Multiple sequence alignment - TraesCS2D01G308500

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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 TraesCS2D01G308500 chr2D 100.000 3793 0 0 1 3793 395559729 395555937 0.000000e+00 7005.0
1 TraesCS2D01G308500 chr2B 93.681 2089 79 13 739 2790 468553263 468551191 0.000000e+00 3077.0
2 TraesCS2D01G308500 chr2B 93.002 886 50 5 2919 3793 468550820 468549936 0.000000e+00 1282.0
3 TraesCS2D01G308500 chr2B 90.116 516 35 7 180 682 468553800 468553288 0.000000e+00 656.0
4 TraesCS2D01G308500 chr2B 89.865 148 5 5 2775 2920 468551041 468550902 8.370000e-42 182.0
5 TraesCS2D01G308500 chr2A 92.823 1895 92 14 1489 3364 533831574 533829705 0.000000e+00 2706.0
6 TraesCS2D01G308500 chr2A 88.303 778 46 14 738 1483 533837503 533836739 0.000000e+00 891.0
7 TraesCS2D01G308500 chr2A 90.108 465 31 4 159 621 533837968 533837517 1.170000e-164 590.0
8 TraesCS2D01G308500 chr2A 87.464 343 37 4 3454 3793 533696202 533695863 1.280000e-104 390.0
9 TraesCS2D01G308500 chr2A 89.583 48 5 0 159 206 272370912 272370865 1.140000e-05 62.1
10 TraesCS2D01G308500 chr6D 86.316 1922 189 35 930 2816 54238260 54240142 0.000000e+00 2025.0
11 TraesCS2D01G308500 chr6D 83.645 428 42 12 1836 2258 54021555 54021959 9.950000e-101 377.0
12 TraesCS2D01G308500 chr6A 86.310 1848 173 45 1021 2817 61007807 61005989 0.000000e+00 1938.0
13 TraesCS2D01G308500 chr6B 88.315 890 77 17 1932 2797 116746834 116745948 0.000000e+00 1042.0
14 TraesCS2D01G308500 chr6B 93.117 523 36 0 1330 1852 116747411 116746889 0.000000e+00 767.0
15 TraesCS2D01G308500 chr6B 90.000 310 24 5 929 1237 116747796 116747493 9.880000e-106 394.0
16 TraesCS2D01G308500 chr6B 92.248 129 10 0 1 129 272401578 272401706 2.330000e-42 183.0
17 TraesCS2D01G308500 chr6B 91.603 131 11 0 1 131 6344835 6344965 8.370000e-42 182.0
18 TraesCS2D01G308500 chr5A 77.157 394 77 13 1333 1718 365253857 365254245 2.290000e-52 217.0
19 TraesCS2D01G308500 chr5A 92.248 129 10 0 1 129 631470369 631470497 2.330000e-42 183.0
20 TraesCS2D01G308500 chr5B 76.081 393 83 11 1333 1718 314193696 314193308 1.080000e-45 195.0
21 TraesCS2D01G308500 chr3D 92.366 131 10 0 1 131 92747694 92747824 1.800000e-43 187.0
22 TraesCS2D01G308500 chr3D 91.603 131 11 0 1 131 585056301 585056171 8.370000e-42 182.0
23 TraesCS2D01G308500 chr3D 90.441 136 13 0 1 136 603057025 603056890 3.010000e-41 180.0
24 TraesCS2D01G308500 chr3D 85.938 64 9 0 160 223 606368427 606368490 6.800000e-08 69.4
25 TraesCS2D01G308500 chr4B 92.248 129 10 0 1 129 2014116 2014244 2.330000e-42 183.0
26 TraesCS2D01G308500 chr3B 92.248 129 10 0 1 129 331935300 331935428 2.330000e-42 183.0
27 TraesCS2D01G308500 chr1D 92.248 129 10 0 1 129 323930293 323930165 2.330000e-42 183.0
28 TraesCS2D01G308500 chr1D 81.366 161 24 6 1564 1721 445589090 445589247 3.980000e-25 126.0
29 TraesCS2D01G308500 chr7D 82.424 165 17 6 3171 3323 102567322 102567158 2.380000e-27 134.0
30 TraesCS2D01G308500 chr1A 80.745 161 25 6 1564 1721 541770987 541771144 1.850000e-23 121.0
31 TraesCS2D01G308500 chr3A 84.375 64 10 0 160 223 737674365 737674302 3.160000e-06 63.9


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 TraesCS2D01G308500 chr2D 395555937 395559729 3792 True 7005.000000 7005 100.000000 1 3793 1 chr2D.!!$R1 3792
1 TraesCS2D01G308500 chr2B 468549936 468553800 3864 True 1299.250000 3077 91.666000 180 3793 4 chr2B.!!$R1 3613
2 TraesCS2D01G308500 chr2A 533829705 533831574 1869 True 2706.000000 2706 92.823000 1489 3364 1 chr2A.!!$R3 1875
3 TraesCS2D01G308500 chr2A 533836739 533837968 1229 True 740.500000 891 89.205500 159 1483 2 chr2A.!!$R4 1324
4 TraesCS2D01G308500 chr6D 54238260 54240142 1882 False 2025.000000 2025 86.316000 930 2816 1 chr6D.!!$F2 1886
5 TraesCS2D01G308500 chr6A 61005989 61007807 1818 True 1938.000000 1938 86.310000 1021 2817 1 chr6A.!!$R1 1796
6 TraesCS2D01G308500 chr6B 116745948 116747796 1848 True 734.333333 1042 90.477333 929 2797 3 chr6B.!!$R1 1868

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
120 121 0.030369 GTGCATGCTCTAGCCAATGC 59.970 55.0 20.33 16.33 45.25 3.56 F
528 536 0.320160 AGAGTACGCGAAAACCACCC 60.320 55.0 15.93 0.00 0.00 4.61 F
533 541 0.320596 ACGCGAAAACCACCCGATAA 60.321 50.0 15.93 0.00 0.00 1.75 F
1930 1995 0.303493 TTCTTGTCACGACTTTGCGC 59.697 50.0 0.00 0.00 33.86 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 1346 0.105964 TCAACCACACCCGAGTCAAG 59.894 55.000 0.00 0.00 0.00 3.02 R
1856 1912 1.195900 GTTGCACGGCGTGATCTTTTA 59.804 47.619 40.94 15.39 35.23 1.52 R
2084 2149 2.168936 TGTTTCAGTTACCCGTGACAGT 59.831 45.455 0.00 0.00 0.00 3.55 R
3639 4015 0.319728 CTCGCCATATCTGTGGGAGG 59.680 60.000 0.00 0.00 39.73 4.30 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
18 19 3.190415 TGGCTCCCTCAGGGTAAAA 57.810 52.632 10.50 0.00 44.74 1.52
19 20 0.696501 TGGCTCCCTCAGGGTAAAAC 59.303 55.000 10.50 0.00 44.74 2.43
20 21 0.392595 GGCTCCCTCAGGGTAAAACG 60.393 60.000 10.50 0.00 44.74 3.60
21 22 0.323957 GCTCCCTCAGGGTAAAACGT 59.676 55.000 10.50 0.00 44.74 3.99
22 23 1.944430 GCTCCCTCAGGGTAAAACGTG 60.944 57.143 10.50 0.00 44.74 4.49
23 24 1.621814 CTCCCTCAGGGTAAAACGTGA 59.378 52.381 10.50 0.00 44.74 4.35
25 26 1.439679 CCTCAGGGTAAAACGTGAGC 58.560 55.000 11.35 0.00 46.53 4.26
26 27 1.439679 CTCAGGGTAAAACGTGAGCC 58.560 55.000 4.91 5.66 43.62 4.70
27 28 0.320073 TCAGGGTAAAACGTGAGCCG 60.320 55.000 7.67 4.41 44.03 5.52
28 29 0.320073 CAGGGTAAAACGTGAGCCGA 60.320 55.000 7.67 0.00 40.70 5.54
29 30 0.393820 AGGGTAAAACGTGAGCCGAA 59.606 50.000 7.67 0.00 40.70 4.30
30 31 1.202675 AGGGTAAAACGTGAGCCGAAA 60.203 47.619 7.67 0.00 40.70 3.46
31 32 1.196127 GGGTAAAACGTGAGCCGAAAG 59.804 52.381 0.00 0.00 40.70 2.62
32 33 1.869132 GGTAAAACGTGAGCCGAAAGT 59.131 47.619 0.00 0.00 40.70 2.66
33 34 2.349155 GGTAAAACGTGAGCCGAAAGTG 60.349 50.000 0.00 0.00 40.70 3.16
34 35 0.661020 AAAACGTGAGCCGAAAGTGG 59.339 50.000 0.00 0.00 40.70 4.00
35 36 1.164041 AAACGTGAGCCGAAAGTGGG 61.164 55.000 0.00 0.00 40.70 4.61
42 43 3.685435 CCGAAAGTGGGCTGCAAT 58.315 55.556 0.50 0.00 0.00 3.56
43 44 1.966762 CCGAAAGTGGGCTGCAATT 59.033 52.632 0.50 0.00 0.00 2.32
44 45 0.318120 CCGAAAGTGGGCTGCAATTT 59.682 50.000 0.50 0.00 0.00 1.82
45 46 1.543802 CCGAAAGTGGGCTGCAATTTA 59.456 47.619 0.50 0.00 0.00 1.40
46 47 2.029470 CCGAAAGTGGGCTGCAATTTAA 60.029 45.455 0.50 0.00 0.00 1.52
47 48 2.986479 CGAAAGTGGGCTGCAATTTAAC 59.014 45.455 0.50 0.00 0.00 2.01
48 49 3.305335 CGAAAGTGGGCTGCAATTTAACT 60.305 43.478 0.50 0.00 0.00 2.24
49 50 3.665745 AAGTGGGCTGCAATTTAACTG 57.334 42.857 0.50 0.00 0.00 3.16
50 51 1.273327 AGTGGGCTGCAATTTAACTGC 59.727 47.619 0.50 0.00 40.35 4.40
51 52 0.243365 TGGGCTGCAATTTAACTGCG 59.757 50.000 0.50 0.00 42.97 5.18
52 53 1.078201 GGGCTGCAATTTAACTGCGC 61.078 55.000 0.00 0.00 42.97 6.09
53 54 1.078201 GGCTGCAATTTAACTGCGCC 61.078 55.000 15.28 15.28 45.26 6.53
54 55 0.388391 GCTGCAATTTAACTGCGCCA 60.388 50.000 4.18 0.00 42.97 5.69
55 56 1.621107 CTGCAATTTAACTGCGCCAG 58.379 50.000 4.18 4.99 42.97 4.85
57 58 1.068610 TGCAATTTAACTGCGCCAGTC 60.069 47.619 4.18 0.00 44.62 3.51
58 59 1.882198 CAATTTAACTGCGCCAGTCG 58.118 50.000 4.18 0.00 44.62 4.18
59 60 0.802494 AATTTAACTGCGCCAGTCGG 59.198 50.000 4.18 0.00 44.62 4.79
60 61 1.024579 ATTTAACTGCGCCAGTCGGG 61.025 55.000 4.18 0.00 44.62 5.14
61 62 2.386064 TTTAACTGCGCCAGTCGGGT 62.386 55.000 4.18 0.00 44.62 5.28
62 63 2.775032 TTAACTGCGCCAGTCGGGTC 62.775 60.000 4.18 0.00 44.62 4.46
64 65 4.379243 CTGCGCCAGTCGGGTCTT 62.379 66.667 4.18 0.00 39.65 3.01
65 66 4.680237 TGCGCCAGTCGGGTCTTG 62.680 66.667 4.18 0.00 39.65 3.02
66 67 4.373116 GCGCCAGTCGGGTCTTGA 62.373 66.667 0.00 0.00 39.65 3.02
67 68 2.342279 CGCCAGTCGGGTCTTGAA 59.658 61.111 0.00 0.00 39.65 2.69
68 69 2.027625 CGCCAGTCGGGTCTTGAAC 61.028 63.158 0.00 0.00 39.65 3.18
69 70 1.371558 GCCAGTCGGGTCTTGAACT 59.628 57.895 0.00 0.00 39.65 3.01
70 71 0.670854 GCCAGTCGGGTCTTGAACTC 60.671 60.000 0.00 0.00 39.65 3.01
71 72 0.679505 CCAGTCGGGTCTTGAACTCA 59.320 55.000 0.00 0.00 0.00 3.41
72 73 1.070134 CCAGTCGGGTCTTGAACTCAA 59.930 52.381 0.00 0.00 0.00 3.02
92 93 4.828072 AAGACCTCTTGGAACTGATACC 57.172 45.455 0.00 0.00 34.38 2.73
93 94 3.791320 AGACCTCTTGGAACTGATACCA 58.209 45.455 0.00 0.00 37.04 3.25
94 95 4.366267 AGACCTCTTGGAACTGATACCAT 58.634 43.478 0.00 0.00 36.02 3.55
95 96 4.163078 AGACCTCTTGGAACTGATACCATG 59.837 45.833 0.00 0.00 36.02 3.66
96 97 3.846588 ACCTCTTGGAACTGATACCATGT 59.153 43.478 0.00 0.00 36.02 3.21
97 98 5.030147 ACCTCTTGGAACTGATACCATGTA 58.970 41.667 0.00 0.00 36.02 2.29
98 99 5.129485 ACCTCTTGGAACTGATACCATGTAG 59.871 44.000 0.00 0.00 36.02 2.74
99 100 5.363868 CCTCTTGGAACTGATACCATGTAGA 59.636 44.000 0.00 0.00 36.02 2.59
100 101 6.127054 CCTCTTGGAACTGATACCATGTAGAA 60.127 42.308 0.00 0.00 36.02 2.10
101 102 6.878317 TCTTGGAACTGATACCATGTAGAAG 58.122 40.000 0.00 0.00 36.02 2.85
102 103 6.440647 TCTTGGAACTGATACCATGTAGAAGT 59.559 38.462 0.00 0.00 36.02 3.01
103 104 5.977635 TGGAACTGATACCATGTAGAAGTG 58.022 41.667 0.00 0.00 0.00 3.16
104 105 4.811557 GGAACTGATACCATGTAGAAGTGC 59.188 45.833 0.00 0.00 0.00 4.40
105 106 5.419542 GAACTGATACCATGTAGAAGTGCA 58.580 41.667 0.00 0.00 0.00 4.57
106 107 5.620738 ACTGATACCATGTAGAAGTGCAT 57.379 39.130 0.00 0.00 0.00 3.96
107 108 5.363101 ACTGATACCATGTAGAAGTGCATG 58.637 41.667 0.00 0.00 44.17 4.06
108 109 4.129380 TGATACCATGTAGAAGTGCATGC 58.871 43.478 11.82 11.82 43.45 4.06
109 110 2.795231 ACCATGTAGAAGTGCATGCT 57.205 45.000 20.33 0.00 43.45 3.79
110 111 2.636830 ACCATGTAGAAGTGCATGCTC 58.363 47.619 20.33 15.94 43.45 4.26
111 112 2.238144 ACCATGTAGAAGTGCATGCTCT 59.762 45.455 20.33 18.23 43.45 4.09
112 113 3.452264 ACCATGTAGAAGTGCATGCTCTA 59.548 43.478 21.70 15.62 43.45 2.43
113 114 4.056740 CCATGTAGAAGTGCATGCTCTAG 58.943 47.826 21.70 7.70 43.45 2.43
114 115 3.170791 TGTAGAAGTGCATGCTCTAGC 57.829 47.619 21.70 16.29 42.50 3.42
115 116 2.159043 TGTAGAAGTGCATGCTCTAGCC 60.159 50.000 21.70 13.81 41.18 3.93
116 117 0.907486 AGAAGTGCATGCTCTAGCCA 59.093 50.000 21.70 0.00 41.18 4.75
117 118 1.280133 AGAAGTGCATGCTCTAGCCAA 59.720 47.619 21.70 0.00 41.18 4.52
118 119 2.092538 AGAAGTGCATGCTCTAGCCAAT 60.093 45.455 21.70 5.92 41.18 3.16
119 120 1.676746 AGTGCATGCTCTAGCCAATG 58.323 50.000 20.22 0.00 41.18 2.82
120 121 0.030369 GTGCATGCTCTAGCCAATGC 59.970 55.000 20.33 16.33 45.25 3.56
121 122 2.411535 GCATGCTCTAGCCAATGCA 58.588 52.632 11.37 0.00 44.74 3.96
122 123 0.742505 GCATGCTCTAGCCAATGCAA 59.257 50.000 11.37 0.00 44.74 4.08
123 124 1.535437 GCATGCTCTAGCCAATGCAAC 60.535 52.381 11.37 2.38 44.74 4.17
124 125 1.746787 CATGCTCTAGCCAATGCAACA 59.253 47.619 0.00 0.00 41.13 3.33
125 126 1.908344 TGCTCTAGCCAATGCAACAA 58.092 45.000 0.00 0.00 41.13 2.83
126 127 2.237643 TGCTCTAGCCAATGCAACAAA 58.762 42.857 0.00 0.00 41.13 2.83
127 128 2.627221 TGCTCTAGCCAATGCAACAAAA 59.373 40.909 0.00 0.00 41.13 2.44
128 129 3.069300 TGCTCTAGCCAATGCAACAAAAA 59.931 39.130 0.00 0.00 41.13 1.94
162 163 8.697067 GCAATGCATTTATACATCAACAGATTC 58.303 33.333 9.83 0.00 0.00 2.52
290 297 5.356882 TCACGTGCTTCTTATTCTTTTGG 57.643 39.130 11.67 0.00 0.00 3.28
295 302 6.128172 ACGTGCTTCTTATTCTTTTGGATGAG 60.128 38.462 0.00 0.00 0.00 2.90
296 303 6.092670 CGTGCTTCTTATTCTTTTGGATGAGA 59.907 38.462 0.00 0.00 0.00 3.27
345 352 0.657312 CAGTTTCACACGCAGAGCAA 59.343 50.000 0.00 0.00 0.00 3.91
347 354 2.480037 CAGTTTCACACGCAGAGCAATA 59.520 45.455 0.00 0.00 0.00 1.90
393 401 6.462500 AGATGACCTCATTACATATGAGTGC 58.538 40.000 10.38 5.87 42.88 4.40
480 488 0.814410 TTCTCCCTCTCCGTCGATCG 60.814 60.000 9.36 9.36 39.52 3.69
486 494 2.064723 CTCTCCGTCGATCGCCATGT 62.065 60.000 11.09 0.00 38.35 3.21
510 518 5.484290 TCCTCCTTTGAGTAACCCTTAAGAG 59.516 44.000 3.36 0.00 36.86 2.85
520 528 2.440409 ACCCTTAAGAGAGTACGCGAA 58.560 47.619 15.93 0.00 0.00 4.70
521 529 2.821969 ACCCTTAAGAGAGTACGCGAAA 59.178 45.455 15.93 0.00 0.00 3.46
528 536 0.320160 AGAGTACGCGAAAACCACCC 60.320 55.000 15.93 0.00 0.00 4.61
533 541 0.320596 ACGCGAAAACCACCCGATAA 60.321 50.000 15.93 0.00 0.00 1.75
553 561 3.323622 TGCCAAGGATCGCAGGAT 58.676 55.556 0.63 0.00 34.96 3.24
624 636 8.598041 AGATGTGGGGACTCAATTATATAGTTC 58.402 37.037 0.00 0.00 37.39 3.01
634 646 8.865090 ACTCAATTATATAGTTCTCAGGACAGG 58.135 37.037 0.00 0.00 0.00 4.00
649 661 0.892755 ACAGGGCGATTACGAGAACA 59.107 50.000 0.00 0.00 42.66 3.18
650 662 1.480954 ACAGGGCGATTACGAGAACAT 59.519 47.619 0.00 0.00 42.66 2.71
651 663 2.128035 CAGGGCGATTACGAGAACATC 58.872 52.381 0.00 0.00 42.66 3.06
652 664 1.754803 AGGGCGATTACGAGAACATCA 59.245 47.619 0.00 0.00 42.66 3.07
653 665 2.365617 AGGGCGATTACGAGAACATCAT 59.634 45.455 0.00 0.00 42.66 2.45
674 686 5.534278 TCATACTTTCACAGCAACAATCCAA 59.466 36.000 0.00 0.00 0.00 3.53
678 690 4.462508 TTCACAGCAACAATCCAAAACA 57.537 36.364 0.00 0.00 0.00 2.83
680 692 4.431809 TCACAGCAACAATCCAAAACAAG 58.568 39.130 0.00 0.00 0.00 3.16
681 693 4.081752 TCACAGCAACAATCCAAAACAAGT 60.082 37.500 0.00 0.00 0.00 3.16
682 694 5.126222 TCACAGCAACAATCCAAAACAAGTA 59.874 36.000 0.00 0.00 0.00 2.24
685 697 5.459762 CAGCAACAATCCAAAACAAGTAGTG 59.540 40.000 0.00 0.00 0.00 2.74
686 698 5.127031 AGCAACAATCCAAAACAAGTAGTGT 59.873 36.000 0.00 0.00 44.64 3.55
688 700 6.559810 CAACAATCCAAAACAAGTAGTGTCA 58.440 36.000 0.00 0.00 40.60 3.58
689 701 6.767524 ACAATCCAAAACAAGTAGTGTCAA 57.232 33.333 0.00 0.00 40.60 3.18
690 702 7.346751 ACAATCCAAAACAAGTAGTGTCAAT 57.653 32.000 0.00 0.00 40.60 2.57
691 703 7.202526 ACAATCCAAAACAAGTAGTGTCAATG 58.797 34.615 0.00 0.00 40.60 2.82
692 704 5.766150 TCCAAAACAAGTAGTGTCAATGG 57.234 39.130 0.00 0.00 40.60 3.16
693 705 5.197451 TCCAAAACAAGTAGTGTCAATGGT 58.803 37.500 0.00 0.00 40.60 3.55
694 706 5.067153 TCCAAAACAAGTAGTGTCAATGGTG 59.933 40.000 0.00 0.00 40.60 4.17
698 710 6.861065 AACAAGTAGTGTCAATGGTGTTAG 57.139 37.500 0.00 0.00 40.60 2.34
699 711 4.755123 ACAAGTAGTGTCAATGGTGTTAGC 59.245 41.667 0.00 0.00 34.38 3.09
700 712 3.939066 AGTAGTGTCAATGGTGTTAGCC 58.061 45.455 0.00 0.00 0.00 3.93
701 713 1.808411 AGTGTCAATGGTGTTAGCCG 58.192 50.000 0.00 0.00 0.00 5.52
703 715 2.027192 AGTGTCAATGGTGTTAGCCGAT 60.027 45.455 0.00 0.00 0.00 4.18
704 716 2.747446 GTGTCAATGGTGTTAGCCGATT 59.253 45.455 0.00 0.00 0.00 3.34
705 717 3.936453 GTGTCAATGGTGTTAGCCGATTA 59.064 43.478 0.00 0.00 0.00 1.75
706 718 4.574828 GTGTCAATGGTGTTAGCCGATTAT 59.425 41.667 0.00 0.00 0.00 1.28
707 719 5.756347 GTGTCAATGGTGTTAGCCGATTATA 59.244 40.000 0.00 0.00 0.00 0.98
708 720 6.259167 GTGTCAATGGTGTTAGCCGATTATAA 59.741 38.462 0.00 0.00 0.00 0.98
709 721 6.995686 TGTCAATGGTGTTAGCCGATTATAAT 59.004 34.615 0.00 0.00 0.00 1.28
710 722 7.500892 TGTCAATGGTGTTAGCCGATTATAATT 59.499 33.333 0.00 0.00 0.00 1.40
711 723 7.803189 GTCAATGGTGTTAGCCGATTATAATTG 59.197 37.037 5.79 5.79 0.00 2.32
712 724 7.717436 TCAATGGTGTTAGCCGATTATAATTGA 59.283 33.333 13.48 0.24 0.00 2.57
713 725 7.672983 ATGGTGTTAGCCGATTATAATTGAG 57.327 36.000 13.48 5.75 0.00 3.02
714 726 5.468746 TGGTGTTAGCCGATTATAATTGAGC 59.531 40.000 13.48 13.77 0.00 4.26
715 727 5.106673 GGTGTTAGCCGATTATAATTGAGCC 60.107 44.000 13.48 2.98 0.00 4.70
716 728 5.001232 TGTTAGCCGATTATAATTGAGCCC 58.999 41.667 13.48 7.35 0.00 5.19
717 729 3.073274 AGCCGATTATAATTGAGCCCC 57.927 47.619 13.48 0.00 0.00 5.80
718 730 2.644798 AGCCGATTATAATTGAGCCCCT 59.355 45.455 13.48 0.80 0.00 4.79
719 731 3.010420 GCCGATTATAATTGAGCCCCTC 58.990 50.000 13.48 0.00 0.00 4.30
720 732 3.559171 GCCGATTATAATTGAGCCCCTCA 60.559 47.826 13.48 0.00 38.87 3.86
721 733 4.256920 CCGATTATAATTGAGCCCCTCAG 58.743 47.826 13.48 0.00 41.75 3.35
722 734 3.686726 CGATTATAATTGAGCCCCTCAGC 59.313 47.826 6.85 0.00 41.75 4.26
723 735 3.508845 TTATAATTGAGCCCCTCAGCC 57.491 47.619 0.00 0.00 41.75 4.85
724 736 0.480252 ATAATTGAGCCCCTCAGCCC 59.520 55.000 0.00 0.00 41.75 5.19
725 737 1.645402 TAATTGAGCCCCTCAGCCCC 61.645 60.000 0.00 0.00 41.75 5.80
726 738 3.978241 ATTGAGCCCCTCAGCCCCT 62.978 63.158 0.00 0.00 41.75 4.79
734 746 3.095163 CTCAGCCCCTCAGCCCAT 61.095 66.667 0.00 0.00 0.00 4.00
735 747 3.414193 TCAGCCCCTCAGCCCATG 61.414 66.667 0.00 0.00 0.00 3.66
736 748 3.414193 CAGCCCCTCAGCCCATGA 61.414 66.667 0.00 0.00 36.21 3.07
842 854 9.270640 GAGAGCTCATGAGATAACATAAACAAT 57.729 33.333 27.04 0.00 0.00 2.71
843 855 9.270640 AGAGCTCATGAGATAACATAAACAATC 57.729 33.333 27.04 3.17 0.00 2.67
857 869 0.957395 ACAATCTGCAACCTGGCTCG 60.957 55.000 0.00 0.00 34.04 5.03
868 880 4.142381 GCAACCTGGCTCGAGATTAATTTT 60.142 41.667 18.75 0.00 0.00 1.82
873 885 3.876914 TGGCTCGAGATTAATTTTGCGAT 59.123 39.130 18.75 0.00 0.00 4.58
875 887 5.050363 TGGCTCGAGATTAATTTTGCGATAC 60.050 40.000 18.75 0.00 0.00 2.24
876 888 5.374898 GCTCGAGATTAATTTTGCGATACC 58.625 41.667 18.75 0.00 0.00 2.73
877 889 5.570262 TCGAGATTAATTTTGCGATACCG 57.430 39.130 0.00 0.00 39.16 4.02
878 890 5.045215 TCGAGATTAATTTTGCGATACCGT 58.955 37.500 0.00 0.00 38.24 4.83
879 891 6.207928 TCGAGATTAATTTTGCGATACCGTA 58.792 36.000 0.00 0.00 38.24 4.02
903 915 3.832171 CGTCGTTGCAGCGAGCTC 61.832 66.667 26.43 13.53 45.94 4.09
912 924 2.520741 AGCGAGCTCCTCCTAGCC 60.521 66.667 8.47 0.00 43.86 3.93
926 938 0.949397 CTAGCCCGTCGCATGTACTA 59.051 55.000 0.00 0.00 41.38 1.82
927 939 0.949397 TAGCCCGTCGCATGTACTAG 59.051 55.000 0.00 0.00 41.38 2.57
937 949 6.304922 CCGTCGCATGTACTAGTATAAATCAC 59.695 42.308 5.75 0.00 0.00 3.06
972 984 2.202878 TCGCATTAGCCCAGACGC 60.203 61.111 0.00 0.00 37.52 5.19
973 985 3.630148 CGCATTAGCCCAGACGCG 61.630 66.667 3.53 3.53 37.52 6.01
974 986 3.272334 GCATTAGCCCAGACGCGG 61.272 66.667 12.47 0.00 33.58 6.46
975 987 2.186903 CATTAGCCCAGACGCGGT 59.813 61.111 12.47 0.00 0.00 5.68
976 988 1.440060 CATTAGCCCAGACGCGGTA 59.560 57.895 12.47 0.00 0.00 4.02
977 989 0.597637 CATTAGCCCAGACGCGGTAG 60.598 60.000 12.47 0.00 0.00 3.18
978 990 1.745320 ATTAGCCCAGACGCGGTAGG 61.745 60.000 12.47 8.66 0.00 3.18
1039 1057 3.188100 CACCATCATCACGCGCGT 61.188 61.111 32.73 32.73 0.00 6.01
1043 1061 3.257561 ATCATCACGCGCGTCTGC 61.258 61.111 35.61 0.00 37.91 4.26
1255 1307 1.072173 AGTCTACTTGTGGCACATGCA 59.928 47.619 27.52 17.46 44.52 3.96
1294 1346 6.961554 CGTGCTGACCTATAATTTGACTTTTC 59.038 38.462 0.00 0.00 0.00 2.29
1311 1363 0.834612 TTCTTGACTCGGGTGTGGTT 59.165 50.000 0.00 0.00 0.00 3.67
1319 1371 3.061848 GGGTGTGGTTGATGGGCG 61.062 66.667 0.00 0.00 0.00 6.13
1320 1372 2.282180 GGTGTGGTTGATGGGCGT 60.282 61.111 0.00 0.00 0.00 5.68
1321 1373 1.003112 GGTGTGGTTGATGGGCGTA 60.003 57.895 0.00 0.00 0.00 4.42
1322 1374 1.303091 GGTGTGGTTGATGGGCGTAC 61.303 60.000 0.00 0.00 0.00 3.67
1323 1375 0.321298 GTGTGGTTGATGGGCGTACT 60.321 55.000 0.00 0.00 0.00 2.73
1324 1376 0.398696 TGTGGTTGATGGGCGTACTT 59.601 50.000 0.00 0.00 0.00 2.24
1325 1377 0.802494 GTGGTTGATGGGCGTACTTG 59.198 55.000 0.00 0.00 0.00 3.16
1326 1378 0.322098 TGGTTGATGGGCGTACTTGG 60.322 55.000 0.00 0.00 0.00 3.61
1327 1379 1.029947 GGTTGATGGGCGTACTTGGG 61.030 60.000 0.00 0.00 0.00 4.12
1328 1380 1.377987 TTGATGGGCGTACTTGGGC 60.378 57.895 0.00 0.00 0.00 5.36
1856 1912 3.706086 ACAAGGTGCAAGTCAAATCCTTT 59.294 39.130 0.00 0.00 33.73 3.11
1930 1995 0.303493 TTCTTGTCACGACTTTGCGC 59.697 50.000 0.00 0.00 33.86 6.09
1965 2030 1.711375 ACGAGCTCCTATGGGGATCTA 59.289 52.381 8.47 0.00 44.15 1.98
2271 2367 1.306997 CCCAAGTCCAGCTCCCCTA 60.307 63.158 0.00 0.00 0.00 3.53
2686 2791 4.353437 GCCGGACCAGAACGACGT 62.353 66.667 5.05 0.00 0.00 4.34
2687 2792 2.337532 CCGGACCAGAACGACGTT 59.662 61.111 14.11 14.11 0.00 3.99
2735 2840 2.363276 TCGGAGCCCACCACGTAT 60.363 61.111 0.00 0.00 0.00 3.06
2901 3182 6.783708 ATCATCCCCGTCTCTTATATTCTC 57.216 41.667 0.00 0.00 0.00 2.87
2930 3294 8.305317 ACGGAGGTAATTACTATTTAGCTGATC 58.695 37.037 15.05 0.00 37.48 2.92
3007 3371 0.958822 GCAAGAAATCCCACGTTGGT 59.041 50.000 5.46 0.00 35.17 3.67
3031 3395 1.742761 ATGAAACCATCTGGACTGCG 58.257 50.000 2.55 0.00 38.94 5.18
3068 3433 2.670229 GCTTCACGAACGACACCATCTA 60.670 50.000 0.14 0.00 0.00 1.98
3201 3566 2.509336 GGACGACACCATCTGCGG 60.509 66.667 0.00 0.00 0.00 5.69
3312 3679 3.002862 GCGTCGGGCACAAAATTATCATA 59.997 43.478 0.00 0.00 42.87 2.15
3452 3826 3.192422 CGCTTTCTCTCTTCTCTCCTTCA 59.808 47.826 0.00 0.00 0.00 3.02
3467 3841 3.501349 TCCTTCATCTTATCCCTCCTCG 58.499 50.000 0.00 0.00 0.00 4.63
3468 3842 3.140332 TCCTTCATCTTATCCCTCCTCGA 59.860 47.826 0.00 0.00 0.00 4.04
3506 3880 3.519930 GGTCGCCCGTCTCTCTCC 61.520 72.222 0.00 0.00 0.00 3.71
3570 3946 0.458025 GACGATCTTTTCCGGCGAGT 60.458 55.000 9.30 0.00 0.00 4.18
3638 4014 1.645455 CATTCGCATGGCTCCTTCG 59.355 57.895 0.00 0.00 0.00 3.79
3639 4015 2.182842 ATTCGCATGGCTCCTTCGC 61.183 57.895 0.00 0.00 0.00 4.70
3655 4031 1.302033 CGCCTCCCACAGATATGGC 60.302 63.158 0.00 0.00 38.55 4.40
3662 4038 0.179048 CCACAGATATGGCGAGGCAA 60.179 55.000 2.86 0.00 31.52 4.52
3676 4052 3.061848 GCAATGTGGTGGGGACGG 61.062 66.667 0.00 0.00 0.00 4.79
3737 4113 3.499918 CACTTCTGGGTGATGAAGACAAC 59.500 47.826 9.33 0.00 41.38 3.32
3744 4120 2.046314 ATGAAGACAACGCCCCCG 60.046 61.111 0.00 0.00 41.14 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.439679 GCTCACGTTTTACCCTGAGG 58.560 55.000 0.00 0.00 40.04 3.86
7 8 1.439679 GGCTCACGTTTTACCCTGAG 58.560 55.000 0.00 0.00 34.43 3.35
8 9 0.320073 CGGCTCACGTTTTACCCTGA 60.320 55.000 0.00 0.00 37.93 3.86
9 10 0.320073 TCGGCTCACGTTTTACCCTG 60.320 55.000 0.00 0.00 44.69 4.45
10 11 0.393820 TTCGGCTCACGTTTTACCCT 59.606 50.000 0.00 0.00 44.69 4.34
11 12 1.196127 CTTTCGGCTCACGTTTTACCC 59.804 52.381 0.00 0.00 44.69 3.69
12 13 1.869132 ACTTTCGGCTCACGTTTTACC 59.131 47.619 0.00 0.00 44.69 2.85
13 14 2.349155 CCACTTTCGGCTCACGTTTTAC 60.349 50.000 0.00 0.00 44.69 2.01
14 15 1.868498 CCACTTTCGGCTCACGTTTTA 59.132 47.619 0.00 0.00 44.69 1.52
15 16 0.661020 CCACTTTCGGCTCACGTTTT 59.339 50.000 0.00 0.00 44.69 2.43
16 17 1.164041 CCCACTTTCGGCTCACGTTT 61.164 55.000 0.00 0.00 44.69 3.60
17 18 1.597027 CCCACTTTCGGCTCACGTT 60.597 57.895 0.00 0.00 44.69 3.99
18 19 2.030562 CCCACTTTCGGCTCACGT 59.969 61.111 0.00 0.00 44.69 4.49
19 20 3.423154 GCCCACTTTCGGCTCACG 61.423 66.667 0.00 0.00 43.48 4.35
25 26 0.318120 AAATTGCAGCCCACTTTCGG 59.682 50.000 0.00 0.00 0.00 4.30
26 27 2.986479 GTTAAATTGCAGCCCACTTTCG 59.014 45.455 0.00 0.00 30.20 3.46
27 28 3.989817 CAGTTAAATTGCAGCCCACTTTC 59.010 43.478 0.00 0.00 30.20 2.62
28 29 3.803368 GCAGTTAAATTGCAGCCCACTTT 60.803 43.478 8.02 0.00 41.17 2.66
29 30 2.289010 GCAGTTAAATTGCAGCCCACTT 60.289 45.455 8.02 0.00 41.17 3.16
30 31 1.273327 GCAGTTAAATTGCAGCCCACT 59.727 47.619 8.02 0.00 41.17 4.00
31 32 1.713597 GCAGTTAAATTGCAGCCCAC 58.286 50.000 8.02 0.00 41.17 4.61
32 33 0.243365 CGCAGTTAAATTGCAGCCCA 59.757 50.000 12.19 0.00 41.59 5.36
33 34 1.078201 GCGCAGTTAAATTGCAGCCC 61.078 55.000 0.30 0.00 41.59 5.19
34 35 1.078201 GGCGCAGTTAAATTGCAGCC 61.078 55.000 21.30 21.30 45.92 4.85
35 36 0.388391 TGGCGCAGTTAAATTGCAGC 60.388 50.000 10.83 13.88 41.59 5.25
36 37 1.068333 ACTGGCGCAGTTAAATTGCAG 60.068 47.619 10.83 5.53 42.59 4.41
37 38 0.958091 ACTGGCGCAGTTAAATTGCA 59.042 45.000 10.83 0.00 42.59 4.08
38 39 1.617740 GACTGGCGCAGTTAAATTGC 58.382 50.000 10.83 3.69 45.44 3.56
39 40 1.465689 CCGACTGGCGCAGTTAAATTG 60.466 52.381 10.83 0.00 45.44 2.32
40 41 0.802494 CCGACTGGCGCAGTTAAATT 59.198 50.000 10.83 0.00 45.44 1.82
41 42 1.024579 CCCGACTGGCGCAGTTAAAT 61.025 55.000 10.83 0.00 45.44 1.40
42 43 1.669760 CCCGACTGGCGCAGTTAAA 60.670 57.895 10.83 0.00 45.44 1.52
43 44 2.047655 CCCGACTGGCGCAGTTAA 60.048 61.111 10.83 0.00 45.44 2.01
44 45 3.291101 GACCCGACTGGCGCAGTTA 62.291 63.158 10.83 0.00 45.44 2.24
45 46 4.681978 GACCCGACTGGCGCAGTT 62.682 66.667 10.83 0.00 45.44 3.16
47 48 4.379243 AAGACCCGACTGGCGCAG 62.379 66.667 10.83 7.58 39.11 5.18
48 49 4.680237 CAAGACCCGACTGGCGCA 62.680 66.667 10.83 0.00 39.11 6.09
49 50 3.876589 TTCAAGACCCGACTGGCGC 62.877 63.158 0.00 0.00 39.11 6.53
50 51 2.027625 GTTCAAGACCCGACTGGCG 61.028 63.158 0.00 0.00 37.83 5.69
51 52 0.670854 GAGTTCAAGACCCGACTGGC 60.671 60.000 0.00 0.00 37.83 4.85
52 53 0.679505 TGAGTTCAAGACCCGACTGG 59.320 55.000 0.00 0.00 41.37 4.00
53 54 2.526304 TTGAGTTCAAGACCCGACTG 57.474 50.000 0.00 0.00 0.00 3.51
71 72 4.168101 TGGTATCAGTTCCAAGAGGTCTT 58.832 43.478 0.00 0.00 36.45 3.01
72 73 3.791320 TGGTATCAGTTCCAAGAGGTCT 58.209 45.455 0.00 0.00 35.89 3.85
73 74 4.080863 ACATGGTATCAGTTCCAAGAGGTC 60.081 45.833 0.00 0.00 37.27 3.85
74 75 3.846588 ACATGGTATCAGTTCCAAGAGGT 59.153 43.478 0.00 0.00 37.27 3.85
75 76 4.494091 ACATGGTATCAGTTCCAAGAGG 57.506 45.455 0.00 0.00 37.27 3.69
76 77 6.471233 TCTACATGGTATCAGTTCCAAGAG 57.529 41.667 0.00 0.00 37.27 2.85
77 78 6.440647 ACTTCTACATGGTATCAGTTCCAAGA 59.559 38.462 0.00 0.00 37.27 3.02
78 79 6.536582 CACTTCTACATGGTATCAGTTCCAAG 59.463 42.308 0.00 0.00 37.27 3.61
79 80 6.406370 CACTTCTACATGGTATCAGTTCCAA 58.594 40.000 0.00 0.00 37.27 3.53
80 81 5.626809 GCACTTCTACATGGTATCAGTTCCA 60.627 44.000 0.00 0.00 38.14 3.53
81 82 4.811557 GCACTTCTACATGGTATCAGTTCC 59.188 45.833 0.00 0.00 0.00 3.62
82 83 5.419542 TGCACTTCTACATGGTATCAGTTC 58.580 41.667 0.00 0.00 0.00 3.01
83 84 5.420725 TGCACTTCTACATGGTATCAGTT 57.579 39.130 0.00 0.00 0.00 3.16
84 85 5.363101 CATGCACTTCTACATGGTATCAGT 58.637 41.667 0.00 0.00 39.98 3.41
85 86 4.212847 GCATGCACTTCTACATGGTATCAG 59.787 45.833 14.21 0.00 43.13 2.90
86 87 4.129380 GCATGCACTTCTACATGGTATCA 58.871 43.478 14.21 0.00 43.13 2.15
87 88 4.739046 GCATGCACTTCTACATGGTATC 57.261 45.455 14.21 0.00 43.13 2.24
90 91 2.795231 AGCATGCACTTCTACATGGT 57.205 45.000 21.98 2.10 46.94 3.55
91 92 2.915349 AGAGCATGCACTTCTACATGG 58.085 47.619 21.98 0.00 43.13 3.66
92 93 3.493877 GCTAGAGCATGCACTTCTACATG 59.506 47.826 22.83 8.90 45.19 3.21
93 94 3.494048 GGCTAGAGCATGCACTTCTACAT 60.494 47.826 22.83 0.00 44.36 2.29
94 95 2.159043 GGCTAGAGCATGCACTTCTACA 60.159 50.000 22.83 3.70 44.36 2.74
95 96 2.159043 TGGCTAGAGCATGCACTTCTAC 60.159 50.000 22.83 12.67 44.36 2.59
96 97 2.110578 TGGCTAGAGCATGCACTTCTA 58.889 47.619 22.83 17.21 44.36 2.10
97 98 0.907486 TGGCTAGAGCATGCACTTCT 59.093 50.000 22.83 17.00 44.36 2.85
98 99 1.742761 TTGGCTAGAGCATGCACTTC 58.257 50.000 22.83 14.30 44.36 3.01
99 100 2.022195 CATTGGCTAGAGCATGCACTT 58.978 47.619 22.83 8.33 44.36 3.16
100 101 1.676746 CATTGGCTAGAGCATGCACT 58.323 50.000 21.45 21.45 44.36 4.40
101 102 0.030369 GCATTGGCTAGAGCATGCAC 59.970 55.000 21.98 14.59 44.74 4.57
102 103 2.411535 GCATTGGCTAGAGCATGCA 58.588 52.632 21.98 0.00 44.74 3.96
103 104 0.742505 TTGCATTGGCTAGAGCATGC 59.257 50.000 10.51 10.51 45.25 4.06
104 105 1.746787 TGTTGCATTGGCTAGAGCATG 59.253 47.619 3.54 0.90 44.36 4.06
105 106 2.133281 TGTTGCATTGGCTAGAGCAT 57.867 45.000 3.54 0.00 44.36 3.79
106 107 1.908344 TTGTTGCATTGGCTAGAGCA 58.092 45.000 3.54 0.00 44.36 4.26
107 108 3.302365 TTTTGTTGCATTGGCTAGAGC 57.698 42.857 0.00 0.00 41.91 4.09
135 136 7.098074 TCTGTTGATGTATAAATGCATTGCA 57.902 32.000 13.82 14.72 44.86 4.08
136 137 8.583810 AATCTGTTGATGTATAAATGCATTGC 57.416 30.769 13.82 0.46 33.17 3.56
137 138 8.898792 CGAATCTGTTGATGTATAAATGCATTG 58.101 33.333 13.82 0.00 33.17 2.82
138 139 8.077991 CCGAATCTGTTGATGTATAAATGCATT 58.922 33.333 5.99 5.99 33.17 3.56
139 140 7.229306 ACCGAATCTGTTGATGTATAAATGCAT 59.771 33.333 0.00 0.00 35.78 3.96
140 141 6.542005 ACCGAATCTGTTGATGTATAAATGCA 59.458 34.615 0.00 0.00 32.44 3.96
141 142 6.959361 ACCGAATCTGTTGATGTATAAATGC 58.041 36.000 0.00 0.00 32.44 3.56
149 150 8.830580 CATTAAGAATACCGAATCTGTTGATGT 58.169 33.333 0.00 0.00 32.44 3.06
150 151 8.830580 ACATTAAGAATACCGAATCTGTTGATG 58.169 33.333 0.00 0.00 32.44 3.07
151 152 8.964476 ACATTAAGAATACCGAATCTGTTGAT 57.036 30.769 0.00 0.00 33.70 2.57
152 153 8.664798 CAACATTAAGAATACCGAATCTGTTGA 58.335 33.333 0.00 0.00 32.15 3.18
153 154 8.664798 TCAACATTAAGAATACCGAATCTGTTG 58.335 33.333 0.00 0.00 31.93 3.33
154 155 8.786826 TCAACATTAAGAATACCGAATCTGTT 57.213 30.769 0.00 0.00 0.00 3.16
155 156 8.964476 ATCAACATTAAGAATACCGAATCTGT 57.036 30.769 0.00 0.00 0.00 3.41
157 158 9.193133 CGTATCAACATTAAGAATACCGAATCT 57.807 33.333 0.00 0.00 0.00 2.40
162 163 9.763465 AAAAACGTATCAACATTAAGAATACCG 57.237 29.630 0.00 0.00 0.00 4.02
237 238 4.344104 CCTTCCATCCCAAAATGTAGTGT 58.656 43.478 0.00 0.00 0.00 3.55
243 244 2.252535 ACCCCTTCCATCCCAAAATG 57.747 50.000 0.00 0.00 0.00 2.32
253 254 2.498481 CACGTGATTACTACCCCTTCCA 59.502 50.000 10.90 0.00 0.00 3.53
290 297 5.180868 ACTGAACTCTGCATGTTTTCTCATC 59.819 40.000 6.67 0.00 0.00 2.92
295 302 4.512944 TCTGACTGAACTCTGCATGTTTTC 59.487 41.667 6.67 5.38 0.00 2.29
296 303 4.274459 GTCTGACTGAACTCTGCATGTTTT 59.726 41.667 0.00 0.00 0.00 2.43
345 352 3.113824 TGGCCCAAATCCAATTTGCTAT 58.886 40.909 0.00 0.00 46.27 2.97
347 354 1.003464 GTGGCCCAAATCCAATTTGCT 59.997 47.619 0.00 0.00 46.27 3.91
393 401 3.499918 ACATCAGAACAGAAAAAGGCTCG 59.500 43.478 0.00 0.00 0.00 5.03
480 488 3.010420 GTTACTCAAAGGAGGACATGGC 58.990 50.000 0.00 0.00 45.81 4.40
486 494 5.408824 TCTTAAGGGTTACTCAAAGGAGGA 58.591 41.667 1.85 0.00 45.81 3.71
510 518 1.620413 CGGGTGGTTTTCGCGTACTC 61.620 60.000 5.77 0.00 36.70 2.59
520 528 0.679960 GGCAGCTTATCGGGTGGTTT 60.680 55.000 0.00 0.00 35.53 3.27
521 529 1.077716 GGCAGCTTATCGGGTGGTT 60.078 57.895 0.00 0.00 35.53 3.67
528 536 1.143305 CGATCCTTGGCAGCTTATCG 58.857 55.000 8.48 8.48 0.00 2.92
533 541 2.124819 CTGCGATCCTTGGCAGCT 60.125 61.111 7.29 0.00 45.76 4.24
550 558 3.399181 TGTGGTGCCTCCGGATCC 61.399 66.667 3.57 0.00 39.52 3.36
553 561 3.625897 CAGTGTGGTGCCTCCGGA 61.626 66.667 2.93 2.93 39.52 5.14
569 577 0.452184 GTGCGTTCTCCTCTCGATCA 59.548 55.000 0.00 0.00 0.00 2.92
606 614 8.861086 TGTCCTGAGAACTATATAATTGAGTCC 58.139 37.037 0.00 0.00 0.00 3.85
624 636 0.249073 CGTAATCGCCCTGTCCTGAG 60.249 60.000 0.00 0.00 0.00 3.35
634 646 4.547532 AGTATGATGTTCTCGTAATCGCC 58.452 43.478 0.00 0.00 36.96 5.54
649 661 5.711506 TGGATTGTTGCTGTGAAAGTATGAT 59.288 36.000 0.00 0.00 0.00 2.45
650 662 5.069318 TGGATTGTTGCTGTGAAAGTATGA 58.931 37.500 0.00 0.00 0.00 2.15
651 663 5.375417 TGGATTGTTGCTGTGAAAGTATG 57.625 39.130 0.00 0.00 0.00 2.39
652 664 6.403866 TTTGGATTGTTGCTGTGAAAGTAT 57.596 33.333 0.00 0.00 0.00 2.12
653 665 5.843673 TTTGGATTGTTGCTGTGAAAGTA 57.156 34.783 0.00 0.00 0.00 2.24
674 686 6.238648 GCTAACACCATTGACACTACTTGTTT 60.239 38.462 0.00 0.00 39.17 2.83
678 690 4.324267 GGCTAACACCATTGACACTACTT 58.676 43.478 0.00 0.00 0.00 2.24
680 692 2.671396 CGGCTAACACCATTGACACTAC 59.329 50.000 0.00 0.00 0.00 2.73
681 693 2.563620 TCGGCTAACACCATTGACACTA 59.436 45.455 0.00 0.00 0.00 2.74
682 694 1.346395 TCGGCTAACACCATTGACACT 59.654 47.619 0.00 0.00 0.00 3.55
685 697 6.854496 TTATAATCGGCTAACACCATTGAC 57.146 37.500 0.00 0.00 0.00 3.18
686 698 7.717436 TCAATTATAATCGGCTAACACCATTGA 59.283 33.333 0.00 0.00 0.00 2.57
688 700 7.308589 GCTCAATTATAATCGGCTAACACCATT 60.309 37.037 0.00 0.00 0.00 3.16
689 701 6.149474 GCTCAATTATAATCGGCTAACACCAT 59.851 38.462 0.00 0.00 0.00 3.55
690 702 5.468746 GCTCAATTATAATCGGCTAACACCA 59.531 40.000 0.00 0.00 0.00 4.17
691 703 5.106673 GGCTCAATTATAATCGGCTAACACC 60.107 44.000 0.00 0.00 0.00 4.16
692 704 5.106673 GGGCTCAATTATAATCGGCTAACAC 60.107 44.000 0.00 0.00 0.00 3.32
693 705 5.001232 GGGCTCAATTATAATCGGCTAACA 58.999 41.667 0.00 0.00 0.00 2.41
694 706 4.395231 GGGGCTCAATTATAATCGGCTAAC 59.605 45.833 0.00 0.55 0.00 2.34
698 710 3.010420 GAGGGGCTCAATTATAATCGGC 58.990 50.000 0.00 3.96 0.00 5.54
699 711 4.256920 CTGAGGGGCTCAATTATAATCGG 58.743 47.826 0.00 0.00 40.18 4.18
700 712 3.686726 GCTGAGGGGCTCAATTATAATCG 59.313 47.826 0.00 0.00 40.18 3.34
701 713 4.013050 GGCTGAGGGGCTCAATTATAATC 58.987 47.826 0.00 0.00 40.18 1.75
703 715 2.108250 GGGCTGAGGGGCTCAATTATAA 59.892 50.000 0.00 0.00 40.18 0.98
704 716 1.705186 GGGCTGAGGGGCTCAATTATA 59.295 52.381 0.00 0.00 40.18 0.98
705 717 0.480252 GGGCTGAGGGGCTCAATTAT 59.520 55.000 0.00 0.00 40.18 1.28
706 718 1.645402 GGGGCTGAGGGGCTCAATTA 61.645 60.000 0.00 0.00 40.18 1.40
707 719 2.685999 GGGCTGAGGGGCTCAATT 59.314 61.111 0.00 0.00 40.18 2.32
708 720 3.424105 GGGGCTGAGGGGCTCAAT 61.424 66.667 0.00 0.00 40.18 2.57
709 721 4.682714 AGGGGCTGAGGGGCTCAA 62.683 66.667 0.00 0.00 44.26 3.02
717 729 3.095163 ATGGGCTGAGGGGCTGAG 61.095 66.667 0.00 0.00 40.65 3.35
718 730 3.414193 CATGGGCTGAGGGGCTGA 61.414 66.667 0.00 0.00 40.65 4.26
719 731 2.693896 GATCATGGGCTGAGGGGCTG 62.694 65.000 0.00 0.00 37.28 4.85
720 732 2.369291 ATCATGGGCTGAGGGGCT 60.369 61.111 0.00 0.00 37.28 5.19
721 733 2.114838 GATCATGGGCTGAGGGGC 59.885 66.667 0.00 0.00 37.28 5.80
722 734 2.838467 GGGATCATGGGCTGAGGGG 61.838 68.421 0.00 0.00 37.28 4.79
723 735 1.773391 AGGGATCATGGGCTGAGGG 60.773 63.158 0.00 0.00 37.28 4.30
724 736 1.454976 CAGGGATCATGGGCTGAGG 59.545 63.158 0.00 0.00 37.28 3.86
725 737 1.058428 TCCAGGGATCATGGGCTGAG 61.058 60.000 14.39 0.00 37.28 3.35
726 738 0.402419 ATCCAGGGATCATGGGCTGA 60.402 55.000 14.39 0.00 38.44 4.26
727 739 2.161581 ATCCAGGGATCATGGGCTG 58.838 57.895 14.39 0.00 38.44 4.85
728 740 4.787592 ATCCAGGGATCATGGGCT 57.212 55.556 14.39 2.49 38.44 5.19
736 748 8.405850 AGTATCTAATCTAACAGATCCAGGGAT 58.594 37.037 0.00 0.00 32.89 3.85
842 854 1.260538 ATCTCGAGCCAGGTTGCAGA 61.261 55.000 7.81 0.00 0.00 4.26
843 855 0.392193 AATCTCGAGCCAGGTTGCAG 60.392 55.000 7.81 0.00 0.00 4.41
857 869 6.074676 ACGTACGGTATCGCAAAATTAATCTC 60.075 38.462 21.06 0.00 40.63 2.75
868 880 0.576798 CGTCTACGTACGGTATCGCA 59.423 55.000 21.06 0.00 39.19 5.10
903 915 3.227276 ATGCGACGGGCTAGGAGG 61.227 66.667 0.00 0.00 44.05 4.30
912 924 6.304922 GTGATTTATACTAGTACATGCGACGG 59.695 42.308 4.31 0.00 0.00 4.79
926 938 3.207265 TGCATGGCGGTGATTTATACT 57.793 42.857 0.00 0.00 0.00 2.12
927 939 4.229096 CAATGCATGGCGGTGATTTATAC 58.771 43.478 0.00 0.00 0.00 1.47
937 949 1.149361 GACATTGCAATGCATGGCGG 61.149 55.000 33.94 14.88 38.76 6.13
972 984 1.064296 CGACTGCTACAGCCTACCG 59.936 63.158 0.00 0.00 41.18 4.02
973 985 1.437986 CCGACTGCTACAGCCTACC 59.562 63.158 0.00 0.00 41.18 3.18
974 986 1.035932 TCCCGACTGCTACAGCCTAC 61.036 60.000 0.00 0.00 41.18 3.18
975 987 0.752009 CTCCCGACTGCTACAGCCTA 60.752 60.000 0.00 0.00 41.18 3.93
976 988 2.037367 TCCCGACTGCTACAGCCT 59.963 61.111 0.00 0.00 41.18 4.58
977 989 2.010582 CTCTCCCGACTGCTACAGCC 62.011 65.000 0.00 0.00 41.18 4.85
978 990 1.032657 TCTCTCCCGACTGCTACAGC 61.033 60.000 0.00 0.00 42.50 4.40
979 991 1.403679 CTTCTCTCCCGACTGCTACAG 59.596 57.143 0.00 0.00 37.52 2.74
980 992 1.004394 TCTTCTCTCCCGACTGCTACA 59.996 52.381 0.00 0.00 0.00 2.74
1039 1057 2.548067 GGGAGAAGACAAGAAACGCAGA 60.548 50.000 0.00 0.00 0.00 4.26
1043 1061 2.288273 ACGAGGGAGAAGACAAGAAACG 60.288 50.000 0.00 0.00 0.00 3.60
1052 1070 1.075698 AGAACCAGACGAGGGAGAAGA 59.924 52.381 0.00 0.00 0.00 2.87
1255 1307 1.536766 CAGCACGTTGACCACAATCAT 59.463 47.619 0.00 0.00 38.32 2.45
1281 1333 6.017440 CACCCGAGTCAAGAAAAGTCAAATTA 60.017 38.462 0.00 0.00 0.00 1.40
1294 1346 0.105964 TCAACCACACCCGAGTCAAG 59.894 55.000 0.00 0.00 0.00 3.02
1311 1363 2.270850 GCCCAAGTACGCCCATCA 59.729 61.111 0.00 0.00 0.00 3.07
1319 1371 3.971109 GACCTGCCGGCCCAAGTAC 62.971 68.421 26.77 7.05 0.00 2.73
1320 1372 3.712907 GACCTGCCGGCCCAAGTA 61.713 66.667 26.77 2.02 0.00 2.24
1601 1657 1.876714 CTCGTACACATTCCGCGGG 60.877 63.158 27.83 12.37 0.00 6.13
1856 1912 1.195900 GTTGCACGGCGTGATCTTTTA 59.804 47.619 40.94 15.39 35.23 1.52
1891 1947 2.515926 ACACGCAGGAGCACTATATG 57.484 50.000 0.00 0.00 42.27 1.78
1965 2030 4.790962 CGCCCAGAGCAGCCATGT 62.791 66.667 0.00 0.00 44.04 3.21
2084 2149 2.168936 TGTTTCAGTTACCCGTGACAGT 59.831 45.455 0.00 0.00 0.00 3.55
2610 2715 4.281947 GCCGGCGTAGAGGTAGCC 62.282 72.222 12.58 0.00 46.88 3.93
2735 2840 2.918802 ACGAGGGGTGCGTTGGTA 60.919 61.111 0.00 0.00 39.18 3.25
2753 2858 0.605319 CAAAGTAGGCGAGGCAACCA 60.605 55.000 0.00 0.00 37.17 3.67
2879 3146 5.641155 TGAGAATATAAGAGACGGGGATGA 58.359 41.667 0.00 0.00 0.00 2.92
2880 3147 5.712446 TCTGAGAATATAAGAGACGGGGATG 59.288 44.000 0.00 0.00 0.00 3.51
2901 3182 7.595502 CAGCTAAATAGTAATTACCTCCGTCTG 59.404 40.741 12.05 8.05 0.00 3.51
2930 3294 4.625972 ACACCTCGGTAAGTTGTTTTTG 57.374 40.909 0.00 0.00 0.00 2.44
3007 3371 5.428253 GCAGTCCAGATGGTTTCATTACTA 58.572 41.667 0.00 0.00 36.34 1.82
3031 3395 3.920412 GTGAAGCAATTTCGGGATCAAAC 59.080 43.478 0.00 0.00 38.71 2.93
3089 3454 2.860136 CAACGCTGTCATGTATCGTCAT 59.140 45.455 0.00 0.00 32.53 3.06
3149 3514 3.686241 CGAGATTCAAATGCAGTCCAGAA 59.314 43.478 0.00 0.00 0.00 3.02
3201 3566 2.033424 GCAGTTGGGAAGGAAATATCGC 59.967 50.000 0.00 0.00 0.00 4.58
3312 3679 6.945218 AGATTCAAAGAGCTCTTCTACACAT 58.055 36.000 28.58 14.57 34.14 3.21
3401 3775 4.385405 GCCCAGAGCTGCGTGACT 62.385 66.667 0.00 0.00 38.99 3.41
3452 3826 1.249407 GCGTCGAGGAGGGATAAGAT 58.751 55.000 9.75 0.00 0.00 2.40
3467 3841 4.666532 GTGTGGTTGCGCTGCGTC 62.667 66.667 24.04 15.82 0.00 5.19
3506 3880 2.443016 CGGAGGTGGAGGAGGGAG 60.443 72.222 0.00 0.00 0.00 4.30
3547 3921 1.708027 CCGGAAAAGATCGTCGTGC 59.292 57.895 0.00 0.00 0.00 5.34
3549 3923 1.804326 CGCCGGAAAAGATCGTCGT 60.804 57.895 5.05 0.00 0.00 4.34
3551 3925 0.458025 ACTCGCCGGAAAAGATCGTC 60.458 55.000 5.05 0.00 0.00 4.20
3552 3926 0.736325 CACTCGCCGGAAAAGATCGT 60.736 55.000 5.05 0.00 0.00 3.73
3553 3927 1.421410 CCACTCGCCGGAAAAGATCG 61.421 60.000 5.05 0.00 0.00 3.69
3612 3988 1.585517 CCATGCGAATGCCACAACA 59.414 52.632 0.00 0.00 41.78 3.33
3638 4014 1.302033 CGCCATATCTGTGGGAGGC 60.302 63.158 0.00 0.00 39.73 4.70
3639 4015 0.319728 CTCGCCATATCTGTGGGAGG 59.680 60.000 0.00 0.00 39.73 4.30
3655 4031 2.751436 CCCCACCACATTGCCTCG 60.751 66.667 0.00 0.00 0.00 4.63
3662 4038 4.344865 GCACCGTCCCCACCACAT 62.345 66.667 0.00 0.00 0.00 3.21
3744 4120 2.174363 AACTTACCGGTTGTAGCACC 57.826 50.000 15.04 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.