Multiple sequence alignment - TraesCS6D01G129900

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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 TraesCS6D01G129900 chr6D 100.000 4432 0 0 1 4432 95726694 95722263 0.000000e+00 8185.0
1 TraesCS6D01G129900 chr6B 96.962 2864 67 11 1 2861 177269182 177272028 0.000000e+00 4789.0
2 TraesCS6D01G129900 chr6B 95.222 879 30 9 2857 3726 177272175 177273050 0.000000e+00 1380.0
3 TraesCS6D01G129900 chr6B 89.496 476 30 12 3723 4182 177273080 177273551 6.390000e-163 584.0
4 TraesCS6D01G129900 chr6A 95.234 2224 66 21 2100 4310 113516276 113518472 0.000000e+00 3483.0
5 TraesCS6D01G129900 chr6A 97.119 1215 34 1 835 2049 113515064 113516277 0.000000e+00 2049.0
6 TraesCS6D01G129900 chr6A 94.760 458 19 2 1 458 113510616 113511068 0.000000e+00 708.0
7 TraesCS6D01G129900 chr6A 94.649 299 8 5 459 755 113511147 113511439 1.450000e-124 457.0
8 TraesCS6D01G129900 chr6A 95.789 95 2 2 2540 2633 250692221 250692314 7.680000e-33 152.0
9 TraesCS6D01G129900 chr6A 100.000 36 0 0 4307 4342 113535629 113535664 2.860000e-07 67.6
10 TraesCS6D01G129900 chr3B 96.939 98 1 2 2547 2643 229298685 229298781 3.550000e-36 163.0
11 TraesCS6D01G129900 chr3B 96.667 90 2 1 2547 2635 217984918 217985007 9.930000e-32 148.0
12 TraesCS6D01G129900 chr3B 89.831 59 6 0 1995 2053 624178805 624178747 4.750000e-10 76.8
13 TraesCS6D01G129900 chr5D 98.876 89 1 0 2547 2635 325476209 325476121 4.590000e-35 159.0
14 TraesCS6D01G129900 chr2B 97.802 91 1 1 2547 2637 37108823 37108912 5.940000e-34 156.0
15 TraesCS6D01G129900 chr7B 95.699 93 2 2 2547 2638 13869113 13869204 9.930000e-32 148.0
16 TraesCS6D01G129900 chr7B 79.775 89 9 6 2005 2085 581389190 581389103 6.190000e-04 56.5
17 TraesCS6D01G129900 chr7B 100.000 30 0 0 2060 2089 677156706 677156735 6.190000e-04 56.5
18 TraesCS6D01G129900 chr1B 95.699 93 3 1 2543 2635 646470988 646470897 9.930000e-32 148.0
19 TraesCS6D01G129900 chr1B 92.857 56 3 1 2003 2057 643590035 643590090 3.670000e-11 80.5
20 TraesCS6D01G129900 chr7D 93.421 76 4 1 2004 2079 167359316 167359390 1.300000e-20 111.0
21 TraesCS6D01G129900 chr7A 89.610 77 6 2 2003 2079 711827742 711827668 3.650000e-16 97.1
22 TraesCS6D01G129900 chrUn 96.000 50 0 2 2000 2049 38926497 38926450 3.670000e-11 80.5
23 TraesCS6D01G129900 chr4D 95.918 49 2 0 2005 2053 16052401 16052449 3.670000e-11 80.5
24 TraesCS6D01G129900 chr1A 94.231 52 3 0 2002 2053 566218077 566218128 3.670000e-11 80.5
25 TraesCS6D01G129900 chr1A 81.319 91 8 6 2005 2087 151773712 151773801 1.030000e-06 65.8
26 TraesCS6D01G129900 chr5B 80.435 92 7 7 2004 2086 69131971 69131882 4.790000e-05 60.2
27 TraesCS6D01G129900 chr4B 80.435 92 6 9 2005 2086 74721776 74721865 4.790000e-05 60.2
28 TraesCS6D01G129900 chr1D 96.875 32 1 0 2053 2084 305586150 305586119 2.000000e-03 54.7


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 TraesCS6D01G129900 chr6D 95722263 95726694 4431 True 8185.00 8185 100.000000 1 4432 1 chr6D.!!$R1 4431
1 TraesCS6D01G129900 chr6B 177269182 177273551 4369 False 2251.00 4789 93.893333 1 4182 3 chr6B.!!$F1 4181
2 TraesCS6D01G129900 chr6A 113510616 113518472 7856 False 1674.25 3483 95.440500 1 4310 4 chr6A.!!$F3 4309

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
645 724 2.568623 AAAGAACAGATTGGCCGAGT 57.431 45.000 0.00 0.0 0.00 4.18 F
1276 4939 1.165270 GTGAGGGTGGTTTTGGATCG 58.835 55.000 0.00 0.0 0.00 3.69 F
2118 5782 2.304180 ACTGTGTGCCTTCAGAAGCTAT 59.696 45.455 4.41 0.0 35.84 2.97 F
3111 6931 1.831106 ACAGTTCTGCGGGTGATGATA 59.169 47.619 0.00 0.0 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 5850 2.452600 ACAGGTGGTGTGGTTTCATT 57.547 45.000 0.00 0.0 38.28 2.57 R
3111 6931 3.634504 TGCAGGCTTGTTCAATATCCAT 58.365 40.909 0.00 0.0 0.00 3.41 R
3317 7137 0.537188 ACGTGGAGGATGAAGCGAAT 59.463 50.000 0.00 0.0 0.00 3.34 R
4332 8207 0.034756 TGTACTTGCGGCACATCAGT 59.965 50.000 0.05 6.2 0.00 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
30 31 4.034279 CGGTAGCAGAGACACTTAGACTAC 59.966 50.000 0.00 0.00 0.00 2.73
91 92 4.722279 CCCCTAGATTAGTTGGAAGTCCTT 59.278 45.833 0.00 0.00 36.82 3.36
227 228 6.563222 TTTATTAAAGTTGTAGCAGCCGTT 57.437 33.333 0.00 0.00 0.00 4.44
312 313 9.408069 GTGGACCTAATCTAATTTGTATAGTCG 57.592 37.037 0.00 0.00 0.00 4.18
342 343 5.948992 AGCTTAAGTTAGTTGCTTTCAGG 57.051 39.130 4.02 0.00 0.00 3.86
405 406 5.434408 TCTATGCATGTTCTGAGCTTGAAT 58.566 37.500 10.16 8.42 0.00 2.57
559 638 5.973565 ACGTAGTCACAGTTTACACTAACAC 59.026 40.000 0.00 0.00 29.74 3.32
643 722 2.813754 CTGAAAAGAACAGATTGGCCGA 59.186 45.455 0.00 0.00 37.54 5.54
645 724 2.568623 AAAGAACAGATTGGCCGAGT 57.431 45.000 0.00 0.00 0.00 4.18
646 725 2.568623 AAGAACAGATTGGCCGAGTT 57.431 45.000 0.00 0.00 0.00 3.01
647 726 2.568623 AGAACAGATTGGCCGAGTTT 57.431 45.000 0.00 0.00 0.00 2.66
648 727 3.695830 AGAACAGATTGGCCGAGTTTA 57.304 42.857 0.00 0.00 0.00 2.01
813 4476 5.774690 ACATGATGGTTCACAGTAATTGGTT 59.225 36.000 0.00 0.00 33.85 3.67
814 4477 5.703978 TGATGGTTCACAGTAATTGGTTG 57.296 39.130 0.00 0.00 0.00 3.77
815 4478 4.522405 TGATGGTTCACAGTAATTGGTTGG 59.478 41.667 0.00 0.00 0.00 3.77
816 4479 3.904717 TGGTTCACAGTAATTGGTTGGT 58.095 40.909 0.00 0.00 0.00 3.67
817 4480 5.050126 TGGTTCACAGTAATTGGTTGGTA 57.950 39.130 0.00 0.00 0.00 3.25
818 4481 4.822896 TGGTTCACAGTAATTGGTTGGTAC 59.177 41.667 0.00 0.00 0.00 3.34
819 4482 5.067954 GGTTCACAGTAATTGGTTGGTACT 58.932 41.667 0.00 0.00 0.00 2.73
826 4489 5.123344 CAGTAATTGGTTGGTACTTGGTAGC 59.877 44.000 0.00 0.64 37.09 3.58
1059 4722 2.504367 ACACGCCAGCAAATTTCTACT 58.496 42.857 0.00 0.00 0.00 2.57
1276 4939 1.165270 GTGAGGGTGGTTTTGGATCG 58.835 55.000 0.00 0.00 0.00 3.69
2053 5717 7.600375 AGACGTTATTACATCCAATATGCTCAG 59.400 37.037 0.00 0.00 0.00 3.35
2054 5718 7.217200 ACGTTATTACATCCAATATGCTCAGT 58.783 34.615 0.00 0.00 0.00 3.41
2080 5744 3.847042 ATATTATGGGACGGAGGGAGA 57.153 47.619 0.00 0.00 0.00 3.71
2118 5782 2.304180 ACTGTGTGCCTTCAGAAGCTAT 59.696 45.455 4.41 0.00 35.84 2.97
2186 5850 7.893302 ACACCCCAAAAGAATCTTTCACATATA 59.107 33.333 8.86 0.00 0.00 0.86
2406 6070 9.093970 GTTTATAGTTTTGGTGTTTTGCTTCTT 57.906 29.630 0.00 0.00 0.00 2.52
2520 6184 8.465201 CCATATTTCTTTCTCTTCTTTTCCCAG 58.535 37.037 0.00 0.00 0.00 4.45
2521 6185 5.774498 TTTCTTTCTCTTCTTTTCCCAGC 57.226 39.130 0.00 0.00 0.00 4.85
2750 6416 6.016024 TGCATAAAAGCAGTCTTGATTTCTGT 60.016 34.615 0.00 0.00 41.73 3.41
2941 6760 9.325198 TGTCTCTACATAAATGCATAAATCGTT 57.675 29.630 0.00 0.00 0.00 3.85
2983 6803 5.048846 TGGAGGGAGCAAATATTCTAACC 57.951 43.478 0.00 0.00 0.00 2.85
3111 6931 1.831106 ACAGTTCTGCGGGTGATGATA 59.169 47.619 0.00 0.00 0.00 2.15
3317 7137 6.405065 GCATGAGGAGAGAAAATAACATTGCA 60.405 38.462 0.00 0.00 0.00 4.08
3452 7272 4.832266 TGACCTGAAGTTGGTTGCAAATAT 59.168 37.500 0.00 0.00 38.03 1.28
3494 7314 4.464947 AGCATAGCCAGATACCCTTTTTC 58.535 43.478 0.00 0.00 0.00 2.29
3495 7315 4.166919 AGCATAGCCAGATACCCTTTTTCT 59.833 41.667 0.00 0.00 0.00 2.52
3496 7316 4.889995 GCATAGCCAGATACCCTTTTTCTT 59.110 41.667 0.00 0.00 0.00 2.52
3569 7389 3.493176 GCATTGCTGGGACAAAGAAGTTT 60.493 43.478 0.16 0.00 38.70 2.66
3588 7408 7.702348 AGAAGTTTCATGAGTTTTACTTTGTGC 59.298 33.333 0.00 0.00 0.00 4.57
3710 7538 2.864097 GCGAGTACATAGCCTGGATGTG 60.864 54.545 7.17 7.17 38.03 3.21
3829 7691 3.926616 TCAGTTTCCATCGTCTCCTTTC 58.073 45.455 0.00 0.00 0.00 2.62
3843 7705 5.220892 CGTCTCCTTTCTCCTGTACACTATC 60.221 48.000 0.00 0.00 0.00 2.08
3867 7729 0.313043 CTGCTTTCAGCTTGGGTGTG 59.687 55.000 0.00 0.00 42.97 3.82
3886 7748 6.435277 GGGTGTGATTTGGATAATGCATAGAT 59.565 38.462 0.00 0.00 0.00 1.98
4074 7945 1.843368 AATCTCCAACATGGGCACAG 58.157 50.000 0.00 0.00 38.32 3.66
4146 8018 1.557371 CCCTTCTCTTTCTCCCCTGTC 59.443 57.143 0.00 0.00 0.00 3.51
4184 8059 1.065564 GCTCTCCTTGAGGTGCATCTT 60.066 52.381 0.00 0.00 42.87 2.40
4219 8094 5.665381 GATGAAGGTGCATCTTTAGTAGC 57.335 43.478 14.71 0.00 41.09 3.58
4276 8151 1.479323 GTCCATGCATGCAGAAATGGT 59.521 47.619 28.57 9.57 40.44 3.55
4289 8164 2.083774 GAAATGGTCGGCTGTTGATCA 58.916 47.619 0.00 0.00 0.00 2.92
4295 8170 0.610174 TCGGCTGTTGATCAGAAGCT 59.390 50.000 23.31 0.00 46.27 3.74
4296 8171 0.725686 CGGCTGTTGATCAGAAGCTG 59.274 55.000 23.31 21.70 46.27 4.24
4297 8172 1.093159 GGCTGTTGATCAGAAGCTGG 58.907 55.000 23.31 3.62 46.27 4.85
4298 8173 0.450983 GCTGTTGATCAGAAGCTGGC 59.549 55.000 19.28 6.00 46.27 4.85
4326 8201 2.592308 GGAGATGGTCCAGTGGGC 59.408 66.667 9.92 7.46 46.10 5.36
4327 8202 2.592308 GAGATGGTCCAGTGGGCC 59.408 66.667 26.96 26.96 0.00 5.80
4328 8203 1.997874 GAGATGGTCCAGTGGGCCT 60.998 63.158 32.47 18.52 33.18 5.19
4329 8204 2.262774 GAGATGGTCCAGTGGGCCTG 62.263 65.000 32.47 0.00 41.15 4.85
4336 8211 3.957586 CAGTGGGCCTGGCACTGA 61.958 66.667 27.39 5.09 46.55 3.41
4337 8212 2.937689 AGTGGGCCTGGCACTGAT 60.938 61.111 23.45 4.80 30.56 2.90
4338 8213 2.753043 GTGGGCCTGGCACTGATG 60.753 66.667 23.45 0.00 30.56 3.07
4339 8214 3.259314 TGGGCCTGGCACTGATGT 61.259 61.111 23.45 0.00 30.56 3.06
4340 8215 2.753043 GGGCCTGGCACTGATGTG 60.753 66.667 22.05 0.00 46.37 3.21
4348 8223 3.659334 CACTGATGTGCCGCAAGT 58.341 55.556 0.00 0.00 37.38 3.16
4349 8224 2.839629 CACTGATGTGCCGCAAGTA 58.160 52.632 0.00 0.00 37.38 2.24
4350 8225 0.443869 CACTGATGTGCCGCAAGTAC 59.556 55.000 0.00 0.00 37.38 2.73
4351 8226 0.034756 ACTGATGTGCCGCAAGTACA 59.965 50.000 0.00 0.00 37.03 2.90
4352 8227 1.155889 CTGATGTGCCGCAAGTACAA 58.844 50.000 0.00 0.00 36.37 2.41
4353 8228 1.739466 CTGATGTGCCGCAAGTACAAT 59.261 47.619 0.00 0.00 36.37 2.71
4354 8229 2.935849 CTGATGTGCCGCAAGTACAATA 59.064 45.455 0.00 0.00 36.37 1.90
4355 8230 2.935849 TGATGTGCCGCAAGTACAATAG 59.064 45.455 0.00 0.00 36.37 1.73
4356 8231 1.083489 TGTGCCGCAAGTACAATAGC 58.917 50.000 0.00 0.00 30.98 2.97
4357 8232 1.083489 GTGCCGCAAGTACAATAGCA 58.917 50.000 0.00 0.00 0.00 3.49
4358 8233 1.062587 GTGCCGCAAGTACAATAGCAG 59.937 52.381 0.00 0.00 0.00 4.24
4359 8234 0.657840 GCCGCAAGTACAATAGCAGG 59.342 55.000 0.00 1.37 0.00 4.85
4360 8235 2.012051 GCCGCAAGTACAATAGCAGGT 61.012 52.381 0.00 0.00 0.00 4.00
4361 8236 1.665679 CCGCAAGTACAATAGCAGGTG 59.334 52.381 0.00 0.00 0.00 4.00
4362 8237 1.062587 CGCAAGTACAATAGCAGGTGC 59.937 52.381 0.00 0.00 42.49 5.01
4363 8238 1.401905 GCAAGTACAATAGCAGGTGCC 59.598 52.381 0.00 0.00 43.38 5.01
4364 8239 2.941415 GCAAGTACAATAGCAGGTGCCT 60.941 50.000 0.00 0.00 43.38 4.75
4365 8240 2.679837 CAAGTACAATAGCAGGTGCCTG 59.320 50.000 13.59 13.59 46.15 4.85
4375 8250 1.242076 CAGGTGCCTGCTTATATGGC 58.758 55.000 5.19 0.00 46.26 4.40
4383 8258 4.696455 GCCTGCTTATATGGCAATTTTGT 58.304 39.130 0.00 0.00 45.46 2.83
4384 8259 4.746611 GCCTGCTTATATGGCAATTTTGTC 59.253 41.667 0.00 0.00 45.46 3.18
4385 8260 5.452356 GCCTGCTTATATGGCAATTTTGTCT 60.452 40.000 0.00 0.00 45.46 3.41
4386 8261 6.239008 GCCTGCTTATATGGCAATTTTGTCTA 60.239 38.462 0.00 0.00 45.46 2.59
4387 8262 7.524367 GCCTGCTTATATGGCAATTTTGTCTAT 60.524 37.037 0.00 0.00 45.46 1.98
4388 8263 9.013229 CCTGCTTATATGGCAATTTTGTCTATA 57.987 33.333 0.00 0.00 39.30 1.31
4418 8293 9.018582 AGAAGAAAGACATGAAAAGATAAAGGG 57.981 33.333 0.00 0.00 0.00 3.95
4419 8294 8.940397 AAGAAAGACATGAAAAGATAAAGGGA 57.060 30.769 0.00 0.00 0.00 4.20
4420 8295 8.940397 AGAAAGACATGAAAAGATAAAGGGAA 57.060 30.769 0.00 0.00 0.00 3.97
4421 8296 9.539194 AGAAAGACATGAAAAGATAAAGGGAAT 57.461 29.630 0.00 0.00 0.00 3.01
4422 8297 9.578439 GAAAGACATGAAAAGATAAAGGGAATG 57.422 33.333 0.00 0.00 0.00 2.67
4423 8298 7.651027 AGACATGAAAAGATAAAGGGAATGG 57.349 36.000 0.00 0.00 0.00 3.16
4424 8299 6.608808 AGACATGAAAAGATAAAGGGAATGGG 59.391 38.462 0.00 0.00 0.00 4.00
4425 8300 5.129320 ACATGAAAAGATAAAGGGAATGGGC 59.871 40.000 0.00 0.00 0.00 5.36
4426 8301 4.946646 TGAAAAGATAAAGGGAATGGGCT 58.053 39.130 0.00 0.00 0.00 5.19
4427 8302 4.956075 TGAAAAGATAAAGGGAATGGGCTC 59.044 41.667 0.00 0.00 0.00 4.70
4428 8303 4.888626 AAAGATAAAGGGAATGGGCTCT 57.111 40.909 0.00 0.00 0.00 4.09
4429 8304 4.888626 AAGATAAAGGGAATGGGCTCTT 57.111 40.909 0.00 0.00 0.00 2.85
4430 8305 5.994416 AAGATAAAGGGAATGGGCTCTTA 57.006 39.130 0.00 0.00 0.00 2.10
4431 8306 6.536684 AAGATAAAGGGAATGGGCTCTTAT 57.463 37.500 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 1.407299 CCTCGTGGATGATTTCCTGCA 60.407 52.381 0.00 0.00 45.68 4.41
227 228 1.423584 TCTCAGTTTCTCCACCTGCA 58.576 50.000 0.00 0.00 0.00 4.41
312 313 6.056236 AGCAACTAACTTAAGCTTATAGCCC 58.944 40.000 7.08 0.00 43.77 5.19
342 343 9.751542 AAACATATCTAACTACTACATCAGCAC 57.248 33.333 0.00 0.00 0.00 4.40
405 406 2.313643 TGGTGTACTCCAGGGTGATCTA 59.686 50.000 12.62 0.00 33.19 1.98
431 432 5.593679 ATCCTTTGCATGGAAGATCAAAG 57.406 39.130 12.14 11.91 42.82 2.77
559 638 7.739825 TCCATCAAGAGGAGGAAGTAATATTG 58.260 38.462 0.00 0.00 0.00 1.90
675 755 1.822990 CCATGGTGAATTGCAGAGCTT 59.177 47.619 2.57 0.00 0.00 3.74
813 4476 2.756760 CCTTCTACGCTACCAAGTACCA 59.243 50.000 0.00 0.00 0.00 3.25
814 4477 2.100418 CCCTTCTACGCTACCAAGTACC 59.900 54.545 0.00 0.00 0.00 3.34
815 4478 2.480932 GCCCTTCTACGCTACCAAGTAC 60.481 54.545 0.00 0.00 0.00 2.73
816 4479 1.753073 GCCCTTCTACGCTACCAAGTA 59.247 52.381 0.00 0.00 0.00 2.24
817 4480 0.535797 GCCCTTCTACGCTACCAAGT 59.464 55.000 0.00 0.00 0.00 3.16
818 4481 0.824759 AGCCCTTCTACGCTACCAAG 59.175 55.000 0.00 0.00 32.26 3.61
819 4482 0.822164 GAGCCCTTCTACGCTACCAA 59.178 55.000 0.00 0.00 34.84 3.67
826 4489 2.969628 ACTGAATGAGCCCTTCTACG 57.030 50.000 0.00 0.00 0.00 3.51
1209 4872 1.750780 GTTGCCCTTGCTAGCTCCC 60.751 63.158 17.23 0.62 38.71 4.30
1264 4927 6.503560 ACCTTATATACCGATCCAAAACCA 57.496 37.500 0.00 0.00 0.00 3.67
1276 4939 8.242729 AGGTTACACACACTACCTTATATACC 57.757 38.462 0.00 0.00 37.75 2.73
1345 5008 9.689976 CACCATTATGTGATCAAACTTTAAACA 57.310 29.630 0.00 0.00 38.55 2.83
1667 5331 9.665719 AGAAATAAGAAGAGAAAAGCTAAGGAG 57.334 33.333 0.00 0.00 0.00 3.69
1992 5656 3.681593 GGTGGGAGTAGTAAACATGCAA 58.318 45.455 0.00 0.00 0.00 4.08
2047 5711 6.516693 CGTCCCATAATATAAGACACTGAGCA 60.517 42.308 0.00 0.00 0.00 4.26
2053 5717 5.337330 CCCTCCGTCCCATAATATAAGACAC 60.337 48.000 0.00 0.00 0.00 3.67
2054 5718 4.775780 CCCTCCGTCCCATAATATAAGACA 59.224 45.833 0.00 0.00 0.00 3.41
2080 5744 6.364976 GCACACAGTACAAAACAAAGAAACTT 59.635 34.615 0.00 0.00 0.00 2.66
2118 5782 9.935241 TTAACTTGAAATGCCAATTATAAGCAA 57.065 25.926 2.41 0.00 40.46 3.91
2186 5850 2.452600 ACAGGTGGTGTGGTTTCATT 57.547 45.000 0.00 0.00 38.28 2.57
2283 5947 5.637006 AAGTAATGCCGCAAGTTTATCAA 57.363 34.783 0.00 0.00 0.00 2.57
2406 6070 4.361783 TGGATCTCCCACTGACTATTTCA 58.638 43.478 0.00 0.00 40.82 2.69
2941 6760 6.042093 CCTCCAGTCATGCTAAGAGGTTATAA 59.958 42.308 17.86 0.00 39.92 0.98
2983 6803 4.053295 CAGCAAAGAACAAAAGTCCATGG 58.947 43.478 4.97 4.97 0.00 3.66
3111 6931 3.634504 TGCAGGCTTGTTCAATATCCAT 58.365 40.909 0.00 0.00 0.00 3.41
3317 7137 0.537188 ACGTGGAGGATGAAGCGAAT 59.463 50.000 0.00 0.00 0.00 3.34
3452 7272 5.016831 TGCTACTTCTCTACATGGTCTTCA 58.983 41.667 0.00 0.00 0.00 3.02
3494 7314 6.830114 ACACTACGAAGAAAACTTCTGAAG 57.170 37.500 15.59 15.59 40.59 3.02
3495 7315 9.622004 CTATACACTACGAAGAAAACTTCTGAA 57.378 33.333 0.00 0.00 40.59 3.02
3496 7316 9.006839 TCTATACACTACGAAGAAAACTTCTGA 57.993 33.333 0.00 0.00 40.59 3.27
3569 7389 5.524281 TGTACGCACAAAGTAAAACTCATGA 59.476 36.000 0.00 0.00 0.00 3.07
3588 7408 3.734231 CGCCACCAATCTAGTATTGTACG 59.266 47.826 11.50 0.00 0.00 3.67
3710 7538 7.360269 CCATTTATGAACTGTGATTTTGTTGGC 60.360 37.037 0.00 0.00 0.00 4.52
3829 7691 4.340666 AGCAGATGTGATAGTGTACAGGAG 59.659 45.833 0.00 0.00 0.00 3.69
3886 7748 6.345298 TGCCGAGACAAAGATAATACATCAA 58.655 36.000 0.00 0.00 0.00 2.57
3896 7758 1.078143 GGCCTGCCGAGACAAAGAT 60.078 57.895 0.00 0.00 0.00 2.40
4042 7913 3.398318 TGGAGATTACCTCACTGGCTA 57.602 47.619 0.00 0.00 43.76 3.93
4083 7954 3.403558 GGCAGAGGGGAGGACACC 61.404 72.222 0.00 0.00 40.50 4.16
4242 8117 1.626356 ATGGACCATGGACCACTCCG 61.626 60.000 33.83 0.00 42.09 4.63
4276 8151 0.610174 AGCTTCTGATCAACAGCCGA 59.390 50.000 18.14 0.00 45.38 5.54
4289 8164 0.689055 TCACTCATGTGCCAGCTTCT 59.311 50.000 0.00 0.00 43.49 2.85
4295 8170 1.208776 CATCTCCTCACTCATGTGCCA 59.791 52.381 0.00 0.00 43.49 4.92
4296 8171 1.474677 CCATCTCCTCACTCATGTGCC 60.475 57.143 0.00 0.00 43.49 5.01
4297 8172 1.209019 ACCATCTCCTCACTCATGTGC 59.791 52.381 0.00 0.00 43.49 4.57
4298 8173 2.158986 GGACCATCTCCTCACTCATGTG 60.159 54.545 0.00 0.00 45.07 3.21
4310 8185 1.997874 AGGCCCACTGGACCATCTC 60.998 63.158 2.83 0.00 42.80 2.75
4311 8186 2.125912 AGGCCCACTGGACCATCT 59.874 61.111 2.83 0.00 42.80 2.90
4312 8187 2.273449 CAGGCCCACTGGACCATC 59.727 66.667 2.83 0.00 42.80 3.51
4320 8195 2.937689 ATCAGTGCCAGGCCCACT 60.938 61.111 9.64 7.27 43.92 4.00
4321 8196 2.753043 CATCAGTGCCAGGCCCAC 60.753 66.667 9.64 0.44 0.00 4.61
4322 8197 3.259314 ACATCAGTGCCAGGCCCA 61.259 61.111 9.64 0.00 0.00 5.36
4323 8198 2.753043 CACATCAGTGCCAGGCCC 60.753 66.667 9.64 0.00 39.21 5.80
4332 8207 0.034756 TGTACTTGCGGCACATCAGT 59.965 50.000 0.05 6.20 0.00 3.41
4333 8208 1.155889 TTGTACTTGCGGCACATCAG 58.844 50.000 0.05 0.00 0.00 2.90
4334 8209 1.819928 ATTGTACTTGCGGCACATCA 58.180 45.000 0.05 0.00 0.00 3.07
4335 8210 2.286418 GCTATTGTACTTGCGGCACATC 60.286 50.000 0.05 0.00 0.00 3.06
4336 8211 1.670811 GCTATTGTACTTGCGGCACAT 59.329 47.619 0.05 0.00 0.00 3.21
4337 8212 1.083489 GCTATTGTACTTGCGGCACA 58.917 50.000 0.05 0.00 0.00 4.57
4338 8213 1.062587 CTGCTATTGTACTTGCGGCAC 59.937 52.381 0.05 0.00 0.00 5.01
4339 8214 1.368641 CTGCTATTGTACTTGCGGCA 58.631 50.000 0.00 0.00 0.00 5.69
4340 8215 0.657840 CCTGCTATTGTACTTGCGGC 59.342 55.000 0.00 0.00 0.00 6.53
4341 8216 1.665679 CACCTGCTATTGTACTTGCGG 59.334 52.381 0.00 0.00 0.00 5.69
4342 8217 1.062587 GCACCTGCTATTGTACTTGCG 59.937 52.381 0.00 0.00 38.21 4.85
4343 8218 1.401905 GGCACCTGCTATTGTACTTGC 59.598 52.381 0.00 0.00 41.70 4.01
4344 8219 2.679837 CAGGCACCTGCTATTGTACTTG 59.320 50.000 3.23 0.00 41.70 3.16
4345 8220 2.991250 CAGGCACCTGCTATTGTACTT 58.009 47.619 3.23 0.00 41.70 2.24
4346 8221 2.698855 CAGGCACCTGCTATTGTACT 57.301 50.000 3.23 0.00 41.70 2.73
4362 8237 6.152932 AGACAAAATTGCCATATAAGCAGG 57.847 37.500 1.60 0.00 42.17 4.85
4392 8267 9.018582 CCCTTTATCTTTTCATGTCTTTCTTCT 57.981 33.333 0.00 0.00 0.00 2.85
4393 8268 9.014297 TCCCTTTATCTTTTCATGTCTTTCTTC 57.986 33.333 0.00 0.00 0.00 2.87
4394 8269 8.940397 TCCCTTTATCTTTTCATGTCTTTCTT 57.060 30.769 0.00 0.00 0.00 2.52
4395 8270 8.940397 TTCCCTTTATCTTTTCATGTCTTTCT 57.060 30.769 0.00 0.00 0.00 2.52
4396 8271 9.578439 CATTCCCTTTATCTTTTCATGTCTTTC 57.422 33.333 0.00 0.00 0.00 2.62
4397 8272 8.534496 CCATTCCCTTTATCTTTTCATGTCTTT 58.466 33.333 0.00 0.00 0.00 2.52
4398 8273 7.124750 CCCATTCCCTTTATCTTTTCATGTCTT 59.875 37.037 0.00 0.00 0.00 3.01
4399 8274 6.608808 CCCATTCCCTTTATCTTTTCATGTCT 59.391 38.462 0.00 0.00 0.00 3.41
4400 8275 6.683861 GCCCATTCCCTTTATCTTTTCATGTC 60.684 42.308 0.00 0.00 0.00 3.06
4401 8276 5.129320 GCCCATTCCCTTTATCTTTTCATGT 59.871 40.000 0.00 0.00 0.00 3.21
4402 8277 5.364735 AGCCCATTCCCTTTATCTTTTCATG 59.635 40.000 0.00 0.00 0.00 3.07
4403 8278 5.532155 AGCCCATTCCCTTTATCTTTTCAT 58.468 37.500 0.00 0.00 0.00 2.57
4404 8279 4.946646 AGCCCATTCCCTTTATCTTTTCA 58.053 39.130 0.00 0.00 0.00 2.69
4405 8280 5.204292 AGAGCCCATTCCCTTTATCTTTTC 58.796 41.667 0.00 0.00 0.00 2.29
4406 8281 5.212472 AGAGCCCATTCCCTTTATCTTTT 57.788 39.130 0.00 0.00 0.00 2.27
4407 8282 4.888626 AGAGCCCATTCCCTTTATCTTT 57.111 40.909 0.00 0.00 0.00 2.52
4408 8283 4.888626 AAGAGCCCATTCCCTTTATCTT 57.111 40.909 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.