Multiple sequence alignment - TraesCS3B01G606200

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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 TraesCS3B01G606200 chr3B 100.000 4036 0 0 1 4036 825491715 825495750 0.000000e+00 7454.0
1 TraesCS3B01G606200 chr3B 98.183 3852 55 11 197 4036 825317816 825313968 0.000000e+00 6711.0
2 TraesCS3B01G606200 chr3B 93.126 2866 161 14 632 3470 824008561 824005705 0.000000e+00 4169.0
3 TraesCS3B01G606200 chr3B 89.976 838 60 14 2633 3470 824048280 824047467 0.000000e+00 1061.0
4 TraesCS3B01G606200 chr3B 90.576 573 29 7 3489 4036 823985454 823984882 0.000000e+00 736.0
5 TraesCS3B01G606200 chr3B 94.604 278 12 3 3588 3864 824027504 824027229 1.040000e-115 427.0
6 TraesCS3B01G606200 chr3B 93.564 202 11 2 1 200 113928440 113928641 2.360000e-77 300.0
7 TraesCS3B01G606200 chr3B 92.611 203 13 2 1 201 19977635 19977837 1.420000e-74 291.0
8 TraesCS3B01G606200 chrUn 96.408 2060 49 6 426 2468 211800407 211802458 0.000000e+00 3371.0
9 TraesCS3B01G606200 chrUn 97.652 1661 36 3 2376 4036 43085119 43083462 0.000000e+00 2848.0
10 TraesCS3B01G606200 chrUn 95.238 84 3 1 200 282 211800193 211800276 9.100000e-27 132.0
11 TraesCS3B01G606200 chrUn 100.000 52 0 0 353 404 211800282 211800333 3.320000e-16 97.1
12 TraesCS3B01G606200 chr5B 95.000 200 8 2 1 198 50533219 50533020 3.030000e-81 313.0
13 TraesCS3B01G606200 chr3A 93.596 203 11 2 1 201 22785998 22785796 6.560000e-78 302.0
14 TraesCS3B01G606200 chr3A 94.000 200 10 2 1 198 65362848 65362649 6.560000e-78 302.0
15 TraesCS3B01G606200 chr3D 93.970 199 11 1 1 198 527633099 527633297 2.360000e-77 300.0
16 TraesCS3B01G606200 chr2A 93.500 200 11 2 1 198 685744298 685744497 3.050000e-76 296.0
17 TraesCS3B01G606200 chr1B 93.103 203 12 2 1 201 661632339 661632541 3.050000e-76 296.0
18 TraesCS3B01G606200 chr5D 92.683 205 13 2 1 203 324351542 324351746 1.100000e-75 294.0


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 TraesCS3B01G606200 chr3B 825491715 825495750 4035 False 7454.000000 7454 100.000000 1 4036 1 chr3B.!!$F3 4035
1 TraesCS3B01G606200 chr3B 825313968 825317816 3848 True 6711.000000 6711 98.183000 197 4036 1 chr3B.!!$R5 3839
2 TraesCS3B01G606200 chr3B 824005705 824008561 2856 True 4169.000000 4169 93.126000 632 3470 1 chr3B.!!$R2 2838
3 TraesCS3B01G606200 chr3B 824047467 824048280 813 True 1061.000000 1061 89.976000 2633 3470 1 chr3B.!!$R4 837
4 TraesCS3B01G606200 chr3B 823984882 823985454 572 True 736.000000 736 90.576000 3489 4036 1 chr3B.!!$R1 547
5 TraesCS3B01G606200 chrUn 43083462 43085119 1657 True 2848.000000 2848 97.652000 2376 4036 1 chrUn.!!$R1 1660
6 TraesCS3B01G606200 chrUn 211800193 211802458 2265 False 1200.033333 3371 97.215333 200 2468 3 chrUn.!!$F1 2268

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
87 88 0.035458 ACGTGCTAGAGCTGGCTTTT 59.965 50.000 7.36 0.0 42.66 2.27 F
88 89 0.723981 CGTGCTAGAGCTGGCTTTTC 59.276 55.000 7.36 0.0 42.66 2.29 F
101 102 1.131315 GGCTTTTCATCAAGAGTCCGC 59.869 52.381 0.00 0.0 0.00 5.54 F
2644 2731 1.458639 GCCAGCAAGGAAGCAGTTGT 61.459 55.000 0.00 0.0 41.22 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2641 2728 1.213182 TGTTGTACCCTGCTTCCACAA 59.787 47.619 0.00 0.0 0.00 3.33 R
2644 2731 2.173782 TCTTTGTTGTACCCTGCTTCCA 59.826 45.455 0.00 0.0 0.00 3.53 R
2745 2832 2.463553 CATGAATGCTTCGCGTCAAT 57.536 45.000 5.77 0.0 31.02 2.57 R
3987 4105 1.001293 GAGATGCATGGGATCACGCTA 59.999 52.381 2.46 0.0 32.69 4.26 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
40 41 9.563748 TGTACTACTTTTTATTATATGGCCCAC 57.436 33.333 0.00 0.00 0.00 4.61
41 42 9.788889 GTACTACTTTTTATTATATGGCCCACT 57.211 33.333 0.00 0.00 0.00 4.00
43 44 9.709387 ACTACTTTTTATTATATGGCCCACTTT 57.291 29.630 0.00 0.00 0.00 2.66
45 46 8.602472 ACTTTTTATTATATGGCCCACTTTCA 57.398 30.769 0.00 0.00 0.00 2.69
46 47 8.474831 ACTTTTTATTATATGGCCCACTTTCAC 58.525 33.333 0.00 0.00 0.00 3.18
47 48 8.602472 TTTTTATTATATGGCCCACTTTCACT 57.398 30.769 0.00 0.00 0.00 3.41
48 49 7.817418 TTTATTATATGGCCCACTTTCACTC 57.183 36.000 0.00 0.00 0.00 3.51
49 50 5.653255 ATTATATGGCCCACTTTCACTCT 57.347 39.130 0.00 0.00 0.00 3.24
50 51 3.567478 ATATGGCCCACTTTCACTCTC 57.433 47.619 0.00 0.00 0.00 3.20
51 52 1.067295 ATGGCCCACTTTCACTCTCA 58.933 50.000 0.00 0.00 0.00 3.27
52 53 0.108585 TGGCCCACTTTCACTCTCAC 59.891 55.000 0.00 0.00 0.00 3.51
53 54 0.108585 GGCCCACTTTCACTCTCACA 59.891 55.000 0.00 0.00 0.00 3.58
54 55 1.476833 GGCCCACTTTCACTCTCACAA 60.477 52.381 0.00 0.00 0.00 3.33
55 56 2.297701 GCCCACTTTCACTCTCACAAA 58.702 47.619 0.00 0.00 0.00 2.83
56 57 2.291741 GCCCACTTTCACTCTCACAAAG 59.708 50.000 0.00 0.00 33.98 2.77
57 58 3.545703 CCCACTTTCACTCTCACAAAGT 58.454 45.455 0.00 0.00 40.28 2.66
59 60 3.945179 CACTTTCACTCTCACAAAGTGC 58.055 45.455 10.03 0.00 45.98 4.40
60 61 2.945668 ACTTTCACTCTCACAAAGTGCC 59.054 45.455 0.00 0.00 43.09 5.01
61 62 3.209410 CTTTCACTCTCACAAAGTGCCT 58.791 45.455 0.00 0.00 43.09 4.75
62 63 4.141711 ACTTTCACTCTCACAAAGTGCCTA 60.142 41.667 0.00 0.00 43.09 3.93
63 64 3.667497 TCACTCTCACAAAGTGCCTAG 57.333 47.619 0.00 0.00 43.09 3.02
64 65 2.300152 TCACTCTCACAAAGTGCCTAGG 59.700 50.000 3.67 3.67 43.09 3.02
65 66 2.300152 CACTCTCACAAAGTGCCTAGGA 59.700 50.000 14.75 0.00 37.88 2.94
66 67 2.564947 ACTCTCACAAAGTGCCTAGGAG 59.435 50.000 14.75 0.00 32.98 3.69
67 68 1.276421 TCTCACAAAGTGCCTAGGAGC 59.724 52.381 14.75 3.68 32.98 4.70
68 69 1.002430 CTCACAAAGTGCCTAGGAGCA 59.998 52.381 14.75 0.22 41.46 4.26
83 84 3.191539 GCACGTGCTAGAGCTGGC 61.192 66.667 32.55 1.87 42.66 4.85
84 85 2.575993 CACGTGCTAGAGCTGGCT 59.424 61.111 0.82 0.00 42.66 4.75
85 86 1.079543 CACGTGCTAGAGCTGGCTT 60.080 57.895 0.82 0.00 42.66 4.35
86 87 0.671781 CACGTGCTAGAGCTGGCTTT 60.672 55.000 0.82 0.00 42.66 3.51
87 88 0.035458 ACGTGCTAGAGCTGGCTTTT 59.965 50.000 7.36 0.00 42.66 2.27
88 89 0.723981 CGTGCTAGAGCTGGCTTTTC 59.276 55.000 7.36 0.00 42.66 2.29
89 90 1.813513 GTGCTAGAGCTGGCTTTTCA 58.186 50.000 7.36 0.00 42.66 2.69
90 91 2.363683 GTGCTAGAGCTGGCTTTTCAT 58.636 47.619 7.36 0.00 42.66 2.57
91 92 2.354199 GTGCTAGAGCTGGCTTTTCATC 59.646 50.000 7.36 0.00 42.66 2.92
92 93 2.026915 TGCTAGAGCTGGCTTTTCATCA 60.027 45.455 7.36 0.00 42.66 3.07
93 94 3.012518 GCTAGAGCTGGCTTTTCATCAA 58.987 45.455 0.00 0.00 38.21 2.57
94 95 3.065095 GCTAGAGCTGGCTTTTCATCAAG 59.935 47.826 0.00 0.00 38.21 3.02
95 96 3.430042 AGAGCTGGCTTTTCATCAAGA 57.570 42.857 0.00 0.00 0.00 3.02
96 97 3.345414 AGAGCTGGCTTTTCATCAAGAG 58.655 45.455 0.00 0.00 0.00 2.85
97 98 3.080319 GAGCTGGCTTTTCATCAAGAGT 58.920 45.455 0.00 0.00 0.00 3.24
98 99 3.080319 AGCTGGCTTTTCATCAAGAGTC 58.920 45.455 0.00 0.00 0.00 3.36
99 100 2.163211 GCTGGCTTTTCATCAAGAGTCC 59.837 50.000 0.00 0.00 0.00 3.85
100 101 2.417933 CTGGCTTTTCATCAAGAGTCCG 59.582 50.000 0.00 0.00 0.00 4.79
101 102 1.131315 GGCTTTTCATCAAGAGTCCGC 59.869 52.381 0.00 0.00 0.00 5.54
102 103 2.079925 GCTTTTCATCAAGAGTCCGCT 58.920 47.619 0.00 0.00 0.00 5.52
103 104 2.485814 GCTTTTCATCAAGAGTCCGCTT 59.514 45.455 0.00 0.00 0.00 4.68
104 105 3.684788 GCTTTTCATCAAGAGTCCGCTTA 59.315 43.478 0.00 0.00 0.00 3.09
105 106 4.436183 GCTTTTCATCAAGAGTCCGCTTAC 60.436 45.833 0.00 0.00 0.00 2.34
106 107 4.537135 TTTCATCAAGAGTCCGCTTACT 57.463 40.909 0.00 0.00 0.00 2.24
107 108 4.537135 TTCATCAAGAGTCCGCTTACTT 57.463 40.909 0.00 0.00 0.00 2.24
108 109 4.537135 TCATCAAGAGTCCGCTTACTTT 57.463 40.909 0.00 0.00 0.00 2.66
109 110 4.495422 TCATCAAGAGTCCGCTTACTTTC 58.505 43.478 0.00 0.00 0.00 2.62
110 111 4.220821 TCATCAAGAGTCCGCTTACTTTCT 59.779 41.667 0.00 0.00 0.00 2.52
111 112 4.175787 TCAAGAGTCCGCTTACTTTCTC 57.824 45.455 0.00 0.00 0.00 2.87
112 113 3.827302 TCAAGAGTCCGCTTACTTTCTCT 59.173 43.478 0.00 0.00 34.37 3.10
113 114 4.082679 TCAAGAGTCCGCTTACTTTCTCTC 60.083 45.833 0.00 0.00 32.20 3.20
114 115 3.692690 AGAGTCCGCTTACTTTCTCTCT 58.307 45.455 0.00 0.00 0.00 3.10
115 116 3.692593 AGAGTCCGCTTACTTTCTCTCTC 59.307 47.826 0.00 0.00 0.00 3.20
116 117 2.756207 AGTCCGCTTACTTTCTCTCTCC 59.244 50.000 0.00 0.00 0.00 3.71
117 118 2.756207 GTCCGCTTACTTTCTCTCTCCT 59.244 50.000 0.00 0.00 0.00 3.69
118 119 3.018149 TCCGCTTACTTTCTCTCTCCTC 58.982 50.000 0.00 0.00 0.00 3.71
119 120 3.020984 CCGCTTACTTTCTCTCTCCTCT 58.979 50.000 0.00 0.00 0.00 3.69
120 121 3.445805 CCGCTTACTTTCTCTCTCCTCTT 59.554 47.826 0.00 0.00 0.00 2.85
121 122 4.439563 CCGCTTACTTTCTCTCTCCTCTTC 60.440 50.000 0.00 0.00 0.00 2.87
122 123 4.398044 CGCTTACTTTCTCTCTCCTCTTCT 59.602 45.833 0.00 0.00 0.00 2.85
123 124 5.448632 CGCTTACTTTCTCTCTCCTCTTCTC 60.449 48.000 0.00 0.00 0.00 2.87
124 125 5.652452 GCTTACTTTCTCTCTCCTCTTCTCT 59.348 44.000 0.00 0.00 0.00 3.10
125 126 6.152831 GCTTACTTTCTCTCTCCTCTTCTCTT 59.847 42.308 0.00 0.00 0.00 2.85
126 127 7.309805 GCTTACTTTCTCTCTCCTCTTCTCTTT 60.310 40.741 0.00 0.00 0.00 2.52
127 128 6.590234 ACTTTCTCTCTCCTCTTCTCTTTC 57.410 41.667 0.00 0.00 0.00 2.62
128 129 5.480422 ACTTTCTCTCTCCTCTTCTCTTTCC 59.520 44.000 0.00 0.00 0.00 3.13
129 130 4.946160 TCTCTCTCCTCTTCTCTTTCCT 57.054 45.455 0.00 0.00 0.00 3.36
130 131 4.855340 TCTCTCTCCTCTTCTCTTTCCTC 58.145 47.826 0.00 0.00 0.00 3.71
131 132 3.954258 CTCTCTCCTCTTCTCTTTCCTCC 59.046 52.174 0.00 0.00 0.00 4.30
132 133 3.335183 TCTCTCCTCTTCTCTTTCCTCCA 59.665 47.826 0.00 0.00 0.00 3.86
133 134 4.093011 CTCTCCTCTTCTCTTTCCTCCAA 58.907 47.826 0.00 0.00 0.00 3.53
134 135 3.835395 TCTCCTCTTCTCTTTCCTCCAAC 59.165 47.826 0.00 0.00 0.00 3.77
135 136 3.837731 CTCCTCTTCTCTTTCCTCCAACT 59.162 47.826 0.00 0.00 0.00 3.16
136 137 5.011982 TCCTCTTCTCTTTCCTCCAACTA 57.988 43.478 0.00 0.00 0.00 2.24
137 138 5.403512 TCCTCTTCTCTTTCCTCCAACTAA 58.596 41.667 0.00 0.00 0.00 2.24
138 139 5.482175 TCCTCTTCTCTTTCCTCCAACTAAG 59.518 44.000 0.00 0.00 0.00 2.18
139 140 5.153950 TCTTCTCTTTCCTCCAACTAAGC 57.846 43.478 0.00 0.00 0.00 3.09
140 141 4.593206 TCTTCTCTTTCCTCCAACTAAGCA 59.407 41.667 0.00 0.00 0.00 3.91
141 142 4.974645 TCTCTTTCCTCCAACTAAGCAA 57.025 40.909 0.00 0.00 0.00 3.91
142 143 4.899502 TCTCTTTCCTCCAACTAAGCAAG 58.100 43.478 0.00 0.00 0.00 4.01
143 144 4.593206 TCTCTTTCCTCCAACTAAGCAAGA 59.407 41.667 0.00 0.00 0.00 3.02
144 145 5.071788 TCTCTTTCCTCCAACTAAGCAAGAA 59.928 40.000 0.00 0.00 0.00 2.52
145 146 5.880901 TCTTTCCTCCAACTAAGCAAGAAT 58.119 37.500 0.00 0.00 0.00 2.40
146 147 7.016153 TCTTTCCTCCAACTAAGCAAGAATA 57.984 36.000 0.00 0.00 0.00 1.75
147 148 7.633789 TCTTTCCTCCAACTAAGCAAGAATAT 58.366 34.615 0.00 0.00 0.00 1.28
148 149 8.768397 TCTTTCCTCCAACTAAGCAAGAATATA 58.232 33.333 0.00 0.00 0.00 0.86
149 150 8.732746 TTTCCTCCAACTAAGCAAGAATATAC 57.267 34.615 0.00 0.00 0.00 1.47
150 151 7.676683 TCCTCCAACTAAGCAAGAATATACT 57.323 36.000 0.00 0.00 0.00 2.12
151 152 8.777578 TCCTCCAACTAAGCAAGAATATACTA 57.222 34.615 0.00 0.00 0.00 1.82
152 153 9.381038 TCCTCCAACTAAGCAAGAATATACTAT 57.619 33.333 0.00 0.00 0.00 2.12
188 189 4.815269 GTCAGCTGACTCAGTTCTATTGT 58.185 43.478 34.54 0.00 41.65 2.71
189 190 5.955488 GTCAGCTGACTCAGTTCTATTGTA 58.045 41.667 34.54 0.00 41.65 2.41
190 191 5.802956 GTCAGCTGACTCAGTTCTATTGTAC 59.197 44.000 34.54 7.02 41.65 2.90
191 192 5.712446 TCAGCTGACTCAGTTCTATTGTACT 59.288 40.000 13.74 0.00 33.43 2.73
192 193 6.209589 TCAGCTGACTCAGTTCTATTGTACTT 59.790 38.462 13.74 0.00 33.43 2.24
193 194 6.309980 CAGCTGACTCAGTTCTATTGTACTTG 59.690 42.308 8.42 0.00 33.43 3.16
194 195 5.062809 GCTGACTCAGTTCTATTGTACTTGC 59.937 44.000 7.89 0.00 33.43 4.01
195 196 6.346477 TGACTCAGTTCTATTGTACTTGCT 57.654 37.500 0.00 0.00 0.00 3.91
283 284 5.910166 CCATGACGACGATTAAACAAAAACA 59.090 36.000 0.00 0.00 0.00 2.83
293 294 7.434013 ACGATTAAACAAAAACAACATGAGGTC 59.566 33.333 0.00 0.00 0.00 3.85
294 295 7.433719 CGATTAAACAAAAACAACATGAGGTCA 59.566 33.333 0.00 0.00 0.00 4.02
295 296 9.260002 GATTAAACAAAAACAACATGAGGTCAT 57.740 29.630 0.00 0.00 36.96 3.06
297 298 9.522804 TTAAACAAAAACAACATGAGGTCATAC 57.477 29.630 0.00 0.00 34.26 2.39
298 299 5.757886 ACAAAAACAACATGAGGTCATACG 58.242 37.500 0.00 0.00 34.26 3.06
300 301 5.356882 AAAACAACATGAGGTCATACGTG 57.643 39.130 0.00 0.00 34.26 4.49
301 302 3.953712 ACAACATGAGGTCATACGTGA 57.046 42.857 0.00 0.00 34.26 4.35
302 303 4.265904 ACAACATGAGGTCATACGTGAA 57.734 40.909 0.00 0.00 35.80 3.18
303 304 4.245660 ACAACATGAGGTCATACGTGAAG 58.754 43.478 0.00 0.00 35.80 3.02
306 307 3.509967 ACATGAGGTCATACGTGAAGTGA 59.490 43.478 0.00 0.00 35.80 3.41
307 308 4.021456 ACATGAGGTCATACGTGAAGTGAA 60.021 41.667 0.00 0.00 35.80 3.18
2641 2728 2.670934 CGCCAGCAAGGAAGCAGT 60.671 61.111 0.00 0.00 41.22 4.40
2644 2731 1.458639 GCCAGCAAGGAAGCAGTTGT 61.459 55.000 0.00 0.00 41.22 3.32
2745 2832 4.707030 CTGCAAGCATCCTGTATTGAAA 57.293 40.909 0.00 0.00 0.00 2.69
2792 2879 7.114095 TGAATGATGAGATGAATTCAGTCCAA 58.886 34.615 14.54 0.00 34.86 3.53
3295 3388 1.004745 TCCAAGGGAAGTTCATGGAGC 59.995 52.381 16.15 0.00 35.33 4.70
3372 3465 6.130298 TGATGACAAAGTACCACAACAAAG 57.870 37.500 0.00 0.00 0.00 2.77
3373 3466 5.650266 TGATGACAAAGTACCACAACAAAGT 59.350 36.000 0.00 0.00 0.00 2.66
3374 3467 6.824196 TGATGACAAAGTACCACAACAAAGTA 59.176 34.615 0.00 0.00 0.00 2.24
3375 3468 6.425577 TGACAAAGTACCACAACAAAGTAC 57.574 37.500 0.00 0.00 37.27 2.73
3376 3469 5.354792 TGACAAAGTACCACAACAAAGTACC 59.645 40.000 0.00 0.00 37.64 3.34
3377 3470 5.254901 ACAAAGTACCACAACAAAGTACCA 58.745 37.500 0.00 0.00 37.64 3.25
3378 3471 5.124297 ACAAAGTACCACAACAAAGTACCAC 59.876 40.000 0.00 0.00 37.64 4.16
3388 3481 5.105554 ACAACAAAGTACCACAGCAAAATGA 60.106 36.000 0.00 0.00 0.00 2.57
3487 3580 5.520376 AAGAGTGGAGTTTGGTTTTGATG 57.480 39.130 0.00 0.00 0.00 3.07
3778 3872 4.160329 AGATAGATATTCACCCGAGGCAA 58.840 43.478 0.00 0.00 0.00 4.52
3895 3989 5.748630 GTCTCTGCAACATGTCGTATTATCA 59.251 40.000 0.00 0.00 0.00 2.15
3987 4105 2.060567 ATGTGTGCAGTCCAGCCTGT 62.061 55.000 0.00 0.00 34.84 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.563748 GTGGGCCATATAATAAAAAGTAGTACA 57.436 33.333 10.70 0.00 0.00 2.90
15 16 9.788889 AGTGGGCCATATAATAAAAAGTAGTAC 57.211 33.333 10.70 0.00 0.00 2.73
17 18 9.709387 AAAGTGGGCCATATAATAAAAAGTAGT 57.291 29.630 10.70 0.00 0.00 2.73
19 20 9.702253 TGAAAGTGGGCCATATAATAAAAAGTA 57.298 29.630 10.70 0.00 0.00 2.24
20 21 8.474831 GTGAAAGTGGGCCATATAATAAAAAGT 58.525 33.333 10.70 0.00 0.00 2.66
21 22 8.695456 AGTGAAAGTGGGCCATATAATAAAAAG 58.305 33.333 10.70 0.00 0.00 2.27
22 23 8.602472 AGTGAAAGTGGGCCATATAATAAAAA 57.398 30.769 10.70 0.00 0.00 1.94
23 24 8.058847 AGAGTGAAAGTGGGCCATATAATAAAA 58.941 33.333 10.70 0.00 0.00 1.52
24 25 7.582719 AGAGTGAAAGTGGGCCATATAATAAA 58.417 34.615 10.70 0.00 0.00 1.40
25 26 7.147391 TGAGAGTGAAAGTGGGCCATATAATAA 60.147 37.037 10.70 0.00 0.00 1.40
26 27 6.328934 TGAGAGTGAAAGTGGGCCATATAATA 59.671 38.462 10.70 0.00 0.00 0.98
27 28 5.132648 TGAGAGTGAAAGTGGGCCATATAAT 59.867 40.000 10.70 0.00 0.00 1.28
28 29 4.473196 TGAGAGTGAAAGTGGGCCATATAA 59.527 41.667 10.70 0.00 0.00 0.98
29 30 4.037222 TGAGAGTGAAAGTGGGCCATATA 58.963 43.478 10.70 0.00 0.00 0.86
30 31 2.846206 TGAGAGTGAAAGTGGGCCATAT 59.154 45.455 10.70 0.00 0.00 1.78
31 32 2.027192 GTGAGAGTGAAAGTGGGCCATA 60.027 50.000 10.70 0.00 0.00 2.74
32 33 1.067295 TGAGAGTGAAAGTGGGCCAT 58.933 50.000 10.70 0.00 0.00 4.40
33 34 0.108585 GTGAGAGTGAAAGTGGGCCA 59.891 55.000 0.00 0.00 0.00 5.36
34 35 0.108585 TGTGAGAGTGAAAGTGGGCC 59.891 55.000 0.00 0.00 0.00 5.80
35 36 1.967319 TTGTGAGAGTGAAAGTGGGC 58.033 50.000 0.00 0.00 0.00 5.36
36 37 3.313526 CACTTTGTGAGAGTGAAAGTGGG 59.686 47.826 13.57 0.00 46.76 4.61
37 38 4.542662 CACTTTGTGAGAGTGAAAGTGG 57.457 45.455 13.57 0.00 46.76 4.00
39 40 2.945668 GGCACTTTGTGAGAGTGAAAGT 59.054 45.455 8.33 0.00 45.72 2.66
40 41 3.209410 AGGCACTTTGTGAGAGTGAAAG 58.791 45.455 8.33 0.00 45.72 2.62
41 42 3.281727 AGGCACTTTGTGAGAGTGAAA 57.718 42.857 8.33 0.00 45.72 2.69
42 43 3.244215 CCTAGGCACTTTGTGAGAGTGAA 60.244 47.826 8.33 0.00 45.72 3.18
43 44 2.300152 CCTAGGCACTTTGTGAGAGTGA 59.700 50.000 8.33 0.00 45.72 3.41
44 45 2.300152 TCCTAGGCACTTTGTGAGAGTG 59.700 50.000 2.96 0.10 45.64 3.51
45 46 2.564947 CTCCTAGGCACTTTGTGAGAGT 59.435 50.000 2.96 0.00 41.75 3.24
46 47 2.676463 GCTCCTAGGCACTTTGTGAGAG 60.676 54.545 2.96 0.00 41.75 3.20
47 48 1.276421 GCTCCTAGGCACTTTGTGAGA 59.724 52.381 2.96 0.00 41.75 3.27
48 49 1.002430 TGCTCCTAGGCACTTTGTGAG 59.998 52.381 2.96 0.00 41.75 3.51
49 50 1.055849 TGCTCCTAGGCACTTTGTGA 58.944 50.000 2.96 0.00 41.75 3.58
50 51 3.631453 TGCTCCTAGGCACTTTGTG 57.369 52.632 2.96 0.00 41.75 3.33
66 67 3.191539 GCCAGCTCTAGCACGTGC 61.192 66.667 32.79 32.79 45.16 5.34
67 68 0.671781 AAAGCCAGCTCTAGCACGTG 60.672 55.000 12.28 12.28 45.16 4.49
68 69 0.035458 AAAAGCCAGCTCTAGCACGT 59.965 50.000 4.54 0.00 45.16 4.49
69 70 0.723981 GAAAAGCCAGCTCTAGCACG 59.276 55.000 4.54 0.00 45.16 5.34
70 71 1.813513 TGAAAAGCCAGCTCTAGCAC 58.186 50.000 4.54 0.00 45.16 4.40
71 72 2.026915 TGATGAAAAGCCAGCTCTAGCA 60.027 45.455 4.54 0.00 45.16 3.49
72 73 2.636830 TGATGAAAAGCCAGCTCTAGC 58.363 47.619 0.00 0.00 42.49 3.42
73 74 4.511527 TCTTGATGAAAAGCCAGCTCTAG 58.488 43.478 0.00 0.00 0.00 2.43
74 75 4.019860 ACTCTTGATGAAAAGCCAGCTCTA 60.020 41.667 0.00 0.00 0.00 2.43
75 76 3.244840 ACTCTTGATGAAAAGCCAGCTCT 60.245 43.478 0.00 0.00 0.00 4.09
76 77 3.080319 ACTCTTGATGAAAAGCCAGCTC 58.920 45.455 0.00 0.00 0.00 4.09
77 78 3.080319 GACTCTTGATGAAAAGCCAGCT 58.920 45.455 0.00 0.00 0.00 4.24
78 79 2.163211 GGACTCTTGATGAAAAGCCAGC 59.837 50.000 0.00 0.00 0.00 4.85
79 80 2.417933 CGGACTCTTGATGAAAAGCCAG 59.582 50.000 0.00 0.00 0.00 4.85
80 81 2.426522 CGGACTCTTGATGAAAAGCCA 58.573 47.619 0.00 0.00 0.00 4.75
81 82 1.131315 GCGGACTCTTGATGAAAAGCC 59.869 52.381 0.00 0.00 0.00 4.35
82 83 2.079925 AGCGGACTCTTGATGAAAAGC 58.920 47.619 0.00 0.00 0.00 3.51
83 84 4.932200 AGTAAGCGGACTCTTGATGAAAAG 59.068 41.667 0.00 0.00 0.00 2.27
84 85 4.894784 AGTAAGCGGACTCTTGATGAAAA 58.105 39.130 0.00 0.00 0.00 2.29
85 86 4.537135 AGTAAGCGGACTCTTGATGAAA 57.463 40.909 0.00 0.00 0.00 2.69
86 87 4.537135 AAGTAAGCGGACTCTTGATGAA 57.463 40.909 0.00 0.00 0.00 2.57
87 88 4.220821 AGAAAGTAAGCGGACTCTTGATGA 59.779 41.667 0.00 0.00 0.00 2.92
88 89 4.499183 AGAAAGTAAGCGGACTCTTGATG 58.501 43.478 0.00 0.00 0.00 3.07
89 90 4.464597 AGAGAAAGTAAGCGGACTCTTGAT 59.535 41.667 0.00 0.00 31.93 2.57
90 91 3.827302 AGAGAAAGTAAGCGGACTCTTGA 59.173 43.478 0.00 0.00 31.93 3.02
91 92 4.082463 AGAGAGAAAGTAAGCGGACTCTTG 60.082 45.833 0.00 0.00 35.34 3.02
92 93 4.083565 AGAGAGAAAGTAAGCGGACTCTT 58.916 43.478 0.00 0.00 35.34 2.85
93 94 3.692593 GAGAGAGAAAGTAAGCGGACTCT 59.307 47.826 0.00 0.00 37.42 3.24
94 95 3.181494 GGAGAGAGAAAGTAAGCGGACTC 60.181 52.174 0.00 0.00 0.00 3.36
95 96 2.756207 GGAGAGAGAAAGTAAGCGGACT 59.244 50.000 0.00 0.00 0.00 3.85
96 97 2.756207 AGGAGAGAGAAAGTAAGCGGAC 59.244 50.000 0.00 0.00 0.00 4.79
97 98 3.018149 GAGGAGAGAGAAAGTAAGCGGA 58.982 50.000 0.00 0.00 0.00 5.54
98 99 3.020984 AGAGGAGAGAGAAAGTAAGCGG 58.979 50.000 0.00 0.00 0.00 5.52
99 100 4.398044 AGAAGAGGAGAGAGAAAGTAAGCG 59.602 45.833 0.00 0.00 0.00 4.68
100 101 5.652452 AGAGAAGAGGAGAGAGAAAGTAAGC 59.348 44.000 0.00 0.00 0.00 3.09
101 102 7.703058 AAGAGAAGAGGAGAGAGAAAGTAAG 57.297 40.000 0.00 0.00 0.00 2.34
102 103 7.177744 GGAAAGAGAAGAGGAGAGAGAAAGTAA 59.822 40.741 0.00 0.00 0.00 2.24
103 104 6.661805 GGAAAGAGAAGAGGAGAGAGAAAGTA 59.338 42.308 0.00 0.00 0.00 2.24
104 105 5.480422 GGAAAGAGAAGAGGAGAGAGAAAGT 59.520 44.000 0.00 0.00 0.00 2.66
105 106 5.716703 AGGAAAGAGAAGAGGAGAGAGAAAG 59.283 44.000 0.00 0.00 0.00 2.62
106 107 5.650283 AGGAAAGAGAAGAGGAGAGAGAAA 58.350 41.667 0.00 0.00 0.00 2.52
107 108 5.261216 GAGGAAAGAGAAGAGGAGAGAGAA 58.739 45.833 0.00 0.00 0.00 2.87
108 109 4.325030 GGAGGAAAGAGAAGAGGAGAGAGA 60.325 50.000 0.00 0.00 0.00 3.10
109 110 3.954258 GGAGGAAAGAGAAGAGGAGAGAG 59.046 52.174 0.00 0.00 0.00 3.20
110 111 3.335183 TGGAGGAAAGAGAAGAGGAGAGA 59.665 47.826 0.00 0.00 0.00 3.10
111 112 3.707316 TGGAGGAAAGAGAAGAGGAGAG 58.293 50.000 0.00 0.00 0.00 3.20
112 113 3.835395 GTTGGAGGAAAGAGAAGAGGAGA 59.165 47.826 0.00 0.00 0.00 3.71
113 114 3.837731 AGTTGGAGGAAAGAGAAGAGGAG 59.162 47.826 0.00 0.00 0.00 3.69
114 115 3.863086 AGTTGGAGGAAAGAGAAGAGGA 58.137 45.455 0.00 0.00 0.00 3.71
115 116 5.729510 CTTAGTTGGAGGAAAGAGAAGAGG 58.270 45.833 0.00 0.00 0.00 3.69
116 117 5.175127 GCTTAGTTGGAGGAAAGAGAAGAG 58.825 45.833 0.00 0.00 0.00 2.85
117 118 4.593206 TGCTTAGTTGGAGGAAAGAGAAGA 59.407 41.667 0.00 0.00 0.00 2.87
118 119 4.899502 TGCTTAGTTGGAGGAAAGAGAAG 58.100 43.478 0.00 0.00 0.00 2.85
119 120 4.974645 TGCTTAGTTGGAGGAAAGAGAA 57.025 40.909 0.00 0.00 0.00 2.87
120 121 4.593206 TCTTGCTTAGTTGGAGGAAAGAGA 59.407 41.667 0.00 0.00 0.00 3.10
121 122 4.899502 TCTTGCTTAGTTGGAGGAAAGAG 58.100 43.478 0.00 0.00 0.00 2.85
122 123 4.974645 TCTTGCTTAGTTGGAGGAAAGA 57.025 40.909 0.00 0.00 0.00 2.52
123 124 7.872113 ATATTCTTGCTTAGTTGGAGGAAAG 57.128 36.000 0.00 0.00 28.75 2.62
124 125 8.548877 AGTATATTCTTGCTTAGTTGGAGGAAA 58.451 33.333 0.00 0.00 28.75 3.13
125 126 8.090788 AGTATATTCTTGCTTAGTTGGAGGAA 57.909 34.615 0.00 0.00 0.00 3.36
126 127 7.676683 AGTATATTCTTGCTTAGTTGGAGGA 57.323 36.000 0.00 0.00 0.00 3.71
166 167 4.815269 ACAATAGAACTGAGTCAGCTGAC 58.185 43.478 34.82 34.82 45.08 3.51
167 168 5.712446 AGTACAATAGAACTGAGTCAGCTGA 59.288 40.000 20.31 13.74 34.37 4.26
168 169 5.960113 AGTACAATAGAACTGAGTCAGCTG 58.040 41.667 20.31 7.63 34.37 4.24
169 170 6.393990 CAAGTACAATAGAACTGAGTCAGCT 58.606 40.000 20.31 8.07 34.37 4.24
170 171 5.062809 GCAAGTACAATAGAACTGAGTCAGC 59.937 44.000 20.31 4.84 34.37 4.26
171 172 6.393990 AGCAAGTACAATAGAACTGAGTCAG 58.606 40.000 18.83 18.83 37.52 3.51
172 173 6.209589 AGAGCAAGTACAATAGAACTGAGTCA 59.790 38.462 0.00 0.00 0.00 3.41
173 174 6.626302 AGAGCAAGTACAATAGAACTGAGTC 58.374 40.000 0.00 0.00 0.00 3.36
174 175 6.597832 AGAGCAAGTACAATAGAACTGAGT 57.402 37.500 0.00 0.00 0.00 3.41
175 176 7.221838 GCTTAGAGCAAGTACAATAGAACTGAG 59.778 40.741 0.00 0.00 41.89 3.35
176 177 7.036220 GCTTAGAGCAAGTACAATAGAACTGA 58.964 38.462 0.00 0.00 41.89 3.41
177 178 7.227992 GCTTAGAGCAAGTACAATAGAACTG 57.772 40.000 0.00 0.00 41.89 3.16
193 194 1.996191 CTTCCACGTCTTGCTTAGAGC 59.004 52.381 0.00 0.00 42.82 4.09
194 195 1.996191 GCTTCCACGTCTTGCTTAGAG 59.004 52.381 0.00 0.00 32.23 2.43
195 196 1.668919 CGCTTCCACGTCTTGCTTAGA 60.669 52.381 0.00 0.00 0.00 2.10
202 203 1.668151 GCCTTCGCTTCCACGTCTT 60.668 57.895 0.00 0.00 0.00 3.01
209 210 2.383527 CGTGTCTGCCTTCGCTTCC 61.384 63.158 0.00 0.00 35.36 3.46
283 284 4.021456 TCACTTCACGTATGACCTCATGTT 60.021 41.667 0.00 0.00 37.15 2.71
293 294 7.758076 TCCAAAGTAGTATTCACTTCACGTATG 59.242 37.037 0.00 0.00 35.19 2.39
294 295 7.833786 TCCAAAGTAGTATTCACTTCACGTAT 58.166 34.615 0.00 0.00 35.19 3.06
295 296 7.218228 TCCAAAGTAGTATTCACTTCACGTA 57.782 36.000 0.00 0.00 35.19 3.57
296 297 6.092955 TCCAAAGTAGTATTCACTTCACGT 57.907 37.500 0.00 0.00 35.19 4.49
297 298 7.416154 TTTCCAAAGTAGTATTCACTTCACG 57.584 36.000 0.00 0.00 35.19 4.35
298 299 9.612620 CAATTTCCAAAGTAGTATTCACTTCAC 57.387 33.333 0.00 0.00 35.19 3.18
2641 2728 1.213182 TGTTGTACCCTGCTTCCACAA 59.787 47.619 0.00 0.00 0.00 3.33
2644 2731 2.173782 TCTTTGTTGTACCCTGCTTCCA 59.826 45.455 0.00 0.00 0.00 3.53
2745 2832 2.463553 CATGAATGCTTCGCGTCAAT 57.536 45.000 5.77 0.00 31.02 2.57
2792 2879 4.101741 ACCTTCTCAGACACTAGTGCTTTT 59.898 41.667 22.90 2.78 0.00 2.27
3295 3388 7.639113 TGCATAGTCTTTAATTTAGGGGTTG 57.361 36.000 0.00 0.00 0.00 3.77
3372 3465 4.829064 TCTGTTCATTTTGCTGTGGTAC 57.171 40.909 0.00 0.00 0.00 3.34
3373 3466 4.321156 GCATCTGTTCATTTTGCTGTGGTA 60.321 41.667 0.00 0.00 0.00 3.25
3374 3467 3.553508 GCATCTGTTCATTTTGCTGTGGT 60.554 43.478 0.00 0.00 0.00 4.16
3375 3468 2.991190 GCATCTGTTCATTTTGCTGTGG 59.009 45.455 0.00 0.00 0.00 4.17
3376 3469 3.909430 AGCATCTGTTCATTTTGCTGTG 58.091 40.909 0.00 0.00 41.79 3.66
3377 3470 4.595762 AAGCATCTGTTCATTTTGCTGT 57.404 36.364 0.00 0.00 42.50 4.40
3378 3471 5.946298 TCTAAGCATCTGTTCATTTTGCTG 58.054 37.500 0.00 0.00 42.50 4.41
3427 3520 7.039784 TCCCTTATAATTTAATGATGTGCAGCC 60.040 37.037 0.00 0.00 0.00 4.85
3462 3555 6.693315 TCAAAACCAAACTCCACTCTTTAG 57.307 37.500 0.00 0.00 0.00 1.85
3463 3556 6.040391 CCATCAAAACCAAACTCCACTCTTTA 59.960 38.462 0.00 0.00 0.00 1.85
3470 3563 2.962421 GTCCCATCAAAACCAAACTCCA 59.038 45.455 0.00 0.00 0.00 3.86
3487 3580 5.509832 TTTAAAGGAAACTAGAGGGTCCC 57.490 43.478 0.00 0.00 42.68 4.46
3895 3989 2.888594 CACCTGACCAATACGAACGAT 58.111 47.619 0.14 0.00 0.00 3.73
3987 4105 1.001293 GAGATGCATGGGATCACGCTA 59.999 52.381 2.46 0.00 32.69 4.26


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

AutoCloner maintained by Alex Coulton.