Multiple sequence alignment - TraesCS3D01G236100

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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 TraesCS3D01G236100 chr3D 100.000 5918 0 0 1 5918 326700856 326694939 0.000000e+00 10929.0
1 TraesCS3D01G236100 chr3D 79.116 498 74 21 1121 1607 326552522 326552044 3.440000e-82 316.0
2 TraesCS3D01G236100 chr3D 94.706 170 9 0 5747 5916 63951218 63951387 1.260000e-66 265.0
3 TraesCS3D01G236100 chr3D 90.323 62 4 2 1840 1900 441125021 441124961 4.920000e-11 80.5
4 TraesCS3D01G236100 chr3D 100.000 32 0 0 1912 1943 582626034 582626003 6.400000e-05 60.2
5 TraesCS3D01G236100 chr3A 91.894 3343 120 39 1 3282 438602934 438606186 0.000000e+00 4532.0
6 TraesCS3D01G236100 chr3A 92.942 1346 63 18 3356 4683 438607348 438608679 0.000000e+00 1930.0
7 TraesCS3D01G236100 chr3A 95.280 678 31 1 4774 5451 438608678 438609354 0.000000e+00 1074.0
8 TraesCS3D01G236100 chr3A 95.669 254 11 0 5448 5701 438609460 438609713 5.520000e-110 409.0
9 TraesCS3D01G236100 chr3A 79.317 498 73 21 1121 1607 438611964 438612442 7.400000e-84 322.0
10 TraesCS3D01G236100 chr3A 93.069 101 3 2 4682 4778 269394411 269394311 1.720000e-30 145.0
11 TraesCS3D01G236100 chr3A 96.154 78 3 0 3280 3357 438607241 438607318 1.730000e-25 128.0
12 TraesCS3D01G236100 chr3A 94.737 38 2 0 1917 1954 513924986 513925023 6.400000e-05 60.2
13 TraesCS3D01G236100 chr3B 97.040 1757 45 5 3994 5746 423806889 423805136 0.000000e+00 2950.0
14 TraesCS3D01G236100 chr3B 95.633 1603 36 11 701 2285 423811354 423809768 0.000000e+00 2542.0
15 TraesCS3D01G236100 chr3B 98.111 1006 17 2 2279 3282 423809726 423808721 0.000000e+00 1751.0
16 TraesCS3D01G236100 chr3B 97.150 386 9 2 3280 3664 423807665 423807281 0.000000e+00 651.0
17 TraesCS3D01G236100 chr3B 96.791 374 11 1 3654 4026 423807261 423806888 1.810000e-174 623.0
18 TraesCS3D01G236100 chr3B 83.859 539 47 22 1 526 423812035 423811524 1.490000e-130 477.0
19 TraesCS3D01G236100 chr3B 78.600 500 79 21 1121 1605 423796453 423795967 7.450000e-79 305.0
20 TraesCS3D01G236100 chr3B 97.391 115 3 0 587 701 423811524 423811410 4.680000e-46 196.0
21 TraesCS3D01G236100 chr5D 95.833 168 7 0 5749 5916 306161264 306161431 7.560000e-69 272.0
22 TraesCS3D01G236100 chr5D 95.238 168 8 0 5751 5918 442613064 442612897 3.520000e-67 267.0
23 TraesCS3D01G236100 chr5D 93.714 175 11 0 5742 5916 216662647 216662821 4.550000e-66 263.0
24 TraesCS3D01G236100 chr5D 86.000 100 12 2 2971 3068 530069385 530069286 8.110000e-19 106.0
25 TraesCS3D01G236100 chr5D 88.506 87 7 3 2978 3062 482103273 482103358 1.050000e-17 102.0
26 TraesCS3D01G236100 chr7D 95.758 165 7 0 5752 5916 68847246 68847410 3.520000e-67 267.0
27 TraesCS3D01G236100 chr7D 95.210 167 8 0 5750 5916 83574340 83574174 1.260000e-66 265.0
28 TraesCS3D01G236100 chr7D 91.351 185 16 0 5732 5916 629864379 629864195 2.740000e-63 254.0
29 TraesCS3D01G236100 chr7D 93.878 49 2 1 3517 3564 3844965 3845013 8.230000e-09 73.1
30 TraesCS3D01G236100 chr7D 94.595 37 2 0 1918 1954 571471667 571471703 2.300000e-04 58.4
31 TraesCS3D01G236100 chr4D 95.783 166 5 1 5751 5916 196858813 196858976 3.520000e-67 267.0
32 TraesCS3D01G236100 chr4D 93.678 174 11 0 5743 5916 433766083 433765910 1.640000e-65 261.0
33 TraesCS3D01G236100 chr4D 93.000 100 4 1 4679 4775 494042369 494042468 6.180000e-30 143.0
34 TraesCS3D01G236100 chr4B 92.523 107 4 2 4682 4784 658516033 658515927 3.690000e-32 150.0
35 TraesCS3D01G236100 chr4B 90.566 106 7 2 4682 4784 595278881 595278776 2.880000e-28 137.0
36 TraesCS3D01G236100 chr4B 93.750 48 2 1 3518 3564 49466804 49466851 2.960000e-08 71.3
37 TraesCS3D01G236100 chr4B 92.000 50 3 1 3517 3565 191655747 191655698 1.060000e-07 69.4
38 TraesCS3D01G236100 chr6A 95.652 92 3 1 3811 3902 548408055 548408145 4.780000e-31 147.0
39 TraesCS3D01G236100 chr6A 87.395 119 8 6 4670 4782 570936865 570936982 4.810000e-26 130.0
40 TraesCS3D01G236100 chr6A 88.636 88 8 2 2977 3062 479543456 479543543 8.110000e-19 106.0
41 TraesCS3D01G236100 chr6A 93.617 47 1 2 3526 3571 79346285 79346330 1.060000e-07 69.4
42 TraesCS3D01G236100 chr7B 93.878 98 3 2 4682 4776 234791514 234791611 1.720000e-30 145.0
43 TraesCS3D01G236100 chr7B 94.505 91 5 0 3812 3902 153326933 153326843 2.220000e-29 141.0
44 TraesCS3D01G236100 chr7B 92.079 101 4 3 4678 4775 288709129 288709030 8.000000e-29 139.0
45 TraesCS3D01G236100 chr7B 88.506 87 9 1 2978 3063 482484951 482485037 2.920000e-18 104.0
46 TraesCS3D01G236100 chr4A 92.308 104 4 4 3803 3905 625404764 625404864 1.720000e-30 145.0
47 TraesCS3D01G236100 chr4A 91.837 49 3 1 3520 3567 629375445 629375397 3.830000e-07 67.6
48 TraesCS3D01G236100 chr7A 96.512 86 3 0 3817 3902 574129324 574129409 6.180000e-30 143.0
49 TraesCS3D01G236100 chr7A 92.405 79 5 1 2985 3062 190473058 190472980 1.740000e-20 111.0
50 TraesCS3D01G236100 chr6D 95.506 89 4 0 3817 3905 122992191 122992103 6.180000e-30 143.0
51 TraesCS3D01G236100 chr6D 92.727 55 2 2 3519 3571 62122873 62122927 1.770000e-10 78.7
52 TraesCS3D01G236100 chrUn 94.565 92 3 2 3813 3904 75423086 75423175 2.220000e-29 141.0
53 TraesCS3D01G236100 chrUn 94.595 37 2 0 1912 1948 385633267 385633231 2.300000e-04 58.4
54 TraesCS3D01G236100 chr1D 93.617 94 5 1 3812 3905 198901716 198901808 8.000000e-29 139.0
55 TraesCS3D01G236100 chr1D 88.136 118 9 2 4682 4796 37458231 37458346 1.030000e-27 135.0
56 TraesCS3D01G236100 chr1D 87.640 89 9 2 2976 3063 372835960 372836047 1.050000e-17 102.0
57 TraesCS3D01G236100 chr1D 84.762 105 9 6 2984 3081 480792851 480792955 1.360000e-16 99.0
58 TraesCS3D01G236100 chr1D 82.716 81 14 0 1212 1292 342873145 342873225 8.230000e-09 73.1
59 TraesCS3D01G236100 chr2D 81.098 164 21 8 1128 1289 92736704 92736859 8.050000e-24 122.0
60 TraesCS3D01G236100 chr2B 81.098 164 21 8 1128 1289 144021269 144021424 8.050000e-24 122.0
61 TraesCS3D01G236100 chr6B 85.149 101 11 3 2977 3075 518388985 518389083 3.770000e-17 100.0
62 TraesCS3D01G236100 chr6B 90.909 55 4 1 3518 3571 135867630 135867576 8.230000e-09 73.1
63 TraesCS3D01G236100 chr6B 95.349 43 2 0 1912 1954 101731985 101731943 1.060000e-07 69.4
64 TraesCS3D01G236100 chr6B 88.679 53 5 1 1996 2047 342982116 342982168 4.950000e-06 63.9
65 TraesCS3D01G236100 chr1B 91.803 61 4 1 1852 1912 277455175 277455234 3.800000e-12 84.2
66 TraesCS3D01G236100 chr1B 95.745 47 1 1 2002 2047 673957635 673957681 2.290000e-09 75.0
67 TraesCS3D01G236100 chr1B 93.023 43 3 0 1912 1954 439444772 439444730 4.950000e-06 63.9
68 TraesCS3D01G236100 chr1A 82.716 81 14 0 1212 1292 442606754 442606834 8.230000e-09 73.1
69 TraesCS3D01G236100 chr5B 93.478 46 2 1 3520 3564 634527000 634526955 3.830000e-07 67.6
70 TraesCS3D01G236100 chr5B 92.500 40 3 0 1873 1912 184767207 184767168 2.300000e-04 58.4
71 TraesCS3D01G236100 chr5B 96.875 32 0 1 1831 1862 56976262 56976232 1.100000e-02 52.8
72 TraesCS3D01G236100 chr2A 100.000 32 0 0 1912 1943 74782107 74782076 6.400000e-05 60.2


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 TraesCS3D01G236100 chr3D 326694939 326700856 5917 True 10929.000000 10929 100.000000 1 5918 1 chr3D.!!$R2 5917
1 TraesCS3D01G236100 chr3A 438602934 438612442 9508 False 1399.166667 4532 91.876000 1 5701 6 chr3A.!!$F2 5700
2 TraesCS3D01G236100 chr3B 423805136 423812035 6899 True 1312.857143 2950 95.139286 1 5746 7 chr3B.!!$R2 5745

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
236 260 2.107031 TGTCAGCCCATGGATAGGATTG 59.893 50.000 15.22 0.75 0.00 2.67 F
674 707 2.748132 CGCCCAAAGCCCTCAATATACA 60.748 50.000 0.00 0.00 38.78 2.29 F
1725 1849 3.941188 CTGGCACCGGTGTGAGGT 61.941 66.667 33.92 0.00 45.76 3.85 F
1947 2087 4.702831 TCAGCGACAATTAATATGGAGCA 58.297 39.130 14.85 0.00 0.00 4.26 F
2928 3121 0.754217 TGGAGATCTACCGTTCCCCG 60.754 60.000 1.43 0.00 0.00 5.73 F
4209 5572 1.000145 GCGTTTCGGTCTCTCCAATC 59.000 55.000 0.00 0.00 35.57 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 1676 0.249120 ACCATTTCATCTCGACGCCA 59.751 50.000 0.0 0.0 0.00 5.69 R
2585 2774 2.816672 TGCGATTCAAGTAACAATGGCA 59.183 40.909 0.0 0.0 40.23 4.92 R
2928 3121 2.876581 AGGGACTCACCAAATTGTTCC 58.123 47.619 0.0 0.0 41.20 3.62 R
3483 4771 2.950781 TCTGGAGATACTGCCTACTGG 58.049 52.381 0.0 0.0 0.00 4.00 R
4754 6118 0.115745 ACTCCCTCCGTCCCAAAGTA 59.884 55.000 0.0 0.0 0.00 2.24 R
5850 7418 0.037605 CGCTTTCGGTCTACAAGGGT 60.038 55.000 0.0 0.0 0.00 4.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 129 3.388024 TCTGTAAGTGGCCATGATACCTC 59.612 47.826 9.72 0.00 33.76 3.85
122 145 5.941058 TGATACCTCTATGCTCTAGTACTGC 59.059 44.000 5.39 0.59 0.00 4.40
130 153 8.105097 TCTATGCTCTAGTACTGCTAATCAAG 57.895 38.462 5.39 0.00 0.00 3.02
219 243 5.473066 TGTGTGAAGAGATTCTCATGTCA 57.527 39.130 15.83 12.17 32.06 3.58
236 260 2.107031 TGTCAGCCCATGGATAGGATTG 59.893 50.000 15.22 0.75 0.00 2.67
271 295 4.299586 TGTCAATCACCTTGCATCCTTA 57.700 40.909 0.00 0.00 34.66 2.69
349 373 8.850454 AATTACGGCAAACAATTGACATATAC 57.150 30.769 13.59 0.00 45.46 1.47
353 377 8.896320 ACGGCAAACAATTGACATATACTATA 57.104 30.769 13.59 0.00 45.46 1.31
389 414 5.540911 ACAAATTTGCTGGTTCACATTAGG 58.459 37.500 18.12 0.00 0.00 2.69
502 531 8.090788 AGTTTCCAGTATGACAGGTATACATT 57.909 34.615 5.01 0.00 39.69 2.71
503 532 9.209048 AGTTTCCAGTATGACAGGTATACATTA 57.791 33.333 5.01 0.00 39.69 1.90
565 594 2.821969 GAGGTCAGGAACATTGCACAAT 59.178 45.455 0.00 0.00 0.00 2.71
646 675 6.018425 CCGAGTTCACCTCATTGATTTCATAG 60.018 42.308 0.00 0.00 40.48 2.23
674 707 2.748132 CGCCCAAAGCCCTCAATATACA 60.748 50.000 0.00 0.00 38.78 2.29
821 910 4.934797 ATGATCTTGTTTCAAGGGAGGA 57.065 40.909 9.18 0.00 0.00 3.71
947 1036 4.792087 GGCAGTCCCGAAGTTTGA 57.208 55.556 0.00 0.00 0.00 2.69
1688 1812 7.435068 TTGACCTGAATTTTTCTGCTAGTAC 57.565 36.000 0.00 0.00 0.00 2.73
1725 1849 3.941188 CTGGCACCGGTGTGAGGT 61.941 66.667 33.92 0.00 45.76 3.85
1802 1926 5.197451 TGAGTTTCACTACAAACCACCATT 58.803 37.500 0.00 0.00 37.01 3.16
1885 2019 8.996988 TTTACTGCAACTTTTGTACTAAATCG 57.003 30.769 2.94 0.00 0.00 3.34
1900 2034 9.263538 TGTACTAAATCGGCGACAATTAATATT 57.736 29.630 13.76 0.00 0.00 1.28
1905 2039 5.509605 TCGGCGACAATTAATATTGATCG 57.490 39.130 4.99 10.22 43.12 3.69
1947 2087 4.702831 TCAGCGACAATTAATATGGAGCA 58.297 39.130 14.85 0.00 0.00 4.26
1986 2126 8.311650 ACTAAATCAGCGACATTAATATGGAC 57.688 34.615 0.00 0.00 36.01 4.02
2028 2168 5.679734 AATCAGCGACAACAATATGGATC 57.320 39.130 0.00 0.00 0.00 3.36
2585 2774 5.766150 TTACTGCTGCTACAATTGTTGTT 57.234 34.783 17.78 0.00 42.22 2.83
2928 3121 0.754217 TGGAGATCTACCGTTCCCCG 60.754 60.000 1.43 0.00 0.00 5.73
2966 3159 8.311836 TGAGTCCCTTCTACTTTGTAGTTTATG 58.688 37.037 4.89 0.00 35.78 1.90
3434 4722 9.765795 AGCAAGGTTGACATTTATATACTAGTC 57.234 33.333 0.00 0.00 0.00 2.59
3513 4801 6.100279 AGGCAGTATCTCCAGAAATGACAATA 59.900 38.462 0.00 0.00 0.00 1.90
3554 4842 9.626045 CTAAATCAAAGACACTTATTTTGGGAC 57.374 33.333 0.00 0.00 33.70 4.46
3557 4845 3.782656 AGACACTTATTTTGGGACGGT 57.217 42.857 0.00 0.00 0.00 4.83
3586 4875 9.984590 AGTACATAATAGGGGTGTGTTTAATTT 57.015 29.630 0.00 0.00 0.00 1.82
3601 4890 9.757227 TGTGTTTAATTTGGGTTTCTTATGAAG 57.243 29.630 0.00 0.00 33.28 3.02
3851 5170 5.516090 TCCAAAATAAGTGTCGCAGTTTTC 58.484 37.500 5.46 0.00 0.00 2.29
3954 5284 4.210120 CAGATTTGATACGGCAGCTACTTC 59.790 45.833 0.00 0.00 0.00 3.01
4180 5543 2.293677 AGTGGTATCGCTAACATCCTCG 59.706 50.000 0.00 0.00 30.95 4.63
4209 5572 1.000145 GCGTTTCGGTCTCTCCAATC 59.000 55.000 0.00 0.00 35.57 2.67
4217 5581 1.280421 GGTCTCTCCAATCTGCCAAGT 59.720 52.381 0.00 0.00 35.97 3.16
4321 5685 8.064222 CCAAGAACACATATATTCATCGACAAC 58.936 37.037 0.00 0.00 0.00 3.32
4622 5986 2.288886 ACAACTTACTGAACTCGGCTCC 60.289 50.000 0.00 0.00 0.00 4.70
4694 6058 6.947644 TTTTTGTTACTACTCCCTTTGTCC 57.052 37.500 0.00 0.00 0.00 4.02
4695 6059 4.628963 TTGTTACTACTCCCTTTGTCCC 57.371 45.455 0.00 0.00 0.00 4.46
4696 6060 3.589641 TGTTACTACTCCCTTTGTCCCA 58.410 45.455 0.00 0.00 0.00 4.37
4697 6061 3.975312 TGTTACTACTCCCTTTGTCCCAA 59.025 43.478 0.00 0.00 0.00 4.12
4698 6062 4.412858 TGTTACTACTCCCTTTGTCCCAAA 59.587 41.667 0.00 0.00 0.00 3.28
4699 6063 5.104024 TGTTACTACTCCCTTTGTCCCAAAA 60.104 40.000 0.00 0.00 0.00 2.44
4700 6064 4.741928 ACTACTCCCTTTGTCCCAAAAT 57.258 40.909 0.00 0.00 0.00 1.82
4701 6065 5.853572 ACTACTCCCTTTGTCCCAAAATA 57.146 39.130 0.00 0.00 0.00 1.40
4702 6066 6.208840 ACTACTCCCTTTGTCCCAAAATAA 57.791 37.500 0.00 0.00 0.00 1.40
4703 6067 6.246163 ACTACTCCCTTTGTCCCAAAATAAG 58.754 40.000 0.00 0.00 0.00 1.73
4704 6068 5.074746 ACTCCCTTTGTCCCAAAATAAGT 57.925 39.130 0.00 0.00 0.00 2.24
4705 6069 4.832823 ACTCCCTTTGTCCCAAAATAAGTG 59.167 41.667 0.00 0.00 0.00 3.16
4706 6070 4.810345 TCCCTTTGTCCCAAAATAAGTGT 58.190 39.130 0.00 0.00 0.00 3.55
4707 6071 4.830600 TCCCTTTGTCCCAAAATAAGTGTC 59.169 41.667 0.00 0.00 0.00 3.67
4708 6072 4.832823 CCCTTTGTCCCAAAATAAGTGTCT 59.167 41.667 0.00 0.00 0.00 3.41
4709 6073 5.048013 CCCTTTGTCCCAAAATAAGTGTCTC 60.048 44.000 0.00 0.00 0.00 3.36
4710 6074 5.534654 CCTTTGTCCCAAAATAAGTGTCTCA 59.465 40.000 0.00 0.00 0.00 3.27
4711 6075 6.040391 CCTTTGTCCCAAAATAAGTGTCTCAA 59.960 38.462 0.00 0.00 0.00 3.02
4712 6076 6.633500 TTGTCCCAAAATAAGTGTCTCAAG 57.367 37.500 0.00 0.00 0.00 3.02
4713 6077 5.070001 TGTCCCAAAATAAGTGTCTCAAGG 58.930 41.667 0.00 0.00 0.00 3.61
4714 6078 5.070685 GTCCCAAAATAAGTGTCTCAAGGT 58.929 41.667 0.00 0.00 0.00 3.50
4715 6079 5.535030 GTCCCAAAATAAGTGTCTCAAGGTT 59.465 40.000 0.00 0.00 0.00 3.50
4716 6080 6.713450 GTCCCAAAATAAGTGTCTCAAGGTTA 59.287 38.462 0.00 0.00 0.00 2.85
4717 6081 6.940298 TCCCAAAATAAGTGTCTCAAGGTTAG 59.060 38.462 0.00 0.00 0.00 2.34
4718 6082 6.715264 CCCAAAATAAGTGTCTCAAGGTTAGT 59.285 38.462 0.00 0.00 0.00 2.24
4719 6083 7.881232 CCCAAAATAAGTGTCTCAAGGTTAGTA 59.119 37.037 0.00 0.00 0.00 1.82
4720 6084 8.718734 CCAAAATAAGTGTCTCAAGGTTAGTAC 58.281 37.037 0.00 0.00 0.00 2.73
4721 6085 9.268268 CAAAATAAGTGTCTCAAGGTTAGTACA 57.732 33.333 0.00 0.00 0.00 2.90
4722 6086 9.841295 AAAATAAGTGTCTCAAGGTTAGTACAA 57.159 29.630 0.00 0.00 0.00 2.41
4723 6087 8.828688 AATAAGTGTCTCAAGGTTAGTACAAC 57.171 34.615 0.00 0.00 0.00 3.32
4724 6088 6.481434 AAGTGTCTCAAGGTTAGTACAACT 57.519 37.500 0.00 0.00 0.00 3.16
4725 6089 6.481434 AGTGTCTCAAGGTTAGTACAACTT 57.519 37.500 0.00 0.00 0.00 2.66
4726 6090 6.885922 AGTGTCTCAAGGTTAGTACAACTTT 58.114 36.000 0.00 0.00 0.00 2.66
4727 6091 6.761714 AGTGTCTCAAGGTTAGTACAACTTTG 59.238 38.462 18.34 18.34 38.21 2.77
4728 6092 6.537660 GTGTCTCAAGGTTAGTACAACTTTGT 59.462 38.462 21.04 0.00 44.86 2.83
4729 6093 7.707893 GTGTCTCAAGGTTAGTACAACTTTGTA 59.292 37.037 21.04 13.72 42.35 2.41
4730 6094 8.259411 TGTCTCAAGGTTAGTACAACTTTGTAA 58.741 33.333 21.04 13.51 44.46 2.41
4731 6095 9.101655 GTCTCAAGGTTAGTACAACTTTGTAAA 57.898 33.333 21.04 12.05 44.46 2.01
4732 6096 9.321562 TCTCAAGGTTAGTACAACTTTGTAAAG 57.678 33.333 21.04 15.57 44.46 1.85
4761 6125 9.490379 AGTATAAAGTTGAGACACTTACTTTGG 57.510 33.333 15.93 0.00 40.11 3.28
4762 6126 7.745620 ATAAAGTTGAGACACTTACTTTGGG 57.254 36.000 15.93 0.00 40.11 4.12
4763 6127 5.367945 AAGTTGAGACACTTACTTTGGGA 57.632 39.130 0.00 0.00 35.10 4.37
4764 6128 4.704965 AGTTGAGACACTTACTTTGGGAC 58.295 43.478 0.00 0.00 0.00 4.46
4765 6129 3.380479 TGAGACACTTACTTTGGGACG 57.620 47.619 0.00 0.00 0.00 4.79
4766 6130 2.036733 TGAGACACTTACTTTGGGACGG 59.963 50.000 0.00 0.00 0.00 4.79
4767 6131 2.298163 GAGACACTTACTTTGGGACGGA 59.702 50.000 0.00 0.00 0.00 4.69
4768 6132 2.299297 AGACACTTACTTTGGGACGGAG 59.701 50.000 0.00 0.00 0.00 4.63
4769 6133 1.346722 ACACTTACTTTGGGACGGAGG 59.653 52.381 0.00 0.00 0.00 4.30
4770 6134 0.981943 ACTTACTTTGGGACGGAGGG 59.018 55.000 0.00 0.00 0.00 4.30
4771 6135 1.272807 CTTACTTTGGGACGGAGGGA 58.727 55.000 0.00 0.00 0.00 4.20
4772 6136 1.207329 CTTACTTTGGGACGGAGGGAG 59.793 57.143 0.00 0.00 0.00 4.30
4965 6424 6.538742 TCTGTTGATTCGCCCTCTTAAATAAG 59.461 38.462 0.00 0.00 34.65 1.73
5012 6471 5.813513 TCTAACTTCGTAGGGTCCTTTTT 57.186 39.130 0.00 0.00 0.00 1.94
5044 6503 7.754625 TGTTGTTTAAGAGGAAGTAAACACAC 58.245 34.615 8.15 9.82 45.28 3.82
5252 6711 9.638239 AAAAAGCTTCGCAGATTCAATTTTATA 57.362 25.926 0.00 0.00 35.04 0.98
5647 7215 4.255833 GATTGCAATCCACCAGTTTTCA 57.744 40.909 26.03 0.00 0.00 2.69
5705 7273 9.381033 CTCCATATATGAGAGATTTTTGCTAGG 57.619 37.037 14.54 0.00 31.15 3.02
5706 7274 8.884323 TCCATATATGAGAGATTTTTGCTAGGT 58.116 33.333 14.54 0.00 0.00 3.08
5720 7288 4.216411 TGCTAGGTTAGATGGTTTGACC 57.784 45.455 0.00 0.00 39.22 4.02
5721 7289 3.054655 TGCTAGGTTAGATGGTTTGACCC 60.055 47.826 0.00 0.00 37.50 4.46
5746 7314 7.175641 CCCTCTTGACATTAGAAGACATGTTTT 59.824 37.037 0.00 0.00 33.62 2.43
5747 7315 8.019669 CCTCTTGACATTAGAAGACATGTTTTG 58.980 37.037 6.32 0.00 33.62 2.44
5748 7316 7.362662 TCTTGACATTAGAAGACATGTTTTGC 58.637 34.615 6.32 0.00 33.62 3.68
5749 7317 6.012658 TGACATTAGAAGACATGTTTTGCC 57.987 37.500 6.32 0.00 33.62 4.52
5751 7319 6.017400 ACATTAGAAGACATGTTTTGCCTG 57.983 37.500 6.32 1.97 28.73 4.85
5752 7320 5.536161 ACATTAGAAGACATGTTTTGCCTGT 59.464 36.000 6.32 2.54 28.73 4.00
5753 7321 6.040842 ACATTAGAAGACATGTTTTGCCTGTT 59.959 34.615 6.32 0.00 28.73 3.16
5754 7322 4.311816 AGAAGACATGTTTTGCCTGTTG 57.688 40.909 6.32 0.00 0.00 3.33
5756 7324 1.688197 AGACATGTTTTGCCTGTTGGG 59.312 47.619 0.00 0.00 38.36 4.12
5757 7325 1.686052 GACATGTTTTGCCTGTTGGGA 59.314 47.619 0.00 0.00 37.23 4.37
5758 7326 2.102252 GACATGTTTTGCCTGTTGGGAA 59.898 45.455 0.00 0.00 42.05 3.97
5762 7330 2.889200 TTTGCCTGTTGGGAAACGT 58.111 47.368 0.00 0.00 46.44 3.99
5763 7331 2.054232 TTTGCCTGTTGGGAAACGTA 57.946 45.000 0.00 0.00 46.44 3.57
5764 7332 1.600023 TTGCCTGTTGGGAAACGTAG 58.400 50.000 0.00 0.00 40.79 3.51
5766 7334 0.887387 GCCTGTTGGGAAACGTAGCA 60.887 55.000 0.00 0.00 37.23 3.49
5767 7335 1.821216 CCTGTTGGGAAACGTAGCAT 58.179 50.000 0.00 0.00 37.23 3.79
5768 7336 1.468520 CCTGTTGGGAAACGTAGCATG 59.531 52.381 0.00 0.00 37.23 4.06
5769 7337 0.878416 TGTTGGGAAACGTAGCATGC 59.122 50.000 10.51 10.51 0.00 4.06
5770 7338 0.878416 GTTGGGAAACGTAGCATGCA 59.122 50.000 21.98 2.77 0.00 3.96
5771 7339 1.268352 GTTGGGAAACGTAGCATGCAA 59.732 47.619 21.98 0.00 0.00 4.08
5772 7340 1.832883 TGGGAAACGTAGCATGCAAT 58.167 45.000 21.98 1.90 0.00 3.56
5773 7341 2.166829 TGGGAAACGTAGCATGCAATT 58.833 42.857 21.98 6.80 0.00 2.32
5776 7344 3.366883 GGGAAACGTAGCATGCAATTTCA 60.367 43.478 21.98 0.00 0.00 2.69
5777 7345 4.233789 GGAAACGTAGCATGCAATTTCAA 58.766 39.130 21.98 0.00 0.00 2.69
5778 7346 4.683781 GGAAACGTAGCATGCAATTTCAAA 59.316 37.500 21.98 0.00 0.00 2.69
5779 7347 5.176590 GGAAACGTAGCATGCAATTTCAAAA 59.823 36.000 21.98 0.00 0.00 2.44
5780 7348 6.292596 GGAAACGTAGCATGCAATTTCAAAAA 60.293 34.615 21.98 0.00 0.00 1.94
5797 7365 2.894307 AAAATTTCCTACGCTCACGC 57.106 45.000 0.00 0.00 45.53 5.34
5798 7366 1.803334 AAATTTCCTACGCTCACGCA 58.197 45.000 0.00 0.00 45.53 5.24
5799 7367 1.803334 AATTTCCTACGCTCACGCAA 58.197 45.000 0.00 0.00 45.53 4.85
5800 7368 1.359848 ATTTCCTACGCTCACGCAAG 58.640 50.000 0.00 0.00 45.53 4.01
5801 7369 0.315886 TTTCCTACGCTCACGCAAGA 59.684 50.000 0.00 0.00 45.53 3.02
5802 7370 0.530744 TTCCTACGCTCACGCAAGAT 59.469 50.000 0.00 0.00 45.53 2.40
5803 7371 0.100682 TCCTACGCTCACGCAAGATC 59.899 55.000 0.00 0.00 45.53 2.75
5804 7372 0.101399 CCTACGCTCACGCAAGATCT 59.899 55.000 0.00 0.00 45.53 2.75
5805 7373 1.333931 CCTACGCTCACGCAAGATCTA 59.666 52.381 0.00 0.00 45.53 1.98
5806 7374 2.030717 CCTACGCTCACGCAAGATCTAT 60.031 50.000 0.00 0.00 45.53 1.98
5807 7375 2.126914 ACGCTCACGCAAGATCTATC 57.873 50.000 0.00 0.00 45.53 2.08
5808 7376 1.678627 ACGCTCACGCAAGATCTATCT 59.321 47.619 0.00 0.00 45.53 1.98
5809 7377 2.879026 ACGCTCACGCAAGATCTATCTA 59.121 45.455 0.00 0.00 45.53 1.98
5814 7382 4.974399 TCACGCAAGATCTATCTAGGAGA 58.026 43.478 0.00 0.00 43.62 3.71
5815 7383 5.565509 TCACGCAAGATCTATCTAGGAGAT 58.434 41.667 0.00 7.55 38.77 2.75
5818 7386 4.157472 CGCAAGATCTATCTAGGAGATGCA 59.843 45.833 11.48 0.00 35.65 3.96
5820 7388 5.047448 GCAAGATCTATCTAGGAGATGCACA 60.047 44.000 11.48 0.00 35.37 4.57
5822 7390 6.588719 AGATCTATCTAGGAGATGCACAAC 57.411 41.667 11.48 0.00 35.37 3.32
5824 7392 6.552725 AGATCTATCTAGGAGATGCACAACAA 59.447 38.462 11.48 0.00 35.37 2.83
5825 7393 5.907207 TCTATCTAGGAGATGCACAACAAC 58.093 41.667 0.00 0.00 35.37 3.32
5826 7394 2.959516 TCTAGGAGATGCACAACAACG 58.040 47.619 0.00 0.00 0.00 4.10
5827 7395 2.560981 TCTAGGAGATGCACAACAACGA 59.439 45.455 0.00 0.00 0.00 3.85
5828 7396 1.800805 AGGAGATGCACAACAACGAG 58.199 50.000 0.00 0.00 0.00 4.18
5829 7397 1.344438 AGGAGATGCACAACAACGAGA 59.656 47.619 0.00 0.00 0.00 4.04
5830 7398 1.728971 GGAGATGCACAACAACGAGAG 59.271 52.381 0.00 0.00 0.00 3.20
5832 7400 0.798776 GATGCACAACAACGAGAGGG 59.201 55.000 0.00 0.00 0.00 4.30
5833 7401 0.606401 ATGCACAACAACGAGAGGGG 60.606 55.000 0.00 0.00 0.00 4.79
5834 7402 1.966451 GCACAACAACGAGAGGGGG 60.966 63.158 0.00 0.00 0.00 5.40
5835 7403 1.752198 CACAACAACGAGAGGGGGA 59.248 57.895 0.00 0.00 0.00 4.81
5837 7405 0.471211 ACAACAACGAGAGGGGGAGA 60.471 55.000 0.00 0.00 0.00 3.71
5838 7406 0.247736 CAACAACGAGAGGGGGAGAG 59.752 60.000 0.00 0.00 0.00 3.20
5839 7407 0.178929 AACAACGAGAGGGGGAGAGT 60.179 55.000 0.00 0.00 0.00 3.24
5840 7408 0.900647 ACAACGAGAGGGGGAGAGTG 60.901 60.000 0.00 0.00 0.00 3.51
5841 7409 0.900647 CAACGAGAGGGGGAGAGTGT 60.901 60.000 0.00 0.00 0.00 3.55
5842 7410 0.900647 AACGAGAGGGGGAGAGTGTG 60.901 60.000 0.00 0.00 0.00 3.82
5843 7411 1.304547 CGAGAGGGGGAGAGTGTGT 60.305 63.158 0.00 0.00 0.00 3.72
5844 7412 1.316706 CGAGAGGGGGAGAGTGTGTC 61.317 65.000 0.00 0.00 0.00 3.67
5845 7413 0.973496 GAGAGGGGGAGAGTGTGTCC 60.973 65.000 0.00 0.00 0.00 4.02
5847 7415 1.536662 AGGGGGAGAGTGTGTCCAC 60.537 63.158 0.00 0.00 42.17 4.02
5849 7417 2.207924 GGGGAGAGTGTGTCCACGT 61.208 63.158 0.00 0.00 46.56 4.49
5850 7418 0.896940 GGGGAGAGTGTGTCCACGTA 60.897 60.000 0.00 0.00 46.56 3.57
5852 7420 0.243095 GGAGAGTGTGTCCACGTACC 59.757 60.000 0.00 0.00 46.56 3.34
5853 7421 0.243095 GAGAGTGTGTCCACGTACCC 59.757 60.000 0.00 0.00 46.56 3.69
5854 7422 0.178970 AGAGTGTGTCCACGTACCCT 60.179 55.000 0.00 0.00 46.56 4.34
5855 7423 0.677842 GAGTGTGTCCACGTACCCTT 59.322 55.000 0.00 0.00 46.56 3.95
5856 7424 0.391597 AGTGTGTCCACGTACCCTTG 59.608 55.000 0.00 0.00 46.56 3.61
5857 7425 0.105408 GTGTGTCCACGTACCCTTGT 59.895 55.000 0.00 0.00 0.00 3.16
5858 7426 1.340889 GTGTGTCCACGTACCCTTGTA 59.659 52.381 0.00 0.00 0.00 2.41
5859 7427 1.614903 TGTGTCCACGTACCCTTGTAG 59.385 52.381 0.00 0.00 0.00 2.74
5860 7428 1.888512 GTGTCCACGTACCCTTGTAGA 59.111 52.381 0.00 0.00 0.00 2.59
5862 7430 1.203287 GTCCACGTACCCTTGTAGACC 59.797 57.143 0.00 0.00 0.00 3.85
5864 7432 1.167851 CACGTACCCTTGTAGACCGA 58.832 55.000 0.00 0.00 0.00 4.69
5865 7433 1.541147 CACGTACCCTTGTAGACCGAA 59.459 52.381 0.00 0.00 0.00 4.30
5866 7434 2.030007 CACGTACCCTTGTAGACCGAAA 60.030 50.000 0.00 0.00 0.00 3.46
5870 7438 0.245539 CCCTTGTAGACCGAAAGCGA 59.754 55.000 0.00 0.00 40.82 4.93
5871 7439 1.337447 CCCTTGTAGACCGAAAGCGAA 60.337 52.381 0.00 0.00 40.82 4.70
5872 7440 2.409975 CCTTGTAGACCGAAAGCGAAA 58.590 47.619 0.00 0.00 40.82 3.46
5873 7441 2.412089 CCTTGTAGACCGAAAGCGAAAG 59.588 50.000 0.00 0.00 40.82 2.62
5893 7461 3.837669 GTTTGACAACGCGGTTGAT 57.162 47.368 22.26 10.59 45.28 2.57
5894 7462 1.394697 GTTTGACAACGCGGTTGATG 58.605 50.000 22.26 11.18 45.28 3.07
5895 7463 1.018148 TTTGACAACGCGGTTGATGT 58.982 45.000 22.26 13.84 45.28 3.06
5896 7464 1.867166 TTGACAACGCGGTTGATGTA 58.133 45.000 22.26 7.55 45.28 2.29
5898 7466 1.269883 TGACAACGCGGTTGATGTAGT 60.270 47.619 22.26 4.69 45.28 2.73
5899 7467 1.389106 GACAACGCGGTTGATGTAGTC 59.611 52.381 22.26 10.01 45.28 2.59
5900 7468 1.269883 ACAACGCGGTTGATGTAGTCA 60.270 47.619 22.26 0.00 45.28 3.41
5901 7469 1.795872 CAACGCGGTTGATGTAGTCAA 59.204 47.619 12.47 0.00 45.28 3.18
5915 7483 9.950680 TTGATGTAGTCAAACTTTTTCTCATTC 57.049 29.630 0.00 0.00 43.64 2.67
5916 7484 9.342308 TGATGTAGTCAAACTTTTTCTCATTCT 57.658 29.630 0.00 0.00 32.78 2.40
5917 7485 9.604626 GATGTAGTCAAACTTTTTCTCATTCTG 57.395 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.335315 TGGAACTAACTGAAAGCACAACAG 59.665 41.667 0.00 0.00 37.60 3.16
50 51 7.012138 AGCATCAAATGACTGACATGAGATTAC 59.988 37.037 0.00 0.00 39.39 1.89
58 59 3.086282 TGCAGCATCAAATGACTGACAT 58.914 40.909 12.45 0.00 41.45 3.06
106 129 7.807433 CACTTGATTAGCAGTACTAGAGCATAG 59.193 40.741 6.47 0.00 30.79 2.23
122 145 7.409697 CGAATCAAATACCCACACTTGATTAG 58.590 38.462 8.44 5.74 44.49 1.73
130 153 2.088423 TGGCGAATCAAATACCCACAC 58.912 47.619 0.00 0.00 0.00 3.82
159 182 6.183359 GCGATTGAAACAGAAATACTTTGCTG 60.183 38.462 0.00 0.00 34.65 4.41
219 243 3.979501 AAACAATCCTATCCATGGGCT 57.020 42.857 13.02 2.14 0.00 5.19
236 260 6.646240 AGGTGATTGACAAATGCAACATAAAC 59.354 34.615 0.00 0.00 0.00 2.01
294 318 2.785713 TGACTGTCATCGTCGTCAAA 57.214 45.000 6.36 0.00 33.84 2.69
360 384 5.069648 TGTGAACCAGCAAATTTGTATCCAA 59.930 36.000 19.03 0.00 0.00 3.53
361 385 4.586421 TGTGAACCAGCAAATTTGTATCCA 59.414 37.500 19.03 7.76 0.00 3.41
363 387 7.489113 CCTAATGTGAACCAGCAAATTTGTATC 59.511 37.037 19.03 10.72 28.99 2.24
378 402 2.916716 CGCATTGTTGCCTAATGTGAAC 59.083 45.455 10.81 0.00 46.57 3.18
436 465 2.997986 GCATCTGCACATTGGAAAAAGG 59.002 45.455 0.00 0.00 41.59 3.11
462 491 9.886132 ATACTGGAAACTAGAAAATCGTATGTT 57.114 29.630 0.00 0.00 0.00 2.71
502 531 4.101114 TGAACTCTCCCTGGCAATAAGTA 58.899 43.478 0.00 0.00 0.00 2.24
503 532 2.912956 TGAACTCTCCCTGGCAATAAGT 59.087 45.455 0.00 0.00 0.00 2.24
508 537 2.237143 CACTATGAACTCTCCCTGGCAA 59.763 50.000 0.00 0.00 0.00 4.52
509 538 1.833630 CACTATGAACTCTCCCTGGCA 59.166 52.381 0.00 0.00 0.00 4.92
565 594 4.816385 CGAGCAGCATTCCCTAATTTTAGA 59.184 41.667 0.00 0.00 32.47 2.10
646 675 3.443925 GGCTTTGGGCGAAGAGGC 61.444 66.667 3.74 3.56 42.94 4.70
674 707 8.709308 AGTAGTATTCTGGAGCAATATTGTTCT 58.291 33.333 25.52 12.53 38.32 3.01
821 910 1.584175 ACGCGTACTCTCTGATCGAT 58.416 50.000 11.67 0.00 0.00 3.59
885 974 3.806507 GCCAAGGAGCCTGAGATAGAATG 60.807 52.174 0.00 0.00 0.00 2.67
913 1002 2.487428 CGTCGCCAGAGTCCAGAG 59.513 66.667 0.00 0.00 0.00 3.35
945 1034 5.064707 GTGCGACTTTCTGCCTTTTATATCA 59.935 40.000 0.00 0.00 0.00 2.15
946 1035 5.502606 GTGCGACTTTCTGCCTTTTATATC 58.497 41.667 0.00 0.00 0.00 1.63
947 1036 4.335594 GGTGCGACTTTCTGCCTTTTATAT 59.664 41.667 0.00 0.00 0.00 0.86
1351 1466 5.964168 GCGAGTTTCATCAGAATTCAATCAG 59.036 40.000 8.44 0.00 32.89 2.90
1352 1467 5.446340 CGCGAGTTTCATCAGAATTCAATCA 60.446 40.000 0.00 0.00 32.89 2.57
1353 1468 4.960354 CGCGAGTTTCATCAGAATTCAATC 59.040 41.667 0.00 0.00 32.89 2.67
1354 1469 4.393062 ACGCGAGTTTCATCAGAATTCAAT 59.607 37.500 15.93 0.00 46.40 2.57
1552 1676 0.249120 ACCATTTCATCTCGACGCCA 59.751 50.000 0.00 0.00 0.00 5.69
1679 1803 6.777213 TTTTTCTCTCCCTAGTACTAGCAG 57.223 41.667 22.39 18.78 31.95 4.24
1680 1804 7.620094 AGAATTTTTCTCTCCCTAGTACTAGCA 59.380 37.037 22.39 11.11 34.07 3.49
1688 1812 6.052360 GCCAGTAGAATTTTTCTCTCCCTAG 58.948 44.000 0.00 0.00 41.14 3.02
1725 1849 5.630415 AATATTACTACTCCCAGCAGCAA 57.370 39.130 0.00 0.00 0.00 3.91
1838 1964 7.984422 AAATCAGCGACATTAATATGGATCA 57.016 32.000 0.00 0.00 36.01 2.92
1885 2019 5.163854 CCTCCGATCAATATTAATTGTCGCC 60.164 44.000 0.00 0.00 42.66 5.54
1900 2034 4.837093 AATACAACTTTCCCTCCGATCA 57.163 40.909 0.00 0.00 0.00 2.92
1905 2039 6.458342 CGCTGATTTAATACAACTTTCCCTCC 60.458 42.308 0.00 0.00 0.00 4.30
1945 2085 5.938125 TGATTTAGTACAACTTTCCCTCTGC 59.062 40.000 0.00 0.00 0.00 4.26
1947 2087 6.174049 GCTGATTTAGTACAACTTTCCCTCT 58.826 40.000 0.00 0.00 0.00 3.69
1986 2126 8.439286 GCTGATTTAGTACAACTTTCTCTCAAG 58.561 37.037 0.00 0.00 0.00 3.02
2028 2168 4.220163 GGACCAAATATACTACTCCCTCCG 59.780 50.000 0.00 0.00 0.00 4.63
2585 2774 2.816672 TGCGATTCAAGTAACAATGGCA 59.183 40.909 0.00 0.00 40.23 4.92
2727 2920 8.417106 TCACTCTTGAATATCATCAGGTAGTTC 58.583 37.037 0.00 0.00 0.00 3.01
2928 3121 2.876581 AGGGACTCACCAAATTGTTCC 58.123 47.619 0.00 0.00 41.20 3.62
2966 3159 9.823647 TGGATCAGAGAGATTACAAGTTAATTC 57.176 33.333 0.00 0.00 37.00 2.17
3032 3225 4.250464 TCCGATCCATATTAATTGTCGCC 58.750 43.478 0.00 0.00 0.00 5.54
3434 4722 9.061610 GTTCGTGTGATTTAGAAAACAATATGG 57.938 33.333 0.00 0.00 0.00 2.74
3456 4744 5.982516 TCAAAAGAAAATGATGTTGGGTTCG 59.017 36.000 0.00 0.00 0.00 3.95
3483 4771 2.950781 TCTGGAGATACTGCCTACTGG 58.049 52.381 0.00 0.00 0.00 4.00
3554 4842 3.006537 CACCCCTATTATGTACTCCACCG 59.993 52.174 0.00 0.00 0.00 4.94
3557 4845 4.627015 ACACACCCCTATTATGTACTCCA 58.373 43.478 0.00 0.00 0.00 3.86
3851 5170 5.560183 CGCAGTTTTGAACTAACCCTAGTTG 60.560 44.000 2.37 0.00 46.31 3.16
4180 5543 1.393883 GACCGAAACGCCAGAATCTTC 59.606 52.381 0.00 0.00 0.00 2.87
4217 5581 0.823460 TGGCATCGTCTCATACAGCA 59.177 50.000 0.00 0.00 0.00 4.41
4245 5609 4.640771 AGTGAAAGTAGCATCCAGGAAA 57.359 40.909 0.00 0.00 0.00 3.13
4321 5685 7.447374 TGGTATCAACTAGGAAAACATGTTG 57.553 36.000 12.82 0.47 39.23 3.33
4622 5986 3.195825 AGAGGACCTTGTATTCAACGGAG 59.804 47.826 0.00 0.00 0.00 4.63
4690 6054 5.070001 CCTTGAGACACTTATTTTGGGACA 58.930 41.667 0.00 0.00 0.00 4.02
4691 6055 5.070685 ACCTTGAGACACTTATTTTGGGAC 58.929 41.667 0.00 0.00 0.00 4.46
4692 6056 5.319043 ACCTTGAGACACTTATTTTGGGA 57.681 39.130 0.00 0.00 0.00 4.37
4693 6057 6.715264 ACTAACCTTGAGACACTTATTTTGGG 59.285 38.462 0.00 0.00 0.00 4.12
4694 6058 7.745620 ACTAACCTTGAGACACTTATTTTGG 57.254 36.000 0.00 0.00 0.00 3.28
4695 6059 9.268268 TGTACTAACCTTGAGACACTTATTTTG 57.732 33.333 0.00 0.00 0.00 2.44
4696 6060 9.841295 TTGTACTAACCTTGAGACACTTATTTT 57.159 29.630 0.00 0.00 0.00 1.82
4697 6061 9.269453 GTTGTACTAACCTTGAGACACTTATTT 57.731 33.333 0.00 0.00 0.00 1.40
4698 6062 8.648693 AGTTGTACTAACCTTGAGACACTTATT 58.351 33.333 0.00 0.00 0.00 1.40
4699 6063 8.191534 AGTTGTACTAACCTTGAGACACTTAT 57.808 34.615 0.00 0.00 0.00 1.73
4700 6064 7.592885 AGTTGTACTAACCTTGAGACACTTA 57.407 36.000 0.00 0.00 0.00 2.24
4701 6065 6.481434 AGTTGTACTAACCTTGAGACACTT 57.519 37.500 0.00 0.00 0.00 3.16
4702 6066 6.481434 AAGTTGTACTAACCTTGAGACACT 57.519 37.500 0.00 0.00 0.00 3.55
4703 6067 6.537660 ACAAAGTTGTACTAACCTTGAGACAC 59.462 38.462 18.30 0.00 40.16 3.67
4704 6068 6.646267 ACAAAGTTGTACTAACCTTGAGACA 58.354 36.000 18.30 0.00 40.16 3.41
4705 6069 8.652810 TTACAAAGTTGTACTAACCTTGAGAC 57.347 34.615 18.30 0.00 42.84 3.36
4706 6070 9.321562 CTTTACAAAGTTGTACTAACCTTGAGA 57.678 33.333 18.30 8.92 42.84 3.27
4707 6071 9.106070 ACTTTACAAAGTTGTACTAACCTTGAG 57.894 33.333 18.30 11.76 46.52 3.02
4735 6099 9.490379 CCAAAGTAAGTGTCTCAACTTTATACT 57.510 33.333 0.00 0.00 39.50 2.12
4736 6100 8.718734 CCCAAAGTAAGTGTCTCAACTTTATAC 58.281 37.037 0.00 0.00 39.50 1.47
4737 6101 8.653191 TCCCAAAGTAAGTGTCTCAACTTTATA 58.347 33.333 0.00 0.00 39.50 0.98
4738 6102 7.444487 GTCCCAAAGTAAGTGTCTCAACTTTAT 59.556 37.037 0.00 0.00 39.50 1.40
4739 6103 6.764560 GTCCCAAAGTAAGTGTCTCAACTTTA 59.235 38.462 0.00 0.00 39.50 1.85
4740 6104 5.589050 GTCCCAAAGTAAGTGTCTCAACTTT 59.411 40.000 0.00 0.00 41.56 2.66
4741 6105 5.123936 GTCCCAAAGTAAGTGTCTCAACTT 58.876 41.667 0.00 0.00 42.89 2.66
4742 6106 4.704965 GTCCCAAAGTAAGTGTCTCAACT 58.295 43.478 0.00 0.00 0.00 3.16
4743 6107 3.493503 CGTCCCAAAGTAAGTGTCTCAAC 59.506 47.826 0.00 0.00 0.00 3.18
4744 6108 3.493699 CCGTCCCAAAGTAAGTGTCTCAA 60.494 47.826 0.00 0.00 0.00 3.02
4745 6109 2.036733 CCGTCCCAAAGTAAGTGTCTCA 59.963 50.000 0.00 0.00 0.00 3.27
4746 6110 2.298163 TCCGTCCCAAAGTAAGTGTCTC 59.702 50.000 0.00 0.00 0.00 3.36
4747 6111 2.299297 CTCCGTCCCAAAGTAAGTGTCT 59.701 50.000 0.00 0.00 0.00 3.41
4748 6112 2.612221 CCTCCGTCCCAAAGTAAGTGTC 60.612 54.545 0.00 0.00 0.00 3.67
4749 6113 1.346722 CCTCCGTCCCAAAGTAAGTGT 59.653 52.381 0.00 0.00 0.00 3.55
4750 6114 1.338769 CCCTCCGTCCCAAAGTAAGTG 60.339 57.143 0.00 0.00 0.00 3.16
4751 6115 0.981943 CCCTCCGTCCCAAAGTAAGT 59.018 55.000 0.00 0.00 0.00 2.24
4752 6116 1.207329 CTCCCTCCGTCCCAAAGTAAG 59.793 57.143 0.00 0.00 0.00 2.34
4753 6117 1.272807 CTCCCTCCGTCCCAAAGTAA 58.727 55.000 0.00 0.00 0.00 2.24
4754 6118 0.115745 ACTCCCTCCGTCCCAAAGTA 59.884 55.000 0.00 0.00 0.00 2.24
4755 6119 0.115745 TACTCCCTCCGTCCCAAAGT 59.884 55.000 0.00 0.00 0.00 2.66
4756 6120 1.497161 ATACTCCCTCCGTCCCAAAG 58.503 55.000 0.00 0.00 0.00 2.77
4757 6121 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
4758 6122 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
4759 6123 2.852714 TTAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
4760 6124 5.813513 TTAATTAATACTCCCTCCGTCCC 57.186 43.478 0.00 0.00 0.00 4.46
5012 6471 3.057586 TCCTCTTAAACAACAGGGGGAA 58.942 45.455 0.00 0.00 30.53 3.97
5013 6472 2.708759 TCCTCTTAAACAACAGGGGGA 58.291 47.619 0.00 0.00 30.53 4.81
5044 6503 1.377725 AGCCAAGATGAGCAACCGG 60.378 57.895 0.00 0.00 0.00 5.28
5073 6532 0.729140 GAACCAACATTTCAGCCGCG 60.729 55.000 0.00 0.00 0.00 6.46
5252 6711 9.912634 CAACACAAAGGTATGAGAAATGTTAAT 57.087 29.630 0.00 0.00 0.00 1.40
5593 7161 8.437360 AAAATTCTTGTTCAAGGAATTTCACC 57.563 30.769 21.04 0.00 44.00 4.02
5647 7215 6.229936 AGCAAATAGACATGCATTTTGGAT 57.770 33.333 17.96 0.00 44.95 3.41
5701 7269 3.780850 AGGGGTCAAACCATCTAACCTAG 59.219 47.826 0.00 0.00 41.02 3.02
5720 7288 5.738909 ACATGTCTTCTAATGTCAAGAGGG 58.261 41.667 0.00 0.00 31.33 4.30
5721 7289 7.678947 AAACATGTCTTCTAATGTCAAGAGG 57.321 36.000 0.00 0.00 35.99 3.69
5746 7314 0.887387 GCTACGTTTCCCAACAGGCA 60.887 55.000 0.00 0.00 34.51 4.75
5747 7315 0.887387 TGCTACGTTTCCCAACAGGC 60.887 55.000 0.00 0.00 34.51 4.85
5748 7316 1.468520 CATGCTACGTTTCCCAACAGG 59.531 52.381 0.00 0.00 32.54 4.00
5749 7317 1.135689 GCATGCTACGTTTCCCAACAG 60.136 52.381 11.37 0.00 32.54 3.16
5751 7319 0.878416 TGCATGCTACGTTTCCCAAC 59.122 50.000 20.33 0.00 0.00 3.77
5752 7320 1.610363 TTGCATGCTACGTTTCCCAA 58.390 45.000 20.33 0.00 0.00 4.12
5753 7321 1.832883 ATTGCATGCTACGTTTCCCA 58.167 45.000 20.33 0.00 0.00 4.37
5754 7322 2.939460 AATTGCATGCTACGTTTCCC 57.061 45.000 20.33 0.00 0.00 3.97
5756 7324 5.820926 TTTGAAATTGCATGCTACGTTTC 57.179 34.783 20.33 20.42 0.00 2.78
5757 7325 6.595772 TTTTTGAAATTGCATGCTACGTTT 57.404 29.167 20.33 13.51 0.00 3.60
5794 7362 4.157656 GCATCTCCTAGATAGATCTTGCGT 59.842 45.833 0.00 0.00 38.32 5.24
5795 7363 4.157472 TGCATCTCCTAGATAGATCTTGCG 59.843 45.833 0.00 0.00 36.48 4.85
5796 7364 5.047448 TGTGCATCTCCTAGATAGATCTTGC 60.047 44.000 0.00 0.69 38.32 4.01
5797 7365 6.587206 TGTGCATCTCCTAGATAGATCTTG 57.413 41.667 0.00 0.00 38.32 3.02
5798 7366 6.552725 TGTTGTGCATCTCCTAGATAGATCTT 59.447 38.462 0.00 0.00 38.32 2.40
5799 7367 6.073981 TGTTGTGCATCTCCTAGATAGATCT 58.926 40.000 0.00 0.00 40.86 2.75
5800 7368 6.338214 TGTTGTGCATCTCCTAGATAGATC 57.662 41.667 0.00 0.00 32.12 2.75
5801 7369 6.520272 GTTGTTGTGCATCTCCTAGATAGAT 58.480 40.000 0.00 0.00 32.12 1.98
5802 7370 5.450550 CGTTGTTGTGCATCTCCTAGATAGA 60.451 44.000 0.00 0.00 32.12 1.98
5803 7371 4.742167 CGTTGTTGTGCATCTCCTAGATAG 59.258 45.833 0.00 0.00 32.12 2.08
5804 7372 4.401202 TCGTTGTTGTGCATCTCCTAGATA 59.599 41.667 0.00 0.00 32.12 1.98
5805 7373 3.195610 TCGTTGTTGTGCATCTCCTAGAT 59.804 43.478 0.00 0.00 34.74 1.98
5806 7374 2.560981 TCGTTGTTGTGCATCTCCTAGA 59.439 45.455 0.00 0.00 0.00 2.43
5807 7375 2.926200 CTCGTTGTTGTGCATCTCCTAG 59.074 50.000 0.00 0.00 0.00 3.02
5808 7376 2.560981 TCTCGTTGTTGTGCATCTCCTA 59.439 45.455 0.00 0.00 0.00 2.94
5809 7377 1.344438 TCTCGTTGTTGTGCATCTCCT 59.656 47.619 0.00 0.00 0.00 3.69
5814 7382 0.606401 CCCCTCTCGTTGTTGTGCAT 60.606 55.000 0.00 0.00 0.00 3.96
5815 7383 1.227823 CCCCTCTCGTTGTTGTGCA 60.228 57.895 0.00 0.00 0.00 4.57
5818 7386 0.471211 TCTCCCCCTCTCGTTGTTGT 60.471 55.000 0.00 0.00 0.00 3.32
5820 7388 0.178929 ACTCTCCCCCTCTCGTTGTT 60.179 55.000 0.00 0.00 0.00 2.83
5822 7390 0.900647 ACACTCTCCCCCTCTCGTTG 60.901 60.000 0.00 0.00 0.00 4.10
5824 7392 1.304547 CACACTCTCCCCCTCTCGT 60.305 63.158 0.00 0.00 0.00 4.18
5825 7393 1.304547 ACACACTCTCCCCCTCTCG 60.305 63.158 0.00 0.00 0.00 4.04
5826 7394 0.973496 GGACACACTCTCCCCCTCTC 60.973 65.000 0.00 0.00 0.00 3.20
5827 7395 1.079438 GGACACACTCTCCCCCTCT 59.921 63.158 0.00 0.00 0.00 3.69
5828 7396 1.229209 TGGACACACTCTCCCCCTC 60.229 63.158 0.00 0.00 0.00 4.30
5829 7397 1.536662 GTGGACACACTCTCCCCCT 60.537 63.158 0.00 0.00 44.29 4.79
5830 7398 2.943978 CGTGGACACACTCTCCCCC 61.944 68.421 3.12 0.00 45.50 5.40
5832 7400 0.243095 GTACGTGGACACACTCTCCC 59.757 60.000 0.00 0.00 45.50 4.30
5833 7401 0.243095 GGTACGTGGACACACTCTCC 59.757 60.000 0.00 0.00 45.50 3.71
5834 7402 0.243095 GGGTACGTGGACACACTCTC 59.757 60.000 0.00 0.00 45.50 3.20
5835 7403 0.178970 AGGGTACGTGGACACACTCT 60.179 55.000 0.00 0.00 45.50 3.24
5837 7405 0.391597 CAAGGGTACGTGGACACACT 59.608 55.000 0.00 0.00 45.50 3.55
5838 7406 0.105408 ACAAGGGTACGTGGACACAC 59.895 55.000 0.00 0.00 44.23 3.82
5839 7407 1.614903 CTACAAGGGTACGTGGACACA 59.385 52.381 0.00 0.00 0.00 3.72
5840 7408 1.888512 TCTACAAGGGTACGTGGACAC 59.111 52.381 0.00 0.00 0.00 3.67
5841 7409 1.888512 GTCTACAAGGGTACGTGGACA 59.111 52.381 0.00 0.00 41.67 4.02
5842 7410 1.203287 GGTCTACAAGGGTACGTGGAC 59.797 57.143 0.00 6.59 41.42 4.02
5843 7411 1.549203 GGTCTACAAGGGTACGTGGA 58.451 55.000 0.00 0.00 0.00 4.02
5844 7412 0.171903 CGGTCTACAAGGGTACGTGG 59.828 60.000 0.00 0.00 0.00 4.94
5845 7413 1.167851 TCGGTCTACAAGGGTACGTG 58.832 55.000 0.00 0.00 0.00 4.49
5847 7415 2.872370 CTTTCGGTCTACAAGGGTACG 58.128 52.381 0.00 0.00 0.00 3.67
5849 7417 1.203052 CGCTTTCGGTCTACAAGGGTA 59.797 52.381 0.00 0.00 0.00 3.69
5850 7418 0.037605 CGCTTTCGGTCTACAAGGGT 60.038 55.000 0.00 0.00 0.00 4.34
5852 7420 2.074547 TTCGCTTTCGGTCTACAAGG 57.925 50.000 0.00 0.00 36.13 3.61
5853 7421 2.159827 GCTTTCGCTTTCGGTCTACAAG 60.160 50.000 0.00 0.00 36.13 3.16
5854 7422 1.796459 GCTTTCGCTTTCGGTCTACAA 59.204 47.619 0.00 0.00 36.13 2.41
5855 7423 1.425412 GCTTTCGCTTTCGGTCTACA 58.575 50.000 0.00 0.00 36.13 2.74
5856 7424 0.365859 CGCTTTCGCTTTCGGTCTAC 59.634 55.000 0.00 0.00 36.13 2.59
5857 7425 0.038892 ACGCTTTCGCTTTCGGTCTA 60.039 50.000 0.00 0.00 39.84 2.59
5858 7426 0.878961 AACGCTTTCGCTTTCGGTCT 60.879 50.000 0.00 0.00 39.84 3.85
5859 7427 0.041576 AAACGCTTTCGCTTTCGGTC 60.042 50.000 0.00 0.00 39.84 4.79
5860 7428 0.316689 CAAACGCTTTCGCTTTCGGT 60.317 50.000 0.00 0.00 39.84 4.69
5862 7430 1.035032 GTCAAACGCTTTCGCTTTCG 58.965 50.000 0.00 0.00 39.84 3.46
5864 7432 2.182014 GTTGTCAAACGCTTTCGCTTT 58.818 42.857 0.00 0.00 39.84 3.51
5865 7433 1.822581 GTTGTCAAACGCTTTCGCTT 58.177 45.000 0.00 0.00 39.84 4.68
5866 7434 3.526825 GTTGTCAAACGCTTTCGCT 57.473 47.368 0.00 0.00 39.84 4.93
5875 7443 1.268335 ACATCAACCGCGTTGTCAAAC 60.268 47.619 16.97 0.00 43.23 2.93
5879 7447 1.389106 GACTACATCAACCGCGTTGTC 59.611 52.381 16.97 5.64 43.23 3.18
5880 7448 1.269883 TGACTACATCAACCGCGTTGT 60.270 47.619 16.97 9.99 43.23 3.32
5881 7449 1.424403 TGACTACATCAACCGCGTTG 58.576 50.000 4.92 10.14 43.99 4.10
5882 7450 2.157834 TTGACTACATCAACCGCGTT 57.842 45.000 4.92 0.00 42.62 4.84
5883 7451 3.898380 TTGACTACATCAACCGCGT 57.102 47.368 4.92 0.00 42.62 6.01
5889 7457 9.950680 GAATGAGAAAAAGTTTGACTACATCAA 57.049 29.630 0.00 0.00 45.92 2.57
5891 7459 9.604626 CAGAATGAGAAAAAGTTTGACTACATC 57.395 33.333 0.00 0.00 39.69 3.06


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

AutoCloner maintained by Alex Coulton.