Multiple sequence alignment - TraesCS3D01G371200

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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 TraesCS3D01G371200 chr3D 100.000 2792 0 0 1 2792 484733474 484736265 0.000000e+00 5156
1 TraesCS3D01G371200 chr3D 91.878 788 62 2 919 1705 484804980 484805766 0.000000e+00 1099
2 TraesCS3D01G371200 chr3D 91.808 708 52 4 998 1705 484726149 484726850 0.000000e+00 981
3 TraesCS3D01G371200 chr3D 86.850 327 37 5 2469 2792 484805781 484806104 7.350000e-96 361
4 TraesCS3D01G371200 chr3D 82.386 176 24 5 1 176 553747721 553747889 2.240000e-31 147
5 TraesCS3D01G371200 chr2D 98.920 741 8 0 1724 2464 39147104 39147844 0.000000e+00 1325
6 TraesCS3D01G371200 chr2D 89.525 716 63 8 1760 2464 67566168 67565454 0.000000e+00 896
7 TraesCS3D01G371200 chr2D 85.119 168 21 4 678 842 298058745 298058911 4.780000e-38 169
8 TraesCS3D01G371200 chr2D 80.861 209 33 2 1 209 111500019 111499818 1.040000e-34 158
9 TraesCS3D01G371200 chr3A 95.521 826 32 1 898 1723 627817168 627817988 0.000000e+00 1315
10 TraesCS3D01G371200 chr3A 89.988 829 63 7 887 1705 627785314 627786132 0.000000e+00 1053
11 TraesCS3D01G371200 chr3A 93.921 329 20 0 2464 2792 627817980 627818308 5.370000e-137 497
12 TraesCS3D01G371200 chr3A 87.538 329 34 7 2469 2792 627786147 627786473 9.440000e-100 374
13 TraesCS3D01G371200 chr3A 91.257 183 11 1 887 1069 627793664 627793841 7.720000e-61 244
14 TraesCS3D01G371200 chr3A 85.119 168 21 4 678 842 228540279 228540113 4.780000e-38 169
15 TraesCS3D01G371200 chr3A 87.611 113 14 0 566 678 627708115 627708227 6.270000e-27 132
16 TraesCS3D01G371200 chr4D 97.841 741 12 1 1724 2464 474981177 474980441 0.000000e+00 1277
17 TraesCS3D01G371200 chr4D 88.873 710 58 13 1760 2464 83867541 83866848 0.000000e+00 854
18 TraesCS3D01G371200 chr4D 75.634 513 80 28 1 509 57470110 57469639 2.180000e-51 213
19 TraesCS3D01G371200 chr4D 78.736 348 50 14 83 425 356880752 356881080 7.840000e-51 211
20 TraesCS3D01G371200 chr3B 90.793 782 60 2 930 1705 647542264 647543039 0.000000e+00 1035
21 TraesCS3D01G371200 chr3B 92.869 603 32 6 1866 2464 817455020 817454425 0.000000e+00 865
22 TraesCS3D01G371200 chr3B 92.053 604 41 4 1864 2464 235803664 235804263 0.000000e+00 843
23 TraesCS3D01G371200 chr3B 81.833 600 90 12 1 595 647541651 647542236 1.160000e-133 486
24 TraesCS3D01G371200 chr3B 86.322 329 38 7 2469 2792 647543054 647543380 4.420000e-93 351
25 TraesCS3D01G371200 chr3B 98.101 158 3 0 1724 1881 235803485 235803642 2.740000e-70 276
26 TraesCS3D01G371200 chr3B 73.546 533 96 24 1 524 465057873 465058369 8.000000e-36 161
27 TraesCS3D01G371200 chr3B 76.125 289 61 8 240 525 598970430 598970147 8.060000e-31 145
28 TraesCS3D01G371200 chr6B 92.586 607 36 6 1864 2466 60592807 60592206 0.000000e+00 863
29 TraesCS3D01G371200 chr6B 92.092 607 39 6 1864 2465 141736708 141736106 0.000000e+00 846
30 TraesCS3D01G371200 chr6B 96.815 157 5 0 1723 1879 141736886 141736730 2.130000e-66 263
31 TraesCS3D01G371200 chr6B 95.679 162 6 1 1720 1881 60592985 60592825 2.760000e-65 259
32 TraesCS3D01G371200 chr6B 75.849 530 90 20 1 525 590025994 590026490 4.650000e-58 235
33 TraesCS3D01G371200 chr6B 77.485 342 70 6 189 529 643531262 643531597 6.100000e-47 198
34 TraesCS3D01G371200 chr6B 79.343 213 31 9 1011 1218 75268455 75268251 1.350000e-28 137
35 TraesCS3D01G371200 chr2B 92.384 604 37 6 1864 2464 517263058 517262461 0.000000e+00 852
36 TraesCS3D01G371200 chr2B 96.835 158 5 0 1724 1881 517263233 517263076 5.930000e-67 265
37 TraesCS3D01G371200 chr2B 94.937 158 8 0 1724 1881 484744487 484744330 5.970000e-62 248
38 TraesCS3D01G371200 chr2B 81.166 223 25 10 678 885 355230745 355230525 2.230000e-36 163
39 TraesCS3D01G371200 chr2B 78.030 264 46 11 255 509 34805725 34805985 3.720000e-34 156
40 TraesCS3D01G371200 chr7A 83.550 462 63 6 1 459 100194282 100194733 1.200000e-113 420
41 TraesCS3D01G371200 chr1B 78.044 501 86 19 30 525 571679408 571679889 7.560000e-76 294
42 TraesCS3D01G371200 chr5A 78.772 391 68 7 1 386 69383944 69384324 5.970000e-62 248
43 TraesCS3D01G371200 chr5A 75.472 530 93 20 2 526 677669776 677670273 1.010000e-54 224
44 TraesCS3D01G371200 chr5A 77.982 327 63 8 118 438 69527171 69527494 2.190000e-46 196
45 TraesCS3D01G371200 chr5D 75.417 480 91 19 57 531 310260948 310260491 1.010000e-49 207
46 TraesCS3D01G371200 chr5D 84.434 212 29 2 678 885 565094083 565093872 3.650000e-49 206
47 TraesCS3D01G371200 chr4A 84.689 209 28 4 678 885 12399778 12399573 3.650000e-49 206
48 TraesCS3D01G371200 chr7B 84.360 211 25 8 678 882 728010910 728011118 1.700000e-47 200
49 TraesCS3D01G371200 chr7B 78.049 205 39 5 677 877 39615062 39615264 1.050000e-24 124
50 TraesCS3D01G371200 chr4B 82.569 218 25 9 677 883 107033309 107033524 2.210000e-41 180
51 TraesCS3D01G371200 chr4B 83.425 181 24 6 679 857 124017520 124017344 2.230000e-36 163
52 TraesCS3D01G371200 chr1D 74.125 514 86 28 1 509 407613841 407613370 4.780000e-38 169
53 TraesCS3D01G371200 chr7D 79.343 213 34 8 679 885 325872442 325872650 1.040000e-29 141
54 TraesCS3D01G371200 chr2A 79.429 175 27 4 1 175 13799331 13799166 6.320000e-22 115


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 TraesCS3D01G371200 chr3D 484733474 484736265 2791 False 5156.0 5156 100.0000 1 2792 1 chr3D.!!$F2 2791
1 TraesCS3D01G371200 chr3D 484726149 484726850 701 False 981.0 981 91.8080 998 1705 1 chr3D.!!$F1 707
2 TraesCS3D01G371200 chr3D 484804980 484806104 1124 False 730.0 1099 89.3640 919 2792 2 chr3D.!!$F4 1873
3 TraesCS3D01G371200 chr2D 39147104 39147844 740 False 1325.0 1325 98.9200 1724 2464 1 chr2D.!!$F1 740
4 TraesCS3D01G371200 chr2D 67565454 67566168 714 True 896.0 896 89.5250 1760 2464 1 chr2D.!!$R1 704
5 TraesCS3D01G371200 chr3A 627817168 627818308 1140 False 906.0 1315 94.7210 898 2792 2 chr3A.!!$F4 1894
6 TraesCS3D01G371200 chr3A 627785314 627786473 1159 False 713.5 1053 88.7630 887 2792 2 chr3A.!!$F3 1905
7 TraesCS3D01G371200 chr4D 474980441 474981177 736 True 1277.0 1277 97.8410 1724 2464 1 chr4D.!!$R3 740
8 TraesCS3D01G371200 chr4D 83866848 83867541 693 True 854.0 854 88.8730 1760 2464 1 chr4D.!!$R2 704
9 TraesCS3D01G371200 chr3B 817454425 817455020 595 True 865.0 865 92.8690 1866 2464 1 chr3B.!!$R2 598
10 TraesCS3D01G371200 chr3B 647541651 647543380 1729 False 624.0 1035 86.3160 1 2792 3 chr3B.!!$F3 2791
11 TraesCS3D01G371200 chr3B 235803485 235804263 778 False 559.5 843 95.0770 1724 2464 2 chr3B.!!$F2 740
12 TraesCS3D01G371200 chr6B 60592206 60592985 779 True 561.0 863 94.1325 1720 2466 2 chr6B.!!$R2 746
13 TraesCS3D01G371200 chr6B 141736106 141736886 780 True 554.5 846 94.4535 1723 2465 2 chr6B.!!$R3 742
14 TraesCS3D01G371200 chr2B 517262461 517263233 772 True 558.5 852 94.6095 1724 2464 2 chr2B.!!$R3 740

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
28 29 0.039764 TCGTGGACCTCACATCCTCT 59.960 55.0 0.00 0.00 46.36 3.69 F
65 66 0.106419 GGACTCCTCCGAGGATGAGT 60.106 60.0 23.73 23.73 44.81 3.41 F
209 211 0.179062 GCAGACGGCAGATTGAGGAT 60.179 55.0 0.00 0.00 43.97 3.24 F
511 516 1.161843 GAAGGAAATTTGCGGGTCGA 58.838 50.0 3.87 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 1552 0.462937 TGTCCACCACGACCACTTTG 60.463 55.000 0.00 0.0 31.35 2.77 R
1560 1582 0.464036 AGGCGACGGCTTCATTATCA 59.536 50.000 19.41 0.0 39.81 2.15 R
1721 1743 3.071023 GTCGACCCATTCCCATCTTGATA 59.929 47.826 3.51 0.0 0.00 2.15 R
2502 2580 0.839946 GGTGGCCTATGGATCACAGT 59.160 55.000 3.32 0.0 32.80 3.55 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
24 25 0.824109 TCCATCGTGGACCTCACATC 59.176 55.000 3.02 0.00 42.67 3.06
26 27 0.826715 CATCGTGGACCTCACATCCT 59.173 55.000 0.00 0.00 46.36 3.24
27 28 1.115467 ATCGTGGACCTCACATCCTC 58.885 55.000 0.00 0.00 46.36 3.71
28 29 0.039764 TCGTGGACCTCACATCCTCT 59.960 55.000 0.00 0.00 46.36 3.69
35 36 0.743688 CCTCACATCCTCTGGAGACG 59.256 60.000 0.00 0.00 34.05 4.18
37 38 0.684479 TCACATCCTCTGGAGACGGG 60.684 60.000 0.00 0.00 34.05 5.28
40 41 1.760086 ATCCTCTGGAGACGGGCAG 60.760 63.158 0.00 0.00 34.05 4.85
54 55 2.435059 GCAGGTTGCGGACTCCTC 60.435 66.667 0.00 0.00 31.71 3.71
65 66 0.106419 GGACTCCTCCGAGGATGAGT 60.106 60.000 23.73 23.73 44.81 3.41
69 70 1.422024 CTCCTCCGAGGATGAGTAGGA 59.578 57.143 17.80 5.98 44.81 2.94
73 74 1.283905 TCCGAGGATGAGTAGGACACA 59.716 52.381 0.00 0.00 0.00 3.72
78 79 2.035632 GGATGAGTAGGACACAGGAGG 58.964 57.143 0.00 0.00 0.00 4.30
81 82 0.966370 GAGTAGGACACAGGAGGCGT 60.966 60.000 0.00 0.00 0.00 5.68
97 98 4.717313 GTCGGGGCCTTGTGTCCC 62.717 72.222 0.84 0.00 41.87 4.46
113 114 2.998097 CCATGTGGGTCGGTCCAT 59.002 61.111 1.26 0.00 39.26 3.41
114 115 1.153168 CCATGTGGGTCGGTCCATC 60.153 63.158 1.26 0.00 39.26 3.51
115 116 1.626356 CCATGTGGGTCGGTCCATCT 61.626 60.000 1.26 0.00 39.26 2.90
116 117 0.179073 CATGTGGGTCGGTCCATCTC 60.179 60.000 1.26 0.00 39.26 2.75
136 137 0.886563 CCGACTCCCGTGTTCTACTT 59.113 55.000 0.00 0.00 36.31 2.24
139 140 3.387397 CGACTCCCGTGTTCTACTTTTT 58.613 45.455 0.00 0.00 0.00 1.94
144 145 3.318839 TCCCGTGTTCTACTTTTTCTCGA 59.681 43.478 0.00 0.00 0.00 4.04
147 148 3.727723 CGTGTTCTACTTTTTCTCGACGT 59.272 43.478 0.00 0.00 0.00 4.34
154 155 1.647702 CTTTTTCTCGACGTAGACCGC 59.352 52.381 0.00 0.00 41.42 5.68
168 169 0.531974 GACCGCACCTTCACTTCACA 60.532 55.000 0.00 0.00 0.00 3.58
182 183 1.466025 TTCACAGGTCTTACCGCCGT 61.466 55.000 0.00 0.00 44.90 5.68
184 185 2.202570 CAGGTCTTACCGCCGTCG 60.203 66.667 0.00 0.00 44.90 5.12
185 186 2.674380 AGGTCTTACCGCCGTCGT 60.674 61.111 0.00 0.00 44.90 4.34
190 192 1.585214 GTCTTACCGCCGTCGTTTATG 59.415 52.381 0.00 0.00 0.00 1.90
191 193 0.299597 CTTACCGCCGTCGTTTATGC 59.700 55.000 0.00 0.00 0.00 3.14
207 209 3.805267 GCAGACGGCAGATTGAGG 58.195 61.111 0.00 0.00 43.97 3.86
209 211 0.179062 GCAGACGGCAGATTGAGGAT 60.179 55.000 0.00 0.00 43.97 3.24
215 217 1.679944 CGGCAGATTGAGGATGTGGTT 60.680 52.381 0.00 0.00 30.00 3.67
216 218 2.419990 CGGCAGATTGAGGATGTGGTTA 60.420 50.000 0.00 0.00 30.00 2.85
217 219 3.745480 CGGCAGATTGAGGATGTGGTTAT 60.745 47.826 0.00 0.00 30.00 1.89
224 226 2.159296 TGAGGATGTGGTTATCGACACG 60.159 50.000 0.00 0.00 40.39 4.49
234 236 5.751990 GTGGTTATCGACACGGAATAGAAAT 59.248 40.000 0.00 0.00 0.00 2.17
244 246 5.411669 ACACGGAATAGAAATGAAGTTGGAC 59.588 40.000 0.00 0.00 0.00 4.02
246 248 4.630069 CGGAATAGAAATGAAGTTGGACGT 59.370 41.667 0.00 0.00 0.00 4.34
250 252 2.036733 AGAAATGAAGTTGGACGTCGGA 59.963 45.455 9.92 0.00 28.93 4.55
279 281 1.211212 GCCGTTGGATAGGTTTAGGGT 59.789 52.381 0.00 0.00 0.00 4.34
281 283 3.493873 GCCGTTGGATAGGTTTAGGGTAG 60.494 52.174 0.00 0.00 0.00 3.18
284 286 4.042884 GTTGGATAGGTTTAGGGTAGGGT 58.957 47.826 0.00 0.00 0.00 4.34
285 287 4.372953 TGGATAGGTTTAGGGTAGGGTT 57.627 45.455 0.00 0.00 0.00 4.11
286 288 4.713283 TGGATAGGTTTAGGGTAGGGTTT 58.287 43.478 0.00 0.00 0.00 3.27
287 289 5.864035 TGGATAGGTTTAGGGTAGGGTTTA 58.136 41.667 0.00 0.00 0.00 2.01
293 295 6.866621 AGGTTTAGGGTAGGGTTTATTTTGT 58.133 36.000 0.00 0.00 0.00 2.83
296 298 7.874016 GGTTTAGGGTAGGGTTTATTTTGTTTG 59.126 37.037 0.00 0.00 0.00 2.93
299 301 7.058023 AGGGTAGGGTTTATTTTGTTTGTTC 57.942 36.000 0.00 0.00 0.00 3.18
331 333 9.464248 GTTTGAAATGTAATGAAAATTCGATGC 57.536 29.630 0.00 0.00 0.00 3.91
349 351 2.247311 GCGTTTGCATGAATCTCGTT 57.753 45.000 0.00 0.00 42.15 3.85
350 352 2.169179 GCGTTTGCATGAATCTCGTTC 58.831 47.619 0.00 0.00 42.15 3.95
352 354 2.774007 GTTTGCATGAATCTCGTTCGG 58.226 47.619 0.00 0.00 39.80 4.30
356 358 3.591023 TGCATGAATCTCGTTCGGTTTA 58.409 40.909 0.00 0.00 39.80 2.01
365 367 8.937884 TGAATCTCGTTCGGTTTATATGAAAAA 58.062 29.630 0.00 0.00 39.80 1.94
366 368 9.931210 GAATCTCGTTCGGTTTATATGAAAAAT 57.069 29.630 0.00 0.00 0.00 1.82
369 371 7.276218 TCTCGTTCGGTTTATATGAAAAATCGT 59.724 33.333 2.88 0.00 40.45 3.73
370 372 7.741198 TCGTTCGGTTTATATGAAAAATCGTT 58.259 30.769 2.88 0.00 40.45 3.85
380 382 4.831741 TGAAAAATCGTTGTGTTTGCAC 57.168 36.364 0.00 0.00 45.44 4.57
446 449 4.424711 GTTGGATGGCGGCCTCCA 62.425 66.667 28.17 28.17 39.78 3.86
473 478 2.364579 TCCGCGGATTGGTACCCT 60.365 61.111 27.28 0.00 0.00 4.34
474 479 2.108362 CCGCGGATTGGTACCCTC 59.892 66.667 24.07 6.23 0.00 4.30
481 486 2.948840 GATTGGTACCCTCGTCCGCG 62.949 65.000 10.07 0.00 39.92 6.46
504 509 1.798813 CGGATGCGGAAGGAAATTTGC 60.799 52.381 0.68 0.68 32.68 3.68
505 510 1.548986 GATGCGGAAGGAAATTTGCG 58.451 50.000 3.87 0.00 43.53 4.85
511 516 1.161843 GAAGGAAATTTGCGGGTCGA 58.838 50.000 3.87 0.00 0.00 4.20
512 517 1.743394 GAAGGAAATTTGCGGGTCGAT 59.257 47.619 3.87 0.00 0.00 3.59
516 521 2.515912 GAAATTTGCGGGTCGATGTTC 58.484 47.619 0.00 0.00 0.00 3.18
562 567 7.826690 AGCAAGGTTAAAACAATGAATATCGT 58.173 30.769 0.00 0.00 0.00 3.73
575 581 8.184192 ACAATGAATATCGTGAAATCTTGTTCC 58.816 33.333 0.00 0.00 0.00 3.62
580 586 3.926616 TCGTGAAATCTTGTTCCTCTCC 58.073 45.455 0.00 0.00 0.00 3.71
584 590 5.106908 CGTGAAATCTTGTTCCTCTCCTTTC 60.107 44.000 0.00 0.00 0.00 2.62
591 597 2.716424 TGTTCCTCTCCTTTCCATTGGT 59.284 45.455 1.86 0.00 0.00 3.67
595 601 4.918588 TCCTCTCCTTTCCATTGGTTTAC 58.081 43.478 1.86 0.00 0.00 2.01
597 603 4.459337 CCTCTCCTTTCCATTGGTTTACAC 59.541 45.833 1.86 0.00 0.00 2.90
599 605 5.640147 TCTCCTTTCCATTGGTTTACACAT 58.360 37.500 1.86 0.00 0.00 3.21
601 607 6.553100 TCTCCTTTCCATTGGTTTACACATTT 59.447 34.615 1.86 0.00 0.00 2.32
603 609 7.213678 TCCTTTCCATTGGTTTACACATTTTC 58.786 34.615 1.86 0.00 0.00 2.29
604 610 7.070571 TCCTTTCCATTGGTTTACACATTTTCT 59.929 33.333 1.86 0.00 0.00 2.52
605 611 8.364142 CCTTTCCATTGGTTTACACATTTTCTA 58.636 33.333 1.86 0.00 0.00 2.10
609 615 9.921637 TCCATTGGTTTACACATTTTCTAAATC 57.078 29.630 1.86 0.00 0.00 2.17
610 616 9.703892 CCATTGGTTTACACATTTTCTAAATCA 57.296 29.630 0.00 0.00 0.00 2.57
613 619 9.522804 TTGGTTTACACATTTTCTAAATCACAC 57.477 29.630 0.00 0.00 0.00 3.82
614 620 8.687242 TGGTTTACACATTTTCTAAATCACACA 58.313 29.630 0.00 0.00 0.00 3.72
615 621 9.691362 GGTTTACACATTTTCTAAATCACACAT 57.309 29.630 0.00 0.00 0.00 3.21
620 626 9.248291 ACACATTTTCTAAATCACACATTTCAC 57.752 29.630 0.00 0.00 0.00 3.18
622 628 9.985730 ACATTTTCTAAATCACACATTTCACAT 57.014 25.926 0.00 0.00 0.00 3.21
625 631 9.474920 TTTTCTAAATCACACATTTCACATTCC 57.525 29.630 0.00 0.00 0.00 3.01
626 632 8.408043 TTCTAAATCACACATTTCACATTCCT 57.592 30.769 0.00 0.00 0.00 3.36
627 633 8.044060 TCTAAATCACACATTTCACATTCCTC 57.956 34.615 0.00 0.00 0.00 3.71
628 634 6.906157 AAATCACACATTTCACATTCCTCT 57.094 33.333 0.00 0.00 0.00 3.69
629 635 6.506500 AATCACACATTTCACATTCCTCTC 57.493 37.500 0.00 0.00 0.00 3.20
630 636 5.233083 TCACACATTTCACATTCCTCTCT 57.767 39.130 0.00 0.00 0.00 3.10
631 637 5.624159 TCACACATTTCACATTCCTCTCTT 58.376 37.500 0.00 0.00 0.00 2.85
632 638 6.064060 TCACACATTTCACATTCCTCTCTTT 58.936 36.000 0.00 0.00 0.00 2.52
633 639 6.547141 TCACACATTTCACATTCCTCTCTTTT 59.453 34.615 0.00 0.00 0.00 2.27
634 640 7.068593 TCACACATTTCACATTCCTCTCTTTTT 59.931 33.333 0.00 0.00 0.00 1.94
635 641 7.380602 CACACATTTCACATTCCTCTCTTTTTC 59.619 37.037 0.00 0.00 0.00 2.29
636 642 7.286316 ACACATTTCACATTCCTCTCTTTTTCT 59.714 33.333 0.00 0.00 0.00 2.52
637 643 8.139989 CACATTTCACATTCCTCTCTTTTTCTT 58.860 33.333 0.00 0.00 0.00 2.52
638 644 8.355913 ACATTTCACATTCCTCTCTTTTTCTTC 58.644 33.333 0.00 0.00 0.00 2.87
639 645 6.545504 TTCACATTCCTCTCTTTTTCTTCG 57.454 37.500 0.00 0.00 0.00 3.79
640 646 4.997395 TCACATTCCTCTCTTTTTCTTCGG 59.003 41.667 0.00 0.00 0.00 4.30
641 647 3.753797 ACATTCCTCTCTTTTTCTTCGGC 59.246 43.478 0.00 0.00 0.00 5.54
642 648 3.485463 TTCCTCTCTTTTTCTTCGGCA 57.515 42.857 0.00 0.00 0.00 5.69
643 649 3.045601 TCCTCTCTTTTTCTTCGGCAG 57.954 47.619 0.00 0.00 0.00 4.85
644 650 2.632996 TCCTCTCTTTTTCTTCGGCAGA 59.367 45.455 0.00 0.00 0.00 4.26
645 651 3.071023 TCCTCTCTTTTTCTTCGGCAGAA 59.929 43.478 0.00 0.00 39.99 3.02
646 652 4.006319 CCTCTCTTTTTCTTCGGCAGAAT 58.994 43.478 0.00 0.00 41.42 2.40
647 653 5.046591 TCCTCTCTTTTTCTTCGGCAGAATA 60.047 40.000 0.00 0.00 41.42 1.75
648 654 5.293079 CCTCTCTTTTTCTTCGGCAGAATAG 59.707 44.000 0.00 0.00 41.42 1.73
649 655 6.037786 TCTCTTTTTCTTCGGCAGAATAGA 57.962 37.500 0.00 0.00 41.42 1.98
650 656 6.464222 TCTCTTTTTCTTCGGCAGAATAGAA 58.536 36.000 0.00 0.00 41.42 2.10
651 657 6.934645 TCTCTTTTTCTTCGGCAGAATAGAAA 59.065 34.615 8.95 8.95 41.42 2.52
652 658 7.118390 TCTCTTTTTCTTCGGCAGAATAGAAAG 59.882 37.037 16.21 16.21 41.42 2.62
653 659 6.710744 TCTTTTTCTTCGGCAGAATAGAAAGT 59.289 34.615 19.29 0.00 41.42 2.66
654 660 7.876068 TCTTTTTCTTCGGCAGAATAGAAAGTA 59.124 33.333 19.29 10.34 41.42 2.24
655 661 7.596749 TTTTCTTCGGCAGAATAGAAAGTAG 57.403 36.000 11.75 0.00 41.42 2.57
656 662 6.525578 TTCTTCGGCAGAATAGAAAGTAGA 57.474 37.500 0.00 0.00 36.51 2.59
657 663 5.892568 TCTTCGGCAGAATAGAAAGTAGAC 58.107 41.667 0.00 0.00 35.56 2.59
658 664 5.417894 TCTTCGGCAGAATAGAAAGTAGACA 59.582 40.000 0.00 0.00 35.56 3.41
659 665 4.995124 TCGGCAGAATAGAAAGTAGACAC 58.005 43.478 0.00 0.00 0.00 3.67
660 666 4.113354 CGGCAGAATAGAAAGTAGACACC 58.887 47.826 0.00 0.00 0.00 4.16
661 667 4.142138 CGGCAGAATAGAAAGTAGACACCT 60.142 45.833 0.00 0.00 0.00 4.00
662 668 5.624738 CGGCAGAATAGAAAGTAGACACCTT 60.625 44.000 0.00 0.00 0.00 3.50
663 669 6.174049 GGCAGAATAGAAAGTAGACACCTTT 58.826 40.000 0.00 0.00 34.93 3.11
664 670 6.092807 GGCAGAATAGAAAGTAGACACCTTTG 59.907 42.308 0.00 0.00 32.47 2.77
665 671 6.651225 GCAGAATAGAAAGTAGACACCTTTGT 59.349 38.462 0.00 0.00 39.32 2.83
680 686 7.027778 ACACCTTTGTCTGAAAAGAATGTAC 57.972 36.000 11.40 0.00 39.12 2.90
681 687 6.828785 ACACCTTTGTCTGAAAAGAATGTACT 59.171 34.615 11.40 0.00 39.12 2.73
682 688 7.012421 ACACCTTTGTCTGAAAAGAATGTACTC 59.988 37.037 11.40 0.00 39.12 2.59
683 689 6.486993 ACCTTTGTCTGAAAAGAATGTACTCC 59.513 38.462 11.40 0.00 39.12 3.85
684 690 6.072452 CCTTTGTCTGAAAAGAATGTACTCCC 60.072 42.308 11.40 0.00 39.12 4.30
685 691 5.825593 TGTCTGAAAAGAATGTACTCCCT 57.174 39.130 0.00 0.00 0.00 4.20
686 692 5.794894 TGTCTGAAAAGAATGTACTCCCTC 58.205 41.667 0.00 0.00 0.00 4.30
687 693 5.179533 GTCTGAAAAGAATGTACTCCCTCC 58.820 45.833 0.00 0.00 0.00 4.30
688 694 4.081642 TCTGAAAAGAATGTACTCCCTCCG 60.082 45.833 0.00 0.00 0.00 4.63
689 695 3.581332 TGAAAAGAATGTACTCCCTCCGT 59.419 43.478 0.00 0.00 0.00 4.69
690 696 4.041198 TGAAAAGAATGTACTCCCTCCGTT 59.959 41.667 0.00 0.00 0.00 4.44
691 697 4.635699 AAAGAATGTACTCCCTCCGTTT 57.364 40.909 0.00 0.00 0.00 3.60
692 698 4.635699 AAGAATGTACTCCCTCCGTTTT 57.364 40.909 0.00 0.00 0.00 2.43
693 699 4.635699 AGAATGTACTCCCTCCGTTTTT 57.364 40.909 0.00 0.00 0.00 1.94
694 700 5.750352 AGAATGTACTCCCTCCGTTTTTA 57.250 39.130 0.00 0.00 0.00 1.52
695 701 6.309389 AGAATGTACTCCCTCCGTTTTTAT 57.691 37.500 0.00 0.00 0.00 1.40
696 702 6.718294 AGAATGTACTCCCTCCGTTTTTATT 58.282 36.000 0.00 0.00 0.00 1.40
697 703 7.173032 AGAATGTACTCCCTCCGTTTTTATTT 58.827 34.615 0.00 0.00 0.00 1.40
698 704 8.323567 AGAATGTACTCCCTCCGTTTTTATTTA 58.676 33.333 0.00 0.00 0.00 1.40
699 705 7.854557 ATGTACTCCCTCCGTTTTTATTTAC 57.145 36.000 0.00 0.00 0.00 2.01
700 706 7.008021 TGTACTCCCTCCGTTTTTATTTACT 57.992 36.000 0.00 0.00 0.00 2.24
701 707 7.099120 TGTACTCCCTCCGTTTTTATTTACTC 58.901 38.462 0.00 0.00 0.00 2.59
702 708 5.494724 ACTCCCTCCGTTTTTATTTACTCC 58.505 41.667 0.00 0.00 0.00 3.85
703 709 4.506758 TCCCTCCGTTTTTATTTACTCCG 58.493 43.478 0.00 0.00 0.00 4.63
704 710 3.064408 CCCTCCGTTTTTATTTACTCCGC 59.936 47.826 0.00 0.00 0.00 5.54
705 711 3.685756 CCTCCGTTTTTATTTACTCCGCA 59.314 43.478 0.00 0.00 0.00 5.69
706 712 4.334481 CCTCCGTTTTTATTTACTCCGCAT 59.666 41.667 0.00 0.00 0.00 4.73
707 713 5.524646 CCTCCGTTTTTATTTACTCCGCATA 59.475 40.000 0.00 0.00 0.00 3.14
708 714 6.204108 CCTCCGTTTTTATTTACTCCGCATAT 59.796 38.462 0.00 0.00 0.00 1.78
709 715 7.385752 CCTCCGTTTTTATTTACTCCGCATATA 59.614 37.037 0.00 0.00 0.00 0.86
710 716 8.659925 TCCGTTTTTATTTACTCCGCATATAA 57.340 30.769 0.00 0.00 0.00 0.98
711 717 8.767085 TCCGTTTTTATTTACTCCGCATATAAG 58.233 33.333 0.00 0.00 0.00 1.73
712 718 7.532884 CCGTTTTTATTTACTCCGCATATAAGC 59.467 37.037 0.00 0.00 0.00 3.09
713 719 8.280497 CGTTTTTATTTACTCCGCATATAAGCT 58.720 33.333 0.00 0.00 0.00 3.74
714 720 9.946165 GTTTTTATTTACTCCGCATATAAGCTT 57.054 29.630 3.48 3.48 0.00 3.74
718 724 9.991906 TTATTTACTCCGCATATAAGCTTTAGT 57.008 29.630 3.20 2.01 0.00 2.24
719 725 7.941795 TTTACTCCGCATATAAGCTTTAGTC 57.058 36.000 3.20 0.00 0.00 2.59
720 726 5.531122 ACTCCGCATATAAGCTTTAGTCA 57.469 39.130 3.20 0.00 0.00 3.41
721 727 5.914033 ACTCCGCATATAAGCTTTAGTCAA 58.086 37.500 3.20 0.00 0.00 3.18
722 728 6.346096 ACTCCGCATATAAGCTTTAGTCAAA 58.654 36.000 3.20 0.00 0.00 2.69
723 729 6.480320 ACTCCGCATATAAGCTTTAGTCAAAG 59.520 38.462 3.20 0.00 43.46 2.77
724 730 6.346096 TCCGCATATAAGCTTTAGTCAAAGT 58.654 36.000 3.20 0.00 42.71 2.66
725 731 6.821665 TCCGCATATAAGCTTTAGTCAAAGTT 59.178 34.615 3.20 0.00 42.71 2.66
726 732 7.982919 TCCGCATATAAGCTTTAGTCAAAGTTA 59.017 33.333 3.20 0.00 42.71 2.24
727 733 8.609176 CCGCATATAAGCTTTAGTCAAAGTTAA 58.391 33.333 3.20 0.00 42.71 2.01
728 734 9.638300 CGCATATAAGCTTTAGTCAAAGTTAAG 57.362 33.333 3.20 0.00 42.71 1.85
981 994 2.122324 TCTCCGAAACCCCACCCA 60.122 61.111 0.00 0.00 0.00 4.51
1092 1111 2.902846 CGCGAGATCCTCCTCCGT 60.903 66.667 0.00 0.00 0.00 4.69
1173 1192 2.190841 CGCCACCGAACCCAAGTTT 61.191 57.895 0.00 0.00 35.94 2.66
1441 1463 1.228644 TCCCTCTTGTCGGTTCCGA 60.229 57.895 10.00 10.00 36.02 4.55
1530 1552 1.743252 CTGCCACTCGAGCCCTTTC 60.743 63.158 13.61 0.00 0.00 2.62
1560 1582 1.257750 TGGTGGACAGCTACGAGCAT 61.258 55.000 9.09 0.00 45.56 3.79
1719 1741 1.229428 TGCTTAAGATGCATAGCGGC 58.771 50.000 6.67 8.81 36.43 6.53
2466 2544 1.506262 CCCGTTCCCATTTTGAGCG 59.494 57.895 0.00 0.00 36.39 5.03
2487 2565 4.615912 GCGGCATACTTGAGTTTGATTTGT 60.616 41.667 5.88 0.00 0.00 2.83
2502 2580 8.033038 AGTTTGATTTGTATAGACAGACGCTAA 58.967 33.333 0.00 0.00 36.76 3.09
2524 2602 1.131638 GTGATCCATAGGCCACCTGA 58.868 55.000 5.01 0.00 34.61 3.86
2548 2626 3.991773 GCTTATTACGGTGACAGTGTTCA 59.008 43.478 0.00 0.00 0.00 3.18
2556 2634 3.614870 CGGTGACAGTGTTCAGATCATCA 60.615 47.826 0.00 0.00 0.00 3.07
2622 2703 4.660938 GCCCGTTTCCCTGCCACT 62.661 66.667 0.00 0.00 0.00 4.00
2669 2750 2.181975 AGGAAGGTCAATTGCAATGGG 58.818 47.619 13.82 8.84 0.00 4.00
2725 2806 1.271379 GCAGAAGCTACTTGGGTTGGA 60.271 52.381 0.00 0.00 37.91 3.53
2738 2819 5.535030 ACTTGGGTTGGAGTTTAAGATTGAC 59.465 40.000 0.00 0.00 0.00 3.18
2743 2824 5.461526 GTTGGAGTTTAAGATTGACAAGGC 58.538 41.667 0.00 0.00 0.00 4.35
2787 2868 3.628942 TGCTGAGGATGTTCATGCATTAC 59.371 43.478 0.00 0.00 31.21 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.539051 CCAGAGGATGTGAGGTCCAC 59.461 60.000 0.00 0.00 45.88 4.02
12 13 0.413434 TCCAGAGGATGTGAGGTCCA 59.587 55.000 0.00 0.00 38.25 4.02
13 14 1.118838 CTCCAGAGGATGTGAGGTCC 58.881 60.000 0.00 0.00 35.94 4.46
14 15 1.754226 GTCTCCAGAGGATGTGAGGTC 59.246 57.143 0.00 0.00 31.05 3.85
15 16 1.859302 GTCTCCAGAGGATGTGAGGT 58.141 55.000 0.00 0.00 31.05 3.85
16 17 0.743688 CGTCTCCAGAGGATGTGAGG 59.256 60.000 0.00 0.00 32.08 3.86
18 19 0.684479 CCCGTCTCCAGAGGATGTGA 60.684 60.000 0.00 0.00 32.08 3.58
20 21 2.060980 GCCCGTCTCCAGAGGATGT 61.061 63.158 0.00 0.00 32.08 3.06
21 22 2.025767 CTGCCCGTCTCCAGAGGATG 62.026 65.000 0.00 0.00 32.08 3.51
24 25 3.465403 CCTGCCCGTCTCCAGAGG 61.465 72.222 0.00 0.00 0.00 3.69
26 27 2.203788 AACCTGCCCGTCTCCAGA 60.204 61.111 0.00 0.00 0.00 3.86
27 28 2.046892 CAACCTGCCCGTCTCCAG 60.047 66.667 0.00 0.00 0.00 3.86
28 29 4.329545 GCAACCTGCCCGTCTCCA 62.330 66.667 0.00 0.00 37.42 3.86
37 38 2.435059 GAGGAGTCCGCAACCTGC 60.435 66.667 8.20 0.00 40.69 4.85
54 55 1.678627 CTGTGTCCTACTCATCCTCGG 59.321 57.143 0.00 0.00 0.00 4.63
65 66 4.013702 GACGCCTCCTGTGTCCTA 57.986 61.111 0.00 0.00 46.60 2.94
97 98 0.179073 GAGATGGACCGACCCACATG 60.179 60.000 0.00 0.00 39.34 3.21
98 99 1.338136 GGAGATGGACCGACCCACAT 61.338 60.000 0.00 0.00 39.34 3.21
110 111 2.442272 ACGGGAGTCGGGAGATGG 60.442 66.667 0.00 0.00 40.62 3.51
136 137 0.592637 TGCGGTCTACGTCGAGAAAA 59.407 50.000 0.00 0.00 46.52 2.29
139 140 2.393768 GGTGCGGTCTACGTCGAGA 61.394 63.158 0.00 0.00 46.52 4.04
144 145 1.177256 AGTGAAGGTGCGGTCTACGT 61.177 55.000 0.00 0.00 46.52 3.57
147 148 1.000506 GTGAAGTGAAGGTGCGGTCTA 59.999 52.381 0.00 0.00 0.00 2.59
154 155 2.918712 AGACCTGTGAAGTGAAGGTG 57.081 50.000 0.00 0.00 44.42 4.00
168 169 1.809567 AAACGACGGCGGTAAGACCT 61.810 55.000 18.49 0.00 43.17 3.85
190 192 0.179062 ATCCTCAATCTGCCGTCTGC 60.179 55.000 0.00 0.00 41.77 4.26
191 193 1.134580 ACATCCTCAATCTGCCGTCTG 60.135 52.381 0.00 0.00 0.00 3.51
196 198 2.134789 AACCACATCCTCAATCTGCC 57.865 50.000 0.00 0.00 0.00 4.85
203 205 2.159296 CGTGTCGATAACCACATCCTCA 60.159 50.000 4.96 0.00 0.00 3.86
207 209 2.572191 TCCGTGTCGATAACCACATC 57.428 50.000 4.96 0.00 0.00 3.06
209 211 3.695556 TCTATTCCGTGTCGATAACCACA 59.304 43.478 4.96 0.00 0.00 4.17
215 217 6.802608 ACTTCATTTCTATTCCGTGTCGATA 58.197 36.000 0.00 0.00 0.00 2.92
216 218 5.661458 ACTTCATTTCTATTCCGTGTCGAT 58.339 37.500 0.00 0.00 0.00 3.59
217 219 5.068234 ACTTCATTTCTATTCCGTGTCGA 57.932 39.130 0.00 0.00 0.00 4.20
224 226 5.220416 CGACGTCCAACTTCATTTCTATTCC 60.220 44.000 10.58 0.00 0.00 3.01
234 236 1.008194 CGTCCGACGTCCAACTTCA 60.008 57.895 12.91 0.00 36.74 3.02
256 258 0.462403 TAAACCTATCCAACGGCGGC 60.462 55.000 13.24 0.00 0.00 6.53
264 266 4.372953 AACCCTACCCTAAACCTATCCA 57.627 45.455 0.00 0.00 0.00 3.41
329 331 1.155889 ACGAGATTCATGCAAACGCA 58.844 45.000 0.00 0.00 45.23 5.24
331 333 2.421523 CGAACGAGATTCATGCAAACG 58.578 47.619 0.00 0.00 37.12 3.60
349 351 7.808672 ACACAACGATTTTTCATATAAACCGA 58.191 30.769 0.00 0.00 0.00 4.69
350 352 8.442605 AACACAACGATTTTTCATATAAACCG 57.557 30.769 0.00 0.00 0.00 4.44
352 354 9.511022 GCAAACACAACGATTTTTCATATAAAC 57.489 29.630 0.00 0.00 0.00 2.01
356 358 7.104326 GTGCAAACACAACGATTTTTCATAT 57.896 32.000 0.00 0.00 46.61 1.78
369 371 4.047822 GAATGGAATTCGTGCAAACACAA 58.952 39.130 0.00 0.00 44.37 3.33
370 372 3.637432 GAATGGAATTCGTGCAAACACA 58.363 40.909 0.00 0.00 44.37 3.72
416 419 2.884997 ATCCAACGCTGCCCGCATAA 62.885 55.000 0.00 0.00 41.76 1.90
442 445 2.202797 CGGACACGGATGCTGGAG 60.203 66.667 0.00 0.00 36.18 3.86
443 446 4.451150 GCGGACACGGATGCTGGA 62.451 66.667 0.00 0.00 41.36 3.86
481 486 0.463833 ATTTCCTTCCGCATCCGTCC 60.464 55.000 0.00 0.00 0.00 4.79
488 493 1.583986 CCGCAAATTTCCTTCCGCA 59.416 52.632 0.00 0.00 0.00 5.69
490 495 0.170339 GACCCGCAAATTTCCTTCCG 59.830 55.000 0.00 0.00 0.00 4.30
493 498 1.472480 CATCGACCCGCAAATTTCCTT 59.528 47.619 0.00 0.00 0.00 3.36
504 509 1.209275 GCATCTCGAACATCGACCCG 61.209 60.000 0.00 0.00 44.82 5.28
505 510 0.876342 GGCATCTCGAACATCGACCC 60.876 60.000 0.00 0.00 44.82 4.46
511 516 2.092968 TGGCTAAAGGCATCTCGAACAT 60.093 45.455 1.52 0.00 46.12 2.71
512 517 1.277842 TGGCTAAAGGCATCTCGAACA 59.722 47.619 1.52 0.00 46.12 3.18
525 530 1.975660 ACCTTGCTTCGTTGGCTAAA 58.024 45.000 0.00 0.00 0.00 1.85
562 567 5.163099 TGGAAAGGAGAGGAACAAGATTTCA 60.163 40.000 0.00 0.00 0.00 2.69
575 581 5.070001 TGTGTAAACCAATGGAAAGGAGAG 58.930 41.667 6.16 0.00 0.00 3.20
580 586 9.757227 TTAGAAAATGTGTAAACCAATGGAAAG 57.243 29.630 6.16 0.00 0.00 2.62
584 590 9.703892 TGATTTAGAAAATGTGTAAACCAATGG 57.296 29.630 0.00 0.00 28.46 3.16
595 601 9.247126 TGTGAAATGTGTGATTTAGAAAATGTG 57.753 29.630 0.00 0.00 0.00 3.21
599 605 9.474920 GGAATGTGAAATGTGTGATTTAGAAAA 57.525 29.630 0.00 0.00 0.00 2.29
601 607 8.408043 AGGAATGTGAAATGTGTGATTTAGAA 57.592 30.769 0.00 0.00 0.00 2.10
603 609 8.048534 AGAGGAATGTGAAATGTGTGATTTAG 57.951 34.615 0.00 0.00 0.00 1.85
604 610 7.884877 AGAGAGGAATGTGAAATGTGTGATTTA 59.115 33.333 0.00 0.00 0.00 1.40
605 611 6.718454 AGAGAGGAATGTGAAATGTGTGATTT 59.282 34.615 0.00 0.00 0.00 2.17
607 613 5.813383 AGAGAGGAATGTGAAATGTGTGAT 58.187 37.500 0.00 0.00 0.00 3.06
609 615 5.954296 AAGAGAGGAATGTGAAATGTGTG 57.046 39.130 0.00 0.00 0.00 3.82
610 616 6.966534 AAAAGAGAGGAATGTGAAATGTGT 57.033 33.333 0.00 0.00 0.00 3.72
611 617 7.655490 AGAAAAAGAGAGGAATGTGAAATGTG 58.345 34.615 0.00 0.00 0.00 3.21
612 618 7.830099 AGAAAAAGAGAGGAATGTGAAATGT 57.170 32.000 0.00 0.00 0.00 2.71
613 619 7.536622 CGAAGAAAAAGAGAGGAATGTGAAATG 59.463 37.037 0.00 0.00 0.00 2.32
614 620 7.308830 CCGAAGAAAAAGAGAGGAATGTGAAAT 60.309 37.037 0.00 0.00 0.00 2.17
615 621 6.017109 CCGAAGAAAAAGAGAGGAATGTGAAA 60.017 38.462 0.00 0.00 0.00 2.69
616 622 5.470098 CCGAAGAAAAAGAGAGGAATGTGAA 59.530 40.000 0.00 0.00 0.00 3.18
617 623 4.997395 CCGAAGAAAAAGAGAGGAATGTGA 59.003 41.667 0.00 0.00 0.00 3.58
618 624 4.378874 GCCGAAGAAAAAGAGAGGAATGTG 60.379 45.833 0.00 0.00 0.00 3.21
619 625 3.753797 GCCGAAGAAAAAGAGAGGAATGT 59.246 43.478 0.00 0.00 0.00 2.71
620 626 3.753272 TGCCGAAGAAAAAGAGAGGAATG 59.247 43.478 0.00 0.00 0.00 2.67
622 628 3.071023 TCTGCCGAAGAAAAAGAGAGGAA 59.929 43.478 0.00 0.00 29.54 3.36
623 629 2.632996 TCTGCCGAAGAAAAAGAGAGGA 59.367 45.455 0.00 0.00 29.54 3.71
624 630 3.045601 TCTGCCGAAGAAAAAGAGAGG 57.954 47.619 0.00 0.00 29.54 3.69
634 640 5.417894 TGTCTACTTTCTATTCTGCCGAAGA 59.582 40.000 0.00 0.00 31.60 2.87
635 641 5.517054 GTGTCTACTTTCTATTCTGCCGAAG 59.483 44.000 0.00 0.00 31.60 3.79
636 642 5.408356 GTGTCTACTTTCTATTCTGCCGAA 58.592 41.667 0.00 0.00 0.00 4.30
637 643 4.142227 GGTGTCTACTTTCTATTCTGCCGA 60.142 45.833 0.00 0.00 0.00 5.54
638 644 4.113354 GGTGTCTACTTTCTATTCTGCCG 58.887 47.826 0.00 0.00 0.00 5.69
639 645 5.346181 AGGTGTCTACTTTCTATTCTGCC 57.654 43.478 0.00 0.00 0.00 4.85
640 646 6.651225 ACAAAGGTGTCTACTTTCTATTCTGC 59.349 38.462 0.00 0.00 36.09 4.26
656 662 6.828785 AGTACATTCTTTTCAGACAAAGGTGT 59.171 34.615 0.00 14.05 42.10 4.16
657 663 7.264373 AGTACATTCTTTTCAGACAAAGGTG 57.736 36.000 0.00 0.00 34.90 4.00
658 664 6.486993 GGAGTACATTCTTTTCAGACAAAGGT 59.513 38.462 0.00 0.00 34.90 3.50
659 665 6.072452 GGGAGTACATTCTTTTCAGACAAAGG 60.072 42.308 0.00 0.00 34.90 3.11
660 666 6.712547 AGGGAGTACATTCTTTTCAGACAAAG 59.287 38.462 0.00 0.00 35.39 2.77
661 667 6.601332 AGGGAGTACATTCTTTTCAGACAAA 58.399 36.000 0.00 0.00 0.00 2.83
662 668 6.187727 AGGGAGTACATTCTTTTCAGACAA 57.812 37.500 0.00 0.00 0.00 3.18
663 669 5.280011 GGAGGGAGTACATTCTTTTCAGACA 60.280 44.000 0.00 0.00 0.00 3.41
664 670 5.179533 GGAGGGAGTACATTCTTTTCAGAC 58.820 45.833 0.00 0.00 0.00 3.51
665 671 4.081642 CGGAGGGAGTACATTCTTTTCAGA 60.082 45.833 0.00 0.00 0.00 3.27
666 672 4.184629 CGGAGGGAGTACATTCTTTTCAG 58.815 47.826 0.00 0.00 0.00 3.02
667 673 3.581332 ACGGAGGGAGTACATTCTTTTCA 59.419 43.478 0.00 0.00 0.00 2.69
668 674 4.203654 ACGGAGGGAGTACATTCTTTTC 57.796 45.455 0.00 0.00 0.00 2.29
669 675 4.635699 AACGGAGGGAGTACATTCTTTT 57.364 40.909 0.00 0.00 0.00 2.27
670 676 4.635699 AAACGGAGGGAGTACATTCTTT 57.364 40.909 0.00 0.00 0.00 2.52
671 677 4.635699 AAAACGGAGGGAGTACATTCTT 57.364 40.909 0.00 0.00 0.00 2.52
672 678 4.635699 AAAAACGGAGGGAGTACATTCT 57.364 40.909 0.00 0.00 0.00 2.40
673 679 6.997239 AATAAAAACGGAGGGAGTACATTC 57.003 37.500 0.00 0.00 0.00 2.67
674 680 8.105197 AGTAAATAAAAACGGAGGGAGTACATT 58.895 33.333 0.00 0.00 0.00 2.71
675 681 7.627311 AGTAAATAAAAACGGAGGGAGTACAT 58.373 34.615 0.00 0.00 0.00 2.29
676 682 7.008021 AGTAAATAAAAACGGAGGGAGTACA 57.992 36.000 0.00 0.00 0.00 2.90
677 683 6.536582 GGAGTAAATAAAAACGGAGGGAGTAC 59.463 42.308 0.00 0.00 0.00 2.73
678 684 6.627953 CGGAGTAAATAAAAACGGAGGGAGTA 60.628 42.308 0.00 0.00 0.00 2.59
679 685 5.494724 GGAGTAAATAAAAACGGAGGGAGT 58.505 41.667 0.00 0.00 0.00 3.85
680 686 4.569564 CGGAGTAAATAAAAACGGAGGGAG 59.430 45.833 0.00 0.00 0.00 4.30
681 687 4.506758 CGGAGTAAATAAAAACGGAGGGA 58.493 43.478 0.00 0.00 0.00 4.20
682 688 3.064408 GCGGAGTAAATAAAAACGGAGGG 59.936 47.826 0.00 0.00 0.00 4.30
683 689 3.685756 TGCGGAGTAAATAAAAACGGAGG 59.314 43.478 0.00 0.00 0.00 4.30
684 690 4.932268 TGCGGAGTAAATAAAAACGGAG 57.068 40.909 0.00 0.00 0.00 4.63
685 691 8.659925 TTATATGCGGAGTAAATAAAAACGGA 57.340 30.769 0.00 0.00 0.00 4.69
686 692 7.532884 GCTTATATGCGGAGTAAATAAAAACGG 59.467 37.037 0.00 0.00 0.00 4.44
687 693 8.280497 AGCTTATATGCGGAGTAAATAAAAACG 58.720 33.333 5.07 0.00 38.13 3.60
688 694 9.946165 AAGCTTATATGCGGAGTAAATAAAAAC 57.054 29.630 0.00 0.00 38.13 2.43
692 698 9.991906 ACTAAAGCTTATATGCGGAGTAAATAA 57.008 29.630 0.00 0.00 38.13 1.40
693 699 9.635520 GACTAAAGCTTATATGCGGAGTAAATA 57.364 33.333 0.00 0.00 38.13 1.40
694 700 8.148351 TGACTAAAGCTTATATGCGGAGTAAAT 58.852 33.333 0.00 0.00 38.13 1.40
695 701 7.494211 TGACTAAAGCTTATATGCGGAGTAAA 58.506 34.615 0.00 5.14 38.13 2.01
696 702 7.046292 TGACTAAAGCTTATATGCGGAGTAA 57.954 36.000 0.00 5.75 38.13 2.24
697 703 6.644248 TGACTAAAGCTTATATGCGGAGTA 57.356 37.500 0.00 0.00 38.13 2.59
698 704 5.531122 TGACTAAAGCTTATATGCGGAGT 57.469 39.130 0.00 11.98 38.13 3.85
699 705 6.480320 ACTTTGACTAAAGCTTATATGCGGAG 59.520 38.462 0.00 6.47 45.72 4.63
700 706 6.346096 ACTTTGACTAAAGCTTATATGCGGA 58.654 36.000 0.00 0.00 45.72 5.54
701 707 6.604735 ACTTTGACTAAAGCTTATATGCGG 57.395 37.500 0.00 1.14 45.72 5.69
702 708 9.638300 CTTAACTTTGACTAAAGCTTATATGCG 57.362 33.333 0.00 0.00 45.72 4.73
864 870 6.566753 GCCTGCTGAAGTCAAACTTACTAAAG 60.567 42.308 0.00 0.00 38.80 1.85
865 871 5.238650 GCCTGCTGAAGTCAAACTTACTAAA 59.761 40.000 0.00 0.00 38.80 1.85
866 872 4.755123 GCCTGCTGAAGTCAAACTTACTAA 59.245 41.667 0.00 0.00 38.80 2.24
867 873 4.040461 AGCCTGCTGAAGTCAAACTTACTA 59.960 41.667 0.00 0.00 38.80 1.82
868 874 3.142174 GCCTGCTGAAGTCAAACTTACT 58.858 45.455 0.00 0.00 38.80 2.24
869 875 3.142174 AGCCTGCTGAAGTCAAACTTAC 58.858 45.455 0.00 0.00 38.80 2.34
870 876 3.181455 TGAGCCTGCTGAAGTCAAACTTA 60.181 43.478 0.00 0.00 38.80 2.24
871 877 2.225467 GAGCCTGCTGAAGTCAAACTT 58.775 47.619 0.00 0.00 41.95 2.66
872 878 1.141657 TGAGCCTGCTGAAGTCAAACT 59.858 47.619 0.00 0.00 0.00 2.66
873 879 1.597742 TGAGCCTGCTGAAGTCAAAC 58.402 50.000 0.00 0.00 0.00 2.93
874 880 2.574006 ATGAGCCTGCTGAAGTCAAA 57.426 45.000 0.00 0.00 0.00 2.69
875 881 2.679059 GCTATGAGCCTGCTGAAGTCAA 60.679 50.000 0.00 0.00 34.48 3.18
876 882 1.134580 GCTATGAGCCTGCTGAAGTCA 60.135 52.381 0.00 0.00 34.48 3.41
877 883 1.138661 AGCTATGAGCCTGCTGAAGTC 59.861 52.381 0.00 0.00 43.77 3.01
878 884 1.202330 AGCTATGAGCCTGCTGAAGT 58.798 50.000 0.00 0.00 43.77 3.01
917 923 8.856490 AGTGTGAAATGTGTGATTTAGAAAAC 57.144 30.769 0.00 0.00 0.00 2.43
1148 1167 1.964373 GGTTCGGTGGCGATGTGTT 60.964 57.895 0.00 0.00 0.00 3.32
1164 1183 2.032071 CGGCGGAGAAACTTGGGT 59.968 61.111 0.00 0.00 0.00 4.51
1357 1379 2.164865 CTGTTGAGGAGGAGCACGCT 62.165 60.000 0.00 0.00 0.00 5.07
1441 1463 2.254546 TGCATGTCTTCAAACTCCGT 57.745 45.000 0.00 0.00 0.00 4.69
1530 1552 0.462937 TGTCCACCACGACCACTTTG 60.463 55.000 0.00 0.00 31.35 2.77
1560 1582 0.464036 AGGCGACGGCTTCATTATCA 59.536 50.000 19.41 0.00 39.81 2.15
1719 1741 4.005650 CGACCCATTCCCATCTTGATATG 58.994 47.826 0.00 0.00 0.00 1.78
1720 1742 3.909995 TCGACCCATTCCCATCTTGATAT 59.090 43.478 0.00 0.00 0.00 1.63
1721 1743 3.071023 GTCGACCCATTCCCATCTTGATA 59.929 47.826 3.51 0.00 0.00 2.15
2382 2460 1.904771 GATGGGTCACATGGGTCGA 59.095 57.895 0.00 0.00 40.72 4.20
2466 2544 9.109393 TCTATACAAATCAAACTCAAGTATGCC 57.891 33.333 0.00 0.00 0.00 4.40
2467 2545 9.922305 GTCTATACAAATCAAACTCAAGTATGC 57.078 33.333 0.00 0.00 0.00 3.14
2487 2565 5.238868 GGATCACAGTTAGCGTCTGTCTATA 59.761 44.000 8.13 0.00 43.14 1.31
2502 2580 0.839946 GGTGGCCTATGGATCACAGT 59.160 55.000 3.32 0.00 32.80 3.55
2524 2602 4.202245 ACACTGTCACCGTAATAAGCAT 57.798 40.909 0.00 0.00 0.00 3.79
2556 2634 1.204146 ACACCGCCATCATCTACCTT 58.796 50.000 0.00 0.00 0.00 3.50
2619 2700 1.071071 TCGGAAACAGGGTTGGTAGTG 59.929 52.381 0.00 0.00 0.00 2.74
2622 2703 2.106857 ACATTCGGAAACAGGGTTGGTA 59.893 45.455 0.00 0.00 0.00 3.25
2669 2750 1.227118 CAACACCCAAACGGCAACC 60.227 57.895 0.00 0.00 33.26 3.77
2725 2806 4.003648 CCTCGCCTTGTCAATCTTAAACT 58.996 43.478 0.00 0.00 0.00 2.66
2738 2819 0.597637 CTATACGTGCCCTCGCCTTG 60.598 60.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.