Multiple sequence alignment - TraesCS1D01G250500

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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 TraesCS1D01G250500 chr1D 100.000 4332 0 0 1 4332 342865079 342860748 0.000000e+00 8000
1 TraesCS1D01G250500 chr1B 93.214 2564 114 28 306 2836 459929320 459926784 0.000000e+00 3716
2 TraesCS1D01G250500 chr1B 92.440 1508 87 12 2832 4332 459926623 459925136 0.000000e+00 2128
3 TraesCS1D01G250500 chr1B 92.045 264 19 1 1 264 459929805 459929544 1.900000e-98 370
4 TraesCS1D01G250500 chr1A 90.181 1935 100 31 2037 3953 442562114 442560252 0.000000e+00 2438
5 TraesCS1D01G250500 chr1A 89.860 1785 95 45 339 2077 442563859 442562115 0.000000e+00 2215
6 TraesCS1D01G250500 chr1A 92.428 383 25 2 3951 4332 442560203 442559824 1.060000e-150 544
7 TraesCS1D01G250500 chr1A 92.827 237 15 1 1 237 442564053 442563819 4.150000e-90 342
8 TraesCS1D01G250500 chr2B 83.186 226 32 5 11 235 798305886 798305666 7.350000e-48 202
9 TraesCS1D01G250500 chr5B 82.203 236 36 5 1 235 686755048 686755278 9.500000e-47 198
10 TraesCS1D01G250500 chr7B 82.743 226 33 5 11 235 486727045 486726825 3.420000e-46 196


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 TraesCS1D01G250500 chr1D 342860748 342865079 4331 True 8000.000000 8000 100.000000 1 4332 1 chr1D.!!$R1 4331
1 TraesCS1D01G250500 chr1B 459925136 459929805 4669 True 2071.333333 3716 92.566333 1 4332 3 chr1B.!!$R1 4331
2 TraesCS1D01G250500 chr1A 442559824 442564053 4229 True 1384.750000 2438 91.324000 1 4332 4 chr1A.!!$R1 4331

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
791 974 0.178990 ACCAAACCCAGAAGGAGCAC 60.179 55.0 0.00 0.0 39.89 4.40 F
834 1023 0.179156 CACATTTGACGGCCAGATGC 60.179 55.0 2.24 0.0 40.06 3.91 F
2263 2548 0.317160 TGAGGTGAGCAACGTACCAG 59.683 55.0 7.18 0.0 36.94 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2762 3057 1.190833 ACTCAGAGGTCCTGCCACAG 61.191 60.000 0.0 0.0 42.62 3.66 R
2783 3078 8.244802 AGTCGAATATCAGTAACATATGGTAGC 58.755 37.037 7.8 0.3 0.00 3.58 R
3583 4044 1.142667 TGGTTGCACAATCTGGTCTGA 59.857 47.619 0.0 0.0 0.00 3.27 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
20 21 3.192541 GGAATTTGGCAAAACACACCT 57.807 42.857 17.70 0.00 0.00 4.00
21 22 4.329462 GGAATTTGGCAAAACACACCTA 57.671 40.909 17.70 0.00 0.00 3.08
38 39 6.868864 ACACACCTATATCAGATAAACGATGC 59.131 38.462 0.00 0.00 0.00 3.91
39 40 6.311445 CACACCTATATCAGATAAACGATGCC 59.689 42.308 0.00 0.00 0.00 4.40
51 52 2.689083 CGATGCCGTTAATGCCAGA 58.311 52.632 0.00 0.00 0.00 3.86
133 134 6.150474 CACTGAACGTGGTTCCCTTATTTTAT 59.850 38.462 6.08 0.00 41.35 1.40
137 138 7.334921 TGAACGTGGTTCCCTTATTTTATACTG 59.665 37.037 6.08 0.00 41.35 2.74
187 188 1.779569 AACGGTTAGCGTTCACTCAG 58.220 50.000 16.58 0.00 0.00 3.35
192 193 3.181530 CGGTTAGCGTTCACTCAGAAATG 60.182 47.826 0.00 0.00 38.13 2.32
318 501 5.236911 TGTTAGTCCACGGTGAAACAATTAC 59.763 40.000 10.28 5.46 39.98 1.89
340 523 2.024176 TCCACTAAAGACTCTGGGCA 57.976 50.000 0.00 0.00 0.00 5.36
347 530 3.515602 AAAGACTCTGGGCATCAGTTT 57.484 42.857 6.26 0.00 43.76 2.66
733 916 0.674581 GGGGTAGGGTTTTTCCGTCG 60.675 60.000 0.00 0.00 37.00 5.12
734 917 0.321346 GGGTAGGGTTTTTCCGTCGA 59.679 55.000 0.00 0.00 37.00 4.20
741 924 1.941975 GGTTTTTCCGTCGAGTTCCAA 59.058 47.619 0.00 0.00 0.00 3.53
783 966 1.971357 GTCAGAGAGACCAAACCCAGA 59.029 52.381 0.00 0.00 41.56 3.86
786 969 1.981495 AGAGAGACCAAACCCAGAAGG 59.019 52.381 0.00 0.00 43.78 3.46
788 971 1.981495 AGAGACCAAACCCAGAAGGAG 59.019 52.381 0.00 0.00 39.89 3.69
789 972 0.402121 AGACCAAACCCAGAAGGAGC 59.598 55.000 0.00 0.00 39.89 4.70
791 974 0.178990 ACCAAACCCAGAAGGAGCAC 60.179 55.000 0.00 0.00 39.89 4.40
792 975 0.895559 CCAAACCCAGAAGGAGCACC 60.896 60.000 0.00 0.00 39.89 5.01
816 1005 0.386858 GTCTTACGCTGACGCTGTCA 60.387 55.000 10.24 10.24 45.53 3.58
821 1010 0.880278 ACGCTGACGCTGTCACATTT 60.880 50.000 7.20 0.00 45.53 2.32
831 1020 2.927004 GTCACATTTGACGGCCAGA 58.073 52.632 2.24 0.00 42.86 3.86
832 1021 1.453155 GTCACATTTGACGGCCAGAT 58.547 50.000 2.24 0.00 42.86 2.90
833 1022 1.131126 GTCACATTTGACGGCCAGATG 59.869 52.381 2.24 8.38 42.86 2.90
834 1023 0.179156 CACATTTGACGGCCAGATGC 60.179 55.000 2.24 0.00 40.06 3.91
835 1024 1.063006 CATTTGACGGCCAGATGCG 59.937 57.895 2.24 0.00 42.61 4.73
847 1036 4.241555 GATGCGGCCGGGTCAGAT 62.242 66.667 29.38 1.71 0.00 2.90
848 1037 4.241555 ATGCGGCCGGGTCAGATC 62.242 66.667 29.38 7.83 0.00 2.75
861 1051 0.323087 TCAGATCCGACGGTCCAGAA 60.323 55.000 14.79 0.00 0.00 3.02
923 1113 1.337167 CGAGGCATCCATCGATTAGCA 60.337 52.381 0.00 0.00 41.40 3.49
924 1114 2.344950 GAGGCATCCATCGATTAGCAG 58.655 52.381 0.00 0.00 0.00 4.24
925 1115 0.801251 GGCATCCATCGATTAGCAGC 59.199 55.000 0.00 0.00 0.00 5.25
926 1116 1.516161 GCATCCATCGATTAGCAGCA 58.484 50.000 0.00 0.00 0.00 4.41
927 1117 1.875514 GCATCCATCGATTAGCAGCAA 59.124 47.619 0.00 0.00 0.00 3.91
928 1118 2.486982 GCATCCATCGATTAGCAGCAAT 59.513 45.455 0.00 0.00 0.00 3.56
929 1119 3.425892 GCATCCATCGATTAGCAGCAATC 60.426 47.826 0.00 1.48 0.00 2.67
954 1144 2.494918 CCGACTCGGCGAAAGGAT 59.505 61.111 12.13 0.00 41.17 3.24
1035 1234 2.334946 GCTGGAGCGGAACATGCAA 61.335 57.895 0.00 0.00 33.85 4.08
1327 1533 0.543749 CCTTCAAGGGCGAGATCCTT 59.456 55.000 0.00 0.00 44.76 3.36
1381 1587 2.154854 TTCACTCGCCTTCTTCACAG 57.845 50.000 0.00 0.00 0.00 3.66
1419 1649 1.202879 TGCCTGGTTTACTGACTTGGG 60.203 52.381 0.00 0.00 0.00 4.12
1529 1764 1.050204 TGGAGCTGCTTTGCCAAATT 58.950 45.000 6.82 0.00 0.00 1.82
1786 2023 7.090173 TGCATAAGTGGTTCTTGCTATTTTTC 58.910 34.615 0.00 0.00 37.56 2.29
1814 2051 6.176183 TCTTCGGTAACTACTAGCTAAGTGT 58.824 40.000 0.00 0.00 39.39 3.55
1893 2130 9.517609 ACTAATATGACTTCACGAATACAACTC 57.482 33.333 0.00 0.00 0.00 3.01
1896 2133 5.447624 TGACTTCACGAATACAACTCAGA 57.552 39.130 0.00 0.00 0.00 3.27
1898 2135 5.196341 ACTTCACGAATACAACTCAGACA 57.804 39.130 0.00 0.00 0.00 3.41
2015 2253 7.768240 AGGAACGAAAAATTGTTTAGAGTTGT 58.232 30.769 0.00 0.00 0.00 3.32
2026 2264 9.668497 AATTGTTTAGAGTTGTATAAGAGGTCC 57.332 33.333 0.00 0.00 0.00 4.46
2077 2359 8.713971 AGGAGATACCACATGTCACAATTAATA 58.286 33.333 0.00 0.00 42.04 0.98
2149 2432 5.184096 TGTTAAGAGTTGCACAAAAGGTTGA 59.816 36.000 0.00 0.00 38.20 3.18
2158 2441 3.380142 CACAAAAGGTTGATCGGTTTGG 58.620 45.455 9.65 0.00 38.20 3.28
2164 2447 2.305927 AGGTTGATCGGTTTGGTGAGAT 59.694 45.455 0.00 0.00 0.00 2.75
2263 2548 0.317160 TGAGGTGAGCAACGTACCAG 59.683 55.000 7.18 0.00 36.94 4.00
2390 2681 5.009210 TGTTGGTTTACTCTTATTGTGGCAC 59.991 40.000 11.55 11.55 0.00 5.01
2462 2757 5.503927 GTGGGATCCATGTGCTATATGAAT 58.496 41.667 15.23 0.00 35.28 2.57
2762 3057 6.128145 GGAAGTGCTCAAGTCCTTTAGAATTC 60.128 42.308 0.00 0.00 28.05 2.17
2783 3078 0.820871 GTGGCAGGACCTCTGAGTAG 59.179 60.000 3.66 0.00 46.18 2.57
2860 3320 8.077991 ACCATTAAGATCATTGCATACAATTCG 58.922 33.333 0.00 0.00 44.21 3.34
2863 3323 9.669353 ATTAAGATCATTGCATACAATTCGTTC 57.331 29.630 0.00 0.00 44.21 3.95
2930 3390 8.498358 TGTTCGCAAATAGCAATCTTGATATAG 58.502 33.333 1.47 0.26 46.13 1.31
2966 3426 4.016444 TCCAAGAAAACCAGCATATGACC 58.984 43.478 6.97 0.00 0.00 4.02
3047 3507 5.423931 TCCTCTGGCATATGTTGTAACTACA 59.576 40.000 4.29 0.00 0.00 2.74
3070 3530 4.081642 ACGAGGCACATAAACTGATAGTGT 60.082 41.667 0.00 0.00 32.99 3.55
3093 3553 8.333908 GTGTGCTAATCTATGAGAAGATGTTTG 58.666 37.037 0.00 0.00 36.34 2.93
3151 3611 4.826616 TCCTGGACCATAATCAGATACCA 58.173 43.478 0.00 0.00 0.00 3.25
3212 3672 7.926020 TGCATATATGTATCCATCCTCTCAT 57.074 36.000 14.14 0.00 32.29 2.90
3247 3707 7.984422 TGGATGCACCATTATCTTATAGTTG 57.016 36.000 4.16 0.00 44.64 3.16
3248 3708 7.744733 TGGATGCACCATTATCTTATAGTTGA 58.255 34.615 4.16 0.00 44.64 3.18
3249 3709 8.385491 TGGATGCACCATTATCTTATAGTTGAT 58.615 33.333 4.16 0.00 44.64 2.57
3356 3816 2.507484 TCCAAACAAGACTCAGCATGG 58.493 47.619 0.00 0.00 36.16 3.66
3376 3836 1.667724 GTCTCCAACTTCCGCATCATG 59.332 52.381 0.00 0.00 0.00 3.07
3377 3837 1.554617 TCTCCAACTTCCGCATCATGA 59.445 47.619 0.00 0.00 0.00 3.07
3378 3838 2.171237 TCTCCAACTTCCGCATCATGAT 59.829 45.455 1.18 1.18 0.00 2.45
3417 3877 1.237285 CCAAGGAAGGTTGCGACTGG 61.237 60.000 3.59 0.00 0.00 4.00
3418 3878 1.600916 AAGGAAGGTTGCGACTGGC 60.601 57.895 3.59 0.00 43.96 4.85
3457 3917 6.183360 CCTGATGTAAAATGTGATGTCATGCT 60.183 38.462 0.00 0.00 0.00 3.79
3471 3931 6.429078 TGATGTCATGCTTATCTAATGGAAGC 59.571 38.462 0.00 0.00 44.71 3.86
3481 3941 2.022428 TCTAATGGAAGCCAGGGTCCTA 60.022 50.000 0.00 0.00 36.75 2.94
3482 3942 1.681229 AATGGAAGCCAGGGTCCTAA 58.319 50.000 0.00 0.00 36.75 2.69
3485 3945 2.124411 TGGAAGCCAGGGTCCTAATAC 58.876 52.381 0.00 0.00 34.77 1.89
3487 3947 2.778270 GGAAGCCAGGGTCCTAATACTT 59.222 50.000 0.00 0.00 0.00 2.24
3492 3952 6.002653 AGCCAGGGTCCTAATACTTTTAAG 57.997 41.667 0.00 0.00 0.00 1.85
3583 4044 5.221126 GGATTCAAGCAGTTGTCTGAACTTT 60.221 40.000 0.00 0.00 43.76 2.66
3630 4093 2.345641 CGCACCTAATCACTTTGTCTCG 59.654 50.000 0.00 0.00 0.00 4.04
3638 4101 5.437289 AATCACTTTGTCTCGCATTTGAA 57.563 34.783 0.00 0.00 0.00 2.69
3654 4117 5.337491 GCATTTGAAGATGGTAATTGGTGGT 60.337 40.000 0.00 0.00 0.00 4.16
3655 4118 5.720371 TTTGAAGATGGTAATTGGTGGTG 57.280 39.130 0.00 0.00 0.00 4.17
3662 4125 2.959707 TGGTAATTGGTGGTGGTTGTTC 59.040 45.455 0.00 0.00 0.00 3.18
3728 4193 5.807520 TCTCAAGTGCGATGAAAGTATCTTC 59.192 40.000 0.00 0.00 0.00 2.87
3794 4259 5.337219 TGACAACACTGCACTAATAAACG 57.663 39.130 0.00 0.00 0.00 3.60
3846 4311 1.555075 TCAGCTGTACCCTTCCATGAC 59.445 52.381 14.67 0.00 0.00 3.06
3877 4342 3.579151 GGTTGTGCCCCTAAAATGGTTAA 59.421 43.478 0.00 0.00 0.00 2.01
3964 4480 4.218417 ACTTCAAATGTAACACTGATGCCC 59.782 41.667 0.00 0.00 0.00 5.36
3982 4498 1.233019 CCTCCTTTGCATATGGAGCG 58.767 55.000 18.94 11.66 43.58 5.03
4010 4526 2.619074 GCTCACCTGCTTAGAACCCAAT 60.619 50.000 0.00 0.00 0.00 3.16
4028 4544 4.533222 CCAATGTGAGTGTAAACGGTTTC 58.467 43.478 9.78 3.08 0.00 2.78
4052 4568 4.083003 TGGATGTTATTCTTTTGTCCACGC 60.083 41.667 0.00 0.00 29.89 5.34
4085 4601 6.143919 GCTGTACAAAGAAATTACAAACTGGC 59.856 38.462 0.00 0.00 0.00 4.85
4144 4660 1.033746 CCGAATGTGCTGCTCCCATT 61.034 55.000 0.00 6.82 0.00 3.16
4146 4662 2.016318 CGAATGTGCTGCTCCCATTAA 58.984 47.619 0.00 0.00 0.00 1.40
4202 4718 1.682854 CAACATGTGGGGTATGATGGC 59.317 52.381 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.850982 CGTTTATCTGATATAGGTGTGTTTTGC 59.149 37.037 0.00 0.00 0.00 3.68
9 10 9.093970 TCGTTTATCTGATATAGGTGTGTTTTG 57.906 33.333 0.00 0.00 0.00 2.44
16 17 5.516696 CGGCATCGTTTATCTGATATAGGTG 59.483 44.000 0.00 1.69 0.00 4.00
38 39 1.376609 GGCACCTCTGGCATTAACGG 61.377 60.000 0.00 0.00 42.66 4.44
39 40 0.392998 AGGCACCTCTGGCATTAACG 60.393 55.000 0.00 0.00 45.63 3.18
51 52 4.074970 CAGTCATCAAAGTTTAGGCACCT 58.925 43.478 0.00 0.00 0.00 4.00
137 138 7.072030 GTGATGTCATTCACAAACTGACTAAC 58.928 38.462 9.29 0.00 44.38 2.34
187 188 5.849357 TTGCAAATTGATGCTCACATTTC 57.151 34.783 0.00 0.00 46.54 2.17
192 193 7.061905 GCTATATGATTGCAAATTGATGCTCAC 59.938 37.037 1.71 0.00 46.54 3.51
290 309 4.141981 TGTTTCACCGTGGACTAACACTAA 60.142 41.667 0.00 0.00 39.19 2.24
292 311 2.168936 TGTTTCACCGTGGACTAACACT 59.831 45.455 0.00 0.00 39.19 3.55
293 312 2.553086 TGTTTCACCGTGGACTAACAC 58.447 47.619 0.00 0.00 37.99 3.32
294 313 2.983907 TGTTTCACCGTGGACTAACA 57.016 45.000 0.00 2.67 0.00 2.41
295 314 4.823790 AATTGTTTCACCGTGGACTAAC 57.176 40.909 0.00 0.23 0.00 2.34
296 315 4.756135 GGTAATTGTTTCACCGTGGACTAA 59.244 41.667 0.00 0.00 0.00 2.24
297 316 4.202336 TGGTAATTGTTTCACCGTGGACTA 60.202 41.667 0.00 0.00 34.94 2.59
298 317 3.143728 GGTAATTGTTTCACCGTGGACT 58.856 45.455 0.00 0.00 0.00 3.85
299 318 2.879646 TGGTAATTGTTTCACCGTGGAC 59.120 45.455 0.00 0.00 34.94 4.02
303 322 3.504520 GTGGATGGTAATTGTTTCACCGT 59.495 43.478 0.00 0.00 34.94 4.83
304 323 3.756434 AGTGGATGGTAATTGTTTCACCG 59.244 43.478 0.00 0.00 34.94 4.94
318 501 2.420687 GCCCAGAGTCTTTAGTGGATGG 60.421 54.545 0.00 0.00 31.04 3.51
347 530 7.011389 GTGTCTGTACTTTGCTATATGATTGCA 59.989 37.037 0.00 0.00 39.16 4.08
570 753 1.343821 CGGCGCGTCAAGTATGTTC 59.656 57.895 12.89 0.00 0.00 3.18
733 916 2.095252 GCTCTCGCCGTTGGAACTC 61.095 63.158 0.00 0.00 0.00 3.01
734 917 2.048127 GCTCTCGCCGTTGGAACT 60.048 61.111 0.00 0.00 0.00 3.01
741 924 2.276116 TTTCCTCTGCTCTCGCCGT 61.276 57.895 0.00 0.00 34.43 5.68
780 963 0.389166 GACACTCGGTGCTCCTTCTG 60.389 60.000 2.85 0.00 36.98 3.02
783 966 1.272769 GTAAGACACTCGGTGCTCCTT 59.727 52.381 2.85 7.61 36.98 3.36
786 969 1.071567 GCGTAAGACACTCGGTGCTC 61.072 60.000 4.23 2.58 43.02 4.26
788 971 1.080705 AGCGTAAGACACTCGGTGC 60.081 57.895 4.23 0.00 43.02 5.01
789 972 2.725644 CAGCGTAAGACACTCGGTG 58.274 57.895 0.00 0.00 44.05 4.94
791 974 0.793478 CGTCAGCGTAAGACACTCGG 60.793 60.000 0.00 0.00 43.02 4.63
792 975 1.396543 GCGTCAGCGTAAGACACTCG 61.397 60.000 0.00 0.00 40.81 4.18
816 1005 1.647545 CGCATCTGGCCGTCAAATGT 61.648 55.000 0.00 0.00 40.31 2.71
830 1019 4.241555 ATCTGACCCGGCCGCATC 62.242 66.667 22.85 19.57 0.00 3.91
831 1020 4.241555 GATCTGACCCGGCCGCAT 62.242 66.667 22.85 9.88 0.00 4.73
835 1024 4.222847 GTCGGATCTGACCCGGCC 62.223 72.222 22.10 0.00 45.27 6.13
841 1030 1.030488 TCTGGACCGTCGGATCTGAC 61.030 60.000 22.64 22.64 35.49 3.51
842 1031 0.323087 TTCTGGACCGTCGGATCTGA 60.323 55.000 20.51 14.80 0.00 3.27
843 1032 0.179134 GTTCTGGACCGTCGGATCTG 60.179 60.000 20.51 12.80 0.00 2.90
844 1033 1.654954 CGTTCTGGACCGTCGGATCT 61.655 60.000 20.51 0.00 0.00 2.75
845 1034 1.226603 CGTTCTGGACCGTCGGATC 60.227 63.158 20.51 11.57 0.00 3.36
847 1036 4.047059 GCGTTCTGGACCGTCGGA 62.047 66.667 20.51 0.00 0.00 4.55
855 1045 4.415332 GAGACGCGGCGTTCTGGA 62.415 66.667 29.98 0.00 41.37 3.86
864 1054 0.318784 GTAATAGCCCTGAGACGCGG 60.319 60.000 12.47 0.00 0.00 6.46
869 1059 1.132817 GGGGGAGTAATAGCCCTGAGA 60.133 57.143 0.00 0.00 44.10 3.27
901 1091 0.678950 TAATCGATGGATGCCTCGCA 59.321 50.000 7.02 0.00 44.86 5.10
976 1175 1.152839 CCTCTCCTCCTCCTCGTCC 60.153 68.421 0.00 0.00 0.00 4.79
1201 1407 3.070060 GTGATCGCCACGACGAAC 58.930 61.111 0.00 3.02 46.59 3.95
1327 1533 2.994995 ATGGTGACGACGGCCTCA 60.995 61.111 0.00 0.00 0.00 3.86
1381 1587 1.334419 GCACTGAGCACATGACACAAC 60.334 52.381 0.00 0.00 44.79 3.32
1419 1649 3.502191 TCTGCAGAACCAACAAACAAC 57.498 42.857 15.67 0.00 0.00 3.32
1562 1797 4.359434 TGCACTGAACTATTAACCACCA 57.641 40.909 0.00 0.00 0.00 4.17
1563 1798 4.379499 GCTTGCACTGAACTATTAACCACC 60.379 45.833 0.00 0.00 0.00 4.61
1603 1838 2.023414 TTCGAGTCCACGGCACAACT 62.023 55.000 0.00 0.00 0.00 3.16
1708 1943 1.609208 AGTTTGGCACATCACCAGAC 58.391 50.000 0.00 0.00 41.44 3.51
1732 1967 3.389329 AGCATACCGATCCATCAGAAGTT 59.611 43.478 0.00 0.00 0.00 2.66
1786 2023 7.227116 ACTTAGCTAGTAGTTACCGAAGATGAG 59.773 40.741 0.00 0.00 34.56 2.90
1814 2051 4.530553 TGAAGTCCATAGTAACAAGCAGGA 59.469 41.667 0.00 0.00 0.00 3.86
1883 2120 7.793902 ACGTGTTTTATGTCTGAGTTGTATTC 58.206 34.615 0.00 0.00 0.00 1.75
2001 2239 9.047947 AGGACCTCTTATACAACTCTAAACAAT 57.952 33.333 0.00 0.00 0.00 2.71
2015 2253 4.534500 TCACAAGCCAAAGGACCTCTTATA 59.466 41.667 0.00 0.00 34.78 0.98
2025 2263 7.153985 TGATTTAATTTCTCACAAGCCAAAGG 58.846 34.615 0.00 0.00 0.00 3.11
2026 2264 8.592105 TTGATTTAATTTCTCACAAGCCAAAG 57.408 30.769 0.00 0.00 0.00 2.77
2149 2432 8.801882 TTTCTTTATTATCTCACCAAACCGAT 57.198 30.769 0.00 0.00 0.00 4.18
2164 2447 9.862371 TGTGCAGTTTGTTTCTTTTCTTTATTA 57.138 25.926 0.00 0.00 0.00 0.98
2220 2505 8.028354 TCACTCACACAAAATAAAATATGCCTG 58.972 33.333 0.00 0.00 0.00 4.85
2263 2548 2.985847 GGTGGTTGGAGGCAGCAC 60.986 66.667 0.00 0.00 41.11 4.40
2329 2620 3.640498 GACCTACCAGTACCCAATAGTCC 59.360 52.174 0.00 0.00 0.00 3.85
2390 2681 4.211794 GCACACACAATTTCATTTCCAAGG 59.788 41.667 0.00 0.00 0.00 3.61
2762 3057 1.190833 ACTCAGAGGTCCTGCCACAG 61.191 60.000 0.00 0.00 42.62 3.66
2783 3078 8.244802 AGTCGAATATCAGTAACATATGGTAGC 58.755 37.037 7.80 0.30 0.00 3.58
2860 3320 9.352191 TCATGGTAGGTAATTAGAGACTAGAAC 57.648 37.037 0.00 0.00 0.00 3.01
2863 3323 9.132923 TGTTCATGGTAGGTAATTAGAGACTAG 57.867 37.037 0.00 0.00 0.00 2.57
2930 3390 5.376854 TTTCTTGGACTGATTAAGCAAGC 57.623 39.130 0.00 0.00 30.28 4.01
3047 3507 4.081642 ACACTATCAGTTTATGTGCCTCGT 60.082 41.667 0.00 0.00 32.49 4.18
3070 3530 6.484643 GCCAAACATCTTCTCATAGATTAGCA 59.515 38.462 0.00 0.00 32.60 3.49
3093 3553 7.390162 TCCAGGAAAATATTCAACATTTTTGCC 59.610 33.333 0.00 0.00 36.09 4.52
3123 3583 4.782691 TCTGATTATGGTCCAGGAAGACAA 59.217 41.667 0.00 0.00 38.59 3.18
3356 3816 1.667724 CATGATGCGGAAGTTGGAGAC 59.332 52.381 0.00 0.00 0.00 3.36
3417 3877 3.758554 ACATCAGGACACAAATTACAGGC 59.241 43.478 0.00 0.00 0.00 4.85
3418 3878 7.447374 TTTACATCAGGACACAAATTACAGG 57.553 36.000 0.00 0.00 0.00 4.00
3457 3917 3.394606 GGACCCTGGCTTCCATTAGATAA 59.605 47.826 7.52 0.00 30.82 1.75
3471 3931 8.873186 TTTTCTTAAAAGTATTAGGACCCTGG 57.127 34.615 0.00 0.00 0.00 4.45
3487 3947 6.378848 ACAGGTGCCAGTTACTTTTTCTTAAA 59.621 34.615 0.00 0.00 0.00 1.52
3492 3952 5.761165 TTACAGGTGCCAGTTACTTTTTC 57.239 39.130 0.00 0.00 0.00 2.29
3535 3996 3.892284 ACATGTCAACCACCACAGTTAA 58.108 40.909 0.00 0.00 0.00 2.01
3552 4013 4.624015 ACAACTGCTTGAATCCAAACATG 58.376 39.130 0.00 0.00 29.16 3.21
3583 4044 1.142667 TGGTTGCACAATCTGGTCTGA 59.857 47.619 0.00 0.00 0.00 3.27
3630 4093 5.111293 CCACCAATTACCATCTTCAAATGC 58.889 41.667 0.00 0.00 0.00 3.56
3638 4101 3.181423 ACAACCACCACCAATTACCATCT 60.181 43.478 0.00 0.00 0.00 2.90
3682 4147 5.645497 AGAGCATTGACTTGTACTTCCATTC 59.355 40.000 0.00 0.00 0.00 2.67
3794 4259 2.949644 AGCGAATGGTGTTTATTAGCCC 59.050 45.455 0.00 0.00 37.00 5.19
3982 4498 4.527509 TCTAAGCAGGTGAGCTATATGC 57.472 45.455 4.90 4.90 45.89 3.14
4010 4526 3.118702 TCCAGAAACCGTTTACACTCACA 60.119 43.478 0.00 0.00 0.00 3.58
4028 4544 5.631026 CGTGGACAAAAGAATAACATCCAG 58.369 41.667 0.00 0.00 35.49 3.86
4052 4568 2.046283 TCTTTGTACAGCGTGACTCG 57.954 50.000 0.00 0.00 43.12 4.18
4085 4601 1.310933 GCATGGACAGTGGCCAAGAG 61.311 60.000 24.84 16.23 39.21 2.85
4144 4660 9.921637 GATTTACACAATCAATTTTGGGACTTA 57.078 29.630 0.00 0.00 34.06 2.24
4146 4662 7.961351 TGATTTACACAATCAATTTTGGGACT 58.039 30.769 0.00 0.00 34.06 3.85
4202 4718 4.511527 AGCTGTTCTAGATTGTCATGTGG 58.488 43.478 0.00 0.00 0.00 4.17
4257 4773 6.757897 ATTTCATAATCGTGGTGTTCATGT 57.242 33.333 0.00 0.00 34.14 3.21
4298 4819 6.357367 AGATTGGTTTGATGGTATCAGGTAC 58.643 40.000 0.00 0.00 40.94 3.34


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

AutoCloner maintained by Alex Coulton.