Multiple sequence alignment - TraesCS4D01G059500

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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 TraesCS4D01G059500 chr4D 100.000 2573 0 0 1 2573 35173270 35170698 0.000000e+00 4752.0
1 TraesCS4D01G059500 chr4D 91.952 1578 86 22 51 1600 35521472 35523036 0.000000e+00 2172.0
2 TraesCS4D01G059500 chr4D 81.905 105 13 4 2 105 43624443 43624344 1.640000e-12 84.2
3 TraesCS4D01G059500 chr4A 86.511 2276 194 68 362 2573 567470407 567472633 0.000000e+00 2398.0
4 TraesCS4D01G059500 chr4A 88.454 1637 118 35 50 1628 567039025 567037402 0.000000e+00 1910.0
5 TraesCS4D01G059500 chr4A 91.667 48 4 0 163 210 37028887 37028840 1.650000e-07 67.6
6 TraesCS4D01G059500 chr4B 90.038 1847 116 37 224 2029 51126009 51124190 0.000000e+00 2329.0
7 TraesCS4D01G059500 chr4B 89.526 1308 91 20 338 1625 51748464 51749745 0.000000e+00 1615.0
8 TraesCS4D01G059500 chr4B 78.261 483 68 15 2100 2573 51121873 51121419 2.520000e-70 276.0
9 TraesCS4D01G059500 chr6A 90.541 74 7 0 2 75 596175967 596175894 5.860000e-17 99.0
10 TraesCS4D01G059500 chr5A 86.076 79 8 3 42 119 570473555 570473479 5.900000e-12 82.4
11 TraesCS4D01G059500 chr2A 91.379 58 3 2 15 72 416014316 416014371 7.630000e-11 78.7
12 TraesCS4D01G059500 chr2A 94.000 50 3 0 2 51 727165630 727165581 2.750000e-10 76.8
13 TraesCS4D01G059500 chr7D 90.196 51 5 0 51 101 63378812 63378762 1.650000e-07 67.6
14 TraesCS4D01G059500 chr1B 86.154 65 6 3 62 124 33083143 33083206 1.650000e-07 67.6
15 TraesCS4D01G059500 chr6D 85.714 63 8 1 9 71 343029223 343029284 5.940000e-07 65.8
16 TraesCS4D01G059500 chr6D 88.235 51 6 0 2 52 3417402 3417352 7.690000e-06 62.1
17 TraesCS4D01G059500 chr6D 84.127 63 9 1 9 71 336478382 336478321 2.760000e-05 60.2
18 TraesCS4D01G059500 chr3D 84.615 65 9 1 9 73 1111504 1111441 2.140000e-06 63.9
19 TraesCS4D01G059500 chr6B 90.909 44 4 0 9 52 450607165 450607208 2.760000e-05 60.2
20 TraesCS4D01G059500 chr5B 89.362 47 2 3 160 205 513849289 513849333 3.580000e-04 56.5


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 TraesCS4D01G059500 chr4D 35170698 35173270 2572 True 4752.0 4752 100.0000 1 2573 1 chr4D.!!$R1 2572
1 TraesCS4D01G059500 chr4D 35521472 35523036 1564 False 2172.0 2172 91.9520 51 1600 1 chr4D.!!$F1 1549
2 TraesCS4D01G059500 chr4A 567470407 567472633 2226 False 2398.0 2398 86.5110 362 2573 1 chr4A.!!$F1 2211
3 TraesCS4D01G059500 chr4A 567037402 567039025 1623 True 1910.0 1910 88.4540 50 1628 1 chr4A.!!$R2 1578
4 TraesCS4D01G059500 chr4B 51748464 51749745 1281 False 1615.0 1615 89.5260 338 1625 1 chr4B.!!$F1 1287
5 TraesCS4D01G059500 chr4B 51121419 51126009 4590 True 1302.5 2329 84.1495 224 2573 2 chr4B.!!$R1 2349

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
24 25 0.02877 CGCGGCAAGTTTCTGTCAAA 59.971 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 1983 0.341258 AGGAGAGGCAGAATGGAGGA 59.659 55.0 0.0 0.0 35.86 3.71 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
17 18 2.127758 CGACACGCGGCAAGTTTC 60.128 61.111 12.47 0.00 36.03 2.78
18 19 2.594962 CGACACGCGGCAAGTTTCT 61.595 57.895 12.47 0.00 36.03 2.52
19 20 1.082756 GACACGCGGCAAGTTTCTG 60.083 57.895 12.47 0.00 0.00 3.02
20 21 1.772063 GACACGCGGCAAGTTTCTGT 61.772 55.000 12.47 1.13 0.00 3.41
21 22 1.082756 CACGCGGCAAGTTTCTGTC 60.083 57.895 12.47 0.00 0.00 3.51
22 23 1.522806 ACGCGGCAAGTTTCTGTCA 60.523 52.632 12.47 0.00 0.00 3.58
23 24 1.092921 ACGCGGCAAGTTTCTGTCAA 61.093 50.000 12.47 0.00 0.00 3.18
24 25 0.028770 CGCGGCAAGTTTCTGTCAAA 59.971 50.000 0.00 0.00 0.00 2.69
25 26 1.532921 CGCGGCAAGTTTCTGTCAAAA 60.533 47.619 0.00 0.00 0.00 2.44
26 27 2.535331 GCGGCAAGTTTCTGTCAAAAA 58.465 42.857 0.00 0.00 0.00 1.94
27 28 3.123050 GCGGCAAGTTTCTGTCAAAAAT 58.877 40.909 0.00 0.00 0.00 1.82
28 29 4.295051 GCGGCAAGTTTCTGTCAAAAATA 58.705 39.130 0.00 0.00 0.00 1.40
29 30 4.742659 GCGGCAAGTTTCTGTCAAAAATAA 59.257 37.500 0.00 0.00 0.00 1.40
30 31 5.233263 GCGGCAAGTTTCTGTCAAAAATAAA 59.767 36.000 0.00 0.00 0.00 1.40
31 32 6.636443 CGGCAAGTTTCTGTCAAAAATAAAC 58.364 36.000 0.00 0.00 0.00 2.01
32 33 6.475402 CGGCAAGTTTCTGTCAAAAATAAACT 59.525 34.615 0.00 0.00 40.98 2.66
33 34 7.515059 CGGCAAGTTTCTGTCAAAAATAAACTG 60.515 37.037 0.00 0.00 39.60 3.16
34 35 7.491048 GGCAAGTTTCTGTCAAAAATAAACTGA 59.509 33.333 0.00 0.00 39.60 3.41
35 36 8.868916 GCAAGTTTCTGTCAAAAATAAACTGAA 58.131 29.630 0.00 0.00 39.60 3.02
68 69 1.816835 TCATCCTCGCGTCACTAAACT 59.183 47.619 5.77 0.00 0.00 2.66
72 73 1.419374 CTCGCGTCACTAAACTTGCT 58.581 50.000 5.77 0.00 0.00 3.91
102 103 5.689383 ACGTTCAGAATTGTAATGTGCTT 57.311 34.783 0.00 0.00 0.00 3.91
103 104 5.451908 ACGTTCAGAATTGTAATGTGCTTG 58.548 37.500 0.00 0.00 0.00 4.01
105 106 5.565259 CGTTCAGAATTGTAATGTGCTTGTC 59.435 40.000 0.00 0.00 0.00 3.18
106 107 6.566564 CGTTCAGAATTGTAATGTGCTTGTCT 60.567 38.462 0.00 0.00 0.00 3.41
117 118 0.249447 TGCTTGTCTCTGACGTGTGG 60.249 55.000 0.00 0.00 34.95 4.17
164 166 7.019774 CCATTATATGGGCTAAACATCATCG 57.980 40.000 0.00 0.00 46.86 3.84
172 183 2.158957 GCTAAACATCATCGAGGGACCA 60.159 50.000 0.00 0.00 0.00 4.02
266 278 2.043953 GAGGGATGTGGTTGCCCC 60.044 66.667 0.00 0.00 43.08 5.80
270 282 2.033448 GATGTGGTTGCCCCGACA 59.967 61.111 0.00 0.00 35.15 4.35
277 289 0.893727 GGTTGCCCCGACAAACAGAT 60.894 55.000 0.00 0.00 37.20 2.90
429 442 7.769719 TTGCGATAATACGAAAGTTTTTGTC 57.230 32.000 0.88 0.00 46.40 3.18
432 445 6.464834 GCGATAATACGAAAGTTTTTGTCTGG 59.535 38.462 0.88 0.00 46.40 3.86
475 498 1.137479 TCGTTTTGTTCCAGTCGAGGT 59.863 47.619 0.00 0.00 0.00 3.85
521 557 1.565156 GATCGCACAAGACGCAACCA 61.565 55.000 0.00 0.00 0.00 3.67
525 561 1.208642 GCACAAGACGCAACCAAAGC 61.209 55.000 0.00 0.00 0.00 3.51
588 632 1.737029 CGGTCGATGTCTTGTGAGCAT 60.737 52.381 0.00 0.00 0.00 3.79
1175 1261 4.025858 GCACCTGCAGCCAGAGGA 62.026 66.667 8.66 0.00 41.77 3.71
1179 1265 1.988956 CCTGCAGCCAGAGGACTCT 60.989 63.158 8.66 0.00 41.77 3.24
1419 1532 4.832608 GGAGCCAAGTACGCCGGG 62.833 72.222 2.18 0.00 0.00 5.73
1612 1726 2.094803 TGTTTGTTTCTGGTGCTGTGTG 60.095 45.455 0.00 0.00 0.00 3.82
1632 1748 1.798283 GTGCACCACCACGTACATAA 58.202 50.000 5.22 0.00 0.00 1.90
1678 1799 6.020440 CAGTGTGTAAAATTGTGCAGAAACAG 60.020 38.462 0.00 0.00 0.00 3.16
1692 1828 9.448438 TGTGCAGAAACAGATATATAAACTTGT 57.552 29.630 0.00 0.00 0.00 3.16
1757 1895 4.159377 TGAAATTAACCGAGCTTTGCTG 57.841 40.909 0.00 0.00 39.88 4.41
1766 1904 2.505557 GCTTTGCTGCATCCACGC 60.506 61.111 1.84 0.00 0.00 5.34
1767 1905 2.202388 CTTTGCTGCATCCACGCG 60.202 61.111 3.53 3.53 33.35 6.01
1778 1916 1.982395 TCCACGCGGAGGATTCACT 60.982 57.895 17.21 0.00 35.91 3.41
1779 1917 0.681887 TCCACGCGGAGGATTCACTA 60.682 55.000 17.21 0.00 35.91 2.74
1787 1925 3.561725 GCGGAGGATTCACTAGGAATTTG 59.438 47.826 7.58 0.00 46.17 2.32
1825 1963 1.007336 CCCACAGTACACGAAGCGTC 61.007 60.000 0.00 0.00 38.32 5.19
1826 1964 1.007336 CCACAGTACACGAAGCGTCC 61.007 60.000 0.00 0.00 38.32 4.79
1827 1965 1.007336 CACAGTACACGAAGCGTCCC 61.007 60.000 0.00 0.00 38.32 4.46
1828 1966 1.445582 CAGTACACGAAGCGTCCCC 60.446 63.158 0.00 0.00 38.32 4.81
1829 1967 2.125793 GTACACGAAGCGTCCCCC 60.126 66.667 0.00 0.00 38.32 5.40
1858 1996 1.704007 CCCTCCTCCTCCATTCTGCC 61.704 65.000 0.00 0.00 0.00 4.85
1859 1997 0.693767 CCTCCTCCTCCATTCTGCCT 60.694 60.000 0.00 0.00 0.00 4.75
1888 2026 2.737180 CGAGATCATGGGTCCCCG 59.263 66.667 5.13 0.00 39.42 5.73
1921 2061 2.689553 TCGCATCAGCAATACAAGGA 57.310 45.000 0.00 0.00 42.27 3.36
1923 2063 2.938451 TCGCATCAGCAATACAAGGAAG 59.062 45.455 0.00 0.00 42.27 3.46
1929 2069 3.073798 TCAGCAATACAAGGAAGTGGGAA 59.926 43.478 0.00 0.00 0.00 3.97
1971 2111 7.215789 TGGTACGGTCATGTTTTTAACTTAGA 58.784 34.615 0.00 0.00 0.00 2.10
1990 2130 7.429633 ACTTAGATTCTGGTATTCAGTCATCG 58.570 38.462 0.00 0.00 43.76 3.84
2017 2157 1.361271 GCAATGGCACCATCATCGG 59.639 57.895 1.88 0.00 40.72 4.18
2030 2170 2.890808 TCATCGGCATGGAGTAAGTC 57.109 50.000 0.00 0.00 0.00 3.01
2070 3224 0.828762 TGCCATTGTGCTTCTTGCCT 60.829 50.000 0.00 0.00 42.00 4.75
2071 3225 0.319405 GCCATTGTGCTTCTTGCCTT 59.681 50.000 0.00 0.00 42.00 4.35
2072 3226 1.670967 GCCATTGTGCTTCTTGCCTTC 60.671 52.381 0.00 0.00 42.00 3.46
2073 3227 1.891150 CCATTGTGCTTCTTGCCTTCT 59.109 47.619 0.00 0.00 42.00 2.85
2074 3228 2.298163 CCATTGTGCTTCTTGCCTTCTT 59.702 45.455 0.00 0.00 42.00 2.52
2077 3231 1.133823 TGTGCTTCTTGCCTTCTTGGA 60.134 47.619 0.00 0.00 42.00 3.53
2091 3245 5.509498 CCTTCTTGGAATTATTGGGAGACA 58.491 41.667 0.00 0.00 38.35 3.41
2094 3248 6.078456 TCTTGGAATTATTGGGAGACATGT 57.922 37.500 0.00 0.00 0.00 3.21
2095 3249 5.887598 TCTTGGAATTATTGGGAGACATGTG 59.112 40.000 1.15 0.00 0.00 3.21
2096 3250 4.535781 TGGAATTATTGGGAGACATGTGG 58.464 43.478 1.15 0.00 0.00 4.17
2098 3252 4.536765 GAATTATTGGGAGACATGTGGGT 58.463 43.478 1.15 0.00 0.00 4.51
2104 4490 1.407437 GGGAGACATGTGGGTGTGATC 60.407 57.143 1.15 0.00 31.16 2.92
2165 4551 7.168905 TCTACAGATTTATCTCGATGGAGCTA 58.831 38.462 0.00 0.00 40.26 3.32
2169 4555 5.362430 AGATTTATCTCGATGGAGCTATCCC 59.638 44.000 0.00 0.00 37.40 3.85
2188 4574 3.344215 CGGAGCGGATGATGCAGC 61.344 66.667 0.00 0.00 33.85 5.25
2218 4604 1.153147 GTCCTCCGGCTCCAATTCC 60.153 63.158 0.00 0.00 0.00 3.01
2231 4617 2.933906 TCCAATTCCGACTAACGAATGC 59.066 45.455 0.00 0.00 45.77 3.56
2277 4663 2.930040 AGTGTGTGAGAGTTGTGTTTCG 59.070 45.455 0.00 0.00 0.00 3.46
2342 4728 2.080693 AGGCGTCGATTTGTTATGCAA 58.919 42.857 0.00 0.00 34.87 4.08
2380 4766 5.595885 CATCTTCTGGTCTACATTGACGAT 58.404 41.667 0.00 0.00 37.81 3.73
2383 4769 6.100004 TCTTCTGGTCTACATTGACGATTTC 58.900 40.000 0.00 0.00 37.81 2.17
2384 4770 4.755411 TCTGGTCTACATTGACGATTTCC 58.245 43.478 0.00 0.00 37.81 3.13
2387 4773 2.864343 GTCTACATTGACGATTTCCCCG 59.136 50.000 0.00 0.00 0.00 5.73
2400 4786 3.399181 CCCCGGCCACTGCTTCTA 61.399 66.667 2.24 0.00 37.74 2.10
2401 4787 2.746375 CCCCGGCCACTGCTTCTAT 61.746 63.158 2.24 0.00 37.74 1.98
2524 4910 9.901172 GAAGACTTCAGAACCCCTAATTATTTA 57.099 33.333 10.42 0.00 0.00 1.40
2556 4951 4.901197 TGTAAGAGCATTGTAAGGGTCA 57.099 40.909 10.48 0.00 39.43 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.127758 GAAACTTGCCGCGTGTCG 60.128 61.111 4.92 0.00 38.08 4.35
1 2 1.082756 CAGAAACTTGCCGCGTGTC 60.083 57.895 4.92 0.00 0.00 3.67
2 3 1.772063 GACAGAAACTTGCCGCGTGT 61.772 55.000 4.92 0.00 0.00 4.49
3 4 1.082756 GACAGAAACTTGCCGCGTG 60.083 57.895 4.92 0.00 0.00 5.34
4 5 1.092921 TTGACAGAAACTTGCCGCGT 61.093 50.000 4.92 0.00 0.00 6.01
5 6 0.028770 TTTGACAGAAACTTGCCGCG 59.971 50.000 0.00 0.00 0.00 6.46
6 7 2.202295 TTTTGACAGAAACTTGCCGC 57.798 45.000 0.00 0.00 0.00 6.53
7 8 6.475402 AGTTTATTTTTGACAGAAACTTGCCG 59.525 34.615 0.00 0.00 37.09 5.69
8 9 7.491048 TCAGTTTATTTTTGACAGAAACTTGCC 59.509 33.333 0.00 0.00 38.06 4.52
9 10 8.406172 TCAGTTTATTTTTGACAGAAACTTGC 57.594 30.769 0.00 0.00 38.06 4.01
28 29 9.082313 AGGATGATAACTTTTGTGATTCAGTTT 57.918 29.630 0.00 0.00 0.00 2.66
29 30 8.641498 AGGATGATAACTTTTGTGATTCAGTT 57.359 30.769 0.00 0.00 0.00 3.16
30 31 7.065085 CGAGGATGATAACTTTTGTGATTCAGT 59.935 37.037 0.00 0.00 0.00 3.41
31 32 7.404985 CGAGGATGATAACTTTTGTGATTCAG 58.595 38.462 0.00 0.00 0.00 3.02
32 33 6.183360 GCGAGGATGATAACTTTTGTGATTCA 60.183 38.462 0.00 0.00 0.00 2.57
33 34 6.195165 GCGAGGATGATAACTTTTGTGATTC 58.805 40.000 0.00 0.00 0.00 2.52
34 35 5.220662 CGCGAGGATGATAACTTTTGTGATT 60.221 40.000 0.00 0.00 0.00 2.57
35 36 4.271049 CGCGAGGATGATAACTTTTGTGAT 59.729 41.667 0.00 0.00 0.00 3.06
36 37 3.616821 CGCGAGGATGATAACTTTTGTGA 59.383 43.478 0.00 0.00 0.00 3.58
37 38 3.370978 ACGCGAGGATGATAACTTTTGTG 59.629 43.478 15.93 0.00 0.00 3.33
38 39 3.596214 ACGCGAGGATGATAACTTTTGT 58.404 40.909 15.93 0.00 0.00 2.83
39 40 3.616821 TGACGCGAGGATGATAACTTTTG 59.383 43.478 15.93 0.00 0.00 2.44
40 41 3.617263 GTGACGCGAGGATGATAACTTTT 59.383 43.478 15.93 0.00 0.00 2.27
41 42 3.119101 AGTGACGCGAGGATGATAACTTT 60.119 43.478 15.93 0.00 0.00 2.66
42 43 2.427453 AGTGACGCGAGGATGATAACTT 59.573 45.455 15.93 0.00 0.00 2.66
43 44 2.025155 AGTGACGCGAGGATGATAACT 58.975 47.619 15.93 0.00 0.00 2.24
44 45 2.493713 AGTGACGCGAGGATGATAAC 57.506 50.000 15.93 0.00 0.00 1.89
45 46 4.097437 AGTTTAGTGACGCGAGGATGATAA 59.903 41.667 15.93 0.00 0.00 1.75
46 47 3.630769 AGTTTAGTGACGCGAGGATGATA 59.369 43.478 15.93 0.00 0.00 2.15
47 48 2.427453 AGTTTAGTGACGCGAGGATGAT 59.573 45.455 15.93 0.00 0.00 2.45
48 49 1.816835 AGTTTAGTGACGCGAGGATGA 59.183 47.619 15.93 0.00 0.00 2.92
86 87 6.148480 GTCAGAGACAAGCACATTACAATTCT 59.852 38.462 0.00 0.00 32.09 2.40
89 90 4.389992 CGTCAGAGACAAGCACATTACAAT 59.610 41.667 0.00 0.00 32.09 2.71
93 94 3.243737 ACACGTCAGAGACAAGCACATTA 60.244 43.478 0.00 0.00 32.09 1.90
94 95 2.138320 CACGTCAGAGACAAGCACATT 58.862 47.619 0.00 0.00 32.09 2.71
95 96 1.069204 ACACGTCAGAGACAAGCACAT 59.931 47.619 0.00 0.00 32.09 3.21
102 103 1.067416 GTGCCACACGTCAGAGACA 59.933 57.895 0.00 0.00 32.09 3.41
103 104 0.249489 AAGTGCCACACGTCAGAGAC 60.249 55.000 0.00 0.00 39.64 3.36
105 106 1.299541 AAAAGTGCCACACGTCAGAG 58.700 50.000 0.00 0.00 39.64 3.35
106 107 1.745232 AAAAAGTGCCACACGTCAGA 58.255 45.000 0.00 0.00 39.64 3.27
266 278 2.480419 GTGAACCCTCATCTGTTTGTCG 59.520 50.000 0.00 0.00 33.05 4.35
270 282 1.420138 ACGGTGAACCCTCATCTGTTT 59.580 47.619 0.00 0.00 33.05 2.83
277 289 0.469331 ACAGAGACGGTGAACCCTCA 60.469 55.000 8.04 0.00 29.87 3.86
313 325 6.969043 TGTCTAATTTGAACCCCATATGTCT 58.031 36.000 1.24 0.00 0.00 3.41
393 406 8.420374 TCGTATTATCGCAAAAAGAAGAAGAT 57.580 30.769 0.00 0.00 0.00 2.40
429 442 5.261216 TGAAGCCTAGGTTTTATTTCCCAG 58.739 41.667 12.62 0.00 0.00 4.45
432 445 6.017852 CGAGATGAAGCCTAGGTTTTATTTCC 60.018 42.308 20.30 9.08 0.00 3.13
475 498 0.872451 AACGTTGTGCATCACGTCGA 60.872 50.000 22.05 0.00 37.14 4.20
521 557 0.940126 CGCATCGCCATCTTAGCTTT 59.060 50.000 0.00 0.00 0.00 3.51
525 561 1.787155 GTACACGCATCGCCATCTTAG 59.213 52.381 0.00 0.00 0.00 2.18
588 632 0.923403 CGATCGACTCCGTACGTACA 59.077 55.000 24.50 6.07 37.05 2.90
1324 1434 1.882623 CCTGTTCTTCTTCTGTTGCCC 59.117 52.381 0.00 0.00 0.00 5.36
1365 1478 2.676121 CAAATGCCGCACCCCTGA 60.676 61.111 0.00 0.00 0.00 3.86
1419 1532 2.523015 CCGTACTTACACGACATCACC 58.477 52.381 0.00 0.00 44.69 4.02
1421 1534 1.814394 AGCCGTACTTACACGACATCA 59.186 47.619 0.00 0.00 44.69 3.07
1620 1734 5.549347 TGTTACATTGGTTATGTACGTGGT 58.451 37.500 0.00 0.00 46.69 4.16
1632 1748 4.402829 TGCAGTGGTATTGTTACATTGGT 58.597 39.130 0.00 0.00 0.00 3.67
1648 1764 8.808032 TCTGCACAATTTTACACACTGCAGTG 62.808 42.308 38.76 38.76 46.61 3.66
1692 1828 6.870971 TCACAGCACGATATACACATAGTA 57.129 37.500 0.00 0.00 37.06 1.82
1693 1829 5.767816 TCACAGCACGATATACACATAGT 57.232 39.130 0.00 0.00 0.00 2.12
1694 1830 5.802451 GGATCACAGCACGATATACACATAG 59.198 44.000 0.00 0.00 0.00 2.23
1706 1842 2.140065 ATACGATGGATCACAGCACG 57.860 50.000 0.00 0.00 34.42 5.34
1742 1878 1.086696 GATGCAGCAAAGCTCGGTTA 58.913 50.000 0.00 0.00 36.40 2.85
1757 1895 2.203070 AATCCTCCGCGTGGATGC 60.203 61.111 24.92 0.00 45.33 3.91
1766 1904 4.572389 CACAAATTCCTAGTGAATCCTCCG 59.428 45.833 6.84 0.00 42.97 4.63
1767 1905 4.884164 CCACAAATTCCTAGTGAATCCTCC 59.116 45.833 6.84 0.00 42.97 4.30
1838 1976 1.704007 GCAGAATGGAGGAGGAGGGG 61.704 65.000 0.00 0.00 35.86 4.79
1844 1982 0.758123 GGAGAGGCAGAATGGAGGAG 59.242 60.000 0.00 0.00 35.86 3.69
1845 1983 0.341258 AGGAGAGGCAGAATGGAGGA 59.659 55.000 0.00 0.00 35.86 3.71
1858 1996 1.791103 GATCTCGCGTGGGAGGAGAG 61.791 65.000 5.77 0.00 39.91 3.20
1859 1997 1.824329 GATCTCGCGTGGGAGGAGA 60.824 63.158 5.77 0.00 40.75 3.71
1888 2026 4.593864 GCGATGGACGGAGGGAGC 62.594 72.222 0.00 0.00 42.83 4.70
1921 2061 1.812708 CGGTCCGAAACTTTCCCACTT 60.813 52.381 4.91 0.00 0.00 3.16
1923 2063 1.232621 CCGGTCCGAAACTTTCCCAC 61.233 60.000 14.39 0.00 0.00 4.61
1929 2069 1.348696 ACCATTACCGGTCCGAAACTT 59.651 47.619 12.40 0.00 32.11 2.66
1971 2111 4.443457 CCACCGATGACTGAATACCAGAAT 60.443 45.833 0.00 0.00 45.78 2.40
1987 2127 1.077501 CCATTGCCTCACCACCGAT 60.078 57.895 0.00 0.00 0.00 4.18
1990 2130 2.283101 TGCCATTGCCTCACCACC 60.283 61.111 0.00 0.00 36.33 4.61
2030 2170 1.383248 AAGGACGAGATGGGGGAGG 60.383 63.158 0.00 0.00 0.00 4.30
2032 2172 0.546747 AACAAGGACGAGATGGGGGA 60.547 55.000 0.00 0.00 0.00 4.81
2033 2173 0.392998 CAACAAGGACGAGATGGGGG 60.393 60.000 0.00 0.00 0.00 5.40
2070 3224 6.377996 CACATGTCTCCCAATAATTCCAAGAA 59.622 38.462 0.00 0.00 0.00 2.52
2071 3225 5.887598 CACATGTCTCCCAATAATTCCAAGA 59.112 40.000 0.00 0.00 0.00 3.02
2072 3226 5.068198 CCACATGTCTCCCAATAATTCCAAG 59.932 44.000 0.00 0.00 0.00 3.61
2073 3227 4.955450 CCACATGTCTCCCAATAATTCCAA 59.045 41.667 0.00 0.00 0.00 3.53
2074 3228 4.535781 CCACATGTCTCCCAATAATTCCA 58.464 43.478 0.00 0.00 0.00 3.53
2077 3231 4.264352 ACACCCACATGTCTCCCAATAATT 60.264 41.667 0.00 0.00 0.00 1.40
2157 4543 2.203640 TCCGCGGGATAGCTCCAT 60.204 61.111 27.83 0.00 44.08 3.41
2188 4574 1.374758 GGAGGACCAAGACGCACAG 60.375 63.158 0.00 0.00 35.97 3.66
2218 4604 1.075542 TGCCAAGCATTCGTTAGTCG 58.924 50.000 0.00 0.00 35.56 4.18
2225 4611 0.526096 CCGGAATTGCCAAGCATTCG 60.526 55.000 0.00 0.00 38.76 3.34
2249 4635 3.005897 ACAACTCTCACACACTCGCTAAT 59.994 43.478 0.00 0.00 0.00 1.73
2252 4638 0.747255 ACAACTCTCACACACTCGCT 59.253 50.000 0.00 0.00 0.00 4.93
2296 4682 0.880278 GGGCATGTATGACGTCGCAT 60.880 55.000 11.62 12.05 36.40 4.73
2348 4734 1.519455 CCAGAAGATGCCGACGACC 60.519 63.158 0.00 0.00 0.00 4.79
2380 4766 3.860930 GAAGCAGTGGCCGGGGAAA 62.861 63.158 2.18 0.00 42.56 3.13
2383 4769 1.407656 TATAGAAGCAGTGGCCGGGG 61.408 60.000 2.18 0.00 42.56 5.73
2384 4770 0.468226 TTATAGAAGCAGTGGCCGGG 59.532 55.000 2.18 0.00 42.56 5.73
2400 4786 6.863126 GCAAACTTGTTAACACATGAGCTTAT 59.137 34.615 8.07 0.00 33.26 1.73
2401 4787 6.205784 GCAAACTTGTTAACACATGAGCTTA 58.794 36.000 8.07 0.00 33.26 3.09
2482 4868 1.556911 TCTTCTTCCCTCTGCATCCAC 59.443 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.