Multiple sequence alignment - TraesCS2B01G510500

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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 TraesCS2B01G510500 chr2B 100.000 2909 0 0 1 2909 706566767 706569675 0.000000e+00 5373.0
1 TraesCS2B01G510500 chr2B 87.341 1335 113 29 484 1792 706698633 706699937 0.000000e+00 1478.0
2 TraesCS2B01G510500 chr2B 86.397 544 40 10 697 1207 770607529 770608071 5.440000e-157 564.0
3 TraesCS2B01G510500 chr2B 92.361 144 11 0 26 169 285796417 285796274 3.800000e-49 206.0
4 TraesCS2B01G510500 chr2B 89.262 149 15 1 24 171 385161276 385161128 4.950000e-43 185.0
5 TraesCS2B01G510500 chr2B 81.328 241 31 8 1732 1972 706421751 706421977 1.780000e-42 183.0
6 TraesCS2B01G510500 chr2B 85.185 189 15 6 1785 1971 706699990 706700167 6.400000e-42 182.0
7 TraesCS2B01G510500 chr2B 82.486 177 17 7 2154 2330 706694945 706695107 3.020000e-30 143.0
8 TraesCS2B01G510500 chr2D 88.723 1543 112 32 586 2092 585519415 585520931 0.000000e+00 1829.0
9 TraesCS2B01G510500 chr2D 87.247 1333 112 26 622 1934 585636025 585637319 0.000000e+00 1467.0
10 TraesCS2B01G510500 chr2D 90.374 187 17 1 2157 2343 585634928 585635113 8.050000e-61 244.0
11 TraesCS2B01G510500 chr2D 87.582 153 12 6 1783 1934 585637356 585637502 1.390000e-38 171.0
12 TraesCS2B01G510500 chr2D 84.444 90 3 5 452 541 585519315 585519393 8.640000e-11 78.7
13 TraesCS2B01G510500 chr2A 90.849 907 47 15 364 1245 719564865 719565760 0.000000e+00 1182.0
14 TraesCS2B01G510500 chr2A 82.934 1418 132 48 618 1977 719685602 719686967 0.000000e+00 1177.0
15 TraesCS2B01G510500 chr2A 90.308 908 72 11 1286 2183 719566240 719567141 0.000000e+00 1175.0
16 TraesCS2B01G510500 chr2A 87.500 1032 100 16 1284 2310 719626411 719627418 0.000000e+00 1164.0
17 TraesCS2B01G510500 chr2A 84.786 585 46 17 458 1008 719573776 719574351 5.480000e-152 547.0
18 TraesCS2B01G510500 chr2A 81.197 585 83 16 2346 2909 165335372 165334794 2.060000e-121 446.0
19 TraesCS2B01G510500 chr2A 88.655 238 26 1 992 1229 719609748 719609984 3.670000e-74 289.0
20 TraesCS2B01G510500 chr2A 89.677 155 14 2 2189 2343 719567710 719567862 2.290000e-46 196.0
21 TraesCS2B01G510500 chr5D 88.183 567 59 5 2346 2907 257170171 257170734 0.000000e+00 669.0
22 TraesCS2B01G510500 chr5D 80.705 596 88 15 2334 2909 114464963 114465551 3.440000e-119 438.0
23 TraesCS2B01G510500 chr5D 86.228 167 19 4 14 178 481480198 481480034 8.280000e-41 178.0
24 TraesCS2B01G510500 chr5D 87.943 141 11 5 216 354 406834391 406834527 8.340000e-36 161.0
25 TraesCS2B01G510500 chr5D 84.298 121 19 0 2789 2909 459918943 459919063 5.090000e-23 119.0
26 TraesCS2B01G510500 chr7B 86.765 544 38 11 697 1207 616817212 616816670 2.510000e-160 575.0
27 TraesCS2B01G510500 chr7B 78.559 583 84 22 2345 2909 488169955 488170514 2.150000e-91 346.0
28 TraesCS2B01G510500 chr7B 86.395 147 16 4 2089 2233 539324223 539324079 1.080000e-34 158.0
29 TraesCS2B01G510500 chr1B 86.581 544 39 11 697 1207 62244917 62245459 1.170000e-158 569.0
30 TraesCS2B01G510500 chr1B 84.220 583 70 12 2346 2909 168590320 168589741 5.480000e-152 547.0
31 TraesCS2B01G510500 chr1B 95.312 192 9 0 170 361 688981579 688981388 3.640000e-79 305.0
32 TraesCS2B01G510500 chr1B 96.226 159 5 1 205 363 354546095 354545938 2.880000e-65 259.0
33 TraesCS2B01G510500 chr1B 88.356 146 17 0 24 169 167712003 167712148 2.980000e-40 176.0
34 TraesCS2B01G510500 chr1B 88.079 151 5 6 176 326 640878114 640877977 1.790000e-37 167.0
35 TraesCS2B01G510500 chr4B 86.754 536 38 10 697 1200 649654645 649654111 1.510000e-157 566.0
36 TraesCS2B01G510500 chr4B 85.517 145 21 0 25 169 71000014 70999870 5.020000e-33 152.0
37 TraesCS2B01G510500 chr5B 86.213 544 41 11 697 1207 250133961 250134503 2.530000e-155 558.0
38 TraesCS2B01G510500 chr6D 81.456 728 89 35 988 1675 436405153 436404432 3.280000e-154 555.0
39 TraesCS2B01G510500 chr6D 81.197 585 81 15 2346 2909 438332194 438332770 7.400000e-121 444.0
40 TraesCS2B01G510500 chr6D 79.393 626 72 19 921 1545 30072826 30073395 3.520000e-104 388.0
41 TraesCS2B01G510500 chr6D 80.220 273 35 13 1799 2058 30073553 30073819 1.380000e-43 187.0
42 TraesCS2B01G510500 chr6D 89.189 148 14 2 25 171 441677604 441677458 1.780000e-42 183.0
43 TraesCS2B01G510500 chr6D 87.755 147 14 4 25 170 448798439 448798296 4.990000e-38 169.0
44 TraesCS2B01G510500 chr6B 83.150 635 73 15 921 1545 57458476 57457866 1.520000e-152 549.0
45 TraesCS2B01G510500 chr6B 93.229 192 11 2 170 361 309272234 309272423 6.140000e-72 281.0
46 TraesCS2B01G510500 chr6B 79.753 405 52 21 1663 2058 57457817 57457434 1.720000e-67 267.0
47 TraesCS2B01G510500 chr6B 91.724 145 12 0 25 169 473283 473427 4.920000e-48 202.0
48 TraesCS2B01G510500 chr7D 82.363 584 76 16 2346 2909 46576971 46576395 1.570000e-132 483.0
49 TraesCS2B01G510500 chr7D 89.500 200 14 4 170 362 549364793 549364992 2.240000e-61 246.0
50 TraesCS2B01G510500 chr7D 96.629 89 3 0 266 354 147991680 147991768 6.490000e-32 148.0
51 TraesCS2B01G510500 chr7D 96.364 55 2 0 237 291 88196907 88196961 1.110000e-14 91.6
52 TraesCS2B01G510500 chr3A 87.409 413 45 5 2346 2752 648267835 648267424 4.390000e-128 468.0
53 TraesCS2B01G510500 chr5A 81.507 584 81 16 2346 2909 650158199 650157623 3.420000e-124 455.0
54 TraesCS2B01G510500 chr5A 86.755 151 14 5 205 354 512445629 512445774 2.320000e-36 163.0
55 TraesCS2B01G510500 chr4D 80.993 584 84 13 2346 2909 391462772 391462196 3.440000e-119 438.0
56 TraesCS2B01G510500 chr6A 86.027 365 40 6 1310 1673 584508166 584507812 5.880000e-102 381.0
57 TraesCS2B01G510500 chr6A 85.246 366 43 9 1310 1674 584531233 584530878 1.650000e-97 366.0
58 TraesCS2B01G510500 chr6A 92.268 194 15 0 170 363 86535462 86535655 2.860000e-70 276.0
59 TraesCS2B01G510500 chr1A 79.110 584 97 14 2346 2909 505218268 505218846 2.120000e-101 379.0
60 TraesCS2B01G510500 chr1D 88.966 145 16 0 25 169 434734670 434734814 2.300000e-41 180.0
61 TraesCS2B01G510500 chr3D 82.081 173 20 8 185 354 102647952 102648116 1.410000e-28 137.0


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 TraesCS2B01G510500 chr2B 706566767 706569675 2908 False 5373.000000 5373 100.0000 1 2909 1 chr2B.!!$F2 2908
1 TraesCS2B01G510500 chr2B 706694945 706700167 5222 False 601.000000 1478 85.0040 484 2330 3 chr2B.!!$F4 1846
2 TraesCS2B01G510500 chr2B 770607529 770608071 542 False 564.000000 564 86.3970 697 1207 1 chr2B.!!$F3 510
3 TraesCS2B01G510500 chr2D 585519315 585520931 1616 False 953.850000 1829 86.5835 452 2092 2 chr2D.!!$F1 1640
4 TraesCS2B01G510500 chr2D 585634928 585637502 2574 False 627.333333 1467 88.4010 622 2343 3 chr2D.!!$F2 1721
5 TraesCS2B01G510500 chr2A 719685602 719686967 1365 False 1177.000000 1177 82.9340 618 1977 1 chr2A.!!$F4 1359
6 TraesCS2B01G510500 chr2A 719626411 719627418 1007 False 1164.000000 1164 87.5000 1284 2310 1 chr2A.!!$F3 1026
7 TraesCS2B01G510500 chr2A 719564865 719567862 2997 False 851.000000 1182 90.2780 364 2343 3 chr2A.!!$F5 1979
8 TraesCS2B01G510500 chr2A 719573776 719574351 575 False 547.000000 547 84.7860 458 1008 1 chr2A.!!$F1 550
9 TraesCS2B01G510500 chr2A 165334794 165335372 578 True 446.000000 446 81.1970 2346 2909 1 chr2A.!!$R1 563
10 TraesCS2B01G510500 chr5D 257170171 257170734 563 False 669.000000 669 88.1830 2346 2907 1 chr5D.!!$F2 561
11 TraesCS2B01G510500 chr5D 114464963 114465551 588 False 438.000000 438 80.7050 2334 2909 1 chr5D.!!$F1 575
12 TraesCS2B01G510500 chr7B 616816670 616817212 542 True 575.000000 575 86.7650 697 1207 1 chr7B.!!$R2 510
13 TraesCS2B01G510500 chr7B 488169955 488170514 559 False 346.000000 346 78.5590 2345 2909 1 chr7B.!!$F1 564
14 TraesCS2B01G510500 chr1B 62244917 62245459 542 False 569.000000 569 86.5810 697 1207 1 chr1B.!!$F1 510
15 TraesCS2B01G510500 chr1B 168589741 168590320 579 True 547.000000 547 84.2200 2346 2909 1 chr1B.!!$R1 563
16 TraesCS2B01G510500 chr4B 649654111 649654645 534 True 566.000000 566 86.7540 697 1200 1 chr4B.!!$R2 503
17 TraesCS2B01G510500 chr5B 250133961 250134503 542 False 558.000000 558 86.2130 697 1207 1 chr5B.!!$F1 510
18 TraesCS2B01G510500 chr6D 436404432 436405153 721 True 555.000000 555 81.4560 988 1675 1 chr6D.!!$R1 687
19 TraesCS2B01G510500 chr6D 438332194 438332770 576 False 444.000000 444 81.1970 2346 2909 1 chr6D.!!$F1 563
20 TraesCS2B01G510500 chr6D 30072826 30073819 993 False 287.500000 388 79.8065 921 2058 2 chr6D.!!$F2 1137
21 TraesCS2B01G510500 chr6B 57457434 57458476 1042 True 408.000000 549 81.4515 921 2058 2 chr6B.!!$R1 1137
22 TraesCS2B01G510500 chr7D 46576395 46576971 576 True 483.000000 483 82.3630 2346 2909 1 chr7D.!!$R1 563
23 TraesCS2B01G510500 chr5A 650157623 650158199 576 True 455.000000 455 81.5070 2346 2909 1 chr5A.!!$R1 563
24 TraesCS2B01G510500 chr4D 391462196 391462772 576 True 438.000000 438 80.9930 2346 2909 1 chr4D.!!$R1 563
25 TraesCS2B01G510500 chr1A 505218268 505218846 578 False 379.000000 379 79.1100 2346 2909 1 chr1A.!!$F1 563

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
197 198 0.038159 CAGGAGGTCAGTGGTTCGAC 60.038 60.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2119 6231 0.321346 GGTGACTGCCCCAAAAATGG 59.679 55.0 0.0 0.0 0.0 3.16 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.463444 GTTAGGTCATTGTGTCACGGC 59.537 52.381 0.00 0.00 0.00 5.68
24 25 0.973632 TAGGTCATTGTGTCACGGCT 59.026 50.000 0.00 0.00 0.00 5.52
25 26 0.973632 AGGTCATTGTGTCACGGCTA 59.026 50.000 0.00 0.00 0.00 3.93
26 27 1.066858 AGGTCATTGTGTCACGGCTAG 60.067 52.381 0.00 0.00 0.00 3.42
30 31 1.134401 CATTGTGTCACGGCTAGGGAT 60.134 52.381 0.00 0.00 33.06 3.85
32 33 1.521681 GTGTCACGGCTAGGGATGC 60.522 63.158 0.00 0.00 33.06 3.91
34 35 1.227380 GTCACGGCTAGGGATGCAG 60.227 63.158 0.00 0.00 33.06 4.41
35 36 2.109799 CACGGCTAGGGATGCAGG 59.890 66.667 0.00 0.00 0.00 4.85
38 39 4.632974 GGCTAGGGATGCAGGGCG 62.633 72.222 0.00 0.00 0.00 6.13
40 41 3.164269 CTAGGGATGCAGGGCGGT 61.164 66.667 0.00 0.00 0.00 5.68
41 42 3.466791 CTAGGGATGCAGGGCGGTG 62.467 68.421 0.00 0.00 0.00 4.94
62 63 4.483243 GATCCGCCCCGCTTCCAA 62.483 66.667 0.00 0.00 0.00 3.53
66 67 4.697756 CGCCCCGCTTCCAAGTCA 62.698 66.667 0.00 0.00 0.00 3.41
68 69 1.901464 GCCCCGCTTCCAAGTCAAA 60.901 57.895 0.00 0.00 0.00 2.69
69 70 1.460273 GCCCCGCTTCCAAGTCAAAA 61.460 55.000 0.00 0.00 0.00 2.44
70 71 1.256812 CCCCGCTTCCAAGTCAAAAT 58.743 50.000 0.00 0.00 0.00 1.82
71 72 1.067635 CCCCGCTTCCAAGTCAAAATG 60.068 52.381 0.00 0.00 0.00 2.32
76 77 3.250762 CGCTTCCAAGTCAAAATGTCTCA 59.749 43.478 0.00 0.00 0.00 3.27
77 78 4.612259 CGCTTCCAAGTCAAAATGTCTCAG 60.612 45.833 0.00 0.00 0.00 3.35
79 80 4.090761 TCCAAGTCAAAATGTCTCAGCT 57.909 40.909 0.00 0.00 0.00 4.24
80 81 4.464008 TCCAAGTCAAAATGTCTCAGCTT 58.536 39.130 0.00 0.00 0.00 3.74
81 82 5.620206 TCCAAGTCAAAATGTCTCAGCTTA 58.380 37.500 0.00 0.00 0.00 3.09
83 84 5.471456 CCAAGTCAAAATGTCTCAGCTTAGT 59.529 40.000 0.00 0.00 0.00 2.24
85 86 7.173218 CCAAGTCAAAATGTCTCAGCTTAGTTA 59.827 37.037 0.00 0.00 0.00 2.24
87 88 9.944376 AAGTCAAAATGTCTCAGCTTAGTTATA 57.056 29.630 0.00 0.00 0.00 0.98
88 89 9.944376 AGTCAAAATGTCTCAGCTTAGTTATAA 57.056 29.630 0.00 0.00 0.00 0.98
99 100 6.038936 TCAGCTTAGTTATAATTTTTCCGGCC 59.961 38.462 0.00 0.00 0.00 6.13
101 102 6.039382 AGCTTAGTTATAATTTTTCCGGCCAG 59.961 38.462 2.24 0.00 0.00 4.85
102 103 6.038936 GCTTAGTTATAATTTTTCCGGCCAGA 59.961 38.462 2.24 0.00 0.00 3.86
103 104 7.255486 GCTTAGTTATAATTTTTCCGGCCAGAT 60.255 37.037 2.24 0.00 0.00 2.90
105 106 7.418337 AGTTATAATTTTTCCGGCCAGATTT 57.582 32.000 2.24 0.00 0.00 2.17
106 107 8.528044 AGTTATAATTTTTCCGGCCAGATTTA 57.472 30.769 2.24 0.00 0.00 1.40
108 109 9.027129 GTTATAATTTTTCCGGCCAGATTTAAC 57.973 33.333 2.24 0.00 0.00 2.01
109 110 5.738619 AATTTTTCCGGCCAGATTTAACT 57.261 34.783 2.24 0.00 0.00 2.24
115 116 4.913784 TCCGGCCAGATTTAACTTACTTT 58.086 39.130 2.24 0.00 0.00 2.66
116 117 4.698304 TCCGGCCAGATTTAACTTACTTTG 59.302 41.667 2.24 0.00 0.00 2.77
117 118 4.698304 CCGGCCAGATTTAACTTACTTTGA 59.302 41.667 2.24 0.00 0.00 2.69
118 119 5.182380 CCGGCCAGATTTAACTTACTTTGAA 59.818 40.000 2.24 0.00 0.00 2.69
121 122 7.118680 CGGCCAGATTTAACTTACTTTGAACTA 59.881 37.037 2.24 0.00 0.00 2.24
122 123 8.789762 GGCCAGATTTAACTTACTTTGAACTAA 58.210 33.333 0.00 0.00 0.00 2.24
137 138 8.982685 ACTTTGAACTAATATCATGTCTATGCG 58.017 33.333 0.00 0.00 34.21 4.73
141 142 3.988976 AATATCATGTCTATGCGGGCT 57.011 42.857 0.00 0.00 34.21 5.19
142 143 3.988976 ATATCATGTCTATGCGGGCTT 57.011 42.857 0.00 0.00 34.21 4.35
145 146 3.044235 TCATGTCTATGCGGGCTTATG 57.956 47.619 0.00 0.00 34.21 1.90
146 147 1.466167 CATGTCTATGCGGGCTTATGC 59.534 52.381 0.00 0.00 38.76 3.14
147 148 0.599991 TGTCTATGCGGGCTTATGCG 60.600 55.000 0.00 0.00 40.82 4.73
148 149 1.005037 TCTATGCGGGCTTATGCGG 60.005 57.895 0.00 0.00 40.82 5.69
149 150 2.031919 TATGCGGGCTTATGCGGG 59.968 61.111 0.00 0.00 40.82 6.13
150 151 2.449031 CTATGCGGGCTTATGCGGGA 62.449 60.000 0.00 0.00 40.82 5.14
151 152 1.836999 TATGCGGGCTTATGCGGGAT 61.837 55.000 0.00 0.00 40.82 3.85
152 153 3.357079 GCGGGCTTATGCGGGATG 61.357 66.667 0.00 0.00 40.82 3.51
154 155 2.985847 GGGCTTATGCGGGATGCC 60.986 66.667 2.70 2.70 45.60 4.40
169 170 4.632974 GCCCGCCTGCATCCCTAG 62.633 72.222 0.00 0.00 0.00 3.02
170 171 3.164269 CCCGCCTGCATCCCTAGT 61.164 66.667 0.00 0.00 0.00 2.57
173 174 1.227380 CGCCTGCATCCCTAGTCAC 60.227 63.158 0.00 0.00 0.00 3.67
174 175 1.227380 GCCTGCATCCCTAGTCACG 60.227 63.158 0.00 0.00 0.00 4.35
175 176 1.443407 CCTGCATCCCTAGTCACGG 59.557 63.158 0.00 0.00 0.00 4.94
177 178 1.960040 CTGCATCCCTAGTCACGGCA 61.960 60.000 0.00 0.00 0.00 5.69
178 179 1.521681 GCATCCCTAGTCACGGCAC 60.522 63.158 0.00 0.00 0.00 5.01
179 180 1.897423 CATCCCTAGTCACGGCACA 59.103 57.895 0.00 0.00 0.00 4.57
181 182 1.330655 ATCCCTAGTCACGGCACAGG 61.331 60.000 0.00 0.00 0.00 4.00
183 184 1.513158 CCTAGTCACGGCACAGGAG 59.487 63.158 0.00 0.00 0.00 3.69
186 187 1.248785 TAGTCACGGCACAGGAGGTC 61.249 60.000 0.00 0.00 0.00 3.85
187 188 2.523168 TCACGGCACAGGAGGTCA 60.523 61.111 0.00 0.00 0.00 4.02
189 190 2.524394 ACGGCACAGGAGGTCAGT 60.524 61.111 0.00 0.00 0.00 3.41
190 191 2.047844 CGGCACAGGAGGTCAGTG 60.048 66.667 0.00 0.00 36.39 3.66
191 192 2.348998 GGCACAGGAGGTCAGTGG 59.651 66.667 0.00 0.00 33.98 4.00
192 193 2.520536 GGCACAGGAGGTCAGTGGT 61.521 63.158 0.00 0.00 33.98 4.16
194 195 0.603975 GCACAGGAGGTCAGTGGTTC 60.604 60.000 0.00 0.00 33.98 3.62
195 196 0.319900 CACAGGAGGTCAGTGGTTCG 60.320 60.000 0.00 0.00 0.00 3.95
197 198 0.038159 CAGGAGGTCAGTGGTTCGAC 60.038 60.000 0.00 0.00 0.00 4.20
199 200 0.244178 GGAGGTCAGTGGTTCGACTC 59.756 60.000 0.00 0.00 32.57 3.36
200 201 0.959553 GAGGTCAGTGGTTCGACTCA 59.040 55.000 0.00 0.00 32.57 3.41
201 202 0.674534 AGGTCAGTGGTTCGACTCAC 59.325 55.000 8.74 8.74 32.57 3.51
202 203 0.319641 GGTCAGTGGTTCGACTCACC 60.320 60.000 12.14 5.85 34.67 4.02
204 205 2.022129 CAGTGGTTCGACTCACCGC 61.022 63.158 9.81 9.81 44.05 5.68
226 227 3.070429 CAAGCGCACTTGTTTTTCTCT 57.930 42.857 11.47 0.00 46.84 3.10
228 229 3.782889 AGCGCACTTGTTTTTCTCTTT 57.217 38.095 11.47 0.00 0.00 2.52
229 230 4.110036 AGCGCACTTGTTTTTCTCTTTT 57.890 36.364 11.47 0.00 0.00 2.27
234 235 6.617529 GCGCACTTGTTTTTCTCTTTTGAAAA 60.618 34.615 0.30 0.00 42.12 2.29
235 236 6.731948 CGCACTTGTTTTTCTCTTTTGAAAAC 59.268 34.615 2.44 0.00 43.09 2.43
236 237 7.568497 CGCACTTGTTTTTCTCTTTTGAAAACA 60.568 33.333 8.92 8.92 43.09 2.83
237 238 7.741652 GCACTTGTTTTTCTCTTTTGAAAACAG 59.258 33.333 11.79 9.59 43.09 3.16
238 239 8.977505 CACTTGTTTTTCTCTTTTGAAAACAGA 58.022 29.630 11.79 0.00 43.09 3.41
246 247 9.846248 TTTCTCTTTTGAAAACAGAAGAAGAAG 57.154 29.630 8.08 0.00 33.59 2.85
253 254 9.981114 TTTGAAAACAGAAGAAGAAGAAAAACT 57.019 25.926 0.00 0.00 0.00 2.66
258 259 7.252965 ACAGAAGAAGAAGAAAAACTACTGC 57.747 36.000 0.00 0.00 0.00 4.40
260 261 7.011857 ACAGAAGAAGAAGAAAAACTACTGCAG 59.988 37.037 13.48 13.48 0.00 4.41
261 262 5.681337 AGAAGAAGAAAAACTACTGCAGC 57.319 39.130 15.27 0.00 0.00 5.25
262 263 4.517075 AGAAGAAGAAAAACTACTGCAGCC 59.483 41.667 15.27 0.00 0.00 4.85
263 264 4.092116 AGAAGAAAAACTACTGCAGCCT 57.908 40.909 15.27 0.00 0.00 4.58
268 269 3.990318 AAAACTACTGCAGCCTGAAAC 57.010 42.857 15.27 0.00 0.00 2.78
272 273 2.304180 ACTACTGCAGCCTGAAACAGAT 59.696 45.455 15.27 0.00 32.44 2.90
276 277 4.338879 ACTGCAGCCTGAAACAGATAAAT 58.661 39.130 15.27 0.00 32.44 1.40
277 278 4.157289 ACTGCAGCCTGAAACAGATAAATG 59.843 41.667 15.27 0.00 32.44 2.32
278 279 3.444742 TGCAGCCTGAAACAGATAAATGG 59.555 43.478 0.00 0.00 32.44 3.16
279 280 3.181483 GCAGCCTGAAACAGATAAATGGG 60.181 47.826 0.00 0.00 32.44 4.00
280 281 3.026694 AGCCTGAAACAGATAAATGGGC 58.973 45.455 0.00 0.00 37.57 5.36
303 304 3.490759 CACCTAACGCGGCTGCAG 61.491 66.667 19.50 10.11 42.97 4.41
304 305 4.760047 ACCTAACGCGGCTGCAGG 62.760 66.667 19.50 18.89 42.97 4.85
323 324 0.800683 GCGCCGGTTAGGAAAATTGC 60.801 55.000 1.90 0.00 45.00 3.56
324 325 0.179148 CGCCGGTTAGGAAAATTGCC 60.179 55.000 1.90 0.00 45.00 4.52
325 326 0.174845 GCCGGTTAGGAAAATTGCCC 59.825 55.000 1.90 0.00 45.00 5.36
326 327 1.847328 CCGGTTAGGAAAATTGCCCT 58.153 50.000 0.00 4.54 45.00 5.19
328 329 3.358118 CCGGTTAGGAAAATTGCCCTTA 58.642 45.455 4.44 0.00 45.00 2.69
330 331 4.381185 CCGGTTAGGAAAATTGCCCTTAAC 60.381 45.833 4.44 7.00 45.00 2.01
331 332 4.381185 CGGTTAGGAAAATTGCCCTTAACC 60.381 45.833 9.92 9.92 35.38 2.85
333 334 2.176045 AGGAAAATTGCCCTTAACCGG 58.824 47.619 0.00 0.00 0.00 5.28
339 340 2.750237 GCCCTTAACCGGCACCTG 60.750 66.667 0.00 0.00 46.27 4.00
340 341 2.750237 CCCTTAACCGGCACCTGC 60.750 66.667 0.00 0.00 41.14 4.85
342 343 2.040544 CCTTAACCGGCACCTGCAG 61.041 63.158 6.78 6.78 44.36 4.41
343 344 2.671619 TTAACCGGCACCTGCAGC 60.672 61.111 8.66 0.00 44.36 5.25
351 352 2.511373 CACCTGCAGCGCCGAATA 60.511 61.111 8.66 0.00 0.00 1.75
352 353 2.202932 ACCTGCAGCGCCGAATAG 60.203 61.111 8.66 0.00 0.00 1.73
353 354 2.969238 CCTGCAGCGCCGAATAGG 60.969 66.667 8.66 1.07 44.97 2.57
354 355 2.106938 CTGCAGCGCCGAATAGGA 59.893 61.111 2.29 0.00 45.00 2.94
356 357 1.078778 TGCAGCGCCGAATAGGAAA 60.079 52.632 2.29 0.00 45.00 3.13
359 360 0.040958 CAGCGCCGAATAGGAAATGC 60.041 55.000 2.29 0.00 45.00 3.56
360 361 1.166531 AGCGCCGAATAGGAAATGCC 61.167 55.000 2.29 0.00 45.00 4.40
520 3726 9.504708 TTCTGCATGAACCAAAAATCATTAATT 57.495 25.926 0.00 0.00 34.12 1.40
710 3947 4.273257 GCCCTCGTAGCTCTCGCC 62.273 72.222 0.00 0.00 36.60 5.54
898 4169 4.024143 GCATGCGCACCGTGAACA 62.024 61.111 14.90 0.00 38.36 3.18
901 4172 1.596752 ATGCGCACCGTGAACAAGA 60.597 52.632 14.90 0.00 0.00 3.02
903 4174 2.954753 GCGCACCGTGAACAAGAGG 61.955 63.158 0.30 0.00 0.00 3.69
948 4225 2.172419 CGTGTTAAACCGCGGCAG 59.828 61.111 28.58 1.05 34.83 4.85
981 4260 2.307768 GCAAGCCTATAAAAGGGGGAC 58.692 52.381 0.00 0.00 46.65 4.46
1238 4585 0.684805 CCCGAGTAAGGACCTCTGCT 60.685 60.000 0.00 0.00 0.00 4.24
1240 4587 2.588620 CCGAGTAAGGACCTCTGCTAT 58.411 52.381 0.00 0.00 0.00 2.97
1268 5072 0.186630 TTGGATCTGGATGCCATGGG 59.813 55.000 15.13 0.00 30.82 4.00
1280 5084 2.929483 CATGGGCCATGGCTACCT 59.071 61.111 34.26 18.44 38.11 3.08
1281 5085 1.231068 CATGGGCCATGGCTACCTT 59.769 57.895 34.26 22.78 38.11 3.50
1282 5086 0.825010 CATGGGCCATGGCTACCTTC 60.825 60.000 34.26 17.64 38.11 3.46
1299 5116 2.420022 CCTTCCCGTCTTACATTTGCTG 59.580 50.000 0.00 0.00 0.00 4.41
1603 5439 3.329300 CCTAATTGGCCTCATCGGG 57.671 57.895 3.32 0.00 0.00 5.14
1687 5523 1.460504 AGATGCTCGACTACAACCGA 58.539 50.000 0.00 0.00 0.00 4.69
1836 5921 3.933332 GTGTTACCGCTTCTAAGAAGCAT 59.067 43.478 19.91 12.93 43.15 3.79
1893 5987 2.287909 TGTGTCGTGTGATCGATGTTCA 60.288 45.455 0.54 0.00 41.78 3.18
1899 5996 4.091365 TCGTGTGATCGATGTTCATTTGTC 59.909 41.667 0.54 0.00 34.85 3.18
1911 6008 7.679634 CGATGTTCATTTGTCAAAAATAAAGCG 59.320 33.333 1.31 0.19 0.00 4.68
2019 6131 4.384846 GTGGTATCTGTACAAAGTCGTGTG 59.615 45.833 0.00 0.00 32.75 3.82
2067 6179 2.697431 GCTAACACGCCATTTTCACA 57.303 45.000 0.00 0.00 0.00 3.58
2068 6180 2.584791 GCTAACACGCCATTTTCACAG 58.415 47.619 0.00 0.00 0.00 3.66
2086 6198 6.500684 TCACAGCATGGAATTAACTCTTTC 57.499 37.500 0.00 0.00 43.62 2.62
2118 6230 6.266203 GACTACATGTCAATCGACTGAATG 57.734 41.667 0.00 7.68 44.73 2.67
2119 6231 4.568359 ACTACATGTCAATCGACTGAATGC 59.432 41.667 0.00 0.00 43.06 3.56
2123 6235 3.346315 TGTCAATCGACTGAATGCCATT 58.654 40.909 0.00 0.00 43.06 3.16
2130 6242 2.674747 CGACTGAATGCCATTTTTGGGG 60.675 50.000 0.00 0.00 0.00 4.96
2159 6271 2.723124 TTTGCCTCTTTGCGATTTCC 57.277 45.000 0.00 0.00 0.00 3.13
2183 6581 0.035458 GCCGTGCCTATTAGGAGCAT 59.965 55.000 14.16 0.00 37.67 3.79
2191 6589 5.409826 GTGCCTATTAGGAGCATGTAATGAC 59.590 44.000 14.16 0.00 42.57 3.06
2192 6590 4.627467 GCCTATTAGGAGCATGTAATGACG 59.373 45.833 14.16 0.00 42.57 4.35
2194 6592 6.363937 CCTATTAGGAGCATGTAATGACGCC 61.364 48.000 3.41 0.00 42.57 5.68
2195 6593 8.684611 CCTATTAGGAGCATGTAATGACGCCA 62.685 46.154 3.41 0.00 42.57 5.69
2196 6594 9.886657 CCTATTAGGAGCATGTAATGACGCCAT 62.887 44.444 3.41 0.00 42.57 4.40
2201 6875 0.179059 ATGTAATGACGCCATCGCCA 60.179 50.000 0.00 0.00 39.84 5.69
2204 6878 0.529773 TAATGACGCCATCGCCAGAC 60.530 55.000 0.00 0.00 39.84 3.51
2265 6939 4.456911 CCGCATCAATGACTAATAGGCAAT 59.543 41.667 0.00 0.00 36.42 3.56
2268 6942 6.293571 CGCATCAATGACTAATAGGCAATTCA 60.294 38.462 0.00 0.00 36.42 2.57
2285 6959 7.342799 AGGCAATTCATACATCCACTTAATTGT 59.657 33.333 0.00 0.00 36.00 2.71
2307 6981 0.313987 TCTACAGGCGCATGGATACG 59.686 55.000 27.21 6.31 42.51 3.06
2326 7000 1.470890 CGTGGAAAACCAACGCCATAT 59.529 47.619 0.00 0.00 32.26 1.78
2327 7001 2.730715 CGTGGAAAACCAACGCCATATG 60.731 50.000 0.00 0.00 32.26 1.78
2333 7007 4.695217 AAACCAACGCCATATGTAACTG 57.305 40.909 1.24 0.00 0.00 3.16
2472 7148 0.250553 CCCAAACCCGCAGTGACTAA 60.251 55.000 0.00 0.00 0.00 2.24
2473 7149 1.613255 CCCAAACCCGCAGTGACTAAT 60.613 52.381 0.00 0.00 0.00 1.73
2481 7157 5.250200 ACCCGCAGTGACTAATGATTTAAA 58.750 37.500 0.00 0.00 0.00 1.52
2654 7335 2.852449 CTCTCTGACCTAGGTGCGATA 58.148 52.381 22.10 7.02 0.00 2.92
2726 7411 4.500116 GTCGAGGAGAGCGGTGGC 62.500 72.222 0.00 0.00 40.37 5.01
2738 7423 1.904771 CGGTGGCCATTCAGAGGTA 59.095 57.895 9.72 0.00 0.00 3.08
2787 7472 4.969196 CGCAGCGGTCACCACAGT 62.969 66.667 7.00 0.00 0.00 3.55
2811 7496 3.458163 CGCCCGAGGTCCAGCTAA 61.458 66.667 0.00 0.00 0.00 3.09
2828 7528 3.257375 AGCTAAATCCGATATACCGTGCA 59.743 43.478 0.00 0.00 0.00 4.57
2829 7529 3.991773 GCTAAATCCGATATACCGTGCAA 59.008 43.478 0.00 0.00 0.00 4.08
2845 7545 1.885157 CAACAATGGCAGTGGCGAT 59.115 52.632 19.96 4.12 40.47 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.073816 CCGTGACACAATGACCTAACC 58.926 52.381 6.37 0.00 0.00 2.85
3 4 1.463444 GCCGTGACACAATGACCTAAC 59.537 52.381 6.37 0.00 0.00 2.34
6 7 0.973632 TAGCCGTGACACAATGACCT 59.026 50.000 6.37 0.00 0.00 3.85
10 11 0.249120 TCCCTAGCCGTGACACAATG 59.751 55.000 6.37 0.00 0.00 2.82
11 12 1.134401 CATCCCTAGCCGTGACACAAT 60.134 52.381 6.37 0.00 0.00 2.71
13 14 1.897423 CATCCCTAGCCGTGACACA 59.103 57.895 6.37 0.00 0.00 3.72
15 16 1.960040 CTGCATCCCTAGCCGTGACA 61.960 60.000 0.00 0.00 0.00 3.58
17 18 2.434843 CCTGCATCCCTAGCCGTGA 61.435 63.158 0.00 0.00 0.00 4.35
19 20 3.164269 CCCTGCATCCCTAGCCGT 61.164 66.667 0.00 0.00 0.00 5.68
20 21 4.632974 GCCCTGCATCCCTAGCCG 62.633 72.222 0.00 0.00 0.00 5.52
23 24 3.164269 ACCGCCCTGCATCCCTAG 61.164 66.667 0.00 0.00 0.00 3.02
24 25 3.479203 CACCGCCCTGCATCCCTA 61.479 66.667 0.00 0.00 0.00 3.53
46 47 4.489771 CTTGGAAGCGGGGCGGAT 62.490 66.667 0.00 0.00 0.00 4.18
50 51 1.460273 TTTTGACTTGGAAGCGGGGC 61.460 55.000 0.00 0.00 0.00 5.80
51 52 1.067635 CATTTTGACTTGGAAGCGGGG 60.068 52.381 0.00 0.00 0.00 5.73
53 54 2.554032 AGACATTTTGACTTGGAAGCGG 59.446 45.455 0.00 0.00 0.00 5.52
54 55 3.250762 TGAGACATTTTGACTTGGAAGCG 59.749 43.478 0.00 0.00 0.00 4.68
55 56 4.791974 CTGAGACATTTTGACTTGGAAGC 58.208 43.478 0.00 0.00 0.00 3.86
56 57 4.518211 AGCTGAGACATTTTGACTTGGAAG 59.482 41.667 0.00 0.00 0.00 3.46
58 59 4.090761 AGCTGAGACATTTTGACTTGGA 57.909 40.909 0.00 0.00 0.00 3.53
60 61 6.551385 ACTAAGCTGAGACATTTTGACTTG 57.449 37.500 4.63 0.00 0.00 3.16
62 63 9.944376 TTATAACTAAGCTGAGACATTTTGACT 57.056 29.630 4.63 0.00 0.00 3.41
70 71 8.879759 CGGAAAAATTATAACTAAGCTGAGACA 58.120 33.333 4.63 0.00 0.00 3.41
71 72 8.336080 CCGGAAAAATTATAACTAAGCTGAGAC 58.664 37.037 4.63 0.00 0.00 3.36
76 77 5.889289 TGGCCGGAAAAATTATAACTAAGCT 59.111 36.000 5.05 0.00 0.00 3.74
77 78 6.038936 TCTGGCCGGAAAAATTATAACTAAGC 59.961 38.462 13.31 0.00 0.00 3.09
79 80 8.528044 AATCTGGCCGGAAAAATTATAACTAA 57.472 30.769 20.61 0.00 0.00 2.24
80 81 8.528044 AAATCTGGCCGGAAAAATTATAACTA 57.472 30.769 20.61 0.00 0.00 2.24
81 82 7.418337 AAATCTGGCCGGAAAAATTATAACT 57.582 32.000 20.61 0.00 0.00 2.24
83 84 8.973182 AGTTAAATCTGGCCGGAAAAATTATAA 58.027 29.630 20.61 7.51 0.00 0.98
85 86 7.418337 AGTTAAATCTGGCCGGAAAAATTAT 57.582 32.000 20.61 0.00 0.00 1.28
87 88 5.738619 AGTTAAATCTGGCCGGAAAAATT 57.261 34.783 20.61 13.60 0.00 1.82
88 89 5.738619 AAGTTAAATCTGGCCGGAAAAAT 57.261 34.783 20.61 9.95 0.00 1.82
89 90 5.771165 AGTAAGTTAAATCTGGCCGGAAAAA 59.229 36.000 20.61 10.36 0.00 1.94
90 91 5.318630 AGTAAGTTAAATCTGGCCGGAAAA 58.681 37.500 20.61 10.74 0.00 2.29
92 93 4.563140 AGTAAGTTAAATCTGGCCGGAA 57.437 40.909 20.61 0.00 0.00 4.30
93 94 4.563140 AAGTAAGTTAAATCTGGCCGGA 57.437 40.909 18.80 18.80 0.00 5.14
94 95 4.698304 TCAAAGTAAGTTAAATCTGGCCGG 59.302 41.667 4.71 4.71 0.00 6.13
115 116 6.398095 CCCGCATAGACATGATATTAGTTCA 58.602 40.000 0.00 0.00 33.67 3.18
116 117 5.292101 GCCCGCATAGACATGATATTAGTTC 59.708 44.000 0.00 0.00 33.67 3.01
117 118 5.046304 AGCCCGCATAGACATGATATTAGTT 60.046 40.000 0.00 0.00 33.67 2.24
118 119 4.467795 AGCCCGCATAGACATGATATTAGT 59.532 41.667 0.00 0.00 33.67 2.24
121 122 3.988976 AGCCCGCATAGACATGATATT 57.011 42.857 0.00 0.00 33.67 1.28
122 123 3.988976 AAGCCCGCATAGACATGATAT 57.011 42.857 0.00 0.00 33.67 1.63
126 127 1.466167 GCATAAGCCCGCATAGACATG 59.534 52.381 0.00 0.00 32.87 3.21
127 128 1.813513 GCATAAGCCCGCATAGACAT 58.186 50.000 0.00 0.00 33.58 3.06
128 129 0.599991 CGCATAAGCCCGCATAGACA 60.600 55.000 0.00 0.00 37.52 3.41
129 130 1.291877 CCGCATAAGCCCGCATAGAC 61.292 60.000 0.00 0.00 37.52 2.59
133 134 3.196207 ATCCCGCATAAGCCCGCAT 62.196 57.895 0.00 0.00 37.52 4.73
135 136 3.357079 CATCCCGCATAAGCCCGC 61.357 66.667 0.00 0.00 37.52 6.13
137 138 2.985847 GGCATCCCGCATAAGCCC 60.986 66.667 0.00 0.00 45.17 5.19
152 153 4.632974 CTAGGGATGCAGGCGGGC 62.633 72.222 0.00 0.00 0.00 6.13
154 155 2.423446 GACTAGGGATGCAGGCGG 59.577 66.667 0.00 0.00 0.00 6.13
156 157 1.227380 CGTGACTAGGGATGCAGGC 60.227 63.158 0.00 0.00 0.00 4.85
157 158 1.443407 CCGTGACTAGGGATGCAGG 59.557 63.158 0.00 0.00 33.64 4.85
158 159 1.227380 GCCGTGACTAGGGATGCAG 60.227 63.158 0.00 0.00 33.64 4.41
161 162 0.179100 CTGTGCCGTGACTAGGGATG 60.179 60.000 0.00 0.00 33.64 3.51
163 164 1.982395 CCTGTGCCGTGACTAGGGA 60.982 63.158 0.00 0.00 33.64 4.20
166 167 1.251527 ACCTCCTGTGCCGTGACTAG 61.252 60.000 0.00 0.00 0.00 2.57
169 170 2.048127 GACCTCCTGTGCCGTGAC 60.048 66.667 0.00 0.00 0.00 3.67
170 171 2.523168 TGACCTCCTGTGCCGTGA 60.523 61.111 0.00 0.00 0.00 4.35
173 174 2.047844 CACTGACCTCCTGTGCCG 60.048 66.667 0.00 0.00 37.79 5.69
174 175 2.056906 AACCACTGACCTCCTGTGCC 62.057 60.000 0.00 0.00 41.61 5.01
175 176 0.603975 GAACCACTGACCTCCTGTGC 60.604 60.000 0.00 0.00 41.61 4.57
177 178 0.469331 TCGAACCACTGACCTCCTGT 60.469 55.000 0.00 0.00 0.00 4.00
178 179 0.038159 GTCGAACCACTGACCTCCTG 60.038 60.000 0.00 0.00 0.00 3.86
179 180 0.178958 AGTCGAACCACTGACCTCCT 60.179 55.000 0.00 0.00 35.71 3.69
181 182 0.959553 TGAGTCGAACCACTGACCTC 59.040 55.000 0.00 0.00 35.71 3.85
183 184 0.319641 GGTGAGTCGAACCACTGACC 60.320 60.000 15.28 6.63 42.52 4.02
186 187 2.022129 GCGGTGAGTCGAACCACTG 61.022 63.158 17.99 17.99 41.35 3.66
187 188 2.338984 GCGGTGAGTCGAACCACT 59.661 61.111 15.28 0.00 37.57 4.00
191 192 3.000080 CTTGCGCGGTGAGTCGAAC 62.000 63.158 8.83 0.00 0.00 3.95
192 193 2.733218 CTTGCGCGGTGAGTCGAA 60.733 61.111 8.83 0.00 0.00 3.71
210 211 6.388259 TTTCAAAAGAGAAAAACAAGTGCG 57.612 33.333 0.00 0.00 34.77 5.34
215 216 9.757227 TCTTCTGTTTTCAAAAGAGAAAAACAA 57.243 25.926 19.82 1.35 45.81 2.83
216 217 9.757227 TTCTTCTGTTTTCAAAAGAGAAAAACA 57.243 25.926 19.82 10.96 45.81 2.83
220 221 9.846248 CTTCTTCTTCTGTTTTCAAAAGAGAAA 57.154 29.630 19.82 8.42 38.02 2.52
222 223 8.792830 TCTTCTTCTTCTGTTTTCAAAAGAGA 57.207 30.769 5.62 5.62 38.02 3.10
234 235 6.823689 TGCAGTAGTTTTTCTTCTTCTTCTGT 59.176 34.615 0.00 0.00 0.00 3.41
235 236 7.251704 TGCAGTAGTTTTTCTTCTTCTTCTG 57.748 36.000 0.00 0.00 0.00 3.02
236 237 6.017523 GCTGCAGTAGTTTTTCTTCTTCTTCT 60.018 38.462 16.64 0.00 0.00 2.85
237 238 6.139435 GCTGCAGTAGTTTTTCTTCTTCTTC 58.861 40.000 16.64 0.00 0.00 2.87
238 239 5.009110 GGCTGCAGTAGTTTTTCTTCTTCTT 59.991 40.000 16.64 0.00 0.00 2.52
240 241 4.517075 AGGCTGCAGTAGTTTTTCTTCTTC 59.483 41.667 16.64 0.00 0.00 2.87
244 245 3.820557 TCAGGCTGCAGTAGTTTTTCTT 58.179 40.909 16.64 0.00 0.00 2.52
246 247 4.202010 TGTTTCAGGCTGCAGTAGTTTTTC 60.202 41.667 16.64 0.00 0.00 2.29
252 253 2.462456 TCTGTTTCAGGCTGCAGTAG 57.538 50.000 16.64 5.72 31.51 2.57
253 254 4.551702 TTATCTGTTTCAGGCTGCAGTA 57.448 40.909 16.64 4.63 31.51 2.74
255 256 4.439700 CCATTTATCTGTTTCAGGCTGCAG 60.440 45.833 10.11 10.11 31.51 4.41
256 257 3.444742 CCATTTATCTGTTTCAGGCTGCA 59.555 43.478 10.34 0.00 31.51 4.41
258 259 3.181483 GCCCATTTATCTGTTTCAGGCTG 60.181 47.826 8.58 8.58 35.00 4.85
260 261 2.101415 GGCCCATTTATCTGTTTCAGGC 59.899 50.000 0.00 0.00 37.14 4.85
261 262 3.364549 TGGCCCATTTATCTGTTTCAGG 58.635 45.455 0.00 0.00 31.51 3.86
262 263 3.181483 GCTGGCCCATTTATCTGTTTCAG 60.181 47.826 0.00 0.00 0.00 3.02
263 264 2.760092 GCTGGCCCATTTATCTGTTTCA 59.240 45.455 0.00 0.00 0.00 2.69
286 287 3.490759 CTGCAGCCGCGTTAGGTG 61.491 66.667 4.92 7.04 42.97 4.00
300 301 4.770874 TTCCTAACCGGCGCCTGC 62.771 66.667 26.68 0.00 41.71 4.85
301 302 1.029947 ATTTTCCTAACCGGCGCCTG 61.030 55.000 26.68 21.87 0.00 4.85
303 304 0.179148 CAATTTTCCTAACCGGCGCC 60.179 55.000 19.07 19.07 0.00 6.53
304 305 0.800683 GCAATTTTCCTAACCGGCGC 60.801 55.000 0.00 0.00 0.00 6.53
305 306 0.179148 GGCAATTTTCCTAACCGGCG 60.179 55.000 0.00 0.00 0.00 6.46
306 307 0.174845 GGGCAATTTTCCTAACCGGC 59.825 55.000 0.00 0.00 0.00 6.13
307 308 1.847328 AGGGCAATTTTCCTAACCGG 58.153 50.000 0.00 0.00 0.00 5.28
309 310 4.381185 CGGTTAAGGGCAATTTTCCTAACC 60.381 45.833 15.75 15.75 35.66 2.85
311 312 3.764972 CCGGTTAAGGGCAATTTTCCTAA 59.235 43.478 0.00 0.00 32.21 2.69
313 314 2.176045 CCGGTTAAGGGCAATTTTCCT 58.824 47.619 0.00 0.00 34.29 3.36
314 315 2.665649 CCGGTTAAGGGCAATTTTCC 57.334 50.000 0.00 0.00 0.00 3.13
323 324 2.750237 GCAGGTGCCGGTTAAGGG 60.750 66.667 1.90 0.00 34.31 3.95
324 325 2.033448 TGCAGGTGCCGGTTAAGG 59.967 61.111 1.90 0.00 41.18 2.69
325 326 2.690778 GCTGCAGGTGCCGGTTAAG 61.691 63.158 17.12 0.00 41.18 1.85
326 327 2.671619 GCTGCAGGTGCCGGTTAA 60.672 61.111 17.12 0.00 41.18 2.01
334 335 2.511373 TATTCGGCGCTGCAGGTG 60.511 61.111 17.12 4.07 0.00 4.00
335 336 2.202932 CTATTCGGCGCTGCAGGT 60.203 61.111 17.12 0.00 0.00 4.00
336 337 2.923426 TTCCTATTCGGCGCTGCAGG 62.923 60.000 17.12 19.62 0.00 4.85
337 338 1.089481 TTTCCTATTCGGCGCTGCAG 61.089 55.000 12.58 10.11 0.00 4.41
338 339 0.463654 ATTTCCTATTCGGCGCTGCA 60.464 50.000 12.58 0.00 0.00 4.41
339 340 0.040958 CATTTCCTATTCGGCGCTGC 60.041 55.000 12.58 0.00 0.00 5.25
340 341 0.040958 GCATTTCCTATTCGGCGCTG 60.041 55.000 10.86 10.86 0.00 5.18
342 343 1.282875 GGCATTTCCTATTCGGCGC 59.717 57.895 0.00 0.00 0.00 6.53
343 344 1.569493 CGGCATTTCCTATTCGGCG 59.431 57.895 0.00 0.00 39.29 6.46
345 346 1.798813 GCTACGGCATTTCCTATTCGG 59.201 52.381 0.00 0.00 38.54 4.30
346 347 1.455786 CGCTACGGCATTTCCTATTCG 59.544 52.381 0.00 0.00 38.60 3.34
347 348 1.194772 GCGCTACGGCATTTCCTATTC 59.805 52.381 0.00 0.00 38.60 1.75
349 350 0.393077 AGCGCTACGGCATTTCCTAT 59.607 50.000 8.99 0.00 38.60 2.57
351 352 1.521681 GAGCGCTACGGCATTTCCT 60.522 57.895 11.50 0.00 38.60 3.36
352 353 1.766143 CTGAGCGCTACGGCATTTCC 61.766 60.000 11.50 0.00 38.60 3.13
353 354 1.084370 ACTGAGCGCTACGGCATTTC 61.084 55.000 11.50 0.00 38.60 2.17
354 355 1.079127 ACTGAGCGCTACGGCATTT 60.079 52.632 11.50 0.00 38.60 2.32
356 357 1.663379 TACACTGAGCGCTACGGCAT 61.663 55.000 11.50 3.91 38.60 4.40
359 360 1.003759 CTACTACACTGAGCGCTACGG 60.004 57.143 11.50 12.06 0.00 4.02
360 361 1.003759 CCTACTACACTGAGCGCTACG 60.004 57.143 11.50 6.93 0.00 3.51
520 3726 0.322456 GGTGCATGCCTGTGGACTTA 60.322 55.000 16.68 0.00 39.95 2.24
522 3728 2.034687 GGTGCATGCCTGTGGACT 59.965 61.111 16.68 0.00 39.95 3.85
623 3829 4.065321 AGAAGGATCAAGCAACGGATAG 57.935 45.455 0.00 0.00 0.00 2.08
710 3947 5.571784 TGCCAAGCTAGAGATTTTTGATG 57.428 39.130 0.00 0.00 0.00 3.07
898 4169 0.179018 AACGCTTGCTGGTTCCTCTT 60.179 50.000 0.00 0.00 0.00 2.85
901 4172 3.749981 CAACGCTTGCTGGTTCCT 58.250 55.556 0.00 0.00 0.00 3.36
948 4225 3.130160 CTTGCGAGGAGGCCAAGC 61.130 66.667 5.01 2.97 0.00 4.01
981 4260 2.338015 GCTGAGTGTGGTGCATGGG 61.338 63.158 0.00 0.00 0.00 4.00
1213 4555 1.335882 GGTCCTTACTCGGGAAGGGG 61.336 65.000 13.16 0.00 43.26 4.79
1216 4558 1.751924 CAGAGGTCCTTACTCGGGAAG 59.248 57.143 0.00 0.00 39.90 3.46
1238 4585 3.657610 TCCAGATCCAAGCAAGAGGATA 58.342 45.455 0.00 0.00 44.44 2.59
1240 4587 1.956869 TCCAGATCCAAGCAAGAGGA 58.043 50.000 0.00 0.00 38.50 3.71
1268 5072 2.203209 CGGGAAGGTAGCCATGGC 60.203 66.667 30.12 30.12 42.33 4.40
1270 5074 0.541863 AAGACGGGAAGGTAGCCATG 59.458 55.000 0.00 0.00 0.00 3.66
1272 5076 1.188863 GTAAGACGGGAAGGTAGCCA 58.811 55.000 0.00 0.00 0.00 4.75
1274 5078 3.538634 AATGTAAGACGGGAAGGTAGC 57.461 47.619 0.00 0.00 0.00 3.58
1276 5080 3.262405 AGCAAATGTAAGACGGGAAGGTA 59.738 43.478 0.00 0.00 0.00 3.08
1277 5081 2.039879 AGCAAATGTAAGACGGGAAGGT 59.960 45.455 0.00 0.00 0.00 3.50
1278 5082 2.420022 CAGCAAATGTAAGACGGGAAGG 59.580 50.000 0.00 0.00 0.00 3.46
1279 5083 3.074412 ACAGCAAATGTAAGACGGGAAG 58.926 45.455 0.00 0.00 41.60 3.46
1280 5084 2.811431 CACAGCAAATGTAAGACGGGAA 59.189 45.455 0.00 0.00 41.41 3.97
1281 5085 2.422597 CACAGCAAATGTAAGACGGGA 58.577 47.619 0.00 0.00 41.41 5.14
1282 5086 1.135689 GCACAGCAAATGTAAGACGGG 60.136 52.381 0.00 0.00 41.41 5.28
1299 5116 0.884704 TGTCGGGAGCAAAGAAGCAC 60.885 55.000 0.00 0.00 36.85 4.40
1538 5356 1.695893 CCGCTGCCACTGTCAATACG 61.696 60.000 0.00 0.00 0.00 3.06
1627 5463 2.513317 TGGGATGATGTTAAGGATGCCA 59.487 45.455 0.00 0.00 34.27 4.92
1734 5573 3.868619 TTGGTAGGTTGGCAAGTACTT 57.131 42.857 15.63 1.12 0.00 2.24
1836 5921 5.666969 ATTGCGCGATATGCTTACTTTTA 57.333 34.783 12.10 0.00 43.27 1.52
1855 5947 5.089411 CGACACACACTCAGAGTAGTATTG 58.911 45.833 1.67 7.35 0.00 1.90
1893 5987 6.359617 CAGACGTCGCTTTATTTTTGACAAAT 59.640 34.615 10.46 0.00 0.00 2.32
1899 5996 4.768145 TCACAGACGTCGCTTTATTTTTG 58.232 39.130 10.46 1.10 0.00 2.44
1911 6008 6.600246 TCACATAGTACTATCACAGACGTC 57.400 41.667 12.62 7.70 0.00 4.34
2062 6174 6.716628 AGAAAGAGTTAATTCCATGCTGTGAA 59.283 34.615 0.00 0.00 0.00 3.18
2064 6176 6.506500 AGAAAGAGTTAATTCCATGCTGTG 57.493 37.500 0.00 0.00 0.00 3.66
2065 6177 6.825721 CCTAGAAAGAGTTAATTCCATGCTGT 59.174 38.462 0.00 0.00 0.00 4.40
2066 6178 6.261826 CCCTAGAAAGAGTTAATTCCATGCTG 59.738 42.308 0.00 0.00 0.00 4.41
2067 6179 6.158695 TCCCTAGAAAGAGTTAATTCCATGCT 59.841 38.462 0.00 0.00 0.00 3.79
2068 6180 6.357367 TCCCTAGAAAGAGTTAATTCCATGC 58.643 40.000 0.00 0.00 0.00 4.06
2119 6231 0.321346 GGTGACTGCCCCAAAAATGG 59.679 55.000 0.00 0.00 0.00 3.16
2123 6235 1.484240 CAAAAGGTGACTGCCCCAAAA 59.516 47.619 0.00 0.00 42.68 2.44
2183 6581 4.118480 GGCGATGGCGTCATTACA 57.882 55.556 2.92 0.00 42.82 2.41
2191 6589 1.069765 ATTAGGTCTGGCGATGGCG 59.930 57.895 0.00 0.00 41.24 5.69
2192 6590 1.510480 GCATTAGGTCTGGCGATGGC 61.510 60.000 0.00 0.00 38.90 4.40
2194 6592 1.534163 CATGCATTAGGTCTGGCGATG 59.466 52.381 0.00 0.00 0.00 3.84
2195 6593 1.888215 CATGCATTAGGTCTGGCGAT 58.112 50.000 0.00 0.00 0.00 4.58
2196 6594 0.815213 GCATGCATTAGGTCTGGCGA 60.815 55.000 14.21 0.00 0.00 5.54
2198 6596 1.066605 CTTGCATGCATTAGGTCTGGC 59.933 52.381 23.37 0.00 0.00 4.85
2201 6875 2.648059 GTCCTTGCATGCATTAGGTCT 58.352 47.619 29.19 0.00 0.00 3.85
2204 6878 1.331756 GTCGTCCTTGCATGCATTAGG 59.668 52.381 26.31 26.31 0.00 2.69
2253 6927 7.749666 AGTGGATGTATGAATTGCCTATTAGT 58.250 34.615 0.00 0.00 0.00 2.24
2265 6939 8.862325 AGACAACAATTAAGTGGATGTATGAA 57.138 30.769 14.03 0.00 0.00 2.57
2268 6942 9.383519 CTGTAGACAACAATTAAGTGGATGTAT 57.616 33.333 14.03 13.60 37.74 2.29
2285 6959 0.541392 ATCCATGCGCCTGTAGACAA 59.459 50.000 11.83 0.00 0.00 3.18
2316 6990 9.198837 TGTAATATACAGTTACATATGGCGTTG 57.801 33.333 7.80 3.15 37.19 4.10
2417 7091 2.411031 CGACTGCGCGTTTGATAGTTTT 60.411 45.455 8.43 0.00 0.00 2.43
2472 7148 9.965824 AATCAGTCAGAAAAACGTTTAAATCAT 57.034 25.926 15.03 0.00 0.00 2.45
2473 7149 9.232082 CAATCAGTCAGAAAAACGTTTAAATCA 57.768 29.630 15.03 0.00 0.00 2.57
2481 7157 2.293399 GCCCAATCAGTCAGAAAAACGT 59.707 45.455 0.00 0.00 0.00 3.99
2539 7215 2.742372 CGGCCGTTAACTGCTGCT 60.742 61.111 19.50 0.00 0.00 4.24
2638 7317 0.039978 CGCTATCGCACCTAGGTCAG 60.040 60.000 12.84 9.21 35.30 3.51
2726 7411 4.133078 GCCATTTCTCTACCTCTGAATGG 58.867 47.826 8.21 8.21 0.00 3.16
2738 7423 3.796764 GCTGCCTAGCCATTTCTCT 57.203 52.632 0.00 0.00 44.33 3.10
2787 7472 3.458163 GACCTCGGGCGGTGATGA 61.458 66.667 0.00 0.00 37.42 2.92
2811 7496 3.462483 TGTTGCACGGTATATCGGATT 57.538 42.857 10.69 0.00 0.00 3.01
2828 7528 0.895100 ACATCGCCACTGCCATTGTT 60.895 50.000 0.00 0.00 0.00 2.83
2829 7529 1.303561 ACATCGCCACTGCCATTGT 60.304 52.632 0.00 0.00 0.00 2.71
2878 7578 2.962786 CAAACGACGACGCCCACA 60.963 61.111 7.30 0.00 43.96 4.17


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

AutoCloner maintained by Alex Coulton.