Multiple sequence alignment - TraesCS5D01G289600

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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 TraesCS5D01G289600 chr5D 100.000 2519 0 0 1 2519 388108795 388111313 0.000000e+00 4652.0
1 TraesCS5D01G289600 chr5D 96.214 766 26 3 1756 2519 66983107 66982343 0.000000e+00 1251.0
2 TraesCS5D01G289600 chr5D 82.927 328 55 1 1194 1521 565748317 565748643 6.810000e-76 294.0
3 TraesCS5D01G289600 chr5D 86.585 82 9 2 2164 2243 66982616 66982697 3.450000e-14 89.8
4 TraesCS5D01G289600 chr5D 83.133 83 14 0 229 311 528849301 528849219 2.690000e-10 76.8
5 TraesCS5D01G289600 chr5A 90.191 1417 80 19 217 1590 491301108 491302508 0.000000e+00 1792.0
6 TraesCS5D01G289600 chr5A 96.057 279 9 2 2239 2517 447363719 447363443 1.060000e-123 453.0
7 TraesCS5D01G289600 chr5A 96.057 279 9 2 2239 2517 681379536 681379812 1.060000e-123 453.0
8 TraesCS5D01G289600 chr5A 89.048 210 10 4 1 201 491300918 491301123 5.380000e-62 248.0
9 TraesCS5D01G289600 chr5A 80.172 232 31 12 266 489 547505206 547505430 2.590000e-35 159.0
10 TraesCS5D01G289600 chr5A 88.889 63 6 1 1661 1723 491302634 491302695 2.690000e-10 76.8
11 TraesCS5D01G289600 chr5B 89.637 743 40 22 882 1590 466844140 466844879 0.000000e+00 911.0
12 TraesCS5D01G289600 chr5B 91.759 631 40 1 217 847 466843286 466843904 0.000000e+00 867.0
13 TraesCS5D01G289600 chr5B 85.061 328 48 1 1194 1521 707395093 707394767 1.440000e-87 333.0
14 TraesCS5D01G289600 chr5B 90.952 210 10 1 1 201 466843092 466843301 8.880000e-70 274.0
15 TraesCS5D01G289600 chr5B 96.403 139 4 1 1619 1757 466844950 466845087 7.010000e-56 228.0
16 TraesCS5D01G289600 chr5B 80.349 229 29 12 244 461 546724735 546724958 2.590000e-35 159.0
17 TraesCS5D01G289600 chr5B 76.812 276 51 11 219 492 478410924 478411188 2.610000e-30 143.0
18 TraesCS5D01G289600 chr5B 88.889 81 7 2 2166 2244 597288108 597288188 5.730000e-17 99.0
19 TraesCS5D01G289600 chr2A 93.333 420 25 2 1757 2174 21749722 21749304 3.560000e-173 617.0
20 TraesCS5D01G289600 chr2A 93.128 422 26 2 1755 2174 718252678 718252258 1.280000e-172 616.0
21 TraesCS5D01G289600 chr2A 78.058 278 51 8 217 487 693154153 693154427 1.550000e-37 167.0
22 TraesCS5D01G289600 chr2A 82.716 162 24 3 41 199 101893855 101893695 9.390000e-30 141.0
23 TraesCS5D01G289600 chr2A 76.259 278 53 11 219 487 768727322 768727049 4.370000e-28 135.0
24 TraesCS5D01G289600 chr7A 93.112 421 26 2 1756 2174 611896404 611895985 4.610000e-172 614.0
25 TraesCS5D01G289600 chr7A 96.057 279 9 2 2239 2517 203845372 203845096 1.060000e-123 453.0
26 TraesCS5D01G289600 chr7A 77.451 204 41 5 1 199 64738731 64738934 1.580000e-22 117.0
27 TraesCS5D01G289600 chr6B 92.925 424 26 3 1753 2174 195250486 195250065 4.610000e-172 614.0
28 TraesCS5D01G289600 chr6B 92.857 420 27 2 1757 2174 86943704 86944122 7.710000e-170 606.0
29 TraesCS5D01G289600 chr6B 80.349 229 35 8 220 440 493355930 493355704 5.570000e-37 165.0
30 TraesCS5D01G289600 chr2B 93.095 420 26 2 1757 2174 25806983 25807401 1.660000e-171 612.0
31 TraesCS5D01G289600 chr2B 79.422 277 48 5 217 486 569538222 569538496 1.190000e-43 187.0
32 TraesCS5D01G289600 chr2B 88.462 78 8 1 2171 2247 99269994 99270071 2.670000e-15 93.5
33 TraesCS5D01G289600 chr7B 92.689 424 27 3 1753 2174 739640524 739640945 2.140000e-170 608.0
34 TraesCS5D01G289600 chr7B 96.057 279 9 2 2239 2517 739640974 739641250 1.060000e-123 453.0
35 TraesCS5D01G289600 chr7B 88.462 78 3 3 2171 2242 639489827 639489904 3.450000e-14 89.8
36 TraesCS5D01G289600 chr4A 92.857 420 27 2 1757 2174 26880756 26881174 7.710000e-170 606.0
37 TraesCS5D01G289600 chr4A 96.057 279 9 2 2239 2517 26881203 26881479 1.060000e-123 453.0
38 TraesCS5D01G289600 chr4A 79.087 263 41 8 231 484 175861249 175860992 4.310000e-38 169.0
39 TraesCS5D01G289600 chr4A 77.723 202 36 6 1 195 737178994 737178795 5.690000e-22 115.0
40 TraesCS5D01G289600 chr4A 82.576 132 14 3 246 369 175893056 175892926 9.530000e-20 108.0
41 TraesCS5D01G289600 chr1D 96.809 282 9 0 2236 2517 380569178 380568897 2.930000e-129 472.0
42 TraesCS5D01G289600 chr1D 82.007 578 67 15 983 1537 246970670 246970107 8.210000e-125 457.0
43 TraesCS5D01G289600 chr1D 77.551 294 43 13 217 489 411058234 411058525 3.360000e-34 156.0
44 TraesCS5D01G289600 chr1D 87.500 80 8 1 2171 2248 74410541 74410462 9.600000e-15 91.6
45 TraesCS5D01G289600 chr1B 96.140 285 10 1 2236 2519 51079417 51079701 4.910000e-127 464.0
46 TraesCS5D01G289600 chr1B 80.711 591 67 20 980 1537 331084018 331084594 1.390000e-112 416.0
47 TraesCS5D01G289600 chr1B 79.936 623 73 22 933 1519 330991402 330992008 6.490000e-111 411.0
48 TraesCS5D01G289600 chr1B 92.308 169 8 3 2006 2174 51079259 51079422 4.190000e-58 235.0
49 TraesCS5D01G289600 chr1B 77.407 270 52 3 220 482 567980672 567980405 4.340000e-33 152.0
50 TraesCS5D01G289600 chr1B 89.474 76 4 4 2171 2242 10201046 10200971 2.670000e-15 93.5
51 TraesCS5D01G289600 chr4B 95.105 286 14 0 2232 2517 570842565 570842280 3.820000e-123 451.0
52 TraesCS5D01G289600 chr1A 80.630 635 77 24 933 1537 300672569 300673187 1.370000e-122 449.0
53 TraesCS5D01G289600 chr1A 79.046 692 94 29 892 1557 300943981 300944647 6.440000e-116 427.0
54 TraesCS5D01G289600 chr4D 81.560 282 39 7 220 490 484062825 484062546 1.170000e-53 220.0
55 TraesCS5D01G289600 chr4D 80.000 165 17 8 217 367 58157597 58157759 9.530000e-20 108.0
56 TraesCS5D01G289600 chr4D 91.304 69 4 2 2182 2249 348048266 348048199 2.670000e-15 93.5
57 TraesCS5D01G289600 chr6D 80.216 278 43 6 217 486 439759086 439759359 5.500000e-47 198.0
58 TraesCS5D01G289600 chr6D 93.333 45 3 0 41 85 57474891 57474847 1.620000e-07 67.6
59 TraesCS5D01G289600 chr3A 74.549 499 88 18 1 487 721342612 721343083 5.540000e-42 182.0
60 TraesCS5D01G289600 chr2D 80.870 230 34 8 219 440 641490036 641489809 3.330000e-39 172.0
61 TraesCS5D01G289600 chr2D 74.888 446 74 29 29 461 429082111 429081691 4.310000e-38 169.0
62 TraesCS5D01G289600 chr2D 90.541 74 5 2 2169 2240 441760371 441760444 2.060000e-16 97.1
63 TraesCS5D01G289600 chr6A 79.151 259 45 3 221 472 570385757 570386013 1.200000e-38 171.0
64 TraesCS5D01G289600 chr6A 88.372 86 8 2 218 302 53065026 53064942 4.430000e-18 102.0
65 TraesCS5D01G289600 chr6A 88.372 86 8 2 218 302 53069202 53069118 4.430000e-18 102.0
66 TraesCS5D01G289600 chr6A 78.824 85 18 0 1 85 72477179 72477095 9.730000e-05 58.4
67 TraesCS5D01G289600 chr7D 78.346 254 43 8 217 461 577917172 577916922 1.210000e-33 154.0
68 TraesCS5D01G289600 chr7D 77.432 257 46 6 219 466 30755851 30756104 2.610000e-30 143.0
69 TraesCS5D01G289600 chr7D 79.293 198 32 8 1 192 139826186 139826380 2.030000e-26 130.0
70 TraesCS5D01G289600 chr7D 76.608 171 32 6 1 165 556999430 556999262 1.240000e-13 87.9
71 TraesCS5D01G289600 chr3D 79.208 202 34 2 256 450 556029974 556029774 1.570000e-27 134.0
72 TraesCS5D01G289600 chr3D 87.805 82 10 0 1198 1279 12848607 12848688 2.060000e-16 97.1
73 TraesCS5D01G289600 chr3B 78.205 156 34 0 1198 1353 18484767 18484922 1.590000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G289600 chr5D 388108795 388111313 2518 False 4652.0 4652 100.00000 1 2519 1 chr5D.!!$F2 2518
1 TraesCS5D01G289600 chr5D 66982343 66983107 764 True 1251.0 1251 96.21400 1756 2519 1 chr5D.!!$R1 763
2 TraesCS5D01G289600 chr5A 491300918 491302695 1777 False 705.6 1792 89.37600 1 1723 3 chr5A.!!$F3 1722
3 TraesCS5D01G289600 chr5B 466843092 466845087 1995 False 570.0 911 92.18775 1 1757 4 chr5B.!!$F4 1756
4 TraesCS5D01G289600 chr7B 739640524 739641250 726 False 530.5 608 94.37300 1753 2517 2 chr7B.!!$F2 764
5 TraesCS5D01G289600 chr4A 26880756 26881479 723 False 529.5 606 94.45700 1757 2517 2 chr4A.!!$F1 760
6 TraesCS5D01G289600 chr1D 246970107 246970670 563 True 457.0 457 82.00700 983 1537 1 chr1D.!!$R2 554
7 TraesCS5D01G289600 chr1B 331084018 331084594 576 False 416.0 416 80.71100 980 1537 1 chr1B.!!$F2 557
8 TraesCS5D01G289600 chr1B 330991402 330992008 606 False 411.0 411 79.93600 933 1519 1 chr1B.!!$F1 586
9 TraesCS5D01G289600 chr1A 300672569 300673187 618 False 449.0 449 80.63000 933 1537 1 chr1A.!!$F1 604
10 TraesCS5D01G289600 chr1A 300943981 300944647 666 False 427.0 427 79.04600 892 1557 1 chr1A.!!$F2 665

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
196 206 0.322277 CTGCCAGGTGCTTCAGATGT 60.322 55.0 0.0 0.0 42.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 2122 2.025699 GTGCCCACCCCTAAGTTTGATA 60.026 50.0 0.0 0.0 0.0 2.15 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
26 27 1.080772 CTCGTAAGTGCGGTGCTCA 60.081 57.895 0.00 0.00 39.48 4.26
27 28 0.666274 CTCGTAAGTGCGGTGCTCAA 60.666 55.000 0.00 0.00 39.48 3.02
111 121 1.602605 TTGACTCGACGGAGCTCCA 60.603 57.895 31.67 11.96 44.48 3.86
139 149 0.549902 TCCTGCCATCTCCTTGGGAA 60.550 55.000 0.00 0.00 36.59 3.97
191 201 0.828762 ATTTGCTGCCAGGTGCTTCA 60.829 50.000 0.00 0.00 42.00 3.02
192 202 1.457823 TTTGCTGCCAGGTGCTTCAG 61.458 55.000 0.00 0.00 42.00 3.02
193 203 2.033141 GCTGCCAGGTGCTTCAGA 59.967 61.111 0.00 0.00 42.00 3.27
194 204 1.378250 GCTGCCAGGTGCTTCAGAT 60.378 57.895 0.00 0.00 42.00 2.90
195 205 1.654954 GCTGCCAGGTGCTTCAGATG 61.655 60.000 0.00 0.00 42.00 2.90
196 206 0.322277 CTGCCAGGTGCTTCAGATGT 60.322 55.000 0.00 0.00 42.00 3.06
197 207 0.983467 TGCCAGGTGCTTCAGATGTA 59.017 50.000 0.00 0.00 42.00 2.29
198 208 1.561076 TGCCAGGTGCTTCAGATGTAT 59.439 47.619 0.00 0.00 42.00 2.29
199 209 2.025981 TGCCAGGTGCTTCAGATGTATT 60.026 45.455 0.00 0.00 42.00 1.89
200 210 2.615912 GCCAGGTGCTTCAGATGTATTC 59.384 50.000 0.00 0.00 36.87 1.75
201 211 3.209410 CCAGGTGCTTCAGATGTATTCC 58.791 50.000 0.00 0.00 0.00 3.01
202 212 3.118112 CCAGGTGCTTCAGATGTATTCCT 60.118 47.826 0.00 0.00 0.00 3.36
203 213 4.521146 CAGGTGCTTCAGATGTATTCCTT 58.479 43.478 0.00 0.00 0.00 3.36
204 214 4.946157 CAGGTGCTTCAGATGTATTCCTTT 59.054 41.667 0.00 0.00 0.00 3.11
205 215 5.416952 CAGGTGCTTCAGATGTATTCCTTTT 59.583 40.000 0.00 0.00 0.00 2.27
206 216 6.012745 AGGTGCTTCAGATGTATTCCTTTTT 58.987 36.000 0.00 0.00 0.00 1.94
221 231 4.748409 TTTTTGCGGGCTTGCTTC 57.252 50.000 4.09 0.00 35.36 3.86
237 247 3.282021 TGCTTCAGATGTATTCAAGGGC 58.718 45.455 0.00 0.00 0.00 5.19
242 252 4.517285 TCAGATGTATTCAAGGGCTCAAC 58.483 43.478 0.00 0.00 0.00 3.18
320 336 1.026718 GGTTGTCATCTCAAGCCGGG 61.027 60.000 2.18 0.00 39.11 5.73
324 340 1.612146 TCATCTCAAGCCGGGTCCA 60.612 57.895 6.62 0.00 0.00 4.02
372 388 4.742201 GGCTCGTTCTGGCAGCGA 62.742 66.667 10.34 13.10 33.66 4.93
375 391 0.806102 GCTCGTTCTGGCAGCGATAA 60.806 55.000 15.79 0.20 34.04 1.75
395 411 2.404923 TGGTCGTTTGGTTGTCTTGA 57.595 45.000 0.00 0.00 0.00 3.02
444 460 4.177165 TGACGTGCTTTATACTTTCGGA 57.823 40.909 0.00 0.00 0.00 4.55
450 466 5.004535 CGTGCTTTATACTTTCGGAGAACTC 59.995 44.000 0.00 0.00 45.90 3.01
582 598 4.526970 ACCCATTCATATCGAAGCACTTT 58.473 39.130 0.00 0.00 36.95 2.66
700 721 2.747446 GCGACACCATGTAATCCAAACT 59.253 45.455 0.00 0.00 0.00 2.66
738 759 3.763897 ACACTCAGGGCCATTTTAATCAC 59.236 43.478 6.18 0.00 0.00 3.06
805 829 2.734606 CCACGTACGCTCATCTGAAAAA 59.265 45.455 16.72 0.00 0.00 1.94
846 870 2.680352 GCCAGAGGTCGGTCAGGA 60.680 66.667 0.00 0.00 0.00 3.86
847 871 3.007973 GCCAGAGGTCGGTCAGGAC 62.008 68.421 0.00 0.00 36.18 3.85
848 872 1.304547 CCAGAGGTCGGTCAGGACT 60.305 63.158 0.00 0.00 37.12 3.85
849 873 1.316706 CCAGAGGTCGGTCAGGACTC 61.317 65.000 0.00 0.00 37.12 3.36
850 874 0.609406 CAGAGGTCGGTCAGGACTCA 60.609 60.000 0.00 0.00 37.12 3.41
851 875 0.322997 AGAGGTCGGTCAGGACTCAG 60.323 60.000 0.00 0.00 37.12 3.35
852 876 1.304547 AGGTCGGTCAGGACTCAGG 60.305 63.158 0.00 0.00 37.12 3.86
860 884 1.188219 TCAGGACTCAGGAGCCACAC 61.188 60.000 10.82 0.00 0.00 3.82
866 890 0.524862 CTCAGGAGCCACACAAATGC 59.475 55.000 0.00 0.00 0.00 3.56
886 1118 1.216977 GCCATGCATGCACATGTGT 59.783 52.632 25.37 2.19 44.88 3.72
947 1197 1.302192 TTCAGTACCCACGGCAAGC 60.302 57.895 0.00 0.00 0.00 4.01
954 1204 2.336088 CCACGGCAAGCCAAGTTG 59.664 61.111 12.19 0.00 35.37 3.16
958 1208 1.372128 CGGCAAGCCAAGTTGAAGC 60.372 57.895 12.19 0.00 35.37 3.86
959 1209 1.799258 CGGCAAGCCAAGTTGAAGCT 61.799 55.000 12.19 2.34 38.88 3.74
960 1210 1.247567 GGCAAGCCAAGTTGAAGCTA 58.752 50.000 6.14 0.00 35.30 3.32
961 1211 1.068264 GGCAAGCCAAGTTGAAGCTAC 60.068 52.381 6.14 2.01 35.30 3.58
989 1240 2.648059 CAGGTAATCAAGAAGGCAGGG 58.352 52.381 0.00 0.00 0.00 4.45
1050 1317 1.579964 CGCTTGTGATCCTGCTGCAA 61.580 55.000 3.02 0.00 0.00 4.08
1414 1726 1.286260 GACGAGTGCGACTCCAACT 59.714 57.895 9.71 0.00 42.12 3.16
1526 1842 2.549282 CGACGCCTGAAAACCGTG 59.451 61.111 0.00 0.00 35.06 4.94
1576 1892 3.075005 ACGACGACCATGGAGGGG 61.075 66.667 21.47 10.31 43.89 4.79
1605 1945 0.098552 TGCTTGTTTCTGTGTGCGTG 59.901 50.000 0.00 0.00 0.00 5.34
1609 1949 1.024046 TGTTTCTGTGTGCGTGTGCT 61.024 50.000 0.00 0.00 43.34 4.40
1610 1950 0.934496 GTTTCTGTGTGCGTGTGCTA 59.066 50.000 0.00 0.00 43.34 3.49
1611 1951 1.329292 GTTTCTGTGTGCGTGTGCTAA 59.671 47.619 0.00 0.00 43.34 3.09
1612 1952 1.657822 TTCTGTGTGCGTGTGCTAAA 58.342 45.000 0.00 0.00 43.34 1.85
1613 1953 1.657822 TCTGTGTGCGTGTGCTAAAA 58.342 45.000 0.00 0.00 43.34 1.52
1615 1955 3.394719 TCTGTGTGCGTGTGCTAAAATA 58.605 40.909 0.00 0.00 43.34 1.40
1617 1957 4.454161 TCTGTGTGCGTGTGCTAAAATAAT 59.546 37.500 0.00 0.00 43.34 1.28
1732 2107 7.691050 CGTCTCCGTTCCAAAATAATTAAAGTC 59.309 37.037 0.00 0.00 0.00 3.01
1777 2152 0.759060 GGGGTGGGCACTTTTGAACT 60.759 55.000 0.00 0.00 0.00 3.01
1797 2172 3.190953 ACTGAAAACCGAAAAACCGAACA 59.809 39.130 0.00 0.00 0.00 3.18
1802 2177 2.635714 ACCGAAAAACCGAACAGAACT 58.364 42.857 0.00 0.00 0.00 3.01
1878 2253 5.536916 AGTGGGAAATTTTATGGTTGTTCGA 59.463 36.000 0.00 0.00 0.00 3.71
1923 2298 1.476488 GTGCCCAAAAGCCGAATACAT 59.524 47.619 0.00 0.00 0.00 2.29
1925 2300 1.748493 GCCCAAAAGCCGAATACATCA 59.252 47.619 0.00 0.00 0.00 3.07
1952 2327 3.499338 ACCGATATGTACGATACCCCAA 58.501 45.455 0.00 0.00 0.00 4.12
2074 2451 8.961294 TCTCACAATCTAACTAGTACTCCTAC 57.039 38.462 0.00 0.00 0.00 3.18
2147 2524 3.200294 TGTTTGCATGCAACATAGTCG 57.800 42.857 31.99 0.00 35.46 4.18
2178 2555 7.501892 CCGTATTCTTCTAGTAAGTACTCCCTT 59.498 40.741 0.00 0.00 37.73 3.95
2203 2580 9.800433 TTCGTTCCATAATGTAAGACGTTAATA 57.200 29.630 0.00 0.00 33.75 0.98
2464 2843 4.033358 CCGAATAAAGCACTGACTGATGTC 59.967 45.833 0.00 0.00 43.20 3.06
2465 2844 4.259570 CGAATAAAGCACTGACTGATGTCG 60.260 45.833 0.00 0.00 45.70 4.35
2493 2872 8.740906 GGTTGCTAGCTCTTGTGATATATACTA 58.259 37.037 17.23 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 3.214328 AGAAGAAGTGTTGCATCCGTTT 58.786 40.909 0.00 0.00 0.00 3.60
27 28 2.851195 AGAAGAAGTGTTGCATCCGTT 58.149 42.857 0.00 0.00 0.00 4.44
94 104 2.033602 TGGAGCTCCGTCGAGTCA 59.966 61.111 27.43 4.53 38.49 3.41
111 121 2.305343 GGAGATGGCAGGAATCTATGCT 59.695 50.000 9.95 0.00 42.19 3.79
139 149 2.225470 ACGAGGAACCCTAACCTTACCT 60.225 50.000 0.00 0.00 36.57 3.08
204 214 0.249405 CTGAAGCAAGCCCGCAAAAA 60.249 50.000 0.00 0.00 0.00 1.94
205 215 1.106351 TCTGAAGCAAGCCCGCAAAA 61.106 50.000 0.00 0.00 0.00 2.44
206 216 0.895100 ATCTGAAGCAAGCCCGCAAA 60.895 50.000 0.00 0.00 0.00 3.68
207 217 1.303561 ATCTGAAGCAAGCCCGCAA 60.304 52.632 0.00 0.00 0.00 4.85
208 218 2.042259 CATCTGAAGCAAGCCCGCA 61.042 57.895 0.00 0.00 0.00 5.69
209 219 0.744414 TACATCTGAAGCAAGCCCGC 60.744 55.000 0.00 0.00 0.00 6.13
210 220 1.959042 ATACATCTGAAGCAAGCCCG 58.041 50.000 0.00 0.00 0.00 6.13
211 221 3.282021 TGAATACATCTGAAGCAAGCCC 58.718 45.455 0.00 0.00 0.00 5.19
212 222 4.201990 CCTTGAATACATCTGAAGCAAGCC 60.202 45.833 0.00 0.00 32.23 4.35
213 223 4.201990 CCCTTGAATACATCTGAAGCAAGC 60.202 45.833 0.00 0.00 32.23 4.01
214 224 4.201990 GCCCTTGAATACATCTGAAGCAAG 60.202 45.833 0.00 0.00 0.00 4.01
215 225 3.696051 GCCCTTGAATACATCTGAAGCAA 59.304 43.478 0.00 0.00 0.00 3.91
216 226 3.054139 AGCCCTTGAATACATCTGAAGCA 60.054 43.478 0.00 0.00 0.00 3.91
217 227 3.549794 AGCCCTTGAATACATCTGAAGC 58.450 45.455 0.00 0.00 0.00 3.86
218 228 4.774124 TGAGCCCTTGAATACATCTGAAG 58.226 43.478 0.00 0.00 0.00 3.02
219 229 4.842531 TGAGCCCTTGAATACATCTGAA 57.157 40.909 0.00 0.00 0.00 3.02
220 230 4.517285 GTTGAGCCCTTGAATACATCTGA 58.483 43.478 0.00 0.00 0.00 3.27
221 231 3.310774 CGTTGAGCCCTTGAATACATCTG 59.689 47.826 0.00 0.00 0.00 2.90
237 247 2.418333 CGCACTCGTCGTCGTTGAG 61.418 63.158 12.69 12.69 38.33 3.02
293 303 1.697432 TGAGATGACAACCGGGAAGTT 59.303 47.619 6.32 0.00 0.00 2.66
320 336 1.523032 CGCCGTTCCCCTATTGGAC 60.523 63.158 0.00 0.00 35.39 4.02
324 340 1.520666 CTGTCGCCGTTCCCCTATT 59.479 57.895 0.00 0.00 0.00 1.73
372 388 5.067273 TCAAGACAACCAAACGACCATTAT 58.933 37.500 0.00 0.00 0.00 1.28
375 391 2.925724 TCAAGACAACCAAACGACCAT 58.074 42.857 0.00 0.00 0.00 3.55
434 450 9.575868 TCTATTATCAGAGTTCTCCGAAAGTAT 57.424 33.333 0.00 0.00 0.00 2.12
500 516 3.431626 CGACAAGGCAATGGGTGTATAGA 60.432 47.826 0.00 0.00 0.00 1.98
582 598 3.057969 ACACAAAGCTGATTGATCGGA 57.942 42.857 5.15 0.00 35.13 4.55
657 678 4.067896 CCATTGCTCCAGCGTTAATATCT 58.932 43.478 0.00 0.00 45.83 1.98
700 721 4.840271 TGAGTGTACCTCGAGATGAGTTA 58.160 43.478 15.71 0.00 43.64 2.24
738 759 2.584418 CATGCTCGAGACAGGGCG 60.584 66.667 18.75 1.01 41.40 6.13
776 797 4.218478 GCGTACGTGGGCATTCGC 62.218 66.667 17.90 0.00 37.17 4.70
778 799 0.810031 ATGAGCGTACGTGGGCATTC 60.810 55.000 17.90 5.49 0.00 2.67
782 803 1.878522 CAGATGAGCGTACGTGGGC 60.879 63.158 17.90 0.50 0.00 5.36
786 807 3.673809 GTCTTTTTCAGATGAGCGTACGT 59.326 43.478 17.90 3.43 32.60 3.57
792 816 6.264088 GGATCAATGTCTTTTTCAGATGAGC 58.736 40.000 0.00 0.00 32.60 4.26
805 829 2.114616 AGAGCTTCCGGATCAATGTCT 58.885 47.619 4.15 0.00 31.91 3.41
846 870 1.901591 CATTTGTGTGGCTCCTGAGT 58.098 50.000 0.00 0.00 0.00 3.41
847 871 0.524862 GCATTTGTGTGGCTCCTGAG 59.475 55.000 0.00 0.00 0.00 3.35
848 872 0.895100 GGCATTTGTGTGGCTCCTGA 60.895 55.000 0.00 0.00 41.09 3.86
849 873 1.588082 GGCATTTGTGTGGCTCCTG 59.412 57.895 0.00 0.00 41.09 3.86
850 874 1.973281 CGGCATTTGTGTGGCTCCT 60.973 57.895 0.00 0.00 42.03 3.69
851 875 2.568090 CGGCATTTGTGTGGCTCC 59.432 61.111 0.00 0.00 42.03 4.70
852 876 2.126346 GCGGCATTTGTGTGGCTC 60.126 61.111 0.00 0.00 42.03 4.70
866 890 2.279186 CATGTGCATGCATGGCGG 60.279 61.111 25.64 8.45 41.70 6.13
886 1118 4.876828 GGCGCCCGCGTATGTGTA 62.877 66.667 18.11 0.00 43.06 2.90
958 1208 4.342378 TCTTGATTACCTGCTAGCCTGTAG 59.658 45.833 13.29 2.18 0.00 2.74
959 1209 4.286707 TCTTGATTACCTGCTAGCCTGTA 58.713 43.478 13.29 10.65 0.00 2.74
960 1210 3.107601 TCTTGATTACCTGCTAGCCTGT 58.892 45.455 13.29 11.72 0.00 4.00
961 1211 3.827008 TCTTGATTACCTGCTAGCCTG 57.173 47.619 13.29 5.60 0.00 4.85
989 1240 1.720301 CTCGCCATTGCTGAAGCTC 59.280 57.895 3.61 0.00 42.66 4.09
1329 1641 2.740714 GATCGTCTTGTGGCACCGC 61.741 63.158 16.26 1.57 0.00 5.68
1414 1726 2.260434 GTCGTCCTTGCAGCCGTA 59.740 61.111 0.00 0.00 0.00 4.02
1576 1892 7.020010 CACACAGAAACAAGCAATCTAGAATC 58.980 38.462 0.00 0.00 0.00 2.52
1605 1945 6.453134 GCGCTCGAGAGATATTATTTTAGCAC 60.453 42.308 21.07 0.00 40.84 4.40
1609 1949 7.120873 ACCTAGCGCTCGAGAGATATTATTTTA 59.879 37.037 21.07 0.00 40.84 1.52
1610 1950 6.071840 ACCTAGCGCTCGAGAGATATTATTTT 60.072 38.462 21.07 0.00 40.84 1.82
1611 1951 5.416326 ACCTAGCGCTCGAGAGATATTATTT 59.584 40.000 21.07 0.00 40.84 1.40
1612 1952 4.944930 ACCTAGCGCTCGAGAGATATTATT 59.055 41.667 21.07 0.00 40.84 1.40
1613 1953 4.519213 ACCTAGCGCTCGAGAGATATTAT 58.481 43.478 21.07 3.57 40.84 1.28
1615 1955 2.785562 ACCTAGCGCTCGAGAGATATT 58.214 47.619 21.07 5.18 40.84 1.28
1617 1957 2.299582 AGTACCTAGCGCTCGAGAGATA 59.700 50.000 21.07 17.05 40.84 1.98
1738 2113 8.665906 CCACCCCTAAGTTTGATATAGGATAAA 58.334 37.037 0.00 0.00 38.81 1.40
1741 2116 5.551977 CCCACCCCTAAGTTTGATATAGGAT 59.448 44.000 0.00 0.00 38.81 3.24
1744 2119 4.104102 TGCCCACCCCTAAGTTTGATATAG 59.896 45.833 0.00 0.00 0.00 1.31
1747 2122 2.025699 GTGCCCACCCCTAAGTTTGATA 60.026 50.000 0.00 0.00 0.00 2.15
1777 2152 3.439476 TCTGTTCGGTTTTTCGGTTTTCA 59.561 39.130 0.00 0.00 0.00 2.69
1797 2172 9.847224 ATAAATCGGTTAATATGGTTCAGTTCT 57.153 29.630 0.00 0.00 0.00 3.01
1878 2253 5.701290 TGAAAACCGAACAAAAACCAAACAT 59.299 32.000 0.00 0.00 0.00 2.71
1952 2327 5.519722 CACTTTCGAAAACAAGGTATTGCT 58.480 37.500 12.41 0.00 40.27 3.91
2074 2451 2.798283 CCATGTTAGTATGGCGTTACGG 59.202 50.000 6.94 0.00 41.02 4.02
2147 2524 6.086785 ACTTACTAGAAGAATACGGCCATC 57.913 41.667 2.24 0.00 0.00 3.51
2178 2555 9.970395 ATATTAACGTCTTACATTATGGAACGA 57.030 29.630 8.44 0.00 0.00 3.85
2348 2727 7.710907 AGAATATGTGTGATGCGTGTAAACTAT 59.289 33.333 0.00 0.00 0.00 2.12
2464 2843 1.067565 TCACAAGAGCTAGCAACCTCG 60.068 52.381 18.83 2.87 33.39 4.63
2465 2844 2.751166 TCACAAGAGCTAGCAACCTC 57.249 50.000 18.83 5.47 0.00 3.85
2493 2872 6.365789 CGAAAACCAAAATACATGCACTCATT 59.634 34.615 0.00 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.