Multiple sequence alignment - TraesCS4D01G126800

Loading Multiple Alignment...

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 TraesCS4D01G126800 chr4D 100.000 4321 0 0 1 4321 111584225 111588545 0.000000e+00 7980.0
1 TraesCS4D01G126800 chr4D 73.942 2245 428 100 775 2899 111053261 111055468 0.000000e+00 760.0
2 TraesCS4D01G126800 chr4D 85.892 241 32 2 95 334 20299927 20300166 5.550000e-64 255.0
3 TraesCS4D01G126800 chr4D 93.333 45 1 2 20 64 154797333 154797375 1.000000e-06 65.8
4 TraesCS4D01G126800 chr4B 95.589 2675 85 14 589 3238 172377252 172379918 0.000000e+00 4255.0
5 TraesCS4D01G126800 chr4B 95.652 644 23 4 3679 4321 172380371 172381010 0.000000e+00 1029.0
6 TraesCS4D01G126800 chr4B 74.297 2062 410 82 775 2754 171143810 171141787 0.000000e+00 761.0
7 TraesCS4D01G126800 chr4B 91.214 387 24 5 3264 3646 172379992 172380372 6.410000e-143 518.0
8 TraesCS4D01G126800 chr4B 88.889 270 14 8 335 589 172376942 172377210 6.970000e-83 318.0
9 TraesCS4D01G126800 chr4B 85.656 244 34 1 95 337 382422990 382423233 5.550000e-64 255.0
10 TraesCS4D01G126800 chr4A 95.331 2656 107 9 589 3231 465548484 465545833 0.000000e+00 4202.0
11 TraesCS4D01G126800 chr4A 98.938 471 5 0 3851 4321 465545047 465544577 0.000000e+00 843.0
12 TraesCS4D01G126800 chr4A 92.091 569 36 4 3211 3774 465545821 465545257 0.000000e+00 793.0
13 TraesCS4D01G126800 chr4A 88.636 264 8 14 331 574 465548790 465548529 7.020000e-78 302.0
14 TraesCS4D01G126800 chr4A 75.634 513 98 16 2269 2754 465891146 465890634 3.360000e-56 230.0
15 TraesCS4D01G126800 chr4A 82.692 104 10 5 3273 3368 565436208 565436105 7.700000e-13 86.1
16 TraesCS4D01G126800 chr6D 89.300 243 25 1 93 334 431455384 431455626 1.950000e-78 303.0
17 TraesCS4D01G126800 chr6D 100.000 35 0 0 23 57 326121607 326121573 1.000000e-06 65.8
18 TraesCS4D01G126800 chr7D 87.552 241 28 2 95 334 469900078 469900317 1.180000e-70 278.0
19 TraesCS4D01G126800 chr7D 100.000 36 0 0 23 58 235701634 235701599 2.790000e-07 67.6
20 TraesCS4D01G126800 chr1D 87.552 241 29 1 95 334 3763961 3763721 1.180000e-70 278.0
21 TraesCS4D01G126800 chr1B 86.475 244 32 1 100 342 19063546 19063789 2.560000e-67 267.0
22 TraesCS4D01G126800 chr1B 85.081 248 33 4 95 341 533813613 533813369 2.580000e-62 250.0
23 TraesCS4D01G126800 chr2B 86.920 237 27 4 100 334 698960513 698960747 3.310000e-66 263.0
24 TraesCS4D01G126800 chr2B 97.297 37 1 0 23 59 690892437 690892401 3.610000e-06 63.9
25 TraesCS4D01G126800 chr5A 86.695 233 29 2 95 325 22633811 22633579 1.540000e-64 257.0
26 TraesCS4D01G126800 chr5A 91.071 56 3 1 1 54 199706648 199706593 1.670000e-09 75.0
27 TraesCS4D01G126800 chr5A 89.091 55 4 2 23 77 126432551 126432499 2.790000e-07 67.6
28 TraesCS4D01G126800 chr5D 83.721 129 11 6 333 452 467760068 467759941 3.530000e-21 113.0
29 TraesCS4D01G126800 chr5D 95.238 42 2 0 23 64 365507363 365507322 2.790000e-07 67.6
30 TraesCS4D01G126800 chr7B 91.463 82 5 1 3273 3352 362043476 362043395 1.270000e-20 111.0
31 TraesCS4D01G126800 chr7B 84.706 85 7 3 3274 3352 153326928 153326844 3.580000e-11 80.5
32 TraesCS4D01G126800 chr7A 90.244 82 6 1 3273 3352 330430217 330430298 5.910000e-19 106.0
33 TraesCS4D01G126800 chr7A 100.000 37 0 0 20 56 688258478 688258442 7.750000e-08 69.4
34 TraesCS4D01G126800 chr3D 88.372 86 4 2 3273 3352 64179038 64179123 9.890000e-17 99.0
35 TraesCS4D01G126800 chr3D 84.158 101 7 5 3261 3352 326697056 326696956 5.950000e-14 89.8
36 TraesCS4D01G126800 chr3A 88.608 79 9 0 3274 3352 95018427 95018349 3.560000e-16 97.1
37 TraesCS4D01G126800 chr5B 82.353 85 12 3 1105 1187 531814787 531814870 2.160000e-08 71.3
38 TraesCS4D01G126800 chr2D 97.368 38 1 0 20 57 203716155 203716192 1.000000e-06 65.8


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 TraesCS4D01G126800 chr4D 111584225 111588545 4320 False 7980 7980 100.000 1 4321 1 chr4D.!!$F3 4320
1 TraesCS4D01G126800 chr4D 111053261 111055468 2207 False 760 760 73.942 775 2899 1 chr4D.!!$F2 2124
2 TraesCS4D01G126800 chr4B 172376942 172381010 4068 False 1530 4255 92.836 335 4321 4 chr4B.!!$F2 3986
3 TraesCS4D01G126800 chr4B 171141787 171143810 2023 True 761 761 74.297 775 2754 1 chr4B.!!$R1 1979
4 TraesCS4D01G126800 chr4A 465544577 465548790 4213 True 1535 4202 93.749 331 4321 4 chr4A.!!$R3 3990
5 TraesCS4D01G126800 chr4A 465890634 465891146 512 True 230 230 75.634 2269 2754 1 chr4A.!!$R1 485

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
262 263 0.035152 TCCCGCTGTAGTCGGTCTTA 60.035 55.0 11.70 0.0 45.09 2.10 F
302 303 0.106149 AGTTGAACCTCGGAAAGCGT 59.894 50.0 0.00 0.0 0.00 5.07 F
1866 1974 0.036732 TCCAGTACAAGCAGGGCAAG 59.963 55.0 0.00 0.0 0.00 4.01 F
2868 3060 1.747709 AGGTCGACGTGTACAGCTAT 58.252 50.0 10.45 0.0 0.00 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1495 0.252012 AAATGGCCCGTGGAATCCAA 60.252 50.000 2.31 0.0 34.18 3.53 R
2124 2253 0.435008 CGAAGAACGCGGACAAGAAG 59.565 55.000 12.47 0.0 34.51 2.85 R
2913 3105 0.323725 CTTTCCCATCCACCACCCAG 60.324 60.000 0.00 0.0 0.00 4.45 R
4072 4480 2.624838 CCATGTGGTGCTCAAGAAGTTT 59.375 45.455 0.00 0.0 0.00 2.66 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
46 47 8.654485 TTAGTCTAAGTTACTACCCATTGTGA 57.346 34.615 0.00 0.00 0.00 3.58
47 48 6.932947 AGTCTAAGTTACTACCCATTGTGAC 58.067 40.000 0.00 0.00 0.00 3.67
48 49 6.724905 AGTCTAAGTTACTACCCATTGTGACT 59.275 38.462 0.00 0.00 35.08 3.41
49 50 7.892241 AGTCTAAGTTACTACCCATTGTGACTA 59.108 37.037 0.00 0.00 32.96 2.59
50 51 8.189460 GTCTAAGTTACTACCCATTGTGACTAG 58.811 40.741 0.00 0.00 32.96 2.57
51 52 6.930068 AAGTTACTACCCATTGTGACTAGT 57.070 37.500 0.00 0.00 32.96 2.57
52 53 6.527057 AGTTACTACCCATTGTGACTAGTC 57.473 41.667 16.32 16.32 32.48 2.59
53 54 6.254522 AGTTACTACCCATTGTGACTAGTCT 58.745 40.000 23.01 0.19 32.48 3.24
54 55 6.724905 AGTTACTACCCATTGTGACTAGTCTT 59.275 38.462 23.01 3.71 32.48 3.01
55 56 7.892241 AGTTACTACCCATTGTGACTAGTCTTA 59.108 37.037 23.01 9.67 32.48 2.10
56 57 6.527057 ACTACCCATTGTGACTAGTCTTAC 57.473 41.667 23.01 14.37 0.00 2.34
57 58 4.451629 ACCCATTGTGACTAGTCTTACG 57.548 45.455 23.01 8.34 0.00 3.18
58 59 4.084287 ACCCATTGTGACTAGTCTTACGA 58.916 43.478 23.01 13.96 0.00 3.43
59 60 4.082354 ACCCATTGTGACTAGTCTTACGAC 60.082 45.833 23.01 13.00 40.54 4.34
60 61 4.421948 CCATTGTGACTAGTCTTACGACC 58.578 47.826 23.01 4.03 41.16 4.79
61 62 3.818961 TTGTGACTAGTCTTACGACCG 57.181 47.619 23.01 0.00 41.16 4.79
62 63 2.079158 TGTGACTAGTCTTACGACCGG 58.921 52.381 23.01 0.00 41.16 5.28
63 64 2.289631 TGTGACTAGTCTTACGACCGGA 60.290 50.000 23.01 0.00 41.16 5.14
64 65 2.095053 GTGACTAGTCTTACGACCGGAC 59.905 54.545 23.01 0.00 41.16 4.79
65 66 2.289631 TGACTAGTCTTACGACCGGACA 60.290 50.000 23.01 0.00 41.16 4.02
66 67 2.744202 GACTAGTCTTACGACCGGACAA 59.256 50.000 15.91 0.00 41.16 3.18
67 68 3.149196 ACTAGTCTTACGACCGGACAAA 58.851 45.455 9.46 0.00 41.16 2.83
68 69 2.719426 AGTCTTACGACCGGACAAAG 57.281 50.000 9.46 9.11 41.16 2.77
69 70 2.233271 AGTCTTACGACCGGACAAAGA 58.767 47.619 9.46 11.52 41.16 2.52
70 71 2.624838 AGTCTTACGACCGGACAAAGAA 59.375 45.455 9.46 0.00 41.16 2.52
71 72 2.728318 GTCTTACGACCGGACAAAGAAC 59.272 50.000 9.46 5.80 33.98 3.01
72 73 2.624838 TCTTACGACCGGACAAAGAACT 59.375 45.455 9.46 0.00 0.00 3.01
73 74 3.820467 TCTTACGACCGGACAAAGAACTA 59.180 43.478 9.46 0.00 0.00 2.24
74 75 2.719426 ACGACCGGACAAAGAACTAG 57.281 50.000 9.46 0.00 0.00 2.57
75 76 1.959282 ACGACCGGACAAAGAACTAGT 59.041 47.619 9.46 0.00 0.00 2.57
76 77 3.149196 ACGACCGGACAAAGAACTAGTA 58.851 45.455 9.46 0.00 0.00 1.82
77 78 3.057946 ACGACCGGACAAAGAACTAGTAC 60.058 47.826 9.46 0.00 0.00 2.73
78 79 3.496155 GACCGGACAAAGAACTAGTACG 58.504 50.000 9.46 0.00 39.23 3.67
79 80 3.149196 ACCGGACAAAGAACTAGTACGA 58.851 45.455 9.46 0.00 41.97 3.43
80 81 3.760684 ACCGGACAAAGAACTAGTACGAT 59.239 43.478 9.46 0.00 41.97 3.73
81 82 4.142513 ACCGGACAAAGAACTAGTACGATC 60.143 45.833 9.46 0.00 41.97 3.69
82 83 4.027065 CGGACAAAGAACTAGTACGATCG 58.973 47.826 14.88 14.88 41.97 3.69
83 84 4.201753 CGGACAAAGAACTAGTACGATCGA 60.202 45.833 24.34 2.23 41.97 3.59
84 85 5.503683 CGGACAAAGAACTAGTACGATCGAT 60.504 44.000 24.34 9.73 41.97 3.59
85 86 5.908499 GGACAAAGAACTAGTACGATCGATC 59.092 44.000 24.34 15.68 0.00 3.69
86 87 5.819059 ACAAAGAACTAGTACGATCGATCC 58.181 41.667 24.34 8.68 0.00 3.36
87 88 5.356190 ACAAAGAACTAGTACGATCGATCCA 59.644 40.000 24.34 5.06 0.00 3.41
88 89 6.127814 ACAAAGAACTAGTACGATCGATCCAA 60.128 38.462 24.34 5.06 0.00 3.53
89 90 5.676532 AGAACTAGTACGATCGATCCAAG 57.323 43.478 24.34 13.85 0.00 3.61
90 91 5.366460 AGAACTAGTACGATCGATCCAAGA 58.634 41.667 24.34 0.00 0.00 3.02
91 92 5.998981 AGAACTAGTACGATCGATCCAAGAT 59.001 40.000 24.34 6.89 0.00 2.40
92 93 7.160049 AGAACTAGTACGATCGATCCAAGATA 58.840 38.462 24.34 5.95 0.00 1.98
93 94 6.724694 ACTAGTACGATCGATCCAAGATAC 57.275 41.667 24.34 10.93 0.00 2.24
94 95 6.465948 ACTAGTACGATCGATCCAAGATACT 58.534 40.000 24.34 17.43 0.00 2.12
95 96 7.609960 ACTAGTACGATCGATCCAAGATACTA 58.390 38.462 24.34 17.61 0.00 1.82
96 97 6.724694 AGTACGATCGATCCAAGATACTAC 57.275 41.667 24.34 8.93 0.00 2.73
97 98 6.465948 AGTACGATCGATCCAAGATACTACT 58.534 40.000 24.34 11.13 0.00 2.57
98 99 6.935771 AGTACGATCGATCCAAGATACTACTT 59.064 38.462 24.34 0.00 0.00 2.24
99 100 6.243811 ACGATCGATCCAAGATACTACTTC 57.756 41.667 24.34 0.00 0.00 3.01
100 101 5.181622 ACGATCGATCCAAGATACTACTTCC 59.818 44.000 24.34 0.00 0.00 3.46
101 102 5.413213 CGATCGATCCAAGATACTACTTCCT 59.587 44.000 19.51 0.00 0.00 3.36
102 103 6.402766 CGATCGATCCAAGATACTACTTCCTC 60.403 46.154 19.51 0.00 0.00 3.71
103 104 5.071370 TCGATCCAAGATACTACTTCCTCC 58.929 45.833 0.00 0.00 0.00 4.30
104 105 4.083217 CGATCCAAGATACTACTTCCTCCG 60.083 50.000 0.00 0.00 0.00 4.63
105 106 4.246712 TCCAAGATACTACTTCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
106 107 4.607239 TCCAAGATACTACTTCCTCCGTT 58.393 43.478 0.00 0.00 0.00 4.44
107 108 4.643784 TCCAAGATACTACTTCCTCCGTTC 59.356 45.833 0.00 0.00 0.00 3.95
108 109 4.202131 CCAAGATACTACTTCCTCCGTTCC 60.202 50.000 0.00 0.00 0.00 3.62
109 110 4.246712 AGATACTACTTCCTCCGTTCCA 57.753 45.455 0.00 0.00 0.00 3.53
110 111 4.607239 AGATACTACTTCCTCCGTTCCAA 58.393 43.478 0.00 0.00 0.00 3.53
111 112 5.021458 AGATACTACTTCCTCCGTTCCAAA 58.979 41.667 0.00 0.00 0.00 3.28
112 113 5.482878 AGATACTACTTCCTCCGTTCCAAAA 59.517 40.000 0.00 0.00 0.00 2.44
113 114 4.635699 ACTACTTCCTCCGTTCCAAAAT 57.364 40.909 0.00 0.00 0.00 1.82
114 115 5.750352 ACTACTTCCTCCGTTCCAAAATA 57.250 39.130 0.00 0.00 0.00 1.40
115 116 6.309389 ACTACTTCCTCCGTTCCAAAATAT 57.691 37.500 0.00 0.00 0.00 1.28
116 117 7.427989 ACTACTTCCTCCGTTCCAAAATATA 57.572 36.000 0.00 0.00 0.00 0.86
117 118 7.498443 ACTACTTCCTCCGTTCCAAAATATAG 58.502 38.462 0.00 0.00 0.00 1.31
118 119 5.123936 ACTTCCTCCGTTCCAAAATATAGC 58.876 41.667 0.00 0.00 0.00 2.97
119 120 4.764050 TCCTCCGTTCCAAAATATAGCA 57.236 40.909 0.00 0.00 0.00 3.49
120 121 5.304686 TCCTCCGTTCCAAAATATAGCAT 57.695 39.130 0.00 0.00 0.00 3.79
121 122 5.063204 TCCTCCGTTCCAAAATATAGCATG 58.937 41.667 0.00 0.00 0.00 4.06
122 123 4.821805 CCTCCGTTCCAAAATATAGCATGT 59.178 41.667 0.00 0.00 0.00 3.21
123 124 5.049405 CCTCCGTTCCAAAATATAGCATGTC 60.049 44.000 0.00 0.00 0.00 3.06
124 125 4.819630 TCCGTTCCAAAATATAGCATGTCC 59.180 41.667 0.00 0.00 0.00 4.02
125 126 4.821805 CCGTTCCAAAATATAGCATGTCCT 59.178 41.667 0.00 0.00 0.00 3.85
126 127 5.049405 CCGTTCCAAAATATAGCATGTCCTC 60.049 44.000 0.00 0.00 0.00 3.71
127 128 5.333339 CGTTCCAAAATATAGCATGTCCTCG 60.333 44.000 0.00 0.00 0.00 4.63
128 129 5.545063 TCCAAAATATAGCATGTCCTCGA 57.455 39.130 0.00 0.00 0.00 4.04
129 130 6.114187 TCCAAAATATAGCATGTCCTCGAT 57.886 37.500 0.00 0.00 0.00 3.59
130 131 6.533730 TCCAAAATATAGCATGTCCTCGATT 58.466 36.000 0.00 0.00 0.00 3.34
131 132 6.998074 TCCAAAATATAGCATGTCCTCGATTT 59.002 34.615 0.00 0.00 0.00 2.17
132 133 7.173218 TCCAAAATATAGCATGTCCTCGATTTC 59.827 37.037 0.00 0.00 0.00 2.17
133 134 7.301054 CAAAATATAGCATGTCCTCGATTTCC 58.699 38.462 0.00 0.00 0.00 3.13
134 135 2.509052 TAGCATGTCCTCGATTTCCG 57.491 50.000 0.00 0.00 40.25 4.30
135 136 0.811616 AGCATGTCCTCGATTTCCGC 60.812 55.000 0.00 0.00 38.37 5.54
136 137 1.776034 GCATGTCCTCGATTTCCGCC 61.776 60.000 0.00 0.00 38.37 6.13
137 138 1.146263 ATGTCCTCGATTTCCGCCC 59.854 57.895 0.00 0.00 38.37 6.13
138 139 1.338136 ATGTCCTCGATTTCCGCCCT 61.338 55.000 0.00 0.00 38.37 5.19
139 140 1.221021 GTCCTCGATTTCCGCCCTT 59.779 57.895 0.00 0.00 38.37 3.95
140 141 0.810426 GTCCTCGATTTCCGCCCTTC 60.810 60.000 0.00 0.00 38.37 3.46
141 142 1.220749 CCTCGATTTCCGCCCTTCA 59.779 57.895 0.00 0.00 38.37 3.02
142 143 0.392461 CCTCGATTTCCGCCCTTCAA 60.392 55.000 0.00 0.00 38.37 2.69
143 144 0.727398 CTCGATTTCCGCCCTTCAAC 59.273 55.000 0.00 0.00 38.37 3.18
144 145 0.323629 TCGATTTCCGCCCTTCAACT 59.676 50.000 0.00 0.00 38.37 3.16
145 146 1.165270 CGATTTCCGCCCTTCAACTT 58.835 50.000 0.00 0.00 0.00 2.66
146 147 1.539827 CGATTTCCGCCCTTCAACTTT 59.460 47.619 0.00 0.00 0.00 2.66
147 148 2.668279 CGATTTCCGCCCTTCAACTTTG 60.668 50.000 0.00 0.00 0.00 2.77
148 149 2.060050 TTTCCGCCCTTCAACTTTGA 57.940 45.000 0.00 0.00 34.92 2.69
149 150 1.314730 TTCCGCCCTTCAACTTTGAC 58.685 50.000 0.00 0.00 36.83 3.18
150 151 0.472471 TCCGCCCTTCAACTTTGACT 59.528 50.000 0.00 0.00 36.83 3.41
151 152 1.695242 TCCGCCCTTCAACTTTGACTA 59.305 47.619 0.00 0.00 36.83 2.59
152 153 2.304761 TCCGCCCTTCAACTTTGACTAT 59.695 45.455 0.00 0.00 36.83 2.12
153 154 3.516300 TCCGCCCTTCAACTTTGACTATA 59.484 43.478 0.00 0.00 36.83 1.31
154 155 4.020039 TCCGCCCTTCAACTTTGACTATAA 60.020 41.667 0.00 0.00 36.83 0.98
155 156 4.698304 CCGCCCTTCAACTTTGACTATAAA 59.302 41.667 0.00 0.00 36.83 1.40
156 157 5.357032 CCGCCCTTCAACTTTGACTATAAAT 59.643 40.000 0.00 0.00 36.83 1.40
157 158 6.127730 CCGCCCTTCAACTTTGACTATAAATT 60.128 38.462 0.00 0.00 36.83 1.82
158 159 7.312899 CGCCCTTCAACTTTGACTATAAATTT 58.687 34.615 0.00 0.00 36.83 1.82
159 160 8.455682 CGCCCTTCAACTTTGACTATAAATTTA 58.544 33.333 0.00 0.00 36.83 1.40
172 173 9.491675 TGACTATAAATTTAAACAACGAGACCA 57.508 29.630 1.21 0.00 0.00 4.02
178 179 5.640218 TTTAAACAACGAGACCAACTACG 57.360 39.130 0.00 0.00 0.00 3.51
179 180 2.144482 AACAACGAGACCAACTACGG 57.856 50.000 0.00 0.00 0.00 4.02
180 181 0.319297 ACAACGAGACCAACTACGGC 60.319 55.000 0.00 0.00 0.00 5.68
181 182 1.080974 AACGAGACCAACTACGGCG 60.081 57.895 4.80 4.80 0.00 6.46
182 183 2.202570 CGAGACCAACTACGGCGG 60.203 66.667 13.24 0.00 0.00 6.13
183 184 2.183555 GAGACCAACTACGGCGGG 59.816 66.667 13.24 4.45 0.00 6.13
184 185 2.283388 AGACCAACTACGGCGGGA 60.283 61.111 13.24 0.00 0.00 5.14
185 186 2.183555 GACCAACTACGGCGGGAG 59.816 66.667 13.24 10.89 0.00 4.30
245 246 9.530129 CGAATTCATTAGTATAATTTTCGCTCC 57.470 33.333 6.22 0.00 0.00 4.70
246 247 9.827411 GAATTCATTAGTATAATTTTCGCTCCC 57.173 33.333 0.00 0.00 0.00 4.30
247 248 7.416154 TTCATTAGTATAATTTTCGCTCCCG 57.584 36.000 0.00 0.00 0.00 5.14
248 249 5.407387 TCATTAGTATAATTTTCGCTCCCGC 59.593 40.000 0.00 0.00 0.00 6.13
249 250 3.470645 AGTATAATTTTCGCTCCCGCT 57.529 42.857 0.00 0.00 0.00 5.52
250 251 3.131396 AGTATAATTTTCGCTCCCGCTG 58.869 45.455 0.00 0.00 0.00 5.18
251 252 2.038387 ATAATTTTCGCTCCCGCTGT 57.962 45.000 0.00 0.00 0.00 4.40
252 253 2.676632 TAATTTTCGCTCCCGCTGTA 57.323 45.000 0.00 0.00 0.00 2.74
253 254 1.369625 AATTTTCGCTCCCGCTGTAG 58.630 50.000 0.00 0.00 0.00 2.74
254 255 0.249398 ATTTTCGCTCCCGCTGTAGT 59.751 50.000 0.00 0.00 0.00 2.73
255 256 0.389426 TTTTCGCTCCCGCTGTAGTC 60.389 55.000 0.00 0.00 0.00 2.59
256 257 2.537792 TTTCGCTCCCGCTGTAGTCG 62.538 60.000 0.00 0.00 0.00 4.18
257 258 4.554363 CGCTCCCGCTGTAGTCGG 62.554 72.222 7.48 7.48 46.05 4.79
258 259 3.450115 GCTCCCGCTGTAGTCGGT 61.450 66.667 11.70 0.00 45.09 4.69
259 260 2.799371 CTCCCGCTGTAGTCGGTC 59.201 66.667 11.70 0.00 45.09 4.79
260 261 1.749638 CTCCCGCTGTAGTCGGTCT 60.750 63.158 11.70 0.00 45.09 3.85
261 262 1.303888 TCCCGCTGTAGTCGGTCTT 60.304 57.895 11.70 0.00 45.09 3.01
262 263 0.035152 TCCCGCTGTAGTCGGTCTTA 60.035 55.000 11.70 0.00 45.09 2.10
263 264 1.030457 CCCGCTGTAGTCGGTCTTAT 58.970 55.000 11.70 0.00 45.09 1.73
264 265 1.407979 CCCGCTGTAGTCGGTCTTATT 59.592 52.381 11.70 0.00 45.09 1.40
265 266 2.460918 CCGCTGTAGTCGGTCTTATTG 58.539 52.381 6.59 0.00 41.85 1.90
266 267 2.460918 CGCTGTAGTCGGTCTTATTGG 58.539 52.381 0.00 0.00 0.00 3.16
267 268 2.159282 CGCTGTAGTCGGTCTTATTGGT 60.159 50.000 0.00 0.00 0.00 3.67
268 269 3.675228 CGCTGTAGTCGGTCTTATTGGTT 60.675 47.826 0.00 0.00 0.00 3.67
269 270 4.439153 CGCTGTAGTCGGTCTTATTGGTTA 60.439 45.833 0.00 0.00 0.00 2.85
270 271 5.041940 GCTGTAGTCGGTCTTATTGGTTAG 58.958 45.833 0.00 0.00 0.00 2.34
271 272 5.163581 GCTGTAGTCGGTCTTATTGGTTAGA 60.164 44.000 0.00 0.00 0.00 2.10
272 273 6.461231 GCTGTAGTCGGTCTTATTGGTTAGAT 60.461 42.308 0.00 0.00 0.00 1.98
273 274 7.414222 TGTAGTCGGTCTTATTGGTTAGATT 57.586 36.000 0.00 0.00 0.00 2.40
274 275 7.844009 TGTAGTCGGTCTTATTGGTTAGATTT 58.156 34.615 0.00 0.00 0.00 2.17
275 276 8.970020 TGTAGTCGGTCTTATTGGTTAGATTTA 58.030 33.333 0.00 0.00 0.00 1.40
276 277 9.978044 GTAGTCGGTCTTATTGGTTAGATTTAT 57.022 33.333 0.00 0.00 0.00 1.40
277 278 8.888579 AGTCGGTCTTATTGGTTAGATTTATG 57.111 34.615 0.00 0.00 0.00 1.90
278 279 7.441458 AGTCGGTCTTATTGGTTAGATTTATGC 59.559 37.037 0.00 0.00 0.00 3.14
279 280 7.441458 GTCGGTCTTATTGGTTAGATTTATGCT 59.559 37.037 0.00 0.00 0.00 3.79
280 281 7.656137 TCGGTCTTATTGGTTAGATTTATGCTC 59.344 37.037 0.00 0.00 0.00 4.26
281 282 7.441157 CGGTCTTATTGGTTAGATTTATGCTCA 59.559 37.037 0.00 0.00 0.00 4.26
282 283 9.120538 GGTCTTATTGGTTAGATTTATGCTCAA 57.879 33.333 0.00 0.00 0.00 3.02
288 289 7.994425 TGGTTAGATTTATGCTCAAAGTTGA 57.006 32.000 0.00 0.00 35.57 3.18
289 290 8.402798 TGGTTAGATTTATGCTCAAAGTTGAA 57.597 30.769 0.00 0.00 36.64 2.69
290 291 8.296713 TGGTTAGATTTATGCTCAAAGTTGAAC 58.703 33.333 0.00 0.00 36.64 3.18
291 292 7.755373 GGTTAGATTTATGCTCAAAGTTGAACC 59.245 37.037 0.00 0.00 36.64 3.62
292 293 8.515414 GTTAGATTTATGCTCAAAGTTGAACCT 58.485 33.333 0.00 0.00 36.64 3.50
293 294 7.150783 AGATTTATGCTCAAAGTTGAACCTC 57.849 36.000 0.00 0.00 36.64 3.85
294 295 5.356882 TTTATGCTCAAAGTTGAACCTCG 57.643 39.130 0.00 0.00 36.64 4.63
295 296 1.593196 TGCTCAAAGTTGAACCTCGG 58.407 50.000 0.00 0.00 36.64 4.63
296 297 1.140052 TGCTCAAAGTTGAACCTCGGA 59.860 47.619 0.00 0.00 36.64 4.55
297 298 2.218603 GCTCAAAGTTGAACCTCGGAA 58.781 47.619 0.00 0.00 36.64 4.30
298 299 2.616842 GCTCAAAGTTGAACCTCGGAAA 59.383 45.455 0.00 0.00 36.64 3.13
299 300 3.304057 GCTCAAAGTTGAACCTCGGAAAG 60.304 47.826 0.00 0.00 36.64 2.62
300 301 2.616842 TCAAAGTTGAACCTCGGAAAGC 59.383 45.455 0.00 0.00 33.55 3.51
301 302 1.226746 AAGTTGAACCTCGGAAAGCG 58.773 50.000 0.00 0.00 0.00 4.68
302 303 0.106149 AGTTGAACCTCGGAAAGCGT 59.894 50.000 0.00 0.00 0.00 5.07
303 304 0.234884 GTTGAACCTCGGAAAGCGTG 59.765 55.000 0.00 0.00 0.00 5.34
304 305 0.882927 TTGAACCTCGGAAAGCGTGG 60.883 55.000 0.00 0.00 0.00 4.94
305 306 1.005394 GAACCTCGGAAAGCGTGGA 60.005 57.895 0.00 0.00 0.00 4.02
306 307 1.289800 GAACCTCGGAAAGCGTGGAC 61.290 60.000 0.00 0.00 0.00 4.02
307 308 2.809601 CCTCGGAAAGCGTGGACG 60.810 66.667 0.00 0.00 43.27 4.79
319 320 2.279250 CGTGGACGCGCTATATTTTG 57.721 50.000 5.73 0.00 0.00 2.44
320 321 1.855978 CGTGGACGCGCTATATTTTGA 59.144 47.619 5.73 0.00 0.00 2.69
321 322 2.283086 CGTGGACGCGCTATATTTTGAA 59.717 45.455 5.73 0.00 0.00 2.69
322 323 3.242155 CGTGGACGCGCTATATTTTGAAA 60.242 43.478 5.73 0.00 0.00 2.69
323 324 4.026407 GTGGACGCGCTATATTTTGAAAC 58.974 43.478 5.73 0.00 0.00 2.78
324 325 3.242155 TGGACGCGCTATATTTTGAAACG 60.242 43.478 5.73 0.00 0.00 3.60
325 326 3.242188 GGACGCGCTATATTTTGAAACGT 60.242 43.478 5.73 0.00 0.00 3.99
326 327 4.026640 GGACGCGCTATATTTTGAAACGTA 60.027 41.667 5.73 0.00 0.00 3.57
327 328 5.332808 GGACGCGCTATATTTTGAAACGTAT 60.333 40.000 5.73 0.00 0.00 3.06
328 329 5.428770 ACGCGCTATATTTTGAAACGTATG 58.571 37.500 5.73 0.00 0.00 2.39
329 330 4.838642 CGCGCTATATTTTGAAACGTATGG 59.161 41.667 5.56 0.00 0.00 2.74
415 416 4.430423 CTTCGCGCCTGAACGTGC 62.430 66.667 0.00 0.00 43.05 5.34
480 498 1.301716 GCACATGTGGGTGACGTCT 60.302 57.895 26.55 0.00 41.32 4.18
512 530 0.112412 GGAAGAAGTGGGGCCTTTGA 59.888 55.000 0.84 0.00 0.00 2.69
526 547 1.751924 CCTTTGACCTCCTCGTCCTAG 59.248 57.143 0.00 0.00 31.35 3.02
615 686 2.281484 TTTCCGCAGTGACAGCCC 60.281 61.111 0.00 0.00 0.00 5.19
675 749 1.910772 ACCGACCAAGCTCAGCTCT 60.911 57.895 0.00 0.00 38.25 4.09
680 754 1.193462 ACCAAGCTCAGCTCTGCTCT 61.193 55.000 0.00 0.00 38.25 4.09
735 821 2.219325 CTTCTGCTCTTCGCCCTCGT 62.219 60.000 0.00 0.00 38.05 4.18
1076 1170 3.948719 GGAACTCCACCGCCCACA 61.949 66.667 0.00 0.00 35.64 4.17
1167 1263 2.125912 CAGAGCTTCGACCACCCG 60.126 66.667 0.00 0.00 0.00 5.28
1305 1401 2.479730 GCTCTCAATGGTGTACGACGAT 60.480 50.000 0.00 0.00 0.00 3.73
1308 1404 1.546923 TCAATGGTGTACGACGATGGT 59.453 47.619 0.00 0.00 0.00 3.55
1317 1413 2.767445 CGACGATGGTGGCGAGGTA 61.767 63.158 0.00 0.00 0.00 3.08
1483 1579 4.400251 CCGGGGTCAGGAGGAGGT 62.400 72.222 0.00 0.00 0.00 3.85
1532 1628 2.260434 GTACAGCTTGGACGGCGA 59.740 61.111 16.62 0.00 34.52 5.54
1790 1898 1.335597 CGACCTCAACAACAGCGAGTA 60.336 52.381 0.00 0.00 0.00 2.59
1866 1974 0.036732 TCCAGTACAAGCAGGGCAAG 59.963 55.000 0.00 0.00 0.00 4.01
2018 2132 3.554342 CCTCGCCATCCAGGAGGG 61.554 72.222 16.57 16.57 42.91 4.30
2124 2253 3.640592 GCTATGGTTCTACTTCTACGGC 58.359 50.000 0.00 0.00 0.00 5.68
2291 2426 3.344064 GCTACTCAGAGCTGCAGAC 57.656 57.895 20.43 10.66 39.50 3.51
2469 2613 5.030147 AGGATCTACCACATGAACTTGGTA 58.970 41.667 11.32 11.32 44.68 3.25
2472 2616 6.351881 GGATCTACCACATGAACTTGGTAAGA 60.352 42.308 12.53 11.85 45.68 2.10
2868 3060 1.747709 AGGTCGACGTGTACAGCTAT 58.252 50.000 10.45 0.00 0.00 2.97
2913 3105 3.181443 TGAAAGGGAAGAGGGTTTCAGAC 60.181 47.826 0.00 0.00 34.72 3.51
3091 3283 1.162698 CCAGTTGGCTGTCTCATGTG 58.837 55.000 0.00 0.00 41.02 3.21
3183 3375 9.299963 GATGAGTCAAGAGATAATGAATATCCG 57.700 37.037 0.00 0.00 41.23 4.18
3200 3393 9.573166 TGAATATCCGGAAATATGATTCAGTTT 57.427 29.630 9.01 0.00 30.52 2.66
3247 3472 6.073276 TGTGTGTGTATACAGCAATCTTTGTC 60.073 38.462 5.62 0.00 37.52 3.18
3254 3479 6.822667 ATACAGCAATCTTTGTCACATCAA 57.177 33.333 0.00 0.00 0.00 2.57
3257 3482 6.154445 ACAGCAATCTTTGTCACATCAAATC 58.846 36.000 0.00 0.00 36.83 2.17
3323 3561 5.041287 GCAGTTCAACCTTAGTTCAAAACC 58.959 41.667 0.00 0.00 32.45 3.27
3327 3565 1.232119 ACCTTAGTTCAAAACCGCGG 58.768 50.000 26.86 26.86 0.00 6.46
3343 3581 1.808512 CGCGGCACTTATTATGGACCA 60.809 52.381 0.00 0.00 0.00 4.02
3352 3590 5.131142 CACTTATTATGGACCAGAGGGAGTT 59.869 44.000 0.00 0.00 38.05 3.01
3368 3606 3.439129 GGGAGTTGAAATTAGAACCCACG 59.561 47.826 0.00 0.00 36.47 4.94
3382 3620 4.156008 AGAACCCACGAATTATGTCTTTGC 59.844 41.667 0.00 0.00 0.00 3.68
3463 3701 3.243359 TGGATTTGTTCTTCTTGCCCT 57.757 42.857 0.00 0.00 0.00 5.19
3466 3704 5.144100 TGGATTTGTTCTTCTTGCCCTAAA 58.856 37.500 0.00 0.00 0.00 1.85
3522 3760 2.417933 GGACAGCAGCACTTAGATTGTG 59.582 50.000 0.00 0.00 38.36 3.33
3527 3765 4.931601 CAGCAGCACTTAGATTGTGAACTA 59.068 41.667 0.00 0.00 37.60 2.24
3656 3898 2.366916 AGATGATACCACAGGCTAGCAC 59.633 50.000 18.24 6.06 0.00 4.40
3676 3918 4.207891 ACAGACCTGATATGTGACAACC 57.792 45.455 3.76 0.00 29.34 3.77
3794 4052 8.306680 ACATGAACAACTAGTACATGTGTTAC 57.693 34.615 23.80 13.58 45.95 2.50
3795 4053 8.148351 ACATGAACAACTAGTACATGTGTTACT 58.852 33.333 23.80 6.81 45.95 2.24
3796 4054 9.634163 CATGAACAACTAGTACATGTGTTACTA 57.366 33.333 9.11 7.68 35.22 1.82
3952 4360 0.329261 CCTCCTCCAGGCATGAAACA 59.671 55.000 0.00 0.00 34.56 2.83
4005 4413 1.068541 GTTGAAATTGCCGTCCAGTCC 60.069 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.263446 TCACAATGGGTAGTAACTTAGACTAAT 57.737 33.333 0.00 0.00 31.33 1.73
21 22 8.526147 GTCACAATGGGTAGTAACTTAGACTAA 58.474 37.037 0.00 0.00 31.33 2.24
22 23 7.892241 AGTCACAATGGGTAGTAACTTAGACTA 59.108 37.037 0.00 0.00 0.00 2.59
23 24 6.724905 AGTCACAATGGGTAGTAACTTAGACT 59.275 38.462 0.00 0.00 0.00 3.24
24 25 6.932947 AGTCACAATGGGTAGTAACTTAGAC 58.067 40.000 0.00 0.00 0.00 2.59
25 26 7.892241 ACTAGTCACAATGGGTAGTAACTTAGA 59.108 37.037 0.00 0.00 0.00 2.10
26 27 8.064336 ACTAGTCACAATGGGTAGTAACTTAG 57.936 38.462 0.00 0.00 0.00 2.18
27 28 7.892241 AGACTAGTCACAATGGGTAGTAACTTA 59.108 37.037 24.44 0.00 0.00 2.24
28 29 6.724905 AGACTAGTCACAATGGGTAGTAACTT 59.275 38.462 24.44 0.00 0.00 2.66
29 30 6.254522 AGACTAGTCACAATGGGTAGTAACT 58.745 40.000 24.44 0.00 0.00 2.24
30 31 6.527057 AGACTAGTCACAATGGGTAGTAAC 57.473 41.667 24.44 0.00 0.00 2.50
31 32 7.148188 CGTAAGACTAGTCACAATGGGTAGTAA 60.148 40.741 24.44 0.00 43.02 2.24
32 33 6.317140 CGTAAGACTAGTCACAATGGGTAGTA 59.683 42.308 24.44 0.00 43.02 1.82
33 34 5.125097 CGTAAGACTAGTCACAATGGGTAGT 59.875 44.000 24.44 0.00 43.02 2.73
34 35 5.356190 TCGTAAGACTAGTCACAATGGGTAG 59.644 44.000 24.44 5.03 45.01 3.18
35 36 5.255687 TCGTAAGACTAGTCACAATGGGTA 58.744 41.667 24.44 1.49 45.01 3.69
36 37 4.084287 TCGTAAGACTAGTCACAATGGGT 58.916 43.478 24.44 0.00 45.01 4.51
37 38 4.713824 TCGTAAGACTAGTCACAATGGG 57.286 45.455 24.44 7.19 45.01 4.00
52 53 3.022607 AGTTCTTTGTCCGGTCGTAAG 57.977 47.619 0.00 4.21 0.00 2.34
53 54 3.569701 ACTAGTTCTTTGTCCGGTCGTAA 59.430 43.478 0.00 0.00 0.00 3.18
54 55 3.149196 ACTAGTTCTTTGTCCGGTCGTA 58.851 45.455 0.00 0.00 0.00 3.43
55 56 1.959282 ACTAGTTCTTTGTCCGGTCGT 59.041 47.619 0.00 0.00 0.00 4.34
56 57 2.719426 ACTAGTTCTTTGTCCGGTCG 57.281 50.000 0.00 0.00 0.00 4.79
57 58 3.189287 TCGTACTAGTTCTTTGTCCGGTC 59.811 47.826 0.00 0.00 0.00 4.79
58 59 3.149196 TCGTACTAGTTCTTTGTCCGGT 58.851 45.455 0.00 0.00 0.00 5.28
59 60 3.837213 TCGTACTAGTTCTTTGTCCGG 57.163 47.619 0.00 0.00 0.00 5.14
60 61 4.027065 CGATCGTACTAGTTCTTTGTCCG 58.973 47.826 7.03 0.00 0.00 4.79
61 62 5.227238 TCGATCGTACTAGTTCTTTGTCC 57.773 43.478 15.94 0.00 0.00 4.02
62 63 5.908499 GGATCGATCGTACTAGTTCTTTGTC 59.092 44.000 18.81 0.00 0.00 3.18
63 64 5.356190 TGGATCGATCGTACTAGTTCTTTGT 59.644 40.000 18.81 0.00 0.00 2.83
64 65 5.817988 TGGATCGATCGTACTAGTTCTTTG 58.182 41.667 18.81 0.00 0.00 2.77
65 66 6.318144 TCTTGGATCGATCGTACTAGTTCTTT 59.682 38.462 18.81 0.00 0.00 2.52
66 67 5.821470 TCTTGGATCGATCGTACTAGTTCTT 59.179 40.000 18.81 0.00 0.00 2.52
67 68 5.366460 TCTTGGATCGATCGTACTAGTTCT 58.634 41.667 18.81 0.00 0.00 3.01
68 69 5.670149 TCTTGGATCGATCGTACTAGTTC 57.330 43.478 18.81 0.00 0.00 3.01
69 70 6.935771 AGTATCTTGGATCGATCGTACTAGTT 59.064 38.462 18.81 9.11 0.00 2.24
70 71 6.465948 AGTATCTTGGATCGATCGTACTAGT 58.534 40.000 18.81 0.00 0.00 2.57
71 72 6.971527 AGTATCTTGGATCGATCGTACTAG 57.028 41.667 18.81 11.31 0.00 2.57
72 73 7.609960 AGTAGTATCTTGGATCGATCGTACTA 58.390 38.462 18.81 18.71 0.00 1.82
73 74 6.465948 AGTAGTATCTTGGATCGATCGTACT 58.534 40.000 18.81 19.51 0.00 2.73
74 75 6.724694 AGTAGTATCTTGGATCGATCGTAC 57.275 41.667 18.81 14.62 0.00 3.67
75 76 6.370994 GGAAGTAGTATCTTGGATCGATCGTA 59.629 42.308 18.81 8.03 0.00 3.43
76 77 5.181622 GGAAGTAGTATCTTGGATCGATCGT 59.818 44.000 18.81 2.13 0.00 3.73
77 78 5.413213 AGGAAGTAGTATCTTGGATCGATCG 59.587 44.000 18.81 9.36 0.00 3.69
78 79 6.127842 GGAGGAAGTAGTATCTTGGATCGATC 60.128 46.154 17.36 17.36 0.00 3.69
79 80 5.712917 GGAGGAAGTAGTATCTTGGATCGAT 59.287 44.000 0.00 0.00 0.00 3.59
80 81 5.071370 GGAGGAAGTAGTATCTTGGATCGA 58.929 45.833 0.00 0.00 0.00 3.59
81 82 4.083217 CGGAGGAAGTAGTATCTTGGATCG 60.083 50.000 0.00 0.00 0.00 3.69
82 83 4.828387 ACGGAGGAAGTAGTATCTTGGATC 59.172 45.833 0.00 0.00 0.00 3.36
83 84 4.805744 ACGGAGGAAGTAGTATCTTGGAT 58.194 43.478 0.00 0.00 0.00 3.41
84 85 4.246712 ACGGAGGAAGTAGTATCTTGGA 57.753 45.455 0.00 0.00 0.00 3.53
85 86 4.202131 GGAACGGAGGAAGTAGTATCTTGG 60.202 50.000 0.00 0.00 0.00 3.61
86 87 4.401519 TGGAACGGAGGAAGTAGTATCTTG 59.598 45.833 0.00 0.00 0.00 3.02
87 88 4.607239 TGGAACGGAGGAAGTAGTATCTT 58.393 43.478 0.00 0.00 0.00 2.40
88 89 4.246712 TGGAACGGAGGAAGTAGTATCT 57.753 45.455 0.00 0.00 0.00 1.98
89 90 4.996788 TTGGAACGGAGGAAGTAGTATC 57.003 45.455 0.00 0.00 0.00 2.24
90 91 5.750352 TTTTGGAACGGAGGAAGTAGTAT 57.250 39.130 0.00 0.00 0.00 2.12
91 92 5.750352 ATTTTGGAACGGAGGAAGTAGTA 57.250 39.130 0.00 0.00 0.00 1.82
92 93 4.635699 ATTTTGGAACGGAGGAAGTAGT 57.364 40.909 0.00 0.00 0.00 2.73
93 94 6.424207 GCTATATTTTGGAACGGAGGAAGTAG 59.576 42.308 0.00 0.00 0.00 2.57
94 95 6.126997 TGCTATATTTTGGAACGGAGGAAGTA 60.127 38.462 0.00 0.00 0.00 2.24
95 96 5.123936 GCTATATTTTGGAACGGAGGAAGT 58.876 41.667 0.00 0.00 0.00 3.01
96 97 5.123227 TGCTATATTTTGGAACGGAGGAAG 58.877 41.667 0.00 0.00 0.00 3.46
97 98 5.105567 TGCTATATTTTGGAACGGAGGAA 57.894 39.130 0.00 0.00 0.00 3.36
98 99 4.764050 TGCTATATTTTGGAACGGAGGA 57.236 40.909 0.00 0.00 0.00 3.71
99 100 4.821805 ACATGCTATATTTTGGAACGGAGG 59.178 41.667 0.00 0.00 0.00 4.30
100 101 5.049405 GGACATGCTATATTTTGGAACGGAG 60.049 44.000 0.00 0.00 0.00 4.63
101 102 4.819630 GGACATGCTATATTTTGGAACGGA 59.180 41.667 0.00 0.00 0.00 4.69
102 103 4.821805 AGGACATGCTATATTTTGGAACGG 59.178 41.667 0.00 0.00 0.00 4.44
103 104 5.333339 CGAGGACATGCTATATTTTGGAACG 60.333 44.000 0.00 0.00 0.00 3.95
104 105 5.758296 TCGAGGACATGCTATATTTTGGAAC 59.242 40.000 0.00 0.00 0.00 3.62
105 106 5.924356 TCGAGGACATGCTATATTTTGGAA 58.076 37.500 0.00 0.00 0.00 3.53
106 107 5.545063 TCGAGGACATGCTATATTTTGGA 57.455 39.130 0.00 0.00 0.00 3.53
107 108 6.808008 AATCGAGGACATGCTATATTTTGG 57.192 37.500 0.00 0.00 0.00 3.28
108 109 7.301054 GGAAATCGAGGACATGCTATATTTTG 58.699 38.462 0.00 0.00 0.00 2.44
109 110 6.147821 CGGAAATCGAGGACATGCTATATTTT 59.852 38.462 0.00 0.00 42.43 1.82
110 111 5.639506 CGGAAATCGAGGACATGCTATATTT 59.360 40.000 0.00 0.00 42.43 1.40
111 112 5.171476 CGGAAATCGAGGACATGCTATATT 58.829 41.667 0.00 0.00 42.43 1.28
112 113 4.748892 CGGAAATCGAGGACATGCTATAT 58.251 43.478 0.00 0.00 42.43 0.86
113 114 3.614150 GCGGAAATCGAGGACATGCTATA 60.614 47.826 0.00 0.00 42.43 1.31
114 115 2.868044 GCGGAAATCGAGGACATGCTAT 60.868 50.000 0.00 0.00 42.43 2.97
115 116 1.538204 GCGGAAATCGAGGACATGCTA 60.538 52.381 0.00 0.00 42.43 3.49
116 117 0.811616 GCGGAAATCGAGGACATGCT 60.812 55.000 0.00 0.00 42.43 3.79
117 118 1.643832 GCGGAAATCGAGGACATGC 59.356 57.895 0.00 0.00 42.43 4.06
118 119 1.160329 GGGCGGAAATCGAGGACATG 61.160 60.000 0.00 0.00 42.43 3.21
119 120 1.146263 GGGCGGAAATCGAGGACAT 59.854 57.895 0.00 0.00 42.43 3.06
120 121 1.550130 AAGGGCGGAAATCGAGGACA 61.550 55.000 0.00 0.00 42.43 4.02
121 122 0.810426 GAAGGGCGGAAATCGAGGAC 60.810 60.000 0.00 0.00 42.43 3.85
122 123 1.261938 TGAAGGGCGGAAATCGAGGA 61.262 55.000 0.00 0.00 42.43 3.71
123 124 0.392461 TTGAAGGGCGGAAATCGAGG 60.392 55.000 0.00 0.00 42.43 4.63
124 125 0.727398 GTTGAAGGGCGGAAATCGAG 59.273 55.000 0.00 0.00 42.43 4.04
125 126 0.323629 AGTTGAAGGGCGGAAATCGA 59.676 50.000 0.00 0.00 42.43 3.59
126 127 1.165270 AAGTTGAAGGGCGGAAATCG 58.835 50.000 0.00 0.00 42.76 3.34
127 128 2.556622 TCAAAGTTGAAGGGCGGAAATC 59.443 45.455 0.00 0.00 33.55 2.17
128 129 2.296190 GTCAAAGTTGAAGGGCGGAAAT 59.704 45.455 0.00 0.00 39.21 2.17
129 130 1.679153 GTCAAAGTTGAAGGGCGGAAA 59.321 47.619 0.00 0.00 39.21 3.13
130 131 1.133915 AGTCAAAGTTGAAGGGCGGAA 60.134 47.619 0.00 0.00 39.21 4.30
131 132 0.472471 AGTCAAAGTTGAAGGGCGGA 59.528 50.000 0.00 0.00 39.21 5.54
132 133 2.178912 TAGTCAAAGTTGAAGGGCGG 57.821 50.000 0.00 0.00 39.21 6.13
133 134 5.873179 TTTATAGTCAAAGTTGAAGGGCG 57.127 39.130 0.00 0.00 39.21 6.13
146 147 9.491675 TGGTCTCGTTGTTTAAATTTATAGTCA 57.508 29.630 0.00 0.00 0.00 3.41
152 153 8.274939 CGTAGTTGGTCTCGTTGTTTAAATTTA 58.725 33.333 0.00 0.00 0.00 1.40
153 154 7.127686 CGTAGTTGGTCTCGTTGTTTAAATTT 58.872 34.615 0.00 0.00 0.00 1.82
154 155 6.293027 CCGTAGTTGGTCTCGTTGTTTAAATT 60.293 38.462 0.00 0.00 0.00 1.82
155 156 5.178067 CCGTAGTTGGTCTCGTTGTTTAAAT 59.822 40.000 0.00 0.00 0.00 1.40
156 157 4.507388 CCGTAGTTGGTCTCGTTGTTTAAA 59.493 41.667 0.00 0.00 0.00 1.52
157 158 4.050553 CCGTAGTTGGTCTCGTTGTTTAA 58.949 43.478 0.00 0.00 0.00 1.52
158 159 3.641648 CCGTAGTTGGTCTCGTTGTTTA 58.358 45.455 0.00 0.00 0.00 2.01
159 160 2.476821 CCGTAGTTGGTCTCGTTGTTT 58.523 47.619 0.00 0.00 0.00 2.83
160 161 1.870993 GCCGTAGTTGGTCTCGTTGTT 60.871 52.381 0.00 0.00 0.00 2.83
161 162 0.319297 GCCGTAGTTGGTCTCGTTGT 60.319 55.000 0.00 0.00 0.00 3.32
162 163 1.342082 CGCCGTAGTTGGTCTCGTTG 61.342 60.000 0.00 0.00 0.00 4.10
163 164 1.080974 CGCCGTAGTTGGTCTCGTT 60.081 57.895 0.00 0.00 0.00 3.85
164 165 2.564975 CGCCGTAGTTGGTCTCGT 59.435 61.111 0.00 0.00 0.00 4.18
165 166 2.202570 CCGCCGTAGTTGGTCTCG 60.203 66.667 0.00 0.00 0.00 4.04
166 167 2.183555 CCCGCCGTAGTTGGTCTC 59.816 66.667 0.00 0.00 0.00 3.36
167 168 2.283388 TCCCGCCGTAGTTGGTCT 60.283 61.111 0.00 0.00 0.00 3.85
168 169 2.183555 CTCCCGCCGTAGTTGGTC 59.816 66.667 0.00 0.00 0.00 4.02
169 170 4.078516 GCTCCCGCCGTAGTTGGT 62.079 66.667 0.00 0.00 0.00 3.67
170 171 3.599285 TTGCTCCCGCCGTAGTTGG 62.599 63.158 0.00 0.00 34.43 3.77
171 172 1.231958 TTTTGCTCCCGCCGTAGTTG 61.232 55.000 0.00 0.00 34.43 3.16
172 173 0.322187 ATTTTGCTCCCGCCGTAGTT 60.322 50.000 0.00 0.00 34.43 2.24
173 174 0.322187 AATTTTGCTCCCGCCGTAGT 60.322 50.000 0.00 0.00 34.43 2.73
174 175 1.658994 TAATTTTGCTCCCGCCGTAG 58.341 50.000 0.00 0.00 34.43 3.51
175 176 2.335316 ATAATTTTGCTCCCGCCGTA 57.665 45.000 0.00 0.00 34.43 4.02
176 177 2.335316 TATAATTTTGCTCCCGCCGT 57.665 45.000 0.00 0.00 34.43 5.68
177 178 5.560966 ATTATATAATTTTGCTCCCGCCG 57.439 39.130 1.91 0.00 34.43 6.46
178 179 6.919721 TCAATTATATAATTTTGCTCCCGCC 58.080 36.000 16.47 0.00 33.88 6.13
179 180 8.810652 TTTCAATTATATAATTTTGCTCCCGC 57.189 30.769 16.47 0.00 33.88 6.13
219 220 9.530129 GGAGCGAAAATTATACTAATGAATTCG 57.470 33.333 0.04 13.03 39.85 3.34
220 221 9.827411 GGGAGCGAAAATTATACTAATGAATTC 57.173 33.333 0.00 0.00 0.00 2.17
221 222 8.504005 CGGGAGCGAAAATTATACTAATGAATT 58.496 33.333 0.00 0.00 0.00 2.17
222 223 8.029642 CGGGAGCGAAAATTATACTAATGAAT 57.970 34.615 0.00 0.00 0.00 2.57
223 224 7.416154 CGGGAGCGAAAATTATACTAATGAA 57.584 36.000 0.00 0.00 0.00 2.57
246 247 2.159282 ACCAATAAGACCGACTACAGCG 60.159 50.000 0.00 0.00 0.00 5.18
247 248 3.521947 ACCAATAAGACCGACTACAGC 57.478 47.619 0.00 0.00 0.00 4.40
248 249 6.446781 TCTAACCAATAAGACCGACTACAG 57.553 41.667 0.00 0.00 0.00 2.74
249 250 7.414222 AATCTAACCAATAAGACCGACTACA 57.586 36.000 0.00 0.00 0.00 2.74
250 251 9.978044 ATAAATCTAACCAATAAGACCGACTAC 57.022 33.333 0.00 0.00 0.00 2.73
251 252 9.976511 CATAAATCTAACCAATAAGACCGACTA 57.023 33.333 0.00 0.00 0.00 2.59
252 253 7.441458 GCATAAATCTAACCAATAAGACCGACT 59.559 37.037 0.00 0.00 0.00 4.18
253 254 7.441458 AGCATAAATCTAACCAATAAGACCGAC 59.559 37.037 0.00 0.00 0.00 4.79
254 255 7.506114 AGCATAAATCTAACCAATAAGACCGA 58.494 34.615 0.00 0.00 0.00 4.69
255 256 7.441157 TGAGCATAAATCTAACCAATAAGACCG 59.559 37.037 0.00 0.00 0.00 4.79
256 257 8.677148 TGAGCATAAATCTAACCAATAAGACC 57.323 34.615 0.00 0.00 0.00 3.85
262 263 9.023962 TCAACTTTGAGCATAAATCTAACCAAT 57.976 29.630 0.00 0.00 32.50 3.16
263 264 8.402798 TCAACTTTGAGCATAAATCTAACCAA 57.597 30.769 0.00 0.00 32.50 3.67
264 265 7.994425 TCAACTTTGAGCATAAATCTAACCA 57.006 32.000 0.00 0.00 32.50 3.67
265 266 7.755373 GGTTCAACTTTGAGCATAAATCTAACC 59.245 37.037 7.93 0.00 39.76 2.85
266 267 8.515414 AGGTTCAACTTTGAGCATAAATCTAAC 58.485 33.333 7.93 0.00 39.76 2.34
267 268 8.635765 AGGTTCAACTTTGAGCATAAATCTAA 57.364 30.769 7.93 0.00 39.76 2.10
268 269 7.064609 CGAGGTTCAACTTTGAGCATAAATCTA 59.935 37.037 7.93 0.00 39.76 1.98
269 270 6.128172 CGAGGTTCAACTTTGAGCATAAATCT 60.128 38.462 7.93 0.00 39.76 2.40
270 271 6.024049 CGAGGTTCAACTTTGAGCATAAATC 58.976 40.000 7.93 0.00 39.76 2.17
271 272 5.106157 CCGAGGTTCAACTTTGAGCATAAAT 60.106 40.000 7.93 0.00 39.76 1.40
272 273 4.215399 CCGAGGTTCAACTTTGAGCATAAA 59.785 41.667 7.93 0.00 39.76 1.40
273 274 3.751175 CCGAGGTTCAACTTTGAGCATAA 59.249 43.478 7.93 0.00 39.76 1.90
274 275 3.007506 TCCGAGGTTCAACTTTGAGCATA 59.992 43.478 7.93 0.00 39.76 3.14
275 276 2.154462 CCGAGGTTCAACTTTGAGCAT 58.846 47.619 7.93 0.70 39.76 3.79
276 277 1.140052 TCCGAGGTTCAACTTTGAGCA 59.860 47.619 7.93 0.00 39.76 4.26
277 278 1.878953 TCCGAGGTTCAACTTTGAGC 58.121 50.000 0.00 0.00 38.61 4.26
278 279 3.304057 GCTTTCCGAGGTTCAACTTTGAG 60.304 47.826 0.00 0.00 38.61 3.02
279 280 2.616842 GCTTTCCGAGGTTCAACTTTGA 59.383 45.455 0.00 0.00 34.92 2.69
280 281 2.602217 CGCTTTCCGAGGTTCAACTTTG 60.602 50.000 0.00 0.00 40.02 2.77
281 282 1.602377 CGCTTTCCGAGGTTCAACTTT 59.398 47.619 0.00 0.00 40.02 2.66
282 283 1.226746 CGCTTTCCGAGGTTCAACTT 58.773 50.000 0.00 0.00 40.02 2.66
283 284 0.106149 ACGCTTTCCGAGGTTCAACT 59.894 50.000 0.00 0.00 41.02 3.16
284 285 0.234884 CACGCTTTCCGAGGTTCAAC 59.765 55.000 0.00 0.00 41.02 3.18
285 286 0.882927 CCACGCTTTCCGAGGTTCAA 60.883 55.000 0.00 0.00 41.93 2.69
286 287 1.301401 CCACGCTTTCCGAGGTTCA 60.301 57.895 0.00 0.00 41.93 3.18
287 288 1.005394 TCCACGCTTTCCGAGGTTC 60.005 57.895 0.00 0.00 46.17 3.62
288 289 1.301479 GTCCACGCTTTCCGAGGTT 60.301 57.895 0.00 0.00 46.17 3.50
289 290 2.342648 GTCCACGCTTTCCGAGGT 59.657 61.111 0.00 0.00 46.17 3.85
300 301 1.855978 TCAAAATATAGCGCGTCCACG 59.144 47.619 8.43 0.00 43.27 4.94
301 302 3.936902 TTCAAAATATAGCGCGTCCAC 57.063 42.857 8.43 0.00 0.00 4.02
302 303 3.242155 CGTTTCAAAATATAGCGCGTCCA 60.242 43.478 8.43 0.00 0.00 4.02
303 304 3.242188 ACGTTTCAAAATATAGCGCGTCC 60.242 43.478 8.43 0.00 0.00 4.79
304 305 3.919827 ACGTTTCAAAATATAGCGCGTC 58.080 40.909 8.43 0.00 0.00 5.19
305 306 5.428770 CATACGTTTCAAAATATAGCGCGT 58.571 37.500 8.43 0.00 0.00 6.01
306 307 4.838642 CCATACGTTTCAAAATATAGCGCG 59.161 41.667 0.00 0.00 0.00 6.86
307 308 5.981174 TCCATACGTTTCAAAATATAGCGC 58.019 37.500 0.00 0.00 0.00 5.92
308 309 7.173863 ACTCCATACGTTTCAAAATATAGCG 57.826 36.000 0.00 0.00 0.00 4.26
309 310 9.472361 TCTACTCCATACGTTTCAAAATATAGC 57.528 33.333 0.00 0.00 0.00 2.97
316 317 9.887406 GAAAAATTCTACTCCATACGTTTCAAA 57.113 29.630 0.00 0.00 0.00 2.69
317 318 9.058174 TGAAAAATTCTACTCCATACGTTTCAA 57.942 29.630 0.00 0.00 30.63 2.69
318 319 8.610248 TGAAAAATTCTACTCCATACGTTTCA 57.390 30.769 0.00 0.00 0.00 2.69
319 320 9.326339 GTTGAAAAATTCTACTCCATACGTTTC 57.674 33.333 0.00 0.00 33.54 2.78
320 321 8.013378 CGTTGAAAAATTCTACTCCATACGTTT 58.987 33.333 0.00 0.00 34.04 3.60
321 322 7.172019 ACGTTGAAAAATTCTACTCCATACGTT 59.828 33.333 0.00 0.00 32.87 3.99
322 323 6.647895 ACGTTGAAAAATTCTACTCCATACGT 59.352 34.615 0.00 0.00 34.04 3.57
323 324 6.953743 CACGTTGAAAAATTCTACTCCATACG 59.046 38.462 0.00 0.00 34.04 3.06
324 325 8.025243 TCACGTTGAAAAATTCTACTCCATAC 57.975 34.615 0.00 0.00 34.04 2.39
325 326 8.786826 ATCACGTTGAAAAATTCTACTCCATA 57.213 30.769 0.00 0.00 34.04 2.74
326 327 7.148239 GGATCACGTTGAAAAATTCTACTCCAT 60.148 37.037 0.00 0.00 34.04 3.41
327 328 6.148811 GGATCACGTTGAAAAATTCTACTCCA 59.851 38.462 0.00 0.00 34.04 3.86
328 329 6.371825 AGGATCACGTTGAAAAATTCTACTCC 59.628 38.462 0.00 3.92 34.04 3.85
329 330 7.365840 AGGATCACGTTGAAAAATTCTACTC 57.634 36.000 0.00 0.00 34.04 2.59
415 416 1.227999 ACGCTGTTGGTGTTGGATCG 61.228 55.000 0.00 0.00 34.69 3.69
480 498 1.479323 CTTCTTCCGGTAATGGGACGA 59.521 52.381 0.00 0.00 32.05 4.20
512 530 1.380112 GGCACTAGGACGAGGAGGT 60.380 63.158 0.00 0.00 0.00 3.85
615 686 0.867753 CGTTAGTGCTCTAGCTGCCG 60.868 60.000 0.00 0.00 42.66 5.69
675 749 4.019312 TCATGGCCGTGCAGAGCA 62.019 61.111 20.86 0.00 35.60 4.26
704 790 3.024782 GCAGAAGCAGAGCACAGCG 62.025 63.158 0.00 0.00 41.58 5.18
880 966 2.298661 GGTGAAGACGGTGGGGGAT 61.299 63.158 0.00 0.00 0.00 3.85
1167 1263 4.083862 GGGAGCAGGGTGTCGGTC 62.084 72.222 0.00 0.00 0.00 4.79
1305 1401 2.420568 GGTCGATACCTCGCCACCA 61.421 63.158 0.00 0.00 44.65 4.17
1399 1495 0.252012 AAATGGCCCGTGGAATCCAA 60.252 50.000 2.31 0.00 34.18 3.53
1465 1561 4.400251 CCTCCTCCTGACCCCGGT 62.400 72.222 0.00 0.00 0.00 5.28
1529 1625 4.760047 ACACGGTCCATGCCTCGC 62.760 66.667 0.00 0.00 0.00 5.03
1532 1628 3.311110 ACGACACGGTCCATGCCT 61.311 61.111 0.00 0.00 0.00 4.75
1536 1632 1.218047 CATCCACGACACGGTCCAT 59.782 57.895 0.00 0.00 0.00 3.41
1947 2055 2.665185 GGCACGTTGAAGTCGGCT 60.665 61.111 0.00 0.00 0.00 5.52
2018 2132 4.596180 CGTCGCATCCGGCAATGC 62.596 66.667 16.26 16.26 46.86 3.56
2124 2253 0.435008 CGAAGAACGCGGACAAGAAG 59.565 55.000 12.47 0.00 34.51 2.85
2291 2426 2.359975 GGAACTTCCTGGTGGCCG 60.360 66.667 0.00 0.00 32.53 6.13
2469 2613 0.779997 AGCAGAACCCCCACATTCTT 59.220 50.000 0.00 0.00 32.77 2.52
2472 2616 1.002134 CGAGCAGAACCCCCACATT 60.002 57.895 0.00 0.00 0.00 2.71
2787 2979 0.845102 ACCCCCTTGTTCCTCGGATT 60.845 55.000 0.00 0.00 0.00 3.01
2913 3105 0.323725 CTTTCCCATCCACCACCCAG 60.324 60.000 0.00 0.00 0.00 4.45
3018 3210 1.153369 ATCCAGCCGTTCATCCACG 60.153 57.895 0.00 0.00 40.02 4.94
3091 3283 6.316640 GGCCTTTTGTTTCTATCTTCCTCTAC 59.683 42.308 0.00 0.00 0.00 2.59
3200 3393 5.184096 ACACACACTAACACATGTCCAAAAA 59.816 36.000 0.00 0.00 0.00 1.94
3270 3496 2.241281 TTGGATCGGAGGGAGTACAA 57.759 50.000 0.00 0.00 0.00 2.41
3323 3561 0.865769 GGTCCATAATAAGTGCCGCG 59.134 55.000 0.00 0.00 0.00 6.46
3327 3565 3.391296 TCCCTCTGGTCCATAATAAGTGC 59.609 47.826 0.00 0.00 0.00 4.40
3343 3581 4.601857 TGGGTTCTAATTTCAACTCCCTCT 59.398 41.667 0.00 0.00 35.20 3.69
3352 3590 7.827236 AGACATAATTCGTGGGTTCTAATTTCA 59.173 33.333 0.00 0.00 0.00 2.69
3368 3606 6.486248 TCACGCATTAGCAAAGACATAATTC 58.514 36.000 0.00 0.00 42.27 2.17
3382 3620 3.562973 AGATTTCTGCCATCACGCATTAG 59.437 43.478 0.00 0.00 38.30 1.73
3466 3704 6.121776 TGATACCACTGTCAAACCAATAGT 57.878 37.500 0.00 0.00 0.00 2.12
3507 3745 7.038048 TGATCTAGTTCACAATCTAAGTGCTG 58.962 38.462 0.00 0.00 36.93 4.41
3508 3746 7.175347 TGATCTAGTTCACAATCTAAGTGCT 57.825 36.000 0.00 0.00 36.93 4.40
3509 3747 6.478344 CCTGATCTAGTTCACAATCTAAGTGC 59.522 42.308 0.00 0.00 36.93 4.40
3610 3852 5.765182 GGTAACTGCTTGCCAACTGATATAT 59.235 40.000 0.00 0.00 32.49 0.86
3656 3898 4.081476 TGAGGTTGTCACATATCAGGTCTG 60.081 45.833 0.00 0.00 0.00 3.51
3689 3931 9.371136 GAGAACATACTGTAAATCTGACAATGA 57.629 33.333 5.47 0.00 0.00 2.57
3729 3971 7.562454 TTGTTTCTGAAATCGTTTTAGGACT 57.438 32.000 6.06 0.00 0.00 3.85
3731 3973 9.296400 CTTTTTGTTTCTGAAATCGTTTTAGGA 57.704 29.630 6.06 0.00 0.00 2.94
3737 3979 7.535139 TCAGTCTTTTTGTTTCTGAAATCGTT 58.465 30.769 6.06 0.00 33.18 3.85
3738 3980 7.083875 TCAGTCTTTTTGTTTCTGAAATCGT 57.916 32.000 6.06 0.00 33.18 3.73
3952 4360 4.739137 GCGAAAGAGTTGATCAGGATAGCT 60.739 45.833 0.00 0.00 0.00 3.32
4072 4480 2.624838 CCATGTGGTGCTCAAGAAGTTT 59.375 45.455 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.