Multiple sequence alignment - TraesCS3D01G268100

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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 TraesCS3D01G268100 chr3D 100.000 4428 0 0 1 4428 372320525 372316098 0.000000e+00 8178.0
1 TraesCS3D01G268100 chr3B 94.995 2158 75 12 576 2721 486383527 486381391 0.000000e+00 3356.0
2 TraesCS3D01G268100 chr3B 92.844 1076 38 8 2714 3773 486381366 486380314 0.000000e+00 1524.0
3 TraesCS3D01G268100 chr3B 87.121 396 38 12 3816 4204 486380311 486379922 1.890000e-118 436.0
4 TraesCS3D01G268100 chr3B 88.211 246 13 8 4193 4428 486379902 486379663 3.370000e-71 279.0
5 TraesCS3D01G268100 chr3B 94.915 177 9 0 1 177 486412223 486412047 1.210000e-70 278.0
6 TraesCS3D01G268100 chr3B 93.478 184 9 2 159 339 486386894 486386711 2.030000e-68 270.0
7 TraesCS3D01G268100 chr3B 89.773 88 9 0 1796 1883 760593439 760593352 3.620000e-21 113.0
8 TraesCS3D01G268100 chr3A 91.856 1142 39 19 565 1687 493717090 493715984 0.000000e+00 1544.0
9 TraesCS3D01G268100 chr3A 89.234 1031 67 24 2493 3520 493715929 493714940 0.000000e+00 1249.0
10 TraesCS3D01G268100 chr3A 86.355 557 47 16 3519 4051 493714848 493714297 8.260000e-162 580.0
11 TraesCS3D01G268100 chr6B 93.571 140 8 1 3798 3936 6050503 6050642 1.610000e-49 207.0
12 TraesCS3D01G268100 chr2D 96.512 86 3 0 1798 1883 595166405 595166490 4.620000e-30 143.0
13 TraesCS3D01G268100 chr2B 91.860 86 7 0 1797 1882 247368623 247368538 2.160000e-23 121.0
14 TraesCS3D01G268100 chr2B 94.872 39 2 0 506 544 105747055 105747017 1.330000e-05 62.1
15 TraesCS3D01G268100 chr2B 92.857 42 2 1 503 544 50742358 50742318 4.780000e-05 60.2
16 TraesCS3D01G268100 chr2B 92.857 42 2 1 503 544 71370479 71370439 4.780000e-05 60.2
17 TraesCS3D01G268100 chr4A 90.805 87 8 0 1796 1882 187263715 187263801 2.800000e-22 117.0
18 TraesCS3D01G268100 chr5D 87.879 99 9 3 1786 1882 354502065 354501968 3.620000e-21 113.0
19 TraesCS3D01G268100 chr7D 88.889 90 10 0 1798 1887 602187852 602187763 1.300000e-20 111.0
20 TraesCS3D01G268100 chr5B 84.762 105 10 5 1783 1883 582391958 582392060 2.820000e-17 100.0
21 TraesCS3D01G268100 chr5B 92.857 42 2 1 503 544 656714655 656714615 4.780000e-05 60.2
22 TraesCS3D01G268100 chr1B 84.615 104 13 3 1802 1904 85441628 85441729 2.820000e-17 100.0
23 TraesCS3D01G268100 chr1B 94.872 39 1 1 506 544 117784235 117784198 4.780000e-05 60.2
24 TraesCS3D01G268100 chrUn 92.857 42 3 0 506 547 57435607 57435566 1.330000e-05 62.1
25 TraesCS3D01G268100 chr7B 92.857 42 2 1 503 544 631598323 631598283 4.780000e-05 60.2
26 TraesCS3D01G268100 chr7A 92.857 42 2 1 503 544 205634416 205634456 4.780000e-05 60.2
27 TraesCS3D01G268100 chr4B 92.857 42 2 1 503 544 471693442 471693402 4.780000e-05 60.2


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 TraesCS3D01G268100 chr3D 372316098 372320525 4427 True 8178.000000 8178 100.000000 1 4428 1 chr3D.!!$R1 4427
1 TraesCS3D01G268100 chr3B 486379663 486386894 7231 True 1173.000000 3356 91.329800 159 4428 5 chr3B.!!$R3 4269
2 TraesCS3D01G268100 chr3A 493714297 493717090 2793 True 1124.333333 1544 89.148333 565 4051 3 chr3A.!!$R1 3486

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
74 75 0.096454 GAGTTTACGCCCGTTGCATC 59.904 55.000 0.00 0.0 41.33 3.91 F
136 137 0.248377 GCGAATGTCATCCTTGCTGC 60.248 55.000 0.00 0.0 0.00 5.25 F
153 154 0.248580 TGCTGTTCGCAGTTTGCTTG 60.249 50.000 0.00 0.0 45.47 4.01 F
155 156 0.248580 CTGTTCGCAGTTTGCTTGCA 60.249 50.000 0.00 0.0 42.25 4.08 F
161 162 0.249573 GCAGTTTGCTTGCATGGTGT 60.250 50.000 1.34 0.0 40.96 4.16 F
1743 4710 1.203225 AGAAGGGGCAAAGGAGCATTT 60.203 47.619 0.00 0.0 35.83 2.32 F
2762 5767 1.686115 GCATTCAACCTACCATGGGCT 60.686 52.381 18.09 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 4513 0.171007 ACTGGGATTGCGAATTTGCG 59.829 50.000 13.01 0.00 37.81 4.85 R
1711 4678 2.038269 CCCTTCTTTGCGCCGCTTA 61.038 57.895 11.67 0.00 0.00 3.09 R
1915 4882 2.401583 ATATTGCAGGCGTCAACTCA 57.598 45.000 0.00 0.00 0.00 3.41 R
2072 5040 7.624360 TTCAGTGACAAAACTACACTTTCAT 57.376 32.000 0.00 0.00 41.93 2.57 R
2213 5183 5.761234 ACAGTTGTTTAGCGAAAATACAGGA 59.239 36.000 0.00 0.00 0.00 3.86 R
2988 6004 0.324943 GGGCACTGCTTCCAGAGTTA 59.675 55.000 0.00 0.00 41.77 2.24 R
3805 6922 0.104855 TCTTTCCAGATCATCCGCGG 59.895 55.000 22.12 22.12 0.00 6.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.627395 TCCAACAAGGAATATGAGCGT 57.373 42.857 0.00 0.00 45.65 5.07
24 25 3.531538 TCCAACAAGGAATATGAGCGTC 58.468 45.455 0.00 0.00 45.65 5.19
25 26 3.055458 TCCAACAAGGAATATGAGCGTCA 60.055 43.478 0.00 0.00 45.65 4.35
26 27 3.063997 CCAACAAGGAATATGAGCGTCAC 59.936 47.826 0.00 0.00 41.22 3.67
27 28 3.895232 ACAAGGAATATGAGCGTCACT 57.105 42.857 0.00 0.00 0.00 3.41
28 29 3.525537 ACAAGGAATATGAGCGTCACTG 58.474 45.455 0.00 0.00 0.00 3.66
29 30 3.055819 ACAAGGAATATGAGCGTCACTGT 60.056 43.478 0.00 0.00 0.00 3.55
30 31 3.444703 AGGAATATGAGCGTCACTGTC 57.555 47.619 0.00 0.00 0.00 3.51
31 32 2.120232 GGAATATGAGCGTCACTGTCG 58.880 52.381 0.00 0.00 0.00 4.35
38 39 4.243383 CGTCACTGTCGCATGTGA 57.757 55.556 4.45 4.45 40.39 3.58
39 40 2.065193 CGTCACTGTCGCATGTGAG 58.935 57.895 9.75 1.22 42.84 3.51
40 41 0.387239 CGTCACTGTCGCATGTGAGA 60.387 55.000 9.75 7.68 42.84 3.27
41 42 1.733718 CGTCACTGTCGCATGTGAGAT 60.734 52.381 9.75 0.00 42.84 2.75
42 43 1.923204 GTCACTGTCGCATGTGAGATC 59.077 52.381 9.75 0.00 42.84 2.75
43 44 1.545582 TCACTGTCGCATGTGAGATCA 59.454 47.619 9.75 3.50 38.15 2.92
44 45 2.029110 TCACTGTCGCATGTGAGATCAA 60.029 45.455 9.75 0.00 38.15 2.57
45 46 2.738314 CACTGTCGCATGTGAGATCAAA 59.262 45.455 9.75 0.00 36.38 2.69
46 47 2.998670 ACTGTCGCATGTGAGATCAAAG 59.001 45.455 9.75 0.00 0.00 2.77
47 48 1.733912 TGTCGCATGTGAGATCAAAGC 59.266 47.619 9.75 0.00 0.00 3.51
48 49 1.733912 GTCGCATGTGAGATCAAAGCA 59.266 47.619 9.75 0.00 0.00 3.91
49 50 2.160219 GTCGCATGTGAGATCAAAGCAA 59.840 45.455 9.75 0.00 0.00 3.91
50 51 2.813172 TCGCATGTGAGATCAAAGCAAA 59.187 40.909 4.45 0.00 0.00 3.68
51 52 3.441222 TCGCATGTGAGATCAAAGCAAAT 59.559 39.130 4.45 0.00 0.00 2.32
52 53 3.546271 CGCATGTGAGATCAAAGCAAATG 59.454 43.478 0.00 0.00 31.84 2.32
53 54 3.306166 GCATGTGAGATCAAAGCAAATGC 59.694 43.478 13.57 13.57 43.53 3.56
54 55 4.490743 CATGTGAGATCAAAGCAAATGCA 58.509 39.130 8.28 0.00 45.16 3.96
55 56 4.168922 TGTGAGATCAAAGCAAATGCAG 57.831 40.909 8.28 0.00 45.16 4.41
56 57 3.822167 TGTGAGATCAAAGCAAATGCAGA 59.178 39.130 8.28 3.16 45.16 4.26
57 58 4.082949 TGTGAGATCAAAGCAAATGCAGAG 60.083 41.667 8.28 0.00 45.16 3.35
58 59 4.077108 TGAGATCAAAGCAAATGCAGAGT 58.923 39.130 8.28 0.00 45.16 3.24
59 60 4.521639 TGAGATCAAAGCAAATGCAGAGTT 59.478 37.500 8.28 0.00 45.16 3.01
60 61 5.010314 TGAGATCAAAGCAAATGCAGAGTTT 59.990 36.000 8.28 0.00 45.16 2.66
61 62 6.207221 TGAGATCAAAGCAAATGCAGAGTTTA 59.793 34.615 8.28 0.00 45.16 2.01
62 63 6.385033 AGATCAAAGCAAATGCAGAGTTTAC 58.615 36.000 8.28 0.00 45.16 2.01
63 64 4.536065 TCAAAGCAAATGCAGAGTTTACG 58.464 39.130 8.28 0.00 45.16 3.18
64 65 2.619013 AGCAAATGCAGAGTTTACGC 57.381 45.000 8.28 0.00 45.16 4.42
65 66 1.200020 AGCAAATGCAGAGTTTACGCC 59.800 47.619 8.28 0.00 45.16 5.68
66 67 1.732405 GCAAATGCAGAGTTTACGCCC 60.732 52.381 0.00 0.00 41.59 6.13
67 68 0.802494 AAATGCAGAGTTTACGCCCG 59.198 50.000 0.00 0.00 0.00 6.13
68 69 0.321298 AATGCAGAGTTTACGCCCGT 60.321 50.000 0.00 0.00 0.00 5.28
69 70 0.321298 ATGCAGAGTTTACGCCCGTT 60.321 50.000 0.00 0.00 0.00 4.44
70 71 1.225376 TGCAGAGTTTACGCCCGTTG 61.225 55.000 0.00 0.00 0.00 4.10
71 72 1.495951 CAGAGTTTACGCCCGTTGC 59.504 57.895 0.00 0.00 0.00 4.17
72 73 1.070105 AGAGTTTACGCCCGTTGCA 59.930 52.632 0.00 0.00 41.33 4.08
73 74 0.321298 AGAGTTTACGCCCGTTGCAT 60.321 50.000 0.00 0.00 41.33 3.96
74 75 0.096454 GAGTTTACGCCCGTTGCATC 59.904 55.000 0.00 0.00 41.33 3.91
75 76 0.604243 AGTTTACGCCCGTTGCATCA 60.604 50.000 0.00 0.00 41.33 3.07
76 77 0.453782 GTTTACGCCCGTTGCATCAC 60.454 55.000 0.00 0.00 41.33 3.06
77 78 0.885150 TTTACGCCCGTTGCATCACA 60.885 50.000 0.00 0.00 41.33 3.58
78 79 1.570347 TTACGCCCGTTGCATCACAC 61.570 55.000 0.00 0.00 41.33 3.82
79 80 4.101790 CGCCCGTTGCATCACACC 62.102 66.667 0.00 0.00 41.33 4.16
80 81 2.672996 GCCCGTTGCATCACACCT 60.673 61.111 0.00 0.00 40.77 4.00
81 82 2.690778 GCCCGTTGCATCACACCTC 61.691 63.158 0.00 0.00 40.77 3.85
82 83 1.003355 CCCGTTGCATCACACCTCT 60.003 57.895 0.00 0.00 0.00 3.69
83 84 0.249120 CCCGTTGCATCACACCTCTA 59.751 55.000 0.00 0.00 0.00 2.43
84 85 1.359848 CCGTTGCATCACACCTCTAC 58.640 55.000 0.00 0.00 0.00 2.59
85 86 1.337728 CCGTTGCATCACACCTCTACA 60.338 52.381 0.00 0.00 0.00 2.74
86 87 1.726791 CGTTGCATCACACCTCTACAC 59.273 52.381 0.00 0.00 0.00 2.90
87 88 2.076863 GTTGCATCACACCTCTACACC 58.923 52.381 0.00 0.00 0.00 4.16
88 89 1.347062 TGCATCACACCTCTACACCA 58.653 50.000 0.00 0.00 0.00 4.17
89 90 1.908619 TGCATCACACCTCTACACCAT 59.091 47.619 0.00 0.00 0.00 3.55
90 91 2.093500 TGCATCACACCTCTACACCATC 60.093 50.000 0.00 0.00 0.00 3.51
91 92 2.814269 CATCACACCTCTACACCATCG 58.186 52.381 0.00 0.00 0.00 3.84
92 93 0.530744 TCACACCTCTACACCATCGC 59.469 55.000 0.00 0.00 0.00 4.58
93 94 0.460284 CACACCTCTACACCATCGCC 60.460 60.000 0.00 0.00 0.00 5.54
94 95 0.902984 ACACCTCTACACCATCGCCA 60.903 55.000 0.00 0.00 0.00 5.69
95 96 0.249120 CACCTCTACACCATCGCCAA 59.751 55.000 0.00 0.00 0.00 4.52
96 97 0.981183 ACCTCTACACCATCGCCAAA 59.019 50.000 0.00 0.00 0.00 3.28
97 98 1.338769 ACCTCTACACCATCGCCAAAC 60.339 52.381 0.00 0.00 0.00 2.93
98 99 1.369625 CTCTACACCATCGCCAAACC 58.630 55.000 0.00 0.00 0.00 3.27
99 100 0.687920 TCTACACCATCGCCAAACCA 59.312 50.000 0.00 0.00 0.00 3.67
100 101 1.280710 TCTACACCATCGCCAAACCAT 59.719 47.619 0.00 0.00 0.00 3.55
101 102 2.502130 TCTACACCATCGCCAAACCATA 59.498 45.455 0.00 0.00 0.00 2.74
102 103 1.750193 ACACCATCGCCAAACCATAG 58.250 50.000 0.00 0.00 0.00 2.23
103 104 0.381801 CACCATCGCCAAACCATAGC 59.618 55.000 0.00 0.00 0.00 2.97
104 105 0.751643 ACCATCGCCAAACCATAGCC 60.752 55.000 0.00 0.00 0.00 3.93
105 106 1.648720 CATCGCCAAACCATAGCCG 59.351 57.895 0.00 0.00 0.00 5.52
106 107 2.186826 ATCGCCAAACCATAGCCGC 61.187 57.895 0.00 0.00 0.00 6.53
107 108 3.887868 CGCCAAACCATAGCCGCC 61.888 66.667 0.00 0.00 0.00 6.13
108 109 2.753849 GCCAAACCATAGCCGCCA 60.754 61.111 0.00 0.00 0.00 5.69
109 110 2.347322 GCCAAACCATAGCCGCCAA 61.347 57.895 0.00 0.00 0.00 4.52
110 111 1.675720 GCCAAACCATAGCCGCCAAT 61.676 55.000 0.00 0.00 0.00 3.16
111 112 1.686355 CCAAACCATAGCCGCCAATA 58.314 50.000 0.00 0.00 0.00 1.90
112 113 2.028130 CCAAACCATAGCCGCCAATAA 58.972 47.619 0.00 0.00 0.00 1.40
113 114 2.627699 CCAAACCATAGCCGCCAATAAT 59.372 45.455 0.00 0.00 0.00 1.28
114 115 3.069443 CCAAACCATAGCCGCCAATAATT 59.931 43.478 0.00 0.00 0.00 1.40
115 116 4.298332 CAAACCATAGCCGCCAATAATTC 58.702 43.478 0.00 0.00 0.00 2.17
116 117 3.222173 ACCATAGCCGCCAATAATTCA 57.778 42.857 0.00 0.00 0.00 2.57
117 118 3.149196 ACCATAGCCGCCAATAATTCAG 58.851 45.455 0.00 0.00 0.00 3.02
118 119 2.095059 CCATAGCCGCCAATAATTCAGC 60.095 50.000 0.00 0.00 0.00 4.26
126 127 4.291540 GCCAATAATTCAGCGAATGTCA 57.708 40.909 4.87 0.00 32.14 3.58
127 128 4.863491 GCCAATAATTCAGCGAATGTCAT 58.137 39.130 4.87 0.00 32.14 3.06
128 129 4.913924 GCCAATAATTCAGCGAATGTCATC 59.086 41.667 4.87 0.00 32.14 2.92
129 130 5.455392 CCAATAATTCAGCGAATGTCATCC 58.545 41.667 4.87 0.00 32.14 3.51
130 131 5.240183 CCAATAATTCAGCGAATGTCATCCT 59.760 40.000 4.87 0.00 32.14 3.24
131 132 6.238842 CCAATAATTCAGCGAATGTCATCCTT 60.239 38.462 4.87 0.00 32.14 3.36
132 133 4.627611 AATTCAGCGAATGTCATCCTTG 57.372 40.909 4.87 0.00 32.14 3.61
133 134 1.372582 TCAGCGAATGTCATCCTTGC 58.627 50.000 0.00 0.00 0.00 4.01
134 135 1.065926 TCAGCGAATGTCATCCTTGCT 60.066 47.619 0.00 0.00 0.00 3.91
135 136 1.063616 CAGCGAATGTCATCCTTGCTG 59.936 52.381 10.90 10.90 41.81 4.41
136 137 0.248377 GCGAATGTCATCCTTGCTGC 60.248 55.000 0.00 0.00 0.00 5.25
137 138 1.376543 CGAATGTCATCCTTGCTGCT 58.623 50.000 0.00 0.00 0.00 4.24
138 139 1.063616 CGAATGTCATCCTTGCTGCTG 59.936 52.381 0.00 0.00 0.00 4.41
139 140 2.089980 GAATGTCATCCTTGCTGCTGT 58.910 47.619 0.00 0.00 0.00 4.40
140 141 2.211250 ATGTCATCCTTGCTGCTGTT 57.789 45.000 0.00 0.00 0.00 3.16
141 142 1.527034 TGTCATCCTTGCTGCTGTTC 58.473 50.000 0.00 0.00 0.00 3.18
142 143 0.445436 GTCATCCTTGCTGCTGTTCG 59.555 55.000 0.00 0.00 0.00 3.95
143 144 1.136147 CATCCTTGCTGCTGTTCGC 59.864 57.895 0.00 0.00 39.77 4.70
151 152 3.826221 TGCTGTTCGCAGTTTGCT 58.174 50.000 0.00 0.00 45.47 3.91
152 153 2.105984 TGCTGTTCGCAGTTTGCTT 58.894 47.368 0.00 0.00 45.47 3.91
153 154 0.248580 TGCTGTTCGCAGTTTGCTTG 60.249 50.000 0.00 0.00 45.47 4.01
154 155 1.543106 GCTGTTCGCAGTTTGCTTGC 61.543 55.000 0.00 0.00 46.58 4.01
155 156 0.248580 CTGTTCGCAGTTTGCTTGCA 60.249 50.000 0.00 0.00 42.25 4.08
156 157 0.385029 TGTTCGCAGTTTGCTTGCAT 59.615 45.000 0.00 0.00 42.25 3.96
157 158 0.780002 GTTCGCAGTTTGCTTGCATG 59.220 50.000 0.00 0.00 42.25 4.06
158 159 0.318869 TTCGCAGTTTGCTTGCATGG 60.319 50.000 1.34 0.00 42.25 3.66
159 160 1.007038 CGCAGTTTGCTTGCATGGT 60.007 52.632 1.34 0.00 42.25 3.55
160 161 1.279527 CGCAGTTTGCTTGCATGGTG 61.280 55.000 1.34 0.00 42.25 4.17
161 162 0.249573 GCAGTTTGCTTGCATGGTGT 60.250 50.000 1.34 0.00 40.96 4.16
162 163 1.807377 GCAGTTTGCTTGCATGGTGTT 60.807 47.619 1.34 0.00 40.96 3.32
204 205 6.462768 CCAAGACCCTGTGATTTCATTTTTGA 60.463 38.462 0.00 0.00 0.00 2.69
315 318 2.233271 CATTTCACCACAAGACTGCCT 58.767 47.619 0.00 0.00 0.00 4.75
405 491 7.762615 TCGATGTTCGACCAAGTTTATAGAAAT 59.237 33.333 0.00 0.00 44.82 2.17
630 3580 3.406764 AGTGATGTTCTCAAAGACCTGC 58.593 45.455 0.00 0.00 35.07 4.85
753 3703 5.218885 CCATACATCGTGCTTGTTTCAAAA 58.781 37.500 0.00 0.00 0.00 2.44
760 3710 3.060607 CGTGCTTGTTTCAAAATTTCCCG 60.061 43.478 0.00 0.00 0.00 5.14
765 3715 5.176774 GCTTGTTTCAAAATTTCCCGGTTAG 59.823 40.000 0.00 0.00 0.00 2.34
1115 4065 1.689582 GGACCTTCCCCTCCATCGT 60.690 63.158 0.00 0.00 0.00 3.73
1197 4147 3.467226 CCGGCCGTATGTGTCCCT 61.467 66.667 26.12 0.00 0.00 4.20
1503 4455 4.580167 TGAGTATGGTATGCATTTTGGAGC 59.420 41.667 3.54 0.00 0.00 4.70
1561 4513 5.302360 TGTTGGTATTCGTTATAGGCCATC 58.698 41.667 5.01 0.00 0.00 3.51
1562 4514 4.182693 TGGTATTCGTTATAGGCCATCG 57.817 45.455 5.01 1.87 0.00 3.84
1563 4515 2.928116 GGTATTCGTTATAGGCCATCGC 59.072 50.000 5.01 0.00 0.00 4.58
1564 4516 2.831685 ATTCGTTATAGGCCATCGCA 57.168 45.000 5.01 0.00 36.38 5.10
1565 4517 2.605837 TTCGTTATAGGCCATCGCAA 57.394 45.000 5.01 0.00 36.38 4.85
1566 4518 2.605837 TCGTTATAGGCCATCGCAAA 57.394 45.000 5.01 0.00 36.38 3.68
1567 4519 3.120321 TCGTTATAGGCCATCGCAAAT 57.880 42.857 5.01 0.00 36.38 2.32
1568 4520 3.472652 TCGTTATAGGCCATCGCAAATT 58.527 40.909 5.01 0.00 36.38 1.82
1687 4654 1.244019 GCTTGCAACAGTAGGTGGGG 61.244 60.000 0.00 0.00 0.00 4.96
1711 4678 7.454225 GGTTAATTATCCTTATCTCACCTGCT 58.546 38.462 5.46 0.00 0.00 4.24
1716 4683 2.362397 TCCTTATCTCACCTGCTAAGCG 59.638 50.000 0.00 0.00 0.00 4.68
1743 4710 1.203225 AGAAGGGGCAAAGGAGCATTT 60.203 47.619 0.00 0.00 35.83 2.32
1755 4722 4.913335 AGGAGCATTTATGTCATTGCAG 57.087 40.909 9.96 0.00 37.56 4.41
1762 4729 9.173939 GAGCATTTATGTCATTGCAGTATTAAC 57.826 33.333 9.96 0.00 37.56 2.01
1806 4773 5.299531 TGTTGATCTCTTATGTACTCCCTCG 59.700 44.000 0.00 0.00 0.00 4.63
1835 4802 8.736244 ACCATAATATAAGACGTTTTTGCAGTT 58.264 29.630 0.00 0.00 0.00 3.16
1870 4837 8.736244 ACTGCAAAAACGTCTTATATTATGGTT 58.264 29.630 0.00 0.00 0.00 3.67
1872 4839 7.906010 TGCAAAAACGTCTTATATTATGGTTCG 59.094 33.333 0.00 0.00 0.00 3.95
1873 4840 7.375017 GCAAAAACGTCTTATATTATGGTTCGG 59.625 37.037 0.00 0.00 0.00 4.30
1883 4850 2.376695 TATGGTTCGGAGGGAGTAGG 57.623 55.000 0.00 0.00 0.00 3.18
2099 5069 9.168451 TGAAAGTGTAGTTTTGTCACTGAAATA 57.832 29.630 0.00 0.00 41.37 1.40
2105 5075 7.661437 TGTAGTTTTGTCACTGAAATATCTGCT 59.339 33.333 0.00 0.00 0.00 4.24
2106 5076 7.516198 AGTTTTGTCACTGAAATATCTGCTT 57.484 32.000 0.00 0.00 0.00 3.91
2107 5077 7.945134 AGTTTTGTCACTGAAATATCTGCTTT 58.055 30.769 0.00 0.00 0.00 3.51
2108 5078 8.416329 AGTTTTGTCACTGAAATATCTGCTTTT 58.584 29.630 0.00 0.00 0.00 2.27
2275 5246 2.189191 TAGCACTGGAGGCTTGCTGG 62.189 60.000 19.07 0.00 46.10 4.85
2284 5255 3.201930 TGGAGGCTTGCTGGTAAATGATA 59.798 43.478 0.00 0.00 0.00 2.15
2285 5256 4.207165 GGAGGCTTGCTGGTAAATGATAA 58.793 43.478 0.00 0.00 0.00 1.75
2286 5257 4.644685 GGAGGCTTGCTGGTAAATGATAAA 59.355 41.667 0.00 0.00 0.00 1.40
2295 5266 8.262601 TGCTGGTAAATGATAAATAGAGAGGA 57.737 34.615 0.00 0.00 0.00 3.71
2353 5324 3.135895 GCTTATAGGGCCAAAGGTACTCA 59.864 47.826 6.18 0.00 38.49 3.41
2377 5348 2.370189 AGGCCATAGCTCATAACTCACC 59.630 50.000 5.01 0.00 39.73 4.02
2379 5350 2.104792 GCCATAGCTCATAACTCACCCA 59.895 50.000 0.00 0.00 35.50 4.51
2467 5438 9.757227 TTTTGGTGAGAACTAAATAAATTGGTG 57.243 29.630 0.00 0.00 32.40 4.17
2531 5502 5.482908 TGTTATTTGTTGCCACAACTTTGT 58.517 33.333 2.27 0.00 42.87 2.83
2711 5682 5.964958 TGATGTTCTGAGGGTCAATTTTC 57.035 39.130 0.00 0.00 0.00 2.29
2731 5734 7.872163 TTTTCATTTGACTATGTGACAATGC 57.128 32.000 0.00 0.00 31.22 3.56
2760 5765 2.142356 TGCATTCAACCTACCATGGG 57.858 50.000 18.09 0.00 0.00 4.00
2762 5767 1.686115 GCATTCAACCTACCATGGGCT 60.686 52.381 18.09 0.00 0.00 5.19
2844 5849 8.429237 TGGATGGGATAGTGTATTTTGTTTTT 57.571 30.769 0.00 0.00 0.00 1.94
2869 5874 5.690409 TGCGAATTAGGATAGAATGACGTTC 59.310 40.000 0.00 0.00 37.08 3.95
2875 5880 4.282496 AGGATAGAATGACGTTCCTCACT 58.718 43.478 3.71 0.00 37.56 3.41
2895 5900 3.328931 ACTTGTCCAGGTGATGAACTCAT 59.671 43.478 0.00 0.00 39.70 2.90
2900 5905 5.053145 GTCCAGGTGATGAACTCATGATAC 58.947 45.833 0.00 0.00 36.57 2.24
2907 5912 6.703607 GGTGATGAACTCATGATACACTAAGG 59.296 42.308 0.00 0.00 36.57 2.69
3022 6038 0.253044 TGCCCTACTTCCATCTGCAC 59.747 55.000 0.00 0.00 0.00 4.57
3030 6046 3.144506 ACTTCCATCTGCACTTGTCTTG 58.855 45.455 0.00 0.00 0.00 3.02
3160 6177 3.496884 GTCATAGGTTCGCAACACTCAAA 59.503 43.478 2.28 0.00 0.00 2.69
3164 6181 3.214328 AGGTTCGCAACACTCAAATCTT 58.786 40.909 2.28 0.00 0.00 2.40
3189 6206 5.819991 ACCATCATGTACATTGTCTTTCCT 58.180 37.500 5.37 0.00 0.00 3.36
3261 6278 0.037326 CTTACGGAGTCTTGCAGCCA 60.037 55.000 0.00 0.00 43.93 4.75
3397 6414 3.769739 ATCACAAACAGTCTACAGCCA 57.230 42.857 0.00 0.00 0.00 4.75
3592 6705 6.547510 AGATTATTCAGGGCTTACAACATTCC 59.452 38.462 0.00 0.00 0.00 3.01
3638 6751 2.032030 GTGTAACGCACAGCAAACTCAT 60.032 45.455 0.00 0.00 46.91 2.90
3664 6777 8.293867 TGGGAAAGAAACTACAAAATCATAACG 58.706 33.333 0.00 0.00 0.00 3.18
3670 6783 6.795098 AACTACAAAATCATAACGTCTGCA 57.205 33.333 0.00 0.00 0.00 4.41
3727 6840 4.118324 TGCATGCACCCATGGAAAATTTG 61.118 43.478 18.46 4.80 45.22 2.32
3819 6939 2.029666 GTCCCGCGGATGATCTGG 59.970 66.667 30.73 7.15 32.73 3.86
3854 6974 2.046314 CCGGCCGTTGGATGAAGT 60.046 61.111 26.12 0.00 0.00 3.01
3860 6980 2.359900 GCCGTTGGATGAAGTGAGAAT 58.640 47.619 0.00 0.00 0.00 2.40
3937 7057 2.988010 TTGTTGCACTCAGTCTCTGT 57.012 45.000 0.00 0.00 32.61 3.41
3950 7070 2.026822 AGTCTCTGTAACATGGGCCTTG 60.027 50.000 17.21 17.21 0.00 3.61
3998 7122 7.257722 TCCATTTTCTTCTTCTGAAACACAAC 58.742 34.615 0.00 0.00 33.77 3.32
3999 7123 7.122650 TCCATTTTCTTCTTCTGAAACACAACT 59.877 33.333 0.00 0.00 33.77 3.16
4000 7124 7.433425 CCATTTTCTTCTTCTGAAACACAACTC 59.567 37.037 0.00 0.00 33.77 3.01
4003 7127 6.227298 TCTTCTTCTGAAACACAACTCTCT 57.773 37.500 0.00 0.00 0.00 3.10
4021 7155 4.797471 TCTCTTCATTGCAACAAAATCGG 58.203 39.130 0.00 0.00 0.00 4.18
4073 7208 5.756195 TGTTGGAGAAACATTTCTGACTG 57.244 39.130 11.54 0.00 46.84 3.51
4074 7209 5.436175 TGTTGGAGAAACATTTCTGACTGA 58.564 37.500 11.54 0.00 46.84 3.41
4139 7275 3.949132 ACAGGGTTGTTGTTGCAAAAAT 58.051 36.364 5.11 0.00 32.28 1.82
4144 7281 7.121907 ACAGGGTTGTTGTTGCAAAAATAAAAT 59.878 29.630 12.55 0.58 32.28 1.82
4147 7284 9.444534 GGGTTGTTGTTGCAAAAATAAAATAAG 57.555 29.630 12.55 0.00 0.00 1.73
4161 7298 7.703058 AATAAAATAAGGAGGCATTATCCGG 57.297 36.000 0.00 0.00 42.02 5.14
4170 7307 1.317613 GCATTATCCGGCCATGAACA 58.682 50.000 2.24 0.00 0.00 3.18
4174 7311 1.705002 TATCCGGCCATGAACAGGGG 61.705 60.000 2.24 0.00 31.86 4.79
4175 7312 4.047125 CCGGCCATGAACAGGGGT 62.047 66.667 2.24 0.00 31.86 4.95
4177 7314 1.301623 CGGCCATGAACAGGGGTAA 59.698 57.895 2.24 0.00 31.86 2.85
4179 7316 1.474330 GGCCATGAACAGGGGTAAAG 58.526 55.000 0.00 0.00 31.86 1.85
4180 7317 1.005450 GGCCATGAACAGGGGTAAAGA 59.995 52.381 0.00 0.00 31.86 2.52
4181 7318 2.556559 GGCCATGAACAGGGGTAAAGAA 60.557 50.000 0.00 0.00 31.86 2.52
4182 7319 2.755103 GCCATGAACAGGGGTAAAGAAG 59.245 50.000 7.58 0.00 31.86 2.85
4185 7322 4.398319 CATGAACAGGGGTAAAGAAGTGT 58.602 43.478 0.00 0.00 0.00 3.55
4204 7370 0.609151 TGATTTTACTCCACCGCCGA 59.391 50.000 0.00 0.00 0.00 5.54
4251 7421 0.250166 GGTGGCCGACTTGTAACACT 60.250 55.000 0.00 0.00 0.00 3.55
4252 7422 1.001181 GGTGGCCGACTTGTAACACTA 59.999 52.381 0.00 0.00 0.00 2.74
4278 7448 4.742201 CTGGCCACACCTCCGTCG 62.742 72.222 0.00 0.00 40.22 5.12
4317 7487 2.420022 CGGCTAAACCTCTCAACAATGG 59.580 50.000 0.00 0.00 35.61 3.16
4336 7506 1.000739 ACATGGATGGGTGGCTTGG 59.999 57.895 0.00 0.00 0.00 3.61
4337 7507 1.307309 CATGGATGGGTGGCTTGGA 59.693 57.895 0.00 0.00 0.00 3.53
4338 7508 0.754217 CATGGATGGGTGGCTTGGAG 60.754 60.000 0.00 0.00 0.00 3.86
4339 7509 2.440980 GGATGGGTGGCTTGGAGC 60.441 66.667 0.00 0.00 41.46 4.70
4393 7567 2.105006 GCTGCAAGTGAGAAGATCCA 57.895 50.000 0.00 0.00 35.30 3.41
4408 7582 7.179872 TGAGAAGATCCAAGAAAGATTGAGAGA 59.820 37.037 0.00 0.00 31.55 3.10
4409 7583 7.558604 AGAAGATCCAAGAAAGATTGAGAGAG 58.441 38.462 0.00 0.00 31.55 3.20
4417 7591 7.364939 CCAAGAAAGATTGAGAGAGGAAGAGAT 60.365 40.741 0.00 0.00 31.55 2.75
4421 7595 9.533253 GAAAGATTGAGAGAGGAAGAGATAAAG 57.467 37.037 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.935203 AGTGACGCTCATATTCCTTGTTG 59.065 43.478 0.00 0.00 0.00 3.33
6 7 3.935203 CAGTGACGCTCATATTCCTTGTT 59.065 43.478 0.00 0.00 0.00 2.83
7 8 3.055819 ACAGTGACGCTCATATTCCTTGT 60.056 43.478 0.00 0.00 0.00 3.16
8 9 3.525537 ACAGTGACGCTCATATTCCTTG 58.474 45.455 0.00 0.00 0.00 3.61
9 10 3.735208 CGACAGTGACGCTCATATTCCTT 60.735 47.826 1.37 0.00 0.00 3.36
10 11 2.223595 CGACAGTGACGCTCATATTCCT 60.224 50.000 1.37 0.00 0.00 3.36
11 12 2.120232 CGACAGTGACGCTCATATTCC 58.880 52.381 1.37 0.00 0.00 3.01
21 22 0.387239 TCTCACATGCGACAGTGACG 60.387 55.000 10.69 10.69 39.65 4.35
22 23 1.923204 GATCTCACATGCGACAGTGAC 59.077 52.381 0.00 0.00 39.65 3.67
23 24 1.545582 TGATCTCACATGCGACAGTGA 59.454 47.619 0.00 0.00 42.06 3.41
24 25 2.000429 TGATCTCACATGCGACAGTG 58.000 50.000 0.00 0.00 37.10 3.66
25 26 2.749280 TTGATCTCACATGCGACAGT 57.251 45.000 0.00 0.00 0.00 3.55
26 27 2.222976 GCTTTGATCTCACATGCGACAG 60.223 50.000 0.00 0.00 0.00 3.51
27 28 1.733912 GCTTTGATCTCACATGCGACA 59.266 47.619 0.00 0.00 0.00 4.35
28 29 1.733912 TGCTTTGATCTCACATGCGAC 59.266 47.619 0.00 0.00 0.00 5.19
29 30 2.097680 TGCTTTGATCTCACATGCGA 57.902 45.000 0.00 0.00 0.00 5.10
30 31 2.905959 TTGCTTTGATCTCACATGCG 57.094 45.000 0.00 0.00 0.00 4.73
31 32 3.306166 GCATTTGCTTTGATCTCACATGC 59.694 43.478 0.00 10.63 36.95 4.06
32 33 4.490743 TGCATTTGCTTTGATCTCACATG 58.509 39.130 3.94 0.00 42.66 3.21
33 34 4.461431 TCTGCATTTGCTTTGATCTCACAT 59.539 37.500 3.94 0.00 42.66 3.21
34 35 3.822167 TCTGCATTTGCTTTGATCTCACA 59.178 39.130 3.94 0.00 42.66 3.58
35 36 4.082895 ACTCTGCATTTGCTTTGATCTCAC 60.083 41.667 3.94 0.00 42.66 3.51
36 37 4.077108 ACTCTGCATTTGCTTTGATCTCA 58.923 39.130 3.94 0.00 42.66 3.27
37 38 4.698583 ACTCTGCATTTGCTTTGATCTC 57.301 40.909 3.94 0.00 42.66 2.75
38 39 5.464030 AAACTCTGCATTTGCTTTGATCT 57.536 34.783 3.94 0.00 42.66 2.75
39 40 5.284660 CGTAAACTCTGCATTTGCTTTGATC 59.715 40.000 3.94 0.00 42.66 2.92
40 41 5.156355 CGTAAACTCTGCATTTGCTTTGAT 58.844 37.500 3.94 0.00 42.66 2.57
41 42 4.536065 CGTAAACTCTGCATTTGCTTTGA 58.464 39.130 3.94 0.00 42.66 2.69
42 43 3.120121 GCGTAAACTCTGCATTTGCTTTG 59.880 43.478 3.94 0.00 42.66 2.77
43 44 3.308530 GCGTAAACTCTGCATTTGCTTT 58.691 40.909 3.94 0.00 42.66 3.51
44 45 2.351738 GGCGTAAACTCTGCATTTGCTT 60.352 45.455 3.94 0.00 42.66 3.91
45 46 1.200020 GGCGTAAACTCTGCATTTGCT 59.800 47.619 3.94 0.00 42.66 3.91
46 47 1.617740 GGCGTAAACTCTGCATTTGC 58.382 50.000 0.00 0.00 42.50 3.68
47 48 1.465689 CGGGCGTAAACTCTGCATTTG 60.466 52.381 0.00 0.00 0.00 2.32
48 49 0.802494 CGGGCGTAAACTCTGCATTT 59.198 50.000 0.00 0.00 0.00 2.32
49 50 0.321298 ACGGGCGTAAACTCTGCATT 60.321 50.000 0.00 0.00 0.00 3.56
50 51 0.321298 AACGGGCGTAAACTCTGCAT 60.321 50.000 0.00 0.00 0.00 3.96
51 52 1.070105 AACGGGCGTAAACTCTGCA 59.930 52.632 0.00 0.00 0.00 4.41
52 53 1.495951 CAACGGGCGTAAACTCTGC 59.504 57.895 0.00 0.00 0.00 4.26
53 54 1.495951 GCAACGGGCGTAAACTCTG 59.504 57.895 0.00 0.00 0.00 3.35
54 55 3.961729 GCAACGGGCGTAAACTCT 58.038 55.556 0.00 0.00 0.00 3.24
63 64 2.672996 AGGTGTGATGCAACGGGC 60.673 61.111 0.00 0.00 40.44 6.13
64 65 0.249120 TAGAGGTGTGATGCAACGGG 59.751 55.000 0.00 0.00 40.44 5.28
65 66 1.337728 TGTAGAGGTGTGATGCAACGG 60.338 52.381 0.00 0.00 40.44 4.44
66 67 1.726791 GTGTAGAGGTGTGATGCAACG 59.273 52.381 0.00 0.00 40.44 4.10
67 68 2.076863 GGTGTAGAGGTGTGATGCAAC 58.923 52.381 0.00 0.00 34.25 4.17
68 69 1.696884 TGGTGTAGAGGTGTGATGCAA 59.303 47.619 0.00 0.00 0.00 4.08
69 70 1.347062 TGGTGTAGAGGTGTGATGCA 58.653 50.000 0.00 0.00 0.00 3.96
70 71 2.555199 GATGGTGTAGAGGTGTGATGC 58.445 52.381 0.00 0.00 0.00 3.91
71 72 2.814269 CGATGGTGTAGAGGTGTGATG 58.186 52.381 0.00 0.00 0.00 3.07
72 73 1.137086 GCGATGGTGTAGAGGTGTGAT 59.863 52.381 0.00 0.00 0.00 3.06
73 74 0.530744 GCGATGGTGTAGAGGTGTGA 59.469 55.000 0.00 0.00 0.00 3.58
74 75 0.460284 GGCGATGGTGTAGAGGTGTG 60.460 60.000 0.00 0.00 0.00 3.82
75 76 0.902984 TGGCGATGGTGTAGAGGTGT 60.903 55.000 0.00 0.00 0.00 4.16
76 77 0.249120 TTGGCGATGGTGTAGAGGTG 59.751 55.000 0.00 0.00 0.00 4.00
77 78 0.981183 TTTGGCGATGGTGTAGAGGT 59.019 50.000 0.00 0.00 0.00 3.85
78 79 1.369625 GTTTGGCGATGGTGTAGAGG 58.630 55.000 0.00 0.00 0.00 3.69
79 80 1.338674 TGGTTTGGCGATGGTGTAGAG 60.339 52.381 0.00 0.00 0.00 2.43
80 81 0.687920 TGGTTTGGCGATGGTGTAGA 59.312 50.000 0.00 0.00 0.00 2.59
81 82 1.750193 ATGGTTTGGCGATGGTGTAG 58.250 50.000 0.00 0.00 0.00 2.74
82 83 2.912771 CTATGGTTTGGCGATGGTGTA 58.087 47.619 0.00 0.00 0.00 2.90
83 84 1.750193 CTATGGTTTGGCGATGGTGT 58.250 50.000 0.00 0.00 0.00 4.16
84 85 0.381801 GCTATGGTTTGGCGATGGTG 59.618 55.000 0.00 0.00 0.00 4.17
85 86 0.751643 GGCTATGGTTTGGCGATGGT 60.752 55.000 0.00 0.00 0.00 3.55
86 87 2.032981 GGCTATGGTTTGGCGATGG 58.967 57.895 0.00 0.00 0.00 3.51
91 92 1.675720 ATTGGCGGCTATGGTTTGGC 61.676 55.000 11.43 0.00 0.00 4.52
92 93 1.686355 TATTGGCGGCTATGGTTTGG 58.314 50.000 15.79 0.00 0.00 3.28
93 94 4.202101 TGAATTATTGGCGGCTATGGTTTG 60.202 41.667 15.79 0.00 0.00 2.93
94 95 3.957497 TGAATTATTGGCGGCTATGGTTT 59.043 39.130 15.79 6.60 0.00 3.27
95 96 3.561143 TGAATTATTGGCGGCTATGGTT 58.439 40.909 15.79 9.90 0.00 3.67
96 97 3.149196 CTGAATTATTGGCGGCTATGGT 58.851 45.455 15.79 1.74 0.00 3.55
97 98 2.095059 GCTGAATTATTGGCGGCTATGG 60.095 50.000 15.79 1.33 0.00 2.74
98 99 2.413239 CGCTGAATTATTGGCGGCTATG 60.413 50.000 15.79 0.00 43.25 2.23
99 100 1.806542 CGCTGAATTATTGGCGGCTAT 59.193 47.619 11.43 11.25 43.25 2.97
100 101 1.202592 TCGCTGAATTATTGGCGGCTA 60.203 47.619 11.43 1.99 46.31 3.93
101 102 0.463654 TCGCTGAATTATTGGCGGCT 60.464 50.000 11.43 0.00 46.31 5.52
102 103 0.380378 TTCGCTGAATTATTGGCGGC 59.620 50.000 17.02 0.00 46.31 6.53
103 104 2.033299 ACATTCGCTGAATTATTGGCGG 59.967 45.455 17.02 7.91 46.31 6.13
105 106 4.291540 TGACATTCGCTGAATTATTGGC 57.708 40.909 1.76 0.00 28.87 4.52
106 107 5.240183 AGGATGACATTCGCTGAATTATTGG 59.760 40.000 1.76 0.00 28.87 3.16
107 108 6.309712 AGGATGACATTCGCTGAATTATTG 57.690 37.500 1.76 0.00 28.87 1.90
108 109 6.732154 CAAGGATGACATTCGCTGAATTATT 58.268 36.000 1.76 0.00 28.87 1.40
109 110 5.278169 GCAAGGATGACATTCGCTGAATTAT 60.278 40.000 3.68 0.00 28.87 1.28
110 111 4.035558 GCAAGGATGACATTCGCTGAATTA 59.964 41.667 3.68 0.00 28.87 1.40
111 112 3.181493 GCAAGGATGACATTCGCTGAATT 60.181 43.478 3.68 0.00 28.87 2.17
112 113 2.357009 GCAAGGATGACATTCGCTGAAT 59.643 45.455 3.68 0.00 31.86 2.57
113 114 1.739466 GCAAGGATGACATTCGCTGAA 59.261 47.619 3.68 0.00 0.00 3.02
114 115 1.065926 AGCAAGGATGACATTCGCTGA 60.066 47.619 3.68 0.00 0.00 4.26
115 116 1.063616 CAGCAAGGATGACATTCGCTG 59.936 52.381 8.65 8.65 39.38 5.18
116 117 1.376543 CAGCAAGGATGACATTCGCT 58.623 50.000 0.00 0.00 0.00 4.93
117 118 0.248377 GCAGCAAGGATGACATTCGC 60.248 55.000 0.00 0.00 0.00 4.70
118 119 1.063616 CAGCAGCAAGGATGACATTCG 59.936 52.381 0.00 0.00 0.00 3.34
119 120 2.089980 ACAGCAGCAAGGATGACATTC 58.910 47.619 0.00 0.00 0.00 2.67
120 121 2.211250 ACAGCAGCAAGGATGACATT 57.789 45.000 0.00 0.00 0.00 2.71
121 122 2.089980 GAACAGCAGCAAGGATGACAT 58.910 47.619 0.00 0.00 0.00 3.06
122 123 1.527034 GAACAGCAGCAAGGATGACA 58.473 50.000 0.00 0.00 0.00 3.58
123 124 0.445436 CGAACAGCAGCAAGGATGAC 59.555 55.000 0.00 0.00 0.00 3.06
124 125 2.845019 CGAACAGCAGCAAGGATGA 58.155 52.632 0.00 0.00 0.00 2.92
142 143 0.249573 ACACCATGCAAGCAAACTGC 60.250 50.000 0.00 0.00 45.46 4.40
143 144 1.862201 CAACACCATGCAAGCAAACTG 59.138 47.619 0.00 0.00 0.00 3.16
144 145 1.202557 CCAACACCATGCAAGCAAACT 60.203 47.619 0.00 0.00 0.00 2.66
145 146 1.219646 CCAACACCATGCAAGCAAAC 58.780 50.000 0.00 0.00 0.00 2.93
146 147 0.106335 CCCAACACCATGCAAGCAAA 59.894 50.000 0.00 0.00 0.00 3.68
147 148 1.047596 ACCCAACACCATGCAAGCAA 61.048 50.000 0.00 0.00 0.00 3.91
148 149 1.047596 AACCCAACACCATGCAAGCA 61.048 50.000 0.00 0.00 0.00 3.91
149 150 0.319813 GAACCCAACACCATGCAAGC 60.320 55.000 0.00 0.00 0.00 4.01
150 151 1.331214 AGAACCCAACACCATGCAAG 58.669 50.000 0.00 0.00 0.00 4.01
151 152 1.411977 CAAGAACCCAACACCATGCAA 59.588 47.619 0.00 0.00 0.00 4.08
152 153 1.039068 CAAGAACCCAACACCATGCA 58.961 50.000 0.00 0.00 0.00 3.96
153 154 0.318120 CCAAGAACCCAACACCATGC 59.682 55.000 0.00 0.00 0.00 4.06
154 155 1.703411 ACCAAGAACCCAACACCATG 58.297 50.000 0.00 0.00 0.00 3.66
155 156 2.445525 AGTACCAAGAACCCAACACCAT 59.554 45.455 0.00 0.00 0.00 3.55
156 157 1.847737 AGTACCAAGAACCCAACACCA 59.152 47.619 0.00 0.00 0.00 4.17
157 158 2.158726 TGAGTACCAAGAACCCAACACC 60.159 50.000 0.00 0.00 0.00 4.16
158 159 2.876550 GTGAGTACCAAGAACCCAACAC 59.123 50.000 0.00 0.00 0.00 3.32
159 160 2.158726 GGTGAGTACCAAGAACCCAACA 60.159 50.000 0.00 0.00 46.71 3.33
160 161 2.501261 GGTGAGTACCAAGAACCCAAC 58.499 52.381 0.00 0.00 46.71 3.77
161 162 2.943036 GGTGAGTACCAAGAACCCAA 57.057 50.000 0.00 0.00 46.71 4.12
217 218 4.744570 TGTATGAAGATCTCCGTGTTCAC 58.255 43.478 0.00 0.00 34.70 3.18
274 277 7.566760 AATGCCATCGTTCTCATACAAATTA 57.433 32.000 0.00 0.00 0.00 1.40
364 450 8.697846 TCGAACATCGATAGTATTTGACTTTT 57.302 30.769 0.00 0.00 44.82 2.27
534 623 5.369993 AGAGGGTAATATTCAACTCCCTTCC 59.630 44.000 12.86 5.54 44.30 3.46
535 624 6.099845 TGAGAGGGTAATATTCAACTCCCTTC 59.900 42.308 12.86 12.22 44.30 3.46
753 3703 5.833131 ACAATAATCATGCTAACCGGGAAAT 59.167 36.000 6.32 0.00 0.00 2.17
760 3710 3.304659 CGCCCACAATAATCATGCTAACC 60.305 47.826 0.00 0.00 0.00 2.85
765 3715 1.675483 TCACGCCCACAATAATCATGC 59.325 47.619 0.00 0.00 0.00 4.06
803 3753 2.755103 GCTGACCCACCCAAAATTCTAG 59.245 50.000 0.00 0.00 0.00 2.43
807 3757 1.416030 GTTGCTGACCCACCCAAAATT 59.584 47.619 0.00 0.00 0.00 1.82
895 3845 1.892474 GGCTTGGGTTGCACAATCTAA 59.108 47.619 0.00 0.00 0.00 2.10
1197 4147 0.383949 GCAAAGTTTCTGCCACGGAA 59.616 50.000 0.00 0.00 33.51 4.30
1232 4182 3.441572 GCAAAGGCATGAAAGCTCTAAGA 59.558 43.478 0.00 0.00 40.72 2.10
1561 4513 0.171007 ACTGGGATTGCGAATTTGCG 59.829 50.000 13.01 0.00 37.81 4.85
1562 4514 2.368655 AACTGGGATTGCGAATTTGC 57.631 45.000 10.99 10.99 0.00 3.68
1563 4515 8.647143 AATTATAAACTGGGATTGCGAATTTG 57.353 30.769 0.00 0.00 0.00 2.32
1564 4516 9.097257 CAAATTATAAACTGGGATTGCGAATTT 57.903 29.630 0.00 0.00 0.00 1.82
1565 4517 7.224557 GCAAATTATAAACTGGGATTGCGAATT 59.775 33.333 0.00 0.00 33.54 2.17
1566 4518 6.701400 GCAAATTATAAACTGGGATTGCGAAT 59.299 34.615 0.00 0.00 33.54 3.34
1567 4519 6.039616 GCAAATTATAAACTGGGATTGCGAA 58.960 36.000 0.00 0.00 33.54 4.70
1568 4520 5.126222 TGCAAATTATAAACTGGGATTGCGA 59.874 36.000 0.00 0.00 43.48 5.10
1609 4561 9.836864 TTCAGATATGAACAATATAACTGCAGT 57.163 29.630 15.25 15.25 33.47 4.40
1687 4654 9.998106 TTAGCAGGTGAGATAAGGATAATTAAC 57.002 33.333 0.00 0.00 0.00 2.01
1711 4678 2.038269 CCCTTCTTTGCGCCGCTTA 61.038 57.895 11.67 0.00 0.00 3.09
1716 4683 2.770132 CTTTGCCCCTTCTTTGCGCC 62.770 60.000 4.18 0.00 0.00 6.53
1730 4697 4.269363 GCAATGACATAAATGCTCCTTTGC 59.731 41.667 3.76 0.00 35.93 3.68
1743 4710 8.962884 ATCAGTGTTAATACTGCAATGACATA 57.037 30.769 23.36 7.15 45.94 2.29
1755 4722 9.988350 CAACTCCACATAAATCAGTGTTAATAC 57.012 33.333 0.00 0.00 33.99 1.89
1762 4729 5.947228 ACACAACTCCACATAAATCAGTG 57.053 39.130 0.00 0.00 35.56 3.66
1806 4773 8.614346 TGCAAAAACGTCTTATATTATGGTACC 58.386 33.333 4.43 4.43 0.00 3.34
1835 4802 7.820044 AAGACGTTTTTGCAGTTCAAATTTA 57.180 28.000 0.00 0.00 43.53 1.40
1861 4828 4.106825 TCCTACTCCCTCCGAACCATAATA 59.893 45.833 0.00 0.00 0.00 0.98
1870 4837 3.181431 CCTTTCTATCCTACTCCCTCCGA 60.181 52.174 0.00 0.00 0.00 4.55
1872 4839 4.472690 TCCTTTCTATCCTACTCCCTCC 57.527 50.000 0.00 0.00 0.00 4.30
1873 4840 5.841783 ACATTCCTTTCTATCCTACTCCCTC 59.158 44.000 0.00 0.00 0.00 4.30
1915 4882 2.401583 ATATTGCAGGCGTCAACTCA 57.598 45.000 0.00 0.00 0.00 3.41
2072 5040 7.624360 TTCAGTGACAAAACTACACTTTCAT 57.376 32.000 0.00 0.00 41.93 2.57
2213 5183 5.761234 ACAGTTGTTTAGCGAAAATACAGGA 59.239 36.000 0.00 0.00 0.00 3.86
2217 5187 9.601971 TGATTAACAGTTGTTTAGCGAAAATAC 57.398 29.630 2.46 0.00 39.31 1.89
2284 5255 6.126863 TGTTTGGATGTGTCCTCTCTATTT 57.873 37.500 0.00 0.00 45.32 1.40
2285 5256 5.762179 TGTTTGGATGTGTCCTCTCTATT 57.238 39.130 0.00 0.00 45.32 1.73
2286 5257 5.762179 TTGTTTGGATGTGTCCTCTCTAT 57.238 39.130 0.00 0.00 45.32 1.98
2295 5266 4.079253 GGACCACTATTGTTTGGATGTGT 58.921 43.478 0.00 0.00 36.28 3.72
2327 5298 2.311841 ACCTTTGGCCCTATAAGCAACT 59.688 45.455 0.00 0.00 0.00 3.16
2353 5324 3.455910 TGAGTTATGAGCTATGGCCTTGT 59.544 43.478 3.32 0.00 39.73 3.16
2377 5348 6.152661 TGAAACCTAATTCTTACAATGCCTGG 59.847 38.462 0.00 0.00 0.00 4.45
2379 5350 7.201732 CGATGAAACCTAATTCTTACAATGCCT 60.202 37.037 0.00 0.00 0.00 4.75
2444 5415 7.504238 ACACACCAATTTATTTAGTTCTCACCA 59.496 33.333 0.00 0.00 0.00 4.17
2445 5416 7.882179 ACACACCAATTTATTTAGTTCTCACC 58.118 34.615 0.00 0.00 0.00 4.02
2531 5502 6.899393 ATGAACCTGTCTGCATTTTAGAAA 57.101 33.333 0.00 0.00 0.00 2.52
2670 5641 7.750229 ACATCATGTGGCATAGTAATAAAGG 57.250 36.000 0.00 0.00 0.00 3.11
2711 5682 7.383029 ACAAAAGCATTGTCACATAGTCAAATG 59.617 33.333 2.38 0.00 0.00 2.32
2731 5734 6.314896 TGGTAGGTTGAATGCAAAAACAAAAG 59.685 34.615 10.52 0.00 35.42 2.27
2787 5792 7.709613 AGAGTCAGATTACGTAACAACAAAAGT 59.290 33.333 10.81 0.00 0.00 2.66
2792 5797 8.355169 ACTTAAGAGTCAGATTACGTAACAACA 58.645 33.333 10.81 0.00 0.00 3.33
2800 5805 6.477033 CCATCCAACTTAAGAGTCAGATTACG 59.523 42.308 10.09 0.00 34.21 3.18
2844 5849 5.597806 ACGTCATTCTATCCTAATTCGCAA 58.402 37.500 0.00 0.00 0.00 4.85
2852 5857 5.446860 AGTGAGGAACGTCATTCTATCCTA 58.553 41.667 2.74 0.00 40.53 2.94
2858 5863 3.555168 GGACAAGTGAGGAACGTCATTCT 60.555 47.826 0.00 0.00 37.48 2.40
2860 5865 2.104111 TGGACAAGTGAGGAACGTCATT 59.896 45.455 0.00 0.00 0.00 2.57
2869 5874 1.625315 TCATCACCTGGACAAGTGAGG 59.375 52.381 8.88 8.88 45.60 3.86
2875 5880 3.327464 TCATGAGTTCATCACCTGGACAA 59.673 43.478 0.00 0.00 41.91 3.18
2895 5900 5.835819 AGCTCATAGAAGCCTTAGTGTATCA 59.164 40.000 0.00 0.00 43.56 2.15
2900 5905 8.116651 TCTATTAGCTCATAGAAGCCTTAGTG 57.883 38.462 14.02 0.00 43.56 2.74
2988 6004 0.324943 GGGCACTGCTTCCAGAGTTA 59.675 55.000 0.00 0.00 41.77 2.24
3022 6038 8.964420 TCTGAGTTTTAAACAAACAAGACAAG 57.036 30.769 10.60 0.00 32.81 3.16
3160 6177 6.656902 AGACAATGTACATGATGGTCAAGAT 58.343 36.000 21.89 7.75 0.00 2.40
3164 6181 5.647658 GGAAAGACAATGTACATGATGGTCA 59.352 40.000 21.89 0.00 0.00 4.02
3189 6206 6.206634 CCTATGAAGTTTAGCAACTCCAACAA 59.793 38.462 0.00 0.00 42.89 2.83
3397 6414 2.462456 TGAGAAGCGCTTTCAGATGT 57.538 45.000 25.84 0.00 38.31 3.06
3441 6458 2.645802 GGTATGTTACCGCAATCCCAA 58.354 47.619 0.00 0.00 39.39 4.12
3638 6751 8.293867 CGTTATGATTTTGTAGTTTCTTTCCCA 58.706 33.333 0.00 0.00 0.00 4.37
3664 6777 9.910511 CATTTCATTAATGCTATTTTTGCAGAC 57.089 29.630 10.76 0.00 44.04 3.51
3802 6919 2.028125 TTCCAGATCATCCGCGGGAC 62.028 60.000 27.83 12.18 32.98 4.46
3805 6922 0.104855 TCTTTCCAGATCATCCGCGG 59.895 55.000 22.12 22.12 0.00 6.46
3806 6923 2.160822 ATCTTTCCAGATCATCCGCG 57.839 50.000 0.00 0.00 34.26 6.46
3854 6974 3.137176 GGGAGATCCAATGGTCATTCTCA 59.863 47.826 18.28 0.00 37.91 3.27
3860 6980 1.496001 CATGGGGAGATCCAATGGTCA 59.504 52.381 0.00 0.00 42.20 4.02
3937 7057 1.342819 GTTGCAACAAGGCCCATGTTA 59.657 47.619 24.52 7.17 38.90 2.41
3978 7102 7.106239 AGAGAGTTGTGTTTCAGAAGAAGAAA 58.894 34.615 0.00 0.00 34.71 2.52
3981 7105 6.536582 TGAAGAGAGTTGTGTTTCAGAAGAAG 59.463 38.462 0.00 0.00 34.71 2.85
3998 7122 4.855388 CCGATTTTGTTGCAATGAAGAGAG 59.145 41.667 0.59 0.00 0.00 3.20
3999 7123 4.278170 ACCGATTTTGTTGCAATGAAGAGA 59.722 37.500 0.59 0.00 0.00 3.10
4000 7124 4.383649 CACCGATTTTGTTGCAATGAAGAG 59.616 41.667 0.59 0.00 0.00 2.85
4003 7127 4.052159 ACACCGATTTTGTTGCAATGAA 57.948 36.364 0.59 0.00 0.00 2.57
4139 7275 5.007682 GCCGGATAATGCCTCCTTATTTTA 58.992 41.667 5.05 0.00 0.00 1.52
4144 7281 0.690762 GGCCGGATAATGCCTCCTTA 59.309 55.000 5.05 0.00 44.46 2.69
4157 7294 3.727258 CCCCTGTTCATGGCCGGA 61.727 66.667 5.05 0.00 0.00 5.14
4161 7298 2.507407 TCTTTACCCCTGTTCATGGC 57.493 50.000 0.00 0.00 0.00 4.40
4167 7304 4.724279 ATCACACTTCTTTACCCCTGTT 57.276 40.909 0.00 0.00 0.00 3.16
4169 7306 6.715264 AGTAAAATCACACTTCTTTACCCCTG 59.285 38.462 0.00 0.00 35.69 4.45
4170 7307 6.849151 AGTAAAATCACACTTCTTTACCCCT 58.151 36.000 0.00 0.00 35.69 4.79
4174 7311 7.570691 CGGTGGAGTAAAATCACACTTCTTTAC 60.571 40.741 0.00 0.00 35.44 2.01
4175 7312 6.425721 CGGTGGAGTAAAATCACACTTCTTTA 59.574 38.462 0.00 0.00 33.45 1.85
4177 7314 4.755123 CGGTGGAGTAAAATCACACTTCTT 59.245 41.667 0.00 0.00 33.45 2.52
4179 7316 3.120304 GCGGTGGAGTAAAATCACACTTC 60.120 47.826 0.00 0.00 33.45 3.01
4180 7317 2.812011 GCGGTGGAGTAAAATCACACTT 59.188 45.455 0.00 0.00 33.45 3.16
4181 7318 2.423577 GCGGTGGAGTAAAATCACACT 58.576 47.619 0.00 0.00 33.45 3.55
4182 7319 1.467342 GGCGGTGGAGTAAAATCACAC 59.533 52.381 0.00 0.00 33.45 3.82
4185 7322 0.609151 TCGGCGGTGGAGTAAAATCA 59.391 50.000 7.21 0.00 0.00 2.57
4317 7487 1.039233 CCAAGCCACCCATCCATGTC 61.039 60.000 0.00 0.00 0.00 3.06
4342 7512 2.872557 CCATGAGCCGCAAGTGTG 59.127 61.111 0.00 0.00 0.00 3.82
4343 7513 3.058160 GCCATGAGCCGCAAGTGT 61.058 61.111 0.00 0.00 34.35 3.55
4356 7529 1.454479 CGGCTCCAGGATTTGCCAT 60.454 57.895 16.59 0.00 45.13 4.40
4357 7530 2.045045 CGGCTCCAGGATTTGCCA 60.045 61.111 16.59 0.00 45.13 4.92
4391 7565 6.047511 TCTTCCTCTCTCAATCTTTCTTGG 57.952 41.667 0.00 0.00 0.00 3.61
4393 7567 7.738437 ATCTCTTCCTCTCTCAATCTTTCTT 57.262 36.000 0.00 0.00 0.00 2.52
4408 7582 1.112113 TCGCCGCTTTATCTCTTCCT 58.888 50.000 0.00 0.00 0.00 3.36
4409 7583 3.661745 TCGCCGCTTTATCTCTTCC 57.338 52.632 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.