Multiple sequence alignment - TraesCS7B01G173800

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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 TraesCS7B01G173800 chr7B 100.000 3957 0 0 1 3957 244886426 244882470 0.000000e+00 7308.0
1 TraesCS7B01G173800 chr7D 94.252 3027 150 12 194 3209 550635824 550638837 0.000000e+00 4604.0
2 TraesCS7B01G173800 chr7D 95.745 94 4 0 1 94 264677009 264676916 6.850000e-33 152.0
3 TraesCS7B01G173800 chr5D 93.987 3027 150 16 193 3209 350369588 350366584 0.000000e+00 4553.0
4 TraesCS7B01G173800 chr5D 93.787 3026 167 10 193 3209 41771427 41768414 0.000000e+00 4527.0
5 TraesCS7B01G173800 chr5D 93.313 3021 175 16 193 3203 320660538 320663541 0.000000e+00 4434.0
6 TraesCS7B01G173800 chr5D 93.188 3024 182 12 193 3204 530733136 530736147 0.000000e+00 4421.0
7 TraesCS7B01G173800 chr5B 93.591 3027 177 9 193 3209 184288881 184291900 0.000000e+00 4499.0
8 TraesCS7B01G173800 chr5B 76.489 638 119 16 3338 3950 515181648 515182279 6.380000e-83 318.0
9 TraesCS7B01G173800 chr6B 93.311 3035 186 7 190 3212 521149809 521146780 0.000000e+00 4464.0
10 TraesCS7B01G173800 chr6B 93.111 3034 187 10 193 3214 197818492 197815469 0.000000e+00 4425.0
11 TraesCS7B01G173800 chr4B 93.583 2992 172 10 193 3173 446326669 446329651 0.000000e+00 4444.0
12 TraesCS7B01G173800 chr4B 77.021 631 121 22 3337 3950 72974914 72974291 1.360000e-89 340.0
13 TraesCS7B01G173800 chr3D 76.992 778 129 29 3206 3950 404975093 404974333 2.220000e-107 399.0
14 TraesCS7B01G173800 chr3D 77.508 618 121 14 3339 3954 183679336 183679937 4.860000e-94 355.0
15 TraesCS7B01G173800 chr2A 79.599 549 99 9 3206 3744 711666069 711665524 8.020000e-102 381.0
16 TraesCS7B01G173800 chr4A 78.369 564 102 14 3399 3950 477876464 477877019 8.140000e-92 348.0
17 TraesCS7B01G173800 chr6D 79.701 468 91 4 3378 3844 310554842 310555306 6.340000e-88 335.0
18 TraesCS7B01G173800 chr6D 79.808 416 80 4 3371 3783 110985036 110984622 2.310000e-77 300.0
19 TraesCS7B01G173800 chr6A 79.826 461 84 9 3378 3833 199986632 199986176 1.060000e-85 327.0
20 TraesCS7B01G173800 chr6A 79.176 437 88 3 3355 3789 450106519 450106084 2.310000e-77 300.0
21 TraesCS7B01G173800 chr3B 81.047 401 74 2 3355 3753 173113860 173114260 6.380000e-83 318.0
22 TraesCS7B01G173800 chr2B 80.630 413 67 11 3345 3753 88410231 88409828 1.380000e-79 307.0
23 TraesCS7B01G173800 chr2B 87.755 49 6 0 3882 3930 646067585 646067633 1.540000e-04 58.4
24 TraesCS7B01G173800 chr7A 90.291 103 4 2 1 100 288867892 288867793 3.210000e-26 130.0
25 TraesCS7B01G173800 chr4D 86.667 60 7 1 3891 3949 170675914 170675855 9.180000e-07 65.8


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 TraesCS7B01G173800 chr7B 244882470 244886426 3956 True 7308 7308 100.000 1 3957 1 chr7B.!!$R1 3956
1 TraesCS7B01G173800 chr7D 550635824 550638837 3013 False 4604 4604 94.252 194 3209 1 chr7D.!!$F1 3015
2 TraesCS7B01G173800 chr5D 350366584 350369588 3004 True 4553 4553 93.987 193 3209 1 chr5D.!!$R2 3016
3 TraesCS7B01G173800 chr5D 41768414 41771427 3013 True 4527 4527 93.787 193 3209 1 chr5D.!!$R1 3016
4 TraesCS7B01G173800 chr5D 320660538 320663541 3003 False 4434 4434 93.313 193 3203 1 chr5D.!!$F1 3010
5 TraesCS7B01G173800 chr5D 530733136 530736147 3011 False 4421 4421 93.188 193 3204 1 chr5D.!!$F2 3011
6 TraesCS7B01G173800 chr5B 184288881 184291900 3019 False 4499 4499 93.591 193 3209 1 chr5B.!!$F1 3016
7 TraesCS7B01G173800 chr5B 515181648 515182279 631 False 318 318 76.489 3338 3950 1 chr5B.!!$F2 612
8 TraesCS7B01G173800 chr6B 521146780 521149809 3029 True 4464 4464 93.311 190 3212 1 chr6B.!!$R2 3022
9 TraesCS7B01G173800 chr6B 197815469 197818492 3023 True 4425 4425 93.111 193 3214 1 chr6B.!!$R1 3021
10 TraesCS7B01G173800 chr4B 446326669 446329651 2982 False 4444 4444 93.583 193 3173 1 chr4B.!!$F1 2980
11 TraesCS7B01G173800 chr4B 72974291 72974914 623 True 340 340 77.021 3337 3950 1 chr4B.!!$R1 613
12 TraesCS7B01G173800 chr3D 404974333 404975093 760 True 399 399 76.992 3206 3950 1 chr3D.!!$R1 744
13 TraesCS7B01G173800 chr3D 183679336 183679937 601 False 355 355 77.508 3339 3954 1 chr3D.!!$F1 615
14 TraesCS7B01G173800 chr2A 711665524 711666069 545 True 381 381 79.599 3206 3744 1 chr2A.!!$R1 538
15 TraesCS7B01G173800 chr4A 477876464 477877019 555 False 348 348 78.369 3399 3950 1 chr4A.!!$F1 551

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
154 155 0.035056 ATCTGGCCCTCAAAAGACCG 60.035 55.0 0.00 0.0 0.00 4.79 F
1541 1571 0.038166 CTGCCACCCAGGTGTACAAT 59.962 55.0 15.49 0.0 44.02 2.71 F
2239 2269 0.466189 CTCACAGGGTGTTGTGGCTT 60.466 55.0 6.33 0.0 46.55 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2145 0.770166 TCCACCCTGGGTCATGACAA 60.770 55.0 26.47 13.47 38.32 3.18 R
2694 2741 0.030504 CAACGCCACTTGTGCATTGA 59.969 50.0 0.00 0.00 0.00 2.57 R
3340 3395 0.107897 TTTGCACTATCCGCCGATGT 60.108 50.0 0.00 0.00 0.00 3.06 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
20 21 3.079960 GATGTAAACGGAGATCGCTGA 57.920 47.619 12.67 0.00 43.89 4.26
21 22 3.444916 GATGTAAACGGAGATCGCTGAA 58.555 45.455 12.67 0.00 43.89 3.02
22 23 2.602878 TGTAAACGGAGATCGCTGAAC 58.397 47.619 12.67 7.58 43.89 3.18
23 24 1.582502 GTAAACGGAGATCGCTGAACG 59.417 52.381 12.67 1.78 43.89 3.95
24 25 0.736325 AAACGGAGATCGCTGAACGG 60.736 55.000 12.67 0.00 43.89 4.44
25 26 2.278857 CGGAGATCGCTGAACGGG 60.279 66.667 0.00 0.00 43.89 5.28
26 27 2.107141 GGAGATCGCTGAACGGGG 59.893 66.667 0.00 0.00 43.89 5.73
27 28 2.107141 GAGATCGCTGAACGGGGG 59.893 66.667 0.00 0.00 43.89 5.40
28 29 2.683933 AGATCGCTGAACGGGGGT 60.684 61.111 0.00 0.00 43.89 4.95
29 30 1.380785 AGATCGCTGAACGGGGGTA 60.381 57.895 0.00 0.00 43.89 3.69
30 31 1.227176 GATCGCTGAACGGGGGTAC 60.227 63.158 0.00 0.00 43.89 3.34
31 32 2.639883 GATCGCTGAACGGGGGTACC 62.640 65.000 2.17 2.17 46.24 3.34
42 43 3.892581 GGGTACCGCGGGTAGTCG 61.893 72.222 31.76 1.69 39.02 4.18
50 51 2.183555 CGGGTAGTCGCCTTCCAC 59.816 66.667 0.00 0.00 30.00 4.02
51 52 2.642254 CGGGTAGTCGCCTTCCACA 61.642 63.158 0.00 0.00 30.00 4.17
52 53 1.079336 GGGTAGTCGCCTTCCACAC 60.079 63.158 0.00 0.00 30.00 3.82
53 54 1.542187 GGGTAGTCGCCTTCCACACT 61.542 60.000 0.00 0.00 30.00 3.55
54 55 0.108756 GGTAGTCGCCTTCCACACTC 60.109 60.000 0.00 0.00 0.00 3.51
55 56 0.108756 GTAGTCGCCTTCCACACTCC 60.109 60.000 0.00 0.00 0.00 3.85
56 57 0.251653 TAGTCGCCTTCCACACTCCT 60.252 55.000 0.00 0.00 0.00 3.69
57 58 1.122019 AGTCGCCTTCCACACTCCTT 61.122 55.000 0.00 0.00 0.00 3.36
58 59 0.606604 GTCGCCTTCCACACTCCTTA 59.393 55.000 0.00 0.00 0.00 2.69
59 60 0.606604 TCGCCTTCCACACTCCTTAC 59.393 55.000 0.00 0.00 0.00 2.34
60 61 0.391263 CGCCTTCCACACTCCTTACC 60.391 60.000 0.00 0.00 0.00 2.85
61 62 0.690762 GCCTTCCACACTCCTTACCA 59.309 55.000 0.00 0.00 0.00 3.25
62 63 1.073284 GCCTTCCACACTCCTTACCAA 59.927 52.381 0.00 0.00 0.00 3.67
63 64 2.876079 GCCTTCCACACTCCTTACCAAG 60.876 54.545 0.00 0.00 0.00 3.61
64 65 2.637872 CCTTCCACACTCCTTACCAAGA 59.362 50.000 0.00 0.00 0.00 3.02
65 66 3.264450 CCTTCCACACTCCTTACCAAGAT 59.736 47.826 0.00 0.00 0.00 2.40
66 67 4.263506 CCTTCCACACTCCTTACCAAGATT 60.264 45.833 0.00 0.00 0.00 2.40
67 68 4.286297 TCCACACTCCTTACCAAGATTG 57.714 45.455 0.00 0.00 0.00 2.67
68 69 3.907474 TCCACACTCCTTACCAAGATTGA 59.093 43.478 0.00 0.00 0.00 2.57
69 70 4.349636 TCCACACTCCTTACCAAGATTGAA 59.650 41.667 0.00 0.00 0.00 2.69
70 71 4.697352 CCACACTCCTTACCAAGATTGAAG 59.303 45.833 0.00 0.00 0.00 3.02
71 72 5.308825 CACACTCCTTACCAAGATTGAAGT 58.691 41.667 0.00 0.00 0.00 3.01
72 73 5.409826 CACACTCCTTACCAAGATTGAAGTC 59.590 44.000 0.00 0.00 0.00 3.01
73 74 4.938226 CACTCCTTACCAAGATTGAAGTCC 59.062 45.833 0.00 0.00 0.00 3.85
74 75 4.184629 CTCCTTACCAAGATTGAAGTCCG 58.815 47.826 0.00 0.00 0.00 4.79
75 76 2.678336 CCTTACCAAGATTGAAGTCCGC 59.322 50.000 0.00 0.00 0.00 5.54
76 77 3.600388 CTTACCAAGATTGAAGTCCGCT 58.400 45.455 0.00 0.00 0.00 5.52
77 78 2.568623 ACCAAGATTGAAGTCCGCTT 57.431 45.000 0.00 0.00 37.71 4.68
78 79 2.863809 ACCAAGATTGAAGTCCGCTTT 58.136 42.857 0.00 0.00 34.61 3.51
79 80 2.554032 ACCAAGATTGAAGTCCGCTTTG 59.446 45.455 0.00 0.00 34.61 2.77
80 81 2.589014 CAAGATTGAAGTCCGCTTTGC 58.411 47.619 0.00 0.00 34.61 3.68
81 82 1.168714 AGATTGAAGTCCGCTTTGCC 58.831 50.000 0.00 0.00 34.61 4.52
82 83 0.881118 GATTGAAGTCCGCTTTGCCA 59.119 50.000 0.00 0.00 34.61 4.92
83 84 1.269448 GATTGAAGTCCGCTTTGCCAA 59.731 47.619 0.00 0.00 34.61 4.52
84 85 1.107114 TTGAAGTCCGCTTTGCCAAA 58.893 45.000 0.00 0.00 34.61 3.28
85 86 0.383949 TGAAGTCCGCTTTGCCAAAC 59.616 50.000 0.00 0.00 34.61 2.93
86 87 0.383949 GAAGTCCGCTTTGCCAAACA 59.616 50.000 0.00 0.00 34.61 2.83
87 88 0.385390 AAGTCCGCTTTGCCAAACAG 59.615 50.000 0.00 0.00 0.00 3.16
88 89 1.007387 GTCCGCTTTGCCAAACAGG 60.007 57.895 0.94 0.94 41.84 4.00
89 90 1.152860 TCCGCTTTGCCAAACAGGA 60.153 52.632 5.13 5.13 41.22 3.86
90 91 0.753479 TCCGCTTTGCCAAACAGGAA 60.753 50.000 6.44 0.00 41.22 3.36
91 92 0.103937 CCGCTTTGCCAAACAGGAAA 59.896 50.000 1.08 0.00 41.22 3.13
92 93 1.208259 CGCTTTGCCAAACAGGAAAC 58.792 50.000 0.00 0.00 41.22 2.78
93 94 1.208259 GCTTTGCCAAACAGGAAACG 58.792 50.000 0.00 0.00 41.22 3.60
94 95 1.208259 CTTTGCCAAACAGGAAACGC 58.792 50.000 0.00 0.00 41.22 4.84
95 96 0.526524 TTTGCCAAACAGGAAACGCG 60.527 50.000 3.53 3.53 41.22 6.01
96 97 1.658686 TTGCCAAACAGGAAACGCGT 61.659 50.000 5.58 5.58 41.22 6.01
97 98 1.065109 GCCAAACAGGAAACGCGTT 59.935 52.632 20.79 20.79 41.22 4.84
98 99 0.526739 GCCAAACAGGAAACGCGTTT 60.527 50.000 35.28 35.28 41.22 3.60
99 100 1.915952 CCAAACAGGAAACGCGTTTT 58.084 45.000 35.06 19.96 41.22 2.43
100 101 2.795331 GCCAAACAGGAAACGCGTTTTA 60.795 45.455 35.06 0.00 41.22 1.52
101 102 2.784928 CCAAACAGGAAACGCGTTTTAC 59.215 45.455 35.06 28.85 41.22 2.01
102 103 2.372148 AACAGGAAACGCGTTTTACG 57.628 45.000 35.06 26.40 45.88 3.18
103 104 6.992583 CCAAACAGGAAACGCGTTTTACGT 62.993 45.833 35.06 26.98 43.00 3.57
109 110 2.299562 ACGCGTTTTACGTTCAGCA 58.700 47.368 5.58 0.00 44.73 4.41
110 111 0.651551 ACGCGTTTTACGTTCAGCAA 59.348 45.000 5.58 0.00 44.73 3.91
111 112 1.305482 CGCGTTTTACGTTCAGCAAG 58.695 50.000 0.00 0.00 44.73 4.01
112 113 1.332552 CGCGTTTTACGTTCAGCAAGT 60.333 47.619 0.00 0.00 44.73 3.16
113 114 2.034076 GCGTTTTACGTTCAGCAAGTG 58.966 47.619 0.00 0.00 44.73 3.16
114 115 2.034076 CGTTTTACGTTCAGCAAGTGC 58.966 47.619 0.00 0.00 36.74 4.40
115 116 2.381589 GTTTTACGTTCAGCAAGTGCC 58.618 47.619 0.00 0.00 43.38 5.01
116 117 0.948678 TTTACGTTCAGCAAGTGCCC 59.051 50.000 0.00 0.00 43.38 5.36
117 118 0.107831 TTACGTTCAGCAAGTGCCCT 59.892 50.000 0.00 0.00 43.38 5.19
118 119 0.107831 TACGTTCAGCAAGTGCCCTT 59.892 50.000 0.00 0.00 43.38 3.95
119 120 0.751643 ACGTTCAGCAAGTGCCCTTT 60.752 50.000 0.00 0.00 43.38 3.11
120 121 1.234821 CGTTCAGCAAGTGCCCTTTA 58.765 50.000 0.00 0.00 43.38 1.85
121 122 1.606668 CGTTCAGCAAGTGCCCTTTAA 59.393 47.619 0.00 0.00 43.38 1.52
122 123 2.604614 CGTTCAGCAAGTGCCCTTTAAC 60.605 50.000 0.00 0.00 43.38 2.01
123 124 1.616159 TCAGCAAGTGCCCTTTAACC 58.384 50.000 0.00 0.00 43.38 2.85
124 125 1.144913 TCAGCAAGTGCCCTTTAACCT 59.855 47.619 0.00 0.00 43.38 3.50
125 126 2.373836 TCAGCAAGTGCCCTTTAACCTA 59.626 45.455 0.00 0.00 43.38 3.08
126 127 3.010138 TCAGCAAGTGCCCTTTAACCTAT 59.990 43.478 0.00 0.00 43.38 2.57
127 128 3.763897 CAGCAAGTGCCCTTTAACCTATT 59.236 43.478 0.00 0.00 43.38 1.73
128 129 4.947388 CAGCAAGTGCCCTTTAACCTATTA 59.053 41.667 0.00 0.00 43.38 0.98
129 130 5.066505 CAGCAAGTGCCCTTTAACCTATTAG 59.933 44.000 0.00 0.00 43.38 1.73
130 131 5.045140 AGCAAGTGCCCTTTAACCTATTAGA 60.045 40.000 0.00 0.00 43.38 2.10
131 132 5.297029 GCAAGTGCCCTTTAACCTATTAGAG 59.703 44.000 0.00 0.00 34.31 2.43
132 133 5.037383 AGTGCCCTTTAACCTATTAGAGC 57.963 43.478 0.00 0.00 0.00 4.09
133 134 4.473559 AGTGCCCTTTAACCTATTAGAGCA 59.526 41.667 0.00 0.00 0.00 4.26
134 135 5.045140 AGTGCCCTTTAACCTATTAGAGCAA 60.045 40.000 0.00 0.00 0.00 3.91
135 136 5.650703 GTGCCCTTTAACCTATTAGAGCAAA 59.349 40.000 0.00 0.00 0.00 3.68
136 137 6.321435 GTGCCCTTTAACCTATTAGAGCAAAT 59.679 38.462 0.00 0.00 0.00 2.32
137 138 6.546034 TGCCCTTTAACCTATTAGAGCAAATC 59.454 38.462 0.00 0.00 0.00 2.17
138 139 6.773200 GCCCTTTAACCTATTAGAGCAAATCT 59.227 38.462 0.00 0.00 42.47 2.40
139 140 7.255277 GCCCTTTAACCTATTAGAGCAAATCTG 60.255 40.741 0.00 0.00 39.20 2.90
140 141 7.229506 CCCTTTAACCTATTAGAGCAAATCTGG 59.770 40.741 0.00 0.00 39.20 3.86
141 142 7.255277 CCTTTAACCTATTAGAGCAAATCTGGC 60.255 40.741 0.00 0.00 39.20 4.85
142 143 4.092116 ACCTATTAGAGCAAATCTGGCC 57.908 45.455 0.00 0.00 39.20 5.36
143 144 3.181439 ACCTATTAGAGCAAATCTGGCCC 60.181 47.826 0.00 0.00 39.20 5.80
144 145 3.073650 CCTATTAGAGCAAATCTGGCCCT 59.926 47.826 0.00 0.00 39.20 5.19
145 146 2.717639 TTAGAGCAAATCTGGCCCTC 57.282 50.000 0.00 0.00 39.20 4.30
146 147 1.583556 TAGAGCAAATCTGGCCCTCA 58.416 50.000 0.00 0.00 39.20 3.86
147 148 0.700564 AGAGCAAATCTGGCCCTCAA 59.299 50.000 0.00 0.00 36.69 3.02
148 149 1.076024 AGAGCAAATCTGGCCCTCAAA 59.924 47.619 0.00 0.00 36.69 2.69
149 150 1.895131 GAGCAAATCTGGCCCTCAAAA 59.105 47.619 0.00 0.00 0.00 2.44
150 151 1.897802 AGCAAATCTGGCCCTCAAAAG 59.102 47.619 0.00 0.00 0.00 2.27
151 152 1.895131 GCAAATCTGGCCCTCAAAAGA 59.105 47.619 0.00 0.00 0.00 2.52
152 153 2.353109 GCAAATCTGGCCCTCAAAAGAC 60.353 50.000 0.00 0.00 0.00 3.01
153 154 2.222227 AATCTGGCCCTCAAAAGACC 57.778 50.000 0.00 0.00 0.00 3.85
154 155 0.035056 ATCTGGCCCTCAAAAGACCG 60.035 55.000 0.00 0.00 0.00 4.79
155 156 2.282180 TGGCCCTCAAAAGACCGC 60.282 61.111 0.00 0.00 0.00 5.68
156 157 3.431725 GGCCCTCAAAAGACCGCG 61.432 66.667 0.00 0.00 0.00 6.46
157 158 4.103103 GCCCTCAAAAGACCGCGC 62.103 66.667 0.00 0.00 0.00 6.86
158 159 3.788766 CCCTCAAAAGACCGCGCG 61.789 66.667 25.67 25.67 0.00 6.86
159 160 4.445545 CCTCAAAAGACCGCGCGC 62.446 66.667 27.36 23.91 0.00 6.86
160 161 4.776953 CTCAAAAGACCGCGCGCG 62.777 66.667 43.73 43.73 39.44 6.86
186 187 3.924507 GGCATGGACCCATCACAC 58.075 61.111 0.00 0.00 33.90 3.82
187 188 1.754234 GGCATGGACCCATCACACC 60.754 63.158 0.00 0.00 33.90 4.16
188 189 1.304282 GCATGGACCCATCACACCT 59.696 57.895 0.00 0.00 33.90 4.00
240 241 4.697756 CCTGGCACGAGCGGGAAA 62.698 66.667 9.17 0.00 43.41 3.13
248 249 2.671070 GCACGAGCGGGAAAAATTTGAT 60.671 45.455 0.00 0.00 0.00 2.57
262 263 3.953712 ATTTGATCCGTTTGGTTTCCC 57.046 42.857 0.00 0.00 36.30 3.97
539 548 0.038526 TCTTCCTCCGTTCGCACTTC 60.039 55.000 0.00 0.00 0.00 3.01
541 550 1.469335 TTCCTCCGTTCGCACTTCCT 61.469 55.000 0.00 0.00 0.00 3.36
549 558 4.717629 CGCACTTCCTCGCCGACA 62.718 66.667 0.00 0.00 0.00 4.35
557 566 4.829518 CTCGCCGACACGCATCGA 62.830 66.667 10.26 0.00 45.13 3.59
644 653 1.819632 GCCGGCGTTCATCTTCCAT 60.820 57.895 12.58 0.00 0.00 3.41
649 658 1.678728 GGCGTTCATCTTCCATCACCA 60.679 52.381 0.00 0.00 0.00 4.17
650 659 1.398390 GCGTTCATCTTCCATCACCAC 59.602 52.381 0.00 0.00 0.00 4.16
651 660 2.009774 CGTTCATCTTCCATCACCACC 58.990 52.381 0.00 0.00 0.00 4.61
652 661 2.615240 CGTTCATCTTCCATCACCACCA 60.615 50.000 0.00 0.00 0.00 4.17
653 662 2.749621 GTTCATCTTCCATCACCACCAC 59.250 50.000 0.00 0.00 0.00 4.16
654 663 1.281867 TCATCTTCCATCACCACCACC 59.718 52.381 0.00 0.00 0.00 4.61
655 664 1.004628 CATCTTCCATCACCACCACCA 59.995 52.381 0.00 0.00 0.00 4.17
685 695 1.228644 TTCAAGCTGCAGCCATGGT 60.229 52.632 34.39 13.75 43.38 3.55
689 699 2.827642 GCTGCAGCCATGGTCTCC 60.828 66.667 28.76 1.69 34.31 3.71
705 715 0.613260 CTCCGTGAGTTCAATCCCCA 59.387 55.000 0.00 0.00 0.00 4.96
784 794 5.104569 TGCATGGTTGATTAGTGGTCTGATA 60.105 40.000 0.00 0.00 0.00 2.15
807 817 3.244875 TGTGAGCTGATATGGTTGGTTGT 60.245 43.478 0.00 0.00 0.00 3.32
858 868 4.818546 GCTAGATGTTCAAGCATGTGGTAT 59.181 41.667 0.00 0.00 36.26 2.73
963 973 5.536538 TGGTCCATTTGTAGCATGTTGTTTA 59.463 36.000 0.00 0.00 0.00 2.01
998 1008 6.041423 TGTTTCTGCTCATAGATTGTCTGA 57.959 37.500 0.00 0.00 0.00 3.27
1006 1016 6.649557 TGCTCATAGATTGTCTGATATGCTTG 59.350 38.462 0.00 0.00 0.00 4.01
1067 1077 6.038603 GTGATGAACCATGTACATGTATGCTT 59.961 38.462 29.25 16.21 37.11 3.91
1079 1090 4.945543 ACATGTATGCTTCTGCTTTCATGA 59.054 37.500 20.89 0.00 45.70 3.07
1088 1099 3.673902 TCTGCTTTCATGAATTGTCCGA 58.326 40.909 9.40 0.00 0.00 4.55
1091 1102 5.294306 TCTGCTTTCATGAATTGTCCGATAC 59.706 40.000 9.40 0.00 0.00 2.24
1165 1176 1.849219 GCAGACGCAAGATCTTAGTCG 59.151 52.381 25.03 21.29 43.62 4.18
1307 1321 0.106708 TCGTTGAGCCAACTCTTGCT 59.893 50.000 13.76 0.00 43.85 3.91
1308 1322 0.236711 CGTTGAGCCAACTCTTGCTG 59.763 55.000 13.76 0.00 43.85 4.41
1309 1323 1.597742 GTTGAGCCAACTCTTGCTGA 58.402 50.000 9.89 0.00 43.85 4.26
1353 1382 1.666872 GCAGCAGCAAAGGCAAAGG 60.667 57.895 0.00 0.00 44.61 3.11
1457 1486 2.258109 GGAGTTAGGACTGACAAGGGT 58.742 52.381 0.00 0.00 35.88 4.34
1490 1520 1.088306 ACTTGAACACCGTTGCGAAA 58.912 45.000 0.00 0.00 0.00 3.46
1507 1537 3.635331 CGAAACAGGTGTTCGAGTTCTA 58.365 45.455 0.39 0.00 37.25 2.10
1541 1571 0.038166 CTGCCACCCAGGTGTACAAT 59.962 55.000 15.49 0.00 44.02 2.71
1635 1665 4.973168 TGAGAACACTTGCTCCATAGTTT 58.027 39.130 0.00 0.00 0.00 2.66
1699 1729 4.783227 ACAGCCCTCTTCCTTTTCATACTA 59.217 41.667 0.00 0.00 0.00 1.82
1906 1936 1.127567 CAGACTTCCCTGGGACACCA 61.128 60.000 16.85 0.00 46.94 4.17
2034 2064 4.460382 GGAGGAGATCAATGTCTTTTGCAA 59.540 41.667 0.00 0.00 0.00 4.08
2040 2070 6.751157 AGATCAATGTCTTTTGCAACATGAA 58.249 32.000 0.00 0.00 36.28 2.57
2115 2145 1.612442 ACCCTGACCTGTATGGCGT 60.612 57.895 0.00 0.00 40.22 5.68
2141 2171 1.852157 ACCCAGGGTGGATTCAGCA 60.852 57.895 11.70 0.00 40.96 4.41
2167 2197 0.825410 CTCTCATGGCAGCTCTCAGT 59.175 55.000 0.00 0.00 0.00 3.41
2239 2269 0.466189 CTCACAGGGTGTTGTGGCTT 60.466 55.000 6.33 0.00 46.55 4.35
2344 2389 1.131218 GATGACGACGACGACGACA 59.869 57.895 25.15 23.86 42.66 4.35
2427 2472 5.222109 TGGTATATACTAACCCCTCACGCTA 60.222 44.000 12.54 0.00 34.69 4.26
2518 2563 2.584835 AGGTTGAACTTGCTATGCCA 57.415 45.000 0.00 0.00 0.00 4.92
2561 2607 4.067896 TCTCTTCTGCTCCATTGTTGTTC 58.932 43.478 0.00 0.00 0.00 3.18
2694 2741 6.424032 GGGTTTATAGTTCATGGGAAGAAGT 58.576 40.000 0.00 0.00 32.62 3.01
2710 2757 0.311790 AAGTCAATGCACAAGTGGCG 59.688 50.000 2.00 0.00 0.00 5.69
2712 2759 0.030638 GTCAATGCACAAGTGGCGTT 59.969 50.000 2.00 0.18 40.93 4.84
2806 2853 4.988598 CACGGAGGCGGCAGTGTT 62.989 66.667 13.08 0.00 30.80 3.32
2841 2888 1.490490 TGGAGCTGTCAAAGTGGAAGT 59.510 47.619 0.00 0.00 0.00 3.01
2864 2911 2.094182 GCTAAGGTGGATCGTCAGTTCA 60.094 50.000 0.00 0.00 0.00 3.18
2913 2960 0.605319 GCCCAGTTCGTCACCATTGA 60.605 55.000 0.00 0.00 0.00 2.57
2919 2966 3.067106 AGTTCGTCACCATTGATGTGTC 58.933 45.455 0.00 0.00 39.48 3.67
2930 2977 3.308878 GATGTGTCGTGGCGTTGGC 62.309 63.158 0.00 0.00 38.90 4.52
2946 2993 1.154413 GGCGTGCTTGTTGTGATCG 60.154 57.895 0.00 0.00 0.00 3.69
3000 3047 1.154488 GCACAACATGTACGCCGTG 60.154 57.895 0.00 3.48 36.08 4.94
3081 3129 3.250040 GCACTTGGGTATTACCTAATGCG 59.750 47.826 19.89 10.66 38.10 4.73
3152 3200 2.760650 CCTATTTTTCCTCAACCAGGCC 59.239 50.000 0.00 0.00 43.08 5.19
3153 3201 2.397044 ATTTTTCCTCAACCAGGCCA 57.603 45.000 5.01 0.00 43.08 5.36
3175 3223 3.019564 GGTTGAGAAGGCTATGCAATGT 58.980 45.455 0.00 0.00 0.00 2.71
3224 3272 1.202758 TGCCCCATATGTTAGCTTCCG 60.203 52.381 1.24 0.00 0.00 4.30
3251 3300 3.126831 GCGTCTCTCATATCCAAACCTG 58.873 50.000 0.00 0.00 0.00 4.00
3252 3301 3.126831 CGTCTCTCATATCCAAACCTGC 58.873 50.000 0.00 0.00 0.00 4.85
3260 3309 6.000246 TCATATCCAAACCTGCAACTCATA 58.000 37.500 0.00 0.00 0.00 2.15
3281 3330 2.916716 ACAACGCTACGTATAAACACGG 59.083 45.455 0.00 0.00 46.12 4.94
3286 3335 3.792956 CGCTACGTATAAACACGGTCAAT 59.207 43.478 0.00 0.00 46.12 2.57
3289 3338 5.743398 GCTACGTATAAACACGGTCAATACA 59.257 40.000 0.00 0.00 46.12 2.29
3290 3339 6.291269 GCTACGTATAAACACGGTCAATACAC 60.291 42.308 0.00 0.00 46.12 2.90
3291 3340 4.558470 ACGTATAAACACGGTCAATACACG 59.442 41.667 0.00 0.00 46.12 4.49
3298 3347 2.739913 CACGGTCAATACACGGTTCATT 59.260 45.455 0.00 0.00 0.00 2.57
3307 3356 1.094785 CACGGTTCATTGGATCACCC 58.905 55.000 0.00 0.00 34.81 4.61
3315 3364 4.868172 TCATTGGATCACCCTTTCATCT 57.132 40.909 0.00 0.00 35.38 2.90
3318 3367 4.934797 TTGGATCACCCTTTCATCTCTT 57.065 40.909 0.00 0.00 35.38 2.85
3319 3368 6.158520 TCATTGGATCACCCTTTCATCTCTTA 59.841 38.462 0.00 0.00 35.38 2.10
3321 3370 6.581388 TGGATCACCCTTTCATCTCTTAAT 57.419 37.500 0.00 0.00 35.38 1.40
3322 3371 6.359804 TGGATCACCCTTTCATCTCTTAATG 58.640 40.000 0.00 0.00 35.38 1.90
3324 3373 6.709846 GGATCACCCTTTCATCTCTTAATGAG 59.290 42.308 0.00 0.00 43.96 2.90
3325 3374 5.431765 TCACCCTTTCATCTCTTAATGAGC 58.568 41.667 0.00 0.00 42.38 4.26
3326 3375 5.045651 TCACCCTTTCATCTCTTAATGAGCA 60.046 40.000 0.00 0.00 42.38 4.26
3327 3376 5.826737 CACCCTTTCATCTCTTAATGAGCAT 59.173 40.000 0.00 0.00 42.38 3.79
3328 3377 5.826737 ACCCTTTCATCTCTTAATGAGCATG 59.173 40.000 0.00 0.00 42.38 4.06
3329 3378 5.826737 CCCTTTCATCTCTTAATGAGCATGT 59.173 40.000 0.00 0.00 42.38 3.21
3333 3388 5.993055 TCATCTCTTAATGAGCATGTCCAA 58.007 37.500 0.00 0.00 42.38 3.53
3335 3390 5.426689 TCTCTTAATGAGCATGTCCAACT 57.573 39.130 0.00 0.00 42.38 3.16
3340 3395 4.558226 AATGAGCATGTCCAACTGAGTA 57.442 40.909 0.00 0.00 0.00 2.59
3429 3506 2.091541 GAAATCACCATTTCCTCGCCA 58.908 47.619 0.00 0.00 41.51 5.69
3430 3507 2.214376 AATCACCATTTCCTCGCCAA 57.786 45.000 0.00 0.00 0.00 4.52
3443 3520 2.531326 GCCAACCCCTTCCCCTTT 59.469 61.111 0.00 0.00 0.00 3.11
3518 3597 1.226717 GTCATCGTCGGAGCTGGAC 60.227 63.158 0.00 0.00 0.00 4.02
3537 3616 1.269936 ACGTGGAACCGTCTGTTAAGG 60.270 52.381 0.00 0.00 35.95 2.69
3552 3631 3.388024 TGTTAAGGCAGAGTCTGAGTTGT 59.612 43.478 24.55 5.97 32.44 3.32
3628 3708 2.720758 CTTCGGCTTCGCTGTCGTG 61.721 63.158 1.93 0.00 36.18 4.35
3675 3755 4.194720 GATGGCGAGTCGGAGCGT 62.195 66.667 15.52 0.00 0.00 5.07
3682 3762 4.421479 AGTCGGAGCGTCTTGGCG 62.421 66.667 0.00 0.00 38.18 5.69
3698 3778 2.030562 CGTTCTTGCGGTGGAGGT 59.969 61.111 0.00 0.00 0.00 3.85
3770 3850 0.039978 GACCGCGACATCGAGATCAT 60.040 55.000 8.23 0.00 41.67 2.45
3799 3881 3.103289 GCGTGTGATCGTCGTGCA 61.103 61.111 0.00 0.00 0.00 4.57
3876 3958 0.894835 TGCTTGTGCCTCATACTCGA 59.105 50.000 0.00 0.00 38.71 4.04
3881 3963 0.867753 GTGCCTCATACTCGAGCGTG 60.868 60.000 13.61 11.76 0.00 5.34
3882 3964 1.313091 TGCCTCATACTCGAGCGTGT 61.313 55.000 13.61 0.00 0.00 4.49
3883 3965 0.592754 GCCTCATACTCGAGCGTGTC 60.593 60.000 13.61 2.64 0.00 3.67
3940 4033 0.824759 ATACCACTTCCGGAGCAGAC 59.175 55.000 10.18 0.00 0.00 3.51
3942 4035 2.651361 CACTTCCGGAGCAGACGT 59.349 61.111 10.18 0.00 0.00 4.34
3950 4043 1.668151 GGAGCAGACGTTGGTGGTC 60.668 63.158 14.06 14.06 37.72 4.02
3954 4047 3.231736 AGACGTTGGTGGTCGGCT 61.232 61.111 0.00 0.00 40.79 5.52
3955 4048 3.041940 GACGTTGGTGGTCGGCTG 61.042 66.667 0.00 0.00 31.86 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.187700 GTTCAGCGATCTCCGTTTACAT 58.812 45.455 0.00 0.00 41.15 2.29
2 3 2.602878 GTTCAGCGATCTCCGTTTACA 58.397 47.619 0.00 0.00 41.15 2.41
3 4 1.582502 CGTTCAGCGATCTCCGTTTAC 59.417 52.381 0.00 0.00 44.77 2.01
4 5 1.468565 CCGTTCAGCGATCTCCGTTTA 60.469 52.381 0.00 0.00 44.77 2.01
5 6 0.736325 CCGTTCAGCGATCTCCGTTT 60.736 55.000 0.00 0.00 44.77 3.60
6 7 1.153823 CCGTTCAGCGATCTCCGTT 60.154 57.895 0.00 0.00 44.77 4.44
7 8 2.490217 CCGTTCAGCGATCTCCGT 59.510 61.111 0.00 0.00 44.77 4.69
8 9 2.278857 CCCGTTCAGCGATCTCCG 60.279 66.667 0.00 0.00 44.77 4.63
9 10 2.107141 CCCCGTTCAGCGATCTCC 59.893 66.667 0.00 0.00 44.77 3.71
10 11 1.389609 TACCCCCGTTCAGCGATCTC 61.390 60.000 0.00 0.00 44.77 2.75
11 12 1.380785 TACCCCCGTTCAGCGATCT 60.381 57.895 0.00 0.00 44.77 2.75
12 13 1.227176 GTACCCCCGTTCAGCGATC 60.227 63.158 0.00 0.00 44.77 3.69
13 14 2.728435 GGTACCCCCGTTCAGCGAT 61.728 63.158 0.00 0.00 44.77 4.58
14 15 3.384532 GGTACCCCCGTTCAGCGA 61.385 66.667 0.00 0.00 44.77 4.93
24 25 3.531207 GACTACCCGCGGTACCCC 61.531 72.222 26.12 6.35 37.09 4.95
25 26 3.892581 CGACTACCCGCGGTACCC 61.893 72.222 26.12 8.03 37.09 3.69
26 27 4.559229 GCGACTACCCGCGGTACC 62.559 72.222 26.12 0.16 45.86 3.34
33 34 2.183555 GTGGAAGGCGACTACCCG 59.816 66.667 0.00 0.00 42.68 5.28
34 35 1.079336 GTGTGGAAGGCGACTACCC 60.079 63.158 0.00 0.00 42.68 3.69
35 36 0.108756 GAGTGTGGAAGGCGACTACC 60.109 60.000 0.00 0.00 42.68 3.18
36 37 0.108756 GGAGTGTGGAAGGCGACTAC 60.109 60.000 0.00 0.00 42.68 2.73
37 38 0.251653 AGGAGTGTGGAAGGCGACTA 60.252 55.000 0.00 0.00 42.68 2.59
39 40 0.606604 TAAGGAGTGTGGAAGGCGAC 59.393 55.000 0.00 0.00 0.00 5.19
40 41 0.606604 GTAAGGAGTGTGGAAGGCGA 59.393 55.000 0.00 0.00 0.00 5.54
41 42 0.391263 GGTAAGGAGTGTGGAAGGCG 60.391 60.000 0.00 0.00 0.00 5.52
42 43 0.690762 TGGTAAGGAGTGTGGAAGGC 59.309 55.000 0.00 0.00 0.00 4.35
43 44 2.637872 TCTTGGTAAGGAGTGTGGAAGG 59.362 50.000 0.00 0.00 0.00 3.46
44 45 4.559862 ATCTTGGTAAGGAGTGTGGAAG 57.440 45.455 0.00 0.00 0.00 3.46
45 46 4.349636 TCAATCTTGGTAAGGAGTGTGGAA 59.650 41.667 0.00 0.00 0.00 3.53
46 47 3.907474 TCAATCTTGGTAAGGAGTGTGGA 59.093 43.478 0.00 0.00 0.00 4.02
47 48 4.286297 TCAATCTTGGTAAGGAGTGTGG 57.714 45.455 0.00 0.00 0.00 4.17
48 49 5.308825 ACTTCAATCTTGGTAAGGAGTGTG 58.691 41.667 0.00 0.00 0.00 3.82
49 50 5.513267 GGACTTCAATCTTGGTAAGGAGTGT 60.513 44.000 0.00 0.00 0.00 3.55
50 51 4.938226 GGACTTCAATCTTGGTAAGGAGTG 59.062 45.833 0.00 0.00 0.00 3.51
51 52 4.322801 CGGACTTCAATCTTGGTAAGGAGT 60.323 45.833 0.00 0.00 0.00 3.85
52 53 4.184629 CGGACTTCAATCTTGGTAAGGAG 58.815 47.826 0.00 0.00 0.00 3.69
53 54 3.618997 GCGGACTTCAATCTTGGTAAGGA 60.619 47.826 0.00 0.00 0.00 3.36
54 55 2.678336 GCGGACTTCAATCTTGGTAAGG 59.322 50.000 0.00 0.00 0.00 2.69
55 56 3.600388 AGCGGACTTCAATCTTGGTAAG 58.400 45.455 0.00 0.00 0.00 2.34
56 57 3.695830 AGCGGACTTCAATCTTGGTAA 57.304 42.857 0.00 0.00 0.00 2.85
57 58 3.695830 AAGCGGACTTCAATCTTGGTA 57.304 42.857 0.00 0.00 0.00 3.25
58 59 2.554032 CAAAGCGGACTTCAATCTTGGT 59.446 45.455 0.00 0.00 34.05 3.67
59 60 2.669391 GCAAAGCGGACTTCAATCTTGG 60.669 50.000 0.00 0.00 34.05 3.61
60 61 2.589014 GCAAAGCGGACTTCAATCTTG 58.411 47.619 0.00 0.00 34.05 3.02
61 62 1.541588 GGCAAAGCGGACTTCAATCTT 59.458 47.619 0.00 0.00 34.05 2.40
62 63 1.168714 GGCAAAGCGGACTTCAATCT 58.831 50.000 0.00 0.00 34.05 2.40
63 64 0.881118 TGGCAAAGCGGACTTCAATC 59.119 50.000 0.00 0.00 34.05 2.67
64 65 1.327303 TTGGCAAAGCGGACTTCAAT 58.673 45.000 0.00 0.00 34.05 2.57
65 66 1.107114 TTTGGCAAAGCGGACTTCAA 58.893 45.000 8.93 0.00 34.05 2.69
66 67 0.383949 GTTTGGCAAAGCGGACTTCA 59.616 50.000 13.94 0.00 34.05 3.02
67 68 0.383949 TGTTTGGCAAAGCGGACTTC 59.616 50.000 13.94 0.00 34.05 3.01
68 69 0.385390 CTGTTTGGCAAAGCGGACTT 59.615 50.000 13.94 0.00 37.90 3.01
69 70 1.455383 CCTGTTTGGCAAAGCGGACT 61.455 55.000 13.94 0.00 0.00 3.85
70 71 1.007387 CCTGTTTGGCAAAGCGGAC 60.007 57.895 13.94 2.16 0.00 4.79
71 72 0.753479 TTCCTGTTTGGCAAAGCGGA 60.753 50.000 20.30 20.30 35.26 5.54
72 73 0.103937 TTTCCTGTTTGGCAAAGCGG 59.896 50.000 13.94 15.92 35.26 5.52
73 74 1.208259 GTTTCCTGTTTGGCAAAGCG 58.792 50.000 13.94 7.16 35.26 4.68
74 75 1.208259 CGTTTCCTGTTTGGCAAAGC 58.792 50.000 13.94 9.04 35.26 3.51
75 76 1.208259 GCGTTTCCTGTTTGGCAAAG 58.792 50.000 13.94 2.02 35.26 2.77
76 77 0.526524 CGCGTTTCCTGTTTGGCAAA 60.527 50.000 8.93 8.93 35.26 3.68
77 78 1.064946 CGCGTTTCCTGTTTGGCAA 59.935 52.632 0.00 0.00 35.26 4.52
78 79 1.658686 AACGCGTTTCCTGTTTGGCA 61.659 50.000 20.79 0.00 35.26 4.92
79 80 0.526739 AAACGCGTTTCCTGTTTGGC 60.527 50.000 30.36 0.00 34.73 4.52
80 81 1.915952 AAAACGCGTTTCCTGTTTGG 58.084 45.000 34.77 0.00 36.07 3.28
81 82 2.461120 CGTAAAACGCGTTTCCTGTTTG 59.539 45.455 34.77 17.40 36.07 2.93
82 83 2.707392 CGTAAAACGCGTTTCCTGTTT 58.293 42.857 34.77 21.40 37.41 2.83
83 84 2.372148 CGTAAAACGCGTTTCCTGTT 57.628 45.000 34.77 22.10 33.65 3.16
93 94 3.710470 GCACTTGCTGAACGTAAAACGC 61.710 50.000 0.00 0.00 40.97 4.84
94 95 2.034076 GCACTTGCTGAACGTAAAACG 58.966 47.619 0.00 0.00 42.17 3.60
95 96 2.381589 GGCACTTGCTGAACGTAAAAC 58.618 47.619 0.38 0.00 41.70 2.43
96 97 1.335496 GGGCACTTGCTGAACGTAAAA 59.665 47.619 0.38 0.00 41.70 1.52
97 98 0.948678 GGGCACTTGCTGAACGTAAA 59.051 50.000 0.38 0.00 41.70 2.01
98 99 0.107831 AGGGCACTTGCTGAACGTAA 59.892 50.000 0.38 0.00 41.70 3.18
99 100 0.107831 AAGGGCACTTGCTGAACGTA 59.892 50.000 0.00 0.00 41.70 3.57
100 101 0.751643 AAAGGGCACTTGCTGAACGT 60.752 50.000 0.00 0.00 41.70 3.99
101 102 1.234821 TAAAGGGCACTTGCTGAACG 58.765 50.000 0.00 0.00 41.70 3.95
102 103 2.288213 GGTTAAAGGGCACTTGCTGAAC 60.288 50.000 0.00 4.76 41.70 3.18
103 104 1.960689 GGTTAAAGGGCACTTGCTGAA 59.039 47.619 0.00 0.00 41.70 3.02
104 105 1.144913 AGGTTAAAGGGCACTTGCTGA 59.855 47.619 0.00 0.00 41.70 4.26
105 106 1.620822 AGGTTAAAGGGCACTTGCTG 58.379 50.000 0.00 0.00 41.70 4.41
106 107 3.739401 ATAGGTTAAAGGGCACTTGCT 57.261 42.857 0.00 0.00 41.70 3.91
107 108 5.190677 TCTAATAGGTTAAAGGGCACTTGC 58.809 41.667 0.00 0.00 36.93 4.01
108 109 5.297029 GCTCTAATAGGTTAAAGGGCACTTG 59.703 44.000 0.00 0.00 36.93 3.16
109 110 5.045140 TGCTCTAATAGGTTAAAGGGCACTT 60.045 40.000 0.00 0.00 38.99 3.16
110 111 4.473559 TGCTCTAATAGGTTAAAGGGCACT 59.526 41.667 0.00 0.00 0.00 4.40
111 112 4.777463 TGCTCTAATAGGTTAAAGGGCAC 58.223 43.478 0.00 0.00 0.00 5.01
112 113 5.444744 TTGCTCTAATAGGTTAAAGGGCA 57.555 39.130 0.00 0.00 0.00 5.36
113 114 6.773200 AGATTTGCTCTAATAGGTTAAAGGGC 59.227 38.462 0.00 0.00 30.26 5.19
114 115 7.229506 CCAGATTTGCTCTAATAGGTTAAAGGG 59.770 40.741 0.00 0.00 31.13 3.95
115 116 7.255277 GCCAGATTTGCTCTAATAGGTTAAAGG 60.255 40.741 0.00 0.00 31.13 3.11
116 117 7.255277 GGCCAGATTTGCTCTAATAGGTTAAAG 60.255 40.741 0.00 0.00 31.13 1.85
117 118 6.546034 GGCCAGATTTGCTCTAATAGGTTAAA 59.454 38.462 0.00 0.00 31.13 1.52
118 119 6.062095 GGCCAGATTTGCTCTAATAGGTTAA 58.938 40.000 0.00 0.00 31.13 2.01
119 120 5.456186 GGGCCAGATTTGCTCTAATAGGTTA 60.456 44.000 4.39 0.00 31.13 2.85
120 121 4.464947 GGCCAGATTTGCTCTAATAGGTT 58.535 43.478 0.00 0.00 31.13 3.50
121 122 3.181439 GGGCCAGATTTGCTCTAATAGGT 60.181 47.826 4.39 0.00 31.13 3.08
122 123 3.073650 AGGGCCAGATTTGCTCTAATAGG 59.926 47.826 6.18 0.00 37.92 2.57
123 124 4.202398 TGAGGGCCAGATTTGCTCTAATAG 60.202 45.833 6.18 0.00 40.39 1.73
124 125 3.716353 TGAGGGCCAGATTTGCTCTAATA 59.284 43.478 6.18 0.00 40.39 0.98
125 126 2.511218 TGAGGGCCAGATTTGCTCTAAT 59.489 45.455 6.18 0.00 40.39 1.73
126 127 1.915489 TGAGGGCCAGATTTGCTCTAA 59.085 47.619 6.18 0.00 40.39 2.10
127 128 1.583556 TGAGGGCCAGATTTGCTCTA 58.416 50.000 6.18 0.00 40.39 2.43
128 129 0.700564 TTGAGGGCCAGATTTGCTCT 59.299 50.000 6.18 0.00 43.83 4.09
129 130 1.549203 TTTGAGGGCCAGATTTGCTC 58.451 50.000 6.18 0.00 0.00 4.26
130 131 1.897802 CTTTTGAGGGCCAGATTTGCT 59.102 47.619 6.18 0.00 0.00 3.91
131 132 1.895131 TCTTTTGAGGGCCAGATTTGC 59.105 47.619 6.18 0.00 0.00 3.68
132 133 2.232208 GGTCTTTTGAGGGCCAGATTTG 59.768 50.000 6.18 0.00 0.00 2.32
133 134 2.529632 GGTCTTTTGAGGGCCAGATTT 58.470 47.619 6.18 0.00 0.00 2.17
134 135 1.614317 CGGTCTTTTGAGGGCCAGATT 60.614 52.381 6.18 0.00 0.00 2.40
135 136 0.035056 CGGTCTTTTGAGGGCCAGAT 60.035 55.000 6.18 0.00 0.00 2.90
136 137 1.374947 CGGTCTTTTGAGGGCCAGA 59.625 57.895 6.18 0.00 0.00 3.86
137 138 2.335712 GCGGTCTTTTGAGGGCCAG 61.336 63.158 6.18 0.00 0.00 4.85
138 139 2.282180 GCGGTCTTTTGAGGGCCA 60.282 61.111 6.18 0.00 0.00 5.36
139 140 3.431725 CGCGGTCTTTTGAGGGCC 61.432 66.667 0.00 0.00 0.00 5.80
140 141 4.103103 GCGCGGTCTTTTGAGGGC 62.103 66.667 8.83 0.00 35.54 5.19
141 142 3.788766 CGCGCGGTCTTTTGAGGG 61.789 66.667 24.84 0.00 0.00 4.30
142 143 4.445545 GCGCGCGGTCTTTTGAGG 62.446 66.667 33.06 0.00 0.00 3.86
143 144 4.776953 CGCGCGCGGTCTTTTGAG 62.777 66.667 43.28 13.53 35.56 3.02
169 170 1.754234 GGTGTGATGGGTCCATGCC 60.754 63.158 7.29 1.25 36.70 4.40
170 171 0.749454 GAGGTGTGATGGGTCCATGC 60.749 60.000 7.29 1.23 36.70 4.06
171 172 0.620030 TGAGGTGTGATGGGTCCATG 59.380 55.000 7.29 0.00 36.70 3.66
172 173 1.213678 CATGAGGTGTGATGGGTCCAT 59.786 52.381 1.54 1.54 39.69 3.41
173 174 0.620030 CATGAGGTGTGATGGGTCCA 59.380 55.000 0.00 0.00 0.00 4.02
174 175 0.107017 CCATGAGGTGTGATGGGTCC 60.107 60.000 0.00 0.00 36.26 4.46
175 176 3.483954 CCATGAGGTGTGATGGGTC 57.516 57.895 0.00 0.00 36.26 4.46
178 179 1.820906 CGCCCATGAGGTGTGATGG 60.821 63.158 0.00 0.00 41.64 3.51
179 180 3.817787 CGCCCATGAGGTGTGATG 58.182 61.111 0.00 0.00 41.64 3.07
185 186 1.603455 CCAAACACGCCCATGAGGT 60.603 57.895 0.00 0.00 38.26 3.85
186 187 1.178534 AACCAAACACGCCCATGAGG 61.179 55.000 0.00 0.00 39.47 3.86
187 188 0.039256 CAACCAAACACGCCCATGAG 60.039 55.000 0.00 0.00 0.00 2.90
188 189 2.037053 CAACCAAACACGCCCATGA 58.963 52.632 0.00 0.00 0.00 3.07
229 230 2.163613 GGATCAAATTTTTCCCGCTCGT 59.836 45.455 5.85 0.00 0.00 4.18
515 524 0.108329 GCGAACGGAGGAAGAATGGA 60.108 55.000 0.00 0.00 0.00 3.41
557 566 1.585006 CTTACCTGCTCGTCGGTGT 59.415 57.895 0.00 0.00 34.76 4.16
608 617 3.382832 CGGTGAAGGAGCTCCGGT 61.383 66.667 26.95 18.99 40.25 5.28
667 677 1.228644 ACCATGGCTGCAGCTTGAA 60.229 52.632 35.82 20.28 41.70 2.69
685 695 0.902531 GGGGATTGAACTCACGGAGA 59.097 55.000 7.76 0.00 33.32 3.71
689 699 3.347216 AGAAATGGGGATTGAACTCACG 58.653 45.455 0.00 0.00 0.00 4.35
705 715 7.122715 TCTAGCTAGAAGGAACAGAGAGAAAT 58.877 38.462 21.26 0.00 0.00 2.17
784 794 3.939740 ACCAACCATATCAGCTCACAT 57.060 42.857 0.00 0.00 0.00 3.21
858 868 9.463902 ACTTCAAACTCTACTACTAATCTAGCA 57.536 33.333 0.00 0.00 0.00 3.49
963 973 9.486497 CTATGAGCAGAAACATACATCTACAAT 57.514 33.333 0.00 0.00 0.00 2.71
998 1008 7.551974 GCTTCATCACTATCATACCAAGCATAT 59.448 37.037 0.00 0.00 35.01 1.78
1006 1016 5.106791 GCACATGCTTCATCACTATCATACC 60.107 44.000 0.00 0.00 38.21 2.73
1067 1077 3.673902 TCGGACAATTCATGAAAGCAGA 58.326 40.909 13.09 5.72 0.00 4.26
1079 1090 2.158841 GCACACAACGTATCGGACAATT 59.841 45.455 0.00 0.00 0.00 2.32
1088 1099 2.930040 GTGAGCATAGCACACAACGTAT 59.070 45.455 13.34 0.00 46.31 3.06
1091 1102 3.955429 GTGAGCATAGCACACAACG 57.045 52.632 13.34 0.00 46.31 4.10
1113 1124 3.067040 TCCTACAATCGTAGCACGCATTA 59.933 43.478 4.15 0.00 43.33 1.90
1165 1176 3.124921 CGGACACGACAATGGCCC 61.125 66.667 0.00 0.00 46.23 5.80
1457 1486 2.727123 TCAAGTGCACCTCCTTGAAA 57.273 45.000 14.63 0.00 42.92 2.69
1490 1520 2.233922 CCCATAGAACTCGAACACCTGT 59.766 50.000 0.00 0.00 0.00 4.00
1507 1537 1.001641 GCAGACACCTCTTGCCCAT 60.002 57.895 0.00 0.00 0.00 4.00
1541 1571 2.251818 CTTCTCCACTTCCTCAGGTGA 58.748 52.381 0.00 0.00 35.69 4.02
1635 1665 1.591703 CGTAGTGCTCTGCCTCCAA 59.408 57.895 0.00 0.00 0.00 3.53
1699 1729 1.898863 AGGAGTAGGCAATGGTGGAT 58.101 50.000 0.00 0.00 0.00 3.41
1927 1957 3.241530 ACAGCGGGCTTGTCAGGA 61.242 61.111 0.00 0.00 0.00 3.86
2034 2064 1.679944 CCTTCACCGCCTCATTCATGT 60.680 52.381 0.00 0.00 0.00 3.21
2040 2070 1.613630 ACCTCCTTCACCGCCTCAT 60.614 57.895 0.00 0.00 0.00 2.90
2073 2103 3.710722 CGAGGGGCTTGCACTCCT 61.711 66.667 0.00 0.00 0.00 3.69
2115 2145 0.770166 TCCACCCTGGGTCATGACAA 60.770 55.000 26.47 13.47 38.32 3.18
2141 2171 1.220206 CTGCCATGAGAGCCTCGTT 59.780 57.895 0.00 0.00 32.35 3.85
2167 2197 1.679139 CCTTGTTGTCAAGCAGGTGA 58.321 50.000 2.85 0.00 46.74 4.02
2314 2344 2.126618 GTCATCGTCGTCGCCACA 60.127 61.111 0.00 0.00 36.96 4.17
2337 2382 4.326278 AGCTACACAAAATGTATGTCGTCG 59.674 41.667 0.00 0.00 43.01 5.12
2427 2472 0.467290 ACCACCGCAAGTTCACCATT 60.467 50.000 0.00 0.00 0.00 3.16
2518 2563 7.395617 AGAGAAGTAAGCATGCATGATCATAT 58.604 34.615 30.64 11.51 0.00 1.78
2561 2607 0.588252 AGCAAGCAAAGTAGCACACG 59.412 50.000 0.00 0.00 36.85 4.49
2694 2741 0.030504 CAACGCCACTTGTGCATTGA 59.969 50.000 0.00 0.00 0.00 2.57
2712 2759 8.003044 ACCCTCTATAGTTGTAGTTGCTATACA 58.997 37.037 0.00 0.00 0.00 2.29
2798 2845 3.034030 GGCACTGTCAACACTGCC 58.966 61.111 15.10 15.10 44.41 4.85
2806 2853 4.577152 CCAACCTTGGCACTGTCA 57.423 55.556 0.00 0.00 42.21 3.58
2841 2888 1.899814 ACTGACGATCCACCTTAGCAA 59.100 47.619 0.00 0.00 0.00 3.91
2884 2931 1.754803 ACGAACTGGGCGAAGATGATA 59.245 47.619 0.00 0.00 0.00 2.15
2913 2960 3.353836 GCCAACGCCACGACACAT 61.354 61.111 0.00 0.00 0.00 3.21
2930 2977 1.003972 ACAACGATCACAACAAGCACG 60.004 47.619 0.00 0.00 0.00 5.34
2936 2983 2.912690 TACCCACAACGATCACAACA 57.087 45.000 0.00 0.00 0.00 3.33
2938 2985 2.147958 GCTTACCCACAACGATCACAA 58.852 47.619 0.00 0.00 0.00 3.33
2946 2993 1.607148 GTTGGTGAGCTTACCCACAAC 59.393 52.381 23.81 17.26 40.09 3.32
3000 3047 0.179184 AACACGACGTTTGGTTGCAC 60.179 50.000 0.00 0.00 32.35 4.57
3081 3129 3.155167 CCTGCGTCCCTAGTCCCC 61.155 72.222 0.00 0.00 0.00 4.81
3152 3200 2.408271 TGCATAGCCTTCTCAACCTG 57.592 50.000 0.00 0.00 0.00 4.00
3153 3201 3.285484 CATTGCATAGCCTTCTCAACCT 58.715 45.455 0.00 0.00 0.00 3.50
3204 3252 1.202758 CGGAAGCTAACATATGGGGCA 60.203 52.381 7.80 0.00 0.00 5.36
3224 3272 2.029560 TGGATATGAGAGACGCAGATGC 60.030 50.000 0.00 0.00 37.78 3.91
3251 3300 1.990563 ACGTAGCGTTGTATGAGTTGC 59.009 47.619 0.00 0.00 36.35 4.17
3252 3301 7.008538 TGTTTATACGTAGCGTTGTATGAGTTG 59.991 37.037 0.08 0.00 41.54 3.16
3260 3309 2.916716 CCGTGTTTATACGTAGCGTTGT 59.083 45.455 0.08 0.00 42.24 3.32
3281 3330 4.634004 TGATCCAATGAACCGTGTATTGAC 59.366 41.667 8.74 3.22 34.55 3.18
3286 3335 2.355310 GGGTGATCCAATGAACCGTGTA 60.355 50.000 0.00 0.00 33.24 2.90
3289 3338 0.991920 AGGGTGATCCAATGAACCGT 59.008 50.000 0.00 0.00 38.24 4.83
3290 3339 2.128771 AAGGGTGATCCAATGAACCG 57.871 50.000 0.00 0.00 38.24 4.44
3291 3340 3.430453 TGAAAGGGTGATCCAATGAACC 58.570 45.455 0.00 0.00 38.24 3.62
3298 3347 6.158520 TCATTAAGAGATGAAAGGGTGATCCA 59.841 38.462 0.00 0.00 33.88 3.41
3315 3364 5.164620 TCAGTTGGACATGCTCATTAAGA 57.835 39.130 0.00 0.00 0.00 2.10
3318 3367 4.558226 ACTCAGTTGGACATGCTCATTA 57.442 40.909 0.00 0.00 0.00 1.90
3319 3368 3.430042 ACTCAGTTGGACATGCTCATT 57.570 42.857 0.00 0.00 0.00 2.57
3321 3370 2.632512 TGTACTCAGTTGGACATGCTCA 59.367 45.455 0.00 0.00 0.00 4.26
3322 3371 3.319137 TGTACTCAGTTGGACATGCTC 57.681 47.619 0.00 0.00 0.00 4.26
3324 3373 2.604914 CGATGTACTCAGTTGGACATGC 59.395 50.000 0.00 0.00 32.75 4.06
3325 3374 3.190079 CCGATGTACTCAGTTGGACATG 58.810 50.000 0.00 0.00 32.75 3.21
3326 3375 2.418746 GCCGATGTACTCAGTTGGACAT 60.419 50.000 0.00 0.00 35.26 3.06
3327 3376 1.067142 GCCGATGTACTCAGTTGGACA 60.067 52.381 0.00 0.00 0.00 4.02
3328 3377 1.641577 GCCGATGTACTCAGTTGGAC 58.358 55.000 0.00 0.00 0.00 4.02
3329 3378 0.172578 CGCCGATGTACTCAGTTGGA 59.827 55.000 0.00 0.00 0.00 3.53
3333 3388 1.880675 CTATCCGCCGATGTACTCAGT 59.119 52.381 0.00 0.00 0.00 3.41
3335 3390 1.607148 CACTATCCGCCGATGTACTCA 59.393 52.381 0.00 0.00 0.00 3.41
3340 3395 0.107897 TTTGCACTATCCGCCGATGT 60.108 50.000 0.00 0.00 0.00 3.06
3395 3451 2.826128 GTGATTTCCTCCACCCTTTTCC 59.174 50.000 0.00 0.00 0.00 3.13
3396 3452 2.826128 GGTGATTTCCTCCACCCTTTTC 59.174 50.000 0.00 0.00 45.30 2.29
3443 3520 0.321210 ACAACCGCATCAATGACCGA 60.321 50.000 6.70 0.00 0.00 4.69
3518 3597 1.425412 CCTTAACAGACGGTTCCACG 58.575 55.000 0.00 0.00 40.96 4.94
3530 3609 3.388024 ACAACTCAGACTCTGCCTTAACA 59.612 43.478 0.62 0.00 0.00 2.41
3533 3612 3.193691 GCTACAACTCAGACTCTGCCTTA 59.806 47.826 0.62 0.00 0.00 2.69
3537 3616 3.311486 AAGCTACAACTCAGACTCTGC 57.689 47.619 0.62 0.00 0.00 4.26
3563 3642 1.963515 TGCTTACTCTGCAGTCTGTCA 59.036 47.619 14.67 3.60 35.31 3.58
3619 3699 2.542907 AAACAAGGGCACGACAGCG 61.543 57.895 0.00 0.00 44.79 5.18
3622 3702 2.485795 GGCAAACAAGGGCACGACA 61.486 57.895 0.00 0.00 0.00 4.35
3628 3708 2.644992 CGTGAGGCAAACAAGGGC 59.355 61.111 0.00 0.00 0.00 5.19
3629 3709 2.644992 GCGTGAGGCAAACAAGGG 59.355 61.111 0.00 0.00 42.87 3.95
3675 3755 2.110213 ACCGCAAGAACGCCAAGA 59.890 55.556 0.00 0.00 43.02 3.02
3682 3762 2.617274 GCACCTCCACCGCAAGAAC 61.617 63.158 0.00 0.00 43.02 3.01
3758 3838 1.269465 CGTGCCAGATGATCTCGATGT 60.269 52.381 0.00 0.00 0.00 3.06
3787 3869 1.444383 GCTGACTGCACGACGATCA 60.444 57.895 0.00 0.00 42.31 2.92
3789 3871 2.504899 CGCTGACTGCACGACGAT 60.505 61.111 0.00 0.00 43.06 3.73
3793 3875 4.724602 GAGGCGCTGACTGCACGA 62.725 66.667 7.64 0.00 43.06 4.35
3819 3901 4.680537 AGTGAGGGAGACGGCGGT 62.681 66.667 13.24 0.00 0.00 5.68
3825 3907 2.183046 GCAGCGAGTGAGGGAGAC 59.817 66.667 0.00 0.00 0.00 3.36
3861 3943 1.313091 ACGCTCGAGTATGAGGCACA 61.313 55.000 15.13 0.00 36.47 4.57
3869 3951 1.428219 CACCGACACGCTCGAGTAT 59.572 57.895 15.13 0.00 46.14 2.12
3919 4012 1.906574 TCTGCTCCGGAAGTGGTATTT 59.093 47.619 5.23 0.00 0.00 1.40
3920 4013 1.207329 GTCTGCTCCGGAAGTGGTATT 59.793 52.381 5.23 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.