Multiple sequence alignment - TraesCS1D01G417000

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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 TraesCS1D01G417000 chr1D 100.000 2524 0 0 737 3260 475502320 475504843 0.000000e+00 4662.0
1 TraesCS1D01G417000 chr1D 100.000 362 0 0 1 362 475501584 475501945 0.000000e+00 669.0
2 TraesCS1D01G417000 chr1D 89.091 55 5 1 1300 1354 46107121 46107068 2.100000e-07 67.6
3 TraesCS1D01G417000 chr1A 93.688 808 23 19 737 1530 571281060 571281853 0.000000e+00 1184.0
4 TraesCS1D01G417000 chr1A 90.000 910 34 24 1809 2676 571282422 571283316 0.000000e+00 1123.0
5 TraesCS1D01G417000 chr1A 97.970 394 6 2 2672 3065 571283548 571283939 0.000000e+00 682.0
6 TraesCS1D01G417000 chr1A 93.973 365 16 4 1 362 571280673 571281034 6.150000e-152 547.0
7 TraesCS1D01G417000 chr1A 88.649 370 25 11 1 355 571348956 571348589 5.000000e-118 435.0
8 TraesCS1D01G417000 chr1A 90.203 296 20 4 1523 1810 571281890 571282184 8.540000e-101 377.0
9 TraesCS1D01G417000 chr1B 93.039 747 29 14 783 1512 661508321 661509061 0.000000e+00 1070.0
10 TraesCS1D01G417000 chr1B 93.065 620 21 7 2446 3065 661510332 661510929 0.000000e+00 887.0
11 TraesCS1D01G417000 chr1B 91.406 640 35 13 1820 2445 661509632 661510265 0.000000e+00 859.0
12 TraesCS1D01G417000 chr1B 97.598 333 7 1 1 332 661507613 661507945 1.310000e-158 569.0
13 TraesCS1D01G417000 chr1B 80.165 363 31 16 4 351 661567334 661566998 1.960000e-57 233.0
14 TraesCS1D01G417000 chr1B 96.078 102 4 0 1709 1810 661509175 661509276 2.010000e-37 167.0
15 TraesCS1D01G417000 chr5D 86.957 138 17 1 210 347 289584852 289584988 1.570000e-33 154.0
16 TraesCS1D01G417000 chr6D 95.385 65 3 0 1291 1355 445057445 445057381 1.600000e-18 104.0
17 TraesCS1D01G417000 chr6D 88.333 60 6 1 1297 1356 112956263 112956321 1.620000e-08 71.3
18 TraesCS1D01G417000 chr4D 92.453 53 4 0 1304 1356 321815851 321815903 3.490000e-10 76.8
19 TraesCS1D01G417000 chr4D 87.302 63 7 1 1297 1359 442750855 442750794 1.620000e-08 71.3
20 TraesCS1D01G417000 chr7D 90.196 51 5 0 1304 1354 134503747 134503797 2.100000e-07 67.6


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 TraesCS1D01G417000 chr1D 475501584 475504843 3259 False 2665.5 4662 100.0000 1 3260 2 chr1D.!!$F1 3259
1 TraesCS1D01G417000 chr1A 571280673 571283939 3266 False 782.6 1184 93.1668 1 3065 5 chr1A.!!$F1 3064
2 TraesCS1D01G417000 chr1B 661507613 661510929 3316 False 710.4 1070 94.2372 1 3065 5 chr1B.!!$F1 3064

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
956 958 1.067516 GCAACTTACGGCCCGACTATA 59.932 52.381 11.71 0.0 0.0 1.31 F
1816 1890 0.764271 TCCAGTGTGTTCTCATGGCA 59.236 50.000 0.00 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2470 0.108615 CCTGGTTTCGATCGAGCTGT 60.109 55.0 18.54 0.0 0.00 4.40 R
3179 3959 0.039617 GCACTGTGCGCCAATAAACA 60.040 50.0 17.93 0.0 31.71 2.83 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
310 312 4.329545 GAGGCCGGCACAGGTGAA 62.330 66.667 30.85 0.00 0.00 3.18
888 890 2.560119 CCATCGCTCTCTCTCCCGG 61.560 68.421 0.00 0.00 0.00 5.73
889 891 1.826054 CATCGCTCTCTCTCCCGGT 60.826 63.158 0.00 0.00 0.00 5.28
953 955 2.047560 GCAACTTACGGCCCGACT 60.048 61.111 11.71 0.00 0.00 4.18
954 956 1.216178 GCAACTTACGGCCCGACTA 59.784 57.895 11.71 0.00 0.00 2.59
956 958 1.067516 GCAACTTACGGCCCGACTATA 59.932 52.381 11.71 0.00 0.00 1.31
959 961 4.479619 CAACTTACGGCCCGACTATATAC 58.520 47.826 11.71 0.00 0.00 1.47
1409 1418 1.191535 CCGACCTCCACATCAGGTAA 58.808 55.000 0.00 0.00 44.87 2.85
1413 1422 1.285280 CCTCCACATCAGGTAACCCA 58.715 55.000 0.00 0.00 37.17 4.51
1534 1599 2.160822 TCAGACAGTTCTTGCAGCTC 57.839 50.000 0.00 0.00 0.00 4.09
1573 1641 4.675190 CAATCGACTTGTCAGATTGCTT 57.325 40.909 21.99 5.25 42.83 3.91
1595 1663 6.252869 GCTTGATAGTGCAGTTCATCATTTTG 59.747 38.462 0.00 0.00 0.00 2.44
1598 1666 7.700505 TGATAGTGCAGTTCATCATTTTGATC 58.299 34.615 0.00 0.00 34.28 2.92
1626 1694 5.829924 CCAAGGATTATGGTTCAGCTAATGT 59.170 40.000 0.00 0.00 33.08 2.71
1654 1722 4.635699 AATCCTCTACCGAAAACCAAGT 57.364 40.909 0.00 0.00 0.00 3.16
1663 1731 2.422127 CCGAAAACCAAGTTGACAGTGT 59.578 45.455 3.87 0.00 0.00 3.55
1687 1759 9.283768 TGTGATTACTGCTCTTTTATTCAGAAA 57.716 29.630 0.00 0.00 0.00 2.52
1694 1766 9.071276 ACTGCTCTTTTATTCAGAAAGAAATGA 57.929 29.630 0.00 0.00 41.21 2.57
1696 1768 9.850628 TGCTCTTTTATTCAGAAAGAAATGATG 57.149 29.630 8.67 6.23 41.21 3.07
1718 1791 6.252599 TGTGCCCTTTTCAGATCATACTAT 57.747 37.500 0.00 0.00 0.00 2.12
1810 1884 2.351157 GCAATGCTTCCAGTGTGTTCTC 60.351 50.000 0.00 0.00 39.15 2.87
1811 1885 2.880268 CAATGCTTCCAGTGTGTTCTCA 59.120 45.455 0.00 0.00 32.68 3.27
1812 1886 2.936919 TGCTTCCAGTGTGTTCTCAT 57.063 45.000 0.00 0.00 0.00 2.90
1816 1890 0.764271 TCCAGTGTGTTCTCATGGCA 59.236 50.000 0.00 0.00 0.00 4.92
1817 1891 0.877071 CCAGTGTGTTCTCATGGCAC 59.123 55.000 0.00 0.00 0.00 5.01
1818 1892 1.544093 CCAGTGTGTTCTCATGGCACT 60.544 52.381 0.00 0.00 40.54 4.40
1849 2272 4.157289 AGCATGAAATTCTTTGCTGATCGT 59.843 37.500 18.31 0.17 0.00 3.73
1856 2279 4.934075 TTCTTTGCTGATCGTCTGAATG 57.066 40.909 0.00 0.00 0.00 2.67
1937 2360 2.384653 GATACCTGAAGAGCGGCCCC 62.385 65.000 0.00 0.00 0.00 5.80
2025 2448 2.722201 ATCCTCGGCGGACCTTGAC 61.722 63.158 7.21 0.00 46.80 3.18
2045 2469 2.034124 CAATCAATCCCCATCCACCAC 58.966 52.381 0.00 0.00 0.00 4.16
2046 2470 1.307878 ATCAATCCCCATCCACCACA 58.692 50.000 0.00 0.00 0.00 4.17
2069 2498 0.818296 CTCGATCGAAACCAGGACCT 59.182 55.000 19.92 0.00 0.00 3.85
2124 2559 6.774673 TCCCTTGTTCAAGTGTGATGTAATA 58.225 36.000 10.93 0.00 32.48 0.98
2125 2560 6.653320 TCCCTTGTTCAAGTGTGATGTAATAC 59.347 38.462 10.93 0.00 32.48 1.89
2249 2684 7.173722 ACAGACATTTTCTCTGGATTGATCTT 58.826 34.615 0.00 0.00 39.69 2.40
2250 2685 7.668886 ACAGACATTTTCTCTGGATTGATCTTT 59.331 33.333 0.00 0.00 39.69 2.52
2578 3122 3.499737 CGAATCAGGCCACCACGC 61.500 66.667 5.01 0.00 0.00 5.34
3036 3816 3.860605 CGCCCATCCCGTGATCCA 61.861 66.667 0.00 0.00 0.00 3.41
3065 3845 0.608308 GCACCCCAAGAACCTACACC 60.608 60.000 0.00 0.00 0.00 4.16
3066 3846 0.321298 CACCCCAAGAACCTACACCG 60.321 60.000 0.00 0.00 0.00 4.94
3067 3847 1.376812 CCCCAAGAACCTACACCGC 60.377 63.158 0.00 0.00 0.00 5.68
3068 3848 1.677552 CCCAAGAACCTACACCGCT 59.322 57.895 0.00 0.00 0.00 5.52
3069 3849 0.899720 CCCAAGAACCTACACCGCTA 59.100 55.000 0.00 0.00 0.00 4.26
3070 3850 1.485066 CCCAAGAACCTACACCGCTAT 59.515 52.381 0.00 0.00 0.00 2.97
3071 3851 2.550978 CCAAGAACCTACACCGCTATG 58.449 52.381 0.00 0.00 0.00 2.23
3072 3852 2.167693 CCAAGAACCTACACCGCTATGA 59.832 50.000 0.00 0.00 0.00 2.15
3073 3853 3.448686 CAAGAACCTACACCGCTATGAG 58.551 50.000 0.00 0.00 0.00 2.90
3074 3854 1.409427 AGAACCTACACCGCTATGAGC 59.591 52.381 0.00 0.00 38.02 4.26
3083 3863 3.486263 GCTATGAGCGCGTTTGGT 58.514 55.556 8.43 0.00 0.00 3.67
3084 3864 1.794222 GCTATGAGCGCGTTTGGTT 59.206 52.632 8.43 0.00 0.00 3.67
3085 3865 0.168128 GCTATGAGCGCGTTTGGTTT 59.832 50.000 8.43 0.00 0.00 3.27
3086 3866 1.401018 GCTATGAGCGCGTTTGGTTTT 60.401 47.619 8.43 0.00 0.00 2.43
3087 3867 2.920647 GCTATGAGCGCGTTTGGTTTTT 60.921 45.455 8.43 0.00 0.00 1.94
3105 3885 4.776795 TTTTTCATTCGGGAAGTTAGCC 57.223 40.909 0.00 0.00 0.00 3.93
3106 3886 3.426787 TTTCATTCGGGAAGTTAGCCA 57.573 42.857 0.00 0.00 0.00 4.75
3107 3887 3.426787 TTCATTCGGGAAGTTAGCCAA 57.573 42.857 0.00 0.00 0.00 4.52
3108 3888 3.426787 TCATTCGGGAAGTTAGCCAAA 57.573 42.857 0.00 0.00 0.00 3.28
3109 3889 3.757270 TCATTCGGGAAGTTAGCCAAAA 58.243 40.909 0.00 0.00 0.00 2.44
3110 3890 4.145807 TCATTCGGGAAGTTAGCCAAAAA 58.854 39.130 0.00 0.00 0.00 1.94
3111 3891 4.770010 TCATTCGGGAAGTTAGCCAAAAAT 59.230 37.500 0.00 0.00 0.00 1.82
3112 3892 5.245075 TCATTCGGGAAGTTAGCCAAAAATT 59.755 36.000 0.00 0.00 0.00 1.82
3113 3893 6.434652 TCATTCGGGAAGTTAGCCAAAAATTA 59.565 34.615 0.00 0.00 0.00 1.40
3114 3894 5.632244 TCGGGAAGTTAGCCAAAAATTAC 57.368 39.130 0.00 0.00 0.00 1.89
3115 3895 5.318630 TCGGGAAGTTAGCCAAAAATTACT 58.681 37.500 0.00 0.00 0.00 2.24
3116 3896 5.771165 TCGGGAAGTTAGCCAAAAATTACTT 59.229 36.000 0.00 0.00 0.00 2.24
3117 3897 6.941436 TCGGGAAGTTAGCCAAAAATTACTTA 59.059 34.615 0.00 0.00 0.00 2.24
3118 3898 7.120138 TCGGGAAGTTAGCCAAAAATTACTTAG 59.880 37.037 0.00 0.00 0.00 2.18
3119 3899 7.094506 CGGGAAGTTAGCCAAAAATTACTTAGT 60.095 37.037 0.00 0.00 0.00 2.24
3120 3900 8.582437 GGGAAGTTAGCCAAAAATTACTTAGTT 58.418 33.333 0.00 0.00 0.00 2.24
3136 3916 6.408107 ACTTAGTTAGTATAGGAAGCTGGC 57.592 41.667 0.00 0.00 34.56 4.85
3137 3917 5.897824 ACTTAGTTAGTATAGGAAGCTGGCA 59.102 40.000 0.00 0.00 34.56 4.92
3138 3918 6.383147 ACTTAGTTAGTATAGGAAGCTGGCAA 59.617 38.462 0.00 0.00 34.56 4.52
3139 3919 5.693769 AGTTAGTATAGGAAGCTGGCAAA 57.306 39.130 0.00 0.00 0.00 3.68
3140 3920 6.062258 AGTTAGTATAGGAAGCTGGCAAAA 57.938 37.500 0.00 0.00 0.00 2.44
3141 3921 6.663734 AGTTAGTATAGGAAGCTGGCAAAAT 58.336 36.000 0.00 0.00 0.00 1.82
3142 3922 7.802117 AGTTAGTATAGGAAGCTGGCAAAATA 58.198 34.615 0.00 0.00 0.00 1.40
3143 3923 8.440771 AGTTAGTATAGGAAGCTGGCAAAATAT 58.559 33.333 0.00 0.00 0.00 1.28
3144 3924 9.720769 GTTAGTATAGGAAGCTGGCAAAATATA 57.279 33.333 0.00 0.00 0.00 0.86
3145 3925 9.720769 TTAGTATAGGAAGCTGGCAAAATATAC 57.279 33.333 0.00 3.48 0.00 1.47
3146 3926 7.168905 AGTATAGGAAGCTGGCAAAATATACC 58.831 38.462 0.00 0.00 0.00 2.73
3147 3927 4.526438 AGGAAGCTGGCAAAATATACCT 57.474 40.909 0.00 0.00 0.00 3.08
3148 3928 4.871822 AGGAAGCTGGCAAAATATACCTT 58.128 39.130 0.00 0.00 0.00 3.50
3149 3929 5.272402 AGGAAGCTGGCAAAATATACCTTT 58.728 37.500 0.00 0.00 0.00 3.11
3150 3930 5.127682 AGGAAGCTGGCAAAATATACCTTTG 59.872 40.000 0.00 5.22 36.94 2.77
3161 3941 8.687824 CAAAATATACCTTTGCTTCATCGTTT 57.312 30.769 0.00 0.00 0.00 3.60
3162 3942 8.798153 CAAAATATACCTTTGCTTCATCGTTTC 58.202 33.333 0.00 0.00 0.00 2.78
3163 3943 2.969443 ACCTTTGCTTCATCGTTTCG 57.031 45.000 0.00 0.00 0.00 3.46
3164 3944 1.535462 ACCTTTGCTTCATCGTTTCGG 59.465 47.619 0.00 0.00 0.00 4.30
3165 3945 1.606606 CTTTGCTTCATCGTTTCGGC 58.393 50.000 0.00 0.00 0.00 5.54
3166 3946 1.197721 CTTTGCTTCATCGTTTCGGCT 59.802 47.619 0.00 0.00 0.00 5.52
3167 3947 0.796312 TTGCTTCATCGTTTCGGCTC 59.204 50.000 0.00 0.00 0.00 4.70
3168 3948 1.345176 GCTTCATCGTTTCGGCTCG 59.655 57.895 0.00 0.00 0.00 5.03
3169 3949 1.999051 CTTCATCGTTTCGGCTCGG 59.001 57.895 0.00 0.00 0.00 4.63
3170 3950 2.025359 CTTCATCGTTTCGGCTCGGC 62.025 60.000 0.00 0.00 0.00 5.54
3171 3951 2.773397 TTCATCGTTTCGGCTCGGCA 62.773 55.000 0.00 0.00 0.00 5.69
3172 3952 2.813908 ATCGTTTCGGCTCGGCAC 60.814 61.111 0.00 0.00 0.00 5.01
3193 3973 1.696988 CCAAGTGTTTATTGGCGCAC 58.303 50.000 10.83 0.00 40.74 5.34
3194 3974 1.000827 CCAAGTGTTTATTGGCGCACA 60.001 47.619 10.83 0.00 40.74 4.57
3195 3975 2.318578 CAAGTGTTTATTGGCGCACAG 58.681 47.619 10.83 0.00 34.59 3.66
3196 3976 1.604604 AGTGTTTATTGGCGCACAGT 58.395 45.000 10.83 3.44 34.59 3.55
3197 3977 1.266718 AGTGTTTATTGGCGCACAGTG 59.733 47.619 10.83 0.00 34.59 3.66
3198 3978 0.039617 TGTTTATTGGCGCACAGTGC 60.040 50.000 16.21 16.21 40.69 4.40
3225 4005 5.866335 TTTTTATCTGCCGTCACGTTTAT 57.134 34.783 0.00 0.00 0.00 1.40
3226 4006 4.850859 TTTATCTGCCGTCACGTTTATG 57.149 40.909 0.00 0.00 0.00 1.90
3227 4007 2.380084 ATCTGCCGTCACGTTTATGT 57.620 45.000 0.00 0.00 0.00 2.29
3228 4008 2.157834 TCTGCCGTCACGTTTATGTT 57.842 45.000 0.00 0.00 0.00 2.71
3229 4009 2.063266 TCTGCCGTCACGTTTATGTTC 58.937 47.619 0.00 0.00 0.00 3.18
3230 4010 1.795872 CTGCCGTCACGTTTATGTTCA 59.204 47.619 0.00 0.00 0.00 3.18
3231 4011 2.415168 CTGCCGTCACGTTTATGTTCAT 59.585 45.455 0.00 0.00 0.00 2.57
3232 4012 2.158645 TGCCGTCACGTTTATGTTCATG 59.841 45.455 0.00 0.00 0.00 3.07
3233 4013 2.769376 CCGTCACGTTTATGTTCATGC 58.231 47.619 0.00 0.00 0.00 4.06
3234 4014 2.415168 CCGTCACGTTTATGTTCATGCT 59.585 45.455 0.00 0.00 0.00 3.79
3235 4015 3.407252 CGTCACGTTTATGTTCATGCTG 58.593 45.455 0.00 0.00 0.00 4.41
3236 4016 3.120683 CGTCACGTTTATGTTCATGCTGT 60.121 43.478 0.00 0.00 0.00 4.40
3237 4017 4.394795 GTCACGTTTATGTTCATGCTGTC 58.605 43.478 0.00 0.00 0.00 3.51
3238 4018 4.152402 GTCACGTTTATGTTCATGCTGTCT 59.848 41.667 0.00 0.00 0.00 3.41
3239 4019 4.388773 TCACGTTTATGTTCATGCTGTCTC 59.611 41.667 0.00 0.00 0.00 3.36
3240 4020 4.152223 CACGTTTATGTTCATGCTGTCTCA 59.848 41.667 0.00 0.00 0.00 3.27
3241 4021 4.937620 ACGTTTATGTTCATGCTGTCTCAT 59.062 37.500 0.00 0.00 0.00 2.90
3242 4022 6.035975 CACGTTTATGTTCATGCTGTCTCATA 59.964 38.462 0.00 0.00 0.00 2.15
3243 4023 6.593770 ACGTTTATGTTCATGCTGTCTCATAA 59.406 34.615 0.00 0.00 0.00 1.90
3244 4024 7.121911 CGTTTATGTTCATGCTGTCTCATAAG 58.878 38.462 0.00 0.00 32.19 1.73
3245 4025 7.201556 CGTTTATGTTCATGCTGTCTCATAAGT 60.202 37.037 0.00 0.00 32.19 2.24
3246 4026 9.098355 GTTTATGTTCATGCTGTCTCATAAGTA 57.902 33.333 0.00 0.00 32.19 2.24
3247 4027 9.836864 TTTATGTTCATGCTGTCTCATAAGTAT 57.163 29.630 0.00 0.00 32.19 2.12
3248 4028 9.836864 TTATGTTCATGCTGTCTCATAAGTATT 57.163 29.630 0.00 0.00 0.00 1.89
3249 4029 7.543947 TGTTCATGCTGTCTCATAAGTATTG 57.456 36.000 0.00 0.00 0.00 1.90
3250 4030 6.037500 TGTTCATGCTGTCTCATAAGTATTGC 59.962 38.462 0.00 0.00 0.00 3.56
3251 4031 5.922053 TCATGCTGTCTCATAAGTATTGCT 58.078 37.500 0.00 0.00 0.00 3.91
3252 4032 6.351711 TCATGCTGTCTCATAAGTATTGCTT 58.648 36.000 0.00 0.00 41.05 3.91
3253 4033 6.825213 TCATGCTGTCTCATAAGTATTGCTTT 59.175 34.615 0.00 0.00 38.57 3.51
3254 4034 6.668541 TGCTGTCTCATAAGTATTGCTTTC 57.331 37.500 0.00 0.00 38.57 2.62
3255 4035 6.409704 TGCTGTCTCATAAGTATTGCTTTCT 58.590 36.000 0.00 0.00 38.57 2.52
3256 4036 6.881065 TGCTGTCTCATAAGTATTGCTTTCTT 59.119 34.615 0.00 0.00 38.57 2.52
3257 4037 7.391554 TGCTGTCTCATAAGTATTGCTTTCTTT 59.608 33.333 0.00 0.00 38.57 2.52
3258 4038 8.239998 GCTGTCTCATAAGTATTGCTTTCTTTT 58.760 33.333 0.00 0.00 38.57 2.27
3259 4039 9.552114 CTGTCTCATAAGTATTGCTTTCTTTTG 57.448 33.333 0.00 0.00 38.57 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 167 2.651361 CGGTGTCCGCTGACTTCT 59.349 61.111 9.79 0.00 41.17 2.85
225 227 2.490217 CGACCACTGCCTCGGTAG 59.510 66.667 0.00 0.00 34.99 3.18
302 304 0.109086 CGATGCTCTCGTTCACCTGT 60.109 55.000 1.70 0.00 42.56 4.00
752 754 3.003763 ACCGCTTCCCTCCCACTC 61.004 66.667 0.00 0.00 0.00 3.51
753 755 3.322466 CACCGCTTCCCTCCCACT 61.322 66.667 0.00 0.00 0.00 4.00
913 915 2.590114 GGTCCACGTAGTTGGGCCT 61.590 63.158 4.53 0.00 45.49 5.19
1470 1487 4.564406 GCTCCAATTCCTCTTCAGTCAAGA 60.564 45.833 0.00 0.00 38.95 3.02
1471 1488 3.688673 GCTCCAATTCCTCTTCAGTCAAG 59.311 47.826 0.00 0.00 0.00 3.02
1472 1489 3.679389 GCTCCAATTCCTCTTCAGTCAA 58.321 45.455 0.00 0.00 0.00 3.18
1513 1534 2.479656 GAGCTGCAAGAACTGTCTGAAG 59.520 50.000 1.02 0.00 34.07 3.02
1534 1599 5.700832 TCGATTGCTTATATTGGGCTAACTG 59.299 40.000 0.00 0.00 0.00 3.16
1573 1641 7.337436 TGATCAAAATGATGAACTGCACTATCA 59.663 33.333 0.00 0.00 37.20 2.15
1595 1663 5.634118 TGAACCATAATCCTTGGGATGATC 58.366 41.667 0.00 0.00 42.27 2.92
1598 1666 3.571401 GCTGAACCATAATCCTTGGGATG 59.429 47.826 0.00 0.00 42.27 3.51
1626 1694 3.973206 TTCGGTAGAGGATTTGCAGAA 57.027 42.857 0.00 0.00 0.00 3.02
1654 1722 4.607293 AGAGCAGTAATCACACTGTCAA 57.393 40.909 5.26 0.00 46.31 3.18
1663 1731 9.725019 TCTTTCTGAATAAAAGAGCAGTAATCA 57.275 29.630 0.00 0.00 37.72 2.57
1680 1752 4.410099 AGGGCACATCATTTCTTTCTGAA 58.590 39.130 0.00 0.00 0.00 3.02
1687 1759 4.410099 TCTGAAAAGGGCACATCATTTCT 58.590 39.130 0.00 0.00 32.60 2.52
1692 1764 3.438216 TGATCTGAAAAGGGCACATCA 57.562 42.857 0.00 0.00 0.00 3.07
1694 1766 5.121380 AGTATGATCTGAAAAGGGCACAT 57.879 39.130 0.00 0.00 0.00 3.21
1695 1767 4.574674 AGTATGATCTGAAAAGGGCACA 57.425 40.909 0.00 0.00 0.00 4.57
1696 1768 6.767902 TCAATAGTATGATCTGAAAAGGGCAC 59.232 38.462 0.00 0.00 0.00 5.01
1718 1791 4.953579 GGGGGTGCTAAATTATGAAGTCAA 59.046 41.667 0.00 0.00 0.00 3.18
1737 1810 1.842381 GAACTCAGGTGGTCAGGGGG 61.842 65.000 0.00 0.00 0.00 5.40
1810 1884 4.445453 TCATGCTTTCTAGTAGTGCCATG 58.555 43.478 0.00 6.75 0.00 3.66
1811 1885 4.760530 TCATGCTTTCTAGTAGTGCCAT 57.239 40.909 0.00 0.00 0.00 4.40
1812 1886 4.551702 TTCATGCTTTCTAGTAGTGCCA 57.448 40.909 0.00 0.00 0.00 4.92
1816 1890 8.239998 GCAAAGAATTTCATGCTTTCTAGTAGT 58.760 33.333 15.78 0.00 35.03 2.73
1817 1891 8.457261 AGCAAAGAATTTCATGCTTTCTAGTAG 58.543 33.333 18.51 0.00 46.36 2.57
1818 1892 8.239314 CAGCAAAGAATTTCATGCTTTCTAGTA 58.761 33.333 20.53 0.00 46.36 1.82
1849 2272 6.660521 AGTGTCTTGGCAAATAATCATTCAGA 59.339 34.615 0.00 0.00 0.00 3.27
1882 2305 7.926555 CGATTAAACATAGTAGGGTTCAGTGAT 59.073 37.037 0.00 0.00 0.00 3.06
1937 2360 1.192146 TGTCCTTCTCCAGGTTCCCG 61.192 60.000 0.00 0.00 44.37 5.14
2021 2444 3.364549 GTGGATGGGGATTGATTGTCAA 58.635 45.455 0.00 0.00 41.09 3.18
2025 2448 2.034124 GTGGTGGATGGGGATTGATTG 58.966 52.381 0.00 0.00 0.00 2.67
2045 2469 0.994995 CTGGTTTCGATCGAGCTGTG 59.005 55.000 18.54 6.52 0.00 3.66
2046 2470 0.108615 CCTGGTTTCGATCGAGCTGT 60.109 55.000 18.54 0.00 0.00 4.40
2069 2498 2.029964 GGTCGTGCTTGGACGGAA 59.970 61.111 14.08 0.00 39.88 4.30
2124 2559 6.552445 AGTATTACAGAGCTGAATTCTGGT 57.448 37.500 15.80 15.80 44.96 4.00
2125 2560 9.553064 AATTAGTATTACAGAGCTGAATTCTGG 57.447 33.333 13.50 4.83 44.96 3.86
2259 2694 7.587037 TCAACAGAAATCCAGAGAAAATGTT 57.413 32.000 0.00 0.00 0.00 2.71
2622 3166 0.249073 CCCGCTTATCCTCTGACACG 60.249 60.000 0.00 0.00 0.00 4.49
3030 3810 0.107508 GTGCAGCTAGCCTTGGATCA 60.108 55.000 12.13 0.00 44.83 2.92
3036 3816 2.490270 CTTGGGGTGCAGCTAGCCTT 62.490 60.000 16.65 0.00 44.83 4.35
3066 3846 0.168128 AAACCAAACGCGCTCATAGC 59.832 50.000 5.73 0.00 38.02 2.97
3067 3847 2.611974 AAAACCAAACGCGCTCATAG 57.388 45.000 5.73 0.00 0.00 2.23
3069 3849 3.957383 AAAAACCAAACGCGCTCAT 57.043 42.105 5.73 0.00 0.00 2.90
3084 3864 4.145807 TGGCTAACTTCCCGAATGAAAAA 58.854 39.130 0.00 0.00 0.00 1.94
3085 3865 3.757270 TGGCTAACTTCCCGAATGAAAA 58.243 40.909 0.00 0.00 0.00 2.29
3086 3866 3.426787 TGGCTAACTTCCCGAATGAAA 57.573 42.857 0.00 0.00 0.00 2.69
3087 3867 3.426787 TTGGCTAACTTCCCGAATGAA 57.573 42.857 0.00 0.00 0.00 2.57
3088 3868 3.426787 TTTGGCTAACTTCCCGAATGA 57.573 42.857 0.00 0.00 0.00 2.57
3089 3869 4.513198 TTTTTGGCTAACTTCCCGAATG 57.487 40.909 0.00 0.00 0.00 2.67
3090 3870 5.738619 AATTTTTGGCTAACTTCCCGAAT 57.261 34.783 0.00 0.00 0.00 3.34
3091 3871 5.771165 AGTAATTTTTGGCTAACTTCCCGAA 59.229 36.000 0.00 0.00 0.00 4.30
3092 3872 5.318630 AGTAATTTTTGGCTAACTTCCCGA 58.681 37.500 0.00 0.00 0.00 5.14
3093 3873 5.638596 AGTAATTTTTGGCTAACTTCCCG 57.361 39.130 0.00 0.00 0.00 5.14
3094 3874 8.118976 ACTAAGTAATTTTTGGCTAACTTCCC 57.881 34.615 0.00 0.00 0.00 3.97
3110 3890 8.586744 GCCAGCTTCCTATACTAACTAAGTAAT 58.413 37.037 0.00 0.00 43.87 1.89
3111 3891 7.562454 TGCCAGCTTCCTATACTAACTAAGTAA 59.438 37.037 0.00 0.00 43.87 2.24
3112 3892 7.064866 TGCCAGCTTCCTATACTAACTAAGTA 58.935 38.462 0.00 0.00 44.76 2.24
3113 3893 5.897824 TGCCAGCTTCCTATACTAACTAAGT 59.102 40.000 0.00 0.00 42.62 2.24
3114 3894 6.406692 TGCCAGCTTCCTATACTAACTAAG 57.593 41.667 0.00 0.00 0.00 2.18
3115 3895 6.801718 TTGCCAGCTTCCTATACTAACTAA 57.198 37.500 0.00 0.00 0.00 2.24
3116 3896 6.801718 TTTGCCAGCTTCCTATACTAACTA 57.198 37.500 0.00 0.00 0.00 2.24
3117 3897 5.693769 TTTGCCAGCTTCCTATACTAACT 57.306 39.130 0.00 0.00 0.00 2.24
3118 3898 6.944234 ATTTTGCCAGCTTCCTATACTAAC 57.056 37.500 0.00 0.00 0.00 2.34
3119 3899 9.720769 GTATATTTTGCCAGCTTCCTATACTAA 57.279 33.333 0.00 0.00 0.00 2.24
3120 3900 8.319146 GGTATATTTTGCCAGCTTCCTATACTA 58.681 37.037 0.00 0.00 0.00 1.82
3121 3901 7.017651 AGGTATATTTTGCCAGCTTCCTATACT 59.982 37.037 0.00 0.00 31.27 2.12
3122 3902 7.168905 AGGTATATTTTGCCAGCTTCCTATAC 58.831 38.462 0.00 0.00 31.27 1.47
3123 3903 7.329746 AGGTATATTTTGCCAGCTTCCTATA 57.670 36.000 0.00 0.00 31.27 1.31
3124 3904 6.206180 AGGTATATTTTGCCAGCTTCCTAT 57.794 37.500 0.00 0.00 31.27 2.57
3125 3905 5.646692 AGGTATATTTTGCCAGCTTCCTA 57.353 39.130 0.00 0.00 31.27 2.94
3126 3906 4.526438 AGGTATATTTTGCCAGCTTCCT 57.474 40.909 0.00 0.00 31.27 3.36
3127 3907 5.351458 CAAAGGTATATTTTGCCAGCTTCC 58.649 41.667 0.00 0.00 31.27 3.46
3136 3916 8.687824 AAACGATGAAGCAAAGGTATATTTTG 57.312 30.769 0.00 7.81 38.30 2.44
3137 3917 7.696453 CGAAACGATGAAGCAAAGGTATATTTT 59.304 33.333 0.00 0.00 0.00 1.82
3138 3918 7.186804 CGAAACGATGAAGCAAAGGTATATTT 58.813 34.615 0.00 0.00 0.00 1.40
3139 3919 6.238374 CCGAAACGATGAAGCAAAGGTATATT 60.238 38.462 0.00 0.00 0.00 1.28
3140 3920 5.236478 CCGAAACGATGAAGCAAAGGTATAT 59.764 40.000 0.00 0.00 0.00 0.86
3141 3921 4.569162 CCGAAACGATGAAGCAAAGGTATA 59.431 41.667 0.00 0.00 0.00 1.47
3142 3922 3.374058 CCGAAACGATGAAGCAAAGGTAT 59.626 43.478 0.00 0.00 0.00 2.73
3143 3923 2.739913 CCGAAACGATGAAGCAAAGGTA 59.260 45.455 0.00 0.00 0.00 3.08
3144 3924 1.535462 CCGAAACGATGAAGCAAAGGT 59.465 47.619 0.00 0.00 0.00 3.50
3145 3925 1.729149 GCCGAAACGATGAAGCAAAGG 60.729 52.381 0.00 0.00 0.00 3.11
3146 3926 1.197721 AGCCGAAACGATGAAGCAAAG 59.802 47.619 0.00 0.00 0.00 2.77
3147 3927 1.196808 GAGCCGAAACGATGAAGCAAA 59.803 47.619 0.00 0.00 0.00 3.68
3148 3928 0.796312 GAGCCGAAACGATGAAGCAA 59.204 50.000 0.00 0.00 0.00 3.91
3149 3929 1.351430 CGAGCCGAAACGATGAAGCA 61.351 55.000 0.00 0.00 0.00 3.91
3150 3930 1.345176 CGAGCCGAAACGATGAAGC 59.655 57.895 0.00 0.00 0.00 3.86
3151 3931 1.999051 CCGAGCCGAAACGATGAAG 59.001 57.895 0.00 0.00 0.00 3.02
3152 3932 2.098233 GCCGAGCCGAAACGATGAA 61.098 57.895 0.00 0.00 0.00 2.57
3153 3933 2.508439 GCCGAGCCGAAACGATGA 60.508 61.111 0.00 0.00 0.00 2.92
3154 3934 2.813474 TGCCGAGCCGAAACGATG 60.813 61.111 0.00 0.00 0.00 3.84
3155 3935 2.813908 GTGCCGAGCCGAAACGAT 60.814 61.111 0.00 0.00 0.00 3.73
3174 3954 1.000827 TGTGCGCCAATAAACACTTGG 60.001 47.619 4.18 0.00 44.94 3.61
3175 3955 2.287547 ACTGTGCGCCAATAAACACTTG 60.288 45.455 4.18 0.00 34.14 3.16
3176 3956 1.953686 ACTGTGCGCCAATAAACACTT 59.046 42.857 4.18 0.00 34.14 3.16
3177 3957 1.266718 CACTGTGCGCCAATAAACACT 59.733 47.619 4.18 0.00 34.14 3.55
3178 3958 1.685302 CACTGTGCGCCAATAAACAC 58.315 50.000 4.18 0.00 0.00 3.32
3179 3959 0.039617 GCACTGTGCGCCAATAAACA 60.040 50.000 17.93 0.00 31.71 2.83
3180 3960 2.724403 GCACTGTGCGCCAATAAAC 58.276 52.632 17.93 0.00 31.71 2.01
3203 3983 5.179742 ACATAAACGTGACGGCAGATAAAAA 59.820 36.000 10.66 0.00 0.00 1.94
3204 3984 4.691685 ACATAAACGTGACGGCAGATAAAA 59.308 37.500 10.66 0.00 0.00 1.52
3205 3985 4.247258 ACATAAACGTGACGGCAGATAAA 58.753 39.130 10.66 0.00 0.00 1.40
3206 3986 3.852286 ACATAAACGTGACGGCAGATAA 58.148 40.909 10.66 0.00 0.00 1.75
3207 3987 3.513680 ACATAAACGTGACGGCAGATA 57.486 42.857 10.66 0.00 0.00 1.98
3208 3988 2.380084 ACATAAACGTGACGGCAGAT 57.620 45.000 10.66 0.00 0.00 2.90
3209 3989 2.063266 GAACATAAACGTGACGGCAGA 58.937 47.619 10.66 0.00 0.00 4.26
3210 3990 1.795872 TGAACATAAACGTGACGGCAG 59.204 47.619 10.66 0.00 0.00 4.85
3211 3991 1.867166 TGAACATAAACGTGACGGCA 58.133 45.000 10.66 0.00 0.00 5.69
3212 3992 2.769376 CATGAACATAAACGTGACGGC 58.231 47.619 10.66 0.00 0.00 5.68
3213 3993 2.415168 AGCATGAACATAAACGTGACGG 59.585 45.455 10.66 0.00 0.00 4.79
3214 3994 3.120683 ACAGCATGAACATAAACGTGACG 60.121 43.478 2.24 2.24 39.69 4.35
3215 3995 4.152402 AGACAGCATGAACATAAACGTGAC 59.848 41.667 0.00 0.00 39.69 3.67
3216 3996 4.314961 AGACAGCATGAACATAAACGTGA 58.685 39.130 0.00 0.00 39.69 4.35
3217 3997 4.152223 TGAGACAGCATGAACATAAACGTG 59.848 41.667 0.00 0.00 39.69 4.49
3218 3998 4.314961 TGAGACAGCATGAACATAAACGT 58.685 39.130 0.00 0.00 39.69 3.99
3219 3999 4.926860 TGAGACAGCATGAACATAAACG 57.073 40.909 0.00 0.00 39.69 3.60
3220 4000 7.978982 ACTTATGAGACAGCATGAACATAAAC 58.021 34.615 0.00 0.00 39.69 2.01
3221 4001 9.836864 ATACTTATGAGACAGCATGAACATAAA 57.163 29.630 0.00 0.00 39.69 1.40
3222 4002 9.836864 AATACTTATGAGACAGCATGAACATAA 57.163 29.630 0.00 0.00 39.69 1.90
3223 4003 9.264719 CAATACTTATGAGACAGCATGAACATA 57.735 33.333 0.00 0.00 39.69 2.29
3224 4004 7.255035 GCAATACTTATGAGACAGCATGAACAT 60.255 37.037 0.00 0.00 39.69 2.71
3225 4005 6.037500 GCAATACTTATGAGACAGCATGAACA 59.962 38.462 0.00 0.00 39.69 3.18
3226 4006 6.259608 AGCAATACTTATGAGACAGCATGAAC 59.740 38.462 0.00 0.00 39.69 3.18
3227 4007 6.351711 AGCAATACTTATGAGACAGCATGAA 58.648 36.000 0.00 0.00 39.69 2.57
3228 4008 5.922053 AGCAATACTTATGAGACAGCATGA 58.078 37.500 0.00 0.00 39.69 3.07
3229 4009 6.615264 AAGCAATACTTATGAGACAGCATG 57.385 37.500 0.00 0.00 38.68 4.06
3230 4010 7.052873 AGAAAGCAATACTTATGAGACAGCAT 58.947 34.615 0.00 0.00 37.75 3.79
3231 4011 6.409704 AGAAAGCAATACTTATGAGACAGCA 58.590 36.000 0.00 0.00 37.75 4.41
3232 4012 6.917217 AGAAAGCAATACTTATGAGACAGC 57.083 37.500 0.00 0.00 37.75 4.40
3233 4013 9.552114 CAAAAGAAAGCAATACTTATGAGACAG 57.448 33.333 0.00 0.00 37.75 3.51


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

AutoCloner maintained by Alex Coulton.