Multiple sequence alignment - TraesCS2B01G259400

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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 TraesCS2B01G259400 chr2B 100.000 3332 0 0 1763 5094 322459780 322463111 0.000000e+00 6154.0
1 TraesCS2B01G259400 chr2B 100.000 1414 0 0 1 1414 322458018 322459431 0.000000e+00 2612.0
2 TraesCS2B01G259400 chr2B 95.597 636 21 3 4159 4787 322645428 322644793 0.000000e+00 1013.0
3 TraesCS2B01G259400 chr2B 95.925 319 11 1 4778 5094 322644831 322644513 2.720000e-142 516.0
4 TraesCS2B01G259400 chr2B 95.349 129 4 1 4037 4165 322645673 322645547 2.400000e-48 204.0
5 TraesCS2B01G259400 chr2B 100.000 41 0 0 4778 4818 322462766 322462806 5.470000e-10 76.8
6 TraesCS2B01G259400 chr2B 100.000 41 0 0 4749 4789 322462795 322462835 5.470000e-10 76.8
7 TraesCS2B01G259400 chr2B 97.368 38 1 0 3017 3054 322460983 322461020 1.180000e-06 65.8
8 TraesCS2B01G259400 chr2B 97.368 38 1 0 2966 3003 322461034 322461071 1.180000e-06 65.8
9 TraesCS2B01G259400 chr2A 95.628 1258 38 9 1763 3003 311156103 311157360 0.000000e+00 2002.0
10 TraesCS2B01G259400 chr2A 97.986 1142 23 0 3017 4158 311157323 311158464 0.000000e+00 1982.0
11 TraesCS2B01G259400 chr2A 95.141 782 30 7 620 1395 311155018 311155797 0.000000e+00 1227.0
12 TraesCS2B01G259400 chr2A 90.166 661 29 7 4162 4786 311158498 311159158 0.000000e+00 828.0
13 TraesCS2B01G259400 chr2D 97.986 1142 23 0 3017 4158 250205399 250206540 0.000000e+00 1982.0
14 TraesCS2B01G259400 chr2D 95.579 1244 39 5 1776 3003 250204193 250205436 0.000000e+00 1978.0
15 TraesCS2B01G259400 chr2D 95.125 800 33 5 620 1414 250203360 250204158 0.000000e+00 1256.0
16 TraesCS2B01G259400 chr2D 95.079 630 26 3 4162 4786 250206574 250207203 0.000000e+00 987.0
17 TraesCS2B01G259400 chr6B 95.016 622 23 3 2 619 182317759 182317142 0.000000e+00 970.0
18 TraesCS2B01G259400 chr4A 94.737 627 22 6 1 620 727271723 727271101 0.000000e+00 965.0
19 TraesCS2B01G259400 chr1A 76.364 605 130 9 21 619 320152120 320151523 3.830000e-81 313.0


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 TraesCS2B01G259400 chr2B 322458018 322463111 5093 False 1508.533333 6154 99.122667 1 5094 6 chr2B.!!$F1 5093
1 TraesCS2B01G259400 chr2B 322644513 322645673 1160 True 577.666667 1013 95.623667 4037 5094 3 chr2B.!!$R1 1057
2 TraesCS2B01G259400 chr2A 311155018 311159158 4140 False 1509.750000 2002 94.730250 620 4786 4 chr2A.!!$F1 4166
3 TraesCS2B01G259400 chr2D 250203360 250207203 3843 False 1550.750000 1982 95.942250 620 4786 4 chr2D.!!$F1 4166
4 TraesCS2B01G259400 chr6B 182317142 182317759 617 True 970.000000 970 95.016000 2 619 1 chr6B.!!$R1 617
5 TraesCS2B01G259400 chr4A 727271101 727271723 622 True 965.000000 965 94.737000 1 620 1 chr4A.!!$R1 619
6 TraesCS2B01G259400 chr1A 320151523 320152120 597 True 313.000000 313 76.364000 21 619 1 chr1A.!!$R1 598

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
226 228 1.065854 GGTAGCTGCTCAAGTGGTCAT 60.066 52.381 4.91 0.00 0.0 3.06 F
1195 1204 1.141591 GATCATTTTGGCGGCGCTTG 61.142 55.000 32.30 19.73 0.0 4.01 F
2995 3026 0.108585 TCCAGTTCTGACCTGTTGCC 59.891 55.000 1.45 0.00 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1361 0.680618 TGGGCAGTGCTTTTGATTGG 59.319 50.0 16.11 0.00 0.00 3.16 R
3027 3058 0.108585 GGCAACAGGTCAGAACTGGA 59.891 55.0 20.03 0.00 40.23 3.86 R
4894 5085 0.168128 GCCCAGAATAACGTGCACAC 59.832 55.0 18.64 0.62 0.00 3.82 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
54 55 2.564947 ACAAAGTGCAGGGTTTTCACAA 59.435 40.909 0.00 0.00 33.44 3.33
90 91 8.626526 GGAAAGTGGAAAGACAAAATACTACAA 58.373 33.333 0.00 0.00 0.00 2.41
126 127 7.596248 TCTTCATACAAATGCTTGAAGAAAAGC 59.404 33.333 18.63 2.01 46.61 3.51
183 185 4.273318 AGGAGCAAAATTATCGCCTCTTT 58.727 39.130 0.00 0.00 0.00 2.52
226 228 1.065854 GGTAGCTGCTCAAGTGGTCAT 60.066 52.381 4.91 0.00 0.00 3.06
399 401 3.811083 ACCGTTTGTTACATTCACAGGA 58.189 40.909 0.00 0.00 0.00 3.86
410 412 8.100791 TGTTACATTCACAGGAAGCTTAATAGT 58.899 33.333 0.00 0.00 36.25 2.12
500 505 5.674052 ACAAGTCTCACTTAGCTGATCAT 57.326 39.130 0.00 0.00 36.03 2.45
509 514 5.366477 TCACTTAGCTGATCATTGTCCCATA 59.634 40.000 0.00 0.00 0.00 2.74
519 524 5.497464 TCATTGTCCCATACTGTTGAAGA 57.503 39.130 0.00 0.00 0.00 2.87
610 616 1.302993 GGGCGCCACCTCTTTGTTA 60.303 57.895 30.85 0.00 39.10 2.41
640 646 8.601845 AAAATGTTTGCTGGAAACCTATAAAC 57.398 30.769 19.86 0.00 43.04 2.01
662 668 5.360591 ACCGGATGTTCTCAGATAACATTC 58.639 41.667 9.46 11.44 45.24 2.67
667 673 7.710907 CGGATGTTCTCAGATAACATTCCTTAA 59.289 37.037 13.81 0.00 45.24 1.85
711 717 4.724697 CGTGCTTTCCGTGCAGCG 62.725 66.667 0.00 0.00 41.41 5.18
753 759 7.385752 GCAGAAGATCCTGATATTTTCTCTCTG 59.614 40.741 3.41 0.00 36.29 3.35
816 822 4.869440 CGCAGCCTGAGAGAGCCG 62.869 72.222 0.00 0.00 0.00 5.52
884 891 1.377725 CTTTCCATGGCGCTCAGGT 60.378 57.895 6.96 0.00 0.00 4.00
885 892 1.651240 CTTTCCATGGCGCTCAGGTG 61.651 60.000 6.96 0.00 0.00 4.00
894 903 1.153647 CGCTCAGGTGGCGTGATTA 60.154 57.895 0.00 0.00 46.37 1.75
905 914 2.100031 CGTGATTAGCGCTGCACCA 61.100 57.895 22.90 9.83 0.00 4.17
918 927 2.981560 GCACCACGGCACAGATTGG 61.982 63.158 0.00 0.00 35.06 3.16
928 937 2.356535 GGCACAGATTGGTGAGGATCTT 60.357 50.000 0.00 0.00 41.32 2.40
1139 1148 3.632145 GCCATATTCCTCCATTCGTTTGT 59.368 43.478 0.00 0.00 0.00 2.83
1140 1149 4.097892 GCCATATTCCTCCATTCGTTTGTT 59.902 41.667 0.00 0.00 0.00 2.83
1195 1204 1.141591 GATCATTTTGGCGGCGCTTG 61.142 55.000 32.30 19.73 0.00 4.01
1222 1232 9.880157 GTCTTTAGTTTTGTATATAGGGTGACA 57.120 33.333 0.00 0.00 0.00 3.58
1259 1269 6.731467 TCATCCTTAAGCTGGTTTTTCCTAT 58.269 36.000 0.00 0.00 37.07 2.57
1281 1291 9.883142 CCTATTTCTCTACAGAGTTTCTTCATT 57.117 33.333 6.16 0.00 42.60 2.57
1302 1312 8.565896 TCATTTTAACTCATCTGTGCTGTAAT 57.434 30.769 0.00 0.00 0.00 1.89
1318 1328 4.786609 GCTGTAATTCCGCTGATTAGTTGC 60.787 45.833 0.00 0.00 0.00 4.17
1357 1367 8.995027 ATTAAAGAGCCATATTGTACCAATCA 57.005 30.769 0.00 0.00 0.00 2.57
1361 1371 7.338800 AGAGCCATATTGTACCAATCAAAAG 57.661 36.000 0.00 0.00 0.00 2.27
1797 1812 7.611213 AGTATTATGTTTGGTTAGCTGTGTC 57.389 36.000 0.00 0.00 0.00 3.67
1992 2007 7.940688 ACCATCTCATTTGCAAGTATGATGATA 59.059 33.333 24.49 14.29 33.92 2.15
2303 2318 4.852134 TGAAGTAACGGTACTGTTAGCA 57.148 40.909 24.45 19.28 39.79 3.49
2317 2332 5.954335 ACTGTTAGCAAATTTGGTAGATGC 58.046 37.500 24.55 17.59 41.53 3.91
2376 2392 5.730550 CATGGGTAGTGTTTAAGCTGACTA 58.269 41.667 0.00 0.00 0.00 2.59
2442 2466 5.738619 TTCTACAGAGCTAAACATGACCA 57.261 39.130 0.00 0.00 0.00 4.02
2529 2554 1.965643 TGAAAGGCAGATGCAGCTTTT 59.034 42.857 0.00 3.67 42.85 2.27
2560 2585 9.575868 TTGTCCTTGGTTAGTGATTTATTACAA 57.424 29.630 0.00 0.00 0.00 2.41
2572 2597 9.182214 AGTGATTTATTACAAGTGATGCTTCAT 57.818 29.630 5.49 0.00 34.69 2.57
2607 2632 6.533723 TGTGTGCTATTTTATTCCTACAGTCG 59.466 38.462 0.00 0.00 0.00 4.18
2646 2671 2.751806 CTCAGTCTTCAAATGCCCCTTC 59.248 50.000 0.00 0.00 0.00 3.46
2810 2841 5.751028 TGTAAAGTTATTGTTTTGTGCCTGC 59.249 36.000 0.00 0.00 0.00 4.85
2869 2900 5.497464 TGGATGTGGAGTTTACTCATTCA 57.503 39.130 11.67 7.52 44.60 2.57
2981 3012 1.141657 ACAGTGTCACATGCTTCCAGT 59.858 47.619 5.62 0.00 0.00 4.00
2982 3013 2.224606 CAGTGTCACATGCTTCCAGTT 58.775 47.619 5.62 0.00 0.00 3.16
2983 3014 2.225019 CAGTGTCACATGCTTCCAGTTC 59.775 50.000 5.62 0.00 0.00 3.01
2984 3015 2.105477 AGTGTCACATGCTTCCAGTTCT 59.895 45.455 5.62 0.00 0.00 3.01
2985 3016 2.225019 GTGTCACATGCTTCCAGTTCTG 59.775 50.000 0.00 0.00 0.00 3.02
2986 3017 2.104622 TGTCACATGCTTCCAGTTCTGA 59.895 45.455 1.00 0.00 0.00 3.27
2987 3018 2.481952 GTCACATGCTTCCAGTTCTGAC 59.518 50.000 1.00 0.00 0.00 3.51
2988 3019 1.808945 CACATGCTTCCAGTTCTGACC 59.191 52.381 1.00 0.00 0.00 4.02
2989 3020 1.701847 ACATGCTTCCAGTTCTGACCT 59.298 47.619 1.00 0.00 0.00 3.85
2990 3021 2.082231 CATGCTTCCAGTTCTGACCTG 58.918 52.381 1.00 0.00 0.00 4.00
2991 3022 1.131638 TGCTTCCAGTTCTGACCTGT 58.868 50.000 1.45 0.00 0.00 4.00
2992 3023 1.490490 TGCTTCCAGTTCTGACCTGTT 59.510 47.619 1.45 0.00 0.00 3.16
2993 3024 1.876156 GCTTCCAGTTCTGACCTGTTG 59.124 52.381 1.45 0.00 0.00 3.33
2994 3025 1.876156 CTTCCAGTTCTGACCTGTTGC 59.124 52.381 1.45 0.00 0.00 4.17
2995 3026 0.108585 TCCAGTTCTGACCTGTTGCC 59.891 55.000 1.45 0.00 0.00 4.52
2996 3027 0.890996 CCAGTTCTGACCTGTTGCCC 60.891 60.000 1.45 0.00 0.00 5.36
2997 3028 0.179020 CAGTTCTGACCTGTTGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
2998 3029 0.773644 AGTTCTGACCTGTTGCCCAT 59.226 50.000 0.00 0.00 0.00 4.00
2999 3030 0.883833 GTTCTGACCTGTTGCCCATG 59.116 55.000 0.00 0.00 0.00 3.66
3000 3031 0.251297 TTCTGACCTGTTGCCCATGG 60.251 55.000 4.14 4.14 0.00 3.66
3001 3032 1.075482 CTGACCTGTTGCCCATGGT 59.925 57.895 11.73 0.00 35.23 3.55
3002 3033 0.327924 CTGACCTGTTGCCCATGGTA 59.672 55.000 11.73 0.00 32.30 3.25
3003 3034 0.774276 TGACCTGTTGCCCATGGTAA 59.226 50.000 11.73 2.56 32.30 2.85
3004 3035 1.173913 GACCTGTTGCCCATGGTAAC 58.826 55.000 11.73 15.44 46.05 2.50
3005 3036 0.251608 ACCTGTTGCCCATGGTAACC 60.252 55.000 20.30 4.68 45.44 2.85
3006 3037 0.251564 CCTGTTGCCCATGGTAACCA 60.252 55.000 20.30 8.39 45.44 3.67
3007 3038 1.176527 CTGTTGCCCATGGTAACCAG 58.823 55.000 20.30 13.06 45.44 4.00
3008 3039 0.480690 TGTTGCCCATGGTAACCAGT 59.519 50.000 20.30 0.00 45.44 4.00
3009 3040 1.133325 TGTTGCCCATGGTAACCAGTT 60.133 47.619 20.30 0.00 45.44 3.16
3010 3041 1.544246 GTTGCCCATGGTAACCAGTTC 59.456 52.381 11.73 0.00 41.34 3.01
3011 3042 1.072266 TGCCCATGGTAACCAGTTCT 58.928 50.000 11.73 0.00 36.75 3.01
3012 3043 1.271871 TGCCCATGGTAACCAGTTCTG 60.272 52.381 11.73 0.00 36.75 3.02
3013 3044 1.004277 GCCCATGGTAACCAGTTCTGA 59.996 52.381 11.73 0.00 36.75 3.27
3014 3045 2.711542 CCCATGGTAACCAGTTCTGAC 58.288 52.381 11.73 0.00 36.75 3.51
3015 3046 2.618045 CCCATGGTAACCAGTTCTGACC 60.618 54.545 11.73 2.32 36.75 4.02
3016 3047 2.305927 CCATGGTAACCAGTTCTGACCT 59.694 50.000 2.57 0.00 36.75 3.85
3017 3048 3.338249 CATGGTAACCAGTTCTGACCTG 58.662 50.000 1.00 0.00 36.75 4.00
3018 3049 2.404559 TGGTAACCAGTTCTGACCTGT 58.595 47.619 1.45 0.00 0.00 4.00
3019 3050 2.367567 TGGTAACCAGTTCTGACCTGTC 59.632 50.000 1.45 0.00 0.00 3.51
3020 3051 2.367567 GGTAACCAGTTCTGACCTGTCA 59.632 50.000 1.45 0.00 38.06 3.58
3021 3052 2.622064 AACCAGTTCTGACCTGTCAC 57.378 50.000 1.45 0.00 35.46 3.67
3022 3053 1.496060 ACCAGTTCTGACCTGTCACA 58.504 50.000 1.45 0.00 35.46 3.58
3023 3054 2.050144 ACCAGTTCTGACCTGTCACAT 58.950 47.619 1.45 0.00 35.46 3.21
3024 3055 2.224378 ACCAGTTCTGACCTGTCACATG 60.224 50.000 1.45 0.00 35.46 3.21
3025 3056 1.802960 CAGTTCTGACCTGTCACATGC 59.197 52.381 0.00 0.00 35.46 4.06
3026 3057 1.696336 AGTTCTGACCTGTCACATGCT 59.304 47.619 0.00 0.00 35.46 3.79
3027 3058 2.105477 AGTTCTGACCTGTCACATGCTT 59.895 45.455 0.00 0.00 35.46 3.91
3028 3059 2.462456 TCTGACCTGTCACATGCTTC 57.538 50.000 0.00 0.00 35.46 3.86
3029 3060 1.002430 TCTGACCTGTCACATGCTTCC 59.998 52.381 0.00 0.00 35.46 3.46
3030 3061 0.764271 TGACCTGTCACATGCTTCCA 59.236 50.000 0.00 0.00 34.14 3.53
3031 3062 1.271001 TGACCTGTCACATGCTTCCAG 60.271 52.381 0.00 0.00 34.14 3.86
3094 3125 4.141482 TGTTGGGGCAGATAAAGGAGATAC 60.141 45.833 0.00 0.00 0.00 2.24
3220 3251 1.141053 GTCGTCATTTCCCTATGGCCT 59.859 52.381 3.32 0.00 0.00 5.19
3556 3587 1.022982 ATCGTGGTGCAGCTGACATG 61.023 55.000 20.43 17.26 0.00 3.21
3637 3668 5.429762 TGAATGTCCTTATTCTGATGGAGGT 59.570 40.000 0.00 0.00 37.81 3.85
3729 3760 5.856839 GAGGATCAGACCGTTTTGGTAATCA 60.857 44.000 0.00 0.00 44.29 2.57
3840 3871 4.855105 TGGCGACAGATATGGTGC 57.145 55.556 0.00 0.00 35.01 5.01
3932 3963 5.820947 GGTGGAAGTTATTACCGTGATGAAT 59.179 40.000 0.00 0.00 0.00 2.57
3940 3971 7.506261 AGTTATTACCGTGATGAATCTAGAGGT 59.494 37.037 0.00 0.00 34.78 3.85
4116 4147 1.280421 GAAGGTCACCTTGGAGCAGAT 59.720 52.381 15.92 0.00 44.82 2.90
4446 4617 3.129871 GACCTGCTTATCTGATGTCAGC 58.870 50.000 5.14 5.97 43.46 4.26
4455 4626 6.092670 GCTTATCTGATGTCAGCTTTGTGTTA 59.907 38.462 5.14 0.00 43.46 2.41
4463 4634 6.449635 TGTCAGCTTTGTGTTAAAATCTGT 57.550 33.333 0.00 0.00 35.66 3.41
4513 4684 7.036829 TGGATGTGCATTTTCAAGATTATGTG 58.963 34.615 0.00 0.00 0.00 3.21
4649 4838 3.006940 TCAACTGGTAAATGACGGATGC 58.993 45.455 0.00 0.00 0.00 3.91
4786 4977 3.126831 CGAGATAGCATCAACCAAGTCC 58.873 50.000 0.00 0.00 0.00 3.85
4787 4978 3.430790 CGAGATAGCATCAACCAAGTCCA 60.431 47.826 0.00 0.00 0.00 4.02
4788 4979 4.712476 GAGATAGCATCAACCAAGTCCAT 58.288 43.478 0.00 0.00 0.00 3.41
4789 4980 5.121380 AGATAGCATCAACCAAGTCCATT 57.879 39.130 0.00 0.00 0.00 3.16
4790 4981 5.513233 AGATAGCATCAACCAAGTCCATTT 58.487 37.500 0.00 0.00 0.00 2.32
4791 4982 3.947910 AGCATCAACCAAGTCCATTTG 57.052 42.857 0.00 0.00 0.00 2.32
4792 4983 3.233507 AGCATCAACCAAGTCCATTTGT 58.766 40.909 0.00 0.00 0.00 2.83
4793 4984 3.006110 AGCATCAACCAAGTCCATTTGTG 59.994 43.478 0.00 0.00 0.00 3.33
4794 4985 3.319755 CATCAACCAAGTCCATTTGTGC 58.680 45.455 0.00 0.00 0.00 4.57
4795 4986 1.336440 TCAACCAAGTCCATTTGTGCG 59.664 47.619 0.00 0.00 0.00 5.34
4796 4987 1.336440 CAACCAAGTCCATTTGTGCGA 59.664 47.619 0.00 0.00 0.00 5.10
4797 4988 1.238439 ACCAAGTCCATTTGTGCGAG 58.762 50.000 0.00 0.00 0.00 5.03
4798 4989 1.202758 ACCAAGTCCATTTGTGCGAGA 60.203 47.619 0.00 0.00 0.00 4.04
4799 4990 2.086869 CCAAGTCCATTTGTGCGAGAT 58.913 47.619 0.00 0.00 0.00 2.75
4800 4991 3.270027 CCAAGTCCATTTGTGCGAGATA 58.730 45.455 0.00 0.00 0.00 1.98
4801 4992 3.310774 CCAAGTCCATTTGTGCGAGATAG 59.689 47.826 0.00 0.00 0.00 2.08
4802 4993 2.555199 AGTCCATTTGTGCGAGATAGC 58.445 47.619 0.00 0.00 37.71 2.97
4803 4994 2.093500 AGTCCATTTGTGCGAGATAGCA 60.093 45.455 0.00 0.00 45.96 3.49
4816 5007 3.430790 CGAGATAGCATCAACCAAGTCCA 60.431 47.826 0.00 0.00 0.00 4.02
4845 5036 3.771479 TGATGCAGGGTGCCTATATAGAG 59.229 47.826 11.53 2.92 44.23 2.43
4888 5079 1.587088 CGGATTTTCAGCGCATGGC 60.587 57.895 11.47 0.00 44.05 4.40
4908 5099 1.126113 CGTCCAGTGTGCACGTTATTC 59.874 52.381 13.13 0.75 36.20 1.75
4945 5138 2.120232 CTTCGTGATCGTATCCTGTGC 58.880 52.381 0.00 0.00 38.33 4.57
4983 5176 4.959839 TGCACAGTCTACCTTGGATATACA 59.040 41.667 0.00 0.00 0.00 2.29
5060 5253 1.877443 ACGAAAAACCGAATGAGGGTG 59.123 47.619 0.00 0.00 37.96 4.61
5075 5268 3.322191 AGGGTGCCCTTTTACAGAAAA 57.678 42.857 3.45 0.00 45.70 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.344679 TCTTTCCACTTTCCATGTTGCATT 59.655 37.500 0.00 0.00 0.00 3.56
90 91 7.002879 AGCATTTGTATGAAGATTCCTATGCT 58.997 34.615 0.00 0.00 33.37 3.79
123 124 3.659183 ATATTGACCTCCTGCTTGCTT 57.341 42.857 0.00 0.00 0.00 3.91
124 125 3.659183 AATATTGACCTCCTGCTTGCT 57.341 42.857 0.00 0.00 0.00 3.91
125 126 4.455606 ACTAATATTGACCTCCTGCTTGC 58.544 43.478 0.00 0.00 0.00 4.01
126 127 8.367911 TGTATACTAATATTGACCTCCTGCTTG 58.632 37.037 4.17 0.00 0.00 4.01
183 185 0.830648 AGTGCCATAGCTTCCGCTTA 59.169 50.000 0.00 0.00 46.47 3.09
226 228 5.375773 TGATGTCTCCTGTTGTGATTTCAA 58.624 37.500 0.00 0.00 0.00 2.69
281 283 2.476852 TATCCCTTGCTTGTGCGGCA 62.477 55.000 0.00 0.00 43.34 5.69
410 412 4.916041 AGCTGCATTATTATGAGCCCTA 57.084 40.909 1.02 0.00 36.46 3.53
509 514 3.327757 TCAGGTTGCCTATCTTCAACAGT 59.672 43.478 7.31 0.00 43.06 3.55
619 625 4.216687 CGGTTTATAGGTTTCCAGCAAACA 59.783 41.667 1.18 0.00 45.66 2.83
620 626 4.380128 CCGGTTTATAGGTTTCCAGCAAAC 60.380 45.833 0.00 0.00 43.43 2.93
621 627 3.759618 CCGGTTTATAGGTTTCCAGCAAA 59.240 43.478 0.00 0.00 0.00 3.68
623 629 2.572556 TCCGGTTTATAGGTTTCCAGCA 59.427 45.455 0.00 0.00 0.00 4.41
624 630 3.271055 TCCGGTTTATAGGTTTCCAGC 57.729 47.619 0.00 0.00 0.00 4.85
625 631 4.777463 ACATCCGGTTTATAGGTTTCCAG 58.223 43.478 0.00 0.00 0.00 3.86
626 632 4.847990 ACATCCGGTTTATAGGTTTCCA 57.152 40.909 0.00 0.00 0.00 3.53
633 639 8.141909 TGTTATCTGAGAACATCCGGTTTATAG 58.858 37.037 13.38 0.00 40.63 1.31
635 641 6.884832 TGTTATCTGAGAACATCCGGTTTAT 58.115 36.000 13.38 0.00 40.63 1.40
636 642 6.288941 TGTTATCTGAGAACATCCGGTTTA 57.711 37.500 13.38 0.00 40.63 2.01
638 644 4.819105 TGTTATCTGAGAACATCCGGTT 57.181 40.909 13.38 0.00 44.10 4.44
640 646 4.752101 GGAATGTTATCTGAGAACATCCGG 59.248 45.833 25.56 0.00 44.75 5.14
662 668 8.311109 TGGCTTTATTTTAGCTTCCTTTTAAGG 58.689 33.333 1.95 1.95 41.72 2.69
667 673 7.039082 TGTCATGGCTTTATTTTAGCTTCCTTT 60.039 33.333 0.00 0.00 38.67 3.11
711 717 2.135139 TCTGCATGTATTCCGAATCGC 58.865 47.619 0.00 0.00 0.00 4.58
753 759 0.749649 AGGGATGAGATGACACGAGC 59.250 55.000 0.00 0.00 0.00 5.03
806 812 0.331954 ACCTAAGGACGGCTCTCTCA 59.668 55.000 0.00 0.00 0.00 3.27
816 822 0.952010 TTGCGCGGAAACCTAAGGAC 60.952 55.000 11.75 0.00 0.00 3.85
900 909 2.562912 CAATCTGTGCCGTGGTGC 59.437 61.111 0.00 0.00 0.00 5.01
905 914 1.003355 CCTCACCAATCTGTGCCGT 60.003 57.895 0.00 0.00 36.17 5.68
918 927 6.310197 CGAAAAAGTCAATCAAGATCCTCAC 58.690 40.000 0.00 0.00 0.00 3.51
928 937 5.766150 AATCACACCGAAAAAGTCAATCA 57.234 34.783 0.00 0.00 0.00 2.57
1139 1148 1.193650 GACGAGCACGCACAATACAAA 59.806 47.619 2.62 0.00 43.96 2.83
1140 1149 0.787787 GACGAGCACGCACAATACAA 59.212 50.000 2.62 0.00 43.96 2.41
1195 1204 9.322773 GTCACCCTATATACAAAACTAAAGACC 57.677 37.037 0.00 0.00 0.00 3.85
1281 1291 6.092122 CGGAATTACAGCACAGATGAGTTAAA 59.908 38.462 0.00 0.00 0.00 1.52
1302 1312 2.881513 TGTTTGCAACTAATCAGCGGAA 59.118 40.909 0.00 0.00 0.00 4.30
1351 1361 0.680618 TGGGCAGTGCTTTTGATTGG 59.319 50.000 16.11 0.00 0.00 3.16
1357 1367 4.082026 GTCTTATTGATGGGCAGTGCTTTT 60.082 41.667 16.11 0.00 0.00 2.27
1361 1371 1.331756 CGTCTTATTGATGGGCAGTGC 59.668 52.381 6.55 6.55 0.00 4.40
1797 1812 5.551760 AACAAGCCATCAAAGTTCTATCG 57.448 39.130 0.00 0.00 0.00 2.92
1840 1855 5.874810 ACGTAACATAACTGAATCATGCACT 59.125 36.000 0.00 0.00 0.00 4.40
2292 2307 6.967199 GCATCTACCAAATTTGCTAACAGTAC 59.033 38.462 12.92 0.00 0.00 2.73
2303 2318 4.041444 TGCCCAAAAGCATCTACCAAATTT 59.959 37.500 0.00 0.00 38.00 1.82
2317 2332 0.319297 GCACTGCTTCTGCCCAAAAG 60.319 55.000 0.00 0.00 38.71 2.27
2356 2372 6.171213 ACATTAGTCAGCTTAAACACTACCC 58.829 40.000 0.00 0.00 0.00 3.69
2389 2413 6.002704 AGCCATGGCAATGAAAATTTGTTTA 58.997 32.000 37.18 0.00 44.88 2.01
2400 2424 4.897076 AGAATTGATTAGCCATGGCAATGA 59.103 37.500 37.18 23.95 44.88 2.57
2442 2466 8.065473 TGCATTAATTTCATATCCAACACTGT 57.935 30.769 0.00 0.00 0.00 3.55
2529 2554 6.783708 AATCACTAACCAAGGACAACAAAA 57.216 33.333 0.00 0.00 0.00 2.44
2560 2585 4.815533 ACACTCACTATGAAGCATCACT 57.184 40.909 0.00 0.00 38.69 3.41
2572 2597 8.615878 AATAAAATAGCACACAACACTCACTA 57.384 30.769 0.00 0.00 0.00 2.74
2646 2671 3.023832 GGTATGTGTCCATTTGAAGGGG 58.976 50.000 0.00 0.00 32.29 4.79
2810 2841 1.531149 CAGTTACTTTGGTCGGTGCTG 59.469 52.381 0.00 0.00 0.00 4.41
2817 2848 1.270678 ACGAGGCCAGTTACTTTGGTC 60.271 52.381 5.01 0.00 40.67 4.02
2934 2965 3.194116 ACAACAATGCCATCAATGAGTCC 59.806 43.478 0.00 0.00 0.00 3.85
2981 3012 0.251297 CCATGGGCAACAGGTCAGAA 60.251 55.000 2.85 0.00 39.74 3.02
2982 3013 1.379916 CCATGGGCAACAGGTCAGA 59.620 57.895 2.85 0.00 39.74 3.27
2983 3014 0.327924 TACCATGGGCAACAGGTCAG 59.672 55.000 18.09 0.00 34.11 3.51
2984 3015 0.774276 TTACCATGGGCAACAGGTCA 59.226 50.000 18.09 0.00 34.11 4.02
2985 3016 1.173913 GTTACCATGGGCAACAGGTC 58.826 55.000 18.09 0.00 34.11 3.85
2986 3017 0.251608 GGTTACCATGGGCAACAGGT 60.252 55.000 24.65 3.61 35.61 4.00
2987 3018 0.251564 TGGTTACCATGGGCAACAGG 60.252 55.000 24.65 0.00 39.74 4.00
2988 3019 1.176527 CTGGTTACCATGGGCAACAG 58.823 55.000 24.65 20.01 31.79 3.16
2989 3020 0.480690 ACTGGTTACCATGGGCAACA 59.519 50.000 24.65 15.67 31.79 3.33
2990 3021 1.544246 GAACTGGTTACCATGGGCAAC 59.456 52.381 18.09 18.37 30.82 4.17
2991 3022 1.427368 AGAACTGGTTACCATGGGCAA 59.573 47.619 18.09 6.83 30.82 4.52
2992 3023 1.072266 AGAACTGGTTACCATGGGCA 58.928 50.000 18.09 0.00 30.82 5.36
2993 3024 1.004277 TCAGAACTGGTTACCATGGGC 59.996 52.381 18.09 5.67 30.82 5.36
2994 3025 2.618045 GGTCAGAACTGGTTACCATGGG 60.618 54.545 18.09 0.00 30.82 4.00
2995 3026 2.305927 AGGTCAGAACTGGTTACCATGG 59.694 50.000 11.19 11.19 30.82 3.66
2996 3027 3.244561 ACAGGTCAGAACTGGTTACCATG 60.245 47.826 20.03 0.00 40.23 3.66
2997 3028 2.979678 ACAGGTCAGAACTGGTTACCAT 59.020 45.455 20.03 0.00 40.23 3.55
2998 3029 2.367567 GACAGGTCAGAACTGGTTACCA 59.632 50.000 20.03 3.29 40.23 3.25
2999 3030 2.367567 TGACAGGTCAGAACTGGTTACC 59.632 50.000 20.03 0.00 40.23 2.85
3000 3031 3.181469 TGTGACAGGTCAGAACTGGTTAC 60.181 47.826 20.03 14.51 40.75 2.50
3001 3032 3.035363 TGTGACAGGTCAGAACTGGTTA 58.965 45.455 20.03 2.58 40.75 2.85
3002 3033 1.837439 TGTGACAGGTCAGAACTGGTT 59.163 47.619 20.03 0.00 40.75 3.67
3003 3034 1.496060 TGTGACAGGTCAGAACTGGT 58.504 50.000 20.03 5.39 40.75 4.00
3004 3035 2.420642 CATGTGACAGGTCAGAACTGG 58.579 52.381 20.03 2.06 40.75 4.00
3005 3036 1.802960 GCATGTGACAGGTCAGAACTG 59.197 52.381 14.44 14.44 40.75 3.16
3006 3037 1.696336 AGCATGTGACAGGTCAGAACT 59.304 47.619 1.66 1.43 40.75 3.01
3007 3038 2.175878 AGCATGTGACAGGTCAGAAC 57.824 50.000 1.66 0.00 40.75 3.01
3008 3039 2.550855 GGAAGCATGTGACAGGTCAGAA 60.551 50.000 1.66 0.00 40.75 3.02
3009 3040 1.002430 GGAAGCATGTGACAGGTCAGA 59.998 52.381 1.66 1.59 40.75 3.27
3010 3041 1.271001 TGGAAGCATGTGACAGGTCAG 60.271 52.381 1.66 0.00 40.75 3.51
3011 3042 0.764271 TGGAAGCATGTGACAGGTCA 59.236 50.000 0.00 0.00 37.24 4.02
3012 3043 1.271054 ACTGGAAGCATGTGACAGGTC 60.271 52.381 0.00 0.00 37.60 3.85
3013 3044 0.767375 ACTGGAAGCATGTGACAGGT 59.233 50.000 0.00 0.00 37.60 4.00
3014 3045 1.808945 GAACTGGAAGCATGTGACAGG 59.191 52.381 0.00 0.00 37.60 4.00
3015 3046 2.483106 CAGAACTGGAAGCATGTGACAG 59.517 50.000 0.00 1.09 37.60 3.51
3016 3047 2.104622 TCAGAACTGGAAGCATGTGACA 59.895 45.455 1.93 0.00 37.60 3.58
3017 3048 2.481952 GTCAGAACTGGAAGCATGTGAC 59.518 50.000 1.93 0.00 39.14 3.67
3018 3049 2.550855 GGTCAGAACTGGAAGCATGTGA 60.551 50.000 1.93 0.00 37.60 3.58
3019 3050 1.808945 GGTCAGAACTGGAAGCATGTG 59.191 52.381 1.93 0.00 37.60 3.21
3020 3051 1.701847 AGGTCAGAACTGGAAGCATGT 59.298 47.619 1.93 0.00 37.60 3.21
3021 3052 2.082231 CAGGTCAGAACTGGAAGCATG 58.918 52.381 7.70 0.00 37.60 4.06
3022 3053 1.701847 ACAGGTCAGAACTGGAAGCAT 59.298 47.619 20.03 0.00 40.23 3.79
3023 3054 1.131638 ACAGGTCAGAACTGGAAGCA 58.868 50.000 20.03 0.00 40.23 3.91
3024 3055 1.876156 CAACAGGTCAGAACTGGAAGC 59.124 52.381 20.03 0.00 40.23 3.86
3025 3056 1.876156 GCAACAGGTCAGAACTGGAAG 59.124 52.381 20.03 9.68 40.23 3.46
3026 3057 1.476833 GGCAACAGGTCAGAACTGGAA 60.477 52.381 20.03 0.00 40.23 3.53
3027 3058 0.108585 GGCAACAGGTCAGAACTGGA 59.891 55.000 20.03 0.00 40.23 3.86
3028 3059 0.890996 GGGCAACAGGTCAGAACTGG 60.891 60.000 20.03 3.92 40.23 4.00
3029 3060 0.179020 TGGGCAACAGGTCAGAACTG 60.179 55.000 14.44 14.44 41.64 3.16
3030 3061 0.773644 ATGGGCAACAGGTCAGAACT 59.226 50.000 0.00 0.00 39.74 3.01
3031 3062 2.290323 ACTATGGGCAACAGGTCAGAAC 60.290 50.000 0.00 0.00 39.74 3.01
3637 3668 1.063114 GGAGAGTACCTTCCAGGCCTA 60.063 57.143 3.98 0.00 39.63 3.93
3729 3760 7.386025 CACCATCATAACGATCATCAACATAGT 59.614 37.037 0.00 0.00 29.21 2.12
3840 3871 2.804527 CCTGATGCATAACGATCACCAG 59.195 50.000 0.00 0.00 0.00 4.00
3877 3908 5.516415 CCCTCCATCTCTCTCATAGCTTCTA 60.516 48.000 0.00 0.00 0.00 2.10
3932 3963 4.543689 CCATAACCACCAGTACCTCTAGA 58.456 47.826 0.00 0.00 0.00 2.43
3940 3971 0.916086 CCCTGCCATAACCACCAGTA 59.084 55.000 0.00 0.00 0.00 2.74
4116 4147 9.314321 GAACTGAATCTTGTATTAAATCTCCGA 57.686 33.333 0.00 0.00 0.00 4.55
4355 4526 0.584396 GACAATGCCGACAACACGAA 59.416 50.000 0.00 0.00 35.09 3.85
4455 4626 7.322664 CAGTGCCAATATTACCAACAGATTTT 58.677 34.615 0.00 0.00 0.00 1.82
4463 4634 3.425659 TGTGCAGTGCCAATATTACCAA 58.574 40.909 13.72 0.00 0.00 3.67
4649 4838 9.799106 ATTATACCAGTAGAATTTCCCTGATTG 57.201 33.333 12.79 2.78 0.00 2.67
4786 4977 4.277258 GTTGATGCTATCTCGCACAAATG 58.723 43.478 0.00 0.00 43.61 2.32
4787 4978 3.313526 GGTTGATGCTATCTCGCACAAAT 59.686 43.478 0.00 0.00 43.61 2.32
4788 4979 2.677836 GGTTGATGCTATCTCGCACAAA 59.322 45.455 0.00 0.00 43.61 2.83
4789 4980 2.279741 GGTTGATGCTATCTCGCACAA 58.720 47.619 0.00 0.00 43.61 3.33
4790 4981 1.206849 TGGTTGATGCTATCTCGCACA 59.793 47.619 0.00 0.00 43.61 4.57
4791 4982 1.939974 TGGTTGATGCTATCTCGCAC 58.060 50.000 0.00 0.00 43.61 5.34
4792 4983 2.093500 ACTTGGTTGATGCTATCTCGCA 60.093 45.455 0.00 0.00 45.10 5.10
4793 4984 2.541762 GACTTGGTTGATGCTATCTCGC 59.458 50.000 0.00 0.00 0.00 5.03
4794 4985 3.126831 GGACTTGGTTGATGCTATCTCG 58.873 50.000 0.00 0.00 0.00 4.04
4795 4986 4.142609 TGGACTTGGTTGATGCTATCTC 57.857 45.455 0.00 0.00 0.00 2.75
4796 4987 4.445448 GGATGGACTTGGTTGATGCTATCT 60.445 45.833 0.00 0.00 0.00 1.98
4797 4988 3.817647 GGATGGACTTGGTTGATGCTATC 59.182 47.826 0.00 0.00 0.00 2.08
4798 4989 3.461085 AGGATGGACTTGGTTGATGCTAT 59.539 43.478 0.00 0.00 0.00 2.97
4799 4990 2.846206 AGGATGGACTTGGTTGATGCTA 59.154 45.455 0.00 0.00 0.00 3.49
4800 4991 1.637553 AGGATGGACTTGGTTGATGCT 59.362 47.619 0.00 0.00 0.00 3.79
4801 4992 2.134789 AGGATGGACTTGGTTGATGC 57.865 50.000 0.00 0.00 0.00 3.91
4802 4993 5.439721 TCATAAGGATGGACTTGGTTGATG 58.560 41.667 0.00 0.00 33.49 3.07
4803 4994 5.715439 TCATAAGGATGGACTTGGTTGAT 57.285 39.130 0.00 0.00 33.49 2.57
4804 4995 5.715439 ATCATAAGGATGGACTTGGTTGA 57.285 39.130 0.00 0.00 34.06 3.18
4816 5007 2.283145 GCACCCTGCATCATAAGGAT 57.717 50.000 0.00 0.00 44.26 3.24
4894 5085 0.168128 GCCCAGAATAACGTGCACAC 59.832 55.000 18.64 0.62 0.00 3.82
4945 5138 0.381801 GTGCAATATTCCAGCGTGGG 59.618 55.000 0.00 0.00 38.32 4.61
4994 5187 2.257034 GTCTTGTTCCGATGTCGTACC 58.743 52.381 1.44 0.00 37.74 3.34
4999 5192 1.007336 ACGCGTCTTGTTCCGATGTC 61.007 55.000 5.58 0.00 0.00 3.06
5060 5253 1.621814 GGGGGTTTTCTGTAAAAGGGC 59.378 52.381 0.00 0.00 35.29 5.19


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

AutoCloner maintained by Alex Coulton.