Multiple sequence alignment - TraesCS2D01G522100

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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 TraesCS2D01G522100 chr2D 100.000 2243 0 0 1 2243 610758380 610756138 0.000000e+00 4143.0
1 TraesCS2D01G522100 chr2D 79.103 847 95 44 792 1591 619312791 619311980 1.990000e-140 508.0
2 TraesCS2D01G522100 chr2D 89.831 59 5 1 1633 1690 557290046 557290104 8.590000e-10 75.0
3 TraesCS2D01G522100 chr2B 89.109 1010 71 20 1242 2243 757394244 757393266 0.000000e+00 1219.0
4 TraesCS2D01G522100 chr2B 87.202 922 54 27 658 1534 757433981 757433079 0.000000e+00 990.0
5 TraesCS2D01G522100 chr2B 84.335 1015 93 29 658 1624 757453474 757452478 0.000000e+00 933.0
6 TraesCS2D01G522100 chr2B 90.838 513 28 3 1736 2243 757433085 757432587 0.000000e+00 669.0
7 TraesCS2D01G522100 chr2B 83.713 571 35 25 658 1188 757562126 757561574 9.310000e-134 486.0
8 TraesCS2D01G522100 chr2B 79.014 791 87 47 792 1540 757567248 757566495 3.370000e-128 468.0
9 TraesCS2D01G522100 chr2B 87.936 373 20 9 897 1244 757394651 757394279 1.240000e-112 416.0
10 TraesCS2D01G522100 chr2B 77.328 741 98 34 875 1591 757016053 757015359 7.560000e-100 374.0
11 TraesCS2D01G522100 chr2B 91.571 261 16 4 3 263 121998182 121998436 2.740000e-94 355.0
12 TraesCS2D01G522100 chr2B 91.188 261 22 1 3 263 11013120 11013379 9.850000e-94 353.0
13 TraesCS2D01G522100 chr2B 87.307 323 23 9 341 655 757454098 757453786 9.850000e-94 353.0
14 TraesCS2D01G522100 chr2B 80.962 478 51 28 770 1244 757241814 757241374 2.130000e-90 342.0
15 TraesCS2D01G522100 chr2B 86.047 172 8 6 486 655 757563831 757563674 1.070000e-38 171.0
16 TraesCS2D01G522100 chr2B 93.548 93 6 0 868 960 757295721 757295629 3.000000e-29 139.0
17 TraesCS2D01G522100 chr2B 84.000 100 9 4 770 868 757394742 757394649 3.070000e-14 89.8
18 TraesCS2D01G522100 chr2B 92.982 57 1 2 262 317 765190869 765190923 1.850000e-11 80.5
19 TraesCS2D01G522100 chr2A 79.087 832 94 43 792 1580 750425317 750424523 1.200000e-137 499.0
20 TraesCS2D01G522100 chr2A 83.721 516 41 16 770 1244 750365674 750365161 4.390000e-122 448.0
21 TraesCS2D01G522100 chr2A 81.733 531 57 21 736 1247 750334616 750334107 7.460000e-110 407.0
22 TraesCS2D01G522100 chr2A 88.333 180 15 5 1365 1544 750365018 750364845 6.280000e-51 211.0
23 TraesCS2D01G522100 chr2A 80.258 233 28 8 1331 1558 750189298 750189517 2.310000e-35 159.0
24 TraesCS2D01G522100 chr2A 97.778 45 1 0 1645 1689 98879580 98879536 6.640000e-11 78.7
25 TraesCS2D01G522100 chr7D 80.889 675 85 26 880 1522 498285349 498284687 2.000000e-135 492.0
26 TraesCS2D01G522100 chr7D 82.463 268 29 10 1329 1591 498251971 498251717 3.750000e-53 219.0
27 TraesCS2D01G522100 chr5B 94.253 261 14 1 3 263 681614890 681614631 4.490000e-107 398.0
28 TraesCS2D01G522100 chr5B 91.011 267 20 3 3 269 297114201 297114463 7.620000e-95 357.0
29 TraesCS2D01G522100 chr5B 91.188 261 20 2 3 263 114905402 114905145 3.540000e-93 351.0
30 TraesCS2D01G522100 chr5B 90.421 261 19 4 3 263 245604700 245604954 2.760000e-89 339.0
31 TraesCS2D01G522100 chr5B 93.878 49 3 0 1637 1685 65238961 65238913 8.590000e-10 75.0
32 TraesCS2D01G522100 chr5B 91.667 48 3 1 267 313 143300754 143300801 5.170000e-07 65.8
33 TraesCS2D01G522100 chr7B 91.765 255 18 2 3 257 642460798 642460547 3.540000e-93 351.0
34 TraesCS2D01G522100 chr7B 93.103 58 4 0 262 319 469799736 469799793 3.970000e-13 86.1
35 TraesCS2D01G522100 chr1B 90.494 263 20 2 1 263 109693834 109694091 2.130000e-90 342.0
36 TraesCS2D01G522100 chr1B 83.399 253 30 7 1291 1539 121011937 121012181 8.060000e-55 224.0
37 TraesCS2D01G522100 chr6B 88.968 281 22 5 3 283 140718967 140718696 2.760000e-89 339.0
38 TraesCS2D01G522100 chr1A 82.996 247 31 5 1374 1620 108778403 108778638 1.740000e-51 213.0
39 TraesCS2D01G522100 chr1A 97.674 43 1 0 1645 1687 372248500 372248458 8.590000e-10 75.0
40 TraesCS2D01G522100 chr1A 97.674 43 1 0 1645 1687 426298537 426298579 8.590000e-10 75.0
41 TraesCS2D01G522100 chr1A 97.674 43 1 0 1645 1687 574488981 574489023 8.590000e-10 75.0
42 TraesCS2D01G522100 chr5D 96.610 59 1 1 262 319 341558379 341558437 1.830000e-16 97.1
43 TraesCS2D01G522100 chr5D 98.148 54 0 1 265 317 386144875 386144928 2.370000e-15 93.5
44 TraesCS2D01G522100 chr4D 97.674 43 1 0 1645 1687 326385088 326385046 8.590000e-10 75.0
45 TraesCS2D01G522100 chr4D 97.674 43 1 0 1645 1687 419197776 419197734 8.590000e-10 75.0
46 TraesCS2D01G522100 chr3D 97.297 37 1 0 281 317 14806295 14806331 1.860000e-06 63.9
47 TraesCS2D01G522100 chr3D 100.000 34 0 0 287 320 388513849 388513882 1.860000e-06 63.9


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 TraesCS2D01G522100 chr2D 610756138 610758380 2242 True 4143.000000 4143 100.000000 1 2243 1 chr2D.!!$R1 2242
1 TraesCS2D01G522100 chr2D 619311980 619312791 811 True 508.000000 508 79.103000 792 1591 1 chr2D.!!$R2 799
2 TraesCS2D01G522100 chr2B 757432587 757433981 1394 True 829.500000 990 89.020000 658 2243 2 chr2B.!!$R5 1585
3 TraesCS2D01G522100 chr2B 757452478 757454098 1620 True 643.000000 933 85.821000 341 1624 2 chr2B.!!$R6 1283
4 TraesCS2D01G522100 chr2B 757393266 757394742 1476 True 574.933333 1219 87.015000 770 2243 3 chr2B.!!$R4 1473
5 TraesCS2D01G522100 chr2B 757561574 757567248 5674 True 375.000000 486 82.924667 486 1540 3 chr2B.!!$R7 1054
6 TraesCS2D01G522100 chr2B 757015359 757016053 694 True 374.000000 374 77.328000 875 1591 1 chr2B.!!$R1 716
7 TraesCS2D01G522100 chr2A 750424523 750425317 794 True 499.000000 499 79.087000 792 1580 1 chr2A.!!$R3 788
8 TraesCS2D01G522100 chr2A 750334107 750334616 509 True 407.000000 407 81.733000 736 1247 1 chr2A.!!$R2 511
9 TraesCS2D01G522100 chr2A 750364845 750365674 829 True 329.500000 448 86.027000 770 1544 2 chr2A.!!$R4 774
10 TraesCS2D01G522100 chr7D 498284687 498285349 662 True 492.000000 492 80.889000 880 1522 1 chr7D.!!$R2 642

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
316 317 0.036732 TCGCCCATTGAAGTTGCTCT 59.963 50.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 6573 0.109412 GTTGTGTCTAGTAGCGGCGT 60.109 55.0 9.37 0.0 0.0 5.68 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.882876 ACATTCGGACGTCGGAGG 59.117 61.111 22.70 20.46 39.77 4.30
18 19 1.676635 ACATTCGGACGTCGGAGGA 60.677 57.895 22.70 12.07 39.77 3.71
19 20 1.064296 CATTCGGACGTCGGAGGAG 59.936 63.158 22.70 14.15 39.77 3.69
20 21 2.119655 ATTCGGACGTCGGAGGAGG 61.120 63.158 22.70 1.41 39.77 4.30
21 22 2.547640 ATTCGGACGTCGGAGGAGGA 62.548 60.000 22.70 10.74 39.77 3.71
23 24 2.360852 GGACGTCGGAGGAGGACA 60.361 66.667 9.92 0.00 34.04 4.02
26 27 1.386533 GACGTCGGAGGAGGACATTA 58.613 55.000 0.00 0.00 34.04 1.90
28 29 0.384669 CGTCGGAGGAGGACATTACC 59.615 60.000 0.00 0.00 34.04 2.85
29 30 0.384669 GTCGGAGGAGGACATTACCG 59.615 60.000 0.00 0.00 41.39 4.02
30 31 0.256752 TCGGAGGAGGACATTACCGA 59.743 55.000 0.00 0.00 45.36 4.69
31 32 0.669077 CGGAGGAGGACATTACCGAG 59.331 60.000 0.00 0.00 42.40 4.63
32 33 1.777941 GGAGGAGGACATTACCGAGT 58.222 55.000 0.00 0.00 34.73 4.18
33 34 1.682323 GGAGGAGGACATTACCGAGTC 59.318 57.143 0.00 0.00 34.73 3.36
34 35 2.376109 GAGGAGGACATTACCGAGTCA 58.624 52.381 0.00 0.00 36.50 3.41
35 36 2.359531 GAGGAGGACATTACCGAGTCAG 59.640 54.545 0.00 0.00 36.50 3.51
36 37 2.025226 AGGAGGACATTACCGAGTCAGA 60.025 50.000 0.00 0.00 36.50 3.27
37 38 2.359531 GGAGGACATTACCGAGTCAGAG 59.640 54.545 0.00 0.00 36.50 3.35
38 39 3.018149 GAGGACATTACCGAGTCAGAGT 58.982 50.000 0.00 0.00 36.50 3.24
39 40 3.018149 AGGACATTACCGAGTCAGAGTC 58.982 50.000 0.00 0.00 36.50 3.36
40 41 2.223294 GGACATTACCGAGTCAGAGTCG 60.223 54.545 19.25 19.25 40.53 4.18
59 60 2.712057 GGAAACCGACGAGTAGTTGA 57.288 50.000 0.00 0.00 36.30 3.18
61 62 2.728318 GGAAACCGACGAGTAGTTGAAC 59.272 50.000 0.00 0.00 36.30 3.18
62 63 3.551659 GGAAACCGACGAGTAGTTGAACT 60.552 47.826 2.37 2.37 36.30 3.01
64 65 3.722728 ACCGACGAGTAGTTGAACTTT 57.277 42.857 1.97 0.00 36.30 2.66
65 66 4.050852 ACCGACGAGTAGTTGAACTTTT 57.949 40.909 1.97 0.00 36.30 2.27
66 67 4.047142 ACCGACGAGTAGTTGAACTTTTC 58.953 43.478 1.97 0.97 36.30 2.29
67 68 4.202090 ACCGACGAGTAGTTGAACTTTTCT 60.202 41.667 1.97 0.06 36.30 2.52
68 69 4.743644 CCGACGAGTAGTTGAACTTTTCTT 59.256 41.667 1.97 0.00 36.30 2.52
69 70 5.233689 CCGACGAGTAGTTGAACTTTTCTTT 59.766 40.000 1.97 0.00 36.30 2.52
70 71 6.238022 CCGACGAGTAGTTGAACTTTTCTTTT 60.238 38.462 1.97 0.00 36.30 2.27
71 72 7.043192 CCGACGAGTAGTTGAACTTTTCTTTTA 60.043 37.037 1.97 0.00 36.30 1.52
72 73 8.485591 CGACGAGTAGTTGAACTTTTCTTTTAT 58.514 33.333 1.97 0.00 36.30 1.40
74 75 9.543783 ACGAGTAGTTGAACTTTTCTTTTATCT 57.456 29.630 1.97 0.00 0.00 1.98
75 76 9.798885 CGAGTAGTTGAACTTTTCTTTTATCTG 57.201 33.333 1.97 0.00 0.00 2.90
81 82 9.155053 GTTGAACTTTTCTTTTATCTGTGTACG 57.845 33.333 0.00 0.00 0.00 3.67
84 85 7.254227 ACTTTTCTTTTATCTGTGTACGCAA 57.746 32.000 10.85 2.41 0.00 4.85
86 87 7.225931 ACTTTTCTTTTATCTGTGTACGCAAGA 59.774 33.333 10.85 10.26 43.62 3.02
88 89 6.462073 TCTTTTATCTGTGTACGCAAGAAC 57.538 37.500 10.85 0.00 43.62 3.01
89 90 6.220930 TCTTTTATCTGTGTACGCAAGAACT 58.779 36.000 10.85 0.10 43.62 3.01
91 92 8.033038 TCTTTTATCTGTGTACGCAAGAACTAT 58.967 33.333 10.85 0.93 43.62 2.12
92 93 7.751047 TTTATCTGTGTACGCAAGAACTATC 57.249 36.000 10.85 0.00 43.62 2.08
95 96 6.694877 TCTGTGTACGCAAGAACTATCTAT 57.305 37.500 10.85 0.00 43.62 1.98
96 97 6.495706 TCTGTGTACGCAAGAACTATCTATG 58.504 40.000 10.85 0.00 43.62 2.23
97 98 6.095021 TCTGTGTACGCAAGAACTATCTATGT 59.905 38.462 10.85 0.00 43.62 2.29
99 100 7.937649 TGTGTACGCAAGAACTATCTATGTAT 58.062 34.615 6.65 0.00 43.62 2.29
100 101 8.074370 TGTGTACGCAAGAACTATCTATGTATC 58.926 37.037 6.65 0.00 43.62 2.24
101 102 7.537991 GTGTACGCAAGAACTATCTATGTATCC 59.462 40.741 0.39 0.00 43.62 2.59
102 103 6.026947 ACGCAAGAACTATCTATGTATCCC 57.973 41.667 0.00 0.00 43.62 3.85
103 104 5.775701 ACGCAAGAACTATCTATGTATCCCT 59.224 40.000 0.00 0.00 43.62 4.20
104 105 6.267928 ACGCAAGAACTATCTATGTATCCCTT 59.732 38.462 0.00 0.00 43.62 3.95
105 106 7.155328 CGCAAGAACTATCTATGTATCCCTTT 58.845 38.462 0.00 0.00 43.02 3.11
106 107 7.657761 CGCAAGAACTATCTATGTATCCCTTTT 59.342 37.037 0.00 0.00 43.02 2.27
107 108 8.994170 GCAAGAACTATCTATGTATCCCTTTTC 58.006 37.037 0.00 0.00 33.77 2.29
111 112 9.360093 GAACTATCTATGTATCCCTTTTCATCG 57.640 37.037 0.00 0.00 0.00 3.84
113 114 6.935240 ATCTATGTATCCCTTTTCATCGGA 57.065 37.500 0.00 0.00 0.00 4.55
114 115 6.740944 TCTATGTATCCCTTTTCATCGGAA 57.259 37.500 0.00 0.00 0.00 4.30
115 116 7.131907 TCTATGTATCCCTTTTCATCGGAAA 57.868 36.000 0.00 0.00 41.13 3.13
134 135 0.446222 AAAAATGACCGGCGATGTCG 59.554 50.000 9.30 0.00 43.27 4.35
153 154 3.726517 CAACGAAGCAGGCGGTGG 61.727 66.667 3.40 0.00 42.38 4.61
154 155 3.936203 AACGAAGCAGGCGGTGGA 61.936 61.111 0.00 0.00 0.00 4.02
155 156 3.883744 AACGAAGCAGGCGGTGGAG 62.884 63.158 0.00 0.00 0.00 3.86
157 158 4.785453 GAAGCAGGCGGTGGAGGG 62.785 72.222 0.00 0.00 0.00 4.30
161 162 4.704833 CAGGCGGTGGAGGGTGTG 62.705 72.222 0.00 0.00 0.00 3.82
179 180 4.544689 CGTGCGCGGAGAGGAGAG 62.545 72.222 12.87 0.00 0.00 3.20
180 181 3.134792 GTGCGCGGAGAGGAGAGA 61.135 66.667 8.83 0.00 0.00 3.10
182 183 3.591835 GCGCGGAGAGGAGAGAGG 61.592 72.222 8.83 0.00 0.00 3.69
183 184 2.904866 CGCGGAGAGGAGAGAGGG 60.905 72.222 0.00 0.00 0.00 4.30
185 186 2.904866 CGGAGAGGAGAGAGGGCG 60.905 72.222 0.00 0.00 0.00 6.13
186 187 2.598467 GGAGAGGAGAGAGGGCGA 59.402 66.667 0.00 0.00 0.00 5.54
188 189 2.123897 AGAGGAGAGAGGGCGAGC 60.124 66.667 0.00 0.00 0.00 5.03
189 190 3.591835 GAGGAGAGAGGGCGAGCG 61.592 72.222 0.00 0.00 0.00 5.03
206 207 2.127758 GCGCACGTTTCCGTCTTG 60.128 61.111 0.30 0.00 46.28 3.02
207 208 2.877974 GCGCACGTTTCCGTCTTGT 61.878 57.895 0.30 0.00 46.28 3.16
208 209 1.083657 CGCACGTTTCCGTCTTGTG 60.084 57.895 0.00 0.00 46.28 3.33
212 213 0.872881 ACGTTTCCGTCTTGTGTCCG 60.873 55.000 0.00 0.00 46.28 4.79
213 214 1.568025 GTTTCCGTCTTGTGTCCGC 59.432 57.895 0.00 0.00 0.00 5.54
214 215 1.952133 TTTCCGTCTTGTGTCCGCG 60.952 57.895 0.00 0.00 0.00 6.46
232 233 3.564027 CCGACGCAAATCCGGCTC 61.564 66.667 0.00 0.00 36.62 4.70
233 234 2.813474 CGACGCAAATCCGGCTCA 60.813 61.111 0.00 0.00 33.03 4.26
234 235 2.387445 CGACGCAAATCCGGCTCAA 61.387 57.895 0.00 0.00 33.03 3.02
235 236 1.873165 GACGCAAATCCGGCTCAAA 59.127 52.632 0.00 0.00 32.31 2.69
237 238 0.671251 ACGCAAATCCGGCTCAAAAA 59.329 45.000 0.00 0.00 0.00 1.94
238 239 1.272212 ACGCAAATCCGGCTCAAAAAT 59.728 42.857 0.00 0.00 0.00 1.82
239 240 1.655099 CGCAAATCCGGCTCAAAAATG 59.345 47.619 0.00 0.00 0.00 2.32
241 242 2.353605 GCAAATCCGGCTCAAAAATGGA 60.354 45.455 0.00 0.00 0.00 3.41
243 244 1.474330 ATCCGGCTCAAAAATGGACC 58.526 50.000 0.00 0.00 0.00 4.46
244 245 0.958382 TCCGGCTCAAAAATGGACCG 60.958 55.000 0.00 0.00 40.30 4.79
246 247 1.890174 GGCTCAAAAATGGACCGGG 59.110 57.895 6.32 0.00 0.00 5.73
247 248 0.610785 GGCTCAAAAATGGACCGGGA 60.611 55.000 6.32 0.00 0.00 5.14
248 249 1.253100 GCTCAAAAATGGACCGGGAA 58.747 50.000 6.32 0.00 0.00 3.97
251 252 2.166254 CTCAAAAATGGACCGGGAATGG 59.834 50.000 6.32 0.00 0.00 3.16
252 253 1.206849 CAAAAATGGACCGGGAATGGG 59.793 52.381 6.32 0.00 0.00 4.00
299 300 3.192922 GGCGGACGAAATGGGTCG 61.193 66.667 0.00 0.00 46.54 4.79
300 301 3.861263 GCGGACGAAATGGGTCGC 61.861 66.667 0.00 0.00 45.00 5.19
301 302 3.192922 CGGACGAAATGGGTCGCC 61.193 66.667 0.00 0.00 45.00 5.54
311 312 4.415783 GGGTCGCCCATTGAAGTT 57.584 55.556 9.72 0.00 44.65 2.66
312 313 1.883021 GGGTCGCCCATTGAAGTTG 59.117 57.895 9.72 0.00 44.65 3.16
314 315 1.244019 GGTCGCCCATTGAAGTTGCT 61.244 55.000 0.00 0.00 0.00 3.91
315 316 0.169009 GTCGCCCATTGAAGTTGCTC 59.831 55.000 0.00 0.00 0.00 4.26
316 317 0.036732 TCGCCCATTGAAGTTGCTCT 59.963 50.000 0.00 0.00 0.00 4.09
317 318 0.883833 CGCCCATTGAAGTTGCTCTT 59.116 50.000 0.00 0.00 39.32 2.85
318 319 2.083774 CGCCCATTGAAGTTGCTCTTA 58.916 47.619 0.00 0.00 36.40 2.10
320 321 3.488047 CGCCCATTGAAGTTGCTCTTATG 60.488 47.826 0.00 0.00 36.40 1.90
321 322 3.696051 GCCCATTGAAGTTGCTCTTATGA 59.304 43.478 0.00 0.00 36.40 2.15
322 323 4.158394 GCCCATTGAAGTTGCTCTTATGAA 59.842 41.667 0.00 0.00 36.40 2.57
323 324 5.644644 CCCATTGAAGTTGCTCTTATGAAC 58.355 41.667 0.00 0.00 36.40 3.18
324 325 5.393461 CCCATTGAAGTTGCTCTTATGAACC 60.393 44.000 0.00 0.00 36.40 3.62
325 326 5.183713 CCATTGAAGTTGCTCTTATGAACCA 59.816 40.000 0.00 0.00 36.40 3.67
326 327 6.294675 CCATTGAAGTTGCTCTTATGAACCAA 60.295 38.462 0.00 0.00 36.40 3.67
327 328 6.707440 TTGAAGTTGCTCTTATGAACCAAA 57.293 33.333 0.00 0.00 36.40 3.28
328 329 6.072112 TGAAGTTGCTCTTATGAACCAAAC 57.928 37.500 0.00 0.00 36.40 2.93
329 330 5.592282 TGAAGTTGCTCTTATGAACCAAACA 59.408 36.000 0.00 0.00 36.40 2.83
330 331 5.695851 AGTTGCTCTTATGAACCAAACAG 57.304 39.130 0.00 0.00 0.00 3.16
331 332 4.520492 AGTTGCTCTTATGAACCAAACAGG 59.480 41.667 0.00 0.00 45.67 4.00
332 333 2.819608 TGCTCTTATGAACCAAACAGGC 59.180 45.455 0.00 0.00 43.14 4.85
333 334 2.164422 GCTCTTATGAACCAAACAGGCC 59.836 50.000 0.00 0.00 43.14 5.19
334 335 3.690460 CTCTTATGAACCAAACAGGCCT 58.310 45.455 0.00 0.00 43.14 5.19
337 338 1.915141 ATGAACCAAACAGGCCTGAG 58.085 50.000 39.19 25.29 43.14 3.35
338 339 0.550914 TGAACCAAACAGGCCTGAGT 59.449 50.000 39.19 24.80 43.14 3.41
339 340 1.064017 TGAACCAAACAGGCCTGAGTT 60.064 47.619 39.19 30.42 43.14 3.01
370 371 0.995024 ACTTGGTGGCAGCCTAGATT 59.005 50.000 14.15 0.00 35.75 2.40
377 378 0.761802 GGCAGCCTAGATTAGCAGGT 59.238 55.000 3.29 0.00 34.18 4.00
379 380 2.368875 GGCAGCCTAGATTAGCAGGTTA 59.631 50.000 3.29 0.00 34.18 2.85
381 382 3.556004 GCAGCCTAGATTAGCAGGTTAGG 60.556 52.174 0.00 0.00 34.18 2.69
447 448 1.499688 TTTGACGAAATGCGCGGTGA 61.500 50.000 8.83 0.00 46.04 4.02
470 471 4.508128 CCACGTACGGGAGCGCAT 62.508 66.667 21.47 0.00 0.00 4.73
515 3448 4.873129 CCATCGGACGGCACTCGG 62.873 72.222 0.00 0.00 44.45 4.63
535 3470 0.985490 AGAGGGAGGGAGCATGGAAC 60.985 60.000 0.00 0.00 0.00 3.62
538 3473 1.153349 GGAGGGAGCATGGAACGAC 60.153 63.158 0.00 0.00 0.00 4.34
576 3511 0.109086 ATCGGCACTCACTCAAGTCG 60.109 55.000 0.00 0.00 0.00 4.18
578 3513 2.375766 GGCACTCACTCAAGTCGCG 61.376 63.158 0.00 0.00 0.00 5.87
636 3576 1.078848 CTTCCCTTCAGTCAGCCGG 60.079 63.158 0.00 0.00 0.00 6.13
726 5211 5.455056 TCTCAAGTCTCAAGTGGTCTAAC 57.545 43.478 0.00 0.00 0.00 2.34
784 5270 4.029520 TCTCTTCTGAGAAGATTCCCAGG 58.970 47.826 23.77 11.40 45.42 4.45
847 5390 0.987294 CTCACCTCCACCCATCACTT 59.013 55.000 0.00 0.00 0.00 3.16
848 5391 0.692476 TCACCTCCACCCATCACTTG 59.308 55.000 0.00 0.00 0.00 3.16
851 5394 1.561542 ACCTCCACCCATCACTTGATC 59.438 52.381 0.00 0.00 31.21 2.92
852 5395 1.133976 CCTCCACCCATCACTTGATCC 60.134 57.143 0.00 0.00 31.21 3.36
904 5461 5.221244 ACAGATAAACACAAAAAGCAGACCC 60.221 40.000 0.00 0.00 0.00 4.46
961 5533 1.601759 GGCCTCAGCTCACTGCAAA 60.602 57.895 0.00 0.00 44.10 3.68
985 5561 1.203063 CCTACATCGATCCTCTCCCCA 60.203 57.143 0.00 0.00 0.00 4.96
997 5573 3.664025 CTCCCCATCGTCGCTTGCA 62.664 63.158 0.00 0.00 0.00 4.08
1135 5740 1.367840 GTGTCCAGCGAGGTGAAGT 59.632 57.895 3.61 0.00 39.02 3.01
1164 5775 3.177249 GTCGACAAGTACGCGCCC 61.177 66.667 11.55 0.00 0.00 6.13
1275 5930 3.002348 GCACAGAAATCGTTAGGCATACC 59.998 47.826 0.00 0.00 0.00 2.73
1356 6039 1.000060 TGTTAGAGTGGGAAACGGACG 60.000 52.381 0.00 0.00 0.00 4.79
1371 6054 6.150140 GGAAACGGACGTATAGTGTAGGATAT 59.850 42.308 0.00 0.00 0.00 1.63
1419 6109 4.411256 TTCGTTTGTCCCTTGAAGTACT 57.589 40.909 0.00 0.00 0.00 2.73
1420 6110 5.534207 TTCGTTTGTCCCTTGAAGTACTA 57.466 39.130 0.00 0.00 0.00 1.82
1421 6111 4.874970 TCGTTTGTCCCTTGAAGTACTAC 58.125 43.478 0.00 0.00 0.00 2.73
1540 6235 2.805099 CTCTTGACCTCTGCAACAACTC 59.195 50.000 0.00 0.00 0.00 3.01
1544 6239 2.224137 TGACCTCTGCAACAACTCTCAG 60.224 50.000 0.00 0.00 0.00 3.35
1547 6242 2.686235 CTCTGCAACAACTCTCAGAGG 58.314 52.381 6.64 0.00 45.23 3.69
1560 6255 7.494952 ACAACTCTCAGAGGTAAGTTTTACAAC 59.505 37.037 6.64 0.00 33.35 3.32
1610 6308 3.845781 AGGCCGACATTCTTACATGAT 57.154 42.857 0.00 0.00 0.00 2.45
1613 6311 3.496130 GGCCGACATTCTTACATGATGAG 59.504 47.826 0.00 0.00 0.00 2.90
1629 6327 7.851228 ACATGATGAGTTGACCTAAATCAGTA 58.149 34.615 0.00 0.00 45.36 2.74
1630 6328 8.321353 ACATGATGAGTTGACCTAAATCAGTAA 58.679 33.333 0.00 0.00 45.36 2.24
1631 6329 8.607459 CATGATGAGTTGACCTAAATCAGTAAC 58.393 37.037 0.00 0.00 45.36 2.50
1632 6330 7.676004 TGATGAGTTGACCTAAATCAGTAACA 58.324 34.615 0.00 0.00 45.36 2.41
1633 6331 8.154203 TGATGAGTTGACCTAAATCAGTAACAA 58.846 33.333 0.00 0.00 45.36 2.83
1634 6332 9.167311 GATGAGTTGACCTAAATCAGTAACAAT 57.833 33.333 0.00 0.00 45.36 2.71
1635 6333 8.918202 TGAGTTGACCTAAATCAGTAACAATT 57.082 30.769 0.00 0.00 38.35 2.32
1687 6385 4.240103 TGCTCACCACGCAGCTGT 62.240 61.111 16.64 0.00 36.53 4.40
1702 6400 2.909965 TGTGCCGGCTGGGTTTTC 60.910 61.111 29.70 8.07 38.44 2.29
1703 6401 3.680786 GTGCCGGCTGGGTTTTCC 61.681 66.667 29.70 0.00 38.44 3.13
1715 6413 1.205820 GTTTTCCGAACCGCTTCCG 59.794 57.895 0.00 0.00 0.00 4.30
1716 6414 1.227615 TTTTCCGAACCGCTTCCGT 60.228 52.632 0.00 0.00 0.00 4.69
1724 6422 3.508840 CCGCTTCCGTGATTGGGC 61.509 66.667 0.00 0.00 0.00 5.36
1752 6450 1.051008 TGCTCTGCACTTCCTCTTCA 58.949 50.000 0.00 0.00 31.71 3.02
1802 6500 0.779358 CCCATATTCCATGGCCAGGA 59.221 55.000 21.32 18.80 37.85 3.86
1816 6514 1.984570 CAGGAGCTTCGACAGGGGA 60.985 63.158 0.00 0.00 0.00 4.81
1817 6515 1.985116 AGGAGCTTCGACAGGGGAC 60.985 63.158 0.00 0.00 0.00 4.46
1871 6570 2.716424 TGATCCACTTCAAGGGGTTCTT 59.284 45.455 16.39 0.00 40.57 2.52
1877 6576 3.668386 CAAGGGGTTCTTGGACGC 58.332 61.111 0.00 0.00 46.81 5.19
1910 6609 4.236935 CACAACCTTTTGCGCAAGATTAT 58.763 39.130 23.68 8.39 36.00 1.28
1919 6618 1.714794 CGCAAGATTATAGGGAGGCG 58.285 55.000 0.00 0.00 43.02 5.52
1966 6665 1.779061 GACGACGCTGCGATTTTCA 59.221 52.632 30.47 0.00 34.83 2.69
1973 6672 1.129251 CGCTGCGATTTTCATCACACT 59.871 47.619 18.66 0.00 0.00 3.55
2032 6731 1.330655 ATCATTCGGCGAGACCACCT 61.331 55.000 10.46 0.00 39.03 4.00
2153 6852 2.906354 CTTCCCGATGAAGTACCTTGG 58.094 52.381 6.52 0.00 44.59 3.61
2171 6870 1.460305 GGCTGCCCCTCTCCATCTA 60.460 63.158 7.66 0.00 0.00 1.98
2194 6893 2.103153 ACTCAAGAGGGTGGACTTCA 57.897 50.000 1.73 0.00 0.00 3.02
2195 6894 2.625639 ACTCAAGAGGGTGGACTTCAT 58.374 47.619 1.73 0.00 0.00 2.57
2196 6895 2.569404 ACTCAAGAGGGTGGACTTCATC 59.431 50.000 1.73 0.00 0.00 2.92
2197 6896 2.836981 CTCAAGAGGGTGGACTTCATCT 59.163 50.000 0.00 0.00 0.00 2.90
2198 6897 3.251484 TCAAGAGGGTGGACTTCATCTT 58.749 45.455 0.00 0.00 0.00 2.40
2199 6898 3.008375 TCAAGAGGGTGGACTTCATCTTG 59.992 47.826 10.29 10.29 43.07 3.02
2200 6899 2.907892 AGAGGGTGGACTTCATCTTGA 58.092 47.619 0.00 0.00 0.00 3.02
2219 6922 2.429971 TGATGACAAGGTTGCTGCAAAA 59.570 40.909 17.80 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.654954 CTCCTCCGACGTCCGAATGT 61.655 60.000 10.58 0.00 41.76 2.71
1 2 1.064296 CTCCTCCGACGTCCGAATG 59.936 63.158 10.58 3.59 41.76 2.67
2 3 2.119655 CCTCCTCCGACGTCCGAAT 61.120 63.158 10.58 0.00 41.76 3.34
4 5 3.709633 TCCTCCTCCGACGTCCGA 61.710 66.667 10.58 8.28 41.76 4.55
5 6 3.507009 GTCCTCCTCCGACGTCCG 61.507 72.222 10.58 3.37 38.18 4.79
7 8 1.065251 GTAATGTCCTCCTCCGACGTC 59.935 57.143 5.18 5.18 32.68 4.34
8 9 1.101331 GTAATGTCCTCCTCCGACGT 58.899 55.000 0.00 0.00 32.68 4.34
9 10 0.384669 GGTAATGTCCTCCTCCGACG 59.615 60.000 0.00 0.00 32.68 5.12
10 11 0.384669 CGGTAATGTCCTCCTCCGAC 59.615 60.000 0.00 0.00 40.29 4.79
11 12 0.256752 TCGGTAATGTCCTCCTCCGA 59.743 55.000 0.00 0.00 43.52 4.55
13 14 1.682323 GACTCGGTAATGTCCTCCTCC 59.318 57.143 0.00 0.00 0.00 4.30
15 16 2.025226 TCTGACTCGGTAATGTCCTCCT 60.025 50.000 0.00 0.00 32.67 3.69
16 17 2.359531 CTCTGACTCGGTAATGTCCTCC 59.640 54.545 0.00 0.00 32.67 4.30
17 18 3.018149 ACTCTGACTCGGTAATGTCCTC 58.982 50.000 0.00 0.00 32.67 3.71
18 19 3.018149 GACTCTGACTCGGTAATGTCCT 58.982 50.000 0.00 0.00 32.67 3.85
19 20 2.223294 CGACTCTGACTCGGTAATGTCC 60.223 54.545 0.00 0.00 32.67 4.02
20 21 2.223294 CCGACTCTGACTCGGTAATGTC 60.223 54.545 15.03 0.00 44.82 3.06
21 22 1.743958 CCGACTCTGACTCGGTAATGT 59.256 52.381 15.03 0.00 44.82 2.71
28 29 3.403276 GGTTTCCGACTCTGACTCG 57.597 57.895 0.50 0.50 0.00 4.18
40 41 2.712057 TCAACTACTCGTCGGTTTCC 57.288 50.000 0.00 0.00 0.00 3.13
41 42 3.636381 AGTTCAACTACTCGTCGGTTTC 58.364 45.455 0.00 0.00 0.00 2.78
43 44 3.722728 AAGTTCAACTACTCGTCGGTT 57.277 42.857 0.00 0.00 0.00 4.44
44 45 3.722728 AAAGTTCAACTACTCGTCGGT 57.277 42.857 0.00 0.00 0.00 4.69
45 46 4.296690 AGAAAAGTTCAACTACTCGTCGG 58.703 43.478 0.00 0.00 0.00 4.79
47 48 9.794653 GATAAAAGAAAAGTTCAACTACTCGTC 57.205 33.333 0.00 0.00 0.00 4.20
56 57 7.853929 GCGTACACAGATAAAAGAAAAGTTCAA 59.146 33.333 0.00 0.00 0.00 2.69
58 59 7.349711 TGCGTACACAGATAAAAGAAAAGTTC 58.650 34.615 0.00 0.00 0.00 3.01
59 60 7.254227 TGCGTACACAGATAAAAGAAAAGTT 57.746 32.000 0.00 0.00 0.00 2.66
61 62 7.572759 TCTTGCGTACACAGATAAAAGAAAAG 58.427 34.615 0.00 0.00 0.00 2.27
62 63 7.485418 TCTTGCGTACACAGATAAAAGAAAA 57.515 32.000 0.00 0.00 0.00 2.29
64 65 6.704493 AGTTCTTGCGTACACAGATAAAAGAA 59.296 34.615 0.00 0.00 31.79 2.52
65 66 6.220930 AGTTCTTGCGTACACAGATAAAAGA 58.779 36.000 0.00 0.00 0.00 2.52
66 67 6.467723 AGTTCTTGCGTACACAGATAAAAG 57.532 37.500 0.00 0.00 0.00 2.27
67 68 8.033038 AGATAGTTCTTGCGTACACAGATAAAA 58.967 33.333 0.00 0.00 0.00 1.52
68 69 7.544622 AGATAGTTCTTGCGTACACAGATAAA 58.455 34.615 0.00 0.00 0.00 1.40
69 70 7.096884 AGATAGTTCTTGCGTACACAGATAA 57.903 36.000 0.00 0.00 0.00 1.75
70 71 6.694877 AGATAGTTCTTGCGTACACAGATA 57.305 37.500 0.00 0.00 0.00 1.98
71 72 5.584253 AGATAGTTCTTGCGTACACAGAT 57.416 39.130 0.00 0.00 0.00 2.90
72 73 6.095021 ACATAGATAGTTCTTGCGTACACAGA 59.905 38.462 0.00 0.00 33.17 3.41
74 75 6.203808 ACATAGATAGTTCTTGCGTACACA 57.796 37.500 0.00 0.00 33.17 3.72
75 76 7.537991 GGATACATAGATAGTTCTTGCGTACAC 59.462 40.741 0.00 0.00 33.17 2.90
76 77 7.309012 GGGATACATAGATAGTTCTTGCGTACA 60.309 40.741 0.00 0.00 39.74 2.90
77 78 7.028361 GGGATACATAGATAGTTCTTGCGTAC 58.972 42.308 0.00 0.00 39.74 3.67
78 79 6.946583 AGGGATACATAGATAGTTCTTGCGTA 59.053 38.462 0.00 0.00 39.74 4.42
79 80 5.775701 AGGGATACATAGATAGTTCTTGCGT 59.224 40.000 0.00 0.00 39.74 5.24
80 81 6.274157 AGGGATACATAGATAGTTCTTGCG 57.726 41.667 0.00 0.00 39.74 4.85
81 82 8.910351 AAAAGGGATACATAGATAGTTCTTGC 57.090 34.615 0.00 0.00 39.74 4.01
85 86 9.360093 CGATGAAAAGGGATACATAGATAGTTC 57.640 37.037 0.00 0.00 39.74 3.01
86 87 8.314751 CCGATGAAAAGGGATACATAGATAGTT 58.685 37.037 0.00 0.00 39.74 2.24
88 89 8.067751 TCCGATGAAAAGGGATACATAGATAG 57.932 38.462 0.00 0.00 39.74 2.08
89 90 8.430573 TTCCGATGAAAAGGGATACATAGATA 57.569 34.615 0.00 0.00 39.74 1.98
91 92 6.740944 TTCCGATGAAAAGGGATACATAGA 57.259 37.500 0.00 0.00 39.74 1.98
92 93 7.801716 TTTTCCGATGAAAAGGGATACATAG 57.198 36.000 0.00 0.00 43.68 2.23
115 116 0.446222 CGACATCGCCGGTCATTTTT 59.554 50.000 1.90 0.00 34.97 1.94
116 117 1.366111 CCGACATCGCCGGTCATTTT 61.366 55.000 1.90 0.00 41.91 1.82
117 118 1.813753 CCGACATCGCCGGTCATTT 60.814 57.895 1.90 0.00 41.91 2.32
118 119 2.202878 CCGACATCGCCGGTCATT 60.203 61.111 1.90 0.00 41.91 2.57
125 126 3.083600 CTTCGTTGCCGACATCGCC 62.084 63.158 0.00 0.00 44.13 5.54
126 127 2.395690 CTTCGTTGCCGACATCGC 59.604 61.111 0.00 0.00 44.13 4.58
128 129 1.421485 CTGCTTCGTTGCCGACATC 59.579 57.895 0.00 0.00 44.13 3.06
129 130 2.034879 CCTGCTTCGTTGCCGACAT 61.035 57.895 0.00 0.00 44.13 3.06
130 131 2.664851 CCTGCTTCGTTGCCGACA 60.665 61.111 0.00 0.00 44.13 4.35
131 132 4.090057 GCCTGCTTCGTTGCCGAC 62.090 66.667 0.00 0.00 44.13 4.79
136 137 3.726517 CCACCGCCTGCTTCGTTG 61.727 66.667 0.00 0.00 0.00 4.10
137 138 3.883744 CTCCACCGCCTGCTTCGTT 62.884 63.158 0.00 0.00 0.00 3.85
138 139 4.379243 CTCCACCGCCTGCTTCGT 62.379 66.667 0.00 0.00 0.00 3.85
140 141 4.785453 CCCTCCACCGCCTGCTTC 62.785 72.222 0.00 0.00 0.00 3.86
144 145 4.704833 CACACCCTCCACCGCCTG 62.705 72.222 0.00 0.00 0.00 4.85
162 163 4.544689 CTCTCCTCTCCGCGCACG 62.545 72.222 8.75 0.00 39.67 5.34
163 164 3.119709 CTCTCTCCTCTCCGCGCAC 62.120 68.421 8.75 0.00 0.00 5.34
164 165 2.826287 CTCTCTCCTCTCCGCGCA 60.826 66.667 8.75 0.00 0.00 6.09
165 166 3.591835 CCTCTCTCCTCTCCGCGC 61.592 72.222 0.00 0.00 0.00 6.86
167 168 3.223589 GCCCTCTCTCCTCTCCGC 61.224 72.222 0.00 0.00 0.00 5.54
168 169 2.904866 CGCCCTCTCTCCTCTCCG 60.905 72.222 0.00 0.00 0.00 4.63
169 170 1.528309 CTCGCCCTCTCTCCTCTCC 60.528 68.421 0.00 0.00 0.00 3.71
170 171 2.193536 GCTCGCCCTCTCTCCTCTC 61.194 68.421 0.00 0.00 0.00 3.20
171 172 2.123897 GCTCGCCCTCTCTCCTCT 60.124 66.667 0.00 0.00 0.00 3.69
172 173 3.591835 CGCTCGCCCTCTCTCCTC 61.592 72.222 0.00 0.00 0.00 3.71
195 196 1.568025 GCGGACACAAGACGGAAAC 59.432 57.895 0.00 0.00 0.00 2.78
196 197 1.952133 CGCGGACACAAGACGGAAA 60.952 57.895 0.00 0.00 0.00 3.13
197 198 2.355363 CGCGGACACAAGACGGAA 60.355 61.111 0.00 0.00 0.00 4.30
215 216 3.564027 GAGCCGGATTTGCGTCGG 61.564 66.667 5.05 0.00 45.84 4.79
217 218 0.239879 TTTTGAGCCGGATTTGCGTC 59.760 50.000 5.05 0.00 0.00 5.19
218 219 0.671251 TTTTTGAGCCGGATTTGCGT 59.329 45.000 5.05 0.00 0.00 5.24
220 221 2.001872 CCATTTTTGAGCCGGATTTGC 58.998 47.619 5.05 0.00 0.00 3.68
221 222 3.253230 GTCCATTTTTGAGCCGGATTTG 58.747 45.455 5.05 0.00 0.00 2.32
222 223 2.233676 GGTCCATTTTTGAGCCGGATTT 59.766 45.455 5.05 0.00 0.00 2.17
223 224 1.824852 GGTCCATTTTTGAGCCGGATT 59.175 47.619 5.05 0.00 0.00 3.01
225 226 0.958382 CGGTCCATTTTTGAGCCGGA 60.958 55.000 5.05 0.00 36.05 5.14
229 230 1.253100 TTCCCGGTCCATTTTTGAGC 58.747 50.000 0.00 0.00 0.00 4.26
230 231 2.166254 CCATTCCCGGTCCATTTTTGAG 59.834 50.000 0.00 0.00 0.00 3.02
231 232 2.175202 CCATTCCCGGTCCATTTTTGA 58.825 47.619 0.00 0.00 0.00 2.69
232 233 1.206849 CCCATTCCCGGTCCATTTTTG 59.793 52.381 0.00 0.00 0.00 2.44
233 234 1.203250 ACCCATTCCCGGTCCATTTTT 60.203 47.619 0.00 0.00 0.00 1.94
234 235 0.411848 ACCCATTCCCGGTCCATTTT 59.588 50.000 0.00 0.00 0.00 1.82
235 236 0.033503 GACCCATTCCCGGTCCATTT 60.034 55.000 0.00 0.00 43.48 2.32
237 238 2.742116 CGACCCATTCCCGGTCCAT 61.742 63.158 0.00 0.00 46.01 3.41
238 239 3.395702 CGACCCATTCCCGGTCCA 61.396 66.667 0.00 0.00 46.01 4.02
239 240 4.171103 CCGACCCATTCCCGGTCC 62.171 72.222 0.00 0.00 46.01 4.46
277 278 4.204891 CATTTCGTCCGCCGCGTC 62.205 66.667 12.58 3.65 36.19 5.19
281 282 3.192922 GACCCATTTCGTCCGCCG 61.193 66.667 0.00 0.00 38.13 6.46
282 283 3.192922 CGACCCATTTCGTCCGCC 61.193 66.667 0.00 0.00 34.16 6.13
283 284 3.861263 GCGACCCATTTCGTCCGC 61.861 66.667 0.00 0.00 41.26 5.54
284 285 3.192922 GGCGACCCATTTCGTCCG 61.193 66.667 0.00 0.00 41.26 4.79
296 297 0.169009 GAGCAACTTCAATGGGCGAC 59.831 55.000 0.00 0.00 0.00 5.19
299 300 3.696051 TCATAAGAGCAACTTCAATGGGC 59.304 43.478 0.00 0.00 39.72 5.36
300 301 5.393461 GGTTCATAAGAGCAACTTCAATGGG 60.393 44.000 0.00 0.00 39.72 4.00
301 302 5.183713 TGGTTCATAAGAGCAACTTCAATGG 59.816 40.000 0.00 0.00 39.72 3.16
303 304 6.899393 TTGGTTCATAAGAGCAACTTCAAT 57.101 33.333 0.00 0.00 39.72 2.57
304 305 6.096141 TGTTTGGTTCATAAGAGCAACTTCAA 59.904 34.615 0.00 0.00 39.72 2.69
305 306 5.592282 TGTTTGGTTCATAAGAGCAACTTCA 59.408 36.000 0.00 0.00 39.72 3.02
306 307 6.072112 TGTTTGGTTCATAAGAGCAACTTC 57.928 37.500 0.00 0.00 39.72 3.01
307 308 5.010012 CCTGTTTGGTTCATAAGAGCAACTT 59.990 40.000 2.10 2.10 42.04 2.66
308 309 4.520492 CCTGTTTGGTTCATAAGAGCAACT 59.480 41.667 0.00 0.00 34.59 3.16
309 310 4.798574 CCTGTTTGGTTCATAAGAGCAAC 58.201 43.478 0.00 0.00 34.59 4.17
310 311 3.255642 GCCTGTTTGGTTCATAAGAGCAA 59.744 43.478 0.00 0.00 38.35 3.91
311 312 2.819608 GCCTGTTTGGTTCATAAGAGCA 59.180 45.455 0.00 0.00 38.35 4.26
312 313 2.164422 GGCCTGTTTGGTTCATAAGAGC 59.836 50.000 0.00 0.00 38.35 4.09
314 315 3.073798 TCAGGCCTGTTTGGTTCATAAGA 59.926 43.478 31.58 4.68 38.35 2.10
315 316 3.420893 TCAGGCCTGTTTGGTTCATAAG 58.579 45.455 31.58 1.23 38.35 1.73
316 317 3.181434 ACTCAGGCCTGTTTGGTTCATAA 60.181 43.478 31.58 7.42 38.35 1.90
317 318 2.375174 ACTCAGGCCTGTTTGGTTCATA 59.625 45.455 31.58 7.96 38.35 2.15
318 319 1.145738 ACTCAGGCCTGTTTGGTTCAT 59.854 47.619 31.58 5.72 38.35 2.57
320 321 1.692411 AACTCAGGCCTGTTTGGTTC 58.308 50.000 31.58 0.00 38.35 3.62
321 322 3.157087 CATAACTCAGGCCTGTTTGGTT 58.843 45.455 31.58 27.88 38.35 3.67
322 323 2.555227 CCATAACTCAGGCCTGTTTGGT 60.555 50.000 31.58 22.37 38.35 3.67
323 324 2.094675 CCATAACTCAGGCCTGTTTGG 58.905 52.381 31.58 24.46 39.35 3.28
324 325 1.474077 GCCATAACTCAGGCCTGTTTG 59.526 52.381 31.58 23.23 45.18 2.93
325 326 1.839424 GCCATAACTCAGGCCTGTTT 58.161 50.000 31.58 25.56 45.18 2.83
326 327 3.577389 GCCATAACTCAGGCCTGTT 57.423 52.632 31.58 21.64 45.18 3.16
332 333 1.732259 GTGAACACGCCATAACTCAGG 59.268 52.381 0.00 0.00 0.00 3.86
333 334 2.688507 AGTGAACACGCCATAACTCAG 58.311 47.619 0.00 0.00 36.20 3.35
334 335 2.805671 CAAGTGAACACGCCATAACTCA 59.194 45.455 0.00 0.00 36.20 3.41
337 338 1.877443 ACCAAGTGAACACGCCATAAC 59.123 47.619 0.00 0.00 36.20 1.89
338 339 1.876799 CACCAAGTGAACACGCCATAA 59.123 47.619 0.00 0.00 35.23 1.90
339 340 1.518325 CACCAAGTGAACACGCCATA 58.482 50.000 0.00 0.00 35.23 2.74
370 371 1.895238 GGTGCGTCCTAACCTGCTA 59.105 57.895 0.00 0.00 33.40 3.49
423 424 1.265462 GCGCATTTCGTCAAACGCAA 61.265 50.000 0.30 0.00 42.21 4.85
470 471 4.302509 TGGAAAACGCGGCTCCGA 62.303 61.111 12.47 1.62 42.83 4.55
515 3448 0.692419 TTCCATGCTCCCTCCCTCTC 60.692 60.000 0.00 0.00 0.00 3.20
600 3540 2.353610 GGGTCGGTCGGTGGTATGT 61.354 63.158 0.00 0.00 0.00 2.29
643 3583 3.879180 ATGGGTGGTGGAAACGGCC 62.879 63.158 0.00 0.00 0.00 6.13
644 3584 2.282887 ATGGGTGGTGGAAACGGC 60.283 61.111 0.00 0.00 0.00 5.68
655 3595 2.862140 GCCAACGTGAAAAAGATGGGTG 60.862 50.000 0.00 0.00 31.88 4.61
656 3596 1.339929 GCCAACGTGAAAAAGATGGGT 59.660 47.619 0.00 0.00 31.88 4.51
726 5211 3.822735 TCTTCTGCTCTGGTGGAAATTTG 59.177 43.478 0.00 0.00 0.00 2.32
784 5270 1.377856 GAGGCTGAAGTGGAAGGGC 60.378 63.158 0.00 0.00 0.00 5.19
847 5390 4.898265 GGAGCTGCTCATATATAGGGATCA 59.102 45.833 28.95 0.00 31.08 2.92
848 5391 4.898265 TGGAGCTGCTCATATATAGGGATC 59.102 45.833 28.95 9.03 31.08 3.36
851 5394 3.771479 TGTGGAGCTGCTCATATATAGGG 59.229 47.826 28.95 0.00 31.08 3.53
852 5395 4.382470 GGTGTGGAGCTGCTCATATATAGG 60.382 50.000 28.95 0.00 31.08 2.57
961 5533 3.436243 GGAGAGGATCGATGTAGGGAAT 58.564 50.000 0.54 0.00 42.67 3.01
985 5561 0.456653 GCCATTTTGCAAGCGACGAT 60.457 50.000 0.00 0.00 0.00 3.73
997 5573 2.229784 CGCTGGAAGAAGAAGCCATTTT 59.770 45.455 0.00 0.00 34.07 1.82
1139 5750 3.313007 TACTTGTCGACGACCGCCG 62.313 63.158 24.33 12.31 45.44 6.46
1164 5775 2.124819 AGCATGGCGAGCAGAAGG 60.125 61.111 3.81 0.00 0.00 3.46
1275 5930 5.067413 ACCATCAACCACTGAGTATACGTAG 59.933 44.000 0.08 2.78 37.52 3.51
1278 5933 4.386867 ACCATCAACCACTGAGTATACG 57.613 45.455 0.00 0.00 37.52 3.06
1280 5935 6.121776 ACAAACCATCAACCACTGAGTATA 57.878 37.500 0.00 0.00 37.52 1.47
1283 5950 3.297134 ACAAACCATCAACCACTGAGT 57.703 42.857 0.00 0.00 37.52 3.41
1371 6054 9.777008 AGAATGAAGGTATAATTTTTGGGGTAA 57.223 29.630 0.00 0.00 0.00 2.85
1419 6109 7.042725 CGACAGAACTCTTTCAATCAACAAGTA 60.043 37.037 0.00 0.00 33.72 2.24
1420 6110 6.238211 CGACAGAACTCTTTCAATCAACAAGT 60.238 38.462 0.00 0.00 33.72 3.16
1421 6111 6.132056 CGACAGAACTCTTTCAATCAACAAG 58.868 40.000 0.00 0.00 33.72 3.16
1469 6160 2.892374 TGCATCGGTGACTATGAACAG 58.108 47.619 0.00 0.00 35.63 3.16
1540 6235 5.469084 GTGGGTTGTAAAACTTACCTCTGAG 59.531 44.000 0.00 0.00 30.93 3.35
1544 6239 4.883006 TGTGTGGGTTGTAAAACTTACCTC 59.117 41.667 0.00 0.00 30.93 3.85
1547 6242 6.628919 ATCTGTGTGGGTTGTAAAACTTAC 57.371 37.500 0.00 0.00 30.93 2.34
1591 6289 3.466836 TCATCATGTAAGAATGTCGGCC 58.533 45.455 0.00 0.00 0.00 6.13
1596 6294 6.715280 AGGTCAACTCATCATGTAAGAATGT 58.285 36.000 0.00 0.00 0.00 2.71
1610 6308 8.918202 AATTGTTACTGATTTAGGTCAACTCA 57.082 30.769 0.00 0.00 0.00 3.41
1638 6336 8.726988 CGAACTATTCTTTCACCTTTTTCCATA 58.273 33.333 0.00 0.00 0.00 2.74
1639 6337 7.593825 CGAACTATTCTTTCACCTTTTTCCAT 58.406 34.615 0.00 0.00 0.00 3.41
1640 6338 6.514376 GCGAACTATTCTTTCACCTTTTTCCA 60.514 38.462 0.00 0.00 0.00 3.53
1689 6387 2.281900 TTCGGAAAACCCAGCCGG 60.282 61.111 0.00 0.00 44.87 6.13
1702 6400 1.740296 AATCACGGAAGCGGTTCGG 60.740 57.895 26.99 26.99 38.61 4.30
1703 6401 1.419922 CAATCACGGAAGCGGTTCG 59.580 57.895 20.14 16.99 32.92 3.95
1715 6413 4.778143 AGACCGCCGCCCAATCAC 62.778 66.667 0.00 0.00 0.00 3.06
1716 6414 4.028490 AAGACCGCCGCCCAATCA 62.028 61.111 0.00 0.00 0.00 2.57
1752 6450 3.340814 ACTCCATTCAGAAGAACGCAT 57.659 42.857 0.00 0.00 36.39 4.73
1802 6500 3.003763 GGGTCCCCTGTCGAAGCT 61.004 66.667 0.00 0.00 0.00 3.74
1831 6530 0.883833 AATTGCCAGGACAAAGAGCG 59.116 50.000 0.00 0.00 32.27 5.03
1838 6537 1.355381 AGTGGATCAATTGCCAGGACA 59.645 47.619 5.15 0.00 34.22 4.02
1871 6570 1.377594 TGTCTAGTAGCGGCGTCCA 60.378 57.895 9.37 0.00 0.00 4.02
1873 6572 0.169672 TTGTGTCTAGTAGCGGCGTC 59.830 55.000 9.37 0.13 0.00 5.19
1874 6573 0.109412 GTTGTGTCTAGTAGCGGCGT 60.109 55.000 9.37 0.00 0.00 5.68
1875 6574 0.801067 GGTTGTGTCTAGTAGCGGCG 60.801 60.000 0.51 0.51 0.00 6.46
1876 6575 0.531200 AGGTTGTGTCTAGTAGCGGC 59.469 55.000 0.00 0.00 0.00 6.53
1877 6576 3.314541 AAAGGTTGTGTCTAGTAGCGG 57.685 47.619 0.00 0.00 0.00 5.52
1878 6577 3.120649 GCAAAAGGTTGTGTCTAGTAGCG 60.121 47.826 0.00 0.00 37.06 4.26
1919 6618 0.600782 TGAAGTACGAACAACCGGGC 60.601 55.000 6.32 0.00 0.00 6.13
1962 6661 4.136796 CCTCCTTTGTCAGTGTGATGAAA 58.863 43.478 0.00 0.00 0.00 2.69
1966 6665 3.328931 ACATCCTCCTTTGTCAGTGTGAT 59.671 43.478 0.00 0.00 0.00 3.06
1973 6672 2.054021 TGTGGACATCCTCCTTTGTCA 58.946 47.619 0.00 0.00 43.20 3.58
2153 6852 1.460305 TAGATGGAGAGGGGCAGCC 60.460 63.158 1.26 1.26 0.00 4.85
2171 6870 2.695585 AGTCCACCCTCTTGAGTTTCT 58.304 47.619 0.00 0.00 0.00 2.52
2197 6896 1.689984 TGCAGCAACCTTGTCATCAA 58.310 45.000 0.00 0.00 0.00 2.57
2198 6897 1.689984 TTGCAGCAACCTTGTCATCA 58.310 45.000 2.83 0.00 0.00 3.07
2199 6898 2.796593 GTTTTGCAGCAACCTTGTCATC 59.203 45.455 7.54 0.00 0.00 2.92
2200 6899 2.431782 AGTTTTGCAGCAACCTTGTCAT 59.568 40.909 7.54 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.