Multiple sequence alignment - TraesCS3A01G343200

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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 TraesCS3A01G343200 chr3A 100.000 6729 0 0 1 6729 590362970 590369698 0.000000e+00 12427.0
1 TraesCS3A01G343200 chr3A 92.349 745 54 3 199 942 383761656 383760914 0.000000e+00 1057.0
2 TraesCS3A01G343200 chr5A 96.444 4387 148 6 1474 5857 256447940 256443559 0.000000e+00 7230.0
3 TraesCS3A01G343200 chr5A 92.709 2414 149 10 3226 5636 628225523 628223134 0.000000e+00 3458.0
4 TraesCS3A01G343200 chr5A 90.819 1721 115 13 1451 3163 628227206 628225521 0.000000e+00 2263.0
5 TraesCS3A01G343200 chr5A 94.675 507 25 2 943 1447 256448442 256447936 0.000000e+00 785.0
6 TraesCS3A01G343200 chr5A 97.087 206 6 0 1 206 377225116 377224911 1.390000e-91 348.0
7 TraesCS3A01G343200 chr7D 93.862 4708 225 25 942 5636 111561536 111566192 0.000000e+00 7035.0
8 TraesCS3A01G343200 chr7D 94.319 3890 169 18 1757 5636 100499141 100495294 0.000000e+00 5912.0
9 TraesCS3A01G343200 chr7D 93.165 673 41 4 936 1606 100525138 100524469 0.000000e+00 983.0
10 TraesCS3A01G343200 chr7D 93.116 552 27 2 5862 6403 261107413 261107963 0.000000e+00 798.0
11 TraesCS3A01G343200 chr7D 92.444 225 15 2 5638 5861 100495261 100495038 3.030000e-83 320.0
12 TraesCS3A01G343200 chr7D 91.129 124 10 1 1602 1724 100499255 100499132 4.170000e-37 167.0
13 TraesCS3A01G343200 chr6A 91.270 4731 308 37 943 5636 604402039 604397377 0.000000e+00 6351.0
14 TraesCS3A01G343200 chr6A 94.558 3804 178 13 1136 4937 174110174 174113950 0.000000e+00 5851.0
15 TraesCS3A01G343200 chr6A 94.894 803 39 2 5007 5808 174113947 174114748 0.000000e+00 1254.0
16 TraesCS3A01G343200 chr6A 94.220 173 10 0 943 1115 174109752 174109924 1.440000e-66 265.0
17 TraesCS3A01G343200 chr6A 92.857 140 10 0 3191 3330 1825118 1825257 3.180000e-48 204.0
18 TraesCS3A01G343200 chr1D 93.134 4122 193 26 1786 5862 33164741 33160665 0.000000e+00 5962.0
19 TraesCS3A01G343200 chr1D 93.058 3241 151 17 2657 5862 91482122 91485323 0.000000e+00 4671.0
20 TraesCS3A01G343200 chr1D 90.920 859 60 6 5862 6705 244997950 244998805 0.000000e+00 1138.0
21 TraesCS3A01G343200 chr1D 93.247 770 48 3 943 1710 33165837 33165070 0.000000e+00 1131.0
22 TraesCS3A01G343200 chr1D 93.252 741 48 2 202 942 244997214 244997952 0.000000e+00 1090.0
23 TraesCS3A01G343200 chr1D 92.105 760 53 5 940 1697 91480423 91481177 0.000000e+00 1064.0
24 TraesCS3A01G343200 chr1D 92.432 740 53 3 204 942 110703561 110702824 0.000000e+00 1053.0
25 TraesCS3A01G343200 chr1D 94.118 629 30 5 1794 2416 91481499 91482126 0.000000e+00 950.0
26 TraesCS3A01G343200 chr1D 93.719 398 24 1 5862 6258 290867842 290868239 4.490000e-166 595.0
27 TraesCS3A01G343200 chr1D 97.087 206 6 0 1 206 112294731 112294936 1.390000e-91 348.0
28 TraesCS3A01G343200 chr1D 88.384 198 22 1 2908 3104 198276901 198277098 3.140000e-58 237.0
29 TraesCS3A01G343200 chr2A 96.526 3195 104 6 2672 5864 667190279 667187090 0.000000e+00 5278.0
30 TraesCS3A01G343200 chr2A 89.579 3253 255 35 942 4158 760026490 760023286 0.000000e+00 4052.0
31 TraesCS3A01G343200 chr2A 95.525 1743 75 3 939 2679 667192880 667191139 0.000000e+00 2784.0
32 TraesCS3A01G343200 chr2A 94.070 1484 65 5 4154 5636 760018648 760017187 0.000000e+00 2231.0
33 TraesCS3A01G343200 chr2A 92.782 859 46 10 5862 6705 394604517 394605374 0.000000e+00 1229.0
34 TraesCS3A01G343200 chr6B 92.569 3647 214 31 2016 5638 253654056 253657669 0.000000e+00 5180.0
35 TraesCS3A01G343200 chr6B 89.585 1037 84 11 943 1969 253653037 253654059 0.000000e+00 1295.0
36 TraesCS3A01G343200 chr6B 78.427 1488 212 52 942 2362 307069342 307070787 0.000000e+00 869.0
37 TraesCS3A01G343200 chr6B 92.411 224 17 0 5635 5858 253657697 253657920 3.030000e-83 320.0
38 TraesCS3A01G343200 chr3D 95.457 2091 66 9 1984 4061 603528179 603530253 0.000000e+00 3308.0
39 TraesCS3A01G343200 chr3D 93.346 1082 38 9 4089 5170 603530240 603531287 0.000000e+00 1568.0
40 TraesCS3A01G343200 chr3D 91.851 859 50 8 5862 6704 424310952 424310098 0.000000e+00 1181.0
41 TraesCS3A01G343200 chr3D 92.289 804 42 8 938 1733 603527385 603528176 0.000000e+00 1123.0
42 TraesCS3A01G343200 chr3D 92.848 741 50 2 202 942 424302407 424301670 0.000000e+00 1072.0
43 TraesCS3A01G343200 chr3D 91.379 696 26 3 5201 5862 603531636 603532331 0.000000e+00 922.0
44 TraesCS3A01G343200 chr3D 92.206 603 32 7 6117 6705 480273175 480273776 0.000000e+00 839.0
45 TraesCS3A01G343200 chr4D 91.841 858 53 10 5862 6705 63493752 63494606 0.000000e+00 1181.0
46 TraesCS3A01G343200 chr4D 91.492 858 56 5 5862 6705 63356614 63357468 0.000000e+00 1164.0
47 TraesCS3A01G343200 chr4D 90.793 858 60 6 5862 6705 121986941 121986089 0.000000e+00 1129.0
48 TraesCS3A01G343200 chr4D 92.194 743 56 2 200 942 122005681 122004941 0.000000e+00 1050.0
49 TraesCS3A01G343200 chr4D 97.087 206 6 0 1 206 386073012 386072807 1.390000e-91 348.0
50 TraesCS3A01G343200 chr5D 91.259 858 59 6 5862 6705 75309768 75310623 0.000000e+00 1155.0
51 TraesCS3A01G343200 chr5D 93.243 740 47 3 204 942 75299751 75300488 0.000000e+00 1086.0
52 TraesCS3A01G343200 chr5D 92.992 742 49 3 202 942 75309031 75309770 0.000000e+00 1079.0
53 TraesCS3A01G343200 chr5D 97.573 206 5 0 1 206 289259275 289259070 2.990000e-93 353.0
54 TraesCS3A01G343200 chr2D 91.047 860 55 12 5862 6705 282420605 282421458 0.000000e+00 1142.0
55 TraesCS3A01G343200 chr2D 92.848 741 50 3 202 942 282419870 282420607 0.000000e+00 1072.0
56 TraesCS3A01G343200 chr2D 97.573 206 5 0 1 206 114938638 114938843 2.990000e-93 353.0
57 TraesCS3A01G343200 chr2D 97.087 206 6 0 1 206 477009964 477009759 1.390000e-91 348.0
58 TraesCS3A01G343200 chr6D 92.308 741 55 2 202 942 284356742 284357480 0.000000e+00 1051.0
59 TraesCS3A01G343200 chr6D 97.087 206 6 0 1 206 185102299 185102094 1.390000e-91 348.0
60 TraesCS3A01G343200 chr6D 84.615 65 8 2 942 1005 427994759 427994696 5.630000e-06 63.9
61 TraesCS3A01G343200 chr4B 86.364 858 96 13 5862 6705 137402384 137401534 0.000000e+00 917.0
62 TraesCS3A01G343200 chr4B 85.135 814 99 18 5862 6666 426858323 426857523 0.000000e+00 813.0
63 TraesCS3A01G343200 chr4B 94.512 492 24 3 5147 5636 657495916 657496406 0.000000e+00 756.0
64 TraesCS3A01G343200 chr4B 94.309 492 25 3 5147 5636 657512969 657513459 0.000000e+00 750.0
65 TraesCS3A01G343200 chr4B 84.341 645 65 22 5233 5865 419760036 419759416 3.470000e-167 599.0
66 TraesCS3A01G343200 chr7B 85.648 857 103 13 5862 6705 96923726 96922877 0.000000e+00 883.0
67 TraesCS3A01G343200 chr4A 97.087 206 6 0 1 206 543771090 543771295 1.390000e-91 348.0
68 TraesCS3A01G343200 chr1A 97.087 206 6 0 1 206 304258688 304258893 1.390000e-91 348.0
69 TraesCS3A01G343200 chr1A 89.950 199 18 2 2908 3105 249048359 249048556 8.660000e-64 255.0


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 TraesCS3A01G343200 chr3A 590362970 590369698 6728 False 12427.000000 12427 100.000000 1 6729 1 chr3A.!!$F1 6728
1 TraesCS3A01G343200 chr3A 383760914 383761656 742 True 1057.000000 1057 92.349000 199 942 1 chr3A.!!$R1 743
2 TraesCS3A01G343200 chr5A 256443559 256448442 4883 True 4007.500000 7230 95.559500 943 5857 2 chr5A.!!$R2 4914
3 TraesCS3A01G343200 chr5A 628223134 628227206 4072 True 2860.500000 3458 91.764000 1451 5636 2 chr5A.!!$R3 4185
4 TraesCS3A01G343200 chr7D 111561536 111566192 4656 False 7035.000000 7035 93.862000 942 5636 1 chr7D.!!$F1 4694
5 TraesCS3A01G343200 chr7D 100495038 100499255 4217 True 2133.000000 5912 92.630667 1602 5861 3 chr7D.!!$R2 4259
6 TraesCS3A01G343200 chr7D 100524469 100525138 669 True 983.000000 983 93.165000 936 1606 1 chr7D.!!$R1 670
7 TraesCS3A01G343200 chr7D 261107413 261107963 550 False 798.000000 798 93.116000 5862 6403 1 chr7D.!!$F2 541
8 TraesCS3A01G343200 chr6A 604397377 604402039 4662 True 6351.000000 6351 91.270000 943 5636 1 chr6A.!!$R1 4693
9 TraesCS3A01G343200 chr6A 174109752 174114748 4996 False 2456.666667 5851 94.557333 943 5808 3 chr6A.!!$F2 4865
10 TraesCS3A01G343200 chr1D 33160665 33165837 5172 True 3546.500000 5962 93.190500 943 5862 2 chr1D.!!$R2 4919
11 TraesCS3A01G343200 chr1D 91480423 91485323 4900 False 2228.333333 4671 93.093667 940 5862 3 chr1D.!!$F4 4922
12 TraesCS3A01G343200 chr1D 244997214 244998805 1591 False 1114.000000 1138 92.086000 202 6705 2 chr1D.!!$F5 6503
13 TraesCS3A01G343200 chr1D 110702824 110703561 737 True 1053.000000 1053 92.432000 204 942 1 chr1D.!!$R1 738
14 TraesCS3A01G343200 chr2A 760023286 760026490 3204 True 4052.000000 4052 89.579000 942 4158 1 chr2A.!!$R2 3216
15 TraesCS3A01G343200 chr2A 667187090 667192880 5790 True 4031.000000 5278 96.025500 939 5864 2 chr2A.!!$R3 4925
16 TraesCS3A01G343200 chr2A 760017187 760018648 1461 True 2231.000000 2231 94.070000 4154 5636 1 chr2A.!!$R1 1482
17 TraesCS3A01G343200 chr2A 394604517 394605374 857 False 1229.000000 1229 92.782000 5862 6705 1 chr2A.!!$F1 843
18 TraesCS3A01G343200 chr6B 253653037 253657920 4883 False 2265.000000 5180 91.521667 943 5858 3 chr6B.!!$F2 4915
19 TraesCS3A01G343200 chr6B 307069342 307070787 1445 False 869.000000 869 78.427000 942 2362 1 chr6B.!!$F1 1420
20 TraesCS3A01G343200 chr3D 603527385 603532331 4946 False 1730.250000 3308 93.117750 938 5862 4 chr3D.!!$F2 4924
21 TraesCS3A01G343200 chr3D 424310098 424310952 854 True 1181.000000 1181 91.851000 5862 6704 1 chr3D.!!$R2 842
22 TraesCS3A01G343200 chr3D 424301670 424302407 737 True 1072.000000 1072 92.848000 202 942 1 chr3D.!!$R1 740
23 TraesCS3A01G343200 chr3D 480273175 480273776 601 False 839.000000 839 92.206000 6117 6705 1 chr3D.!!$F1 588
24 TraesCS3A01G343200 chr4D 63493752 63494606 854 False 1181.000000 1181 91.841000 5862 6705 1 chr4D.!!$F2 843
25 TraesCS3A01G343200 chr4D 63356614 63357468 854 False 1164.000000 1164 91.492000 5862 6705 1 chr4D.!!$F1 843
26 TraesCS3A01G343200 chr4D 121986089 121986941 852 True 1129.000000 1129 90.793000 5862 6705 1 chr4D.!!$R1 843
27 TraesCS3A01G343200 chr4D 122004941 122005681 740 True 1050.000000 1050 92.194000 200 942 1 chr4D.!!$R2 742
28 TraesCS3A01G343200 chr5D 75309031 75310623 1592 False 1117.000000 1155 92.125500 202 6705 2 chr5D.!!$F2 6503
29 TraesCS3A01G343200 chr5D 75299751 75300488 737 False 1086.000000 1086 93.243000 204 942 1 chr5D.!!$F1 738
30 TraesCS3A01G343200 chr2D 282419870 282421458 1588 False 1107.000000 1142 91.947500 202 6705 2 chr2D.!!$F2 6503
31 TraesCS3A01G343200 chr6D 284356742 284357480 738 False 1051.000000 1051 92.308000 202 942 1 chr6D.!!$F1 740
32 TraesCS3A01G343200 chr4B 137401534 137402384 850 True 917.000000 917 86.364000 5862 6705 1 chr4B.!!$R1 843
33 TraesCS3A01G343200 chr4B 426857523 426858323 800 True 813.000000 813 85.135000 5862 6666 1 chr4B.!!$R3 804
34 TraesCS3A01G343200 chr4B 419759416 419760036 620 True 599.000000 599 84.341000 5233 5865 1 chr4B.!!$R2 632
35 TraesCS3A01G343200 chr7B 96922877 96923726 849 True 883.000000 883 85.648000 5862 6705 1 chr7B.!!$R1 843

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
44 45 0.106708 TGCAGATATGGCCTCGGAAC 59.893 55.000 3.32 0.0 0.00 3.62 F
45 46 0.106708 GCAGATATGGCCTCGGAACA 59.893 55.000 3.32 0.0 0.00 3.18 F
249 250 0.114168 TACCTTGCATTGCCAACCCT 59.886 50.000 6.12 0.0 0.00 4.34 F
1518 1809 0.400213 AACTCCAAAGCCCACGATCA 59.600 50.000 0.00 0.0 0.00 2.92 F
1606 1904 1.006639 GACTCCTCTCCCTCTCACCTT 59.993 57.143 0.00 0.0 0.00 3.50 F
1873 2441 1.271217 GGAAAGTGGTTTAGGACGGCT 60.271 52.381 0.00 0.0 0.00 5.52 F
2810 4268 1.020861 CATGCTCGCTGTTGGCACTA 61.021 55.000 0.00 0.0 41.91 2.74 F
3906 5384 0.322546 GAGGCACCGGATCCTTGTTT 60.323 55.000 9.46 0.0 31.71 2.83 F
4588 6068 1.002430 TGGCCTCAACTTCTGCTACTG 59.998 52.381 3.32 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1837 0.179129 GATAGGGTTTTCGCGGTCGA 60.179 55.000 6.13 0.00 43.89 4.20 R
1724 2039 2.043852 GGAGCCGGAGAGAGTGGA 60.044 66.667 5.05 0.00 0.00 4.02 R
1864 2432 2.693591 CAACTTCCATCTAGCCGTCCTA 59.306 50.000 0.00 0.00 0.00 2.94 R
2724 4182 1.552337 AGCTACTGTCATGTGTGAGGG 59.448 52.381 0.00 0.00 34.36 4.30 R
2810 4268 1.674441 CTTGCACGATTCTGCCATGAT 59.326 47.619 0.00 0.00 36.21 2.45 R
3847 5325 1.561076 CTGGGACCATGAGGAACATCA 59.439 52.381 0.00 0.00 37.07 3.07 R
4765 6245 1.170290 ACTTGTACCCTGCGGTTTGC 61.170 55.000 0.00 0.00 40.58 3.68 R
5664 7498 1.077716 GCCCAAACTAGGCCGTGAT 60.078 57.895 0.00 0.00 45.16 3.06 R
5929 7763 1.194781 AGTGCGAGTCCATGGGTTCT 61.195 55.000 13.02 8.28 0.00 3.01 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
21 22 4.421033 GGTTAAACTTGACAAGCCTAGC 57.579 45.455 15.24 8.41 0.00 3.42
22 23 3.818773 GGTTAAACTTGACAAGCCTAGCA 59.181 43.478 15.24 0.00 0.00 3.49
23 24 4.459337 GGTTAAACTTGACAAGCCTAGCAT 59.541 41.667 15.24 0.00 0.00 3.79
24 25 5.646360 GGTTAAACTTGACAAGCCTAGCATA 59.354 40.000 15.24 0.00 0.00 3.14
25 26 6.318900 GGTTAAACTTGACAAGCCTAGCATAT 59.681 38.462 15.24 0.00 0.00 1.78
26 27 5.824904 AAACTTGACAAGCCTAGCATATG 57.175 39.130 15.24 0.00 0.00 1.78
27 28 3.209410 ACTTGACAAGCCTAGCATATGC 58.791 45.455 20.36 20.36 42.49 3.14
28 29 3.208594 CTTGACAAGCCTAGCATATGCA 58.791 45.455 28.62 13.96 45.16 3.96
29 30 2.842457 TGACAAGCCTAGCATATGCAG 58.158 47.619 28.62 21.34 45.16 4.41
30 31 2.435437 TGACAAGCCTAGCATATGCAGA 59.565 45.455 28.62 15.32 45.16 4.26
31 32 3.072038 TGACAAGCCTAGCATATGCAGAT 59.928 43.478 28.62 13.30 45.16 2.90
32 33 4.284234 TGACAAGCCTAGCATATGCAGATA 59.716 41.667 28.62 12.13 45.16 1.98
33 34 5.046087 TGACAAGCCTAGCATATGCAGATAT 60.046 40.000 28.62 10.85 45.16 1.63
34 35 5.183969 ACAAGCCTAGCATATGCAGATATG 58.816 41.667 28.62 20.14 43.12 1.78
35 36 4.418973 AGCCTAGCATATGCAGATATGG 57.581 45.455 28.62 19.31 41.29 2.74
36 37 2.877168 GCCTAGCATATGCAGATATGGC 59.123 50.000 28.62 23.85 41.29 4.40
37 38 3.474600 CCTAGCATATGCAGATATGGCC 58.525 50.000 28.62 0.00 41.29 5.36
38 39 3.136077 CCTAGCATATGCAGATATGGCCT 59.864 47.826 28.62 7.20 41.29 5.19
39 40 3.278668 AGCATATGCAGATATGGCCTC 57.721 47.619 28.62 0.00 41.29 4.70
40 41 1.938577 GCATATGCAGATATGGCCTCG 59.061 52.381 22.84 0.00 41.29 4.63
41 42 2.558378 CATATGCAGATATGGCCTCGG 58.442 52.381 3.32 0.00 38.45 4.63
42 43 1.937191 TATGCAGATATGGCCTCGGA 58.063 50.000 3.32 0.00 0.00 4.55
43 44 1.059098 ATGCAGATATGGCCTCGGAA 58.941 50.000 3.32 0.00 0.00 4.30
44 45 0.106708 TGCAGATATGGCCTCGGAAC 59.893 55.000 3.32 0.00 0.00 3.62
45 46 0.106708 GCAGATATGGCCTCGGAACA 59.893 55.000 3.32 0.00 0.00 3.18
46 47 1.871080 CAGATATGGCCTCGGAACAC 58.129 55.000 3.32 0.00 0.00 3.32
47 48 1.414181 CAGATATGGCCTCGGAACACT 59.586 52.381 3.32 0.00 0.00 3.55
48 49 1.414181 AGATATGGCCTCGGAACACTG 59.586 52.381 3.32 0.00 0.00 3.66
49 50 1.412710 GATATGGCCTCGGAACACTGA 59.587 52.381 3.32 0.00 0.00 3.41
50 51 0.824109 TATGGCCTCGGAACACTGAG 59.176 55.000 3.32 0.00 36.94 3.35
51 52 0.904865 ATGGCCTCGGAACACTGAGA 60.905 55.000 3.32 0.00 38.81 3.27
52 53 1.079750 GGCCTCGGAACACTGAGAC 60.080 63.158 0.00 0.00 38.81 3.36
53 54 1.079750 GCCTCGGAACACTGAGACC 60.080 63.158 7.52 0.00 38.81 3.85
54 55 1.213013 CCTCGGAACACTGAGACCG 59.787 63.158 7.52 0.00 45.61 4.79
57 58 3.580904 CGGAACACTGAGACCGAAA 57.419 52.632 0.00 0.00 46.94 3.46
58 59 1.419374 CGGAACACTGAGACCGAAAG 58.581 55.000 0.00 0.00 46.94 2.62
78 79 7.288317 GAAAGGTCGAGCATGAATCATATAG 57.712 40.000 18.15 0.00 0.00 1.31
79 80 5.991933 AGGTCGAGCATGAATCATATAGT 57.008 39.130 18.15 0.00 0.00 2.12
80 81 7.468141 AAGGTCGAGCATGAATCATATAGTA 57.532 36.000 18.15 0.00 0.00 1.82
81 82 7.094508 AGGTCGAGCATGAATCATATAGTAG 57.905 40.000 18.15 0.00 0.00 2.57
82 83 6.887002 AGGTCGAGCATGAATCATATAGTAGA 59.113 38.462 18.15 0.00 0.00 2.59
83 84 7.559533 AGGTCGAGCATGAATCATATAGTAGAT 59.440 37.037 18.15 0.00 0.00 1.98
84 85 8.841300 GGTCGAGCATGAATCATATAGTAGATA 58.159 37.037 10.30 0.00 0.00 1.98
117 118 4.510038 GTGATGTTCACCATTGAAAGCT 57.490 40.909 0.00 0.00 43.52 3.74
118 119 5.627499 GTGATGTTCACCATTGAAAGCTA 57.373 39.130 0.00 0.00 43.52 3.32
119 120 5.393962 GTGATGTTCACCATTGAAAGCTAC 58.606 41.667 0.00 0.00 43.52 3.58
120 121 5.182001 GTGATGTTCACCATTGAAAGCTACT 59.818 40.000 0.00 0.00 43.52 2.57
121 122 5.412594 TGATGTTCACCATTGAAAGCTACTC 59.587 40.000 0.00 0.00 43.52 2.59
122 123 4.072131 TGTTCACCATTGAAAGCTACTCC 58.928 43.478 0.00 0.00 43.52 3.85
123 124 4.072131 GTTCACCATTGAAAGCTACTCCA 58.928 43.478 0.00 0.00 43.52 3.86
124 125 4.574674 TCACCATTGAAAGCTACTCCAT 57.425 40.909 0.00 0.00 0.00 3.41
125 126 4.517285 TCACCATTGAAAGCTACTCCATC 58.483 43.478 0.00 0.00 0.00 3.51
126 127 4.225942 TCACCATTGAAAGCTACTCCATCT 59.774 41.667 0.00 0.00 0.00 2.90
127 128 4.574013 CACCATTGAAAGCTACTCCATCTC 59.426 45.833 0.00 0.00 0.00 2.75
128 129 4.225942 ACCATTGAAAGCTACTCCATCTCA 59.774 41.667 0.00 0.00 0.00 3.27
129 130 4.574013 CCATTGAAAGCTACTCCATCTCAC 59.426 45.833 0.00 0.00 0.00 3.51
130 131 3.510388 TGAAAGCTACTCCATCTCACG 57.490 47.619 0.00 0.00 0.00 4.35
131 132 2.826128 TGAAAGCTACTCCATCTCACGT 59.174 45.455 0.00 0.00 0.00 4.49
132 133 2.949451 AAGCTACTCCATCTCACGTG 57.051 50.000 9.94 9.94 0.00 4.49
133 134 2.130272 AGCTACTCCATCTCACGTGA 57.870 50.000 18.88 18.88 0.00 4.35
134 135 2.660572 AGCTACTCCATCTCACGTGAT 58.339 47.619 20.40 1.42 0.00 3.06
135 136 2.360483 AGCTACTCCATCTCACGTGATG 59.640 50.000 20.40 15.30 42.38 3.07
136 137 2.359214 GCTACTCCATCTCACGTGATGA 59.641 50.000 20.40 18.00 44.71 2.92
137 138 3.005261 GCTACTCCATCTCACGTGATGAT 59.995 47.826 20.40 19.36 44.71 2.45
138 139 3.724508 ACTCCATCTCACGTGATGATC 57.275 47.619 20.40 0.00 44.71 2.92
139 140 2.033927 ACTCCATCTCACGTGATGATCG 59.966 50.000 20.40 15.51 44.71 3.69
140 141 1.338020 TCCATCTCACGTGATGATCGG 59.662 52.381 20.40 21.82 44.71 4.18
141 142 1.338020 CCATCTCACGTGATGATCGGA 59.662 52.381 20.40 12.04 44.71 4.55
142 143 2.389059 CATCTCACGTGATGATCGGAC 58.611 52.381 20.40 0.00 44.71 4.79
143 144 1.459450 TCTCACGTGATGATCGGACA 58.541 50.000 20.40 0.00 36.48 4.02
144 145 2.024414 TCTCACGTGATGATCGGACAT 58.976 47.619 20.40 0.00 36.48 3.06
145 146 2.122564 CTCACGTGATGATCGGACATG 58.877 52.381 20.40 0.00 36.48 3.21
146 147 1.202405 TCACGTGATGATCGGACATGG 60.202 52.381 15.76 0.00 29.99 3.66
147 148 0.824109 ACGTGATGATCGGACATGGT 59.176 50.000 0.00 0.00 0.00 3.55
148 149 1.207089 ACGTGATGATCGGACATGGTT 59.793 47.619 0.00 0.00 0.00 3.67
149 150 2.279741 CGTGATGATCGGACATGGTTT 58.720 47.619 0.00 0.00 0.00 3.27
150 151 3.118920 ACGTGATGATCGGACATGGTTTA 60.119 43.478 0.00 0.00 0.00 2.01
151 152 3.490896 CGTGATGATCGGACATGGTTTAG 59.509 47.826 0.00 0.00 0.00 1.85
152 153 4.442706 GTGATGATCGGACATGGTTTAGT 58.557 43.478 0.00 0.00 0.00 2.24
153 154 4.876107 GTGATGATCGGACATGGTTTAGTT 59.124 41.667 0.00 0.00 0.00 2.24
154 155 4.875536 TGATGATCGGACATGGTTTAGTTG 59.124 41.667 0.00 0.00 0.00 3.16
155 156 4.545208 TGATCGGACATGGTTTAGTTGA 57.455 40.909 0.00 0.00 0.00 3.18
156 157 5.097742 TGATCGGACATGGTTTAGTTGAT 57.902 39.130 0.00 0.00 0.00 2.57
157 158 6.228616 TGATCGGACATGGTTTAGTTGATA 57.771 37.500 0.00 0.00 0.00 2.15
158 159 6.826668 TGATCGGACATGGTTTAGTTGATAT 58.173 36.000 0.00 0.00 0.00 1.63
159 160 6.705825 TGATCGGACATGGTTTAGTTGATATG 59.294 38.462 0.00 0.00 0.00 1.78
160 161 5.364778 TCGGACATGGTTTAGTTGATATGG 58.635 41.667 0.00 0.00 0.00 2.74
161 162 5.129650 TCGGACATGGTTTAGTTGATATGGA 59.870 40.000 0.00 0.00 0.00 3.41
162 163 5.997746 CGGACATGGTTTAGTTGATATGGAT 59.002 40.000 0.00 0.00 0.00 3.41
163 164 6.147821 CGGACATGGTTTAGTTGATATGGATC 59.852 42.308 0.00 0.00 0.00 3.36
164 165 6.998074 GGACATGGTTTAGTTGATATGGATCA 59.002 38.462 0.00 0.00 40.45 2.92
165 166 7.041098 GGACATGGTTTAGTTGATATGGATCAC 60.041 40.741 0.00 0.00 41.92 3.06
166 167 6.483307 ACATGGTTTAGTTGATATGGATCACG 59.517 38.462 0.00 0.00 41.92 4.35
167 168 4.814234 TGGTTTAGTTGATATGGATCACGC 59.186 41.667 0.00 0.00 41.92 5.34
168 169 4.084537 GGTTTAGTTGATATGGATCACGCG 60.085 45.833 3.53 3.53 41.92 6.01
169 170 4.577834 TTAGTTGATATGGATCACGCGA 57.422 40.909 15.93 0.00 41.92 5.87
170 171 3.667497 AGTTGATATGGATCACGCGAT 57.333 42.857 15.93 0.00 41.92 4.58
171 172 3.579709 AGTTGATATGGATCACGCGATC 58.420 45.455 15.93 6.11 46.34 3.69
182 183 5.183817 GATCACGCGATCATTTAGATGAC 57.816 43.478 15.93 0.00 46.33 3.06
183 184 4.307443 TCACGCGATCATTTAGATGACT 57.693 40.909 15.93 0.00 44.64 3.41
184 185 5.432885 TCACGCGATCATTTAGATGACTA 57.567 39.130 15.93 0.00 44.64 2.59
185 186 5.452777 TCACGCGATCATTTAGATGACTAG 58.547 41.667 15.93 0.00 44.64 2.57
186 187 5.238650 TCACGCGATCATTTAGATGACTAGA 59.761 40.000 15.93 0.00 44.64 2.43
187 188 5.340932 CACGCGATCATTTAGATGACTAGAC 59.659 44.000 15.93 0.00 44.64 2.59
188 189 4.551509 CGCGATCATTTAGATGACTAGACG 59.448 45.833 0.00 2.22 44.64 4.18
189 190 4.854291 GCGATCATTTAGATGACTAGACGG 59.146 45.833 0.00 0.00 44.64 4.79
190 191 5.334957 GCGATCATTTAGATGACTAGACGGA 60.335 44.000 0.00 0.00 44.64 4.69
191 192 6.623986 GCGATCATTTAGATGACTAGACGGAT 60.624 42.308 0.00 0.00 44.64 4.18
192 193 6.744993 CGATCATTTAGATGACTAGACGGATG 59.255 42.308 0.00 0.00 44.64 3.51
193 194 6.961360 TCATTTAGATGACTAGACGGATGT 57.039 37.500 0.00 0.00 37.37 3.06
194 195 6.971602 TCATTTAGATGACTAGACGGATGTC 58.028 40.000 0.00 0.00 40.13 3.06
195 196 6.773200 TCATTTAGATGACTAGACGGATGTCT 59.227 38.462 0.00 3.19 45.83 3.41
196 197 7.937394 TCATTTAGATGACTAGACGGATGTCTA 59.063 37.037 0.00 5.16 44.08 2.59
197 198 8.735315 CATTTAGATGACTAGACGGATGTCTAT 58.265 37.037 5.67 0.00 44.16 1.98
249 250 0.114168 TACCTTGCATTGCCAACCCT 59.886 50.000 6.12 0.00 0.00 4.34
287 288 3.255642 GGCAACACACAACATCTTGGTAT 59.744 43.478 0.00 0.00 0.00 2.73
393 395 9.274206 TGCCGCTAAACAATATGTACATTATTA 57.726 29.630 14.77 6.11 0.00 0.98
410 412 8.533569 ACATTATTAAGTGAACATAAAGGGGG 57.466 34.615 0.00 0.00 0.00 5.40
468 470 2.682594 TGTAGCAGGACTCCATAGCAT 58.317 47.619 0.00 0.00 0.00 3.79
502 504 1.272258 TGGACACGGTCTAGACATGGA 60.272 52.381 23.91 7.77 32.47 3.41
507 509 1.478510 ACGGTCTAGACATGGAAGCAG 59.521 52.381 23.91 6.21 0.00 4.24
738 740 0.583438 CAACTGAACAGTGCTCACGG 59.417 55.000 8.25 0.00 41.58 4.94
763 765 1.011333 CACGAACGGAACCACACTTT 58.989 50.000 0.00 0.00 0.00 2.66
793 796 2.028748 TCCTTACCTCGTAACCAACAGC 60.029 50.000 0.00 0.00 0.00 4.40
794 797 2.289195 CCTTACCTCGTAACCAACAGCA 60.289 50.000 0.00 0.00 0.00 4.41
811 814 2.220363 CAGCAATCAATCTCGGATCACG 59.780 50.000 0.00 0.00 46.11 4.35
887 890 6.073873 GCAATGCAAATTACTTAGTGTGCAAA 60.074 34.615 15.05 0.00 44.39 3.68
888 891 7.360269 GCAATGCAAATTACTTAGTGTGCAAAT 60.360 33.333 15.05 7.82 44.39 2.32
940 943 1.648116 TACTTACGAACTGGGCCCTT 58.352 50.000 25.70 10.23 0.00 3.95
1066 1070 1.761198 GTAGCCCCTTAATGACGGACT 59.239 52.381 0.00 0.00 0.00 3.85
1116 1120 2.660064 CGACCAACTGGGCCTAGCT 61.660 63.158 17.38 0.00 41.34 3.32
1264 1499 9.540538 TCCTAATCAAAATAGATGGAACCAAAA 57.459 29.630 0.00 0.00 0.00 2.44
1372 1622 6.491394 CAAAGACACCAAAATACGAAACTGA 58.509 36.000 0.00 0.00 0.00 3.41
1387 1662 0.953727 ACTGATTGAAGCAAAGCGCA 59.046 45.000 11.47 0.00 46.13 6.09
1506 1788 5.378332 TCTTTTCGACCCATTTAACTCCAA 58.622 37.500 0.00 0.00 0.00 3.53
1518 1809 0.400213 AACTCCAAAGCCCACGATCA 59.600 50.000 0.00 0.00 0.00 2.92
1546 1837 4.434354 AGCCTCGCGTCTCTCCCT 62.434 66.667 5.77 0.00 0.00 4.20
1606 1904 1.006639 GACTCCTCTCCCTCTCACCTT 59.993 57.143 0.00 0.00 0.00 3.50
1729 2044 4.954118 TCCGCCACCACCTCCACT 62.954 66.667 0.00 0.00 0.00 4.00
1815 2383 4.411927 GCTCCTAGATCTATGTCAAGGGA 58.588 47.826 2.11 3.85 0.00 4.20
1864 2432 3.222603 GTGGTCATGAGGAAAGTGGTTT 58.777 45.455 0.00 0.00 0.00 3.27
1873 2441 1.271217 GGAAAGTGGTTTAGGACGGCT 60.271 52.381 0.00 0.00 0.00 5.52
1886 2454 1.480954 GGACGGCTAGATGGAAGTTGA 59.519 52.381 0.00 0.00 0.00 3.18
1947 2516 2.291217 GCTCCCCCTTCTTCACAATCTT 60.291 50.000 0.00 0.00 0.00 2.40
2054 2630 1.550524 TCGCTGTGAAGGTGATAAGCT 59.449 47.619 0.00 0.00 0.00 3.74
2310 2893 1.961394 AGTTTCTGAGGTCGTGCTGTA 59.039 47.619 0.00 0.00 0.00 2.74
2506 3097 8.421249 TTGTTTTCTCCATGGAATAGTTTGAT 57.579 30.769 17.00 0.00 0.00 2.57
2699 4157 2.206576 ATGCACCCTTCTTTGTCCTC 57.793 50.000 0.00 0.00 0.00 3.71
2810 4268 1.020861 CATGCTCGCTGTTGGCACTA 61.021 55.000 0.00 0.00 41.91 2.74
2859 4317 3.457234 CATGCAGGTGTCGTGTGTATAT 58.543 45.455 0.00 0.00 0.00 0.86
3229 4702 8.536175 AGAAAAGAACCATTACTTGAAAACCAA 58.464 29.630 0.00 0.00 0.00 3.67
3244 4717 9.092876 CTTGAAAACCAACTATGAGATAGACTC 57.907 37.037 0.00 0.00 45.11 3.36
3847 5325 4.160252 GGTTGTGATTGTTATGCTGGGAAT 59.840 41.667 0.00 0.00 0.00 3.01
3894 5372 3.798202 CTGTTAGTATGGAAGAGGCACC 58.202 50.000 0.00 0.00 0.00 5.01
3906 5384 0.322546 GAGGCACCGGATCCTTGTTT 60.323 55.000 9.46 0.00 31.71 2.83
3918 5396 4.398044 GGATCCTTGTTTTCGCATTCCTTA 59.602 41.667 3.84 0.00 0.00 2.69
4390 5870 3.960102 AGATGACCTTGGCAAAAACTCAA 59.040 39.130 0.00 0.00 0.00 3.02
4588 6068 1.002430 TGGCCTCAACTTCTGCTACTG 59.998 52.381 3.32 0.00 0.00 2.74
4606 6086 6.921857 TGCTACTGTAGTACTTGAGTTTTGTC 59.078 38.462 15.71 0.00 0.00 3.18
4624 6104 4.787381 TGTCATGTGTGTTTGTTAGTCG 57.213 40.909 0.00 0.00 0.00 4.18
4719 6199 8.948631 TCTGAATTTCTTCTGTATCATGTACC 57.051 34.615 0.00 0.00 33.42 3.34
4720 6200 8.539544 TCTGAATTTCTTCTGTATCATGTACCA 58.460 33.333 0.00 0.00 33.42 3.25
4744 6224 4.994852 TGCAGGATAACAAGTACAGACAAC 59.005 41.667 0.00 0.00 0.00 3.32
4876 6357 9.987272 TGGAGACATGATTTCTGTTACTATATG 57.013 33.333 0.00 0.00 33.40 1.78
5020 6501 9.487790 AAGAAAATTACATTGTTACATTGTGGG 57.512 29.630 19.23 0.00 31.72 4.61
5087 6568 7.704899 TGTGTACTATGCACATGTATTAGTCAC 59.295 37.037 14.39 18.01 41.32 3.67
5138 6619 9.482627 GATACTTTGTTATTCTCATCTGTAGGG 57.517 37.037 0.00 0.00 0.00 3.53
5148 6629 5.144100 TCTCATCTGTAGGGATTTCTCCTC 58.856 45.833 0.00 0.00 41.74 3.71
5255 7054 1.133181 TGCCATCAGGAGGGTTGACA 61.133 55.000 1.61 0.00 36.89 3.58
5297 7098 9.344772 ACAACCTTTGTAGTTATATGTTTGTCA 57.655 29.630 0.00 0.00 43.27 3.58
5520 7323 9.611284 CATTATGATTTACGGAACACATTATGG 57.389 33.333 12.95 0.00 30.18 2.74
5528 7331 3.692101 CGGAACACATTATGGTAAAGGCA 59.308 43.478 0.00 0.00 0.00 4.75
5664 7498 1.270625 GGTCCATGACGAACTGTTCCA 60.271 52.381 14.48 8.25 32.65 3.53
5728 7562 1.375396 CGGCCAAGAACCGTCATGA 60.375 57.895 2.24 0.00 45.70 3.07
5729 7563 0.744414 CGGCCAAGAACCGTCATGAT 60.744 55.000 2.24 0.00 45.70 2.45
5817 7651 4.156556 GCATGACAGTTTTTGGCTGATCTA 59.843 41.667 0.00 0.00 35.09 1.98
5929 7763 0.816018 CGCACTTTACCCACACCACA 60.816 55.000 0.00 0.00 0.00 4.17
5940 7774 0.110295 CACACCACAGAACCCATGGA 59.890 55.000 15.22 0.00 36.94 3.41
5989 7823 1.066858 GCATTCCGACAGAACTCTCCA 60.067 52.381 0.00 0.00 37.29 3.86
6015 7849 0.973632 ATGACACTCTTACGGCCACA 59.026 50.000 2.24 0.00 0.00 4.17
6079 7918 2.666317 AGCAAAGGCAAAACTACCACT 58.334 42.857 0.00 0.00 44.61 4.00
6124 7963 1.684983 ACGGGGACACGATACCATAAG 59.315 52.381 0.00 0.00 37.61 1.73
6127 7966 3.006537 CGGGGACACGATACCATAAGAAT 59.993 47.826 0.00 0.00 35.47 2.40
6228 8069 0.108585 AAGGCATGACAACAGGACGT 59.891 50.000 0.00 0.00 41.08 4.34
6631 8498 8.839310 ATATATCACTAGTTCAAGCATTCACC 57.161 34.615 0.00 0.00 0.00 4.02
6641 8508 7.168219 AGTTCAAGCATTCACCTCTATTAACA 58.832 34.615 0.00 0.00 0.00 2.41
6662 8529 6.774354 ACAAAGCATTTTGATCATGACAAC 57.226 33.333 0.00 0.00 45.21 3.32
6721 8593 8.456904 ACAATGAATCAATGTTCAAGAAATCG 57.543 30.769 0.00 0.00 41.09 3.34
6722 8594 8.084073 ACAATGAATCAATGTTCAAGAAATCGT 58.916 29.630 0.00 0.00 41.09 3.73
6723 8595 8.918658 CAATGAATCAATGTTCAAGAAATCGTT 58.081 29.630 0.00 0.00 41.09 3.85
6726 8598 9.393249 TGAATCAATGTTCAAGAAATCGTTAAC 57.607 29.630 0.00 0.00 35.31 2.01
6727 8599 9.612620 GAATCAATGTTCAAGAAATCGTTAACT 57.387 29.630 3.71 0.00 0.00 2.24
6728 8600 8.955061 ATCAATGTTCAAGAAATCGTTAACTG 57.045 30.769 3.71 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.629079 ATGCTAGGCTTGTCAAGTTTAAC 57.371 39.130 14.03 3.88 0.00 2.01
3 4 5.296780 GCATATGCTAGGCTTGTCAAGTTTA 59.703 40.000 20.64 6.30 38.21 2.01
5 6 3.629398 GCATATGCTAGGCTTGTCAAGTT 59.371 43.478 20.64 5.83 38.21 2.66
6 7 3.209410 GCATATGCTAGGCTTGTCAAGT 58.791 45.455 20.64 0.00 38.21 3.16
7 8 3.208594 TGCATATGCTAGGCTTGTCAAG 58.791 45.455 27.13 8.31 42.66 3.02
8 9 3.118298 TCTGCATATGCTAGGCTTGTCAA 60.118 43.478 27.13 2.68 42.66 3.18
9 10 2.435437 TCTGCATATGCTAGGCTTGTCA 59.565 45.455 27.13 3.19 42.66 3.58
10 11 3.117491 TCTGCATATGCTAGGCTTGTC 57.883 47.619 27.13 0.00 42.66 3.18
11 12 3.784511 ATCTGCATATGCTAGGCTTGT 57.215 42.857 27.13 3.63 42.66 3.16
12 13 4.575236 CCATATCTGCATATGCTAGGCTTG 59.425 45.833 27.13 16.61 40.47 4.01
13 14 4.778579 CCATATCTGCATATGCTAGGCTT 58.221 43.478 27.13 13.37 40.47 4.35
14 15 3.433314 GCCATATCTGCATATGCTAGGCT 60.433 47.826 27.13 15.16 40.47 4.58
15 16 2.877168 GCCATATCTGCATATGCTAGGC 59.123 50.000 27.13 23.29 40.47 3.93
16 17 3.136077 AGGCCATATCTGCATATGCTAGG 59.864 47.826 27.13 18.76 40.47 3.02
17 18 4.378774 GAGGCCATATCTGCATATGCTAG 58.621 47.826 27.13 21.08 40.47 3.42
18 19 3.181472 CGAGGCCATATCTGCATATGCTA 60.181 47.826 27.13 16.23 40.47 3.49
19 20 2.419713 CGAGGCCATATCTGCATATGCT 60.420 50.000 27.13 10.98 40.47 3.79
20 21 1.938577 CGAGGCCATATCTGCATATGC 59.061 52.381 21.09 21.09 40.47 3.14
21 22 2.169144 TCCGAGGCCATATCTGCATATG 59.831 50.000 5.01 0.00 41.20 1.78
22 23 2.470990 TCCGAGGCCATATCTGCATAT 58.529 47.619 5.01 0.00 0.00 1.78
23 24 1.937191 TCCGAGGCCATATCTGCATA 58.063 50.000 5.01 0.00 0.00 3.14
24 25 1.059098 TTCCGAGGCCATATCTGCAT 58.941 50.000 5.01 0.00 0.00 3.96
25 26 0.106708 GTTCCGAGGCCATATCTGCA 59.893 55.000 5.01 0.00 0.00 4.41
26 27 0.106708 TGTTCCGAGGCCATATCTGC 59.893 55.000 5.01 0.00 0.00 4.26
27 28 1.414181 AGTGTTCCGAGGCCATATCTG 59.586 52.381 5.01 0.00 0.00 2.90
28 29 1.414181 CAGTGTTCCGAGGCCATATCT 59.586 52.381 5.01 0.00 0.00 1.98
29 30 1.412710 TCAGTGTTCCGAGGCCATATC 59.587 52.381 5.01 0.00 0.00 1.63
30 31 1.414181 CTCAGTGTTCCGAGGCCATAT 59.586 52.381 5.01 0.00 0.00 1.78
31 32 0.824109 CTCAGTGTTCCGAGGCCATA 59.176 55.000 5.01 0.00 0.00 2.74
32 33 0.904865 TCTCAGTGTTCCGAGGCCAT 60.905 55.000 5.01 0.00 0.00 4.40
33 34 1.533033 TCTCAGTGTTCCGAGGCCA 60.533 57.895 5.01 0.00 0.00 5.36
34 35 1.079750 GTCTCAGTGTTCCGAGGCC 60.080 63.158 0.00 0.00 0.00 5.19
35 36 1.079750 GGTCTCAGTGTTCCGAGGC 60.080 63.158 0.00 0.00 32.98 4.70
36 37 1.213013 CGGTCTCAGTGTTCCGAGG 59.787 63.158 14.52 0.00 44.86 4.63
37 38 2.254471 TCGGTCTCAGTGTTCCGAG 58.746 57.895 16.96 0.00 45.49 4.63
39 40 1.419374 CTTTCGGTCTCAGTGTTCCG 58.581 55.000 13.85 13.85 43.65 4.30
40 41 1.070289 ACCTTTCGGTCTCAGTGTTCC 59.930 52.381 0.00 0.00 40.27 3.62
41 42 2.528041 ACCTTTCGGTCTCAGTGTTC 57.472 50.000 0.00 0.00 40.27 3.18
52 53 1.594862 GATTCATGCTCGACCTTTCGG 59.405 52.381 0.00 0.00 45.90 4.30
54 55 6.870965 ACTATATGATTCATGCTCGACCTTTC 59.129 38.462 9.46 0.00 0.00 2.62
55 56 6.763355 ACTATATGATTCATGCTCGACCTTT 58.237 36.000 9.46 0.00 0.00 3.11
56 57 6.352016 ACTATATGATTCATGCTCGACCTT 57.648 37.500 9.46 0.00 0.00 3.50
57 58 5.991933 ACTATATGATTCATGCTCGACCT 57.008 39.130 9.46 0.00 0.00 3.85
58 59 7.089770 TCTACTATATGATTCATGCTCGACC 57.910 40.000 9.46 0.00 0.00 4.79
91 92 6.349611 GCTTTCAATGGTGAACATCACTATGT 60.350 38.462 9.66 0.00 45.90 2.29
92 93 6.032094 GCTTTCAATGGTGAACATCACTATG 58.968 40.000 9.66 7.08 45.90 2.23
94 95 5.316167 AGCTTTCAATGGTGAACATCACTA 58.684 37.500 10.06 4.82 46.19 2.74
95 96 4.147321 AGCTTTCAATGGTGAACATCACT 58.853 39.130 10.06 0.00 46.19 3.41
96 97 4.510038 AGCTTTCAATGGTGAACATCAC 57.490 40.909 1.88 1.88 43.52 3.06
97 98 5.316167 AGTAGCTTTCAATGGTGAACATCA 58.684 37.500 0.00 0.00 43.52 3.07
98 99 5.163713 GGAGTAGCTTTCAATGGTGAACATC 60.164 44.000 0.00 0.00 43.52 3.06
99 100 4.702131 GGAGTAGCTTTCAATGGTGAACAT 59.298 41.667 0.00 0.00 43.52 2.71
100 101 4.072131 GGAGTAGCTTTCAATGGTGAACA 58.928 43.478 0.00 0.00 43.52 3.18
101 102 4.072131 TGGAGTAGCTTTCAATGGTGAAC 58.928 43.478 0.00 0.00 43.52 3.18
102 103 4.365514 TGGAGTAGCTTTCAATGGTGAA 57.634 40.909 0.00 0.00 42.12 3.18
103 104 4.225942 AGATGGAGTAGCTTTCAATGGTGA 59.774 41.667 0.00 0.00 0.00 4.02
104 105 4.521146 AGATGGAGTAGCTTTCAATGGTG 58.479 43.478 0.00 0.00 0.00 4.17
105 106 4.225942 TGAGATGGAGTAGCTTTCAATGGT 59.774 41.667 0.00 0.00 0.00 3.55
106 107 4.574013 GTGAGATGGAGTAGCTTTCAATGG 59.426 45.833 0.00 0.00 0.00 3.16
107 108 4.269603 CGTGAGATGGAGTAGCTTTCAATG 59.730 45.833 0.00 0.00 0.00 2.82
108 109 4.081420 ACGTGAGATGGAGTAGCTTTCAAT 60.081 41.667 0.00 0.00 0.00 2.57
109 110 3.258372 ACGTGAGATGGAGTAGCTTTCAA 59.742 43.478 0.00 0.00 0.00 2.69
110 111 2.826128 ACGTGAGATGGAGTAGCTTTCA 59.174 45.455 0.00 0.00 0.00 2.69
111 112 3.119459 TCACGTGAGATGGAGTAGCTTTC 60.119 47.826 15.76 0.00 0.00 2.62
112 113 2.826128 TCACGTGAGATGGAGTAGCTTT 59.174 45.455 15.76 0.00 0.00 3.51
113 114 2.447443 TCACGTGAGATGGAGTAGCTT 58.553 47.619 15.76 0.00 0.00 3.74
114 115 2.130272 TCACGTGAGATGGAGTAGCT 57.870 50.000 15.76 0.00 0.00 3.32
115 116 2.359214 TCATCACGTGAGATGGAGTAGC 59.641 50.000 24.41 0.00 44.30 3.58
116 117 4.612486 CGATCATCACGTGAGATGGAGTAG 60.612 50.000 24.41 9.72 44.30 2.57
117 118 3.251004 CGATCATCACGTGAGATGGAGTA 59.749 47.826 24.41 2.74 44.30 2.59
118 119 2.033927 CGATCATCACGTGAGATGGAGT 59.966 50.000 24.41 8.11 44.30 3.85
119 120 2.606551 CCGATCATCACGTGAGATGGAG 60.607 54.545 26.12 19.00 44.30 3.86
120 121 1.338020 CCGATCATCACGTGAGATGGA 59.662 52.381 26.12 20.22 44.30 3.41
121 122 1.338020 TCCGATCATCACGTGAGATGG 59.662 52.381 24.41 22.63 44.30 3.51
122 123 2.223572 TGTCCGATCATCACGTGAGATG 60.224 50.000 24.41 17.82 45.28 2.90
123 124 2.024414 TGTCCGATCATCACGTGAGAT 58.976 47.619 24.41 23.15 40.92 2.75
124 125 1.459450 TGTCCGATCATCACGTGAGA 58.541 50.000 24.41 19.81 40.92 3.27
125 126 2.122564 CATGTCCGATCATCACGTGAG 58.877 52.381 24.41 15.36 40.92 3.51
126 127 1.202405 CCATGTCCGATCATCACGTGA 60.202 52.381 22.48 22.48 42.06 4.35
127 128 1.211743 CCATGTCCGATCATCACGTG 58.788 55.000 9.94 9.94 0.00 4.49
128 129 0.824109 ACCATGTCCGATCATCACGT 59.176 50.000 0.00 0.00 0.00 4.49
129 130 1.939974 AACCATGTCCGATCATCACG 58.060 50.000 0.00 0.00 0.00 4.35
130 131 4.442706 ACTAAACCATGTCCGATCATCAC 58.557 43.478 0.00 0.00 0.00 3.06
131 132 4.753516 ACTAAACCATGTCCGATCATCA 57.246 40.909 0.00 0.00 0.00 3.07
132 133 5.116180 TCAACTAAACCATGTCCGATCATC 58.884 41.667 0.00 0.00 0.00 2.92
133 134 5.097742 TCAACTAAACCATGTCCGATCAT 57.902 39.130 0.00 0.00 0.00 2.45
134 135 4.545208 TCAACTAAACCATGTCCGATCA 57.455 40.909 0.00 0.00 0.00 2.92
135 136 6.147821 CCATATCAACTAAACCATGTCCGATC 59.852 42.308 0.00 0.00 0.00 3.69
136 137 5.997746 CCATATCAACTAAACCATGTCCGAT 59.002 40.000 0.00 0.00 0.00 4.18
137 138 5.129650 TCCATATCAACTAAACCATGTCCGA 59.870 40.000 0.00 0.00 0.00 4.55
138 139 5.364778 TCCATATCAACTAAACCATGTCCG 58.635 41.667 0.00 0.00 0.00 4.79
139 140 6.998074 TGATCCATATCAACTAAACCATGTCC 59.002 38.462 0.00 0.00 39.20 4.02
140 141 7.307396 CGTGATCCATATCAACTAAACCATGTC 60.307 40.741 0.00 0.00 43.69 3.06
141 142 6.483307 CGTGATCCATATCAACTAAACCATGT 59.517 38.462 0.00 0.00 43.69 3.21
142 143 6.566564 GCGTGATCCATATCAACTAAACCATG 60.567 42.308 0.00 0.00 43.69 3.66
143 144 5.470098 GCGTGATCCATATCAACTAAACCAT 59.530 40.000 0.00 0.00 43.69 3.55
144 145 4.814234 GCGTGATCCATATCAACTAAACCA 59.186 41.667 0.00 0.00 43.69 3.67
145 146 4.084537 CGCGTGATCCATATCAACTAAACC 60.085 45.833 0.00 0.00 43.69 3.27
146 147 4.743151 TCGCGTGATCCATATCAACTAAAC 59.257 41.667 5.77 0.00 43.69 2.01
147 148 4.939271 TCGCGTGATCCATATCAACTAAA 58.061 39.130 5.77 0.00 43.69 1.85
148 149 4.577834 TCGCGTGATCCATATCAACTAA 57.422 40.909 5.77 0.00 43.69 2.24
149 150 4.733850 GATCGCGTGATCCATATCAACTA 58.266 43.478 25.22 0.00 43.69 2.24
150 151 3.579709 GATCGCGTGATCCATATCAACT 58.420 45.455 25.22 0.00 43.69 3.16
151 152 3.980238 GATCGCGTGATCCATATCAAC 57.020 47.619 25.22 0.44 43.69 3.18
161 162 4.876125 AGTCATCTAAATGATCGCGTGAT 58.124 39.130 12.10 12.10 43.62 3.06
162 163 4.307443 AGTCATCTAAATGATCGCGTGA 57.693 40.909 5.77 0.00 43.62 4.35
163 164 5.340932 GTCTAGTCATCTAAATGATCGCGTG 59.659 44.000 5.77 0.00 43.62 5.34
164 165 5.453648 GTCTAGTCATCTAAATGATCGCGT 58.546 41.667 5.77 0.00 43.62 6.01
165 166 4.551509 CGTCTAGTCATCTAAATGATCGCG 59.448 45.833 0.00 0.00 43.62 5.87
166 167 4.854291 CCGTCTAGTCATCTAAATGATCGC 59.146 45.833 0.00 0.00 43.62 4.58
167 168 6.242508 TCCGTCTAGTCATCTAAATGATCG 57.757 41.667 0.00 0.00 43.62 3.69
168 169 7.598278 ACATCCGTCTAGTCATCTAAATGATC 58.402 38.462 0.00 0.00 43.62 2.92
169 170 7.531857 ACATCCGTCTAGTCATCTAAATGAT 57.468 36.000 0.00 0.00 43.62 2.45
170 171 6.961360 ACATCCGTCTAGTCATCTAAATGA 57.039 37.500 0.00 0.00 39.63 2.57
185 186 3.255888 TGCCACATAGATAGACATCCGTC 59.744 47.826 0.00 0.00 42.95 4.79
186 187 3.005897 GTGCCACATAGATAGACATCCGT 59.994 47.826 0.00 0.00 0.00 4.69
187 188 3.579709 GTGCCACATAGATAGACATCCG 58.420 50.000 0.00 0.00 0.00 4.18
188 189 3.307059 GGGTGCCACATAGATAGACATCC 60.307 52.174 0.00 0.00 0.00 3.51
189 190 3.307059 GGGGTGCCACATAGATAGACATC 60.307 52.174 0.00 0.00 0.00 3.06
190 191 2.639839 GGGGTGCCACATAGATAGACAT 59.360 50.000 0.00 0.00 0.00 3.06
191 192 2.047061 GGGGTGCCACATAGATAGACA 58.953 52.381 0.00 0.00 0.00 3.41
192 193 1.000955 CGGGGTGCCACATAGATAGAC 59.999 57.143 0.00 0.00 0.00 2.59
193 194 1.338107 CGGGGTGCCACATAGATAGA 58.662 55.000 0.00 0.00 0.00 1.98
194 195 0.321671 CCGGGGTGCCACATAGATAG 59.678 60.000 0.00 0.00 0.00 2.08
195 196 1.764571 GCCGGGGTGCCACATAGATA 61.765 60.000 2.18 0.00 0.00 1.98
196 197 3.120086 GCCGGGGTGCCACATAGAT 62.120 63.158 2.18 0.00 0.00 1.98
197 198 3.792736 GCCGGGGTGCCACATAGA 61.793 66.667 2.18 0.00 0.00 1.98
198 199 3.757248 GAGCCGGGGTGCCACATAG 62.757 68.421 2.05 0.00 0.00 2.23
227 228 2.027285 GGGTTGGCAATGCAAGGTAAAT 60.027 45.455 7.79 0.00 0.00 1.40
249 250 3.008266 TGTTGCCAGAAGACATGATCTCA 59.992 43.478 0.00 0.00 36.27 3.27
287 288 7.681939 AGTTTCAATAAAGCGGTGATTTCTA 57.318 32.000 0.00 0.00 0.00 2.10
325 327 4.403015 TGCAACTTGATGTAATGTCACG 57.597 40.909 0.00 0.00 0.00 4.35
393 395 1.716503 AGGCCCCCTTTATGTTCACTT 59.283 47.619 0.00 0.00 0.00 3.16
410 412 1.281899 GTAGATGTTGTGCTCGAGGC 58.718 55.000 15.58 7.24 42.22 4.70
421 423 0.541392 TCCGCTGCCATGTAGATGTT 59.459 50.000 0.00 0.00 0.00 2.71
468 470 0.251877 TGTCCACATCGGTGTCCCTA 60.252 55.000 0.00 0.00 43.71 3.53
502 504 2.166664 GTCTAACTGGATCGGACTGCTT 59.833 50.000 0.00 0.00 0.00 3.91
507 509 3.447944 AGGAAAGTCTAACTGGATCGGAC 59.552 47.826 0.00 0.00 0.00 4.79
723 725 2.636778 TTCGCCGTGAGCACTGTTCA 62.637 55.000 0.00 0.00 44.04 3.18
738 740 2.170273 GTTCCGTTCGTGCTTCGC 59.830 61.111 0.00 0.00 39.67 4.70
763 765 2.322658 ACGAGGTAAGGAGTTGAACCA 58.677 47.619 0.00 0.00 34.29 3.67
773 775 2.289195 TGCTGTTGGTTACGAGGTAAGG 60.289 50.000 0.00 0.00 0.00 2.69
774 776 3.034721 TGCTGTTGGTTACGAGGTAAG 57.965 47.619 0.00 0.00 0.00 2.34
811 814 4.021894 AGACTGACTGTTGTGGTATCACTC 60.022 45.833 7.81 1.53 43.94 3.51
915 918 3.369157 GGCCCAGTTCGTAAGTAAGTCAT 60.369 47.826 0.00 0.00 39.48 3.06
940 943 6.869913 CGGATTAACAGGTTTCTTGTAGTGTA 59.130 38.462 0.00 0.00 0.00 2.90
1066 1070 1.039068 TTTCGTGACGGTACCTCCAA 58.961 50.000 10.90 0.00 35.57 3.53
1116 1120 0.400093 GAAGGGGGAAGCTAGGCCTA 60.400 60.000 13.09 13.09 0.00 3.93
1230 1465 8.715998 CCATCTATTTTGATTAGGATCGTTGAG 58.284 37.037 0.00 0.00 34.91 3.02
1235 1470 7.661437 TGGTTCCATCTATTTTGATTAGGATCG 59.339 37.037 0.00 0.00 34.91 3.69
1249 1484 8.771521 TCATCATTCATTTTGGTTCCATCTAT 57.228 30.769 0.00 0.00 0.00 1.98
1290 1537 1.842052 TGGCCTCACGTGTCTGTATA 58.158 50.000 16.51 0.00 0.00 1.47
1372 1622 0.310543 TTCGTGCGCTTTGCTTCAAT 59.689 45.000 9.73 0.00 46.63 2.57
1387 1662 5.123227 TGACTTGAATGTTTTCTCCTTCGT 58.877 37.500 0.00 0.00 32.78 3.85
1506 1788 1.609208 GCCAATATGATCGTGGGCTT 58.391 50.000 15.80 0.00 38.37 4.35
1538 1829 3.617143 TTCGCGGTCGAGGGAGAGA 62.617 63.158 6.13 0.00 46.34 3.10
1546 1837 0.179129 GATAGGGTTTTCGCGGTCGA 60.179 55.000 6.13 0.00 43.89 4.20
1606 1904 3.244215 GCTGGACATGGATCTAAATCGGA 60.244 47.826 0.00 0.00 32.24 4.55
1641 1947 2.586245 CTGGAGATCGGCAGCCAA 59.414 61.111 13.30 0.00 0.00 4.52
1724 2039 2.043852 GGAGCCGGAGAGAGTGGA 60.044 66.667 5.05 0.00 0.00 4.02
1729 2044 4.144727 GAGGGGGAGCCGGAGAGA 62.145 72.222 5.05 0.00 0.00 3.10
1864 2432 2.693591 CAACTTCCATCTAGCCGTCCTA 59.306 50.000 0.00 0.00 0.00 2.94
1873 2441 3.454812 GGGTAGGCTTCAACTTCCATCTA 59.545 47.826 0.00 0.00 0.00 1.98
1947 2516 4.704103 ACCTCCTCTCCCAGCGCA 62.704 66.667 11.47 0.00 0.00 6.09
2182 2761 6.033831 CAGTCGCATCAACATTTATGGAAAAC 59.966 38.462 0.00 0.00 0.00 2.43
2268 2851 6.947464 ACTATGTAAGCACCCCACATATATC 58.053 40.000 0.00 0.00 35.28 1.63
2381 2972 7.362920 GCTTTAAGCATCCCATCTTTTCAGTTA 60.363 37.037 12.54 0.00 41.89 2.24
2724 4182 1.552337 AGCTACTGTCATGTGTGAGGG 59.448 52.381 0.00 0.00 34.36 4.30
2810 4268 1.674441 CTTGCACGATTCTGCCATGAT 59.326 47.619 0.00 0.00 36.21 2.45
2859 4317 9.613428 ACGAAGATATTTAAGGATCAACAATGA 57.387 29.630 0.00 0.00 40.57 2.57
3244 4717 7.482654 TCTATCAACCAAGCTTAAATGATCG 57.517 36.000 18.06 14.03 0.00 3.69
3382 4856 2.676121 CAATGGCCAGGGTCGCAA 60.676 61.111 13.05 0.00 0.00 4.85
3470 4944 6.330278 ACTTTTCTCAAGCCTAAAACAACAC 58.670 36.000 0.00 0.00 0.00 3.32
3657 5133 8.624776 CCAGATTTACCATGAGATTTAGGAAAC 58.375 37.037 0.00 0.00 0.00 2.78
3847 5325 1.561076 CTGGGACCATGAGGAACATCA 59.439 52.381 0.00 0.00 37.07 3.07
3894 5372 2.477863 GGAATGCGAAAACAAGGATCCG 60.478 50.000 5.98 0.00 0.00 4.18
3906 5384 3.674997 ACAAGAGCTTAAGGAATGCGAA 58.325 40.909 4.29 0.00 0.00 4.70
3918 5396 7.147949 CCATTTATTCTCCATCAACAAGAGCTT 60.148 37.037 0.00 0.00 0.00 3.74
4239 5717 6.642950 CGAACTACTCACTCTTGAAACAAGAT 59.357 38.462 13.34 3.08 0.00 2.40
4374 5852 5.293324 GGTAAAAGTTGAGTTTTTGCCAAGG 59.707 40.000 11.13 0.00 44.59 3.61
4588 6068 7.011109 ACACACATGACAAAACTCAAGTACTAC 59.989 37.037 0.00 0.00 0.00 2.73
4606 6086 5.451023 GTCAAACGACTAACAAACACACATG 59.549 40.000 0.00 0.00 0.00 3.21
4624 6104 3.042887 GTGTGCCGAATGAAAGTCAAAC 58.957 45.455 0.00 0.00 0.00 2.93
4719 6199 5.178061 TGTCTGTACTTGTTATCCTGCATG 58.822 41.667 0.00 0.00 0.00 4.06
4720 6200 5.420725 TGTCTGTACTTGTTATCCTGCAT 57.579 39.130 0.00 0.00 0.00 3.96
4744 6224 1.482593 CTCTACTTGGTACCCTGCAGG 59.517 57.143 26.87 26.87 43.78 4.85
4765 6245 1.170290 ACTTGTACCCTGCGGTTTGC 61.170 55.000 0.00 0.00 40.58 3.68
5020 6501 6.829811 ACCTCTGTATTCTTACTGTAGGACTC 59.170 42.308 0.00 0.00 33.66 3.36
5255 7054 2.676342 GGTTGTCACTCGTGTTCTTGTT 59.324 45.455 0.00 0.00 0.00 2.83
5297 7098 6.127563 GGAACCGGTACAATCCAATTTACATT 60.128 38.462 16.67 0.00 32.08 2.71
5520 7323 8.829612 CCCAATTTTGATCAAATATGCCTTTAC 58.170 33.333 21.10 0.00 33.60 2.01
5528 7331 8.269317 ACATTCAGCCCAATTTTGATCAAATAT 58.731 29.630 21.10 13.99 33.60 1.28
5664 7498 1.077716 GCCCAAACTAGGCCGTGAT 60.078 57.895 0.00 0.00 45.16 3.06
5728 7562 8.232513 CGCATCATAATTTGACATTGTAGCTAT 58.767 33.333 0.00 0.00 37.11 2.97
5729 7563 7.440856 TCGCATCATAATTTGACATTGTAGCTA 59.559 33.333 0.00 0.00 37.11 3.32
5817 7651 3.457380 ACATGACAGTCCTTAGCCATCAT 59.543 43.478 0.00 0.00 0.00 2.45
5858 7692 2.816083 CGCGCCCACGGATAACAA 60.816 61.111 0.00 0.00 40.57 2.83
5929 7763 1.194781 AGTGCGAGTCCATGGGTTCT 61.195 55.000 13.02 8.28 0.00 3.01
5940 7774 2.579201 CCGAATGGGAGTGCGAGT 59.421 61.111 0.00 0.00 38.47 4.18
5989 7823 3.009723 CCGTAAGAGTGTCATGGCAATT 58.990 45.455 0.00 0.00 43.02 2.32
6015 7849 2.122547 AGTGGGGAGTTGGTCGGT 60.123 61.111 0.00 0.00 0.00 4.69
6048 7882 1.450312 CCTTTGCTAGGCTGGGTCG 60.450 63.158 0.00 0.00 37.17 4.79
6079 7918 2.550606 GGACTGTTTATTTGCCACGACA 59.449 45.455 0.00 0.00 0.00 4.35
6124 7963 5.944007 ACATAACCTTGTGGACCTGTTATTC 59.056 40.000 0.00 0.00 37.04 1.75
6127 7966 4.595781 AGACATAACCTTGTGGACCTGTTA 59.404 41.667 0.00 0.00 37.04 2.41
6228 8069 1.766496 CTTTATGGGGAGGCCGTTAGA 59.234 52.381 0.00 0.00 0.00 2.10
6378 8238 9.612066 TTGTTTCTAAGTGATATGTGATGCATA 57.388 29.630 0.00 0.00 43.47 3.14
6610 8477 5.046014 AGAGGTGAATGCTTGAACTAGTGAT 60.046 40.000 0.00 0.00 0.00 3.06
6641 8508 6.105397 AGGTTGTCATGATCAAAATGCTTT 57.895 33.333 0.00 0.00 0.00 3.51
6696 8568 8.084073 ACGATTTCTTGAACATTGATTCATTGT 58.916 29.630 8.09 8.09 38.37 2.71


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

AutoCloner maintained by Alex Coulton.