Multiple sequence alignment - TraesCS6D01G037900

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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 TraesCS6D01G037900 chr6D 100.000 3530 0 0 1 3530 15699602 15696073 0.000000e+00 6519.0
1 TraesCS6D01G037900 chr6D 85.171 2367 259 57 703 3013 15748288 15745958 0.000000e+00 2342.0
2 TraesCS6D01G037900 chr6D 89.506 1782 171 12 781 2553 15711790 15710016 0.000000e+00 2241.0
3 TraesCS6D01G037900 chr6D 85.200 1777 241 15 785 2547 15799489 15797721 0.000000e+00 1805.0
4 TraesCS6D01G037900 chr6D 87.084 1564 198 2 983 2545 15419630 15418070 0.000000e+00 1766.0
5 TraesCS6D01G037900 chr6D 97.403 154 4 0 84 237 49274890 49275043 2.700000e-66 263.0
6 TraesCS6D01G037900 chr6D 97.297 37 1 0 3494 3530 15793030 15793066 2.940000e-06 63.9
7 TraesCS6D01G037900 chr6D 100.000 30 0 0 3501 3530 15668589 15668560 4.920000e-04 56.5
8 TraesCS6D01G037900 chr6A 92.731 2724 141 28 262 2965 16376843 16374157 0.000000e+00 3880.0
9 TraesCS6D01G037900 chr6A 86.488 2235 233 38 785 2963 16388427 16386206 0.000000e+00 2390.0
10 TraesCS6D01G037900 chr6A 87.220 1565 196 3 984 2547 16400714 16399153 0.000000e+00 1779.0
11 TraesCS6D01G037900 chr6A 87.088 1549 193 3 983 2529 15953431 15951888 0.000000e+00 1746.0
12 TraesCS6D01G037900 chr6A 82.308 520 46 17 3024 3530 16374052 16373566 3.280000e-110 409.0
13 TraesCS6D01G037900 chr6A 96.000 50 2 0 2966 3015 16374104 16374153 8.120000e-12 82.4
14 TraesCS6D01G037900 chr6A 96.875 32 1 0 3499 3530 16362835 16362804 2.000000e-03 54.7
15 TraesCS6D01G037900 chr6A 96.875 32 1 0 3499 3530 16367524 16367493 2.000000e-03 54.7
16 TraesCS6D01G037900 chrUn 94.240 1632 70 8 1899 3528 356328126 356329735 0.000000e+00 2471.0
17 TraesCS6D01G037900 chrUn 94.125 1634 70 9 1899 3530 76448929 76447320 0.000000e+00 2462.0
18 TraesCS6D01G037900 chr6B 86.764 2191 218 36 780 2921 27780020 27777853 0.000000e+00 2374.0
19 TraesCS6D01G037900 chr6B 94.033 419 17 3 695 1107 27711964 27711548 2.310000e-176 628.0
20 TraesCS6D01G037900 chr6B 90.909 429 30 5 240 664 27712559 27712136 5.110000e-158 568.0
21 TraesCS6D01G037900 chr6B 100.000 30 0 0 3501 3530 27694745 27694716 4.920000e-04 56.5
22 TraesCS6D01G037900 chr7D 92.040 201 10 3 237 434 83761061 83761258 9.650000e-71 278.0
23 TraesCS6D01G037900 chr7D 95.349 86 3 1 1 85 83760984 83761069 6.150000e-28 135.0
24 TraesCS6D01G037900 chr2D 92.040 201 10 3 237 434 238090304 238090107 9.650000e-71 278.0
25 TraesCS6D01G037900 chr2D 95.349 86 3 1 1 85 238090381 238090296 6.150000e-28 135.0
26 TraesCS6D01G037900 chr2B 98.701 154 2 0 84 237 92501107 92500954 1.250000e-69 274.0
27 TraesCS6D01G037900 chr1A 96.732 153 5 0 85 237 512458806 512458654 4.520000e-64 255.0
28 TraesCS6D01G037900 chr1A 95.364 151 7 0 86 236 85335769 85335619 1.270000e-59 241.0
29 TraesCS6D01G037900 chr5D 97.902 143 3 0 86 228 434559496 434559354 7.570000e-62 248.0
30 TraesCS6D01G037900 chr7B 94.231 156 9 0 86 241 336472998 336472843 4.550000e-59 239.0
31 TraesCS6D01G037900 chr5B 94.737 152 7 1 85 236 323857011 323857161 5.890000e-58 235.0
32 TraesCS6D01G037900 chr5A 94.702 151 8 0 86 236 697878262 697878112 5.890000e-58 235.0
33 TraesCS6D01G037900 chr3A 94.702 151 8 0 86 236 655785238 655785388 5.890000e-58 235.0


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 TraesCS6D01G037900 chr6D 15696073 15699602 3529 True 6519.0 6519 100.0000 1 3530 1 chr6D.!!$R3 3529
1 TraesCS6D01G037900 chr6D 15745958 15748288 2330 True 2342.0 2342 85.1710 703 3013 1 chr6D.!!$R5 2310
2 TraesCS6D01G037900 chr6D 15710016 15711790 1774 True 2241.0 2241 89.5060 781 2553 1 chr6D.!!$R4 1772
3 TraesCS6D01G037900 chr6D 15797721 15799489 1768 True 1805.0 1805 85.2000 785 2547 1 chr6D.!!$R6 1762
4 TraesCS6D01G037900 chr6D 15418070 15419630 1560 True 1766.0 1766 87.0840 983 2545 1 chr6D.!!$R1 1562
5 TraesCS6D01G037900 chr6A 16386206 16388427 2221 True 2390.0 2390 86.4880 785 2963 1 chr6A.!!$R4 2178
6 TraesCS6D01G037900 chr6A 16373566 16376843 3277 True 2144.5 3880 87.5195 262 3530 2 chr6A.!!$R6 3268
7 TraesCS6D01G037900 chr6A 16399153 16400714 1561 True 1779.0 1779 87.2200 984 2547 1 chr6A.!!$R5 1563
8 TraesCS6D01G037900 chr6A 15951888 15953431 1543 True 1746.0 1746 87.0880 983 2529 1 chr6A.!!$R1 1546
9 TraesCS6D01G037900 chrUn 356328126 356329735 1609 False 2471.0 2471 94.2400 1899 3528 1 chrUn.!!$F1 1629
10 TraesCS6D01G037900 chrUn 76447320 76448929 1609 True 2462.0 2462 94.1250 1899 3530 1 chrUn.!!$R1 1631
11 TraesCS6D01G037900 chr6B 27777853 27780020 2167 True 2374.0 2374 86.7640 780 2921 1 chr6B.!!$R2 2141
12 TraesCS6D01G037900 chr6B 27711548 27712559 1011 True 598.0 628 92.4710 240 1107 2 chr6B.!!$R3 867

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
217 218 0.028110 GCCTCGTCCGCAAAATCATC 59.972 55.0 0.0 0.0 0.0 2.92 F
225 226 0.168788 CGCAAAATCATCGGCTGTGT 59.831 50.0 0.0 0.0 0.0 3.72 F
1431 1629 0.395862 TCCTCATCGGTGTCTCCCTC 60.396 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 1629 0.798776 GACATGAGACAAAGGTGGCG 59.201 55.0 0.00 0.0 38.10 5.69 R
1590 1788 1.996786 GCCATGCCATGAAGGACGTG 61.997 60.0 6.18 0.0 41.22 4.49 R
3354 3667 0.182775 ACCTGGAAAGTTCAACGGCT 59.817 50.0 0.00 0.0 0.00 5.52 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
17 18 2.279918 ACGGCGTTCGCTTTCACT 60.280 55.556 6.77 0.00 43.89 3.41
18 19 1.007038 ACGGCGTTCGCTTTCACTA 60.007 52.632 6.77 0.00 43.89 2.74
19 20 0.598158 ACGGCGTTCGCTTTCACTAA 60.598 50.000 6.77 0.00 43.89 2.24
20 21 0.179258 CGGCGTTCGCTTTCACTAAC 60.179 55.000 16.40 0.00 0.00 2.34
21 22 0.863144 GGCGTTCGCTTTCACTAACA 59.137 50.000 16.40 0.00 0.00 2.41
22 23 1.136336 GGCGTTCGCTTTCACTAACAG 60.136 52.381 16.40 0.00 0.00 3.16
23 24 1.525619 GCGTTCGCTTTCACTAACAGT 59.474 47.619 9.99 0.00 0.00 3.55
25 26 2.538449 CGTTCGCTTTCACTAACAGTGT 59.462 45.455 6.23 0.00 46.03 3.55
26 27 3.361724 CGTTCGCTTTCACTAACAGTGTC 60.362 47.826 0.00 0.00 46.03 3.67
27 28 2.750948 TCGCTTTCACTAACAGTGTCC 58.249 47.619 0.00 0.00 46.03 4.02
28 29 2.364324 TCGCTTTCACTAACAGTGTCCT 59.636 45.455 0.00 0.00 46.03 3.85
29 30 2.731976 CGCTTTCACTAACAGTGTCCTC 59.268 50.000 0.00 0.00 46.03 3.71
30 31 3.553096 CGCTTTCACTAACAGTGTCCTCT 60.553 47.826 0.00 0.00 46.03 3.69
31 32 4.321008 CGCTTTCACTAACAGTGTCCTCTA 60.321 45.833 0.00 0.00 46.03 2.43
32 33 5.539048 GCTTTCACTAACAGTGTCCTCTAA 58.461 41.667 0.00 0.00 46.03 2.10
33 34 5.989777 GCTTTCACTAACAGTGTCCTCTAAA 59.010 40.000 0.00 0.00 46.03 1.85
34 35 6.073711 GCTTTCACTAACAGTGTCCTCTAAAC 60.074 42.308 0.00 0.00 46.03 2.01
35 36 6.726490 TTCACTAACAGTGTCCTCTAAACT 57.274 37.500 0.00 0.00 46.03 2.66
36 37 6.726490 TCACTAACAGTGTCCTCTAAACTT 57.274 37.500 0.00 0.00 46.03 2.66
37 38 6.513180 TCACTAACAGTGTCCTCTAAACTTG 58.487 40.000 0.00 0.00 46.03 3.16
38 39 5.696724 CACTAACAGTGTCCTCTAAACTTGG 59.303 44.000 0.00 0.00 41.19 3.61
39 40 4.772886 AACAGTGTCCTCTAAACTTGGT 57.227 40.909 0.00 0.00 0.00 3.67
40 41 4.338379 ACAGTGTCCTCTAAACTTGGTC 57.662 45.455 0.00 0.00 0.00 4.02
41 42 3.709653 ACAGTGTCCTCTAAACTTGGTCA 59.290 43.478 0.00 0.00 0.00 4.02
42 43 4.163458 ACAGTGTCCTCTAAACTTGGTCAA 59.837 41.667 0.00 0.00 0.00 3.18
43 44 5.163195 ACAGTGTCCTCTAAACTTGGTCAAT 60.163 40.000 0.00 0.00 0.00 2.57
44 45 5.765182 CAGTGTCCTCTAAACTTGGTCAATT 59.235 40.000 0.00 0.00 0.00 2.32
45 46 5.765182 AGTGTCCTCTAAACTTGGTCAATTG 59.235 40.000 0.00 0.00 0.00 2.32
46 47 5.048713 GTGTCCTCTAAACTTGGTCAATTGG 60.049 44.000 5.42 0.00 0.00 3.16
47 48 5.070685 GTCCTCTAAACTTGGTCAATTGGT 58.929 41.667 5.42 0.00 0.00 3.67
48 49 5.181433 GTCCTCTAAACTTGGTCAATTGGTC 59.819 44.000 5.42 0.00 0.00 4.02
49 50 4.459337 CCTCTAAACTTGGTCAATTGGTCC 59.541 45.833 5.42 9.33 0.00 4.46
50 51 5.316987 CTCTAAACTTGGTCAATTGGTCCT 58.683 41.667 17.02 4.34 0.00 3.85
51 52 5.313712 TCTAAACTTGGTCAATTGGTCCTC 58.686 41.667 17.02 1.55 0.00 3.71
52 53 3.884037 AACTTGGTCAATTGGTCCTCT 57.116 42.857 17.02 2.66 0.00 3.69
53 54 3.425162 ACTTGGTCAATTGGTCCTCTC 57.575 47.619 17.02 0.00 0.00 3.20
54 55 2.040412 ACTTGGTCAATTGGTCCTCTCC 59.960 50.000 17.02 6.22 0.00 3.71
55 56 0.991920 TGGTCAATTGGTCCTCTCCC 59.008 55.000 17.02 3.19 0.00 4.30
56 57 0.991920 GGTCAATTGGTCCTCTCCCA 59.008 55.000 5.42 0.00 0.00 4.37
57 58 1.354368 GGTCAATTGGTCCTCTCCCAA 59.646 52.381 5.42 0.00 45.55 4.12
58 59 2.225017 GGTCAATTGGTCCTCTCCCAAA 60.225 50.000 5.42 0.00 44.70 3.28
59 60 2.820197 GTCAATTGGTCCTCTCCCAAAC 59.180 50.000 5.42 0.00 44.70 2.93
60 61 2.716424 TCAATTGGTCCTCTCCCAAACT 59.284 45.455 5.42 0.00 44.70 2.66
61 62 3.140144 TCAATTGGTCCTCTCCCAAACTT 59.860 43.478 5.42 0.00 44.70 2.66
62 63 2.656947 TTGGTCCTCTCCCAAACTTG 57.343 50.000 0.00 0.00 38.98 3.16
63 64 1.518367 TGGTCCTCTCCCAAACTTGT 58.482 50.000 0.00 0.00 0.00 3.16
64 65 1.850345 TGGTCCTCTCCCAAACTTGTT 59.150 47.619 0.00 0.00 0.00 2.83
65 66 2.243736 TGGTCCTCTCCCAAACTTGTTT 59.756 45.455 0.00 0.00 0.00 2.83
66 67 2.623416 GGTCCTCTCCCAAACTTGTTTG 59.377 50.000 16.64 16.64 0.00 2.93
72 73 2.592212 CCAAACTTGTTTGGCGCTG 58.408 52.632 25.97 8.22 44.15 5.18
73 74 0.179113 CCAAACTTGTTTGGCGCTGT 60.179 50.000 25.97 0.00 44.15 4.40
74 75 1.639280 CAAACTTGTTTGGCGCTGTT 58.361 45.000 16.00 0.00 0.00 3.16
75 76 2.480416 CCAAACTTGTTTGGCGCTGTTA 60.480 45.455 25.97 0.00 44.15 2.41
76 77 3.380142 CAAACTTGTTTGGCGCTGTTAT 58.620 40.909 16.00 0.00 0.00 1.89
77 78 4.541779 CAAACTTGTTTGGCGCTGTTATA 58.458 39.130 16.00 0.00 0.00 0.98
78 79 4.839668 AACTTGTTTGGCGCTGTTATAA 57.160 36.364 7.64 0.00 0.00 0.98
79 80 4.839668 ACTTGTTTGGCGCTGTTATAAA 57.160 36.364 7.64 0.00 0.00 1.40
80 81 4.542735 ACTTGTTTGGCGCTGTTATAAAC 58.457 39.130 7.64 10.06 33.20 2.01
81 82 3.562567 TGTTTGGCGCTGTTATAAACC 57.437 42.857 7.64 0.00 31.96 3.27
82 83 3.150767 TGTTTGGCGCTGTTATAAACCT 58.849 40.909 7.64 0.00 31.96 3.50
83 84 3.570550 TGTTTGGCGCTGTTATAAACCTT 59.429 39.130 7.64 0.00 31.96 3.50
84 85 4.760715 TGTTTGGCGCTGTTATAAACCTTA 59.239 37.500 7.64 0.00 31.96 2.69
85 86 4.950434 TTGGCGCTGTTATAAACCTTAC 57.050 40.909 7.64 0.00 0.00 2.34
86 87 2.931325 TGGCGCTGTTATAAACCTTACG 59.069 45.455 7.64 0.00 0.00 3.18
87 88 2.286025 GGCGCTGTTATAAACCTTACGG 59.714 50.000 7.64 0.00 0.00 4.02
88 89 3.189285 GCGCTGTTATAAACCTTACGGA 58.811 45.455 0.00 0.00 0.00 4.69
89 90 3.618150 GCGCTGTTATAAACCTTACGGAA 59.382 43.478 0.00 0.00 0.00 4.30
90 91 4.271776 GCGCTGTTATAAACCTTACGGAAT 59.728 41.667 0.00 0.00 0.00 3.01
91 92 5.463061 GCGCTGTTATAAACCTTACGGAATA 59.537 40.000 0.00 0.00 0.00 1.75
92 93 6.346359 GCGCTGTTATAAACCTTACGGAATAG 60.346 42.308 0.00 0.00 0.00 1.73
93 94 6.346359 CGCTGTTATAAACCTTACGGAATAGC 60.346 42.308 0.00 0.00 0.00 2.97
94 95 6.704937 GCTGTTATAAACCTTACGGAATAGCT 59.295 38.462 0.00 0.00 29.42 3.32
95 96 7.307219 GCTGTTATAAACCTTACGGAATAGCTG 60.307 40.741 0.00 0.00 29.42 4.24
96 97 6.480981 TGTTATAAACCTTACGGAATAGCTGC 59.519 38.462 0.00 0.00 0.00 5.25
97 98 3.343941 AAACCTTACGGAATAGCTGCA 57.656 42.857 1.02 0.00 0.00 4.41
98 99 2.311124 ACCTTACGGAATAGCTGCAC 57.689 50.000 1.02 0.00 0.00 4.57
99 100 1.553248 ACCTTACGGAATAGCTGCACA 59.447 47.619 1.02 0.00 0.00 4.57
100 101 1.933853 CCTTACGGAATAGCTGCACAC 59.066 52.381 1.02 0.00 0.00 3.82
101 102 2.616960 CTTACGGAATAGCTGCACACA 58.383 47.619 1.02 0.00 0.00 3.72
102 103 2.004583 TACGGAATAGCTGCACACAC 57.995 50.000 1.02 0.00 0.00 3.82
103 104 1.014044 ACGGAATAGCTGCACACACG 61.014 55.000 1.02 3.44 0.00 4.49
104 105 0.735978 CGGAATAGCTGCACACACGA 60.736 55.000 1.02 0.00 0.00 4.35
105 106 0.721718 GGAATAGCTGCACACACGAC 59.278 55.000 1.02 0.00 0.00 4.34
106 107 0.721718 GAATAGCTGCACACACGACC 59.278 55.000 1.02 0.00 0.00 4.79
107 108 0.321671 AATAGCTGCACACACGACCT 59.678 50.000 1.02 0.00 0.00 3.85
108 109 0.321671 ATAGCTGCACACACGACCTT 59.678 50.000 1.02 0.00 0.00 3.50
109 110 0.105964 TAGCTGCACACACGACCTTT 59.894 50.000 1.02 0.00 0.00 3.11
110 111 0.748005 AGCTGCACACACGACCTTTT 60.748 50.000 1.02 0.00 0.00 2.27
111 112 0.941542 GCTGCACACACGACCTTTTA 59.058 50.000 0.00 0.00 0.00 1.52
112 113 1.535462 GCTGCACACACGACCTTTTAT 59.465 47.619 0.00 0.00 0.00 1.40
113 114 2.665519 GCTGCACACACGACCTTTTATG 60.666 50.000 0.00 0.00 0.00 1.90
114 115 1.265635 TGCACACACGACCTTTTATGC 59.734 47.619 0.00 0.00 0.00 3.14
115 116 1.265635 GCACACACGACCTTTTATGCA 59.734 47.619 0.00 0.00 0.00 3.96
116 117 2.916111 CACACACGACCTTTTATGCAC 58.084 47.619 0.00 0.00 0.00 4.57
117 118 1.529438 ACACACGACCTTTTATGCACG 59.471 47.619 0.00 0.00 0.00 5.34
118 119 1.795872 CACACGACCTTTTATGCACGA 59.204 47.619 0.00 0.00 0.00 4.35
119 120 1.796459 ACACGACCTTTTATGCACGAC 59.204 47.619 0.00 0.00 0.00 4.34
120 121 1.795872 CACGACCTTTTATGCACGACA 59.204 47.619 0.00 0.00 0.00 4.35
121 122 2.066262 ACGACCTTTTATGCACGACAG 58.934 47.619 0.00 0.00 0.00 3.51
122 123 1.393539 CGACCTTTTATGCACGACAGG 59.606 52.381 0.00 0.00 0.00 4.00
123 124 2.423577 GACCTTTTATGCACGACAGGT 58.576 47.619 8.34 8.34 37.35 4.00
131 132 4.169102 CACGACAGGTGGACGATG 57.831 61.111 0.00 0.00 43.16 3.84
132 133 1.446099 CACGACAGGTGGACGATGG 60.446 63.158 0.00 0.00 43.16 3.51
133 134 1.906824 ACGACAGGTGGACGATGGT 60.907 57.895 0.00 0.00 0.00 3.55
134 135 0.609957 ACGACAGGTGGACGATGGTA 60.610 55.000 0.00 0.00 0.00 3.25
135 136 0.100682 CGACAGGTGGACGATGGTAG 59.899 60.000 0.00 0.00 0.00 3.18
136 137 0.460311 GACAGGTGGACGATGGTAGG 59.540 60.000 0.00 0.00 0.00 3.18
137 138 0.040646 ACAGGTGGACGATGGTAGGA 59.959 55.000 0.00 0.00 0.00 2.94
138 139 1.343075 ACAGGTGGACGATGGTAGGAT 60.343 52.381 0.00 0.00 0.00 3.24
139 140 1.341531 CAGGTGGACGATGGTAGGATC 59.658 57.143 0.00 0.00 0.00 3.36
140 141 1.218196 AGGTGGACGATGGTAGGATCT 59.782 52.381 0.00 0.00 0.00 2.75
141 142 1.341531 GGTGGACGATGGTAGGATCTG 59.658 57.143 0.00 0.00 0.00 2.90
142 143 2.307768 GTGGACGATGGTAGGATCTGA 58.692 52.381 0.00 0.00 0.00 3.27
143 144 2.894126 GTGGACGATGGTAGGATCTGAT 59.106 50.000 0.00 0.00 0.00 2.90
144 145 2.893489 TGGACGATGGTAGGATCTGATG 59.107 50.000 0.00 0.00 0.00 3.07
145 146 2.894126 GGACGATGGTAGGATCTGATGT 59.106 50.000 0.00 0.00 0.00 3.06
146 147 3.322254 GGACGATGGTAGGATCTGATGTT 59.678 47.826 0.00 0.00 0.00 2.71
147 148 4.302455 GACGATGGTAGGATCTGATGTTG 58.698 47.826 0.00 0.00 0.00 3.33
148 149 3.062763 CGATGGTAGGATCTGATGTTGC 58.937 50.000 0.00 0.00 0.00 4.17
149 150 3.244009 CGATGGTAGGATCTGATGTTGCT 60.244 47.826 0.00 0.00 0.00 3.91
150 151 4.712476 GATGGTAGGATCTGATGTTGCTT 58.288 43.478 0.00 0.00 0.00 3.91
151 152 5.509670 CGATGGTAGGATCTGATGTTGCTTA 60.510 44.000 0.00 0.00 0.00 3.09
152 153 5.282055 TGGTAGGATCTGATGTTGCTTAG 57.718 43.478 0.00 0.00 0.00 2.18
153 154 4.101585 TGGTAGGATCTGATGTTGCTTAGG 59.898 45.833 0.00 0.00 0.00 2.69
154 155 4.101741 GGTAGGATCTGATGTTGCTTAGGT 59.898 45.833 0.00 0.00 0.00 3.08
155 156 5.304614 GGTAGGATCTGATGTTGCTTAGGTA 59.695 44.000 0.00 0.00 0.00 3.08
156 157 6.014156 GGTAGGATCTGATGTTGCTTAGGTAT 60.014 42.308 0.00 0.00 0.00 2.73
157 158 5.862845 AGGATCTGATGTTGCTTAGGTATG 58.137 41.667 0.00 0.00 0.00 2.39
158 159 4.999950 GGATCTGATGTTGCTTAGGTATGG 59.000 45.833 0.00 0.00 0.00 2.74
159 160 5.221722 GGATCTGATGTTGCTTAGGTATGGA 60.222 44.000 0.00 0.00 0.00 3.41
160 161 5.282055 TCTGATGTTGCTTAGGTATGGAG 57.718 43.478 0.00 0.00 0.00 3.86
161 162 4.101585 TCTGATGTTGCTTAGGTATGGAGG 59.898 45.833 0.00 0.00 0.00 4.30
162 163 3.136443 TGATGTTGCTTAGGTATGGAGGG 59.864 47.826 0.00 0.00 0.00 4.30
163 164 2.840511 TGTTGCTTAGGTATGGAGGGA 58.159 47.619 0.00 0.00 0.00 4.20
164 165 3.393687 TGTTGCTTAGGTATGGAGGGAT 58.606 45.455 0.00 0.00 0.00 3.85
165 166 3.785887 TGTTGCTTAGGTATGGAGGGATT 59.214 43.478 0.00 0.00 0.00 3.01
166 167 4.141482 TGTTGCTTAGGTATGGAGGGATTC 60.141 45.833 0.00 0.00 0.00 2.52
167 168 3.664320 TGCTTAGGTATGGAGGGATTCA 58.336 45.455 0.00 0.00 0.00 2.57
168 169 4.044308 TGCTTAGGTATGGAGGGATTCAA 58.956 43.478 0.00 0.00 0.00 2.69
169 170 4.665009 TGCTTAGGTATGGAGGGATTCAAT 59.335 41.667 0.00 0.00 0.00 2.57
170 171 5.221925 TGCTTAGGTATGGAGGGATTCAATC 60.222 44.000 0.00 0.00 0.00 2.67
186 187 7.440523 GATTCAATCCAACGATTATTAGCCT 57.559 36.000 0.00 0.00 36.54 4.58
187 188 6.618287 TTCAATCCAACGATTATTAGCCTG 57.382 37.500 0.00 0.00 36.54 4.85
188 189 5.680619 TCAATCCAACGATTATTAGCCTGT 58.319 37.500 0.00 0.00 36.54 4.00
189 190 5.527214 TCAATCCAACGATTATTAGCCTGTG 59.473 40.000 0.00 0.00 36.54 3.66
190 191 4.481368 TCCAACGATTATTAGCCTGTGT 57.519 40.909 0.00 0.00 0.00 3.72
191 192 4.439057 TCCAACGATTATTAGCCTGTGTC 58.561 43.478 0.00 0.00 0.00 3.67
192 193 3.245284 CCAACGATTATTAGCCTGTGTCG 59.755 47.826 0.00 0.00 0.00 4.35
193 194 3.795623 ACGATTATTAGCCTGTGTCGT 57.204 42.857 0.00 0.00 36.19 4.34
194 195 3.703420 ACGATTATTAGCCTGTGTCGTC 58.297 45.455 0.00 0.00 36.23 4.20
195 196 3.050619 CGATTATTAGCCTGTGTCGTCC 58.949 50.000 0.00 0.00 0.00 4.79
196 197 3.490249 CGATTATTAGCCTGTGTCGTCCA 60.490 47.826 0.00 0.00 0.00 4.02
197 198 4.632153 GATTATTAGCCTGTGTCGTCCAT 58.368 43.478 0.00 0.00 0.00 3.41
198 199 2.315925 ATTAGCCTGTGTCGTCCATG 57.684 50.000 0.00 0.00 0.00 3.66
199 200 0.391130 TTAGCCTGTGTCGTCCATGC 60.391 55.000 0.00 0.00 0.00 4.06
200 201 2.238847 TAGCCTGTGTCGTCCATGCC 62.239 60.000 0.00 0.00 0.00 4.40
201 202 2.665000 CCTGTGTCGTCCATGCCT 59.335 61.111 0.00 0.00 0.00 4.75
202 203 1.448540 CCTGTGTCGTCCATGCCTC 60.449 63.158 0.00 0.00 0.00 4.70
203 204 1.807165 CTGTGTCGTCCATGCCTCG 60.807 63.158 0.00 0.00 0.00 4.63
204 205 2.261671 GTGTCGTCCATGCCTCGT 59.738 61.111 0.00 0.00 0.00 4.18
205 206 1.805945 GTGTCGTCCATGCCTCGTC 60.806 63.158 0.00 0.00 0.00 4.20
206 207 2.202756 GTCGTCCATGCCTCGTCC 60.203 66.667 0.00 0.00 0.00 4.79
207 208 3.822192 TCGTCCATGCCTCGTCCG 61.822 66.667 0.00 0.00 0.00 4.79
209 210 4.451150 GTCCATGCCTCGTCCGCA 62.451 66.667 0.00 0.00 41.28 5.69
210 211 3.700970 TCCATGCCTCGTCCGCAA 61.701 61.111 0.00 0.00 40.22 4.85
211 212 2.745884 CCATGCCTCGTCCGCAAA 60.746 61.111 0.00 0.00 40.22 3.68
212 213 2.331893 CCATGCCTCGTCCGCAAAA 61.332 57.895 0.00 0.00 40.22 2.44
213 214 1.656818 CCATGCCTCGTCCGCAAAAT 61.657 55.000 0.00 0.00 40.22 1.82
214 215 0.248215 CATGCCTCGTCCGCAAAATC 60.248 55.000 0.00 0.00 40.22 2.17
215 216 0.676466 ATGCCTCGTCCGCAAAATCA 60.676 50.000 0.00 0.00 40.22 2.57
216 217 0.676466 TGCCTCGTCCGCAAAATCAT 60.676 50.000 0.00 0.00 32.05 2.45
217 218 0.028110 GCCTCGTCCGCAAAATCATC 59.972 55.000 0.00 0.00 0.00 2.92
218 219 0.301687 CCTCGTCCGCAAAATCATCG 59.698 55.000 0.00 0.00 0.00 3.84
219 220 0.301687 CTCGTCCGCAAAATCATCGG 59.698 55.000 0.00 0.00 44.16 4.18
220 221 1.297598 CGTCCGCAAAATCATCGGC 60.298 57.895 0.00 0.00 42.65 5.54
221 222 1.705337 CGTCCGCAAAATCATCGGCT 61.705 55.000 0.00 0.00 42.65 5.52
222 223 0.248215 GTCCGCAAAATCATCGGCTG 60.248 55.000 0.00 0.00 42.65 4.85
223 224 0.676466 TCCGCAAAATCATCGGCTGT 60.676 50.000 0.00 0.00 42.65 4.40
224 225 0.523968 CCGCAAAATCATCGGCTGTG 60.524 55.000 0.00 0.00 36.53 3.66
225 226 0.168788 CGCAAAATCATCGGCTGTGT 59.831 50.000 0.00 0.00 0.00 3.72
226 227 1.396648 CGCAAAATCATCGGCTGTGTA 59.603 47.619 0.00 0.00 0.00 2.90
227 228 2.537529 CGCAAAATCATCGGCTGTGTAG 60.538 50.000 0.00 0.00 0.00 2.74
309 320 9.483489 TCTTGATTAATACTACTACCCACAGAA 57.517 33.333 0.00 0.00 0.00 3.02
416 427 2.159490 ACGGTTTGCAGTAACACAACAC 60.159 45.455 3.80 0.00 0.00 3.32
538 549 9.807649 GTAGGATCAAGTACGTTTTAGGAATAA 57.192 33.333 0.00 0.00 0.00 1.40
541 552 8.601476 GGATCAAGTACGTTTTAGGAATAACTG 58.399 37.037 0.00 0.00 0.00 3.16
551 562 7.574967 CGTTTTAGGAATAACTGAACCTGCAAT 60.575 37.037 0.00 0.00 34.42 3.56
576 587 3.130516 TCGCAGTCAGATCGAATAAACCT 59.869 43.478 0.00 0.00 0.00 3.50
582 593 7.148474 GCAGTCAGATCGAATAAACCTTTTACA 60.148 37.037 0.00 0.00 0.00 2.41
596 607 7.492352 AACCTTTTACATACAGTGTCAACTC 57.508 36.000 0.00 0.00 42.29 3.01
613 624 3.393089 ACTCTTTGCACTGTCCTGTAG 57.607 47.619 0.00 0.00 0.00 2.74
651 666 4.515028 ATGCCCTGCACTGCATATATAT 57.485 40.909 14.81 0.00 45.89 0.86
660 675 7.440556 CCTGCACTGCATATATATTATCTCCAC 59.559 40.741 3.64 0.00 38.13 4.02
690 825 5.860941 AGTAGCATGTAGTACAATCTGCT 57.139 39.130 25.38 25.38 42.52 4.24
692 827 7.348080 AGTAGCATGTAGTACAATCTGCTTA 57.652 36.000 26.59 14.55 38.40 3.09
693 828 7.203910 AGTAGCATGTAGTACAATCTGCTTAC 58.796 38.462 26.59 21.50 38.40 2.34
698 854 7.653713 GCATGTAGTACAATCTGCTTACTATGT 59.346 37.037 16.60 0.00 31.09 2.29
887 1047 0.525761 GTCTCTCGAGCAGCAACTCT 59.474 55.000 7.81 0.00 34.35 3.24
924 1106 1.043673 ACCTAGAGCTACCCCTTGCG 61.044 60.000 0.00 0.00 0.00 4.85
974 1162 3.752339 GCAAGCAAAGCTCCCCGG 61.752 66.667 0.00 0.00 38.25 5.73
1197 1395 4.479993 GCTGCGCCACTCATCCCT 62.480 66.667 4.18 0.00 0.00 4.20
1398 1596 1.434188 TTGATGGTCCTGGCGGATAT 58.566 50.000 0.00 0.00 42.43 1.63
1407 1605 4.406003 GGTCCTGGCGGATATATCACTATT 59.594 45.833 14.60 0.00 42.43 1.73
1431 1629 0.395862 TCCTCATCGGTGTCTCCCTC 60.396 60.000 0.00 0.00 0.00 4.30
1601 1799 1.302511 GTGGTGCCACGTCCTTCAT 60.303 57.895 5.53 0.00 37.19 2.57
1602 1800 1.302431 TGGTGCCACGTCCTTCATG 60.302 57.895 0.00 0.00 0.00 3.07
1680 1878 1.076485 GCTCACCATGGGGCAAGAT 60.076 57.895 18.09 0.00 37.90 2.40
1785 1983 5.357257 GTCACCAACTATCGTACATGGATT 58.643 41.667 0.00 0.00 35.16 3.01
1935 2133 1.299541 CAAATATCTTCGCACGGCCT 58.700 50.000 0.00 0.00 0.00 5.19
2007 2205 4.013728 CCCGTCTTTGGAACATTTGGATA 58.986 43.478 0.00 0.00 39.30 2.59
2352 2550 1.277580 CCATGCTCCTCCCTCCAAGT 61.278 60.000 0.00 0.00 0.00 3.16
2519 2717 4.204028 ACCAAACAGCACGCCCCT 62.204 61.111 0.00 0.00 0.00 4.79
2723 2944 9.142014 TGCAATAAGGGCTTGTAATATGTTATT 57.858 29.630 0.00 0.00 0.00 1.40
3029 3338 0.319297 AGCAACTTACGGTCCGTGAC 60.319 55.000 27.20 6.79 41.39 3.67
3037 3346 1.035139 ACGGTCCGTGACACTTTAGT 58.965 50.000 18.08 0.00 39.18 2.24
3061 3370 1.319541 GATGGCAATGCAGCTCTGAT 58.680 50.000 7.79 0.00 34.17 2.90
3062 3371 1.001268 GATGGCAATGCAGCTCTGATG 60.001 52.381 7.79 0.00 34.17 3.07
3134 3443 0.523072 ATAAGCTGTGCAAACTGGCG 59.477 50.000 0.00 0.00 36.28 5.69
3207 3516 5.424121 AACTTCTCGTTGAATGTTTGAGG 57.576 39.130 0.00 0.00 33.72 3.86
3211 3520 1.879380 TCGTTGAATGTTTGAGGCCTG 59.121 47.619 12.00 0.00 0.00 4.85
3307 3620 7.652727 TGCTACTTATCTGATACTAGTTGCTG 58.347 38.462 23.50 0.00 38.06 4.41
3319 3632 8.518702 TGATACTAGTTGCTGCTTATCTGATAG 58.481 37.037 0.00 0.00 0.00 2.08
3320 3633 6.723298 ACTAGTTGCTGCTTATCTGATAGT 57.277 37.500 0.00 0.00 0.00 2.12
3321 3634 7.825331 ACTAGTTGCTGCTTATCTGATAGTA 57.175 36.000 0.00 0.00 0.00 1.82
3362 3687 1.000955 GAAACTCCTCTCAGCCGTTGA 59.999 52.381 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.179258 GTTAGTGAAAGCGAACGCCG 60.179 55.000 15.44 0.00 43.17 6.46
2 3 0.863144 TGTTAGTGAAAGCGAACGCC 59.137 50.000 15.44 1.52 43.17 5.68
3 4 1.525619 ACTGTTAGTGAAAGCGAACGC 59.474 47.619 11.31 11.31 42.33 4.84
15 16 5.365895 ACCAAGTTTAGAGGACACTGTTAGT 59.634 40.000 0.00 0.00 0.00 2.24
16 17 5.855045 ACCAAGTTTAGAGGACACTGTTAG 58.145 41.667 0.00 0.00 0.00 2.34
17 18 5.364446 TGACCAAGTTTAGAGGACACTGTTA 59.636 40.000 0.00 0.00 0.00 2.41
18 19 4.163458 TGACCAAGTTTAGAGGACACTGTT 59.837 41.667 0.00 0.00 0.00 3.16
19 20 3.709653 TGACCAAGTTTAGAGGACACTGT 59.290 43.478 0.00 0.00 0.00 3.55
20 21 4.336889 TGACCAAGTTTAGAGGACACTG 57.663 45.455 0.00 0.00 0.00 3.66
21 22 5.568620 ATTGACCAAGTTTAGAGGACACT 57.431 39.130 0.00 0.00 0.00 3.55
22 23 5.048713 CCAATTGACCAAGTTTAGAGGACAC 60.049 44.000 7.12 0.00 0.00 3.67
23 24 5.070001 CCAATTGACCAAGTTTAGAGGACA 58.930 41.667 7.12 0.00 0.00 4.02
24 25 5.070685 ACCAATTGACCAAGTTTAGAGGAC 58.929 41.667 7.12 0.00 0.00 3.85
25 26 5.313712 GACCAATTGACCAAGTTTAGAGGA 58.686 41.667 7.12 0.00 0.00 3.71
26 27 4.459337 GGACCAATTGACCAAGTTTAGAGG 59.541 45.833 7.12 0.00 0.00 3.69
27 28 5.316987 AGGACCAATTGACCAAGTTTAGAG 58.683 41.667 18.75 0.00 0.00 2.43
28 29 5.073144 AGAGGACCAATTGACCAAGTTTAGA 59.927 40.000 18.75 0.00 0.00 2.10
29 30 5.316987 AGAGGACCAATTGACCAAGTTTAG 58.683 41.667 18.75 0.00 0.00 1.85
30 31 5.313712 GAGAGGACCAATTGACCAAGTTTA 58.686 41.667 18.75 0.00 0.00 2.01
31 32 4.145052 GAGAGGACCAATTGACCAAGTTT 58.855 43.478 18.75 3.36 0.00 2.66
32 33 3.498661 GGAGAGGACCAATTGACCAAGTT 60.499 47.826 18.75 3.65 0.00 2.66
33 34 2.040412 GGAGAGGACCAATTGACCAAGT 59.960 50.000 18.75 4.58 0.00 3.16
34 35 2.619074 GGGAGAGGACCAATTGACCAAG 60.619 54.545 18.75 1.66 0.00 3.61
35 36 1.354368 GGGAGAGGACCAATTGACCAA 59.646 52.381 18.75 0.00 0.00 3.67
36 37 0.991920 GGGAGAGGACCAATTGACCA 59.008 55.000 18.75 0.00 0.00 4.02
37 38 0.991920 TGGGAGAGGACCAATTGACC 59.008 55.000 7.12 10.06 34.44 4.02
38 39 2.820197 GTTTGGGAGAGGACCAATTGAC 59.180 50.000 7.12 0.40 46.55 3.18
39 40 2.716424 AGTTTGGGAGAGGACCAATTGA 59.284 45.455 7.12 0.00 46.55 2.57
40 41 3.160679 AGTTTGGGAGAGGACCAATTG 57.839 47.619 0.00 0.00 46.55 2.32
41 42 3.117131 ACAAGTTTGGGAGAGGACCAATT 60.117 43.478 0.00 0.00 46.55 2.32
42 43 2.447047 ACAAGTTTGGGAGAGGACCAAT 59.553 45.455 0.00 0.00 46.55 3.16
43 44 1.850345 ACAAGTTTGGGAGAGGACCAA 59.150 47.619 0.00 0.00 45.73 3.67
44 45 1.518367 ACAAGTTTGGGAGAGGACCA 58.482 50.000 0.00 0.00 35.88 4.02
45 46 2.623416 CAAACAAGTTTGGGAGAGGACC 59.377 50.000 15.95 0.00 44.47 4.46
46 47 3.990318 CAAACAAGTTTGGGAGAGGAC 57.010 47.619 15.95 0.00 44.47 3.85
55 56 1.639280 AACAGCGCCAAACAAGTTTG 58.361 45.000 16.62 16.62 46.93 2.93
56 57 3.726291 ATAACAGCGCCAAACAAGTTT 57.274 38.095 2.29 0.00 0.00 2.66
57 58 4.839668 TTATAACAGCGCCAAACAAGTT 57.160 36.364 2.29 0.55 0.00 2.66
58 59 4.542735 GTTTATAACAGCGCCAAACAAGT 58.457 39.130 2.29 0.00 0.00 3.16
59 60 3.917985 GGTTTATAACAGCGCCAAACAAG 59.082 43.478 2.29 0.00 32.11 3.16
60 61 3.570550 AGGTTTATAACAGCGCCAAACAA 59.429 39.130 2.29 0.00 32.11 2.83
61 62 3.150767 AGGTTTATAACAGCGCCAAACA 58.849 40.909 2.29 0.00 32.11 2.83
62 63 3.842732 AGGTTTATAACAGCGCCAAAC 57.157 42.857 2.29 5.35 0.00 2.93
63 64 4.142859 CGTAAGGTTTATAACAGCGCCAAA 60.143 41.667 2.29 0.00 0.00 3.28
64 65 3.371591 CGTAAGGTTTATAACAGCGCCAA 59.628 43.478 2.29 0.00 0.00 4.52
65 66 2.931325 CGTAAGGTTTATAACAGCGCCA 59.069 45.455 2.29 0.00 0.00 5.69
66 67 3.580794 CGTAAGGTTTATAACAGCGCC 57.419 47.619 2.29 0.00 0.00 6.53
81 82 2.348666 GTGTGTGCAGCTATTCCGTAAG 59.651 50.000 0.00 0.00 0.00 2.34
82 83 2.343101 GTGTGTGCAGCTATTCCGTAA 58.657 47.619 0.00 0.00 0.00 3.18
83 84 1.734377 CGTGTGTGCAGCTATTCCGTA 60.734 52.381 0.00 0.00 0.00 4.02
84 85 1.014044 CGTGTGTGCAGCTATTCCGT 61.014 55.000 0.00 0.00 0.00 4.69
85 86 0.735978 TCGTGTGTGCAGCTATTCCG 60.736 55.000 0.00 0.00 0.00 4.30
86 87 0.721718 GTCGTGTGTGCAGCTATTCC 59.278 55.000 0.00 0.00 0.00 3.01
87 88 0.721718 GGTCGTGTGTGCAGCTATTC 59.278 55.000 0.00 0.00 0.00 1.75
88 89 0.321671 AGGTCGTGTGTGCAGCTATT 59.678 50.000 0.00 0.00 0.00 1.73
89 90 0.321671 AAGGTCGTGTGTGCAGCTAT 59.678 50.000 0.00 0.00 0.00 2.97
90 91 0.105964 AAAGGTCGTGTGTGCAGCTA 59.894 50.000 0.00 0.00 0.00 3.32
91 92 0.748005 AAAAGGTCGTGTGTGCAGCT 60.748 50.000 0.00 0.00 0.00 4.24
92 93 0.941542 TAAAAGGTCGTGTGTGCAGC 59.058 50.000 0.00 0.00 0.00 5.25
93 94 2.665519 GCATAAAAGGTCGTGTGTGCAG 60.666 50.000 0.00 0.00 0.00 4.41
94 95 1.265635 GCATAAAAGGTCGTGTGTGCA 59.734 47.619 0.00 0.00 0.00 4.57
95 96 1.265635 TGCATAAAAGGTCGTGTGTGC 59.734 47.619 0.00 0.00 0.00 4.57
96 97 2.661709 CGTGCATAAAAGGTCGTGTGTG 60.662 50.000 0.00 0.00 0.00 3.82
97 98 1.529438 CGTGCATAAAAGGTCGTGTGT 59.471 47.619 0.00 0.00 0.00 3.72
98 99 1.795872 TCGTGCATAAAAGGTCGTGTG 59.204 47.619 0.00 0.00 0.00 3.82
99 100 1.796459 GTCGTGCATAAAAGGTCGTGT 59.204 47.619 0.00 0.00 0.00 4.49
100 101 1.795872 TGTCGTGCATAAAAGGTCGTG 59.204 47.619 0.00 0.00 0.00 4.35
101 102 2.066262 CTGTCGTGCATAAAAGGTCGT 58.934 47.619 0.00 0.00 0.00 4.34
102 103 1.393539 CCTGTCGTGCATAAAAGGTCG 59.606 52.381 0.00 0.00 0.00 4.79
103 104 2.159627 CACCTGTCGTGCATAAAAGGTC 59.840 50.000 9.61 0.00 35.87 3.85
104 105 2.151202 CACCTGTCGTGCATAAAAGGT 58.849 47.619 7.22 7.22 38.57 3.50
105 106 1.468520 CCACCTGTCGTGCATAAAAGG 59.531 52.381 6.07 6.07 41.53 3.11
106 107 2.159627 GTCCACCTGTCGTGCATAAAAG 59.840 50.000 0.00 0.00 41.53 2.27
107 108 2.147958 GTCCACCTGTCGTGCATAAAA 58.852 47.619 0.00 0.00 41.53 1.52
108 109 1.803334 GTCCACCTGTCGTGCATAAA 58.197 50.000 0.00 0.00 41.53 1.40
109 110 0.389296 CGTCCACCTGTCGTGCATAA 60.389 55.000 0.00 0.00 41.53 1.90
110 111 1.214325 CGTCCACCTGTCGTGCATA 59.786 57.895 0.00 0.00 41.53 3.14
111 112 1.888436 ATCGTCCACCTGTCGTGCAT 61.888 55.000 0.00 0.00 41.53 3.96
112 113 2.570284 ATCGTCCACCTGTCGTGCA 61.570 57.895 0.00 0.00 41.53 4.57
113 114 2.094659 CATCGTCCACCTGTCGTGC 61.095 63.158 0.00 0.00 41.53 5.34
114 115 1.446099 CCATCGTCCACCTGTCGTG 60.446 63.158 0.00 0.00 42.62 4.35
115 116 0.609957 TACCATCGTCCACCTGTCGT 60.610 55.000 0.00 0.00 0.00 4.34
116 117 0.100682 CTACCATCGTCCACCTGTCG 59.899 60.000 0.00 0.00 0.00 4.35
117 118 0.460311 CCTACCATCGTCCACCTGTC 59.540 60.000 0.00 0.00 0.00 3.51
118 119 0.040646 TCCTACCATCGTCCACCTGT 59.959 55.000 0.00 0.00 0.00 4.00
119 120 1.341531 GATCCTACCATCGTCCACCTG 59.658 57.143 0.00 0.00 0.00 4.00
120 121 1.218196 AGATCCTACCATCGTCCACCT 59.782 52.381 0.00 0.00 0.00 4.00
121 122 1.341531 CAGATCCTACCATCGTCCACC 59.658 57.143 0.00 0.00 0.00 4.61
122 123 2.307768 TCAGATCCTACCATCGTCCAC 58.692 52.381 0.00 0.00 0.00 4.02
123 124 2.748209 TCAGATCCTACCATCGTCCA 57.252 50.000 0.00 0.00 0.00 4.02
124 125 2.894126 ACATCAGATCCTACCATCGTCC 59.106 50.000 0.00 0.00 0.00 4.79
125 126 4.302455 CAACATCAGATCCTACCATCGTC 58.698 47.826 0.00 0.00 0.00 4.20
126 127 3.493350 GCAACATCAGATCCTACCATCGT 60.493 47.826 0.00 0.00 0.00 3.73
127 128 3.062763 GCAACATCAGATCCTACCATCG 58.937 50.000 0.00 0.00 0.00 3.84
128 129 4.348863 AGCAACATCAGATCCTACCATC 57.651 45.455 0.00 0.00 0.00 3.51
129 130 4.785346 AAGCAACATCAGATCCTACCAT 57.215 40.909 0.00 0.00 0.00 3.55
130 131 4.101585 CCTAAGCAACATCAGATCCTACCA 59.898 45.833 0.00 0.00 0.00 3.25
131 132 4.101741 ACCTAAGCAACATCAGATCCTACC 59.898 45.833 0.00 0.00 0.00 3.18
132 133 5.283457 ACCTAAGCAACATCAGATCCTAC 57.717 43.478 0.00 0.00 0.00 3.18
133 134 6.014242 CCATACCTAAGCAACATCAGATCCTA 60.014 42.308 0.00 0.00 0.00 2.94
134 135 5.221803 CCATACCTAAGCAACATCAGATCCT 60.222 44.000 0.00 0.00 0.00 3.24
135 136 4.999950 CCATACCTAAGCAACATCAGATCC 59.000 45.833 0.00 0.00 0.00 3.36
136 137 5.858381 TCCATACCTAAGCAACATCAGATC 58.142 41.667 0.00 0.00 0.00 2.75
137 138 5.221803 CCTCCATACCTAAGCAACATCAGAT 60.222 44.000 0.00 0.00 0.00 2.90
138 139 4.101585 CCTCCATACCTAAGCAACATCAGA 59.898 45.833 0.00 0.00 0.00 3.27
139 140 4.384056 CCTCCATACCTAAGCAACATCAG 58.616 47.826 0.00 0.00 0.00 2.90
140 141 3.136443 CCCTCCATACCTAAGCAACATCA 59.864 47.826 0.00 0.00 0.00 3.07
141 142 3.391296 TCCCTCCATACCTAAGCAACATC 59.609 47.826 0.00 0.00 0.00 3.06
142 143 3.393687 TCCCTCCATACCTAAGCAACAT 58.606 45.455 0.00 0.00 0.00 2.71
143 144 2.840511 TCCCTCCATACCTAAGCAACA 58.159 47.619 0.00 0.00 0.00 3.33
144 145 4.141482 TGAATCCCTCCATACCTAAGCAAC 60.141 45.833 0.00 0.00 0.00 4.17
145 146 4.044308 TGAATCCCTCCATACCTAAGCAA 58.956 43.478 0.00 0.00 0.00 3.91
146 147 3.664320 TGAATCCCTCCATACCTAAGCA 58.336 45.455 0.00 0.00 0.00 3.91
147 148 4.706842 TTGAATCCCTCCATACCTAAGC 57.293 45.455 0.00 0.00 0.00 3.09
148 149 5.810095 GGATTGAATCCCTCCATACCTAAG 58.190 45.833 13.26 0.00 43.88 2.18
149 150 5.843019 GGATTGAATCCCTCCATACCTAA 57.157 43.478 13.26 0.00 43.88 2.69
162 163 7.041098 ACAGGCTAATAATCGTTGGATTGAATC 60.041 37.037 0.00 0.00 42.72 2.52
163 164 6.772716 ACAGGCTAATAATCGTTGGATTGAAT 59.227 34.615 0.00 0.00 42.72 2.57
164 165 6.038161 CACAGGCTAATAATCGTTGGATTGAA 59.962 38.462 0.00 0.00 42.72 2.69
165 166 5.527214 CACAGGCTAATAATCGTTGGATTGA 59.473 40.000 0.00 0.00 42.72 2.57
166 167 5.296780 ACACAGGCTAATAATCGTTGGATTG 59.703 40.000 0.00 0.00 42.72 2.67
167 168 5.437060 ACACAGGCTAATAATCGTTGGATT 58.563 37.500 0.00 0.00 44.81 3.01
168 169 5.036117 ACACAGGCTAATAATCGTTGGAT 57.964 39.130 0.00 0.00 0.00 3.41
169 170 4.439057 GACACAGGCTAATAATCGTTGGA 58.561 43.478 0.00 0.00 0.00 3.53
170 171 3.245284 CGACACAGGCTAATAATCGTTGG 59.755 47.826 0.00 0.00 0.00 3.77
171 172 3.863424 ACGACACAGGCTAATAATCGTTG 59.137 43.478 0.00 0.00 38.06 4.10
172 173 4.110482 GACGACACAGGCTAATAATCGTT 58.890 43.478 11.17 0.00 41.05 3.85
173 174 3.490419 GGACGACACAGGCTAATAATCGT 60.490 47.826 10.08 10.08 43.42 3.73
174 175 3.050619 GGACGACACAGGCTAATAATCG 58.949 50.000 0.00 0.00 0.00 3.34
175 176 4.054780 TGGACGACACAGGCTAATAATC 57.945 45.455 0.00 0.00 0.00 1.75
176 177 4.380531 CATGGACGACACAGGCTAATAAT 58.619 43.478 0.00 0.00 0.00 1.28
177 178 3.792401 CATGGACGACACAGGCTAATAA 58.208 45.455 0.00 0.00 0.00 1.40
178 179 2.483013 GCATGGACGACACAGGCTAATA 60.483 50.000 7.80 0.00 41.90 0.98
179 180 1.743772 GCATGGACGACACAGGCTAAT 60.744 52.381 7.80 0.00 41.90 1.73
180 181 0.391130 GCATGGACGACACAGGCTAA 60.391 55.000 7.80 0.00 41.90 3.09
181 182 1.218047 GCATGGACGACACAGGCTA 59.782 57.895 7.80 0.00 41.90 3.93
182 183 2.046892 GCATGGACGACACAGGCT 60.047 61.111 7.80 0.00 41.90 4.58
183 184 3.127533 GGCATGGACGACACAGGC 61.128 66.667 0.00 6.80 44.16 4.85
184 185 1.448540 GAGGCATGGACGACACAGG 60.449 63.158 0.00 0.00 0.00 4.00
185 186 1.807165 CGAGGCATGGACGACACAG 60.807 63.158 0.00 0.00 0.00 3.66
186 187 2.261361 CGAGGCATGGACGACACA 59.739 61.111 0.00 0.00 0.00 3.72
187 188 1.805945 GACGAGGCATGGACGACAC 60.806 63.158 0.00 0.00 0.00 3.67
188 189 2.571757 GACGAGGCATGGACGACA 59.428 61.111 0.00 0.00 0.00 4.35
189 190 2.202756 GGACGAGGCATGGACGAC 60.203 66.667 0.00 0.00 0.00 4.34
190 191 3.822192 CGGACGAGGCATGGACGA 61.822 66.667 0.00 0.00 0.00 4.20
192 193 3.950794 TTGCGGACGAGGCATGGAC 62.951 63.158 0.00 0.00 40.62 4.02
193 194 2.739849 TTTTGCGGACGAGGCATGGA 62.740 55.000 0.00 0.00 40.62 3.41
194 195 1.656818 ATTTTGCGGACGAGGCATGG 61.657 55.000 0.00 0.00 40.62 3.66
195 196 0.248215 GATTTTGCGGACGAGGCATG 60.248 55.000 0.00 0.00 40.62 4.06
196 197 0.676466 TGATTTTGCGGACGAGGCAT 60.676 50.000 0.00 0.00 40.62 4.40
197 198 0.676466 ATGATTTTGCGGACGAGGCA 60.676 50.000 0.00 0.00 38.93 4.75
198 199 0.028110 GATGATTTTGCGGACGAGGC 59.972 55.000 0.00 0.00 0.00 4.70
199 200 0.301687 CGATGATTTTGCGGACGAGG 59.698 55.000 0.00 0.00 0.00 4.63
200 201 3.786955 CGATGATTTTGCGGACGAG 57.213 52.632 0.00 0.00 0.00 4.18
206 207 0.168788 ACACAGCCGATGATTTTGCG 59.831 50.000 0.00 0.00 0.00 4.85
207 208 2.792542 GCTACACAGCCGATGATTTTGC 60.793 50.000 0.00 0.00 42.37 3.68
208 209 3.056952 GCTACACAGCCGATGATTTTG 57.943 47.619 0.00 0.00 42.37 2.44
220 221 4.256920 AGGTTTAGAGCAATGCTACACAG 58.743 43.478 8.12 0.00 39.88 3.66
221 222 4.286297 AGGTTTAGAGCAATGCTACACA 57.714 40.909 8.12 0.00 39.88 3.72
222 223 6.737254 TTAAGGTTTAGAGCAATGCTACAC 57.263 37.500 8.12 2.34 39.88 2.90
223 224 6.940298 AGTTTAAGGTTTAGAGCAATGCTACA 59.060 34.615 8.12 0.00 39.88 2.74
224 225 7.379098 AGTTTAAGGTTTAGAGCAATGCTAC 57.621 36.000 8.12 1.98 39.88 3.58
225 226 8.319146 ACTAGTTTAAGGTTTAGAGCAATGCTA 58.681 33.333 8.12 0.00 39.88 3.49
226 227 7.168905 ACTAGTTTAAGGTTTAGAGCAATGCT 58.831 34.615 7.79 7.79 43.88 3.79
227 228 7.334671 AGACTAGTTTAAGGTTTAGAGCAATGC 59.665 37.037 0.00 0.00 0.00 3.56
228 229 8.779354 AGACTAGTTTAAGGTTTAGAGCAATG 57.221 34.615 0.00 0.00 0.00 2.82
255 256 0.468648 GCGGGGAGCTGGTAGTAATT 59.531 55.000 0.00 0.00 44.04 1.40
269 270 0.465705 TCAAGATCTAGCTTGCGGGG 59.534 55.000 0.00 0.00 43.78 5.73
416 427 3.127203 ACTGCAGAGCTAACTACAGTACG 59.873 47.826 23.35 0.00 41.09 3.67
486 497 7.239972 GCTAAGTACAAATCAAGAGCTCTTTG 58.760 38.462 26.44 22.52 33.11 2.77
538 549 1.680735 TGCGAAAATTGCAGGTTCAGT 59.319 42.857 6.83 0.00 37.44 3.41
551 562 5.163893 GGTTTATTCGATCTGACTGCGAAAA 60.164 40.000 13.30 8.28 45.54 2.29
576 587 7.066404 TGCAAAGAGTTGACACTGTATGTAAAA 59.934 33.333 0.00 0.00 43.56 1.52
582 593 4.708177 AGTGCAAAGAGTTGACACTGTAT 58.292 39.130 12.51 0.00 43.86 2.29
596 607 2.550830 ACCTACAGGACAGTGCAAAG 57.449 50.000 1.29 0.00 38.94 2.77
613 624 4.081697 AGGGCATTAATTGTTGCAAGTACC 60.082 41.667 0.00 7.36 40.66 3.34
664 679 9.078990 AGCAGATTGTACTACATGCTACTTATA 57.921 33.333 12.24 0.00 39.39 0.98
665 680 7.957002 AGCAGATTGTACTACATGCTACTTAT 58.043 34.615 12.24 0.00 39.39 1.73
764 920 7.315247 TGTCTCTTTCAATCGTTTTTCTTCA 57.685 32.000 0.00 0.00 0.00 3.02
887 1047 7.039644 GCTCTAGGTATCAAGGTTCTAATGCTA 60.040 40.741 0.00 0.00 0.00 3.49
924 1106 1.896465 AGCTGAAGTGTGGACTAGGAC 59.104 52.381 0.00 0.00 0.00 3.85
978 1166 2.033141 TCTTGTGCTGAGGCTGGC 59.967 61.111 0.00 0.00 39.59 4.85
1197 1395 1.107945 TGAGGTTGTCGCGGATGATA 58.892 50.000 6.13 0.00 0.00 2.15
1299 1497 4.344865 GGGCCAAGGAGGTCGCAA 62.345 66.667 4.39 0.00 45.54 4.85
1356 1554 1.529438 ACGGACATACAAAACACAGCG 59.471 47.619 0.00 0.00 0.00 5.18
1359 1557 4.816925 TCAATGACGGACATACAAAACACA 59.183 37.500 0.00 0.00 38.38 3.72
1368 1566 3.038280 AGGACCATCAATGACGGACATA 58.962 45.455 1.02 0.00 38.38 2.29
1398 1596 4.082733 CCGATGAGGAAGCGAATAGTGATA 60.083 45.833 0.00 0.00 45.00 2.15
1407 1605 0.965866 AGACACCGATGAGGAAGCGA 60.966 55.000 0.00 0.00 45.00 4.93
1431 1629 0.798776 GACATGAGACAAAGGTGGCG 59.201 55.000 0.00 0.00 38.10 5.69
1515 1713 2.088096 ACCACCCATGTCACCCCAA 61.088 57.895 0.00 0.00 0.00 4.12
1590 1788 1.996786 GCCATGCCATGAAGGACGTG 61.997 60.000 6.18 0.00 41.22 4.49
1680 1878 4.955335 TCCTTAGGTTACCATCAGGAAGA 58.045 43.478 12.16 0.00 38.69 2.87
1785 1983 5.586243 GCAGTAGCCATAGATGAAGACAAAA 59.414 40.000 0.00 0.00 33.58 2.44
2007 2205 3.314331 CCACCGGCTGTCTGGAGT 61.314 66.667 0.00 0.00 41.45 3.85
2519 2717 6.854496 AAAAACTGAAGACTTATACGTGCA 57.146 33.333 0.00 0.00 0.00 4.57
2582 2796 3.839353 CTCGATCCCAGGGGCATGC 62.839 68.421 9.90 9.90 34.68 4.06
3029 3338 4.793216 GCATTGCCATCGTAAACTAAAGTG 59.207 41.667 0.00 0.00 0.00 3.16
3037 3346 1.401552 GAGCTGCATTGCCATCGTAAA 59.598 47.619 6.12 0.00 0.00 2.01
3061 3370 4.956085 TCCTTATTTCTAATAGCAGCGCA 58.044 39.130 11.47 0.00 0.00 6.09
3062 3371 5.064071 GGATCCTTATTTCTAATAGCAGCGC 59.936 44.000 3.84 0.00 0.00 5.92
3134 3443 4.979815 AGCGCCAACAAATTAAGTAAACAC 59.020 37.500 2.29 0.00 0.00 3.32
3207 3516 5.540719 ACCTACTCTCATACTAATTCCAGGC 59.459 44.000 0.00 0.00 0.00 4.85
3319 3632 9.837525 TTTCACTTTCGTCTCTCTTATTAGTAC 57.162 33.333 0.00 0.00 0.00 2.73
3320 3633 9.837525 GTTTCACTTTCGTCTCTCTTATTAGTA 57.162 33.333 0.00 0.00 0.00 1.82
3321 3634 8.578151 AGTTTCACTTTCGTCTCTCTTATTAGT 58.422 33.333 0.00 0.00 0.00 2.24
3335 3648 2.734079 GCTGAGAGGAGTTTCACTTTCG 59.266 50.000 0.00 0.00 0.00 3.46
3354 3667 0.182775 ACCTGGAAAGTTCAACGGCT 59.817 50.000 0.00 0.00 0.00 5.52
3362 3687 4.657039 TGGTGAGTAAGTACCTGGAAAGTT 59.343 41.667 0.00 0.00 37.84 2.66


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

AutoCloner maintained by Alex Coulton.