Multiple sequence alignment - TraesCS3A01G129400

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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 TraesCS3A01G129400 chr3A 100.000 4218 0 0 1 4218 106664310 106660093 0.000000e+00 7790.0
1 TraesCS3A01G129400 chr3A 78.770 829 111 36 1036 1838 106678868 106678079 2.930000e-136 496.0
2 TraesCS3A01G129400 chr3A 79.603 706 105 25 2017 2703 106677887 106677202 1.780000e-128 470.0
3 TraesCS3A01G129400 chr3A 81.159 276 47 5 3085 3358 106674680 106674408 2.550000e-52 217.0
4 TraesCS3A01G129400 chr3A 96.825 126 3 1 3362 3486 106660828 106660703 4.270000e-50 209.0
5 TraesCS3A01G129400 chr3A 96.825 126 3 1 3483 3608 106660949 106660825 4.270000e-50 209.0
6 TraesCS3A01G129400 chr3D 89.287 2455 145 61 1119 3486 90375061 90372638 0.000000e+00 2968.0
7 TraesCS3A01G129400 chr3D 89.219 1011 63 13 34 1018 90376139 90375149 0.000000e+00 1221.0
8 TraesCS3A01G129400 chr3D 93.001 743 29 8 3483 4218 90372761 90372035 0.000000e+00 1062.0
9 TraesCS3A01G129400 chr3D 76.932 828 103 45 1033 1838 90381676 90380915 1.420000e-104 390.0
10 TraesCS3A01G129400 chr3D 83.158 380 42 10 2331 2703 90380436 90380072 1.130000e-85 327.0
11 TraesCS3A01G129400 chr3D 88.636 220 25 0 2017 2236 90380724 90380505 6.950000e-68 268.0
12 TraesCS3A01G129400 chr3D 88.148 135 13 3 3225 3358 90379455 90379323 1.570000e-34 158.0
13 TraesCS3A01G129400 chr3B 93.029 1248 65 12 2253 3486 139779226 139777987 0.000000e+00 1803.0
14 TraesCS3A01G129400 chr3B 91.993 1149 64 13 1119 2251 139780392 139779256 0.000000e+00 1587.0
15 TraesCS3A01G129400 chr3B 92.123 749 39 12 3483 4218 139778106 139777365 0.000000e+00 1038.0
16 TraesCS3A01G129400 chr3B 87.791 729 54 18 304 1018 139781181 139780474 0.000000e+00 821.0
17 TraesCS3A01G129400 chr3B 78.403 1102 144 46 2330 3358 139833177 139832097 7.700000e-177 630.0
18 TraesCS3A01G129400 chr3B 79.484 775 112 28 1033 1785 139834439 139833690 1.350000e-139 507.0
19 TraesCS3A01G129400 chr3B 91.327 196 17 0 2021 2216 139833454 139833259 6.950000e-68 268.0
20 TraesCS3A01G129400 chr3B 84.568 162 21 2 69 228 542724285 542724126 1.570000e-34 158.0
21 TraesCS3A01G129400 chr5A 90.865 416 23 6 1780 2184 311157982 311157571 1.030000e-150 544.0
22 TraesCS3A01G129400 chr4A 83.575 207 34 0 2028 2234 592530375 592530581 1.200000e-45 195.0
23 TraesCS3A01G129400 chr4A 83.575 207 34 0 2028 2234 592816719 592816925 1.200000e-45 195.0
24 TraesCS3A01G129400 chr4A 83.575 207 34 0 2028 2234 593096932 593097138 1.200000e-45 195.0
25 TraesCS3A01G129400 chr5B 82.323 198 21 5 72 257 355641537 355641342 4.370000e-35 159.0
26 TraesCS3A01G129400 chr5B 85.417 96 10 2 72 165 355641546 355641639 3.470000e-16 97.1
27 TraesCS3A01G129400 chr5B 84.375 96 11 2 72 165 355640526 355640619 1.620000e-14 91.6
28 TraesCS3A01G129400 chr1A 84.177 158 12 8 72 228 104240048 104240193 1.580000e-29 141.0
29 TraesCS3A01G129400 chr2A 90.625 96 9 0 136 231 751644353 751644258 1.230000e-25 128.0
30 TraesCS3A01G129400 chr4B 83.969 131 19 2 2555 2683 20361098 20361228 1.590000e-24 124.0
31 TraesCS3A01G129400 chr4D 83.206 131 20 2 2555 2683 10835135 10835265 7.410000e-23 119.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G129400 chr3A 106660093 106664310 4217 True 2736.000000 7790 97.883333 1 4218 3 chr3A.!!$R1 4217
1 TraesCS3A01G129400 chr3A 106674408 106678868 4460 True 394.333333 496 79.844000 1036 3358 3 chr3A.!!$R2 2322
2 TraesCS3A01G129400 chr3D 90372035 90381676 9641 True 913.428571 2968 86.911571 34 4218 7 chr3D.!!$R1 4184
3 TraesCS3A01G129400 chr3B 139777365 139781181 3816 True 1312.250000 1803 91.234000 304 4218 4 chr3B.!!$R2 3914
4 TraesCS3A01G129400 chr3B 139832097 139834439 2342 True 468.333333 630 83.071333 1033 3358 3 chr3B.!!$R3 2325

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
815 6351 0.250381 TTTTGCCCCATTTGCTGCTG 60.250 50.0 0.0 0.0 0.0 4.41 F
1773 7361 0.107831 GTGGTGGGACTGCTACAACA 59.892 55.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 7941 0.031857 TTGCAAACACCCTTGATGCG 59.968 50.0 0.0 0.0 40.04 4.73 R
3566 11451 0.035152 TCTGAATTGGTGCCGCAGAT 60.035 50.0 0.0 0.0 31.24 2.90 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
19 20 2.928801 AACTGGCTGACACATACACA 57.071 45.000 0.00 0.00 0.00 3.72
20 21 2.169832 ACTGGCTGACACATACACAC 57.830 50.000 0.00 0.00 0.00 3.82
21 22 1.070821 CTGGCTGACACATACACACG 58.929 55.000 0.00 0.00 0.00 4.49
22 23 0.948623 TGGCTGACACATACACACGC 60.949 55.000 0.00 0.00 0.00 5.34
23 24 1.416049 GCTGACACATACACACGCG 59.584 57.895 3.53 3.53 0.00 6.01
25 26 2.265965 CTGACACATACACACGCGCG 62.266 60.000 30.96 30.96 0.00 6.86
26 27 3.680072 GACACATACACACGCGCGC 62.680 63.158 32.58 23.91 0.00 6.86
50 5555 3.774702 GAAACGTCGCCTGTCGCC 61.775 66.667 0.00 0.00 38.27 5.54
67 5572 2.351418 TCGCCGAGCATTCATTTGTAAG 59.649 45.455 0.00 0.00 0.00 2.34
92 5597 0.896226 GGTTCGGCTCCTCTACAGTT 59.104 55.000 0.00 0.00 0.00 3.16
105 5610 7.468906 GCTCCTCTACAGTTATGTTACTACTGG 60.469 44.444 13.86 0.00 42.70 4.00
106 5611 6.320672 TCCTCTACAGTTATGTTACTACTGGC 59.679 42.308 13.86 0.00 42.70 4.85
130 5635 5.235516 CACCCGTAGTTACTTGTTCAATCT 58.764 41.667 0.00 0.00 0.00 2.40
132 5637 4.092968 CCCGTAGTTACTTGTTCAATCTGC 59.907 45.833 0.00 0.00 0.00 4.26
133 5638 4.092968 CCGTAGTTACTTGTTCAATCTGCC 59.907 45.833 0.00 0.00 0.00 4.85
152 5657 2.755650 CCGTTCAATCTAATCGGAGGG 58.244 52.381 0.00 0.00 43.22 4.30
177 5682 3.110705 CCCTTTCTCTCCATCCTTCTCA 58.889 50.000 0.00 0.00 0.00 3.27
185 5690 1.220169 CCATCCTTCTCATCGCAGCG 61.220 60.000 9.06 9.06 0.00 5.18
190 5695 1.737196 CTTCTCATCGCAGCGACGTG 61.737 60.000 22.28 16.10 39.18 4.49
192 5697 1.226295 CTCATCGCAGCGACGTGTA 60.226 57.895 22.28 5.16 39.18 2.90
232 5748 1.669115 CTTGCTGTCCACCGACCAG 60.669 63.158 0.00 0.00 38.32 4.00
245 5761 1.067846 CCGACCAGTGATGAACTCGAA 60.068 52.381 0.00 0.00 36.83 3.71
246 5762 2.254459 CGACCAGTGATGAACTCGAAG 58.746 52.381 0.00 0.00 36.83 3.79
260 5776 3.442996 CGAAGAACTCGGCCTCAAT 57.557 52.632 0.00 0.00 44.20 2.57
273 5789 0.806102 CCTCAATGGCCGTGTACTCG 60.806 60.000 10.28 10.28 0.00 4.18
288 5813 0.803740 ACTCGACGTGCTCCTTCTAC 59.196 55.000 0.00 0.00 0.00 2.59
295 5820 4.674623 CGACGTGCTCCTTCTACTTGTATT 60.675 45.833 0.00 0.00 0.00 1.89
302 5827 5.986741 GCTCCTTCTACTTGTATTTCTAGCC 59.013 44.000 0.00 0.00 0.00 3.93
304 5829 6.875076 TCCTTCTACTTGTATTTCTAGCCAC 58.125 40.000 0.00 0.00 0.00 5.01
352 5877 1.766143 GCGATCTTGGTGCGTGATCC 61.766 60.000 0.00 0.00 34.70 3.36
369 5894 0.395586 TCCACACCCATGGCATTAGC 60.396 55.000 6.09 0.00 39.85 3.09
372 5897 0.332632 ACACCCATGGCATTAGCTGT 59.667 50.000 6.09 0.00 41.70 4.40
521 6050 5.441500 TGCAATTCGGGGAATGAAATACTA 58.558 37.500 0.00 0.00 32.14 1.82
525 6054 4.411256 TCGGGGAATGAAATACTACACC 57.589 45.455 0.00 0.00 0.00 4.16
527 6056 3.118186 CGGGGAATGAAATACTACACCCA 60.118 47.826 0.00 0.00 37.99 4.51
549 6083 6.930722 CCCATTTAATAAACCATCAAGCCATC 59.069 38.462 0.00 0.00 0.00 3.51
553 6087 1.255882 AAACCATCAAGCCATCGCAA 58.744 45.000 0.00 0.00 37.52 4.85
554 6088 0.813184 AACCATCAAGCCATCGCAAG 59.187 50.000 0.00 0.00 37.52 4.01
601 6135 3.118454 CTGGAAATGGCGTCGCGT 61.118 61.111 11.75 0.00 0.00 6.01
615 6149 2.652496 GCGTCGCGTTTTTGGCAA 60.652 55.556 5.77 0.00 0.00 4.52
616 6150 2.635305 GCGTCGCGTTTTTGGCAAG 61.635 57.895 5.77 0.00 0.00 4.01
659 6193 1.000274 GGGATAACCGCATGGCATTTC 60.000 52.381 0.00 0.00 39.70 2.17
664 6198 2.788640 CCGCATGGCATTTCTGGGG 61.789 63.158 7.42 7.42 36.77 4.96
750 6285 6.036517 CCTGCGCTGATTTGGATATCTATAAC 59.963 42.308 16.65 0.00 0.00 1.89
755 6290 7.043125 CGCTGATTTGGATATCTATAACATCCG 60.043 40.741 2.05 0.52 41.02 4.18
783 6318 1.284982 CTGCCACGACAAACGAGAGG 61.285 60.000 0.00 0.00 45.77 3.69
815 6351 0.250381 TTTTGCCCCATTTGCTGCTG 60.250 50.000 0.00 0.00 0.00 4.41
863 6399 2.650765 GTCTCGCGCGTGTATGTATAAG 59.349 50.000 30.98 15.45 0.00 1.73
981 6522 0.575859 CGATTCAGCTGCTGATCGTG 59.424 55.000 32.36 21.87 40.39 4.35
982 6523 0.935898 GATTCAGCTGCTGATCGTGG 59.064 55.000 30.80 3.80 40.39 4.94
983 6524 0.251354 ATTCAGCTGCTGATCGTGGT 59.749 50.000 30.80 11.64 40.39 4.16
984 6525 0.894835 TTCAGCTGCTGATCGTGGTA 59.105 50.000 30.80 13.09 40.39 3.25
985 6526 0.457443 TCAGCTGCTGATCGTGGTAG 59.543 55.000 27.35 0.00 35.39 3.18
986 6527 1.142748 AGCTGCTGATCGTGGTAGC 59.857 57.895 0.00 12.60 40.53 3.58
987 6528 1.153568 GCTGCTGATCGTGGTAGCA 60.154 57.895 14.57 10.29 44.45 3.49
988 6529 0.531532 GCTGCTGATCGTGGTAGCAT 60.532 55.000 14.57 0.00 45.38 3.79
1006 6547 3.262660 AGCATCGGTGATCATCATGGTAT 59.737 43.478 16.42 0.00 0.00 2.73
1007 6548 3.373130 GCATCGGTGATCATCATGGTATG 59.627 47.826 6.80 2.87 0.00 2.39
1018 6559 0.597377 CATGGTATGCGCGTCAGCTA 60.597 55.000 4.79 0.00 42.32 3.32
1019 6560 0.318441 ATGGTATGCGCGTCAGCTAT 59.682 50.000 4.79 0.00 42.32 2.97
1020 6561 0.597377 TGGTATGCGCGTCAGCTATG 60.597 55.000 4.79 0.00 42.32 2.23
1022 6563 0.941463 GTATGCGCGTCAGCTATGCT 60.941 55.000 4.79 0.00 42.32 3.79
1023 6564 0.664466 TATGCGCGTCAGCTATGCTC 60.664 55.000 4.79 0.00 42.32 4.26
1024 6565 2.279120 GCGCGTCAGCTATGCTCT 60.279 61.111 8.43 0.00 42.32 4.09
1025 6566 1.008424 GCGCGTCAGCTATGCTCTA 60.008 57.895 8.43 0.00 42.32 2.43
1027 6568 0.661780 CGCGTCAGCTATGCTCTACC 60.662 60.000 0.00 0.00 42.32 3.18
1044 6585 2.713895 ACCGTCGCTCATCATCTATG 57.286 50.000 0.00 0.00 36.88 2.23
1098 6653 3.715097 AGAGGGCTGCAGCAGGAC 61.715 66.667 37.63 24.04 44.36 3.85
1099 6654 4.025858 GAGGGCTGCAGCAGGACA 62.026 66.667 37.63 0.00 44.36 4.02
1100 6655 3.336568 AGGGCTGCAGCAGGACAT 61.337 61.111 37.63 17.18 44.36 3.06
1101 6656 3.138798 GGGCTGCAGCAGGACATG 61.139 66.667 37.63 0.00 44.36 3.21
1104 6659 3.506096 CTGCAGCAGGACATGGCG 61.506 66.667 15.35 0.00 34.54 5.69
1108 6666 4.479993 AGCAGGACATGGCGCCTC 62.480 66.667 29.70 17.20 34.54 4.70
1202 6766 1.602771 GAAAGGGGAAGGGACTCGG 59.397 63.158 0.00 0.00 38.49 4.63
1265 6829 6.043243 AGACGGATGATTCCAAGGTATAACAT 59.957 38.462 0.00 0.00 42.74 2.71
1274 6841 4.647853 TCCAAGGTATAACATCAGCGTACT 59.352 41.667 0.00 0.00 0.00 2.73
1281 6855 3.454371 AACATCAGCGTACTCCCATAC 57.546 47.619 0.00 0.00 0.00 2.39
1344 6922 6.475076 CGGTCAGATCAGATCTTTCTTACTTG 59.525 42.308 10.51 0.00 37.58 3.16
1394 6976 2.202492 CAGGCGTTCGAGGAGACG 60.202 66.667 3.06 3.06 0.00 4.18
1526 7108 1.540267 TGCAGGTAAAAACCATCCGG 58.460 50.000 0.00 0.00 38.77 5.14
1577 7160 2.362397 GCATGACCCATCTTCGTCTCTA 59.638 50.000 0.00 0.00 0.00 2.43
1593 7176 4.033587 CGTCTCTAGTCTCTAGCACAAGAC 59.966 50.000 1.89 1.89 41.81 3.01
1594 7177 4.938832 GTCTCTAGTCTCTAGCACAAGACA 59.061 45.833 10.87 0.00 43.52 3.41
1621 7207 2.180159 TAACCGAGGCTGGTGCTTCC 62.180 60.000 9.00 0.00 42.89 3.46
1662 7250 2.515523 CGCCAAGCTCCATCTGGG 60.516 66.667 3.61 0.00 35.41 4.45
1773 7361 0.107831 GTGGTGGGACTGCTACAACA 59.892 55.000 0.00 0.00 0.00 3.33
1807 7395 2.234414 CAGCATACCTGGGCAAACAAAT 59.766 45.455 0.00 0.00 37.93 2.32
1817 7405 1.999024 GGCAAACAAATATGGCCGTTG 59.001 47.619 0.77 4.66 36.21 4.10
1861 7449 8.998377 TCATATATACATACATTGTGCACAACC 58.002 33.333 33.29 0.00 39.48 3.77
1862 7450 9.002600 CATATATACATACATTGTGCACAACCT 57.997 33.333 33.29 22.38 39.48 3.50
1863 7451 3.921119 ACATACATTGTGCACAACCTG 57.079 42.857 33.29 28.42 38.86 4.00
1864 7452 3.485394 ACATACATTGTGCACAACCTGA 58.515 40.909 33.29 19.05 38.86 3.86
1865 7453 3.253188 ACATACATTGTGCACAACCTGAC 59.747 43.478 33.29 0.00 38.86 3.51
1866 7454 0.662619 ACATTGTGCACAACCTGACG 59.337 50.000 33.29 18.80 38.86 4.35
1885 7476 1.684049 CTGACGCCCCTCCTCTCTT 60.684 63.158 0.00 0.00 0.00 2.85
1950 7541 5.067674 CACACAATCCCTCTTTCAGTTTCAA 59.932 40.000 0.00 0.00 0.00 2.69
1966 7564 5.641209 CAGTTTCAATCTGGAACTAGTCAGG 59.359 44.000 10.73 0.00 0.00 3.86
1982 7580 5.869649 AGTCAGGCATATGTATGTGTGTA 57.130 39.130 4.29 0.00 36.11 2.90
2012 7613 1.561076 TCATCCAGGCTTGCACATACT 59.439 47.619 0.00 0.00 0.00 2.12
2015 7616 1.073763 TCCAGGCTTGCACATACTTGT 59.926 47.619 0.00 0.00 36.15 3.16
2239 7881 2.666098 ATCCACAGCGGTACACCCC 61.666 63.158 0.00 0.00 35.57 4.95
2254 7896 3.419858 CCCCCTCCTTCACTGCAT 58.580 61.111 0.00 0.00 0.00 3.96
2255 7897 1.077212 CCCCCTCCTTCACTGCATG 60.077 63.158 0.00 0.00 0.00 4.06
2257 7899 1.001764 CCCTCCTTCACTGCATGCA 60.002 57.895 21.29 21.29 0.00 3.96
2278 7950 2.615447 ACATTGCAGTATCGCATCAAGG 59.385 45.455 0.00 0.00 42.62 3.61
2289 7988 1.501169 GCATCAAGGGTGTTTGCAAC 58.499 50.000 0.00 0.00 36.00 4.17
2477 8189 2.965671 ATATATGCAGGCCTGTGCTT 57.034 45.000 32.81 20.49 44.32 3.91
2540 8255 4.848357 AGTAGCATACATTGAGCAAGGTT 58.152 39.130 5.82 0.00 46.26 3.50
2541 8256 5.989477 AGTAGCATACATTGAGCAAGGTTA 58.011 37.500 5.82 0.00 46.26 2.85
2545 8260 4.497006 GCATACATTGAGCAAGGTTAGCTG 60.497 45.833 5.82 1.77 43.58 4.24
2552 8274 3.315191 TGAGCAAGGTTAGCTGTTTTGAC 59.685 43.478 0.00 0.00 43.58 3.18
2597 8319 1.104577 GGAGGTGCCGGTGAAAAACA 61.105 55.000 1.90 0.00 0.00 2.83
2599 8321 1.135333 GAGGTGCCGGTGAAAAACAAA 59.865 47.619 1.90 0.00 0.00 2.83
2714 8452 0.097499 CTACATGCATGTGTGTGCCG 59.903 55.000 36.72 15.12 44.43 5.69
2734 8481 3.435671 CCGTCAGTTCAAAGATACCAACC 59.564 47.826 0.00 0.00 0.00 3.77
2735 8482 3.435671 CGTCAGTTCAAAGATACCAACCC 59.564 47.826 0.00 0.00 0.00 4.11
2761 8511 5.130350 GGTTGCATACACCATGGTAGTATT 58.870 41.667 25.14 14.72 34.97 1.89
2831 8604 1.329599 AGCGAACACGTTCCTTTTCAC 59.670 47.619 4.40 0.00 36.27 3.18
2866 8639 5.938279 TGACTGAAGTACGGTATCCTATCT 58.062 41.667 0.00 0.00 38.34 1.98
2976 8777 2.806434 ACTGAAACCATATTGGCTGCA 58.194 42.857 0.50 0.00 42.67 4.41
3172 11053 4.608170 AATCCTAAATGCCCAAGGAAGA 57.392 40.909 0.00 0.00 42.53 2.87
3220 11101 1.900351 CTTCCGTGGCCTCTGATCA 59.100 57.895 3.32 0.00 0.00 2.92
3221 11102 0.179089 CTTCCGTGGCCTCTGATCAG 60.179 60.000 17.07 17.07 0.00 2.90
3222 11103 0.614697 TTCCGTGGCCTCTGATCAGA 60.615 55.000 23.75 23.75 35.85 3.27
3235 11116 1.474478 TGATCAGAAGTGCTCTCCGTC 59.526 52.381 0.00 0.00 29.07 4.79
3288 11170 2.030007 GCAAGTGCAGAAATGCTTACCA 60.030 45.455 0.00 0.00 41.59 3.25
3449 11334 2.682893 CACCGAGGTGCTTATCTGC 58.317 57.895 9.54 0.00 39.39 4.26
3454 11339 0.533755 GAGGTGCTTATCTGCGGCAT 60.534 55.000 1.75 0.00 38.27 4.40
3484 11369 5.119931 GAGTATCTCGCATGATTCTGTCT 57.880 43.478 0.00 0.00 0.00 3.41
3485 11370 5.119931 AGTATCTCGCATGATTCTGTCTC 57.880 43.478 0.00 0.00 0.00 3.36
3486 11371 4.582240 AGTATCTCGCATGATTCTGTCTCA 59.418 41.667 0.00 0.00 0.00 3.27
3487 11372 4.603989 ATCTCGCATGATTCTGTCTCAT 57.396 40.909 0.00 0.00 33.65 2.90
3488 11373 5.718724 ATCTCGCATGATTCTGTCTCATA 57.281 39.130 0.00 0.00 32.18 2.15
3489 11374 5.718724 TCTCGCATGATTCTGTCTCATAT 57.281 39.130 0.00 0.00 32.18 1.78
3490 11375 5.707931 TCTCGCATGATTCTGTCTCATATC 58.292 41.667 0.00 0.00 32.18 1.63
3491 11376 5.476254 TCTCGCATGATTCTGTCTCATATCT 59.524 40.000 0.00 0.00 32.18 1.98
3492 11377 5.467705 TCGCATGATTCTGTCTCATATCTG 58.532 41.667 0.00 0.00 32.18 2.90
3493 11378 5.010415 TCGCATGATTCTGTCTCATATCTGT 59.990 40.000 0.00 0.00 32.18 3.41
3494 11379 5.345472 CGCATGATTCTGTCTCATATCTGTC 59.655 44.000 0.00 0.00 32.18 3.51
3495 11380 6.221659 GCATGATTCTGTCTCATATCTGTCA 58.778 40.000 0.00 0.00 32.18 3.58
3496 11381 6.874664 GCATGATTCTGTCTCATATCTGTCAT 59.125 38.462 0.00 0.00 32.18 3.06
3497 11382 7.148557 GCATGATTCTGTCTCATATCTGTCATG 60.149 40.741 0.00 0.00 41.08 3.07
3498 11383 6.221659 TGATTCTGTCTCATATCTGTCATGC 58.778 40.000 0.00 0.00 0.00 4.06
3499 11384 4.597404 TCTGTCTCATATCTGTCATGCC 57.403 45.455 0.00 0.00 0.00 4.40
3500 11385 4.221530 TCTGTCTCATATCTGTCATGCCT 58.778 43.478 0.00 0.00 0.00 4.75
3501 11386 5.388654 TCTGTCTCATATCTGTCATGCCTA 58.611 41.667 0.00 0.00 0.00 3.93
3502 11387 5.242615 TCTGTCTCATATCTGTCATGCCTAC 59.757 44.000 0.00 0.00 0.00 3.18
3503 11388 4.895297 TGTCTCATATCTGTCATGCCTACA 59.105 41.667 0.00 0.00 0.00 2.74
3504 11389 5.363580 TGTCTCATATCTGTCATGCCTACAA 59.636 40.000 0.00 0.00 0.00 2.41
3505 11390 5.694006 GTCTCATATCTGTCATGCCTACAAC 59.306 44.000 0.00 0.00 0.00 3.32
3506 11391 5.600069 TCTCATATCTGTCATGCCTACAACT 59.400 40.000 0.00 0.00 0.00 3.16
3507 11392 6.098838 TCTCATATCTGTCATGCCTACAACTT 59.901 38.462 0.00 0.00 0.00 2.66
3508 11393 6.283694 TCATATCTGTCATGCCTACAACTTC 58.716 40.000 0.00 0.00 0.00 3.01
3509 11394 4.833478 ATCTGTCATGCCTACAACTTCT 57.167 40.909 0.00 0.00 0.00 2.85
3510 11395 4.193826 TCTGTCATGCCTACAACTTCTC 57.806 45.455 0.00 0.00 0.00 2.87
3511 11396 3.578282 TCTGTCATGCCTACAACTTCTCA 59.422 43.478 0.00 0.00 0.00 3.27
3512 11397 4.040339 TCTGTCATGCCTACAACTTCTCAA 59.960 41.667 0.00 0.00 0.00 3.02
3513 11398 4.910195 TGTCATGCCTACAACTTCTCAAT 58.090 39.130 0.00 0.00 0.00 2.57
3514 11399 4.696877 TGTCATGCCTACAACTTCTCAATG 59.303 41.667 0.00 0.00 0.00 2.82
3515 11400 4.697352 GTCATGCCTACAACTTCTCAATGT 59.303 41.667 0.00 0.00 0.00 2.71
3516 11401 5.874810 GTCATGCCTACAACTTCTCAATGTA 59.125 40.000 0.00 0.00 0.00 2.29
3517 11402 6.540189 GTCATGCCTACAACTTCTCAATGTAT 59.460 38.462 0.00 0.00 0.00 2.29
3518 11403 6.539826 TCATGCCTACAACTTCTCAATGTATG 59.460 38.462 0.00 0.00 0.00 2.39
3519 11404 5.185454 TGCCTACAACTTCTCAATGTATGG 58.815 41.667 0.00 0.00 0.00 2.74
3520 11405 4.035675 GCCTACAACTTCTCAATGTATGGC 59.964 45.833 0.00 0.00 37.04 4.40
3521 11406 4.576463 CCTACAACTTCTCAATGTATGGCC 59.424 45.833 0.00 0.00 0.00 5.36
3522 11407 4.032960 ACAACTTCTCAATGTATGGCCA 57.967 40.909 8.56 8.56 0.00 5.36
3523 11408 4.603131 ACAACTTCTCAATGTATGGCCAT 58.397 39.130 24.45 24.45 0.00 4.40
3524 11409 5.018809 ACAACTTCTCAATGTATGGCCATT 58.981 37.500 26.37 2.81 35.45 3.16
3525 11410 5.126061 ACAACTTCTCAATGTATGGCCATTC 59.874 40.000 26.37 20.17 32.81 2.67
3526 11411 5.121380 ACTTCTCAATGTATGGCCATTCT 57.879 39.130 26.37 2.16 32.81 2.40
3527 11412 5.513233 ACTTCTCAATGTATGGCCATTCTT 58.487 37.500 26.37 14.42 32.81 2.52
3528 11413 5.591877 ACTTCTCAATGTATGGCCATTCTTC 59.408 40.000 26.37 12.64 32.81 2.87
3529 11414 5.378230 TCTCAATGTATGGCCATTCTTCT 57.622 39.130 26.37 0.29 32.81 2.85
3530 11415 6.499106 TCTCAATGTATGGCCATTCTTCTA 57.501 37.500 26.37 0.34 32.81 2.10
3531 11416 7.083062 TCTCAATGTATGGCCATTCTTCTAT 57.917 36.000 26.37 5.27 32.81 1.98
3532 11417 7.164122 TCTCAATGTATGGCCATTCTTCTATC 58.836 38.462 26.37 5.39 32.81 2.08
3533 11418 7.016957 TCTCAATGTATGGCCATTCTTCTATCT 59.983 37.037 26.37 0.00 32.81 1.98
3534 11419 8.206126 TCAATGTATGGCCATTCTTCTATCTA 57.794 34.615 26.37 0.00 32.81 1.98
3535 11420 8.829746 TCAATGTATGGCCATTCTTCTATCTAT 58.170 33.333 26.37 2.55 32.81 1.98
3560 11445 4.399004 ACTATAAGCAAGAGCACTGAGG 57.601 45.455 0.00 0.00 45.49 3.86
3561 11446 3.772025 ACTATAAGCAAGAGCACTGAGGT 59.228 43.478 0.00 0.00 45.49 3.85
3562 11447 2.462456 TAAGCAAGAGCACTGAGGTG 57.538 50.000 0.00 0.00 45.49 4.00
3572 11457 1.284657 CACTGAGGTGCTTATCTGCG 58.715 55.000 0.00 0.00 36.61 5.18
3573 11458 0.176680 ACTGAGGTGCTTATCTGCGG 59.823 55.000 0.00 0.00 35.36 5.69
3574 11459 1.153369 TGAGGTGCTTATCTGCGGC 60.153 57.895 0.00 0.00 35.36 6.53
3575 11460 1.153369 GAGGTGCTTATCTGCGGCA 60.153 57.895 1.29 1.29 35.36 5.69
3578 11463 2.668024 TGCTTATCTGCGGCACCA 59.332 55.556 0.00 0.00 35.36 4.17
3579 11464 1.002746 TGCTTATCTGCGGCACCAA 60.003 52.632 0.00 0.00 35.36 3.67
3580 11465 0.394216 TGCTTATCTGCGGCACCAAT 60.394 50.000 0.00 0.00 35.36 3.16
3581 11466 0.740737 GCTTATCTGCGGCACCAATT 59.259 50.000 0.00 0.00 0.00 2.32
3582 11467 1.268743 GCTTATCTGCGGCACCAATTC 60.269 52.381 0.00 0.00 0.00 2.17
3583 11468 2.016318 CTTATCTGCGGCACCAATTCA 58.984 47.619 0.00 0.00 0.00 2.57
3584 11469 1.667236 TATCTGCGGCACCAATTCAG 58.333 50.000 0.00 0.00 0.00 3.02
3585 11470 0.035152 ATCTGCGGCACCAATTCAGA 60.035 50.000 0.00 0.00 38.05 3.27
3586 11471 0.674581 TCTGCGGCACCAATTCAGAG 60.675 55.000 0.00 0.00 31.07 3.35
3587 11472 0.957395 CTGCGGCACCAATTCAGAGT 60.957 55.000 0.00 0.00 0.00 3.24
3588 11473 0.323302 TGCGGCACCAATTCAGAGTA 59.677 50.000 0.00 0.00 0.00 2.59
3589 11474 1.065491 TGCGGCACCAATTCAGAGTAT 60.065 47.619 0.00 0.00 0.00 2.12
3590 11475 1.599542 GCGGCACCAATTCAGAGTATC 59.400 52.381 0.00 0.00 0.00 2.24
3684 11569 0.527565 CACAAACCTAGCCATGGCAC 59.472 55.000 37.18 10.61 44.88 5.01
3734 11624 2.738314 GTGGTTCAATTGAAAGCATGCC 59.262 45.455 22.07 17.23 35.58 4.40
3829 11721 3.388024 GGTACTCCATTATCCTCAGCACA 59.612 47.826 0.00 0.00 0.00 4.57
3832 11724 2.104451 CTCCATTATCCTCAGCACAGCT 59.896 50.000 0.00 0.00 40.77 4.24
3847 11739 3.370366 GCACAGCTTCAGACTTGATGTAG 59.630 47.826 0.00 0.00 32.27 2.74
3857 11749 1.977854 ACTTGATGTAGGACCTGCACA 59.022 47.619 15.13 11.80 0.00 4.57
3862 11756 0.250295 TGTAGGACCTGCACAGCAAC 60.250 55.000 8.39 0.00 38.41 4.17
3872 11766 2.792674 CTGCACAGCAACAACATTTCTG 59.207 45.455 0.00 0.00 38.41 3.02
3874 11768 3.068448 TGCACAGCAACAACATTTCTGAT 59.932 39.130 0.00 0.00 34.76 2.90
3900 11796 2.158623 GGTCCATGGCTGATGTCCATTA 60.159 50.000 6.96 0.00 42.11 1.90
4046 11949 2.364973 TACCTGATGCTCCGGCCA 60.365 61.111 2.24 0.00 37.74 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.605457 CGTGTGTATGTGTCAGCCAGT 60.605 52.381 0.00 0.00 0.00 4.00
3 4 0.948623 GCGTGTGTATGTGTCAGCCA 60.949 55.000 0.00 0.00 0.00 4.75
4 5 1.787847 GCGTGTGTATGTGTCAGCC 59.212 57.895 0.00 0.00 0.00 4.85
5 6 1.416049 CGCGTGTGTATGTGTCAGC 59.584 57.895 0.00 0.00 0.00 4.26
6 7 1.416049 GCGCGTGTGTATGTGTCAG 59.584 57.895 8.43 0.00 0.00 3.51
8 9 2.390288 CGCGCGTGTGTATGTGTC 59.610 61.111 24.19 0.00 0.00 3.67
9 10 3.773630 GCGCGCGTGTGTATGTGT 61.774 61.111 32.35 0.00 0.00 3.72
10 11 4.826605 CGCGCGCGTGTGTATGTG 62.827 66.667 42.49 13.34 34.35 3.21
44 5549 0.447406 CAAATGAATGCTCGGCGACA 59.553 50.000 4.99 10.18 0.00 4.35
50 5555 3.093574 CACGCTTACAAATGAATGCTCG 58.906 45.455 0.00 0.00 0.00 5.03
92 5597 1.758280 CGGGTGGCCAGTAGTAACATA 59.242 52.381 5.11 0.00 0.00 2.29
105 5610 2.071540 GAACAAGTAACTACGGGTGGC 58.928 52.381 0.00 0.00 0.00 5.01
106 5611 3.389925 TGAACAAGTAACTACGGGTGG 57.610 47.619 0.00 0.00 0.00 4.61
130 5635 2.483013 CCTCCGATTAGATTGAACGGCA 60.483 50.000 0.00 0.00 42.73 5.69
132 5637 2.755650 CCCTCCGATTAGATTGAACGG 58.244 52.381 0.00 0.00 44.09 4.44
133 5638 2.135933 GCCCTCCGATTAGATTGAACG 58.864 52.381 0.00 0.00 0.00 3.95
152 5657 1.843206 AGGATGGAGAGAAAGGGAAGC 59.157 52.381 0.00 0.00 0.00 3.86
161 5666 1.959985 GCGATGAGAAGGATGGAGAGA 59.040 52.381 0.00 0.00 0.00 3.10
177 5682 0.797249 GAAGTACACGTCGCTGCGAT 60.797 55.000 28.51 14.48 38.42 4.58
185 5690 0.883833 TTCCTCGGGAAGTACACGTC 59.116 55.000 0.00 0.00 46.47 4.34
206 5711 3.423154 GGACAGCAAGAACGCCCG 61.423 66.667 0.00 0.00 0.00 6.13
260 5776 2.979676 ACGTCGAGTACACGGCCA 60.980 61.111 11.66 0.00 41.73 5.36
273 5789 2.726832 ACAAGTAGAAGGAGCACGTC 57.273 50.000 0.00 0.00 0.00 4.34
288 5813 3.766151 TCGTCGTGGCTAGAAATACAAG 58.234 45.455 0.00 0.00 0.00 3.16
295 5820 1.816835 ACAAGATCGTCGTGGCTAGAA 59.183 47.619 0.00 0.00 30.01 2.10
302 5827 5.504755 GCTGAAATTTTACAAGATCGTCGTG 59.495 40.000 0.00 0.94 32.10 4.35
304 5829 5.617609 TGCTGAAATTTTACAAGATCGTCG 58.382 37.500 0.00 0.00 0.00 5.12
352 5877 0.742505 CAGCTAATGCCATGGGTGTG 59.257 55.000 15.13 0.00 40.80 3.82
357 5882 1.679680 CCTTCACAGCTAATGCCATGG 59.320 52.381 7.63 7.63 40.80 3.66
369 5894 5.119694 GGTAGCTAGGATTTTCCTTCACAG 58.880 45.833 0.59 0.00 46.91 3.66
372 5897 4.108570 TGGGTAGCTAGGATTTTCCTTCA 58.891 43.478 0.59 0.00 46.91 3.02
404 5929 2.514824 GAGATGGACGGCTTGGGC 60.515 66.667 0.00 0.00 37.82 5.36
405 5930 2.202932 CGAGATGGACGGCTTGGG 60.203 66.667 0.00 0.00 0.00 4.12
521 6050 6.351796 GGCTTGATGGTTTATTAAATGGGTGT 60.352 38.462 0.00 0.00 0.00 4.16
525 6054 6.642131 CGATGGCTTGATGGTTTATTAAATGG 59.358 38.462 0.00 0.00 0.00 3.16
527 6056 6.183360 TGCGATGGCTTGATGGTTTATTAAAT 60.183 34.615 0.15 0.00 40.82 1.40
549 6083 1.380515 TCCCTCCTCTCCTCTTGCG 60.381 63.158 0.00 0.00 0.00 4.85
553 6087 1.619975 TCCGTCCCTCCTCTCCTCT 60.620 63.158 0.00 0.00 0.00 3.69
554 6088 1.454295 GTCCGTCCCTCCTCTCCTC 60.454 68.421 0.00 0.00 0.00 3.71
555 6089 2.684735 GTCCGTCCCTCCTCTCCT 59.315 66.667 0.00 0.00 0.00 3.69
556 6090 2.829458 CGTCCGTCCCTCCTCTCC 60.829 72.222 0.00 0.00 0.00 3.71
557 6091 3.519930 GCGTCCGTCCCTCCTCTC 61.520 72.222 0.00 0.00 0.00 3.20
601 6135 2.026879 GCCTTGCCAAAAACGCGA 59.973 55.556 15.93 0.00 0.00 5.87
628 6162 4.189580 TTATCCCGCCCAGCTGCC 62.190 66.667 8.66 0.00 0.00 4.85
640 6174 1.956477 AGAAATGCCATGCGGTTATCC 59.044 47.619 0.00 0.00 33.28 2.59
664 6198 1.816214 GAGATTAGCTGCACGCGAGC 61.816 60.000 21.99 21.99 45.59 5.03
678 6212 2.642807 TCCCCGTTTGAAAGAGGAGATT 59.357 45.455 1.46 0.00 0.00 2.40
750 6285 2.633657 GCAGTAATGCCGCGGATG 59.366 61.111 33.48 17.04 0.00 3.51
790 6325 3.189702 CAGCAAATGGGGCAAAAATTCAG 59.810 43.478 0.00 0.00 0.00 3.02
800 6336 4.807039 CGCAGCAGCAAATGGGGC 62.807 66.667 0.82 0.00 42.27 5.80
863 6399 2.603110 CCGTGTGCTCATGTGTATGTAC 59.397 50.000 7.19 0.00 35.73 2.90
905 6441 4.980903 GTTGCAAGCACCGCCGTG 62.981 66.667 0.00 0.34 43.35 4.94
981 6522 2.820059 TGATGATCACCGATGCTACC 57.180 50.000 0.00 0.00 0.00 3.18
982 6523 2.998670 CCATGATGATCACCGATGCTAC 59.001 50.000 0.00 0.00 0.00 3.58
983 6524 2.634453 ACCATGATGATCACCGATGCTA 59.366 45.455 0.00 0.00 0.00 3.49
984 6525 1.419012 ACCATGATGATCACCGATGCT 59.581 47.619 0.00 0.00 0.00 3.79
985 6526 1.888215 ACCATGATGATCACCGATGC 58.112 50.000 0.00 0.00 0.00 3.91
986 6527 3.373130 GCATACCATGATGATCACCGATG 59.627 47.826 0.00 0.35 0.00 3.84
987 6528 3.603532 GCATACCATGATGATCACCGAT 58.396 45.455 0.00 0.00 0.00 4.18
988 6529 2.610232 CGCATACCATGATGATCACCGA 60.610 50.000 0.00 0.00 0.00 4.69
1006 6547 1.724582 TAGAGCATAGCTGACGCGCA 61.725 55.000 5.73 4.25 39.88 6.09
1007 6548 1.008424 TAGAGCATAGCTGACGCGC 60.008 57.895 5.73 0.00 39.88 6.86
1018 6559 0.312416 GATGAGCGACGGTAGAGCAT 59.688 55.000 0.00 0.00 0.00 3.79
1019 6560 1.029947 TGATGAGCGACGGTAGAGCA 61.030 55.000 0.00 0.00 0.00 4.26
1020 6561 0.312416 ATGATGAGCGACGGTAGAGC 59.688 55.000 0.00 0.00 0.00 4.09
1022 6563 1.968704 AGATGATGAGCGACGGTAGA 58.031 50.000 0.00 0.00 0.00 2.59
1023 6564 3.189495 ACATAGATGATGAGCGACGGTAG 59.811 47.826 0.00 0.00 39.06 3.18
1024 6565 3.058224 CACATAGATGATGAGCGACGGTA 60.058 47.826 0.00 0.00 39.06 4.02
1025 6566 1.957177 ACATAGATGATGAGCGACGGT 59.043 47.619 0.00 0.00 39.06 4.83
1027 6568 3.005341 ACACATAGATGATGAGCGACG 57.995 47.619 0.00 0.00 39.06 5.12
1044 6585 0.592247 CACGTCAGGCAAAGCAACAC 60.592 55.000 0.00 0.00 0.00 3.32
1096 6651 2.514824 GGAAGGAGGCGCCATGTC 60.515 66.667 31.54 17.95 40.02 3.06
1098 6653 2.203126 GAGGAAGGAGGCGCCATG 60.203 66.667 31.54 0.00 40.02 3.66
1099 6654 3.854669 CGAGGAAGGAGGCGCCAT 61.855 66.667 31.54 14.28 40.02 4.40
1130 6688 1.007271 CGACACCACGAGAAGCAGT 60.007 57.895 0.00 0.00 35.09 4.40
1202 6766 0.727398 GGAAAGCCATGACGCTGTAC 59.273 55.000 0.00 0.00 39.64 2.90
1265 6829 1.977056 ATCGTATGGGAGTACGCTGA 58.023 50.000 0.00 0.00 45.20 4.26
1344 6922 0.530870 GACGGAGGGTGCAGATAAGC 60.531 60.000 0.00 0.00 0.00 3.09
1394 6976 2.821366 CTGCATGCCGAGTCCCAC 60.821 66.667 16.68 0.00 0.00 4.61
1406 6988 4.827087 CCGCCGCTGTCTCTGCAT 62.827 66.667 0.00 0.00 0.00 3.96
1519 7101 3.961197 TCGTCGATCGCCGGATGG 61.961 66.667 19.14 0.00 39.67 3.51
1577 7160 6.975196 ATGATATGTCTTGTGCTAGAGACT 57.025 37.500 9.87 0.89 42.13 3.24
1593 7176 5.111989 CACCAGCCTCGGTTATATGATATG 58.888 45.833 0.00 0.00 37.07 1.78
1594 7177 4.383118 GCACCAGCCTCGGTTATATGATAT 60.383 45.833 0.00 0.00 37.07 1.63
1656 7244 1.286248 AACGACTTTAGGCCCCAGAT 58.714 50.000 0.00 0.00 0.00 2.90
1662 7250 2.161012 GGCTTGTTAACGACTTTAGGCC 59.839 50.000 0.00 0.00 0.00 5.19
1773 7361 3.264450 AGGTATGCTGCTGTTACCTTCTT 59.736 43.478 17.81 3.56 42.36 2.52
1854 7442 2.939022 GTCAGCGTCAGGTTGTGC 59.061 61.111 0.00 0.00 0.00 4.57
1861 7449 4.803426 GAGGGGCGTCAGCGTCAG 62.803 72.222 0.00 0.00 45.79 3.51
1866 7454 3.844090 GAGAGGAGGGGCGTCAGC 61.844 72.222 0.00 0.00 44.18 4.26
1885 7476 2.307496 ATGGCATTTCTGTGGGAACA 57.693 45.000 0.00 0.00 33.13 3.18
1950 7541 4.904251 ACATATGCCTGACTAGTTCCAGAT 59.096 41.667 12.07 3.08 32.37 2.90
1966 7564 8.397906 AGTTTCAACATACACACATACATATGC 58.602 33.333 1.58 0.00 37.19 3.14
1982 7580 3.446442 AGCCTGGATGAGTTTCAACAT 57.554 42.857 0.00 0.00 0.00 2.71
2239 7881 1.001764 TGCATGCAGTGAAGGAGGG 60.002 57.895 18.46 0.00 0.00 4.30
2265 7937 2.477863 GCAAACACCCTTGATGCGATAC 60.478 50.000 0.00 0.00 32.31 2.24
2269 7941 0.031857 TTGCAAACACCCTTGATGCG 59.968 50.000 0.00 0.00 40.04 4.73
2289 7988 1.610038 TGCAAACATGCTTCAGGAGTG 59.390 47.619 2.22 0.00 35.49 3.51
2510 8222 5.918011 GCTCAATGTATGCTACTCAGTAGAC 59.082 44.000 16.61 5.65 38.29 2.59
2515 8227 4.510711 CCTTGCTCAATGTATGCTACTCAG 59.489 45.833 0.00 0.00 0.00 3.35
2540 8255 7.172532 CACTACACAATAAGGTCAAAACAGCTA 59.827 37.037 0.00 0.00 0.00 3.32
2541 8256 6.017109 CACTACACAATAAGGTCAAAACAGCT 60.017 38.462 0.00 0.00 0.00 4.24
2545 8260 6.435428 CCACACTACACAATAAGGTCAAAAC 58.565 40.000 0.00 0.00 0.00 2.43
2552 8274 3.689649 GCTTCCCACACTACACAATAAGG 59.310 47.826 0.00 0.00 0.00 2.69
2597 8319 5.768164 ACTGTAATTCTTTCCACCATCGTTT 59.232 36.000 0.00 0.00 0.00 3.60
2599 8321 4.906618 ACTGTAATTCTTTCCACCATCGT 58.093 39.130 0.00 0.00 0.00 3.73
2714 8452 4.394729 TGGGTTGGTATCTTTGAACTGAC 58.605 43.478 0.00 0.00 0.00 3.51
2761 8511 9.928618 TCATAACATCATATAAGTTTGGGGAAA 57.071 29.630 0.00 0.00 0.00 3.13
2831 8604 2.289072 ACTTCAGTCATGTTGAGGTCCG 60.289 50.000 10.36 0.00 30.07 4.79
2866 8639 3.181469 GGGCAATAGAACTGGTCGATGTA 60.181 47.826 0.00 0.00 0.00 2.29
2976 8777 1.331214 CACACCACCTTCCTGCAAAT 58.669 50.000 0.00 0.00 0.00 2.32
3010 8811 2.423373 CCCCCGGATGTTGATGAATCTT 60.423 50.000 0.73 0.00 0.00 2.40
3172 11053 3.883744 CTTCACCTTGCCCGCGACT 62.884 63.158 8.23 0.00 0.00 4.18
3208 11089 0.251354 GCACTTCTGATCAGAGGCCA 59.749 55.000 29.18 13.62 37.99 5.36
3220 11101 0.889638 TCACGACGGAGAGCACTTCT 60.890 55.000 0.00 0.00 39.43 2.85
3221 11102 0.039437 TTCACGACGGAGAGCACTTC 60.039 55.000 0.00 0.00 0.00 3.01
3222 11103 0.318784 GTTCACGACGGAGAGCACTT 60.319 55.000 0.00 0.00 0.00 3.16
3235 11116 2.412870 TGTCCAAGCACTATGTTCACG 58.587 47.619 0.00 0.00 0.00 4.35
3288 11170 0.663688 CTCACGTAGCGCTCACCTAT 59.336 55.000 16.34 0.00 0.00 2.57
3300 11182 1.283029 ACTACTACCCTGCCTCACGTA 59.717 52.381 0.00 0.00 0.00 3.57
3443 11328 3.181462 ACTCTGAATTGATGCCGCAGATA 60.181 43.478 0.00 0.00 35.32 1.98
3449 11334 3.672397 CGAGATACTCTGAATTGATGCCG 59.328 47.826 0.00 0.00 0.00 5.69
3454 11339 5.520376 TCATGCGAGATACTCTGAATTGA 57.480 39.130 0.00 0.00 0.00 2.57
3482 11367 5.600069 AGTTGTAGGCATGACAGATATGAGA 59.400 40.000 0.00 0.00 0.00 3.27
3483 11368 5.851720 AGTTGTAGGCATGACAGATATGAG 58.148 41.667 0.00 0.00 0.00 2.90
3484 11369 5.876651 AGTTGTAGGCATGACAGATATGA 57.123 39.130 0.00 0.00 0.00 2.15
3485 11370 6.286758 AGAAGTTGTAGGCATGACAGATATG 58.713 40.000 0.00 0.00 0.00 1.78
3486 11371 6.098838 TGAGAAGTTGTAGGCATGACAGATAT 59.901 38.462 0.00 0.00 0.00 1.63
3487 11372 5.422012 TGAGAAGTTGTAGGCATGACAGATA 59.578 40.000 0.00 0.00 0.00 1.98
3488 11373 4.223700 TGAGAAGTTGTAGGCATGACAGAT 59.776 41.667 0.00 0.00 0.00 2.90
3489 11374 3.578282 TGAGAAGTTGTAGGCATGACAGA 59.422 43.478 0.00 0.00 0.00 3.41
3490 11375 3.930336 TGAGAAGTTGTAGGCATGACAG 58.070 45.455 0.00 0.00 0.00 3.51
3491 11376 4.350368 TTGAGAAGTTGTAGGCATGACA 57.650 40.909 0.00 0.00 0.00 3.58
3492 11377 4.697352 ACATTGAGAAGTTGTAGGCATGAC 59.303 41.667 0.00 0.00 0.00 3.06
3493 11378 4.910195 ACATTGAGAAGTTGTAGGCATGA 58.090 39.130 0.00 0.00 0.00 3.07
3494 11379 6.238566 CCATACATTGAGAAGTTGTAGGCATG 60.239 42.308 0.00 0.00 30.03 4.06
3495 11380 5.824624 CCATACATTGAGAAGTTGTAGGCAT 59.175 40.000 0.00 0.00 30.03 4.40
3496 11381 5.185454 CCATACATTGAGAAGTTGTAGGCA 58.815 41.667 0.00 0.00 30.03 4.75
3497 11382 4.035675 GCCATACATTGAGAAGTTGTAGGC 59.964 45.833 0.00 0.00 35.28 3.93
3498 11383 4.576463 GGCCATACATTGAGAAGTTGTAGG 59.424 45.833 0.00 0.00 30.03 3.18
3499 11384 5.185454 TGGCCATACATTGAGAAGTTGTAG 58.815 41.667 0.00 0.00 30.03 2.74
3500 11385 5.172687 TGGCCATACATTGAGAAGTTGTA 57.827 39.130 0.00 0.00 0.00 2.41
3501 11386 4.032960 TGGCCATACATTGAGAAGTTGT 57.967 40.909 0.00 0.00 0.00 3.32
3502 11387 5.359009 AGAATGGCCATACATTGAGAAGTTG 59.641 40.000 21.15 0.00 40.92 3.16
3503 11388 5.513233 AGAATGGCCATACATTGAGAAGTT 58.487 37.500 21.15 0.00 40.92 2.66
3504 11389 5.121380 AGAATGGCCATACATTGAGAAGT 57.879 39.130 21.15 0.00 40.92 3.01
3505 11390 5.826737 AGAAGAATGGCCATACATTGAGAAG 59.173 40.000 21.15 0.00 40.92 2.85
3506 11391 5.759059 AGAAGAATGGCCATACATTGAGAA 58.241 37.500 21.15 0.00 40.92 2.87
3507 11392 5.378230 AGAAGAATGGCCATACATTGAGA 57.622 39.130 21.15 0.00 40.92 3.27
3508 11393 7.166851 AGATAGAAGAATGGCCATACATTGAG 58.833 38.462 21.15 0.00 40.92 3.02
3509 11394 7.083062 AGATAGAAGAATGGCCATACATTGA 57.917 36.000 21.15 4.08 40.92 2.57
3534 11419 8.310382 CCTCAGTGCTCTTGCTTATAGTATTAT 58.690 37.037 0.00 0.00 40.48 1.28
3535 11420 7.287927 ACCTCAGTGCTCTTGCTTATAGTATTA 59.712 37.037 0.00 0.00 40.48 0.98
3536 11421 6.098982 ACCTCAGTGCTCTTGCTTATAGTATT 59.901 38.462 0.00 0.00 40.48 1.89
3537 11422 5.600484 ACCTCAGTGCTCTTGCTTATAGTAT 59.400 40.000 0.00 0.00 40.48 2.12
3538 11423 4.956700 ACCTCAGTGCTCTTGCTTATAGTA 59.043 41.667 0.00 0.00 40.48 1.82
3539 11424 3.772025 ACCTCAGTGCTCTTGCTTATAGT 59.228 43.478 0.00 0.00 40.48 2.12
3540 11425 4.118410 CACCTCAGTGCTCTTGCTTATAG 58.882 47.826 0.00 0.00 37.14 1.31
3541 11426 4.128925 CACCTCAGTGCTCTTGCTTATA 57.871 45.455 0.00 0.00 37.14 0.98
3542 11427 2.983229 CACCTCAGTGCTCTTGCTTAT 58.017 47.619 0.00 0.00 37.14 1.73
3543 11428 2.462456 CACCTCAGTGCTCTTGCTTA 57.538 50.000 0.00 0.00 37.14 3.09
3544 11429 3.319135 CACCTCAGTGCTCTTGCTT 57.681 52.632 0.00 0.00 37.14 3.91
3554 11439 0.176680 CCGCAGATAAGCACCTCAGT 59.823 55.000 0.00 0.00 0.00 3.41
3555 11440 1.156645 GCCGCAGATAAGCACCTCAG 61.157 60.000 0.00 0.00 0.00 3.35
3556 11441 1.153369 GCCGCAGATAAGCACCTCA 60.153 57.895 0.00 0.00 0.00 3.86
3557 11442 1.153369 TGCCGCAGATAAGCACCTC 60.153 57.895 0.00 0.00 0.00 3.85
3558 11443 2.989639 TGCCGCAGATAAGCACCT 59.010 55.556 0.00 0.00 0.00 4.00
3561 11446 0.394216 ATTGGTGCCGCAGATAAGCA 60.394 50.000 0.00 0.00 0.00 3.91
3562 11447 0.740737 AATTGGTGCCGCAGATAAGC 59.259 50.000 0.00 0.00 0.00 3.09
3563 11448 2.016318 TGAATTGGTGCCGCAGATAAG 58.984 47.619 0.00 0.00 0.00 1.73
3564 11449 2.016318 CTGAATTGGTGCCGCAGATAA 58.984 47.619 0.00 0.00 0.00 1.75
3565 11450 1.209261 TCTGAATTGGTGCCGCAGATA 59.791 47.619 0.00 0.00 31.24 1.98
3566 11451 0.035152 TCTGAATTGGTGCCGCAGAT 60.035 50.000 0.00 0.00 31.24 2.90
3567 11452 0.674581 CTCTGAATTGGTGCCGCAGA 60.675 55.000 0.00 0.00 34.71 4.26
3568 11453 0.957395 ACTCTGAATTGGTGCCGCAG 60.957 55.000 0.00 0.00 0.00 5.18
3569 11454 0.323302 TACTCTGAATTGGTGCCGCA 59.677 50.000 0.00 0.00 0.00 5.69
3570 11455 1.599542 GATACTCTGAATTGGTGCCGC 59.400 52.381 0.00 0.00 0.00 6.53
3571 11456 3.126831 GAGATACTCTGAATTGGTGCCG 58.873 50.000 0.00 0.00 0.00 5.69
3572 11457 3.126831 CGAGATACTCTGAATTGGTGCC 58.873 50.000 0.00 0.00 0.00 5.01
3573 11458 2.541762 GCGAGATACTCTGAATTGGTGC 59.458 50.000 0.00 0.00 0.00 5.01
3574 11459 3.785486 TGCGAGATACTCTGAATTGGTG 58.215 45.455 0.00 0.00 0.00 4.17
3575 11460 4.100035 TCATGCGAGATACTCTGAATTGGT 59.900 41.667 0.00 0.00 0.00 3.67
3576 11461 4.625028 TCATGCGAGATACTCTGAATTGG 58.375 43.478 0.00 0.00 0.00 3.16
3577 11462 6.645827 AGAATCATGCGAGATACTCTGAATTG 59.354 38.462 0.00 0.00 0.00 2.32
3578 11463 6.645827 CAGAATCATGCGAGATACTCTGAATT 59.354 38.462 11.56 0.00 36.00 2.17
3579 11464 6.157904 CAGAATCATGCGAGATACTCTGAAT 58.842 40.000 11.56 0.00 36.00 2.57
3580 11465 5.068329 ACAGAATCATGCGAGATACTCTGAA 59.932 40.000 18.92 0.00 36.00 3.02
3581 11466 4.582240 ACAGAATCATGCGAGATACTCTGA 59.418 41.667 18.92 0.00 36.00 3.27
3582 11467 4.869215 ACAGAATCATGCGAGATACTCTG 58.131 43.478 13.88 13.88 38.19 3.35
3583 11468 4.826733 AGACAGAATCATGCGAGATACTCT 59.173 41.667 0.00 0.00 0.00 3.24
3584 11469 5.048782 AGAGACAGAATCATGCGAGATACTC 60.049 44.000 0.00 0.00 0.00 2.59
3585 11470 4.826733 AGAGACAGAATCATGCGAGATACT 59.173 41.667 0.00 0.00 0.00 2.12
3586 11471 4.916831 CAGAGACAGAATCATGCGAGATAC 59.083 45.833 0.00 0.00 0.00 2.24
3587 11472 4.823989 TCAGAGACAGAATCATGCGAGATA 59.176 41.667 0.00 0.00 0.00 1.98
3588 11473 3.635836 TCAGAGACAGAATCATGCGAGAT 59.364 43.478 0.00 0.00 0.00 2.75
3589 11474 3.019564 TCAGAGACAGAATCATGCGAGA 58.980 45.455 0.00 0.00 0.00 4.04
3590 11475 3.114809 GTCAGAGACAGAATCATGCGAG 58.885 50.000 0.00 0.00 32.09 5.03
3591 11476 2.159184 GGTCAGAGACAGAATCATGCGA 60.159 50.000 0.00 0.00 33.68 5.10
3592 11477 2.200067 GGTCAGAGACAGAATCATGCG 58.800 52.381 0.00 0.00 33.68 4.73
3593 11478 2.200067 CGGTCAGAGACAGAATCATGC 58.800 52.381 0.00 0.00 33.68 4.06
3594 11479 2.819115 CCGGTCAGAGACAGAATCATG 58.181 52.381 0.00 0.00 33.68 3.07
3595 11480 1.137872 GCCGGTCAGAGACAGAATCAT 59.862 52.381 1.90 0.00 33.68 2.45
3596 11481 0.532573 GCCGGTCAGAGACAGAATCA 59.467 55.000 1.90 0.00 33.68 2.57
3597 11482 0.179097 GGCCGGTCAGAGACAGAATC 60.179 60.000 0.00 0.00 33.68 2.52
3598 11483 1.901085 GGCCGGTCAGAGACAGAAT 59.099 57.895 0.00 0.00 33.68 2.40
3599 11484 2.636412 CGGCCGGTCAGAGACAGAA 61.636 63.158 20.10 0.00 33.68 3.02
3600 11485 3.062466 CGGCCGGTCAGAGACAGA 61.062 66.667 20.10 0.00 33.68 3.41
3601 11486 2.636412 TTCGGCCGGTCAGAGACAG 61.636 63.158 27.83 0.00 33.68 3.51
3602 11487 2.599281 TTCGGCCGGTCAGAGACA 60.599 61.111 27.83 0.00 33.68 3.41
3603 11488 2.126031 GTTCGGCCGGTCAGAGAC 60.126 66.667 27.83 9.01 0.00 3.36
3684 11569 3.438781 TGCAAACTACTAATTCTTGGCGG 59.561 43.478 0.00 0.00 0.00 6.13
3734 11624 1.599071 AGCTCAATTCACACACACACG 59.401 47.619 0.00 0.00 0.00 4.49
3805 11697 3.898123 TGCTGAGGATAATGGAGTACCTC 59.102 47.826 0.00 0.00 44.90 3.85
3829 11721 3.196685 GGTCCTACATCAAGTCTGAAGCT 59.803 47.826 0.00 0.00 34.49 3.74
3832 11724 3.055819 GCAGGTCCTACATCAAGTCTGAA 60.056 47.826 0.00 0.00 34.49 3.02
3847 11739 1.360192 GTTGTTGCTGTGCAGGTCC 59.640 57.895 1.11 0.00 40.61 4.46
3857 11749 5.536161 ACCAAGTATCAGAAATGTTGTTGCT 59.464 36.000 0.00 0.00 0.00 3.91
3862 11756 6.405065 CCATGGACCAAGTATCAGAAATGTTG 60.405 42.308 5.56 0.00 0.00 3.33
3872 11766 3.144506 CATCAGCCATGGACCAAGTATC 58.855 50.000 18.40 0.00 0.00 2.24
3874 11768 1.915489 ACATCAGCCATGGACCAAGTA 59.085 47.619 18.40 0.00 36.72 2.24
3900 11796 3.181467 CCTCTAGCTGCTCTGCTATTGTT 60.181 47.826 4.91 0.00 43.54 2.83


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

AutoCloner maintained by Alex Coulton.