Multiple sequence alignment - TraesCS6A01G315400

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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 TraesCS6A01G315400 chr6A 100.000 3665 0 0 1 3665 551985359 551981695 0.000000e+00 6769
1 TraesCS6A01G315400 chr6D 95.796 2355 59 13 801 3125 405587837 405585493 0.000000e+00 3764
2 TraesCS6A01G315400 chr6D 94.019 418 23 1 3248 3665 405585495 405585080 1.860000e-177 632
3 TraesCS6A01G315400 chr6D 90.643 171 16 0 3101 3271 363593405 363593575 1.020000e-55 228
4 TraesCS6A01G315400 chr6D 96.269 134 4 1 3123 3256 329858472 329858340 6.160000e-53 219
5 TraesCS6A01G315400 chr6B 95.576 2351 68 10 801 3126 609846623 609844284 0.000000e+00 3733
6 TraesCS6A01G315400 chr6B 92.823 418 14 5 3248 3665 609844287 609843886 3.150000e-165 592
7 TraesCS6A01G315400 chr6B 92.517 147 11 0 3125 3271 644808897 644809043 1.030000e-50 211
8 TraesCS6A01G315400 chr4A 94.195 758 9 8 3 726 146053958 146054714 0.000000e+00 1123
9 TraesCS6A01G315400 chr3A 93.165 790 15 10 1 755 718558918 718558133 0.000000e+00 1123
10 TraesCS6A01G315400 chr3B 94.513 729 10 3 1 700 702169140 702169867 0.000000e+00 1098
11 TraesCS6A01G315400 chr3B 91.558 154 13 0 3117 3270 672783973 672783820 2.870000e-51 213
12 TraesCS6A01G315400 chr7A 93.204 721 9 8 1 693 473891727 473891019 0.000000e+00 1024
13 TraesCS6A01G315400 chr7A 95.519 491 17 5 215 703 193581543 193581056 0.000000e+00 780
14 TraesCS6A01G315400 chr7A 87.387 444 25 18 1 415 193582049 193581608 7.120000e-132 481
15 TraesCS6A01G315400 chr5A 93.383 665 13 5 1 638 396367834 396367174 0.000000e+00 955
16 TraesCS6A01G315400 chr7B 91.892 703 8 4 29 703 373778738 373779419 0.000000e+00 937
17 TraesCS6A01G315400 chr2B 87.855 774 50 27 1 743 272680423 272679663 0.000000e+00 869
18 TraesCS6A01G315400 chr2B 92.292 493 32 6 252 741 765482242 765482731 0.000000e+00 695
19 TraesCS6A01G315400 chr2B 90.161 498 20 12 1 470 765481713 765482209 4.020000e-174 621
20 TraesCS6A01G315400 chr2B 93.243 148 5 4 3125 3270 578606501 578606357 2.870000e-51 213
21 TraesCS6A01G315400 chr1A 95.178 477 16 7 247 722 464082810 464083280 0.000000e+00 747
22 TraesCS6A01G315400 chr1A 91.400 500 12 5 1 470 464082312 464082810 0.000000e+00 656
23 TraesCS6A01G315400 chr7D 89.087 504 33 17 215 703 522362059 522361563 1.130000e-169 606
24 TraesCS6A01G315400 chr4B 98.438 128 2 0 3124 3251 55925904 55926031 3.680000e-55 226
25 TraesCS6A01G315400 chr2D 96.269 134 4 1 3123 3256 305940018 305939886 6.160000e-53 219
26 TraesCS6A01G315400 chr2D 96.269 134 4 1 3123 3256 516381922 516381790 6.160000e-53 219
27 TraesCS6A01G315400 chr1D 96.269 134 3 2 3123 3256 141715473 141715604 6.160000e-53 219


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 TraesCS6A01G315400 chr6A 551981695 551985359 3664 True 6769.0 6769 100.0000 1 3665 1 chr6A.!!$R1 3664
1 TraesCS6A01G315400 chr6D 405585080 405587837 2757 True 2198.0 3764 94.9075 801 3665 2 chr6D.!!$R2 2864
2 TraesCS6A01G315400 chr6B 609843886 609846623 2737 True 2162.5 3733 94.1995 801 3665 2 chr6B.!!$R1 2864
3 TraesCS6A01G315400 chr4A 146053958 146054714 756 False 1123.0 1123 94.1950 3 726 1 chr4A.!!$F1 723
4 TraesCS6A01G315400 chr3A 718558133 718558918 785 True 1123.0 1123 93.1650 1 755 1 chr3A.!!$R1 754
5 TraesCS6A01G315400 chr3B 702169140 702169867 727 False 1098.0 1098 94.5130 1 700 1 chr3B.!!$F1 699
6 TraesCS6A01G315400 chr7A 473891019 473891727 708 True 1024.0 1024 93.2040 1 693 1 chr7A.!!$R1 692
7 TraesCS6A01G315400 chr7A 193581056 193582049 993 True 630.5 780 91.4530 1 703 2 chr7A.!!$R2 702
8 TraesCS6A01G315400 chr5A 396367174 396367834 660 True 955.0 955 93.3830 1 638 1 chr5A.!!$R1 637
9 TraesCS6A01G315400 chr7B 373778738 373779419 681 False 937.0 937 91.8920 29 703 1 chr7B.!!$F1 674
10 TraesCS6A01G315400 chr2B 272679663 272680423 760 True 869.0 869 87.8550 1 743 1 chr2B.!!$R1 742
11 TraesCS6A01G315400 chr2B 765481713 765482731 1018 False 658.0 695 91.2265 1 741 2 chr2B.!!$F1 740
12 TraesCS6A01G315400 chr1A 464082312 464083280 968 False 701.5 747 93.2890 1 722 2 chr1A.!!$F1 721

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
971 1565 3.090532 AGCCTCCGAATCCCCCAC 61.091 66.667 0.0 0.0 0.0 4.61 F
1735 2335 0.314935 GGAGACGGTGTTTGGTCGTA 59.685 55.000 0.0 0.0 38.2 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2548 0.244178 GATATCTTCGACCCCTCGGC 59.756 60.0 0.00 0.0 40.58 5.54 R
3228 3832 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
922 1503 4.826274 TCTCAGAACCCACCATAGAAAG 57.174 45.455 0.00 0.00 0.00 2.62
923 1504 3.519510 TCTCAGAACCCACCATAGAAAGG 59.480 47.826 0.00 0.00 0.00 3.11
971 1565 3.090532 AGCCTCCGAATCCCCCAC 61.091 66.667 0.00 0.00 0.00 4.61
1115 1709 1.227556 CATCCTCCCCGCCGTTAAG 60.228 63.158 0.00 0.00 0.00 1.85
1242 1842 2.792599 GTCGCGTCTCTGTCCGAT 59.207 61.111 5.77 0.00 31.96 4.18
1620 2220 1.676967 CAACCTCAGGAAGCTGGCC 60.677 63.158 0.00 0.00 0.00 5.36
1686 2286 1.450312 CAACATCCTCCTGGACGCC 60.450 63.158 0.00 0.00 46.51 5.68
1734 2334 1.068585 GGAGACGGTGTTTGGTCGT 59.931 57.895 0.00 0.00 38.20 4.34
1735 2335 0.314935 GGAGACGGTGTTTGGTCGTA 59.685 55.000 0.00 0.00 38.20 3.43
1779 2379 0.387202 CCGAGACCTACAGCATCCTG 59.613 60.000 0.00 0.00 44.80 3.86
1860 2460 0.321564 TTGAGATGAAGCACACCCCG 60.322 55.000 0.00 0.00 0.00 5.73
1903 2503 2.886081 CTATTGACTCGTTCTGCAGCT 58.114 47.619 9.47 0.00 0.00 4.24
1948 2548 4.392940 AGAGTTGTTTGAGTTCATGAGGG 58.607 43.478 0.00 0.00 0.00 4.30
1977 2577 3.223435 GTCGAAGATATCCTCTCCCACA 58.777 50.000 0.00 0.00 40.67 4.17
2052 2652 2.481568 TGAGTGCTTTGAGCTGATTTCG 59.518 45.455 0.00 0.00 42.97 3.46
2133 2733 3.614092 CATGTGCTTGGTGGATAGACTT 58.386 45.455 0.00 0.00 0.00 3.01
2318 2918 8.210265 TGTTCATACTTACAATATGCTGATGGA 58.790 33.333 0.00 0.00 31.26 3.41
2362 2962 2.205074 CACACAGGGCACTCGATATTC 58.795 52.381 0.00 0.00 0.00 1.75
2409 3009 2.686405 TCGACGTGCTGTTGATACCTAT 59.314 45.455 0.00 0.00 36.01 2.57
2448 3048 3.068024 GGCTGTTTGATTGTGGAAGAACA 59.932 43.478 0.00 0.00 0.00 3.18
2457 3057 1.412710 TGTGGAAGAACAGAAGACGCT 59.587 47.619 0.00 0.00 0.00 5.07
2532 3132 4.056740 AGTTCGATTCTATCATGCTGCAG 58.943 43.478 10.11 10.11 0.00 4.41
2656 3256 7.984617 AGAAGAAGAAGAGCATTGGTATTAGAC 59.015 37.037 0.00 0.00 0.00 2.59
2677 3277 3.701542 ACGGAGATGAGTTCTGCAAGATA 59.298 43.478 0.00 0.00 46.36 1.98
2678 3278 4.343526 ACGGAGATGAGTTCTGCAAGATAT 59.656 41.667 0.00 0.00 46.36 1.63
2679 3279 5.536538 ACGGAGATGAGTTCTGCAAGATATA 59.463 40.000 0.00 0.00 46.36 0.86
2825 3429 8.608598 AGTACTTATTTTGCCTACTTTTCCCTA 58.391 33.333 0.00 0.00 0.00 3.53
2897 3501 0.771127 ACCAAAGGGCAGCTAACAGA 59.229 50.000 0.00 0.00 37.90 3.41
3099 3703 5.408356 ACTTGTGTGTTAGATACATCCGTC 58.592 41.667 0.00 0.00 39.39 4.79
3100 3704 4.023739 TGTGTGTTAGATACATCCGTCG 57.976 45.455 0.00 0.00 39.39 5.12
3101 3705 3.441222 TGTGTGTTAGATACATCCGTCGT 59.559 43.478 0.00 0.00 39.39 4.34
3115 3719 5.751990 ACATCCGTCGTATCTAAACAAATCC 59.248 40.000 0.00 0.00 0.00 3.01
3119 3723 5.006358 CCGTCGTATCTAAACAAATCCAAGG 59.994 44.000 0.00 0.00 0.00 3.61
3122 3726 5.941058 TCGTATCTAAACAAATCCAAGGCAA 59.059 36.000 0.00 0.00 0.00 4.52
3123 3727 6.093495 TCGTATCTAAACAAATCCAAGGCAAG 59.907 38.462 0.00 0.00 0.00 4.01
3124 3728 6.128007 CGTATCTAAACAAATCCAAGGCAAGT 60.128 38.462 0.00 0.00 0.00 3.16
3125 3729 7.065324 CGTATCTAAACAAATCCAAGGCAAGTA 59.935 37.037 0.00 0.00 0.00 2.24
3126 3730 6.569179 TCTAAACAAATCCAAGGCAAGTAC 57.431 37.500 0.00 0.00 0.00 2.73
3127 3731 6.303839 TCTAAACAAATCCAAGGCAAGTACT 58.696 36.000 0.00 0.00 0.00 2.73
3128 3732 5.453567 AAACAAATCCAAGGCAAGTACTC 57.546 39.130 0.00 0.00 0.00 2.59
3129 3733 3.421844 ACAAATCCAAGGCAAGTACTCC 58.578 45.455 0.00 0.00 0.00 3.85
3130 3734 2.755103 CAAATCCAAGGCAAGTACTCCC 59.245 50.000 0.00 0.00 0.00 4.30
3131 3735 1.972588 ATCCAAGGCAAGTACTCCCT 58.027 50.000 8.79 8.79 0.00 4.20
3132 3736 1.276622 TCCAAGGCAAGTACTCCCTC 58.723 55.000 13.68 0.00 0.00 4.30
3133 3737 0.253327 CCAAGGCAAGTACTCCCTCC 59.747 60.000 13.68 5.34 0.00 4.30
3134 3738 0.108138 CAAGGCAAGTACTCCCTCCG 60.108 60.000 13.68 6.54 0.00 4.63
3135 3739 0.544595 AAGGCAAGTACTCCCTCCGT 60.545 55.000 13.68 1.59 0.00 4.69
3136 3740 0.971447 AGGCAAGTACTCCCTCCGTC 60.971 60.000 8.79 0.00 0.00 4.79
3137 3741 0.971447 GGCAAGTACTCCCTCCGTCT 60.971 60.000 0.00 0.00 0.00 4.18
3138 3742 0.173708 GCAAGTACTCCCTCCGTCTG 59.826 60.000 0.00 0.00 0.00 3.51
3139 3743 0.818296 CAAGTACTCCCTCCGTCTGG 59.182 60.000 0.00 0.00 0.00 3.86
3140 3744 0.702902 AAGTACTCCCTCCGTCTGGA 59.297 55.000 0.00 0.00 43.88 3.86
3141 3745 0.702902 AGTACTCCCTCCGTCTGGAA 59.297 55.000 0.00 0.00 45.87 3.53
3142 3746 1.076677 AGTACTCCCTCCGTCTGGAAA 59.923 52.381 0.00 0.00 45.87 3.13
3143 3747 2.108970 GTACTCCCTCCGTCTGGAAAT 58.891 52.381 0.00 0.00 45.87 2.17
3144 3748 2.544844 ACTCCCTCCGTCTGGAAATA 57.455 50.000 0.00 0.00 45.87 1.40
3145 3749 2.108970 ACTCCCTCCGTCTGGAAATAC 58.891 52.381 0.00 0.00 45.87 1.89
3146 3750 2.292323 ACTCCCTCCGTCTGGAAATACT 60.292 50.000 0.00 0.00 45.87 2.12
3147 3751 2.766828 CTCCCTCCGTCTGGAAATACTT 59.233 50.000 0.00 0.00 45.87 2.24
3148 3752 2.500098 TCCCTCCGTCTGGAAATACTTG 59.500 50.000 0.00 0.00 45.87 3.16
3149 3753 2.236395 CCCTCCGTCTGGAAATACTTGT 59.764 50.000 0.00 0.00 45.87 3.16
3150 3754 3.522553 CCTCCGTCTGGAAATACTTGTC 58.477 50.000 0.00 0.00 45.87 3.18
3151 3755 3.056107 CCTCCGTCTGGAAATACTTGTCA 60.056 47.826 0.00 0.00 45.87 3.58
3152 3756 4.383118 CCTCCGTCTGGAAATACTTGTCAT 60.383 45.833 0.00 0.00 45.87 3.06
3153 3757 4.755411 TCCGTCTGGAAATACTTGTCATC 58.245 43.478 0.00 0.00 42.85 2.92
3154 3758 4.221924 TCCGTCTGGAAATACTTGTCATCA 59.778 41.667 0.00 0.00 42.85 3.07
3155 3759 4.935205 CCGTCTGGAAATACTTGTCATCAA 59.065 41.667 0.00 0.00 37.49 2.57
3156 3760 5.411361 CCGTCTGGAAATACTTGTCATCAAA 59.589 40.000 0.00 0.00 37.49 2.69
3157 3761 6.072728 CCGTCTGGAAATACTTGTCATCAAAA 60.073 38.462 0.00 0.00 37.49 2.44
3158 3762 7.362056 CCGTCTGGAAATACTTGTCATCAAAAT 60.362 37.037 0.00 0.00 37.49 1.82
3159 3763 7.482743 CGTCTGGAAATACTTGTCATCAAAATG 59.517 37.037 0.00 0.00 32.87 2.32
3160 3764 7.756722 GTCTGGAAATACTTGTCATCAAAATGG 59.243 37.037 0.00 0.00 33.42 3.16
3161 3765 7.669304 TCTGGAAATACTTGTCATCAAAATGGA 59.331 33.333 0.00 0.00 33.42 3.41
3162 3766 8.365060 TGGAAATACTTGTCATCAAAATGGAT 57.635 30.769 0.00 0.00 33.42 3.41
3163 3767 9.473007 TGGAAATACTTGTCATCAAAATGGATA 57.527 29.630 0.00 0.00 33.42 2.59
3170 3774 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
3171 3775 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
3172 3776 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
3173 3777 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
3174 3778 8.260114 GTCATCAAAATGGATAAAAAGGGATGT 58.740 33.333 0.00 0.00 33.42 3.06
3175 3779 9.486123 TCATCAAAATGGATAAAAAGGGATGTA 57.514 29.630 0.00 0.00 33.42 2.29
3178 3782 9.713684 TCAAAATGGATAAAAAGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
3184 3788 9.225682 TGGATAAAAAGGGATGTATCTAGAACT 57.774 33.333 0.00 0.00 0.00 3.01
3208 3812 9.845214 ACTAAAATATGTCTAGATACATCCCCT 57.155 33.333 0.00 0.00 40.52 4.79
3216 3820 8.561536 TGTCTAGATACATCCCCTTTTATTCA 57.438 34.615 0.00 0.00 0.00 2.57
3217 3821 9.170890 TGTCTAGATACATCCCCTTTTATTCAT 57.829 33.333 0.00 0.00 0.00 2.57
3222 3826 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
3225 3829 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
3226 3830 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
3227 3831 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
3228 3832 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
3229 3833 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
3230 3834 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
3237 3841 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
3238 3842 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
3239 3843 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
3240 3844 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
3241 3845 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3242 3846 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3243 3847 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3244 3848 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3245 3849 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3246 3850 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3329 3933 5.125097 AGTTTGCTGCCTGAGATAAATTCAG 59.875 40.000 0.00 0.00 41.34 3.02
3349 3953 8.807948 ATTCAGTTTAACCTATGCAACAGTAT 57.192 30.769 0.00 0.00 0.00 2.12
3364 3968 7.966812 TGCAACAGTATATTGTAGATGGATCT 58.033 34.615 0.78 0.00 40.86 2.75
3506 4110 2.816087 TGCCTGAAAGAAATGCAGAGAC 59.184 45.455 0.00 0.00 34.07 3.36
3512 4116 5.809001 TGAAAGAAATGCAGAGACACCTAT 58.191 37.500 0.00 0.00 0.00 2.57
3516 4120 4.223700 AGAAATGCAGAGACACCTATGTGA 59.776 41.667 5.05 0.00 45.76 3.58
3570 4174 9.628746 TGGGTTTTTCTCGCTATTTTAATTTAC 57.371 29.630 0.00 0.00 0.00 2.01
3606 4210 5.491078 TGTAAATAATCTGGAACCTGGACCT 59.509 40.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
484 1017 2.666317 CCACTTGAAAGACCAGGGTTT 58.334 47.619 0.00 0.00 0.00 3.27
791 1364 9.927668 CATTACACACATTTTTCCTTAAATCCT 57.072 29.630 0.00 0.00 0.00 3.24
792 1365 9.921637 TCATTACACACATTTTTCCTTAAATCC 57.078 29.630 0.00 0.00 0.00 3.01
795 1368 9.959749 GACTCATTACACACATTTTTCCTTAAA 57.040 29.630 0.00 0.00 0.00 1.52
796 1369 8.573035 GGACTCATTACACACATTTTTCCTTAA 58.427 33.333 0.00 0.00 0.00 1.85
797 1370 7.721842 TGGACTCATTACACACATTTTTCCTTA 59.278 33.333 0.00 0.00 0.00 2.69
798 1371 6.549364 TGGACTCATTACACACATTTTTCCTT 59.451 34.615 0.00 0.00 0.00 3.36
799 1372 6.068010 TGGACTCATTACACACATTTTTCCT 58.932 36.000 0.00 0.00 0.00 3.36
884 1458 2.200955 GAGAAGAGGGAAGGGGATTGT 58.799 52.381 0.00 0.00 0.00 2.71
943 1524 1.301401 CGGAGGCTGAAAACGGACA 60.301 57.895 0.00 0.00 0.00 4.02
944 1525 0.601841 TTCGGAGGCTGAAAACGGAC 60.602 55.000 0.00 0.00 0.00 4.79
945 1526 0.323629 ATTCGGAGGCTGAAAACGGA 59.676 50.000 0.00 0.00 32.18 4.69
946 1527 0.727398 GATTCGGAGGCTGAAAACGG 59.273 55.000 0.00 0.00 32.18 4.44
948 1529 1.095600 GGGATTCGGAGGCTGAAAAC 58.904 55.000 0.00 0.00 32.18 2.43
949 1530 0.034477 GGGGATTCGGAGGCTGAAAA 60.034 55.000 0.00 0.00 32.18 2.29
1110 1704 3.865830 GCCTGAGCGCGGCTTAAC 61.866 66.667 16.45 0.00 44.17 2.01
1242 1842 0.179076 TCACCGCGTCGTAGATCCTA 60.179 55.000 4.92 0.00 40.67 2.94
1404 2004 0.108615 CGTAGTTGTCCTGCTGGGAG 60.109 60.000 10.07 0.00 46.10 4.30
1686 2286 1.651240 CCATCCCGCACTTGCAGAAG 61.651 60.000 1.48 0.00 42.21 2.85
1734 2334 2.840038 TCCCTGCAGCTTCTTCTTCATA 59.160 45.455 8.66 0.00 0.00 2.15
1735 2335 1.632409 TCCCTGCAGCTTCTTCTTCAT 59.368 47.619 8.66 0.00 0.00 2.57
1779 2379 3.039134 CGGCACCACCCAAAGAAC 58.961 61.111 0.00 0.00 33.26 3.01
1860 2460 3.123621 CAGCAATGTACGTGAAGTTCTCC 59.876 47.826 0.00 0.00 0.00 3.71
1903 2503 0.537188 GCCTCCGAGATCAAACCAGA 59.463 55.000 0.00 0.00 0.00 3.86
1948 2548 0.244178 GATATCTTCGACCCCTCGGC 59.756 60.000 0.00 0.00 40.58 5.54
2052 2652 3.563808 TGCAGCCACGTTTAATCATATCC 59.436 43.478 0.00 0.00 0.00 2.59
2331 2931 1.489481 CCCTGTGTGGCTCTCTCATA 58.511 55.000 0.00 0.00 0.00 2.15
2362 2962 3.257393 CTCTCTTGTCCATTTCAGTCCG 58.743 50.000 0.00 0.00 0.00 4.79
2409 3009 6.795144 AACAGCCCATCAATCATTATTTCA 57.205 33.333 0.00 0.00 0.00 2.69
2532 3132 0.249031 GGTTGCCAACAGCTGACAAC 60.249 55.000 23.35 24.31 44.23 3.32
2656 3256 2.662006 TCTTGCAGAACTCATCTCCG 57.338 50.000 0.00 0.00 35.73 4.63
2679 3279 8.942338 TCTTGACTATTCGTGCTAACAATAAT 57.058 30.769 0.00 0.00 0.00 1.28
2768 3372 2.146342 ACTGTACAGAATGCAGCACAC 58.854 47.619 29.30 0.00 44.44 3.82
2825 3429 1.076438 AACTTAGGCCCTCCTTGCTT 58.924 50.000 0.00 0.00 40.66 3.91
2897 3501 9.944376 AAATACACATTAGAGTACATTGTGTCT 57.056 29.630 16.98 4.34 45.63 3.41
2947 3551 6.483974 TGTAGCAACCGTTTTGATTCTAAAGA 59.516 34.615 0.00 0.00 0.00 2.52
3099 3703 5.811399 TGCCTTGGATTTGTTTAGATACG 57.189 39.130 0.00 0.00 0.00 3.06
3100 3704 7.158099 ACTTGCCTTGGATTTGTTTAGATAC 57.842 36.000 0.00 0.00 0.00 2.24
3101 3705 8.107095 AGTACTTGCCTTGGATTTGTTTAGATA 58.893 33.333 0.00 0.00 0.00 1.98
3107 3711 3.826729 GGAGTACTTGCCTTGGATTTGTT 59.173 43.478 0.00 0.00 0.00 2.83
3119 3723 0.173708 CAGACGGAGGGAGTACTTGC 59.826 60.000 0.00 0.00 0.00 4.01
3122 3726 0.702902 TTCCAGACGGAGGGAGTACT 59.297 55.000 0.00 0.00 44.10 2.73
3123 3727 1.553706 TTTCCAGACGGAGGGAGTAC 58.446 55.000 0.00 0.00 44.10 2.73
3124 3728 2.544844 ATTTCCAGACGGAGGGAGTA 57.455 50.000 0.00 0.00 44.10 2.59
3125 3729 2.108970 GTATTTCCAGACGGAGGGAGT 58.891 52.381 0.00 0.00 44.10 3.85
3126 3730 2.389715 AGTATTTCCAGACGGAGGGAG 58.610 52.381 0.00 0.00 44.10 4.30
3127 3731 2.500098 CAAGTATTTCCAGACGGAGGGA 59.500 50.000 0.00 0.00 44.10 4.20
3128 3732 2.236395 ACAAGTATTTCCAGACGGAGGG 59.764 50.000 0.00 0.00 44.10 4.30
3129 3733 3.056107 TGACAAGTATTTCCAGACGGAGG 60.056 47.826 0.00 0.00 44.10 4.30
3130 3734 4.188247 TGACAAGTATTTCCAGACGGAG 57.812 45.455 0.00 0.00 44.10 4.63
3131 3735 4.221924 TGATGACAAGTATTTCCAGACGGA 59.778 41.667 0.00 0.00 40.60 4.69
3132 3736 4.503910 TGATGACAAGTATTTCCAGACGG 58.496 43.478 0.00 0.00 0.00 4.79
3133 3737 6.480524 TTTGATGACAAGTATTTCCAGACG 57.519 37.500 0.00 0.00 37.32 4.18
3134 3738 7.756722 CCATTTTGATGACAAGTATTTCCAGAC 59.243 37.037 0.00 0.00 37.32 3.51
3135 3739 7.669304 TCCATTTTGATGACAAGTATTTCCAGA 59.331 33.333 0.00 0.00 37.32 3.86
3136 3740 7.829725 TCCATTTTGATGACAAGTATTTCCAG 58.170 34.615 0.00 0.00 37.32 3.86
3137 3741 7.773489 TCCATTTTGATGACAAGTATTTCCA 57.227 32.000 0.00 0.00 37.32 3.53
3144 3748 8.096414 CCCTTTTTATCCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
3145 3749 8.313292 TCCCTTTTTATCCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
3146 3750 8.200024 TCCCTTTTTATCCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
3147 3751 7.789202 TCCCTTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
3148 3752 8.260114 ACATCCCTTTTTATCCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
3149 3753 8.378115 ACATCCCTTTTTATCCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
3152 3756 9.713684 AGATACATCCCTTTTTATCCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
3158 3762 9.225682 AGTTCTAGATACATCCCTTTTTATCCA 57.774 33.333 0.00 0.00 0.00 3.41
3182 3786 9.845214 AGGGGATGTATCTAGACATATTTTAGT 57.155 33.333 0.00 0.00 40.18 2.24
3190 3794 9.170890 TGAATAAAAGGGGATGTATCTAGACAT 57.829 33.333 0.00 0.00 42.82 3.06
3191 3795 8.561536 TGAATAAAAGGGGATGTATCTAGACA 57.438 34.615 0.00 0.00 0.00 3.41
3196 3800 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
3199 3803 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
3200 3804 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
3201 3805 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
3202 3806 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
3203 3807 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
3204 3808 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
3212 3816 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
3213 3817 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
3214 3818 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
3215 3819 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
3216 3820 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
3217 3821 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
3218 3822 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3219 3823 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3220 3824 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3221 3825 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3222 3826 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3223 3827 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3224 3828 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3225 3829 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3226 3830 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3227 3831 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3228 3832 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3229 3833 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3230 3834 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3231 3835 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3232 3836 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
3233 3837 0.032813 ATTACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
3234 3838 0.846015 TATTACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
3235 3839 1.544691 CATATTACTCCCTCCGTCCGG 59.455 57.143 0.00 0.00 0.00 5.14
3236 3840 1.544691 CCATATTACTCCCTCCGTCCG 59.455 57.143 0.00 0.00 0.00 4.79
3237 3841 2.885616 TCCATATTACTCCCTCCGTCC 58.114 52.381 0.00 0.00 0.00 4.79
3238 3842 3.128938 CGATCCATATTACTCCCTCCGTC 59.871 52.174 0.00 0.00 0.00 4.79
3239 3843 3.090037 CGATCCATATTACTCCCTCCGT 58.910 50.000 0.00 0.00 0.00 4.69
3240 3844 2.427453 CCGATCCATATTACTCCCTCCG 59.573 54.545 0.00 0.00 0.00 4.63
3241 3845 3.702045 CTCCGATCCATATTACTCCCTCC 59.298 52.174 0.00 0.00 0.00 4.30
3242 3846 3.702045 CCTCCGATCCATATTACTCCCTC 59.298 52.174 0.00 0.00 0.00 4.30
3243 3847 3.566775 CCCTCCGATCCATATTACTCCCT 60.567 52.174 0.00 0.00 0.00 4.20
3244 3848 2.766828 CCCTCCGATCCATATTACTCCC 59.233 54.545 0.00 0.00 0.00 4.30
3245 3849 3.702045 CTCCCTCCGATCCATATTACTCC 59.298 52.174 0.00 0.00 0.00 3.85
3246 3850 4.345854 ACTCCCTCCGATCCATATTACTC 58.654 47.826 0.00 0.00 0.00 2.59
3364 3968 5.170021 ACACGCTGGTTTGTCGTTTATATA 58.830 37.500 0.00 0.00 33.84 0.86
3570 4174 9.276590 TCCAGATTATTTACATCATAGCTTGTG 57.723 33.333 0.00 0.00 0.00 3.33
3590 4194 5.536497 AAAAATAGGTCCAGGTTCCAGAT 57.464 39.130 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.