Multiple sequence alignment - TraesCS5D01G036200

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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 TraesCS5D01G036200 chr5D 100.000 1954 0 0 1 1954 35500869 35498916 0.000000e+00 3609.0
1 TraesCS5D01G036200 chr5D 90.918 1013 67 20 557 1564 35286834 35285842 0.000000e+00 1338.0
2 TraesCS5D01G036200 chr5D 100.000 664 0 0 2187 2850 35498683 35498020 0.000000e+00 1227.0
3 TraesCS5D01G036200 chr5D 80.082 487 62 25 542 1011 35393418 35393886 2.120000e-86 329.0
4 TraesCS5D01G036200 chr5D 84.030 263 30 8 699 961 35329669 35329919 2.840000e-60 243.0
5 TraesCS5D01G036200 chr5D 81.746 252 21 12 1570 1819 35285808 35285580 1.350000e-43 187.0
6 TraesCS5D01G036200 chr5A 92.234 1365 74 18 267 1617 24150521 24149175 0.000000e+00 1905.0
7 TraesCS5D01G036200 chr5A 91.463 656 50 3 2199 2849 24061918 24061264 0.000000e+00 896.0
8 TraesCS5D01G036200 chr5A 86.098 856 81 19 745 1565 23919543 23918691 0.000000e+00 887.0
9 TraesCS5D01G036200 chr5A 85.222 609 56 15 972 1564 24184969 24185559 1.890000e-166 595.0
10 TraesCS5D01G036200 chr5A 93.662 284 10 3 1615 1898 24139291 24139016 4.390000e-113 418.0
11 TraesCS5D01G036200 chr5A 82.938 422 36 16 699 1119 23941719 23942105 5.840000e-92 348.0
12 TraesCS5D01G036200 chr5A 73.480 592 141 12 2218 2803 572347535 572348116 2.880000e-50 209.0
13 TraesCS5D01G036200 chr5A 84.034 119 9 4 1688 1796 23918647 23918529 3.880000e-19 106.0
14 TraesCS5D01G036200 chrUn 89.945 1263 102 18 556 1811 266220246 266219002 0.000000e+00 1605.0
15 TraesCS5D01G036200 chrUn 89.945 1263 102 18 556 1811 266247041 266245797 0.000000e+00 1605.0
16 TraesCS5D01G036200 chrUn 88.089 722 58 22 658 1366 440671519 440670813 0.000000e+00 832.0
17 TraesCS5D01G036200 chrUn 93.103 435 20 4 1368 1796 271386826 271387256 1.860000e-176 628.0
18 TraesCS5D01G036200 chrUn 93.103 435 20 4 1368 1796 271394972 271395402 1.860000e-176 628.0
19 TraesCS5D01G036200 chrUn 93.103 435 20 4 1368 1796 428762914 428763344 1.860000e-176 628.0
20 TraesCS5D01G036200 chrUn 78.281 640 89 31 466 1081 268031273 268031886 1.610000e-97 366.0
21 TraesCS5D01G036200 chrUn 78.244 501 66 23 466 951 268030745 268031217 6.010000e-72 281.0
22 TraesCS5D01G036200 chrUn 78.244 501 66 23 466 951 324441714 324441242 6.010000e-72 281.0
23 TraesCS5D01G036200 chrUn 85.652 230 27 5 782 1011 274029214 274028991 1.320000e-58 237.0
24 TraesCS5D01G036200 chrUn 79.913 229 37 7 545 770 383760376 383760154 2.940000e-35 159.0
25 TraesCS5D01G036200 chr4A 90.071 564 52 4 2253 2815 624347050 624346490 0.000000e+00 728.0
26 TraesCS5D01G036200 chr4A 73.220 590 146 10 2218 2803 598669763 598670344 1.340000e-48 204.0
27 TraesCS5D01G036200 chr4A 93.878 98 5 1 1846 1942 624348630 624348533 2.290000e-31 147.0
28 TraesCS5D01G036200 chr1D 83.882 577 79 9 2218 2791 70593486 70592921 3.230000e-149 538.0
29 TraesCS5D01G036200 chr1D 95.876 97 4 0 1846 1942 70593609 70593513 1.060000e-34 158.0
30 TraesCS5D01G036200 chr7A 90.690 290 21 2 1123 1409 3945516 3945802 5.760000e-102 381.0
31 TraesCS5D01G036200 chr2A 90.071 282 22 5 1123 1401 734773572 734773850 7.510000e-96 361.0
32 TraesCS5D01G036200 chr2A 74.024 589 143 9 2218 2803 755446700 755446119 6.140000e-57 231.0
33 TraesCS5D01G036200 chr2A 73.390 590 145 10 2218 2803 41470809 41471390 2.880000e-50 209.0
34 TraesCS5D01G036200 chr1A 73.220 590 146 10 2218 2803 11679309 11679890 1.340000e-48 204.0
35 TraesCS5D01G036200 chr3D 74.843 159 35 4 2218 2373 47177144 47177300 1.830000e-07 67.6
36 TraesCS5D01G036200 chr7B 97.059 34 1 0 355 388 528756279 528756246 1.100000e-04 58.4
37 TraesCS5D01G036200 chr2B 94.444 36 1 1 1906 1940 648905853 648905818 1.000000e-03 54.7


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 TraesCS5D01G036200 chr5D 35498020 35500869 2849 True 2418.0 3609 100.0000 1 2850 2 chr5D.!!$R2 2849
1 TraesCS5D01G036200 chr5D 35285580 35286834 1254 True 762.5 1338 86.3320 557 1819 2 chr5D.!!$R1 1262
2 TraesCS5D01G036200 chr5A 24149175 24150521 1346 True 1905.0 1905 92.2340 267 1617 1 chr5A.!!$R3 1350
3 TraesCS5D01G036200 chr5A 24061264 24061918 654 True 896.0 896 91.4630 2199 2849 1 chr5A.!!$R1 650
4 TraesCS5D01G036200 chr5A 24184969 24185559 590 False 595.0 595 85.2220 972 1564 1 chr5A.!!$F2 592
5 TraesCS5D01G036200 chr5A 23918529 23919543 1014 True 496.5 887 85.0660 745 1796 2 chr5A.!!$R4 1051
6 TraesCS5D01G036200 chr5A 572347535 572348116 581 False 209.0 209 73.4800 2218 2803 1 chr5A.!!$F3 585
7 TraesCS5D01G036200 chrUn 266219002 266220246 1244 True 1605.0 1605 89.9450 556 1811 1 chrUn.!!$R1 1255
8 TraesCS5D01G036200 chrUn 266245797 266247041 1244 True 1605.0 1605 89.9450 556 1811 1 chrUn.!!$R2 1255
9 TraesCS5D01G036200 chrUn 440670813 440671519 706 True 832.0 832 88.0890 658 1366 1 chrUn.!!$R6 708
10 TraesCS5D01G036200 chrUn 268030745 268031886 1141 False 323.5 366 78.2625 466 1081 2 chrUn.!!$F4 615
11 TraesCS5D01G036200 chr4A 624346490 624348630 2140 True 437.5 728 91.9745 1846 2815 2 chr4A.!!$R1 969
12 TraesCS5D01G036200 chr4A 598669763 598670344 581 False 204.0 204 73.2200 2218 2803 1 chr4A.!!$F1 585
13 TraesCS5D01G036200 chr1D 70592921 70593609 688 True 348.0 538 89.8790 1846 2791 2 chr1D.!!$R1 945
14 TraesCS5D01G036200 chr2A 755446119 755446700 581 True 231.0 231 74.0240 2218 2803 1 chr2A.!!$R1 585
15 TraesCS5D01G036200 chr2A 41470809 41471390 581 False 209.0 209 73.3900 2218 2803 1 chr2A.!!$F1 585
16 TraesCS5D01G036200 chr1A 11679309 11679890 581 False 204.0 204 73.2200 2218 2803 1 chr1A.!!$F1 585

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
187 188 0.036022 GTTTGCTCTGCCTCCTCTGT 59.964 55.0 0.00 0.00 0.0 3.41 F
911 1460 0.108520 TGTCTTTATGGTCGACGGCC 60.109 55.0 12.68 12.68 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 2248 0.892814 GGCTACGTACTCCGCCCTAT 60.893 60.0 11.52 0.0 41.42 2.57 R
2699 4766 0.179059 TTCAAGCTCCGCAACAGACA 60.179 50.0 0.00 0.0 0.00 3.41 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 2.721425 TGAAACTTTCCCGACCAAGT 57.279 45.000 0.00 0.00 34.58 3.16
20 21 3.007473 TGAAACTTTCCCGACCAAGTT 57.993 42.857 0.00 0.00 43.61 2.66
21 22 2.685897 TGAAACTTTCCCGACCAAGTTG 59.314 45.455 0.00 0.00 41.42 3.16
22 23 1.687563 AACTTTCCCGACCAAGTTGG 58.312 50.000 20.76 20.76 40.87 3.77
23 24 0.822121 ACTTTCCCGACCAAGTTGGC 60.822 55.000 22.25 13.30 42.67 4.52
24 25 1.524008 CTTTCCCGACCAAGTTGGCC 61.524 60.000 22.25 10.32 42.67 5.36
25 26 2.987355 TTTCCCGACCAAGTTGGCCC 62.987 60.000 22.25 12.77 42.67 5.80
27 28 3.966543 CCGACCAAGTTGGCCCCT 61.967 66.667 22.25 1.60 42.67 4.79
28 29 2.598787 CCGACCAAGTTGGCCCCTA 61.599 63.158 22.25 0.00 42.67 3.53
29 30 1.377229 CGACCAAGTTGGCCCCTAA 59.623 57.895 22.25 0.00 42.67 2.69
30 31 0.958876 CGACCAAGTTGGCCCCTAAC 60.959 60.000 22.25 0.00 42.67 2.34
31 32 0.111639 GACCAAGTTGGCCCCTAACA 59.888 55.000 22.25 0.00 42.67 2.41
32 33 0.783850 ACCAAGTTGGCCCCTAACAT 59.216 50.000 22.25 0.00 42.67 2.71
33 34 1.149077 ACCAAGTTGGCCCCTAACATT 59.851 47.619 22.25 0.00 42.67 2.71
34 35 1.550072 CCAAGTTGGCCCCTAACATTG 59.450 52.381 9.46 5.19 0.00 2.82
35 36 2.524306 CAAGTTGGCCCCTAACATTGA 58.476 47.619 0.00 0.00 0.00 2.57
36 37 3.099141 CAAGTTGGCCCCTAACATTGAT 58.901 45.455 0.00 0.00 0.00 2.57
37 38 3.018423 AGTTGGCCCCTAACATTGATC 57.982 47.619 0.00 0.00 0.00 2.92
38 39 2.311542 AGTTGGCCCCTAACATTGATCA 59.688 45.455 0.00 0.00 0.00 2.92
39 40 3.052642 AGTTGGCCCCTAACATTGATCAT 60.053 43.478 0.00 0.00 0.00 2.45
40 41 4.167892 AGTTGGCCCCTAACATTGATCATA 59.832 41.667 0.00 0.00 0.00 2.15
41 42 5.079643 GTTGGCCCCTAACATTGATCATAT 58.920 41.667 0.00 0.00 0.00 1.78
42 43 4.922206 TGGCCCCTAACATTGATCATATC 58.078 43.478 0.00 0.00 0.00 1.63
43 44 4.353489 TGGCCCCTAACATTGATCATATCA 59.647 41.667 0.00 0.00 37.55 2.15
44 45 5.015497 TGGCCCCTAACATTGATCATATCAT 59.985 40.000 0.00 0.00 39.39 2.45
45 46 5.591877 GGCCCCTAACATTGATCATATCATC 59.408 44.000 0.00 0.00 39.39 2.92
46 47 5.591877 GCCCCTAACATTGATCATATCATCC 59.408 44.000 0.00 0.00 39.39 3.51
47 48 6.579849 GCCCCTAACATTGATCATATCATCCT 60.580 42.308 0.00 0.00 39.39 3.24
48 49 7.052873 CCCCTAACATTGATCATATCATCCTC 58.947 42.308 0.00 0.00 39.39 3.71
49 50 6.760298 CCCTAACATTGATCATATCATCCTCG 59.240 42.308 0.00 0.00 39.39 4.63
50 51 7.326454 CCTAACATTGATCATATCATCCTCGT 58.674 38.462 0.00 0.00 39.39 4.18
51 52 7.821359 CCTAACATTGATCATATCATCCTCGTT 59.179 37.037 0.00 0.00 39.39 3.85
52 53 9.860898 CTAACATTGATCATATCATCCTCGTTA 57.139 33.333 0.00 0.00 39.39 3.18
54 55 8.539770 ACATTGATCATATCATCCTCGTTAAC 57.460 34.615 0.00 0.00 39.39 2.01
55 56 8.150296 ACATTGATCATATCATCCTCGTTAACA 58.850 33.333 6.39 0.00 39.39 2.41
56 57 7.946655 TTGATCATATCATCCTCGTTAACAC 57.053 36.000 6.39 0.00 39.39 3.32
57 58 6.149633 TGATCATATCATCCTCGTTAACACG 58.850 40.000 6.39 0.00 40.16 4.49
58 59 6.238925 TGATCATATCATCCTCGTTAACACGT 60.239 38.462 6.39 0.00 39.92 4.49
59 60 7.995611 TGATCATATCATCCTCGTTAACACGTC 60.996 40.741 6.39 0.00 39.92 4.34
72 73 2.805546 ACGTCTCGTGTGTGCACT 59.194 55.556 19.41 0.00 43.16 4.40
73 74 1.141019 ACGTCTCGTGTGTGCACTT 59.859 52.632 19.41 0.00 43.16 3.16
74 75 0.870307 ACGTCTCGTGTGTGCACTTC 60.870 55.000 19.41 11.68 43.16 3.01
75 76 0.595053 CGTCTCGTGTGTGCACTTCT 60.595 55.000 19.41 0.00 43.16 2.85
76 77 1.571919 GTCTCGTGTGTGCACTTCTT 58.428 50.000 19.41 0.00 43.16 2.52
77 78 1.258982 GTCTCGTGTGTGCACTTCTTG 59.741 52.381 19.41 4.43 43.16 3.02
78 79 1.136110 TCTCGTGTGTGCACTTCTTGA 59.864 47.619 19.41 8.59 43.16 3.02
79 80 1.933181 CTCGTGTGTGCACTTCTTGAA 59.067 47.619 19.41 0.00 43.16 2.69
80 81 2.545526 CTCGTGTGTGCACTTCTTGAAT 59.454 45.455 19.41 0.00 43.16 2.57
81 82 2.543848 TCGTGTGTGCACTTCTTGAATC 59.456 45.455 19.41 0.00 43.16 2.52
82 83 2.287644 CGTGTGTGCACTTCTTGAATCA 59.712 45.455 19.41 1.02 43.16 2.57
83 84 3.058708 CGTGTGTGCACTTCTTGAATCAT 60.059 43.478 19.41 0.00 43.16 2.45
84 85 4.555313 CGTGTGTGCACTTCTTGAATCATT 60.555 41.667 19.41 0.00 43.16 2.57
85 86 4.913924 GTGTGTGCACTTCTTGAATCATTC 59.086 41.667 19.41 0.00 42.13 2.67
86 87 4.022935 TGTGTGCACTTCTTGAATCATTCC 60.023 41.667 19.41 0.00 0.00 3.01
87 88 3.507233 TGTGCACTTCTTGAATCATTCCC 59.493 43.478 19.41 0.00 0.00 3.97
88 89 3.507233 GTGCACTTCTTGAATCATTCCCA 59.493 43.478 10.32 0.00 0.00 4.37
89 90 4.022068 GTGCACTTCTTGAATCATTCCCAA 60.022 41.667 10.32 0.00 0.00 4.12
90 91 4.219070 TGCACTTCTTGAATCATTCCCAAG 59.781 41.667 0.00 0.00 38.79 3.61
91 92 4.741342 CACTTCTTGAATCATTCCCAAGC 58.259 43.478 0.00 0.00 37.71 4.01
92 93 4.219070 CACTTCTTGAATCATTCCCAAGCA 59.781 41.667 0.00 0.00 37.71 3.91
93 94 4.219288 ACTTCTTGAATCATTCCCAAGCAC 59.781 41.667 0.00 0.00 37.71 4.40
94 95 3.765381 TCTTGAATCATTCCCAAGCACA 58.235 40.909 0.00 0.00 37.71 4.57
95 96 3.507233 TCTTGAATCATTCCCAAGCACAC 59.493 43.478 0.00 0.00 37.71 3.82
96 97 3.159213 TGAATCATTCCCAAGCACACT 57.841 42.857 0.00 0.00 0.00 3.55
97 98 2.821378 TGAATCATTCCCAAGCACACTG 59.179 45.455 0.00 0.00 0.00 3.66
98 99 2.592102 ATCATTCCCAAGCACACTGT 57.408 45.000 0.00 0.00 0.00 3.55
99 100 2.363306 TCATTCCCAAGCACACTGTT 57.637 45.000 0.00 0.00 0.00 3.16
100 101 2.665165 TCATTCCCAAGCACACTGTTT 58.335 42.857 0.00 0.00 0.00 2.83
101 102 2.622942 TCATTCCCAAGCACACTGTTTC 59.377 45.455 0.00 0.00 0.00 2.78
102 103 1.398692 TTCCCAAGCACACTGTTTCC 58.601 50.000 0.00 0.00 0.00 3.13
103 104 0.467290 TCCCAAGCACACTGTTTCCC 60.467 55.000 0.00 0.00 0.00 3.97
104 105 1.463553 CCCAAGCACACTGTTTCCCC 61.464 60.000 0.00 0.00 0.00 4.81
105 106 1.463553 CCAAGCACACTGTTTCCCCC 61.464 60.000 0.00 0.00 0.00 5.40
119 120 3.525221 CCCCCGACAAATCCATGC 58.475 61.111 0.00 0.00 0.00 4.06
120 121 2.127232 CCCCCGACAAATCCATGCC 61.127 63.158 0.00 0.00 0.00 4.40
121 122 2.127232 CCCCGACAAATCCATGCCC 61.127 63.158 0.00 0.00 0.00 5.36
122 123 1.076777 CCCGACAAATCCATGCCCT 60.077 57.895 0.00 0.00 0.00 5.19
123 124 1.103398 CCCGACAAATCCATGCCCTC 61.103 60.000 0.00 0.00 0.00 4.30
124 125 0.394216 CCGACAAATCCATGCCCTCA 60.394 55.000 0.00 0.00 0.00 3.86
125 126 1.462616 CGACAAATCCATGCCCTCAA 58.537 50.000 0.00 0.00 0.00 3.02
126 127 1.133025 CGACAAATCCATGCCCTCAAC 59.867 52.381 0.00 0.00 0.00 3.18
127 128 1.478105 GACAAATCCATGCCCTCAACC 59.522 52.381 0.00 0.00 0.00 3.77
128 129 1.203162 ACAAATCCATGCCCTCAACCA 60.203 47.619 0.00 0.00 0.00 3.67
129 130 1.205417 CAAATCCATGCCCTCAACCAC 59.795 52.381 0.00 0.00 0.00 4.16
130 131 0.706433 AATCCATGCCCTCAACCACT 59.294 50.000 0.00 0.00 0.00 4.00
131 132 0.257039 ATCCATGCCCTCAACCACTC 59.743 55.000 0.00 0.00 0.00 3.51
132 133 1.133181 TCCATGCCCTCAACCACTCA 61.133 55.000 0.00 0.00 0.00 3.41
133 134 0.679002 CCATGCCCTCAACCACTCAG 60.679 60.000 0.00 0.00 0.00 3.35
134 135 0.325933 CATGCCCTCAACCACTCAGA 59.674 55.000 0.00 0.00 0.00 3.27
135 136 0.617413 ATGCCCTCAACCACTCAGAG 59.383 55.000 0.00 0.00 0.00 3.35
136 137 0.471780 TGCCCTCAACCACTCAGAGA 60.472 55.000 3.79 0.00 0.00 3.10
137 138 0.687354 GCCCTCAACCACTCAGAGAA 59.313 55.000 3.79 0.00 0.00 2.87
138 139 1.609320 GCCCTCAACCACTCAGAGAAC 60.609 57.143 3.79 0.00 0.00 3.01
139 140 1.974236 CCCTCAACCACTCAGAGAACT 59.026 52.381 3.79 0.00 0.00 3.01
140 141 2.028567 CCCTCAACCACTCAGAGAACTC 60.029 54.545 3.79 0.00 0.00 3.01
141 142 2.352225 CCTCAACCACTCAGAGAACTCG 60.352 54.545 3.79 0.00 34.09 4.18
142 143 2.294791 CTCAACCACTCAGAGAACTCGT 59.705 50.000 3.79 0.00 34.09 4.18
143 144 2.293677 TCAACCACTCAGAGAACTCGTC 59.706 50.000 3.79 0.00 34.09 4.20
144 145 2.279935 ACCACTCAGAGAACTCGTCT 57.720 50.000 3.79 0.00 40.25 4.18
151 152 3.410098 GAGAACTCGTCTCCACTGC 57.590 57.895 0.00 0.00 46.32 4.40
152 153 0.109039 GAGAACTCGTCTCCACTGCC 60.109 60.000 0.00 0.00 46.32 4.85
153 154 1.444553 GAACTCGTCTCCACTGCCG 60.445 63.158 0.00 0.00 0.00 5.69
154 155 3.575351 AACTCGTCTCCACTGCCGC 62.575 63.158 0.00 0.00 0.00 6.53
177 178 4.748679 GCAGCCGCGTTTGCTCTG 62.749 66.667 20.61 11.46 40.26 3.35
178 179 4.748679 CAGCCGCGTTTGCTCTGC 62.749 66.667 4.92 0.00 36.81 4.26
181 182 3.793144 CCGCGTTTGCTCTGCCTC 61.793 66.667 4.92 0.00 39.65 4.70
182 183 3.793144 CGCGTTTGCTCTGCCTCC 61.793 66.667 0.00 0.00 39.65 4.30
183 184 2.359230 GCGTTTGCTCTGCCTCCT 60.359 61.111 0.00 0.00 38.39 3.69
184 185 2.394563 GCGTTTGCTCTGCCTCCTC 61.395 63.158 0.00 0.00 38.39 3.71
185 186 1.294780 CGTTTGCTCTGCCTCCTCT 59.705 57.895 0.00 0.00 0.00 3.69
186 187 1.018226 CGTTTGCTCTGCCTCCTCTG 61.018 60.000 0.00 0.00 0.00 3.35
187 188 0.036022 GTTTGCTCTGCCTCCTCTGT 59.964 55.000 0.00 0.00 0.00 3.41
188 189 0.767375 TTTGCTCTGCCTCCTCTGTT 59.233 50.000 0.00 0.00 0.00 3.16
189 190 0.322975 TTGCTCTGCCTCCTCTGTTC 59.677 55.000 0.00 0.00 0.00 3.18
190 191 1.220477 GCTCTGCCTCCTCTGTTCC 59.780 63.158 0.00 0.00 0.00 3.62
191 192 1.904032 CTCTGCCTCCTCTGTTCCC 59.096 63.158 0.00 0.00 0.00 3.97
192 193 0.617249 CTCTGCCTCCTCTGTTCCCT 60.617 60.000 0.00 0.00 0.00 4.20
193 194 0.616111 TCTGCCTCCTCTGTTCCCTC 60.616 60.000 0.00 0.00 0.00 4.30
194 195 0.617249 CTGCCTCCTCTGTTCCCTCT 60.617 60.000 0.00 0.00 0.00 3.69
195 196 0.710588 TGCCTCCTCTGTTCCCTCTA 59.289 55.000 0.00 0.00 0.00 2.43
196 197 1.342474 TGCCTCCTCTGTTCCCTCTAG 60.342 57.143 0.00 0.00 0.00 2.43
197 198 1.408969 CCTCCTCTGTTCCCTCTAGC 58.591 60.000 0.00 0.00 0.00 3.42
198 199 1.063266 CCTCCTCTGTTCCCTCTAGCT 60.063 57.143 0.00 0.00 0.00 3.32
199 200 2.306847 CTCCTCTGTTCCCTCTAGCTC 58.693 57.143 0.00 0.00 0.00 4.09
200 201 1.926665 TCCTCTGTTCCCTCTAGCTCT 59.073 52.381 0.00 0.00 0.00 4.09
201 202 2.313342 TCCTCTGTTCCCTCTAGCTCTT 59.687 50.000 0.00 0.00 0.00 2.85
202 203 3.528078 TCCTCTGTTCCCTCTAGCTCTTA 59.472 47.826 0.00 0.00 0.00 2.10
203 204 4.169068 TCCTCTGTTCCCTCTAGCTCTTAT 59.831 45.833 0.00 0.00 0.00 1.73
204 205 5.372959 TCCTCTGTTCCCTCTAGCTCTTATA 59.627 44.000 0.00 0.00 0.00 0.98
205 206 5.475564 CCTCTGTTCCCTCTAGCTCTTATAC 59.524 48.000 0.00 0.00 0.00 1.47
206 207 5.386924 TCTGTTCCCTCTAGCTCTTATACC 58.613 45.833 0.00 0.00 0.00 2.73
207 208 5.103643 TCTGTTCCCTCTAGCTCTTATACCA 60.104 44.000 0.00 0.00 0.00 3.25
208 209 4.894114 TGTTCCCTCTAGCTCTTATACCAC 59.106 45.833 0.00 0.00 0.00 4.16
209 210 5.141910 GTTCCCTCTAGCTCTTATACCACT 58.858 45.833 0.00 0.00 0.00 4.00
210 211 5.405063 TCCCTCTAGCTCTTATACCACTT 57.595 43.478 0.00 0.00 0.00 3.16
211 212 5.778542 TCCCTCTAGCTCTTATACCACTTT 58.221 41.667 0.00 0.00 0.00 2.66
212 213 6.203072 TCCCTCTAGCTCTTATACCACTTTT 58.797 40.000 0.00 0.00 0.00 2.27
213 214 6.672657 TCCCTCTAGCTCTTATACCACTTTTT 59.327 38.462 0.00 0.00 0.00 1.94
214 215 6.987404 CCCTCTAGCTCTTATACCACTTTTTC 59.013 42.308 0.00 0.00 0.00 2.29
215 216 6.987404 CCTCTAGCTCTTATACCACTTTTTCC 59.013 42.308 0.00 0.00 0.00 3.13
216 217 7.147637 CCTCTAGCTCTTATACCACTTTTTCCT 60.148 40.741 0.00 0.00 0.00 3.36
217 218 7.783042 TCTAGCTCTTATACCACTTTTTCCTC 58.217 38.462 0.00 0.00 0.00 3.71
218 219 5.746284 AGCTCTTATACCACTTTTTCCTCC 58.254 41.667 0.00 0.00 0.00 4.30
219 220 5.489278 AGCTCTTATACCACTTTTTCCTCCT 59.511 40.000 0.00 0.00 0.00 3.69
220 221 5.818336 GCTCTTATACCACTTTTTCCTCCTC 59.182 44.000 0.00 0.00 0.00 3.71
221 222 6.352308 GCTCTTATACCACTTTTTCCTCCTCT 60.352 42.308 0.00 0.00 0.00 3.69
222 223 6.947464 TCTTATACCACTTTTTCCTCCTCTG 58.053 40.000 0.00 0.00 0.00 3.35
223 224 6.500751 TCTTATACCACTTTTTCCTCCTCTGT 59.499 38.462 0.00 0.00 0.00 3.41
224 225 3.953542 ACCACTTTTTCCTCCTCTGTT 57.046 42.857 0.00 0.00 0.00 3.16
225 226 6.697641 ATACCACTTTTTCCTCCTCTGTTA 57.302 37.500 0.00 0.00 0.00 2.41
226 227 4.974399 ACCACTTTTTCCTCCTCTGTTAG 58.026 43.478 0.00 0.00 0.00 2.34
227 228 4.412528 ACCACTTTTTCCTCCTCTGTTAGT 59.587 41.667 0.00 0.00 0.00 2.24
228 229 4.998033 CCACTTTTTCCTCCTCTGTTAGTC 59.002 45.833 0.00 0.00 0.00 2.59
229 230 4.998033 CACTTTTTCCTCCTCTGTTAGTCC 59.002 45.833 0.00 0.00 0.00 3.85
230 231 4.908481 ACTTTTTCCTCCTCTGTTAGTCCT 59.092 41.667 0.00 0.00 0.00 3.85
231 232 6.014499 CACTTTTTCCTCCTCTGTTAGTCCTA 60.014 42.308 0.00 0.00 0.00 2.94
232 233 6.557633 ACTTTTTCCTCCTCTGTTAGTCCTAA 59.442 38.462 0.00 0.00 0.00 2.69
233 234 7.237887 ACTTTTTCCTCCTCTGTTAGTCCTAAT 59.762 37.037 0.00 0.00 0.00 1.73
234 235 8.674925 TTTTTCCTCCTCTGTTAGTCCTAATA 57.325 34.615 0.00 0.00 0.00 0.98
235 236 8.855804 TTTTCCTCCTCTGTTAGTCCTAATAT 57.144 34.615 0.00 0.00 0.00 1.28
236 237 9.947189 TTTTCCTCCTCTGTTAGTCCTAATATA 57.053 33.333 0.00 0.00 0.00 0.86
237 238 9.589461 TTTCCTCCTCTGTTAGTCCTAATATAG 57.411 37.037 0.00 0.00 0.00 1.31
239 240 6.378848 CCTCCTCTGTTAGTCCTAATATAGGC 59.621 46.154 9.16 0.00 45.82 3.93
240 241 5.944599 TCCTCTGTTAGTCCTAATATAGGCG 59.055 44.000 9.16 0.00 45.82 5.52
241 242 5.393243 CCTCTGTTAGTCCTAATATAGGCGC 60.393 48.000 0.00 0.00 45.82 6.53
242 243 5.322754 TCTGTTAGTCCTAATATAGGCGCT 58.677 41.667 7.64 0.00 45.82 5.92
243 244 5.183331 TCTGTTAGTCCTAATATAGGCGCTG 59.817 44.000 7.64 0.00 45.82 5.18
244 245 4.174762 GTTAGTCCTAATATAGGCGCTGC 58.825 47.826 7.64 0.00 45.82 5.25
245 246 2.530701 AGTCCTAATATAGGCGCTGCT 58.469 47.619 7.64 0.00 45.82 4.24
246 247 2.900546 AGTCCTAATATAGGCGCTGCTT 59.099 45.455 7.64 0.00 45.82 3.91
247 248 3.056465 AGTCCTAATATAGGCGCTGCTTC 60.056 47.826 7.64 0.00 45.82 3.86
248 249 2.233922 TCCTAATATAGGCGCTGCTTCC 59.766 50.000 7.64 0.00 45.82 3.46
249 250 2.234908 CCTAATATAGGCGCTGCTTCCT 59.765 50.000 7.64 13.49 39.48 3.36
250 251 2.464157 AATATAGGCGCTGCTTCCTC 57.536 50.000 7.64 0.00 34.02 3.71
251 252 1.638529 ATATAGGCGCTGCTTCCTCT 58.361 50.000 7.64 7.13 34.02 3.69
252 253 0.962489 TATAGGCGCTGCTTCCTCTC 59.038 55.000 7.64 0.00 34.02 3.20
253 254 1.753368 ATAGGCGCTGCTTCCTCTCC 61.753 60.000 7.64 0.00 34.02 3.71
254 255 2.863019 TAGGCGCTGCTTCCTCTCCT 62.863 60.000 7.64 0.00 34.02 3.69
255 256 2.511145 GCGCTGCTTCCTCTCCTG 60.511 66.667 0.00 0.00 0.00 3.86
256 257 2.511145 CGCTGCTTCCTCTCCTGC 60.511 66.667 0.00 0.00 0.00 4.85
257 258 2.124778 GCTGCTTCCTCTCCTGCC 60.125 66.667 0.00 0.00 0.00 4.85
258 259 2.668120 GCTGCTTCCTCTCCTGCCT 61.668 63.158 0.00 0.00 0.00 4.75
259 260 1.521616 CTGCTTCCTCTCCTGCCTC 59.478 63.158 0.00 0.00 0.00 4.70
260 261 1.970352 CTGCTTCCTCTCCTGCCTCC 61.970 65.000 0.00 0.00 0.00 4.30
261 262 1.688884 GCTTCCTCTCCTGCCTCCT 60.689 63.158 0.00 0.00 0.00 3.69
262 263 1.970352 GCTTCCTCTCCTGCCTCCTG 61.970 65.000 0.00 0.00 0.00 3.86
263 264 0.617249 CTTCCTCTCCTGCCTCCTGT 60.617 60.000 0.00 0.00 0.00 4.00
264 265 0.616111 TTCCTCTCCTGCCTCCTGTC 60.616 60.000 0.00 0.00 0.00 3.51
265 266 2.063378 CCTCTCCTGCCTCCTGTCC 61.063 68.421 0.00 0.00 0.00 4.02
275 276 2.122413 TCCTGTCCAGCCACCACT 60.122 61.111 0.00 0.00 0.00 4.00
369 370 9.810545 CTCTCTAATTAACCCTCTTTAGTTCAG 57.189 37.037 0.00 0.00 0.00 3.02
518 520 8.504815 CATTTCCTAGCTTCATCATTCATAGTG 58.495 37.037 0.00 0.00 0.00 2.74
566 578 7.254932 GCCATCTTAACAGCCTACTTAAGAATG 60.255 40.741 10.09 2.93 40.60 2.67
666 682 3.525537 CATTAGAGAACATGCCACGACT 58.474 45.455 0.00 0.00 0.00 4.18
732 748 6.975772 TCTGTCAAATCAAAACTAAAAACCCG 59.024 34.615 0.00 0.00 0.00 5.28
839 856 2.106683 GGAACAATCGGCGACAGGG 61.107 63.158 13.76 4.41 0.00 4.45
843 860 0.250553 ACAATCGGCGACAGGGAAAA 60.251 50.000 13.76 0.00 0.00 2.29
856 874 6.148976 GCGACAGGGAAAAGTAAAAGTAGAAT 59.851 38.462 0.00 0.00 0.00 2.40
877 1426 1.509703 CGAGGCATGGTCATCATCAG 58.490 55.000 0.00 0.00 32.92 2.90
878 1427 1.202615 CGAGGCATGGTCATCATCAGT 60.203 52.381 0.00 0.00 32.92 3.41
879 1428 2.744166 CGAGGCATGGTCATCATCAGTT 60.744 50.000 0.00 0.00 32.92 3.16
880 1429 2.877168 GAGGCATGGTCATCATCAGTTC 59.123 50.000 0.00 0.00 32.92 3.01
881 1430 2.240414 AGGCATGGTCATCATCAGTTCA 59.760 45.455 0.00 0.00 32.92 3.18
882 1431 3.117625 AGGCATGGTCATCATCAGTTCAT 60.118 43.478 0.00 0.00 32.92 2.57
883 1432 3.252701 GGCATGGTCATCATCAGTTCATC 59.747 47.826 0.00 0.00 32.92 2.92
884 1433 3.881089 GCATGGTCATCATCAGTTCATCA 59.119 43.478 0.00 0.00 32.92 3.07
885 1434 4.261072 GCATGGTCATCATCAGTTCATCAC 60.261 45.833 0.00 0.00 32.92 3.06
899 1448 7.676004 TCAGTTCATCACTACCATTGTCTTTA 58.324 34.615 0.00 0.00 32.76 1.85
911 1460 0.108520 TGTCTTTATGGTCGACGGCC 60.109 55.000 12.68 12.68 0.00 6.13
926 1475 0.319383 CGGCCGAGATTGGATCTGAG 60.319 60.000 24.07 0.00 40.38 3.35
938 1487 1.954362 GATCTGAGCGTGAGGTGGCT 61.954 60.000 0.00 0.00 45.11 4.75
954 1503 1.589716 GGCTGTTGGCGCAAATCTCT 61.590 55.000 10.83 0.00 42.94 3.10
1254 1844 0.249615 CCACGTCGATCCAGCATCAT 60.250 55.000 0.00 0.00 0.00 2.45
1255 1845 1.135046 CACGTCGATCCAGCATCATC 58.865 55.000 0.00 0.00 0.00 2.92
1256 1846 1.035923 ACGTCGATCCAGCATCATCT 58.964 50.000 0.00 0.00 0.00 2.90
1401 2000 3.923864 TGCGTCGACCAGTGGCTT 61.924 61.111 9.78 0.00 0.00 4.35
1536 2143 1.665264 TTCGTTCCGGCCGTATAGCA 61.665 55.000 26.12 0.03 0.00 3.49
1613 2248 1.454295 TACGGAGCCGCCATGTAGA 60.454 57.895 9.14 0.00 44.19 2.59
1697 2335 4.593956 TCTCTCTCTATGAAGACACAGCA 58.406 43.478 0.00 0.00 0.00 4.41
1738 2383 2.860735 GACATCCGTTCCTCGATTGAAG 59.139 50.000 0.00 0.00 42.86 3.02
1751 2396 3.058708 TCGATTGAAGTGCAGAAGCTTTG 60.059 43.478 0.00 2.27 42.74 2.77
1784 2429 2.877168 CGTACTCTATCTAACCGCCTGT 59.123 50.000 0.00 0.00 0.00 4.00
1819 2464 5.965922 GGCAGTGCCTAGAAATTATTTTGT 58.034 37.500 27.48 0.00 46.69 2.83
1820 2465 6.398095 GGCAGTGCCTAGAAATTATTTTGTT 58.602 36.000 27.48 0.00 46.69 2.83
1821 2466 6.873605 GGCAGTGCCTAGAAATTATTTTGTTT 59.126 34.615 27.48 0.00 46.69 2.83
1822 2467 7.387673 GGCAGTGCCTAGAAATTATTTTGTTTT 59.612 33.333 27.48 0.00 46.69 2.43
1823 2468 8.773645 GCAGTGCCTAGAAATTATTTTGTTTTT 58.226 29.630 2.85 0.00 0.00 1.94
1887 2532 8.060090 GCATGCTTTATTGAATCAAAGTAATGC 58.940 33.333 11.37 14.84 41.34 3.56
1942 2587 4.947388 GCCCAATCAAACATGTCTACCTAA 59.053 41.667 0.00 0.00 0.00 2.69
1944 2589 6.071616 GCCCAATCAAACATGTCTACCTAAAA 60.072 38.462 0.00 0.00 0.00 1.52
1946 2591 7.312899 CCAATCAAACATGTCTACCTAAAACC 58.687 38.462 0.00 0.00 0.00 3.27
1947 2592 6.737254 ATCAAACATGTCTACCTAAAACCG 57.263 37.500 0.00 0.00 0.00 4.44
1949 2594 2.981898 ACATGTCTACCTAAAACCGGC 58.018 47.619 0.00 0.00 0.00 6.13
1950 2595 2.303600 ACATGTCTACCTAAAACCGGCA 59.696 45.455 0.00 0.00 0.00 5.69
1951 2596 2.754946 TGTCTACCTAAAACCGGCAG 57.245 50.000 0.00 0.00 0.00 4.85
1953 2598 2.232941 TGTCTACCTAAAACCGGCAGAG 59.767 50.000 0.00 0.00 0.00 3.35
2222 2867 2.293677 GCTGCTGCCTACGTCTAGATTA 59.706 50.000 3.85 0.00 0.00 1.75
2230 2875 4.218852 GCCTACGTCTAGATTATGAGCCTT 59.781 45.833 0.00 0.00 0.00 4.35
2262 4328 4.982295 AGTTTCTGCGCTCAAATAAAAACC 59.018 37.500 9.73 0.00 0.00 3.27
2269 4335 4.298332 CGCTCAAATAAAAACCTGCAAGT 58.702 39.130 0.00 0.00 0.00 3.16
2438 4505 4.989279 TCTCTGCAAGCAAAAGTTTCTT 57.011 36.364 0.00 0.00 0.00 2.52
2439 4506 4.675510 TCTCTGCAAGCAAAAGTTTCTTG 58.324 39.130 11.05 11.05 39.95 3.02
2477 4544 1.150992 CCCCCGTAAACCACCACAA 59.849 57.895 0.00 0.00 0.00 3.33
2478 4545 0.891904 CCCCCGTAAACCACCACAAG 60.892 60.000 0.00 0.00 0.00 3.16
2480 4547 1.477195 CCCCGTAAACCACCACAAGAA 60.477 52.381 0.00 0.00 0.00 2.52
2481 4548 2.299521 CCCGTAAACCACCACAAGAAA 58.700 47.619 0.00 0.00 0.00 2.52
2536 4603 3.480679 CTGCCACAGCTCCACCACA 62.481 63.158 0.00 0.00 40.80 4.17
2782 4853 1.732259 CCACAACGTAACAGCCATCTC 59.268 52.381 0.00 0.00 0.00 2.75
2808 4879 3.051081 ACTTTGAGTGATCCAGCTGTC 57.949 47.619 13.81 5.09 0.00 3.51
2820 4891 1.137086 CCAGCTGTCGTTGTAGCCTAT 59.863 52.381 13.81 0.00 40.76 2.57
2825 4896 3.797256 GCTGTCGTTGTAGCCTATAAGTG 59.203 47.826 0.00 0.00 33.89 3.16
2833 4904 7.604927 TCGTTGTAGCCTATAAGTGTTTTGATT 59.395 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.034179 CCAACTTGGTCGGGAAAGTTTC 59.966 50.000 7.09 7.09 42.51 2.78
2 3 2.028876 CCAACTTGGTCGGGAAAGTTT 58.971 47.619 0.00 0.00 42.51 2.66
3 4 1.687563 CCAACTTGGTCGGGAAAGTT 58.312 50.000 0.00 4.96 45.22 2.66
4 5 0.822121 GCCAACTTGGTCGGGAAAGT 60.822 55.000 9.63 0.00 40.46 2.66
5 6 1.524008 GGCCAACTTGGTCGGGAAAG 61.524 60.000 9.63 0.00 40.46 2.62
7 8 2.114411 GGCCAACTTGGTCGGGAA 59.886 61.111 9.63 0.00 40.46 3.97
8 9 3.961414 GGGCCAACTTGGTCGGGA 61.961 66.667 4.39 0.00 44.85 5.14
10 11 2.132089 TTAGGGGCCAACTTGGTCGG 62.132 60.000 4.39 0.00 44.85 4.79
11 12 0.958876 GTTAGGGGCCAACTTGGTCG 60.959 60.000 4.39 0.00 44.85 4.79
12 13 0.111639 TGTTAGGGGCCAACTTGGTC 59.888 55.000 4.39 6.78 42.67 4.02
13 14 0.783850 ATGTTAGGGGCCAACTTGGT 59.216 50.000 4.39 0.00 40.46 3.67
14 15 1.550072 CAATGTTAGGGGCCAACTTGG 59.450 52.381 4.39 3.10 41.55 3.61
15 16 2.524306 TCAATGTTAGGGGCCAACTTG 58.476 47.619 4.39 8.79 0.00 3.16
16 17 2.990740 TCAATGTTAGGGGCCAACTT 57.009 45.000 4.39 0.00 0.00 2.66
17 18 2.311542 TGATCAATGTTAGGGGCCAACT 59.688 45.455 4.39 4.45 0.00 3.16
18 19 2.733956 TGATCAATGTTAGGGGCCAAC 58.266 47.619 4.39 2.27 0.00 3.77
19 20 3.686227 ATGATCAATGTTAGGGGCCAA 57.314 42.857 4.39 0.00 0.00 4.52
20 21 4.353489 TGATATGATCAATGTTAGGGGCCA 59.647 41.667 4.39 0.00 36.11 5.36
21 22 4.922206 TGATATGATCAATGTTAGGGGCC 58.078 43.478 0.00 0.00 36.11 5.80
22 23 5.591877 GGATGATATGATCAATGTTAGGGGC 59.408 44.000 0.00 0.00 43.50 5.80
23 24 6.966751 AGGATGATATGATCAATGTTAGGGG 58.033 40.000 0.00 0.00 43.50 4.79
24 25 6.760298 CGAGGATGATATGATCAATGTTAGGG 59.240 42.308 0.00 0.00 43.50 3.53
25 26 7.326454 ACGAGGATGATATGATCAATGTTAGG 58.674 38.462 0.00 0.00 43.50 2.69
26 27 8.768957 AACGAGGATGATATGATCAATGTTAG 57.231 34.615 0.00 0.00 43.50 2.34
28 29 8.993121 GTTAACGAGGATGATATGATCAATGTT 58.007 33.333 0.00 7.26 43.50 2.71
29 30 8.150296 TGTTAACGAGGATGATATGATCAATGT 58.850 33.333 0.00 0.00 43.50 2.71
30 31 8.438513 GTGTTAACGAGGATGATATGATCAATG 58.561 37.037 0.00 0.00 43.50 2.82
31 32 8.539770 GTGTTAACGAGGATGATATGATCAAT 57.460 34.615 0.00 0.00 43.50 2.57
32 33 7.946655 GTGTTAACGAGGATGATATGATCAA 57.053 36.000 0.00 0.00 43.50 2.57
63 64 4.022935 GGAATGATTCAAGAAGTGCACACA 60.023 41.667 21.04 5.09 0.00 3.72
64 65 4.479619 GGAATGATTCAAGAAGTGCACAC 58.520 43.478 21.04 12.64 0.00 3.82
65 66 3.507233 GGGAATGATTCAAGAAGTGCACA 59.493 43.478 21.04 0.00 0.00 4.57
66 67 3.507233 TGGGAATGATTCAAGAAGTGCAC 59.493 43.478 9.40 9.40 0.00 4.57
67 68 3.765381 TGGGAATGATTCAAGAAGTGCA 58.235 40.909 7.56 0.00 0.00 4.57
68 69 4.741342 CTTGGGAATGATTCAAGAAGTGC 58.259 43.478 7.56 0.00 39.97 4.40
69 70 4.219070 TGCTTGGGAATGATTCAAGAAGTG 59.781 41.667 7.56 0.00 39.97 3.16
70 71 4.219288 GTGCTTGGGAATGATTCAAGAAGT 59.781 41.667 7.56 0.00 39.97 3.01
71 72 4.219070 TGTGCTTGGGAATGATTCAAGAAG 59.781 41.667 7.56 6.60 39.97 2.85
72 73 4.022068 GTGTGCTTGGGAATGATTCAAGAA 60.022 41.667 7.56 0.00 39.97 2.52
73 74 3.507233 GTGTGCTTGGGAATGATTCAAGA 59.493 43.478 7.56 0.00 39.97 3.02
74 75 3.508793 AGTGTGCTTGGGAATGATTCAAG 59.491 43.478 7.56 5.03 40.38 3.02
75 76 3.256383 CAGTGTGCTTGGGAATGATTCAA 59.744 43.478 7.56 0.00 0.00 2.69
76 77 2.821378 CAGTGTGCTTGGGAATGATTCA 59.179 45.455 7.56 0.00 0.00 2.57
77 78 2.821969 ACAGTGTGCTTGGGAATGATTC 59.178 45.455 0.00 0.00 0.00 2.52
78 79 2.880443 ACAGTGTGCTTGGGAATGATT 58.120 42.857 0.00 0.00 0.00 2.57
79 80 2.592102 ACAGTGTGCTTGGGAATGAT 57.408 45.000 0.00 0.00 0.00 2.45
80 81 2.363306 AACAGTGTGCTTGGGAATGA 57.637 45.000 0.00 0.00 0.00 2.57
81 82 2.288395 GGAAACAGTGTGCTTGGGAATG 60.288 50.000 0.00 0.00 0.00 2.67
82 83 1.963515 GGAAACAGTGTGCTTGGGAAT 59.036 47.619 0.00 0.00 0.00 3.01
83 84 1.398692 GGAAACAGTGTGCTTGGGAA 58.601 50.000 0.00 0.00 0.00 3.97
84 85 0.467290 GGGAAACAGTGTGCTTGGGA 60.467 55.000 0.00 0.00 0.00 4.37
85 86 1.463553 GGGGAAACAGTGTGCTTGGG 61.464 60.000 0.00 0.00 0.00 4.12
86 87 1.463553 GGGGGAAACAGTGTGCTTGG 61.464 60.000 0.00 0.00 0.00 3.61
87 88 2.041153 GGGGGAAACAGTGTGCTTG 58.959 57.895 0.00 0.00 0.00 4.01
88 89 4.599036 GGGGGAAACAGTGTGCTT 57.401 55.556 0.00 0.00 0.00 3.91
102 103 2.127232 GGCATGGATTTGTCGGGGG 61.127 63.158 0.00 0.00 0.00 5.40
103 104 2.127232 GGGCATGGATTTGTCGGGG 61.127 63.158 0.00 0.00 0.00 5.73
104 105 1.076777 AGGGCATGGATTTGTCGGG 60.077 57.895 0.00 0.00 0.00 5.14
105 106 0.394216 TGAGGGCATGGATTTGTCGG 60.394 55.000 0.00 0.00 0.00 4.79
106 107 1.133025 GTTGAGGGCATGGATTTGTCG 59.867 52.381 0.00 0.00 0.00 4.35
107 108 1.478105 GGTTGAGGGCATGGATTTGTC 59.522 52.381 0.00 0.00 0.00 3.18
108 109 1.203162 TGGTTGAGGGCATGGATTTGT 60.203 47.619 0.00 0.00 0.00 2.83
109 110 1.205417 GTGGTTGAGGGCATGGATTTG 59.795 52.381 0.00 0.00 0.00 2.32
110 111 1.077663 AGTGGTTGAGGGCATGGATTT 59.922 47.619 0.00 0.00 0.00 2.17
111 112 0.706433 AGTGGTTGAGGGCATGGATT 59.294 50.000 0.00 0.00 0.00 3.01
112 113 0.257039 GAGTGGTTGAGGGCATGGAT 59.743 55.000 0.00 0.00 0.00 3.41
113 114 1.133181 TGAGTGGTTGAGGGCATGGA 61.133 55.000 0.00 0.00 0.00 3.41
114 115 0.679002 CTGAGTGGTTGAGGGCATGG 60.679 60.000 0.00 0.00 0.00 3.66
115 116 0.325933 TCTGAGTGGTTGAGGGCATG 59.674 55.000 0.00 0.00 0.00 4.06
116 117 0.617413 CTCTGAGTGGTTGAGGGCAT 59.383 55.000 0.00 0.00 0.00 4.40
117 118 0.471780 TCTCTGAGTGGTTGAGGGCA 60.472 55.000 4.32 0.00 0.00 5.36
118 119 0.687354 TTCTCTGAGTGGTTGAGGGC 59.313 55.000 4.32 0.00 0.00 5.19
119 120 1.974236 AGTTCTCTGAGTGGTTGAGGG 59.026 52.381 4.32 0.00 0.00 4.30
120 121 2.352225 CGAGTTCTCTGAGTGGTTGAGG 60.352 54.545 4.32 0.00 0.00 3.86
121 122 2.294791 ACGAGTTCTCTGAGTGGTTGAG 59.705 50.000 4.32 0.00 0.00 3.02
122 123 2.293677 GACGAGTTCTCTGAGTGGTTGA 59.706 50.000 4.32 0.00 0.00 3.18
123 124 2.294791 AGACGAGTTCTCTGAGTGGTTG 59.705 50.000 4.32 0.00 0.00 3.77
124 125 2.554893 GAGACGAGTTCTCTGAGTGGTT 59.445 50.000 4.32 0.00 46.68 3.67
125 126 2.156098 GAGACGAGTTCTCTGAGTGGT 58.844 52.381 4.32 0.00 46.68 4.16
126 127 2.911819 GAGACGAGTTCTCTGAGTGG 57.088 55.000 4.32 0.00 46.68 4.00
134 135 1.867919 CGGCAGTGGAGACGAGTTCT 61.868 60.000 0.00 0.00 37.23 3.01
135 136 1.444553 CGGCAGTGGAGACGAGTTC 60.445 63.158 0.00 0.00 0.00 3.01
136 137 2.651361 CGGCAGTGGAGACGAGTT 59.349 61.111 0.00 0.00 0.00 3.01
137 138 4.057428 GCGGCAGTGGAGACGAGT 62.057 66.667 0.00 0.00 0.00 4.18
160 161 4.748679 CAGAGCAAACGCGGCTGC 62.749 66.667 22.59 22.59 42.78 5.25
161 162 4.748679 GCAGAGCAAACGCGGCTG 62.749 66.667 13.13 9.13 42.78 4.85
164 165 3.793144 GAGGCAGAGCAAACGCGG 61.793 66.667 12.47 0.00 0.00 6.46
165 166 3.793144 GGAGGCAGAGCAAACGCG 61.793 66.667 3.53 3.53 0.00 6.01
166 167 2.359230 AGGAGGCAGAGCAAACGC 60.359 61.111 0.00 0.00 0.00 4.84
167 168 1.018226 CAGAGGAGGCAGAGCAAACG 61.018 60.000 0.00 0.00 0.00 3.60
168 169 0.036022 ACAGAGGAGGCAGAGCAAAC 59.964 55.000 0.00 0.00 0.00 2.93
169 170 0.767375 AACAGAGGAGGCAGAGCAAA 59.233 50.000 0.00 0.00 0.00 3.68
170 171 0.322975 GAACAGAGGAGGCAGAGCAA 59.677 55.000 0.00 0.00 0.00 3.91
171 172 1.548357 GGAACAGAGGAGGCAGAGCA 61.548 60.000 0.00 0.00 0.00 4.26
172 173 1.220477 GGAACAGAGGAGGCAGAGC 59.780 63.158 0.00 0.00 0.00 4.09
173 174 0.617249 AGGGAACAGAGGAGGCAGAG 60.617 60.000 0.00 0.00 0.00 3.35
174 175 0.616111 GAGGGAACAGAGGAGGCAGA 60.616 60.000 0.00 0.00 0.00 4.26
175 176 0.617249 AGAGGGAACAGAGGAGGCAG 60.617 60.000 0.00 0.00 0.00 4.85
176 177 0.710588 TAGAGGGAACAGAGGAGGCA 59.289 55.000 0.00 0.00 0.00 4.75
177 178 1.408969 CTAGAGGGAACAGAGGAGGC 58.591 60.000 0.00 0.00 0.00 4.70
178 179 1.063266 AGCTAGAGGGAACAGAGGAGG 60.063 57.143 0.00 0.00 0.00 4.30
179 180 2.091885 AGAGCTAGAGGGAACAGAGGAG 60.092 54.545 0.00 0.00 0.00 3.69
180 181 1.926665 AGAGCTAGAGGGAACAGAGGA 59.073 52.381 0.00 0.00 0.00 3.71
181 182 2.452600 AGAGCTAGAGGGAACAGAGG 57.547 55.000 0.00 0.00 0.00 3.69
182 183 5.475564 GGTATAAGAGCTAGAGGGAACAGAG 59.524 48.000 0.00 0.00 0.00 3.35
183 184 5.103643 TGGTATAAGAGCTAGAGGGAACAGA 60.104 44.000 0.00 0.00 0.00 3.41
184 185 5.010213 GTGGTATAAGAGCTAGAGGGAACAG 59.990 48.000 0.00 0.00 0.00 3.16
185 186 4.894114 GTGGTATAAGAGCTAGAGGGAACA 59.106 45.833 0.00 0.00 0.00 3.18
186 187 5.141910 AGTGGTATAAGAGCTAGAGGGAAC 58.858 45.833 0.00 0.00 0.00 3.62
187 188 5.405063 AGTGGTATAAGAGCTAGAGGGAA 57.595 43.478 0.00 0.00 0.00 3.97
188 189 5.405063 AAGTGGTATAAGAGCTAGAGGGA 57.595 43.478 0.00 0.00 0.00 4.20
189 190 6.487299 AAAAGTGGTATAAGAGCTAGAGGG 57.513 41.667 0.00 0.00 0.00 4.30
190 191 6.987404 GGAAAAAGTGGTATAAGAGCTAGAGG 59.013 42.308 0.00 0.00 0.00 3.69
191 192 7.787028 AGGAAAAAGTGGTATAAGAGCTAGAG 58.213 38.462 0.00 0.00 0.00 2.43
192 193 7.147707 GGAGGAAAAAGTGGTATAAGAGCTAGA 60.148 40.741 0.00 0.00 0.00 2.43
193 194 6.987404 GGAGGAAAAAGTGGTATAAGAGCTAG 59.013 42.308 0.00 0.00 0.00 3.42
194 195 6.672657 AGGAGGAAAAAGTGGTATAAGAGCTA 59.327 38.462 0.00 0.00 0.00 3.32
195 196 5.489278 AGGAGGAAAAAGTGGTATAAGAGCT 59.511 40.000 0.00 0.00 0.00 4.09
196 197 5.746284 AGGAGGAAAAAGTGGTATAAGAGC 58.254 41.667 0.00 0.00 0.00 4.09
197 198 7.044798 CAGAGGAGGAAAAAGTGGTATAAGAG 58.955 42.308 0.00 0.00 0.00 2.85
198 199 6.500751 ACAGAGGAGGAAAAAGTGGTATAAGA 59.499 38.462 0.00 0.00 0.00 2.10
199 200 6.712276 ACAGAGGAGGAAAAAGTGGTATAAG 58.288 40.000 0.00 0.00 0.00 1.73
200 201 6.697641 ACAGAGGAGGAAAAAGTGGTATAA 57.302 37.500 0.00 0.00 0.00 0.98
201 202 6.697641 AACAGAGGAGGAAAAAGTGGTATA 57.302 37.500 0.00 0.00 0.00 1.47
202 203 5.584551 AACAGAGGAGGAAAAAGTGGTAT 57.415 39.130 0.00 0.00 0.00 2.73
203 204 5.605488 ACTAACAGAGGAGGAAAAAGTGGTA 59.395 40.000 0.00 0.00 0.00 3.25
204 205 3.953542 AACAGAGGAGGAAAAAGTGGT 57.046 42.857 0.00 0.00 0.00 4.16
205 206 4.974399 ACTAACAGAGGAGGAAAAAGTGG 58.026 43.478 0.00 0.00 0.00 4.00
206 207 4.998033 GGACTAACAGAGGAGGAAAAAGTG 59.002 45.833 0.00 0.00 0.00 3.16
207 208 4.908481 AGGACTAACAGAGGAGGAAAAAGT 59.092 41.667 0.00 0.00 0.00 2.66
208 209 5.491323 AGGACTAACAGAGGAGGAAAAAG 57.509 43.478 0.00 0.00 0.00 2.27
209 210 7.569599 ATTAGGACTAACAGAGGAGGAAAAA 57.430 36.000 0.00 0.00 0.00 1.94
210 211 8.855804 ATATTAGGACTAACAGAGGAGGAAAA 57.144 34.615 0.00 0.00 0.00 2.29
211 212 9.589461 CTATATTAGGACTAACAGAGGAGGAAA 57.411 37.037 0.00 0.00 0.00 3.13
229 230 3.194542 AGAGGAAGCAGCGCCTATATTAG 59.805 47.826 2.29 0.00 33.84 1.73
230 231 3.165875 AGAGGAAGCAGCGCCTATATTA 58.834 45.455 2.29 0.00 33.84 0.98
231 232 1.974236 AGAGGAAGCAGCGCCTATATT 59.026 47.619 2.29 0.00 33.84 1.28
232 233 1.548269 GAGAGGAAGCAGCGCCTATAT 59.452 52.381 2.29 0.51 33.84 0.86
233 234 0.962489 GAGAGGAAGCAGCGCCTATA 59.038 55.000 2.29 0.00 33.84 1.31
234 235 1.745264 GAGAGGAAGCAGCGCCTAT 59.255 57.895 2.29 6.99 33.84 2.57
235 236 2.427245 GGAGAGGAAGCAGCGCCTA 61.427 63.158 2.29 0.00 33.84 3.93
236 237 3.780173 GGAGAGGAAGCAGCGCCT 61.780 66.667 2.29 9.38 37.18 5.52
237 238 3.780173 AGGAGAGGAAGCAGCGCC 61.780 66.667 2.29 0.00 0.00 6.53
238 239 2.511145 CAGGAGAGGAAGCAGCGC 60.511 66.667 0.00 0.00 0.00 5.92
239 240 2.511145 GCAGGAGAGGAAGCAGCG 60.511 66.667 0.00 0.00 0.00 5.18
240 241 2.124778 GGCAGGAGAGGAAGCAGC 60.125 66.667 0.00 0.00 0.00 5.25
241 242 1.521616 GAGGCAGGAGAGGAAGCAG 59.478 63.158 0.00 0.00 0.00 4.24
242 243 1.992277 GGAGGCAGGAGAGGAAGCA 60.992 63.158 0.00 0.00 0.00 3.91
243 244 1.688884 AGGAGGCAGGAGAGGAAGC 60.689 63.158 0.00 0.00 0.00 3.86
244 245 0.617249 ACAGGAGGCAGGAGAGGAAG 60.617 60.000 0.00 0.00 0.00 3.46
245 246 0.616111 GACAGGAGGCAGGAGAGGAA 60.616 60.000 0.00 0.00 0.00 3.36
246 247 1.000993 GACAGGAGGCAGGAGAGGA 59.999 63.158 0.00 0.00 0.00 3.71
247 248 2.063378 GGACAGGAGGCAGGAGAGG 61.063 68.421 0.00 0.00 0.00 3.69
248 249 1.305633 TGGACAGGAGGCAGGAGAG 60.306 63.158 0.00 0.00 0.00 3.20
249 250 1.305633 CTGGACAGGAGGCAGGAGA 60.306 63.158 0.00 0.00 0.00 3.71
250 251 3.028921 GCTGGACAGGAGGCAGGAG 62.029 68.421 1.01 0.00 0.00 3.69
251 252 3.005539 GCTGGACAGGAGGCAGGA 61.006 66.667 1.01 0.00 0.00 3.86
252 253 4.106925 GGCTGGACAGGAGGCAGG 62.107 72.222 1.01 0.00 36.06 4.85
253 254 3.324930 TGGCTGGACAGGAGGCAG 61.325 66.667 1.01 0.00 40.80 4.85
254 255 3.640407 GTGGCTGGACAGGAGGCA 61.640 66.667 1.01 0.00 43.23 4.75
255 256 4.416738 GGTGGCTGGACAGGAGGC 62.417 72.222 1.01 0.00 36.55 4.70
256 257 2.930019 TGGTGGCTGGACAGGAGG 60.930 66.667 1.01 0.00 0.00 4.30
257 258 2.177594 GAGTGGTGGCTGGACAGGAG 62.178 65.000 1.01 0.00 0.00 3.69
258 259 2.122413 AGTGGTGGCTGGACAGGA 60.122 61.111 1.01 0.00 0.00 3.86
259 260 2.348998 GAGTGGTGGCTGGACAGG 59.651 66.667 1.01 0.00 0.00 4.00
260 261 2.219875 AGGAGTGGTGGCTGGACAG 61.220 63.158 0.00 0.00 0.00 3.51
261 262 2.122413 AGGAGTGGTGGCTGGACA 60.122 61.111 0.00 0.00 0.00 4.02
262 263 2.348998 CAGGAGTGGTGGCTGGAC 59.651 66.667 0.00 0.00 0.00 4.02
263 264 3.640407 GCAGGAGTGGTGGCTGGA 61.640 66.667 0.00 0.00 0.00 3.86
264 265 4.729918 GGCAGGAGTGGTGGCTGG 62.730 72.222 0.00 0.00 37.50 4.85
275 276 0.116342 TGGTACAAGAGGAGGCAGGA 59.884 55.000 0.00 0.00 31.92 3.86
338 339 7.434927 AAAGAGGGTTAATTAGAGAGTACCC 57.565 40.000 11.43 11.43 36.47 3.69
343 344 9.810545 CTGAACTAAAGAGGGTTAATTAGAGAG 57.189 37.037 0.00 0.00 0.00 3.20
437 438 2.769095 GGCTACTCTTGGAACCTCTCAT 59.231 50.000 0.00 0.00 0.00 2.90
438 439 2.180276 GGCTACTCTTGGAACCTCTCA 58.820 52.381 0.00 0.00 0.00 3.27
518 520 7.488322 TGGCCTTATTAGTTGATTGTTTATGC 58.512 34.615 3.32 0.00 0.00 3.14
566 578 4.061596 GCTACTAATGATGGAGGAACAGC 58.938 47.826 0.00 0.00 0.00 4.40
603 619 1.131638 AAACTGTGCCTCCTGACAGA 58.868 50.000 3.32 0.00 41.90 3.41
604 620 1.972872 AAAACTGTGCCTCCTGACAG 58.027 50.000 0.00 0.00 44.38 3.51
605 621 3.181445 ACATAAAACTGTGCCTCCTGACA 60.181 43.478 0.00 0.00 0.00 3.58
606 622 3.412386 ACATAAAACTGTGCCTCCTGAC 58.588 45.455 0.00 0.00 0.00 3.51
608 624 4.074970 AGAACATAAAACTGTGCCTCCTG 58.925 43.478 0.00 0.00 0.00 3.86
666 682 1.829222 CGCCAGTAAAGAAGGTAGGGA 59.171 52.381 0.00 0.00 0.00 4.20
732 748 8.480643 TCTCTTCAAATTTTCTTACGAGGATC 57.519 34.615 0.00 0.00 0.00 3.36
839 856 6.022208 GCCTCGCATTCTACTTTTACTTTTC 58.978 40.000 0.00 0.00 0.00 2.29
843 860 4.202245 TGCCTCGCATTCTACTTTTACT 57.798 40.909 0.00 0.00 31.71 2.24
856 874 0.533531 GATGATGACCATGCCTCGCA 60.534 55.000 0.00 0.00 44.86 5.10
877 1426 7.697691 CCATAAAGACAATGGTAGTGATGAAC 58.302 38.462 0.00 0.00 39.30 3.18
878 1427 7.864108 CCATAAAGACAATGGTAGTGATGAA 57.136 36.000 0.00 0.00 39.30 2.57
899 1448 2.423898 AATCTCGGCCGTCGACCAT 61.424 57.895 27.15 10.06 43.74 3.55
911 1460 1.066152 TCACGCTCAGATCCAATCTCG 59.934 52.381 0.00 0.00 37.58 4.04
918 1467 1.142748 CCACCTCACGCTCAGATCC 59.857 63.158 0.00 0.00 0.00 3.36
926 1475 3.357079 CCAACAGCCACCTCACGC 61.357 66.667 0.00 0.00 0.00 5.34
938 1487 1.580942 GCAGAGATTTGCGCCAACA 59.419 52.632 4.18 0.00 33.90 3.33
954 1503 7.483691 CGTATATATATACTTTCTGCGTGTGCA 59.516 37.037 23.98 0.00 41.51 4.57
1505 2112 1.586154 GGAACGAACGGTCCCGACTA 61.586 60.000 18.98 0.00 45.91 2.59
1536 2143 3.660501 TTGAGTACGACACATCTTGCT 57.339 42.857 0.00 0.00 0.00 3.91
1613 2248 0.892814 GGCTACGTACTCCGCCCTAT 60.893 60.000 11.52 0.00 41.42 2.57
1671 2306 6.306643 TGTGTCTTCATAGAGAGAGAGAGA 57.693 41.667 0.00 0.00 0.00 3.10
1672 2307 5.008019 GCTGTGTCTTCATAGAGAGAGAGAG 59.992 48.000 0.00 0.00 37.27 3.20
1674 2309 4.639755 TGCTGTGTCTTCATAGAGAGAGAG 59.360 45.833 0.00 0.00 37.27 3.20
1675 2310 4.593956 TGCTGTGTCTTCATAGAGAGAGA 58.406 43.478 0.00 0.00 37.27 3.10
1676 2311 4.979943 TGCTGTGTCTTCATAGAGAGAG 57.020 45.455 0.00 0.00 37.90 3.20
1697 2335 5.488341 TGTCCGAGCTAGCTTCTAAATTTT 58.512 37.500 20.42 0.00 0.00 1.82
1738 2383 3.111098 CAAACTCACAAAGCTTCTGCAC 58.889 45.455 0.00 0.00 42.74 4.57
1751 2396 6.434018 AGATAGAGTACGTACCAAACTCAC 57.566 41.667 21.80 9.77 41.69 3.51
1784 2429 1.247567 GCACTGCCTTAGCCTTTTGA 58.752 50.000 0.00 0.00 38.69 2.69
1887 2532 4.466370 TGACCCAACTCTTGTACCTATGAG 59.534 45.833 0.00 0.00 0.00 2.90
2194 2839 4.457496 TAGGCAGCAGCGGCACTC 62.457 66.667 19.73 1.92 44.61 3.51
2195 2840 4.767255 GTAGGCAGCAGCGGCACT 62.767 66.667 19.73 15.23 44.61 4.40
2222 2867 7.542130 CGCAGAAACTTTAATTTTAAGGCTCAT 59.458 33.333 0.00 0.00 0.00 2.90
2230 2875 8.810652 ATTTGAGCGCAGAAACTTTAATTTTA 57.189 26.923 11.47 0.00 0.00 1.52
2262 4328 6.034044 CGTAGCTCTAGTTTTTCTACTTGCAG 59.966 42.308 0.00 0.00 0.00 4.41
2305 4371 0.249447 TGGTCCGAATGCAGCTATCG 60.249 55.000 11.95 11.95 36.39 2.92
2335 4402 4.163078 CAGGGAGTAGTCAAGGACATCAAT 59.837 45.833 0.00 0.00 34.60 2.57
2438 4505 3.396560 GCATCACTGATTCGATGATCCA 58.603 45.455 3.65 0.00 41.28 3.41
2439 4506 2.740981 GGCATCACTGATTCGATGATCC 59.259 50.000 3.65 0.00 41.28 3.36
2477 4544 8.404765 CAAAATTGCATTTACCTTGGTTTTTCT 58.595 29.630 0.00 0.00 0.00 2.52
2478 4545 7.647318 CCAAAATTGCATTTACCTTGGTTTTTC 59.353 33.333 12.22 0.00 0.00 2.29
2480 4547 6.605194 ACCAAAATTGCATTTACCTTGGTTTT 59.395 30.769 17.31 2.81 36.66 2.43
2481 4548 6.125719 ACCAAAATTGCATTTACCTTGGTTT 58.874 32.000 17.31 3.33 36.66 3.27
2561 4628 0.856641 GCGCTGTCAAAGTGAACGTA 59.143 50.000 0.00 0.00 38.83 3.57
2677 4744 8.522830 AGACAATATCATTCGTGGACAATTTTT 58.477 29.630 0.00 0.00 0.00 1.94
2699 4766 0.179059 TTCAAGCTCCGCAACAGACA 60.179 50.000 0.00 0.00 0.00 3.41
2782 4853 3.188048 GCTGGATCACTCAAAGTTCACAG 59.812 47.826 0.00 0.00 0.00 3.66
2808 4879 6.715344 TCAAAACACTTATAGGCTACAACG 57.285 37.500 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.