Multiple sequence alignment - TraesCS7A01G115400

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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 TraesCS7A01G115400 chr7A 100.000 3033 0 0 1 3033 71668854 71671886 0.000000e+00 5602.0
1 TraesCS7A01G115400 chr7D 90.502 2769 108 58 1 2691 68418555 68415864 0.000000e+00 3513.0
2 TraesCS7A01G115400 chr7D 93.750 48 1 2 2987 3033 541421871 541421917 1.510000e-08 71.3
3 TraesCS7A01G115400 chr7B 90.786 1552 65 41 1 1521 9701480 9702984 0.000000e+00 2002.0
4 TraesCS7A01G115400 chr7B 91.990 1161 38 19 1546 2691 9703261 9704381 0.000000e+00 1578.0
5 TraesCS7A01G115400 chr7B 97.727 44 0 1 2836 2878 9705424 9705467 1.170000e-09 75.0
6 TraesCS7A01G115400 chr7B 97.727 44 0 1 2836 2878 9705472 9705515 1.170000e-09 75.0
7 TraesCS7A01G115400 chr7B 97.727 44 0 1 2836 2878 9705520 9705563 1.170000e-09 75.0
8 TraesCS7A01G115400 chr7B 97.727 44 0 1 2836 2878 9705568 9705611 1.170000e-09 75.0
9 TraesCS7A01G115400 chr7B 97.727 44 0 1 2836 2878 9705616 9705659 1.170000e-09 75.0
10 TraesCS7A01G115400 chr7B 97.727 44 0 1 2836 2878 9705664 9705707 1.170000e-09 75.0
11 TraesCS7A01G115400 chr7B 100.000 35 0 0 2836 2870 9705712 9705746 7.020000e-07 65.8
12 TraesCS7A01G115400 chr3D 85.047 214 32 0 1812 2025 107678834 107678621 5.090000e-53 219.0
13 TraesCS7A01G115400 chr3B 85.047 214 32 0 1812 2025 158716003 158715790 5.090000e-53 219.0
14 TraesCS7A01G115400 chr3A 84.332 217 34 0 1809 2025 124176269 124176485 2.370000e-51 213.0


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 TraesCS7A01G115400 chr7A 71668854 71671886 3032 False 5602.000000 5602 100.000000 1 3033 1 chr7A.!!$F1 3032
1 TraesCS7A01G115400 chr7D 68415864 68418555 2691 True 3513.000000 3513 90.502000 1 2691 1 chr7D.!!$R1 2690
2 TraesCS7A01G115400 chr7B 9701480 9705746 4266 False 455.088889 2002 96.570889 1 2878 9 chr7B.!!$F1 2877

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
984 1050 0.592148 GCCGGTCGATCTACACTAGG 59.408 60.0 1.9 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2930 4430 0.034186 TATCTGGGCCAGTTTGCAGG 60.034 55.0 31.6 6.1 32.61 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
114 124 1.134280 CAGGGACAGGTGGAGCATTAG 60.134 57.143 0.00 0.00 0.00 1.73
472 498 3.680786 CCCAGTCACCGTCTCGCA 61.681 66.667 0.00 0.00 0.00 5.10
570 596 1.438059 CGCAACGCAAACCTACACG 60.438 57.895 0.00 0.00 0.00 4.49
579 605 1.764571 AAACCTACACGCCAGCAGGA 61.765 55.000 0.00 0.00 36.89 3.86
580 606 2.172483 AACCTACACGCCAGCAGGAG 62.172 60.000 0.00 0.00 41.02 3.69
582 608 3.300934 CTACACGCCAGCAGGAGCA 62.301 63.158 0.00 0.00 45.49 4.26
734 770 2.217750 CACGTCCACAGAACCAATTCA 58.782 47.619 0.00 0.00 37.29 2.57
736 772 3.253188 CACGTCCACAGAACCAATTCAAT 59.747 43.478 0.00 0.00 37.29 2.57
741 777 6.173339 GTCCACAGAACCAATTCAATAGAGA 58.827 40.000 0.00 0.00 37.29 3.10
800 836 1.323271 CCAAGGAGTGCTAGAGCGGA 61.323 60.000 0.00 0.00 45.83 5.54
835 871 0.620030 TGGTCTGGACATGGACATGG 59.380 55.000 15.94 0.00 42.91 3.66
838 874 1.278985 GTCTGGACATGGACATGGACA 59.721 52.381 15.94 12.42 42.91 4.02
839 875 2.092753 GTCTGGACATGGACATGGACAT 60.093 50.000 15.94 0.00 42.91 3.06
842 878 1.212688 GGACATGGACATGGACATGGA 59.787 52.381 25.79 1.10 46.60 3.41
843 879 2.357050 GGACATGGACATGGACATGGAA 60.357 50.000 25.79 2.43 46.60 3.53
844 880 2.684881 GACATGGACATGGACATGGAAC 59.315 50.000 25.79 16.81 46.60 3.62
845 881 2.041485 ACATGGACATGGACATGGAACA 59.959 45.455 25.79 11.42 46.60 3.18
846 882 3.293337 CATGGACATGGACATGGAACAT 58.707 45.455 18.75 12.90 42.91 2.71
847 883 3.067601 CATGGACATGGACATGGAACATG 59.932 47.826 20.63 20.63 45.56 3.21
848 884 6.521891 CATGGACATGGACATGGAACATGC 62.522 50.000 21.44 14.45 44.32 4.06
935 971 3.997021 ACTTCCTCAATTCACAGCTTACG 59.003 43.478 0.00 0.00 0.00 3.18
939 975 3.932710 CCTCAATTCACAGCTTACGCTTA 59.067 43.478 0.00 0.00 46.47 3.09
953 1006 0.820871 CGCTTACTCTTGCTCCCTCT 59.179 55.000 0.00 0.00 0.00 3.69
954 1007 1.470632 CGCTTACTCTTGCTCCCTCTG 60.471 57.143 0.00 0.00 0.00 3.35
955 1008 1.742071 GCTTACTCTTGCTCCCTCTGC 60.742 57.143 0.00 0.00 0.00 4.26
963 1020 2.433994 GCTCCCTCTGCTGCTAGCT 61.434 63.158 17.23 0.00 42.97 3.32
978 1044 1.733360 CTAGCTAGCCGGTCGATCTAC 59.267 57.143 12.13 0.00 0.00 2.59
982 1048 2.763933 CTAGCCGGTCGATCTACACTA 58.236 52.381 1.90 0.00 0.00 2.74
983 1049 1.595466 AGCCGGTCGATCTACACTAG 58.405 55.000 1.90 0.00 0.00 2.57
984 1050 0.592148 GCCGGTCGATCTACACTAGG 59.408 60.000 1.90 0.00 0.00 3.02
998 1064 2.113777 ACACTAGGAAGAAGGAAGGGGA 59.886 50.000 0.00 0.00 0.00 4.81
1047 1113 2.197324 GTTGGCAGGGTTGTGGGA 59.803 61.111 0.00 0.00 0.00 4.37
1065 1131 2.113243 GAGACGTGCTGGACCCCTTT 62.113 60.000 0.00 0.00 0.00 3.11
1403 1471 1.273606 TGTGCTAGCTCTCTGGTGTTC 59.726 52.381 17.23 0.00 0.00 3.18
1460 1534 5.514204 GGAACATTGATTTTCGATGCTTCTG 59.486 40.000 4.92 0.00 41.03 3.02
1472 1550 4.275689 TCGATGCTTCTGTTGACATGTTTT 59.724 37.500 0.00 0.00 0.00 2.43
1481 1559 8.994429 TTCTGTTGACATGTTTTATGTTTGTT 57.006 26.923 0.00 0.00 31.52 2.83
1484 1562 8.404889 TGTTGACATGTTTTATGTTTGTTCTG 57.595 30.769 0.00 0.00 31.52 3.02
1531 1868 9.039870 AGCTCGATCTTAAATATATGCTTATGC 57.960 33.333 2.46 0.00 40.20 3.14
1587 1925 4.293648 TGCACGCGTGTACTGCCT 62.294 61.111 36.80 0.00 0.00 4.75
1690 2031 9.507329 TTGTAGCTCAGTTGAATAATTTCTCTT 57.493 29.630 0.00 0.00 32.78 2.85
1726 2073 2.477754 CACTAGCTCATGTGTGTGTGTG 59.522 50.000 0.00 0.00 0.00 3.82
1727 2074 2.103094 ACTAGCTCATGTGTGTGTGTGT 59.897 45.455 0.00 0.00 0.00 3.72
1728 2075 1.302366 AGCTCATGTGTGTGTGTGTG 58.698 50.000 0.00 0.00 0.00 3.82
1729 2076 1.016627 GCTCATGTGTGTGTGTGTGT 58.983 50.000 0.00 0.00 0.00 3.72
1730 2077 1.268184 GCTCATGTGTGTGTGTGTGTG 60.268 52.381 0.00 0.00 0.00 3.82
1731 2078 2.009051 CTCATGTGTGTGTGTGTGTGT 58.991 47.619 0.00 0.00 0.00 3.72
1732 2079 1.736681 TCATGTGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
1733 2080 0.451383 ATGTGTGTGTGTGTGTGTGC 59.549 50.000 0.00 0.00 0.00 4.57
1734 2081 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
1735 2082 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
1736 2083 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
1822 2169 1.133976 GGGCAGGAAGTGATGTGCTAT 60.134 52.381 0.00 0.00 36.15 2.97
1957 2304 1.215647 CGCCGAGCTCTACAACCTT 59.784 57.895 12.85 0.00 0.00 3.50
1966 2313 4.354162 TACAACCTTGGCCCGCCC 62.354 66.667 0.00 0.00 34.56 6.13
2033 2380 2.945668 GGCAGGAGGATGTACAATTGAC 59.054 50.000 13.59 6.76 0.00 3.18
2047 2394 0.923729 ATTGACCTACCCATGGCCCA 60.924 55.000 6.09 0.00 0.00 5.36
2207 2563 4.380841 TGATCGATGTAAAACTAGCCGT 57.619 40.909 0.54 0.00 0.00 5.68
2209 2565 5.276270 TGATCGATGTAAAACTAGCCGTAC 58.724 41.667 0.54 0.00 0.00 3.67
2249 2605 8.852135 TCAACGGCTAATTAATTAATTAAGGGG 58.148 33.333 24.08 16.39 37.60 4.79
2250 2606 7.770366 ACGGCTAATTAATTAATTAAGGGGG 57.230 36.000 24.08 16.12 37.60 5.40
2366 2726 1.155889 CACGCCATGTGCAACTTAGA 58.844 50.000 0.00 0.00 42.70 2.10
2394 2754 2.843730 TGGTACATATCTGCAGGTTGGT 59.156 45.455 15.13 11.00 0.00 3.67
2395 2755 3.118408 TGGTACATATCTGCAGGTTGGTC 60.118 47.826 15.13 5.78 0.00 4.02
2396 2756 3.134804 GGTACATATCTGCAGGTTGGTCT 59.865 47.826 15.13 0.00 0.00 3.85
2397 2757 4.384208 GGTACATATCTGCAGGTTGGTCTT 60.384 45.833 15.13 0.00 0.00 3.01
2398 2758 3.614092 ACATATCTGCAGGTTGGTCTTG 58.386 45.455 15.13 3.66 0.00 3.02
2399 2759 3.264193 ACATATCTGCAGGTTGGTCTTGA 59.736 43.478 15.13 0.00 0.00 3.02
2400 2760 2.191128 ATCTGCAGGTTGGTCTTGAC 57.809 50.000 15.13 0.00 0.00 3.18
2486 2846 5.705441 GGGAGACAAACATGTAATTGACAGA 59.295 40.000 15.51 0.00 42.79 3.41
2487 2847 6.375455 GGGAGACAAACATGTAATTGACAGAT 59.625 38.462 15.51 0.00 42.79 2.90
2575 2935 4.095483 GCCTTGTACAACTTCCTCATGATG 59.905 45.833 3.59 0.00 0.00 3.07
2659 3021 5.364778 ACAATATTAATGTCTGGTGCGCTA 58.635 37.500 9.73 0.00 0.00 4.26
2660 3022 5.466728 ACAATATTAATGTCTGGTGCGCTAG 59.533 40.000 9.73 3.91 0.00 3.42
2661 3023 1.651987 TTAATGTCTGGTGCGCTAGC 58.348 50.000 9.73 4.06 45.41 3.42
2662 3024 0.824109 TAATGTCTGGTGCGCTAGCT 59.176 50.000 13.93 0.00 45.42 3.32
2670 3032 1.303309 GGTGCGCTAGCTCATCAATT 58.697 50.000 13.07 0.00 45.42 2.32
2693 4069 9.890629 AATTTGTGTCTTATACTAGATGCTTCA 57.109 29.630 0.00 0.00 0.00 3.02
2694 4070 8.932945 TTTGTGTCTTATACTAGATGCTTCAG 57.067 34.615 0.00 0.75 0.00 3.02
2696 4072 6.322456 TGTGTCTTATACTAGATGCTTCAGCT 59.678 38.462 0.00 0.00 42.66 4.24
2702 4078 2.026449 ACTAGATGCTTCAGCTGCCTTT 60.026 45.455 9.47 0.00 42.66 3.11
2705 4081 2.126580 GCTTCAGCTGCCTTTGCG 60.127 61.111 9.47 0.00 41.78 4.85
2708 4084 2.504461 CTTCAGCTGCCTTTGCGTCG 62.504 60.000 9.47 0.00 41.78 5.12
2714 4090 2.301902 CTGCCTTTGCGTCGATCAGC 62.302 60.000 0.00 0.00 41.78 4.26
2720 4096 0.243636 TTGCGTCGATCAGCAGAAGA 59.756 50.000 11.79 0.00 44.72 2.87
2721 4097 0.456824 TGCGTCGATCAGCAGAAGAC 60.457 55.000 8.72 7.66 38.59 3.01
2722 4098 0.456824 GCGTCGATCAGCAGAAGACA 60.457 55.000 14.90 0.00 36.13 3.41
2723 4099 1.263776 CGTCGATCAGCAGAAGACAC 58.736 55.000 14.90 0.00 36.13 3.67
2724 4100 1.401539 CGTCGATCAGCAGAAGACACA 60.402 52.381 14.90 0.00 36.13 3.72
2727 4103 1.067283 CGATCAGCAGAAGACACACCT 60.067 52.381 0.00 0.00 0.00 4.00
2728 4104 2.611473 CGATCAGCAGAAGACACACCTT 60.611 50.000 0.00 0.00 0.00 3.50
2729 4105 3.406764 GATCAGCAGAAGACACACCTTT 58.593 45.455 0.00 0.00 0.00 3.11
2730 4106 3.281727 TCAGCAGAAGACACACCTTTT 57.718 42.857 0.00 0.00 0.00 2.27
2731 4107 3.620488 TCAGCAGAAGACACACCTTTTT 58.380 40.909 0.00 0.00 0.00 1.94
2755 4131 6.751514 TTTTTAGAAACAGCAGAAGACACA 57.248 33.333 0.00 0.00 0.00 3.72
2757 4133 2.565841 AGAAACAGCAGAAGACACACC 58.434 47.619 0.00 0.00 0.00 4.16
2759 4135 2.717639 AACAGCAGAAGACACACCTT 57.282 45.000 0.00 0.00 0.00 3.50
2760 4136 2.717639 ACAGCAGAAGACACACCTTT 57.282 45.000 0.00 0.00 0.00 3.11
2761 4137 3.004752 ACAGCAGAAGACACACCTTTT 57.995 42.857 0.00 0.00 0.00 2.27
2763 4139 3.129287 ACAGCAGAAGACACACCTTTTTG 59.871 43.478 0.00 0.00 0.00 2.44
2764 4140 3.129287 CAGCAGAAGACACACCTTTTTGT 59.871 43.478 0.00 0.00 0.00 2.83
2765 4141 3.763897 AGCAGAAGACACACCTTTTTGTT 59.236 39.130 0.00 0.00 0.00 2.83
2766 4142 4.220602 AGCAGAAGACACACCTTTTTGTTT 59.779 37.500 0.00 0.00 0.00 2.83
2767 4143 4.929211 GCAGAAGACACACCTTTTTGTTTT 59.071 37.500 0.00 0.00 0.00 2.43
2768 4144 5.408299 GCAGAAGACACACCTTTTTGTTTTT 59.592 36.000 0.00 0.00 0.00 1.94
2770 4146 6.644592 CAGAAGACACACCTTTTTGTTTTTGA 59.355 34.615 0.00 0.00 0.00 2.69
2771 4147 6.868339 AGAAGACACACCTTTTTGTTTTTGAG 59.132 34.615 0.00 0.00 0.00 3.02
2773 4149 5.925969 AGACACACCTTTTTGTTTTTGAGTG 59.074 36.000 0.00 0.00 0.00 3.51
2774 4150 5.848406 ACACACCTTTTTGTTTTTGAGTGA 58.152 33.333 0.00 0.00 0.00 3.41
2775 4151 6.284459 ACACACCTTTTTGTTTTTGAGTGAA 58.716 32.000 0.00 0.00 0.00 3.18
2776 4152 6.423604 ACACACCTTTTTGTTTTTGAGTGAAG 59.576 34.615 0.00 0.00 0.00 3.02
2780 4156 5.868801 CCTTTTTGTTTTTGAGTGAAGCAGA 59.131 36.000 0.00 0.00 0.00 4.26
2782 4158 6.949578 TTTTGTTTTTGAGTGAAGCAGAAG 57.050 33.333 0.00 0.00 0.00 2.85
2783 4159 5.895636 TTGTTTTTGAGTGAAGCAGAAGA 57.104 34.783 0.00 0.00 0.00 2.87
2784 4160 5.895636 TGTTTTTGAGTGAAGCAGAAGAA 57.104 34.783 0.00 0.00 0.00 2.52
2785 4161 5.883661 TGTTTTTGAGTGAAGCAGAAGAAG 58.116 37.500 0.00 0.00 0.00 2.85
2786 4162 5.647658 TGTTTTTGAGTGAAGCAGAAGAAGA 59.352 36.000 0.00 0.00 0.00 2.87
2789 4165 3.722147 TGAGTGAAGCAGAAGAAGACAC 58.278 45.455 0.00 0.00 0.00 3.67
2791 4167 3.462021 AGTGAAGCAGAAGAAGACACAC 58.538 45.455 0.00 0.00 0.00 3.82
2793 4169 2.435805 TGAAGCAGAAGAAGACACACCT 59.564 45.455 0.00 0.00 0.00 4.00
2795 4171 4.100963 TGAAGCAGAAGAAGACACACCTAA 59.899 41.667 0.00 0.00 0.00 2.69
2796 4172 4.689612 AGCAGAAGAAGACACACCTAAA 57.310 40.909 0.00 0.00 0.00 1.85
2797 4173 4.381411 AGCAGAAGAAGACACACCTAAAC 58.619 43.478 0.00 0.00 0.00 2.01
2798 4174 4.127171 GCAGAAGAAGACACACCTAAACA 58.873 43.478 0.00 0.00 0.00 2.83
2799 4175 4.757149 GCAGAAGAAGACACACCTAAACAT 59.243 41.667 0.00 0.00 0.00 2.71
2800 4176 5.932303 GCAGAAGAAGACACACCTAAACATA 59.068 40.000 0.00 0.00 0.00 2.29
2802 4178 7.413438 GCAGAAGAAGACACACCTAAACATATG 60.413 40.741 0.00 0.00 0.00 1.78
2804 4180 8.157476 AGAAGAAGACACACCTAAACATATGTT 58.843 33.333 15.47 15.47 40.50 2.71
2806 4182 9.787435 AAGAAGACACACCTAAACATATGTTTA 57.213 29.630 29.95 29.95 45.47 2.01
2830 4206 6.180472 AGGTGTTCCTAAACATATGTTCCAG 58.820 40.000 21.02 18.86 46.58 3.86
2831 4207 5.944007 GGTGTTCCTAAACATATGTTCCAGT 59.056 40.000 21.02 8.50 46.58 4.00
2832 4208 7.037873 AGGTGTTCCTAAACATATGTTCCAGTA 60.038 37.037 21.02 9.18 46.58 2.74
2833 4209 7.608761 GGTGTTCCTAAACATATGTTCCAGTAA 59.391 37.037 21.02 11.60 46.58 2.24
2879 4379 1.952296 GCCATGGGCTTCTCATACTTG 59.048 52.381 15.13 0.00 46.69 3.16
2880 4380 1.952296 CCATGGGCTTCTCATACTTGC 59.048 52.381 2.85 0.00 0.00 4.01
2881 4381 1.600957 CATGGGCTTCTCATACTTGCG 59.399 52.381 0.00 0.00 0.00 4.85
2882 4382 0.107703 TGGGCTTCTCATACTTGCGG 60.108 55.000 0.00 0.00 0.00 5.69
2883 4383 1.440145 GGGCTTCTCATACTTGCGGC 61.440 60.000 0.00 0.00 0.00 6.53
2884 4384 1.440145 GGCTTCTCATACTTGCGGCC 61.440 60.000 0.00 0.00 0.00 6.13
2885 4385 0.462759 GCTTCTCATACTTGCGGCCT 60.463 55.000 0.00 0.00 0.00 5.19
2886 4386 1.293924 CTTCTCATACTTGCGGCCTG 58.706 55.000 0.00 0.00 0.00 4.85
2887 4387 0.901827 TTCTCATACTTGCGGCCTGA 59.098 50.000 0.00 0.00 0.00 3.86
2888 4388 0.175760 TCTCATACTTGCGGCCTGAC 59.824 55.000 0.00 0.00 0.00 3.51
2889 4389 1.148157 CTCATACTTGCGGCCTGACG 61.148 60.000 0.00 0.00 0.00 4.35
2890 4390 2.173669 CATACTTGCGGCCTGACGG 61.174 63.158 0.00 0.00 0.00 4.79
2901 4401 2.350458 CCTGACGGGCCCCAAATTG 61.350 63.158 18.66 2.75 0.00 2.32
2902 4402 2.283532 TGACGGGCCCCAAATTGG 60.284 61.111 18.66 4.74 37.25 3.16
2903 4403 2.036572 GACGGGCCCCAAATTGGA 59.963 61.111 18.66 0.00 40.96 3.53
2904 4404 2.283604 ACGGGCCCCAAATTGGAC 60.284 61.111 18.66 5.00 40.96 4.02
2905 4405 3.448340 CGGGCCCCAAATTGGACG 61.448 66.667 18.66 8.59 40.96 4.79
2906 4406 2.283604 GGGCCCCAAATTGGACGT 60.284 61.111 12.23 0.00 40.96 4.34
2908 4408 1.605165 GGCCCCAAATTGGACGTGA 60.605 57.895 14.62 0.00 40.96 4.35
2909 4409 1.182385 GGCCCCAAATTGGACGTGAA 61.182 55.000 14.62 0.00 40.96 3.18
2910 4410 0.038618 GCCCCAAATTGGACGTGAAC 60.039 55.000 14.62 0.00 40.96 3.18
2912 4412 2.785562 CCCCAAATTGGACGTGAACTA 58.214 47.619 14.62 0.00 40.96 2.24
2913 4413 2.486592 CCCCAAATTGGACGTGAACTAC 59.513 50.000 14.62 0.00 40.96 2.73
2922 4422 3.901225 CGTGAACTACGCTGAAACG 57.099 52.632 0.00 0.00 46.92 3.60
2923 4423 1.126079 CGTGAACTACGCTGAAACGT 58.874 50.000 0.00 0.00 46.92 3.99
2929 4429 3.713963 ACGCTGAAACGTGGTCAC 58.286 55.556 0.00 0.00 46.28 3.67
2930 4430 1.885850 ACGCTGAAACGTGGTCACC 60.886 57.895 0.00 0.00 46.28 4.02
2931 4431 2.604174 CGCTGAAACGTGGTCACCC 61.604 63.158 0.00 0.00 0.00 4.61
2932 4432 1.227853 GCTGAAACGTGGTCACCCT 60.228 57.895 0.00 0.00 0.00 4.34
2933 4433 1.507141 GCTGAAACGTGGTCACCCTG 61.507 60.000 0.00 0.00 0.00 4.45
2934 4434 1.507141 CTGAAACGTGGTCACCCTGC 61.507 60.000 0.00 0.00 0.00 4.85
2935 4435 1.525077 GAAACGTGGTCACCCTGCA 60.525 57.895 0.00 0.00 0.00 4.41
2936 4436 1.077357 AAACGTGGTCACCCTGCAA 60.077 52.632 0.00 0.00 0.00 4.08
2937 4437 0.681564 AAACGTGGTCACCCTGCAAA 60.682 50.000 0.00 0.00 0.00 3.68
2938 4438 1.381165 AACGTGGTCACCCTGCAAAC 61.381 55.000 0.00 0.00 0.00 2.93
2939 4439 1.525995 CGTGGTCACCCTGCAAACT 60.526 57.895 0.00 0.00 0.00 2.66
2940 4440 1.785041 CGTGGTCACCCTGCAAACTG 61.785 60.000 0.00 0.00 0.00 3.16
2941 4441 1.152777 TGGTCACCCTGCAAACTGG 60.153 57.895 0.00 0.00 34.74 4.00
2942 4442 2.564721 GGTCACCCTGCAAACTGGC 61.565 63.158 0.00 0.00 33.65 4.85
2943 4443 2.203480 TCACCCTGCAAACTGGCC 60.203 61.111 0.00 0.00 33.65 5.36
2944 4444 3.305516 CACCCTGCAAACTGGCCC 61.306 66.667 0.00 0.00 33.65 5.80
2945 4445 3.831637 ACCCTGCAAACTGGCCCA 61.832 61.111 0.00 0.00 33.65 5.36
2946 4446 2.993264 CCCTGCAAACTGGCCCAG 60.993 66.667 9.83 9.83 37.52 4.45
2947 4447 2.115910 CCTGCAAACTGGCCCAGA 59.884 61.111 19.90 0.00 35.18 3.86
2948 4448 1.304713 CCTGCAAACTGGCCCAGAT 60.305 57.895 19.90 1.48 35.18 2.90
2949 4449 0.034186 CCTGCAAACTGGCCCAGATA 60.034 55.000 19.90 0.00 35.18 1.98
2950 4450 1.386533 CTGCAAACTGGCCCAGATAG 58.613 55.000 19.90 7.22 35.18 2.08
2951 4451 0.698238 TGCAAACTGGCCCAGATAGT 59.302 50.000 19.90 0.00 35.18 2.12
2952 4452 1.098050 GCAAACTGGCCCAGATAGTG 58.902 55.000 19.90 10.22 35.18 2.74
2964 4464 3.520290 CAGATAGTGGAACGGCTAACA 57.480 47.619 0.00 0.00 45.86 2.41
2965 4465 3.857052 CAGATAGTGGAACGGCTAACAA 58.143 45.455 0.00 0.00 45.86 2.83
2966 4466 4.250464 CAGATAGTGGAACGGCTAACAAA 58.750 43.478 0.00 0.00 45.86 2.83
2967 4467 4.330074 CAGATAGTGGAACGGCTAACAAAG 59.670 45.833 0.00 0.00 45.86 2.77
2968 4468 2.632987 AGTGGAACGGCTAACAAAGT 57.367 45.000 0.00 0.00 45.86 2.66
2969 4469 2.927028 AGTGGAACGGCTAACAAAGTT 58.073 42.857 0.00 0.00 45.86 2.66
2970 4470 2.616842 AGTGGAACGGCTAACAAAGTTG 59.383 45.455 0.00 0.00 45.86 3.16
2971 4471 1.950909 TGGAACGGCTAACAAAGTTGG 59.049 47.619 0.00 0.00 0.00 3.77
2972 4472 1.268625 GGAACGGCTAACAAAGTTGGG 59.731 52.381 0.00 0.00 0.00 4.12
2973 4473 0.671796 AACGGCTAACAAAGTTGGGC 59.328 50.000 9.25 9.25 0.00 5.36
2974 4474 1.176619 ACGGCTAACAAAGTTGGGCC 61.177 55.000 12.73 13.62 38.28 5.80
2975 4475 1.584495 GGCTAACAAAGTTGGGCCG 59.416 57.895 8.30 0.00 34.65 6.13
2976 4476 1.584495 GCTAACAAAGTTGGGCCGG 59.416 57.895 0.00 0.00 0.00 6.13
2977 4477 1.584495 CTAACAAAGTTGGGCCGGC 59.416 57.895 21.18 21.18 0.00 6.13
2978 4478 1.873270 CTAACAAAGTTGGGCCGGCC 61.873 60.000 38.57 38.57 0.00 6.13
3004 4504 3.719214 GGCACCCTATTTCTCGCG 58.281 61.111 0.00 0.00 0.00 5.87
3005 4505 1.153429 GGCACCCTATTTCTCGCGT 60.153 57.895 5.77 0.00 0.00 6.01
3006 4506 0.743345 GGCACCCTATTTCTCGCGTT 60.743 55.000 5.77 0.00 0.00 4.84
3007 4507 0.651031 GCACCCTATTTCTCGCGTTC 59.349 55.000 5.77 0.00 0.00 3.95
3008 4508 2.004583 CACCCTATTTCTCGCGTTCA 57.995 50.000 5.77 0.00 0.00 3.18
3009 4509 2.343101 CACCCTATTTCTCGCGTTCAA 58.657 47.619 5.77 0.00 0.00 2.69
3010 4510 2.093783 CACCCTATTTCTCGCGTTCAAC 59.906 50.000 5.77 0.00 0.00 3.18
3011 4511 1.323534 CCCTATTTCTCGCGTTCAACG 59.676 52.381 5.28 5.28 45.88 4.10
3012 4512 2.256174 CCTATTTCTCGCGTTCAACGA 58.744 47.619 15.79 0.00 46.05 3.85
3017 4517 2.633099 TCGCGTTCAACGAGACGA 59.367 55.556 15.79 10.69 44.93 4.20
3018 4518 1.439858 TCGCGTTCAACGAGACGAG 60.440 57.895 15.79 3.09 44.93 4.18
3019 4519 1.439858 CGCGTTCAACGAGACGAGA 60.440 57.895 15.79 0.00 46.05 4.04
3020 4520 1.389204 CGCGTTCAACGAGACGAGAG 61.389 60.000 15.79 0.00 46.05 3.20
3021 4521 1.066114 GCGTTCAACGAGACGAGAGG 61.066 60.000 15.79 0.00 46.05 3.69
3022 4522 0.516001 CGTTCAACGAGACGAGAGGA 59.484 55.000 3.01 0.00 46.05 3.71
3023 4523 1.130749 CGTTCAACGAGACGAGAGGAT 59.869 52.381 3.01 0.00 46.05 3.24
3024 4524 2.520979 GTTCAACGAGACGAGAGGATG 58.479 52.381 0.00 0.00 0.00 3.51
3025 4525 0.452184 TCAACGAGACGAGAGGATGC 59.548 55.000 0.00 0.00 0.00 3.91
3026 4526 0.863538 CAACGAGACGAGAGGATGCG 60.864 60.000 0.00 0.00 0.00 4.73
3027 4527 2.352915 CGAGACGAGAGGATGCGC 60.353 66.667 0.00 0.00 0.00 6.09
3028 4528 2.829206 CGAGACGAGAGGATGCGCT 61.829 63.158 9.73 0.00 0.00 5.92
3029 4529 1.008995 GAGACGAGAGGATGCGCTC 60.009 63.158 9.73 7.93 0.00 5.03
3032 4532 4.263209 CGAGAGGATGCGCTCGCT 62.263 66.667 25.27 5.40 45.97 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.487762 CCCTTTGAGCGCATCTTTTACA 59.512 45.455 11.47 0.00 0.00 2.41
374 400 4.699522 AGGTGTCGAAAGCCCGCC 62.700 66.667 0.00 0.00 34.04 6.13
375 401 2.668550 AAGGTGTCGAAAGCCCGC 60.669 61.111 0.00 0.00 0.00 6.13
472 498 4.455606 GGAATGTCTGCCAATTAGCTAGT 58.544 43.478 0.00 0.00 0.00 2.57
551 577 1.823260 CGTGTAGGTTTGCGTTGCGA 61.823 55.000 0.00 0.00 0.00 5.10
597 623 4.737649 GCAAATTAATGGTGGCTTCTAGGC 60.738 45.833 0.00 0.00 41.77 3.93
598 624 4.498009 CGCAAATTAATGGTGGCTTCTAGG 60.498 45.833 0.00 0.00 0.00 3.02
599 625 4.096382 ACGCAAATTAATGGTGGCTTCTAG 59.904 41.667 0.00 0.00 0.00 2.43
600 626 4.013728 ACGCAAATTAATGGTGGCTTCTA 58.986 39.130 0.00 0.00 0.00 2.10
605 631 1.639280 CCACGCAAATTAATGGTGGC 58.361 50.000 12.48 3.99 41.37 5.01
711 747 1.121378 TTGGTTCTGTGGACGTGGTA 58.879 50.000 0.00 0.00 0.00 3.25
734 770 2.623878 TCTCGTCGCCTCTCTCTATT 57.376 50.000 0.00 0.00 0.00 1.73
736 772 2.485903 GAATCTCGTCGCCTCTCTCTA 58.514 52.381 0.00 0.00 0.00 2.43
741 777 1.749638 ACGGAATCTCGTCGCCTCT 60.750 57.895 0.00 0.00 39.34 3.69
790 826 2.027460 GCTGCTCTCCGCTCTAGC 59.973 66.667 0.00 0.00 40.11 3.42
835 871 0.682209 AGCCTGGCATGTTCCATGTC 60.682 55.000 22.65 1.96 35.22 3.06
838 874 0.395311 CTCAGCCTGGCATGTTCCAT 60.395 55.000 22.65 0.00 35.22 3.41
839 875 1.001764 CTCAGCCTGGCATGTTCCA 60.002 57.895 22.65 0.00 34.42 3.53
840 876 2.413142 GCTCAGCCTGGCATGTTCC 61.413 63.158 22.65 0.00 0.00 3.62
842 878 0.541296 AAAGCTCAGCCTGGCATGTT 60.541 50.000 22.65 5.30 0.00 2.71
843 879 0.541296 AAAAGCTCAGCCTGGCATGT 60.541 50.000 22.65 0.00 0.00 3.21
844 880 0.172803 GAAAAGCTCAGCCTGGCATG 59.827 55.000 22.65 15.67 0.00 4.06
845 881 1.310933 CGAAAAGCTCAGCCTGGCAT 61.311 55.000 22.65 2.87 0.00 4.40
846 882 1.968017 CGAAAAGCTCAGCCTGGCA 60.968 57.895 22.65 0.00 0.00 4.92
847 883 2.694760 CCGAAAAGCTCAGCCTGGC 61.695 63.158 11.65 11.65 0.00 4.85
848 884 2.694760 GCCGAAAAGCTCAGCCTGG 61.695 63.158 0.00 0.00 0.00 4.45
849 885 2.694760 GGCCGAAAAGCTCAGCCTG 61.695 63.158 0.00 0.00 43.46 4.85
850 886 2.360475 GGCCGAAAAGCTCAGCCT 60.360 61.111 0.00 0.00 43.46 4.58
851 887 2.536997 TAGGGCCGAAAAGCTCAGCC 62.537 60.000 0.00 0.00 45.75 4.85
852 888 0.464554 ATAGGGCCGAAAAGCTCAGC 60.465 55.000 0.00 0.00 34.85 4.26
935 971 1.742071 GCAGAGGGAGCAAGAGTAAGC 60.742 57.143 0.00 0.00 0.00 3.09
937 973 1.552337 CAGCAGAGGGAGCAAGAGTAA 59.448 52.381 0.00 0.00 0.00 2.24
939 975 1.981636 CAGCAGAGGGAGCAAGAGT 59.018 57.895 0.00 0.00 0.00 3.24
963 1020 2.549563 CCTAGTGTAGATCGACCGGCTA 60.550 54.545 0.00 0.00 0.00 3.93
978 1044 2.834113 TCCCCTTCCTTCTTCCTAGTG 58.166 52.381 0.00 0.00 0.00 2.74
982 1048 2.313041 CCATTTCCCCTTCCTTCTTCCT 59.687 50.000 0.00 0.00 0.00 3.36
983 1049 2.739943 CCATTTCCCCTTCCTTCTTCC 58.260 52.381 0.00 0.00 0.00 3.46
984 1050 2.103373 GCCATTTCCCCTTCCTTCTTC 58.897 52.381 0.00 0.00 0.00 2.87
998 1064 2.938798 TGTCCCTCCCGGCCATTT 60.939 61.111 2.24 0.00 0.00 2.32
1047 1113 2.147387 AAAGGGGTCCAGCACGTCT 61.147 57.895 0.00 0.00 0.00 4.18
1065 1131 2.446994 AGGTTGGTGGTCCGGACA 60.447 61.111 34.40 18.59 36.30 4.02
1235 1301 3.681897 CGAGCACTTTCAGAGCTTAACAT 59.318 43.478 0.00 0.00 42.16 2.71
1236 1302 3.059884 CGAGCACTTTCAGAGCTTAACA 58.940 45.455 0.00 0.00 42.16 2.41
1240 1306 0.952984 GGCGAGCACTTTCAGAGCTT 60.953 55.000 0.00 0.00 42.16 3.74
1430 1499 4.013728 TCGAAAATCAATGTTCCCCGAAT 58.986 39.130 0.00 0.00 0.00 3.34
1460 1534 7.516627 GCCAGAACAAACATAAAACATGTCAAC 60.517 37.037 0.00 0.00 0.00 3.18
1472 1550 2.954989 TGTGCTTGCCAGAACAAACATA 59.045 40.909 0.00 0.00 35.36 2.29
1481 1559 0.391228 TTAGTCGTGTGCTTGCCAGA 59.609 50.000 0.00 0.00 0.00 3.86
1484 1562 4.403453 CTTTAATTAGTCGTGTGCTTGCC 58.597 43.478 0.00 0.00 0.00 4.52
1548 1886 7.116090 GTGCACATCATGATCAATACTAGAGAC 59.884 40.741 13.17 0.00 0.00 3.36
1587 1925 0.546507 TGGGTCTACCATCACCTGCA 60.547 55.000 0.81 0.00 46.80 4.41
1669 2010 7.121907 AGGGAAAGAGAAATTATTCAACTGAGC 59.878 37.037 0.00 0.00 38.06 4.26
1690 2031 6.849151 TGAGCTAGTGTGTATATCTAGGGAA 58.151 40.000 0.00 0.00 33.81 3.97
1732 2079 4.559386 GTAGATGCACACGCGCGC 62.559 66.667 32.58 23.91 42.97 6.86
1733 2080 2.516589 ATGTAGATGCACACGCGCG 61.517 57.895 30.96 30.96 42.97 6.86
1734 2081 1.011904 CATGTAGATGCACACGCGC 60.012 57.895 5.73 0.00 42.97 6.86
1735 2082 0.025384 CACATGTAGATGCACACGCG 59.975 55.000 3.53 3.53 42.97 6.01
1736 2083 1.078709 ACACATGTAGATGCACACGC 58.921 50.000 0.00 0.00 39.24 5.34
1737 2084 2.068519 ACACACATGTAGATGCACACG 58.931 47.619 0.00 0.00 37.26 4.49
1738 2085 2.413239 GCACACACATGTAGATGCACAC 60.413 50.000 17.82 0.00 36.72 3.82
1739 2086 1.805943 GCACACACATGTAGATGCACA 59.194 47.619 17.82 0.00 36.72 4.57
1740 2087 1.805943 TGCACACACATGTAGATGCAC 59.194 47.619 20.27 7.53 36.72 4.57
1741 2088 2.078392 CTGCACACACATGTAGATGCA 58.922 47.619 21.85 21.85 36.72 3.96
1742 2089 1.399440 CCTGCACACACATGTAGATGC 59.601 52.381 16.52 16.52 36.72 3.91
1743 2090 1.399440 GCCTGCACACACATGTAGATG 59.601 52.381 0.00 0.00 36.72 2.90
1744 2091 1.280133 AGCCTGCACACACATGTAGAT 59.720 47.619 0.00 0.00 36.72 1.98
1745 2092 0.686789 AGCCTGCACACACATGTAGA 59.313 50.000 0.00 0.00 36.72 2.59
1795 2142 1.738099 CACTTCCTGCCCGAACGAG 60.738 63.158 0.00 0.00 0.00 4.18
1822 2169 2.750637 GTCGGACGAGGGCTCTCA 60.751 66.667 15.40 0.00 39.95 3.27
2011 2358 2.575735 TCAATTGTACATCCTCCTGCCA 59.424 45.455 5.13 0.00 0.00 4.92
2033 2380 2.067605 TACGTGGGCCATGGGTAGG 61.068 63.158 28.48 4.06 0.00 3.18
2056 2403 0.319813 AATTTGCTGACTTTGCGGGC 60.320 50.000 0.00 0.00 0.00 6.13
2062 2413 5.460646 CACGTTGGATAATTTGCTGACTTT 58.539 37.500 0.00 0.00 0.00 2.66
2197 2553 3.924686 GCATATATGCGTACGGCTAGTTT 59.075 43.478 21.33 0.00 44.67 2.66
2250 2606 3.073650 AGCCATTGATCTAGGGTTCATCC 59.926 47.826 9.54 0.00 0.00 3.51
2251 2607 4.363991 AGCCATTGATCTAGGGTTCATC 57.636 45.455 9.54 0.00 0.00 2.92
2252 2608 4.467769 CAAGCCATTGATCTAGGGTTCAT 58.532 43.478 9.54 0.00 40.84 2.57
2366 2726 3.576118 CTGCAGATATGTACCAGGTAGCT 59.424 47.826 8.42 0.00 0.00 3.32
2394 2754 4.471904 AGTGAACACACAAGAGTCAAGA 57.528 40.909 7.68 0.00 37.04 3.02
2395 2755 6.653183 CATAAGTGAACACACAAGAGTCAAG 58.347 40.000 7.68 0.00 37.04 3.02
2396 2756 5.007626 GCATAAGTGAACACACAAGAGTCAA 59.992 40.000 7.68 0.00 37.04 3.18
2397 2757 4.511454 GCATAAGTGAACACACAAGAGTCA 59.489 41.667 7.68 0.00 37.04 3.41
2398 2758 4.376413 CGCATAAGTGAACACACAAGAGTC 60.376 45.833 7.68 0.00 37.04 3.36
2399 2759 3.494626 CGCATAAGTGAACACACAAGAGT 59.505 43.478 7.68 0.00 37.04 3.24
2400 2760 3.494626 ACGCATAAGTGAACACACAAGAG 59.505 43.478 7.68 0.12 37.04 2.85
2486 2846 5.667539 ATCACTGTGTCTTGTAGCAGTAT 57.332 39.130 7.79 0.00 39.82 2.12
2487 2847 6.152831 ACATATCACTGTGTCTTGTAGCAGTA 59.847 38.462 7.79 0.00 39.82 2.74
2553 2913 5.491070 TCATCATGAGGAAGTTGTACAAGG 58.509 41.667 8.98 0.00 0.00 3.61
2575 2935 7.934457 ACTTGACACTTGATTATATTGCCATC 58.066 34.615 0.00 0.00 0.00 3.51
2659 3021 9.539825 CTAGTATAAGACACAAATTGATGAGCT 57.460 33.333 0.00 0.00 0.00 4.09
2660 3022 9.534565 TCTAGTATAAGACACAAATTGATGAGC 57.465 33.333 0.00 0.00 0.00 4.26
2670 3032 6.980978 GCTGAAGCATCTAGTATAAGACACAA 59.019 38.462 0.00 0.00 41.59 3.33
2693 4069 2.046892 ATCGACGCAAAGGCAGCT 60.047 55.556 0.00 0.00 41.24 4.24
2694 4070 2.301902 CTGATCGACGCAAAGGCAGC 62.302 60.000 0.00 0.00 41.24 5.25
2696 4072 2.390599 GCTGATCGACGCAAAGGCA 61.391 57.895 0.00 0.00 41.24 4.75
2702 4078 0.456824 GTCTTCTGCTGATCGACGCA 60.457 55.000 5.85 5.85 34.54 5.24
2705 4081 1.989165 GTGTGTCTTCTGCTGATCGAC 59.011 52.381 13.26 13.26 0.00 4.20
2708 4084 2.758736 AGGTGTGTCTTCTGCTGATC 57.241 50.000 0.00 0.00 0.00 2.92
2732 4108 6.404293 GGTGTGTCTTCTGCTGTTTCTAAAAA 60.404 38.462 0.00 0.00 0.00 1.94
2733 4109 5.065988 GGTGTGTCTTCTGCTGTTTCTAAAA 59.934 40.000 0.00 0.00 0.00 1.52
2735 4111 4.127171 GGTGTGTCTTCTGCTGTTTCTAA 58.873 43.478 0.00 0.00 0.00 2.10
2737 4113 2.171448 AGGTGTGTCTTCTGCTGTTTCT 59.829 45.455 0.00 0.00 0.00 2.52
2738 4114 2.565841 AGGTGTGTCTTCTGCTGTTTC 58.434 47.619 0.00 0.00 0.00 2.78
2739 4115 2.717639 AGGTGTGTCTTCTGCTGTTT 57.282 45.000 0.00 0.00 0.00 2.83
2741 4117 2.717639 AAAGGTGTGTCTTCTGCTGT 57.282 45.000 0.00 0.00 0.00 4.40
2742 4118 3.129287 ACAAAAAGGTGTGTCTTCTGCTG 59.871 43.478 0.00 0.00 0.00 4.41
2743 4119 3.356290 ACAAAAAGGTGTGTCTTCTGCT 58.644 40.909 0.00 0.00 0.00 4.24
2744 4120 3.782889 ACAAAAAGGTGTGTCTTCTGC 57.217 42.857 0.00 0.00 0.00 4.26
2747 4123 6.645003 ACTCAAAAACAAAAAGGTGTGTCTTC 59.355 34.615 0.00 0.00 0.00 2.87
2748 4124 6.423604 CACTCAAAAACAAAAAGGTGTGTCTT 59.576 34.615 0.00 0.00 0.00 3.01
2749 4125 5.925969 CACTCAAAAACAAAAAGGTGTGTCT 59.074 36.000 0.00 0.00 0.00 3.41
2751 4127 5.848406 TCACTCAAAAACAAAAAGGTGTGT 58.152 33.333 0.00 0.00 0.00 3.72
2752 4128 6.618379 GCTTCACTCAAAAACAAAAAGGTGTG 60.618 38.462 0.00 0.00 0.00 3.82
2753 4129 5.408299 GCTTCACTCAAAAACAAAAAGGTGT 59.592 36.000 0.00 0.00 0.00 4.16
2755 4131 5.546526 TGCTTCACTCAAAAACAAAAAGGT 58.453 33.333 0.00 0.00 0.00 3.50
2757 4133 6.949578 TCTGCTTCACTCAAAAACAAAAAG 57.050 33.333 0.00 0.00 0.00 2.27
2759 4135 6.686630 TCTTCTGCTTCACTCAAAAACAAAA 58.313 32.000 0.00 0.00 0.00 2.44
2760 4136 6.266168 TCTTCTGCTTCACTCAAAAACAAA 57.734 33.333 0.00 0.00 0.00 2.83
2761 4137 5.895636 TCTTCTGCTTCACTCAAAAACAA 57.104 34.783 0.00 0.00 0.00 2.83
2763 4139 5.968261 GTCTTCTTCTGCTTCACTCAAAAAC 59.032 40.000 0.00 0.00 0.00 2.43
2764 4140 5.647658 TGTCTTCTTCTGCTTCACTCAAAAA 59.352 36.000 0.00 0.00 0.00 1.94
2765 4141 5.065218 GTGTCTTCTTCTGCTTCACTCAAAA 59.935 40.000 0.00 0.00 0.00 2.44
2766 4142 4.572389 GTGTCTTCTTCTGCTTCACTCAAA 59.428 41.667 0.00 0.00 0.00 2.69
2767 4143 4.122776 GTGTCTTCTTCTGCTTCACTCAA 58.877 43.478 0.00 0.00 0.00 3.02
2768 4144 3.132824 TGTGTCTTCTTCTGCTTCACTCA 59.867 43.478 0.00 0.00 0.00 3.41
2770 4146 3.462021 GTGTGTCTTCTTCTGCTTCACT 58.538 45.455 0.00 0.00 0.00 3.41
2771 4147 2.545946 GGTGTGTCTTCTTCTGCTTCAC 59.454 50.000 0.00 0.00 0.00 3.18
2773 4149 3.118905 AGGTGTGTCTTCTTCTGCTTC 57.881 47.619 0.00 0.00 0.00 3.86
2774 4150 4.689612 TTAGGTGTGTCTTCTTCTGCTT 57.310 40.909 0.00 0.00 0.00 3.91
2775 4151 4.141711 TGTTTAGGTGTGTCTTCTTCTGCT 60.142 41.667 0.00 0.00 0.00 4.24
2776 4152 4.127171 TGTTTAGGTGTGTCTTCTTCTGC 58.873 43.478 0.00 0.00 0.00 4.26
2780 4156 8.691661 AAACATATGTTTAGGTGTGTCTTCTT 57.308 30.769 28.20 2.60 45.47 2.52
2804 4180 7.827236 CTGGAACATATGTTTAGGAACACCTAA 59.173 37.037 21.63 4.84 43.27 2.69
2805 4181 7.037873 ACTGGAACATATGTTTAGGAACACCTA 60.038 37.037 21.63 3.71 43.27 3.08
2806 4182 6.180472 CTGGAACATATGTTTAGGAACACCT 58.820 40.000 21.63 0.00 43.27 4.00
2807 4183 5.944007 ACTGGAACATATGTTTAGGAACACC 59.056 40.000 21.63 15.24 43.27 4.16
2808 4184 8.556213 TTACTGGAACATATGTTTAGGAACAC 57.444 34.615 21.63 6.80 43.27 3.32
2809 4185 9.173021 CATTACTGGAACATATGTTTAGGAACA 57.827 33.333 23.14 14.94 44.14 3.18
2810 4186 8.621286 CCATTACTGGAACATATGTTTAGGAAC 58.379 37.037 23.14 11.80 46.37 3.62
2811 4187 7.777910 CCCATTACTGGAACATATGTTTAGGAA 59.222 37.037 21.63 22.47 46.37 3.36
2812 4188 7.287061 CCCATTACTGGAACATATGTTTAGGA 58.713 38.462 21.63 16.31 46.37 2.94
2813 4189 6.016276 GCCCATTACTGGAACATATGTTTAGG 60.016 42.308 21.63 15.58 46.37 2.69
2814 4190 6.772716 AGCCCATTACTGGAACATATGTTTAG 59.227 38.462 21.63 22.02 46.37 1.85
2815 4191 6.668645 AGCCCATTACTGGAACATATGTTTA 58.331 36.000 21.63 13.07 46.37 2.01
2816 4192 5.518865 AGCCCATTACTGGAACATATGTTT 58.481 37.500 21.63 8.93 46.37 2.83
2817 4193 5.129368 AGCCCATTACTGGAACATATGTT 57.871 39.130 20.93 20.93 46.37 2.71
2818 4194 4.796110 AGCCCATTACTGGAACATATGT 57.204 40.909 1.41 1.41 46.37 2.29
2819 4195 4.520492 GGAAGCCCATTACTGGAACATATG 59.480 45.833 0.00 0.00 46.37 1.78
2820 4196 4.729868 GGAAGCCCATTACTGGAACATAT 58.270 43.478 0.00 0.00 46.37 1.78
2821 4197 3.433031 CGGAAGCCCATTACTGGAACATA 60.433 47.826 0.00 0.00 46.37 2.29
2822 4198 2.683742 CGGAAGCCCATTACTGGAACAT 60.684 50.000 0.00 0.00 46.37 2.71
2823 4199 1.339631 CGGAAGCCCATTACTGGAACA 60.340 52.381 0.00 0.00 46.37 3.18
2824 4200 1.379527 CGGAAGCCCATTACTGGAAC 58.620 55.000 0.00 0.00 46.37 3.62
2825 4201 3.873781 CGGAAGCCCATTACTGGAA 57.126 52.632 0.00 0.00 46.37 3.53
2883 4383 2.037208 AATTTGGGGCCCGTCAGG 59.963 61.111 19.83 0.00 39.47 3.86
2884 4384 2.350458 CCAATTTGGGGCCCGTCAG 61.350 63.158 19.83 6.47 32.67 3.51
2885 4385 2.283532 CCAATTTGGGGCCCGTCA 60.284 61.111 19.83 6.08 32.67 4.35
2886 4386 2.036572 TCCAATTTGGGGCCCGTC 59.963 61.111 19.83 2.70 38.32 4.79
2887 4387 2.283604 GTCCAATTTGGGGCCCGT 60.284 61.111 19.83 3.16 38.32 5.28
2888 4388 3.448340 CGTCCAATTTGGGGCCCG 61.448 66.667 19.83 2.16 38.32 6.13
2889 4389 2.283604 ACGTCCAATTTGGGGCCC 60.284 61.111 18.17 18.17 38.32 5.80
2890 4390 1.182385 TTCACGTCCAATTTGGGGCC 61.182 55.000 15.37 0.00 38.32 5.80
2894 4394 3.449322 CGTAGTTCACGTCCAATTTGG 57.551 47.619 9.28 9.28 45.82 3.28
2905 4405 1.191647 CCACGTTTCAGCGTAGTTCAC 59.808 52.381 0.00 0.00 43.83 3.18
2906 4406 1.202440 ACCACGTTTCAGCGTAGTTCA 60.202 47.619 0.00 0.00 43.83 3.18
2908 4408 1.202440 TGACCACGTTTCAGCGTAGTT 60.202 47.619 0.00 0.00 43.83 2.24
2909 4409 0.386476 TGACCACGTTTCAGCGTAGT 59.614 50.000 0.00 0.00 43.83 2.73
2910 4410 0.782384 GTGACCACGTTTCAGCGTAG 59.218 55.000 0.00 0.00 43.83 3.51
2912 4412 1.885850 GGTGACCACGTTTCAGCGT 60.886 57.895 9.67 0.00 46.88 5.07
2913 4413 2.935955 GGTGACCACGTTTCAGCG 59.064 61.111 9.67 0.00 32.21 5.18
2925 4425 2.564721 GGCCAGTTTGCAGGGTGAC 61.565 63.158 0.00 0.00 0.00 3.67
2926 4426 2.203480 GGCCAGTTTGCAGGGTGA 60.203 61.111 0.00 0.00 0.00 4.02
2927 4427 3.305516 GGGCCAGTTTGCAGGGTG 61.306 66.667 4.39 0.00 0.00 4.61
2928 4428 3.815407 CTGGGCCAGTTTGCAGGGT 62.815 63.158 25.74 0.00 0.00 4.34
2929 4429 2.793317 ATCTGGGCCAGTTTGCAGGG 62.793 60.000 31.60 5.30 32.61 4.45
2930 4430 0.034186 TATCTGGGCCAGTTTGCAGG 60.034 55.000 31.60 6.10 32.61 4.85
2931 4431 1.340405 ACTATCTGGGCCAGTTTGCAG 60.340 52.381 31.60 22.14 32.61 4.41
2932 4432 0.698238 ACTATCTGGGCCAGTTTGCA 59.302 50.000 31.60 13.93 32.61 4.08
2933 4433 1.098050 CACTATCTGGGCCAGTTTGC 58.902 55.000 31.60 0.00 32.61 3.68
2934 4434 1.281867 TCCACTATCTGGGCCAGTTTG 59.718 52.381 31.60 25.18 41.06 2.93
2935 4435 1.668826 TCCACTATCTGGGCCAGTTT 58.331 50.000 31.60 22.17 41.06 2.66
2936 4436 1.282157 GTTCCACTATCTGGGCCAGTT 59.718 52.381 31.60 25.76 41.06 3.16
2937 4437 0.912486 GTTCCACTATCTGGGCCAGT 59.088 55.000 31.60 21.05 41.06 4.00
2938 4438 0.179073 CGTTCCACTATCTGGGCCAG 60.179 60.000 28.01 28.01 41.06 4.85
2939 4439 1.622607 CCGTTCCACTATCTGGGCCA 61.623 60.000 5.85 5.85 41.06 5.36
2940 4440 1.146263 CCGTTCCACTATCTGGGCC 59.854 63.158 0.00 0.00 41.06 5.80
2941 4441 1.523938 GCCGTTCCACTATCTGGGC 60.524 63.158 0.00 0.00 41.06 5.36
2942 4442 1.410004 TAGCCGTTCCACTATCTGGG 58.590 55.000 0.00 0.00 41.06 4.45
2943 4443 2.167693 TGTTAGCCGTTCCACTATCTGG 59.832 50.000 0.00 0.00 42.29 3.86
2944 4444 3.520290 TGTTAGCCGTTCCACTATCTG 57.480 47.619 0.00 0.00 0.00 2.90
2945 4445 4.020485 ACTTTGTTAGCCGTTCCACTATCT 60.020 41.667 0.00 0.00 0.00 1.98
2946 4446 4.251268 ACTTTGTTAGCCGTTCCACTATC 58.749 43.478 0.00 0.00 0.00 2.08
2947 4447 4.281898 ACTTTGTTAGCCGTTCCACTAT 57.718 40.909 0.00 0.00 0.00 2.12
2948 4448 3.756933 ACTTTGTTAGCCGTTCCACTA 57.243 42.857 0.00 0.00 0.00 2.74
2949 4449 2.616842 CAACTTTGTTAGCCGTTCCACT 59.383 45.455 0.00 0.00 0.00 4.00
2950 4450 2.287368 CCAACTTTGTTAGCCGTTCCAC 60.287 50.000 0.00 0.00 0.00 4.02
2951 4451 1.950909 CCAACTTTGTTAGCCGTTCCA 59.049 47.619 0.00 0.00 0.00 3.53
2952 4452 1.268625 CCCAACTTTGTTAGCCGTTCC 59.731 52.381 0.00 0.00 0.00 3.62
2953 4453 1.335597 GCCCAACTTTGTTAGCCGTTC 60.336 52.381 0.00 0.00 0.00 3.95
2954 4454 0.671796 GCCCAACTTTGTTAGCCGTT 59.328 50.000 0.00 0.00 0.00 4.44
2955 4455 1.176619 GGCCCAACTTTGTTAGCCGT 61.177 55.000 0.00 0.00 30.68 5.68
2956 4456 1.584495 GGCCCAACTTTGTTAGCCG 59.416 57.895 0.00 0.00 30.68 5.52
2957 4457 1.584495 CGGCCCAACTTTGTTAGCC 59.416 57.895 0.00 11.39 35.09 3.93
2958 4458 1.584495 CCGGCCCAACTTTGTTAGC 59.416 57.895 0.00 0.00 0.00 3.09
2959 4459 1.584495 GCCGGCCCAACTTTGTTAG 59.416 57.895 18.11 0.00 0.00 2.34
2960 4460 1.904378 GGCCGGCCCAACTTTGTTA 60.904 57.895 36.64 0.00 0.00 2.41
2961 4461 3.230990 GGCCGGCCCAACTTTGTT 61.231 61.111 36.64 0.00 0.00 2.83
2978 4478 2.546114 AATAGGGTGCCCGTTTCCCG 62.546 60.000 0.98 0.00 45.27 5.14
2979 4479 0.323999 AAATAGGGTGCCCGTTTCCC 60.324 55.000 0.98 0.00 41.95 3.97
2980 4480 1.100510 GAAATAGGGTGCCCGTTTCC 58.899 55.000 20.56 10.02 41.95 3.13
2981 4481 2.014857 GAGAAATAGGGTGCCCGTTTC 58.985 52.381 22.24 22.24 41.46 2.78
2982 4482 1.677820 CGAGAAATAGGGTGCCCGTTT 60.678 52.381 11.56 11.56 41.95 3.60
2983 4483 0.107848 CGAGAAATAGGGTGCCCGTT 60.108 55.000 0.98 0.00 41.95 4.44
2984 4484 1.520666 CGAGAAATAGGGTGCCCGT 59.479 57.895 0.98 0.00 41.95 5.28
2985 4485 1.887707 GCGAGAAATAGGGTGCCCG 60.888 63.158 0.98 0.00 41.95 6.13
2986 4486 1.887707 CGCGAGAAATAGGGTGCCC 60.888 63.158 0.00 0.00 0.00 5.36
2987 4487 0.743345 AACGCGAGAAATAGGGTGCC 60.743 55.000 15.93 0.00 33.74 5.01
2988 4488 0.651031 GAACGCGAGAAATAGGGTGC 59.349 55.000 15.93 0.00 33.74 5.01
2989 4489 2.004583 TGAACGCGAGAAATAGGGTG 57.995 50.000 15.93 0.00 33.74 4.61
2990 4490 2.344025 GTTGAACGCGAGAAATAGGGT 58.656 47.619 15.93 0.00 34.95 4.34
2991 4491 1.323534 CGTTGAACGCGAGAAATAGGG 59.676 52.381 15.93 0.00 33.65 3.53
2992 4492 2.256174 TCGTTGAACGCGAGAAATAGG 58.744 47.619 15.93 0.00 42.21 2.57
3000 4500 1.439858 CTCGTCTCGTTGAACGCGA 60.440 57.895 15.93 14.83 42.21 5.87
3001 4501 1.389204 CTCTCGTCTCGTTGAACGCG 61.389 60.000 13.62 11.18 42.21 6.01
3002 4502 1.066114 CCTCTCGTCTCGTTGAACGC 61.066 60.000 13.62 0.00 42.21 4.84
3003 4503 0.516001 TCCTCTCGTCTCGTTGAACG 59.484 55.000 12.12 12.12 44.19 3.95
3004 4504 2.520979 CATCCTCTCGTCTCGTTGAAC 58.479 52.381 0.00 0.00 0.00 3.18
3005 4505 1.135373 GCATCCTCTCGTCTCGTTGAA 60.135 52.381 0.00 0.00 0.00 2.69
3006 4506 0.452184 GCATCCTCTCGTCTCGTTGA 59.548 55.000 0.00 0.00 0.00 3.18
3007 4507 0.863538 CGCATCCTCTCGTCTCGTTG 60.864 60.000 0.00 0.00 0.00 4.10
3008 4508 1.429825 CGCATCCTCTCGTCTCGTT 59.570 57.895 0.00 0.00 0.00 3.85
3009 4509 3.102985 CGCATCCTCTCGTCTCGT 58.897 61.111 0.00 0.00 0.00 4.18
3010 4510 2.352915 GCGCATCCTCTCGTCTCG 60.353 66.667 0.30 0.00 0.00 4.04
3011 4511 1.008995 GAGCGCATCCTCTCGTCTC 60.009 63.158 11.47 0.00 0.00 3.36
3012 4512 2.829206 CGAGCGCATCCTCTCGTCT 61.829 63.158 11.47 0.00 44.95 4.18
3013 4513 2.352915 CGAGCGCATCCTCTCGTC 60.353 66.667 11.47 0.00 44.95 4.20


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

AutoCloner maintained by Alex Coulton.