Multiple sequence alignment - TraesCS5A01G194500

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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 TraesCS5A01G194500 chr5A 100.000 6238 0 0 1 6238 398188267 398194504 0.000000e+00 11520.0
1 TraesCS5A01G194500 chr5A 84.868 304 44 2 3610 3912 401954335 401954637 7.860000e-79 305.0
2 TraesCS5A01G194500 chr5A 90.968 155 10 3 11 162 595886802 595886955 8.200000e-49 206.0
3 TraesCS5A01G194500 chr5A 97.222 36 1 0 538 573 496564272 496564237 1.880000e-05 62.1
4 TraesCS5A01G194500 chr5A 94.737 38 1 1 538 574 568891615 568891578 2.430000e-04 58.4
5 TraesCS5A01G194500 chr5D 95.238 4788 175 19 1473 6238 300948683 300943927 0.000000e+00 7529.0
6 TraesCS5A01G194500 chr5D 95.743 1104 39 5 576 1679 300949680 300948585 0.000000e+00 1772.0
7 TraesCS5A01G194500 chr5D 85.149 303 45 0 3610 3912 297151519 297151217 1.690000e-80 311.0
8 TraesCS5A01G194500 chr5D 85.135 296 26 5 159 453 300953913 300953635 2.850000e-73 287.0
9 TraesCS5A01G194500 chr5D 89.714 175 13 4 6064 6235 503265298 503265470 1.050000e-52 219.0
10 TraesCS5A01G194500 chr5D 76.923 169 35 4 2548 2714 297152446 297152280 6.660000e-15 93.5
11 TraesCS5A01G194500 chr5D 97.500 40 1 0 5768 5807 439641756 439641795 1.120000e-07 69.4
12 TraesCS5A01G194500 chr5B 96.022 4198 144 17 1488 5674 344286473 344290658 0.000000e+00 6806.0
13 TraesCS5A01G194500 chr5B 94.823 1101 52 5 576 1676 344285458 344286553 0.000000e+00 1712.0
14 TraesCS5A01G194500 chr5B 88.276 290 24 7 159 447 344281688 344281968 7.750000e-89 339.0
15 TraesCS5A01G194500 chr5B 85.149 303 45 0 3610 3912 337189754 337189452 1.690000e-80 311.0
16 TraesCS5A01G194500 chr5B 89.714 175 13 4 6064 6235 679664843 679665015 1.050000e-52 219.0
17 TraesCS5A01G194500 chr5B 97.143 35 1 0 538 572 450041873 450041839 6.750000e-05 60.2
18 TraesCS5A01G194500 chr5B 100.000 28 0 0 5887 5914 545190631 545190658 1.100000e-02 52.8
19 TraesCS5A01G194500 chrUn 89.888 178 14 3 6064 6238 416411451 416411275 6.290000e-55 226.0
20 TraesCS5A01G194500 chrUn 89.714 175 13 4 6064 6235 43670747 43670919 1.050000e-52 219.0
21 TraesCS5A01G194500 chr7D 89.326 178 13 4 6064 6238 595072169 595071995 1.050000e-52 219.0
22 TraesCS5A01G194500 chr7D 95.455 44 2 0 5874 5917 88715142 88715185 3.120000e-08 71.3
23 TraesCS5A01G194500 chr7D 84.286 70 9 2 5749 5816 265692538 265692607 4.040000e-07 67.6
24 TraesCS5A01G194500 chr7D 96.970 33 1 0 540 572 81375782 81375814 8.740000e-04 56.5
25 TraesCS5A01G194500 chr6D 89.714 175 13 4 6064 6235 389245815 389245987 1.050000e-52 219.0
26 TraesCS5A01G194500 chr6D 89.697 165 14 1 1 162 381526634 381526470 2.280000e-49 207.0
27 TraesCS5A01G194500 chr1A 89.326 178 14 4 6064 6238 526831030 526830855 1.050000e-52 219.0
28 TraesCS5A01G194500 chr1A 89.326 178 14 4 6064 6238 526831508 526831333 1.050000e-52 219.0
29 TraesCS5A01G194500 chr3A 89.441 161 17 0 1 161 93909677 93909517 2.950000e-48 204.0
30 TraesCS5A01G194500 chr7B 89.308 159 13 3 3 161 584028863 584029017 4.930000e-46 196.0
31 TraesCS5A01G194500 chr7B 83.562 73 9 2 5753 5824 245993819 245993889 1.450000e-06 65.8
32 TraesCS5A01G194500 chr4A 90.066 151 15 0 11 161 651824411 651824261 4.930000e-46 196.0
33 TraesCS5A01G194500 chr4A 88.272 162 19 0 1 162 24564545 24564706 1.770000e-45 195.0
34 TraesCS5A01G194500 chr3D 88.415 164 13 5 1 162 64696019 64695860 6.380000e-45 193.0
35 TraesCS5A01G194500 chr1B 87.654 162 18 2 1 162 370368839 370368680 2.970000e-43 187.0
36 TraesCS5A01G194500 chr4D 87.730 163 14 5 1 163 445102208 445102364 1.070000e-42 185.0
37 TraesCS5A01G194500 chr4D 85.294 68 7 3 5812 5878 338442167 338442232 4.040000e-07 67.6
38 TraesCS5A01G194500 chr3B 93.878 49 3 0 5768 5816 507132311 507132359 2.410000e-09 75.0
39 TraesCS5A01G194500 chr3B 96.970 33 1 0 540 572 545410097 545410129 8.740000e-04 56.5
40 TraesCS5A01G194500 chr2B 90.909 55 4 1 5763 5816 679898246 679898300 8.670000e-09 73.1
41 TraesCS5A01G194500 chr2A 90.909 55 4 1 5763 5816 706752901 706752955 8.670000e-09 73.1
42 TraesCS5A01G194500 chr2D 89.091 55 5 1 5763 5816 566988998 566989052 4.040000e-07 67.6
43 TraesCS5A01G194500 chr2D 89.796 49 5 0 5768 5816 179329839 179329791 5.220000e-06 63.9
44 TraesCS5A01G194500 chr2D 94.737 38 1 1 538 574 76557695 76557658 2.430000e-04 58.4
45 TraesCS5A01G194500 chr2D 96.970 33 1 0 540 572 410234547 410234515 8.740000e-04 56.5
46 TraesCS5A01G194500 chr4B 93.182 44 2 1 5874 5917 669918118 669918076 5.220000e-06 63.9
47 TraesCS5A01G194500 chr4B 97.059 34 1 0 5827 5860 417537423 417537456 2.430000e-04 58.4
48 TraesCS5A01G194500 chr1D 92.683 41 1 2 540 578 490330003 490329963 2.430000e-04 58.4
49 TraesCS5A01G194500 chr6B 96.970 33 1 0 540 572 672051859 672051827 8.740000e-04 56.5
50 TraesCS5A01G194500 chr6A 100.000 29 0 0 5887 5915 60491892 60491864 3.000000e-03 54.7


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 TraesCS5A01G194500 chr5A 398188267 398194504 6237 False 11520.000000 11520 100.000000 1 6238 1 chr5A.!!$F1 6237
1 TraesCS5A01G194500 chr5D 300943927 300953913 9986 True 3196.000000 7529 92.038667 159 6238 3 chr5D.!!$R2 6079
2 TraesCS5A01G194500 chr5D 297151217 297152446 1229 True 202.250000 311 81.036000 2548 3912 2 chr5D.!!$R1 1364
3 TraesCS5A01G194500 chr5B 344281688 344290658 8970 False 2952.333333 6806 93.040333 159 5674 3 chr5B.!!$F3 5515
4 TraesCS5A01G194500 chr1A 526830855 526831508 653 True 219.000000 219 89.326000 6064 6238 2 chr1A.!!$R1 174

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
110 111 0.036388 GGCTGAAAGTGATGGGACGA 60.036 55.000 0.00 0.0 35.30 4.20 F
1004 5707 0.242017 GTCTGTGCAAGGTGAATGCC 59.758 55.000 0.00 0.0 43.16 4.40 F
2036 6847 0.108662 CCATCTCAGCTGTACGCACA 60.109 55.000 14.67 0.0 42.61 4.57 F
2095 6906 0.322975 GGCAGCAGAGTTGAGGAAGA 59.677 55.000 0.00 0.0 0.00 2.87 F
2138 6949 0.834687 TCAGTTTCGCTACCAGGGGT 60.835 55.000 0.00 0.0 40.16 4.95 F
2698 7512 1.067565 TGCTAGTGCTTCCAACTCTCG 60.068 52.381 0.00 0.0 40.48 4.04 F
2764 7578 1.275573 GGACGCTACTCCAAGGAAAGT 59.724 52.381 0.00 0.0 0.00 2.66 F
4240 9215 1.134670 AGCGAGCTAACTAAAGGCTGG 60.135 52.381 0.00 0.0 36.37 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1556 6259 0.390340 CCCTGTCCATGTGTGTCTCG 60.390 60.000 0.00 0.0 0.00 4.04 R
2624 7438 0.102481 CTGGAGCCATCAATGCTTGC 59.898 55.000 0.00 0.0 39.69 4.01 R
3102 7919 1.314730 ACAACAACACCGGGAACATC 58.685 50.000 6.32 0.0 0.00 3.06 R
3482 8306 2.491693 CCAACAATCCACCACCACATAC 59.508 50.000 0.00 0.0 0.00 2.39 R
3556 8380 3.806949 AAGCTAATTCAGGTTGACCCA 57.193 42.857 0.00 0.0 43.32 4.51 R
4235 9210 1.214589 CTGCATGCAGTTTCCAGCC 59.785 57.895 34.76 0.0 39.10 4.85 R
4581 9556 3.181520 GGTTGATGAATCTTCCGACGTTG 60.182 47.826 0.00 0.0 0.00 4.10 R
6152 11611 0.753111 GATGGCCCGGAGAAAGCAAT 60.753 55.000 0.73 0.0 0.00 3.56 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
31 32 2.702592 TTTTCGTTGTGTGAGAGGGT 57.297 45.000 0.00 0.00 0.00 4.34
32 33 1.948104 TTTCGTTGTGTGAGAGGGTG 58.052 50.000 0.00 0.00 0.00 4.61
33 34 1.116308 TTCGTTGTGTGAGAGGGTGA 58.884 50.000 0.00 0.00 0.00 4.02
34 35 1.338107 TCGTTGTGTGAGAGGGTGAT 58.662 50.000 0.00 0.00 0.00 3.06
35 36 1.000843 TCGTTGTGTGAGAGGGTGATG 59.999 52.381 0.00 0.00 0.00 3.07
36 37 1.160137 GTTGTGTGAGAGGGTGATGC 58.840 55.000 0.00 0.00 0.00 3.91
37 38 0.320683 TTGTGTGAGAGGGTGATGCG 60.321 55.000 0.00 0.00 0.00 4.73
38 39 1.184970 TGTGTGAGAGGGTGATGCGA 61.185 55.000 0.00 0.00 0.00 5.10
39 40 0.037326 GTGTGAGAGGGTGATGCGAA 60.037 55.000 0.00 0.00 0.00 4.70
40 41 0.684535 TGTGAGAGGGTGATGCGAAA 59.315 50.000 0.00 0.00 0.00 3.46
41 42 1.079503 GTGAGAGGGTGATGCGAAAC 58.920 55.000 0.00 0.00 0.00 2.78
42 43 0.976641 TGAGAGGGTGATGCGAAACT 59.023 50.000 0.00 0.00 0.00 2.66
43 44 2.094182 GTGAGAGGGTGATGCGAAACTA 60.094 50.000 0.00 0.00 0.00 2.24
44 45 2.565391 TGAGAGGGTGATGCGAAACTAA 59.435 45.455 0.00 0.00 0.00 2.24
45 46 3.007506 TGAGAGGGTGATGCGAAACTAAA 59.992 43.478 0.00 0.00 0.00 1.85
46 47 3.335579 AGAGGGTGATGCGAAACTAAAC 58.664 45.455 0.00 0.00 0.00 2.01
47 48 3.008049 AGAGGGTGATGCGAAACTAAACT 59.992 43.478 0.00 0.00 0.00 2.66
48 49 3.074412 AGGGTGATGCGAAACTAAACTG 58.926 45.455 0.00 0.00 0.00 3.16
49 50 2.161609 GGGTGATGCGAAACTAAACTGG 59.838 50.000 0.00 0.00 0.00 4.00
50 51 2.812011 GGTGATGCGAAACTAAACTGGT 59.188 45.455 0.00 0.00 0.00 4.00
51 52 3.364964 GGTGATGCGAAACTAAACTGGTG 60.365 47.826 0.00 0.00 0.00 4.17
52 53 2.811431 TGATGCGAAACTAAACTGGTGG 59.189 45.455 0.00 0.00 0.00 4.61
53 54 1.600023 TGCGAAACTAAACTGGTGGG 58.400 50.000 0.00 0.00 0.00 4.61
54 55 1.141254 TGCGAAACTAAACTGGTGGGA 59.859 47.619 0.00 0.00 0.00 4.37
55 56 2.224670 TGCGAAACTAAACTGGTGGGAT 60.225 45.455 0.00 0.00 0.00 3.85
56 57 2.161609 GCGAAACTAAACTGGTGGGATG 59.838 50.000 0.00 0.00 0.00 3.51
57 58 2.747446 CGAAACTAAACTGGTGGGATGG 59.253 50.000 0.00 0.00 0.00 3.51
58 59 2.899303 AACTAAACTGGTGGGATGGG 57.101 50.000 0.00 0.00 0.00 4.00
59 60 0.999712 ACTAAACTGGTGGGATGGGG 59.000 55.000 0.00 0.00 0.00 4.96
60 61 0.258774 CTAAACTGGTGGGATGGGGG 59.741 60.000 0.00 0.00 0.00 5.40
61 62 0.178828 TAAACTGGTGGGATGGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
62 63 1.509548 AAACTGGTGGGATGGGGGAG 61.510 60.000 0.00 0.00 0.00 4.30
63 64 3.099170 CTGGTGGGATGGGGGAGG 61.099 72.222 0.00 0.00 0.00 4.30
64 65 4.777546 TGGTGGGATGGGGGAGGG 62.778 72.222 0.00 0.00 0.00 4.30
66 67 4.448340 GTGGGATGGGGGAGGGGA 62.448 72.222 0.00 0.00 0.00 4.81
67 68 4.448340 TGGGATGGGGGAGGGGAC 62.448 72.222 0.00 0.00 0.00 4.46
69 70 4.492303 GGATGGGGGAGGGGACGA 62.492 72.222 0.00 0.00 0.00 4.20
70 71 2.366435 GATGGGGGAGGGGACGAA 60.366 66.667 0.00 0.00 0.00 3.85
71 72 1.999002 GATGGGGGAGGGGACGAAA 60.999 63.158 0.00 0.00 0.00 3.46
72 73 1.542881 ATGGGGGAGGGGACGAAAA 60.543 57.895 0.00 0.00 0.00 2.29
73 74 1.143970 ATGGGGGAGGGGACGAAAAA 61.144 55.000 0.00 0.00 0.00 1.94
92 93 3.291809 AAACCCAGCGAAATAAAACGG 57.708 42.857 0.00 0.00 0.00 4.44
93 94 0.524414 ACCCAGCGAAATAAAACGGC 59.476 50.000 0.00 0.00 0.00 5.68
94 95 0.808755 CCCAGCGAAATAAAACGGCT 59.191 50.000 0.00 0.00 0.00 5.52
95 96 1.467374 CCCAGCGAAATAAAACGGCTG 60.467 52.381 4.45 4.45 35.37 4.85
96 97 1.466950 CCAGCGAAATAAAACGGCTGA 59.533 47.619 12.45 0.00 36.55 4.26
97 98 2.095466 CCAGCGAAATAAAACGGCTGAA 60.095 45.455 12.45 0.00 36.55 3.02
98 99 3.560503 CAGCGAAATAAAACGGCTGAAA 58.439 40.909 0.00 0.00 36.55 2.69
99 100 3.603770 CAGCGAAATAAAACGGCTGAAAG 59.396 43.478 0.00 0.00 36.55 2.62
100 101 3.252458 AGCGAAATAAAACGGCTGAAAGT 59.748 39.130 0.00 0.00 35.30 2.66
101 102 3.360758 GCGAAATAAAACGGCTGAAAGTG 59.639 43.478 0.00 0.00 35.30 3.16
102 103 4.778904 CGAAATAAAACGGCTGAAAGTGA 58.221 39.130 0.00 0.00 35.30 3.41
103 104 5.390613 CGAAATAAAACGGCTGAAAGTGAT 58.609 37.500 0.00 0.00 35.30 3.06
104 105 5.283717 CGAAATAAAACGGCTGAAAGTGATG 59.716 40.000 0.00 0.00 35.30 3.07
105 106 4.701956 ATAAAACGGCTGAAAGTGATGG 57.298 40.909 0.00 0.00 35.30 3.51
106 107 1.247567 AAACGGCTGAAAGTGATGGG 58.752 50.000 0.00 0.00 35.30 4.00
107 108 0.400213 AACGGCTGAAAGTGATGGGA 59.600 50.000 0.00 0.00 35.30 4.37
108 109 0.321653 ACGGCTGAAAGTGATGGGAC 60.322 55.000 0.00 0.00 35.30 4.46
109 110 1.361668 CGGCTGAAAGTGATGGGACG 61.362 60.000 0.00 0.00 35.30 4.79
110 111 0.036388 GGCTGAAAGTGATGGGACGA 60.036 55.000 0.00 0.00 35.30 4.20
111 112 1.610624 GGCTGAAAGTGATGGGACGAA 60.611 52.381 0.00 0.00 35.30 3.85
112 113 2.151202 GCTGAAAGTGATGGGACGAAA 58.849 47.619 0.00 0.00 35.30 3.46
113 114 2.552315 GCTGAAAGTGATGGGACGAAAA 59.448 45.455 0.00 0.00 35.30 2.29
114 115 3.191371 GCTGAAAGTGATGGGACGAAAAT 59.809 43.478 0.00 0.00 35.30 1.82
115 116 4.394920 GCTGAAAGTGATGGGACGAAAATA 59.605 41.667 0.00 0.00 35.30 1.40
116 117 5.106317 GCTGAAAGTGATGGGACGAAAATAA 60.106 40.000 0.00 0.00 35.30 1.40
117 118 6.569610 GCTGAAAGTGATGGGACGAAAATAAA 60.570 38.462 0.00 0.00 35.30 1.40
118 119 7.461182 TGAAAGTGATGGGACGAAAATAAAT 57.539 32.000 0.00 0.00 0.00 1.40
119 120 7.535139 TGAAAGTGATGGGACGAAAATAAATC 58.465 34.615 0.00 0.00 0.00 2.17
120 121 7.175816 TGAAAGTGATGGGACGAAAATAAATCA 59.824 33.333 0.00 0.00 0.00 2.57
121 122 7.645058 AAGTGATGGGACGAAAATAAATCAT 57.355 32.000 0.00 0.00 0.00 2.45
122 123 7.031226 AGTGATGGGACGAAAATAAATCATG 57.969 36.000 0.00 0.00 0.00 3.07
123 124 6.039717 AGTGATGGGACGAAAATAAATCATGG 59.960 38.462 0.00 0.00 0.00 3.66
124 125 6.039270 GTGATGGGACGAAAATAAATCATGGA 59.961 38.462 0.00 0.00 0.00 3.41
125 126 6.777091 TGATGGGACGAAAATAAATCATGGAT 59.223 34.615 0.00 0.00 0.00 3.41
126 127 7.941790 TGATGGGACGAAAATAAATCATGGATA 59.058 33.333 0.00 0.00 0.00 2.59
127 128 7.504924 TGGGACGAAAATAAATCATGGATAC 57.495 36.000 0.00 0.00 0.00 2.24
128 129 7.287061 TGGGACGAAAATAAATCATGGATACT 58.713 34.615 0.00 0.00 37.61 2.12
129 130 8.433599 TGGGACGAAAATAAATCATGGATACTA 58.566 33.333 0.00 0.00 37.61 1.82
130 131 9.449719 GGGACGAAAATAAATCATGGATACTAT 57.550 33.333 0.00 0.00 37.61 2.12
141 142 8.682936 AATCATGGATACTATTCAACCAACTC 57.317 34.615 0.00 0.00 34.28 3.01
142 143 7.194112 TCATGGATACTATTCAACCAACTCA 57.806 36.000 0.00 0.00 34.28 3.41
143 144 7.629157 TCATGGATACTATTCAACCAACTCAA 58.371 34.615 0.00 0.00 34.28 3.02
144 145 8.106462 TCATGGATACTATTCAACCAACTCAAA 58.894 33.333 0.00 0.00 34.28 2.69
145 146 7.681939 TGGATACTATTCAACCAACTCAAAC 57.318 36.000 0.00 0.00 37.61 2.93
146 147 7.227873 TGGATACTATTCAACCAACTCAAACA 58.772 34.615 0.00 0.00 37.61 2.83
147 148 7.888021 TGGATACTATTCAACCAACTCAAACAT 59.112 33.333 0.00 0.00 37.61 2.71
148 149 8.739972 GGATACTATTCAACCAACTCAAACATT 58.260 33.333 0.00 0.00 0.00 2.71
152 153 9.349713 ACTATTCAACCAACTCAAACATTAAGA 57.650 29.630 0.00 0.00 0.00 2.10
153 154 9.831737 CTATTCAACCAACTCAAACATTAAGAG 57.168 33.333 0.00 0.00 35.56 2.85
154 155 7.639113 TTCAACCAACTCAAACATTAAGAGT 57.361 32.000 0.00 0.00 43.98 3.24
155 156 8.740123 TTCAACCAACTCAAACATTAAGAGTA 57.260 30.769 0.00 0.00 41.45 2.59
156 157 8.378172 TCAACCAACTCAAACATTAAGAGTAG 57.622 34.615 0.00 0.00 41.45 2.57
157 158 8.208224 TCAACCAACTCAAACATTAAGAGTAGA 58.792 33.333 0.00 0.00 41.45 2.59
176 177 9.052365 AGAGTAGAGATTTATTTTTCCTCTGGT 57.948 33.333 0.00 0.00 35.93 4.00
244 245 7.634671 AAAAACCCCGAAACCAATAGTATAG 57.365 36.000 0.00 0.00 0.00 1.31
245 246 5.963214 AACCCCGAAACCAATAGTATAGT 57.037 39.130 0.00 0.00 0.00 2.12
311 312 9.772973 AAACGCTTTTATAGTATGTGATGGATA 57.227 29.630 0.00 0.00 0.00 2.59
369 370 7.308589 CCAGATTTAAGGAGACGTGAATTTTGT 60.309 37.037 0.00 0.00 28.70 2.83
379 380 4.822026 ACGTGAATTTTGTGGAACCAAAA 58.178 34.783 0.00 2.01 45.43 2.44
410 411 1.411041 ATAGGTCAGGTCGGTTAGGC 58.589 55.000 0.00 0.00 0.00 3.93
447 448 3.005472 ACACACAGTACAGACATAAGCGT 59.995 43.478 0.00 0.00 0.00 5.07
449 450 4.447724 CACACAGTACAGACATAAGCGTTT 59.552 41.667 0.00 0.00 0.00 3.60
453 454 8.195436 ACACAGTACAGACATAAGCGTTTATAT 58.805 33.333 4.07 0.00 0.00 0.86
454 455 9.673454 CACAGTACAGACATAAGCGTTTATATA 57.327 33.333 4.07 0.00 0.00 0.86
470 471 8.703823 CGTTTATATATACGCGCATATACTCA 57.296 34.615 18.84 7.01 0.00 3.41
471 472 9.326339 CGTTTATATATACGCGCATATACTCAT 57.674 33.333 18.84 8.83 0.00 2.90
477 478 2.995939 ACGCGCATATACTCATCCAATG 59.004 45.455 5.73 0.00 0.00 2.82
481 482 4.452114 GCGCATATACTCATCCAATGAACA 59.548 41.667 0.30 0.00 39.11 3.18
483 484 5.388786 CGCATATACTCATCCAATGAACACG 60.389 44.000 0.00 0.00 39.11 4.49
484 485 5.466728 GCATATACTCATCCAATGAACACGT 59.533 40.000 0.00 0.00 39.11 4.49
489 490 2.990514 TCATCCAATGAACACGTACACG 59.009 45.455 0.00 0.00 39.95 4.49
499 500 1.475280 ACACGTACACGCACATCCTAT 59.525 47.619 0.85 0.00 44.43 2.57
500 501 2.094390 ACACGTACACGCACATCCTATT 60.094 45.455 0.85 0.00 44.43 1.73
580 5283 0.968901 TACCACGGTCCTCATTCGCT 60.969 55.000 0.00 0.00 0.00 4.93
591 5294 2.093973 CCTCATTCGCTGTTAGGTCAGT 60.094 50.000 0.00 0.00 37.70 3.41
739 5442 7.466746 TTCTCTTCCCCAAACATAGATTTTG 57.533 36.000 0.00 0.00 34.31 2.44
740 5443 6.552008 TCTCTTCCCCAAACATAGATTTTGT 58.448 36.000 0.00 0.00 32.92 2.83
742 5445 7.176690 TCTCTTCCCCAAACATAGATTTTGTTC 59.823 37.037 0.00 0.00 36.32 3.18
745 5448 7.610580 TCCCCAAACATAGATTTTGTTCTTT 57.389 32.000 0.00 0.00 36.32 2.52
747 5450 7.930865 TCCCCAAACATAGATTTTGTTCTTTTG 59.069 33.333 0.00 0.00 36.32 2.44
754 5457 9.868277 ACATAGATTTTGTTCTTTTGTTGTTGA 57.132 25.926 0.00 0.00 0.00 3.18
945 5648 1.600636 CACCCACATCGCCAACAGT 60.601 57.895 0.00 0.00 0.00 3.55
1004 5707 0.242017 GTCTGTGCAAGGTGAATGCC 59.758 55.000 0.00 0.00 43.16 4.40
1102 5805 6.774170 AGGGTTTGGTTCTTATCTTTTACGTT 59.226 34.615 0.00 0.00 0.00 3.99
1103 5806 7.286087 AGGGTTTGGTTCTTATCTTTTACGTTT 59.714 33.333 0.00 0.00 0.00 3.60
1144 5847 6.039382 CCTTTCTTTTATCCGGATTTGTAGGG 59.961 42.308 24.71 11.72 0.00 3.53
1351 6054 1.153369 CCAATGGCGTCATCGAGGT 60.153 57.895 1.37 0.00 39.71 3.85
1354 6057 0.465705 AATGGCGTCATCGAGGTCAT 59.534 50.000 1.37 0.00 43.15 3.06
1358 6061 1.067212 GGCGTCATCGAGGTCATAGTT 59.933 52.381 0.00 0.00 39.71 2.24
1443 6146 4.689549 TGGCGGAGGGGACGAAGA 62.690 66.667 0.00 0.00 0.00 2.87
1556 6259 2.741055 GGAGAGGAAGGAGGGCAGC 61.741 68.421 0.00 0.00 0.00 5.25
1650 6353 2.365635 AGACCGAGGGGATGGTGG 60.366 66.667 0.00 0.00 38.99 4.61
1688 6499 4.681978 GAGGCGCAACCGTCCAGT 62.682 66.667 10.83 0.00 46.52 4.00
1695 6506 3.484806 AACCGTCCAGTGGTGGCA 61.485 61.111 19.21 0.00 44.60 4.92
1767 6578 0.398696 TGCTGCCCCGAAGAGTTTTA 59.601 50.000 0.00 0.00 0.00 1.52
1928 6739 2.094906 GGAAAACAGAACGGGTAATGGC 60.095 50.000 0.00 0.00 0.00 4.40
1963 6774 1.350351 AGAGGATGGGCATGATACAGC 59.650 52.381 0.00 0.00 0.00 4.40
1976 6787 5.586339 CATGATACAGCGAGAAAGAAGAGA 58.414 41.667 0.00 0.00 0.00 3.10
2035 6846 1.424493 GCCATCTCAGCTGTACGCAC 61.424 60.000 14.67 0.00 42.61 5.34
2036 6847 0.108662 CCATCTCAGCTGTACGCACA 60.109 55.000 14.67 0.00 42.61 4.57
2060 6871 2.352805 CCTGGCTGTGGAAGGGAC 59.647 66.667 0.00 0.00 0.00 4.46
2095 6906 0.322975 GGCAGCAGAGTTGAGGAAGA 59.677 55.000 0.00 0.00 0.00 2.87
2138 6949 0.834687 TCAGTTTCGCTACCAGGGGT 60.835 55.000 0.00 0.00 40.16 4.95
2167 6978 2.351276 GGATGCCTTGACCACGGT 59.649 61.111 0.00 0.00 0.00 4.83
2173 6984 1.302511 CCTTGACCACGGTTCCAGG 60.303 63.158 0.00 0.00 0.00 4.45
2306 7120 1.519408 GAAGCTTGCGGAAAGGTACA 58.481 50.000 2.10 0.00 45.87 2.90
2307 7121 1.877443 GAAGCTTGCGGAAAGGTACAA 59.123 47.619 2.10 0.00 45.87 2.41
2309 7123 1.202770 AGCTTGCGGAAAGGTACAACT 60.203 47.619 0.00 0.00 44.77 3.16
2310 7124 2.038033 AGCTTGCGGAAAGGTACAACTA 59.962 45.455 0.00 0.00 44.77 2.24
2311 7125 2.809696 GCTTGCGGAAAGGTACAACTAA 59.190 45.455 0.00 0.00 36.30 2.24
2376 7190 1.522668 CAAGCGACCAAAGGATGTCA 58.477 50.000 0.00 0.00 0.00 3.58
2446 7260 3.005367 ACGCCGGAAAACAAGAATTCAAT 59.995 39.130 5.05 0.00 0.00 2.57
2484 7298 2.753055 TAGTAACACGAAGCATGGCA 57.247 45.000 0.00 0.00 0.00 4.92
2698 7512 1.067565 TGCTAGTGCTTCCAACTCTCG 60.068 52.381 0.00 0.00 40.48 4.04
2711 7525 4.079901 TCCAACTCTCGTACTCCTAGGAAT 60.080 45.833 13.77 5.21 0.00 3.01
2764 7578 1.275573 GGACGCTACTCCAAGGAAAGT 59.724 52.381 0.00 0.00 0.00 2.66
2768 7582 5.163478 GGACGCTACTCCAAGGAAAGTATTA 60.163 44.000 0.00 0.00 0.00 0.98
2816 7630 2.159198 GGCCGTGCATGAGAAAATTGAT 60.159 45.455 7.72 0.00 0.00 2.57
2848 7662 3.618351 ACTCTTGCTTGGAAGATGATGG 58.382 45.455 5.11 0.00 31.51 3.51
2858 7672 3.980022 TGGAAGATGATGGCAACCCTATA 59.020 43.478 0.00 0.00 0.00 1.31
2866 7680 3.140325 TGGCAACCCTATAGCATTAGC 57.860 47.619 0.00 0.00 42.56 3.09
3024 7841 5.391203 GCCGAGGAACAACAATTACGTAATT 60.391 40.000 24.43 24.43 36.39 1.40
3032 7849 9.453325 GAACAACAATTACGTAATTTTGGAAGA 57.547 29.630 31.54 8.85 33.88 2.87
3048 7865 2.555227 GGAAGAATTGACCTTGAGGCCA 60.555 50.000 5.01 0.00 39.32 5.36
3290 8107 8.256605 TCTAGCTCGGACGAGTTAATATATACT 58.743 37.037 21.14 9.29 43.70 2.12
3440 8264 1.546476 AGTAGAAGTGAAGTCGGGCAG 59.454 52.381 0.00 0.00 0.00 4.85
3461 8285 6.039717 GGCAGTCTAAATCCAAGCAAATATCA 59.960 38.462 0.00 0.00 0.00 2.15
3482 8306 7.572523 ATCAACATACACTTATGATGGGTTG 57.427 36.000 0.00 0.00 38.45 3.77
3556 8380 8.990163 TTCAAGTACAAGTTAAAAAGGATCCT 57.010 30.769 9.02 9.02 0.00 3.24
3593 8417 8.723942 AATTAGCTTTACACATAGTCAAGGAG 57.276 34.615 0.00 0.00 33.10 3.69
4060 9035 8.510243 TTGTACCGAGTCTAAGTATATGTTCA 57.490 34.615 0.00 0.00 0.00 3.18
4143 9118 6.716934 TTGGCTCATAAACCAAACTTGTTA 57.283 33.333 0.00 0.00 42.87 2.41
4152 9127 9.541143 CATAAACCAAACTTGTTAACCTGAATT 57.459 29.630 2.48 0.00 0.00 2.17
4180 9155 4.467082 TGGCAGTATTCTTTTGCATTGGAT 59.533 37.500 0.00 0.00 39.54 3.41
4222 9197 8.538409 AGTCACAAAATTTCATTGGAATTAGC 57.462 30.769 3.32 0.00 31.93 3.09
4235 9210 6.903883 TTGGAATTAGCGAGCTAACTAAAG 57.096 37.500 18.39 0.00 40.76 1.85
4240 9215 1.134670 AGCGAGCTAACTAAAGGCTGG 60.135 52.381 0.00 0.00 36.37 4.85
4546 9521 2.225496 ACCTCTGAGACAATGGAGGAGT 60.225 50.000 13.78 0.00 45.79 3.85
4877 9852 4.665833 TGTTCGTATCCGATGGAAATCT 57.334 40.909 0.00 0.00 43.80 2.40
4897 9872 3.455910 TCTGTCCTATAATGGCAGTGCTT 59.544 43.478 16.11 4.86 34.86 3.91
5038 10013 1.416030 CCTTTTTGGGTGTTTGGGAGG 59.584 52.381 0.00 0.00 0.00 4.30
5051 10026 2.276732 TGGGAGGCTTTGAAAGAGTG 57.723 50.000 9.48 0.00 0.00 3.51
5070 10045 4.362677 AGTGGTATGAAGTGTCCAGGTAT 58.637 43.478 0.00 0.00 0.00 2.73
5139 10114 3.541632 TGAGGTTTGACTGTTGGTCTTC 58.458 45.455 0.00 0.00 44.74 2.87
5148 10123 4.038763 TGACTGTTGGTCTTCGTTATGACT 59.961 41.667 0.00 0.00 44.74 3.41
5204 10179 5.474876 ACATTCTCCTGTTGAAATCTTCACC 59.525 40.000 0.00 0.00 39.87 4.02
5221 10196 0.397254 ACCTGGACCTGGAGGATACG 60.397 60.000 23.36 0.00 46.39 3.06
5297 10272 2.431057 AGGACTAAAGATGGTGGCTACG 59.569 50.000 0.00 0.00 0.00 3.51
5380 10355 3.177884 TGCACAAGGACTGCCCCT 61.178 61.111 0.00 0.00 38.42 4.79
5440 10415 1.405526 GCTGCCGATAGAAGTTGTGGA 60.406 52.381 0.00 0.00 39.76 4.02
5453 10428 5.491078 AGAAGTTGTGGATTCATACCCCTTA 59.509 40.000 0.00 0.00 0.00 2.69
5523 10498 4.813697 CCTATCTTAAAGAGTTGCAGCTCC 59.186 45.833 24.95 9.10 36.20 4.70
5525 10500 5.683876 ATCTTAAAGAGTTGCAGCTCCTA 57.316 39.130 24.95 14.84 36.20 2.94
5618 10593 7.175641 GCTACCATGCAACTTCAGGAAATATAT 59.824 37.037 0.00 0.00 0.00 0.86
5693 10668 1.402968 GCCATGTTGCGAGATGAACAT 59.597 47.619 12.62 2.41 42.29 2.71
6039 11019 8.528044 TGTTTTGGGGATACAAATAATAGACC 57.472 34.615 0.00 0.00 39.80 3.85
6061 11041 4.202161 CCGTGGAGACATAAGCTAGACATT 60.202 45.833 0.00 0.00 46.14 2.71
6062 11042 5.352284 CGTGGAGACATAAGCTAGACATTT 58.648 41.667 0.00 0.00 46.14 2.32
6079 11059 6.643388 AGACATTTCTTTTTCAAACCTGCTT 58.357 32.000 0.00 0.00 0.00 3.91
6080 11060 6.758416 AGACATTTCTTTTTCAAACCTGCTTC 59.242 34.615 0.00 0.00 0.00 3.86
6084 11064 3.130340 TCTTTTTCAAACCTGCTTCGCTT 59.870 39.130 0.00 0.00 0.00 4.68
6164 11623 6.226787 AGTCCTATGATTATTGCTTTCTCCG 58.773 40.000 0.00 0.00 0.00 4.63
6166 11625 4.697352 CCTATGATTATTGCTTTCTCCGGG 59.303 45.833 0.00 0.00 0.00 5.73
6169 11628 0.329931 TTATTGCTTTCTCCGGGCCA 59.670 50.000 4.39 0.00 0.00 5.36
6221 11681 0.258774 GTACAATCCCATGCCACCCT 59.741 55.000 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.680841 CACCCTCTCACACAACGAAAAA 59.319 45.455 0.00 0.00 0.00 1.94
12 13 2.093394 TCACCCTCTCACACAACGAAAA 60.093 45.455 0.00 0.00 0.00 2.29
13 14 1.483004 TCACCCTCTCACACAACGAAA 59.517 47.619 0.00 0.00 0.00 3.46
14 15 1.116308 TCACCCTCTCACACAACGAA 58.884 50.000 0.00 0.00 0.00 3.85
15 16 1.000843 CATCACCCTCTCACACAACGA 59.999 52.381 0.00 0.00 0.00 3.85
16 17 1.432514 CATCACCCTCTCACACAACG 58.567 55.000 0.00 0.00 0.00 4.10
17 18 1.160137 GCATCACCCTCTCACACAAC 58.840 55.000 0.00 0.00 0.00 3.32
18 19 0.320683 CGCATCACCCTCTCACACAA 60.321 55.000 0.00 0.00 0.00 3.33
19 20 1.184970 TCGCATCACCCTCTCACACA 61.185 55.000 0.00 0.00 0.00 3.72
20 21 0.037326 TTCGCATCACCCTCTCACAC 60.037 55.000 0.00 0.00 0.00 3.82
21 22 0.684535 TTTCGCATCACCCTCTCACA 59.315 50.000 0.00 0.00 0.00 3.58
22 23 1.079503 GTTTCGCATCACCCTCTCAC 58.920 55.000 0.00 0.00 0.00 3.51
23 24 0.976641 AGTTTCGCATCACCCTCTCA 59.023 50.000 0.00 0.00 0.00 3.27
24 25 2.961526 TAGTTTCGCATCACCCTCTC 57.038 50.000 0.00 0.00 0.00 3.20
25 26 3.008049 AGTTTAGTTTCGCATCACCCTCT 59.992 43.478 0.00 0.00 0.00 3.69
26 27 3.125316 CAGTTTAGTTTCGCATCACCCTC 59.875 47.826 0.00 0.00 0.00 4.30
27 28 3.074412 CAGTTTAGTTTCGCATCACCCT 58.926 45.455 0.00 0.00 0.00 4.34
28 29 2.161609 CCAGTTTAGTTTCGCATCACCC 59.838 50.000 0.00 0.00 0.00 4.61
29 30 2.812011 ACCAGTTTAGTTTCGCATCACC 59.188 45.455 0.00 0.00 0.00 4.02
30 31 3.364964 CCACCAGTTTAGTTTCGCATCAC 60.365 47.826 0.00 0.00 0.00 3.06
31 32 2.811431 CCACCAGTTTAGTTTCGCATCA 59.189 45.455 0.00 0.00 0.00 3.07
32 33 2.161609 CCCACCAGTTTAGTTTCGCATC 59.838 50.000 0.00 0.00 0.00 3.91
33 34 2.159382 CCCACCAGTTTAGTTTCGCAT 58.841 47.619 0.00 0.00 0.00 4.73
34 35 1.141254 TCCCACCAGTTTAGTTTCGCA 59.859 47.619 0.00 0.00 0.00 5.10
35 36 1.886886 TCCCACCAGTTTAGTTTCGC 58.113 50.000 0.00 0.00 0.00 4.70
36 37 2.747446 CCATCCCACCAGTTTAGTTTCG 59.253 50.000 0.00 0.00 0.00 3.46
37 38 3.089284 CCCATCCCACCAGTTTAGTTTC 58.911 50.000 0.00 0.00 0.00 2.78
38 39 2.225267 CCCCATCCCACCAGTTTAGTTT 60.225 50.000 0.00 0.00 0.00 2.66
39 40 1.357761 CCCCATCCCACCAGTTTAGTT 59.642 52.381 0.00 0.00 0.00 2.24
40 41 0.999712 CCCCATCCCACCAGTTTAGT 59.000 55.000 0.00 0.00 0.00 2.24
41 42 0.258774 CCCCCATCCCACCAGTTTAG 59.741 60.000 0.00 0.00 0.00 1.85
42 43 0.178828 TCCCCCATCCCACCAGTTTA 60.179 55.000 0.00 0.00 0.00 2.01
43 44 1.467190 TCCCCCATCCCACCAGTTT 60.467 57.895 0.00 0.00 0.00 2.66
44 45 1.930656 CTCCCCCATCCCACCAGTT 60.931 63.158 0.00 0.00 0.00 3.16
45 46 2.286425 CTCCCCCATCCCACCAGT 60.286 66.667 0.00 0.00 0.00 4.00
46 47 3.099170 CCTCCCCCATCCCACCAG 61.099 72.222 0.00 0.00 0.00 4.00
47 48 4.777546 CCCTCCCCCATCCCACCA 62.778 72.222 0.00 0.00 0.00 4.17
49 50 4.448340 TCCCCTCCCCCATCCCAC 62.448 72.222 0.00 0.00 0.00 4.61
50 51 4.448340 GTCCCCTCCCCCATCCCA 62.448 72.222 0.00 0.00 0.00 4.37
52 53 4.492303 TCGTCCCCTCCCCCATCC 62.492 72.222 0.00 0.00 0.00 3.51
53 54 1.568118 TTTTCGTCCCCTCCCCCATC 61.568 60.000 0.00 0.00 0.00 3.51
54 55 1.143970 TTTTTCGTCCCCTCCCCCAT 61.144 55.000 0.00 0.00 0.00 4.00
55 56 1.775046 TTTTTCGTCCCCTCCCCCA 60.775 57.895 0.00 0.00 0.00 4.96
56 57 3.173323 TTTTTCGTCCCCTCCCCC 58.827 61.111 0.00 0.00 0.00 5.40
70 71 4.052608 CCGTTTTATTTCGCTGGGTTTTT 58.947 39.130 0.00 0.00 0.00 1.94
71 72 3.644823 CCGTTTTATTTCGCTGGGTTTT 58.355 40.909 0.00 0.00 0.00 2.43
72 73 2.608506 GCCGTTTTATTTCGCTGGGTTT 60.609 45.455 0.00 0.00 0.00 3.27
73 74 1.068125 GCCGTTTTATTTCGCTGGGTT 60.068 47.619 0.00 0.00 0.00 4.11
74 75 0.524414 GCCGTTTTATTTCGCTGGGT 59.476 50.000 0.00 0.00 0.00 4.51
75 76 0.808755 AGCCGTTTTATTTCGCTGGG 59.191 50.000 0.00 0.00 0.00 4.45
76 77 1.466950 TCAGCCGTTTTATTTCGCTGG 59.533 47.619 7.44 0.00 34.61 4.85
77 78 2.892373 TCAGCCGTTTTATTTCGCTG 57.108 45.000 0.00 0.00 34.89 5.18
78 79 3.252458 ACTTTCAGCCGTTTTATTTCGCT 59.748 39.130 0.00 0.00 0.00 4.93
79 80 3.360758 CACTTTCAGCCGTTTTATTTCGC 59.639 43.478 0.00 0.00 0.00 4.70
80 81 4.778904 TCACTTTCAGCCGTTTTATTTCG 58.221 39.130 0.00 0.00 0.00 3.46
81 82 5.572896 CCATCACTTTCAGCCGTTTTATTTC 59.427 40.000 0.00 0.00 0.00 2.17
82 83 5.469479 CCATCACTTTCAGCCGTTTTATTT 58.531 37.500 0.00 0.00 0.00 1.40
83 84 4.082245 CCCATCACTTTCAGCCGTTTTATT 60.082 41.667 0.00 0.00 0.00 1.40
84 85 3.443681 CCCATCACTTTCAGCCGTTTTAT 59.556 43.478 0.00 0.00 0.00 1.40
85 86 2.817258 CCCATCACTTTCAGCCGTTTTA 59.183 45.455 0.00 0.00 0.00 1.52
86 87 1.613437 CCCATCACTTTCAGCCGTTTT 59.387 47.619 0.00 0.00 0.00 2.43
87 88 1.202879 TCCCATCACTTTCAGCCGTTT 60.203 47.619 0.00 0.00 0.00 3.60
88 89 0.400213 TCCCATCACTTTCAGCCGTT 59.600 50.000 0.00 0.00 0.00 4.44
89 90 0.321653 GTCCCATCACTTTCAGCCGT 60.322 55.000 0.00 0.00 0.00 5.68
90 91 1.361668 CGTCCCATCACTTTCAGCCG 61.362 60.000 0.00 0.00 0.00 5.52
91 92 0.036388 TCGTCCCATCACTTTCAGCC 60.036 55.000 0.00 0.00 0.00 4.85
92 93 1.808411 TTCGTCCCATCACTTTCAGC 58.192 50.000 0.00 0.00 0.00 4.26
93 94 6.494893 TTATTTTCGTCCCATCACTTTCAG 57.505 37.500 0.00 0.00 0.00 3.02
94 95 6.885952 TTTATTTTCGTCCCATCACTTTCA 57.114 33.333 0.00 0.00 0.00 2.69
95 96 7.535139 TGATTTATTTTCGTCCCATCACTTTC 58.465 34.615 0.00 0.00 0.00 2.62
96 97 7.461182 TGATTTATTTTCGTCCCATCACTTT 57.539 32.000 0.00 0.00 0.00 2.66
97 98 7.416664 CCATGATTTATTTTCGTCCCATCACTT 60.417 37.037 0.00 0.00 0.00 3.16
98 99 6.039717 CCATGATTTATTTTCGTCCCATCACT 59.960 38.462 0.00 0.00 0.00 3.41
99 100 6.039270 TCCATGATTTATTTTCGTCCCATCAC 59.961 38.462 0.00 0.00 0.00 3.06
100 101 6.125719 TCCATGATTTATTTTCGTCCCATCA 58.874 36.000 0.00 0.00 0.00 3.07
101 102 6.633500 TCCATGATTTATTTTCGTCCCATC 57.367 37.500 0.00 0.00 0.00 3.51
102 103 7.944554 AGTATCCATGATTTATTTTCGTCCCAT 59.055 33.333 0.00 0.00 0.00 4.00
103 104 7.287061 AGTATCCATGATTTATTTTCGTCCCA 58.713 34.615 0.00 0.00 0.00 4.37
104 105 7.745620 AGTATCCATGATTTATTTTCGTCCC 57.254 36.000 0.00 0.00 0.00 4.46
115 116 9.125026 GAGTTGGTTGAATAGTATCCATGATTT 57.875 33.333 0.00 0.00 0.00 2.17
116 117 8.274322 TGAGTTGGTTGAATAGTATCCATGATT 58.726 33.333 0.00 0.00 0.00 2.57
117 118 7.805163 TGAGTTGGTTGAATAGTATCCATGAT 58.195 34.615 0.00 0.00 0.00 2.45
118 119 7.194112 TGAGTTGGTTGAATAGTATCCATGA 57.806 36.000 0.00 0.00 0.00 3.07
119 120 7.864108 TTGAGTTGGTTGAATAGTATCCATG 57.136 36.000 0.00 0.00 0.00 3.66
120 121 7.888021 TGTTTGAGTTGGTTGAATAGTATCCAT 59.112 33.333 0.00 0.00 0.00 3.41
121 122 7.227873 TGTTTGAGTTGGTTGAATAGTATCCA 58.772 34.615 0.00 0.00 0.00 3.41
122 123 7.681939 TGTTTGAGTTGGTTGAATAGTATCC 57.318 36.000 0.00 0.00 0.00 2.59
126 127 9.349713 TCTTAATGTTTGAGTTGGTTGAATAGT 57.650 29.630 0.00 0.00 0.00 2.12
127 128 9.831737 CTCTTAATGTTTGAGTTGGTTGAATAG 57.168 33.333 0.00 0.00 0.00 1.73
128 129 9.349713 ACTCTTAATGTTTGAGTTGGTTGAATA 57.650 29.630 0.00 0.00 37.76 1.75
129 130 8.237811 ACTCTTAATGTTTGAGTTGGTTGAAT 57.762 30.769 0.00 0.00 37.76 2.57
130 131 7.639113 ACTCTTAATGTTTGAGTTGGTTGAA 57.361 32.000 0.00 0.00 37.76 2.69
131 132 8.208224 TCTACTCTTAATGTTTGAGTTGGTTGA 58.792 33.333 0.00 0.00 40.86 3.18
132 133 8.378172 TCTACTCTTAATGTTTGAGTTGGTTG 57.622 34.615 0.00 0.00 40.86 3.77
133 134 8.429641 TCTCTACTCTTAATGTTTGAGTTGGTT 58.570 33.333 0.00 0.00 40.86 3.67
134 135 7.963532 TCTCTACTCTTAATGTTTGAGTTGGT 58.036 34.615 0.00 0.00 40.86 3.67
135 136 9.442047 AATCTCTACTCTTAATGTTTGAGTTGG 57.558 33.333 0.00 0.00 40.86 3.77
149 150 9.898152 CCAGAGGAAAAATAAATCTCTACTCTT 57.102 33.333 0.00 0.00 33.95 2.85
150 151 9.052365 ACCAGAGGAAAAATAAATCTCTACTCT 57.948 33.333 0.00 0.00 33.95 3.24
225 226 8.810041 ACTATAACTATACTATTGGTTTCGGGG 58.190 37.037 0.00 0.00 0.00 5.73
260 261 9.979578 TTTTTACACTAGTTTTCATCATTGCAT 57.020 25.926 0.00 0.00 0.00 3.96
326 327 4.112634 TCTGGTTTCTAGGCCAATTGTT 57.887 40.909 5.01 0.00 33.93 2.83
391 392 1.411041 GCCTAACCGACCTGACCTAT 58.589 55.000 0.00 0.00 0.00 2.57
398 399 0.544595 AAGACTGGCCTAACCGACCT 60.545 55.000 3.32 0.00 43.94 3.85
423 424 5.158494 CGCTTATGTCTGTACTGTGTGTAA 58.842 41.667 0.00 0.00 32.25 2.41
425 426 3.005472 ACGCTTATGTCTGTACTGTGTGT 59.995 43.478 0.00 0.00 0.00 3.72
426 427 3.575630 ACGCTTATGTCTGTACTGTGTG 58.424 45.455 0.00 0.00 0.00 3.82
447 448 9.836076 GGATGAGTATATGCGCGTATATATAAA 57.164 33.333 30.69 21.51 30.55 1.40
449 450 8.556213 TGGATGAGTATATGCGCGTATATATA 57.444 34.615 30.69 22.35 30.55 0.86
453 454 5.570234 TTGGATGAGTATATGCGCGTATA 57.430 39.130 22.47 22.47 0.00 1.47
454 455 4.450082 TTGGATGAGTATATGCGCGTAT 57.550 40.909 24.52 24.52 0.00 3.06
455 456 3.926821 TTGGATGAGTATATGCGCGTA 57.073 42.857 12.53 12.53 0.00 4.42
456 457 2.812358 TTGGATGAGTATATGCGCGT 57.188 45.000 8.43 7.55 0.00 6.01
457 458 3.253230 TCATTGGATGAGTATATGCGCG 58.747 45.455 0.00 0.00 33.59 6.86
458 459 4.452114 TGTTCATTGGATGAGTATATGCGC 59.548 41.667 0.00 0.00 40.94 6.09
459 460 5.388786 CGTGTTCATTGGATGAGTATATGCG 60.389 44.000 0.00 0.00 40.94 4.73
460 461 5.466728 ACGTGTTCATTGGATGAGTATATGC 59.533 40.000 0.00 0.00 40.94 3.14
461 462 7.651704 TGTACGTGTTCATTGGATGAGTATATG 59.348 37.037 0.00 0.00 40.94 1.78
462 463 7.652105 GTGTACGTGTTCATTGGATGAGTATAT 59.348 37.037 0.00 0.00 40.94 0.86
463 464 6.976349 GTGTACGTGTTCATTGGATGAGTATA 59.024 38.462 0.00 0.00 40.94 1.47
464 465 5.810587 GTGTACGTGTTCATTGGATGAGTAT 59.189 40.000 0.00 0.00 40.94 2.12
465 466 5.165676 GTGTACGTGTTCATTGGATGAGTA 58.834 41.667 0.00 0.00 40.94 2.59
466 467 3.994392 GTGTACGTGTTCATTGGATGAGT 59.006 43.478 0.00 0.00 40.94 3.41
467 468 3.060761 CGTGTACGTGTTCATTGGATGAG 59.939 47.826 0.00 0.00 36.16 2.90
468 469 2.990514 CGTGTACGTGTTCATTGGATGA 59.009 45.455 0.00 0.00 34.21 2.92
469 470 2.473868 GCGTGTACGTGTTCATTGGATG 60.474 50.000 0.00 0.00 42.22 3.51
470 471 1.730064 GCGTGTACGTGTTCATTGGAT 59.270 47.619 0.00 0.00 42.22 3.41
471 472 1.141645 GCGTGTACGTGTTCATTGGA 58.858 50.000 0.00 0.00 42.22 3.53
477 478 0.437295 GGATGTGCGTGTACGTGTTC 59.563 55.000 0.00 0.00 42.22 3.18
481 482 2.953466 AATAGGATGTGCGTGTACGT 57.047 45.000 6.27 0.00 42.22 3.57
528 5209 8.587608 GCCCATCAGGATTCAAATTTGATATAA 58.412 33.333 21.10 7.21 38.24 0.98
529 5210 7.951806 AGCCCATCAGGATTCAAATTTGATATA 59.048 33.333 21.10 7.58 38.24 0.86
536 5217 3.036091 CCAGCCCATCAGGATTCAAATT 58.964 45.455 0.00 0.00 38.24 1.82
544 5225 0.768221 GTATCCCCAGCCCATCAGGA 60.768 60.000 0.00 0.00 38.24 3.86
546 5227 1.061905 TGGTATCCCCAGCCCATCAG 61.062 60.000 0.00 0.00 38.72 2.90
570 5251 2.093973 ACTGACCTAACAGCGAATGAGG 60.094 50.000 0.00 0.00 41.06 3.86
574 5255 3.963428 AAGACTGACCTAACAGCGAAT 57.037 42.857 0.00 0.00 41.06 3.34
706 5409 4.837093 TTGGGGAAGAGAAATATGTCGT 57.163 40.909 0.00 0.00 0.00 4.34
707 5410 4.941263 TGTTTGGGGAAGAGAAATATGTCG 59.059 41.667 0.00 0.00 0.00 4.35
709 5412 7.872138 TCTATGTTTGGGGAAGAGAAATATGT 58.128 34.615 0.00 0.00 0.00 2.29
739 5442 8.595533 GGAGAAATTCTTCAACAACAAAAGAAC 58.404 33.333 0.00 0.00 40.67 3.01
740 5443 8.310382 TGGAGAAATTCTTCAACAACAAAAGAA 58.690 29.630 0.60 0.00 41.71 2.52
742 5445 8.477984 TTGGAGAAATTCTTCAACAACAAAAG 57.522 30.769 12.43 0.00 37.08 2.27
745 5448 7.382110 TGTTTGGAGAAATTCTTCAACAACAA 58.618 30.769 15.78 0.00 41.44 2.83
747 5450 9.185192 CTATGTTTGGAGAAATTCTTCAACAAC 57.815 33.333 15.78 12.77 41.44 3.32
753 5456 9.890352 GCATATCTATGTTTGGAGAAATTCTTC 57.110 33.333 0.00 0.00 36.11 2.87
754 5457 9.412460 TGCATATCTATGTTTGGAGAAATTCTT 57.588 29.630 0.00 0.00 36.11 2.52
982 5685 1.603802 CATTCACCTTGCACAGACGTT 59.396 47.619 0.00 0.00 0.00 3.99
1004 5707 1.433879 CGTACCAAGAGGAGCCGAG 59.566 63.158 0.00 0.00 38.69 4.63
1098 5801 3.243602 GGCACTTTAATCAACCCAAACGT 60.244 43.478 0.00 0.00 0.00 3.99
1144 5847 0.883833 CACCATCAGAACACAAGCCC 59.116 55.000 0.00 0.00 0.00 5.19
1351 6054 1.686325 GGCCGCCTCCTCAACTATGA 61.686 60.000 0.71 0.00 0.00 2.15
1354 6057 2.284331 TGGCCGCCTCCTCAACTA 60.284 61.111 11.61 0.00 0.00 2.24
1378 6081 4.436998 CCGCCGAGGAAACGCTCT 62.437 66.667 0.00 0.00 45.00 4.09
1411 6114 1.622607 CGCCAACCCCTCAGTATCCA 61.623 60.000 0.00 0.00 0.00 3.41
1443 6146 2.359900 GTCGATTGCATCTCCAACCTT 58.640 47.619 0.00 0.00 0.00 3.50
1522 6225 3.147595 CCTCCGGCATCGTCTCCA 61.148 66.667 0.00 0.00 33.95 3.86
1556 6259 0.390340 CCCTGTCCATGTGTGTCTCG 60.390 60.000 0.00 0.00 0.00 4.04
1650 6353 1.621672 CCACCCTCCTTCCTCAGCTC 61.622 65.000 0.00 0.00 0.00 4.09
1767 6578 0.956633 CCATTGACAGCAGCAACAGT 59.043 50.000 0.00 0.00 0.00 3.55
1928 6739 4.574013 CCATCCTCTTTTCTCTCCAATTCG 59.426 45.833 0.00 0.00 0.00 3.34
1963 6774 5.174395 ACATCAACCATCTCTTCTTTCTCG 58.826 41.667 0.00 0.00 0.00 4.04
1976 6787 4.641989 GGATTTACAGCAGACATCAACCAT 59.358 41.667 0.00 0.00 0.00 3.55
2054 6865 1.053424 TTCCAGTAACAGCGTCCCTT 58.947 50.000 0.00 0.00 0.00 3.95
2060 6871 0.602638 TGCCAGTTCCAGTAACAGCG 60.603 55.000 0.00 0.00 40.59 5.18
2095 6906 1.676014 GCGTGGCTTCCAATACTGACT 60.676 52.381 0.00 0.00 34.18 3.41
2138 6949 0.618680 AGGCATCCACTACAGAGGCA 60.619 55.000 0.00 0.00 42.63 4.75
2167 6978 1.073763 CACCATGACCTGAACCTGGAA 59.926 52.381 0.00 0.00 0.00 3.53
2173 6984 1.168714 GGAAGCACCATGACCTGAAC 58.831 55.000 0.00 0.00 38.79 3.18
2205 7016 1.938577 CACCTCATTGGAAGCATCTCG 59.061 52.381 0.00 0.00 39.71 4.04
2306 7120 9.790389 CGACTTCTCACATAAGTCTTATTAGTT 57.210 33.333 12.60 0.00 46.94 2.24
2307 7121 8.958506 ACGACTTCTCACATAAGTCTTATTAGT 58.041 33.333 12.60 0.00 46.94 2.24
2309 7123 8.737175 ACACGACTTCTCACATAAGTCTTATTA 58.263 33.333 12.60 0.00 46.94 0.98
2310 7124 7.603651 ACACGACTTCTCACATAAGTCTTATT 58.396 34.615 12.60 0.00 46.94 1.40
2311 7125 7.159322 ACACGACTTCTCACATAAGTCTTAT 57.841 36.000 12.60 0.00 46.94 1.73
2334 7148 3.803778 CCCTTTGTCTTTGCATCAACAAC 59.196 43.478 7.55 0.00 31.76 3.32
2376 7190 4.620982 TCTCGCAATGTATCATTCATCGT 58.379 39.130 0.00 0.00 0.00 3.73
2428 7242 9.229784 CATCATCTATTGAATTCTTGTTTTCCG 57.770 33.333 7.05 0.00 38.03 4.30
2446 7260 4.948847 ACTATTTGAGCGCACATCATCTA 58.051 39.130 11.47 0.00 0.00 1.98
2484 7298 5.769662 TGCCATAACTCTTCAACTTCACAAT 59.230 36.000 0.00 0.00 0.00 2.71
2615 7429 3.065786 CCATCAATGCTTGCACGATTAGT 59.934 43.478 0.00 0.00 0.00 2.24
2624 7438 0.102481 CTGGAGCCATCAATGCTTGC 59.898 55.000 0.00 0.00 39.69 4.01
2698 7512 7.514784 GGAAGAGACTTATTCCTAGGAGTAC 57.485 44.000 13.29 3.27 40.73 2.73
2711 7525 5.418209 CGGTTTCTTAGGAGGAAGAGACTTA 59.582 44.000 6.75 0.00 39.40 2.24
2784 7598 2.526120 GCACGGCCGATGTAGAAGC 61.526 63.158 35.90 17.14 0.00 3.86
2816 7630 3.196469 CCAAGCAAGAGTACTCTCCATGA 59.804 47.826 25.34 0.00 41.26 3.07
2858 7672 4.651540 TCCTTTCAGGGACAGCTAATGCT 61.652 47.826 0.00 0.00 42.83 3.79
2866 7680 6.660949 ACATAATTCTTTCCTTTCAGGGACAG 59.339 38.462 0.00 0.00 35.59 3.51
3024 7841 3.573967 GCCTCAAGGTCAATTCTTCCAAA 59.426 43.478 0.00 0.00 37.57 3.28
3102 7919 1.314730 ACAACAACACCGGGAACATC 58.685 50.000 6.32 0.00 0.00 3.06
3290 8107 2.987125 GCTTTACCTCCGGAGCCA 59.013 61.111 26.87 12.58 0.00 4.75
3323 8140 4.012374 CCTTAAGCTTTTGATCCTCTGCA 58.988 43.478 3.20 0.00 0.00 4.41
3461 8285 8.052748 ACATACAACCCATCATAAGTGTATGTT 58.947 33.333 17.24 6.30 44.61 2.71
3482 8306 2.491693 CCAACAATCCACCACCACATAC 59.508 50.000 0.00 0.00 0.00 2.39
3556 8380 3.806949 AAGCTAATTCAGGTTGACCCA 57.193 42.857 0.00 0.00 43.32 4.51
3857 8826 3.911155 GAGCGGCTTTGCGTGAACG 62.911 63.158 2.97 0.00 40.67 3.95
4060 9035 7.345653 TCTCATATTTCACCAACATCTAGGACT 59.654 37.037 0.00 0.00 0.00 3.85
4152 9127 3.386078 TGCAAAAGAATACTGCCAACCAA 59.614 39.130 0.00 0.00 35.13 3.67
4180 9155 7.575414 TTGTGACTTCAATTTAACCTAAGCA 57.425 32.000 0.00 0.00 0.00 3.91
4222 9197 2.961526 TCCAGCCTTTAGTTAGCTCG 57.038 50.000 0.00 0.00 33.70 5.03
4235 9210 1.214589 CTGCATGCAGTTTCCAGCC 59.785 57.895 34.76 0.00 39.10 4.85
4240 9215 4.565531 GCACCTGCATGCAGTTTC 57.434 55.556 38.22 21.69 45.39 2.78
4467 9442 5.012239 CCCTTCCAAAGTTCTTCATCATCA 58.988 41.667 0.00 0.00 0.00 3.07
4581 9556 3.181520 GGTTGATGAATCTTCCGACGTTG 60.182 47.826 0.00 0.00 0.00 4.10
4877 9852 3.931907 AAGCACTGCCATTATAGGACA 57.068 42.857 0.00 0.00 0.00 4.02
5038 10013 5.239525 ACACTTCATACCACTCTTTCAAAGC 59.760 40.000 0.00 0.00 0.00 3.51
5051 10026 4.755266 ACATACCTGGACACTTCATACC 57.245 45.455 0.00 0.00 0.00 2.73
5092 10067 9.632638 ATGTTATAGCCAGTACAATCTCATTTT 57.367 29.630 0.00 0.00 0.00 1.82
5139 10114 5.462068 TGATTCTGCGGAATTAGTCATAACG 59.538 40.000 21.52 0.00 41.68 3.18
5148 10123 5.581126 AAATGCTTGATTCTGCGGAATTA 57.419 34.783 21.52 15.11 41.68 1.40
5204 10179 1.776662 TTCGTATCCTCCAGGTCCAG 58.223 55.000 0.00 0.00 36.34 3.86
5221 10196 8.733458 TCCATACAAGCTAATCATTGCATATTC 58.267 33.333 0.00 0.00 0.00 1.75
5297 10272 4.427661 ACGCAGCTCCGAGCACTC 62.428 66.667 22.29 9.38 45.56 3.51
5380 10355 4.143543 TCCACAGTTGAGCAAAATGATGA 58.856 39.130 6.60 0.88 37.30 2.92
5523 10498 6.959361 ACACTGAAAACTTTACATGCAGTAG 58.041 36.000 0.00 0.00 33.78 2.57
5525 10500 5.835113 ACACTGAAAACTTTACATGCAGT 57.165 34.783 0.00 0.00 35.70 4.40
5618 10593 5.013704 ACATGTGGGAACAGTAGGAATGTTA 59.986 40.000 0.00 0.00 44.46 2.41
5720 10695 8.023128 AGAAAAATGATTGTCTTACATGGTTCG 58.977 33.333 0.00 0.00 28.04 3.95
5954 10933 6.610830 AGGTGATCCTGACTTTTTAAGGAAA 58.389 36.000 0.00 0.00 43.20 3.13
5955 10934 6.200878 AGGTGATCCTGACTTTTTAAGGAA 57.799 37.500 0.00 0.00 43.20 3.36
6039 11019 4.576216 ATGTCTAGCTTATGTCTCCACG 57.424 45.455 0.00 0.00 0.00 4.94
6079 11059 6.642707 TTCTTTTTCCTTAAATGGAAGCGA 57.357 33.333 0.00 0.00 45.58 4.93
6080 11060 7.889589 AATTCTTTTTCCTTAAATGGAAGCG 57.110 32.000 0.00 0.00 45.58 4.68
6084 11064 8.417884 ACGTGAAATTCTTTTTCCTTAAATGGA 58.582 29.630 0.00 0.00 0.00 3.41
6152 11611 0.753111 GATGGCCCGGAGAAAGCAAT 60.753 55.000 0.73 0.00 0.00 3.56
6164 11623 1.758122 ATGCTTTTCCCGATGGCCC 60.758 57.895 0.00 0.00 0.00 5.80
6166 11625 0.817013 TTCATGCTTTTCCCGATGGC 59.183 50.000 0.00 0.00 0.00 4.40
6191 11650 2.172505 TGGGATTGTACCATTCGAGCAT 59.827 45.455 0.00 0.00 31.83 3.79
6192 11651 1.557371 TGGGATTGTACCATTCGAGCA 59.443 47.619 0.00 0.00 31.83 4.26
6206 11665 1.607225 TTCTAGGGTGGCATGGGATT 58.393 50.000 0.00 0.00 0.00 3.01
6212 11671 2.091665 CCCTTTCATTCTAGGGTGGCAT 60.092 50.000 0.00 0.00 45.12 4.40


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

AutoCloner maintained by Alex Coulton.