Multiple sequence alignment - TraesCS3B01G112200

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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 TraesCS3B01G112200 chr3B 100.000 2774 0 0 1 2774 78524392 78521619 0.000000e+00 5123
1 TraesCS3B01G112200 chr3B 88.350 103 9 2 1981 2082 778627432 778627332 1.350000e-23 121
2 TraesCS3B01G112200 chr3D 94.695 1018 26 11 1548 2550 48870226 48869222 0.000000e+00 1555
3 TraesCS3B01G112200 chr3D 94.028 787 18 8 295 1072 48882786 48882020 0.000000e+00 1166
4 TraesCS3B01G112200 chr3D 97.291 443 5 2 1070 1512 48870658 48870223 0.000000e+00 745
5 TraesCS3B01G112200 chr3D 95.197 229 6 3 2550 2774 48868548 48868321 9.450000e-95 357
6 TraesCS3B01G112200 chr3A 92.777 983 32 10 816 1783 61438259 61437301 0.000000e+00 1386
7 TraesCS3B01G112200 chr3A 80.021 1897 274 61 302 2165 103017790 103019614 0.000000e+00 1306
8 TraesCS3B01G112200 chr3A 90.430 512 14 5 291 793 61438740 61438255 2.330000e-180 641
9 TraesCS3B01G112200 chr3A 90.647 278 15 8 1870 2143 61437296 61437026 2.630000e-95 359
10 TraesCS3B01G112200 chr3A 92.444 225 5 5 2326 2550 61437045 61436833 7.460000e-81 311
11 TraesCS3B01G112200 chr3A 93.204 103 1 4 2676 2774 61436394 61436294 2.230000e-31 147
12 TraesCS3B01G112200 chr4D 93.134 670 23 9 1887 2550 141361311 141360659 0.000000e+00 961
13 TraesCS3B01G112200 chr2D 79.154 1348 233 24 452 1782 1624491 1623175 0.000000e+00 889
14 TraesCS3B01G112200 chr2D 83.902 205 16 10 1904 2108 648871264 648871077 2.200000e-41 180
15 TraesCS3B01G112200 chr2B 78.963 1331 236 24 452 1777 10214768 10216059 0.000000e+00 867
16 TraesCS3B01G112200 chr2B 80.242 248 46 1 445 689 319359800 319360047 1.700000e-42 183
17 TraesCS3B01G112200 chr2B 98.969 97 1 0 1 97 366650666 366650570 1.020000e-39 174
18 TraesCS3B01G112200 chr2B 97.059 102 3 0 1 102 378481176 378481277 3.670000e-39 172
19 TraesCS3B01G112200 chr2B 97.980 99 2 0 1 99 600576155 600576253 3.670000e-39 172
20 TraesCS3B01G112200 chr2B 97.980 99 2 0 1 99 754502710 754502808 3.670000e-39 172
21 TraesCS3B01G112200 chr2B 86.408 103 11 2 1981 2082 786389645 786389745 2.920000e-20 110
22 TraesCS3B01G112200 chr5B 97.170 106 2 1 1 105 59309095 59309200 7.890000e-41 178
23 TraesCS3B01G112200 chr7B 100.000 95 0 0 1 95 318093942 318093848 2.840000e-40 176
24 TraesCS3B01G112200 chr7B 97.059 102 3 0 1 102 673186236 673186135 3.670000e-39 172
25 TraesCS3B01G112200 chr7B 87.379 103 10 2 1981 2082 688412980 688413080 6.280000e-22 115
26 TraesCS3B01G112200 chr6B 95.283 106 5 0 1 106 148783630 148783525 4.750000e-38 169
27 TraesCS3B01G112200 chr6B 92.308 117 7 2 1 117 674119696 674119582 6.150000e-37 165
28 TraesCS3B01G112200 chr6B 87.379 103 10 2 1981 2082 692624781 692624881 6.280000e-22 115
29 TraesCS3B01G112200 chr1B 85.577 104 12 2 1981 2083 39180949 39180848 3.780000e-19 106


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 TraesCS3B01G112200 chr3B 78521619 78524392 2773 True 5123.000000 5123 100.000000 1 2774 1 chr3B.!!$R1 2773
1 TraesCS3B01G112200 chr3D 48882020 48882786 766 True 1166.000000 1166 94.028000 295 1072 1 chr3D.!!$R1 777
2 TraesCS3B01G112200 chr3D 48868321 48870658 2337 True 885.666667 1555 95.727667 1070 2774 3 chr3D.!!$R2 1704
3 TraesCS3B01G112200 chr3A 103017790 103019614 1824 False 1306.000000 1306 80.021000 302 2165 1 chr3A.!!$F1 1863
4 TraesCS3B01G112200 chr3A 61436294 61438740 2446 True 568.800000 1386 91.900400 291 2774 5 chr3A.!!$R1 2483
5 TraesCS3B01G112200 chr4D 141360659 141361311 652 True 961.000000 961 93.134000 1887 2550 1 chr4D.!!$R1 663
6 TraesCS3B01G112200 chr2D 1623175 1624491 1316 True 889.000000 889 79.154000 452 1782 1 chr2D.!!$R1 1330
7 TraesCS3B01G112200 chr2B 10214768 10216059 1291 False 867.000000 867 78.963000 452 1777 1 chr2B.!!$F1 1325

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
90 91 0.033405 CCTAGTCCGGAACTCCCTCA 60.033 60.0 5.23 0.0 39.55 3.86 F
291 292 0.098376 ACTCGGCGAGACGACAATAC 59.902 55.0 40.35 0.0 38.06 1.89 F
1418 1436 0.177604 GATGACCTGCCAGAGGAGTG 59.822 60.0 0.00 0.0 46.33 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1439 0.523968 CAATTCATTCGGCTGCCACG 60.524 55.0 20.29 5.67 0.0 4.94 R
1423 1441 0.527113 CACAATTCATTCGGCTGCCA 59.473 50.0 20.29 0.00 0.0 4.92 R
2634 3383 2.795231 ATTGCACTGGACACTATGCT 57.205 45.0 0.00 0.00 38.9 3.79 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
31 32 9.605275 TTCAATCTTGTATCTTCATAGTCTTGG 57.395 33.333 0.00 0.00 0.00 3.61
32 33 8.981659 TCAATCTTGTATCTTCATAGTCTTGGA 58.018 33.333 0.00 0.00 0.00 3.53
33 34 9.258826 CAATCTTGTATCTTCATAGTCTTGGAG 57.741 37.037 0.00 0.00 0.00 3.86
34 35 7.962995 TCTTGTATCTTCATAGTCTTGGAGT 57.037 36.000 0.00 0.00 0.00 3.85
35 36 8.001881 TCTTGTATCTTCATAGTCTTGGAGTC 57.998 38.462 0.00 0.00 0.00 3.36
36 37 6.716934 TGTATCTTCATAGTCTTGGAGTCC 57.283 41.667 0.73 0.73 0.00 3.85
37 38 4.927978 ATCTTCATAGTCTTGGAGTCCG 57.072 45.455 4.30 0.00 0.00 4.79
38 39 3.964411 TCTTCATAGTCTTGGAGTCCGA 58.036 45.455 4.30 0.84 0.00 4.55
39 40 3.695060 TCTTCATAGTCTTGGAGTCCGAC 59.305 47.826 4.30 6.89 0.00 4.79
40 41 2.376109 TCATAGTCTTGGAGTCCGACC 58.624 52.381 12.19 0.00 0.00 4.79
41 42 1.065701 CATAGTCTTGGAGTCCGACCG 59.934 57.143 12.19 0.00 0.00 4.79
42 43 0.325933 TAGTCTTGGAGTCCGACCGA 59.674 55.000 12.19 0.00 0.00 4.69
43 44 0.323542 AGTCTTGGAGTCCGACCGAT 60.324 55.000 12.19 0.00 0.00 4.18
44 45 0.179134 GTCTTGGAGTCCGACCGATG 60.179 60.000 4.30 0.00 0.00 3.84
45 46 0.323087 TCTTGGAGTCCGACCGATGA 60.323 55.000 4.30 0.00 0.00 2.92
46 47 0.747255 CTTGGAGTCCGACCGATGAT 59.253 55.000 4.30 0.00 0.00 2.45
47 48 0.459899 TTGGAGTCCGACCGATGATG 59.540 55.000 4.30 0.00 0.00 3.07
48 49 0.395173 TGGAGTCCGACCGATGATGA 60.395 55.000 4.30 0.00 0.00 2.92
49 50 0.962489 GGAGTCCGACCGATGATGAT 59.038 55.000 0.00 0.00 0.00 2.45
50 51 2.160205 GGAGTCCGACCGATGATGATA 58.840 52.381 0.00 0.00 0.00 2.15
51 52 2.162608 GGAGTCCGACCGATGATGATAG 59.837 54.545 0.00 0.00 0.00 2.08
52 53 2.814919 GAGTCCGACCGATGATGATAGT 59.185 50.000 0.00 0.00 0.00 2.12
53 54 3.223435 AGTCCGACCGATGATGATAGTT 58.777 45.455 0.00 0.00 0.00 2.24
54 55 3.253677 AGTCCGACCGATGATGATAGTTC 59.746 47.826 0.00 0.00 0.00 3.01
55 56 2.225727 TCCGACCGATGATGATAGTTCG 59.774 50.000 0.00 0.00 0.00 3.95
58 59 2.732412 CCGATGATGATAGTTCGGCT 57.268 50.000 0.00 0.00 43.91 5.52
59 60 3.850122 CCGATGATGATAGTTCGGCTA 57.150 47.619 0.00 0.00 43.91 3.93
60 61 4.377839 CCGATGATGATAGTTCGGCTAT 57.622 45.455 0.00 1.08 43.91 2.97
72 73 3.557290 GGCTATCCGGACACCCCC 61.557 72.222 6.12 0.00 0.00 5.40
73 74 2.446036 GCTATCCGGACACCCCCT 60.446 66.667 6.12 0.00 0.00 4.79
74 75 1.152398 GCTATCCGGACACCCCCTA 60.152 63.158 6.12 0.00 0.00 3.53
75 76 1.186267 GCTATCCGGACACCCCCTAG 61.186 65.000 6.12 3.64 0.00 3.02
76 77 0.187851 CTATCCGGACACCCCCTAGT 59.812 60.000 6.12 0.00 0.00 2.57
77 78 0.186873 TATCCGGACACCCCCTAGTC 59.813 60.000 6.12 0.00 0.00 2.59
80 81 2.762875 GGACACCCCCTAGTCCGG 60.763 72.222 0.00 0.00 44.23 5.14
81 82 2.361771 GACACCCCCTAGTCCGGA 59.638 66.667 0.00 0.00 0.00 5.14
82 83 1.305549 GACACCCCCTAGTCCGGAA 60.306 63.158 5.23 0.00 0.00 4.30
83 84 1.611474 GACACCCCCTAGTCCGGAAC 61.611 65.000 5.23 0.00 0.00 3.62
84 85 1.305887 CACCCCCTAGTCCGGAACT 60.306 63.158 5.23 8.86 42.33 3.01
85 86 1.001376 ACCCCCTAGTCCGGAACTC 59.999 63.158 5.23 0.00 39.55 3.01
86 87 1.761271 CCCCCTAGTCCGGAACTCC 60.761 68.421 5.23 0.00 39.55 3.85
87 88 1.761271 CCCCTAGTCCGGAACTCCC 60.761 68.421 5.23 0.00 39.55 4.30
88 89 1.310373 CCCTAGTCCGGAACTCCCT 59.690 63.158 5.23 0.05 39.55 4.20
89 90 0.756070 CCCTAGTCCGGAACTCCCTC 60.756 65.000 5.23 0.00 39.55 4.30
90 91 0.033405 CCTAGTCCGGAACTCCCTCA 60.033 60.000 5.23 0.00 39.55 3.86
91 92 1.618888 CCTAGTCCGGAACTCCCTCAA 60.619 57.143 5.23 0.00 39.55 3.02
92 93 1.751924 CTAGTCCGGAACTCCCTCAAG 59.248 57.143 5.23 0.00 39.55 3.02
93 94 0.905337 AGTCCGGAACTCCCTCAAGG 60.905 60.000 5.23 0.00 30.02 3.61
94 95 0.903454 GTCCGGAACTCCCTCAAGGA 60.903 60.000 5.23 0.00 44.91 3.36
95 96 0.903454 TCCGGAACTCCCTCAAGGAC 60.903 60.000 0.00 0.00 40.93 3.85
96 97 1.597461 CGGAACTCCCTCAAGGACC 59.403 63.158 0.00 0.00 40.93 4.46
97 98 0.905337 CGGAACTCCCTCAAGGACCT 60.905 60.000 0.00 0.00 40.93 3.85
98 99 1.363246 GGAACTCCCTCAAGGACCTT 58.637 55.000 0.00 0.00 40.93 3.50
99 100 1.003696 GGAACTCCCTCAAGGACCTTG 59.996 57.143 25.87 25.87 40.93 3.61
100 101 1.003696 GAACTCCCTCAAGGACCTTGG 59.996 57.143 29.76 20.79 40.93 3.61
101 102 0.842467 ACTCCCTCAAGGACCTTGGG 60.842 60.000 29.76 27.56 40.93 4.12
102 103 2.203549 CTCCCTCAAGGACCTTGGGC 62.204 65.000 29.76 0.00 40.33 5.36
103 104 2.356667 CCTCAAGGACCTTGGGCC 59.643 66.667 29.76 2.61 40.33 5.80
104 105 2.538141 CCTCAAGGACCTTGGGCCA 61.538 63.158 29.76 12.85 40.33 5.36
105 106 1.303643 CTCAAGGACCTTGGGCCAC 60.304 63.158 29.76 0.00 41.33 5.01
106 107 2.283173 CAAGGACCTTGGGCCACC 60.283 66.667 24.42 3.71 37.77 4.61
107 108 2.452491 AAGGACCTTGGGCCACCT 60.452 61.111 14.87 6.67 37.76 4.00
108 109 2.539081 AAGGACCTTGGGCCACCTC 61.539 63.158 14.87 4.96 37.76 3.85
109 110 3.256960 GGACCTTGGGCCACCTCA 61.257 66.667 5.23 0.00 37.76 3.86
110 111 2.840753 GGACCTTGGGCCACCTCAA 61.841 63.158 5.23 0.00 37.76 3.02
111 112 1.603739 GACCTTGGGCCACCTCAAC 60.604 63.158 5.23 0.00 37.76 3.18
112 113 2.672996 CCTTGGGCCACCTCAACG 60.673 66.667 5.23 0.00 37.76 4.10
113 114 2.429930 CTTGGGCCACCTCAACGA 59.570 61.111 5.23 0.00 37.76 3.85
114 115 1.228124 CTTGGGCCACCTCAACGAA 60.228 57.895 5.23 0.00 37.76 3.85
115 116 0.821711 CTTGGGCCACCTCAACGAAA 60.822 55.000 5.23 0.00 37.76 3.46
116 117 0.178975 TTGGGCCACCTCAACGAAAT 60.179 50.000 5.23 0.00 37.76 2.17
117 118 0.693622 TGGGCCACCTCAACGAAATA 59.306 50.000 0.00 0.00 37.76 1.40
118 119 1.283613 TGGGCCACCTCAACGAAATAT 59.716 47.619 0.00 0.00 37.76 1.28
119 120 2.291282 TGGGCCACCTCAACGAAATATT 60.291 45.455 0.00 0.00 37.76 1.28
120 121 2.758423 GGGCCACCTCAACGAAATATTT 59.242 45.455 4.39 0.00 0.00 1.40
121 122 3.428862 GGGCCACCTCAACGAAATATTTG 60.429 47.826 4.39 1.06 0.00 2.32
122 123 3.442273 GGCCACCTCAACGAAATATTTGA 59.558 43.478 5.17 0.00 0.00 2.69
123 124 4.412207 GCCACCTCAACGAAATATTTGAC 58.588 43.478 5.17 0.00 0.00 3.18
124 125 4.083003 GCCACCTCAACGAAATATTTGACA 60.083 41.667 5.17 0.00 0.00 3.58
125 126 5.563867 GCCACCTCAACGAAATATTTGACAA 60.564 40.000 5.17 0.00 0.00 3.18
126 127 6.086222 CCACCTCAACGAAATATTTGACAAG 58.914 40.000 5.17 0.00 0.00 3.16
127 128 6.293955 CCACCTCAACGAAATATTTGACAAGT 60.294 38.462 5.17 0.00 0.00 3.16
128 129 6.578545 CACCTCAACGAAATATTTGACAAGTG 59.421 38.462 5.17 1.45 0.00 3.16
129 130 6.086222 CCTCAACGAAATATTTGACAAGTGG 58.914 40.000 5.17 0.00 0.00 4.00
130 131 6.007936 TCAACGAAATATTTGACAAGTGGG 57.992 37.500 5.17 0.00 0.00 4.61
131 132 5.048364 TCAACGAAATATTTGACAAGTGGGG 60.048 40.000 5.17 0.00 0.00 4.96
132 133 4.403734 ACGAAATATTTGACAAGTGGGGT 58.596 39.130 5.17 0.00 0.00 4.95
133 134 4.457949 ACGAAATATTTGACAAGTGGGGTC 59.542 41.667 5.17 0.00 35.83 4.46
134 135 4.457603 CGAAATATTTGACAAGTGGGGTCA 59.542 41.667 5.17 0.00 43.12 4.02
138 139 2.818751 TTGACAAGTGGGGTCAACTT 57.181 45.000 4.02 0.00 46.95 2.66
139 140 2.051334 TGACAAGTGGGGTCAACTTG 57.949 50.000 13.30 13.30 41.96 3.16
142 143 0.944386 CAAGTGGGGTCAACTTGTCG 59.056 55.000 7.90 0.00 36.89 4.35
143 144 0.179029 AAGTGGGGTCAACTTGTCGG 60.179 55.000 0.00 0.00 0.00 4.79
144 145 1.147600 GTGGGGTCAACTTGTCGGT 59.852 57.895 0.00 0.00 0.00 4.69
145 146 0.464916 GTGGGGTCAACTTGTCGGTT 60.465 55.000 0.00 0.00 0.00 4.44
146 147 0.256464 TGGGGTCAACTTGTCGGTTT 59.744 50.000 0.00 0.00 0.00 3.27
147 148 1.341187 TGGGGTCAACTTGTCGGTTTT 60.341 47.619 0.00 0.00 0.00 2.43
148 149 1.066454 GGGGTCAACTTGTCGGTTTTG 59.934 52.381 0.00 0.00 0.00 2.44
149 150 1.535226 GGGTCAACTTGTCGGTTTTGC 60.535 52.381 0.00 0.00 0.00 3.68
150 151 1.404035 GGTCAACTTGTCGGTTTTGCT 59.596 47.619 0.00 0.00 0.00 3.91
151 152 2.614983 GGTCAACTTGTCGGTTTTGCTA 59.385 45.455 0.00 0.00 0.00 3.49
152 153 3.252458 GGTCAACTTGTCGGTTTTGCTAT 59.748 43.478 0.00 0.00 0.00 2.97
153 154 4.261447 GGTCAACTTGTCGGTTTTGCTATT 60.261 41.667 0.00 0.00 0.00 1.73
154 155 5.278604 GTCAACTTGTCGGTTTTGCTATTT 58.721 37.500 0.00 0.00 0.00 1.40
155 156 5.746721 GTCAACTTGTCGGTTTTGCTATTTT 59.253 36.000 0.00 0.00 0.00 1.82
156 157 6.254804 GTCAACTTGTCGGTTTTGCTATTTTT 59.745 34.615 0.00 0.00 0.00 1.94
157 158 6.474102 TCAACTTGTCGGTTTTGCTATTTTTC 59.526 34.615 0.00 0.00 0.00 2.29
158 159 4.973663 ACTTGTCGGTTTTGCTATTTTTCG 59.026 37.500 0.00 0.00 0.00 3.46
159 160 4.555348 TGTCGGTTTTGCTATTTTTCGT 57.445 36.364 0.00 0.00 0.00 3.85
160 161 5.670149 TGTCGGTTTTGCTATTTTTCGTA 57.330 34.783 0.00 0.00 0.00 3.43
161 162 5.681880 TGTCGGTTTTGCTATTTTTCGTAG 58.318 37.500 0.00 0.00 0.00 3.51
162 163 5.084055 GTCGGTTTTGCTATTTTTCGTAGG 58.916 41.667 0.00 0.00 0.00 3.18
163 164 4.756135 TCGGTTTTGCTATTTTTCGTAGGT 59.244 37.500 0.00 0.00 0.00 3.08
164 165 4.849383 CGGTTTTGCTATTTTTCGTAGGTG 59.151 41.667 0.00 0.00 0.00 4.00
165 166 5.334260 CGGTTTTGCTATTTTTCGTAGGTGA 60.334 40.000 0.00 0.00 0.00 4.02
166 167 6.440436 GGTTTTGCTATTTTTCGTAGGTGAA 58.560 36.000 0.00 0.00 0.00 3.18
167 168 7.088272 GGTTTTGCTATTTTTCGTAGGTGAAT 58.912 34.615 0.00 0.00 0.00 2.57
168 169 8.238631 GGTTTTGCTATTTTTCGTAGGTGAATA 58.761 33.333 0.00 0.00 0.00 1.75
169 170 9.783256 GTTTTGCTATTTTTCGTAGGTGAATAT 57.217 29.630 0.00 0.00 0.00 1.28
179 180 8.570096 TTTCGTAGGTGAATATAAGACAATCG 57.430 34.615 0.00 0.00 0.00 3.34
180 181 6.147581 TCGTAGGTGAATATAAGACAATCGC 58.852 40.000 0.00 0.00 0.00 4.58
181 182 5.059343 CGTAGGTGAATATAAGACAATCGCG 59.941 44.000 0.00 0.00 0.00 5.87
182 183 4.945246 AGGTGAATATAAGACAATCGCGT 58.055 39.130 5.77 0.00 0.00 6.01
183 184 5.357257 AGGTGAATATAAGACAATCGCGTT 58.643 37.500 5.77 0.00 0.00 4.84
184 185 5.462398 AGGTGAATATAAGACAATCGCGTTC 59.538 40.000 5.77 0.00 0.00 3.95
185 186 5.333111 GGTGAATATAAGACAATCGCGTTCC 60.333 44.000 5.77 0.00 0.00 3.62
186 187 5.233476 GTGAATATAAGACAATCGCGTTCCA 59.767 40.000 5.77 0.00 0.00 3.53
187 188 5.233476 TGAATATAAGACAATCGCGTTCCAC 59.767 40.000 5.77 0.00 0.00 4.02
188 189 2.442212 TAAGACAATCGCGTTCCACA 57.558 45.000 5.77 0.00 0.00 4.17
189 190 1.808411 AAGACAATCGCGTTCCACAT 58.192 45.000 5.77 0.00 0.00 3.21
190 191 1.808411 AGACAATCGCGTTCCACATT 58.192 45.000 5.77 0.00 0.00 2.71
191 192 1.464608 AGACAATCGCGTTCCACATTG 59.535 47.619 5.77 10.20 33.27 2.82
192 193 1.463056 GACAATCGCGTTCCACATTGA 59.537 47.619 19.08 0.00 31.78 2.57
193 194 1.876799 ACAATCGCGTTCCACATTGAA 59.123 42.857 19.08 0.00 31.78 2.69
194 195 2.487762 ACAATCGCGTTCCACATTGAAT 59.512 40.909 19.08 0.00 31.78 2.57
195 196 2.830772 ATCGCGTTCCACATTGAATG 57.169 45.000 5.77 3.16 34.94 2.67
202 203 5.594724 CGTTCCACATTGAATGCATTTTT 57.405 34.783 14.33 0.00 0.00 1.94
233 234 6.573664 TTTTGTGACCTGACTTGAATATGG 57.426 37.500 0.00 0.00 0.00 2.74
234 235 4.908601 TGTGACCTGACTTGAATATGGT 57.091 40.909 0.00 0.00 0.00 3.55
235 236 6.367374 TTGTGACCTGACTTGAATATGGTA 57.633 37.500 0.00 0.00 0.00 3.25
236 237 5.730550 TGTGACCTGACTTGAATATGGTAC 58.269 41.667 0.00 0.00 0.00 3.34
237 238 5.483937 TGTGACCTGACTTGAATATGGTACT 59.516 40.000 0.00 0.00 0.00 2.73
238 239 6.666113 TGTGACCTGACTTGAATATGGTACTA 59.334 38.462 0.00 0.00 0.00 1.82
239 240 7.179516 TGTGACCTGACTTGAATATGGTACTAA 59.820 37.037 0.00 0.00 0.00 2.24
240 241 8.038944 GTGACCTGACTTGAATATGGTACTAAA 58.961 37.037 0.00 0.00 0.00 1.85
241 242 8.768397 TGACCTGACTTGAATATGGTACTAAAT 58.232 33.333 0.00 0.00 0.00 1.40
242 243 9.614792 GACCTGACTTGAATATGGTACTAAATT 57.385 33.333 0.00 0.00 0.00 1.82
243 244 9.396022 ACCTGACTTGAATATGGTACTAAATTG 57.604 33.333 0.00 0.00 0.00 2.32
244 245 9.396022 CCTGACTTGAATATGGTACTAAATTGT 57.604 33.333 0.00 0.00 0.00 2.71
253 254 9.788889 AATATGGTACTAAATTGTTACCTAGCC 57.211 33.333 10.31 0.00 0.00 3.93
254 255 5.663456 TGGTACTAAATTGTTACCTAGCCG 58.337 41.667 10.31 0.00 0.00 5.52
255 256 5.052481 GGTACTAAATTGTTACCTAGCCGG 58.948 45.833 0.00 0.00 39.35 6.13
263 264 4.813346 ACCTAGCCGGTGGTTTTG 57.187 55.556 1.90 0.00 46.80 2.44
264 265 1.074248 ACCTAGCCGGTGGTTTTGG 59.926 57.895 1.90 0.00 46.80 3.28
265 266 1.677633 CCTAGCCGGTGGTTTTGGG 60.678 63.158 1.90 0.00 0.00 4.12
266 267 2.282603 TAGCCGGTGGTTTTGGGC 60.283 61.111 1.90 0.00 45.91 5.36
268 269 3.541713 GCCGGTGGTTTTGGGCAA 61.542 61.111 1.90 0.00 44.91 4.52
269 270 3.095347 GCCGGTGGTTTTGGGCAAA 62.095 57.895 1.90 0.00 44.91 3.68
270 271 1.751563 CCGGTGGTTTTGGGCAAAT 59.248 52.632 0.00 0.00 0.00 2.32
271 272 0.969894 CCGGTGGTTTTGGGCAAATA 59.030 50.000 0.00 0.00 0.00 1.40
272 273 1.344763 CCGGTGGTTTTGGGCAAATAA 59.655 47.619 0.00 0.00 0.00 1.40
273 274 2.409012 CGGTGGTTTTGGGCAAATAAC 58.591 47.619 0.00 0.00 0.00 1.89
274 275 2.036604 CGGTGGTTTTGGGCAAATAACT 59.963 45.455 0.00 0.00 0.00 2.24
275 276 3.659786 GGTGGTTTTGGGCAAATAACTC 58.340 45.455 0.00 0.00 0.00 3.01
276 277 3.313690 GTGGTTTTGGGCAAATAACTCG 58.686 45.455 0.00 0.00 0.00 4.18
277 278 2.297597 TGGTTTTGGGCAAATAACTCGG 59.702 45.455 0.00 0.00 0.00 4.63
278 279 2.333926 GTTTTGGGCAAATAACTCGGC 58.666 47.619 0.00 0.00 0.00 5.54
279 280 0.523966 TTTGGGCAAATAACTCGGCG 59.476 50.000 0.00 0.00 0.00 6.46
280 281 0.321741 TTGGGCAAATAACTCGGCGA 60.322 50.000 10.14 10.14 0.00 5.54
281 282 0.742990 TGGGCAAATAACTCGGCGAG 60.743 55.000 33.42 33.42 35.52 5.03
282 283 0.461339 GGGCAAATAACTCGGCGAGA 60.461 55.000 40.35 21.84 33.32 4.04
283 284 0.651031 GGCAAATAACTCGGCGAGAC 59.349 55.000 40.35 19.55 33.32 3.36
284 285 0.297820 GCAAATAACTCGGCGAGACG 59.702 55.000 40.35 21.56 33.32 4.18
285 286 1.904144 CAAATAACTCGGCGAGACGA 58.096 50.000 40.35 24.71 41.13 4.20
286 287 1.582502 CAAATAACTCGGCGAGACGAC 59.417 52.381 40.35 0.00 38.06 4.34
287 288 0.806868 AATAACTCGGCGAGACGACA 59.193 50.000 40.35 20.50 38.06 4.35
288 289 0.806868 ATAACTCGGCGAGACGACAA 59.193 50.000 40.35 19.15 38.06 3.18
289 290 0.806868 TAACTCGGCGAGACGACAAT 59.193 50.000 40.35 15.91 38.06 2.71
290 291 0.806868 AACTCGGCGAGACGACAATA 59.193 50.000 40.35 0.00 38.06 1.90
291 292 0.098376 ACTCGGCGAGACGACAATAC 59.902 55.000 40.35 0.00 38.06 1.89
292 293 0.377554 CTCGGCGAGACGACAATACT 59.622 55.000 32.07 0.00 38.06 2.12
293 294 1.596260 CTCGGCGAGACGACAATACTA 59.404 52.381 32.07 0.00 38.06 1.82
329 330 2.203070 GCCGCCGTTCTGATCCAT 60.203 61.111 0.00 0.00 0.00 3.41
450 451 4.023622 CAGGGTCATACTGAGTAGATCGTG 60.024 50.000 0.00 4.92 38.20 4.35
500 509 3.743269 CGTAAATCTGGGGGTGTATGACC 60.743 52.174 0.00 0.00 45.28 4.02
715 731 2.229784 GTCTCCAAAAAGCCAGGTGATG 59.770 50.000 0.00 0.00 0.00 3.07
962 978 3.127352 GAAGACGCGGGCGATCTCT 62.127 63.158 20.98 9.40 42.83 3.10
963 979 1.783031 GAAGACGCGGGCGATCTCTA 61.783 60.000 20.98 0.00 42.83 2.43
964 980 2.051166 GACGCGGGCGATCTCTAC 60.051 66.667 20.98 0.00 42.83 2.59
965 981 2.827190 ACGCGGGCGATCTCTACA 60.827 61.111 20.98 0.00 42.83 2.74
966 982 2.131294 GACGCGGGCGATCTCTACAT 62.131 60.000 20.98 0.00 42.83 2.29
967 983 1.730902 CGCGGGCGATCTCTACATG 60.731 63.158 7.38 0.00 42.83 3.21
968 984 1.660355 GCGGGCGATCTCTACATGA 59.340 57.895 0.00 0.00 0.00 3.07
969 985 0.244994 GCGGGCGATCTCTACATGAT 59.755 55.000 0.00 0.00 0.00 2.45
993 1009 3.319405 ACATCATCGATCAGGTCCTACAC 59.681 47.826 0.00 0.00 0.00 2.90
1095 1112 2.981302 CACTGCGACATCCTCCCA 59.019 61.111 0.00 0.00 0.00 4.37
1418 1436 0.177604 GATGACCTGCCAGAGGAGTG 59.822 60.000 0.00 0.00 46.33 3.51
1419 1437 1.908340 ATGACCTGCCAGAGGAGTGC 61.908 60.000 0.00 0.00 46.33 4.40
1420 1438 2.527624 ACCTGCCAGAGGAGTGCA 60.528 61.111 0.00 0.00 46.33 4.57
1421 1439 2.046507 CCTGCCAGAGGAGTGCAC 60.047 66.667 9.40 9.40 46.33 4.57
1422 1440 2.433838 CTGCCAGAGGAGTGCACG 60.434 66.667 12.01 0.00 0.00 5.34
1423 1441 3.231889 CTGCCAGAGGAGTGCACGT 62.232 63.158 12.01 0.00 0.00 4.49
1490 1510 0.600057 GGCAGGTTCTTCTTTGCTGG 59.400 55.000 0.00 0.00 36.79 4.85
1652 1687 0.537143 AATGGCACCAGCAAAGACGA 60.537 50.000 0.00 0.00 44.61 4.20
1653 1688 0.322816 ATGGCACCAGCAAAGACGAT 60.323 50.000 0.00 0.00 44.61 3.73
1654 1689 1.236616 TGGCACCAGCAAAGACGATG 61.237 55.000 0.00 0.00 44.61 3.84
1656 1691 1.503542 CACCAGCAAAGACGATGGC 59.496 57.895 0.00 0.00 46.69 4.40
1657 1692 1.073025 ACCAGCAAAGACGATGGCA 59.927 52.632 0.00 0.00 46.69 4.92
1658 1693 0.537143 ACCAGCAAAGACGATGGCAA 60.537 50.000 0.00 0.00 46.69 4.52
1659 1694 0.109597 CCAGCAAAGACGATGGCAAC 60.110 55.000 0.00 0.00 35.29 4.17
1742 1786 6.412653 CACAAGTCCAAACGTTACATGTTTAC 59.587 38.462 2.30 1.94 35.31 2.01
1821 1865 3.779759 CTCAACTTCAGCTAGCTAGTGG 58.220 50.000 18.86 15.88 0.00 4.00
1901 1947 4.274459 AGTTTACTCTTGCTGCTCTTTGTG 59.726 41.667 0.00 0.00 0.00 3.33
1993 2060 3.973206 TCCTGTGGTATGATGAAACGT 57.027 42.857 0.00 0.00 0.00 3.99
1994 2061 5.356426 CATCCTGTGGTATGATGAAACGTA 58.644 41.667 0.00 0.00 38.49 3.57
1995 2062 4.751060 TCCTGTGGTATGATGAAACGTAC 58.249 43.478 0.00 0.00 0.00 3.67
1996 2063 4.464951 TCCTGTGGTATGATGAAACGTACT 59.535 41.667 0.00 0.00 34.06 2.73
1997 2064 4.566759 CCTGTGGTATGATGAAACGTACTG 59.433 45.833 0.00 0.00 34.06 2.74
1998 2065 5.142061 TGTGGTATGATGAAACGTACTGT 57.858 39.130 0.00 0.00 34.06 3.55
2244 2317 0.798776 CTCATTCAAGGCACGGACAC 59.201 55.000 0.00 0.00 0.00 3.67
2259 2332 1.269257 GGACACAACTTTGAGCCAAGC 60.269 52.381 0.00 0.00 0.00 4.01
2321 2395 0.958822 GCCACCAATCGTTCACCTTT 59.041 50.000 0.00 0.00 0.00 3.11
2588 3337 8.248253 TCGCTGATCAATACTTTAGTAGTCAAA 58.752 33.333 0.00 0.00 38.33 2.69
2745 3499 6.859112 ATCACTACACTACCAAGACTGAAT 57.141 37.500 0.00 0.00 0.00 2.57
2746 3500 7.956328 ATCACTACACTACCAAGACTGAATA 57.044 36.000 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.605275 CCAAGACTATGAAGATACAAGATTGAA 57.395 33.333 0.00 0.00 0.00 2.69
6 7 8.981659 TCCAAGACTATGAAGATACAAGATTGA 58.018 33.333 0.00 0.00 0.00 2.57
8 9 8.986991 ACTCCAAGACTATGAAGATACAAGATT 58.013 33.333 0.00 0.00 0.00 2.40
9 10 8.546083 ACTCCAAGACTATGAAGATACAAGAT 57.454 34.615 0.00 0.00 0.00 2.40
10 11 7.068839 GGACTCCAAGACTATGAAGATACAAGA 59.931 40.741 0.00 0.00 0.00 3.02
11 12 7.206687 GGACTCCAAGACTATGAAGATACAAG 58.793 42.308 0.00 0.00 0.00 3.16
12 13 6.183360 CGGACTCCAAGACTATGAAGATACAA 60.183 42.308 0.00 0.00 0.00 2.41
13 14 5.299531 CGGACTCCAAGACTATGAAGATACA 59.700 44.000 0.00 0.00 0.00 2.29
14 15 5.531659 TCGGACTCCAAGACTATGAAGATAC 59.468 44.000 0.00 0.00 0.00 2.24
15 16 5.531659 GTCGGACTCCAAGACTATGAAGATA 59.468 44.000 0.00 0.00 32.58 1.98
16 17 4.339814 GTCGGACTCCAAGACTATGAAGAT 59.660 45.833 0.00 0.00 32.58 2.40
17 18 3.695060 GTCGGACTCCAAGACTATGAAGA 59.305 47.826 0.00 0.00 32.58 2.87
18 19 3.181485 GGTCGGACTCCAAGACTATGAAG 60.181 52.174 8.23 0.00 35.42 3.02
19 20 2.758979 GGTCGGACTCCAAGACTATGAA 59.241 50.000 8.23 0.00 35.42 2.57
20 21 2.376109 GGTCGGACTCCAAGACTATGA 58.624 52.381 8.23 0.00 35.42 2.15
21 22 1.065701 CGGTCGGACTCCAAGACTATG 59.934 57.143 8.23 0.00 35.42 2.23
22 23 1.064906 TCGGTCGGACTCCAAGACTAT 60.065 52.381 8.23 0.00 35.42 2.12
23 24 0.325933 TCGGTCGGACTCCAAGACTA 59.674 55.000 8.23 0.00 35.42 2.59
24 25 0.323542 ATCGGTCGGACTCCAAGACT 60.324 55.000 8.23 0.00 35.42 3.24
25 26 0.179134 CATCGGTCGGACTCCAAGAC 60.179 60.000 8.23 0.00 0.00 3.01
26 27 0.323087 TCATCGGTCGGACTCCAAGA 60.323 55.000 8.23 1.38 0.00 3.02
27 28 0.747255 ATCATCGGTCGGACTCCAAG 59.253 55.000 8.23 0.00 0.00 3.61
28 29 0.459899 CATCATCGGTCGGACTCCAA 59.540 55.000 8.23 0.00 0.00 3.53
29 30 0.395173 TCATCATCGGTCGGACTCCA 60.395 55.000 8.23 0.00 0.00 3.86
30 31 0.962489 ATCATCATCGGTCGGACTCC 59.038 55.000 8.23 0.00 0.00 3.85
31 32 2.814919 ACTATCATCATCGGTCGGACTC 59.185 50.000 8.23 0.00 0.00 3.36
32 33 2.865079 ACTATCATCATCGGTCGGACT 58.135 47.619 8.23 0.00 0.00 3.85
33 34 3.566523 GAACTATCATCATCGGTCGGAC 58.433 50.000 0.00 0.00 0.00 4.79
34 35 2.225727 CGAACTATCATCATCGGTCGGA 59.774 50.000 0.00 0.00 32.54 4.55
35 36 2.585845 CGAACTATCATCATCGGTCGG 58.414 52.381 0.00 0.00 32.54 4.79
55 56 2.668106 TAGGGGGTGTCCGGATAGCC 62.668 65.000 34.24 34.24 39.05 3.93
56 57 1.152398 TAGGGGGTGTCCGGATAGC 60.152 63.158 20.91 20.91 36.01 2.97
57 58 0.187851 ACTAGGGGGTGTCCGGATAG 59.812 60.000 7.81 5.89 36.01 2.08
58 59 0.186873 GACTAGGGGGTGTCCGGATA 59.813 60.000 7.81 0.10 36.01 2.59
59 60 1.075450 GACTAGGGGGTGTCCGGAT 60.075 63.158 7.81 0.00 36.01 4.18
60 61 2.361771 GACTAGGGGGTGTCCGGA 59.638 66.667 0.00 0.00 36.01 5.14
61 62 2.762875 GGACTAGGGGGTGTCCGG 60.763 72.222 0.00 0.00 42.51 5.14
63 64 2.762875 CCGGACTAGGGGGTGTCC 60.763 72.222 0.00 0.00 46.69 4.02
64 65 1.305549 TTCCGGACTAGGGGGTGTC 60.306 63.158 1.83 0.00 0.00 3.67
65 66 1.611556 GTTCCGGACTAGGGGGTGT 60.612 63.158 1.83 0.00 0.00 4.16
66 67 1.305887 AGTTCCGGACTAGGGGGTG 60.306 63.158 1.83 0.00 36.65 4.61
67 68 1.001376 GAGTTCCGGACTAGGGGGT 59.999 63.158 1.83 0.00 39.19 4.95
68 69 1.761271 GGAGTTCCGGACTAGGGGG 60.761 68.421 1.83 0.00 39.19 5.40
69 70 1.761271 GGGAGTTCCGGACTAGGGG 60.761 68.421 1.83 0.00 39.19 4.79
70 71 0.756070 GAGGGAGTTCCGGACTAGGG 60.756 65.000 1.83 0.00 39.19 3.53
71 72 0.033405 TGAGGGAGTTCCGGACTAGG 60.033 60.000 1.83 0.00 39.19 3.02
72 73 1.751924 CTTGAGGGAGTTCCGGACTAG 59.248 57.143 1.83 0.00 39.19 2.57
73 74 1.618888 CCTTGAGGGAGTTCCGGACTA 60.619 57.143 1.83 0.00 39.19 2.59
74 75 0.905337 CCTTGAGGGAGTTCCGGACT 60.905 60.000 1.83 4.69 42.70 3.85
75 76 0.903454 TCCTTGAGGGAGTTCCGGAC 60.903 60.000 1.83 0.00 39.58 4.79
76 77 0.903454 GTCCTTGAGGGAGTTCCGGA 60.903 60.000 0.00 0.00 46.10 5.14
77 78 1.597461 GTCCTTGAGGGAGTTCCGG 59.403 63.158 0.00 0.00 46.10 5.14
78 79 0.905337 AGGTCCTTGAGGGAGTTCCG 60.905 60.000 0.00 0.00 46.10 4.30
79 80 1.003696 CAAGGTCCTTGAGGGAGTTCC 59.996 57.143 25.15 0.00 46.10 3.62
80 81 1.003696 CCAAGGTCCTTGAGGGAGTTC 59.996 57.143 29.91 0.00 46.10 3.01
81 82 1.068121 CCAAGGTCCTTGAGGGAGTT 58.932 55.000 29.91 0.00 46.10 3.01
82 83 0.842467 CCCAAGGTCCTTGAGGGAGT 60.842 60.000 29.91 0.00 46.10 3.85
83 84 1.994463 CCCAAGGTCCTTGAGGGAG 59.006 63.158 29.91 14.21 46.10 4.30
84 85 2.231380 GCCCAAGGTCCTTGAGGGA 61.231 63.158 29.91 0.00 43.42 4.20
85 86 2.356667 GCCCAAGGTCCTTGAGGG 59.643 66.667 29.91 24.10 43.42 4.30
86 87 2.356667 GGCCCAAGGTCCTTGAGG 59.643 66.667 29.91 26.75 43.42 3.86
87 88 1.303643 GTGGCCCAAGGTCCTTGAG 60.304 63.158 29.91 19.97 43.42 3.02
88 89 2.840753 GGTGGCCCAAGGTCCTTGA 61.841 63.158 29.91 9.73 43.42 3.02
89 90 2.283173 GGTGGCCCAAGGTCCTTG 60.283 66.667 22.89 22.89 40.75 3.61
90 91 2.452491 AGGTGGCCCAAGGTCCTT 60.452 61.111 0.00 0.00 0.00 3.36
91 92 2.936032 GAGGTGGCCCAAGGTCCT 60.936 66.667 0.00 0.00 0.00 3.85
92 93 2.840753 TTGAGGTGGCCCAAGGTCC 61.841 63.158 0.00 0.00 0.00 4.46
93 94 1.603739 GTTGAGGTGGCCCAAGGTC 60.604 63.158 0.00 0.00 0.00 3.85
94 95 2.520968 GTTGAGGTGGCCCAAGGT 59.479 61.111 0.00 0.00 0.00 3.50
95 96 2.672996 CGTTGAGGTGGCCCAAGG 60.673 66.667 0.00 0.00 0.00 3.61
96 97 0.821711 TTTCGTTGAGGTGGCCCAAG 60.822 55.000 0.00 0.00 0.00 3.61
97 98 0.178975 ATTTCGTTGAGGTGGCCCAA 60.179 50.000 0.00 0.00 0.00 4.12
98 99 0.693622 TATTTCGTTGAGGTGGCCCA 59.306 50.000 0.00 0.00 0.00 5.36
99 100 2.052782 ATATTTCGTTGAGGTGGCCC 57.947 50.000 0.00 0.00 0.00 5.80
100 101 3.442273 TCAAATATTTCGTTGAGGTGGCC 59.558 43.478 0.00 0.00 30.41 5.36
101 102 4.083003 TGTCAAATATTTCGTTGAGGTGGC 60.083 41.667 0.00 0.00 34.52 5.01
102 103 5.621197 TGTCAAATATTTCGTTGAGGTGG 57.379 39.130 0.00 0.00 34.52 4.61
103 104 6.578545 CACTTGTCAAATATTTCGTTGAGGTG 59.421 38.462 0.00 0.85 34.52 4.00
104 105 6.293955 CCACTTGTCAAATATTTCGTTGAGGT 60.294 38.462 0.00 0.00 34.52 3.85
105 106 6.086222 CCACTTGTCAAATATTTCGTTGAGG 58.914 40.000 0.00 0.00 34.52 3.86
106 107 6.086222 CCCACTTGTCAAATATTTCGTTGAG 58.914 40.000 0.00 0.00 34.52 3.02
107 108 5.048364 CCCCACTTGTCAAATATTTCGTTGA 60.048 40.000 0.00 0.00 0.00 3.18
108 109 5.160641 CCCCACTTGTCAAATATTTCGTTG 58.839 41.667 0.00 0.00 0.00 4.10
109 110 4.830600 ACCCCACTTGTCAAATATTTCGTT 59.169 37.500 0.00 0.00 0.00 3.85
110 111 4.403734 ACCCCACTTGTCAAATATTTCGT 58.596 39.130 0.00 0.00 0.00 3.85
111 112 4.457603 TGACCCCACTTGTCAAATATTTCG 59.542 41.667 0.00 0.00 39.66 3.46
112 113 5.975693 TGACCCCACTTGTCAAATATTTC 57.024 39.130 0.00 0.00 39.66 2.17
120 121 2.051334 CAAGTTGACCCCACTTGTCA 57.949 50.000 0.00 0.00 40.80 3.58
123 124 0.944386 CGACAAGTTGACCCCACTTG 59.056 55.000 10.54 10.55 44.43 3.16
124 125 0.179029 CCGACAAGTTGACCCCACTT 60.179 55.000 10.54 0.00 0.00 3.16
125 126 1.342672 ACCGACAAGTTGACCCCACT 61.343 55.000 10.54 0.00 0.00 4.00
126 127 0.464916 AACCGACAAGTTGACCCCAC 60.465 55.000 10.54 0.00 0.00 4.61
127 128 0.256464 AAACCGACAAGTTGACCCCA 59.744 50.000 10.54 0.00 0.00 4.96
128 129 1.066454 CAAAACCGACAAGTTGACCCC 59.934 52.381 10.54 0.00 0.00 4.95
129 130 1.535226 GCAAAACCGACAAGTTGACCC 60.535 52.381 10.54 0.00 0.00 4.46
130 131 1.404035 AGCAAAACCGACAAGTTGACC 59.596 47.619 10.54 0.00 0.00 4.02
131 132 2.844122 AGCAAAACCGACAAGTTGAC 57.156 45.000 10.54 2.00 0.00 3.18
132 133 5.508200 AAATAGCAAAACCGACAAGTTGA 57.492 34.783 10.54 0.00 0.00 3.18
133 134 6.559521 CGAAAAATAGCAAAACCGACAAGTTG 60.560 38.462 0.00 0.00 0.00 3.16
134 135 5.457473 CGAAAAATAGCAAAACCGACAAGTT 59.543 36.000 0.00 0.00 0.00 2.66
135 136 4.973663 CGAAAAATAGCAAAACCGACAAGT 59.026 37.500 0.00 0.00 0.00 3.16
136 137 4.973663 ACGAAAAATAGCAAAACCGACAAG 59.026 37.500 0.00 0.00 0.00 3.16
137 138 4.922719 ACGAAAAATAGCAAAACCGACAA 58.077 34.783 0.00 0.00 0.00 3.18
138 139 4.555348 ACGAAAAATAGCAAAACCGACA 57.445 36.364 0.00 0.00 0.00 4.35
139 140 5.084055 CCTACGAAAAATAGCAAAACCGAC 58.916 41.667 0.00 0.00 0.00 4.79
140 141 4.756135 ACCTACGAAAAATAGCAAAACCGA 59.244 37.500 0.00 0.00 0.00 4.69
141 142 4.849383 CACCTACGAAAAATAGCAAAACCG 59.151 41.667 0.00 0.00 0.00 4.44
142 143 6.004408 TCACCTACGAAAAATAGCAAAACC 57.996 37.500 0.00 0.00 0.00 3.27
143 144 9.783256 ATATTCACCTACGAAAAATAGCAAAAC 57.217 29.630 0.00 0.00 0.00 2.43
153 154 9.027129 CGATTGTCTTATATTCACCTACGAAAA 57.973 33.333 0.00 0.00 0.00 2.29
154 155 7.168637 GCGATTGTCTTATATTCACCTACGAAA 59.831 37.037 0.00 0.00 0.00 3.46
155 156 6.639686 GCGATTGTCTTATATTCACCTACGAA 59.360 38.462 0.00 0.00 0.00 3.85
156 157 6.147581 GCGATTGTCTTATATTCACCTACGA 58.852 40.000 0.00 0.00 0.00 3.43
157 158 5.059343 CGCGATTGTCTTATATTCACCTACG 59.941 44.000 0.00 0.00 0.00 3.51
158 159 5.919141 ACGCGATTGTCTTATATTCACCTAC 59.081 40.000 15.93 0.00 0.00 3.18
159 160 6.080648 ACGCGATTGTCTTATATTCACCTA 57.919 37.500 15.93 0.00 0.00 3.08
160 161 4.945246 ACGCGATTGTCTTATATTCACCT 58.055 39.130 15.93 0.00 0.00 4.00
161 162 5.333111 GGAACGCGATTGTCTTATATTCACC 60.333 44.000 15.93 0.00 0.00 4.02
162 163 5.233476 TGGAACGCGATTGTCTTATATTCAC 59.767 40.000 15.93 0.00 0.00 3.18
163 164 5.233476 GTGGAACGCGATTGTCTTATATTCA 59.767 40.000 15.93 0.00 0.00 2.57
164 165 5.233476 TGTGGAACGCGATTGTCTTATATTC 59.767 40.000 15.93 0.39 45.01 1.75
165 166 5.113383 TGTGGAACGCGATTGTCTTATATT 58.887 37.500 15.93 0.00 45.01 1.28
166 167 4.689071 TGTGGAACGCGATTGTCTTATAT 58.311 39.130 15.93 0.00 45.01 0.86
167 168 4.112716 TGTGGAACGCGATTGTCTTATA 57.887 40.909 15.93 0.00 45.01 0.98
168 169 2.967362 TGTGGAACGCGATTGTCTTAT 58.033 42.857 15.93 0.00 45.01 1.73
169 170 2.442212 TGTGGAACGCGATTGTCTTA 57.558 45.000 15.93 0.00 45.01 2.10
170 171 1.808411 ATGTGGAACGCGATTGTCTT 58.192 45.000 15.93 0.00 45.01 3.01
171 172 1.464608 CAATGTGGAACGCGATTGTCT 59.535 47.619 15.93 0.00 45.01 3.41
172 173 1.463056 TCAATGTGGAACGCGATTGTC 59.537 47.619 15.93 4.05 45.01 3.18
173 174 1.518325 TCAATGTGGAACGCGATTGT 58.482 45.000 15.93 0.00 45.01 2.71
174 175 2.610219 TTCAATGTGGAACGCGATTG 57.390 45.000 15.93 11.55 45.01 2.67
175 176 2.731968 GCATTCAATGTGGAACGCGATT 60.732 45.455 15.93 2.74 45.01 3.34
176 177 1.202177 GCATTCAATGTGGAACGCGAT 60.202 47.619 15.93 0.00 45.01 4.58
177 178 0.167908 GCATTCAATGTGGAACGCGA 59.832 50.000 15.93 0.00 45.01 5.87
178 179 0.109827 TGCATTCAATGTGGAACGCG 60.110 50.000 3.53 3.53 45.01 6.01
179 180 2.282701 ATGCATTCAATGTGGAACGC 57.717 45.000 0.00 0.00 42.39 4.84
180 181 5.594724 AAAAATGCATTCAATGTGGAACG 57.405 34.783 13.38 0.00 42.39 3.95
209 210 6.549364 ACCATATTCAAGTCAGGTCACAAAAA 59.451 34.615 0.00 0.00 0.00 1.94
210 211 6.068010 ACCATATTCAAGTCAGGTCACAAAA 58.932 36.000 0.00 0.00 0.00 2.44
211 212 5.630121 ACCATATTCAAGTCAGGTCACAAA 58.370 37.500 0.00 0.00 0.00 2.83
212 213 5.241403 ACCATATTCAAGTCAGGTCACAA 57.759 39.130 0.00 0.00 0.00 3.33
213 214 4.908601 ACCATATTCAAGTCAGGTCACA 57.091 40.909 0.00 0.00 0.00 3.58
214 215 5.978814 AGTACCATATTCAAGTCAGGTCAC 58.021 41.667 0.00 0.00 0.00 3.67
215 216 7.727578 TTAGTACCATATTCAAGTCAGGTCA 57.272 36.000 0.00 0.00 0.00 4.02
216 217 9.614792 AATTTAGTACCATATTCAAGTCAGGTC 57.385 33.333 0.00 0.00 0.00 3.85
217 218 9.396022 CAATTTAGTACCATATTCAAGTCAGGT 57.604 33.333 0.00 0.00 0.00 4.00
218 219 9.396022 ACAATTTAGTACCATATTCAAGTCAGG 57.604 33.333 0.00 0.00 0.00 3.86
227 228 9.788889 GGCTAGGTAACAATTTAGTACCATATT 57.211 33.333 10.25 0.00 41.41 1.28
228 229 8.092687 CGGCTAGGTAACAATTTAGTACCATAT 58.907 37.037 10.25 0.00 41.41 1.78
229 230 7.436118 CGGCTAGGTAACAATTTAGTACCATA 58.564 38.462 10.25 2.30 41.41 2.74
230 231 6.285990 CGGCTAGGTAACAATTTAGTACCAT 58.714 40.000 10.25 1.51 41.41 3.55
231 232 5.395546 CCGGCTAGGTAACAATTTAGTACCA 60.396 44.000 10.25 0.00 41.41 3.25
232 233 5.052481 CCGGCTAGGTAACAATTTAGTACC 58.948 45.833 0.00 2.09 41.41 3.34
248 249 2.340328 GCCCAAAACCACCGGCTAG 61.340 63.158 0.00 0.00 38.41 3.42
249 250 2.282603 GCCCAAAACCACCGGCTA 60.283 61.111 0.00 0.00 38.41 3.93
250 251 4.531426 TGCCCAAAACCACCGGCT 62.531 61.111 0.00 0.00 42.15 5.52
251 252 2.390306 ATTTGCCCAAAACCACCGGC 62.390 55.000 0.00 0.00 41.99 6.13
252 253 0.969894 TATTTGCCCAAAACCACCGG 59.030 50.000 0.00 0.00 33.56 5.28
253 254 2.036604 AGTTATTTGCCCAAAACCACCG 59.963 45.455 0.00 0.00 33.56 4.94
254 255 3.659786 GAGTTATTTGCCCAAAACCACC 58.340 45.455 0.00 0.00 33.56 4.61
255 256 3.313690 CGAGTTATTTGCCCAAAACCAC 58.686 45.455 0.00 0.00 33.56 4.16
256 257 2.297597 CCGAGTTATTTGCCCAAAACCA 59.702 45.455 0.00 0.00 33.56 3.67
257 258 2.929161 GCCGAGTTATTTGCCCAAAACC 60.929 50.000 0.00 0.00 33.56 3.27
258 259 2.333926 GCCGAGTTATTTGCCCAAAAC 58.666 47.619 0.00 0.00 33.56 2.43
259 260 1.068194 CGCCGAGTTATTTGCCCAAAA 60.068 47.619 0.00 0.00 33.56 2.44
260 261 0.523966 CGCCGAGTTATTTGCCCAAA 59.476 50.000 0.00 0.00 34.46 3.28
261 262 0.321741 TCGCCGAGTTATTTGCCCAA 60.322 50.000 0.00 0.00 0.00 4.12
262 263 0.742990 CTCGCCGAGTTATTTGCCCA 60.743 55.000 5.82 0.00 0.00 5.36
263 264 0.461339 TCTCGCCGAGTTATTTGCCC 60.461 55.000 14.64 0.00 0.00 5.36
264 265 0.651031 GTCTCGCCGAGTTATTTGCC 59.349 55.000 14.64 0.00 0.00 4.52
265 266 0.297820 CGTCTCGCCGAGTTATTTGC 59.702 55.000 14.64 0.00 0.00 3.68
266 267 1.582502 GTCGTCTCGCCGAGTTATTTG 59.417 52.381 14.64 0.00 37.56 2.32
267 268 1.200716 TGTCGTCTCGCCGAGTTATTT 59.799 47.619 14.64 0.00 37.56 1.40
268 269 0.806868 TGTCGTCTCGCCGAGTTATT 59.193 50.000 14.64 0.00 37.56 1.40
269 270 0.806868 TTGTCGTCTCGCCGAGTTAT 59.193 50.000 14.64 0.00 37.56 1.89
270 271 0.806868 ATTGTCGTCTCGCCGAGTTA 59.193 50.000 14.64 0.00 37.56 2.24
271 272 0.806868 TATTGTCGTCTCGCCGAGTT 59.193 50.000 14.64 0.00 37.56 3.01
272 273 0.098376 GTATTGTCGTCTCGCCGAGT 59.902 55.000 14.64 0.00 37.56 4.18
273 274 0.377554 AGTATTGTCGTCTCGCCGAG 59.622 55.000 8.05 8.05 37.56 4.63
274 275 1.655484 TAGTATTGTCGTCTCGCCGA 58.345 50.000 0.00 0.00 33.79 5.54
275 276 2.107178 GTTAGTATTGTCGTCTCGCCG 58.893 52.381 0.00 0.00 0.00 6.46
276 277 2.098770 AGGTTAGTATTGTCGTCTCGCC 59.901 50.000 0.00 0.00 0.00 5.54
277 278 3.417690 AGGTTAGTATTGTCGTCTCGC 57.582 47.619 0.00 0.00 0.00 5.03
278 279 4.574013 AGGTAGGTTAGTATTGTCGTCTCG 59.426 45.833 0.00 0.00 0.00 4.04
279 280 5.008514 GGAGGTAGGTTAGTATTGTCGTCTC 59.991 48.000 0.00 0.00 0.00 3.36
280 281 4.886489 GGAGGTAGGTTAGTATTGTCGTCT 59.114 45.833 0.00 0.00 0.00 4.18
281 282 4.886489 AGGAGGTAGGTTAGTATTGTCGTC 59.114 45.833 0.00 0.00 0.00 4.20
282 283 4.864726 AGGAGGTAGGTTAGTATTGTCGT 58.135 43.478 0.00 0.00 0.00 4.34
283 284 4.277921 GGAGGAGGTAGGTTAGTATTGTCG 59.722 50.000 0.00 0.00 0.00 4.35
284 285 4.588106 GGGAGGAGGTAGGTTAGTATTGTC 59.412 50.000 0.00 0.00 0.00 3.18
285 286 4.234693 AGGGAGGAGGTAGGTTAGTATTGT 59.765 45.833 0.00 0.00 0.00 2.71
286 287 4.817286 AGGGAGGAGGTAGGTTAGTATTG 58.183 47.826 0.00 0.00 0.00 1.90
287 288 4.140734 GGAGGGAGGAGGTAGGTTAGTATT 60.141 50.000 0.00 0.00 0.00 1.89
288 289 3.402025 GGAGGGAGGAGGTAGGTTAGTAT 59.598 52.174 0.00 0.00 0.00 2.12
289 290 2.788215 GGAGGGAGGAGGTAGGTTAGTA 59.212 54.545 0.00 0.00 0.00 1.82
290 291 1.574821 GGAGGGAGGAGGTAGGTTAGT 59.425 57.143 0.00 0.00 0.00 2.24
291 292 1.133104 GGGAGGGAGGAGGTAGGTTAG 60.133 61.905 0.00 0.00 0.00 2.34
292 293 0.939698 GGGAGGGAGGAGGTAGGTTA 59.060 60.000 0.00 0.00 0.00 2.85
293 294 1.710972 GGGAGGGAGGAGGTAGGTT 59.289 63.158 0.00 0.00 0.00 3.50
329 330 3.420214 GATCTACCGGCGGCGAACA 62.420 63.158 34.49 15.73 0.00 3.18
468 477 2.199236 CCAGATTTACGAACCGCCTAC 58.801 52.381 0.00 0.00 0.00 3.18
469 478 1.137479 CCCAGATTTACGAACCGCCTA 59.863 52.381 0.00 0.00 0.00 3.93
500 509 1.007011 CGAATAGACGCGTTTGAGCTG 60.007 52.381 15.53 0.00 34.40 4.24
567 577 4.189188 GCGCGGCCGTCTCTTCTA 62.189 66.667 28.70 0.00 36.67 2.10
715 731 3.501458 GACTACCGGCGGCCTCATC 62.501 68.421 28.71 13.07 0.00 2.92
967 983 5.398603 AGGACCTGATCGATGATGTAATC 57.601 43.478 0.54 0.00 45.83 1.75
968 984 5.775195 TGTAGGACCTGATCGATGATGTAAT 59.225 40.000 0.54 0.00 0.00 1.89
969 985 5.009710 GTGTAGGACCTGATCGATGATGTAA 59.990 44.000 0.54 0.00 0.00 2.41
993 1009 2.591715 GATTCCGCCATGTCCGGG 60.592 66.667 18.43 2.86 45.60 5.73
1095 1112 2.692368 ATGATCCACGGGGGCAGT 60.692 61.111 2.42 0.00 36.21 4.40
1418 1436 4.465512 CATTCGGCTGCCACGTGC 62.466 66.667 20.29 6.53 41.77 5.34
1419 1437 1.647545 ATTCATTCGGCTGCCACGTG 61.648 55.000 20.29 9.08 0.00 4.49
1420 1438 0.960364 AATTCATTCGGCTGCCACGT 60.960 50.000 20.29 0.00 0.00 4.49
1421 1439 0.523968 CAATTCATTCGGCTGCCACG 60.524 55.000 20.29 5.67 0.00 4.94
1422 1440 0.527565 ACAATTCATTCGGCTGCCAC 59.472 50.000 20.29 0.00 0.00 5.01
1423 1441 0.527113 CACAATTCATTCGGCTGCCA 59.473 50.000 20.29 0.00 0.00 4.92
1490 1510 7.750458 TGTCGAATTTCATGTCATTAAAGAAGC 59.250 33.333 0.00 0.00 0.00 3.86
1597 1617 5.576384 TGCAGTTGAAATTGTCTTTGTTGAC 59.424 36.000 0.00 0.00 37.47 3.18
1598 1618 5.718146 TGCAGTTGAAATTGTCTTTGTTGA 58.282 33.333 0.00 0.00 0.00 3.18
1642 1677 1.317613 TTGTTGCCATCGTCTTTGCT 58.682 45.000 0.00 0.00 0.00 3.91
1807 1851 3.578716 AGTCAAAACCACTAGCTAGCTGA 59.421 43.478 27.68 10.36 0.00 4.26
1821 1865 5.079406 CACGCACACATACATAGTCAAAAC 58.921 41.667 0.00 0.00 0.00 2.43
1854 1898 7.880195 ACTGAACTGATAGCAAATTAAGTCACT 59.120 33.333 0.00 0.00 0.00 3.41
1901 1947 1.270839 TGCTGTAAACAGGGAGCAGAC 60.271 52.381 11.86 0.00 43.94 3.51
1993 2060 6.955851 AGGGAGGTACAATTTACAGTACAGTA 59.044 38.462 0.00 0.00 41.74 2.74
1994 2061 5.783875 AGGGAGGTACAATTTACAGTACAGT 59.216 40.000 0.00 0.00 41.74 3.55
1995 2062 6.106673 CAGGGAGGTACAATTTACAGTACAG 58.893 44.000 0.00 0.00 41.74 2.74
1996 2063 5.046159 CCAGGGAGGTACAATTTACAGTACA 60.046 44.000 0.00 0.00 41.74 2.90
1997 2064 5.425630 CCAGGGAGGTACAATTTACAGTAC 58.574 45.833 0.00 0.00 39.80 2.73
1998 2065 5.687166 CCAGGGAGGTACAATTTACAGTA 57.313 43.478 0.00 0.00 0.00 2.74
2244 2317 3.347958 TTTACGCTTGGCTCAAAGTTG 57.652 42.857 0.00 0.00 0.00 3.16
2259 2332 9.864034 ATGAAGAAGCGACATAAATAATTTACG 57.136 29.630 0.00 0.00 0.00 3.18
2428 2502 8.371699 CACCCATAAATACAAAGGGAAGAAAAA 58.628 33.333 2.29 0.00 42.25 1.94
2429 2503 7.730784 TCACCCATAAATACAAAGGGAAGAAAA 59.269 33.333 2.29 0.00 42.25 2.29
2433 2507 8.940397 ATATCACCCATAAATACAAAGGGAAG 57.060 34.615 2.29 0.00 42.25 3.46
2507 2581 3.190535 GCTGTAATTCCCTTTTCGAAGCA 59.809 43.478 0.00 0.00 0.00 3.91
2555 3304 8.033038 ACTAAAGTATTGATCAGCGAAGTTACA 58.967 33.333 0.00 0.00 0.00 2.41
2588 3337 6.764560 ACCGTGTAGTTTCTTCAAGTTTACAT 59.235 34.615 0.00 0.00 0.00 2.29
2634 3383 2.795231 ATTGCACTGGACACTATGCT 57.205 45.000 0.00 0.00 38.90 3.79
2635 3384 3.428045 GGAAATTGCACTGGACACTATGC 60.428 47.826 0.00 0.00 38.59 3.14


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

AutoCloner maintained by Alex Coulton.