Multiple sequence alignment - TraesCS1B01G354300

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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 TraesCS1B01G354300 chr1B 100.000 2603 0 0 1 2603 584142653 584140051 0.000000e+00 4807
1 TraesCS1B01G354300 chr1B 100.000 1355 0 0 2924 4278 584139730 584138376 0.000000e+00 2503
2 TraesCS1B01G354300 chr1A 96.819 2609 70 11 1 2603 531225408 531222807 0.000000e+00 4346
3 TraesCS1B01G354300 chr1A 84.828 725 39 31 2940 3643 531222783 531222109 0.000000e+00 664
4 TraesCS1B01G354300 chr1A 86.063 574 41 14 3738 4278 531222102 531221535 7.970000e-162 580
5 TraesCS1B01G354300 chr1D 96.587 2608 73 12 1 2603 432789124 432786528 0.000000e+00 4309
6 TraesCS1B01G354300 chr1D 88.253 1362 88 40 2940 4264 432786522 432785196 0.000000e+00 1563


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 TraesCS1B01G354300 chr1B 584138376 584142653 4277 True 3655.000000 4807 100.000000 1 4278 2 chr1B.!!$R1 4277
1 TraesCS1B01G354300 chr1A 531221535 531225408 3873 True 1863.333333 4346 89.236667 1 4278 3 chr1A.!!$R1 4277
2 TraesCS1B01G354300 chr1D 432785196 432789124 3928 True 2936.000000 4309 92.420000 1 4264 2 chr1D.!!$R1 4263

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
693 699 2.287977 AAGGCTTGGGTTTCTACACC 57.712 50.000 0.00 0.00 35.88 4.16 F
1665 1672 3.264450 AGGCAGCTGTTTTAGGTATGTCT 59.736 43.478 16.64 0.00 34.81 3.41 F
3092 3101 0.747255 TGAAGAGGGAGCACGCTATC 59.253 55.000 0.00 3.92 39.38 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1834 2.023673 CAAGCTGACCAGTTTGTTGGA 58.976 47.619 15.48 0.0 42.35 3.53 R
3095 3104 0.041833 AGGACTCCAGCTTCTGCCTA 59.958 55.000 0.00 0.0 40.80 3.93 R
4216 4302 0.036875 CCTCCCTTCTTCCGCACTTT 59.963 55.000 0.00 0.0 0.00 2.66 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
94 95 7.348201 GTTCTCGATGATTTTATCACCACATC 58.652 38.462 0.00 0.00 43.01 3.06
122 123 4.923893 TGAACTTTGAGATGCACAAACAG 58.076 39.130 0.00 0.00 34.30 3.16
316 317 4.641396 TGTTCATTGTCTTGATTCTCGGT 58.359 39.130 0.00 0.00 0.00 4.69
322 323 2.897326 TGTCTTGATTCTCGGTCTCCAA 59.103 45.455 0.00 0.00 0.00 3.53
538 540 9.988815 GACCTGTATCTGATTATGTGATAAGTT 57.011 33.333 0.00 0.00 0.00 2.66
605 611 6.144402 CAGGTTTGCAGATGTCAAATTTGTAC 59.856 38.462 17.47 14.01 36.06 2.90
693 699 2.287977 AAGGCTTGGGTTTCTACACC 57.712 50.000 0.00 0.00 35.88 4.16
737 743 4.024556 CACAGTCTGTTGATGTTCAAGTCC 60.025 45.833 1.67 0.00 37.00 3.85
894 900 4.989168 CCGGAGCTATATAAACAACCTGAC 59.011 45.833 0.00 0.00 0.00 3.51
1210 1216 8.084073 CCTTAGAAAAATCTGAATGAAGCACAA 58.916 33.333 0.00 0.00 0.00 3.33
1328 1335 4.693095 GGAACTCTCCTTTTCTGCTACTTG 59.307 45.833 0.00 0.00 38.88 3.16
1665 1672 3.264450 AGGCAGCTGTTTTAGGTATGTCT 59.736 43.478 16.64 0.00 34.81 3.41
1710 1717 7.261325 TCTTTAGGCGATAGATGATTAGATGC 58.739 38.462 0.00 0.00 39.76 3.91
1740 1747 5.417580 GCCTATGTGAAAGAAATTGGTGGTA 59.582 40.000 0.00 0.00 0.00 3.25
1743 1750 7.393234 CCTATGTGAAAGAAATTGGTGGTAGAA 59.607 37.037 0.00 0.00 0.00 2.10
1903 1910 3.253188 GCACATGGCTAAACTCAGTTTCA 59.747 43.478 5.92 0.00 37.01 2.69
1947 1955 9.454859 TTGTTTGGTTTTGTAAAAGGAAATCAT 57.545 25.926 0.00 0.00 0.00 2.45
2086 2095 6.004574 ACACTGCTTCTAGATATCGGATGTA 58.995 40.000 0.00 2.16 0.00 2.29
2090 2099 7.066887 ACTGCTTCTAGATATCGGATGTATCTG 59.933 40.741 11.74 0.00 38.85 2.90
2128 2137 5.175859 GTGTCCTCAATTCTCGAAACCATA 58.824 41.667 0.00 0.00 0.00 2.74
2199 2208 2.969821 TTGGTTGGTGGTGCTTCTAT 57.030 45.000 0.00 0.00 0.00 1.98
2227 2236 6.385649 TTGTTTTACTTTAAGTGCCTCAGG 57.614 37.500 8.00 0.00 0.00 3.86
2237 2246 1.985159 AGTGCCTCAGGGAATGTGTAA 59.015 47.619 0.00 0.00 33.58 2.41
2262 2271 6.322491 ACCAGAGTTTTTCTTTTTCTTGACG 58.678 36.000 0.00 0.00 32.41 4.35
2320 2329 2.929398 CACGCAGTACTAATCATGTGCA 59.071 45.455 0.00 0.00 41.61 4.57
2459 2468 8.472413 AGAGCTGACATTTTGCATTTGTTATAT 58.528 29.630 0.00 0.00 0.00 0.86
2500 2509 7.533289 AGTTTTGGGCTTAAGCTTAACATAA 57.467 32.000 25.88 16.68 41.70 1.90
2597 2606 4.429854 AAATGCTGAAGGGTATCTCTCC 57.570 45.455 0.00 0.00 0.00 3.71
2989 2998 5.181245 CGACATGTGGTTTTCTATCCAAAGT 59.819 40.000 1.15 0.00 35.38 2.66
2996 3005 8.598916 TGTGGTTTTCTATCCAAAGTATACAGA 58.401 33.333 5.50 0.00 35.38 3.41
3086 3095 2.421619 CAGAAAGTGAAGAGGGAGCAC 58.578 52.381 0.00 0.00 0.00 4.40
3092 3101 0.747255 TGAAGAGGGAGCACGCTATC 59.253 55.000 0.00 3.92 39.38 2.08
3095 3104 0.397816 AGAGGGAGCACGCTATCCTT 60.398 55.000 12.80 0.00 39.38 3.36
3116 3125 1.127343 GGCAGAAGCTGGAGTCCTAT 58.873 55.000 11.33 0.00 41.70 2.57
3131 3140 6.447084 TGGAGTCCTATTTCCAGGTAATCTTT 59.553 38.462 11.33 0.00 38.53 2.52
3132 3141 6.768381 GGAGTCCTATTTCCAGGTAATCTTTG 59.232 42.308 0.41 0.00 36.99 2.77
3134 3143 7.339482 AGTCCTATTTCCAGGTAATCTTTGTC 58.661 38.462 0.00 0.00 36.99 3.18
3136 3145 7.775561 GTCCTATTTCCAGGTAATCTTTGTCAT 59.224 37.037 0.00 0.00 36.99 3.06
3137 3146 7.993183 TCCTATTTCCAGGTAATCTTTGTCATC 59.007 37.037 0.00 0.00 36.99 2.92
3139 3148 4.503714 TCCAGGTAATCTTTGTCATCCC 57.496 45.455 0.00 0.00 0.00 3.85
3140 3149 3.202151 TCCAGGTAATCTTTGTCATCCCC 59.798 47.826 0.00 0.00 0.00 4.81
3141 3150 3.053693 CCAGGTAATCTTTGTCATCCCCA 60.054 47.826 0.00 0.00 0.00 4.96
3142 3151 4.202441 CAGGTAATCTTTGTCATCCCCAG 58.798 47.826 0.00 0.00 0.00 4.45
3143 3152 2.952310 GGTAATCTTTGTCATCCCCAGC 59.048 50.000 0.00 0.00 0.00 4.85
3144 3153 3.372025 GGTAATCTTTGTCATCCCCAGCT 60.372 47.826 0.00 0.00 0.00 4.24
3145 3154 3.463048 AATCTTTGTCATCCCCAGCTT 57.537 42.857 0.00 0.00 0.00 3.74
3146 3155 2.496899 TCTTTGTCATCCCCAGCTTC 57.503 50.000 0.00 0.00 0.00 3.86
3147 3156 1.704628 TCTTTGTCATCCCCAGCTTCA 59.295 47.619 0.00 0.00 0.00 3.02
3148 3157 2.309755 TCTTTGTCATCCCCAGCTTCAT 59.690 45.455 0.00 0.00 0.00 2.57
3149 3158 2.425143 TTGTCATCCCCAGCTTCATC 57.575 50.000 0.00 0.00 0.00 2.92
3150 3159 1.588239 TGTCATCCCCAGCTTCATCT 58.412 50.000 0.00 0.00 0.00 2.90
3151 3160 1.487976 TGTCATCCCCAGCTTCATCTC 59.512 52.381 0.00 0.00 0.00 2.75
3152 3161 1.767681 GTCATCCCCAGCTTCATCTCT 59.232 52.381 0.00 0.00 0.00 3.10
3153 3162 2.172293 GTCATCCCCAGCTTCATCTCTT 59.828 50.000 0.00 0.00 0.00 2.85
3154 3163 2.172082 TCATCCCCAGCTTCATCTCTTG 59.828 50.000 0.00 0.00 0.00 3.02
3155 3164 0.914644 TCCCCAGCTTCATCTCTTGG 59.085 55.000 0.00 0.00 0.00 3.61
3156 3165 0.106819 CCCCAGCTTCATCTCTTGGG 60.107 60.000 0.82 0.82 35.02 4.12
3157 3166 0.914644 CCCAGCTTCATCTCTTGGGA 59.085 55.000 1.59 0.00 37.29 4.37
3158 3167 1.134159 CCCAGCTTCATCTCTTGGGAG 60.134 57.143 1.59 0.00 40.73 4.30
3159 3168 1.666054 CAGCTTCATCTCTTGGGAGC 58.334 55.000 0.00 0.00 39.31 4.70
3160 3169 1.209990 CAGCTTCATCTCTTGGGAGCT 59.790 52.381 0.00 0.00 42.30 4.09
3161 3170 1.209990 AGCTTCATCTCTTGGGAGCTG 59.790 52.381 0.00 0.00 41.00 4.24
3162 3171 1.666054 CTTCATCTCTTGGGAGCTGC 58.334 55.000 0.00 0.00 39.31 5.25
3163 3172 0.254178 TTCATCTCTTGGGAGCTGCC 59.746 55.000 18.95 18.95 39.31 4.85
3174 3183 2.441532 AGCTGCCCATCATGGTGC 60.442 61.111 2.07 6.56 35.17 5.01
3175 3184 2.441532 GCTGCCCATCATGGTGCT 60.442 61.111 15.69 0.00 35.17 4.40
3176 3185 2.487532 GCTGCCCATCATGGTGCTC 61.488 63.158 15.69 6.50 35.17 4.26
3180 3189 0.178998 GCCCATCATGGTGCTCATCT 60.179 55.000 2.07 0.00 35.17 2.90
3190 3199 0.938637 GTGCTCATCTGATCTCGCCG 60.939 60.000 0.00 0.00 0.00 6.46
3191 3200 2.021039 GCTCATCTGATCTCGCCGC 61.021 63.158 0.00 0.00 0.00 6.53
3278 3287 1.838112 CAGGCCTGGAAGCATGTAAA 58.162 50.000 26.14 0.00 39.62 2.01
3280 3289 0.457443 GGCCTGGAAGCATGTAAAGC 59.543 55.000 0.00 0.00 0.00 3.51
3281 3290 0.099436 GCCTGGAAGCATGTAAAGCG 59.901 55.000 0.00 0.00 37.01 4.68
3282 3291 0.099436 CCTGGAAGCATGTAAAGCGC 59.901 55.000 0.00 0.00 37.01 5.92
3283 3292 1.089920 CTGGAAGCATGTAAAGCGCT 58.910 50.000 2.64 2.64 37.68 5.92
3284 3293 0.804364 TGGAAGCATGTAAAGCGCTG 59.196 50.000 12.58 0.00 35.79 5.18
3285 3294 0.099436 GGAAGCATGTAAAGCGCTGG 59.901 55.000 12.58 0.00 35.79 4.85
3286 3295 0.524180 GAAGCATGTAAAGCGCTGGC 60.524 55.000 12.58 8.53 35.79 4.85
3307 3323 1.596934 CTGGCGCTTTACAGGGAGA 59.403 57.895 7.64 0.00 34.82 3.71
3321 3337 9.090103 CTTTACAGGGAGATGAACCAGTATATA 57.910 37.037 0.00 0.00 0.00 0.86
3325 3341 7.617723 ACAGGGAGATGAACCAGTATATATCTC 59.382 40.741 0.00 0.00 39.66 2.75
3326 3342 7.838696 CAGGGAGATGAACCAGTATATATCTCT 59.161 40.741 0.00 0.00 40.04 3.10
3406 3422 3.266510 TGGGTGCTAGCTAGTTCATTG 57.733 47.619 21.62 0.00 0.00 2.82
3423 3439 5.114764 TCATTGATGCCTGAAAGATACCA 57.885 39.130 0.00 0.00 34.07 3.25
3568 3593 1.333524 CGAGCTTGCAAGTGTCTGTTG 60.334 52.381 26.55 8.33 0.00 3.33
3610 3650 3.311106 AGCTTGTGAATGAATGTTTGCG 58.689 40.909 0.00 0.00 0.00 4.85
3645 3685 8.193438 AGCTGGAAAGCAATAGTCATATTTTTC 58.807 33.333 0.00 0.00 37.25 2.29
3646 3686 8.193438 GCTGGAAAGCAATAGTCATATTTTTCT 58.807 33.333 0.00 0.00 32.99 2.52
3661 3703 9.125026 TCATATTTTTCTTTATCCTCTCAAGGC 57.875 33.333 0.00 0.00 43.02 4.35
3667 3709 1.131638 TATCCTCTCAAGGCGCCATT 58.868 50.000 31.54 17.17 43.02 3.16
3668 3710 0.465097 ATCCTCTCAAGGCGCCATTG 60.465 55.000 31.54 27.02 43.02 2.82
3677 3719 3.509575 TCAAGGCGCCATTGAATAAAGTT 59.490 39.130 31.54 6.23 33.85 2.66
3685 3727 6.021596 CGCCATTGAATAAAGTTGACTACAC 58.978 40.000 0.00 0.00 0.00 2.90
3749 3795 7.383102 ACACTATGAACACATTGATTCTTCC 57.617 36.000 0.00 0.00 0.00 3.46
3826 3872 7.899178 TTTTTATGTGCGATCTTTGTAGAGA 57.101 32.000 0.00 0.00 32.92 3.10
3827 3873 7.899178 TTTTATGTGCGATCTTTGTAGAGAA 57.101 32.000 0.00 0.00 32.92 2.87
3828 3874 6.887376 TTATGTGCGATCTTTGTAGAGAAC 57.113 37.500 0.00 0.00 32.92 3.01
3829 3875 3.585862 TGTGCGATCTTTGTAGAGAACC 58.414 45.455 0.00 0.00 32.92 3.62
3879 3939 1.340017 GCCCTTATTGTCCAGACTGCA 60.340 52.381 0.00 0.00 0.00 4.41
3881 3941 2.749621 CCCTTATTGTCCAGACTGCAAC 59.250 50.000 0.00 0.00 0.00 4.17
4025 4104 1.188863 TACTGAGCTAACGGGGGAAC 58.811 55.000 0.00 0.00 0.00 3.62
4072 4152 4.944619 TGACTGAGCTACCAAGGATATG 57.055 45.455 0.00 0.00 0.00 1.78
4151 4237 1.447317 CGCTTTGTGGCCTGACTGTT 61.447 55.000 3.32 0.00 0.00 3.16
4172 4258 3.636231 TCGCAACCACTCTGGGGG 61.636 66.667 0.00 0.00 43.37 5.40
4176 4262 3.322466 AACCACTCTGGGGGCGAG 61.322 66.667 0.00 0.00 43.37 5.03
4223 4315 2.095567 CCAAGATGAACTCCAAAGTGCG 60.096 50.000 0.00 0.00 33.14 5.34
4256 4350 1.568025 GAAAAACTTCGCGCCGACT 59.432 52.632 0.00 0.00 34.89 4.18
4274 4368 2.620585 GACTCAAACTTTTGCCTCTGCT 59.379 45.455 0.00 0.00 38.05 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 3.918591 GTGCATCTCAAAGTTCAAGCATG 59.081 43.478 0.00 0.00 32.98 4.06
122 123 7.949690 AAGGGGAATGGTATAACAAAACTAC 57.050 36.000 0.00 0.00 0.00 2.73
316 317 2.625314 CTCGGTCTGAGCATATTGGAGA 59.375 50.000 7.70 0.00 38.03 3.71
322 323 1.001746 CATGCCTCGGTCTGAGCATAT 59.998 52.381 14.44 2.84 43.82 1.78
640 646 5.773680 GTCTATGCAGATGGGTTACTACCTA 59.226 44.000 0.00 0.00 39.47 3.08
693 699 5.006386 GTGATGCTCCTCCTTTATATTGGG 58.994 45.833 0.00 0.00 0.00 4.12
737 743 7.194278 CAGCATCTATTCACATTTTGGAGAAG 58.806 38.462 0.00 0.00 0.00 2.85
894 900 5.047847 TCTCTGGTTGTAGAAAGTTGAACG 58.952 41.667 0.00 0.00 0.00 3.95
1288 1294 9.337396 GGAGAGTTCCAAAATGGTTAAATTTTT 57.663 29.630 0.00 0.00 43.45 1.94
1290 1296 8.262601 AGGAGAGTTCCAAAATGGTTAAATTT 57.737 30.769 0.00 0.00 46.64 1.82
1291 1297 7.855784 AGGAGAGTTCCAAAATGGTTAAATT 57.144 32.000 0.00 0.00 46.64 1.82
1292 1298 7.855784 AAGGAGAGTTCCAAAATGGTTAAAT 57.144 32.000 0.00 0.00 46.64 1.40
1328 1335 9.169468 CCATATCAACGCACATTAAAATAAGAC 57.831 33.333 0.00 0.00 0.00 3.01
1578 1585 3.526534 GATACTTCTCCCTGCAGTGTTC 58.473 50.000 13.81 0.00 0.00 3.18
1710 1717 4.707030 TTTCTTTCACATAGGCATGCAG 57.293 40.909 21.36 8.54 35.39 4.41
1740 1747 6.944862 ACAAATTCAACAGCCTCTAAGATTCT 59.055 34.615 0.00 0.00 0.00 2.40
1743 1750 6.571150 GCAACAAATTCAACAGCCTCTAAGAT 60.571 38.462 0.00 0.00 0.00 2.40
1827 1834 2.023673 CAAGCTGACCAGTTTGTTGGA 58.976 47.619 15.48 0.00 42.35 3.53
1903 1910 7.160726 CCAAACAATTATCACTTTTCACCCAT 58.839 34.615 0.00 0.00 0.00 4.00
1939 1946 9.860898 ATTAAGTTCTGCAAACTTATGATTTCC 57.139 29.630 23.02 0.00 40.96 3.13
1943 1951 9.453572 TCAGATTAAGTTCTGCAAACTTATGAT 57.546 29.630 23.02 17.88 42.37 2.45
1947 1955 7.719633 AGGTTCAGATTAAGTTCTGCAAACTTA 59.280 33.333 20.62 20.62 42.37 2.24
2009 2018 4.814234 ACAAATAGTCAACAGCTCGTTTGA 59.186 37.500 0.00 4.73 34.86 2.69
2183 2192 4.584327 AAAACATAGAAGCACCACCAAC 57.416 40.909 0.00 0.00 0.00 3.77
2199 2208 8.088981 TGAGGCACTTAAAGTAAAACAAAAACA 58.911 29.630 0.00 0.00 41.55 2.83
2227 2236 7.039313 AGAAAAACTCTGGTTTACACATTCC 57.961 36.000 0.00 0.00 43.90 3.01
2237 2246 6.806739 CGTCAAGAAAAAGAAAAACTCTGGTT 59.193 34.615 0.00 0.00 33.37 3.67
2262 2271 3.572255 AATCTCTGCGTTAGGAGATCTCC 59.428 47.826 31.27 31.27 45.21 3.71
2459 2468 6.708949 CCCAAAACTTTACAGCAGAGTAGTAA 59.291 38.462 0.00 0.00 0.00 2.24
2923 2932 2.091333 AGCAGGGACCCTCAAAAAGAAA 60.091 45.455 11.23 0.00 0.00 2.52
2924 2933 1.499007 AGCAGGGACCCTCAAAAAGAA 59.501 47.619 11.23 0.00 0.00 2.52
2925 2934 1.149101 AGCAGGGACCCTCAAAAAGA 58.851 50.000 11.23 0.00 0.00 2.52
2926 2935 2.001076 AAGCAGGGACCCTCAAAAAG 57.999 50.000 11.23 0.00 0.00 2.27
2927 2936 3.603965 TTAAGCAGGGACCCTCAAAAA 57.396 42.857 11.23 0.04 0.00 1.94
2928 2937 3.825908 ATTAAGCAGGGACCCTCAAAA 57.174 42.857 11.23 3.24 0.00 2.44
2929 2938 3.825908 AATTAAGCAGGGACCCTCAAA 57.174 42.857 11.23 2.86 0.00 2.69
2930 2939 3.850173 ACTAATTAAGCAGGGACCCTCAA 59.150 43.478 11.23 2.85 0.00 3.02
2931 2940 3.460825 ACTAATTAAGCAGGGACCCTCA 58.539 45.455 11.23 0.00 0.00 3.86
2932 2941 4.200092 CAACTAATTAAGCAGGGACCCTC 58.800 47.826 11.23 5.95 0.00 4.30
2933 2942 3.053619 CCAACTAATTAAGCAGGGACCCT 60.054 47.826 7.44 7.44 0.00 4.34
2934 2943 3.288092 CCAACTAATTAAGCAGGGACCC 58.712 50.000 0.59 0.59 0.00 4.46
2935 2944 3.964411 ACCAACTAATTAAGCAGGGACC 58.036 45.455 0.00 0.00 0.00 4.46
2936 2945 5.066117 GCTAACCAACTAATTAAGCAGGGAC 59.934 44.000 0.00 0.00 0.00 4.46
2937 2946 5.190677 GCTAACCAACTAATTAAGCAGGGA 58.809 41.667 0.00 0.00 0.00 4.20
2938 2947 4.947388 TGCTAACCAACTAATTAAGCAGGG 59.053 41.667 2.38 0.00 0.00 4.45
2989 2998 6.605849 GCGTCGGTAGTGATTAATCTGTATA 58.394 40.000 16.24 2.07 0.00 1.47
2996 3005 2.357009 AGACGCGTCGGTAGTGATTAAT 59.643 45.455 31.56 8.29 34.09 1.40
3086 3095 1.342819 AGCTTCTGCCTAAGGATAGCG 59.657 52.381 0.00 0.00 40.80 4.26
3092 3101 0.908198 ACTCCAGCTTCTGCCTAAGG 59.092 55.000 0.00 0.00 40.80 2.69
3095 3104 0.041833 AGGACTCCAGCTTCTGCCTA 59.958 55.000 0.00 0.00 40.80 3.93
3116 3125 5.261216 GGGATGACAAAGATTACCTGGAAA 58.739 41.667 0.00 0.00 0.00 3.13
3131 3140 1.487976 GAGATGAAGCTGGGGATGACA 59.512 52.381 0.00 0.00 0.00 3.58
3132 3141 1.767681 AGAGATGAAGCTGGGGATGAC 59.232 52.381 0.00 0.00 0.00 3.06
3134 3143 2.573369 CAAGAGATGAAGCTGGGGATG 58.427 52.381 0.00 0.00 0.00 3.51
3136 3145 0.914644 CCAAGAGATGAAGCTGGGGA 59.085 55.000 0.00 0.00 0.00 4.81
3137 3146 0.106819 CCCAAGAGATGAAGCTGGGG 60.107 60.000 0.00 0.00 0.00 4.96
3139 3148 1.746516 GCTCCCAAGAGATGAAGCTGG 60.747 57.143 0.00 0.00 43.39 4.85
3140 3149 1.209990 AGCTCCCAAGAGATGAAGCTG 59.790 52.381 0.00 0.00 43.39 4.24
3141 3150 1.582389 AGCTCCCAAGAGATGAAGCT 58.418 50.000 0.00 0.00 43.39 3.74
3155 3164 1.826921 CACCATGATGGGCAGCTCC 60.827 63.158 17.04 0.00 43.37 4.70
3156 3165 2.487532 GCACCATGATGGGCAGCTC 61.488 63.158 17.04 0.00 43.37 4.09
3157 3166 2.441532 GCACCATGATGGGCAGCT 60.442 61.111 17.04 0.00 43.37 4.24
3158 3167 2.441532 AGCACCATGATGGGCAGC 60.442 61.111 21.45 18.42 43.37 5.25
3159 3168 0.467474 ATGAGCACCATGATGGGCAG 60.467 55.000 21.45 10.91 43.37 4.85
3160 3169 0.466739 GATGAGCACCATGATGGGCA 60.467 55.000 21.45 12.46 43.37 5.36
3161 3170 0.178998 AGATGAGCACCATGATGGGC 60.179 55.000 17.04 15.62 43.37 5.36
3162 3171 1.142262 TCAGATGAGCACCATGATGGG 59.858 52.381 17.04 6.01 43.37 4.00
3163 3172 2.632987 TCAGATGAGCACCATGATGG 57.367 50.000 10.53 10.53 45.02 3.51
3169 3178 0.103755 GCGAGATCAGATGAGCACCA 59.896 55.000 0.42 0.00 31.88 4.17
3170 3179 0.599728 GGCGAGATCAGATGAGCACC 60.600 60.000 0.42 0.00 31.88 5.01
3171 3180 0.938637 CGGCGAGATCAGATGAGCAC 60.939 60.000 0.00 0.00 31.88 4.40
3174 3183 1.728778 CGCGGCGAGATCAGATGAG 60.729 63.158 19.16 0.00 0.00 2.90
3175 3184 2.332869 CGCGGCGAGATCAGATGA 59.667 61.111 19.16 0.00 0.00 2.92
3176 3185 2.026734 ACGCGGCGAGATCAGATG 59.973 61.111 30.94 0.00 0.00 2.90
3180 3189 1.650314 TAGAACACGCGGCGAGATCA 61.650 55.000 30.94 12.73 0.00 2.92
3190 3199 5.501715 CCATGTCATGTTATTAGAACACGC 58.498 41.667 11.84 0.00 32.37 5.34
3191 3200 5.501715 GCCATGTCATGTTATTAGAACACG 58.498 41.667 11.84 0.00 32.37 4.49
3321 3337 5.019470 TCTGCAACGATCCCATATAGAGAT 58.981 41.667 0.00 0.00 0.00 2.75
3325 3341 4.790765 TCTCTGCAACGATCCCATATAG 57.209 45.455 0.00 0.00 0.00 1.31
3326 3342 5.304357 TCTTTCTCTGCAACGATCCCATATA 59.696 40.000 0.00 0.00 0.00 0.86
3330 3346 1.623311 TCTTTCTCTGCAACGATCCCA 59.377 47.619 0.00 0.00 0.00 4.37
3406 3422 9.624373 ATCATTATATGGTATCTTTCAGGCATC 57.376 33.333 0.00 0.00 0.00 3.91
3449 3465 9.900710 GGCGTCCTTATGATTATAGTATGATAG 57.099 37.037 0.00 0.00 0.00 2.08
3450 3466 9.416284 TGGCGTCCTTATGATTATAGTATGATA 57.584 33.333 0.00 0.00 0.00 2.15
3451 3467 8.306313 TGGCGTCCTTATGATTATAGTATGAT 57.694 34.615 0.00 0.00 0.00 2.45
3452 3468 7.712204 TGGCGTCCTTATGATTATAGTATGA 57.288 36.000 0.00 0.00 0.00 2.15
3453 3469 7.981789 ACATGGCGTCCTTATGATTATAGTATG 59.018 37.037 0.00 0.00 0.00 2.39
3454 3470 8.079211 ACATGGCGTCCTTATGATTATAGTAT 57.921 34.615 0.00 0.00 0.00 2.12
3471 3487 1.600636 CAGGACACCAACATGGCGT 60.601 57.895 0.00 0.00 42.67 5.68
3610 3650 0.169894 GCTTTCCAGCTAGCTGTTGC 59.830 55.000 36.14 28.68 43.51 4.17
3645 3685 1.134401 TGGCGCCTTGAGAGGATAAAG 60.134 52.381 29.70 0.00 46.74 1.85
3646 3686 0.908910 TGGCGCCTTGAGAGGATAAA 59.091 50.000 29.70 0.00 46.74 1.40
3660 3702 4.096732 AGTCAACTTTATTCAATGGCGC 57.903 40.909 0.00 0.00 0.00 6.53
3661 3703 6.021596 GTGTAGTCAACTTTATTCAATGGCG 58.978 40.000 0.00 0.00 0.00 5.69
3677 3719 5.487488 AGTGAGGGGATTAAATGTGTAGTCA 59.513 40.000 0.00 0.00 0.00 3.41
3685 3727 4.599041 TGGTCAAGTGAGGGGATTAAATG 58.401 43.478 0.00 0.00 0.00 2.32
3690 3732 3.117131 AGTTTTGGTCAAGTGAGGGGATT 60.117 43.478 0.00 0.00 0.00 3.01
3723 3765 8.946085 GGAAGAATCAATGTGTTCATAGTGTAA 58.054 33.333 4.59 0.00 33.49 2.41
3812 3858 7.976734 AGATTTACTGGTTCTCTACAAAGATCG 59.023 37.037 0.00 0.00 0.00 3.69
3879 3939 2.124653 TCCGCACAACAACCCGTT 60.125 55.556 0.00 0.00 38.83 4.44
3881 3941 2.184167 AACTCCGCACAACAACCCG 61.184 57.895 0.00 0.00 0.00 5.28
4025 4104 4.634883 CCCATCACAGAGATTTCTCAACTG 59.365 45.833 10.07 2.67 45.21 3.16
4072 4152 4.787598 CAACAAGTTTGGCATAGTGAGAC 58.212 43.478 0.00 0.00 0.00 3.36
4151 4237 0.320374 CCCAGAGTGGTTGCGACTTA 59.680 55.000 3.59 0.00 35.17 2.24
4172 4258 2.380433 ATCATCTCTGCCTGCCTCGC 62.380 60.000 0.00 0.00 0.00 5.03
4176 4262 2.883386 CCTTTTATCATCTCTGCCTGCC 59.117 50.000 0.00 0.00 0.00 4.85
4216 4302 0.036875 CCTCCCTTCTTCCGCACTTT 59.963 55.000 0.00 0.00 0.00 2.66
4218 4304 2.294078 CCCTCCCTTCTTCCGCACT 61.294 63.158 0.00 0.00 0.00 4.40
4223 4315 1.081481 TTTTCCCCCTCCCTTCTTCC 58.919 55.000 0.00 0.00 0.00 3.46
4256 4350 1.603802 CGAGCAGAGGCAAAAGTTTGA 59.396 47.619 7.96 0.00 44.61 2.69


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

AutoCloner maintained by Alex Coulton.