Multiple sequence alignment - TraesCS5B01G303500

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 TraesCS5B01G303500 chr5B 100.000 3297 0 0 973 4269 487833484 487830188 0.000000e+00 6089
1 TraesCS5B01G303500 chr5B 100.000 557 0 0 1 557 487834456 487833900 0.000000e+00 1029
2 TraesCS5B01G303500 chr5B 78.240 1250 196 45 992 2206 487920046 487918838 0.000000e+00 732
3 TraesCS5B01G303500 chr5A 97.156 2356 65 2 973 3326 512423077 512420722 0.000000e+00 3978
4 TraesCS5B01G303500 chr5A 96.774 589 16 2 3340 3928 512420334 512419749 0.000000e+00 979
5 TraesCS5B01G303500 chr5A 75.859 2009 330 94 992 2921 512454265 512452333 0.000000e+00 880
6 TraesCS5B01G303500 chr5A 95.427 328 6 7 233 557 512423469 512423148 8.190000e-142 514
7 TraesCS5B01G303500 chr5A 92.541 362 5 9 3911 4269 512419734 512419392 2.290000e-137 499
8 TraesCS5B01G303500 chr5D 95.320 1218 45 5 989 2206 406829451 406828246 0.000000e+00 1923
9 TraesCS5B01G303500 chr5D 97.892 996 19 2 2333 3326 406828147 406827152 0.000000e+00 1722
10 TraesCS5B01G303500 chr5D 95.606 933 31 8 3340 4269 406826766 406825841 0.000000e+00 1487
11 TraesCS5B01G303500 chr5D 77.778 2007 313 80 992 2921 406953503 406951553 0.000000e+00 1112
12 TraesCS5B01G303500 chr5D 87.591 822 70 9 2518 3326 406897665 406896863 0.000000e+00 924
13 TraesCS5B01G303500 chr5D 98.621 290 3 1 224 513 406830139 406829851 2.940000e-141 512
14 TraesCS5B01G303500 chr5D 80.500 200 34 5 2027 2222 406897958 406897760 9.560000e-32 148
15 TraesCS5B01G303500 chr5D 84.298 121 14 3 2232 2348 406897789 406897670 3.490000e-21 113
16 TraesCS5B01G303500 chr6B 89.098 266 27 2 3341 3605 367380935 367380671 3.180000e-86 329


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 TraesCS5B01G303500 chr5B 487830188 487834456 4268 True 3559.0 6089 100.000000 1 4269 2 chr5B.!!$R2 4268
1 TraesCS5B01G303500 chr5B 487918838 487920046 1208 True 732.0 732 78.240000 992 2206 1 chr5B.!!$R1 1214
2 TraesCS5B01G303500 chr5A 512419392 512423469 4077 True 1492.5 3978 95.474500 233 4269 4 chr5A.!!$R2 4036
3 TraesCS5B01G303500 chr5A 512452333 512454265 1932 True 880.0 880 75.859000 992 2921 1 chr5A.!!$R1 1929
4 TraesCS5B01G303500 chr5D 406825841 406830139 4298 True 1411.0 1923 96.859750 224 4269 4 chr5D.!!$R2 4045
5 TraesCS5B01G303500 chr5D 406951553 406953503 1950 True 1112.0 1112 77.778000 992 2921 1 chr5D.!!$R1 1929
6 TraesCS5B01G303500 chr5D 406896863 406897958 1095 True 395.0 924 84.129667 2027 3326 3 chr5D.!!$R3 1299

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
59 60 0.035458 GCTAGTGAGGTGCAGTGGTT 59.965 55.0 0.00 0.0 31.55 3.67 F
83 84 0.094730 CGGCAACTGCTTTAGCGTAC 59.905 55.0 1.06 0.0 45.83 3.67 F
139 140 0.112412 ACCGCTCTGTCCCCATTTTT 59.888 50.0 0.00 0.0 0.00 1.94 F
476 479 0.178981 ATGATCCCGCCCTCCATTTG 60.179 55.0 0.00 0.0 0.00 2.32 F
1542 1568 0.320247 AACAGCTTGAGCAGGAGACG 60.320 55.0 5.70 0.0 45.16 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 1971 0.108138 ACATTCGCCCTTCTCCTTCG 60.108 55.000 0.00 0.0 0.00 3.79 R
1953 2003 6.365970 TCATCAATTATAGGCCTTCTCCTC 57.634 41.667 12.58 0.0 37.66 3.71 R
2121 2175 1.202806 CCTTGCACCAGAGGTTCAGAA 60.203 52.381 0.00 0.0 29.63 3.02 R
2430 2541 1.491668 GGGTTTCAAAAGGGGTGTGT 58.508 50.000 0.00 0.0 0.00 3.72 R
3332 3514 0.242017 CAAGGTGCAAGTGCTTAGGC 59.758 55.000 4.69 0.0 42.66 3.93 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.238583 AGGGTCTAATTGTGTTCTCTTTCG 58.761 41.667 0.00 0.00 0.00 3.46
24 25 4.142881 GGGTCTAATTGTGTTCTCTTTCGC 60.143 45.833 0.00 0.00 0.00 4.70
25 26 4.451096 GGTCTAATTGTGTTCTCTTTCGCA 59.549 41.667 0.00 0.00 0.00 5.10
26 27 5.122396 GGTCTAATTGTGTTCTCTTTCGCAT 59.878 40.000 0.00 0.00 0.00 4.73
27 28 6.348540 GGTCTAATTGTGTTCTCTTTCGCATT 60.349 38.462 0.00 0.00 0.00 3.56
28 29 6.521133 GTCTAATTGTGTTCTCTTTCGCATTG 59.479 38.462 0.00 0.00 0.00 2.82
29 30 5.437289 AATTGTGTTCTCTTTCGCATTGA 57.563 34.783 0.00 0.00 0.00 2.57
30 31 5.633830 ATTGTGTTCTCTTTCGCATTGAT 57.366 34.783 0.00 0.00 0.00 2.57
31 32 6.741992 ATTGTGTTCTCTTTCGCATTGATA 57.258 33.333 0.00 0.00 0.00 2.15
32 33 6.552859 TTGTGTTCTCTTTCGCATTGATAA 57.447 33.333 0.00 0.00 0.00 1.75
33 34 5.927030 TGTGTTCTCTTTCGCATTGATAAC 58.073 37.500 0.00 0.00 0.00 1.89
34 35 5.468409 TGTGTTCTCTTTCGCATTGATAACA 59.532 36.000 0.00 0.00 0.00 2.41
35 36 6.149308 TGTGTTCTCTTTCGCATTGATAACAT 59.851 34.615 0.00 0.00 32.38 2.71
36 37 6.684555 GTGTTCTCTTTCGCATTGATAACATC 59.315 38.462 0.00 0.00 32.38 3.06
37 38 6.595326 TGTTCTCTTTCGCATTGATAACATCT 59.405 34.615 0.00 0.00 0.00 2.90
38 39 7.763985 TGTTCTCTTTCGCATTGATAACATCTA 59.236 33.333 0.00 0.00 0.00 1.98
39 40 8.604035 GTTCTCTTTCGCATTGATAACATCTAA 58.396 33.333 0.00 0.00 0.00 2.10
40 41 8.357796 TCTCTTTCGCATTGATAACATCTAAG 57.642 34.615 0.00 0.00 0.00 2.18
41 42 6.948353 TCTTTCGCATTGATAACATCTAAGC 58.052 36.000 0.00 0.00 0.00 3.09
42 43 6.763135 TCTTTCGCATTGATAACATCTAAGCT 59.237 34.615 0.00 0.00 0.00 3.74
43 44 7.926018 TCTTTCGCATTGATAACATCTAAGCTA 59.074 33.333 0.00 0.00 0.00 3.32
44 45 7.643528 TTCGCATTGATAACATCTAAGCTAG 57.356 36.000 0.00 0.00 0.00 3.42
45 46 6.749139 TCGCATTGATAACATCTAAGCTAGT 58.251 36.000 0.00 0.00 0.00 2.57
46 47 6.642540 TCGCATTGATAACATCTAAGCTAGTG 59.357 38.462 0.00 0.00 0.00 2.74
47 48 6.642540 CGCATTGATAACATCTAAGCTAGTGA 59.357 38.462 0.00 0.00 0.00 3.41
48 49 7.148836 CGCATTGATAACATCTAAGCTAGTGAG 60.149 40.741 0.00 0.00 0.00 3.51
49 50 7.117523 GCATTGATAACATCTAAGCTAGTGAGG 59.882 40.741 0.00 0.00 0.00 3.86
50 51 7.661536 TTGATAACATCTAAGCTAGTGAGGT 57.338 36.000 0.00 0.00 33.85 3.85
51 52 7.043961 TGATAACATCTAAGCTAGTGAGGTG 57.956 40.000 0.00 0.00 32.39 4.00
52 53 3.810310 ACATCTAAGCTAGTGAGGTGC 57.190 47.619 0.00 0.00 32.39 5.01
53 54 3.099905 ACATCTAAGCTAGTGAGGTGCA 58.900 45.455 0.00 0.00 32.39 4.57
54 55 3.131933 ACATCTAAGCTAGTGAGGTGCAG 59.868 47.826 0.00 0.00 32.39 4.41
55 56 2.808919 TCTAAGCTAGTGAGGTGCAGT 58.191 47.619 0.00 0.00 32.39 4.40
56 57 2.493675 TCTAAGCTAGTGAGGTGCAGTG 59.506 50.000 0.00 0.00 32.39 3.66
57 58 0.322975 AAGCTAGTGAGGTGCAGTGG 59.677 55.000 0.00 0.00 32.39 4.00
58 59 0.833834 AGCTAGTGAGGTGCAGTGGT 60.834 55.000 0.00 0.00 31.55 4.16
59 60 0.035458 GCTAGTGAGGTGCAGTGGTT 59.965 55.000 0.00 0.00 31.55 3.67
60 61 1.275291 GCTAGTGAGGTGCAGTGGTTA 59.725 52.381 0.00 0.00 31.55 2.85
61 62 2.093447 GCTAGTGAGGTGCAGTGGTTAT 60.093 50.000 0.00 0.00 31.55 1.89
62 63 3.619979 GCTAGTGAGGTGCAGTGGTTATT 60.620 47.826 0.00 0.00 31.55 1.40
63 64 2.783135 AGTGAGGTGCAGTGGTTATTG 58.217 47.619 0.00 0.00 0.00 1.90
64 65 1.200020 GTGAGGTGCAGTGGTTATTGC 59.800 52.381 0.00 0.00 39.72 3.56
65 66 0.447801 GAGGTGCAGTGGTTATTGCG 59.552 55.000 0.00 0.00 41.94 4.85
66 67 0.960364 AGGTGCAGTGGTTATTGCGG 60.960 55.000 0.00 0.00 41.94 5.69
67 68 1.154035 GTGCAGTGGTTATTGCGGC 60.154 57.895 0.00 0.00 41.94 6.53
68 69 1.602041 TGCAGTGGTTATTGCGGCA 60.602 52.632 0.00 0.00 41.94 5.69
69 70 1.175347 TGCAGTGGTTATTGCGGCAA 61.175 50.000 18.85 18.85 41.94 4.52
70 71 0.732538 GCAGTGGTTATTGCGGCAAC 60.733 55.000 18.94 6.12 29.62 4.17
71 72 0.881118 CAGTGGTTATTGCGGCAACT 59.119 50.000 18.94 7.27 0.00 3.16
72 73 0.881118 AGTGGTTATTGCGGCAACTG 59.119 50.000 18.94 0.00 0.00 3.16
73 74 0.732538 GTGGTTATTGCGGCAACTGC 60.733 55.000 18.94 10.28 41.14 4.40
74 75 0.893270 TGGTTATTGCGGCAACTGCT 60.893 50.000 18.94 4.56 41.70 4.24
75 76 0.243636 GGTTATTGCGGCAACTGCTT 59.756 50.000 18.94 4.15 41.70 3.91
76 77 1.336795 GGTTATTGCGGCAACTGCTTT 60.337 47.619 18.94 3.35 41.70 3.51
77 78 2.094957 GGTTATTGCGGCAACTGCTTTA 60.095 45.455 18.94 2.27 41.70 1.85
78 79 3.171277 GTTATTGCGGCAACTGCTTTAG 58.829 45.455 18.94 0.00 41.70 1.85
79 80 0.109132 ATTGCGGCAACTGCTTTAGC 60.109 50.000 18.94 0.00 41.70 3.09
80 81 2.202349 GCGGCAACTGCTTTAGCG 60.202 61.111 1.06 0.00 45.83 4.26
81 82 2.966309 GCGGCAACTGCTTTAGCGT 61.966 57.895 1.06 0.00 45.83 5.07
82 83 1.632046 GCGGCAACTGCTTTAGCGTA 61.632 55.000 1.06 0.00 45.83 4.42
83 84 0.094730 CGGCAACTGCTTTAGCGTAC 59.905 55.000 1.06 0.00 45.83 3.67
84 85 1.153353 GGCAACTGCTTTAGCGTACA 58.847 50.000 1.06 0.00 45.83 2.90
85 86 1.136057 GGCAACTGCTTTAGCGTACAC 60.136 52.381 1.06 0.00 45.83 2.90
86 87 1.529438 GCAACTGCTTTAGCGTACACA 59.471 47.619 0.00 0.00 45.83 3.72
87 88 2.159627 GCAACTGCTTTAGCGTACACAT 59.840 45.455 0.00 0.00 45.83 3.21
88 89 3.736213 CAACTGCTTTAGCGTACACATG 58.264 45.455 0.00 0.00 45.83 3.21
89 90 1.732259 ACTGCTTTAGCGTACACATGC 59.268 47.619 0.00 0.00 45.83 4.06
91 92 2.416547 CTGCTTTAGCGTACACATGCTT 59.583 45.455 0.00 0.00 44.94 3.91
92 93 2.159430 TGCTTTAGCGTACACATGCTTG 59.841 45.455 0.00 0.00 44.94 4.01
93 94 2.159627 GCTTTAGCGTACACATGCTTGT 59.840 45.455 0.00 0.00 44.94 3.16
94 95 3.364964 GCTTTAGCGTACACATGCTTGTT 60.365 43.478 1.83 0.00 44.94 2.83
95 96 4.394795 CTTTAGCGTACACATGCTTGTTC 58.605 43.478 1.83 0.00 44.94 3.18
96 97 1.877637 AGCGTACACATGCTTGTTCA 58.122 45.000 1.83 0.00 44.94 3.18
97 98 2.217750 AGCGTACACATGCTTGTTCAA 58.782 42.857 1.83 0.00 44.94 2.69
98 99 2.813754 AGCGTACACATGCTTGTTCAAT 59.186 40.909 1.83 0.00 44.94 2.57
99 100 3.253188 AGCGTACACATGCTTGTTCAATT 59.747 39.130 1.83 0.00 44.94 2.32
100 101 3.603770 GCGTACACATGCTTGTTCAATTC 59.396 43.478 1.83 0.00 32.34 2.17
101 102 4.158384 CGTACACATGCTTGTTCAATTCC 58.842 43.478 1.83 0.00 32.34 3.01
102 103 3.665745 ACACATGCTTGTTCAATTCCC 57.334 42.857 1.83 0.00 32.34 3.97
103 104 2.964464 ACACATGCTTGTTCAATTCCCA 59.036 40.909 1.83 0.00 32.34 4.37
104 105 3.243839 ACACATGCTTGTTCAATTCCCAC 60.244 43.478 1.83 0.00 32.34 4.61
105 106 3.006110 CACATGCTTGTTCAATTCCCACT 59.994 43.478 1.83 0.00 32.34 4.00
106 107 4.218200 CACATGCTTGTTCAATTCCCACTA 59.782 41.667 1.83 0.00 32.34 2.74
107 108 4.218417 ACATGCTTGTTCAATTCCCACTAC 59.782 41.667 0.00 0.00 29.55 2.73
108 109 4.098914 TGCTTGTTCAATTCCCACTACT 57.901 40.909 0.00 0.00 0.00 2.57
109 110 4.072131 TGCTTGTTCAATTCCCACTACTC 58.928 43.478 0.00 0.00 0.00 2.59
110 111 3.125316 GCTTGTTCAATTCCCACTACTCG 59.875 47.826 0.00 0.00 0.00 4.18
111 112 2.695359 TGTTCAATTCCCACTACTCGC 58.305 47.619 0.00 0.00 0.00 5.03
112 113 2.037902 TGTTCAATTCCCACTACTCGCA 59.962 45.455 0.00 0.00 0.00 5.10
113 114 3.071479 GTTCAATTCCCACTACTCGCAA 58.929 45.455 0.00 0.00 0.00 4.85
114 115 3.410631 TCAATTCCCACTACTCGCAAA 57.589 42.857 0.00 0.00 0.00 3.68
115 116 3.745799 TCAATTCCCACTACTCGCAAAA 58.254 40.909 0.00 0.00 0.00 2.44
116 117 4.331968 TCAATTCCCACTACTCGCAAAAT 58.668 39.130 0.00 0.00 0.00 1.82
117 118 5.492895 TCAATTCCCACTACTCGCAAAATA 58.507 37.500 0.00 0.00 0.00 1.40
118 119 5.353123 TCAATTCCCACTACTCGCAAAATAC 59.647 40.000 0.00 0.00 0.00 1.89
119 120 4.546829 TTCCCACTACTCGCAAAATACT 57.453 40.909 0.00 0.00 0.00 2.12
120 121 5.664294 TTCCCACTACTCGCAAAATACTA 57.336 39.130 0.00 0.00 0.00 1.82
121 122 5.002464 TCCCACTACTCGCAAAATACTAC 57.998 43.478 0.00 0.00 0.00 2.73
122 123 4.117685 CCCACTACTCGCAAAATACTACC 58.882 47.826 0.00 0.00 0.00 3.18
123 124 3.795101 CCACTACTCGCAAAATACTACCG 59.205 47.826 0.00 0.00 0.00 4.02
124 125 3.242248 CACTACTCGCAAAATACTACCGC 59.758 47.826 0.00 0.00 0.00 5.68
125 126 2.667473 ACTCGCAAAATACTACCGCT 57.333 45.000 0.00 0.00 0.00 5.52
126 127 2.537401 ACTCGCAAAATACTACCGCTC 58.463 47.619 0.00 0.00 0.00 5.03
127 128 2.165845 ACTCGCAAAATACTACCGCTCT 59.834 45.455 0.00 0.00 0.00 4.09
128 129 2.535984 CTCGCAAAATACTACCGCTCTG 59.464 50.000 0.00 0.00 0.00 3.35
129 130 2.094390 TCGCAAAATACTACCGCTCTGT 60.094 45.455 0.00 0.00 0.00 3.41
130 131 2.281762 CGCAAAATACTACCGCTCTGTC 59.718 50.000 0.00 0.00 0.00 3.51
131 132 2.608090 GCAAAATACTACCGCTCTGTCC 59.392 50.000 0.00 0.00 0.00 4.02
132 133 3.195661 CAAAATACTACCGCTCTGTCCC 58.804 50.000 0.00 0.00 0.00 4.46
133 134 1.411041 AATACTACCGCTCTGTCCCC 58.589 55.000 0.00 0.00 0.00 4.81
134 135 0.260816 ATACTACCGCTCTGTCCCCA 59.739 55.000 0.00 0.00 0.00 4.96
135 136 0.260816 TACTACCGCTCTGTCCCCAT 59.739 55.000 0.00 0.00 0.00 4.00
136 137 0.617820 ACTACCGCTCTGTCCCCATT 60.618 55.000 0.00 0.00 0.00 3.16
137 138 0.541863 CTACCGCTCTGTCCCCATTT 59.458 55.000 0.00 0.00 0.00 2.32
138 139 0.988832 TACCGCTCTGTCCCCATTTT 59.011 50.000 0.00 0.00 0.00 1.82
139 140 0.112412 ACCGCTCTGTCCCCATTTTT 59.888 50.000 0.00 0.00 0.00 1.94
158 159 1.083489 TTTTTACCGAGCGATGCTGG 58.917 50.000 0.00 0.99 39.88 4.85
175 176 2.595655 GGCCGGCCCATTACTTCT 59.404 61.111 36.64 0.00 0.00 2.85
176 177 1.076995 GGCCGGCCCATTACTTCTT 60.077 57.895 36.64 0.00 0.00 2.52
177 178 1.384222 GGCCGGCCCATTACTTCTTG 61.384 60.000 36.64 0.00 0.00 3.02
178 179 2.004808 GCCGGCCCATTACTTCTTGC 62.005 60.000 18.11 0.00 0.00 4.01
179 180 1.384222 CCGGCCCATTACTTCTTGCC 61.384 60.000 0.00 0.00 35.55 4.52
180 181 0.394352 CGGCCCATTACTTCTTGCCT 60.394 55.000 0.00 0.00 36.74 4.75
181 182 1.852633 GGCCCATTACTTCTTGCCTT 58.147 50.000 0.00 0.00 35.99 4.35
182 183 1.751351 GGCCCATTACTTCTTGCCTTC 59.249 52.381 0.00 0.00 35.99 3.46
183 184 1.401905 GCCCATTACTTCTTGCCTTCG 59.598 52.381 0.00 0.00 0.00 3.79
184 185 2.939640 GCCCATTACTTCTTGCCTTCGA 60.940 50.000 0.00 0.00 0.00 3.71
185 186 2.939103 CCCATTACTTCTTGCCTTCGAG 59.061 50.000 0.00 0.00 0.00 4.04
186 187 2.352960 CCATTACTTCTTGCCTTCGAGC 59.647 50.000 0.00 0.00 0.00 5.03
187 188 1.710013 TTACTTCTTGCCTTCGAGCG 58.290 50.000 0.00 0.00 34.65 5.03
188 189 0.736325 TACTTCTTGCCTTCGAGCGC 60.736 55.000 0.00 0.00 34.65 5.92
189 190 2.742372 TTCTTGCCTTCGAGCGCC 60.742 61.111 2.29 0.00 34.65 6.53
190 191 3.529341 TTCTTGCCTTCGAGCGCCA 62.529 57.895 2.29 0.00 34.65 5.69
191 192 3.494336 CTTGCCTTCGAGCGCCAG 61.494 66.667 2.29 0.00 34.65 4.85
192 193 3.939837 CTTGCCTTCGAGCGCCAGA 62.940 63.158 2.29 0.00 34.65 3.86
193 194 3.315142 TTGCCTTCGAGCGCCAGAT 62.315 57.895 2.29 0.00 34.65 2.90
194 195 3.267860 GCCTTCGAGCGCCAGATG 61.268 66.667 2.29 6.20 0.00 2.90
195 196 2.587194 CCTTCGAGCGCCAGATGG 60.587 66.667 16.40 16.40 38.53 3.51
205 206 4.587056 CCAGATGGCTTAAGGGGC 57.413 61.111 4.29 0.00 0.00 5.80
206 207 1.526917 CCAGATGGCTTAAGGGGCG 60.527 63.158 4.29 0.00 34.31 6.13
207 208 2.189499 CAGATGGCTTAAGGGGCGC 61.189 63.158 0.00 0.00 34.31 6.53
208 209 2.907407 GATGGCTTAAGGGGCGCC 60.907 66.667 21.18 21.18 44.02 6.53
209 210 4.875713 ATGGCTTAAGGGGCGCCG 62.876 66.667 22.54 6.34 46.67 6.46
211 212 4.789123 GGCTTAAGGGGCGCCGAA 62.789 66.667 22.54 10.84 33.64 4.30
212 213 3.202706 GCTTAAGGGGCGCCGAAG 61.203 66.667 22.54 24.35 0.00 3.79
213 214 2.582436 CTTAAGGGGCGCCGAAGA 59.418 61.111 22.54 2.46 0.00 2.87
214 215 1.521681 CTTAAGGGGCGCCGAAGAG 60.522 63.158 22.54 10.63 0.00 2.85
215 216 2.925162 CTTAAGGGGCGCCGAAGAGG 62.925 65.000 22.54 5.46 44.97 3.69
216 217 3.968837 TAAGGGGCGCCGAAGAGGA 62.969 63.158 22.54 0.00 45.00 3.71
319 320 3.454375 GTCCGATGAAAAAGGCGAGATA 58.546 45.455 0.00 0.00 0.00 1.98
396 398 5.447144 GCAAAATAATCCCGCCAAAATTGAC 60.447 40.000 0.00 0.00 0.00 3.18
476 479 0.178981 ATGATCCCGCCCTCCATTTG 60.179 55.000 0.00 0.00 0.00 2.32
535 538 2.521708 CAATCCAATCCCGCCCCC 60.522 66.667 0.00 0.00 0.00 5.40
547 550 2.888447 CGCCCCCATCTCATCTCCC 61.888 68.421 0.00 0.00 0.00 4.30
1122 1128 3.885521 GACGTCCCCTCCTACGCG 61.886 72.222 3.53 3.53 42.74 6.01
1155 1161 4.864334 CCAGAGGTGCCCATCGCC 62.864 72.222 0.00 0.00 45.76 5.54
1464 1479 4.130118 GGTATGTGATGATCACCCTTGAC 58.870 47.826 21.68 11.98 46.40 3.18
1529 1552 1.353694 AGGATTTGAGCCTGAACAGCT 59.646 47.619 0.00 0.00 45.23 4.24
1542 1568 0.320247 AACAGCTTGAGCAGGAGACG 60.320 55.000 5.70 0.00 45.16 4.18
1574 1600 5.049818 CGTTTCCTGAGGATATCATTTCTGC 60.050 44.000 0.04 0.00 37.28 4.26
1910 1957 0.393537 CCATCTCCACCACCTCAAGC 60.394 60.000 0.00 0.00 0.00 4.01
1924 1971 1.537202 CTCAAGCACAAGGTAACAGGC 59.463 52.381 0.00 0.00 41.41 4.85
1953 2003 1.482593 AGGGCGAATGTACAGGAGAAG 59.517 52.381 0.33 0.00 0.00 2.85
2118 2172 4.130570 GGATAAGCCAAAAGGACAGCCTT 61.131 47.826 0.00 0.00 46.37 4.35
2232 2286 1.196808 GCCGATGTTGTGAATGTTCGT 59.803 47.619 0.00 0.00 0.00 3.85
2253 2322 1.524165 CTCTGATGCTCAGCCTGCC 60.524 63.158 0.00 0.00 43.95 4.85
2264 2333 2.515523 GCCTGCCGATGCTGTGAT 60.516 61.111 0.00 0.00 38.71 3.06
2430 2541 9.349713 GATCTATCTCCAGTAAGAGAAGAAGAA 57.650 37.037 0.00 0.00 45.70 2.52
2468 2600 1.374252 CTGGTCGAAGTGGAACCCG 60.374 63.158 0.00 0.00 37.80 5.28
2522 2660 4.513692 TGTACCACTAACACATTGCAGTTC 59.486 41.667 0.00 0.00 0.00 3.01
2922 3091 1.454276 TCGAGCGCTAAACTTTGAACG 59.546 47.619 11.50 5.56 0.00 3.95
3013 3183 8.202137 TCCTGGTTTAGAATAGTGCTATGTTAC 58.798 37.037 0.00 0.00 0.00 2.50
3322 3504 3.317711 TCAATTTGATTGCTGACACCGTT 59.682 39.130 0.00 0.00 40.05 4.44
3326 3508 0.798776 GATTGCTGACACCGTTCAGG 59.201 55.000 7.74 0.00 42.95 3.86
3338 3520 3.166489 CCGTTCAGGTTAGAGCCTAAG 57.834 52.381 0.00 0.00 37.04 2.18
3370 3926 7.575365 CACCTTGCCTTCATGTTTTAAATTTC 58.425 34.615 0.00 0.00 0.00 2.17
3425 3981 7.559897 AGGAACTTTTATTTGTTTCTCACCTGA 59.440 33.333 0.00 0.00 27.25 3.86
3590 4146 3.696051 TGCCTAAATCTTGCAATGGAGAC 59.304 43.478 0.00 0.00 30.85 3.36
3616 4172 6.655425 AGTGTTAAGAATAGGGCTGAAGTTTC 59.345 38.462 0.00 0.00 0.00 2.78
3649 4205 5.469084 GTCTGTCCAGTTAAGGTACCAAAAG 59.531 44.000 15.94 4.50 0.00 2.27
3716 4272 3.879998 TGTTGCTCACCTGAAAGTTACA 58.120 40.909 0.00 0.00 0.00 2.41
3856 4412 9.019764 GTTTACGCATAATGCATCTTATTGTTT 57.980 29.630 0.00 0.00 45.36 2.83
3897 4453 0.325296 ATGGTCTTACGCCAGGGAGA 60.325 55.000 0.00 0.00 39.65 3.71
3901 4457 0.687757 TCTTACGCCAGGGAGAGCAT 60.688 55.000 0.00 0.00 0.00 3.79
4039 4627 5.534654 CAGGACCAAAGGTTAGTGATTTTGA 59.465 40.000 0.00 0.00 35.25 2.69
4088 4678 8.117988 GCAATGCATGTTTATTTTGGTTAGATG 58.882 33.333 0.00 0.00 0.00 2.90
4131 4722 8.093927 TCAGTCATATTCACATTCACAGTGTTA 58.906 33.333 0.00 0.00 38.16 2.41
4200 4792 5.336150 TGAAGGAGAGATCTGTTGATGTC 57.664 43.478 0.00 0.00 41.61 3.06
4205 4797 4.161189 GGAGAGATCTGTTGATGTCCAAGA 59.839 45.833 0.00 0.00 42.07 3.02
4216 4808 6.828273 TGTTGATGTCCAAGATAGGTTAATGG 59.172 38.462 0.00 0.00 35.03 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.238583 CGAAAGAGAACACAATTAGACCCT 58.761 41.667 0.00 0.00 0.00 4.34
1 2 4.142881 GCGAAAGAGAACACAATTAGACCC 60.143 45.833 0.00 0.00 0.00 4.46
2 3 4.451096 TGCGAAAGAGAACACAATTAGACC 59.549 41.667 0.00 0.00 0.00 3.85
4 5 6.426633 TCAATGCGAAAGAGAACACAATTAGA 59.573 34.615 0.00 0.00 0.00 2.10
5 6 6.602179 TCAATGCGAAAGAGAACACAATTAG 58.398 36.000 0.00 0.00 0.00 1.73
6 7 6.552859 TCAATGCGAAAGAGAACACAATTA 57.447 33.333 0.00 0.00 0.00 1.40
7 8 5.437289 TCAATGCGAAAGAGAACACAATT 57.563 34.783 0.00 0.00 0.00 2.32
9 10 6.017523 TGTTATCAATGCGAAAGAGAACACAA 60.018 34.615 5.57 0.00 38.22 3.33
10 11 5.468409 TGTTATCAATGCGAAAGAGAACACA 59.532 36.000 5.57 0.00 38.22 3.72
11 12 5.927030 TGTTATCAATGCGAAAGAGAACAC 58.073 37.500 5.57 0.00 38.22 3.32
12 13 6.595326 AGATGTTATCAATGCGAAAGAGAACA 59.405 34.615 10.62 10.62 44.41 3.18
13 14 7.009568 AGATGTTATCAATGCGAAAGAGAAC 57.990 36.000 1.02 1.02 34.90 3.01
14 15 8.716646 TTAGATGTTATCAATGCGAAAGAGAA 57.283 30.769 0.00 0.00 0.00 2.87
15 16 7.042456 GCTTAGATGTTATCAATGCGAAAGAGA 60.042 37.037 0.00 0.00 0.00 3.10
16 17 7.042187 AGCTTAGATGTTATCAATGCGAAAGAG 60.042 37.037 0.00 0.00 0.00 2.85
17 18 6.763135 AGCTTAGATGTTATCAATGCGAAAGA 59.237 34.615 0.00 0.00 0.00 2.52
18 19 6.952743 AGCTTAGATGTTATCAATGCGAAAG 58.047 36.000 0.00 0.00 0.00 2.62
19 20 6.925610 AGCTTAGATGTTATCAATGCGAAA 57.074 33.333 0.00 0.00 0.00 3.46
20 21 7.169813 CACTAGCTTAGATGTTATCAATGCGAA 59.830 37.037 0.00 0.00 0.00 4.70
21 22 6.642540 CACTAGCTTAGATGTTATCAATGCGA 59.357 38.462 0.00 0.00 0.00 5.10
22 23 6.642540 TCACTAGCTTAGATGTTATCAATGCG 59.357 38.462 0.00 0.00 0.00 4.73
23 24 7.117523 CCTCACTAGCTTAGATGTTATCAATGC 59.882 40.741 0.00 0.00 0.00 3.56
24 25 8.147058 ACCTCACTAGCTTAGATGTTATCAATG 58.853 37.037 0.00 0.00 0.00 2.82
25 26 8.147058 CACCTCACTAGCTTAGATGTTATCAAT 58.853 37.037 0.00 0.00 0.00 2.57
26 27 7.492524 CACCTCACTAGCTTAGATGTTATCAA 58.507 38.462 0.00 0.00 0.00 2.57
27 28 6.461648 GCACCTCACTAGCTTAGATGTTATCA 60.462 42.308 0.00 0.00 0.00 2.15
28 29 5.923684 GCACCTCACTAGCTTAGATGTTATC 59.076 44.000 0.00 0.00 0.00 1.75
29 30 5.363868 TGCACCTCACTAGCTTAGATGTTAT 59.636 40.000 0.00 0.00 0.00 1.89
30 31 4.709886 TGCACCTCACTAGCTTAGATGTTA 59.290 41.667 0.00 0.00 0.00 2.41
31 32 3.515502 TGCACCTCACTAGCTTAGATGTT 59.484 43.478 0.00 0.00 0.00 2.71
32 33 3.099905 TGCACCTCACTAGCTTAGATGT 58.900 45.455 0.00 0.00 0.00 3.06
33 34 3.131933 ACTGCACCTCACTAGCTTAGATG 59.868 47.826 0.00 0.00 0.00 2.90
34 35 3.131933 CACTGCACCTCACTAGCTTAGAT 59.868 47.826 0.00 0.00 0.00 1.98
35 36 2.493675 CACTGCACCTCACTAGCTTAGA 59.506 50.000 0.00 0.00 0.00 2.10
36 37 2.417924 CCACTGCACCTCACTAGCTTAG 60.418 54.545 0.00 0.00 0.00 2.18
37 38 1.550524 CCACTGCACCTCACTAGCTTA 59.449 52.381 0.00 0.00 0.00 3.09
38 39 0.322975 CCACTGCACCTCACTAGCTT 59.677 55.000 0.00 0.00 0.00 3.74
39 40 0.833834 ACCACTGCACCTCACTAGCT 60.834 55.000 0.00 0.00 0.00 3.32
40 41 0.035458 AACCACTGCACCTCACTAGC 59.965 55.000 0.00 0.00 0.00 3.42
41 42 3.895232 ATAACCACTGCACCTCACTAG 57.105 47.619 0.00 0.00 0.00 2.57
42 43 3.868369 GCAATAACCACTGCACCTCACTA 60.868 47.826 0.00 0.00 38.48 2.74
43 44 2.783135 CAATAACCACTGCACCTCACT 58.217 47.619 0.00 0.00 0.00 3.41
44 45 1.200020 GCAATAACCACTGCACCTCAC 59.800 52.381 0.00 0.00 38.48 3.51
45 46 1.533625 GCAATAACCACTGCACCTCA 58.466 50.000 0.00 0.00 38.48 3.86
46 47 0.447801 CGCAATAACCACTGCACCTC 59.552 55.000 0.00 0.00 38.52 3.85
47 48 0.960364 CCGCAATAACCACTGCACCT 60.960 55.000 0.00 0.00 38.52 4.00
48 49 1.506262 CCGCAATAACCACTGCACC 59.494 57.895 0.00 0.00 38.52 5.01
49 50 1.154035 GCCGCAATAACCACTGCAC 60.154 57.895 0.00 0.00 38.52 4.57
50 51 1.175347 TTGCCGCAATAACCACTGCA 61.175 50.000 0.38 0.00 38.52 4.41
51 52 0.732538 GTTGCCGCAATAACCACTGC 60.733 55.000 9.46 0.00 35.14 4.40
52 53 0.881118 AGTTGCCGCAATAACCACTG 59.119 50.000 9.46 0.00 0.00 3.66
53 54 0.881118 CAGTTGCCGCAATAACCACT 59.119 50.000 9.46 0.00 0.00 4.00
54 55 0.732538 GCAGTTGCCGCAATAACCAC 60.733 55.000 9.46 0.00 34.31 4.16
55 56 0.893270 AGCAGTTGCCGCAATAACCA 60.893 50.000 9.46 0.00 43.38 3.67
56 57 0.243636 AAGCAGTTGCCGCAATAACC 59.756 50.000 9.46 0.00 43.38 2.85
57 58 2.064573 AAAGCAGTTGCCGCAATAAC 57.935 45.000 9.46 0.00 43.38 1.89
58 59 2.415357 GCTAAAGCAGTTGCCGCAATAA 60.415 45.455 9.46 0.00 43.38 1.40
59 60 1.132262 GCTAAAGCAGTTGCCGCAATA 59.868 47.619 9.46 0.00 43.38 1.90
60 61 0.109132 GCTAAAGCAGTTGCCGCAAT 60.109 50.000 9.46 0.00 43.38 3.56
61 62 1.285641 GCTAAAGCAGTTGCCGCAA 59.714 52.632 0.38 0.38 43.38 4.85
62 63 2.953821 GCTAAAGCAGTTGCCGCA 59.046 55.556 0.00 0.00 43.38 5.69
63 64 1.632046 TACGCTAAAGCAGTTGCCGC 61.632 55.000 2.44 0.00 43.38 6.53
64 65 0.094730 GTACGCTAAAGCAGTTGCCG 59.905 55.000 2.44 0.00 43.38 5.69
65 66 1.136057 GTGTACGCTAAAGCAGTTGCC 60.136 52.381 2.44 0.00 43.38 4.52
66 67 1.529438 TGTGTACGCTAAAGCAGTTGC 59.471 47.619 8.10 0.00 42.21 4.17
67 68 3.736213 CATGTGTACGCTAAAGCAGTTG 58.264 45.455 8.10 0.00 42.21 3.16
68 69 2.159627 GCATGTGTACGCTAAAGCAGTT 59.840 45.455 8.10 0.00 42.21 3.16
69 70 1.732259 GCATGTGTACGCTAAAGCAGT 59.268 47.619 8.10 4.05 42.21 4.40
70 71 2.002586 AGCATGTGTACGCTAAAGCAG 58.997 47.619 8.10 0.00 42.21 4.24
71 72 2.093306 AGCATGTGTACGCTAAAGCA 57.907 45.000 8.10 0.00 42.21 3.91
72 73 2.159627 ACAAGCATGTGTACGCTAAAGC 59.840 45.455 8.10 6.44 38.69 3.51
73 74 4.084066 TGAACAAGCATGTGTACGCTAAAG 60.084 41.667 8.10 0.00 40.46 1.85
74 75 3.810386 TGAACAAGCATGTGTACGCTAAA 59.190 39.130 8.10 0.00 40.46 1.85
75 76 3.394719 TGAACAAGCATGTGTACGCTAA 58.605 40.909 8.10 0.00 40.46 3.09
76 77 3.033368 TGAACAAGCATGTGTACGCTA 57.967 42.857 8.10 0.00 40.46 4.26
77 78 1.877637 TGAACAAGCATGTGTACGCT 58.122 45.000 8.10 0.00 40.46 5.07
78 79 2.679355 TTGAACAAGCATGTGTACGC 57.321 45.000 0.00 0.00 40.46 4.42
79 80 4.158384 GGAATTGAACAAGCATGTGTACG 58.842 43.478 0.00 0.00 40.46 3.67
80 81 4.022416 TGGGAATTGAACAAGCATGTGTAC 60.022 41.667 0.00 0.00 40.46 2.90
81 82 4.022416 GTGGGAATTGAACAAGCATGTGTA 60.022 41.667 0.00 0.00 40.46 2.90
82 83 2.964464 TGGGAATTGAACAAGCATGTGT 59.036 40.909 0.00 0.00 40.46 3.72
83 84 3.006110 AGTGGGAATTGAACAAGCATGTG 59.994 43.478 0.00 0.00 40.46 3.21
84 85 3.233507 AGTGGGAATTGAACAAGCATGT 58.766 40.909 0.00 0.00 43.14 3.21
85 86 3.947910 AGTGGGAATTGAACAAGCATG 57.052 42.857 0.00 0.00 0.00 4.06
86 87 4.666512 AGTAGTGGGAATTGAACAAGCAT 58.333 39.130 0.00 0.00 0.00 3.79
87 88 4.072131 GAGTAGTGGGAATTGAACAAGCA 58.928 43.478 0.00 0.00 0.00 3.91
88 89 3.125316 CGAGTAGTGGGAATTGAACAAGC 59.875 47.826 0.00 0.00 0.00 4.01
89 90 3.125316 GCGAGTAGTGGGAATTGAACAAG 59.875 47.826 0.00 0.00 0.00 3.16
90 91 3.071479 GCGAGTAGTGGGAATTGAACAA 58.929 45.455 0.00 0.00 0.00 2.83
91 92 2.037902 TGCGAGTAGTGGGAATTGAACA 59.962 45.455 0.00 0.00 0.00 3.18
92 93 2.695359 TGCGAGTAGTGGGAATTGAAC 58.305 47.619 0.00 0.00 0.00 3.18
93 94 3.410631 TTGCGAGTAGTGGGAATTGAA 57.589 42.857 0.00 0.00 0.00 2.69
94 95 3.410631 TTTGCGAGTAGTGGGAATTGA 57.589 42.857 0.00 0.00 0.00 2.57
95 96 4.701956 ATTTTGCGAGTAGTGGGAATTG 57.298 40.909 0.00 0.00 0.00 2.32
96 97 5.497474 AGTATTTTGCGAGTAGTGGGAATT 58.503 37.500 0.00 0.00 0.00 2.17
97 98 5.099042 AGTATTTTGCGAGTAGTGGGAAT 57.901 39.130 0.00 0.00 0.00 3.01
98 99 4.546829 AGTATTTTGCGAGTAGTGGGAA 57.453 40.909 0.00 0.00 0.00 3.97
99 100 4.142093 GGTAGTATTTTGCGAGTAGTGGGA 60.142 45.833 0.00 0.00 0.00 4.37
100 101 4.117685 GGTAGTATTTTGCGAGTAGTGGG 58.882 47.826 0.00 0.00 0.00 4.61
101 102 3.795101 CGGTAGTATTTTGCGAGTAGTGG 59.205 47.826 0.00 0.00 0.00 4.00
102 103 3.242248 GCGGTAGTATTTTGCGAGTAGTG 59.758 47.826 0.00 0.00 0.00 2.74
103 104 3.129988 AGCGGTAGTATTTTGCGAGTAGT 59.870 43.478 0.00 0.00 0.00 2.73
104 105 3.703420 AGCGGTAGTATTTTGCGAGTAG 58.297 45.455 0.00 0.00 0.00 2.57
105 106 3.379372 AGAGCGGTAGTATTTTGCGAGTA 59.621 43.478 0.00 0.00 0.00 2.59
106 107 2.165845 AGAGCGGTAGTATTTTGCGAGT 59.834 45.455 0.00 0.00 0.00 4.18
107 108 2.535984 CAGAGCGGTAGTATTTTGCGAG 59.464 50.000 0.00 0.00 0.00 5.03
108 109 2.094390 ACAGAGCGGTAGTATTTTGCGA 60.094 45.455 0.00 0.00 0.00 5.10
109 110 2.268298 ACAGAGCGGTAGTATTTTGCG 58.732 47.619 0.00 0.00 0.00 4.85
110 111 2.608090 GGACAGAGCGGTAGTATTTTGC 59.392 50.000 0.00 0.00 0.00 3.68
111 112 3.195661 GGGACAGAGCGGTAGTATTTTG 58.804 50.000 0.00 0.00 0.00 2.44
112 113 2.169978 GGGGACAGAGCGGTAGTATTTT 59.830 50.000 0.00 0.00 0.00 1.82
113 114 1.761198 GGGGACAGAGCGGTAGTATTT 59.239 52.381 0.00 0.00 0.00 1.40
114 115 1.342674 TGGGGACAGAGCGGTAGTATT 60.343 52.381 0.00 0.00 35.01 1.89
115 116 0.260816 TGGGGACAGAGCGGTAGTAT 59.739 55.000 0.00 0.00 35.01 2.12
116 117 1.693034 TGGGGACAGAGCGGTAGTA 59.307 57.895 0.00 0.00 35.01 1.82
117 118 2.443781 TGGGGACAGAGCGGTAGT 59.556 61.111 0.00 0.00 35.01 2.73
139 140 1.083489 CCAGCATCGCTCGGTAAAAA 58.917 50.000 0.00 0.00 36.40 1.94
140 141 0.742990 CCCAGCATCGCTCGGTAAAA 60.743 55.000 0.00 0.00 36.40 1.52
141 142 1.153449 CCCAGCATCGCTCGGTAAA 60.153 57.895 0.00 0.00 36.40 2.01
142 143 2.499205 CCCAGCATCGCTCGGTAA 59.501 61.111 0.00 0.00 36.40 2.85
143 144 4.221422 GCCCAGCATCGCTCGGTA 62.221 66.667 1.58 0.00 39.12 4.02
158 159 1.076995 AAGAAGTAATGGGCCGGCC 60.077 57.895 38.57 38.57 0.00 6.13
159 160 2.004808 GCAAGAAGTAATGGGCCGGC 62.005 60.000 21.18 21.18 0.00 6.13
160 161 1.384222 GGCAAGAAGTAATGGGCCGG 61.384 60.000 0.00 0.00 0.00 6.13
161 162 0.394352 AGGCAAGAAGTAATGGGCCG 60.394 55.000 0.00 0.00 45.79 6.13
162 163 1.751351 GAAGGCAAGAAGTAATGGGCC 59.249 52.381 0.00 0.00 41.65 5.80
163 164 1.401905 CGAAGGCAAGAAGTAATGGGC 59.598 52.381 0.00 0.00 0.00 5.36
164 165 2.939103 CTCGAAGGCAAGAAGTAATGGG 59.061 50.000 0.00 0.00 0.00 4.00
165 166 2.352960 GCTCGAAGGCAAGAAGTAATGG 59.647 50.000 0.00 0.00 0.00 3.16
166 167 2.029728 CGCTCGAAGGCAAGAAGTAATG 59.970 50.000 0.00 0.00 0.00 1.90
167 168 2.271800 CGCTCGAAGGCAAGAAGTAAT 58.728 47.619 0.00 0.00 0.00 1.89
168 169 1.710013 CGCTCGAAGGCAAGAAGTAA 58.290 50.000 0.00 0.00 0.00 2.24
169 170 0.736325 GCGCTCGAAGGCAAGAAGTA 60.736 55.000 0.00 0.00 0.00 2.24
170 171 2.029844 GCGCTCGAAGGCAAGAAGT 61.030 57.895 0.00 0.00 0.00 3.01
171 172 2.744768 GGCGCTCGAAGGCAAGAAG 61.745 63.158 7.64 0.00 0.00 2.85
172 173 2.742372 GGCGCTCGAAGGCAAGAA 60.742 61.111 7.64 0.00 0.00 2.52
173 174 3.939837 CTGGCGCTCGAAGGCAAGA 62.940 63.158 7.64 0.00 43.59 3.02
174 175 3.494336 CTGGCGCTCGAAGGCAAG 61.494 66.667 7.64 7.63 43.59 4.01
175 176 3.315142 ATCTGGCGCTCGAAGGCAA 62.315 57.895 7.64 8.91 43.59 4.52
176 177 3.774528 ATCTGGCGCTCGAAGGCA 61.775 61.111 7.64 14.45 42.00 4.75
177 178 3.267860 CATCTGGCGCTCGAAGGC 61.268 66.667 7.64 7.10 0.00 4.35
178 179 2.587194 CCATCTGGCGCTCGAAGG 60.587 66.667 7.64 6.86 0.00 3.46
188 189 1.526917 CGCCCCTTAAGCCATCTGG 60.527 63.158 0.00 0.00 38.53 3.86
189 190 2.189499 GCGCCCCTTAAGCCATCTG 61.189 63.158 0.00 0.00 0.00 2.90
190 191 2.193248 GCGCCCCTTAAGCCATCT 59.807 61.111 0.00 0.00 0.00 2.90
194 195 4.789123 TTCGGCGCCCCTTAAGCC 62.789 66.667 23.46 0.00 46.88 4.35
195 196 3.202706 CTTCGGCGCCCCTTAAGC 61.203 66.667 23.46 0.00 0.00 3.09
196 197 1.521681 CTCTTCGGCGCCCCTTAAG 60.522 63.158 23.46 18.60 0.00 1.85
197 198 2.582436 CTCTTCGGCGCCCCTTAA 59.418 61.111 23.46 9.42 0.00 1.85
198 199 3.467226 CCTCTTCGGCGCCCCTTA 61.467 66.667 23.46 3.11 0.00 2.69
206 207 4.135153 TGAGCGCTCCTCTTCGGC 62.135 66.667 33.23 7.51 41.35 5.54
207 208 1.938657 TTCTGAGCGCTCCTCTTCGG 61.939 60.000 33.23 14.47 41.35 4.30
208 209 0.109086 TTTCTGAGCGCTCCTCTTCG 60.109 55.000 33.23 14.75 41.35 3.79
209 210 1.639280 CTTTCTGAGCGCTCCTCTTC 58.361 55.000 33.23 10.17 41.35 2.87
210 211 0.390998 GCTTTCTGAGCGCTCCTCTT 60.391 55.000 33.23 0.00 42.46 2.85
211 212 1.217779 GCTTTCTGAGCGCTCCTCT 59.782 57.895 33.23 0.00 42.46 3.69
212 213 3.792904 GCTTTCTGAGCGCTCCTC 58.207 61.111 33.23 11.79 42.46 3.71
220 221 3.971032 AAAAGAACCGTGCTTTCTGAG 57.029 42.857 4.89 0.00 34.68 3.35
221 222 3.442273 ACAAAAAGAACCGTGCTTTCTGA 59.558 39.130 11.66 0.00 34.68 3.27
222 223 3.769536 ACAAAAAGAACCGTGCTTTCTG 58.230 40.909 4.89 4.43 34.68 3.02
272 273 0.400213 ACCAATTTCCTCCTCGCACA 59.600 50.000 0.00 0.00 0.00 4.57
1159 1165 3.474570 GAGATGCCCCGACAGCCT 61.475 66.667 0.00 0.00 0.00 4.58
1464 1479 1.326213 ACTCTGCTCCACCATCCTCG 61.326 60.000 0.00 0.00 0.00 4.63
1529 1552 0.832135 AGGGAACGTCTCCTGCTCAA 60.832 55.000 8.61 0.00 44.68 3.02
1625 1651 4.083802 GGCGCAATATTTCTGGTGTATCTC 60.084 45.833 10.83 0.00 0.00 2.75
1823 1864 5.009010 GCTGGTTCTTCATCTTCTTCAACAA 59.991 40.000 0.00 0.00 0.00 2.83
1910 1957 1.156736 CCTTCGCCTGTTACCTTGTG 58.843 55.000 0.00 0.00 0.00 3.33
1924 1971 0.108138 ACATTCGCCCTTCTCCTTCG 60.108 55.000 0.00 0.00 0.00 3.79
1953 2003 6.365970 TCATCAATTATAGGCCTTCTCCTC 57.634 41.667 12.58 0.00 37.66 3.71
2118 2172 3.011566 TGCACCAGAGGTTCAGAAAAA 57.988 42.857 0.00 0.00 31.02 1.94
2121 2175 1.202806 CCTTGCACCAGAGGTTCAGAA 60.203 52.381 0.00 0.00 29.63 3.02
2253 2322 1.726248 TCACGAACAATCACAGCATCG 59.274 47.619 0.00 0.00 36.45 3.84
2264 2333 1.601903 GTGCATCCTTGTCACGAACAA 59.398 47.619 0.00 7.66 45.60 2.83
2430 2541 1.491668 GGGTTTCAAAAGGGGTGTGT 58.508 50.000 0.00 0.00 0.00 3.72
2468 2600 2.266055 CTCCAAGTCCAGACCGCC 59.734 66.667 0.00 0.00 0.00 6.13
2545 2683 5.203528 ACCGAATGGGAAATGAGATTCAAT 58.796 37.500 0.00 0.00 40.75 2.57
2554 2692 2.607635 CGTCAGTACCGAATGGGAAATG 59.392 50.000 0.00 0.00 40.75 2.32
2922 3091 4.073293 TGAACTGAAGGGAAACAGAGTC 57.927 45.455 0.00 0.00 37.54 3.36
3013 3183 4.184629 ACACGAAGCTTAGAAGGCATAAG 58.815 43.478 13.94 0.00 34.09 1.73
3322 3504 2.821437 AGTGCTTAGGCTCTAACCTGA 58.179 47.619 0.00 0.00 41.34 3.86
3326 3508 2.416893 GTGCAAGTGCTTAGGCTCTAAC 59.583 50.000 4.69 0.00 40.78 2.34
3327 3509 2.615493 GGTGCAAGTGCTTAGGCTCTAA 60.615 50.000 4.69 0.00 40.78 2.10
3328 3510 1.066143 GGTGCAAGTGCTTAGGCTCTA 60.066 52.381 4.69 0.00 40.78 2.43
3329 3511 0.322008 GGTGCAAGTGCTTAGGCTCT 60.322 55.000 4.69 0.00 43.06 4.09
3330 3512 0.322008 AGGTGCAAGTGCTTAGGCTC 60.322 55.000 4.69 0.00 42.66 4.70
3332 3514 0.242017 CAAGGTGCAAGTGCTTAGGC 59.758 55.000 4.69 0.00 42.66 3.93
3333 3515 0.242017 GCAAGGTGCAAGTGCTTAGG 59.758 55.000 4.69 0.00 44.26 2.69
3334 3516 3.780925 GCAAGGTGCAAGTGCTTAG 57.219 52.632 4.69 0.00 44.26 2.18
3370 3926 1.885887 TGGCTTTTTCTTGGTGGATCG 59.114 47.619 0.00 0.00 0.00 3.69
3590 4146 5.491982 ACTTCAGCCCTATTCTTAACACTG 58.508 41.667 0.00 0.00 0.00 3.66
3616 4172 2.867109 ACTGGACAGACATCAAAGGG 57.133 50.000 6.29 0.00 0.00 3.95
3620 4176 4.974645 ACCTTAACTGGACAGACATCAA 57.025 40.909 6.29 0.00 0.00 2.57
3649 4205 4.498177 GGCTTGTTCTTGGAGAGTGAAAAC 60.498 45.833 0.00 0.00 0.00 2.43
3856 4412 6.294453 CCATTCAGTAAGGTGCATGTAAACAA 60.294 38.462 0.00 0.00 0.00 2.83
3897 4453 0.798776 GTAGCTTGTTGTGCGATGCT 59.201 50.000 0.00 0.00 35.28 3.79
3901 4457 0.105964 AGGTGTAGCTTGTTGTGCGA 59.894 50.000 0.00 0.00 35.28 5.10
3934 4522 8.890472 GGGGCCCAGATATCACATATATTTATA 58.110 37.037 26.86 0.00 0.00 0.98
4039 4627 5.298777 GCTCAATCCTGAAGCTAACATTGAT 59.701 40.000 0.00 0.00 0.00 2.57
4088 4678 5.001232 TGACTGAATTAGCACACCTAAACC 58.999 41.667 0.00 0.00 39.36 3.27
4094 4685 6.316140 TGTGAATATGACTGAATTAGCACACC 59.684 38.462 0.00 0.00 0.00 4.16
4131 4722 8.526147 GGCATAAATAAGACTTGGCATCATATT 58.474 33.333 0.00 0.00 33.49 1.28
4200 4792 7.283329 AGAAGCTAACCATTAACCTATCTTGG 58.717 38.462 0.00 0.00 0.00 3.61
4205 4797 7.092399 ACCTTGAGAAGCTAACCATTAACCTAT 60.092 37.037 0.00 0.00 0.00 2.57
4216 4808 3.748568 CAGGTGAACCTTGAGAAGCTAAC 59.251 47.826 0.00 0.00 46.09 2.34


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

AutoCloner maintained by Alex Coulton.