Multiple sequence alignment - TraesCS1A01G069600

Loading Multiple Alignment...

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 TraesCS1A01G069600 chr1A 100.000 2931 0 0 897 3827 52238284 52235354 0.000000e+00 5413
1 TraesCS1A01G069600 chr1A 100.000 613 0 0 1 613 52239180 52238568 0.000000e+00 1133
2 TraesCS1A01G069600 chr1D 97.573 2101 43 3 925 3022 52577081 52574986 0.000000e+00 3591
3 TraesCS1A01G069600 chr1D 90.511 822 46 20 3013 3827 52574835 52574039 0.000000e+00 1057
4 TraesCS1A01G069600 chr1D 86.032 630 46 18 1 613 52577706 52577102 4.170000e-179 638
5 TraesCS1A01G069600 chr1B 95.674 2173 60 11 899 3066 83640804 83638661 0.000000e+00 3461
6 TraesCS1A01G069600 chr1B 87.500 744 40 22 3110 3827 83638133 83637417 0.000000e+00 809
7 TraesCS1A01G069600 chr1B 87.863 585 31 19 45 613 83641364 83640804 0.000000e+00 651
8 TraesCS1A01G069600 chr3B 85.827 381 44 9 1609 1983 822832864 822833240 2.770000e-106 396
9 TraesCS1A01G069600 chr3B 81.875 320 47 9 1636 1951 101799735 101800047 3.790000e-65 259
10 TraesCS1A01G069600 chr3A 85.372 376 48 7 1609 1979 749282505 749282878 2.160000e-102 383
11 TraesCS1A01G069600 chr5B 81.102 381 65 7 1573 1950 141574543 141574167 8.040000e-77 298
12 TraesCS1A01G069600 chr5D 80.840 381 66 7 1573 1950 129478244 129477868 3.740000e-75 292
13 TraesCS1A01G069600 chr5A 80.840 381 66 7 1573 1950 144707953 144707577 3.740000e-75 292
14 TraesCS1A01G069600 chr3D 81.761 318 49 8 1636 1950 63007300 63007611 1.360000e-64 257


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 TraesCS1A01G069600 chr1A 52235354 52239180 3826 True 3273.000000 5413 100.000000 1 3827 2 chr1A.!!$R1 3826
1 TraesCS1A01G069600 chr1D 52574039 52577706 3667 True 1762.000000 3591 91.372000 1 3827 3 chr1D.!!$R1 3826
2 TraesCS1A01G069600 chr1B 83637417 83641364 3947 True 1640.333333 3461 90.345667 45 3827 3 chr1B.!!$R1 3782

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
134 138 0.178903 TACCCACAGCTCCACTCCTT 60.179 55.0 0.0 0.0 0.0 3.36 F
447 465 0.331278 TCATCAATCCCACCACCACC 59.669 55.0 0.0 0.0 0.0 4.61 F
923 964 0.456995 CCGAGCAAGAACCGTCTCTC 60.457 60.0 0.0 0.0 30.7 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1154 2.915659 ACGACCCGCCTGAACTCA 60.916 61.111 0.00 0.00 0.00 3.41 R
1701 1742 3.241530 TGCACGAAGGGGCACTCT 61.242 61.111 0.00 0.00 37.04 3.24 R
2846 2891 0.103208 GAGCCAGTGATCGATCGGTT 59.897 55.000 20.03 13.09 0.00 4.44 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 3.963383 AGACAACCACACGAAACATTC 57.037 42.857 0.00 0.00 0.00 2.67
32 33 2.616842 GACAACCACACGAAACATTCCT 59.383 45.455 0.00 0.00 0.00 3.36
41 42 5.856455 CACACGAAACATTCCTAACATTTCC 59.144 40.000 0.00 0.00 0.00 3.13
88 89 2.545526 ACACAGAGAAGAAACACATGCG 59.454 45.455 0.00 0.00 0.00 4.73
134 138 0.178903 TACCCACAGCTCCACTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
135 139 1.062488 ACCCACAGCTCCACTCCTTT 61.062 55.000 0.00 0.00 0.00 3.11
143 147 1.946283 GCTCCACTCCTTTTTCCTCCG 60.946 57.143 0.00 0.00 0.00 4.63
147 151 1.537202 CACTCCTTTTTCCTCCGCAAG 59.463 52.381 0.00 0.00 0.00 4.01
154 158 3.708563 TTTTCCTCCGCAAGAAAACAG 57.291 42.857 0.00 0.00 43.02 3.16
156 160 2.631160 TCCTCCGCAAGAAAACAGAA 57.369 45.000 0.00 0.00 43.02 3.02
160 164 4.340950 TCCTCCGCAAGAAAACAGAAAAAT 59.659 37.500 0.00 0.00 43.02 1.82
161 165 5.533154 TCCTCCGCAAGAAAACAGAAAAATA 59.467 36.000 0.00 0.00 43.02 1.40
164 168 7.384932 CCTCCGCAAGAAAACAGAAAAATAAAT 59.615 33.333 0.00 0.00 43.02 1.40
166 170 8.547069 TCCGCAAGAAAACAGAAAAATAAATTG 58.453 29.630 0.00 0.00 43.02 2.32
167 171 8.334632 CCGCAAGAAAACAGAAAAATAAATTGT 58.665 29.630 0.00 0.00 43.02 2.71
213 217 3.862063 GACTTGTGCGCGTTGGCTG 62.862 63.158 8.43 0.00 36.88 4.85
284 289 1.743996 GGAGGCGAGAAAGAAAGCAT 58.256 50.000 0.00 0.00 0.00 3.79
285 290 2.087646 GGAGGCGAGAAAGAAAGCATT 58.912 47.619 0.00 0.00 0.00 3.56
286 291 2.489722 GGAGGCGAGAAAGAAAGCATTT 59.510 45.455 0.00 0.00 43.98 2.32
313 323 3.260380 TCTGTTAAACAATGGGGGCAATG 59.740 43.478 0.00 0.00 0.00 2.82
358 376 2.944129 AGCTAGAGAGAGAAAGGCGAT 58.056 47.619 0.00 0.00 0.00 4.58
359 377 2.622942 AGCTAGAGAGAGAAAGGCGATG 59.377 50.000 0.00 0.00 0.00 3.84
360 378 2.288152 GCTAGAGAGAGAAAGGCGATGG 60.288 54.545 0.00 0.00 0.00 3.51
361 379 0.463620 AGAGAGAGAAAGGCGATGGC 59.536 55.000 0.00 0.00 38.90 4.40
362 380 0.873743 GAGAGAGAAAGGCGATGGCG 60.874 60.000 0.00 0.00 41.24 5.69
363 381 1.141881 GAGAGAAAGGCGATGGCGA 59.858 57.895 0.00 0.00 41.24 5.54
364 382 0.873743 GAGAGAAAGGCGATGGCGAG 60.874 60.000 0.00 0.00 41.24 5.03
365 383 1.884926 GAGAAAGGCGATGGCGAGG 60.885 63.158 0.00 0.00 41.24 4.63
366 384 2.897350 GAAAGGCGATGGCGAGGG 60.897 66.667 0.00 0.00 41.24 4.30
372 390 4.637489 CGATGGCGAGGGCGAGAG 62.637 72.222 0.00 0.00 41.24 3.20
373 391 3.219928 GATGGCGAGGGCGAGAGA 61.220 66.667 0.00 0.00 41.24 3.10
374 392 3.206211 GATGGCGAGGGCGAGAGAG 62.206 68.421 0.00 0.00 41.24 3.20
447 465 0.331278 TCATCAATCCCACCACCACC 59.669 55.000 0.00 0.00 0.00 4.61
448 466 0.684153 CATCAATCCCACCACCACCC 60.684 60.000 0.00 0.00 0.00 4.61
609 650 4.566004 TCAATCAAGAACGTACTGGAAGG 58.434 43.478 0.00 0.00 39.30 3.46
611 652 4.884668 ATCAAGAACGTACTGGAAGGAA 57.115 40.909 0.00 0.00 39.30 3.36
612 653 4.252971 TCAAGAACGTACTGGAAGGAAG 57.747 45.455 0.00 0.00 39.30 3.46
922 963 1.179814 ACCGAGCAAGAACCGTCTCT 61.180 55.000 0.00 0.00 30.70 3.10
923 964 0.456995 CCGAGCAAGAACCGTCTCTC 60.457 60.000 0.00 0.00 30.70 3.20
924 965 0.456995 CGAGCAAGAACCGTCTCTCC 60.457 60.000 0.00 0.00 30.70 3.71
925 966 0.892063 GAGCAAGAACCGTCTCTCCT 59.108 55.000 0.00 0.00 30.70 3.69
926 967 0.892063 AGCAAGAACCGTCTCTCCTC 59.108 55.000 0.00 0.00 30.70 3.71
935 976 4.507916 TCTCTCCTCTCCCCGGCG 62.508 72.222 0.00 0.00 0.00 6.46
967 1008 3.804873 AGAACGCAGAGTCTCTTTTGAAC 59.195 43.478 0.00 0.00 0.00 3.18
969 1010 1.801178 CGCAGAGTCTCTTTTGAACCC 59.199 52.381 0.00 0.00 0.00 4.11
1701 1742 0.611062 CCTACTCCCACGACTGGACA 60.611 60.000 0.00 0.00 40.55 4.02
2162 2203 1.502231 CTGTTCGACAAGGTGTCCAG 58.498 55.000 2.91 1.67 44.20 3.86
2271 2312 1.215647 GGACTACACCGACCTGCTG 59.784 63.158 0.00 0.00 0.00 4.41
2847 2892 3.980989 CACCCCGTCGACGACCAA 61.981 66.667 37.65 0.00 43.02 3.67
2848 2893 3.982241 ACCCCGTCGACGACCAAC 61.982 66.667 37.65 0.00 43.02 3.77
2900 2945 5.394115 GCTGACCAAAGTTCTTTCCTTCAAA 60.394 40.000 0.00 0.00 0.00 2.69
3187 3876 4.114073 CAAGATTTGCTTTGTGTGCTTCA 58.886 39.130 0.00 0.00 33.60 3.02
3201 3890 5.152097 GTGTGCTTCATTGTCTCTTGATTG 58.848 41.667 0.00 0.00 0.00 2.67
3214 3903 5.855395 GTCTCTTGATTGATCAAACTTGTGC 59.145 40.000 13.09 0.00 45.26 4.57
3248 3943 5.559770 TCTTCTCATGCCAAAGTACATCAA 58.440 37.500 0.00 0.00 0.00 2.57
3249 3944 6.182627 TCTTCTCATGCCAAAGTACATCAAT 58.817 36.000 0.00 0.00 0.00 2.57
3250 3945 5.823209 TCTCATGCCAAAGTACATCAATG 57.177 39.130 0.00 0.00 0.00 2.82
3251 3946 4.641541 TCTCATGCCAAAGTACATCAATGG 59.358 41.667 0.00 0.00 0.00 3.16
3252 3947 4.598022 TCATGCCAAAGTACATCAATGGA 58.402 39.130 0.00 0.00 32.82 3.41
3253 3948 5.015515 TCATGCCAAAGTACATCAATGGAA 58.984 37.500 0.00 0.00 32.82 3.53
3254 3949 5.657745 TCATGCCAAAGTACATCAATGGAAT 59.342 36.000 0.00 0.00 32.82 3.01
3255 3950 5.581126 TGCCAAAGTACATCAATGGAATC 57.419 39.130 0.00 0.00 32.82 2.52
3300 3995 9.845214 ATATAGTATATGTTCTTGGTTCCTCCT 57.155 33.333 1.68 0.00 37.07 3.69
3301 3996 6.487299 AGTATATGTTCTTGGTTCCTCCTC 57.513 41.667 0.00 0.00 37.07 3.71
3302 3997 4.779993 ATATGTTCTTGGTTCCTCCTCC 57.220 45.455 0.00 0.00 37.07 4.30
3314 4009 3.050523 TCCTCCTCCATGATCACATCA 57.949 47.619 0.00 0.00 44.55 3.07
3326 4022 6.321945 CCATGATCACATCACCCTTTATTTGA 59.678 38.462 0.00 0.00 43.01 2.69
3327 4023 7.014905 CCATGATCACATCACCCTTTATTTGAT 59.985 37.037 0.00 0.00 43.01 2.57
3328 4024 7.959658 TGATCACATCACCCTTTATTTGATT 57.040 32.000 0.00 0.00 33.59 2.57
3329 4025 7.999679 TGATCACATCACCCTTTATTTGATTC 58.000 34.615 0.00 0.00 33.59 2.52
3330 4026 6.773976 TCACATCACCCTTTATTTGATTCC 57.226 37.500 0.00 0.00 0.00 3.01
3351 4047 3.322828 CCATTCCATGTCCATTCCATTCC 59.677 47.826 0.00 0.00 0.00 3.01
3382 4078 8.786826 AGAGTGGATCATAAATAAAAACGTCA 57.213 30.769 0.00 0.00 0.00 4.35
3384 4080 7.985476 AGTGGATCATAAATAAAAACGTCAGG 58.015 34.615 0.00 0.00 0.00 3.86
3385 4081 7.067008 AGTGGATCATAAATAAAAACGTCAGGG 59.933 37.037 0.00 0.00 0.00 4.45
3386 4082 6.320164 TGGATCATAAATAAAAACGTCAGGGG 59.680 38.462 0.00 0.00 0.00 4.79
3388 4084 7.230712 GGATCATAAATAAAAACGTCAGGGGAT 59.769 37.037 0.00 0.00 0.00 3.85
3389 4085 7.562454 TCATAAATAAAAACGTCAGGGGATC 57.438 36.000 0.00 0.00 0.00 3.36
3390 4086 6.544564 TCATAAATAAAAACGTCAGGGGATCC 59.455 38.462 1.92 1.92 0.00 3.36
3391 4087 2.389962 TAAAAACGTCAGGGGATCCG 57.610 50.000 5.45 0.00 38.33 4.18
3393 4089 2.814913 AAAACGTCAGGGGATCCGGC 62.815 60.000 5.45 0.00 38.33 6.13
3395 4091 3.917760 CGTCAGGGGATCCGGCTC 61.918 72.222 5.45 0.00 38.33 4.70
3396 4092 3.551407 GTCAGGGGATCCGGCTCC 61.551 72.222 16.35 16.35 38.33 4.70
3437 4151 3.201290 GTCATAGGATGTGAACTGCAGG 58.799 50.000 19.93 0.00 0.00 4.85
3453 4167 1.098050 CAGGGCAATCACAGGTTAGC 58.902 55.000 0.00 0.00 0.00 3.09
3489 4205 3.439932 GCGTCATGCACCGATTATTAG 57.560 47.619 6.45 0.00 45.45 1.73
3490 4206 2.800544 GCGTCATGCACCGATTATTAGT 59.199 45.455 6.45 0.00 45.45 2.24
3498 4214 4.872664 GCACCGATTATTAGTAGTGCTCT 58.127 43.478 5.73 0.00 45.40 4.09
3504 4220 8.298140 ACCGATTATTAGTAGTGCTCTCAATAC 58.702 37.037 0.00 0.00 42.32 1.89
3505 4221 8.297426 CCGATTATTAGTAGTGCTCTCAATACA 58.703 37.037 5.83 0.00 43.87 2.29
3551 4268 2.652530 CACCCAAAGCAAGCGCAT 59.347 55.556 11.47 0.00 42.27 4.73
3552 4269 1.882311 CACCCAAAGCAAGCGCATA 59.118 52.632 11.47 0.00 42.27 3.14
3553 4270 0.179156 CACCCAAAGCAAGCGCATAG 60.179 55.000 11.47 0.00 42.27 2.23
3599 4316 0.674895 GCTGTGGGTTAGGCACAGAG 60.675 60.000 5.72 0.00 46.55 3.35
3600 4317 0.036010 CTGTGGGTTAGGCACAGAGG 60.036 60.000 0.00 0.00 46.55 3.69
3641 4358 0.676466 CTGGGCATAAGCGTCACCAA 60.676 55.000 0.00 0.00 43.41 3.67
3653 4371 2.159517 GCGTCACCAAGATAAGCTTTGG 60.160 50.000 12.45 12.45 33.60 3.28
3676 4394 6.881065 TGGTTATCTGCTCATTATCCTAATGC 59.119 38.462 2.65 0.00 0.00 3.56
3689 4407 3.429492 TCCTAATGCTGCCAATGTTGAA 58.571 40.909 0.00 0.00 0.00 2.69
3712 4430 7.769970 TGAATTTTTCCTTTGACAAGAGCATTT 59.230 29.630 0.00 0.00 30.57 2.32
3743 4461 1.935400 ATTGGACCTGGGGCATCCA 60.935 57.895 0.00 0.00 44.79 3.41
3753 4471 0.178767 GGGGCATCCATTTTCCTTGC 59.821 55.000 0.00 0.00 35.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.740585 TGTTTCGTGTGGTTGTCTTGG 59.259 47.619 0.00 0.00 0.00 3.61
13 14 4.035792 TGTTAGGAATGTTTCGTGTGGTTG 59.964 41.667 0.00 0.00 0.00 3.77
30 31 4.909696 TTGTGTGTGTGGAAATGTTAGG 57.090 40.909 0.00 0.00 0.00 2.69
32 33 6.516739 TCTTTTGTGTGTGTGGAAATGTTA 57.483 33.333 0.00 0.00 0.00 2.41
110 111 0.107831 GTGGAGCTGTGGGTACAACA 59.892 55.000 0.00 0.00 35.37 3.33
120 121 1.777272 AGGAAAAAGGAGTGGAGCTGT 59.223 47.619 0.00 0.00 0.00 4.40
134 138 3.283751 TCTGTTTTCTTGCGGAGGAAAA 58.716 40.909 20.30 20.30 37.43 2.29
135 139 2.925724 TCTGTTTTCTTGCGGAGGAAA 58.074 42.857 10.15 10.15 37.43 3.13
160 164 8.289618 CCTCTCATTTCGTTTCTCAACAATTTA 58.710 33.333 0.00 0.00 32.54 1.40
161 165 7.141363 CCTCTCATTTCGTTTCTCAACAATTT 58.859 34.615 0.00 0.00 32.54 1.82
164 168 4.515191 CCCTCTCATTTCGTTTCTCAACAA 59.485 41.667 0.00 0.00 32.54 2.83
166 170 4.315803 TCCCTCTCATTTCGTTTCTCAAC 58.684 43.478 0.00 0.00 0.00 3.18
167 171 4.617253 TCCCTCTCATTTCGTTTCTCAA 57.383 40.909 0.00 0.00 0.00 3.02
213 217 1.304464 CCTGGTCAAAAGGAGGGCC 60.304 63.158 0.00 0.00 36.91 5.80
256 261 2.543687 TTCTCGCCTCCGCTTTCGAG 62.544 60.000 4.34 4.34 46.78 4.04
361 379 2.904866 CTCCCTCTCTCGCCCTCG 60.905 72.222 0.00 0.00 0.00 4.63
362 380 1.528309 CTCTCCCTCTCTCGCCCTC 60.528 68.421 0.00 0.00 0.00 4.30
363 381 1.994885 CTCTCTCCCTCTCTCGCCCT 61.995 65.000 0.00 0.00 0.00 5.19
364 382 1.528309 CTCTCTCCCTCTCTCGCCC 60.528 68.421 0.00 0.00 0.00 6.13
365 383 0.818040 GTCTCTCTCCCTCTCTCGCC 60.818 65.000 0.00 0.00 0.00 5.54
366 384 0.818040 GGTCTCTCTCCCTCTCTCGC 60.818 65.000 0.00 0.00 0.00 5.03
367 385 0.544223 TGGTCTCTCTCCCTCTCTCG 59.456 60.000 0.00 0.00 0.00 4.04
368 386 2.174639 TGATGGTCTCTCTCCCTCTCTC 59.825 54.545 0.00 0.00 0.00 3.20
369 387 2.091885 GTGATGGTCTCTCTCCCTCTCT 60.092 54.545 0.00 0.00 0.00 3.10
370 388 2.306847 GTGATGGTCTCTCTCCCTCTC 58.693 57.143 0.00 0.00 0.00 3.20
371 389 1.643286 TGTGATGGTCTCTCTCCCTCT 59.357 52.381 0.00 0.00 0.00 3.69
372 390 2.031120 CTGTGATGGTCTCTCTCCCTC 58.969 57.143 0.00 0.00 0.00 4.30
373 391 1.964344 GCTGTGATGGTCTCTCTCCCT 60.964 57.143 0.00 0.00 0.00 4.20
374 392 0.463620 GCTGTGATGGTCTCTCTCCC 59.536 60.000 0.00 0.00 0.00 4.30
375 393 1.484038 AGCTGTGATGGTCTCTCTCC 58.516 55.000 0.00 0.00 0.00 3.71
447 465 0.550147 TGGAGGAGAAAAGGAGGGGG 60.550 60.000 0.00 0.00 0.00 5.40
448 466 0.621082 GTGGAGGAGAAAAGGAGGGG 59.379 60.000 0.00 0.00 0.00 4.79
583 624 5.547465 TCCAGTACGTTCTTGATTGATTGT 58.453 37.500 0.00 0.00 0.00 2.71
896 937 1.270893 GGTTCTTGCTCGGTTCTTCCT 60.271 52.381 0.00 0.00 0.00 3.36
897 938 1.157585 GGTTCTTGCTCGGTTCTTCC 58.842 55.000 0.00 0.00 0.00 3.46
906 947 0.892063 AGGAGAGACGGTTCTTGCTC 59.108 55.000 0.00 0.00 29.47 4.26
909 950 1.474879 GGAGAGGAGAGACGGTTCTTG 59.525 57.143 0.00 0.00 29.47 3.02
924 965 2.423898 TTAAGAGCGCCGGGGAGAG 61.424 63.158 24.68 0.00 0.00 3.20
925 966 2.363276 TTAAGAGCGCCGGGGAGA 60.363 61.111 24.68 0.00 0.00 3.71
926 967 2.202892 GTTAAGAGCGCCGGGGAG 60.203 66.667 24.68 0.00 0.00 4.30
935 976 1.914700 CTCTGCGTTCTCGTTAAGAGC 59.085 52.381 0.00 0.00 46.44 4.09
967 1008 1.003839 TGTCCGCTGCTAACAAGGG 60.004 57.895 0.00 0.00 0.00 3.95
969 1010 1.639298 GCCTGTCCGCTGCTAACAAG 61.639 60.000 0.00 0.00 0.00 3.16
1113 1154 2.915659 ACGACCCGCCTGAACTCA 60.916 61.111 0.00 0.00 0.00 3.41
1701 1742 3.241530 TGCACGAAGGGGCACTCT 61.242 61.111 0.00 0.00 37.04 3.24
2742 2786 3.244215 TGACAAGAGAGTTCACCCATGAC 60.244 47.826 0.00 0.00 33.38 3.06
2837 2881 1.371337 ATCGATCGGTTGGTCGTCGA 61.371 55.000 16.41 11.61 42.05 4.20
2844 2889 1.154205 GCCAGTGATCGATCGGTTGG 61.154 60.000 26.10 26.10 0.00 3.77
2845 2890 0.179100 AGCCAGTGATCGATCGGTTG 60.179 55.000 20.03 16.32 0.00 3.77
2846 2891 0.103208 GAGCCAGTGATCGATCGGTT 59.897 55.000 20.03 13.09 0.00 4.44
2847 2892 1.037579 TGAGCCAGTGATCGATCGGT 61.038 55.000 20.03 8.34 0.00 4.69
2848 2893 0.316522 ATGAGCCAGTGATCGATCGG 59.683 55.000 20.03 15.77 0.00 4.18
3174 3863 4.825546 AGAGACAATGAAGCACACAAAG 57.174 40.909 0.00 0.00 0.00 2.77
3187 3876 8.080417 CACAAGTTTGATCAATCAAGAGACAAT 58.920 33.333 16.79 0.00 46.34 2.71
3201 3890 8.454106 AGAGTACAATATTGCACAAGTTTGATC 58.546 33.333 18.78 6.88 0.00 2.92
3214 3903 7.558161 TTGGCATGAGAAGAGTACAATATTG 57.442 36.000 14.01 14.01 0.00 1.90
3248 3943 4.019174 GGTGAACACTTCCATGATTCCAT 58.981 43.478 0.00 0.00 0.00 3.41
3249 3944 3.181435 TGGTGAACACTTCCATGATTCCA 60.181 43.478 0.00 0.00 0.00 3.53
3250 3945 3.420893 TGGTGAACACTTCCATGATTCC 58.579 45.455 0.00 0.00 0.00 3.01
3251 3946 3.119708 GCTGGTGAACACTTCCATGATTC 60.120 47.826 0.00 0.00 0.00 2.52
3252 3947 2.821969 GCTGGTGAACACTTCCATGATT 59.178 45.455 0.00 0.00 0.00 2.57
3253 3948 2.224843 TGCTGGTGAACACTTCCATGAT 60.225 45.455 0.00 0.00 0.00 2.45
3254 3949 1.142667 TGCTGGTGAACACTTCCATGA 59.857 47.619 0.00 0.00 0.00 3.07
3255 3950 1.608055 TGCTGGTGAACACTTCCATG 58.392 50.000 4.96 0.00 0.00 3.66
3300 3995 5.651612 ATAAAGGGTGATGTGATCATGGA 57.348 39.130 0.00 0.00 42.04 3.41
3301 3996 6.321945 TCAAATAAAGGGTGATGTGATCATGG 59.678 38.462 0.00 0.00 42.04 3.66
3302 3997 7.337480 TCAAATAAAGGGTGATGTGATCATG 57.663 36.000 0.00 0.00 42.04 3.07
3314 4009 7.128234 CATGGAATGGAATCAAATAAAGGGT 57.872 36.000 0.00 0.00 41.79 4.34
3377 4073 4.779733 AGCCGGATCCCCTGACGT 62.780 66.667 5.05 0.00 0.00 4.34
3379 4075 3.551407 GGAGCCGGATCCCCTGAC 61.551 72.222 28.96 0.78 32.79 3.51
3385 4081 3.237741 CAGGAGGGAGCCGGATCC 61.238 72.222 31.09 31.09 38.76 3.36
3386 4082 1.753368 CTTCAGGAGGGAGCCGGATC 61.753 65.000 12.38 12.38 32.19 3.36
3388 4084 2.364317 CTTCAGGAGGGAGCCGGA 60.364 66.667 5.05 0.00 0.00 5.14
3389 4085 2.685380 ACTTCAGGAGGGAGCCGG 60.685 66.667 0.00 0.00 0.00 6.13
3390 4086 2.581354 CACTTCAGGAGGGAGCCG 59.419 66.667 0.00 0.00 0.00 5.52
3391 4087 2.993853 CCACTTCAGGAGGGAGCC 59.006 66.667 0.00 0.00 0.00 4.70
3393 4089 1.601171 CAGCCACTTCAGGAGGGAG 59.399 63.158 0.00 0.00 0.00 4.30
3395 4091 2.227036 ACCAGCCACTTCAGGAGGG 61.227 63.158 0.00 0.00 31.77 4.30
3396 4092 1.002868 CACCAGCCACTTCAGGAGG 60.003 63.158 0.00 0.00 0.00 4.30
3437 4151 3.375299 CACTAAGCTAACCTGTGATTGCC 59.625 47.826 0.00 0.00 0.00 4.52
3453 4167 1.067821 GACGCCTCCATCTCCACTAAG 59.932 57.143 0.00 0.00 0.00 2.18
3504 4220 7.082602 GCACTTGCCTTTCTGATGATATATTG 58.917 38.462 0.00 0.00 34.31 1.90
3505 4221 7.211966 GCACTTGCCTTTCTGATGATATATT 57.788 36.000 0.00 0.00 34.31 1.28
3599 4316 2.525105 TTTGGGCCTAATTCCTGTCC 57.475 50.000 0.85 0.00 0.00 4.02
3600 4317 4.711846 AGATTTTTGGGCCTAATTCCTGTC 59.288 41.667 0.85 0.00 0.00 3.51
3641 4358 5.994250 TGAGCAGATAACCAAAGCTTATCT 58.006 37.500 0.00 0.49 40.22 1.98
3653 4371 7.413877 GCAGCATTAGGATAATGAGCAGATAAC 60.414 40.741 12.53 0.00 33.43 1.89
3676 4394 6.260493 TCAAAGGAAAAATTCAACATTGGCAG 59.740 34.615 0.00 0.00 0.00 4.85
3689 4407 8.510243 AAAAATGCTCTTGTCAAAGGAAAAAT 57.490 26.923 0.00 0.00 33.90 1.82
3712 4430 5.514834 CCCAGGTCCAATGTTCTAGAAGAAA 60.515 44.000 5.12 0.00 35.75 2.52
3786 4504 7.119699 GGACATCAACACTTGTTTCATCATCTA 59.880 37.037 0.00 0.00 35.83 1.98
3787 4505 6.072286 GGACATCAACACTTGTTTCATCATCT 60.072 38.462 0.00 0.00 35.83 2.90


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

AutoCloner maintained by Alex Coulton.