Multiple sequence alignment - TraesCS1A01G336500

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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 TraesCS1A01G336500 chr1A 100.000 3110 0 0 1 3110 524285626 524288735 0.000000e+00 5744
1 TraesCS1A01G336500 chr1A 90.972 1584 94 11 703 2243 522972135 522973712 0.000000e+00 2087
2 TraesCS1A01G336500 chr1A 91.418 1072 73 7 1185 2243 524700924 524701989 0.000000e+00 1452
3 TraesCS1A01G336500 chr1A 95.221 858 25 7 328 1184 526621454 526622296 0.000000e+00 1343
4 TraesCS1A01G336500 chr1A 93.837 860 30 11 331 1184 524700051 524700893 0.000000e+00 1273
5 TraesCS1A01G336500 chr1A 95.058 688 34 0 1431 2118 526622770 526623457 0.000000e+00 1083
6 TraesCS1A01G336500 chr1A 89.863 730 59 9 2395 3110 523083881 523083153 0.000000e+00 924
7 TraesCS1A01G336500 chr1A 91.480 669 44 4 523 1183 524599123 524599786 0.000000e+00 907
8 TraesCS1A01G336500 chr1A 89.178 730 63 10 2395 3110 525062960 525063687 0.000000e+00 896
9 TraesCS1A01G336500 chr1A 84.106 755 88 17 1406 2142 524600558 524601298 0.000000e+00 701
10 TraesCS1A01G336500 chr1A 93.204 309 20 1 1810 2118 524611362 524611669 1.310000e-123 453
11 TraesCS1A01G336500 chr1A 92.123 292 22 1 2113 2404 525050967 525051257 8.030000e-111 411
12 TraesCS1A01G336500 chr1A 95.547 247 10 1 1186 1432 526622329 526622574 8.080000e-106 394
13 TraesCS1A01G336500 chr1A 90.068 292 28 1 2113 2404 523095971 523095681 8.140000e-101 377
14 TraesCS1A01G336500 chr1A 89.916 119 7 2 331 444 522971762 522971880 6.950000e-32 148
15 TraesCS1A01G336500 chr1D 94.425 1130 59 2 1182 2307 427634223 427635352 0.000000e+00 1735
16 TraesCS1A01G336500 chr1D 88.930 804 51 14 379 1177 427633113 427633883 0.000000e+00 957
17 TraesCS1A01G336500 chr1B 95.401 935 43 0 1185 2119 580212116 580213050 0.000000e+00 1489
18 TraesCS1A01G336500 chr1B 96.288 889 31 2 1185 2072 579944257 579945144 0.000000e+00 1458
19 TraesCS1A01G336500 chr1B 91.492 811 46 10 379 1184 579943434 579944226 0.000000e+00 1094
20 TraesCS1A01G336500 chr1B 91.642 682 33 5 523 1184 580211408 580212085 0.000000e+00 922


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 TraesCS1A01G336500 chr1A 524285626 524288735 3109 False 5744.0 5744 100.000000 1 3110 1 chr1A.!!$F1 3109
1 TraesCS1A01G336500 chr1A 524700051 524701989 1938 False 1362.5 1452 92.627500 331 2243 2 chr1A.!!$F7 1912
2 TraesCS1A01G336500 chr1A 522971762 522973712 1950 False 1117.5 2087 90.444000 331 2243 2 chr1A.!!$F5 1912
3 TraesCS1A01G336500 chr1A 526621454 526623457 2003 False 940.0 1343 95.275333 328 2118 3 chr1A.!!$F8 1790
4 TraesCS1A01G336500 chr1A 523083153 523083881 728 True 924.0 924 89.863000 2395 3110 1 chr1A.!!$R1 715
5 TraesCS1A01G336500 chr1A 525062960 525063687 727 False 896.0 896 89.178000 2395 3110 1 chr1A.!!$F4 715
6 TraesCS1A01G336500 chr1A 524599123 524601298 2175 False 804.0 907 87.793000 523 2142 2 chr1A.!!$F6 1619
7 TraesCS1A01G336500 chr1D 427633113 427635352 2239 False 1346.0 1735 91.677500 379 2307 2 chr1D.!!$F1 1928
8 TraesCS1A01G336500 chr1B 579943434 579945144 1710 False 1276.0 1458 93.890000 379 2072 2 chr1B.!!$F1 1693
9 TraesCS1A01G336500 chr1B 580211408 580213050 1642 False 1205.5 1489 93.521500 523 2119 2 chr1B.!!$F2 1596

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
94 95 0.039035 ACTGCTCGACCTCTCCTCTT 59.961 55.0 0.0 0.0 0.0 2.85 F
182 183 0.109039 GCTCGTCCACTCCTTGTCTC 60.109 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 2991 1.270907 ACTTCAGTGGTAGGAGCAGG 58.729 55.0 0.0 0.0 0.0 4.85 R
2158 3312 5.761234 AGTTAAAGCAGTCCAACGTAAATGA 59.239 36.0 0.0 0.0 0.0 2.57 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
81 82 4.864334 CCCGGCCATGGACTGCTC 62.864 72.222 18.40 0.00 0.00 4.26
83 84 4.147449 CGGCCATGGACTGCTCGA 62.147 66.667 18.40 0.00 0.00 4.04
84 85 2.512515 GGCCATGGACTGCTCGAC 60.513 66.667 18.40 0.00 0.00 4.20
85 86 2.512515 GCCATGGACTGCTCGACC 60.513 66.667 18.40 0.00 0.00 4.79
86 87 3.023949 GCCATGGACTGCTCGACCT 62.024 63.158 18.40 0.00 0.00 3.85
87 88 1.142748 CCATGGACTGCTCGACCTC 59.857 63.158 5.56 0.00 0.00 3.85
88 89 1.326213 CCATGGACTGCTCGACCTCT 61.326 60.000 5.56 0.00 0.00 3.69
89 90 0.102120 CATGGACTGCTCGACCTCTC 59.898 60.000 0.00 0.00 0.00 3.20
90 91 1.040339 ATGGACTGCTCGACCTCTCC 61.040 60.000 0.00 0.00 0.00 3.71
91 92 1.379309 GGACTGCTCGACCTCTCCT 60.379 63.158 0.00 0.00 0.00 3.69
92 93 1.381165 GGACTGCTCGACCTCTCCTC 61.381 65.000 0.00 0.00 0.00 3.71
93 94 0.393808 GACTGCTCGACCTCTCCTCT 60.394 60.000 0.00 0.00 0.00 3.69
94 95 0.039035 ACTGCTCGACCTCTCCTCTT 59.961 55.000 0.00 0.00 0.00 2.85
95 96 0.738389 CTGCTCGACCTCTCCTCTTC 59.262 60.000 0.00 0.00 0.00 2.87
96 97 0.681564 TGCTCGACCTCTCCTCTTCC 60.682 60.000 0.00 0.00 0.00 3.46
97 98 0.681564 GCTCGACCTCTCCTCTTCCA 60.682 60.000 0.00 0.00 0.00 3.53
98 99 1.388547 CTCGACCTCTCCTCTTCCAG 58.611 60.000 0.00 0.00 0.00 3.86
99 100 0.681564 TCGACCTCTCCTCTTCCAGC 60.682 60.000 0.00 0.00 0.00 4.85
100 101 1.813192 GACCTCTCCTCTTCCAGCG 59.187 63.158 0.00 0.00 0.00 5.18
101 102 2.291457 GACCTCTCCTCTTCCAGCGC 62.291 65.000 0.00 0.00 0.00 5.92
102 103 2.354401 CCTCTCCTCTTCCAGCGCA 61.354 63.158 11.47 0.00 0.00 6.09
103 104 1.684386 CCTCTCCTCTTCCAGCGCAT 61.684 60.000 11.47 0.00 0.00 4.73
104 105 0.530211 CTCTCCTCTTCCAGCGCATG 60.530 60.000 11.47 4.88 0.00 4.06
147 148 4.849329 CGCTCGCGTACCCAGGAC 62.849 72.222 5.77 0.00 34.35 3.85
148 149 4.849329 GCTCGCGTACCCAGGACG 62.849 72.222 5.77 0.00 43.19 4.79
149 150 3.129502 CTCGCGTACCCAGGACGA 61.130 66.667 5.77 0.00 42.98 4.20
150 151 2.672651 TCGCGTACCCAGGACGAA 60.673 61.111 5.77 0.00 42.98 3.85
151 152 2.202570 CGCGTACCCAGGACGAAG 60.203 66.667 2.99 0.00 42.98 3.79
152 153 2.508663 GCGTACCCAGGACGAAGC 60.509 66.667 2.99 0.00 42.98 3.86
153 154 2.183555 CGTACCCAGGACGAAGCC 59.816 66.667 0.00 0.00 42.98 4.35
154 155 2.582978 GTACCCAGGACGAAGCCC 59.417 66.667 0.00 0.00 0.00 5.19
155 156 3.072468 TACCCAGGACGAAGCCCG 61.072 66.667 0.00 0.00 45.44 6.13
177 178 3.382832 CCCGCTCGTCCACTCCTT 61.383 66.667 0.00 0.00 0.00 3.36
178 179 2.125912 CCGCTCGTCCACTCCTTG 60.126 66.667 0.00 0.00 0.00 3.61
179 180 2.651361 CGCTCGTCCACTCCTTGT 59.349 61.111 0.00 0.00 0.00 3.16
180 181 1.444553 CGCTCGTCCACTCCTTGTC 60.445 63.158 0.00 0.00 0.00 3.18
181 182 1.867919 CGCTCGTCCACTCCTTGTCT 61.868 60.000 0.00 0.00 0.00 3.41
182 183 0.109039 GCTCGTCCACTCCTTGTCTC 60.109 60.000 0.00 0.00 0.00 3.36
183 184 0.528470 CTCGTCCACTCCTTGTCTCC 59.472 60.000 0.00 0.00 0.00 3.71
184 185 0.898789 TCGTCCACTCCTTGTCTCCC 60.899 60.000 0.00 0.00 0.00 4.30
185 186 1.185618 CGTCCACTCCTTGTCTCCCA 61.186 60.000 0.00 0.00 0.00 4.37
186 187 0.321996 GTCCACTCCTTGTCTCCCAC 59.678 60.000 0.00 0.00 0.00 4.61
187 188 1.185618 TCCACTCCTTGTCTCCCACG 61.186 60.000 0.00 0.00 0.00 4.94
188 189 1.374758 CACTCCTTGTCTCCCACGC 60.375 63.158 0.00 0.00 0.00 5.34
189 190 1.534235 ACTCCTTGTCTCCCACGCT 60.534 57.895 0.00 0.00 0.00 5.07
190 191 1.079543 CTCCTTGTCTCCCACGCTG 60.080 63.158 0.00 0.00 0.00 5.18
191 192 2.046892 CCTTGTCTCCCACGCTGG 60.047 66.667 0.00 0.00 37.25 4.85
192 193 2.743928 CTTGTCTCCCACGCTGGC 60.744 66.667 0.00 0.00 35.79 4.85
193 194 4.329545 TTGTCTCCCACGCTGGCC 62.330 66.667 0.00 0.00 35.79 5.36
235 236 4.400961 GTCTGCTTGCCCGGCTCT 62.401 66.667 11.61 0.00 0.00 4.09
236 237 4.087892 TCTGCTTGCCCGGCTCTC 62.088 66.667 11.61 0.00 0.00 3.20
240 241 3.764466 CTTGCCCGGCTCTCGTCT 61.764 66.667 11.61 0.00 37.11 4.18
241 242 3.708220 CTTGCCCGGCTCTCGTCTC 62.708 68.421 11.61 0.00 37.11 3.36
245 246 3.878519 CCGGCTCTCGTCTCCGTC 61.879 72.222 0.00 0.00 41.46 4.79
246 247 4.225340 CGGCTCTCGTCTCCGTCG 62.225 72.222 0.00 0.00 38.47 5.12
247 248 4.539881 GGCTCTCGTCTCCGTCGC 62.540 72.222 0.00 0.00 35.01 5.19
248 249 4.539881 GCTCTCGTCTCCGTCGCC 62.540 72.222 0.00 0.00 35.01 5.54
249 250 4.225340 CTCTCGTCTCCGTCGCCG 62.225 72.222 0.00 0.00 35.01 6.46
293 294 3.387091 GCCCCCGCCCGAATTTTT 61.387 61.111 0.00 0.00 0.00 1.94
316 317 3.055719 GCAGCCGGCAAGCAAGTA 61.056 61.111 31.22 0.00 43.97 2.24
317 318 3.044059 GCAGCCGGCAAGCAAGTAG 62.044 63.158 31.22 11.12 43.97 2.57
318 319 1.672356 CAGCCGGCAAGCAAGTAGT 60.672 57.895 31.54 0.00 34.23 2.73
319 320 1.376037 AGCCGGCAAGCAAGTAGTC 60.376 57.895 31.54 0.00 34.23 2.59
320 321 2.740714 GCCGGCAAGCAAGTAGTCG 61.741 63.158 24.80 0.00 0.00 4.18
321 322 1.080093 CCGGCAAGCAAGTAGTCGA 60.080 57.895 0.00 0.00 0.00 4.20
322 323 1.078759 CCGGCAAGCAAGTAGTCGAG 61.079 60.000 0.00 0.00 0.00 4.04
323 324 0.388649 CGGCAAGCAAGTAGTCGAGT 60.389 55.000 0.00 0.00 0.00 4.18
324 325 1.135489 CGGCAAGCAAGTAGTCGAGTA 60.135 52.381 0.00 0.00 0.00 2.59
325 326 2.531206 GGCAAGCAAGTAGTCGAGTAG 58.469 52.381 0.00 0.00 0.00 2.57
326 327 2.531206 GCAAGCAAGTAGTCGAGTAGG 58.469 52.381 0.00 0.00 0.00 3.18
354 355 0.779997 AAGGTTCTGCAATGGGGAGT 59.220 50.000 0.00 0.00 36.18 3.85
438 443 2.028484 GGCCGGAATGACGCGATA 59.972 61.111 15.93 0.02 0.00 2.92
439 444 1.374252 GGCCGGAATGACGCGATAT 60.374 57.895 15.93 3.08 0.00 1.63
610 672 6.266786 TCGCTATATACATCTTCCCTTGTTGA 59.733 38.462 0.00 0.00 0.00 3.18
723 796 4.162690 GATCCGGCGGGTCTGCTT 62.163 66.667 31.13 5.19 34.52 3.91
1020 1093 3.357079 GGTCACTGCAACGGCCTG 61.357 66.667 0.00 0.00 40.13 4.85
1029 1102 2.038975 AACGGCCTGCTCCTCCTA 59.961 61.111 0.00 0.00 0.00 2.94
1125 1198 3.214328 AGGCTTCATGAAACACGACTTT 58.786 40.909 9.88 0.00 0.00 2.66
1801 2952 6.698008 ACAATGATGAAACACTTGACAGAA 57.302 33.333 0.00 0.00 0.00 3.02
1840 2991 1.662629 CAGACAACGATGATGCCACTC 59.337 52.381 0.00 0.00 0.00 3.51
1849 3000 0.325577 TGATGCCACTCCTGCTCCTA 60.326 55.000 0.00 0.00 0.00 2.94
1950 3101 0.950836 TTTTGCACATGTCCCTCACG 59.049 50.000 0.00 0.00 0.00 4.35
2226 3380 6.992063 AAACATAATCTCTACAAGTGGCTG 57.008 37.500 0.00 0.00 0.00 4.85
2246 3400 7.442364 GTGGCTGCTTCTAATGAGTCATATTAA 59.558 37.037 5.94 0.34 0.00 1.40
2279 3433 7.736881 TCCTATTACTTGGTGTATGTGGTTA 57.263 36.000 0.00 0.00 0.00 2.85
2296 3450 7.931578 TGTGGTTATTTCTACATGGTTAAGG 57.068 36.000 0.00 0.00 0.00 2.69
2307 3461 5.453567 ACATGGTTAAGGCTTTTCAGTTC 57.546 39.130 4.45 0.00 0.00 3.01
2308 3462 5.140454 ACATGGTTAAGGCTTTTCAGTTCT 58.860 37.500 4.45 0.00 0.00 3.01
2309 3463 6.303839 ACATGGTTAAGGCTTTTCAGTTCTA 58.696 36.000 4.45 0.00 0.00 2.10
2310 3464 6.948309 ACATGGTTAAGGCTTTTCAGTTCTAT 59.052 34.615 4.45 0.00 0.00 1.98
2311 3465 7.451566 ACATGGTTAAGGCTTTTCAGTTCTATT 59.548 33.333 4.45 0.00 0.00 1.73
2312 3466 7.833285 TGGTTAAGGCTTTTCAGTTCTATTT 57.167 32.000 4.45 0.00 0.00 1.40
2313 3467 8.927675 TGGTTAAGGCTTTTCAGTTCTATTTA 57.072 30.769 4.45 0.00 0.00 1.40
2314 3468 9.010029 TGGTTAAGGCTTTTCAGTTCTATTTAG 57.990 33.333 4.45 0.00 0.00 1.85
2315 3469 9.227777 GGTTAAGGCTTTTCAGTTCTATTTAGA 57.772 33.333 4.45 0.00 0.00 2.10
2339 3493 9.520515 AGATATGTAATGTTCCAAACTGAACTT 57.479 29.630 5.61 0.00 43.96 2.66
2340 3494 9.559958 GATATGTAATGTTCCAAACTGAACTTG 57.440 33.333 5.61 0.00 43.96 3.16
2341 3495 6.767524 TGTAATGTTCCAAACTGAACTTGT 57.232 33.333 5.61 0.00 43.96 3.16
2342 3496 6.559810 TGTAATGTTCCAAACTGAACTTGTG 58.440 36.000 5.61 0.00 43.96 3.33
2343 3497 5.913137 AATGTTCCAAACTGAACTTGTGA 57.087 34.783 5.61 0.00 43.96 3.58
2344 3498 4.695217 TGTTCCAAACTGAACTTGTGAC 57.305 40.909 5.61 0.00 43.96 3.67
2345 3499 3.442273 TGTTCCAAACTGAACTTGTGACC 59.558 43.478 5.61 0.00 43.96 4.02
2346 3500 3.358111 TCCAAACTGAACTTGTGACCA 57.642 42.857 0.00 0.00 0.00 4.02
2347 3501 3.897239 TCCAAACTGAACTTGTGACCAT 58.103 40.909 0.00 0.00 0.00 3.55
2348 3502 4.277476 TCCAAACTGAACTTGTGACCATT 58.723 39.130 0.00 0.00 0.00 3.16
2349 3503 5.441500 TCCAAACTGAACTTGTGACCATTA 58.558 37.500 0.00 0.00 0.00 1.90
2350 3504 5.530915 TCCAAACTGAACTTGTGACCATTAG 59.469 40.000 0.00 0.00 0.00 1.73
2351 3505 5.530915 CCAAACTGAACTTGTGACCATTAGA 59.469 40.000 0.00 0.00 0.00 2.10
2352 3506 6.039270 CCAAACTGAACTTGTGACCATTAGAA 59.961 38.462 0.00 0.00 0.00 2.10
2353 3507 7.416213 CCAAACTGAACTTGTGACCATTAGAAA 60.416 37.037 0.00 0.00 0.00 2.52
2354 3508 7.639113 AACTGAACTTGTGACCATTAGAAAA 57.361 32.000 0.00 0.00 0.00 2.29
2355 3509 7.027778 ACTGAACTTGTGACCATTAGAAAAC 57.972 36.000 0.00 0.00 0.00 2.43
2356 3510 6.601613 ACTGAACTTGTGACCATTAGAAAACA 59.398 34.615 0.00 0.00 0.00 2.83
2357 3511 7.285401 ACTGAACTTGTGACCATTAGAAAACAT 59.715 33.333 0.00 0.00 0.00 2.71
2358 3512 8.006298 TGAACTTGTGACCATTAGAAAACATT 57.994 30.769 0.00 0.00 0.00 2.71
2359 3513 7.920151 TGAACTTGTGACCATTAGAAAACATTG 59.080 33.333 0.00 0.00 0.00 2.82
2360 3514 6.215845 ACTTGTGACCATTAGAAAACATTGC 58.784 36.000 0.00 0.00 0.00 3.56
2361 3515 6.040842 ACTTGTGACCATTAGAAAACATTGCT 59.959 34.615 0.00 0.00 0.00 3.91
2362 3516 6.403866 TGTGACCATTAGAAAACATTGCTT 57.596 33.333 0.00 0.00 0.00 3.91
2363 3517 6.815089 TGTGACCATTAGAAAACATTGCTTT 58.185 32.000 0.00 0.00 0.00 3.51
2364 3518 7.271511 TGTGACCATTAGAAAACATTGCTTTT 58.728 30.769 0.00 0.00 0.00 2.27
2365 3519 7.437862 TGTGACCATTAGAAAACATTGCTTTTC 59.562 33.333 12.57 12.57 39.50 2.29
2367 3521 8.203485 TGACCATTAGAAAACATTGCTTTTCTT 58.797 29.630 21.23 10.81 44.56 2.52
2368 3522 8.962884 ACCATTAGAAAACATTGCTTTTCTTT 57.037 26.923 21.23 12.85 44.56 2.52
2369 3523 9.394767 ACCATTAGAAAACATTGCTTTTCTTTT 57.605 25.926 21.23 12.64 44.56 2.27
2373 3527 9.593134 TTAGAAAACATTGCTTTTCTTTTAGCA 57.407 25.926 21.23 0.00 44.56 3.49
2374 3528 7.909267 AGAAAACATTGCTTTTCTTTTAGCAC 58.091 30.769 15.29 0.00 44.56 4.40
2375 3529 7.765819 AGAAAACATTGCTTTTCTTTTAGCACT 59.234 29.630 15.29 0.00 44.56 4.40
2376 3530 8.940768 AAAACATTGCTTTTCTTTTAGCACTA 57.059 26.923 0.00 0.00 46.28 2.74
2377 3531 8.579682 AAACATTGCTTTTCTTTTAGCACTAG 57.420 30.769 0.00 0.00 46.28 2.57
2378 3532 7.510549 ACATTGCTTTTCTTTTAGCACTAGA 57.489 32.000 0.00 0.00 46.28 2.43
2379 3533 7.363431 ACATTGCTTTTCTTTTAGCACTAGAC 58.637 34.615 0.00 0.00 46.28 2.59
2380 3534 7.229506 ACATTGCTTTTCTTTTAGCACTAGACT 59.770 33.333 0.00 0.00 46.28 3.24
2381 3535 7.568199 TTGCTTTTCTTTTAGCACTAGACTT 57.432 32.000 0.00 0.00 46.28 3.01
2382 3536 7.568199 TGCTTTTCTTTTAGCACTAGACTTT 57.432 32.000 0.00 0.00 42.12 2.66
2383 3537 7.996385 TGCTTTTCTTTTAGCACTAGACTTTT 58.004 30.769 0.00 0.00 42.12 2.27
2384 3538 9.116067 TGCTTTTCTTTTAGCACTAGACTTTTA 57.884 29.630 0.00 0.00 42.12 1.52
2385 3539 9.383462 GCTTTTCTTTTAGCACTAGACTTTTAC 57.617 33.333 0.00 0.00 37.35 2.01
2388 3542 8.603242 TTCTTTTAGCACTAGACTTTTACTGG 57.397 34.615 0.00 0.00 0.00 4.00
2389 3543 7.732996 TCTTTTAGCACTAGACTTTTACTGGT 58.267 34.615 0.00 0.00 0.00 4.00
2390 3544 7.871463 TCTTTTAGCACTAGACTTTTACTGGTC 59.129 37.037 0.00 0.00 0.00 4.02
2391 3545 6.659745 TTAGCACTAGACTTTTACTGGTCA 57.340 37.500 0.00 0.00 35.18 4.02
2392 3546 4.884247 AGCACTAGACTTTTACTGGTCAC 58.116 43.478 0.00 0.00 35.18 3.67
2393 3547 4.589374 AGCACTAGACTTTTACTGGTCACT 59.411 41.667 0.00 0.00 35.18 3.41
2409 3563 2.413453 GTCACTTTGGTCGAAGATGAGC 59.587 50.000 5.07 0.00 40.67 4.26
2410 3564 1.734465 CACTTTGGTCGAAGATGAGCC 59.266 52.381 5.07 0.00 40.67 4.70
2453 3607 3.365472 ACATTTTGATGCTTAGTCCCCC 58.635 45.455 0.00 0.00 0.00 5.40
2457 3611 2.734755 TGATGCTTAGTCCCCCATTG 57.265 50.000 0.00 0.00 0.00 2.82
2478 3633 5.801531 TGTGTACATCATGATACTACCCC 57.198 43.478 8.15 5.51 0.00 4.95
2488 3643 5.601313 TCATGATACTACCCCTGTTCTAACC 59.399 44.000 0.00 0.00 0.00 2.85
2513 3668 5.809562 ACAAACATGAATTTCTCGCAACAAA 59.190 32.000 0.00 0.00 0.00 2.83
2570 3725 9.106070 ACATAAGTATTCGGGTTTTATCTTCAC 57.894 33.333 0.00 0.00 0.00 3.18
2583 3738 8.932791 GGTTTTATCTTCACGAAATCTAGACAA 58.067 33.333 0.00 0.00 0.00 3.18
2589 3744 9.906660 ATCTTCACGAAATCTAGACAATCTATC 57.093 33.333 0.00 0.00 0.00 2.08
2590 3745 8.903820 TCTTCACGAAATCTAGACAATCTATCA 58.096 33.333 0.00 0.00 0.00 2.15
2667 3830 6.120220 ACCTAAAATGGTACCAACTGCTATC 58.880 40.000 20.76 0.00 38.79 2.08
2672 3835 1.538419 GGTACCAACTGCTATCGCTCC 60.538 57.143 7.15 0.00 36.97 4.70
2724 3887 6.144078 ACAAAAGTGTTGCTTACCTTTAGG 57.856 37.500 0.00 0.00 36.17 2.69
2730 3893 7.215719 AGTGTTGCTTACCTTTAGGAATTTC 57.784 36.000 2.06 0.00 38.94 2.17
2793 3959 4.985538 TCAACTTAGCCCTCATTTGACTT 58.014 39.130 0.00 0.00 0.00 3.01
2805 3971 6.405842 CCCTCATTTGACTTGGCCTAAAATAC 60.406 42.308 3.32 0.00 0.00 1.89
2806 3972 6.405842 CCTCATTTGACTTGGCCTAAAATACC 60.406 42.308 3.32 0.00 0.00 2.73
2834 4000 2.434336 TGGTAGAATCCAATCCACTCCG 59.566 50.000 0.00 0.00 34.24 4.63
2838 4004 0.179073 AATCCAATCCACTCCGAGCG 60.179 55.000 0.00 0.00 0.00 5.03
2845 4011 0.738975 TCCACTCCGAGCGAATACAG 59.261 55.000 0.00 0.00 0.00 2.74
2846 4012 0.738975 CCACTCCGAGCGAATACAGA 59.261 55.000 0.00 0.00 0.00 3.41
2851 4017 0.924090 CCGAGCGAATACAGACAAGC 59.076 55.000 0.00 0.00 0.00 4.01
2853 4019 1.794076 CGAGCGAATACAGACAAGCGA 60.794 52.381 0.00 0.00 0.00 4.93
2860 4026 3.895232 ATACAGACAAGCGAAGATGGT 57.105 42.857 0.00 0.00 0.00 3.55
2883 4049 3.856900 TGCATAGCCCTAGGTAGAATCA 58.143 45.455 8.29 0.00 0.00 2.57
2888 4054 2.370189 AGCCCTAGGTAGAATCACATGC 59.630 50.000 8.29 0.00 0.00 4.06
2905 4071 3.134442 ACATGCAAAAGGTGTCCAAACAT 59.866 39.130 0.00 0.00 37.81 2.71
2918 4084 1.272212 CCAAACATAGGCCACAACCAC 59.728 52.381 5.01 0.00 0.00 4.16
2921 4087 0.109723 ACATAGGCCACAACCACGTT 59.890 50.000 5.01 0.00 0.00 3.99
2973 4139 0.110238 CGGACATGTTCGGTTGCTTG 60.110 55.000 19.23 0.00 0.00 4.01
2979 4145 0.592637 TGTTCGGTTGCTTGCATCTG 59.407 50.000 6.24 6.24 0.00 2.90
2982 4148 0.592637 TCGGTTGCTTGCATCTGTTG 59.407 50.000 10.97 0.00 0.00 3.33
3015 4183 2.832129 TGAGTGACCCATAGAGGTTGAC 59.168 50.000 0.00 0.00 41.42 3.18
3018 4186 2.832129 GTGACCCATAGAGGTTGACTGA 59.168 50.000 0.00 0.00 41.42 3.41
3025 4193 5.295950 CCATAGAGGTTGACTGAGCTAATG 58.704 45.833 0.00 0.00 0.00 1.90
3034 4202 2.935201 GACTGAGCTAATGCAACCTCTG 59.065 50.000 0.00 1.25 42.74 3.35
3049 4217 3.233507 ACCTCTGAACCATGTTTTGCAT 58.766 40.909 0.00 0.00 38.60 3.96
3091 4259 0.833287 GCCCTAGGTTGCATGAGAGA 59.167 55.000 8.29 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 4.864334 GAGCAGTCCATGGCCGGG 62.864 72.222 6.96 6.93 0.00 5.73
66 67 4.147449 TCGAGCAGTCCATGGCCG 62.147 66.667 6.96 3.69 0.00 6.13
67 68 2.512515 GTCGAGCAGTCCATGGCC 60.513 66.667 6.96 0.00 0.00 5.36
68 69 2.512515 GGTCGAGCAGTCCATGGC 60.513 66.667 6.96 2.00 0.00 4.40
69 70 1.142748 GAGGTCGAGCAGTCCATGG 59.857 63.158 18.15 4.97 0.00 3.66
70 71 0.102120 GAGAGGTCGAGCAGTCCATG 59.898 60.000 18.15 0.00 0.00 3.66
71 72 1.040339 GGAGAGGTCGAGCAGTCCAT 61.040 60.000 23.25 1.31 0.00 3.41
72 73 1.679305 GGAGAGGTCGAGCAGTCCA 60.679 63.158 23.25 0.00 0.00 4.02
73 74 1.379309 AGGAGAGGTCGAGCAGTCC 60.379 63.158 21.56 21.56 0.00 3.85
74 75 0.393808 AGAGGAGAGGTCGAGCAGTC 60.394 60.000 18.15 12.14 0.00 3.51
75 76 0.039035 AAGAGGAGAGGTCGAGCAGT 59.961 55.000 18.15 2.53 0.00 4.40
76 77 0.738389 GAAGAGGAGAGGTCGAGCAG 59.262 60.000 18.15 0.00 0.00 4.24
77 78 0.681564 GGAAGAGGAGAGGTCGAGCA 60.682 60.000 18.15 0.00 0.00 4.26
78 79 0.681564 TGGAAGAGGAGAGGTCGAGC 60.682 60.000 6.48 6.48 0.00 5.03
79 80 1.388547 CTGGAAGAGGAGAGGTCGAG 58.611 60.000 0.00 0.00 34.07 4.04
80 81 0.681564 GCTGGAAGAGGAGAGGTCGA 60.682 60.000 0.00 0.00 34.07 4.20
81 82 1.813192 GCTGGAAGAGGAGAGGTCG 59.187 63.158 0.00 0.00 34.07 4.79
82 83 1.813192 CGCTGGAAGAGGAGAGGTC 59.187 63.158 0.00 0.00 34.07 3.85
83 84 2.355193 GCGCTGGAAGAGGAGAGGT 61.355 63.158 0.00 0.00 34.07 3.85
84 85 1.684386 ATGCGCTGGAAGAGGAGAGG 61.684 60.000 9.73 0.00 37.59 3.69
85 86 0.530211 CATGCGCTGGAAGAGGAGAG 60.530 60.000 9.73 0.00 37.59 3.20
86 87 1.519246 CATGCGCTGGAAGAGGAGA 59.481 57.895 9.73 0.00 37.59 3.71
87 88 4.121691 CATGCGCTGGAAGAGGAG 57.878 61.111 9.73 0.00 37.59 3.69
130 131 4.849329 GTCCTGGGTACGCGAGCG 62.849 72.222 15.93 16.38 46.03 5.03
131 132 4.849329 CGTCCTGGGTACGCGAGC 62.849 72.222 15.93 6.12 33.04 5.03
132 133 2.594119 CTTCGTCCTGGGTACGCGAG 62.594 65.000 15.93 0.00 40.12 5.03
133 134 2.672651 TTCGTCCTGGGTACGCGA 60.673 61.111 15.93 0.00 40.12 5.87
134 135 2.202570 CTTCGTCCTGGGTACGCG 60.203 66.667 3.53 3.53 40.12 6.01
135 136 2.508663 GCTTCGTCCTGGGTACGC 60.509 66.667 2.35 2.35 40.12 4.42
136 137 2.183555 GGCTTCGTCCTGGGTACG 59.816 66.667 1.78 1.78 41.64 3.67
137 138 2.582978 GGGCTTCGTCCTGGGTAC 59.417 66.667 0.00 0.00 0.00 3.34
138 139 3.072468 CGGGCTTCGTCCTGGGTA 61.072 66.667 0.00 0.00 0.00 3.69
160 161 3.382832 AAGGAGTGGACGAGCGGG 61.383 66.667 0.00 0.00 0.00 6.13
161 162 2.125912 CAAGGAGTGGACGAGCGG 60.126 66.667 0.00 0.00 0.00 5.52
162 163 1.444553 GACAAGGAGTGGACGAGCG 60.445 63.158 0.00 0.00 0.00 5.03
163 164 0.109039 GAGACAAGGAGTGGACGAGC 60.109 60.000 0.00 0.00 0.00 5.03
164 165 0.528470 GGAGACAAGGAGTGGACGAG 59.472 60.000 0.00 0.00 0.00 4.18
165 166 0.898789 GGGAGACAAGGAGTGGACGA 60.899 60.000 0.00 0.00 0.00 4.20
166 167 1.185618 TGGGAGACAAGGAGTGGACG 61.186 60.000 0.00 0.00 0.00 4.79
167 168 0.321996 GTGGGAGACAAGGAGTGGAC 59.678 60.000 0.00 0.00 0.00 4.02
168 169 1.185618 CGTGGGAGACAAGGAGTGGA 61.186 60.000 0.00 0.00 0.00 4.02
169 170 1.293498 CGTGGGAGACAAGGAGTGG 59.707 63.158 0.00 0.00 0.00 4.00
170 171 1.374758 GCGTGGGAGACAAGGAGTG 60.375 63.158 0.00 0.00 0.00 3.51
171 172 1.534235 AGCGTGGGAGACAAGGAGT 60.534 57.895 0.00 0.00 0.00 3.85
172 173 1.079543 CAGCGTGGGAGACAAGGAG 60.080 63.158 0.00 0.00 0.00 3.69
173 174 2.583441 CCAGCGTGGGAGACAAGGA 61.583 63.158 0.00 0.00 32.67 3.36
174 175 2.046892 CCAGCGTGGGAGACAAGG 60.047 66.667 0.00 0.00 32.67 3.61
175 176 2.743928 GCCAGCGTGGGAGACAAG 60.744 66.667 6.23 0.00 38.19 3.16
176 177 4.329545 GGCCAGCGTGGGAGACAA 62.330 66.667 0.00 0.00 38.19 3.18
218 219 4.400961 AGAGCCGGGCAAGCAGAC 62.401 66.667 23.09 3.38 0.00 3.51
219 220 4.087892 GAGAGCCGGGCAAGCAGA 62.088 66.667 23.09 0.00 0.00 4.26
223 224 3.708220 GAGACGAGAGCCGGGCAAG 62.708 68.421 23.09 11.35 43.93 4.01
224 225 3.760035 GAGACGAGAGCCGGGCAA 61.760 66.667 23.09 0.00 43.93 4.52
276 277 3.387091 AAAAATTCGGGCGGGGGC 61.387 61.111 0.00 0.00 0.00 5.80
299 300 3.044059 CTACTTGCTTGCCGGCTGC 62.044 63.158 29.70 29.33 41.77 5.25
300 301 1.639298 GACTACTTGCTTGCCGGCTG 61.639 60.000 29.70 21.00 0.00 4.85
301 302 1.376037 GACTACTTGCTTGCCGGCT 60.376 57.895 29.70 7.80 0.00 5.52
302 303 2.740714 CGACTACTTGCTTGCCGGC 61.741 63.158 22.73 22.73 0.00 6.13
303 304 1.078759 CTCGACTACTTGCTTGCCGG 61.079 60.000 0.00 0.00 0.00 6.13
304 305 0.388649 ACTCGACTACTTGCTTGCCG 60.389 55.000 0.00 0.00 0.00 5.69
305 306 2.531206 CTACTCGACTACTTGCTTGCC 58.469 52.381 0.00 0.00 0.00 4.52
306 307 2.531206 CCTACTCGACTACTTGCTTGC 58.469 52.381 0.00 0.00 0.00 4.01
307 308 2.753452 TCCCTACTCGACTACTTGCTTG 59.247 50.000 0.00 0.00 0.00 4.01
308 309 3.083122 TCCCTACTCGACTACTTGCTT 57.917 47.619 0.00 0.00 0.00 3.91
309 310 2.803030 TCCCTACTCGACTACTTGCT 57.197 50.000 0.00 0.00 0.00 3.91
310 311 2.544069 GCATCCCTACTCGACTACTTGC 60.544 54.545 0.00 0.00 0.00 4.01
311 312 2.952978 AGCATCCCTACTCGACTACTTG 59.047 50.000 0.00 0.00 0.00 3.16
312 313 3.117813 AGAGCATCCCTACTCGACTACTT 60.118 47.826 0.00 0.00 37.99 2.24
313 314 2.440253 AGAGCATCCCTACTCGACTACT 59.560 50.000 0.00 0.00 37.99 2.57
314 315 2.853705 AGAGCATCCCTACTCGACTAC 58.146 52.381 0.00 0.00 37.99 2.73
315 316 4.505215 CCTTAGAGCATCCCTACTCGACTA 60.505 50.000 0.00 0.00 37.99 2.59
316 317 3.482436 CTTAGAGCATCCCTACTCGACT 58.518 50.000 0.00 0.00 37.99 4.18
317 318 2.554893 CCTTAGAGCATCCCTACTCGAC 59.445 54.545 0.00 0.00 37.99 4.20
318 319 2.175069 ACCTTAGAGCATCCCTACTCGA 59.825 50.000 0.00 0.00 37.99 4.04
319 320 2.588620 ACCTTAGAGCATCCCTACTCG 58.411 52.381 0.00 0.00 37.99 4.18
320 321 4.038642 CAGAACCTTAGAGCATCCCTACTC 59.961 50.000 0.00 0.00 33.66 2.59
321 322 3.964031 CAGAACCTTAGAGCATCCCTACT 59.036 47.826 0.00 0.00 33.66 2.57
322 323 3.493524 GCAGAACCTTAGAGCATCCCTAC 60.494 52.174 0.00 0.00 33.66 3.18
323 324 2.700897 GCAGAACCTTAGAGCATCCCTA 59.299 50.000 0.00 0.00 33.66 3.53
324 325 1.488393 GCAGAACCTTAGAGCATCCCT 59.512 52.381 0.00 0.00 33.66 4.20
325 326 1.210478 TGCAGAACCTTAGAGCATCCC 59.790 52.381 0.00 0.00 33.66 3.85
326 327 2.698855 TGCAGAACCTTAGAGCATCC 57.301 50.000 0.00 0.00 33.66 3.51
354 355 1.079819 CTCTTCTTCAGCCGGCGAA 60.080 57.895 23.20 24.32 0.00 4.70
438 443 2.224161 GCAGAGCTATTCCGGACTTGAT 60.224 50.000 1.83 0.00 0.00 2.57
439 444 1.137086 GCAGAGCTATTCCGGACTTGA 59.863 52.381 1.83 0.00 0.00 3.02
610 672 2.483889 GCTTTGCTTCTACCTCGGCTAT 60.484 50.000 0.00 0.00 0.00 2.97
1102 1175 2.808543 AGTCGTGTTTCATGAAGCCTTC 59.191 45.455 18.27 0.00 30.77 3.46
1437 2570 1.678728 CGTGCATGGTATTGGGTGACT 60.679 52.381 0.00 0.00 0.00 3.41
1801 2952 3.010138 TCTGAATCCCATTCCGGTTTCTT 59.990 43.478 0.00 0.00 38.50 2.52
1840 2991 1.270907 ACTTCAGTGGTAGGAGCAGG 58.729 55.000 0.00 0.00 0.00 4.85
2037 3188 7.907056 TATCCAGCAAGGCGTGTATACACAC 62.907 48.000 30.17 22.74 43.27 3.82
2158 3312 5.761234 AGTTAAAGCAGTCCAACGTAAATGA 59.239 36.000 0.00 0.00 0.00 2.57
2206 3360 4.701765 AGCAGCCACTTGTAGAGATTATG 58.298 43.478 0.00 0.00 0.00 1.90
2218 3372 3.008375 TGACTCATTAGAAGCAGCCACTT 59.992 43.478 0.00 0.00 0.00 3.16
2256 3410 8.974060 AATAACCACATACACCAAGTAATAGG 57.026 34.615 0.00 0.00 36.05 2.57
2279 3433 7.451566 ACTGAAAAGCCTTAACCATGTAGAAAT 59.548 33.333 0.00 0.00 0.00 2.17
2324 3478 3.442273 TGGTCACAAGTTCAGTTTGGAAC 59.558 43.478 0.00 0.00 45.87 3.62
2325 3479 3.691575 TGGTCACAAGTTCAGTTTGGAA 58.308 40.909 0.00 0.00 0.00 3.53
2326 3480 3.358111 TGGTCACAAGTTCAGTTTGGA 57.642 42.857 0.00 0.00 0.00 3.53
2327 3481 4.654091 AATGGTCACAAGTTCAGTTTGG 57.346 40.909 0.00 0.00 0.00 3.28
2328 3482 6.618287 TCTAATGGTCACAAGTTCAGTTTG 57.382 37.500 0.00 0.00 0.00 2.93
2329 3483 7.639113 TTTCTAATGGTCACAAGTTCAGTTT 57.361 32.000 0.00 0.00 0.00 2.66
2330 3484 7.122055 TGTTTTCTAATGGTCACAAGTTCAGTT 59.878 33.333 0.00 0.00 0.00 3.16
2331 3485 6.601613 TGTTTTCTAATGGTCACAAGTTCAGT 59.398 34.615 0.00 0.00 0.00 3.41
2332 3486 7.026631 TGTTTTCTAATGGTCACAAGTTCAG 57.973 36.000 0.00 0.00 0.00 3.02
2333 3487 7.581213 ATGTTTTCTAATGGTCACAAGTTCA 57.419 32.000 0.00 0.00 0.00 3.18
2334 3488 7.096065 GCAATGTTTTCTAATGGTCACAAGTTC 60.096 37.037 0.00 0.00 0.00 3.01
2335 3489 6.701400 GCAATGTTTTCTAATGGTCACAAGTT 59.299 34.615 0.00 0.00 0.00 2.66
2336 3490 6.040842 AGCAATGTTTTCTAATGGTCACAAGT 59.959 34.615 0.00 0.00 0.00 3.16
2337 3491 6.449698 AGCAATGTTTTCTAATGGTCACAAG 58.550 36.000 0.00 0.00 0.00 3.16
2338 3492 6.403866 AGCAATGTTTTCTAATGGTCACAA 57.596 33.333 0.00 0.00 0.00 3.33
2339 3493 6.403866 AAGCAATGTTTTCTAATGGTCACA 57.596 33.333 0.00 0.00 0.00 3.58
2340 3494 7.713764 AAAAGCAATGTTTTCTAATGGTCAC 57.286 32.000 0.00 0.00 0.00 3.67
2341 3495 7.945033 GAAAAGCAATGTTTTCTAATGGTCA 57.055 32.000 0.00 0.00 41.38 4.02
2358 3512 7.568199 AAAGTCTAGTGCTAAAAGAAAAGCA 57.432 32.000 0.00 0.00 46.11 3.91
2359 3513 9.383462 GTAAAAGTCTAGTGCTAAAAGAAAAGC 57.617 33.333 0.00 0.00 39.25 3.51
2362 3516 9.052759 CCAGTAAAAGTCTAGTGCTAAAAGAAA 57.947 33.333 0.00 0.00 0.00 2.52
2363 3517 8.208903 ACCAGTAAAAGTCTAGTGCTAAAAGAA 58.791 33.333 0.00 0.00 0.00 2.52
2364 3518 7.732996 ACCAGTAAAAGTCTAGTGCTAAAAGA 58.267 34.615 0.00 0.00 0.00 2.52
2365 3519 7.656137 TGACCAGTAAAAGTCTAGTGCTAAAAG 59.344 37.037 0.00 0.00 34.02 2.27
2366 3520 7.440255 GTGACCAGTAAAAGTCTAGTGCTAAAA 59.560 37.037 0.00 0.00 34.02 1.52
2367 3521 6.927381 GTGACCAGTAAAAGTCTAGTGCTAAA 59.073 38.462 0.00 0.00 34.02 1.85
2368 3522 6.267014 AGTGACCAGTAAAAGTCTAGTGCTAA 59.733 38.462 0.00 0.00 34.02 3.09
2369 3523 5.773680 AGTGACCAGTAAAAGTCTAGTGCTA 59.226 40.000 0.00 0.00 34.02 3.49
2370 3524 4.589374 AGTGACCAGTAAAAGTCTAGTGCT 59.411 41.667 0.00 0.00 34.02 4.40
2371 3525 4.884247 AGTGACCAGTAAAAGTCTAGTGC 58.116 43.478 0.00 0.00 34.02 4.40
2372 3526 6.202954 CCAAAGTGACCAGTAAAAGTCTAGTG 59.797 42.308 0.00 0.00 34.02 2.74
2373 3527 6.126854 ACCAAAGTGACCAGTAAAAGTCTAGT 60.127 38.462 0.00 0.00 34.02 2.57
2374 3528 6.289064 ACCAAAGTGACCAGTAAAAGTCTAG 58.711 40.000 0.00 0.00 34.02 2.43
2375 3529 6.243216 ACCAAAGTGACCAGTAAAAGTCTA 57.757 37.500 0.00 0.00 34.02 2.59
2376 3530 5.112129 ACCAAAGTGACCAGTAAAAGTCT 57.888 39.130 0.00 0.00 34.02 3.24
2377 3531 4.025145 CGACCAAAGTGACCAGTAAAAGTC 60.025 45.833 0.00 0.00 0.00 3.01
2378 3532 3.875134 CGACCAAAGTGACCAGTAAAAGT 59.125 43.478 0.00 0.00 0.00 2.66
2379 3533 4.124238 TCGACCAAAGTGACCAGTAAAAG 58.876 43.478 0.00 0.00 0.00 2.27
2380 3534 4.139859 TCGACCAAAGTGACCAGTAAAA 57.860 40.909 0.00 0.00 0.00 1.52
2381 3535 3.823281 TCGACCAAAGTGACCAGTAAA 57.177 42.857 0.00 0.00 0.00 2.01
2382 3536 3.385433 TCTTCGACCAAAGTGACCAGTAA 59.615 43.478 0.00 0.00 0.00 2.24
2383 3537 2.960384 TCTTCGACCAAAGTGACCAGTA 59.040 45.455 0.00 0.00 0.00 2.74
2384 3538 1.760613 TCTTCGACCAAAGTGACCAGT 59.239 47.619 0.00 0.00 0.00 4.00
2385 3539 2.526304 TCTTCGACCAAAGTGACCAG 57.474 50.000 0.00 0.00 0.00 4.00
2386 3540 2.367241 TCATCTTCGACCAAAGTGACCA 59.633 45.455 0.00 0.00 0.00 4.02
2387 3541 2.996621 CTCATCTTCGACCAAAGTGACC 59.003 50.000 0.00 0.00 0.00 4.02
2388 3542 2.413453 GCTCATCTTCGACCAAAGTGAC 59.587 50.000 0.00 0.00 0.00 3.67
2389 3543 2.612972 GGCTCATCTTCGACCAAAGTGA 60.613 50.000 0.00 0.00 0.00 3.41
2390 3544 1.734465 GGCTCATCTTCGACCAAAGTG 59.266 52.381 0.00 0.00 0.00 3.16
2391 3545 1.347707 TGGCTCATCTTCGACCAAAGT 59.652 47.619 0.00 0.00 0.00 2.66
2392 3546 1.734465 GTGGCTCATCTTCGACCAAAG 59.266 52.381 0.00 0.00 30.82 2.77
2393 3547 1.347707 AGTGGCTCATCTTCGACCAAA 59.652 47.619 0.00 0.00 30.82 3.28
2409 3563 5.353678 GTCTCTCATTTGAATGAAGGAGTGG 59.646 44.000 16.27 3.23 44.20 4.00
2410 3564 5.936372 TGTCTCTCATTTGAATGAAGGAGTG 59.064 40.000 16.27 3.75 44.20 3.51
2453 3607 6.650807 GGGGTAGTATCATGATGTACACAATG 59.349 42.308 23.52 11.66 0.00 2.82
2457 3611 5.304614 ACAGGGGTAGTATCATGATGTACAC 59.695 44.000 18.72 18.23 0.00 2.90
2478 3633 8.137437 AGAAATTCATGTTTGTGGTTAGAACAG 58.863 33.333 0.00 0.00 36.80 3.16
2488 3643 4.739228 TGTTGCGAGAAATTCATGTTTGTG 59.261 37.500 0.00 0.00 0.00 3.33
2538 3693 7.989416 AAAACCCGAATACTTATGTTTCTCA 57.011 32.000 0.00 0.00 0.00 3.27
2555 3710 5.796350 AGATTTCGTGAAGATAAAACCCG 57.204 39.130 0.00 0.00 0.00 5.28
2636 3799 9.621629 CAGTTGGTACCATTTTAGGTAATGATA 57.378 33.333 17.17 0.00 45.24 2.15
2643 3806 4.382386 AGCAGTTGGTACCATTTTAGGT 57.618 40.909 17.17 7.28 45.72 3.08
2667 3830 1.399440 CATGTCCTTGTTGATGGAGCG 59.601 52.381 0.00 0.00 32.36 5.03
2672 3835 7.275183 TCTAGATAACCATGTCCTTGTTGATG 58.725 38.462 0.00 0.00 0.00 3.07
2767 3933 6.015940 AGTCAAATGAGGGCTAAGTTGAAAAG 60.016 38.462 0.00 0.00 0.00 2.27
2777 3943 1.340991 GGCCAAGTCAAATGAGGGCTA 60.341 52.381 15.88 0.00 41.28 3.93
2780 3946 2.806945 TAGGCCAAGTCAAATGAGGG 57.193 50.000 5.01 0.00 0.00 4.30
2806 3972 3.571401 GGATTGGATTCTACCATTGCCTG 59.429 47.826 0.00 0.00 39.82 4.85
2834 4000 1.909376 TCGCTTGTCTGTATTCGCTC 58.091 50.000 0.00 0.00 0.00 5.03
2838 4004 4.184629 ACCATCTTCGCTTGTCTGTATTC 58.815 43.478 0.00 0.00 0.00 1.75
2845 4011 1.266718 TGCAAACCATCTTCGCTTGTC 59.733 47.619 0.00 0.00 0.00 3.18
2846 4012 1.317613 TGCAAACCATCTTCGCTTGT 58.682 45.000 0.00 0.00 0.00 3.16
2851 4017 1.334869 GGGCTATGCAAACCATCTTCG 59.665 52.381 0.00 0.00 35.34 3.79
2853 4019 2.834638 AGGGCTATGCAAACCATCTT 57.165 45.000 0.00 0.00 35.34 2.40
2860 4026 4.658435 TGATTCTACCTAGGGCTATGCAAA 59.342 41.667 14.81 0.00 0.00 3.68
2883 4049 2.499289 TGTTTGGACACCTTTTGCATGT 59.501 40.909 0.00 0.00 0.00 3.21
2888 4054 3.306019 GGCCTATGTTTGGACACCTTTTG 60.306 47.826 0.00 0.00 38.91 2.44
2905 4071 0.398696 ATGAACGTGGTTGTGGCCTA 59.601 50.000 3.32 0.00 0.00 3.93
2957 4123 0.961019 ATGCAAGCAACCGAACATGT 59.039 45.000 0.00 0.00 0.00 3.21
2973 4139 1.598701 GCAAGGGGTCCAACAGATGC 61.599 60.000 0.00 0.00 0.00 3.91
2979 4145 0.251341 ACTCATGCAAGGGGTCCAAC 60.251 55.000 0.00 0.00 0.00 3.77
2982 4148 0.678048 GTCACTCATGCAAGGGGTCC 60.678 60.000 0.00 0.00 0.00 4.46
3015 4183 3.257469 TCAGAGGTTGCATTAGCTCAG 57.743 47.619 17.43 10.96 43.39 3.35
3018 4186 2.040278 TGGTTCAGAGGTTGCATTAGCT 59.960 45.455 0.00 0.00 42.74 3.32
3025 4193 3.383761 CAAAACATGGTTCAGAGGTTGC 58.616 45.455 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.