Multiple sequence alignment - TraesCS7A01G311900

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 TraesCS7A01G311900 chr7A 100.000 5195 0 0 1 5195 442947263 442952457 0.000000e+00 9594
1 TraesCS7A01G311900 chr7A 89.684 475 32 6 1505 1974 442947699 442948161 1.610000e-164 590
2 TraesCS7A01G311900 chr7A 89.684 475 32 6 437 899 442948767 442949236 1.610000e-164 590
3 TraesCS7A01G311900 chr7A 89.474 133 14 0 1385 1517 442947485 442947617 8.950000e-38 169
4 TraesCS7A01G311900 chr7A 89.474 133 14 0 223 355 442948647 442948779 8.950000e-38 169
5 TraesCS7A01G311900 chr7B 94.440 3813 132 21 1414 5195 387642233 387645996 0.000000e+00 5794
6 TraesCS7A01G311900 chr7B 90.316 475 28 6 437 899 387642324 387642792 1.600000e-169 606
7 TraesCS7A01G311900 chr7B 84.615 429 36 12 897 1301 117793343 117792921 2.910000e-107 399
8 TraesCS7A01G311900 chr7B 94.186 86 4 1 1299 1384 117792873 117792789 4.220000e-26 130
9 TraesCS7A01G311900 chr7D 95.489 2793 96 6 1385 4153 390904732 390907518 0.000000e+00 4433
10 TraesCS7A01G311900 chr7D 91.009 1001 46 14 4207 5195 390907526 390908494 0.000000e+00 1310
11 TraesCS7A01G311900 chr7D 89.662 474 32 6 437 898 390904852 390905320 5.790000e-164 588
12 TraesCS7A01G311900 chr7D 93.793 145 7 2 1 144 228862751 228862608 3.150000e-52 217
13 TraesCS7A01G311900 chr7D 93.793 145 6 3 1 143 105575154 105575297 1.130000e-51 215
14 TraesCS7A01G311900 chr7D 90.698 86 7 1 1299 1384 48125777 48125861 4.250000e-21 113
15 TraesCS7A01G311900 chr5D 94.483 145 6 2 1 144 386566035 386566178 6.770000e-54 222
16 TraesCS7A01G311900 chr4A 93.836 146 6 3 1 144 415013295 415013439 3.150000e-52 217
17 TraesCS7A01G311900 chr4A 93.023 86 5 1 1299 1384 736525108 736525024 1.960000e-24 124
18 TraesCS7A01G311900 chr3D 93.836 146 6 3 1 144 92756889 92757033 3.150000e-52 217
19 TraesCS7A01G311900 chr3A 93.836 146 6 3 1 144 730179502 730179646 3.150000e-52 217
20 TraesCS7A01G311900 chr6D 93.103 145 8 2 1 144 197925495 197925352 1.470000e-50 211
21 TraesCS7A01G311900 chr4D 93.103 145 8 2 1 144 40726201 40726344 1.470000e-50 211
22 TraesCS7A01G311900 chr1D 93.151 146 7 3 1 144 292737242 292737098 1.470000e-50 211
23 TraesCS7A01G311900 chr6B 91.398 93 7 1 1299 1391 169104601 169104510 5.460000e-25 126
24 TraesCS7A01G311900 chrUn 90.909 88 6 2 1297 1384 56268222 56268307 3.290000e-22 117
25 TraesCS7A01G311900 chrUn 89.655 87 7 2 1299 1385 64204629 64204545 5.500000e-20 110
26 TraesCS7A01G311900 chr3B 90.805 87 7 1 1299 1385 820135569 820135654 1.180000e-21 115
27 TraesCS7A01G311900 chr4B 89.655 87 8 1 1299 1385 656915220 656915135 5.500000e-20 110
28 TraesCS7A01G311900 chr5B 89.655 87 6 3 1299 1384 346623440 346623356 1.980000e-19 108


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 TraesCS7A01G311900 chr7A 442947263 442952457 5194 False 9594.000000 9594 100.000000 1 5195 1 chr7A.!!$F1 5194
1 TraesCS7A01G311900 chr7A 442947485 442949236 1751 False 379.500000 590 89.579000 223 1974 4 chr7A.!!$F2 1751
2 TraesCS7A01G311900 chr7B 387642233 387645996 3763 False 3200.000000 5794 92.378000 437 5195 2 chr7B.!!$F1 4758
3 TraesCS7A01G311900 chr7B 117792789 117793343 554 True 264.500000 399 89.400500 897 1384 2 chr7B.!!$R1 487
4 TraesCS7A01G311900 chr7D 390904732 390908494 3762 False 2110.333333 4433 92.053333 437 5195 3 chr7D.!!$F3 4758

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
68 69 0.032017 ACTCCCCCTCTCGTTGCTAT 60.032 55.000 0.00 0.00 0.00 2.97 F
72 73 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96 F
133 134 0.110678 TACGTTCCCCAACATTGCCA 59.889 50.000 0.00 0.00 32.14 4.92 F
135 136 0.173255 CGTTCCCCAACATTGCCATC 59.827 55.000 0.00 0.00 32.14 3.51 F
172 173 0.179062 GGAGCTACAGTGGGCATCAG 60.179 60.000 11.81 0.00 0.00 2.90 F
173 174 0.813210 GAGCTACAGTGGGCATCAGC 60.813 60.000 11.81 2.99 41.10 4.26 F
2368 2456 1.337728 ACGAATTGATGGAGCGTGTGA 60.338 47.619 0.00 0.00 33.52 3.58 F
3048 3154 1.002366 CCATACTTCAGCACGCAGAC 58.998 55.000 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2080 7.329226 CGTGTAGGTAAAATTTTCTTAGACCGA 59.671 37.037 6.72 2.77 0.00 4.69 R
2091 2179 8.997323 CAGGAAAGGTCTGAATATATGCTTAAG 58.003 37.037 0.00 0.00 34.36 1.85 R
2217 2305 0.749454 CGGCTTTCTCCCCAGGAATG 60.749 60.000 0.00 0.00 0.00 2.67 R
2368 2456 1.616159 CACCAACCTTTCCATTCGGT 58.384 50.000 0.00 0.00 0.00 4.69 R
2476 2564 4.450976 ACAGACTTGTGAAAGTACATGCA 58.549 39.130 0.00 0.00 35.83 3.96 R
2512 2600 0.735978 TACGGAACACTCTGCATGCG 60.736 55.000 14.09 8.20 0.00 4.73 R
3434 3542 0.323178 ACCTCCCGCTAGAAGAACGA 60.323 55.000 0.00 0.00 0.00 3.85 R
4902 5029 0.119155 TCTCCCTCCCCATGTGAAGT 59.881 55.000 0.00 0.00 0.00 3.01 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
20 21 3.198680 CGTTGATAAACGCTTCCGC 57.801 52.632 1.55 0.00 39.43 5.54
21 22 0.719465 CGTTGATAAACGCTTCCGCT 59.281 50.000 1.55 0.00 39.43 5.52
22 23 1.127951 CGTTGATAAACGCTTCCGCTT 59.872 47.619 1.55 0.00 39.43 4.68
23 24 2.346244 CGTTGATAAACGCTTCCGCTTA 59.654 45.455 1.55 0.00 39.43 3.09
24 25 3.667050 GTTGATAAACGCTTCCGCTTAC 58.333 45.455 0.00 0.00 38.22 2.34
25 26 2.962125 TGATAAACGCTTCCGCTTACA 58.038 42.857 0.00 0.00 38.22 2.41
26 27 2.927477 TGATAAACGCTTCCGCTTACAG 59.073 45.455 0.00 0.00 38.22 2.74
27 28 2.443887 TAAACGCTTCCGCTTACAGT 57.556 45.000 0.00 0.00 38.22 3.55
28 29 1.145803 AAACGCTTCCGCTTACAGTC 58.854 50.000 0.00 0.00 38.22 3.51
29 30 0.317479 AACGCTTCCGCTTACAGTCT 59.683 50.000 0.00 0.00 38.22 3.24
30 31 1.171308 ACGCTTCCGCTTACAGTCTA 58.829 50.000 0.00 0.00 38.22 2.59
31 32 1.135460 ACGCTTCCGCTTACAGTCTAC 60.135 52.381 0.00 0.00 38.22 2.59
32 33 1.546834 GCTTCCGCTTACAGTCTACG 58.453 55.000 0.00 0.00 0.00 3.51
33 34 1.131883 GCTTCCGCTTACAGTCTACGA 59.868 52.381 0.00 0.00 0.00 3.43
34 35 2.791849 GCTTCCGCTTACAGTCTACGAG 60.792 54.545 0.00 0.00 0.00 4.18
35 36 1.376543 TCCGCTTACAGTCTACGAGG 58.623 55.000 0.00 0.00 0.00 4.63
36 37 0.381089 CCGCTTACAGTCTACGAGGG 59.619 60.000 0.00 0.00 0.00 4.30
37 38 1.093159 CGCTTACAGTCTACGAGGGT 58.907 55.000 0.00 0.00 0.00 4.34
38 39 2.283298 CGCTTACAGTCTACGAGGGTA 58.717 52.381 0.00 0.00 0.00 3.69
39 40 2.031437 CGCTTACAGTCTACGAGGGTAC 59.969 54.545 0.00 0.00 0.00 3.34
40 41 3.012518 GCTTACAGTCTACGAGGGTACA 58.987 50.000 0.00 0.00 0.00 2.90
41 42 3.631227 GCTTACAGTCTACGAGGGTACAT 59.369 47.826 0.00 0.00 0.00 2.29
42 43 4.818546 GCTTACAGTCTACGAGGGTACATA 59.181 45.833 0.00 0.00 0.00 2.29
43 44 5.049543 GCTTACAGTCTACGAGGGTACATAG 60.050 48.000 0.00 0.00 0.00 2.23
44 45 4.767578 ACAGTCTACGAGGGTACATAGA 57.232 45.455 0.00 0.00 0.00 1.98
45 46 4.450053 ACAGTCTACGAGGGTACATAGAC 58.550 47.826 0.00 4.14 42.52 2.59
46 47 4.080695 ACAGTCTACGAGGGTACATAGACA 60.081 45.833 16.28 0.00 43.94 3.41
47 48 4.880120 CAGTCTACGAGGGTACATAGACAA 59.120 45.833 16.28 0.00 43.94 3.18
48 49 4.880696 AGTCTACGAGGGTACATAGACAAC 59.119 45.833 16.28 0.10 43.94 3.32
49 50 4.637534 GTCTACGAGGGTACATAGACAACA 59.362 45.833 12.11 0.00 42.02 3.33
50 51 3.863142 ACGAGGGTACATAGACAACAC 57.137 47.619 0.00 0.00 0.00 3.32
51 52 3.428532 ACGAGGGTACATAGACAACACT 58.571 45.455 0.00 0.00 0.00 3.55
52 53 3.442977 ACGAGGGTACATAGACAACACTC 59.557 47.826 0.00 0.00 39.74 3.51
53 54 3.181489 CGAGGGTACATAGACAACACTCC 60.181 52.174 0.00 0.00 39.94 3.85
54 55 3.105283 AGGGTACATAGACAACACTCCC 58.895 50.000 0.00 0.00 0.00 4.30
55 56 2.169978 GGGTACATAGACAACACTCCCC 59.830 54.545 0.00 0.00 0.00 4.81
56 57 2.169978 GGTACATAGACAACACTCCCCC 59.830 54.545 0.00 0.00 0.00 5.40
57 58 2.344093 ACATAGACAACACTCCCCCT 57.656 50.000 0.00 0.00 0.00 4.79
58 59 2.188817 ACATAGACAACACTCCCCCTC 58.811 52.381 0.00 0.00 0.00 4.30
59 60 2.225650 ACATAGACAACACTCCCCCTCT 60.226 50.000 0.00 0.00 0.00 3.69
60 61 2.233305 TAGACAACACTCCCCCTCTC 57.767 55.000 0.00 0.00 0.00 3.20
61 62 0.900647 AGACAACACTCCCCCTCTCG 60.901 60.000 0.00 0.00 0.00 4.04
62 63 1.152312 ACAACACTCCCCCTCTCGT 60.152 57.895 0.00 0.00 0.00 4.18
63 64 0.763223 ACAACACTCCCCCTCTCGTT 60.763 55.000 0.00 0.00 0.00 3.85
64 65 0.320771 CAACACTCCCCCTCTCGTTG 60.321 60.000 0.00 0.00 0.00 4.10
65 66 2.113243 AACACTCCCCCTCTCGTTGC 62.113 60.000 0.00 0.00 0.00 4.17
66 67 2.120718 ACTCCCCCTCTCGTTGCT 59.879 61.111 0.00 0.00 0.00 3.91
67 68 0.970937 CACTCCCCCTCTCGTTGCTA 60.971 60.000 0.00 0.00 0.00 3.49
68 69 0.032017 ACTCCCCCTCTCGTTGCTAT 60.032 55.000 0.00 0.00 0.00 2.97
69 70 0.390860 CTCCCCCTCTCGTTGCTATG 59.609 60.000 0.00 0.00 0.00 2.23
70 71 1.227674 CCCCCTCTCGTTGCTATGC 60.228 63.158 0.00 0.00 0.00 3.14
71 72 1.522092 CCCCTCTCGTTGCTATGCA 59.478 57.895 0.00 0.00 36.47 3.96
72 73 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
73 74 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
74 75 1.202568 CCCTCTCGTTGCTATGCATCA 60.203 52.381 0.19 0.00 38.76 3.07
75 76 1.863454 CCTCTCGTTGCTATGCATCAC 59.137 52.381 0.19 0.00 38.76 3.06
76 77 1.863454 CTCTCGTTGCTATGCATCACC 59.137 52.381 0.19 0.00 38.76 4.02
77 78 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
78 79 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
79 80 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
80 81 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
81 82 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
82 83 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
83 84 2.786777 TGCTATGCATCACCATGATCC 58.213 47.619 0.19 0.00 34.28 3.36
84 85 2.374170 TGCTATGCATCACCATGATCCT 59.626 45.455 0.19 0.00 34.28 3.24
85 86 2.747989 GCTATGCATCACCATGATCCTG 59.252 50.000 0.19 0.00 34.28 3.86
86 87 3.809678 GCTATGCATCACCATGATCCTGT 60.810 47.826 0.19 0.00 34.28 4.00
87 88 2.047002 TGCATCACCATGATCCTGTG 57.953 50.000 0.00 0.00 34.28 3.66
88 89 1.282738 TGCATCACCATGATCCTGTGT 59.717 47.619 0.00 0.00 34.28 3.72
89 90 1.674441 GCATCACCATGATCCTGTGTG 59.326 52.381 0.00 10.98 34.28 3.82
90 91 2.942752 GCATCACCATGATCCTGTGTGT 60.943 50.000 14.49 0.00 34.28 3.72
91 92 2.477845 TCACCATGATCCTGTGTGTG 57.522 50.000 14.49 8.57 0.00 3.82
92 93 0.806868 CACCATGATCCTGTGTGTGC 59.193 55.000 0.00 0.00 0.00 4.57
93 94 0.674581 ACCATGATCCTGTGTGTGCG 60.675 55.000 0.00 0.00 0.00 5.34
94 95 0.674581 CCATGATCCTGTGTGTGCGT 60.675 55.000 0.00 0.00 0.00 5.24
95 96 1.405391 CCATGATCCTGTGTGTGCGTA 60.405 52.381 0.00 0.00 0.00 4.42
96 97 1.929169 CATGATCCTGTGTGTGCGTAG 59.071 52.381 0.00 0.00 0.00 3.51
97 98 0.246360 TGATCCTGTGTGTGCGTAGG 59.754 55.000 0.00 0.00 0.00 3.18
98 99 0.530744 GATCCTGTGTGTGCGTAGGA 59.469 55.000 0.00 0.00 43.01 2.94
99 100 0.973632 ATCCTGTGTGTGCGTAGGAA 59.026 50.000 0.00 0.00 42.20 3.36
100 101 0.753867 TCCTGTGTGTGCGTAGGAAA 59.246 50.000 0.00 0.00 36.44 3.13
101 102 1.346395 TCCTGTGTGTGCGTAGGAAAT 59.654 47.619 0.00 0.00 36.44 2.17
102 103 2.151202 CCTGTGTGTGCGTAGGAAATT 58.849 47.619 0.00 0.00 31.91 1.82
103 104 2.552315 CCTGTGTGTGCGTAGGAAATTT 59.448 45.455 0.00 0.00 31.91 1.82
104 105 3.004315 CCTGTGTGTGCGTAGGAAATTTT 59.996 43.478 0.00 0.00 31.91 1.82
105 106 4.499019 CCTGTGTGTGCGTAGGAAATTTTT 60.499 41.667 0.00 0.00 31.91 1.94
106 107 4.355437 TGTGTGTGCGTAGGAAATTTTTG 58.645 39.130 0.00 0.00 0.00 2.44
107 108 4.096532 TGTGTGTGCGTAGGAAATTTTTGA 59.903 37.500 0.00 0.00 0.00 2.69
108 109 5.038033 GTGTGTGCGTAGGAAATTTTTGAA 58.962 37.500 0.00 0.00 0.00 2.69
109 110 5.517054 GTGTGTGCGTAGGAAATTTTTGAAA 59.483 36.000 0.00 0.00 0.00 2.69
110 111 6.200097 GTGTGTGCGTAGGAAATTTTTGAAAT 59.800 34.615 0.00 0.00 0.00 2.17
111 112 6.758886 TGTGTGCGTAGGAAATTTTTGAAATT 59.241 30.769 0.00 0.00 0.00 1.82
112 113 7.921214 TGTGTGCGTAGGAAATTTTTGAAATTA 59.079 29.630 0.00 0.00 0.00 1.40
113 114 8.211838 GTGTGCGTAGGAAATTTTTGAAATTAC 58.788 33.333 0.00 0.00 0.00 1.89
114 115 8.138712 TGTGCGTAGGAAATTTTTGAAATTACT 58.861 29.630 0.00 4.52 0.00 2.24
115 116 9.615295 GTGCGTAGGAAATTTTTGAAATTACTA 57.385 29.630 0.00 3.76 0.00 1.82
116 117 9.615295 TGCGTAGGAAATTTTTGAAATTACTAC 57.385 29.630 18.73 18.73 32.65 2.73
117 118 8.782327 GCGTAGGAAATTTTTGAAATTACTACG 58.218 33.333 29.83 29.83 44.82 3.51
118 119 9.815936 CGTAGGAAATTTTTGAAATTACTACGT 57.184 29.630 28.22 0.00 41.82 3.57
121 122 9.687210 AGGAAATTTTTGAAATTACTACGTTCC 57.313 29.630 0.00 0.00 0.00 3.62
122 123 8.918658 GGAAATTTTTGAAATTACTACGTTCCC 58.081 33.333 0.00 0.00 0.00 3.97
123 124 8.821147 AAATTTTTGAAATTACTACGTTCCCC 57.179 30.769 0.00 0.00 0.00 4.81
124 125 6.956202 TTTTTGAAATTACTACGTTCCCCA 57.044 33.333 0.00 0.00 0.00 4.96
125 126 6.956202 TTTTGAAATTACTACGTTCCCCAA 57.044 33.333 0.00 0.00 0.00 4.12
126 127 5.945466 TTGAAATTACTACGTTCCCCAAC 57.055 39.130 0.00 0.00 0.00 3.77
127 128 4.970711 TGAAATTACTACGTTCCCCAACA 58.029 39.130 0.00 0.00 32.14 3.33
128 129 5.562635 TGAAATTACTACGTTCCCCAACAT 58.437 37.500 0.00 0.00 32.14 2.71
129 130 6.005198 TGAAATTACTACGTTCCCCAACATT 58.995 36.000 0.00 0.00 32.14 2.71
130 131 5.890424 AATTACTACGTTCCCCAACATTG 57.110 39.130 0.00 0.00 32.14 2.82
131 132 1.530323 ACTACGTTCCCCAACATTGC 58.470 50.000 0.00 0.00 32.14 3.56
132 133 0.808755 CTACGTTCCCCAACATTGCC 59.191 55.000 0.00 0.00 32.14 4.52
133 134 0.110678 TACGTTCCCCAACATTGCCA 59.889 50.000 0.00 0.00 32.14 4.92
134 135 0.541764 ACGTTCCCCAACATTGCCAT 60.542 50.000 0.00 0.00 32.14 4.40
135 136 0.173255 CGTTCCCCAACATTGCCATC 59.827 55.000 0.00 0.00 32.14 3.51
136 137 1.265236 GTTCCCCAACATTGCCATCA 58.735 50.000 0.00 0.00 32.14 3.07
137 138 1.066929 GTTCCCCAACATTGCCATCAC 60.067 52.381 0.00 0.00 32.14 3.06
138 139 0.964860 TCCCCAACATTGCCATCACG 60.965 55.000 0.00 0.00 0.00 4.35
139 140 1.512230 CCCAACATTGCCATCACGG 59.488 57.895 0.00 0.00 38.11 4.94
140 141 1.512230 CCAACATTGCCATCACGGG 59.488 57.895 0.00 0.00 34.06 5.28
157 158 1.371183 GGCCAACCCAAAAAGGAGC 59.629 57.895 0.00 0.00 41.22 4.70
158 159 1.121407 GGCCAACCCAAAAAGGAGCT 61.121 55.000 0.00 0.00 41.22 4.09
159 160 1.627864 GCCAACCCAAAAAGGAGCTA 58.372 50.000 0.00 0.00 41.22 3.32
160 161 1.272490 GCCAACCCAAAAAGGAGCTAC 59.728 52.381 0.00 0.00 41.22 3.58
161 162 2.593026 CCAACCCAAAAAGGAGCTACA 58.407 47.619 0.00 0.00 41.22 2.74
162 163 2.558359 CCAACCCAAAAAGGAGCTACAG 59.442 50.000 0.00 0.00 41.22 2.74
163 164 3.222603 CAACCCAAAAAGGAGCTACAGT 58.777 45.455 0.00 0.00 41.22 3.55
164 165 2.863809 ACCCAAAAAGGAGCTACAGTG 58.136 47.619 0.00 0.00 41.22 3.66
165 166 2.162681 CCCAAAAAGGAGCTACAGTGG 58.837 52.381 0.00 0.00 41.22 4.00
166 167 2.162681 CCAAAAAGGAGCTACAGTGGG 58.837 52.381 0.00 0.00 41.22 4.61
167 168 1.541588 CAAAAAGGAGCTACAGTGGGC 59.458 52.381 0.00 0.00 0.00 5.36
168 169 0.771127 AAAAGGAGCTACAGTGGGCA 59.229 50.000 0.00 0.00 0.00 5.36
169 170 0.995024 AAAGGAGCTACAGTGGGCAT 59.005 50.000 0.00 0.00 0.00 4.40
170 171 0.543749 AAGGAGCTACAGTGGGCATC 59.456 55.000 0.00 7.02 0.00 3.91
171 172 0.618680 AGGAGCTACAGTGGGCATCA 60.619 55.000 0.00 0.00 0.00 3.07
172 173 0.179062 GGAGCTACAGTGGGCATCAG 60.179 60.000 11.81 0.00 0.00 2.90
173 174 0.813210 GAGCTACAGTGGGCATCAGC 60.813 60.000 11.81 2.99 41.10 4.26
183 184 3.181367 GCATCAGCCACCTGTTCG 58.819 61.111 0.00 0.00 40.09 3.95
184 185 2.401766 GCATCAGCCACCTGTTCGG 61.402 63.158 0.00 0.00 40.09 4.30
185 186 1.746615 CATCAGCCACCTGTTCGGG 60.747 63.158 0.00 0.00 40.09 5.14
206 207 3.195698 GCCTAAGGCGCCGAACAG 61.196 66.667 23.20 16.01 39.62 3.16
207 208 2.511600 CCTAAGGCGCCGAACAGG 60.512 66.667 23.20 20.97 44.97 4.00
208 209 2.577059 CTAAGGCGCCGAACAGGA 59.423 61.111 23.20 1.11 45.00 3.86
209 210 1.519455 CTAAGGCGCCGAACAGGAG 60.519 63.158 23.20 7.78 45.00 3.69
214 215 2.202676 CGCCGAACAGGAGCTCTC 60.203 66.667 14.64 3.76 45.00 3.20
1990 2078 6.367983 ACAGATTGTTGCTATGGTGGAATAT 58.632 36.000 0.00 0.00 0.00 1.28
1992 2080 6.263842 CAGATTGTTGCTATGGTGGAATATGT 59.736 38.462 0.00 0.00 0.00 2.29
2091 2179 2.442413 AGGCAGAGAGTGACTACTGAC 58.558 52.381 18.70 16.67 45.98 3.51
2323 2411 6.149474 CGTTCCTACAGGTTCAGAAATTGATT 59.851 38.462 0.00 0.00 35.27 2.57
2368 2456 1.337728 ACGAATTGATGGAGCGTGTGA 60.338 47.619 0.00 0.00 33.52 3.58
2512 2600 1.003839 TCTGTTGATGCCACCGGAC 60.004 57.895 9.46 0.00 0.00 4.79
2524 2612 3.190849 CCGGACGCATGCAGAGTG 61.191 66.667 19.57 2.94 0.00 3.51
2762 2850 1.344438 CTCCAGTGCCAAGCGGATATA 59.656 52.381 0.00 0.00 0.00 0.86
2775 2863 7.553044 GCCAAGCGGATATATAGGTTTTTCTAT 59.447 37.037 3.27 0.00 34.63 1.98
2871 2959 4.062991 GGTTCGGAACTGACTTTATGTGT 58.937 43.478 19.40 0.00 0.00 3.72
2892 2980 7.156673 TGTGTCTACAAAGTTACTGGGATAAC 58.843 38.462 0.00 0.00 33.22 1.89
2908 2996 4.327680 GGATAACAAAGACAAGCTCAGGT 58.672 43.478 0.00 0.00 0.00 4.00
2949 3037 1.454663 GGAAGATGGCCCTTGGAGC 60.455 63.158 0.00 0.00 0.00 4.70
2973 3079 4.346418 AGGGAGTATGACTGCTTGATAAGG 59.654 45.833 0.00 0.00 36.73 2.69
3048 3154 1.002366 CCATACTTCAGCACGCAGAC 58.998 55.000 0.00 0.00 0.00 3.51
3125 3231 6.836007 AGGGATGAATTACAATCTCTTTTCCC 59.164 38.462 0.00 0.00 38.54 3.97
3250 3358 6.687604 ACTGTGTGTCTTATTTTTAATGGCC 58.312 36.000 0.00 0.00 0.00 5.36
3389 3497 3.648339 GCAATTGAGAAGGTTGCAGAA 57.352 42.857 10.34 0.00 45.57 3.02
3434 3542 3.377172 CACTGGACCAGTTCGAAACTTTT 59.623 43.478 25.03 0.00 42.59 2.27
3478 3586 5.404096 TGACAAAGATATTGCTCGACGTTA 58.596 37.500 0.00 0.00 0.00 3.18
3479 3587 5.865013 TGACAAAGATATTGCTCGACGTTAA 59.135 36.000 0.00 0.00 0.00 2.01
3480 3588 6.366604 TGACAAAGATATTGCTCGACGTTAAA 59.633 34.615 0.00 0.00 0.00 1.52
3481 3589 7.095565 TGACAAAGATATTGCTCGACGTTAAAA 60.096 33.333 0.00 0.00 0.00 1.52
3482 3590 7.577979 ACAAAGATATTGCTCGACGTTAAAAA 58.422 30.769 0.00 0.00 0.00 1.94
3559 3667 0.681733 TCCTTCAGGGCTATGCGATC 59.318 55.000 0.00 0.00 35.41 3.69
3572 3680 0.249120 TGCGATCCGAATTGTGTCCT 59.751 50.000 0.00 0.00 0.00 3.85
3589 3697 4.890581 GTGTCCTGATGTATGTCCTCTAGT 59.109 45.833 0.00 0.00 0.00 2.57
3862 3970 2.306805 TGCATCCTTGACTTCACTGGAT 59.693 45.455 6.99 6.99 38.89 3.41
3914 4022 3.384168 TCTAGGGCTGTGATTGGTATGT 58.616 45.455 0.00 0.00 0.00 2.29
3937 4045 6.041409 TGTTATGCAAAGGGAAATCAAGTGAA 59.959 34.615 0.00 0.00 0.00 3.18
3978 4086 3.153919 TCGGGGTTTTGGAATTGAAGAG 58.846 45.455 0.00 0.00 0.00 2.85
4254 4369 5.066505 ACTCATGACAGTTTTGTTGACTTCC 59.933 40.000 0.00 0.00 37.76 3.46
4388 4503 3.960102 ACAAGAGCCTGAAATCCAAAACA 59.040 39.130 0.00 0.00 0.00 2.83
4436 4551 3.589988 TCTCTTGCTGATTTCGAACTCC 58.410 45.455 12.40 0.00 0.00 3.85
4437 4552 3.006859 TCTCTTGCTGATTTCGAACTCCA 59.993 43.478 12.40 2.29 0.00 3.86
4503 4618 5.835819 TCTTCTGCCTGTAGTAAGATGCTAT 59.164 40.000 0.00 0.00 0.00 2.97
4511 4626 7.039923 GCCTGTAGTAAGATGCTATGTTAGGTA 60.040 40.741 0.00 0.00 0.00 3.08
4534 4652 7.755373 GGTACCTTTTGAGAAATGTTCTAATGC 59.245 37.037 4.06 0.00 40.87 3.56
4548 4666 5.068591 TGTTCTAATGCTCGCTGGTTATCTA 59.931 40.000 0.00 0.00 0.00 1.98
4633 4751 2.353889 CTCTGATCGATGGTGCCAAAAG 59.646 50.000 0.54 0.00 0.00 2.27
4645 4767 6.569127 TGGTGCCAAAAGGAAGTATATCTA 57.431 37.500 0.00 0.00 0.00 1.98
4720 4842 1.782181 GCTTTCAGAGCGACCGTTC 59.218 57.895 0.00 0.00 42.46 3.95
4721 4843 0.667792 GCTTTCAGAGCGACCGTTCT 60.668 55.000 2.97 2.97 42.46 3.01
4794 4918 4.985538 TTCCACTTTACGCCAAGAAAAA 57.014 36.364 1.32 0.00 0.00 1.94
4878 5005 8.147058 AGATATCAAGTGGTAATACAAGAGCAG 58.853 37.037 5.32 0.00 0.00 4.24
4901 5028 6.036844 CAGATGTACATATGCACAGCCATATC 59.963 42.308 18.44 8.43 36.52 1.63
4902 5029 5.226194 TGTACATATGCACAGCCATATCA 57.774 39.130 4.57 0.00 36.52 2.15
4903 5030 4.996758 TGTACATATGCACAGCCATATCAC 59.003 41.667 4.57 0.00 36.52 3.06
4904 5031 4.362470 ACATATGCACAGCCATATCACT 57.638 40.909 1.58 0.00 36.52 3.41
4905 5032 4.722220 ACATATGCACAGCCATATCACTT 58.278 39.130 1.58 0.00 36.52 3.16
4906 5033 4.758674 ACATATGCACAGCCATATCACTTC 59.241 41.667 1.58 0.00 36.52 3.01
4907 5034 2.785540 TGCACAGCCATATCACTTCA 57.214 45.000 0.00 0.00 0.00 3.02
4908 5035 2.358957 TGCACAGCCATATCACTTCAC 58.641 47.619 0.00 0.00 0.00 3.18
4909 5036 2.290197 TGCACAGCCATATCACTTCACA 60.290 45.455 0.00 0.00 0.00 3.58
4910 5037 2.947652 GCACAGCCATATCACTTCACAT 59.052 45.455 0.00 0.00 0.00 3.21
4911 5038 3.242969 GCACAGCCATATCACTTCACATG 60.243 47.826 0.00 0.00 0.00 3.21
4912 5039 3.314357 CACAGCCATATCACTTCACATGG 59.686 47.826 0.00 0.00 40.80 3.66
4913 5040 2.882761 CAGCCATATCACTTCACATGGG 59.117 50.000 0.00 0.00 38.70 4.00
4914 5041 2.158564 AGCCATATCACTTCACATGGGG 60.159 50.000 0.00 0.00 38.70 4.96
4915 5042 2.158623 GCCATATCACTTCACATGGGGA 60.159 50.000 0.00 0.00 38.70 4.81
4916 5043 3.748083 CCATATCACTTCACATGGGGAG 58.252 50.000 0.11 0.11 35.33 4.30
4917 5044 3.497405 CCATATCACTTCACATGGGGAGG 60.497 52.174 8.49 2.71 35.33 4.30
4918 5045 0.921896 ATCACTTCACATGGGGAGGG 59.078 55.000 8.49 2.83 0.00 4.30
4919 5046 0.178876 TCACTTCACATGGGGAGGGA 60.179 55.000 3.24 3.24 0.00 4.20
4920 5047 0.254178 CACTTCACATGGGGAGGGAG 59.746 60.000 8.49 0.00 0.00 4.30
4921 5048 0.119155 ACTTCACATGGGGAGGGAGA 59.881 55.000 8.49 0.00 0.00 3.71
4922 5049 0.835941 CTTCACATGGGGAGGGAGAG 59.164 60.000 0.00 0.00 0.00 3.20
4923 5050 0.621571 TTCACATGGGGAGGGAGAGG 60.622 60.000 0.00 0.00 0.00 3.69
4936 5063 1.227497 GAGAGGGATGCTGGCTTCG 60.227 63.158 3.10 0.00 0.00 3.79
4990 5117 4.080582 CCCAACATCCTACATACAGTCCAA 60.081 45.833 0.00 0.00 0.00 3.53
5084 5211 2.097825 CCCCAAAGATCAAGCTCCAAG 58.902 52.381 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.223294 CCTCGTAGACTGTAAGCGGAAG 60.223 54.545 0.00 0.00 37.60 3.46
15 16 1.741706 CCTCGTAGACTGTAAGCGGAA 59.258 52.381 0.00 0.00 37.60 4.30
16 17 1.376543 CCTCGTAGACTGTAAGCGGA 58.623 55.000 0.00 0.00 37.60 5.54
17 18 0.381089 CCCTCGTAGACTGTAAGCGG 59.619 60.000 0.00 0.00 37.60 5.52
18 19 1.093159 ACCCTCGTAGACTGTAAGCG 58.907 55.000 0.00 0.00 37.60 4.68
19 20 3.012518 TGTACCCTCGTAGACTGTAAGC 58.987 50.000 0.00 0.00 37.60 3.09
20 21 6.202570 GTCTATGTACCCTCGTAGACTGTAAG 59.797 46.154 14.80 0.00 45.71 2.34
21 22 6.051717 GTCTATGTACCCTCGTAGACTGTAA 58.948 44.000 14.80 0.00 45.71 2.41
22 23 5.605534 GTCTATGTACCCTCGTAGACTGTA 58.394 45.833 14.80 0.00 45.71 2.74
23 24 4.450053 GTCTATGTACCCTCGTAGACTGT 58.550 47.826 14.80 0.00 45.71 3.55
27 28 4.637534 GTGTTGTCTATGTACCCTCGTAGA 59.362 45.833 0.00 0.00 34.71 2.59
28 29 4.639310 AGTGTTGTCTATGTACCCTCGTAG 59.361 45.833 0.00 0.00 0.00 3.51
29 30 4.592942 AGTGTTGTCTATGTACCCTCGTA 58.407 43.478 0.00 0.00 0.00 3.43
30 31 3.428532 AGTGTTGTCTATGTACCCTCGT 58.571 45.455 0.00 0.00 0.00 4.18
31 32 3.181489 GGAGTGTTGTCTATGTACCCTCG 60.181 52.174 0.00 0.00 0.00 4.63
32 33 3.132467 GGGAGTGTTGTCTATGTACCCTC 59.868 52.174 0.00 0.00 32.93 4.30
33 34 3.105283 GGGAGTGTTGTCTATGTACCCT 58.895 50.000 0.00 0.00 32.93 4.34
34 35 2.169978 GGGGAGTGTTGTCTATGTACCC 59.830 54.545 0.00 0.00 0.00 3.69
35 36 2.169978 GGGGGAGTGTTGTCTATGTACC 59.830 54.545 0.00 0.00 0.00 3.34
36 37 3.105283 AGGGGGAGTGTTGTCTATGTAC 58.895 50.000 0.00 0.00 0.00 2.90
37 38 3.012502 AGAGGGGGAGTGTTGTCTATGTA 59.987 47.826 0.00 0.00 0.00 2.29
38 39 2.188817 GAGGGGGAGTGTTGTCTATGT 58.811 52.381 0.00 0.00 0.00 2.29
39 40 2.432510 GAGAGGGGGAGTGTTGTCTATG 59.567 54.545 0.00 0.00 0.00 2.23
40 41 2.753247 GAGAGGGGGAGTGTTGTCTAT 58.247 52.381 0.00 0.00 0.00 1.98
41 42 1.616187 CGAGAGGGGGAGTGTTGTCTA 60.616 57.143 0.00 0.00 0.00 2.59
42 43 0.900647 CGAGAGGGGGAGTGTTGTCT 60.901 60.000 0.00 0.00 0.00 3.41
43 44 1.186267 ACGAGAGGGGGAGTGTTGTC 61.186 60.000 0.00 0.00 0.00 3.18
44 45 0.763223 AACGAGAGGGGGAGTGTTGT 60.763 55.000 0.00 0.00 0.00 3.32
45 46 0.320771 CAACGAGAGGGGGAGTGTTG 60.321 60.000 0.00 0.00 0.00 3.33
46 47 2.058675 CAACGAGAGGGGGAGTGTT 58.941 57.895 0.00 0.00 0.00 3.32
47 48 2.584391 GCAACGAGAGGGGGAGTGT 61.584 63.158 0.00 0.00 0.00 3.55
48 49 0.970937 TAGCAACGAGAGGGGGAGTG 60.971 60.000 0.00 0.00 0.00 3.51
49 50 0.032017 ATAGCAACGAGAGGGGGAGT 60.032 55.000 0.00 0.00 0.00 3.85
50 51 0.390860 CATAGCAACGAGAGGGGGAG 59.609 60.000 0.00 0.00 0.00 4.30
51 52 1.686325 GCATAGCAACGAGAGGGGGA 61.686 60.000 0.00 0.00 0.00 4.81
52 53 1.227674 GCATAGCAACGAGAGGGGG 60.228 63.158 0.00 0.00 0.00 5.40
53 54 0.107456 ATGCATAGCAACGAGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
54 55 1.202568 TGATGCATAGCAACGAGAGGG 60.203 52.381 0.00 0.00 43.62 4.30
55 56 1.863454 GTGATGCATAGCAACGAGAGG 59.137 52.381 0.00 0.00 43.62 3.69
56 57 1.863454 GGTGATGCATAGCAACGAGAG 59.137 52.381 0.00 0.00 43.62 3.20
57 58 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
58 59 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
59 60 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
60 61 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
61 62 3.057736 GGATCATGGTGATGCATAGCAAC 60.058 47.826 0.00 0.00 43.55 4.17
62 63 3.151554 GGATCATGGTGATGCATAGCAA 58.848 45.455 0.00 0.00 43.55 3.91
63 64 2.374170 AGGATCATGGTGATGCATAGCA 59.626 45.455 12.83 4.86 46.03 3.49
64 65 2.747989 CAGGATCATGGTGATGCATAGC 59.252 50.000 12.83 0.00 46.03 2.97
65 66 3.751698 CACAGGATCATGGTGATGCATAG 59.248 47.826 12.66 5.87 46.03 2.23
66 67 3.136992 ACACAGGATCATGGTGATGCATA 59.863 43.478 12.66 0.00 46.03 3.14
67 68 2.092049 ACACAGGATCATGGTGATGCAT 60.092 45.455 12.66 0.00 46.03 3.96
68 69 1.282738 ACACAGGATCATGGTGATGCA 59.717 47.619 12.66 0.00 46.03 3.96
69 70 1.674441 CACACAGGATCATGGTGATGC 59.326 52.381 18.31 3.59 44.29 3.91
70 71 2.681344 CACACACAGGATCATGGTGATG 59.319 50.000 25.47 18.22 37.20 3.07
71 72 2.942752 GCACACACAGGATCATGGTGAT 60.943 50.000 25.47 13.21 40.34 3.06
72 73 1.611410 GCACACACAGGATCATGGTGA 60.611 52.381 25.47 0.00 36.42 4.02
73 74 0.806868 GCACACACAGGATCATGGTG 59.193 55.000 20.27 20.27 38.47 4.17
74 75 0.674581 CGCACACACAGGATCATGGT 60.675 55.000 12.66 4.08 0.00 3.55
75 76 0.674581 ACGCACACACAGGATCATGG 60.675 55.000 12.66 3.43 0.00 3.66
76 77 1.929169 CTACGCACACACAGGATCATG 59.071 52.381 5.68 5.68 0.00 3.07
77 78 1.134699 CCTACGCACACACAGGATCAT 60.135 52.381 0.00 0.00 0.00 2.45
78 79 0.246360 CCTACGCACACACAGGATCA 59.754 55.000 0.00 0.00 0.00 2.92
79 80 0.530744 TCCTACGCACACACAGGATC 59.469 55.000 0.00 0.00 32.20 3.36
80 81 0.973632 TTCCTACGCACACACAGGAT 59.026 50.000 0.00 0.00 37.06 3.24
81 82 0.753867 TTTCCTACGCACACACAGGA 59.246 50.000 0.00 0.00 35.38 3.86
82 83 1.808411 ATTTCCTACGCACACACAGG 58.192 50.000 0.00 0.00 0.00 4.00
83 84 3.896648 AAATTTCCTACGCACACACAG 57.103 42.857 0.00 0.00 0.00 3.66
84 85 4.096532 TCAAAAATTTCCTACGCACACACA 59.903 37.500 0.00 0.00 0.00 3.72
85 86 4.602995 TCAAAAATTTCCTACGCACACAC 58.397 39.130 0.00 0.00 0.00 3.82
86 87 4.902443 TCAAAAATTTCCTACGCACACA 57.098 36.364 0.00 0.00 0.00 3.72
87 88 6.763303 ATTTCAAAAATTTCCTACGCACAC 57.237 33.333 0.00 0.00 0.00 3.82
88 89 8.138712 AGTAATTTCAAAAATTTCCTACGCACA 58.861 29.630 3.24 0.00 0.00 4.57
89 90 8.515473 AGTAATTTCAAAAATTTCCTACGCAC 57.485 30.769 3.24 0.00 0.00 5.34
90 91 9.615295 GTAGTAATTTCAAAAATTTCCTACGCA 57.385 29.630 3.24 0.00 0.00 5.24
91 92 8.782327 CGTAGTAATTTCAAAAATTTCCTACGC 58.218 33.333 24.45 10.35 38.26 4.42
92 93 9.815936 ACGTAGTAATTTCAAAAATTTCCTACG 57.184 29.630 28.37 28.37 41.94 3.51
95 96 9.687210 GGAACGTAGTAATTTCAAAAATTTCCT 57.313 29.630 3.24 3.62 45.00 3.36
96 97 8.918658 GGGAACGTAGTAATTTCAAAAATTTCC 58.081 33.333 3.24 3.13 45.00 3.13
97 98 8.918658 GGGGAACGTAGTAATTTCAAAAATTTC 58.081 33.333 3.24 0.00 45.00 2.17
98 99 8.422566 TGGGGAACGTAGTAATTTCAAAAATTT 58.577 29.630 3.24 0.00 45.00 1.82
99 100 7.953752 TGGGGAACGTAGTAATTTCAAAAATT 58.046 30.769 0.00 3.43 45.00 1.82
100 101 7.527568 TGGGGAACGTAGTAATTTCAAAAAT 57.472 32.000 0.00 0.00 45.00 1.82
101 102 6.956202 TGGGGAACGTAGTAATTTCAAAAA 57.044 33.333 0.00 0.00 45.00 1.94
102 103 6.320672 TGTTGGGGAACGTAGTAATTTCAAAA 59.679 34.615 0.00 0.00 45.00 2.44
103 104 5.826737 TGTTGGGGAACGTAGTAATTTCAAA 59.173 36.000 0.00 0.00 45.00 2.69
104 105 5.374921 TGTTGGGGAACGTAGTAATTTCAA 58.625 37.500 0.00 0.00 45.00 2.69
105 106 4.970711 TGTTGGGGAACGTAGTAATTTCA 58.029 39.130 0.00 0.00 45.00 2.69
106 107 6.319399 CAATGTTGGGGAACGTAGTAATTTC 58.681 40.000 0.00 0.00 45.00 2.17
107 108 5.336134 GCAATGTTGGGGAACGTAGTAATTT 60.336 40.000 0.00 0.00 45.00 1.82
108 109 4.157105 GCAATGTTGGGGAACGTAGTAATT 59.843 41.667 0.00 0.00 45.00 1.40
109 110 3.692593 GCAATGTTGGGGAACGTAGTAAT 59.307 43.478 0.00 0.00 45.00 1.89
110 111 3.075884 GCAATGTTGGGGAACGTAGTAA 58.924 45.455 0.00 0.00 45.00 2.24
111 112 2.616001 GGCAATGTTGGGGAACGTAGTA 60.616 50.000 0.00 0.00 45.00 1.82
113 114 0.808755 GGCAATGTTGGGGAACGTAG 59.191 55.000 0.00 0.00 0.00 3.51
114 115 0.110678 TGGCAATGTTGGGGAACGTA 59.889 50.000 0.00 0.00 0.00 3.57
115 116 0.541764 ATGGCAATGTTGGGGAACGT 60.542 50.000 0.00 0.00 0.00 3.99
116 117 0.173255 GATGGCAATGTTGGGGAACG 59.827 55.000 0.00 0.00 0.00 3.95
117 118 1.066929 GTGATGGCAATGTTGGGGAAC 60.067 52.381 0.00 0.00 0.00 3.62
118 119 1.265236 GTGATGGCAATGTTGGGGAA 58.735 50.000 0.00 0.00 0.00 3.97
119 120 0.964860 CGTGATGGCAATGTTGGGGA 60.965 55.000 0.00 0.00 0.00 4.81
120 121 1.512230 CGTGATGGCAATGTTGGGG 59.488 57.895 0.00 0.00 0.00 4.96
121 122 1.512230 CCGTGATGGCAATGTTGGG 59.488 57.895 0.00 0.00 0.00 4.12
122 123 1.512230 CCCGTGATGGCAATGTTGG 59.488 57.895 0.00 0.00 35.87 3.77
139 140 1.121407 AGCTCCTTTTTGGGTTGGCC 61.121 55.000 0.00 0.00 36.20 5.36
140 141 1.272490 GTAGCTCCTTTTTGGGTTGGC 59.728 52.381 0.00 0.00 36.20 4.52
141 142 2.558359 CTGTAGCTCCTTTTTGGGTTGG 59.442 50.000 0.00 0.00 36.20 3.77
142 143 3.004734 CACTGTAGCTCCTTTTTGGGTTG 59.995 47.826 0.00 0.00 36.20 3.77
143 144 3.222603 CACTGTAGCTCCTTTTTGGGTT 58.777 45.455 0.00 0.00 36.20 4.11
144 145 2.489073 CCACTGTAGCTCCTTTTTGGGT 60.489 50.000 0.00 0.00 36.20 4.51
145 146 2.162681 CCACTGTAGCTCCTTTTTGGG 58.837 52.381 0.00 0.00 36.20 4.12
146 147 2.162681 CCCACTGTAGCTCCTTTTTGG 58.837 52.381 0.00 0.00 37.10 3.28
147 148 1.541588 GCCCACTGTAGCTCCTTTTTG 59.458 52.381 0.00 0.00 0.00 2.44
148 149 1.144913 TGCCCACTGTAGCTCCTTTTT 59.855 47.619 0.00 0.00 0.00 1.94
149 150 0.771127 TGCCCACTGTAGCTCCTTTT 59.229 50.000 0.00 0.00 0.00 2.27
150 151 0.995024 ATGCCCACTGTAGCTCCTTT 59.005 50.000 0.00 0.00 0.00 3.11
151 152 0.543749 GATGCCCACTGTAGCTCCTT 59.456 55.000 0.00 0.00 0.00 3.36
152 153 0.618680 TGATGCCCACTGTAGCTCCT 60.619 55.000 0.00 0.00 0.00 3.69
153 154 0.179062 CTGATGCCCACTGTAGCTCC 60.179 60.000 0.00 0.00 0.00 4.70
154 155 0.813210 GCTGATGCCCACTGTAGCTC 60.813 60.000 0.00 0.00 0.00 4.09
155 156 1.222936 GCTGATGCCCACTGTAGCT 59.777 57.895 0.00 0.00 0.00 3.32
156 157 3.819188 GCTGATGCCCACTGTAGC 58.181 61.111 0.00 0.00 0.00 3.58
166 167 2.401766 CCGAACAGGTGGCTGATGC 61.402 63.158 0.00 0.00 35.04 3.91
167 168 1.746615 CCCGAACAGGTGGCTGATG 60.747 63.158 0.00 0.00 38.74 3.07
168 169 2.671070 CCCGAACAGGTGGCTGAT 59.329 61.111 0.00 0.00 38.74 2.90
169 170 4.329545 GCCCGAACAGGTGGCTGA 62.330 66.667 0.00 0.00 42.01 4.26
189 190 3.195698 CTGTTCGGCGCCTTAGGC 61.196 66.667 26.68 14.22 46.75 3.93
190 191 2.511600 CCTGTTCGGCGCCTTAGG 60.512 66.667 26.68 20.88 0.00 2.69
191 192 1.519455 CTCCTGTTCGGCGCCTTAG 60.519 63.158 26.68 16.04 0.00 2.18
192 193 2.577059 CTCCTGTTCGGCGCCTTA 59.423 61.111 26.68 9.93 0.00 2.69
196 197 4.443266 AGAGCTCCTGTTCGGCGC 62.443 66.667 10.93 0.00 43.98 6.53
197 198 2.202676 GAGAGCTCCTGTTCGGCG 60.203 66.667 10.93 0.00 0.00 6.46
198 199 2.185608 GGAGAGCTCCTGTTCGGC 59.814 66.667 10.93 0.00 46.16 5.54
207 208 1.519013 CTTGCAGCGAGGAGAGCTC 60.519 63.158 5.27 5.27 44.06 4.09
209 210 3.194308 GCTTGCAGCGAGGAGAGC 61.194 66.667 11.92 0.00 0.00 4.09
210 211 2.511145 GGCTTGCAGCGAGGAGAG 60.511 66.667 11.92 0.00 43.62 3.20
211 212 2.513026 GAAGGCTTGCAGCGAGGAGA 62.513 60.000 3.46 0.00 43.62 3.71
212 213 2.046507 AAGGCTTGCAGCGAGGAG 60.047 61.111 11.92 0.00 43.62 3.69
213 214 2.046892 GAAGGCTTGCAGCGAGGA 60.047 61.111 3.46 0.00 43.62 3.71
214 215 1.712977 GATGAAGGCTTGCAGCGAGG 61.713 60.000 3.46 0.00 43.62 4.63
215 216 1.712977 GGATGAAGGCTTGCAGCGAG 61.713 60.000 3.46 5.11 43.62 5.03
216 217 1.746615 GGATGAAGGCTTGCAGCGA 60.747 57.895 3.46 0.00 43.62 4.93
217 218 1.989966 CTGGATGAAGGCTTGCAGCG 61.990 60.000 3.46 0.00 43.62 5.18
218 219 1.807886 CTGGATGAAGGCTTGCAGC 59.192 57.895 3.46 5.43 41.46 5.25
219 220 1.664321 GGCTGGATGAAGGCTTGCAG 61.664 60.000 3.46 2.68 39.56 4.41
220 221 1.679977 GGCTGGATGAAGGCTTGCA 60.680 57.895 3.46 2.93 39.56 4.08
221 222 3.204418 GGCTGGATGAAGGCTTGC 58.796 61.111 3.46 0.00 39.56 4.01
1990 2078 8.149647 TGTAGGTAAAATTTTCTTAGACCGACA 58.850 33.333 21.86 21.86 38.33 4.35
1992 2080 7.329226 CGTGTAGGTAAAATTTTCTTAGACCGA 59.671 37.037 6.72 2.77 0.00 4.69
2091 2179 8.997323 CAGGAAAGGTCTGAATATATGCTTAAG 58.003 37.037 0.00 0.00 34.36 1.85
2217 2305 0.749454 CGGCTTTCTCCCCAGGAATG 60.749 60.000 0.00 0.00 0.00 2.67
2368 2456 1.616159 CACCAACCTTTCCATTCGGT 58.384 50.000 0.00 0.00 0.00 4.69
2476 2564 4.450976 ACAGACTTGTGAAAGTACATGCA 58.549 39.130 0.00 0.00 35.83 3.96
2512 2600 0.735978 TACGGAACACTCTGCATGCG 60.736 55.000 14.09 8.20 0.00 4.73
2524 2612 9.360093 CCTAATCAATTCATAGAGATACGGAAC 57.640 37.037 0.00 0.00 0.00 3.62
2654 2742 1.069427 GGCTGCCAAACAATGTGCA 59.931 52.632 15.17 0.00 35.07 4.57
2679 2767 5.178996 CAGCATGAGATTAACAGTATGAGCC 59.821 44.000 0.00 0.00 36.43 4.70
2775 2863 4.744570 CGTGCAGAGGTTCAGAATAACTA 58.255 43.478 0.00 0.00 0.00 2.24
2871 2959 8.653191 TCTTTGTTATCCCAGTAACTTTGTAGA 58.347 33.333 0.00 0.00 35.94 2.59
2892 2980 3.070018 CCACTACCTGAGCTTGTCTTTG 58.930 50.000 0.00 0.00 0.00 2.77
2908 2996 4.279420 CCACTCATTCGAGATCATCCACTA 59.721 45.833 0.00 0.00 42.34 2.74
2949 3037 3.834489 ATCAAGCAGTCATACTCCCTG 57.166 47.619 0.00 0.00 0.00 4.45
3125 3231 3.334583 TCAAATCTTCTGAACCCTCCG 57.665 47.619 0.00 0.00 0.00 4.63
3132 3238 7.174772 TCCATGAAATCGTTCAAATCTTCTGAA 59.825 33.333 0.00 0.00 46.66 3.02
3434 3542 0.323178 ACCTCCCGCTAGAAGAACGA 60.323 55.000 0.00 0.00 0.00 3.85
3479 3587 3.055891 GGGTCCAATGTGCTAGCATTTTT 60.056 43.478 22.51 11.93 37.00 1.94
3480 3588 2.497273 GGGTCCAATGTGCTAGCATTTT 59.503 45.455 22.51 14.50 37.00 1.82
3481 3589 2.102578 GGGTCCAATGTGCTAGCATTT 58.897 47.619 22.51 14.87 37.00 2.32
3482 3590 1.005805 TGGGTCCAATGTGCTAGCATT 59.994 47.619 22.51 9.42 39.42 3.56
3483 3591 0.625316 TGGGTCCAATGTGCTAGCAT 59.375 50.000 22.51 2.08 0.00 3.79
3559 3667 4.191544 ACATACATCAGGACACAATTCGG 58.808 43.478 0.00 0.00 0.00 4.30
3589 3697 1.080093 CCAGTTTCGCTCGCACCTA 60.080 57.895 0.00 0.00 0.00 3.08
3650 3758 3.891049 ACTTGTGAAGCTTTTCAGAGGT 58.109 40.909 0.00 0.00 31.38 3.85
3652 3760 4.096984 ACCAACTTGTGAAGCTTTTCAGAG 59.903 41.667 0.00 6.48 0.00 3.35
3862 3970 6.487828 AGGGAGATCACATTCATCTTTTTCA 58.512 36.000 0.00 0.00 30.30 2.69
3914 4022 6.493115 TCTTCACTTGATTTCCCTTTGCATAA 59.507 34.615 0.00 0.00 0.00 1.90
3937 4045 2.957402 TTGGCTTGTCAAGGACATCT 57.043 45.000 14.40 0.00 42.40 2.90
3978 4086 1.298014 CTGGAGAGGGTGCAGTTCC 59.702 63.158 0.00 0.00 39.73 3.62
4022 4130 7.276658 CGAACCATTATTATCAGTAGCCATCTC 59.723 40.741 0.00 0.00 0.00 2.75
4111 4222 6.152379 GGCAACTTCTAAACAGAATTTCCTG 58.848 40.000 0.00 0.00 39.93 3.86
4113 4224 6.084326 TGGCAACTTCTAAACAGAATTTCC 57.916 37.500 0.00 0.00 37.61 3.13
4220 4331 4.955811 ACTGTCATGAGTGTTAGGTTGA 57.044 40.909 0.00 0.00 0.00 3.18
4254 4369 6.546428 TCCAGGACAGATTAACCTAAAGAG 57.454 41.667 0.00 0.00 32.35 2.85
4388 4503 4.022359 ACCCTAAGATCTAACACCCCAT 57.978 45.455 0.00 0.00 0.00 4.00
4396 4511 7.633772 GCAAGAGATCACAACCCTAAGATCTAA 60.634 40.741 0.00 0.00 45.18 2.10
4503 4618 7.996644 AGAACATTTCTCAAAAGGTACCTAACA 59.003 33.333 16.67 0.00 38.36 2.41
4511 4626 7.530426 AGCATTAGAACATTTCTCAAAAGGT 57.470 32.000 0.00 0.00 40.88 3.50
4534 4652 7.494625 TGGAAATTAAACTAGATAACCAGCGAG 59.505 37.037 0.00 0.00 0.00 5.03
4548 4666 6.655003 ACGACAGTCATCATGGAAATTAAACT 59.345 34.615 0.41 0.00 0.00 2.66
4645 4767 7.015584 GGGGATTGAAGAAACATTTATGCCTAT 59.984 37.037 0.00 0.00 0.00 2.57
4662 4784 4.803452 AGTGACAAGAAAAGGGGATTGAA 58.197 39.130 0.00 0.00 0.00 2.69
4718 4840 7.504238 TGTTATTGAAGCAAACTTTAGGGAGAA 59.496 33.333 0.00 0.00 35.82 2.87
4720 4842 7.214467 TGTTATTGAAGCAAACTTTAGGGAG 57.786 36.000 0.00 0.00 35.82 4.30
4721 4843 7.775053 ATGTTATTGAAGCAAACTTTAGGGA 57.225 32.000 0.00 0.00 35.82 4.20
4794 4918 3.359033 ACTGGATTGTGTTGCTGCATAT 58.641 40.909 1.84 0.00 0.00 1.78
4878 5005 5.876460 TGATATGGCTGTGCATATGTACATC 59.124 40.000 24.27 20.24 39.79 3.06
4901 5028 0.254178 CTCCCTCCCCATGTGAAGTG 59.746 60.000 0.00 0.00 0.00 3.16
4902 5029 0.119155 TCTCCCTCCCCATGTGAAGT 59.881 55.000 0.00 0.00 0.00 3.01
4903 5030 0.835941 CTCTCCCTCCCCATGTGAAG 59.164 60.000 0.00 0.00 0.00 3.02
4904 5031 0.621571 CCTCTCCCTCCCCATGTGAA 60.622 60.000 0.00 0.00 0.00 3.18
4905 5032 1.003442 CCTCTCCCTCCCCATGTGA 59.997 63.158 0.00 0.00 0.00 3.58
4906 5033 2.074948 CCCTCTCCCTCCCCATGTG 61.075 68.421 0.00 0.00 0.00 3.21
4907 5034 1.617181 ATCCCTCTCCCTCCCCATGT 61.617 60.000 0.00 0.00 0.00 3.21
4908 5035 1.132554 CATCCCTCTCCCTCCCCATG 61.133 65.000 0.00 0.00 0.00 3.66
4909 5036 1.241327 CATCCCTCTCCCTCCCCAT 59.759 63.158 0.00 0.00 0.00 4.00
4910 5037 2.705410 CATCCCTCTCCCTCCCCA 59.295 66.667 0.00 0.00 0.00 4.96
4911 5038 2.851588 GCATCCCTCTCCCTCCCC 60.852 72.222 0.00 0.00 0.00 4.81
4912 5039 2.146061 CAGCATCCCTCTCCCTCCC 61.146 68.421 0.00 0.00 0.00 4.30
4913 5040 2.146061 CCAGCATCCCTCTCCCTCC 61.146 68.421 0.00 0.00 0.00 4.30
4914 5041 2.817056 GCCAGCATCCCTCTCCCTC 61.817 68.421 0.00 0.00 0.00 4.30
4915 5042 2.771762 GCCAGCATCCCTCTCCCT 60.772 66.667 0.00 0.00 0.00 4.20
4916 5043 2.336484 GAAGCCAGCATCCCTCTCCC 62.336 65.000 0.00 0.00 0.00 4.30
4917 5044 1.148048 GAAGCCAGCATCCCTCTCC 59.852 63.158 0.00 0.00 0.00 3.71
4918 5045 1.227497 CGAAGCCAGCATCCCTCTC 60.227 63.158 0.00 0.00 0.00 3.20
4919 5046 2.739996 CCGAAGCCAGCATCCCTCT 61.740 63.158 0.00 0.00 0.00 3.69
4920 5047 2.203126 CCGAAGCCAGCATCCCTC 60.203 66.667 0.00 0.00 0.00 4.30
4921 5048 3.801997 CCCGAAGCCAGCATCCCT 61.802 66.667 0.00 0.00 0.00 4.20
4922 5049 4.115199 ACCCGAAGCCAGCATCCC 62.115 66.667 0.00 0.00 0.00 3.85
4923 5050 2.514824 GACCCGAAGCCAGCATCC 60.515 66.667 0.00 0.00 0.00 3.51
4936 5063 3.444388 TGTTGTGTACAGTTTTTGGACCC 59.556 43.478 0.00 0.00 40.16 4.46
4990 5117 3.270433 AGACATGGGTTCCCTTTGATCAT 59.730 43.478 9.43 0.00 0.00 2.45
5006 5133 4.497966 CGAAGCATGCAATTGTTAGACATG 59.502 41.667 21.98 14.91 40.80 3.21
5084 5211 3.119352 GGTGTTTCTTGATGATTCCCTGC 60.119 47.826 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.