Multiple sequence alignment - TraesCS1A01G190400

Loading Multiple Alignment...

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 TraesCS1A01G190400 chr1A 100.000 2462 0 0 1 2462 344190787 344188326 0.000000e+00 4547.0
1 TraesCS1A01G190400 chr1A 83.438 960 98 36 803 1714 400955357 400956303 0.000000e+00 835.0
2 TraesCS1A01G190400 chr1A 88.352 704 54 17 803 1486 401227525 401226830 0.000000e+00 821.0
3 TraesCS1A01G190400 chr1A 77.399 323 57 14 1855 2171 400956823 400957135 7.000000e-41 178.0
4 TraesCS1A01G190400 chr1B 94.042 1628 77 12 588 2204 344376046 344374428 0.000000e+00 2451.0
5 TraesCS1A01G190400 chr1B 88.756 667 56 13 803 1466 434335207 434335857 0.000000e+00 798.0
6 TraesCS1A01G190400 chr1B 90.494 263 21 4 2202 2462 344374347 344374087 6.520000e-91 344.0
7 TraesCS1A01G190400 chr1B 87.931 58 3 4 576 632 595016409 595016463 5.680000e-07 65.8
8 TraesCS1A01G190400 chr1D 95.497 866 32 2 685 1550 271838126 271837268 0.000000e+00 1376.0
9 TraesCS1A01G190400 chr1D 92.741 923 56 7 1548 2462 271837021 271836102 0.000000e+00 1323.0
10 TraesCS1A01G190400 chr1D 96.099 282 11 0 37 318 51920193 51920474 6.200000e-126 460.0
11 TraesCS1A01G190400 chr1D 80.791 354 62 5 1830 2179 321709695 321709344 3.120000e-69 272.0
12 TraesCS1A01G190400 chr1D 85.787 197 21 5 452 643 271840376 271840182 4.150000e-48 202.0
13 TraesCS1A01G190400 chr1D 90.667 150 12 2 320 468 271841233 271841085 5.370000e-47 198.0
14 TraesCS1A01G190400 chr1D 88.667 150 15 2 320 468 271840798 271840650 5.410000e-42 182.0
15 TraesCS1A01G190400 chr2D 89.577 662 47 17 812 1463 399347438 399348087 0.000000e+00 821.0
16 TraesCS1A01G190400 chr4A 87.781 712 67 15 772 1469 23614736 23614031 0.000000e+00 815.0
17 TraesCS1A01G190400 chr4A 87.677 706 68 14 774 1466 23844239 23843540 0.000000e+00 804.0
18 TraesCS1A01G190400 chr4A 89.982 569 48 7 1772 2335 479396125 479395561 0.000000e+00 726.0
19 TraesCS1A01G190400 chr4A 90.265 113 9 2 2331 2442 479395296 479395185 1.970000e-31 147.0
20 TraesCS1A01G190400 chr2B 88.705 664 53 15 812 1465 473299734 473300385 0.000000e+00 791.0
21 TraesCS1A01G190400 chr2B 91.045 268 17 1 1385 1652 247943200 247942940 3.010000e-94 355.0
22 TraesCS1A01G190400 chr7D 90.909 363 28 5 2091 2451 58207068 58206709 1.320000e-132 483.0
23 TraesCS1A01G190400 chr7D 93.009 329 17 3 1772 2095 58212732 58212405 2.220000e-130 475.0
24 TraesCS1A01G190400 chrUn 96.454 282 10 0 37 318 354077453 354077172 1.330000e-127 466.0
25 TraesCS1A01G190400 chr6A 96.454 282 10 0 37 318 370486197 370485916 1.330000e-127 466.0
26 TraesCS1A01G190400 chr6A 88.312 308 25 3 1385 1689 73016795 73017094 2.330000e-95 359.0
27 TraesCS1A01G190400 chr6A 87.013 308 29 3 1385 1689 72997758 72998057 1.090000e-88 337.0
28 TraesCS1A01G190400 chr5B 96.140 285 11 0 37 321 63468047 63467763 1.330000e-127 466.0
29 TraesCS1A01G190400 chr5B 85.207 169 23 2 2009 2176 63849883 63849716 3.260000e-39 172.0
30 TraesCS1A01G190400 chr3D 96.454 282 10 0 37 318 589269903 589270184 1.330000e-127 466.0
31 TraesCS1A01G190400 chr3B 96.454 282 10 0 37 318 101917701 101917420 1.330000e-127 466.0
32 TraesCS1A01G190400 chr3A 96.454 282 10 0 37 318 164854297 164854578 1.330000e-127 466.0
33 TraesCS1A01G190400 chr6D 96.099 282 11 0 37 318 168264182 168263901 6.200000e-126 460.0
34 TraesCS1A01G190400 chr5D 96.099 282 11 0 37 318 432429292 432429011 6.200000e-126 460.0
35 TraesCS1A01G190400 chr5D 83.799 179 19 6 1998 2169 58684917 58684742 7.050000e-36 161.0
36 TraesCS1A01G190400 chr7A 87.931 58 3 4 576 632 496840917 496840971 5.680000e-07 65.8
37 TraesCS1A01G190400 chr5A 87.931 58 3 4 576 632 596595558 596595504 5.680000e-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 TraesCS1A01G190400 chr1A 344188326 344190787 2461 True 4547.0 4547 100.0000 1 2462 1 chr1A.!!$R1 2461
1 TraesCS1A01G190400 chr1A 401226830 401227525 695 True 821.0 821 88.3520 803 1486 1 chr1A.!!$R2 683
2 TraesCS1A01G190400 chr1A 400955357 400957135 1778 False 506.5 835 80.4185 803 2171 2 chr1A.!!$F1 1368
3 TraesCS1A01G190400 chr1B 344374087 344376046 1959 True 1397.5 2451 92.2680 588 2462 2 chr1B.!!$R1 1874
4 TraesCS1A01G190400 chr1B 434335207 434335857 650 False 798.0 798 88.7560 803 1466 1 chr1B.!!$F1 663
5 TraesCS1A01G190400 chr1D 271836102 271841233 5131 True 656.2 1376 90.6718 320 2462 5 chr1D.!!$R2 2142
6 TraesCS1A01G190400 chr2D 399347438 399348087 649 False 821.0 821 89.5770 812 1463 1 chr2D.!!$F1 651
7 TraesCS1A01G190400 chr4A 23614031 23614736 705 True 815.0 815 87.7810 772 1469 1 chr4A.!!$R1 697
8 TraesCS1A01G190400 chr4A 23843540 23844239 699 True 804.0 804 87.6770 774 1466 1 chr4A.!!$R2 692
9 TraesCS1A01G190400 chr4A 479395185 479396125 940 True 436.5 726 90.1235 1772 2442 2 chr4A.!!$R3 670
10 TraesCS1A01G190400 chr2B 473299734 473300385 651 False 791.0 791 88.7050 812 1465 1 chr2B.!!$F1 653

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
476 1202 0.105964 TCCACCTGACCGACTGTTTG 59.894 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 4878 1.135373 CAATGCAGCTGGCTCTCAAAG 60.135 52.381 17.12 0.0 45.15 2.77 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
18 19 2.109431 CCAATGATGACAAGGCCGG 58.891 57.895 0.00 0.00 0.00 6.13
19 20 0.394216 CCAATGATGACAAGGCCGGA 60.394 55.000 5.05 0.00 0.00 5.14
20 21 1.683943 CAATGATGACAAGGCCGGAT 58.316 50.000 5.05 0.00 0.00 4.18
21 22 1.605710 CAATGATGACAAGGCCGGATC 59.394 52.381 5.05 0.00 0.00 3.36
22 23 0.839277 ATGATGACAAGGCCGGATCA 59.161 50.000 5.05 3.47 0.00 2.92
23 24 0.839277 TGATGACAAGGCCGGATCAT 59.161 50.000 5.05 15.85 34.50 2.45
24 25 1.202687 TGATGACAAGGCCGGATCATC 60.203 52.381 26.63 26.63 45.07 2.92
25 26 0.109342 ATGACAAGGCCGGATCATCC 59.891 55.000 5.05 0.00 0.00 3.51
26 27 1.227973 GACAAGGCCGGATCATCCC 60.228 63.158 5.05 0.00 31.13 3.85
27 28 1.983119 GACAAGGCCGGATCATCCCA 61.983 60.000 5.05 0.00 31.13 4.37
28 29 1.526917 CAAGGCCGGATCATCCCAC 60.527 63.158 5.05 0.00 31.13 4.61
29 30 2.000701 AAGGCCGGATCATCCCACA 61.001 57.895 5.05 0.00 31.13 4.17
30 31 2.203209 GGCCGGATCATCCCACAC 60.203 66.667 5.05 0.00 31.13 3.82
31 32 2.588877 GCCGGATCATCCCACACG 60.589 66.667 5.05 0.00 31.13 4.49
32 33 2.108976 CCGGATCATCCCACACGG 59.891 66.667 0.00 0.00 31.13 4.94
47 48 4.707791 CGGGGCCCGTAAATATCC 57.292 61.111 36.52 0.00 42.73 2.59
48 49 1.002990 CGGGGCCCGTAAATATCCC 60.003 63.158 36.52 0.00 42.73 3.85
49 50 1.770749 CGGGGCCCGTAAATATCCCA 61.771 60.000 36.52 0.00 42.73 4.37
50 51 0.702316 GGGGCCCGTAAATATCCCAT 59.298 55.000 17.79 0.00 38.72 4.00
51 52 1.076513 GGGGCCCGTAAATATCCCATT 59.923 52.381 17.79 0.00 38.72 3.16
52 53 2.492010 GGGGCCCGTAAATATCCCATTT 60.492 50.000 17.79 0.00 38.72 2.32
53 54 3.245336 GGGGCCCGTAAATATCCCATTTA 60.245 47.826 17.79 0.00 38.72 1.40
54 55 4.409187 GGGCCCGTAAATATCCCATTTAA 58.591 43.478 5.69 0.00 36.96 1.52
55 56 4.833938 GGGCCCGTAAATATCCCATTTAAA 59.166 41.667 5.69 0.00 36.96 1.52
56 57 5.304871 GGGCCCGTAAATATCCCATTTAAAA 59.695 40.000 5.69 0.00 36.96 1.52
57 58 6.183360 GGGCCCGTAAATATCCCATTTAAAAA 60.183 38.462 5.69 0.00 36.96 1.94
80 81 7.698836 AAATTGAAACAATCAGGACTTTTCG 57.301 32.000 0.00 0.00 39.77 3.46
81 82 4.829064 TGAAACAATCAGGACTTTTCGG 57.171 40.909 0.00 0.00 33.04 4.30
82 83 4.456535 TGAAACAATCAGGACTTTTCGGA 58.543 39.130 0.00 0.00 33.04 4.55
83 84 4.515191 TGAAACAATCAGGACTTTTCGGAG 59.485 41.667 0.00 0.00 33.04 4.63
84 85 4.351874 AACAATCAGGACTTTTCGGAGA 57.648 40.909 0.00 0.00 0.00 3.71
85 86 4.559862 ACAATCAGGACTTTTCGGAGAT 57.440 40.909 0.00 0.00 35.04 2.75
86 87 4.911390 ACAATCAGGACTTTTCGGAGATT 58.089 39.130 0.00 0.00 35.04 2.40
87 88 4.697352 ACAATCAGGACTTTTCGGAGATTG 59.303 41.667 0.00 0.00 43.75 2.67
88 89 3.334583 TCAGGACTTTTCGGAGATTGG 57.665 47.619 0.00 0.00 35.04 3.16
89 90 2.903784 TCAGGACTTTTCGGAGATTGGA 59.096 45.455 0.00 0.00 35.04 3.53
90 91 3.519510 TCAGGACTTTTCGGAGATTGGAT 59.480 43.478 0.00 0.00 35.04 3.41
91 92 3.624861 CAGGACTTTTCGGAGATTGGATG 59.375 47.826 0.00 0.00 35.04 3.51
92 93 2.356069 GGACTTTTCGGAGATTGGATGC 59.644 50.000 0.00 0.00 35.04 3.91
93 94 3.009723 GACTTTTCGGAGATTGGATGCA 58.990 45.455 0.00 0.00 35.04 3.96
94 95 3.012518 ACTTTTCGGAGATTGGATGCAG 58.987 45.455 0.00 0.00 35.04 4.41
95 96 1.382522 TTTCGGAGATTGGATGCAGC 58.617 50.000 0.00 0.00 35.04 5.25
96 97 0.543277 TTCGGAGATTGGATGCAGCT 59.457 50.000 0.22 0.00 35.04 4.24
97 98 1.413118 TCGGAGATTGGATGCAGCTA 58.587 50.000 0.22 0.00 0.00 3.32
98 99 1.973515 TCGGAGATTGGATGCAGCTAT 59.026 47.619 0.22 0.00 0.00 2.97
99 100 2.369860 TCGGAGATTGGATGCAGCTATT 59.630 45.455 0.22 0.00 0.00 1.73
100 101 3.578282 TCGGAGATTGGATGCAGCTATTA 59.422 43.478 0.22 0.00 0.00 0.98
101 102 4.040339 TCGGAGATTGGATGCAGCTATTAA 59.960 41.667 0.22 0.00 0.00 1.40
102 103 4.940046 CGGAGATTGGATGCAGCTATTAAT 59.060 41.667 0.22 0.00 0.00 1.40
103 104 5.413833 CGGAGATTGGATGCAGCTATTAATT 59.586 40.000 0.22 0.00 0.00 1.40
104 105 6.402983 CGGAGATTGGATGCAGCTATTAATTC 60.403 42.308 0.22 0.00 0.00 2.17
105 106 6.432162 GGAGATTGGATGCAGCTATTAATTCA 59.568 38.462 0.22 0.00 0.00 2.57
106 107 7.122353 GGAGATTGGATGCAGCTATTAATTCAT 59.878 37.037 0.22 0.00 0.00 2.57
107 108 7.827701 AGATTGGATGCAGCTATTAATTCATG 58.172 34.615 0.22 0.00 0.00 3.07
108 109 7.668469 AGATTGGATGCAGCTATTAATTCATGA 59.332 33.333 0.22 0.00 0.00 3.07
109 110 7.770366 TTGGATGCAGCTATTAATTCATGAT 57.230 32.000 0.22 0.00 0.00 2.45
110 111 7.387119 TGGATGCAGCTATTAATTCATGATC 57.613 36.000 0.22 0.00 0.00 2.92
111 112 7.173032 TGGATGCAGCTATTAATTCATGATCT 58.827 34.615 0.22 0.00 0.00 2.75
112 113 7.120726 TGGATGCAGCTATTAATTCATGATCTG 59.879 37.037 0.22 0.00 0.00 2.90
113 114 6.812879 TGCAGCTATTAATTCATGATCTGG 57.187 37.500 0.00 0.00 0.00 3.86
114 115 5.182570 TGCAGCTATTAATTCATGATCTGGC 59.817 40.000 0.00 0.00 0.00 4.85
115 116 5.182570 GCAGCTATTAATTCATGATCTGGCA 59.817 40.000 0.00 0.00 0.00 4.92
116 117 6.127703 GCAGCTATTAATTCATGATCTGGCAT 60.128 38.462 0.00 0.00 0.00 4.40
117 118 7.251281 CAGCTATTAATTCATGATCTGGCATG 58.749 38.462 0.00 0.00 45.41 4.06
118 119 6.946583 AGCTATTAATTCATGATCTGGCATGT 59.053 34.615 0.00 0.00 44.59 3.21
119 120 8.105197 AGCTATTAATTCATGATCTGGCATGTA 58.895 33.333 0.00 0.00 44.59 2.29
120 121 8.180267 GCTATTAATTCATGATCTGGCATGTAC 58.820 37.037 0.00 0.00 44.59 2.90
121 122 9.223099 CTATTAATTCATGATCTGGCATGTACA 57.777 33.333 0.00 0.00 44.59 2.90
122 123 7.500720 TTAATTCATGATCTGGCATGTACAG 57.499 36.000 11.80 11.80 44.59 2.74
124 125 4.758773 TCATGATCTGGCATGTACAGAA 57.241 40.909 20.81 10.08 46.89 3.02
125 126 5.300411 TCATGATCTGGCATGTACAGAAT 57.700 39.130 20.81 11.53 46.89 2.40
126 127 5.061179 TCATGATCTGGCATGTACAGAATG 58.939 41.667 20.81 19.42 46.89 2.67
127 128 4.758773 TGATCTGGCATGTACAGAATGA 57.241 40.909 20.81 9.19 46.89 2.57
128 129 5.101648 TGATCTGGCATGTACAGAATGAA 57.898 39.130 20.81 8.59 46.89 2.57
129 130 5.499313 TGATCTGGCATGTACAGAATGAAA 58.501 37.500 20.81 7.29 46.89 2.69
130 131 5.945191 TGATCTGGCATGTACAGAATGAAAA 59.055 36.000 20.81 2.96 46.89 2.29
131 132 5.627499 TCTGGCATGTACAGAATGAAAAC 57.373 39.130 16.55 0.00 41.66 2.43
132 133 5.316167 TCTGGCATGTACAGAATGAAAACT 58.684 37.500 16.55 0.00 41.66 2.66
133 134 5.769662 TCTGGCATGTACAGAATGAAAACTT 59.230 36.000 16.55 0.00 41.66 2.66
134 135 6.012658 TGGCATGTACAGAATGAAAACTTC 57.987 37.500 0.33 0.00 39.69 3.01
135 136 5.534278 TGGCATGTACAGAATGAAAACTTCA 59.466 36.000 0.33 0.00 45.01 3.02
149 150 7.278211 TGAAAACTTCATTCTCGATTCTACG 57.722 36.000 0.00 0.00 34.08 3.51
150 151 7.088272 TGAAAACTTCATTCTCGATTCTACGA 58.912 34.615 0.00 0.00 36.43 3.43
151 152 7.273598 TGAAAACTTCATTCTCGATTCTACGAG 59.726 37.037 11.11 11.11 45.80 4.18
166 167 9.148460 CGATTCTACGAGAATTTTTATGAAAGC 57.852 33.333 10.21 0.00 44.41 3.51
167 168 9.148460 GATTCTACGAGAATTTTTATGAAAGCG 57.852 33.333 10.21 0.00 44.41 4.68
168 169 7.591006 TCTACGAGAATTTTTATGAAAGCGT 57.409 32.000 0.00 0.00 0.00 5.07
169 170 8.025243 TCTACGAGAATTTTTATGAAAGCGTT 57.975 30.769 0.00 0.00 0.00 4.84
170 171 8.500773 TCTACGAGAATTTTTATGAAAGCGTTT 58.499 29.630 0.00 0.00 0.00 3.60
171 172 7.548673 ACGAGAATTTTTATGAAAGCGTTTC 57.451 32.000 0.00 4.24 40.08 2.78
184 185 4.574599 AAGCGTTTCATTTGCTTCTCTT 57.425 36.364 0.00 0.00 45.24 2.85
185 186 4.152607 AGCGTTTCATTTGCTTCTCTTC 57.847 40.909 0.00 0.00 34.80 2.87
186 187 3.565482 AGCGTTTCATTTGCTTCTCTTCA 59.435 39.130 0.00 0.00 34.80 3.02
187 188 4.036734 AGCGTTTCATTTGCTTCTCTTCAA 59.963 37.500 0.00 0.00 34.80 2.69
188 189 4.919754 GCGTTTCATTTGCTTCTCTTCAAT 59.080 37.500 0.00 0.00 0.00 2.57
189 190 5.164119 GCGTTTCATTTGCTTCTCTTCAATG 60.164 40.000 0.00 0.00 0.00 2.82
190 191 5.344128 CGTTTCATTTGCTTCTCTTCAATGG 59.656 40.000 0.00 0.00 0.00 3.16
191 192 6.449698 GTTTCATTTGCTTCTCTTCAATGGA 58.550 36.000 0.00 0.00 0.00 3.41
192 193 6.653526 TTCATTTGCTTCTCTTCAATGGAA 57.346 33.333 0.00 0.00 0.00 3.53
206 207 6.678568 TTCAATGGAAGCTTTATTTTCCCA 57.321 33.333 0.00 1.22 41.75 4.37
207 208 6.284891 TCAATGGAAGCTTTATTTTCCCAG 57.715 37.500 0.00 0.00 41.75 4.45
208 209 6.015918 TCAATGGAAGCTTTATTTTCCCAGA 58.984 36.000 0.00 0.00 41.75 3.86
209 210 6.496565 TCAATGGAAGCTTTATTTTCCCAGAA 59.503 34.615 0.00 0.00 41.75 3.02
210 211 7.180766 TCAATGGAAGCTTTATTTTCCCAGAAT 59.819 33.333 0.00 0.00 41.75 2.40
211 212 6.284891 TGGAAGCTTTATTTTCCCAGAATG 57.715 37.500 0.00 0.00 41.75 2.67
212 213 5.779771 TGGAAGCTTTATTTTCCCAGAATGT 59.220 36.000 0.00 0.00 41.75 2.71
213 214 6.951198 TGGAAGCTTTATTTTCCCAGAATGTA 59.049 34.615 0.00 0.00 41.75 2.29
214 215 7.619302 TGGAAGCTTTATTTTCCCAGAATGTAT 59.381 33.333 0.00 0.00 41.75 2.29
215 216 8.138074 GGAAGCTTTATTTTCCCAGAATGTATC 58.862 37.037 0.00 0.00 37.48 2.24
216 217 7.588497 AGCTTTATTTTCCCAGAATGTATCC 57.412 36.000 0.00 0.00 0.00 2.59
217 218 7.357471 AGCTTTATTTTCCCAGAATGTATCCT 58.643 34.615 0.00 0.00 0.00 3.24
218 219 8.502738 AGCTTTATTTTCCCAGAATGTATCCTA 58.497 33.333 0.00 0.00 0.00 2.94
219 220 9.131791 GCTTTATTTTCCCAGAATGTATCCTAA 57.868 33.333 0.00 0.00 0.00 2.69
226 227 7.896383 TCCCAGAATGTATCCTAATTTTTGG 57.104 36.000 0.00 0.00 0.00 3.28
227 228 6.323739 TCCCAGAATGTATCCTAATTTTTGGC 59.676 38.462 0.00 0.00 0.00 4.52
228 229 6.462909 CCCAGAATGTATCCTAATTTTTGGCC 60.463 42.308 0.00 0.00 0.00 5.36
229 230 6.324770 CCAGAATGTATCCTAATTTTTGGCCT 59.675 38.462 3.32 0.00 0.00 5.19
230 231 7.505585 CCAGAATGTATCCTAATTTTTGGCCTA 59.494 37.037 3.32 0.00 0.00 3.93
231 232 8.912988 CAGAATGTATCCTAATTTTTGGCCTAA 58.087 33.333 3.32 0.00 0.00 2.69
232 233 9.660544 AGAATGTATCCTAATTTTTGGCCTAAT 57.339 29.630 3.32 0.00 0.00 1.73
235 236 9.660544 ATGTATCCTAATTTTTGGCCTAATTCT 57.339 29.630 3.32 0.00 0.00 2.40
236 237 9.487442 TGTATCCTAATTTTTGGCCTAATTCTT 57.513 29.630 3.32 0.00 0.00 2.52
237 238 9.967346 GTATCCTAATTTTTGGCCTAATTCTTC 57.033 33.333 3.32 0.00 0.00 2.87
238 239 8.844865 ATCCTAATTTTTGGCCTAATTCTTCT 57.155 30.769 3.32 0.00 0.00 2.85
239 240 8.664669 TCCTAATTTTTGGCCTAATTCTTCTT 57.335 30.769 3.32 0.00 0.00 2.52
240 241 8.749354 TCCTAATTTTTGGCCTAATTCTTCTTC 58.251 33.333 3.32 0.00 0.00 2.87
241 242 8.753133 CCTAATTTTTGGCCTAATTCTTCTTCT 58.247 33.333 3.32 0.00 0.00 2.85
242 243 9.578439 CTAATTTTTGGCCTAATTCTTCTTCTG 57.422 33.333 3.32 0.00 0.00 3.02
243 244 7.781324 ATTTTTGGCCTAATTCTTCTTCTGA 57.219 32.000 3.32 0.00 0.00 3.27
244 245 7.781324 TTTTTGGCCTAATTCTTCTTCTGAT 57.219 32.000 3.32 0.00 0.00 2.90
245 246 6.764308 TTTGGCCTAATTCTTCTTCTGATG 57.236 37.500 3.32 0.00 0.00 3.07
246 247 5.698741 TGGCCTAATTCTTCTTCTGATGA 57.301 39.130 3.32 0.00 0.00 2.92
247 248 6.257994 TGGCCTAATTCTTCTTCTGATGAT 57.742 37.500 3.32 0.00 0.00 2.45
248 249 6.294473 TGGCCTAATTCTTCTTCTGATGATC 58.706 40.000 3.32 0.00 0.00 2.92
249 250 5.407995 GGCCTAATTCTTCTTCTGATGATCG 59.592 44.000 0.00 0.00 0.00 3.69
250 251 6.219473 GCCTAATTCTTCTTCTGATGATCGA 58.781 40.000 0.00 0.00 0.00 3.59
251 252 6.873076 GCCTAATTCTTCTTCTGATGATCGAT 59.127 38.462 0.00 0.00 0.00 3.59
252 253 7.387397 GCCTAATTCTTCTTCTGATGATCGATT 59.613 37.037 0.00 0.00 0.00 3.34
253 254 8.924691 CCTAATTCTTCTTCTGATGATCGATTC 58.075 37.037 0.00 0.00 0.00 2.52
254 255 9.473640 CTAATTCTTCTTCTGATGATCGATTCA 57.526 33.333 0.00 0.00 39.12 2.57
255 256 8.728337 AATTCTTCTTCTGATGATCGATTCAA 57.272 30.769 0.00 0.00 38.03 2.69
256 257 7.531280 TTCTTCTTCTGATGATCGATTCAAC 57.469 36.000 0.00 0.00 38.03 3.18
257 258 6.045318 TCTTCTTCTGATGATCGATTCAACC 58.955 40.000 0.00 0.00 38.03 3.77
258 259 5.604758 TCTTCTGATGATCGATTCAACCT 57.395 39.130 0.00 0.00 38.03 3.50
259 260 5.595885 TCTTCTGATGATCGATTCAACCTC 58.404 41.667 0.00 0.00 38.03 3.85
260 261 5.362143 TCTTCTGATGATCGATTCAACCTCT 59.638 40.000 0.00 0.00 38.03 3.69
261 262 4.941657 TCTGATGATCGATTCAACCTCTG 58.058 43.478 0.00 0.00 38.03 3.35
262 263 4.646492 TCTGATGATCGATTCAACCTCTGA 59.354 41.667 0.00 1.92 38.03 3.27
263 264 5.303845 TCTGATGATCGATTCAACCTCTGAT 59.696 40.000 0.00 0.00 38.03 2.90
264 265 6.491403 TCTGATGATCGATTCAACCTCTGATA 59.509 38.462 0.00 0.00 38.03 2.15
265 266 7.014615 TCTGATGATCGATTCAACCTCTGATAA 59.985 37.037 0.00 0.00 38.03 1.75
266 267 7.500141 TGATGATCGATTCAACCTCTGATAAA 58.500 34.615 0.00 0.00 38.03 1.40
267 268 7.986889 TGATGATCGATTCAACCTCTGATAAAA 59.013 33.333 0.00 0.00 38.03 1.52
268 269 8.737168 ATGATCGATTCAACCTCTGATAAAAA 57.263 30.769 0.00 0.00 38.03 1.94
294 295 8.971032 AGATAGATCTTGGGTCTATTTCATCT 57.029 34.615 0.00 0.00 38.63 2.90
295 296 9.034800 AGATAGATCTTGGGTCTATTTCATCTC 57.965 37.037 0.00 0.00 38.63 2.75
296 297 8.971032 ATAGATCTTGGGTCTATTTCATCTCT 57.029 34.615 0.00 0.00 35.85 3.10
297 298 7.688918 AGATCTTGGGTCTATTTCATCTCTT 57.311 36.000 0.00 0.00 0.00 2.85
298 299 7.734942 AGATCTTGGGTCTATTTCATCTCTTC 58.265 38.462 0.00 0.00 0.00 2.87
299 300 6.874278 TCTTGGGTCTATTTCATCTCTTCA 57.126 37.500 0.00 0.00 0.00 3.02
300 301 7.257790 TCTTGGGTCTATTTCATCTCTTCAA 57.742 36.000 0.00 0.00 0.00 2.69
301 302 7.106239 TCTTGGGTCTATTTCATCTCTTCAAC 58.894 38.462 0.00 0.00 0.00 3.18
302 303 6.373005 TGGGTCTATTTCATCTCTTCAACA 57.627 37.500 0.00 0.00 0.00 3.33
303 304 6.778821 TGGGTCTATTTCATCTCTTCAACAA 58.221 36.000 0.00 0.00 0.00 2.83
304 305 6.881065 TGGGTCTATTTCATCTCTTCAACAAG 59.119 38.462 0.00 0.00 0.00 3.16
305 306 6.881602 GGGTCTATTTCATCTCTTCAACAAGT 59.118 38.462 0.00 0.00 0.00 3.16
306 307 7.391833 GGGTCTATTTCATCTCTTCAACAAGTT 59.608 37.037 0.00 0.00 0.00 2.66
307 308 8.787852 GGTCTATTTCATCTCTTCAACAAGTTT 58.212 33.333 0.00 0.00 0.00 2.66
318 319 9.998106 TCTCTTCAACAAGTTTAGTAATAAGCT 57.002 29.630 0.00 0.00 0.00 3.74
332 333 4.373156 AATAAGCTGTTGACCTCACCTT 57.627 40.909 0.00 0.00 0.00 3.50
335 336 1.490490 AGCTGTTGACCTCACCTTTGA 59.510 47.619 0.00 0.00 0.00 2.69
459 895 3.748568 GCGATTCTAATTGGATGACCTCC 59.251 47.826 0.00 0.00 45.19 4.30
467 1193 1.908483 GGATGACCTCCACCTGACC 59.092 63.158 0.00 0.00 44.26 4.02
470 1196 1.258445 ATGACCTCCACCTGACCGAC 61.258 60.000 0.00 0.00 0.00 4.79
474 1200 1.472662 CCTCCACCTGACCGACTGTT 61.473 60.000 0.00 0.00 0.00 3.16
475 1201 0.393077 CTCCACCTGACCGACTGTTT 59.607 55.000 0.00 0.00 0.00 2.83
476 1202 0.105964 TCCACCTGACCGACTGTTTG 59.894 55.000 0.00 0.00 0.00 2.93
501 1227 0.745128 AAGTCCAAACGTGTCCGCAA 60.745 50.000 0.00 0.00 37.70 4.85
505 1231 1.532007 TCCAAACGTGTCCGCAAATAC 59.468 47.619 0.00 0.00 37.70 1.89
511 1237 1.326548 CGTGTCCGCAAATACTTAGGC 59.673 52.381 0.00 0.00 0.00 3.93
535 1261 4.149221 CCTTCGGCGAAAACCAAAAATTAC 59.851 41.667 23.81 0.00 0.00 1.89
536 1262 4.303086 TCGGCGAAAACCAAAAATTACA 57.697 36.364 7.35 0.00 0.00 2.41
540 1266 4.318475 GGCGAAAACCAAAAATTACAGCAC 60.318 41.667 0.00 0.00 0.00 4.40
550 1276 7.062848 CCAAAAATTACAGCACGTCAAAATTC 58.937 34.615 0.00 0.00 0.00 2.17
551 1277 6.432802 AAAATTACAGCACGTCAAAATTCG 57.567 33.333 0.00 0.00 0.00 3.34
552 1278 2.587612 TACAGCACGTCAAAATTCGC 57.412 45.000 0.00 0.00 0.00 4.70
554 1280 1.069906 ACAGCACGTCAAAATTCGCTC 60.070 47.619 0.00 0.00 0.00 5.03
558 1284 1.262950 CACGTCAAAATTCGCTCCACA 59.737 47.619 0.00 0.00 0.00 4.17
559 1285 1.531149 ACGTCAAAATTCGCTCCACAG 59.469 47.619 0.00 0.00 0.00 3.66
560 1286 1.798223 CGTCAAAATTCGCTCCACAGA 59.202 47.619 0.00 0.00 0.00 3.41
562 1288 3.120199 CGTCAAAATTCGCTCCACAGAAT 60.120 43.478 0.00 0.00 38.58 2.40
563 1289 4.406943 GTCAAAATTCGCTCCACAGAATC 58.593 43.478 0.00 0.00 36.20 2.52
564 1290 4.154918 GTCAAAATTCGCTCCACAGAATCT 59.845 41.667 0.00 0.00 36.20 2.40
565 1291 4.393062 TCAAAATTCGCTCCACAGAATCTC 59.607 41.667 0.00 0.00 36.20 2.75
610 1341 4.129148 GCTCCCCCGGCTCCATTT 62.129 66.667 0.00 0.00 0.00 2.32
643 1374 5.784578 AACGAAACCAAAAGCTTAATCCT 57.215 34.783 0.00 0.00 0.00 3.24
644 1375 5.121221 ACGAAACCAAAAGCTTAATCCTG 57.879 39.130 0.00 0.00 0.00 3.86
647 1378 5.629435 CGAAACCAAAAGCTTAATCCTGTTC 59.371 40.000 0.00 0.00 0.00 3.18
706 3451 2.046938 CTATTCGCGCCTTCCCCTA 58.953 57.895 0.00 0.00 0.00 3.53
798 3543 0.933097 CAGCAAATCAGGATCGTCCG 59.067 55.000 0.00 0.00 42.75 4.79
1350 4141 0.517316 GCTACAACAAGAAGCCCACG 59.483 55.000 0.00 0.00 0.00 4.94
1537 4340 5.335191 GCTCAATGGAAATCGGTGGAATATC 60.335 44.000 0.00 0.00 0.00 1.63
1674 4742 3.200605 TGATGCATGTCCCAACTATCTGT 59.799 43.478 2.46 0.00 0.00 3.41
1691 4759 9.634021 AACTATCTGTCTGATCTCTGTTATGTA 57.366 33.333 0.00 0.00 36.65 2.29
1707 4775 9.161629 TCTGTTATGTAATGGTAGTTGATGTTG 57.838 33.333 0.00 0.00 0.00 3.33
1720 4788 7.755822 GGTAGTTGATGTTGTGTTTTTGTTACA 59.244 33.333 0.00 0.00 0.00 2.41
1747 4815 3.817709 TTTTGCTTTTGGAGACTTGGG 57.182 42.857 0.00 0.00 0.00 4.12
1750 4818 1.202927 TGCTTTTGGAGACTTGGGAGG 60.203 52.381 0.00 0.00 0.00 4.30
1779 4850 2.676076 CCAATTTGGCTGAAGAAACCG 58.324 47.619 1.71 0.00 0.00 4.44
1907 5375 9.778993 CTCTTTGTGACATAAAGATACCAAATG 57.221 33.333 22.80 9.04 41.71 2.32
1909 5377 9.912634 CTTTGTGACATAAAGATACCAAATGTT 57.087 29.630 17.19 0.00 37.33 2.71
2064 5538 3.645884 CCTGGTGAGTGCTTCATTTTTG 58.354 45.455 0.00 0.00 38.29 2.44
2176 5650 2.706890 GGCTCCTGTTTTCCATCGTTA 58.293 47.619 0.00 0.00 0.00 3.18
2179 5653 3.424433 GCTCCTGTTTTCCATCGTTAACG 60.424 47.826 21.85 21.85 41.45 3.18
2238 5795 2.057316 CAGAGATATTTCGAGGCTGCG 58.943 52.381 0.00 0.00 0.00 5.18
2243 5800 2.238847 TATTTCGAGGCTGCGCAGGT 62.239 55.000 36.47 8.65 0.00 4.00
2266 5823 8.004215 AGGTATGGTTTTCAAGATATAATGCCA 58.996 33.333 0.00 0.00 0.00 4.92
2287 5845 7.853299 TGCCAATCTTTTACATACTGTACCTA 58.147 34.615 0.00 0.00 31.69 3.08
2290 5848 8.262227 CCAATCTTTTACATACTGTACCTACCA 58.738 37.037 0.00 0.00 31.69 3.25
2291 5849 9.832445 CAATCTTTTACATACTGTACCTACCAT 57.168 33.333 0.00 0.00 31.69 3.55
2292 5850 9.832445 AATCTTTTACATACTGTACCTACCATG 57.168 33.333 0.00 0.00 31.69 3.66
2293 5851 8.370266 TCTTTTACATACTGTACCTACCATGT 57.630 34.615 0.00 0.00 31.69 3.21
2294 5852 9.478238 TCTTTTACATACTGTACCTACCATGTA 57.522 33.333 0.00 0.00 31.69 2.29
2311 5869 5.932303 ACCATGTAATCGGATGCTAATACAC 59.068 40.000 2.50 0.00 0.00 2.90
2381 6208 0.107017 AACCAGCAGCTCAACACAGT 60.107 50.000 0.00 0.00 0.00 3.55
2383 6210 0.533531 CCAGCAGCTCAACACAGTCA 60.534 55.000 0.00 0.00 0.00 3.41
2384 6211 0.866427 CAGCAGCTCAACACAGTCAG 59.134 55.000 0.00 0.00 0.00 3.51
2413 6240 5.399858 CAGCAAACGTACTACAGTCTACAT 58.600 41.667 0.00 0.00 0.00 2.29
2422 6249 6.128090 CGTACTACAGTCTACATGGAGAACAA 60.128 42.308 9.89 0.00 32.57 2.83
2444 6272 3.334583 TTCTACACAGAATGGACTGCC 57.665 47.619 0.00 0.00 43.62 4.85
2456 6284 2.334977 TGGACTGCCAGAAAGTAGGAA 58.665 47.619 0.00 0.00 39.92 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.394216 TCCGGCCTTGTCATCATTGG 60.394 55.000 0.00 0.00 0.00 3.16
1 2 1.605710 GATCCGGCCTTGTCATCATTG 59.394 52.381 0.00 0.00 0.00 2.82
2 3 1.212688 TGATCCGGCCTTGTCATCATT 59.787 47.619 0.00 0.00 0.00 2.57
3 4 0.839277 TGATCCGGCCTTGTCATCAT 59.161 50.000 0.00 0.00 0.00 2.45
4 5 0.839277 ATGATCCGGCCTTGTCATCA 59.161 50.000 0.00 0.00 0.00 3.07
5 6 1.517242 GATGATCCGGCCTTGTCATC 58.483 55.000 18.97 18.97 39.88 2.92
6 7 0.109342 GGATGATCCGGCCTTGTCAT 59.891 55.000 11.86 11.86 34.23 3.06
7 8 1.526887 GGATGATCCGGCCTTGTCA 59.473 57.895 0.00 1.84 0.00 3.58
8 9 1.227973 GGGATGATCCGGCCTTGTC 60.228 63.158 5.22 0.00 37.43 3.18
9 10 2.000701 TGGGATGATCCGGCCTTGT 61.001 57.895 5.22 0.00 37.43 3.16
10 11 1.526917 GTGGGATGATCCGGCCTTG 60.527 63.158 5.22 0.00 37.43 3.61
11 12 2.000701 TGTGGGATGATCCGGCCTT 61.001 57.895 5.22 0.00 37.43 4.35
12 13 2.366837 TGTGGGATGATCCGGCCT 60.367 61.111 5.22 0.00 37.43 5.19
13 14 2.203209 GTGTGGGATGATCCGGCC 60.203 66.667 5.22 0.00 37.43 6.13
14 15 2.588877 CGTGTGGGATGATCCGGC 60.589 66.667 5.22 1.20 37.43 6.13
15 16 2.108976 CCGTGTGGGATGATCCGG 59.891 66.667 5.22 0.00 37.43 5.14
31 32 0.702316 ATGGGATATTTACGGGCCCC 59.298 55.000 18.66 0.00 38.02 5.80
32 33 2.597578 AATGGGATATTTACGGGCCC 57.402 50.000 13.57 13.57 39.29 5.80
33 34 6.408107 TTTTAAATGGGATATTTACGGGCC 57.592 37.500 0.00 0.00 0.00 5.80
54 55 8.603181 CGAAAAGTCCTGATTGTTTCAATTTTT 58.397 29.630 0.00 0.00 32.78 1.94
55 56 7.224557 CCGAAAAGTCCTGATTGTTTCAATTTT 59.775 33.333 0.00 0.00 32.78 1.82
56 57 6.701400 CCGAAAAGTCCTGATTGTTTCAATTT 59.299 34.615 0.00 0.00 32.78 1.82
57 58 6.040391 TCCGAAAAGTCCTGATTGTTTCAATT 59.960 34.615 0.00 0.00 32.78 2.32
58 59 5.534654 TCCGAAAAGTCCTGATTGTTTCAAT 59.465 36.000 0.00 0.00 32.78 2.57
59 60 4.884744 TCCGAAAAGTCCTGATTGTTTCAA 59.115 37.500 0.00 0.00 32.78 2.69
60 61 4.456535 TCCGAAAAGTCCTGATTGTTTCA 58.543 39.130 0.00 0.00 0.00 2.69
61 62 4.755123 TCTCCGAAAAGTCCTGATTGTTTC 59.245 41.667 0.00 0.00 0.00 2.78
62 63 4.714632 TCTCCGAAAAGTCCTGATTGTTT 58.285 39.130 0.00 0.00 0.00 2.83
63 64 4.351874 TCTCCGAAAAGTCCTGATTGTT 57.648 40.909 0.00 0.00 0.00 2.83
64 65 4.559862 ATCTCCGAAAAGTCCTGATTGT 57.440 40.909 0.00 0.00 0.00 2.71
65 66 4.095483 CCAATCTCCGAAAAGTCCTGATTG 59.905 45.833 0.00 0.00 39.03 2.67
66 67 4.019321 TCCAATCTCCGAAAAGTCCTGATT 60.019 41.667 0.00 0.00 0.00 2.57
67 68 3.519510 TCCAATCTCCGAAAAGTCCTGAT 59.480 43.478 0.00 0.00 0.00 2.90
68 69 2.903784 TCCAATCTCCGAAAAGTCCTGA 59.096 45.455 0.00 0.00 0.00 3.86
69 70 3.334583 TCCAATCTCCGAAAAGTCCTG 57.665 47.619 0.00 0.00 0.00 3.86
70 71 3.878778 CATCCAATCTCCGAAAAGTCCT 58.121 45.455 0.00 0.00 0.00 3.85
71 72 2.356069 GCATCCAATCTCCGAAAAGTCC 59.644 50.000 0.00 0.00 0.00 3.85
72 73 3.009723 TGCATCCAATCTCCGAAAAGTC 58.990 45.455 0.00 0.00 0.00 3.01
73 74 3.012518 CTGCATCCAATCTCCGAAAAGT 58.987 45.455 0.00 0.00 0.00 2.66
74 75 2.223433 GCTGCATCCAATCTCCGAAAAG 60.223 50.000 0.00 0.00 0.00 2.27
75 76 1.745087 GCTGCATCCAATCTCCGAAAA 59.255 47.619 0.00 0.00 0.00 2.29
76 77 1.065199 AGCTGCATCCAATCTCCGAAA 60.065 47.619 1.02 0.00 0.00 3.46
77 78 0.543277 AGCTGCATCCAATCTCCGAA 59.457 50.000 1.02 0.00 0.00 4.30
78 79 1.413118 TAGCTGCATCCAATCTCCGA 58.587 50.000 1.02 0.00 0.00 4.55
79 80 2.469274 ATAGCTGCATCCAATCTCCG 57.531 50.000 1.02 0.00 0.00 4.63
80 81 6.432162 TGAATTAATAGCTGCATCCAATCTCC 59.568 38.462 1.02 0.00 0.00 3.71
81 82 7.444629 TGAATTAATAGCTGCATCCAATCTC 57.555 36.000 1.02 0.00 0.00 2.75
82 83 7.668469 TCATGAATTAATAGCTGCATCCAATCT 59.332 33.333 1.02 0.00 0.00 2.40
83 84 7.823665 TCATGAATTAATAGCTGCATCCAATC 58.176 34.615 1.02 0.00 0.00 2.67
84 85 7.770366 TCATGAATTAATAGCTGCATCCAAT 57.230 32.000 1.02 0.00 0.00 3.16
85 86 7.668469 AGATCATGAATTAATAGCTGCATCCAA 59.332 33.333 0.00 0.00 0.00 3.53
86 87 7.120726 CAGATCATGAATTAATAGCTGCATCCA 59.879 37.037 0.00 0.00 0.00 3.41
87 88 7.415318 CCAGATCATGAATTAATAGCTGCATCC 60.415 40.741 0.00 0.00 0.00 3.51
88 89 7.473366 CCAGATCATGAATTAATAGCTGCATC 58.527 38.462 0.00 0.00 0.00 3.91
89 90 6.127703 GCCAGATCATGAATTAATAGCTGCAT 60.128 38.462 0.00 0.00 0.00 3.96
90 91 5.182570 GCCAGATCATGAATTAATAGCTGCA 59.817 40.000 0.00 0.00 0.00 4.41
91 92 5.182570 TGCCAGATCATGAATTAATAGCTGC 59.817 40.000 0.00 0.00 0.00 5.25
92 93 6.812879 TGCCAGATCATGAATTAATAGCTG 57.187 37.500 0.00 0.00 0.00 4.24
93 94 6.946583 ACATGCCAGATCATGAATTAATAGCT 59.053 34.615 0.00 0.00 44.94 3.32
94 95 7.154435 ACATGCCAGATCATGAATTAATAGC 57.846 36.000 0.00 0.00 44.94 2.97
95 96 9.223099 TGTACATGCCAGATCATGAATTAATAG 57.777 33.333 0.00 0.00 44.94 1.73
96 97 9.223099 CTGTACATGCCAGATCATGAATTAATA 57.777 33.333 0.00 0.00 44.94 0.98
97 98 7.940688 TCTGTACATGCCAGATCATGAATTAAT 59.059 33.333 10.72 0.00 44.94 1.40
98 99 7.281841 TCTGTACATGCCAGATCATGAATTAA 58.718 34.615 10.72 0.00 44.94 1.40
99 100 6.829849 TCTGTACATGCCAGATCATGAATTA 58.170 36.000 10.72 0.00 44.94 1.40
100 101 5.687780 TCTGTACATGCCAGATCATGAATT 58.312 37.500 10.72 0.00 44.94 2.17
101 102 5.300411 TCTGTACATGCCAGATCATGAAT 57.700 39.130 10.72 0.00 44.94 2.57
102 103 4.758773 TCTGTACATGCCAGATCATGAA 57.241 40.909 10.72 0.00 44.94 2.57
103 104 4.758773 TTCTGTACATGCCAGATCATGA 57.241 40.909 14.44 0.00 44.94 3.07
104 105 5.061179 TCATTCTGTACATGCCAGATCATG 58.939 41.667 14.44 14.90 46.86 3.07
105 106 5.300411 TCATTCTGTACATGCCAGATCAT 57.700 39.130 14.44 5.71 38.66 2.45
106 107 4.758773 TCATTCTGTACATGCCAGATCA 57.241 40.909 14.44 3.86 38.66 2.92
107 108 6.094603 AGTTTTCATTCTGTACATGCCAGATC 59.905 38.462 14.44 0.00 38.66 2.75
108 109 5.948162 AGTTTTCATTCTGTACATGCCAGAT 59.052 36.000 14.44 4.94 38.66 2.90
109 110 5.316167 AGTTTTCATTCTGTACATGCCAGA 58.684 37.500 10.72 10.72 37.18 3.86
110 111 5.633830 AGTTTTCATTCTGTACATGCCAG 57.366 39.130 0.00 6.64 0.00 4.85
111 112 5.534278 TGAAGTTTTCATTCTGTACATGCCA 59.466 36.000 0.00 0.00 34.08 4.92
112 113 6.012658 TGAAGTTTTCATTCTGTACATGCC 57.987 37.500 0.00 0.00 34.08 4.40
124 125 7.759886 TCGTAGAATCGAGAATGAAGTTTTCAT 59.240 33.333 0.00 0.00 42.16 2.57
125 126 7.088272 TCGTAGAATCGAGAATGAAGTTTTCA 58.912 34.615 0.00 0.00 38.27 2.69
126 127 7.507672 TCGTAGAATCGAGAATGAAGTTTTC 57.492 36.000 0.00 0.00 34.85 2.29
140 141 9.148460 GCTTTCATAAAAATTCTCGTAGAATCG 57.852 33.333 9.54 0.00 43.67 3.34
141 142 9.148460 CGCTTTCATAAAAATTCTCGTAGAATC 57.852 33.333 9.54 0.00 43.67 2.52
142 143 8.665685 ACGCTTTCATAAAAATTCTCGTAGAAT 58.334 29.630 4.81 4.81 46.22 2.40
143 144 8.025243 ACGCTTTCATAAAAATTCTCGTAGAA 57.975 30.769 0.79 0.79 38.78 2.10
144 145 7.591006 ACGCTTTCATAAAAATTCTCGTAGA 57.409 32.000 0.00 0.00 0.00 2.59
145 146 8.655378 AAACGCTTTCATAAAAATTCTCGTAG 57.345 30.769 0.00 0.00 0.00 3.51
146 147 8.283992 TGAAACGCTTTCATAAAAATTCTCGTA 58.716 29.630 8.47 0.00 44.21 3.43
147 148 7.136119 TGAAACGCTTTCATAAAAATTCTCGT 58.864 30.769 8.47 0.00 44.21 4.18
148 149 7.547285 TGAAACGCTTTCATAAAAATTCTCG 57.453 32.000 8.47 0.00 44.21 4.04
161 162 4.540824 AGAGAAGCAAATGAAACGCTTTC 58.459 39.130 0.00 4.24 45.63 2.62
162 163 4.574599 AGAGAAGCAAATGAAACGCTTT 57.425 36.364 0.00 0.00 45.63 3.51
164 165 3.565482 TGAAGAGAAGCAAATGAAACGCT 59.435 39.130 0.00 0.00 37.68 5.07
165 166 3.888934 TGAAGAGAAGCAAATGAAACGC 58.111 40.909 0.00 0.00 0.00 4.84
166 167 5.344128 CCATTGAAGAGAAGCAAATGAAACG 59.656 40.000 0.00 0.00 0.00 3.60
167 168 6.449698 TCCATTGAAGAGAAGCAAATGAAAC 58.550 36.000 0.00 0.00 0.00 2.78
168 169 6.653526 TCCATTGAAGAGAAGCAAATGAAA 57.346 33.333 0.00 0.00 0.00 2.69
169 170 6.653526 TTCCATTGAAGAGAAGCAAATGAA 57.346 33.333 0.00 0.00 0.00 2.57
183 184 6.496565 TCTGGGAAAATAAAGCTTCCATTGAA 59.503 34.615 0.00 0.00 42.56 2.69
184 185 6.015918 TCTGGGAAAATAAAGCTTCCATTGA 58.984 36.000 0.00 0.00 42.56 2.57
185 186 6.284891 TCTGGGAAAATAAAGCTTCCATTG 57.715 37.500 0.00 0.00 42.56 2.82
186 187 6.933514 TTCTGGGAAAATAAAGCTTCCATT 57.066 33.333 0.00 0.00 42.56 3.16
187 188 6.441604 ACATTCTGGGAAAATAAAGCTTCCAT 59.558 34.615 0.00 0.00 42.56 3.41
188 189 5.779771 ACATTCTGGGAAAATAAAGCTTCCA 59.220 36.000 0.00 0.00 42.56 3.53
189 190 6.286240 ACATTCTGGGAAAATAAAGCTTCC 57.714 37.500 0.00 0.00 40.44 3.46
190 191 8.138074 GGATACATTCTGGGAAAATAAAGCTTC 58.862 37.037 0.00 0.00 0.00 3.86
191 192 7.841222 AGGATACATTCTGGGAAAATAAAGCTT 59.159 33.333 0.00 0.00 41.41 3.74
192 193 7.357471 AGGATACATTCTGGGAAAATAAAGCT 58.643 34.615 0.00 0.00 41.41 3.74
193 194 7.588497 AGGATACATTCTGGGAAAATAAAGC 57.412 36.000 0.00 0.00 41.41 3.51
200 201 8.757877 CCAAAAATTAGGATACATTCTGGGAAA 58.242 33.333 0.00 0.00 41.41 3.13
201 202 7.147742 GCCAAAAATTAGGATACATTCTGGGAA 60.148 37.037 0.00 0.00 41.41 3.97
202 203 6.323739 GCCAAAAATTAGGATACATTCTGGGA 59.676 38.462 0.00 0.00 41.41 4.37
203 204 6.462909 GGCCAAAAATTAGGATACATTCTGGG 60.463 42.308 0.00 0.00 41.41 4.45
204 205 6.324770 AGGCCAAAAATTAGGATACATTCTGG 59.675 38.462 5.01 0.00 41.41 3.86
205 206 7.352079 AGGCCAAAAATTAGGATACATTCTG 57.648 36.000 5.01 0.00 41.41 3.02
206 207 9.660544 ATTAGGCCAAAAATTAGGATACATTCT 57.339 29.630 5.01 0.00 41.41 2.40
209 210 9.660544 AGAATTAGGCCAAAAATTAGGATACAT 57.339 29.630 5.01 0.00 41.41 2.29
210 211 9.487442 AAGAATTAGGCCAAAAATTAGGATACA 57.513 29.630 5.01 0.00 41.41 2.29
211 212 9.967346 GAAGAATTAGGCCAAAAATTAGGATAC 57.033 33.333 5.01 0.00 0.00 2.24
212 213 9.936329 AGAAGAATTAGGCCAAAAATTAGGATA 57.064 29.630 5.01 0.00 0.00 2.59
213 214 8.844865 AGAAGAATTAGGCCAAAAATTAGGAT 57.155 30.769 5.01 0.00 0.00 3.24
214 215 8.664669 AAGAAGAATTAGGCCAAAAATTAGGA 57.335 30.769 5.01 0.00 0.00 2.94
215 216 8.753133 AGAAGAAGAATTAGGCCAAAAATTAGG 58.247 33.333 5.01 0.00 0.00 2.69
216 217 9.578439 CAGAAGAAGAATTAGGCCAAAAATTAG 57.422 33.333 5.01 0.00 0.00 1.73
217 218 9.308000 TCAGAAGAAGAATTAGGCCAAAAATTA 57.692 29.630 5.01 0.00 0.00 1.40
218 219 8.193953 TCAGAAGAAGAATTAGGCCAAAAATT 57.806 30.769 5.01 8.03 0.00 1.82
219 220 7.781324 TCAGAAGAAGAATTAGGCCAAAAAT 57.219 32.000 5.01 0.00 0.00 1.82
220 221 7.451255 TCATCAGAAGAAGAATTAGGCCAAAAA 59.549 33.333 5.01 0.00 0.00 1.94
221 222 6.947733 TCATCAGAAGAAGAATTAGGCCAAAA 59.052 34.615 5.01 0.00 0.00 2.44
222 223 6.484288 TCATCAGAAGAAGAATTAGGCCAAA 58.516 36.000 5.01 0.00 0.00 3.28
223 224 6.065976 TCATCAGAAGAAGAATTAGGCCAA 57.934 37.500 5.01 0.00 0.00 4.52
224 225 5.698741 TCATCAGAAGAAGAATTAGGCCA 57.301 39.130 5.01 0.00 0.00 5.36
225 226 5.407995 CGATCATCAGAAGAAGAATTAGGCC 59.592 44.000 0.00 0.00 0.00 5.19
226 227 6.219473 TCGATCATCAGAAGAAGAATTAGGC 58.781 40.000 0.00 0.00 0.00 3.93
227 228 8.830201 AATCGATCATCAGAAGAAGAATTAGG 57.170 34.615 0.00 0.00 0.00 2.69
228 229 9.473640 TGAATCGATCATCAGAAGAAGAATTAG 57.526 33.333 0.00 0.00 31.50 1.73
229 230 9.822185 TTGAATCGATCATCAGAAGAAGAATTA 57.178 29.630 0.00 0.00 38.03 1.40
230 231 8.610896 GTTGAATCGATCATCAGAAGAAGAATT 58.389 33.333 0.00 0.00 38.03 2.17
231 232 7.226325 GGTTGAATCGATCATCAGAAGAAGAAT 59.774 37.037 0.00 0.00 38.03 2.40
232 233 6.536582 GGTTGAATCGATCATCAGAAGAAGAA 59.463 38.462 0.00 0.00 38.03 2.52
233 234 6.045318 GGTTGAATCGATCATCAGAAGAAGA 58.955 40.000 0.00 0.00 38.03 2.87
234 235 6.047870 AGGTTGAATCGATCATCAGAAGAAG 58.952 40.000 0.00 0.00 38.03 2.85
235 236 5.982356 AGGTTGAATCGATCATCAGAAGAA 58.018 37.500 0.00 0.00 38.03 2.52
236 237 5.362143 AGAGGTTGAATCGATCATCAGAAGA 59.638 40.000 0.00 0.00 38.03 2.87
237 238 5.462729 CAGAGGTTGAATCGATCATCAGAAG 59.537 44.000 0.00 0.00 38.03 2.85
238 239 5.127682 TCAGAGGTTGAATCGATCATCAGAA 59.872 40.000 0.00 0.00 38.03 3.02
239 240 4.646492 TCAGAGGTTGAATCGATCATCAGA 59.354 41.667 0.00 0.00 38.03 3.27
240 241 4.941657 TCAGAGGTTGAATCGATCATCAG 58.058 43.478 0.00 0.00 38.03 2.90
241 242 5.541953 ATCAGAGGTTGAATCGATCATCA 57.458 39.130 0.00 0.00 39.77 3.07
242 243 7.953158 TTTATCAGAGGTTGAATCGATCATC 57.047 36.000 0.00 0.00 39.77 2.92
243 244 8.737168 TTTTTATCAGAGGTTGAATCGATCAT 57.263 30.769 0.00 0.00 39.77 2.45
269 270 8.971032 AGATGAAATAGACCCAAGATCTATCT 57.029 34.615 0.00 0.00 38.23 1.98
270 271 9.034800 AGAGATGAAATAGACCCAAGATCTATC 57.965 37.037 0.00 0.00 38.23 2.08
271 272 8.971032 AGAGATGAAATAGACCCAAGATCTAT 57.029 34.615 0.00 0.00 40.41 1.98
272 273 8.789767 AAGAGATGAAATAGACCCAAGATCTA 57.210 34.615 0.00 0.00 33.27 1.98
273 274 7.346698 TGAAGAGATGAAATAGACCCAAGATCT 59.653 37.037 0.00 0.00 0.00 2.75
274 275 7.504403 TGAAGAGATGAAATAGACCCAAGATC 58.496 38.462 0.00 0.00 0.00 2.75
275 276 7.443302 TGAAGAGATGAAATAGACCCAAGAT 57.557 36.000 0.00 0.00 0.00 2.40
276 277 6.874278 TGAAGAGATGAAATAGACCCAAGA 57.126 37.500 0.00 0.00 0.00 3.02
277 278 6.881065 TGTTGAAGAGATGAAATAGACCCAAG 59.119 38.462 0.00 0.00 0.00 3.61
278 279 6.778821 TGTTGAAGAGATGAAATAGACCCAA 58.221 36.000 0.00 0.00 0.00 4.12
279 280 6.373005 TGTTGAAGAGATGAAATAGACCCA 57.627 37.500 0.00 0.00 0.00 4.51
280 281 6.881602 ACTTGTTGAAGAGATGAAATAGACCC 59.118 38.462 0.00 0.00 32.98 4.46
281 282 7.913674 ACTTGTTGAAGAGATGAAATAGACC 57.086 36.000 0.00 0.00 32.98 3.85
292 293 9.998106 AGCTTATTACTAAACTTGTTGAAGAGA 57.002 29.630 0.00 0.00 32.98 3.10
294 295 9.555727 ACAGCTTATTACTAAACTTGTTGAAGA 57.444 29.630 0.00 0.00 32.98 2.87
296 297 9.944663 CAACAGCTTATTACTAAACTTGTTGAA 57.055 29.630 7.53 0.00 31.92 2.69
297 298 9.332502 TCAACAGCTTATTACTAAACTTGTTGA 57.667 29.630 10.97 10.97 33.99 3.18
298 299 9.382244 GTCAACAGCTTATTACTAAACTTGTTG 57.618 33.333 7.08 7.08 31.76 3.33
299 300 8.565416 GGTCAACAGCTTATTACTAAACTTGTT 58.435 33.333 0.00 0.00 0.00 2.83
300 301 7.937394 AGGTCAACAGCTTATTACTAAACTTGT 59.063 33.333 0.00 0.00 0.00 3.16
301 302 8.324163 AGGTCAACAGCTTATTACTAAACTTG 57.676 34.615 0.00 0.00 0.00 3.16
302 303 8.154856 TGAGGTCAACAGCTTATTACTAAACTT 58.845 33.333 0.00 0.00 0.00 2.66
303 304 7.603024 GTGAGGTCAACAGCTTATTACTAAACT 59.397 37.037 0.00 0.00 0.00 2.66
304 305 7.148457 GGTGAGGTCAACAGCTTATTACTAAAC 60.148 40.741 0.00 0.00 32.77 2.01
305 306 6.877322 GGTGAGGTCAACAGCTTATTACTAAA 59.123 38.462 0.00 0.00 32.77 1.85
306 307 6.212791 AGGTGAGGTCAACAGCTTATTACTAA 59.787 38.462 0.00 0.00 42.22 2.24
307 308 5.720041 AGGTGAGGTCAACAGCTTATTACTA 59.280 40.000 0.00 0.00 42.22 1.82
308 309 4.532521 AGGTGAGGTCAACAGCTTATTACT 59.467 41.667 0.00 0.00 42.22 2.24
309 310 4.833390 AGGTGAGGTCAACAGCTTATTAC 58.167 43.478 0.00 0.00 42.22 1.89
315 316 1.490490 TCAAAGGTGAGGTCAACAGCT 59.510 47.619 0.00 0.00 45.87 4.24
316 317 1.604278 GTCAAAGGTGAGGTCAACAGC 59.396 52.381 0.00 0.00 35.62 4.40
317 318 2.874701 CTGTCAAAGGTGAGGTCAACAG 59.125 50.000 0.00 0.00 35.62 3.16
318 319 2.421388 CCTGTCAAAGGTGAGGTCAACA 60.421 50.000 0.00 0.00 41.74 3.33
332 333 3.053544 CCTACTCTACTCCTCCCTGTCAA 60.054 52.174 0.00 0.00 0.00 3.18
335 336 2.861261 TCCTACTCTACTCCTCCCTGT 58.139 52.381 0.00 0.00 0.00 4.00
381 817 9.068008 CATTTTCCAAATTGATTTTTGCATAGC 57.932 29.630 0.00 0.00 35.67 2.97
399 835 7.545265 GGACATCGATTTTTCATTCATTTTCCA 59.455 33.333 0.00 0.00 0.00 3.53
418 854 2.450160 GCCAAATAAAAGCGGACATCG 58.550 47.619 0.00 0.00 42.76 3.84
420 856 2.559998 CGCCAAATAAAAGCGGACAT 57.440 45.000 0.00 0.00 45.88 3.06
459 895 0.813610 TGCAAACAGTCGGTCAGGTG 60.814 55.000 0.00 0.00 0.00 4.00
460 896 0.532862 CTGCAAACAGTCGGTCAGGT 60.533 55.000 0.00 0.00 39.22 4.00
464 1190 1.261619 CTTGTCTGCAAACAGTCGGTC 59.738 52.381 0.00 0.00 44.77 4.79
467 1193 1.261619 GGACTTGTCTGCAAACAGTCG 59.738 52.381 13.17 2.09 44.77 4.18
470 1196 3.438360 GTTTGGACTTGTCTGCAAACAG 58.562 45.455 20.27 0.00 46.30 3.16
474 1200 1.400142 CACGTTTGGACTTGTCTGCAA 59.600 47.619 0.61 0.00 0.00 4.08
475 1201 1.013596 CACGTTTGGACTTGTCTGCA 58.986 50.000 0.61 0.00 0.00 4.41
476 1202 1.003866 GACACGTTTGGACTTGTCTGC 60.004 52.381 8.40 0.00 46.09 4.26
520 1246 5.517054 TGACGTGCTGTAATTTTTGGTTTTC 59.483 36.000 0.00 0.00 0.00 2.29
535 1261 1.595609 GAGCGAATTTTGACGTGCTG 58.404 50.000 0.00 0.00 31.88 4.41
536 1262 0.517316 GGAGCGAATTTTGACGTGCT 59.483 50.000 0.00 0.00 34.96 4.40
540 1266 1.798223 TCTGTGGAGCGAATTTTGACG 59.202 47.619 0.00 0.00 0.00 4.35
550 1276 1.135257 AGAACGAGATTCTGTGGAGCG 60.135 52.381 0.00 0.00 46.44 5.03
551 1277 2.663826 AGAACGAGATTCTGTGGAGC 57.336 50.000 0.00 0.00 46.44 4.70
580 1311 2.818132 GGAGCTCCCCTGTGATCG 59.182 66.667 23.19 0.00 0.00 3.69
610 1341 8.573035 AGCTTTTGGTTTCGTTTTCTATATGAA 58.427 29.630 0.00 0.00 0.00 2.57
798 3543 0.452784 GCGTTCGATGCTGTTTCCAC 60.453 55.000 3.12 0.00 0.00 4.02
1350 4141 1.287503 GATCTCGCGGGAGGTGATC 59.712 63.158 27.01 19.03 40.85 2.92
1537 4340 4.336153 ACCAACCCAACTACAAACTAAACG 59.664 41.667 0.00 0.00 0.00 3.60
1674 4742 8.768501 ACTACCATTACATAACAGAGATCAGA 57.231 34.615 0.00 0.00 0.00 3.27
1691 4759 7.327214 ACAAAAACACAACATCAACTACCATT 58.673 30.769 0.00 0.00 0.00 3.16
1707 4775 8.174422 AGCAAAATCATGTTGTAACAAAAACAC 58.826 29.630 1.10 0.00 43.03 3.32
1720 4788 6.165700 AGTCTCCAAAAGCAAAATCATGTT 57.834 33.333 0.00 0.00 0.00 2.71
1722 4790 5.407387 CCAAGTCTCCAAAAGCAAAATCATG 59.593 40.000 0.00 0.00 0.00 3.07
1804 4878 1.135373 CAATGCAGCTGGCTCTCAAAG 60.135 52.381 17.12 0.00 45.15 2.77
1907 5375 6.640907 CCTGCAACACCAGTATTTTCTTAAAC 59.359 38.462 0.00 0.00 0.00 2.01
1909 5377 5.278758 GCCTGCAACACCAGTATTTTCTTAA 60.279 40.000 0.00 0.00 0.00 1.85
2176 5650 3.042887 GTTTGCAAGAATTTCTCGCGTT 58.957 40.909 5.77 0.00 0.00 4.84
2179 5653 2.406357 GCAGTTTGCAAGAATTTCTCGC 59.594 45.455 2.28 2.28 44.26 5.03
2238 5795 7.809806 GCATTATATCTTGAAAACCATACCTGC 59.190 37.037 0.00 0.00 0.00 4.85
2282 5840 4.157246 AGCATCCGATTACATGGTAGGTA 58.843 43.478 0.00 0.00 0.00 3.08
2287 5845 5.932303 GTGTATTAGCATCCGATTACATGGT 59.068 40.000 0.00 0.00 35.04 3.55
2290 5848 5.639506 GCAGTGTATTAGCATCCGATTACAT 59.360 40.000 0.00 0.00 0.00 2.29
2291 5849 4.988540 GCAGTGTATTAGCATCCGATTACA 59.011 41.667 0.00 0.00 0.00 2.41
2292 5850 4.988540 TGCAGTGTATTAGCATCCGATTAC 59.011 41.667 0.00 0.00 32.55 1.89
2293 5851 5.208463 TGCAGTGTATTAGCATCCGATTA 57.792 39.130 0.00 0.00 32.55 1.75
2294 5852 4.071961 TGCAGTGTATTAGCATCCGATT 57.928 40.909 0.00 0.00 32.55 3.34
2311 5869 4.256110 TCAGTACCTGAATGTCAATGCAG 58.744 43.478 0.00 0.00 37.57 4.41
2381 6208 2.557056 AGTACGTTTGCTGCTCTACTGA 59.443 45.455 0.00 0.00 0.00 3.41
2383 6210 3.504906 TGTAGTACGTTTGCTGCTCTACT 59.495 43.478 0.00 1.55 0.00 2.57
2384 6211 3.829948 TGTAGTACGTTTGCTGCTCTAC 58.170 45.455 0.00 0.00 0.00 2.59
2413 6240 6.430925 CCATTCTGTGTAGAAATTGTTCTCCA 59.569 38.462 0.00 0.00 45.47 3.86
2422 6249 4.263462 TGGCAGTCCATTCTGTGTAGAAAT 60.263 41.667 0.00 0.00 45.47 2.17
2435 6263 2.551270 TCCTACTTTCTGGCAGTCCAT 58.449 47.619 15.27 1.99 42.51 3.41


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

AutoCloner maintained by Alex Coulton.