Multiple sequence alignment - TraesCS6D01G192800

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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 TraesCS6D01G192800 chr6D 100.000 2600 0 0 1 2600 266954870 266952271 0.000000e+00 4802.0
1 TraesCS6D01G192800 chr6D 97.143 35 1 0 38 72 100520423 100520457 2.790000e-05 60.2
2 TraesCS6D01G192800 chr6D 76.852 108 19 5 1 102 78788961 78789068 3.610000e-04 56.5
3 TraesCS6D01G192800 chr6D 100.000 28 0 0 44 71 382350185 382350158 5.000000e-03 52.8
4 TraesCS6D01G192800 chr6A 95.303 1767 51 13 771 2525 379656295 379654549 0.000000e+00 2774.0
5 TraesCS6D01G192800 chr6A 95.146 103 5 0 189 291 379656389 379656287 2.070000e-36 163.0
6 TraesCS6D01G192800 chr6B 95.141 1379 45 11 782 2151 415035906 415034541 0.000000e+00 2156.0
7 TraesCS6D01G192800 chr6B 94.276 297 15 2 2230 2525 415028964 415028669 1.100000e-123 453.0
8 TraesCS6D01G192800 chr6B 85.106 329 39 7 426 749 578462324 578462647 6.940000e-86 327.0
9 TraesCS6D01G192800 chr6B 88.889 108 7 2 189 291 415036060 415035953 7.550000e-26 128.0
10 TraesCS6D01G192800 chr6B 95.652 46 2 0 1353 1398 624698847 624698892 9.980000e-10 75.0
11 TraesCS6D01G192800 chr6B 93.478 46 3 0 1353 1398 195273270 195273315 4.640000e-08 69.4
12 TraesCS6D01G192800 chr6B 82.500 80 5 5 1 71 702267828 702267749 7.770000e-06 62.1
13 TraesCS6D01G192800 chr6B 94.595 37 2 0 66 102 429677458 429677422 1.000000e-04 58.4
14 TraesCS6D01G192800 chr5B 84.167 480 74 2 291 770 359269625 359269148 5.070000e-127 464.0
15 TraesCS6D01G192800 chr5B 85.714 406 56 2 362 767 441540117 441540520 6.650000e-116 427.0
16 TraesCS6D01G192800 chr5B 92.000 50 3 1 134 183 466652510 466652558 4.640000e-08 69.4
17 TraesCS6D01G192800 chr5B 88.235 51 4 1 138 188 619924273 619924225 2.790000e-05 60.2
18 TraesCS6D01G192800 chr5D 84.444 450 60 7 329 770 527180059 527179612 3.970000e-118 435.0
19 TraesCS6D01G192800 chr7A 81.836 523 70 21 269 773 85647320 85646805 1.440000e-112 416.0
20 TraesCS6D01G192800 chr7A 87.006 354 42 3 426 778 617692227 617691877 1.880000e-106 396.0
21 TraesCS6D01G192800 chr7A 97.059 34 1 0 38 71 13052839 13052806 1.000000e-04 58.4
22 TraesCS6D01G192800 chr3A 84.298 363 51 6 395 756 726422391 726422034 1.480000e-92 350.0
23 TraesCS6D01G192800 chr7D 83.240 358 48 9 426 780 374767782 374768130 4.180000e-83 318.0
24 TraesCS6D01G192800 chr7D 94.444 36 2 0 67 102 57036288 57036253 3.610000e-04 56.5
25 TraesCS6D01G192800 chr7D 94.444 36 2 0 67 102 181702006 181701971 3.610000e-04 56.5
26 TraesCS6D01G192800 chr1B 82.857 350 54 6 426 774 571431218 571430874 2.510000e-80 309.0
27 TraesCS6D01G192800 chr3B 83.069 189 28 4 288 476 561025523 561025707 4.450000e-38 169.0
28 TraesCS6D01G192800 chr3B 100.000 30 0 0 150 179 502646175 502646204 3.610000e-04 56.5
29 TraesCS6D01G192800 chr3B 94.444 36 2 0 67 102 666171590 666171625 3.610000e-04 56.5
30 TraesCS6D01G192800 chr5A 90.741 54 5 0 1345 1398 401505898 401505845 3.590000e-09 73.1
31 TraesCS6D01G192800 chr5A 90.741 54 4 1 131 183 491240776 491240829 1.290000e-08 71.3
32 TraesCS6D01G192800 chr5A 97.059 34 1 0 38 71 514460086 514460053 1.000000e-04 58.4
33 TraesCS6D01G192800 chr5A 94.444 36 0 2 38 72 386180444 386180478 1.000000e-03 54.7
34 TraesCS6D01G192800 chr4D 93.478 46 3 0 1353 1398 358472686 358472641 4.640000e-08 69.4
35 TraesCS6D01G192800 chr4D 94.595 37 2 0 66 102 61237870 61237834 1.000000e-04 58.4
36 TraesCS6D01G192800 chr4D 94.444 36 2 0 67 102 14170043 14170078 3.610000e-04 56.5
37 TraesCS6D01G192800 chr1A 93.478 46 3 0 1353 1398 577819031 577819076 4.640000e-08 69.4
38 TraesCS6D01G192800 chr4A 97.222 36 1 0 67 102 52607275 52607240 7.770000e-06 62.1
39 TraesCS6D01G192800 chr3D 100.000 32 0 0 148 179 429086092 429086061 2.790000e-05 60.2
40 TraesCS6D01G192800 chr7B 97.059 34 1 0 38 71 31131696 31131663 1.000000e-04 58.4
41 TraesCS6D01G192800 chr2A 97.059 34 1 0 38 71 666029907 666029874 1.000000e-04 58.4
42 TraesCS6D01G192800 chr2D 94.444 36 2 0 67 102 416512231 416512196 3.610000e-04 56.5


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 TraesCS6D01G192800 chr6D 266952271 266954870 2599 True 4802.0 4802 100.0000 1 2600 1 chr6D.!!$R1 2599
1 TraesCS6D01G192800 chr6A 379654549 379656389 1840 True 1468.5 2774 95.2245 189 2525 2 chr6A.!!$R1 2336
2 TraesCS6D01G192800 chr6B 415034541 415036060 1519 True 1142.0 2156 92.0150 189 2151 2 chr6B.!!$R4 1962
3 TraesCS6D01G192800 chr7A 85646805 85647320 515 True 416.0 416 81.8360 269 773 1 chr7A.!!$R2 504

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
692 728 0.188342 AAAGGATGGTGTGTGGGCTT 59.812 50.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2230 0.034059 GTGTGCCCTCCGATCTATGG 59.966 60.0 0.0 0.0 0.0 2.74 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
23 24 5.914033 CTCCCTCCGTTTCATAATGTAAGA 58.086 41.667 0.00 0.00 0.00 2.10
24 25 5.667466 TCCCTCCGTTTCATAATGTAAGAC 58.333 41.667 0.00 0.00 0.00 3.01
25 26 5.424252 TCCCTCCGTTTCATAATGTAAGACT 59.576 40.000 0.00 0.00 0.00 3.24
26 27 6.070424 TCCCTCCGTTTCATAATGTAAGACTT 60.070 38.462 0.00 0.00 0.00 3.01
27 28 6.598064 CCCTCCGTTTCATAATGTAAGACTTT 59.402 38.462 0.00 0.00 0.00 2.66
28 29 7.120726 CCCTCCGTTTCATAATGTAAGACTTTT 59.879 37.037 0.00 0.00 0.00 2.27
29 30 8.512138 CCTCCGTTTCATAATGTAAGACTTTTT 58.488 33.333 0.00 0.00 0.00 1.94
53 54 9.828852 TTTTTACACTAAACGCCTTACATTATG 57.171 29.630 0.00 0.00 0.00 1.90
54 55 7.542534 TTACACTAAACGCCTTACATTATGG 57.457 36.000 0.00 0.00 0.00 2.74
55 56 4.879545 ACACTAAACGCCTTACATTATGGG 59.120 41.667 0.00 0.00 0.00 4.00
56 57 5.120399 CACTAAACGCCTTACATTATGGGA 58.880 41.667 0.00 0.00 0.00 4.37
57 58 5.007332 CACTAAACGCCTTACATTATGGGAC 59.993 44.000 0.00 0.00 0.00 4.46
58 59 2.234300 ACGCCTTACATTATGGGACG 57.766 50.000 0.00 0.30 0.00 4.79
59 60 1.758280 ACGCCTTACATTATGGGACGA 59.242 47.619 0.00 0.00 0.00 4.20
60 61 2.168936 ACGCCTTACATTATGGGACGAA 59.831 45.455 0.00 0.00 0.00 3.85
61 62 2.800544 CGCCTTACATTATGGGACGAAG 59.199 50.000 0.00 0.00 0.00 3.79
62 63 3.139077 GCCTTACATTATGGGACGAAGG 58.861 50.000 0.00 3.06 35.99 3.46
63 64 3.740115 CCTTACATTATGGGACGAAGGG 58.260 50.000 0.00 0.00 0.00 3.95
64 65 3.389983 CCTTACATTATGGGACGAAGGGA 59.610 47.826 0.00 0.00 0.00 4.20
65 66 4.503296 CCTTACATTATGGGACGAAGGGAG 60.503 50.000 0.00 0.00 0.00 4.30
66 67 2.478292 ACATTATGGGACGAAGGGAGT 58.522 47.619 0.00 0.00 0.00 3.85
67 68 3.649843 ACATTATGGGACGAAGGGAGTA 58.350 45.455 0.00 0.00 0.00 2.59
68 69 4.232091 ACATTATGGGACGAAGGGAGTAT 58.768 43.478 0.00 0.00 0.00 2.12
69 70 4.658901 ACATTATGGGACGAAGGGAGTATT 59.341 41.667 0.00 0.00 0.00 1.89
70 71 5.132144 ACATTATGGGACGAAGGGAGTATTT 59.868 40.000 0.00 0.00 0.00 1.40
71 72 5.703730 TTATGGGACGAAGGGAGTATTTT 57.296 39.130 0.00 0.00 0.00 1.82
72 73 3.343941 TGGGACGAAGGGAGTATTTTG 57.656 47.619 0.00 0.00 0.00 2.44
73 74 2.907696 TGGGACGAAGGGAGTATTTTGA 59.092 45.455 0.00 0.00 0.00 2.69
74 75 3.328343 TGGGACGAAGGGAGTATTTTGAA 59.672 43.478 0.00 0.00 0.00 2.69
75 76 3.939592 GGGACGAAGGGAGTATTTTGAAG 59.060 47.826 0.00 0.00 0.00 3.02
76 77 4.565028 GGGACGAAGGGAGTATTTTGAAGT 60.565 45.833 0.00 0.00 0.00 3.01
77 78 4.392138 GGACGAAGGGAGTATTTTGAAGTG 59.608 45.833 0.00 0.00 0.00 3.16
78 79 4.969484 ACGAAGGGAGTATTTTGAAGTGT 58.031 39.130 0.00 0.00 0.00 3.55
79 80 6.105397 ACGAAGGGAGTATTTTGAAGTGTA 57.895 37.500 0.00 0.00 0.00 2.90
80 81 6.164176 ACGAAGGGAGTATTTTGAAGTGTAG 58.836 40.000 0.00 0.00 0.00 2.74
81 82 6.014840 ACGAAGGGAGTATTTTGAAGTGTAGA 60.015 38.462 0.00 0.00 0.00 2.59
82 83 7.042335 CGAAGGGAGTATTTTGAAGTGTAGAT 58.958 38.462 0.00 0.00 0.00 1.98
83 84 7.549488 CGAAGGGAGTATTTTGAAGTGTAGATT 59.451 37.037 0.00 0.00 0.00 2.40
84 85 8.794335 AAGGGAGTATTTTGAAGTGTAGATTC 57.206 34.615 0.00 0.00 0.00 2.52
85 86 7.918076 AGGGAGTATTTTGAAGTGTAGATTCA 58.082 34.615 0.00 0.00 34.93 2.57
86 87 7.824779 AGGGAGTATTTTGAAGTGTAGATTCAC 59.175 37.037 0.00 0.00 36.44 3.18
88 89 8.874816 GGAGTATTTTGAAGTGTAGATTCACTC 58.125 37.037 0.00 0.00 46.25 3.51
89 90 9.424319 GAGTATTTTGAAGTGTAGATTCACTCA 57.576 33.333 0.00 0.00 46.25 3.41
90 91 9.950496 AGTATTTTGAAGTGTAGATTCACTCAT 57.050 29.630 0.00 0.00 46.25 2.90
93 94 8.908786 TTTTGAAGTGTAGATTCACTCATTCT 57.091 30.769 0.00 0.00 46.25 2.40
94 95 7.895975 TTGAAGTGTAGATTCACTCATTCTG 57.104 36.000 0.00 0.00 46.25 3.02
95 96 5.871524 TGAAGTGTAGATTCACTCATTCTGC 59.128 40.000 0.00 0.00 46.25 4.26
96 97 5.674052 AGTGTAGATTCACTCATTCTGCT 57.326 39.130 0.00 0.00 44.07 4.24
97 98 6.047511 AGTGTAGATTCACTCATTCTGCTT 57.952 37.500 0.00 0.00 44.07 3.91
98 99 6.105333 AGTGTAGATTCACTCATTCTGCTTC 58.895 40.000 0.00 0.00 44.07 3.86
99 100 5.005203 GTGTAGATTCACTCATTCTGCTTCG 59.995 44.000 0.00 0.00 35.68 3.79
100 101 4.199432 AGATTCACTCATTCTGCTTCGT 57.801 40.909 0.00 0.00 0.00 3.85
101 102 5.330455 AGATTCACTCATTCTGCTTCGTA 57.670 39.130 0.00 0.00 0.00 3.43
102 103 5.105752 AGATTCACTCATTCTGCTTCGTAC 58.894 41.667 0.00 0.00 0.00 3.67
103 104 3.934457 TCACTCATTCTGCTTCGTACA 57.066 42.857 0.00 0.00 0.00 2.90
104 105 4.456280 TCACTCATTCTGCTTCGTACAT 57.544 40.909 0.00 0.00 0.00 2.29
105 106 4.820897 TCACTCATTCTGCTTCGTACATT 58.179 39.130 0.00 0.00 0.00 2.71
106 107 4.864806 TCACTCATTCTGCTTCGTACATTC 59.135 41.667 0.00 0.00 0.00 2.67
107 108 4.627035 CACTCATTCTGCTTCGTACATTCA 59.373 41.667 0.00 0.00 0.00 2.57
108 109 4.627467 ACTCATTCTGCTTCGTACATTCAC 59.373 41.667 0.00 0.00 0.00 3.18
109 110 4.820897 TCATTCTGCTTCGTACATTCACT 58.179 39.130 0.00 0.00 0.00 3.41
110 111 4.864806 TCATTCTGCTTCGTACATTCACTC 59.135 41.667 0.00 0.00 0.00 3.51
111 112 3.934457 TCTGCTTCGTACATTCACTCA 57.066 42.857 0.00 0.00 0.00 3.41
112 113 4.456280 TCTGCTTCGTACATTCACTCAT 57.544 40.909 0.00 0.00 0.00 2.90
113 114 4.820897 TCTGCTTCGTACATTCACTCATT 58.179 39.130 0.00 0.00 0.00 2.57
114 115 4.864806 TCTGCTTCGTACATTCACTCATTC 59.135 41.667 0.00 0.00 0.00 2.67
115 116 4.820897 TGCTTCGTACATTCACTCATTCT 58.179 39.130 0.00 0.00 0.00 2.40
116 117 4.627035 TGCTTCGTACATTCACTCATTCTG 59.373 41.667 0.00 0.00 0.00 3.02
117 118 4.493220 GCTTCGTACATTCACTCATTCTGC 60.493 45.833 0.00 0.00 0.00 4.26
118 119 4.456280 TCGTACATTCACTCATTCTGCT 57.544 40.909 0.00 0.00 0.00 4.24
119 120 4.424626 TCGTACATTCACTCATTCTGCTC 58.575 43.478 0.00 0.00 0.00 4.26
120 121 3.553511 CGTACATTCACTCATTCTGCTCC 59.446 47.826 0.00 0.00 0.00 4.70
121 122 2.625737 ACATTCACTCATTCTGCTCCG 58.374 47.619 0.00 0.00 0.00 4.63
122 123 2.027745 ACATTCACTCATTCTGCTCCGT 60.028 45.455 0.00 0.00 0.00 4.69
123 124 3.195610 ACATTCACTCATTCTGCTCCGTA 59.804 43.478 0.00 0.00 0.00 4.02
124 125 2.941453 TCACTCATTCTGCTCCGTAC 57.059 50.000 0.00 0.00 0.00 3.67
125 126 2.447443 TCACTCATTCTGCTCCGTACT 58.553 47.619 0.00 0.00 0.00 2.73
126 127 2.826128 TCACTCATTCTGCTCCGTACTT 59.174 45.455 0.00 0.00 0.00 2.24
127 128 4.014406 TCACTCATTCTGCTCCGTACTTA 58.986 43.478 0.00 0.00 0.00 2.24
128 129 4.096532 TCACTCATTCTGCTCCGTACTTAG 59.903 45.833 0.00 0.00 0.00 2.18
129 130 4.017808 ACTCATTCTGCTCCGTACTTAGT 58.982 43.478 0.00 0.00 0.00 2.24
130 131 4.463186 ACTCATTCTGCTCCGTACTTAGTT 59.537 41.667 0.00 0.00 0.00 2.24
131 132 4.995124 TCATTCTGCTCCGTACTTAGTTC 58.005 43.478 0.00 0.00 0.00 3.01
132 133 3.863142 TTCTGCTCCGTACTTAGTTCC 57.137 47.619 0.00 0.00 0.00 3.62
133 134 3.083122 TCTGCTCCGTACTTAGTTCCT 57.917 47.619 0.00 0.00 0.00 3.36
134 135 4.226427 TCTGCTCCGTACTTAGTTCCTA 57.774 45.455 0.00 0.00 0.00 2.94
135 136 4.789807 TCTGCTCCGTACTTAGTTCCTAT 58.210 43.478 0.00 0.00 0.00 2.57
136 137 5.198965 TCTGCTCCGTACTTAGTTCCTATT 58.801 41.667 0.00 0.00 0.00 1.73
137 138 6.359804 TCTGCTCCGTACTTAGTTCCTATTA 58.640 40.000 0.00 0.00 0.00 0.98
138 139 6.830324 TCTGCTCCGTACTTAGTTCCTATTAA 59.170 38.462 0.00 0.00 0.00 1.40
139 140 7.340232 TCTGCTCCGTACTTAGTTCCTATTAAA 59.660 37.037 0.00 0.00 0.00 1.52
140 141 7.839907 TGCTCCGTACTTAGTTCCTATTAAAA 58.160 34.615 0.00 0.00 0.00 1.52
141 142 8.480501 TGCTCCGTACTTAGTTCCTATTAAAAT 58.519 33.333 0.00 0.00 0.00 1.82
142 143 8.976471 GCTCCGTACTTAGTTCCTATTAAAATC 58.024 37.037 0.00 0.00 0.00 2.17
176 177 9.743581 AAGAACTTATATTTAAAAACGGAGGGA 57.256 29.630 0.00 0.00 0.00 4.20
177 178 9.392259 AGAACTTATATTTAAAAACGGAGGGAG 57.608 33.333 0.00 0.00 0.00 4.30
178 179 9.170734 GAACTTATATTTAAAAACGGAGGGAGT 57.829 33.333 0.00 0.00 0.00 3.85
179 180 8.502105 ACTTATATTTAAAAACGGAGGGAGTG 57.498 34.615 0.00 0.00 0.00 3.51
180 181 7.555195 ACTTATATTTAAAAACGGAGGGAGTGG 59.445 37.037 0.00 0.00 0.00 4.00
181 182 3.581265 TTTAAAAACGGAGGGAGTGGT 57.419 42.857 0.00 0.00 0.00 4.16
182 183 4.703379 TTTAAAAACGGAGGGAGTGGTA 57.297 40.909 0.00 0.00 0.00 3.25
183 184 2.556144 AAAAACGGAGGGAGTGGTAC 57.444 50.000 0.00 0.00 0.00 3.34
184 185 1.725803 AAAACGGAGGGAGTGGTACT 58.274 50.000 0.00 0.00 0.00 2.73
185 186 1.264295 AAACGGAGGGAGTGGTACTC 58.736 55.000 0.39 0.39 44.32 2.59
186 187 0.408700 AACGGAGGGAGTGGTACTCT 59.591 55.000 8.68 0.00 44.46 3.24
187 188 1.293062 ACGGAGGGAGTGGTACTCTA 58.707 55.000 8.68 0.00 44.46 2.43
302 308 0.386113 TTTGTTTTGGGGCGTGCTAC 59.614 50.000 0.00 0.00 0.00 3.58
319 325 2.011741 TACGCATCCGTCGGCTGATT 62.012 55.000 19.00 6.71 46.39 2.57
344 350 0.899720 TTAAAGATCAGCCGGGTCGT 59.100 50.000 1.27 0.00 0.00 4.34
359 365 1.957177 GGTCGTGAGCCATCAGATCTA 59.043 52.381 0.00 0.00 35.66 1.98
361 367 3.759086 GGTCGTGAGCCATCAGATCTATA 59.241 47.826 0.00 0.00 35.66 1.31
362 368 4.380023 GGTCGTGAGCCATCAGATCTATAC 60.380 50.000 0.00 0.00 35.66 1.47
364 370 4.457257 TCGTGAGCCATCAGATCTATACTG 59.543 45.833 0.00 0.00 35.66 2.74
365 371 4.493547 GTGAGCCATCAGATCTATACTGC 58.506 47.826 0.00 0.00 35.66 4.40
366 372 4.021632 GTGAGCCATCAGATCTATACTGCA 60.022 45.833 0.00 0.00 35.66 4.41
367 373 4.776308 TGAGCCATCAGATCTATACTGCAT 59.224 41.667 0.00 0.00 35.61 3.96
368 374 5.105432 TGAGCCATCAGATCTATACTGCATC 60.105 44.000 0.00 0.00 35.61 3.91
369 375 4.776308 AGCCATCAGATCTATACTGCATCA 59.224 41.667 0.00 0.00 35.61 3.07
370 376 5.247792 AGCCATCAGATCTATACTGCATCAA 59.752 40.000 0.00 0.00 35.61 2.57
371 377 5.581479 GCCATCAGATCTATACTGCATCAAG 59.419 44.000 0.00 0.00 35.61 3.02
372 378 5.581479 CCATCAGATCTATACTGCATCAAGC 59.419 44.000 0.00 0.00 45.96 4.01
384 390 0.235665 CATCAAGCGCTCAAACGTGT 59.764 50.000 12.06 0.00 34.88 4.49
391 397 1.462541 GCGCTCAAACGTGTCTTCATC 60.463 52.381 0.00 0.00 34.88 2.92
400 406 2.877786 ACGTGTCTTCATCATTGCAACA 59.122 40.909 0.00 0.00 0.00 3.33
404 410 3.884693 TGTCTTCATCATTGCAACACAGT 59.115 39.130 0.00 0.00 0.00 3.55
405 411 4.338964 TGTCTTCATCATTGCAACACAGTT 59.661 37.500 0.00 0.00 0.00 3.16
406 412 5.163530 TGTCTTCATCATTGCAACACAGTTT 60.164 36.000 0.00 0.00 0.00 2.66
457 463 5.584649 CGGTCTTGTTGCAGGATTATTTCTA 59.415 40.000 0.00 0.00 0.00 2.10
463 469 6.908825 TGTTGCAGGATTATTTCTACAACAC 58.091 36.000 7.38 0.00 40.66 3.32
477 483 2.937469 CAACACAGGTCTTGTTGCAA 57.063 45.000 0.00 0.00 45.36 4.08
478 484 3.229276 CAACACAGGTCTTGTTGCAAA 57.771 42.857 0.00 0.00 45.36 3.68
480 486 3.951775 ACACAGGTCTTGTTGCAAAAA 57.048 38.095 0.00 0.00 38.16 1.94
523 558 6.396459 TTTTTGCAACTTTTTACAACCGAG 57.604 33.333 0.00 0.00 0.00 4.63
525 560 4.705337 TGCAACTTTTTACAACCGAGTT 57.295 36.364 0.00 0.00 0.00 3.01
552 587 5.461032 TTGTAATTCCTTTTGCAACCGAT 57.539 34.783 0.00 0.00 0.00 4.18
570 605 4.037923 ACCGATGTCTTGTTGCAGAAAAAT 59.962 37.500 0.00 0.00 0.00 1.82
571 606 4.984161 CCGATGTCTTGTTGCAGAAAAATT 59.016 37.500 0.00 0.00 0.00 1.82
604 640 7.081976 AGATATTTTGTTGCAAAACGTAGACC 58.918 34.615 0.00 0.00 0.00 3.85
605 641 3.423996 TTTGTTGCAAAACGTAGACCC 57.576 42.857 0.00 0.00 0.00 4.46
608 644 0.938713 TTGCAAAACGTAGACCCGTG 59.061 50.000 0.00 0.00 41.65 4.94
614 650 4.679662 CAAAACGTAGACCCGTGATAGAT 58.320 43.478 0.00 0.00 41.65 1.98
624 660 3.205338 CCCGTGATAGATCATTGCAACA 58.795 45.455 0.00 0.00 39.30 3.33
628 664 5.050769 CCGTGATAGATCATTGCAACACTAC 60.051 44.000 0.00 0.00 39.30 2.73
629 665 5.050769 CGTGATAGATCATTGCAACACTACC 60.051 44.000 0.00 0.00 39.30 3.18
638 674 6.000840 TCATTGCAACACTACCTATGTTTCA 58.999 36.000 0.00 0.00 38.22 2.69
674 710 2.938823 GCAGAAGCGCGTTCGACAA 61.939 57.895 8.43 0.00 40.49 3.18
680 716 1.225745 GCGCGTTCGACAAAGGATG 60.226 57.895 8.43 0.00 38.10 3.51
689 725 1.247567 GACAAAGGATGGTGTGTGGG 58.752 55.000 0.00 0.00 0.00 4.61
690 726 0.827507 ACAAAGGATGGTGTGTGGGC 60.828 55.000 0.00 0.00 0.00 5.36
692 728 0.188342 AAAGGATGGTGTGTGGGCTT 59.812 50.000 0.00 0.00 0.00 4.35
709 745 1.539496 GCTTTCACTGGGACACGTGTA 60.539 52.381 23.44 5.16 38.18 2.90
722 758 2.291043 CGTGTAAGGCAGGGGAGGT 61.291 63.158 0.00 0.00 0.00 3.85
770 806 4.506625 CCAGGTGATGGTAAGAGTTTTCCA 60.507 45.833 0.00 0.00 44.91 3.53
771 807 5.256474 CAGGTGATGGTAAGAGTTTTCCAT 58.744 41.667 0.00 0.00 44.35 3.41
774 810 6.209391 AGGTGATGGTAAGAGTTTTCCATTTG 59.791 38.462 0.00 0.00 42.48 2.32
775 811 6.015434 GGTGATGGTAAGAGTTTTCCATTTGT 60.015 38.462 0.00 0.00 42.48 2.83
776 812 7.433680 GTGATGGTAAGAGTTTTCCATTTGTT 58.566 34.615 0.00 0.00 42.48 2.83
777 813 7.926018 GTGATGGTAAGAGTTTTCCATTTGTTT 59.074 33.333 0.00 0.00 42.48 2.83
852 897 1.901159 TGAAATGGGCCTGTCCAAATG 59.099 47.619 4.53 0.00 40.62 2.32
942 987 2.726351 CGCCTCCAGTCCCTCTTCC 61.726 68.421 0.00 0.00 0.00 3.46
943 988 1.306568 GCCTCCAGTCCCTCTTCCT 60.307 63.158 0.00 0.00 0.00 3.36
1104 1149 2.974698 GCCGCCGATTCCATGGAG 60.975 66.667 15.53 4.30 0.00 3.86
1335 1380 1.867363 AGTCCCTGAAGAAGGCGTAT 58.133 50.000 0.00 0.00 45.89 3.06
1805 1850 3.667282 CGTCCGTCCGTGTCTGGT 61.667 66.667 0.00 0.00 0.00 4.00
1827 1872 2.862541 TGATTGGTTTCAGGTGGTGAG 58.137 47.619 0.00 0.00 36.21 3.51
1847 1892 5.065602 GTGAGCTGCTGATGTTATCATTGAA 59.934 40.000 7.01 0.00 38.85 2.69
1891 1936 3.622630 TGGTAGCTCCTCTAACTCTGAC 58.377 50.000 0.00 0.00 35.96 3.51
1938 1984 6.092670 GGATGATAATAGCTTTGCGCAATCTA 59.907 38.462 25.64 25.26 42.61 1.98
1939 1985 6.859420 TGATAATAGCTTTGCGCAATCTAA 57.141 33.333 25.64 13.76 42.61 2.10
1942 1988 7.388776 TGATAATAGCTTTGCGCAATCTAATCT 59.611 33.333 25.64 12.18 42.61 2.40
1959 2005 2.943449 TCTTTTTCGCGTTTTTGGGT 57.057 40.000 5.77 0.00 0.00 4.51
1960 2006 3.233684 TCTTTTTCGCGTTTTTGGGTT 57.766 38.095 5.77 0.00 0.00 4.11
1981 2027 6.080406 GGTTTGAAAAGTAGAGCTTCATTCG 58.920 40.000 0.00 0.00 36.17 3.34
2016 2062 2.046217 GAACCCGGGAACTCCAGC 60.046 66.667 32.02 2.58 37.91 4.85
2031 2077 1.120530 CCAGCCTTACTCCGGTACAT 58.879 55.000 0.00 0.00 0.00 2.29
2076 2126 0.961857 ATGAGCTGCAACATTCGCCA 60.962 50.000 1.02 0.00 0.00 5.69
2077 2127 1.171549 TGAGCTGCAACATTCGCCAA 61.172 50.000 1.02 0.00 0.00 4.52
2135 2185 3.591977 ACCTACTAAGCCCTTCCATTTGT 59.408 43.478 0.00 0.00 0.00 2.83
2157 2207 2.242926 TCAGGATCGGAAGGATAGCAG 58.757 52.381 0.00 0.00 34.82 4.24
2174 2224 9.830186 AGGATAGCAGTTCTATTCTTATTCCTA 57.170 33.333 0.00 0.00 40.02 2.94
2179 2229 9.207868 AGCAGTTCTATTCTTATTCCTAGTCTT 57.792 33.333 0.00 0.00 0.00 3.01
2180 2230 9.471084 GCAGTTCTATTCTTATTCCTAGTCTTC 57.529 37.037 0.00 0.00 0.00 2.87
2192 2242 4.912586 TCCTAGTCTTCCATAGATCGGAG 58.087 47.826 0.00 0.00 34.79 4.63
2235 2285 6.533730 TGAGTATGACTTGGTTGTGATTTCT 58.466 36.000 0.00 0.00 0.00 2.52
2479 2529 5.181433 GGAAGCTTGGTTCGACTAGAAAATT 59.819 40.000 2.10 0.00 41.10 1.82
2487 2537 6.426937 TGGTTCGACTAGAAAATTCCTGAAAG 59.573 38.462 0.00 0.00 41.10 2.62
2522 2572 5.681337 TGAGATCAGTATGTGAGACGATC 57.319 43.478 0.00 0.00 39.07 3.69
2525 2575 7.164803 TGAGATCAGTATGTGAGACGATCTAT 58.835 38.462 0.00 0.00 39.07 1.98
2526 2576 7.118971 TGAGATCAGTATGTGAGACGATCTATG 59.881 40.741 0.00 0.00 39.07 2.23
2527 2577 5.948992 TCAGTATGTGAGACGATCTATGG 57.051 43.478 0.00 0.00 37.40 2.74
2528 2578 5.621193 TCAGTATGTGAGACGATCTATGGA 58.379 41.667 0.00 0.00 37.40 3.41
2529 2579 6.062095 TCAGTATGTGAGACGATCTATGGAA 58.938 40.000 0.00 0.00 37.40 3.53
2530 2580 6.546034 TCAGTATGTGAGACGATCTATGGAAA 59.454 38.462 0.00 0.00 37.40 3.13
2531 2581 7.231519 TCAGTATGTGAGACGATCTATGGAAAT 59.768 37.037 0.00 0.00 37.40 2.17
2532 2582 7.869937 CAGTATGTGAGACGATCTATGGAAATT 59.130 37.037 0.00 0.00 0.00 1.82
2533 2583 7.869937 AGTATGTGAGACGATCTATGGAAATTG 59.130 37.037 0.00 0.00 0.00 2.32
2534 2584 6.220726 TGTGAGACGATCTATGGAAATTGA 57.779 37.500 0.00 0.00 0.00 2.57
2535 2585 6.276091 TGTGAGACGATCTATGGAAATTGAG 58.724 40.000 0.00 0.00 0.00 3.02
2536 2586 6.096846 TGTGAGACGATCTATGGAAATTGAGA 59.903 38.462 0.00 0.00 0.00 3.27
2537 2587 7.151308 GTGAGACGATCTATGGAAATTGAGAT 58.849 38.462 0.00 0.00 0.00 2.75
2538 2588 7.328249 GTGAGACGATCTATGGAAATTGAGATC 59.672 40.741 0.00 0.00 40.54 2.75
2539 2589 7.014615 TGAGACGATCTATGGAAATTGAGATCA 59.985 37.037 10.43 0.00 42.94 2.92
2540 2590 7.377398 AGACGATCTATGGAAATTGAGATCAG 58.623 38.462 10.43 6.38 42.94 2.90
2541 2591 7.015098 AGACGATCTATGGAAATTGAGATCAGT 59.985 37.037 10.43 8.81 42.94 3.41
2542 2592 8.183104 ACGATCTATGGAAATTGAGATCAGTA 57.817 34.615 10.43 0.00 42.94 2.74
2543 2593 8.811017 ACGATCTATGGAAATTGAGATCAGTAT 58.189 33.333 10.43 0.00 42.94 2.12
2544 2594 9.085250 CGATCTATGGAAATTGAGATCAGTATG 57.915 37.037 10.43 0.00 42.94 2.39
2545 2595 9.941325 GATCTATGGAAATTGAGATCAGTATGT 57.059 33.333 5.98 0.00 42.53 2.29
2549 2599 7.734924 TGGAAATTGAGATCAGTATGTATGC 57.265 36.000 0.00 0.00 37.40 3.14
2550 2600 6.712095 TGGAAATTGAGATCAGTATGTATGCC 59.288 38.462 0.00 0.00 37.40 4.40
2551 2601 6.150140 GGAAATTGAGATCAGTATGTATGCCC 59.850 42.308 0.00 0.00 37.40 5.36
2552 2602 5.830799 ATTGAGATCAGTATGTATGCCCA 57.169 39.130 0.00 0.00 37.40 5.36
2553 2603 5.830799 TTGAGATCAGTATGTATGCCCAT 57.169 39.130 0.00 0.00 37.40 4.00
2554 2604 5.411831 TGAGATCAGTATGTATGCCCATC 57.588 43.478 0.00 0.00 37.40 3.51
2555 2605 4.082026 TGAGATCAGTATGTATGCCCATCG 60.082 45.833 0.00 0.00 37.40 3.84
2556 2606 3.834813 AGATCAGTATGTATGCCCATCGT 59.165 43.478 0.00 0.00 37.40 3.73
2557 2607 3.385193 TCAGTATGTATGCCCATCGTG 57.615 47.619 0.00 0.00 37.40 4.35
2558 2608 2.698274 TCAGTATGTATGCCCATCGTGT 59.302 45.455 0.00 0.00 37.40 4.49
2559 2609 2.802247 CAGTATGTATGCCCATCGTGTG 59.198 50.000 0.00 0.00 0.00 3.82
2560 2610 1.531149 GTATGTATGCCCATCGTGTGC 59.469 52.381 0.00 0.00 0.00 4.57
2561 2611 0.181114 ATGTATGCCCATCGTGTGCT 59.819 50.000 0.00 0.00 0.00 4.40
2562 2612 0.827368 TGTATGCCCATCGTGTGCTA 59.173 50.000 0.00 0.00 0.00 3.49
2563 2613 1.202521 TGTATGCCCATCGTGTGCTAG 60.203 52.381 0.00 0.00 0.00 3.42
2564 2614 1.119684 TATGCCCATCGTGTGCTAGT 58.880 50.000 0.00 0.00 0.00 2.57
2565 2615 1.119684 ATGCCCATCGTGTGCTAGTA 58.880 50.000 0.00 0.00 0.00 1.82
2566 2616 0.899019 TGCCCATCGTGTGCTAGTAA 59.101 50.000 0.00 0.00 0.00 2.24
2567 2617 1.484653 TGCCCATCGTGTGCTAGTAAT 59.515 47.619 0.00 0.00 0.00 1.89
2568 2618 2.093181 TGCCCATCGTGTGCTAGTAATT 60.093 45.455 0.00 0.00 0.00 1.40
2569 2619 2.287915 GCCCATCGTGTGCTAGTAATTG 59.712 50.000 0.00 0.00 0.00 2.32
2570 2620 3.531538 CCCATCGTGTGCTAGTAATTGT 58.468 45.455 0.00 0.00 0.00 2.71
2571 2621 4.689071 CCCATCGTGTGCTAGTAATTGTA 58.311 43.478 0.00 0.00 0.00 2.41
2572 2622 4.506654 CCCATCGTGTGCTAGTAATTGTAC 59.493 45.833 0.00 0.00 0.00 2.90
2573 2623 5.106442 CCATCGTGTGCTAGTAATTGTACA 58.894 41.667 0.00 0.00 32.12 2.90
2574 2624 5.579119 CCATCGTGTGCTAGTAATTGTACAA 59.421 40.000 11.41 11.41 31.25 2.41
2575 2625 6.455113 CCATCGTGTGCTAGTAATTGTACAAC 60.455 42.308 11.22 0.00 31.25 3.32
2576 2626 5.775686 TCGTGTGCTAGTAATTGTACAACT 58.224 37.500 11.22 7.20 31.25 3.16
2577 2627 5.631929 TCGTGTGCTAGTAATTGTACAACTG 59.368 40.000 11.22 1.54 31.25 3.16
2578 2628 5.163992 CGTGTGCTAGTAATTGTACAACTGG 60.164 44.000 11.22 7.78 31.25 4.00
2579 2629 5.699458 GTGTGCTAGTAATTGTACAACTGGT 59.301 40.000 11.22 0.00 31.25 4.00
2580 2630 6.204108 GTGTGCTAGTAATTGTACAACTGGTT 59.796 38.462 11.22 3.88 31.25 3.67
2581 2631 6.425721 TGTGCTAGTAATTGTACAACTGGTTC 59.574 38.462 11.22 5.15 32.12 3.62
2582 2632 6.649557 GTGCTAGTAATTGTACAACTGGTTCT 59.350 38.462 11.22 6.62 32.12 3.01
2583 2633 7.172703 GTGCTAGTAATTGTACAACTGGTTCTT 59.827 37.037 11.22 1.98 32.12 2.52
2584 2634 7.172532 TGCTAGTAATTGTACAACTGGTTCTTG 59.827 37.037 11.22 6.36 32.12 3.02
2585 2635 7.172703 GCTAGTAATTGTACAACTGGTTCTTGT 59.827 37.037 11.22 0.00 35.92 3.16
2586 2636 9.701098 CTAGTAATTGTACAACTGGTTCTTGTA 57.299 33.333 11.22 0.00 33.79 2.41
2588 2638 8.999431 AGTAATTGTACAACTGGTTCTTGTATG 58.001 33.333 11.22 0.00 36.68 2.39
2589 2639 7.817418 AATTGTACAACTGGTTCTTGTATGT 57.183 32.000 11.22 0.00 36.68 2.29
2590 2640 6.854496 TTGTACAACTGGTTCTTGTATGTC 57.146 37.500 3.59 0.00 36.68 3.06
2591 2641 6.169557 TGTACAACTGGTTCTTGTATGTCT 57.830 37.500 0.00 0.00 36.68 3.41
2592 2642 6.588204 TGTACAACTGGTTCTTGTATGTCTT 58.412 36.000 0.00 0.00 36.68 3.01
2593 2643 7.728148 TGTACAACTGGTTCTTGTATGTCTTA 58.272 34.615 0.00 0.00 36.68 2.10
2594 2644 8.372459 TGTACAACTGGTTCTTGTATGTCTTAT 58.628 33.333 0.00 0.00 36.68 1.73
2595 2645 9.216117 GTACAACTGGTTCTTGTATGTCTTATT 57.784 33.333 0.00 0.00 36.68 1.40
2596 2646 8.691661 ACAACTGGTTCTTGTATGTCTTATTT 57.308 30.769 0.00 0.00 29.81 1.40
2597 2647 9.131791 ACAACTGGTTCTTGTATGTCTTATTTT 57.868 29.630 0.00 0.00 29.81 1.82
2598 2648 9.965824 CAACTGGTTCTTGTATGTCTTATTTTT 57.034 29.630 0.00 0.00 0.00 1.94
2599 2649 9.965824 AACTGGTTCTTGTATGTCTTATTTTTG 57.034 29.630 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.753921 GTCTTACATTATGAAACGGAGGGAG 59.246 44.000 0.00 0.00 0.00 4.30
1 2 5.424252 AGTCTTACATTATGAAACGGAGGGA 59.576 40.000 0.00 0.00 0.00 4.20
2 3 5.671493 AGTCTTACATTATGAAACGGAGGG 58.329 41.667 0.00 0.00 0.00 4.30
3 4 7.611213 AAAGTCTTACATTATGAAACGGAGG 57.389 36.000 0.00 0.00 0.00 4.30
27 28 9.828852 CATAATGTAAGGCGTTTAGTGTAAAAA 57.171 29.630 0.00 0.00 0.00 1.94
28 29 8.452534 CCATAATGTAAGGCGTTTAGTGTAAAA 58.547 33.333 0.00 0.00 0.00 1.52
29 30 7.066043 CCCATAATGTAAGGCGTTTAGTGTAAA 59.934 37.037 0.00 0.00 0.00 2.01
30 31 6.539464 CCCATAATGTAAGGCGTTTAGTGTAA 59.461 38.462 0.00 0.00 0.00 2.41
31 32 6.050432 CCCATAATGTAAGGCGTTTAGTGTA 58.950 40.000 0.00 0.00 0.00 2.90
32 33 4.879545 CCCATAATGTAAGGCGTTTAGTGT 59.120 41.667 0.00 0.00 0.00 3.55
33 34 5.007332 GTCCCATAATGTAAGGCGTTTAGTG 59.993 44.000 0.00 0.00 0.00 2.74
34 35 5.121105 GTCCCATAATGTAAGGCGTTTAGT 58.879 41.667 0.00 0.00 0.00 2.24
35 36 4.210537 CGTCCCATAATGTAAGGCGTTTAG 59.789 45.833 0.00 0.00 0.00 1.85
36 37 4.121317 CGTCCCATAATGTAAGGCGTTTA 58.879 43.478 0.00 0.00 0.00 2.01
37 38 2.940410 CGTCCCATAATGTAAGGCGTTT 59.060 45.455 0.00 0.00 0.00 3.60
38 39 2.168936 TCGTCCCATAATGTAAGGCGTT 59.831 45.455 0.00 0.00 0.00 4.84
39 40 1.758280 TCGTCCCATAATGTAAGGCGT 59.242 47.619 0.00 0.00 0.00 5.68
40 41 2.519377 TCGTCCCATAATGTAAGGCG 57.481 50.000 0.00 0.00 0.00 5.52
41 42 3.139077 CCTTCGTCCCATAATGTAAGGC 58.861 50.000 0.00 0.00 0.00 4.35
42 43 3.389983 TCCCTTCGTCCCATAATGTAAGG 59.610 47.826 0.00 0.00 33.37 2.69
43 44 4.101119 ACTCCCTTCGTCCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
44 45 4.035112 ACTCCCTTCGTCCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
45 46 3.649843 ACTCCCTTCGTCCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
46 47 2.478292 ACTCCCTTCGTCCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
47 48 4.891992 ATACTCCCTTCGTCCCATAATG 57.108 45.455 0.00 0.00 0.00 1.90
48 49 5.906772 AAATACTCCCTTCGTCCCATAAT 57.093 39.130 0.00 0.00 0.00 1.28
49 50 5.190132 TCAAAATACTCCCTTCGTCCCATAA 59.810 40.000 0.00 0.00 0.00 1.90
50 51 4.717778 TCAAAATACTCCCTTCGTCCCATA 59.282 41.667 0.00 0.00 0.00 2.74
51 52 3.521937 TCAAAATACTCCCTTCGTCCCAT 59.478 43.478 0.00 0.00 0.00 4.00
52 53 2.907696 TCAAAATACTCCCTTCGTCCCA 59.092 45.455 0.00 0.00 0.00 4.37
53 54 3.622166 TCAAAATACTCCCTTCGTCCC 57.378 47.619 0.00 0.00 0.00 4.46
54 55 4.392138 CACTTCAAAATACTCCCTTCGTCC 59.608 45.833 0.00 0.00 0.00 4.79
55 56 4.995487 ACACTTCAAAATACTCCCTTCGTC 59.005 41.667 0.00 0.00 0.00 4.20
56 57 4.969484 ACACTTCAAAATACTCCCTTCGT 58.031 39.130 0.00 0.00 0.00 3.85
57 58 6.395629 TCTACACTTCAAAATACTCCCTTCG 58.604 40.000 0.00 0.00 0.00 3.79
58 59 8.794335 AATCTACACTTCAAAATACTCCCTTC 57.206 34.615 0.00 0.00 0.00 3.46
59 60 8.383175 TGAATCTACACTTCAAAATACTCCCTT 58.617 33.333 0.00 0.00 29.96 3.95
60 61 7.824779 GTGAATCTACACTTCAAAATACTCCCT 59.175 37.037 0.00 0.00 37.73 4.20
61 62 7.975750 GTGAATCTACACTTCAAAATACTCCC 58.024 38.462 0.00 0.00 37.73 4.30
75 76 5.005203 CGAAGCAGAATGAGTGAATCTACAC 59.995 44.000 0.00 0.00 39.69 2.90
76 77 5.105063 CGAAGCAGAATGAGTGAATCTACA 58.895 41.667 0.00 0.00 39.69 2.74
77 78 5.105752 ACGAAGCAGAATGAGTGAATCTAC 58.894 41.667 0.00 0.00 39.69 2.59
78 79 5.330455 ACGAAGCAGAATGAGTGAATCTA 57.670 39.130 0.00 0.00 39.69 1.98
79 80 4.199432 ACGAAGCAGAATGAGTGAATCT 57.801 40.909 0.00 0.00 39.69 2.40
80 81 4.864806 TGTACGAAGCAGAATGAGTGAATC 59.135 41.667 0.00 0.00 39.69 2.52
81 82 4.820897 TGTACGAAGCAGAATGAGTGAAT 58.179 39.130 0.00 0.00 39.69 2.57
82 83 4.251543 TGTACGAAGCAGAATGAGTGAA 57.748 40.909 0.00 0.00 39.69 3.18
83 84 3.934457 TGTACGAAGCAGAATGAGTGA 57.066 42.857 0.00 0.00 39.69 3.41
84 85 4.627035 TGAATGTACGAAGCAGAATGAGTG 59.373 41.667 0.00 0.00 39.69 3.51
85 86 4.627467 GTGAATGTACGAAGCAGAATGAGT 59.373 41.667 0.00 0.00 39.69 3.41
86 87 4.867047 AGTGAATGTACGAAGCAGAATGAG 59.133 41.667 0.00 0.00 39.69 2.90
87 88 4.820897 AGTGAATGTACGAAGCAGAATGA 58.179 39.130 0.00 0.00 39.69 2.57
88 89 4.627035 TGAGTGAATGTACGAAGCAGAATG 59.373 41.667 0.00 0.00 40.87 2.67
89 90 4.820897 TGAGTGAATGTACGAAGCAGAAT 58.179 39.130 0.00 0.00 0.00 2.40
90 91 4.251543 TGAGTGAATGTACGAAGCAGAA 57.748 40.909 0.00 0.00 0.00 3.02
91 92 3.934457 TGAGTGAATGTACGAAGCAGA 57.066 42.857 0.00 0.00 0.00 4.26
92 93 4.867047 AGAATGAGTGAATGTACGAAGCAG 59.133 41.667 0.00 0.00 0.00 4.24
93 94 4.627035 CAGAATGAGTGAATGTACGAAGCA 59.373 41.667 0.00 0.00 39.69 3.91
94 95 4.493220 GCAGAATGAGTGAATGTACGAAGC 60.493 45.833 0.00 0.00 39.69 3.86
95 96 4.867047 AGCAGAATGAGTGAATGTACGAAG 59.133 41.667 0.00 0.00 39.69 3.79
96 97 4.820897 AGCAGAATGAGTGAATGTACGAA 58.179 39.130 0.00 0.00 39.69 3.85
97 98 4.424626 GAGCAGAATGAGTGAATGTACGA 58.575 43.478 0.00 0.00 39.69 3.43
98 99 3.553511 GGAGCAGAATGAGTGAATGTACG 59.446 47.826 0.00 0.00 39.69 3.67
99 100 3.553511 CGGAGCAGAATGAGTGAATGTAC 59.446 47.826 0.00 0.00 39.69 2.90
100 101 3.195610 ACGGAGCAGAATGAGTGAATGTA 59.804 43.478 0.00 0.00 39.69 2.29
101 102 2.027745 ACGGAGCAGAATGAGTGAATGT 60.028 45.455 0.00 0.00 39.69 2.71
102 103 2.625737 ACGGAGCAGAATGAGTGAATG 58.374 47.619 0.00 0.00 39.69 2.67
103 104 3.449018 AGTACGGAGCAGAATGAGTGAAT 59.551 43.478 0.00 0.00 39.69 2.57
104 105 2.826128 AGTACGGAGCAGAATGAGTGAA 59.174 45.455 0.00 0.00 39.69 3.18
105 106 2.447443 AGTACGGAGCAGAATGAGTGA 58.553 47.619 0.00 0.00 39.69 3.41
106 107 2.949451 AGTACGGAGCAGAATGAGTG 57.051 50.000 0.00 0.00 39.69 3.51
107 108 4.017808 ACTAAGTACGGAGCAGAATGAGT 58.982 43.478 0.00 0.00 39.69 3.41
108 109 4.640789 ACTAAGTACGGAGCAGAATGAG 57.359 45.455 0.00 0.00 39.69 2.90
109 110 4.142227 GGAACTAAGTACGGAGCAGAATGA 60.142 45.833 0.00 0.00 39.69 2.57
110 111 4.113354 GGAACTAAGTACGGAGCAGAATG 58.887 47.826 0.00 0.00 40.87 2.67
111 112 4.024670 AGGAACTAAGTACGGAGCAGAAT 58.975 43.478 0.00 0.00 36.02 2.40
112 113 3.428532 AGGAACTAAGTACGGAGCAGAA 58.571 45.455 0.00 0.00 36.02 3.02
113 114 3.083122 AGGAACTAAGTACGGAGCAGA 57.917 47.619 0.00 0.00 36.02 4.26
150 151 9.743581 TCCCTCCGTTTTTAAATATAAGTTCTT 57.256 29.630 0.00 0.00 0.00 2.52
151 152 9.392259 CTCCCTCCGTTTTTAAATATAAGTTCT 57.608 33.333 0.00 0.00 0.00 3.01
152 153 9.170734 ACTCCCTCCGTTTTTAAATATAAGTTC 57.829 33.333 0.00 0.00 0.00 3.01
153 154 8.953313 CACTCCCTCCGTTTTTAAATATAAGTT 58.047 33.333 0.00 0.00 0.00 2.66
154 155 7.555195 CCACTCCCTCCGTTTTTAAATATAAGT 59.445 37.037 0.00 0.00 0.00 2.24
155 156 7.555195 ACCACTCCCTCCGTTTTTAAATATAAG 59.445 37.037 0.00 0.00 0.00 1.73
156 157 7.404481 ACCACTCCCTCCGTTTTTAAATATAA 58.596 34.615 0.00 0.00 0.00 0.98
157 158 6.961042 ACCACTCCCTCCGTTTTTAAATATA 58.039 36.000 0.00 0.00 0.00 0.86
158 159 5.823312 ACCACTCCCTCCGTTTTTAAATAT 58.177 37.500 0.00 0.00 0.00 1.28
159 160 5.245584 ACCACTCCCTCCGTTTTTAAATA 57.754 39.130 0.00 0.00 0.00 1.40
160 161 4.108501 ACCACTCCCTCCGTTTTTAAAT 57.891 40.909 0.00 0.00 0.00 1.40
161 162 3.581265 ACCACTCCCTCCGTTTTTAAA 57.419 42.857 0.00 0.00 0.00 1.52
162 163 3.647590 AGTACCACTCCCTCCGTTTTTAA 59.352 43.478 0.00 0.00 0.00 1.52
163 164 3.242011 AGTACCACTCCCTCCGTTTTTA 58.758 45.455 0.00 0.00 0.00 1.52
164 165 2.038164 GAGTACCACTCCCTCCGTTTTT 59.962 50.000 0.00 0.00 39.28 1.94
165 166 1.622312 GAGTACCACTCCCTCCGTTTT 59.378 52.381 0.00 0.00 39.28 2.43
166 167 1.203149 AGAGTACCACTCCCTCCGTTT 60.203 52.381 2.74 0.00 46.18 3.60
167 168 0.408700 AGAGTACCACTCCCTCCGTT 59.591 55.000 2.74 0.00 46.18 4.44
168 169 1.293062 TAGAGTACCACTCCCTCCGT 58.707 55.000 2.74 0.00 46.18 4.69
169 170 2.660670 ATAGAGTACCACTCCCTCCG 57.339 55.000 2.74 0.00 46.18 4.63
170 171 8.104838 AGTATATATAGAGTACCACTCCCTCC 57.895 42.308 2.74 0.00 46.18 4.30
172 173 9.802210 AGTAGTATATATAGAGTACCACTCCCT 57.198 37.037 15.60 0.00 46.18 4.20
173 174 9.835389 CAGTAGTATATATAGAGTACCACTCCC 57.165 40.741 15.60 0.00 46.18 4.30
174 175 9.328845 GCAGTAGTATATATAGAGTACCACTCC 57.671 40.741 15.60 0.00 46.18 3.85
175 176 9.887629 TGCAGTAGTATATATAGAGTACCACTC 57.112 37.037 15.60 0.00 45.38 3.51
224 225 6.791303 TCTTGCAGTTTTTAAGAACACGAAT 58.209 32.000 11.10 0.00 31.94 3.34
227 228 7.449934 AATTCTTGCAGTTTTTAAGAACACG 57.550 32.000 11.10 3.40 41.57 4.49
241 242 5.603170 ATTCCACCCATTAATTCTTGCAG 57.397 39.130 0.00 0.00 0.00 4.41
302 308 1.705337 AAAATCAGCCGACGGATGCG 61.705 55.000 26.87 4.58 39.19 4.73
324 330 1.276989 ACGACCCGGCTGATCTTTAAA 59.723 47.619 0.00 0.00 0.00 1.52
325 331 0.899720 ACGACCCGGCTGATCTTTAA 59.100 50.000 0.00 0.00 0.00 1.52
326 332 0.174845 CACGACCCGGCTGATCTTTA 59.825 55.000 0.00 0.00 0.00 1.85
344 350 4.154942 TGCAGTATAGATCTGATGGCTCA 58.845 43.478 5.18 0.00 35.20 4.26
359 365 2.028420 TTGAGCGCTTGATGCAGTAT 57.972 45.000 13.26 0.00 43.06 2.12
361 367 0.239347 GTTTGAGCGCTTGATGCAGT 59.761 50.000 13.26 0.00 43.06 4.40
362 368 0.791983 CGTTTGAGCGCTTGATGCAG 60.792 55.000 13.26 0.00 43.06 4.41
364 370 1.061799 CACGTTTGAGCGCTTGATGC 61.062 55.000 13.26 0.00 38.57 3.91
365 371 0.235665 ACACGTTTGAGCGCTTGATG 59.764 50.000 13.26 8.81 34.88 3.07
366 372 0.512952 GACACGTTTGAGCGCTTGAT 59.487 50.000 13.26 0.00 34.88 2.57
367 373 0.529773 AGACACGTTTGAGCGCTTGA 60.530 50.000 13.26 0.00 34.88 3.02
368 374 0.304705 AAGACACGTTTGAGCGCTTG 59.695 50.000 13.26 7.26 34.88 4.01
369 375 0.582005 GAAGACACGTTTGAGCGCTT 59.418 50.000 13.26 0.00 34.88 4.68
370 376 0.529773 TGAAGACACGTTTGAGCGCT 60.530 50.000 11.27 11.27 34.88 5.92
371 377 0.512952 ATGAAGACACGTTTGAGCGC 59.487 50.000 0.00 0.00 34.88 5.92
372 378 1.792367 TGATGAAGACACGTTTGAGCG 59.208 47.619 0.00 0.00 37.94 5.03
373 379 4.153986 CAATGATGAAGACACGTTTGAGC 58.846 43.478 0.00 0.00 0.00 4.26
374 380 4.153986 GCAATGATGAAGACACGTTTGAG 58.846 43.478 0.00 0.00 0.00 3.02
375 381 3.563390 TGCAATGATGAAGACACGTTTGA 59.437 39.130 0.00 0.00 0.00 2.69
376 382 3.887741 TGCAATGATGAAGACACGTTTG 58.112 40.909 0.00 0.00 0.00 2.93
377 383 4.202000 TGTTGCAATGATGAAGACACGTTT 60.202 37.500 0.59 0.00 0.00 3.60
378 384 3.314913 TGTTGCAATGATGAAGACACGTT 59.685 39.130 0.59 0.00 0.00 3.99
379 385 2.877786 TGTTGCAATGATGAAGACACGT 59.122 40.909 0.59 0.00 0.00 4.49
380 386 3.228749 GTGTTGCAATGATGAAGACACG 58.771 45.455 0.59 0.00 30.86 4.49
384 390 5.518848 AAACTGTGTTGCAATGATGAAGA 57.481 34.783 0.59 0.00 0.00 2.87
400 406 5.852282 AGTAATCCTGCAACAAAAACTGT 57.148 34.783 0.00 0.00 41.27 3.55
432 438 3.627395 ATAATCCTGCAACAAGACCGA 57.373 42.857 0.00 0.00 0.00 4.69
433 439 4.396166 AGAAATAATCCTGCAACAAGACCG 59.604 41.667 0.00 0.00 0.00 4.79
502 537 5.061920 ACTCGGTTGTAAAAAGTTGCAAA 57.938 34.783 0.00 0.00 40.44 3.68
529 564 5.263968 TCGGTTGCAAAAGGAATTACAAA 57.736 34.783 0.00 0.00 0.00 2.83
532 567 4.805219 ACATCGGTTGCAAAAGGAATTAC 58.195 39.130 0.00 0.00 0.00 1.89
533 568 4.764823 AGACATCGGTTGCAAAAGGAATTA 59.235 37.500 0.00 0.00 0.00 1.40
538 573 2.034558 ACAAGACATCGGTTGCAAAAGG 59.965 45.455 0.00 0.00 0.00 3.11
539 574 3.354089 ACAAGACATCGGTTGCAAAAG 57.646 42.857 0.00 0.00 0.00 2.27
552 587 8.994429 TTAGAAAATTTTTCTGCAACAAGACA 57.006 26.923 27.05 7.00 0.00 3.41
588 624 0.939419 ACGGGTCTACGTTTTGCAAC 59.061 50.000 0.00 0.00 46.25 4.17
591 627 1.435577 ATCACGGGTCTACGTTTTGC 58.564 50.000 0.00 0.00 46.25 3.68
604 640 3.873361 AGTGTTGCAATGATCTATCACGG 59.127 43.478 0.59 0.00 40.03 4.94
605 641 5.050769 GGTAGTGTTGCAATGATCTATCACG 60.051 44.000 0.59 0.00 40.03 4.35
608 644 7.875041 ACATAGGTAGTGTTGCAATGATCTATC 59.125 37.037 0.59 4.13 0.00 2.08
614 650 6.000840 TGAAACATAGGTAGTGTTGCAATGA 58.999 36.000 0.59 0.00 41.07 2.57
638 674 4.645535 TCTGCAACAGAAGCTATGTTTCT 58.354 39.130 13.13 0.00 38.80 2.52
674 710 0.188342 AAAGCCCACACACCATCCTT 59.812 50.000 0.00 0.00 0.00 3.36
680 716 1.455383 CCAGTGAAAGCCCACACACC 61.455 60.000 0.00 0.00 39.42 4.16
689 725 0.814010 ACACGTGTCCCAGTGAAAGC 60.814 55.000 17.22 0.00 40.56 3.51
690 726 2.519377 TACACGTGTCCCAGTGAAAG 57.481 50.000 27.16 0.00 40.56 2.62
692 728 1.069513 CCTTACACGTGTCCCAGTGAA 59.930 52.381 27.16 11.08 40.56 3.18
749 785 4.993705 TGGAAAACTCTTACCATCACCT 57.006 40.909 0.00 0.00 0.00 4.00
767 803 5.529430 ACATGTGTCTCGTAAAACAAATGGA 59.471 36.000 0.00 0.00 42.80 3.41
770 806 8.696410 AAAAACATGTGTCTCGTAAAACAAAT 57.304 26.923 0.00 0.00 0.00 2.32
771 807 9.063739 GTAAAAACATGTGTCTCGTAAAACAAA 57.936 29.630 0.00 0.00 0.00 2.83
774 810 8.603983 TTGTAAAAACATGTGTCTCGTAAAAC 57.396 30.769 0.00 0.00 0.00 2.43
775 811 9.622004 TTTTGTAAAAACATGTGTCTCGTAAAA 57.378 25.926 0.00 0.44 0.00 1.52
776 812 9.622004 TTTTTGTAAAAACATGTGTCTCGTAAA 57.378 25.926 0.00 0.00 33.29 2.01
942 987 1.944177 TGGGTTTGGGAGAGAGAGAG 58.056 55.000 0.00 0.00 0.00 3.20
943 988 2.415983 TTGGGTTTGGGAGAGAGAGA 57.584 50.000 0.00 0.00 0.00 3.10
1443 1488 2.433145 TTCTGCAGCTTCGAGCCG 60.433 61.111 9.47 0.00 43.77 5.52
1805 1850 3.636300 CTCACCACCTGAAACCAATCAAA 59.364 43.478 0.00 0.00 0.00 2.69
1827 1872 5.496133 AGTTCAATGATAACATCAGCAGC 57.504 39.130 0.00 0.00 43.53 5.25
1891 1936 5.010922 TCCACAACATCCCAAATCAAAAGAG 59.989 40.000 0.00 0.00 0.00 2.85
1938 1984 3.787785 ACCCAAAAACGCGAAAAAGATT 58.212 36.364 15.93 0.00 0.00 2.40
1939 1985 3.446310 ACCCAAAAACGCGAAAAAGAT 57.554 38.095 15.93 0.00 0.00 2.40
1942 1988 3.323243 TCAAACCCAAAAACGCGAAAAA 58.677 36.364 15.93 0.00 0.00 1.94
1959 2005 6.861065 ACGAATGAAGCTCTACTTTTCAAA 57.139 33.333 0.00 0.00 39.29 2.69
1960 2006 6.861065 AACGAATGAAGCTCTACTTTTCAA 57.139 33.333 0.00 0.00 39.29 2.69
1981 2027 5.006746 CGGGTTCTTATCACAGCTGATAAAC 59.993 44.000 23.35 10.63 45.01 2.01
2016 2062 3.021695 TGAGTGATGTACCGGAGTAAGG 58.978 50.000 9.46 0.00 0.00 2.69
2031 2077 6.449635 AACTGCTAAACAATTTGTGAGTGA 57.550 33.333 2.13 0.00 0.00 3.41
2068 2118 1.209127 GTTGTCCCGTTGGCGAATG 59.791 57.895 0.00 0.00 41.33 2.67
2076 2126 3.662247 TTTGTGTTTTGTTGTCCCGTT 57.338 38.095 0.00 0.00 0.00 4.44
2077 2127 3.732471 CGATTTGTGTTTTGTTGTCCCGT 60.732 43.478 0.00 0.00 0.00 5.28
2116 2166 5.636123 TGAAACAAATGGAAGGGCTTAGTA 58.364 37.500 0.00 0.00 0.00 1.82
2135 2185 3.038280 TGCTATCCTTCCGATCCTGAAA 58.962 45.455 0.00 0.00 31.92 2.69
2168 2218 5.893500 TCCGATCTATGGAAGACTAGGAAT 58.106 41.667 0.00 0.00 36.93 3.01
2174 2224 2.883026 CCCTCCGATCTATGGAAGACT 58.117 52.381 0.00 0.00 36.93 3.24
2179 2229 0.105709 TGTGCCCTCCGATCTATGGA 60.106 55.000 0.00 0.00 0.00 3.41
2180 2230 0.034059 GTGTGCCCTCCGATCTATGG 59.966 60.000 0.00 0.00 0.00 2.74
2202 2252 3.801050 CCAAGTCATACTCAAGCTGATCG 59.199 47.826 0.00 0.00 0.00 3.69
2235 2285 1.725641 CACGATCCTTTGTAGCAGCA 58.274 50.000 0.00 0.00 0.00 4.41
2479 2529 5.879763 TCAATTTCCATCTGTCTTTCAGGA 58.120 37.500 0.00 0.00 43.76 3.86
2487 2537 7.714377 ACATACTGATCTCAATTTCCATCTGTC 59.286 37.037 0.00 0.00 31.93 3.51
2525 2575 6.712095 GGCATACATACTGATCTCAATTTCCA 59.288 38.462 0.00 0.00 0.00 3.53
2526 2576 6.150140 GGGCATACATACTGATCTCAATTTCC 59.850 42.308 0.00 0.00 0.00 3.13
2527 2577 6.712095 TGGGCATACATACTGATCTCAATTTC 59.288 38.462 0.00 0.00 0.00 2.17
2528 2578 6.604171 TGGGCATACATACTGATCTCAATTT 58.396 36.000 0.00 0.00 0.00 1.82
2529 2579 6.191657 TGGGCATACATACTGATCTCAATT 57.808 37.500 0.00 0.00 0.00 2.32
2530 2580 5.830799 TGGGCATACATACTGATCTCAAT 57.169 39.130 0.00 0.00 0.00 2.57
2531 2581 5.567423 CGATGGGCATACATACTGATCTCAA 60.567 44.000 0.00 0.00 0.00 3.02
2532 2582 4.082026 CGATGGGCATACATACTGATCTCA 60.082 45.833 0.00 0.00 0.00 3.27
2533 2583 4.081972 ACGATGGGCATACATACTGATCTC 60.082 45.833 0.00 0.00 0.00 2.75
2534 2584 3.834813 ACGATGGGCATACATACTGATCT 59.165 43.478 0.00 0.00 0.00 2.75
2535 2585 3.928992 CACGATGGGCATACATACTGATC 59.071 47.826 0.00 0.00 0.00 2.92
2536 2586 3.324846 ACACGATGGGCATACATACTGAT 59.675 43.478 0.00 0.00 0.00 2.90
2537 2587 2.698274 ACACGATGGGCATACATACTGA 59.302 45.455 0.00 0.00 0.00 3.41
2538 2588 2.802247 CACACGATGGGCATACATACTG 59.198 50.000 0.00 0.00 0.00 2.74
2539 2589 3.111853 CACACGATGGGCATACATACT 57.888 47.619 0.00 0.00 0.00 2.12
2549 2599 3.531538 ACAATTACTAGCACACGATGGG 58.468 45.455 0.00 0.00 0.00 4.00
2550 2600 5.106442 TGTACAATTACTAGCACACGATGG 58.894 41.667 0.00 0.00 0.00 3.51
2551 2601 6.310467 AGTTGTACAATTACTAGCACACGATG 59.690 38.462 12.26 0.00 0.00 3.84
2552 2602 6.310467 CAGTTGTACAATTACTAGCACACGAT 59.690 38.462 12.26 0.00 0.00 3.73
2553 2603 5.631929 CAGTTGTACAATTACTAGCACACGA 59.368 40.000 12.26 0.00 0.00 4.35
2554 2604 5.163992 CCAGTTGTACAATTACTAGCACACG 60.164 44.000 12.26 0.00 0.00 4.49
2555 2605 5.699458 ACCAGTTGTACAATTACTAGCACAC 59.301 40.000 12.26 0.00 0.00 3.82
2556 2606 5.860611 ACCAGTTGTACAATTACTAGCACA 58.139 37.500 12.26 0.00 0.00 4.57
2557 2607 6.649557 AGAACCAGTTGTACAATTACTAGCAC 59.350 38.462 12.26 0.00 0.00 4.40
2558 2608 6.765403 AGAACCAGTTGTACAATTACTAGCA 58.235 36.000 12.26 0.00 0.00 3.49
2559 2609 7.172703 ACAAGAACCAGTTGTACAATTACTAGC 59.827 37.037 12.26 0.00 36.35 3.42
2560 2610 8.603242 ACAAGAACCAGTTGTACAATTACTAG 57.397 34.615 12.26 0.77 36.35 2.57
2562 2612 8.999431 CATACAAGAACCAGTTGTACAATTACT 58.001 33.333 12.26 1.83 41.87 2.24
2563 2613 8.780249 ACATACAAGAACCAGTTGTACAATTAC 58.220 33.333 12.26 0.00 41.87 1.89
2564 2614 8.911918 ACATACAAGAACCAGTTGTACAATTA 57.088 30.769 12.26 0.00 41.87 1.40
2565 2615 7.719633 AGACATACAAGAACCAGTTGTACAATT 59.280 33.333 12.26 4.40 41.87 2.32
2566 2616 7.224297 AGACATACAAGAACCAGTTGTACAAT 58.776 34.615 12.26 0.00 41.87 2.71
2567 2617 6.588204 AGACATACAAGAACCAGTTGTACAA 58.412 36.000 3.59 3.59 41.87 2.41
2568 2618 6.169557 AGACATACAAGAACCAGTTGTACA 57.830 37.500 0.00 0.00 41.87 2.90
2569 2619 8.773404 ATAAGACATACAAGAACCAGTTGTAC 57.227 34.615 0.00 0.00 41.87 2.90
2570 2620 9.787435 AAATAAGACATACAAGAACCAGTTGTA 57.213 29.630 0.00 0.00 42.92 2.41
2571 2621 8.691661 AAATAAGACATACAAGAACCAGTTGT 57.308 30.769 0.00 0.00 41.11 3.32
2572 2622 9.965824 AAAAATAAGACATACAAGAACCAGTTG 57.034 29.630 0.00 0.00 0.00 3.16
2573 2623 9.965824 CAAAAATAAGACATACAAGAACCAGTT 57.034 29.630 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.