Multiple sequence alignment - TraesCS3D01G145300

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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 TraesCS3D01G145300 chr3D 100.000 3167 0 0 1 3167 108955440 108952274 0.000000e+00 5849
1 TraesCS3D01G145300 chr3D 84.568 1134 140 23 1079 2203 109271400 109270293 0.000000e+00 1092
2 TraesCS3D01G145300 chr3B 96.186 1914 40 8 540 2434 160368582 160366683 0.000000e+00 3099
3 TraesCS3D01G145300 chr3B 84.000 1125 144 22 1079 2195 160640887 160639791 0.000000e+00 1048
4 TraesCS3D01G145300 chr3B 96.679 542 14 2 1 538 160369221 160368680 0.000000e+00 898
5 TraesCS3D01G145300 chr3B 96.787 498 15 1 1 497 160374761 160374264 0.000000e+00 830
6 TraesCS3D01G145300 chr3B 91.971 274 15 7 2426 2696 160366639 160366370 8.290000e-101 377
7 TraesCS3D01G145300 chr3B 89.899 198 16 3 2742 2938 160364864 160364670 5.240000e-63 252
8 TraesCS3D01G145300 chr3A 90.072 1944 125 26 423 2352 121478855 121480744 0.000000e+00 2459
9 TraesCS3D01G145300 chr3A 83.967 1210 157 22 994 2195 121235625 121236805 0.000000e+00 1125
10 TraesCS3D01G145300 chr3A 87.869 643 72 1 1553 2195 121317894 121318530 0.000000e+00 750
11 TraesCS3D01G145300 chr3A 85.714 490 61 4 994 1477 121317353 121317839 2.820000e-140 508
12 TraesCS3D01G145300 chr3A 85.115 477 45 15 1970 2427 121482457 121482926 6.190000e-127 464
13 TraesCS3D01G145300 chr5D 82.727 1100 158 20 1079 2167 27540212 27541290 0.000000e+00 950
14 TraesCS3D01G145300 chr4B 78.710 1132 181 40 1076 2169 666359560 666360669 0.000000e+00 701
15 TraesCS3D01G145300 chr4B 78.622 1132 182 41 1076 2169 666254881 666255990 0.000000e+00 695
16 TraesCS3D01G145300 chr4B 78.534 1132 183 41 1076 2169 666388557 666389666 0.000000e+00 689
17 TraesCS3D01G145300 chr4B 78.534 1132 183 40 1076 2169 666410744 666411853 0.000000e+00 689
18 TraesCS3D01G145300 chr4B 78.269 1132 186 40 1076 2169 666301691 666302800 0.000000e+00 673
19 TraesCS3D01G145300 chr4B 83.034 613 93 6 1558 2169 666331640 666332242 2.150000e-151 545
20 TraesCS3D01G145300 chr5B 81.782 752 109 22 1079 1817 20628514 20627778 3.490000e-169 604
21 TraesCS3D01G145300 chr5A 81.806 753 107 22 1079 1817 18857289 18858025 3.490000e-169 604
22 TraesCS3D01G145300 chrUn 79.405 874 132 29 1326 2169 329101337 329100482 9.850000e-160 573
23 TraesCS3D01G145300 chrUn 79.405 874 132 29 1326 2169 380933331 380932476 9.850000e-160 573


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 TraesCS3D01G145300 chr3D 108952274 108955440 3166 True 5849.0 5849 100.00000 1 3167 1 chr3D.!!$R1 3166
1 TraesCS3D01G145300 chr3D 109270293 109271400 1107 True 1092.0 1092 84.56800 1079 2203 1 chr3D.!!$R2 1124
2 TraesCS3D01G145300 chr3B 160364670 160369221 4551 True 1156.5 3099 93.68375 1 2938 4 chr3B.!!$R3 2937
3 TraesCS3D01G145300 chr3B 160639791 160640887 1096 True 1048.0 1048 84.00000 1079 2195 1 chr3B.!!$R2 1116
4 TraesCS3D01G145300 chr3A 121478855 121482926 4071 False 1461.5 2459 87.59350 423 2427 2 chr3A.!!$F3 2004
5 TraesCS3D01G145300 chr3A 121235625 121236805 1180 False 1125.0 1125 83.96700 994 2195 1 chr3A.!!$F1 1201
6 TraesCS3D01G145300 chr3A 121317353 121318530 1177 False 629.0 750 86.79150 994 2195 2 chr3A.!!$F2 1201
7 TraesCS3D01G145300 chr5D 27540212 27541290 1078 False 950.0 950 82.72700 1079 2167 1 chr5D.!!$F1 1088
8 TraesCS3D01G145300 chr4B 666359560 666360669 1109 False 701.0 701 78.71000 1076 2169 1 chr4B.!!$F4 1093
9 TraesCS3D01G145300 chr4B 666254881 666255990 1109 False 695.0 695 78.62200 1076 2169 1 chr4B.!!$F1 1093
10 TraesCS3D01G145300 chr4B 666388557 666389666 1109 False 689.0 689 78.53400 1076 2169 1 chr4B.!!$F5 1093
11 TraesCS3D01G145300 chr4B 666410744 666411853 1109 False 689.0 689 78.53400 1076 2169 1 chr4B.!!$F6 1093
12 TraesCS3D01G145300 chr4B 666301691 666302800 1109 False 673.0 673 78.26900 1076 2169 1 chr4B.!!$F2 1093
13 TraesCS3D01G145300 chr4B 666331640 666332242 602 False 545.0 545 83.03400 1558 2169 1 chr4B.!!$F3 611
14 TraesCS3D01G145300 chr5B 20627778 20628514 736 True 604.0 604 81.78200 1079 1817 1 chr5B.!!$R1 738
15 TraesCS3D01G145300 chr5A 18857289 18858025 736 False 604.0 604 81.80600 1079 1817 1 chr5A.!!$F1 738
16 TraesCS3D01G145300 chrUn 329100482 329101337 855 True 573.0 573 79.40500 1326 2169 1 chrUn.!!$R1 843
17 TraesCS3D01G145300 chrUn 380932476 380933331 855 True 573.0 573 79.40500 1326 2169 1 chrUn.!!$R2 843

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
904 1011 1.007038 GACGACACGCTAACCCACA 60.007 57.895 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2887 6798 0.370273 CTAATGGTTGTCGCGACTGC 59.63 55.0 36.27 27.36 37.91 4.4 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
44 45 6.783708 AACACCAAAATTTGTAGAAGTGGA 57.216 33.333 13.63 0.00 0.00 4.02
319 321 1.669115 CTCACAGACACCCCGCAAG 60.669 63.158 0.00 0.00 0.00 4.01
333 335 1.068264 CCGCAAGAAAAGAAGAAGCCC 60.068 52.381 0.00 0.00 43.02 5.19
391 393 8.738199 TCCGACATTTAGATTACGTTCATATC 57.262 34.615 0.00 0.00 0.00 1.63
447 449 4.164796 ACCTCTATGAGATGTGGATGCAAA 59.835 41.667 0.00 0.00 0.00 3.68
531 536 4.989168 GTGGAGTAGGTGTGAACTTAACAG 59.011 45.833 0.00 0.00 0.00 3.16
607 708 8.561738 AGAAAAATACAGGACGTAAACATCAT 57.438 30.769 0.00 0.00 32.59 2.45
621 722 8.726068 ACGTAAACATCATTTTCATACATCACA 58.274 29.630 0.00 0.00 0.00 3.58
622 723 8.998989 CGTAAACATCATTTTCATACATCACAC 58.001 33.333 0.00 0.00 0.00 3.82
623 724 9.838975 GTAAACATCATTTTCATACATCACACA 57.161 29.630 0.00 0.00 0.00 3.72
821 928 4.884668 TCTACGGAATTCCTCAAAGTGT 57.115 40.909 22.05 12.65 0.00 3.55
834 941 5.526111 TCCTCAAAGTGTAAAAAGGTCTTCG 59.474 40.000 0.00 0.00 0.00 3.79
904 1011 1.007038 GACGACACGCTAACCCACA 60.007 57.895 0.00 0.00 0.00 4.17
1025 1143 0.392461 TCTTCCACGCCATACCTTGC 60.392 55.000 0.00 0.00 0.00 4.01
1083 1204 2.203294 ACGGCGGGTTTTGAGCTT 60.203 55.556 13.24 0.00 0.00 3.74
1541 1778 5.119588 TCTGCTACGTTTACTTATGTTGTGC 59.880 40.000 0.00 0.00 0.00 4.57
1542 1779 4.750598 TGCTACGTTTACTTATGTTGTGCA 59.249 37.500 0.00 0.00 0.00 4.57
1543 1780 5.410132 TGCTACGTTTACTTATGTTGTGCAT 59.590 36.000 0.00 0.00 41.42 3.96
1544 1781 5.732647 GCTACGTTTACTTATGTTGTGCATG 59.267 40.000 0.00 0.00 38.47 4.06
1668 1952 1.079543 GCAGCTCGTGGACTGTGAT 60.080 57.895 0.00 0.00 36.26 3.06
1798 2082 0.530650 CAGCTGTGACGTGGACAAGT 60.531 55.000 5.25 0.00 0.00 3.16
1799 2083 0.249489 AGCTGTGACGTGGACAAGTC 60.249 55.000 10.75 10.75 39.68 3.01
2055 2339 3.055094 ACAAGTACTGGATCGCCAAGAAT 60.055 43.478 3.64 0.00 45.41 2.40
2392 4787 1.806758 GCATTGCGGTGGATTGTGC 60.807 57.895 0.00 0.00 0.00 4.57
2460 4907 2.458592 GCTTTGCTGCGGTAATACTG 57.541 50.000 0.00 0.00 0.00 2.74
2478 4925 9.220767 GTAATACTGAAAGAAATCCAGAACACT 57.779 33.333 0.00 0.00 37.43 3.55
2509 4956 7.550906 ACTTTGATGAGGTAAGAGATAACTTGC 59.449 37.037 0.00 0.00 29.31 4.01
2510 4957 5.592054 TGATGAGGTAAGAGATAACTTGCG 58.408 41.667 0.00 0.00 29.31 4.85
2529 4976 7.425606 ACTTGCGAGAAAAATAACAGTTCATT 58.574 30.769 8.31 0.00 0.00 2.57
2671 5120 6.932901 ACATTAACAGAAATTGAATGCACG 57.067 33.333 0.00 0.00 31.98 5.34
2727 6607 7.744087 TTAATCAATGCTACACAAACTGAGT 57.256 32.000 0.00 0.00 0.00 3.41
2748 6628 5.075493 AGTTTCCATCTTTCATGTGAAGCT 58.925 37.500 0.00 0.00 35.21 3.74
2806 6716 6.689561 TCTCCATGTTAAATCCCTAGACCTA 58.310 40.000 0.00 0.00 0.00 3.08
2814 6724 9.623000 TGTTAAATCCCTAGACCTATTTTTAGC 57.377 33.333 0.00 0.00 0.00 3.09
2817 6727 8.753497 AAATCCCTAGACCTATTTTTAGCTTG 57.247 34.615 0.00 0.00 0.00 4.01
2840 6751 6.356556 TGAATCCATAGACCACCTACAAATG 58.643 40.000 0.00 0.00 0.00 2.32
2887 6798 4.713824 TTCACCTAACTACACGGATGAG 57.286 45.455 0.00 0.00 0.00 2.90
2888 6799 2.426024 TCACCTAACTACACGGATGAGC 59.574 50.000 0.00 0.00 0.00 4.26
2891 6802 2.427453 CCTAACTACACGGATGAGCAGT 59.573 50.000 0.00 0.00 0.00 4.40
2894 6805 0.867753 CTACACGGATGAGCAGTCGC 60.868 60.000 0.00 0.00 38.99 5.19
2896 6807 3.440415 ACGGATGAGCAGTCGCGA 61.440 61.111 3.71 3.71 45.49 5.87
2916 6827 4.236935 CGACAACCATTAGCAAGCAAAAT 58.763 39.130 0.00 0.00 0.00 1.82
2935 6846 1.218316 GGACGACCAGGACACATCC 59.782 63.158 0.00 0.00 46.69 3.51
2946 6857 2.980568 GGACACATCCCGTAATGTTCA 58.019 47.619 0.00 0.00 37.78 3.18
2947 6858 3.541632 GGACACATCCCGTAATGTTCAT 58.458 45.455 0.00 0.00 37.78 2.57
2948 6859 4.699637 GGACACATCCCGTAATGTTCATA 58.300 43.478 0.00 0.00 37.78 2.15
2949 6860 5.120399 GGACACATCCCGTAATGTTCATAA 58.880 41.667 0.00 0.00 37.78 1.90
2950 6861 5.763204 GGACACATCCCGTAATGTTCATAAT 59.237 40.000 0.00 0.00 37.78 1.28
2951 6862 6.293407 GGACACATCCCGTAATGTTCATAATG 60.293 42.308 0.00 0.00 37.78 1.90
2952 6863 6.119536 ACACATCCCGTAATGTTCATAATGT 58.880 36.000 0.00 0.00 37.78 2.71
2953 6864 6.601613 ACACATCCCGTAATGTTCATAATGTT 59.398 34.615 0.00 0.00 37.78 2.71
2954 6865 7.132213 CACATCCCGTAATGTTCATAATGTTC 58.868 38.462 0.00 0.00 37.78 3.18
2955 6866 5.977171 TCCCGTAATGTTCATAATGTTCG 57.023 39.130 0.00 0.00 0.00 3.95
2956 6867 5.421277 TCCCGTAATGTTCATAATGTTCGT 58.579 37.500 0.00 0.00 0.00 3.85
2957 6868 6.571605 TCCCGTAATGTTCATAATGTTCGTA 58.428 36.000 0.00 0.00 0.00 3.43
2958 6869 7.040494 TCCCGTAATGTTCATAATGTTCGTAA 58.960 34.615 0.00 0.00 0.00 3.18
2959 6870 7.711772 TCCCGTAATGTTCATAATGTTCGTAAT 59.288 33.333 0.00 0.00 0.00 1.89
2960 6871 8.980610 CCCGTAATGTTCATAATGTTCGTAATA 58.019 33.333 0.00 0.00 0.00 0.98
2967 6878 9.929722 TGTTCATAATGTTCGTAATATCAAAGC 57.070 29.630 0.00 0.00 0.00 3.51
2968 6879 9.382244 GTTCATAATGTTCGTAATATCAAAGCC 57.618 33.333 0.00 0.00 0.00 4.35
2969 6880 8.669946 TCATAATGTTCGTAATATCAAAGCCA 57.330 30.769 0.00 0.00 0.00 4.75
2970 6881 8.556194 TCATAATGTTCGTAATATCAAAGCCAC 58.444 33.333 0.00 0.00 0.00 5.01
2971 6882 6.751514 AATGTTCGTAATATCAAAGCCACA 57.248 33.333 0.00 0.00 0.00 4.17
2972 6883 6.751514 ATGTTCGTAATATCAAAGCCACAA 57.248 33.333 0.00 0.00 0.00 3.33
2973 6884 6.561737 TGTTCGTAATATCAAAGCCACAAA 57.438 33.333 0.00 0.00 0.00 2.83
2974 6885 6.375377 TGTTCGTAATATCAAAGCCACAAAC 58.625 36.000 0.00 0.00 0.00 2.93
2975 6886 6.205853 TGTTCGTAATATCAAAGCCACAAACT 59.794 34.615 0.00 0.00 0.00 2.66
2976 6887 6.811253 TCGTAATATCAAAGCCACAAACTT 57.189 33.333 0.00 0.00 0.00 2.66
2977 6888 6.607689 TCGTAATATCAAAGCCACAAACTTG 58.392 36.000 0.00 0.00 0.00 3.16
2978 6889 6.428465 TCGTAATATCAAAGCCACAAACTTGA 59.572 34.615 0.00 0.00 0.00 3.02
2979 6890 7.041030 TCGTAATATCAAAGCCACAAACTTGAA 60.041 33.333 0.00 0.00 0.00 2.69
2980 6891 7.593273 CGTAATATCAAAGCCACAAACTTGAAA 59.407 33.333 0.00 0.00 0.00 2.69
2981 6892 9.255304 GTAATATCAAAGCCACAAACTTGAAAA 57.745 29.630 0.00 0.00 0.00 2.29
2982 6893 8.729805 AATATCAAAGCCACAAACTTGAAAAA 57.270 26.923 0.00 0.00 0.00 1.94
2983 6894 6.667007 ATCAAAGCCACAAACTTGAAAAAG 57.333 33.333 0.00 0.00 0.00 2.27
2984 6895 4.934602 TCAAAGCCACAAACTTGAAAAAGG 59.065 37.500 0.00 0.00 0.00 3.11
2985 6896 4.551702 AAGCCACAAACTTGAAAAAGGT 57.448 36.364 0.00 0.00 0.00 3.50
2986 6897 4.551702 AGCCACAAACTTGAAAAAGGTT 57.448 36.364 0.00 0.00 0.00 3.50
2987 6898 4.503910 AGCCACAAACTTGAAAAAGGTTC 58.496 39.130 0.00 0.00 0.00 3.62
2988 6899 4.020662 AGCCACAAACTTGAAAAAGGTTCA 60.021 37.500 0.00 0.00 0.00 3.18
2989 6900 4.092821 GCCACAAACTTGAAAAAGGTTCAC 59.907 41.667 0.00 0.00 0.00 3.18
2990 6901 5.233988 CCACAAACTTGAAAAAGGTTCACA 58.766 37.500 0.00 0.00 0.00 3.58
2991 6902 5.698545 CCACAAACTTGAAAAAGGTTCACAA 59.301 36.000 0.00 0.00 0.00 3.33
2992 6903 6.203723 CCACAAACTTGAAAAAGGTTCACAAA 59.796 34.615 0.00 0.00 0.00 2.83
2993 6904 7.094848 CCACAAACTTGAAAAAGGTTCACAAAT 60.095 33.333 0.00 0.00 0.00 2.32
2994 6905 8.288913 CACAAACTTGAAAAAGGTTCACAAATT 58.711 29.630 0.00 0.00 0.00 1.82
2995 6906 8.845227 ACAAACTTGAAAAAGGTTCACAAATTT 58.155 25.926 0.00 0.00 0.00 1.82
2996 6907 9.116054 CAAACTTGAAAAAGGTTCACAAATTTG 57.884 29.630 16.67 16.67 33.75 2.32
2997 6908 8.614469 AACTTGAAAAAGGTTCACAAATTTGA 57.386 26.923 24.64 0.00 0.00 2.69
2998 6909 8.791327 ACTTGAAAAAGGTTCACAAATTTGAT 57.209 26.923 24.64 6.33 0.00 2.57
2999 6910 9.883142 ACTTGAAAAAGGTTCACAAATTTGATA 57.117 25.926 24.64 8.96 0.00 2.15
3045 6956 9.583765 AAATTGTTGGGAATTGAAAAATGTTTG 57.416 25.926 0.00 0.00 0.00 2.93
3046 6957 7.693969 TTGTTGGGAATTGAAAAATGTTTGT 57.306 28.000 0.00 0.00 0.00 2.83
3047 6958 8.792830 TTGTTGGGAATTGAAAAATGTTTGTA 57.207 26.923 0.00 0.00 0.00 2.41
3048 6959 8.792830 TGTTGGGAATTGAAAAATGTTTGTAA 57.207 26.923 0.00 0.00 0.00 2.41
3049 6960 9.231297 TGTTGGGAATTGAAAAATGTTTGTAAA 57.769 25.926 0.00 0.00 0.00 2.01
3078 6989 5.665916 AAAAATGCTCGGGAAAATGATCT 57.334 34.783 0.00 0.00 0.00 2.75
3079 6990 5.665916 AAAATGCTCGGGAAAATGATCTT 57.334 34.783 0.00 0.00 0.00 2.40
3080 6991 4.644103 AATGCTCGGGAAAATGATCTTG 57.356 40.909 0.00 0.00 0.00 3.02
3081 6992 2.368439 TGCTCGGGAAAATGATCTTGG 58.632 47.619 0.00 0.00 0.00 3.61
3082 6993 2.026356 TGCTCGGGAAAATGATCTTGGA 60.026 45.455 0.00 0.00 0.00 3.53
3083 6994 3.016736 GCTCGGGAAAATGATCTTGGAA 58.983 45.455 0.00 0.00 0.00 3.53
3084 6995 3.181496 GCTCGGGAAAATGATCTTGGAAC 60.181 47.826 0.00 0.00 0.00 3.62
3085 6996 3.352648 TCGGGAAAATGATCTTGGAACC 58.647 45.455 0.00 0.00 0.00 3.62
3086 6997 3.088532 CGGGAAAATGATCTTGGAACCA 58.911 45.455 0.00 0.00 0.00 3.67
3087 6998 3.509575 CGGGAAAATGATCTTGGAACCAA 59.490 43.478 6.12 6.12 0.00 3.67
3088 6999 4.021544 CGGGAAAATGATCTTGGAACCAAA 60.022 41.667 7.68 0.39 35.33 3.28
3089 7000 5.510520 CGGGAAAATGATCTTGGAACCAAAA 60.511 40.000 7.68 0.00 35.33 2.44
3090 7001 6.295249 GGGAAAATGATCTTGGAACCAAAAA 58.705 36.000 7.68 0.03 35.33 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.311109 ACTTCTACAAATTTTGGTGTTTGTCTT 58.689 29.630 13.42 0.00 44.73 3.01
31 32 1.707989 TGCCCCATCCACTTCTACAAA 59.292 47.619 0.00 0.00 0.00 2.83
32 33 1.367346 TGCCCCATCCACTTCTACAA 58.633 50.000 0.00 0.00 0.00 2.41
44 45 3.775261 GCATAATTCCATTTGCCCCAT 57.225 42.857 0.00 0.00 0.00 4.00
319 321 1.197949 GTCTGCGGGCTTCTTCTTTTC 59.802 52.381 0.00 0.00 0.00 2.29
333 335 2.078849 TGTGTCTATTGTGGTCTGCG 57.921 50.000 0.00 0.00 0.00 5.18
391 393 6.461640 TCCTTCGAAAGTTTCTAAAGGTAGG 58.538 40.000 28.23 18.67 39.42 3.18
556 657 5.429435 ACTTTTGTAGTATAATTCCCCGGGA 59.571 40.000 26.32 1.94 34.56 5.14
557 658 5.687780 ACTTTTGTAGTATAATTCCCCGGG 58.312 41.667 15.80 15.80 34.56 5.73
571 672 9.807386 CGTCCTGTATTTTTCTAACTTTTGTAG 57.193 33.333 0.00 0.00 0.00 2.74
593 694 8.394877 TGATGTATGAAAATGATGTTTACGTCC 58.605 33.333 0.00 0.00 0.00 4.79
607 708 8.402798 AGGTTGTTATGTGTGATGTATGAAAA 57.597 30.769 0.00 0.00 0.00 2.29
621 722 3.188460 GTCATTGCACGAGGTTGTTATGT 59.812 43.478 0.00 0.00 0.00 2.29
622 723 3.436704 AGTCATTGCACGAGGTTGTTATG 59.563 43.478 0.00 0.00 0.00 1.90
623 724 3.674997 AGTCATTGCACGAGGTTGTTAT 58.325 40.909 0.00 0.00 0.00 1.89
624 725 3.120321 AGTCATTGCACGAGGTTGTTA 57.880 42.857 0.00 0.00 0.00 2.41
625 726 1.967319 AGTCATTGCACGAGGTTGTT 58.033 45.000 0.00 0.00 0.00 2.83
821 928 3.258872 TGATCCGTCCGAAGACCTTTTTA 59.741 43.478 0.00 0.00 40.12 1.52
834 941 1.096967 TGTGCATGCATGATCCGTCC 61.097 55.000 30.64 10.88 0.00 4.79
904 1011 2.221906 ATAGGCGCCTTGTTCGACGT 62.222 55.000 37.74 8.78 40.48 4.34
1025 1143 2.031012 TGAGGCACAAGAGCACGG 59.969 61.111 0.00 0.00 35.83 4.94
1491 1724 5.498393 TGTAGGAGCGGTTCTATATAGGAG 58.502 45.833 5.80 1.08 0.00 3.69
1492 1725 5.498393 CTGTAGGAGCGGTTCTATATAGGA 58.502 45.833 5.80 0.00 0.00 2.94
1493 1726 4.096682 GCTGTAGGAGCGGTTCTATATAGG 59.903 50.000 5.80 0.00 38.15 2.57
1494 1727 5.238006 GCTGTAGGAGCGGTTCTATATAG 57.762 47.826 5.80 3.10 38.15 1.31
1561 1845 2.046988 CGCCCAGCATGACACTGA 60.047 61.111 0.00 0.00 39.69 3.41
1799 2083 2.954753 GCCTGGTTGTCGAACAGCG 61.955 63.158 0.00 0.00 42.69 5.18
2316 2604 8.087136 TGTGCATTATCACTGCTGAAAAATAAA 58.913 29.630 0.00 0.00 40.34 1.40
2319 2607 6.028146 TGTGCATTATCACTGCTGAAAAAT 57.972 33.333 0.00 0.00 40.34 1.82
2392 4787 5.365021 AACTGGAGAGTTGATGGGATTAG 57.635 43.478 0.00 0.00 41.12 1.73
2460 4907 7.484140 AGTCAAAAGTGTTCTGGATTTCTTTC 58.516 34.615 0.00 0.00 0.00 2.62
2550 4997 8.410673 TCTTGGGTACATACAAAGCATTTTTA 57.589 30.769 0.00 0.00 35.03 1.52
2630 5078 9.632807 TGTTAATGTATGGCATTGTTTTCTTAC 57.367 29.630 4.78 0.00 46.40 2.34
2631 5079 9.853555 CTGTTAATGTATGGCATTGTTTTCTTA 57.146 29.630 4.78 0.00 46.40 2.10
2633 5081 8.121305 TCTGTTAATGTATGGCATTGTTTTCT 57.879 30.769 4.78 0.00 46.40 2.52
2634 5082 8.755696 TTCTGTTAATGTATGGCATTGTTTTC 57.244 30.769 4.78 0.00 46.40 2.29
2635 5083 9.723601 ATTTCTGTTAATGTATGGCATTGTTTT 57.276 25.926 4.78 0.00 46.40 2.43
2639 5087 8.929827 TCAATTTCTGTTAATGTATGGCATTG 57.070 30.769 4.78 0.00 46.40 2.82
2644 5092 8.810427 GTGCATTCAATTTCTGTTAATGTATGG 58.190 33.333 0.00 0.00 31.65 2.74
2652 5100 6.746104 CAAACGTGCATTCAATTTCTGTTA 57.254 33.333 0.00 0.00 0.00 2.41
2727 6607 5.048504 GTGAGCTTCACATGAAAGATGGAAA 60.049 40.000 14.18 0.00 46.22 3.13
2748 6628 6.647334 TTTTATTTGAGCTCCATGTTGTGA 57.353 33.333 12.15 0.00 0.00 3.58
2800 6710 9.566432 CTATGGATTCAAGCTAAAAATAGGTCT 57.434 33.333 0.00 0.00 0.00 3.85
2806 6716 7.068716 GGTGGTCTATGGATTCAAGCTAAAAAT 59.931 37.037 0.00 0.00 0.00 1.82
2814 6724 5.614324 TGTAGGTGGTCTATGGATTCAAG 57.386 43.478 0.00 0.00 0.00 3.02
2817 6727 6.591935 TCATTTGTAGGTGGTCTATGGATTC 58.408 40.000 0.00 0.00 0.00 2.52
2861 6772 5.320549 TCCGTGTAGTTAGGTGAATCTTC 57.679 43.478 0.00 0.00 0.00 2.87
2864 6775 5.258456 TCATCCGTGTAGTTAGGTGAATC 57.742 43.478 0.00 0.00 0.00 2.52
2887 6798 0.370273 CTAATGGTTGTCGCGACTGC 59.630 55.000 36.27 27.36 37.91 4.40
2888 6799 0.370273 GCTAATGGTTGTCGCGACTG 59.630 55.000 36.27 17.61 0.00 3.51
2891 6802 1.075542 CTTGCTAATGGTTGTCGCGA 58.924 50.000 3.71 3.71 0.00 5.87
2894 6805 2.987413 TTGCTTGCTAATGGTTGTCG 57.013 45.000 0.00 0.00 0.00 4.35
2896 6807 4.040217 TCCATTTTGCTTGCTAATGGTTGT 59.960 37.500 24.61 0.00 45.43 3.32
2916 6827 1.541310 GGATGTGTCCTGGTCGTCCA 61.541 60.000 16.34 0.39 41.60 4.02
2941 6852 9.929722 GCTTTGATATTACGAACATTATGAACA 57.070 29.630 0.00 0.00 0.00 3.18
2942 6853 9.382244 GGCTTTGATATTACGAACATTATGAAC 57.618 33.333 0.00 0.00 0.00 3.18
2943 6854 9.114952 TGGCTTTGATATTACGAACATTATGAA 57.885 29.630 0.00 0.00 0.00 2.57
2944 6855 8.556194 GTGGCTTTGATATTACGAACATTATGA 58.444 33.333 0.00 0.00 0.00 2.15
2945 6856 8.341903 TGTGGCTTTGATATTACGAACATTATG 58.658 33.333 0.00 0.00 0.00 1.90
2946 6857 8.445275 TGTGGCTTTGATATTACGAACATTAT 57.555 30.769 0.00 0.00 0.00 1.28
2947 6858 7.851387 TGTGGCTTTGATATTACGAACATTA 57.149 32.000 0.00 0.00 0.00 1.90
2948 6859 6.751514 TGTGGCTTTGATATTACGAACATT 57.248 33.333 0.00 0.00 0.00 2.71
2949 6860 6.751514 TTGTGGCTTTGATATTACGAACAT 57.248 33.333 0.00 0.00 0.00 2.71
2950 6861 6.205853 AGTTTGTGGCTTTGATATTACGAACA 59.794 34.615 0.00 0.00 35.76 3.18
2951 6862 6.608610 AGTTTGTGGCTTTGATATTACGAAC 58.391 36.000 0.00 0.00 34.31 3.95
2952 6863 6.811253 AGTTTGTGGCTTTGATATTACGAA 57.189 33.333 0.00 0.00 0.00 3.85
2953 6864 6.428465 TCAAGTTTGTGGCTTTGATATTACGA 59.572 34.615 0.00 0.00 0.00 3.43
2954 6865 6.607689 TCAAGTTTGTGGCTTTGATATTACG 58.392 36.000 0.00 0.00 0.00 3.18
2955 6866 8.810652 TTTCAAGTTTGTGGCTTTGATATTAC 57.189 30.769 0.00 0.00 0.00 1.89
2956 6867 9.823647 TTTTTCAAGTTTGTGGCTTTGATATTA 57.176 25.926 0.00 0.00 0.00 0.98
2957 6868 8.729805 TTTTTCAAGTTTGTGGCTTTGATATT 57.270 26.923 0.00 0.00 0.00 1.28
2958 6869 7.442062 CCTTTTTCAAGTTTGTGGCTTTGATAT 59.558 33.333 0.00 0.00 0.00 1.63
2959 6870 6.760770 CCTTTTTCAAGTTTGTGGCTTTGATA 59.239 34.615 0.00 0.00 0.00 2.15
2960 6871 5.585844 CCTTTTTCAAGTTTGTGGCTTTGAT 59.414 36.000 0.00 0.00 0.00 2.57
2961 6872 4.934602 CCTTTTTCAAGTTTGTGGCTTTGA 59.065 37.500 0.00 0.00 0.00 2.69
2962 6873 4.694982 ACCTTTTTCAAGTTTGTGGCTTTG 59.305 37.500 0.00 0.00 0.00 2.77
2963 6874 4.905429 ACCTTTTTCAAGTTTGTGGCTTT 58.095 34.783 0.00 0.00 0.00 3.51
2964 6875 4.551702 ACCTTTTTCAAGTTTGTGGCTT 57.448 36.364 0.00 0.00 0.00 4.35
2965 6876 4.020662 TGAACCTTTTTCAAGTTTGTGGCT 60.021 37.500 0.00 0.00 0.00 4.75
2966 6877 4.092821 GTGAACCTTTTTCAAGTTTGTGGC 59.907 41.667 0.00 0.00 0.00 5.01
2967 6878 5.233988 TGTGAACCTTTTTCAAGTTTGTGG 58.766 37.500 0.00 0.00 0.00 4.17
2968 6879 6.777526 TTGTGAACCTTTTTCAAGTTTGTG 57.222 33.333 0.00 0.00 0.00 3.33
2969 6880 7.977789 ATTTGTGAACCTTTTTCAAGTTTGT 57.022 28.000 0.00 0.00 0.00 2.83
2970 6881 9.116054 CAAATTTGTGAACCTTTTTCAAGTTTG 57.884 29.630 10.15 0.00 38.37 2.93
2971 6882 9.061435 TCAAATTTGTGAACCTTTTTCAAGTTT 57.939 25.926 17.47 0.00 31.66 2.66
2972 6883 8.614469 TCAAATTTGTGAACCTTTTTCAAGTT 57.386 26.923 17.47 0.00 0.00 2.66
2973 6884 8.791327 ATCAAATTTGTGAACCTTTTTCAAGT 57.209 26.923 17.47 0.00 0.00 3.16
3019 6930 9.583765 CAAACATTTTTCAATTCCCAACAATTT 57.416 25.926 0.00 0.00 0.00 1.82
3020 6931 8.747471 ACAAACATTTTTCAATTCCCAACAATT 58.253 25.926 0.00 0.00 0.00 2.32
3021 6932 8.291191 ACAAACATTTTTCAATTCCCAACAAT 57.709 26.923 0.00 0.00 0.00 2.71
3022 6933 7.693969 ACAAACATTTTTCAATTCCCAACAA 57.306 28.000 0.00 0.00 0.00 2.83
3023 6934 8.792830 TTACAAACATTTTTCAATTCCCAACA 57.207 26.923 0.00 0.00 0.00 3.33
3056 6967 5.665916 AGATCATTTTCCCGAGCATTTTT 57.334 34.783 0.00 0.00 0.00 1.94
3057 6968 5.413499 CAAGATCATTTTCCCGAGCATTTT 58.587 37.500 0.00 0.00 0.00 1.82
3058 6969 4.142093 CCAAGATCATTTTCCCGAGCATTT 60.142 41.667 0.00 0.00 0.00 2.32
3059 6970 3.382546 CCAAGATCATTTTCCCGAGCATT 59.617 43.478 0.00 0.00 0.00 3.56
3060 6971 2.954318 CCAAGATCATTTTCCCGAGCAT 59.046 45.455 0.00 0.00 0.00 3.79
3061 6972 2.026356 TCCAAGATCATTTTCCCGAGCA 60.026 45.455 0.00 0.00 0.00 4.26
3062 6973 2.643551 TCCAAGATCATTTTCCCGAGC 58.356 47.619 0.00 0.00 0.00 5.03
3063 6974 3.378427 GGTTCCAAGATCATTTTCCCGAG 59.622 47.826 0.00 0.00 0.00 4.63
3064 6975 3.245087 TGGTTCCAAGATCATTTTCCCGA 60.245 43.478 0.00 0.00 0.00 5.14
3065 6976 3.088532 TGGTTCCAAGATCATTTTCCCG 58.911 45.455 0.00 0.00 0.00 5.14
3066 6977 5.482163 TTTGGTTCCAAGATCATTTTCCC 57.518 39.130 4.44 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.