Multiple sequence alignment - TraesCS5B01G042100

Loading Multiple Alignment...

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 TraesCS5B01G042100 chr5B 100.000 2384 0 0 1 2384 46747584 46745201 0.000000e+00 4403
1 TraesCS5B01G042100 chr5B 92.923 1413 82 8 155 1567 46768559 46767165 0.000000e+00 2039
2 TraesCS5B01G042100 chr5B 87.316 1695 169 24 173 1860 46636096 46634441 0.000000e+00 1897
3 TraesCS5B01G042100 chr5B 84.494 1580 214 23 205 1775 48146273 48147830 0.000000e+00 1531
4 TraesCS5B01G042100 chr5B 82.640 1659 239 32 210 1859 46152976 46151358 0.000000e+00 1423
5 TraesCS5B01G042100 chr5B 85.185 432 37 13 1575 2002 46766611 46766203 3.670000e-113 418
6 TraesCS5B01G042100 chr5B 87.336 229 28 1 1990 2218 46634214 46633987 6.540000e-66 261
7 TraesCS5B01G042100 chr5B 80.180 333 48 10 202 524 46771222 46770898 1.420000e-57 233
8 TraesCS5B01G042100 chr5B 91.111 135 11 1 1859 1993 46770125 46769992 5.230000e-42 182
9 TraesCS5B01G042100 chr5B 94.565 92 5 0 43 134 46764552 46764643 2.470000e-30 143
10 TraesCS5B01G042100 chr5A 89.011 1547 125 23 326 1858 36942966 36941451 0.000000e+00 1873
11 TraesCS5B01G042100 chr5A 86.778 1732 156 36 155 1861 36826971 36825288 0.000000e+00 1862
12 TraesCS5B01G042100 chr5A 84.393 1589 203 21 202 1778 37402367 37400812 0.000000e+00 1519
13 TraesCS5B01G042100 chr5A 92.150 293 20 3 2093 2384 36820721 36820431 6.130000e-111 411
14 TraesCS5B01G042100 chr5A 94.142 239 14 0 1859 2097 36825217 36824979 4.840000e-97 364
15 TraesCS5B01G042100 chr5A 91.176 136 11 1 1859 1993 36945044 36944909 1.460000e-42 183
16 TraesCS5B01G042100 chr5A 87.417 151 18 1 1708 1858 37400767 37400618 3.150000e-39 172
17 TraesCS5B01G042100 chr5A 93.258 89 6 0 155 243 36943384 36943296 5.350000e-27 132
18 TraesCS5B01G042100 chr5A 86.607 112 14 1 2019 2130 37168194 37168084 3.220000e-24 122
19 TraesCS5B01G042100 chr5D 91.740 1247 59 12 155 1386 45897681 45898898 0.000000e+00 1692
20 TraesCS5B01G042100 chr5D 85.920 1527 168 23 173 1697 45938659 45940140 0.000000e+00 1585
21 TraesCS5B01G042100 chr5D 86.032 1482 189 10 322 1796 46128577 46127107 0.000000e+00 1574
22 TraesCS5B01G042100 chr5D 93.924 395 23 1 1988 2381 45913266 45913660 1.580000e-166 595
23 TraesCS5B01G042100 chr5D 98.450 129 2 0 1859 1987 45912463 45912591 6.630000e-56 228
24 TraesCS5B01G042100 chr5D 93.182 132 9 0 1859 1990 45896267 45896398 6.720000e-46 195
25 TraesCS5B01G042100 chr5D 98.165 109 2 0 26 134 45897521 45897629 8.700000e-45 191
26 TraesCS5B01G042100 chr2A 81.644 365 51 11 155 517 734772918 734773268 3.000000e-74 289
27 TraesCS5B01G042100 chr7A 88.073 109 13 0 26 134 646943391 646943283 1.920000e-26 130
28 TraesCS5B01G042100 chr6B 88.073 109 13 0 26 134 91152827 91152719 1.920000e-26 130
29 TraesCS5B01G042100 chr2B 87.156 109 14 0 26 134 776450015 776450123 8.950000e-25 124


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 TraesCS5B01G042100 chr5B 46745201 46747584 2383 True 4403.000000 4403 100.000000 1 2384 1 chr5B.!!$R2 2383
1 TraesCS5B01G042100 chr5B 48146273 48147830 1557 False 1531.000000 1531 84.494000 205 1775 1 chr5B.!!$F2 1570
2 TraesCS5B01G042100 chr5B 46151358 46152976 1618 True 1423.000000 1423 82.640000 210 1859 1 chr5B.!!$R1 1649
3 TraesCS5B01G042100 chr5B 46633987 46636096 2109 True 1079.000000 1897 87.326000 173 2218 2 chr5B.!!$R3 2045
4 TraesCS5B01G042100 chr5B 46766203 46771222 5019 True 718.000000 2039 87.349750 155 2002 4 chr5B.!!$R4 1847
5 TraesCS5B01G042100 chr5A 36824979 36826971 1992 True 1113.000000 1862 90.460000 155 2097 2 chr5A.!!$R3 1942
6 TraesCS5B01G042100 chr5A 37400618 37402367 1749 True 845.500000 1519 85.905000 202 1858 2 chr5A.!!$R5 1656
7 TraesCS5B01G042100 chr5A 36941451 36945044 3593 True 729.333333 1873 91.148333 155 1993 3 chr5A.!!$R4 1838
8 TraesCS5B01G042100 chr5D 45938659 45940140 1481 False 1585.000000 1585 85.920000 173 1697 1 chr5D.!!$F1 1524
9 TraesCS5B01G042100 chr5D 46127107 46128577 1470 True 1574.000000 1574 86.032000 322 1796 1 chr5D.!!$R1 1474
10 TraesCS5B01G042100 chr5D 45896267 45898898 2631 False 692.666667 1692 94.362333 26 1990 3 chr5D.!!$F2 1964
11 TraesCS5B01G042100 chr5D 45912463 45913660 1197 False 411.500000 595 96.187000 1859 2381 2 chr5D.!!$F3 522

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
65 66 0.030638 CTGGTTTTCGTTGCCAGTGG 59.969 55.0 4.2 4.2 43.42 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 6612 0.035725 CGGTTAACCCCTCCCTCAAC 60.036 60.0 19.09 0.0 0.0 3.18 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 8.854979 TTTAATTCACGATCAAATGCTTATGG 57.145 30.769 0.00 0.00 0.00 2.74
35 36 2.618241 TCACGATCAAATGCTTATGGGC 59.382 45.455 0.00 0.00 0.00 5.36
36 37 1.956477 ACGATCAAATGCTTATGGGCC 59.044 47.619 0.00 0.00 0.00 5.80
38 39 2.229792 GATCAAATGCTTATGGGCCGA 58.770 47.619 0.00 0.00 0.00 5.54
39 40 1.679139 TCAAATGCTTATGGGCCGAG 58.321 50.000 0.00 0.00 0.00 4.63
40 41 0.670162 CAAATGCTTATGGGCCGAGG 59.330 55.000 0.00 0.00 0.00 4.63
42 43 3.832237 ATGCTTATGGGCCGAGGCG 62.832 63.158 8.14 0.00 43.06 5.52
43 44 4.547367 GCTTATGGGCCGAGGCGT 62.547 66.667 8.14 0.00 43.06 5.68
45 46 4.215742 TTATGGGCCGAGGCGTCG 62.216 66.667 21.30 21.30 46.39 5.12
53 54 3.041940 CGAGGCGTCGCTGGTTTT 61.042 61.111 16.57 0.00 39.88 2.43
54 55 2.861006 GAGGCGTCGCTGGTTTTC 59.139 61.111 18.11 0.00 0.00 2.29
55 56 3.011760 GAGGCGTCGCTGGTTTTCG 62.012 63.158 18.11 0.00 0.00 3.46
56 57 3.343421 GGCGTCGCTGGTTTTCGT 61.343 61.111 18.11 0.00 0.00 3.85
57 58 2.629763 GCGTCGCTGGTTTTCGTT 59.370 55.556 10.68 0.00 0.00 3.85
58 59 1.721133 GCGTCGCTGGTTTTCGTTG 60.721 57.895 10.68 0.00 0.00 4.10
60 61 1.370051 GTCGCTGGTTTTCGTTGCC 60.370 57.895 0.00 0.00 0.00 4.52
61 62 1.820056 TCGCTGGTTTTCGTTGCCA 60.820 52.632 0.00 0.00 0.00 4.92
65 66 0.030638 CTGGTTTTCGTTGCCAGTGG 59.969 55.000 4.20 4.20 43.42 4.00
66 67 0.394488 TGGTTTTCGTTGCCAGTGGA 60.394 50.000 15.20 0.00 0.00 4.02
68 69 1.335872 GGTTTTCGTTGCCAGTGGATG 60.336 52.381 15.20 0.00 0.00 3.51
69 70 0.313672 TTTTCGTTGCCAGTGGATGC 59.686 50.000 15.20 0.00 0.00 3.91
70 71 0.537143 TTTCGTTGCCAGTGGATGCT 60.537 50.000 15.20 0.00 0.00 3.79
72 73 0.955428 TCGTTGCCAGTGGATGCTTC 60.955 55.000 15.20 0.00 0.00 3.86
73 74 0.957395 CGTTGCCAGTGGATGCTTCT 60.957 55.000 15.20 0.00 0.00 2.85
74 75 0.524862 GTTGCCAGTGGATGCTTCTG 59.475 55.000 15.20 3.82 0.00 3.02
75 76 1.246056 TTGCCAGTGGATGCTTCTGC 61.246 55.000 15.20 0.00 40.20 4.26
76 77 2.413142 GCCAGTGGATGCTTCTGCC 61.413 63.158 15.20 0.00 38.71 4.85
77 78 2.110967 CCAGTGGATGCTTCTGCCG 61.111 63.158 1.68 0.00 38.71 5.69
79 80 1.078848 AGTGGATGCTTCTGCCGTC 60.079 57.895 0.00 0.00 38.71 4.79
80 81 2.125552 TGGATGCTTCTGCCGTCG 60.126 61.111 0.00 0.00 38.71 5.12
81 82 2.892425 GGATGCTTCTGCCGTCGG 60.892 66.667 6.99 6.99 38.71 4.79
83 84 1.227380 GATGCTTCTGCCGTCGGAT 60.227 57.895 17.49 0.00 38.71 4.18
84 85 1.493950 GATGCTTCTGCCGTCGGATG 61.494 60.000 17.49 6.53 38.71 3.51
85 86 2.892425 GCTTCTGCCGTCGGATGG 60.892 66.667 17.49 12.04 0.00 3.51
91 92 2.960129 GCCGTCGGATGGCTTACG 60.960 66.667 29.56 5.14 46.66 3.18
92 93 2.802792 CCGTCGGATGGCTTACGA 59.197 61.111 4.91 3.23 37.53 3.43
94 95 1.143969 CCGTCGGATGGCTTACGAAC 61.144 60.000 9.49 3.79 38.46 3.95
95 96 1.469126 CGTCGGATGGCTTACGAACG 61.469 60.000 9.49 11.44 38.46 3.95
96 97 1.140161 TCGGATGGCTTACGAACGG 59.860 57.895 5.08 0.00 33.21 4.44
97 98 1.153706 CGGATGGCTTACGAACGGT 60.154 57.895 0.00 0.00 0.00 4.83
98 99 1.418342 CGGATGGCTTACGAACGGTG 61.418 60.000 0.00 0.00 0.00 4.94
100 101 0.108520 GATGGCTTACGAACGGTGGA 60.109 55.000 0.00 0.00 0.00 4.02
101 102 0.539986 ATGGCTTACGAACGGTGGAT 59.460 50.000 0.00 0.00 0.00 3.41
102 103 1.184431 TGGCTTACGAACGGTGGATA 58.816 50.000 0.00 0.00 0.00 2.59
103 104 1.135024 TGGCTTACGAACGGTGGATAC 60.135 52.381 0.00 0.00 0.00 2.24
104 105 1.194495 GCTTACGAACGGTGGATACG 58.806 55.000 0.00 0.00 42.51 3.06
115 116 3.339061 TGGATACGCACATCACGTC 57.661 52.632 0.00 0.00 43.88 4.34
117 118 0.874607 GGATACGCACATCACGTCCC 60.875 60.000 0.00 0.00 43.88 4.46
118 119 0.102481 GATACGCACATCACGTCCCT 59.898 55.000 0.00 0.00 43.88 4.20
119 120 0.102481 ATACGCACATCACGTCCCTC 59.898 55.000 0.00 0.00 43.88 4.30
120 121 0.963856 TACGCACATCACGTCCCTCT 60.964 55.000 0.00 0.00 43.88 3.69
121 122 1.807165 CGCACATCACGTCCCTCTG 60.807 63.158 0.00 0.00 0.00 3.35
122 123 2.103042 GCACATCACGTCCCTCTGC 61.103 63.158 0.00 0.00 0.00 4.26
123 124 1.293179 CACATCACGTCCCTCTGCA 59.707 57.895 0.00 0.00 0.00 4.41
124 125 0.738762 CACATCACGTCCCTCTGCAG 60.739 60.000 7.63 7.63 0.00 4.41
125 126 1.188219 ACATCACGTCCCTCTGCAGT 61.188 55.000 14.67 0.00 0.00 4.40
126 127 0.817654 CATCACGTCCCTCTGCAGTA 59.182 55.000 14.67 0.00 0.00 2.74
127 128 1.107114 ATCACGTCCCTCTGCAGTAG 58.893 55.000 14.67 9.71 0.00 2.57
128 129 1.153745 CACGTCCCTCTGCAGTAGC 60.154 63.158 14.67 0.35 42.57 3.58
129 130 2.352032 ACGTCCCTCTGCAGTAGCC 61.352 63.158 14.67 0.00 41.13 3.93
130 131 2.055042 CGTCCCTCTGCAGTAGCCT 61.055 63.158 14.67 0.00 41.13 4.58
132 133 0.972983 GTCCCTCTGCAGTAGCCTGA 60.973 60.000 14.67 0.56 41.50 3.86
133 134 0.685785 TCCCTCTGCAGTAGCCTGAG 60.686 60.000 14.67 1.45 41.50 3.35
135 136 0.975040 CCTCTGCAGTAGCCTGAGGT 60.975 60.000 14.67 0.00 46.43 3.85
138 139 0.175302 CTGCAGTAGCCTGAGGTGAG 59.825 60.000 5.25 0.00 41.50 3.51
140 141 0.972983 GCAGTAGCCTGAGGTGAGGA 60.973 60.000 0.00 0.00 41.50 3.71
141 142 1.786937 CAGTAGCCTGAGGTGAGGAT 58.213 55.000 0.00 0.00 41.50 3.24
142 143 1.686052 CAGTAGCCTGAGGTGAGGATC 59.314 57.143 0.00 0.00 41.50 3.36
143 144 1.044611 GTAGCCTGAGGTGAGGATCC 58.955 60.000 2.48 2.48 34.69 3.36
144 145 0.937441 TAGCCTGAGGTGAGGATCCT 59.063 55.000 16.13 16.13 34.69 3.24
147 148 1.407989 GCCTGAGGTGAGGATCCTTTG 60.408 57.143 17.42 1.58 34.69 2.77
148 149 1.912043 CCTGAGGTGAGGATCCTTTGT 59.088 52.381 17.42 0.72 34.69 2.83
149 150 2.093235 CCTGAGGTGAGGATCCTTTGTC 60.093 54.545 17.42 11.09 34.69 3.18
150 151 1.909302 TGAGGTGAGGATCCTTTGTCC 59.091 52.381 17.42 15.15 35.20 4.02
152 153 2.305927 GAGGTGAGGATCCTTTGTCCAA 59.694 50.000 17.42 0.00 38.25 3.53
153 154 2.716424 AGGTGAGGATCCTTTGTCCAAA 59.284 45.455 17.42 0.00 38.25 3.28
171 3020 0.685660 AAGTCCAAACCCTCGTCTCC 59.314 55.000 0.00 0.00 0.00 3.71
307 3188 4.489771 CGCATCCTCCCCACACCC 62.490 72.222 0.00 0.00 0.00 4.61
308 3189 4.489771 GCATCCTCCCCACACCCG 62.490 72.222 0.00 0.00 0.00 5.28
309 3190 4.489771 CATCCTCCCCACACCCGC 62.490 72.222 0.00 0.00 0.00 6.13
481 3613 2.108976 GGCATTCTCCATCGGCGA 59.891 61.111 13.87 13.87 0.00 5.54
560 3692 1.297456 ACGTCTCCGTCTTCCTCGTC 61.297 60.000 0.00 0.00 46.28 4.20
566 3698 1.280133 TCCGTCTTCCTCGTCCTCTTA 59.720 52.381 0.00 0.00 0.00 2.10
728 3861 3.964688 TGAAGACCACCACTGAAGTAGAA 59.035 43.478 0.00 0.00 0.00 2.10
734 3867 3.589988 CACCACTGAAGTAGAATCGCTT 58.410 45.455 0.00 0.00 0.00 4.68
806 3949 0.031721 AAACACTCGAGGTCCACGTC 59.968 55.000 18.41 0.00 0.00 4.34
851 3994 6.456795 AATCTTGCAAAATTACTAGAGGGC 57.543 37.500 0.00 0.00 0.00 5.19
868 4011 1.499502 GCAAGAAAGGAGCAGACGC 59.500 57.895 0.00 0.00 38.99 5.19
972 4115 2.036572 GGCCGATGGGGGACAAAA 59.963 61.111 0.00 0.00 34.16 2.44
981 4124 2.915137 GGGACAAAAGGGGCGCAA 60.915 61.111 10.83 0.00 0.00 4.85
1068 4211 1.019673 CAATGCCTTCCATGGACGAG 58.980 55.000 19.45 12.77 33.49 4.18
1392 4535 3.428316 CCCGCAAAATTTAGTACGCCAAT 60.428 43.478 0.00 0.00 0.00 3.16
1572 5270 0.899720 ATGAGGTTGCCATGCCTTTG 59.100 50.000 0.00 0.00 34.81 2.77
1593 5291 4.144297 TGTGTTTCCAGAGATCTTTTGGG 58.856 43.478 20.82 10.61 32.76 4.12
1608 5307 3.810310 TTTGGGGTAAGCAGTTTGTTG 57.190 42.857 0.00 0.00 0.00 3.33
1723 5541 7.015584 TCTGCTCAGTTTAATATCTGGCTCATA 59.984 37.037 0.00 0.00 32.93 2.15
1724 5542 6.931281 TGCTCAGTTTAATATCTGGCTCATAC 59.069 38.462 0.00 0.00 32.93 2.39
2039 6655 5.990120 ACAAAAATTGAGAGAGGGATTGG 57.010 39.130 0.00 0.00 0.00 3.16
2047 6663 4.895836 TGAGAGAGGGATTGGGAAGAATA 58.104 43.478 0.00 0.00 0.00 1.75
2111 6727 1.918293 CCCTACTGCTGGGTGGACA 60.918 63.158 0.00 0.00 39.82 4.02
2121 6737 0.774096 TGGGTGGACAGAAATCCCCA 60.774 55.000 0.00 0.00 38.06 4.96
2166 6782 5.183904 ACTGAACAAAGCCTAATGTGGATTC 59.816 40.000 0.00 0.00 34.26 2.52
2173 6789 1.327460 CCTAATGTGGATTCGTGTGCG 59.673 52.381 0.00 0.00 39.92 5.34
2196 6812 1.224870 GCCCCTCTGTTTAGCTCCC 59.775 63.158 0.00 0.00 0.00 4.30
2203 6819 1.203313 TCTGTTTAGCTCCCCTCCTGT 60.203 52.381 0.00 0.00 0.00 4.00
2279 6895 1.000827 CTCGCTCTGCCGACATAATCT 60.001 52.381 0.00 0.00 33.12 2.40
2286 6902 1.688735 TGCCGACATAATCTAGCAGCT 59.311 47.619 0.00 0.00 32.30 4.24
2309 6925 8.540388 AGCTTATGAGAAAAGTCAGGTAATGTA 58.460 33.333 0.00 0.00 0.00 2.29
2312 6928 9.832445 TTATGAGAAAAGTCAGGTAATGTATCC 57.168 33.333 0.00 0.00 0.00 2.59
2346 6962 8.715191 TGCATATGGGTAATTTCATTTGTTTC 57.285 30.769 4.56 0.00 0.00 2.78
2382 6999 8.879759 TCGTTTTGTATCTGTCATTTCTATTCC 58.120 33.333 0.00 0.00 0.00 3.01
2383 7000 8.122952 CGTTTTGTATCTGTCATTTCTATTCCC 58.877 37.037 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.299963 CCATAAGCATTTGATCGTGAATTAAAA 57.700 29.630 0.00 0.00 0.00 1.52
8 9 7.920151 CCCATAAGCATTTGATCGTGAATTAAA 59.080 33.333 0.00 0.00 0.00 1.52
9 10 7.424803 CCCATAAGCATTTGATCGTGAATTAA 58.575 34.615 0.00 0.00 0.00 1.40
10 11 6.514870 GCCCATAAGCATTTGATCGTGAATTA 60.515 38.462 0.00 0.00 0.00 1.40
11 12 5.737063 GCCCATAAGCATTTGATCGTGAATT 60.737 40.000 0.00 0.00 0.00 2.17
12 13 4.261741 GCCCATAAGCATTTGATCGTGAAT 60.262 41.667 0.00 0.00 0.00 2.57
13 14 3.066621 GCCCATAAGCATTTGATCGTGAA 59.933 43.478 0.00 0.00 0.00 3.18
14 15 2.618241 GCCCATAAGCATTTGATCGTGA 59.382 45.455 0.00 0.00 0.00 4.35
15 16 2.287788 GGCCCATAAGCATTTGATCGTG 60.288 50.000 0.00 0.00 0.00 4.35
16 17 1.956477 GGCCCATAAGCATTTGATCGT 59.044 47.619 0.00 0.00 0.00 3.73
17 18 1.069022 CGGCCCATAAGCATTTGATCG 60.069 52.381 0.00 0.00 0.00 3.69
18 19 2.227388 CTCGGCCCATAAGCATTTGATC 59.773 50.000 0.00 0.00 0.00 2.92
19 20 2.233271 CTCGGCCCATAAGCATTTGAT 58.767 47.619 0.00 0.00 0.00 2.57
20 21 1.679139 CTCGGCCCATAAGCATTTGA 58.321 50.000 0.00 0.00 0.00 2.69
24 25 2.113986 GCCTCGGCCCATAAGCAT 59.886 61.111 0.00 0.00 34.56 3.79
25 26 4.545706 CGCCTCGGCCCATAAGCA 62.546 66.667 0.00 0.00 37.98 3.91
26 27 4.547367 ACGCCTCGGCCCATAAGC 62.547 66.667 0.00 0.00 37.98 3.09
28 29 4.215742 CGACGCCTCGGCCCATAA 62.216 66.667 0.00 0.00 36.16 1.90
36 37 3.011760 GAAAACCAGCGACGCCTCG 62.012 63.158 17.79 6.54 43.28 4.63
38 39 3.041940 CGAAAACCAGCGACGCCT 61.042 61.111 17.79 0.50 0.00 5.52
39 40 2.888998 AACGAAAACCAGCGACGCC 61.889 57.895 17.79 0.00 0.00 5.68
40 41 1.721133 CAACGAAAACCAGCGACGC 60.721 57.895 13.03 13.03 0.00 5.19
42 43 1.370051 GGCAACGAAAACCAGCGAC 60.370 57.895 0.00 0.00 0.00 5.19
43 44 1.781025 CTGGCAACGAAAACCAGCGA 61.781 55.000 0.00 0.00 44.16 4.93
45 46 4.633980 CTGGCAACGAAAACCAGC 57.366 55.556 0.00 0.00 44.16 4.85
47 48 0.394488 TCCACTGGCAACGAAAACCA 60.394 50.000 0.00 0.00 42.51 3.67
48 49 0.958822 ATCCACTGGCAACGAAAACC 59.041 50.000 0.00 0.00 42.51 3.27
49 50 1.930371 GCATCCACTGGCAACGAAAAC 60.930 52.381 0.00 0.00 42.51 2.43
51 52 0.537143 AGCATCCACTGGCAACGAAA 60.537 50.000 0.00 0.00 42.51 3.46
52 53 0.537143 AAGCATCCACTGGCAACGAA 60.537 50.000 0.00 0.00 42.51 3.85
53 54 0.955428 GAAGCATCCACTGGCAACGA 60.955 55.000 0.00 0.00 42.51 3.85
54 55 0.957395 AGAAGCATCCACTGGCAACG 60.957 55.000 0.00 0.00 42.51 4.10
55 56 0.524862 CAGAAGCATCCACTGGCAAC 59.475 55.000 0.00 0.00 0.00 4.17
56 57 1.246056 GCAGAAGCATCCACTGGCAA 61.246 55.000 0.00 0.00 41.58 4.52
57 58 1.676635 GCAGAAGCATCCACTGGCA 60.677 57.895 0.00 0.00 41.58 4.92
58 59 2.413142 GGCAGAAGCATCCACTGGC 61.413 63.158 0.00 0.00 46.30 4.85
60 61 1.364626 GACGGCAGAAGCATCCACTG 61.365 60.000 0.00 0.00 44.61 3.66
61 62 1.078848 GACGGCAGAAGCATCCACT 60.079 57.895 0.00 0.00 44.61 4.00
62 63 2.456119 CGACGGCAGAAGCATCCAC 61.456 63.158 0.00 0.00 44.61 4.02
63 64 2.125552 CGACGGCAGAAGCATCCA 60.126 61.111 0.00 0.00 44.61 3.41
65 66 1.227380 ATCCGACGGCAGAAGCATC 60.227 57.895 9.66 0.00 44.61 3.91
66 67 1.522355 CATCCGACGGCAGAAGCAT 60.522 57.895 9.66 0.00 44.61 3.79
68 69 2.892425 CCATCCGACGGCAGAAGC 60.892 66.667 9.66 0.00 41.10 3.86
75 76 1.140161 TTCGTAAGCCATCCGACGG 59.860 57.895 7.84 7.84 36.02 4.79
76 77 1.469126 CGTTCGTAAGCCATCCGACG 61.469 60.000 0.00 0.00 36.66 5.12
77 78 1.143969 CCGTTCGTAAGCCATCCGAC 61.144 60.000 0.00 0.00 37.18 4.79
79 80 1.153706 ACCGTTCGTAAGCCATCCG 60.154 57.895 0.00 0.00 37.18 4.18
80 81 1.087771 CCACCGTTCGTAAGCCATCC 61.088 60.000 0.00 0.00 37.18 3.51
81 82 0.108520 TCCACCGTTCGTAAGCCATC 60.109 55.000 0.00 0.00 37.18 3.51
83 84 1.135024 GTATCCACCGTTCGTAAGCCA 60.135 52.381 0.00 0.00 37.18 4.75
84 85 1.564207 GTATCCACCGTTCGTAAGCC 58.436 55.000 0.00 0.00 37.18 4.35
85 86 1.194495 CGTATCCACCGTTCGTAAGC 58.806 55.000 0.00 0.00 37.18 3.09
86 87 1.194495 GCGTATCCACCGTTCGTAAG 58.806 55.000 0.00 0.00 0.00 2.34
87 88 0.525311 TGCGTATCCACCGTTCGTAA 59.475 50.000 0.00 0.00 0.00 3.18
88 89 0.179166 GTGCGTATCCACCGTTCGTA 60.179 55.000 0.00 0.00 0.00 3.43
89 90 1.444895 GTGCGTATCCACCGTTCGT 60.445 57.895 0.00 0.00 0.00 3.85
91 92 0.928229 GATGTGCGTATCCACCGTTC 59.072 55.000 0.00 0.00 34.85 3.95
92 93 0.248012 TGATGTGCGTATCCACCGTT 59.752 50.000 0.00 0.00 34.85 4.44
94 95 1.479420 CGTGATGTGCGTATCCACCG 61.479 60.000 0.00 0.00 34.85 4.94
95 96 0.459585 ACGTGATGTGCGTATCCACC 60.460 55.000 0.00 0.00 41.06 4.61
96 97 0.921347 GACGTGATGTGCGTATCCAC 59.079 55.000 0.00 0.00 43.04 4.02
97 98 0.179121 GGACGTGATGTGCGTATCCA 60.179 55.000 0.00 0.00 43.04 3.41
98 99 0.874607 GGGACGTGATGTGCGTATCC 60.875 60.000 0.00 0.00 43.04 2.59
100 101 0.102481 GAGGGACGTGATGTGCGTAT 59.898 55.000 0.00 0.00 43.04 3.06
101 102 0.963856 AGAGGGACGTGATGTGCGTA 60.964 55.000 0.00 0.00 43.04 4.42
102 103 2.261671 GAGGGACGTGATGTGCGT 59.738 61.111 0.00 0.00 45.86 5.24
103 104 1.807165 CAGAGGGACGTGATGTGCG 60.807 63.158 0.00 0.00 40.35 5.34
104 105 2.103042 GCAGAGGGACGTGATGTGC 61.103 63.158 0.00 0.00 38.37 4.57
106 107 1.188219 ACTGCAGAGGGACGTGATGT 61.188 55.000 23.35 0.00 0.00 3.06
108 109 1.107114 CTACTGCAGAGGGACGTGAT 58.893 55.000 23.35 0.00 0.00 3.06
109 110 1.595993 GCTACTGCAGAGGGACGTGA 61.596 60.000 23.35 0.00 39.41 4.35
110 111 1.153745 GCTACTGCAGAGGGACGTG 60.154 63.158 23.35 2.03 39.41 4.49
113 114 0.972983 TCAGGCTACTGCAGAGGGAC 60.973 60.000 23.35 11.76 44.54 4.46
114 115 0.685785 CTCAGGCTACTGCAGAGGGA 60.686 60.000 23.35 7.79 44.54 4.20
115 116 1.821936 CTCAGGCTACTGCAGAGGG 59.178 63.158 23.35 10.65 44.54 4.30
117 118 0.175302 CACCTCAGGCTACTGCAGAG 59.825 60.000 23.35 14.33 44.54 3.35
118 119 0.251787 TCACCTCAGGCTACTGCAGA 60.252 55.000 23.35 2.95 44.54 4.26
119 120 0.175302 CTCACCTCAGGCTACTGCAG 59.825 60.000 13.48 13.48 44.54 4.41
120 121 1.260538 CCTCACCTCAGGCTACTGCA 61.261 60.000 0.00 0.00 44.54 4.41
121 122 0.972983 TCCTCACCTCAGGCTACTGC 60.973 60.000 0.00 0.00 44.54 4.40
122 123 1.686052 GATCCTCACCTCAGGCTACTG 59.314 57.143 0.00 0.00 46.30 2.74
123 124 1.412361 GGATCCTCACCTCAGGCTACT 60.412 57.143 3.84 0.00 32.91 2.57
124 125 1.044611 GGATCCTCACCTCAGGCTAC 58.955 60.000 3.84 0.00 32.91 3.58
125 126 0.937441 AGGATCCTCACCTCAGGCTA 59.063 55.000 9.02 0.00 32.91 3.93
126 127 0.043940 AAGGATCCTCACCTCAGGCT 59.956 55.000 16.52 0.00 36.67 4.58
127 128 0.915364 AAAGGATCCTCACCTCAGGC 59.085 55.000 16.52 0.00 36.67 4.85
128 129 1.912043 ACAAAGGATCCTCACCTCAGG 59.088 52.381 16.52 0.00 36.67 3.86
129 130 2.093235 GGACAAAGGATCCTCACCTCAG 60.093 54.545 16.52 2.81 36.67 3.35
130 131 1.909302 GGACAAAGGATCCTCACCTCA 59.091 52.381 16.52 0.00 36.67 3.86
132 133 2.044793 TGGACAAAGGATCCTCACCT 57.955 50.000 16.52 0.00 39.69 4.00
133 134 2.879103 TTGGACAAAGGATCCTCACC 57.121 50.000 16.52 15.68 37.13 4.02
144 145 3.028130 GAGGGTTTGGACTTTGGACAAA 58.972 45.455 0.00 0.00 0.00 2.83
147 148 1.235724 CGAGGGTTTGGACTTTGGAC 58.764 55.000 0.00 0.00 0.00 4.02
148 149 0.841289 ACGAGGGTTTGGACTTTGGA 59.159 50.000 0.00 0.00 0.00 3.53
149 150 1.202770 AGACGAGGGTTTGGACTTTGG 60.203 52.381 0.00 0.00 0.00 3.28
150 151 2.143925 GAGACGAGGGTTTGGACTTTG 58.856 52.381 0.00 0.00 0.00 2.77
152 153 0.685660 GGAGACGAGGGTTTGGACTT 59.314 55.000 0.00 0.00 0.00 3.01
153 154 0.471211 TGGAGACGAGGGTTTGGACT 60.471 55.000 0.00 0.00 0.00 3.85
171 3020 1.032114 GCCGAGATTGGGGAAGGTTG 61.032 60.000 0.00 0.00 0.00 3.77
195 3059 4.148645 GGCGCGACGGAAGAAAGC 62.149 66.667 12.10 0.00 0.00 3.51
308 3189 3.770040 GTGGGATTTTGGGCGGGC 61.770 66.667 0.00 0.00 0.00 6.13
309 3190 1.264045 ATTGTGGGATTTTGGGCGGG 61.264 55.000 0.00 0.00 0.00 6.13
310 3191 0.108233 CATTGTGGGATTTTGGGCGG 60.108 55.000 0.00 0.00 0.00 6.13
311 3192 0.108233 CCATTGTGGGATTTTGGGCG 60.108 55.000 0.00 0.00 32.67 6.13
312 3193 0.392863 GCCATTGTGGGATTTTGGGC 60.393 55.000 0.00 0.00 38.19 5.36
316 3197 1.350071 TGCTGCCATTGTGGGATTTT 58.650 45.000 0.00 0.00 37.20 1.82
560 3692 1.076332 CGGCGTTCTTGGTTAAGAGG 58.924 55.000 0.00 0.00 43.41 3.69
566 3698 1.597027 CACCTCGGCGTTCTTGGTT 60.597 57.895 6.85 0.00 0.00 3.67
734 3867 3.616821 CGAGACAATCATTTCGCAGGTAA 59.383 43.478 0.00 0.00 0.00 2.85
851 3994 0.667487 TCGCGTCTGCTCCTTTCTTG 60.667 55.000 5.77 0.00 39.65 3.02
868 4011 0.593128 CCCTTGCACCTTGAAAGTCG 59.407 55.000 0.00 0.00 0.00 4.18
972 4115 1.200519 TAGTTATGTCTTGCGCCCCT 58.799 50.000 4.18 0.00 0.00 4.79
981 4124 6.204301 GCTGCATGTCATCAATAGTTATGTCT 59.796 38.462 0.00 0.00 0.00 3.41
1068 4211 3.525537 TCTTTTGTCATCATCCTCGAGC 58.474 45.455 6.99 0.00 0.00 5.03
1572 5270 3.507622 CCCCAAAAGATCTCTGGAAACAC 59.492 47.826 20.51 0.00 35.60 3.32
1790 5625 5.346822 CAGCTGGCATTCAAAATGTAAGTTC 59.653 40.000 5.57 0.00 0.00 3.01
1996 6612 0.035725 CGGTTAACCCCTCCCTCAAC 60.036 60.000 19.09 0.00 0.00 3.18
2039 6655 6.853490 AGGGATTAAACCTCCATATTCTTCC 58.147 40.000 1.37 0.00 31.01 3.46
2121 6737 3.074857 TGATGGGGCTCTAATACCCTT 57.925 47.619 0.00 0.00 46.19 3.95
2173 6789 1.745489 CTAAACAGAGGGGCGCACC 60.745 63.158 24.88 24.88 39.11 5.01
2196 6812 3.965539 CTTCGGGCAGCACAGGAGG 62.966 68.421 0.00 0.00 0.00 4.30
2203 6819 2.769652 AAATCCAGCTTCGGGCAGCA 62.770 55.000 0.00 0.00 42.84 4.41
2245 6861 4.933064 CGAGATCCACGAGCCGGC 62.933 72.222 21.89 21.89 0.00 6.13
2279 6895 5.046304 ACCTGACTTTTCTCATAAGCTGCTA 60.046 40.000 0.90 0.00 0.00 3.49
2286 6902 9.832445 GGATACATTACCTGACTTTTCTCATAA 57.168 33.333 0.00 0.00 0.00 1.90
2309 6925 1.472201 CCATATGCAGCTATCGCGGAT 60.472 52.381 6.13 0.75 42.32 4.18
2312 6928 0.390340 ACCCATATGCAGCTATCGCG 60.390 55.000 0.00 0.00 42.32 5.87
2346 6962 8.279800 TGACAGATACAAAACGAAATTGTGTAG 58.720 33.333 12.94 7.29 40.95 2.74
2357 6974 8.122952 GGGAATAGAAATGACAGATACAAAACG 58.877 37.037 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.