 2110 6.255215 CAGTAGTTTTTATTATGGGCACACG 58.745 40.000 0.00 0.00 0.00 4.49
2068 2111 4.104696 AGTTTTTATTATGGGCACACGC 57.895 40.909 0.00 0.00 37.44 5.34
2069 2112 3.761752 AGTTTTTATTATGGGCACACGCT 59.238 39.130 0.00 0.00 38.60 5.07
2070 2113 3.773860 TTTTATTATGGGCACACGCTG 57.226 42.857 0.00 0.00 38.60 5.18
2071 2114 2.411628 TTATTATGGGCACACGCTGT 57.588 45.000 0.00 0.00 38.60 4.40
2072 2115 3.545366 TTATTATGGGCACACGCTGTA 57.455 42.857 0.00 0.00 38.60 2.74
2073 2116 1.953559 ATTATGGGCACACGCTGTAG 58.046 50.000 0.00 0.00 38.60 2.74
2074 2117 0.611200 TTATGGGCACACGCTGTAGT 59.389 50.000 0.00 0.00 38.60 2.73
2075 2118 0.611200 TATGGGCACACGCTGTAGTT 59.389 50.000 0.00 0.00 38.60 2.24
2076 2119 0.250727 ATGGGCACACGCTGTAGTTT 60.251 50.000 0.00 0.00 38.60 2.66
2077 2120 0.464735 TGGGCACACGCTGTAGTTTT 60.465 50.000 0.00 0.00 38.60 2.43
2078 2121 0.666374 GGGCACACGCTGTAGTTTTT 59.334 50.000 0.00 0.00 38.60 1.94
2079 2122 1.874872 GGGCACACGCTGTAGTTTTTA 59.125 47.619 0.00 0.00 38.60 1.52
2080 2123 2.486592 GGGCACACGCTGTAGTTTTTAT 59.513 45.455 0.00 0.00 38.60 1.40
2081 2124 3.057806 GGGCACACGCTGTAGTTTTTATT 60.058 43.478 0.00 0.00 38.60 1.40
2082 2125 4.154556 GGGCACACGCTGTAGTTTTTATTA 59.845 41.667 0.00 0.00 38.60 0.98
2083 2126 5.163693 GGGCACACGCTGTAGTTTTTATTAT 60.164 40.000 0.00 0.00 38.60 1.28
2104 2147 2.082231 GAGCAAGAGAAGATGCAGCAA 58.918 47.619 4.07 0.00 44.95 3.91
2147 2193 4.410225 AGCATGTTGTCTGGCTGG 57.590 55.556 0.00 0.00 34.83 4.85
2160 2206 2.413142 GGCTGGCTGTTGATCCTGC 61.413 63.158 0.00 0.00 43.76 4.85
2166 2212 2.837591 TGGCTGTTGATCCTGCTTACTA 59.162 45.455 0.00 0.00 0.00 1.82
2283 2546 5.403766 CGAGATCCTGCTGACACAATATAAC 59.596 44.000 0.00 0.00 0.00 1.89
2348 2611 1.563924 TAGCGCTGGTTTCCTTCCTA 58.436 50.000 22.90 0.00 0.00 2.94
2460 2821 4.024133 TGTGTCCATGAAGTCAACATTTCG 60.024 41.667 0.00 0.00 0.00 3.46
2466 2827 5.976534 CCATGAAGTCAACATTTCGTTTCAA 59.023 36.000 0.00 0.00 34.86 2.69
2474 2835 5.635280 TCAACATTTCGTTTCAAAGCAACAA 59.365 32.000 0.00 0.00 34.86 2.83
2480 2841 4.992688 TCGTTTCAAAGCAACAACATTCT 58.007 34.783 0.00 0.00 0.00 2.40
2491 2853 4.495349 GCAACAACATTCTCATCTCATCCG 60.495 45.833 0.00 0.00 0.00 4.18
2498 2862 4.535526 TTCTCATCTCATCCGTCACAAA 57.464 40.909 0.00 0.00 0.00 2.83
2603 2987 2.490115 CTCAGTCAGTCAGTACAGGGTC 59.510 54.545 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.643334 CCAGATTCTGCATTCTCCAAATCA 59.357 41.667 8.23 0.00 0.00 2.57
33 34 5.067936 ACAGTTATTGTGTAGATCGAGGGAG 59.932 44.000 0.00 0.00 38.99 4.30
50 51 0.739561 GCGACCGGAGAGACAGTTAT 59.260 55.000 9.46 0.00 0.00 1.89
56 57 1.359475 GGTATGCGACCGGAGAGAC 59.641 63.158 9.46 0.00 38.87 3.36
82 83 0.325296 AGATTGTGGAGCCTACGGGA 60.325 55.000 0.00 0.00 33.58 5.14
89 90 0.038166 TTGGGACAGATTGTGGAGCC 59.962 55.000 0.00 0.00 42.39 4.70
94 95 4.023193 GGTTGTAAGTTGGGACAGATTGTG 60.023 45.833 0.00 0.00 42.39 3.33
96 97 4.398319 AGGTTGTAAGTTGGGACAGATTG 58.602 43.478 0.00 0.00 42.39 2.67
113 114 8.283291 GTGTGTTAGAAGACAAATCTAAGGTTG 58.717 37.037 0.00 0.00 39.40 3.77
163 164 3.316029 TCCATATTCTGCATTCGCCAAAG 59.684 43.478 0.00 0.00 37.32 2.77
169 170 2.156504 GCGACTCCATATTCTGCATTCG 59.843 50.000 0.00 0.00 0.00 3.34
187 188 3.599343 AGTTATTGTGCAGATCAAGCGA 58.401 40.909 0.00 0.00 33.85 4.93
188 189 3.620374 AGAGTTATTGTGCAGATCAAGCG 59.380 43.478 0.00 0.00 33.85 4.68
189 190 4.874966 AGAGAGTTATTGTGCAGATCAAGC 59.125 41.667 0.00 0.00 0.00 4.01
192 193 6.341316 GGTTAGAGAGTTATTGTGCAGATCA 58.659 40.000 0.00 0.00 0.00 2.92
198 199 3.858247 ACCGGTTAGAGAGTTATTGTGC 58.142 45.455 0.00 0.00 0.00 4.57
229 230 8.939929 CAGTTTCTTGAGCTTACAGAAATCATA 58.060 33.333 15.18 0.00 32.25 2.15
252 253 6.153680 TGTTGTTCAATAAAAACCAGGACAGT 59.846 34.615 0.00 0.00 0.00 3.55
274 275 1.843851 TGGGCCGGATAGAAGATTGTT 59.156 47.619 5.05 0.00 0.00 2.83
338 339 3.347216 TGGTTGCTAGAGAAATTGAGGC 58.653 45.455 0.00 0.00 0.00 4.70
354 355 0.817634 TCTTGCCCGTCAGTTGGTTG 60.818 55.000 0.00 0.00 0.00 3.77
397 398 5.010012 TGGAAAGAAAGCTCCATTGAAAGTC 59.990 40.000 0.00 0.00 36.79 3.01
399 400 5.458041 TGGAAAGAAAGCTCCATTGAAAG 57.542 39.130 0.00 0.00 36.79 2.62
459 460 1.968017 CAATCTGGTGCACGCAGGT 60.968 57.895 25.49 20.02 0.00 4.00
491 492 1.061812 AGGCCATGAGGAGGACTACAT 60.062 52.381 5.01 0.00 44.68 2.29
496 497 0.394899 CCAAAGGCCATGAGGAGGAC 60.395 60.000 5.01 0.00 36.89 3.85
499 500 1.272092 TGAACCAAAGGCCATGAGGAG 60.272 52.381 5.01 0.00 36.89 3.69
501 502 1.273327 GTTGAACCAAAGGCCATGAGG 59.727 52.381 5.01 3.40 38.23 3.86
552 553 9.733556 TTACAGAAAAATGCCTTGATCTTAGTA 57.266 29.630 0.00 0.00 0.00 1.82
605 606 3.553095 AAGGCCGTCAGCTTCCACC 62.553 63.158 0.00 0.00 43.05 4.61
655 656 1.828595 TGCATCAATGAGGCTGCAAAT 59.171 42.857 20.62 0.00 41.33 2.32
662 663 2.028748 ACAAGGTTTGCATCAATGAGGC 60.029 45.455 13.41 13.41 39.95 4.70
696 697 6.349300 GCAGATCTTATACACCTTTCCTGAA 58.651 40.000 0.00 0.00 0.00 3.02
727 728 6.595716 ACAGCTATAACCTCACTGTTTTCATC 59.404 38.462 0.00 0.00 38.38 2.92
729 730 5.865085 ACAGCTATAACCTCACTGTTTTCA 58.135 37.500 0.00 0.00 38.38 2.69
730 731 5.932303 TGACAGCTATAACCTCACTGTTTTC 59.068 40.000 0.00 0.00 41.45 2.29
736 737 4.130286 GCTTGACAGCTATAACCTCACT 57.870 45.455 0.00 0.00 43.51 3.41
771 772 1.153369 ATCATGTTCCCGTCCGCTG 60.153 57.895 0.00 0.00 0.00 5.18
852 856 5.300539 TGAAATGTAGCCAAGCAACTTTACA 59.699 36.000 0.00 0.00 0.00 2.41
915 919 3.131396 CCATTCATACAGGCTACCGTTC 58.869 50.000 0.00 0.00 0.00 3.95
954 958 6.071108 ACTGTCTAGTTGTACTACTAGTCGGA 60.071 42.308 33.93 20.41 45.08 4.55
956 960 7.593875 AACTGTCTAGTTGTACTACTAGTCG 57.406 40.000 30.67 24.29 45.17 4.18
977 984 0.107410 TGTCGGCCAGTTCAACAACT 60.107 50.000 2.24 0.00 44.26 3.16
1026 1033 1.595093 GGTGCATGTAACACAGCCCC 61.595 60.000 0.00 0.00 39.87 5.80
1047 1054 1.414181 GCTATAGCAGGAGAGCAACCA 59.586 52.381 20.01 0.00 41.59 3.67
1123 1130 1.923227 GCTAGGCCAAAGTCCGCAAC 61.923 60.000 5.01 0.00 0.00 4.17
1150 1157 1.247567 GGCTCACCAGCTTTAAGCAA 58.752 50.000 19.63 0.00 45.56 3.91
1227 1234 8.007405 AGTTCAAAATAACCAAAGTTAGCACT 57.993 30.769 0.00 0.00 41.66 4.40
1230 1237 6.581166 CCGAGTTCAAAATAACCAAAGTTAGC 59.419 38.462 0.00 0.00 41.66 3.09
1259 1273 6.147821 GCAAGTCACTTGTCACACAGTTATAT 59.852 38.462 18.89 0.00 42.77 0.86
1283 1297 5.009110 AGCTTCCAAACTCTAGAAAAAGTGC 59.991 40.000 0.00 0.00 0.00 4.40
1287 1301 5.607477 TCGAGCTTCCAAACTCTAGAAAAA 58.393 37.500 0.00 0.00 0.00 1.94
1379 1398 1.756172 CGCCCCCACCATTTGCATA 60.756 57.895 0.00 0.00 0.00 3.14
1380 1399 3.076278 CGCCCCCACCATTTGCAT 61.076 61.111 0.00 0.00 0.00 3.96
1475 1497 1.539929 GGCTGGATCTCGAACATCTGG 60.540 57.143 0.00 0.54 0.00 3.86
1480 1502 2.025155 GAGTAGGCTGGATCTCGAACA 58.975 52.381 0.00 0.00 0.00 3.18
1481 1503 2.785713 GAGTAGGCTGGATCTCGAAC 57.214 55.000 0.00 0.00 0.00 3.95
1594 1616 3.484557 CGTGTAGTGTTTTTCAGCGTTGT 60.485 43.478 0.00 0.00 0.00 3.32
1665 1687 0.657840 AGTGCGTGTCTCTTTGCAAC 59.342 50.000 0.00 0.00 39.34 4.17
1668 1690 1.082496 GCAGTGCGTGTCTCTTTGC 60.082 57.895 0.00 0.00 0.00 3.68
1680 1702 4.680171 AGTAAGAATAAAACCGCAGTGC 57.320 40.909 4.58 4.58 0.00 4.40
1706 1728 8.507249 CCTTCCAGTTTCATTTAGACAAACTAG 58.493 37.037 0.00 0.00 38.11 2.57
1716 1738 3.078837 GTCGCCCTTCCAGTTTCATTTA 58.921 45.455 0.00 0.00 0.00 1.40
1721 1743 1.235281 GGTGTCGCCCTTCCAGTTTC 61.235 60.000 0.00 0.00 0.00 2.78
1735 1757 4.032104 CGTAATAAAACTACAGCCGGTGTC 59.968 45.833 6.48 0.00 40.94 3.67
1740 1762 6.968904 TCTTACTCGTAATAAAACTACAGCCG 59.031 38.462 0.00 0.00 0.00 5.52
1813 1835 4.892934 AGTAAAAAGGATCAACAGCCACAA 59.107 37.500 0.00 0.00 0.00 3.33
1823 1845 7.010160 ACTGAATCCCAAAGTAAAAAGGATCA 58.990 34.615 0.00 0.00 36.30 2.92
1838 1860 5.768164 GTCCTTGACTTTAAACTGAATCCCA 59.232 40.000 0.00 0.00 0.00 4.37
1839 1861 6.004574 AGTCCTTGACTTTAAACTGAATCCC 58.995 40.000 0.00 0.00 40.28 3.85
1840 1862 6.710744 TCAGTCCTTGACTTTAAACTGAATCC 59.289 38.462 0.81 0.00 41.37 3.01
1860 1882 7.009357 GTGTTTATTCCGATACTCTGTTCAGTC 59.991 40.741 0.00 0.00 0.00 3.51
1875 1897 2.676342 GCAGTACCAGGTGTTTATTCCG 59.324 50.000 0.76 0.00 0.00 4.30
1878 1900 4.725490 ACTTGCAGTACCAGGTGTTTATT 58.275 39.130 0.76 0.00 0.00 1.40
1886 1908 3.540211 CAGGACTTGCAGTACCAGG 57.460 57.895 7.63 0.00 25.63 4.45
1898 1929 1.065551 GTTTTTCAGCGTTGCAGGACT 59.934 47.619 0.00 0.00 0.00 3.85
1921 1952 3.199727 TGGCTTAGGAACTGCATCATGTA 59.800 43.478 0.00 0.00 41.52 2.29
1922 1953 2.025981 TGGCTTAGGAACTGCATCATGT 60.026 45.455 0.00 0.00 41.52 3.21
1954 1988 2.218603 TCTGAAACTTTTGGCGACCTC 58.781 47.619 0.00 0.00 0.00 3.85
1979 2013 3.328382 AGTAAGAATAACAGCACGGCA 57.672 42.857 0.00 0.00 0.00 5.69
2058 2101 0.464735 AAAACTACAGCGTGTGCCCA 60.465 50.000 1.58 0.00 44.31 5.36
2059 2102 0.666374 AAAAACTACAGCGTGTGCCC 59.334 50.000 1.58 0.00 44.31 5.36
2061 2104 6.539324 TCATAATAAAAACTACAGCGTGTGC 58.461 36.000 1.58 0.00 43.24 4.57
2062 2105 6.682863 GCTCATAATAAAAACTACAGCGTGTG 59.317 38.462 1.58 0.00 0.00 3.82
2064 2107 6.771076 TGCTCATAATAAAAACTACAGCGTG 58.229 36.000 0.00 0.00 0.00 5.34
2065 2108 6.978343 TGCTCATAATAAAAACTACAGCGT 57.022 33.333 0.00 0.00 0.00 5.07
2066 2109 7.684670 TCTTGCTCATAATAAAAACTACAGCG 58.315 34.615 0.00 0.00 0.00 5.18
2067 2110 8.883731 TCTCTTGCTCATAATAAAAACTACAGC 58.116 33.333 0.00 0.00 0.00 4.40
2073 2116 9.230932 GCATCTTCTCTTGCTCATAATAAAAAC 57.769 33.333 0.00 0.00 35.95 2.43
2074 2117 8.959548 TGCATCTTCTCTTGCTCATAATAAAAA 58.040 29.630 0.00 0.00 39.60 1.94
2075 2118 8.510243 TGCATCTTCTCTTGCTCATAATAAAA 57.490 30.769 0.00 0.00 39.60 1.52
2076 2119 7.255035 GCTGCATCTTCTCTTGCTCATAATAAA 60.255 37.037 0.00 0.00 39.60 1.40
2077 2120 6.204301 GCTGCATCTTCTCTTGCTCATAATAA 59.796 38.462 0.00 0.00 39.60 1.40
2078 2121 5.699915 GCTGCATCTTCTCTTGCTCATAATA 59.300 40.000 0.00 0.00 39.60 0.98
2079 2122 4.515944 GCTGCATCTTCTCTTGCTCATAAT 59.484 41.667 0.00 0.00 39.60 1.28
2080 2123 3.875727 GCTGCATCTTCTCTTGCTCATAA 59.124 43.478 0.00 0.00 39.60 1.90
2081 2124 3.118519 TGCTGCATCTTCTCTTGCTCATA 60.119 43.478 0.00 0.00 39.60 2.15
2082 2125 2.290464 GCTGCATCTTCTCTTGCTCAT 58.710 47.619 0.00 0.00 39.60 2.90
2083 2126 1.002773 TGCTGCATCTTCTCTTGCTCA 59.997 47.619 0.00 0.00 39.60 4.26
2114 2160 3.194755 ACATGCTGACATTGCACATTCAT 59.805 39.130 0.00 0.00 43.59 2.57
2147 2193 4.697514 TCATAGTAAGCAGGATCAACAGC 58.302 43.478 0.00 0.00 0.00 4.40
2160 2206 9.706691 TGACTTTAAACTGAACCTCATAGTAAG 57.293 33.333 0.00 0.00 0.00 2.34
2166 2212 6.486993 GTCCTTGACTTTAAACTGAACCTCAT 59.513 38.462 0.00 0.00 0.00 2.90
2207 2469 4.762251 AGGTTTAAAGGAAGACTGCATCAC 59.238 41.667 0.00 0.00 0.00 3.06
2326 2589 2.504175 AGGAAGGAAACCAGCGCTAATA 59.496 45.455 10.99 0.00 0.00 0.98
2327 2590 1.282157 AGGAAGGAAACCAGCGCTAAT 59.718 47.619 10.99 0.00 0.00 1.73
2329 2592 1.480954 CTAGGAAGGAAACCAGCGCTA 59.519 52.381 10.99 0.00 0.00 4.26
2330 2593 0.250513 CTAGGAAGGAAACCAGCGCT 59.749 55.000 2.64 2.64 0.00 5.92
2331 2594 1.369839 GCTAGGAAGGAAACCAGCGC 61.370 60.000 0.00 0.00 0.00 5.92
2332 2595 0.036388 TGCTAGGAAGGAAACCAGCG 60.036 55.000 0.00 0.00 35.75 5.18
2338 2601 6.539173 TCTTACATTGTTGCTAGGAAGGAAA 58.461 36.000 0.00 0.00 34.53 3.13
2348 2611 7.164122 TCTTCAGATCTTCTTACATTGTTGCT 58.836 34.615 0.00 0.00 0.00 3.91
2460 2821 6.698766 AGATGAGAATGTTGTTGCTTTGAAAC 59.301 34.615 0.00 0.00 0.00 2.78
2466 2827 5.125097 GGATGAGATGAGAATGTTGTTGCTT 59.875 40.000 0.00 0.00 0.00 3.91
2474 2835 3.448660 TGTGACGGATGAGATGAGAATGT 59.551 43.478 0.00 0.00 0.00 2.71
2491 2853 1.333258 GCTTGTGAGCTCGTTTGTGAC 60.333 52.381 9.64 0.00 45.65 3.67
2558 2942 5.234757 GTGTGCAAAGCAAAATTGAGAATGA 59.765 36.000 0.00 0.00 41.47 2.57


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

AutoCloner maintained by Alex Coulton.