Multiple sequence alignment - TraesCS2D01G347700

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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 TraesCS2D01G347700 chr2D 100.000 3988 0 0 1 3988 445744020 445740033 0.000000e+00 7365
1 TraesCS2D01G347700 chr2B 95.865 2757 86 11 575 3315 524029111 524026367 0.000000e+00 4434
2 TraesCS2D01G347700 chr2B 89.619 578 44 9 3 577 524029705 524029141 0.000000e+00 721
3 TraesCS2D01G347700 chr2B 84.942 684 53 20 3317 3988 524026228 524025583 0.000000e+00 647
4 TraesCS2D01G347700 chr2A 94.067 2680 102 23 1000 3641 588380793 588378133 0.000000e+00 4015
5 TraesCS2D01G347700 chr2A 87.590 556 38 11 4 551 588381770 588381238 2.040000e-172 616
6 TraesCS2D01G347700 chr2A 85.934 391 36 13 575 957 588381176 588380797 2.230000e-107 399


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 TraesCS2D01G347700 chr2D 445740033 445744020 3987 True 7365.000000 7365 100.000 1 3988 1 chr2D.!!$R1 3987
1 TraesCS2D01G347700 chr2B 524025583 524029705 4122 True 1934.000000 4434 90.142 3 3988 3 chr2B.!!$R1 3985
2 TraesCS2D01G347700 chr2A 588378133 588381770 3637 True 1676.666667 4015 89.197 4 3641 3 chr2A.!!$R1 3637

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
639 687 0.107831 CCACACTCGACTTTTGGGGA 59.892 55.0 0.0 0.0 35.64 4.81 F
1797 1859 0.179009 AAGCAGAGTGTGTGCCACAT 60.179 50.0 0.0 0.0 46.32 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 1955 2.680339 GACACTGAATTTAGCAGCTCCC 59.320 50.0 0.0 0.0 36.86 4.30 R
3573 3791 0.179176 GCAAACACACGCAACACTCA 60.179 50.0 0.0 0.0 0.00 3.41 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
39 40 1.202348 GCCGTTGCTAGGATTTTTGCT 59.798 47.619 0.00 0.00 33.53 3.91
102 109 4.201628 CGTCGCTCCTCTTAGTTCAATTTG 60.202 45.833 0.00 0.00 0.00 2.32
127 134 2.931649 ACCGGTGGGGATTCCGTT 60.932 61.111 6.12 0.00 39.97 4.44
138 145 1.128692 GGATTCCGTTGCTGTTCTTCG 59.871 52.381 0.00 0.00 0.00 3.79
143 150 0.655733 CGTTGCTGTTCTTCGGTTGT 59.344 50.000 0.00 0.00 0.00 3.32
173 180 1.737793 GGCGTGATCTGACGGAAATTT 59.262 47.619 7.59 0.00 39.81 1.82
186 193 2.476185 CGGAAATTTGGTGAGATGTCGC 60.476 50.000 0.00 0.00 0.00 5.19
208 215 2.614983 TGCGTTTAGTGGGTTTCAGTTC 59.385 45.455 0.00 0.00 0.00 3.01
223 230 0.395724 AGTTCCGGGGATTTGGATGC 60.396 55.000 0.00 0.00 33.42 3.91
227 234 0.395586 CCGGGGATTTGGATGCTGAA 60.396 55.000 0.00 0.00 0.00 3.02
439 447 3.282021 TGGATAGATTTGGTTCTGCTGC 58.718 45.455 0.00 0.00 0.00 5.25
444 452 3.077359 AGATTTGGTTCTGCTGCTGTAC 58.923 45.455 0.00 4.41 0.00 2.90
445 453 2.638480 TTTGGTTCTGCTGCTGTACT 57.362 45.000 14.00 0.00 0.00 2.73
446 454 3.762407 TTTGGTTCTGCTGCTGTACTA 57.238 42.857 14.00 7.14 0.00 1.82
502 511 2.037367 AGGAGCTAGCGTGGGTCA 59.963 61.111 9.55 0.00 33.45 4.02
537 546 0.250727 TACTTGCAGTCCACCCTTGC 60.251 55.000 0.00 0.00 38.30 4.01
552 561 2.136196 CTTGCGGGCGGCTTGTTTTA 62.136 55.000 18.19 0.00 44.05 1.52
554 563 1.214325 GCGGGCGGCTTGTTTTATT 59.786 52.632 9.56 0.00 39.11 1.40
557 573 0.174845 GGGCGGCTTGTTTTATTCCC 59.825 55.000 9.56 0.00 0.00 3.97
598 646 5.705441 AGTCGATTTCCAGATTTTTGCTACA 59.295 36.000 0.00 0.00 0.00 2.74
600 648 6.305638 GTCGATTTCCAGATTTTTGCTACAAC 59.694 38.462 0.00 0.00 0.00 3.32
602 650 4.864704 TTCCAGATTTTTGCTACAACCC 57.135 40.909 0.00 0.00 0.00 4.11
604 652 4.415596 TCCAGATTTTTGCTACAACCCAT 58.584 39.130 0.00 0.00 0.00 4.00
605 653 4.220382 TCCAGATTTTTGCTACAACCCATG 59.780 41.667 0.00 0.00 0.00 3.66
606 654 4.021192 CCAGATTTTTGCTACAACCCATGT 60.021 41.667 0.00 0.00 46.36 3.21
607 655 5.184864 CCAGATTTTTGCTACAACCCATGTA 59.815 40.000 0.00 0.00 43.63 2.29
608 656 6.092748 CAGATTTTTGCTACAACCCATGTAC 58.907 40.000 0.00 0.00 43.63 2.90
639 687 0.107831 CCACACTCGACTTTTGGGGA 59.892 55.000 0.00 0.00 35.64 4.81
667 715 1.176527 ATGGATTTGGAAGTGGCACG 58.823 50.000 12.71 0.00 0.00 5.34
669 717 1.212751 GATTTGGAAGTGGCACGCC 59.787 57.895 20.96 20.96 41.54 5.68
989 1041 6.852420 AACTACTGAAGATAACTGGTAGCA 57.148 37.500 0.00 0.00 32.91 3.49
990 1042 6.458232 ACTACTGAAGATAACTGGTAGCAG 57.542 41.667 20.16 20.16 32.91 4.24
991 1043 4.130286 ACTGAAGATAACTGGTAGCAGC 57.870 45.455 21.58 5.54 0.00 5.25
992 1044 3.515502 ACTGAAGATAACTGGTAGCAGCA 59.484 43.478 21.58 10.36 0.00 4.41
993 1045 4.163078 ACTGAAGATAACTGGTAGCAGCAT 59.837 41.667 21.58 14.64 0.00 3.79
994 1046 5.363868 ACTGAAGATAACTGGTAGCAGCATA 59.636 40.000 21.58 14.89 0.00 3.14
995 1047 5.847304 TGAAGATAACTGGTAGCAGCATAG 58.153 41.667 21.58 0.00 0.00 2.23
996 1048 4.264460 AGATAACTGGTAGCAGCATAGC 57.736 45.455 21.58 16.57 0.00 2.97
1160 1212 6.182039 ACTTGTTTGATCGTTCATACATGG 57.818 37.500 23.71 18.59 41.46 3.66
1343 1397 6.072783 GCTCATGCAAATTCCCTAGTATTCTC 60.073 42.308 0.00 0.00 39.41 2.87
1344 1398 6.299141 TCATGCAAATTCCCTAGTATTCTCC 58.701 40.000 0.00 0.00 0.00 3.71
1359 1414 3.426787 TTCTCCCGGCACTAAATTTCA 57.573 42.857 0.00 0.00 0.00 2.69
1360 1415 3.426787 TCTCCCGGCACTAAATTTCAA 57.573 42.857 0.00 0.00 0.00 2.69
1361 1416 3.757270 TCTCCCGGCACTAAATTTCAAA 58.243 40.909 0.00 0.00 0.00 2.69
1364 1419 4.082845 TCCCGGCACTAAATTTCAAATCA 58.917 39.130 0.00 0.00 0.00 2.57
1630 1692 5.559148 ATTGGGAGAGTTCCATCACTATC 57.441 43.478 0.00 0.00 45.98 2.08
1797 1859 0.179009 AAGCAGAGTGTGTGCCACAT 60.179 50.000 0.00 0.00 46.32 3.21
1891 1955 9.755804 TTTGAGCTTGATATCTATGTACTCAAG 57.244 33.333 12.17 12.17 43.51 3.02
1908 1972 3.614092 TCAAGGGAGCTGCTAAATTCAG 58.386 45.455 0.15 0.00 34.79 3.02
1958 2025 9.929180 GCAGTCATATATTTTCATACAGGACTA 57.071 33.333 0.00 0.00 0.00 2.59
2084 2154 2.079925 GCTTGAAGGTGTGTCATCTCC 58.920 52.381 0.00 0.00 0.00 3.71
2177 2247 8.344098 CAATTTTGGAAAATGCATGTTTGTACT 58.656 29.630 2.99 0.00 38.53 2.73
2235 2306 7.829725 TGTGTATTGATTCTTGCTTAAATGCT 58.170 30.769 0.00 0.00 0.00 3.79
2740 2811 6.475504 TCACCTTCTCATGTGTCATATGTTT 58.524 36.000 9.16 0.00 34.14 2.83
2771 2842 1.341531 GTAGCCGATGGAGCACAGTAT 59.658 52.381 0.00 0.00 0.00 2.12
2873 2944 4.363138 CTTCAAAGAAGAACTTGGTTGGC 58.637 43.478 0.52 0.00 38.98 4.52
2879 2950 4.218312 AGAAGAACTTGGTTGGCTCAAAT 58.782 39.130 0.00 0.00 0.00 2.32
3028 3099 5.128033 TGAAAAAGATGATCCTGGCCATA 57.872 39.130 5.51 0.00 0.00 2.74
3030 3101 4.803329 AAAAGATGATCCTGGCCATAGT 57.197 40.909 5.51 0.00 0.00 2.12
3031 3102 3.784511 AAGATGATCCTGGCCATAGTG 57.215 47.619 5.51 0.00 0.00 2.74
3042 3113 4.299155 CTGGCCATAGTGTCGTATACAAG 58.701 47.826 5.51 0.00 40.63 3.16
3045 3116 5.105269 TGGCCATAGTGTCGTATACAAGAAA 60.105 40.000 0.00 0.00 40.63 2.52
3129 3200 3.802685 GTGATAGGTTCAAGTATGCGTCC 59.197 47.826 0.00 0.00 35.70 4.79
3353 3563 6.357367 TGAGAGCTTGTTCTTTCTTTAAGGT 58.643 36.000 0.00 0.00 34.46 3.50
3398 3608 7.173218 CAGTAGTTCAGATTTAAGGAAGCACAA 59.827 37.037 0.00 0.00 0.00 3.33
3399 3609 7.885399 AGTAGTTCAGATTTAAGGAAGCACAAT 59.115 33.333 0.00 0.00 0.00 2.71
3415 3625 5.376625 AGCACAATCTCAACAAAGGACTTA 58.623 37.500 0.00 0.00 0.00 2.24
3456 3669 4.065321 AGCGAGGGATCTGTTAGATTTG 57.935 45.455 0.00 0.00 34.53 2.32
3460 3673 5.220681 GCGAGGGATCTGTTAGATTTGTTTC 60.221 44.000 0.00 0.00 34.53 2.78
3514 3732 8.464404 ACCATAATGATTTGAGTTCATGTCAAG 58.536 33.333 0.00 0.00 35.39 3.02
3537 3755 1.071385 ACCCGATCCTCTCATGAATGC 59.929 52.381 0.00 0.00 0.00 3.56
3573 3791 8.622157 GTGTATCAGTGTAGTGTATGATAGTGT 58.378 37.037 0.00 0.00 35.81 3.55
3574 3792 8.621286 TGTATCAGTGTAGTGTATGATAGTGTG 58.379 37.037 0.00 0.00 35.81 3.82
3608 3826 3.315191 TGTTTGCCTTGAACTCTTGCTAC 59.685 43.478 0.00 0.00 0.00 3.58
3654 3872 9.239551 GGTAATATCTACCCTCACAAACTTTTT 57.760 33.333 3.85 0.00 0.00 1.94
3664 3882 6.272318 CCTCACAAACTTTTTACTGCAATCA 58.728 36.000 0.00 0.00 0.00 2.57
3665 3883 6.198966 CCTCACAAACTTTTTACTGCAATCAC 59.801 38.462 0.00 0.00 0.00 3.06
3666 3884 6.862209 TCACAAACTTTTTACTGCAATCACT 58.138 32.000 0.00 0.00 0.00 3.41
3680 3898 5.415415 GCAATCACTGCCAGTAATAGAAG 57.585 43.478 0.00 0.00 46.13 2.85
3681 3899 5.118990 GCAATCACTGCCAGTAATAGAAGA 58.881 41.667 0.00 0.00 46.13 2.87
3682 3900 5.236047 GCAATCACTGCCAGTAATAGAAGAG 59.764 44.000 0.00 0.00 46.13 2.85
3683 3901 6.577103 CAATCACTGCCAGTAATAGAAGAGA 58.423 40.000 0.00 0.00 0.00 3.10
3684 3902 5.584253 TCACTGCCAGTAATAGAAGAGAC 57.416 43.478 0.00 0.00 0.00 3.36
3685 3903 5.265191 TCACTGCCAGTAATAGAAGAGACT 58.735 41.667 0.00 0.00 0.00 3.24
3686 3904 5.717178 TCACTGCCAGTAATAGAAGAGACTT 59.283 40.000 0.00 0.00 0.00 3.01
3712 3930 2.704725 AACACATCATTGTTGTCGCC 57.295 45.000 0.00 0.00 38.31 5.54
3713 3931 1.603456 ACACATCATTGTTGTCGCCA 58.397 45.000 0.00 0.00 32.34 5.69
3714 3932 1.266718 ACACATCATTGTTGTCGCCAC 59.733 47.619 0.00 0.00 32.34 5.01
3715 3933 0.881118 ACATCATTGTTGTCGCCACC 59.119 50.000 0.00 0.00 29.55 4.61
3716 3934 1.167851 CATCATTGTTGTCGCCACCT 58.832 50.000 0.00 0.00 0.00 4.00
3717 3935 1.131126 CATCATTGTTGTCGCCACCTC 59.869 52.381 0.00 0.00 0.00 3.85
3718 3936 0.107643 TCATTGTTGTCGCCACCTCA 59.892 50.000 0.00 0.00 0.00 3.86
3719 3937 0.238289 CATTGTTGTCGCCACCTCAC 59.762 55.000 0.00 0.00 0.00 3.51
3720 3938 0.889186 ATTGTTGTCGCCACCTCACC 60.889 55.000 0.00 0.00 0.00 4.02
3721 3939 3.041940 GTTGTCGCCACCTCACCG 61.042 66.667 0.00 0.00 0.00 4.94
3722 3940 3.228017 TTGTCGCCACCTCACCGA 61.228 61.111 0.00 0.00 0.00 4.69
3723 3941 2.579657 TTGTCGCCACCTCACCGAT 61.580 57.895 0.00 0.00 33.24 4.18
3724 3942 2.509336 GTCGCCACCTCACCGATG 60.509 66.667 0.00 0.00 33.24 3.84
3725 3943 4.451150 TCGCCACCTCACCGATGC 62.451 66.667 0.00 0.00 0.00 3.91
3739 3957 5.116180 TCACCGATGCCACTTAGAAAATAG 58.884 41.667 0.00 0.00 0.00 1.73
3776 3994 9.268282 AGAGACCTATTAAGACTGGAATTAACA 57.732 33.333 0.00 0.00 0.00 2.41
3807 4025 8.711170 TGATTATTAACGAAGGATCCCTTTAGT 58.289 33.333 8.55 0.55 44.82 2.24
3808 4026 9.557061 GATTATTAACGAAGGATCCCTTTAGTT 57.443 33.333 8.55 12.11 44.82 2.24
3816 4034 3.190415 TCCCTTTAGTTGCTGGGGA 57.810 52.632 0.00 0.00 43.15 4.81
3817 4035 1.681229 TCCCTTTAGTTGCTGGGGAT 58.319 50.000 0.00 0.00 40.84 3.85
3819 4037 1.686115 CCCTTTAGTTGCTGGGGATGG 60.686 57.143 0.00 0.00 39.42 3.51
3832 4050 1.003464 GGGGATGGCATTTGCAAAAGT 59.997 47.619 17.19 0.00 44.36 2.66
3855 4075 6.991531 AGTTTTTATGGCAAATTCTTCAAGCA 59.008 30.769 0.00 0.00 0.00 3.91
3868 4088 3.069872 TCTTCAAGCACACATGGCAATTT 59.930 39.130 0.00 0.00 0.00 1.82
3880 4100 5.470777 CACATGGCAATTTCTTTGGAAACAT 59.529 36.000 0.00 0.00 43.16 2.71
3884 4104 9.550406 CATGGCAATTTCTTTGGAAACATATAT 57.450 29.630 0.00 0.00 43.16 0.86
3885 4105 9.768662 ATGGCAATTTCTTTGGAAACATATATC 57.231 29.630 0.00 0.00 43.16 1.63
3886 4106 8.756927 TGGCAATTTCTTTGGAAACATATATCA 58.243 29.630 0.00 0.00 43.16 2.15
3941 4162 1.755179 CCATGTCGCCTGAAGGAATT 58.245 50.000 0.00 0.00 37.39 2.17
3960 4181 6.919721 GGAATTGCCTAACTTTCAACACATA 58.080 36.000 0.00 0.00 0.00 2.29
3967 4188 6.090763 GCCTAACTTTCAACACATAAATTGCC 59.909 38.462 0.00 0.00 0.00 4.52
3970 4191 3.650070 TTCAACACATAAATTGCCGCA 57.350 38.095 0.00 0.00 0.00 5.69
3974 4195 4.811024 TCAACACATAAATTGCCGCAAAAA 59.189 33.333 10.42 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.567385 GAGGCGCGCTCTCCTCTG 62.567 72.222 32.29 2.19 44.19 3.35
102 109 2.600735 ATCCCCACCGGTCCTCTACC 62.601 65.000 2.59 0.00 45.77 3.18
113 120 2.046285 CAGCAACGGAATCCCCACC 61.046 63.158 0.00 0.00 34.14 4.61
127 134 0.934496 CGAACAACCGAAGAACAGCA 59.066 50.000 0.00 0.00 0.00 4.41
173 180 2.125952 CGCAGCGACATCTCACCA 60.126 61.111 9.98 0.00 0.00 4.17
186 193 2.218603 ACTGAAACCCACTAAACGCAG 58.781 47.619 0.00 0.00 0.00 5.18
208 215 0.395586 TTCAGCATCCAAATCCCCGG 60.396 55.000 0.00 0.00 0.00 5.73
223 230 1.078567 GGGGCACAGAGCTCTTCAG 60.079 63.158 15.27 5.67 45.61 3.02
244 251 2.494073 AGAGAGGTCGTCATCCAAAGAC 59.506 50.000 0.00 0.00 0.00 3.01
246 253 2.493675 TCAGAGAGGTCGTCATCCAAAG 59.506 50.000 0.00 0.00 0.00 2.77
247 254 2.525368 TCAGAGAGGTCGTCATCCAAA 58.475 47.619 0.00 0.00 0.00 3.28
325 332 0.947180 GAACCGCAGACGCAACCTAA 60.947 55.000 0.00 0.00 38.40 2.69
326 333 1.373748 GAACCGCAGACGCAACCTA 60.374 57.895 0.00 0.00 38.40 3.08
444 452 7.824289 TGGTCCAGAATTGAGATTTTGTACTAG 59.176 37.037 0.00 0.00 0.00 2.57
445 453 7.685481 TGGTCCAGAATTGAGATTTTGTACTA 58.315 34.615 0.00 0.00 0.00 1.82
446 454 6.542821 TGGTCCAGAATTGAGATTTTGTACT 58.457 36.000 0.00 0.00 0.00 2.73
502 511 6.795098 TGCAAGTACGAAATCAATAACAGT 57.205 33.333 0.00 0.00 0.00 3.55
537 546 0.179148 GGAATAAAACAAGCCGCCCG 60.179 55.000 0.00 0.00 0.00 6.13
547 556 2.764010 GTGGACCATGGGGGAATAAAAC 59.236 50.000 18.09 0.00 41.15 2.43
552 561 0.850883 AGTGTGGACCATGGGGGAAT 60.851 55.000 18.09 0.00 41.15 3.01
554 563 0.620410 CTAGTGTGGACCATGGGGGA 60.620 60.000 18.09 0.00 41.15 4.81
557 573 1.482593 GACTCTAGTGTGGACCATGGG 59.517 57.143 18.09 0.00 0.00 4.00
598 646 3.307480 GGCAGAACACTAGTACATGGGTT 60.307 47.826 5.61 5.61 0.00 4.11
600 648 2.420129 GGGCAGAACACTAGTACATGGG 60.420 54.545 0.00 0.00 0.00 4.00
602 650 3.262420 GTGGGCAGAACACTAGTACATG 58.738 50.000 0.00 0.00 35.98 3.21
604 652 2.036733 GTGTGGGCAGAACACTAGTACA 59.963 50.000 0.00 0.00 43.69 2.90
605 653 2.685100 GTGTGGGCAGAACACTAGTAC 58.315 52.381 0.00 0.00 43.69 2.73
627 675 1.318576 AAAGTGCTCCCCAAAAGTCG 58.681 50.000 0.00 0.00 0.00 4.18
639 687 5.047092 CCACTTCCAAATCCATAAAAGTGCT 60.047 40.000 7.38 0.00 41.25 4.40
667 715 8.067751 AGATAAAAATCCTAAAGGTTTGAGGC 57.932 34.615 0.00 0.00 36.34 4.70
887 939 5.949735 AGACAATTGGCTACATTAAAACGG 58.050 37.500 13.57 0.00 0.00 4.44
989 1041 0.181114 TGCCTTCATTCCGCTATGCT 59.819 50.000 0.00 0.00 0.00 3.79
990 1042 0.308993 GTGCCTTCATTCCGCTATGC 59.691 55.000 0.00 0.00 0.00 3.14
991 1043 0.947244 GGTGCCTTCATTCCGCTATG 59.053 55.000 0.00 0.00 0.00 2.23
992 1044 0.546122 TGGTGCCTTCATTCCGCTAT 59.454 50.000 0.00 0.00 0.00 2.97
993 1045 0.546122 ATGGTGCCTTCATTCCGCTA 59.454 50.000 0.00 0.00 0.00 4.26
994 1046 0.749454 GATGGTGCCTTCATTCCGCT 60.749 55.000 0.00 0.00 0.00 5.52
995 1047 1.729881 GATGGTGCCTTCATTCCGC 59.270 57.895 0.00 0.00 0.00 5.54
996 1048 2.016961 CGATGGTGCCTTCATTCCG 58.983 57.895 5.21 0.00 0.00 4.30
1343 1397 4.448537 TGATTTGAAATTTAGTGCCGGG 57.551 40.909 2.18 0.00 0.00 5.73
1344 1398 6.254157 CAGAATGATTTGAAATTTAGTGCCGG 59.746 38.462 0.00 0.00 39.69 6.13
1361 1416 9.890629 TGTTTGAGTAATTACTAGCAGAATGAT 57.109 29.630 18.03 0.00 39.45 2.45
1514 1574 6.942576 GGAGGAAATATTGCATATGTAGTGGT 59.057 38.462 4.29 0.00 0.00 4.16
1576 1638 8.429641 AGACTACCTGAGAAAAGAAACACAATA 58.570 33.333 0.00 0.00 0.00 1.90
1797 1859 3.388024 GTCTTATGCAGGATACCAGACCA 59.612 47.826 0.00 0.00 37.17 4.02
1869 1933 7.013220 TCCCTTGAGTACATAGATATCAAGCT 58.987 38.462 5.32 0.00 43.45 3.74
1891 1955 2.680339 GACACTGAATTTAGCAGCTCCC 59.320 50.000 0.00 0.00 36.86 4.30
1908 1972 3.705072 AGGGTAGTAGGCATAGTTGACAC 59.295 47.826 0.00 0.00 30.96 3.67
2177 2247 6.483307 CACTTGGTGAAGTATGACAAGAGAAA 59.517 38.462 9.41 0.00 40.68 2.52
2209 2279 8.472413 AGCATTTAAGCAAGAATCAATACACAT 58.528 29.630 0.00 0.00 36.85 3.21
2210 2280 7.829725 AGCATTTAAGCAAGAATCAATACACA 58.170 30.769 0.00 0.00 36.85 3.72
2235 2306 6.264744 GTGAACTATAGATGCACCCTGTAGTA 59.735 42.308 20.14 9.17 37.51 1.82
2706 2777 3.120468 TGAGAAGGTGATGATGGGAGA 57.880 47.619 0.00 0.00 0.00 3.71
2740 2811 1.391933 ATCGGCTACATGCACGAGGA 61.392 55.000 0.00 0.00 43.51 3.71
2873 2944 2.202518 CTTGCGCCGCCATTTGAG 60.203 61.111 6.63 0.00 0.00 3.02
3042 3113 6.032880 GCTGCGAGTAGACAAATGAATTTTTC 59.967 38.462 0.00 0.00 0.00 2.29
3045 3116 4.436050 CGCTGCGAGTAGACAAATGAATTT 60.436 41.667 18.66 0.00 0.00 1.82
3129 3200 4.507388 CACATTTGCAGGTTTAACAACTGG 59.493 41.667 0.00 0.00 30.71 4.00
3372 3582 6.650807 TGTGCTTCCTTAAATCTGAACTACTG 59.349 38.462 0.00 0.00 0.00 2.74
3398 3608 5.295292 CGCATGATAAGTCCTTTGTTGAGAT 59.705 40.000 0.00 0.00 0.00 2.75
3399 3609 4.631377 CGCATGATAAGTCCTTTGTTGAGA 59.369 41.667 0.00 0.00 0.00 3.27
3456 3669 9.089601 GTAGCTAACAGATTTCCTTAGAGAAAC 57.910 37.037 0.00 0.00 38.51 2.78
3477 3690 7.564793 TCAAATCATTATGGTGTACTGTAGCT 58.435 34.615 0.00 0.00 0.00 3.32
3484 3697 8.677300 ACATGAACTCAAATCATTATGGTGTAC 58.323 33.333 0.00 0.00 35.38 2.90
3485 3698 8.806429 ACATGAACTCAAATCATTATGGTGTA 57.194 30.769 0.00 0.00 35.38 2.90
3487 3700 7.764331 TGACATGAACTCAAATCATTATGGTG 58.236 34.615 0.00 0.00 35.38 4.17
3489 3702 8.680001 TCTTGACATGAACTCAAATCATTATGG 58.320 33.333 0.00 0.00 35.38 2.74
3492 3705 9.897744 GTTTCTTGACATGAACTCAAATCATTA 57.102 29.630 0.00 0.00 35.38 1.90
3514 3732 3.543680 TTCATGAGAGGATCGGGTTTC 57.456 47.619 0.00 0.00 42.67 2.78
3537 3755 7.224753 ACACTACACTGATACACAAACTCAAAG 59.775 37.037 0.00 0.00 0.00 2.77
3573 3791 0.179176 GCAAACACACGCAACACTCA 60.179 50.000 0.00 0.00 0.00 3.41
3574 3792 0.865639 GGCAAACACACGCAACACTC 60.866 55.000 0.00 0.00 0.00 3.51
3664 3882 6.613153 AAAGTCTCTTCTATTACTGGCAGT 57.387 37.500 25.34 25.34 0.00 4.40
3665 3883 9.606631 AAATAAAGTCTCTTCTATTACTGGCAG 57.393 33.333 14.16 14.16 0.00 4.85
3666 3884 9.601217 GAAATAAAGTCTCTTCTATTACTGGCA 57.399 33.333 0.00 0.00 0.00 4.92
3675 3893 9.996554 TGATGTGTTGAAATAAAGTCTCTTCTA 57.003 29.630 0.00 0.00 0.00 2.10
3676 3894 8.908786 TGATGTGTTGAAATAAAGTCTCTTCT 57.091 30.769 0.00 0.00 0.00 2.85
3678 3896 9.903682 CAATGATGTGTTGAAATAAAGTCTCTT 57.096 29.630 0.00 0.00 0.00 2.85
3679 3897 9.071276 ACAATGATGTGTTGAAATAAAGTCTCT 57.929 29.630 0.00 0.00 38.69 3.10
3680 3898 9.683069 AACAATGATGTGTTGAAATAAAGTCTC 57.317 29.630 0.00 0.00 40.22 3.36
3712 3930 0.249120 TAAGTGGCATCGGTGAGGTG 59.751 55.000 0.00 0.00 0.00 4.00
3713 3931 0.537188 CTAAGTGGCATCGGTGAGGT 59.463 55.000 0.00 0.00 0.00 3.85
3714 3932 0.824109 TCTAAGTGGCATCGGTGAGG 59.176 55.000 0.00 0.00 0.00 3.86
3715 3933 2.672961 TTCTAAGTGGCATCGGTGAG 57.327 50.000 0.00 0.00 0.00 3.51
3716 3934 3.410631 TTTTCTAAGTGGCATCGGTGA 57.589 42.857 0.00 0.00 0.00 4.02
3717 3935 5.116180 TCTATTTTCTAAGTGGCATCGGTG 58.884 41.667 0.00 0.00 0.00 4.94
3718 3936 5.353394 TCTATTTTCTAAGTGGCATCGGT 57.647 39.130 0.00 0.00 0.00 4.69
3719 3937 5.007724 GGTTCTATTTTCTAAGTGGCATCGG 59.992 44.000 0.00 0.00 0.00 4.18
3720 3938 5.817816 AGGTTCTATTTTCTAAGTGGCATCG 59.182 40.000 0.00 0.00 0.00 3.84
3721 3939 8.732746 TTAGGTTCTATTTTCTAAGTGGCATC 57.267 34.615 0.00 0.00 0.00 3.91
3722 3940 9.528489 TTTTAGGTTCTATTTTCTAAGTGGCAT 57.472 29.630 0.00 0.00 0.00 4.40
3723 3941 8.927675 TTTTAGGTTCTATTTTCTAAGTGGCA 57.072 30.769 0.00 0.00 0.00 4.92
3776 3994 9.421399 AGGGATCCTTCGTTAATAATCATTTTT 57.579 29.630 12.58 0.00 0.00 1.94
3792 4010 3.282885 CCAGCAACTAAAGGGATCCTTC 58.717 50.000 12.58 0.00 43.92 3.46
3807 4025 1.901654 GCAAATGCCATCCCCAGCAA 61.902 55.000 0.00 0.00 43.36 3.91
3808 4026 2.360767 GCAAATGCCATCCCCAGCA 61.361 57.895 0.00 0.00 44.45 4.41
3816 4034 6.679843 CCATAAAAACTTTTGCAAATGCCAT 58.320 32.000 21.35 8.41 41.18 4.40
3817 4035 5.506982 GCCATAAAAACTTTTGCAAATGCCA 60.507 36.000 21.35 3.28 41.18 4.92
3819 4037 5.517904 TGCCATAAAAACTTTTGCAAATGC 58.482 33.333 21.35 0.00 42.50 3.56
3832 4050 6.765036 TGTGCTTGAAGAATTTGCCATAAAAA 59.235 30.769 0.00 0.00 0.00 1.94
3853 4073 2.481185 CCAAAGAAATTGCCATGTGTGC 59.519 45.455 0.00 0.00 37.73 4.57
3855 4075 4.686191 TTCCAAAGAAATTGCCATGTGT 57.314 36.364 0.00 0.00 37.73 3.72
3880 4100 6.314152 TCCGTTGTTTGCGAGAATTTGATATA 59.686 34.615 0.00 0.00 0.00 0.86
3884 4104 2.614520 TCCGTTGTTTGCGAGAATTTGA 59.385 40.909 0.00 0.00 0.00 2.69
3885 4105 2.993545 TCCGTTGTTTGCGAGAATTTG 58.006 42.857 0.00 0.00 0.00 2.32
3886 4106 3.915437 ATCCGTTGTTTGCGAGAATTT 57.085 38.095 0.00 0.00 0.00 1.82
3888 4108 3.564511 CAAATCCGTTGTTTGCGAGAAT 58.435 40.909 0.00 0.00 32.08 2.40
3890 4110 2.679355 CAAATCCGTTGTTTGCGAGA 57.321 45.000 0.00 0.00 32.08 4.04
3941 4162 6.644592 GCAATTTATGTGTTGAAAGTTAGGCA 59.355 34.615 0.00 0.00 0.00 4.75
3945 4166 5.631512 GCGGCAATTTATGTGTTGAAAGTTA 59.368 36.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.