Multiple sequence alignment - TraesCS3D01G220600

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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 TraesCS3D01G220600 chr3D 100.000 2363 0 0 1 2363 301347716 301345354 0.000000e+00 4364
1 TraesCS3D01G220600 chr3D 88.571 210 22 2 151 360 169728220 169728427 1.080000e-63 254
2 TraesCS3D01G220600 chr3D 89.394 198 17 3 163 360 141467105 141467298 1.810000e-61 246
3 TraesCS3D01G220600 chr3D 95.105 143 7 0 2221 2363 281328919 281328777 2.360000e-55 226
4 TraesCS3D01G220600 chr3D 89.714 175 15 2 186 360 405513320 405513491 1.100000e-53 220
5 TraesCS3D01G220600 chr1A 95.773 1987 51 5 410 2363 510300993 510299007 0.000000e+00 3173
6 TraesCS3D01G220600 chr1A 90.173 753 64 8 1233 1980 214889047 214888300 0.000000e+00 972
7 TraesCS3D01G220600 chr1A 88.480 816 55 18 1366 2177 111988174 111987394 0.000000e+00 950
8 TraesCS3D01G220600 chr1A 92.576 229 15 2 810 1038 503459916 503460142 6.300000e-86 327
9 TraesCS3D01G220600 chr1A 90.830 229 19 2 810 1038 503557538 503557312 2.950000e-79 305
10 TraesCS3D01G220600 chr1A 93.237 207 12 2 1973 2177 214731034 214730828 1.060000e-78 303
11 TraesCS3D01G220600 chr1A 87.970 266 15 7 163 411 510301964 510301699 4.940000e-77 298
12 TraesCS3D01G220600 chr1A 89.956 229 21 2 810 1038 503584799 503584573 6.390000e-76 294
13 TraesCS3D01G220600 chr1A 95.804 143 6 0 2221 2363 111987162 111987020 5.080000e-57 231
14 TraesCS3D01G220600 chr1A 92.079 101 8 0 2263 2363 14361566 14361666 2.450000e-30 143
15 TraesCS3D01G220600 chr6D 96.661 1767 36 3 619 2363 436501209 436499444 0.000000e+00 2915
16 TraesCS3D01G220600 chr6D 100.000 60 0 0 410 469 436501280 436501221 6.900000e-21 111
17 TraesCS3D01G220600 chr1B 92.857 952 56 11 1233 2177 130938880 130937934 0.000000e+00 1371
18 TraesCS3D01G220600 chr1B 91.983 923 60 11 1262 2177 223853437 223852522 0.000000e+00 1282
19 TraesCS3D01G220600 chr1B 92.222 810 47 9 1346 2150 575124514 575125312 0.000000e+00 1133
20 TraesCS3D01G220600 chr1B 96.429 140 4 1 2221 2359 575126211 575126350 1.830000e-56 230
21 TraesCS3D01G220600 chr1B 92.361 144 4 3 2219 2362 130937252 130937116 5.150000e-47 198
22 TraesCS3D01G220600 chr2B 92.511 948 57 9 1236 2177 697436996 697436057 0.000000e+00 1345
23 TraesCS3D01G220600 chr2B 92.105 114 5 2 694 807 282994324 282994215 8.740000e-35 158
24 TraesCS3D01G220600 chr7B 92.194 474 31 5 1365 1836 73924345 73923876 0.000000e+00 665
25 TraesCS3D01G220600 chr7B 91.954 261 16 5 1920 2177 73923879 73923621 6.210000e-96 361
26 TraesCS3D01G220600 chr7B 95.804 143 6 0 2221 2363 73923389 73923247 5.080000e-57 231
27 TraesCS3D01G220600 chr1D 92.178 473 32 5 1681 2149 51927142 51927613 0.000000e+00 664
28 TraesCS3D01G220600 chr1D 97.368 152 4 0 1 152 135839678 135839527 2.330000e-65 259
29 TraesCS3D01G220600 chr1D 96.732 153 4 1 1 152 416437128 416436976 1.080000e-63 254
30 TraesCS3D01G220600 chr3A 91.156 441 32 5 1399 1836 565340941 565341377 2.020000e-165 592
31 TraesCS3D01G220600 chr3A 95.804 143 6 0 2221 2363 565341864 565342006 5.080000e-57 231
32 TraesCS3D01G220600 chr4D 88.283 367 33 6 1819 2177 12700176 12699812 4.670000e-117 431
33 TraesCS3D01G220600 chr4D 96.711 152 5 0 1 152 134165750 134165901 1.080000e-63 254
34 TraesCS3D01G220600 chr4D 83.682 239 33 5 1 238 328841981 328842214 1.100000e-53 220
35 TraesCS3D01G220600 chr4B 88.011 367 34 6 1819 2177 23404485 23404121 2.170000e-115 425
36 TraesCS3D01G220600 chr2A 92.520 254 17 2 1366 1619 191918516 191918265 1.730000e-96 363
37 TraesCS3D01G220600 chr2A 95.804 143 6 0 2221 2363 426713295 426713437 5.080000e-57 231
38 TraesCS3D01G220600 chr4A 84.469 367 44 8 1819 2177 589603268 589602907 1.340000e-92 350
39 TraesCS3D01G220600 chr4A 97.368 152 4 0 1 152 4750249 4750400 2.330000e-65 259
40 TraesCS3D01G220600 chr4A 89.000 200 21 1 161 360 350842233 350842431 1.810000e-61 246
41 TraesCS3D01G220600 chr4A 88.500 200 22 1 161 360 257179924 257179726 8.440000e-60 241
42 TraesCS3D01G220600 chr4A 87.940 199 21 3 163 360 257481970 257481774 5.080000e-57 231
43 TraesCS3D01G220600 chr4A 95.455 132 6 0 2232 2363 599902798 599902667 6.620000e-51 211
44 TraesCS3D01G220600 chr5B 92.174 230 17 1 810 1038 637397265 637397494 8.150000e-85 324
45 TraesCS3D01G220600 chr6B 92.444 225 17 0 810 1034 463261172 463261396 2.930000e-84 322
46 TraesCS3D01G220600 chr6B 93.069 101 7 0 2263 2363 705327770 705327870 5.260000e-32 148
47 TraesCS3D01G220600 chr6B 88.298 94 8 2 1681 1771 705326927 705327020 2.480000e-20 110
48 TraesCS3D01G220600 chr7A 90.435 230 16 3 810 1038 518161876 518162100 4.940000e-77 298
49 TraesCS3D01G220600 chr7A 94.697 132 7 0 2232 2363 193579385 193579516 3.080000e-49 206
50 TraesCS3D01G220600 chr5A 97.368 152 4 0 1 152 170780790 170780639 2.330000e-65 259
51 TraesCS3D01G220600 chr5A 87.000 200 24 2 161 360 648901120 648901317 8.500000e-55 224
52 TraesCS3D01G220600 chr6A 96.711 152 5 0 1 152 404476844 404476995 1.080000e-63 254
53 TraesCS3D01G220600 chr5D 96.711 152 5 0 1 152 195637128 195637279 1.080000e-63 254
54 TraesCS3D01G220600 chr5D 97.059 136 4 0 2221 2356 119464985 119464850 1.830000e-56 230
55 TraesCS3D01G220600 chrUn 90.860 186 17 0 161 346 131944783 131944598 1.400000e-62 250
56 TraesCS3D01G220600 chr3B 95.804 143 6 0 2221 2363 646713888 646713746 5.080000e-57 231
57 TraesCS3D01G220600 chr2D 83.682 239 33 5 1 238 407382142 407381909 1.100000e-53 220


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 TraesCS3D01G220600 chr3D 301345354 301347716 2362 True 4364.0 4364 100.000000 1 2363 1 chr3D.!!$R2 2362
1 TraesCS3D01G220600 chr1A 510299007 510301964 2957 True 1735.5 3173 91.871500 163 2363 2 chr1A.!!$R6 2200
2 TraesCS3D01G220600 chr1A 214888300 214889047 747 True 972.0 972 90.173000 1233 1980 1 chr1A.!!$R2 747
3 TraesCS3D01G220600 chr1A 111987020 111988174 1154 True 590.5 950 92.142000 1366 2363 2 chr1A.!!$R5 997
4 TraesCS3D01G220600 chr6D 436499444 436501280 1836 True 1513.0 2915 98.330500 410 2363 2 chr6D.!!$R1 1953
5 TraesCS3D01G220600 chr1B 223852522 223853437 915 True 1282.0 1282 91.983000 1262 2177 1 chr1B.!!$R1 915
6 TraesCS3D01G220600 chr1B 130937116 130938880 1764 True 784.5 1371 92.609000 1233 2362 2 chr1B.!!$R2 1129
7 TraesCS3D01G220600 chr1B 575124514 575126350 1836 False 681.5 1133 94.325500 1346 2359 2 chr1B.!!$F1 1013
8 TraesCS3D01G220600 chr2B 697436057 697436996 939 True 1345.0 1345 92.511000 1236 2177 1 chr2B.!!$R2 941
9 TraesCS3D01G220600 chr7B 73923247 73924345 1098 True 419.0 665 93.317333 1365 2363 3 chr7B.!!$R1 998
10 TraesCS3D01G220600 chr3A 565340941 565342006 1065 False 411.5 592 93.480000 1399 2363 2 chr3A.!!$F1 964

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
488 1213 1.575244 TGCTCTGACTGCGATTATGC 58.425 50.0 0.0 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 2419 4.165372 TCCATAGTTTGGTTGGGGATAGAC 59.835 45.833 0.0 0.0 46.52 2.59 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
22 23 5.514274 CTTAAACCTTTGCTTGTCCTCAA 57.486 39.130 0.00 0.00 0.00 3.02
31 32 2.907910 CTTGTCCTCAAGCAATTCGG 57.092 50.000 0.00 0.00 43.34 4.30
32 33 2.154462 CTTGTCCTCAAGCAATTCGGT 58.846 47.619 0.00 0.00 43.34 4.69
33 34 2.270352 TGTCCTCAAGCAATTCGGTT 57.730 45.000 0.00 0.00 35.07 4.44
43 44 5.957842 AAGCAATTCGGTTGATAAACTGA 57.042 34.783 0.00 0.00 40.37 3.41
87 88 9.515020 TTTTACAAACTCTGTTTGCTCTTATTG 57.485 29.630 19.19 0.00 39.64 1.90
88 89 6.699575 ACAAACTCTGTTTGCTCTTATTGT 57.300 33.333 19.19 0.00 32.99 2.71
89 90 7.100458 ACAAACTCTGTTTGCTCTTATTGTT 57.900 32.000 19.19 0.00 32.99 2.83
90 91 6.974622 ACAAACTCTGTTTGCTCTTATTGTTG 59.025 34.615 19.19 0.00 32.99 3.33
91 92 6.699575 AACTCTGTTTGCTCTTATTGTTGT 57.300 33.333 0.00 0.00 0.00 3.32
92 93 7.801716 AACTCTGTTTGCTCTTATTGTTGTA 57.198 32.000 0.00 0.00 0.00 2.41
93 94 7.801716 ACTCTGTTTGCTCTTATTGTTGTAA 57.198 32.000 0.00 0.00 0.00 2.41
94 95 8.220755 ACTCTGTTTGCTCTTATTGTTGTAAA 57.779 30.769 0.00 0.00 0.00 2.01
95 96 8.850156 ACTCTGTTTGCTCTTATTGTTGTAAAT 58.150 29.630 0.00 0.00 0.00 1.40
108 109 9.796120 TTATTGTTGTAAATATGTAAAGCCAGC 57.204 29.630 0.00 0.00 0.00 4.85
109 110 6.825944 TGTTGTAAATATGTAAAGCCAGCA 57.174 33.333 0.00 0.00 0.00 4.41
110 111 7.403312 TGTTGTAAATATGTAAAGCCAGCAT 57.597 32.000 0.00 0.00 0.00 3.79
111 112 7.835822 TGTTGTAAATATGTAAAGCCAGCATT 58.164 30.769 0.00 0.00 0.00 3.56
112 113 7.973388 TGTTGTAAATATGTAAAGCCAGCATTC 59.027 33.333 0.00 0.00 0.00 2.67
113 114 7.637631 TGTAAATATGTAAAGCCAGCATTCA 57.362 32.000 0.00 0.00 0.00 2.57
114 115 8.060931 TGTAAATATGTAAAGCCAGCATTCAA 57.939 30.769 0.00 0.00 0.00 2.69
115 116 8.190122 TGTAAATATGTAAAGCCAGCATTCAAG 58.810 33.333 0.00 0.00 0.00 3.02
116 117 6.780457 AATATGTAAAGCCAGCATTCAAGT 57.220 33.333 0.00 0.00 0.00 3.16
117 118 6.780457 ATATGTAAAGCCAGCATTCAAGTT 57.220 33.333 0.00 0.00 0.00 2.66
118 119 4.935352 TGTAAAGCCAGCATTCAAGTTT 57.065 36.364 0.00 0.00 0.00 2.66
119 120 5.275067 TGTAAAGCCAGCATTCAAGTTTT 57.725 34.783 0.00 0.00 0.00 2.43
120 121 5.288804 TGTAAAGCCAGCATTCAAGTTTTC 58.711 37.500 0.00 0.00 0.00 2.29
121 122 4.405116 AAAGCCAGCATTCAAGTTTTCA 57.595 36.364 0.00 0.00 0.00 2.69
122 123 3.655276 AGCCAGCATTCAAGTTTTCAG 57.345 42.857 0.00 0.00 0.00 3.02
123 124 2.064014 GCCAGCATTCAAGTTTTCAGC 58.936 47.619 0.00 0.00 0.00 4.26
124 125 2.546373 GCCAGCATTCAAGTTTTCAGCA 60.546 45.455 0.00 0.00 0.00 4.41
125 126 3.719924 CCAGCATTCAAGTTTTCAGCAA 58.280 40.909 0.00 0.00 0.00 3.91
126 127 4.121317 CCAGCATTCAAGTTTTCAGCAAA 58.879 39.130 0.00 0.00 0.00 3.68
127 128 4.210537 CCAGCATTCAAGTTTTCAGCAAAG 59.789 41.667 0.00 0.00 0.00 2.77
128 129 5.045215 CAGCATTCAAGTTTTCAGCAAAGA 58.955 37.500 0.00 0.00 0.00 2.52
129 130 5.694910 CAGCATTCAAGTTTTCAGCAAAGAT 59.305 36.000 0.00 0.00 0.00 2.40
130 131 6.202188 CAGCATTCAAGTTTTCAGCAAAGATT 59.798 34.615 0.00 0.00 0.00 2.40
131 132 7.383029 CAGCATTCAAGTTTTCAGCAAAGATTA 59.617 33.333 0.00 0.00 0.00 1.75
132 133 8.092687 AGCATTCAAGTTTTCAGCAAAGATTAT 58.907 29.630 0.00 0.00 0.00 1.28
133 134 9.357652 GCATTCAAGTTTTCAGCAAAGATTATA 57.642 29.630 0.00 0.00 0.00 0.98
143 144 8.856153 TTCAGCAAAGATTATAACTAACCACA 57.144 30.769 0.00 0.00 0.00 4.17
144 145 9.461312 TTCAGCAAAGATTATAACTAACCACAT 57.539 29.630 0.00 0.00 0.00 3.21
145 146 9.461312 TCAGCAAAGATTATAACTAACCACATT 57.539 29.630 0.00 0.00 0.00 2.71
146 147 9.722056 CAGCAAAGATTATAACTAACCACATTC 57.278 33.333 0.00 0.00 0.00 2.67
147 148 8.612619 AGCAAAGATTATAACTAACCACATTCG 58.387 33.333 0.00 0.00 0.00 3.34
148 149 7.376072 GCAAAGATTATAACTAACCACATTCGC 59.624 37.037 0.00 0.00 0.00 4.70
149 150 8.394877 CAAAGATTATAACTAACCACATTCGCA 58.605 33.333 0.00 0.00 0.00 5.10
150 151 8.500753 AAGATTATAACTAACCACATTCGCAA 57.499 30.769 0.00 0.00 0.00 4.85
151 152 8.677148 AGATTATAACTAACCACATTCGCAAT 57.323 30.769 0.00 0.00 0.00 3.56
152 153 8.774586 AGATTATAACTAACCACATTCGCAATC 58.225 33.333 0.00 0.00 0.00 2.67
153 154 8.677148 ATTATAACTAACCACATTCGCAATCT 57.323 30.769 0.00 0.00 0.00 2.40
154 155 8.500753 TTATAACTAACCACATTCGCAATCTT 57.499 30.769 0.00 0.00 0.00 2.40
155 156 5.705609 AACTAACCACATTCGCAATCTTT 57.294 34.783 0.00 0.00 0.00 2.52
156 157 5.705609 ACTAACCACATTCGCAATCTTTT 57.294 34.783 0.00 0.00 0.00 2.27
157 158 5.699839 ACTAACCACATTCGCAATCTTTTC 58.300 37.500 0.00 0.00 0.00 2.29
158 159 3.575965 ACCACATTCGCAATCTTTTCC 57.424 42.857 0.00 0.00 0.00 3.13
159 160 3.157087 ACCACATTCGCAATCTTTTCCT 58.843 40.909 0.00 0.00 0.00 3.36
160 161 3.191371 ACCACATTCGCAATCTTTTCCTC 59.809 43.478 0.00 0.00 0.00 3.71
161 162 3.428045 CCACATTCGCAATCTTTTCCTCC 60.428 47.826 0.00 0.00 0.00 4.30
209 210 2.759535 TGGGTTCACCGTCATAATACGA 59.240 45.455 0.00 0.00 45.68 3.43
219 220 3.918591 CGTCATAATACGATTCTTCCCGG 59.081 47.826 0.00 0.00 45.68 5.73
220 221 4.558095 CGTCATAATACGATTCTTCCCGGT 60.558 45.833 0.00 0.00 45.68 5.28
235 236 8.726870 TTCTTCCCGGTAATTTATACTTTCAG 57.273 34.615 0.00 0.00 0.00 3.02
239 240 7.622713 TCCCGGTAATTTATACTTTCAGTTCA 58.377 34.615 0.00 0.00 0.00 3.18
285 286 3.861689 GGTACTAAATTTCGTCCGTCCAG 59.138 47.826 0.00 0.00 0.00 3.86
303 304 4.562789 GTCCAGTTTTGTTTTCACAGCTTC 59.437 41.667 0.00 0.00 33.22 3.86
308 309 7.115378 CCAGTTTTGTTTTCACAGCTTCATATC 59.885 37.037 0.00 0.00 33.22 1.63
375 393 4.031129 CTGGCTGCTCTGGCTGGT 62.031 66.667 0.00 0.00 39.59 4.00
408 426 2.469516 CGGCATGGACCTAAACGCC 61.470 63.158 0.00 0.00 36.16 5.68
488 1213 1.575244 TGCTCTGACTGCGATTATGC 58.425 50.000 0.00 0.00 0.00 3.14
534 1259 6.183360 GCTCTGCAGAATAGATATGCTAGCTA 60.183 42.308 18.85 6.33 41.87 3.32
674 1399 4.037923 GGTTGTCCAACATGTGTTTCTCAT 59.962 41.667 11.89 0.00 42.85 2.90
759 1484 5.163663 TGTTGGCCTAAATATTCTCTTTGCG 60.164 40.000 3.32 0.00 0.00 4.85
1003 1738 7.426456 CAGTTACGATTTAGTCAACATTGATGC 59.574 37.037 0.00 0.00 39.73 3.91
1077 1812 2.371841 ACTTATAGAATGGGATGCGCCA 59.628 45.455 4.18 0.00 38.95 5.69
1108 1843 2.425592 CACGGTCCCAACAGCTGA 59.574 61.111 23.35 0.00 0.00 4.26
1129 1864 1.978712 GCGAGTCTCCACGATCGACA 61.979 60.000 24.34 3.60 37.35 4.35
1190 1925 0.299597 GACAAGCGTTCGTTCGTGTT 59.700 50.000 4.37 0.00 0.00 3.32
1465 2201 2.603075 ATGCCAGTACCACACCAAAT 57.397 45.000 0.00 0.00 0.00 2.32
1679 2419 5.387788 TGGGATCATCAATTCCTTGGTATG 58.612 41.667 0.00 0.00 33.53 2.39
1941 2687 6.560003 TCTCTGTATCCTATTTCTTGCCAA 57.440 37.500 0.00 0.00 0.00 4.52
2359 3937 5.361427 TGTCAGGTTTCGACTCAAATTGTA 58.639 37.500 0.00 0.00 34.37 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.514274 TTGAGGACAAGCAAAGGTTTAAG 57.486 39.130 0.00 0.00 0.00 1.85
1 2 5.514274 CTTGAGGACAAGCAAAGGTTTAA 57.486 39.130 0.00 0.00 45.19 1.52
13 14 2.270352 ACCGAATTGCTTGAGGACAA 57.730 45.000 0.00 0.00 34.65 3.18
14 15 1.879380 CAACCGAATTGCTTGAGGACA 59.121 47.619 0.00 0.00 0.00 4.02
15 16 2.151202 TCAACCGAATTGCTTGAGGAC 58.849 47.619 0.00 0.00 38.29 3.85
16 17 2.559698 TCAACCGAATTGCTTGAGGA 57.440 45.000 0.00 0.00 38.29 3.71
17 18 4.963276 TTATCAACCGAATTGCTTGAGG 57.037 40.909 0.00 0.00 38.29 3.86
18 19 5.796935 CAGTTTATCAACCGAATTGCTTGAG 59.203 40.000 0.00 0.00 38.29 3.02
19 20 5.471797 TCAGTTTATCAACCGAATTGCTTGA 59.528 36.000 0.00 0.00 38.29 3.02
20 21 5.698832 TCAGTTTATCAACCGAATTGCTTG 58.301 37.500 0.00 0.00 38.29 4.01
21 22 5.957842 TCAGTTTATCAACCGAATTGCTT 57.042 34.783 0.00 0.00 38.29 3.91
22 23 5.957842 TTCAGTTTATCAACCGAATTGCT 57.042 34.783 0.00 0.00 38.29 3.91
23 24 6.088085 CACTTTCAGTTTATCAACCGAATTGC 59.912 38.462 0.00 0.00 38.29 3.56
24 25 7.359595 TCACTTTCAGTTTATCAACCGAATTG 58.640 34.615 0.00 0.00 39.94 2.32
25 26 7.504924 TCACTTTCAGTTTATCAACCGAATT 57.495 32.000 0.00 0.00 30.87 2.17
26 27 7.687941 ATCACTTTCAGTTTATCAACCGAAT 57.312 32.000 0.00 0.00 30.87 3.34
27 28 8.610248 TTATCACTTTCAGTTTATCAACCGAA 57.390 30.769 0.00 0.00 32.70 4.30
28 29 8.610248 TTTATCACTTTCAGTTTATCAACCGA 57.390 30.769 0.00 0.00 32.70 4.69
29 30 8.717821 TCTTTATCACTTTCAGTTTATCAACCG 58.282 33.333 0.00 0.00 32.70 4.44
61 62 9.515020 CAATAAGAGCAAACAGAGTTTGTAAAA 57.485 29.630 19.93 6.80 39.73 1.52
62 63 8.682710 ACAATAAGAGCAAACAGAGTTTGTAAA 58.317 29.630 19.93 6.25 39.73 2.01
63 64 8.220755 ACAATAAGAGCAAACAGAGTTTGTAA 57.779 30.769 19.93 5.98 39.73 2.41
64 65 7.801716 ACAATAAGAGCAAACAGAGTTTGTA 57.198 32.000 19.93 8.25 39.73 2.41
65 66 6.699575 ACAATAAGAGCAAACAGAGTTTGT 57.300 33.333 19.93 9.81 43.45 2.83
66 67 6.974622 ACAACAATAAGAGCAAACAGAGTTTG 59.025 34.615 16.07 16.07 0.00 2.93
67 68 7.100458 ACAACAATAAGAGCAAACAGAGTTT 57.900 32.000 0.00 0.00 0.00 2.66
68 69 6.699575 ACAACAATAAGAGCAAACAGAGTT 57.300 33.333 0.00 0.00 0.00 3.01
69 70 7.801716 TTACAACAATAAGAGCAAACAGAGT 57.198 32.000 0.00 0.00 0.00 3.24
82 83 9.796120 GCTGGCTTTACATATTTACAACAATAA 57.204 29.630 0.00 0.00 0.00 1.40
83 84 8.961634 TGCTGGCTTTACATATTTACAACAATA 58.038 29.630 0.00 0.00 0.00 1.90
84 85 7.835822 TGCTGGCTTTACATATTTACAACAAT 58.164 30.769 0.00 0.00 0.00 2.71
85 86 7.220741 TGCTGGCTTTACATATTTACAACAA 57.779 32.000 0.00 0.00 0.00 2.83
86 87 6.825944 TGCTGGCTTTACATATTTACAACA 57.174 33.333 0.00 0.00 0.00 3.33
87 88 7.973388 TGAATGCTGGCTTTACATATTTACAAC 59.027 33.333 0.00 0.00 0.00 3.32
88 89 8.060931 TGAATGCTGGCTTTACATATTTACAA 57.939 30.769 0.00 0.00 0.00 2.41
89 90 7.637631 TGAATGCTGGCTTTACATATTTACA 57.362 32.000 0.00 0.00 0.00 2.41
90 91 8.190784 ACTTGAATGCTGGCTTTACATATTTAC 58.809 33.333 0.00 0.00 0.00 2.01
91 92 8.292444 ACTTGAATGCTGGCTTTACATATTTA 57.708 30.769 0.00 0.00 0.00 1.40
92 93 7.174107 ACTTGAATGCTGGCTTTACATATTT 57.826 32.000 0.00 0.00 0.00 1.40
93 94 6.780457 ACTTGAATGCTGGCTTTACATATT 57.220 33.333 0.00 0.00 0.00 1.28
94 95 6.780457 AACTTGAATGCTGGCTTTACATAT 57.220 33.333 0.00 0.00 0.00 1.78
95 96 6.588719 AAACTTGAATGCTGGCTTTACATA 57.411 33.333 0.00 0.00 0.00 2.29
96 97 5.473066 AAACTTGAATGCTGGCTTTACAT 57.527 34.783 0.00 0.00 0.00 2.29
97 98 4.935352 AAACTTGAATGCTGGCTTTACA 57.065 36.364 0.00 0.00 0.00 2.41
98 99 5.288804 TGAAAACTTGAATGCTGGCTTTAC 58.711 37.500 0.00 0.00 0.00 2.01
99 100 5.528043 TGAAAACTTGAATGCTGGCTTTA 57.472 34.783 0.00 0.00 0.00 1.85
100 101 4.374399 CTGAAAACTTGAATGCTGGCTTT 58.626 39.130 0.00 0.00 0.00 3.51
101 102 3.801293 GCTGAAAACTTGAATGCTGGCTT 60.801 43.478 0.00 0.00 0.00 4.35
102 103 2.288640 GCTGAAAACTTGAATGCTGGCT 60.289 45.455 0.00 0.00 0.00 4.75
103 104 2.064014 GCTGAAAACTTGAATGCTGGC 58.936 47.619 0.00 0.00 0.00 4.85
104 105 3.374220 TGCTGAAAACTTGAATGCTGG 57.626 42.857 0.00 0.00 0.00 4.85
105 106 5.045215 TCTTTGCTGAAAACTTGAATGCTG 58.955 37.500 0.00 0.00 0.00 4.41
106 107 5.266733 TCTTTGCTGAAAACTTGAATGCT 57.733 34.783 0.00 0.00 0.00 3.79
107 108 6.535274 AATCTTTGCTGAAAACTTGAATGC 57.465 33.333 0.00 0.00 0.00 3.56
117 118 9.290988 TGTGGTTAGTTATAATCTTTGCTGAAA 57.709 29.630 0.00 0.00 0.00 2.69
118 119 8.856153 TGTGGTTAGTTATAATCTTTGCTGAA 57.144 30.769 0.00 0.00 0.00 3.02
119 120 9.461312 AATGTGGTTAGTTATAATCTTTGCTGA 57.539 29.630 0.00 0.00 0.00 4.26
120 121 9.722056 GAATGTGGTTAGTTATAATCTTTGCTG 57.278 33.333 0.00 0.00 0.00 4.41
121 122 8.612619 CGAATGTGGTTAGTTATAATCTTTGCT 58.387 33.333 0.00 0.00 0.00 3.91
122 123 7.376072 GCGAATGTGGTTAGTTATAATCTTTGC 59.624 37.037 0.00 0.00 0.00 3.68
123 124 8.394877 TGCGAATGTGGTTAGTTATAATCTTTG 58.605 33.333 0.00 0.00 0.00 2.77
124 125 8.500753 TGCGAATGTGGTTAGTTATAATCTTT 57.499 30.769 0.00 0.00 0.00 2.52
125 126 8.500753 TTGCGAATGTGGTTAGTTATAATCTT 57.499 30.769 0.00 0.00 0.00 2.40
126 127 8.677148 ATTGCGAATGTGGTTAGTTATAATCT 57.323 30.769 0.00 0.00 0.00 2.40
127 128 8.774586 AGATTGCGAATGTGGTTAGTTATAATC 58.225 33.333 0.00 0.00 0.00 1.75
128 129 8.677148 AGATTGCGAATGTGGTTAGTTATAAT 57.323 30.769 0.00 0.00 0.00 1.28
129 130 8.500753 AAGATTGCGAATGTGGTTAGTTATAA 57.499 30.769 0.00 0.00 0.00 0.98
130 131 8.500753 AAAGATTGCGAATGTGGTTAGTTATA 57.499 30.769 0.00 0.00 0.00 0.98
131 132 7.391148 AAAGATTGCGAATGTGGTTAGTTAT 57.609 32.000 0.00 0.00 0.00 1.89
132 133 6.811253 AAAGATTGCGAATGTGGTTAGTTA 57.189 33.333 0.00 0.00 0.00 2.24
133 134 5.705609 AAAGATTGCGAATGTGGTTAGTT 57.294 34.783 0.00 0.00 0.00 2.24
134 135 5.335661 GGAAAAGATTGCGAATGTGGTTAGT 60.336 40.000 0.00 0.00 0.00 2.24
135 136 5.095490 GGAAAAGATTGCGAATGTGGTTAG 58.905 41.667 0.00 0.00 0.00 2.34
136 137 4.764823 AGGAAAAGATTGCGAATGTGGTTA 59.235 37.500 0.00 0.00 31.21 2.85
137 138 3.573967 AGGAAAAGATTGCGAATGTGGTT 59.426 39.130 0.00 0.00 31.21 3.67
138 139 3.157087 AGGAAAAGATTGCGAATGTGGT 58.843 40.909 0.00 0.00 31.21 4.16
139 140 3.428045 GGAGGAAAAGATTGCGAATGTGG 60.428 47.826 0.00 0.00 31.21 4.17
140 141 3.441572 AGGAGGAAAAGATTGCGAATGTG 59.558 43.478 0.00 0.00 31.21 3.21
141 142 3.690460 AGGAGGAAAAGATTGCGAATGT 58.310 40.909 0.00 0.00 31.21 2.71
142 143 5.818136 TTAGGAGGAAAAGATTGCGAATG 57.182 39.130 0.00 0.00 31.21 2.67
143 144 8.697507 ATTATTAGGAGGAAAAGATTGCGAAT 57.302 30.769 0.00 0.00 31.21 3.34
144 145 9.621629 TTATTATTAGGAGGAAAAGATTGCGAA 57.378 29.630 0.00 0.00 31.21 4.70
145 146 9.621629 TTTATTATTAGGAGGAAAAGATTGCGA 57.378 29.630 0.00 0.00 31.21 5.10
146 147 9.884465 CTTTATTATTAGGAGGAAAAGATTGCG 57.116 33.333 0.00 0.00 31.21 4.85
147 148 9.684448 GCTTTATTATTAGGAGGAAAAGATTGC 57.316 33.333 0.00 0.00 0.00 3.56
150 151 9.057089 CGTGCTTTATTATTAGGAGGAAAAGAT 57.943 33.333 0.00 0.00 0.00 2.40
151 152 7.497909 CCGTGCTTTATTATTAGGAGGAAAAGA 59.502 37.037 0.00 0.00 0.00 2.52
152 153 7.497909 TCCGTGCTTTATTATTAGGAGGAAAAG 59.502 37.037 0.00 0.00 0.00 2.27
153 154 7.340256 TCCGTGCTTTATTATTAGGAGGAAAA 58.660 34.615 0.00 0.00 0.00 2.29
154 155 6.891388 TCCGTGCTTTATTATTAGGAGGAAA 58.109 36.000 0.00 0.00 0.00 3.13
155 156 6.488769 TCCGTGCTTTATTATTAGGAGGAA 57.511 37.500 0.00 0.00 0.00 3.36
156 157 6.681729 ATCCGTGCTTTATTATTAGGAGGA 57.318 37.500 0.00 0.00 0.00 3.71
157 158 6.934645 TCAATCCGTGCTTTATTATTAGGAGG 59.065 38.462 0.00 0.00 0.00 4.30
158 159 7.657761 AGTCAATCCGTGCTTTATTATTAGGAG 59.342 37.037 0.00 0.00 0.00 3.69
159 160 7.506114 AGTCAATCCGTGCTTTATTATTAGGA 58.494 34.615 0.00 0.00 0.00 2.94
160 161 7.095187 GGAGTCAATCCGTGCTTTATTATTAGG 60.095 40.741 0.00 0.00 38.67 2.69
161 162 7.797819 GGAGTCAATCCGTGCTTTATTATTAG 58.202 38.462 0.00 0.00 38.67 1.73
209 210 9.338622 CTGAAAGTATAAATTACCGGGAAGAAT 57.661 33.333 4.81 0.41 0.00 2.40
239 240 9.016438 ACCACCTCACGTATATGTTTTAAATTT 57.984 29.630 0.00 0.00 0.00 1.82
285 286 7.434897 TGTGATATGAAGCTGTGAAAACAAAAC 59.565 33.333 0.00 0.00 0.00 2.43
303 304 5.540400 AATTTTCTGGCCCATGTGATATG 57.460 39.130 0.00 0.00 0.00 1.78
308 309 2.078392 GCAAATTTTCTGGCCCATGTG 58.922 47.619 0.00 0.00 0.00 3.21
359 376 4.340246 CACCAGCCAGAGCAGCCA 62.340 66.667 0.00 0.00 43.56 4.75
394 412 1.632965 GGGGAGGCGTTTAGGTCCAT 61.633 60.000 0.00 0.00 0.00 3.41
408 426 4.195416 GAGTGATTAGCTTTCAAGGGGAG 58.805 47.826 0.00 0.00 0.00 4.30
495 1220 5.793817 TCTGCAGAGCTAATTGTTAACTGA 58.206 37.500 13.74 0.00 0.00 3.41
506 1231 6.602410 AGCATATCTATTCTGCAGAGCTAA 57.398 37.500 17.43 1.82 38.37 3.09
514 1239 6.039616 GGTGTAGCTAGCATATCTATTCTGC 58.960 44.000 18.83 0.00 36.15 4.26
534 1259 3.054361 CCTAATCCTGGTTTGCTAGGTGT 60.054 47.826 0.21 0.00 43.13 4.16
582 1307 5.174398 CACACATGTTTCTTTGCTGATCAAC 59.826 40.000 0.00 0.00 33.73 3.18
674 1399 4.229582 AGAGGGGTGTTGAAGGCATTAATA 59.770 41.667 0.00 0.00 0.00 0.98
759 1484 8.821894 CAAGTCTGAACTAATAATAAGAGCACC 58.178 37.037 0.00 0.00 33.48 5.01
1003 1738 3.575965 AATAAGCTTTTTGCAGACGGG 57.424 42.857 3.20 0.00 45.94 5.28
1057 1792 2.744202 GTGGCGCATCCCATTCTATAAG 59.256 50.000 10.83 0.00 37.20 1.73
1060 1795 0.250901 GGTGGCGCATCCCATTCTAT 60.251 55.000 10.83 0.00 37.20 1.98
1108 1843 2.792599 GATCGTGGAGACTCGCGT 59.207 61.111 5.77 0.00 46.27 6.01
1129 1864 4.796231 GCACAGACGGACGGCGAT 62.796 66.667 16.62 0.00 0.00 4.58
1220 1955 2.680352 ACGACAGCGATCTGGGGT 60.680 61.111 0.00 0.00 44.54 4.95
1465 2201 5.284861 TCAGTGTCCTACAGCAAAAGTTA 57.715 39.130 0.00 0.00 0.00 2.24
1679 2419 4.165372 TCCATAGTTTGGTTGGGGATAGAC 59.835 45.833 0.00 0.00 46.52 2.59
2110 2857 7.333528 AGAACATTGCTCTTCTACAACAAAA 57.666 32.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.