Multiple sequence alignment - TraesCS2D01G174400

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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 TraesCS2D01G174400 chr2D 100.000 3690 0 0 1 3690 117841943 117838254 0.000000e+00 6815
1 TraesCS2D01G174400 chr2D 90.909 583 39 5 3111 3681 331607228 331607808 0.000000e+00 771
2 TraesCS2D01G174400 chr2D 88.496 113 9 4 3016 3125 382450347 382450458 2.310000e-27 134
3 TraesCS2D01G174400 chr2B 91.622 2972 169 42 786 3690 168623043 168620085 0.000000e+00 4036
4 TraesCS2D01G174400 chr2B 86.978 599 46 18 3111 3681 581713608 581713014 0.000000e+00 645
5 TraesCS2D01G174400 chr2A 95.325 2246 89 6 786 3027 119089156 119086923 0.000000e+00 3552
6 TraesCS2D01G174400 chr2A 85.366 615 23 26 198 785 119089764 119089190 3.200000e-160 575
7 TraesCS2D01G174400 chr5B 92.586 580 31 5 3111 3681 455170743 455170167 0.000000e+00 822
8 TraesCS2D01G174400 chr1D 92.414 580 33 6 3111 3681 225403866 225403289 0.000000e+00 817
9 TraesCS2D01G174400 chr1D 89.880 583 46 6 3113 3686 423306578 423307156 0.000000e+00 737
10 TraesCS2D01G174400 chr1A 92.201 577 34 7 3111 3678 477660810 477661384 0.000000e+00 806
11 TraesCS2D01G174400 chr1A 88.165 583 58 5 3113 3686 519420181 519420761 0.000000e+00 684
12 TraesCS2D01G174400 chr1A 87.611 113 7 7 3016 3125 381310101 381310209 1.390000e-24 124
13 TraesCS2D01G174400 chr7A 92.028 577 36 5 3111 3678 167255826 167256401 0.000000e+00 802
14 TraesCS2D01G174400 chr4D 91.724 580 37 6 3111 3681 242938843 242938266 0.000000e+00 795
15 TraesCS2D01G174400 chr4D 88.034 117 9 5 3013 3125 57872992 57872877 2.310000e-27 134
16 TraesCS2D01G174400 chr7D 91.681 577 37 6 3111 3678 548866750 548867324 0.000000e+00 789
17 TraesCS2D01G174400 chr7D 89.320 103 8 3 3026 3125 236843013 236842911 3.870000e-25 126
18 TraesCS2D01G174400 chr6D 93.474 521 33 1 3111 3631 158356663 158356144 0.000000e+00 773
19 TraesCS2D01G174400 chr6B 90.829 567 42 6 3111 3677 487538419 487537863 0.000000e+00 750
20 TraesCS2D01G174400 chr7B 89.358 592 35 10 3113 3681 427378278 427377692 0.000000e+00 719
21 TraesCS2D01G174400 chr7B 88.393 112 9 4 3017 3125 627311832 627311722 8.320000e-27 132
22 TraesCS2D01G174400 chr1B 87.952 581 58 5 3111 3683 181171846 181171270 0.000000e+00 675
23 TraesCS2D01G174400 chr4B 86.538 520 40 4 3175 3686 182772195 182772692 2.510000e-151 545
24 TraesCS2D01G174400 chr6A 91.429 105 5 4 3024 3125 540045311 540045414 1.380000e-29 141
25 TraesCS2D01G174400 chr6A 89.216 102 8 3 3026 3125 34544542 34544442 1.390000e-24 124
26 TraesCS2D01G174400 chr5D 87.500 120 9 5 3009 3125 277252227 277252111 2.310000e-27 134


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 TraesCS2D01G174400 chr2D 117838254 117841943 3689 True 6815.0 6815 100.0000 1 3690 1 chr2D.!!$R1 3689
1 TraesCS2D01G174400 chr2D 331607228 331607808 580 False 771.0 771 90.9090 3111 3681 1 chr2D.!!$F1 570
2 TraesCS2D01G174400 chr2B 168620085 168623043 2958 True 4036.0 4036 91.6220 786 3690 1 chr2B.!!$R1 2904
3 TraesCS2D01G174400 chr2B 581713014 581713608 594 True 645.0 645 86.9780 3111 3681 1 chr2B.!!$R2 570
4 TraesCS2D01G174400 chr2A 119086923 119089764 2841 True 2063.5 3552 90.3455 198 3027 2 chr2A.!!$R1 2829
5 TraesCS2D01G174400 chr5B 455170167 455170743 576 True 822.0 822 92.5860 3111 3681 1 chr5B.!!$R1 570
6 TraesCS2D01G174400 chr1D 225403289 225403866 577 True 817.0 817 92.4140 3111 3681 1 chr1D.!!$R1 570
7 TraesCS2D01G174400 chr1D 423306578 423307156 578 False 737.0 737 89.8800 3113 3686 1 chr1D.!!$F1 573
8 TraesCS2D01G174400 chr1A 477660810 477661384 574 False 806.0 806 92.2010 3111 3678 1 chr1A.!!$F2 567
9 TraesCS2D01G174400 chr1A 519420181 519420761 580 False 684.0 684 88.1650 3113 3686 1 chr1A.!!$F3 573
10 TraesCS2D01G174400 chr7A 167255826 167256401 575 False 802.0 802 92.0280 3111 3678 1 chr7A.!!$F1 567
11 TraesCS2D01G174400 chr4D 242938266 242938843 577 True 795.0 795 91.7240 3111 3681 1 chr4D.!!$R2 570
12 TraesCS2D01G174400 chr7D 548866750 548867324 574 False 789.0 789 91.6810 3111 3678 1 chr7D.!!$F1 567
13 TraesCS2D01G174400 chr6D 158356144 158356663 519 True 773.0 773 93.4740 3111 3631 1 chr6D.!!$R1 520
14 TraesCS2D01G174400 chr6B 487537863 487538419 556 True 750.0 750 90.8290 3111 3677 1 chr6B.!!$R1 566
15 TraesCS2D01G174400 chr7B 427377692 427378278 586 True 719.0 719 89.3580 3113 3681 1 chr7B.!!$R1 568
16 TraesCS2D01G174400 chr1B 181171270 181171846 576 True 675.0 675 87.9520 3111 3683 1 chr1B.!!$R1 572

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
288 289 0.035152 TCAACCAGCATCATCCGCTT 60.035 50.0 0.0 0.0 37.72 4.68 F
290 291 0.035152 AACCAGCATCATCCGCTTGA 60.035 50.0 0.0 0.0 37.72 3.02 F
505 514 0.101399 GAGAGACGCCGATCATGTGT 59.899 55.0 0.0 0.0 0.00 3.72 F
650 669 0.390340 CCGATGATGACGCCCATAGG 60.390 60.0 0.0 0.0 35.17 2.57 F
1333 1425 0.541764 TTGGAAGCAATGTGGGGGAC 60.542 55.0 0.0 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2262 0.326264 GGTCAAGCTGTCCACCAGAT 59.674 55.000 0.00 0.00 44.49 2.90 R
2176 2268 1.429930 TACTTGGGTCAAGCTGTCCA 58.570 50.000 7.48 0.00 44.43 4.02 R
2348 2440 3.754965 TCCACAAAGGAATTCCAGACAG 58.245 45.455 26.22 12.93 45.65 3.51 R
2441 2533 5.725490 ACCCATCTCTTCTCTAATGGATCT 58.275 41.667 1.85 0.00 40.98 2.75 R
3080 3195 1.068741 GGTCGCGAGATCTTATGGGTT 59.931 52.381 10.24 0.00 45.19 4.11 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
19 20 0.036765 TCTGCCGCGTTATGGTTCTT 60.037 50.000 4.92 0.00 0.00 2.52
20 21 0.373716 CTGCCGCGTTATGGTTCTTC 59.626 55.000 4.92 0.00 0.00 2.87
21 22 0.036765 TGCCGCGTTATGGTTCTTCT 60.037 50.000 4.92 0.00 0.00 2.85
22 23 1.084289 GCCGCGTTATGGTTCTTCTT 58.916 50.000 4.92 0.00 0.00 2.52
23 24 1.467342 GCCGCGTTATGGTTCTTCTTT 59.533 47.619 4.92 0.00 0.00 2.52
24 25 2.727916 GCCGCGTTATGGTTCTTCTTTG 60.728 50.000 4.92 0.00 0.00 2.77
25 26 2.739913 CCGCGTTATGGTTCTTCTTTGA 59.260 45.455 4.92 0.00 0.00 2.69
26 27 3.187637 CCGCGTTATGGTTCTTCTTTGAA 59.812 43.478 4.92 0.00 0.00 2.69
27 28 4.319911 CCGCGTTATGGTTCTTCTTTGAAA 60.320 41.667 4.92 0.00 0.00 2.69
28 29 4.846137 CGCGTTATGGTTCTTCTTTGAAAG 59.154 41.667 0.00 0.00 0.00 2.62
29 30 5.333798 CGCGTTATGGTTCTTCTTTGAAAGA 60.334 40.000 3.02 3.02 33.50 2.52
30 31 6.435428 GCGTTATGGTTCTTCTTTGAAAGAA 58.565 36.000 18.32 18.32 44.82 2.52
31 32 6.915843 GCGTTATGGTTCTTCTTTGAAAGAAA 59.084 34.615 19.62 6.64 46.13 2.52
32 33 7.434013 GCGTTATGGTTCTTCTTTGAAAGAAAA 59.566 33.333 19.62 13.90 46.13 2.29
33 34 9.296400 CGTTATGGTTCTTCTTTGAAAGAAAAA 57.704 29.630 19.62 11.56 46.13 1.94
37 38 8.716646 TGGTTCTTCTTTGAAAGAAAAATTCC 57.283 30.769 19.62 12.43 46.13 3.01
38 39 8.539544 TGGTTCTTCTTTGAAAGAAAAATTCCT 58.460 29.630 19.62 0.00 46.13 3.36
39 40 9.383519 GGTTCTTCTTTGAAAGAAAAATTCCTT 57.616 29.630 19.62 0.00 46.13 3.36
41 42 9.942850 TTCTTCTTTGAAAGAAAAATTCCTTGT 57.057 25.926 19.62 0.00 46.13 3.16
42 43 9.369904 TCTTCTTTGAAAGAAAAATTCCTTGTG 57.630 29.630 19.62 5.54 46.13 3.33
43 44 7.538303 TCTTTGAAAGAAAAATTCCTTGTGC 57.462 32.000 4.94 0.00 33.83 4.57
44 45 7.102346 TCTTTGAAAGAAAAATTCCTTGTGCA 58.898 30.769 4.94 0.00 33.83 4.57
45 46 7.605691 TCTTTGAAAGAAAAATTCCTTGTGCAA 59.394 29.630 4.94 0.00 33.83 4.08
46 47 7.862512 TTGAAAGAAAAATTCCTTGTGCAAT 57.137 28.000 0.00 0.00 0.00 3.56
47 48 7.862512 TGAAAGAAAAATTCCTTGTGCAATT 57.137 28.000 0.00 0.00 0.00 2.32
48 49 7.695820 TGAAAGAAAAATTCCTTGTGCAATTG 58.304 30.769 0.00 0.00 0.00 2.32
49 50 6.622833 AAGAAAAATTCCTTGTGCAATTGG 57.377 33.333 7.72 0.00 0.00 3.16
50 51 5.065235 AGAAAAATTCCTTGTGCAATTGGG 58.935 37.500 7.72 0.00 0.00 4.12
51 52 4.703379 AAAATTCCTTGTGCAATTGGGA 57.297 36.364 7.72 1.77 0.00 4.37
52 53 4.914177 AAATTCCTTGTGCAATTGGGAT 57.086 36.364 7.72 0.00 0.00 3.85
53 54 3.899052 ATTCCTTGTGCAATTGGGATG 57.101 42.857 7.72 0.00 0.00 3.51
54 55 1.559368 TCCTTGTGCAATTGGGATGG 58.441 50.000 7.72 0.00 0.00 3.51
55 56 1.203162 TCCTTGTGCAATTGGGATGGT 60.203 47.619 7.72 0.00 0.00 3.55
56 57 1.066716 CCTTGTGCAATTGGGATGGTG 60.067 52.381 7.72 0.00 0.00 4.17
57 58 1.894466 CTTGTGCAATTGGGATGGTGA 59.106 47.619 7.72 0.00 0.00 4.02
58 59 1.548081 TGTGCAATTGGGATGGTGAG 58.452 50.000 7.72 0.00 0.00 3.51
59 60 1.075212 TGTGCAATTGGGATGGTGAGA 59.925 47.619 7.72 0.00 0.00 3.27
60 61 1.747355 GTGCAATTGGGATGGTGAGAG 59.253 52.381 7.72 0.00 0.00 3.20
61 62 1.355381 TGCAATTGGGATGGTGAGAGT 59.645 47.619 7.72 0.00 0.00 3.24
62 63 2.575735 TGCAATTGGGATGGTGAGAGTA 59.424 45.455 7.72 0.00 0.00 2.59
63 64 3.010027 TGCAATTGGGATGGTGAGAGTAA 59.990 43.478 7.72 0.00 0.00 2.24
64 65 4.016444 GCAATTGGGATGGTGAGAGTAAA 58.984 43.478 7.72 0.00 0.00 2.01
65 66 4.462483 GCAATTGGGATGGTGAGAGTAAAA 59.538 41.667 7.72 0.00 0.00 1.52
66 67 5.047377 GCAATTGGGATGGTGAGAGTAAAAA 60.047 40.000 7.72 0.00 0.00 1.94
67 68 6.351286 GCAATTGGGATGGTGAGAGTAAAAAT 60.351 38.462 7.72 0.00 0.00 1.82
68 69 7.260603 CAATTGGGATGGTGAGAGTAAAAATC 58.739 38.462 0.00 0.00 0.00 2.17
69 70 4.855340 TGGGATGGTGAGAGTAAAAATCC 58.145 43.478 0.00 0.00 32.94 3.01
70 71 4.207955 GGGATGGTGAGAGTAAAAATCCC 58.792 47.826 2.23 2.23 43.63 3.85
71 72 4.207955 GGATGGTGAGAGTAAAAATCCCC 58.792 47.826 0.00 0.00 0.00 4.81
72 73 3.732048 TGGTGAGAGTAAAAATCCCCC 57.268 47.619 0.00 0.00 0.00 5.40
98 99 5.907866 CCCCCTTATTTTGTTACGAATGT 57.092 39.130 0.00 0.00 0.00 2.71
99 100 5.646606 CCCCCTTATTTTGTTACGAATGTG 58.353 41.667 0.00 0.00 0.00 3.21
100 101 5.184287 CCCCCTTATTTTGTTACGAATGTGT 59.816 40.000 0.00 0.00 0.00 3.72
101 102 6.319399 CCCCTTATTTTGTTACGAATGTGTC 58.681 40.000 0.00 0.00 0.00 3.67
102 103 6.150474 CCCCTTATTTTGTTACGAATGTGTCT 59.850 38.462 0.00 0.00 0.00 3.41
103 104 7.308951 CCCCTTATTTTGTTACGAATGTGTCTT 60.309 37.037 0.00 0.00 0.00 3.01
104 105 8.079809 CCCTTATTTTGTTACGAATGTGTCTTT 58.920 33.333 0.00 0.00 0.00 2.52
105 106 8.901748 CCTTATTTTGTTACGAATGTGTCTTTG 58.098 33.333 0.00 0.00 0.00 2.77
106 107 9.445786 CTTATTTTGTTACGAATGTGTCTTTGT 57.554 29.630 0.00 0.00 0.00 2.83
109 110 8.996988 TTTTGTTACGAATGTGTCTTTGTATC 57.003 30.769 0.00 0.00 0.00 2.24
110 111 7.716768 TTGTTACGAATGTGTCTTTGTATCA 57.283 32.000 0.00 0.00 0.00 2.15
111 112 7.899178 TGTTACGAATGTGTCTTTGTATCAT 57.101 32.000 0.00 0.00 0.00 2.45
112 113 8.317891 TGTTACGAATGTGTCTTTGTATCATT 57.682 30.769 0.00 0.00 0.00 2.57
113 114 8.440059 TGTTACGAATGTGTCTTTGTATCATTC 58.560 33.333 0.00 0.00 40.15 2.67
114 115 8.656849 GTTACGAATGTGTCTTTGTATCATTCT 58.343 33.333 12.20 4.90 40.87 2.40
115 116 7.065216 ACGAATGTGTCTTTGTATCATTCTG 57.935 36.000 12.20 9.13 40.87 3.02
116 117 6.873605 ACGAATGTGTCTTTGTATCATTCTGA 59.126 34.615 12.20 0.00 40.87 3.27
117 118 7.148573 ACGAATGTGTCTTTGTATCATTCTGAC 60.149 37.037 12.20 0.00 40.87 3.51
118 119 6.653273 ATGTGTCTTTGTATCATTCTGACG 57.347 37.500 0.00 0.00 0.00 4.35
119 120 4.929211 TGTGTCTTTGTATCATTCTGACGG 59.071 41.667 0.00 0.00 0.00 4.79
120 121 3.932710 TGTCTTTGTATCATTCTGACGGC 59.067 43.478 0.00 0.00 0.00 5.68
121 122 3.309954 GTCTTTGTATCATTCTGACGGCC 59.690 47.826 0.00 0.00 0.00 6.13
122 123 3.055458 TCTTTGTATCATTCTGACGGCCA 60.055 43.478 2.24 0.00 0.00 5.36
123 124 2.309528 TGTATCATTCTGACGGCCAC 57.690 50.000 2.24 0.00 0.00 5.01
124 125 1.552792 TGTATCATTCTGACGGCCACA 59.447 47.619 2.24 0.77 0.00 4.17
125 126 2.027653 TGTATCATTCTGACGGCCACAA 60.028 45.455 2.24 0.00 0.00 3.33
126 127 2.425143 ATCATTCTGACGGCCACAAT 57.575 45.000 2.24 0.00 0.00 2.71
127 128 3.558931 ATCATTCTGACGGCCACAATA 57.441 42.857 2.24 0.00 0.00 1.90
128 129 3.558931 TCATTCTGACGGCCACAATAT 57.441 42.857 2.24 0.00 0.00 1.28
129 130 3.466836 TCATTCTGACGGCCACAATATC 58.533 45.455 2.24 0.00 0.00 1.63
130 131 3.118445 TCATTCTGACGGCCACAATATCA 60.118 43.478 2.24 0.00 0.00 2.15
131 132 2.602257 TCTGACGGCCACAATATCAG 57.398 50.000 2.24 5.71 38.51 2.90
132 133 0.940126 CTGACGGCCACAATATCAGC 59.060 55.000 2.24 0.00 31.14 4.26
133 134 0.541392 TGACGGCCACAATATCAGCT 59.459 50.000 2.24 0.00 0.00 4.24
134 135 1.065491 TGACGGCCACAATATCAGCTT 60.065 47.619 2.24 0.00 0.00 3.74
135 136 1.331756 GACGGCCACAATATCAGCTTG 59.668 52.381 2.24 0.00 0.00 4.01
136 137 1.340017 ACGGCCACAATATCAGCTTGT 60.340 47.619 2.24 0.00 37.31 3.16
137 138 2.093181 ACGGCCACAATATCAGCTTGTA 60.093 45.455 2.24 0.00 35.15 2.41
138 139 2.942376 CGGCCACAATATCAGCTTGTAA 59.058 45.455 2.24 0.00 35.15 2.41
139 140 3.242739 CGGCCACAATATCAGCTTGTAAC 60.243 47.826 2.24 0.00 35.15 2.50
140 141 3.694072 GGCCACAATATCAGCTTGTAACA 59.306 43.478 0.00 0.00 35.15 2.41
141 142 4.438744 GGCCACAATATCAGCTTGTAACAC 60.439 45.833 0.00 0.00 35.15 3.32
142 143 4.438744 GCCACAATATCAGCTTGTAACACC 60.439 45.833 0.00 0.00 35.15 4.16
143 144 4.943705 CCACAATATCAGCTTGTAACACCT 59.056 41.667 0.00 0.00 35.15 4.00
144 145 5.065218 CCACAATATCAGCTTGTAACACCTC 59.935 44.000 0.00 0.00 35.15 3.85
145 146 4.870426 ACAATATCAGCTTGTAACACCTCG 59.130 41.667 0.00 0.00 35.15 4.63
146 147 5.109210 CAATATCAGCTTGTAACACCTCGA 58.891 41.667 0.00 0.00 0.00 4.04
147 148 3.895232 ATCAGCTTGTAACACCTCGAT 57.105 42.857 0.00 0.00 0.00 3.59
148 149 3.232213 TCAGCTTGTAACACCTCGATC 57.768 47.619 0.00 0.00 0.00 3.69
149 150 2.094182 TCAGCTTGTAACACCTCGATCC 60.094 50.000 0.00 0.00 0.00 3.36
150 151 1.135083 AGCTTGTAACACCTCGATCCG 60.135 52.381 0.00 0.00 0.00 4.18
151 152 1.403780 GCTTGTAACACCTCGATCCGT 60.404 52.381 0.00 0.00 0.00 4.69
152 153 2.159338 GCTTGTAACACCTCGATCCGTA 60.159 50.000 0.00 0.00 0.00 4.02
153 154 3.692576 CTTGTAACACCTCGATCCGTAG 58.307 50.000 0.00 0.00 0.00 3.51
154 155 2.989909 TGTAACACCTCGATCCGTAGA 58.010 47.619 0.00 0.00 0.00 2.59
155 156 2.679837 TGTAACACCTCGATCCGTAGAC 59.320 50.000 0.00 0.00 0.00 2.59
156 157 0.731417 AACACCTCGATCCGTAGACG 59.269 55.000 0.00 0.00 39.44 4.18
157 158 1.009900 CACCTCGATCCGTAGACGC 60.010 63.158 0.00 0.00 38.18 5.19
158 159 1.450848 ACCTCGATCCGTAGACGCA 60.451 57.895 0.00 0.00 38.18 5.24
159 160 1.028330 ACCTCGATCCGTAGACGCAA 61.028 55.000 0.00 0.00 38.18 4.85
161 162 0.317103 CTCGATCCGTAGACGCAAGG 60.317 60.000 0.00 0.00 46.39 3.61
162 163 1.299165 CGATCCGTAGACGCAAGGG 60.299 63.158 0.00 0.00 46.39 3.95
163 164 1.591863 GATCCGTAGACGCAAGGGC 60.592 63.158 0.00 0.00 46.39 5.19
173 174 2.819595 GCAAGGGCGCGATCAGAA 60.820 61.111 12.10 0.00 0.00 3.02
174 175 2.182842 GCAAGGGCGCGATCAGAAT 61.183 57.895 12.10 0.00 0.00 2.40
175 176 1.718757 GCAAGGGCGCGATCAGAATT 61.719 55.000 12.10 0.00 0.00 2.17
176 177 0.305922 CAAGGGCGCGATCAGAATTC 59.694 55.000 12.10 0.00 0.00 2.17
177 178 0.107703 AAGGGCGCGATCAGAATTCA 60.108 50.000 12.10 0.00 0.00 2.57
178 179 0.531532 AGGGCGCGATCAGAATTCAG 60.532 55.000 12.10 0.00 0.00 3.02
179 180 0.530650 GGGCGCGATCAGAATTCAGA 60.531 55.000 12.10 5.51 0.00 3.27
180 181 1.290203 GGCGCGATCAGAATTCAGAA 58.710 50.000 12.10 0.00 0.00 3.02
181 182 1.665679 GGCGCGATCAGAATTCAGAAA 59.334 47.619 12.10 0.00 0.00 2.52
182 183 2.537730 GGCGCGATCAGAATTCAGAAAC 60.538 50.000 12.10 3.67 0.00 2.78
183 184 2.537730 GCGCGATCAGAATTCAGAAACC 60.538 50.000 12.10 0.00 0.00 3.27
184 185 2.672874 CGCGATCAGAATTCAGAAACCA 59.327 45.455 0.00 0.00 0.00 3.67
185 186 3.242220 CGCGATCAGAATTCAGAAACCAG 60.242 47.826 0.00 0.00 0.00 4.00
186 187 3.064545 GCGATCAGAATTCAGAAACCAGG 59.935 47.826 8.44 0.00 0.00 4.45
187 188 4.507710 CGATCAGAATTCAGAAACCAGGA 58.492 43.478 8.44 0.00 0.00 3.86
188 189 4.569966 CGATCAGAATTCAGAAACCAGGAG 59.430 45.833 8.44 0.00 0.00 3.69
189 190 3.679389 TCAGAATTCAGAAACCAGGAGC 58.321 45.455 8.44 0.00 0.00 4.70
190 191 2.417933 CAGAATTCAGAAACCAGGAGCG 59.582 50.000 8.44 0.00 0.00 5.03
191 192 2.303022 AGAATTCAGAAACCAGGAGCGA 59.697 45.455 8.44 0.00 0.00 4.93
192 193 3.054802 AGAATTCAGAAACCAGGAGCGAT 60.055 43.478 8.44 0.00 0.00 4.58
193 194 4.162320 AGAATTCAGAAACCAGGAGCGATA 59.838 41.667 8.44 0.00 0.00 2.92
194 195 3.973206 TTCAGAAACCAGGAGCGATAA 57.027 42.857 0.00 0.00 0.00 1.75
195 196 4.487714 TTCAGAAACCAGGAGCGATAAT 57.512 40.909 0.00 0.00 0.00 1.28
196 197 3.797039 TCAGAAACCAGGAGCGATAATG 58.203 45.455 0.00 0.00 0.00 1.90
220 221 1.591248 CGAACAGCGAAATGAAACCG 58.409 50.000 0.00 0.00 44.57 4.44
229 230 2.603560 CGAAATGAAACCGCTAGTCTCC 59.396 50.000 0.00 0.00 0.00 3.71
233 234 2.457598 TGAAACCGCTAGTCTCCTCAT 58.542 47.619 0.00 0.00 0.00 2.90
236 237 4.464951 TGAAACCGCTAGTCTCCTCATAAA 59.535 41.667 0.00 0.00 0.00 1.40
238 239 5.416271 AACCGCTAGTCTCCTCATAAAAA 57.584 39.130 0.00 0.00 0.00 1.94
288 289 0.035152 TCAACCAGCATCATCCGCTT 60.035 50.000 0.00 0.00 37.72 4.68
289 290 0.099968 CAACCAGCATCATCCGCTTG 59.900 55.000 0.00 0.00 37.72 4.01
290 291 0.035152 AACCAGCATCATCCGCTTGA 60.035 50.000 0.00 0.00 37.72 3.02
291 292 0.182061 ACCAGCATCATCCGCTTGAT 59.818 50.000 0.00 0.00 37.72 2.57
298 299 3.635433 CATCCGCTTGATGCAAAGG 57.365 52.632 0.00 0.00 44.16 3.11
299 300 1.097232 CATCCGCTTGATGCAAAGGA 58.903 50.000 0.00 0.00 44.16 3.36
300 301 1.098050 ATCCGCTTGATGCAAAGGAC 58.902 50.000 0.00 0.00 43.06 3.85
301 302 1.135315 CCGCTTGATGCAAAGGACG 59.865 57.895 0.00 0.00 43.06 4.79
302 303 1.512734 CGCTTGATGCAAAGGACGC 60.513 57.895 0.00 0.00 43.06 5.19
303 304 1.153958 GCTTGATGCAAAGGACGCC 60.154 57.895 0.00 0.00 42.31 5.68
310 311 0.179032 TGCAAAGGACGCCTGAGAAA 60.179 50.000 0.00 0.00 32.13 2.52
330 331 5.728741 AGAAACTGGGGAGAAGAACATATCT 59.271 40.000 0.00 0.00 41.32 1.98
363 364 1.232621 GGTTACTGACAACCACCGGC 61.233 60.000 0.00 0.00 46.14 6.13
367 368 4.572571 TGACAACCACCGGCCACC 62.573 66.667 0.00 0.00 0.00 4.61
462 463 3.123674 GTTCGCCACGATCTGTTCT 57.876 52.632 0.00 0.00 35.23 3.01
463 464 0.716108 GTTCGCCACGATCTGTTCTG 59.284 55.000 0.00 0.00 35.23 3.02
471 472 1.291184 CGATCTGTTCTGTTGGCGCA 61.291 55.000 10.83 0.00 0.00 6.09
500 501 1.018148 GAGAAGAGAGACGCCGATCA 58.982 55.000 0.00 0.00 0.00 2.92
505 514 0.101399 GAGAGACGCCGATCATGTGT 59.899 55.000 0.00 0.00 0.00 3.72
507 516 1.756375 GAGACGCCGATCATGTGTGC 61.756 60.000 3.39 0.00 0.00 4.57
573 582 2.190578 GGCTATTGGGCTGTCGCT 59.809 61.111 0.00 0.00 37.53 4.93
616 626 3.603671 GCGCTCCCGGTAGGTAGG 61.604 72.222 0.00 0.00 36.75 3.18
617 627 2.123982 CGCTCCCGGTAGGTAGGT 60.124 66.667 0.00 0.00 36.75 3.08
618 628 1.755783 CGCTCCCGGTAGGTAGGTT 60.756 63.158 0.00 0.00 36.75 3.50
619 629 0.466189 CGCTCCCGGTAGGTAGGTTA 60.466 60.000 0.00 0.00 36.75 2.85
620 630 1.326328 GCTCCCGGTAGGTAGGTTAG 58.674 60.000 0.00 0.00 36.75 2.34
622 632 2.305009 CTCCCGGTAGGTAGGTTAGTG 58.695 57.143 0.00 0.00 36.75 2.74
623 633 1.640670 TCCCGGTAGGTAGGTTAGTGT 59.359 52.381 0.00 0.00 36.75 3.55
624 634 2.849943 TCCCGGTAGGTAGGTTAGTGTA 59.150 50.000 0.00 0.00 36.75 2.90
641 660 1.961394 TGTAGGGTAGCCGATGATGAC 59.039 52.381 5.06 0.00 0.00 3.06
642 661 1.068472 GTAGGGTAGCCGATGATGACG 60.068 57.143 5.06 0.00 0.00 4.35
643 662 1.664965 GGGTAGCCGATGATGACGC 60.665 63.158 0.00 0.00 0.00 5.19
644 663 1.664965 GGTAGCCGATGATGACGCC 60.665 63.158 0.00 0.00 0.00 5.68
645 664 1.664965 GTAGCCGATGATGACGCCC 60.665 63.158 0.00 0.00 0.00 6.13
646 665 2.131067 TAGCCGATGATGACGCCCA 61.131 57.895 0.00 0.00 0.00 5.36
647 666 1.471829 TAGCCGATGATGACGCCCAT 61.472 55.000 0.00 0.00 38.43 4.00
648 667 1.005037 GCCGATGATGACGCCCATA 60.005 57.895 0.00 0.00 35.17 2.74
649 668 1.016130 GCCGATGATGACGCCCATAG 61.016 60.000 0.00 0.00 35.17 2.23
650 669 0.390340 CCGATGATGACGCCCATAGG 60.390 60.000 0.00 0.00 35.17 2.57
686 706 1.870055 CGAACCCAGCAAAGCAGCAT 61.870 55.000 0.00 0.00 36.85 3.79
813 878 1.271108 TGTGCGTGTCTCTCTCTCTCT 60.271 52.381 0.00 0.00 0.00 3.10
814 879 1.396996 GTGCGTGTCTCTCTCTCTCTC 59.603 57.143 0.00 0.00 0.00 3.20
815 880 1.014352 GCGTGTCTCTCTCTCTCTCC 58.986 60.000 0.00 0.00 0.00 3.71
816 881 1.286501 CGTGTCTCTCTCTCTCTCCG 58.713 60.000 0.00 0.00 0.00 4.63
817 882 1.134936 CGTGTCTCTCTCTCTCTCCGA 60.135 57.143 0.00 0.00 0.00 4.55
824 889 0.745128 TCTCTCTCTCCGACTTCCGC 60.745 60.000 0.00 0.00 36.84 5.54
856 921 7.011482 CGCAGATTTAGTTTAGCTCCAAAGTAT 59.989 37.037 0.00 0.00 0.00 2.12
869 945 5.023533 TCCAAAGTATAGCAGATTTCGCT 57.976 39.130 0.00 0.00 43.62 4.93
881 957 2.187599 ATTTCGCTGCAACTGACGCC 62.188 55.000 0.00 0.00 0.00 5.68
1096 1176 2.017049 CCAATCCTTTTCCAGGTAGCG 58.983 52.381 0.00 0.00 44.37 4.26
1097 1177 2.618045 CCAATCCTTTTCCAGGTAGCGT 60.618 50.000 0.00 0.00 44.37 5.07
1110 1190 1.206371 GGTAGCGTTCCTTCCAAGCTA 59.794 52.381 0.00 0.00 39.14 3.32
1121 1201 4.080863 TCCTTCCAAGCTAGAATCTGTTCC 60.081 45.833 0.00 0.00 34.81 3.62
1133 1213 2.935481 TGTTCCCCAGCCCCTCTG 60.935 66.667 0.00 0.00 42.49 3.35
1142 1222 0.612732 CAGCCCCTCTGCATTCCAAA 60.613 55.000 0.00 0.00 35.78 3.28
1166 1249 4.448210 TCAAAGGCAGTTCTAACTCGTTT 58.552 39.130 0.00 1.17 37.08 3.60
1168 1251 2.767505 AGGCAGTTCTAACTCGTTTGG 58.232 47.619 0.00 0.00 37.08 3.28
1173 1256 4.986659 GCAGTTCTAACTCGTTTGGTCTTA 59.013 41.667 0.00 0.00 37.08 2.10
1201 1284 3.589951 ATAACAGCAGCATGGGATCTT 57.410 42.857 0.00 0.00 35.86 2.40
1216 1299 4.662179 TGGGATCTTAGGCATTCTCTCAAT 59.338 41.667 0.00 0.00 0.00 2.57
1237 1320 3.901797 CTCAAGGAAAGCGCCGGGT 62.902 63.158 2.29 0.00 0.00 5.28
1315 1407 3.442977 GCCAAGAGATTGTGATTGCTCTT 59.557 43.478 0.00 0.00 45.69 2.85
1333 1425 0.541764 TTGGAAGCAATGTGGGGGAC 60.542 55.000 0.00 0.00 0.00 4.46
1396 1488 1.140852 TCGGGCATAAAGATCACCAGG 59.859 52.381 0.00 0.00 0.00 4.45
1423 1515 3.834799 CTGTACGAGACCGCCCCC 61.835 72.222 0.00 0.00 39.95 5.40
1435 1527 2.504519 GCCCCCGAGTATGTGACC 59.495 66.667 0.00 0.00 0.00 4.02
1534 1626 3.117663 AGGAGATCGAGAGGGATATAGGC 60.118 52.174 0.00 0.00 0.00 3.93
1543 1635 2.181021 GATATAGGCCGGACCGCG 59.819 66.667 1.76 0.00 46.52 6.46
1576 1668 1.005630 CCCAAGGCCGATCGATCTC 60.006 63.158 22.43 13.68 0.00 2.75
1684 1776 1.151668 CGCCTCTTGTTGACCTTCTG 58.848 55.000 0.00 0.00 0.00 3.02
1859 1951 3.375699 GATTGGAGTGAGAGGACCCTTA 58.624 50.000 0.00 0.00 0.00 2.69
1912 2004 3.925299 GCTTTAGTGACGGAGGTAAGTTC 59.075 47.826 0.00 0.00 0.00 3.01
2077 2169 2.689983 GGATGCAATCGTCAAAATCCCT 59.310 45.455 0.00 0.00 46.86 4.20
2161 2253 1.422531 AGAGAGGAGCCACCATGATC 58.577 55.000 0.00 0.00 42.04 2.92
2170 2262 4.392047 GAGCCACCATGATCAATGATGTA 58.608 43.478 0.00 0.00 38.72 2.29
2176 2268 6.002082 CACCATGATCAATGATGTATCTGGT 58.998 40.000 0.00 1.60 38.72 4.00
2348 2440 1.996191 CACGGTTAAGAGAAGCTGAGC 59.004 52.381 0.00 0.00 0.00 4.26
2441 2533 6.757897 ATCTTGAAATAATCAACGGCTTGA 57.242 33.333 2.63 2.63 43.08 3.02
2453 2545 3.742433 ACGGCTTGAGATCCATTAGAG 57.258 47.619 0.00 0.00 0.00 2.43
2495 2587 0.892358 AGGTGCTTCACATGTGCCAG 60.892 55.000 21.38 18.59 35.86 4.85
2696 2788 3.120923 GCGCATGGTCAAATGAAAAAGTG 60.121 43.478 0.30 0.00 0.00 3.16
2869 2961 7.088589 AGCTTGTGTATAACTTTTGCCATAG 57.911 36.000 0.00 0.00 0.00 2.23
2908 3000 4.157120 GCGCCGGCTCCTTCCTAA 62.157 66.667 26.68 0.00 35.83 2.69
3003 3095 3.074412 GGCTGCTACTAAGTTTTCTGCA 58.926 45.455 0.00 0.00 0.00 4.41
3037 3150 5.098893 TGCAACACTATCAACAACAACAAC 58.901 37.500 0.00 0.00 0.00 3.32
3045 3158 3.583806 TCAACAACAACAACAAAGCCTG 58.416 40.909 0.00 0.00 0.00 4.85
3052 3165 3.627577 ACAACAACAAAGCCTGTAGTCTG 59.372 43.478 0.00 0.00 37.23 3.51
3065 3178 4.451900 CTGTAGTCTGAAACAAGTTGGGT 58.548 43.478 7.96 0.00 0.00 4.51
3066 3179 5.454187 CCTGTAGTCTGAAACAAGTTGGGTA 60.454 44.000 7.96 0.00 0.00 3.69
3068 3181 4.086706 AGTCTGAAACAAGTTGGGTAGG 57.913 45.455 7.96 0.00 0.00 3.18
3069 3182 2.552743 GTCTGAAACAAGTTGGGTAGGC 59.447 50.000 7.96 0.00 0.00 3.93
3070 3183 2.441750 TCTGAAACAAGTTGGGTAGGCT 59.558 45.455 7.96 0.00 0.00 4.58
3075 3190 4.717279 AACAAGTTGGGTAGGCTTAGAA 57.283 40.909 7.96 0.00 0.00 2.10
3080 3195 3.908103 AGTTGGGTAGGCTTAGAAGTGAA 59.092 43.478 0.00 0.00 0.00 3.18
3083 3198 3.008704 TGGGTAGGCTTAGAAGTGAAACC 59.991 47.826 0.00 0.00 37.80 3.27
3152 3270 3.100671 GGTGATACTCCAGTCCTTCAGT 58.899 50.000 0.00 0.00 0.00 3.41
3193 3311 2.259618 CCATGTCAAGTTCGGTCTACG 58.740 52.381 0.00 0.00 46.11 3.51
3305 3461 2.096069 CAGACGATGTTGGACAAGCTTG 60.096 50.000 24.84 24.84 0.00 4.01
3401 3558 1.019673 ATCCATCTCAACATGCGCAC 58.980 50.000 14.90 0.00 0.00 5.34
3542 3699 2.369860 TCTTGTCACAGAGAATGCCAGT 59.630 45.455 0.00 0.00 0.00 4.00
3578 3736 2.173356 TCATCCATCCGGCTTTGATTCT 59.827 45.455 0.00 0.00 0.00 2.40
3686 3852 3.134804 GCTAACCTCCTCCTTCTTATGCA 59.865 47.826 0.00 0.00 0.00 3.96
3687 3853 4.384208 GCTAACCTCCTCCTTCTTATGCAA 60.384 45.833 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.036765 AAGAACCATAACGCGGCAGA 60.037 50.000 12.47 0.00 0.00 4.26
1 2 0.373716 GAAGAACCATAACGCGGCAG 59.626 55.000 12.47 0.00 0.00 4.85
3 4 1.084289 AAGAAGAACCATAACGCGGC 58.916 50.000 12.47 0.00 0.00 6.53
5 6 4.398549 TTCAAAGAAGAACCATAACGCG 57.601 40.909 3.53 3.53 0.00 6.01
6 7 5.997385 TCTTTCAAAGAAGAACCATAACGC 58.003 37.500 0.00 0.00 33.83 4.84
19 20 7.102346 TGCACAAGGAATTTTTCTTTCAAAGA 58.898 30.769 0.00 0.00 35.26 2.52
20 21 7.306205 TGCACAAGGAATTTTTCTTTCAAAG 57.694 32.000 0.00 0.00 0.00 2.77
21 22 7.678947 TTGCACAAGGAATTTTTCTTTCAAA 57.321 28.000 0.00 0.00 0.00 2.69
22 23 7.862512 ATTGCACAAGGAATTTTTCTTTCAA 57.137 28.000 0.00 0.00 31.03 2.69
23 24 7.201714 CCAATTGCACAAGGAATTTTTCTTTCA 60.202 33.333 0.00 0.00 42.23 2.69
24 25 7.134163 CCAATTGCACAAGGAATTTTTCTTTC 58.866 34.615 0.00 0.00 42.23 2.62
25 26 6.039605 CCCAATTGCACAAGGAATTTTTCTTT 59.960 34.615 0.00 0.00 42.23 2.52
26 27 5.532032 CCCAATTGCACAAGGAATTTTTCTT 59.468 36.000 0.00 0.00 42.23 2.52
27 28 5.065235 CCCAATTGCACAAGGAATTTTTCT 58.935 37.500 0.00 0.00 42.23 2.52
28 29 5.062528 TCCCAATTGCACAAGGAATTTTTC 58.937 37.500 0.00 0.00 42.23 2.29
29 30 5.046288 TCCCAATTGCACAAGGAATTTTT 57.954 34.783 0.00 0.00 42.23 1.94
30 31 4.703379 TCCCAATTGCACAAGGAATTTT 57.297 36.364 0.00 0.00 42.23 1.82
31 32 4.566070 CCATCCCAATTGCACAAGGAATTT 60.566 41.667 0.00 0.00 42.23 1.82
32 33 3.054948 CCATCCCAATTGCACAAGGAATT 60.055 43.478 0.00 0.00 45.21 2.17
33 34 2.502538 CCATCCCAATTGCACAAGGAAT 59.497 45.455 0.00 0.00 37.39 3.01
34 35 1.901159 CCATCCCAATTGCACAAGGAA 59.099 47.619 0.00 0.00 0.00 3.36
35 36 1.203162 ACCATCCCAATTGCACAAGGA 60.203 47.619 0.00 1.09 0.00 3.36
36 37 1.066716 CACCATCCCAATTGCACAAGG 60.067 52.381 0.00 0.49 0.00 3.61
37 38 1.894466 TCACCATCCCAATTGCACAAG 59.106 47.619 0.00 0.00 0.00 3.16
38 39 1.894466 CTCACCATCCCAATTGCACAA 59.106 47.619 0.00 0.00 0.00 3.33
39 40 1.075212 TCTCACCATCCCAATTGCACA 59.925 47.619 0.00 0.00 0.00 4.57
40 41 1.747355 CTCTCACCATCCCAATTGCAC 59.253 52.381 0.00 0.00 0.00 4.57
41 42 1.355381 ACTCTCACCATCCCAATTGCA 59.645 47.619 0.00 0.00 0.00 4.08
42 43 2.134789 ACTCTCACCATCCCAATTGC 57.865 50.000 0.00 0.00 0.00 3.56
43 44 6.588719 TTTTTACTCTCACCATCCCAATTG 57.411 37.500 0.00 0.00 0.00 2.32
44 45 6.381133 GGATTTTTACTCTCACCATCCCAATT 59.619 38.462 0.00 0.00 0.00 2.32
45 46 5.893824 GGATTTTTACTCTCACCATCCCAAT 59.106 40.000 0.00 0.00 0.00 3.16
46 47 5.261216 GGATTTTTACTCTCACCATCCCAA 58.739 41.667 0.00 0.00 0.00 4.12
47 48 4.325030 GGGATTTTTACTCTCACCATCCCA 60.325 45.833 9.10 0.00 45.47 4.37
48 49 4.207955 GGGATTTTTACTCTCACCATCCC 58.792 47.826 0.00 0.00 41.26 3.85
49 50 4.207955 GGGGATTTTTACTCTCACCATCC 58.792 47.826 0.00 0.00 32.45 3.51
50 51 4.207955 GGGGGATTTTTACTCTCACCATC 58.792 47.826 0.00 0.00 33.93 3.51
51 52 4.251103 GGGGGATTTTTACTCTCACCAT 57.749 45.455 0.00 0.00 33.93 3.55
52 53 3.732048 GGGGGATTTTTACTCTCACCA 57.268 47.619 0.00 0.00 33.93 4.17
76 77 5.184287 ACACATTCGTAACAAAATAAGGGGG 59.816 40.000 0.00 0.00 0.00 5.40
77 78 6.150474 AGACACATTCGTAACAAAATAAGGGG 59.850 38.462 0.00 0.00 0.00 4.79
78 79 7.141100 AGACACATTCGTAACAAAATAAGGG 57.859 36.000 0.00 0.00 0.00 3.95
79 80 8.901748 CAAAGACACATTCGTAACAAAATAAGG 58.098 33.333 0.00 0.00 0.00 2.69
80 81 9.445786 ACAAAGACACATTCGTAACAAAATAAG 57.554 29.630 0.00 0.00 0.00 1.73
83 84 9.607285 GATACAAAGACACATTCGTAACAAAAT 57.393 29.630 0.00 0.00 0.00 1.82
84 85 8.613482 TGATACAAAGACACATTCGTAACAAAA 58.387 29.630 0.00 0.00 0.00 2.44
85 86 8.144155 TGATACAAAGACACATTCGTAACAAA 57.856 30.769 0.00 0.00 0.00 2.83
86 87 7.716768 TGATACAAAGACACATTCGTAACAA 57.283 32.000 0.00 0.00 0.00 2.83
87 88 7.899178 ATGATACAAAGACACATTCGTAACA 57.101 32.000 0.00 0.00 0.00 2.41
88 89 8.656849 AGAATGATACAAAGACACATTCGTAAC 58.343 33.333 0.00 0.00 46.12 2.50
89 90 8.655970 CAGAATGATACAAAGACACATTCGTAA 58.344 33.333 0.00 0.00 46.12 3.18
90 91 8.032451 TCAGAATGATACAAAGACACATTCGTA 58.968 33.333 0.00 0.00 42.56 3.43
91 92 6.873605 TCAGAATGATACAAAGACACATTCGT 59.126 34.615 0.00 0.00 42.56 3.85
92 93 7.294676 TCAGAATGATACAAAGACACATTCG 57.705 36.000 0.00 0.00 42.56 3.34
109 110 3.205338 TGATATTGTGGCCGTCAGAATG 58.795 45.455 5.65 0.00 39.34 2.67
110 111 3.470709 CTGATATTGTGGCCGTCAGAAT 58.529 45.455 0.00 0.60 41.46 2.40
111 112 2.905075 CTGATATTGTGGCCGTCAGAA 58.095 47.619 0.00 0.00 38.81 3.02
112 113 1.473257 GCTGATATTGTGGCCGTCAGA 60.473 52.381 16.95 5.13 38.81 3.27
113 114 0.940126 GCTGATATTGTGGCCGTCAG 59.060 55.000 0.00 6.02 39.35 3.51
114 115 0.541392 AGCTGATATTGTGGCCGTCA 59.459 50.000 0.00 0.00 0.00 4.35
115 116 1.331756 CAAGCTGATATTGTGGCCGTC 59.668 52.381 0.00 0.00 0.00 4.79
116 117 1.340017 ACAAGCTGATATTGTGGCCGT 60.340 47.619 0.00 0.00 39.36 5.68
117 118 1.382522 ACAAGCTGATATTGTGGCCG 58.617 50.000 0.00 0.00 39.36 6.13
118 119 3.694072 TGTTACAAGCTGATATTGTGGCC 59.306 43.478 0.00 0.00 40.92 5.36
119 120 4.438744 GGTGTTACAAGCTGATATTGTGGC 60.439 45.833 1.74 0.00 40.92 5.01
120 121 4.943705 AGGTGTTACAAGCTGATATTGTGG 59.056 41.667 1.74 0.00 40.92 4.17
121 122 5.220472 CGAGGTGTTACAAGCTGATATTGTG 60.220 44.000 1.74 0.00 40.92 3.33
122 123 4.870426 CGAGGTGTTACAAGCTGATATTGT 59.130 41.667 0.00 0.00 43.15 2.71
123 124 5.109210 TCGAGGTGTTACAAGCTGATATTG 58.891 41.667 0.00 0.00 0.00 1.90
124 125 5.339008 TCGAGGTGTTACAAGCTGATATT 57.661 39.130 0.00 0.00 0.00 1.28
125 126 5.509840 GGATCGAGGTGTTACAAGCTGATAT 60.510 44.000 0.00 0.00 0.00 1.63
126 127 4.202121 GGATCGAGGTGTTACAAGCTGATA 60.202 45.833 0.00 0.00 0.00 2.15
127 128 3.430929 GGATCGAGGTGTTACAAGCTGAT 60.431 47.826 0.00 0.00 0.00 2.90
128 129 2.094182 GGATCGAGGTGTTACAAGCTGA 60.094 50.000 0.00 0.00 0.00 4.26
129 130 2.271800 GGATCGAGGTGTTACAAGCTG 58.728 52.381 0.00 0.00 0.00 4.24
130 131 1.135083 CGGATCGAGGTGTTACAAGCT 60.135 52.381 0.00 0.00 0.00 3.74
131 132 1.278238 CGGATCGAGGTGTTACAAGC 58.722 55.000 0.00 0.00 0.00 4.01
132 133 2.649331 ACGGATCGAGGTGTTACAAG 57.351 50.000 0.00 0.00 0.00 3.16
133 134 3.127548 GTCTACGGATCGAGGTGTTACAA 59.872 47.826 0.00 0.00 0.00 2.41
134 135 2.679837 GTCTACGGATCGAGGTGTTACA 59.320 50.000 0.00 0.00 0.00 2.41
135 136 2.286067 CGTCTACGGATCGAGGTGTTAC 60.286 54.545 0.00 0.00 35.37 2.50
136 137 1.935873 CGTCTACGGATCGAGGTGTTA 59.064 52.381 0.00 0.00 35.37 2.41
137 138 0.731417 CGTCTACGGATCGAGGTGTT 59.269 55.000 0.00 0.00 35.37 3.32
138 139 1.712977 GCGTCTACGGATCGAGGTGT 61.713 60.000 4.49 0.00 40.23 4.16
139 140 1.009900 GCGTCTACGGATCGAGGTG 60.010 63.158 4.49 0.00 40.23 4.00
140 141 1.028330 TTGCGTCTACGGATCGAGGT 61.028 55.000 4.49 0.00 39.94 3.85
141 142 0.317103 CTTGCGTCTACGGATCGAGG 60.317 60.000 4.49 0.00 39.94 4.63
142 143 0.317103 CCTTGCGTCTACGGATCGAG 60.317 60.000 4.49 0.00 39.94 4.04
143 144 1.721664 CCCTTGCGTCTACGGATCGA 61.722 60.000 4.49 0.00 39.94 3.59
144 145 1.299165 CCCTTGCGTCTACGGATCG 60.299 63.158 4.49 0.00 39.94 3.69
145 146 1.591863 GCCCTTGCGTCTACGGATC 60.592 63.158 4.49 0.00 39.94 3.36
146 147 2.499685 GCCCTTGCGTCTACGGAT 59.500 61.111 4.49 0.00 39.94 4.18
156 157 1.718757 AATTCTGATCGCGCCCTTGC 61.719 55.000 0.00 0.00 0.00 4.01
157 158 0.305922 GAATTCTGATCGCGCCCTTG 59.694 55.000 0.00 0.00 0.00 3.61
158 159 0.107703 TGAATTCTGATCGCGCCCTT 60.108 50.000 0.00 0.00 0.00 3.95
159 160 0.531532 CTGAATTCTGATCGCGCCCT 60.532 55.000 0.00 0.00 0.00 5.19
160 161 0.530650 TCTGAATTCTGATCGCGCCC 60.531 55.000 10.68 0.00 0.00 6.13
161 162 1.290203 TTCTGAATTCTGATCGCGCC 58.710 50.000 14.89 0.00 0.00 6.53
162 163 2.537730 GGTTTCTGAATTCTGATCGCGC 60.538 50.000 14.89 0.00 0.00 6.86
163 164 2.672874 TGGTTTCTGAATTCTGATCGCG 59.327 45.455 14.89 0.00 0.00 5.87
164 165 3.064545 CCTGGTTTCTGAATTCTGATCGC 59.935 47.826 14.89 8.65 0.00 4.58
165 166 4.507710 TCCTGGTTTCTGAATTCTGATCG 58.492 43.478 14.89 3.78 0.00 3.69
166 167 4.335037 GCTCCTGGTTTCTGAATTCTGATC 59.665 45.833 14.89 11.16 0.00 2.92
167 168 4.268359 GCTCCTGGTTTCTGAATTCTGAT 58.732 43.478 14.89 0.00 0.00 2.90
168 169 3.679389 GCTCCTGGTTTCTGAATTCTGA 58.321 45.455 10.68 10.68 0.00 3.27
169 170 2.417933 CGCTCCTGGTTTCTGAATTCTG 59.582 50.000 7.05 6.50 0.00 3.02
170 171 2.303022 TCGCTCCTGGTTTCTGAATTCT 59.697 45.455 7.05 0.00 0.00 2.40
171 172 2.699954 TCGCTCCTGGTTTCTGAATTC 58.300 47.619 0.00 0.00 0.00 2.17
172 173 2.859165 TCGCTCCTGGTTTCTGAATT 57.141 45.000 0.00 0.00 0.00 2.17
173 174 4.487714 TTATCGCTCCTGGTTTCTGAAT 57.512 40.909 0.00 0.00 0.00 2.57
174 175 3.973206 TTATCGCTCCTGGTTTCTGAA 57.027 42.857 0.00 0.00 0.00 3.02
175 176 3.197766 ACATTATCGCTCCTGGTTTCTGA 59.802 43.478 0.00 0.00 0.00 3.27
176 177 3.310774 CACATTATCGCTCCTGGTTTCTG 59.689 47.826 0.00 0.00 0.00 3.02
177 178 3.197766 TCACATTATCGCTCCTGGTTTCT 59.802 43.478 0.00 0.00 0.00 2.52
178 179 3.531538 TCACATTATCGCTCCTGGTTTC 58.468 45.455 0.00 0.00 0.00 2.78
179 180 3.627395 TCACATTATCGCTCCTGGTTT 57.373 42.857 0.00 0.00 0.00 3.27
180 181 3.733337 GATCACATTATCGCTCCTGGTT 58.267 45.455 0.00 0.00 0.00 3.67
181 182 2.288457 CGATCACATTATCGCTCCTGGT 60.288 50.000 0.00 0.00 41.93 4.00
182 183 2.029918 TCGATCACATTATCGCTCCTGG 60.030 50.000 1.51 0.00 46.51 4.45
183 184 3.288809 TCGATCACATTATCGCTCCTG 57.711 47.619 1.51 0.00 46.51 3.86
184 185 3.068165 TGTTCGATCACATTATCGCTCCT 59.932 43.478 1.51 0.00 46.51 3.69
185 186 3.381045 TGTTCGATCACATTATCGCTCC 58.619 45.455 1.51 0.00 46.51 4.70
186 187 3.121194 GCTGTTCGATCACATTATCGCTC 60.121 47.826 1.51 0.00 46.51 5.03
187 188 2.797156 GCTGTTCGATCACATTATCGCT 59.203 45.455 1.51 0.00 46.51 4.93
188 189 2.408991 CGCTGTTCGATCACATTATCGC 60.409 50.000 1.51 0.00 46.51 4.58
248 249 6.817765 TGATTTCGCTAGAGGTTCATTTTT 57.182 33.333 0.00 0.00 0.00 1.94
253 254 3.007506 TGGTTGATTTCGCTAGAGGTTCA 59.992 43.478 0.00 0.00 0.00 3.18
261 262 2.984562 TGATGCTGGTTGATTTCGCTA 58.015 42.857 0.00 0.00 0.00 4.26
288 289 0.674581 CTCAGGCGTCCTTTGCATCA 60.675 55.000 0.00 0.00 0.00 3.07
289 290 0.391661 TCTCAGGCGTCCTTTGCATC 60.392 55.000 0.00 0.00 0.00 3.91
290 291 0.036732 TTCTCAGGCGTCCTTTGCAT 59.963 50.000 0.00 0.00 0.00 3.96
291 292 0.179032 TTTCTCAGGCGTCCTTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
292 293 0.238553 GTTTCTCAGGCGTCCTTTGC 59.761 55.000 0.00 0.00 0.00 3.68
293 294 1.532868 CAGTTTCTCAGGCGTCCTTTG 59.467 52.381 0.00 0.00 0.00 2.77
294 295 1.543429 CCAGTTTCTCAGGCGTCCTTT 60.543 52.381 0.00 0.00 0.00 3.11
295 296 0.035458 CCAGTTTCTCAGGCGTCCTT 59.965 55.000 0.00 0.00 0.00 3.36
296 297 1.674057 CCAGTTTCTCAGGCGTCCT 59.326 57.895 0.00 0.00 0.00 3.85
297 298 1.376037 CCCAGTTTCTCAGGCGTCC 60.376 63.158 0.00 0.00 0.00 4.79
298 299 1.376037 CCCCAGTTTCTCAGGCGTC 60.376 63.158 0.00 0.00 0.00 5.19
299 300 1.831652 CTCCCCAGTTTCTCAGGCGT 61.832 60.000 0.00 0.00 0.00 5.68
300 301 1.078848 CTCCCCAGTTTCTCAGGCG 60.079 63.158 0.00 0.00 0.00 5.52
301 302 0.693049 TTCTCCCCAGTTTCTCAGGC 59.307 55.000 0.00 0.00 0.00 4.85
302 303 2.260822 TCTTCTCCCCAGTTTCTCAGG 58.739 52.381 0.00 0.00 0.00 3.86
303 304 3.071602 TGTTCTTCTCCCCAGTTTCTCAG 59.928 47.826 0.00 0.00 0.00 3.35
310 311 3.135530 GCAGATATGTTCTTCTCCCCAGT 59.864 47.826 0.00 0.00 29.93 4.00
369 370 2.202388 TTCGTCGCGACTTAGCCG 60.202 61.111 33.94 21.32 34.89 5.52
370 371 1.154073 ACTTCGTCGCGACTTAGCC 60.154 57.895 33.94 9.89 34.89 3.93
371 372 1.403972 CCACTTCGTCGCGACTTAGC 61.404 60.000 33.94 10.66 34.89 3.09
372 373 1.403972 GCCACTTCGTCGCGACTTAG 61.404 60.000 33.94 29.46 34.89 2.18
373 374 1.443194 GCCACTTCGTCGCGACTTA 60.443 57.895 33.94 20.74 34.89 2.24
374 375 2.733593 GCCACTTCGTCGCGACTT 60.734 61.111 33.94 14.76 34.89 3.01
458 459 3.579626 GAGCGTGCGCCAACAGAAC 62.580 63.158 13.21 0.00 43.17 3.01
459 460 3.345808 GAGCGTGCGCCAACAGAA 61.346 61.111 13.21 0.00 43.17 3.02
471 472 0.746563 CTCTCTTCTCCGAGGAGCGT 60.747 60.000 14.07 0.00 41.71 5.07
500 501 2.186160 CCCACACACACGCACACAT 61.186 57.895 0.00 0.00 0.00 3.21
505 514 4.168291 TGAGCCCACACACACGCA 62.168 61.111 0.00 0.00 0.00 5.24
507 516 3.349006 GCTGAGCCCACACACACG 61.349 66.667 0.00 0.00 0.00 4.49
573 582 1.868498 GGCTTGTTACGTACAGTGCAA 59.132 47.619 0.00 2.57 38.76 4.08
616 626 2.954318 TCATCGGCTACCCTACACTAAC 59.046 50.000 0.00 0.00 0.00 2.34
617 627 3.301794 TCATCGGCTACCCTACACTAA 57.698 47.619 0.00 0.00 0.00 2.24
618 628 3.154710 CATCATCGGCTACCCTACACTA 58.845 50.000 0.00 0.00 0.00 2.74
619 629 1.964223 CATCATCGGCTACCCTACACT 59.036 52.381 0.00 0.00 0.00 3.55
620 630 1.961394 TCATCATCGGCTACCCTACAC 59.039 52.381 0.00 0.00 0.00 2.90
622 632 1.068472 CGTCATCATCGGCTACCCTAC 60.068 57.143 0.00 0.00 0.00 3.18
623 633 1.244816 CGTCATCATCGGCTACCCTA 58.755 55.000 0.00 0.00 0.00 3.53
624 634 2.041976 CGTCATCATCGGCTACCCT 58.958 57.895 0.00 0.00 0.00 4.34
645 664 4.214119 CGGATTGTTTACTCCATGCCTATG 59.786 45.833 0.00 0.00 0.00 2.23
646 665 4.102524 TCGGATTGTTTACTCCATGCCTAT 59.897 41.667 0.00 0.00 0.00 2.57
647 666 3.452990 TCGGATTGTTTACTCCATGCCTA 59.547 43.478 0.00 0.00 0.00 3.93
648 667 2.238646 TCGGATTGTTTACTCCATGCCT 59.761 45.455 0.00 0.00 0.00 4.75
649 668 2.639065 TCGGATTGTTTACTCCATGCC 58.361 47.619 0.00 0.00 0.00 4.40
650 669 3.181500 GGTTCGGATTGTTTACTCCATGC 60.181 47.826 0.00 0.00 0.00 4.06
651 670 3.377172 GGGTTCGGATTGTTTACTCCATG 59.623 47.826 0.00 0.00 0.00 3.66
652 671 3.009695 TGGGTTCGGATTGTTTACTCCAT 59.990 43.478 0.00 0.00 0.00 3.41
797 862 1.134936 TCGGAGAGAGAGAGAGACACG 60.135 57.143 0.00 0.00 0.00 4.49
824 889 3.060473 GCTAAACTAAATCTGCGGCGTAG 60.060 47.826 19.29 19.29 0.00 3.51
881 957 1.880340 GGAGTGAATCTGCTCGGCG 60.880 63.158 0.00 0.00 32.83 6.46
1096 1176 4.837972 ACAGATTCTAGCTTGGAAGGAAC 58.162 43.478 0.00 0.00 0.00 3.62
1097 1177 5.491982 GAACAGATTCTAGCTTGGAAGGAA 58.508 41.667 0.00 0.00 31.55 3.36
1121 1201 2.123982 GAATGCAGAGGGGCTGGG 60.124 66.667 0.00 0.00 45.03 4.45
1133 1213 3.667360 ACTGCCTTTGAATTTGGAATGC 58.333 40.909 0.00 0.00 0.00 3.56
1142 1222 4.642429 ACGAGTTAGAACTGCCTTTGAAT 58.358 39.130 0.00 0.00 39.88 2.57
1166 1249 8.428852 TGCTGCTGTTATATTAAGATAAGACCA 58.571 33.333 2.79 0.00 0.00 4.02
1173 1256 6.782986 TCCCATGCTGCTGTTATATTAAGAT 58.217 36.000 0.00 0.00 0.00 2.40
1201 1284 3.657610 TGAGGGATTGAGAGAATGCCTA 58.342 45.455 7.38 0.00 46.56 3.93
1216 1299 2.351276 GGCGCTTTCCTTGAGGGA 59.649 61.111 7.64 0.00 43.41 4.20
1281 1364 2.674380 CTTGGCCGGCAGAGCTTT 60.674 61.111 30.85 0.00 0.00 3.51
1286 1369 1.078214 CAATCTCTTGGCCGGCAGA 60.078 57.895 30.85 22.60 0.00 4.26
1293 1385 3.015327 AGAGCAATCACAATCTCTTGGC 58.985 45.455 0.00 0.00 36.64 4.52
1315 1407 1.076549 GTCCCCCACATTGCTTCCA 59.923 57.895 0.00 0.00 0.00 3.53
1333 1425 2.254459 CTGTCGAACGAACTGATCCTG 58.746 52.381 0.00 0.00 0.00 3.86
1396 1488 1.801913 CTCGTACAGACAGGCGTGC 60.802 63.158 6.26 0.00 0.00 5.34
1423 1515 0.525668 GCTGGTCGGTCACATACTCG 60.526 60.000 0.00 0.00 0.00 4.18
1543 1635 1.347243 TTGGGCCGTACCTTATCCCC 61.347 60.000 0.00 0.00 39.10 4.81
1576 1668 3.850122 TCGCCATACAGGAGAATATCG 57.150 47.619 0.00 0.00 43.76 2.92
1859 1951 2.311542 TCAAGTTAAGCACCCCCATGAT 59.688 45.455 0.00 0.00 0.00 2.45
1931 2023 1.342174 CAACAACTTGGCCTGAGCAAT 59.658 47.619 3.32 0.00 42.56 3.56
2077 2169 1.956869 TCAGCTTCCCTTCCATCTCA 58.043 50.000 0.00 0.00 0.00 3.27
2161 2253 3.562973 GCTGTCCACCAGATACATCATTG 59.437 47.826 0.00 0.00 44.49 2.82
2170 2262 0.326264 GGTCAAGCTGTCCACCAGAT 59.674 55.000 0.00 0.00 44.49 2.90
2176 2268 1.429930 TACTTGGGTCAAGCTGTCCA 58.570 50.000 7.48 0.00 44.43 4.02
2317 2409 5.872635 TCTCTTAACCGTGTGTATAACTCG 58.127 41.667 0.00 0.00 43.64 4.18
2348 2440 3.754965 TCCACAAAGGAATTCCAGACAG 58.245 45.455 26.22 12.93 45.65 3.51
2441 2533 5.725490 ACCCATCTCTTCTCTAATGGATCT 58.275 41.667 1.85 0.00 40.98 2.75
2453 2545 6.819146 CCTAAACTCACTTTACCCATCTCTTC 59.181 42.308 0.00 0.00 0.00 2.87
2495 2587 8.095169 TCTTTTCCTTGAGAGTCCAAGTAATAC 58.905 37.037 15.76 0.00 41.34 1.89
2696 2788 1.269448 TCAATTCTTTTCTGGCGGTGC 59.731 47.619 0.00 0.00 0.00 5.01
2869 2961 5.569059 CGCAAGAAAATGTACATCTTTGGTC 59.431 40.000 9.23 0.00 43.02 4.02
2908 3000 6.976934 TTACCTTTGCTTCCTTGAAGATTT 57.023 33.333 7.98 0.00 41.71 2.17
3037 3150 4.576463 ACTTGTTTCAGACTACAGGCTTTG 59.424 41.667 0.00 0.00 0.00 2.77
3045 3158 4.995487 CCTACCCAACTTGTTTCAGACTAC 59.005 45.833 0.00 0.00 0.00 2.73
3052 3165 4.648651 TCTAAGCCTACCCAACTTGTTTC 58.351 43.478 0.00 0.00 0.00 2.78
3065 3178 6.442564 TCTTATGGGTTTCACTTCTAAGCCTA 59.557 38.462 0.00 0.00 41.36 3.93
3066 3179 5.250774 TCTTATGGGTTTCACTTCTAAGCCT 59.749 40.000 0.00 0.00 41.36 4.58
3068 3181 7.051000 AGATCTTATGGGTTTCACTTCTAAGC 58.949 38.462 0.00 0.00 0.00 3.09
3069 3182 7.436673 CGAGATCTTATGGGTTTCACTTCTAAG 59.563 40.741 0.00 0.00 0.00 2.18
3070 3183 7.265673 CGAGATCTTATGGGTTTCACTTCTAA 58.734 38.462 0.00 0.00 0.00 2.10
3075 3190 3.738281 CGCGAGATCTTATGGGTTTCACT 60.738 47.826 0.00 0.00 0.00 3.41
3080 3195 1.068741 GGTCGCGAGATCTTATGGGTT 59.931 52.381 10.24 0.00 45.19 4.11
3083 3198 2.128035 GTTGGTCGCGAGATCTTATGG 58.872 52.381 10.24 0.00 43.23 2.74
3152 3270 3.354467 GGAGGAGTCCGTAAAGAGAGAA 58.646 50.000 2.76 0.00 31.37 2.87
3193 3311 2.961526 TAATGTCAAGAGAGGTCGGC 57.038 50.000 0.00 0.00 0.00 5.54
3305 3461 1.653151 GGGTAGCACCGATTGAAGAC 58.347 55.000 0.00 0.00 39.83 3.01
3401 3558 1.910580 ATGGTTAGGTGTGGCGGAGG 61.911 60.000 0.00 0.00 0.00 4.30
3542 3699 1.340017 GGATGAAGTGGTGCCAAGCTA 60.340 52.381 0.00 0.00 0.00 3.32
3578 3736 9.288576 GGAATATTGATGAAGATGTGAACCATA 57.711 33.333 0.00 0.00 32.56 2.74


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

AutoCloner maintained by Alex Coulton.