Multiple sequence alignment - TraesCS2D01G117300

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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 TraesCS2D01G117300 chr2D 100.000 2347 0 0 1 2347 66822139 66819793 0.000000e+00 4335.0
1 TraesCS2D01G117300 chr2B 92.944 1488 78 15 865 2347 104805631 104807096 0.000000e+00 2141.0
2 TraesCS2D01G117300 chr2B 92.331 326 15 9 1 318 104804904 104805227 2.750000e-124 455.0
3 TraesCS2D01G117300 chr2B 92.737 179 13 0 367 545 104805226 104805404 2.310000e-65 259.0
4 TraesCS2D01G117300 chr2B 95.041 121 6 0 581 701 104805406 104805526 8.560000e-45 191.0
5 TraesCS2D01G117300 chr2B 95.652 69 1 1 774 842 796806520 796806454 2.470000e-20 110.0
6 TraesCS2D01G117300 chr2A 92.154 650 38 5 1331 1976 68178956 68179596 0.000000e+00 905.0
7 TraesCS2D01G117300 chr2A 94.639 429 20 3 1 428 68156220 68156646 0.000000e+00 662.0
8 TraesCS2D01G117300 chr2A 95.556 405 17 1 931 1335 68159301 68159704 0.000000e+00 647.0
9 TraesCS2D01G117300 chr2A 91.522 460 29 6 1890 2346 68179947 68180399 1.980000e-175 625.0
10 TraesCS2D01G117300 chr2A 95.810 358 15 0 423 780 68158687 68159044 1.560000e-161 579.0
11 TraesCS2D01G117300 chr2A 84.672 274 33 6 1474 1746 68179594 68179859 4.970000e-67 265.0
12 TraesCS2D01G117300 chr2A 97.170 106 2 1 840 945 68159042 68159146 6.660000e-41 178.0
13 TraesCS2D01G117300 chr6D 95.385 65 1 1 778 842 62122799 62122737 4.130000e-18 102.0
14 TraesCS2D01G117300 chr6D 89.474 76 6 1 766 841 18498548 18498621 6.900000e-16 95.3
15 TraesCS2D01G117300 chr6B 92.958 71 4 1 781 850 151609055 151608985 4.130000e-18 102.0
16 TraesCS2D01G117300 chr4D 94.118 68 2 2 778 843 444255146 444255079 4.130000e-18 102.0
17 TraesCS2D01G117300 chr4D 90.411 73 6 1 769 841 301747398 301747469 6.900000e-16 95.3
18 TraesCS2D01G117300 chr4B 95.385 65 2 1 778 841 661199831 661199895 4.130000e-18 102.0
19 TraesCS2D01G117300 chr6A 92.857 70 2 1 775 844 404350476 404350542 5.340000e-17 99.0
20 TraesCS2D01G117300 chr1A 91.667 72 4 1 778 849 58274650 58274581 5.340000e-17 99.0


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 TraesCS2D01G117300 chr2D 66819793 66822139 2346 True 4335.000000 4335 100.000000 1 2347 1 chr2D.!!$R1 2346
1 TraesCS2D01G117300 chr2B 104804904 104807096 2192 False 761.500000 2141 93.263250 1 2347 4 chr2B.!!$F1 2346
2 TraesCS2D01G117300 chr2A 68178956 68180399 1443 False 598.333333 905 89.449333 1331 2346 3 chr2A.!!$F2 1015
3 TraesCS2D01G117300 chr2A 68156220 68159704 3484 False 516.500000 662 95.793750 1 1335 4 chr2A.!!$F1 1334

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
792 2884 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 4966 0.322322 TTACCGAACGCCAAGACCAT 59.678 50.0 0.0 0.0 0.0 3.55 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
71 78 3.332919 ACAGTTCTGACTATGCTTGCTG 58.667 45.455 6.83 0.00 33.90 4.41
81 88 6.527423 TGACTATGCTTGCTGATGATATTCA 58.473 36.000 0.00 0.00 0.00 2.57
120 127 7.760131 AAATGTTATGCACATGTTATGAAGC 57.240 32.000 0.00 0.00 46.23 3.86
160 167 5.643379 TGCAACTTCTTGTCTCTGTTTTT 57.357 34.783 0.00 0.00 0.00 1.94
320 328 2.670414 GTGTAAGTCACTCAGCTGCATC 59.330 50.000 9.47 0.00 43.13 3.91
321 329 1.923204 GTAAGTCACTCAGCTGCATCG 59.077 52.381 9.47 0.00 0.00 3.84
336 344 2.159393 TGCATCGTGATTGCTTTTAGGC 60.159 45.455 0.00 0.00 0.00 3.93
361 369 7.095017 GCTGTTAGAACTTAGAATTGCTGAACT 60.095 37.037 0.00 0.00 0.00 3.01
551 2604 8.250332 AGAAAAATTACAGAACAAAAGACAGCA 58.750 29.630 0.00 0.00 0.00 4.41
569 2622 8.169977 AGACAGCAGAGATTTTTATGTCAAAA 57.830 30.769 5.36 0.00 38.38 2.44
729 2815 5.074804 AGTTTTCGGTATTTAGTTTGGGCT 58.925 37.500 0.00 0.00 0.00 5.19
733 2825 2.681344 CGGTATTTAGTTTGGGCTCACC 59.319 50.000 0.00 0.00 40.81 4.02
734 2826 3.621461 CGGTATTTAGTTTGGGCTCACCT 60.621 47.826 0.00 0.00 41.11 4.00
735 2827 4.341487 GGTATTTAGTTTGGGCTCACCTT 58.659 43.478 0.00 0.00 41.11 3.50
736 2828 4.770531 GGTATTTAGTTTGGGCTCACCTTT 59.229 41.667 0.00 0.00 41.11 3.11
737 2829 5.245301 GGTATTTAGTTTGGGCTCACCTTTT 59.755 40.000 0.00 0.00 41.11 2.27
738 2830 4.929819 TTTAGTTTGGGCTCACCTTTTC 57.070 40.909 0.00 0.00 41.11 2.29
739 2831 2.755952 AGTTTGGGCTCACCTTTTCT 57.244 45.000 0.00 0.00 41.11 2.52
740 2832 3.032265 AGTTTGGGCTCACCTTTTCTT 57.968 42.857 0.00 0.00 41.11 2.52
741 2833 4.178956 AGTTTGGGCTCACCTTTTCTTA 57.821 40.909 0.00 0.00 41.11 2.10
742 2834 4.542697 AGTTTGGGCTCACCTTTTCTTAA 58.457 39.130 0.00 0.00 41.11 1.85
786 2878 8.483758 TCAATTAAGTTAGAACATACTCCCTCC 58.516 37.037 0.00 0.00 0.00 4.30
787 2879 6.461110 TTAAGTTAGAACATACTCCCTCCG 57.539 41.667 0.00 0.00 0.00 4.63
788 2880 3.978610 AGTTAGAACATACTCCCTCCGT 58.021 45.455 0.00 0.00 0.00 4.69
789 2881 3.952967 AGTTAGAACATACTCCCTCCGTC 59.047 47.826 0.00 0.00 0.00 4.79
790 2882 1.777941 AGAACATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
791 2883 0.751452 GAACATACTCCCTCCGTCCC 59.249 60.000 0.00 0.00 0.00 4.46
792 2884 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
793 2885 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
794 2886 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
795 2887 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
796 2888 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
797 2889 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
798 2890 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
799 2891 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
800 2892 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
801 2893 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
802 2894 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
803 2895 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
804 2896 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
805 2897 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
806 2898 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
807 2899 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
808 2900 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
809 2901 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
810 2902 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
811 2903 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
812 2904 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
813 2905 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
814 2906 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
815 2907 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
816 2908 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
822 2914 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
823 2915 9.880157 AAGTGACTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
824 2916 9.530633 AGTGACTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
825 2917 9.310716 GTGACTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
826 2918 9.309516 TGACTCAACTTTGTACTAACTTTAGTG 57.690 33.333 11.24 0.00 43.44 2.74
827 2919 8.658499 ACTCAACTTTGTACTAACTTTAGTGG 57.342 34.615 11.24 1.06 43.44 4.00
828 2920 7.713942 ACTCAACTTTGTACTAACTTTAGTGGG 59.286 37.037 11.24 0.00 43.44 4.61
829 2921 7.794041 TCAACTTTGTACTAACTTTAGTGGGA 58.206 34.615 11.24 0.00 43.44 4.37
830 2922 7.712205 TCAACTTTGTACTAACTTTAGTGGGAC 59.288 37.037 11.24 3.43 43.44 4.46
831 2923 6.218746 ACTTTGTACTAACTTTAGTGGGACG 58.781 40.000 11.24 1.52 43.44 4.79
832 2924 4.789012 TGTACTAACTTTAGTGGGACGG 57.211 45.455 11.24 0.00 43.44 4.79
833 2925 4.406456 TGTACTAACTTTAGTGGGACGGA 58.594 43.478 11.24 0.00 43.44 4.69
834 2926 4.460382 TGTACTAACTTTAGTGGGACGGAG 59.540 45.833 11.24 0.00 43.44 4.63
835 2927 2.830321 ACTAACTTTAGTGGGACGGAGG 59.170 50.000 0.70 0.00 42.13 4.30
836 2928 0.981943 AACTTTAGTGGGACGGAGGG 59.018 55.000 0.00 0.00 0.00 4.30
837 2929 0.115745 ACTTTAGTGGGACGGAGGGA 59.884 55.000 0.00 0.00 0.00 4.20
838 2930 0.824759 CTTTAGTGGGACGGAGGGAG 59.175 60.000 0.00 0.00 0.00 4.30
839 2931 0.115745 TTTAGTGGGACGGAGGGAGT 59.884 55.000 0.00 0.00 0.00 3.85
840 2932 1.002069 TTAGTGGGACGGAGGGAGTA 58.998 55.000 0.00 0.00 0.00 2.59
841 2933 0.257039 TAGTGGGACGGAGGGAGTAC 59.743 60.000 0.00 0.00 0.00 2.73
1008 3269 4.822685 TGGTATGCAGGCAATGAAATTT 57.177 36.364 0.00 0.00 31.22 1.82
1119 3380 0.241749 CTGATGCGTGCACAATGGTT 59.758 50.000 18.64 0.00 0.00 3.67
1134 3395 1.447314 GGTTAGACCTCGTTGGCCG 60.447 63.158 0.00 0.00 40.22 6.13
1218 3479 9.747898 AACATAATAGTAACACCCAATCTTTCA 57.252 29.630 0.00 0.00 0.00 2.69
1241 3502 1.605710 GCCATGGTCGGAATTGATCAG 59.394 52.381 14.67 0.00 31.32 2.90
1321 3582 3.282021 TGAAGCTGGATCCTACAAATGC 58.718 45.455 14.23 5.99 0.00 3.56
1328 3589 6.214208 AGCTGGATCCTACAAATGCTGATATA 59.786 38.462 14.23 0.00 0.00 0.86
1356 3617 5.163281 TGCTTTAAGGTAACCGTTCCATA 57.837 39.130 0.00 0.00 37.17 2.74
1361 3622 7.699391 GCTTTAAGGTAACCGTTCCATATTTTC 59.301 37.037 0.00 0.00 37.17 2.29
1382 3643 5.337219 TCATTTTGCGTAGTATTATGCGG 57.663 39.130 5.14 0.00 43.37 5.69
1396 3657 4.065281 GCGGTAGTGGTCGGCAGT 62.065 66.667 0.00 0.00 0.00 4.40
1417 3678 3.305361 GTGTCTTCCGTAACTAATTCGGC 59.695 47.826 0.00 0.00 43.35 5.54
1515 3776 5.633830 ATTTGCGAGTTCTGAATGTTGAT 57.366 34.783 0.00 0.00 0.00 2.57
1585 3846 3.932545 TGTTGTTGTGTTTCTTGCTGT 57.067 38.095 0.00 0.00 0.00 4.40
1592 3853 4.044336 TGTGTTTCTTGCTGTCATTTGG 57.956 40.909 0.00 0.00 0.00 3.28
1742 4003 4.360951 AACTGACAGATTTTCCGGGTAA 57.639 40.909 10.08 0.00 0.00 2.85
1820 4081 5.104693 TCTGGATGGCCGAGTTATAAAAAGA 60.105 40.000 0.00 0.00 36.79 2.52
1860 4121 4.396166 GGATTTTCTGTCATGACCGAATGT 59.604 41.667 26.80 19.77 35.14 2.71
1996 4700 2.472695 TCAGAGTTACAATTGCGGCT 57.527 45.000 5.05 0.42 0.00 5.52
1999 4703 2.076863 AGAGTTACAATTGCGGCTGTC 58.923 47.619 5.05 0.00 0.00 3.51
2048 4752 7.264294 ACATAGGGAAGAGGATCCAATTATC 57.736 40.000 15.82 1.71 41.55 1.75
2061 4766 6.150140 GGATCCAATTATCCTGTTGCTATGTC 59.850 42.308 6.95 0.00 41.99 3.06
2095 4801 7.500992 TGTTATACTATTTGCTCTCTGGGAAG 58.499 38.462 0.00 0.00 0.00 3.46
2188 4894 0.381801 AACGGCTGTGCTGAAAAGTG 59.618 50.000 0.00 0.00 38.46 3.16
2191 4897 0.040958 GGCTGTGCTGAAAAGTGACG 60.041 55.000 0.00 0.00 0.00 4.35
2258 4964 5.067805 AGGACCTGTTTTGAACTAGCTTTTG 59.932 40.000 0.00 0.00 0.00 2.44
2259 4965 5.163550 GGACCTGTTTTGAACTAGCTTTTGT 60.164 40.000 0.00 0.00 0.00 2.83
2260 4966 6.038936 GGACCTGTTTTGAACTAGCTTTTGTA 59.961 38.462 0.00 0.00 0.00 2.41
2261 4967 7.255486 GGACCTGTTTTGAACTAGCTTTTGTAT 60.255 37.037 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 127 6.624423 AGTTGCATTTAGAAGTTAGCAATGG 58.376 36.000 0.00 0.00 42.90 3.16
130 137 7.041508 ACAGAGACAAGAAGTTGCATTTAGAAG 60.042 37.037 0.00 0.00 37.14 2.85
131 138 6.767902 ACAGAGACAAGAAGTTGCATTTAGAA 59.232 34.615 0.00 0.00 37.14 2.10
320 328 3.559238 AACAGCCTAAAAGCAATCACG 57.441 42.857 0.00 0.00 34.23 4.35
321 329 5.880054 TCTAACAGCCTAAAAGCAATCAC 57.120 39.130 0.00 0.00 34.23 3.06
336 344 8.316640 AGTTCAGCAATTCTAAGTTCTAACAG 57.683 34.615 0.00 0.00 0.00 3.16
361 369 0.673437 GGTGTTGCAGCCAGCTTTAA 59.327 50.000 9.60 0.00 45.94 1.52
545 2598 8.078596 AGTTTTGACATAAAAATCTCTGCTGTC 58.921 33.333 0.00 0.00 32.02 3.51
551 2604 9.533253 CACCAAAGTTTTGACATAAAAATCTCT 57.467 29.630 6.18 0.00 40.55 3.10
569 2622 4.953579 ACAAATCACAAGTACCACCAAAGT 59.046 37.500 0.00 0.00 0.00 2.66
729 2815 9.255304 GCAACATTTGTATTTAAGAAAAGGTGA 57.745 29.630 0.00 0.00 0.00 4.02
761 2853 7.438459 CGGAGGGAGTATGTTCTAACTTAATTG 59.562 40.741 0.00 0.00 0.00 2.32
780 2872 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
781 2873 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
782 2874 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
783 2875 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
784 2876 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
785 2877 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
786 2878 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
787 2879 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
788 2880 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
789 2881 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
790 2882 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
796 2888 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
797 2889 8.788325 AAAGTTAGTACAAAGTTGAGTCACTT 57.212 30.769 0.00 0.00 38.74 3.16
798 2890 9.530633 CTAAAGTTAGTACAAAGTTGAGTCACT 57.469 33.333 0.00 0.00 0.00 3.41
799 2891 9.310716 ACTAAAGTTAGTACAAAGTTGAGTCAC 57.689 33.333 1.81 0.00 41.92 3.67
800 2892 9.309516 CACTAAAGTTAGTACAAAGTTGAGTCA 57.690 33.333 3.46 0.00 41.82 3.41
801 2893 8.762426 CCACTAAAGTTAGTACAAAGTTGAGTC 58.238 37.037 3.46 0.00 41.82 3.36
802 2894 7.713942 CCCACTAAAGTTAGTACAAAGTTGAGT 59.286 37.037 3.46 0.00 41.82 3.41
803 2895 7.929785 TCCCACTAAAGTTAGTACAAAGTTGAG 59.070 37.037 3.46 0.00 41.82 3.02
804 2896 7.712205 GTCCCACTAAAGTTAGTACAAAGTTGA 59.288 37.037 3.46 0.00 41.82 3.18
805 2897 7.306983 CGTCCCACTAAAGTTAGTACAAAGTTG 60.307 40.741 3.46 0.00 41.82 3.16
806 2898 6.703165 CGTCCCACTAAAGTTAGTACAAAGTT 59.297 38.462 3.46 0.00 41.82 2.66
807 2899 6.218746 CGTCCCACTAAAGTTAGTACAAAGT 58.781 40.000 3.46 0.00 41.82 2.66
808 2900 5.636543 CCGTCCCACTAAAGTTAGTACAAAG 59.363 44.000 3.46 0.00 41.82 2.77
809 2901 5.304101 TCCGTCCCACTAAAGTTAGTACAAA 59.696 40.000 3.46 0.00 41.82 2.83
810 2902 4.832266 TCCGTCCCACTAAAGTTAGTACAA 59.168 41.667 3.46 0.00 41.82 2.41
811 2903 4.406456 TCCGTCCCACTAAAGTTAGTACA 58.594 43.478 3.46 0.00 41.82 2.90
812 2904 4.142293 CCTCCGTCCCACTAAAGTTAGTAC 60.142 50.000 3.46 0.00 41.82 2.73
813 2905 4.019174 CCTCCGTCCCACTAAAGTTAGTA 58.981 47.826 3.46 0.00 41.82 1.82
814 2906 2.830321 CCTCCGTCCCACTAAAGTTAGT 59.170 50.000 0.00 0.00 44.42 2.24
815 2907 2.167900 CCCTCCGTCCCACTAAAGTTAG 59.832 54.545 0.00 0.00 36.82 2.34
816 2908 2.181975 CCCTCCGTCCCACTAAAGTTA 58.818 52.381 0.00 0.00 0.00 2.24
817 2909 0.981943 CCCTCCGTCCCACTAAAGTT 59.018 55.000 0.00 0.00 0.00 2.66
818 2910 0.115745 TCCCTCCGTCCCACTAAAGT 59.884 55.000 0.00 0.00 0.00 2.66
819 2911 0.824759 CTCCCTCCGTCCCACTAAAG 59.175 60.000 0.00 0.00 0.00 1.85
820 2912 0.115745 ACTCCCTCCGTCCCACTAAA 59.884 55.000 0.00 0.00 0.00 1.85
821 2913 1.002069 TACTCCCTCCGTCCCACTAA 58.998 55.000 0.00 0.00 0.00 2.24
822 2914 0.257039 GTACTCCCTCCGTCCCACTA 59.743 60.000 0.00 0.00 0.00 2.74
823 2915 1.000107 GTACTCCCTCCGTCCCACT 60.000 63.158 0.00 0.00 0.00 4.00
824 2916 0.686769 ATGTACTCCCTCCGTCCCAC 60.687 60.000 0.00 0.00 0.00 4.61
825 2917 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
826 2918 1.201424 AAATGTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
827 2919 4.476628 TTAAAATGTACTCCCTCCGTCC 57.523 45.455 0.00 0.00 0.00 4.79
828 2920 6.997239 AATTTAAAATGTACTCCCTCCGTC 57.003 37.500 0.00 0.00 0.00 4.79
829 2921 6.943718 TCAAATTTAAAATGTACTCCCTCCGT 59.056 34.615 0.00 0.00 0.00 4.69
830 2922 7.385778 TCAAATTTAAAATGTACTCCCTCCG 57.614 36.000 0.00 0.00 0.00 4.63
831 2923 8.803235 AGTTCAAATTTAAAATGTACTCCCTCC 58.197 33.333 9.41 0.00 0.00 4.30
883 2975 2.932614 AGCATTGCTAGCTACAAACTCG 59.067 45.455 17.23 0.00 41.32 4.18
937 3029 7.740805 TGGTAGTGATGCATACACCAATATTA 58.259 34.615 19.27 7.27 38.82 0.98
1008 3269 4.836825 CAAGATCTTTTGGACTAGGCTCA 58.163 43.478 4.86 0.00 0.00 4.26
1134 3395 2.676839 GCCTTTTCGGTAGTAGCCTTTC 59.323 50.000 0.00 0.00 34.25 2.62
1209 3470 3.251729 CCGACCATGGCTATGAAAGATTG 59.748 47.826 13.04 0.00 36.36 2.67
1218 3479 3.072915 TGATCAATTCCGACCATGGCTAT 59.927 43.478 13.04 0.00 0.00 2.97
1241 3502 3.375299 CCTGTAAATAGACACCAAGCAGC 59.625 47.826 0.00 0.00 0.00 5.25
1356 3617 7.378461 CCGCATAATACTACGCAAAATGAAAAT 59.622 33.333 0.00 0.00 0.00 1.82
1361 3622 5.090652 ACCGCATAATACTACGCAAAATG 57.909 39.130 0.00 0.00 0.00 2.32
1382 3643 0.317479 AAGACACTGCCGACCACTAC 59.683 55.000 0.00 0.00 0.00 2.73
1417 3678 4.607293 TTCGGTCATCCAGATCTAATGG 57.393 45.455 14.24 5.49 39.33 3.16
1470 3731 3.817084 TCTGTCAATGCTGTCTTTTCAGG 59.183 43.478 0.00 0.00 36.12 3.86
1472 3733 6.395426 AATTCTGTCAATGCTGTCTTTTCA 57.605 33.333 0.00 0.00 0.00 2.69
1473 3734 6.346359 GCAAATTCTGTCAATGCTGTCTTTTC 60.346 38.462 0.00 0.00 34.29 2.29
1515 3776 5.523552 AGCAAATTACGATCATGATCAACGA 59.476 36.000 30.13 15.83 37.69 3.85
1564 3825 4.233789 GACAGCAAGAAACACAACAACAA 58.766 39.130 0.00 0.00 0.00 2.83
1585 3846 3.277715 TGCATAGATTCACGCCAAATGA 58.722 40.909 0.00 0.00 0.00 2.57
1592 3853 5.692204 AGTATTACACTGCATAGATTCACGC 59.308 40.000 0.00 0.00 35.62 5.34
1718 3979 3.568430 ACCCGGAAAATCTGTCAGTTTTC 59.432 43.478 20.73 20.73 41.36 2.29
1721 3982 2.951229 ACCCGGAAAATCTGTCAGTT 57.049 45.000 0.73 0.00 0.00 3.16
1731 3992 4.002316 CGGTAATTCTGTTACCCGGAAAA 58.998 43.478 0.73 0.00 41.70 2.29
1736 3997 2.094078 TGACCGGTAATTCTGTTACCCG 60.094 50.000 7.34 7.37 40.96 5.28
1742 4003 4.345859 TTTGAGTGACCGGTAATTCTGT 57.654 40.909 15.09 0.00 0.00 3.41
1860 4121 2.101917 GCGTGTAGTATAAAGGGCTGGA 59.898 50.000 0.00 0.00 0.00 3.86
1996 4700 6.745116 TGTATCTCGAGTTTTCAGAAAGACA 58.255 36.000 13.13 0.21 0.00 3.41
1999 4703 9.015577 GTAGATGTATCTCGAGTTTTCAGAAAG 57.984 37.037 13.13 0.00 38.32 2.62
2048 4752 2.048444 AGCATGGACATAGCAACAGG 57.952 50.000 0.00 0.00 0.00 4.00
2061 4766 8.408601 AGAGCAAATAGTATAACAAAAGCATGG 58.591 33.333 0.00 0.00 0.00 3.66
2095 4801 3.548268 GTGAGATTTCTGCACTACTACGC 59.452 47.826 0.00 0.00 0.00 4.42
2191 4897 1.936547 CTGCATAAGAACGAAGCCCTC 59.063 52.381 0.00 0.00 0.00 4.30
2258 4964 0.390735 ACCGAACGCCAAGACCATAC 60.391 55.000 0.00 0.00 0.00 2.39
2259 4965 1.184431 TACCGAACGCCAAGACCATA 58.816 50.000 0.00 0.00 0.00 2.74
2260 4966 0.322322 TTACCGAACGCCAAGACCAT 59.678 50.000 0.00 0.00 0.00 3.55
2261 4967 0.322322 ATTACCGAACGCCAAGACCA 59.678 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.