Multiple sequence alignment - TraesCS6A01G153200

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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 TraesCS6A01G153200 chr6A 100.000 5576 0 0 1 5576 140426236 140431811 0 10298
1 TraesCS6A01G153200 chr3A 94.114 5403 285 18 195 5576 647248385 647253775 0 8185
2 TraesCS6A01G153200 chr2A 93.564 5407 311 22 195 5576 184075720 184081114 0 8022
3 TraesCS6A01G153200 chr2A 92.474 2033 127 18 195 2210 78648936 78646913 0 2883
4 TraesCS6A01G153200 chr2A 92.376 2020 131 17 205 2210 184086303 184088313 0 2856
5 TraesCS6A01G153200 chr2B 92.560 5618 364 29 1 5576 219375183 219380788 0 8010
6 TraesCS6A01G153200 chr2B 93.110 4441 262 24 1 4407 310927531 310923101 0 6466
7 TraesCS6A01G153200 chr2B 92.366 2227 145 19 1 2210 310917243 310915025 0 3147
8 TraesCS6A01G153200 chr2B 92.183 2226 153 17 1 2210 219385528 219387748 0 3127
9 TraesCS6A01G153200 chr2B 92.007 2227 154 18 1 2210 175064245 175066464 0 3105
10 TraesCS6A01G153200 chr2D 92.492 5607 352 40 1 5576 143543052 143548620 0 7958
11 TraesCS6A01G153200 chr7D 91.970 5629 364 46 1 5576 368314310 368319903 0 7810
12 TraesCS6A01G153200 chr1A 94.497 3289 175 6 1 3287 376865088 376868372 0 5066
13 TraesCS6A01G153200 chrUn 94.407 3290 179 5 1 3287 293664418 293661131 0 5051
14 TraesCS6A01G153200 chrUn 94.965 1132 46 3 4112 5242 374936915 374935794 0 1764
15 TraesCS6A01G153200 chr6D 90.950 3359 259 31 1 3351 85382930 85379609 0 4477
16 TraesCS6A01G153200 chr6D 93.517 1450 78 8 4142 5576 85374709 85373261 0 2143
17 TraesCS6A01G153200 chr3B 89.243 3291 280 42 2326 5576 796295834 796299090 0 4048
18 TraesCS6A01G153200 chr3B 89.000 3291 289 41 2327 5576 132170833 132174091 0 4004
19 TraesCS6A01G153200 chr4B 88.867 2039 184 22 3564 5576 353285227 353283206 0 2468
20 TraesCS6A01G153200 chr4B 88.720 2039 185 22 3565 5576 353444557 353442537 0 2449
21 TraesCS6A01G153200 chr4B 88.671 2039 188 20 3564 5576 353364264 353362243 0 2446


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 TraesCS6A01G153200 chr6A 140426236 140431811 5575 False 10298 10298 100.000 1 5576 1 chr6A.!!$F1 5575
1 TraesCS6A01G153200 chr3A 647248385 647253775 5390 False 8185 8185 94.114 195 5576 1 chr3A.!!$F1 5381
2 TraesCS6A01G153200 chr2A 184075720 184081114 5394 False 8022 8022 93.564 195 5576 1 chr2A.!!$F1 5381
3 TraesCS6A01G153200 chr2A 78646913 78648936 2023 True 2883 2883 92.474 195 2210 1 chr2A.!!$R1 2015
4 TraesCS6A01G153200 chr2A 184086303 184088313 2010 False 2856 2856 92.376 205 2210 1 chr2A.!!$F2 2005
5 TraesCS6A01G153200 chr2B 219375183 219380788 5605 False 8010 8010 92.560 1 5576 1 chr2B.!!$F2 5575
6 TraesCS6A01G153200 chr2B 310923101 310927531 4430 True 6466 6466 93.110 1 4407 1 chr2B.!!$R2 4406
7 TraesCS6A01G153200 chr2B 310915025 310917243 2218 True 3147 3147 92.366 1 2210 1 chr2B.!!$R1 2209
8 TraesCS6A01G153200 chr2B 219385528 219387748 2220 False 3127 3127 92.183 1 2210 1 chr2B.!!$F3 2209
9 TraesCS6A01G153200 chr2B 175064245 175066464 2219 False 3105 3105 92.007 1 2210 1 chr2B.!!$F1 2209
10 TraesCS6A01G153200 chr2D 143543052 143548620 5568 False 7958 7958 92.492 1 5576 1 chr2D.!!$F1 5575
11 TraesCS6A01G153200 chr7D 368314310 368319903 5593 False 7810 7810 91.970 1 5576 1 chr7D.!!$F1 5575
12 TraesCS6A01G153200 chr1A 376865088 376868372 3284 False 5066 5066 94.497 1 3287 1 chr1A.!!$F1 3286
13 TraesCS6A01G153200 chrUn 293661131 293664418 3287 True 5051 5051 94.407 1 3287 1 chrUn.!!$R1 3286
14 TraesCS6A01G153200 chrUn 374935794 374936915 1121 True 1764 1764 94.965 4112 5242 1 chrUn.!!$R2 1130
15 TraesCS6A01G153200 chr6D 85379609 85382930 3321 True 4477 4477 90.950 1 3351 1 chr6D.!!$R2 3350
16 TraesCS6A01G153200 chr6D 85373261 85374709 1448 True 2143 2143 93.517 4142 5576 1 chr6D.!!$R1 1434
17 TraesCS6A01G153200 chr3B 796295834 796299090 3256 False 4048 4048 89.243 2326 5576 1 chr3B.!!$F2 3250
18 TraesCS6A01G153200 chr3B 132170833 132174091 3258 False 4004 4004 89.000 2327 5576 1 chr3B.!!$F1 3249
19 TraesCS6A01G153200 chr4B 353283206 353285227 2021 True 2468 2468 88.867 3564 5576 1 chr4B.!!$R1 2012
20 TraesCS6A01G153200 chr4B 353442537 353444557 2020 True 2449 2449 88.720 3565 5576 1 chr4B.!!$R3 2011
21 TraesCS6A01G153200 chr4B 353362243 353364264 2021 True 2446 2446 88.671 3564 5576 1 chr4B.!!$R2 2012

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
197 198 2.262292 CAAAGCCATGGCAACCGG 59.738 61.111 37.18 18.06 44.88 5.28 F
578 587 2.447408 TTCTGGATAGACACGGGCTA 57.553 50.000 0.00 0.00 31.21 3.93 F
1474 1495 1.000506 GTTCCTTGGTCTAGTCGTGCA 59.999 52.381 0.00 0.00 0.00 4.57 F
2965 2998 0.100682 CGATAGTCCCACACACTCGG 59.899 60.000 0.00 0.00 31.12 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1078 1099 0.601558 TGCCCGAGTCACAACTACTC 59.398 55.0 0.0 0.0 40.01 2.59 R
1484 1505 0.682292 TGGTACAAGTCGTCCATGCA 59.318 50.0 0.0 0.0 31.92 3.96 R
3359 3392 0.402121 GGAGAAGGTGGAGCAAGGTT 59.598 55.0 0.0 0.0 0.00 3.50 R
4750 4854 0.476808 TGGGGTAATGGTGGAGGTGT 60.477 55.0 0.0 0.0 0.00 4.16 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
85 86 4.306600 CACGTTCATATATAGCAGGCACA 58.693 43.478 0.00 0.00 0.00 4.57
163 164 3.372660 GTAGCAGTAGGATGTGGCTAC 57.627 52.381 6.38 6.38 46.71 3.58
197 198 2.262292 CAAAGCCATGGCAACCGG 59.738 61.111 37.18 18.06 44.88 5.28
578 587 2.447408 TTCTGGATAGACACGGGCTA 57.553 50.000 0.00 0.00 31.21 3.93
940 961 6.778821 TCTCCTTGACCATGTCTTGATAAAA 58.221 36.000 0.00 0.00 33.15 1.52
941 962 7.230747 TCTCCTTGACCATGTCTTGATAAAAA 58.769 34.615 0.00 0.00 33.15 1.94
1078 1099 6.927936 CCAGATCAGGTGAAGTATCTGTATTG 59.072 42.308 9.58 0.00 42.39 1.90
1091 1112 8.582657 AGTATCTGTATTGAGTAGTTGTGACT 57.417 34.615 0.00 0.00 39.97 3.41
1212 1233 5.723672 ACATAGGGTATCACATTAGGACG 57.276 43.478 0.00 0.00 0.00 4.79
1338 1359 2.185387 GGGTAAGAAGGTGGCTGTAGA 58.815 52.381 0.00 0.00 0.00 2.59
1432 1453 2.296190 GGTGGAAAAGCAAAGGTAGTGG 59.704 50.000 0.00 0.00 0.00 4.00
1474 1495 1.000506 GTTCCTTGGTCTAGTCGTGCA 59.999 52.381 0.00 0.00 0.00 4.57
1586 1607 0.824109 CTGGGATAGGAAGTGCGTCA 59.176 55.000 0.00 0.00 0.00 4.35
1639 1660 3.749064 ACGTCGCTCTGTCGCCAT 61.749 61.111 0.00 0.00 32.10 4.40
1727 1749 8.367911 ACATAGTATTTTGAGATAATGGCTCGA 58.632 33.333 0.00 0.00 35.15 4.04
1742 1764 1.663379 CTCGATGGTGGTAGCCGTGA 61.663 60.000 0.00 0.00 0.00 4.35
1833 1856 3.594603 ATACGTACTCAGCTGCACTTT 57.405 42.857 9.47 0.00 0.00 2.66
1869 1893 4.161377 AGCAAGAGAGTTATGAGAACTCCC 59.839 45.833 15.60 4.85 45.82 4.30
1943 1967 5.749109 CGGTTATTCTGAAGTGGAGTATGAC 59.251 44.000 0.00 0.00 0.00 3.06
1949 1973 6.701145 TCTGAAGTGGAGTATGACTATGAC 57.299 41.667 0.00 0.00 0.00 3.06
1950 1974 6.427441 TCTGAAGTGGAGTATGACTATGACT 58.573 40.000 0.00 0.00 0.00 3.41
2046 2071 1.404583 CGATCTATCATCATGGCCGCA 60.405 52.381 0.00 0.00 0.00 5.69
2049 2074 3.979101 TCTATCATCATGGCCGCATAA 57.021 42.857 0.00 0.00 0.00 1.90
2098 2123 6.737254 TGTAATAAAAGCTTGCCTACTCAC 57.263 37.500 0.00 0.00 0.00 3.51
2126 2151 2.233676 TGCTCCGTCTTGTACATGACAT 59.766 45.455 30.28 0.00 38.07 3.06
2166 2191 0.880278 GGCGCAACTCTGAAGTGACA 60.880 55.000 10.83 0.00 35.36 3.58
2210 2235 2.125832 ACGTAATGGGGCGTCACG 60.126 61.111 0.00 0.00 36.54 4.35
2214 2239 0.463116 GTAATGGGGCGTCACGGAAT 60.463 55.000 0.00 0.00 0.00 3.01
2231 2256 3.305676 CGGAATAGGTGGTATCAGAGCAG 60.306 52.174 0.00 0.00 35.85 4.24
2555 2587 4.102524 TCTTGGTTGAGCTTCTTGGTCTTA 59.897 41.667 0.00 0.00 43.13 2.10
2622 2654 2.498885 GTTCCACGGGGTACTTAGTCAT 59.501 50.000 2.12 0.00 32.14 3.06
2703 2735 1.211703 TGTTTCAGCACTTCAGGGTGA 59.788 47.619 0.00 0.00 40.66 4.02
2740 2772 3.488778 TTACACCTTTTCCACGCCTAA 57.511 42.857 0.00 0.00 0.00 2.69
2760 2792 0.173708 CACCCTCTCCTTCAGTACGC 59.826 60.000 0.00 0.00 0.00 4.42
2830 2862 2.895372 CCTACGCCCATTGTCGCC 60.895 66.667 0.00 0.00 0.00 5.54
2920 2953 2.738587 TTTTACCACCACCAGCTTCA 57.261 45.000 0.00 0.00 0.00 3.02
2927 2960 1.529010 CCACCAGCTTCAACTGCCA 60.529 57.895 0.00 0.00 36.29 4.92
2949 2982 1.035932 CGTCCACCTCTGTACCCGAT 61.036 60.000 0.00 0.00 0.00 4.18
2958 2991 1.285667 TCTGTACCCGATAGTCCCACA 59.714 52.381 0.00 0.00 0.00 4.17
2965 2998 0.100682 CGATAGTCCCACACACTCGG 59.899 60.000 0.00 0.00 31.12 4.63
3037 3070 1.304713 ACGTCCCTCCACACCGTAT 60.305 57.895 0.00 0.00 0.00 3.06
3103 3136 2.659610 GCCACTCTTCAGAGGCGT 59.340 61.111 8.70 0.00 45.22 5.68
3110 3143 0.756294 TCTTCAGAGGCGTTGTTCCA 59.244 50.000 0.00 0.00 0.00 3.53
3123 3156 0.550914 TGTTCCAAGCTTGAGTGGGT 59.449 50.000 28.05 0.00 35.46 4.51
3292 3325 3.372133 CCTCTCAGGTTGCTCCTACTCTA 60.372 52.174 1.02 0.00 46.24 2.43
3359 3392 0.178903 ACCAGGTTCTCCAGCTACCA 60.179 55.000 5.43 0.00 34.32 3.25
3363 3396 0.984995 GGTTCTCCAGCTACCAACCT 59.015 55.000 8.22 0.00 34.74 3.50
3413 3446 1.531149 ACTTTTCAGTGATTGGCGTCG 59.469 47.619 0.00 0.00 0.00 5.12
3488 3521 1.899814 AGTACCTTCATGTCGCTTCCA 59.100 47.619 0.00 0.00 0.00 3.53
3503 3536 1.616865 CTTCCAACGTCACACCCTCTA 59.383 52.381 0.00 0.00 0.00 2.43
3538 3571 3.450904 TGAGTACCCTCTTAGCACCATT 58.549 45.455 0.00 0.00 38.61 3.16
3588 3621 1.070445 GTGTGTCTCTGCCTGCACT 59.930 57.895 0.00 0.00 33.44 4.40
3825 3872 1.405821 CGTAGCTACCCTTCCAGAGTG 59.594 57.143 18.16 0.00 0.00 3.51
3833 3880 0.394192 CCTTCCAGAGTGTGCACAGA 59.606 55.000 22.40 10.97 0.00 3.41
3867 3914 4.156922 CAGACTAGTTCCGACAGACAGATT 59.843 45.833 0.00 0.00 0.00 2.40
3911 3958 2.950309 CCAGGTACACGTGTAGATAGCT 59.050 50.000 28.02 20.26 0.00 3.32
4072 4120 8.918658 CATGCCTCCATATTCATTTTAAATTCG 58.081 33.333 0.00 0.00 0.00 3.34
4230 4282 3.314080 CCTTTGGTACATCACGTGTTTGT 59.686 43.478 23.30 23.30 42.29 2.83
4407 4483 7.093333 TGACTTGTGATTAATCTCTTGCCTCTA 60.093 37.037 16.24 0.00 0.00 2.43
4531 4632 3.323751 AATTGATGCTCCAAAACAGGC 57.676 42.857 0.00 0.00 0.00 4.85
4678 4782 4.761235 AGTCAGTCGTTCGAAGACAATA 57.239 40.909 21.65 9.74 40.84 1.90
4863 4967 9.347240 CTAGAACACCAGAATAAATTCATGGAT 57.653 33.333 19.37 0.00 39.23 3.41
4864 4968 8.004087 AGAACACCAGAATAAATTCATGGATG 57.996 34.615 19.37 16.26 39.23 3.51
4877 4981 4.322080 TCATGGATGAGATGTTCGGTAC 57.678 45.455 0.00 0.00 32.11 3.34
4919 5023 3.312736 AAACCCAGAACAAGGTGTCAT 57.687 42.857 0.00 0.00 36.19 3.06
4958 5062 4.086706 AGACTAGACCACCAACCTTTTG 57.913 45.455 0.00 0.00 0.00 2.44
5075 5179 3.066291 TGCGTCCCATCAGTTAATTGT 57.934 42.857 0.00 0.00 0.00 2.71
5078 5182 3.689649 GCGTCCCATCAGTTAATTGTTCT 59.310 43.478 0.00 0.00 0.00 3.01
5174 5278 5.049267 AGAGGAGATTTCGAGATAACTACGC 60.049 44.000 0.00 0.00 0.00 4.42
5250 5354 4.839668 GTCTAAGACCATCGCAGAGTAT 57.160 45.455 0.00 0.00 43.63 2.12
5552 5657 2.280552 CCGTCCGTCCTCCTTTCCA 61.281 63.158 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.576550 TGCCTGCTATATATGAACGTGGA 59.423 43.478 0.00 0.00 0.00 4.02
85 86 6.339730 TGAAGTGCTTCAAATTTCACAACAT 58.660 32.000 11.72 0.00 45.56 2.71
163 164 0.602638 TTGCTGCTAACGGTGTGGAG 60.603 55.000 0.00 0.00 0.00 3.86
242 243 2.901840 CAGCCACACGCACAAGGT 60.902 61.111 0.00 0.00 41.38 3.50
336 338 0.176680 CACCACTCAATCCTAGCGCT 59.823 55.000 17.26 17.26 0.00 5.92
502 507 3.844090 GCCCGCTCACCTCTCTCC 61.844 72.222 0.00 0.00 0.00 3.71
778 787 3.394674 TCTAAACATCCAGCAACACGA 57.605 42.857 0.00 0.00 0.00 4.35
822 843 9.613428 TCGACTCCTGATAATTATTTCACAAAT 57.387 29.630 0.00 0.00 34.90 2.32
940 961 1.286553 TGACCCATAGCCCGGAATTTT 59.713 47.619 0.73 0.00 0.00 1.82
941 962 0.923358 TGACCCATAGCCCGGAATTT 59.077 50.000 0.73 0.00 0.00 1.82
942 963 1.149101 ATGACCCATAGCCCGGAATT 58.851 50.000 0.73 0.00 0.00 2.17
943 964 1.149101 AATGACCCATAGCCCGGAAT 58.851 50.000 0.73 0.00 0.00 3.01
1078 1099 0.601558 TGCCCGAGTCACAACTACTC 59.398 55.000 0.00 0.00 40.01 2.59
1091 1112 2.018355 TATAATGTAGCCCTGCCCGA 57.982 50.000 0.00 0.00 0.00 5.14
1127 1148 2.771943 TCACCAACATAAGCTCCCCTAG 59.228 50.000 0.00 0.00 0.00 3.02
1212 1233 1.081442 GTAAGCGCCAGTTGGTTGC 60.081 57.895 2.29 8.79 38.44 4.17
1322 1343 0.608640 CCGTCTACAGCCACCTTCTT 59.391 55.000 0.00 0.00 0.00 2.52
1338 1359 0.613012 GGGTGACTGTACCTACCCGT 60.613 60.000 7.83 0.00 42.96 5.28
1432 1453 1.162698 GAACCTTTAACCAGCCCGTC 58.837 55.000 0.00 0.00 0.00 4.79
1474 1495 1.295423 GTCCATGCACTACCCGTGT 59.705 57.895 0.00 0.00 45.57 4.49
1484 1505 0.682292 TGGTACAAGTCGTCCATGCA 59.318 50.000 0.00 0.00 31.92 3.96
1574 1595 1.003355 CCCACATGACGCACTTCCT 60.003 57.895 0.00 0.00 0.00 3.36
1586 1607 4.447138 TGTGTTAGAGGAAAACCCACAT 57.553 40.909 0.00 0.00 37.41 3.21
1727 1749 2.987125 GGTCACGGCTACCACCAT 59.013 61.111 0.00 0.00 36.96 3.55
1833 1856 7.391148 AACTCTCTTGCTCTAAAAACAACAA 57.609 32.000 0.00 0.00 0.00 2.83
1869 1893 4.592485 AAGTACCATTCTCTATCGCCTG 57.408 45.455 0.00 0.00 0.00 4.85
1943 1967 5.460419 GCCTTGATTGTCGACTTAGTCATAG 59.540 44.000 17.92 13.08 32.09 2.23
1949 1973 5.592054 TCATAGCCTTGATTGTCGACTTAG 58.408 41.667 17.92 6.56 0.00 2.18
1950 1974 5.592104 TCATAGCCTTGATTGTCGACTTA 57.408 39.130 17.92 5.22 0.00 2.24
2046 2071 4.463186 ACCTCAAGTGTCGACTAAGCTTAT 59.537 41.667 17.92 0.00 0.00 1.73
2049 2074 2.029828 CACCTCAAGTGTCGACTAAGCT 60.030 50.000 17.92 6.88 41.93 3.74
2126 2151 4.565652 GCCAGGATCAGTTAAGGAGAACAA 60.566 45.833 0.00 0.00 0.00 2.83
2166 2191 1.080025 GTCAGGCGTAACGGAAGCT 60.080 57.895 0.00 0.00 32.41 3.74
2210 2235 3.556004 GCTGCTCTGATACCACCTATTCC 60.556 52.174 0.00 0.00 0.00 3.01
2214 2239 1.032794 CGCTGCTCTGATACCACCTA 58.967 55.000 0.00 0.00 0.00 3.08
2231 2256 4.689345 AGTACATGACTGTTTCCTTAACGC 59.311 41.667 0.00 0.00 39.72 4.84
2461 2488 7.230108 CCACTCATCATCCTACATTAAGCAATT 59.770 37.037 0.00 0.00 0.00 2.32
2555 2587 0.968405 GGTGCAATCAACACACCCAT 59.032 50.000 0.00 0.00 46.65 4.00
2622 2654 2.182827 AGCTCTCAGGAATGTGCACTA 58.817 47.619 19.41 4.84 0.00 2.74
2716 2748 1.335496 GCGTGGAAAAGGTGTAAAGCA 59.665 47.619 0.00 0.00 0.00 3.91
2740 2772 1.546961 CGTACTGAAGGAGAGGGTGT 58.453 55.000 0.00 0.00 0.00 4.16
2920 2953 2.100879 GAGGTGGACGAGTGGCAGTT 62.101 60.000 0.00 0.00 0.00 3.16
2927 2960 0.611340 GGGTACAGAGGTGGACGAGT 60.611 60.000 0.00 0.00 38.61 4.18
2958 2991 3.626924 GGTGGTCTGCCCGAGTGT 61.627 66.667 0.00 0.00 35.15 3.55
2965 2998 4.416738 GGAGCTGGGTGGTCTGCC 62.417 72.222 0.00 0.00 42.40 4.85
3037 3070 2.189191 GAGGTGCAGGTGGATGCTCA 62.189 60.000 0.00 0.00 46.63 4.26
3110 3143 1.972872 CTGTTCACCCACTCAAGCTT 58.027 50.000 0.00 0.00 0.00 3.74
3123 3156 0.969149 AGTGGACATCTCGCTGTTCA 59.031 50.000 0.00 0.00 32.10 3.18
3166 3199 0.988678 GAGGGTTGAGGGCCATACCT 60.989 60.000 17.64 11.97 45.57 3.08
3266 3299 0.980423 GGAGCAACCTGAGAGGAAGT 59.020 55.000 0.00 0.00 37.67 3.01
3292 3325 1.071228 GGTGGGACTACAACGGAACTT 59.929 52.381 0.00 0.00 0.00 2.66
3359 3392 0.402121 GGAGAAGGTGGAGCAAGGTT 59.598 55.000 0.00 0.00 0.00 3.50
3363 3396 0.909610 ATCGGGAGAAGGTGGAGCAA 60.910 55.000 0.00 0.00 45.37 3.91
3413 3446 3.130340 AGTGCTAGAAGCTCTGAGTAAGC 59.870 47.826 6.53 8.72 42.72 3.09
3488 3521 1.045407 TGCTTAGAGGGTGTGACGTT 58.955 50.000 0.00 0.00 0.00 3.99
3538 3571 1.583495 CGTCAGACTCGGGTGCACTA 61.583 60.000 17.98 1.75 0.00 2.74
3588 3621 0.903454 GGGGTCGAGGGAAGAAGTCA 60.903 60.000 0.00 0.00 0.00 3.41
3771 3817 5.928839 CCTTTCCAGATATGTACAGAATCCG 59.071 44.000 14.36 7.12 0.00 4.18
3825 3872 1.336517 TGGCTAACTACGTCTGTGCAC 60.337 52.381 10.75 10.75 0.00 4.57
3833 3880 3.693578 GGAACTAGTCTGGCTAACTACGT 59.306 47.826 0.00 0.00 0.00 3.57
3867 3914 2.303600 ACAAAAGTATACCTGCCGACCA 59.696 45.455 0.00 0.00 0.00 4.02
3911 3958 1.407299 GCACATCATCAGGCTACCACA 60.407 52.381 0.00 0.00 0.00 4.17
4072 4120 3.849911 GCAAGGAGCATAAAAAGAACCC 58.150 45.455 0.00 0.00 44.79 4.11
4189 4240 6.127535 CCAAAGGCATGTACTTGAATGAAGAT 60.128 38.462 12.65 0.00 35.42 2.40
4334 4391 2.431454 TGCACACACAAGTTCTTCACA 58.569 42.857 0.00 0.00 0.00 3.58
4466 4556 7.226772 CGGCATACTAGAAAATTTTGCAAAAC 58.773 34.615 26.05 13.68 0.00 2.43
4467 4557 6.128688 GCGGCATACTAGAAAATTTTGCAAAA 60.129 34.615 25.76 25.76 0.00 2.44
4468 4558 5.347364 GCGGCATACTAGAAAATTTTGCAAA 59.653 36.000 8.05 8.05 0.00 3.68
4469 4559 4.862018 GCGGCATACTAGAAAATTTTGCAA 59.138 37.500 8.47 0.00 0.00 4.08
4531 4632 5.468072 AGCTCAAACAGTACATTTCACTCTG 59.532 40.000 0.00 0.00 0.00 3.35
4593 4695 8.859236 AGGTTATAACGATAGCTACTACATGA 57.141 34.615 9.46 0.00 42.67 3.07
4621 4725 2.671070 CGATCTGGTGGGCAAGGT 59.329 61.111 0.00 0.00 0.00 3.50
4678 4782 3.372025 GGTGCTAAATCTGATGGGTTCCT 60.372 47.826 0.00 0.00 0.00 3.36
4745 4849 2.574824 GGTAATGGTGGAGGTGTAGGTT 59.425 50.000 0.00 0.00 0.00 3.50
4750 4854 0.476808 TGGGGTAATGGTGGAGGTGT 60.477 55.000 0.00 0.00 0.00 4.16
4863 4967 3.275999 TCTCATCGTACCGAACATCTCA 58.724 45.455 0.00 0.00 39.99 3.27
4864 4968 3.304123 CCTCTCATCGTACCGAACATCTC 60.304 52.174 0.00 0.00 39.99 2.75
4877 4981 0.534412 AGTCAGTTGGCCTCTCATCG 59.466 55.000 3.32 0.00 0.00 3.84
4958 5062 2.213499 CTAATGGATCTGTGGCGGTTC 58.787 52.381 0.00 0.00 0.00 3.62
5075 5179 2.343506 CACCATGTGGCAGCAAGAA 58.656 52.632 0.00 0.00 39.32 2.52
5271 5375 1.227380 CTCTGGTGCATAGCGGGAC 60.227 63.158 0.00 0.00 0.00 4.46
5552 5657 2.559381 AGGTGGTCTAGGAGCTTGAT 57.441 50.000 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.