Multiple sequence alignment - TraesCS7D01G520000

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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 TraesCS7D01G520000 chr7D 100.000 2582 0 0 1 2582 617736771 617734190 0.000000e+00 4769.0
1 TraesCS7D01G520000 chr7D 82.716 162 22 5 188 347 200770579 200770422 3.460000e-29 139.0
2 TraesCS7D01G520000 chr7A 92.659 1662 89 14 831 2464 711583880 711582224 0.000000e+00 2362.0
3 TraesCS7D01G520000 chr7A 91.148 610 48 4 1853 2460 711580946 711580341 0.000000e+00 822.0
4 TraesCS7D01G520000 chr7A 87.048 664 62 14 188 839 711584840 711584189 0.000000e+00 728.0
5 TraesCS7D01G520000 chr7A 95.918 49 2 0 1809 1857 711581180 711581132 2.130000e-11 80.5
6 TraesCS7D01G520000 chr7B 88.335 1886 130 35 202 2033 711756969 711755120 0.000000e+00 2182.0
7 TraesCS7D01G520000 chr7B 88.509 322 30 6 2147 2465 711752197 711751880 1.450000e-102 383.0
8 TraesCS7D01G520000 chr7B 89.655 232 18 5 202 429 711772666 711772437 9.040000e-75 291.0
9 TraesCS7D01G520000 chr6B 81.368 687 77 33 876 1537 38877602 38878262 1.770000e-141 512.0
10 TraesCS7D01G520000 chr6B 83.835 532 63 15 975 1496 59723180 59723698 3.860000e-133 484.0
11 TraesCS7D01G520000 chr6B 83.871 527 64 14 975 1496 29060618 29060108 1.390000e-132 483.0
12 TraesCS7D01G520000 chr6B 83.810 525 63 11 975 1496 28980244 28979739 1.800000e-131 479.0
13 TraesCS7D01G520000 chr6B 83.585 530 61 18 975 1496 58812382 58812893 8.360000e-130 473.0
14 TraesCS7D01G520000 chr6A 83.099 568 63 20 975 1537 16802044 16801505 1.070000e-133 486.0
15 TraesCS7D01G520000 chr6A 82.487 571 67 15 973 1537 16658710 16658167 1.080000e-128 470.0
16 TraesCS7D01G520000 chr6A 86.154 260 22 9 925 1177 16683330 16683582 4.230000e-68 268.0
17 TraesCS7D01G520000 chr6D 80.799 651 92 24 863 1496 16307383 16306749 1.800000e-131 479.0
18 TraesCS7D01G520000 chr6D 83.208 530 70 13 970 1496 16523201 16522688 3.890000e-128 468.0
19 TraesCS7D01G520000 chr6D 81.930 570 66 20 973 1537 16529537 16529000 5.070000e-122 448.0
20 TraesCS7D01G520000 chr3A 80.155 645 82 29 975 1599 746261394 746262012 8.480000e-120 440.0
21 TraesCS7D01G520000 chr3D 81.193 553 77 19 975 1521 611407314 611407845 1.100000e-113 420.0
22 TraesCS7D01G520000 chr2D 89.944 179 18 0 10 188 63395960 63395782 5.560000e-57 231.0
23 TraesCS7D01G520000 chr4A 84.058 138 17 4 52 188 673956535 673956402 7.500000e-26 128.0
24 TraesCS7D01G520000 chrUn 87.273 110 14 0 80 189 345013074 345013183 2.700000e-25 126.0
25 TraesCS7D01G520000 chr2B 86.726 113 15 0 80 192 98614299 98614187 2.700000e-25 126.0
26 TraesCS7D01G520000 chr2B 86.726 113 15 0 80 192 98619142 98619030 2.700000e-25 126.0


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 TraesCS7D01G520000 chr7D 617734190 617736771 2581 True 4769.000 4769 100.00000 1 2582 1 chr7D.!!$R2 2581
1 TraesCS7D01G520000 chr7A 711580341 711584840 4499 True 998.125 2362 91.69325 188 2464 4 chr7A.!!$R1 2276
2 TraesCS7D01G520000 chr7B 711751880 711756969 5089 True 1282.500 2182 88.42200 202 2465 2 chr7B.!!$R2 2263
3 TraesCS7D01G520000 chr6B 38877602 38878262 660 False 512.000 512 81.36800 876 1537 1 chr6B.!!$F1 661
4 TraesCS7D01G520000 chr6B 59723180 59723698 518 False 484.000 484 83.83500 975 1496 1 chr6B.!!$F3 521
5 TraesCS7D01G520000 chr6B 29060108 29060618 510 True 483.000 483 83.87100 975 1496 1 chr6B.!!$R2 521
6 TraesCS7D01G520000 chr6B 28979739 28980244 505 True 479.000 479 83.81000 975 1496 1 chr6B.!!$R1 521
7 TraesCS7D01G520000 chr6B 58812382 58812893 511 False 473.000 473 83.58500 975 1496 1 chr6B.!!$F2 521
8 TraesCS7D01G520000 chr6A 16801505 16802044 539 True 486.000 486 83.09900 975 1537 1 chr6A.!!$R2 562
9 TraesCS7D01G520000 chr6A 16658167 16658710 543 True 470.000 470 82.48700 973 1537 1 chr6A.!!$R1 564
10 TraesCS7D01G520000 chr6D 16306749 16307383 634 True 479.000 479 80.79900 863 1496 1 chr6D.!!$R1 633
11 TraesCS7D01G520000 chr6D 16522688 16523201 513 True 468.000 468 83.20800 970 1496 1 chr6D.!!$R2 526
12 TraesCS7D01G520000 chr6D 16529000 16529537 537 True 448.000 448 81.93000 973 1537 1 chr6D.!!$R3 564
13 TraesCS7D01G520000 chr3A 746261394 746262012 618 False 440.000 440 80.15500 975 1599 1 chr3A.!!$F1 624
14 TraesCS7D01G520000 chr3D 611407314 611407845 531 False 420.000 420 81.19300 975 1521 1 chr3D.!!$F1 546

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
145 146 0.104671 TTGCAGGGCAACAAAGAAGC 59.895 50.0 0.00 0.0 43.99 3.86 F
183 184 0.961019 TCCACATGCAAGTTGAAGCC 59.039 50.0 7.16 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 1899 0.182775 GTGGTCTTGGTGGACTTGGT 59.817 55.000 0.00 0.0 36.55 3.67 R
2145 2614 1.818060 GTTATGGCCAGTCACAATGCA 59.182 47.619 13.05 0.0 0.00 3.96 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
38 39 8.885722 AGAACAAAATATATGGCTTTGCAATTG 58.114 29.630 0.00 0.00 34.15 2.32
39 40 8.564509 AACAAAATATATGGCTTTGCAATTGT 57.435 26.923 7.40 0.02 34.15 2.71
40 41 7.976826 ACAAAATATATGGCTTTGCAATTGTG 58.023 30.769 7.40 0.00 34.15 3.33
41 42 7.607223 ACAAAATATATGGCTTTGCAATTGTGT 59.393 29.630 7.40 0.00 34.15 3.72
42 43 7.775397 AAATATATGGCTTTGCAATTGTGTC 57.225 32.000 7.40 0.00 0.00 3.67
43 44 4.804868 ATATGGCTTTGCAATTGTGTCA 57.195 36.364 7.40 0.00 0.00 3.58
44 45 2.975732 TGGCTTTGCAATTGTGTCAA 57.024 40.000 7.40 0.00 0.00 3.18
45 46 3.472283 TGGCTTTGCAATTGTGTCAAT 57.528 38.095 7.40 0.00 0.00 2.57
46 47 3.806380 TGGCTTTGCAATTGTGTCAATT 58.194 36.364 7.40 2.42 0.00 2.32
47 48 4.953667 TGGCTTTGCAATTGTGTCAATTA 58.046 34.783 7.40 0.00 0.00 1.40
48 49 4.749099 TGGCTTTGCAATTGTGTCAATTAC 59.251 37.500 7.40 3.61 0.00 1.89
49 50 4.990426 GGCTTTGCAATTGTGTCAATTACT 59.010 37.500 7.40 0.00 0.00 2.24
50 51 6.155827 GGCTTTGCAATTGTGTCAATTACTA 58.844 36.000 7.40 0.00 0.00 1.82
51 52 6.644592 GGCTTTGCAATTGTGTCAATTACTAA 59.355 34.615 7.40 5.26 0.00 2.24
52 53 7.170658 GGCTTTGCAATTGTGTCAATTACTAAA 59.829 33.333 7.40 8.14 0.00 1.85
53 54 8.711457 GCTTTGCAATTGTGTCAATTACTAAAT 58.289 29.630 7.40 0.00 0.00 1.40
113 114 9.099454 ACTACTTTAGTAAGTTTGCTCATATGC 57.901 33.333 0.00 0.00 41.85 3.14
114 115 9.319143 CTACTTTAGTAAGTTTGCTCATATGCT 57.681 33.333 0.00 0.00 41.85 3.79
115 116 8.567285 ACTTTAGTAAGTTTGCTCATATGCTT 57.433 30.769 0.00 0.00 41.85 3.91
116 117 8.669243 ACTTTAGTAAGTTTGCTCATATGCTTC 58.331 33.333 0.00 0.00 41.85 3.86
117 118 7.553881 TTAGTAAGTTTGCTCATATGCTTCC 57.446 36.000 0.00 0.00 0.00 3.46
118 119 5.749462 AGTAAGTTTGCTCATATGCTTCCT 58.251 37.500 0.00 0.00 0.00 3.36
119 120 6.889198 AGTAAGTTTGCTCATATGCTTCCTA 58.111 36.000 0.00 0.00 0.00 2.94
120 121 7.512992 AGTAAGTTTGCTCATATGCTTCCTAT 58.487 34.615 0.00 0.00 0.00 2.57
121 122 6.630444 AAGTTTGCTCATATGCTTCCTATG 57.370 37.500 0.00 0.00 0.00 2.23
122 123 5.933617 AGTTTGCTCATATGCTTCCTATGA 58.066 37.500 0.00 0.00 35.05 2.15
123 124 6.540995 AGTTTGCTCATATGCTTCCTATGAT 58.459 36.000 0.00 0.00 35.60 2.45
124 125 7.683578 AGTTTGCTCATATGCTTCCTATGATA 58.316 34.615 0.00 0.00 35.60 2.15
125 126 8.327271 AGTTTGCTCATATGCTTCCTATGATAT 58.673 33.333 0.00 0.00 35.60 1.63
126 127 8.954350 GTTTGCTCATATGCTTCCTATGATATT 58.046 33.333 0.00 0.00 35.60 1.28
127 128 9.524496 TTTGCTCATATGCTTCCTATGATATTT 57.476 29.630 0.00 0.00 35.60 1.40
128 129 8.502105 TGCTCATATGCTTCCTATGATATTTG 57.498 34.615 0.00 0.00 35.60 2.32
129 130 7.066645 TGCTCATATGCTTCCTATGATATTTGC 59.933 37.037 0.00 0.00 35.60 3.68
130 131 7.066645 GCTCATATGCTTCCTATGATATTTGCA 59.933 37.037 0.00 0.00 35.60 4.08
131 132 8.502105 TCATATGCTTCCTATGATATTTGCAG 57.498 34.615 0.00 0.00 32.13 4.41
132 133 7.555195 TCATATGCTTCCTATGATATTTGCAGG 59.445 37.037 0.00 0.00 32.13 4.85
133 134 4.401022 TGCTTCCTATGATATTTGCAGGG 58.599 43.478 0.00 0.00 0.00 4.45
134 135 3.192212 GCTTCCTATGATATTTGCAGGGC 59.808 47.826 0.00 0.00 0.00 5.19
135 136 4.401022 CTTCCTATGATATTTGCAGGGCA 58.599 43.478 0.00 0.00 36.47 5.36
145 146 0.104671 TTGCAGGGCAACAAAGAAGC 59.895 50.000 0.00 0.00 43.99 3.86
146 147 3.241446 TTGCAGGGCAACAAAGAAGCC 62.241 52.381 0.00 0.00 43.99 4.35
151 152 1.869774 GGCAACAAAGAAGCCCAAAG 58.130 50.000 0.00 0.00 42.58 2.77
152 153 1.138859 GGCAACAAAGAAGCCCAAAGT 59.861 47.619 0.00 0.00 42.58 2.66
153 154 2.419990 GGCAACAAAGAAGCCCAAAGTT 60.420 45.455 0.00 0.00 42.58 2.66
154 155 2.866156 GCAACAAAGAAGCCCAAAGTTC 59.134 45.455 0.00 0.00 0.00 3.01
155 156 3.678529 GCAACAAAGAAGCCCAAAGTTCA 60.679 43.478 0.00 0.00 0.00 3.18
156 157 4.502962 CAACAAAGAAGCCCAAAGTTCAA 58.497 39.130 0.00 0.00 0.00 2.69
157 158 4.817318 ACAAAGAAGCCCAAAGTTCAAA 57.183 36.364 0.00 0.00 0.00 2.69
158 159 4.503910 ACAAAGAAGCCCAAAGTTCAAAC 58.496 39.130 0.00 0.00 0.00 2.93
159 160 3.819564 AAGAAGCCCAAAGTTCAAACC 57.180 42.857 0.00 0.00 0.00 3.27
160 161 2.745968 AGAAGCCCAAAGTTCAAACCA 58.254 42.857 0.00 0.00 0.00 3.67
161 162 3.103742 AGAAGCCCAAAGTTCAAACCAA 58.896 40.909 0.00 0.00 0.00 3.67
162 163 3.132824 AGAAGCCCAAAGTTCAAACCAAG 59.867 43.478 0.00 0.00 0.00 3.61
163 164 2.745968 AGCCCAAAGTTCAAACCAAGA 58.254 42.857 0.00 0.00 0.00 3.02
164 165 3.308401 AGCCCAAAGTTCAAACCAAGAT 58.692 40.909 0.00 0.00 0.00 2.40
165 166 3.321968 AGCCCAAAGTTCAAACCAAGATC 59.678 43.478 0.00 0.00 0.00 2.75
166 167 3.554960 GCCCAAAGTTCAAACCAAGATCC 60.555 47.826 0.00 0.00 0.00 3.36
167 168 3.640967 CCCAAAGTTCAAACCAAGATCCA 59.359 43.478 0.00 0.00 0.00 3.41
168 169 4.501400 CCCAAAGTTCAAACCAAGATCCAC 60.501 45.833 0.00 0.00 0.00 4.02
169 170 4.099266 CCAAAGTTCAAACCAAGATCCACA 59.901 41.667 0.00 0.00 0.00 4.17
170 171 5.221501 CCAAAGTTCAAACCAAGATCCACAT 60.222 40.000 0.00 0.00 0.00 3.21
171 172 5.458041 AAGTTCAAACCAAGATCCACATG 57.542 39.130 0.00 0.00 0.00 3.21
172 173 3.256631 AGTTCAAACCAAGATCCACATGC 59.743 43.478 0.00 0.00 0.00 4.06
173 174 2.874014 TCAAACCAAGATCCACATGCA 58.126 42.857 0.00 0.00 0.00 3.96
174 175 3.229293 TCAAACCAAGATCCACATGCAA 58.771 40.909 0.00 0.00 0.00 4.08
175 176 3.256383 TCAAACCAAGATCCACATGCAAG 59.744 43.478 0.00 0.00 0.00 4.01
176 177 2.592102 ACCAAGATCCACATGCAAGT 57.408 45.000 0.00 0.00 0.00 3.16
177 178 2.880443 ACCAAGATCCACATGCAAGTT 58.120 42.857 0.00 0.00 0.00 2.66
178 179 2.559668 ACCAAGATCCACATGCAAGTTG 59.440 45.455 0.00 0.00 0.00 3.16
179 180 2.821378 CCAAGATCCACATGCAAGTTGA 59.179 45.455 7.16 0.00 0.00 3.18
180 181 3.256383 CCAAGATCCACATGCAAGTTGAA 59.744 43.478 7.16 0.00 0.00 2.69
181 182 4.482386 CAAGATCCACATGCAAGTTGAAG 58.518 43.478 7.16 0.00 0.00 3.02
182 183 2.490903 AGATCCACATGCAAGTTGAAGC 59.509 45.455 7.16 0.00 0.00 3.86
183 184 0.961019 TCCACATGCAAGTTGAAGCC 59.039 50.000 7.16 0.00 0.00 4.35
184 185 0.963962 CCACATGCAAGTTGAAGCCT 59.036 50.000 7.16 0.00 0.00 4.58
185 186 1.068055 CCACATGCAAGTTGAAGCCTC 60.068 52.381 7.16 0.00 0.00 4.70
186 187 1.884579 CACATGCAAGTTGAAGCCTCT 59.115 47.619 7.16 0.00 0.00 3.69
187 188 2.295349 CACATGCAAGTTGAAGCCTCTT 59.705 45.455 7.16 0.00 0.00 2.85
188 189 2.555757 ACATGCAAGTTGAAGCCTCTTC 59.444 45.455 7.16 0.00 0.00 2.87
189 190 2.645838 TGCAAGTTGAAGCCTCTTCT 57.354 45.000 7.16 0.00 0.00 2.85
190 191 2.936202 TGCAAGTTGAAGCCTCTTCTT 58.064 42.857 7.16 0.00 0.00 2.52
191 192 3.290710 TGCAAGTTGAAGCCTCTTCTTT 58.709 40.909 7.16 0.00 0.00 2.52
192 193 3.701040 TGCAAGTTGAAGCCTCTTCTTTT 59.299 39.130 7.16 0.00 0.00 2.27
193 194 4.887071 TGCAAGTTGAAGCCTCTTCTTTTA 59.113 37.500 7.16 0.00 0.00 1.52
194 195 5.536161 TGCAAGTTGAAGCCTCTTCTTTTAT 59.464 36.000 7.16 0.00 0.00 1.40
195 196 6.089476 GCAAGTTGAAGCCTCTTCTTTTATC 58.911 40.000 7.16 0.00 0.00 1.75
196 197 6.072230 GCAAGTTGAAGCCTCTTCTTTTATCT 60.072 38.462 7.16 0.00 0.00 1.98
197 198 7.525759 CAAGTTGAAGCCTCTTCTTTTATCTC 58.474 38.462 0.00 0.00 0.00 2.75
198 199 6.176896 AGTTGAAGCCTCTTCTTTTATCTCC 58.823 40.000 7.91 0.00 0.00 3.71
199 200 6.012945 AGTTGAAGCCTCTTCTTTTATCTCCT 60.013 38.462 7.91 0.00 0.00 3.69
200 201 5.738909 TGAAGCCTCTTCTTTTATCTCCTG 58.261 41.667 7.91 0.00 0.00 3.86
252 253 6.968131 TTGAAGATACTGGTTTTCGATGAG 57.032 37.500 0.00 0.00 0.00 2.90
254 255 4.744795 AGATACTGGTTTTCGATGAGCT 57.255 40.909 0.00 0.00 0.00 4.09
266 267 4.537135 TCGATGAGCTCAAGTTTAACCT 57.463 40.909 22.50 0.00 0.00 3.50
275 276 6.455647 AGCTCAAGTTTAACCTTTTAATGGC 58.544 36.000 0.00 0.00 0.00 4.40
277 278 6.104146 TCAAGTTTAACCTTTTAATGGCCC 57.896 37.500 0.00 0.00 0.00 5.80
314 315 6.821160 TGTCACTATTCCGATCTGCATTTTAA 59.179 34.615 0.00 0.00 0.00 1.52
315 316 7.498900 TGTCACTATTCCGATCTGCATTTTAAT 59.501 33.333 0.00 0.00 0.00 1.40
355 356 5.970317 TTTCAATGTGTGAAGATGATGCT 57.030 34.783 0.00 0.00 46.85 3.79
398 404 9.462174 CTTGATAGTTGAAAAAGTGCACAATTA 57.538 29.630 21.04 4.95 0.00 1.40
459 465 8.882736 GTGTTGAATGTACATATTGAGATGTGA 58.117 33.333 9.21 0.00 40.31 3.58
463 469 9.617523 TGAATGTACATATTGAGATGTGAATGT 57.382 29.630 9.21 0.00 40.31 2.71
487 493 9.986833 TGTTGATCGTTTATGATTACAATTCAG 57.013 29.630 0.00 0.00 0.00 3.02
506 512 3.253188 TCAGAATAGCAGCCAAACAACAC 59.747 43.478 0.00 0.00 0.00 3.32
574 586 3.737850 TGCAATCAAAATCCCACCAAAC 58.262 40.909 0.00 0.00 0.00 2.93
608 620 7.605410 GTAAGAACGAGGTTTCATCCATTTA 57.395 36.000 0.00 0.00 0.00 1.40
613 625 3.063452 CGAGGTTTCATCCATTTACACCG 59.937 47.826 0.00 0.00 0.00 4.94
615 627 4.658063 AGGTTTCATCCATTTACACCGAA 58.342 39.130 0.00 0.00 0.00 4.30
631 643 9.896263 TTTACACCGAATAAAATGAAAACCTAC 57.104 29.630 0.00 0.00 0.00 3.18
650 662 3.324930 TGGGTGCCAGAGGAGCTG 61.325 66.667 0.00 0.00 44.49 4.24
660 672 3.133003 GCCAGAGGAGCTGTACAGAAATA 59.867 47.826 27.08 0.00 43.33 1.40
701 718 5.355071 TCAACCCAATGAAATGAGATCGAAG 59.645 40.000 0.00 0.00 0.00 3.79
715 732 1.370414 CGAAGGTGCCAAACAAGCG 60.370 57.895 0.00 0.00 0.00 4.68
734 754 3.135994 GCGGTAAATGAATACGACCCAT 58.864 45.455 0.00 0.00 0.00 4.00
779 799 3.306433 CCGGTTCCCCAAATTTCGAATTT 60.306 43.478 0.00 0.00 0.00 1.82
790 814 4.839668 ATTTCGAATTTCGTTTCCCACA 57.160 36.364 17.61 0.00 41.35 4.17
792 816 2.841215 TCGAATTTCGTTTCCCACAGT 58.159 42.857 17.61 0.00 41.35 3.55
801 825 3.768468 GTTTCCCACAGTGAAAAACGA 57.232 42.857 0.62 0.00 33.80 3.85
802 826 3.691498 GTTTCCCACAGTGAAAAACGAG 58.309 45.455 0.62 0.00 33.80 4.18
815 839 7.540745 CAGTGAAAAACGAGGAAAAGAAGAAAA 59.459 33.333 0.00 0.00 0.00 2.29
817 841 8.373256 GTGAAAAACGAGGAAAAGAAGAAAAAG 58.627 33.333 0.00 0.00 0.00 2.27
820 844 6.378710 AACGAGGAAAAGAAGAAAAAGGAG 57.621 37.500 0.00 0.00 0.00 3.69
823 847 6.773200 ACGAGGAAAAGAAGAAAAAGGAGAAT 59.227 34.615 0.00 0.00 0.00 2.40
824 848 7.937394 ACGAGGAAAAGAAGAAAAAGGAGAATA 59.063 33.333 0.00 0.00 0.00 1.75
825 849 8.231161 CGAGGAAAAGAAGAAAAAGGAGAATAC 58.769 37.037 0.00 0.00 0.00 1.89
826 850 9.290988 GAGGAAAAGAAGAAAAAGGAGAATACT 57.709 33.333 0.00 0.00 0.00 2.12
900 1242 1.147600 CCCTATAAAACCCGCGCCT 59.852 57.895 0.00 0.00 0.00 5.52
935 1300 1.772819 ATCCACCATCCGATCCAGCC 61.773 60.000 0.00 0.00 0.00 4.85
936 1301 2.280389 CACCATCCGATCCAGCCG 60.280 66.667 0.00 0.00 0.00 5.52
937 1302 4.241555 ACCATCCGATCCAGCCGC 62.242 66.667 0.00 0.00 0.00 6.53
938 1303 4.996434 CCATCCGATCCAGCCGCC 62.996 72.222 0.00 0.00 0.00 6.13
997 1375 1.754226 CCGGAGAGAAGAAGAAGGAGG 59.246 57.143 0.00 0.00 0.00 4.30
1197 1590 1.585521 CGGTCGATCTTTCCCGTCG 60.586 63.158 1.98 0.00 35.78 5.12
1443 1862 1.178534 CCAACATCAACCCCGTGCTT 61.179 55.000 0.00 0.00 0.00 3.91
1480 1899 1.595993 CGAGAAGGCCGACAAGGAGA 61.596 60.000 0.00 0.00 45.00 3.71
1537 1977 1.304464 GCCAAGTCCCCCAAGAAGG 60.304 63.158 0.00 0.00 37.03 3.46
1542 1982 4.033776 TCCCCCAAGAAGGCTGCG 62.034 66.667 0.00 0.00 35.39 5.18
1548 1988 1.003355 CAAGAAGGCTGCGGAGGAA 60.003 57.895 5.93 0.00 0.00 3.36
1559 1999 2.671963 GGAGGAAACCACCGCCAC 60.672 66.667 0.00 0.00 46.63 5.01
1560 2000 2.671963 GAGGAAACCACCGCCACC 60.672 66.667 0.00 0.00 34.73 4.61
1561 2001 4.636435 AGGAAACCACCGCCACCG 62.636 66.667 0.00 0.00 34.73 4.94
1562 2002 4.629523 GGAAACCACCGCCACCGA 62.630 66.667 0.00 0.00 36.29 4.69
1563 2003 3.047877 GAAACCACCGCCACCGAG 61.048 66.667 0.00 0.00 36.29 4.63
1564 2004 4.636435 AAACCACCGCCACCGAGG 62.636 66.667 0.00 0.00 41.84 4.63
1568 2008 4.436998 CACCGCCACCGAGGAGAC 62.437 72.222 0.00 0.00 40.01 3.36
1626 2084 1.895707 GCGAGCCTTGGCTGCATAT 60.896 57.895 19.84 0.00 0.00 1.78
1629 2087 0.950116 GAGCCTTGGCTGCATATGAC 59.050 55.000 19.84 0.00 0.00 3.06
1652 2110 2.401766 GGGAGCCTGTCATGTTGCG 61.402 63.158 0.00 0.00 0.00 4.85
1694 2158 3.054166 TCGTTCATGGTTGTCGTTAGTG 58.946 45.455 0.00 0.00 0.00 2.74
1748 2212 5.220777 CGGAAGCTGAAAACTGAACTGTTTA 60.221 40.000 9.47 0.00 38.98 2.01
1779 2248 7.665145 TCAGTCTTTACCATGTCAATTTGATCA 59.335 33.333 1.78 0.00 0.00 2.92
1780 2249 8.464404 CAGTCTTTACCATGTCAATTTGATCAT 58.536 33.333 1.78 5.68 0.00 2.45
1893 2362 3.066621 TGATGTGTTTGGCAGTGAAAGTC 59.933 43.478 0.00 0.00 0.00 3.01
1903 2372 2.622942 GCAGTGAAAGTCATTTGGGTGA 59.377 45.455 0.00 0.00 0.00 4.02
1956 2425 4.572389 GCAAACAACGGATGATCTACAGAT 59.428 41.667 0.00 0.00 37.51 2.90
1985 2454 6.456795 TGATGATATAGATGAGTAAGCCCG 57.543 41.667 0.00 0.00 0.00 6.13
2009 2478 2.089201 CCGGTATTGTTCCTTGTTCCC 58.911 52.381 0.00 0.00 0.00 3.97
2011 2480 2.486592 CGGTATTGTTCCTTGTTCCCAC 59.513 50.000 0.00 0.00 0.00 4.61
2019 2488 4.086457 GTTCCTTGTTCCCACCAATACAT 58.914 43.478 0.00 0.00 0.00 2.29
2021 2490 5.522315 TCCTTGTTCCCACCAATACATAA 57.478 39.130 0.00 0.00 0.00 1.90
2025 2494 6.039717 CCTTGTTCCCACCAATACATAAGATG 59.960 42.308 0.00 0.00 0.00 2.90
2064 2533 2.953466 GCATTTGCATGATCACCAGT 57.047 45.000 0.00 0.00 41.59 4.00
2145 2614 2.205022 TTAGCTTGCCATTGTCTGCT 57.795 45.000 0.00 0.00 34.92 4.24
2158 5471 0.520404 GTCTGCTGCATTGTGACTGG 59.480 55.000 1.31 0.00 0.00 4.00
2237 5550 2.867975 CACGGGTACGAGAAACAACTTT 59.132 45.455 0.00 0.00 44.60 2.66
2298 5611 6.651225 CCCAGGTAAACAGCTATCTATTAAGC 59.349 42.308 0.00 0.00 39.08 3.09
2300 5613 5.927115 AGGTAAACAGCTATCTATTAAGCGC 59.073 40.000 0.00 0.00 43.63 5.92
2316 5629 1.016627 GCGCATAGCCATGTCTGAAA 58.983 50.000 0.30 0.00 40.81 2.69
2334 5647 6.798959 GTCTGAAATAATCAATCCGCTATTGC 59.201 38.462 4.27 0.00 44.03 3.56
2337 5650 5.536554 AATAATCAATCCGCTATTGCTCG 57.463 39.130 0.00 0.00 44.03 5.03
2378 7576 9.994432 GAGATTTAAGGTATGATGTTTGAACAG 57.006 33.333 2.77 0.00 43.04 3.16
2389 7587 6.119536 TGATGTTTGAACAGTTAGGTCTTGT 58.880 36.000 2.77 0.00 43.04 3.16
2390 7588 7.276658 TGATGTTTGAACAGTTAGGTCTTGTA 58.723 34.615 2.77 0.00 43.04 2.41
2466 7665 4.109877 CCATGGGGATTTAAGAGCATCT 57.890 45.455 2.85 0.00 43.11 2.90
2467 7666 4.077822 CCATGGGGATTTAAGAGCATCTC 58.922 47.826 2.85 0.00 40.65 2.75
2468 7667 5.050876 CCATGGGGATTTAAGAGCATCTCC 61.051 50.000 2.85 0.00 40.65 3.71
2477 7676 2.833244 GAGCATCTCCACTAGGGCT 58.167 57.895 0.00 0.00 38.46 5.19
2478 7677 0.678950 GAGCATCTCCACTAGGGCTC 59.321 60.000 0.00 0.00 42.07 4.70
2479 7678 0.762461 AGCATCTCCACTAGGGCTCC 60.762 60.000 0.00 0.00 32.85 4.70
2480 7679 1.763546 GCATCTCCACTAGGGCTCCC 61.764 65.000 0.00 0.00 36.21 4.30
2481 7680 0.399091 CATCTCCACTAGGGCTCCCA 60.399 60.000 7.82 0.00 38.92 4.37
2482 7681 0.343372 ATCTCCACTAGGGCTCCCAA 59.657 55.000 7.82 0.00 38.92 4.12
2483 7682 0.325671 TCTCCACTAGGGCTCCCAAG 60.326 60.000 7.82 0.00 38.92 3.61
2484 7683 0.325671 CTCCACTAGGGCTCCCAAGA 60.326 60.000 7.82 0.00 38.92 3.02
2485 7684 0.617820 TCCACTAGGGCTCCCAAGAC 60.618 60.000 7.82 0.00 38.92 3.01
2486 7685 1.517832 CACTAGGGCTCCCAAGACG 59.482 63.158 7.82 0.00 38.92 4.18
2487 7686 2.359967 ACTAGGGCTCCCAAGACGC 61.360 63.158 7.82 0.00 38.92 5.19
2488 7687 3.081409 TAGGGCTCCCAAGACGCC 61.081 66.667 7.82 0.00 43.03 5.68
2505 7704 4.293610 CCCCCACAGCCACTTTTT 57.706 55.556 0.00 0.00 0.00 1.94
2506 7705 1.747774 CCCCCACAGCCACTTTTTG 59.252 57.895 0.00 0.00 0.00 2.44
2514 7713 2.339712 CCACTTTTTGGGCGCTGG 59.660 61.111 7.64 0.00 42.54 4.85
2515 7714 2.356194 CACTTTTTGGGCGCTGGC 60.356 61.111 7.64 0.00 38.90 4.85
2516 7715 2.837291 ACTTTTTGGGCGCTGGCA 60.837 55.556 7.64 0.00 42.47 4.92
2517 7716 2.420890 CTTTTTGGGCGCTGGCAA 59.579 55.556 7.64 0.00 42.47 4.52
2518 7717 1.004679 CTTTTTGGGCGCTGGCAAT 60.005 52.632 7.64 0.00 42.47 3.56
2519 7718 0.246086 CTTTTTGGGCGCTGGCAATA 59.754 50.000 7.64 0.00 42.47 1.90
2520 7719 0.681733 TTTTTGGGCGCTGGCAATAA 59.318 45.000 7.64 0.00 42.47 1.40
2521 7720 0.681733 TTTTGGGCGCTGGCAATAAA 59.318 45.000 7.64 0.00 42.47 1.40
2522 7721 0.681733 TTTGGGCGCTGGCAATAAAA 59.318 45.000 7.64 0.00 42.47 1.52
2523 7722 0.681733 TTGGGCGCTGGCAATAAAAA 59.318 45.000 7.64 0.00 42.47 1.94
2539 7738 2.820845 AAAAAGCTCCCACCCACAC 58.179 52.632 0.00 0.00 0.00 3.82
2540 7739 0.759060 AAAAAGCTCCCACCCACACC 60.759 55.000 0.00 0.00 0.00 4.16
2541 7740 2.656698 AAAAGCTCCCACCCACACCC 62.657 60.000 0.00 0.00 0.00 4.61
2547 7746 3.182263 CCACCCACACCCCCAGAA 61.182 66.667 0.00 0.00 0.00 3.02
2548 7747 2.115266 CACCCACACCCCCAGAAC 59.885 66.667 0.00 0.00 0.00 3.01
2549 7748 3.566210 ACCCACACCCCCAGAACG 61.566 66.667 0.00 0.00 0.00 3.95
2550 7749 3.566210 CCCACACCCCCAGAACGT 61.566 66.667 0.00 0.00 0.00 3.99
2551 7750 2.513895 CCACACCCCCAGAACGTT 59.486 61.111 0.00 0.00 0.00 3.99
2552 7751 1.896660 CCACACCCCCAGAACGTTG 60.897 63.158 5.00 0.00 0.00 4.10
2553 7752 1.153046 CACACCCCCAGAACGTTGT 60.153 57.895 5.00 0.00 0.00 3.32
2554 7753 0.750182 CACACCCCCAGAACGTTGTT 60.750 55.000 5.00 0.00 0.00 2.83
2555 7754 0.033894 ACACCCCCAGAACGTTGTTT 60.034 50.000 5.00 0.00 0.00 2.83
2556 7755 1.107945 CACCCCCAGAACGTTGTTTT 58.892 50.000 5.00 0.00 0.00 2.43
2557 7756 1.107945 ACCCCCAGAACGTTGTTTTG 58.892 50.000 5.00 0.00 0.00 2.44
2558 7757 0.249280 CCCCCAGAACGTTGTTTTGC 60.249 55.000 5.00 0.00 0.00 3.68
2559 7758 0.593773 CCCCAGAACGTTGTTTTGCG 60.594 55.000 5.00 0.00 0.00 4.85
2560 7759 1.206115 CCCAGAACGTTGTTTTGCGC 61.206 55.000 5.00 0.00 0.00 6.09
2561 7760 1.206115 CCAGAACGTTGTTTTGCGCC 61.206 55.000 5.00 0.00 0.00 6.53
2562 7761 1.298041 AGAACGTTGTTTTGCGCCG 60.298 52.632 5.00 0.75 0.00 6.46
2563 7762 2.278271 AACGTTGTTTTGCGCCGG 60.278 55.556 4.18 0.00 0.00 6.13
2564 7763 2.649843 GAACGTTGTTTTGCGCCGGA 62.650 55.000 5.00 0.00 0.00 5.14
2565 7764 2.065906 AACGTTGTTTTGCGCCGGAT 62.066 50.000 5.05 0.00 0.00 4.18
2566 7765 1.371145 CGTTGTTTTGCGCCGGATT 60.371 52.632 5.05 0.00 0.00 3.01
2567 7766 0.937231 CGTTGTTTTGCGCCGGATTT 60.937 50.000 5.05 0.00 0.00 2.17
2568 7767 0.506506 GTTGTTTTGCGCCGGATTTG 59.493 50.000 5.05 0.00 0.00 2.32
2569 7768 0.598680 TTGTTTTGCGCCGGATTTGG 60.599 50.000 5.05 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.885722 CAATTGCAAAGCCATATATTTTGTTCT 58.114 29.630 1.71 0.00 34.98 3.01
13 14 8.667463 ACAATTGCAAAGCCATATATTTTGTTC 58.333 29.630 1.71 0.00 34.98 3.18
14 15 8.452534 CACAATTGCAAAGCCATATATTTTGTT 58.547 29.630 1.71 0.00 34.98 2.83
15 16 7.607223 ACACAATTGCAAAGCCATATATTTTGT 59.393 29.630 1.71 1.79 34.98 2.83
16 17 7.976826 ACACAATTGCAAAGCCATATATTTTG 58.023 30.769 1.71 1.10 35.47 2.44
17 18 7.823310 TGACACAATTGCAAAGCCATATATTTT 59.177 29.630 1.71 0.00 0.00 1.82
18 19 7.329499 TGACACAATTGCAAAGCCATATATTT 58.671 30.769 1.71 0.00 0.00 1.40
19 20 6.876155 TGACACAATTGCAAAGCCATATATT 58.124 32.000 1.71 0.00 0.00 1.28
20 21 6.468333 TGACACAATTGCAAAGCCATATAT 57.532 33.333 1.71 0.00 0.00 0.86
21 22 5.911378 TGACACAATTGCAAAGCCATATA 57.089 34.783 1.71 0.00 0.00 0.86
22 23 4.804868 TGACACAATTGCAAAGCCATAT 57.195 36.364 1.71 0.00 0.00 1.78
23 24 4.597404 TTGACACAATTGCAAAGCCATA 57.403 36.364 1.71 0.00 0.00 2.74
24 25 3.472283 TTGACACAATTGCAAAGCCAT 57.528 38.095 1.71 0.00 0.00 4.40
25 26 2.975732 TTGACACAATTGCAAAGCCA 57.024 40.000 1.71 0.00 0.00 4.75
26 27 4.990426 AGTAATTGACACAATTGCAAAGCC 59.010 37.500 20.51 0.00 0.00 4.35
27 28 7.636259 TTAGTAATTGACACAATTGCAAAGC 57.364 32.000 20.51 0.00 0.00 3.51
87 88 9.099454 GCATATGAGCAAACTTACTAAAGTAGT 57.901 33.333 6.97 0.00 45.37 2.73
88 89 9.319143 AGCATATGAGCAAACTTACTAAAGTAG 57.681 33.333 6.97 0.00 40.09 2.57
89 90 9.667107 AAGCATATGAGCAAACTTACTAAAGTA 57.333 29.630 6.97 0.00 40.09 2.24
90 91 8.567285 AAGCATATGAGCAAACTTACTAAAGT 57.433 30.769 6.97 0.00 41.63 2.66
91 92 8.125448 GGAAGCATATGAGCAAACTTACTAAAG 58.875 37.037 6.97 0.00 36.45 1.85
92 93 7.829211 AGGAAGCATATGAGCAAACTTACTAAA 59.171 33.333 6.97 0.00 36.85 1.85
93 94 7.338710 AGGAAGCATATGAGCAAACTTACTAA 58.661 34.615 6.97 0.00 36.85 2.24
94 95 6.889198 AGGAAGCATATGAGCAAACTTACTA 58.111 36.000 6.97 0.00 36.85 1.82
95 96 5.749462 AGGAAGCATATGAGCAAACTTACT 58.251 37.500 6.97 2.21 36.85 2.24
96 97 7.442364 TCATAGGAAGCATATGAGCAAACTTAC 59.558 37.037 6.97 0.00 35.29 2.34
97 98 7.508687 TCATAGGAAGCATATGAGCAAACTTA 58.491 34.615 6.97 0.00 35.29 2.24
98 99 6.359804 TCATAGGAAGCATATGAGCAAACTT 58.640 36.000 6.97 0.00 35.29 2.66
99 100 5.933617 TCATAGGAAGCATATGAGCAAACT 58.066 37.500 6.97 0.00 35.29 2.66
100 101 6.814506 ATCATAGGAAGCATATGAGCAAAC 57.185 37.500 6.97 0.00 41.61 2.93
101 102 9.524496 AAATATCATAGGAAGCATATGAGCAAA 57.476 29.630 6.97 0.00 41.61 3.68
102 103 8.953313 CAAATATCATAGGAAGCATATGAGCAA 58.047 33.333 6.97 0.00 41.61 3.91
103 104 7.066645 GCAAATATCATAGGAAGCATATGAGCA 59.933 37.037 6.97 0.19 41.61 4.26
104 105 7.066645 TGCAAATATCATAGGAAGCATATGAGC 59.933 37.037 6.97 5.90 41.61 4.26
105 106 8.502105 TGCAAATATCATAGGAAGCATATGAG 57.498 34.615 6.97 0.00 41.61 2.90
106 107 7.555195 CCTGCAAATATCATAGGAAGCATATGA 59.445 37.037 6.97 4.54 42.29 2.15
107 108 7.201794 CCCTGCAAATATCATAGGAAGCATATG 60.202 40.741 0.00 0.00 32.87 1.78
108 109 6.832384 CCCTGCAAATATCATAGGAAGCATAT 59.168 38.462 0.00 0.00 0.00 1.78
109 110 6.182627 CCCTGCAAATATCATAGGAAGCATA 58.817 40.000 0.00 0.00 0.00 3.14
110 111 5.014858 CCCTGCAAATATCATAGGAAGCAT 58.985 41.667 0.00 0.00 0.00 3.79
111 112 4.401022 CCCTGCAAATATCATAGGAAGCA 58.599 43.478 0.00 0.00 0.00 3.91
112 113 3.192212 GCCCTGCAAATATCATAGGAAGC 59.808 47.826 0.00 0.00 0.00 3.86
113 114 4.401022 TGCCCTGCAAATATCATAGGAAG 58.599 43.478 0.00 0.00 34.76 3.46
114 115 4.451891 TGCCCTGCAAATATCATAGGAA 57.548 40.909 0.00 0.00 34.76 3.36
115 116 4.451891 TTGCCCTGCAAATATCATAGGA 57.548 40.909 0.00 0.00 45.96 2.94
126 127 0.104671 GCTTCTTTGTTGCCCTGCAA 59.895 50.000 0.00 0.00 46.80 4.08
127 128 1.741525 GCTTCTTTGTTGCCCTGCA 59.258 52.632 0.00 0.00 36.47 4.41
128 129 1.005748 GGCTTCTTTGTTGCCCTGC 60.006 57.895 0.00 0.00 40.71 4.85
132 133 1.138859 ACTTTGGGCTTCTTTGTTGCC 59.861 47.619 0.00 0.00 45.42 4.52
133 134 2.602257 ACTTTGGGCTTCTTTGTTGC 57.398 45.000 0.00 0.00 0.00 4.17
134 135 4.122143 TGAACTTTGGGCTTCTTTGTTG 57.878 40.909 0.00 0.00 0.00 3.33
135 136 4.817318 TTGAACTTTGGGCTTCTTTGTT 57.183 36.364 0.00 0.00 0.00 2.83
136 137 4.503910 GTTTGAACTTTGGGCTTCTTTGT 58.496 39.130 0.00 0.00 0.00 2.83
137 138 3.871006 GGTTTGAACTTTGGGCTTCTTTG 59.129 43.478 0.00 0.00 0.00 2.77
138 139 3.517500 TGGTTTGAACTTTGGGCTTCTTT 59.482 39.130 0.00 0.00 0.00 2.52
139 140 3.103742 TGGTTTGAACTTTGGGCTTCTT 58.896 40.909 0.00 0.00 0.00 2.52
140 141 2.745968 TGGTTTGAACTTTGGGCTTCT 58.254 42.857 0.00 0.00 0.00 2.85
141 142 3.132111 TCTTGGTTTGAACTTTGGGCTTC 59.868 43.478 0.00 0.00 0.00 3.86
142 143 3.103742 TCTTGGTTTGAACTTTGGGCTT 58.896 40.909 0.00 0.00 0.00 4.35
143 144 2.745968 TCTTGGTTTGAACTTTGGGCT 58.254 42.857 0.00 0.00 0.00 5.19
144 145 3.554960 GGATCTTGGTTTGAACTTTGGGC 60.555 47.826 0.00 0.00 0.00 5.36
145 146 3.640967 TGGATCTTGGTTTGAACTTTGGG 59.359 43.478 0.00 0.00 0.00 4.12
146 147 4.099266 TGTGGATCTTGGTTTGAACTTTGG 59.901 41.667 0.00 0.00 0.00 3.28
147 148 5.261209 TGTGGATCTTGGTTTGAACTTTG 57.739 39.130 0.00 0.00 0.00 2.77
148 149 5.739935 GCATGTGGATCTTGGTTTGAACTTT 60.740 40.000 0.00 0.00 0.00 2.66
149 150 4.262164 GCATGTGGATCTTGGTTTGAACTT 60.262 41.667 0.00 0.00 0.00 2.66
150 151 3.256631 GCATGTGGATCTTGGTTTGAACT 59.743 43.478 0.00 0.00 0.00 3.01
151 152 3.005684 TGCATGTGGATCTTGGTTTGAAC 59.994 43.478 0.00 0.00 0.00 3.18
152 153 3.229293 TGCATGTGGATCTTGGTTTGAA 58.771 40.909 0.00 0.00 0.00 2.69
153 154 2.874014 TGCATGTGGATCTTGGTTTGA 58.126 42.857 0.00 0.00 0.00 2.69
154 155 3.006110 ACTTGCATGTGGATCTTGGTTTG 59.994 43.478 4.14 0.00 0.00 2.93
155 156 3.233507 ACTTGCATGTGGATCTTGGTTT 58.766 40.909 4.14 0.00 0.00 3.27
156 157 2.880443 ACTTGCATGTGGATCTTGGTT 58.120 42.857 4.14 0.00 0.00 3.67
157 158 2.559668 CAACTTGCATGTGGATCTTGGT 59.440 45.455 5.94 0.00 0.00 3.67
158 159 2.821378 TCAACTTGCATGTGGATCTTGG 59.179 45.455 5.94 0.00 0.00 3.61
159 160 4.482386 CTTCAACTTGCATGTGGATCTTG 58.518 43.478 10.41 2.57 0.00 3.02
160 161 3.057033 GCTTCAACTTGCATGTGGATCTT 60.057 43.478 10.41 0.00 0.00 2.40
161 162 2.490903 GCTTCAACTTGCATGTGGATCT 59.509 45.455 10.41 0.00 0.00 2.75
162 163 2.416431 GGCTTCAACTTGCATGTGGATC 60.416 50.000 10.41 6.12 0.00 3.36
163 164 1.547372 GGCTTCAACTTGCATGTGGAT 59.453 47.619 10.41 0.00 0.00 3.41
164 165 0.961019 GGCTTCAACTTGCATGTGGA 59.039 50.000 5.94 5.82 0.00 4.02
165 166 0.963962 AGGCTTCAACTTGCATGTGG 59.036 50.000 5.94 3.15 0.00 4.17
166 167 1.884579 AGAGGCTTCAACTTGCATGTG 59.115 47.619 5.94 1.45 0.00 3.21
167 168 2.283145 AGAGGCTTCAACTTGCATGT 57.717 45.000 0.00 0.00 0.00 3.21
168 169 2.818432 AGAAGAGGCTTCAACTTGCATG 59.182 45.455 9.56 0.00 0.00 4.06
169 170 3.151912 AGAAGAGGCTTCAACTTGCAT 57.848 42.857 9.56 0.00 0.00 3.96
170 171 2.645838 AGAAGAGGCTTCAACTTGCA 57.354 45.000 9.56 0.00 0.00 4.08
171 172 3.998099 AAAGAAGAGGCTTCAACTTGC 57.002 42.857 9.56 0.00 0.00 4.01
172 173 7.361628 GGAGATAAAAGAAGAGGCTTCAACTTG 60.362 40.741 9.56 0.00 0.00 3.16
173 174 6.657117 GGAGATAAAAGAAGAGGCTTCAACTT 59.343 38.462 9.56 0.20 0.00 2.66
174 175 6.012945 AGGAGATAAAAGAAGAGGCTTCAACT 60.013 38.462 9.56 0.00 0.00 3.16
175 176 6.093357 CAGGAGATAAAAGAAGAGGCTTCAAC 59.907 42.308 9.56 0.00 0.00 3.18
176 177 6.176183 CAGGAGATAAAAGAAGAGGCTTCAA 58.824 40.000 9.56 0.00 0.00 2.69
177 178 5.249393 ACAGGAGATAAAAGAAGAGGCTTCA 59.751 40.000 9.56 0.00 0.00 3.02
178 179 5.739959 ACAGGAGATAAAAGAAGAGGCTTC 58.260 41.667 0.00 0.00 0.00 3.86
179 180 5.770685 ACAGGAGATAAAAGAAGAGGCTT 57.229 39.130 0.00 0.00 0.00 4.35
180 181 5.129650 GGTACAGGAGATAAAAGAAGAGGCT 59.870 44.000 0.00 0.00 0.00 4.58
181 182 5.104900 TGGTACAGGAGATAAAAGAAGAGGC 60.105 44.000 0.00 0.00 0.00 4.70
182 183 6.546428 TGGTACAGGAGATAAAAGAAGAGG 57.454 41.667 0.00 0.00 0.00 3.69
183 184 6.481644 GCATGGTACAGGAGATAAAAGAAGAG 59.518 42.308 0.00 0.00 46.40 2.85
184 185 6.156949 AGCATGGTACAGGAGATAAAAGAAGA 59.843 38.462 0.00 0.00 46.40 2.87
185 186 6.352516 AGCATGGTACAGGAGATAAAAGAAG 58.647 40.000 0.00 0.00 46.40 2.85
186 187 6.313519 AGCATGGTACAGGAGATAAAAGAA 57.686 37.500 0.00 0.00 46.40 2.52
187 188 5.957771 AGCATGGTACAGGAGATAAAAGA 57.042 39.130 0.00 0.00 46.40 2.52
188 189 8.682936 ATTAAGCATGGTACAGGAGATAAAAG 57.317 34.615 0.00 0.00 46.40 2.27
189 190 9.555727 GTATTAAGCATGGTACAGGAGATAAAA 57.444 33.333 0.00 0.00 46.40 1.52
190 191 8.710239 TGTATTAAGCATGGTACAGGAGATAAA 58.290 33.333 0.00 0.00 46.40 1.40
191 192 8.257602 TGTATTAAGCATGGTACAGGAGATAA 57.742 34.615 0.00 0.00 46.40 1.75
192 193 7.849322 TGTATTAAGCATGGTACAGGAGATA 57.151 36.000 0.00 0.00 46.40 1.98
193 194 6.747414 TGTATTAAGCATGGTACAGGAGAT 57.253 37.500 0.00 0.00 46.40 2.75
194 195 6.553953 TTGTATTAAGCATGGTACAGGAGA 57.446 37.500 0.00 0.00 46.40 3.71
195 196 6.823689 AGTTTGTATTAAGCATGGTACAGGAG 59.176 38.462 0.00 0.00 46.40 3.69
196 197 6.717289 AGTTTGTATTAAGCATGGTACAGGA 58.283 36.000 0.00 0.00 46.40 3.86
200 201 9.931210 GTTCATAGTTTGTATTAAGCATGGTAC 57.069 33.333 0.00 0.00 0.00 3.34
252 253 5.637810 GGCCATTAAAAGGTTAAACTTGAGC 59.362 40.000 6.51 4.02 32.98 4.26
254 255 5.841783 AGGGCCATTAAAAGGTTAAACTTGA 59.158 36.000 6.51 0.00 32.98 3.02
266 267 6.269769 ACAAGATCTTTGAAGGGCCATTAAAA 59.730 34.615 12.10 12.10 0.00 1.52
275 276 6.317391 GGAATAGTGACAAGATCTTTGAAGGG 59.683 42.308 4.86 0.00 0.00 3.95
277 278 6.813649 TCGGAATAGTGACAAGATCTTTGAAG 59.186 38.462 4.86 0.00 0.00 3.02
336 337 3.128764 AGCAGCATCATCTTCACACATTG 59.871 43.478 0.00 0.00 0.00 2.82
487 493 3.641437 TGTGTTGTTTGGCTGCTATTC 57.359 42.857 0.00 0.00 0.00 1.75
506 512 4.205588 GCGATTTGTGTAATGCATGTCATG 59.794 41.667 8.56 8.56 35.13 3.07
591 603 3.063452 CGGTGTAAATGGATGAAACCTCG 59.937 47.826 0.00 0.00 0.00 4.63
595 607 8.973835 TTTTATTCGGTGTAAATGGATGAAAC 57.026 30.769 0.00 0.00 0.00 2.78
608 620 6.717997 AGGTAGGTTTTCATTTTATTCGGTGT 59.282 34.615 0.00 0.00 0.00 4.16
613 625 7.320399 CACCCAGGTAGGTTTTCATTTTATTC 58.680 38.462 0.00 0.00 38.39 1.75
615 627 5.186992 GCACCCAGGTAGGTTTTCATTTTAT 59.813 40.000 0.00 0.00 38.39 1.40
642 654 4.392921 TGCTATTTCTGTACAGCTCCTC 57.607 45.455 18.45 6.04 35.05 3.71
660 672 6.297582 TGGGTTGAAAATGAAATGAAATGCT 58.702 32.000 0.00 0.00 0.00 3.79
677 694 4.842574 TCGATCTCATTTCATTGGGTTGA 58.157 39.130 0.00 0.00 0.00 3.18
701 718 0.386113 TTTACCGCTTGTTTGGCACC 59.614 50.000 0.00 0.00 0.00 5.01
715 732 4.070009 GGGATGGGTCGTATTCATTTACC 58.930 47.826 0.00 0.00 0.00 2.85
734 754 5.548056 GGGAGAATGGATAAACATAGAGGGA 59.452 44.000 0.00 0.00 0.00 4.20
779 799 3.768468 GTTTTTCACTGTGGGAAACGA 57.232 42.857 17.51 2.80 34.23 3.85
790 814 6.753107 TTCTTCTTTTCCTCGTTTTTCACT 57.247 33.333 0.00 0.00 0.00 3.41
792 816 7.544217 CCTTTTTCTTCTTTTCCTCGTTTTTCA 59.456 33.333 0.00 0.00 0.00 2.69
815 839 7.525692 GCACGGATATTTCCTAGTATTCTCCTT 60.526 40.741 0.46 0.00 40.17 3.36
817 841 6.100668 GCACGGATATTTCCTAGTATTCTCC 58.899 44.000 0.46 0.00 40.17 3.71
820 844 5.467705 ACGCACGGATATTTCCTAGTATTC 58.532 41.667 0.46 0.00 40.17 1.75
823 847 4.581824 AGAACGCACGGATATTTCCTAGTA 59.418 41.667 0.46 0.00 40.17 1.82
824 848 3.383825 AGAACGCACGGATATTTCCTAGT 59.616 43.478 0.46 0.00 40.17 2.57
825 849 3.736252 CAGAACGCACGGATATTTCCTAG 59.264 47.826 0.46 0.00 40.17 3.02
826 850 3.382227 TCAGAACGCACGGATATTTCCTA 59.618 43.478 0.46 0.00 40.17 2.94
900 1242 1.068083 GATTGGATGAGCGGCGAGA 59.932 57.895 12.98 0.00 0.00 4.04
909 1251 1.506025 TCGGATGGTGGATTGGATGA 58.494 50.000 0.00 0.00 0.00 2.92
957 1322 3.901797 GACGTGGGCAGGAGGGTTG 62.902 68.421 0.00 0.00 0.00 3.77
997 1375 2.190578 CTTCCACCCGGCCATCTC 59.809 66.667 2.24 0.00 0.00 2.75
1197 1590 2.049063 ACAAGGCAGACGCTCGAC 60.049 61.111 0.00 0.00 38.60 4.20
1443 1862 2.291043 GGCGGTCTTCTTGGGGAGA 61.291 63.158 0.00 0.00 0.00 3.71
1480 1899 0.182775 GTGGTCTTGGTGGACTTGGT 59.817 55.000 0.00 0.00 36.55 3.67
1537 1977 3.056328 GGTGGTTTCCTCCGCAGC 61.056 66.667 0.00 0.00 39.49 5.25
1542 1982 2.671963 GTGGCGGTGGTTTCCTCC 60.672 66.667 0.00 0.00 34.16 4.30
1557 1997 4.436998 GTGGCGGTCTCCTCGGTG 62.437 72.222 0.00 0.00 0.00 4.94
1564 2004 4.208686 CTAGGCGGTGGCGGTCTC 62.209 72.222 0.00 0.00 41.24 3.36
1569 2009 4.208686 GTCTCCTAGGCGGTGGCG 62.209 72.222 2.96 0.00 41.24 5.69
1570 2010 3.851128 GGTCTCCTAGGCGGTGGC 61.851 72.222 2.96 0.00 38.90 5.01
1571 2011 3.528370 CGGTCTCCTAGGCGGTGG 61.528 72.222 2.96 0.00 0.00 4.61
1572 2012 4.208686 GCGGTCTCCTAGGCGGTG 62.209 72.222 2.96 0.00 0.00 4.94
1626 2084 4.316823 ACAGGCTCCCTCCGGTCA 62.317 66.667 0.00 0.00 28.15 4.02
1629 2087 2.765807 ATGACAGGCTCCCTCCGG 60.766 66.667 0.00 0.00 0.00 5.14
1652 2110 2.953466 TACATACAGGACGCAACTCC 57.047 50.000 0.00 0.00 0.00 3.85
1729 2193 5.243426 TGGTAAACAGTTCAGTTTTCAGC 57.757 39.130 0.00 0.00 41.58 4.26
1748 2212 5.241403 TGACATGGTAAAGACTGAATGGT 57.759 39.130 0.00 0.00 0.00 3.55
1893 2362 5.212532 TCTTTTCACCAATCACCCAAATG 57.787 39.130 0.00 0.00 0.00 2.32
1903 2372 4.021719 CACCTGCATCTTCTTTTCACCAAT 60.022 41.667 0.00 0.00 0.00 3.16
1985 2454 4.573607 GGAACAAGGAACAATACCGGATAC 59.426 45.833 9.46 0.00 0.00 2.24
2000 2469 5.505780 TCTTATGTATTGGTGGGAACAAGG 58.494 41.667 0.00 0.00 46.06 3.61
2021 2490 8.864087 TGCAGAGAGTATTACATATGTTCATCT 58.136 33.333 14.77 10.45 0.00 2.90
2145 2614 1.818060 GTTATGGCCAGTCACAATGCA 59.182 47.619 13.05 0.00 0.00 3.96
2158 5471 5.472137 TGTACCTCTGTTTTTCAGTTATGGC 59.528 40.000 0.00 0.00 43.97 4.40
2187 5500 4.000988 TGGAAAAGAAATAGCTGACCGAC 58.999 43.478 0.00 0.00 0.00 4.79
2237 5550 2.151202 CAAGCTTTAAGACGAGGGCAA 58.849 47.619 0.00 0.00 0.00 4.52
2298 5611 5.179929 TGATTATTTCAGACATGGCTATGCG 59.820 40.000 10.37 0.00 37.85 4.73
2300 5613 8.242053 GGATTGATTATTTCAGACATGGCTATG 58.758 37.037 0.00 8.74 36.65 2.23
2308 5621 7.520453 GCAATAGCGGATTGATTATTTCAGACA 60.520 37.037 15.97 0.00 46.94 3.41
2334 5647 4.720649 TCTCCTTGATCAGTAAACCGAG 57.279 45.455 0.00 0.00 0.00 4.63
2337 5650 7.829706 ACCTTAAATCTCCTTGATCAGTAAACC 59.170 37.037 0.00 0.00 33.57 3.27
2366 7564 6.619801 ACAAGACCTAACTGTTCAAACATC 57.380 37.500 0.00 0.00 38.41 3.06
2378 7576 8.611654 TGACCTAACAAAATACAAGACCTAAC 57.388 34.615 0.00 0.00 0.00 2.34
2389 7587 6.224584 TGACGTGTGATGACCTAACAAAATA 58.775 36.000 0.00 0.00 0.00 1.40
2390 7588 5.060506 TGACGTGTGATGACCTAACAAAAT 58.939 37.500 0.00 0.00 0.00 1.82
2460 7659 0.762461 GGAGCCCTAGTGGAGATGCT 60.762 60.000 1.75 0.00 36.23 3.79
2461 7660 1.751563 GGAGCCCTAGTGGAGATGC 59.248 63.158 1.75 0.00 35.39 3.91
2462 7661 0.399091 TGGGAGCCCTAGTGGAGATG 60.399 60.000 7.16 0.00 35.39 2.90
2463 7662 0.343372 TTGGGAGCCCTAGTGGAGAT 59.657 55.000 7.16 0.00 35.39 2.75
2464 7663 0.325671 CTTGGGAGCCCTAGTGGAGA 60.326 60.000 7.16 0.00 34.91 3.71
2465 7664 0.325671 TCTTGGGAGCCCTAGTGGAG 60.326 60.000 15.11 1.52 39.41 3.86
2466 7665 0.617820 GTCTTGGGAGCCCTAGTGGA 60.618 60.000 15.11 0.00 39.41 4.02
2467 7666 1.908483 GTCTTGGGAGCCCTAGTGG 59.092 63.158 15.11 0.00 39.41 4.00
2468 7667 1.517832 CGTCTTGGGAGCCCTAGTG 59.482 63.158 15.11 7.12 39.41 2.74
2469 7668 2.359967 GCGTCTTGGGAGCCCTAGT 61.360 63.158 15.11 0.00 39.41 2.57
2470 7669 2.501610 GCGTCTTGGGAGCCCTAG 59.498 66.667 10.31 10.31 39.69 3.02
2471 7670 3.081409 GGCGTCTTGGGAGCCCTA 61.081 66.667 7.16 0.00 44.80 3.53
2488 7687 1.747774 CAAAAAGTGGCTGTGGGGG 59.252 57.895 0.00 0.00 0.00 5.40
2489 7688 1.747774 CCAAAAAGTGGCTGTGGGG 59.252 57.895 0.00 0.00 41.72 4.96
2498 7697 2.356194 GCCAGCGCCCAAAAAGTG 60.356 61.111 2.29 0.00 0.00 3.16
2499 7698 1.757423 ATTGCCAGCGCCCAAAAAGT 61.757 50.000 2.29 0.00 0.00 2.66
2500 7699 0.246086 TATTGCCAGCGCCCAAAAAG 59.754 50.000 2.29 0.00 0.00 2.27
2501 7700 0.681733 TTATTGCCAGCGCCCAAAAA 59.318 45.000 2.29 0.00 0.00 1.94
2502 7701 0.681733 TTTATTGCCAGCGCCCAAAA 59.318 45.000 2.29 0.00 0.00 2.44
2503 7702 0.681733 TTTTATTGCCAGCGCCCAAA 59.318 45.000 2.29 0.00 0.00 3.28
2504 7703 0.681733 TTTTTATTGCCAGCGCCCAA 59.318 45.000 2.29 5.93 0.00 4.12
2505 7704 2.355946 TTTTTATTGCCAGCGCCCA 58.644 47.368 2.29 0.00 0.00 5.36
2521 7720 0.759060 GGTGTGGGTGGGAGCTTTTT 60.759 55.000 0.00 0.00 0.00 1.94
2522 7721 1.152546 GGTGTGGGTGGGAGCTTTT 60.153 57.895 0.00 0.00 0.00 2.27
2523 7722 2.520968 GGTGTGGGTGGGAGCTTT 59.479 61.111 0.00 0.00 0.00 3.51
2524 7723 3.580319 GGGTGTGGGTGGGAGCTT 61.580 66.667 0.00 0.00 0.00 3.74
2530 7729 3.182263 TTCTGGGGGTGTGGGTGG 61.182 66.667 0.00 0.00 0.00 4.61
2531 7730 2.115266 GTTCTGGGGGTGTGGGTG 59.885 66.667 0.00 0.00 0.00 4.61
2532 7731 3.566210 CGTTCTGGGGGTGTGGGT 61.566 66.667 0.00 0.00 0.00 4.51
2533 7732 3.128032 AACGTTCTGGGGGTGTGGG 62.128 63.158 0.00 0.00 0.00 4.61
2534 7733 1.896660 CAACGTTCTGGGGGTGTGG 60.897 63.158 0.00 0.00 0.00 4.17
2535 7734 0.750182 AACAACGTTCTGGGGGTGTG 60.750 55.000 0.00 0.00 0.00 3.82
2536 7735 0.033894 AAACAACGTTCTGGGGGTGT 60.034 50.000 0.00 0.00 0.00 4.16
2537 7736 1.107945 AAAACAACGTTCTGGGGGTG 58.892 50.000 0.00 0.00 0.00 4.61
2538 7737 1.107945 CAAAACAACGTTCTGGGGGT 58.892 50.000 0.00 0.00 0.00 4.95
2539 7738 0.249280 GCAAAACAACGTTCTGGGGG 60.249 55.000 0.00 0.00 0.00 5.40
2540 7739 0.593773 CGCAAAACAACGTTCTGGGG 60.594 55.000 0.00 0.00 0.00 4.96
2541 7740 1.206115 GCGCAAAACAACGTTCTGGG 61.206 55.000 0.30 3.50 0.00 4.45
2542 7741 1.206115 GGCGCAAAACAACGTTCTGG 61.206 55.000 10.83 0.00 0.00 3.86
2543 7742 1.528248 CGGCGCAAAACAACGTTCTG 61.528 55.000 10.83 0.00 0.00 3.02
2544 7743 1.298041 CGGCGCAAAACAACGTTCT 60.298 52.632 10.83 0.00 0.00 3.01
2545 7744 2.290082 CCGGCGCAAAACAACGTTC 61.290 57.895 10.83 0.00 0.00 3.95
2546 7745 2.065906 ATCCGGCGCAAAACAACGTT 62.066 50.000 10.83 0.00 0.00 3.99
2547 7746 2.065906 AATCCGGCGCAAAACAACGT 62.066 50.000 10.83 0.00 0.00 3.99
2548 7747 0.937231 AAATCCGGCGCAAAACAACG 60.937 50.000 10.83 0.43 0.00 4.10
2549 7748 0.506506 CAAATCCGGCGCAAAACAAC 59.493 50.000 10.83 0.00 0.00 3.32
2550 7749 0.598680 CCAAATCCGGCGCAAAACAA 60.599 50.000 10.83 0.00 0.00 2.83
2551 7750 1.006805 CCAAATCCGGCGCAAAACA 60.007 52.632 10.83 0.00 0.00 2.83
2552 7751 2.379634 GCCAAATCCGGCGCAAAAC 61.380 57.895 10.83 0.00 43.52 2.43
2553 7752 2.048690 GCCAAATCCGGCGCAAAA 60.049 55.556 10.83 0.00 43.52 2.44


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

AutoCloner maintained by Alex Coulton.