Multiple sequence alignment - TraesCS1D01G407700

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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 TraesCS1D01G407700 chr1D 100.000 3230 0 0 1 3230 470526349 470523120 0.000000e+00 5965.0
1 TraesCS1D01G407700 chr1D 92.922 1441 92 6 873 2313 470198289 470199719 0.000000e+00 2087.0
2 TraesCS1D01G407700 chr1D 83.416 1405 198 24 789 2181 470189901 470191282 0.000000e+00 1271.0
3 TraesCS1D01G407700 chr1D 80.125 1278 220 20 981 2248 470077553 470078806 0.000000e+00 922.0
4 TraesCS1D01G407700 chr1D 92.952 227 15 1 5 230 199680069 199679843 2.400000e-86 329.0
5 TraesCS1D01G407700 chr1D 88.942 208 17 4 2850 3057 470536054 470535853 5.350000e-63 252.0
6 TraesCS1D01G407700 chr1D 78.641 206 26 11 2646 2836 470536568 470536366 1.570000e-23 121.0
7 TraesCS1D01G407700 chr1D 75.714 210 30 7 2645 2836 470544713 470544507 5.740000e-13 86.1
8 TraesCS1D01G407700 chr1B 94.207 1847 59 17 509 2321 653239063 653237231 0.000000e+00 2774.0
9 TraesCS1D01G407700 chr1B 92.734 1679 97 10 649 2311 652638490 652640159 0.000000e+00 2401.0
10 TraesCS1D01G407700 chr1B 88.610 1554 155 13 788 2340 652632931 652634463 0.000000e+00 1869.0
11 TraesCS1D01G407700 chr1B 81.801 2154 255 82 346 2441 652574134 652576208 0.000000e+00 1679.0
12 TraesCS1D01G407700 chr1B 89.413 954 49 19 2312 3230 653237207 653236271 0.000000e+00 1155.0
13 TraesCS1D01G407700 chr1B 80.520 1576 226 46 687 2232 652569644 652571168 0.000000e+00 1134.0
14 TraesCS1D01G407700 chr1B 79.652 1263 222 17 999 2248 652459744 652460984 0.000000e+00 876.0
15 TraesCS1D01G407700 chr1B 80.127 785 133 16 972 1745 652467685 652468457 6.050000e-157 564.0
16 TraesCS1D01G407700 chr1B 91.985 262 15 2 227 488 653239776 653239521 2.370000e-96 363.0
17 TraesCS1D01G407700 chr1B 92.340 235 14 1 1 231 565328332 565328566 6.680000e-87 331.0
18 TraesCS1D01G407700 chr1B 78.161 522 99 10 1798 2314 652468540 652469051 5.200000e-83 318.0
19 TraesCS1D01G407700 chr1B 87.302 189 24 0 2648 2836 683109466 683109278 1.950000e-52 217.0
20 TraesCS1D01G407700 chr1B 84.103 195 28 2 2645 2836 653683563 653683369 5.500000e-43 185.0
21 TraesCS1D01G407700 chr1B 84.375 192 20 7 2645 2836 653526788 653526607 2.560000e-41 180.0
22 TraesCS1D01G407700 chr1B 80.786 229 21 15 2312 2533 652577265 652577477 1.200000e-34 158.0
23 TraesCS1D01G407700 chr1B 77.143 210 27 10 2645 2836 653836020 653836226 5.700000e-18 102.0
24 TraesCS1D01G407700 chr1B 91.489 47 4 0 2579 2625 652577492 652577538 7.480000e-07 65.8
25 TraesCS1D01G407700 chr1A 80.799 1552 232 40 789 2315 563783399 563784909 0.000000e+00 1155.0
26 TraesCS1D01G407700 chr1A 81.766 1212 157 40 688 1879 563791086 563792253 0.000000e+00 955.0
27 TraesCS1D01G407700 chr1A 80.599 768 122 18 990 1745 563695358 563696110 4.680000e-158 568.0
28 TraesCS1D01G407700 chr1A 85.149 303 11 6 2931 3228 564118120 564117847 2.450000e-71 279.0
29 TraesCS1D01G407700 chr1A 82.039 206 18 12 2645 2836 564130859 564130659 1.200000e-34 158.0
30 TraesCS1D01G407700 chr1A 77.251 211 25 10 2645 2836 564140214 564140008 5.700000e-18 102.0
31 TraesCS1D01G407700 chr7A 93.590 234 9 4 1 230 521555508 521555739 8.580000e-91 344.0
32 TraesCS1D01G407700 chr5B 93.450 229 13 2 3 230 699665782 699666009 3.990000e-89 339.0
33 TraesCS1D01G407700 chr3B 93.421 228 14 1 3 230 527907232 527907458 1.440000e-88 337.0
34 TraesCS1D01G407700 chr6D 93.392 227 14 1 5 230 420535640 420535866 5.160000e-88 335.0
35 TraesCS1D01G407700 chr3D 92.982 228 15 1 5 231 70273864 70274091 6.680000e-87 331.0
36 TraesCS1D01G407700 chr7D 92.952 227 15 1 5 230 543606126 543606352 2.400000e-86 329.0
37 TraesCS1D01G407700 chr2B 90.708 226 20 1 6 230 395539517 395539742 1.880000e-77 300.0


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 TraesCS1D01G407700 chr1D 470523120 470526349 3229 True 5965.000000 5965 100.000000 1 3230 1 chr1D.!!$R2 3229
1 TraesCS1D01G407700 chr1D 470198289 470199719 1430 False 2087.000000 2087 92.922000 873 2313 1 chr1D.!!$F3 1440
2 TraesCS1D01G407700 chr1D 470189901 470191282 1381 False 1271.000000 1271 83.416000 789 2181 1 chr1D.!!$F2 1392
3 TraesCS1D01G407700 chr1D 470077553 470078806 1253 False 922.000000 922 80.125000 981 2248 1 chr1D.!!$F1 1267
4 TraesCS1D01G407700 chr1B 652638490 652640159 1669 False 2401.000000 2401 92.734000 649 2311 1 chr1B.!!$F4 1662
5 TraesCS1D01G407700 chr1B 652632931 652634463 1532 False 1869.000000 1869 88.610000 788 2340 1 chr1B.!!$F3 1552
6 TraesCS1D01G407700 chr1B 653236271 653239776 3505 True 1430.666667 2774 91.868333 227 3230 3 chr1B.!!$R4 3003
7 TraesCS1D01G407700 chr1B 652459744 652460984 1240 False 876.000000 876 79.652000 999 2248 1 chr1B.!!$F2 1249
8 TraesCS1D01G407700 chr1B 652569644 652577538 7894 False 759.200000 1679 83.649000 346 2625 4 chr1B.!!$F7 2279
9 TraesCS1D01G407700 chr1B 652467685 652469051 1366 False 441.000000 564 79.144000 972 2314 2 chr1B.!!$F6 1342
10 TraesCS1D01G407700 chr1A 563783399 563784909 1510 False 1155.000000 1155 80.799000 789 2315 1 chr1A.!!$F2 1526
11 TraesCS1D01G407700 chr1A 563791086 563792253 1167 False 955.000000 955 81.766000 688 1879 1 chr1A.!!$F3 1191
12 TraesCS1D01G407700 chr1A 563695358 563696110 752 False 568.000000 568 80.599000 990 1745 1 chr1A.!!$F1 755

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
143 144 0.193069 ATCCATCTCCCTAGCCAGCT 59.807 55.0 0.0 0.0 0.0 4.24 F
827 1303 0.254462 CCCTCCTCTTGCTTCTTCCC 59.746 60.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1055 1559 0.179034 CAATCCTGCTAGGTCCAGCC 60.179 60.000 9.85 0.0 41.04 4.85 R
2584 9145 1.002087 CCTGACGTTCAAGGGCTACTT 59.998 52.381 5.26 0.0 41.00 2.24 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
35 36 9.823647 TTTGGACAGAAAATAAATAAGCAAACA 57.176 25.926 0.00 0.00 0.00 2.83
36 37 9.474920 TTGGACAGAAAATAAATAAGCAAACAG 57.525 29.630 0.00 0.00 0.00 3.16
37 38 8.637986 TGGACAGAAAATAAATAAGCAAACAGT 58.362 29.630 0.00 0.00 0.00 3.55
38 39 9.476202 GGACAGAAAATAAATAAGCAAACAGTT 57.524 29.630 0.00 0.00 0.00 3.16
53 54 8.409358 AGCAAACAGTTTTATTATGGAAGACT 57.591 30.769 0.00 0.00 0.00 3.24
54 55 8.299570 AGCAAACAGTTTTATTATGGAAGACTG 58.700 33.333 0.00 4.93 39.04 3.51
55 56 8.296713 GCAAACAGTTTTATTATGGAAGACTGA 58.703 33.333 11.63 0.00 37.17 3.41
56 57 9.831737 CAAACAGTTTTATTATGGAAGACTGAG 57.168 33.333 11.63 0.66 37.17 3.35
57 58 9.793259 AAACAGTTTTATTATGGAAGACTGAGA 57.207 29.630 11.63 0.00 37.17 3.27
58 59 9.793259 AACAGTTTTATTATGGAAGACTGAGAA 57.207 29.630 11.63 0.00 37.17 2.87
59 60 9.965902 ACAGTTTTATTATGGAAGACTGAGAAT 57.034 29.630 11.63 0.00 37.17 2.40
61 62 9.965902 AGTTTTATTATGGAAGACTGAGAATGT 57.034 29.630 0.00 0.00 0.00 2.71
62 63 9.994432 GTTTTATTATGGAAGACTGAGAATGTG 57.006 33.333 0.00 0.00 0.00 3.21
63 64 9.958180 TTTTATTATGGAAGACTGAGAATGTGA 57.042 29.630 0.00 0.00 0.00 3.58
64 65 9.605275 TTTATTATGGAAGACTGAGAATGTGAG 57.395 33.333 0.00 0.00 0.00 3.51
65 66 6.857437 TTATGGAAGACTGAGAATGTGAGA 57.143 37.500 0.00 0.00 0.00 3.27
66 67 5.954153 ATGGAAGACTGAGAATGTGAGAT 57.046 39.130 0.00 0.00 0.00 2.75
67 68 8.539117 TTATGGAAGACTGAGAATGTGAGATA 57.461 34.615 0.00 0.00 0.00 1.98
68 69 7.615039 ATGGAAGACTGAGAATGTGAGATAT 57.385 36.000 0.00 0.00 0.00 1.63
69 70 6.814043 TGGAAGACTGAGAATGTGAGATATG 58.186 40.000 0.00 0.00 0.00 1.78
70 71 6.183360 TGGAAGACTGAGAATGTGAGATATGG 60.183 42.308 0.00 0.00 0.00 2.74
71 72 6.041409 GGAAGACTGAGAATGTGAGATATGGA 59.959 42.308 0.00 0.00 0.00 3.41
72 73 6.653526 AGACTGAGAATGTGAGATATGGAG 57.346 41.667 0.00 0.00 0.00 3.86
73 74 6.135454 AGACTGAGAATGTGAGATATGGAGT 58.865 40.000 0.00 0.00 0.00 3.85
74 75 6.040729 AGACTGAGAATGTGAGATATGGAGTG 59.959 42.308 0.00 0.00 0.00 3.51
75 76 4.953667 TGAGAATGTGAGATATGGAGTGC 58.046 43.478 0.00 0.00 0.00 4.40
76 77 3.986572 GAGAATGTGAGATATGGAGTGCG 59.013 47.826 0.00 0.00 0.00 5.34
77 78 2.827800 ATGTGAGATATGGAGTGCGG 57.172 50.000 0.00 0.00 0.00 5.69
78 79 0.752658 TGTGAGATATGGAGTGCGGG 59.247 55.000 0.00 0.00 0.00 6.13
79 80 0.753262 GTGAGATATGGAGTGCGGGT 59.247 55.000 0.00 0.00 0.00 5.28
80 81 1.139058 GTGAGATATGGAGTGCGGGTT 59.861 52.381 0.00 0.00 0.00 4.11
81 82 2.364324 GTGAGATATGGAGTGCGGGTTA 59.636 50.000 0.00 0.00 0.00 2.85
82 83 3.035363 TGAGATATGGAGTGCGGGTTAA 58.965 45.455 0.00 0.00 0.00 2.01
83 84 3.646162 TGAGATATGGAGTGCGGGTTAAT 59.354 43.478 0.00 0.00 0.00 1.40
84 85 4.102524 TGAGATATGGAGTGCGGGTTAATT 59.897 41.667 0.00 0.00 0.00 1.40
85 86 5.048846 AGATATGGAGTGCGGGTTAATTT 57.951 39.130 0.00 0.00 0.00 1.82
86 87 5.063880 AGATATGGAGTGCGGGTTAATTTC 58.936 41.667 0.00 0.00 0.00 2.17
87 88 2.871096 TGGAGTGCGGGTTAATTTCT 57.129 45.000 0.00 0.00 0.00 2.52
88 89 3.985019 TGGAGTGCGGGTTAATTTCTA 57.015 42.857 0.00 0.00 0.00 2.10
89 90 4.289238 TGGAGTGCGGGTTAATTTCTAA 57.711 40.909 0.00 0.00 0.00 2.10
90 91 4.653868 TGGAGTGCGGGTTAATTTCTAAA 58.346 39.130 0.00 0.00 0.00 1.85
91 92 5.258051 TGGAGTGCGGGTTAATTTCTAAAT 58.742 37.500 0.00 0.00 0.00 1.40
92 93 6.416415 TGGAGTGCGGGTTAATTTCTAAATA 58.584 36.000 0.00 0.00 0.00 1.40
93 94 6.885376 TGGAGTGCGGGTTAATTTCTAAATAA 59.115 34.615 0.00 0.00 0.00 1.40
94 95 7.558444 TGGAGTGCGGGTTAATTTCTAAATAAT 59.442 33.333 0.00 0.00 0.00 1.28
95 96 9.059260 GGAGTGCGGGTTAATTTCTAAATAATA 57.941 33.333 0.00 0.00 0.00 0.98
97 98 9.841295 AGTGCGGGTTAATTTCTAAATAATAGA 57.159 29.630 0.00 0.00 0.00 1.98
119 120 7.158099 AGAAGGACTATTTTGCAAATGTACC 57.842 36.000 13.65 12.60 0.00 3.34
120 121 6.719370 AGAAGGACTATTTTGCAAATGTACCA 59.281 34.615 13.65 0.00 0.00 3.25
121 122 6.909550 AGGACTATTTTGCAAATGTACCAA 57.090 33.333 13.65 0.00 0.00 3.67
122 123 6.687604 AGGACTATTTTGCAAATGTACCAAC 58.312 36.000 13.65 0.37 0.00 3.77
123 124 5.867174 GGACTATTTTGCAAATGTACCAACC 59.133 40.000 13.65 6.12 0.00 3.77
124 125 6.412362 ACTATTTTGCAAATGTACCAACCA 57.588 33.333 13.65 0.00 0.00 3.67
125 126 7.003402 ACTATTTTGCAAATGTACCAACCAT 57.997 32.000 13.65 1.88 0.00 3.55
126 127 7.096551 ACTATTTTGCAAATGTACCAACCATC 58.903 34.615 13.65 0.00 0.00 3.51
127 128 3.951775 TTGCAAATGTACCAACCATCC 57.048 42.857 0.00 0.00 0.00 3.51
128 129 2.881734 TGCAAATGTACCAACCATCCA 58.118 42.857 0.00 0.00 0.00 3.41
129 130 3.439154 TGCAAATGTACCAACCATCCAT 58.561 40.909 0.00 0.00 0.00 3.41
130 131 3.446873 TGCAAATGTACCAACCATCCATC 59.553 43.478 0.00 0.00 0.00 3.51
131 132 3.701040 GCAAATGTACCAACCATCCATCT 59.299 43.478 0.00 0.00 0.00 2.90
132 133 4.202050 GCAAATGTACCAACCATCCATCTC 60.202 45.833 0.00 0.00 0.00 2.75
133 134 3.864789 ATGTACCAACCATCCATCTCC 57.135 47.619 0.00 0.00 0.00 3.71
134 135 1.843851 TGTACCAACCATCCATCTCCC 59.156 52.381 0.00 0.00 0.00 4.30
135 136 2.127708 GTACCAACCATCCATCTCCCT 58.872 52.381 0.00 0.00 0.00 4.20
136 137 2.587060 ACCAACCATCCATCTCCCTA 57.413 50.000 0.00 0.00 0.00 3.53
137 138 2.412591 ACCAACCATCCATCTCCCTAG 58.587 52.381 0.00 0.00 0.00 3.02
138 139 1.072965 CCAACCATCCATCTCCCTAGC 59.927 57.143 0.00 0.00 0.00 3.42
139 140 1.072965 CAACCATCCATCTCCCTAGCC 59.927 57.143 0.00 0.00 0.00 3.93
140 141 0.268869 ACCATCCATCTCCCTAGCCA 59.731 55.000 0.00 0.00 0.00 4.75
141 142 0.982704 CCATCCATCTCCCTAGCCAG 59.017 60.000 0.00 0.00 0.00 4.85
142 143 0.324285 CATCCATCTCCCTAGCCAGC 59.676 60.000 0.00 0.00 0.00 4.85
143 144 0.193069 ATCCATCTCCCTAGCCAGCT 59.807 55.000 0.00 0.00 0.00 4.24
144 145 0.470833 TCCATCTCCCTAGCCAGCTC 60.471 60.000 0.00 0.00 0.00 4.09
145 146 0.762082 CCATCTCCCTAGCCAGCTCA 60.762 60.000 0.00 0.00 0.00 4.26
146 147 1.350071 CATCTCCCTAGCCAGCTCAT 58.650 55.000 0.00 0.00 0.00 2.90
147 148 1.275856 CATCTCCCTAGCCAGCTCATC 59.724 57.143 0.00 0.00 0.00 2.92
148 149 0.560193 TCTCCCTAGCCAGCTCATCT 59.440 55.000 0.00 0.00 0.00 2.90
149 150 0.968405 CTCCCTAGCCAGCTCATCTC 59.032 60.000 0.00 0.00 0.00 2.75
150 151 0.470833 TCCCTAGCCAGCTCATCTCC 60.471 60.000 0.00 0.00 0.00 3.71
151 152 1.479368 CCCTAGCCAGCTCATCTCCC 61.479 65.000 0.00 0.00 0.00 4.30
152 153 0.471591 CCTAGCCAGCTCATCTCCCT 60.472 60.000 0.00 0.00 0.00 4.20
153 154 0.968405 CTAGCCAGCTCATCTCCCTC 59.032 60.000 0.00 0.00 0.00 4.30
154 155 0.560193 TAGCCAGCTCATCTCCCTCT 59.440 55.000 0.00 0.00 0.00 3.69
155 156 0.560193 AGCCAGCTCATCTCCCTCTA 59.440 55.000 0.00 0.00 0.00 2.43
156 157 1.149711 AGCCAGCTCATCTCCCTCTAT 59.850 52.381 0.00 0.00 0.00 1.98
157 158 1.977129 GCCAGCTCATCTCCCTCTATT 59.023 52.381 0.00 0.00 0.00 1.73
158 159 2.371510 GCCAGCTCATCTCCCTCTATTT 59.628 50.000 0.00 0.00 0.00 1.40
159 160 3.181446 GCCAGCTCATCTCCCTCTATTTT 60.181 47.826 0.00 0.00 0.00 1.82
160 161 4.387598 CCAGCTCATCTCCCTCTATTTTG 58.612 47.826 0.00 0.00 0.00 2.44
161 162 4.141528 CCAGCTCATCTCCCTCTATTTTGT 60.142 45.833 0.00 0.00 0.00 2.83
162 163 5.070981 CCAGCTCATCTCCCTCTATTTTGTA 59.929 44.000 0.00 0.00 0.00 2.41
163 164 6.239829 CCAGCTCATCTCCCTCTATTTTGTAT 60.240 42.308 0.00 0.00 0.00 2.29
164 165 6.873076 CAGCTCATCTCCCTCTATTTTGTATC 59.127 42.308 0.00 0.00 0.00 2.24
165 166 6.013812 AGCTCATCTCCCTCTATTTTGTATCC 60.014 42.308 0.00 0.00 0.00 2.59
166 167 6.239714 GCTCATCTCCCTCTATTTTGTATCCA 60.240 42.308 0.00 0.00 0.00 3.41
167 168 7.690301 GCTCATCTCCCTCTATTTTGTATCCAA 60.690 40.741 0.00 0.00 0.00 3.53
168 169 8.280258 TCATCTCCCTCTATTTTGTATCCAAT 57.720 34.615 0.00 0.00 0.00 3.16
169 170 8.159447 TCATCTCCCTCTATTTTGTATCCAATG 58.841 37.037 0.00 0.00 0.00 2.82
170 171 6.841601 TCTCCCTCTATTTTGTATCCAATGG 58.158 40.000 0.00 0.00 0.00 3.16
171 172 5.385198 TCCCTCTATTTTGTATCCAATGGC 58.615 41.667 0.00 0.00 0.00 4.40
172 173 5.134339 TCCCTCTATTTTGTATCCAATGGCT 59.866 40.000 0.00 0.00 0.00 4.75
173 174 5.835280 CCCTCTATTTTGTATCCAATGGCTT 59.165 40.000 0.00 0.00 0.00 4.35
174 175 7.004086 CCCTCTATTTTGTATCCAATGGCTTA 58.996 38.462 0.00 0.00 0.00 3.09
175 176 7.671398 CCCTCTATTTTGTATCCAATGGCTTAT 59.329 37.037 0.00 0.00 0.00 1.73
176 177 8.734386 CCTCTATTTTGTATCCAATGGCTTATC 58.266 37.037 0.00 0.00 0.00 1.75
177 178 9.512588 CTCTATTTTGTATCCAATGGCTTATCT 57.487 33.333 0.00 0.00 0.00 1.98
208 209 3.102052 CATTGGGTGCATGAATTAGGC 57.898 47.619 0.00 0.00 36.42 3.93
209 210 1.484038 TTGGGTGCATGAATTAGGCC 58.516 50.000 0.00 0.00 34.56 5.19
210 211 0.751277 TGGGTGCATGAATTAGGCCG 60.751 55.000 0.00 0.00 34.56 6.13
211 212 1.455383 GGGTGCATGAATTAGGCCGG 61.455 60.000 0.00 0.00 34.56 6.13
212 213 0.751643 GGTGCATGAATTAGGCCGGT 60.752 55.000 1.90 0.00 34.56 5.28
213 214 0.381801 GTGCATGAATTAGGCCGGTG 59.618 55.000 1.90 0.00 34.56 4.94
214 215 1.360192 GCATGAATTAGGCCGGTGC 59.640 57.895 1.90 0.00 0.00 5.01
215 216 1.383456 GCATGAATTAGGCCGGTGCA 61.383 55.000 1.90 0.00 40.13 4.57
216 217 0.381801 CATGAATTAGGCCGGTGCAC 59.618 55.000 8.80 8.80 40.13 4.57
217 218 0.255890 ATGAATTAGGCCGGTGCACT 59.744 50.000 17.98 0.00 40.13 4.40
218 219 0.676466 TGAATTAGGCCGGTGCACTG 60.676 55.000 19.25 19.25 40.13 3.66
219 220 1.376609 GAATTAGGCCGGTGCACTGG 61.377 60.000 36.14 36.14 45.30 4.00
220 221 1.847798 AATTAGGCCGGTGCACTGGA 61.848 55.000 42.58 25.34 45.36 3.86
221 222 1.635817 ATTAGGCCGGTGCACTGGAT 61.636 55.000 42.58 31.56 45.36 3.41
222 223 0.978667 TTAGGCCGGTGCACTGGATA 60.979 55.000 42.58 30.58 45.36 2.59
223 224 1.682451 TAGGCCGGTGCACTGGATAC 61.682 60.000 42.58 30.52 45.36 2.24
224 225 2.267642 GCCGGTGCACTGGATACA 59.732 61.111 42.58 0.00 45.36 2.29
225 226 1.153168 GCCGGTGCACTGGATACAT 60.153 57.895 42.58 0.00 45.36 2.29
239 240 2.326529 ATACATCCTCGGGGCCTCCA 62.327 60.000 0.84 0.00 34.36 3.86
244 245 2.765807 CTCGGGGCCTCCATGTCT 60.766 66.667 0.84 0.00 34.36 3.41
246 247 4.227134 CGGGGCCTCCATGTCTCG 62.227 72.222 0.84 0.00 34.36 4.04
247 248 2.764128 GGGGCCTCCATGTCTCGA 60.764 66.667 0.84 0.00 35.00 4.04
260 261 1.600957 TGTCTCGACGACGTCTTCTTT 59.399 47.619 24.36 0.00 45.87 2.52
261 262 2.232524 GTCTCGACGACGTCTTCTTTC 58.767 52.381 24.36 7.52 40.69 2.62
262 263 1.136419 TCTCGACGACGTCTTCTTTCG 60.136 52.381 24.36 14.71 40.69 3.46
272 273 0.756294 TCTTCTTTCGGTGTGAGGCA 59.244 50.000 0.00 0.00 0.00 4.75
278 279 4.720902 CGGTGTGAGGCATGCCCA 62.721 66.667 33.14 25.83 36.58 5.36
287 288 1.200760 AGGCATGCCCACTGTGAGTA 61.201 55.000 33.14 0.00 36.58 2.59
342 343 6.422701 CGCGGGTTATAACATCTAAAATCTCA 59.577 38.462 17.16 0.00 0.00 3.27
449 450 1.335496 TCTTTTGCGGGAAAAACCTCG 59.665 47.619 8.74 0.00 38.98 4.63
458 459 3.252458 CGGGAAAAACCTCGTTTGAAGAT 59.748 43.478 0.00 0.00 35.80 2.40
459 460 4.261447 CGGGAAAAACCTCGTTTGAAGATT 60.261 41.667 0.00 0.00 35.80 2.40
460 461 5.220381 GGGAAAAACCTCGTTTGAAGATTC 58.780 41.667 0.00 0.00 35.80 2.52
461 462 5.220381 GGAAAAACCTCGTTTGAAGATTCC 58.780 41.667 3.27 3.27 35.80 3.01
462 463 5.009710 GGAAAAACCTCGTTTGAAGATTCCT 59.990 40.000 9.09 0.00 35.89 3.36
507 523 5.079643 ACCTGGCAAAATGTTTACTCTGAT 58.920 37.500 0.00 0.00 0.00 2.90
557 995 6.768861 TCTGATTTTTCTTTTACCGAGTTCCA 59.231 34.615 0.00 0.00 0.00 3.53
564 1002 4.215399 TCTTTTACCGAGTTCCATTGCTTG 59.785 41.667 0.00 0.00 0.00 4.01
568 1006 1.135972 CCGAGTTCCATTGCTTGTTCG 60.136 52.381 0.00 0.00 0.00 3.95
579 1017 0.733150 GCTTGTTCGAGGTATTGGGC 59.267 55.000 0.00 0.00 0.00 5.36
580 1018 1.679032 GCTTGTTCGAGGTATTGGGCT 60.679 52.381 0.00 0.00 0.00 5.19
591 1029 3.117512 AGGTATTGGGCTATGTTTGGAGG 60.118 47.826 0.00 0.00 0.00 4.30
626 1064 2.191128 AAATCAGCGAAGAAGCAGGT 57.809 45.000 0.00 0.00 40.15 4.00
651 1089 1.964223 ACTACTGACTGAGTGTGTGGG 59.036 52.381 0.00 0.00 35.96 4.61
818 1294 1.827969 CTGTCTGGTACCCTCCTCTTG 59.172 57.143 10.07 0.00 0.00 3.02
823 1299 1.203313 TGGTACCCTCCTCTTGCTTCT 60.203 52.381 10.07 0.00 0.00 2.85
824 1300 1.909986 GGTACCCTCCTCTTGCTTCTT 59.090 52.381 0.00 0.00 0.00 2.52
825 1301 2.093394 GGTACCCTCCTCTTGCTTCTTC 60.093 54.545 0.00 0.00 0.00 2.87
826 1302 0.988063 ACCCTCCTCTTGCTTCTTCC 59.012 55.000 0.00 0.00 0.00 3.46
827 1303 0.254462 CCCTCCTCTTGCTTCTTCCC 59.746 60.000 0.00 0.00 0.00 3.97
828 1304 1.284313 CCTCCTCTTGCTTCTTCCCT 58.716 55.000 0.00 0.00 0.00 4.20
829 1305 1.209261 CCTCCTCTTGCTTCTTCCCTC 59.791 57.143 0.00 0.00 0.00 4.30
830 1306 1.905215 CTCCTCTTGCTTCTTCCCTCA 59.095 52.381 0.00 0.00 0.00 3.86
831 1307 1.625818 TCCTCTTGCTTCTTCCCTCAC 59.374 52.381 0.00 0.00 0.00 3.51
832 1308 1.339535 CCTCTTGCTTCTTCCCTCACC 60.340 57.143 0.00 0.00 0.00 4.02
833 1309 1.627834 CTCTTGCTTCTTCCCTCACCT 59.372 52.381 0.00 0.00 0.00 4.00
834 1310 2.039613 CTCTTGCTTCTTCCCTCACCTT 59.960 50.000 0.00 0.00 0.00 3.50
835 1311 2.443255 TCTTGCTTCTTCCCTCACCTTT 59.557 45.455 0.00 0.00 0.00 3.11
1055 1559 2.187946 GTCATGGTCAGCCCTCCG 59.812 66.667 0.00 0.00 0.00 4.63
1071 1575 2.759973 CGGCTGGACCTAGCAGGA 60.760 66.667 15.09 0.00 45.46 3.86
1252 6580 0.111253 CTTCCCTGGTTGTGGCTTCT 59.889 55.000 0.00 0.00 0.00 2.85
1269 6597 3.775202 CTTCTCAGGGTACGAGAATGTG 58.225 50.000 10.82 0.00 45.82 3.21
1285 6613 3.876236 TGTGTGGCAGCTGGCTCA 61.876 61.111 36.39 34.75 44.01 4.26
2109 7467 5.716228 AGACTATGCCTATGATGAGGAGAAG 59.284 44.000 0.00 0.00 39.15 2.85
2281 7641 0.107312 CTATGCAAGCTGCTCCCTGT 60.107 55.000 1.00 0.00 45.31 4.00
2317 8873 5.278709 CCATGCTATGGTTGTTGTTGTTGTA 60.279 40.000 6.93 0.00 45.54 2.41
2352 8908 2.403378 GCAAGCCGGGAATGCGTTA 61.403 57.895 2.18 0.00 0.00 3.18
2364 8920 7.675637 GCCGGGAATGCGTTAGTATAAATTATC 60.676 40.741 2.18 0.00 0.00 1.75
2470 9027 2.568956 AGCTGTTATCTGCACAAGAGGA 59.431 45.455 5.59 0.00 38.67 3.71
2497 9058 4.953667 TGCTACTGTGGATGAATGATCTC 58.046 43.478 0.00 0.00 0.00 2.75
2504 9065 5.323581 TGTGGATGAATGATCTCAAAACCA 58.676 37.500 0.00 0.39 0.00 3.67
2521 9082 1.747355 ACCATGTTGCTGCTTATCTGC 59.253 47.619 0.00 0.00 39.73 4.26
2525 9086 2.632377 TGTTGCTGCTTATCTGCCTAC 58.368 47.619 0.00 0.00 38.68 3.18
2528 9089 4.101585 TGTTGCTGCTTATCTGCCTACTAT 59.898 41.667 0.00 0.00 38.68 2.12
2529 9090 4.527509 TGCTGCTTATCTGCCTACTATC 57.472 45.455 0.00 0.00 38.68 2.08
2530 9091 4.155709 TGCTGCTTATCTGCCTACTATCT 58.844 43.478 0.00 0.00 38.68 1.98
2531 9092 4.590647 TGCTGCTTATCTGCCTACTATCTT 59.409 41.667 0.00 0.00 38.68 2.40
2558 9119 3.808728 TGTTGGTCTCTTTCTTGGTCTG 58.191 45.455 0.00 0.00 0.00 3.51
2559 9120 2.550180 GTTGGTCTCTTTCTTGGTCTGC 59.450 50.000 0.00 0.00 0.00 4.26
2567 9128 4.401022 TCTTTCTTGGTCTGCATTGTCAT 58.599 39.130 0.00 0.00 0.00 3.06
2582 9143 4.551702 TTGTCATCCTGTAGCTAGCAAA 57.448 40.909 18.83 0.86 0.00 3.68
2584 9145 5.869649 TGTCATCCTGTAGCTAGCAAATA 57.130 39.130 18.83 1.80 0.00 1.40
2591 9162 4.991687 CCTGTAGCTAGCAAATAAGTAGCC 59.008 45.833 18.83 0.00 40.11 3.93
2705 9277 4.408596 TGCCATACAGATACAAGACATGGA 59.591 41.667 0.00 0.00 34.64 3.41
2721 9293 1.234821 TGGAGCCGAATGTGTTCAAC 58.765 50.000 0.00 0.00 33.86 3.18
2730 9302 0.593128 ATGTGTTCAACGCCTTGCTC 59.407 50.000 0.00 0.00 0.00 4.26
2731 9303 1.082756 GTGTTCAACGCCTTGCTCG 60.083 57.895 0.00 0.00 0.00 5.03
2765 9337 0.465705 GACTCGATGCCCAAGATGGA 59.534 55.000 0.00 0.00 40.96 3.41
2766 9338 0.467384 ACTCGATGCCCAAGATGGAG 59.533 55.000 0.00 0.00 40.96 3.86
2768 9340 0.982852 TCGATGCCCAAGATGGAGGT 60.983 55.000 0.00 0.00 40.96 3.85
2769 9341 0.816825 CGATGCCCAAGATGGAGGTG 60.817 60.000 0.00 0.00 40.96 4.00
2845 9427 5.043903 CGGATAGGTTTGATACTGTGACTG 58.956 45.833 0.00 0.00 0.00 3.51
2867 9449 3.407424 TGTTCCTGGAATGTCTCACTG 57.593 47.619 13.07 0.00 0.00 3.66
2877 9459 5.483937 TGGAATGTCTCACTGTATTGGTACT 59.516 40.000 0.00 0.00 0.00 2.73
2900 9482 7.372714 ACTGTGTGTACGTAAATCTCATGTTA 58.627 34.615 0.00 0.00 0.00 2.41
2935 9517 2.282039 CCGGCCAGGGAAAATGCAA 61.282 57.895 2.24 0.00 35.97 4.08
2936 9518 1.079888 CGGCCAGGGAAAATGCAAC 60.080 57.895 2.24 0.00 0.00 4.17
2943 9525 1.202879 AGGGAAAATGCAACACCGAGA 60.203 47.619 0.00 0.00 0.00 4.04
2949 9531 2.831685 ATGCAACACCGAGAGTTGTA 57.168 45.000 13.43 10.58 46.09 2.41
2952 9534 2.805671 TGCAACACCGAGAGTTGTATTG 59.194 45.455 13.43 0.00 46.09 1.90
2968 9550 8.809468 AGTTGTATTGTATCTACTCTCACTGA 57.191 34.615 0.00 0.00 0.00 3.41
2969 9551 9.244292 AGTTGTATTGTATCTACTCTCACTGAA 57.756 33.333 0.00 0.00 0.00 3.02
3012 9594 4.304110 TCAGCTAACAAGTTACCAAGACG 58.696 43.478 0.00 0.00 0.00 4.18
3042 9630 4.071961 AGCACACATGAACTGTACAGAA 57.928 40.909 29.30 14.11 35.91 3.02
3043 9631 4.645535 AGCACACATGAACTGTACAGAAT 58.354 39.130 29.30 16.81 35.91 2.40
3044 9632 4.692625 AGCACACATGAACTGTACAGAATC 59.307 41.667 29.30 23.59 35.91 2.52
3053 9641 1.390123 CTGTACAGAATCGGTGTTGCG 59.610 52.381 18.45 0.00 0.00 4.85
3070 9658 3.353836 GTTTGCCCAAGCGAGCGA 61.354 61.111 0.00 0.00 44.31 4.93
3071 9659 3.049674 TTTGCCCAAGCGAGCGAG 61.050 61.111 0.00 0.00 44.31 5.03
3079 9667 4.218578 AGCGAGCGAGCTCCCATG 62.219 66.667 18.19 6.45 45.67 3.66
3140 9731 3.525545 GGGTACGACGGCTCCTCC 61.526 72.222 0.00 0.00 0.00 4.30
3196 9787 2.187946 CGCCTCTTCTTGCCGGAT 59.812 61.111 5.05 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.823647 TGTTTGCTTATTTATTTTCTGTCCAAA 57.176 25.926 0.00 0.00 0.00 3.28
10 11 9.474920 CTGTTTGCTTATTTATTTTCTGTCCAA 57.525 29.630 0.00 0.00 0.00 3.53
11 12 8.637986 ACTGTTTGCTTATTTATTTTCTGTCCA 58.362 29.630 0.00 0.00 0.00 4.02
12 13 9.476202 AACTGTTTGCTTATTTATTTTCTGTCC 57.524 29.630 0.00 0.00 0.00 4.02
27 28 8.860088 AGTCTTCCATAATAAAACTGTTTGCTT 58.140 29.630 6.53 6.23 0.00 3.91
28 29 8.299570 CAGTCTTCCATAATAAAACTGTTTGCT 58.700 33.333 6.53 0.00 0.00 3.91
29 30 8.296713 TCAGTCTTCCATAATAAAACTGTTTGC 58.703 33.333 6.53 0.00 35.37 3.68
30 31 9.831737 CTCAGTCTTCCATAATAAAACTGTTTG 57.168 33.333 6.53 0.00 35.37 2.93
31 32 9.793259 TCTCAGTCTTCCATAATAAAACTGTTT 57.207 29.630 0.00 0.00 35.37 2.83
32 33 9.793259 TTCTCAGTCTTCCATAATAAAACTGTT 57.207 29.630 0.00 0.00 35.37 3.16
33 34 9.965902 ATTCTCAGTCTTCCATAATAAAACTGT 57.034 29.630 0.00 0.00 35.37 3.55
35 36 9.965902 ACATTCTCAGTCTTCCATAATAAAACT 57.034 29.630 0.00 0.00 0.00 2.66
36 37 9.994432 CACATTCTCAGTCTTCCATAATAAAAC 57.006 33.333 0.00 0.00 0.00 2.43
37 38 9.958180 TCACATTCTCAGTCTTCCATAATAAAA 57.042 29.630 0.00 0.00 0.00 1.52
38 39 9.605275 CTCACATTCTCAGTCTTCCATAATAAA 57.395 33.333 0.00 0.00 0.00 1.40
39 40 8.981659 TCTCACATTCTCAGTCTTCCATAATAA 58.018 33.333 0.00 0.00 0.00 1.40
40 41 8.539117 TCTCACATTCTCAGTCTTCCATAATA 57.461 34.615 0.00 0.00 0.00 0.98
41 42 7.429374 TCTCACATTCTCAGTCTTCCATAAT 57.571 36.000 0.00 0.00 0.00 1.28
42 43 6.857437 TCTCACATTCTCAGTCTTCCATAA 57.143 37.500 0.00 0.00 0.00 1.90
43 44 8.583296 CATATCTCACATTCTCAGTCTTCCATA 58.417 37.037 0.00 0.00 0.00 2.74
44 45 5.954153 ATCTCACATTCTCAGTCTTCCAT 57.046 39.130 0.00 0.00 0.00 3.41
45 46 6.183360 CCATATCTCACATTCTCAGTCTTCCA 60.183 42.308 0.00 0.00 0.00 3.53
46 47 6.041409 TCCATATCTCACATTCTCAGTCTTCC 59.959 42.308 0.00 0.00 0.00 3.46
47 48 7.048629 TCCATATCTCACATTCTCAGTCTTC 57.951 40.000 0.00 0.00 0.00 2.87
48 49 6.610830 ACTCCATATCTCACATTCTCAGTCTT 59.389 38.462 0.00 0.00 0.00 3.01
49 50 6.040729 CACTCCATATCTCACATTCTCAGTCT 59.959 42.308 0.00 0.00 0.00 3.24
50 51 6.215121 CACTCCATATCTCACATTCTCAGTC 58.785 44.000 0.00 0.00 0.00 3.51
51 52 5.453057 GCACTCCATATCTCACATTCTCAGT 60.453 44.000 0.00 0.00 0.00 3.41
52 53 4.989797 GCACTCCATATCTCACATTCTCAG 59.010 45.833 0.00 0.00 0.00 3.35
53 54 4.500375 CGCACTCCATATCTCACATTCTCA 60.500 45.833 0.00 0.00 0.00 3.27
54 55 3.986572 CGCACTCCATATCTCACATTCTC 59.013 47.826 0.00 0.00 0.00 2.87
55 56 3.244009 CCGCACTCCATATCTCACATTCT 60.244 47.826 0.00 0.00 0.00 2.40
56 57 3.062763 CCGCACTCCATATCTCACATTC 58.937 50.000 0.00 0.00 0.00 2.67
57 58 2.224378 CCCGCACTCCATATCTCACATT 60.224 50.000 0.00 0.00 0.00 2.71
58 59 1.345741 CCCGCACTCCATATCTCACAT 59.654 52.381 0.00 0.00 0.00 3.21
59 60 0.752658 CCCGCACTCCATATCTCACA 59.247 55.000 0.00 0.00 0.00 3.58
60 61 0.753262 ACCCGCACTCCATATCTCAC 59.247 55.000 0.00 0.00 0.00 3.51
61 62 1.496060 AACCCGCACTCCATATCTCA 58.504 50.000 0.00 0.00 0.00 3.27
62 63 3.746045 TTAACCCGCACTCCATATCTC 57.254 47.619 0.00 0.00 0.00 2.75
63 64 4.706842 AATTAACCCGCACTCCATATCT 57.293 40.909 0.00 0.00 0.00 1.98
64 65 5.063880 AGAAATTAACCCGCACTCCATATC 58.936 41.667 0.00 0.00 0.00 1.63
65 66 5.048846 AGAAATTAACCCGCACTCCATAT 57.951 39.130 0.00 0.00 0.00 1.78
66 67 4.497291 AGAAATTAACCCGCACTCCATA 57.503 40.909 0.00 0.00 0.00 2.74
67 68 3.366052 AGAAATTAACCCGCACTCCAT 57.634 42.857 0.00 0.00 0.00 3.41
68 69 2.871096 AGAAATTAACCCGCACTCCA 57.129 45.000 0.00 0.00 0.00 3.86
69 70 5.830000 ATTTAGAAATTAACCCGCACTCC 57.170 39.130 0.00 0.00 0.00 3.85
71 72 9.841295 TCTATTATTTAGAAATTAACCCGCACT 57.159 29.630 0.00 0.00 0.00 4.40
93 94 8.903820 GGTACATTTGCAAAATAGTCCTTCTAT 58.096 33.333 17.19 0.00 40.68 1.98
94 95 7.885922 TGGTACATTTGCAAAATAGTCCTTCTA 59.114 33.333 17.19 0.00 0.00 2.10
95 96 6.719370 TGGTACATTTGCAAAATAGTCCTTCT 59.281 34.615 17.19 0.00 0.00 2.85
96 97 6.919721 TGGTACATTTGCAAAATAGTCCTTC 58.080 36.000 17.19 7.13 0.00 3.46
97 98 6.909550 TGGTACATTTGCAAAATAGTCCTT 57.090 33.333 17.19 0.00 0.00 3.36
98 99 6.295067 GGTTGGTACATTTGCAAAATAGTCCT 60.295 38.462 17.19 0.00 39.30 3.85
99 100 5.867174 GGTTGGTACATTTGCAAAATAGTCC 59.133 40.000 17.19 14.64 39.30 3.85
100 101 6.451393 TGGTTGGTACATTTGCAAAATAGTC 58.549 36.000 17.19 7.06 39.30 2.59
101 102 6.412362 TGGTTGGTACATTTGCAAAATAGT 57.588 33.333 17.19 16.57 39.30 2.12
102 103 6.534793 GGATGGTTGGTACATTTGCAAAATAG 59.465 38.462 17.19 11.59 39.30 1.73
103 104 6.014242 TGGATGGTTGGTACATTTGCAAAATA 60.014 34.615 17.19 9.10 39.30 1.40
104 105 5.221803 TGGATGGTTGGTACATTTGCAAAAT 60.222 36.000 17.19 10.14 39.30 1.82
105 106 4.101585 TGGATGGTTGGTACATTTGCAAAA 59.898 37.500 17.19 0.00 39.30 2.44
106 107 3.643320 TGGATGGTTGGTACATTTGCAAA 59.357 39.130 15.44 15.44 39.30 3.68
107 108 3.234353 TGGATGGTTGGTACATTTGCAA 58.766 40.909 0.00 0.00 39.30 4.08
108 109 2.881734 TGGATGGTTGGTACATTTGCA 58.118 42.857 0.00 0.00 39.30 4.08
109 110 3.701040 AGATGGATGGTTGGTACATTTGC 59.299 43.478 0.00 0.00 39.30 3.68
110 111 4.339247 GGAGATGGATGGTTGGTACATTTG 59.661 45.833 0.00 0.00 39.30 2.32
111 112 4.536765 GGAGATGGATGGTTGGTACATTT 58.463 43.478 0.00 0.00 39.30 2.32
112 113 3.117512 GGGAGATGGATGGTTGGTACATT 60.118 47.826 0.00 0.00 39.30 2.71
113 114 2.443255 GGGAGATGGATGGTTGGTACAT 59.557 50.000 0.00 0.00 39.30 2.29
114 115 1.843851 GGGAGATGGATGGTTGGTACA 59.156 52.381 0.00 0.00 0.00 2.90
115 116 2.127708 AGGGAGATGGATGGTTGGTAC 58.872 52.381 0.00 0.00 0.00 3.34
116 117 2.587060 AGGGAGATGGATGGTTGGTA 57.413 50.000 0.00 0.00 0.00 3.25
117 118 2.412591 CTAGGGAGATGGATGGTTGGT 58.587 52.381 0.00 0.00 0.00 3.67
118 119 1.072965 GCTAGGGAGATGGATGGTTGG 59.927 57.143 0.00 0.00 0.00 3.77
119 120 1.072965 GGCTAGGGAGATGGATGGTTG 59.927 57.143 0.00 0.00 0.00 3.77
120 121 1.345422 TGGCTAGGGAGATGGATGGTT 60.345 52.381 0.00 0.00 0.00 3.67
121 122 0.268869 TGGCTAGGGAGATGGATGGT 59.731 55.000 0.00 0.00 0.00 3.55
122 123 0.982704 CTGGCTAGGGAGATGGATGG 59.017 60.000 0.00 0.00 0.00 3.51
123 124 0.324285 GCTGGCTAGGGAGATGGATG 59.676 60.000 0.00 0.00 0.00 3.51
124 125 0.193069 AGCTGGCTAGGGAGATGGAT 59.807 55.000 0.00 0.00 0.00 3.41
125 126 0.470833 GAGCTGGCTAGGGAGATGGA 60.471 60.000 0.00 0.00 0.00 3.41
126 127 0.762082 TGAGCTGGCTAGGGAGATGG 60.762 60.000 0.00 0.00 0.00 3.51
127 128 1.275856 GATGAGCTGGCTAGGGAGATG 59.724 57.143 0.00 0.00 0.00 2.90
128 129 1.149711 AGATGAGCTGGCTAGGGAGAT 59.850 52.381 0.00 0.00 0.00 2.75
129 130 0.560193 AGATGAGCTGGCTAGGGAGA 59.440 55.000 0.00 0.00 0.00 3.71
130 131 0.968405 GAGATGAGCTGGCTAGGGAG 59.032 60.000 0.00 0.00 0.00 4.30
131 132 0.470833 GGAGATGAGCTGGCTAGGGA 60.471 60.000 0.00 0.00 0.00 4.20
132 133 1.479368 GGGAGATGAGCTGGCTAGGG 61.479 65.000 0.00 0.00 0.00 3.53
133 134 0.471591 AGGGAGATGAGCTGGCTAGG 60.472 60.000 0.00 0.00 0.00 3.02
134 135 0.968405 GAGGGAGATGAGCTGGCTAG 59.032 60.000 0.00 0.00 0.00 3.42
135 136 0.560193 AGAGGGAGATGAGCTGGCTA 59.440 55.000 0.00 0.00 0.00 3.93
136 137 0.560193 TAGAGGGAGATGAGCTGGCT 59.440 55.000 0.00 0.00 0.00 4.75
137 138 1.643310 ATAGAGGGAGATGAGCTGGC 58.357 55.000 0.00 0.00 0.00 4.85
138 139 4.141528 ACAAAATAGAGGGAGATGAGCTGG 60.142 45.833 0.00 0.00 0.00 4.85
139 140 5.033589 ACAAAATAGAGGGAGATGAGCTG 57.966 43.478 0.00 0.00 0.00 4.24
140 141 6.013812 GGATACAAAATAGAGGGAGATGAGCT 60.014 42.308 0.00 0.00 0.00 4.09
141 142 6.169800 GGATACAAAATAGAGGGAGATGAGC 58.830 44.000 0.00 0.00 0.00 4.26
188 189 2.224113 GGCCTAATTCATGCACCCAATG 60.224 50.000 0.00 0.00 0.00 2.82
189 190 2.041701 GGCCTAATTCATGCACCCAAT 58.958 47.619 0.00 0.00 0.00 3.16
190 191 1.484038 GGCCTAATTCATGCACCCAA 58.516 50.000 0.00 0.00 0.00 4.12
191 192 0.751277 CGGCCTAATTCATGCACCCA 60.751 55.000 0.00 0.00 0.00 4.51
192 193 1.455383 CCGGCCTAATTCATGCACCC 61.455 60.000 0.00 0.00 0.00 4.61
193 194 0.751643 ACCGGCCTAATTCATGCACC 60.752 55.000 0.00 0.00 0.00 5.01
194 195 0.381801 CACCGGCCTAATTCATGCAC 59.618 55.000 0.00 0.00 0.00 4.57
195 196 1.383456 GCACCGGCCTAATTCATGCA 61.383 55.000 0.00 0.00 0.00 3.96
196 197 1.360192 GCACCGGCCTAATTCATGC 59.640 57.895 0.00 0.00 0.00 4.06
197 198 0.381801 GTGCACCGGCCTAATTCATG 59.618 55.000 5.22 0.00 40.13 3.07
198 199 0.255890 AGTGCACCGGCCTAATTCAT 59.744 50.000 14.63 0.00 40.13 2.57
199 200 0.676466 CAGTGCACCGGCCTAATTCA 60.676 55.000 14.63 0.00 40.13 2.57
200 201 1.376609 CCAGTGCACCGGCCTAATTC 61.377 60.000 14.63 0.00 40.13 2.17
201 202 1.378514 CCAGTGCACCGGCCTAATT 60.379 57.895 14.63 0.00 40.13 1.40
202 203 1.635817 ATCCAGTGCACCGGCCTAAT 61.636 55.000 14.67 0.00 40.13 1.73
203 204 0.978667 TATCCAGTGCACCGGCCTAA 60.979 55.000 14.67 0.00 40.13 2.69
204 205 1.382009 TATCCAGTGCACCGGCCTA 60.382 57.895 14.67 5.75 40.13 3.93
205 206 2.687200 TATCCAGTGCACCGGCCT 60.687 61.111 14.67 6.73 40.13 5.19
206 207 2.513897 GTATCCAGTGCACCGGCC 60.514 66.667 14.67 0.00 40.13 6.13
207 208 1.153168 ATGTATCCAGTGCACCGGC 60.153 57.895 14.67 1.20 41.68 6.13
208 209 0.532862 GGATGTATCCAGTGCACCGG 60.533 60.000 13.28 13.28 46.38 5.28
209 210 2.992089 GGATGTATCCAGTGCACCG 58.008 57.895 14.63 2.26 46.38 4.94
219 220 1.545706 GGAGGCCCCGAGGATGTATC 61.546 65.000 0.00 0.00 33.47 2.24
220 221 1.536662 GGAGGCCCCGAGGATGTAT 60.537 63.158 0.00 0.00 33.47 2.29
221 222 2.122989 GGAGGCCCCGAGGATGTA 60.123 66.667 0.00 0.00 33.47 2.29
222 223 3.721172 ATGGAGGCCCCGAGGATGT 62.721 63.158 0.00 0.00 37.93 3.06
223 224 2.851102 ATGGAGGCCCCGAGGATG 60.851 66.667 0.00 0.00 37.93 3.51
224 225 2.851102 CATGGAGGCCCCGAGGAT 60.851 66.667 0.00 0.00 37.93 3.24
225 226 4.414956 ACATGGAGGCCCCGAGGA 62.415 66.667 0.00 0.00 37.93 3.71
244 245 0.110509 CCGAAAGAAGACGTCGTCGA 60.111 55.000 22.80 0.00 39.60 4.20
246 247 1.050767 CACCGAAAGAAGACGTCGTC 58.949 55.000 21.86 21.86 0.00 4.20
247 248 0.383231 ACACCGAAAGAAGACGTCGT 59.617 50.000 10.46 6.85 0.00 4.34
260 261 4.408821 GGGCATGCCTCACACCGA 62.409 66.667 34.70 0.00 36.10 4.69
261 262 4.720902 TGGGCATGCCTCACACCG 62.721 66.667 34.70 0.00 36.10 4.94
262 263 3.064324 GTGGGCATGCCTCACACC 61.064 66.667 34.70 21.85 37.29 4.16
272 273 2.573462 AGAACATACTCACAGTGGGCAT 59.427 45.455 0.00 0.00 0.00 4.40
287 288 3.703001 AAACGAGACCCATGAGAACAT 57.297 42.857 0.00 0.00 37.19 2.71
400 401 6.800892 TGCTTTTGAGAAACAAACAAAATTGC 59.199 30.769 0.00 0.00 46.32 3.56
449 450 5.277490 GCCAAAAGCAAAGGAATCTTCAAAC 60.277 40.000 0.00 0.00 42.97 2.93
529 967 8.897872 AACTCGGTAAAAGAAAAATCAGAGTA 57.102 30.769 0.00 0.00 34.62 2.59
542 980 4.023193 ACAAGCAATGGAACTCGGTAAAAG 60.023 41.667 0.00 0.00 0.00 2.27
543 981 3.886505 ACAAGCAATGGAACTCGGTAAAA 59.113 39.130 0.00 0.00 0.00 1.52
557 995 3.016736 CCCAATACCTCGAACAAGCAAT 58.983 45.455 0.00 0.00 0.00 3.56
564 1002 3.470645 ACATAGCCCAATACCTCGAAC 57.529 47.619 0.00 0.00 0.00 3.95
568 1006 4.137543 CTCCAAACATAGCCCAATACCTC 58.862 47.826 0.00 0.00 0.00 3.85
579 1017 8.802267 TCTTTAAATCCAAACCTCCAAACATAG 58.198 33.333 0.00 0.00 0.00 2.23
580 1018 8.713708 TCTTTAAATCCAAACCTCCAAACATA 57.286 30.769 0.00 0.00 0.00 2.29
591 1029 8.293114 TCGCTGATTTTTCTTTAAATCCAAAC 57.707 30.769 0.00 0.00 41.62 2.93
651 1089 3.009115 TACTGAGCCCAGGCCCAC 61.009 66.667 4.70 0.00 44.60 4.61
674 1112 1.507141 CTTGCCCGTGTGACCAAGTC 61.507 60.000 0.00 0.00 32.22 3.01
704 1159 3.775654 GGCGGGAGTGGAGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
818 1294 1.614583 GGGAAAGGTGAGGGAAGAAGC 60.615 57.143 0.00 0.00 0.00 3.86
823 1299 1.462627 ACGGGGAAAGGTGAGGGAA 60.463 57.895 0.00 0.00 0.00 3.97
824 1300 1.916777 GACGGGGAAAGGTGAGGGA 60.917 63.158 0.00 0.00 0.00 4.20
825 1301 2.669240 GACGGGGAAAGGTGAGGG 59.331 66.667 0.00 0.00 0.00 4.30
826 1302 2.669240 GGACGGGGAAAGGTGAGG 59.331 66.667 0.00 0.00 0.00 3.86
827 1303 2.108278 AACGGACGGGGAAAGGTGAG 62.108 60.000 0.00 0.00 0.00 3.51
828 1304 1.698067 AAACGGACGGGGAAAGGTGA 61.698 55.000 0.00 0.00 0.00 4.02
829 1305 0.820482 AAAACGGACGGGGAAAGGTG 60.820 55.000 0.00 0.00 0.00 4.00
830 1306 0.106569 AAAAACGGACGGGGAAAGGT 60.107 50.000 0.00 0.00 0.00 3.50
831 1307 0.312729 CAAAAACGGACGGGGAAAGG 59.687 55.000 0.00 0.00 0.00 3.11
832 1308 0.318360 GCAAAAACGGACGGGGAAAG 60.318 55.000 0.00 0.00 0.00 2.62
833 1309 0.752376 AGCAAAAACGGACGGGGAAA 60.752 50.000 0.00 0.00 0.00 3.13
834 1310 1.152922 AGCAAAAACGGACGGGGAA 60.153 52.632 0.00 0.00 0.00 3.97
835 1311 1.598685 GAGCAAAAACGGACGGGGA 60.599 57.895 0.00 0.00 0.00 4.81
891 1387 1.368641 CACTTAGCGTGCATAGCCAA 58.631 50.000 12.59 5.80 36.72 4.52
1055 1559 0.179034 CAATCCTGCTAGGTCCAGCC 60.179 60.000 9.85 0.00 41.04 4.85
1071 1575 1.378250 GAGCAGGCTGAGCACCAAT 60.378 57.895 20.86 0.00 0.00 3.16
1252 6580 2.029380 CACACACATTCTCGTACCCTGA 60.029 50.000 0.00 0.00 0.00 3.86
1269 6597 2.360852 ATGAGCCAGCTGCCACAC 60.361 61.111 8.66 0.00 42.71 3.82
1285 6613 0.248661 CCGTCATCGCGTGAGAAGAT 60.249 55.000 5.77 0.00 37.56 2.40
2109 7467 2.858941 GGAATAGACGCCGAAAGAAGTC 59.141 50.000 0.00 0.00 37.50 3.01
2281 7641 5.745312 CCATAGCATGGTCAGATAACCTA 57.255 43.478 0.00 0.00 45.54 3.08
2304 7664 4.762765 ACCACAGAACTACAACAACAACAA 59.237 37.500 0.00 0.00 0.00 2.83
2317 8873 3.503748 GCTTGCAGAATAACCACAGAACT 59.496 43.478 0.00 0.00 0.00 3.01
2364 8920 6.201044 CACTTACACAGAGTAACCAAGTTCAG 59.799 42.308 0.00 0.00 37.77 3.02
2470 9027 3.354948 TTCATCCACAGTAGCAGCAAT 57.645 42.857 0.00 0.00 0.00 3.56
2497 9058 4.624024 CAGATAAGCAGCAACATGGTTTTG 59.376 41.667 0.00 0.00 41.01 2.44
2504 9065 2.431954 AGGCAGATAAGCAGCAACAT 57.568 45.000 0.00 0.00 35.83 2.71
2521 9082 4.526970 ACCAACATGCCAAAGATAGTAGG 58.473 43.478 0.00 0.00 0.00 3.18
2525 9086 4.521146 AGAGACCAACATGCCAAAGATAG 58.479 43.478 0.00 0.00 0.00 2.08
2528 9089 2.957402 AGAGACCAACATGCCAAAGA 57.043 45.000 0.00 0.00 0.00 2.52
2529 9090 3.571401 AGAAAGAGACCAACATGCCAAAG 59.429 43.478 0.00 0.00 0.00 2.77
2530 9091 3.565307 AGAAAGAGACCAACATGCCAAA 58.435 40.909 0.00 0.00 0.00 3.28
2531 9092 3.228188 AGAAAGAGACCAACATGCCAA 57.772 42.857 0.00 0.00 0.00 4.52
2539 9100 2.172505 TGCAGACCAAGAAAGAGACCAA 59.827 45.455 0.00 0.00 0.00 3.67
2558 9119 2.805099 GCTAGCTACAGGATGACAATGC 59.195 50.000 7.70 0.00 39.69 3.56
2559 9120 4.063998 TGCTAGCTACAGGATGACAATG 57.936 45.455 17.23 0.00 39.69 2.82
2567 9128 5.221461 GGCTACTTATTTGCTAGCTACAGGA 60.221 44.000 17.23 0.37 34.48 3.86
2582 9143 3.118738 CCTGACGTTCAAGGGCTACTTAT 60.119 47.826 5.26 0.00 37.29 1.73
2584 9145 1.002087 CCTGACGTTCAAGGGCTACTT 59.998 52.381 5.26 0.00 41.00 2.24
2591 9162 2.680841 TGAAACAACCTGACGTTCAAGG 59.319 45.455 10.41 10.41 29.93 3.61
2705 9277 1.574428 GCGTTGAACACATTCGGCT 59.426 52.632 0.00 0.00 37.69 5.52
2721 9293 1.078759 AGACGAAATCGAGCAAGGCG 61.079 55.000 10.16 0.00 43.02 5.52
2730 9302 2.438583 GAGTCGGTGTAGACGAAATCG 58.561 52.381 0.48 0.48 45.26 3.34
2731 9303 2.094894 TCGAGTCGGTGTAGACGAAATC 59.905 50.000 13.54 0.00 45.26 2.17
2765 9337 3.322466 CGACTTCCCCTGCCACCT 61.322 66.667 0.00 0.00 0.00 4.00
2766 9338 4.410400 CCGACTTCCCCTGCCACC 62.410 72.222 0.00 0.00 0.00 4.61
2830 9412 5.527214 CAGGAACAACAGTCACAGTATCAAA 59.473 40.000 0.00 0.00 0.00 2.69
2845 9427 3.499918 CAGTGAGACATTCCAGGAACAAC 59.500 47.826 3.18 0.00 0.00 3.32
2877 9459 8.766000 ATTAACATGAGATTTACGTACACACA 57.234 30.769 0.00 0.00 0.00 3.72
2885 9467 9.110617 GCATGATCAATTAACATGAGATTTACG 57.889 33.333 17.09 0.00 42.41 3.18
2886 9468 9.955208 TGCATGATCAATTAACATGAGATTTAC 57.045 29.630 17.09 4.37 42.41 2.01
2900 9482 1.965643 CCGGGGATTGCATGATCAATT 59.034 47.619 0.00 0.00 36.85 2.32
2935 9517 5.916661 AGATACAATACAACTCTCGGTGT 57.083 39.130 0.00 0.00 0.00 4.16
2936 9518 7.012515 AGAGTAGATACAATACAACTCTCGGTG 59.987 40.741 0.00 0.00 39.48 4.94
2943 9525 8.809468 TCAGTGAGAGTAGATACAATACAACT 57.191 34.615 0.00 0.00 0.00 3.16
2949 9531 7.763528 CAGCTTTTCAGTGAGAGTAGATACAAT 59.236 37.037 0.00 0.00 0.00 2.71
2952 9534 6.626302 ACAGCTTTTCAGTGAGAGTAGATAC 58.374 40.000 0.00 0.00 0.00 2.24
2992 9574 3.064931 GCGTCTTGGTAACTTGTTAGCT 58.935 45.455 19.12 0.00 37.61 3.32
2999 9581 2.224670 TGGGATTGCGTCTTGGTAACTT 60.225 45.455 0.00 0.00 37.61 2.66
3012 9594 0.889994 TCATGTGTGCTTGGGATTGC 59.110 50.000 0.00 0.00 0.00 3.56
3042 9630 2.642700 GGCAAACGCAACACCGAT 59.357 55.556 0.00 0.00 0.00 4.18
3043 9631 3.587933 GGGCAAACGCAACACCGA 61.588 61.111 0.00 0.00 0.00 4.69
3044 9632 3.417275 TTGGGCAAACGCAACACCG 62.417 57.895 0.00 0.00 43.13 4.94
3053 9641 3.314388 CTCGCTCGCTTGGGCAAAC 62.314 63.158 0.00 0.00 38.60 2.93
3069 9657 0.761187 TAGCATGACCATGGGAGCTC 59.239 55.000 20.81 4.71 39.16 4.09
3070 9658 0.471617 GTAGCATGACCATGGGAGCT 59.528 55.000 18.09 19.86 39.16 4.09
3071 9659 0.882042 CGTAGCATGACCATGGGAGC 60.882 60.000 18.09 13.77 39.16 4.70
3073 9661 1.829456 CCGTAGCATGACCATGGGA 59.171 57.895 18.09 1.83 39.16 4.37
3074 9662 1.893808 GCCGTAGCATGACCATGGG 60.894 63.158 18.09 0.00 39.16 4.00
3075 9663 1.153188 TGCCGTAGCATGACCATGG 60.153 57.895 11.19 11.19 46.52 3.66
3076 9664 4.538233 TGCCGTAGCATGACCATG 57.462 55.556 0.00 5.67 46.52 3.66


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

AutoCloner maintained by Alex Coulton.