Multiple sequence alignment - TraesCS4D01G194200

Loading Multiple Alignment...

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 TraesCS4D01G194200 chr4D 100.000 4611 0 0 1 4611 337149729 337154339 0.000000e+00 8516.0
1 TraesCS4D01G194200 chr4D 85.872 453 39 7 2965 3416 439783654 439783226 4.200000e-125 459.0
2 TraesCS4D01G194200 chr4D 100.000 40 0 0 3928 3967 337153621 337153660 1.780000e-09 75.0
3 TraesCS4D01G194200 chr4D 100.000 40 0 0 3893 3932 337153656 337153695 1.780000e-09 75.0
4 TraesCS4D01G194200 chr4B 92.839 3910 167 47 76 3932 416302898 416306747 0.000000e+00 5565.0
5 TraesCS4D01G194200 chr4B 88.202 712 48 21 3928 4611 416306708 416307411 0.000000e+00 817.0
6 TraesCS4D01G194200 chr4A 92.544 1985 79 29 1977 3934 135615828 135613886 0.000000e+00 2782.0
7 TraesCS4D01G194200 chr4A 94.200 1362 57 12 591 1943 135617179 135615831 0.000000e+00 2058.0
8 TraesCS4D01G194200 chr4A 90.428 491 28 11 3928 4409 135613927 135613447 3.030000e-176 628.0
9 TraesCS4D01G194200 chr4A 93.258 267 14 1 139 405 135617935 135617673 1.560000e-104 390.0
10 TraesCS4D01G194200 chr4A 92.169 166 7 1 433 592 135617618 135617453 3.590000e-56 230.0
11 TraesCS4D01G194200 chr4A 97.143 35 1 0 417 451 135617674 135617640 4.980000e-05 60.2
12 TraesCS4D01G194200 chr2B 86.957 460 48 11 2959 3416 746113580 746114029 1.480000e-139 507.0
13 TraesCS4D01G194200 chr2B 89.136 405 44 0 1123 1527 770767404 770767000 5.320000e-139 505.0
14 TraesCS4D01G194200 chr2B 86.849 403 53 0 1124 1526 64778504 64778102 7.040000e-123 451.0
15 TraesCS4D01G194200 chr2B 87.952 249 22 3 3609 3856 746115014 746115255 2.100000e-73 287.0
16 TraesCS4D01G194200 chr2B 84.667 150 18 3 3012 3159 707174346 707174200 1.340000e-30 145.0
17 TraesCS4D01G194200 chrUn 88.889 405 45 0 1123 1527 17299752 17299348 2.480000e-137 499.0
18 TraesCS4D01G194200 chrUn 88.000 200 24 0 3154 3353 17298413 17298214 2.140000e-58 237.0
19 TraesCS4D01G194200 chr2A 88.889 405 45 0 1123 1527 758449596 758449192 2.480000e-137 499.0
20 TraesCS4D01G194200 chr2A 87.626 396 49 0 1131 1526 41992682 41993077 1.170000e-125 460.0
21 TraesCS4D01G194200 chr2A 91.489 282 18 3 3135 3416 644310939 644310664 2.600000e-102 383.0
22 TraesCS4D01G194200 chr2A 88.618 246 23 2 3612 3856 644309339 644309098 1.250000e-75 294.0
23 TraesCS4D01G194200 chr2D 86.849 403 53 0 1124 1526 37055749 37055347 7.040000e-123 451.0
24 TraesCS4D01G194200 chr2D 86.600 403 54 0 1124 1526 37074381 37073979 3.270000e-121 446.0
25 TraesCS4D01G194200 chr3B 82.159 454 56 12 2965 3416 333941887 333941457 2.620000e-97 366.0
26 TraesCS4D01G194200 chr3B 91.981 212 16 1 3612 3822 333940470 333940259 3.490000e-76 296.0


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 TraesCS4D01G194200 chr4D 337149729 337154339 4610 False 2888.666667 8516 100.000000 1 4611 3 chr4D.!!$F1 4610
1 TraesCS4D01G194200 chr4B 416302898 416307411 4513 False 3191.000000 5565 90.520500 76 4611 2 chr4B.!!$F1 4535
2 TraesCS4D01G194200 chr4A 135613447 135617935 4488 True 1024.700000 2782 93.290333 139 4409 6 chr4A.!!$R1 4270
3 TraesCS4D01G194200 chr2B 746113580 746115255 1675 False 397.000000 507 87.454500 2959 3856 2 chr2B.!!$F1 897
4 TraesCS4D01G194200 chrUn 17298214 17299752 1538 True 368.000000 499 88.444500 1123 3353 2 chrUn.!!$R1 2230
5 TraesCS4D01G194200 chr2A 644309098 644310939 1841 True 338.500000 383 90.053500 3135 3856 2 chr2A.!!$R2 721
6 TraesCS4D01G194200 chr3B 333940259 333941887 1628 True 331.000000 366 87.070000 2965 3822 2 chr3B.!!$R1 857

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
186 193 0.106918 GGTTGGGTGGTGACTTGTCA 60.107 55.0 0.00 0.00 0.00 3.58 F
598 661 0.170116 GCGGCGAATCCAATGAACAA 59.830 50.0 12.98 0.00 34.01 2.83 F
1215 1564 0.606604 GGGACTTCAACCTCACGCTA 59.393 55.0 0.00 0.00 0.00 4.26 F
2025 2391 0.037447 TGCACCCGGTTGAATCATGA 59.963 50.0 1.77 0.00 0.00 3.07 F
2744 3116 0.330604 AGCACATCCAGGACATGCTT 59.669 50.0 19.69 7.78 44.01 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1973 1.086696 CACCGCCTGAATCGACAAAT 58.913 50.000 0.00 0.00 0.0 2.32 R
1801 2155 1.348036 GAACAGAGTAGGGGCAGTTGT 59.652 52.381 0.00 0.00 0.0 3.32 R
3070 3449 0.108424 ACGGCAGCAGAGATCAGAAC 60.108 55.000 0.00 0.00 0.0 3.01 R
3071 3450 0.108472 CACGGCAGCAGAGATCAGAA 60.108 55.000 0.00 0.00 0.0 3.02 R
3935 5476 0.109179 TGCATGTTGGATTGCGCTTC 60.109 50.000 9.73 5.59 41.8 3.86 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 3.987594 AAGGGGAGGAATGCAACTC 57.012 52.632 7.64 7.64 0.00 3.01
20 21 1.376649 AAGGGGAGGAATGCAACTCT 58.623 50.000 13.79 1.81 0.00 3.24
21 22 0.915364 AGGGGAGGAATGCAACTCTC 59.085 55.000 13.79 10.84 0.00 3.20
22 23 0.620556 GGGGAGGAATGCAACTCTCA 59.379 55.000 15.46 0.00 0.00 3.27
23 24 1.680249 GGGGAGGAATGCAACTCTCAC 60.680 57.143 15.46 11.42 0.00 3.51
24 25 1.280421 GGGAGGAATGCAACTCTCACT 59.720 52.381 13.79 0.00 0.00 3.41
25 26 2.626840 GGAGGAATGCAACTCTCACTC 58.373 52.381 13.79 6.09 0.00 3.51
26 27 2.235898 GGAGGAATGCAACTCTCACTCT 59.764 50.000 13.79 0.00 0.00 3.24
27 28 3.520569 GAGGAATGCAACTCTCACTCTC 58.479 50.000 8.63 0.00 0.00 3.20
28 29 2.902486 AGGAATGCAACTCTCACTCTCA 59.098 45.455 0.00 0.00 0.00 3.27
29 30 2.999355 GGAATGCAACTCTCACTCTCAC 59.001 50.000 0.00 0.00 0.00 3.51
30 31 3.555795 GGAATGCAACTCTCACTCTCACA 60.556 47.826 0.00 0.00 0.00 3.58
31 32 3.977134 ATGCAACTCTCACTCTCACAT 57.023 42.857 0.00 0.00 0.00 3.21
32 33 3.036075 TGCAACTCTCACTCTCACATG 57.964 47.619 0.00 0.00 0.00 3.21
33 34 2.289257 TGCAACTCTCACTCTCACATGG 60.289 50.000 0.00 0.00 0.00 3.66
34 35 2.028658 GCAACTCTCACTCTCACATGGA 60.029 50.000 0.00 0.00 0.00 3.41
35 36 3.369261 GCAACTCTCACTCTCACATGGAT 60.369 47.826 0.00 0.00 0.00 3.41
36 37 4.431809 CAACTCTCACTCTCACATGGATC 58.568 47.826 0.00 0.00 0.00 3.36
37 38 3.706183 ACTCTCACTCTCACATGGATCA 58.294 45.455 0.00 0.00 0.00 2.92
38 39 4.092279 ACTCTCACTCTCACATGGATCAA 58.908 43.478 0.00 0.00 0.00 2.57
39 40 4.715792 ACTCTCACTCTCACATGGATCAAT 59.284 41.667 0.00 0.00 0.00 2.57
40 41 5.163426 ACTCTCACTCTCACATGGATCAATC 60.163 44.000 0.00 0.00 0.00 2.67
41 42 4.713321 TCTCACTCTCACATGGATCAATCA 59.287 41.667 0.00 0.00 0.00 2.57
42 43 4.763073 TCACTCTCACATGGATCAATCAC 58.237 43.478 0.00 0.00 0.00 3.06
43 44 4.468868 TCACTCTCACATGGATCAATCACT 59.531 41.667 0.00 0.00 0.00 3.41
44 45 4.809958 CACTCTCACATGGATCAATCACTC 59.190 45.833 0.00 0.00 0.00 3.51
45 46 4.715792 ACTCTCACATGGATCAATCACTCT 59.284 41.667 0.00 0.00 0.00 3.24
46 47 5.163426 ACTCTCACATGGATCAATCACTCTC 60.163 44.000 0.00 0.00 0.00 3.20
47 48 4.961099 TCTCACATGGATCAATCACTCTCT 59.039 41.667 0.00 0.00 0.00 3.10
48 49 5.068855 TCTCACATGGATCAATCACTCTCTC 59.931 44.000 0.00 0.00 0.00 3.20
49 50 4.100653 TCACATGGATCAATCACTCTCTCC 59.899 45.833 0.00 0.00 0.00 3.71
50 51 3.069300 ACATGGATCAATCACTCTCTCCG 59.931 47.826 0.00 0.00 0.00 4.63
51 52 1.410517 TGGATCAATCACTCTCTCCGC 59.589 52.381 0.00 0.00 0.00 5.54
52 53 1.601663 GGATCAATCACTCTCTCCGCG 60.602 57.143 0.00 0.00 0.00 6.46
53 54 1.335182 GATCAATCACTCTCTCCGCGA 59.665 52.381 8.23 0.00 0.00 5.87
54 55 1.393603 TCAATCACTCTCTCCGCGAT 58.606 50.000 8.23 0.00 0.00 4.58
55 56 1.335182 TCAATCACTCTCTCCGCGATC 59.665 52.381 8.23 0.00 0.00 3.69
56 57 0.671251 AATCACTCTCTCCGCGATCC 59.329 55.000 8.23 0.00 0.00 3.36
57 58 0.179004 ATCACTCTCTCCGCGATCCT 60.179 55.000 8.23 0.00 0.00 3.24
58 59 0.816018 TCACTCTCTCCGCGATCCTC 60.816 60.000 8.23 0.00 0.00 3.71
59 60 0.817634 CACTCTCTCCGCGATCCTCT 60.818 60.000 8.23 0.00 0.00 3.69
60 61 0.817634 ACTCTCTCCGCGATCCTCTG 60.818 60.000 8.23 0.00 0.00 3.35
61 62 1.514678 CTCTCTCCGCGATCCTCTGG 61.515 65.000 8.23 0.00 0.00 3.86
62 63 1.527148 CTCTCCGCGATCCTCTGGA 60.527 63.158 8.23 0.00 35.55 3.86
63 64 1.791103 CTCTCCGCGATCCTCTGGAC 61.791 65.000 8.23 0.00 32.98 4.02
64 65 3.187699 CTCCGCGATCCTCTGGACG 62.188 68.421 8.23 0.00 32.98 4.79
65 66 4.933064 CCGCGATCCTCTGGACGC 62.933 72.222 8.23 17.13 43.32 5.19
66 67 4.933064 CGCGATCCTCTGGACGCC 62.933 72.222 19.43 8.89 43.60 5.68
67 68 3.532155 GCGATCCTCTGGACGCCT 61.532 66.667 16.62 0.00 42.09 5.52
68 69 3.082579 GCGATCCTCTGGACGCCTT 62.083 63.158 16.62 0.00 42.09 4.35
69 70 1.517832 CGATCCTCTGGACGCCTTT 59.482 57.895 0.00 0.00 32.98 3.11
70 71 0.528684 CGATCCTCTGGACGCCTTTC 60.529 60.000 0.00 0.00 32.98 2.62
71 72 0.179070 GATCCTCTGGACGCCTTTCC 60.179 60.000 0.00 0.00 32.98 3.13
72 73 1.627297 ATCCTCTGGACGCCTTTCCC 61.627 60.000 0.00 0.00 32.98 3.97
73 74 2.592993 CCTCTGGACGCCTTTCCCA 61.593 63.158 0.00 0.00 34.33 4.37
74 75 1.078848 CTCTGGACGCCTTTCCCAG 60.079 63.158 0.00 0.00 46.64 4.45
75 76 2.527951 CTCTGGACGCCTTTCCCAGG 62.528 65.000 0.00 0.00 45.62 4.45
82 83 3.646715 CCTTTCCCAGGCCGTCCA 61.647 66.667 0.00 0.00 35.13 4.02
83 84 2.359975 CTTTCCCAGGCCGTCCAC 60.360 66.667 0.00 0.00 33.74 4.02
84 85 2.852075 TTTCCCAGGCCGTCCACT 60.852 61.111 0.00 0.00 33.74 4.00
104 105 3.325135 ACTTCTCCTTAAGTGGTGTCAGG 59.675 47.826 0.97 0.00 38.28 3.86
118 119 2.357881 CAGGCTCTGCGCTGACAA 60.358 61.111 13.46 0.00 39.13 3.18
119 120 1.744368 CAGGCTCTGCGCTGACAAT 60.744 57.895 13.46 0.00 39.13 2.71
129 130 2.639327 GCTGACAATGGTGGCCCAC 61.639 63.158 4.93 4.93 45.65 4.61
131 132 0.962356 CTGACAATGGTGGCCCACTC 60.962 60.000 14.71 3.33 45.65 3.51
173 180 1.243342 ACGTGTCATGCATGGTTGGG 61.243 55.000 25.97 13.98 38.39 4.12
186 193 0.106918 GGTTGGGTGGTGACTTGTCA 60.107 55.000 0.00 0.00 0.00 3.58
209 216 1.902508 GACTGGGTCCAGAATGTCAGA 59.097 52.381 22.46 0.00 46.30 3.27
240 247 3.391049 GTGTCTGTGTCTGGGTTTACTC 58.609 50.000 0.00 0.00 0.00 2.59
287 294 2.037527 ACCGGACTCCACCTCTCC 59.962 66.667 9.46 0.00 0.00 3.71
297 304 0.250234 CCACCTCTCCGCATTCAAGA 59.750 55.000 0.00 0.00 0.00 3.02
341 348 3.712881 GTCCGTGCACGAGTTGGC 61.713 66.667 39.10 20.87 43.02 4.52
494 541 2.051345 GACTTGCGCCACAAACCG 60.051 61.111 4.18 0.00 37.96 4.44
563 626 0.941542 TCTCGCCACCAAAAACGAAG 59.058 50.000 0.00 0.00 33.61 3.79
598 661 0.170116 GCGGCGAATCCAATGAACAA 59.830 50.000 12.98 0.00 34.01 2.83
645 981 3.451178 ACGTGAACCTACATAATGCTCCT 59.549 43.478 0.00 0.00 0.00 3.69
732 1068 1.448922 CCGTGGTTTTCCTTTCGCCA 61.449 55.000 0.00 0.00 41.38 5.69
786 1122 2.359478 CTTCCCACGAAACCCCCG 60.359 66.667 0.00 0.00 0.00 5.73
942 1283 1.772979 AAAACCCCACGTCCCCTCT 60.773 57.895 0.00 0.00 0.00 3.69
1012 1361 2.815211 CAGCGATGGACACCCACG 60.815 66.667 0.00 0.00 46.98 4.94
1215 1564 0.606604 GGGACTTCAACCTCACGCTA 59.393 55.000 0.00 0.00 0.00 4.26
1532 1885 2.351276 CTGCCACCAGGTACCCAC 59.649 66.667 8.74 0.00 37.19 4.61
1550 1903 3.788766 GCACGCGCGTTTCCTCAT 61.789 61.111 35.90 5.97 0.00 2.90
1560 1913 2.159338 GCGTTTCCTCATCATGCATTGT 60.159 45.455 0.00 0.00 0.00 2.71
1588 1941 3.509575 CCTCATTCGATTCCTCCCTCTAG 59.490 52.174 0.00 0.00 0.00 2.43
1593 1946 2.431057 TCGATTCCTCCCTCTAGTTTGC 59.569 50.000 0.00 0.00 0.00 3.68
1614 1967 1.819288 TGACTCGATCTGGTTGGTCTC 59.181 52.381 0.00 0.00 0.00 3.36
1620 1973 3.830178 TCGATCTGGTTGGTCTCTTGTTA 59.170 43.478 0.00 0.00 0.00 2.41
1801 2155 1.993391 CTTCCTCGCCCCCAGGTAA 60.993 63.158 0.00 0.00 34.57 2.85
1827 2184 0.824759 CCCCTACTCTGTTCTTCCGG 59.175 60.000 0.00 0.00 0.00 5.14
1843 2200 1.592131 CGGGTTGTCGTTTCCGTGA 60.592 57.895 0.00 0.00 37.92 4.35
1854 2213 1.454653 GTTTCCGTGAACGTAGTGCTC 59.545 52.381 1.75 0.00 45.00 4.26
1922 2281 7.176690 ACTTTATCTTGGATCATGGAACGTTTT 59.823 33.333 0.46 0.00 0.00 2.43
1924 2283 4.393834 TCTTGGATCATGGAACGTTTTCA 58.606 39.130 0.46 4.92 32.80 2.69
1964 2323 6.758886 CCGTAGATCTTAACTCTTGATTTGCT 59.241 38.462 0.00 0.00 0.00 3.91
1971 2337 9.944376 ATCTTAACTCTTGATTTGCTGTACTAA 57.056 29.630 0.00 0.00 0.00 2.24
1975 2341 6.759272 ACTCTTGATTTGCTGTACTAACTGA 58.241 36.000 0.00 0.00 0.00 3.41
1986 2352 5.737635 GCTGTACTAACTGATGGGAGCTTAG 60.738 48.000 0.00 0.00 0.00 2.18
2008 2374 8.770438 TTAGGATTTTATCACCACAAAAATGC 57.230 30.769 0.00 0.00 39.67 3.56
2009 2375 6.767456 AGGATTTTATCACCACAAAAATGCA 58.233 32.000 11.89 0.00 40.96 3.96
2013 2379 0.387202 TCACCACAAAAATGCACCCG 59.613 50.000 0.00 0.00 0.00 5.28
2020 2386 2.103941 ACAAAAATGCACCCGGTTGAAT 59.896 40.909 1.77 0.00 0.00 2.57
2021 2387 2.736192 CAAAAATGCACCCGGTTGAATC 59.264 45.455 1.77 0.00 0.00 2.52
2022 2388 1.626686 AAATGCACCCGGTTGAATCA 58.373 45.000 1.77 0.00 0.00 2.57
2023 2389 1.851304 AATGCACCCGGTTGAATCAT 58.149 45.000 1.77 0.00 0.00 2.45
2024 2390 1.105457 ATGCACCCGGTTGAATCATG 58.895 50.000 1.77 0.00 0.00 3.07
2025 2391 0.037447 TGCACCCGGTTGAATCATGA 59.963 50.000 1.77 0.00 0.00 3.07
2026 2392 0.451783 GCACCCGGTTGAATCATGAC 59.548 55.000 1.77 0.00 0.00 3.06
2027 2393 1.950484 GCACCCGGTTGAATCATGACT 60.950 52.381 1.77 0.00 0.00 3.41
2170 2536 6.949578 ACTGAACTGTGTTGTGAAAAATTG 57.050 33.333 0.00 0.00 0.00 2.32
2268 2634 4.669809 TTGTCGCCGGCCCCAAAT 62.670 61.111 23.46 0.00 0.00 2.32
2306 2672 1.153804 GAAGGCCTTCGTCGACCTC 60.154 63.158 29.09 4.50 0.00 3.85
2321 2687 4.742201 CTCGTGGACGCCAGTGGG 62.742 72.222 12.15 3.56 39.60 4.61
2465 2831 2.038975 TACCTCTTCGCAGGCCCT 59.961 61.111 0.00 0.00 36.98 5.19
2744 3116 0.330604 AGCACATCCAGGACATGCTT 59.669 50.000 19.69 7.78 44.01 3.91
2768 3140 3.418068 GACAGTGCAGTGCTCGCC 61.418 66.667 21.57 3.93 0.00 5.54
2836 3208 3.385384 CTGCGGGTGAGCTCCTGA 61.385 66.667 12.15 0.00 36.02 3.86
2837 3209 2.685017 TGCGGGTGAGCTCCTGAT 60.685 61.111 12.15 0.00 36.02 2.90
2838 3210 2.249413 CTGCGGGTGAGCTCCTGATT 62.249 60.000 12.15 0.00 36.02 2.57
2839 3211 1.522580 GCGGGTGAGCTCCTGATTC 60.523 63.158 12.15 0.00 36.02 2.52
2881 3259 5.682212 GCATGTTTCCTCCTTGTTTGTCTTT 60.682 40.000 0.00 0.00 0.00 2.52
2882 3260 5.323371 TGTTTCCTCCTTGTTTGTCTTTG 57.677 39.130 0.00 0.00 0.00 2.77
2883 3261 4.770010 TGTTTCCTCCTTGTTTGTCTTTGT 59.230 37.500 0.00 0.00 0.00 2.83
2884 3262 4.981806 TTCCTCCTTGTTTGTCTTTGTG 57.018 40.909 0.00 0.00 0.00 3.33
2885 3263 4.229304 TCCTCCTTGTTTGTCTTTGTGA 57.771 40.909 0.00 0.00 0.00 3.58
2899 3277 3.066621 TCTTTGTGATGTCTTGTTGTGCC 59.933 43.478 0.00 0.00 0.00 5.01
3004 3383 4.430765 CTCGGGTACGCGCAAGGT 62.431 66.667 25.81 0.00 40.69 3.50
3062 3441 2.708325 GGGAGCTTCCAGGTGAGATATT 59.292 50.000 6.02 0.00 38.64 1.28
3065 3444 3.387962 AGCTTCCAGGTGAGATATTCCA 58.612 45.455 0.00 0.00 0.00 3.53
3067 3446 3.118261 GCTTCCAGGTGAGATATTCCACA 60.118 47.826 9.62 0.00 35.13 4.17
3069 3448 5.688807 CTTCCAGGTGAGATATTCCACAAT 58.311 41.667 9.62 0.00 35.13 2.71
3070 3449 5.039920 TCCAGGTGAGATATTCCACAATG 57.960 43.478 9.62 7.73 35.13 2.82
3071 3450 4.474651 TCCAGGTGAGATATTCCACAATGT 59.525 41.667 9.62 0.00 35.13 2.71
3102 3484 1.005294 CTGCCGTGTGCTGCAATTTC 61.005 55.000 2.77 0.00 42.00 2.17
3132 3516 3.419915 CGTGCTGTTTCTAATGTGATGC 58.580 45.455 0.00 0.00 0.00 3.91
3565 4795 0.543174 AAGAGCTTCTCGAGTGGGGT 60.543 55.000 13.13 9.15 35.36 4.95
3620 5146 0.404040 CCCCCAGTAGACCAAGCAAA 59.596 55.000 0.00 0.00 0.00 3.68
3641 5170 2.834549 ACTTGCCTGCATCAGTAGTAGT 59.165 45.455 0.00 0.00 0.00 2.73
3766 5301 1.473257 GCCATCGCCTGTGTTCTATCA 60.473 52.381 0.00 0.00 0.00 2.15
3809 5344 4.876125 TGAGATATTTCTAGCTTGCCTCG 58.124 43.478 0.00 0.00 30.30 4.63
3910 5451 2.728839 CGAGGAATCTAGAAGCGCAATC 59.271 50.000 11.47 7.77 0.00 2.67
3911 5452 3.063485 GAGGAATCTAGAAGCGCAATCC 58.937 50.000 11.47 0.00 0.00 3.01
3912 5453 2.435805 AGGAATCTAGAAGCGCAATCCA 59.564 45.455 11.47 0.00 0.00 3.41
3913 5454 3.118261 AGGAATCTAGAAGCGCAATCCAA 60.118 43.478 11.47 0.00 0.00 3.53
3914 5455 3.002759 GGAATCTAGAAGCGCAATCCAAC 59.997 47.826 11.47 0.00 0.00 3.77
3915 5456 2.760634 TCTAGAAGCGCAATCCAACA 57.239 45.000 11.47 0.00 0.00 3.33
3916 5457 3.266510 TCTAGAAGCGCAATCCAACAT 57.733 42.857 11.47 0.00 0.00 2.71
3917 5458 2.938451 TCTAGAAGCGCAATCCAACATG 59.062 45.455 11.47 0.00 0.00 3.21
3918 5459 0.171903 AGAAGCGCAATCCAACATGC 59.828 50.000 11.47 0.00 39.17 4.06
3919 5460 0.109179 GAAGCGCAATCCAACATGCA 60.109 50.000 11.47 0.00 42.68 3.96
3920 5461 0.533491 AAGCGCAATCCAACATGCAT 59.467 45.000 11.47 0.00 42.68 3.96
3921 5462 0.179121 AGCGCAATCCAACATGCATG 60.179 50.000 25.09 25.09 42.68 4.06
3922 5463 1.149361 GCGCAATCCAACATGCATGG 61.149 55.000 29.41 14.99 42.68 3.66
3927 5468 3.157727 TCCAACATGCATGGACTCG 57.842 52.632 29.41 12.75 41.98 4.18
3928 5469 0.392863 TCCAACATGCATGGACTCGG 60.393 55.000 29.41 20.15 41.98 4.63
3929 5470 0.392863 CCAACATGCATGGACTCGGA 60.393 55.000 29.41 0.00 40.56 4.55
3930 5471 1.452110 CAACATGCATGGACTCGGAA 58.548 50.000 29.41 0.00 0.00 4.30
3931 5472 2.019249 CAACATGCATGGACTCGGAAT 58.981 47.619 29.41 3.16 0.00 3.01
3932 5473 1.959042 ACATGCATGGACTCGGAATC 58.041 50.000 29.41 0.00 0.00 2.52
3933 5474 1.487976 ACATGCATGGACTCGGAATCT 59.512 47.619 29.41 1.84 0.00 2.40
3934 5475 2.700371 ACATGCATGGACTCGGAATCTA 59.300 45.455 29.41 0.00 0.00 1.98
3935 5476 3.244009 ACATGCATGGACTCGGAATCTAG 60.244 47.826 29.41 0.00 0.00 2.43
3936 5477 2.666317 TGCATGGACTCGGAATCTAGA 58.334 47.619 0.00 0.00 0.00 2.43
3937 5478 3.031013 TGCATGGACTCGGAATCTAGAA 58.969 45.455 0.00 0.00 0.00 2.10
3938 5479 3.068732 TGCATGGACTCGGAATCTAGAAG 59.931 47.826 0.00 0.00 0.00 2.85
3939 5480 3.648009 CATGGACTCGGAATCTAGAAGC 58.352 50.000 0.00 0.00 0.00 3.86
3940 5481 1.676529 TGGACTCGGAATCTAGAAGCG 59.323 52.381 0.00 0.00 0.00 4.68
3941 5482 1.600912 GGACTCGGAATCTAGAAGCGC 60.601 57.143 0.00 0.00 0.00 5.92
3942 5483 1.065701 GACTCGGAATCTAGAAGCGCA 59.934 52.381 11.47 0.00 0.00 6.09
3943 5484 1.476891 ACTCGGAATCTAGAAGCGCAA 59.523 47.619 11.47 0.00 0.00 4.85
3944 5485 2.101582 ACTCGGAATCTAGAAGCGCAAT 59.898 45.455 11.47 0.00 0.00 3.56
3945 5486 2.728839 CTCGGAATCTAGAAGCGCAATC 59.271 50.000 11.47 7.77 0.00 2.67
3998 5543 8.925161 TTGCAAATATGATAGTTTTGGTTAGC 57.075 30.769 0.00 0.00 32.33 3.09
3999 5544 8.292444 TGCAAATATGATAGTTTTGGTTAGCT 57.708 30.769 0.00 0.00 32.33 3.32
4020 5565 6.234723 GCTAGAAAGTGAGCTAATAATGGC 57.765 41.667 0.00 0.00 35.73 4.40
4066 5611 3.003480 CAGTTCGGCCCTTTTTCTAGAG 58.997 50.000 0.00 0.00 0.00 2.43
4198 5745 2.564947 GTGGGTTTTGATATTGCCACCA 59.435 45.455 0.00 0.00 0.00 4.17
4300 5853 2.357056 CCCCCGTTTATGTGGGCA 59.643 61.111 0.00 0.00 44.58 5.36
4330 5885 3.703420 CAAATATCAGAGGCTGCTTTGC 58.297 45.455 0.00 0.00 0.00 3.68
4359 5914 6.541111 AAAGTGAGATAACGACAACCTTTC 57.459 37.500 0.00 0.00 0.00 2.62
4409 5964 2.414594 GGTATCCGCCGCTACGTT 59.585 61.111 0.00 0.00 0.00 3.99
4410 5965 1.659644 GGTATCCGCCGCTACGTTC 60.660 63.158 0.00 0.00 0.00 3.95
4414 5969 2.221906 ATCCGCCGCTACGTTCTGTT 62.222 55.000 0.00 0.00 0.00 3.16
4415 5970 2.025418 CCGCCGCTACGTTCTGTTT 61.025 57.895 0.00 0.00 0.00 2.83
4417 5972 0.179258 CGCCGCTACGTTCTGTTTTC 60.179 55.000 0.00 0.00 0.00 2.29
4442 6018 2.540515 CGTCACGCTGGTTCAGATTAT 58.459 47.619 0.00 0.00 32.44 1.28
4447 6023 3.310774 CACGCTGGTTCAGATTATGGAAG 59.689 47.826 0.00 0.00 32.44 3.46
4448 6024 3.197766 ACGCTGGTTCAGATTATGGAAGA 59.802 43.478 0.00 0.00 32.44 2.87
4449 6025 3.806521 CGCTGGTTCAGATTATGGAAGAG 59.193 47.826 0.00 0.00 32.44 2.85
4458 6034 7.849804 TCAGATTATGGAAGAGTAAAAGCAC 57.150 36.000 0.00 0.00 0.00 4.40
4459 6035 7.624549 TCAGATTATGGAAGAGTAAAAGCACT 58.375 34.615 0.00 0.00 0.00 4.40
4460 6036 8.103305 TCAGATTATGGAAGAGTAAAAGCACTT 58.897 33.333 0.00 0.00 0.00 3.16
4475 6052 2.976882 AGCACTTCAGGTACCCAACTTA 59.023 45.455 8.74 0.00 0.00 2.24
4476 6053 3.587506 AGCACTTCAGGTACCCAACTTAT 59.412 43.478 8.74 0.00 0.00 1.73
4480 6057 6.055588 CACTTCAGGTACCCAACTTATATGG 58.944 44.000 8.74 0.00 37.71 2.74
4489 6066 7.174946 GGTACCCAACTTATATGGAATGTGATG 59.825 40.741 0.00 0.00 40.56 3.07
4503 6080 9.857656 ATGGAATGTGATGATTTAGTCTTACAT 57.142 29.630 0.00 0.00 31.50 2.29
4507 6084 9.793252 AATGTGATGATTTAGTCTTACATTTGC 57.207 29.630 0.00 0.00 34.66 3.68
4532 6110 1.123928 GCAGCTCTACCATACCCAGT 58.876 55.000 0.00 0.00 0.00 4.00
4538 6116 3.270877 CTCTACCATACCCAGTTTGCAC 58.729 50.000 0.00 0.00 0.00 4.57
4550 6128 4.566545 CAGTTTGCACTGGATGTGTTTA 57.433 40.909 0.00 0.00 46.10 2.01
4551 6129 5.125100 CAGTTTGCACTGGATGTGTTTAT 57.875 39.130 0.00 0.00 46.10 1.40
4554 6132 7.144661 CAGTTTGCACTGGATGTGTTTATTTA 58.855 34.615 0.00 0.00 46.10 1.40
4560 6140 6.180472 CACTGGATGTGTTTATTTAGTCCCT 58.820 40.000 0.00 0.00 41.53 4.20
4581 6161 1.267532 GCCTATCACAACGCGACAATG 60.268 52.381 15.93 8.81 0.00 2.82
4587 6168 3.737172 AACGCGACAATGGCAGCC 61.737 61.111 15.93 3.66 0.00 4.85
4594 6175 2.283388 CAATGGCAGCCAGGTGGT 60.283 61.111 21.51 0.00 36.75 4.16
4607 6188 3.982241 GTGGTCGGACCGGTCGTT 61.982 66.667 27.68 0.00 42.58 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.505819 GAGAGTTGCATTCCTCCCCTTA 59.494 50.000 0.00 0.00 0.00 2.69
1 2 1.283321 GAGAGTTGCATTCCTCCCCTT 59.717 52.381 0.00 0.00 0.00 3.95
2 3 0.915364 GAGAGTTGCATTCCTCCCCT 59.085 55.000 0.00 0.00 0.00 4.79
4 5 1.280421 AGTGAGAGTTGCATTCCTCCC 59.720 52.381 0.00 0.00 0.00 4.30
6 7 3.056250 TGAGAGTGAGAGTTGCATTCCTC 60.056 47.826 0.00 0.00 0.00 3.71
7 8 2.902486 TGAGAGTGAGAGTTGCATTCCT 59.098 45.455 0.00 0.00 0.00 3.36
8 9 2.999355 GTGAGAGTGAGAGTTGCATTCC 59.001 50.000 0.00 0.00 0.00 3.01
9 10 3.657634 TGTGAGAGTGAGAGTTGCATTC 58.342 45.455 0.00 0.00 0.00 2.67
10 11 3.758755 TGTGAGAGTGAGAGTTGCATT 57.241 42.857 0.00 0.00 0.00 3.56
11 12 3.597255 CATGTGAGAGTGAGAGTTGCAT 58.403 45.455 0.00 0.00 0.00 3.96
12 13 2.289257 CCATGTGAGAGTGAGAGTTGCA 60.289 50.000 0.00 0.00 0.00 4.08
13 14 2.028658 TCCATGTGAGAGTGAGAGTTGC 60.029 50.000 0.00 0.00 0.00 4.17
14 15 3.949842 TCCATGTGAGAGTGAGAGTTG 57.050 47.619 0.00 0.00 0.00 3.16
15 16 4.092279 TGATCCATGTGAGAGTGAGAGTT 58.908 43.478 0.00 0.00 0.00 3.01
16 17 3.706183 TGATCCATGTGAGAGTGAGAGT 58.294 45.455 0.00 0.00 0.00 3.24
17 18 4.732672 TTGATCCATGTGAGAGTGAGAG 57.267 45.455 0.00 0.00 0.00 3.20
18 19 4.713321 TGATTGATCCATGTGAGAGTGAGA 59.287 41.667 0.00 0.00 0.00 3.27
19 20 4.809958 GTGATTGATCCATGTGAGAGTGAG 59.190 45.833 0.00 0.00 0.00 3.51
20 21 4.468868 AGTGATTGATCCATGTGAGAGTGA 59.531 41.667 0.00 0.00 0.00 3.41
21 22 4.767478 AGTGATTGATCCATGTGAGAGTG 58.233 43.478 0.00 0.00 0.00 3.51
22 23 4.715792 AGAGTGATTGATCCATGTGAGAGT 59.284 41.667 0.00 0.00 0.00 3.24
23 24 5.069383 AGAGAGTGATTGATCCATGTGAGAG 59.931 44.000 0.00 0.00 0.00 3.20
24 25 4.961099 AGAGAGTGATTGATCCATGTGAGA 59.039 41.667 0.00 0.00 0.00 3.27
25 26 5.279255 AGAGAGTGATTGATCCATGTGAG 57.721 43.478 0.00 0.00 0.00 3.51
26 27 4.100653 GGAGAGAGTGATTGATCCATGTGA 59.899 45.833 0.00 0.00 0.00 3.58
27 28 4.378774 GGAGAGAGTGATTGATCCATGTG 58.621 47.826 0.00 0.00 0.00 3.21
28 29 3.069300 CGGAGAGAGTGATTGATCCATGT 59.931 47.826 0.00 0.00 0.00 3.21
29 30 3.651206 CGGAGAGAGTGATTGATCCATG 58.349 50.000 0.00 0.00 0.00 3.66
30 31 2.036992 GCGGAGAGAGTGATTGATCCAT 59.963 50.000 0.00 0.00 0.00 3.41
31 32 1.410517 GCGGAGAGAGTGATTGATCCA 59.589 52.381 0.00 0.00 0.00 3.41
32 33 1.601663 CGCGGAGAGAGTGATTGATCC 60.602 57.143 0.00 0.00 0.00 3.36
33 34 1.335182 TCGCGGAGAGAGTGATTGATC 59.665 52.381 6.13 0.00 0.00 2.92
34 35 1.393603 TCGCGGAGAGAGTGATTGAT 58.606 50.000 6.13 0.00 0.00 2.57
35 36 1.335182 GATCGCGGAGAGAGTGATTGA 59.665 52.381 6.13 0.00 41.36 2.57
36 37 1.601663 GGATCGCGGAGAGAGTGATTG 60.602 57.143 6.13 0.00 41.36 2.67
37 38 0.671251 GGATCGCGGAGAGAGTGATT 59.329 55.000 6.13 0.00 41.36 2.57
38 39 0.179004 AGGATCGCGGAGAGAGTGAT 60.179 55.000 6.13 0.00 41.36 3.06
39 40 0.816018 GAGGATCGCGGAGAGAGTGA 60.816 60.000 6.13 0.00 41.36 3.41
40 41 0.817634 AGAGGATCGCGGAGAGAGTG 60.818 60.000 6.13 0.00 41.36 3.51
41 42 0.817634 CAGAGGATCGCGGAGAGAGT 60.818 60.000 6.13 0.00 41.36 3.24
42 43 1.514678 CCAGAGGATCGCGGAGAGAG 61.515 65.000 6.13 0.00 41.36 3.20
43 44 1.527148 CCAGAGGATCGCGGAGAGA 60.527 63.158 6.13 0.00 42.67 3.10
44 45 1.527148 TCCAGAGGATCGCGGAGAG 60.527 63.158 6.13 0.00 42.67 3.20
45 46 1.824329 GTCCAGAGGATCGCGGAGA 60.824 63.158 6.13 0.00 41.30 3.71
46 47 2.725008 GTCCAGAGGATCGCGGAG 59.275 66.667 6.13 0.00 41.30 4.63
47 48 3.209812 CGTCCAGAGGATCGCGGA 61.210 66.667 6.13 0.00 42.67 5.54
48 49 4.933064 GCGTCCAGAGGATCGCGG 62.933 72.222 6.13 0.00 42.67 6.46
49 50 4.933064 GGCGTCCAGAGGATCGCG 62.933 72.222 19.06 0.00 45.60 5.87
50 51 2.579684 AAAGGCGTCCAGAGGATCGC 62.580 60.000 18.17 18.17 44.73 4.58
51 52 0.528684 GAAAGGCGTCCAGAGGATCG 60.529 60.000 0.00 0.00 42.67 3.69
52 53 0.179070 GGAAAGGCGTCCAGAGGATC 60.179 60.000 5.49 0.00 37.65 3.36
53 54 1.627297 GGGAAAGGCGTCCAGAGGAT 61.627 60.000 11.67 0.00 39.70 3.24
54 55 2.291043 GGGAAAGGCGTCCAGAGGA 61.291 63.158 11.67 0.00 39.70 3.71
55 56 2.269241 GGGAAAGGCGTCCAGAGG 59.731 66.667 11.67 0.00 39.70 3.69
56 57 3.068881 TGGGAAAGGCGTCCAGAG 58.931 61.111 11.67 0.00 39.70 3.35
58 59 2.045926 CCTGGGAAAGGCGTCCAG 60.046 66.667 11.67 10.84 45.57 3.86
66 67 2.359975 GTGGACGGCCTGGGAAAG 60.360 66.667 9.82 0.00 34.31 2.62
67 68 2.406002 GAAGTGGACGGCCTGGGAAA 62.406 60.000 9.82 0.00 34.31 3.13
68 69 2.852075 AAGTGGACGGCCTGGGAA 60.852 61.111 9.82 0.00 34.31 3.97
69 70 3.319198 GAAGTGGACGGCCTGGGA 61.319 66.667 9.82 0.00 34.31 4.37
70 71 3.316573 GAGAAGTGGACGGCCTGGG 62.317 68.421 9.82 0.00 34.31 4.45
71 72 2.266055 GAGAAGTGGACGGCCTGG 59.734 66.667 9.82 0.00 34.31 4.45
72 73 1.831652 AAGGAGAAGTGGACGGCCTG 61.832 60.000 9.82 0.00 34.31 4.85
73 74 0.252103 TAAGGAGAAGTGGACGGCCT 60.252 55.000 9.82 0.00 34.31 5.19
74 75 0.611714 TTAAGGAGAAGTGGACGGCC 59.388 55.000 0.00 0.00 0.00 6.13
75 76 1.275573 ACTTAAGGAGAAGTGGACGGC 59.724 52.381 7.53 0.00 38.25 5.68
82 83 3.325135 CCTGACACCACTTAAGGAGAAGT 59.675 47.826 7.53 0.00 40.35 3.01
83 84 3.866449 GCCTGACACCACTTAAGGAGAAG 60.866 52.174 7.53 0.00 0.00 2.85
84 85 2.038557 GCCTGACACCACTTAAGGAGAA 59.961 50.000 7.53 0.00 0.00 2.87
129 130 1.757340 GAGGTACCTGGGACCGGAG 60.757 68.421 22.10 0.00 42.21 4.63
131 132 3.145551 CGAGGTACCTGGGACCGG 61.146 72.222 22.10 14.54 42.21 5.28
159 166 0.899253 CACCACCCAACCATGCATGA 60.899 55.000 28.31 0.00 0.00 3.07
161 168 0.899717 GTCACCACCCAACCATGCAT 60.900 55.000 0.00 0.00 0.00 3.96
173 180 2.549754 CCAGTCATTGACAAGTCACCAC 59.450 50.000 18.57 0.44 39.66 4.16
186 193 2.644299 TGACATTCTGGACCCAGTCATT 59.356 45.455 15.06 0.26 43.96 2.57
240 247 4.045104 CGTCAATGACCTCCGAAAGATAG 58.955 47.826 7.91 0.00 0.00 2.08
287 294 2.512885 GCACTGTCATTCTTGAATGCG 58.487 47.619 16.09 10.40 32.48 4.73
297 304 0.874390 AATCGCAACGCACTGTCATT 59.126 45.000 0.00 0.00 0.00 2.57
494 541 3.723348 GCGTGGGACAGCGGTTTC 61.723 66.667 0.00 0.00 41.80 2.78
520 567 3.744155 CTTCCTTCCCTGGGGGCC 61.744 72.222 14.00 0.00 43.94 5.80
589 652 6.449698 ACAAGGCTAGAATGTTTGTTCATTG 58.550 36.000 0.00 0.00 38.03 2.82
598 661 2.644798 AGTGGGACAAGGCTAGAATGTT 59.355 45.455 0.00 0.00 44.16 2.71
732 1068 3.447742 CAAAACTCGCCTGCTTTTCTTT 58.552 40.909 0.00 0.00 0.00 2.52
786 1122 2.660064 CGGGATGGGGATCGGGATC 61.660 68.421 0.00 0.00 37.11 3.36
992 1341 2.509336 GGGTGTCCATCGCTGTCG 60.509 66.667 0.00 0.00 0.00 4.35
993 1342 1.741770 GTGGGTGTCCATCGCTGTC 60.742 63.158 0.00 0.00 46.09 3.51
994 1343 2.347490 GTGGGTGTCCATCGCTGT 59.653 61.111 0.00 0.00 46.09 4.40
1550 1903 1.634973 TGAGGAAGGGACAATGCATGA 59.365 47.619 0.00 0.00 0.00 3.07
1560 1913 2.700897 GAGGAATCGAATGAGGAAGGGA 59.299 50.000 0.00 0.00 0.00 4.20
1588 1941 2.086054 ACCAGATCGAGTCAGCAAAC 57.914 50.000 0.00 0.00 0.00 2.93
1593 1946 1.821753 AGACCAACCAGATCGAGTCAG 59.178 52.381 0.00 0.00 0.00 3.51
1614 1967 4.334443 CGCCTGAATCGACAAATAACAAG 58.666 43.478 0.00 0.00 0.00 3.16
1620 1973 1.086696 CACCGCCTGAATCGACAAAT 58.913 50.000 0.00 0.00 0.00 2.32
1801 2155 1.348036 GAACAGAGTAGGGGCAGTTGT 59.652 52.381 0.00 0.00 0.00 3.32
1843 2200 4.158579 TGATCAGATTCAGAGCACTACGTT 59.841 41.667 0.00 0.00 0.00 3.99
1945 2304 9.944376 TTAGTACAGCAAATCAAGAGTTAAGAT 57.056 29.630 0.00 0.00 0.00 2.40
1964 2323 4.649674 CCTAAGCTCCCATCAGTTAGTACA 59.350 45.833 0.00 0.00 0.00 2.90
1971 2337 4.870021 AAAATCCTAAGCTCCCATCAGT 57.130 40.909 0.00 0.00 0.00 3.41
1975 2341 5.134339 TGGTGATAAAATCCTAAGCTCCCAT 59.866 40.000 0.00 0.00 0.00 4.00
1986 2352 6.128309 GGTGCATTTTTGTGGTGATAAAATCC 60.128 38.462 0.00 0.00 31.14 3.01
2008 2374 2.113860 AGTCATGATTCAACCGGGTG 57.886 50.000 15.24 15.24 0.00 4.61
2009 2375 2.039746 TGAAGTCATGATTCAACCGGGT 59.960 45.455 6.32 0.00 33.85 5.28
2013 2379 6.441093 TGCTAATGAAGTCATGATTCAACC 57.559 37.500 18.28 10.88 39.92 3.77
2020 2386 8.515695 AATTCTCAATGCTAATGAAGTCATGA 57.484 30.769 0.00 0.00 36.56 3.07
2047 2413 7.281774 ACAGATAGCATCAAAATTCACGATCTT 59.718 33.333 0.00 0.00 0.00 2.40
2124 2490 4.204799 TCATCAGATGGCTTCAAATGGAG 58.795 43.478 10.67 0.00 0.00 3.86
2125 2491 4.239428 TCATCAGATGGCTTCAAATGGA 57.761 40.909 10.67 0.00 0.00 3.41
2126 2492 4.401519 AGTTCATCAGATGGCTTCAAATGG 59.598 41.667 10.67 0.00 0.00 3.16
2127 2493 5.124936 TCAGTTCATCAGATGGCTTCAAATG 59.875 40.000 10.67 6.71 0.00 2.32
2128 2494 5.258841 TCAGTTCATCAGATGGCTTCAAAT 58.741 37.500 10.67 0.00 0.00 2.32
2170 2536 1.404391 CCATCTTGTTGCTCATCCTGC 59.596 52.381 0.00 0.00 0.00 4.85
2306 2672 3.014085 ATACCCACTGGCGTCCACG 62.014 63.158 0.00 0.00 43.27 4.94
2321 2687 5.178252 CGATGGCATTATAGCATAGGCATAC 59.822 44.000 0.00 0.00 44.14 2.39
2465 2831 4.700692 ACAGAGCTGTAGTCGTTGAAGATA 59.299 41.667 0.41 0.00 42.90 1.98
2629 3001 2.511659 TGTAGTTCTCGTAGGCAGTGT 58.488 47.619 0.00 0.00 0.00 3.55
2633 3005 2.753452 CCTCTTGTAGTTCTCGTAGGCA 59.247 50.000 0.00 0.00 0.00 4.75
2744 3116 1.365999 CACTGCACTGTCACCCGTA 59.634 57.895 0.00 0.00 0.00 4.02
2768 3140 2.701780 CCAGGAGTCACCGGTCTCG 61.702 68.421 2.59 0.00 44.74 4.04
2832 3204 5.649395 ACCATCACAACATTGTAGAATCAGG 59.351 40.000 0.00 3.23 39.91 3.86
2833 3205 6.549061 CACCATCACAACATTGTAGAATCAG 58.451 40.000 0.00 0.00 39.91 2.90
2834 3206 5.106197 GCACCATCACAACATTGTAGAATCA 60.106 40.000 0.00 0.00 39.91 2.57
2835 3207 5.106197 TGCACCATCACAACATTGTAGAATC 60.106 40.000 0.00 0.00 39.91 2.52
2836 3208 4.766373 TGCACCATCACAACATTGTAGAAT 59.234 37.500 0.00 0.00 39.91 2.40
2837 3209 4.140536 TGCACCATCACAACATTGTAGAA 58.859 39.130 0.00 0.00 39.91 2.10
2838 3210 3.749226 TGCACCATCACAACATTGTAGA 58.251 40.909 0.00 0.00 39.91 2.59
2839 3211 4.082625 ACATGCACCATCACAACATTGTAG 60.083 41.667 0.00 0.00 39.91 2.74
2881 3259 2.049888 TGGCACAACAAGACATCACA 57.950 45.000 0.00 0.00 31.92 3.58
2899 3277 3.069443 ACAAACAACCAACCCTGCTTATG 59.931 43.478 0.00 0.00 0.00 1.90
3004 3383 1.154814 TAACACGCTTGTCGCTTGCA 61.155 50.000 0.00 0.00 41.24 4.08
3062 3441 3.262660 AGCAGAGATCAGAACATTGTGGA 59.737 43.478 0.00 0.00 0.00 4.02
3065 3444 3.008330 GCAGCAGAGATCAGAACATTGT 58.992 45.455 0.00 0.00 0.00 2.71
3067 3446 2.641305 GGCAGCAGAGATCAGAACATT 58.359 47.619 0.00 0.00 0.00 2.71
3069 3448 0.108472 CGGCAGCAGAGATCAGAACA 60.108 55.000 0.00 0.00 0.00 3.18
3070 3449 0.108424 ACGGCAGCAGAGATCAGAAC 60.108 55.000 0.00 0.00 0.00 3.01
3071 3450 0.108472 CACGGCAGCAGAGATCAGAA 60.108 55.000 0.00 0.00 0.00 3.02
3424 3818 0.528017 TCACCTGCGCAACACAAAAA 59.472 45.000 13.05 0.00 0.00 1.94
3556 4320 2.928396 ACCCTGGAACCCCACTCG 60.928 66.667 0.00 0.00 37.58 4.18
3559 4323 1.539124 AGAGACCCTGGAACCCCAC 60.539 63.158 0.00 0.00 37.58 4.61
3565 4795 2.596851 GGCAGCAGAGACCCTGGAA 61.597 63.158 0.00 0.00 43.13 3.53
3620 5146 2.834549 ACTACTACTGATGCAGGCAAGT 59.165 45.455 0.00 0.70 35.51 3.16
3641 5170 4.685467 TGCGTGCTGCTGCTGCTA 62.685 61.111 27.67 14.32 46.63 3.49
3766 5301 5.308014 TCATAATCTTCGTAGCATTGGCAT 58.692 37.500 0.00 0.00 44.61 4.40
3797 5332 1.869767 CAAATAGCCGAGGCAAGCTAG 59.130 52.381 17.18 0.00 44.36 3.42
3809 5344 1.247567 AGGCACACACACAAATAGCC 58.752 50.000 0.00 0.00 40.85 3.93
3910 5451 0.392863 TCCGAGTCCATGCATGTTGG 60.393 55.000 24.58 18.55 35.45 3.77
3911 5452 1.452110 TTCCGAGTCCATGCATGTTG 58.548 50.000 24.58 11.03 0.00 3.33
3912 5453 2.092753 AGATTCCGAGTCCATGCATGTT 60.093 45.455 24.58 10.34 0.00 2.71
3913 5454 1.487976 AGATTCCGAGTCCATGCATGT 59.512 47.619 24.58 6.98 0.00 3.21
3914 5455 2.251409 AGATTCCGAGTCCATGCATG 57.749 50.000 20.19 20.19 0.00 4.06
3915 5456 3.234353 TCTAGATTCCGAGTCCATGCAT 58.766 45.455 0.00 0.00 0.00 3.96
3916 5457 2.666317 TCTAGATTCCGAGTCCATGCA 58.334 47.619 0.00 0.00 0.00 3.96
3917 5458 3.648009 CTTCTAGATTCCGAGTCCATGC 58.352 50.000 0.00 0.00 0.00 4.06
3918 5459 3.648009 GCTTCTAGATTCCGAGTCCATG 58.352 50.000 0.00 0.00 0.00 3.66
3919 5460 2.294791 CGCTTCTAGATTCCGAGTCCAT 59.705 50.000 0.00 0.00 0.00 3.41
3920 5461 1.676529 CGCTTCTAGATTCCGAGTCCA 59.323 52.381 0.00 0.00 0.00 4.02
3921 5462 1.600912 GCGCTTCTAGATTCCGAGTCC 60.601 57.143 0.00 0.00 0.00 3.85
3922 5463 1.065701 TGCGCTTCTAGATTCCGAGTC 59.934 52.381 9.73 0.00 0.00 3.36
3923 5464 1.103803 TGCGCTTCTAGATTCCGAGT 58.896 50.000 9.73 0.00 0.00 4.18
3924 5465 2.209838 TTGCGCTTCTAGATTCCGAG 57.790 50.000 9.73 0.00 0.00 4.63
3925 5466 2.545952 GGATTGCGCTTCTAGATTCCGA 60.546 50.000 9.73 0.00 0.00 4.55
3926 5467 1.795286 GGATTGCGCTTCTAGATTCCG 59.205 52.381 9.73 0.00 0.00 4.30
3927 5468 2.838736 TGGATTGCGCTTCTAGATTCC 58.161 47.619 9.73 3.01 0.00 3.01
3928 5469 3.623060 TGTTGGATTGCGCTTCTAGATTC 59.377 43.478 9.73 0.00 0.00 2.52
3929 5470 3.609853 TGTTGGATTGCGCTTCTAGATT 58.390 40.909 9.73 0.00 0.00 2.40
3930 5471 3.266510 TGTTGGATTGCGCTTCTAGAT 57.733 42.857 9.73 0.00 0.00 1.98
3931 5472 2.760634 TGTTGGATTGCGCTTCTAGA 57.239 45.000 9.73 0.00 0.00 2.43
3932 5473 2.540361 GCATGTTGGATTGCGCTTCTAG 60.540 50.000 9.73 0.00 0.00 2.43
3933 5474 1.401552 GCATGTTGGATTGCGCTTCTA 59.598 47.619 9.73 0.23 0.00 2.10
3934 5475 0.171903 GCATGTTGGATTGCGCTTCT 59.828 50.000 9.73 0.00 0.00 2.85
3935 5476 0.109179 TGCATGTTGGATTGCGCTTC 60.109 50.000 9.73 5.59 41.80 3.86
3936 5477 0.533491 ATGCATGTTGGATTGCGCTT 59.467 45.000 9.73 0.00 41.80 4.68
3937 5478 0.179121 CATGCATGTTGGATTGCGCT 60.179 50.000 18.91 0.00 41.80 5.92
3938 5479 1.149361 CCATGCATGTTGGATTGCGC 61.149 55.000 24.58 0.00 41.80 6.09
3939 5480 0.456628 TCCATGCATGTTGGATTGCG 59.543 50.000 24.58 6.69 41.80 4.85
3940 5481 1.479323 AGTCCATGCATGTTGGATTGC 59.521 47.619 24.58 5.95 44.75 3.56
3941 5482 2.223409 CGAGTCCATGCATGTTGGATTG 60.223 50.000 24.58 8.13 44.75 2.67
3942 5483 2.019249 CGAGTCCATGCATGTTGGATT 58.981 47.619 24.58 13.81 44.75 3.01
3943 5484 1.671979 CGAGTCCATGCATGTTGGAT 58.328 50.000 24.58 7.55 44.75 3.41
3944 5485 0.392863 CCGAGTCCATGCATGTTGGA 60.393 55.000 24.58 14.53 40.96 3.53
3945 5486 0.392863 TCCGAGTCCATGCATGTTGG 60.393 55.000 24.58 18.55 35.45 3.77
3987 5528 5.690816 GCTCACTTTCTAGCTAACCAAAAC 58.309 41.667 0.00 0.00 35.80 2.43
3997 5542 5.760253 TGCCATTATTAGCTCACTTTCTAGC 59.240 40.000 0.00 0.00 39.08 3.42
3998 5543 7.519649 GCTTGCCATTATTAGCTCACTTTCTAG 60.520 40.741 0.00 0.00 0.00 2.43
3999 5544 6.260936 GCTTGCCATTATTAGCTCACTTTCTA 59.739 38.462 0.00 0.00 0.00 2.10
4020 5565 3.187227 CCACAAGTTGCAGTACTAGCTTG 59.813 47.826 16.39 16.39 39.16 4.01
4066 5611 6.147328 ACTTGCTCCAGAATTAGTACGTTTTC 59.853 38.462 0.00 0.00 0.00 2.29
4286 5838 4.406533 TGGTGCCCACATAAACGG 57.593 55.556 0.40 0.00 0.00 4.44
4300 5853 2.632377 CTCTGATATTTGCGGTGTGGT 58.368 47.619 0.00 0.00 0.00 4.16
4330 5885 6.183359 GGTTGTCGTTATCTCACTTTTCTACG 60.183 42.308 0.00 0.00 0.00 3.51
4359 5914 2.605338 CCTTGTCACATGCGGAAACTTG 60.605 50.000 0.00 0.00 0.00 3.16
4409 5964 2.661504 CGTGACGCATTGAAAACAGA 57.338 45.000 0.00 0.00 0.00 3.41
4435 6011 7.856145 AGTGCTTTTACTCTTCCATAATCTG 57.144 36.000 0.00 0.00 0.00 2.90
4442 6018 4.141482 ACCTGAAGTGCTTTTACTCTTCCA 60.141 41.667 0.00 0.00 38.69 3.53
4506 6083 3.243201 GGTATGGTAGAGCTGCATTTTGC 60.243 47.826 1.02 0.00 45.29 3.68
4507 6084 3.316308 GGGTATGGTAGAGCTGCATTTTG 59.684 47.826 1.02 0.00 0.00 2.44
4516 6093 2.289565 GCAAACTGGGTATGGTAGAGC 58.710 52.381 0.00 0.00 0.00 4.09
4520 6097 3.066291 CAGTGCAAACTGGGTATGGTA 57.934 47.619 0.00 0.00 34.28 3.25
4538 6116 5.066505 GCAGGGACTAAATAAACACATCCAG 59.933 44.000 0.00 0.00 36.02 3.86
4550 6128 4.683400 CGTTGTGATAGGCAGGGACTAAAT 60.683 45.833 0.00 0.00 36.02 1.40
4551 6129 3.369052 CGTTGTGATAGGCAGGGACTAAA 60.369 47.826 0.00 0.00 36.02 1.85
4554 6132 0.537188 CGTTGTGATAGGCAGGGACT 59.463 55.000 0.00 0.00 43.88 3.85
4556 6134 1.220749 GCGTTGTGATAGGCAGGGA 59.779 57.895 0.00 0.00 0.00 4.20
4560 6140 0.319986 TTGTCGCGTTGTGATAGGCA 60.320 50.000 5.77 0.00 0.00 4.75
4587 6168 4.065281 GACCGGTCCGACCACCTG 62.065 72.222 24.75 5.28 38.47 4.00


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

AutoCloner maintained by Alex Coulton.