Multiple sequence alignment - TraesCS5D01G322900

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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 TraesCS5D01G322900 chr5D 100.000 4129 0 0 1 4129 414811926 414807798 0.000000e+00 7625
1 TraesCS5D01G322900 chr5B 93.059 3688 152 46 8 3621 500531345 500527688 0.000000e+00 5297
2 TraesCS5D01G322900 chr5A 92.473 3255 139 40 938 4129 527491689 527488478 0.000000e+00 4556
3 TraesCS5D01G322900 chr5A 86.561 945 47 30 1 902 527492598 527491691 0.000000e+00 968
4 TraesCS5D01G322900 chr7A 78.829 803 144 18 1286 2074 280071595 280070805 6.120000e-143 518
5 TraesCS5D01G322900 chr7A 75.279 627 129 17 2151 2754 280070689 280070066 4.070000e-70 276
6 TraesCS5D01G322900 chr7D 78.234 804 149 17 1283 2067 258238051 258237255 3.710000e-135 492
7 TraesCS5D01G322900 chr7D 76.592 628 119 17 2151 2754 258237155 258236532 1.850000e-83 320
8 TraesCS5D01G322900 chr7B 78.261 805 147 19 1283 2067 237509471 237508675 3.710000e-135 492


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 TraesCS5D01G322900 chr5D 414807798 414811926 4128 True 7625 7625 100.000 1 4129 1 chr5D.!!$R1 4128
1 TraesCS5D01G322900 chr5B 500527688 500531345 3657 True 5297 5297 93.059 8 3621 1 chr5B.!!$R1 3613
2 TraesCS5D01G322900 chr5A 527488478 527492598 4120 True 2762 4556 89.517 1 4129 2 chr5A.!!$R1 4128
3 TraesCS5D01G322900 chr7A 280070066 280071595 1529 True 397 518 77.054 1286 2754 2 chr7A.!!$R1 1468
4 TraesCS5D01G322900 chr7D 258236532 258238051 1519 True 406 492 77.413 1283 2754 2 chr7D.!!$R1 1471
5 TraesCS5D01G322900 chr7B 237508675 237509471 796 True 492 492 78.261 1283 2067 1 chr7B.!!$R1 784

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
894 1002 0.251916 TTGAATCGATCGCCCTGGTT 59.748 50.000 11.09 0.00 0.00 3.67 F
903 1011 0.903942 TCGCCCTGGTTATTACGGTT 59.096 50.000 0.00 0.00 0.00 4.44 F
1062 1177 1.286880 CCGAACCAAAGCAAGGCAG 59.713 57.895 0.00 0.00 0.00 4.85 F
2419 2597 0.665068 CGGACATTCACGTTGACGGA 60.665 55.000 8.52 0.03 44.95 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1906 1.448119 CTCAGCTCGCGGACCTCATA 61.448 60.000 6.13 0.00 0.0 2.15 R
1937 2064 2.582226 TGGTCGTCGATGATGCGC 60.582 61.111 11.16 0.00 0.0 6.09 R
2945 3152 2.037121 TCACCTGGCACGTCCATATATG 59.963 50.000 5.68 5.68 45.5 1.78 R
3744 3963 0.109723 TGTTACTGTTCACCCTGGGC 59.890 55.000 14.08 0.00 0.0 5.36 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
106 107 0.948623 CTCATTTGGACGTGACGGCA 60.949 55.000 14.80 0.00 36.10 5.69
172 179 2.849142 ATGCACGCGGACGAATTTGC 62.849 55.000 12.47 9.28 43.93 3.68
318 329 4.996976 ACGGAGTAGCTGCAGTTG 57.003 55.556 16.64 0.00 41.94 3.16
480 509 4.682334 CCACAGTGGGCATGGGCA 62.682 66.667 12.40 0.00 43.71 5.36
491 520 0.466922 GCATGGGCAATGGAGCTACT 60.467 55.000 3.59 0.00 40.72 2.57
541 583 1.696336 CATGTGCCTGCCTACTCCTAT 59.304 52.381 0.00 0.00 0.00 2.57
542 584 2.767644 TGTGCCTGCCTACTCCTATA 57.232 50.000 0.00 0.00 0.00 1.31
543 585 2.317040 TGTGCCTGCCTACTCCTATAC 58.683 52.381 0.00 0.00 0.00 1.47
544 586 2.091278 TGTGCCTGCCTACTCCTATACT 60.091 50.000 0.00 0.00 0.00 2.12
545 587 3.139584 TGTGCCTGCCTACTCCTATACTA 59.860 47.826 0.00 0.00 0.00 1.82
546 588 3.759618 GTGCCTGCCTACTCCTATACTAG 59.240 52.174 0.00 0.00 0.00 2.57
549 591 4.263594 GCCTGCCTACTCCTATACTAGAGT 60.264 50.000 0.00 0.00 0.00 3.24
564 606 3.358076 GAGTTGCTAGCTCGGCCGT 62.358 63.158 27.15 8.80 0.00 5.68
608 650 3.969642 GAGCAAAACCGCATGGCCG 62.970 63.158 0.00 0.00 39.70 6.13
659 701 4.907034 CTCCACCGCCGATCGTCG 62.907 72.222 12.22 12.22 40.07 5.12
729 811 2.467826 CCTACGTCCGTCTCCGTCC 61.468 68.421 0.00 0.00 38.43 4.79
730 812 2.806856 CTACGTCCGTCTCCGTCCG 61.807 68.421 0.00 0.00 38.43 4.79
757 846 4.530857 GGATGCCCCTCCACGACG 62.531 72.222 0.00 0.00 35.24 5.12
788 877 4.730613 GCAGTTACCGCGATCATCAATTTT 60.731 41.667 8.23 0.00 0.00 1.82
793 882 2.114056 CGCGATCATCAATTTTGGCAG 58.886 47.619 0.00 0.00 0.00 4.85
820 926 2.877335 CTGCACCGTTACTACTTCTCC 58.123 52.381 0.00 0.00 0.00 3.71
824 930 3.087031 CACCGTTACTACTTCTCCCTCA 58.913 50.000 0.00 0.00 0.00 3.86
842 948 4.602696 GCACTGATGATGCGCGCC 62.603 66.667 30.77 15.18 32.45 6.53
843 949 4.289379 CACTGATGATGCGCGCCG 62.289 66.667 30.77 11.10 0.00 6.46
866 974 6.243551 CGTATCATCATCAACGCCATTAATC 58.756 40.000 0.00 0.00 0.00 1.75
894 1002 0.251916 TTGAATCGATCGCCCTGGTT 59.748 50.000 11.09 0.00 0.00 3.67
903 1011 0.903942 TCGCCCTGGTTATTACGGTT 59.096 50.000 0.00 0.00 0.00 4.44
907 1015 1.405797 CCCTGGTTATTACGGTTCGCA 60.406 52.381 0.00 0.00 0.00 5.10
908 1016 2.557317 CCTGGTTATTACGGTTCGCAT 58.443 47.619 0.00 0.00 0.00 4.73
912 1020 2.288729 GGTTATTACGGTTCGCATTCCC 59.711 50.000 0.00 0.00 0.00 3.97
918 1026 2.513897 GTTCGCATTCCCCTCCCG 60.514 66.667 0.00 0.00 0.00 5.14
933 1041 4.933064 CCGCGATGGAGCTCCGTC 62.933 72.222 35.96 35.96 46.19 4.79
935 1043 4.933064 GCGATGGAGCTCCGTCCG 62.933 72.222 37.89 32.51 46.80 4.79
936 1044 3.518998 CGATGGAGCTCCGTCCGT 61.519 66.667 37.89 18.86 46.80 4.69
937 1045 2.413765 GATGGAGCTCCGTCCGTC 59.586 66.667 35.90 20.65 44.42 4.79
1062 1177 1.286880 CCGAACCAAAGCAAGGCAG 59.713 57.895 0.00 0.00 0.00 4.85
1124 1239 1.639298 GGCTGCTGTACCTTTCGCTG 61.639 60.000 0.00 0.00 0.00 5.18
1418 1533 2.035155 TTCTCCCTCGGCGAGACA 59.965 61.111 36.47 21.03 36.11 3.41
1779 1906 4.400961 GCACCGGCAAGGAGAGCT 62.401 66.667 0.00 0.00 45.00 4.09
1781 1908 1.826024 CACCGGCAAGGAGAGCTAT 59.174 57.895 0.00 0.00 45.00 2.97
1937 2064 2.372690 CGTGAACAGCTTCGTCGGG 61.373 63.158 0.00 0.00 0.00 5.14
2083 2216 0.681564 TGTGCAACCGAACCCAAACT 60.682 50.000 0.00 0.00 34.36 2.66
2091 2224 1.072648 CCGAACCCAAACTAACTCCCA 59.927 52.381 0.00 0.00 0.00 4.37
2129 2268 1.325338 CACGTTTCGTTTCGTTCCAGT 59.675 47.619 0.00 0.00 38.32 4.00
2419 2597 0.665068 CGGACATTCACGTTGACGGA 60.665 55.000 8.52 0.03 44.95 4.69
2911 3118 2.799412 CGCTTATCCTGATGAGCAACTC 59.201 50.000 19.82 0.00 46.87 3.01
3164 3371 7.918033 CCTATTCCGATCATAATGCTACTAGTG 59.082 40.741 5.39 0.00 0.00 2.74
3181 3391 2.467880 AGTGGTACCTGGTATGGTGAG 58.532 52.381 14.36 0.00 41.05 3.51
3193 3403 3.430929 GGTATGGTGAGACACAGTGGATC 60.431 52.174 5.31 2.95 35.86 3.36
3200 3410 2.431057 GAGACACAGTGGATCGGGTATT 59.569 50.000 5.31 0.00 0.00 1.89
3202 3412 3.383825 AGACACAGTGGATCGGGTATTAC 59.616 47.826 5.31 0.00 0.00 1.89
3203 3413 2.100252 ACACAGTGGATCGGGTATTACG 59.900 50.000 5.31 0.00 0.00 3.18
3208 3418 1.334556 TGGATCGGGTATTACGACGTG 59.665 52.381 11.56 0.00 43.78 4.49
3211 3421 0.099259 TCGGGTATTACGACGTGCAG 59.901 55.000 11.56 0.00 35.12 4.41
3251 3462 6.961360 TCAAAATATGTACACCAACCAACA 57.039 33.333 0.00 0.00 0.00 3.33
3252 3463 7.348080 TCAAAATATGTACACCAACCAACAA 57.652 32.000 0.00 0.00 0.00 2.83
3253 3464 7.782049 TCAAAATATGTACACCAACCAACAAA 58.218 30.769 0.00 0.00 0.00 2.83
3254 3465 7.707035 TCAAAATATGTACACCAACCAACAAAC 59.293 33.333 0.00 0.00 0.00 2.93
3304 3515 2.834549 AGATTCTTGTCCCGTGATCAGT 59.165 45.455 0.00 0.00 0.00 3.41
3314 3525 1.068402 CCGTGATCAGTTGCAATGCAA 60.068 47.619 17.55 17.55 46.80 4.08
3610 3829 1.081242 GCCACCATCTTTGTGCACG 60.081 57.895 13.13 0.00 32.30 5.34
3631 3850 0.108585 ACATCCAACGTTGCTGTCCT 59.891 50.000 22.93 4.17 0.00 3.85
3706 3925 4.327982 TCACTGCCATATAAGCTCAGTC 57.672 45.455 0.00 0.00 36.01 3.51
3713 3932 4.499865 GCCATATAAGCTCAGTCGTTCAGA 60.500 45.833 0.00 0.00 0.00 3.27
3728 3947 3.927142 CGTTCAGACATGGAGTTTCTACC 59.073 47.826 0.00 0.00 0.00 3.18
3744 3963 0.179032 TACCCTTGGGTGCATATGCG 60.179 55.000 22.21 8.17 45.83 4.73
3758 3977 2.535485 TATGCGCCCAGGGTGAACAG 62.535 60.000 24.58 1.17 34.74 3.16
3767 3986 2.028476 CCAGGGTGAACAGTAACATCGA 60.028 50.000 0.00 0.00 0.00 3.59
3786 4005 7.996385 ACATCGACTAAAATAAGATTTTGGGG 58.004 34.615 11.27 4.79 0.00 4.96
3787 4006 7.832187 ACATCGACTAAAATAAGATTTTGGGGA 59.168 33.333 11.27 8.72 0.00 4.81
3788 4007 7.619964 TCGACTAAAATAAGATTTTGGGGAC 57.380 36.000 11.27 3.89 0.00 4.46
3790 4009 7.886446 TCGACTAAAATAAGATTTTGGGGACTT 59.114 33.333 11.27 0.00 0.00 3.01
3791 4010 8.520351 CGACTAAAATAAGATTTTGGGGACTTT 58.480 33.333 11.27 0.00 0.00 2.66
3843 4073 6.756299 ACAAACATGCAAAATTTCTTGGTT 57.244 29.167 0.00 0.00 0.00 3.67
3869 4099 4.749245 AACATTTGTGGACATCTTCGTC 57.251 40.909 0.00 0.00 35.03 4.20
3871 4101 4.133820 ACATTTGTGGACATCTTCGTCAA 58.866 39.130 0.00 0.00 37.66 3.18
3899 4130 8.437360 AAAAGTTCTAAAAAGGGCATTTCTTG 57.563 30.769 0.00 0.00 0.00 3.02
3900 4131 6.731292 AGTTCTAAAAAGGGCATTTCTTGT 57.269 33.333 0.00 0.00 0.00 3.16
3901 4132 7.124573 AGTTCTAAAAAGGGCATTTCTTGTT 57.875 32.000 0.00 0.00 0.00 2.83
3902 4133 7.210174 AGTTCTAAAAAGGGCATTTCTTGTTC 58.790 34.615 0.00 0.00 0.00 3.18
3903 4134 6.723298 TCTAAAAAGGGCATTTCTTGTTCA 57.277 33.333 0.00 0.00 0.00 3.18
3904 4135 6.748132 TCTAAAAAGGGCATTTCTTGTTCAG 58.252 36.000 0.00 0.00 0.00 3.02
3905 4136 5.612725 AAAAAGGGCATTTCTTGTTCAGA 57.387 34.783 0.00 0.00 0.00 3.27
3906 4137 4.590850 AAAGGGCATTTCTTGTTCAGAC 57.409 40.909 0.00 0.00 0.00 3.51
3909 4140 3.823304 AGGGCATTTCTTGTTCAGACTTC 59.177 43.478 0.00 0.00 0.00 3.01
3910 4141 3.823304 GGGCATTTCTTGTTCAGACTTCT 59.177 43.478 0.00 0.00 0.00 2.85
3911 4142 4.320788 GGGCATTTCTTGTTCAGACTTCTG 60.321 45.833 0.00 0.00 45.08 3.02
3912 4143 4.276926 GGCATTTCTTGTTCAGACTTCTGT 59.723 41.667 6.15 0.00 44.12 3.41
3913 4144 5.447573 GCATTTCTTGTTCAGACTTCTGTC 58.552 41.667 6.15 2.54 44.12 3.51
3967 4225 5.852282 AGTAAAACATTTGTGGTGAAGCT 57.148 34.783 0.00 0.00 0.00 3.74
4047 4313 2.994995 TGACGACGCACCATCCCT 60.995 61.111 0.00 0.00 0.00 4.20
4049 4315 2.047274 ACGACGCACCATCCCTTG 60.047 61.111 0.00 0.00 0.00 3.61
4110 4376 0.670546 CTCTGGTGGTTACGTGGCAG 60.671 60.000 0.00 0.00 0.00 4.85
4112 4378 3.419759 GGTGGTTACGTGGCAGCG 61.420 66.667 0.00 7.71 37.94 5.18
4113 4379 3.419759 GTGGTTACGTGGCAGCGG 61.420 66.667 0.00 0.00 35.98 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 179 0.734309 TGCCATACGCATTCTGCAAG 59.266 50.000 0.00 0.00 45.36 4.01
199 206 0.027979 TACGCTACGTCGTATGTGGC 59.972 55.000 16.41 11.04 43.15 5.01
318 329 1.678123 CCATCCATCCATCCAGCGATC 60.678 57.143 0.00 0.00 0.00 3.69
491 520 1.800805 GCTGCTTCAGTTCAGTAGCA 58.199 50.000 5.28 0.00 46.18 3.49
541 583 1.948145 GCCGAGCTAGCAACTCTAGTA 59.052 52.381 18.83 0.00 45.22 1.82
542 584 0.741915 GCCGAGCTAGCAACTCTAGT 59.258 55.000 18.83 0.00 45.22 2.57
543 585 0.031449 GGCCGAGCTAGCAACTCTAG 59.969 60.000 18.83 1.60 46.01 2.43
544 586 1.725557 CGGCCGAGCTAGCAACTCTA 61.726 60.000 24.07 0.00 31.71 2.43
545 587 2.896443 GGCCGAGCTAGCAACTCT 59.104 61.111 18.83 0.00 31.71 3.24
546 588 2.583593 CGGCCGAGCTAGCAACTC 60.584 66.667 24.07 4.84 0.00 3.01
549 591 4.143333 GGACGGCCGAGCTAGCAA 62.143 66.667 35.90 0.00 0.00 3.91
564 606 3.621805 TGGGCAACGAGAAGCGGA 61.622 61.111 0.00 0.00 46.49 5.54
608 650 3.055719 CATGGGGTGGCACGTGAC 61.056 66.667 22.23 19.45 0.00 3.67
658 700 4.692475 AAAACGACCGGGGGAGCG 62.692 66.667 6.32 3.77 0.00 5.03
659 701 3.053896 CAAAACGACCGGGGGAGC 61.054 66.667 6.32 0.00 0.00 4.70
660 702 3.053896 GCAAAACGACCGGGGGAG 61.054 66.667 6.32 0.00 0.00 4.30
671 713 3.846602 CTGGCCTGGCACGCAAAAC 62.847 63.158 22.05 0.25 0.00 2.43
672 714 3.604667 CTGGCCTGGCACGCAAAA 61.605 61.111 22.05 0.00 0.00 2.44
729 811 2.592861 GGCATCCAAGGCTAGCCG 60.593 66.667 27.83 14.71 41.95 5.52
730 812 2.203408 GGGCATCCAAGGCTAGCC 60.203 66.667 27.19 27.19 44.48 3.93
757 846 3.484547 CGGTAACTGCGGGCGTTC 61.485 66.667 0.00 0.00 0.00 3.95
813 919 1.554160 CATCAGTGCTGAGGGAGAAGT 59.446 52.381 7.96 0.00 43.61 3.01
820 926 1.773054 GCGCATCATCAGTGCTGAGG 61.773 60.000 0.30 4.32 43.61 3.86
824 930 3.570638 GCGCGCATCATCAGTGCT 61.571 61.111 29.10 0.00 40.37 4.40
841 947 1.864565 TGGCGTTGATGATGATACGG 58.135 50.000 0.00 0.00 34.76 4.02
842 948 5.590104 TTAATGGCGTTGATGATGATACG 57.410 39.130 1.27 0.00 37.09 3.06
843 949 7.132694 TGATTAATGGCGTTGATGATGATAC 57.867 36.000 0.95 0.00 0.00 2.24
894 1002 1.764134 AGGGGAATGCGAACCGTAATA 59.236 47.619 0.00 0.00 0.00 0.98
907 1015 3.560251 CCATCGCGGGAGGGGAAT 61.560 66.667 24.02 0.00 40.45 3.01
908 1016 4.789173 TCCATCGCGGGAGGGGAA 62.789 66.667 29.56 11.62 44.27 3.97
918 1026 4.933064 CGGACGGAGCTCCATCGC 62.933 72.222 31.67 18.40 35.14 4.58
1062 1177 1.523711 TCGCCATGGATTCTTCGCC 60.524 57.895 18.40 0.00 0.00 5.54
1109 1224 2.399356 GGCCAGCGAAAGGTACAGC 61.399 63.158 0.00 0.00 41.81 4.40
1779 1906 1.448119 CTCAGCTCGCGGACCTCATA 61.448 60.000 6.13 0.00 0.00 2.15
1781 1908 3.443925 CTCAGCTCGCGGACCTCA 61.444 66.667 6.13 0.00 0.00 3.86
1937 2064 2.582226 TGGTCGTCGATGATGCGC 60.582 61.111 11.16 0.00 0.00 6.09
1973 2100 3.591254 GAAGTCCTTGACGGCGGCT 62.591 63.158 16.45 0.00 37.67 5.52
2083 2216 2.868839 GCTGTGTACGCTTTGGGAGTTA 60.869 50.000 8.10 0.00 0.00 2.24
2091 2224 3.637714 CGTGGCTGTGTACGCTTT 58.362 55.556 8.10 0.00 33.25 3.51
2129 2268 4.466370 ACCAAAGATGAACGTATCAGAGGA 59.534 41.667 1.38 0.00 42.53 3.71
2419 2597 3.125376 GCCAGCGGGGATGAGGAAT 62.125 63.158 4.64 0.00 40.01 3.01
2911 3118 4.073293 ACTAGGTAATTCATCCCTTGCG 57.927 45.455 0.00 0.00 0.00 4.85
2945 3152 2.037121 TCACCTGGCACGTCCATATATG 59.963 50.000 5.68 5.68 45.50 1.78
3038 3245 2.158682 TCTTACAGGGCAGTTGCAGAAA 60.159 45.455 6.43 0.00 44.36 2.52
3132 3339 8.899427 AGCATTATGATCGGAATAGGATAATG 57.101 34.615 11.18 11.18 37.06 1.90
3164 3371 2.167900 GTGTCTCACCATACCAGGTACC 59.832 54.545 2.73 2.73 40.77 3.34
3181 3391 2.981859 AATACCCGATCCACTGTGTC 57.018 50.000 7.08 0.00 0.00 3.67
3193 3403 0.099259 TCTGCACGTCGTAATACCCG 59.901 55.000 0.00 0.00 0.00 5.28
3200 3410 1.209383 GCTCTGTCTGCACGTCGTA 59.791 57.895 0.00 0.00 0.00 3.43
3202 3412 2.085262 CAGCTCTGTCTGCACGTCG 61.085 63.158 0.00 0.00 0.00 5.12
3203 3413 1.735920 CCAGCTCTGTCTGCACGTC 60.736 63.158 0.00 0.00 32.87 4.34
3208 3418 4.697514 TGATATTTACCAGCTCTGTCTGC 58.302 43.478 0.00 0.00 32.87 4.26
3250 3461 3.624777 AGACCTGGATATGCTTGGTTTG 58.375 45.455 0.00 0.00 0.00 2.93
3251 3462 4.227300 TGTAGACCTGGATATGCTTGGTTT 59.773 41.667 0.00 9.80 0.00 3.27
3252 3463 3.780294 TGTAGACCTGGATATGCTTGGTT 59.220 43.478 0.00 6.81 0.00 3.67
3253 3464 3.384168 TGTAGACCTGGATATGCTTGGT 58.616 45.455 11.00 11.00 0.00 3.67
3254 3465 3.389329 ACTGTAGACCTGGATATGCTTGG 59.611 47.826 0.00 0.73 0.00 3.61
3304 3515 2.791383 AACTTAGCGTTGCATTGCAA 57.209 40.000 19.77 19.77 46.80 4.08
3314 3525 4.155826 TCAGCATTTGCAATAACTTAGCGT 59.844 37.500 0.00 0.00 45.16 5.07
3610 3829 1.069227 GGACAGCAACGTTGGATGTTC 60.069 52.381 28.33 18.26 0.00 3.18
3631 3850 8.846211 AGCAAACAGTAACAGATTTTTAGCTTA 58.154 29.630 0.00 0.00 0.00 3.09
3706 3925 3.927142 GGTAGAAACTCCATGTCTGAACG 59.073 47.826 0.00 0.00 0.00 3.95
3713 3932 2.308866 CCCAAGGGTAGAAACTCCATGT 59.691 50.000 0.00 0.00 0.00 3.21
3728 3947 2.723746 GCGCATATGCACCCAAGG 59.276 61.111 26.52 10.01 42.21 3.61
3744 3963 0.109723 TGTTACTGTTCACCCTGGGC 59.890 55.000 14.08 0.00 0.00 5.36
3745 3964 2.711542 GATGTTACTGTTCACCCTGGG 58.288 52.381 12.28 12.28 0.00 4.45
3748 3967 2.897969 AGTCGATGTTACTGTTCACCCT 59.102 45.455 0.00 0.00 0.00 4.34
3809 4039 6.915544 TTTGCATGTTTGTAAAGCATTCAA 57.084 29.167 0.00 0.00 45.92 2.69
3848 4078 4.133820 TGACGAAGATGTCCACAAATGTT 58.866 39.130 0.00 0.00 38.11 2.71
3896 4127 2.721603 CGTCGACAGAAGTCTGAACAAG 59.278 50.000 17.16 2.09 46.59 3.16
3898 4129 1.674441 ACGTCGACAGAAGTCTGAACA 59.326 47.619 17.16 0.00 46.59 3.18
3899 4130 2.402640 ACGTCGACAGAAGTCTGAAC 57.597 50.000 17.16 8.70 46.59 3.18
3900 4131 3.431922 AAACGTCGACAGAAGTCTGAA 57.568 42.857 17.16 0.00 46.59 3.02
3901 4132 3.431922 AAAACGTCGACAGAAGTCTGA 57.568 42.857 17.16 0.00 46.59 3.27
3903 4134 3.121544 GGAAAAACGTCGACAGAAGTCT 58.878 45.455 17.16 0.00 42.73 3.24
3904 4135 2.861935 TGGAAAAACGTCGACAGAAGTC 59.138 45.455 17.16 6.68 38.11 3.01
3905 4136 2.896168 TGGAAAAACGTCGACAGAAGT 58.104 42.857 17.16 1.80 40.73 3.01
3906 4137 3.493129 TGATGGAAAAACGTCGACAGAAG 59.507 43.478 17.16 1.08 0.00 2.85
3909 4140 3.493129 TCTTGATGGAAAAACGTCGACAG 59.507 43.478 17.16 10.90 0.00 3.51
3910 4141 3.459145 TCTTGATGGAAAAACGTCGACA 58.541 40.909 17.16 0.00 0.00 4.35
3911 4142 4.461992 TTCTTGATGGAAAAACGTCGAC 57.538 40.909 5.18 5.18 0.00 4.20
3912 4143 4.573201 AGTTTCTTGATGGAAAAACGTCGA 59.427 37.500 0.00 0.00 37.02 4.20
3913 4144 4.844267 AGTTTCTTGATGGAAAAACGTCG 58.156 39.130 0.00 0.00 37.02 5.12
3914 4145 6.507929 GCAAAGTTTCTTGATGGAAAAACGTC 60.508 38.462 0.00 0.00 37.02 4.34
3915 4146 5.290885 GCAAAGTTTCTTGATGGAAAAACGT 59.709 36.000 0.00 0.00 37.02 3.99
3916 4147 5.290643 TGCAAAGTTTCTTGATGGAAAAACG 59.709 36.000 0.00 0.00 37.02 3.60
3982 4240 4.176752 GATGGAGACCCCGCCACC 62.177 72.222 0.00 0.00 45.01 4.61
3984 4242 4.731853 TGGATGGAGACCCCGCCA 62.732 66.667 0.00 0.00 46.23 5.69
3987 4245 3.083349 TGCTGGATGGAGACCCCG 61.083 66.667 0.00 0.00 37.93 5.73
4033 4299 3.499737 GCAAGGGATGGTGCGTCG 61.500 66.667 0.00 0.00 0.00 5.12
4035 4301 2.045926 GAGCAAGGGATGGTGCGT 60.046 61.111 0.00 0.00 40.59 5.24
4041 4307 2.515523 CAGCCGGAGCAAGGGATG 60.516 66.667 5.05 0.00 43.56 3.51
4084 4350 3.022406 ACGTAACCACCAGAGATAGGAC 58.978 50.000 0.00 0.00 0.00 3.85
4089 4355 0.249398 GCCACGTAACCACCAGAGAT 59.751 55.000 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.