Multiple sequence alignment - TraesCS3D01G168700

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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 TraesCS3D01G168700 chr3D 100.000 5083 0 0 1 5083 143456408 143461490 0.000000e+00 9387.0
1 TraesCS3D01G168700 chr3D 81.013 79 15 0 3688 3766 382806515 382806437 4.250000e-06 63.9
2 TraesCS3D01G168700 chr3D 78.351 97 20 1 3688 3783 382753654 382753558 1.530000e-05 62.1
3 TraesCS3D01G168700 chr3B 94.922 3761 142 24 405 4149 207120256 207123983 0.000000e+00 5842.0
4 TraesCS3D01G168700 chr3B 96.903 452 8 3 4637 5083 207127887 207128337 0.000000e+00 752.0
5 TraesCS3D01G168700 chr3B 94.601 426 16 2 4169 4589 207124040 207124463 0.000000e+00 652.0
6 TraesCS3D01G168700 chr3B 96.721 61 1 1 4578 4638 207126102 207126161 3.240000e-17 100.0
7 TraesCS3D01G168700 chr3B 80.769 78 15 0 3688 3765 498367161 498367084 1.530000e-05 62.1
8 TraesCS3D01G168700 chrUn 96.581 3100 91 5 1026 4113 188197775 188194679 0.000000e+00 5123.0
9 TraesCS3D01G168700 chrUn 94.800 750 25 8 4099 4844 188194665 188193926 0.000000e+00 1157.0
10 TraesCS3D01G168700 chrUn 83.705 583 53 19 148 715 188198478 188197923 3.510000e-141 512.0
11 TraesCS3D01G168700 chrUn 95.885 243 9 1 4841 5083 188193864 188193623 4.770000e-105 392.0
12 TraesCS3D01G168700 chr2B 94.226 433 24 1 3217 3648 576586355 576585923 0.000000e+00 660.0
13 TraesCS3D01G168700 chr2B 74.380 847 167 40 3002 3831 105539553 105540366 2.950000e-82 316.0
14 TraesCS3D01G168700 chr4D 84.181 354 35 12 904 1240 127102143 127101794 1.770000e-84 324.0
15 TraesCS3D01G168700 chr4D 76.677 313 65 7 3294 3602 397094852 397094544 3.150000e-37 167.0
16 TraesCS3D01G168700 chr4D 94.667 75 4 0 1304 1378 127101790 127101716 3.220000e-22 117.0
17 TraesCS3D01G168700 chr4D 92.000 50 4 0 3724 3773 84545735 84545686 2.540000e-08 71.3
18 TraesCS3D01G168700 chr2D 75.862 638 125 24 3201 3831 65690705 65690090 1.070000e-76 298.0
19 TraesCS3D01G168700 chr2A 73.248 856 182 36 2990 3831 68880263 68881085 8.390000e-68 268.0
20 TraesCS3D01G168700 chr4A 76.677 313 65 7 3294 3602 54107726 54107418 3.150000e-37 167.0
21 TraesCS3D01G168700 chr4A 91.549 71 6 0 260 330 214377629 214377559 1.160000e-16 99.0
22 TraesCS3D01G168700 chr4A 92.000 50 4 0 3724 3773 497440567 497440518 2.540000e-08 71.3
23 TraesCS3D01G168700 chr7B 97.368 38 1 0 3292 3329 376934983 376934946 1.180000e-06 65.8
24 TraesCS3D01G168700 chr6D 91.111 45 4 0 3729 3773 473103183 473103227 1.530000e-05 62.1
25 TraesCS3D01G168700 chr3A 79.310 87 16 2 3689 3774 505723416 505723331 5.500000e-05 60.2
26 TraesCS3D01G168700 chr5A 96.774 31 1 0 362 392 56831652 56831622 9.000000e-03 52.8


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 TraesCS3D01G168700 chr3D 143456408 143461490 5082 False 9387.0 9387 100.00000 1 5083 1 chr3D.!!$F1 5082
1 TraesCS3D01G168700 chr3B 207120256 207128337 8081 False 1836.5 5842 95.78675 405 5083 4 chr3B.!!$F1 4678
2 TraesCS3D01G168700 chrUn 188193623 188198478 4855 True 1796.0 5123 92.74275 148 5083 4 chrUn.!!$R1 4935
3 TraesCS3D01G168700 chr2B 105539553 105540366 813 False 316.0 316 74.38000 3002 3831 1 chr2B.!!$F1 829
4 TraesCS3D01G168700 chr2D 65690090 65690705 615 True 298.0 298 75.86200 3201 3831 1 chr2D.!!$R1 630
5 TraesCS3D01G168700 chr2A 68880263 68881085 822 False 268.0 268 73.24800 2990 3831 1 chr2A.!!$F1 841

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
254 257 0.094730 GCGGTGACAAATAGCGTGTC 59.905 55.0 0.0 6.08 44.67 3.67 F
502 514 0.107654 GGGACGGATCAAACCTCCTG 60.108 60.0 0.0 0.00 32.14 3.86 F
2412 2444 0.468226 TCCCCTCGGAAATTGGATCG 59.532 55.0 0.0 0.00 34.19 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2037 0.320374 TTCAGCCGGTTCGAGAACAT 59.680 50.000 16.56 0.0 42.85 2.71 R
2439 2471 1.078848 AGAGAGCATGTTGCCGTCC 60.079 57.895 0.00 0.0 46.52 4.79 R
4287 4401 0.313043 GAACACCGCCGCTAGCTATA 59.687 55.000 13.93 0.0 40.39 1.31 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
17 18 4.415783 AAAAGCTTGCGGTAGGGG 57.584 55.556 0.00 0.00 0.00 4.79
18 19 1.977009 AAAAGCTTGCGGTAGGGGC 60.977 57.895 0.00 0.00 0.00 5.80
19 20 2.706952 AAAAGCTTGCGGTAGGGGCA 62.707 55.000 0.00 0.00 38.93 5.36
23 24 3.960136 TTGCGGTAGGGGCAAGCA 61.960 61.111 0.00 0.00 44.79 3.91
24 25 3.499461 TTGCGGTAGGGGCAAGCAA 62.499 57.895 0.00 0.00 44.79 3.91
25 26 2.675075 GCGGTAGGGGCAAGCAAA 60.675 61.111 0.00 0.00 0.00 3.68
26 27 2.989881 GCGGTAGGGGCAAGCAAAC 61.990 63.158 0.00 0.00 0.00 2.93
27 28 2.686816 CGGTAGGGGCAAGCAAACG 61.687 63.158 0.00 0.00 0.00 3.60
28 29 2.340328 GGTAGGGGCAAGCAAACGG 61.340 63.158 0.00 0.00 0.00 4.44
29 30 2.034999 TAGGGGCAAGCAAACGGG 59.965 61.111 0.00 0.00 0.00 5.28
32 33 4.662961 GGGCAAGCAAACGGGCAC 62.663 66.667 0.00 0.00 35.83 5.01
33 34 3.910490 GGCAAGCAAACGGGCACA 61.910 61.111 0.00 0.00 35.83 4.57
34 35 2.105930 GCAAGCAAACGGGCACAA 59.894 55.556 0.00 0.00 35.83 3.33
35 36 2.237066 GCAAGCAAACGGGCACAAC 61.237 57.895 0.00 0.00 35.83 3.32
36 37 1.140589 CAAGCAAACGGGCACAACA 59.859 52.632 0.00 0.00 35.83 3.33
37 38 0.249405 CAAGCAAACGGGCACAACAT 60.249 50.000 0.00 0.00 35.83 2.71
38 39 0.463620 AAGCAAACGGGCACAACATT 59.536 45.000 0.00 0.00 35.83 2.71
39 40 0.249405 AGCAAACGGGCACAACATTG 60.249 50.000 0.00 0.00 35.83 2.82
40 41 1.220817 GCAAACGGGCACAACATTGG 61.221 55.000 0.00 0.00 0.00 3.16
41 42 0.387202 CAAACGGGCACAACATTGGA 59.613 50.000 0.00 0.00 0.00 3.53
42 43 0.673437 AAACGGGCACAACATTGGAG 59.327 50.000 0.00 0.00 0.00 3.86
43 44 1.805428 AACGGGCACAACATTGGAGC 61.805 55.000 0.00 0.12 34.11 4.70
44 45 1.973281 CGGGCACAACATTGGAGCT 60.973 57.895 10.00 0.00 34.90 4.09
45 46 1.588082 GGGCACAACATTGGAGCTG 59.412 57.895 0.00 0.00 34.90 4.24
46 47 1.588082 GGCACAACATTGGAGCTGG 59.412 57.895 0.00 0.00 34.90 4.85
47 48 1.588082 GCACAACATTGGAGCTGGG 59.412 57.895 0.00 0.00 32.77 4.45
48 49 1.588082 CACAACATTGGAGCTGGGC 59.412 57.895 0.00 0.00 0.00 5.36
49 50 1.153524 ACAACATTGGAGCTGGGCA 59.846 52.632 0.00 0.00 0.00 5.36
50 51 0.251922 ACAACATTGGAGCTGGGCAT 60.252 50.000 0.00 0.00 0.00 4.40
51 52 0.174845 CAACATTGGAGCTGGGCATG 59.825 55.000 0.00 0.00 0.00 4.06
52 53 0.974010 AACATTGGAGCTGGGCATGG 60.974 55.000 0.00 0.00 0.00 3.66
53 54 2.131709 CATTGGAGCTGGGCATGGG 61.132 63.158 0.00 0.00 0.00 4.00
54 55 3.384555 ATTGGAGCTGGGCATGGGG 62.385 63.158 0.00 0.00 0.00 4.96
62 63 2.358619 GGGCATGGGGCACTTGTA 59.641 61.111 4.43 0.00 44.81 2.41
63 64 1.304879 GGGCATGGGGCACTTGTAA 60.305 57.895 4.43 0.00 44.81 2.41
64 65 1.322538 GGGCATGGGGCACTTGTAAG 61.323 60.000 4.43 0.00 44.81 2.34
65 66 3.264574 GCATGGGGCACTTGTAAGA 57.735 52.632 4.43 0.00 43.97 2.10
66 67 1.098050 GCATGGGGCACTTGTAAGAG 58.902 55.000 4.43 0.00 43.97 2.85
67 68 1.614317 GCATGGGGCACTTGTAAGAGT 60.614 52.381 4.43 0.00 43.97 3.24
77 78 3.108376 ACTTGTAAGAGTGATCCCCTCC 58.892 50.000 6.01 0.00 0.00 4.30
78 79 1.776662 TGTAAGAGTGATCCCCTCCG 58.223 55.000 6.01 0.00 0.00 4.63
79 80 1.006758 TGTAAGAGTGATCCCCTCCGT 59.993 52.381 6.01 0.00 0.00 4.69
80 81 1.409427 GTAAGAGTGATCCCCTCCGTG 59.591 57.143 6.01 0.00 0.00 4.94
81 82 1.617947 AAGAGTGATCCCCTCCGTGC 61.618 60.000 6.01 0.00 0.00 5.34
82 83 2.039624 AGTGATCCCCTCCGTGCT 59.960 61.111 0.00 0.00 0.00 4.40
83 84 2.022240 GAGTGATCCCCTCCGTGCTC 62.022 65.000 0.00 0.00 0.00 4.26
84 85 2.764128 TGATCCCCTCCGTGCTCC 60.764 66.667 0.00 0.00 0.00 4.70
85 86 3.551407 GATCCCCTCCGTGCTCCC 61.551 72.222 0.00 0.00 0.00 4.30
86 87 4.095400 ATCCCCTCCGTGCTCCCT 62.095 66.667 0.00 0.00 0.00 4.20
89 90 3.775654 CCCTCCGTGCTCCCTGTC 61.776 72.222 0.00 0.00 0.00 3.51
90 91 2.997315 CCTCCGTGCTCCCTGTCA 60.997 66.667 0.00 0.00 0.00 3.58
91 92 2.575993 CTCCGTGCTCCCTGTCAG 59.424 66.667 0.00 0.00 0.00 3.51
92 93 2.997315 TCCGTGCTCCCTGTCAGG 60.997 66.667 12.40 12.40 34.30 3.86
93 94 3.314331 CCGTGCTCCCTGTCAGGT 61.314 66.667 17.85 0.00 31.93 4.00
94 95 2.262915 CGTGCTCCCTGTCAGGTC 59.737 66.667 17.85 7.05 31.93 3.85
95 96 2.665603 GTGCTCCCTGTCAGGTCC 59.334 66.667 17.85 6.00 31.93 4.46
96 97 1.915769 GTGCTCCCTGTCAGGTCCT 60.916 63.158 17.85 0.00 31.93 3.85
97 98 0.614979 GTGCTCCCTGTCAGGTCCTA 60.615 60.000 17.85 0.00 31.93 2.94
98 99 0.339859 TGCTCCCTGTCAGGTCCTAT 59.660 55.000 17.85 0.00 31.93 2.57
99 100 0.755686 GCTCCCTGTCAGGTCCTATG 59.244 60.000 17.85 1.25 31.93 2.23
100 101 1.689575 GCTCCCTGTCAGGTCCTATGA 60.690 57.143 17.85 5.69 31.93 2.15
101 102 2.752030 CTCCCTGTCAGGTCCTATGAA 58.248 52.381 17.85 0.00 31.93 2.57
102 103 3.312890 CTCCCTGTCAGGTCCTATGAAT 58.687 50.000 17.85 0.00 31.93 2.57
103 104 3.713764 CTCCCTGTCAGGTCCTATGAATT 59.286 47.826 17.85 0.00 31.93 2.17
104 105 3.455910 TCCCTGTCAGGTCCTATGAATTG 59.544 47.826 17.85 0.00 31.93 2.32
105 106 3.455910 CCCTGTCAGGTCCTATGAATTGA 59.544 47.826 17.85 0.00 31.93 2.57
106 107 4.446371 CCTGTCAGGTCCTATGAATTGAC 58.554 47.826 11.09 0.00 36.97 3.18
107 108 4.080919 CCTGTCAGGTCCTATGAATTGACA 60.081 45.833 11.09 12.23 40.73 3.58
108 109 5.491070 CTGTCAGGTCCTATGAATTGACAA 58.509 41.667 13.20 0.00 41.59 3.18
109 110 5.245531 TGTCAGGTCCTATGAATTGACAAC 58.754 41.667 11.09 0.00 40.37 3.32
110 111 4.636206 GTCAGGTCCTATGAATTGACAACC 59.364 45.833 0.00 0.00 36.68 3.77
111 112 4.288366 TCAGGTCCTATGAATTGACAACCA 59.712 41.667 0.00 0.00 0.00 3.67
112 113 5.009631 CAGGTCCTATGAATTGACAACCAA 58.990 41.667 0.00 0.00 39.41 3.67
113 114 5.653769 CAGGTCCTATGAATTGACAACCAAT 59.346 40.000 0.00 0.00 46.86 3.16
114 115 5.888161 AGGTCCTATGAATTGACAACCAATC 59.112 40.000 0.00 0.00 44.28 2.67
115 116 5.652014 GGTCCTATGAATTGACAACCAATCA 59.348 40.000 0.00 0.00 44.28 2.57
116 117 6.322201 GGTCCTATGAATTGACAACCAATCAT 59.678 38.462 10.57 10.57 44.28 2.45
117 118 7.502226 GGTCCTATGAATTGACAACCAATCATA 59.498 37.037 11.33 11.33 44.28 2.15
118 119 8.902806 GTCCTATGAATTGACAACCAATCATAA 58.097 33.333 12.26 2.16 44.28 1.90
119 120 8.902806 TCCTATGAATTGACAACCAATCATAAC 58.097 33.333 12.26 0.00 44.28 1.89
120 121 8.137437 CCTATGAATTGACAACCAATCATAACC 58.863 37.037 12.26 0.00 44.28 2.85
121 122 7.722949 ATGAATTGACAACCAATCATAACCT 57.277 32.000 0.00 0.00 44.28 3.50
122 123 7.537596 TGAATTGACAACCAATCATAACCTT 57.462 32.000 0.00 0.00 44.28 3.50
123 124 7.601856 TGAATTGACAACCAATCATAACCTTC 58.398 34.615 0.00 0.00 44.28 3.46
124 125 7.451255 TGAATTGACAACCAATCATAACCTTCT 59.549 33.333 0.00 0.00 44.28 2.85
125 126 6.573664 TTGACAACCAATCATAACCTTCTG 57.426 37.500 0.00 0.00 0.00 3.02
126 127 5.875224 TGACAACCAATCATAACCTTCTGA 58.125 37.500 0.00 0.00 0.00 3.27
127 128 5.939883 TGACAACCAATCATAACCTTCTGAG 59.060 40.000 0.00 0.00 0.00 3.35
128 129 4.702131 ACAACCAATCATAACCTTCTGAGC 59.298 41.667 0.00 0.00 0.00 4.26
129 130 4.851639 ACCAATCATAACCTTCTGAGCT 57.148 40.909 0.00 0.00 0.00 4.09
130 131 4.775236 ACCAATCATAACCTTCTGAGCTC 58.225 43.478 6.82 6.82 0.00 4.09
131 132 3.806521 CCAATCATAACCTTCTGAGCTCG 59.193 47.826 9.64 4.19 0.00 5.03
132 133 3.742433 ATCATAACCTTCTGAGCTCGG 57.258 47.619 16.98 16.98 0.00 4.63
133 134 2.457598 TCATAACCTTCTGAGCTCGGT 58.542 47.619 21.88 13.47 0.00 4.69
134 135 2.166459 TCATAACCTTCTGAGCTCGGTG 59.834 50.000 21.88 15.17 0.00 4.94
135 136 1.629043 TAACCTTCTGAGCTCGGTGT 58.371 50.000 21.88 14.41 0.00 4.16
136 137 1.629043 AACCTTCTGAGCTCGGTGTA 58.371 50.000 21.88 8.27 0.00 2.90
137 138 0.889306 ACCTTCTGAGCTCGGTGTAC 59.111 55.000 21.88 0.00 0.00 2.90
138 139 0.173708 CCTTCTGAGCTCGGTGTACC 59.826 60.000 21.88 0.00 0.00 3.34
139 140 0.173708 CTTCTGAGCTCGGTGTACCC 59.826 60.000 21.88 0.00 0.00 3.69
140 141 0.251653 TTCTGAGCTCGGTGTACCCT 60.252 55.000 21.88 0.00 0.00 4.34
141 142 0.251653 TCTGAGCTCGGTGTACCCTT 60.252 55.000 21.88 0.00 0.00 3.95
142 143 0.108615 CTGAGCTCGGTGTACCCTTG 60.109 60.000 14.84 0.00 0.00 3.61
143 144 0.541063 TGAGCTCGGTGTACCCTTGA 60.541 55.000 9.64 0.00 0.00 3.02
144 145 0.606604 GAGCTCGGTGTACCCTTGAA 59.393 55.000 0.00 0.00 0.00 2.69
145 146 0.320697 AGCTCGGTGTACCCTTGAAC 59.679 55.000 0.00 0.00 0.00 3.18
146 147 1.012486 GCTCGGTGTACCCTTGAACG 61.012 60.000 0.00 0.00 0.00 3.95
151 152 1.145803 GTGTACCCTTGAACGTGCTC 58.854 55.000 0.00 0.00 0.00 4.26
154 155 1.529865 GTACCCTTGAACGTGCTCAAC 59.470 52.381 0.00 0.00 32.00 3.18
156 157 0.868406 CCCTTGAACGTGCTCAACTC 59.132 55.000 0.00 0.00 32.00 3.01
178 179 3.245122 CCCTCCAAGTTTAGGCCAAAGTA 60.245 47.826 5.01 0.00 0.00 2.24
183 184 4.825085 CCAAGTTTAGGCCAAAGTACTCAA 59.175 41.667 5.01 0.00 0.00 3.02
219 220 3.270877 AGACCGCCAATAAGAATGTGTC 58.729 45.455 0.00 0.00 0.00 3.67
221 222 2.290641 ACCGCCAATAAGAATGTGTCCA 60.291 45.455 0.00 0.00 0.00 4.02
222 223 2.355756 CCGCCAATAAGAATGTGTCCAG 59.644 50.000 0.00 0.00 0.00 3.86
225 226 3.355378 CCAATAAGAATGTGTCCAGCCA 58.645 45.455 0.00 0.00 0.00 4.75
226 227 3.379372 CCAATAAGAATGTGTCCAGCCAG 59.621 47.826 0.00 0.00 0.00 4.85
228 229 0.773644 AAGAATGTGTCCAGCCAGGT 59.226 50.000 0.00 0.00 39.02 4.00
229 230 1.656587 AGAATGTGTCCAGCCAGGTA 58.343 50.000 0.00 0.00 39.02 3.08
240 243 3.470888 CCAGGTAGGGGAGCGGTG 61.471 72.222 0.00 0.00 0.00 4.94
245 248 1.675219 GTAGGGGAGCGGTGACAAA 59.325 57.895 0.00 0.00 0.00 2.83
246 249 0.252197 GTAGGGGAGCGGTGACAAAT 59.748 55.000 0.00 0.00 0.00 2.32
248 251 0.541863 AGGGGAGCGGTGACAAATAG 59.458 55.000 0.00 0.00 0.00 1.73
249 252 1.095807 GGGGAGCGGTGACAAATAGC 61.096 60.000 0.00 0.00 0.00 2.97
250 253 1.429148 GGGAGCGGTGACAAATAGCG 61.429 60.000 0.00 0.00 41.52 4.26
251 254 0.739813 GGAGCGGTGACAAATAGCGT 60.740 55.000 0.00 0.00 40.78 5.07
252 255 0.370273 GAGCGGTGACAAATAGCGTG 59.630 55.000 0.00 0.00 40.78 5.34
253 256 0.320421 AGCGGTGACAAATAGCGTGT 60.320 50.000 0.00 0.00 40.78 4.49
254 257 0.094730 GCGGTGACAAATAGCGTGTC 59.905 55.000 0.00 6.08 44.67 3.67
255 258 0.365523 CGGTGACAAATAGCGTGTCG 59.634 55.000 7.90 0.00 46.89 4.35
256 259 0.719465 GGTGACAAATAGCGTGTCGG 59.281 55.000 7.90 0.00 46.89 4.79
257 260 0.094730 GTGACAAATAGCGTGTCGGC 59.905 55.000 7.90 0.00 46.89 5.54
259 262 1.349259 GACAAATAGCGTGTCGGCGT 61.349 55.000 6.85 0.00 36.35 5.68
261 264 0.165079 CAAATAGCGTGTCGGCGTTT 59.835 50.000 6.85 0.00 38.18 3.60
262 265 0.869730 AAATAGCGTGTCGGCGTTTT 59.130 45.000 6.85 0.00 38.18 2.43
277 280 3.928375 GGCGTTTTCGGAGTTCTATACAA 59.072 43.478 0.00 0.00 44.29 2.41
278 281 4.201656 GGCGTTTTCGGAGTTCTATACAAC 60.202 45.833 0.00 0.00 44.29 3.32
289 292 6.710597 AGTTCTATACAACTCCTATTCGCA 57.289 37.500 0.00 0.00 30.25 5.10
307 310 2.214376 CAGTTGGTGCCCTAATTCCA 57.786 50.000 0.00 0.00 0.00 3.53
338 341 2.897972 CTTTAGGGGCGGTAGCGT 59.102 61.111 16.63 0.00 46.35 5.07
340 343 1.078988 TTTAGGGGCGGTAGCGTTG 60.079 57.895 16.63 0.00 46.35 4.10
341 344 2.524951 TTTAGGGGCGGTAGCGTTGG 62.525 60.000 16.63 0.00 46.35 3.77
349 352 0.940519 CGGTAGCGTTGGTCGTTTGA 60.941 55.000 6.07 0.00 42.13 2.69
403 406 8.945481 TTGTGTTTGAGATGTTTTGATGATTT 57.055 26.923 0.00 0.00 0.00 2.17
404 407 8.945481 TGTGTTTGAGATGTTTTGATGATTTT 57.055 26.923 0.00 0.00 0.00 1.82
469 481 6.819397 AGTAAACAGCCTAAATTTCTCACC 57.181 37.500 0.00 0.00 0.00 4.02
482 494 2.203640 TCACCGACAGGACCAGCT 60.204 61.111 0.00 0.00 41.02 4.24
483 495 2.047844 CACCGACAGGACCAGCTG 60.048 66.667 6.78 6.78 41.02 4.24
484 496 3.314331 ACCGACAGGACCAGCTGG 61.314 66.667 31.60 31.60 41.02 4.85
485 497 4.087892 CCGACAGGACCAGCTGGG 62.088 72.222 35.42 20.37 41.02 4.45
486 498 2.997315 CGACAGGACCAGCTGGGA 60.997 66.667 35.42 0.00 41.15 4.37
487 499 2.665603 GACAGGACCAGCTGGGAC 59.334 66.667 35.42 26.31 41.15 4.46
488 500 3.302347 GACAGGACCAGCTGGGACG 62.302 68.421 35.42 22.21 41.15 4.79
489 501 4.087892 CAGGACCAGCTGGGACGG 62.088 72.222 35.42 23.26 41.15 4.79
490 502 4.316823 AGGACCAGCTGGGACGGA 62.317 66.667 35.42 0.00 41.15 4.69
491 503 3.083997 GGACCAGCTGGGACGGAT 61.084 66.667 35.42 14.69 41.15 4.18
492 504 2.501610 GACCAGCTGGGACGGATC 59.498 66.667 35.42 19.38 41.15 3.36
496 508 1.026718 CCAGCTGGGACGGATCAAAC 61.027 60.000 26.14 0.00 40.01 2.93
502 514 0.107654 GGGACGGATCAAACCTCCTG 60.108 60.000 0.00 0.00 32.14 3.86
503 515 0.744771 GGACGGATCAAACCTCCTGC 60.745 60.000 0.00 0.00 0.00 4.85
505 517 0.693049 ACGGATCAAACCTCCTGCTT 59.307 50.000 0.00 0.00 0.00 3.91
508 520 1.272147 GGATCAAACCTCCTGCTTGGT 60.272 52.381 0.00 0.00 38.35 3.67
537 549 2.581354 CCACTTCTCAGAGGCCCG 59.419 66.667 0.00 0.00 0.00 6.13
557 569 1.668751 GAACCGAGACAAAACACAGCA 59.331 47.619 0.00 0.00 0.00 4.41
566 578 0.877071 AAAACACAGCAGCATCTCGG 59.123 50.000 0.00 0.00 0.00 4.63
567 579 1.580845 AAACACAGCAGCATCTCGGC 61.581 55.000 0.00 0.00 36.06 5.54
568 580 3.561213 CACAGCAGCATCTCGGCG 61.561 66.667 0.00 0.00 40.93 6.46
589 601 2.019951 CGCCACAGTAGAAACGCGT 61.020 57.895 5.58 5.58 35.15 6.01
742 759 2.454941 CCCCCACCCCACTCTACT 59.545 66.667 0.00 0.00 0.00 2.57
743 760 1.689582 CCCCCACCCCACTCTACTC 60.690 68.421 0.00 0.00 0.00 2.59
790 807 3.184683 CGTGCTCAGCTCGCTTCC 61.185 66.667 8.39 0.00 38.59 3.46
791 808 3.184683 GTGCTCAGCTCGCTTCCG 61.185 66.667 0.00 0.00 0.00 4.30
825 842 1.687146 CTCAGCTCAGCTACCCCCA 60.687 63.158 0.00 0.00 36.40 4.96
829 846 3.082579 GCTCAGCTACCCCCACTCG 62.083 68.421 0.00 0.00 0.00 4.18
830 847 1.682684 CTCAGCTACCCCCACTCGT 60.683 63.158 0.00 0.00 0.00 4.18
831 848 1.229082 TCAGCTACCCCCACTCGTT 60.229 57.895 0.00 0.00 0.00 3.85
832 849 1.218316 CAGCTACCCCCACTCGTTC 59.782 63.158 0.00 0.00 0.00 3.95
833 850 2.183555 GCTACCCCCACTCGTTCG 59.816 66.667 0.00 0.00 0.00 3.95
840 857 2.372690 CCCACTCGTTCGCTTGTCG 61.373 63.158 0.00 0.00 40.15 4.35
848 865 2.939261 TTCGCTTGTCGTCTCCCCC 61.939 63.158 0.00 0.00 39.67 5.40
862 879 2.551413 CCCCCATCCATCCCCATCC 61.551 68.421 0.00 0.00 0.00 3.51
937 954 2.885644 CCATGTCGCCGTCCTTCG 60.886 66.667 0.00 0.00 39.52 3.79
947 964 2.273179 CGTCCTTCGTCTGACCCCA 61.273 63.158 1.55 0.00 34.52 4.96
950 967 0.761323 TCCTTCGTCTGACCCCAACA 60.761 55.000 1.55 0.00 0.00 3.33
977 994 4.999939 CGCGCCCAGCCAAACAAC 63.000 66.667 0.00 0.00 44.76 3.32
1214 1246 3.151022 GGAGGTCTCGCTCCCCAG 61.151 72.222 0.00 0.00 33.81 4.45
1812 1844 1.006102 CAACAACTCGCTCTCCGGT 60.006 57.895 0.00 0.00 37.59 5.28
1872 1904 6.901857 TCAGGAGCATAGATATCTCCATGAAT 59.098 38.462 16.49 6.53 46.71 2.57
1908 1940 1.153628 CCCGGATGACCTGTTCGAC 60.154 63.158 0.73 0.00 0.00 4.20
2092 2124 0.666577 GGACTTGTCCGACAACTCCG 60.667 60.000 18.57 9.48 33.55 4.63
2241 2273 0.976641 TGTCCAAGAACAGGCTCGAT 59.023 50.000 0.00 0.00 0.00 3.59
2412 2444 0.468226 TCCCCTCGGAAATTGGATCG 59.532 55.000 0.00 0.00 34.19 3.69
2568 2600 0.973632 TCCGTTCTTGGAAGCAGCTA 59.026 50.000 0.00 0.00 34.30 3.32
2682 2714 2.738521 CGTCTCACCGGCCAAGTG 60.739 66.667 15.30 15.30 36.54 3.16
2751 2783 2.280835 CCAGCTCAGTGGTCAGCTA 58.719 57.895 4.62 0.00 44.47 3.32
2791 2823 2.828128 GCATACCGCAGCAGCTTCC 61.828 63.158 0.00 0.00 41.79 3.46
2826 2858 2.359850 TGTGGAGACATTGCCGGC 60.360 61.111 22.73 22.73 46.14 6.13
2841 2873 2.684843 CGGCTTGTGCTCTGCTTCC 61.685 63.158 4.85 0.00 39.59 3.46
2872 2904 4.208632 GGAACCACTCTGGCATCG 57.791 61.111 0.00 0.00 42.67 3.84
2964 2996 1.002087 AGGTACCGGAGCTTCAACAAG 59.998 52.381 9.46 0.00 29.01 3.16
2988 3020 4.140599 CTGAAGGCCGAGCGCTCT 62.141 66.667 32.88 15.88 37.74 4.09
3671 3716 2.530177 ACGTGCATGTAAGTCTGATCG 58.470 47.619 10.57 0.00 0.00 3.69
3684 3729 6.532365 AAGTCTGATCGAAAGTTGTTCTTC 57.468 37.500 0.00 0.00 35.02 2.87
3917 3962 1.067295 TCAGCAGGGTCCTGAACATT 58.933 50.000 20.22 0.00 46.30 2.71
4093 4138 5.402997 AGCAGTGTCTAGGTAAGGTAAAC 57.597 43.478 0.00 0.00 0.00 2.01
4094 4139 5.085219 AGCAGTGTCTAGGTAAGGTAAACT 58.915 41.667 0.00 0.00 0.00 2.66
4097 4142 6.071728 GCAGTGTCTAGGTAAGGTAAACTACA 60.072 42.308 0.00 0.00 0.00 2.74
4113 4189 2.993899 ACTACAGAGCATAACACGTTGC 59.006 45.455 1.65 1.65 39.17 4.17
4132 4208 3.801997 CCCCTTCCATGGCTCGCT 61.802 66.667 6.96 0.00 0.00 4.93
4133 4209 2.203126 CCCTTCCATGGCTCGCTC 60.203 66.667 6.96 0.00 0.00 5.03
4152 4228 3.678529 GCTCAGCTCTGGGTAAGAAAGAG 60.679 52.174 0.00 0.00 40.38 2.85
4165 4241 7.147707 TGGGTAAGAAAGAGCCTAAGTAGAATC 60.148 40.741 0.00 0.00 35.40 2.52
4188 4302 0.109597 GTGCTGATTTTGACCGCTGG 60.110 55.000 0.00 0.00 0.00 4.85
4191 4305 1.813513 CTGATTTTGACCGCTGGACT 58.186 50.000 1.50 0.00 0.00 3.85
4212 4326 0.670546 CTTGTTGTCGACGCCTCCAT 60.671 55.000 11.62 0.00 0.00 3.41
4223 4337 2.124983 CCTCCATCGCCACTGTGG 60.125 66.667 22.46 22.46 41.55 4.17
4287 4401 1.132500 GTGGGAGTTAGGGCATAGCT 58.868 55.000 0.00 0.00 0.00 3.32
4288 4402 2.090719 AGTGGGAGTTAGGGCATAGCTA 60.091 50.000 0.00 0.00 0.00 3.32
4312 4426 2.775032 TAGCGGCGGTGTTCTTGGTC 62.775 60.000 23.33 0.00 0.00 4.02
4536 4658 1.938125 CGGTTGTTGCACATCGACA 59.062 52.632 0.00 0.00 37.30 4.35
4551 4673 0.319040 CGACAGTATCTCCGGGCATG 60.319 60.000 0.00 0.00 0.00 4.06
4566 4688 2.897326 GGGCATGTAACTTGGTTTTCCT 59.103 45.455 0.00 0.00 41.38 3.36
4585 6357 5.466127 TCCTGGGTCCAGCTATTTATTTT 57.534 39.130 11.36 0.00 42.35 1.82
4586 6358 5.200483 TCCTGGGTCCAGCTATTTATTTTG 58.800 41.667 11.36 0.00 42.35 2.44
4859 8424 8.445275 TCACATGTACATACAGAAACAGTTTT 57.555 30.769 8.32 0.00 39.92 2.43
4867 8432 1.329292 CAGAAACAGTTTTCGTCGGCA 59.671 47.619 0.00 0.00 45.15 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.977009 GCCCCTACCGCAAGCTTTT 60.977 57.895 0.00 0.00 0.00 2.27
1 2 2.361230 GCCCCTACCGCAAGCTTT 60.361 61.111 0.00 0.00 0.00 3.51
2 3 3.204467 TTGCCCCTACCGCAAGCTT 62.204 57.895 0.00 0.00 41.17 3.74
3 4 3.646715 TTGCCCCTACCGCAAGCT 61.647 61.111 0.00 0.00 41.17 3.74
6 7 2.985539 TTTGCTTGCCCCTACCGCAA 62.986 55.000 0.00 0.00 43.71 4.85
7 8 3.499461 TTTGCTTGCCCCTACCGCA 62.499 57.895 0.00 0.00 0.00 5.69
8 9 2.675075 TTTGCTTGCCCCTACCGC 60.675 61.111 0.00 0.00 0.00 5.68
9 10 2.686816 CGTTTGCTTGCCCCTACCG 61.687 63.158 0.00 0.00 0.00 4.02
10 11 2.340328 CCGTTTGCTTGCCCCTACC 61.340 63.158 0.00 0.00 0.00 3.18
11 12 2.340328 CCCGTTTGCTTGCCCCTAC 61.340 63.158 0.00 0.00 0.00 3.18
12 13 2.034999 CCCGTTTGCTTGCCCCTA 59.965 61.111 0.00 0.00 0.00 3.53
15 16 4.662961 GTGCCCGTTTGCTTGCCC 62.663 66.667 0.00 0.00 0.00 5.36
16 17 3.438017 TTGTGCCCGTTTGCTTGCC 62.438 57.895 0.00 0.00 0.00 4.52
17 18 2.105930 TTGTGCCCGTTTGCTTGC 59.894 55.556 0.00 0.00 0.00 4.01
18 19 0.249405 ATGTTGTGCCCGTTTGCTTG 60.249 50.000 0.00 0.00 0.00 4.01
19 20 0.463620 AATGTTGTGCCCGTTTGCTT 59.536 45.000 0.00 0.00 0.00 3.91
20 21 0.249405 CAATGTTGTGCCCGTTTGCT 60.249 50.000 0.00 0.00 0.00 3.91
21 22 1.220817 CCAATGTTGTGCCCGTTTGC 61.221 55.000 0.00 0.00 0.00 3.68
22 23 0.387202 TCCAATGTTGTGCCCGTTTG 59.613 50.000 0.00 0.00 0.00 2.93
23 24 0.673437 CTCCAATGTTGTGCCCGTTT 59.327 50.000 0.00 0.00 0.00 3.60
24 25 1.805428 GCTCCAATGTTGTGCCCGTT 61.805 55.000 0.00 0.00 0.00 4.44
25 26 2.268076 GCTCCAATGTTGTGCCCGT 61.268 57.895 0.00 0.00 0.00 5.28
26 27 1.973281 AGCTCCAATGTTGTGCCCG 60.973 57.895 0.00 0.00 0.00 6.13
27 28 1.588082 CAGCTCCAATGTTGTGCCC 59.412 57.895 0.00 0.00 0.00 5.36
28 29 1.588082 CCAGCTCCAATGTTGTGCC 59.412 57.895 0.00 0.00 0.00 5.01
29 30 1.588082 CCCAGCTCCAATGTTGTGC 59.412 57.895 0.00 0.00 0.00 4.57
30 31 1.180456 TGCCCAGCTCCAATGTTGTG 61.180 55.000 0.00 0.00 0.00 3.33
31 32 0.251922 ATGCCCAGCTCCAATGTTGT 60.252 50.000 0.00 0.00 0.00 3.32
32 33 0.174845 CATGCCCAGCTCCAATGTTG 59.825 55.000 0.00 0.00 0.00 3.33
33 34 0.974010 CCATGCCCAGCTCCAATGTT 60.974 55.000 0.00 0.00 0.00 2.71
34 35 1.380785 CCATGCCCAGCTCCAATGT 60.381 57.895 0.00 0.00 0.00 2.71
35 36 2.131709 CCCATGCCCAGCTCCAATG 61.132 63.158 0.00 0.00 0.00 2.82
36 37 2.281091 CCCATGCCCAGCTCCAAT 59.719 61.111 0.00 0.00 0.00 3.16
37 38 4.064768 CCCCATGCCCAGCTCCAA 62.065 66.667 0.00 0.00 0.00 3.53
43 44 2.497792 TACAAGTGCCCCATGCCCAG 62.498 60.000 0.00 0.00 40.16 4.45
44 45 2.086599 TTACAAGTGCCCCATGCCCA 62.087 55.000 0.00 0.00 40.16 5.36
45 46 1.304879 TTACAAGTGCCCCATGCCC 60.305 57.895 0.00 0.00 40.16 5.36
46 47 0.323360 TCTTACAAGTGCCCCATGCC 60.323 55.000 0.00 0.00 40.16 4.40
47 48 1.098050 CTCTTACAAGTGCCCCATGC 58.902 55.000 0.00 0.00 41.77 4.06
48 49 2.086869 CACTCTTACAAGTGCCCCATG 58.913 52.381 0.00 0.00 40.18 3.66
49 50 1.985159 TCACTCTTACAAGTGCCCCAT 59.015 47.619 0.00 0.00 45.12 4.00
50 51 1.429930 TCACTCTTACAAGTGCCCCA 58.570 50.000 0.00 0.00 45.12 4.96
51 52 2.633488 GATCACTCTTACAAGTGCCCC 58.367 52.381 0.00 0.00 45.12 5.80
52 53 2.633488 GGATCACTCTTACAAGTGCCC 58.367 52.381 0.00 0.55 45.12 5.36
53 54 2.633488 GGGATCACTCTTACAAGTGCC 58.367 52.381 0.00 0.00 45.12 5.01
54 55 2.237392 AGGGGATCACTCTTACAAGTGC 59.763 50.000 0.00 0.00 45.12 4.40
55 56 3.118592 GGAGGGGATCACTCTTACAAGTG 60.119 52.174 14.10 0.00 46.54 3.16
56 57 3.108376 GGAGGGGATCACTCTTACAAGT 58.892 50.000 14.10 0.00 35.34 3.16
57 58 2.101582 CGGAGGGGATCACTCTTACAAG 59.898 54.545 14.10 0.00 35.34 3.16
58 59 2.108168 CGGAGGGGATCACTCTTACAA 58.892 52.381 14.10 0.00 35.34 2.41
59 60 1.006758 ACGGAGGGGATCACTCTTACA 59.993 52.381 14.10 0.00 35.34 2.41
60 61 1.409427 CACGGAGGGGATCACTCTTAC 59.591 57.143 14.10 0.83 35.34 2.34
61 62 1.776662 CACGGAGGGGATCACTCTTA 58.223 55.000 14.10 0.00 35.34 2.10
62 63 1.617947 GCACGGAGGGGATCACTCTT 61.618 60.000 14.10 2.45 35.34 2.85
63 64 2.060980 GCACGGAGGGGATCACTCT 61.061 63.158 14.10 1.68 35.34 3.24
64 65 2.022240 GAGCACGGAGGGGATCACTC 62.022 65.000 7.85 7.85 0.00 3.51
65 66 2.039624 AGCACGGAGGGGATCACT 59.960 61.111 0.00 0.00 0.00 3.41
66 67 2.501610 GAGCACGGAGGGGATCAC 59.498 66.667 0.00 0.00 0.00 3.06
67 68 2.764128 GGAGCACGGAGGGGATCA 60.764 66.667 0.00 0.00 0.00 2.92
68 69 3.551407 GGGAGCACGGAGGGGATC 61.551 72.222 0.00 0.00 0.00 3.36
69 70 4.095400 AGGGAGCACGGAGGGGAT 62.095 66.667 0.00 0.00 0.00 3.85
72 73 3.775654 GACAGGGAGCACGGAGGG 61.776 72.222 0.00 0.00 0.00 4.30
73 74 2.997315 TGACAGGGAGCACGGAGG 60.997 66.667 0.00 0.00 0.00 4.30
74 75 2.575993 CTGACAGGGAGCACGGAG 59.424 66.667 0.00 0.00 0.00 4.63
75 76 2.997315 CCTGACAGGGAGCACGGA 60.997 66.667 14.26 0.00 0.00 4.69
76 77 3.302347 GACCTGACAGGGAGCACGG 62.302 68.421 25.34 0.00 40.58 4.94
77 78 2.262915 GACCTGACAGGGAGCACG 59.737 66.667 25.34 0.00 40.58 5.34
78 79 0.614979 TAGGACCTGACAGGGAGCAC 60.615 60.000 25.34 10.19 40.58 4.40
79 80 0.339859 ATAGGACCTGACAGGGAGCA 59.660 55.000 25.34 8.37 40.58 4.26
80 81 0.755686 CATAGGACCTGACAGGGAGC 59.244 60.000 25.34 13.60 40.58 4.70
81 82 2.461300 TCATAGGACCTGACAGGGAG 57.539 55.000 25.34 8.32 40.58 4.30
82 83 2.940514 TTCATAGGACCTGACAGGGA 57.059 50.000 25.34 8.98 40.58 4.20
83 84 3.455910 TCAATTCATAGGACCTGACAGGG 59.544 47.826 25.34 6.64 40.58 4.45
84 85 4.080919 TGTCAATTCATAGGACCTGACAGG 60.081 45.833 20.45 20.45 38.77 4.00
85 86 5.089970 TGTCAATTCATAGGACCTGACAG 57.910 43.478 13.83 0.00 38.77 3.51
86 87 5.245531 GTTGTCAATTCATAGGACCTGACA 58.754 41.667 13.83 13.83 40.48 3.58
87 88 4.636206 GGTTGTCAATTCATAGGACCTGAC 59.364 45.833 3.53 9.89 36.27 3.51
88 89 4.288366 TGGTTGTCAATTCATAGGACCTGA 59.712 41.667 3.53 0.00 0.00 3.86
89 90 4.588899 TGGTTGTCAATTCATAGGACCTG 58.411 43.478 3.53 0.00 0.00 4.00
90 91 4.927267 TGGTTGTCAATTCATAGGACCT 57.073 40.909 0.00 0.00 0.00 3.85
91 92 5.652014 TGATTGGTTGTCAATTCATAGGACC 59.348 40.000 0.00 0.00 45.36 4.46
92 93 6.757897 TGATTGGTTGTCAATTCATAGGAC 57.242 37.500 0.00 0.00 45.36 3.85
93 94 8.902806 GTTATGATTGGTTGTCAATTCATAGGA 58.097 33.333 0.00 0.00 45.36 2.94
94 95 8.137437 GGTTATGATTGGTTGTCAATTCATAGG 58.863 37.037 0.00 0.00 45.36 2.57
95 96 8.906867 AGGTTATGATTGGTTGTCAATTCATAG 58.093 33.333 0.00 0.00 45.36 2.23
96 97 8.821686 AGGTTATGATTGGTTGTCAATTCATA 57.178 30.769 0.00 0.00 45.36 2.15
97 98 7.722949 AGGTTATGATTGGTTGTCAATTCAT 57.277 32.000 0.00 0.00 45.36 2.57
98 99 7.451255 AGAAGGTTATGATTGGTTGTCAATTCA 59.549 33.333 0.00 0.00 45.36 2.57
99 100 7.756722 CAGAAGGTTATGATTGGTTGTCAATTC 59.243 37.037 0.00 0.00 45.36 2.17
100 101 7.451255 TCAGAAGGTTATGATTGGTTGTCAATT 59.549 33.333 0.00 0.00 45.36 2.32
102 103 6.303054 TCAGAAGGTTATGATTGGTTGTCAA 58.697 36.000 0.00 0.00 40.01 3.18
103 104 5.875224 TCAGAAGGTTATGATTGGTTGTCA 58.125 37.500 0.00 0.00 0.00 3.58
104 105 5.163713 GCTCAGAAGGTTATGATTGGTTGTC 60.164 44.000 0.00 0.00 0.00 3.18
105 106 4.702131 GCTCAGAAGGTTATGATTGGTTGT 59.298 41.667 0.00 0.00 0.00 3.32
106 107 4.946157 AGCTCAGAAGGTTATGATTGGTTG 59.054 41.667 0.00 0.00 0.00 3.77
107 108 5.184892 AGCTCAGAAGGTTATGATTGGTT 57.815 39.130 0.00 0.00 0.00 3.67
108 109 4.681781 CGAGCTCAGAAGGTTATGATTGGT 60.682 45.833 15.40 0.00 32.07 3.67
109 110 3.806521 CGAGCTCAGAAGGTTATGATTGG 59.193 47.826 15.40 0.00 32.07 3.16
110 111 3.806521 CCGAGCTCAGAAGGTTATGATTG 59.193 47.826 15.40 0.00 32.07 2.67
111 112 3.452627 ACCGAGCTCAGAAGGTTATGATT 59.547 43.478 15.40 0.00 32.17 2.57
112 113 3.034635 ACCGAGCTCAGAAGGTTATGAT 58.965 45.455 15.40 0.00 32.17 2.45
113 114 2.166459 CACCGAGCTCAGAAGGTTATGA 59.834 50.000 15.40 0.00 34.25 2.15
114 115 2.093973 ACACCGAGCTCAGAAGGTTATG 60.094 50.000 15.40 3.99 34.25 1.90
115 116 2.180276 ACACCGAGCTCAGAAGGTTAT 58.820 47.619 15.40 0.70 34.25 1.89
116 117 1.629043 ACACCGAGCTCAGAAGGTTA 58.371 50.000 15.40 0.00 34.25 2.85
117 118 1.272769 GTACACCGAGCTCAGAAGGTT 59.727 52.381 15.40 6.51 34.25 3.50
118 119 0.889306 GTACACCGAGCTCAGAAGGT 59.111 55.000 15.40 9.92 37.49 3.50
119 120 0.173708 GGTACACCGAGCTCAGAAGG 59.826 60.000 15.40 9.21 0.00 3.46
120 121 0.173708 GGGTACACCGAGCTCAGAAG 59.826 60.000 15.40 3.67 36.71 2.85
121 122 0.251653 AGGGTACACCGAGCTCAGAA 60.252 55.000 15.40 0.00 46.96 3.02
122 123 0.251653 AAGGGTACACCGAGCTCAGA 60.252 55.000 15.40 0.00 46.96 3.27
123 124 0.108615 CAAGGGTACACCGAGCTCAG 60.109 60.000 15.40 4.66 46.96 3.35
124 125 0.541063 TCAAGGGTACACCGAGCTCA 60.541 55.000 15.40 0.00 46.96 4.26
125 126 0.606604 TTCAAGGGTACACCGAGCTC 59.393 55.000 2.73 2.73 46.96 4.09
126 127 0.320697 GTTCAAGGGTACACCGAGCT 59.679 55.000 0.00 0.00 46.96 4.09
127 128 1.012486 CGTTCAAGGGTACACCGAGC 61.012 60.000 0.00 0.00 46.96 5.03
128 129 0.316204 ACGTTCAAGGGTACACCGAG 59.684 55.000 0.00 0.00 46.96 4.63
129 130 0.032403 CACGTTCAAGGGTACACCGA 59.968 55.000 0.00 0.00 46.96 4.69
130 131 1.562575 GCACGTTCAAGGGTACACCG 61.563 60.000 0.00 0.00 46.96 4.94
131 132 0.250166 AGCACGTTCAAGGGTACACC 60.250 55.000 0.00 0.00 40.67 4.16
132 133 1.145803 GAGCACGTTCAAGGGTACAC 58.854 55.000 0.00 0.00 0.00 2.90
133 134 0.753867 TGAGCACGTTCAAGGGTACA 59.246 50.000 0.00 0.00 0.00 2.90
134 135 1.529865 GTTGAGCACGTTCAAGGGTAC 59.470 52.381 2.93 0.00 37.72 3.34
135 136 1.414919 AGTTGAGCACGTTCAAGGGTA 59.585 47.619 2.93 0.00 37.72 3.69
136 137 0.180406 AGTTGAGCACGTTCAAGGGT 59.820 50.000 2.93 0.00 37.72 4.34
137 138 0.868406 GAGTTGAGCACGTTCAAGGG 59.132 55.000 2.93 0.00 37.72 3.95
138 139 0.868406 GGAGTTGAGCACGTTCAAGG 59.132 55.000 2.93 0.00 37.72 3.61
139 140 0.868406 GGGAGTTGAGCACGTTCAAG 59.132 55.000 2.93 0.00 37.72 3.02
140 141 0.468226 AGGGAGTTGAGCACGTTCAA 59.532 50.000 0.00 0.00 34.83 2.69
141 142 0.033504 GAGGGAGTTGAGCACGTTCA 59.966 55.000 0.00 0.00 0.00 3.18
142 143 0.670854 GGAGGGAGTTGAGCACGTTC 60.671 60.000 0.00 0.00 0.00 3.95
143 144 1.371558 GGAGGGAGTTGAGCACGTT 59.628 57.895 0.00 0.00 0.00 3.99
144 145 1.407656 TTGGAGGGAGTTGAGCACGT 61.408 55.000 0.00 0.00 0.00 4.49
145 146 0.671781 CTTGGAGGGAGTTGAGCACG 60.672 60.000 0.00 0.00 0.00 5.34
146 147 0.398318 ACTTGGAGGGAGTTGAGCAC 59.602 55.000 0.00 0.00 0.00 4.40
151 152 2.437413 GCCTAAACTTGGAGGGAGTTG 58.563 52.381 0.00 0.00 37.41 3.16
154 155 0.991920 TGGCCTAAACTTGGAGGGAG 59.008 55.000 3.32 0.00 33.04 4.30
156 157 2.171003 CTTTGGCCTAAACTTGGAGGG 58.829 52.381 3.32 0.00 33.04 4.30
183 184 1.235948 GGTCTCGTGACTCACCTCGT 61.236 60.000 16.45 0.00 42.54 4.18
219 220 3.483869 GCTCCCCTACCTGGCTGG 61.484 72.222 9.11 9.11 42.93 4.85
225 226 2.363925 GTCACCGCTCCCCTACCT 60.364 66.667 0.00 0.00 0.00 3.08
226 227 1.833787 TTTGTCACCGCTCCCCTACC 61.834 60.000 0.00 0.00 0.00 3.18
228 229 1.760613 CTATTTGTCACCGCTCCCCTA 59.239 52.381 0.00 0.00 0.00 3.53
229 230 0.541863 CTATTTGTCACCGCTCCCCT 59.458 55.000 0.00 0.00 0.00 4.79
239 242 1.348538 CGCCGACACGCTATTTGTCA 61.349 55.000 4.29 0.00 43.09 3.58
240 243 1.343821 CGCCGACACGCTATTTGTC 59.656 57.895 0.00 0.00 40.10 3.18
245 248 1.680105 CGAAAACGCCGACACGCTAT 61.680 55.000 0.00 0.00 36.19 2.97
246 249 2.366584 CGAAAACGCCGACACGCTA 61.367 57.895 0.00 0.00 36.19 4.26
248 251 4.712873 CCGAAAACGCCGACACGC 62.713 66.667 0.00 0.00 36.19 5.34
249 252 2.995450 CTCCGAAAACGCCGACACG 61.995 63.158 0.00 0.00 39.50 4.49
250 253 1.493134 AACTCCGAAAACGCCGACAC 61.493 55.000 0.00 0.00 0.00 3.67
251 254 1.216941 GAACTCCGAAAACGCCGACA 61.217 55.000 0.00 0.00 0.00 4.35
252 255 0.942884 AGAACTCCGAAAACGCCGAC 60.943 55.000 0.00 0.00 0.00 4.79
253 256 0.597568 TAGAACTCCGAAAACGCCGA 59.402 50.000 0.00 0.00 0.00 5.54
254 257 1.636988 ATAGAACTCCGAAAACGCCG 58.363 50.000 0.00 0.00 0.00 6.46
255 258 3.514645 TGTATAGAACTCCGAAAACGCC 58.485 45.455 0.00 0.00 0.00 5.68
256 259 4.624452 AGTTGTATAGAACTCCGAAAACGC 59.376 41.667 9.39 0.00 29.85 4.84
257 260 6.315274 GAGTTGTATAGAACTCCGAAAACG 57.685 41.667 25.22 0.00 44.16 3.60
278 281 1.009829 GCACCAACTGCGAATAGGAG 58.990 55.000 0.00 0.00 44.60 3.69
307 310 2.299867 CCCTAAAGCATTGGCAAGTGTT 59.700 45.455 5.96 0.00 44.61 3.32
338 341 3.586100 TCGAGATCATCAAACGACCAA 57.414 42.857 0.00 0.00 0.00 3.67
340 343 4.806247 AGATTTCGAGATCATCAAACGACC 59.194 41.667 17.33 0.00 32.89 4.79
341 344 5.957304 GAGATTTCGAGATCATCAAACGAC 58.043 41.667 17.33 0.00 32.89 4.34
409 412 8.925161 TTTCAAAAACGATCAAATCTTCTGTT 57.075 26.923 0.00 0.00 0.00 3.16
410 413 8.925161 TTTTCAAAAACGATCAAATCTTCTGT 57.075 26.923 0.00 0.00 0.00 3.41
442 450 9.649167 GTGAGAAATTTAGGCTGTTTACTAGTA 57.351 33.333 0.00 0.00 0.00 1.82
444 455 7.201530 CGGTGAGAAATTTAGGCTGTTTACTAG 60.202 40.741 0.00 0.00 0.00 2.57
446 457 5.411669 CGGTGAGAAATTTAGGCTGTTTACT 59.588 40.000 0.00 0.00 0.00 2.24
469 481 2.997315 TCCCAGCTGGTCCTGTCG 60.997 66.667 30.63 13.94 34.77 4.35
482 494 0.546747 AGGAGGTTTGATCCGTCCCA 60.547 55.000 5.80 0.00 42.02 4.37
483 495 0.107654 CAGGAGGTTTGATCCGTCCC 60.108 60.000 5.80 0.00 42.02 4.46
484 496 0.744771 GCAGGAGGTTTGATCCGTCC 60.745 60.000 2.08 2.08 42.02 4.79
485 497 0.250513 AGCAGGAGGTTTGATCCGTC 59.749 55.000 0.00 0.00 42.02 4.79
486 498 0.693049 AAGCAGGAGGTTTGATCCGT 59.307 50.000 0.00 0.00 42.02 4.69
487 499 1.089920 CAAGCAGGAGGTTTGATCCG 58.910 55.000 0.00 0.00 39.82 4.18
488 500 1.272147 ACCAAGCAGGAGGTTTGATCC 60.272 52.381 1.83 0.00 39.82 3.36
489 501 2.206576 ACCAAGCAGGAGGTTTGATC 57.793 50.000 1.83 0.00 39.82 2.92
490 502 3.356529 CTACCAAGCAGGAGGTTTGAT 57.643 47.619 1.83 0.00 39.82 2.57
491 503 2.859165 CTACCAAGCAGGAGGTTTGA 57.141 50.000 1.83 0.00 39.82 2.69
503 515 2.203209 GGGCCGGATGCTACCAAG 60.203 66.667 5.05 0.00 40.92 3.61
508 520 2.690881 AAGTGGGGCCGGATGCTA 60.691 61.111 5.05 0.00 40.92 3.49
537 549 1.668751 TGCTGTGTTTTGTCTCGGTTC 59.331 47.619 0.00 0.00 0.00 3.62
567 579 3.109547 TTTCTACTGTGGCGCGCG 61.110 61.111 28.44 28.44 0.00 6.86
568 580 2.474712 GTTTCTACTGTGGCGCGC 59.525 61.111 25.94 25.94 0.00 6.86
569 581 2.769617 CGTTTCTACTGTGGCGCG 59.230 61.111 0.00 0.00 0.00 6.86
732 749 1.236628 CCGGTATCGAGTAGAGTGGG 58.763 60.000 0.00 0.00 39.00 4.61
734 751 1.872313 GACCCGGTATCGAGTAGAGTG 59.128 57.143 0.00 0.00 39.00 3.51
739 756 3.713902 GGAGACCCGGTATCGAGTA 57.286 57.895 6.11 0.00 39.00 2.59
740 757 4.575180 GGAGACCCGGTATCGAGT 57.425 61.111 6.11 0.00 39.00 4.18
789 806 4.834453 CAGAGCAGAGCAGGGCGG 62.834 72.222 0.00 0.00 34.54 6.13
791 808 4.098722 AGCAGAGCAGAGCAGGGC 62.099 66.667 0.00 0.00 0.00 5.19
792 809 2.187424 GAGCAGAGCAGAGCAGGG 59.813 66.667 0.00 0.00 0.00 4.45
793 810 1.153529 CTGAGCAGAGCAGAGCAGG 60.154 63.158 0.00 0.00 35.39 4.85
825 842 0.385723 GAGACGACAAGCGAACGAGT 60.386 55.000 0.00 0.00 44.57 4.18
829 846 1.737008 GGGGAGACGACAAGCGAAC 60.737 63.158 0.00 0.00 44.57 3.95
830 847 2.654877 GGGGAGACGACAAGCGAA 59.345 61.111 0.00 0.00 44.57 4.70
831 848 3.379445 GGGGGAGACGACAAGCGA 61.379 66.667 0.00 0.00 44.57 4.93
833 850 1.153349 GATGGGGGAGACGACAAGC 60.153 63.158 0.00 0.00 0.00 4.01
840 857 2.156774 GGGGATGGATGGGGGAGAC 61.157 68.421 0.00 0.00 0.00 3.36
848 865 3.334581 TCTTATTGGGATGGGGATGGATG 59.665 47.826 0.00 0.00 0.00 3.51
862 879 1.755179 CTGGTGGGTGCTCTTATTGG 58.245 55.000 0.00 0.00 0.00 3.16
937 954 2.668550 GGCGTGTTGGGGTCAGAC 60.669 66.667 0.00 0.00 0.00 3.51
1768 1800 3.621394 GATCTGAACGGCGCTCGC 61.621 66.667 16.48 5.60 43.89 5.03
1770 1802 1.941734 CTCGATCTGAACGGCGCTC 60.942 63.158 6.90 4.64 0.00 5.03
1860 1892 1.546029 CCGAGGCGATTCATGGAGATA 59.454 52.381 0.00 0.00 0.00 1.98
1908 1940 3.494336 CTCTCCAGCTTTGGCGCG 61.494 66.667 0.00 0.00 44.37 6.86
2005 2037 0.320374 TTCAGCCGGTTCGAGAACAT 59.680 50.000 16.56 0.00 42.85 2.71
2412 2444 1.805945 CTCGTACAGCTTGGCGACC 60.806 63.158 0.00 0.00 0.00 4.79
2439 2471 1.078848 AGAGAGCATGTTGCCGTCC 60.079 57.895 0.00 0.00 46.52 4.79
2508 2540 2.563179 AGATAGCGAGTTGTTGTGGAGT 59.437 45.455 0.00 0.00 0.00 3.85
2745 2777 1.496060 CATACTGGGGTGGTAGCTGA 58.504 55.000 0.00 0.00 0.00 4.26
2751 2783 1.002624 CGTTGCATACTGGGGTGGT 60.003 57.895 0.00 0.00 0.00 4.16
2811 2843 1.675310 CAAGCCGGCAATGTCTCCA 60.675 57.895 31.54 0.00 0.00 3.86
2826 2858 0.879765 CTTGGGAAGCAGAGCACAAG 59.120 55.000 0.00 0.00 0.00 3.16
2838 2870 1.827792 TCCCTGAACTTCCTTGGGAA 58.172 50.000 10.27 0.00 43.27 3.97
2841 2873 1.144913 TGGTTCCCTGAACTTCCTTGG 59.855 52.381 6.89 0.00 41.70 3.61
2871 2903 1.946156 CGACCGCATCATCCAGACG 60.946 63.158 0.00 0.00 0.00 4.18
2872 2904 0.032678 ATCGACCGCATCATCCAGAC 59.967 55.000 0.00 0.00 0.00 3.51
2928 2960 0.537188 ACCTCCAGTAGAACCATGCG 59.463 55.000 0.00 0.00 0.00 4.73
2964 2996 2.358247 TCGGCCTTCAGTTTCGCC 60.358 61.111 0.00 0.00 38.07 5.54
2988 3020 4.250464 GGAACGATGTCAGTGTCCATTTA 58.750 43.478 0.00 0.00 0.00 1.40
3186 3230 2.844451 GCTGTTGTTGGCCGCAGAA 61.844 57.895 12.96 0.00 0.00 3.02
3189 3233 2.832661 AAGCTGTTGTTGGCCGCA 60.833 55.556 0.00 0.00 0.00 5.69
3196 3240 1.961277 CGGCCTCGAAGCTGTTGTT 60.961 57.895 6.68 0.00 39.00 2.83
3671 3716 5.640732 TCTGCACAAAGAAGAACAACTTTC 58.359 37.500 0.00 0.00 39.13 2.62
3684 3729 1.385743 GTACGCGTACTCTGCACAAAG 59.614 52.381 35.66 0.00 33.45 2.77
3791 3836 1.514443 GTCCTTCTCGCCGAACTCG 60.514 63.158 0.00 0.00 39.44 4.18
3917 3962 4.519437 CTCGCGCAGATGAGGCCA 62.519 66.667 8.75 0.00 0.00 5.36
4093 4138 2.348666 GGCAACGTGTTATGCTCTGTAG 59.651 50.000 9.61 0.00 42.20 2.74
4094 4139 2.343101 GGCAACGTGTTATGCTCTGTA 58.657 47.619 9.61 0.00 42.20 2.74
4097 4142 0.676782 GGGGCAACGTGTTATGCTCT 60.677 55.000 9.54 0.00 42.74 4.09
4140 4216 6.541934 TTCTACTTAGGCTCTTTCTTACCC 57.458 41.667 0.00 0.00 0.00 3.69
4152 4228 3.868077 CAGCACTGTGATTCTACTTAGGC 59.132 47.826 12.86 0.00 0.00 3.93
4165 4241 1.664016 GCGGTCAAAATCAGCACTGTG 60.664 52.381 2.76 2.76 0.00 3.66
4188 4302 1.201825 GCGTCGACAACAAGCAGTC 59.798 57.895 17.16 0.00 0.00 3.51
4191 4305 1.954146 GAGGCGTCGACAACAAGCA 60.954 57.895 17.16 0.00 0.00 3.91
4223 4337 0.607489 AGCACACATCAACTCCAGGC 60.607 55.000 0.00 0.00 0.00 4.85
4257 4371 0.765510 AACTCCCACTTGTCCTCCAC 59.234 55.000 0.00 0.00 0.00 4.02
4287 4401 0.313043 GAACACCGCCGCTAGCTATA 59.687 55.000 13.93 0.00 40.39 1.31
4288 4402 1.067582 GAACACCGCCGCTAGCTAT 59.932 57.895 13.93 0.00 40.39 2.97
4312 4426 0.737715 GCCCACAGACAGCTAGAACG 60.738 60.000 0.00 0.00 0.00 3.95
4536 4658 2.679082 AGTTACATGCCCGGAGATACT 58.321 47.619 0.73 0.00 0.00 2.12
4551 4673 2.889045 GGACCCAGGAAAACCAAGTTAC 59.111 50.000 0.00 0.00 0.00 2.50
4566 4688 4.941713 ACCAAAATAAATAGCTGGACCCA 58.058 39.130 0.00 0.00 0.00 4.51
4585 6357 2.367241 TCTGTTCCGAGTTTGATGACCA 59.633 45.455 0.00 0.00 0.00 4.02
4586 6358 2.996621 CTCTGTTCCGAGTTTGATGACC 59.003 50.000 0.00 0.00 0.00 4.02
4859 8424 3.039588 GAACCGCTTTGCCGACGA 61.040 61.111 0.00 0.00 0.00 4.20
4867 8432 1.463553 CCCAAGCCTTGAACCGCTTT 61.464 55.000 5.89 0.00 42.61 3.51
5003 8568 2.892852 TGAAAGCCAATCCAAACTCCAG 59.107 45.455 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.