Multiple sequence alignment - TraesCS2A01G512400

Loading Multiple Alignment...

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 TraesCS2A01G512400 chr2A 100.000 2432 0 0 520 2951 737342269 737339838 0.000000e+00 4492.0
1 TraesCS2A01G512400 chr2A 100.000 83 0 0 1 83 737342788 737342706 1.420000e-33 154.0
2 TraesCS2A01G512400 chr2D 93.629 1915 77 21 995 2881 605910446 605908549 0.000000e+00 2819.0
3 TraesCS2A01G512400 chr2D 92.325 443 22 8 520 962 605910943 605910513 1.160000e-173 619.0
4 TraesCS2A01G512400 chr2D 88.060 67 4 2 17 83 605911002 605910940 3.150000e-10 76.8
5 TraesCS2A01G512400 chr2B 93.462 1912 82 23 997 2881 736757292 736755397 0.000000e+00 2798.0
6 TraesCS2A01G512400 chr2B 91.667 444 21 9 525 962 736757794 736757361 4.210000e-168 601.0
7 TraesCS2A01G512400 chr7D 98.113 53 1 0 1349 1401 579339586 579339534 3.130000e-15 93.5
8 TraesCS2A01G512400 chr5D 75.460 163 28 10 1327 1483 412352410 412352566 5.280000e-08 69.4
9 TraesCS2A01G512400 chr5A 79.167 96 18 2 1327 1421 524217821 524217915 6.830000e-07 65.8
10 TraesCS2A01G512400 chr5B 80.233 86 13 4 1327 1410 496485443 496485526 8.830000e-06 62.1


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 TraesCS2A01G512400 chr2A 737339838 737342788 2950 True 2323.0 4492 100.0000 1 2951 2 chr2A.!!$R1 2950
1 TraesCS2A01G512400 chr2D 605908549 605911002 2453 True 1171.6 2819 91.3380 17 2881 3 chr2D.!!$R1 2864
2 TraesCS2A01G512400 chr2B 736755397 736757794 2397 True 1699.5 2798 92.5645 525 2881 2 chr2B.!!$R1 2356

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
64 65 0.31716 ATGACGCCGAGTTTCACTCA 59.683 50.0 4.82 0.0 45.3 3.41 F
965 972 0.46187 CACGCCGATTGATTCTCCCA 60.462 55.0 0.00 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1442 0.109412 CGTTCTCGTCCAGGTACACC 60.109 60.0 0.0 0.0 0.0 4.16 R
2924 3019 0.037232 GCTGTACCAACGCTCCTTCT 60.037 55.0 0.0 0.0 0.0 2.85 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
49 50 3.457234 TCAATGTCAGATGCCGTATGAC 58.543 45.455 4.74 4.74 46.70 3.06
51 52 2.217112 GTCAGATGCCGTATGACGC 58.783 57.895 0.00 0.00 39.07 5.19
58 59 1.808390 GCCGTATGACGCCGAGTTT 60.808 57.895 0.00 0.00 40.91 2.66
59 60 1.749609 GCCGTATGACGCCGAGTTTC 61.750 60.000 0.00 0.00 40.91 2.78
60 61 0.457166 CCGTATGACGCCGAGTTTCA 60.457 55.000 0.00 0.00 40.91 2.69
61 62 0.638746 CGTATGACGCCGAGTTTCAC 59.361 55.000 0.00 0.00 33.65 3.18
62 63 1.731424 CGTATGACGCCGAGTTTCACT 60.731 52.381 0.00 0.00 33.65 3.41
63 64 1.918609 GTATGACGCCGAGTTTCACTC 59.081 52.381 0.00 0.00 41.71 3.51
64 65 0.317160 ATGACGCCGAGTTTCACTCA 59.683 50.000 4.82 0.00 45.30 3.41
65 66 0.596600 TGACGCCGAGTTTCACTCAC 60.597 55.000 4.82 0.00 45.30 3.51
539 540 2.752238 ACCGCGTCCTCCTCTGAG 60.752 66.667 4.92 0.00 38.42 3.35
545 546 1.382009 GTCCTCCTCTGAGACCCCC 60.382 68.421 6.17 0.00 41.42 5.40
546 547 1.862138 TCCTCCTCTGAGACCCCCA 60.862 63.158 6.17 0.00 41.42 4.96
547 548 1.687493 CCTCCTCTGAGACCCCCAC 60.687 68.421 6.17 0.00 41.42 4.61
548 549 2.037367 TCCTCTGAGACCCCCACG 59.963 66.667 6.17 0.00 0.00 4.94
549 550 3.775654 CCTCTGAGACCCCCACGC 61.776 72.222 6.17 0.00 0.00 5.34
550 551 2.681778 CTCTGAGACCCCCACGCT 60.682 66.667 0.00 0.00 0.00 5.07
571 572 2.158769 TCATACCATGATGACACCAGCC 60.159 50.000 0.00 0.00 33.59 4.85
578 579 1.608717 GATGACACCAGCCCGAGAGT 61.609 60.000 0.00 0.00 0.00 3.24
602 603 2.901042 GTCCTCCTACAAGGCCGG 59.099 66.667 0.00 0.00 36.29 6.13
729 730 3.708734 CGAACAACGTGCCCCGAC 61.709 66.667 0.00 0.00 40.70 4.79
800 801 2.284995 AGCCTCCACTCACTCCCC 60.285 66.667 0.00 0.00 0.00 4.81
801 802 2.284995 GCCTCCACTCACTCCCCT 60.285 66.667 0.00 0.00 0.00 4.79
822 823 3.571590 TGCTACTTGAACCCACCAAAAT 58.428 40.909 0.00 0.00 0.00 1.82
826 827 5.448632 GCTACTTGAACCCACCAAAATATCG 60.449 44.000 0.00 0.00 0.00 2.92
829 830 2.490115 TGAACCCACCAAAATATCGCAC 59.510 45.455 0.00 0.00 0.00 5.34
845 846 1.615262 CACCTTCCTCCCCCAATCC 59.385 63.158 0.00 0.00 0.00 3.01
873 874 2.282958 AAGCTGGGTCGACCGAGA 60.283 61.111 40.63 21.81 43.58 4.04
874 875 2.344203 AAGCTGGGTCGACCGAGAG 61.344 63.158 40.63 29.01 43.58 3.20
875 882 2.750637 GCTGGGTCGACCGAGAGA 60.751 66.667 40.63 17.25 43.58 3.10
962 969 0.811616 AGCCACGCCGATTGATTCTC 60.812 55.000 0.00 0.00 0.00 2.87
963 970 1.776034 GCCACGCCGATTGATTCTCC 61.776 60.000 0.00 0.00 0.00 3.71
964 971 1.160329 CCACGCCGATTGATTCTCCC 61.160 60.000 0.00 0.00 0.00 4.30
965 972 0.461870 CACGCCGATTGATTCTCCCA 60.462 55.000 0.00 0.00 0.00 4.37
968 975 1.151668 GCCGATTGATTCTCCCATCG 58.848 55.000 0.00 0.00 0.00 3.84
970 977 2.838736 CCGATTGATTCTCCCATCGTT 58.161 47.619 0.00 0.00 0.00 3.85
972 979 2.802816 CGATTGATTCTCCCATCGTTCC 59.197 50.000 0.00 0.00 0.00 3.62
973 980 3.741075 CGATTGATTCTCCCATCGTTCCA 60.741 47.826 0.00 0.00 0.00 3.53
974 981 3.931907 TTGATTCTCCCATCGTTCCAT 57.068 42.857 0.00 0.00 0.00 3.41
978 985 1.054406 TCTCCCATCGTTCCATCCCC 61.054 60.000 0.00 0.00 0.00 4.81
979 986 1.307430 TCCCATCGTTCCATCCCCA 60.307 57.895 0.00 0.00 0.00 4.96
980 987 1.152963 CCCATCGTTCCATCCCCAC 60.153 63.158 0.00 0.00 0.00 4.61
981 988 1.523711 CCATCGTTCCATCCCCACG 60.524 63.158 0.00 0.00 35.18 4.94
984 991 2.593468 ATCGTTCCATCCCCACGCAG 62.593 60.000 0.00 0.00 33.85 5.18
986 993 3.329889 TTCCATCCCCACGCAGCT 61.330 61.111 0.00 0.00 0.00 4.24
987 994 3.329542 TTCCATCCCCACGCAGCTC 62.330 63.158 0.00 0.00 0.00 4.09
989 996 3.790437 CATCCCCACGCAGCTCCT 61.790 66.667 0.00 0.00 0.00 3.69
991 998 3.335356 ATCCCCACGCAGCTCCTTG 62.335 63.158 0.00 0.00 0.00 3.61
1185 1226 2.331132 GGGTTCGTCGTCCTCGTCT 61.331 63.158 8.53 0.00 38.33 4.18
1186 1227 1.021390 GGGTTCGTCGTCCTCGTCTA 61.021 60.000 8.53 0.00 38.33 2.59
1187 1228 0.798776 GGTTCGTCGTCCTCGTCTAA 59.201 55.000 0.00 0.00 38.33 2.10
1704 1745 2.100631 GCCGTCCATCTTCACCACG 61.101 63.158 0.00 0.00 0.00 4.94
1792 1833 2.513026 CTTCGAGGTGGAGCAGGTGG 62.513 65.000 0.00 0.00 0.00 4.61
1863 1904 3.736482 CTCGCTCGCCCACTACGTC 62.736 68.421 0.00 0.00 0.00 4.34
1980 2021 3.035942 CGCACTTTGATTAATTAGCCGC 58.964 45.455 0.00 0.00 0.00 6.53
2133 2178 3.678072 AGTGTAACAATCAATCGTGACGG 59.322 43.478 4.70 0.00 41.43 4.79
2155 2200 3.487376 GCATGATTGATCGCCTCGAAAAA 60.487 43.478 0.00 0.00 39.99 1.94
2205 2250 3.760684 ACTTTGACAGATTGCTTGGGATC 59.239 43.478 0.00 0.00 0.00 3.36
2253 2303 2.482664 GGATCCATCCATCCATCGATCG 60.483 54.545 9.36 9.36 46.38 3.69
2255 2305 0.107993 CCATCCATCCATCGATCGGG 60.108 60.000 16.41 9.78 0.00 5.14
2305 2366 1.734837 TTGCGTGCGTTGCTCGATA 60.735 52.632 16.21 2.64 46.28 2.92
2308 2369 0.850217 GCGTGCGTTGCTCGATAATA 59.150 50.000 16.21 0.00 46.28 0.98
2311 2372 3.522362 CGTGCGTTGCTCGATAATAAAG 58.478 45.455 7.40 0.00 46.28 1.85
2331 2392 5.408079 AAGGTGGTGGGATCATATTCATT 57.592 39.130 0.00 0.00 0.00 2.57
2367 2429 0.861837 GTCATTAATGAGCGAGGGCG 59.138 55.000 18.47 0.00 46.35 6.13
2412 2474 0.965866 AGAAGTGTCTCGGATCGGCA 60.966 55.000 0.00 0.00 0.00 5.69
2438 2500 0.317160 TCATTGGAGTCGCTGTCGTT 59.683 50.000 0.00 0.00 36.96 3.85
2513 2584 2.359975 GGCTCAACGAACTGGGGG 60.360 66.667 0.00 0.00 0.00 5.40
2514 2585 3.056328 GCTCAACGAACTGGGGGC 61.056 66.667 0.00 0.00 0.00 5.80
2515 2586 2.429930 CTCAACGAACTGGGGGCA 59.570 61.111 0.00 0.00 0.00 5.36
2516 2587 1.002134 CTCAACGAACTGGGGGCAT 60.002 57.895 0.00 0.00 0.00 4.40
2517 2588 0.251916 CTCAACGAACTGGGGGCATA 59.748 55.000 0.00 0.00 0.00 3.14
2529 2600 1.533469 GGGGCATAGCGTATCCTCGT 61.533 60.000 0.00 0.00 0.00 4.18
2532 2603 1.269998 GGCATAGCGTATCCTCGTCTT 59.730 52.381 0.00 0.00 0.00 3.01
2541 2612 2.770164 ATCCTCGTCTTGACCCTTTG 57.230 50.000 0.00 0.00 0.00 2.77
2590 2661 1.472878 GTCTACGTGGCAGTGATCAGA 59.527 52.381 0.00 0.00 0.00 3.27
2596 2667 0.764271 TGGCAGTGATCAGACACCAA 59.236 50.000 0.00 0.00 41.12 3.67
2601 2672 2.745821 CAGTGATCAGACACCAACCATG 59.254 50.000 0.00 0.00 41.12 3.66
2608 2679 1.203038 AGACACCAACCATGATGCCAA 60.203 47.619 0.00 0.00 0.00 4.52
2615 2686 4.183101 CCAACCATGATGCCAATACAAAC 58.817 43.478 0.00 0.00 0.00 2.93
2682 2766 3.686726 GGGACAGTGCTACAGATCAAAAG 59.313 47.826 0.00 0.00 0.00 2.27
2685 2769 4.136796 ACAGTGCTACAGATCAAAAGCAA 58.863 39.130 14.94 1.19 45.81 3.91
2690 2774 7.170320 CAGTGCTACAGATCAAAAGCAATTTTT 59.830 33.333 14.94 0.91 45.81 1.94
2798 2893 0.108756 GGTTAGTGGTCAGCTCGGAC 60.109 60.000 0.00 0.00 37.06 4.79
2842 2937 4.776953 GTGCGCGATCGTGTGTGC 62.777 66.667 27.68 17.98 41.81 4.57
2881 2976 7.777910 AGGACGATCATAAATTGGATTTGGTTA 59.222 33.333 0.00 0.00 33.82 2.85
2882 2977 8.410141 GGACGATCATAAATTGGATTTGGTTAA 58.590 33.333 0.00 0.00 33.82 2.01
2883 2978 9.233232 GACGATCATAAATTGGATTTGGTTAAC 57.767 33.333 0.00 0.00 33.82 2.01
2884 2979 8.966868 ACGATCATAAATTGGATTTGGTTAACT 58.033 29.630 5.42 0.00 33.82 2.24
2885 2980 9.801873 CGATCATAAATTGGATTTGGTTAACTT 57.198 29.630 5.42 0.00 33.82 2.66
2915 3010 3.421919 AAATGGATTTGGTTTGCAGGG 57.578 42.857 0.00 0.00 0.00 4.45
2916 3011 2.028561 ATGGATTTGGTTTGCAGGGT 57.971 45.000 0.00 0.00 0.00 4.34
2917 3012 2.685106 TGGATTTGGTTTGCAGGGTA 57.315 45.000 0.00 0.00 0.00 3.69
2918 3013 3.182887 TGGATTTGGTTTGCAGGGTAT 57.817 42.857 0.00 0.00 0.00 2.73
2919 3014 2.830923 TGGATTTGGTTTGCAGGGTATG 59.169 45.455 0.00 0.00 0.00 2.39
2920 3015 2.168313 GGATTTGGTTTGCAGGGTATGG 59.832 50.000 0.00 0.00 0.00 2.74
2921 3016 2.685106 TTTGGTTTGCAGGGTATGGA 57.315 45.000 0.00 0.00 0.00 3.41
2922 3017 2.685106 TTGGTTTGCAGGGTATGGAA 57.315 45.000 0.00 0.00 37.48 3.53
2923 3018 2.685106 TGGTTTGCAGGGTATGGAAA 57.315 45.000 0.00 0.00 45.75 3.13
2929 3024 3.085952 TGCAGGGTATGGAAAAGAAGG 57.914 47.619 0.00 0.00 0.00 3.46
2930 3025 2.647299 TGCAGGGTATGGAAAAGAAGGA 59.353 45.455 0.00 0.00 0.00 3.36
2931 3026 3.282885 GCAGGGTATGGAAAAGAAGGAG 58.717 50.000 0.00 0.00 0.00 3.69
2932 3027 3.282885 CAGGGTATGGAAAAGAAGGAGC 58.717 50.000 0.00 0.00 0.00 4.70
2933 3028 2.092914 AGGGTATGGAAAAGAAGGAGCG 60.093 50.000 0.00 0.00 0.00 5.03
2934 3029 2.355818 GGGTATGGAAAAGAAGGAGCGT 60.356 50.000 0.00 0.00 0.00 5.07
2935 3030 3.344515 GGTATGGAAAAGAAGGAGCGTT 58.655 45.455 0.00 0.00 0.00 4.84
2936 3031 3.127030 GGTATGGAAAAGAAGGAGCGTTG 59.873 47.826 0.00 0.00 0.00 4.10
2937 3032 1.604604 TGGAAAAGAAGGAGCGTTGG 58.395 50.000 0.00 0.00 0.00 3.77
2938 3033 1.133915 TGGAAAAGAAGGAGCGTTGGT 60.134 47.619 0.00 0.00 0.00 3.67
2939 3034 2.105134 TGGAAAAGAAGGAGCGTTGGTA 59.895 45.455 0.00 0.00 0.00 3.25
2940 3035 2.483106 GGAAAAGAAGGAGCGTTGGTAC 59.517 50.000 0.00 0.00 0.00 3.34
2941 3036 2.922740 AAAGAAGGAGCGTTGGTACA 57.077 45.000 0.00 0.00 0.00 2.90
2942 3037 2.457366 AAGAAGGAGCGTTGGTACAG 57.543 50.000 0.00 0.00 42.39 2.74
2943 3038 0.037232 AGAAGGAGCGTTGGTACAGC 60.037 55.000 0.00 0.00 42.39 4.40
2944 3039 1.003718 AAGGAGCGTTGGTACAGCC 60.004 57.895 0.00 0.00 42.39 4.85
2945 3040 1.481056 AAGGAGCGTTGGTACAGCCT 61.481 55.000 0.00 0.00 42.39 4.58
2946 3041 1.741770 GGAGCGTTGGTACAGCCTG 60.742 63.158 0.00 0.00 42.39 4.85
2947 3042 2.358737 AGCGTTGGTACAGCCTGC 60.359 61.111 0.00 0.00 42.39 4.85
2948 3043 3.431725 GCGTTGGTACAGCCTGCC 61.432 66.667 0.00 0.00 42.39 4.85
2949 3044 2.746277 CGTTGGTACAGCCTGCCC 60.746 66.667 0.00 0.00 42.39 5.36
2950 3045 2.361230 GTTGGTACAGCCTGCCCC 60.361 66.667 0.00 0.00 42.39 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108709 TGAGAATTTGCGCATTGGCC 60.109 50.000 12.75 0.00 36.38 5.36
1 2 1.712401 TTGAGAATTTGCGCATTGGC 58.288 45.000 12.75 1.23 0.00 4.52
2 3 4.628333 AGAAATTGAGAATTTGCGCATTGG 59.372 37.500 12.75 0.00 40.97 3.16
3 4 5.346551 TGAGAAATTGAGAATTTGCGCATTG 59.653 36.000 12.75 0.00 40.97 2.82
4 5 5.472148 TGAGAAATTGAGAATTTGCGCATT 58.528 33.333 12.75 2.45 40.97 3.56
5 6 5.063180 TGAGAAATTGAGAATTTGCGCAT 57.937 34.783 12.75 0.00 40.97 4.73
6 7 4.502171 TGAGAAATTGAGAATTTGCGCA 57.498 36.364 5.66 5.66 40.97 6.09
7 8 5.097529 TGATGAGAAATTGAGAATTTGCGC 58.902 37.500 0.00 0.00 40.97 6.09
8 9 7.274904 ACATTGATGAGAAATTGAGAATTTGCG 59.725 33.333 0.00 0.00 40.97 4.85
9 10 8.475331 ACATTGATGAGAAATTGAGAATTTGC 57.525 30.769 0.00 0.00 40.97 3.68
10 11 9.634163 TGACATTGATGAGAAATTGAGAATTTG 57.366 29.630 0.00 0.00 40.97 2.32
11 12 9.856488 CTGACATTGATGAGAAATTGAGAATTT 57.144 29.630 0.00 0.00 43.43 1.82
12 13 9.239551 TCTGACATTGATGAGAAATTGAGAATT 57.760 29.630 0.00 0.00 0.00 2.17
13 14 8.803397 TCTGACATTGATGAGAAATTGAGAAT 57.197 30.769 0.00 0.00 0.00 2.40
14 15 8.674607 CATCTGACATTGATGAGAAATTGAGAA 58.325 33.333 0.00 0.00 42.68 2.87
15 16 7.201705 GCATCTGACATTGATGAGAAATTGAGA 60.202 37.037 8.48 0.00 42.68 3.27
58 59 4.751600 GTGTGTGAATGAATGAGTGAGTGA 59.248 41.667 0.00 0.00 0.00 3.41
59 60 4.512571 TGTGTGTGAATGAATGAGTGAGTG 59.487 41.667 0.00 0.00 0.00 3.51
60 61 4.707105 TGTGTGTGAATGAATGAGTGAGT 58.293 39.130 0.00 0.00 0.00 3.41
523 524 2.438614 TCTCAGAGGAGGACGCGG 60.439 66.667 12.47 0.00 41.69 6.46
539 540 1.696097 ATGGTATGAGCGTGGGGGTC 61.696 60.000 0.00 0.00 43.52 4.46
545 546 2.541346 GTGTCATCATGGTATGAGCGTG 59.459 50.000 0.00 0.00 43.53 5.34
546 547 2.483714 GGTGTCATCATGGTATGAGCGT 60.484 50.000 0.00 0.00 43.53 5.07
547 548 2.138320 GGTGTCATCATGGTATGAGCG 58.862 52.381 0.00 0.00 43.53 5.03
548 549 3.136763 CTGGTGTCATCATGGTATGAGC 58.863 50.000 0.00 0.00 43.53 4.26
549 550 3.136763 GCTGGTGTCATCATGGTATGAG 58.863 50.000 0.00 0.00 43.53 2.90
550 551 2.158769 GGCTGGTGTCATCATGGTATGA 60.159 50.000 0.00 0.00 44.55 2.15
571 572 3.056628 AGGACGTACGTACTCTCGG 57.943 57.895 27.42 9.75 33.15 4.63
578 579 2.632377 CCTTGTAGGAGGACGTACGTA 58.368 52.381 22.87 0.66 37.67 3.57
619 620 1.063806 GCTGACTACTGAACGCTGTG 58.936 55.000 0.00 0.00 0.00 3.66
620 621 0.673985 TGCTGACTACTGAACGCTGT 59.326 50.000 0.00 0.00 0.00 4.40
622 623 0.389166 GCTGCTGACTACTGAACGCT 60.389 55.000 0.00 0.00 0.00 5.07
800 801 2.270352 TTGGTGGGTTCAAGTAGCAG 57.730 50.000 0.00 0.00 0.00 4.24
801 802 2.738587 TTTGGTGGGTTCAAGTAGCA 57.261 45.000 0.00 0.00 0.00 3.49
822 823 1.764854 GGGGGAGGAAGGTGCGATA 60.765 63.158 0.00 0.00 0.00 2.92
826 827 1.076705 GATTGGGGGAGGAAGGTGC 60.077 63.158 0.00 0.00 0.00 5.01
829 830 1.692749 TCGGATTGGGGGAGGAAGG 60.693 63.158 0.00 0.00 0.00 3.46
862 863 0.386985 GTGTGTTCTCTCGGTCGACC 60.387 60.000 25.28 25.28 0.00 4.79
873 874 0.810031 GCCTCGTGTGTGTGTGTTCT 60.810 55.000 0.00 0.00 0.00 3.01
874 875 1.641677 GCCTCGTGTGTGTGTGTTC 59.358 57.895 0.00 0.00 0.00 3.18
875 882 1.817941 GGCCTCGTGTGTGTGTGTT 60.818 57.895 0.00 0.00 0.00 3.32
962 969 1.152963 GTGGGGATGGAACGATGGG 60.153 63.158 0.00 0.00 0.00 4.00
963 970 1.523711 CGTGGGGATGGAACGATGG 60.524 63.158 0.00 0.00 39.64 3.51
964 971 2.180204 GCGTGGGGATGGAACGATG 61.180 63.158 0.00 0.00 39.64 3.84
965 972 2.189521 GCGTGGGGATGGAACGAT 59.810 61.111 0.00 0.00 39.64 3.73
968 975 3.134127 GCTGCGTGGGGATGGAAC 61.134 66.667 0.00 0.00 0.00 3.62
970 977 3.785859 GAGCTGCGTGGGGATGGA 61.786 66.667 0.00 0.00 0.00 3.41
972 979 3.335356 AAGGAGCTGCGTGGGGATG 62.335 63.158 0.00 0.00 0.00 3.51
973 980 3.011517 AAGGAGCTGCGTGGGGAT 61.012 61.111 0.00 0.00 0.00 3.85
974 981 4.020617 CAAGGAGCTGCGTGGGGA 62.021 66.667 13.22 0.00 0.00 4.81
981 988 2.899339 GATCGCCCAAGGAGCTGC 60.899 66.667 0.00 0.00 0.00 5.25
984 991 1.958205 CATCGATCGCCCAAGGAGC 60.958 63.158 11.09 0.00 0.00 4.70
986 993 0.104855 CTTCATCGATCGCCCAAGGA 59.895 55.000 11.09 0.00 0.00 3.36
987 994 0.179073 ACTTCATCGATCGCCCAAGG 60.179 55.000 11.09 0.00 0.00 3.61
989 996 0.179084 GGACTTCATCGATCGCCCAA 60.179 55.000 11.09 1.27 0.00 4.12
991 998 0.034059 ATGGACTTCATCGATCGCCC 59.966 55.000 11.09 3.34 0.00 6.13
992 999 1.423395 GATGGACTTCATCGATCGCC 58.577 55.000 11.09 4.38 42.29 5.54
1169 1210 1.784816 CGTTAGACGAGGACGACGAAC 60.785 57.143 0.00 0.00 46.05 3.95
1170 1211 0.439985 CGTTAGACGAGGACGACGAA 59.560 55.000 0.00 0.00 46.05 3.85
1174 1215 2.780643 CGCGTTAGACGAGGACGA 59.219 61.111 4.46 0.00 46.05 4.20
1401 1442 0.109412 CGTTCTCGTCCAGGTACACC 60.109 60.000 0.00 0.00 0.00 4.16
1792 1833 1.517242 CACAGGAACTCCTTGCTCAC 58.483 55.000 0.00 0.00 46.09 3.51
2133 2178 1.220529 TTCGAGGCGATCAATCATGC 58.779 50.000 0.00 0.00 35.23 4.06
2187 2232 1.554617 TCGATCCCAAGCAATCTGTCA 59.445 47.619 0.00 0.00 0.00 3.58
2205 2250 0.371301 CACCAGCACATGTCGAATCG 59.629 55.000 0.00 0.00 0.00 3.34
2253 2303 5.277779 GCAAAGGAAAATGTAAAAGCAACCC 60.278 40.000 0.00 0.00 0.00 4.11
2255 2305 5.277779 GGGCAAAGGAAAATGTAAAAGCAAC 60.278 40.000 0.00 0.00 0.00 4.17
2305 2366 6.921412 TGAATATGATCCCACCACCTTTATT 58.079 36.000 0.00 0.00 0.00 1.40
2308 2369 4.879295 TGAATATGATCCCACCACCTTT 57.121 40.909 0.00 0.00 0.00 3.11
2311 2372 4.262164 GCAAATGAATATGATCCCACCACC 60.262 45.833 0.00 0.00 0.00 4.61
2331 2392 1.158434 GACCAAAATACGACGGGCAA 58.842 50.000 0.00 0.00 0.00 4.52
2367 2429 3.928992 TCAGATCAGATCAAAGCAACGAC 59.071 43.478 13.14 0.00 0.00 4.34
2412 2474 1.620819 AGCGACTCCAATGAACTGACT 59.379 47.619 0.00 0.00 0.00 3.41
2452 2518 2.280628 GACATCTTCCACGGATCCAAC 58.719 52.381 13.41 0.00 0.00 3.77
2474 2540 1.574428 GGACGTTGCTGCGAAACAT 59.426 52.632 7.42 0.00 35.59 2.71
2513 2584 2.031069 TCAAGACGAGGATACGCTATGC 60.031 50.000 0.00 0.00 46.39 3.14
2514 2585 3.556513 GTCAAGACGAGGATACGCTATG 58.443 50.000 0.00 0.00 46.39 2.23
2515 2586 2.553172 GGTCAAGACGAGGATACGCTAT 59.447 50.000 0.00 0.00 46.39 2.97
2516 2587 1.945394 GGTCAAGACGAGGATACGCTA 59.055 52.381 0.00 0.00 46.39 4.26
2517 2588 0.739561 GGTCAAGACGAGGATACGCT 59.260 55.000 0.00 0.00 46.39 5.07
2529 2600 2.554344 GGCATACCACAAAGGGTCAAGA 60.554 50.000 0.00 0.00 43.89 3.02
2532 2603 0.774276 TGGCATACCACAAAGGGTCA 59.226 50.000 0.00 0.00 42.67 4.02
2590 2661 1.941377 ATTGGCATCATGGTTGGTGT 58.059 45.000 0.00 0.00 36.28 4.16
2596 2667 3.351740 TCGTTTGTATTGGCATCATGGT 58.648 40.909 0.00 0.00 0.00 3.55
2601 2672 2.161410 TGTGCTCGTTTGTATTGGCATC 59.839 45.455 0.00 0.00 32.38 3.91
2608 2679 3.398406 TCACACATGTGCTCGTTTGTAT 58.602 40.909 25.68 0.00 45.25 2.29
2615 2686 1.925185 CAGAGATCACACATGTGCTCG 59.075 52.381 25.68 14.26 43.63 5.03
2682 2766 5.759763 AGTCAATCAAGTTGGGAAAAATTGC 59.240 36.000 2.34 2.16 38.39 3.56
2685 2769 6.282930 CACAGTCAATCAAGTTGGGAAAAAT 58.717 36.000 2.34 0.00 38.39 1.82
2690 2774 2.158623 AGCACAGTCAATCAAGTTGGGA 60.159 45.455 2.34 0.00 38.39 4.37
2842 2937 0.824109 TCGTCCTATGAGCTGTTGGG 59.176 55.000 0.00 0.00 0.00 4.12
2893 2988 4.143543 CCCTGCAAACCAAATCCATTTTT 58.856 39.130 0.00 0.00 0.00 1.94
2894 2989 3.138098 ACCCTGCAAACCAAATCCATTTT 59.862 39.130 0.00 0.00 0.00 1.82
2895 2990 2.710471 ACCCTGCAAACCAAATCCATTT 59.290 40.909 0.00 0.00 0.00 2.32
2896 2991 2.337849 ACCCTGCAAACCAAATCCATT 58.662 42.857 0.00 0.00 0.00 3.16
2897 2992 2.028561 ACCCTGCAAACCAAATCCAT 57.971 45.000 0.00 0.00 0.00 3.41
2898 2993 2.685106 TACCCTGCAAACCAAATCCA 57.315 45.000 0.00 0.00 0.00 3.41
2899 2994 2.168313 CCATACCCTGCAAACCAAATCC 59.832 50.000 0.00 0.00 0.00 3.01
2900 2995 3.096092 TCCATACCCTGCAAACCAAATC 58.904 45.455 0.00 0.00 0.00 2.17
2901 2996 3.182887 TCCATACCCTGCAAACCAAAT 57.817 42.857 0.00 0.00 0.00 2.32
2902 2997 2.685106 TCCATACCCTGCAAACCAAA 57.315 45.000 0.00 0.00 0.00 3.28
2903 2998 2.685106 TTCCATACCCTGCAAACCAA 57.315 45.000 0.00 0.00 0.00 3.67
2904 2999 2.685106 TTTCCATACCCTGCAAACCA 57.315 45.000 0.00 0.00 0.00 3.67
2905 3000 3.161866 TCTTTTCCATACCCTGCAAACC 58.838 45.455 0.00 0.00 0.00 3.27
2906 3001 4.321974 CCTTCTTTTCCATACCCTGCAAAC 60.322 45.833 0.00 0.00 0.00 2.93
2907 3002 3.831911 CCTTCTTTTCCATACCCTGCAAA 59.168 43.478 0.00 0.00 0.00 3.68
2908 3003 3.075283 TCCTTCTTTTCCATACCCTGCAA 59.925 43.478 0.00 0.00 0.00 4.08
2909 3004 2.647299 TCCTTCTTTTCCATACCCTGCA 59.353 45.455 0.00 0.00 0.00 4.41
2910 3005 3.282885 CTCCTTCTTTTCCATACCCTGC 58.717 50.000 0.00 0.00 0.00 4.85
2911 3006 3.282885 GCTCCTTCTTTTCCATACCCTG 58.717 50.000 0.00 0.00 0.00 4.45
2912 3007 2.092914 CGCTCCTTCTTTTCCATACCCT 60.093 50.000 0.00 0.00 0.00 4.34
2913 3008 2.289565 CGCTCCTTCTTTTCCATACCC 58.710 52.381 0.00 0.00 0.00 3.69
2914 3009 2.987232 ACGCTCCTTCTTTTCCATACC 58.013 47.619 0.00 0.00 0.00 2.73
2915 3010 3.127030 CCAACGCTCCTTCTTTTCCATAC 59.873 47.826 0.00 0.00 0.00 2.39
2916 3011 3.244770 ACCAACGCTCCTTCTTTTCCATA 60.245 43.478 0.00 0.00 0.00 2.74
2917 3012 2.162681 CCAACGCTCCTTCTTTTCCAT 58.837 47.619 0.00 0.00 0.00 3.41
2918 3013 1.133915 ACCAACGCTCCTTCTTTTCCA 60.134 47.619 0.00 0.00 0.00 3.53
2919 3014 1.605753 ACCAACGCTCCTTCTTTTCC 58.394 50.000 0.00 0.00 0.00 3.13
2920 3015 3.135994 TGTACCAACGCTCCTTCTTTTC 58.864 45.455 0.00 0.00 0.00 2.29
2921 3016 3.139077 CTGTACCAACGCTCCTTCTTTT 58.861 45.455 0.00 0.00 0.00 2.27
2922 3017 2.767505 CTGTACCAACGCTCCTTCTTT 58.232 47.619 0.00 0.00 0.00 2.52
2923 3018 1.608283 GCTGTACCAACGCTCCTTCTT 60.608 52.381 0.00 0.00 0.00 2.52
2924 3019 0.037232 GCTGTACCAACGCTCCTTCT 60.037 55.000 0.00 0.00 0.00 2.85
2925 3020 1.019805 GGCTGTACCAACGCTCCTTC 61.020 60.000 0.00 0.00 38.86 3.46
2926 3021 1.003718 GGCTGTACCAACGCTCCTT 60.004 57.895 0.00 0.00 38.86 3.36
2927 3022 1.913762 AGGCTGTACCAACGCTCCT 60.914 57.895 0.00 0.00 43.14 3.69
2928 3023 1.741770 CAGGCTGTACCAACGCTCC 60.742 63.158 6.28 0.00 43.14 4.70
2929 3024 2.391389 GCAGGCTGTACCAACGCTC 61.391 63.158 17.16 0.00 43.14 5.03
2930 3025 2.358737 GCAGGCTGTACCAACGCT 60.359 61.111 17.16 0.00 43.14 5.07
2931 3026 3.431725 GGCAGGCTGTACCAACGC 61.432 66.667 17.16 0.00 43.14 4.84
2932 3027 2.746277 GGGCAGGCTGTACCAACG 60.746 66.667 17.16 0.00 43.14 4.10
2933 3028 2.361230 GGGGCAGGCTGTACCAAC 60.361 66.667 24.78 9.91 43.14 3.77


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

AutoCloner maintained by Alex Coulton.