Multiple sequence alignment - TraesCS7D01G492000

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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 TraesCS7D01G492000 chr7D 100.000 5844 0 0 1 5844 600882342 600888185 0.000000e+00 10792.0
1 TraesCS7D01G492000 chr7D 92.366 262 14 5 4830 5087 600923285 600923544 9.250000e-98 368.0
2 TraesCS7D01G492000 chr7D 90.206 194 18 1 4417 4610 600921953 600922145 9.720000e-63 252.0
3 TraesCS7D01G492000 chr7D 78.963 328 48 7 4507 4833 600922003 600922310 2.760000e-48 204.0
4 TraesCS7D01G492000 chr7D 83.333 210 26 7 3030 3233 611261584 611261378 1.000000e-42 185.0
5 TraesCS7D01G492000 chr7D 84.112 107 17 0 5335 5441 546768870 546768976 2.880000e-18 104.0
6 TraesCS7D01G492000 chr7B 95.111 4664 143 32 474 5087 680112976 680117604 0.000000e+00 7271.0
7 TraesCS7D01G492000 chr7A 93.078 5042 202 58 116 5094 692876152 692881109 0.000000e+00 7241.0
8 TraesCS7D01G492000 chr7A 92.368 380 17 3 5064 5438 692881108 692881480 1.120000e-146 531.0
9 TraesCS7D01G492000 chr7A 83.788 586 66 14 4507 5087 692896613 692897174 4.010000e-146 529.0
10 TraesCS7D01G492000 chr7A 94.444 324 15 1 5524 5844 692881528 692881851 4.070000e-136 496.0
11 TraesCS7D01G492000 chr7A 90.722 194 18 0 4417 4610 692896562 692896755 5.810000e-65 259.0
12 TraesCS7D01G492000 chr7A 79.733 375 49 14 2510 2867 285424310 285423946 4.520000e-61 246.0
13 TraesCS7D01G492000 chr7A 84.112 107 17 0 5335 5441 630043683 630043789 2.880000e-18 104.0
14 TraesCS7D01G492000 chr4D 93.733 367 17 4 5081 5445 482951852 482952214 3.980000e-151 545.0
15 TraesCS7D01G492000 chr4D 88.957 163 17 1 5450 5611 482952167 482952329 3.570000e-47 200.0
16 TraesCS7D01G492000 chr4D 76.015 271 42 15 2568 2834 464045846 464045595 1.030000e-22 119.0
17 TraesCS7D01G492000 chr4B 78.306 673 98 25 5088 5740 7743748 7743104 1.970000e-104 390.0
18 TraesCS7D01G492000 chr4B 83.333 216 28 6 3018 3232 416249222 416249014 5.980000e-45 193.0
19 TraesCS7D01G492000 chr4B 82.828 198 31 3 3043 3239 369037687 369037882 2.160000e-39 174.0
20 TraesCS7D01G492000 chr4B 80.165 121 21 3 5450 5568 14582855 14582736 2.900000e-13 87.9
21 TraesCS7D01G492000 chr3B 74.964 687 92 38 5085 5737 20832366 20831726 5.850000e-60 243.0
22 TraesCS7D01G492000 chr3B 74.672 687 94 39 5087 5737 296066965 296066323 1.270000e-56 231.0
23 TraesCS7D01G492000 chr3B 74.085 656 107 39 5088 5711 718680947 718681571 1.650000e-50 211.0
24 TraesCS7D01G492000 chr3B 75.551 454 62 25 5290 5736 752377877 752378288 1.670000e-40 178.0
25 TraesCS7D01G492000 chr3B 82.381 210 25 10 3025 3233 8853136 8853334 7.790000e-39 172.0
26 TraesCS7D01G492000 chr3B 97.183 71 2 0 5765 5835 811044496 811044566 2.860000e-23 121.0
27 TraesCS7D01G492000 chr3B 81.818 110 19 1 5450 5558 752379231 752379340 2.240000e-14 91.6
28 TraesCS7D01G492000 chr5B 74.771 654 91 36 5088 5711 599313106 599313715 5.890000e-55 226.0
29 TraesCS7D01G492000 chr6D 73.049 679 145 31 3355 4009 105821720 105821056 7.680000e-49 206.0
30 TraesCS7D01G492000 chr6D 73.843 562 105 31 1797 2342 105822402 105821867 1.000000e-42 185.0
31 TraesCS7D01G492000 chr6D 91.200 125 11 0 4331 4455 105820659 105820535 2.800000e-38 171.0
32 TraesCS7D01G492000 chr6D 77.174 184 25 16 2568 2747 79703213 79703383 2.240000e-14 91.6
33 TraesCS7D01G492000 chr6D 86.207 87 8 4 2768 2853 156802853 156802936 2.240000e-14 91.6
34 TraesCS7D01G492000 chr5D 84.579 214 25 5 3027 3233 278634173 278633961 7.680000e-49 206.0
35 TraesCS7D01G492000 chr5D 82.379 227 32 3 3018 3237 278633962 278634187 2.150000e-44 191.0
36 TraesCS7D01G492000 chr5D 76.852 216 29 15 2551 2763 459928787 459928590 1.040000e-17 102.0
37 TraesCS7D01G492000 chr6A 73.009 678 145 32 3355 4009 128444608 128443946 2.760000e-48 204.0
38 TraesCS7D01G492000 chr6A 90.400 125 12 0 4331 4455 128443571 128443447 1.300000e-36 165.0
39 TraesCS7D01G492000 chr6A 73.145 566 107 31 1797 2342 128446068 128445528 1.690000e-35 161.0
40 TraesCS7D01G492000 chr6A 86.207 87 9 3 2768 2853 212117179 212117095 2.240000e-14 91.6
41 TraesCS7D01G492000 chr6B 74.373 558 96 34 1797 2333 192352900 192352369 1.660000e-45 195.0
42 TraesCS7D01G492000 chr6B 72.526 677 151 31 3355 4009 192351305 192350642 2.780000e-43 187.0
43 TraesCS7D01G492000 chr6B 84.925 199 13 6 5571 5752 8377069 8376871 1.000000e-42 185.0
44 TraesCS7D01G492000 chr6B 90.400 125 12 0 4331 4455 192350244 192350120 1.300000e-36 165.0
45 TraesCS7D01G492000 chr6B 80.000 90 15 3 2574 2661 687787546 687787458 4.890000e-06 63.9
46 TraesCS7D01G492000 chr2A 77.188 377 58 13 2510 2884 243122306 243122656 1.660000e-45 195.0
47 TraesCS7D01G492000 chr2A 82.063 223 38 2 5450 5670 686222924 686223146 7.730000e-44 189.0
48 TraesCS7D01G492000 chr2A 75.636 275 53 10 2568 2839 174751798 174751535 2.210000e-24 124.0
49 TraesCS7D01G492000 chr2A 92.000 75 5 1 5088 5162 686221882 686221955 2.880000e-18 104.0
50 TraesCS7D01G492000 chr5A 82.819 227 28 5 3021 3237 369628529 369628304 5.980000e-45 193.0
51 TraesCS7D01G492000 chr5A 74.909 275 54 13 2568 2839 494869308 494869046 1.720000e-20 111.0
52 TraesCS7D01G492000 chr5A 78.022 182 33 6 2568 2747 573054800 573054624 2.230000e-19 108.0
53 TraesCS7D01G492000 chr3A 77.391 345 54 9 5296 5635 40291644 40291319 3.600000e-42 183.0
54 TraesCS7D01G492000 chr3A 86.747 83 11 0 5363 5445 40290712 40290630 6.240000e-15 93.5
55 TraesCS7D01G492000 chr3A 76.842 190 27 12 2574 2761 728693913 728694087 2.240000e-14 91.6
56 TraesCS7D01G492000 chr1A 78.800 250 36 9 2608 2854 45692548 45692313 1.010000e-32 152.0
57 TraesCS7D01G492000 chr1D 75.368 272 42 19 2568 2834 462135136 462135387 2.230000e-19 108.0
58 TraesCS7D01G492000 chr3D 97.674 43 1 0 5793 5835 603948430 603948472 2.260000e-09 75.0
59 TraesCS7D01G492000 chrUn 100.000 37 0 0 5655 5691 287696882 287696918 1.050000e-07 69.4
60 TraesCS7D01G492000 chrUn 100.000 37 0 0 5655 5691 287709086 287709122 1.050000e-07 69.4
61 TraesCS7D01G492000 chrUn 100.000 37 0 0 5655 5691 294705099 294705135 1.050000e-07 69.4
62 TraesCS7D01G492000 chr1B 97.297 37 1 0 5808 5844 497300093 497300057 4.890000e-06 63.9


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 TraesCS7D01G492000 chr7D 600882342 600888185 5843 False 10792.000000 10792 100.000000 1 5844 1 chr7D.!!$F2 5843
1 TraesCS7D01G492000 chr7D 600921953 600923544 1591 False 274.666667 368 87.178333 4417 5087 3 chr7D.!!$F3 670
2 TraesCS7D01G492000 chr7B 680112976 680117604 4628 False 7271.000000 7271 95.111000 474 5087 1 chr7B.!!$F1 4613
3 TraesCS7D01G492000 chr7A 692876152 692881851 5699 False 2756.000000 7241 93.296667 116 5844 3 chr7A.!!$F2 5728
4 TraesCS7D01G492000 chr7A 692896562 692897174 612 False 394.000000 529 87.255000 4417 5087 2 chr7A.!!$F3 670
5 TraesCS7D01G492000 chr4B 7743104 7743748 644 True 390.000000 390 78.306000 5088 5740 1 chr4B.!!$R1 652
6 TraesCS7D01G492000 chr3B 20831726 20832366 640 True 243.000000 243 74.964000 5085 5737 1 chr3B.!!$R1 652
7 TraesCS7D01G492000 chr3B 296066323 296066965 642 True 231.000000 231 74.672000 5087 5737 1 chr3B.!!$R2 650
8 TraesCS7D01G492000 chr3B 718680947 718681571 624 False 211.000000 211 74.085000 5088 5711 1 chr3B.!!$F2 623
9 TraesCS7D01G492000 chr5B 599313106 599313715 609 False 226.000000 226 74.771000 5088 5711 1 chr5B.!!$F1 623

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
425 435 0.030638 CGAGTGGGCTGGTTTTGTTG 59.969 55.0 0.00 0.00 0.00 3.33 F
429 439 0.107945 TGGGCTGGTTTTGTTGCAAC 60.108 50.0 22.83 22.83 0.00 4.17 F
533 543 0.371989 TATCGAATGCACGCGTTTGG 59.628 50.0 10.22 2.96 0.00 3.28 F
1279 1322 0.608308 GGTAGGTTGGGGAACTGTGC 60.608 60.0 0.00 0.00 0.00 4.57 F
2345 2404 1.154197 GGAGGTAACGGTGCAACTTC 58.846 55.0 0.00 0.00 46.39 3.01 F
3840 3902 2.363306 TGTTGACAGCAAACCCTGAT 57.637 45.0 0.00 0.00 35.42 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1830 3.193479 GGAATGTTGCTCAAAGGGTTAGG 59.807 47.826 0.00 0.00 0.00 2.69 R
2020 2076 4.935808 AGGTCACCAGCTAAATAAACTTCG 59.064 41.667 0.00 0.00 0.00 3.79 R
2677 2737 3.446799 TGTGCACTTTTTGAGCATTGAC 58.553 40.909 19.41 0.00 43.59 3.18 R
3023 3083 1.560505 CAGCCATAAGCCCCAAAAGT 58.439 50.000 0.00 0.00 45.47 2.66 R
3889 3951 2.770164 ATGGTAGCCATCGATTAGCC 57.230 50.000 12.45 4.42 40.74 3.93 R
5246 6360 0.440371 GCAAAGCGAAGAGGAACGAG 59.560 55.000 0.00 0.00 0.00 4.18 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 3.532155 AGGCAGACGAGATCCCGC 61.532 66.667 0.00 0.00 0.00 6.13
18 19 4.593864 GGCAGACGAGATCCCGCC 62.594 72.222 0.00 0.00 38.78 6.13
19 20 4.933064 GCAGACGAGATCCCGCCG 62.933 72.222 0.00 0.00 0.00 6.46
20 21 4.933064 CAGACGAGATCCCGCCGC 62.933 72.222 0.00 0.00 0.00 6.53
25 26 4.593864 GAGATCCCGCCGCCAGTC 62.594 72.222 0.00 0.00 0.00 3.51
45 46 3.556306 GCTGGCCGCCTACCCATA 61.556 66.667 11.61 0.00 0.00 2.74
46 47 2.895424 GCTGGCCGCCTACCCATAT 61.895 63.158 11.61 0.00 0.00 1.78
47 48 1.761174 CTGGCCGCCTACCCATATT 59.239 57.895 11.61 0.00 0.00 1.28
48 49 0.110486 CTGGCCGCCTACCCATATTT 59.890 55.000 11.61 0.00 0.00 1.40
49 50 0.179004 TGGCCGCCTACCCATATTTG 60.179 55.000 11.61 0.00 0.00 2.32
50 51 0.893727 GGCCGCCTACCCATATTTGG 60.894 60.000 0.71 0.00 43.23 3.28
60 61 2.826674 CCATATTTGGGTGTGGGACT 57.173 50.000 0.00 0.00 39.56 3.85
61 62 3.100207 CCATATTTGGGTGTGGGACTT 57.900 47.619 0.00 0.00 39.56 3.01
62 63 3.023832 CCATATTTGGGTGTGGGACTTC 58.976 50.000 0.00 0.00 39.56 3.01
63 64 3.309121 CCATATTTGGGTGTGGGACTTCT 60.309 47.826 0.00 0.00 39.56 2.85
64 65 2.586648 ATTTGGGTGTGGGACTTCTC 57.413 50.000 0.00 0.00 0.00 2.87
65 66 0.476771 TTTGGGTGTGGGACTTCTCC 59.523 55.000 0.00 0.00 35.50 3.71
66 67 1.764571 TTGGGTGTGGGACTTCTCCG 61.765 60.000 0.00 0.00 37.46 4.63
67 68 2.047179 GGTGTGGGACTTCTCCGC 60.047 66.667 0.00 0.00 37.46 5.54
68 69 2.432628 GTGTGGGACTTCTCCGCG 60.433 66.667 0.00 0.00 37.46 6.46
69 70 2.915659 TGTGGGACTTCTCCGCGT 60.916 61.111 4.92 0.00 37.46 6.01
70 71 2.432628 GTGGGACTTCTCCGCGTG 60.433 66.667 4.92 0.00 37.46 5.34
71 72 3.691342 TGGGACTTCTCCGCGTGG 61.691 66.667 9.28 9.28 37.46 4.94
73 74 4.070552 GGACTTCTCCGCGTGGCT 62.071 66.667 11.05 0.00 34.14 4.75
74 75 2.048127 GACTTCTCCGCGTGGCTT 60.048 61.111 11.05 0.00 34.14 4.35
75 76 2.357517 ACTTCTCCGCGTGGCTTG 60.358 61.111 11.05 3.04 34.14 4.01
76 77 3.793144 CTTCTCCGCGTGGCTTGC 61.793 66.667 11.05 0.00 34.14 4.01
77 78 4.617520 TTCTCCGCGTGGCTTGCA 62.618 61.111 11.05 0.00 34.14 4.08
80 81 3.932580 CTCCGCGTGGCTTGCAGTA 62.933 63.158 11.05 0.00 34.14 2.74
81 82 3.490759 CCGCGTGGCTTGCAGTAG 61.491 66.667 0.00 0.00 0.00 2.57
82 83 4.152625 CGCGTGGCTTGCAGTAGC 62.153 66.667 0.00 1.52 40.48 3.58
83 84 2.743928 GCGTGGCTTGCAGTAGCT 60.744 61.111 10.12 0.00 42.74 3.32
84 85 3.031964 GCGTGGCTTGCAGTAGCTG 62.032 63.158 10.12 2.66 42.74 4.24
99 100 3.715854 GCTGCCAAGCTCAATTCAG 57.284 52.632 0.00 0.00 46.60 3.02
100 101 0.458025 GCTGCCAAGCTCAATTCAGC 60.458 55.000 0.00 0.00 46.60 4.26
101 102 0.179171 CTGCCAAGCTCAATTCAGCG 60.179 55.000 0.00 0.00 44.82 5.18
102 103 0.890542 TGCCAAGCTCAATTCAGCGT 60.891 50.000 0.00 0.00 44.82 5.07
103 104 0.455633 GCCAAGCTCAATTCAGCGTG 60.456 55.000 10.19 10.19 45.39 5.34
104 105 0.877071 CCAAGCTCAATTCAGCGTGT 59.123 50.000 15.32 0.00 44.63 4.49
105 106 1.400629 CCAAGCTCAATTCAGCGTGTG 60.401 52.381 15.32 6.18 44.63 3.82
106 107 0.239347 AAGCTCAATTCAGCGTGTGC 59.761 50.000 0.00 0.00 44.82 4.57
107 108 0.886043 AGCTCAATTCAGCGTGTGCA 60.886 50.000 0.00 0.00 44.82 4.57
108 109 0.169672 GCTCAATTCAGCGTGTGCAT 59.830 50.000 0.00 0.00 46.23 3.96
109 110 1.398041 GCTCAATTCAGCGTGTGCATA 59.602 47.619 0.00 0.00 46.23 3.14
110 111 2.538333 GCTCAATTCAGCGTGTGCATAG 60.538 50.000 0.00 0.00 46.23 2.23
111 112 2.674852 CTCAATTCAGCGTGTGCATAGT 59.325 45.455 0.00 0.00 46.23 2.12
112 113 3.073678 TCAATTCAGCGTGTGCATAGTT 58.926 40.909 0.00 0.00 46.23 2.24
113 114 3.501828 TCAATTCAGCGTGTGCATAGTTT 59.498 39.130 0.00 0.00 46.23 2.66
114 115 4.023279 TCAATTCAGCGTGTGCATAGTTTT 60.023 37.500 0.00 0.00 46.23 2.43
138 139 0.038067 TTTACTAGTTGCAGCGCCGA 60.038 50.000 2.29 0.00 0.00 5.54
161 163 0.402121 AACTTTCCCCACCTGCTCTC 59.598 55.000 0.00 0.00 0.00 3.20
162 164 0.474660 ACTTTCCCCACCTGCTCTCT 60.475 55.000 0.00 0.00 0.00 3.10
163 165 0.035630 CTTTCCCCACCTGCTCTCTG 60.036 60.000 0.00 0.00 0.00 3.35
164 166 0.768221 TTTCCCCACCTGCTCTCTGT 60.768 55.000 0.00 0.00 0.00 3.41
165 167 0.116342 TTCCCCACCTGCTCTCTGTA 59.884 55.000 0.00 0.00 0.00 2.74
166 168 0.614979 TCCCCACCTGCTCTCTGTAC 60.615 60.000 0.00 0.00 0.00 2.90
167 169 0.616111 CCCCACCTGCTCTCTGTACT 60.616 60.000 0.00 0.00 0.00 2.73
168 170 0.820871 CCCACCTGCTCTCTGTACTC 59.179 60.000 0.00 0.00 0.00 2.59
169 171 1.618345 CCCACCTGCTCTCTGTACTCT 60.618 57.143 0.00 0.00 0.00 3.24
170 172 1.476085 CCACCTGCTCTCTGTACTCTG 59.524 57.143 0.00 0.00 0.00 3.35
171 173 2.166829 CACCTGCTCTCTGTACTCTGT 58.833 52.381 0.00 0.00 0.00 3.41
172 174 3.348119 CACCTGCTCTCTGTACTCTGTA 58.652 50.000 0.00 0.00 0.00 2.74
173 175 3.376859 CACCTGCTCTCTGTACTCTGTAG 59.623 52.174 0.00 0.00 0.00 2.74
174 176 2.357637 CCTGCTCTCTGTACTCTGTAGC 59.642 54.545 0.00 0.00 0.00 3.58
210 212 4.559862 ACTGTAGCTTATGCAGGTCTTT 57.440 40.909 0.00 0.00 45.21 2.52
216 218 5.379706 AGCTTATGCAGGTCTTTAGGAAT 57.620 39.130 3.16 0.00 42.74 3.01
230 232 2.119655 GGAATCTGCTGCTGCCTGG 61.120 63.158 13.47 3.77 38.71 4.45
255 257 2.279120 CCGCACCTCGAGCTGATC 60.279 66.667 11.97 0.00 41.67 2.92
259 261 0.809241 GCACCTCGAGCTGATCAAGG 60.809 60.000 11.97 8.57 0.00 3.61
266 268 1.470632 CGAGCTGATCAAGGAGTGGAC 60.471 57.143 0.00 0.00 0.00 4.02
268 270 1.086634 GCTGATCAAGGAGTGGACGC 61.087 60.000 0.00 0.00 0.00 5.19
273 275 2.031163 AAGGAGTGGACGCTGTGC 59.969 61.111 0.00 0.00 0.00 4.57
284 286 3.271586 GCTGTGCAGCGTGTCACA 61.272 61.111 8.50 5.83 45.29 3.58
287 289 3.649986 GTGCAGCGTGTCACACCC 61.650 66.667 1.24 0.00 33.63 4.61
293 295 2.032528 CGTGTCACACCCATGGCT 59.967 61.111 6.09 0.00 0.00 4.75
294 296 2.327343 CGTGTCACACCCATGGCTG 61.327 63.158 6.09 5.73 0.00 4.85
295 297 1.973281 GTGTCACACCCATGGCTGG 60.973 63.158 11.77 3.20 42.73 4.85
321 331 0.315251 CCTCTCGTTGACTGCAGTGA 59.685 55.000 27.27 14.64 0.00 3.41
331 341 1.294780 CTGCAGTGAGGGTGGACTC 59.705 63.158 5.25 0.00 37.99 3.36
332 342 1.152247 TGCAGTGAGGGTGGACTCT 60.152 57.895 0.00 0.00 38.32 3.24
342 352 0.321122 GGTGGACTCTTCTGTGCTGG 60.321 60.000 0.00 0.00 0.00 4.85
343 353 0.952984 GTGGACTCTTCTGTGCTGGC 60.953 60.000 0.00 0.00 0.00 4.85
347 357 0.761187 ACTCTTCTGTGCTGGCTCAA 59.239 50.000 0.00 0.00 0.00 3.02
348 358 1.155042 CTCTTCTGTGCTGGCTCAAC 58.845 55.000 0.00 0.00 0.00 3.18
353 363 0.040958 CTGTGCTGGCTCAACGTTTC 60.041 55.000 0.00 0.00 0.00 2.78
355 365 2.250939 TGCTGGCTCAACGTTTCCG 61.251 57.895 0.00 0.00 40.83 4.30
367 377 2.497304 CGTTTCCGTACCGAAATGTG 57.503 50.000 16.28 6.49 35.11 3.21
368 378 2.060284 CGTTTCCGTACCGAAATGTGA 58.940 47.619 16.28 0.00 35.11 3.58
369 379 2.669434 CGTTTCCGTACCGAAATGTGAT 59.331 45.455 16.28 0.00 35.11 3.06
370 380 3.482923 CGTTTCCGTACCGAAATGTGATG 60.483 47.826 16.28 0.00 35.11 3.07
373 383 1.663643 CCGTACCGAAATGTGATGGTG 59.336 52.381 0.00 0.00 35.93 4.17
377 387 3.915437 ACCGAAATGTGATGGTGTTTC 57.085 42.857 0.00 0.00 32.33 2.78
382 392 2.183478 ATGTGATGGTGTTTCGCTCA 57.817 45.000 0.00 0.00 0.00 4.26
383 393 1.511850 TGTGATGGTGTTTCGCTCAG 58.488 50.000 0.00 0.00 0.00 3.35
384 394 0.798776 GTGATGGTGTTTCGCTCAGG 59.201 55.000 0.00 0.00 0.00 3.86
385 395 0.955428 TGATGGTGTTTCGCTCAGGC 60.955 55.000 0.00 0.00 0.00 4.85
386 396 1.648467 GATGGTGTTTCGCTCAGGCC 61.648 60.000 0.00 0.00 34.44 5.19
387 397 3.423154 GGTGTTTCGCTCAGGCCG 61.423 66.667 0.00 0.00 34.44 6.13
388 398 4.090057 GTGTTTCGCTCAGGCCGC 62.090 66.667 0.00 0.00 34.44 6.53
389 399 4.617520 TGTTTCGCTCAGGCCGCA 62.618 61.111 0.00 0.00 34.44 5.69
390 400 3.127533 GTTTCGCTCAGGCCGCAT 61.128 61.111 0.00 0.00 34.44 4.73
391 401 3.126879 TTTCGCTCAGGCCGCATG 61.127 61.111 0.00 0.00 34.44 4.06
392 402 3.604129 TTTCGCTCAGGCCGCATGA 62.604 57.895 7.61 7.61 34.44 3.07
393 403 2.874648 TTTCGCTCAGGCCGCATGAT 62.875 55.000 8.39 0.00 34.44 2.45
394 404 2.874648 TTCGCTCAGGCCGCATGATT 62.875 55.000 8.39 0.00 34.44 2.57
395 405 1.595109 CGCTCAGGCCGCATGATTA 60.595 57.895 8.39 0.00 34.44 1.75
396 406 1.835483 CGCTCAGGCCGCATGATTAC 61.835 60.000 8.39 0.80 34.44 1.89
397 407 0.815213 GCTCAGGCCGCATGATTACA 60.815 55.000 8.39 0.00 0.00 2.41
398 408 1.888215 CTCAGGCCGCATGATTACAT 58.112 50.000 8.39 0.00 37.19 2.29
425 435 0.030638 CGAGTGGGCTGGTTTTGTTG 59.969 55.000 0.00 0.00 0.00 3.33
429 439 0.107945 TGGGCTGGTTTTGTTGCAAC 60.108 50.000 22.83 22.83 0.00 4.17
438 448 2.280835 TTGTTGCAACAACAGGGCA 58.719 47.368 35.10 16.35 43.45 5.36
441 451 2.132996 TTGCAACAACAGGGCAGGG 61.133 57.895 0.00 0.00 38.97 4.45
448 458 2.133641 AACAGGGCAGGGTGTTTGC 61.134 57.895 0.00 0.00 40.80 3.68
453 463 2.050077 GCAGGGTGTTTGCGCTTC 60.050 61.111 9.73 0.00 0.00 3.86
462 472 1.208259 GTTTGCGCTTCCCTTTTGTG 58.792 50.000 9.73 0.00 0.00 3.33
472 482 4.340381 GCTTCCCTTTTGTGATCAGCATAT 59.660 41.667 0.00 0.00 0.00 1.78
491 501 6.398095 GCATATATATGGCTATGCGTATGGA 58.602 40.000 21.50 0.00 40.41 3.41
513 523 3.689347 AGGCTTGTGAATTGTGATGCTA 58.311 40.909 0.00 0.00 0.00 3.49
516 526 6.066690 AGGCTTGTGAATTGTGATGCTATAT 58.933 36.000 0.00 0.00 0.00 0.86
517 527 6.206243 AGGCTTGTGAATTGTGATGCTATATC 59.794 38.462 0.00 0.00 0.00 1.63
518 528 6.075918 GCTTGTGAATTGTGATGCTATATCG 58.924 40.000 0.00 0.00 0.00 2.92
520 530 7.518848 GCTTGTGAATTGTGATGCTATATCGAA 60.519 37.037 0.00 0.00 0.00 3.71
521 531 7.967890 TGTGAATTGTGATGCTATATCGAAT 57.032 32.000 0.00 0.00 0.00 3.34
522 532 7.799784 TGTGAATTGTGATGCTATATCGAATG 58.200 34.615 0.00 0.00 0.00 2.67
523 533 6.740002 GTGAATTGTGATGCTATATCGAATGC 59.260 38.462 0.00 0.00 0.00 3.56
524 534 6.427547 TGAATTGTGATGCTATATCGAATGCA 59.572 34.615 7.28 7.28 39.83 3.96
525 535 5.596268 TTGTGATGCTATATCGAATGCAC 57.404 39.130 7.05 0.00 38.29 4.57
526 536 3.674753 TGTGATGCTATATCGAATGCACG 59.325 43.478 7.05 0.00 38.29 5.34
527 537 2.667969 TGATGCTATATCGAATGCACGC 59.332 45.455 7.05 4.47 38.29 5.34
529 539 1.060713 GCTATATCGAATGCACGCGT 58.939 50.000 5.58 5.58 0.00 6.01
530 540 1.455786 GCTATATCGAATGCACGCGTT 59.544 47.619 10.22 0.00 0.00 4.84
531 541 2.096909 GCTATATCGAATGCACGCGTTT 60.097 45.455 10.22 0.07 0.00 3.60
532 542 2.367399 ATATCGAATGCACGCGTTTG 57.633 45.000 10.22 0.00 0.00 2.93
533 543 0.371989 TATCGAATGCACGCGTTTGG 59.628 50.000 10.22 2.96 0.00 3.28
534 544 1.295357 ATCGAATGCACGCGTTTGGA 61.295 50.000 10.22 9.37 0.00 3.53
535 545 1.082431 CGAATGCACGCGTTTGGAA 60.082 52.632 10.22 0.00 0.00 3.53
536 546 0.658829 CGAATGCACGCGTTTGGAAA 60.659 50.000 10.22 0.00 0.00 3.13
537 547 1.052287 GAATGCACGCGTTTGGAAAG 58.948 50.000 10.22 0.00 0.00 2.62
538 548 0.939106 AATGCACGCGTTTGGAAAGC 60.939 50.000 10.22 9.07 0.00 3.51
539 549 2.025441 GCACGCGTTTGGAAAGCA 59.975 55.556 10.22 0.00 0.00 3.91
540 550 1.371635 GCACGCGTTTGGAAAGCAT 60.372 52.632 10.22 0.00 0.00 3.79
541 551 1.337110 GCACGCGTTTGGAAAGCATC 61.337 55.000 10.22 0.00 0.00 3.91
542 552 1.059657 CACGCGTTTGGAAAGCATCG 61.060 55.000 10.22 0.00 0.00 3.84
543 553 2.145905 CGCGTTTGGAAAGCATCGC 61.146 57.895 0.00 0.00 40.19 4.58
544 554 1.801512 GCGTTTGGAAAGCATCGCC 60.802 57.895 0.00 0.00 38.16 5.54
545 555 1.511887 CGTTTGGAAAGCATCGCCG 60.512 57.895 0.00 0.00 0.00 6.46
546 556 1.579429 GTTTGGAAAGCATCGCCGT 59.421 52.632 0.00 0.00 0.00 5.68
547 557 0.800012 GTTTGGAAAGCATCGCCGTA 59.200 50.000 0.00 0.00 0.00 4.02
548 558 1.400494 GTTTGGAAAGCATCGCCGTAT 59.600 47.619 0.00 0.00 0.00 3.06
581 591 1.428448 TGCTATATCGAATGCACGCC 58.572 50.000 0.00 0.00 0.00 5.68
608 618 2.491621 CATCGCCGTCTCTGCTGA 59.508 61.111 0.00 0.00 0.00 4.26
609 619 1.875813 CATCGCCGTCTCTGCTGAC 60.876 63.158 0.00 0.00 0.00 3.51
610 620 2.343426 ATCGCCGTCTCTGCTGACA 61.343 57.895 0.00 0.00 36.82 3.58
622 632 3.007635 TCTGCTGACATGCTCTCATTTG 58.992 45.455 0.00 0.00 0.00 2.32
686 698 4.651962 GGGCCTTGAGAGATAGGATATACC 59.348 50.000 0.84 0.00 39.35 2.73
710 722 3.940209 ACACACATTGGCATGTTAAGG 57.060 42.857 0.00 0.00 41.16 2.69
718 730 3.370840 TGGCATGTTAAGGAGAAGCAT 57.629 42.857 0.00 0.00 0.00 3.79
786 804 1.464608 CCGCAACATTGTGAGGTACTG 59.535 52.381 6.74 0.00 41.55 2.74
791 809 4.499696 GCAACATTGTGAGGTACTGCTTTT 60.500 41.667 0.00 0.00 41.55 2.27
795 813 7.524717 ACATTGTGAGGTACTGCTTTTTAAT 57.475 32.000 0.00 0.00 41.55 1.40
876 895 1.271856 TCCCCGATTTGTGCAGTAGA 58.728 50.000 0.00 0.00 0.00 2.59
877 896 1.626321 TCCCCGATTTGTGCAGTAGAA 59.374 47.619 0.00 0.00 0.00 2.10
878 897 2.009774 CCCCGATTTGTGCAGTAGAAG 58.990 52.381 0.00 0.00 0.00 2.85
879 898 2.615493 CCCCGATTTGTGCAGTAGAAGT 60.615 50.000 0.00 0.00 0.00 3.01
881 900 4.250464 CCCGATTTGTGCAGTAGAAGTTA 58.750 43.478 0.00 0.00 0.00 2.24
882 901 4.092968 CCCGATTTGTGCAGTAGAAGTTAC 59.907 45.833 0.00 0.00 0.00 2.50
883 902 4.201589 CCGATTTGTGCAGTAGAAGTTACG 60.202 45.833 0.00 0.00 0.00 3.18
884 903 4.619760 CGATTTGTGCAGTAGAAGTTACGA 59.380 41.667 0.00 0.00 0.00 3.43
885 904 5.442909 CGATTTGTGCAGTAGAAGTTACGAC 60.443 44.000 0.00 0.00 0.00 4.34
886 905 3.293311 TGTGCAGTAGAAGTTACGACC 57.707 47.619 0.00 0.00 0.00 4.79
994 1037 8.523915 ACATATTCTTTTATCAGGTGCATTCA 57.476 30.769 0.00 0.00 0.00 2.57
996 1039 4.944962 TCTTTTATCAGGTGCATTCACG 57.055 40.909 0.00 0.00 44.03 4.35
1231 1274 5.398711 CGCGGTGAGTCTAGTTTGTTATATC 59.601 44.000 0.00 0.00 0.00 1.63
1279 1322 0.608308 GGTAGGTTGGGGAACTGTGC 60.608 60.000 0.00 0.00 0.00 4.57
1328 1371 7.545265 TCCAAGTGCTTATTTGTTGATAATTGC 59.455 33.333 0.00 0.00 0.00 3.56
1480 1524 3.415212 ACTTGATCTGGTGTTGACATGG 58.585 45.455 0.00 0.00 0.00 3.66
1533 1577 6.910536 ATGTACCGAATAGCTTTTGAAGAG 57.089 37.500 0.00 0.00 0.00 2.85
1677 1733 9.915629 AAATTAGACGCTATGATCCTTAGTTAG 57.084 33.333 0.00 0.00 0.00 2.34
1876 1932 4.019591 GGACATGGAGGTAAGGTTACTTGT 60.020 45.833 0.00 0.00 37.53 3.16
1881 1937 4.657039 TGGAGGTAAGGTTACTTGTGAAGT 59.343 41.667 0.11 0.00 45.40 3.01
1899 1955 5.239525 GTGAAGTCTAGTGCCTTTTCATTGT 59.760 40.000 0.00 0.00 0.00 2.71
2020 2076 2.952310 ACACAGGGAAGTTCTCAAAAGC 59.048 45.455 5.34 0.00 0.00 3.51
2345 2404 1.154197 GGAGGTAACGGTGCAACTTC 58.846 55.000 0.00 0.00 46.39 3.01
2703 2763 3.924144 TGCTCAAAAAGTGCACAAAACT 58.076 36.364 21.04 0.00 41.43 2.66
2704 2764 4.314121 TGCTCAAAAAGTGCACAAAACTT 58.686 34.783 21.04 0.24 41.43 2.66
2706 2766 5.081394 GCTCAAAAAGTGCACAAAACTTTG 58.919 37.500 21.04 18.11 44.93 2.77
2784 2844 3.749609 GGCAGAAATTTTGCAAGATGCTT 59.250 39.130 19.78 0.89 45.31 3.91
2847 2907 4.497473 TTGGATTTGGTTTGATCACGTC 57.503 40.909 0.00 0.00 0.00 4.34
2896 2956 7.466725 CGAGAGTAGAACATTCACTCTCCTTAG 60.467 44.444 26.92 18.37 46.05 2.18
3086 3147 5.070981 TCCTCCCATCTTATGCTAGAAGTTG 59.929 44.000 0.00 0.00 0.00 3.16
3246 3307 7.967890 AAGAACTGGCCTTTAATTCAATTTG 57.032 32.000 3.32 0.00 0.00 2.32
3542 3604 9.733556 TTTAACATGTGAAGTTATACACAGGAT 57.266 29.630 16.40 8.86 46.82 3.24
3840 3902 2.363306 TGTTGACAGCAAACCCTGAT 57.637 45.000 0.00 0.00 35.42 2.90
3879 3941 4.829492 AGTTCAGCTTCTGCCATTACTTTT 59.171 37.500 0.00 0.00 40.80 2.27
3889 3951 3.438781 TGCCATTACTTTTAACTCCTGCG 59.561 43.478 0.00 0.00 0.00 5.18
4013 4075 4.352009 TGTGATGGCATTTGGTAAATCCT 58.648 39.130 0.00 0.00 37.07 3.24
4030 4092 7.125356 GGTAAATCCTTCTCTTAGTAGGGTTCA 59.875 40.741 0.00 0.00 35.39 3.18
4083 4145 5.569355 TCCTTGAACATTCAATGGAAGCTA 58.431 37.500 16.57 2.45 45.26 3.32
4116 4178 7.872138 TCTCATATCCCAAATTCCTACTTTGT 58.128 34.615 0.00 0.00 32.83 2.83
4147 4209 7.659390 AGTTATTAGCTATGAGCCTTCAACATC 59.341 37.037 0.00 0.00 43.77 3.06
4279 4341 4.952460 AGTGCCGAGTTACTTCTGTAAAA 58.048 39.130 0.00 0.00 39.96 1.52
4756 4819 0.237761 CTCAACTCTGCTGCTGTTGC 59.762 55.000 20.23 0.00 40.34 4.17
4939 5980 1.077086 TGGGTTGAGCATGCATGGT 59.923 52.632 30.31 30.31 41.89 3.55
5050 6095 6.509418 TTTTTGTGCTGTTTCTCTGTAACT 57.491 33.333 0.00 0.00 0.00 2.24
5242 6356 4.345547 CACTTATCCTAGTTCCCCTCTTCC 59.654 50.000 0.00 0.00 0.00 3.46
5243 6357 4.235636 ACTTATCCTAGTTCCCCTCTTCCT 59.764 45.833 0.00 0.00 0.00 3.36
5244 6358 3.805360 ATCCTAGTTCCCCTCTTCCTT 57.195 47.619 0.00 0.00 0.00 3.36
5245 6359 3.117552 TCCTAGTTCCCCTCTTCCTTC 57.882 52.381 0.00 0.00 0.00 3.46
5246 6360 2.120312 CCTAGTTCCCCTCTTCCTTCC 58.880 57.143 0.00 0.00 0.00 3.46
5247 6361 2.293251 CCTAGTTCCCCTCTTCCTTCCT 60.293 54.545 0.00 0.00 0.00 3.36
5248 6362 1.959710 AGTTCCCCTCTTCCTTCCTC 58.040 55.000 0.00 0.00 0.00 3.71
5426 6580 1.267574 ACCTCCATCATCGGCACACT 61.268 55.000 0.00 0.00 0.00 3.55
5428 6582 1.269988 CCTCCATCATCGGCACACTAG 60.270 57.143 0.00 0.00 0.00 2.57
5429 6583 1.410517 CTCCATCATCGGCACACTAGT 59.589 52.381 0.00 0.00 0.00 2.57
5438 6592 2.809601 CACACTAGTGCCGCCGTC 60.810 66.667 22.90 0.00 39.21 4.79
5439 6593 4.065281 ACACTAGTGCCGCCGTCC 62.065 66.667 22.90 0.00 0.00 4.79
5440 6594 4.063967 CACTAGTGCCGCCGTCCA 62.064 66.667 10.54 0.00 0.00 4.02
5441 6595 4.065281 ACTAGTGCCGCCGTCCAC 62.065 66.667 0.00 0.00 0.00 4.02
5442 6596 3.760035 CTAGTGCCGCCGTCCACT 61.760 66.667 11.49 11.49 44.02 4.00
5443 6597 3.296709 CTAGTGCCGCCGTCCACTT 62.297 63.158 11.92 0.00 42.02 3.16
5444 6598 3.291101 TAGTGCCGCCGTCCACTTC 62.291 63.158 11.92 0.00 42.02 3.01
5494 6648 3.991051 CCAGCACCGACGTCCACT 61.991 66.667 10.58 0.00 0.00 4.00
5503 6657 2.446994 ACGTCCACTTCCCCCACA 60.447 61.111 0.00 0.00 0.00 4.17
5613 6771 3.338250 ACCATGGCCATCACCGGT 61.338 61.111 17.61 17.64 31.64 5.28
5644 6802 4.391830 GCAAGAATCGACCTGTACATGAAA 59.608 41.667 0.00 0.00 0.00 2.69
5750 6914 5.538118 TCTGGACTTGCGTACATATAATGG 58.462 41.667 0.00 0.00 32.39 3.16
5756 6920 7.431084 GGACTTGCGTACATATAATGGTTTTTG 59.569 37.037 0.00 0.00 33.60 2.44
5761 6925 6.196353 GCGTACATATAATGGTTTTTGTGCTG 59.804 38.462 0.00 0.00 33.60 4.41
5800 6964 9.363763 AGACTAGGTTTTAGTTAATCTTAACGC 57.636 33.333 7.08 0.00 45.77 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.532155 GCGGGATCTCGTCTGCCT 61.532 66.667 17.85 0.00 0.00 4.75
1 2 4.593864 GGCGGGATCTCGTCTGCC 62.594 72.222 17.85 10.28 39.76 4.85
2 3 4.933064 CGGCGGGATCTCGTCTGC 62.933 72.222 18.86 4.96 31.91 4.26
3 4 4.933064 GCGGCGGGATCTCGTCTG 62.933 72.222 18.86 15.00 31.91 3.51
8 9 4.593864 GACTGGCGGCGGGATCTC 62.594 72.222 23.06 6.57 0.00 2.75
29 30 0.110486 AAATATGGGTAGGCGGCCAG 59.890 55.000 23.09 0.00 0.00 4.85
30 31 0.179004 CAAATATGGGTAGGCGGCCA 60.179 55.000 23.09 4.27 0.00 5.36
31 32 0.893727 CCAAATATGGGTAGGCGGCC 60.894 60.000 12.11 12.11 43.51 6.13
32 33 2.641197 CCAAATATGGGTAGGCGGC 58.359 57.895 0.00 0.00 43.51 6.53
42 43 3.947834 GAGAAGTCCCACACCCAAATATG 59.052 47.826 0.00 0.00 0.00 1.78
43 44 3.053619 GGAGAAGTCCCACACCCAAATAT 60.054 47.826 0.00 0.00 36.76 1.28
44 45 2.307686 GGAGAAGTCCCACACCCAAATA 59.692 50.000 0.00 0.00 36.76 1.40
45 46 1.075536 GGAGAAGTCCCACACCCAAAT 59.924 52.381 0.00 0.00 36.76 2.32
46 47 0.476771 GGAGAAGTCCCACACCCAAA 59.523 55.000 0.00 0.00 36.76 3.28
47 48 1.764571 CGGAGAAGTCCCACACCCAA 61.765 60.000 0.00 0.00 40.20 4.12
48 49 2.214216 CGGAGAAGTCCCACACCCA 61.214 63.158 0.00 0.00 40.20 4.51
49 50 2.663196 CGGAGAAGTCCCACACCC 59.337 66.667 0.00 0.00 40.20 4.61
50 51 2.047179 GCGGAGAAGTCCCACACC 60.047 66.667 0.00 0.00 40.20 4.16
51 52 2.432628 CGCGGAGAAGTCCCACAC 60.433 66.667 0.00 0.00 40.20 3.82
52 53 2.915659 ACGCGGAGAAGTCCCACA 60.916 61.111 12.47 0.00 40.20 4.17
53 54 2.432628 CACGCGGAGAAGTCCCAC 60.433 66.667 12.47 0.00 40.20 4.61
54 55 3.691342 CCACGCGGAGAAGTCCCA 61.691 66.667 12.47 0.00 40.20 4.37
56 57 3.591254 AAGCCACGCGGAGAAGTCC 62.591 63.158 12.47 0.00 39.88 3.85
57 58 2.048127 AAGCCACGCGGAGAAGTC 60.048 61.111 12.47 0.00 0.00 3.01
58 59 2.357517 CAAGCCACGCGGAGAAGT 60.358 61.111 12.47 0.00 0.00 3.01
59 60 3.793144 GCAAGCCACGCGGAGAAG 61.793 66.667 12.47 0.00 0.00 2.85
60 61 4.617520 TGCAAGCCACGCGGAGAA 62.618 61.111 12.47 0.00 0.00 2.87
62 63 3.932580 TACTGCAAGCCACGCGGAG 62.933 63.158 12.47 1.22 39.15 4.63
63 64 3.932580 CTACTGCAAGCCACGCGGA 62.933 63.158 12.47 0.00 39.15 5.54
64 65 3.490759 CTACTGCAAGCCACGCGG 61.491 66.667 12.47 0.00 41.71 6.46
65 66 4.152625 GCTACTGCAAGCCACGCG 62.153 66.667 3.53 3.53 37.60 6.01
66 67 2.743928 AGCTACTGCAAGCCACGC 60.744 61.111 6.77 0.00 43.86 5.34
67 68 3.171987 CAGCTACTGCAAGCCACG 58.828 61.111 6.77 0.00 43.86 4.94
82 83 0.179171 CGCTGAATTGAGCTTGGCAG 60.179 55.000 15.09 0.00 36.77 4.85
83 84 0.890542 ACGCTGAATTGAGCTTGGCA 60.891 50.000 15.09 0.00 36.77 4.92
84 85 0.455633 CACGCTGAATTGAGCTTGGC 60.456 55.000 15.09 0.00 35.20 4.52
85 86 0.877071 ACACGCTGAATTGAGCTTGG 59.123 50.000 23.40 11.70 41.36 3.61
86 87 1.959747 CACACGCTGAATTGAGCTTG 58.040 50.000 19.31 19.31 42.44 4.01
87 88 0.239347 GCACACGCTGAATTGAGCTT 59.761 50.000 15.09 2.34 36.77 3.74
88 89 0.886043 TGCACACGCTGAATTGAGCT 60.886 50.000 15.09 0.00 39.64 4.09
89 90 0.169672 ATGCACACGCTGAATTGAGC 59.830 50.000 6.86 6.86 39.64 4.26
90 91 2.674852 ACTATGCACACGCTGAATTGAG 59.325 45.455 0.00 0.00 39.64 3.02
91 92 2.698803 ACTATGCACACGCTGAATTGA 58.301 42.857 0.00 0.00 39.64 2.57
92 93 3.476295 AACTATGCACACGCTGAATTG 57.524 42.857 0.00 0.00 39.64 2.32
93 94 4.503741 AAAACTATGCACACGCTGAATT 57.496 36.364 0.00 0.00 39.64 2.17
94 95 4.503741 AAAAACTATGCACACGCTGAAT 57.496 36.364 0.00 0.00 39.64 2.57
95 96 3.980646 AAAAACTATGCACACGCTGAA 57.019 38.095 0.00 0.00 39.64 3.02
120 121 0.038067 TTCGGCGCTGCAACTAGTAA 60.038 50.000 12.58 0.00 0.00 2.24
121 122 0.734942 GTTCGGCGCTGCAACTAGTA 60.735 55.000 12.58 0.00 0.00 1.82
128 129 4.961511 AGTTCGTTCGGCGCTGCA 62.962 61.111 12.58 0.00 41.07 4.41
134 135 1.598685 TGGGGAAAGTTCGTTCGGC 60.599 57.895 0.00 0.00 0.00 5.54
138 139 0.822121 GCAGGTGGGGAAAGTTCGTT 60.822 55.000 0.00 0.00 0.00 3.85
142 143 0.402121 GAGAGCAGGTGGGGAAAGTT 59.598 55.000 0.00 0.00 0.00 2.66
161 163 4.334203 CAGACTACAGGCTACAGAGTACAG 59.666 50.000 0.00 0.00 0.00 2.74
162 164 4.262617 CAGACTACAGGCTACAGAGTACA 58.737 47.826 0.00 0.00 0.00 2.90
163 165 4.095185 CACAGACTACAGGCTACAGAGTAC 59.905 50.000 1.84 0.00 0.00 2.73
164 166 4.262617 CACAGACTACAGGCTACAGAGTA 58.737 47.826 1.84 0.00 0.00 2.59
165 167 3.085533 CACAGACTACAGGCTACAGAGT 58.914 50.000 1.84 0.00 0.00 3.24
166 168 2.159310 GCACAGACTACAGGCTACAGAG 60.159 54.545 1.84 0.00 0.00 3.35
167 169 1.819288 GCACAGACTACAGGCTACAGA 59.181 52.381 1.84 0.00 0.00 3.41
168 170 1.821753 AGCACAGACTACAGGCTACAG 59.178 52.381 0.00 0.00 32.09 2.74
169 171 1.924731 AGCACAGACTACAGGCTACA 58.075 50.000 0.00 0.00 32.09 2.74
170 172 3.423996 GTAGCACAGACTACAGGCTAC 57.576 52.381 6.38 6.38 46.71 3.58
171 173 3.017442 CAGTAGCACAGACTACAGGCTA 58.983 50.000 4.67 0.00 44.14 3.93
172 174 1.821753 CAGTAGCACAGACTACAGGCT 59.178 52.381 4.67 0.00 44.14 4.58
173 175 1.546476 ACAGTAGCACAGACTACAGGC 59.454 52.381 4.67 0.00 44.14 4.85
174 176 4.624336 CTACAGTAGCACAGACTACAGG 57.376 50.000 4.67 0.00 44.14 4.00
210 212 0.179702 CAGGCAGCAGCAGATTCCTA 59.820 55.000 2.65 0.00 44.61 2.94
237 239 3.069980 GATCAGCTCGAGGTGCGGT 62.070 63.158 34.11 23.46 42.77 5.68
238 240 2.279120 GATCAGCTCGAGGTGCGG 60.279 66.667 34.11 15.89 42.77 5.69
239 241 1.144565 CTTGATCAGCTCGAGGTGCG 61.145 60.000 34.11 16.60 42.77 5.34
240 242 0.809241 CCTTGATCAGCTCGAGGTGC 60.809 60.000 34.11 23.35 46.88 5.01
241 243 3.359194 CCTTGATCAGCTCGAGGTG 57.641 57.895 33.38 33.38 46.88 4.00
244 246 1.202394 CCACTCCTTGATCAGCTCGAG 60.202 57.143 8.45 8.45 35.40 4.04
251 253 0.247460 CAGCGTCCACTCCTTGATCA 59.753 55.000 0.00 0.00 0.00 2.92
255 257 2.320587 GCACAGCGTCCACTCCTTG 61.321 63.158 0.00 0.00 0.00 3.61
259 261 3.418068 GCTGCACAGCGTCCACTC 61.418 66.667 6.92 0.00 45.29 3.51
268 270 2.628106 GTGTGACACGCTGCACAG 59.372 61.111 11.93 0.00 44.78 3.66
273 275 2.327343 CCATGGGTGTGACACGCTG 61.327 63.158 28.76 22.84 45.53 5.18
305 315 0.668706 CCCTCACTGCAGTCAACGAG 60.669 60.000 18.64 19.43 0.00 4.18
314 324 0.764369 AAGAGTCCACCCTCACTGCA 60.764 55.000 0.00 0.00 33.75 4.41
315 325 0.036858 GAAGAGTCCACCCTCACTGC 60.037 60.000 0.00 0.00 33.75 4.40
321 331 0.472734 AGCACAGAAGAGTCCACCCT 60.473 55.000 0.00 0.00 0.00 4.34
331 341 0.882042 ACGTTGAGCCAGCACAGAAG 60.882 55.000 0.00 0.00 0.00 2.85
332 342 0.463654 AACGTTGAGCCAGCACAGAA 60.464 50.000 0.00 0.00 0.00 3.02
355 365 4.668177 CGAAACACCATCACATTTCGGTAC 60.668 45.833 9.48 0.00 45.95 3.34
356 366 3.433957 CGAAACACCATCACATTTCGGTA 59.566 43.478 9.48 0.00 45.95 4.02
357 367 2.225491 CGAAACACCATCACATTTCGGT 59.775 45.455 9.48 0.00 45.95 4.69
358 368 2.850321 CGAAACACCATCACATTTCGG 58.150 47.619 9.48 0.00 45.95 4.30
360 370 3.058293 TGAGCGAAACACCATCACATTTC 60.058 43.478 0.00 0.00 0.00 2.17
361 371 2.884012 TGAGCGAAACACCATCACATTT 59.116 40.909 0.00 0.00 0.00 2.32
363 373 2.079158 CTGAGCGAAACACCATCACAT 58.921 47.619 0.00 0.00 0.00 3.21
364 374 1.511850 CTGAGCGAAACACCATCACA 58.488 50.000 0.00 0.00 0.00 3.58
365 375 0.798776 CCTGAGCGAAACACCATCAC 59.201 55.000 0.00 0.00 0.00 3.06
366 376 0.955428 GCCTGAGCGAAACACCATCA 60.955 55.000 0.00 0.00 0.00 3.07
367 377 1.648467 GGCCTGAGCGAAACACCATC 61.648 60.000 0.00 0.00 41.24 3.51
368 378 1.675641 GGCCTGAGCGAAACACCAT 60.676 57.895 0.00 0.00 41.24 3.55
369 379 2.281484 GGCCTGAGCGAAACACCA 60.281 61.111 0.00 0.00 41.24 4.17
370 380 3.423154 CGGCCTGAGCGAAACACC 61.423 66.667 0.00 0.00 41.24 4.16
373 383 3.127533 ATGCGGCCTGAGCGAAAC 61.128 61.111 0.00 0.00 41.24 2.78
377 387 1.595109 TAATCATGCGGCCTGAGCG 60.595 57.895 13.26 0.00 41.24 5.03
378 388 0.815213 TGTAATCATGCGGCCTGAGC 60.815 55.000 13.26 0.00 38.76 4.26
389 399 4.262207 CCACTCGTAGGAGCATGTAATCAT 60.262 45.833 12.30 0.00 44.48 2.45
390 400 3.068165 CCACTCGTAGGAGCATGTAATCA 59.932 47.826 12.30 0.00 44.48 2.57
391 401 3.553096 CCCACTCGTAGGAGCATGTAATC 60.553 52.174 12.30 0.00 44.48 1.75
392 402 2.365617 CCCACTCGTAGGAGCATGTAAT 59.634 50.000 12.30 0.00 44.48 1.89
393 403 1.754803 CCCACTCGTAGGAGCATGTAA 59.245 52.381 12.30 0.00 44.48 2.41
394 404 1.399714 CCCACTCGTAGGAGCATGTA 58.600 55.000 12.30 0.00 44.48 2.29
395 405 1.961180 GCCCACTCGTAGGAGCATGT 61.961 60.000 12.30 0.00 44.48 3.21
396 406 1.227380 GCCCACTCGTAGGAGCATG 60.227 63.158 12.30 4.43 44.48 4.06
397 407 1.381872 AGCCCACTCGTAGGAGCAT 60.382 57.895 12.30 0.00 44.48 3.79
398 408 2.037367 AGCCCACTCGTAGGAGCA 59.963 61.111 12.30 0.00 44.48 4.26
399 409 2.496817 CAGCCCACTCGTAGGAGC 59.503 66.667 12.30 0.00 44.48 4.70
400 410 1.258445 AACCAGCCCACTCGTAGGAG 61.258 60.000 10.86 10.86 46.13 3.69
401 411 0.834687 AAACCAGCCCACTCGTAGGA 60.835 55.000 0.00 0.00 0.00 2.94
402 412 0.036306 AAAACCAGCCCACTCGTAGG 59.964 55.000 0.00 0.00 0.00 3.18
403 413 1.156736 CAAAACCAGCCCACTCGTAG 58.843 55.000 0.00 0.00 0.00 3.51
404 414 0.470766 ACAAAACCAGCCCACTCGTA 59.529 50.000 0.00 0.00 0.00 3.43
405 415 0.395173 AACAAAACCAGCCCACTCGT 60.395 50.000 0.00 0.00 0.00 4.18
406 416 0.030638 CAACAAAACCAGCCCACTCG 59.969 55.000 0.00 0.00 0.00 4.18
409 419 0.107945 TTGCAACAAAACCAGCCCAC 60.108 50.000 0.00 0.00 0.00 4.61
425 435 2.521708 ACCCTGCCCTGTTGTTGC 60.522 61.111 0.00 0.00 0.00 4.17
429 439 1.741525 CAAACACCCTGCCCTGTTG 59.258 57.895 0.00 0.00 30.88 3.33
438 448 2.597510 GGGAAGCGCAAACACCCT 60.598 61.111 11.47 0.00 37.75 4.34
441 451 1.208259 CAAAAGGGAAGCGCAAACAC 58.792 50.000 11.47 0.58 0.00 3.32
448 458 1.135575 GCTGATCACAAAAGGGAAGCG 60.136 52.381 0.00 0.00 0.00 4.68
453 463 7.415989 GCCATATATATGCTGATCACAAAAGGG 60.416 40.741 16.08 0.00 32.40 3.95
472 482 4.442893 GCCTTCCATACGCATAGCCATATA 60.443 45.833 0.00 0.00 0.00 0.86
491 501 2.895404 AGCATCACAATTCACAAGCCTT 59.105 40.909 0.00 0.00 0.00 4.35
513 523 1.003972 CCAAACGCGTGCATTCGATAT 60.004 47.619 14.98 0.00 0.00 1.63
516 526 1.499688 TTCCAAACGCGTGCATTCGA 61.500 50.000 14.98 0.00 0.00 3.71
517 527 0.658829 TTTCCAAACGCGTGCATTCG 60.659 50.000 14.98 8.68 0.00 3.34
518 528 1.052287 CTTTCCAAACGCGTGCATTC 58.948 50.000 14.98 0.00 0.00 2.67
520 530 1.371635 GCTTTCCAAACGCGTGCAT 60.372 52.632 14.98 0.00 0.00 3.96
521 531 2.025441 GCTTTCCAAACGCGTGCA 59.975 55.556 14.98 0.00 0.00 4.57
522 532 1.337110 GATGCTTTCCAAACGCGTGC 61.337 55.000 14.98 10.96 0.00 5.34
523 533 1.059657 CGATGCTTTCCAAACGCGTG 61.060 55.000 14.98 0.00 0.00 5.34
524 534 1.206578 CGATGCTTTCCAAACGCGT 59.793 52.632 5.58 5.58 0.00 6.01
525 535 2.145905 GCGATGCTTTCCAAACGCG 61.146 57.895 3.53 3.53 40.92 6.01
526 536 1.801512 GGCGATGCTTTCCAAACGC 60.802 57.895 0.00 0.00 45.49 4.84
527 537 1.511887 CGGCGATGCTTTCCAAACG 60.512 57.895 0.00 0.00 0.00 3.60
529 539 1.745232 ATACGGCGATGCTTTCCAAA 58.255 45.000 16.62 0.00 0.00 3.28
530 540 2.101750 TCTATACGGCGATGCTTTCCAA 59.898 45.455 16.62 0.00 0.00 3.53
531 541 1.684450 TCTATACGGCGATGCTTTCCA 59.316 47.619 16.62 0.00 0.00 3.53
532 542 2.329379 CTCTATACGGCGATGCTTTCC 58.671 52.381 16.62 0.00 0.00 3.13
533 543 1.721926 GCTCTATACGGCGATGCTTTC 59.278 52.381 16.62 0.00 0.00 2.62
534 544 1.341531 AGCTCTATACGGCGATGCTTT 59.658 47.619 16.62 0.00 0.00 3.51
535 545 0.962489 AGCTCTATACGGCGATGCTT 59.038 50.000 16.62 0.00 0.00 3.91
536 546 0.242286 CAGCTCTATACGGCGATGCT 59.758 55.000 16.62 10.34 0.00 3.79
537 547 1.347817 GCAGCTCTATACGGCGATGC 61.348 60.000 16.62 8.10 0.00 3.91
538 548 0.039165 TGCAGCTCTATACGGCGATG 60.039 55.000 16.62 0.00 0.00 3.84
539 549 0.891373 ATGCAGCTCTATACGGCGAT 59.109 50.000 16.62 5.41 0.00 4.58
540 550 1.530323 TATGCAGCTCTATACGGCGA 58.470 50.000 16.62 0.00 0.00 5.54
541 551 2.568696 ATATGCAGCTCTATACGGCG 57.431 50.000 4.80 4.80 0.00 6.46
542 552 4.590400 CAAATATGCAGCTCTATACGGC 57.410 45.455 0.00 0.00 0.00 5.68
566 576 1.603802 CCAAAGGCGTGCATTCGATAT 59.396 47.619 0.24 0.00 0.00 1.63
570 580 0.039617 TTTCCAAAGGCGTGCATTCG 60.040 50.000 0.00 0.00 0.00 3.34
581 591 0.179189 GACGGCGATGCTTTCCAAAG 60.179 55.000 16.62 0.00 39.03 2.77
608 618 4.298103 AGGAAGACAAATGAGAGCATGT 57.702 40.909 0.00 0.00 34.26 3.21
609 619 5.640189 AAAGGAAGACAAATGAGAGCATG 57.360 39.130 0.00 0.00 34.26 4.06
610 620 5.771666 TGAAAAGGAAGACAAATGAGAGCAT 59.228 36.000 0.00 0.00 35.92 3.79
622 632 2.548057 TGCACGACATGAAAAGGAAGAC 59.452 45.455 0.00 0.00 0.00 3.01
686 698 1.164411 ACATGCCAATGTGTGTACCG 58.836 50.000 0.00 0.00 45.51 4.02
710 722 2.941720 CCAAGTAGCTCCAATGCTTCTC 59.058 50.000 0.00 0.00 43.74 2.87
850 868 1.886655 GCACAAATCGGGGAAGAGGTT 60.887 52.381 0.00 0.00 0.00 3.50
876 895 4.925646 GGAAACAGATTACGGTCGTAACTT 59.074 41.667 16.62 3.93 42.44 2.66
877 896 4.022068 TGGAAACAGATTACGGTCGTAACT 60.022 41.667 16.62 12.94 38.41 2.24
878 897 4.236935 TGGAAACAGATTACGGTCGTAAC 58.763 43.478 16.62 11.26 38.41 2.50
879 898 4.517952 TGGAAACAGATTACGGTCGTAA 57.482 40.909 16.61 16.61 39.22 3.18
881 900 3.389925 TTGGAAACAGATTACGGTCGT 57.610 42.857 0.69 0.69 44.54 4.34
929 954 2.537560 GCATACTGCCAAGCGCGAT 61.538 57.895 12.10 0.00 42.08 4.58
994 1037 4.776308 ACTAAGGTAAACTCCCATCTTCGT 59.224 41.667 0.00 0.00 0.00 3.85
996 1039 6.407865 GGGTACTAAGGTAAACTCCCATCTTC 60.408 46.154 0.00 0.00 33.32 2.87
1231 1274 8.147058 AGTGTCAGCTATACTTATGATTTCTGG 58.853 37.037 0.00 0.00 0.00 3.86
1241 1284 7.580910 ACCTACCTTAGTGTCAGCTATACTTA 58.419 38.462 2.54 0.00 31.17 2.24
1279 1322 8.059461 TGGATATGTATACCTAGTATCCCTGTG 58.941 40.741 19.95 0.00 39.89 3.66
1328 1371 7.529158 TCATGTGCACAGATTTGTAAACATAG 58.471 34.615 25.84 9.38 39.02 2.23
1480 1524 3.656559 AGTTGATCATTTTTGGCACAGC 58.343 40.909 0.00 0.00 42.39 4.40
1533 1577 7.965045 TGTTGCAATAACAAAACCAAAAGTAC 58.035 30.769 0.59 0.00 0.00 2.73
1677 1733 3.665173 GCACTATGCTACAGCTTCAAC 57.335 47.619 2.44 0.00 40.96 3.18
1774 1830 3.193479 GGAATGTTGCTCAAAGGGTTAGG 59.807 47.826 0.00 0.00 0.00 2.69
1876 1932 5.376625 ACAATGAAAAGGCACTAGACTTCA 58.623 37.500 0.00 0.00 44.19 3.02
1881 1937 6.003326 TCATGAACAATGAAAAGGCACTAGA 58.997 36.000 0.00 0.00 42.49 2.43
2020 2076 4.935808 AGGTCACCAGCTAAATAAACTTCG 59.064 41.667 0.00 0.00 0.00 3.79
2677 2737 3.446799 TGTGCACTTTTTGAGCATTGAC 58.553 40.909 19.41 0.00 43.59 3.18
2701 2761 9.218440 ACAAAATCAATGTTCAAAGTTCAAAGT 57.782 25.926 0.00 0.00 0.00 2.66
2784 2844 9.897744 GAGACATCAAACTTTATCAAATGTTCA 57.102 29.630 0.00 0.00 33.24 3.18
2896 2956 9.472361 AAGAACCGTACATATATTACACATGAC 57.528 33.333 0.00 0.00 0.00 3.06
3019 3079 3.526019 AGCCATAAGCCCCAAAAGTACTA 59.474 43.478 0.00 0.00 45.47 1.82
3023 3083 1.560505 CAGCCATAAGCCCCAAAAGT 58.439 50.000 0.00 0.00 45.47 2.66
3889 3951 2.770164 ATGGTAGCCATCGATTAGCC 57.230 50.000 12.45 4.42 40.74 3.93
4065 4127 6.259550 ACTTGTAGCTTCCATTGAATGTTC 57.740 37.500 4.27 0.00 0.00 3.18
4083 4145 7.675619 AGGAATTTGGGATATGAGAAAACTTGT 59.324 33.333 0.00 0.00 0.00 3.16
4116 4178 9.899661 TGAAGGCTCATAGCTAATAACTTAAAA 57.100 29.630 0.00 0.00 41.99 1.52
4223 4285 3.201290 GTGCTCATGGATGAAATCGACT 58.799 45.455 0.00 0.00 46.86 4.18
5162 6236 4.038042 CCCACTTCTCTATCGCAGATTACA 59.962 45.833 0.00 0.00 45.12 2.41
5242 6356 0.528470 AGCGAAGAGGAACGAGGAAG 59.472 55.000 0.00 0.00 0.00 3.46
5243 6357 0.966920 AAGCGAAGAGGAACGAGGAA 59.033 50.000 0.00 0.00 0.00 3.36
5244 6358 0.966920 AAAGCGAAGAGGAACGAGGA 59.033 50.000 0.00 0.00 0.00 3.71
5245 6359 1.071605 CAAAGCGAAGAGGAACGAGG 58.928 55.000 0.00 0.00 0.00 4.63
5246 6360 0.440371 GCAAAGCGAAGAGGAACGAG 59.560 55.000 0.00 0.00 0.00 4.18
5247 6361 0.949105 GGCAAAGCGAAGAGGAACGA 60.949 55.000 0.00 0.00 0.00 3.85
5248 6362 1.227999 TGGCAAAGCGAAGAGGAACG 61.228 55.000 0.00 0.00 0.00 3.95
5426 6580 3.291101 GAAGTGGACGGCGGCACTA 62.291 63.158 17.61 0.00 0.00 2.74
5446 6600 4.980805 GAAGTGGACGGCGGCACA 62.981 66.667 17.61 7.58 0.00 4.57
5486 6640 2.446994 TGTGGGGGAAGTGGACGT 60.447 61.111 0.00 0.00 0.00 4.34
5494 6648 4.284550 GGTGCAGCTGTGGGGGAA 62.285 66.667 16.64 0.00 0.00 3.97
5516 6670 2.204291 TGGGGGAGTTGAGGGCAT 60.204 61.111 0.00 0.00 0.00 4.40
5521 6675 4.410400 GGCCGTGGGGGAGTTGAG 62.410 72.222 0.00 0.00 38.47 3.02
5613 6771 1.442769 GTCGATTCTTGCAAGCCTCA 58.557 50.000 21.99 0.99 0.00 3.86
5675 6839 2.149578 CAGGTTCTTCTTGGACAGCAG 58.850 52.381 0.00 0.00 0.00 4.24
5750 6914 2.223805 CCTCCTTGGACAGCACAAAAAC 60.224 50.000 0.00 0.00 38.35 2.43
5756 6920 1.623811 TCTAACCTCCTTGGACAGCAC 59.376 52.381 0.00 0.00 39.71 4.40
5761 6925 3.710724 ACCTAGTCTAACCTCCTTGGAC 58.289 50.000 0.00 0.00 39.99 4.02
5800 6964 5.389098 GCAATCTAAACAAGCATGCAAACAG 60.389 40.000 21.98 8.91 36.84 3.16


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

AutoCloner maintained by Alex Coulton.