Multiple sequence alignment - TraesCS6B01G407300

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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 TraesCS6B01G407300 chr6B 100.000 4061 0 0 1 4061 681831750 681835810 0.000000e+00 7500.0
1 TraesCS6B01G407300 chr6B 95.463 3857 135 13 221 4061 681170278 681174110 0.000000e+00 6117.0
2 TraesCS6B01G407300 chr6B 81.103 852 157 4 1025 1873 680931394 680932244 0.000000e+00 678.0
3 TraesCS6B01G407300 chr6B 79.234 992 180 19 1052 2030 680737183 680736205 0.000000e+00 667.0
4 TraesCS6B01G407300 chr6B 79.818 659 116 11 2161 2813 681077805 681078452 7.950000e-127 464.0
5 TraesCS6B01G407300 chr6B 80.989 526 74 12 3557 4057 710142520 710143044 1.060000e-105 394.0
6 TraesCS6B01G407300 chr6B 82.004 489 61 12 3594 4057 710232898 710232412 1.370000e-104 390.0
7 TraesCS6B01G407300 chr6D 89.824 3862 328 27 221 4059 449503163 449506982 0.000000e+00 4894.0
8 TraesCS6B01G407300 chr6D 90.137 3508 283 23 224 3722 449766811 449770264 0.000000e+00 4503.0
9 TraesCS6B01G407300 chr6D 80.230 521 78 11 3557 4058 420161528 420161014 6.410000e-98 368.0
10 TraesCS6B01G407300 chr6A 89.166 3655 308 43 221 3843 595327829 595331427 0.000000e+00 4475.0
11 TraesCS6B01G407300 chr6A 79.725 947 172 14 1046 1981 594990110 594989173 0.000000e+00 667.0
12 TraesCS6B01G407300 chr6A 78.941 774 128 24 1870 2635 595414869 595415615 1.010000e-135 494.0
13 TraesCS6B01G407300 chr6A 77.912 661 124 17 2161 2813 595179578 595180224 3.810000e-105 392.0
14 TraesCS6B01G407300 chr6A 93.478 46 3 0 3124 3169 563262581 563262536 7.280000e-08 69.4
15 TraesCS6B01G407300 chrUn 81.852 810 147 0 1052 1861 214050846 214050037 0.000000e+00 682.0
16 TraesCS6B01G407300 chrUn 81.522 828 153 0 1025 1852 240294212 240295039 0.000000e+00 682.0
17 TraesCS6B01G407300 chr5D 83.366 517 62 8 3557 4049 9391608 9392124 1.330000e-124 457.0
18 TraesCS6B01G407300 chr5D 97.817 229 4 1 1 229 328979341 328979568 1.060000e-105 394.0
19 TraesCS6B01G407300 chr7B 98.268 231 4 0 1 231 205926944 205926714 4.890000e-109 405.0
20 TraesCS6B01G407300 chr7B 98.673 226 3 0 1 226 388959284 388959059 6.320000e-108 401.0
21 TraesCS6B01G407300 chr7B 95.102 245 9 3 1 244 39606201 39606443 2.290000e-102 383.0
22 TraesCS6B01G407300 chr2B 99.103 223 2 0 1 223 393803325 393803547 6.320000e-108 401.0
23 TraesCS6B01G407300 chr1D 98.673 226 2 1 1 225 208318863 208319088 2.270000e-107 399.0
24 TraesCS6B01G407300 chr5B 81.061 528 72 14 3556 4059 594754130 594753607 2.940000e-106 396.0
25 TraesCS6B01G407300 chr2D 98.655 223 3 0 1 223 204148758 204148980 2.940000e-106 396.0
26 TraesCS6B01G407300 chr2D 80.779 411 54 12 3557 3942 383561663 383561253 8.530000e-77 298.0
27 TraesCS6B01G407300 chr7D 97.009 234 5 2 1 233 98206540 98206308 3.810000e-105 392.0
28 TraesCS6B01G407300 chr1B 95.102 245 7 5 1 244 461370180 461369940 8.240000e-102 381.0
29 TraesCS6B01G407300 chr1B 80.702 513 72 14 3557 4044 402785790 402785280 1.380000e-99 374.0
30 TraesCS6B01G407300 chr2A 79.769 519 76 16 3565 4059 706267144 706266631 2.320000e-92 350.0
31 TraesCS6B01G407300 chr1A 78.912 294 38 9 3556 3828 99339247 99339537 1.160000e-40 178.0


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 TraesCS6B01G407300 chr6B 681831750 681835810 4060 False 7500 7500 100.000 1 4061 1 chr6B.!!$F4 4060
1 TraesCS6B01G407300 chr6B 681170278 681174110 3832 False 6117 6117 95.463 221 4061 1 chr6B.!!$F3 3840
2 TraesCS6B01G407300 chr6B 680931394 680932244 850 False 678 678 81.103 1025 1873 1 chr6B.!!$F1 848
3 TraesCS6B01G407300 chr6B 680736205 680737183 978 True 667 667 79.234 1052 2030 1 chr6B.!!$R1 978
4 TraesCS6B01G407300 chr6B 681077805 681078452 647 False 464 464 79.818 2161 2813 1 chr6B.!!$F2 652
5 TraesCS6B01G407300 chr6B 710142520 710143044 524 False 394 394 80.989 3557 4057 1 chr6B.!!$F5 500
6 TraesCS6B01G407300 chr6D 449503163 449506982 3819 False 4894 4894 89.824 221 4059 1 chr6D.!!$F1 3838
7 TraesCS6B01G407300 chr6D 449766811 449770264 3453 False 4503 4503 90.137 224 3722 1 chr6D.!!$F2 3498
8 TraesCS6B01G407300 chr6D 420161014 420161528 514 True 368 368 80.230 3557 4058 1 chr6D.!!$R1 501
9 TraesCS6B01G407300 chr6A 595327829 595331427 3598 False 4475 4475 89.166 221 3843 1 chr6A.!!$F2 3622
10 TraesCS6B01G407300 chr6A 594989173 594990110 937 True 667 667 79.725 1046 1981 1 chr6A.!!$R2 935
11 TraesCS6B01G407300 chr6A 595414869 595415615 746 False 494 494 78.941 1870 2635 1 chr6A.!!$F3 765
12 TraesCS6B01G407300 chr6A 595179578 595180224 646 False 392 392 77.912 2161 2813 1 chr6A.!!$F1 652
13 TraesCS6B01G407300 chrUn 214050037 214050846 809 True 682 682 81.852 1052 1861 1 chrUn.!!$R1 809
14 TraesCS6B01G407300 chrUn 240294212 240295039 827 False 682 682 81.522 1025 1852 1 chrUn.!!$F1 827
15 TraesCS6B01G407300 chr5D 9391608 9392124 516 False 457 457 83.366 3557 4049 1 chr5D.!!$F1 492
16 TraesCS6B01G407300 chr5B 594753607 594754130 523 True 396 396 81.061 3556 4059 1 chr5B.!!$R1 503
17 TraesCS6B01G407300 chr1B 402785280 402785790 510 True 374 374 80.702 3557 4044 1 chr1B.!!$R1 487
18 TraesCS6B01G407300 chr2A 706266631 706267144 513 True 350 350 79.769 3565 4059 1 chr2A.!!$R1 494

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
147 148 0.035820 TAAACATCGTGTCCCCTGCC 60.036 55.000 0.00 0.00 0.00 4.85 F
647 654 0.038159 GACGCTGTGTTGCCTAGAGT 60.038 55.000 0.00 0.00 0.00 3.24 F
895 903 1.072331 GTCCATGTGTTGAGGTGAGGT 59.928 52.381 0.00 0.00 0.00 3.85 F
1595 1618 1.278337 GTCACGTTGTGCGCATTCA 59.722 52.632 15.91 4.58 46.11 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1009 1017 0.336737 AGGTCCTCGAAGTGATCCCT 59.663 55.0 0.00 0.00 0.00 4.20 R
1595 1618 2.198304 GAGACCCGGGGCACAAATCT 62.198 60.0 32.91 18.91 0.00 2.40 R
2739 2789 0.179156 CCATCAACGTGCAATCCAGC 60.179 55.0 0.00 0.00 0.00 4.85 R
3245 3318 0.316204 ACACATGCAAAGCAAGAGGC 59.684 50.0 0.92 0.00 43.62 4.70 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
21 22 4.965200 CATAGGCTAGCTTCTAGGGTTT 57.035 45.455 15.72 0.00 0.00 3.27
23 24 6.031751 CATAGGCTAGCTTCTAGGGTTTAG 57.968 45.833 15.72 0.00 0.00 1.85
24 25 2.701423 AGGCTAGCTTCTAGGGTTTAGC 59.299 50.000 15.72 0.00 34.32 3.09
25 26 2.224329 GGCTAGCTTCTAGGGTTTAGCC 60.224 54.545 15.72 15.56 44.26 3.93
26 27 2.701423 GCTAGCTTCTAGGGTTTAGCCT 59.299 50.000 7.70 5.72 37.43 4.58
27 28 3.243941 GCTAGCTTCTAGGGTTTAGCCTC 60.244 52.174 7.70 0.00 37.43 4.70
28 29 3.123392 AGCTTCTAGGGTTTAGCCTCT 57.877 47.619 3.32 0.00 37.43 3.69
29 30 4.267341 AGCTTCTAGGGTTTAGCCTCTA 57.733 45.455 3.32 0.00 37.43 2.43
30 31 3.962063 AGCTTCTAGGGTTTAGCCTCTAC 59.038 47.826 3.32 0.00 37.43 2.59
31 32 3.243468 GCTTCTAGGGTTTAGCCTCTACG 60.243 52.174 3.32 0.00 37.43 3.51
32 33 3.939740 TCTAGGGTTTAGCCTCTACGA 57.060 47.619 3.32 0.00 37.43 3.43
33 34 4.450305 TCTAGGGTTTAGCCTCTACGAT 57.550 45.455 3.32 0.00 37.43 3.73
34 35 4.396522 TCTAGGGTTTAGCCTCTACGATC 58.603 47.826 3.32 0.00 37.43 3.69
35 36 3.315880 AGGGTTTAGCCTCTACGATCT 57.684 47.619 0.00 0.00 37.43 2.75
36 37 3.224269 AGGGTTTAGCCTCTACGATCTC 58.776 50.000 0.00 0.00 37.43 2.75
37 38 2.030981 GGGTTTAGCCTCTACGATCTCG 60.031 54.545 0.00 0.00 40.54 4.04
38 39 4.551164 GGGTTTAGCCTCTACGATCTCGT 61.551 52.174 10.40 10.40 45.75 4.18
39 40 6.558908 GGGTTTAGCCTCTACGATCTCGTG 62.559 54.167 15.08 5.81 44.52 4.35
54 55 4.703645 TCTCGTGGTAGATCAACTCTTG 57.296 45.455 0.00 0.00 35.28 3.02
55 56 4.079970 TCTCGTGGTAGATCAACTCTTGT 58.920 43.478 0.00 0.00 35.28 3.16
56 57 5.250982 TCTCGTGGTAGATCAACTCTTGTA 58.749 41.667 0.00 0.00 35.28 2.41
57 58 5.708697 TCTCGTGGTAGATCAACTCTTGTAA 59.291 40.000 0.00 0.00 35.28 2.41
58 59 6.377429 TCTCGTGGTAGATCAACTCTTGTAAT 59.623 38.462 0.00 0.00 35.28 1.89
59 60 7.555195 TCTCGTGGTAGATCAACTCTTGTAATA 59.445 37.037 0.00 0.00 35.28 0.98
60 61 7.478322 TCGTGGTAGATCAACTCTTGTAATAC 58.522 38.462 0.00 0.00 35.28 1.89
61 62 7.338703 TCGTGGTAGATCAACTCTTGTAATACT 59.661 37.037 0.00 0.00 35.28 2.12
62 63 7.644551 CGTGGTAGATCAACTCTTGTAATACTC 59.355 40.741 0.00 0.00 35.28 2.59
63 64 8.467598 GTGGTAGATCAACTCTTGTAATACTCA 58.532 37.037 0.00 0.00 35.28 3.41
64 65 9.201989 TGGTAGATCAACTCTTGTAATACTCAT 57.798 33.333 0.00 0.00 35.28 2.90
84 85 8.325421 ACTCATATCATCAAGATCAATCAAGC 57.675 34.615 0.00 0.00 38.19 4.01
85 86 7.937394 ACTCATATCATCAAGATCAATCAAGCA 59.063 33.333 0.00 0.00 38.19 3.91
86 87 8.324163 TCATATCATCAAGATCAATCAAGCAG 57.676 34.615 0.00 0.00 38.19 4.24
87 88 7.390718 TCATATCATCAAGATCAATCAAGCAGG 59.609 37.037 0.00 0.00 38.19 4.85
88 89 5.106876 TCATCAAGATCAATCAAGCAGGA 57.893 39.130 0.00 0.00 0.00 3.86
89 90 5.503002 TCATCAAGATCAATCAAGCAGGAA 58.497 37.500 0.00 0.00 0.00 3.36
90 91 5.589050 TCATCAAGATCAATCAAGCAGGAAG 59.411 40.000 0.00 0.00 0.00 3.46
91 92 4.914983 TCAAGATCAATCAAGCAGGAAGT 58.085 39.130 0.00 0.00 0.00 3.01
92 93 6.053632 TCAAGATCAATCAAGCAGGAAGTA 57.946 37.500 0.00 0.00 0.00 2.24
93 94 6.111382 TCAAGATCAATCAAGCAGGAAGTAG 58.889 40.000 0.00 0.00 0.00 2.57
94 95 5.033589 AGATCAATCAAGCAGGAAGTAGG 57.966 43.478 0.00 0.00 0.00 3.18
95 96 3.634397 TCAATCAAGCAGGAAGTAGGG 57.366 47.619 0.00 0.00 0.00 3.53
96 97 2.912956 TCAATCAAGCAGGAAGTAGGGT 59.087 45.455 0.00 0.00 0.00 4.34
97 98 4.101114 TCAATCAAGCAGGAAGTAGGGTA 58.899 43.478 0.00 0.00 0.00 3.69
98 99 4.721776 TCAATCAAGCAGGAAGTAGGGTAT 59.278 41.667 0.00 0.00 0.00 2.73
99 100 5.191722 TCAATCAAGCAGGAAGTAGGGTATT 59.808 40.000 0.00 0.00 0.00 1.89
100 101 6.385759 TCAATCAAGCAGGAAGTAGGGTATTA 59.614 38.462 0.00 0.00 0.00 0.98
101 102 5.609533 TCAAGCAGGAAGTAGGGTATTAC 57.390 43.478 0.00 0.00 0.00 1.89
102 103 4.407945 TCAAGCAGGAAGTAGGGTATTACC 59.592 45.833 4.11 4.11 37.60 2.85
103 104 4.282292 AGCAGGAAGTAGGGTATTACCT 57.718 45.455 12.54 2.07 44.75 3.08
104 105 4.224762 AGCAGGAAGTAGGGTATTACCTC 58.775 47.826 12.54 2.11 42.09 3.85
105 106 3.324268 GCAGGAAGTAGGGTATTACCTCC 59.676 52.174 12.54 10.66 42.09 4.30
106 107 4.553678 CAGGAAGTAGGGTATTACCTCCA 58.446 47.826 16.39 0.80 42.09 3.86
107 108 5.155905 CAGGAAGTAGGGTATTACCTCCAT 58.844 45.833 16.39 4.17 42.09 3.41
108 109 5.246429 CAGGAAGTAGGGTATTACCTCCATC 59.754 48.000 16.39 8.41 42.09 3.51
109 110 4.220163 GGAAGTAGGGTATTACCTCCATCG 59.780 50.000 12.54 0.00 42.09 3.84
110 111 4.736611 AGTAGGGTATTACCTCCATCGA 57.263 45.455 12.54 0.00 42.09 3.59
111 112 4.664392 AGTAGGGTATTACCTCCATCGAG 58.336 47.826 12.54 0.00 42.09 4.04
112 113 3.897657 AGGGTATTACCTCCATCGAGA 57.102 47.619 12.54 0.00 38.52 4.04
113 114 3.768878 AGGGTATTACCTCCATCGAGAG 58.231 50.000 12.54 0.00 38.52 3.20
119 120 3.610669 CTCCATCGAGAGGGCCCG 61.611 72.222 18.44 4.06 38.52 6.13
120 121 4.137615 TCCATCGAGAGGGCCCGA 62.138 66.667 18.44 10.63 39.25 5.14
121 122 3.154473 CCATCGAGAGGGCCCGAA 61.154 66.667 18.44 1.01 38.36 4.30
122 123 2.107141 CATCGAGAGGGCCCGAAC 59.893 66.667 18.44 12.45 38.36 3.95
123 124 3.155167 ATCGAGAGGGCCCGAACC 61.155 66.667 18.44 7.31 38.36 3.62
124 125 3.680920 ATCGAGAGGGCCCGAACCT 62.681 63.158 18.44 12.55 42.18 3.50
125 126 4.148825 CGAGAGGGCCCGAACCTG 62.149 72.222 18.44 1.23 38.79 4.00
126 127 3.787001 GAGAGGGCCCGAACCTGG 61.787 72.222 18.44 0.00 38.79 4.45
134 135 3.970205 CCCGAACCTGGGTAAACAT 57.030 52.632 0.00 0.00 44.76 2.71
135 136 1.746470 CCCGAACCTGGGTAAACATC 58.254 55.000 0.00 0.00 44.76 3.06
136 137 1.365699 CCGAACCTGGGTAAACATCG 58.634 55.000 0.00 4.42 0.00 3.84
137 138 1.338389 CCGAACCTGGGTAAACATCGT 60.338 52.381 0.00 0.00 0.00 3.73
138 139 1.730064 CGAACCTGGGTAAACATCGTG 59.270 52.381 0.00 0.00 0.00 4.35
139 140 2.774687 GAACCTGGGTAAACATCGTGT 58.225 47.619 0.00 0.00 0.00 4.49
140 141 2.467566 ACCTGGGTAAACATCGTGTC 57.532 50.000 0.00 0.00 0.00 3.67
141 142 1.002773 ACCTGGGTAAACATCGTGTCC 59.997 52.381 0.00 0.00 0.00 4.02
142 143 1.677820 CCTGGGTAAACATCGTGTCCC 60.678 57.143 0.00 0.00 35.85 4.46
143 144 0.325602 TGGGTAAACATCGTGTCCCC 59.674 55.000 9.39 10.06 34.88 4.81
144 145 0.616891 GGGTAAACATCGTGTCCCCT 59.383 55.000 10.47 0.00 32.86 4.79
145 146 1.677820 GGGTAAACATCGTGTCCCCTG 60.678 57.143 10.47 0.00 32.86 4.45
146 147 1.084289 GTAAACATCGTGTCCCCTGC 58.916 55.000 0.00 0.00 0.00 4.85
147 148 0.035820 TAAACATCGTGTCCCCTGCC 60.036 55.000 0.00 0.00 0.00 4.85
148 149 1.779061 AAACATCGTGTCCCCTGCCT 61.779 55.000 0.00 0.00 0.00 4.75
149 150 2.185310 AACATCGTGTCCCCTGCCTC 62.185 60.000 0.00 0.00 0.00 4.70
150 151 3.083997 ATCGTGTCCCCTGCCTCC 61.084 66.667 0.00 0.00 0.00 4.30
151 152 3.625632 ATCGTGTCCCCTGCCTCCT 62.626 63.158 0.00 0.00 0.00 3.69
152 153 4.087892 CGTGTCCCCTGCCTCCTG 62.088 72.222 0.00 0.00 0.00 3.86
153 154 2.930562 GTGTCCCCTGCCTCCTGT 60.931 66.667 0.00 0.00 0.00 4.00
154 155 2.121963 TGTCCCCTGCCTCCTGTT 60.122 61.111 0.00 0.00 0.00 3.16
155 156 1.159905 TGTCCCCTGCCTCCTGTTA 59.840 57.895 0.00 0.00 0.00 2.41
156 157 1.198759 TGTCCCCTGCCTCCTGTTAC 61.199 60.000 0.00 0.00 0.00 2.50
157 158 1.615424 TCCCCTGCCTCCTGTTACC 60.615 63.158 0.00 0.00 0.00 2.85
158 159 1.923395 CCCCTGCCTCCTGTTACCA 60.923 63.158 0.00 0.00 0.00 3.25
159 160 1.281925 CCCCTGCCTCCTGTTACCAT 61.282 60.000 0.00 0.00 0.00 3.55
160 161 0.625849 CCCTGCCTCCTGTTACCATT 59.374 55.000 0.00 0.00 0.00 3.16
161 162 1.843851 CCCTGCCTCCTGTTACCATTA 59.156 52.381 0.00 0.00 0.00 1.90
162 163 2.158755 CCCTGCCTCCTGTTACCATTAG 60.159 54.545 0.00 0.00 0.00 1.73
163 164 2.565841 CTGCCTCCTGTTACCATTAGC 58.434 52.381 0.00 0.00 0.00 3.09
164 165 1.211949 TGCCTCCTGTTACCATTAGCC 59.788 52.381 0.00 0.00 0.00 3.93
165 166 1.490910 GCCTCCTGTTACCATTAGCCT 59.509 52.381 0.00 0.00 0.00 4.58
166 167 2.092375 GCCTCCTGTTACCATTAGCCTT 60.092 50.000 0.00 0.00 0.00 4.35
167 168 3.135895 GCCTCCTGTTACCATTAGCCTTA 59.864 47.826 0.00 0.00 0.00 2.69
168 169 4.743955 GCCTCCTGTTACCATTAGCCTTAG 60.744 50.000 0.00 0.00 0.00 2.18
169 170 4.654262 CCTCCTGTTACCATTAGCCTTAGA 59.346 45.833 0.00 0.00 0.00 2.10
170 171 5.453480 CCTCCTGTTACCATTAGCCTTAGAC 60.453 48.000 0.00 0.00 0.00 2.59
171 172 4.098960 TCCTGTTACCATTAGCCTTAGACG 59.901 45.833 0.00 0.00 0.00 4.18
172 173 3.788937 TGTTACCATTAGCCTTAGACGC 58.211 45.455 0.00 0.00 0.00 5.19
173 174 3.196039 TGTTACCATTAGCCTTAGACGCA 59.804 43.478 0.00 0.00 0.00 5.24
174 175 2.311124 ACCATTAGCCTTAGACGCAC 57.689 50.000 0.00 0.00 0.00 5.34
175 176 1.553248 ACCATTAGCCTTAGACGCACA 59.447 47.619 0.00 0.00 0.00 4.57
176 177 2.205074 CCATTAGCCTTAGACGCACAG 58.795 52.381 0.00 0.00 0.00 3.66
177 178 2.418746 CCATTAGCCTTAGACGCACAGT 60.419 50.000 0.00 0.00 0.00 3.55
178 179 3.262420 CATTAGCCTTAGACGCACAGTT 58.738 45.455 0.00 0.00 0.00 3.16
179 180 2.649331 TAGCCTTAGACGCACAGTTC 57.351 50.000 0.00 0.00 0.00 3.01
180 181 0.388649 AGCCTTAGACGCACAGTTCG 60.389 55.000 0.00 0.00 0.00 3.95
181 182 1.352156 GCCTTAGACGCACAGTTCGG 61.352 60.000 0.00 0.00 0.00 4.30
182 183 0.736325 CCTTAGACGCACAGTTCGGG 60.736 60.000 0.00 0.00 0.00 5.14
183 184 0.242825 CTTAGACGCACAGTTCGGGA 59.757 55.000 0.00 0.00 0.00 5.14
184 185 0.038892 TTAGACGCACAGTTCGGGAC 60.039 55.000 0.00 0.00 0.00 4.46
185 186 1.870055 TAGACGCACAGTTCGGGACC 61.870 60.000 0.00 0.00 0.00 4.46
186 187 4.309950 ACGCACAGTTCGGGACCC 62.310 66.667 0.00 0.00 0.00 4.46
188 189 4.717313 GCACAGTTCGGGACCCCC 62.717 72.222 4.46 0.00 41.09 5.40
189 190 2.928396 CACAGTTCGGGACCCCCT 60.928 66.667 4.46 0.00 42.67 4.79
190 191 1.611261 CACAGTTCGGGACCCCCTA 60.611 63.158 4.46 0.00 42.67 3.53
191 192 1.611556 ACAGTTCGGGACCCCCTAC 60.612 63.158 4.46 0.29 42.67 3.18
192 193 2.040114 AGTTCGGGACCCCCTACC 59.960 66.667 4.46 0.00 42.67 3.18
193 194 3.085947 GTTCGGGACCCCCTACCC 61.086 72.222 4.46 0.00 42.67 3.69
197 198 3.759101 GGGACCCCCTACCCGAGA 61.759 72.222 0.00 0.00 41.34 4.04
198 199 2.613421 GGACCCCCTACCCGAGAT 59.387 66.667 0.00 0.00 0.00 2.75
199 200 1.533513 GGACCCCCTACCCGAGATC 60.534 68.421 0.00 0.00 0.00 2.75
200 201 1.533513 GACCCCCTACCCGAGATCC 60.534 68.421 0.00 0.00 0.00 3.36
201 202 2.600769 CCCCCTACCCGAGATCCG 60.601 72.222 0.00 0.00 38.18 4.18
202 203 3.303928 CCCCTACCCGAGATCCGC 61.304 72.222 0.00 0.00 36.84 5.54
203 204 3.303928 CCCTACCCGAGATCCGCC 61.304 72.222 0.00 0.00 36.84 6.13
204 205 3.671411 CCTACCCGAGATCCGCCG 61.671 72.222 0.00 0.00 36.84 6.46
205 206 3.671411 CTACCCGAGATCCGCCGG 61.671 72.222 0.00 0.00 44.94 6.13
206 207 4.511246 TACCCGAGATCCGCCGGT 62.511 66.667 1.63 11.60 43.93 5.28
208 209 4.157120 CCCGAGATCCGCCGGTTT 62.157 66.667 1.63 0.00 43.93 3.27
209 210 2.125269 CCGAGATCCGCCGGTTTT 60.125 61.111 1.63 0.00 40.78 2.43
210 211 2.461110 CCGAGATCCGCCGGTTTTG 61.461 63.158 1.63 0.00 40.78 2.44
211 212 1.447140 CGAGATCCGCCGGTTTTGA 60.447 57.895 1.63 0.00 0.00 2.69
212 213 1.693083 CGAGATCCGCCGGTTTTGAC 61.693 60.000 1.63 0.00 0.00 3.18
213 214 0.672401 GAGATCCGCCGGTTTTGACA 60.672 55.000 1.63 0.00 0.00 3.58
214 215 0.953960 AGATCCGCCGGTTTTGACAC 60.954 55.000 1.63 0.00 0.00 3.67
215 216 1.918868 GATCCGCCGGTTTTGACACC 61.919 60.000 1.63 0.00 0.00 4.16
271 272 0.968405 GCAAAGGGGACAAAGATGCA 59.032 50.000 0.00 0.00 32.80 3.96
333 335 7.559897 GGAAGACAATACAGGGGAAAATGAATA 59.440 37.037 0.00 0.00 0.00 1.75
335 337 8.697507 AGACAATACAGGGGAAAATGAATATC 57.302 34.615 0.00 0.00 0.00 1.63
347 349 6.377327 AAAATGAATATCATCGAACGGCTT 57.623 33.333 0.00 0.00 35.76 4.35
357 359 3.022401 GAACGGCTTTGCGCGATCA 62.022 57.895 12.10 0.00 40.44 2.92
422 426 3.390521 CCACACCTAGCCTCGGCA 61.391 66.667 11.02 0.00 44.88 5.69
641 648 4.059459 CGACGACGCTGTGTTGCC 62.059 66.667 8.48 0.00 35.13 4.52
647 654 0.038159 GACGCTGTGTTGCCTAGAGT 60.038 55.000 0.00 0.00 0.00 3.24
651 658 1.543429 GCTGTGTTGCCTAGAGTTGGT 60.543 52.381 0.00 0.00 0.00 3.67
695 703 2.039787 TCCCCATGCCTACGACCA 59.960 61.111 0.00 0.00 0.00 4.02
895 903 1.072331 GTCCATGTGTTGAGGTGAGGT 59.928 52.381 0.00 0.00 0.00 3.85
979 987 7.138054 TCTTTCCTCTCCTGTAGAACTTTTT 57.862 36.000 0.00 0.00 32.46 1.94
1020 1042 3.550437 ATGCACACTAGGGATCACTTC 57.450 47.619 0.87 0.00 0.00 3.01
1022 1044 1.476891 GCACACTAGGGATCACTTCGA 59.523 52.381 0.87 0.00 0.00 3.71
1032 1054 1.819288 GATCACTTCGAGGACCTCACA 59.181 52.381 21.49 4.15 0.00 3.58
1281 1303 2.125106 GATGACCCCGAGCACACC 60.125 66.667 0.00 0.00 0.00 4.16
1286 1308 2.046892 CCCCGAGCACACCTTCAG 60.047 66.667 0.00 0.00 0.00 3.02
1407 1429 4.210611 TCCTCTGAATCTCATCTCCCAT 57.789 45.455 0.00 0.00 0.00 4.00
1595 1618 1.278337 GTCACGTTGTGCGCATTCA 59.722 52.632 15.91 4.58 46.11 2.57
1630 1653 3.133721 GGGTCTCATCTCACTGCAACTAT 59.866 47.826 0.00 0.00 0.00 2.12
1735 1758 1.686355 TTTTTGTCGTGATGGCCAGT 58.314 45.000 13.05 0.00 0.00 4.00
1886 1911 4.815846 TCTCGTTTTTACCCTTGGTGTTAC 59.184 41.667 0.00 0.00 36.19 2.50
1890 1915 6.152492 TCGTTTTTACCCTTGGTGTTACTTTT 59.848 34.615 0.00 0.00 36.19 2.27
2068 2104 5.687730 CGTGATCGATATTTCTAGTGCTTGT 59.312 40.000 0.00 0.00 39.71 3.16
2089 2126 6.827586 TGTGGTGTAGTTTTGTTTCTCTTT 57.172 33.333 0.00 0.00 0.00 2.52
2592 2638 3.785486 TCACATTAGCATCAAGACTCCG 58.215 45.455 0.00 0.00 0.00 4.63
2767 2817 1.313772 CACGTTGATGGGGTTCACAA 58.686 50.000 0.00 0.00 0.00 3.33
2847 2919 8.217111 TGCCATTCTTGTAAATCACTATCCATA 58.783 33.333 0.00 0.00 0.00 2.74
2955 3028 4.694760 TTGGAGTCCTCATATGGATGTG 57.305 45.455 11.33 0.00 38.52 3.21
3159 3232 1.299976 CTCCACCACCACCTAAGCC 59.700 63.158 0.00 0.00 0.00 4.35
3457 3536 9.130661 TGTTTGTTTTTCCTTAATGAGAGATGA 57.869 29.630 0.00 0.00 0.00 2.92
3676 3761 1.806542 GCTTCGCCAGATCAGTTTTGA 59.193 47.619 0.00 0.00 37.81 2.69
3870 3981 0.172578 CGTGATCCTTGGCACTACGA 59.827 55.000 0.00 0.00 32.98 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.224329 GGCTAAACCCTAGAAGCTAGCC 60.224 54.545 12.13 13.65 43.27 3.93
5 6 2.701423 AGGCTAAACCCTAGAAGCTAGC 59.299 50.000 6.62 6.62 40.58 3.42
6 7 4.219919 AGAGGCTAAACCCTAGAAGCTAG 58.780 47.826 0.00 0.00 40.58 3.42
7 8 4.267341 AGAGGCTAAACCCTAGAAGCTA 57.733 45.455 0.00 0.00 40.58 3.32
8 9 3.123392 AGAGGCTAAACCCTAGAAGCT 57.877 47.619 0.00 0.00 40.58 3.74
9 10 3.243468 CGTAGAGGCTAAACCCTAGAAGC 60.243 52.174 0.00 0.00 40.58 3.86
10 11 4.205587 TCGTAGAGGCTAAACCCTAGAAG 58.794 47.826 0.00 0.00 40.58 2.85
11 12 4.240881 TCGTAGAGGCTAAACCCTAGAA 57.759 45.455 0.00 0.00 40.58 2.10
12 13 3.939740 TCGTAGAGGCTAAACCCTAGA 57.060 47.619 0.00 0.00 40.58 2.43
13 14 4.400120 AGATCGTAGAGGCTAAACCCTAG 58.600 47.826 0.00 0.00 43.63 3.02
14 15 4.396522 GAGATCGTAGAGGCTAAACCCTA 58.603 47.826 0.00 0.00 43.63 3.53
15 16 3.224269 GAGATCGTAGAGGCTAAACCCT 58.776 50.000 0.00 0.00 43.63 4.34
16 17 2.030981 CGAGATCGTAGAGGCTAAACCC 60.031 54.545 0.00 0.00 43.63 4.11
17 18 3.270962 CGAGATCGTAGAGGCTAAACC 57.729 52.381 0.00 0.00 43.63 3.27
32 33 4.707448 ACAAGAGTTGATCTACCACGAGAT 59.293 41.667 3.54 0.00 37.23 2.75
33 34 4.079970 ACAAGAGTTGATCTACCACGAGA 58.920 43.478 3.54 0.00 37.23 4.04
34 35 4.442375 ACAAGAGTTGATCTACCACGAG 57.558 45.455 3.54 1.07 37.23 4.18
35 36 5.970317 TTACAAGAGTTGATCTACCACGA 57.030 39.130 3.54 0.00 37.23 4.35
36 37 7.481642 AGTATTACAAGAGTTGATCTACCACG 58.518 38.462 3.54 0.00 37.23 4.94
37 38 8.467598 TGAGTATTACAAGAGTTGATCTACCAC 58.532 37.037 3.54 0.00 37.23 4.16
38 39 8.589701 TGAGTATTACAAGAGTTGATCTACCA 57.410 34.615 3.54 0.00 37.23 3.25
58 59 9.433153 GCTTGATTGATCTTGATGATATGAGTA 57.567 33.333 0.00 0.00 35.14 2.59
59 60 7.937394 TGCTTGATTGATCTTGATGATATGAGT 59.063 33.333 0.00 0.00 35.14 3.41
60 61 8.324163 TGCTTGATTGATCTTGATGATATGAG 57.676 34.615 0.00 0.00 35.14 2.90
61 62 7.390718 CCTGCTTGATTGATCTTGATGATATGA 59.609 37.037 0.00 0.00 35.14 2.15
62 63 7.390718 TCCTGCTTGATTGATCTTGATGATATG 59.609 37.037 0.00 0.00 35.14 1.78
63 64 7.459234 TCCTGCTTGATTGATCTTGATGATAT 58.541 34.615 0.00 0.00 35.14 1.63
64 65 6.834107 TCCTGCTTGATTGATCTTGATGATA 58.166 36.000 0.00 0.00 35.14 2.15
65 66 5.691896 TCCTGCTTGATTGATCTTGATGAT 58.308 37.500 0.00 0.00 38.27 2.45
66 67 5.106876 TCCTGCTTGATTGATCTTGATGA 57.893 39.130 0.00 0.00 0.00 2.92
67 68 5.357314 ACTTCCTGCTTGATTGATCTTGATG 59.643 40.000 0.00 0.00 0.00 3.07
68 69 5.507637 ACTTCCTGCTTGATTGATCTTGAT 58.492 37.500 0.00 0.00 0.00 2.57
69 70 4.914983 ACTTCCTGCTTGATTGATCTTGA 58.085 39.130 0.00 0.00 0.00 3.02
70 71 5.296283 CCTACTTCCTGCTTGATTGATCTTG 59.704 44.000 0.00 0.00 0.00 3.02
71 72 5.435291 CCTACTTCCTGCTTGATTGATCTT 58.565 41.667 0.00 0.00 0.00 2.40
72 73 4.141528 CCCTACTTCCTGCTTGATTGATCT 60.142 45.833 0.00 0.00 0.00 2.75
73 74 4.133078 CCCTACTTCCTGCTTGATTGATC 58.867 47.826 0.00 0.00 0.00 2.92
74 75 3.525199 ACCCTACTTCCTGCTTGATTGAT 59.475 43.478 0.00 0.00 0.00 2.57
75 76 2.912956 ACCCTACTTCCTGCTTGATTGA 59.087 45.455 0.00 0.00 0.00 2.57
76 77 3.356529 ACCCTACTTCCTGCTTGATTG 57.643 47.619 0.00 0.00 0.00 2.67
77 78 5.717119 AATACCCTACTTCCTGCTTGATT 57.283 39.130 0.00 0.00 0.00 2.57
78 79 5.071923 GGTAATACCCTACTTCCTGCTTGAT 59.928 44.000 0.00 0.00 30.04 2.57
79 80 4.407945 GGTAATACCCTACTTCCTGCTTGA 59.592 45.833 0.00 0.00 30.04 3.02
80 81 4.409247 AGGTAATACCCTACTTCCTGCTTG 59.591 45.833 5.71 0.00 39.75 4.01
81 82 4.632292 AGGTAATACCCTACTTCCTGCTT 58.368 43.478 5.71 0.00 39.75 3.91
82 83 4.224762 GAGGTAATACCCTACTTCCTGCT 58.775 47.826 5.71 0.00 39.75 4.24
83 84 3.324268 GGAGGTAATACCCTACTTCCTGC 59.676 52.174 5.71 0.00 42.18 4.85
84 85 4.553678 TGGAGGTAATACCCTACTTCCTG 58.446 47.826 13.63 0.00 44.50 3.86
85 86 4.913154 TGGAGGTAATACCCTACTTCCT 57.087 45.455 13.63 0.00 44.50 3.36
86 87 4.220163 CGATGGAGGTAATACCCTACTTCC 59.780 50.000 5.71 6.77 44.47 3.46
87 88 5.075493 TCGATGGAGGTAATACCCTACTTC 58.925 45.833 5.71 4.12 39.75 3.01
88 89 5.070823 TCGATGGAGGTAATACCCTACTT 57.929 43.478 5.71 0.00 39.75 2.24
89 90 4.353191 TCTCGATGGAGGTAATACCCTACT 59.647 45.833 5.71 0.00 39.75 2.57
90 91 4.660168 TCTCGATGGAGGTAATACCCTAC 58.340 47.826 5.71 0.00 39.75 3.18
91 92 4.263816 CCTCTCGATGGAGGTAATACCCTA 60.264 50.000 11.66 0.00 45.65 3.53
92 93 3.500654 CCTCTCGATGGAGGTAATACCCT 60.501 52.174 11.66 0.00 45.65 4.34
93 94 2.826725 CCTCTCGATGGAGGTAATACCC 59.173 54.545 11.66 0.00 45.65 3.69
102 103 3.610669 CGGGCCCTCTCGATGGAG 61.611 72.222 22.43 0.00 41.89 3.86
103 104 3.672338 TTCGGGCCCTCTCGATGGA 62.672 63.158 22.43 3.53 35.25 3.41
104 105 3.154473 TTCGGGCCCTCTCGATGG 61.154 66.667 22.43 0.54 35.25 3.51
105 106 2.107141 GTTCGGGCCCTCTCGATG 59.893 66.667 22.43 1.43 35.25 3.84
106 107 3.155167 GGTTCGGGCCCTCTCGAT 61.155 66.667 22.43 0.00 35.25 3.59
107 108 4.377760 AGGTTCGGGCCCTCTCGA 62.378 66.667 22.43 9.26 0.00 4.04
108 109 4.148825 CAGGTTCGGGCCCTCTCG 62.149 72.222 22.43 6.49 0.00 4.04
109 110 3.787001 CCAGGTTCGGGCCCTCTC 61.787 72.222 22.43 9.34 0.00 3.20
117 118 1.338389 ACGATGTTTACCCAGGTTCGG 60.338 52.381 11.39 0.00 30.52 4.30
118 119 1.730064 CACGATGTTTACCCAGGTTCG 59.270 52.381 6.36 6.36 31.96 3.95
119 120 2.740447 GACACGATGTTTACCCAGGTTC 59.260 50.000 0.00 0.00 0.00 3.62
120 121 2.551504 GGACACGATGTTTACCCAGGTT 60.552 50.000 0.00 0.00 0.00 3.50
121 122 1.002773 GGACACGATGTTTACCCAGGT 59.997 52.381 0.00 0.00 0.00 4.00
122 123 1.677820 GGGACACGATGTTTACCCAGG 60.678 57.143 0.00 0.00 37.50 4.45
123 124 1.677820 GGGGACACGATGTTTACCCAG 60.678 57.143 0.00 0.00 38.30 4.45
124 125 0.325602 GGGGACACGATGTTTACCCA 59.674 55.000 0.00 0.00 38.30 4.51
125 126 0.616891 AGGGGACACGATGTTTACCC 59.383 55.000 13.43 13.43 38.53 3.69
126 127 1.734163 CAGGGGACACGATGTTTACC 58.266 55.000 0.00 0.00 0.00 2.85
127 128 1.084289 GCAGGGGACACGATGTTTAC 58.916 55.000 0.00 0.00 0.00 2.01
128 129 0.035820 GGCAGGGGACACGATGTTTA 60.036 55.000 0.00 0.00 0.00 2.01
129 130 1.303317 GGCAGGGGACACGATGTTT 60.303 57.895 0.00 0.00 0.00 2.83
130 131 2.185310 GAGGCAGGGGACACGATGTT 62.185 60.000 0.00 0.00 0.00 2.71
131 132 2.607750 AGGCAGGGGACACGATGT 60.608 61.111 0.00 0.00 0.00 3.06
132 133 2.187946 GAGGCAGGGGACACGATG 59.812 66.667 0.00 0.00 0.00 3.84
133 134 3.083997 GGAGGCAGGGGACACGAT 61.084 66.667 0.00 0.00 0.00 3.73
134 135 4.316823 AGGAGGCAGGGGACACGA 62.317 66.667 0.00 0.00 0.00 4.35
135 136 4.087892 CAGGAGGCAGGGGACACG 62.088 72.222 0.00 0.00 0.00 4.49
136 137 1.198759 TAACAGGAGGCAGGGGACAC 61.199 60.000 0.00 0.00 0.00 3.67
137 138 1.159905 TAACAGGAGGCAGGGGACA 59.840 57.895 0.00 0.00 0.00 4.02
138 139 1.602771 GTAACAGGAGGCAGGGGAC 59.397 63.158 0.00 0.00 0.00 4.46
139 140 1.615424 GGTAACAGGAGGCAGGGGA 60.615 63.158 0.00 0.00 0.00 4.81
140 141 1.923395 TGGTAACAGGAGGCAGGGG 60.923 63.158 0.00 0.00 46.17 4.79
141 142 3.820425 TGGTAACAGGAGGCAGGG 58.180 61.111 0.00 0.00 46.17 4.45
152 153 3.554731 GTGCGTCTAAGGCTAATGGTAAC 59.445 47.826 0.00 0.00 0.00 2.50
153 154 3.196039 TGTGCGTCTAAGGCTAATGGTAA 59.804 43.478 0.00 0.00 0.00 2.85
154 155 2.761767 TGTGCGTCTAAGGCTAATGGTA 59.238 45.455 0.00 0.00 0.00 3.25
155 156 1.553248 TGTGCGTCTAAGGCTAATGGT 59.447 47.619 0.00 0.00 0.00 3.55
156 157 2.205074 CTGTGCGTCTAAGGCTAATGG 58.795 52.381 0.00 0.00 0.00 3.16
157 158 2.893637 ACTGTGCGTCTAAGGCTAATG 58.106 47.619 0.00 0.00 0.00 1.90
158 159 3.522553 GAACTGTGCGTCTAAGGCTAAT 58.477 45.455 0.00 0.00 0.00 1.73
159 160 2.670229 CGAACTGTGCGTCTAAGGCTAA 60.670 50.000 0.00 0.00 0.00 3.09
160 161 1.135489 CGAACTGTGCGTCTAAGGCTA 60.135 52.381 0.00 0.00 0.00 3.93
161 162 0.388649 CGAACTGTGCGTCTAAGGCT 60.389 55.000 0.00 0.00 0.00 4.58
162 163 1.352156 CCGAACTGTGCGTCTAAGGC 61.352 60.000 7.51 0.00 0.00 4.35
163 164 0.736325 CCCGAACTGTGCGTCTAAGG 60.736 60.000 7.51 0.00 0.00 2.69
164 165 0.242825 TCCCGAACTGTGCGTCTAAG 59.757 55.000 7.51 0.00 0.00 2.18
165 166 0.038892 GTCCCGAACTGTGCGTCTAA 60.039 55.000 7.51 0.00 0.00 2.10
166 167 1.582968 GTCCCGAACTGTGCGTCTA 59.417 57.895 7.51 0.00 0.00 2.59
167 168 2.338984 GTCCCGAACTGTGCGTCT 59.661 61.111 7.51 0.00 0.00 4.18
168 169 2.737376 GGTCCCGAACTGTGCGTC 60.737 66.667 7.51 0.00 0.00 5.19
169 170 4.309950 GGGTCCCGAACTGTGCGT 62.310 66.667 7.51 0.00 0.00 5.24
171 172 4.717313 GGGGGTCCCGAACTGTGC 62.717 72.222 0.48 0.00 36.85 4.57
180 181 3.097429 ATCTCGGGTAGGGGGTCCC 62.097 68.421 0.00 0.00 45.90 4.46
181 182 1.533513 GATCTCGGGTAGGGGGTCC 60.534 68.421 0.00 0.00 0.00 4.46
182 183 1.533513 GGATCTCGGGTAGGGGGTC 60.534 68.421 0.00 0.00 0.00 4.46
183 184 2.613421 GGATCTCGGGTAGGGGGT 59.387 66.667 0.00 0.00 0.00 4.95
184 185 2.600769 CGGATCTCGGGTAGGGGG 60.601 72.222 0.00 0.00 34.75 5.40
185 186 3.303928 GCGGATCTCGGGTAGGGG 61.304 72.222 5.87 0.00 39.69 4.79
186 187 3.303928 GGCGGATCTCGGGTAGGG 61.304 72.222 5.87 0.00 39.69 3.53
187 188 3.671411 CGGCGGATCTCGGGTAGG 61.671 72.222 0.00 0.00 39.69 3.18
188 189 3.671411 CCGGCGGATCTCGGGTAG 61.671 72.222 24.41 0.00 42.32 3.18
193 194 1.447140 TCAAAACCGGCGGATCTCG 60.447 57.895 35.78 16.34 42.76 4.04
194 195 0.672401 TGTCAAAACCGGCGGATCTC 60.672 55.000 35.78 16.90 0.00 2.75
195 196 0.953960 GTGTCAAAACCGGCGGATCT 60.954 55.000 35.78 13.84 0.00 2.75
196 197 1.500396 GTGTCAAAACCGGCGGATC 59.500 57.895 35.78 9.52 0.00 3.36
197 198 1.969589 GGTGTCAAAACCGGCGGAT 60.970 57.895 35.78 20.37 0.00 4.18
198 199 2.592287 GGTGTCAAAACCGGCGGA 60.592 61.111 35.78 6.54 0.00 5.54
204 205 0.580104 CGAGTGACGGTGTCAAAACC 59.420 55.000 0.49 0.00 44.49 3.27
205 206 0.042448 GCGAGTGACGGTGTCAAAAC 60.042 55.000 0.49 0.00 44.49 2.43
206 207 1.155424 GGCGAGTGACGGTGTCAAAA 61.155 55.000 0.49 0.00 44.49 2.44
207 208 1.593209 GGCGAGTGACGGTGTCAAA 60.593 57.895 0.49 0.00 44.49 2.69
208 209 2.028484 GGCGAGTGACGGTGTCAA 59.972 61.111 0.49 0.00 44.49 3.18
209 210 4.337060 CGGCGAGTGACGGTGTCA 62.337 66.667 0.00 0.00 45.13 3.58
216 217 1.141881 ATCATGGTCGGCGAGTGAC 59.858 57.895 11.20 0.00 35.60 3.67
217 218 1.141665 CATCATGGTCGGCGAGTGA 59.858 57.895 11.20 15.65 0.00 3.41
218 219 2.528743 GCATCATGGTCGGCGAGTG 61.529 63.158 11.20 10.27 0.00 3.51
219 220 2.202932 GCATCATGGTCGGCGAGT 60.203 61.111 11.20 0.00 0.00 4.18
230 231 0.817654 TCCGTCTTCACTCGCATCAT 59.182 50.000 0.00 0.00 0.00 2.45
271 272 1.463444 GTATTTCGTTCCTGCGCAACT 59.537 47.619 13.05 0.00 0.00 3.16
333 335 1.715585 CGCAAAGCCGTTCGATGAT 59.284 52.632 0.00 0.00 0.00 2.45
335 337 2.574212 GCGCAAAGCCGTTCGATG 60.574 61.111 0.30 0.00 40.81 3.84
347 349 2.765122 TCATTGGATATGATCGCGCAA 58.235 42.857 8.75 0.00 0.00 4.85
357 359 2.430465 GCCTCACGCATCATTGGATAT 58.570 47.619 0.00 0.00 37.47 1.63
550 554 1.078918 CCTGTGCGGCTCATTCTCA 60.079 57.895 5.08 0.00 0.00 3.27
641 648 1.339151 GCCTTGACCCACCAACTCTAG 60.339 57.143 0.00 0.00 0.00 2.43
647 654 4.196778 TGCGCCTTGACCCACCAA 62.197 61.111 4.18 0.00 0.00 3.67
651 658 3.825160 GACAGTGCGCCTTGACCCA 62.825 63.158 14.26 0.00 0.00 4.51
695 703 1.003718 GTGAAGGTTGCTAGGGCGT 60.004 57.895 0.00 0.00 42.25 5.68
910 918 8.511604 AGGTCGATTCATCATCAAACTAAAAT 57.488 30.769 0.00 0.00 0.00 1.82
979 987 2.112297 GCCGAACAGGTTGTGGGA 59.888 61.111 4.34 0.00 43.70 4.37
1009 1017 0.336737 AGGTCCTCGAAGTGATCCCT 59.663 55.000 0.00 0.00 0.00 4.20
1020 1042 1.177401 TGTCATCTGTGAGGTCCTCG 58.823 55.000 14.34 0.14 34.36 4.63
1022 1044 2.114616 GGATGTCATCTGTGAGGTCCT 58.885 52.381 12.54 0.00 36.69 3.85
1032 1054 2.125233 ACATGCCAGAGGATGTCATCT 58.875 47.619 12.54 0.00 37.51 2.90
1162 1184 1.278238 CGCTTGTATCTCGGGAACAC 58.722 55.000 0.00 0.00 0.00 3.32
1248 1270 4.324022 GGGTCATCATCAGGATATGCATCA 60.324 45.833 0.19 0.00 33.95 3.07
1281 1303 5.309323 TCAACAACTTGGTGTTTCTGAAG 57.691 39.130 6.70 0.00 39.73 3.02
1286 1308 7.096640 CGTAATCAATCAACAACTTGGTGTTTC 60.097 37.037 6.70 0.00 39.73 2.78
1407 1429 1.490490 AGGTGCAAGGTCTTCAAGTGA 59.510 47.619 0.00 0.00 0.00 3.41
1595 1618 2.198304 GAGACCCGGGGCACAAATCT 62.198 60.000 32.91 18.91 0.00 2.40
1735 1758 4.600111 ACAGAAAGGGTTACTACAATCCCA 59.400 41.667 0.00 0.00 42.12 4.37
1886 1911 8.507249 CAAGAGAAACTACTAATGGTGGAAAAG 58.493 37.037 0.00 0.00 0.00 2.27
1890 1915 6.269077 TCACAAGAGAAACTACTAATGGTGGA 59.731 38.462 0.00 0.00 0.00 4.02
2068 2104 6.827586 ACAAAGAGAAACAAAACTACACCA 57.172 33.333 0.00 0.00 0.00 4.17
2592 2638 4.207165 ACTTACAATATGTGGATGGTGCC 58.793 43.478 0.00 0.00 0.00 5.01
2739 2789 0.179156 CCATCAACGTGCAATCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
2767 2817 9.942850 CTAAACCCTTTGAAATTTAATGGTCAT 57.057 29.630 0.00 0.00 0.00 3.06
2797 2869 9.780413 GCAAATTTTCAAACCAAATTAACAGAA 57.220 25.926 0.00 0.00 33.56 3.02
2819 2891 7.395772 TGGATAGTGATTTACAAGAATGGCAAA 59.604 33.333 0.00 0.00 0.00 3.68
2955 3028 7.065324 TCACAAGTTTATTACGAATCATCCACC 59.935 37.037 0.00 0.00 0.00 4.61
3002 3075 2.320745 TAGATCGCGTCAGTAGGTCA 57.679 50.000 5.77 0.00 0.00 4.02
3159 3232 2.332063 ATGTGTCCAAGCCTAATCCG 57.668 50.000 0.00 0.00 0.00 4.18
3245 3318 0.316204 ACACATGCAAAGCAAGAGGC 59.684 50.000 0.92 0.00 43.62 4.70
3457 3536 3.223674 ACAAAGTCCGGGTCTGATTTT 57.776 42.857 0.00 0.00 0.00 1.82
3676 3761 2.094545 GCGGCAACCATGAGAAGAAATT 60.095 45.455 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.