Multiple sequence alignment - TraesCS5A01G554200

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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 TraesCS5A01G554200 chr5A 100.000 2697 0 0 1 2697 706238761 706241457 0.000000e+00 4981.0
1 TraesCS5A01G554200 chr5A 100.000 2465 0 0 2905 5369 706241665 706244129 0.000000e+00 4553.0
2 TraesCS5A01G554200 chr4B 89.246 2055 136 36 307 2326 667880737 667878733 0.000000e+00 2492.0
3 TraesCS5A01G554200 chr4B 91.051 1598 99 24 2905 4495 667877719 667876159 0.000000e+00 2119.0
4 TraesCS5A01G554200 chr4B 84.140 372 39 11 2319 2685 667878398 667878042 5.150000e-90 342.0
5 TraesCS5A01G554200 chr4B 84.615 104 12 3 205 307 667881276 667881176 3.420000e-17 100.0
6 TraesCS5A01G554200 chrUn 95.330 1456 39 12 2909 4351 29785039 29786478 0.000000e+00 2285.0
7 TraesCS5A01G554200 chrUn 92.237 1082 59 13 775 1853 29782953 29784012 0.000000e+00 1509.0
8 TraesCS5A01G554200 chrUn 89.972 708 58 9 1858 2559 29784150 29784850 0.000000e+00 902.0
9 TraesCS5A01G554200 chrUn 93.398 515 24 3 4780 5284 29787049 29787563 0.000000e+00 754.0
10 TraesCS5A01G554200 chrUn 90.612 490 29 8 4268 4744 29786461 29786946 7.590000e-178 634.0
11 TraesCS5A01G554200 chrUn 87.138 311 30 7 1 307 29781366 29781670 1.430000e-90 344.0
12 TraesCS5A01G554200 chrUn 93.953 215 12 1 524 737 29782751 29782965 1.870000e-84 324.0
13 TraesCS5A01G554200 chrUn 84.681 235 21 1 307 526 29782378 29782612 2.520000e-53 220.0
14 TraesCS5A01G554200 chrUn 87.778 90 5 2 4268 4351 29786425 29786514 3.420000e-17 100.0
15 TraesCS5A01G554200 chrUn 97.222 36 1 0 4744 4779 29786985 29787020 1.610000e-05 62.1
16 TraesCS5A01G554200 chr2B 80.619 1357 184 48 2937 4262 244571077 244569769 0.000000e+00 976.0
17 TraesCS5A01G554200 chr2B 87.398 246 26 5 1871 2113 244571802 244571559 1.470000e-70 278.0
18 TraesCS5A01G554200 chr2A 80.162 1356 192 50 2937 4262 202048926 202047618 0.000000e+00 942.0
19 TraesCS5A01G554200 chr2A 89.552 201 19 2 1922 2121 202049582 202049383 2.480000e-63 254.0
20 TraesCS5A01G554200 chr2D 81.014 848 113 26 3434 4262 188503588 188502770 9.810000e-177 630.0
21 TraesCS5A01G554200 chr2D 86.450 369 39 4 2937 3305 188504056 188503699 1.400000e-105 394.0
22 TraesCS5A01G554200 chr2D 84.146 82 10 1 987 1068 188505343 188505265 5.770000e-10 76.8


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 TraesCS5A01G554200 chr5A 706238761 706244129 5368 False 4767.000000 4981 100.0000 1 5369 2 chr5A.!!$F1 5368
1 TraesCS5A01G554200 chr4B 667876159 667881276 5117 True 1263.250000 2492 87.2630 205 4495 4 chr4B.!!$R1 4290
2 TraesCS5A01G554200 chrUn 29781366 29787563 6197 False 713.410000 2285 91.2321 1 5284 10 chrUn.!!$F1 5283
3 TraesCS5A01G554200 chr2B 244569769 244571802 2033 True 627.000000 976 84.0085 1871 4262 2 chr2B.!!$R1 2391
4 TraesCS5A01G554200 chr2A 202047618 202049582 1964 True 598.000000 942 84.8570 1922 4262 2 chr2A.!!$R1 2340
5 TraesCS5A01G554200 chr2D 188502770 188505343 2573 True 366.933333 630 83.8700 987 4262 3 chr2D.!!$R1 3275

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
743 1755 0.037605 GCCGCGTATGGTATAAGGCT 60.038 55.0 4.92 0.00 39.92 4.58 F
1439 2455 0.517316 CGCCTACAAGCAGTTGTTCC 59.483 55.0 0.00 0.00 45.00 3.62 F
2326 4100 0.995024 AACAAGGCATGGCTAGACCT 59.005 50.0 23.63 2.96 40.22 3.85 F
2688 4469 0.102481 CTTGATGCAAGGCAGATGGC 59.898 55.0 0.00 0.00 43.65 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 4116 0.908180 GGATCGGGGTATGGGGTAGG 60.908 65.000 0.00 0.0 0.00 3.18 R
2346 4120 1.140134 ATTGGGATCGGGGTATGGGG 61.140 60.000 0.00 0.0 0.00 4.96 R
4253 6253 1.376037 CCACCGAGGCCTTGAACTC 60.376 63.158 22.68 0.0 0.00 3.01 R
4527 6612 1.202486 TCGGCTTATTTCTAGGGCACG 60.202 52.381 0.00 0.0 30.77 5.34 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
45 46 7.763528 ACTCATGCACTTTCAAAAATGTTTACA 59.236 29.630 0.00 0.00 0.00 2.41
73 75 6.493449 TTCCAAAAAGCCAAAAAGTCAAAG 57.507 33.333 0.00 0.00 0.00 2.77
163 165 6.943981 TCCGCAATAAAAATCAGTAGAATCG 58.056 36.000 0.00 0.00 0.00 3.34
181 183 9.206870 GTAGAATCGACTATAGCTACAGTTACT 57.793 37.037 6.05 4.83 31.08 2.24
187 189 6.347079 CGACTATAGCTACAGTTACTGCTCTC 60.347 46.154 12.80 0.00 37.02 3.20
188 190 5.766174 ACTATAGCTACAGTTACTGCTCTCC 59.234 44.000 12.80 0.00 37.02 3.71
191 193 4.204012 AGCTACAGTTACTGCTCTCCTAG 58.796 47.826 12.80 6.67 34.37 3.02
200 202 0.105964 TGCTCTCCTAGGTAGCCTGG 60.106 60.000 25.99 7.85 34.61 4.45
202 204 1.152735 TCTCCTAGGTAGCCTGGCG 60.153 63.158 13.96 0.00 34.61 5.69
243 245 3.376859 TGTGTTTCAGCGACAATTTGTCT 59.623 39.130 23.29 6.71 44.85 3.41
248 250 3.202097 TCAGCGACAATTTGTCTCAACA 58.798 40.909 23.29 4.91 44.85 3.33
287 289 4.456662 TCCCTTAGTTTTGGGCTTTGTA 57.543 40.909 0.00 0.00 43.04 2.41
288 290 4.146564 TCCCTTAGTTTTGGGCTTTGTAC 58.853 43.478 0.00 0.00 43.04 2.90
289 291 3.057806 CCCTTAGTTTTGGGCTTTGTACG 60.058 47.826 0.00 0.00 36.61 3.67
290 292 3.816523 CCTTAGTTTTGGGCTTTGTACGA 59.183 43.478 0.00 0.00 0.00 3.43
292 294 3.982576 AGTTTTGGGCTTTGTACGAAG 57.017 42.857 17.30 17.30 0.00 3.79
345 1200 1.146982 ACAAGGCCAACAATAGGTGGT 59.853 47.619 5.01 0.00 0.00 4.16
411 1281 3.666883 TTACAACAAACTCAGCACACG 57.333 42.857 0.00 0.00 0.00 4.49
412 1282 0.098728 ACAACAAACTCAGCACACGC 59.901 50.000 0.00 0.00 38.99 5.34
415 1285 4.000557 AAACTCAGCACACGCGCG 62.001 61.111 30.96 30.96 45.49 6.86
428 1298 2.725699 CGCGCGTGCATTACTGTCA 61.726 57.895 24.19 0.00 42.97 3.58
429 1299 1.059369 GCGCGTGCATTACTGTCAG 59.941 57.895 17.66 0.00 42.15 3.51
439 1309 3.491792 GCATTACTGTCAGCCCTAGACTC 60.492 52.174 0.00 0.00 36.94 3.36
495 1365 5.821470 TCGGTTTGTACAAATTCCAACACTA 59.179 36.000 23.11 0.00 32.36 2.74
517 1387 8.331022 CACTATTCCTCAATCACAACTTTATCG 58.669 37.037 0.00 0.00 0.00 2.92
521 1391 6.100004 TCCTCAATCACAACTTTATCGAGTC 58.900 40.000 0.00 0.00 0.00 3.36
552 1563 7.280356 TGTTCCTAAAGTTCTCTAGTTTTGCT 58.720 34.615 0.00 0.00 31.84 3.91
583 1594 4.789012 ATGGCTTTGGAAACACATGTAG 57.211 40.909 0.00 0.00 42.67 2.74
650 1662 3.551250 GCTAGATTACAGAGGAGTTCGGC 60.551 52.174 0.00 0.00 0.00 5.54
660 1672 1.579932 GAGTTCGGCTGAGACGTGA 59.420 57.895 7.91 0.00 34.61 4.35
666 1678 1.361668 CGGCTGAGACGTGAATTGGG 61.362 60.000 0.00 0.00 0.00 4.12
730 1742 2.587194 GATCTGCATCAGCCGCGT 60.587 61.111 4.92 0.00 41.13 6.01
743 1755 0.037605 GCCGCGTATGGTATAAGGCT 60.038 55.000 4.92 0.00 39.92 4.58
748 1760 2.875933 GCGTATGGTATAAGGCTGCAAA 59.124 45.455 0.50 0.00 0.00 3.68
749 1761 3.303791 GCGTATGGTATAAGGCTGCAAAC 60.304 47.826 0.50 0.00 0.00 2.93
750 1762 3.250040 CGTATGGTATAAGGCTGCAAACC 59.750 47.826 0.50 1.72 0.00 3.27
757 1769 1.549203 AAGGCTGCAAACCGATGATT 58.451 45.000 0.50 0.00 0.00 2.57
760 1772 1.474077 GGCTGCAAACCGATGATTTCT 59.526 47.619 0.50 0.00 0.00 2.52
762 1774 3.487544 GGCTGCAAACCGATGATTTCTAC 60.488 47.826 0.50 0.00 0.00 2.59
787 1799 1.538047 AAGCTTGGCTGTGTATGGTG 58.462 50.000 0.00 0.00 39.62 4.17
818 1830 1.609208 AATCAGTTCACAAAGCGCCT 58.391 45.000 2.29 0.00 0.00 5.52
821 1833 1.333619 TCAGTTCACAAAGCGCCTTTC 59.666 47.619 2.29 0.00 30.60 2.62
855 1867 8.430801 ACAAGCTTATTTCTGACATATCTGAC 57.569 34.615 0.00 0.00 32.96 3.51
866 1878 5.423015 TGACATATCTGACTGGAAAAGCTC 58.577 41.667 0.00 0.00 0.00 4.09
867 1879 5.046376 TGACATATCTGACTGGAAAAGCTCA 60.046 40.000 0.00 0.00 0.00 4.26
868 1880 5.181748 ACATATCTGACTGGAAAAGCTCAC 58.818 41.667 0.00 0.00 0.00 3.51
869 1881 2.550830 TCTGACTGGAAAAGCTCACC 57.449 50.000 0.00 0.00 0.00 4.02
870 1882 1.072331 TCTGACTGGAAAAGCTCACCC 59.928 52.381 0.00 0.00 0.00 4.61
871 1883 1.072965 CTGACTGGAAAAGCTCACCCT 59.927 52.381 0.00 0.00 0.00 4.34
872 1884 1.494721 TGACTGGAAAAGCTCACCCTT 59.505 47.619 0.00 0.00 0.00 3.95
886 1898 1.153756 CCCTTGGTTCACTGGCCTT 59.846 57.895 3.32 0.00 0.00 4.35
892 1904 1.098050 GGTTCACTGGCCTTGCTATG 58.902 55.000 3.32 0.00 0.00 2.23
899 1911 2.113986 GCCTTGCTATGGGCGGAT 59.886 61.111 0.00 0.00 45.43 4.18
942 1954 9.794719 ATAAATAGACCCCTTAATTAAGCTCAC 57.205 33.333 18.18 10.02 32.02 3.51
960 1972 4.012374 CTCACTGCCATATCCAACAAACT 58.988 43.478 0.00 0.00 0.00 2.66
983 1995 7.275920 ACTATTTGTTGTAGAGGATCATCCAC 58.724 38.462 6.42 0.00 39.61 4.02
984 1996 5.497464 TTTGTTGTAGAGGATCATCCACA 57.503 39.130 6.42 4.49 39.61 4.17
985 1997 4.471904 TGTTGTAGAGGATCATCCACAC 57.528 45.455 8.15 5.17 39.61 3.82
1084 2096 6.996879 CACCATCCATTCAACTCAATCTCTAT 59.003 38.462 0.00 0.00 0.00 1.98
1085 2097 7.501559 CACCATCCATTCAACTCAATCTCTATT 59.498 37.037 0.00 0.00 0.00 1.73
1086 2098 7.718753 ACCATCCATTCAACTCAATCTCTATTC 59.281 37.037 0.00 0.00 0.00 1.75
1087 2099 7.937942 CCATCCATTCAACTCAATCTCTATTCT 59.062 37.037 0.00 0.00 0.00 2.40
1088 2100 8.991026 CATCCATTCAACTCAATCTCTATTCTC 58.009 37.037 0.00 0.00 0.00 2.87
1089 2101 8.316497 TCCATTCAACTCAATCTCTATTCTCT 57.684 34.615 0.00 0.00 0.00 3.10
1090 2102 9.426534 TCCATTCAACTCAATCTCTATTCTCTA 57.573 33.333 0.00 0.00 0.00 2.43
1250 2266 7.614124 TTGTACTAACCTTGACTTCGTTTTT 57.386 32.000 0.00 0.00 0.00 1.94
1320 2336 2.680352 GGGTGACGAGCTCAGGGA 60.680 66.667 15.40 0.00 0.00 4.20
1439 2455 0.517316 CGCCTACAAGCAGTTGTTCC 59.483 55.000 0.00 0.00 45.00 3.62
1469 2485 1.644509 TGAGGCTGGACTGAAGCTAA 58.355 50.000 0.00 0.00 40.64 3.09
1513 2529 2.358247 GGTGGCAACGTCGGTGAT 60.358 61.111 16.01 0.00 42.51 3.06
1673 2689 3.305720 AGATCTGCCGTCCAGGTTAATA 58.694 45.455 0.00 0.00 42.05 0.98
1699 2719 1.400142 CACCACTCTAGCTCTCTCGTG 59.600 57.143 0.00 0.00 0.00 4.35
1786 2813 4.216042 GCAAATACAAGCAAAAGGCCAAAT 59.784 37.500 5.01 0.00 46.50 2.32
1853 2880 6.388394 AGAGTGAAAAGAATCTAGGGCCTAAT 59.612 38.462 15.43 8.39 0.00 1.73
1868 3028 3.691609 GGCCTAATCACAGGAAGAACAAG 59.308 47.826 0.00 0.00 38.00 3.16
1926 3087 7.875971 TGGTAGAAAGCTTTGATTCTTCTTTC 58.124 34.615 18.30 0.00 41.52 2.62
1931 3092 3.509184 AGCTTTGATTCTTCTTTCTGGCC 59.491 43.478 0.00 0.00 0.00 5.36
1945 3106 2.661718 TCTGGCCGTGACAGATGTATA 58.338 47.619 5.45 0.00 43.49 1.47
2070 3231 2.549082 CCATCCTATCCTCAGAGCCAT 58.451 52.381 0.00 0.00 0.00 4.40
2106 3267 2.628178 AGGCATCGGAGAATTCATCGTA 59.372 45.455 8.44 2.48 43.58 3.43
2152 3313 7.761038 AAATATTTCCTCTTTTGTTCCGACT 57.239 32.000 0.00 0.00 0.00 4.18
2196 3620 2.752903 GTGATGACCAAAGGCGGTTTAT 59.247 45.455 0.00 0.00 40.22 1.40
2233 3659 7.534239 GTGACGATCTACATTGGAAAAGTTTTC 59.466 37.037 18.30 18.30 0.00 2.29
2237 3663 7.959651 CGATCTACATTGGAAAAGTTTTCTCAG 59.040 37.037 23.89 15.16 0.00 3.35
2250 3676 1.021202 TTCTCAGCAAACCAACACCG 58.979 50.000 0.00 0.00 0.00 4.94
2261 3687 3.726291 ACCAACACCGAAATGAAAAGG 57.274 42.857 0.00 0.00 0.00 3.11
2268 3694 4.459337 ACACCGAAATGAAAAGGGATTCTC 59.541 41.667 0.00 0.00 0.00 2.87
2322 4096 2.408271 TCAGAACAAGGCATGGCTAG 57.592 50.000 23.63 8.57 0.00 3.42
2326 4100 0.995024 AACAAGGCATGGCTAGACCT 59.005 50.000 23.63 2.96 40.22 3.85
2357 4133 0.105349 TTCTCCTACCCCATACCCCG 60.105 60.000 0.00 0.00 0.00 5.73
2370 4146 3.561143 CATACCCCGATCCCAATTTTCA 58.439 45.455 0.00 0.00 0.00 2.69
2416 4192 8.846943 AAGACATCATACAAACTTGACACATA 57.153 30.769 0.00 0.00 0.00 2.29
2417 4193 9.453572 AAGACATCATACAAACTTGACACATAT 57.546 29.630 0.00 0.00 0.00 1.78
2559 4337 6.586344 TCCAAAATGGTTTTCTGCACATTAA 58.414 32.000 0.00 0.00 39.03 1.40
2560 4338 7.222872 TCCAAAATGGTTTTCTGCACATTAAT 58.777 30.769 0.00 0.00 39.03 1.40
2561 4339 7.718753 TCCAAAATGGTTTTCTGCACATTAATT 59.281 29.630 0.00 0.00 39.03 1.40
2562 4340 7.804129 CCAAAATGGTTTTCTGCACATTAATTG 59.196 33.333 0.00 2.11 33.54 2.32
2573 4351 6.663093 TCTGCACATTAATTGTAGTCCCAATT 59.337 34.615 12.06 4.73 44.81 2.32
2574 4352 7.178274 TCTGCACATTAATTGTAGTCCCAATTT 59.822 33.333 4.66 0.00 41.11 1.82
2585 4363 4.890158 AGTCCCAATTTTTCATTGACCC 57.110 40.909 0.00 0.00 0.00 4.46
2586 4364 3.258123 AGTCCCAATTTTTCATTGACCCG 59.742 43.478 0.00 0.00 0.00 5.28
2587 4365 2.028567 TCCCAATTTTTCATTGACCCGC 60.029 45.455 0.00 0.00 0.00 6.13
2609 4387 9.345517 CCCGCAATATTTCAAGTTCATATATTG 57.654 33.333 5.84 5.84 40.00 1.90
2662 4443 8.387039 TCTATATGGTGAGATTAGTGAGCTAGT 58.613 37.037 0.00 0.00 0.00 2.57
2688 4469 0.102481 CTTGATGCAAGGCAGATGGC 59.898 55.000 0.00 0.00 43.65 4.40
2693 4474 3.685954 ATGCAAGGCAGATGGCACAGA 62.686 52.381 9.22 0.00 42.90 3.41
2694 4475 4.934587 ATGCAAGGCAGATGGCACAGAT 62.935 50.000 9.22 0.00 42.90 2.90
2968 4898 6.209391 CACCATTAAAGACAAAAGGACTCCAT 59.791 38.462 0.00 0.00 0.00 3.41
3099 5029 4.508128 TTCCTCGCGATGCCGGAC 62.508 66.667 10.36 0.00 36.06 4.79
3375 5326 9.772973 AGAAGTAGTGTATGATAAACAACAACA 57.227 29.630 0.00 0.00 0.00 3.33
3378 5329 9.332502 AGTAGTGTATGATAAACAACAACAACA 57.667 29.630 0.00 0.00 0.00 3.33
3379 5330 9.938670 GTAGTGTATGATAAACAACAACAACAA 57.061 29.630 0.00 0.00 0.00 2.83
3380 5331 8.850454 AGTGTATGATAAACAACAACAACAAC 57.150 30.769 0.00 0.00 0.00 3.32
3381 5332 8.462811 AGTGTATGATAAACAACAACAACAACA 58.537 29.630 0.00 0.00 0.00 3.33
3382 5333 9.077674 GTGTATGATAAACAACAACAACAACAA 57.922 29.630 0.00 0.00 0.00 2.83
3383 5334 9.077674 TGTATGATAAACAACAACAACAACAAC 57.922 29.630 0.00 0.00 0.00 3.32
3384 5335 9.077674 GTATGATAAACAACAACAACAACAACA 57.922 29.630 0.00 0.00 0.00 3.33
3385 5336 7.946655 TGATAAACAACAACAACAACAACAA 57.053 28.000 0.00 0.00 0.00 2.83
3386 5337 7.788055 TGATAAACAACAACAACAACAACAAC 58.212 30.769 0.00 0.00 0.00 3.32
3387 5338 7.438160 TGATAAACAACAACAACAACAACAACA 59.562 29.630 0.00 0.00 0.00 3.33
3388 5339 6.422776 AAACAACAACAACAACAACAACAA 57.577 29.167 0.00 0.00 0.00 2.83
3392 5343 6.963805 ACAACAACAACAACAACAACAAAAAG 59.036 30.769 0.00 0.00 0.00 2.27
3532 5510 2.437180 CAAGCCATGCAGCCGAGA 60.437 61.111 0.00 0.00 0.00 4.04
3567 5545 9.080097 GGGTACTACAACTTACATGATAGAGAT 57.920 37.037 0.00 0.00 0.00 2.75
3605 5583 1.444895 GCATGCTCAAAAGGCACCG 60.445 57.895 11.37 0.00 42.69 4.94
3701 5701 5.262804 AGAACTAGTCCAACAGGTAGGTAG 58.737 45.833 0.00 0.00 0.00 3.18
3708 5708 2.038557 CCAACAGGTAGGTAGCTTGTGT 59.961 50.000 0.00 0.00 30.45 3.72
3716 5716 2.175202 AGGTAGCTTGTGTCTCCAGAG 58.825 52.381 0.00 0.00 0.00 3.35
3873 5873 3.244875 ACAACACCATACTCAGGAATGCA 60.245 43.478 0.00 0.00 0.00 3.96
4034 6034 0.958822 GTTAGTGCCACAACCCCTTG 59.041 55.000 0.00 0.00 0.00 3.61
4053 6053 5.470777 CCCTTGTTCATGCATGTCAAAAATT 59.529 36.000 25.43 0.00 0.00 1.82
4086 6086 8.938906 AGGAATCATTAATTTGTTGATTTGCAC 58.061 29.630 9.96 4.53 39.52 4.57
4095 6095 1.476488 GTTGATTTGCACCGGCCTATT 59.524 47.619 0.00 0.00 40.13 1.73
4105 6105 3.365969 GCACCGGCCTATTACAATAATGC 60.366 47.826 0.00 0.00 0.00 3.56
4253 6253 3.865929 AAGAGCACACCGACCTGCG 62.866 63.158 0.00 0.00 38.51 5.18
4284 6287 3.809013 GGTGGCATCGGTGGGGAT 61.809 66.667 0.00 0.00 0.00 3.85
4368 6443 3.065306 CTCCCTGCCACCGTGTAA 58.935 61.111 0.00 0.00 0.00 2.41
4381 6456 5.636837 CCACCGTGTAATGAAACCTTTATG 58.363 41.667 0.00 0.00 0.00 1.90
4507 6592 2.912956 TCAGTGCTGGAAGGGTTAATCT 59.087 45.455 0.00 0.00 0.00 2.40
4533 6618 1.816074 TGTGAGAATTAACCGTGCCC 58.184 50.000 0.00 0.00 0.00 5.36
4534 6619 1.349688 TGTGAGAATTAACCGTGCCCT 59.650 47.619 0.00 0.00 0.00 5.19
4536 6621 3.195661 GTGAGAATTAACCGTGCCCTAG 58.804 50.000 0.00 0.00 0.00 3.02
4538 6623 3.516300 TGAGAATTAACCGTGCCCTAGAA 59.484 43.478 0.00 0.00 0.00 2.10
4539 6624 4.020039 TGAGAATTAACCGTGCCCTAGAAA 60.020 41.667 0.00 0.00 0.00 2.52
4574 6659 7.136822 AGGATAAATAAGATGTGGTGCTACA 57.863 36.000 0.00 0.00 34.63 2.74
4634 6719 5.593679 CATCAAGAGGATGCTTTTCCAAT 57.406 39.130 0.00 0.00 46.35 3.16
4691 6776 7.806487 CCATTATGTGCATATGAGTGAATGAAC 59.194 37.037 6.97 0.00 32.98 3.18
4695 6780 6.380995 TGTGCATATGAGTGAATGAACAAAC 58.619 36.000 6.97 0.00 38.44 2.93
4699 6784 8.959548 TGCATATGAGTGAATGAACAAACTATT 58.040 29.630 6.97 0.00 0.00 1.73
4771 6895 0.810031 ACGATTACCACTCGCATGGC 60.810 55.000 4.80 0.00 44.33 4.40
4819 6971 5.979288 ACTAAGTGTCCAATCTACTTCGT 57.021 39.130 0.00 0.00 36.22 3.85
4894 7046 7.361889 TCGTAATCAAGCCGTAAATTTTGTA 57.638 32.000 0.00 0.00 0.00 2.41
4908 7060 7.006742 CGTAAATTTTGTATGTAGTTTGGTCGC 59.993 37.037 0.00 0.00 0.00 5.19
4916 7068 2.796031 TGTAGTTTGGTCGCAGTTTACG 59.204 45.455 0.00 0.00 0.00 3.18
4930 7082 4.090210 GCAGTTTACGAAGCTACTCAAGAC 59.910 45.833 0.00 0.00 0.00 3.01
4968 7120 1.165270 CTTGGTGAACCGGTCAATCC 58.835 55.000 8.04 9.33 38.23 3.01
4970 7122 0.036164 TGGTGAACCGGTCAATCCTG 59.964 55.000 8.04 0.00 38.23 3.86
4983 7142 5.355350 CGGTCAATCCTGCTAAAGAAATTCT 59.645 40.000 0.00 0.00 0.00 2.40
5115 7276 7.180051 GGATCTACCTGAGATATTTCTGGACAT 59.820 40.741 21.53 11.75 45.48 3.06
5135 7296 6.206829 GGACATCAATTTACCTGGGCTAATAC 59.793 42.308 0.00 0.00 0.00 1.89
5234 7395 8.330302 GGTAACAATACATGATTTGGTACGTAC 58.670 37.037 17.56 17.56 43.67 3.67
5248 7409 1.448985 ACGTACCAAAGCATCGCAAT 58.551 45.000 0.00 0.00 0.00 3.56
5281 7442 4.638421 AGTCAAGTTCGAATGGTTTGTTGA 59.362 37.500 0.00 0.25 0.00 3.18
5282 7443 5.299279 AGTCAAGTTCGAATGGTTTGTTGAT 59.701 36.000 0.00 0.00 0.00 2.57
5283 7444 5.399301 GTCAAGTTCGAATGGTTTGTTGATG 59.601 40.000 0.00 0.00 0.00 3.07
5284 7445 5.067153 TCAAGTTCGAATGGTTTGTTGATGT 59.933 36.000 0.00 0.00 0.00 3.06
5285 7446 6.261158 TCAAGTTCGAATGGTTTGTTGATGTA 59.739 34.615 0.00 0.00 0.00 2.29
5286 7447 6.241207 AGTTCGAATGGTTTGTTGATGTAG 57.759 37.500 0.00 0.00 0.00 2.74
5287 7448 5.763204 AGTTCGAATGGTTTGTTGATGTAGT 59.237 36.000 0.00 0.00 0.00 2.73
5288 7449 5.856126 TCGAATGGTTTGTTGATGTAGTC 57.144 39.130 0.00 0.00 0.00 2.59
5289 7450 5.301555 TCGAATGGTTTGTTGATGTAGTCA 58.698 37.500 0.00 0.00 34.25 3.41
5290 7451 5.760743 TCGAATGGTTTGTTGATGTAGTCAA 59.239 36.000 0.00 0.00 44.36 3.18
5301 7462 5.766150 TGATGTAGTCAACAAGGTTTTGG 57.234 39.130 0.00 0.00 42.70 3.28
5302 7463 5.441500 TGATGTAGTCAACAAGGTTTTGGA 58.558 37.500 0.00 0.00 42.70 3.53
5303 7464 6.068010 TGATGTAGTCAACAAGGTTTTGGAT 58.932 36.000 0.00 0.00 42.70 3.41
5304 7465 5.766150 TGTAGTCAACAAGGTTTTGGATG 57.234 39.130 0.00 0.00 38.66 3.51
5305 7466 4.582656 TGTAGTCAACAAGGTTTTGGATGG 59.417 41.667 0.00 0.00 38.66 3.51
5306 7467 3.642141 AGTCAACAAGGTTTTGGATGGT 58.358 40.909 0.00 0.00 38.66 3.55
5307 7468 3.636764 AGTCAACAAGGTTTTGGATGGTC 59.363 43.478 0.00 0.00 38.66 4.02
5308 7469 2.621055 TCAACAAGGTTTTGGATGGTCG 59.379 45.455 0.00 0.00 38.66 4.79
5309 7470 2.621055 CAACAAGGTTTTGGATGGTCGA 59.379 45.455 0.00 0.00 38.66 4.20
5310 7471 3.154827 ACAAGGTTTTGGATGGTCGAT 57.845 42.857 0.00 0.00 38.66 3.59
5311 7472 2.819608 ACAAGGTTTTGGATGGTCGATG 59.180 45.455 0.00 0.00 38.66 3.84
5312 7473 3.081061 CAAGGTTTTGGATGGTCGATGA 58.919 45.455 0.00 0.00 0.00 2.92
5313 7474 3.652057 AGGTTTTGGATGGTCGATGAT 57.348 42.857 0.00 0.00 0.00 2.45
5314 7475 3.282021 AGGTTTTGGATGGTCGATGATG 58.718 45.455 0.00 0.00 0.00 3.07
5315 7476 2.358898 GGTTTTGGATGGTCGATGATGG 59.641 50.000 0.00 0.00 0.00 3.51
5316 7477 2.346766 TTTGGATGGTCGATGATGGG 57.653 50.000 0.00 0.00 0.00 4.00
5317 7478 1.212375 TTGGATGGTCGATGATGGGT 58.788 50.000 0.00 0.00 0.00 4.51
5318 7479 2.095604 TGGATGGTCGATGATGGGTA 57.904 50.000 0.00 0.00 0.00 3.69
5319 7480 1.970640 TGGATGGTCGATGATGGGTAG 59.029 52.381 0.00 0.00 0.00 3.18
5320 7481 2.248248 GGATGGTCGATGATGGGTAGA 58.752 52.381 0.00 0.00 0.00 2.59
5321 7482 2.834549 GGATGGTCGATGATGGGTAGAT 59.165 50.000 0.00 0.00 0.00 1.98
5322 7483 3.118956 GGATGGTCGATGATGGGTAGATC 60.119 52.174 0.00 0.00 0.00 2.75
5323 7484 1.886542 TGGTCGATGATGGGTAGATCG 59.113 52.381 0.00 0.00 40.26 3.69
5324 7485 1.402984 GGTCGATGATGGGTAGATCGC 60.403 57.143 0.00 0.00 39.05 4.58
5325 7486 0.888619 TCGATGATGGGTAGATCGCC 59.111 55.000 0.00 1.32 39.05 5.54
5326 7487 0.891373 CGATGATGGGTAGATCGCCT 59.109 55.000 8.83 0.00 33.26 5.52
5327 7488 1.273606 CGATGATGGGTAGATCGCCTT 59.726 52.381 8.83 0.00 33.26 4.35
5328 7489 2.672478 CGATGATGGGTAGATCGCCTTC 60.672 54.545 8.83 7.31 33.26 3.46
5329 7490 1.048601 TGATGGGTAGATCGCCTTCC 58.951 55.000 8.83 0.00 0.00 3.46
5333 7494 3.688553 GGTAGATCGCCTTCCCAAG 57.311 57.895 2.63 0.00 0.00 3.61
5364 7525 5.343307 AAAAATCCTCACTTTGCAACAGT 57.657 34.783 0.00 3.44 0.00 3.55
5365 7526 5.343307 AAAATCCTCACTTTGCAACAGTT 57.657 34.783 0.00 0.00 0.00 3.16
5366 7527 4.574599 AATCCTCACTTTGCAACAGTTC 57.425 40.909 0.00 0.00 0.00 3.01
5367 7528 2.297701 TCCTCACTTTGCAACAGTTCC 58.702 47.619 0.00 0.00 0.00 3.62
5368 7529 2.092429 TCCTCACTTTGCAACAGTTCCT 60.092 45.455 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.857777 AAGTGCATGAGTATTAGCAAGATC 57.142 37.500 0.00 0.00 38.91 2.75
20 21 8.129161 TGTAAACATTTTTGAAAGTGCATGAG 57.871 30.769 0.00 0.00 0.00 2.90
45 46 6.883756 TGACTTTTTGGCTTTTTGGAAATTCT 59.116 30.769 0.00 0.00 0.00 2.40
107 109 3.425122 TTTTTCTCCACCGGTTCCC 57.575 52.632 2.97 0.00 0.00 3.97
126 128 8.669946 TTTTTATTGCGGATTTTCCTTTTCTT 57.330 26.923 0.00 0.00 33.30 2.52
134 136 9.567848 TTCTACTGATTTTTATTGCGGATTTTC 57.432 29.630 0.00 0.00 0.00 2.29
136 138 9.736023 GATTCTACTGATTTTTATTGCGGATTT 57.264 29.630 0.00 0.00 0.00 2.17
137 139 8.070171 CGATTCTACTGATTTTTATTGCGGATT 58.930 33.333 0.00 0.00 0.00 3.01
138 140 7.441157 TCGATTCTACTGATTTTTATTGCGGAT 59.559 33.333 0.00 0.00 0.00 4.18
139 141 6.759356 TCGATTCTACTGATTTTTATTGCGGA 59.241 34.615 0.00 0.00 0.00 5.54
140 142 6.846283 GTCGATTCTACTGATTTTTATTGCGG 59.154 38.462 0.00 0.00 0.00 5.69
161 163 5.366460 AGCAGTAACTGTAGCTATAGTCGA 58.634 41.667 21.74 11.42 35.19 4.20
163 165 6.072893 GGAGAGCAGTAACTGTAGCTATAGTC 60.073 46.154 21.74 11.54 37.48 2.59
181 183 0.105964 CCAGGCTACCTAGGAGAGCA 60.106 60.000 29.38 7.05 37.98 4.26
243 245 7.378181 GGAATTTCTTATTCTTTGCCTGTTGA 58.622 34.615 0.00 0.00 0.00 3.18
248 250 7.895962 ACTAAGGGAATTTCTTATTCTTTGCCT 59.104 33.333 0.00 0.00 39.46 4.75
287 289 1.597461 GCTTAGGGGAGTGCTTCGT 59.403 57.895 0.00 0.00 0.00 3.85
288 290 1.153349 GGCTTAGGGGAGTGCTTCG 60.153 63.158 0.00 0.00 0.00 3.79
289 291 0.328258 TTGGCTTAGGGGAGTGCTTC 59.672 55.000 0.00 0.00 0.00 3.86
290 292 0.038310 GTTGGCTTAGGGGAGTGCTT 59.962 55.000 0.00 0.00 0.00 3.91
292 294 0.034089 ATGTTGGCTTAGGGGAGTGC 60.034 55.000 0.00 0.00 0.00 4.40
296 300 1.367346 TGTGATGTTGGCTTAGGGGA 58.633 50.000 0.00 0.00 0.00 4.81
345 1200 2.076100 CTTTCTCAAGTGCATACGCCA 58.924 47.619 0.00 0.00 37.32 5.69
411 1281 1.059369 CTGACAGTAATGCACGCGC 59.941 57.895 5.73 0.00 39.24 6.86
412 1282 1.059369 GCTGACAGTAATGCACGCG 59.941 57.895 3.53 3.53 0.00 6.01
415 1285 2.168521 TCTAGGGCTGACAGTAATGCAC 59.831 50.000 3.99 0.00 0.00 4.57
419 1289 3.052490 AGGAGTCTAGGGCTGACAGTAAT 60.052 47.826 3.99 0.00 36.94 1.89
439 1309 3.199946 TGTAAACCATGGGCTTCTAGAGG 59.800 47.826 18.09 0.00 0.00 3.69
495 1365 7.106239 ACTCGATAAAGTTGTGATTGAGGAAT 58.894 34.615 11.75 0.00 35.99 3.01
517 1387 6.391537 AGAACTTTAGGAACAATCTCGACTC 58.608 40.000 0.00 0.00 0.00 3.36
521 1391 7.540299 ACTAGAGAACTTTAGGAACAATCTCG 58.460 38.462 0.00 0.00 37.49 4.04
552 1563 5.127845 TGTTTCCAAAGCCATTGTCTAACAA 59.872 36.000 0.00 0.00 42.95 2.83
583 1594 2.877691 GCATCCCGGCACAAGTTC 59.122 61.111 0.00 0.00 0.00 3.01
650 1662 1.676014 GGGACCCAATTCACGTCTCAG 60.676 57.143 5.33 0.00 0.00 3.35
660 1672 4.881157 ATAGCTAACTTGGGACCCAATT 57.119 40.909 26.44 18.35 43.07 2.32
666 1678 9.476928 TCCTTATCTATATAGCTAACTTGGGAC 57.523 37.037 4.75 0.00 0.00 4.46
730 1742 3.134985 TCGGTTTGCAGCCTTATACCATA 59.865 43.478 7.63 0.00 0.00 2.74
743 1755 3.013921 GGGTAGAAATCATCGGTTTGCA 58.986 45.455 0.00 0.00 0.00 4.08
748 1760 5.104485 AGCTTAAAGGGTAGAAATCATCGGT 60.104 40.000 0.00 0.00 0.00 4.69
749 1761 5.368989 AGCTTAAAGGGTAGAAATCATCGG 58.631 41.667 0.00 0.00 0.00 4.18
750 1762 6.238484 CCAAGCTTAAAGGGTAGAAATCATCG 60.238 42.308 0.00 0.00 0.00 3.84
757 1769 3.073946 ACAGCCAAGCTTAAAGGGTAGAA 59.926 43.478 0.00 0.00 36.40 2.10
760 1772 2.107552 ACACAGCCAAGCTTAAAGGGTA 59.892 45.455 0.00 0.00 36.40 3.69
762 1774 1.620822 ACACAGCCAAGCTTAAAGGG 58.379 50.000 0.00 0.00 36.40 3.95
787 1799 6.959671 TGTGAACTGATTTTGGTTTTGTTC 57.040 33.333 0.00 0.00 34.66 3.18
821 1833 4.394300 CAGAAATAAGCTTGTCCAGTCAGG 59.606 45.833 9.86 0.00 39.47 3.86
855 1867 1.251251 CCAAGGGTGAGCTTTTCCAG 58.749 55.000 0.00 0.00 0.00 3.86
866 1878 1.903404 GGCCAGTGAACCAAGGGTG 60.903 63.158 0.00 0.00 35.34 4.61
867 1879 1.655114 AAGGCCAGTGAACCAAGGGT 61.655 55.000 5.01 0.00 37.65 4.34
868 1880 1.153756 AAGGCCAGTGAACCAAGGG 59.846 57.895 5.01 0.00 0.00 3.95
869 1881 1.809567 GCAAGGCCAGTGAACCAAGG 61.810 60.000 5.01 0.00 0.00 3.61
870 1882 0.825010 AGCAAGGCCAGTGAACCAAG 60.825 55.000 5.01 0.00 0.00 3.61
871 1883 0.476338 TAGCAAGGCCAGTGAACCAA 59.524 50.000 5.01 0.00 0.00 3.67
872 1884 0.698238 ATAGCAAGGCCAGTGAACCA 59.302 50.000 5.01 0.00 0.00 3.67
886 1898 1.644509 AGATGTATCCGCCCATAGCA 58.355 50.000 0.00 0.00 44.04 3.49
892 1904 5.063880 ACTATGAAAAAGATGTATCCGCCC 58.936 41.667 0.00 0.00 0.00 6.13
960 1972 7.047891 GTGTGGATGATCCTCTACAACAAATA 58.952 38.462 16.65 0.00 38.21 1.40
974 1986 0.393402 TGCTGGCTGTGTGGATGATC 60.393 55.000 0.00 0.00 0.00 2.92
983 1995 2.273179 ATTGTGGCTGCTGGCTGTG 61.273 57.895 17.87 0.00 41.46 3.66
984 1996 2.116772 ATTGTGGCTGCTGGCTGT 59.883 55.556 17.87 0.00 41.46 4.40
985 1997 2.571757 CATTGTGGCTGCTGGCTG 59.428 61.111 17.87 4.37 41.46 4.85
1084 2096 3.260632 TGTAGTGCATGGTGCTTAGAGAA 59.739 43.478 3.41 0.00 45.31 2.87
1085 2097 2.831526 TGTAGTGCATGGTGCTTAGAGA 59.168 45.455 3.41 0.00 45.31 3.10
1086 2098 3.251479 TGTAGTGCATGGTGCTTAGAG 57.749 47.619 3.41 0.00 45.31 2.43
1087 2099 3.334691 GTTGTAGTGCATGGTGCTTAGA 58.665 45.455 3.41 0.00 45.31 2.10
1088 2100 2.420022 GGTTGTAGTGCATGGTGCTTAG 59.580 50.000 3.41 0.00 45.31 2.18
1089 2101 2.224646 TGGTTGTAGTGCATGGTGCTTA 60.225 45.455 3.41 0.00 45.31 3.09
1090 2102 1.247567 GGTTGTAGTGCATGGTGCTT 58.752 50.000 3.41 0.00 45.31 3.91
1163 2178 6.891388 TCACCCTTTGAACTAGAGTGTTTAA 58.109 36.000 0.00 0.00 0.00 1.52
1167 2182 4.409247 ACTTCACCCTTTGAACTAGAGTGT 59.591 41.667 0.00 0.00 39.45 3.55
1250 2266 5.123186 CGTCCAGCTATTTATTTCCACAACA 59.877 40.000 0.00 0.00 0.00 3.33
1320 2336 1.277557 CTACCAGCCTCTTCAGTTGCT 59.722 52.381 0.00 0.00 33.52 3.91
1439 2455 2.045242 AGCCTCATGCACCAGCTG 60.045 61.111 6.78 6.78 44.83 4.24
1469 2485 2.381911 GTGGAATGACATGATGGCCTT 58.618 47.619 3.32 0.00 0.00 4.35
1513 2529 0.174845 GGATCGGGATGTTGACGACA 59.825 55.000 0.00 0.00 43.71 4.35
1673 2689 4.615513 AGAGAGCTAGAGTGGTGGTTTAT 58.384 43.478 0.00 0.00 0.00 1.40
1763 2790 2.765122 TGGCCTTTTGCTTGTATTTGC 58.235 42.857 3.32 0.00 40.92 3.68
1786 2813 8.759481 TCTGTTGATATATATTTTTGGCACCA 57.241 30.769 0.00 0.00 0.00 4.17
1823 2850 7.275920 GCCCTAGATTCTTTTCACTCTTGATA 58.724 38.462 0.00 0.00 0.00 2.15
1824 2851 6.118852 GCCCTAGATTCTTTTCACTCTTGAT 58.881 40.000 0.00 0.00 0.00 2.57
1826 2853 4.637977 GGCCCTAGATTCTTTTCACTCTTG 59.362 45.833 0.00 0.00 0.00 3.02
1827 2854 4.538089 AGGCCCTAGATTCTTTTCACTCTT 59.462 41.667 0.00 0.00 0.00 2.85
1828 2855 4.107820 AGGCCCTAGATTCTTTTCACTCT 58.892 43.478 0.00 0.00 0.00 3.24
1829 2856 4.495690 AGGCCCTAGATTCTTTTCACTC 57.504 45.455 0.00 0.00 0.00 3.51
1842 2869 3.309296 TCTTCCTGTGATTAGGCCCTAG 58.691 50.000 0.00 0.00 37.76 3.02
1846 2873 3.350219 TGTTCTTCCTGTGATTAGGCC 57.650 47.619 0.00 0.00 37.76 5.19
1853 2880 5.105106 TCACAACTACTTGTTCTTCCTGTGA 60.105 40.000 0.00 0.00 38.66 3.58
1868 3028 9.988350 CATTGTACCTATCAAAATCACAACTAC 57.012 33.333 0.00 0.00 0.00 2.73
1926 3087 2.362397 AGTATACATCTGTCACGGCCAG 59.638 50.000 2.24 0.00 0.00 4.85
1931 3092 7.327032 CCATGTAATCAGTATACATCTGTCACG 59.673 40.741 5.50 0.00 40.96 4.35
1945 3106 3.689347 TGAAGCTTGCCATGTAATCAGT 58.311 40.909 2.10 0.00 0.00 3.41
2070 3231 1.213619 TGCCTGGGAATGACCATCCA 61.214 55.000 0.00 0.00 40.36 3.41
2133 3294 9.374838 GTATATTAGTCGGAACAAAAGAGGAAA 57.625 33.333 0.00 0.00 0.00 3.13
2233 3659 1.021202 TTCGGTGTTGGTTTGCTGAG 58.979 50.000 0.00 0.00 0.00 3.35
2237 3663 2.500509 TCATTTCGGTGTTGGTTTGC 57.499 45.000 0.00 0.00 0.00 3.68
2326 4100 3.769844 GGGTAGGAGAACTGATGAAGTCA 59.230 47.826 0.00 0.00 38.56 3.41
2342 4116 0.908180 GGATCGGGGTATGGGGTAGG 60.908 65.000 0.00 0.00 0.00 3.18
2346 4120 1.140134 ATTGGGATCGGGGTATGGGG 61.140 60.000 0.00 0.00 0.00 4.96
2438 4214 5.446143 TGTTGCACAAACGAATCCTATTT 57.554 34.783 0.00 0.00 42.10 1.40
2439 4215 5.643379 ATGTTGCACAAACGAATCCTATT 57.357 34.783 0.00 0.00 42.10 1.73
2467 4243 8.960591 CCCAAGACAGTTATCATTTGAAGTATT 58.039 33.333 0.00 0.00 0.00 1.89
2474 4250 6.588719 TTTCCCCAAGACAGTTATCATTTG 57.411 37.500 0.00 0.00 0.00 2.32
2559 4337 7.386059 GGTCAATGAAAAATTGGGACTACAAT 58.614 34.615 0.00 0.00 42.56 2.71
2560 4338 6.239458 GGGTCAATGAAAAATTGGGACTACAA 60.239 38.462 0.00 0.00 34.41 2.41
2561 4339 5.245075 GGGTCAATGAAAAATTGGGACTACA 59.755 40.000 0.00 0.00 0.00 2.74
2562 4340 5.621329 CGGGTCAATGAAAAATTGGGACTAC 60.621 44.000 0.00 0.00 0.00 2.73
2573 4351 6.030548 TGAAATATTGCGGGTCAATGAAAA 57.969 33.333 0.82 0.00 44.62 2.29
2574 4352 5.651387 TGAAATATTGCGGGTCAATGAAA 57.349 34.783 0.82 0.00 44.62 2.69
2650 4431 4.709886 TCAAGGTATGCACTAGCTCACTAA 59.290 41.667 0.00 0.00 42.74 2.24
2677 4458 2.634815 CTATCTGTGCCATCTGCCTT 57.365 50.000 0.00 0.00 40.16 4.35
3007 4937 3.983988 CAGGTACTTATCATAGCACTGCG 59.016 47.826 0.00 0.00 34.60 5.18
3099 5029 2.567169 TCTGGGGAGTGTCATTGTACTG 59.433 50.000 0.00 0.00 0.00 2.74
3374 5325 7.166628 TGTGTACTTTTTGTTGTTGTTGTTG 57.833 32.000 0.00 0.00 0.00 3.33
3375 5326 7.772332 TTGTGTACTTTTTGTTGTTGTTGTT 57.228 28.000 0.00 0.00 0.00 2.83
3376 5327 7.772332 TTTGTGTACTTTTTGTTGTTGTTGT 57.228 28.000 0.00 0.00 0.00 3.32
3377 5328 9.312146 GAATTTGTGTACTTTTTGTTGTTGTTG 57.688 29.630 0.00 0.00 0.00 3.33
3378 5329 9.046296 TGAATTTGTGTACTTTTTGTTGTTGTT 57.954 25.926 0.00 0.00 0.00 2.83
3379 5330 8.594881 TGAATTTGTGTACTTTTTGTTGTTGT 57.405 26.923 0.00 0.00 0.00 3.32
3382 5333 9.651913 AGAATGAATTTGTGTACTTTTTGTTGT 57.348 25.926 0.00 0.00 0.00 3.32
3532 5510 3.173965 AGTTGTAGTACCCAGCTGTGAT 58.826 45.455 13.81 0.00 0.00 3.06
3605 5583 4.143305 CGCAAGTGAAGTTAAGACTAGCAC 60.143 45.833 0.00 0.00 39.60 4.40
3663 5641 1.741401 TTCTTCCGGTGCGCTCATG 60.741 57.895 9.73 1.00 0.00 3.07
3701 5701 2.731976 CGTAAACTCTGGAGACACAAGC 59.268 50.000 4.49 0.00 35.60 4.01
3708 5708 4.077108 TGTCTAAGCGTAAACTCTGGAGA 58.923 43.478 4.49 0.00 0.00 3.71
3716 5716 7.588488 GTCTATCAGAGATGTCTAAGCGTAAAC 59.412 40.741 0.00 0.00 36.29 2.01
4034 6034 8.763356 TCTGTTTAATTTTTGACATGCATGAAC 58.237 29.630 32.75 23.52 0.00 3.18
4086 6086 5.643379 ATTGCATTATTGTAATAGGCCGG 57.357 39.130 0.00 0.00 36.54 6.13
4105 6105 7.063074 GTCATGAGGCTGAAAAGAATCAAATTG 59.937 37.037 0.00 0.00 0.00 2.32
4221 6221 1.710244 TGCTCTTCAAAGGGGAATGGA 59.290 47.619 0.00 0.00 0.00 3.41
4253 6253 1.376037 CCACCGAGGCCTTGAACTC 60.376 63.158 22.68 0.00 0.00 3.01
4284 6287 2.391130 ACCAGTGGGGCCTTCAACA 61.391 57.895 15.21 0.00 42.05 3.33
4336 6411 3.415087 GAGCTCCCCACCCATGCT 61.415 66.667 0.87 0.00 36.63 3.79
4368 6443 8.993424 AGGTACTGTAGATCATAAAGGTTTCAT 58.007 33.333 0.00 0.00 37.18 2.57
4381 6456 8.656849 CACACAACATAAAAGGTACTGTAGATC 58.343 37.037 0.00 0.00 40.86 2.75
4492 6567 6.150140 CACAAAGAGAAGATTAACCCTTCCAG 59.850 42.308 13.04 5.11 40.54 3.86
4524 6609 2.640184 GCTTATTTCTAGGGCACGGTT 58.360 47.619 0.00 0.00 0.00 4.44
4527 6612 1.202486 TCGGCTTATTTCTAGGGCACG 60.202 52.381 0.00 0.00 30.77 5.34
4528 6613 2.614829 TCGGCTTATTTCTAGGGCAC 57.385 50.000 0.00 0.00 30.77 5.01
4529 6614 2.703536 TCATCGGCTTATTTCTAGGGCA 59.296 45.455 0.00 0.00 30.77 5.36
4530 6615 3.330267 CTCATCGGCTTATTTCTAGGGC 58.670 50.000 0.00 0.00 0.00 5.19
4536 6621 9.436957 TCTTATTTATCCTCATCGGCTTATTTC 57.563 33.333 0.00 0.00 0.00 2.17
4538 6623 9.388506 CATCTTATTTATCCTCATCGGCTTATT 57.611 33.333 0.00 0.00 0.00 1.40
4539 6624 8.543774 ACATCTTATTTATCCTCATCGGCTTAT 58.456 33.333 0.00 0.00 0.00 1.73
4617 6702 3.022406 GCTCATTGGAAAAGCATCCTCT 58.978 45.455 5.04 0.00 40.35 3.69
4618 6703 3.022406 AGCTCATTGGAAAAGCATCCTC 58.978 45.455 5.04 0.00 40.35 3.71
4632 6717 4.959210 AGGTCTGATGTACTACAGCTCATT 59.041 41.667 6.05 0.00 35.18 2.57
4634 6719 3.969553 AGGTCTGATGTACTACAGCTCA 58.030 45.455 6.05 0.09 35.18 4.26
4714 6799 7.307694 CAAAATGATGGACCCATATACAATCG 58.692 38.462 0.82 0.00 36.70 3.34
4771 6895 8.080083 AGTTTACCACGTAACATTAGTCAAAG 57.920 34.615 2.07 0.00 0.00 2.77
4825 6977 7.123355 ACTCTTGATCCAAAATGGTCAAAAA 57.877 32.000 12.29 6.30 37.22 1.94
4871 7023 7.694784 ACATACAAAATTTACGGCTTGATTACG 59.305 33.333 0.00 0.00 0.00 3.18
4894 7046 3.430895 CGTAAACTGCGACCAAACTACAT 59.569 43.478 0.00 0.00 0.00 2.29
4908 7060 4.321217 CGTCTTGAGTAGCTTCGTAAACTG 59.679 45.833 0.00 0.00 0.00 3.16
4916 7068 6.975772 AGTTTATGATCGTCTTGAGTAGCTTC 59.024 38.462 0.00 0.00 0.00 3.86
4930 7082 9.098355 TCACCAAGAAAAGATAGTTTATGATCG 57.902 33.333 0.00 0.00 0.00 3.69
4952 7104 1.305930 GCAGGATTGACCGGTTCACC 61.306 60.000 9.42 10.69 44.74 4.02
4983 7142 5.135191 TCCCCACCCATGAACAATGAATATA 59.865 40.000 0.00 0.00 38.72 0.86
5051 7212 7.362056 GGCAATGCTGAATAAGAAAGAACTGTA 60.362 37.037 4.82 0.00 0.00 2.74
5057 7218 6.153170 TCAATGGCAATGCTGAATAAGAAAGA 59.847 34.615 4.82 0.00 0.00 2.52
5135 7296 1.930908 AAACGTCGACTCTAGCCGGG 61.931 60.000 14.70 0.00 0.00 5.73
5151 7312 3.917985 GCACGTGACCCATATTTTCAAAC 59.082 43.478 22.23 0.00 0.00 2.93
5228 7389 2.081725 TTGCGATGCTTTGGTACGTA 57.918 45.000 0.00 0.00 0.00 3.57
5234 7395 1.531677 CGGTGTATTGCGATGCTTTGG 60.532 52.381 3.52 0.00 0.00 3.28
5242 7403 0.457853 GACTGAGCGGTGTATTGCGA 60.458 55.000 0.00 0.00 35.87 5.10
5243 7404 0.735978 TGACTGAGCGGTGTATTGCG 60.736 55.000 0.00 0.00 35.87 4.85
5248 7409 1.335597 CGAACTTGACTGAGCGGTGTA 60.336 52.381 0.00 0.00 0.00 2.90
5281 7442 5.243730 CCATCCAAAACCTTGTTGACTACAT 59.756 40.000 0.00 0.00 36.44 2.29
5282 7443 4.582656 CCATCCAAAACCTTGTTGACTACA 59.417 41.667 0.00 0.00 34.12 2.74
5283 7444 4.583073 ACCATCCAAAACCTTGTTGACTAC 59.417 41.667 0.00 0.00 0.00 2.73
5284 7445 4.798882 ACCATCCAAAACCTTGTTGACTA 58.201 39.130 0.00 0.00 0.00 2.59
5285 7446 3.636764 GACCATCCAAAACCTTGTTGACT 59.363 43.478 0.00 0.00 0.00 3.41
5286 7447 3.550030 CGACCATCCAAAACCTTGTTGAC 60.550 47.826 0.00 0.00 0.00 3.18
5287 7448 2.621055 CGACCATCCAAAACCTTGTTGA 59.379 45.455 0.00 0.00 0.00 3.18
5288 7449 2.621055 TCGACCATCCAAAACCTTGTTG 59.379 45.455 0.00 0.00 0.00 3.33
5289 7450 2.938838 TCGACCATCCAAAACCTTGTT 58.061 42.857 0.00 0.00 0.00 2.83
5290 7451 2.649531 TCGACCATCCAAAACCTTGT 57.350 45.000 0.00 0.00 0.00 3.16
5291 7452 3.081061 TCATCGACCATCCAAAACCTTG 58.919 45.455 0.00 0.00 0.00 3.61
5292 7453 3.433306 TCATCGACCATCCAAAACCTT 57.567 42.857 0.00 0.00 0.00 3.50
5293 7454 3.282021 CATCATCGACCATCCAAAACCT 58.718 45.455 0.00 0.00 0.00 3.50
5294 7455 2.358898 CCATCATCGACCATCCAAAACC 59.641 50.000 0.00 0.00 0.00 3.27
5295 7456 2.358898 CCCATCATCGACCATCCAAAAC 59.641 50.000 0.00 0.00 0.00 2.43
5296 7457 2.025416 ACCCATCATCGACCATCCAAAA 60.025 45.455 0.00 0.00 0.00 2.44
5297 7458 1.563879 ACCCATCATCGACCATCCAAA 59.436 47.619 0.00 0.00 0.00 3.28
5298 7459 1.212375 ACCCATCATCGACCATCCAA 58.788 50.000 0.00 0.00 0.00 3.53
5299 7460 1.970640 CTACCCATCATCGACCATCCA 59.029 52.381 0.00 0.00 0.00 3.41
5300 7461 2.248248 TCTACCCATCATCGACCATCC 58.752 52.381 0.00 0.00 0.00 3.51
5301 7462 3.428180 CGATCTACCCATCATCGACCATC 60.428 52.174 0.00 0.00 41.61 3.51
5302 7463 2.493675 CGATCTACCCATCATCGACCAT 59.506 50.000 0.00 0.00 41.61 3.55
5303 7464 1.886542 CGATCTACCCATCATCGACCA 59.113 52.381 0.00 0.00 41.61 4.02
5304 7465 1.402984 GCGATCTACCCATCATCGACC 60.403 57.143 4.79 0.00 41.61 4.79
5305 7466 1.402984 GGCGATCTACCCATCATCGAC 60.403 57.143 4.79 0.00 41.61 4.20
5306 7467 0.888619 GGCGATCTACCCATCATCGA 59.111 55.000 4.79 0.00 41.61 3.59
5307 7468 0.891373 AGGCGATCTACCCATCATCG 59.109 55.000 0.00 0.00 41.92 3.84
5308 7469 2.354203 GGAAGGCGATCTACCCATCATC 60.354 54.545 0.00 0.00 0.00 2.92
5309 7470 1.625818 GGAAGGCGATCTACCCATCAT 59.374 52.381 0.00 0.00 0.00 2.45
5310 7471 1.048601 GGAAGGCGATCTACCCATCA 58.951 55.000 0.00 0.00 0.00 3.07
5311 7472 0.321996 GGGAAGGCGATCTACCCATC 59.678 60.000 0.00 0.00 40.20 3.51
5312 7473 0.399949 TGGGAAGGCGATCTACCCAT 60.400 55.000 0.00 0.00 44.50 4.00
5313 7474 1.002403 TGGGAAGGCGATCTACCCA 59.998 57.895 0.00 0.00 46.74 4.51
5314 7475 0.106894 CTTGGGAAGGCGATCTACCC 59.893 60.000 0.00 0.00 40.79 3.69
5315 7476 0.106894 CCTTGGGAAGGCGATCTACC 59.893 60.000 0.00 0.00 42.78 3.18
5316 7477 3.688553 CCTTGGGAAGGCGATCTAC 57.311 57.895 0.00 0.00 42.78 2.59
5342 7503 5.343307 ACTGTTGCAAAGTGAGGATTTTT 57.657 34.783 0.00 0.00 0.00 1.94
5343 7504 5.343307 AACTGTTGCAAAGTGAGGATTTT 57.657 34.783 0.00 0.00 0.00 1.82
5344 7505 4.202151 GGAACTGTTGCAAAGTGAGGATTT 60.202 41.667 0.00 0.00 0.00 2.17
5345 7506 3.319122 GGAACTGTTGCAAAGTGAGGATT 59.681 43.478 0.00 0.00 0.00 3.01
5346 7507 2.887152 GGAACTGTTGCAAAGTGAGGAT 59.113 45.455 0.00 0.00 0.00 3.24
5347 7508 2.092429 AGGAACTGTTGCAAAGTGAGGA 60.092 45.455 14.52 0.00 37.18 3.71
5348 7509 2.301346 AGGAACTGTTGCAAAGTGAGG 58.699 47.619 14.52 0.00 37.18 3.86


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

AutoCloner maintained by Alex Coulton.