Multiple sequence alignment - TraesCS2B01G145900

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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 TraesCS2B01G145900 chr2B 100.000 3881 0 0 1 3881 111666213 111662333 0.000000e+00 7167.0
1 TraesCS2B01G145900 chr2B 98.966 870 9 0 1 870 111666343 111667212 0.000000e+00 1557.0
2 TraesCS2B01G145900 chr2A 94.601 2019 81 9 938 2946 73177616 73175616 0.000000e+00 3099.0
3 TraesCS2B01G145900 chr2A 93.363 678 42 3 3048 3724 73175265 73174590 0.000000e+00 1000.0
4 TraesCS2B01G145900 chr2A 96.178 157 6 0 3723 3879 73174519 73174363 1.380000e-64 257.0
5 TraesCS2B01G145900 chr2D 94.300 2035 81 10 938 2952 73590545 73588526 0.000000e+00 3083.0
6 TraesCS2B01G145900 chr2D 90.701 785 53 11 2957 3724 73588262 73587481 0.000000e+00 1027.0
7 TraesCS2B01G145900 chr2D 96.178 157 6 0 3723 3879 73587410 73587254 1.380000e-64 257.0
8 TraesCS2B01G145900 chr2D 100.000 30 0 0 2942 2971 73588311 73588282 5.420000e-04 56.5
9 TraesCS2B01G145900 chr7D 81.839 892 109 37 2 870 499525227 499526088 0.000000e+00 701.0


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 TraesCS2B01G145900 chr2B 111662333 111666213 3880 True 7167.000 7167 100.00000 1 3881 1 chr2B.!!$R1 3880
1 TraesCS2B01G145900 chr2B 111666343 111667212 869 False 1557.000 1557 98.96600 1 870 1 chr2B.!!$F1 869
2 TraesCS2B01G145900 chr2A 73174363 73177616 3253 True 1452.000 3099 94.71400 938 3879 3 chr2A.!!$R1 2941
3 TraesCS2B01G145900 chr2D 73587254 73590545 3291 True 1105.875 3083 95.29475 938 3879 4 chr2D.!!$R1 2941
4 TraesCS2B01G145900 chr7D 499525227 499526088 861 False 701.000 701 81.83900 2 870 1 chr7D.!!$F1 868

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
905 940 0.322456 GCGCCTATCATTGCCCCATA 60.322 55.0 0.00 0.0 0.00 2.74 F
1026 1062 0.543883 AGCTCAAGGCCTCTCTCACA 60.544 55.0 5.23 0.0 43.05 3.58 F
1227 1281 0.757935 CCAATGGCTTCATCCAGGGG 60.758 60.0 0.00 0.0 39.89 4.79 F
1869 1923 0.881118 TTCGCCAAATGGAGCTTGAC 59.119 50.0 2.98 0.0 37.39 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2232 0.037303 CATGGTCTCCACTGCAGGTT 59.963 55.0 19.93 0.0 35.80 3.50 R
2718 2772 0.251916 TATACCACTGCCACTGTGCC 59.748 55.0 1.29 0.0 33.08 5.01 R
2863 2918 0.788391 CTTGACTTGTTCGGGTACGC 59.212 55.0 0.00 0.0 40.69 4.42 R
3262 3592 0.827507 TTGGAGTTTTCCCTGCAGCC 60.828 55.0 8.66 1.6 43.33 4.85 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
45 47 2.270205 CTGGAATCAGCCGCACCT 59.730 61.111 0.00 0.00 33.86 4.00
284 309 6.966435 ATTTTTGCTTCAAATGATTACCGG 57.034 33.333 0.00 0.00 33.19 5.28
385 411 5.929415 TCGGAATAAATTTTTGCTTCAACCC 59.071 36.000 0.00 0.00 0.00 4.11
798 833 2.865119 TTCTCTCTCAGGCAATGCAA 57.135 45.000 7.79 0.00 0.00 4.08
884 919 3.299977 GGTTTGGGCCGGTCAACC 61.300 66.667 12.10 12.10 0.00 3.77
894 929 2.588034 GGTCAACCGGCGCCTATC 60.588 66.667 26.68 8.51 0.00 2.08
895 930 2.185867 GTCAACCGGCGCCTATCA 59.814 61.111 26.68 0.73 0.00 2.15
896 931 1.227556 GTCAACCGGCGCCTATCAT 60.228 57.895 26.68 2.76 0.00 2.45
897 932 0.814010 GTCAACCGGCGCCTATCATT 60.814 55.000 26.68 8.27 0.00 2.57
898 933 0.813610 TCAACCGGCGCCTATCATTG 60.814 55.000 26.68 19.49 0.00 2.82
899 934 2.186826 AACCGGCGCCTATCATTGC 61.187 57.895 26.68 0.00 0.00 3.56
900 935 3.357079 CCGGCGCCTATCATTGCC 61.357 66.667 26.68 0.00 44.09 4.52
901 936 3.357079 CGGCGCCTATCATTGCCC 61.357 66.667 26.68 0.00 44.71 5.36
902 937 2.985847 GGCGCCTATCATTGCCCC 60.986 66.667 22.15 0.00 41.70 5.80
903 938 2.203337 GCGCCTATCATTGCCCCA 60.203 61.111 0.00 0.00 0.00 4.96
904 939 1.604593 GCGCCTATCATTGCCCCAT 60.605 57.895 0.00 0.00 0.00 4.00
905 940 0.322456 GCGCCTATCATTGCCCCATA 60.322 55.000 0.00 0.00 0.00 2.74
906 941 1.683011 GCGCCTATCATTGCCCCATAT 60.683 52.381 0.00 0.00 0.00 1.78
907 942 2.292267 CGCCTATCATTGCCCCATATC 58.708 52.381 0.00 0.00 0.00 1.63
908 943 2.356022 CGCCTATCATTGCCCCATATCA 60.356 50.000 0.00 0.00 0.00 2.15
909 944 3.686405 CGCCTATCATTGCCCCATATCAT 60.686 47.826 0.00 0.00 0.00 2.45
910 945 4.444733 CGCCTATCATTGCCCCATATCATA 60.445 45.833 0.00 0.00 0.00 2.15
911 946 5.638133 GCCTATCATTGCCCCATATCATAT 58.362 41.667 0.00 0.00 0.00 1.78
912 947 6.073314 GCCTATCATTGCCCCATATCATATT 58.927 40.000 0.00 0.00 0.00 1.28
913 948 6.015688 GCCTATCATTGCCCCATATCATATTG 60.016 42.308 0.00 0.00 0.00 1.90
914 949 5.864418 ATCATTGCCCCATATCATATTGC 57.136 39.130 0.00 0.00 0.00 3.56
915 950 4.675038 TCATTGCCCCATATCATATTGCA 58.325 39.130 0.00 0.00 0.00 4.08
916 951 5.274015 TCATTGCCCCATATCATATTGCAT 58.726 37.500 0.00 0.00 0.00 3.96
917 952 5.361571 TCATTGCCCCATATCATATTGCATC 59.638 40.000 0.00 0.00 0.00 3.91
918 953 4.319037 TGCCCCATATCATATTGCATCA 57.681 40.909 0.00 0.00 0.00 3.07
919 954 4.675038 TGCCCCATATCATATTGCATCAA 58.325 39.130 0.00 0.00 0.00 2.57
920 955 5.274015 TGCCCCATATCATATTGCATCAAT 58.726 37.500 0.00 0.00 37.80 2.57
921 956 6.433441 TGCCCCATATCATATTGCATCAATA 58.567 36.000 2.23 2.23 40.04 1.90
922 957 6.896307 TGCCCCATATCATATTGCATCAATAA 59.104 34.615 3.72 0.00 39.34 1.40
923 958 7.399478 TGCCCCATATCATATTGCATCAATAAA 59.601 33.333 3.72 0.00 39.34 1.40
924 959 7.924412 GCCCCATATCATATTGCATCAATAAAG 59.076 37.037 3.72 1.27 39.34 1.85
925 960 7.924412 CCCCATATCATATTGCATCAATAAAGC 59.076 37.037 3.72 0.00 39.34 3.51
926 961 8.471609 CCCATATCATATTGCATCAATAAAGCA 58.528 33.333 3.72 0.00 39.34 3.91
927 962 9.516314 CCATATCATATTGCATCAATAAAGCAG 57.484 33.333 3.72 0.00 39.34 4.24
928 963 9.516314 CATATCATATTGCATCAATAAAGCAGG 57.484 33.333 3.72 0.00 39.34 4.85
929 964 7.770366 ATCATATTGCATCAATAAAGCAGGA 57.230 32.000 3.72 0.00 39.34 3.86
930 965 7.210718 TCATATTGCATCAATAAAGCAGGAG 57.789 36.000 3.72 0.00 39.34 3.69
931 966 6.774170 TCATATTGCATCAATAAAGCAGGAGT 59.226 34.615 3.72 0.00 39.34 3.85
932 967 7.938490 TCATATTGCATCAATAAAGCAGGAGTA 59.062 33.333 3.72 0.00 39.34 2.59
933 968 5.818136 TTGCATCAATAAAGCAGGAGTAC 57.182 39.130 0.00 0.00 39.72 2.73
934 969 5.102953 TGCATCAATAAAGCAGGAGTACT 57.897 39.130 0.00 0.00 33.75 2.73
935 970 5.500234 TGCATCAATAAAGCAGGAGTACTT 58.500 37.500 0.00 0.00 33.75 2.24
936 971 5.355071 TGCATCAATAAAGCAGGAGTACTTG 59.645 40.000 0.00 0.00 33.75 3.16
952 987 8.822805 AGGAGTACTTGAAACATAATCCACTTA 58.177 33.333 0.00 0.00 35.89 2.24
1017 1053 1.135721 CAGCCATAAAAGCTCAAGGCC 59.864 52.381 0.00 0.00 42.97 5.19
1018 1054 1.006400 AGCCATAAAAGCTCAAGGCCT 59.994 47.619 0.00 0.00 42.97 5.19
1019 1055 1.406898 GCCATAAAAGCTCAAGGCCTC 59.593 52.381 5.23 0.00 43.05 4.70
1020 1056 2.947695 GCCATAAAAGCTCAAGGCCTCT 60.948 50.000 5.23 0.00 43.05 3.69
1021 1057 2.948315 CCATAAAAGCTCAAGGCCTCTC 59.052 50.000 5.23 0.00 43.05 3.20
1022 1058 3.371380 CCATAAAAGCTCAAGGCCTCTCT 60.371 47.826 5.23 0.00 43.05 3.10
1023 1059 2.488204 AAAAGCTCAAGGCCTCTCTC 57.512 50.000 5.23 0.00 43.05 3.20
1024 1060 1.356124 AAAGCTCAAGGCCTCTCTCA 58.644 50.000 5.23 0.00 43.05 3.27
1025 1061 0.612744 AAGCTCAAGGCCTCTCTCAC 59.387 55.000 5.23 0.00 43.05 3.51
1026 1062 0.543883 AGCTCAAGGCCTCTCTCACA 60.544 55.000 5.23 0.00 43.05 3.58
1043 1079 3.727726 TCACACACACACCATGAACTAG 58.272 45.455 0.00 0.00 0.00 2.57
1045 1081 4.342665 TCACACACACACCATGAACTAGTA 59.657 41.667 0.00 0.00 0.00 1.82
1047 1083 4.344102 ACACACACACCATGAACTAGTACT 59.656 41.667 0.00 0.00 0.00 2.73
1048 1084 4.686091 CACACACACCATGAACTAGTACTG 59.314 45.833 5.39 0.00 0.00 2.74
1227 1281 0.757935 CCAATGGCTTCATCCAGGGG 60.758 60.000 0.00 0.00 39.89 4.79
1482 1536 2.284699 CCGGAGAGGGACCTGGTT 60.285 66.667 0.00 0.00 35.97 3.67
1548 1602 1.816224 GTCGAGGCTCTCTGTCTCTTT 59.184 52.381 13.50 0.00 44.79 2.52
1561 1615 1.134401 GTCTCTTTGGGCGGATGATGA 60.134 52.381 0.00 0.00 0.00 2.92
1574 1628 2.092914 GGATGATGAAGGAAGGGTTCGT 60.093 50.000 0.00 0.00 0.00 3.85
1578 1632 1.072505 GAAGGAAGGGTTCGTGCCA 59.927 57.895 0.00 0.00 0.00 4.92
1584 1638 2.897172 AAGGGTTCGTGCCAAACCGT 62.897 55.000 6.06 4.26 45.90 4.83
1638 1692 4.980805 GCCGGTGCGTTGGAGACA 62.981 66.667 1.90 0.00 39.83 3.41
1660 1714 1.202879 GGAAGTGGGTCCATGTGTTCA 60.203 52.381 0.00 0.00 37.65 3.18
1759 1813 1.569493 CTTGCGTTGGAGGTGTTCG 59.431 57.895 0.00 0.00 0.00 3.95
1761 1815 4.072088 GCGTTGGAGGTGTTCGCG 62.072 66.667 0.00 0.00 37.74 5.87
1762 1816 2.355363 CGTTGGAGGTGTTCGCGA 60.355 61.111 3.71 3.71 0.00 5.87
1765 1819 2.867855 TTGGAGGTGTTCGCGAGCT 61.868 57.895 23.51 11.18 0.00 4.09
1782 1836 1.371183 CTTGAGGGCGAGGAACACA 59.629 57.895 0.00 0.00 0.00 3.72
1869 1923 0.881118 TTCGCCAAATGGAGCTTGAC 59.119 50.000 2.98 0.00 37.39 3.18
2004 2058 3.565902 GCATAGGGTTAATCCTTGAGCAC 59.434 47.826 13.80 0.00 38.30 4.40
2034 2088 1.198094 TGGTTGATCTCCTTGCCCGA 61.198 55.000 8.50 0.00 0.00 5.14
2151 2205 3.087031 CCACAAGAATGTCAAGATGGCT 58.913 45.455 0.00 0.00 37.82 4.75
2174 2228 6.035327 GCTGAAATTGTCATAACTGAAATGGC 59.965 38.462 0.00 0.00 35.07 4.40
2178 2232 3.419943 TGTCATAACTGAAATGGCAGCA 58.580 40.909 0.00 0.00 39.51 4.41
2432 2486 2.570752 AGCAAGGTCATGTCACAGAGAT 59.429 45.455 0.00 0.00 0.00 2.75
2574 2628 3.380142 TGTCAAAAATCTCCGCTTTTGC 58.620 40.909 3.05 0.00 40.66 3.68
2613 2667 4.392921 TGCTAAGCTAGTGTCCAAGATC 57.607 45.455 0.00 0.00 0.00 2.75
2718 2772 8.307483 TGGTAGAAGAGAATCAGTTAAACTCTG 58.693 37.037 0.00 0.00 37.87 3.35
2746 2800 9.881441 CACAGTGGCAGTGGTATACAGTATGTT 62.881 44.444 25.12 0.00 40.95 2.71
2803 2858 9.262358 CTTGTTTACTCTTTAGTAGGATATGCC 57.738 37.037 0.00 0.00 39.36 4.40
2805 2860 7.567622 TGTTTACTCTTTAGTAGGATATGCCCT 59.432 37.037 0.00 0.00 39.36 5.19
2817 2872 3.840437 TGCCCTTGCACAGTTGTC 58.160 55.556 0.00 0.00 44.23 3.18
2826 2881 3.198409 TGCACAGTTGTCTGAGTCAAT 57.802 42.857 0.00 0.00 43.76 2.57
2854 2909 6.371825 GTGTAGTCTGGGGATAAGTTCAAAAG 59.628 42.308 0.00 0.00 0.00 2.27
2863 2918 7.829211 TGGGGATAAGTTCAAAAGTCTTGATAG 59.171 37.037 0.00 0.00 0.00 2.08
2866 2921 7.064728 GGATAAGTTCAAAAGTCTTGATAGCGT 59.935 37.037 0.00 0.00 0.00 5.07
2870 2925 4.501071 TCAAAAGTCTTGATAGCGTACCC 58.499 43.478 0.00 0.00 0.00 3.69
2874 2929 2.098770 AGTCTTGATAGCGTACCCGAAC 59.901 50.000 0.00 0.00 35.63 3.95
2880 2935 1.246649 TAGCGTACCCGAACAAGTCA 58.753 50.000 0.00 0.00 35.63 3.41
2890 2945 3.363970 CCCGAACAAGTCAAGAAACATCG 60.364 47.826 0.00 0.00 0.00 3.84
2901 2956 5.049405 GTCAAGAAACATCGTGAACTCCAAT 60.049 40.000 0.00 0.00 30.61 3.16
2905 2960 2.881074 ACATCGTGAACTCCAATCGAG 58.119 47.619 0.00 0.00 44.95 4.04
2917 2972 5.674525 ACTCCAATCGAGCTAATGAAATCA 58.325 37.500 0.00 0.00 43.01 2.57
2989 3304 8.273780 ACTTGACTGAATATCTTGATGAAACC 57.726 34.615 0.00 0.00 0.00 3.27
2992 3307 5.185454 ACTGAATATCTTGATGAAACCGCA 58.815 37.500 0.00 0.00 0.00 5.69
3007 3323 2.668625 ACCGCAAAGGGGTTAAGAAAA 58.331 42.857 0.00 0.00 46.84 2.29
3023 3339 9.397280 GGTTAAGAAAAGCTAGAAATACCAGAT 57.603 33.333 0.00 0.00 0.00 2.90
3033 3349 9.207868 AGCTAGAAATACCAGATTAGTCTCTTT 57.792 33.333 0.00 0.00 30.42 2.52
3037 3353 8.049721 AGAAATACCAGATTAGTCTCTTTTGGG 58.950 37.037 0.00 0.00 30.42 4.12
3096 3426 4.893241 GTGGAACTTTGCACGTCG 57.107 55.556 0.00 0.00 39.66 5.12
3141 3471 8.121305 TGTAACTGCATTATGTCCTTGAAAAT 57.879 30.769 0.00 0.00 0.00 1.82
3145 3475 6.096001 ACTGCATTATGTCCTTGAAAATCTCC 59.904 38.462 0.00 0.00 0.00 3.71
3166 3496 4.035017 CCGAAAATATTACAAGCAAGGCG 58.965 43.478 0.00 0.00 0.00 5.52
3196 3526 8.197439 CCCATAACAAATGAGAGGGTTAATTTC 58.803 37.037 0.00 0.00 30.41 2.17
3262 3592 5.359292 TGAGTATCTCTCTGACCAAGACATG 59.641 44.000 0.00 0.00 43.13 3.21
3316 3646 5.324409 ACTGAAAAGAATACATGCAAGGGA 58.676 37.500 0.00 0.00 0.00 4.20
3317 3647 5.954150 ACTGAAAAGAATACATGCAAGGGAT 59.046 36.000 0.00 0.00 0.00 3.85
3318 3648 6.096001 ACTGAAAAGAATACATGCAAGGGATC 59.904 38.462 0.00 0.00 0.00 3.36
3319 3649 5.951148 TGAAAAGAATACATGCAAGGGATCA 59.049 36.000 0.00 0.00 0.00 2.92
3320 3650 6.095860 TGAAAAGAATACATGCAAGGGATCAG 59.904 38.462 0.00 0.00 0.00 2.90
3327 3657 4.091549 ACATGCAAGGGATCAGTTCATTT 58.908 39.130 0.00 0.00 0.00 2.32
3330 3660 4.012374 TGCAAGGGATCAGTTCATTTCTC 58.988 43.478 0.00 0.00 0.00 2.87
3403 3733 6.823689 TCTGCACTTCCTATTCATAAAAGGTC 59.176 38.462 0.00 0.00 0.00 3.85
3405 3735 7.118723 TGCACTTCCTATTCATAAAAGGTCAT 58.881 34.615 0.00 0.00 0.00 3.06
3416 3748 8.579850 TTCATAAAAGGTCATTGCAGTAGATT 57.420 30.769 0.00 0.00 0.00 2.40
3417 3749 7.988737 TCATAAAAGGTCATTGCAGTAGATTG 58.011 34.615 0.00 0.00 0.00 2.67
3423 3755 4.272018 GGTCATTGCAGTAGATTGTAGCAG 59.728 45.833 0.00 0.00 36.47 4.24
3424 3756 5.111989 GTCATTGCAGTAGATTGTAGCAGA 58.888 41.667 0.00 0.00 36.47 4.26
3434 3766 7.928167 CAGTAGATTGTAGCAGACCATATGAAA 59.072 37.037 3.65 0.00 0.00 2.69
3449 3781 9.494271 GACCATATGAAATGTTCTGCTATTCTA 57.506 33.333 3.65 0.00 0.00 2.10
3501 3833 3.582647 TGCAAGGAGTCCAGTATTTCTCA 59.417 43.478 12.86 0.00 0.00 3.27
3508 3840 5.104259 AGTCCAGTATTTCTCATTGGGAC 57.896 43.478 0.00 0.00 42.94 4.46
3626 3958 4.758674 GGAGGGAACAAAGTTACAAGGTAC 59.241 45.833 0.00 0.00 0.00 3.34
3674 4006 3.155093 AGTTTGAGCACTGCAAAGTTG 57.845 42.857 3.30 0.00 35.89 3.16
3684 4016 5.997746 AGCACTGCAAAGTTGTATAGAAGAA 59.002 36.000 3.30 0.00 0.00 2.52
3742 4146 3.146847 GCTCTAGACCTCTTCCTAGCTC 58.853 54.545 0.00 0.00 34.02 4.09
3805 4209 1.889170 ACAGTCTGCGATGAAGTCTGA 59.111 47.619 0.00 0.00 35.30 3.27
3812 4216 1.748493 GCGATGAAGTCTGAGAGTCCT 59.252 52.381 0.00 0.00 0.00 3.85
3824 4228 5.186021 GTCTGAGAGTCCTAGAACAAATCCA 59.814 44.000 0.00 0.00 0.00 3.41
3847 4251 3.895998 TGTATGATGTGCCTATTGCCAA 58.104 40.909 0.00 0.00 40.16 4.52
3879 4283 2.292267 CCTCAACGATAGGCTGCAAAT 58.708 47.619 0.50 0.00 43.77 2.32
3880 4284 3.466836 CCTCAACGATAGGCTGCAAATA 58.533 45.455 0.50 0.00 43.77 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
284 309 5.061920 ACGATCTGAGTAACTGGAAACTC 57.938 43.478 0.00 0.00 42.04 3.01
385 411 5.519722 AGAAACTGCGAAACCAGTAAAATG 58.480 37.500 0.00 0.00 44.86 2.32
737 772 4.227134 CTCCCCACGCGCATAGCT 62.227 66.667 5.73 0.00 45.59 3.32
877 912 2.588034 GATAGGCGCCGGTTGACC 60.588 66.667 23.20 3.46 0.00 4.02
878 913 0.814010 AATGATAGGCGCCGGTTGAC 60.814 55.000 23.20 11.15 0.00 3.18
879 914 0.813610 CAATGATAGGCGCCGGTTGA 60.814 55.000 23.20 4.11 0.00 3.18
880 915 1.648720 CAATGATAGGCGCCGGTTG 59.351 57.895 23.20 17.71 0.00 3.77
881 916 2.186826 GCAATGATAGGCGCCGGTT 61.187 57.895 23.20 9.99 0.00 4.44
882 917 2.591715 GCAATGATAGGCGCCGGT 60.592 61.111 23.20 14.30 0.00 5.28
883 918 3.357079 GGCAATGATAGGCGCCGG 61.357 66.667 23.20 0.00 34.26 6.13
884 919 3.357079 GGGCAATGATAGGCGCCG 61.357 66.667 23.20 5.73 45.85 6.46
886 921 0.322456 TATGGGGCAATGATAGGCGC 60.322 55.000 0.00 0.00 43.40 6.53
887 922 2.292267 GATATGGGGCAATGATAGGCG 58.708 52.381 0.00 0.00 0.00 5.52
888 923 3.370840 TGATATGGGGCAATGATAGGC 57.629 47.619 0.00 0.00 0.00 3.93
889 924 6.015688 GCAATATGATATGGGGCAATGATAGG 60.016 42.308 0.00 0.00 0.00 2.57
890 925 6.548251 TGCAATATGATATGGGGCAATGATAG 59.452 38.462 4.79 0.00 0.00 2.08
891 926 6.433441 TGCAATATGATATGGGGCAATGATA 58.567 36.000 4.79 0.00 0.00 2.15
892 927 5.274015 TGCAATATGATATGGGGCAATGAT 58.726 37.500 4.79 0.00 0.00 2.45
893 928 4.675038 TGCAATATGATATGGGGCAATGA 58.325 39.130 4.79 0.00 0.00 2.57
894 929 5.128008 TGATGCAATATGATATGGGGCAATG 59.872 40.000 9.66 0.00 33.09 2.82
895 930 5.274015 TGATGCAATATGATATGGGGCAAT 58.726 37.500 9.66 1.96 33.09 3.56
896 931 4.675038 TGATGCAATATGATATGGGGCAA 58.325 39.130 9.66 0.00 33.09 4.52
897 932 4.319037 TGATGCAATATGATATGGGGCA 57.681 40.909 8.48 8.48 0.00 5.36
898 933 5.864418 ATTGATGCAATATGATATGGGGC 57.136 39.130 0.00 0.00 31.77 5.80
899 934 7.924412 GCTTTATTGATGCAATATGATATGGGG 59.076 37.037 0.00 0.00 36.41 4.96
900 935 8.471609 TGCTTTATTGATGCAATATGATATGGG 58.528 33.333 0.00 0.00 36.41 4.00
901 936 9.516314 CTGCTTTATTGATGCAATATGATATGG 57.484 33.333 0.00 0.00 36.41 2.74
902 937 9.516314 CCTGCTTTATTGATGCAATATGATATG 57.484 33.333 0.00 0.00 36.41 1.78
903 938 9.470399 TCCTGCTTTATTGATGCAATATGATAT 57.530 29.630 0.00 0.00 36.41 1.63
904 939 8.866970 TCCTGCTTTATTGATGCAATATGATA 57.133 30.769 0.00 0.00 36.41 2.15
905 940 7.450634 ACTCCTGCTTTATTGATGCAATATGAT 59.549 33.333 0.00 0.00 36.41 2.45
906 941 6.774170 ACTCCTGCTTTATTGATGCAATATGA 59.226 34.615 0.00 0.00 36.41 2.15
907 942 6.978338 ACTCCTGCTTTATTGATGCAATATG 58.022 36.000 0.00 0.00 36.41 1.78
908 943 7.941238 AGTACTCCTGCTTTATTGATGCAATAT 59.059 33.333 0.00 0.00 36.41 1.28
909 944 7.282585 AGTACTCCTGCTTTATTGATGCAATA 58.717 34.615 0.00 0.00 37.89 1.90
910 945 6.125029 AGTACTCCTGCTTTATTGATGCAAT 58.875 36.000 0.00 0.00 37.89 3.56
911 946 5.500234 AGTACTCCTGCTTTATTGATGCAA 58.500 37.500 0.00 0.00 37.89 4.08
912 947 5.102953 AGTACTCCTGCTTTATTGATGCA 57.897 39.130 0.00 0.00 36.98 3.96
913 948 5.586243 TCAAGTACTCCTGCTTTATTGATGC 59.414 40.000 0.00 0.00 0.00 3.91
914 949 7.615582 TTCAAGTACTCCTGCTTTATTGATG 57.384 36.000 0.00 0.00 0.00 3.07
915 950 7.665559 TGTTTCAAGTACTCCTGCTTTATTGAT 59.334 33.333 0.00 0.00 0.00 2.57
916 951 6.995686 TGTTTCAAGTACTCCTGCTTTATTGA 59.004 34.615 0.00 0.00 0.00 2.57
917 952 7.202016 TGTTTCAAGTACTCCTGCTTTATTG 57.798 36.000 0.00 0.00 0.00 1.90
918 953 9.515226 TTATGTTTCAAGTACTCCTGCTTTATT 57.485 29.630 0.00 0.00 0.00 1.40
919 954 9.686683 ATTATGTTTCAAGTACTCCTGCTTTAT 57.313 29.630 0.00 0.00 0.00 1.40
920 955 9.162764 GATTATGTTTCAAGTACTCCTGCTTTA 57.837 33.333 0.00 0.00 0.00 1.85
921 956 7.121315 GGATTATGTTTCAAGTACTCCTGCTTT 59.879 37.037 0.00 0.00 0.00 3.51
922 957 6.599638 GGATTATGTTTCAAGTACTCCTGCTT 59.400 38.462 0.00 0.00 0.00 3.91
923 958 6.116126 GGATTATGTTTCAAGTACTCCTGCT 58.884 40.000 0.00 0.00 0.00 4.24
924 959 5.880332 TGGATTATGTTTCAAGTACTCCTGC 59.120 40.000 0.00 0.00 0.00 4.85
925 960 7.106239 AGTGGATTATGTTTCAAGTACTCCTG 58.894 38.462 0.00 0.00 0.00 3.86
926 961 7.259088 AGTGGATTATGTTTCAAGTACTCCT 57.741 36.000 0.00 0.00 0.00 3.69
927 962 7.923414 AAGTGGATTATGTTTCAAGTACTCC 57.077 36.000 0.00 0.00 0.00 3.85
928 963 9.654663 ACTAAGTGGATTATGTTTCAAGTACTC 57.345 33.333 0.00 0.00 0.00 2.59
932 967 9.349713 TGAAACTAAGTGGATTATGTTTCAAGT 57.650 29.630 14.12 0.00 41.73 3.16
935 970 9.295825 ACATGAAACTAAGTGGATTATGTTTCA 57.704 29.630 17.37 17.37 44.40 2.69
952 987 9.768662 ATTTAGAAAATGCAAGAACATGAAACT 57.231 25.926 0.00 0.00 0.00 2.66
1017 1053 2.036346 TCATGGTGTGTGTGTGAGAGAG 59.964 50.000 0.00 0.00 0.00 3.20
1018 1054 2.038659 TCATGGTGTGTGTGTGAGAGA 58.961 47.619 0.00 0.00 0.00 3.10
1019 1055 2.531522 TCATGGTGTGTGTGTGAGAG 57.468 50.000 0.00 0.00 0.00 3.20
1020 1056 2.170397 AGTTCATGGTGTGTGTGTGAGA 59.830 45.455 0.00 0.00 0.00 3.27
1021 1057 2.564771 AGTTCATGGTGTGTGTGTGAG 58.435 47.619 0.00 0.00 0.00 3.51
1022 1058 2.708216 AGTTCATGGTGTGTGTGTGA 57.292 45.000 0.00 0.00 0.00 3.58
1023 1059 3.466836 ACTAGTTCATGGTGTGTGTGTG 58.533 45.455 0.00 0.00 0.00 3.82
1024 1060 3.838244 ACTAGTTCATGGTGTGTGTGT 57.162 42.857 0.00 0.00 0.00 3.72
1025 1061 4.686091 CAGTACTAGTTCATGGTGTGTGTG 59.314 45.833 0.00 0.00 0.00 3.82
1026 1062 4.344102 ACAGTACTAGTTCATGGTGTGTGT 59.656 41.667 0.00 0.00 0.00 3.72
1043 1079 5.628134 GTTTGCTATTGGCTTGTACAGTAC 58.372 41.667 3.49 3.49 42.39 2.73
1045 1081 3.188460 CGTTTGCTATTGGCTTGTACAGT 59.812 43.478 0.00 0.00 42.39 3.55
1047 1083 2.095466 GCGTTTGCTATTGGCTTGTACA 60.095 45.455 0.00 0.00 42.39 2.90
1048 1084 2.515912 GCGTTTGCTATTGGCTTGTAC 58.484 47.619 0.00 0.00 42.39 2.90
1458 1512 1.144936 GTCCCTCTCCGGCATCTTG 59.855 63.158 0.00 0.00 0.00 3.02
1482 1536 0.249120 AGATCATGGCGTTCCACGAA 59.751 50.000 0.00 0.00 46.92 3.85
1536 1590 0.541998 TCCGCCCAAAGAGACAGAGA 60.542 55.000 0.00 0.00 0.00 3.10
1548 1602 0.181114 CTTCCTTCATCATCCGCCCA 59.819 55.000 0.00 0.00 0.00 5.36
1561 1615 0.106419 TTTGGCACGAACCCTTCCTT 60.106 50.000 0.00 0.00 0.00 3.36
1574 1628 2.203280 CAGTCCCACGGTTTGGCA 60.203 61.111 0.00 0.00 45.37 4.92
1578 1632 0.253610 TGACAACAGTCCCACGGTTT 59.746 50.000 0.00 0.00 34.38 3.27
1584 1638 2.280797 GCGCTGACAACAGTCCCA 60.281 61.111 0.00 0.00 45.04 4.37
1638 1692 0.772124 ACACATGGACCCACTTCCCT 60.772 55.000 0.00 0.00 34.33 4.20
1660 1714 2.035632 CCGGAGCCTGTTCTTCTCTAT 58.964 52.381 0.00 0.00 0.00 1.98
1747 1801 2.357034 GCTCGCGAACACCTCCAA 60.357 61.111 11.33 0.00 0.00 3.53
1761 1815 1.448717 GTTCCTCGCCCTCAAGCTC 60.449 63.158 0.00 0.00 0.00 4.09
1762 1816 2.217038 TGTTCCTCGCCCTCAAGCT 61.217 57.895 0.00 0.00 0.00 3.74
1765 1819 0.321564 CATGTGTTCCTCGCCCTCAA 60.322 55.000 0.00 0.00 0.00 3.02
1833 1887 1.068610 CGAAACATGTCCAACGCCATT 60.069 47.619 0.00 0.00 0.00 3.16
1869 1923 0.102481 CATCCGGTACCACTCTTCCG 59.898 60.000 13.54 0.00 42.22 4.30
2004 2058 2.216046 AGATCAACCATGCACGCATAG 58.784 47.619 3.80 0.00 34.91 2.23
2034 2088 3.133721 GTGCCTCTTGTAGATGACCAGAT 59.866 47.826 0.00 0.00 29.84 2.90
2151 2205 6.990798 TGCCATTTCAGTTATGACAATTTCA 58.009 32.000 0.00 0.00 39.11 2.69
2174 2228 1.071987 TCTCCACTGCAGGTTGCTG 59.928 57.895 19.93 6.47 45.31 4.41
2178 2232 0.037303 CATGGTCTCCACTGCAGGTT 59.963 55.000 19.93 0.00 35.80 3.50
2295 2349 0.674581 CCATCTCAACCGAGCTGCAA 60.675 55.000 1.02 0.00 39.30 4.08
2574 2628 2.070783 GCAAACTTGTGGCAATCCATG 58.929 47.619 0.00 0.00 45.62 3.66
2613 2667 4.436852 CGAACCACAATTTCCCGTTGATAG 60.437 45.833 0.00 0.00 0.00 2.08
2718 2772 0.251916 TATACCACTGCCACTGTGCC 59.748 55.000 1.29 0.00 33.08 5.01
2761 2815 5.429957 AAACAAGAACTAGCAAGCAGAAG 57.570 39.130 0.00 0.00 0.00 2.85
2778 2833 8.208903 GGGCATATCCTACTAAAGAGTAAACAA 58.791 37.037 0.00 0.00 37.72 2.83
2802 2857 1.233019 CTCAGACAACTGTGCAAGGG 58.767 55.000 0.00 0.00 43.81 3.95
2803 2858 1.869767 GACTCAGACAACTGTGCAAGG 59.130 52.381 0.00 0.00 43.81 3.61
2805 2860 2.689553 TGACTCAGACAACTGTGCAA 57.310 45.000 0.00 0.00 43.81 4.08
2817 2872 4.240888 CCAGACTACACACATTGACTCAG 58.759 47.826 0.00 0.00 0.00 3.35
2826 2881 3.786553 ACTTATCCCCAGACTACACACA 58.213 45.455 0.00 0.00 0.00 3.72
2854 2909 2.159338 TGTTCGGGTACGCTATCAAGAC 60.159 50.000 8.43 0.00 40.69 3.01
2863 2918 0.788391 CTTGACTTGTTCGGGTACGC 59.212 55.000 0.00 0.00 40.69 4.42
2866 2921 4.139859 TGTTTCTTGACTTGTTCGGGTA 57.860 40.909 0.00 0.00 0.00 3.69
2870 2925 4.026062 TCACGATGTTTCTTGACTTGTTCG 60.026 41.667 0.00 0.00 0.00 3.95
2874 2929 5.409643 AGTTCACGATGTTTCTTGACTTG 57.590 39.130 0.00 0.00 30.56 3.16
2880 2935 4.152402 CGATTGGAGTTCACGATGTTTCTT 59.848 41.667 0.00 0.00 0.00 2.52
2890 2945 4.433615 TCATTAGCTCGATTGGAGTTCAC 58.566 43.478 0.00 0.00 45.03 3.18
2901 2956 8.893219 ATAACTGAATGATTTCATTAGCTCGA 57.107 30.769 5.80 0.00 45.72 4.04
2917 2972 7.380536 ACATGTGTGCAAATGAATAACTGAAT 58.619 30.769 9.14 0.00 0.00 2.57
2989 3304 2.296190 AGCTTTTCTTAACCCCTTTGCG 59.704 45.455 0.00 0.00 0.00 4.85
2992 3307 9.021807 GTATTTCTAGCTTTTCTTAACCCCTTT 57.978 33.333 0.00 0.00 0.00 3.11
3007 3323 8.776061 AAGAGACTAATCTGGTATTTCTAGCT 57.224 34.615 0.00 0.00 34.34 3.32
3023 3339 8.212312 TGTATTAACACACCCAAAAGAGACTAA 58.788 33.333 0.00 0.00 0.00 2.24
3026 3342 6.870971 TGTATTAACACACCCAAAAGAGAC 57.129 37.500 0.00 0.00 0.00 3.36
3033 3349 4.584743 TGTGCAATGTATTAACACACCCAA 59.415 37.500 0.00 0.00 38.78 4.12
3037 3353 8.977505 AGATTTTTGTGCAATGTATTAACACAC 58.022 29.630 10.42 0.00 38.78 3.82
3093 3423 6.367969 ACAAGGACTACATTGACAATTACGAC 59.632 38.462 0.00 0.00 39.71 4.34
3096 3426 9.216117 AGTTACAAGGACTACATTGACAATTAC 57.784 33.333 0.00 0.00 39.71 1.89
3141 3471 5.065988 GCCTTGCTTGTAATATTTTCGGAGA 59.934 40.000 0.00 0.00 0.00 3.71
3145 3475 3.482110 GCGCCTTGCTTGTAATATTTTCG 59.518 43.478 0.00 0.00 41.73 3.46
3211 3541 2.344093 TGGAAGCTCCTATATCCCCC 57.656 55.000 0.00 0.00 37.46 5.40
3262 3592 0.827507 TTGGAGTTTTCCCTGCAGCC 60.828 55.000 8.66 1.60 43.33 4.85
3289 3619 6.805271 CCTTGCATGTATTCTTTTCAGTTCTG 59.195 38.462 0.00 0.00 0.00 3.02
3316 3646 8.463930 TTTGTTACTTGGAGAAATGAACTGAT 57.536 30.769 0.00 0.00 0.00 2.90
3317 3647 7.873719 TTTGTTACTTGGAGAAATGAACTGA 57.126 32.000 0.00 0.00 0.00 3.41
3318 3648 8.571336 AGATTTGTTACTTGGAGAAATGAACTG 58.429 33.333 0.00 0.00 0.00 3.16
3319 3649 8.697507 AGATTTGTTACTTGGAGAAATGAACT 57.302 30.769 0.00 0.00 0.00 3.01
3359 3689 7.712639 AGTGCAGAATATTCGTATGATTCACTT 59.287 33.333 9.78 0.00 32.96 3.16
3363 3693 7.386299 AGGAAGTGCAGAATATTCGTATGATTC 59.614 37.037 9.78 10.52 0.00 2.52
3366 3696 6.161855 AGGAAGTGCAGAATATTCGTATGA 57.838 37.500 9.78 0.00 0.00 2.15
3403 3733 4.272018 GGTCTGCTACAATCTACTGCAATG 59.728 45.833 0.00 0.00 33.07 2.82
3405 3735 3.260632 TGGTCTGCTACAATCTACTGCAA 59.739 43.478 0.00 0.00 33.07 4.08
3416 3748 6.653020 AGAACATTTCATATGGTCTGCTACA 58.347 36.000 4.61 0.00 43.78 2.74
3423 3755 8.388484 AGAATAGCAGAACATTTCATATGGTC 57.612 34.615 2.13 0.00 36.05 4.02
3491 3823 9.084533 GTATCTCTAGTCCCAATGAGAAATACT 57.915 37.037 0.00 0.00 38.77 2.12
3501 3833 7.125811 TGCTTTTACAGTATCTCTAGTCCCAAT 59.874 37.037 0.00 0.00 0.00 3.16
3508 3840 9.685828 GTAAGGATGCTTTTACAGTATCTCTAG 57.314 37.037 4.26 0.00 42.73 2.43
3626 3958 2.135933 GGACAGAACAAACCTCTGACG 58.864 52.381 6.83 0.00 42.51 4.35
3714 4046 3.067601 GGAAGAGGTCTAGAGCTTACTGC 59.932 52.174 24.54 16.17 39.57 4.40
3742 4146 7.194278 CAGACTCCAGAGCAATCATATTTTTG 58.806 38.462 0.00 0.00 0.00 2.44
3805 4209 6.380079 ACATTGGATTTGTTCTAGGACTCT 57.620 37.500 2.07 0.00 0.00 3.24
3812 4216 7.201812 GGCACATCATACATTGGATTTGTTCTA 60.202 37.037 0.00 0.00 0.00 2.10
3824 4228 4.472496 TGGCAATAGGCACATCATACATT 58.528 39.130 0.00 0.00 46.46 2.71


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

AutoCloner maintained by Alex Coulton.