Multiple sequence alignment - TraesCS1A01G127300

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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 TraesCS1A01G127300 chr1A 100.000 2308 0 0 1 2308 154076351 154078658 0.000000e+00 4263
1 TraesCS1A01G127300 chr1A 95.746 1481 58 5 302 1779 554468375 554466897 0.000000e+00 2381
2 TraesCS1A01G127300 chr5D 95.878 1480 53 5 303 1779 483798902 483797428 0.000000e+00 2388
3 TraesCS1A01G127300 chr5D 95.003 1481 66 7 302 1779 6210993 6209518 0.000000e+00 2318
4 TraesCS1A01G127300 chr5D 90.110 273 10 1 2 274 6266228 6265973 2.840000e-89 339
5 TraesCS1A01G127300 chr5D 89.051 274 13 6 1 274 329158232 329157976 7.950000e-85 324
6 TraesCS1A01G127300 chr5D 88.686 274 14 1 1 274 6167200 6166944 3.700000e-83 318
7 TraesCS1A01G127300 chr3B 95.679 1481 56 7 302 1779 201503228 201504703 0.000000e+00 2374
8 TraesCS1A01G127300 chr3B 91.610 1478 101 13 308 1779 460161730 460160270 0.000000e+00 2021
9 TraesCS1A01G127300 chr3B 93.282 521 35 0 1788 2308 253772510 253773030 0.000000e+00 769
10 TraesCS1A01G127300 chr3B 89.781 274 11 2 1 274 101910434 101910178 3.670000e-88 335
11 TraesCS1A01G127300 chr2D 94.936 1481 54 6 302 1779 28723771 28725233 0.000000e+00 2300
12 TraesCS1A01G127300 chr2D 94.245 139 8 0 136 274 246163294 246163156 1.800000e-51 213
13 TraesCS1A01G127300 chr6B 96.376 1214 37 4 442 1652 579206857 579205648 0.000000e+00 1991
14 TraesCS1A01G127300 chr1B 95.389 1106 46 5 302 1404 633725721 633726824 0.000000e+00 1755
15 TraesCS1A01G127300 chr1B 93.321 524 31 3 1788 2308 340816254 340816776 0.000000e+00 771
16 TraesCS1A01G127300 chr5A 94.981 1076 46 5 710 1779 684322666 684323739 0.000000e+00 1681
17 TraesCS1A01G127300 chr5A 100.000 79 0 0 357 435 137031711 137031789 1.850000e-31 147
18 TraesCS1A01G127300 chr5A 91.089 101 4 1 305 405 38202810 38202715 5.170000e-27 132
19 TraesCS1A01G127300 chr7A 92.125 800 56 6 303 1100 707518069 707517275 0.000000e+00 1122
20 TraesCS1A01G127300 chr4B 94.073 523 28 3 1788 2308 243087122 243086601 0.000000e+00 791
21 TraesCS1A01G127300 chr1D 93.678 522 32 1 1788 2308 84154857 84155378 0.000000e+00 780
22 TraesCS1A01G127300 chr1D 93.499 523 31 2 1788 2308 191406213 191405692 0.000000e+00 774
23 TraesCS1A01G127300 chr1D 89.781 274 11 1 1 274 254444752 254445008 3.670000e-88 335
24 TraesCS1A01G127300 chr1D 88.321 274 15 2 1 274 51862321 51862065 1.720000e-81 313
25 TraesCS1A01G127300 chr1D 88.321 274 15 7 1 274 246422230 246422486 1.720000e-81 313
26 TraesCS1A01G127300 chr1D 88.000 200 7 3 1 200 30128461 30128643 1.070000e-53 220
27 TraesCS1A01G127300 chr4D 93.295 522 33 2 1788 2308 284190455 284189935 0.000000e+00 769
28 TraesCS1A01G127300 chr4D 93.295 522 34 1 1788 2308 328064083 328064604 0.000000e+00 769
29 TraesCS1A01G127300 chr4A 93.282 521 35 0 1788 2308 91501551 91501031 0.000000e+00 769
30 TraesCS1A01G127300 chr4A 93.197 147 10 0 128 274 43730328 43730474 1.390000e-52 217
31 TraesCS1A01G127300 chr7D 93.295 522 32 3 1788 2308 453333011 453333530 0.000000e+00 767
32 TraesCS1A01G127300 chr7D 97.600 125 3 0 1 125 231579220 231579096 4.990000e-52 215
33 TraesCS1A01G127300 chr2B 89.051 274 13 6 1 274 641861177 641861433 7.950000e-85 324
34 TraesCS1A01G127300 chr2B 86.131 274 9 4 1 274 799650117 799649873 3.780000e-68 268
35 TraesCS1A01G127300 chr6A 88.686 274 14 1 1 274 592504876 592505132 3.700000e-83 318
36 TraesCS1A01G127300 chr3D 88.686 274 13 4 1 274 200308545 200308290 3.700000e-83 318


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 TraesCS1A01G127300 chr1A 154076351 154078658 2307 False 4263 4263 100.000 1 2308 1 chr1A.!!$F1 2307
1 TraesCS1A01G127300 chr1A 554466897 554468375 1478 True 2381 2381 95.746 302 1779 1 chr1A.!!$R1 1477
2 TraesCS1A01G127300 chr5D 483797428 483798902 1474 True 2388 2388 95.878 303 1779 1 chr5D.!!$R5 1476
3 TraesCS1A01G127300 chr5D 6209518 6210993 1475 True 2318 2318 95.003 302 1779 1 chr5D.!!$R2 1477
4 TraesCS1A01G127300 chr3B 201503228 201504703 1475 False 2374 2374 95.679 302 1779 1 chr3B.!!$F1 1477
5 TraesCS1A01G127300 chr3B 460160270 460161730 1460 True 2021 2021 91.610 308 1779 1 chr3B.!!$R2 1471
6 TraesCS1A01G127300 chr3B 253772510 253773030 520 False 769 769 93.282 1788 2308 1 chr3B.!!$F2 520
7 TraesCS1A01G127300 chr2D 28723771 28725233 1462 False 2300 2300 94.936 302 1779 1 chr2D.!!$F1 1477
8 TraesCS1A01G127300 chr6B 579205648 579206857 1209 True 1991 1991 96.376 442 1652 1 chr6B.!!$R1 1210
9 TraesCS1A01G127300 chr1B 633725721 633726824 1103 False 1755 1755 95.389 302 1404 1 chr1B.!!$F2 1102
10 TraesCS1A01G127300 chr1B 340816254 340816776 522 False 771 771 93.321 1788 2308 1 chr1B.!!$F1 520
11 TraesCS1A01G127300 chr5A 684322666 684323739 1073 False 1681 1681 94.981 710 1779 1 chr5A.!!$F2 1069
12 TraesCS1A01G127300 chr7A 707517275 707518069 794 True 1122 1122 92.125 303 1100 1 chr7A.!!$R1 797
13 TraesCS1A01G127300 chr4B 243086601 243087122 521 True 791 791 94.073 1788 2308 1 chr4B.!!$R1 520
14 TraesCS1A01G127300 chr1D 84154857 84155378 521 False 780 780 93.678 1788 2308 1 chr1D.!!$F2 520
15 TraesCS1A01G127300 chr1D 191405692 191406213 521 True 774 774 93.499 1788 2308 1 chr1D.!!$R2 520
16 TraesCS1A01G127300 chr4D 284189935 284190455 520 True 769 769 93.295 1788 2308 1 chr4D.!!$R1 520
17 TraesCS1A01G127300 chr4D 328064083 328064604 521 False 769 769 93.295 1788 2308 1 chr4D.!!$F1 520
18 TraesCS1A01G127300 chr4A 91501031 91501551 520 True 769 769 93.282 1788 2308 1 chr4A.!!$R1 520
19 TraesCS1A01G127300 chr7D 453333011 453333530 519 False 767 767 93.295 1788 2308 1 chr7D.!!$F1 520

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
47 48 0.179084 ACCACGAGATGTATTGGCCG 60.179 55.0 0.0 0.0 31.76 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 1905 0.243907 CACACATCGACCGACTCCTT 59.756 55.0 0.0 0.0 0.0 3.36 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
29 30 8.324163 ACCTCAGAACAATACATTCTTGTTAC 57.676 34.615 1.74 0.00 44.56 2.50
30 31 7.390718 ACCTCAGAACAATACATTCTTGTTACC 59.609 37.037 1.74 0.00 44.56 2.85
31 32 7.390440 CCTCAGAACAATACATTCTTGTTACCA 59.610 37.037 1.74 0.00 44.56 3.25
32 33 8.094798 TCAGAACAATACATTCTTGTTACCAC 57.905 34.615 1.74 0.00 44.56 4.16
33 34 7.015289 CAGAACAATACATTCTTGTTACCACG 58.985 38.462 1.74 0.00 44.56 4.94
34 35 6.932400 AGAACAATACATTCTTGTTACCACGA 59.068 34.615 1.74 0.00 44.56 4.35
35 36 6.721571 ACAATACATTCTTGTTACCACGAG 57.278 37.500 0.00 0.00 37.28 4.18
36 37 6.460781 ACAATACATTCTTGTTACCACGAGA 58.539 36.000 0.00 0.00 41.15 4.04
37 38 7.103641 ACAATACATTCTTGTTACCACGAGAT 58.896 34.615 0.00 0.00 42.23 2.75
38 39 7.064609 ACAATACATTCTTGTTACCACGAGATG 59.935 37.037 0.00 0.00 42.23 2.90
39 40 4.894784 ACATTCTTGTTACCACGAGATGT 58.105 39.130 0.00 0.00 42.23 3.06
40 41 6.032956 ACATTCTTGTTACCACGAGATGTA 57.967 37.500 0.00 0.00 42.23 2.29
41 42 6.640518 ACATTCTTGTTACCACGAGATGTAT 58.359 36.000 0.00 0.00 42.23 2.29
42 43 7.103641 ACATTCTTGTTACCACGAGATGTATT 58.896 34.615 0.00 0.00 42.23 1.89
43 44 6.961359 TTCTTGTTACCACGAGATGTATTG 57.039 37.500 0.00 0.00 42.23 1.90
44 45 5.416083 TCTTGTTACCACGAGATGTATTGG 58.584 41.667 0.00 0.00 38.38 3.16
45 46 3.527533 TGTTACCACGAGATGTATTGGC 58.472 45.455 0.00 0.00 31.76 4.52
46 47 2.870411 GTTACCACGAGATGTATTGGCC 59.130 50.000 0.00 0.00 31.76 5.36
47 48 0.179084 ACCACGAGATGTATTGGCCG 60.179 55.000 0.00 0.00 31.76 6.13
48 49 1.498865 CCACGAGATGTATTGGCCGC 61.499 60.000 0.00 0.00 0.00 6.53
49 50 0.530650 CACGAGATGTATTGGCCGCT 60.531 55.000 0.00 0.00 0.00 5.52
50 51 1.037493 ACGAGATGTATTGGCCGCTA 58.963 50.000 0.00 0.00 0.00 4.26
51 52 1.269621 ACGAGATGTATTGGCCGCTAC 60.270 52.381 0.00 2.63 0.00 3.58
52 53 1.269569 CGAGATGTATTGGCCGCTACA 60.270 52.381 16.85 16.85 32.75 2.74
53 54 2.408050 GAGATGTATTGGCCGCTACAG 58.592 52.381 18.68 0.00 31.79 2.74
54 55 2.035961 GAGATGTATTGGCCGCTACAGA 59.964 50.000 18.68 1.46 31.79 3.41
55 56 2.634940 AGATGTATTGGCCGCTACAGAT 59.365 45.455 18.68 9.67 31.79 2.90
56 57 2.526304 TGTATTGGCCGCTACAGATC 57.474 50.000 11.98 0.00 0.00 2.75
57 58 1.760029 TGTATTGGCCGCTACAGATCA 59.240 47.619 11.98 0.00 0.00 2.92
58 59 2.368548 TGTATTGGCCGCTACAGATCAT 59.631 45.455 11.98 0.00 0.00 2.45
59 60 2.645838 ATTGGCCGCTACAGATCATT 57.354 45.000 0.00 0.00 0.00 2.57
60 61 2.418368 TTGGCCGCTACAGATCATTT 57.582 45.000 0.00 0.00 0.00 2.32
61 62 1.667236 TGGCCGCTACAGATCATTTG 58.333 50.000 0.00 0.00 0.00 2.32
62 63 1.209261 TGGCCGCTACAGATCATTTGA 59.791 47.619 0.00 0.00 0.00 2.69
63 64 2.158769 TGGCCGCTACAGATCATTTGAT 60.159 45.455 0.00 0.00 37.51 2.57
64 65 2.880890 GGCCGCTACAGATCATTTGATT 59.119 45.455 0.00 0.00 34.37 2.57
65 66 3.304257 GGCCGCTACAGATCATTTGATTG 60.304 47.826 0.00 0.00 34.37 2.67
66 67 3.304257 GCCGCTACAGATCATTTGATTGG 60.304 47.826 0.00 0.00 34.37 3.16
67 68 4.129380 CCGCTACAGATCATTTGATTGGA 58.871 43.478 0.00 0.00 34.37 3.53
68 69 4.576053 CCGCTACAGATCATTTGATTGGAA 59.424 41.667 0.00 0.00 34.37 3.53
69 70 5.240183 CCGCTACAGATCATTTGATTGGAAT 59.760 40.000 0.00 0.00 34.37 3.01
70 71 6.369005 CGCTACAGATCATTTGATTGGAATC 58.631 40.000 0.00 0.00 34.37 2.52
71 72 6.017687 CGCTACAGATCATTTGATTGGAATCA 60.018 38.462 0.00 0.00 43.28 2.57
84 85 6.416415 TGATTGGAATCAAATTTGGAATGGG 58.584 36.000 17.90 0.00 42.11 4.00
85 86 5.839517 TTGGAATCAAATTTGGAATGGGT 57.160 34.783 17.90 0.00 0.00 4.51
86 87 6.942163 TTGGAATCAAATTTGGAATGGGTA 57.058 33.333 17.90 0.00 0.00 3.69
87 88 7.507797 TTGGAATCAAATTTGGAATGGGTAT 57.492 32.000 17.90 0.00 0.00 2.73
88 89 8.615360 TTGGAATCAAATTTGGAATGGGTATA 57.385 30.769 17.90 0.00 0.00 1.47
89 90 8.017418 TGGAATCAAATTTGGAATGGGTATAC 57.983 34.615 17.90 0.00 0.00 1.47
90 91 7.843760 TGGAATCAAATTTGGAATGGGTATACT 59.156 33.333 17.90 0.00 0.00 2.12
91 92 8.704668 GGAATCAAATTTGGAATGGGTATACTT 58.295 33.333 17.90 0.00 0.00 2.24
92 93 9.533253 GAATCAAATTTGGAATGGGTATACTTG 57.467 33.333 17.90 0.00 0.00 3.16
93 94 8.837099 ATCAAATTTGGAATGGGTATACTTGA 57.163 30.769 17.90 1.02 0.00 3.02
94 95 8.062065 TCAAATTTGGAATGGGTATACTTGAC 57.938 34.615 17.90 0.00 0.00 3.18
95 96 6.693315 AATTTGGAATGGGTATACTTGACG 57.307 37.500 2.25 0.00 0.00 4.35
96 97 5.423704 TTTGGAATGGGTATACTTGACGA 57.576 39.130 2.25 0.00 0.00 4.20
97 98 5.623956 TTGGAATGGGTATACTTGACGAT 57.376 39.130 2.25 0.00 0.00 3.73
98 99 4.956085 TGGAATGGGTATACTTGACGATG 58.044 43.478 2.25 0.00 0.00 3.84
99 100 4.651962 TGGAATGGGTATACTTGACGATGA 59.348 41.667 2.25 0.00 0.00 2.92
100 101 4.989168 GGAATGGGTATACTTGACGATGAC 59.011 45.833 2.25 0.00 0.00 3.06
101 102 3.703286 TGGGTATACTTGACGATGACG 57.297 47.619 2.25 0.00 45.75 4.35
102 103 3.281158 TGGGTATACTTGACGATGACGA 58.719 45.455 2.25 0.00 42.66 4.20
103 104 3.887110 TGGGTATACTTGACGATGACGAT 59.113 43.478 2.25 0.00 42.66 3.73
104 105 5.065235 TGGGTATACTTGACGATGACGATA 58.935 41.667 2.25 0.00 42.66 2.92
105 106 5.708697 TGGGTATACTTGACGATGACGATAT 59.291 40.000 2.25 0.00 42.66 1.63
106 107 6.028368 GGGTATACTTGACGATGACGATATG 58.972 44.000 2.25 0.00 42.66 1.78
107 108 6.128090 GGGTATACTTGACGATGACGATATGA 60.128 42.308 2.25 0.00 42.66 2.15
108 109 7.303261 GGTATACTTGACGATGACGATATGAA 58.697 38.462 2.25 0.00 42.66 2.57
109 110 7.968956 GGTATACTTGACGATGACGATATGAAT 59.031 37.037 2.25 0.00 42.66 2.57
110 111 9.001049 GTATACTTGACGATGACGATATGAATC 57.999 37.037 0.00 0.00 42.66 2.52
111 112 5.831997 ACTTGACGATGACGATATGAATCA 58.168 37.500 0.00 0.00 42.66 2.57
112 113 5.687730 ACTTGACGATGACGATATGAATCAC 59.312 40.000 0.00 0.00 42.66 3.06
113 114 5.438761 TGACGATGACGATATGAATCACT 57.561 39.130 0.00 0.00 42.66 3.41
114 115 5.831997 TGACGATGACGATATGAATCACTT 58.168 37.500 0.00 0.00 42.66 3.16
115 116 5.687285 TGACGATGACGATATGAATCACTTG 59.313 40.000 0.00 0.00 42.66 3.16
116 117 5.831997 ACGATGACGATATGAATCACTTGA 58.168 37.500 0.00 0.00 42.66 3.02
117 118 6.273071 ACGATGACGATATGAATCACTTGAA 58.727 36.000 0.00 0.00 42.66 2.69
118 119 6.756542 ACGATGACGATATGAATCACTTGAAA 59.243 34.615 0.00 0.00 42.66 2.69
119 120 7.277760 ACGATGACGATATGAATCACTTGAAAA 59.722 33.333 0.00 0.00 42.66 2.29
120 121 8.116136 CGATGACGATATGAATCACTTGAAAAA 58.884 33.333 0.00 0.00 42.66 1.94
121 122 9.941664 GATGACGATATGAATCACTTGAAAAAT 57.058 29.630 0.00 0.00 31.93 1.82
129 130 7.945033 TGAATCACTTGAAAAATAAAGGCAC 57.055 32.000 0.00 0.00 0.00 5.01
149 150 8.880878 AGGCACTTGAAAAATAAACGTATTTT 57.119 26.923 3.68 3.68 43.10 1.82
171 172 7.441890 TTTTTCGGTTGCAGATCTATTACAA 57.558 32.000 0.00 0.00 0.00 2.41
172 173 6.662414 TTTCGGTTGCAGATCTATTACAAG 57.338 37.500 0.00 0.00 0.00 3.16
173 174 5.592104 TCGGTTGCAGATCTATTACAAGA 57.408 39.130 0.00 0.00 0.00 3.02
174 175 6.161855 TCGGTTGCAGATCTATTACAAGAT 57.838 37.500 0.00 0.00 38.95 2.40
188 189 9.060347 TCTATTACAAGATCAATTCAGATTGGC 57.940 33.333 0.00 0.00 42.36 4.52
189 190 7.893124 ATTACAAGATCAATTCAGATTGGCT 57.107 32.000 0.00 0.00 42.36 4.75
190 191 5.831702 ACAAGATCAATTCAGATTGGCTC 57.168 39.130 0.00 0.00 42.36 4.70
191 192 5.507637 ACAAGATCAATTCAGATTGGCTCT 58.492 37.500 0.00 0.97 42.36 4.09
192 193 5.950549 ACAAGATCAATTCAGATTGGCTCTT 59.049 36.000 0.00 9.81 42.36 2.85
193 194 6.266323 CAAGATCAATTCAGATTGGCTCTTG 58.734 40.000 19.06 19.06 44.79 3.02
194 195 4.888239 AGATCAATTCAGATTGGCTCTTGG 59.112 41.667 0.00 0.00 42.36 3.61
195 196 4.038271 TCAATTCAGATTGGCTCTTGGT 57.962 40.909 0.00 0.00 42.36 3.67
196 197 4.012374 TCAATTCAGATTGGCTCTTGGTC 58.988 43.478 0.00 0.00 42.36 4.02
197 198 2.099141 TTCAGATTGGCTCTTGGTCG 57.901 50.000 0.00 0.00 29.16 4.79
198 199 0.976641 TCAGATTGGCTCTTGGTCGT 59.023 50.000 0.00 0.00 29.16 4.34
199 200 1.347707 TCAGATTGGCTCTTGGTCGTT 59.652 47.619 0.00 0.00 29.16 3.85
200 201 2.154462 CAGATTGGCTCTTGGTCGTTT 58.846 47.619 0.00 0.00 29.16 3.60
201 202 3.007506 TCAGATTGGCTCTTGGTCGTTTA 59.992 43.478 0.00 0.00 29.16 2.01
202 203 3.125316 CAGATTGGCTCTTGGTCGTTTAC 59.875 47.826 0.00 0.00 29.16 2.01
203 204 2.623878 TTGGCTCTTGGTCGTTTACA 57.376 45.000 0.00 0.00 0.00 2.41
204 205 2.623878 TGGCTCTTGGTCGTTTACAA 57.376 45.000 0.00 0.00 0.00 2.41
205 206 2.215196 TGGCTCTTGGTCGTTTACAAC 58.785 47.619 0.00 0.00 0.00 3.32
206 207 2.215196 GGCTCTTGGTCGTTTACAACA 58.785 47.619 0.00 0.00 0.00 3.33
207 208 2.812011 GGCTCTTGGTCGTTTACAACAT 59.188 45.455 0.00 0.00 0.00 2.71
208 209 3.364964 GGCTCTTGGTCGTTTACAACATG 60.365 47.826 0.00 0.00 0.00 3.21
209 210 3.810373 CTCTTGGTCGTTTACAACATGC 58.190 45.455 0.00 0.00 0.00 4.06
210 211 3.206964 TCTTGGTCGTTTACAACATGCA 58.793 40.909 0.00 0.00 0.00 3.96
211 212 3.249799 TCTTGGTCGTTTACAACATGCAG 59.750 43.478 0.00 0.00 0.00 4.41
212 213 2.566913 TGGTCGTTTACAACATGCAGT 58.433 42.857 0.00 0.00 0.00 4.40
213 214 2.946329 TGGTCGTTTACAACATGCAGTT 59.054 40.909 0.00 0.00 42.42 3.16
214 215 3.002862 TGGTCGTTTACAACATGCAGTTC 59.997 43.478 0.00 0.00 38.74 3.01
215 216 3.002862 GGTCGTTTACAACATGCAGTTCA 59.997 43.478 0.00 0.00 38.74 3.18
216 217 4.496673 GGTCGTTTACAACATGCAGTTCAA 60.497 41.667 0.00 0.00 38.74 2.69
217 218 5.031578 GTCGTTTACAACATGCAGTTCAAA 58.968 37.500 0.00 0.00 38.74 2.69
218 219 5.513495 GTCGTTTACAACATGCAGTTCAAAA 59.487 36.000 0.00 0.00 38.74 2.44
219 220 6.034044 GTCGTTTACAACATGCAGTTCAAAAA 59.966 34.615 0.00 0.00 38.74 1.94
220 221 6.754209 TCGTTTACAACATGCAGTTCAAAAAT 59.246 30.769 0.00 0.00 38.74 1.82
221 222 7.915923 TCGTTTACAACATGCAGTTCAAAAATA 59.084 29.630 0.00 0.00 38.74 1.40
222 223 8.698854 CGTTTACAACATGCAGTTCAAAAATAT 58.301 29.630 0.00 0.00 38.74 1.28
227 228 9.075519 ACAACATGCAGTTCAAAAATATATTCG 57.924 29.630 0.00 0.00 38.74 3.34
228 229 9.075519 CAACATGCAGTTCAAAAATATATTCGT 57.924 29.630 0.00 0.00 38.74 3.85
230 231 9.935682 ACATGCAGTTCAAAAATATATTCGTAG 57.064 29.630 0.00 0.00 0.00 3.51
233 234 9.378551 TGCAGTTCAAAAATATATTCGTAGAGT 57.621 29.630 0.00 0.00 38.43 3.24
248 249 8.951954 ATTCGTAGAGTATTCATACGTCAATC 57.048 34.615 0.00 0.00 42.14 2.67
249 250 6.587651 TCGTAGAGTATTCATACGTCAATCG 58.412 40.000 0.00 0.00 42.14 3.34
250 251 6.421801 TCGTAGAGTATTCATACGTCAATCGA 59.578 38.462 0.00 0.00 42.14 3.59
251 252 7.042523 TCGTAGAGTATTCATACGTCAATCGAA 60.043 37.037 0.00 0.00 42.14 3.71
252 253 7.585210 CGTAGAGTATTCATACGTCAATCGAAA 59.415 37.037 0.00 0.00 42.86 3.46
253 254 7.681125 AGAGTATTCATACGTCAATCGAAAC 57.319 36.000 0.00 0.00 42.86 2.78
254 255 6.696148 AGAGTATTCATACGTCAATCGAAACC 59.304 38.462 0.00 0.00 42.86 3.27
255 256 6.334989 AGTATTCATACGTCAATCGAAACCA 58.665 36.000 0.00 0.00 42.86 3.67
256 257 6.814644 AGTATTCATACGTCAATCGAAACCAA 59.185 34.615 0.00 0.00 42.86 3.67
257 258 4.914312 TCATACGTCAATCGAAACCAAC 57.086 40.909 0.00 0.00 42.86 3.77
258 259 4.562082 TCATACGTCAATCGAAACCAACT 58.438 39.130 0.00 0.00 42.86 3.16
259 260 4.624024 TCATACGTCAATCGAAACCAACTC 59.376 41.667 0.00 0.00 42.86 3.01
260 261 2.140717 ACGTCAATCGAAACCAACTCC 58.859 47.619 0.00 0.00 42.86 3.85
261 262 1.463444 CGTCAATCGAAACCAACTCCC 59.537 52.381 0.00 0.00 42.86 4.30
262 263 1.810755 GTCAATCGAAACCAACTCCCC 59.189 52.381 0.00 0.00 0.00 4.81
263 264 1.422024 TCAATCGAAACCAACTCCCCA 59.578 47.619 0.00 0.00 0.00 4.96
264 265 2.158593 TCAATCGAAACCAACTCCCCAA 60.159 45.455 0.00 0.00 0.00 4.12
265 266 2.625790 CAATCGAAACCAACTCCCCAAA 59.374 45.455 0.00 0.00 0.00 3.28
266 267 1.682740 TCGAAACCAACTCCCCAAAC 58.317 50.000 0.00 0.00 0.00 2.93
267 268 1.213430 TCGAAACCAACTCCCCAAACT 59.787 47.619 0.00 0.00 0.00 2.66
268 269 2.028876 CGAAACCAACTCCCCAAACTT 58.971 47.619 0.00 0.00 0.00 2.66
269 270 2.429250 CGAAACCAACTCCCCAAACTTT 59.571 45.455 0.00 0.00 0.00 2.66
270 271 3.736740 CGAAACCAACTCCCCAAACTTTG 60.737 47.826 0.00 0.00 0.00 2.77
290 291 4.463050 TGGTACAAAACTCCATCCCTTT 57.537 40.909 0.00 0.00 31.92 3.11
291 292 5.586155 TGGTACAAAACTCCATCCCTTTA 57.414 39.130 0.00 0.00 31.92 1.85
292 293 5.318630 TGGTACAAAACTCCATCCCTTTAC 58.681 41.667 0.00 0.00 31.92 2.01
293 294 5.073965 TGGTACAAAACTCCATCCCTTTACT 59.926 40.000 0.00 0.00 31.92 2.24
294 295 6.272792 TGGTACAAAACTCCATCCCTTTACTA 59.727 38.462 0.00 0.00 31.92 1.82
295 296 6.596888 GGTACAAAACTCCATCCCTTTACTAC 59.403 42.308 0.00 0.00 0.00 2.73
296 297 6.195600 ACAAAACTCCATCCCTTTACTACA 57.804 37.500 0.00 0.00 0.00 2.74
297 298 6.607019 ACAAAACTCCATCCCTTTACTACAA 58.393 36.000 0.00 0.00 0.00 2.41
298 299 7.064229 ACAAAACTCCATCCCTTTACTACAAA 58.936 34.615 0.00 0.00 0.00 2.83
299 300 7.728532 ACAAAACTCCATCCCTTTACTACAAAT 59.271 33.333 0.00 0.00 0.00 2.32
300 301 7.703058 AAACTCCATCCCTTTACTACAAATG 57.297 36.000 0.00 0.00 0.00 2.32
370 371 4.842531 TGTAGAAATTCTGGGATCTGCA 57.157 40.909 5.64 0.00 33.12 4.41
436 437 7.324135 GGAACAGATAACTCGATCGATTTCTAC 59.676 40.741 22.05 14.65 0.00 2.59
440 441 8.017946 CAGATAACTCGATCGATTTCTACATCA 58.982 37.037 22.05 5.64 0.00 3.07
519 520 3.056607 GCAGCAGTGTTATGAAAACCCAT 60.057 43.478 0.00 0.00 0.00 4.00
531 532 4.724399 TGAAAACCCATGAGAAGCAACTA 58.276 39.130 0.00 0.00 0.00 2.24
595 596 3.194968 GTCGATACTGAAGTTCCCCAAGA 59.805 47.826 0.00 0.00 0.00 3.02
605 606 1.075601 TTCCCCAAGATGTGCTTCCT 58.924 50.000 0.00 0.00 33.60 3.36
622 623 6.595716 GTGCTTCCTGATACTGTATTTGAAGT 59.404 38.462 22.09 0.00 0.00 3.01
701 702 1.682087 GGAGGGTTGAATGTAGGTGCC 60.682 57.143 0.00 0.00 0.00 5.01
703 704 1.654023 GGGTTGAATGTAGGTGCCGC 61.654 60.000 0.00 0.00 0.00 6.53
836 841 2.265367 TCTTGTGATAGGCCCTGTTCA 58.735 47.619 0.00 0.00 0.00 3.18
988 994 7.390823 TGATGGTAGCAAGAGTAACAATACAA 58.609 34.615 0.00 0.00 34.29 2.41
1114 1127 2.789323 ATTATACCTCCCGGACCAGT 57.211 50.000 0.73 0.00 0.00 4.00
1142 1155 2.654385 TGTTTCAGAGGGGGAATCCATT 59.346 45.455 0.09 0.00 37.22 3.16
1195 1211 0.185175 GTGGGAGGTTTTGGTCAGGT 59.815 55.000 0.00 0.00 0.00 4.00
1244 1260 2.351706 TACGTGTCCAAGGCCTTTTT 57.648 45.000 17.61 0.00 0.00 1.94
1352 1368 4.691326 ATTTCTAGGTCTCGGGATTTCC 57.309 45.455 0.00 0.00 0.00 3.13
1384 1400 7.858879 TCAAGTTGGTAAAAAGCTTCGATTTAC 59.141 33.333 18.05 18.05 38.29 2.01
1393 1409 6.509418 AAAGCTTCGATTTACTGGCAATTA 57.491 33.333 0.00 0.00 0.00 1.40
1512 1544 6.461640 CAAAAGAAGAGAATCCAAGGCAAAT 58.538 36.000 0.00 0.00 33.66 2.32
1528 1560 4.923281 AGGCAAATGCGAGAACAATAAAAC 59.077 37.500 0.00 0.00 43.26 2.43
1557 1589 5.860648 TTCTTCCTTTTAGGAGGGATTGT 57.139 39.130 5.18 0.00 46.73 2.71
1567 1599 3.379452 AGGAGGGATTGTAGGTCTTCTG 58.621 50.000 0.00 0.00 0.00 3.02
1723 1755 8.414003 CCTCTTTTTCTTTTGCTTAGGTTTAGT 58.586 33.333 0.00 0.00 0.00 2.24
1747 1779 1.975680 GGTAGTGGACAAACAGAGGGA 59.024 52.381 0.00 0.00 0.00 4.20
1764 1796 1.686587 GGGAAAGAAAATATGGCGGGG 59.313 52.381 0.00 0.00 0.00 5.73
1873 1905 7.898014 TGAACTTAATACTCTAGATGCAGGA 57.102 36.000 0.00 0.00 0.00 3.86
2014 2049 5.631026 GCTTTTCTATCAATTGCTCGACAA 58.369 37.500 0.00 3.49 44.01 3.18
2030 2065 3.502595 TCGACAATAATTTGTTCGCCCAA 59.497 39.130 0.00 0.00 46.01 4.12
2126 2163 8.494016 AGTTTCCAATCTACTATTTTCCTTCG 57.506 34.615 0.00 0.00 0.00 3.79
2293 2331 1.373590 CCCTTTATCGCGTTGGGTGG 61.374 60.000 5.77 2.91 33.49 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.431887 GTAACAAGAATGTATTGTTCTGAGGTA 57.568 33.333 7.29 0.00 45.33 3.08
4 5 7.390718 GGTAACAAGAATGTATTGTTCTGAGGT 59.609 37.037 7.29 0.00 45.33 3.85
5 6 7.752695 GGTAACAAGAATGTATTGTTCTGAGG 58.247 38.462 7.29 0.00 45.33 3.86
25 26 2.870411 GGCCAATACATCTCGTGGTAAC 59.130 50.000 0.00 0.00 33.43 2.50
26 27 2.482316 CGGCCAATACATCTCGTGGTAA 60.482 50.000 2.24 0.00 33.43 2.85
27 28 1.067974 CGGCCAATACATCTCGTGGTA 59.932 52.381 2.24 0.00 33.43 3.25
28 29 0.179084 CGGCCAATACATCTCGTGGT 60.179 55.000 2.24 0.00 33.43 4.16
29 30 1.498865 GCGGCCAATACATCTCGTGG 61.499 60.000 2.24 0.00 0.00 4.94
30 31 0.530650 AGCGGCCAATACATCTCGTG 60.531 55.000 2.24 0.00 0.00 4.35
31 32 1.037493 TAGCGGCCAATACATCTCGT 58.963 50.000 2.24 0.00 0.00 4.18
32 33 1.269569 TGTAGCGGCCAATACATCTCG 60.270 52.381 11.97 0.00 0.00 4.04
33 34 2.035961 TCTGTAGCGGCCAATACATCTC 59.964 50.000 15.42 0.00 31.79 2.75
34 35 2.039418 TCTGTAGCGGCCAATACATCT 58.961 47.619 15.42 0.00 31.79 2.90
35 36 2.526304 TCTGTAGCGGCCAATACATC 57.474 50.000 15.42 0.00 31.79 3.06
36 37 2.368548 TGATCTGTAGCGGCCAATACAT 59.631 45.455 15.42 4.29 31.79 2.29
37 38 1.760029 TGATCTGTAGCGGCCAATACA 59.240 47.619 14.54 14.54 0.00 2.29
38 39 2.526304 TGATCTGTAGCGGCCAATAC 57.474 50.000 2.24 5.39 0.00 1.89
39 40 3.769739 AATGATCTGTAGCGGCCAATA 57.230 42.857 2.24 0.00 0.00 1.90
40 41 2.620115 CAAATGATCTGTAGCGGCCAAT 59.380 45.455 2.24 0.00 0.00 3.16
41 42 2.016318 CAAATGATCTGTAGCGGCCAA 58.984 47.619 2.24 0.00 0.00 4.52
42 43 1.209261 TCAAATGATCTGTAGCGGCCA 59.791 47.619 2.24 0.00 0.00 5.36
43 44 1.953559 TCAAATGATCTGTAGCGGCC 58.046 50.000 0.00 0.00 0.00 6.13
44 45 3.304257 CCAATCAAATGATCTGTAGCGGC 60.304 47.826 0.00 0.00 32.75 6.53
45 46 4.129380 TCCAATCAAATGATCTGTAGCGG 58.871 43.478 0.00 0.00 32.75 5.52
46 47 5.739752 TTCCAATCAAATGATCTGTAGCG 57.260 39.130 0.00 0.00 32.75 4.26
47 48 7.268199 TGATTCCAATCAAATGATCTGTAGC 57.732 36.000 0.00 0.00 42.11 3.58
60 61 6.012683 ACCCATTCCAAATTTGATTCCAATCA 60.013 34.615 19.86 0.00 43.28 2.57
61 62 6.417258 ACCCATTCCAAATTTGATTCCAATC 58.583 36.000 19.86 0.00 35.97 2.67
62 63 6.391479 ACCCATTCCAAATTTGATTCCAAT 57.609 33.333 19.86 6.60 31.46 3.16
63 64 5.839517 ACCCATTCCAAATTTGATTCCAA 57.160 34.783 19.86 4.67 0.00 3.53
64 65 7.843760 AGTATACCCATTCCAAATTTGATTCCA 59.156 33.333 19.86 0.00 0.00 3.53
65 66 8.250143 AGTATACCCATTCCAAATTTGATTCC 57.750 34.615 19.86 0.00 0.00 3.01
66 67 9.533253 CAAGTATACCCATTCCAAATTTGATTC 57.467 33.333 19.86 0.96 0.00 2.52
67 68 9.265862 TCAAGTATACCCATTCCAAATTTGATT 57.734 29.630 19.86 0.93 0.00 2.57
68 69 8.695456 GTCAAGTATACCCATTCCAAATTTGAT 58.305 33.333 19.86 3.13 0.00 2.57
69 70 7.148154 CGTCAAGTATACCCATTCCAAATTTGA 60.148 37.037 19.86 0.52 0.00 2.69
70 71 6.972328 CGTCAAGTATACCCATTCCAAATTTG 59.028 38.462 11.40 11.40 0.00 2.32
71 72 6.887545 TCGTCAAGTATACCCATTCCAAATTT 59.112 34.615 0.00 0.00 0.00 1.82
72 73 6.419791 TCGTCAAGTATACCCATTCCAAATT 58.580 36.000 0.00 0.00 0.00 1.82
73 74 5.996644 TCGTCAAGTATACCCATTCCAAAT 58.003 37.500 0.00 0.00 0.00 2.32
74 75 5.423704 TCGTCAAGTATACCCATTCCAAA 57.576 39.130 0.00 0.00 0.00 3.28
75 76 5.129650 TCATCGTCAAGTATACCCATTCCAA 59.870 40.000 0.00 0.00 0.00 3.53
76 77 4.651962 TCATCGTCAAGTATACCCATTCCA 59.348 41.667 0.00 0.00 0.00 3.53
77 78 4.989168 GTCATCGTCAAGTATACCCATTCC 59.011 45.833 0.00 0.00 0.00 3.01
78 79 4.680110 CGTCATCGTCAAGTATACCCATTC 59.320 45.833 0.00 0.00 0.00 2.67
79 80 4.340097 TCGTCATCGTCAAGTATACCCATT 59.660 41.667 0.00 0.00 38.33 3.16
80 81 3.887110 TCGTCATCGTCAAGTATACCCAT 59.113 43.478 0.00 0.00 38.33 4.00
81 82 3.281158 TCGTCATCGTCAAGTATACCCA 58.719 45.455 0.00 0.00 38.33 4.51
82 83 3.976793 TCGTCATCGTCAAGTATACCC 57.023 47.619 0.00 0.00 38.33 3.69
83 84 6.839033 TCATATCGTCATCGTCAAGTATACC 58.161 40.000 0.00 0.00 38.33 2.73
84 85 8.897457 ATTCATATCGTCATCGTCAAGTATAC 57.103 34.615 0.00 0.00 38.33 1.47
85 86 8.726988 TGATTCATATCGTCATCGTCAAGTATA 58.273 33.333 0.00 0.00 38.33 1.47
86 87 7.539022 GTGATTCATATCGTCATCGTCAAGTAT 59.461 37.037 0.00 0.00 38.33 2.12
87 88 6.856426 GTGATTCATATCGTCATCGTCAAGTA 59.144 38.462 0.00 0.00 38.33 2.24
88 89 5.687730 GTGATTCATATCGTCATCGTCAAGT 59.312 40.000 0.00 0.00 38.33 3.16
89 90 5.917447 AGTGATTCATATCGTCATCGTCAAG 59.083 40.000 0.00 0.00 38.33 3.02
90 91 5.831997 AGTGATTCATATCGTCATCGTCAA 58.168 37.500 0.00 0.00 38.33 3.18
91 92 5.438761 AGTGATTCATATCGTCATCGTCA 57.561 39.130 0.00 0.00 38.33 4.35
92 93 5.915196 TCAAGTGATTCATATCGTCATCGTC 59.085 40.000 0.00 0.00 38.33 4.20
93 94 5.831997 TCAAGTGATTCATATCGTCATCGT 58.168 37.500 0.00 0.00 38.33 3.73
94 95 6.753897 TTCAAGTGATTCATATCGTCATCG 57.246 37.500 0.00 0.00 33.23 3.84
95 96 9.941664 ATTTTTCAAGTGATTCATATCGTCATC 57.058 29.630 0.00 0.00 33.23 2.92
103 104 9.638239 GTGCCTTTATTTTTCAAGTGATTCATA 57.362 29.630 0.00 0.00 0.00 2.15
104 105 8.370182 AGTGCCTTTATTTTTCAAGTGATTCAT 58.630 29.630 0.00 0.00 0.00 2.57
105 106 7.725251 AGTGCCTTTATTTTTCAAGTGATTCA 58.275 30.769 0.00 0.00 0.00 2.57
106 107 8.490355 CAAGTGCCTTTATTTTTCAAGTGATTC 58.510 33.333 0.00 0.00 0.00 2.52
107 108 8.203485 TCAAGTGCCTTTATTTTTCAAGTGATT 58.797 29.630 0.00 0.00 0.00 2.57
108 109 7.725251 TCAAGTGCCTTTATTTTTCAAGTGAT 58.275 30.769 0.00 0.00 0.00 3.06
109 110 7.106439 TCAAGTGCCTTTATTTTTCAAGTGA 57.894 32.000 0.00 0.00 0.00 3.41
110 111 7.769272 TTCAAGTGCCTTTATTTTTCAAGTG 57.231 32.000 0.00 0.00 0.00 3.16
111 112 8.785329 TTTTCAAGTGCCTTTATTTTTCAAGT 57.215 26.923 0.00 0.00 0.00 3.16
118 119 9.320352 ACGTTTATTTTTCAAGTGCCTTTATTT 57.680 25.926 0.00 0.00 0.00 1.40
119 120 8.880878 ACGTTTATTTTTCAAGTGCCTTTATT 57.119 26.923 0.00 0.00 0.00 1.40
121 122 9.968870 AATACGTTTATTTTTCAAGTGCCTTTA 57.031 25.926 0.00 0.00 0.00 1.85
122 123 8.880878 AATACGTTTATTTTTCAAGTGCCTTT 57.119 26.923 0.00 0.00 0.00 3.11
123 124 8.880878 AAATACGTTTATTTTTCAAGTGCCTT 57.119 26.923 0.00 0.00 34.75 4.35
124 125 8.880878 AAAATACGTTTATTTTTCAAGTGCCT 57.119 26.923 0.00 0.00 42.76 4.75
147 148 7.389330 TCTTGTAATAGATCTGCAACCGAAAAA 59.611 33.333 5.18 0.00 0.00 1.94
148 149 6.876789 TCTTGTAATAGATCTGCAACCGAAAA 59.123 34.615 5.18 0.00 0.00 2.29
149 150 6.403049 TCTTGTAATAGATCTGCAACCGAAA 58.597 36.000 5.18 0.00 0.00 3.46
150 151 5.972935 TCTTGTAATAGATCTGCAACCGAA 58.027 37.500 5.18 0.00 0.00 4.30
151 152 5.592104 TCTTGTAATAGATCTGCAACCGA 57.408 39.130 5.18 0.00 0.00 4.69
152 153 5.985530 TGATCTTGTAATAGATCTGCAACCG 59.014 40.000 5.18 0.00 46.94 4.44
153 154 7.792374 TTGATCTTGTAATAGATCTGCAACC 57.208 36.000 5.18 0.00 46.94 3.77
154 155 9.875675 GAATTGATCTTGTAATAGATCTGCAAC 57.124 33.333 5.18 0.88 46.94 4.17
155 156 9.617523 TGAATTGATCTTGTAATAGATCTGCAA 57.382 29.630 5.18 4.80 46.94 4.08
156 157 9.269453 CTGAATTGATCTTGTAATAGATCTGCA 57.731 33.333 5.18 0.00 46.94 4.41
157 158 9.486497 TCTGAATTGATCTTGTAATAGATCTGC 57.514 33.333 5.18 0.00 46.94 4.26
162 163 9.060347 GCCAATCTGAATTGATCTTGTAATAGA 57.940 33.333 0.00 0.00 44.25 1.98
163 164 9.064706 AGCCAATCTGAATTGATCTTGTAATAG 57.935 33.333 0.00 0.00 44.25 1.73
164 165 8.985315 AGCCAATCTGAATTGATCTTGTAATA 57.015 30.769 0.00 0.00 44.25 0.98
165 166 7.778853 AGAGCCAATCTGAATTGATCTTGTAAT 59.221 33.333 0.00 0.00 44.25 1.89
166 167 7.114754 AGAGCCAATCTGAATTGATCTTGTAA 58.885 34.615 0.00 0.00 44.25 2.41
167 168 6.656902 AGAGCCAATCTGAATTGATCTTGTA 58.343 36.000 0.00 0.00 44.25 2.41
168 169 5.507637 AGAGCCAATCTGAATTGATCTTGT 58.492 37.500 0.00 0.00 44.25 3.16
169 170 6.266323 CAAGAGCCAATCTGAATTGATCTTG 58.734 40.000 19.71 19.71 46.17 3.02
170 171 5.360144 CCAAGAGCCAATCTGAATTGATCTT 59.640 40.000 10.32 10.32 44.25 2.40
171 172 4.888239 CCAAGAGCCAATCTGAATTGATCT 59.112 41.667 0.00 1.16 44.25 2.75
172 173 4.643784 ACCAAGAGCCAATCTGAATTGATC 59.356 41.667 0.00 0.00 44.25 2.92
173 174 4.607239 ACCAAGAGCCAATCTGAATTGAT 58.393 39.130 0.00 0.00 44.25 2.57
174 175 4.012374 GACCAAGAGCCAATCTGAATTGA 58.988 43.478 0.00 0.00 44.25 2.57
175 176 3.181503 CGACCAAGAGCCAATCTGAATTG 60.182 47.826 0.00 0.00 41.69 2.32
176 177 3.012518 CGACCAAGAGCCAATCTGAATT 58.987 45.455 0.00 0.00 38.67 2.17
177 178 2.026822 ACGACCAAGAGCCAATCTGAAT 60.027 45.455 0.00 0.00 38.67 2.57
178 179 1.347707 ACGACCAAGAGCCAATCTGAA 59.652 47.619 0.00 0.00 38.67 3.02
179 180 0.976641 ACGACCAAGAGCCAATCTGA 59.023 50.000 0.00 0.00 38.67 3.27
180 181 1.813513 AACGACCAAGAGCCAATCTG 58.186 50.000 0.00 0.00 38.67 2.90
181 182 2.568623 AAACGACCAAGAGCCAATCT 57.431 45.000 0.00 0.00 41.27 2.40
182 183 3.071479 TGTAAACGACCAAGAGCCAATC 58.929 45.455 0.00 0.00 0.00 2.67
183 184 3.134574 TGTAAACGACCAAGAGCCAAT 57.865 42.857 0.00 0.00 0.00 3.16
184 185 2.614983 GTTGTAAACGACCAAGAGCCAA 59.385 45.455 0.00 0.00 36.92 4.52
185 186 2.215196 GTTGTAAACGACCAAGAGCCA 58.785 47.619 0.00 0.00 36.92 4.75
186 187 2.963498 GTTGTAAACGACCAAGAGCC 57.037 50.000 0.00 0.00 36.92 4.70
201 202 9.075519 CGAATATATTTTTGAACTGCATGTTGT 57.924 29.630 0.00 0.00 39.30 3.32
202 203 9.075519 ACGAATATATTTTTGAACTGCATGTTG 57.924 29.630 0.00 0.00 39.30 3.33
204 205 9.935682 CTACGAATATATTTTTGAACTGCATGT 57.064 29.630 0.00 0.00 0.00 3.21
207 208 9.378551 ACTCTACGAATATATTTTTGAACTGCA 57.621 29.630 0.00 0.00 0.00 4.41
223 224 7.745155 CGATTGACGTATGAATACTCTACGAAT 59.255 37.037 8.17 0.00 40.38 3.34
224 225 7.042523 TCGATTGACGTATGAATACTCTACGAA 60.043 37.037 8.17 0.00 40.38 3.85
225 226 6.421801 TCGATTGACGTATGAATACTCTACGA 59.578 38.462 8.17 0.00 40.38 3.43
226 227 6.587651 TCGATTGACGTATGAATACTCTACG 58.412 40.000 0.00 0.00 42.84 3.51
227 228 8.680261 GTTTCGATTGACGTATGAATACTCTAC 58.320 37.037 0.00 0.00 43.13 2.59
228 229 7.859377 GGTTTCGATTGACGTATGAATACTCTA 59.141 37.037 0.00 0.00 43.13 2.43
229 230 6.696148 GGTTTCGATTGACGTATGAATACTCT 59.304 38.462 0.00 0.00 43.13 3.24
230 231 6.474427 TGGTTTCGATTGACGTATGAATACTC 59.526 38.462 0.00 0.00 43.13 2.59
231 232 6.334989 TGGTTTCGATTGACGTATGAATACT 58.665 36.000 0.00 0.00 43.13 2.12
232 233 6.578020 TGGTTTCGATTGACGTATGAATAC 57.422 37.500 0.00 0.00 43.13 1.89
233 234 6.814644 AGTTGGTTTCGATTGACGTATGAATA 59.185 34.615 0.00 0.00 43.13 1.75
234 235 5.642063 AGTTGGTTTCGATTGACGTATGAAT 59.358 36.000 0.00 0.00 43.13 2.57
235 236 4.992319 AGTTGGTTTCGATTGACGTATGAA 59.008 37.500 0.00 0.00 43.13 2.57
236 237 4.562082 AGTTGGTTTCGATTGACGTATGA 58.438 39.130 0.00 0.00 43.13 2.15
237 238 4.201685 GGAGTTGGTTTCGATTGACGTATG 60.202 45.833 0.00 0.00 43.13 2.39
238 239 3.930848 GGAGTTGGTTTCGATTGACGTAT 59.069 43.478 0.00 0.00 43.13 3.06
239 240 3.319755 GGAGTTGGTTTCGATTGACGTA 58.680 45.455 0.00 0.00 43.13 3.57
240 241 2.140717 GGAGTTGGTTTCGATTGACGT 58.859 47.619 0.00 0.00 43.13 4.34
241 242 1.463444 GGGAGTTGGTTTCGATTGACG 59.537 52.381 0.00 0.00 44.09 4.35
242 243 1.810755 GGGGAGTTGGTTTCGATTGAC 59.189 52.381 0.00 0.00 0.00 3.18
243 244 1.422024 TGGGGAGTTGGTTTCGATTGA 59.578 47.619 0.00 0.00 0.00 2.57
244 245 1.904287 TGGGGAGTTGGTTTCGATTG 58.096 50.000 0.00 0.00 0.00 2.67
245 246 2.626266 GTTTGGGGAGTTGGTTTCGATT 59.374 45.455 0.00 0.00 0.00 3.34
246 247 2.158519 AGTTTGGGGAGTTGGTTTCGAT 60.159 45.455 0.00 0.00 0.00 3.59
247 248 1.213430 AGTTTGGGGAGTTGGTTTCGA 59.787 47.619 0.00 0.00 0.00 3.71
248 249 1.687563 AGTTTGGGGAGTTGGTTTCG 58.312 50.000 0.00 0.00 0.00 3.46
249 250 3.792401 CAAAGTTTGGGGAGTTGGTTTC 58.208 45.455 7.78 0.00 0.00 2.78
250 251 3.904800 CAAAGTTTGGGGAGTTGGTTT 57.095 42.857 7.78 0.00 0.00 3.27
262 263 5.983118 GGATGGAGTTTTGTACCAAAGTTTG 59.017 40.000 8.73 8.73 37.24 2.93
263 264 5.069914 GGGATGGAGTTTTGTACCAAAGTTT 59.930 40.000 1.62 0.00 37.24 2.66
264 265 4.587262 GGGATGGAGTTTTGTACCAAAGTT 59.413 41.667 1.62 0.00 37.24 2.66
265 266 4.141018 AGGGATGGAGTTTTGTACCAAAGT 60.141 41.667 0.00 0.00 37.24 2.66
266 267 4.407365 AGGGATGGAGTTTTGTACCAAAG 58.593 43.478 0.00 0.00 37.24 2.77
267 268 4.463050 AGGGATGGAGTTTTGTACCAAA 57.537 40.909 0.00 0.00 37.24 3.28
268 269 4.463050 AAGGGATGGAGTTTTGTACCAA 57.537 40.909 0.00 0.00 37.24 3.67
269 270 4.463050 AAAGGGATGGAGTTTTGTACCA 57.537 40.909 0.00 0.00 38.09 3.25
270 271 5.567430 AGTAAAGGGATGGAGTTTTGTACC 58.433 41.667 0.00 0.00 0.00 3.34
271 272 7.163441 TGTAGTAAAGGGATGGAGTTTTGTAC 58.837 38.462 0.00 0.00 0.00 2.90
272 273 7.319052 TGTAGTAAAGGGATGGAGTTTTGTA 57.681 36.000 0.00 0.00 0.00 2.41
273 274 6.195600 TGTAGTAAAGGGATGGAGTTTTGT 57.804 37.500 0.00 0.00 0.00 2.83
274 275 7.519032 TTTGTAGTAAAGGGATGGAGTTTTG 57.481 36.000 0.00 0.00 0.00 2.44
275 276 7.178451 CCATTTGTAGTAAAGGGATGGAGTTTT 59.822 37.037 0.00 0.00 35.68 2.43
276 277 6.663523 CCATTTGTAGTAAAGGGATGGAGTTT 59.336 38.462 0.00 0.00 35.68 2.66
277 278 6.011981 TCCATTTGTAGTAAAGGGATGGAGTT 60.012 38.462 2.03 0.00 37.30 3.01
278 279 5.491078 TCCATTTGTAGTAAAGGGATGGAGT 59.509 40.000 2.03 0.00 37.30 3.85
279 280 6.001449 TCCATTTGTAGTAAAGGGATGGAG 57.999 41.667 2.03 0.00 37.30 3.86
280 281 6.590656 ATCCATTTGTAGTAAAGGGATGGA 57.409 37.500 15.29 4.81 45.67 3.41
281 282 6.833416 TGAATCCATTTGTAGTAAAGGGATGG 59.167 38.462 16.36 2.37 46.40 3.51
282 283 7.880160 TGAATCCATTTGTAGTAAAGGGATG 57.120 36.000 16.36 0.00 46.40 3.51
284 285 7.410174 ACATGAATCCATTTGTAGTAAAGGGA 58.590 34.615 8.03 8.03 43.16 4.20
285 286 7.645058 ACATGAATCCATTTGTAGTAAAGGG 57.355 36.000 0.00 0.00 32.77 3.95
290 291 9.387397 TCCCTATACATGAATCCATTTGTAGTA 57.613 33.333 0.00 0.00 28.28 1.82
291 292 8.275187 TCCCTATACATGAATCCATTTGTAGT 57.725 34.615 0.00 0.00 28.28 2.73
292 293 9.003658 GTTCCCTATACATGAATCCATTTGTAG 57.996 37.037 0.00 0.00 29.41 2.74
293 294 8.723365 AGTTCCCTATACATGAATCCATTTGTA 58.277 33.333 0.00 0.00 0.00 2.41
294 295 7.586349 AGTTCCCTATACATGAATCCATTTGT 58.414 34.615 0.00 0.00 0.00 2.83
295 296 9.224267 CTAGTTCCCTATACATGAATCCATTTG 57.776 37.037 0.00 0.00 0.00 2.32
296 297 9.170890 TCTAGTTCCCTATACATGAATCCATTT 57.829 33.333 0.00 0.00 0.00 2.32
297 298 8.742125 TCTAGTTCCCTATACATGAATCCATT 57.258 34.615 0.00 0.00 0.00 3.16
298 299 8.923838 ATCTAGTTCCCTATACATGAATCCAT 57.076 34.615 0.00 0.00 0.00 3.41
299 300 8.742125 AATCTAGTTCCCTATACATGAATCCA 57.258 34.615 0.00 0.00 0.00 3.41
344 345 7.500227 TGCAGATCCCAGAATTTCTACAATAAG 59.500 37.037 0.00 0.00 0.00 1.73
459 460 7.984422 ATGCATTTGAAATATATGTCCGAGA 57.016 32.000 0.00 0.00 0.00 4.04
504 505 5.076182 TGCTTCTCATGGGTTTTCATAACA 58.924 37.500 0.00 0.00 0.00 2.41
519 520 4.883083 ACAATTCGTCTAGTTGCTTCTCA 58.117 39.130 0.00 0.00 0.00 3.27
531 532 4.675146 GCAATTGGCACATACAATTCGTCT 60.675 41.667 7.72 0.00 44.29 4.18
595 596 6.653020 TCAAATACAGTATCAGGAAGCACAT 58.347 36.000 0.00 0.00 0.00 3.21
622 623 9.424319 GCATATCATAAGGAATTCGAAGAACTA 57.576 33.333 3.35 0.00 45.90 2.24
701 702 0.657840 CCTCGGGCAAAATAAGAGCG 59.342 55.000 0.00 0.00 0.00 5.03
703 704 3.248602 CGAATCCTCGGGCAAAATAAGAG 59.751 47.826 0.00 0.00 41.57 2.85
808 812 4.706962 AGGGCCTATCACAAGAATGTTTTC 59.293 41.667 2.82 0.00 37.82 2.29
836 841 9.886132 AGACAATTTCACTATATTTCTTACCGT 57.114 29.630 0.00 0.00 0.00 4.83
1114 1127 3.593942 TCCCCCTCTGAAACAAGAAGTA 58.406 45.455 0.00 0.00 0.00 2.24
1195 1211 0.665835 AAGCACGATTTTTGCGTCCA 59.334 45.000 0.00 0.00 45.15 4.02
1203 1219 3.071874 TGGATCCTGAAGCACGATTTT 57.928 42.857 14.23 0.00 0.00 1.82
1244 1260 3.536956 ATAACGGATGCGGAGAAGAAA 57.463 42.857 12.44 0.00 0.00 2.52
1252 1268 0.453793 TGCCAAAATAACGGATGCGG 59.546 50.000 12.44 0.00 0.00 5.69
1375 1391 8.958119 ATTCTAGTAATTGCCAGTAAATCGAA 57.042 30.769 0.00 0.00 0.00 3.71
1464 1496 9.599056 TTGCATGGGATATAAATAAGGAATTCA 57.401 29.630 7.93 0.00 0.00 2.57
1512 1544 9.959749 AGAAATTTTAGTTTTATTGTTCTCGCA 57.040 25.926 0.00 0.00 0.00 5.10
1528 1560 8.879427 TCCCTCCTAAAAGGAAGAAATTTTAG 57.121 34.615 9.43 9.43 45.28 1.85
1546 1578 3.012959 TCAGAAGACCTACAATCCCTCCT 59.987 47.826 0.00 0.00 0.00 3.69
1557 1589 5.238868 CCGAATAGACGATTCAGAAGACCTA 59.761 44.000 8.72 0.00 43.76 3.08
1567 1599 3.444916 TCTTGTGCCGAATAGACGATTC 58.555 45.455 0.00 0.00 40.65 2.52
1662 1694 8.491958 ACATACCCGAATAAAGGAGAAATAGTT 58.508 33.333 0.00 0.00 0.00 2.24
1672 1704 5.057149 CCAAGAGACATACCCGAATAAAGG 58.943 45.833 0.00 0.00 0.00 3.11
1723 1755 2.557056 CTCTGTTTGTCCACTACCTCGA 59.443 50.000 0.00 0.00 0.00 4.04
1779 1811 9.819267 GGAAGTAACTCAAGCAATAGTAATACT 57.181 33.333 0.00 0.00 0.00 2.12
1780 1812 9.819267 AGGAAGTAACTCAAGCAATAGTAATAC 57.181 33.333 0.00 0.00 0.00 1.89
1782 1814 8.763601 AGAGGAAGTAACTCAAGCAATAGTAAT 58.236 33.333 0.00 0.00 37.43 1.89
1783 1815 8.135382 AGAGGAAGTAACTCAAGCAATAGTAA 57.865 34.615 0.00 0.00 37.43 2.24
1784 1816 7.719871 AGAGGAAGTAACTCAAGCAATAGTA 57.280 36.000 0.00 0.00 37.43 1.82
1785 1817 6.613153 AGAGGAAGTAACTCAAGCAATAGT 57.387 37.500 0.00 0.00 37.43 2.12
1786 1818 6.693545 CGTAGAGGAAGTAACTCAAGCAATAG 59.306 42.308 0.00 0.00 37.43 1.73
1801 1833 4.909696 AGATGACATGACGTAGAGGAAG 57.090 45.455 0.00 0.00 0.00 3.46
1873 1905 0.243907 CACACATCGACCGACTCCTT 59.756 55.000 0.00 0.00 0.00 3.36
1982 2016 6.519315 CAATTGATAGAAAAGCGCAAAGTTG 58.481 36.000 11.47 0.00 0.00 3.16
2025 2060 7.885297 TCAAGATAGCAAATAATATGTTGGGC 58.115 34.615 0.00 0.00 34.86 5.36


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

AutoCloner maintained by Alex Coulton.