Multiple sequence alignment - TraesCS5D01G522400

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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 TraesCS5D01G522400 chr5D 100.000 4094 0 0 1 4094 543054137 543058230 0.000000e+00 7561
1 TraesCS5D01G522400 chr5D 97.836 647 13 1 1 646 139430097 139429451 0.000000e+00 1116
2 TraesCS5D01G522400 chr5D 97.840 648 11 3 1 646 277073506 277072860 0.000000e+00 1116
3 TraesCS5D01G522400 chr4A 93.126 3273 141 29 863 4094 626121771 626118542 0.000000e+00 4721
4 TraesCS5D01G522400 chr5B 91.435 3304 145 58 868 4091 684491574 684494819 0.000000e+00 4407
5 TraesCS5D01G522400 chr5B 84.875 800 56 31 644 1417 684487839 684488599 0.000000e+00 747
6 TraesCS5D01G522400 chr7D 97.988 646 12 1 1 645 90529940 90530585 0.000000e+00 1120
7 TraesCS5D01G522400 chr7D 97.840 648 11 3 1 646 121773095 121772449 0.000000e+00 1116
8 TraesCS5D01G522400 chr7D 97.538 650 12 4 1 648 546261291 546260644 0.000000e+00 1109
9 TraesCS5D01G522400 chr7D 89.810 422 30 4 1971 2386 529382526 529382940 2.800000e-146 529
10 TraesCS5D01G522400 chr7D 89.810 422 30 4 1971 2386 529384989 529384575 2.800000e-146 529
11 TraesCS5D01G522400 chr7D 85.714 329 20 8 2483 2795 529382974 529383291 5.110000e-84 322
12 TraesCS5D01G522400 chr7D 85.714 329 20 8 2483 2795 529384541 529384224 5.110000e-84 322
13 TraesCS5D01G522400 chrUn 97.840 648 12 2 1 646 95194771 95195418 0.000000e+00 1118
14 TraesCS5D01G522400 chrUn 88.376 628 53 10 1270 1880 118864807 118864183 0.000000e+00 737
15 TraesCS5D01G522400 chr2D 97.840 648 11 3 1 646 377646605 377647251 0.000000e+00 1116
16 TraesCS5D01G522400 chr2D 97.836 647 13 1 1 646 441724728 441724082 0.000000e+00 1116
17 TraesCS5D01G522400 chr4D 97.542 651 13 3 1 649 488436969 488436320 0.000000e+00 1110
18 TraesCS5D01G522400 chr6B 85.185 216 23 6 2345 2557 38982854 38983063 3.210000e-51 213


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 TraesCS5D01G522400 chr5D 543054137 543058230 4093 False 7561.0 7561 100.000 1 4094 1 chr5D.!!$F1 4093
1 TraesCS5D01G522400 chr5D 139429451 139430097 646 True 1116.0 1116 97.836 1 646 1 chr5D.!!$R1 645
2 TraesCS5D01G522400 chr5D 277072860 277073506 646 True 1116.0 1116 97.840 1 646 1 chr5D.!!$R2 645
3 TraesCS5D01G522400 chr4A 626118542 626121771 3229 True 4721.0 4721 93.126 863 4094 1 chr4A.!!$R1 3231
4 TraesCS5D01G522400 chr5B 684487839 684494819 6980 False 2577.0 4407 88.155 644 4091 2 chr5B.!!$F1 3447
5 TraesCS5D01G522400 chr7D 90529940 90530585 645 False 1120.0 1120 97.988 1 645 1 chr7D.!!$F1 644
6 TraesCS5D01G522400 chr7D 121772449 121773095 646 True 1116.0 1116 97.840 1 646 1 chr7D.!!$R1 645
7 TraesCS5D01G522400 chr7D 546260644 546261291 647 True 1109.0 1109 97.538 1 648 1 chr7D.!!$R2 647
8 TraesCS5D01G522400 chr7D 529382526 529383291 765 False 425.5 529 87.762 1971 2795 2 chr7D.!!$F2 824
9 TraesCS5D01G522400 chr7D 529384224 529384989 765 True 425.5 529 87.762 1971 2795 2 chr7D.!!$R3 824
10 TraesCS5D01G522400 chrUn 95194771 95195418 647 False 1118.0 1118 97.840 1 646 1 chrUn.!!$F1 645
11 TraesCS5D01G522400 chrUn 118864183 118864807 624 True 737.0 737 88.376 1270 1880 1 chrUn.!!$R1 610
12 TraesCS5D01G522400 chr2D 377646605 377647251 646 False 1116.0 1116 97.840 1 646 1 chr2D.!!$F1 645
13 TraesCS5D01G522400 chr2D 441724082 441724728 646 True 1116.0 1116 97.836 1 646 1 chr2D.!!$R1 645
14 TraesCS5D01G522400 chr4D 488436320 488436969 649 True 1110.0 1110 97.542 1 649 1 chr4D.!!$R1 648

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
818 824 0.386838 TCATCACATCAGATCGCGCT 59.613 50.000 5.56 0.00 0.00 5.92 F
819 825 0.507358 CATCACATCAGATCGCGCTG 59.493 55.000 5.56 3.93 37.24 5.18 F
820 826 1.220169 ATCACATCAGATCGCGCTGC 61.220 55.000 5.56 0.00 35.86 5.25 F
1344 4960 2.103340 GCGCTCGAGGAGGAGAAC 59.897 66.667 15.58 0.00 36.08 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 6037 1.148759 GAAATCTGAGAGACGCCGCC 61.149 60.000 0.00 0.0 0.00 6.13 R
2405 6041 3.170791 TGATGGAAATCTGAGAGACGC 57.829 47.619 0.00 0.0 0.00 5.19 R
2686 6330 4.404098 GGTGCCGTTCGGGTGGAT 62.404 66.667 13.16 0.0 38.44 3.41 R
3171 6840 0.179936 AGTAGAATGCAGGCAGGCTC 59.820 55.000 0.00 0.0 34.04 4.70 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
501 504 1.769716 TTGGTACGTGGATGGGTGCA 61.770 55.000 0.00 0.00 0.00 4.57
629 633 3.368531 GGAACGGAGACTATCAACAGCTT 60.369 47.826 0.00 0.00 0.00 3.74
651 655 7.665559 AGCTTCATTAGGAGTAGAGATGAGTAG 59.334 40.741 0.00 0.00 0.00 2.57
660 664 7.942341 AGGAGTAGAGATGAGTAGATCGAAAAT 59.058 37.037 0.00 0.00 0.00 1.82
702 706 3.840890 TTGTGTGGAATAATTGCGGTC 57.159 42.857 0.00 0.00 0.00 4.79
703 707 1.735018 TGTGTGGAATAATTGCGGTCG 59.265 47.619 0.00 0.00 0.00 4.79
704 708 2.004017 GTGTGGAATAATTGCGGTCGA 58.996 47.619 0.00 0.00 0.00 4.20
705 709 2.004017 TGTGGAATAATTGCGGTCGAC 58.996 47.619 7.13 7.13 0.00 4.20
706 710 2.004017 GTGGAATAATTGCGGTCGACA 58.996 47.619 18.91 0.00 0.00 4.35
738 742 2.105993 GCCCCGGAAATATCTACCTTGT 59.894 50.000 0.73 0.00 0.00 3.16
739 743 3.434596 GCCCCGGAAATATCTACCTTGTT 60.435 47.826 0.73 0.00 0.00 2.83
746 752 6.458342 CGGAAATATCTACCTTGTTGCTTTCC 60.458 42.308 0.00 0.00 37.05 3.13
766 772 3.135895 TCCTCTCCCGGTGAAAATTATCC 59.864 47.826 0.00 0.00 0.00 2.59
771 777 2.618709 CCCGGTGAAAATTATCCTCAGC 59.381 50.000 0.00 0.00 34.90 4.26
805 811 4.361451 AAGAAAATGTCGGCATCATCAC 57.639 40.909 1.37 0.00 33.50 3.06
809 815 2.625695 ATGTCGGCATCATCACATCA 57.374 45.000 0.00 0.00 0.00 3.07
810 816 1.944032 TGTCGGCATCATCACATCAG 58.056 50.000 0.00 0.00 0.00 2.90
811 817 1.481772 TGTCGGCATCATCACATCAGA 59.518 47.619 0.00 0.00 0.00 3.27
812 818 2.103601 TGTCGGCATCATCACATCAGAT 59.896 45.455 0.00 0.00 0.00 2.90
813 819 2.735663 GTCGGCATCATCACATCAGATC 59.264 50.000 0.00 0.00 0.00 2.75
814 820 1.725164 CGGCATCATCACATCAGATCG 59.275 52.381 0.00 0.00 0.00 3.69
815 821 1.463831 GGCATCATCACATCAGATCGC 59.536 52.381 0.00 0.00 0.00 4.58
816 822 1.126296 GCATCATCACATCAGATCGCG 59.874 52.381 0.00 0.00 0.00 5.87
817 823 1.126296 CATCATCACATCAGATCGCGC 59.874 52.381 0.00 0.00 0.00 6.86
818 824 0.386838 TCATCACATCAGATCGCGCT 59.613 50.000 5.56 0.00 0.00 5.92
819 825 0.507358 CATCACATCAGATCGCGCTG 59.493 55.000 5.56 3.93 37.24 5.18
820 826 1.220169 ATCACATCAGATCGCGCTGC 61.220 55.000 5.56 0.00 35.86 5.25
821 827 2.587194 ACATCAGATCGCGCTGCC 60.587 61.111 5.56 0.00 35.86 4.85
822 828 3.344215 CATCAGATCGCGCTGCCC 61.344 66.667 5.56 0.00 35.86 5.36
823 829 3.853487 ATCAGATCGCGCTGCCCA 61.853 61.111 5.56 0.00 35.86 5.36
824 830 3.804153 ATCAGATCGCGCTGCCCAG 62.804 63.158 5.56 0.00 35.86 4.45
840 846 3.252284 AGTGCCCACCCCAGACAG 61.252 66.667 0.00 0.00 0.00 3.51
843 849 4.729918 GCCCACCCCAGACAGCAG 62.730 72.222 0.00 0.00 0.00 4.24
844 850 2.930019 CCCACCCCAGACAGCAGA 60.930 66.667 0.00 0.00 0.00 4.26
1285 4898 2.376109 GATCCCTCAACGTCTACCTCA 58.624 52.381 0.00 0.00 0.00 3.86
1341 4957 3.591835 GAGGCGCTCGAGGAGGAG 61.592 72.222 15.58 0.00 37.11 3.69
1344 4960 2.103340 GCGCTCGAGGAGGAGAAC 59.897 66.667 15.58 0.00 36.08 3.01
1345 4961 2.411504 GCGCTCGAGGAGGAGAACT 61.412 63.158 15.58 0.00 36.08 3.01
1448 5079 4.849329 CTACGTCTCCACCGCGGC 62.849 72.222 28.58 6.59 33.14 6.53
1958 5589 2.791383 GAGGTGATCGATCTGACCAG 57.209 55.000 27.58 0.00 0.00 4.00
2686 6330 1.807755 GCAGCTTCGCCATCTACATGA 60.808 52.381 0.00 0.00 30.57 3.07
2688 6332 2.735663 CAGCTTCGCCATCTACATGATC 59.264 50.000 0.00 0.00 32.05 2.92
2841 6493 0.322322 TTTCGAACCCGCACCACTAT 59.678 50.000 0.00 0.00 35.37 2.12
3030 6682 1.118838 ACTGGCTCAGCATAGAGGAC 58.881 55.000 0.00 0.00 36.15 3.85
3049 6704 2.038329 ATGCCCAGCCTGCACATT 59.962 55.556 0.00 0.00 42.38 2.71
3050 6705 0.752743 GATGCCCAGCCTGCACATTA 60.753 55.000 0.07 0.00 42.38 1.90
3053 6708 1.741327 GCCCAGCCTGCACATTATGG 61.741 60.000 0.00 0.00 0.00 2.74
3096 6751 3.122297 CAAGAAGATCGGCTGCTAGAAG 58.878 50.000 0.00 0.00 29.90 2.85
3097 6752 1.068434 AGAAGATCGGCTGCTAGAAGC 59.932 52.381 15.07 15.07 42.82 3.86
3098 6753 1.068434 GAAGATCGGCTGCTAGAAGCT 59.932 52.381 22.34 2.25 42.97 3.74
3101 6756 3.791539 CGGCTGCTAGAAGCTGTG 58.208 61.111 22.07 9.25 43.37 3.66
3102 6757 1.079543 CGGCTGCTAGAAGCTGTGT 60.080 57.895 22.07 0.00 43.37 3.72
3103 6758 1.080995 CGGCTGCTAGAAGCTGTGTC 61.081 60.000 22.07 4.69 43.37 3.67
3104 6759 0.742635 GGCTGCTAGAAGCTGTGTCC 60.743 60.000 22.34 0.42 42.97 4.02
3105 6760 0.248843 GCTGCTAGAAGCTGTGTCCT 59.751 55.000 16.15 0.00 42.97 3.85
3106 6761 2.006056 GCTGCTAGAAGCTGTGTCCTG 61.006 57.143 16.15 0.00 42.97 3.86
3107 6762 1.547820 CTGCTAGAAGCTGTGTCCTGA 59.452 52.381 0.00 0.00 42.97 3.86
3108 6763 2.168106 CTGCTAGAAGCTGTGTCCTGAT 59.832 50.000 0.00 0.00 42.97 2.90
3115 6784 3.195471 AGCTGTGTCCTGATGATGATG 57.805 47.619 0.00 0.00 0.00 3.07
3128 6797 4.102681 TGATGATGATGTCAAGGAGAGCAT 59.897 41.667 0.00 0.00 40.97 3.79
3129 6798 3.805207 TGATGATGTCAAGGAGAGCATG 58.195 45.455 0.00 0.00 32.31 4.06
3130 6799 3.199289 TGATGATGTCAAGGAGAGCATGT 59.801 43.478 0.00 0.00 32.31 3.21
3131 6800 3.257469 TGATGTCAAGGAGAGCATGTC 57.743 47.619 0.00 0.00 0.00 3.06
3132 6801 2.568509 TGATGTCAAGGAGAGCATGTCA 59.431 45.455 0.00 0.00 0.00 3.58
3162 6831 6.039270 TGTGCTGTATATAAATGTTTGCCCTC 59.961 38.462 0.00 0.00 0.00 4.30
3163 6832 6.263168 GTGCTGTATATAAATGTTTGCCCTCT 59.737 38.462 0.00 0.00 0.00 3.69
3164 6833 7.444183 GTGCTGTATATAAATGTTTGCCCTCTA 59.556 37.037 0.00 0.00 0.00 2.43
3165 6834 7.661437 TGCTGTATATAAATGTTTGCCCTCTAG 59.339 37.037 0.00 0.00 0.00 2.43
3166 6835 7.661847 GCTGTATATAAATGTTTGCCCTCTAGT 59.338 37.037 0.00 0.00 0.00 2.57
3167 6836 8.902540 TGTATATAAATGTTTGCCCTCTAGTG 57.097 34.615 0.00 0.00 0.00 2.74
3168 6837 6.884280 ATATAAATGTTTGCCCTCTAGTGC 57.116 37.500 0.00 0.00 0.00 4.40
3169 6838 2.584835 AATGTTTGCCCTCTAGTGCA 57.415 45.000 1.20 1.20 35.27 4.57
3170 6839 2.119801 ATGTTTGCCCTCTAGTGCAG 57.880 50.000 0.00 0.00 38.95 4.41
3171 6840 0.036732 TGTTTGCCCTCTAGTGCAGG 59.963 55.000 0.00 0.00 38.95 4.85
3172 6841 0.324943 GTTTGCCCTCTAGTGCAGGA 59.675 55.000 0.00 0.00 38.95 3.86
3173 6842 0.615331 TTTGCCCTCTAGTGCAGGAG 59.385 55.000 0.00 0.00 38.95 3.69
3174 6843 1.903877 TTGCCCTCTAGTGCAGGAGC 61.904 60.000 0.00 1.20 38.95 4.70
3175 6844 3.100503 GCCCTCTAGTGCAGGAGCC 62.101 68.421 0.00 0.00 41.13 4.70
3176 6845 1.382420 CCCTCTAGTGCAGGAGCCT 60.382 63.158 0.00 0.00 41.13 4.58
3188 6857 0.984961 AGGAGCCTGCCTGCATTCTA 60.985 55.000 0.00 0.00 36.76 2.10
3191 6860 1.414181 GAGCCTGCCTGCATTCTACTA 59.586 52.381 0.00 0.00 0.00 1.82
3196 6865 4.498682 GCCTGCCTGCATTCTACTAAATTG 60.499 45.833 0.00 0.00 0.00 2.32
3197 6866 4.037208 CCTGCCTGCATTCTACTAAATTGG 59.963 45.833 0.00 0.00 0.00 3.16
3244 6913 0.698238 AGGCCATGTAAAGTGAGGCA 59.302 50.000 5.01 0.00 46.96 4.75
3247 6916 2.497273 GGCCATGTAAAGTGAGGCAATT 59.503 45.455 0.00 0.00 46.96 2.32
3262 6931 4.773013 AGGCAATTTTCAGGCAAATATGG 58.227 39.130 0.00 0.00 0.00 2.74
3333 7004 7.805071 CCACTTGTTAATTTGTAGCAAGAGAAG 59.195 37.037 14.41 0.00 37.77 2.85
3408 7090 3.059352 GTGCATACACTGGGAAGAACT 57.941 47.619 0.00 0.00 43.85 3.01
3458 7140 5.026790 ACTCTACAGGCTAACAGGAATTCT 58.973 41.667 5.23 0.00 0.00 2.40
3484 7166 9.936759 TTCTTATCTTACAATCATACACACACA 57.063 29.630 0.00 0.00 0.00 3.72
3485 7167 9.366216 TCTTATCTTACAATCATACACACACAC 57.634 33.333 0.00 0.00 0.00 3.82
3486 7168 9.150348 CTTATCTTACAATCATACACACACACA 57.850 33.333 0.00 0.00 0.00 3.72
3527 7209 3.094386 TGCGGACCAAGCAATATCC 57.906 52.632 0.00 0.00 42.18 2.59
3573 7256 5.005094 GGCTCTACCGACAATCTATCTAGT 58.995 45.833 0.00 0.00 0.00 2.57
3637 7320 2.743718 CATTCCGCGCCCCTAGAT 59.256 61.111 0.00 0.00 0.00 1.98
3682 7365 2.936160 ATAGGCTCTGCTGCTCCCGA 62.936 60.000 0.00 0.00 0.00 5.14
3745 7428 1.933247 CTCTCGCATCCAGTCCTTTC 58.067 55.000 0.00 0.00 0.00 2.62
3772 7455 1.541147 CTTTGAAGCCAGCCGAAATCA 59.459 47.619 0.00 0.00 0.00 2.57
3979 7662 6.854892 CGAAATTCTCTGCCATATCATTGTTC 59.145 38.462 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.712152 AGCCAAATCAACGAATCTCTTTT 57.288 34.783 0.00 0.00 0.00 2.27
212 213 9.452287 ACATTAATGCAATTTGCTTTAGGAAAT 57.548 25.926 21.19 13.85 45.86 2.17
238 239 4.487714 AGCCAAATCAACGGATCTCTTA 57.512 40.909 0.00 0.00 31.88 2.10
501 504 2.612115 CTCCTGAGGCCCCAACCT 60.612 66.667 0.00 0.00 45.04 3.50
620 624 5.952347 TCTCTACTCCTAATGAAGCTGTTGA 59.048 40.000 0.00 0.00 0.00 3.18
625 629 6.372931 ACTCATCTCTACTCCTAATGAAGCT 58.627 40.000 0.00 0.00 0.00 3.74
629 633 8.038351 CGATCTACTCATCTCTACTCCTAATGA 58.962 40.741 0.00 0.00 0.00 2.57
679 683 4.743493 ACCGCAATTATTCCACACAAATC 58.257 39.130 0.00 0.00 0.00 2.17
684 688 2.004017 TCGACCGCAATTATTCCACAC 58.996 47.619 0.00 0.00 0.00 3.82
702 706 0.386731 GGGGCAAATTTGTCGTGTCG 60.387 55.000 19.03 0.00 32.44 4.35
703 707 0.386731 CGGGGCAAATTTGTCGTGTC 60.387 55.000 19.03 4.29 32.44 3.67
704 708 1.657556 CGGGGCAAATTTGTCGTGT 59.342 52.632 19.03 0.00 32.44 4.49
705 709 1.080839 CCGGGGCAAATTTGTCGTG 60.081 57.895 19.03 12.09 32.44 4.35
706 710 0.824182 TTCCGGGGCAAATTTGTCGT 60.824 50.000 19.03 0.00 32.44 4.34
738 742 1.125093 TCACCGGGAGAGGAAAGCAA 61.125 55.000 6.32 0.00 34.73 3.91
739 743 1.125093 TTCACCGGGAGAGGAAAGCA 61.125 55.000 6.32 0.00 34.73 3.91
746 752 4.141711 TGAGGATAATTTTCACCGGGAGAG 60.142 45.833 6.32 0.00 0.00 3.20
766 772 1.811359 CTTTTTCTGGCTGAGGCTGAG 59.189 52.381 14.65 0.00 37.37 3.35
771 777 5.205759 ACATTTTCTTTTTCTGGCTGAGG 57.794 39.130 0.00 0.00 0.00 3.86
805 811 3.344215 GGGCAGCGCGATCTGATG 61.344 66.667 12.10 0.00 36.19 3.07
809 815 4.827087 CACTGGGCAGCGCGATCT 62.827 66.667 12.10 0.00 0.00 2.75
821 827 4.351054 GTCTGGGGTGGGCACTGG 62.351 72.222 0.00 0.00 0.00 4.00
822 828 3.557903 CTGTCTGGGGTGGGCACTG 62.558 68.421 0.00 0.00 0.00 3.66
823 829 3.252284 CTGTCTGGGGTGGGCACT 61.252 66.667 0.00 0.00 0.00 4.40
840 846 2.813042 GGACGTGCTCTGCTCTGC 60.813 66.667 0.00 0.00 0.00 4.26
841 847 1.153862 GAGGACGTGCTCTGCTCTG 60.154 63.158 27.63 0.00 0.00 3.35
842 848 0.897863 AAGAGGACGTGCTCTGCTCT 60.898 55.000 35.92 20.21 0.00 4.09
843 849 0.457681 GAAGAGGACGTGCTCTGCTC 60.458 60.000 35.92 26.89 0.00 4.26
844 850 1.181741 TGAAGAGGACGTGCTCTGCT 61.182 55.000 36.11 24.80 0.00 4.24
1236 4849 2.883253 GAGACGAAGAGCAGCGCC 60.883 66.667 2.29 0.00 0.00 6.53
1266 4879 2.100989 GTGAGGTAGACGTTGAGGGAT 58.899 52.381 0.00 0.00 0.00 3.85
1783 5414 2.322212 CGTCATCGGAGACCTCGAT 58.678 57.895 0.00 0.00 46.64 3.59
1923 5554 1.298413 CTCGATGTGCCGGTAGTCG 60.298 63.158 17.50 17.50 38.88 4.18
1966 5597 2.025418 CGAAGTAGGCGGCGTTGTT 61.025 57.895 9.37 0.00 0.00 2.83
2010 5641 3.670377 GGGTTGAAGTGGTGCGCC 61.670 66.667 10.11 10.11 0.00 6.53
2250 5886 1.927895 CGTTCCCGGAGAAGATCTTG 58.072 55.000 14.00 0.00 34.29 3.02
2401 6037 1.148759 GAAATCTGAGAGACGCCGCC 61.149 60.000 0.00 0.00 0.00 6.13
2405 6041 3.170791 TGATGGAAATCTGAGAGACGC 57.829 47.619 0.00 0.00 0.00 5.19
2406 6042 5.003692 TCTTGATGGAAATCTGAGAGACG 57.996 43.478 0.00 0.00 0.00 4.18
2407 6043 5.294060 GCTTCTTGATGGAAATCTGAGAGAC 59.706 44.000 0.00 0.00 0.00 3.36
2686 6330 4.404098 GGTGCCGTTCGGGTGGAT 62.404 66.667 13.16 0.00 38.44 3.41
2996 6648 1.757306 CAGTGGCAGTCCTGGAACT 59.243 57.895 0.00 0.00 0.00 3.01
2997 6649 4.386413 CAGTGGCAGTCCTGGAAC 57.614 61.111 0.00 0.00 0.00 3.62
3046 6701 1.470098 GGCATAGCGAAGGCCATAATG 59.530 52.381 5.01 0.67 46.92 1.90
3047 6702 1.826385 GGCATAGCGAAGGCCATAAT 58.174 50.000 5.01 0.00 46.92 1.28
3053 6708 2.263741 CCATGGGCATAGCGAAGGC 61.264 63.158 2.85 0.00 40.37 4.35
3078 6733 1.068434 AGCTTCTAGCAGCCGATCTTC 59.932 52.381 10.97 0.00 45.56 2.87
3096 6751 2.871022 GACATCATCATCAGGACACAGC 59.129 50.000 0.00 0.00 0.00 4.40
3097 6752 4.133013 TGACATCATCATCAGGACACAG 57.867 45.455 0.00 0.00 29.99 3.66
3098 6753 4.510571 CTTGACATCATCATCAGGACACA 58.489 43.478 0.00 0.00 37.11 3.72
3099 6754 3.875727 CCTTGACATCATCATCAGGACAC 59.124 47.826 0.00 0.00 37.47 3.67
3100 6755 3.776417 TCCTTGACATCATCATCAGGACA 59.224 43.478 0.00 0.00 38.80 4.02
3101 6756 4.100653 TCTCCTTGACATCATCATCAGGAC 59.899 45.833 0.00 0.00 38.80 3.85
3102 6757 4.292643 TCTCCTTGACATCATCATCAGGA 58.707 43.478 0.52 0.52 40.61 3.86
3103 6758 4.633175 CTCTCCTTGACATCATCATCAGG 58.367 47.826 0.00 0.00 36.86 3.86
3104 6759 4.059511 GCTCTCCTTGACATCATCATCAG 58.940 47.826 0.00 0.00 37.11 2.90
3105 6760 3.453353 TGCTCTCCTTGACATCATCATCA 59.547 43.478 0.00 0.00 37.11 3.07
3106 6761 4.069300 TGCTCTCCTTGACATCATCATC 57.931 45.455 0.00 0.00 37.11 2.92
3107 6762 4.141459 ACATGCTCTCCTTGACATCATCAT 60.141 41.667 0.00 0.00 37.11 2.45
3108 6763 3.199289 ACATGCTCTCCTTGACATCATCA 59.801 43.478 0.00 0.00 34.65 3.07
3128 6797 3.843893 ATATACAGCACAGGCATGACA 57.156 42.857 4.84 0.00 44.61 3.58
3129 6798 6.205464 ACATTTATATACAGCACAGGCATGAC 59.795 38.462 4.84 0.00 44.61 3.06
3130 6799 6.298361 ACATTTATATACAGCACAGGCATGA 58.702 36.000 4.84 0.00 44.61 3.07
3131 6800 6.564709 ACATTTATATACAGCACAGGCATG 57.435 37.500 0.00 0.00 44.61 4.06
3132 6801 7.428020 CAAACATTTATATACAGCACAGGCAT 58.572 34.615 0.00 0.00 44.61 4.40
3169 6838 0.984961 TAGAATGCAGGCAGGCTCCT 60.985 55.000 0.00 0.31 36.78 3.69
3170 6839 0.817229 GTAGAATGCAGGCAGGCTCC 60.817 60.000 0.00 0.00 34.04 4.70
3171 6840 0.179936 AGTAGAATGCAGGCAGGCTC 59.820 55.000 0.00 0.00 34.04 4.70
3172 6841 1.500474 TAGTAGAATGCAGGCAGGCT 58.500 50.000 0.00 0.00 34.04 4.58
3173 6842 2.332063 TTAGTAGAATGCAGGCAGGC 57.668 50.000 0.00 0.00 0.00 4.85
3174 6843 4.037208 CCAATTTAGTAGAATGCAGGCAGG 59.963 45.833 0.00 0.00 0.00 4.85
3175 6844 4.641989 ACCAATTTAGTAGAATGCAGGCAG 59.358 41.667 0.00 0.00 0.00 4.85
3176 6845 4.599041 ACCAATTTAGTAGAATGCAGGCA 58.401 39.130 0.00 0.00 0.00 4.75
3197 6866 5.019785 CTGGGGAAATACAGGTACAGTAC 57.980 47.826 1.59 1.59 31.94 2.73
3215 6884 3.593442 TTACATGGCCTTATTCCTGGG 57.407 47.619 3.32 0.00 0.00 4.45
3244 6913 6.371595 TTGGTCCATATTTGCCTGAAAATT 57.628 33.333 0.00 0.00 32.16 1.82
3247 6916 6.171921 CAATTTGGTCCATATTTGCCTGAAA 58.828 36.000 4.91 0.00 0.00 2.69
3262 6931 4.101430 ACATATCCCAATGGCAATTTGGTC 59.899 41.667 16.51 0.00 41.74 4.02
3333 7004 5.181690 TGTAGAATTGCTTCAAACCACAC 57.818 39.130 0.00 0.00 33.56 3.82
3408 7090 8.366401 TGAATTTTTGTTTATGATCTTGCCTCA 58.634 29.630 0.00 0.00 0.00 3.86
3458 7140 9.936759 TGTGTGTGTATGATTGTAAGATAAGAA 57.063 29.630 0.00 0.00 0.00 2.52
3483 7165 9.692749 ATGAGTTATATCGGTATTTGTAGTGTG 57.307 33.333 0.00 0.00 0.00 3.82
3484 7166 9.692749 CATGAGTTATATCGGTATTTGTAGTGT 57.307 33.333 0.00 0.00 0.00 3.55
3485 7167 8.648097 GCATGAGTTATATCGGTATTTGTAGTG 58.352 37.037 0.00 0.00 0.00 2.74
3486 7168 7.541091 CGCATGAGTTATATCGGTATTTGTAGT 59.459 37.037 0.00 0.00 0.00 2.73
3527 7209 0.534652 GGAGCAGCAGAAGCCTATGG 60.535 60.000 0.00 0.00 43.56 2.74
3573 7256 0.327924 ATGGTGGCGAAGGTCATTCA 59.672 50.000 0.00 0.00 37.83 2.57
3637 7320 0.537143 AATGGTTCCAGTGCTTCGCA 60.537 50.000 0.00 0.00 35.60 5.10
3661 7344 0.182299 GGGAGCAGCAGAGCCTATTT 59.818 55.000 0.00 0.00 34.23 1.40
3682 7365 1.679898 CCTTCTCACCCTTCCGCTT 59.320 57.895 0.00 0.00 0.00 4.68
3688 7371 1.075659 GCAAGCCCTTCTCACCCTT 59.924 57.895 0.00 0.00 0.00 3.95
3739 7422 2.494059 CTTCAAAGGTGCTCGAAAGGA 58.506 47.619 0.00 0.00 0.00 3.36
3745 7428 1.871772 CTGGCTTCAAAGGTGCTCG 59.128 57.895 0.00 0.00 0.00 5.03
3772 7455 1.270412 TGGTTCACGCCGATGTTAACT 60.270 47.619 7.22 0.00 0.00 2.24
3979 7662 3.474600 CTGGCTATTTGAGATCCTGGTG 58.525 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.