Multiple sequence alignment - TraesCS1B01G153000

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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 TraesCS1B01G153000 chr1B 100.000 2585 0 0 1 2585 248232814 248235398 0.000000e+00 4774.0
1 TraesCS1B01G153000 chr3A 89.918 2440 181 32 175 2585 688138573 688140976 0.000000e+00 3083.0
2 TraesCS1B01G153000 chr3A 90.400 250 21 2 2322 2568 364197308 364197059 2.480000e-85 326.0
3 TraesCS1B01G153000 chr3A 90.909 132 7 3 1780 1906 364198152 364198021 3.420000e-39 172.0
4 TraesCS1B01G153000 chrUn 93.700 1238 49 10 1356 2585 90338671 90339887 0.000000e+00 1827.0
5 TraesCS1B01G153000 chrUn 93.700 1238 49 10 1356 2585 290522896 290524112 0.000000e+00 1827.0
6 TraesCS1B01G153000 chr1A 94.613 1151 44 9 1445 2585 9820058 9818916 0.000000e+00 1766.0
7 TraesCS1B01G153000 chr1A 91.429 245 20 1 958 1201 9820302 9820058 4.120000e-88 335.0
8 TraesCS1B01G153000 chr1A 79.412 272 37 9 171 423 9839263 9838992 9.510000e-40 174.0
9 TraesCS1B01G153000 chr1A 83.051 177 24 5 4 176 573498081 573497907 3.440000e-34 156.0
10 TraesCS1B01G153000 chr2B 91.958 1144 82 8 637 1772 440826655 440827796 0.000000e+00 1594.0
11 TraesCS1B01G153000 chr2D 91.243 1142 92 6 637 1772 371702005 371703144 0.000000e+00 1548.0
12 TraesCS1B01G153000 chr2D 96.552 58 2 0 171 228 648543142 648543085 2.120000e-16 97.1
13 TraesCS1B01G153000 chr2A 89.108 1166 94 8 637 1772 502336382 502337544 0.000000e+00 1419.0
14 TraesCS1B01G153000 chr2A 86.452 155 14 5 27 176 359427019 359427171 2.060000e-36 163.0
15 TraesCS1B01G153000 chr3B 88.327 831 57 18 1771 2585 799775383 799776189 0.000000e+00 961.0
16 TraesCS1B01G153000 chr3B 82.495 497 58 14 170 642 799774559 799775050 2.390000e-110 409.0
17 TraesCS1B01G153000 chr3B 91.165 249 20 1 2322 2568 375499368 375499120 1.150000e-88 337.0
18 TraesCS1B01G153000 chr3B 88.060 134 12 2 1780 1909 375500182 375500049 3.440000e-34 156.0
19 TraesCS1B01G153000 chr3B 96.970 33 1 0 171 203 71131586 71131554 3.590000e-04 56.5
20 TraesCS1B01G153000 chr7B 91.607 560 37 7 1771 2326 693971709 693972262 0.000000e+00 765.0
21 TraesCS1B01G153000 chr7B 82.341 487 66 10 167 635 693970884 693971368 3.100000e-109 405.0
22 TraesCS1B01G153000 chr6B 88.557 603 45 5 1986 2585 337884423 337885004 0.000000e+00 710.0
23 TraesCS1B01G153000 chr6B 88.696 230 14 6 1771 2000 337876124 337876341 1.180000e-68 270.0
24 TraesCS1B01G153000 chr3D 91.165 249 19 3 2322 2568 275995946 275996193 4.120000e-88 335.0
25 TraesCS1B01G153000 chr3D 81.377 247 24 8 1926 2157 275995216 275995455 5.680000e-42 182.0
26 TraesCS1B01G153000 chr3D 84.181 177 21 6 4 176 119240358 119240531 5.720000e-37 165.0
27 TraesCS1B01G153000 chr3D 87.692 130 12 2 1781 1906 275995030 275995159 5.760000e-32 148.0
28 TraesCS1B01G153000 chr4B 93.182 220 7 4 1932 2151 97560292 97560081 1.490000e-82 316.0
29 TraesCS1B01G153000 chr4B 81.402 371 38 15 170 515 662414555 662414919 9.110000e-70 274.0
30 TraesCS1B01G153000 chr4B 85.119 168 18 6 4 167 440069986 440069822 5.720000e-37 165.0
31 TraesCS1B01G153000 chr4B 86.184 152 14 7 28 176 237441146 237440999 9.580000e-35 158.0
32 TraesCS1B01G153000 chr4D 87.640 178 18 4 2 176 405806489 405806313 1.210000e-48 204.0
33 TraesCS1B01G153000 chr4D 87.640 178 17 5 2 176 405846073 405845898 4.360000e-48 202.0
34 TraesCS1B01G153000 chr1D 84.000 175 24 4 4 176 477245043 477244871 5.720000e-37 165.0
35 TraesCS1B01G153000 chr7D 83.523 176 20 8 6 176 12870622 12870793 3.440000e-34 156.0
36 TraesCS1B01G153000 chr5B 92.958 71 5 0 566 636 452134400 452134330 1.270000e-18 104.0
37 TraesCS1B01G153000 chr6D 93.333 60 2 1 171 228 104078292 104078233 1.270000e-13 87.9
38 TraesCS1B01G153000 chr6D 95.745 47 2 0 179 225 45507079 45507033 2.760000e-10 76.8
39 TraesCS1B01G153000 chr5D 100.000 31 0 0 171 201 458813023 458813053 9.990000e-05 58.4


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 TraesCS1B01G153000 chr1B 248232814 248235398 2584 False 4774.000000 4774 100.000000 1 2585 1 chr1B.!!$F1 2584
1 TraesCS1B01G153000 chr3A 688138573 688140976 2403 False 3083.000000 3083 89.918000 175 2585 1 chr3A.!!$F1 2410
2 TraesCS1B01G153000 chr3A 364197059 364198152 1093 True 249.000000 326 90.654500 1780 2568 2 chr3A.!!$R1 788
3 TraesCS1B01G153000 chrUn 90338671 90339887 1216 False 1827.000000 1827 93.700000 1356 2585 1 chrUn.!!$F1 1229
4 TraesCS1B01G153000 chrUn 290522896 290524112 1216 False 1827.000000 1827 93.700000 1356 2585 1 chrUn.!!$F2 1229
5 TraesCS1B01G153000 chr1A 9818916 9820302 1386 True 1050.500000 1766 93.021000 958 2585 2 chr1A.!!$R3 1627
6 TraesCS1B01G153000 chr2B 440826655 440827796 1141 False 1594.000000 1594 91.958000 637 1772 1 chr2B.!!$F1 1135
7 TraesCS1B01G153000 chr2D 371702005 371703144 1139 False 1548.000000 1548 91.243000 637 1772 1 chr2D.!!$F1 1135
8 TraesCS1B01G153000 chr2A 502336382 502337544 1162 False 1419.000000 1419 89.108000 637 1772 1 chr2A.!!$F2 1135
9 TraesCS1B01G153000 chr3B 799774559 799776189 1630 False 685.000000 961 85.411000 170 2585 2 chr3B.!!$F1 2415
10 TraesCS1B01G153000 chr3B 375499120 375500182 1062 True 246.500000 337 89.612500 1780 2568 2 chr3B.!!$R2 788
11 TraesCS1B01G153000 chr7B 693970884 693972262 1378 False 585.000000 765 86.974000 167 2326 2 chr7B.!!$F1 2159
12 TraesCS1B01G153000 chr6B 337884423 337885004 581 False 710.000000 710 88.557000 1986 2585 1 chr6B.!!$F2 599
13 TraesCS1B01G153000 chr3D 275995030 275996193 1163 False 221.666667 335 86.744667 1781 2568 3 chr3D.!!$F2 787

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
423 447 0.467384 AAGCATCCCCAGTCAGATCG 59.533 55.0 0.0 0.0 0.0 3.69 F
1229 1316 0.538287 GTTTCCTGCTGCTCAACCCT 60.538 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 1491 0.321671 CCTCTTCGATGGTGTGGTGT 59.678 55.000 0.0 0.0 0.0 4.16 R
2527 3079 1.409521 CCCTCAACACCAAACCACTCA 60.410 52.381 0.0 0.0 0.0 3.41 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
68 69 7.694388 AAAAGCTTCGTCCATTTCTAAAAAC 57.306 32.000 0.00 0.00 0.00 2.43
69 70 6.635030 AAGCTTCGTCCATTTCTAAAAACT 57.365 33.333 0.00 0.00 0.00 2.66
70 71 6.635030 AGCTTCGTCCATTTCTAAAAACTT 57.365 33.333 0.00 0.00 0.00 2.66
71 72 7.039313 AGCTTCGTCCATTTCTAAAAACTTT 57.961 32.000 0.00 0.00 0.00 2.66
72 73 7.489160 AGCTTCGTCCATTTCTAAAAACTTTT 58.511 30.769 0.00 0.00 0.00 2.27
73 74 8.626526 AGCTTCGTCCATTTCTAAAAACTTTTA 58.373 29.630 0.00 0.00 0.00 1.52
74 75 9.406828 GCTTCGTCCATTTCTAAAAACTTTTAT 57.593 29.630 0.00 0.00 32.69 1.40
105 106 4.787260 AAAAACAACACCACGGTAGTTT 57.213 36.364 7.43 7.43 32.34 2.66
106 107 4.787260 AAAACAACACCACGGTAGTTTT 57.213 36.364 15.15 15.15 34.78 2.43
107 108 3.768468 AACAACACCACGGTAGTTTTG 57.232 42.857 4.43 4.43 0.00 2.44
108 109 2.713877 ACAACACCACGGTAGTTTTGT 58.286 42.857 5.59 5.59 0.00 2.83
109 110 3.083293 ACAACACCACGGTAGTTTTGTT 58.917 40.909 5.59 0.00 34.69 2.83
110 111 4.260170 ACAACACCACGGTAGTTTTGTTA 58.740 39.130 5.59 0.00 33.38 2.41
111 112 4.699257 ACAACACCACGGTAGTTTTGTTAA 59.301 37.500 5.59 0.00 33.38 2.01
112 113 5.182760 ACAACACCACGGTAGTTTTGTTAAA 59.817 36.000 5.59 0.00 33.38 1.52
113 114 5.893897 ACACCACGGTAGTTTTGTTAAAA 57.106 34.783 0.00 0.00 0.00 1.52
114 115 6.264841 ACACCACGGTAGTTTTGTTAAAAA 57.735 33.333 0.00 0.00 32.82 1.94
127 128 4.886247 TGTTAAAAACAACCTCAGTCCG 57.114 40.909 0.00 0.00 38.72 4.79
128 129 4.515361 TGTTAAAAACAACCTCAGTCCGA 58.485 39.130 0.00 0.00 38.72 4.55
129 130 4.573201 TGTTAAAAACAACCTCAGTCCGAG 59.427 41.667 0.00 0.00 38.72 4.63
130 131 3.277142 AAAAACAACCTCAGTCCGAGT 57.723 42.857 0.00 0.00 40.48 4.18
131 132 3.277142 AAAACAACCTCAGTCCGAGTT 57.723 42.857 0.00 0.00 40.48 3.01
132 133 4.411256 AAAACAACCTCAGTCCGAGTTA 57.589 40.909 0.00 0.00 40.48 2.24
133 134 3.662247 AACAACCTCAGTCCGAGTTAG 57.338 47.619 0.00 0.00 40.48 2.34
134 135 2.595238 ACAACCTCAGTCCGAGTTAGT 58.405 47.619 0.00 0.00 40.48 2.24
135 136 2.963782 ACAACCTCAGTCCGAGTTAGTT 59.036 45.455 0.00 0.00 40.48 2.24
136 137 3.005578 ACAACCTCAGTCCGAGTTAGTTC 59.994 47.826 0.00 0.00 40.48 3.01
137 138 3.157750 ACCTCAGTCCGAGTTAGTTCT 57.842 47.619 0.00 0.00 40.48 3.01
138 139 4.298103 ACCTCAGTCCGAGTTAGTTCTA 57.702 45.455 0.00 0.00 40.48 2.10
139 140 4.857679 ACCTCAGTCCGAGTTAGTTCTAT 58.142 43.478 0.00 0.00 40.48 1.98
140 141 5.262804 ACCTCAGTCCGAGTTAGTTCTATT 58.737 41.667 0.00 0.00 40.48 1.73
141 142 5.357596 ACCTCAGTCCGAGTTAGTTCTATTC 59.642 44.000 0.00 0.00 40.48 1.75
142 143 5.357314 CCTCAGTCCGAGTTAGTTCTATTCA 59.643 44.000 0.00 0.00 40.48 2.57
143 144 6.127703 CCTCAGTCCGAGTTAGTTCTATTCAA 60.128 42.308 0.00 0.00 40.48 2.69
144 145 7.223260 TCAGTCCGAGTTAGTTCTATTCAAA 57.777 36.000 0.00 0.00 0.00 2.69
145 146 7.837863 TCAGTCCGAGTTAGTTCTATTCAAAT 58.162 34.615 0.00 0.00 0.00 2.32
146 147 7.974501 TCAGTCCGAGTTAGTTCTATTCAAATC 59.025 37.037 0.00 0.00 0.00 2.17
147 148 7.759886 CAGTCCGAGTTAGTTCTATTCAAATCA 59.240 37.037 0.00 0.00 0.00 2.57
148 149 8.478877 AGTCCGAGTTAGTTCTATTCAAATCAT 58.521 33.333 0.00 0.00 0.00 2.45
149 150 9.745880 GTCCGAGTTAGTTCTATTCAAATCATA 57.254 33.333 0.00 0.00 0.00 2.15
164 165 9.902684 ATTCAAATCATATAAAATTGCACCCAA 57.097 25.926 0.00 0.00 35.01 4.12
165 166 9.730705 TTCAAATCATATAAAATTGCACCCAAA 57.269 25.926 0.00 0.00 34.05 3.28
172 173 9.558396 CATATAAAATTGCACCCAAACCATATT 57.442 29.630 0.00 0.00 34.05 1.28
193 194 1.303091 AACCCATTAACAGTCGCGGC 61.303 55.000 0.21 0.21 0.00 6.53
195 196 1.095228 CCCATTAACAGTCGCGGCAT 61.095 55.000 15.58 0.23 0.00 4.40
218 220 1.190833 CGCCTCCTCCTGCTATCCAT 61.191 60.000 0.00 0.00 0.00 3.41
243 245 7.999679 TGTCATCACAAGAAGACAAAAAGAAT 58.000 30.769 1.56 0.00 46.11 2.40
260 262 7.796958 AAAAGAATAACAAGTTAGCGATTGC 57.203 32.000 0.00 0.00 43.24 3.56
287 293 4.212150 GCAGTAAAGAGCGAGACAAAAAC 58.788 43.478 0.00 0.00 0.00 2.43
289 295 5.435557 CAGTAAAGAGCGAGACAAAAACAG 58.564 41.667 0.00 0.00 0.00 3.16
290 296 3.971032 AAAGAGCGAGACAAAAACAGG 57.029 42.857 0.00 0.00 0.00 4.00
291 297 1.230324 AGAGCGAGACAAAAACAGGC 58.770 50.000 0.00 0.00 0.00 4.85
292 298 1.202698 AGAGCGAGACAAAAACAGGCT 60.203 47.619 0.00 0.00 0.00 4.58
306 329 1.202639 ACAGGCTCGTCATCAACACAA 60.203 47.619 0.00 0.00 0.00 3.33
312 335 1.579429 GTCATCAACACAACCGCCC 59.421 57.895 0.00 0.00 0.00 6.13
314 337 1.900981 CATCAACACAACCGCCCCA 60.901 57.895 0.00 0.00 0.00 4.96
335 358 1.686587 TCCTGTGCTCGTTTCTCTCAA 59.313 47.619 0.00 0.00 0.00 3.02
383 407 1.086634 GGAGAACCACGAGCATGAGC 61.087 60.000 0.00 0.00 37.27 4.26
404 428 1.737735 CCACAATCGCGTCAGCAGA 60.738 57.895 5.77 0.00 45.49 4.26
414 438 1.300963 GTCAGCAGAAGCATCCCCA 59.699 57.895 0.00 0.00 45.49 4.96
415 439 0.747283 GTCAGCAGAAGCATCCCCAG 60.747 60.000 0.00 0.00 45.49 4.45
423 447 0.467384 AAGCATCCCCAGTCAGATCG 59.533 55.000 0.00 0.00 0.00 3.69
426 450 1.050988 CATCCCCAGTCAGATCGGGT 61.051 60.000 6.41 0.00 38.40 5.28
540 564 2.716864 GGCTCTAGCTCGTCGTCC 59.283 66.667 1.39 0.00 41.70 4.79
542 566 2.113433 GCTCTAGCTCGTCGTCCCA 61.113 63.158 0.00 0.00 38.21 4.37
569 593 0.745845 GGCACGTGCTCTTCATCCAT 60.746 55.000 36.84 0.00 41.70 3.41
639 663 2.626780 CGTGCTCGAGGTGGAGACA 61.627 63.158 15.58 0.00 39.71 3.41
691 776 1.133009 GGAGGAGGAGGATAGGAGCAA 60.133 57.143 0.00 0.00 0.00 3.91
789 875 1.304134 TCGCTGCAGACTACCTCCA 60.304 57.895 20.43 0.00 0.00 3.86
881 967 1.589630 CCCATCACGGACGTTCTCA 59.410 57.895 0.00 0.00 36.56 3.27
916 1002 1.153309 CATGCCTCTCATCGTGCCA 60.153 57.895 0.00 0.00 31.79 4.92
977 1063 1.069775 AATACCCAACCCGTTCCTGT 58.930 50.000 0.00 0.00 0.00 4.00
1065 1152 2.434359 CTCAAGGCCCGACGGAAC 60.434 66.667 17.49 7.62 0.00 3.62
1066 1153 2.920912 TCAAGGCCCGACGGAACT 60.921 61.111 17.49 10.09 0.00 3.01
1088 1175 2.260869 GGCTGTTGTGGTGCACGAT 61.261 57.895 11.45 0.00 37.14 3.73
1137 1224 2.202878 GCGACGGGAGCTGCAATA 60.203 61.111 7.79 0.00 0.00 1.90
1229 1316 0.538287 GTTTCCTGCTGCTCAACCCT 60.538 55.000 0.00 0.00 0.00 4.34
1309 1396 1.805943 CCGATGTGCTCAACAATGACA 59.194 47.619 0.00 0.00 43.61 3.58
1334 1421 1.303236 CCATTGAACGGCTGGTGGA 60.303 57.895 0.00 0.00 0.00 4.02
1335 1422 0.680921 CCATTGAACGGCTGGTGGAT 60.681 55.000 0.00 0.00 0.00 3.41
1381 1468 5.488341 GTGACAAGATCTTGGTTAGGCTAA 58.512 41.667 33.11 2.04 44.45 3.09
1527 1614 0.671163 CCGTTAACCGTGCAAGGCTA 60.671 55.000 19.37 8.26 33.66 3.93
1915 2098 9.657121 GATTAAGCTTGTGAGTTTATAATCAGC 57.343 33.333 9.86 0.00 30.15 4.26
1981 2168 6.376018 TGGGTGCAAGTATTTCTATTTGGTAC 59.624 38.462 0.00 0.00 0.00 3.34
1982 2169 6.602009 GGGTGCAAGTATTTCTATTTGGTACT 59.398 38.462 0.00 0.00 0.00 2.73
1983 2170 7.415206 GGGTGCAAGTATTTCTATTTGGTACTG 60.415 40.741 0.00 0.00 0.00 2.74
1984 2171 7.120726 GGTGCAAGTATTTCTATTTGGTACTGT 59.879 37.037 0.00 0.00 0.00 3.55
2010 2199 8.840833 ATTTAACTTGATAATTGCCGGTTTTT 57.159 26.923 1.90 0.00 0.00 1.94
2140 2354 5.178438 CAGCTCTCAGTCAAACTTCTTTACC 59.822 44.000 0.00 0.00 0.00 2.85
2213 2475 5.728898 GCTTTTATATGCACTGAGCTGTGTC 60.729 44.000 6.11 0.26 45.94 3.67
2257 2522 7.716799 TGCATTACTTCATTTTAGTTCCCAT 57.283 32.000 0.00 0.00 0.00 4.00
2275 2540 7.176690 AGTTCCCATGAATTAAACGTCAAAGAT 59.823 33.333 0.00 0.00 31.98 2.40
2320 2869 5.407407 AGAAGTCGATAAGCCAGAAGAAA 57.593 39.130 0.00 0.00 0.00 2.52
2527 3079 6.723298 TGTGTAGTTGGGATTTCAAATGTT 57.277 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 7.979537 AGTTTTTAGAAATGGACGAAGCTTTTT 59.020 29.630 0.00 0.00 0.00 1.94
44 45 7.489160 AGTTTTTAGAAATGGACGAAGCTTTT 58.511 30.769 0.00 0.00 0.00 2.27
45 46 7.039313 AGTTTTTAGAAATGGACGAAGCTTT 57.961 32.000 0.00 0.00 0.00 3.51
46 47 6.635030 AGTTTTTAGAAATGGACGAAGCTT 57.365 33.333 0.00 0.00 0.00 3.74
47 48 6.635030 AAGTTTTTAGAAATGGACGAAGCT 57.365 33.333 0.00 0.00 0.00 3.74
48 49 7.694388 AAAAGTTTTTAGAAATGGACGAAGC 57.306 32.000 0.00 0.00 0.00 3.86
84 85 4.787260 AAACTACCGTGGTGTTGTTTTT 57.213 36.364 0.72 0.00 39.85 1.94
85 86 4.787260 AAAACTACCGTGGTGTTGTTTT 57.213 36.364 18.03 18.03 43.93 2.43
86 87 3.506844 ACAAAACTACCGTGGTGTTGTTT 59.493 39.130 15.82 7.62 40.84 2.83
87 88 3.083293 ACAAAACTACCGTGGTGTTGTT 58.917 40.909 15.82 3.35 40.84 2.83
88 89 2.713877 ACAAAACTACCGTGGTGTTGT 58.286 42.857 15.82 15.82 39.45 3.32
89 90 3.768468 AACAAAACTACCGTGGTGTTG 57.232 42.857 14.63 14.63 37.76 3.33
90 91 5.893897 TTTAACAAAACTACCGTGGTGTT 57.106 34.783 0.72 1.74 35.95 3.32
91 92 5.893897 TTTTAACAAAACTACCGTGGTGT 57.106 34.783 0.72 0.00 0.00 4.16
92 93 6.557593 GTTTTTAACAAAACTACCGTGGTG 57.442 37.500 0.72 0.00 45.80 4.17
103 104 7.838983 CTCGGACTGAGGTTGTTTTTAACAAAA 60.839 37.037 3.07 0.00 43.33 2.44
104 105 6.403855 CTCGGACTGAGGTTGTTTTTAACAAA 60.404 38.462 3.07 0.00 43.33 2.83
105 106 5.065474 CTCGGACTGAGGTTGTTTTTAACAA 59.935 40.000 3.07 1.10 43.70 2.83
106 107 4.515361 TCGGACTGAGGTTGTTTTTAACA 58.485 39.130 0.00 0.00 40.21 2.41
107 108 5.065602 AACTCGGACTGAGGTTGTTTTTAAC 59.934 40.000 15.76 0.00 44.19 2.01
108 109 5.187687 AACTCGGACTGAGGTTGTTTTTAA 58.812 37.500 15.76 0.00 44.19 1.52
109 110 4.773013 AACTCGGACTGAGGTTGTTTTTA 58.227 39.130 15.76 0.00 44.19 1.52
110 111 3.617284 AACTCGGACTGAGGTTGTTTTT 58.383 40.909 15.76 0.00 44.19 1.94
111 112 3.277142 AACTCGGACTGAGGTTGTTTT 57.723 42.857 15.76 0.00 44.19 2.43
112 113 3.387050 ACTAACTCGGACTGAGGTTGTTT 59.613 43.478 15.76 3.14 46.24 2.83
113 114 2.963782 ACTAACTCGGACTGAGGTTGTT 59.036 45.455 15.76 4.31 46.24 2.83
114 115 2.595238 ACTAACTCGGACTGAGGTTGT 58.405 47.619 15.76 12.94 44.19 3.32
115 116 3.256136 AGAACTAACTCGGACTGAGGTTG 59.744 47.826 15.76 12.28 44.19 3.77
116 117 3.498334 AGAACTAACTCGGACTGAGGTT 58.502 45.455 15.76 9.71 44.19 3.50
120 121 6.829229 TTGAATAGAACTAACTCGGACTGA 57.171 37.500 0.00 0.00 0.00 3.41
121 122 7.759886 TGATTTGAATAGAACTAACTCGGACTG 59.240 37.037 0.00 0.00 0.00 3.51
122 123 7.837863 TGATTTGAATAGAACTAACTCGGACT 58.162 34.615 0.00 0.00 0.00 3.85
123 124 8.649973 ATGATTTGAATAGAACTAACTCGGAC 57.350 34.615 0.00 0.00 0.00 4.79
138 139 9.902684 TTGGGTGCAATTTTATATGATTTGAAT 57.097 25.926 0.00 0.00 0.00 2.57
139 140 9.730705 TTTGGGTGCAATTTTATATGATTTGAA 57.269 25.926 0.00 0.00 0.00 2.69
140 141 9.160496 GTTTGGGTGCAATTTTATATGATTTGA 57.840 29.630 0.00 0.00 0.00 2.69
141 142 8.397148 GGTTTGGGTGCAATTTTATATGATTTG 58.603 33.333 0.00 0.00 0.00 2.32
142 143 8.105829 TGGTTTGGGTGCAATTTTATATGATTT 58.894 29.630 0.00 0.00 0.00 2.17
143 144 7.628234 TGGTTTGGGTGCAATTTTATATGATT 58.372 30.769 0.00 0.00 0.00 2.57
144 145 7.192852 TGGTTTGGGTGCAATTTTATATGAT 57.807 32.000 0.00 0.00 0.00 2.45
145 146 6.611613 TGGTTTGGGTGCAATTTTATATGA 57.388 33.333 0.00 0.00 0.00 2.15
146 147 9.558396 AATATGGTTTGGGTGCAATTTTATATG 57.442 29.630 0.00 0.00 0.00 1.78
149 150 9.965902 TTTAATATGGTTTGGGTGCAATTTTAT 57.034 25.926 0.00 0.00 0.00 1.40
150 151 9.220767 GTTTAATATGGTTTGGGTGCAATTTTA 57.779 29.630 0.00 0.00 0.00 1.52
151 152 7.175816 GGTTTAATATGGTTTGGGTGCAATTTT 59.824 33.333 0.00 0.00 0.00 1.82
152 153 6.657117 GGTTTAATATGGTTTGGGTGCAATTT 59.343 34.615 0.00 0.00 0.00 1.82
153 154 6.176896 GGTTTAATATGGTTTGGGTGCAATT 58.823 36.000 0.00 0.00 0.00 2.32
154 155 5.338789 GGGTTTAATATGGTTTGGGTGCAAT 60.339 40.000 0.00 0.00 0.00 3.56
155 156 4.020128 GGGTTTAATATGGTTTGGGTGCAA 60.020 41.667 0.00 0.00 0.00 4.08
156 157 3.515901 GGGTTTAATATGGTTTGGGTGCA 59.484 43.478 0.00 0.00 0.00 4.57
157 158 3.515901 TGGGTTTAATATGGTTTGGGTGC 59.484 43.478 0.00 0.00 0.00 5.01
158 159 5.948742 ATGGGTTTAATATGGTTTGGGTG 57.051 39.130 0.00 0.00 0.00 4.61
159 160 7.458170 TGTTAATGGGTTTAATATGGTTTGGGT 59.542 33.333 0.00 0.00 32.56 4.51
160 161 7.852263 TGTTAATGGGTTTAATATGGTTTGGG 58.148 34.615 0.00 0.00 32.56 4.12
161 162 8.536175 ACTGTTAATGGGTTTAATATGGTTTGG 58.464 33.333 0.00 0.00 32.56 3.28
162 163 9.581099 GACTGTTAATGGGTTTAATATGGTTTG 57.419 33.333 0.00 0.00 32.56 2.93
163 164 8.463607 CGACTGTTAATGGGTTTAATATGGTTT 58.536 33.333 0.00 0.00 32.56 3.27
164 165 7.415877 GCGACTGTTAATGGGTTTAATATGGTT 60.416 37.037 0.00 0.00 32.56 3.67
165 166 6.038936 GCGACTGTTAATGGGTTTAATATGGT 59.961 38.462 0.00 0.00 32.56 3.55
172 173 2.348660 CCGCGACTGTTAATGGGTTTA 58.651 47.619 8.23 0.00 0.00 2.01
193 194 4.559063 CAGGAGGAGGCGCCCATG 62.559 72.222 26.15 12.17 37.37 3.66
205 207 3.070590 TGTGATGACATGGATAGCAGGAG 59.929 47.826 0.00 0.00 0.00 3.69
206 208 3.040477 TGTGATGACATGGATAGCAGGA 58.960 45.455 0.00 0.00 0.00 3.86
207 209 3.480505 TGTGATGACATGGATAGCAGG 57.519 47.619 0.00 0.00 0.00 4.85
243 245 2.413796 CCACGCAATCGCTAACTTGTTA 59.586 45.455 0.00 0.00 39.84 2.41
260 262 1.078759 CTCGCTCTTTACTGCCCACG 61.079 60.000 0.00 0.00 0.00 4.94
269 275 3.250040 GCCTGTTTTTGTCTCGCTCTTTA 59.750 43.478 0.00 0.00 0.00 1.85
287 293 1.195448 GTTGTGTTGATGACGAGCCTG 59.805 52.381 0.00 0.00 0.00 4.85
289 295 0.517316 GGTTGTGTTGATGACGAGCC 59.483 55.000 0.00 0.00 0.00 4.70
290 296 0.163788 CGGTTGTGTTGATGACGAGC 59.836 55.000 0.00 0.00 0.00 5.03
291 297 0.163788 GCGGTTGTGTTGATGACGAG 59.836 55.000 0.00 0.00 0.00 4.18
292 298 1.225376 GGCGGTTGTGTTGATGACGA 61.225 55.000 0.00 0.00 0.00 4.20
294 300 1.579429 GGGCGGTTGTGTTGATGAC 59.421 57.895 0.00 0.00 0.00 3.06
312 335 1.066573 AGAGAAACGAGCACAGGATGG 60.067 52.381 0.00 0.00 43.62 3.51
314 337 1.895798 TGAGAGAAACGAGCACAGGAT 59.104 47.619 0.00 0.00 0.00 3.24
354 378 2.606826 GGTTCTCCTCCCGGTGGT 60.607 66.667 0.00 0.00 0.00 4.16
383 407 3.071459 GCTGACGCGATTGTGGTCG 62.071 63.158 15.93 0.00 44.14 4.79
392 416 1.807165 GATGCTTCTGCTGACGCGA 60.807 57.895 15.93 7.01 39.91 5.87
397 421 1.203441 ACTGGGGATGCTTCTGCTGA 61.203 55.000 0.00 0.00 40.48 4.26
404 428 0.467384 CGATCTGACTGGGGATGCTT 59.533 55.000 0.00 0.00 0.00 3.91
414 438 1.954362 GCTGAGCACCCGATCTGACT 61.954 60.000 0.00 0.00 0.00 3.41
415 439 1.520342 GCTGAGCACCCGATCTGAC 60.520 63.158 0.00 0.00 0.00 3.51
469 493 1.472201 GCCTGCTCGATCTTGATGTGA 60.472 52.381 0.00 0.00 0.00 3.58
515 539 2.045242 AGCTAGAGCCGTCGTGGA 60.045 61.111 0.00 0.00 43.38 4.02
561 585 1.475034 GGAGCCGTGCTTATGGATGAA 60.475 52.381 0.00 0.00 39.88 2.57
564 588 1.069765 CGGAGCCGTGCTTATGGAT 59.930 57.895 0.00 0.00 39.88 3.41
667 691 0.039035 CCTATCCTCCTCCTCCTCGG 59.961 65.000 0.00 0.00 0.00 4.63
775 861 0.831711 TGCTGTGGAGGTAGTCTGCA 60.832 55.000 0.00 0.00 41.66 4.41
850 936 3.792053 GATGGGCCCGTAGAGTGCG 62.792 68.421 19.13 0.00 0.00 5.34
853 939 2.423898 CGTGATGGGCCCGTAGAGT 61.424 63.158 19.13 0.00 0.00 3.24
908 994 2.738521 GTCGCAGTGTGGCACGAT 60.739 61.111 13.77 0.19 39.64 3.73
909 995 3.911698 AGTCGCAGTGTGGCACGA 61.912 61.111 13.77 2.78 39.64 4.35
1065 1152 3.663176 CACCACAACAGCCGGCAG 61.663 66.667 31.54 24.99 0.00 4.85
1084 1171 4.760047 GCCAGACCCGCACATCGT 62.760 66.667 0.00 0.00 36.19 3.73
1088 1175 3.321648 AGATGCCAGACCCGCACA 61.322 61.111 0.00 0.00 39.49 4.57
1134 1221 0.032678 CGATGACGAGGCCAGCTATT 59.967 55.000 5.01 0.00 42.66 1.73
1137 1224 4.521062 GCGATGACGAGGCCAGCT 62.521 66.667 5.01 0.00 42.66 4.24
1204 1291 4.389576 GCAGCAGGAAACACGCGG 62.390 66.667 12.47 1.27 36.26 6.46
1211 1298 0.250901 GAGGGTTGAGCAGCAGGAAA 60.251 55.000 0.00 0.00 0.00 3.13
1229 1316 1.003839 AGGCGTTTCATCCAAGCGA 60.004 52.632 0.00 0.00 40.95 4.93
1354 1441 3.884037 AACCAAGATCTTGTCACCCTT 57.116 42.857 29.03 10.88 38.85 3.95
1404 1491 0.321671 CCTCTTCGATGGTGTGGTGT 59.678 55.000 0.00 0.00 0.00 4.16
1440 1527 5.221742 GCATAGTAGGCTAGGATGGTTCTTT 60.222 44.000 14.35 0.00 31.18 2.52
1527 1614 4.335416 CATTGAGGTGGTGTACAAGGAAT 58.665 43.478 0.00 0.00 0.00 3.01
1610 1724 4.824537 TGAAACCATCCTTGAATCGTGAAA 59.175 37.500 0.00 0.00 0.00 2.69
1915 2098 3.936453 TGGCACTAAAAGCAATACTACCG 59.064 43.478 0.00 0.00 0.00 4.02
1981 2168 7.703328 ACCGGCAATTATCAAGTTAAATACAG 58.297 34.615 0.00 0.00 0.00 2.74
1982 2169 7.633193 ACCGGCAATTATCAAGTTAAATACA 57.367 32.000 0.00 0.00 0.00 2.29
1983 2170 8.920509 AAACCGGCAATTATCAAGTTAAATAC 57.079 30.769 0.00 0.00 0.00 1.89
1984 2171 9.930693 AAAAACCGGCAATTATCAAGTTAAATA 57.069 25.926 0.00 0.00 0.00 1.40
2010 2199 5.612725 ATCTTTGGCCTTTGTTTCTTCAA 57.387 34.783 3.32 0.00 0.00 2.69
2140 2354 4.934075 TTTCAGCAGATTGAAGTGATCG 57.066 40.909 0.00 0.00 38.25 3.69
2320 2869 4.897670 AGCAAAAGCATAAGGCCTTATCAT 59.102 37.500 31.28 20.84 46.50 2.45
2418 2967 7.486407 AAGAAAATGAATGGGCATTACTTCT 57.514 32.000 0.00 0.00 37.12 2.85
2431 2980 6.940430 ATGGTCCAAGGAAAGAAAATGAAT 57.060 33.333 0.00 0.00 0.00 2.57
2508 3060 6.015519 CCACTCAACATTTGAAATCCCAACTA 60.016 38.462 0.00 0.00 39.58 2.24
2511 3063 4.653341 ACCACTCAACATTTGAAATCCCAA 59.347 37.500 0.00 0.00 39.58 4.12
2527 3079 1.409521 CCCTCAACACCAAACCACTCA 60.410 52.381 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.