Multiple sequence alignment - TraesCS4B01G304200

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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 TraesCS4B01G304200 chr4B 100.000 3167 0 0 1 3167 592195851 592192685 0.000000e+00 5849.0
1 TraesCS4B01G304200 chr4B 88.302 1419 127 13 999 2405 592079602 592078211 0.000000e+00 1664.0
2 TraesCS4B01G304200 chr4B 88.152 1418 131 9 999 2405 592188049 592186658 0.000000e+00 1653.0
3 TraesCS4B01G304200 chr4B 88.368 1238 132 9 956 2184 591909390 591908156 0.000000e+00 1478.0
4 TraesCS4B01G304200 chr4A 91.215 2584 177 26 599 3165 678040769 678038219 0.000000e+00 3469.0
5 TraesCS4B01G304200 chr4A 88.967 1423 133 9 999 2410 677988869 677987460 0.000000e+00 1736.0
6 TraesCS4B01G304200 chr4A 89.562 1188 109 9 999 2171 677958525 677957338 0.000000e+00 1493.0
7 TraesCS4B01G304200 chr4A 91.254 343 19 5 208 543 678041209 678040871 1.040000e-124 457.0
8 TraesCS4B01G304200 chr4A 92.793 111 7 1 1 110 445990321 445990431 3.270000e-35 159.0
9 TraesCS4B01G304200 chr4D 95.728 1662 57 6 599 2259 470149001 470147353 0.000000e+00 2663.0
10 TraesCS4B01G304200 chr4D 90.407 1178 104 4 999 2167 470138363 470137186 0.000000e+00 1541.0
11 TraesCS4B01G304200 chr4D 90.576 1146 99 1 1031 2167 470130302 470129157 0.000000e+00 1509.0
12 TraesCS4B01G304200 chr4D 86.584 1379 132 32 832 2171 470122021 470120657 0.000000e+00 1472.0
13 TraesCS4B01G304200 chr4D 92.241 348 20 5 206 552 470149428 470149087 1.320000e-133 486.0
14 TraesCS4B01G304200 chr4D 83.951 162 19 4 2292 2452 470147356 470147201 7.080000e-32 148.0
15 TraesCS4B01G304200 chr4D 87.273 110 8 5 1 109 297776164 297776268 1.540000e-23 121.0
16 TraesCS4B01G304200 chr1A 78.895 507 87 12 2437 2937 561586853 561586361 3.050000e-85 326.0
17 TraesCS4B01G304200 chr1A 77.030 505 103 8 2436 2937 561591988 561591494 8.650000e-71 278.0
18 TraesCS4B01G304200 chr3D 78.992 476 88 8 2461 2933 584353148 584353614 6.590000e-82 315.0
19 TraesCS4B01G304200 chr3D 79.841 377 75 1 2441 2816 501309619 501309243 1.120000e-69 274.0
20 TraesCS4B01G304200 chr3D 87.611 113 8 1 1 113 545796230 545796336 3.320000e-25 126.0
21 TraesCS4B01G304200 chr7B 78.497 479 88 9 2461 2937 703244223 703243758 1.850000e-77 300.0
22 TraesCS4B01G304200 chr6D 77.734 503 100 10 2437 2937 13062774 13062282 6.640000e-77 298.0
23 TraesCS4B01G304200 chr1D 77.800 509 93 13 2436 2937 468745655 468745160 2.390000e-76 296.0
24 TraesCS4B01G304200 chr1D 93.636 110 7 0 1 110 383180672 383180781 7.030000e-37 165.0
25 TraesCS4B01G304200 chr7D 80.282 355 67 3 2464 2816 230998615 230998262 6.740000e-67 265.0
26 TraesCS4B01G304200 chr7D 90.000 110 10 1 1 109 168500589 168500480 1.180000e-29 141.0
27 TraesCS4B01G304200 chr5B 92.793 111 8 0 1 111 361013934 361014044 9.090000e-36 161.0
28 TraesCS4B01G304200 chr2D 92.593 108 8 0 1 108 194806287 194806394 4.230000e-34 156.0
29 TraesCS4B01G304200 chr2D 87.931 58 6 1 111 168 591272015 591271959 2.040000e-07 67.6
30 TraesCS4B01G304200 chr2A 88.991 109 5 2 1 108 5385806 5385908 9.220000e-26 128.0
31 TraesCS4B01G304200 chr2A 89.320 103 10 1 1 102 431082134 431082236 9.220000e-26 128.0
32 TraesCS4B01G304200 chr2A 89.286 56 6 0 119 174 655848450 655848505 1.580000e-08 71.3
33 TraesCS4B01G304200 chr7A 93.617 47 2 1 111 156 199002498 199002452 5.670000e-08 69.4
34 TraesCS4B01G304200 chr6B 83.333 60 10 0 111 170 624024728 624024787 4.410000e-04 56.5


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 TraesCS4B01G304200 chr4B 592192685 592195851 3166 True 5849 5849 100.0000 1 3167 1 chr4B.!!$R4 3166
1 TraesCS4B01G304200 chr4B 592078211 592079602 1391 True 1664 1664 88.3020 999 2405 1 chr4B.!!$R2 1406
2 TraesCS4B01G304200 chr4B 592186658 592188049 1391 True 1653 1653 88.1520 999 2405 1 chr4B.!!$R3 1406
3 TraesCS4B01G304200 chr4B 591908156 591909390 1234 True 1478 1478 88.3680 956 2184 1 chr4B.!!$R1 1228
4 TraesCS4B01G304200 chr4A 678038219 678041209 2990 True 1963 3469 91.2345 208 3165 2 chr4A.!!$R3 2957
5 TraesCS4B01G304200 chr4A 677987460 677988869 1409 True 1736 1736 88.9670 999 2410 1 chr4A.!!$R2 1411
6 TraesCS4B01G304200 chr4A 677957338 677958525 1187 True 1493 1493 89.5620 999 2171 1 chr4A.!!$R1 1172
7 TraesCS4B01G304200 chr4D 470137186 470138363 1177 True 1541 1541 90.4070 999 2167 1 chr4D.!!$R3 1168
8 TraesCS4B01G304200 chr4D 470129157 470130302 1145 True 1509 1509 90.5760 1031 2167 1 chr4D.!!$R2 1136
9 TraesCS4B01G304200 chr4D 470120657 470122021 1364 True 1472 1472 86.5840 832 2171 1 chr4D.!!$R1 1339
10 TraesCS4B01G304200 chr4D 470147201 470149428 2227 True 1099 2663 90.6400 206 2452 3 chr4D.!!$R4 2246

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
152 153 0.028374 GACGTTTGTTTGGGGTCGTG 59.972 55.0 0.00 0.00 0.00 4.35 F
168 169 0.036306 CGTGGGTTAGAGTTGCCCTT 59.964 55.0 0.00 0.00 42.77 3.95 F
383 384 0.251608 TGACATCCTGGACTCGGTCA 60.252 55.0 14.55 14.55 33.68 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1038 1144 1.79517 TTGGCGTCTTTGCTGCTTCC 61.795 55.000 0.00 0.00 34.52 3.46 R
1347 1462 2.99545 GCACGACACGGCGTACAAG 61.995 63.158 14.22 7.34 43.59 3.16 R
2186 2310 0.25363 ACACCACCCCCATACTCCAT 60.254 55.000 0.00 0.00 0.00 3.41 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
69 70 9.593134 TTTTGTTATGCTTCATTTTGTTGTACT 57.407 25.926 0.00 0.00 0.00 2.73
70 71 9.593134 TTTGTTATGCTTCATTTTGTTGTACTT 57.407 25.926 0.00 0.00 0.00 2.24
71 72 8.572828 TGTTATGCTTCATTTTGTTGTACTTG 57.427 30.769 0.00 0.00 0.00 3.16
72 73 7.651304 TGTTATGCTTCATTTTGTTGTACTTGG 59.349 33.333 0.00 0.00 0.00 3.61
73 74 4.367450 TGCTTCATTTTGTTGTACTTGGC 58.633 39.130 0.00 0.00 0.00 4.52
74 75 3.740832 GCTTCATTTTGTTGTACTTGGCC 59.259 43.478 0.00 0.00 0.00 5.36
75 76 4.501400 GCTTCATTTTGTTGTACTTGGCCT 60.501 41.667 3.32 0.00 0.00 5.19
76 77 4.846779 TCATTTTGTTGTACTTGGCCTC 57.153 40.909 3.32 0.00 0.00 4.70
77 78 3.572255 TCATTTTGTTGTACTTGGCCTCC 59.428 43.478 3.32 0.00 0.00 4.30
78 79 1.600023 TTTGTTGTACTTGGCCTCCG 58.400 50.000 3.32 0.00 0.00 4.63
79 80 0.250553 TTGTTGTACTTGGCCTCCGG 60.251 55.000 3.32 0.00 0.00 5.14
89 90 3.620785 GCCTCCGGCGGATGAGAT 61.621 66.667 31.30 0.00 39.62 2.75
90 91 2.341543 CCTCCGGCGGATGAGATG 59.658 66.667 31.23 16.45 0.00 2.90
91 92 2.203082 CCTCCGGCGGATGAGATGA 61.203 63.158 31.23 3.96 0.00 2.92
92 93 1.288439 CTCCGGCGGATGAGATGAG 59.712 63.158 31.23 11.40 0.00 2.90
93 94 2.152297 CTCCGGCGGATGAGATGAGG 62.152 65.000 31.23 10.58 0.00 3.86
94 95 2.356793 CGGCGGATGAGATGAGGC 60.357 66.667 0.00 0.00 0.00 4.70
95 96 2.824546 GGCGGATGAGATGAGGCA 59.175 61.111 0.00 0.00 0.00 4.75
96 97 1.301558 GGCGGATGAGATGAGGCAG 60.302 63.158 0.00 0.00 0.00 4.85
97 98 1.744639 GCGGATGAGATGAGGCAGA 59.255 57.895 0.00 0.00 0.00 4.26
98 99 0.105593 GCGGATGAGATGAGGCAGAA 59.894 55.000 0.00 0.00 0.00 3.02
99 100 1.873069 GCGGATGAGATGAGGCAGAAG 60.873 57.143 0.00 0.00 0.00 2.85
100 101 1.685517 CGGATGAGATGAGGCAGAAGA 59.314 52.381 0.00 0.00 0.00 2.87
101 102 2.299582 CGGATGAGATGAGGCAGAAGAT 59.700 50.000 0.00 0.00 0.00 2.40
102 103 3.666274 GGATGAGATGAGGCAGAAGATG 58.334 50.000 0.00 0.00 0.00 2.90
120 121 3.784412 CGGCCGCACGAACGAAAT 61.784 61.111 14.67 0.00 35.47 2.17
121 122 2.097728 GGCCGCACGAACGAAATC 59.902 61.111 0.14 0.00 34.06 2.17
122 123 2.097728 GCCGCACGAACGAAATCC 59.902 61.111 0.14 0.00 34.06 3.01
123 124 2.394136 CCGCACGAACGAAATCCG 59.606 61.111 0.14 0.00 45.44 4.18
124 125 2.089936 CCGCACGAACGAAATCCGA 61.090 57.895 0.14 0.00 41.76 4.55
125 126 1.619526 CCGCACGAACGAAATCCGAA 61.620 55.000 0.14 0.00 41.76 4.30
126 127 0.515717 CGCACGAACGAAATCCGAAC 60.516 55.000 0.14 0.00 41.76 3.95
127 128 0.509499 GCACGAACGAAATCCGAACA 59.491 50.000 0.14 0.00 41.76 3.18
128 129 1.070443 GCACGAACGAAATCCGAACAA 60.070 47.619 0.14 0.00 41.76 2.83
129 130 2.600320 GCACGAACGAAATCCGAACAAA 60.600 45.455 0.14 0.00 41.76 2.83
130 131 3.609475 CACGAACGAAATCCGAACAAAA 58.391 40.909 0.14 0.00 41.76 2.44
131 132 3.416352 CACGAACGAAATCCGAACAAAAC 59.584 43.478 0.14 0.00 41.76 2.43
132 133 2.643801 CGAACGAAATCCGAACAAAACG 59.356 45.455 0.00 0.00 41.76 3.60
141 142 2.162371 CGAACAAAACGGACGTTTGT 57.838 45.000 21.57 17.61 46.22 2.83
142 143 2.507866 CGAACAAAACGGACGTTTGTT 58.492 42.857 21.57 23.06 46.22 2.83
143 144 2.909863 CGAACAAAACGGACGTTTGTTT 59.090 40.909 21.57 16.91 46.22 2.83
144 145 3.241084 CGAACAAAACGGACGTTTGTTTG 60.241 43.478 21.57 22.24 46.22 2.93
145 146 2.597520 ACAAAACGGACGTTTGTTTGG 58.402 42.857 21.57 16.01 46.22 3.28
146 147 1.921230 CAAAACGGACGTTTGTTTGGG 59.079 47.619 21.57 10.33 46.22 4.12
147 148 0.456628 AAACGGACGTTTGTTTGGGG 59.543 50.000 20.42 0.00 45.34 4.96
148 149 0.680601 AACGGACGTTTGTTTGGGGT 60.681 50.000 3.99 0.00 34.22 4.95
149 150 1.096967 ACGGACGTTTGTTTGGGGTC 61.097 55.000 0.00 0.00 0.00 4.46
150 151 1.650363 GGACGTTTGTTTGGGGTCG 59.350 57.895 0.00 0.00 0.00 4.79
151 152 1.096967 GGACGTTTGTTTGGGGTCGT 61.097 55.000 0.00 0.00 0.00 4.34
152 153 0.028374 GACGTTTGTTTGGGGTCGTG 59.972 55.000 0.00 0.00 0.00 4.35
153 154 1.357334 CGTTTGTTTGGGGTCGTGG 59.643 57.895 0.00 0.00 0.00 4.94
154 155 1.737201 GTTTGTTTGGGGTCGTGGG 59.263 57.895 0.00 0.00 0.00 4.61
155 156 1.038681 GTTTGTTTGGGGTCGTGGGT 61.039 55.000 0.00 0.00 0.00 4.51
156 157 0.324460 TTTGTTTGGGGTCGTGGGTT 60.324 50.000 0.00 0.00 0.00 4.11
157 158 0.549950 TTGTTTGGGGTCGTGGGTTA 59.450 50.000 0.00 0.00 0.00 2.85
158 159 0.108963 TGTTTGGGGTCGTGGGTTAG 59.891 55.000 0.00 0.00 0.00 2.34
159 160 0.397564 GTTTGGGGTCGTGGGTTAGA 59.602 55.000 0.00 0.00 0.00 2.10
160 161 0.688487 TTTGGGGTCGTGGGTTAGAG 59.312 55.000 0.00 0.00 0.00 2.43
161 162 0.472352 TTGGGGTCGTGGGTTAGAGT 60.472 55.000 0.00 0.00 0.00 3.24
162 163 0.472352 TGGGGTCGTGGGTTAGAGTT 60.472 55.000 0.00 0.00 0.00 3.01
163 164 0.036671 GGGGTCGTGGGTTAGAGTTG 60.037 60.000 0.00 0.00 0.00 3.16
164 165 0.672711 GGGTCGTGGGTTAGAGTTGC 60.673 60.000 0.00 0.00 0.00 4.17
165 166 0.672711 GGTCGTGGGTTAGAGTTGCC 60.673 60.000 0.00 0.00 0.00 4.52
166 167 0.672711 GTCGTGGGTTAGAGTTGCCC 60.673 60.000 0.00 0.00 42.64 5.36
167 168 0.834687 TCGTGGGTTAGAGTTGCCCT 60.835 55.000 0.00 0.00 42.77 5.19
168 169 0.036306 CGTGGGTTAGAGTTGCCCTT 59.964 55.000 0.00 0.00 42.77 3.95
169 170 1.276989 CGTGGGTTAGAGTTGCCCTTA 59.723 52.381 0.00 0.00 42.77 2.69
170 171 2.677037 CGTGGGTTAGAGTTGCCCTTAG 60.677 54.545 0.00 0.00 42.77 2.18
171 172 2.570302 GTGGGTTAGAGTTGCCCTTAGA 59.430 50.000 0.00 0.00 42.77 2.10
172 173 3.008704 GTGGGTTAGAGTTGCCCTTAGAA 59.991 47.826 0.00 0.00 42.77 2.10
173 174 3.008704 TGGGTTAGAGTTGCCCTTAGAAC 59.991 47.826 0.00 0.00 42.77 3.01
174 175 3.263681 GGGTTAGAGTTGCCCTTAGAACT 59.736 47.826 0.00 0.00 39.31 3.01
175 176 4.254492 GGTTAGAGTTGCCCTTAGAACTG 58.746 47.826 0.00 0.00 32.47 3.16
176 177 4.254492 GTTAGAGTTGCCCTTAGAACTGG 58.746 47.826 0.00 0.00 32.47 4.00
177 178 2.339769 AGAGTTGCCCTTAGAACTGGT 58.660 47.619 0.00 0.00 32.47 4.00
178 179 2.039084 AGAGTTGCCCTTAGAACTGGTG 59.961 50.000 0.00 0.00 32.47 4.17
179 180 1.073923 AGTTGCCCTTAGAACTGGTGG 59.926 52.381 0.00 0.00 31.09 4.61
180 181 1.145571 TTGCCCTTAGAACTGGTGGT 58.854 50.000 0.00 0.00 0.00 4.16
181 182 1.145571 TGCCCTTAGAACTGGTGGTT 58.854 50.000 0.00 0.00 41.40 3.67
182 183 1.497286 TGCCCTTAGAACTGGTGGTTT 59.503 47.619 0.00 0.00 38.41 3.27
183 184 2.091555 TGCCCTTAGAACTGGTGGTTTT 60.092 45.455 0.00 0.00 38.41 2.43
184 185 2.963101 GCCCTTAGAACTGGTGGTTTTT 59.037 45.455 0.00 0.00 38.41 1.94
383 384 0.251608 TGACATCCTGGACTCGGTCA 60.252 55.000 14.55 14.55 33.68 4.02
409 414 3.366724 GCCGTGGCATAAAACTAAAAAGC 59.633 43.478 5.89 0.00 41.49 3.51
418 423 9.971922 GGCATAAAACTAAAAAGCATATCAGAT 57.028 29.630 0.00 0.00 0.00 2.90
456 465 7.129457 TGAAGGATAGCAGATGTTTGTCTAT 57.871 36.000 0.00 0.00 0.00 1.98
457 466 8.250143 TGAAGGATAGCAGATGTTTGTCTATA 57.750 34.615 0.00 0.00 0.00 1.31
458 467 8.874156 TGAAGGATAGCAGATGTTTGTCTATAT 58.126 33.333 0.00 0.00 0.00 0.86
459 468 9.149225 GAAGGATAGCAGATGTTTGTCTATATG 57.851 37.037 0.00 0.00 0.00 1.78
461 470 9.044646 AGGATAGCAGATGTTTGTCTATATGAT 57.955 33.333 0.00 0.00 0.00 2.45
552 569 6.473758 ACTCATGAGTCAGTGTACAGTACTA 58.526 40.000 22.89 0.00 36.92 1.82
553 570 6.596106 ACTCATGAGTCAGTGTACAGTACTAG 59.404 42.308 22.89 5.07 36.92 2.57
555 572 6.940867 TCATGAGTCAGTGTACAGTACTAGTT 59.059 38.462 12.07 0.00 0.00 2.24
556 573 7.447545 TCATGAGTCAGTGTACAGTACTAGTTT 59.552 37.037 12.07 0.00 0.00 2.66
557 574 7.578310 TGAGTCAGTGTACAGTACTAGTTTT 57.422 36.000 12.07 0.00 0.00 2.43
577 594 3.530265 TTTAGATGCCCGTGTATTCGT 57.470 42.857 0.00 0.00 0.00 3.85
581 598 0.535335 ATGCCCGTGTATTCGTCTGT 59.465 50.000 0.00 0.00 0.00 3.41
582 599 0.389296 TGCCCGTGTATTCGTCTGTG 60.389 55.000 0.00 0.00 0.00 3.66
583 600 1.693083 GCCCGTGTATTCGTCTGTGC 61.693 60.000 0.00 0.00 0.00 4.57
584 601 1.410737 CCCGTGTATTCGTCTGTGCG 61.411 60.000 0.00 0.00 0.00 5.34
585 602 0.731514 CCGTGTATTCGTCTGTGCGT 60.732 55.000 0.00 0.00 0.00 5.24
586 603 0.633733 CGTGTATTCGTCTGTGCGTC 59.366 55.000 0.00 0.00 0.00 5.19
587 604 1.728179 CGTGTATTCGTCTGTGCGTCT 60.728 52.381 0.00 0.00 0.00 4.18
588 605 2.475022 CGTGTATTCGTCTGTGCGTCTA 60.475 50.000 0.00 0.00 0.00 2.59
592 609 1.460504 TTCGTCTGTGCGTCTAGGAT 58.539 50.000 0.00 0.00 0.00 3.24
606 662 6.708949 TGCGTCTAGGATTATTGGGAAAATAC 59.291 38.462 0.00 0.00 0.00 1.89
863 932 3.194968 GGGTCGAACTTCACATCTTCCTA 59.805 47.826 0.00 0.00 0.00 2.94
884 953 6.497259 TCCTACTCCTATATAAACCCTTGCAG 59.503 42.308 0.00 0.00 0.00 4.41
923 992 0.469070 AGCTCTCATCCCATCTGTGC 59.531 55.000 0.00 0.00 0.00 4.57
924 993 0.879400 GCTCTCATCCCATCTGTGCG 60.879 60.000 0.00 0.00 0.00 5.34
995 1095 2.611518 ACTTGCAGCTAAGCTAAGACG 58.388 47.619 12.10 0.00 36.40 4.18
996 1096 1.929836 CTTGCAGCTAAGCTAAGACGG 59.070 52.381 0.00 0.00 36.40 4.79
1026 1132 0.603707 TCACAACTGCTAGTGCCAGC 60.604 55.000 0.00 0.00 42.15 4.85
1419 1534 1.174078 TGTCCACGTCGTCCTTGCTA 61.174 55.000 0.00 0.00 0.00 3.49
1524 1639 2.187946 CTGCTCACCATCGGTCCC 59.812 66.667 0.00 0.00 31.02 4.46
1597 1712 2.180017 CGTACTGGACCGGGTTCG 59.820 66.667 6.32 0.00 0.00 3.95
1797 1912 1.129437 GCCATCAAGAGCGACTTCAAC 59.871 52.381 0.00 0.00 36.61 3.18
1860 1975 4.194640 CCAAGTACTACCTAGTGCTCGTA 58.805 47.826 0.00 0.00 46.34 3.43
2184 2308 2.151202 TGAAGACCGGCAAATTCTGTC 58.849 47.619 0.00 0.00 0.00 3.51
2185 2309 2.224523 TGAAGACCGGCAAATTCTGTCT 60.225 45.455 0.00 0.00 37.88 3.41
2186 2310 3.007506 TGAAGACCGGCAAATTCTGTCTA 59.992 43.478 0.00 0.00 35.34 2.59
2187 2311 3.914426 AGACCGGCAAATTCTGTCTAT 57.086 42.857 0.00 0.00 34.68 1.98
2188 2312 3.535561 AGACCGGCAAATTCTGTCTATG 58.464 45.455 0.00 0.00 34.68 2.23
2189 2313 2.614057 GACCGGCAAATTCTGTCTATGG 59.386 50.000 0.00 0.00 0.00 2.74
2190 2314 2.238646 ACCGGCAAATTCTGTCTATGGA 59.761 45.455 0.00 0.00 0.00 3.41
2191 2315 2.874701 CCGGCAAATTCTGTCTATGGAG 59.125 50.000 0.00 0.00 0.00 3.86
2192 2316 3.535561 CGGCAAATTCTGTCTATGGAGT 58.464 45.455 0.00 0.00 0.00 3.85
2196 2320 5.471456 GGCAAATTCTGTCTATGGAGTATGG 59.529 44.000 0.00 0.00 0.00 2.74
2198 2322 5.832539 AATTCTGTCTATGGAGTATGGGG 57.167 43.478 0.00 0.00 0.00 4.96
2201 2325 2.634940 CTGTCTATGGAGTATGGGGGTG 59.365 54.545 0.00 0.00 0.00 4.61
2290 2414 7.608153 TCGTAAGACATTGTTTCATTCTAGGA 58.392 34.615 0.00 0.00 45.01 2.94
2311 2459 4.276926 GGAAACACAGAGAAATCAAGTGCT 59.723 41.667 0.00 0.00 33.69 4.40
2312 2460 5.470098 GGAAACACAGAGAAATCAAGTGCTA 59.530 40.000 0.00 0.00 33.69 3.49
2313 2461 5.931441 AACACAGAGAAATCAAGTGCTAC 57.069 39.130 0.00 0.00 33.69 3.58
2314 2462 3.990469 ACACAGAGAAATCAAGTGCTACG 59.010 43.478 0.00 0.00 33.69 3.51
2452 2604 4.955925 TGACTTTTGTTTTGCGAGAAGA 57.044 36.364 0.00 0.00 0.00 2.87
2453 2605 5.499139 TGACTTTTGTTTTGCGAGAAGAT 57.501 34.783 0.00 0.00 0.00 2.40
2456 2608 5.514279 ACTTTTGTTTTGCGAGAAGATCAG 58.486 37.500 0.00 0.00 0.00 2.90
2458 2610 1.806542 TGTTTTGCGAGAAGATCAGGC 59.193 47.619 0.00 0.00 0.00 4.85
2459 2611 1.806542 GTTTTGCGAGAAGATCAGGCA 59.193 47.619 0.00 0.00 0.00 4.75
2492 2644 7.492352 AGATATAACGGAAATACAAGGCAAC 57.508 36.000 0.00 0.00 0.00 4.17
2521 2673 9.977762 AAACATAATAAAAATTACGTCGAGGTC 57.022 29.630 15.00 0.00 0.00 3.85
2524 2676 8.770828 CATAATAAAAATTACGTCGAGGTCCAT 58.229 33.333 15.00 5.57 0.00 3.41
2525 2677 4.939509 AAAAATTACGTCGAGGTCCATG 57.060 40.909 15.00 0.00 0.00 3.66
2546 2698 2.730928 GGACCATCAAACAAACATTGCG 59.269 45.455 0.00 0.00 0.00 4.85
2547 2699 3.551863 GGACCATCAAACAAACATTGCGA 60.552 43.478 0.00 0.00 0.00 5.10
2549 2701 2.730928 CCATCAAACAAACATTGCGACC 59.269 45.455 0.00 0.00 0.00 4.79
2552 2704 2.159366 TCAAACAAACATTGCGACCGTT 60.159 40.909 0.00 0.00 0.00 4.44
2562 2714 0.459585 TGCGACCGTTAGAATGAGCC 60.460 55.000 0.00 0.00 0.00 4.70
2568 2720 0.597637 CGTTAGAATGAGCCGCCGAT 60.598 55.000 0.00 0.00 0.00 4.18
2569 2721 0.861837 GTTAGAATGAGCCGCCGATG 59.138 55.000 0.00 0.00 0.00 3.84
2592 2744 2.203070 CTGCCGCCACTCCCATAC 60.203 66.667 0.00 0.00 0.00 2.39
2594 2746 3.792736 GCCGCCACTCCCATACCA 61.793 66.667 0.00 0.00 0.00 3.25
2597 2749 0.748005 CCGCCACTCCCATACCAAAG 60.748 60.000 0.00 0.00 0.00 2.77
2600 2752 0.331278 CCACTCCCATACCAAAGCCA 59.669 55.000 0.00 0.00 0.00 4.75
2606 2758 0.034186 CCATACCAAAGCCAGCCTGA 60.034 55.000 0.00 0.00 0.00 3.86
2608 2760 0.034089 ATACCAAAGCCAGCCTGACC 60.034 55.000 0.00 0.00 0.00 4.02
2609 2761 2.137177 TACCAAAGCCAGCCTGACCC 62.137 60.000 0.00 0.00 0.00 4.46
2618 2770 2.187946 GCCTGACCCTGTCGATGG 59.812 66.667 0.00 0.00 34.95 3.51
2621 2773 1.296392 CTGACCCTGTCGATGGCAA 59.704 57.895 0.00 0.00 34.95 4.52
2626 2778 2.264480 CTGTCGATGGCAACCGGA 59.736 61.111 9.46 0.00 0.00 5.14
2629 2781 0.535328 TGTCGATGGCAACCGGAAAA 60.535 50.000 9.46 0.00 0.00 2.29
2635 2787 3.127895 CGATGGCAACCGGAAAATCTTTA 59.872 43.478 9.46 0.00 0.00 1.85
2655 2807 3.065306 CACGTGCCCCTAAGACCA 58.935 61.111 0.82 0.00 0.00 4.02
2658 2810 2.125106 GTGCCCCTAAGACCAGCG 60.125 66.667 0.00 0.00 0.00 5.18
2659 2811 2.606519 TGCCCCTAAGACCAGCGT 60.607 61.111 0.00 0.00 0.00 5.07
2668 2820 3.386237 GACCAGCGTCCCAGAGCT 61.386 66.667 0.00 0.00 45.74 4.09
2679 2831 1.107114 CCCAGAGCTGTAGTCATCGT 58.893 55.000 0.00 0.00 0.00 3.73
2680 2832 1.066303 CCCAGAGCTGTAGTCATCGTC 59.934 57.143 0.00 0.00 0.00 4.20
2700 2852 5.063438 TCGTCGTTGAATCCTTGAATTGATC 59.937 40.000 0.00 0.00 0.00 2.92
2705 2857 7.174772 TCGTTGAATCCTTGAATTGATCTGAAA 59.825 33.333 0.00 0.00 0.00 2.69
2717 2869 7.231115 TGAATTGATCTGAAAAATCTGACACCA 59.769 33.333 0.00 0.00 0.00 4.17
2725 2877 7.390440 TCTGAAAAATCTGACACCAAATATCGT 59.610 33.333 0.00 0.00 0.00 3.73
2727 2879 7.807433 TGAAAAATCTGACACCAAATATCGTTG 59.193 33.333 0.00 0.00 0.00 4.10
2731 2883 5.060506 TCTGACACCAAATATCGTTGTTGT 58.939 37.500 0.00 0.00 36.90 3.32
2732 2884 5.178623 TCTGACACCAAATATCGTTGTTGTC 59.821 40.000 9.65 9.65 45.84 3.18
2749 2901 4.725556 TTGTCTATGCACGACAAGAAAC 57.274 40.909 22.51 0.01 44.03 2.78
2756 2908 1.534163 GCACGACAAGAAACCCTAACC 59.466 52.381 0.00 0.00 0.00 2.85
2758 2910 3.064931 CACGACAAGAAACCCTAACCTC 58.935 50.000 0.00 0.00 0.00 3.85
2782 2934 3.612251 CCGAGGAGCCGGTAGAAA 58.388 61.111 1.90 0.00 44.23 2.52
2791 2943 1.000955 AGCCGGTAGAAATCTATGCCG 59.999 52.381 1.90 10.82 37.65 5.69
2794 2946 2.947852 CGGTAGAAATCTATGCCGGAG 58.052 52.381 5.05 0.00 35.62 4.63
2798 2950 3.099267 AGAAATCTATGCCGGAGTTCG 57.901 47.619 5.05 0.00 40.99 3.95
2816 2968 2.173519 TCGGTCTAATTCGTCCCAACT 58.826 47.619 0.00 0.00 0.00 3.16
2817 2969 2.165030 TCGGTCTAATTCGTCCCAACTC 59.835 50.000 0.00 0.00 0.00 3.01
2818 2970 2.737679 CGGTCTAATTCGTCCCAACTCC 60.738 54.545 0.00 0.00 0.00 3.85
2819 2971 2.419713 GGTCTAATTCGTCCCAACTCCC 60.420 54.545 0.00 0.00 0.00 4.30
2820 2972 2.235402 GTCTAATTCGTCCCAACTCCCA 59.765 50.000 0.00 0.00 0.00 4.37
2821 2973 2.907696 TCTAATTCGTCCCAACTCCCAA 59.092 45.455 0.00 0.00 0.00 4.12
2822 2974 2.899303 AATTCGTCCCAACTCCCAAT 57.101 45.000 0.00 0.00 0.00 3.16
2823 2975 2.128771 ATTCGTCCCAACTCCCAATG 57.871 50.000 0.00 0.00 0.00 2.82
2824 2976 1.060729 TTCGTCCCAACTCCCAATGA 58.939 50.000 0.00 0.00 0.00 2.57
2831 2983 2.497273 CCCAACTCCCAATGAATGAACC 59.503 50.000 0.00 0.00 0.00 3.62
2842 2994 0.106967 GAATGAACCTGAGGAGGGCC 60.107 60.000 4.99 0.00 44.84 5.80
2846 2998 4.787280 ACCTGAGGAGGGCCGGAG 62.787 72.222 5.05 0.00 44.84 4.63
2847 2999 4.787280 CCTGAGGAGGGCCGGAGT 62.787 72.222 5.05 0.00 39.96 3.85
2865 3017 2.249844 GTCCGGAAGACCAACTCAAA 57.750 50.000 5.23 0.00 39.84 2.69
2872 3024 4.574828 CGGAAGACCAACTCAAAGAAGAAA 59.425 41.667 0.00 0.00 35.59 2.52
2873 3025 5.504173 CGGAAGACCAACTCAAAGAAGAAAC 60.504 44.000 0.00 0.00 35.59 2.78
2874 3026 5.357032 GGAAGACCAACTCAAAGAAGAAACA 59.643 40.000 0.00 0.00 35.97 2.83
2875 3027 5.819825 AGACCAACTCAAAGAAGAAACAC 57.180 39.130 0.00 0.00 0.00 3.32
2877 3029 3.377172 ACCAACTCAAAGAAGAAACACCG 59.623 43.478 0.00 0.00 0.00 4.94
2883 3035 2.554032 CAAAGAAGAAACACCGCCATCT 59.446 45.455 0.00 0.00 0.00 2.90
2884 3036 1.813513 AGAAGAAACACCGCCATCTG 58.186 50.000 0.00 0.00 0.00 2.90
2892 3044 0.606401 CACCGCCATCTGTCCAAACT 60.606 55.000 0.00 0.00 0.00 2.66
2896 3048 1.743996 GCCATCTGTCCAAACTCCTC 58.256 55.000 0.00 0.00 0.00 3.71
2900 3052 0.104672 TCTGTCCAAACTCCTCCCCA 60.105 55.000 0.00 0.00 0.00 4.96
2901 3053 0.995024 CTGTCCAAACTCCTCCCCAT 59.005 55.000 0.00 0.00 0.00 4.00
2902 3054 0.991920 TGTCCAAACTCCTCCCCATC 59.008 55.000 0.00 0.00 0.00 3.51
2914 3066 4.119155 TCCTCCCCATCAAGGACTAAAAT 58.881 43.478 0.00 0.00 41.22 1.82
2916 3068 4.079787 CCTCCCCATCAAGGACTAAAATCA 60.080 45.833 0.00 0.00 41.22 2.57
2920 3072 5.770162 CCCCATCAAGGACTAAAATCATACC 59.230 44.000 0.00 0.00 41.22 2.73
2931 3083 9.425577 GGACTAAAATCATACCTATCTACAAGC 57.574 37.037 0.00 0.00 0.00 4.01
2952 3104 5.305139 GCCGGAGCTTTTATTGACTTAAA 57.695 39.130 5.05 0.00 35.50 1.52
2953 3105 5.705902 GCCGGAGCTTTTATTGACTTAAAA 58.294 37.500 5.05 0.00 35.50 1.52
2954 3106 5.571741 GCCGGAGCTTTTATTGACTTAAAAC 59.428 40.000 5.05 0.00 35.50 2.43
2955 3107 6.674066 CCGGAGCTTTTATTGACTTAAAACA 58.326 36.000 0.00 0.00 30.16 2.83
2997 3149 7.988737 TGCAAACATCTCATTGTAAAGATAGG 58.011 34.615 0.00 0.00 31.10 2.57
3026 3179 9.822185 ACAAAAGATGCAGAAGTTAATTTTTCT 57.178 25.926 0.00 0.00 34.09 2.52
3098 3251 2.348591 CGACTTCTCCGTGCAAAGAAAC 60.349 50.000 2.16 3.07 31.45 2.78
3107 3260 4.759693 TCCGTGCAAAGAAACAATGAGTAT 59.240 37.500 0.00 0.00 0.00 2.12
3112 3265 8.110612 CGTGCAAAGAAACAATGAGTATACTAG 58.889 37.037 5.09 0.00 0.00 2.57
3150 3303 1.834188 TGAGTACACCTGCGATGAGA 58.166 50.000 0.00 0.00 0.00 3.27
3165 3318 6.758254 TGCGATGAGAAATGATATTCTACCA 58.242 36.000 0.00 0.00 39.70 3.25
3166 3319 6.870439 TGCGATGAGAAATGATATTCTACCAG 59.130 38.462 0.00 0.00 39.70 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 9.593134 AGTACAACAAAATGAAGCATAACAAAA 57.407 25.926 0.00 0.00 0.00 2.44
44 45 9.593134 AAGTACAACAAAATGAAGCATAACAAA 57.407 25.926 0.00 0.00 0.00 2.83
45 46 9.029243 CAAGTACAACAAAATGAAGCATAACAA 57.971 29.630 0.00 0.00 0.00 2.83
46 47 7.651304 CCAAGTACAACAAAATGAAGCATAACA 59.349 33.333 0.00 0.00 0.00 2.41
47 48 7.359181 GCCAAGTACAACAAAATGAAGCATAAC 60.359 37.037 0.00 0.00 0.00 1.89
48 49 6.644592 GCCAAGTACAACAAAATGAAGCATAA 59.355 34.615 0.00 0.00 0.00 1.90
49 50 6.155827 GCCAAGTACAACAAAATGAAGCATA 58.844 36.000 0.00 0.00 0.00 3.14
50 51 4.990426 GCCAAGTACAACAAAATGAAGCAT 59.010 37.500 0.00 0.00 0.00 3.79
51 52 4.367450 GCCAAGTACAACAAAATGAAGCA 58.633 39.130 0.00 0.00 0.00 3.91
52 53 3.740832 GGCCAAGTACAACAAAATGAAGC 59.259 43.478 0.00 0.00 0.00 3.86
53 54 5.200368 AGGCCAAGTACAACAAAATGAAG 57.800 39.130 5.01 0.00 0.00 3.02
54 55 4.038642 GGAGGCCAAGTACAACAAAATGAA 59.961 41.667 5.01 0.00 0.00 2.57
55 56 3.572255 GGAGGCCAAGTACAACAAAATGA 59.428 43.478 5.01 0.00 0.00 2.57
56 57 3.611530 CGGAGGCCAAGTACAACAAAATG 60.612 47.826 5.01 0.00 0.00 2.32
57 58 2.556622 CGGAGGCCAAGTACAACAAAAT 59.443 45.455 5.01 0.00 0.00 1.82
58 59 1.950909 CGGAGGCCAAGTACAACAAAA 59.049 47.619 5.01 0.00 0.00 2.44
59 60 1.600023 CGGAGGCCAAGTACAACAAA 58.400 50.000 5.01 0.00 0.00 2.83
60 61 0.250553 CCGGAGGCCAAGTACAACAA 60.251 55.000 5.01 0.00 46.14 2.83
61 62 1.373435 CCGGAGGCCAAGTACAACA 59.627 57.895 5.01 0.00 46.14 3.33
62 63 4.296265 CCGGAGGCCAAGTACAAC 57.704 61.111 5.01 0.00 46.14 3.32
74 75 1.288439 CTCATCTCATCCGCCGGAG 59.712 63.158 13.12 0.00 34.05 4.63
75 76 2.203082 CCTCATCTCATCCGCCGGA 61.203 63.158 8.97 8.97 35.55 5.14
76 77 2.341543 CCTCATCTCATCCGCCGG 59.658 66.667 0.00 0.00 0.00 6.13
77 78 2.356793 GCCTCATCTCATCCGCCG 60.357 66.667 0.00 0.00 0.00 6.46
78 79 1.301558 CTGCCTCATCTCATCCGCC 60.302 63.158 0.00 0.00 0.00 6.13
79 80 0.105593 TTCTGCCTCATCTCATCCGC 59.894 55.000 0.00 0.00 0.00 5.54
80 81 1.685517 TCTTCTGCCTCATCTCATCCG 59.314 52.381 0.00 0.00 0.00 4.18
81 82 3.666274 CATCTTCTGCCTCATCTCATCC 58.334 50.000 0.00 0.00 0.00 3.51
82 83 3.068560 GCATCTTCTGCCTCATCTCATC 58.931 50.000 0.00 0.00 45.66 2.92
83 84 3.128852 GCATCTTCTGCCTCATCTCAT 57.871 47.619 0.00 0.00 45.66 2.90
84 85 2.616634 GCATCTTCTGCCTCATCTCA 57.383 50.000 0.00 0.00 45.66 3.27
103 104 3.695933 GATTTCGTTCGTGCGGCCG 62.696 63.158 24.05 24.05 0.00 6.13
104 105 2.097728 GATTTCGTTCGTGCGGCC 59.902 61.111 0.00 0.00 0.00 6.13
105 106 2.097728 GGATTTCGTTCGTGCGGC 59.902 61.111 0.00 0.00 0.00 6.53
106 107 1.619526 TTCGGATTTCGTTCGTGCGG 61.620 55.000 2.16 0.00 40.32 5.69
107 108 0.515717 GTTCGGATTTCGTTCGTGCG 60.516 55.000 0.00 0.00 40.32 5.34
108 109 0.509499 TGTTCGGATTTCGTTCGTGC 59.491 50.000 0.00 0.00 40.32 5.34
109 110 2.934107 TTGTTCGGATTTCGTTCGTG 57.066 45.000 0.00 0.00 40.32 4.35
110 111 3.610495 GTTTTGTTCGGATTTCGTTCGT 58.390 40.909 0.00 0.00 40.32 3.85
111 112 2.643801 CGTTTTGTTCGGATTTCGTTCG 59.356 45.455 0.00 0.00 40.32 3.95
121 122 1.202054 ACAAACGTCCGTTTTGTTCGG 60.202 47.619 14.55 5.92 44.84 4.30
122 123 2.162371 ACAAACGTCCGTTTTGTTCG 57.838 45.000 14.55 6.56 44.84 3.95
123 124 3.059702 CCAAACAAACGTCCGTTTTGTTC 59.940 43.478 21.50 0.00 44.84 3.18
124 125 2.987821 CCAAACAAACGTCCGTTTTGTT 59.012 40.909 14.55 16.95 44.84 2.83
125 126 2.597520 CCAAACAAACGTCCGTTTTGT 58.402 42.857 14.55 12.86 44.84 2.83
126 127 1.921230 CCCAAACAAACGTCCGTTTTG 59.079 47.619 14.55 10.82 44.84 2.44
127 128 1.135053 CCCCAAACAAACGTCCGTTTT 60.135 47.619 14.55 4.97 44.84 2.43
129 130 0.680601 ACCCCAAACAAACGTCCGTT 60.681 50.000 0.00 0.00 40.45 4.44
130 131 1.077572 ACCCCAAACAAACGTCCGT 60.078 52.632 0.00 0.00 0.00 4.69
131 132 1.650363 GACCCCAAACAAACGTCCG 59.350 57.895 0.00 0.00 0.00 4.79
132 133 1.096967 ACGACCCCAAACAAACGTCC 61.097 55.000 0.00 0.00 0.00 4.79
133 134 0.028374 CACGACCCCAAACAAACGTC 59.972 55.000 0.00 0.00 31.82 4.34
134 135 1.378124 CCACGACCCCAAACAAACGT 61.378 55.000 0.00 0.00 34.40 3.99
135 136 1.357334 CCACGACCCCAAACAAACG 59.643 57.895 0.00 0.00 0.00 3.60
136 137 1.038681 ACCCACGACCCCAAACAAAC 61.039 55.000 0.00 0.00 0.00 2.93
137 138 0.324460 AACCCACGACCCCAAACAAA 60.324 50.000 0.00 0.00 0.00 2.83
138 139 0.549950 TAACCCACGACCCCAAACAA 59.450 50.000 0.00 0.00 0.00 2.83
139 140 0.108963 CTAACCCACGACCCCAAACA 59.891 55.000 0.00 0.00 0.00 2.83
140 141 0.397564 TCTAACCCACGACCCCAAAC 59.602 55.000 0.00 0.00 0.00 2.93
141 142 0.688487 CTCTAACCCACGACCCCAAA 59.312 55.000 0.00 0.00 0.00 3.28
142 143 0.472352 ACTCTAACCCACGACCCCAA 60.472 55.000 0.00 0.00 0.00 4.12
143 144 0.472352 AACTCTAACCCACGACCCCA 60.472 55.000 0.00 0.00 0.00 4.96
144 145 0.036671 CAACTCTAACCCACGACCCC 60.037 60.000 0.00 0.00 0.00 4.95
145 146 0.672711 GCAACTCTAACCCACGACCC 60.673 60.000 0.00 0.00 0.00 4.46
146 147 0.672711 GGCAACTCTAACCCACGACC 60.673 60.000 0.00 0.00 0.00 4.79
147 148 0.672711 GGGCAACTCTAACCCACGAC 60.673 60.000 0.00 0.00 43.64 4.34
148 149 0.834687 AGGGCAACTCTAACCCACGA 60.835 55.000 0.00 0.00 46.88 4.35
149 150 0.036306 AAGGGCAACTCTAACCCACG 59.964 55.000 0.00 0.00 46.88 4.94
150 151 2.570302 TCTAAGGGCAACTCTAACCCAC 59.430 50.000 0.00 0.00 46.88 4.61
151 152 2.910544 TCTAAGGGCAACTCTAACCCA 58.089 47.619 0.00 0.00 46.88 4.51
152 153 3.263681 AGTTCTAAGGGCAACTCTAACCC 59.736 47.826 0.00 0.00 44.62 4.11
153 154 4.254492 CAGTTCTAAGGGCAACTCTAACC 58.746 47.826 0.00 0.00 30.06 2.85
154 155 4.254492 CCAGTTCTAAGGGCAACTCTAAC 58.746 47.826 0.00 0.00 30.06 2.34
155 156 3.908103 ACCAGTTCTAAGGGCAACTCTAA 59.092 43.478 0.00 0.00 30.06 2.10
156 157 3.260884 CACCAGTTCTAAGGGCAACTCTA 59.739 47.826 0.00 0.00 30.06 2.43
157 158 2.039084 CACCAGTTCTAAGGGCAACTCT 59.961 50.000 0.00 0.00 30.06 3.24
158 159 2.427506 CACCAGTTCTAAGGGCAACTC 58.572 52.381 0.00 0.00 30.06 3.01
159 160 1.073923 CCACCAGTTCTAAGGGCAACT 59.926 52.381 0.00 0.00 32.87 3.16
160 161 1.202891 ACCACCAGTTCTAAGGGCAAC 60.203 52.381 0.00 0.00 0.00 4.17
161 162 1.145571 ACCACCAGTTCTAAGGGCAA 58.854 50.000 0.00 0.00 0.00 4.52
162 163 1.145571 AACCACCAGTTCTAAGGGCA 58.854 50.000 0.00 0.00 30.99 5.36
163 164 2.287977 AAACCACCAGTTCTAAGGGC 57.712 50.000 0.00 0.00 37.88 5.19
195 196 7.040062 CCAACAACCACCAGTCTATCATAAAAA 60.040 37.037 0.00 0.00 0.00 1.94
196 197 6.432783 CCAACAACCACCAGTCTATCATAAAA 59.567 38.462 0.00 0.00 0.00 1.52
197 198 5.943416 CCAACAACCACCAGTCTATCATAAA 59.057 40.000 0.00 0.00 0.00 1.40
198 199 5.013704 ACCAACAACCACCAGTCTATCATAA 59.986 40.000 0.00 0.00 0.00 1.90
199 200 4.534500 ACCAACAACCACCAGTCTATCATA 59.466 41.667 0.00 0.00 0.00 2.15
200 201 3.330701 ACCAACAACCACCAGTCTATCAT 59.669 43.478 0.00 0.00 0.00 2.45
201 202 2.708861 ACCAACAACCACCAGTCTATCA 59.291 45.455 0.00 0.00 0.00 2.15
202 203 3.418684 ACCAACAACCACCAGTCTATC 57.581 47.619 0.00 0.00 0.00 2.08
203 204 3.486383 CAACCAACAACCACCAGTCTAT 58.514 45.455 0.00 0.00 0.00 1.98
204 205 2.422235 CCAACCAACAACCACCAGTCTA 60.422 50.000 0.00 0.00 0.00 2.59
205 206 1.684869 CCAACCAACAACCACCAGTCT 60.685 52.381 0.00 0.00 0.00 3.24
206 207 0.744281 CCAACCAACAACCACCAGTC 59.256 55.000 0.00 0.00 0.00 3.51
207 208 0.040499 ACCAACCAACAACCACCAGT 59.960 50.000 0.00 0.00 0.00 4.00
208 209 1.190643 AACCAACCAACAACCACCAG 58.809 50.000 0.00 0.00 0.00 4.00
209 210 2.526888 TAACCAACCAACAACCACCA 57.473 45.000 0.00 0.00 0.00 4.17
250 251 6.312141 TGGATTTGACCAATCTCATCAGTA 57.688 37.500 0.00 0.00 41.22 2.74
383 384 2.128771 AGTTTTATGCCACGGCTCAT 57.871 45.000 9.92 0.00 42.51 2.90
441 450 8.824159 ACTGTATCATATAGACAAACATCTGC 57.176 34.615 0.00 0.00 0.00 4.26
457 466 9.319143 GAGCAAACTCATTTAGTACTGTATCAT 57.681 33.333 5.39 0.00 42.93 2.45
458 467 8.703604 GAGCAAACTCATTTAGTACTGTATCA 57.296 34.615 5.39 0.00 42.93 2.15
555 572 4.255301 ACGAATACACGGGCATCTAAAAA 58.745 39.130 0.00 0.00 37.61 1.94
556 573 3.864243 ACGAATACACGGGCATCTAAAA 58.136 40.909 0.00 0.00 37.61 1.52
557 574 3.131577 AGACGAATACACGGGCATCTAAA 59.868 43.478 0.00 0.00 37.61 1.85
559 576 2.034179 CAGACGAATACACGGGCATCTA 59.966 50.000 0.00 0.00 37.61 1.98
560 577 1.112113 AGACGAATACACGGGCATCT 58.888 50.000 0.00 0.00 37.61 2.90
564 581 1.693083 GCACAGACGAATACACGGGC 61.693 60.000 0.00 0.00 37.61 6.13
565 582 1.410737 CGCACAGACGAATACACGGG 61.411 60.000 0.00 0.00 37.61 5.28
566 583 0.731514 ACGCACAGACGAATACACGG 60.732 55.000 0.00 0.00 37.61 4.94
567 584 0.633733 GACGCACAGACGAATACACG 59.366 55.000 0.00 0.00 36.70 4.49
569 586 2.096980 CCTAGACGCACAGACGAATACA 59.903 50.000 0.00 0.00 36.70 2.29
570 587 2.353889 TCCTAGACGCACAGACGAATAC 59.646 50.000 0.00 0.00 36.70 1.89
572 589 1.460504 TCCTAGACGCACAGACGAAT 58.539 50.000 0.00 0.00 36.70 3.34
573 590 1.460504 ATCCTAGACGCACAGACGAA 58.539 50.000 0.00 0.00 36.70 3.85
574 591 1.460504 AATCCTAGACGCACAGACGA 58.539 50.000 0.00 0.00 36.70 4.20
575 592 3.627732 ATAATCCTAGACGCACAGACG 57.372 47.619 0.00 0.00 39.50 4.18
577 594 3.069586 CCCAATAATCCTAGACGCACAGA 59.930 47.826 0.00 0.00 0.00 3.41
581 598 4.764050 TTTCCCAATAATCCTAGACGCA 57.236 40.909 0.00 0.00 0.00 5.24
582 599 6.148976 GGTATTTTCCCAATAATCCTAGACGC 59.851 42.308 0.00 0.00 0.00 5.19
583 600 6.653740 GGGTATTTTCCCAATAATCCTAGACG 59.346 42.308 0.00 0.00 46.30 4.18
584 601 7.997773 GGGTATTTTCCCAATAATCCTAGAC 57.002 40.000 0.00 0.00 46.30 2.59
606 662 4.821260 TGCATACTTGTATATGTTGCTGGG 59.179 41.667 0.00 0.00 35.36 4.45
612 668 9.840427 GAAACTTGTTGCATACTTGTATATGTT 57.160 29.630 0.00 0.00 35.36 2.71
613 669 8.458843 GGAAACTTGTTGCATACTTGTATATGT 58.541 33.333 0.00 0.00 35.36 2.29
615 671 8.458843 GTGGAAACTTGTTGCATACTTGTATAT 58.541 33.333 0.00 0.00 0.00 0.86
616 672 7.445707 TGTGGAAACTTGTTGCATACTTGTATA 59.554 33.333 0.00 0.00 0.00 1.47
863 932 4.412199 TGCTGCAAGGGTTTATATAGGAGT 59.588 41.667 0.00 0.00 0.00 3.85
884 953 0.250727 TGTGTTAGACAGGGGCTTGC 60.251 55.000 0.00 0.00 0.00 4.01
923 992 0.470080 TGCCCTCTCTAATCCTCCCG 60.470 60.000 0.00 0.00 0.00 5.14
924 993 1.905894 GATGCCCTCTCTAATCCTCCC 59.094 57.143 0.00 0.00 0.00 4.30
1038 1144 1.795170 TTGGCGTCTTTGCTGCTTCC 61.795 55.000 0.00 0.00 34.52 3.46
1347 1462 2.995450 GCACGACACGGCGTACAAG 61.995 63.158 14.22 7.34 43.59 3.16
2184 2308 1.699634 CACCACCCCCATACTCCATAG 59.300 57.143 0.00 0.00 0.00 2.23
2185 2309 1.010294 ACACCACCCCCATACTCCATA 59.990 52.381 0.00 0.00 0.00 2.74
2186 2310 0.253630 ACACCACCCCCATACTCCAT 60.254 55.000 0.00 0.00 0.00 3.41
2187 2311 0.418245 TACACCACCCCCATACTCCA 59.582 55.000 0.00 0.00 0.00 3.86
2188 2312 1.129058 CTACACCACCCCCATACTCC 58.871 60.000 0.00 0.00 0.00 3.85
2189 2313 1.875488 ACTACACCACCCCCATACTC 58.125 55.000 0.00 0.00 0.00 2.59
2190 2314 3.495186 TTACTACACCACCCCCATACT 57.505 47.619 0.00 0.00 0.00 2.12
2191 2315 4.783560 AATTACTACACCACCCCCATAC 57.216 45.455 0.00 0.00 0.00 2.39
2192 2316 7.468752 AAATAATTACTACACCACCCCCATA 57.531 36.000 0.00 0.00 0.00 2.74
2196 2320 7.949690 AGAAAAATAATTACTACACCACCCC 57.050 36.000 0.00 0.00 0.00 4.95
2243 2367 8.997621 ACGAAATGCTTGTTACTCTATTCTTA 57.002 30.769 0.00 0.00 0.00 2.10
2248 2372 8.033038 TGTCTTACGAAATGCTTGTTACTCTAT 58.967 33.333 0.00 0.00 0.00 1.98
2259 2383 6.312399 TGAAACAATGTCTTACGAAATGCT 57.688 33.333 0.00 0.00 0.00 3.79
2290 2414 5.050091 CGTAGCACTTGATTTCTCTGTGTTT 60.050 40.000 0.00 0.00 32.79 2.83
2411 2563 8.990163 AAGTCAATAAAAGACCTCCTTTAACA 57.010 30.769 0.00 0.00 43.90 2.41
2415 2567 8.306313 ACAAAAGTCAATAAAAGACCTCCTTT 57.694 30.769 0.00 0.00 46.47 3.11
2422 2574 7.890763 TCGCAAAACAAAAGTCAATAAAAGAC 58.109 30.769 0.00 0.00 36.26 3.01
2423 2575 7.971168 TCTCGCAAAACAAAAGTCAATAAAAGA 59.029 29.630 0.00 0.00 0.00 2.52
2439 2591 1.806542 TGCCTGATCTTCTCGCAAAAC 59.193 47.619 0.00 0.00 0.00 2.43
2472 2624 5.250200 TGAGTTGCCTTGTATTTCCGTTAT 58.750 37.500 0.00 0.00 0.00 1.89
2473 2625 4.643463 TGAGTTGCCTTGTATTTCCGTTA 58.357 39.130 0.00 0.00 0.00 3.18
2483 2635 9.777297 ATTTTTATTATGTTTGAGTTGCCTTGT 57.223 25.926 0.00 0.00 0.00 3.16
2497 2649 7.765360 TGGACCTCGACGTAATTTTTATTATGT 59.235 33.333 0.00 0.00 38.53 2.29
2521 2673 4.540359 ATGTTTGTTTGATGGTCCATGG 57.460 40.909 9.76 4.97 0.00 3.66
2524 2676 3.726607 GCAATGTTTGTTTGATGGTCCA 58.273 40.909 0.00 0.00 0.00 4.02
2525 2677 2.730928 CGCAATGTTTGTTTGATGGTCC 59.269 45.455 0.00 0.00 0.00 4.46
2531 2683 1.402259 ACGGTCGCAATGTTTGTTTGA 59.598 42.857 0.00 0.00 0.00 2.69
2533 2685 2.570442 AACGGTCGCAATGTTTGTTT 57.430 40.000 0.00 0.00 0.00 2.83
2537 2689 3.749088 TCATTCTAACGGTCGCAATGTTT 59.251 39.130 0.00 0.00 0.00 2.83
2539 2691 2.930040 CTCATTCTAACGGTCGCAATGT 59.070 45.455 0.00 0.00 0.00 2.71
2546 2698 1.152383 GGCGGCTCATTCTAACGGTC 61.152 60.000 0.00 0.00 0.00 4.79
2547 2699 1.153429 GGCGGCTCATTCTAACGGT 60.153 57.895 0.00 0.00 0.00 4.83
2549 2701 0.597637 ATCGGCGGCTCATTCTAACG 60.598 55.000 7.21 0.00 0.00 3.18
2552 2704 1.300931 GCATCGGCGGCTCATTCTA 60.301 57.895 7.21 0.00 0.00 2.10
2574 2726 4.175337 TATGGGAGTGGCGGCAGC 62.175 66.667 13.91 7.67 44.18 5.25
2578 2730 0.748005 CTTTGGTATGGGAGTGGCGG 60.748 60.000 0.00 0.00 0.00 6.13
2583 2735 0.034089 GCTGGCTTTGGTATGGGAGT 60.034 55.000 0.00 0.00 0.00 3.85
2592 2744 2.677875 GGGTCAGGCTGGCTTTGG 60.678 66.667 19.90 0.00 0.00 3.28
2594 2746 2.417558 GACAGGGTCAGGCTGGCTTT 62.418 60.000 19.90 4.50 32.09 3.51
2597 2749 4.767255 CGACAGGGTCAGGCTGGC 62.767 72.222 15.73 13.70 32.09 4.85
2600 2752 2.362369 CCATCGACAGGGTCAGGCT 61.362 63.158 0.00 0.00 32.09 4.58
2606 2758 2.351276 GGTTGCCATCGACAGGGT 59.649 61.111 7.75 0.00 0.00 4.34
2608 2760 2.796483 TTCCGGTTGCCATCGACAGG 62.796 60.000 0.00 1.40 41.58 4.00
2609 2761 0.953471 TTTCCGGTTGCCATCGACAG 60.953 55.000 0.00 0.00 0.00 3.51
2618 2770 3.612423 GTGCATAAAGATTTTCCGGTTGC 59.388 43.478 0.00 0.00 0.00 4.17
2621 2773 3.078837 ACGTGCATAAAGATTTTCCGGT 58.921 40.909 0.00 0.00 0.00 5.28
2626 2778 2.094234 GGGGCACGTGCATAAAGATTTT 60.094 45.455 38.60 0.00 44.36 1.82
2629 2781 0.255890 AGGGGCACGTGCATAAAGAT 59.744 50.000 38.60 16.02 44.36 2.40
2635 2787 1.078426 GTCTTAGGGGCACGTGCAT 60.078 57.895 38.60 26.23 44.36 3.96
2655 2807 1.304547 ACTACAGCTCTGGGACGCT 60.305 57.895 1.66 0.00 36.83 5.07
2658 2810 1.066303 CGATGACTACAGCTCTGGGAC 59.934 57.143 1.66 0.00 34.19 4.46
2659 2811 1.341089 ACGATGACTACAGCTCTGGGA 60.341 52.381 1.66 0.00 34.19 4.37
2668 2820 3.442625 AGGATTCAACGACGATGACTACA 59.557 43.478 7.37 0.00 0.00 2.74
2679 2831 6.172630 TCAGATCAATTCAAGGATTCAACGA 58.827 36.000 0.00 0.00 0.00 3.85
2680 2832 6.426980 TCAGATCAATTCAAGGATTCAACG 57.573 37.500 0.00 0.00 0.00 4.10
2700 2852 7.530010 ACGATATTTGGTGTCAGATTTTTCAG 58.470 34.615 0.00 0.00 0.00 3.02
2705 2857 6.817765 ACAACGATATTTGGTGTCAGATTT 57.182 33.333 0.00 0.00 0.00 2.17
2708 2860 5.605564 CAACAACGATATTTGGTGTCAGA 57.394 39.130 0.66 0.00 39.05 3.27
2717 2869 5.579119 TCGTGCATAGACAACAACGATATTT 59.421 36.000 0.00 0.00 0.00 1.40
2731 2883 2.301870 AGGGTTTCTTGTCGTGCATAGA 59.698 45.455 0.00 0.00 0.00 1.98
2732 2884 2.699954 AGGGTTTCTTGTCGTGCATAG 58.300 47.619 0.00 0.00 0.00 2.23
2766 2918 1.033574 AGATTTCTACCGGCTCCTCG 58.966 55.000 0.00 0.00 0.00 4.63
2773 2925 2.080286 CCGGCATAGATTTCTACCGG 57.920 55.000 16.67 16.67 45.54 5.28
2774 2926 2.296471 ACTCCGGCATAGATTTCTACCG 59.704 50.000 0.00 8.81 37.65 4.02
2791 2943 2.480932 GGGACGAATTAGACCGAACTCC 60.481 54.545 0.00 0.00 0.00 3.85
2794 2946 2.660189 TGGGACGAATTAGACCGAAC 57.340 50.000 0.00 0.00 0.00 3.95
2798 2950 2.419713 GGGAGTTGGGACGAATTAGACC 60.420 54.545 0.00 0.00 0.00 3.85
2816 2968 2.918934 TCCTCAGGTTCATTCATTGGGA 59.081 45.455 0.00 0.00 0.00 4.37
2817 2969 3.285484 CTCCTCAGGTTCATTCATTGGG 58.715 50.000 0.00 0.00 0.00 4.12
2818 2970 3.285484 CCTCCTCAGGTTCATTCATTGG 58.715 50.000 0.00 0.00 34.60 3.16
2819 2971 3.285484 CCCTCCTCAGGTTCATTCATTG 58.715 50.000 0.00 0.00 38.30 2.82
2820 2972 2.357569 GCCCTCCTCAGGTTCATTCATT 60.358 50.000 0.00 0.00 38.30 2.57
2821 2973 1.213926 GCCCTCCTCAGGTTCATTCAT 59.786 52.381 0.00 0.00 38.30 2.57
2822 2974 0.620556 GCCCTCCTCAGGTTCATTCA 59.379 55.000 0.00 0.00 38.30 2.57
2823 2975 0.106967 GGCCCTCCTCAGGTTCATTC 60.107 60.000 0.00 0.00 38.30 2.67
2824 2976 1.915078 CGGCCCTCCTCAGGTTCATT 61.915 60.000 0.00 0.00 38.30 2.57
2831 2983 3.151022 GACTCCGGCCCTCCTCAG 61.151 72.222 0.00 0.00 0.00 3.35
2846 2998 2.143925 CTTTGAGTTGGTCTTCCGGAC 58.856 52.381 1.83 0.00 43.79 4.79
2847 2999 2.043992 TCTTTGAGTTGGTCTTCCGGA 58.956 47.619 0.00 0.00 36.30 5.14
2857 3009 3.363178 GCGGTGTTTCTTCTTTGAGTTG 58.637 45.455 0.00 0.00 0.00 3.16
2863 3015 2.554032 CAGATGGCGGTGTTTCTTCTTT 59.446 45.455 0.00 0.00 0.00 2.52
2865 3017 1.072331 ACAGATGGCGGTGTTTCTTCT 59.928 47.619 0.00 0.00 0.00 2.85
2872 3024 0.889186 GTTTGGACAGATGGCGGTGT 60.889 55.000 0.00 0.00 0.00 4.16
2873 3025 0.606401 AGTTTGGACAGATGGCGGTG 60.606 55.000 0.00 0.00 0.00 4.94
2874 3026 0.321653 GAGTTTGGACAGATGGCGGT 60.322 55.000 0.00 0.00 0.00 5.68
2875 3027 1.026718 GGAGTTTGGACAGATGGCGG 61.027 60.000 0.00 0.00 0.00 6.13
2877 3029 1.680249 GGAGGAGTTTGGACAGATGGC 60.680 57.143 0.00 0.00 0.00 4.40
2883 3035 0.991920 GATGGGGAGGAGTTTGGACA 59.008 55.000 0.00 0.00 0.00 4.02
2884 3036 0.991920 TGATGGGGAGGAGTTTGGAC 59.008 55.000 0.00 0.00 0.00 4.02
2892 3044 2.961536 TTAGTCCTTGATGGGGAGGA 57.038 50.000 0.00 0.00 39.69 3.71
2896 3048 5.770162 GGTATGATTTTAGTCCTTGATGGGG 59.230 44.000 0.00 0.00 36.20 4.96
2914 3066 4.079970 CTCCGGCTTGTAGATAGGTATGA 58.920 47.826 0.00 0.00 0.00 2.15
2916 3068 2.826725 GCTCCGGCTTGTAGATAGGTAT 59.173 50.000 0.00 0.00 35.22 2.73
2931 3083 6.674066 TGTTTTAAGTCAATAAAAGCTCCGG 58.326 36.000 0.00 0.00 35.91 5.14
2950 3102 6.127196 TGCATAGTCTTTTGAAACCCTGTTTT 60.127 34.615 0.00 0.00 0.00 2.43
2952 3104 4.892934 TGCATAGTCTTTTGAAACCCTGTT 59.107 37.500 0.00 0.00 0.00 3.16
2953 3105 4.469657 TGCATAGTCTTTTGAAACCCTGT 58.530 39.130 0.00 0.00 0.00 4.00
2954 3106 5.452078 TTGCATAGTCTTTTGAAACCCTG 57.548 39.130 0.00 0.00 0.00 4.45
2955 3107 5.362430 TGTTTGCATAGTCTTTTGAAACCCT 59.638 36.000 0.00 0.00 0.00 4.34
3026 3179 8.668653 TCCCATAATTTCTGCCATCTCTTTATA 58.331 33.333 0.00 0.00 0.00 0.98
3098 3251 3.885358 TGCGACGCTAGTATACTCATTG 58.115 45.455 22.08 0.90 0.00 2.82
3129 3282 2.760650 TCTCATCGCAGGTGTACTCATT 59.239 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.