Multiple sequence alignment - TraesCS2D01G362000

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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 TraesCS2D01G362000 chr2D 100.000 4046 0 0 1 4046 468094854 468098899 0.000000e+00 7472.0
1 TraesCS2D01G362000 chr2D 80.654 765 101 28 607 1361 392512105 392512832 2.130000e-152 549.0
2 TraesCS2D01G362000 chr2D 77.197 421 56 20 2228 2625 392513692 392514095 4.100000e-50 209.0
3 TraesCS2D01G362000 chr2D 92.391 92 7 0 1 92 392510905 392510996 9.120000e-27 132.0
4 TraesCS2D01G362000 chr2D 81.928 83 15 0 3709 3791 536530656 536530574 2.020000e-08 71.3
5 TraesCS2D01G362000 chr2D 81.081 74 14 0 3718 3791 144553804 144553731 4.370000e-05 60.2
6 TraesCS2D01G362000 chr2B 95.952 2001 59 11 1 1991 546423956 546425944 0.000000e+00 3227.0
7 TraesCS2D01G362000 chr2B 77.928 1554 228 56 450 1974 464433617 464435084 0.000000e+00 863.0
8 TraesCS2D01G362000 chr2B 96.107 488 9 3 2286 2767 546426306 546426789 0.000000e+00 787.0
9 TraesCS2D01G362000 chr2B 85.515 573 34 14 3163 3688 546427154 546427724 1.640000e-153 553.0
10 TraesCS2D01G362000 chr2B 96.667 300 10 0 2767 3066 546426847 546427146 2.170000e-137 499.0
11 TraesCS2D01G362000 chr2B 95.500 200 9 0 2088 2287 546425946 546426145 1.810000e-83 320.0
12 TraesCS2D01G362000 chr2B 91.489 235 17 2 3812 4046 546427802 546428033 1.810000e-83 320.0
13 TraesCS2D01G362000 chr2B 81.720 372 48 16 2768 3121 464441891 464442260 3.960000e-75 292.0
14 TraesCS2D01G362000 chr2B 76.886 411 62 21 2231 2625 464441115 464441508 6.860000e-48 202.0
15 TraesCS2D01G362000 chr2B 92.391 92 7 0 1 92 464432537 464432628 9.120000e-27 132.0
16 TraesCS2D01G362000 chr3B 78.182 2035 323 79 1 1994 380868369 380870323 0.000000e+00 1186.0
17 TraesCS2D01G362000 chr3B 79.545 352 53 12 3712 4044 403402995 403402644 2.430000e-57 233.0
18 TraesCS2D01G362000 chr3B 90.909 55 3 2 3445 3498 125879585 125879638 5.610000e-09 73.1
19 TraesCS2D01G362000 chr3B 90.909 55 3 2 3445 3498 125897276 125897329 5.610000e-09 73.1
20 TraesCS2D01G362000 chr2A 78.466 1421 206 42 450 1850 530351497 530352837 0.000000e+00 837.0
21 TraesCS2D01G362000 chr2A 84.211 304 34 9 2797 3087 530355685 530355987 2.380000e-72 283.0
22 TraesCS2D01G362000 chr2A 81.871 171 29 1 3828 3996 14907305 14907475 4.220000e-30 143.0
23 TraesCS2D01G362000 chr2A 91.304 92 8 0 1 92 530350600 530350691 4.250000e-25 126.0
24 TraesCS2D01G362000 chr3D 79.023 348 56 11 1 338 288096347 288096687 5.260000e-54 222.0
25 TraesCS2D01G362000 chr3D 99.020 102 1 0 1988 2089 290583814 290583915 2.480000e-42 183.0
26 TraesCS2D01G362000 chr3A 78.448 348 48 17 1 338 377648298 377648628 6.860000e-48 202.0
27 TraesCS2D01G362000 chr6A 100.000 98 0 0 1993 2090 23355174 23355077 8.930000e-42 182.0
28 TraesCS2D01G362000 chr6A 94.231 52 2 1 3457 3507 59711300 59711351 1.210000e-10 78.7
29 TraesCS2D01G362000 chr6B 78.498 293 48 15 3765 4046 440568252 440568540 1.160000e-40 178.0
30 TraesCS2D01G362000 chr7B 98.000 100 2 0 1993 2092 159510698 159510599 1.490000e-39 174.0
31 TraesCS2D01G362000 chr7B 75.942 345 66 12 3713 4046 477380795 477381133 1.160000e-35 161.0
32 TraesCS2D01G362000 chr7B 84.906 106 13 2 3944 4046 210802220 210802325 1.990000e-18 104.0
33 TraesCS2D01G362000 chr7B 85.075 67 10 0 3711 3777 238600030 238600096 7.260000e-08 69.4
34 TraesCS2D01G362000 chr7B 84.375 64 8 2 3713 3775 654708013 654707951 1.210000e-05 62.1
35 TraesCS2D01G362000 chr5D 93.913 115 7 0 1978 2092 513514550 513514664 1.490000e-39 174.0
36 TraesCS2D01G362000 chr4D 95.413 109 5 0 1992 2100 306239611 306239503 1.490000e-39 174.0
37 TraesCS2D01G362000 chr4D 90.625 64 4 2 3454 3516 81986954 81986892 2.590000e-12 84.2
38 TraesCS2D01G362000 chr4D 90.909 55 5 0 3444 3498 100565926 100565980 1.560000e-09 75.0
39 TraesCS2D01G362000 chr7D 95.455 110 2 3 1993 2101 489010687 489010794 5.380000e-39 172.0
40 TraesCS2D01G362000 chr7D 93.478 46 3 0 3732 3777 259299864 259299909 7.260000e-08 69.4
41 TraesCS2D01G362000 chr1A 93.805 113 7 0 1990 2102 202096701 202096813 1.930000e-38 171.0
42 TraesCS2D01G362000 chr1B 92.500 120 4 3 1986 2102 334446242 334446125 2.500000e-37 167.0
43 TraesCS2D01G362000 chr4A 95.192 104 4 1 1992 2095 543742079 543742181 3.240000e-36 163.0
44 TraesCS2D01G362000 chr4A 94.118 51 3 0 3456 3506 643061157 643061207 1.210000e-10 78.7
45 TraesCS2D01G362000 chr7A 76.056 355 60 17 3710 4044 173641109 173641458 1.160000e-35 161.0
46 TraesCS2D01G362000 chr6D 80.952 168 28 2 3873 4037 434506757 434506923 3.280000e-26 130.0
47 TraesCS2D01G362000 chr6D 97.872 47 1 0 3452 3498 104977544 104977590 9.320000e-12 82.4
48 TraesCS2D01G362000 chr5B 80.153 131 16 8 3730 3854 237820593 237820719 5.570000e-14 89.8
49 TraesCS2D01G362000 chr5A 89.831 59 4 2 3440 3498 390157085 390157029 1.560000e-09 75.0
50 TraesCS2D01G362000 chr5A 84.932 73 11 0 3710 3782 580866412 580866340 1.560000e-09 75.0


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 TraesCS2D01G362000 chr2D 468094854 468098899 4045 False 7472.000000 7472 100.000000 1 4046 1 chr2D.!!$F1 4045
1 TraesCS2D01G362000 chr2D 392510905 392514095 3190 False 296.666667 549 83.414000 1 2625 3 chr2D.!!$F2 2624
2 TraesCS2D01G362000 chr2B 546423956 546428033 4077 False 951.000000 3227 93.538333 1 4046 6 chr2B.!!$F3 4045
3 TraesCS2D01G362000 chr2B 464432537 464435084 2547 False 497.500000 863 85.159500 1 1974 2 chr2B.!!$F1 1973
4 TraesCS2D01G362000 chr2B 464441115 464442260 1145 False 247.000000 292 79.303000 2231 3121 2 chr2B.!!$F2 890
5 TraesCS2D01G362000 chr3B 380868369 380870323 1954 False 1186.000000 1186 78.182000 1 1994 1 chr3B.!!$F3 1993
6 TraesCS2D01G362000 chr2A 530350600 530355987 5387 False 415.333333 837 84.660333 1 3087 3 chr2A.!!$F2 3086

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
594 1470 0.396556 ACACGGGGAAGCAAAACCTT 60.397 50.0 0.0 0.0 0.0 3.50 F
2007 4722 0.252103 AAGCTACTCCCTCCGTTCCA 60.252 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2072 4787 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.0 0.0 0.0 0.0 3.53 R
3805 7215 0.038166 TTCAATGGGGAGAGGTGTGC 59.962 55.0 0.0 0.0 0.0 4.57 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
131 133 1.663702 CGTCCTTCTGTCGCGGTTT 60.664 57.895 6.13 0.00 0.00 3.27
244 263 0.533308 TACCGTGGTGTTTGCCTGTC 60.533 55.000 0.72 0.00 0.00 3.51
370 391 8.752005 TGGAATATTAAACCATCTCCTTTCTG 57.248 34.615 0.00 0.00 0.00 3.02
594 1470 0.396556 ACACGGGGAAGCAAAACCTT 60.397 50.000 0.00 0.00 0.00 3.50
659 1550 7.482169 TCCATATCCACTATGTATCTTGGTC 57.518 40.000 0.00 0.00 36.27 4.02
702 1598 8.858094 TGCAAATCCATGCTAATGTGATTATTA 58.142 29.630 0.67 0.00 46.54 0.98
881 1778 5.599999 AGACATTGAGGTGAGTGGTATAC 57.400 43.478 0.00 0.00 0.00 1.47
1018 1918 1.073444 AGATGGGCGATGCAATGAGAT 59.927 47.619 0.00 0.00 0.00 2.75
1019 1919 1.884579 GATGGGCGATGCAATGAGATT 59.115 47.619 0.00 0.00 0.00 2.40
1131 2032 6.151817 GTCATCTGGCCATTCTTTTAAGTTCT 59.848 38.462 5.51 0.00 0.00 3.01
1386 2306 2.058705 TGAAATGGTGGTCCTGGTACA 58.941 47.619 0.00 0.00 34.23 2.90
1401 2321 8.036575 GGTCCTGGTACAATTTTATTAAAACCC 58.963 37.037 3.78 1.59 38.70 4.11
1429 2349 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
1492 2420 9.474313 ACAGTAGAAGAACTAGATGAAGAAGAT 57.526 33.333 0.00 0.00 0.00 2.40
1654 2593 3.361794 ACAGATCGAAGATGATGACGG 57.638 47.619 0.00 0.00 45.12 4.79
1676 2618 3.059597 GCGATGATGAAGGTTTCGGTATG 60.060 47.826 0.00 0.00 0.00 2.39
1858 2817 4.689612 AGTTGACCTGACACAGTTACAT 57.310 40.909 0.00 0.00 0.00 2.29
1869 2828 9.599866 CCTGACACAGTTACATCTCAAAATATA 57.400 33.333 0.00 0.00 0.00 0.86
1921 3222 4.034975 GCTTGTTCTGTATGAAGCATCTCC 59.965 45.833 0.00 0.00 40.47 3.71
1999 4714 7.833285 TTTTTCAAAATGTAAGCTACTCCCT 57.167 32.000 0.00 0.00 0.00 4.20
2000 4715 7.448748 TTTTCAAAATGTAAGCTACTCCCTC 57.551 36.000 0.00 0.00 0.00 4.30
2001 4716 5.099042 TCAAAATGTAAGCTACTCCCTCC 57.901 43.478 0.00 0.00 0.00 4.30
2002 4717 3.821421 AAATGTAAGCTACTCCCTCCG 57.179 47.619 0.00 0.00 0.00 4.63
2003 4718 2.456073 ATGTAAGCTACTCCCTCCGT 57.544 50.000 0.00 0.00 0.00 4.69
2004 4719 2.226962 TGTAAGCTACTCCCTCCGTT 57.773 50.000 0.00 0.00 0.00 4.44
2005 4720 2.097825 TGTAAGCTACTCCCTCCGTTC 58.902 52.381 0.00 0.00 0.00 3.95
2006 4721 1.408340 GTAAGCTACTCCCTCCGTTCC 59.592 57.143 0.00 0.00 0.00 3.62
2007 4722 0.252103 AAGCTACTCCCTCCGTTCCA 60.252 55.000 0.00 0.00 0.00 3.53
2008 4723 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2009 4724 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
2010 4725 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
2011 4726 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
2012 4727 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
2013 4728 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2014 4729 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2015 4730 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2016 4731 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2017 4732 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2018 4733 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2019 4734 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2020 4735 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2021 4736 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2022 4737 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2023 4738 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2024 4739 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2025 4740 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2026 4741 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2027 4742 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2028 4743 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2029 4744 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2030 4745 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
2031 4746 8.531146 CCAAAATAGATGACCCAACTTTGTATT 58.469 33.333 0.00 0.00 0.00 1.89
2035 4750 9.975218 AATAGATGACCCAACTTTGTATTAACT 57.025 29.630 0.00 0.00 0.00 2.24
2036 4751 9.975218 ATAGATGACCCAACTTTGTATTAACTT 57.025 29.630 0.00 0.00 0.00 2.66
2037 4752 8.706322 AGATGACCCAACTTTGTATTAACTTT 57.294 30.769 0.00 0.00 0.00 2.66
2038 4753 8.576442 AGATGACCCAACTTTGTATTAACTTTG 58.424 33.333 0.00 0.00 0.00 2.77
2039 4754 7.648039 TGACCCAACTTTGTATTAACTTTGT 57.352 32.000 0.00 0.00 0.00 2.83
2040 4755 8.749026 TGACCCAACTTTGTATTAACTTTGTA 57.251 30.769 0.00 0.00 0.00 2.41
2041 4756 8.623030 TGACCCAACTTTGTATTAACTTTGTAC 58.377 33.333 0.00 0.00 0.00 2.90
2042 4757 8.756486 ACCCAACTTTGTATTAACTTTGTACT 57.244 30.769 0.00 0.00 0.00 2.73
2043 4758 9.850198 ACCCAACTTTGTATTAACTTTGTACTA 57.150 29.630 0.00 0.00 0.00 1.82
2079 4794 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2080 4795 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2081 4796 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2082 4797 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2083 4798 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2084 4799 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2085 4800 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2086 4801 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2154 4870 6.416455 TGTGTGAAGCGTTTATTGTCATTTTC 59.584 34.615 0.00 0.00 0.00 2.29
2197 4913 6.356556 TGCATTAGATATAGCAACAGTTGGT 58.643 36.000 21.26 21.26 44.64 3.67
2211 4927 2.940410 CAGTTGGTGTTAAGTGGACGTT 59.060 45.455 0.00 0.00 0.00 3.99
2583 5667 4.156008 CCAACAAAGAAGGTAGGCACATAC 59.844 45.833 0.00 0.00 0.00 2.39
2597 5681 4.097714 GGCACATACACGTTCATCATTTG 58.902 43.478 0.00 0.00 0.00 2.32
2695 5963 3.370953 GCCTGATCCTGTTCCACATAACT 60.371 47.826 0.00 0.00 0.00 2.24
2700 5968 6.170506 TGATCCTGTTCCACATAACTTGTAC 58.829 40.000 0.00 0.00 36.57 2.90
2742 6017 5.690409 GCATGACTATCATTTGATTGCCAAG 59.310 40.000 0.00 0.00 34.28 3.61
2809 6153 1.134340 TGTGCCGTACAGGAAACAAGT 60.134 47.619 7.77 0.00 45.00 3.16
2847 6191 6.655003 AGATGCCCATATTCATAGTAAAACCG 59.345 38.462 0.00 0.00 0.00 4.44
3033 6388 1.859080 GACAACACGTCTTGGAGTCAC 59.141 52.381 8.46 0.00 41.81 3.67
3055 6410 2.348605 CTGCGCCTGAGGAGACTAGC 62.349 65.000 6.36 0.00 44.43 3.42
3056 6411 2.418910 GCGCCTGAGGAGACTAGCA 61.419 63.158 6.36 0.00 44.43 3.49
3061 6416 1.000771 TGAGGAGACTAGCACCGCT 60.001 57.895 0.00 0.00 44.43 5.52
3062 6417 1.315981 TGAGGAGACTAGCACCGCTG 61.316 60.000 0.00 0.00 44.43 5.18
3063 6418 1.304547 AGGAGACTAGCACCGCTGT 60.305 57.895 0.00 0.00 40.10 4.40
3064 6419 0.034380 AGGAGACTAGCACCGCTGTA 60.034 55.000 0.00 0.00 40.10 2.74
3065 6420 0.815734 GGAGACTAGCACCGCTGTAA 59.184 55.000 0.00 0.00 40.10 2.41
3114 6473 3.902150 TGTCTACTTCAGCAAAGTCTCG 58.098 45.455 7.68 0.38 45.28 4.04
3115 6474 2.664085 GTCTACTTCAGCAAAGTCTCGC 59.336 50.000 7.68 0.00 45.28 5.03
3121 6480 3.435186 GCAAAGTCTCGCCTGCCC 61.435 66.667 0.00 0.00 0.00 5.36
3122 6481 2.348998 CAAAGTCTCGCCTGCCCT 59.651 61.111 0.00 0.00 0.00 5.19
3123 6482 1.302832 CAAAGTCTCGCCTGCCCTT 60.303 57.895 0.00 0.00 0.00 3.95
3124 6483 0.890996 CAAAGTCTCGCCTGCCCTTT 60.891 55.000 0.00 0.00 0.00 3.11
3125 6484 0.606673 AAAGTCTCGCCTGCCCTTTC 60.607 55.000 0.00 0.00 0.00 2.62
3126 6485 2.436824 GTCTCGCCTGCCCTTTCC 60.437 66.667 0.00 0.00 0.00 3.13
3127 6486 2.927856 TCTCGCCTGCCCTTTCCA 60.928 61.111 0.00 0.00 0.00 3.53
3128 6487 2.437359 CTCGCCTGCCCTTTCCAG 60.437 66.667 0.00 0.00 0.00 3.86
3144 6503 6.722328 CCTTTCCAGGGAGTAAATAAACTCT 58.278 40.000 4.20 0.00 44.42 3.24
3145 6504 6.824196 CCTTTCCAGGGAGTAAATAAACTCTC 59.176 42.308 4.20 0.01 45.75 3.20
3153 6512 8.732746 GGGAGTAAATAAACTCTCTAATGCAA 57.267 34.615 0.00 0.00 42.68 4.08
3154 6513 9.174166 GGGAGTAAATAAACTCTCTAATGCAAA 57.826 33.333 0.00 0.00 42.68 3.68
3155 6514 9.989869 GGAGTAAATAAACTCTCTAATGCAAAC 57.010 33.333 0.00 0.00 44.42 2.93
3162 6521 6.487689 AACTCTCTAATGCAAACTGTAAGC 57.512 37.500 0.00 0.00 37.60 3.09
3163 6522 5.799213 ACTCTCTAATGCAAACTGTAAGCT 58.201 37.500 0.00 0.00 37.60 3.74
3164 6523 6.234177 ACTCTCTAATGCAAACTGTAAGCTT 58.766 36.000 3.48 3.48 37.60 3.74
3165 6524 7.386851 ACTCTCTAATGCAAACTGTAAGCTTA 58.613 34.615 0.86 0.86 37.60 3.09
3166 6525 8.043710 ACTCTCTAATGCAAACTGTAAGCTTAT 58.956 33.333 9.88 0.00 37.60 1.73
3167 6526 9.534565 CTCTCTAATGCAAACTGTAAGCTTATA 57.465 33.333 9.88 6.06 37.60 0.98
3168 6527 9.314321 TCTCTAATGCAAACTGTAAGCTTATAC 57.686 33.333 9.88 0.34 37.60 1.47
3196 6555 8.514594 GTTGCAAATCTATGGCAGCTAATAATA 58.485 33.333 0.00 0.00 38.97 0.98
3345 6704 3.064545 GCAACACTCAGATTGTGGATAGC 59.935 47.826 0.00 0.00 39.52 2.97
3384 6754 4.024048 GTCCATTTGTGTTCATGTCTTCGT 60.024 41.667 0.00 0.00 0.00 3.85
3470 6850 5.452341 TCTTATGTACTCCCTCTGTCTCA 57.548 43.478 0.00 0.00 0.00 3.27
3480 6860 9.742144 GTACTCCCTCTGTCTCATAATATAAGA 57.258 37.037 0.00 0.00 0.00 2.10
3482 6862 7.396055 ACTCCCTCTGTCTCATAATATAAGAGC 59.604 40.741 0.00 0.00 0.00 4.09
3497 6877 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
3499 6879 4.054780 AGAGCGTTTTTGACACTACAGA 57.945 40.909 0.00 0.00 0.00 3.41
3509 6889 9.485206 GTTTTTGACACTACAGAGGAGTAATTA 57.515 33.333 0.00 0.00 0.00 1.40
3510 6890 9.485206 TTTTTGACACTACAGAGGAGTAATTAC 57.515 33.333 7.57 7.57 0.00 1.89
3511 6891 7.770366 TTGACACTACAGAGGAGTAATTACA 57.230 36.000 17.65 0.00 0.00 2.41
3512 6892 7.956328 TGACACTACAGAGGAGTAATTACAT 57.044 36.000 17.65 3.25 0.00 2.29
3513 6893 7.772166 TGACACTACAGAGGAGTAATTACATG 58.228 38.462 17.65 9.90 0.00 3.21
3515 6895 6.668283 ACACTACAGAGGAGTAATTACATGGT 59.332 38.462 17.65 8.87 0.00 3.55
3516 6896 7.837689 ACACTACAGAGGAGTAATTACATGGTA 59.162 37.037 17.65 9.44 0.00 3.25
3517 6897 8.136165 CACTACAGAGGAGTAATTACATGGTAC 58.864 40.741 17.65 0.00 0.00 3.34
3536 6919 5.772672 TGGTACACCGTCCTAAAAGTACTTA 59.227 40.000 8.92 0.00 39.43 2.24
3543 6926 8.253113 CACCGTCCTAAAAGTACTTATAAAGGA 58.747 37.037 8.92 14.61 0.00 3.36
3562 6945 2.232941 GGATAGTTTGACAGTCCGGACA 59.767 50.000 35.00 13.13 0.00 4.02
3565 6948 0.935196 GTTTGACAGTCCGGACACAC 59.065 55.000 35.00 23.69 0.00 3.82
3573 6956 0.108019 GTCCGGACACACCTTTTCCT 59.892 55.000 29.75 0.00 36.31 3.36
3590 6973 6.238925 CCTTTTCCTGTAAACCGAAGACAAAT 60.239 38.462 0.00 0.00 0.00 2.32
3591 6974 5.682943 TTCCTGTAAACCGAAGACAAATG 57.317 39.130 0.00 0.00 0.00 2.32
3592 6975 4.069304 TCCTGTAAACCGAAGACAAATGG 58.931 43.478 0.00 0.00 0.00 3.16
3608 7013 3.329929 AATGGTGGAGACTTTACGGAC 57.670 47.619 0.00 0.00 0.00 4.79
3616 7021 1.815003 AGACTTTACGGACGTTCGGAT 59.185 47.619 22.31 2.38 0.00 4.18
3624 7029 1.231958 GGACGTTCGGATTGTTGCCA 61.232 55.000 0.00 0.00 0.00 4.92
3626 7031 1.154488 CGTTCGGATTGTTGCCACG 60.154 57.895 0.00 0.00 0.00 4.94
3627 7032 1.442017 GTTCGGATTGTTGCCACGC 60.442 57.895 0.00 0.00 0.00 5.34
3629 7034 1.573829 TTCGGATTGTTGCCACGCTC 61.574 55.000 0.00 0.00 0.00 5.03
3631 7036 2.202349 GATTGTTGCCACGCTCGC 60.202 61.111 0.00 0.00 0.00 5.03
3651 7056 1.416401 CGTATGACTAACCTGGCCCAT 59.584 52.381 0.00 0.00 0.00 4.00
3657 7062 2.492088 GACTAACCTGGCCCATCAAAAC 59.508 50.000 0.00 0.00 0.00 2.43
3658 7063 2.158385 ACTAACCTGGCCCATCAAAACA 60.158 45.455 0.00 0.00 0.00 2.83
3659 7064 1.047801 AACCTGGCCCATCAAAACAC 58.952 50.000 0.00 0.00 0.00 3.32
3660 7065 0.105760 ACCTGGCCCATCAAAACACA 60.106 50.000 0.00 0.00 0.00 3.72
3661 7066 1.269012 CCTGGCCCATCAAAACACAT 58.731 50.000 0.00 0.00 0.00 3.21
3664 7069 3.496515 CCTGGCCCATCAAAACACATTTT 60.497 43.478 0.00 0.00 38.61 1.82
3665 7070 3.737850 TGGCCCATCAAAACACATTTTC 58.262 40.909 0.00 0.00 35.79 2.29
3677 7082 0.039527 ACATTTTCCGCGTGCTTTCC 60.040 50.000 4.92 0.00 0.00 3.13
3683 7088 1.080093 CCGCGTGCTTTCCTGTCTA 60.080 57.895 4.92 0.00 0.00 2.59
3688 7093 3.323243 GCGTGCTTTCCTGTCTAAAGTA 58.677 45.455 0.00 0.00 36.52 2.24
3691 7096 4.143094 CGTGCTTTCCTGTCTAAAGTAAGC 60.143 45.833 0.00 0.00 36.52 3.09
3692 7097 4.998033 GTGCTTTCCTGTCTAAAGTAAGCT 59.002 41.667 0.00 0.00 36.52 3.74
3693 7098 4.997395 TGCTTTCCTGTCTAAAGTAAGCTG 59.003 41.667 0.00 0.00 36.52 4.24
3694 7099 4.142795 GCTTTCCTGTCTAAAGTAAGCTGC 60.143 45.833 0.00 0.00 36.52 5.25
3695 7100 3.611766 TCCTGTCTAAAGTAAGCTGCC 57.388 47.619 0.00 0.00 0.00 4.85
3696 7101 2.094182 TCCTGTCTAAAGTAAGCTGCCG 60.094 50.000 0.00 0.00 0.00 5.69
3697 7102 1.661112 CTGTCTAAAGTAAGCTGCCGC 59.339 52.381 0.00 0.00 0.00 6.53
3707 7112 2.089854 AGCTGCCGCTTTTATGTCG 58.910 52.632 0.00 0.00 46.47 4.35
3708 7113 1.062525 GCTGCCGCTTTTATGTCGG 59.937 57.895 0.00 0.00 45.46 4.79
3709 7114 1.721487 CTGCCGCTTTTATGTCGGG 59.279 57.895 2.02 0.00 43.11 5.14
3710 7115 1.003112 TGCCGCTTTTATGTCGGGT 60.003 52.632 2.02 0.00 43.11 5.28
3711 7116 1.022451 TGCCGCTTTTATGTCGGGTC 61.022 55.000 2.02 0.00 43.11 4.46
3712 7117 1.022451 GCCGCTTTTATGTCGGGTCA 61.022 55.000 2.02 0.00 43.11 4.02
3713 7118 1.006832 CCGCTTTTATGTCGGGTCAG 58.993 55.000 0.00 0.00 39.52 3.51
3714 7119 0.373716 CGCTTTTATGTCGGGTCAGC 59.626 55.000 0.00 0.00 0.00 4.26
3715 7120 1.739067 GCTTTTATGTCGGGTCAGCT 58.261 50.000 0.00 0.00 0.00 4.24
3716 7121 1.398390 GCTTTTATGTCGGGTCAGCTG 59.602 52.381 7.63 7.63 0.00 4.24
3717 7122 1.398390 CTTTTATGTCGGGTCAGCTGC 59.602 52.381 9.47 4.04 0.00 5.25
3718 7123 0.392461 TTTATGTCGGGTCAGCTGCC 60.392 55.000 9.47 13.62 0.00 4.85
3719 7124 2.572095 TTATGTCGGGTCAGCTGCCG 62.572 60.000 22.44 22.44 0.00 5.69
3724 7129 2.985847 GGGTCAGCTGCCGCTTTT 60.986 61.111 9.47 0.00 46.47 2.27
3725 7130 1.674322 GGGTCAGCTGCCGCTTTTA 60.674 57.895 9.47 0.00 46.47 1.52
3726 7131 1.032114 GGGTCAGCTGCCGCTTTTAT 61.032 55.000 9.47 0.00 46.47 1.40
3727 7132 0.099436 GGTCAGCTGCCGCTTTTATG 59.901 55.000 9.47 0.00 46.47 1.90
3728 7133 0.804989 GTCAGCTGCCGCTTTTATGT 59.195 50.000 9.47 0.00 46.47 2.29
3729 7134 1.086696 TCAGCTGCCGCTTTTATGTC 58.913 50.000 9.47 0.00 46.47 3.06
3730 7135 0.247814 CAGCTGCCGCTTTTATGTCG 60.248 55.000 0.00 0.00 46.47 4.35
3731 7136 1.062525 GCTGCCGCTTTTATGTCGG 59.937 57.895 0.00 0.00 45.46 4.79
3778 7188 4.189188 CTGGCATTGCAGCGGCTC 62.189 66.667 10.92 0.00 41.91 4.70
3826 7236 2.162681 CACACCTCTCCCCATTGAAAC 58.837 52.381 0.00 0.00 0.00 2.78
3828 7238 1.003118 CACCTCTCCCCATTGAAACGA 59.997 52.381 0.00 0.00 0.00 3.85
3832 7242 2.939103 CTCTCCCCATTGAAACGACATC 59.061 50.000 0.00 0.00 0.00 3.06
3833 7243 2.571653 TCTCCCCATTGAAACGACATCT 59.428 45.455 0.00 0.00 0.00 2.90
3861 7271 1.343465 CGCCTACCTCCATTAATCGGT 59.657 52.381 6.03 6.03 0.00 4.69
3862 7272 2.767505 GCCTACCTCCATTAATCGGTG 58.232 52.381 9.70 5.42 0.00 4.94
3863 7273 2.104281 GCCTACCTCCATTAATCGGTGT 59.896 50.000 9.70 8.11 0.00 4.16
3864 7274 3.433173 GCCTACCTCCATTAATCGGTGTT 60.433 47.826 9.70 0.00 0.00 3.32
3868 7278 2.097466 CCTCCATTAATCGGTGTTGTGC 59.903 50.000 4.51 0.00 0.00 4.57
3906 7316 2.797278 CCCCGAGCGCCAATAGTCT 61.797 63.158 2.29 0.00 0.00 3.24
3923 7333 1.153449 CTGTTCCTATGCCGGCGAA 60.153 57.895 23.90 16.21 0.00 4.70
3951 7361 0.252467 ACCTCTCTGGCTGCCTACTT 60.252 55.000 21.03 0.00 40.22 2.24
3952 7362 0.177604 CCTCTCTGGCTGCCTACTTG 59.822 60.000 21.03 7.34 0.00 3.16
3955 7365 0.107312 CTCTGGCTGCCTACTTGCAT 60.107 55.000 21.03 0.00 41.16 3.96
3983 7393 3.121463 CGCTATATAAACGTGTCCAAGCG 60.121 47.826 14.20 14.20 43.34 4.68
3987 7397 0.030504 TAAACGTGTCCAAGCGTCGA 59.969 50.000 0.00 0.00 40.70 4.20
4024 7434 1.036707 CTCCCGTTCTCTCCATCTCC 58.963 60.000 0.00 0.00 0.00 3.71
4039 7449 1.416243 TCTCCTTGTACAACACCCGT 58.584 50.000 3.59 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 133 4.377134 AGGGTTAAATAACTAGGCCTGGA 58.623 43.478 24.81 0.54 36.47 3.86
178 188 3.842796 GCGCTAATCGACTTCAGATTTGC 60.843 47.826 0.00 12.74 45.96 3.68
244 263 0.443869 CAGACCGGAACAAAGCATCG 59.556 55.000 9.46 0.00 0.00 3.84
370 391 5.511729 GCATGCCAGTAAAGATTACGAAAAC 59.488 40.000 6.36 0.00 0.00 2.43
501 1373 5.050634 CGACACTCTCGGAATAACACAAAAA 60.051 40.000 0.00 0.00 38.87 1.94
562 1435 3.966979 TCCCCGTGTAGTATGAACACTA 58.033 45.455 4.99 0.00 44.05 2.74
702 1598 7.814107 CCAAGTATGTCTGCACACAAAATAAAT 59.186 33.333 0.00 0.00 34.48 1.40
751 1648 3.099905 TGAGCACCTAGTACAGCTGAAT 58.900 45.455 23.35 8.03 37.48 2.57
756 1653 2.231478 TCAGTTGAGCACCTAGTACAGC 59.769 50.000 0.00 0.00 0.00 4.40
881 1778 1.869767 GAAGCTGTTCAGGATATGCCG 59.130 52.381 1.97 0.00 43.43 5.69
947 1846 4.157656 TGTCCACAACCTGAACAAAAGAAG 59.842 41.667 0.00 0.00 0.00 2.85
1018 1918 3.069016 TCGTTTGCTCTGTTCTCCAGTAA 59.931 43.478 0.00 0.00 42.19 2.24
1019 1919 2.626266 TCGTTTGCTCTGTTCTCCAGTA 59.374 45.455 0.00 0.00 42.19 2.74
1144 2045 8.229253 AGTCAACATTTCATGTGCATATACAT 57.771 30.769 0.00 0.00 44.07 2.29
1386 2306 9.688091 GAGAGAGAGAGGGGTTTTAATAAAATT 57.312 33.333 1.21 0.00 32.22 1.82
1401 2321 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1473 2401 9.651913 GTTCTTCATCTTCTTCATCTAGTTCTT 57.348 33.333 0.00 0.00 0.00 2.52
1654 2593 1.369625 ACCGAAACCTTCATCATCGC 58.630 50.000 0.00 0.00 32.46 4.58
1676 2618 1.537202 GTGACATTTGACTGGTCTGGC 59.463 52.381 2.38 0.00 32.84 4.85
1869 2828 8.993424 ACTATATGTTTGGAAGGATAGTTCAGT 58.007 33.333 0.00 0.00 28.11 3.41
1875 2834 9.950496 AAGCATACTATATGTTTGGAAGGATAG 57.050 33.333 0.00 0.00 0.00 2.08
1921 3222 3.005554 ACACATCAAGAAGAGGAATGCG 58.994 45.455 0.00 0.00 0.00 4.73
1992 4707 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
1993 4708 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
1994 4709 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1995 4710 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1996 4711 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1997 4712 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1998 4713 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1999 4714 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2000 4715 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2001 4716 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2002 4717 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2003 4718 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2004 4719 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2005 4720 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2009 4724 9.975218 AGTTAATACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
2010 4725 9.975218 AAGTTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
2011 4726 9.802039 AAAGTTAATACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
2012 4727 8.576442 CAAAGTTAATACAAAGTTGGGTCATCT 58.424 33.333 0.00 0.00 0.00 2.90
2013 4728 8.357402 ACAAAGTTAATACAAAGTTGGGTCATC 58.643 33.333 0.00 0.00 0.00 2.92
2014 4729 8.245195 ACAAAGTTAATACAAAGTTGGGTCAT 57.755 30.769 0.00 0.00 0.00 3.06
2015 4730 7.648039 ACAAAGTTAATACAAAGTTGGGTCA 57.352 32.000 0.00 0.00 0.00 4.02
2016 4731 8.843262 AGTACAAAGTTAATACAAAGTTGGGTC 58.157 33.333 0.00 0.00 0.00 4.46
2017 4732 8.756486 AGTACAAAGTTAATACAAAGTTGGGT 57.244 30.769 0.00 0.00 0.00 4.51
2053 4768 8.717821 CGTTCCAAAATAGATGACTCAACTTTA 58.282 33.333 0.00 0.00 0.00 1.85
2054 4769 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2055 4770 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2056 4771 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2057 4772 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2058 4773 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2059 4774 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2060 4775 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2061 4776 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2062 4777 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2063 4778 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2064 4779 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2065 4780 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2066 4781 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2067 4782 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2068 4783 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
2069 4784 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
2070 4785 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
2071 4786 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
2072 4787 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2073 4788 0.627451 TAGCTACTCCCTCCGTTCCA 59.373 55.000 0.00 0.00 0.00 3.53
2074 4789 1.772836 TTAGCTACTCCCTCCGTTCC 58.227 55.000 0.00 0.00 0.00 3.62
2075 4790 4.583907 AGTTATTAGCTACTCCCTCCGTTC 59.416 45.833 0.00 0.00 0.00 3.95
2076 4791 4.544683 AGTTATTAGCTACTCCCTCCGTT 58.455 43.478 0.00 0.00 0.00 4.44
2077 4792 4.181799 AGTTATTAGCTACTCCCTCCGT 57.818 45.455 0.00 0.00 0.00 4.69
2078 4793 5.335819 GCTTAGTTATTAGCTACTCCCTCCG 60.336 48.000 0.00 0.00 34.57 4.63
2079 4794 5.776208 AGCTTAGTTATTAGCTACTCCCTCC 59.224 44.000 0.00 0.00 45.46 4.30
2080 4795 6.904463 AGCTTAGTTATTAGCTACTCCCTC 57.096 41.667 0.00 0.00 45.46 4.30
2081 4796 6.839657 TGAAGCTTAGTTATTAGCTACTCCCT 59.160 38.462 0.00 0.00 46.53 4.20
2082 4797 7.052142 TGAAGCTTAGTTATTAGCTACTCCC 57.948 40.000 0.00 0.00 46.53 4.30
2083 4798 8.943909 TTTGAAGCTTAGTTATTAGCTACTCC 57.056 34.615 0.00 0.00 46.53 3.85
2154 4870 5.404466 TGCAAATTGAAAACCTATCCCAG 57.596 39.130 0.00 0.00 0.00 4.45
2197 4913 3.472283 TGGCTTAACGTCCACTTAACA 57.528 42.857 0.00 0.00 0.00 2.41
2208 4924 4.497473 TCTGGTTCAAAATGGCTTAACG 57.503 40.909 0.00 0.00 0.00 3.18
2211 4927 6.928492 GTGAATTTCTGGTTCAAAATGGCTTA 59.072 34.615 0.00 0.00 37.34 3.09
2583 5667 3.663564 CGGTGAAACAAATGATGAACGTG 59.336 43.478 0.00 0.00 39.98 4.49
2597 5681 3.060363 CAGTACAAGCGATACGGTGAAAC 59.940 47.826 0.00 0.00 37.73 2.78
2695 5963 4.507710 CAAGATAAGCTGCCTCAGTACAA 58.492 43.478 0.00 0.00 33.43 2.41
2700 5968 1.307097 GCCAAGATAAGCTGCCTCAG 58.693 55.000 0.00 0.00 34.12 3.35
2742 6017 4.584327 AACAGCAACATAAACAAGGACC 57.416 40.909 0.00 0.00 0.00 4.46
2809 6153 3.686622 GCATCTTAGATGCCACGGA 57.313 52.632 30.61 0.00 39.01 4.69
3033 6388 1.227205 GTCTCCTCAGGCGCAGATG 60.227 63.158 10.83 4.75 0.00 2.90
3052 6407 1.445410 CGTGCTTACAGCGGTGCTA 60.445 57.895 15.82 3.67 46.26 3.49
3055 6410 1.695893 CCATCGTGCTTACAGCGGTG 61.696 60.000 14.13 14.13 46.26 4.94
3056 6411 1.447838 CCATCGTGCTTACAGCGGT 60.448 57.895 0.00 0.00 46.26 5.68
3073 6430 5.182001 AGACAATTACATTCTGAGTTGCACC 59.818 40.000 0.00 0.00 0.00 5.01
3077 6434 9.208022 TGAAGTAGACAATTACATTCTGAGTTG 57.792 33.333 0.00 0.00 0.00 3.16
3081 6438 7.386059 TGCTGAAGTAGACAATTACATTCTGA 58.614 34.615 0.00 0.00 0.00 3.27
3121 6480 7.625469 AGAGAGTTTATTTACTCCCTGGAAAG 58.375 38.462 0.00 0.00 44.50 2.62
3122 6481 7.569599 AGAGAGTTTATTTACTCCCTGGAAA 57.430 36.000 0.00 0.00 44.50 3.13
3123 6482 8.674925 TTAGAGAGTTTATTTACTCCCTGGAA 57.325 34.615 0.00 0.00 44.50 3.53
3124 6483 8.705594 CATTAGAGAGTTTATTTACTCCCTGGA 58.294 37.037 0.00 0.00 44.50 3.86
3125 6484 7.442666 GCATTAGAGAGTTTATTTACTCCCTGG 59.557 40.741 0.00 0.00 44.50 4.45
3126 6485 7.987458 TGCATTAGAGAGTTTATTTACTCCCTG 59.013 37.037 0.00 0.00 44.50 4.45
3127 6486 8.090788 TGCATTAGAGAGTTTATTTACTCCCT 57.909 34.615 0.00 0.00 44.50 4.20
3128 6487 8.732746 TTGCATTAGAGAGTTTATTTACTCCC 57.267 34.615 0.00 0.00 44.50 4.30
3129 6488 9.989869 GTTTGCATTAGAGAGTTTATTTACTCC 57.010 33.333 0.00 0.00 44.50 3.85
3136 6495 8.669243 GCTTACAGTTTGCATTAGAGAGTTTAT 58.331 33.333 0.00 0.00 0.00 1.40
3137 6496 7.878127 AGCTTACAGTTTGCATTAGAGAGTTTA 59.122 33.333 0.00 0.00 0.00 2.01
3138 6497 6.712547 AGCTTACAGTTTGCATTAGAGAGTTT 59.287 34.615 0.00 0.00 0.00 2.66
3139 6498 6.234177 AGCTTACAGTTTGCATTAGAGAGTT 58.766 36.000 0.00 0.00 0.00 3.01
3140 6499 5.799213 AGCTTACAGTTTGCATTAGAGAGT 58.201 37.500 0.00 0.00 0.00 3.24
3141 6500 6.734104 AAGCTTACAGTTTGCATTAGAGAG 57.266 37.500 0.00 0.00 0.00 3.20
3142 6501 9.314321 GTATAAGCTTACAGTTTGCATTAGAGA 57.686 33.333 8.70 0.00 0.00 3.10
3143 6502 9.319143 AGTATAAGCTTACAGTTTGCATTAGAG 57.681 33.333 8.70 0.00 0.00 2.43
3144 6503 9.098355 CAGTATAAGCTTACAGTTTGCATTAGA 57.902 33.333 8.70 0.00 0.00 2.10
3145 6504 8.883731 ACAGTATAAGCTTACAGTTTGCATTAG 58.116 33.333 8.70 0.00 0.00 1.73
3146 6505 8.786826 ACAGTATAAGCTTACAGTTTGCATTA 57.213 30.769 8.70 0.00 0.00 1.90
3147 6506 7.687941 ACAGTATAAGCTTACAGTTTGCATT 57.312 32.000 8.70 0.00 0.00 3.56
3148 6507 7.530010 CAACAGTATAAGCTTACAGTTTGCAT 58.470 34.615 8.70 0.00 31.74 3.96
3149 6508 6.567701 GCAACAGTATAAGCTTACAGTTTGCA 60.568 38.462 23.51 0.00 31.74 4.08
3150 6509 5.795441 GCAACAGTATAAGCTTACAGTTTGC 59.205 40.000 8.70 15.12 31.74 3.68
3151 6510 6.898041 TGCAACAGTATAAGCTTACAGTTTG 58.102 36.000 8.70 9.73 31.74 2.93
3152 6511 7.504924 TTGCAACAGTATAAGCTTACAGTTT 57.495 32.000 8.70 0.00 31.74 2.66
3153 6512 7.504924 TTTGCAACAGTATAAGCTTACAGTT 57.495 32.000 8.70 6.33 33.61 3.16
3154 6513 7.607991 AGATTTGCAACAGTATAAGCTTACAGT 59.392 33.333 8.70 0.00 0.00 3.55
3155 6514 7.978982 AGATTTGCAACAGTATAAGCTTACAG 58.021 34.615 8.70 0.00 0.00 2.74
3156 6515 7.921786 AGATTTGCAACAGTATAAGCTTACA 57.078 32.000 8.70 0.00 0.00 2.41
3157 6516 9.869844 CATAGATTTGCAACAGTATAAGCTTAC 57.130 33.333 8.70 0.00 0.00 2.34
3158 6517 9.056005 CCATAGATTTGCAACAGTATAAGCTTA 57.944 33.333 8.99 8.99 0.00 3.09
3159 6518 7.469181 GCCATAGATTTGCAACAGTATAAGCTT 60.469 37.037 3.48 3.48 0.00 3.74
3160 6519 6.016777 GCCATAGATTTGCAACAGTATAAGCT 60.017 38.462 0.00 0.00 0.00 3.74
3161 6520 6.145535 GCCATAGATTTGCAACAGTATAAGC 58.854 40.000 0.00 0.00 0.00 3.09
3162 6521 7.263100 TGCCATAGATTTGCAACAGTATAAG 57.737 36.000 0.00 0.00 30.85 1.73
3163 6522 6.238731 GCTGCCATAGATTTGCAACAGTATAA 60.239 38.462 0.00 0.00 34.06 0.98
3164 6523 5.239306 GCTGCCATAGATTTGCAACAGTATA 59.761 40.000 0.00 0.00 34.06 1.47
3165 6524 4.037208 GCTGCCATAGATTTGCAACAGTAT 59.963 41.667 0.00 0.00 34.06 2.12
3166 6525 3.378112 GCTGCCATAGATTTGCAACAGTA 59.622 43.478 0.00 0.00 34.06 2.74
3167 6526 2.165030 GCTGCCATAGATTTGCAACAGT 59.835 45.455 0.00 0.00 34.06 3.55
3168 6527 2.426024 AGCTGCCATAGATTTGCAACAG 59.574 45.455 0.00 1.49 34.06 3.16
3196 6555 7.724506 TCTTTCTAACACGGATATATCTGGACT 59.275 37.037 22.69 10.47 37.50 3.85
3239 6598 7.750229 ATTCTTCAACTGCTCTGAATTTGTA 57.250 32.000 0.00 0.00 32.53 2.41
3345 6704 3.319137 TGGACAAATCGGAACAGAGAG 57.681 47.619 0.00 0.00 0.00 3.20
3384 6754 4.159693 AGAAACATACATAGGCTCACACGA 59.840 41.667 0.00 0.00 0.00 4.35
3459 6839 6.151985 ACGCTCTTATATTATGAGACAGAGGG 59.848 42.308 8.36 8.36 42.53 4.30
3482 6862 4.369182 ACTCCTCTGTAGTGTCAAAAACG 58.631 43.478 0.00 0.00 0.00 3.60
3496 6876 6.281405 GGTGTACCATGTAATTACTCCTCTG 58.719 44.000 16.33 6.48 35.64 3.35
3497 6877 5.068723 CGGTGTACCATGTAATTACTCCTCT 59.931 44.000 16.33 0.00 35.14 3.69
3499 6879 4.713321 ACGGTGTACCATGTAATTACTCCT 59.287 41.667 16.33 0.00 35.14 3.69
3509 6889 3.325716 ACTTTTAGGACGGTGTACCATGT 59.674 43.478 1.50 0.00 35.14 3.21
3510 6890 3.934068 ACTTTTAGGACGGTGTACCATG 58.066 45.455 1.50 0.00 35.14 3.66
3511 6891 4.774200 AGTACTTTTAGGACGGTGTACCAT 59.226 41.667 1.50 0.00 35.14 3.55
3512 6892 4.151883 AGTACTTTTAGGACGGTGTACCA 58.848 43.478 1.50 0.00 35.14 3.25
3513 6893 4.790765 AGTACTTTTAGGACGGTGTACC 57.209 45.455 0.00 0.00 33.06 3.34
3516 6896 8.037166 CCTTTATAAGTACTTTTAGGACGGTGT 58.963 37.037 14.49 0.00 0.00 4.16
3517 6897 8.253113 TCCTTTATAAGTACTTTTAGGACGGTG 58.747 37.037 14.49 0.00 0.00 4.94
3518 6898 8.366359 TCCTTTATAAGTACTTTTAGGACGGT 57.634 34.615 14.49 0.00 0.00 4.83
3536 6919 5.424252 TCCGGACTGTCAAACTATCCTTTAT 59.576 40.000 10.38 0.00 0.00 1.40
3543 6926 2.631062 TGTGTCCGGACTGTCAAACTAT 59.369 45.455 33.39 0.00 0.00 2.12
3551 6934 0.544697 AAAAGGTGTGTCCGGACTGT 59.455 50.000 33.39 6.91 41.99 3.55
3562 6945 3.564053 TCGGTTTACAGGAAAAGGTGT 57.436 42.857 0.00 0.00 0.00 4.16
3565 6948 4.131596 TGTCTTCGGTTTACAGGAAAAGG 58.868 43.478 0.00 0.00 0.00 3.11
3573 6956 3.566322 CCACCATTTGTCTTCGGTTTACA 59.434 43.478 0.00 0.00 0.00 2.41
3590 6973 0.599558 CGTCCGTAAAGTCTCCACCA 59.400 55.000 0.00 0.00 0.00 4.17
3591 6974 0.600057 ACGTCCGTAAAGTCTCCACC 59.400 55.000 0.00 0.00 0.00 4.61
3592 6975 2.323059 GAACGTCCGTAAAGTCTCCAC 58.677 52.381 0.00 0.00 0.00 4.02
3626 7031 1.478137 CAGGTTAGTCATACGCGAGC 58.522 55.000 15.93 0.00 0.00 5.03
3627 7032 1.864435 GCCAGGTTAGTCATACGCGAG 60.864 57.143 15.93 1.66 0.00 5.03
3629 7034 0.874607 GGCCAGGTTAGTCATACGCG 60.875 60.000 3.53 3.53 0.00 6.01
3631 7036 0.828022 TGGGCCAGGTTAGTCATACG 59.172 55.000 0.00 0.00 0.00 3.06
3651 7056 2.455032 CACGCGGAAAATGTGTTTTGA 58.545 42.857 12.47 0.00 37.65 2.69
3657 7062 1.052287 GAAAGCACGCGGAAAATGTG 58.948 50.000 12.47 0.00 36.70 3.21
3658 7063 0.039527 GGAAAGCACGCGGAAAATGT 60.040 50.000 12.47 0.00 0.00 2.71
3659 7064 0.240945 AGGAAAGCACGCGGAAAATG 59.759 50.000 12.47 0.00 0.00 2.32
3660 7065 0.240945 CAGGAAAGCACGCGGAAAAT 59.759 50.000 12.47 0.00 0.00 1.82
3661 7066 1.098712 ACAGGAAAGCACGCGGAAAA 61.099 50.000 12.47 0.00 0.00 2.29
3664 7069 1.529152 TAGACAGGAAAGCACGCGGA 61.529 55.000 12.47 0.00 0.00 5.54
3665 7070 0.669318 TTAGACAGGAAAGCACGCGG 60.669 55.000 12.47 0.00 0.00 6.46
3677 7082 1.661112 GCGGCAGCTTACTTTAGACAG 59.339 52.381 0.00 0.00 41.01 3.51
3691 7096 1.024579 ACCCGACATAAAAGCGGCAG 61.025 55.000 1.45 0.00 43.52 4.85
3692 7097 1.003112 ACCCGACATAAAAGCGGCA 60.003 52.632 1.45 0.00 43.52 5.69
3693 7098 1.022451 TGACCCGACATAAAAGCGGC 61.022 55.000 0.00 0.00 43.52 6.53
3694 7099 1.006832 CTGACCCGACATAAAAGCGG 58.993 55.000 0.00 0.00 44.42 5.52
3695 7100 0.373716 GCTGACCCGACATAAAAGCG 59.626 55.000 0.00 0.00 0.00 4.68
3696 7101 1.398390 CAGCTGACCCGACATAAAAGC 59.602 52.381 8.42 0.00 0.00 3.51
3697 7102 1.398390 GCAGCTGACCCGACATAAAAG 59.602 52.381 20.43 0.00 0.00 2.27
3698 7103 1.448985 GCAGCTGACCCGACATAAAA 58.551 50.000 20.43 0.00 0.00 1.52
3699 7104 0.392461 GGCAGCTGACCCGACATAAA 60.392 55.000 20.43 0.00 0.00 1.40
3700 7105 1.220749 GGCAGCTGACCCGACATAA 59.779 57.895 20.43 0.00 0.00 1.90
3701 7106 2.900273 GGCAGCTGACCCGACATA 59.100 61.111 20.43 0.00 0.00 2.29
3713 7118 1.062525 CCGACATAAAAGCGGCAGC 59.937 57.895 0.00 0.00 45.58 5.25
3718 7123 0.742990 TCTGGGCCGACATAAAAGCG 60.743 55.000 0.00 0.00 0.00 4.68
3719 7124 1.017387 CTCTGGGCCGACATAAAAGC 58.983 55.000 0.00 0.00 0.00 3.51
3720 7125 1.017387 GCTCTGGGCCGACATAAAAG 58.983 55.000 0.00 0.00 34.27 2.27
3721 7126 0.742990 CGCTCTGGGCCGACATAAAA 60.743 55.000 0.00 0.00 37.74 1.52
3722 7127 1.153449 CGCTCTGGGCCGACATAAA 60.153 57.895 0.00 0.00 37.74 1.40
3723 7128 2.499205 CGCTCTGGGCCGACATAA 59.501 61.111 0.00 0.00 37.74 1.90
3724 7129 3.536917 CCGCTCTGGGCCGACATA 61.537 66.667 0.00 0.00 37.74 2.29
3803 7213 0.962356 CAATGGGGAGAGGTGTGCAC 60.962 60.000 10.75 10.75 0.00 4.57
3805 7215 0.038166 TTCAATGGGGAGAGGTGTGC 59.962 55.000 0.00 0.00 0.00 4.57
3807 7217 1.271379 CGTTTCAATGGGGAGAGGTGT 60.271 52.381 0.00 0.00 0.00 4.16
3808 7218 1.003118 TCGTTTCAATGGGGAGAGGTG 59.997 52.381 0.00 0.00 0.00 4.00
3809 7219 1.003233 GTCGTTTCAATGGGGAGAGGT 59.997 52.381 0.00 0.00 0.00 3.85
3810 7220 1.003118 TGTCGTTTCAATGGGGAGAGG 59.997 52.381 0.00 0.00 0.00 3.69
3811 7221 2.472695 TGTCGTTTCAATGGGGAGAG 57.527 50.000 0.00 0.00 0.00 3.20
3812 7222 2.571653 AGATGTCGTTTCAATGGGGAGA 59.428 45.455 0.00 0.00 0.00 3.71
3813 7223 2.679837 CAGATGTCGTTTCAATGGGGAG 59.320 50.000 0.00 0.00 0.00 4.30
3814 7224 2.710377 CAGATGTCGTTTCAATGGGGA 58.290 47.619 0.00 0.00 0.00 4.81
3815 7225 1.133025 GCAGATGTCGTTTCAATGGGG 59.867 52.381 0.00 0.00 0.00 4.96
3816 7226 1.133025 GGCAGATGTCGTTTCAATGGG 59.867 52.381 0.00 0.00 0.00 4.00
3817 7227 2.086869 AGGCAGATGTCGTTTCAATGG 58.913 47.619 0.00 0.00 0.00 3.16
3818 7228 2.730090 GCAGGCAGATGTCGTTTCAATG 60.730 50.000 0.00 0.00 0.00 2.82
3861 7271 2.037251 GAGTAGGTTCCTCAGCACAACA 59.963 50.000 0.00 0.00 0.00 3.33
3862 7272 2.613223 GGAGTAGGTTCCTCAGCACAAC 60.613 54.545 0.00 0.00 34.27 3.32
3863 7273 1.623811 GGAGTAGGTTCCTCAGCACAA 59.376 52.381 0.00 0.00 34.27 3.33
3864 7274 1.267121 GGAGTAGGTTCCTCAGCACA 58.733 55.000 0.00 0.00 34.27 4.57
3868 7278 1.817209 GCCGGAGTAGGTTCCTCAG 59.183 63.158 5.05 0.00 34.96 3.35
3900 7310 1.344763 GCCGGCATAGGAACAGACTAT 59.655 52.381 24.80 0.00 0.00 2.12
3902 7312 1.522569 GCCGGCATAGGAACAGACT 59.477 57.895 24.80 0.00 0.00 3.24
3906 7316 1.448893 GTTCGCCGGCATAGGAACA 60.449 57.895 28.94 5.00 38.82 3.18
3923 7333 3.679389 CAGCCAGAGAGGTGTTTAATGT 58.321 45.455 0.00 0.00 40.61 2.71
3951 7361 0.899019 TTATATAGCGGGCGGATGCA 59.101 50.000 0.00 0.00 45.35 3.96
3952 7362 1.664151 GTTTATATAGCGGGCGGATGC 59.336 52.381 0.00 0.00 41.71 3.91
3955 7365 0.961019 ACGTTTATATAGCGGGCGGA 59.039 50.000 11.62 0.00 0.00 5.54
3983 7393 2.548057 TGAATTGTGGTTCTTGCTCGAC 59.452 45.455 0.00 0.00 0.00 4.20
3987 7397 2.887152 GGAGTGAATTGTGGTTCTTGCT 59.113 45.455 0.00 0.00 0.00 3.91
4024 7434 1.804151 CCATGACGGGTGTTGTACAAG 59.196 52.381 8.98 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.