Multiple sequence alignment - TraesCS5B01G045800

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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 TraesCS5B01G045800 chr5B 100.000 3480 0 0 1 3480 51063368 51059889 0.000000e+00 6427.0
1 TraesCS5B01G045800 chr5B 95.802 1453 50 3 886 2331 50529911 50531359 0.000000e+00 2335.0
2 TraesCS5B01G045800 chr5B 84.165 1263 172 18 1054 2306 48981044 48979800 0.000000e+00 1199.0
3 TraesCS5B01G045800 chr5B 83.525 1220 168 18 1104 2303 48931306 48930100 0.000000e+00 1109.0
4 TraesCS5B01G045800 chr5B 82.324 1239 158 28 1095 2311 50226679 50227878 0.000000e+00 1018.0
5 TraesCS5B01G045800 chr5B 92.455 729 15 8 2756 3451 50531944 50532665 0.000000e+00 1005.0
6 TraesCS5B01G045800 chr5B 93.803 355 14 6 2405 2752 50531487 50531840 8.560000e-146 527.0
7 TraesCS5B01G045800 chr5B 88.498 313 30 2 2191 2503 50805539 50805845 1.180000e-99 374.0
8 TraesCS5B01G045800 chr5B 88.312 231 25 2 4 234 51147740 51147512 3.420000e-70 276.0
9 TraesCS5B01G045800 chr5B 86.486 148 17 3 2572 2716 50853295 50853442 3.600000e-35 159.0
10 TraesCS5B01G045800 chr5B 92.000 100 8 0 2407 2506 50805486 50805387 1.300000e-29 141.0
11 TraesCS5B01G045800 chr5B 90.909 99 7 2 303 400 638930519 638930422 7.840000e-27 132.0
12 TraesCS5B01G045800 chr5D 89.571 1889 127 37 883 2716 48315253 48313380 0.000000e+00 2333.0
13 TraesCS5B01G045800 chr5D 83.714 1271 169 27 1054 2306 46847654 46846404 0.000000e+00 1166.0
14 TraesCS5B01G045800 chr5D 83.266 1231 152 26 1095 2311 47280669 47281859 0.000000e+00 1083.0
15 TraesCS5B01G045800 chr5D 83.156 1223 163 29 1105 2303 46732753 46731550 0.000000e+00 1077.0
16 TraesCS5B01G045800 chr5D 82.405 682 58 25 1871 2506 48033611 48034276 3.950000e-149 538.0
17 TraesCS5B01G045800 chr5D 93.294 343 23 0 1536 1878 48032280 48032622 1.110000e-139 507.0
18 TraesCS5B01G045800 chr5D 81.981 616 70 20 1913 2503 47916498 47917097 5.220000e-133 484.0
19 TraesCS5B01G045800 chr5D 86.318 402 42 7 885 1284 48021440 48021830 3.210000e-115 425.0
20 TraesCS5B01G045800 chr5D 86.726 226 28 2 1 226 48020726 48020949 2.070000e-62 250.0
21 TraesCS5B01G045800 chr5D 82.213 253 21 18 3026 3271 48034982 48035217 2.740000e-46 196.0
22 TraesCS5B01G045800 chr5D 80.000 240 25 13 596 812 48315491 48315252 4.650000e-34 156.0
23 TraesCS5B01G045800 chr5D 94.444 90 5 0 302 391 293405673 293405762 4.680000e-29 139.0
24 TraesCS5B01G045800 chr5D 80.412 97 14 3 498 589 366913994 366914090 6.230000e-08 69.4
25 TraesCS5B01G045800 chr5A 90.293 1329 76 17 1180 2471 38055694 38054382 0.000000e+00 1690.0
26 TraesCS5B01G045800 chr5A 84.444 900 122 11 1409 2306 37780630 37779747 0.000000e+00 870.0
27 TraesCS5B01G045800 chr5A 85.586 222 16 12 3026 3242 37997350 37997560 5.850000e-53 219.0
28 TraesCS5B01G045800 chr5A 84.076 157 7 13 936 1081 37997061 37997210 6.060000e-28 135.0
29 TraesCS5B01G045800 chr5A 82.143 112 8 3 600 699 37996936 37997047 6.190000e-13 86.1
30 TraesCS5B01G045800 chr5A 100.000 29 0 0 1077 1105 37997192 37997220 2.000000e-03 54.7
31 TraesCS5B01G045800 chr4A 95.556 90 4 0 306 395 488112417 488112506 1.010000e-30 145.0
32 TraesCS5B01G045800 chr4A 93.548 93 6 0 307 399 537597921 537598013 4.680000e-29 139.0
33 TraesCS5B01G045800 chr7D 95.402 87 4 0 307 393 343752012 343751926 4.680000e-29 139.0
34 TraesCS5B01G045800 chr1A 92.632 95 7 0 304 398 115948014 115948108 1.680000e-28 137.0
35 TraesCS5B01G045800 chr1A 90.909 55 5 0 538 592 377221553 377221499 1.340000e-09 75.0
36 TraesCS5B01G045800 chr2A 94.318 88 5 0 304 391 685469228 685469141 6.060000e-28 135.0
37 TraesCS5B01G045800 chr7B 91.000 100 8 1 306 405 199270365 199270463 2.180000e-27 134.0
38 TraesCS5B01G045800 chr7B 77.093 227 31 12 2586 2799 13705423 13705205 1.020000e-20 111.0
39 TraesCS5B01G045800 chr6B 94.253 87 5 0 306 392 688544516 688544430 2.180000e-27 134.0
40 TraesCS5B01G045800 chr6B 75.113 221 36 8 386 589 63401621 63401839 6.190000e-13 86.1
41 TraesCS5B01G045800 chr3B 75.122 205 34 16 2756 2954 45154037 45153844 2.880000e-11 80.5
42 TraesCS5B01G045800 chr1B 89.655 58 3 2 1024 1081 523237228 523237282 1.730000e-08 71.3
43 TraesCS5B01G045800 chr1B 89.091 55 3 1 1027 1081 523230239 523230290 8.060000e-07 65.8


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 TraesCS5B01G045800 chr5B 51059889 51063368 3479 True 6427.000000 6427 100.000000 1 3480 1 chr5B.!!$R4 3479
1 TraesCS5B01G045800 chr5B 50529911 50532665 2754 False 1289.000000 2335 94.020000 886 3451 3 chr5B.!!$F4 2565
2 TraesCS5B01G045800 chr5B 48979800 48981044 1244 True 1199.000000 1199 84.165000 1054 2306 1 chr5B.!!$R2 1252
3 TraesCS5B01G045800 chr5B 48930100 48931306 1206 True 1109.000000 1109 83.525000 1104 2303 1 chr5B.!!$R1 1199
4 TraesCS5B01G045800 chr5B 50226679 50227878 1199 False 1018.000000 1018 82.324000 1095 2311 1 chr5B.!!$F1 1216
5 TraesCS5B01G045800 chr5D 48313380 48315491 2111 True 1244.500000 2333 84.785500 596 2716 2 chr5D.!!$R3 2120
6 TraesCS5B01G045800 chr5D 46846404 46847654 1250 True 1166.000000 1166 83.714000 1054 2306 1 chr5D.!!$R2 1252
7 TraesCS5B01G045800 chr5D 47280669 47281859 1190 False 1083.000000 1083 83.266000 1095 2311 1 chr5D.!!$F1 1216
8 TraesCS5B01G045800 chr5D 46731550 46732753 1203 True 1077.000000 1077 83.156000 1105 2303 1 chr5D.!!$R1 1198
9 TraesCS5B01G045800 chr5D 47916498 47917097 599 False 484.000000 484 81.981000 1913 2503 1 chr5D.!!$F2 590
10 TraesCS5B01G045800 chr5D 48032280 48035217 2937 False 413.666667 538 85.970667 1536 3271 3 chr5D.!!$F6 1735
11 TraesCS5B01G045800 chr5D 48020726 48021830 1104 False 337.500000 425 86.522000 1 1284 2 chr5D.!!$F5 1283
12 TraesCS5B01G045800 chr5A 38054382 38055694 1312 True 1690.000000 1690 90.293000 1180 2471 1 chr5A.!!$R2 1291
13 TraesCS5B01G045800 chr5A 37779747 37780630 883 True 870.000000 870 84.444000 1409 2306 1 chr5A.!!$R1 897

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
170 171 0.106708 GACATATGGCGAGGCTCCAA 59.893 55.0 9.32 0.0 37.13 3.53 F
275 276 0.173255 CCATGGCGTGTTTGATTCCC 59.827 55.0 0.00 0.0 0.00 3.97 F
740 789 0.462047 ACGATTCTCCGCATGTTCCC 60.462 55.0 0.00 0.0 0.00 3.97 F
746 795 0.811281 CTCCGCATGTTCCCCTTTTC 59.189 55.0 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1300 1390 2.031163 GACCTTGCTGCTGTCCGT 59.969 61.111 0.0 0.0 0.00 4.69 R
2150 3273 3.758023 CCTTGATGTAAATGACACTGGCA 59.242 43.478 0.0 0.0 42.17 4.92 R
2414 3601 2.548057 ACAGCGTCAATTCGACACAAAT 59.452 40.909 8.2 0.0 45.70 2.32 R
2682 3972 4.141711 GCTAGAATCATACCCAGTCACCAA 60.142 45.833 0.0 0.0 0.00 3.67 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
25 26 6.018507 GCCAAGATTCATGCAATTAATCCAAC 60.019 38.462 12.73 1.70 37.59 3.77
26 27 6.199531 CCAAGATTCATGCAATTAATCCAACG 59.800 38.462 12.73 0.00 37.59 4.10
34 35 3.181500 GCAATTAATCCAACGGTCCACTC 60.181 47.826 0.00 0.00 0.00 3.51
36 37 1.548081 TAATCCAACGGTCCACTCGA 58.452 50.000 0.00 0.00 0.00 4.04
38 39 1.183030 ATCCAACGGTCCACTCGACA 61.183 55.000 0.00 0.00 43.95 4.35
40 41 0.320421 CCAACGGTCCACTCGACATT 60.320 55.000 0.00 0.00 43.95 2.71
41 42 1.508632 CAACGGTCCACTCGACATTT 58.491 50.000 0.00 0.00 43.95 2.32
46 47 1.079503 GTCCACTCGACATTTGCTCC 58.920 55.000 0.00 0.00 41.54 4.70
52 53 4.549458 CACTCGACATTTGCTCCAAAATT 58.451 39.130 0.00 0.00 36.90 1.82
58 59 5.294734 ACATTTGCTCCAAAATTGTTCCT 57.705 34.783 0.00 0.00 36.90 3.36
63 64 3.826157 TGCTCCAAAATTGTTCCTACCAG 59.174 43.478 0.00 0.00 0.00 4.00
120 121 8.665643 TGATCTTGATGCAAATTTCTGTTTTT 57.334 26.923 0.00 0.00 0.00 1.94
121 122 8.552865 TGATCTTGATGCAAATTTCTGTTTTTG 58.447 29.630 0.00 0.00 36.21 2.44
122 123 8.665643 ATCTTGATGCAAATTTCTGTTTTTGA 57.334 26.923 0.00 0.00 35.34 2.69
131 132 9.213819 GCAAATTTCTGTTTTTGAGAAATGTTC 57.786 29.630 8.17 0.00 45.35 3.18
134 135 7.504922 TTTCTGTTTTTGAGAAATGTTCGTG 57.495 32.000 0.00 0.00 35.07 4.35
168 169 4.683432 GACATATGGCGAGGCTCC 57.317 61.111 9.32 1.49 0.00 4.70
170 171 0.106708 GACATATGGCGAGGCTCCAA 59.893 55.000 9.32 0.00 37.13 3.53
213 214 9.738832 CAAAATGTGATGATGCTAAATGTATGA 57.261 29.630 0.00 0.00 0.00 2.15
214 215 9.740239 AAAATGTGATGATGCTAAATGTATGAC 57.260 29.630 0.00 0.00 0.00 3.06
217 218 6.018832 TGTGATGATGCTAAATGTATGACACG 60.019 38.462 0.00 0.00 0.00 4.49
220 221 4.808895 TGATGCTAAATGTATGACACGGTC 59.191 41.667 0.00 0.00 0.00 4.79
226 227 6.037172 GCTAAATGTATGACACGGTCAGAATT 59.963 38.462 11.50 8.44 46.04 2.17
227 228 6.817765 AAATGTATGACACGGTCAGAATTT 57.182 33.333 11.50 12.33 46.04 1.82
228 229 6.817765 AATGTATGACACGGTCAGAATTTT 57.182 33.333 11.50 1.58 46.04 1.82
229 230 5.605564 TGTATGACACGGTCAGAATTTTG 57.394 39.130 11.50 0.00 46.04 2.44
230 231 4.454161 TGTATGACACGGTCAGAATTTTGG 59.546 41.667 11.50 0.00 46.04 3.28
231 232 1.606668 TGACACGGTCAGAATTTTGGC 59.393 47.619 3.02 0.00 37.67 4.52
232 233 1.606668 GACACGGTCAGAATTTTGGCA 59.393 47.619 2.74 0.00 32.09 4.92
233 234 2.228822 GACACGGTCAGAATTTTGGCAT 59.771 45.455 2.74 0.00 32.09 4.40
234 235 2.627699 ACACGGTCAGAATTTTGGCATT 59.372 40.909 2.74 0.00 0.00 3.56
235 236 2.988493 CACGGTCAGAATTTTGGCATTG 59.012 45.455 2.74 0.00 0.00 2.82
236 237 2.890311 ACGGTCAGAATTTTGGCATTGA 59.110 40.909 2.74 0.00 0.00 2.57
237 238 3.511146 ACGGTCAGAATTTTGGCATTGAT 59.489 39.130 2.74 0.00 0.00 2.57
238 239 4.704540 ACGGTCAGAATTTTGGCATTGATA 59.295 37.500 2.74 0.00 0.00 2.15
239 240 5.360714 ACGGTCAGAATTTTGGCATTGATAT 59.639 36.000 2.74 0.00 0.00 1.63
240 241 5.916883 CGGTCAGAATTTTGGCATTGATATC 59.083 40.000 2.74 0.00 0.00 1.63
241 242 6.459985 CGGTCAGAATTTTGGCATTGATATCA 60.460 38.462 0.00 0.00 0.00 2.15
242 243 7.267128 GGTCAGAATTTTGGCATTGATATCAA 58.733 34.615 20.07 20.07 40.51 2.57
243 244 7.765360 GGTCAGAATTTTGGCATTGATATCAAA 59.235 33.333 21.50 4.31 39.55 2.69
244 245 9.321562 GTCAGAATTTTGGCATTGATATCAAAT 57.678 29.630 21.50 6.49 39.55 2.32
245 246 9.320352 TCAGAATTTTGGCATTGATATCAAATG 57.680 29.630 21.50 18.71 39.55 2.32
246 247 9.320352 CAGAATTTTGGCATTGATATCAAATGA 57.680 29.630 21.50 0.00 39.55 2.57
247 248 9.893634 AGAATTTTGGCATTGATATCAAATGAA 57.106 25.926 21.50 9.66 39.55 2.57
250 251 8.843885 TTTTGGCATTGATATCAAATGAAACA 57.156 26.923 21.50 14.98 39.55 2.83
251 252 9.451002 TTTTGGCATTGATATCAAATGAAACAT 57.549 25.926 21.50 0.24 39.55 2.71
252 253 9.451002 TTTGGCATTGATATCAAATGAAACATT 57.549 25.926 21.50 0.00 39.55 2.71
253 254 9.451002 TTGGCATTGATATCAAATGAAACATTT 57.549 25.926 21.50 4.22 39.55 2.32
254 255 9.100554 TGGCATTGATATCAAATGAAACATTTC 57.899 29.630 21.50 0.00 39.55 2.17
255 256 9.321562 GGCATTGATATCAAATGAAACATTTCT 57.678 29.630 21.50 0.00 39.55 2.52
261 262 9.472361 GATATCAAATGAAACATTTCTCCATGG 57.528 33.333 4.97 4.97 38.02 3.66
262 263 5.481105 TCAAATGAAACATTTCTCCATGGC 58.519 37.500 6.96 0.00 38.02 4.40
263 264 3.788333 ATGAAACATTTCTCCATGGCG 57.212 42.857 6.96 0.00 38.02 5.69
264 265 2.513753 TGAAACATTTCTCCATGGCGT 58.486 42.857 6.96 0.00 38.02 5.68
265 266 2.228582 TGAAACATTTCTCCATGGCGTG 59.771 45.455 6.96 0.00 38.02 5.34
266 267 1.909700 AACATTTCTCCATGGCGTGT 58.090 45.000 6.96 0.00 0.00 4.49
267 268 1.909700 ACATTTCTCCATGGCGTGTT 58.090 45.000 6.96 0.00 0.00 3.32
268 269 2.238521 ACATTTCTCCATGGCGTGTTT 58.761 42.857 6.96 0.00 0.00 2.83
269 270 2.030007 ACATTTCTCCATGGCGTGTTTG 60.030 45.455 6.96 2.97 0.00 2.93
270 271 1.974265 TTTCTCCATGGCGTGTTTGA 58.026 45.000 6.96 0.00 0.00 2.69
271 272 2.198827 TTCTCCATGGCGTGTTTGAT 57.801 45.000 6.96 0.00 0.00 2.57
272 273 2.198827 TCTCCATGGCGTGTTTGATT 57.801 45.000 6.96 0.00 0.00 2.57
273 274 2.083774 TCTCCATGGCGTGTTTGATTC 58.916 47.619 6.96 0.00 0.00 2.52
274 275 1.133025 CTCCATGGCGTGTTTGATTCC 59.867 52.381 6.96 0.00 0.00 3.01
275 276 0.173255 CCATGGCGTGTTTGATTCCC 59.827 55.000 0.00 0.00 0.00 3.97
276 277 0.887247 CATGGCGTGTTTGATTCCCA 59.113 50.000 0.00 0.00 0.00 4.37
277 278 1.271934 CATGGCGTGTTTGATTCCCAA 59.728 47.619 0.00 0.00 0.00 4.12
278 279 1.626686 TGGCGTGTTTGATTCCCAAT 58.373 45.000 0.00 0.00 34.23 3.16
279 280 1.967066 TGGCGTGTTTGATTCCCAATT 59.033 42.857 0.00 0.00 34.23 2.32
280 281 2.366916 TGGCGTGTTTGATTCCCAATTT 59.633 40.909 0.00 0.00 34.23 1.82
287 288 6.571344 CGTGTTTGATTCCCAATTTATGTGGA 60.571 38.462 0.00 0.00 38.54 4.02
289 290 5.596836 TTGATTCCCAATTTATGTGGAGC 57.403 39.130 0.00 0.00 38.54 4.70
298 299 1.288508 TTATGTGGAGCAGGCCCCAT 61.289 55.000 0.00 3.70 34.58 4.00
299 300 1.288508 TATGTGGAGCAGGCCCCATT 61.289 55.000 0.00 0.00 34.58 3.16
306 307 1.202769 AGCAGGCCCCATTGCAAAAT 61.203 50.000 16.24 0.00 42.67 1.82
307 308 0.540923 GCAGGCCCCATTGCAAAATA 59.459 50.000 1.71 0.00 40.02 1.40
308 309 1.743431 GCAGGCCCCATTGCAAAATAC 60.743 52.381 1.71 0.00 40.02 1.89
309 310 1.832998 CAGGCCCCATTGCAAAATACT 59.167 47.619 1.71 0.00 0.00 2.12
310 311 3.030291 CAGGCCCCATTGCAAAATACTA 58.970 45.455 1.71 0.00 0.00 1.82
311 312 3.031013 AGGCCCCATTGCAAAATACTAC 58.969 45.455 1.71 0.00 0.00 2.73
312 313 2.102420 GGCCCCATTGCAAAATACTACC 59.898 50.000 1.71 0.00 0.00 3.18
313 314 3.031013 GCCCCATTGCAAAATACTACCT 58.969 45.455 1.71 0.00 0.00 3.08
314 315 3.068165 GCCCCATTGCAAAATACTACCTC 59.932 47.826 1.71 0.00 0.00 3.85
315 316 3.636764 CCCCATTGCAAAATACTACCTCC 59.363 47.826 1.71 0.00 0.00 4.30
316 317 4.277476 CCCATTGCAAAATACTACCTCCA 58.723 43.478 1.71 0.00 0.00 3.86
317 318 4.895297 CCCATTGCAAAATACTACCTCCAT 59.105 41.667 1.71 0.00 0.00 3.41
318 319 6.068010 CCCATTGCAAAATACTACCTCCATA 58.932 40.000 1.71 0.00 0.00 2.74
319 320 6.549364 CCCATTGCAAAATACTACCTCCATAA 59.451 38.462 1.71 0.00 0.00 1.90
320 321 7.069331 CCCATTGCAAAATACTACCTCCATAAA 59.931 37.037 1.71 0.00 0.00 1.40
321 322 7.920682 CCATTGCAAAATACTACCTCCATAAAC 59.079 37.037 1.71 0.00 0.00 2.01
322 323 8.686334 CATTGCAAAATACTACCTCCATAAACT 58.314 33.333 1.71 0.00 0.00 2.66
323 324 9.914834 ATTGCAAAATACTACCTCCATAAACTA 57.085 29.630 1.71 0.00 0.00 2.24
324 325 9.742144 TTGCAAAATACTACCTCCATAAACTAA 57.258 29.630 0.00 0.00 0.00 2.24
325 326 9.914834 TGCAAAATACTACCTCCATAAACTAAT 57.085 29.630 0.00 0.00 0.00 1.73
406 407 9.545105 CAGAGAGAGTAGAATGCAATAGAAAAT 57.455 33.333 0.00 0.00 0.00 1.82
426 427 8.084073 AGAAAATTATCACATTTATGCCCATCG 58.916 33.333 0.00 0.00 0.00 3.84
428 429 7.994425 AATTATCACATTTATGCCCATCGTA 57.006 32.000 0.00 0.00 0.00 3.43
443 444 3.373748 CCATCGTACATTGCTTGTGCTAA 59.626 43.478 3.49 0.00 38.66 3.09
448 449 5.023920 CGTACATTGCTTGTGCTAATTGAG 58.976 41.667 3.49 0.00 38.66 3.02
457 458 5.122869 GCTTGTGCTAATTGAGTGAGATTCA 59.877 40.000 0.00 0.00 36.03 2.57
459 460 9.911857 GCTTGTGCTAATTGAGTGAGATTCACG 62.912 44.444 3.77 0.00 43.13 4.35
490 491 8.925161 TTTTATTGCATAGGTTGTTTAGCATC 57.075 30.769 0.00 0.00 0.00 3.91
491 492 7.637631 TTATTGCATAGGTTGTTTAGCATCA 57.362 32.000 0.00 0.00 0.00 3.07
493 494 3.947196 TGCATAGGTTGTTTAGCATCAGG 59.053 43.478 0.00 0.00 0.00 3.86
499 500 0.676466 TGTTTAGCATCAGGGCACGG 60.676 55.000 0.00 0.00 35.83 4.94
508 520 2.035626 AGGGCACGGTTCCCATTG 59.964 61.111 18.25 0.00 46.36 2.82
514 526 1.871822 GCACGGTTCCCATTGTTTTGG 60.872 52.381 0.00 0.00 36.46 3.28
515 527 1.683917 CACGGTTCCCATTGTTTTGGA 59.316 47.619 0.00 0.00 39.25 3.53
516 528 2.298729 CACGGTTCCCATTGTTTTGGAT 59.701 45.455 0.00 0.00 39.25 3.41
519 531 5.358442 CACGGTTCCCATTGTTTTGGATATA 59.642 40.000 0.00 0.00 39.25 0.86
520 532 5.952947 ACGGTTCCCATTGTTTTGGATATAA 59.047 36.000 0.00 0.00 39.25 0.98
521 533 6.127563 ACGGTTCCCATTGTTTTGGATATAAC 60.128 38.462 0.00 0.00 39.25 1.89
522 534 6.127591 CGGTTCCCATTGTTTTGGATATAACA 60.128 38.462 0.00 0.00 39.25 2.41
525 537 8.962679 GTTCCCATTGTTTTGGATATAACACTA 58.037 33.333 0.00 0.00 39.25 2.74
526 538 8.746052 TCCCATTGTTTTGGATATAACACTAG 57.254 34.615 0.00 0.00 39.25 2.57
527 539 8.333235 TCCCATTGTTTTGGATATAACACTAGT 58.667 33.333 0.00 0.00 39.25 2.57
529 541 9.396022 CCATTGTTTTGGATATAACACTAGTCT 57.604 33.333 0.00 0.00 39.25 3.24
568 580 4.209080 GTCAAAAGCCGAAACTCAATTTGG 59.791 41.667 0.00 0.00 0.00 3.28
588 600 1.994779 GCAATGCTATTTGGCACACAC 59.005 47.619 0.00 0.00 45.36 3.82
589 601 2.609350 CAATGCTATTTGGCACACACC 58.391 47.619 0.00 0.00 45.36 4.16
590 602 1.921982 ATGCTATTTGGCACACACCA 58.078 45.000 0.00 0.00 45.36 4.17
594 626 3.380954 TGCTATTTGGCACACACCATATG 59.619 43.478 0.00 0.00 40.13 1.78
694 737 1.065199 ACCCATGCCTATGTGACACTG 60.065 52.381 7.20 0.00 32.21 3.66
700 743 2.015588 GCCTATGTGACACTGCTGCAT 61.016 52.381 1.31 0.00 0.00 3.96
701 744 1.669265 CCTATGTGACACTGCTGCATG 59.331 52.381 1.31 6.66 0.00 4.06
702 745 2.624636 CTATGTGACACTGCTGCATGA 58.375 47.619 1.31 0.00 0.00 3.07
703 746 2.124277 ATGTGACACTGCTGCATGAT 57.876 45.000 1.31 0.00 0.00 2.45
704 747 1.161843 TGTGACACTGCTGCATGATG 58.838 50.000 1.31 4.96 0.00 3.07
705 748 1.270947 TGTGACACTGCTGCATGATGA 60.271 47.619 1.31 0.00 0.00 2.92
720 769 1.002134 ATGACGGGCCCACAAGAAG 60.002 57.895 24.92 5.71 0.00 2.85
730 779 2.622436 CCCACAAGAAGACGATTCTCC 58.378 52.381 7.85 0.00 0.00 3.71
740 789 0.462047 ACGATTCTCCGCATGTTCCC 60.462 55.000 0.00 0.00 0.00 3.97
746 795 0.811281 CTCCGCATGTTCCCCTTTTC 59.189 55.000 0.00 0.00 0.00 2.29
757 806 5.313712 TGTTCCCCTTTTCTATTGACAGTC 58.686 41.667 0.00 0.00 0.00 3.51
761 810 6.369629 TCCCCTTTTCTATTGACAGTCAAAA 58.630 36.000 19.92 7.39 40.12 2.44
762 811 7.010160 TCCCCTTTTCTATTGACAGTCAAAAT 58.990 34.615 19.92 7.32 40.12 1.82
777 835 7.138736 ACAGTCAAAATATCTTCACAAAACCG 58.861 34.615 0.00 0.00 0.00 4.44
786 844 3.882888 TCTTCACAAAACCGCTCTGAAAT 59.117 39.130 0.00 0.00 0.00 2.17
800 863 6.146184 CCGCTCTGAAATTATATGTACCACAG 59.854 42.308 0.00 0.00 0.00 3.66
813 876 6.726490 ATGTACCACAGTTCCGATATTACT 57.274 37.500 0.00 0.00 0.00 2.24
814 877 6.140303 TGTACCACAGTTCCGATATTACTC 57.860 41.667 0.00 0.00 0.00 2.59
815 878 5.889853 TGTACCACAGTTCCGATATTACTCT 59.110 40.000 0.00 0.00 0.00 3.24
816 879 5.517322 ACCACAGTTCCGATATTACTCTC 57.483 43.478 0.00 0.00 0.00 3.20
817 880 5.202004 ACCACAGTTCCGATATTACTCTCT 58.798 41.667 0.00 0.00 0.00 3.10
818 881 5.299782 ACCACAGTTCCGATATTACTCTCTC 59.700 44.000 0.00 0.00 0.00 3.20
819 882 5.278561 CCACAGTTCCGATATTACTCTCTCC 60.279 48.000 0.00 0.00 0.00 3.71
820 883 4.515944 ACAGTTCCGATATTACTCTCTCCG 59.484 45.833 0.00 0.00 0.00 4.63
821 884 4.515944 CAGTTCCGATATTACTCTCTCCGT 59.484 45.833 0.00 0.00 0.00 4.69
822 885 5.008811 CAGTTCCGATATTACTCTCTCCGTT 59.991 44.000 0.00 0.00 0.00 4.44
823 886 5.239087 AGTTCCGATATTACTCTCTCCGTTC 59.761 44.000 0.00 0.00 0.00 3.95
824 887 4.070716 TCCGATATTACTCTCTCCGTTCC 58.929 47.826 0.00 0.00 0.00 3.62
825 888 3.120269 CCGATATTACTCTCTCCGTTCCG 60.120 52.174 0.00 0.00 0.00 4.30
826 889 3.744942 CGATATTACTCTCTCCGTTCCGA 59.255 47.826 0.00 0.00 0.00 4.55
827 890 4.212847 CGATATTACTCTCTCCGTTCCGAA 59.787 45.833 0.00 0.00 0.00 4.30
828 891 5.106634 CGATATTACTCTCTCCGTTCCGAAT 60.107 44.000 0.00 0.00 0.00 3.34
829 892 6.568081 CGATATTACTCTCTCCGTTCCGAATT 60.568 42.308 0.00 0.00 0.00 2.17
830 893 7.360691 CGATATTACTCTCTCCGTTCCGAATTA 60.361 40.741 0.00 0.00 0.00 1.40
831 894 3.779271 ACTCTCTCCGTTCCGAATTAC 57.221 47.619 0.00 0.00 0.00 1.89
832 895 3.354467 ACTCTCTCCGTTCCGAATTACT 58.646 45.455 0.00 0.00 0.00 2.24
833 896 4.521146 ACTCTCTCCGTTCCGAATTACTA 58.479 43.478 0.00 0.00 0.00 1.82
834 897 4.335037 ACTCTCTCCGTTCCGAATTACTAC 59.665 45.833 0.00 0.00 0.00 2.73
835 898 4.521146 TCTCTCCGTTCCGAATTACTACT 58.479 43.478 0.00 0.00 0.00 2.57
836 899 4.946157 TCTCTCCGTTCCGAATTACTACTT 59.054 41.667 0.00 0.00 0.00 2.24
837 900 6.115446 TCTCTCCGTTCCGAATTACTACTTA 58.885 40.000 0.00 0.00 0.00 2.24
838 901 6.769822 TCTCTCCGTTCCGAATTACTACTTAT 59.230 38.462 0.00 0.00 0.00 1.73
839 902 6.963796 TCTCCGTTCCGAATTACTACTTATC 58.036 40.000 0.00 0.00 0.00 1.75
840 903 6.769822 TCTCCGTTCCGAATTACTACTTATCT 59.230 38.462 0.00 0.00 0.00 1.98
841 904 7.284034 TCTCCGTTCCGAATTACTACTTATCTT 59.716 37.037 0.00 0.00 0.00 2.40
842 905 7.198390 TCCGTTCCGAATTACTACTTATCTTG 58.802 38.462 0.00 0.00 0.00 3.02
843 906 7.067372 TCCGTTCCGAATTACTACTTATCTTGA 59.933 37.037 0.00 0.00 0.00 3.02
844 907 7.703621 CCGTTCCGAATTACTACTTATCTTGAA 59.296 37.037 0.00 0.00 0.00 2.69
845 908 9.245962 CGTTCCGAATTACTACTTATCTTGAAT 57.754 33.333 0.00 0.00 0.00 2.57
871 934 8.762481 TTGTCTAGATACATATGTACCACAGT 57.238 34.615 17.69 0.83 32.72 3.55
872 935 8.392372 TGTCTAGATACATATGTACCACAGTC 57.608 38.462 17.69 10.23 32.72 3.51
873 936 8.218488 TGTCTAGATACATATGTACCACAGTCT 58.782 37.037 17.69 16.26 32.72 3.24
874 937 9.722184 GTCTAGATACATATGTACCACAGTCTA 57.278 37.037 17.69 16.48 32.72 2.59
878 941 9.588096 AGATACATATGTACCACAGTCTATTGA 57.412 33.333 17.69 0.00 32.72 2.57
879 942 9.627395 GATACATATGTACCACAGTCTATTGAC 57.373 37.037 17.69 0.00 37.10 3.18
880 943 7.418337 ACATATGTACCACAGTCTATTGACA 57.582 36.000 6.56 0.00 45.20 3.58
881 944 7.492524 ACATATGTACCACAGTCTATTGACAG 58.507 38.462 6.56 4.19 45.20 3.51
882 945 7.124298 ACATATGTACCACAGTCTATTGACAGT 59.876 37.037 6.56 4.84 45.20 3.55
883 946 8.630037 CATATGTACCACAGTCTATTGACAGTA 58.370 37.037 9.96 3.44 45.20 2.74
884 947 6.510879 TGTACCACAGTCTATTGACAGTAG 57.489 41.667 9.96 3.69 45.20 2.57
969 1032 1.227853 GGGAAGACTGCACACCGTT 60.228 57.895 0.00 0.00 0.00 4.44
970 1033 1.228657 GGGAAGACTGCACACCGTTC 61.229 60.000 0.00 0.00 0.00 3.95
982 1053 1.068127 ACACCGTTCACAGGACTACAC 59.932 52.381 0.00 0.00 0.00 2.90
1010 1081 2.315176 CCAAACATCCACCACTCCAAA 58.685 47.619 0.00 0.00 0.00 3.28
1751 1856 3.119096 GGAGACGGTTGCCTTCGC 61.119 66.667 0.00 0.00 0.00 4.70
2150 3273 1.228003 AGATCGCCGTCCTCTCGAT 60.228 57.895 0.00 0.00 44.44 3.59
2324 3456 1.071471 GGCAGCGGCAGGTATGTAT 59.929 57.895 11.88 0.00 43.71 2.29
2341 3489 5.568620 ATGTATTCACCTACCAATCTCCC 57.431 43.478 0.00 0.00 0.00 4.30
2345 3495 3.042059 TCACCTACCAATCTCCCTACC 57.958 52.381 0.00 0.00 0.00 3.18
2411 3598 8.038944 AGAAGATTTTGAATTGTTCATGGATGG 58.961 33.333 0.00 0.00 39.84 3.51
2414 3601 9.204337 AGATTTTGAATTGTTCATGGATGGATA 57.796 29.630 0.00 0.00 39.84 2.59
2682 3972 9.522804 GATGATCTGTTTAGTTTCGTCTAGAAT 57.477 33.333 0.00 0.00 38.86 2.40
2737 4028 7.630513 GCTTATGCATCTCTAGGTCTATTCTCC 60.631 44.444 0.19 0.00 39.41 3.71
2753 4044 9.988815 GTCTATTCTCCAATCTAATGCTTCTTA 57.011 33.333 0.00 0.00 0.00 2.10
2799 4191 4.334759 GTCATCCATTCACATTGTCAGGAG 59.665 45.833 0.00 0.00 0.00 3.69
2800 4192 3.354948 TCCATTCACATTGTCAGGAGG 57.645 47.619 0.00 0.00 0.00 4.30
2801 4193 2.912295 TCCATTCACATTGTCAGGAGGA 59.088 45.455 0.00 0.00 0.00 3.71
2860 4253 8.044060 TGATCGCTCTTGTCTTTTTATGAAAT 57.956 30.769 0.00 0.00 0.00 2.17
2974 4497 9.143155 AGTAAACATAACTGACTTCCCATTTTT 57.857 29.630 0.00 0.00 0.00 1.94
3009 4532 0.304098 TGTGGTTACGCGGTTTTTCG 59.696 50.000 12.47 0.00 0.00 3.46
3023 4546 4.149747 CGGTTTTTCGATTTTCCACATTGG 59.850 41.667 0.00 0.00 39.43 3.16
3066 4589 4.809426 GGTAGTCAAACGTCCCTGATATTG 59.191 45.833 0.00 0.00 0.00 1.90
3264 4791 5.457140 CGCTCAGATTAGGAGATTCAGTAC 58.543 45.833 0.00 0.00 34.24 2.73
3313 4841 2.550606 CTGGCGGCAGTTTGTTAAAGTA 59.449 45.455 29.42 0.00 0.00 2.24
3337 4865 6.083487 TCATTTTGGAGGAAATCTGGAGAT 57.917 37.500 0.00 0.00 36.07 2.75
3451 4995 6.264518 AGACATGATTAAATCAGCATGCATGA 59.735 34.615 30.64 19.63 43.53 3.07
3452 4996 6.993079 ACATGATTAAATCAGCATGCATGAT 58.007 32.000 30.64 22.50 43.53 2.45
3453 4997 7.441836 ACATGATTAAATCAGCATGCATGATT 58.558 30.769 30.64 26.27 46.69 2.57
3454 4998 8.581578 ACATGATTAAATCAGCATGCATGATTA 58.418 29.630 29.28 16.57 44.57 1.75
3455 4999 9.418045 CATGATTAAATCAGCATGCATGATTAA 57.582 29.630 29.28 24.25 44.57 1.40
3456 5000 9.990360 ATGATTAAATCAGCATGCATGATTAAA 57.010 25.926 29.28 22.20 44.57 1.52
3457 5001 9.471084 TGATTAAATCAGCATGCATGATTAAAG 57.529 29.630 29.28 12.19 44.57 1.85
3458 5002 9.687210 GATTAAATCAGCATGCATGATTAAAGA 57.313 29.630 29.28 17.29 44.57 2.52
3460 5004 9.872721 TTAAATCAGCATGCATGATTAAAGAAA 57.127 25.926 29.28 20.33 44.57 2.52
3461 5005 8.780846 AAATCAGCATGCATGATTAAAGAAAA 57.219 26.923 29.28 2.08 44.57 2.29
3462 5006 8.780846 AATCAGCATGCATGATTAAAGAAAAA 57.219 26.923 30.64 1.04 43.75 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.498481 TCGAGTGGACCGTTGGATTAAT 59.502 45.455 0.00 0.00 0.00 1.40
25 26 0.670546 AGCAAATGTCGAGTGGACCG 60.671 55.000 2.56 0.00 45.46 4.79
26 27 1.079503 GAGCAAATGTCGAGTGGACC 58.920 55.000 2.56 0.00 45.46 4.46
34 35 4.150451 GGAACAATTTTGGAGCAAATGTCG 59.850 41.667 0.00 0.00 33.19 4.35
36 37 5.294734 AGGAACAATTTTGGAGCAAATGT 57.705 34.783 0.00 0.00 33.19 2.71
38 39 5.306678 TGGTAGGAACAATTTTGGAGCAAAT 59.693 36.000 0.00 0.00 33.19 2.32
40 41 4.219115 TGGTAGGAACAATTTTGGAGCAA 58.781 39.130 0.00 0.00 0.00 3.91
41 42 3.826157 CTGGTAGGAACAATTTTGGAGCA 59.174 43.478 0.00 0.00 0.00 4.26
46 47 6.158598 CCAATGTCTGGTAGGAACAATTTTG 58.841 40.000 0.00 0.00 40.78 2.44
101 102 8.489990 TTTCTCAAAAACAGAAATTTGCATCA 57.510 26.923 0.00 0.00 35.40 3.07
103 104 8.895737 ACATTTCTCAAAAACAGAAATTTGCAT 58.104 25.926 0.00 0.00 44.67 3.96
110 111 7.061673 CACACGAACATTTCTCAAAAACAGAAA 59.938 33.333 0.00 0.00 42.63 2.52
114 115 4.560819 GCACACGAACATTTCTCAAAAACA 59.439 37.500 0.00 0.00 0.00 2.83
120 121 2.286950 GCTTGCACACGAACATTTCTCA 60.287 45.455 0.00 0.00 0.00 3.27
121 122 2.286950 TGCTTGCACACGAACATTTCTC 60.287 45.455 0.00 0.00 0.00 2.87
122 123 1.675483 TGCTTGCACACGAACATTTCT 59.325 42.857 0.00 0.00 0.00 2.52
131 132 2.177531 GCTCCATGCTTGCACACG 59.822 61.111 0.00 0.00 38.95 4.49
189 190 8.905850 TGTCATACATTTAGCATCATCACATTT 58.094 29.630 0.00 0.00 0.00 2.32
213 214 1.686355 TGCCAAAATTCTGACCGTGT 58.314 45.000 0.00 0.00 0.00 4.49
214 215 2.988493 CAATGCCAAAATTCTGACCGTG 59.012 45.455 0.00 0.00 0.00 4.94
217 218 6.808829 TGATATCAATGCCAAAATTCTGACC 58.191 36.000 1.98 0.00 0.00 4.02
220 221 9.320352 TCATTTGATATCAATGCCAAAATTCTG 57.680 29.630 18.61 0.00 35.55 3.02
226 227 9.451002 AATGTTTCATTTGATATCAATGCCAAA 57.549 25.926 18.61 12.01 35.55 3.28
227 228 9.451002 AAATGTTTCATTTGATATCAATGCCAA 57.549 25.926 18.61 4.17 35.55 4.52
228 229 9.100554 GAAATGTTTCATTTGATATCAATGCCA 57.899 29.630 18.61 14.12 37.15 4.92
229 230 9.321562 AGAAATGTTTCATTTGATATCAATGCC 57.678 29.630 18.61 10.26 39.61 4.40
235 236 9.472361 CCATGGAGAAATGTTTCATTTGATATC 57.528 33.333 5.56 0.00 39.61 1.63
236 237 7.929785 GCCATGGAGAAATGTTTCATTTGATAT 59.070 33.333 18.40 0.83 39.61 1.63
237 238 7.267128 GCCATGGAGAAATGTTTCATTTGATA 58.733 34.615 18.40 0.00 39.61 2.15
238 239 6.110707 GCCATGGAGAAATGTTTCATTTGAT 58.889 36.000 18.40 1.96 39.61 2.57
239 240 5.481105 GCCATGGAGAAATGTTTCATTTGA 58.519 37.500 18.40 0.00 39.61 2.69
240 241 4.327898 CGCCATGGAGAAATGTTTCATTTG 59.672 41.667 18.40 0.00 39.61 2.32
241 242 4.021192 ACGCCATGGAGAAATGTTTCATTT 60.021 37.500 23.45 7.32 39.61 2.32
242 243 3.511146 ACGCCATGGAGAAATGTTTCATT 59.489 39.130 23.45 0.00 39.61 2.57
243 244 3.091545 ACGCCATGGAGAAATGTTTCAT 58.908 40.909 23.45 0.00 39.61 2.57
244 245 2.228582 CACGCCATGGAGAAATGTTTCA 59.771 45.455 23.45 0.00 39.61 2.69
245 246 2.228822 ACACGCCATGGAGAAATGTTTC 59.771 45.455 23.45 0.00 37.45 2.78
246 247 2.238521 ACACGCCATGGAGAAATGTTT 58.761 42.857 23.45 0.00 0.00 2.83
247 248 1.909700 ACACGCCATGGAGAAATGTT 58.090 45.000 23.45 0.00 0.00 2.71
248 249 1.909700 AACACGCCATGGAGAAATGT 58.090 45.000 23.45 13.20 0.00 2.71
249 250 2.228582 TCAAACACGCCATGGAGAAATG 59.771 45.455 23.45 12.51 0.00 2.32
250 251 2.513753 TCAAACACGCCATGGAGAAAT 58.486 42.857 23.45 3.77 0.00 2.17
251 252 1.974265 TCAAACACGCCATGGAGAAA 58.026 45.000 23.45 0.00 0.00 2.52
252 253 2.198827 ATCAAACACGCCATGGAGAA 57.801 45.000 23.45 0.60 0.00 2.87
253 254 2.083774 GAATCAAACACGCCATGGAGA 58.916 47.619 23.45 0.00 0.00 3.71
254 255 1.133025 GGAATCAAACACGCCATGGAG 59.867 52.381 18.40 16.40 0.00 3.86
255 256 1.173043 GGAATCAAACACGCCATGGA 58.827 50.000 18.40 0.00 0.00 3.41
256 257 0.173255 GGGAATCAAACACGCCATGG 59.827 55.000 7.63 7.63 0.00 3.66
257 258 0.887247 TGGGAATCAAACACGCCATG 59.113 50.000 0.00 0.00 0.00 3.66
258 259 1.626686 TTGGGAATCAAACACGCCAT 58.373 45.000 0.00 0.00 31.46 4.40
259 260 1.626686 ATTGGGAATCAAACACGCCA 58.373 45.000 0.00 0.00 39.05 5.69
260 261 2.741759 AATTGGGAATCAAACACGCC 57.258 45.000 0.00 0.00 39.05 5.68
261 262 5.062058 CACATAAATTGGGAATCAAACACGC 59.938 40.000 0.00 0.00 39.05 5.34
262 263 5.576384 CCACATAAATTGGGAATCAAACACG 59.424 40.000 0.00 0.00 39.05 4.49
263 264 6.696411 TCCACATAAATTGGGAATCAAACAC 58.304 36.000 0.00 0.00 39.05 3.32
264 265 6.574073 GCTCCACATAAATTGGGAATCAAACA 60.574 38.462 0.00 0.00 39.05 2.83
265 266 5.812127 GCTCCACATAAATTGGGAATCAAAC 59.188 40.000 0.00 0.00 39.05 2.93
266 267 5.483231 TGCTCCACATAAATTGGGAATCAAA 59.517 36.000 0.00 0.00 39.05 2.69
267 268 5.022122 TGCTCCACATAAATTGGGAATCAA 58.978 37.500 0.00 0.00 40.01 2.57
268 269 4.608269 TGCTCCACATAAATTGGGAATCA 58.392 39.130 0.00 0.00 34.56 2.57
269 270 4.038402 CCTGCTCCACATAAATTGGGAATC 59.962 45.833 0.00 0.00 34.56 2.52
270 271 3.962718 CCTGCTCCACATAAATTGGGAAT 59.037 43.478 0.00 0.00 34.56 3.01
271 272 3.364549 CCTGCTCCACATAAATTGGGAA 58.635 45.455 0.00 0.00 34.56 3.97
272 273 2.949963 GCCTGCTCCACATAAATTGGGA 60.950 50.000 0.00 0.00 34.56 4.37
273 274 1.410153 GCCTGCTCCACATAAATTGGG 59.590 52.381 0.00 0.00 34.56 4.12
274 275 1.410153 GGCCTGCTCCACATAAATTGG 59.590 52.381 0.00 0.00 35.18 3.16
275 276 1.410153 GGGCCTGCTCCACATAAATTG 59.590 52.381 0.84 0.00 0.00 2.32
276 277 1.689258 GGGGCCTGCTCCACATAAATT 60.689 52.381 0.84 0.00 36.36 1.82
277 278 0.106015 GGGGCCTGCTCCACATAAAT 60.106 55.000 0.84 0.00 36.36 1.40
278 279 1.306296 GGGGCCTGCTCCACATAAA 59.694 57.895 0.84 0.00 36.36 1.40
279 280 1.928046 TGGGGCCTGCTCCACATAA 60.928 57.895 6.65 0.00 42.59 1.90
280 281 2.286045 TGGGGCCTGCTCCACATA 60.286 61.111 6.65 0.00 42.59 2.29
287 288 1.202769 ATTTTGCAATGGGGCCTGCT 61.203 50.000 16.14 0.00 39.38 4.24
289 290 1.832998 AGTATTTTGCAATGGGGCCTG 59.167 47.619 0.84 0.00 0.00 4.85
298 299 9.742144 TTAGTTTATGGAGGTAGTATTTTGCAA 57.258 29.630 0.00 0.00 0.00 4.08
299 300 9.914834 ATTAGTTTATGGAGGTAGTATTTTGCA 57.085 29.630 0.00 0.00 0.00 4.08
371 372 8.972127 TGCATTCTACTCTCTCTGTAAACTAAT 58.028 33.333 0.00 0.00 0.00 1.73
372 373 8.349568 TGCATTCTACTCTCTCTGTAAACTAA 57.650 34.615 0.00 0.00 0.00 2.24
373 374 7.939784 TGCATTCTACTCTCTCTGTAAACTA 57.060 36.000 0.00 0.00 0.00 2.24
374 375 6.842437 TGCATTCTACTCTCTCTGTAAACT 57.158 37.500 0.00 0.00 0.00 2.66
375 376 9.243637 CTATTGCATTCTACTCTCTCTGTAAAC 57.756 37.037 0.00 0.00 0.00 2.01
376 377 9.190317 TCTATTGCATTCTACTCTCTCTGTAAA 57.810 33.333 0.00 0.00 0.00 2.01
377 378 8.753497 TCTATTGCATTCTACTCTCTCTGTAA 57.247 34.615 0.00 0.00 0.00 2.41
378 379 8.753497 TTCTATTGCATTCTACTCTCTCTGTA 57.247 34.615 0.00 0.00 0.00 2.74
379 380 7.652524 TTCTATTGCATTCTACTCTCTCTGT 57.347 36.000 0.00 0.00 0.00 3.41
380 381 8.939201 TTTTCTATTGCATTCTACTCTCTCTG 57.061 34.615 0.00 0.00 0.00 3.35
406 407 6.292150 TGTACGATGGGCATAAATGTGATAA 58.708 36.000 0.00 0.00 0.00 1.75
408 409 4.713553 TGTACGATGGGCATAAATGTGAT 58.286 39.130 0.00 0.00 0.00 3.06
409 410 4.143986 TGTACGATGGGCATAAATGTGA 57.856 40.909 0.00 0.00 0.00 3.58
412 413 4.022935 AGCAATGTACGATGGGCATAAATG 60.023 41.667 0.00 0.00 0.00 2.32
420 421 1.202177 GCACAAGCAATGTACGATGGG 60.202 52.381 0.00 0.00 41.46 4.00
426 427 5.796935 CACTCAATTAGCACAAGCAATGTAC 59.203 40.000 0.00 0.00 41.46 2.90
428 429 4.520111 TCACTCAATTAGCACAAGCAATGT 59.480 37.500 0.00 0.00 45.34 2.71
448 449 8.600625 TGCAATAAAATACTACGTGAATCTCAC 58.399 33.333 0.00 0.00 43.65 3.51
457 458 8.726870 ACAACCTATGCAATAAAATACTACGT 57.273 30.769 0.00 0.00 0.00 3.57
485 486 2.045926 GAACCGTGCCCTGATGCT 60.046 61.111 0.00 0.00 0.00 3.79
499 500 7.836842 AGTGTTATATCCAAAACAATGGGAAC 58.163 34.615 0.00 0.00 41.05 3.62
519 531 8.147058 CAGCCTCATATTATGAAGACTAGTGTT 58.853 37.037 4.69 4.69 39.11 3.32
520 532 7.288852 ACAGCCTCATATTATGAAGACTAGTGT 59.711 37.037 0.00 0.00 39.11 3.55
521 533 7.665690 ACAGCCTCATATTATGAAGACTAGTG 58.334 38.462 0.00 2.47 39.11 2.74
522 534 7.507277 TGACAGCCTCATATTATGAAGACTAGT 59.493 37.037 7.73 0.00 39.11 2.57
525 537 6.737720 TGACAGCCTCATATTATGAAGACT 57.262 37.500 7.73 3.17 39.11 3.24
526 538 7.792374 TTTGACAGCCTCATATTATGAAGAC 57.208 36.000 7.73 1.13 39.11 3.01
527 539 7.012704 GCTTTTGACAGCCTCATATTATGAAGA 59.987 37.037 7.73 0.00 39.11 2.87
529 541 7.031226 GCTTTTGACAGCCTCATATTATGAA 57.969 36.000 7.73 0.00 39.11 2.57
530 542 6.624352 GCTTTTGACAGCCTCATATTATGA 57.376 37.500 6.23 6.23 37.76 2.15
555 567 6.973229 AATAGCATTGCCAAATTGAGTTTC 57.027 33.333 4.70 0.00 0.00 2.78
568 580 1.994779 GTGTGTGCCAAATAGCATTGC 59.005 47.619 0.00 0.00 46.24 3.56
588 600 8.587608 AGTATGGAAATAAATGGTTGCATATGG 58.412 33.333 4.56 0.00 39.33 2.74
641 673 5.856986 GGCCGAAGAAGTTTTGAATTTAGTC 59.143 40.000 0.00 0.00 0.00 2.59
694 737 3.589881 GGCCCGTCATCATGCAGC 61.590 66.667 0.00 0.00 0.00 5.25
700 743 1.773856 TTCTTGTGGGCCCGTCATCA 61.774 55.000 19.37 8.29 0.00 3.07
701 744 1.002624 TTCTTGTGGGCCCGTCATC 60.003 57.895 19.37 5.54 0.00 2.92
702 745 1.002134 CTTCTTGTGGGCCCGTCAT 60.002 57.895 19.37 0.00 0.00 3.06
703 746 2.144078 TCTTCTTGTGGGCCCGTCA 61.144 57.895 19.37 16.51 0.00 4.35
704 747 1.671379 GTCTTCTTGTGGGCCCGTC 60.671 63.158 19.37 13.77 0.00 4.79
705 748 2.430367 GTCTTCTTGTGGGCCCGT 59.570 61.111 19.37 0.00 0.00 5.28
720 769 0.931005 GGAACATGCGGAGAATCGTC 59.069 55.000 0.00 0.00 34.37 4.20
730 779 3.694072 TCAATAGAAAAGGGGAACATGCG 59.306 43.478 0.00 0.00 0.00 4.73
757 806 6.306356 CAGAGCGGTTTTGTGAAGATATTTTG 59.694 38.462 0.00 0.00 0.00 2.44
761 810 4.832248 TCAGAGCGGTTTTGTGAAGATAT 58.168 39.130 0.00 0.00 0.00 1.63
762 811 4.265904 TCAGAGCGGTTTTGTGAAGATA 57.734 40.909 0.00 0.00 0.00 1.98
765 821 3.691049 TTTCAGAGCGGTTTTGTGAAG 57.309 42.857 0.00 0.00 0.00 3.02
767 823 5.957842 ATAATTTCAGAGCGGTTTTGTGA 57.042 34.783 0.00 0.00 0.00 3.58
777 835 8.438676 AACTGTGGTACATATAATTTCAGAGC 57.561 34.615 0.00 0.00 44.52 4.09
800 863 5.435820 AACGGAGAGAGTAATATCGGAAC 57.564 43.478 0.00 0.00 0.00 3.62
845 908 9.197306 ACTGTGGTACATATGTATCTAGACAAA 57.803 33.333 24.94 12.09 44.52 2.83
846 909 8.762481 ACTGTGGTACATATGTATCTAGACAA 57.238 34.615 24.94 7.34 44.52 3.18
847 910 8.218488 AGACTGTGGTACATATGTATCTAGACA 58.782 37.037 24.94 19.83 44.52 3.41
848 911 8.624367 AGACTGTGGTACATATGTATCTAGAC 57.376 38.462 24.94 20.92 44.52 2.59
852 915 9.588096 TCAATAGACTGTGGTACATATGTATCT 57.412 33.333 23.34 18.97 44.52 1.98
853 916 9.627395 GTCAATAGACTGTGGTACATATGTATC 57.373 37.037 18.27 17.98 40.79 2.24
854 917 9.143155 TGTCAATAGACTGTGGTACATATGTAT 57.857 33.333 18.27 1.53 43.27 2.29
855 918 8.528044 TGTCAATAGACTGTGGTACATATGTA 57.472 34.615 11.62 11.62 43.27 2.29
856 919 7.418337 TGTCAATAGACTGTGGTACATATGT 57.582 36.000 13.93 13.93 43.27 2.29
857 920 7.936950 CTGTCAATAGACTGTGGTACATATG 57.063 40.000 0.00 0.00 43.27 1.78
868 931 7.386299 AGTTTGCTTTCTACTGTCAATAGACTG 59.614 37.037 0.00 0.00 45.20 3.51
869 932 7.386299 CAGTTTGCTTTCTACTGTCAATAGACT 59.614 37.037 0.00 0.00 45.20 3.24
870 933 7.513968 CAGTTTGCTTTCTACTGTCAATAGAC 58.486 38.462 0.00 0.00 45.19 2.59
871 934 7.658179 CAGTTTGCTTTCTACTGTCAATAGA 57.342 36.000 0.00 0.00 35.65 1.98
879 942 5.527582 ACCAAGTACAGTTTGCTTTCTACTG 59.472 40.000 0.00 0.00 43.72 2.74
880 943 5.681639 ACCAAGTACAGTTTGCTTTCTACT 58.318 37.500 0.00 0.00 0.00 2.57
881 944 6.373186 AACCAAGTACAGTTTGCTTTCTAC 57.627 37.500 0.00 0.00 0.00 2.59
882 945 7.399245 AAAACCAAGTACAGTTTGCTTTCTA 57.601 32.000 8.79 0.00 36.36 2.10
883 946 5.914898 AAACCAAGTACAGTTTGCTTTCT 57.085 34.783 7.61 0.00 34.97 2.52
884 947 6.961359 AAAAACCAAGTACAGTTTGCTTTC 57.039 33.333 8.79 0.00 36.36 2.62
909 972 6.649155 AGGTTGCAACTTTAATTCCAAGTTT 58.351 32.000 27.64 0.00 41.58 2.66
982 1053 1.156736 GTGGATGTTTGGGTGACTCG 58.843 55.000 0.00 0.00 0.00 4.18
1300 1390 2.031163 GACCTTGCTGCTGTCCGT 59.969 61.111 0.00 0.00 0.00 4.69
2150 3273 3.758023 CCTTGATGTAAATGACACTGGCA 59.242 43.478 0.00 0.00 42.17 4.92
2237 3360 5.213675 ACAAGAGAAAAGTACTCGTCTTCG 58.786 41.667 9.10 4.87 39.12 3.79
2324 3456 3.013648 AGGTAGGGAGATTGGTAGGTGAA 59.986 47.826 0.00 0.00 0.00 3.18
2341 3489 5.291971 AGCAAATGCAAAACTGAAAGGTAG 58.708 37.500 8.28 0.00 45.16 3.18
2345 3495 5.721876 TCAAGCAAATGCAAAACTGAAAG 57.278 34.783 8.28 0.00 45.16 2.62
2411 3598 4.957967 CAGCGTCAATTCGACACAAATATC 59.042 41.667 8.20 0.00 45.70 1.63
2414 3601 2.548057 ACAGCGTCAATTCGACACAAAT 59.452 40.909 8.20 0.00 45.70 2.32
2682 3972 4.141711 GCTAGAATCATACCCAGTCACCAA 60.142 45.833 0.00 0.00 0.00 3.67
2737 4028 9.745880 ATCAGCAAATTAAGAAGCATTAGATTG 57.254 29.630 0.00 0.00 0.00 2.67
2753 4044 7.994911 TGACTAATAGTGGATGATCAGCAAATT 59.005 33.333 13.85 8.56 0.00 1.82
2754 4045 7.512130 TGACTAATAGTGGATGATCAGCAAAT 58.488 34.615 13.85 2.93 0.00 2.32
2799 4191 9.196552 CATGGAAAAATAAAACTTCTTCAGTCC 57.803 33.333 0.00 0.00 32.94 3.85
2800 4192 9.750125 ACATGGAAAAATAAAACTTCTTCAGTC 57.250 29.630 0.00 0.00 32.94 3.51
2892 4360 9.474920 TGTTTGGAAATAACAAGCTTAATTCAG 57.525 29.630 0.00 0.00 32.89 3.02
3009 4532 4.082125 AGACTGACCCAATGTGGAAAATC 58.918 43.478 0.00 0.00 40.96 2.17
3023 4546 2.558359 CCCAACATGGAAAAGACTGACC 59.442 50.000 0.00 0.00 40.96 4.02
3066 4589 4.745125 GGAACCTGAAAAGTAAAGCAAAGC 59.255 41.667 0.00 0.00 0.00 3.51
3313 4841 6.083487 TCTCCAGATTTCCTCCAAAATGAT 57.917 37.500 0.00 0.00 0.00 2.45
3328 4856 2.305927 ACGAACCCAAACATCTCCAGAT 59.694 45.455 0.00 0.00 34.56 2.90
3337 4865 4.927978 AATTCATCAACGAACCCAAACA 57.072 36.364 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.