Multiple sequence alignment - TraesCS3B01G029600

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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 TraesCS3B01G029600 chr3B 100.000 2870 0 0 1 2870 13509569 13512438 0.000000e+00 5301
1 TraesCS3B01G029600 chr3B 95.965 2602 72 8 196 2781 13528782 13531366 0.000000e+00 4193
2 TraesCS3B01G029600 chr3B 94.911 1749 68 11 605 2335 726424352 726426097 0.000000e+00 2717
3 TraesCS3B01G029600 chr3B 91.121 687 39 5 604 1275 575259575 575260254 0.000000e+00 911
4 TraesCS3B01G029600 chr3B 97.191 534 15 0 2336 2869 761348906 761349439 0.000000e+00 904
5 TraesCS3B01G029600 chr3B 97.009 535 16 0 2336 2870 808790139 808789605 0.000000e+00 900
6 TraesCS3B01G029600 chr3B 96.822 535 17 0 2336 2870 771565277 771565811 0.000000e+00 894
7 TraesCS3B01G029600 chr3B 96.654 538 18 0 2333 2870 813988119 813988656 0.000000e+00 894
8 TraesCS3B01G029600 chr1B 96.613 1742 47 5 604 2335 539849943 539848204 0.000000e+00 2880
9 TraesCS3B01G029600 chr1B 89.936 1560 119 11 606 2145 548830933 548829392 0.000000e+00 1977
10 TraesCS3B01G029600 chr5D 92.066 1752 94 12 604 2335 388593172 388594898 0.000000e+00 2423
11 TraesCS3B01G029600 chr7D 92.030 1744 106 16 606 2335 525733739 525735463 0.000000e+00 2420
12 TraesCS3B01G029600 chr2B 91.205 1751 110 13 605 2335 80552660 80550934 0.000000e+00 2340
13 TraesCS3B01G029600 chr1A 90.365 1754 111 27 604 2335 572001397 571999680 0.000000e+00 2250
14 TraesCS3B01G029600 chr2A 90.234 1751 115 22 602 2335 38507335 38505624 0.000000e+00 2235
15 TraesCS3B01G029600 chr6A 89.675 1753 125 26 605 2335 116690038 116691756 0.000000e+00 2183
16 TraesCS3B01G029600 chr6D 89.493 828 58 8 603 1415 45675920 45676733 0.000000e+00 1020
17 TraesCS3B01G029600 chr6B 97.575 536 13 0 2335 2870 14262141 14262676 0.000000e+00 918
18 TraesCS3B01G029600 chr6B 97.196 535 15 0 2336 2870 659286999 659287533 0.000000e+00 905
19 TraesCS3B01G029600 chr5B 96.828 536 17 0 2335 2870 697365669 697365134 0.000000e+00 896
20 TraesCS3B01G029600 chr7B 96.822 535 17 0 2336 2870 694450938 694451472 0.000000e+00 894
21 TraesCS3B01G029600 chr3A 84.719 445 28 19 196 607 700365809 700365372 2.660000e-110 409
22 TraesCS3B01G029600 chr3D 80.930 215 16 5 1 196 5222097 5221889 2.300000e-31 147
23 TraesCS3B01G029600 chr3D 90.000 110 11 0 1 110 9420055 9420164 2.980000e-30 143
24 TraesCS3B01G029600 chrUn 92.105 76 6 0 121 196 36508180 36508105 1.090000e-19 108


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 TraesCS3B01G029600 chr3B 13509569 13512438 2869 False 5301 5301 100.000 1 2870 1 chr3B.!!$F1 2869
1 TraesCS3B01G029600 chr3B 13528782 13531366 2584 False 4193 4193 95.965 196 2781 1 chr3B.!!$F2 2585
2 TraesCS3B01G029600 chr3B 726424352 726426097 1745 False 2717 2717 94.911 605 2335 1 chr3B.!!$F4 1730
3 TraesCS3B01G029600 chr3B 575259575 575260254 679 False 911 911 91.121 604 1275 1 chr3B.!!$F3 671
4 TraesCS3B01G029600 chr3B 761348906 761349439 533 False 904 904 97.191 2336 2869 1 chr3B.!!$F5 533
5 TraesCS3B01G029600 chr3B 808789605 808790139 534 True 900 900 97.009 2336 2870 1 chr3B.!!$R1 534
6 TraesCS3B01G029600 chr3B 771565277 771565811 534 False 894 894 96.822 2336 2870 1 chr3B.!!$F6 534
7 TraesCS3B01G029600 chr3B 813988119 813988656 537 False 894 894 96.654 2333 2870 1 chr3B.!!$F7 537
8 TraesCS3B01G029600 chr1B 539848204 539849943 1739 True 2880 2880 96.613 604 2335 1 chr1B.!!$R1 1731
9 TraesCS3B01G029600 chr1B 548829392 548830933 1541 True 1977 1977 89.936 606 2145 1 chr1B.!!$R2 1539
10 TraesCS3B01G029600 chr5D 388593172 388594898 1726 False 2423 2423 92.066 604 2335 1 chr5D.!!$F1 1731
11 TraesCS3B01G029600 chr7D 525733739 525735463 1724 False 2420 2420 92.030 606 2335 1 chr7D.!!$F1 1729
12 TraesCS3B01G029600 chr2B 80550934 80552660 1726 True 2340 2340 91.205 605 2335 1 chr2B.!!$R1 1730
13 TraesCS3B01G029600 chr1A 571999680 572001397 1717 True 2250 2250 90.365 604 2335 1 chr1A.!!$R1 1731
14 TraesCS3B01G029600 chr2A 38505624 38507335 1711 True 2235 2235 90.234 602 2335 1 chr2A.!!$R1 1733
15 TraesCS3B01G029600 chr6A 116690038 116691756 1718 False 2183 2183 89.675 605 2335 1 chr6A.!!$F1 1730
16 TraesCS3B01G029600 chr6D 45675920 45676733 813 False 1020 1020 89.493 603 1415 1 chr6D.!!$F1 812
17 TraesCS3B01G029600 chr6B 14262141 14262676 535 False 918 918 97.575 2335 2870 1 chr6B.!!$F1 535
18 TraesCS3B01G029600 chr6B 659286999 659287533 534 False 905 905 97.196 2336 2870 1 chr6B.!!$F2 534
19 TraesCS3B01G029600 chr5B 697365134 697365669 535 True 896 896 96.828 2335 2870 1 chr5B.!!$R1 535
20 TraesCS3B01G029600 chr7B 694450938 694451472 534 False 894 894 96.822 2336 2870 1 chr7B.!!$F1 534

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
161 162 0.106868 TAGCACGACTGGCTAGGCTA 60.107 55.0 18.18 1.37 42.62 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 1994 1.059098 TCTTTGCCTGCTCCTCAAGA 58.941 50.0 0.0 0.0 0.0 3.02 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
27 28 4.659172 CACTTGCTTCCCGGCCCA 62.659 66.667 0.00 0.00 0.00 5.36
28 29 3.661648 ACTTGCTTCCCGGCCCAT 61.662 61.111 0.00 0.00 0.00 4.00
29 30 3.142838 CTTGCTTCCCGGCCCATG 61.143 66.667 0.00 0.00 0.00 3.66
30 31 3.944250 CTTGCTTCCCGGCCCATGT 62.944 63.158 0.00 0.00 0.00 3.21
31 32 4.738998 TGCTTCCCGGCCCATGTG 62.739 66.667 0.00 0.00 0.00 3.21
33 34 4.738998 CTTCCCGGCCCATGTGCA 62.739 66.667 1.71 0.00 0.00 4.57
34 35 4.059304 TTCCCGGCCCATGTGCAT 62.059 61.111 1.71 0.00 0.00 3.96
35 36 3.598747 TTCCCGGCCCATGTGCATT 62.599 57.895 1.71 0.00 0.00 3.56
36 37 3.840594 CCCGGCCCATGTGCATTG 61.841 66.667 1.71 0.00 0.00 2.82
37 38 4.517815 CCGGCCCATGTGCATTGC 62.518 66.667 1.71 0.46 0.00 3.56
38 39 4.858433 CGGCCCATGTGCATTGCG 62.858 66.667 1.71 0.00 0.00 4.85
39 40 3.451004 GGCCCATGTGCATTGCGA 61.451 61.111 1.71 0.00 0.00 5.10
40 41 2.788640 GGCCCATGTGCATTGCGAT 61.789 57.895 1.71 0.00 0.00 4.58
41 42 1.590525 GCCCATGTGCATTGCGATG 60.591 57.895 9.80 9.80 36.32 3.84
49 50 4.557605 CATTGCGATGCCACGGCC 62.558 66.667 5.42 0.00 41.09 6.13
65 66 3.697747 CCGCCCAGTCAACCCGTA 61.698 66.667 0.00 0.00 0.00 4.02
66 67 2.433664 CGCCCAGTCAACCCGTAC 60.434 66.667 0.00 0.00 0.00 3.67
67 68 2.939261 CGCCCAGTCAACCCGTACT 61.939 63.158 0.00 0.00 0.00 2.73
68 69 1.375523 GCCCAGTCAACCCGTACTG 60.376 63.158 0.00 0.00 42.25 2.74
70 71 4.278956 CAGTCAACCCGTACTGGC 57.721 61.111 2.78 0.00 39.55 4.85
71 72 1.369692 CAGTCAACCCGTACTGGCA 59.630 57.895 2.78 0.00 39.55 4.92
72 73 0.949105 CAGTCAACCCGTACTGGCAC 60.949 60.000 2.78 0.00 39.55 5.01
73 74 1.670083 GTCAACCCGTACTGGCACC 60.670 63.158 2.78 0.00 35.87 5.01
74 75 2.740826 CAACCCGTACTGGCACCG 60.741 66.667 2.78 0.00 35.87 4.94
75 76 4.011517 AACCCGTACTGGCACCGG 62.012 66.667 0.00 0.00 41.37 5.28
80 81 4.016706 GTACTGGCACCGGCACCT 62.017 66.667 14.06 0.00 43.71 4.00
81 82 3.702048 TACTGGCACCGGCACCTC 61.702 66.667 14.06 0.00 43.71 3.85
120 121 4.227134 CGCCATGGCCGTCTAGCT 62.227 66.667 30.79 0.00 37.98 3.32
121 122 2.856628 CGCCATGGCCGTCTAGCTA 61.857 63.158 30.79 0.00 37.98 3.32
122 123 1.005630 GCCATGGCCGTCTAGCTAG 60.006 63.158 27.24 15.01 34.56 3.42
123 124 1.668294 CCATGGCCGTCTAGCTAGG 59.332 63.158 20.58 7.03 0.00 3.02
124 125 0.827925 CCATGGCCGTCTAGCTAGGA 60.828 60.000 20.58 4.94 0.00 2.94
125 126 0.600557 CATGGCCGTCTAGCTAGGAG 59.399 60.000 20.58 13.92 0.00 3.69
126 127 0.540830 ATGGCCGTCTAGCTAGGAGG 60.541 60.000 20.58 21.96 0.00 4.30
127 128 1.150992 GGCCGTCTAGCTAGGAGGA 59.849 63.158 28.13 7.76 0.00 3.71
128 129 1.174078 GGCCGTCTAGCTAGGAGGAC 61.174 65.000 28.13 24.50 0.00 3.85
129 130 0.179012 GCCGTCTAGCTAGGAGGACT 60.179 60.000 28.13 0.00 0.00 3.85
130 131 1.600023 CCGTCTAGCTAGGAGGACTG 58.400 60.000 22.85 8.25 0.00 3.51
131 132 1.600023 CGTCTAGCTAGGAGGACTGG 58.400 60.000 20.58 0.00 0.00 4.00
132 133 1.816183 CGTCTAGCTAGGAGGACTGGG 60.816 61.905 20.58 0.00 0.00 4.45
133 134 0.186386 TCTAGCTAGGAGGACTGGGC 59.814 60.000 20.58 0.00 0.00 5.36
134 135 1.152735 TAGCTAGGAGGACTGGGCG 60.153 63.158 0.00 0.00 35.43 6.13
135 136 4.228567 GCTAGGAGGACTGGGCGC 62.229 72.222 0.00 0.00 0.00 6.53
136 137 2.759973 CTAGGAGGACTGGGCGCA 60.760 66.667 10.83 2.47 0.00 6.09
137 138 2.759973 TAGGAGGACTGGGCGCAG 60.760 66.667 27.57 27.57 0.00 5.18
138 139 3.296842 TAGGAGGACTGGGCGCAGA 62.297 63.158 34.63 9.82 0.00 4.26
139 140 2.589610 TAGGAGGACTGGGCGCAGAT 62.590 60.000 34.63 20.23 0.00 2.90
140 141 2.202987 GAGGACTGGGCGCAGATG 60.203 66.667 34.63 12.25 0.00 2.90
141 142 4.479993 AGGACTGGGCGCAGATGC 62.480 66.667 34.63 22.84 37.78 3.91
142 143 4.479993 GGACTGGGCGCAGATGCT 62.480 66.667 34.63 14.41 39.32 3.79
143 144 2.501128 GACTGGGCGCAGATGCTA 59.499 61.111 34.63 0.00 39.32 3.49
144 145 1.593750 GACTGGGCGCAGATGCTAG 60.594 63.158 34.63 9.98 39.32 3.42
145 146 2.971413 CTGGGCGCAGATGCTAGC 60.971 66.667 25.55 8.10 39.32 3.42
146 147 3.745240 CTGGGCGCAGATGCTAGCA 62.745 63.158 25.55 21.85 39.32 3.49
147 148 3.275338 GGGCGCAGATGCTAGCAC 61.275 66.667 22.07 14.04 39.32 4.40
148 149 3.634072 GGCGCAGATGCTAGCACG 61.634 66.667 22.07 19.72 39.32 5.34
149 150 2.583319 GCGCAGATGCTAGCACGA 60.583 61.111 22.07 0.00 39.32 4.35
150 151 2.864931 GCGCAGATGCTAGCACGAC 61.865 63.158 22.07 14.41 39.32 4.34
151 152 1.226802 CGCAGATGCTAGCACGACT 60.227 57.895 22.07 16.48 39.32 4.18
152 153 1.477826 CGCAGATGCTAGCACGACTG 61.478 60.000 28.52 28.52 39.32 3.51
153 154 1.150567 GCAGATGCTAGCACGACTGG 61.151 60.000 30.97 20.64 38.21 4.00
159 160 3.207354 TAGCACGACTGGCTAGGC 58.793 61.111 9.85 9.85 42.62 3.93
160 161 1.379977 TAGCACGACTGGCTAGGCT 60.380 57.895 18.18 2.42 42.62 4.58
161 162 0.106868 TAGCACGACTGGCTAGGCTA 60.107 55.000 18.18 1.37 42.62 3.93
162 163 1.066587 GCACGACTGGCTAGGCTAG 59.933 63.158 17.33 17.33 42.85 3.42
163 164 1.736586 CACGACTGGCTAGGCTAGG 59.263 63.158 22.40 8.99 41.48 3.02
164 165 1.038130 CACGACTGGCTAGGCTAGGT 61.038 60.000 22.40 12.13 41.48 3.08
165 166 0.549950 ACGACTGGCTAGGCTAGGTA 59.450 55.000 22.40 0.00 41.48 3.08
166 167 1.240256 CGACTGGCTAGGCTAGGTAG 58.760 60.000 22.40 8.39 41.48 3.18
167 168 1.623163 GACTGGCTAGGCTAGGTAGG 58.377 60.000 22.40 0.00 41.48 3.18
168 169 0.935194 ACTGGCTAGGCTAGGTAGGT 59.065 55.000 22.40 2.57 41.48 3.08
169 170 2.107901 GACTGGCTAGGCTAGGTAGGTA 59.892 54.545 22.40 0.00 41.48 3.08
170 171 2.108601 ACTGGCTAGGCTAGGTAGGTAG 59.891 54.545 22.40 5.45 41.48 3.18
171 172 2.375845 CTGGCTAGGCTAGGTAGGTAGA 59.624 54.545 22.40 0.00 33.47 2.59
172 173 2.994581 TGGCTAGGCTAGGTAGGTAGAT 59.005 50.000 22.40 0.00 0.00 1.98
173 174 3.245300 TGGCTAGGCTAGGTAGGTAGATG 60.245 52.174 22.40 0.00 0.00 2.90
174 175 3.358118 GCTAGGCTAGGTAGGTAGATGG 58.642 54.545 22.40 0.00 0.00 3.51
175 176 3.010361 GCTAGGCTAGGTAGGTAGATGGA 59.990 52.174 22.40 0.00 0.00 3.41
176 177 4.508763 GCTAGGCTAGGTAGGTAGATGGAA 60.509 50.000 22.40 0.00 0.00 3.53
177 178 4.768807 AGGCTAGGTAGGTAGATGGAAT 57.231 45.455 0.00 0.00 0.00 3.01
178 179 5.880279 AGGCTAGGTAGGTAGATGGAATA 57.120 43.478 0.00 0.00 0.00 1.75
179 180 5.833340 AGGCTAGGTAGGTAGATGGAATAG 58.167 45.833 0.00 0.00 0.00 1.73
180 181 5.316453 AGGCTAGGTAGGTAGATGGAATAGT 59.684 44.000 0.00 0.00 0.00 2.12
181 182 5.419471 GGCTAGGTAGGTAGATGGAATAGTG 59.581 48.000 0.00 0.00 0.00 2.74
182 183 5.105675 GCTAGGTAGGTAGATGGAATAGTGC 60.106 48.000 0.00 0.00 0.00 4.40
183 184 4.816126 AGGTAGGTAGATGGAATAGTGCA 58.184 43.478 0.00 0.00 0.00 4.57
184 185 4.835615 AGGTAGGTAGATGGAATAGTGCAG 59.164 45.833 0.00 0.00 0.00 4.41
185 186 4.021016 GGTAGGTAGATGGAATAGTGCAGG 60.021 50.000 0.00 0.00 0.00 4.85
186 187 2.370189 AGGTAGATGGAATAGTGCAGGC 59.630 50.000 0.00 0.00 0.00 4.85
187 188 2.104792 GGTAGATGGAATAGTGCAGGCA 59.895 50.000 0.00 0.00 0.00 4.75
188 189 3.244700 GGTAGATGGAATAGTGCAGGCAT 60.245 47.826 0.00 0.00 0.00 4.40
189 190 4.020218 GGTAGATGGAATAGTGCAGGCATA 60.020 45.833 0.00 0.00 0.00 3.14
190 191 4.923516 AGATGGAATAGTGCAGGCATAT 57.076 40.909 0.00 0.00 0.00 1.78
191 192 6.127054 GGTAGATGGAATAGTGCAGGCATATA 60.127 42.308 0.00 0.00 0.00 0.86
192 193 6.572182 AGATGGAATAGTGCAGGCATATAT 57.428 37.500 0.00 0.00 0.00 0.86
193 194 7.681259 AGATGGAATAGTGCAGGCATATATA 57.319 36.000 0.00 0.00 0.00 0.86
194 195 7.733969 AGATGGAATAGTGCAGGCATATATAG 58.266 38.462 0.00 0.00 0.00 1.31
204 205 6.934645 GTGCAGGCATATATAGAAACCAAGTA 59.065 38.462 0.00 0.00 0.00 2.24
357 358 1.744368 AGCGCATCTGGAGCAGTTG 60.744 57.895 11.47 0.00 45.74 3.16
360 361 3.392595 GCATCTGGAGCAGTTGCGC 62.393 63.158 0.00 0.00 43.84 6.09
491 492 4.814294 GAAGACGTCCGGGCGCAT 62.814 66.667 31.52 15.34 34.88 4.73
782 783 2.933287 ATCTGGCCCACCGGTCAA 60.933 61.111 2.59 0.00 45.31 3.18
889 898 2.574399 GGCTCGCTCGTCTTCCTT 59.426 61.111 0.00 0.00 0.00 3.36
939 957 1.615883 TCACTCACTCTGTTCCTCTGC 59.384 52.381 0.00 0.00 0.00 4.26
969 987 4.384056 TCTCCACTGCTTCTTTTCTTCTG 58.616 43.478 0.00 0.00 0.00 3.02
1181 1228 6.844388 AGTTCATATATGGGAGGTGTAGTTGA 59.156 38.462 12.78 0.00 0.00 3.18
1182 1229 7.514127 AGTTCATATATGGGAGGTGTAGTTGAT 59.486 37.037 12.78 0.00 0.00 2.57
1630 1682 9.474313 TGAAGAATAAAGCCCACTGTAAATTAT 57.526 29.630 0.00 0.00 0.00 1.28
1734 1787 4.573900 CCAAGCTCTGGGATATGTATCAC 58.426 47.826 6.96 0.00 42.17 3.06
1794 1847 7.201866 GCTCATGAGATAGAGGTTGAGAAACTA 60.202 40.741 27.04 0.00 34.00 2.24
1806 1859 6.270231 AGGTTGAGAAACTAAAGAAGGAGCTA 59.730 38.462 0.00 0.00 0.00 3.32
1941 1994 6.715280 TGAACTTAAGGAGAAGAAGCATCAT 58.285 36.000 7.53 0.00 0.00 2.45
1964 2017 1.101331 GAGGAGCAGGCAAAGATTGG 58.899 55.000 0.00 0.00 0.00 3.16
1979 2032 4.614967 AGATTGGGGTTCAAATGGAGAT 57.385 40.909 0.00 0.00 39.05 2.75
2137 2192 4.162888 TCATTGCTGATCTCTTGAAGGCTA 59.837 41.667 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.944250 ATGGGCCGGGAAGCAAGTG 62.944 63.158 2.18 0.00 0.00 3.16
11 12 3.661648 ATGGGCCGGGAAGCAAGT 61.662 61.111 2.18 0.00 0.00 3.16
12 13 3.142838 CATGGGCCGGGAAGCAAG 61.143 66.667 2.18 0.00 0.00 4.01
13 14 3.978193 ACATGGGCCGGGAAGCAA 61.978 61.111 2.18 0.00 0.00 3.91
14 15 4.738998 CACATGGGCCGGGAAGCA 62.739 66.667 2.18 0.00 0.00 3.91
16 17 4.738998 TGCACATGGGCCGGGAAG 62.739 66.667 19.33 0.00 0.00 3.46
17 18 3.598747 AATGCACATGGGCCGGGAA 62.599 57.895 19.33 0.00 0.00 3.97
18 19 4.059304 AATGCACATGGGCCGGGA 62.059 61.111 19.33 0.00 0.00 5.14
19 20 3.840594 CAATGCACATGGGCCGGG 61.841 66.667 19.33 2.01 0.00 5.73
20 21 4.517815 GCAATGCACATGGGCCGG 62.518 66.667 19.33 7.91 0.00 6.13
21 22 4.858433 CGCAATGCACATGGGCCG 62.858 66.667 19.33 9.94 0.00 6.13
22 23 2.788640 ATCGCAATGCACATGGGCC 61.789 57.895 19.33 0.00 0.00 5.80
23 24 1.590525 CATCGCAATGCACATGGGC 60.591 57.895 14.67 14.67 0.00 5.36
24 25 4.722008 CATCGCAATGCACATGGG 57.278 55.556 5.91 11.00 0.00 4.00
32 33 4.557605 GGCCGTGGCATCGCAATG 62.558 66.667 13.76 0.00 44.11 2.82
48 49 3.697747 TACGGGTTGACTGGGCGG 61.698 66.667 0.00 0.00 0.00 6.13
49 50 2.433664 GTACGGGTTGACTGGGCG 60.434 66.667 0.00 0.00 0.00 6.13
50 51 1.375523 CAGTACGGGTTGACTGGGC 60.376 63.158 0.00 0.00 39.55 5.36
53 54 0.949105 GTGCCAGTACGGGTTGACTG 60.949 60.000 13.86 0.00 42.29 3.51
54 55 1.370064 GTGCCAGTACGGGTTGACT 59.630 57.895 13.86 0.00 34.06 3.41
55 56 1.670083 GGTGCCAGTACGGGTTGAC 60.670 63.158 13.86 7.94 34.06 3.18
56 57 2.745037 GGTGCCAGTACGGGTTGA 59.255 61.111 13.86 0.00 34.06 3.18
57 58 2.740826 CGGTGCCAGTACGGGTTG 60.741 66.667 13.86 0.00 34.06 3.77
58 59 4.011517 CCGGTGCCAGTACGGGTT 62.012 66.667 13.86 0.00 43.69 4.11
63 64 3.952628 GAGGTGCCGGTGCCAGTAC 62.953 68.421 16.72 0.00 36.33 2.73
64 65 3.702048 GAGGTGCCGGTGCCAGTA 61.702 66.667 16.72 0.00 36.33 2.74
104 105 1.005630 CTAGCTAGACGGCCATGGC 60.006 63.158 29.47 29.47 41.06 4.40
105 106 0.827925 TCCTAGCTAGACGGCCATGG 60.828 60.000 22.70 7.63 0.00 3.66
106 107 0.600557 CTCCTAGCTAGACGGCCATG 59.399 60.000 22.70 2.72 0.00 3.66
107 108 0.540830 CCTCCTAGCTAGACGGCCAT 60.541 60.000 22.70 0.00 0.00 4.40
108 109 1.152735 CCTCCTAGCTAGACGGCCA 60.153 63.158 22.70 0.00 0.00 5.36
109 110 1.150992 TCCTCCTAGCTAGACGGCC 59.849 63.158 22.70 0.00 0.00 6.13
110 111 0.179012 AGTCCTCCTAGCTAGACGGC 60.179 60.000 22.70 15.38 34.41 5.68
111 112 1.600023 CAGTCCTCCTAGCTAGACGG 58.400 60.000 22.70 19.60 34.41 4.79
112 113 1.600023 CCAGTCCTCCTAGCTAGACG 58.400 60.000 22.70 11.71 34.41 4.18
113 114 1.989706 CCCAGTCCTCCTAGCTAGAC 58.010 60.000 22.70 12.15 0.00 2.59
114 115 0.186386 GCCCAGTCCTCCTAGCTAGA 59.814 60.000 22.70 7.45 0.00 2.43
115 116 1.175983 CGCCCAGTCCTCCTAGCTAG 61.176 65.000 14.20 14.20 0.00 3.42
116 117 1.152735 CGCCCAGTCCTCCTAGCTA 60.153 63.158 0.00 0.00 0.00 3.32
117 118 2.443016 CGCCCAGTCCTCCTAGCT 60.443 66.667 0.00 0.00 0.00 3.32
118 119 4.228567 GCGCCCAGTCCTCCTAGC 62.229 72.222 0.00 0.00 0.00 3.42
119 120 2.759973 TGCGCCCAGTCCTCCTAG 60.760 66.667 4.18 0.00 0.00 3.02
120 121 2.589610 ATCTGCGCCCAGTCCTCCTA 62.590 60.000 4.18 0.00 40.09 2.94
121 122 3.991924 ATCTGCGCCCAGTCCTCCT 62.992 63.158 4.18 0.00 40.09 3.69
122 123 3.474570 ATCTGCGCCCAGTCCTCC 61.475 66.667 4.18 0.00 40.09 4.30
123 124 2.202987 CATCTGCGCCCAGTCCTC 60.203 66.667 4.18 0.00 40.09 3.71
124 125 4.479993 GCATCTGCGCCCAGTCCT 62.480 66.667 4.18 0.00 40.09 3.85
134 135 1.150567 CCAGTCGTGCTAGCATCTGC 61.151 60.000 27.03 17.21 42.49 4.26
135 136 1.150567 GCCAGTCGTGCTAGCATCTG 61.151 60.000 22.51 24.95 32.00 2.90
136 137 1.142748 GCCAGTCGTGCTAGCATCT 59.857 57.895 22.51 16.23 32.00 2.90
137 138 0.385751 TAGCCAGTCGTGCTAGCATC 59.614 55.000 22.51 14.23 40.23 3.91
138 139 2.504920 TAGCCAGTCGTGCTAGCAT 58.495 52.632 22.51 0.74 40.23 3.79
139 140 4.012138 TAGCCAGTCGTGCTAGCA 57.988 55.556 14.93 14.93 40.23 3.49
142 143 0.106868 TAGCCTAGCCAGTCGTGCTA 60.107 55.000 0.00 0.00 40.23 3.49
143 144 1.379977 TAGCCTAGCCAGTCGTGCT 60.380 57.895 0.00 0.00 42.81 4.40
144 145 1.066587 CTAGCCTAGCCAGTCGTGC 59.933 63.158 0.00 0.00 0.00 5.34
145 146 1.038130 ACCTAGCCTAGCCAGTCGTG 61.038 60.000 0.00 0.00 0.00 4.35
146 147 0.549950 TACCTAGCCTAGCCAGTCGT 59.450 55.000 0.00 0.00 0.00 4.34
147 148 1.240256 CTACCTAGCCTAGCCAGTCG 58.760 60.000 0.00 0.00 0.00 4.18
148 149 1.133419 ACCTACCTAGCCTAGCCAGTC 60.133 57.143 0.00 0.00 0.00 3.51
149 150 0.935194 ACCTACCTAGCCTAGCCAGT 59.065 55.000 0.00 0.00 0.00 4.00
150 151 2.375845 TCTACCTACCTAGCCTAGCCAG 59.624 54.545 0.00 0.00 0.00 4.85
151 152 2.425818 TCTACCTACCTAGCCTAGCCA 58.574 52.381 0.00 0.00 0.00 4.75
152 153 3.358118 CATCTACCTACCTAGCCTAGCC 58.642 54.545 0.00 0.00 0.00 3.93
153 154 3.010361 TCCATCTACCTACCTAGCCTAGC 59.990 52.174 0.00 0.00 0.00 3.42
154 155 4.931027 TCCATCTACCTACCTAGCCTAG 57.069 50.000 0.00 0.00 0.00 3.02
155 156 5.880279 ATTCCATCTACCTACCTAGCCTA 57.120 43.478 0.00 0.00 0.00 3.93
156 157 4.768807 ATTCCATCTACCTACCTAGCCT 57.231 45.455 0.00 0.00 0.00 4.58
157 158 5.419471 CACTATTCCATCTACCTACCTAGCC 59.581 48.000 0.00 0.00 0.00 3.93
158 159 5.105675 GCACTATTCCATCTACCTACCTAGC 60.106 48.000 0.00 0.00 0.00 3.42
159 160 6.010850 TGCACTATTCCATCTACCTACCTAG 58.989 44.000 0.00 0.00 0.00 3.02
160 161 5.960704 TGCACTATTCCATCTACCTACCTA 58.039 41.667 0.00 0.00 0.00 3.08
161 162 4.816126 TGCACTATTCCATCTACCTACCT 58.184 43.478 0.00 0.00 0.00 3.08
162 163 4.021016 CCTGCACTATTCCATCTACCTACC 60.021 50.000 0.00 0.00 0.00 3.18
163 164 4.561734 GCCTGCACTATTCCATCTACCTAC 60.562 50.000 0.00 0.00 0.00 3.18
164 165 3.578716 GCCTGCACTATTCCATCTACCTA 59.421 47.826 0.00 0.00 0.00 3.08
165 166 2.370189 GCCTGCACTATTCCATCTACCT 59.630 50.000 0.00 0.00 0.00 3.08
166 167 2.104792 TGCCTGCACTATTCCATCTACC 59.895 50.000 0.00 0.00 0.00 3.18
167 168 3.475566 TGCCTGCACTATTCCATCTAC 57.524 47.619 0.00 0.00 0.00 2.59
168 169 7.681259 ATATATGCCTGCACTATTCCATCTA 57.319 36.000 0.00 0.00 0.00 1.98
169 170 4.923516 ATATGCCTGCACTATTCCATCT 57.076 40.909 0.00 0.00 0.00 2.90
170 171 7.730084 TCTATATATGCCTGCACTATTCCATC 58.270 38.462 0.00 0.00 0.00 3.51
171 172 7.681259 TCTATATATGCCTGCACTATTCCAT 57.319 36.000 0.00 0.00 0.00 3.41
172 173 7.494922 TTCTATATATGCCTGCACTATTCCA 57.505 36.000 0.00 0.00 0.00 3.53
173 174 7.281100 GGTTTCTATATATGCCTGCACTATTCC 59.719 40.741 0.00 0.00 0.00 3.01
174 175 7.824289 TGGTTTCTATATATGCCTGCACTATTC 59.176 37.037 0.00 0.00 0.00 1.75
175 176 7.689299 TGGTTTCTATATATGCCTGCACTATT 58.311 34.615 0.00 0.00 0.00 1.73
176 177 7.257790 TGGTTTCTATATATGCCTGCACTAT 57.742 36.000 0.00 0.00 0.00 2.12
177 178 6.680148 TGGTTTCTATATATGCCTGCACTA 57.320 37.500 0.00 0.00 0.00 2.74
178 179 5.567037 TGGTTTCTATATATGCCTGCACT 57.433 39.130 0.00 0.00 0.00 4.40
179 180 5.765182 ACTTGGTTTCTATATATGCCTGCAC 59.235 40.000 0.00 0.00 0.00 4.57
180 181 5.940617 ACTTGGTTTCTATATATGCCTGCA 58.059 37.500 0.00 0.00 0.00 4.41
181 182 7.979444 TTACTTGGTTTCTATATATGCCTGC 57.021 36.000 0.00 0.00 0.00 4.85
182 183 8.784043 GGTTTACTTGGTTTCTATATATGCCTG 58.216 37.037 0.00 0.00 0.00 4.85
183 184 7.660208 CGGTTTACTTGGTTTCTATATATGCCT 59.340 37.037 0.00 0.00 0.00 4.75
184 185 7.094933 CCGGTTTACTTGGTTTCTATATATGCC 60.095 40.741 0.00 0.00 0.00 4.40
185 186 7.094933 CCCGGTTTACTTGGTTTCTATATATGC 60.095 40.741 0.00 0.00 0.00 3.14
186 187 7.389607 CCCCGGTTTACTTGGTTTCTATATATG 59.610 40.741 0.00 0.00 0.00 1.78
187 188 7.293062 TCCCCGGTTTACTTGGTTTCTATATAT 59.707 37.037 0.00 0.00 0.00 0.86
188 189 6.614906 TCCCCGGTTTACTTGGTTTCTATATA 59.385 38.462 0.00 0.00 0.00 0.86
189 190 5.429435 TCCCCGGTTTACTTGGTTTCTATAT 59.571 40.000 0.00 0.00 0.00 0.86
190 191 4.782156 TCCCCGGTTTACTTGGTTTCTATA 59.218 41.667 0.00 0.00 0.00 1.31
191 192 3.588396 TCCCCGGTTTACTTGGTTTCTAT 59.412 43.478 0.00 0.00 0.00 1.98
192 193 2.978278 TCCCCGGTTTACTTGGTTTCTA 59.022 45.455 0.00 0.00 0.00 2.10
193 194 1.776063 TCCCCGGTTTACTTGGTTTCT 59.224 47.619 0.00 0.00 0.00 2.52
194 195 2.275134 TCCCCGGTTTACTTGGTTTC 57.725 50.000 0.00 0.00 0.00 2.78
204 205 2.596338 CGCTTGGTTCCCCGGTTT 60.596 61.111 0.00 0.00 0.00 3.27
232 233 2.359531 TGGTCGCGGTTCTTTGATTTTT 59.640 40.909 6.13 0.00 0.00 1.94
233 234 1.950909 TGGTCGCGGTTCTTTGATTTT 59.049 42.857 6.13 0.00 0.00 1.82
234 235 1.600023 TGGTCGCGGTTCTTTGATTT 58.400 45.000 6.13 0.00 0.00 2.17
235 236 1.737793 GATGGTCGCGGTTCTTTGATT 59.262 47.619 6.13 0.00 0.00 2.57
236 237 1.369625 GATGGTCGCGGTTCTTTGAT 58.630 50.000 6.13 0.00 0.00 2.57
281 282 4.899239 GGGCGTCATGGAGGCTCG 62.899 72.222 8.69 0.00 42.20 5.03
360 361 2.193248 GGAAGAAGGGGCGGATGG 59.807 66.667 0.00 0.00 0.00 3.51
362 363 3.097162 GGGGAAGAAGGGGCGGAT 61.097 66.667 0.00 0.00 0.00 4.18
403 404 2.348104 CGACGACCATGTGGGAGGA 61.348 63.158 3.77 0.00 41.15 3.71
436 437 2.746277 GTGATGGTGGCGGTGGTC 60.746 66.667 0.00 0.00 0.00 4.02
437 438 4.697756 CGTGATGGTGGCGGTGGT 62.698 66.667 0.00 0.00 0.00 4.16
445 446 2.597117 GATTTGGCCGCGTGATGGTG 62.597 60.000 4.92 0.00 0.00 4.17
457 458 0.881118 TTCACGGCAGAAGATTTGGC 59.119 50.000 0.00 0.00 37.72 4.52
516 517 1.252904 TACGGGCCTAGTTGAGCGTT 61.253 55.000 0.84 0.00 0.00 4.84
518 519 1.226888 GTACGGGCCTAGTTGAGCG 60.227 63.158 0.84 0.00 0.00 5.03
627 628 4.295141 TGAGGGACGGTTACATGAAATT 57.705 40.909 0.00 0.00 0.00 1.82
723 724 3.402110 ACGCTTCAATCAGTCATCAACA 58.598 40.909 0.00 0.00 0.00 3.33
939 957 0.896923 AAGCAGTGGAGAGCAGAGAG 59.103 55.000 0.00 0.00 0.00 3.20
969 987 4.838486 CGTCGCCGGAGTGAGAGC 62.838 72.222 5.05 0.00 31.79 4.09
1181 1228 9.823647 GCTACAGCAGGAAACACATATATATAT 57.176 33.333 0.00 0.00 41.59 0.86
1204 1251 3.093814 TCACAGTATCCGGAGTTTGCTA 58.906 45.455 11.34 0.00 0.00 3.49
1321 1368 4.225942 TCCTATGAATCTTCTGCCTGTGTT 59.774 41.667 0.00 0.00 0.00 3.32
1630 1682 8.474025 ACAGTTCACACAATCCTGAAAATTTAA 58.526 29.630 0.00 0.00 0.00 1.52
1734 1787 2.424246 GACTCTACCAAGGTTCTCCTCG 59.576 54.545 0.00 0.00 44.35 4.63
1941 1994 1.059098 TCTTTGCCTGCTCCTCAAGA 58.941 50.000 0.00 0.00 0.00 3.02
1964 2017 4.440663 GCTTAAGCATCTCCATTTGAACCC 60.441 45.833 22.59 0.00 41.59 4.11
1979 2032 5.368145 TCTGTTCTTTCTTGAGCTTAAGCA 58.632 37.500 28.39 6.82 45.16 3.91
2137 2192 2.787994 CTTCTCTTTGCACCCATGACT 58.212 47.619 0.00 0.00 0.00 3.41
2397 2452 2.443324 CCCCATTGGTCCCGGTTT 59.557 61.111 0.00 0.00 0.00 3.27
2463 2518 1.065491 CAGATGAACCGGGACCAATGA 60.065 52.381 6.32 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.