Multiple sequence alignment - TraesCS1A01G254800

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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 TraesCS1A01G254800 chr1A 100.000 3185 0 0 1 3185 446235432 446238616 0.000000e+00 5882
1 TraesCS1A01G254800 chr1A 98.837 86 1 0 2775 2860 133417547 133417462 1.530000e-33 154
2 TraesCS1A01G254800 chr1D 92.430 2761 100 31 97 2777 346020718 346023449 0.000000e+00 3840
3 TraesCS1A01G254800 chr1D 79.039 229 32 12 2858 3083 346023447 346023662 3.310000e-30 143
4 TraesCS1A01G254800 chr1B 91.243 2695 127 42 109 2742 463830862 463833508 0.000000e+00 3568
5 TraesCS1A01G254800 chr1B 82.500 320 33 8 2858 3159 463833531 463833845 3.150000e-65 259
6 TraesCS1A01G254800 chr1B 93.750 112 7 0 2 113 463823831 463823942 5.460000e-38 169
7 TraesCS1A01G254800 chr3D 98.851 87 1 0 2774 2860 12881744 12881658 4.250000e-34 156
8 TraesCS1A01G254800 chr3B 98.851 87 1 0 2774 2860 15111023 15111109 4.250000e-34 156
9 TraesCS1A01G254800 chr7A 95.789 95 4 0 2765 2859 210000865 210000959 1.530000e-33 154
10 TraesCS1A01G254800 chr5A 97.753 89 2 0 2772 2860 328936582 328936670 1.530000e-33 154
11 TraesCS1A01G254800 chr5A 97.753 89 2 0 2772 2860 674574369 674574281 1.530000e-33 154
12 TraesCS1A01G254800 chr5A 82.738 168 25 3 1640 1807 11754084 11754247 2.560000e-31 147
13 TraesCS1A01G254800 chr6D 93.878 98 6 0 2763 2860 470635720 470635623 7.120000e-32 148
14 TraesCS1A01G254800 chr5B 96.591 88 3 0 2772 2859 293544198 293544285 2.560000e-31 147
15 TraesCS1A01G254800 chr2A 92.079 101 8 0 2760 2860 522494857 522494957 3.310000e-30 143


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 TraesCS1A01G254800 chr1A 446235432 446238616 3184 False 5882.0 5882 100.0000 1 3185 1 chr1A.!!$F1 3184
1 TraesCS1A01G254800 chr1D 346020718 346023662 2944 False 1991.5 3840 85.7345 97 3083 2 chr1D.!!$F1 2986
2 TraesCS1A01G254800 chr1B 463830862 463833845 2983 False 1913.5 3568 86.8715 109 3159 2 chr1B.!!$F2 3050

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
99 100 0.100861 GAGGAGCAGCTACGGTACAC 59.899 60.0 0.0 0.0 0.00 2.90 F
525 539 0.108329 AGTTGATAACTCCCACCGCG 60.108 55.0 0.0 0.0 37.02 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 1276 1.153823 CCTGTTCCCGTCGCAGTAG 60.154 63.158 0.0 0.0 0.0 2.57 R
2361 2452 0.988832 ACGTTGCTATCCCTTTCCCA 59.011 50.000 0.0 0.0 0.0 4.37 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
24 25 2.257034 GTTAGATCCAACGACACGACC 58.743 52.381 0.00 0.00 0.00 4.79
25 26 1.536940 TAGATCCAACGACACGACCA 58.463 50.000 0.00 0.00 0.00 4.02
26 27 0.243907 AGATCCAACGACACGACCAG 59.756 55.000 0.00 0.00 0.00 4.00
27 28 0.242825 GATCCAACGACACGACCAGA 59.757 55.000 0.00 0.00 0.00 3.86
28 29 0.677288 ATCCAACGACACGACCAGAA 59.323 50.000 0.00 0.00 0.00 3.02
29 30 0.249155 TCCAACGACACGACCAGAAC 60.249 55.000 0.00 0.00 0.00 3.01
30 31 0.528901 CCAACGACACGACCAGAACA 60.529 55.000 0.00 0.00 0.00 3.18
31 32 0.575390 CAACGACACGACCAGAACAC 59.425 55.000 0.00 0.00 0.00 3.32
32 33 0.173935 AACGACACGACCAGAACACA 59.826 50.000 0.00 0.00 0.00 3.72
33 34 0.387929 ACGACACGACCAGAACACAT 59.612 50.000 0.00 0.00 0.00 3.21
34 35 1.610038 ACGACACGACCAGAACACATA 59.390 47.619 0.00 0.00 0.00 2.29
35 36 1.983605 CGACACGACCAGAACACATAC 59.016 52.381 0.00 0.00 0.00 2.39
36 37 2.606065 CGACACGACCAGAACACATACA 60.606 50.000 0.00 0.00 0.00 2.29
37 38 2.729882 GACACGACCAGAACACATACAC 59.270 50.000 0.00 0.00 0.00 2.90
38 39 1.719246 CACGACCAGAACACATACACG 59.281 52.381 0.00 0.00 0.00 4.49
39 40 1.610038 ACGACCAGAACACATACACGA 59.390 47.619 0.00 0.00 0.00 4.35
40 41 2.251040 CGACCAGAACACATACACGAG 58.749 52.381 0.00 0.00 0.00 4.18
41 42 1.993370 GACCAGAACACATACACGAGC 59.007 52.381 0.00 0.00 0.00 5.03
42 43 0.992072 CCAGAACACATACACGAGCG 59.008 55.000 0.00 0.00 0.00 5.03
43 44 0.366871 CAGAACACATACACGAGCGC 59.633 55.000 0.00 0.00 0.00 5.92
44 45 0.736325 AGAACACATACACGAGCGCC 60.736 55.000 2.29 0.00 0.00 6.53
45 46 2.009625 GAACACATACACGAGCGCCG 62.010 60.000 15.25 15.25 45.44 6.46
46 47 3.913573 CACATACACGAGCGCCGC 61.914 66.667 16.48 0.00 43.32 6.53
47 48 4.429212 ACATACACGAGCGCCGCA 62.429 61.111 13.36 4.66 43.32 5.69
48 49 3.913573 CATACACGAGCGCCGCAC 61.914 66.667 13.36 3.45 43.32 5.34
60 61 3.357079 CCGCACCTGACAAGCCAC 61.357 66.667 0.00 0.00 0.00 5.01
61 62 2.591429 CGCACCTGACAAGCCACA 60.591 61.111 0.00 0.00 0.00 4.17
62 63 2.896801 CGCACCTGACAAGCCACAC 61.897 63.158 0.00 0.00 0.00 3.82
63 64 1.823470 GCACCTGACAAGCCACACA 60.823 57.895 0.00 0.00 0.00 3.72
64 65 2.024918 CACCTGACAAGCCACACAC 58.975 57.895 0.00 0.00 0.00 3.82
65 66 0.747644 CACCTGACAAGCCACACACA 60.748 55.000 0.00 0.00 0.00 3.72
66 67 0.748005 ACCTGACAAGCCACACACAC 60.748 55.000 0.00 0.00 0.00 3.82
67 68 1.447317 CCTGACAAGCCACACACACC 61.447 60.000 0.00 0.00 0.00 4.16
68 69 0.747644 CTGACAAGCCACACACACCA 60.748 55.000 0.00 0.00 0.00 4.17
69 70 1.029408 TGACAAGCCACACACACCAC 61.029 55.000 0.00 0.00 0.00 4.16
70 71 1.001517 ACAAGCCACACACACCACA 60.002 52.632 0.00 0.00 0.00 4.17
71 72 1.031571 ACAAGCCACACACACCACAG 61.032 55.000 0.00 0.00 0.00 3.66
72 73 2.120909 AAGCCACACACACCACAGC 61.121 57.895 0.00 0.00 0.00 4.40
73 74 3.952675 GCCACACACACCACAGCG 61.953 66.667 0.00 0.00 0.00 5.18
74 75 3.279116 CCACACACACCACAGCGG 61.279 66.667 0.00 0.00 42.50 5.52
75 76 2.203001 CACACACACCACAGCGGA 60.203 61.111 0.00 0.00 38.63 5.54
76 77 2.108976 ACACACACCACAGCGGAG 59.891 61.111 0.00 0.00 38.63 4.63
94 95 2.811101 CTGGAGGAGCAGCTACGG 59.189 66.667 0.00 0.00 0.00 4.02
95 96 2.037367 TGGAGGAGCAGCTACGGT 59.963 61.111 0.00 0.00 0.00 4.83
96 97 0.752009 CTGGAGGAGCAGCTACGGTA 60.752 60.000 0.00 0.00 0.00 4.02
97 98 1.035932 TGGAGGAGCAGCTACGGTAC 61.036 60.000 0.00 0.00 0.00 3.34
98 99 1.035932 GGAGGAGCAGCTACGGTACA 61.036 60.000 0.00 0.00 0.00 2.90
99 100 0.100861 GAGGAGCAGCTACGGTACAC 59.899 60.000 0.00 0.00 0.00 2.90
119 120 1.320507 GCACCAAACCCGTCCTAAAA 58.679 50.000 0.00 0.00 0.00 1.52
126 127 0.399075 ACCCGTCCTAAAACCCAGTG 59.601 55.000 0.00 0.00 0.00 3.66
142 146 2.686470 TGCCCCTCCAGCTCAGAG 60.686 66.667 3.65 3.65 0.00 3.35
199 203 3.161450 ACCACCGTCACTGCCACT 61.161 61.111 0.00 0.00 0.00 4.00
200 204 2.111043 CCACCGTCACTGCCACTT 59.889 61.111 0.00 0.00 0.00 3.16
300 304 2.862674 TTACTGCCGCGGAACCATCC 62.863 60.000 33.48 9.92 42.80 3.51
383 388 2.202892 GTCATCCCCTCCGAACGC 60.203 66.667 0.00 0.00 0.00 4.84
438 443 3.423154 GTTTGAGCCACCGAGCCG 61.423 66.667 0.00 0.00 0.00 5.52
457 462 0.110373 GCTAAAAACCGCGACAGGTG 60.110 55.000 8.23 0.00 45.21 4.00
513 527 2.169352 GCAGAGGAAGCCAGAGTTGATA 59.831 50.000 0.00 0.00 0.00 2.15
524 538 3.855159 AGTTGATAACTCCCACCGC 57.145 52.632 0.00 0.00 37.02 5.68
525 539 0.108329 AGTTGATAACTCCCACCGCG 60.108 55.000 0.00 0.00 37.02 6.46
526 540 1.448893 TTGATAACTCCCACCGCGC 60.449 57.895 0.00 0.00 0.00 6.86
653 714 2.750166 GCAAAGCCTTCCTTCTTCTACC 59.250 50.000 0.00 0.00 31.99 3.18
658 719 1.137282 CCTTCCTTCTTCTACCGGAGC 59.863 57.143 9.46 0.00 0.00 4.70
755 829 2.717390 TCCTCCACGAGAAAGAGAGAG 58.283 52.381 0.00 0.00 0.00 3.20
837 925 4.811761 GCACCGCGCGCCTTTAAG 62.812 66.667 27.36 11.74 0.00 1.85
841 929 3.564027 CGCGCGCCTTTAAGGGAG 61.564 66.667 27.72 5.27 35.37 4.30
842 930 3.202706 GCGCGCCTTTAAGGGAGG 61.203 66.667 23.24 0.00 35.37 4.30
843 931 2.513897 CGCGCCTTTAAGGGAGGG 60.514 66.667 13.42 8.97 35.37 4.30
844 932 2.124278 GCGCCTTTAAGGGAGGGG 60.124 66.667 13.42 6.10 46.72 4.79
885 973 1.363145 TTAAAGATTCCCACGCCGCG 61.363 55.000 12.14 12.14 0.00 6.46
920 1008 3.195698 GCCACGAGGTTGATCGGC 61.196 66.667 0.00 0.00 46.91 5.54
1032 1120 3.110178 GCTGTCGTGGCGGTGTAC 61.110 66.667 0.00 0.00 0.00 2.90
1372 1463 2.436824 GCTCCAACCTCCGCTTCC 60.437 66.667 0.00 0.00 0.00 3.46
1503 1594 4.695993 TCCATTGCGTCGCTGCCA 62.696 61.111 19.50 0.00 0.00 4.92
1554 1645 4.489771 CTCACCGGTGGCATCCCC 62.490 72.222 33.40 0.00 0.00 4.81
1797 1888 2.493973 CTCTCCGTGCTCCAGCTC 59.506 66.667 0.00 0.00 42.66 4.09
2190 2281 1.941403 AATGGAGGGGCTGACATGGG 61.941 60.000 0.00 0.00 0.00 4.00
2204 2295 2.677289 ATGGGTGGCTGCTCTCAGG 61.677 63.158 0.00 0.00 40.65 3.86
2216 2307 0.318441 CTCTCAGGAGCCACGACAAA 59.682 55.000 0.00 0.00 32.43 2.83
2217 2308 0.756294 TCTCAGGAGCCACGACAAAA 59.244 50.000 0.00 0.00 0.00 2.44
2223 2314 1.136057 GGAGCCACGACAAAAACGATC 60.136 52.381 0.00 0.00 34.70 3.69
2252 2343 3.237741 GCCTCTGATCGGGGAGGG 61.238 72.222 22.25 12.57 46.58 4.30
2378 2469 3.161866 TGTTTGGGAAAGGGATAGCAAC 58.838 45.455 0.00 0.00 0.00 4.17
2393 2484 1.409064 AGCAACGTCACAGACAGAAGA 59.591 47.619 0.00 0.00 32.09 2.87
2394 2485 2.159099 AGCAACGTCACAGACAGAAGAA 60.159 45.455 0.00 0.00 32.09 2.52
2395 2486 2.033662 GCAACGTCACAGACAGAAGAAC 60.034 50.000 0.00 0.00 32.09 3.01
2498 2590 8.349568 TGTTGTATAGACAGTGAGTGAGTAAT 57.650 34.615 0.00 0.00 36.76 1.89
2499 2591 9.457436 TGTTGTATAGACAGTGAGTGAGTAATA 57.543 33.333 0.00 0.00 36.76 0.98
2502 2594 9.067986 TGTATAGACAGTGAGTGAGTAATATGG 57.932 37.037 0.00 0.00 0.00 2.74
2503 2595 5.269505 AGACAGTGAGTGAGTAATATGGC 57.730 43.478 0.00 0.00 0.00 4.40
2602 2715 6.580791 GCATTCGCTGTTGAAATTTGTAGTAA 59.419 34.615 0.00 0.00 34.30 2.24
2650 2763 5.627499 TGATGAACAATGGTTACAAGCTC 57.373 39.130 0.00 0.00 37.36 4.09
2674 2787 0.457851 TTCTTTTGGTTGGCGTGGTG 59.542 50.000 0.00 0.00 0.00 4.17
2688 2801 2.223021 GCGTGGTGTATAAGCATGTGTG 60.223 50.000 0.00 0.00 43.81 3.82
2689 2802 3.000041 CGTGGTGTATAAGCATGTGTGT 59.000 45.455 0.00 0.00 38.84 3.72
2710 2823 4.680567 TGTTGTTGATTGCATTTCGTGATG 59.319 37.500 0.00 0.00 0.00 3.07
2777 2890 3.319972 TCACGTTGTACTTGGCTTCTACT 59.680 43.478 0.00 0.00 0.00 2.57
2778 2891 3.673809 CACGTTGTACTTGGCTTCTACTC 59.326 47.826 0.00 0.00 0.00 2.59
2779 2892 3.251571 CGTTGTACTTGGCTTCTACTCC 58.748 50.000 0.00 0.00 0.00 3.85
2780 2893 3.597255 GTTGTACTTGGCTTCTACTCCC 58.403 50.000 0.00 0.00 0.00 4.30
2781 2894 3.185880 TGTACTTGGCTTCTACTCCCT 57.814 47.619 0.00 0.00 0.00 4.20
2782 2895 3.097614 TGTACTTGGCTTCTACTCCCTC 58.902 50.000 0.00 0.00 0.00 4.30
2783 2896 2.632763 ACTTGGCTTCTACTCCCTCT 57.367 50.000 0.00 0.00 0.00 3.69
2784 2897 2.183679 ACTTGGCTTCTACTCCCTCTG 58.816 52.381 0.00 0.00 0.00 3.35
2785 2898 2.183679 CTTGGCTTCTACTCCCTCTGT 58.816 52.381 0.00 0.00 0.00 3.41
2786 2899 3.245658 ACTTGGCTTCTACTCCCTCTGTA 60.246 47.826 0.00 0.00 0.00 2.74
2787 2900 3.468071 TGGCTTCTACTCCCTCTGTAA 57.532 47.619 0.00 0.00 0.00 2.41
2788 2901 3.786553 TGGCTTCTACTCCCTCTGTAAA 58.213 45.455 0.00 0.00 0.00 2.01
2789 2902 3.514309 TGGCTTCTACTCCCTCTGTAAAC 59.486 47.826 0.00 0.00 0.00 2.01
2790 2903 3.770388 GGCTTCTACTCCCTCTGTAAACT 59.230 47.826 0.00 0.00 0.00 2.66
2791 2904 4.954826 GGCTTCTACTCCCTCTGTAAACTA 59.045 45.833 0.00 0.00 0.00 2.24
2792 2905 5.421374 GGCTTCTACTCCCTCTGTAAACTAA 59.579 44.000 0.00 0.00 0.00 2.24
2793 2906 6.098552 GGCTTCTACTCCCTCTGTAAACTAAT 59.901 42.308 0.00 0.00 0.00 1.73
2794 2907 7.287235 GGCTTCTACTCCCTCTGTAAACTAATA 59.713 40.741 0.00 0.00 0.00 0.98
2795 2908 8.862085 GCTTCTACTCCCTCTGTAAACTAATAT 58.138 37.037 0.00 0.00 0.00 1.28
2801 2914 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2802 2915 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2803 2916 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2804 2917 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2805 2918 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2812 2925 8.868635 AACTAATATAAGAGCGTTTAGACCAC 57.131 34.615 0.00 0.00 0.00 4.16
2813 2926 8.235359 ACTAATATAAGAGCGTTTAGACCACT 57.765 34.615 0.00 0.00 0.00 4.00
2814 2927 9.347240 ACTAATATAAGAGCGTTTAGACCACTA 57.653 33.333 0.00 0.00 0.00 2.74
2817 2930 9.530633 AATATAAGAGCGTTTAGACCACTAAAG 57.469 33.333 0.00 0.00 45.42 1.85
2818 2931 4.868314 AGAGCGTTTAGACCACTAAAGT 57.132 40.909 0.00 0.00 45.42 2.66
2819 2932 5.972107 AGAGCGTTTAGACCACTAAAGTA 57.028 39.130 0.00 0.00 45.42 2.24
2820 2933 5.952033 AGAGCGTTTAGACCACTAAAGTAG 58.048 41.667 0.00 0.00 45.42 2.57
2821 2934 5.476254 AGAGCGTTTAGACCACTAAAGTAGT 59.524 40.000 0.00 0.00 45.42 2.73
2835 2948 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2836 2949 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2837 2950 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2838 2951 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2850 2963 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2851 2964 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2852 2965 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2853 2966 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2854 2967 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2855 2968 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2856 2969 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2857 2970 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2858 2971 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2859 2972 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
2863 2976 2.270297 TTTACGGAGGGAGTACGCGC 62.270 60.000 5.73 5.50 0.00 6.86
2898 3011 2.981400 TCATAATGCATGCATCTGCG 57.019 45.000 32.25 20.26 45.30 5.18
2913 3026 0.107993 CTGCGGATCTCAAGCCTGAA 60.108 55.000 0.00 0.00 0.00 3.02
2914 3027 0.391661 TGCGGATCTCAAGCCTGAAC 60.392 55.000 0.00 0.00 0.00 3.18
2915 3028 0.107945 GCGGATCTCAAGCCTGAACT 60.108 55.000 0.00 0.00 0.00 3.01
2916 3029 1.933247 CGGATCTCAAGCCTGAACTC 58.067 55.000 0.00 0.00 0.00 3.01
2917 3030 1.480137 CGGATCTCAAGCCTGAACTCT 59.520 52.381 0.00 0.00 0.00 3.24
2918 3031 2.738000 CGGATCTCAAGCCTGAACTCTG 60.738 54.545 0.00 0.00 0.00 3.35
2919 3032 2.419851 GGATCTCAAGCCTGAACTCTGG 60.420 54.545 0.00 0.00 37.93 3.86
2920 3033 0.979665 TCTCAAGCCTGAACTCTGGG 59.020 55.000 4.96 0.00 35.73 4.45
2921 3034 0.035630 CTCAAGCCTGAACTCTGGGG 60.036 60.000 4.96 0.00 35.73 4.96
2922 3035 0.768221 TCAAGCCTGAACTCTGGGGT 60.768 55.000 4.96 0.00 35.73 4.95
2973 3106 2.358615 AGATTTGCGCCGCTGTGA 60.359 55.556 11.67 0.00 0.00 3.58
2974 3107 1.965930 AGATTTGCGCCGCTGTGAA 60.966 52.632 11.67 0.16 0.00 3.18
2995 3128 8.018520 TGTGAACTTATTAAACAACTTATGGCG 58.981 33.333 0.00 0.00 0.00 5.69
3004 3137 3.009723 ACAACTTATGGCGGAGTGATTG 58.990 45.455 0.00 0.00 0.00 2.67
3010 3143 2.690778 GGCGGAGTGATTGTGGCAC 61.691 63.158 11.55 11.55 36.53 5.01
3028 3161 3.003793 GGCACAAAGAAAGTGGTCTTCTC 59.996 47.826 0.00 0.00 36.84 2.87
3030 3163 3.871594 CACAAAGAAAGTGGTCTTCTCGT 59.128 43.478 0.00 0.00 36.84 4.18
3037 3170 3.919223 AGTGGTCTTCTCGTAGTGAAC 57.081 47.619 0.00 0.00 34.94 3.18
3038 3171 3.488363 AGTGGTCTTCTCGTAGTGAACT 58.512 45.455 0.00 0.00 34.94 3.01
3039 3172 3.502979 AGTGGTCTTCTCGTAGTGAACTC 59.497 47.826 0.00 0.00 34.94 3.01
3040 3173 3.502979 GTGGTCTTCTCGTAGTGAACTCT 59.497 47.826 0.00 0.00 34.94 3.24
3041 3174 3.502595 TGGTCTTCTCGTAGTGAACTCTG 59.497 47.826 0.00 0.00 34.94 3.35
3042 3175 3.494232 GTCTTCTCGTAGTGAACTCTGC 58.506 50.000 0.00 0.00 34.94 4.26
3067 3200 6.342906 TCTGCATCATTTCCATTGATTTTCC 58.657 36.000 0.00 0.00 31.50 3.13
3086 3219 1.933115 CTTTTGACCCCGCATTCCCG 61.933 60.000 0.00 0.00 0.00 5.14
3104 3237 1.135972 CCGGTGAATTCACTTTGCTCG 60.136 52.381 31.81 25.10 45.73 5.03
3112 3245 3.041940 ACTTTGCTCGGTTCGGCG 61.042 61.111 0.00 0.00 0.00 6.46
3113 3246 3.788766 CTTTGCTCGGTTCGGCGG 61.789 66.667 7.21 0.00 0.00 6.13
3125 3258 3.053896 CGGCGGTTCCCCTGTTTC 61.054 66.667 0.00 0.00 0.00 2.78
3126 3259 2.675423 GGCGGTTCCCCTGTTTCC 60.675 66.667 0.00 0.00 0.00 3.13
3134 3267 1.814429 TCCCCTGTTTCCTCTTGTCA 58.186 50.000 0.00 0.00 0.00 3.58
3136 3269 2.716424 TCCCCTGTTTCCTCTTGTCATT 59.284 45.455 0.00 0.00 0.00 2.57
3143 3276 6.656693 CCTGTTTCCTCTTGTCATTATCAACT 59.343 38.462 0.00 0.00 0.00 3.16
3153 3286 6.048732 TGTCATTATCAACTGGTCAAGCTA 57.951 37.500 0.00 0.00 0.00 3.32
3159 3292 5.649782 ATCAACTGGTCAAGCTATTTTGG 57.350 39.130 0.00 0.00 0.00 3.28
3160 3293 4.469657 TCAACTGGTCAAGCTATTTTGGT 58.530 39.130 0.00 0.00 0.00 3.67
3161 3294 4.892934 TCAACTGGTCAAGCTATTTTGGTT 59.107 37.500 0.00 0.00 0.00 3.67
3162 3295 5.009610 TCAACTGGTCAAGCTATTTTGGTTC 59.990 40.000 0.00 0.00 0.00 3.62
3163 3296 3.502211 ACTGGTCAAGCTATTTTGGTTCG 59.498 43.478 0.00 0.00 0.00 3.95
3164 3297 3.745799 TGGTCAAGCTATTTTGGTTCGA 58.254 40.909 0.00 0.00 0.00 3.71
3165 3298 4.138290 TGGTCAAGCTATTTTGGTTCGAA 58.862 39.130 0.00 0.00 0.00 3.71
3166 3299 4.023536 TGGTCAAGCTATTTTGGTTCGAAC 60.024 41.667 20.14 20.14 0.00 3.95
3167 3300 4.023536 GGTCAAGCTATTTTGGTTCGAACA 60.024 41.667 28.24 12.75 0.00 3.18
3168 3301 5.147162 GTCAAGCTATTTTGGTTCGAACAG 58.853 41.667 28.24 16.94 0.00 3.16
3169 3302 3.831715 AGCTATTTTGGTTCGAACAGC 57.168 42.857 28.24 24.66 0.00 4.40
3170 3303 3.412386 AGCTATTTTGGTTCGAACAGCT 58.588 40.909 28.24 26.25 33.45 4.24
3171 3304 3.821033 AGCTATTTTGGTTCGAACAGCTT 59.179 39.130 28.24 13.97 34.60 3.74
3172 3305 4.278419 AGCTATTTTGGTTCGAACAGCTTT 59.722 37.500 28.24 12.89 34.60 3.51
3173 3306 4.617223 GCTATTTTGGTTCGAACAGCTTTC 59.383 41.667 28.24 11.34 0.00 2.62
3174 3307 4.647424 ATTTTGGTTCGAACAGCTTTCA 57.353 36.364 28.24 13.78 0.00 2.69
3175 3308 3.414549 TTTGGTTCGAACAGCTTTCAC 57.585 42.857 28.24 9.94 0.00 3.18
3176 3309 1.305201 TGGTTCGAACAGCTTTCACC 58.695 50.000 28.24 10.25 0.00 4.02
3177 3310 1.134220 TGGTTCGAACAGCTTTCACCT 60.134 47.619 28.24 0.00 0.00 4.00
3178 3311 1.531578 GGTTCGAACAGCTTTCACCTC 59.468 52.381 28.24 3.97 0.00 3.85
3179 3312 1.192534 GTTCGAACAGCTTTCACCTCG 59.807 52.381 23.12 0.00 0.00 4.63
3180 3313 0.387929 TCGAACAGCTTTCACCTCGT 59.612 50.000 8.64 0.00 0.00 4.18
3181 3314 0.508641 CGAACAGCTTTCACCTCGTG 59.491 55.000 8.64 0.00 34.45 4.35
3182 3315 1.583054 GAACAGCTTTCACCTCGTGT 58.417 50.000 0.00 0.00 34.79 4.49
3183 3316 1.527311 GAACAGCTTTCACCTCGTGTC 59.473 52.381 0.00 0.00 34.79 3.67
3184 3317 0.249911 ACAGCTTTCACCTCGTGTCC 60.250 55.000 0.00 0.00 34.79 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.257034 GGTCGTGTCGTTGGATCTAAC 58.743 52.381 11.69 11.69 0.00 2.34
5 6 1.887854 TGGTCGTGTCGTTGGATCTAA 59.112 47.619 0.00 0.00 0.00 2.10
6 7 1.471287 CTGGTCGTGTCGTTGGATCTA 59.529 52.381 0.00 0.00 0.00 1.98
7 8 0.243907 CTGGTCGTGTCGTTGGATCT 59.756 55.000 0.00 0.00 0.00 2.75
8 9 0.242825 TCTGGTCGTGTCGTTGGATC 59.757 55.000 0.00 0.00 0.00 3.36
9 10 0.677288 TTCTGGTCGTGTCGTTGGAT 59.323 50.000 0.00 0.00 0.00 3.41
10 11 0.249155 GTTCTGGTCGTGTCGTTGGA 60.249 55.000 0.00 0.00 0.00 3.53
11 12 0.528901 TGTTCTGGTCGTGTCGTTGG 60.529 55.000 0.00 0.00 0.00 3.77
12 13 0.575390 GTGTTCTGGTCGTGTCGTTG 59.425 55.000 0.00 0.00 0.00 4.10
13 14 0.173935 TGTGTTCTGGTCGTGTCGTT 59.826 50.000 0.00 0.00 0.00 3.85
14 15 0.387929 ATGTGTTCTGGTCGTGTCGT 59.612 50.000 0.00 0.00 0.00 4.34
15 16 1.983605 GTATGTGTTCTGGTCGTGTCG 59.016 52.381 0.00 0.00 0.00 4.35
16 17 2.729882 GTGTATGTGTTCTGGTCGTGTC 59.270 50.000 0.00 0.00 0.00 3.67
17 18 2.750948 GTGTATGTGTTCTGGTCGTGT 58.249 47.619 0.00 0.00 0.00 4.49
18 19 1.719246 CGTGTATGTGTTCTGGTCGTG 59.281 52.381 0.00 0.00 0.00 4.35
19 20 1.610038 TCGTGTATGTGTTCTGGTCGT 59.390 47.619 0.00 0.00 0.00 4.34
20 21 2.251040 CTCGTGTATGTGTTCTGGTCG 58.749 52.381 0.00 0.00 0.00 4.79
21 22 1.993370 GCTCGTGTATGTGTTCTGGTC 59.007 52.381 0.00 0.00 0.00 4.02
22 23 1.668919 CGCTCGTGTATGTGTTCTGGT 60.669 52.381 0.00 0.00 0.00 4.00
23 24 0.992072 CGCTCGTGTATGTGTTCTGG 59.008 55.000 0.00 0.00 0.00 3.86
24 25 0.366871 GCGCTCGTGTATGTGTTCTG 59.633 55.000 0.00 0.00 0.00 3.02
25 26 0.736325 GGCGCTCGTGTATGTGTTCT 60.736 55.000 7.64 0.00 0.00 3.01
26 27 1.708027 GGCGCTCGTGTATGTGTTC 59.292 57.895 7.64 0.00 0.00 3.18
27 28 2.092291 CGGCGCTCGTGTATGTGTT 61.092 57.895 7.64 0.00 0.00 3.32
28 29 2.506217 CGGCGCTCGTGTATGTGT 60.506 61.111 7.64 0.00 0.00 3.72
29 30 3.913573 GCGGCGCTCGTGTATGTG 61.914 66.667 26.86 0.00 41.72 3.21
30 31 4.429212 TGCGGCGCTCGTGTATGT 62.429 61.111 33.26 0.00 41.72 2.29
31 32 3.913573 GTGCGGCGCTCGTGTATG 61.914 66.667 33.26 0.00 41.72 2.39
43 44 3.357079 GTGGCTTGTCAGGTGCGG 61.357 66.667 0.00 0.00 0.00 5.69
44 45 2.591429 TGTGGCTTGTCAGGTGCG 60.591 61.111 0.00 0.00 0.00 5.34
45 46 1.823470 TGTGTGGCTTGTCAGGTGC 60.823 57.895 0.00 0.00 0.00 5.01
46 47 0.747644 TGTGTGTGGCTTGTCAGGTG 60.748 55.000 0.00 0.00 0.00 4.00
47 48 0.748005 GTGTGTGTGGCTTGTCAGGT 60.748 55.000 0.00 0.00 0.00 4.00
48 49 1.447317 GGTGTGTGTGGCTTGTCAGG 61.447 60.000 0.00 0.00 0.00 3.86
49 50 0.747644 TGGTGTGTGTGGCTTGTCAG 60.748 55.000 0.00 0.00 0.00 3.51
50 51 1.029408 GTGGTGTGTGTGGCTTGTCA 61.029 55.000 0.00 0.00 0.00 3.58
51 52 1.029408 TGTGGTGTGTGTGGCTTGTC 61.029 55.000 0.00 0.00 0.00 3.18
52 53 1.001517 TGTGGTGTGTGTGGCTTGT 60.002 52.632 0.00 0.00 0.00 3.16
53 54 1.729276 CTGTGGTGTGTGTGGCTTG 59.271 57.895 0.00 0.00 0.00 4.01
54 55 2.120909 GCTGTGGTGTGTGTGGCTT 61.121 57.895 0.00 0.00 0.00 4.35
55 56 2.516930 GCTGTGGTGTGTGTGGCT 60.517 61.111 0.00 0.00 0.00 4.75
56 57 3.952675 CGCTGTGGTGTGTGTGGC 61.953 66.667 0.00 0.00 0.00 5.01
57 58 3.279116 CCGCTGTGGTGTGTGTGG 61.279 66.667 0.00 0.00 0.00 4.17
58 59 2.203001 TCCGCTGTGGTGTGTGTG 60.203 61.111 7.20 0.00 39.52 3.82
59 60 2.108976 CTCCGCTGTGGTGTGTGT 59.891 61.111 7.20 0.00 39.52 3.72
60 61 3.349006 GCTCCGCTGTGGTGTGTG 61.349 66.667 7.20 0.00 39.52 3.82
61 62 3.550431 AGCTCCGCTGTGGTGTGT 61.550 61.111 7.20 0.00 37.57 3.72
77 78 0.752009 TACCGTAGCTGCTCCTCCAG 60.752 60.000 4.91 0.00 35.93 3.86
78 79 1.035932 GTACCGTAGCTGCTCCTCCA 61.036 60.000 4.91 0.00 0.00 3.86
79 80 1.035932 TGTACCGTAGCTGCTCCTCC 61.036 60.000 4.91 0.00 0.00 4.30
80 81 0.100861 GTGTACCGTAGCTGCTCCTC 59.899 60.000 4.91 0.00 0.00 3.71
81 82 1.654954 CGTGTACCGTAGCTGCTCCT 61.655 60.000 4.91 0.00 0.00 3.69
82 83 1.226603 CGTGTACCGTAGCTGCTCC 60.227 63.158 4.91 0.00 0.00 4.70
83 84 1.872679 GCGTGTACCGTAGCTGCTC 60.873 63.158 4.91 0.00 39.32 4.26
84 85 2.181021 GCGTGTACCGTAGCTGCT 59.819 61.111 7.57 7.57 39.32 4.24
85 86 2.126228 TGCGTGTACCGTAGCTGC 60.126 61.111 0.00 0.00 39.32 5.25
86 87 1.804326 GGTGCGTGTACCGTAGCTG 60.804 63.158 13.59 0.00 44.69 4.24
87 88 2.570181 GGTGCGTGTACCGTAGCT 59.430 61.111 13.59 0.00 44.69 3.32
89 90 0.785979 GTTTGGTGCGTGTACCGTAG 59.214 55.000 2.66 0.00 43.87 3.51
90 91 0.599728 GGTTTGGTGCGTGTACCGTA 60.600 55.000 2.66 0.00 43.87 4.02
91 92 1.888638 GGTTTGGTGCGTGTACCGT 60.889 57.895 2.66 0.00 43.87 4.83
92 93 2.609759 GGGTTTGGTGCGTGTACCG 61.610 63.158 2.66 0.00 43.87 4.02
93 94 2.609759 CGGGTTTGGTGCGTGTACC 61.610 63.158 0.00 0.00 41.24 3.34
94 95 1.834458 GACGGGTTTGGTGCGTGTAC 61.834 60.000 0.00 0.00 0.00 2.90
95 96 1.594836 GACGGGTTTGGTGCGTGTA 60.595 57.895 0.00 0.00 0.00 2.90
96 97 2.898343 GACGGGTTTGGTGCGTGT 60.898 61.111 0.00 0.00 0.00 4.49
97 98 2.718747 TAGGACGGGTTTGGTGCGTG 62.719 60.000 0.00 0.00 0.00 5.34
98 99 2.042404 TTAGGACGGGTTTGGTGCGT 62.042 55.000 0.00 0.00 0.00 5.24
99 100 0.885596 TTTAGGACGGGTTTGGTGCG 60.886 55.000 0.00 0.00 0.00 5.34
100 101 1.001048 GTTTTAGGACGGGTTTGGTGC 60.001 52.381 0.00 0.00 0.00 5.01
126 127 1.557269 TTTCTCTGAGCTGGAGGGGC 61.557 60.000 11.82 0.00 0.00 5.80
232 236 0.249489 CGAGATTCATCCGTGGTCCC 60.249 60.000 0.00 0.00 0.00 4.46
358 362 4.195334 AGGGGATGACATGCGGGC 62.195 66.667 0.42 0.00 0.00 6.13
438 443 0.110373 CACCTGTCGCGGTTTTTAGC 60.110 55.000 6.13 0.00 34.29 3.09
467 472 1.136872 CTTTCTCTCCTTCGCGAGCG 61.137 60.000 9.59 11.64 41.35 5.03
632 693 2.750166 GGTAGAAGAAGGAAGGCTTTGC 59.250 50.000 0.00 0.00 0.00 3.68
653 714 3.057547 CTCACTCCACTCCGCTCCG 62.058 68.421 0.00 0.00 0.00 4.63
767 841 1.274703 TGAGGGGAGGAATGGAGCAC 61.275 60.000 0.00 0.00 0.00 4.40
768 842 1.082766 TGAGGGGAGGAATGGAGCA 59.917 57.895 0.00 0.00 0.00 4.26
769 843 1.529309 GTGAGGGGAGGAATGGAGC 59.471 63.158 0.00 0.00 0.00 4.70
770 844 1.826024 CGTGAGGGGAGGAATGGAG 59.174 63.158 0.00 0.00 0.00 3.86
837 925 4.500826 GTCCTCCCCTCCCCTCCC 62.501 77.778 0.00 0.00 0.00 4.30
839 927 4.862823 CCGTCCTCCCCTCCCCTC 62.863 77.778 0.00 0.00 0.00 4.30
893 981 4.200283 CTCGTGGCGGGAGAGCTC 62.200 72.222 5.27 5.27 37.29 4.09
920 1008 5.460646 TGCAAGAAGGAAGAATTAAAAGCG 58.539 37.500 0.00 0.00 0.00 4.68
967 1055 1.807573 CCTCGGTTCAAGCTCGCTC 60.808 63.158 0.00 0.00 0.00 5.03
968 1056 2.262915 CCTCGGTTCAAGCTCGCT 59.737 61.111 0.00 0.00 0.00 4.93
969 1057 3.491652 GCCTCGGTTCAAGCTCGC 61.492 66.667 0.00 0.00 0.00 5.03
970 1058 3.181967 CGCCTCGGTTCAAGCTCG 61.182 66.667 0.00 0.00 0.00 5.03
971 1059 3.491652 GCGCCTCGGTTCAAGCTC 61.492 66.667 0.00 0.00 0.00 4.09
1025 1113 2.388232 GCCGCCAAGAAGTACACCG 61.388 63.158 0.00 0.00 0.00 4.94
1068 1159 2.995574 AGGAAGTCCACCGGGTCG 60.996 66.667 6.32 0.00 38.89 4.79
1185 1276 1.153823 CCTGTTCCCGTCGCAGTAG 60.154 63.158 0.00 0.00 0.00 2.57
1372 1463 2.328099 GGTTCTTGCTGACGGCCAG 61.328 63.158 2.24 1.92 45.67 4.85
1503 1594 2.366916 GAGGATGAGGTTGGTGATCGAT 59.633 50.000 0.00 0.00 0.00 3.59
1797 1888 1.630244 CGGAGAAGAAGTTGCGCTGG 61.630 60.000 9.73 0.00 0.00 4.85
1909 2000 2.125512 CAGGTACAGCTGCCCGAC 60.126 66.667 15.27 6.87 0.00 4.79
1911 2002 1.741770 GTTCAGGTACAGCTGCCCG 60.742 63.158 15.27 10.47 0.00 6.13
2204 2295 1.461888 CGATCGTTTTTGTCGTGGCTC 60.462 52.381 7.03 0.00 0.00 4.70
2216 2307 4.524318 ATCCGGCGGCGATCGTTT 62.524 61.111 34.49 7.39 41.72 3.60
2217 2308 4.944372 GATCCGGCGGCGATCGTT 62.944 66.667 34.49 11.26 41.72 3.85
2252 2343 2.026822 TCCATTCTTGTCCTTGCTCCTC 60.027 50.000 0.00 0.00 0.00 3.71
2318 2409 6.597562 TCCACAGTAAAACACCAGTAATCTT 58.402 36.000 0.00 0.00 0.00 2.40
2321 2412 9.528489 AATAATCCACAGTAAAACACCAGTAAT 57.472 29.630 0.00 0.00 0.00 1.89
2357 2448 3.161866 GTTGCTATCCCTTTCCCAAACA 58.838 45.455 0.00 0.00 0.00 2.83
2361 2452 0.988832 ACGTTGCTATCCCTTTCCCA 59.011 50.000 0.00 0.00 0.00 4.37
2365 2456 2.301870 TCTGTGACGTTGCTATCCCTTT 59.698 45.455 0.00 0.00 0.00 3.11
2367 2458 1.204941 GTCTGTGACGTTGCTATCCCT 59.795 52.381 0.00 0.00 0.00 4.20
2378 2469 3.448686 ACTTGTTCTTCTGTCTGTGACG 58.551 45.455 0.00 0.00 34.95 4.35
2393 2484 7.440856 CCACAATTATTAAAGCACCAACTTGTT 59.559 33.333 0.00 0.00 0.00 2.83
2394 2485 6.928492 CCACAATTATTAAAGCACCAACTTGT 59.072 34.615 0.00 0.00 0.00 3.16
2395 2486 6.928492 ACCACAATTATTAAAGCACCAACTTG 59.072 34.615 0.00 0.00 0.00 3.16
2441 2533 4.020573 AGCACATACACTTACACCAGCTAA 60.021 41.667 0.00 0.00 0.00 3.09
2498 2590 3.071457 ACCATCTCATCGTCATTGCCATA 59.929 43.478 0.00 0.00 0.00 2.74
2499 2591 2.158711 ACCATCTCATCGTCATTGCCAT 60.159 45.455 0.00 0.00 0.00 4.40
2500 2592 1.210234 ACCATCTCATCGTCATTGCCA 59.790 47.619 0.00 0.00 0.00 4.92
2502 2594 1.600957 CCACCATCTCATCGTCATTGC 59.399 52.381 0.00 0.00 0.00 3.56
2503 2595 2.610833 CACCACCATCTCATCGTCATTG 59.389 50.000 0.00 0.00 0.00 2.82
2588 2701 9.478768 TCGTACAACATCTTACTACAAATTTCA 57.521 29.630 0.00 0.00 0.00 2.69
2596 2709 8.906636 TTCAATCTCGTACAACATCTTACTAC 57.093 34.615 0.00 0.00 0.00 2.73
2597 2710 9.516314 CATTCAATCTCGTACAACATCTTACTA 57.484 33.333 0.00 0.00 0.00 1.82
2598 2711 8.251026 TCATTCAATCTCGTACAACATCTTACT 58.749 33.333 0.00 0.00 0.00 2.24
2602 2715 7.905604 TTTCATTCAATCTCGTACAACATCT 57.094 32.000 0.00 0.00 0.00 2.90
2650 2763 1.134175 ACGCCAACCAAAAGAACTGTG 59.866 47.619 0.00 0.00 0.00 3.66
2674 2787 6.033831 GCAATCAACAACACACATGCTTATAC 59.966 38.462 0.00 0.00 0.00 1.47
2688 2801 4.681025 ACATCACGAAATGCAATCAACAAC 59.319 37.500 0.00 0.00 0.00 3.32
2689 2802 4.869215 ACATCACGAAATGCAATCAACAA 58.131 34.783 0.00 0.00 0.00 2.83
2710 2823 5.282055 TCCCATGATCTCTCACACATAAC 57.718 43.478 0.00 0.00 33.22 1.89
2777 2890 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2778 2891 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2779 2892 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2786 2899 9.310716 GTGGTCTAAACGCTCTTATATTAGTTT 57.689 33.333 0.00 0.00 36.11 2.66
2787 2900 8.693625 AGTGGTCTAAACGCTCTTATATTAGTT 58.306 33.333 0.00 0.00 0.00 2.24
2788 2901 8.235359 AGTGGTCTAAACGCTCTTATATTAGT 57.765 34.615 0.00 0.00 0.00 2.24
2791 2904 9.530633 CTTTAGTGGTCTAAACGCTCTTATATT 57.469 33.333 0.00 0.00 40.05 1.28
2792 2905 8.693625 ACTTTAGTGGTCTAAACGCTCTTATAT 58.306 33.333 0.00 0.00 40.05 0.86
2793 2906 8.059798 ACTTTAGTGGTCTAAACGCTCTTATA 57.940 34.615 0.00 0.00 40.05 0.98
2794 2907 6.932947 ACTTTAGTGGTCTAAACGCTCTTAT 58.067 36.000 0.00 0.00 40.05 1.73
2795 2908 6.336842 ACTTTAGTGGTCTAAACGCTCTTA 57.663 37.500 0.00 0.00 40.05 2.10
2796 2909 5.211174 ACTTTAGTGGTCTAAACGCTCTT 57.789 39.130 0.00 0.00 40.05 2.85
2797 2910 4.868314 ACTTTAGTGGTCTAAACGCTCT 57.132 40.909 0.00 0.00 40.05 4.09
2798 2911 5.707931 ACTACTTTAGTGGTCTAAACGCTC 58.292 41.667 0.00 0.00 40.05 5.03
2799 2912 5.718724 ACTACTTTAGTGGTCTAAACGCT 57.281 39.130 0.00 0.00 40.05 5.07
2800 2913 6.098017 ATCACTACTTTAGTGGTCTAAACGC 58.902 40.000 12.33 0.00 46.78 4.84
2811 2924 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2812 2925 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2824 2937 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2825 2938 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2826 2939 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2827 2940 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2828 2941 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2829 2942 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2830 2943 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2831 2944 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2832 2945 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2833 2946 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2834 2947 8.233190 CGTACTCCCTCCGTAAACTAATATAAG 58.767 40.741 0.00 0.00 0.00 1.73
2835 2948 7.308589 GCGTACTCCCTCCGTAAACTAATATAA 60.309 40.741 0.00 0.00 0.00 0.98
2836 2949 6.149474 GCGTACTCCCTCCGTAAACTAATATA 59.851 42.308 0.00 0.00 0.00 0.86
2837 2950 5.048434 GCGTACTCCCTCCGTAAACTAATAT 60.048 44.000 0.00 0.00 0.00 1.28
2838 2951 4.275936 GCGTACTCCCTCCGTAAACTAATA 59.724 45.833 0.00 0.00 0.00 0.98
2839 2952 3.067320 GCGTACTCCCTCCGTAAACTAAT 59.933 47.826 0.00 0.00 0.00 1.73
2840 2953 2.423538 GCGTACTCCCTCCGTAAACTAA 59.576 50.000 0.00 0.00 0.00 2.24
2841 2954 2.017049 GCGTACTCCCTCCGTAAACTA 58.983 52.381 0.00 0.00 0.00 2.24
2842 2955 0.813821 GCGTACTCCCTCCGTAAACT 59.186 55.000 0.00 0.00 0.00 2.66
2843 2956 0.524180 CGCGTACTCCCTCCGTAAAC 60.524 60.000 0.00 0.00 0.00 2.01
2844 2957 1.802636 CGCGTACTCCCTCCGTAAA 59.197 57.895 0.00 0.00 0.00 2.01
2845 2958 2.764314 GCGCGTACTCCCTCCGTAA 61.764 63.158 8.43 0.00 0.00 3.18
2846 2959 2.310327 TAGCGCGTACTCCCTCCGTA 62.310 60.000 8.43 0.00 0.00 4.02
2847 2960 3.687321 TAGCGCGTACTCCCTCCGT 62.687 63.158 8.43 0.00 0.00 4.69
2848 2961 2.894565 CTAGCGCGTACTCCCTCCG 61.895 68.421 8.43 0.00 0.00 4.63
2849 2962 3.032339 CTAGCGCGTACTCCCTCC 58.968 66.667 8.43 0.00 0.00 4.30
2850 2963 2.332159 GCTAGCGCGTACTCCCTC 59.668 66.667 8.43 0.00 0.00 4.30
2851 2964 3.217743 GGCTAGCGCGTACTCCCT 61.218 66.667 8.43 0.00 36.88 4.20
2852 2965 4.281947 GGGCTAGCGCGTACTCCC 62.282 72.222 16.68 10.42 36.88 4.30
2853 2966 3.196913 GAGGGCTAGCGCGTACTCC 62.197 68.421 24.23 10.69 36.88 3.85
2854 2967 2.188161 AGAGGGCTAGCGCGTACTC 61.188 63.158 24.23 16.61 36.88 2.59
2855 2968 2.124236 AGAGGGCTAGCGCGTACT 60.124 61.111 24.23 20.50 36.88 2.73
2856 2969 2.026301 CAGAGGGCTAGCGCGTAC 59.974 66.667 24.23 18.85 36.88 3.67
2857 2970 2.124445 TCAGAGGGCTAGCGCGTA 60.124 61.111 24.23 9.74 36.88 4.42
2858 2971 3.522731 CTCAGAGGGCTAGCGCGT 61.523 66.667 24.23 14.12 36.88 6.01
2859 2972 4.940593 GCTCAGAGGGCTAGCGCG 62.941 72.222 24.23 11.88 36.88 6.86
2863 2976 4.613925 TTATGATTGCTCAGAGGGCTAG 57.386 45.455 0.00 0.00 34.12 3.42
2898 3011 2.419851 CCAGAGTTCAGGCTTGAGATCC 60.420 54.545 0.00 0.00 34.15 3.36
2913 3026 1.352352 CACAAATCAGGACCCCAGAGT 59.648 52.381 0.00 0.00 0.00 3.24
2914 3027 1.630369 TCACAAATCAGGACCCCAGAG 59.370 52.381 0.00 0.00 0.00 3.35
2915 3028 1.741028 TCACAAATCAGGACCCCAGA 58.259 50.000 0.00 0.00 0.00 3.86
2916 3029 2.814805 ATCACAAATCAGGACCCCAG 57.185 50.000 0.00 0.00 0.00 4.45
2917 3030 3.591527 AGTAATCACAAATCAGGACCCCA 59.408 43.478 0.00 0.00 0.00 4.96
2918 3031 4.236527 AGTAATCACAAATCAGGACCCC 57.763 45.455 0.00 0.00 0.00 4.95
2919 3032 4.142381 GCAAGTAATCACAAATCAGGACCC 60.142 45.833 0.00 0.00 0.00 4.46
2920 3033 4.702131 AGCAAGTAATCACAAATCAGGACC 59.298 41.667 0.00 0.00 0.00 4.46
2921 3034 5.886960 AGCAAGTAATCACAAATCAGGAC 57.113 39.130 0.00 0.00 0.00 3.85
2922 3035 5.335897 GCAAGCAAGTAATCACAAATCAGGA 60.336 40.000 0.00 0.00 0.00 3.86
2973 3106 7.392393 ACTCCGCCATAAGTTGTTTAATAAGTT 59.608 33.333 0.60 0.60 0.00 2.66
2974 3107 6.882678 ACTCCGCCATAAGTTGTTTAATAAGT 59.117 34.615 0.00 0.00 0.00 2.24
2995 3128 2.229792 TCTTTGTGCCACAATCACTCC 58.770 47.619 11.67 0.00 38.00 3.85
3004 3137 2.024414 AGACCACTTTCTTTGTGCCAC 58.976 47.619 0.00 0.00 34.38 5.01
3010 3143 5.175856 CACTACGAGAAGACCACTTTCTTTG 59.824 44.000 0.00 0.00 35.90 2.77
3028 3161 1.068264 TGCAGAGCAGAGTTCACTACG 60.068 52.381 0.00 0.00 33.32 3.51
3030 3163 2.827921 TGATGCAGAGCAGAGTTCACTA 59.172 45.455 0.00 0.00 43.65 2.74
3037 3170 2.640184 TGGAAATGATGCAGAGCAGAG 58.360 47.619 0.00 0.00 43.65 3.35
3038 3171 2.793288 TGGAAATGATGCAGAGCAGA 57.207 45.000 0.00 0.00 43.65 4.26
3039 3172 3.380320 TCAATGGAAATGATGCAGAGCAG 59.620 43.478 0.00 0.00 43.65 4.24
3040 3173 3.358118 TCAATGGAAATGATGCAGAGCA 58.642 40.909 0.00 0.00 44.86 4.26
3041 3174 4.585955 ATCAATGGAAATGATGCAGAGC 57.414 40.909 0.00 0.00 36.21 4.09
3042 3175 6.479001 GGAAAATCAATGGAAATGATGCAGAG 59.521 38.462 0.00 0.00 37.58 3.35
3067 3200 1.890174 GGGAATGCGGGGTCAAAAG 59.110 57.895 0.00 0.00 0.00 2.27
3113 3246 2.158667 TGACAAGAGGAAACAGGGGAAC 60.159 50.000 0.00 0.00 0.00 3.62
3121 3254 6.431234 ACCAGTTGATAATGACAAGAGGAAAC 59.569 38.462 0.00 0.00 0.00 2.78
3125 3258 5.491070 TGACCAGTTGATAATGACAAGAGG 58.509 41.667 0.00 0.00 0.00 3.69
3126 3259 6.402983 GCTTGACCAGTTGATAATGACAAGAG 60.403 42.308 0.00 0.00 35.13 2.85
3134 3267 7.397192 ACCAAAATAGCTTGACCAGTTGATAAT 59.603 33.333 0.00 0.00 0.00 1.28
3136 3269 6.245408 ACCAAAATAGCTTGACCAGTTGATA 58.755 36.000 0.00 0.00 0.00 2.15
3143 3276 3.745799 TCGAACCAAAATAGCTTGACCA 58.254 40.909 0.00 0.00 0.00 4.02
3153 3286 4.359706 GTGAAAGCTGTTCGAACCAAAAT 58.640 39.130 24.78 9.07 0.00 1.82


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

AutoCloner maintained by Alex Coulton.