Multiple sequence alignment - TraesCS3A01G351100

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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 TraesCS3A01G351100 chr3A 100.000 3812 0 0 1 3812 599582384 599578573 0.000000e+00 7040.0
1 TraesCS3A01G351100 chr3A 93.103 87 3 1 2817 2903 189319084 189319167 1.440000e-24 124.0
2 TraesCS3A01G351100 chr3D 96.964 2108 54 3 712 2816 456648358 456646258 0.000000e+00 3530.0
3 TraesCS3A01G351100 chr3D 90.302 464 37 7 88 544 456650240 456649778 5.450000e-168 601.0
4 TraesCS3A01G351100 chr3D 95.402 87 1 1 2817 2903 160891117 160891034 6.640000e-28 135.0
5 TraesCS3A01G351100 chr3D 92.405 79 4 1 641 717 456649746 456649668 1.120000e-20 111.0
6 TraesCS3A01G351100 chr3B 96.249 2133 62 7 687 2816 603536958 603534841 0.000000e+00 3480.0
7 TraesCS3A01G351100 chr3B 83.415 814 127 5 2940 3751 3956142 3955335 0.000000e+00 749.0
8 TraesCS3A01G351100 chr3B 88.596 342 24 10 273 610 603537765 603537435 5.930000e-108 401.0
9 TraesCS3A01G351100 chr3B 95.402 87 1 1 2817 2903 237632799 237632716 6.640000e-28 135.0
10 TraesCS3A01G351100 chr3B 84.091 132 18 3 526 656 296519285 296519414 1.440000e-24 124.0
11 TraesCS3A01G351100 chr7D 90.504 1527 115 17 1295 2806 529718397 529716886 0.000000e+00 1989.0
12 TraesCS3A01G351100 chr7D 88.519 270 31 0 999 1268 529718662 529718393 1.020000e-85 327.0
13 TraesCS3A01G351100 chr7D 95.082 61 3 0 16 76 3639705 3639645 3.130000e-16 97.1
14 TraesCS3A01G351100 chr7B 90.039 1526 124 16 1295 2806 567802726 567801215 0.000000e+00 1951.0
15 TraesCS3A01G351100 chr7B 89.630 270 28 0 999 1268 567802991 567802722 1.010000e-90 344.0
16 TraesCS3A01G351100 chr7B 90.909 88 7 1 1 88 533378783 533378869 2.410000e-22 117.0
17 TraesCS3A01G351100 chr7B 90.361 83 7 1 526 608 445461621 445461702 1.450000e-19 108.0
18 TraesCS3A01G351100 chr7B 85.106 94 9 4 526 616 408147041 408147132 1.460000e-14 91.6
19 TraesCS3A01G351100 chr7A 91.828 1138 89 4 1671 2806 609262640 609263775 0.000000e+00 1583.0
20 TraesCS3A01G351100 chr7A 85.320 688 70 16 997 1655 609261561 609262246 0.000000e+00 682.0
21 TraesCS3A01G351100 chr7A 78.650 815 153 15 2941 3750 611324331 611323533 4.360000e-144 521.0
22 TraesCS3A01G351100 chr6B 83.572 1534 180 38 751 2231 8141155 8139641 0.000000e+00 1371.0
23 TraesCS3A01G351100 chr6B 87.577 1143 106 12 1697 2812 704447088 704445955 0.000000e+00 1291.0
24 TraesCS3A01G351100 chr6B 88.093 907 80 17 1685 2578 8235175 8236066 0.000000e+00 1051.0
25 TraesCS3A01G351100 chr6B 79.049 778 144 14 2941 3714 687065374 687064612 2.030000e-142 516.0
26 TraesCS3A01G351100 chr6B 89.286 308 29 3 1351 1656 704447637 704447332 2.150000e-102 383.0
27 TraesCS3A01G351100 chr6B 87.702 309 37 1 1347 1655 8234787 8235094 3.620000e-95 359.0
28 TraesCS3A01G351100 chr6B 86.544 327 39 5 976 1299 704447958 704447634 4.680000e-94 355.0
29 TraesCS3A01G351100 chr6B 85.538 325 45 2 987 1310 8234471 8234794 4.720000e-89 339.0
30 TraesCS3A01G351100 chr6D 83.036 1568 160 46 708 2207 4372745 4374274 0.000000e+00 1325.0
31 TraesCS3A01G351100 chr6D 81.933 869 113 18 1914 2770 4363424 4362588 0.000000e+00 695.0
32 TraesCS3A01G351100 chr6D 86.943 314 41 0 1001 1314 4364281 4363968 1.680000e-93 353.0
33 TraesCS3A01G351100 chr1A 88.750 880 95 2 2933 3811 578555208 578554332 0.000000e+00 1074.0
34 TraesCS3A01G351100 chr2D 84.455 817 122 3 2936 3751 428867344 428866532 0.000000e+00 800.0
35 TraesCS3A01G351100 chr2D 81.560 141 18 6 522 656 296720140 296720278 4.030000e-20 110.0
36 TraesCS3A01G351100 chr1D 84.005 819 127 2 2934 3751 378320640 378319825 0.000000e+00 784.0
37 TraesCS3A01G351100 chr1D 82.394 142 14 9 522 656 185128782 185128645 3.110000e-21 113.0
38 TraesCS3A01G351100 chrUn 82.927 820 129 7 2934 3751 30075825 30076635 0.000000e+00 728.0
39 TraesCS3A01G351100 chr4A 78.877 748 143 13 3004 3746 737721013 737721750 3.420000e-135 492.0
40 TraesCS3A01G351100 chr1B 77.586 812 167 12 2940 3746 419411625 419410824 9.580000e-131 477.0
41 TraesCS3A01G351100 chr1B 83.333 102 12 4 522 618 41963906 41964007 5.250000e-14 89.8
42 TraesCS3A01G351100 chr5D 96.591 88 3 0 1 88 511939178 511939091 3.070000e-31 147.0
43 TraesCS3A01G351100 chr5D 89.655 87 8 1 1 87 555039176 555039261 4.030000e-20 110.0
44 TraesCS3A01G351100 chr5D 83.810 105 8 8 522 618 459384557 459384454 1.460000e-14 91.6
45 TraesCS3A01G351100 chr2B 94.186 86 5 0 2 87 596102697 596102782 8.590000e-27 132.0
46 TraesCS3A01G351100 chr2B 84.158 101 9 5 522 616 364920412 364920313 1.460000e-14 91.6
47 TraesCS3A01G351100 chr4B 89.655 87 9 0 1 87 419999491 419999405 1.120000e-20 111.0
48 TraesCS3A01G351100 chr5B 92.424 66 5 0 22 87 75744400 75744465 1.130000e-15 95.3
49 TraesCS3A01G351100 chr2A 100.000 28 0 0 60 87 10980460 10980487 7.000000e-03 52.8


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 TraesCS3A01G351100 chr3A 599578573 599582384 3811 True 7040.000000 7040 100.000000 1 3812 1 chr3A.!!$R1 3811
1 TraesCS3A01G351100 chr3D 456646258 456650240 3982 True 1414.000000 3530 93.223667 88 2816 3 chr3D.!!$R2 2728
2 TraesCS3A01G351100 chr3B 603534841 603537765 2924 True 1940.500000 3480 92.422500 273 2816 2 chr3B.!!$R3 2543
3 TraesCS3A01G351100 chr3B 3955335 3956142 807 True 749.000000 749 83.415000 2940 3751 1 chr3B.!!$R1 811
4 TraesCS3A01G351100 chr7D 529716886 529718662 1776 True 1158.000000 1989 89.511500 999 2806 2 chr7D.!!$R2 1807
5 TraesCS3A01G351100 chr7B 567801215 567802991 1776 True 1147.500000 1951 89.834500 999 2806 2 chr7B.!!$R1 1807
6 TraesCS3A01G351100 chr7A 609261561 609263775 2214 False 1132.500000 1583 88.574000 997 2806 2 chr7A.!!$F1 1809
7 TraesCS3A01G351100 chr7A 611323533 611324331 798 True 521.000000 521 78.650000 2941 3750 1 chr7A.!!$R1 809
8 TraesCS3A01G351100 chr6B 8139641 8141155 1514 True 1371.000000 1371 83.572000 751 2231 1 chr6B.!!$R1 1480
9 TraesCS3A01G351100 chr6B 704445955 704447958 2003 True 676.333333 1291 87.802333 976 2812 3 chr6B.!!$R3 1836
10 TraesCS3A01G351100 chr6B 8234471 8236066 1595 False 583.000000 1051 87.111000 987 2578 3 chr6B.!!$F1 1591
11 TraesCS3A01G351100 chr6B 687064612 687065374 762 True 516.000000 516 79.049000 2941 3714 1 chr6B.!!$R2 773
12 TraesCS3A01G351100 chr6D 4372745 4374274 1529 False 1325.000000 1325 83.036000 708 2207 1 chr6D.!!$F1 1499
13 TraesCS3A01G351100 chr6D 4362588 4364281 1693 True 524.000000 695 84.438000 1001 2770 2 chr6D.!!$R1 1769
14 TraesCS3A01G351100 chr1A 578554332 578555208 876 True 1074.000000 1074 88.750000 2933 3811 1 chr1A.!!$R1 878
15 TraesCS3A01G351100 chr2D 428866532 428867344 812 True 800.000000 800 84.455000 2936 3751 1 chr2D.!!$R1 815
16 TraesCS3A01G351100 chr1D 378319825 378320640 815 True 784.000000 784 84.005000 2934 3751 1 chr1D.!!$R2 817
17 TraesCS3A01G351100 chrUn 30075825 30076635 810 False 728.000000 728 82.927000 2934 3751 1 chrUn.!!$F1 817
18 TraesCS3A01G351100 chr4A 737721013 737721750 737 False 492.000000 492 78.877000 3004 3746 1 chr4A.!!$F1 742
19 TraesCS3A01G351100 chr1B 419410824 419411625 801 True 477.000000 477 77.586000 2940 3746 1 chr1B.!!$R1 806

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
733 2487 0.040425 GGTAGCACCAAAACGCTGTG 60.040 55.0 0.0 0.0 39.3 3.66 F
835 2597 0.103572 AACTCACACGTAACCGCAGT 59.896 50.0 0.0 0.0 37.7 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 4103 1.025113 TTCTCGCTCGAGTCCGTCAT 61.025 55.0 15.13 0.0 42.49 3.06 R
2816 5600 0.035036 TTAACAATCACGGCCGGTCA 59.965 50.0 31.76 13.2 0.00 4.02 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
17 18 2.671963 GGGTTGGCCGTGTTCCTC 60.672 66.667 0.00 0.00 34.97 3.71
18 19 2.112297 GGTTGGCCGTGTTCCTCA 59.888 61.111 0.00 0.00 0.00 3.86
19 20 2.258726 GGTTGGCCGTGTTCCTCAC 61.259 63.158 0.00 0.00 43.03 3.51
20 21 2.112297 TTGGCCGTGTTCCTCACC 59.888 61.111 0.00 0.00 43.51 4.02
21 22 2.448582 TTGGCCGTGTTCCTCACCT 61.449 57.895 0.00 0.00 43.51 4.00
22 23 1.122632 TTGGCCGTGTTCCTCACCTA 61.123 55.000 0.00 0.00 43.51 3.08
23 24 0.907704 TGGCCGTGTTCCTCACCTAT 60.908 55.000 0.00 0.00 43.51 2.57
24 25 0.252197 GGCCGTGTTCCTCACCTATT 59.748 55.000 0.00 0.00 43.51 1.73
25 26 1.369625 GCCGTGTTCCTCACCTATTG 58.630 55.000 0.00 0.00 43.51 1.90
26 27 1.066430 GCCGTGTTCCTCACCTATTGA 60.066 52.381 0.00 0.00 43.51 2.57
27 28 2.420129 GCCGTGTTCCTCACCTATTGAT 60.420 50.000 0.00 0.00 43.51 2.57
28 29 3.458189 CCGTGTTCCTCACCTATTGATC 58.542 50.000 0.00 0.00 43.51 2.92
29 30 3.118775 CCGTGTTCCTCACCTATTGATCA 60.119 47.826 0.00 0.00 43.51 2.92
30 31 4.503910 CGTGTTCCTCACCTATTGATCAA 58.496 43.478 11.26 11.26 43.51 2.57
31 32 5.118990 CGTGTTCCTCACCTATTGATCAAT 58.881 41.667 23.75 23.75 43.51 2.57
32 33 5.235186 CGTGTTCCTCACCTATTGATCAATC 59.765 44.000 23.95 6.83 43.51 2.67
33 34 6.115446 GTGTTCCTCACCTATTGATCAATCA 58.885 40.000 23.95 9.29 40.84 2.57
34 35 6.599244 GTGTTCCTCACCTATTGATCAATCAA 59.401 38.462 23.95 7.44 44.01 2.57
35 36 7.121168 GTGTTCCTCACCTATTGATCAATCAAA 59.879 37.037 23.95 6.71 43.60 2.69
49 50 8.421249 TGATCAATCAAATTAACCCTCTTTGT 57.579 30.769 0.00 0.00 33.08 2.83
50 51 9.527157 TGATCAATCAAATTAACCCTCTTTGTA 57.473 29.630 0.00 0.00 33.08 2.41
56 57 9.855021 ATCAAATTAACCCTCTTTGTAAAATCG 57.145 29.630 0.00 0.00 32.89 3.34
57 58 8.852135 TCAAATTAACCCTCTTTGTAAAATCGT 58.148 29.630 0.00 0.00 32.89 3.73
58 59 8.911662 CAAATTAACCCTCTTTGTAAAATCGTG 58.088 33.333 0.00 0.00 0.00 4.35
59 60 7.754851 ATTAACCCTCTTTGTAAAATCGTGT 57.245 32.000 0.00 0.00 0.00 4.49
60 61 8.851541 ATTAACCCTCTTTGTAAAATCGTGTA 57.148 30.769 0.00 0.00 0.00 2.90
61 62 8.674263 TTAACCCTCTTTGTAAAATCGTGTAA 57.326 30.769 0.00 0.00 0.00 2.41
62 63 6.549912 ACCCTCTTTGTAAAATCGTGTAAC 57.450 37.500 0.00 0.00 0.00 2.50
63 64 6.293698 ACCCTCTTTGTAAAATCGTGTAACT 58.706 36.000 0.00 0.00 31.75 2.24
64 65 6.426025 ACCCTCTTTGTAAAATCGTGTAACTC 59.574 38.462 0.00 0.00 31.75 3.01
65 66 6.425721 CCCTCTTTGTAAAATCGTGTAACTCA 59.574 38.462 0.00 0.00 31.75 3.41
66 67 7.119262 CCCTCTTTGTAAAATCGTGTAACTCAT 59.881 37.037 0.00 0.00 31.75 2.90
67 68 8.504005 CCTCTTTGTAAAATCGTGTAACTCATT 58.496 33.333 0.00 0.00 31.75 2.57
68 69 9.878599 CTCTTTGTAAAATCGTGTAACTCATTT 57.121 29.630 0.00 0.00 30.86 2.32
69 70 9.658475 TCTTTGTAAAATCGTGTAACTCATTTG 57.342 29.630 0.00 0.00 30.31 2.32
70 71 9.445786 CTTTGTAAAATCGTGTAACTCATTTGT 57.554 29.630 0.00 0.00 30.31 2.83
72 73 9.866936 TTGTAAAATCGTGTAACTCATTTGTAC 57.133 29.630 0.00 0.00 30.31 2.90
73 74 8.215792 TGTAAAATCGTGTAACTCATTTGTACG 58.784 33.333 0.00 0.00 30.31 3.67
74 75 6.774354 AAATCGTGTAACTCATTTGTACGT 57.226 33.333 0.00 0.00 32.68 3.57
75 76 5.756950 ATCGTGTAACTCATTTGTACGTG 57.243 39.130 0.00 0.00 32.68 4.49
76 77 4.609947 TCGTGTAACTCATTTGTACGTGT 58.390 39.130 0.00 0.00 32.68 4.49
77 78 5.756849 TCGTGTAACTCATTTGTACGTGTA 58.243 37.500 0.00 0.00 32.68 2.90
78 79 5.852755 TCGTGTAACTCATTTGTACGTGTAG 59.147 40.000 0.00 0.00 32.68 2.74
79 80 5.442390 CGTGTAACTCATTTGTACGTGTAGC 60.442 44.000 0.00 0.00 31.75 3.58
80 81 8.522167 CGTGTAACTCATTTGTACGTGTAGCG 62.522 46.154 0.00 0.00 40.29 4.26
102 103 2.520982 TCGGTGAGGATAGGCCCG 60.521 66.667 0.00 0.00 39.98 6.13
122 123 0.251165 ACACGGGTGAAATTCAGGGG 60.251 55.000 5.71 0.00 0.00 4.79
150 153 6.015940 GGCTGAATAGAATATGGAAGGGTTTG 60.016 42.308 0.00 0.00 0.00 2.93
158 161 2.561478 TGGAAGGGTTTGTAGCAGTC 57.439 50.000 0.00 0.00 0.00 3.51
162 165 0.608640 AGGGTTTGTAGCAGTCTCGG 59.391 55.000 0.00 0.00 0.00 4.63
168 171 2.080286 TGTAGCAGTCTCGGAAAAGC 57.920 50.000 0.00 0.00 0.00 3.51
190 194 3.879427 TGTACGTGTAGCATTTTTGCAC 58.121 40.909 0.00 0.00 37.25 4.57
194 198 3.546617 CGTGTAGCATTTTTGCACGTAA 58.453 40.909 7.53 0.00 45.07 3.18
210 214 8.803201 TTGCACGTAAAACATATTTTCATGAA 57.197 26.923 3.38 3.38 38.91 2.57
213 217 8.365210 GCACGTAAAACATATTTTCATGAACAG 58.635 33.333 7.89 0.00 38.91 3.16
226 230 2.717580 TGAACAGTGCTACACCTACG 57.282 50.000 0.00 0.00 34.49 3.51
248 252 9.555040 CTACGAACAAGTTACGTTAAGTTTTAC 57.445 33.333 12.84 0.00 40.61 2.01
249 253 7.958674 ACGAACAAGTTACGTTAAGTTTTACA 58.041 30.769 0.00 0.00 36.91 2.41
250 254 8.603181 ACGAACAAGTTACGTTAAGTTTTACAT 58.397 29.630 0.00 0.00 36.91 2.29
287 291 2.148723 ATTGTGATTGCGGGTGGGGA 62.149 55.000 0.00 0.00 0.00 4.81
314 318 0.178906 CCCCACCCACCCTGAAAATT 60.179 55.000 0.00 0.00 0.00 1.82
330 335 2.437085 AATTAGGGGGCCGAAGAAAG 57.563 50.000 0.00 0.00 0.00 2.62
334 339 1.074248 GGGGGCCGAAGAAAGTTGA 59.926 57.895 0.00 0.00 0.00 3.18
358 363 9.887406 TGATGAAGGAAAATTACGTAAACTTTC 57.113 29.630 24.42 24.42 0.00 2.62
360 365 7.918643 TGAAGGAAAATTACGTAAACTTTCGT 58.081 30.769 24.91 23.78 42.82 3.85
372 377 8.189709 ACGTAAACTTTCGTTAACTTCTTTCT 57.810 30.769 3.71 0.00 36.93 2.52
563 579 6.228995 AGTCTCAGTCGATGTTATATCCGTA 58.771 40.000 0.00 0.00 0.00 4.02
591 607 1.680735 ACATTGAGAGCCGTGCAAAAA 59.319 42.857 0.00 0.00 0.00 1.94
595 611 3.451141 TGAGAGCCGTGCAAAAATTTT 57.549 38.095 0.00 0.00 0.00 1.82
600 616 4.394610 AGAGCCGTGCAAAAATTTTGTTTT 59.605 33.333 18.28 0.00 0.00 2.43
602 618 6.092807 AGAGCCGTGCAAAAATTTTGTTTTAA 59.907 30.769 18.28 0.00 0.00 1.52
603 619 6.790282 AGCCGTGCAAAAATTTTGTTTTAAT 58.210 28.000 18.28 1.01 0.00 1.40
604 620 7.254137 AGCCGTGCAAAAATTTTGTTTTAATT 58.746 26.923 18.28 0.00 0.00 1.40
605 621 7.757173 AGCCGTGCAAAAATTTTGTTTTAATTT 59.243 25.926 18.28 0.00 36.91 1.82
606 622 8.376203 GCCGTGCAAAAATTTTGTTTTAATTTT 58.624 25.926 18.28 0.00 43.39 1.82
650 666 2.160205 CCGACTGAGACCTAGTCACAA 58.840 52.381 0.00 0.00 43.65 3.33
717 1156 3.523792 ACTTTTAGGGTGCCTGTAGGTA 58.476 45.455 0.00 0.00 34.61 3.08
732 2486 0.179029 AGGTAGCACCAAAACGCTGT 60.179 50.000 7.86 0.00 41.95 4.40
733 2487 0.040425 GGTAGCACCAAAACGCTGTG 60.040 55.000 0.00 0.00 39.30 3.66
835 2597 0.103572 AACTCACACGTAACCGCAGT 59.896 50.000 0.00 0.00 37.70 4.40
836 2598 0.318445 ACTCACACGTAACCGCAGTC 60.318 55.000 0.00 0.00 37.70 3.51
837 2599 1.007038 TCACACGTAACCGCAGTCC 60.007 57.895 0.00 0.00 37.70 3.85
838 2600 2.049802 ACACGTAACCGCAGTCCG 60.050 61.111 0.00 0.00 37.70 4.79
839 2601 3.475774 CACGTAACCGCAGTCCGC 61.476 66.667 0.00 0.00 37.70 5.54
840 2602 3.980989 ACGTAACCGCAGTCCGCA 61.981 61.111 0.00 0.00 42.60 5.69
841 2603 3.179265 CGTAACCGCAGTCCGCAG 61.179 66.667 0.00 0.00 42.60 5.18
857 2619 2.219216 CCGCAGCACAAGTTCAAAAATG 59.781 45.455 0.00 0.00 0.00 2.32
861 2634 4.114073 CAGCACAAGTTCAAAAATGCAGA 58.886 39.130 0.00 0.00 35.51 4.26
944 2727 0.326595 TCAGTCGCTCTCTGTCTCCT 59.673 55.000 0.00 0.00 34.86 3.69
1005 2795 5.478679 CACTGTAGGTAGGAATAGGATGGAG 59.521 48.000 0.00 0.00 0.00 3.86
1056 2846 1.576421 CGTGGCAAGCCTGAAGAAC 59.424 57.895 12.96 0.00 36.94 3.01
1190 2983 1.067416 ACGACAAGCTGCTCGTCAA 59.933 52.632 19.68 0.00 38.80 3.18
1692 3984 2.742053 TCTTTTCGTTGCTATGTCCTGC 59.258 45.455 0.00 0.00 0.00 4.85
1995 4734 1.003839 GATGGTGGACAGCAACGGA 60.004 57.895 8.36 0.00 42.53 4.69
2650 5434 2.352422 GCCACAGGCTCACCATCA 59.648 61.111 0.00 0.00 46.69 3.07
2813 5597 3.936453 GCATTGTACGTCCCAATGTAAGA 59.064 43.478 27.74 1.03 46.91 2.10
2816 5600 2.829720 TGTACGTCCCAATGTAAGAGCT 59.170 45.455 0.00 0.00 0.00 4.09
2817 5601 2.386661 ACGTCCCAATGTAAGAGCTG 57.613 50.000 0.00 0.00 0.00 4.24
2818 5602 1.899814 ACGTCCCAATGTAAGAGCTGA 59.100 47.619 0.00 0.00 0.00 4.26
2819 5603 2.271800 CGTCCCAATGTAAGAGCTGAC 58.728 52.381 0.00 0.00 0.00 3.51
2820 5604 2.633488 GTCCCAATGTAAGAGCTGACC 58.367 52.381 0.00 0.00 0.00 4.02
2821 5605 1.207089 TCCCAATGTAAGAGCTGACCG 59.793 52.381 0.00 0.00 0.00 4.79
2822 5606 1.656652 CCAATGTAAGAGCTGACCGG 58.343 55.000 0.00 0.00 0.00 5.28
2823 5607 1.009829 CAATGTAAGAGCTGACCGGC 58.990 55.000 0.00 0.00 0.00 6.13
2824 5608 0.107654 AATGTAAGAGCTGACCGGCC 60.108 55.000 0.00 0.00 0.00 6.13
2825 5609 2.202756 GTAAGAGCTGACCGGCCG 60.203 66.667 21.04 21.04 0.00 6.13
2826 5610 2.678934 TAAGAGCTGACCGGCCGT 60.679 61.111 26.12 12.57 0.00 5.68
2827 5611 3.001902 TAAGAGCTGACCGGCCGTG 62.002 63.158 26.12 18.04 0.00 4.94
2829 5613 4.148825 GAGCTGACCGGCCGTGAT 62.149 66.667 26.12 9.24 0.00 3.06
2830 5614 3.665675 GAGCTGACCGGCCGTGATT 62.666 63.158 26.12 4.75 0.00 2.57
2831 5615 3.499737 GCTGACCGGCCGTGATTG 61.500 66.667 26.12 10.93 0.00 2.67
2832 5616 2.047274 CTGACCGGCCGTGATTGT 60.047 61.111 26.12 14.64 0.00 2.71
2833 5617 1.671054 CTGACCGGCCGTGATTGTT 60.671 57.895 26.12 0.00 0.00 2.83
2834 5618 0.390603 CTGACCGGCCGTGATTGTTA 60.391 55.000 26.12 10.07 0.00 2.41
2835 5619 0.035036 TGACCGGCCGTGATTGTTAA 59.965 50.000 26.12 4.15 0.00 2.01
2836 5620 1.158434 GACCGGCCGTGATTGTTAAA 58.842 50.000 26.12 0.00 0.00 1.52
2837 5621 0.876399 ACCGGCCGTGATTGTTAAAC 59.124 50.000 26.12 0.00 0.00 2.01
2838 5622 0.875728 CCGGCCGTGATTGTTAAACA 59.124 50.000 26.12 0.00 0.00 2.83
2839 5623 1.135803 CCGGCCGTGATTGTTAAACAG 60.136 52.381 26.12 0.00 0.00 3.16
2840 5624 1.135803 CGGCCGTGATTGTTAAACAGG 60.136 52.381 19.50 0.00 0.00 4.00
2841 5625 1.201414 GGCCGTGATTGTTAAACAGGG 59.799 52.381 0.00 0.00 40.89 4.45
2842 5626 2.156098 GCCGTGATTGTTAAACAGGGA 58.844 47.619 12.69 0.00 40.55 4.20
2843 5627 2.554893 GCCGTGATTGTTAAACAGGGAA 59.445 45.455 12.69 0.00 40.55 3.97
2844 5628 3.610821 GCCGTGATTGTTAAACAGGGAAC 60.611 47.826 12.69 0.00 40.55 3.62
2845 5629 3.364565 CCGTGATTGTTAAACAGGGAACG 60.365 47.826 0.00 4.34 40.55 3.95
2846 5630 3.249080 CGTGATTGTTAAACAGGGAACGT 59.751 43.478 0.00 0.00 0.00 3.99
2855 5639 3.532896 CAGGGAACGTGCATGTACT 57.467 52.632 12.96 8.42 37.42 2.73
2856 5640 2.665649 CAGGGAACGTGCATGTACTA 57.334 50.000 12.96 0.00 37.42 1.82
2857 5641 3.179443 CAGGGAACGTGCATGTACTAT 57.821 47.619 12.96 0.00 37.42 2.12
2858 5642 2.866156 CAGGGAACGTGCATGTACTATG 59.134 50.000 12.96 5.97 37.42 2.23
2859 5643 2.500098 AGGGAACGTGCATGTACTATGT 59.500 45.455 12.96 0.00 0.00 2.29
2860 5644 3.702548 AGGGAACGTGCATGTACTATGTA 59.297 43.478 12.96 0.00 0.00 2.29
2861 5645 4.160814 AGGGAACGTGCATGTACTATGTAA 59.839 41.667 12.96 0.00 0.00 2.41
2862 5646 4.269363 GGGAACGTGCATGTACTATGTAAC 59.731 45.833 12.96 1.91 0.00 2.50
2863 5647 5.107133 GGAACGTGCATGTACTATGTAACT 58.893 41.667 12.96 0.00 0.00 2.24
2864 5648 5.005394 GGAACGTGCATGTACTATGTAACTG 59.995 44.000 12.96 0.00 0.00 3.16
2865 5649 4.430007 ACGTGCATGTACTATGTAACTGG 58.570 43.478 10.57 0.00 0.00 4.00
2866 5650 3.245284 CGTGCATGTACTATGTAACTGGC 59.755 47.826 12.30 0.00 0.00 4.85
2867 5651 4.188462 GTGCATGTACTATGTAACTGGCA 58.812 43.478 6.69 0.00 0.00 4.92
2868 5652 4.034048 GTGCATGTACTATGTAACTGGCAC 59.966 45.833 6.69 0.00 38.32 5.01
2869 5653 3.560068 GCATGTACTATGTAACTGGCACC 59.440 47.826 0.00 0.00 0.00 5.01
2870 5654 3.513680 TGTACTATGTAACTGGCACCG 57.486 47.619 0.00 0.00 0.00 4.94
2871 5655 2.199236 GTACTATGTAACTGGCACCGC 58.801 52.381 0.00 0.00 0.00 5.68
2872 5656 0.902531 ACTATGTAACTGGCACCGCT 59.097 50.000 0.00 0.00 0.00 5.52
2873 5657 1.290203 CTATGTAACTGGCACCGCTG 58.710 55.000 0.00 0.00 0.00 5.18
2874 5658 0.742990 TATGTAACTGGCACCGCTGC 60.743 55.000 0.00 0.00 43.41 5.25
2875 5659 2.358737 GTAACTGGCACCGCTGCT 60.359 61.111 2.19 0.00 43.66 4.24
2876 5660 2.358615 TAACTGGCACCGCTGCTG 60.359 61.111 2.19 0.00 43.66 4.41
2893 5677 2.744787 CTGCAAGCAATGATCGTACC 57.255 50.000 0.00 0.00 0.00 3.34
2894 5678 2.283298 CTGCAAGCAATGATCGTACCT 58.717 47.619 0.00 0.00 0.00 3.08
2895 5679 2.009051 TGCAAGCAATGATCGTACCTG 58.991 47.619 0.00 0.00 0.00 4.00
2896 5680 2.279741 GCAAGCAATGATCGTACCTGA 58.720 47.619 0.00 0.00 0.00 3.86
2897 5681 2.677836 GCAAGCAATGATCGTACCTGAA 59.322 45.455 0.00 0.00 0.00 3.02
2898 5682 3.313526 GCAAGCAATGATCGTACCTGAAT 59.686 43.478 0.00 0.00 0.00 2.57
2899 5683 4.201950 GCAAGCAATGATCGTACCTGAATT 60.202 41.667 0.00 0.00 0.00 2.17
2900 5684 5.677091 GCAAGCAATGATCGTACCTGAATTT 60.677 40.000 0.00 0.00 0.00 1.82
2901 5685 6.324819 CAAGCAATGATCGTACCTGAATTTT 58.675 36.000 0.00 0.00 0.00 1.82
2902 5686 5.883661 AGCAATGATCGTACCTGAATTTTG 58.116 37.500 0.00 0.00 0.00 2.44
2903 5687 5.647658 AGCAATGATCGTACCTGAATTTTGA 59.352 36.000 0.00 0.00 0.00 2.69
2904 5688 6.319658 AGCAATGATCGTACCTGAATTTTGAT 59.680 34.615 0.00 0.00 0.00 2.57
2905 5689 6.974622 GCAATGATCGTACCTGAATTTTGATT 59.025 34.615 0.00 0.00 0.00 2.57
2906 5690 7.166473 GCAATGATCGTACCTGAATTTTGATTC 59.834 37.037 0.00 0.00 0.00 2.52
2907 5691 7.864108 ATGATCGTACCTGAATTTTGATTCA 57.136 32.000 2.28 2.28 38.14 2.57
2908 5692 7.072177 TGATCGTACCTGAATTTTGATTCAC 57.928 36.000 0.00 0.00 35.80 3.18
2909 5693 5.873179 TCGTACCTGAATTTTGATTCACC 57.127 39.130 0.00 0.00 35.80 4.02
2910 5694 5.556915 TCGTACCTGAATTTTGATTCACCT 58.443 37.500 0.00 0.00 35.80 4.00
2911 5695 5.642063 TCGTACCTGAATTTTGATTCACCTC 59.358 40.000 0.00 0.00 35.80 3.85
2912 5696 5.411361 CGTACCTGAATTTTGATTCACCTCA 59.589 40.000 0.00 0.00 35.80 3.86
2913 5697 6.094048 CGTACCTGAATTTTGATTCACCTCAT 59.906 38.462 0.00 0.00 35.80 2.90
2914 5698 6.521151 ACCTGAATTTTGATTCACCTCATC 57.479 37.500 0.00 0.00 35.80 2.92
2915 5699 6.012113 ACCTGAATTTTGATTCACCTCATCA 58.988 36.000 0.00 0.00 35.80 3.07
2916 5700 6.152323 ACCTGAATTTTGATTCACCTCATCAG 59.848 38.462 0.00 0.00 35.80 2.90
2917 5701 6.376299 CCTGAATTTTGATTCACCTCATCAGA 59.624 38.462 13.22 0.00 35.80 3.27
2918 5702 7.149569 TGAATTTTGATTCACCTCATCAGAC 57.850 36.000 0.00 0.00 35.80 3.51
2919 5703 5.808042 ATTTTGATTCACCTCATCAGACG 57.192 39.130 0.00 0.00 32.20 4.18
2920 5704 4.535526 TTTGATTCACCTCATCAGACGA 57.464 40.909 0.00 0.00 32.20 4.20
2921 5705 3.510388 TGATTCACCTCATCAGACGAC 57.490 47.619 0.00 0.00 0.00 4.34
2922 5706 3.092301 TGATTCACCTCATCAGACGACT 58.908 45.455 0.00 0.00 0.00 4.18
2923 5707 3.129462 TGATTCACCTCATCAGACGACTC 59.871 47.826 0.00 0.00 0.00 3.36
2924 5708 1.087501 TCACCTCATCAGACGACTCG 58.912 55.000 0.00 0.00 0.00 4.18
2925 5709 1.087501 CACCTCATCAGACGACTCGA 58.912 55.000 5.20 0.00 0.00 4.04
2926 5710 1.673400 CACCTCATCAGACGACTCGAT 59.327 52.381 5.20 0.00 0.00 3.59
2927 5711 1.944024 ACCTCATCAGACGACTCGATC 59.056 52.381 5.20 0.00 0.00 3.69
2959 5743 2.704616 CGTTGGCACGTCACGTTT 59.295 55.556 0.00 0.00 41.84 3.60
2971 5755 1.227734 CACGTTTGTCCCCGACCTT 60.228 57.895 0.00 0.00 0.00 3.50
2985 5769 3.049674 CCTTGTCGCGGCACACAT 61.050 61.111 15.66 0.00 0.00 3.21
3001 5785 3.838271 ATGCTCACCGCCGACGAT 61.838 61.111 0.00 0.00 43.93 3.73
3154 5938 0.259647 TAGCTAGGGTTGACCGCCTA 59.740 55.000 0.00 0.00 46.96 3.93
3390 6174 0.682852 CCTACCACCACTTCGACCAA 59.317 55.000 0.00 0.00 0.00 3.67
3393 6177 2.358322 ACCACCACTTCGACCAAATT 57.642 45.000 0.00 0.00 0.00 1.82
3412 6196 0.179111 TCGATTCACATCTCGCCCAC 60.179 55.000 0.00 0.00 34.94 4.61
3425 6209 3.160585 CCCACCTCTTCAGGCACA 58.839 61.111 0.00 0.00 45.05 4.57
3625 6411 2.665185 GGCGCGACTTCACTGGTT 60.665 61.111 12.10 0.00 0.00 3.67
3673 6465 1.374947 CCACCGTCCAACCAGACAT 59.625 57.895 0.00 0.00 36.52 3.06
3693 6485 3.880040 CCATATGGTGTGGCAGTGA 57.120 52.632 14.09 0.00 0.00 3.41
3765 6557 3.237741 GGATCCGCTGGAGGAGGG 61.238 72.222 0.00 0.00 44.55 4.30
3811 6603 3.237741 GGGCGATGGGAGGAGGAG 61.238 72.222 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.340789 GTGAGGAACACGGCCAAC 58.659 61.111 2.24 0.00 39.78 3.77
7 8 9.935477 TGATTGATCAATAGGTGAGGAACACGG 62.935 44.444 20.75 0.00 40.95 4.94
10 11 6.312141 TGATTGATCAATAGGTGAGGAACA 57.688 37.500 20.75 7.83 40.43 3.18
11 12 7.630242 TTTGATTGATCAATAGGTGAGGAAC 57.370 36.000 20.75 5.35 45.30 3.62
12 13 8.827832 AATTTGATTGATCAATAGGTGAGGAA 57.172 30.769 20.75 7.56 45.30 3.36
13 14 9.919416 TTAATTTGATTGATCAATAGGTGAGGA 57.081 29.630 20.75 2.20 45.30 3.71
14 15 9.956720 GTTAATTTGATTGATCAATAGGTGAGG 57.043 33.333 20.75 0.00 45.30 3.86
15 16 9.956720 GGTTAATTTGATTGATCAATAGGTGAG 57.043 33.333 20.75 0.00 45.30 3.51
16 17 8.912988 GGGTTAATTTGATTGATCAATAGGTGA 58.087 33.333 20.75 6.45 45.30 4.02
17 18 8.917088 AGGGTTAATTTGATTGATCAATAGGTG 58.083 33.333 20.75 0.00 45.30 4.00
18 19 9.136323 GAGGGTTAATTTGATTGATCAATAGGT 57.864 33.333 20.75 0.00 45.30 3.08
19 20 9.359653 AGAGGGTTAATTTGATTGATCAATAGG 57.640 33.333 20.75 0.00 45.30 2.57
22 23 9.880157 CAAAGAGGGTTAATTTGATTGATCAAT 57.120 29.630 20.85 20.85 45.30 2.57
23 24 8.869109 ACAAAGAGGGTTAATTTGATTGATCAA 58.131 29.630 11.26 11.26 44.42 2.57
24 25 8.421249 ACAAAGAGGGTTAATTTGATTGATCA 57.579 30.769 5.68 0.00 37.37 2.92
30 31 9.855021 CGATTTTACAAAGAGGGTTAATTTGAT 57.145 29.630 5.68 0.00 37.37 2.57
31 32 8.852135 ACGATTTTACAAAGAGGGTTAATTTGA 58.148 29.630 5.68 0.00 37.37 2.69
32 33 8.911662 CACGATTTTACAAAGAGGGTTAATTTG 58.088 33.333 0.00 0.00 39.32 2.32
33 34 8.635328 ACACGATTTTACAAAGAGGGTTAATTT 58.365 29.630 0.00 0.00 0.00 1.82
34 35 8.173542 ACACGATTTTACAAAGAGGGTTAATT 57.826 30.769 0.00 0.00 0.00 1.40
35 36 7.754851 ACACGATTTTACAAAGAGGGTTAAT 57.245 32.000 0.00 0.00 0.00 1.40
36 37 8.558700 GTTACACGATTTTACAAAGAGGGTTAA 58.441 33.333 0.00 0.00 0.00 2.01
37 38 7.933033 AGTTACACGATTTTACAAAGAGGGTTA 59.067 33.333 0.00 0.00 0.00 2.85
38 39 6.769341 AGTTACACGATTTTACAAAGAGGGTT 59.231 34.615 0.00 0.00 0.00 4.11
39 40 6.293698 AGTTACACGATTTTACAAAGAGGGT 58.706 36.000 0.00 0.00 0.00 4.34
40 41 6.425721 TGAGTTACACGATTTTACAAAGAGGG 59.574 38.462 0.00 0.00 0.00 4.30
41 42 7.416154 TGAGTTACACGATTTTACAAAGAGG 57.584 36.000 0.00 0.00 0.00 3.69
42 43 9.878599 AAATGAGTTACACGATTTTACAAAGAG 57.121 29.630 0.00 0.00 0.00 2.85
43 44 9.658475 CAAATGAGTTACACGATTTTACAAAGA 57.342 29.630 0.00 0.00 0.00 2.52
44 45 9.445786 ACAAATGAGTTACACGATTTTACAAAG 57.554 29.630 0.00 0.00 0.00 2.77
46 47 9.866936 GTACAAATGAGTTACACGATTTTACAA 57.133 29.630 0.00 0.00 0.00 2.41
47 48 8.215792 CGTACAAATGAGTTACACGATTTTACA 58.784 33.333 0.00 0.00 30.78 2.41
48 49 8.216453 ACGTACAAATGAGTTACACGATTTTAC 58.784 33.333 5.43 0.00 32.60 2.01
49 50 8.215792 CACGTACAAATGAGTTACACGATTTTA 58.784 33.333 5.43 0.00 32.60 1.52
50 51 7.067116 CACGTACAAATGAGTTACACGATTTT 58.933 34.615 5.43 0.00 32.60 1.82
51 52 6.201425 ACACGTACAAATGAGTTACACGATTT 59.799 34.615 5.43 0.00 32.60 2.17
52 53 5.693104 ACACGTACAAATGAGTTACACGATT 59.307 36.000 5.43 0.00 32.60 3.34
53 54 5.224888 ACACGTACAAATGAGTTACACGAT 58.775 37.500 5.43 0.00 32.60 3.73
54 55 4.609947 ACACGTACAAATGAGTTACACGA 58.390 39.130 5.43 0.00 32.60 4.35
55 56 4.959631 ACACGTACAAATGAGTTACACG 57.040 40.909 0.00 0.00 33.80 4.49
56 57 5.442390 CGCTACACGTACAAATGAGTTACAC 60.442 44.000 0.00 0.00 36.87 2.90
57 58 4.618067 CGCTACACGTACAAATGAGTTACA 59.382 41.667 0.00 0.00 36.87 2.41
58 59 5.109815 CGCTACACGTACAAATGAGTTAC 57.890 43.478 0.00 0.00 36.87 2.50
73 74 1.467035 CCTCACCGAGTAACGCTACAC 60.467 57.143 0.00 0.00 41.07 2.90
74 75 0.806868 CCTCACCGAGTAACGCTACA 59.193 55.000 0.00 0.00 41.07 2.74
75 76 1.089920 TCCTCACCGAGTAACGCTAC 58.910 55.000 0.00 0.00 41.07 3.58
76 77 2.048444 ATCCTCACCGAGTAACGCTA 57.952 50.000 0.00 0.00 41.07 4.26
77 78 1.948145 CTATCCTCACCGAGTAACGCT 59.052 52.381 0.00 0.00 41.07 5.07
78 79 1.001597 CCTATCCTCACCGAGTAACGC 60.002 57.143 0.00 0.00 41.07 4.84
79 80 1.001597 GCCTATCCTCACCGAGTAACG 60.002 57.143 0.00 0.00 42.18 3.18
80 81 1.340568 GGCCTATCCTCACCGAGTAAC 59.659 57.143 0.00 0.00 0.00 2.50
81 82 1.700955 GGCCTATCCTCACCGAGTAA 58.299 55.000 0.00 0.00 0.00 2.24
82 83 0.178970 GGGCCTATCCTCACCGAGTA 60.179 60.000 0.84 0.00 34.39 2.59
83 84 1.457831 GGGCCTATCCTCACCGAGT 60.458 63.158 0.84 0.00 34.39 4.18
84 85 3.460995 GGGCCTATCCTCACCGAG 58.539 66.667 0.84 0.00 34.39 4.63
86 87 2.520982 TCGGGCCTATCCTCACCG 60.521 66.667 0.84 0.00 45.52 4.94
87 88 1.760875 TGTCGGGCCTATCCTCACC 60.761 63.158 0.84 0.00 34.39 4.02
88 89 1.442148 GTGTCGGGCCTATCCTCAC 59.558 63.158 0.84 0.58 34.39 3.51
89 90 2.125326 CGTGTCGGGCCTATCCTCA 61.125 63.158 0.84 0.00 34.39 3.86
90 91 2.728817 CGTGTCGGGCCTATCCTC 59.271 66.667 0.84 0.00 34.39 3.71
91 92 2.838225 CCGTGTCGGGCCTATCCT 60.838 66.667 0.84 0.00 44.15 3.24
102 103 1.165270 CCCTGAATTTCACCCGTGTC 58.835 55.000 0.00 0.00 0.00 3.67
122 123 5.495640 CCTTCCATATTCTATTCAGCCTCC 58.504 45.833 0.00 0.00 0.00 4.30
150 153 1.996191 CAGCTTTTCCGAGACTGCTAC 59.004 52.381 0.00 0.00 0.00 3.58
158 161 1.779569 ACACGTACAGCTTTTCCGAG 58.220 50.000 0.00 0.00 0.00 4.63
162 165 4.663636 AATGCTACACGTACAGCTTTTC 57.336 40.909 18.23 0.00 38.63 2.29
168 171 3.906008 GTGCAAAAATGCTACACGTACAG 59.094 43.478 2.22 0.00 35.49 2.74
190 194 8.365210 GCACTGTTCATGAAAATATGTTTTACG 58.635 33.333 10.35 0.00 37.65 3.18
194 198 8.575589 TGTAGCACTGTTCATGAAAATATGTTT 58.424 29.630 10.35 2.90 0.00 2.83
210 214 1.958579 TGTTCGTAGGTGTAGCACTGT 59.041 47.619 0.00 0.00 34.40 3.55
213 217 3.022607 ACTTGTTCGTAGGTGTAGCAC 57.977 47.619 0.00 0.00 0.00 4.40
248 252 6.256975 CACAATTTGCCAACTGGATCATTATG 59.743 38.462 0.00 0.00 37.39 1.90
249 253 6.154877 TCACAATTTGCCAACTGGATCATTAT 59.845 34.615 0.00 0.00 37.39 1.28
250 254 5.479724 TCACAATTTGCCAACTGGATCATTA 59.520 36.000 0.00 0.00 37.39 1.90
295 299 0.178906 AATTTTCAGGGTGGGTGGGG 60.179 55.000 0.00 0.00 0.00 4.96
314 318 0.326927 CAACTTTCTTCGGCCCCCTA 59.673 55.000 0.00 0.00 0.00 3.53
330 335 9.673454 AAGTTTACGTAATTTTCCTTCATCAAC 57.327 29.630 9.18 0.00 0.00 3.18
334 339 8.562052 ACGAAAGTTTACGTAATTTTCCTTCAT 58.438 29.630 24.83 12.65 46.40 2.57
358 363 7.373493 TCCTACACCTAAGAAAGAAGTTAACG 58.627 38.462 0.00 0.00 0.00 3.18
499 508 5.880054 AATTTACCGAGACAGGTCAAATG 57.120 39.130 1.84 0.00 44.68 2.32
563 579 4.437239 CACGGCTCTCAATGTAAGATCTT 58.563 43.478 13.56 13.56 0.00 2.40
618 634 2.957006 TCTCAGTCGGCTAGGATTTACC 59.043 50.000 0.00 0.00 39.35 2.85
619 635 3.243468 GGTCTCAGTCGGCTAGGATTTAC 60.243 52.174 0.00 0.00 0.00 2.01
620 636 2.957006 GGTCTCAGTCGGCTAGGATTTA 59.043 50.000 0.00 0.00 0.00 1.40
621 637 1.757699 GGTCTCAGTCGGCTAGGATTT 59.242 52.381 0.00 0.00 0.00 2.17
622 638 1.063567 AGGTCTCAGTCGGCTAGGATT 60.064 52.381 0.00 0.00 0.00 3.01
625 641 1.134037 ACTAGGTCTCAGTCGGCTAGG 60.134 57.143 0.00 0.00 0.00 3.02
628 644 0.328592 TGACTAGGTCTCAGTCGGCT 59.671 55.000 0.00 0.00 44.44 5.52
629 645 0.452585 GTGACTAGGTCTCAGTCGGC 59.547 60.000 0.00 0.00 44.44 5.54
630 646 1.822506 TGTGACTAGGTCTCAGTCGG 58.177 55.000 0.00 0.00 44.44 4.79
636 652 5.552178 AGAAAATGGTTGTGACTAGGTCTC 58.448 41.667 0.00 0.00 33.15 3.36
732 2486 5.544176 AGGAAGACAAATACAGAGGAGAACA 59.456 40.000 0.00 0.00 0.00 3.18
733 2487 6.043854 AGGAAGACAAATACAGAGGAGAAC 57.956 41.667 0.00 0.00 0.00 3.01
786 2548 1.034838 TGCTTGGCAGTCCAACGTTT 61.035 50.000 0.00 0.00 46.89 3.60
835 2597 1.098869 TTTTGAACTTGTGCTGCGGA 58.901 45.000 0.00 0.00 0.00 5.54
836 2598 1.919918 TTTTTGAACTTGTGCTGCGG 58.080 45.000 0.00 0.00 0.00 5.69
837 2599 2.347846 GCATTTTTGAACTTGTGCTGCG 60.348 45.455 0.00 0.00 0.00 5.18
838 2600 2.608546 TGCATTTTTGAACTTGTGCTGC 59.391 40.909 0.00 0.00 33.95 5.25
839 2601 4.114073 TCTGCATTTTTGAACTTGTGCTG 58.886 39.130 0.00 0.00 33.95 4.41
840 2602 4.098349 TCTCTGCATTTTTGAACTTGTGCT 59.902 37.500 0.00 0.00 33.95 4.40
841 2603 4.362279 TCTCTGCATTTTTGAACTTGTGC 58.638 39.130 0.00 0.00 0.00 4.57
857 2619 0.545646 ATTCCTTGCCTCCTCTCTGC 59.454 55.000 0.00 0.00 0.00 4.26
861 2634 1.211456 CTGGATTCCTTGCCTCCTCT 58.789 55.000 3.95 0.00 0.00 3.69
944 2727 1.152943 CCTCCTGGACCTCGATCGA 60.153 63.158 18.32 18.32 34.57 3.59
1056 2846 4.410400 GGGTTCTCGGCCACCAGG 62.410 72.222 11.82 0.00 34.36 4.45
1692 3984 2.727607 CGCCATTTGTAATCACACGGTG 60.728 50.000 6.58 6.58 33.30 4.94
1774 4103 1.025113 TTCTCGCTCGAGTCCGTCAT 61.025 55.000 15.13 0.00 42.49 3.06
2650 5434 4.923942 CATGGCGAGGCAGGCGAT 62.924 66.667 5.43 0.00 39.82 4.58
2813 5597 3.706373 AATCACGGCCGGTCAGCT 61.706 61.111 31.76 3.35 0.00 4.24
2816 5600 0.035036 TTAACAATCACGGCCGGTCA 59.965 50.000 31.76 13.20 0.00 4.02
2817 5601 1.135888 GTTTAACAATCACGGCCGGTC 60.136 52.381 31.76 0.00 0.00 4.79
2818 5602 0.876399 GTTTAACAATCACGGCCGGT 59.124 50.000 31.76 14.70 0.00 5.28
2819 5603 0.875728 TGTTTAACAATCACGGCCGG 59.124 50.000 31.76 18.67 0.00 6.13
2820 5604 1.135803 CCTGTTTAACAATCACGGCCG 60.136 52.381 26.86 26.86 0.00 6.13
2821 5605 1.201414 CCCTGTTTAACAATCACGGCC 59.799 52.381 0.00 0.00 0.00 6.13
2822 5606 2.156098 TCCCTGTTTAACAATCACGGC 58.844 47.619 0.00 0.00 0.00 5.68
2823 5607 3.364565 CGTTCCCTGTTTAACAATCACGG 60.365 47.826 0.00 0.00 0.00 4.94
2824 5608 3.249080 ACGTTCCCTGTTTAACAATCACG 59.751 43.478 13.50 13.50 0.00 4.35
2825 5609 4.533222 CACGTTCCCTGTTTAACAATCAC 58.467 43.478 0.00 0.00 0.00 3.06
2826 5610 3.003897 GCACGTTCCCTGTTTAACAATCA 59.996 43.478 0.00 0.00 0.00 2.57
2827 5611 3.003897 TGCACGTTCCCTGTTTAACAATC 59.996 43.478 0.00 0.00 0.00 2.67
2828 5612 2.952978 TGCACGTTCCCTGTTTAACAAT 59.047 40.909 0.00 0.00 0.00 2.71
2829 5613 2.366533 TGCACGTTCCCTGTTTAACAA 58.633 42.857 0.00 0.00 0.00 2.83
2830 5614 2.039818 TGCACGTTCCCTGTTTAACA 57.960 45.000 0.00 0.00 0.00 2.41
2831 5615 2.292292 ACATGCACGTTCCCTGTTTAAC 59.708 45.455 0.00 0.00 0.00 2.01
2832 5616 2.577700 ACATGCACGTTCCCTGTTTAA 58.422 42.857 0.00 0.00 0.00 1.52
2833 5617 2.264005 ACATGCACGTTCCCTGTTTA 57.736 45.000 0.00 0.00 0.00 2.01
2834 5618 1.877443 GTACATGCACGTTCCCTGTTT 59.123 47.619 0.00 0.00 0.00 2.83
2835 5619 1.071699 AGTACATGCACGTTCCCTGTT 59.928 47.619 0.00 0.00 0.00 3.16
2836 5620 0.685097 AGTACATGCACGTTCCCTGT 59.315 50.000 0.00 0.00 0.00 4.00
2837 5621 2.665649 TAGTACATGCACGTTCCCTG 57.334 50.000 0.00 0.00 0.00 4.45
2838 5622 2.500098 ACATAGTACATGCACGTTCCCT 59.500 45.455 0.00 0.00 0.00 4.20
2839 5623 2.901249 ACATAGTACATGCACGTTCCC 58.099 47.619 0.00 0.00 0.00 3.97
2840 5624 5.005394 CAGTTACATAGTACATGCACGTTCC 59.995 44.000 0.00 0.00 0.00 3.62
2841 5625 5.005394 CCAGTTACATAGTACATGCACGTTC 59.995 44.000 0.00 0.00 0.00 3.95
2842 5626 4.868171 CCAGTTACATAGTACATGCACGTT 59.132 41.667 0.00 0.00 0.00 3.99
2843 5627 4.430007 CCAGTTACATAGTACATGCACGT 58.570 43.478 0.00 0.00 0.00 4.49
2844 5628 3.245284 GCCAGTTACATAGTACATGCACG 59.755 47.826 0.00 0.00 0.00 5.34
2845 5629 4.034048 GTGCCAGTTACATAGTACATGCAC 59.966 45.833 0.00 0.00 37.10 4.57
2846 5630 4.188462 GTGCCAGTTACATAGTACATGCA 58.812 43.478 0.00 0.00 0.00 3.96
2847 5631 3.560068 GGTGCCAGTTACATAGTACATGC 59.440 47.826 0.00 0.00 0.00 4.06
2848 5632 3.802139 CGGTGCCAGTTACATAGTACATG 59.198 47.826 0.00 0.00 0.00 3.21
2849 5633 3.740141 GCGGTGCCAGTTACATAGTACAT 60.740 47.826 0.00 0.00 0.00 2.29
2850 5634 2.417651 GCGGTGCCAGTTACATAGTACA 60.418 50.000 0.00 0.00 0.00 2.90
2851 5635 2.159142 AGCGGTGCCAGTTACATAGTAC 60.159 50.000 0.00 0.00 0.00 2.73
2852 5636 2.104967 AGCGGTGCCAGTTACATAGTA 58.895 47.619 0.00 0.00 0.00 1.82
2853 5637 0.902531 AGCGGTGCCAGTTACATAGT 59.097 50.000 0.00 0.00 0.00 2.12
2854 5638 1.290203 CAGCGGTGCCAGTTACATAG 58.710 55.000 0.00 0.00 0.00 2.23
2855 5639 0.742990 GCAGCGGTGCCAGTTACATA 60.743 55.000 28.58 0.00 44.72 2.29
2856 5640 2.040544 GCAGCGGTGCCAGTTACAT 61.041 57.895 28.58 0.00 44.72 2.29
2857 5641 2.668212 GCAGCGGTGCCAGTTACA 60.668 61.111 28.58 0.00 44.72 2.41
2873 5657 1.268234 GGTACGATCATTGCTTGCAGC 60.268 52.381 0.00 1.70 42.82 5.25
2874 5658 2.031314 CAGGTACGATCATTGCTTGCAG 59.969 50.000 0.00 0.00 0.00 4.41
2875 5659 2.009051 CAGGTACGATCATTGCTTGCA 58.991 47.619 0.00 0.00 0.00 4.08
2876 5660 2.279741 TCAGGTACGATCATTGCTTGC 58.720 47.619 0.00 0.00 0.00 4.01
2877 5661 5.490139 AATTCAGGTACGATCATTGCTTG 57.510 39.130 0.00 0.00 0.00 4.01
2878 5662 6.150976 TCAAAATTCAGGTACGATCATTGCTT 59.849 34.615 0.00 0.00 0.00 3.91
2879 5663 5.647658 TCAAAATTCAGGTACGATCATTGCT 59.352 36.000 0.00 0.00 0.00 3.91
2880 5664 5.879237 TCAAAATTCAGGTACGATCATTGC 58.121 37.500 0.00 0.00 0.00 3.56
2881 5665 8.183536 TGAATCAAAATTCAGGTACGATCATTG 58.816 33.333 0.00 0.00 44.94 2.82
2882 5666 8.279970 TGAATCAAAATTCAGGTACGATCATT 57.720 30.769 0.00 0.00 44.94 2.57
2883 5667 7.864108 TGAATCAAAATTCAGGTACGATCAT 57.136 32.000 0.00 0.00 44.94 2.45
2895 5679 6.092670 TCGTCTGATGAGGTGAATCAAAATTC 59.907 38.462 0.00 0.00 41.48 2.17
2896 5680 5.939883 TCGTCTGATGAGGTGAATCAAAATT 59.060 36.000 0.00 0.00 33.76 1.82
2897 5681 5.352569 GTCGTCTGATGAGGTGAATCAAAAT 59.647 40.000 0.00 0.00 33.76 1.82
2898 5682 4.690748 GTCGTCTGATGAGGTGAATCAAAA 59.309 41.667 0.00 0.00 33.76 2.44
2899 5683 4.021104 AGTCGTCTGATGAGGTGAATCAAA 60.021 41.667 0.00 0.00 33.76 2.69
2900 5684 3.511540 AGTCGTCTGATGAGGTGAATCAA 59.488 43.478 0.00 0.00 33.76 2.57
2901 5685 3.092301 AGTCGTCTGATGAGGTGAATCA 58.908 45.455 0.00 0.00 33.13 2.57
2902 5686 3.701241 GAGTCGTCTGATGAGGTGAATC 58.299 50.000 0.00 0.00 0.00 2.52
2903 5687 2.098280 CGAGTCGTCTGATGAGGTGAAT 59.902 50.000 3.82 0.00 0.00 2.57
2904 5688 1.468914 CGAGTCGTCTGATGAGGTGAA 59.531 52.381 3.82 0.00 0.00 3.18
2905 5689 1.087501 CGAGTCGTCTGATGAGGTGA 58.912 55.000 3.82 0.00 0.00 4.02
2906 5690 1.087501 TCGAGTCGTCTGATGAGGTG 58.912 55.000 13.12 0.00 0.00 4.00
2907 5691 1.944024 GATCGAGTCGTCTGATGAGGT 59.056 52.381 13.12 0.00 0.00 3.85
2908 5692 1.070242 CGATCGAGTCGTCTGATGAGG 60.070 57.143 10.26 0.00 45.19 3.86
2909 5693 2.292948 CGATCGAGTCGTCTGATGAG 57.707 55.000 10.26 0.00 45.19 2.90
2919 5703 1.370657 GCCATCGGACGATCGAGTC 60.371 63.158 24.34 9.84 42.69 3.36
2920 5704 2.722487 GCCATCGGACGATCGAGT 59.278 61.111 24.34 0.00 42.69 4.18
2921 5705 2.427575 CGCCATCGGACGATCGAG 60.428 66.667 24.34 12.58 42.69 4.04
2922 5706 2.898343 TCGCCATCGGACGATCGA 60.898 61.111 24.34 12.46 43.61 3.59
2923 5707 2.726180 GTCGCCATCGGACGATCG 60.726 66.667 14.88 14.88 40.90 3.69
2924 5708 2.726180 CGTCGCCATCGGACGATC 60.726 66.667 8.50 0.00 40.90 3.69
2925 5709 4.925576 GCGTCGCCATCGGACGAT 62.926 66.667 17.32 0.65 40.90 3.73
3001 5785 0.548031 GGTGGAGATGGATCTTGCCA 59.452 55.000 0.00 0.00 43.23 4.92
3032 5816 4.695928 CCGTCTATCGATCAGAACCATCTA 59.304 45.833 0.00 0.00 42.86 1.98
3033 5817 3.504134 CCGTCTATCGATCAGAACCATCT 59.496 47.826 0.00 0.00 42.86 2.90
3232 6016 2.202797 CCAGGTGTCTCGCATCCG 60.203 66.667 0.00 0.00 0.00 4.18
3253 6037 3.157252 GATCCGGCAGCTCTCCCA 61.157 66.667 0.00 0.00 0.00 4.37
3284 6068 2.607750 ACCCTCATGGCGGTGAGT 60.608 61.111 15.66 0.39 43.22 3.41
3390 6174 2.213499 GGGCGAGATGTGAATCGAATT 58.787 47.619 0.00 0.00 41.40 2.17
3393 6177 0.179111 GTGGGCGAGATGTGAATCGA 60.179 55.000 0.00 0.00 41.40 3.59
3412 6196 1.770658 TCCCATATGTGCCTGAAGAGG 59.229 52.381 1.24 0.00 43.19 3.69
3425 6209 5.078573 AGGAAACCCTAGATCTCTCCCATAT 59.921 44.000 0.00 0.00 30.72 1.78
3580 6364 1.562672 AATCTCCCCCACCTTGGTCG 61.563 60.000 0.00 0.00 35.17 4.79
3657 6446 1.302511 GCATGTCTGGTTGGACGGT 60.303 57.895 0.00 0.00 38.91 4.83
3765 6557 4.329545 TCCCACTTGTCGCCAGCC 62.330 66.667 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.