Multiple sequence alignment - TraesCS2B01G446400

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 TraesCS2B01G446400 chr2B 100.000 5188 0 0 1 5188 639214124 639219311 0.000000e+00 9581.0
1 TraesCS2B01G446400 chr2B 98.806 335 2 2 649 981 639214440 639214774 3.460000e-166 595.0
2 TraesCS2B01G446400 chr2B 98.806 335 2 2 317 651 639214772 639215104 3.460000e-166 595.0
3 TraesCS2B01G446400 chr2B 96.591 88 1 1 250 335 76882505 76882592 1.510000e-30 145.0
4 TraesCS2B01G446400 chr2B 92.424 66 4 1 4480 4544 639218540 639218605 5.530000e-15 93.5
5 TraesCS2B01G446400 chr2B 92.424 66 4 1 4417 4482 639218603 639218667 5.530000e-15 93.5
6 TraesCS2B01G446400 chr2A 90.442 2783 176 44 2219 4950 679882683 679885426 0.000000e+00 3583.0
7 TraesCS2B01G446400 chr2A 88.353 1494 129 21 743 2217 679881529 679882996 0.000000e+00 1753.0
8 TraesCS2B01G446400 chr2A 94.161 274 16 0 4912 5185 679885435 679885708 8.030000e-113 418.0
9 TraesCS2B01G446400 chr2A 91.391 151 3 7 246 392 679881330 679881474 1.140000e-46 198.0
10 TraesCS2B01G446400 chr2A 97.619 84 0 1 252 335 756836296 756836215 5.420000e-30 143.0
11 TraesCS2B01G446400 chr2A 91.228 57 4 1 4417 4473 679884964 679885019 5.570000e-10 76.8
12 TraesCS2B01G446400 chr2D 91.742 2095 117 20 3105 5188 537214936 537216985 0.000000e+00 2859.0
13 TraesCS2B01G446400 chr2D 84.757 1417 142 43 833 2217 537212589 537213963 0.000000e+00 1352.0
14 TraesCS2B01G446400 chr2D 85.878 871 65 30 2219 3050 537214090 537214941 0.000000e+00 874.0
15 TraesCS2B01G446400 chr2D 88.503 374 28 2 1845 2217 537214037 537214396 6.170000e-119 438.0
16 TraesCS2B01G446400 chr2D 85.204 196 20 7 154 344 537212095 537212286 5.300000e-45 193.0
17 TraesCS2B01G446400 chr2D 97.619 84 0 1 252 335 625437211 625437292 5.420000e-30 143.0
18 TraesCS2B01G446400 chr5D 76.471 595 76 31 3197 3783 558893672 558893134 1.110000e-66 265.0
19 TraesCS2B01G446400 chr5D 96.471 85 1 1 250 334 95306998 95307080 7.010000e-29 139.0
20 TraesCS2B01G446400 chr7A 94.898 98 1 3 244 337 292419 292322 3.240000e-32 150.0
21 TraesCS2B01G446400 chr6B 94.565 92 3 2 245 335 41858417 41858507 1.950000e-29 141.0
22 TraesCS2B01G446400 chr5A 95.455 88 2 1 250 337 90607120 90607205 7.010000e-29 139.0


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 TraesCS2B01G446400 chr2B 639214124 639219311 5187 False 9581.00 9581 100.0000 1 5188 1 chr2B.!!$F2 5187
1 TraesCS2B01G446400 chr2B 639214440 639218667 4227 False 344.25 595 95.6150 317 4544 4 chr2B.!!$F3 4227
2 TraesCS2B01G446400 chr2A 679881330 679885708 4378 False 1205.76 3583 91.1150 246 5185 5 chr2A.!!$F1 4939
3 TraesCS2B01G446400 chr2D 537212095 537216985 4890 False 1143.20 2859 87.2168 154 5188 5 chr2D.!!$F2 5034
4 TraesCS2B01G446400 chr5D 558893134 558893672 538 True 265.00 265 76.4710 3197 3783 1 chr5D.!!$R1 586

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
33 34 0.036306 CCAAACACGCCCTAGGAGTT 59.964 55.0 11.48 6.69 32.34 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4567 5039 1.863454 CTGCTCACATGATTCTACGCC 59.137 52.381 0.0 0.0 0.0 5.68 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
20 21 2.966050 GTTGCAAACTGAACCCAAACA 58.034 42.857 0.00 0.00 45.32 2.83
21 22 2.663826 TGCAAACTGAACCCAAACAC 57.336 45.000 0.00 0.00 0.00 3.32
22 23 1.135257 TGCAAACTGAACCCAAACACG 60.135 47.619 0.00 0.00 0.00 4.49
23 24 1.555477 CAAACTGAACCCAAACACGC 58.445 50.000 0.00 0.00 0.00 5.34
24 25 0.458260 AAACTGAACCCAAACACGCC 59.542 50.000 0.00 0.00 0.00 5.68
25 26 1.388837 AACTGAACCCAAACACGCCC 61.389 55.000 0.00 0.00 0.00 6.13
26 27 1.528309 CTGAACCCAAACACGCCCT 60.528 57.895 0.00 0.00 0.00 5.19
27 28 0.250553 CTGAACCCAAACACGCCCTA 60.251 55.000 0.00 0.00 0.00 3.53
28 29 0.250553 TGAACCCAAACACGCCCTAG 60.251 55.000 0.00 0.00 0.00 3.02
29 30 0.958876 GAACCCAAACACGCCCTAGG 60.959 60.000 0.06 0.06 0.00 3.02
30 31 1.420532 AACCCAAACACGCCCTAGGA 61.421 55.000 11.48 0.00 0.00 2.94
31 32 1.078426 CCCAAACACGCCCTAGGAG 60.078 63.158 11.48 6.50 0.00 3.69
32 33 1.677552 CCAAACACGCCCTAGGAGT 59.322 57.895 11.48 7.23 35.79 3.85
33 34 0.036306 CCAAACACGCCCTAGGAGTT 59.964 55.000 11.48 6.69 32.34 3.01
34 35 1.156736 CAAACACGCCCTAGGAGTTG 58.843 55.000 11.48 6.13 32.34 3.16
35 36 0.036306 AAACACGCCCTAGGAGTTGG 59.964 55.000 11.48 2.00 32.34 3.77
36 37 2.125106 CACGCCCTAGGAGTTGGC 60.125 66.667 11.48 3.30 41.85 4.52
37 38 2.284699 ACGCCCTAGGAGTTGGCT 60.285 61.111 11.48 0.00 43.12 4.75
38 39 1.001248 ACGCCCTAGGAGTTGGCTA 59.999 57.895 11.48 0.00 43.12 3.93
39 40 1.328430 ACGCCCTAGGAGTTGGCTAC 61.328 60.000 11.48 0.00 43.12 3.58
40 41 1.327690 CGCCCTAGGAGTTGGCTACA 61.328 60.000 11.48 0.00 43.12 2.74
41 42 0.466124 GCCCTAGGAGTTGGCTACAG 59.534 60.000 11.48 0.00 42.01 2.74
42 43 1.867363 CCCTAGGAGTTGGCTACAGT 58.133 55.000 11.48 0.00 0.00 3.55
43 44 2.188817 CCCTAGGAGTTGGCTACAGTT 58.811 52.381 11.48 0.00 0.00 3.16
44 45 2.093447 CCCTAGGAGTTGGCTACAGTTG 60.093 54.545 11.48 0.00 0.00 3.16
45 46 2.832129 CCTAGGAGTTGGCTACAGTTGA 59.168 50.000 1.05 0.00 0.00 3.18
46 47 3.452627 CCTAGGAGTTGGCTACAGTTGAT 59.547 47.826 1.05 0.00 0.00 2.57
47 48 4.080863 CCTAGGAGTTGGCTACAGTTGATT 60.081 45.833 1.05 0.00 0.00 2.57
48 49 5.128827 CCTAGGAGTTGGCTACAGTTGATTA 59.871 44.000 1.05 0.00 0.00 1.75
49 50 5.700402 AGGAGTTGGCTACAGTTGATTAT 57.300 39.130 1.24 0.00 0.00 1.28
50 51 5.431765 AGGAGTTGGCTACAGTTGATTATG 58.568 41.667 1.24 0.00 0.00 1.90
51 52 4.576463 GGAGTTGGCTACAGTTGATTATGG 59.424 45.833 1.24 0.00 0.00 2.74
52 53 5.179452 AGTTGGCTACAGTTGATTATGGT 57.821 39.130 1.24 0.00 0.00 3.55
53 54 5.570320 AGTTGGCTACAGTTGATTATGGTT 58.430 37.500 1.24 0.00 0.00 3.67
54 55 5.415701 AGTTGGCTACAGTTGATTATGGTTG 59.584 40.000 1.24 0.00 0.00 3.77
55 56 4.269183 TGGCTACAGTTGATTATGGTTGG 58.731 43.478 0.00 0.00 0.00 3.77
56 57 4.018870 TGGCTACAGTTGATTATGGTTGGA 60.019 41.667 0.00 0.00 0.00 3.53
57 58 5.133221 GGCTACAGTTGATTATGGTTGGAT 58.867 41.667 0.00 0.00 0.00 3.41
58 59 5.009010 GGCTACAGTTGATTATGGTTGGATG 59.991 44.000 0.00 0.00 0.00 3.51
59 60 4.989279 ACAGTTGATTATGGTTGGATGC 57.011 40.909 0.00 0.00 0.00 3.91
60 61 3.378112 ACAGTTGATTATGGTTGGATGCG 59.622 43.478 0.00 0.00 0.00 4.73
61 62 3.627123 CAGTTGATTATGGTTGGATGCGA 59.373 43.478 0.00 0.00 0.00 5.10
62 63 3.627577 AGTTGATTATGGTTGGATGCGAC 59.372 43.478 0.00 0.00 0.00 5.19
63 64 3.274095 TGATTATGGTTGGATGCGACA 57.726 42.857 6.95 0.00 0.00 4.35
64 65 3.615155 TGATTATGGTTGGATGCGACAA 58.385 40.909 6.95 0.00 0.00 3.18
65 66 3.627123 TGATTATGGTTGGATGCGACAAG 59.373 43.478 6.95 0.00 0.00 3.16
66 67 3.342377 TTATGGTTGGATGCGACAAGA 57.658 42.857 6.95 0.00 0.00 3.02
67 68 2.425143 ATGGTTGGATGCGACAAGAT 57.575 45.000 6.95 0.00 0.00 2.40
68 69 3.558931 ATGGTTGGATGCGACAAGATA 57.441 42.857 6.95 0.00 0.00 1.98
69 70 2.905075 TGGTTGGATGCGACAAGATAG 58.095 47.619 6.95 0.00 0.00 2.08
70 71 1.599542 GGTTGGATGCGACAAGATAGC 59.400 52.381 6.95 0.00 0.00 2.97
71 72 1.599542 GTTGGATGCGACAAGATAGCC 59.400 52.381 0.00 0.00 0.00 3.93
72 73 0.829990 TGGATGCGACAAGATAGCCA 59.170 50.000 0.00 0.00 0.00 4.75
73 74 1.417517 TGGATGCGACAAGATAGCCAT 59.582 47.619 0.00 0.00 0.00 4.40
74 75 2.072298 GGATGCGACAAGATAGCCATC 58.928 52.381 0.00 0.00 0.00 3.51
75 76 1.723542 GATGCGACAAGATAGCCATCG 59.276 52.381 0.00 0.00 36.20 3.84
77 78 2.136649 CGACAAGATAGCCATCGCG 58.863 57.895 0.00 0.00 41.18 5.87
78 79 0.595053 CGACAAGATAGCCATCGCGT 60.595 55.000 5.77 0.00 41.18 6.01
79 80 0.855349 GACAAGATAGCCATCGCGTG 59.145 55.000 5.77 3.64 41.18 5.34
80 81 1.154205 ACAAGATAGCCATCGCGTGC 61.154 55.000 5.77 8.03 41.18 5.34
81 82 1.595382 AAGATAGCCATCGCGTGCC 60.595 57.895 5.77 0.00 41.18 5.01
82 83 2.029666 GATAGCCATCGCGTGCCT 59.970 61.111 5.77 1.43 41.18 4.75
83 84 2.280389 ATAGCCATCGCGTGCCTG 60.280 61.111 5.77 0.00 41.18 4.85
84 85 2.699576 GATAGCCATCGCGTGCCTGA 62.700 60.000 5.77 0.00 41.18 3.86
85 86 2.310327 ATAGCCATCGCGTGCCTGAA 62.310 55.000 5.77 0.00 41.18 3.02
86 87 2.906182 TAGCCATCGCGTGCCTGAAG 62.906 60.000 5.77 0.00 41.18 3.02
87 88 3.869272 CCATCGCGTGCCTGAAGC 61.869 66.667 5.77 0.00 44.14 3.86
88 89 2.816958 CATCGCGTGCCTGAAGCT 60.817 61.111 5.77 0.00 44.23 3.74
89 90 2.816958 ATCGCGTGCCTGAAGCTG 60.817 61.111 5.77 0.00 44.23 4.24
106 107 2.328989 GCACGCGCATGCATATGT 59.671 55.556 25.28 6.89 45.39 2.29
107 108 2.007114 GCACGCGCATGCATATGTG 61.007 57.895 25.28 19.03 45.39 3.21
108 109 1.352753 CACGCGCATGCATATGTGT 59.647 52.632 19.57 11.02 44.68 3.72
109 110 4.199130 CGCGCATGCATATGTGTG 57.801 55.556 19.57 0.00 45.45 3.82
110 111 2.007114 CGCGCATGCATATGTGTGC 61.007 57.895 19.57 17.50 45.07 4.57
116 117 4.620437 GCATATGTGTGCGGCATG 57.380 55.556 5.72 0.00 35.10 4.06
117 118 1.659335 GCATATGTGTGCGGCATGC 60.659 57.895 9.90 9.90 46.70 4.06
132 133 2.344504 CATGCGTGCATTGGTTAACA 57.655 45.000 8.10 0.00 33.90 2.41
133 134 2.670479 CATGCGTGCATTGGTTAACAA 58.330 42.857 8.10 0.00 44.54 2.83
134 135 2.126914 TGCGTGCATTGGTTAACAAC 57.873 45.000 8.10 0.00 42.94 3.32
135 136 1.678627 TGCGTGCATTGGTTAACAACT 59.321 42.857 8.10 0.00 42.94 3.16
136 137 2.099921 TGCGTGCATTGGTTAACAACTT 59.900 40.909 8.10 0.00 42.94 2.66
137 138 2.724174 GCGTGCATTGGTTAACAACTTC 59.276 45.455 8.10 0.00 42.94 3.01
138 139 3.793801 GCGTGCATTGGTTAACAACTTCA 60.794 43.478 8.10 0.00 42.94 3.02
139 140 4.545610 CGTGCATTGGTTAACAACTTCAT 58.454 39.130 8.10 0.00 42.94 2.57
140 141 4.981674 CGTGCATTGGTTAACAACTTCATT 59.018 37.500 8.10 0.00 42.94 2.57
141 142 5.116983 CGTGCATTGGTTAACAACTTCATTC 59.883 40.000 8.10 0.00 42.94 2.67
142 143 5.405269 GTGCATTGGTTAACAACTTCATTCC 59.595 40.000 8.10 0.00 42.94 3.01
143 144 5.304101 TGCATTGGTTAACAACTTCATTCCT 59.696 36.000 8.10 0.00 42.94 3.36
144 145 5.863935 GCATTGGTTAACAACTTCATTCCTC 59.136 40.000 8.10 0.00 42.94 3.71
145 146 6.516527 GCATTGGTTAACAACTTCATTCCTCA 60.517 38.462 8.10 0.00 42.94 3.86
146 147 7.432869 CATTGGTTAACAACTTCATTCCTCAA 58.567 34.615 8.10 0.00 42.94 3.02
147 148 6.633500 TGGTTAACAACTTCATTCCTCAAG 57.367 37.500 8.10 0.00 0.00 3.02
148 149 5.009610 TGGTTAACAACTTCATTCCTCAAGC 59.990 40.000 8.10 0.00 0.00 4.01
149 150 3.904136 AACAACTTCATTCCTCAAGCG 57.096 42.857 0.00 0.00 0.00 4.68
150 151 2.851195 ACAACTTCATTCCTCAAGCGT 58.149 42.857 0.00 0.00 0.00 5.07
151 152 2.549754 ACAACTTCATTCCTCAAGCGTG 59.450 45.455 0.00 0.00 0.00 5.34
152 153 1.160137 ACTTCATTCCTCAAGCGTGC 58.840 50.000 0.00 0.00 0.00 5.34
165 166 5.163913 CCTCAAGCGTGCTAGCAATTATATC 60.164 44.000 21.29 3.88 40.15 1.63
170 171 5.707298 AGCGTGCTAGCAATTATATCCAAAT 59.293 36.000 21.29 0.00 40.15 2.32
205 206 7.606073 TGTATTTCAGTAATAAGCTTCTGCACA 59.394 33.333 0.00 4.22 42.74 4.57
207 208 6.668541 TTCAGTAATAAGCTTCTGCACATC 57.331 37.500 0.00 0.00 42.74 3.06
214 215 1.090052 GCTTCTGCACATCCCGTACC 61.090 60.000 0.00 0.00 39.41 3.34
215 216 0.462047 CTTCTGCACATCCCGTACCC 60.462 60.000 0.00 0.00 0.00 3.69
217 218 2.680707 TGCACATCCCGTACCCGA 60.681 61.111 0.00 0.00 35.63 5.14
218 219 2.233605 CTGCACATCCCGTACCCGAA 62.234 60.000 0.00 0.00 35.63 4.30
219 220 1.145377 GCACATCCCGTACCCGAAT 59.855 57.895 0.00 0.00 35.63 3.34
220 221 0.390124 GCACATCCCGTACCCGAATA 59.610 55.000 0.00 0.00 35.63 1.75
222 223 2.683968 CACATCCCGTACCCGAATATG 58.316 52.381 0.00 0.00 35.63 1.78
223 224 2.036733 CACATCCCGTACCCGAATATGT 59.963 50.000 0.00 0.00 35.63 2.29
224 225 2.701951 ACATCCCGTACCCGAATATGTT 59.298 45.455 0.00 0.00 35.63 2.71
225 226 3.896888 ACATCCCGTACCCGAATATGTTA 59.103 43.478 0.00 0.00 35.63 2.41
226 227 4.021719 ACATCCCGTACCCGAATATGTTAG 60.022 45.833 0.00 0.00 35.63 2.34
228 229 3.318839 TCCCGTACCCGAATATGTTAGTG 59.681 47.826 0.00 0.00 35.63 2.74
229 230 3.054878 CCGTACCCGAATATGTTAGTGC 58.945 50.000 0.00 0.00 35.63 4.40
230 231 3.243636 CCGTACCCGAATATGTTAGTGCT 60.244 47.826 0.00 0.00 35.63 4.40
231 232 4.022935 CCGTACCCGAATATGTTAGTGCTA 60.023 45.833 0.00 0.00 35.63 3.49
233 234 5.278169 CGTACCCGAATATGTTAGTGCTAGT 60.278 44.000 0.00 0.00 35.63 2.57
236 237 6.412214 ACCCGAATATGTTAGTGCTAGTTTT 58.588 36.000 0.00 0.00 0.00 2.43
237 238 6.315393 ACCCGAATATGTTAGTGCTAGTTTTG 59.685 38.462 0.00 0.00 0.00 2.44
238 239 6.238374 CCCGAATATGTTAGTGCTAGTTTTGG 60.238 42.308 0.00 0.00 0.00 3.28
241 242 7.254455 CGAATATGTTAGTGCTAGTTTTGGAGG 60.254 40.741 0.00 0.00 0.00 4.30
243 244 5.298989 TGTTAGTGCTAGTTTTGGAGGAA 57.701 39.130 0.00 0.00 0.00 3.36
244 245 5.686753 TGTTAGTGCTAGTTTTGGAGGAAA 58.313 37.500 0.00 0.00 0.00 3.13
4567 5039 4.737054 CTTTGATGGAAATTGGGAACTCG 58.263 43.478 0.00 0.00 0.00 4.18
4574 5046 0.899720 AATTGGGAACTCGGCGTAGA 59.100 50.000 6.85 0.00 0.00 2.59
4593 5065 5.750547 CGTAGAATCATGTGAGCAGTTATGT 59.249 40.000 0.00 0.00 0.00 2.29
4633 5105 4.721132 TCCCATTTTTCTAAAGTGACGGT 58.279 39.130 0.00 0.00 0.00 4.83
4661 5133 4.507710 TGCTCAGCCAGTAGAACTATTTG 58.492 43.478 0.00 0.00 0.00 2.32
4695 5167 6.603201 CAGGACATTTTACATAACCACCTCAT 59.397 38.462 0.00 0.00 0.00 2.90
4701 5173 2.985896 ACATAACCACCTCATTGACCG 58.014 47.619 0.00 0.00 0.00 4.79
4704 5176 1.056660 AACCACCTCATTGACCGTCT 58.943 50.000 0.00 0.00 0.00 4.18
4770 5242 0.036010 ATGGTCAGGAAACGAGCCAG 60.036 55.000 0.00 0.00 32.84 4.85
4821 5294 2.741228 GCTTCAGCTACCCTCTCATGTG 60.741 54.545 0.00 0.00 38.21 3.21
4880 5356 5.050490 TGGATTAGCTTTAATCGACAGAGC 58.950 41.667 0.00 3.82 37.33 4.09
4970 5495 5.339008 ACTTCTTCAGCGTATCCACAATA 57.661 39.130 0.00 0.00 0.00 1.90
4973 5498 4.933330 TCTTCAGCGTATCCACAATACTC 58.067 43.478 0.00 0.00 38.50 2.59
5008 5533 2.094854 GCTGCCTTGGATCACTGAAAAG 60.095 50.000 0.00 0.00 0.00 2.27
5026 5551 7.757624 ACTGAAAAGAAAGCAAAATCGTGTTAA 59.242 29.630 0.00 0.00 0.00 2.01
5063 5588 5.412526 TGTTTTAAACGTAGGCTGAACTG 57.587 39.130 0.00 0.00 0.00 3.16
5071 5596 2.804572 CGTAGGCTGAACTGATGGATGG 60.805 54.545 0.00 0.00 0.00 3.51
5102 5627 3.967332 AATTTTGATCAAGGTGGCTGG 57.033 42.857 8.41 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.670905 GTGTTTGGGTTCAGTTTGCAAC 59.329 45.455 0.00 0.00 0.00 4.17
1 2 2.672478 CGTGTTTGGGTTCAGTTTGCAA 60.672 45.455 0.00 0.00 0.00 4.08
2 3 1.135257 CGTGTTTGGGTTCAGTTTGCA 60.135 47.619 0.00 0.00 0.00 4.08
3 4 1.555477 CGTGTTTGGGTTCAGTTTGC 58.445 50.000 0.00 0.00 0.00 3.68
4 5 1.555477 GCGTGTTTGGGTTCAGTTTG 58.445 50.000 0.00 0.00 0.00 2.93
5 6 0.458260 GGCGTGTTTGGGTTCAGTTT 59.542 50.000 0.00 0.00 0.00 2.66
6 7 1.388837 GGGCGTGTTTGGGTTCAGTT 61.389 55.000 0.00 0.00 0.00 3.16
7 8 1.826487 GGGCGTGTTTGGGTTCAGT 60.826 57.895 0.00 0.00 0.00 3.41
8 9 0.250553 TAGGGCGTGTTTGGGTTCAG 60.251 55.000 0.00 0.00 0.00 3.02
9 10 0.250553 CTAGGGCGTGTTTGGGTTCA 60.251 55.000 0.00 0.00 0.00 3.18
10 11 0.958876 CCTAGGGCGTGTTTGGGTTC 60.959 60.000 0.00 0.00 0.00 3.62
11 12 1.074248 CCTAGGGCGTGTTTGGGTT 59.926 57.895 0.00 0.00 0.00 4.11
12 13 1.838073 CTCCTAGGGCGTGTTTGGGT 61.838 60.000 9.46 0.00 0.00 4.51
13 14 1.078426 CTCCTAGGGCGTGTTTGGG 60.078 63.158 9.46 0.00 0.00 4.12
14 15 0.036306 AACTCCTAGGGCGTGTTTGG 59.964 55.000 9.46 0.00 0.00 3.28
15 16 1.156736 CAACTCCTAGGGCGTGTTTG 58.843 55.000 9.46 0.23 0.00 2.93
16 17 0.036306 CCAACTCCTAGGGCGTGTTT 59.964 55.000 9.46 0.00 0.00 2.83
17 18 1.677552 CCAACTCCTAGGGCGTGTT 59.322 57.895 9.46 6.73 0.00 3.32
18 19 2.955881 GCCAACTCCTAGGGCGTGT 61.956 63.158 9.46 0.37 38.04 4.49
19 20 2.125106 GCCAACTCCTAGGGCGTG 60.125 66.667 9.46 4.28 38.04 5.34
23 24 1.867363 ACTGTAGCCAACTCCTAGGG 58.133 55.000 9.46 2.03 0.00 3.53
24 25 2.832129 TCAACTGTAGCCAACTCCTAGG 59.168 50.000 0.82 0.82 0.00 3.02
25 26 4.744795 ATCAACTGTAGCCAACTCCTAG 57.255 45.455 0.00 0.00 0.00 3.02
26 27 6.408092 CCATAATCAACTGTAGCCAACTCCTA 60.408 42.308 0.00 0.00 0.00 2.94
27 28 5.431765 CATAATCAACTGTAGCCAACTCCT 58.568 41.667 0.00 0.00 0.00 3.69
28 29 4.576463 CCATAATCAACTGTAGCCAACTCC 59.424 45.833 0.00 0.00 0.00 3.85
29 30 5.186198 ACCATAATCAACTGTAGCCAACTC 58.814 41.667 0.00 0.00 0.00 3.01
30 31 5.179452 ACCATAATCAACTGTAGCCAACT 57.821 39.130 0.00 0.00 0.00 3.16
31 32 5.393027 CCAACCATAATCAACTGTAGCCAAC 60.393 44.000 0.00 0.00 0.00 3.77
32 33 4.704540 CCAACCATAATCAACTGTAGCCAA 59.295 41.667 0.00 0.00 0.00 4.52
33 34 4.018870 TCCAACCATAATCAACTGTAGCCA 60.019 41.667 0.00 0.00 0.00 4.75
34 35 4.523083 TCCAACCATAATCAACTGTAGCC 58.477 43.478 0.00 0.00 0.00 3.93
35 36 5.506317 GCATCCAACCATAATCAACTGTAGC 60.506 44.000 0.00 0.00 0.00 3.58
36 37 5.277490 CGCATCCAACCATAATCAACTGTAG 60.277 44.000 0.00 0.00 0.00 2.74
37 38 4.574421 CGCATCCAACCATAATCAACTGTA 59.426 41.667 0.00 0.00 0.00 2.74
38 39 3.378112 CGCATCCAACCATAATCAACTGT 59.622 43.478 0.00 0.00 0.00 3.55
39 40 3.627123 TCGCATCCAACCATAATCAACTG 59.373 43.478 0.00 0.00 0.00 3.16
40 41 3.627577 GTCGCATCCAACCATAATCAACT 59.372 43.478 0.00 0.00 0.00 3.16
41 42 3.376859 TGTCGCATCCAACCATAATCAAC 59.623 43.478 0.00 0.00 0.00 3.18
42 43 3.615155 TGTCGCATCCAACCATAATCAA 58.385 40.909 0.00 0.00 0.00 2.57
43 44 3.274095 TGTCGCATCCAACCATAATCA 57.726 42.857 0.00 0.00 0.00 2.57
44 45 3.876914 TCTTGTCGCATCCAACCATAATC 59.123 43.478 0.00 0.00 0.00 1.75
45 46 3.884895 TCTTGTCGCATCCAACCATAAT 58.115 40.909 0.00 0.00 0.00 1.28
46 47 3.342377 TCTTGTCGCATCCAACCATAA 57.658 42.857 0.00 0.00 0.00 1.90
47 48 3.558931 ATCTTGTCGCATCCAACCATA 57.441 42.857 0.00 0.00 0.00 2.74
48 49 2.425143 ATCTTGTCGCATCCAACCAT 57.575 45.000 0.00 0.00 0.00 3.55
49 50 2.905075 CTATCTTGTCGCATCCAACCA 58.095 47.619 0.00 0.00 0.00 3.67
50 51 1.599542 GCTATCTTGTCGCATCCAACC 59.400 52.381 0.00 0.00 0.00 3.77
51 52 1.599542 GGCTATCTTGTCGCATCCAAC 59.400 52.381 0.00 0.00 0.00 3.77
52 53 1.209261 TGGCTATCTTGTCGCATCCAA 59.791 47.619 0.00 0.00 0.00 3.53
53 54 0.829990 TGGCTATCTTGTCGCATCCA 59.170 50.000 0.00 0.00 0.00 3.41
54 55 2.072298 GATGGCTATCTTGTCGCATCC 58.928 52.381 2.25 0.00 0.00 3.51
55 56 1.723542 CGATGGCTATCTTGTCGCATC 59.276 52.381 8.55 0.00 0.00 3.91
56 57 1.788258 CGATGGCTATCTTGTCGCAT 58.212 50.000 8.55 0.00 0.00 4.73
57 58 3.272766 CGATGGCTATCTTGTCGCA 57.727 52.632 8.55 0.00 0.00 5.10
59 60 0.595053 ACGCGATGGCTATCTTGTCG 60.595 55.000 15.93 8.50 36.88 4.35
60 61 0.855349 CACGCGATGGCTATCTTGTC 59.145 55.000 15.93 0.00 36.88 3.18
61 62 1.154205 GCACGCGATGGCTATCTTGT 61.154 55.000 15.93 3.55 36.88 3.16
62 63 1.566563 GCACGCGATGGCTATCTTG 59.433 57.895 15.93 0.00 36.88 3.02
63 64 4.033894 GCACGCGATGGCTATCTT 57.966 55.556 15.93 0.00 36.88 2.40
70 71 3.869272 GCTTCAGGCACGCGATGG 61.869 66.667 15.93 2.40 41.35 3.51
71 72 2.816958 AGCTTCAGGCACGCGATG 60.817 61.111 15.93 8.90 44.79 3.84
72 73 2.816958 CAGCTTCAGGCACGCGAT 60.817 61.111 15.93 0.00 44.79 4.58
89 90 2.007114 CACATATGCATGCGCGTGC 61.007 57.895 40.52 40.52 45.25 5.34
90 91 0.926628 CACACATATGCATGCGCGTG 60.927 55.000 25.25 25.25 42.97 5.34
91 92 1.352753 CACACATATGCATGCGCGT 59.647 52.632 14.09 0.00 42.97 6.01
92 93 2.007114 GCACACATATGCATGCGCG 61.007 57.895 14.09 0.00 45.39 6.86
93 94 3.912157 GCACACATATGCATGCGC 58.088 55.556 14.09 0.00 45.39 6.09
95 96 1.659335 GCCGCACACATATGCATGC 60.659 57.895 11.82 11.82 46.47 4.06
96 97 0.312729 ATGCCGCACACATATGCATG 59.687 50.000 10.16 2.43 46.47 4.06
97 98 0.312729 CATGCCGCACACATATGCAT 59.687 50.000 3.79 3.79 46.47 3.96
98 99 1.728672 CATGCCGCACACATATGCA 59.271 52.632 1.58 0.00 46.47 3.96
99 100 1.659335 GCATGCCGCACACATATGC 60.659 57.895 6.36 0.00 41.79 3.14
100 101 1.369568 CGCATGCCGCACACATATG 60.370 57.895 13.15 0.00 42.60 1.78
101 102 1.819208 ACGCATGCCGCACACATAT 60.819 52.632 13.15 0.00 42.60 1.78
102 103 2.435762 ACGCATGCCGCACACATA 60.436 55.556 13.15 0.00 42.60 2.29
103 104 4.105733 CACGCATGCCGCACACAT 62.106 61.111 13.15 0.00 42.60 3.21
113 114 2.344504 TGTTAACCAATGCACGCATG 57.655 45.000 5.06 0.00 36.68 4.06
114 115 2.295909 AGTTGTTAACCAATGCACGCAT 59.704 40.909 2.48 0.00 38.46 4.73
115 116 1.678627 AGTTGTTAACCAATGCACGCA 59.321 42.857 2.48 0.00 35.02 5.24
116 117 2.415697 AGTTGTTAACCAATGCACGC 57.584 45.000 2.48 0.00 35.02 5.34
117 118 3.958704 TGAAGTTGTTAACCAATGCACG 58.041 40.909 2.48 0.00 35.02 5.34
118 119 5.405269 GGAATGAAGTTGTTAACCAATGCAC 59.595 40.000 2.48 0.00 35.02 4.57
119 120 5.304101 AGGAATGAAGTTGTTAACCAATGCA 59.696 36.000 2.48 0.00 35.02 3.96
120 121 5.783111 AGGAATGAAGTTGTTAACCAATGC 58.217 37.500 2.48 0.00 35.02 3.56
121 122 6.980593 TGAGGAATGAAGTTGTTAACCAATG 58.019 36.000 2.48 0.00 35.02 2.82
122 123 7.595819 TTGAGGAATGAAGTTGTTAACCAAT 57.404 32.000 2.48 0.00 35.02 3.16
123 124 6.460953 GCTTGAGGAATGAAGTTGTTAACCAA 60.461 38.462 2.48 0.00 0.00 3.67
124 125 5.009610 GCTTGAGGAATGAAGTTGTTAACCA 59.990 40.000 2.48 0.00 0.00 3.67
125 126 5.461526 GCTTGAGGAATGAAGTTGTTAACC 58.538 41.667 2.48 0.00 0.00 2.85
126 127 5.147162 CGCTTGAGGAATGAAGTTGTTAAC 58.853 41.667 0.00 0.00 0.00 2.01
127 128 4.819630 ACGCTTGAGGAATGAAGTTGTTAA 59.180 37.500 0.00 0.00 0.00 2.01
128 129 4.213270 CACGCTTGAGGAATGAAGTTGTTA 59.787 41.667 0.00 0.00 0.00 2.41
129 130 3.003689 CACGCTTGAGGAATGAAGTTGTT 59.996 43.478 0.00 0.00 0.00 2.83
130 131 2.549754 CACGCTTGAGGAATGAAGTTGT 59.450 45.455 0.00 0.00 0.00 3.32
131 132 2.666619 GCACGCTTGAGGAATGAAGTTG 60.667 50.000 0.00 0.00 0.00 3.16
132 133 1.537202 GCACGCTTGAGGAATGAAGTT 59.463 47.619 0.00 0.00 0.00 2.66
133 134 1.160137 GCACGCTTGAGGAATGAAGT 58.840 50.000 0.00 0.00 0.00 3.01
134 135 1.446907 AGCACGCTTGAGGAATGAAG 58.553 50.000 0.00 0.00 0.00 3.02
135 136 2.621338 CTAGCACGCTTGAGGAATGAA 58.379 47.619 0.00 0.00 0.00 2.57
136 137 1.740380 GCTAGCACGCTTGAGGAATGA 60.740 52.381 10.63 0.00 0.00 2.57
137 138 0.654683 GCTAGCACGCTTGAGGAATG 59.345 55.000 10.63 0.00 0.00 2.67
138 139 0.250234 TGCTAGCACGCTTGAGGAAT 59.750 50.000 14.93 0.00 0.00 3.01
139 140 0.034756 TTGCTAGCACGCTTGAGGAA 59.965 50.000 19.17 0.00 0.00 3.36
140 141 0.250234 ATTGCTAGCACGCTTGAGGA 59.750 50.000 19.17 0.00 0.00 3.71
141 142 1.089920 AATTGCTAGCACGCTTGAGG 58.910 50.000 19.17 0.00 0.00 3.86
142 143 5.163913 GGATATAATTGCTAGCACGCTTGAG 60.164 44.000 19.17 0.00 0.00 3.02
143 144 4.690748 GGATATAATTGCTAGCACGCTTGA 59.309 41.667 19.17 1.05 0.00 3.02
144 145 4.452114 TGGATATAATTGCTAGCACGCTTG 59.548 41.667 19.17 0.00 0.00 4.01
145 146 4.641396 TGGATATAATTGCTAGCACGCTT 58.359 39.130 19.17 13.63 0.00 4.68
146 147 4.271696 TGGATATAATTGCTAGCACGCT 57.728 40.909 19.17 7.28 0.00 5.07
147 148 5.356882 TTTGGATATAATTGCTAGCACGC 57.643 39.130 19.17 1.65 0.00 5.34
180 181 7.974675 TGTGCAGAAGCTTATTACTGAAATAC 58.025 34.615 15.12 8.96 42.74 1.89
185 186 5.118990 GGATGTGCAGAAGCTTATTACTGA 58.881 41.667 15.12 0.00 42.74 3.41
199 200 2.202878 CGGGTACGGGATGTGCAG 60.203 66.667 0.00 0.00 34.44 4.41
205 206 4.021719 CACTAACATATTCGGGTACGGGAT 60.022 45.833 0.00 0.00 41.39 3.85
207 208 3.645884 CACTAACATATTCGGGTACGGG 58.354 50.000 0.00 0.00 41.39 5.28
214 215 6.537301 TCCAAAACTAGCACTAACATATTCGG 59.463 38.462 0.00 0.00 0.00 4.30
215 216 7.254455 CCTCCAAAACTAGCACTAACATATTCG 60.254 40.741 0.00 0.00 0.00 3.34
217 218 7.630082 TCCTCCAAAACTAGCACTAACATATT 58.370 34.615 0.00 0.00 0.00 1.28
218 219 7.195374 TCCTCCAAAACTAGCACTAACATAT 57.805 36.000 0.00 0.00 0.00 1.78
219 220 6.614694 TCCTCCAAAACTAGCACTAACATA 57.385 37.500 0.00 0.00 0.00 2.29
220 221 5.499004 TCCTCCAAAACTAGCACTAACAT 57.501 39.130 0.00 0.00 0.00 2.71
222 223 5.529800 TGTTTCCTCCAAAACTAGCACTAAC 59.470 40.000 0.00 0.00 39.39 2.34
223 224 5.686753 TGTTTCCTCCAAAACTAGCACTAA 58.313 37.500 0.00 0.00 39.39 2.24
224 225 5.298989 TGTTTCCTCCAAAACTAGCACTA 57.701 39.130 0.00 0.00 39.39 2.74
225 226 4.164843 TGTTTCCTCCAAAACTAGCACT 57.835 40.909 0.00 0.00 39.39 4.40
226 227 4.097286 TGTTGTTTCCTCCAAAACTAGCAC 59.903 41.667 0.00 0.00 39.39 4.40
228 229 4.911514 TGTTGTTTCCTCCAAAACTAGC 57.088 40.909 0.00 0.00 39.39 3.42
229 230 5.270853 CGTTGTTGTTTCCTCCAAAACTAG 58.729 41.667 0.00 0.00 39.39 2.57
230 231 4.096682 CCGTTGTTGTTTCCTCCAAAACTA 59.903 41.667 1.73 0.00 39.39 2.24
231 232 3.119280 CCGTTGTTGTTTCCTCCAAAACT 60.119 43.478 1.73 0.00 39.39 2.66
233 234 2.166664 CCCGTTGTTGTTTCCTCCAAAA 59.833 45.455 0.00 0.00 0.00 2.44
236 237 0.466555 CCCCGTTGTTGTTTCCTCCA 60.467 55.000 0.00 0.00 0.00 3.86
237 238 1.176619 CCCCCGTTGTTGTTTCCTCC 61.177 60.000 0.00 0.00 0.00 4.30
238 239 0.466739 ACCCCCGTTGTTGTTTCCTC 60.467 55.000 0.00 0.00 0.00 3.71
241 242 1.605232 CTACACCCCCGTTGTTGTTTC 59.395 52.381 0.00 0.00 0.00 2.78
243 244 0.820482 GCTACACCCCCGTTGTTGTT 60.820 55.000 0.00 0.00 0.00 2.83
244 245 1.228033 GCTACACCCCCGTTGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
4567 5039 1.863454 CTGCTCACATGATTCTACGCC 59.137 52.381 0.00 0.00 0.00 5.68
4574 5046 6.579666 ACAAACATAACTGCTCACATGATT 57.420 33.333 0.00 0.00 0.00 2.57
4633 5105 2.110578 TCTACTGGCTGAGCAATAGCA 58.889 47.619 6.82 0.00 45.49 3.49
4661 5133 5.957842 TGTAAAATGTCCTGAATGTGTCC 57.042 39.130 0.00 0.00 0.00 4.02
4695 5167 4.537135 ATTCAAAGCTCTAGACGGTCAA 57.463 40.909 11.27 0.00 0.00 3.18
4701 5173 6.976636 AGCTACAAATTCAAAGCTCTAGAC 57.023 37.500 3.29 0.00 41.35 2.59
4730 5202 6.437162 ACCATTCATGTTGCCTTTGTATAGTT 59.563 34.615 0.00 0.00 0.00 2.24
4739 5211 2.173519 CCTGACCATTCATGTTGCCTT 58.826 47.619 0.00 0.00 0.00 4.35
4742 5214 3.578688 GTTTCCTGACCATTCATGTTGC 58.421 45.455 0.00 0.00 0.00 4.17
4840 5313 7.127339 AGCTAATCCACAAGAAGGAATAAGGTA 59.873 37.037 0.00 0.00 38.93 3.08
4853 5329 6.535150 TCTGTCGATTAAAGCTAATCCACAAG 59.465 38.462 9.87 5.96 41.87 3.16
4880 5356 2.351726 CCGGCCATTCTTTTTCTCTACG 59.648 50.000 2.24 0.00 0.00 3.51
4973 5498 2.173382 CAGCGCCCTTCGTTTTCG 59.827 61.111 2.29 0.00 45.64 3.46
5008 5533 3.972502 AGCGTTAACACGATTTTGCTTTC 59.027 39.130 6.39 0.00 44.36 2.62
5026 5551 7.806014 ACGTTTAAAACAAAATATCATCAGCGT 59.194 29.630 0.00 0.00 0.00 5.07
5063 5588 1.737838 TTCAAGTGACGCCATCCATC 58.262 50.000 0.00 0.00 0.00 3.51
5071 5596 5.117592 CCTTGATCAAAATTTCAAGTGACGC 59.882 40.000 9.88 2.66 44.70 5.19
5102 5627 1.551883 AGCAAATTTCCCATGACCTGC 59.448 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.