Multiple sequence alignment - TraesCS6D01G367000

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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 TraesCS6D01G367000 chr6D 100.000 2752 0 0 1 2752 454997521 454994770 0.000000e+00 5083.0
1 TraesCS6D01G367000 chr6D 82.148 1322 153 54 709 1976 455421595 455422887 0.000000e+00 1057.0
2 TraesCS6D01G367000 chr6D 83.437 1129 135 37 776 1879 455425079 455426180 0.000000e+00 1002.0
3 TraesCS6D01G367000 chr6D 83.201 1137 146 27 852 1975 454968146 454967042 0.000000e+00 1000.0
4 TraesCS6D01G367000 chr6D 82.901 1117 139 28 894 1991 454962837 454961754 0.000000e+00 957.0
5 TraesCS6D01G367000 chr6D 80.822 146 15 6 2349 2483 454960451 454960308 4.850000e-18 102.0
6 TraesCS6D01G367000 chr6B 93.709 1526 84 8 445 1963 692095359 692093839 0.000000e+00 2276.0
7 TraesCS6D01G367000 chr6B 91.088 1167 87 10 797 1958 691944716 691945870 0.000000e+00 1563.0
8 TraesCS6D01G367000 chr6B 83.986 1124 140 31 776 1879 692574232 692575335 0.000000e+00 1042.0
9 TraesCS6D01G367000 chr6B 82.840 1148 153 30 852 1975 692044860 692043733 0.000000e+00 989.0
10 TraesCS6D01G367000 chr6B 82.696 1150 151 33 852 1975 691976044 691977171 0.000000e+00 977.0
11 TraesCS6D01G367000 chr6B 86.357 667 66 14 2102 2752 692091932 692091275 0.000000e+00 704.0
12 TraesCS6D01G367000 chr6B 86.378 646 70 12 2114 2752 692074829 692074195 0.000000e+00 689.0
13 TraesCS6D01G367000 chr6B 90.261 421 41 0 80 500 692095778 692095358 4.010000e-153 551.0
14 TraesCS6D01G367000 chr6B 84.513 226 9 10 576 801 691944336 691944535 1.670000e-47 200.0
15 TraesCS6D01G367000 chr6B 89.865 148 8 4 2370 2510 692092097 692091950 1.680000e-42 183.0
16 TraesCS6D01G367000 chr6B 91.111 135 8 2 2380 2510 692074993 692074859 2.180000e-41 180.0
17 TraesCS6D01G367000 chr6B 87.500 80 6 2 2387 2462 691977457 691977536 3.770000e-14 89.8
18 TraesCS6D01G367000 chr6A 90.633 1580 92 21 579 2124 601265081 601263524 0.000000e+00 2047.0
19 TraesCS6D01G367000 chr6A 84.383 1159 128 38 776 1909 602131267 602132397 0.000000e+00 1088.0
20 TraesCS6D01G367000 chr6A 83.608 1153 158 20 852 1991 601257154 601256020 0.000000e+00 1053.0
21 TraesCS6D01G367000 chr6A 81.264 1329 165 47 700 1975 602075320 602076617 0.000000e+00 998.0
22 TraesCS6D01G367000 chr6A 82.259 1133 133 32 852 1968 601241816 601240736 0.000000e+00 917.0
23 TraesCS6D01G367000 chr6A 87.500 80 6 2 2387 2462 601240442 601240363 3.770000e-14 89.8
24 TraesCS6D01G367000 chrUn 88.642 854 72 7 1296 2124 79450181 79449328 0.000000e+00 1016.0
25 TraesCS6D01G367000 chrUn 86.842 646 66 13 2114 2752 79448833 79448200 0.000000e+00 704.0
26 TraesCS6D01G367000 chrUn 85.233 386 32 13 2131 2510 79449229 79448863 9.310000e-100 374.0
27 TraesCS6D01G367000 chr1A 80.107 563 101 5 21 572 554782843 554783405 2.550000e-110 409.0
28 TraesCS6D01G367000 chr4D 80.000 510 90 6 75 573 504197475 504196967 1.560000e-97 366.0
29 TraesCS6D01G367000 chr3A 78.697 568 101 15 21 573 644816964 644817526 7.250000e-96 361.0
30 TraesCS6D01G367000 chr2A 77.778 585 115 8 1 572 70042791 70042209 2.030000e-91 346.0
31 TraesCS6D01G367000 chr2D 77.436 585 118 9 1 573 13127133 13126551 1.220000e-88 337.0
32 TraesCS6D01G367000 chr2D 76.752 585 123 7 1 573 164743440 164742857 5.720000e-82 315.0
33 TraesCS6D01G367000 chr1D 76.621 586 114 11 1 573 458152343 458151768 4.450000e-78 302.0
34 TraesCS6D01G367000 chr7D 76.148 566 116 15 24 573 561805449 561806011 2.090000e-71 279.0
35 TraesCS6D01G367000 chr4B 77.007 461 89 12 131 576 575652747 575652289 5.890000e-62 248.0
36 TraesCS6D01G367000 chr5A 80.162 247 38 9 2099 2337 514762691 514762934 1.010000e-39 174.0
37 TraesCS6D01G367000 chr5D 75.635 197 33 11 2097 2284 326401268 326401078 1.760000e-12 84.2


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 TraesCS6D01G367000 chr6D 454994770 454997521 2751 True 5083.0 5083 100.000000 1 2752 1 chr6D.!!$R2 2751
1 TraesCS6D01G367000 chr6D 455421595 455426180 4585 False 1029.5 1057 82.792500 709 1976 2 chr6D.!!$F1 1267
2 TraesCS6D01G367000 chr6D 454967042 454968146 1104 True 1000.0 1000 83.201000 852 1975 1 chr6D.!!$R1 1123
3 TraesCS6D01G367000 chr6D 454960308 454962837 2529 True 529.5 957 81.861500 894 2483 2 chr6D.!!$R3 1589
4 TraesCS6D01G367000 chr6B 692574232 692575335 1103 False 1042.0 1042 83.986000 776 1879 1 chr6B.!!$F1 1103
5 TraesCS6D01G367000 chr6B 692043733 692044860 1127 True 989.0 989 82.840000 852 1975 1 chr6B.!!$R1 1123
6 TraesCS6D01G367000 chr6B 692091275 692095778 4503 True 928.5 2276 90.048000 80 2752 4 chr6B.!!$R3 2672
7 TraesCS6D01G367000 chr6B 691944336 691945870 1534 False 881.5 1563 87.800500 576 1958 2 chr6B.!!$F2 1382
8 TraesCS6D01G367000 chr6B 691976044 691977536 1492 False 533.4 977 85.098000 852 2462 2 chr6B.!!$F3 1610
9 TraesCS6D01G367000 chr6B 692074195 692074993 798 True 434.5 689 88.744500 2114 2752 2 chr6B.!!$R2 638
10 TraesCS6D01G367000 chr6A 601263524 601265081 1557 True 2047.0 2047 90.633000 579 2124 1 chr6A.!!$R2 1545
11 TraesCS6D01G367000 chr6A 602131267 602132397 1130 False 1088.0 1088 84.383000 776 1909 1 chr6A.!!$F2 1133
12 TraesCS6D01G367000 chr6A 601256020 601257154 1134 True 1053.0 1053 83.608000 852 1991 1 chr6A.!!$R1 1139
13 TraesCS6D01G367000 chr6A 602075320 602076617 1297 False 998.0 998 81.264000 700 1975 1 chr6A.!!$F1 1275
14 TraesCS6D01G367000 chr6A 601240363 601241816 1453 True 503.4 917 84.879500 852 2462 2 chr6A.!!$R3 1610
15 TraesCS6D01G367000 chrUn 79448200 79450181 1981 True 698.0 1016 86.905667 1296 2752 3 chrUn.!!$R1 1456
16 TraesCS6D01G367000 chr1A 554782843 554783405 562 False 409.0 409 80.107000 21 572 1 chr1A.!!$F1 551
17 TraesCS6D01G367000 chr4D 504196967 504197475 508 True 366.0 366 80.000000 75 573 1 chr4D.!!$R1 498
18 TraesCS6D01G367000 chr3A 644816964 644817526 562 False 361.0 361 78.697000 21 573 1 chr3A.!!$F1 552
19 TraesCS6D01G367000 chr2A 70042209 70042791 582 True 346.0 346 77.778000 1 572 1 chr2A.!!$R1 571
20 TraesCS6D01G367000 chr2D 13126551 13127133 582 True 337.0 337 77.436000 1 573 1 chr2D.!!$R1 572
21 TraesCS6D01G367000 chr2D 164742857 164743440 583 True 315.0 315 76.752000 1 573 1 chr2D.!!$R2 572
22 TraesCS6D01G367000 chr1D 458151768 458152343 575 True 302.0 302 76.621000 1 573 1 chr1D.!!$R1 572
23 TraesCS6D01G367000 chr7D 561805449 561806011 562 False 279.0 279 76.148000 24 573 1 chr7D.!!$F1 549

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
713 796 0.035881 CCGACTGGATGGATCATGGG 59.964 60.0 0.0 0.0 37.49 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 7267 0.329261 CTGGTGATGAGGGCTTCCAA 59.671 55.0 0.0 0.0 0.0 3.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.453521 CGATGGATCCCGACCCTTATA 58.546 52.381 9.90 0.00 0.00 0.98
42 43 3.709587 GATGGATCCCGACCCTTATAGA 58.290 50.000 9.90 0.00 0.00 1.98
59 60 6.183361 CCTTATAGATGGGAGGGTTTCGTTTA 60.183 42.308 0.00 0.00 0.00 2.01
68 69 4.393990 GGAGGGTTTCGTTTATAGGTGTTG 59.606 45.833 0.00 0.00 0.00 3.33
71 72 6.532826 AGGGTTTCGTTTATAGGTGTTGTTA 58.467 36.000 0.00 0.00 0.00 2.41
90 91 9.646427 TGTTGTTATGAGTTTTGTTAGCTTTTT 57.354 25.926 0.00 0.00 0.00 1.94
119 120 0.456221 CAGTAAGATGAGGCGACGGT 59.544 55.000 0.00 0.00 0.00 4.83
150 151 4.586306 AAGATGGAATACGGTTTTCCCT 57.414 40.909 22.30 15.33 41.68 4.20
327 336 2.688446 TCGATCTACGCCTCTTCATTGT 59.312 45.455 0.00 0.00 42.26 2.71
489 553 1.613836 AGACGTCGTTAGGTGGTCTT 58.386 50.000 10.46 0.00 34.49 3.01
506 572 4.701651 TGGTCTTGAGCTGGATGTAAATTG 59.298 41.667 0.00 0.00 0.00 2.32
511 578 8.462016 GTCTTGAGCTGGATGTAAATTGTATTT 58.538 33.333 0.00 0.00 0.00 1.40
713 796 0.035881 CCGACTGGATGGATCATGGG 59.964 60.000 0.00 0.00 37.49 4.00
726 809 3.887716 GGATCATGGGTCTGATTCAAAGG 59.112 47.826 0.00 0.00 36.01 3.11
914 1221 3.039011 CACCCTGCCTATAAGTACCACT 58.961 50.000 0.00 0.00 0.00 4.00
917 1224 2.700897 CCTGCCTATAAGTACCACTGCT 59.299 50.000 0.00 0.00 0.00 4.24
937 1246 4.951715 TGCTTATCTTTGCTCAATCCACAT 59.048 37.500 0.00 0.00 0.00 3.21
964 1280 1.751351 AGCACTCGACAGCTATAGCAA 59.249 47.619 26.07 5.68 45.16 3.91
1175 1577 6.480651 TCTTAATTTGTCAGCTTCGTTGTGTA 59.519 34.615 0.00 0.00 0.00 2.90
1283 1696 1.396543 CGGACGACTTCTTCTTCGCG 61.397 60.000 0.00 0.00 38.88 5.87
1499 5322 2.045926 GGCTTCATCACCACCGCT 60.046 61.111 0.00 0.00 0.00 5.52
1789 5615 0.036388 TGGCAACTCTCCATCCGTTC 60.036 55.000 0.00 0.00 37.61 3.95
1945 5804 7.515643 AGTGTATGTTCATTTTAGTAACGTGC 58.484 34.615 0.00 0.00 0.00 5.34
1993 7010 5.640732 ACATTTGATACATTTCTTGACCGC 58.359 37.500 0.00 0.00 0.00 5.68
2000 7017 4.582701 ACATTTCTTGACCGCAAATTCA 57.417 36.364 0.00 0.00 32.73 2.57
2014 7031 4.947147 TTCACAGGGGCACGCACC 62.947 66.667 0.73 0.73 46.88 5.01
2056 7093 0.459585 GCCTCACGATCCGCAAAGTA 60.460 55.000 0.00 0.00 0.00 2.24
2058 7095 1.135083 CCTCACGATCCGCAAAGTAGT 60.135 52.381 0.00 0.00 0.00 2.73
2074 7111 2.252072 TAGTTGGTCCCGCATGAGGC 62.252 60.000 10.45 0.00 39.90 4.70
2094 7161 7.781056 TGAGGCCATGATTATTTTAAAGTTCC 58.219 34.615 5.01 0.00 0.00 3.62
2095 7162 7.619302 TGAGGCCATGATTATTTTAAAGTTCCT 59.381 33.333 5.01 0.00 0.00 3.36
2122 7189 8.535690 TTTTTGAAACTTATGTTTTTGTCGGT 57.464 26.923 8.03 0.00 45.36 4.69
2123 7190 7.743520 TTTGAAACTTATGTTTTTGTCGGTC 57.256 32.000 8.03 0.00 45.36 4.79
2125 7192 6.259638 TGAAACTTATGTTTTTGTCGGTCAC 58.740 36.000 8.03 0.00 45.36 3.67
2127 7194 5.668558 ACTTATGTTTTTGTCGGTCACTC 57.331 39.130 0.00 0.00 0.00 3.51
2128 7195 5.120399 ACTTATGTTTTTGTCGGTCACTCA 58.880 37.500 0.00 0.00 0.00 3.41
2129 7196 5.763204 ACTTATGTTTTTGTCGGTCACTCAT 59.237 36.000 0.00 0.00 0.00 2.90
2131 7198 5.607119 ATGTTTTTGTCGGTCACTCATAC 57.393 39.130 0.00 0.00 0.00 2.39
2132 7199 3.810941 TGTTTTTGTCGGTCACTCATACC 59.189 43.478 0.00 0.00 0.00 2.73
2134 7201 3.755112 TTTGTCGGTCACTCATACCAA 57.245 42.857 0.00 0.00 36.78 3.67
2135 7202 3.313012 TTGTCGGTCACTCATACCAAG 57.687 47.619 0.00 0.00 36.78 3.61
2137 7204 2.631062 TGTCGGTCACTCATACCAAGTT 59.369 45.455 0.00 0.00 36.78 2.66
2138 7205 3.070446 TGTCGGTCACTCATACCAAGTTT 59.930 43.478 0.00 0.00 36.78 2.66
2139 7206 3.678548 GTCGGTCACTCATACCAAGTTTC 59.321 47.826 0.00 0.00 36.78 2.78
2140 7207 2.666508 CGGTCACTCATACCAAGTTTCG 59.333 50.000 0.00 0.00 36.78 3.46
2141 7208 3.613193 CGGTCACTCATACCAAGTTTCGA 60.613 47.826 0.00 0.00 36.78 3.71
2143 7210 4.389077 GGTCACTCATACCAAGTTTCGAAG 59.611 45.833 0.00 0.00 36.96 3.79
2146 7213 5.465390 TCACTCATACCAAGTTTCGAAGTTG 59.535 40.000 12.97 12.97 40.66 3.16
2147 7214 5.465390 CACTCATACCAAGTTTCGAAGTTGA 59.535 40.000 18.90 9.82 43.02 3.18
2148 7215 6.018262 CACTCATACCAAGTTTCGAAGTTGAA 60.018 38.462 18.90 10.16 43.02 2.69
2149 7216 6.540914 ACTCATACCAAGTTTCGAAGTTGAAA 59.459 34.615 18.90 9.90 43.02 2.69
2180 7247 8.795786 TGAGAATTTAAAAACTCATCCAAACG 57.204 30.769 17.68 0.00 35.01 3.60
2189 7256 8.934507 AAAAACTCATCCAAACGTATTCAAAA 57.065 26.923 0.00 0.00 0.00 2.44
2198 7265 6.657117 TCCAAACGTATTCAAAATGGATCTCA 59.343 34.615 0.00 0.00 30.90 3.27
2199 7266 7.339212 TCCAAACGTATTCAAAATGGATCTCAT 59.661 33.333 0.00 0.00 37.79 2.90
2210 7277 1.925255 TGGATCTCATTTGGAAGCCCT 59.075 47.619 0.00 0.00 0.00 5.19
2211 7278 2.092212 TGGATCTCATTTGGAAGCCCTC 60.092 50.000 0.00 0.00 0.00 4.30
2213 7280 3.436180 GGATCTCATTTGGAAGCCCTCAT 60.436 47.826 0.00 0.00 0.00 2.90
2214 7281 3.287867 TCTCATTTGGAAGCCCTCATC 57.712 47.619 0.00 0.00 0.00 2.92
2215 7282 2.577563 TCTCATTTGGAAGCCCTCATCA 59.422 45.455 0.00 0.00 0.00 3.07
2217 7284 1.753073 CATTTGGAAGCCCTCATCACC 59.247 52.381 0.00 0.00 0.00 4.02
2221 7288 0.620556 GGAAGCCCTCATCACCAGAA 59.379 55.000 0.00 0.00 0.00 3.02
2222 7289 1.004745 GGAAGCCCTCATCACCAGAAA 59.995 52.381 0.00 0.00 0.00 2.52
2223 7290 2.087646 GAAGCCCTCATCACCAGAAAC 58.912 52.381 0.00 0.00 0.00 2.78
2229 7296 3.441572 CCCTCATCACCAGAAACATGAAC 59.558 47.826 0.00 0.00 0.00 3.18
2230 7297 3.441572 CCTCATCACCAGAAACATGAACC 59.558 47.826 0.00 0.00 0.00 3.62
2232 7299 4.074259 TCATCACCAGAAACATGAACCTG 58.926 43.478 0.00 2.92 0.00 4.00
2237 7304 5.298276 TCACCAGAAACATGAACCTGTAAAC 59.702 40.000 0.00 0.00 0.00 2.01
2238 7305 4.274950 ACCAGAAACATGAACCTGTAAACG 59.725 41.667 0.00 0.00 0.00 3.60
2240 7307 5.008217 CCAGAAACATGAACCTGTAAACGAA 59.992 40.000 0.00 0.00 0.00 3.85
2245 7312 9.453325 GAAACATGAACCTGTAAACGAAATTTA 57.547 29.630 0.00 0.00 0.00 1.40
2247 7314 9.974980 AACATGAACCTGTAAACGAAATTTAAT 57.025 25.926 0.00 0.00 34.50 1.40
2248 7315 9.974980 ACATGAACCTGTAAACGAAATTTAATT 57.025 25.926 0.00 0.00 34.50 1.40
2299 7549 6.522946 TGATTGAAATCACATGCCAAAAGAA 58.477 32.000 1.55 0.00 40.32 2.52
2357 7607 6.770746 AATTCAATCCTCTCACATTCCTTG 57.229 37.500 0.00 0.00 0.00 3.61
2495 8999 2.477176 AAGCGCGTGTTTGGCTTCA 61.477 52.632 8.43 0.00 43.02 3.02
2510 9014 6.601741 TTGGCTTCAATTGTTCAACATTTC 57.398 33.333 5.13 0.00 0.00 2.17
2522 9026 7.094508 TGTTCAACATTTCTACACACACAAT 57.905 32.000 0.00 0.00 0.00 2.71
2525 9029 6.502652 TCAACATTTCTACACACACAATTGG 58.497 36.000 10.83 1.35 0.00 3.16
2545 9049 8.571336 CAATTGGTCTCATCTAAAAAGTCAACT 58.429 33.333 0.00 0.00 0.00 3.16
2586 9091 7.480760 AGCTGGAATGGCTAAGAAATTAAAA 57.519 32.000 0.00 0.00 38.36 1.52
2587 9092 7.550712 AGCTGGAATGGCTAAGAAATTAAAAG 58.449 34.615 0.00 0.00 38.36 2.27
2588 9093 6.758416 GCTGGAATGGCTAAGAAATTAAAAGG 59.242 38.462 0.00 0.00 0.00 3.11
2606 9111 1.384222 GGGGCCACATTTCATCGGTC 61.384 60.000 4.39 0.00 0.00 4.79
2623 9128 1.680249 GGTCTTCCCATGGTTGCTCTC 60.680 57.143 11.73 0.00 0.00 3.20
2632 9137 1.743252 GGTTGCTCTCTCTTGCCCG 60.743 63.158 0.00 0.00 0.00 6.13
2642 9147 4.025401 CTTGCCCGCGTCCACAAC 62.025 66.667 4.92 0.00 0.00 3.32
2650 9155 3.931247 CGTCCACAACCGGGGTCA 61.931 66.667 6.32 0.00 0.00 4.02
2659 9164 2.765807 CCGGGGTCATGCTCCTCT 60.766 66.667 0.00 0.00 34.84 3.69
2662 9167 1.997874 GGGGTCATGCTCCTCTGGT 60.998 63.158 6.70 0.00 33.93 4.00
2669 9174 1.833630 CATGCTCCTCTGGTAGACCAA 59.166 52.381 2.42 0.00 46.97 3.67
2670 9175 2.254152 TGCTCCTCTGGTAGACCAAT 57.746 50.000 2.42 0.00 46.97 3.16
2671 9176 2.111384 TGCTCCTCTGGTAGACCAATC 58.889 52.381 2.42 0.00 46.97 2.67
2672 9177 1.067821 GCTCCTCTGGTAGACCAATCG 59.932 57.143 2.42 0.00 46.97 3.34
2673 9178 1.683917 CTCCTCTGGTAGACCAATCGG 59.316 57.143 2.42 3.88 46.97 4.18
2739 9250 6.533012 CCAATGTTGTTATTGTTGTTCACACA 59.467 34.615 0.00 0.00 36.54 3.72
2741 9252 6.260870 TGTTGTTATTGTTGTTCACACACT 57.739 33.333 0.00 0.00 33.98 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.172505 TCCATCGCATTTACATGGTCCT 59.827 45.455 0.00 0.00 38.62 3.85
14 15 1.270625 GGTCGGGATCCATCGCATTTA 60.271 52.381 15.23 0.00 39.45 1.40
16 17 1.071471 GGTCGGGATCCATCGCATT 59.929 57.895 15.23 0.00 39.45 3.56
17 18 2.743718 GGTCGGGATCCATCGCAT 59.256 61.111 15.23 0.00 39.45 4.73
40 41 4.102681 CCTATAAACGAAACCCTCCCATCT 59.897 45.833 0.00 0.00 0.00 2.90
42 43 3.784202 ACCTATAAACGAAACCCTCCCAT 59.216 43.478 0.00 0.00 0.00 4.00
51 52 8.836268 ACTCATAACAACACCTATAAACGAAA 57.164 30.769 0.00 0.00 0.00 3.46
59 60 8.512138 GCTAACAAAACTCATAACAACACCTAT 58.488 33.333 0.00 0.00 0.00 2.57
90 91 4.774124 CCTCATCTTACTGAGAATGGCAA 58.226 43.478 0.00 0.00 44.48 4.52
119 120 7.120923 ACCGTATTCCATCTTTAGAAAGCTA 57.879 36.000 0.00 0.00 35.99 3.32
233 240 6.006449 ACAAGCAGATCCACTAAAGACAAAT 58.994 36.000 0.00 0.00 0.00 2.32
327 336 0.179004 ACCAGAACAACATCCGCCAA 60.179 50.000 0.00 0.00 0.00 4.52
411 420 0.247736 GCTCCTCACTCATCGGTGTT 59.752 55.000 0.00 0.00 38.28 3.32
489 553 8.347004 TCAAAATACAATTTACATCCAGCTCA 57.653 30.769 0.00 0.00 0.00 4.26
511 578 7.276658 TGTGAAGGTAGTACAAAGAACATCAA 58.723 34.615 2.06 0.00 0.00 2.57
573 641 5.125900 AGCAGTTGCACATGATAATGCTTAA 59.874 36.000 0.00 0.00 45.16 1.85
574 642 4.641541 AGCAGTTGCACATGATAATGCTTA 59.358 37.500 0.00 0.00 45.16 3.09
713 796 1.470098 ACATGCGCCTTTGAATCAGAC 59.530 47.619 4.18 0.00 0.00 3.51
726 809 1.766143 GCTACCTGCTACACATGCGC 61.766 60.000 0.00 0.00 38.95 6.09
754 837 7.418942 GCCAATCAAATGGGGATATAGTTGTTT 60.419 37.037 0.00 0.00 41.01 2.83
755 838 6.041979 GCCAATCAAATGGGGATATAGTTGTT 59.958 38.462 0.00 0.00 41.01 2.83
914 1221 4.334552 TGTGGATTGAGCAAAGATAAGCA 58.665 39.130 0.00 0.00 0.00 3.91
917 1224 5.508567 TGGATGTGGATTGAGCAAAGATAA 58.491 37.500 0.00 0.00 0.00 1.75
937 1246 1.967535 CTGTCGAGTGCTTCCTGGA 59.032 57.895 0.00 0.00 0.00 3.86
964 1280 1.471684 GCTTGCTTGCTATCAGCTTGT 59.528 47.619 0.00 0.00 42.97 3.16
1175 1577 1.301244 CGTGTCAGCAAGAGCCAGT 60.301 57.895 0.00 0.00 43.56 4.00
1283 1696 2.269241 CCGGCCTTCTTGAGACCC 59.731 66.667 0.00 0.00 0.00 4.46
1789 5615 2.088950 ACACACCGTTATTCTTCCGG 57.911 50.000 0.00 0.00 46.93 5.14
1945 5804 9.003658 GTAATATACACATCAAGAAATGGAGGG 57.996 37.037 0.00 0.00 0.00 4.30
1984 7001 1.879380 CCTGTGAATTTGCGGTCAAGA 59.121 47.619 0.00 0.00 33.12 3.02
1993 7010 1.080569 GCGTGCCCCTGTGAATTTG 60.081 57.895 0.00 0.00 0.00 2.32
2056 7093 2.671070 CCTCATGCGGGACCAACT 59.329 61.111 0.00 0.00 0.00 3.16
2058 7095 4.424711 GGCCTCATGCGGGACCAA 62.425 66.667 3.43 0.00 42.61 3.67
2102 7169 6.492254 AGTGACCGACAAAAACATAAGTTTC 58.508 36.000 0.00 0.00 46.79 2.78
2106 7173 5.666969 TGAGTGACCGACAAAAACATAAG 57.333 39.130 0.00 0.00 0.00 1.73
2109 7176 4.454504 GGTATGAGTGACCGACAAAAACAT 59.545 41.667 0.00 0.00 0.00 2.71
2110 7177 3.810941 GGTATGAGTGACCGACAAAAACA 59.189 43.478 0.00 0.00 0.00 2.83
2111 7178 3.810941 TGGTATGAGTGACCGACAAAAAC 59.189 43.478 0.00 0.00 40.09 2.43
2112 7179 4.074627 TGGTATGAGTGACCGACAAAAA 57.925 40.909 0.00 0.00 40.09 1.94
2113 7180 3.755112 TGGTATGAGTGACCGACAAAA 57.245 42.857 0.00 0.00 40.09 2.44
2117 7184 3.314541 AACTTGGTATGAGTGACCGAC 57.685 47.619 0.00 0.00 40.09 4.79
2118 7185 3.613193 CGAAACTTGGTATGAGTGACCGA 60.613 47.826 0.00 0.00 40.09 4.69
2120 7187 3.921677 TCGAAACTTGGTATGAGTGACC 58.078 45.455 0.00 0.00 37.49 4.02
2121 7188 4.989168 ACTTCGAAACTTGGTATGAGTGAC 59.011 41.667 0.00 0.00 0.00 3.67
2122 7189 5.209818 ACTTCGAAACTTGGTATGAGTGA 57.790 39.130 0.00 0.00 0.00 3.41
2123 7190 5.465390 TCAACTTCGAAACTTGGTATGAGTG 59.535 40.000 12.88 0.00 0.00 3.51
2125 7192 6.539649 TTCAACTTCGAAACTTGGTATGAG 57.460 37.500 12.88 0.00 0.00 2.90
2154 7221 9.410556 CGTTTGGATGAGTTTTTAAATTCTCAT 57.589 29.630 23.46 23.46 46.11 2.90
2155 7222 8.410141 ACGTTTGGATGAGTTTTTAAATTCTCA 58.590 29.630 18.46 18.46 40.43 3.27
2156 7223 8.797266 ACGTTTGGATGAGTTTTTAAATTCTC 57.203 30.769 11.03 11.03 0.00 2.87
2164 7231 8.934507 TTTTGAATACGTTTGGATGAGTTTTT 57.065 26.923 0.00 0.00 0.00 1.94
2165 7232 8.977505 CATTTTGAATACGTTTGGATGAGTTTT 58.022 29.630 0.00 0.00 0.00 2.43
2169 7236 6.851609 TCCATTTTGAATACGTTTGGATGAG 58.148 36.000 0.00 0.00 0.00 2.90
2174 7241 6.851609 TGAGATCCATTTTGAATACGTTTGG 58.148 36.000 0.00 0.00 0.00 3.28
2175 7242 8.915871 AATGAGATCCATTTTGAATACGTTTG 57.084 30.769 0.00 0.00 42.55 2.93
2188 7255 3.052338 AGGGCTTCCAAATGAGATCCATT 60.052 43.478 4.21 4.21 46.86 3.16
2189 7256 2.517127 AGGGCTTCCAAATGAGATCCAT 59.483 45.455 0.00 0.00 36.99 3.41
2198 7265 1.358787 TGGTGATGAGGGCTTCCAAAT 59.641 47.619 0.00 0.00 0.00 2.32
2199 7266 0.776810 TGGTGATGAGGGCTTCCAAA 59.223 50.000 0.00 0.00 0.00 3.28
2200 7267 0.329261 CTGGTGATGAGGGCTTCCAA 59.671 55.000 0.00 0.00 0.00 3.53
2201 7268 0.547471 TCTGGTGATGAGGGCTTCCA 60.547 55.000 0.00 0.00 0.00 3.53
2202 7269 0.620556 TTCTGGTGATGAGGGCTTCC 59.379 55.000 0.00 0.00 0.00 3.46
2204 7271 1.425066 TGTTTCTGGTGATGAGGGCTT 59.575 47.619 0.00 0.00 0.00 4.35
2205 7272 1.067295 TGTTTCTGGTGATGAGGGCT 58.933 50.000 0.00 0.00 0.00 5.19
2206 7273 1.747355 CATGTTTCTGGTGATGAGGGC 59.253 52.381 0.00 0.00 0.00 5.19
2210 7277 4.074259 CAGGTTCATGTTTCTGGTGATGA 58.926 43.478 0.00 0.00 0.00 2.92
2211 7278 3.822735 ACAGGTTCATGTTTCTGGTGATG 59.177 43.478 13.35 0.00 0.00 3.07
2213 7280 3.576078 ACAGGTTCATGTTTCTGGTGA 57.424 42.857 13.35 0.00 0.00 4.02
2214 7281 5.519722 GTTTACAGGTTCATGTTTCTGGTG 58.480 41.667 13.35 0.00 34.56 4.17
2215 7282 4.274950 CGTTTACAGGTTCATGTTTCTGGT 59.725 41.667 13.35 2.03 34.56 4.00
2217 7284 5.666969 TCGTTTACAGGTTCATGTTTCTG 57.333 39.130 0.00 1.74 34.56 3.02
2221 7288 9.974980 ATTAAATTTCGTTTACAGGTTCATGTT 57.025 25.926 0.00 0.00 34.56 2.71
2222 7289 9.974980 AATTAAATTTCGTTTACAGGTTCATGT 57.025 25.926 0.00 0.00 37.19 3.21
2272 7522 6.971527 TTTGGCATGTGATTTCAATCATTC 57.028 33.333 5.53 0.00 46.17 2.67
2273 7523 7.162761 TCTTTTGGCATGTGATTTCAATCATT 58.837 30.769 5.53 0.00 46.17 2.57
2280 7530 6.293571 CCCTTTTTCTTTTGGCATGTGATTTC 60.294 38.462 0.00 0.00 0.00 2.17
2281 7531 5.532032 CCCTTTTTCTTTTGGCATGTGATTT 59.468 36.000 0.00 0.00 0.00 2.17
2283 7533 4.505390 CCCCTTTTTCTTTTGGCATGTGAT 60.505 41.667 0.00 0.00 0.00 3.06
2284 7534 3.181456 CCCCTTTTTCTTTTGGCATGTGA 60.181 43.478 0.00 0.00 0.00 3.58
2285 7535 3.140623 CCCCTTTTTCTTTTGGCATGTG 58.859 45.455 0.00 0.00 0.00 3.21
2286 7536 2.106338 CCCCCTTTTTCTTTTGGCATGT 59.894 45.455 0.00 0.00 0.00 3.21
2287 7537 2.781923 CCCCCTTTTTCTTTTGGCATG 58.218 47.619 0.00 0.00 0.00 4.06
2288 7538 1.073763 GCCCCCTTTTTCTTTTGGCAT 59.926 47.619 0.00 0.00 37.36 4.40
2289 7539 0.472044 GCCCCCTTTTTCTTTTGGCA 59.528 50.000 0.00 0.00 37.36 4.92
2290 7540 0.764890 AGCCCCCTTTTTCTTTTGGC 59.235 50.000 0.00 0.00 37.68 4.52
2291 7541 1.543208 GCAGCCCCCTTTTTCTTTTGG 60.543 52.381 0.00 0.00 0.00 3.28
2321 7571 6.769822 AGAGGATTGAATTTGTAGCATAGGTG 59.230 38.462 0.00 0.00 0.00 4.00
2322 7572 6.904626 AGAGGATTGAATTTGTAGCATAGGT 58.095 36.000 0.00 0.00 0.00 3.08
2324 7574 7.496920 TGTGAGAGGATTGAATTTGTAGCATAG 59.503 37.037 0.00 0.00 0.00 2.23
2325 7575 7.337938 TGTGAGAGGATTGAATTTGTAGCATA 58.662 34.615 0.00 0.00 0.00 3.14
2326 7576 6.182627 TGTGAGAGGATTGAATTTGTAGCAT 58.817 36.000 0.00 0.00 0.00 3.79
2327 7577 5.559770 TGTGAGAGGATTGAATTTGTAGCA 58.440 37.500 0.00 0.00 0.00 3.49
2328 7578 6.690194 ATGTGAGAGGATTGAATTTGTAGC 57.310 37.500 0.00 0.00 0.00 3.58
2329 7579 7.555554 AGGAATGTGAGAGGATTGAATTTGTAG 59.444 37.037 0.00 0.00 0.00 2.74
2330 7580 7.405292 AGGAATGTGAGAGGATTGAATTTGTA 58.595 34.615 0.00 0.00 0.00 2.41
2331 7581 6.251471 AGGAATGTGAGAGGATTGAATTTGT 58.749 36.000 0.00 0.00 0.00 2.83
2332 7582 6.770746 AGGAATGTGAGAGGATTGAATTTG 57.229 37.500 0.00 0.00 0.00 2.32
2333 7583 6.950041 TCAAGGAATGTGAGAGGATTGAATTT 59.050 34.615 0.00 0.00 0.00 1.82
2334 7584 6.376581 GTCAAGGAATGTGAGAGGATTGAATT 59.623 38.462 0.00 0.00 0.00 2.17
2335 7585 5.884792 GTCAAGGAATGTGAGAGGATTGAAT 59.115 40.000 0.00 0.00 0.00 2.57
2336 7586 5.248640 GTCAAGGAATGTGAGAGGATTGAA 58.751 41.667 0.00 0.00 0.00 2.69
2337 7587 4.621510 CGTCAAGGAATGTGAGAGGATTGA 60.622 45.833 0.00 0.00 0.00 2.57
2338 7588 3.620374 CGTCAAGGAATGTGAGAGGATTG 59.380 47.826 0.00 0.00 0.00 2.67
2416 7749 9.909644 TGTTTAGTCTATGTAGAACAACTCTTC 57.090 33.333 0.00 0.00 35.41 2.87
2421 7754 9.859692 GTTGTTGTTTAGTCTATGTAGAACAAC 57.140 33.333 20.60 20.60 43.61 3.32
2495 8999 7.542890 TGTGTGTGTAGAAATGTTGAACAATT 58.457 30.769 0.62 0.00 0.00 2.32
2510 9014 5.240891 AGATGAGACCAATTGTGTGTGTAG 58.759 41.667 4.43 0.00 0.00 2.74
2522 9026 8.519799 AAAGTTGACTTTTTAGATGAGACCAA 57.480 30.769 3.37 0.00 43.07 3.67
2545 9049 6.832520 TCCAGCTTGCAAGATACATTAAAA 57.167 33.333 30.39 0.93 0.00 1.52
2549 9053 4.098960 CCATTCCAGCTTGCAAGATACATT 59.901 41.667 30.39 7.08 0.00 2.71
2586 9091 1.076777 CCGATGAAATGTGGCCCCT 60.077 57.895 0.00 0.00 0.00 4.79
2587 9092 1.379843 ACCGATGAAATGTGGCCCC 60.380 57.895 0.00 0.00 0.00 5.80
2588 9093 0.394352 AGACCGATGAAATGTGGCCC 60.394 55.000 0.00 0.00 0.00 5.80
2606 9111 1.558756 AGAGAGAGCAACCATGGGAAG 59.441 52.381 18.09 6.33 0.00 3.46
2623 9128 4.680237 TGTGGACGCGGGCAAGAG 62.680 66.667 12.47 0.00 0.00 2.85
2642 9147 2.765807 AGAGGAGCATGACCCCGG 60.766 66.667 0.00 0.00 0.00 5.73
2648 9153 1.007118 TGGTCTACCAGAGGAGCATGA 59.993 52.381 0.00 0.00 42.01 3.07
2669 9174 4.931661 ACCGATATCTACAAACACCGAT 57.068 40.909 0.34 0.00 0.00 4.18
2670 9175 4.082081 ACAACCGATATCTACAAACACCGA 60.082 41.667 0.34 0.00 0.00 4.69
2671 9176 4.178540 ACAACCGATATCTACAAACACCG 58.821 43.478 0.34 0.00 0.00 4.94
2672 9177 5.410439 ACAACAACCGATATCTACAAACACC 59.590 40.000 0.34 0.00 0.00 4.16
2673 9178 6.476243 ACAACAACCGATATCTACAAACAC 57.524 37.500 0.34 0.00 0.00 3.32
2674 9179 7.820386 ACATACAACAACCGATATCTACAAACA 59.180 33.333 0.34 0.00 0.00 2.83
2721 9232 9.295214 CATTTAAGTGTGTGAACAACAATAACA 57.705 29.630 0.00 0.00 41.57 2.41


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

AutoCloner maintained by Alex Coulton.