Multiple sequence alignment - TraesCS2D01G084400

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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 TraesCS2D01G084400 chr2D 100.000 3170 0 0 1 3170 36575593 36578762 0.000000e+00 5854.0
1 TraesCS2D01G084400 chr2D 89.028 319 32 3 1411 1729 3751523 3751208 2.960000e-105 392.0
2 TraesCS2D01G084400 chr2D 86.692 263 22 10 2917 3170 470959002 470959260 2.410000e-71 279.0
3 TraesCS2D01G084400 chr2D 77.778 306 28 22 1029 1308 3752307 3752016 5.480000e-33 152.0
4 TraesCS2D01G084400 chr2D 97.368 38 1 0 1336 1373 3751556 3751519 7.340000e-07 65.8
5 TraesCS2D01G084400 chr2A 91.511 2297 107 29 636 2903 40554548 40556785 0.000000e+00 3081.0
6 TraesCS2D01G084400 chr2A 84.000 600 33 21 56 626 40553681 40554246 4.690000e-143 518.0
7 TraesCS2D01G084400 chr2B 87.858 2059 112 61 635 2630 62983546 62985529 0.000000e+00 2290.0
8 TraesCS2D01G084400 chr2B 88.300 641 48 14 1 623 62978404 62979035 0.000000e+00 743.0
9 TraesCS2D01G084400 chr2B 86.871 457 55 4 1345 1800 62976438 62976890 1.010000e-139 507.0
10 TraesCS2D01G084400 chr7A 90.037 271 15 2 2910 3170 732859751 732860019 1.090000e-89 340.0
11 TraesCS2D01G084400 chr7A 88.603 272 17 5 2910 3170 732858792 732858524 5.100000e-83 318.0
12 TraesCS2D01G084400 chr7A 95.745 47 2 0 1305 1351 524214564 524214518 3.390000e-10 76.8
13 TraesCS2D01G084400 chr1A 88.031 259 19 7 2914 3170 6496338 6496090 2.390000e-76 296.0
14 TraesCS2D01G084400 chr7D 89.121 239 20 5 2938 3170 598745657 598745895 3.090000e-75 292.0
15 TraesCS2D01G084400 chr7D 86.585 246 24 7 2928 3170 156824228 156824467 2.420000e-66 263.0
16 TraesCS2D01G084400 chr7B 87.452 263 22 7 2909 3170 544472140 544471888 3.090000e-75 292.0
17 TraesCS2D01G084400 chr7B 93.617 47 3 0 1305 1351 256489385 256489339 1.580000e-08 71.3
18 TraesCS2D01G084400 chr5D 87.448 239 24 5 2938 3170 446077679 446077441 1.450000e-68 270.0
19 TraesCS2D01G084400 chrUn 89.862 217 10 6 2964 3170 424042276 424042062 5.210000e-68 268.0
20 TraesCS2D01G084400 chr5A 91.566 166 14 0 1881 2046 568595291 568595456 2.460000e-56 230.0
21 TraesCS2D01G084400 chr1B 88.816 152 16 1 1895 2046 82080245 82080395 5.400000e-43 185.0
22 TraesCS2D01G084400 chr1B 91.489 47 4 0 1305 1351 540133938 540133892 7.340000e-07 65.8
23 TraesCS2D01G084400 chr4D 97.368 76 2 0 1971 2046 456510518 456510593 2.570000e-26 130.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G084400 chr2D 36575593 36578762 3169 False 5854.000000 5854 100.0000 1 3170 1 chr2D.!!$F1 3169
1 TraesCS2D01G084400 chr2D 3751208 3752307 1099 True 203.266667 392 88.0580 1029 1729 3 chr2D.!!$R1 700
2 TraesCS2D01G084400 chr2A 40553681 40556785 3104 False 1799.500000 3081 87.7555 56 2903 2 chr2A.!!$F1 2847
3 TraesCS2D01G084400 chr2B 62983546 62985529 1983 False 2290.000000 2290 87.8580 635 2630 1 chr2B.!!$F1 1995
4 TraesCS2D01G084400 chr2B 62976438 62979035 2597 False 625.000000 743 87.5855 1 1800 2 chr2B.!!$F2 1799

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
507 530 0.109342 CCCACTCATGATGCCCCTAC 59.891 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2381 3385 0.108138 GTTCTCGTCCCAGGGTGATG 60.108 60.0 5.01 0.0 0.0 3.07 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
27 28 3.094386 TGCCAACAGACAACTGGTC 57.906 52.632 0.00 0.00 42.75 4.02
34 35 2.426023 GACAACTGGTCCCTGCGT 59.574 61.111 0.00 0.00 40.83 5.24
35 36 1.227853 GACAACTGGTCCCTGCGTT 60.228 57.895 0.00 0.00 40.83 4.84
36 37 1.507141 GACAACTGGTCCCTGCGTTG 61.507 60.000 0.00 0.00 40.83 4.10
37 38 2.113139 AACTGGTCCCTGCGTTGG 59.887 61.111 0.00 0.00 0.00 3.77
41 42 4.660938 GGTCCCTGCGTTGGGCTT 62.661 66.667 9.57 0.00 46.67 4.35
42 43 3.056328 GTCCCTGCGTTGGGCTTC 61.056 66.667 9.57 1.02 46.67 3.86
43 44 3.249189 TCCCTGCGTTGGGCTTCT 61.249 61.111 9.57 0.00 46.67 2.85
44 45 2.747855 CCCTGCGTTGGGCTTCTC 60.748 66.667 2.06 0.00 44.05 2.87
45 46 2.032528 CCTGCGTTGGGCTTCTCA 59.967 61.111 0.00 0.00 44.05 3.27
46 47 1.600636 CCTGCGTTGGGCTTCTCAA 60.601 57.895 0.00 0.00 44.05 3.02
47 48 1.172180 CCTGCGTTGGGCTTCTCAAA 61.172 55.000 0.00 0.00 44.05 2.69
48 49 0.883833 CTGCGTTGGGCTTCTCAAAT 59.116 50.000 0.00 0.00 44.05 2.32
49 50 2.083774 CTGCGTTGGGCTTCTCAAATA 58.916 47.619 0.00 0.00 44.05 1.40
50 51 1.810151 TGCGTTGGGCTTCTCAAATAC 59.190 47.619 0.00 0.00 44.05 1.89
51 52 2.084546 GCGTTGGGCTTCTCAAATACT 58.915 47.619 0.00 0.00 39.11 2.12
52 53 3.267483 GCGTTGGGCTTCTCAAATACTA 58.733 45.455 0.00 0.00 39.11 1.82
53 54 3.687698 GCGTTGGGCTTCTCAAATACTAA 59.312 43.478 0.00 0.00 39.11 2.24
54 55 4.201822 GCGTTGGGCTTCTCAAATACTAAG 60.202 45.833 0.00 0.00 39.11 2.18
55 56 4.935808 CGTTGGGCTTCTCAAATACTAAGT 59.064 41.667 0.00 0.00 0.00 2.24
56 57 5.411669 CGTTGGGCTTCTCAAATACTAAGTT 59.588 40.000 0.00 0.00 0.00 2.66
57 58 6.072673 CGTTGGGCTTCTCAAATACTAAGTTT 60.073 38.462 0.00 0.00 0.00 2.66
58 59 7.306213 GTTGGGCTTCTCAAATACTAAGTTTC 58.694 38.462 0.00 0.00 0.00 2.78
59 60 6.779860 TGGGCTTCTCAAATACTAAGTTTCT 58.220 36.000 0.00 0.00 0.00 2.52
60 61 6.879458 TGGGCTTCTCAAATACTAAGTTTCTC 59.121 38.462 0.00 0.00 0.00 2.87
61 62 7.106890 GGGCTTCTCAAATACTAAGTTTCTCT 58.893 38.462 0.00 0.00 0.00 3.10
62 63 7.065204 GGGCTTCTCAAATACTAAGTTTCTCTG 59.935 40.741 0.00 0.00 0.00 3.35
63 64 7.819900 GGCTTCTCAAATACTAAGTTTCTCTGA 59.180 37.037 0.00 0.00 0.00 3.27
64 65 9.377312 GCTTCTCAAATACTAAGTTTCTCTGAT 57.623 33.333 0.00 0.00 0.00 2.90
79 80 7.343057 AGTTTCTCTGATTGAAAAGGAGGTTTT 59.657 33.333 0.00 0.00 41.29 2.43
122 127 2.238847 GACCGATAGCTGTGGCCACA 62.239 60.000 35.49 35.49 39.73 4.17
149 155 2.629137 TGACGTCCCAGTTAAACTAGCA 59.371 45.455 14.12 0.00 0.00 3.49
157 163 4.390909 CCCAGTTAAACTAGCACTTTACCG 59.609 45.833 0.00 0.00 0.00 4.02
159 165 3.999001 AGTTAAACTAGCACTTTACCGCC 59.001 43.478 0.00 0.00 0.00 6.13
160 166 1.435577 AAACTAGCACTTTACCGCCG 58.564 50.000 0.00 0.00 0.00 6.46
161 167 0.390735 AACTAGCACTTTACCGCCGG 60.391 55.000 0.00 0.00 0.00 6.13
169 181 2.030628 CACTTTACCGCCGGACAAAAAT 60.031 45.455 11.71 0.00 0.00 1.82
171 183 1.606903 TTACCGCCGGACAAAAATGT 58.393 45.000 11.71 0.00 0.00 2.71
173 185 0.312729 ACCGCCGGACAAAAATGTTC 59.687 50.000 11.71 0.00 0.00 3.18
176 188 2.226912 CCGCCGGACAAAAATGTTCTTA 59.773 45.455 5.05 0.00 0.00 2.10
180 192 5.404066 CGCCGGACAAAAATGTTCTTAAATT 59.596 36.000 5.05 0.00 0.00 1.82
183 195 8.218441 GCCGGACAAAAATGTTCTTAAATTAAC 58.782 33.333 5.05 0.00 0.00 2.01
185 197 9.250624 CGGACAAAAATGTTCTTAAATTAACCA 57.749 29.630 0.00 0.00 0.00 3.67
188 200 9.606631 ACAAAAATGTTCTTAAATTAACCAGCA 57.393 25.926 0.00 0.00 0.00 4.41
189 201 9.862585 CAAAAATGTTCTTAAATTAACCAGCAC 57.137 29.630 0.00 0.00 0.00 4.40
190 202 8.601845 AAAATGTTCTTAAATTAACCAGCACC 57.398 30.769 0.00 0.00 0.00 5.01
191 203 5.365403 TGTTCTTAAATTAACCAGCACCG 57.635 39.130 0.00 0.00 0.00 4.94
192 204 4.822896 TGTTCTTAAATTAACCAGCACCGT 59.177 37.500 0.00 0.00 0.00 4.83
193 205 5.299782 TGTTCTTAAATTAACCAGCACCGTT 59.700 36.000 0.00 0.00 0.00 4.44
194 206 6.183360 TGTTCTTAAATTAACCAGCACCGTTT 60.183 34.615 0.00 0.00 0.00 3.60
195 207 6.394025 TCTTAAATTAACCAGCACCGTTTT 57.606 33.333 0.00 0.00 0.00 2.43
196 208 7.507733 TCTTAAATTAACCAGCACCGTTTTA 57.492 32.000 0.00 0.00 0.00 1.52
197 209 7.938715 TCTTAAATTAACCAGCACCGTTTTAA 58.061 30.769 0.00 0.00 0.00 1.52
198 210 8.578151 TCTTAAATTAACCAGCACCGTTTTAAT 58.422 29.630 0.00 0.00 0.00 1.40
199 211 9.198837 CTTAAATTAACCAGCACCGTTTTAATT 57.801 29.630 0.00 0.00 35.05 1.40
400 423 2.944557 CGACACGTCGCCGATCTG 60.945 66.667 6.65 0.00 46.50 2.90
401 424 2.483745 GACACGTCGCCGATCTGA 59.516 61.111 0.00 0.00 37.88 3.27
402 425 1.868251 GACACGTCGCCGATCTGAC 60.868 63.158 0.00 0.00 37.88 3.51
403 426 2.579787 CACGTCGCCGATCTGACC 60.580 66.667 0.00 0.00 37.88 4.02
404 427 3.823330 ACGTCGCCGATCTGACCC 61.823 66.667 0.00 0.00 37.88 4.46
405 428 4.907034 CGTCGCCGATCTGACCCG 62.907 72.222 0.00 0.00 35.63 5.28
411 434 3.900892 CGATCTGACCCGGACCCG 61.901 72.222 0.73 0.66 39.44 5.28
425 448 1.982073 GACCCGGATCGCTTTGCTTG 61.982 60.000 0.73 0.00 0.00 4.01
440 463 3.498774 TGCTTGCCTCTCTTCTTTTCT 57.501 42.857 0.00 0.00 0.00 2.52
446 469 4.168101 TGCCTCTCTTCTTTTCTTCCCTA 58.832 43.478 0.00 0.00 0.00 3.53
455 478 8.214721 TCTTCTTTTCTTCCCTACCTTAATCA 57.785 34.615 0.00 0.00 0.00 2.57
467 490 1.341531 CCTTAATCATCGAGCGGTCCT 59.658 52.381 9.39 0.00 0.00 3.85
486 509 3.371063 GTCGAGGTCGGCCACTCA 61.371 66.667 9.71 0.00 38.15 3.41
487 510 3.062466 TCGAGGTCGGCCACTCAG 61.062 66.667 9.71 10.53 40.29 3.35
506 529 1.708993 GCCCACTCATGATGCCCCTA 61.709 60.000 0.00 0.00 0.00 3.53
507 530 0.109342 CCCACTCATGATGCCCCTAC 59.891 60.000 0.00 0.00 0.00 3.18
519 542 1.722636 GCCCCTACGTACTCCACTCG 61.723 65.000 0.00 0.00 0.00 4.18
531 561 2.445274 CCACTCGTGGTTGATCGTG 58.555 57.895 7.93 0.00 45.53 4.35
551 581 4.267349 TGTCAAAACACTAGCTAGGGTC 57.733 45.455 28.43 15.96 39.47 4.46
554 584 3.003480 CAAAACACTAGCTAGGGTCTGC 58.997 50.000 28.43 0.00 39.47 4.26
564 594 0.902984 TAGGGTCTGCGAGGAAAGCA 60.903 55.000 0.00 0.00 42.99 3.91
565 595 1.302511 GGGTCTGCGAGGAAAGCAA 60.303 57.895 0.00 0.00 44.67 3.91
566 596 0.678048 GGGTCTGCGAGGAAAGCAAT 60.678 55.000 0.00 0.00 44.67 3.56
626 656 1.299468 GAGATCGTGTGGCTAGGCG 60.299 63.158 12.19 0.00 0.00 5.52
627 657 2.005960 GAGATCGTGTGGCTAGGCGT 62.006 60.000 12.19 0.00 0.00 5.68
629 659 2.005960 GATCGTGTGGCTAGGCGTCT 62.006 60.000 12.19 0.00 0.00 4.18
630 660 2.284798 ATCGTGTGGCTAGGCGTCTG 62.285 60.000 12.19 2.04 0.00 3.51
631 661 2.657237 GTGTGGCTAGGCGTCTGT 59.343 61.111 12.19 0.00 0.00 3.41
632 662 1.888018 GTGTGGCTAGGCGTCTGTA 59.112 57.895 12.19 0.00 0.00 2.74
633 663 0.458025 GTGTGGCTAGGCGTCTGTAC 60.458 60.000 12.19 3.55 0.00 2.90
700 1022 0.800683 TAATTGCGGCGTCGAGTCAG 60.801 55.000 16.53 0.00 39.00 3.51
771 1093 7.122948 GTCTCCATCCTTCTTTGACTAGACTAA 59.877 40.741 0.00 0.00 0.00 2.24
834 1156 2.361992 TGTCCGGCCGAGCTCTAA 60.362 61.111 30.73 1.09 0.00 2.10
983 1342 2.496899 TGCAGGCTAGGAAAGAAAGG 57.503 50.000 0.00 0.00 0.00 3.11
1083 1454 2.353958 CTGCAGCTCCACCACCAT 59.646 61.111 0.00 0.00 0.00 3.55
1839 2673 1.153549 GATCGAGGCGCTGAAAGGT 60.154 57.895 7.64 0.00 0.00 3.50
1956 2790 0.531200 CGGAGCCGGAGACTAAAACT 59.469 55.000 5.05 0.00 35.56 2.66
2189 3161 9.624697 CCGATAAGACTGTAGTAGTAGTAGTAG 57.375 40.741 0.00 0.00 40.53 2.57
2227 3199 6.762108 AGTTTAATTAACACGCGAGAAGATG 58.238 36.000 15.93 0.68 39.30 2.90
2266 3241 5.652891 GGATGATCACCCTACGTGTAGATAT 59.347 44.000 0.00 0.00 43.51 1.63
2267 3242 6.827251 GGATGATCACCCTACGTGTAGATATA 59.173 42.308 0.00 0.00 43.51 0.86
2324 3320 4.457496 CGATCAGGCTGCCGGTGT 62.457 66.667 18.24 8.74 0.00 4.16
2333 3329 0.882927 GCTGCCGGTGTCTGTAACAA 60.883 55.000 1.90 0.00 40.31 2.83
2374 3378 3.502211 GCTAATAATCATCACCCGGTTGG 59.498 47.826 0.00 0.00 41.37 3.77
2396 3400 0.838554 TTTCCATCACCCTGGGACGA 60.839 55.000 22.23 15.70 36.89 4.20
2400 3404 0.108138 CATCACCCTGGGACGAGAAC 60.108 60.000 22.23 0.00 0.00 3.01
2401 3405 1.605058 ATCACCCTGGGACGAGAACG 61.605 60.000 22.23 0.00 45.75 3.95
2402 3406 2.116772 ACCCTGGGACGAGAACGA 59.883 61.111 22.23 0.00 42.66 3.85
2403 3407 1.305046 ACCCTGGGACGAGAACGAT 60.305 57.895 22.23 0.00 42.66 3.73
2432 4036 4.326826 TCAGTTAAAAGGGCAGAGATGTG 58.673 43.478 0.00 0.00 0.00 3.21
2458 4062 3.422655 CATGTGTGATCTTGCGTTCATG 58.577 45.455 0.00 0.00 0.00 3.07
2459 4063 1.805943 TGTGTGATCTTGCGTTCATGG 59.194 47.619 0.00 0.00 0.00 3.66
2480 4084 3.896272 GGGTATACTCTCGGAGTTGGAAT 59.104 47.826 11.09 3.11 40.28 3.01
2482 4086 4.583489 GGTATACTCTCGGAGTTGGAATGA 59.417 45.833 11.09 0.00 40.28 2.57
2483 4087 5.068723 GGTATACTCTCGGAGTTGGAATGAA 59.931 44.000 11.09 0.00 40.28 2.57
2484 4088 3.601443 ACTCTCGGAGTTGGAATGAAG 57.399 47.619 4.69 0.00 40.28 3.02
2485 4089 2.275318 CTCTCGGAGTTGGAATGAAGC 58.725 52.381 4.69 0.00 0.00 3.86
2486 4090 1.623311 TCTCGGAGTTGGAATGAAGCA 59.377 47.619 4.69 0.00 0.00 3.91
2487 4091 1.734465 CTCGGAGTTGGAATGAAGCAC 59.266 52.381 0.00 0.00 0.00 4.40
2488 4092 1.071542 TCGGAGTTGGAATGAAGCACA 59.928 47.619 0.00 0.00 0.00 4.57
2489 4093 1.197721 CGGAGTTGGAATGAAGCACAC 59.802 52.381 0.00 0.00 0.00 3.82
2490 4094 1.197721 GGAGTTGGAATGAAGCACACG 59.802 52.381 0.00 0.00 0.00 4.49
2491 4095 1.873591 GAGTTGGAATGAAGCACACGT 59.126 47.619 0.00 0.00 0.00 4.49
2492 4096 1.603802 AGTTGGAATGAAGCACACGTG 59.396 47.619 15.48 15.48 0.00 4.49
2536 4546 4.709397 AGTTTGTGATTCCACTCCAAAACA 59.291 37.500 0.00 0.00 43.55 2.83
2540 4550 4.041723 GTGATTCCACTCCAAAACAAACG 58.958 43.478 0.00 0.00 40.10 3.60
2646 4656 1.689813 TGTTAGTTCGAGGGTGCAGAA 59.310 47.619 0.00 0.00 0.00 3.02
2647 4657 2.288825 TGTTAGTTCGAGGGTGCAGAAG 60.289 50.000 0.00 0.00 0.00 2.85
2648 4658 0.246635 TAGTTCGAGGGTGCAGAAGC 59.753 55.000 0.00 0.00 42.57 3.86
2674 4684 0.035739 GGGCCGTGTAAACCAGAAGA 59.964 55.000 0.00 0.00 0.00 2.87
2747 4757 7.254727 GCTCATTGCCACTTTGATTTAAACAAA 60.255 33.333 12.34 12.34 34.60 2.83
2748 4758 8.498054 TCATTGCCACTTTGATTTAAACAAAA 57.502 26.923 13.32 7.00 36.91 2.44
2749 4759 8.950210 TCATTGCCACTTTGATTTAAACAAAAA 58.050 25.926 13.32 7.80 36.91 1.94
2766 4776 3.540314 AAAAACAGCTCAATGCCACAA 57.460 38.095 0.00 0.00 44.23 3.33
2872 4885 2.570302 TGCCAACTAGAAGACTAACCCC 59.430 50.000 0.00 0.00 0.00 4.95
2887 4900 0.179018 ACCCCAAACTGAGCACTCAC 60.179 55.000 0.00 0.00 35.46 3.51
2890 4903 1.538512 CCCAAACTGAGCACTCACATG 59.461 52.381 0.00 0.00 35.46 3.21
2903 4916 2.125512 ACATGCGCGAGGTTCCTC 60.126 61.111 12.10 8.66 0.00 3.71
2904 4917 2.892425 CATGCGCGAGGTTCCTCC 60.892 66.667 12.10 5.53 0.00 4.30
2907 4920 4.388499 GCGCGAGGTTCCTCCCAA 62.388 66.667 12.10 0.00 36.75 4.12
2908 4921 2.434359 CGCGAGGTTCCTCCCAAC 60.434 66.667 0.00 0.77 36.75 3.77
2909 4922 2.046217 GCGAGGTTCCTCCCAACC 60.046 66.667 12.54 0.00 45.66 3.77
2910 4923 2.669240 CGAGGTTCCTCCCAACCC 59.331 66.667 12.54 0.00 46.39 4.11
2911 4924 1.918800 CGAGGTTCCTCCCAACCCT 60.919 63.158 12.54 0.00 46.39 4.34
2913 4926 1.541620 AGGTTCCTCCCAACCCTCC 60.542 63.158 0.00 0.00 46.39 4.30
2914 4927 2.613482 GGTTCCTCCCAACCCTCCC 61.613 68.421 0.00 0.00 40.18 4.30
2915 4928 1.850755 GTTCCTCCCAACCCTCCCA 60.851 63.158 0.00 0.00 0.00 4.37
2917 4930 3.339093 CCTCCCAACCCTCCCACC 61.339 72.222 0.00 0.00 0.00 4.61
2918 4931 3.339093 CTCCCAACCCTCCCACCC 61.339 72.222 0.00 0.00 0.00 4.61
2921 4934 3.661648 CCAACCCTCCCACCCCAG 61.662 72.222 0.00 0.00 0.00 4.45
2922 4935 4.366684 CAACCCTCCCACCCCAGC 62.367 72.222 0.00 0.00 0.00 4.85
2930 4943 4.785453 CCACCCCAGCCGCTCTTC 62.785 72.222 0.00 0.00 0.00 2.87
2931 4944 4.785453 CACCCCAGCCGCTCTTCC 62.785 72.222 0.00 0.00 0.00 3.46
2933 4946 4.168291 CCCCAGCCGCTCTTCCTC 62.168 72.222 0.00 0.00 0.00 3.71
2934 4947 4.168291 CCCAGCCGCTCTTCCTCC 62.168 72.222 0.00 0.00 0.00 4.30
2935 4948 4.168291 CCAGCCGCTCTTCCTCCC 62.168 72.222 0.00 0.00 0.00 4.30
2936 4949 3.393970 CAGCCGCTCTTCCTCCCA 61.394 66.667 0.00 0.00 0.00 4.37
2937 4950 2.607750 AGCCGCTCTTCCTCCCAA 60.608 61.111 0.00 0.00 0.00 4.12
2938 4951 2.436824 GCCGCTCTTCCTCCCAAC 60.437 66.667 0.00 0.00 0.00 3.77
2939 4952 2.269241 CCGCTCTTCCTCCCAACC 59.731 66.667 0.00 0.00 0.00 3.77
2940 4953 2.269241 CGCTCTTCCTCCCAACCC 59.731 66.667 0.00 0.00 0.00 4.11
2941 4954 2.294078 CGCTCTTCCTCCCAACCCT 61.294 63.158 0.00 0.00 0.00 4.34
2942 4955 0.976073 CGCTCTTCCTCCCAACCCTA 60.976 60.000 0.00 0.00 0.00 3.53
2943 4956 0.833949 GCTCTTCCTCCCAACCCTAG 59.166 60.000 0.00 0.00 0.00 3.02
2944 4957 0.833949 CTCTTCCTCCCAACCCTAGC 59.166 60.000 0.00 0.00 0.00 3.42
2945 4958 0.620700 TCTTCCTCCCAACCCTAGCC 60.621 60.000 0.00 0.00 0.00 3.93
2946 4959 1.972660 CTTCCTCCCAACCCTAGCCG 61.973 65.000 0.00 0.00 0.00 5.52
2947 4960 4.176752 CCTCCCAACCCTAGCCGC 62.177 72.222 0.00 0.00 0.00 6.53
2948 4961 4.176752 CTCCCAACCCTAGCCGCC 62.177 72.222 0.00 0.00 0.00 6.13
2952 4965 4.176752 CAACCCTAGCCGCCCCTC 62.177 72.222 0.00 0.00 0.00 4.30
2957 4970 4.548513 CTAGCCGCCCCTCCTCCT 62.549 72.222 0.00 0.00 0.00 3.69
2958 4971 4.541648 TAGCCGCCCCTCCTCCTC 62.542 72.222 0.00 0.00 0.00 3.71
2964 4977 4.825679 CCCCTCCTCCTCACCCCC 62.826 77.778 0.00 0.00 0.00 5.40
2985 4998 4.074854 CCCCCTCTTCCCTTCCTC 57.925 66.667 0.00 0.00 0.00 3.71
2986 4999 2.066999 CCCCCTCTTCCCTTCCTCG 61.067 68.421 0.00 0.00 0.00 4.63
2987 5000 2.736826 CCCCTCTTCCCTTCCTCGC 61.737 68.421 0.00 0.00 0.00 5.03
2988 5001 2.736826 CCCTCTTCCCTTCCTCGCC 61.737 68.421 0.00 0.00 0.00 5.54
2989 5002 2.496817 CTCTTCCCTTCCTCGCCG 59.503 66.667 0.00 0.00 0.00 6.46
2990 5003 3.724914 CTCTTCCCTTCCTCGCCGC 62.725 68.421 0.00 0.00 0.00 6.53
2991 5004 4.840005 CTTCCCTTCCTCGCCGCC 62.840 72.222 0.00 0.00 0.00 6.13
3031 5044 2.751436 CCAAGGATGGTGGTGGCG 60.751 66.667 0.00 0.00 42.18 5.69
3032 5045 2.751436 CAAGGATGGTGGTGGCGG 60.751 66.667 0.00 0.00 0.00 6.13
3033 5046 4.047125 AAGGATGGTGGTGGCGGG 62.047 66.667 0.00 0.00 0.00 6.13
3051 5064 2.999063 GCCTTGGTTGCCCTGCAT 60.999 61.111 0.00 0.00 38.76 3.96
3052 5065 3.010413 GCCTTGGTTGCCCTGCATC 62.010 63.158 0.00 0.00 38.76 3.91
3053 5066 1.304713 CCTTGGTTGCCCTGCATCT 60.305 57.895 0.00 0.00 38.76 2.90
3054 5067 1.601419 CCTTGGTTGCCCTGCATCTG 61.601 60.000 0.00 0.00 38.76 2.90
3055 5068 2.221906 CTTGGTTGCCCTGCATCTGC 62.222 60.000 0.00 0.00 38.76 4.26
3056 5069 3.818787 GGTTGCCCTGCATCTGCG 61.819 66.667 0.00 0.00 45.83 5.18
3057 5070 3.058160 GTTGCCCTGCATCTGCGT 61.058 61.111 0.00 0.00 45.83 5.24
3058 5071 3.057548 TTGCCCTGCATCTGCGTG 61.058 61.111 0.00 0.00 45.83 5.34
3062 5075 4.100084 CCTGCATCTGCGTGGGGA 62.100 66.667 6.24 0.00 45.83 4.81
3063 5076 2.046023 CTGCATCTGCGTGGGGAA 60.046 61.111 0.00 0.00 45.83 3.97
3064 5077 2.359850 TGCATCTGCGTGGGGAAC 60.360 61.111 0.00 0.00 45.83 3.62
3077 5090 3.231298 GGAACCCCGGATCAGGAG 58.769 66.667 14.13 2.02 0.00 3.69
3078 5091 2.506472 GAACCCCGGATCAGGAGC 59.494 66.667 14.13 0.00 0.00 4.70
3079 5092 3.447025 GAACCCCGGATCAGGAGCG 62.447 68.421 14.13 2.95 0.00 5.03
3095 5108 3.746889 CGGCGGCTCAATTGGCAA 61.747 61.111 17.16 0.68 0.00 4.52
3096 5109 2.182537 GGCGGCTCAATTGGCAAG 59.817 61.111 17.16 12.42 0.00 4.01
3097 5110 2.182537 GCGGCTCAATTGGCAAGG 59.817 61.111 17.16 0.24 0.00 3.61
3098 5111 2.182537 CGGCTCAATTGGCAAGGC 59.817 61.111 17.16 13.12 0.00 4.35
3099 5112 2.638354 CGGCTCAATTGGCAAGGCA 61.638 57.895 16.26 0.00 35.46 4.75
3100 5113 1.079612 GGCTCAATTGGCAAGGCAC 60.080 57.895 17.16 0.00 35.78 5.01
3101 5114 1.667151 GCTCAATTGGCAAGGCACA 59.333 52.632 5.96 0.00 0.00 4.57
3102 5115 0.033781 GCTCAATTGGCAAGGCACAA 59.966 50.000 5.96 0.00 0.00 3.33
3103 5116 1.787012 CTCAATTGGCAAGGCACAAC 58.213 50.000 5.96 0.00 0.00 3.32
3104 5117 0.392336 TCAATTGGCAAGGCACAACC 59.608 50.000 5.96 0.00 39.61 3.77
3105 5118 0.945265 CAATTGGCAAGGCACAACCG 60.945 55.000 5.96 0.00 46.52 4.44
3106 5119 2.098426 AATTGGCAAGGCACAACCGG 62.098 55.000 5.96 0.00 46.52 5.28
3109 5122 2.671619 GCAAGGCACAACCGGCTA 60.672 61.111 0.00 0.00 46.52 3.93
3110 5123 2.690778 GCAAGGCACAACCGGCTAG 61.691 63.158 0.00 0.00 46.52 3.42
3111 5124 2.359975 AAGGCACAACCGGCTAGC 60.360 61.111 6.04 6.04 46.52 3.42
3112 5125 3.190738 AAGGCACAACCGGCTAGCA 62.191 57.895 18.24 0.00 46.52 3.49
3113 5126 3.127533 GGCACAACCGGCTAGCAG 61.128 66.667 18.24 13.09 0.00 4.24
3114 5127 3.804193 GCACAACCGGCTAGCAGC 61.804 66.667 18.24 4.63 41.46 5.25
3136 5149 4.838152 CGGGCGGTGGATCTGGTG 62.838 72.222 0.00 0.00 0.00 4.17
3137 5150 3.717294 GGGCGGTGGATCTGGTGT 61.717 66.667 0.00 0.00 0.00 4.16
3138 5151 2.125106 GGCGGTGGATCTGGTGTC 60.125 66.667 0.00 0.00 0.00 3.67
3139 5152 2.125106 GCGGTGGATCTGGTGTCC 60.125 66.667 0.00 0.00 36.26 4.02
3140 5153 2.584608 CGGTGGATCTGGTGTCCC 59.415 66.667 0.00 0.00 34.76 4.46
3141 5154 2.584608 GGTGGATCTGGTGTCCCG 59.415 66.667 0.00 0.00 34.76 5.14
3142 5155 2.584608 GTGGATCTGGTGTCCCGG 59.415 66.667 0.00 0.00 38.61 5.73
3143 5156 3.399181 TGGATCTGGTGTCCCGGC 61.399 66.667 0.00 0.00 37.01 6.13
3144 5157 4.176752 GGATCTGGTGTCCCGGCC 62.177 72.222 0.00 0.00 37.01 6.13
3145 5158 4.530857 GATCTGGTGTCCCGGCCG 62.531 72.222 21.04 21.04 37.01 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.595382 GTCTGTTGGCAGTGCTCGT 60.595 57.895 16.11 0.00 43.05 4.18
2 3 1.159713 TTGTCTGTTGGCAGTGCTCG 61.160 55.000 16.11 0.00 43.05 5.03
4 5 0.107017 AGTTGTCTGTTGGCAGTGCT 60.107 50.000 16.11 0.00 43.05 4.40
5 6 0.029834 CAGTTGTCTGTTGGCAGTGC 59.970 55.000 6.55 6.55 43.05 4.40
7 8 0.255890 ACCAGTTGTCTGTTGGCAGT 59.744 50.000 0.00 0.00 43.05 4.40
8 9 0.947244 GACCAGTTGTCTGTTGGCAG 59.053 55.000 0.00 0.00 43.87 4.85
9 10 0.465460 GGACCAGTTGTCTGTTGGCA 60.465 55.000 0.00 0.00 43.89 4.92
10 11 1.172812 GGGACCAGTTGTCTGTTGGC 61.173 60.000 0.00 0.00 43.89 4.52
12 13 1.597742 CAGGGACCAGTTGTCTGTTG 58.402 55.000 0.00 0.00 43.89 3.33
15 16 1.669115 CGCAGGGACCAGTTGTCTG 60.669 63.158 0.00 0.00 43.89 3.51
16 17 1.696097 AACGCAGGGACCAGTTGTCT 61.696 55.000 0.00 0.00 43.89 3.41
17 18 1.227853 AACGCAGGGACCAGTTGTC 60.228 57.895 0.00 0.00 43.67 3.18
18 19 1.525995 CAACGCAGGGACCAGTTGT 60.526 57.895 12.84 0.00 39.11 3.32
19 20 2.260869 CCAACGCAGGGACCAGTTG 61.261 63.158 13.63 13.63 42.37 3.16
20 21 2.113139 CCAACGCAGGGACCAGTT 59.887 61.111 0.00 0.00 0.00 3.16
28 29 1.172180 TTTGAGAAGCCCAACGCAGG 61.172 55.000 0.00 0.00 41.38 4.85
29 30 0.883833 ATTTGAGAAGCCCAACGCAG 59.116 50.000 0.00 0.00 41.38 5.18
30 31 1.810151 GTATTTGAGAAGCCCAACGCA 59.190 47.619 0.00 0.00 41.38 5.24
31 32 2.084546 AGTATTTGAGAAGCCCAACGC 58.915 47.619 0.00 0.00 37.98 4.84
32 33 4.935808 ACTTAGTATTTGAGAAGCCCAACG 59.064 41.667 0.00 0.00 0.00 4.10
33 34 6.819397 AACTTAGTATTTGAGAAGCCCAAC 57.181 37.500 0.00 0.00 0.00 3.77
34 35 7.231467 AGAAACTTAGTATTTGAGAAGCCCAA 58.769 34.615 0.00 0.00 0.00 4.12
35 36 6.779860 AGAAACTTAGTATTTGAGAAGCCCA 58.220 36.000 0.00 0.00 0.00 5.36
36 37 7.065204 CAGAGAAACTTAGTATTTGAGAAGCCC 59.935 40.741 0.00 0.00 0.00 5.19
37 38 7.819900 TCAGAGAAACTTAGTATTTGAGAAGCC 59.180 37.037 0.00 0.00 0.00 4.35
38 39 8.764524 TCAGAGAAACTTAGTATTTGAGAAGC 57.235 34.615 0.00 0.00 0.00 3.86
48 49 9.712305 CTCCTTTTCAATCAGAGAAACTTAGTA 57.288 33.333 0.00 0.00 34.94 1.82
49 50 7.663493 CCTCCTTTTCAATCAGAGAAACTTAGT 59.337 37.037 0.00 0.00 34.94 2.24
50 51 7.663493 ACCTCCTTTTCAATCAGAGAAACTTAG 59.337 37.037 0.00 0.00 34.94 2.18
51 52 7.518188 ACCTCCTTTTCAATCAGAGAAACTTA 58.482 34.615 0.00 0.00 34.94 2.24
52 53 6.368805 ACCTCCTTTTCAATCAGAGAAACTT 58.631 36.000 0.00 0.00 34.94 2.66
53 54 5.946486 ACCTCCTTTTCAATCAGAGAAACT 58.054 37.500 0.00 0.00 34.94 2.66
54 55 6.641169 AACCTCCTTTTCAATCAGAGAAAC 57.359 37.500 0.00 0.00 34.94 2.78
55 56 7.468631 CGAAAACCTCCTTTTCAATCAGAGAAA 60.469 37.037 6.41 0.00 45.74 2.52
56 57 6.017109 CGAAAACCTCCTTTTCAATCAGAGAA 60.017 38.462 6.41 0.00 45.74 2.87
57 58 5.470098 CGAAAACCTCCTTTTCAATCAGAGA 59.530 40.000 6.41 0.00 45.74 3.10
58 59 5.470098 TCGAAAACCTCCTTTTCAATCAGAG 59.530 40.000 6.41 0.00 45.74 3.35
59 60 5.373222 TCGAAAACCTCCTTTTCAATCAGA 58.627 37.500 6.41 0.00 45.74 3.27
60 61 5.689383 TCGAAAACCTCCTTTTCAATCAG 57.311 39.130 6.41 0.00 45.74 2.90
61 62 6.648879 ATTCGAAAACCTCCTTTTCAATCA 57.351 33.333 0.00 0.00 45.74 2.57
62 63 7.148967 CGAAATTCGAAAACCTCCTTTTCAATC 60.149 37.037 10.18 0.00 45.74 2.67
63 64 6.640907 CGAAATTCGAAAACCTCCTTTTCAAT 59.359 34.615 10.18 3.36 45.74 2.57
64 65 5.974751 CGAAATTCGAAAACCTCCTTTTCAA 59.025 36.000 10.18 1.61 45.74 2.69
65 66 5.297278 TCGAAATTCGAAAACCTCCTTTTCA 59.703 36.000 16.25 0.00 46.90 2.69
66 67 5.754778 TCGAAATTCGAAAACCTCCTTTTC 58.245 37.500 16.25 4.30 46.90 2.29
67 68 5.761165 TCGAAATTCGAAAACCTCCTTTT 57.239 34.783 16.25 0.00 46.90 2.27
114 119 3.420943 GTCACTGTGTGTGGCCAC 58.579 61.111 29.67 29.67 44.95 5.01
122 127 1.405872 TAACTGGGACGTCACTGTGT 58.594 50.000 28.05 19.77 31.60 3.72
128 133 2.629137 TGCTAGTTTAACTGGGACGTCA 59.371 45.455 18.91 0.00 0.00 4.35
149 155 1.677942 TTTTTGTCCGGCGGTAAAGT 58.322 45.000 27.32 0.00 0.00 2.66
157 163 6.779115 AATTTAAGAACATTTTTGTCCGGC 57.221 33.333 0.00 0.00 0.00 6.13
159 165 9.250624 TGGTTAATTTAAGAACATTTTTGTCCG 57.749 29.630 0.00 0.00 0.00 4.79
169 181 4.822896 ACGGTGCTGGTTAATTTAAGAACA 59.177 37.500 0.00 0.00 0.00 3.18
171 183 6.394025 AAACGGTGCTGGTTAATTTAAGAA 57.606 33.333 0.00 0.00 0.00 2.52
173 185 8.751302 ATTAAAACGGTGCTGGTTAATTTAAG 57.249 30.769 0.00 0.00 0.00 1.85
176 188 9.713713 ATTAATTAAAACGGTGCTGGTTAATTT 57.286 25.926 1.21 0.00 36.37 1.82
180 192 7.450124 TGATTAATTAAAACGGTGCTGGTTA 57.550 32.000 1.21 0.00 0.00 2.85
183 195 5.575218 GGTTGATTAATTAAAACGGTGCTGG 59.425 40.000 1.21 0.00 0.00 4.85
185 197 6.334102 TGGTTGATTAATTAAAACGGTGCT 57.666 33.333 1.21 0.00 0.00 4.40
186 198 5.061684 GCTGGTTGATTAATTAAAACGGTGC 59.938 40.000 1.21 5.19 0.00 5.01
187 199 6.088883 GTGCTGGTTGATTAATTAAAACGGTG 59.911 38.462 1.21 0.00 0.00 4.94
188 200 6.015772 AGTGCTGGTTGATTAATTAAAACGGT 60.016 34.615 1.21 0.00 0.00 4.83
189 201 6.307800 CAGTGCTGGTTGATTAATTAAAACGG 59.692 38.462 1.21 0.06 0.00 4.44
190 202 6.183359 GCAGTGCTGGTTGATTAATTAAAACG 60.183 38.462 8.18 0.00 0.00 3.60
191 203 6.090763 GGCAGTGCTGGTTGATTAATTAAAAC 59.909 38.462 16.11 3.35 0.00 2.43
192 204 6.162777 GGCAGTGCTGGTTGATTAATTAAAA 58.837 36.000 16.11 0.00 0.00 1.52
193 205 5.621104 CGGCAGTGCTGGTTGATTAATTAAA 60.621 40.000 16.66 0.00 0.00 1.52
194 206 4.142491 CGGCAGTGCTGGTTGATTAATTAA 60.142 41.667 16.66 0.00 0.00 1.40
195 207 3.376859 CGGCAGTGCTGGTTGATTAATTA 59.623 43.478 16.66 0.00 0.00 1.40
196 208 2.164219 CGGCAGTGCTGGTTGATTAATT 59.836 45.455 16.66 0.00 0.00 1.40
197 209 1.745087 CGGCAGTGCTGGTTGATTAAT 59.255 47.619 16.66 0.00 0.00 1.40
198 210 1.164411 CGGCAGTGCTGGTTGATTAA 58.836 50.000 16.66 0.00 0.00 1.40
199 211 1.305219 GCGGCAGTGCTGGTTGATTA 61.305 55.000 25.02 0.00 35.15 1.75
200 212 2.629656 GCGGCAGTGCTGGTTGATT 61.630 57.895 25.02 0.00 35.15 2.57
224 236 7.194607 TGTTTGAAGATGTTTTTGTTTTGCA 57.805 28.000 0.00 0.00 0.00 4.08
295 317 2.357034 GGAAGCTGCCGTTGTCGA 60.357 61.111 0.00 0.00 39.71 4.20
404 427 2.890474 CAAAGCGATCCGGGTCCG 60.890 66.667 9.71 7.90 39.44 4.79
405 428 3.202706 GCAAAGCGATCCGGGTCC 61.203 66.667 9.71 1.71 0.00 4.46
406 429 1.745489 AAGCAAAGCGATCCGGGTC 60.745 57.895 4.00 4.00 0.00 4.46
407 430 2.040544 CAAGCAAAGCGATCCGGGT 61.041 57.895 0.00 0.00 0.00 5.28
408 431 2.793946 CAAGCAAAGCGATCCGGG 59.206 61.111 0.00 0.00 0.00 5.73
409 432 2.100991 GCAAGCAAAGCGATCCGG 59.899 61.111 0.00 0.00 0.00 5.14
410 433 2.100991 GGCAAGCAAAGCGATCCG 59.899 61.111 0.00 0.00 0.00 4.18
411 434 1.028868 AGAGGCAAGCAAAGCGATCC 61.029 55.000 0.00 0.00 0.00 3.36
412 435 0.376502 GAGAGGCAAGCAAAGCGATC 59.623 55.000 0.00 0.00 0.00 3.69
413 436 0.035630 AGAGAGGCAAGCAAAGCGAT 60.036 50.000 0.00 0.00 0.00 4.58
425 448 3.712016 AGGGAAGAAAAGAAGAGAGGC 57.288 47.619 0.00 0.00 0.00 4.70
440 463 3.005472 CGCTCGATGATTAAGGTAGGGAA 59.995 47.826 0.00 0.00 0.00 3.97
446 469 1.068741 GGACCGCTCGATGATTAAGGT 59.931 52.381 0.00 0.00 0.00 3.50
455 478 3.518998 CGACCAGGACCGCTCGAT 61.519 66.667 0.00 0.00 0.00 3.59
486 509 2.599597 GGGCATCATGAGTGGGCT 59.400 61.111 14.96 0.00 0.00 5.19
487 510 1.708993 TAGGGGCATCATGAGTGGGC 61.709 60.000 0.09 5.71 0.00 5.36
531 561 4.246458 CAGACCCTAGCTAGTGTTTTGAC 58.754 47.826 19.31 2.25 0.00 3.18
551 581 1.138247 GCCATTGCTTTCCTCGCAG 59.862 57.895 0.00 0.00 38.80 5.18
554 584 2.793946 CCGCCATTGCTTTCCTCG 59.206 61.111 0.00 0.00 34.43 4.63
609 639 2.005960 GACGCCTAGCCACACGATCT 62.006 60.000 0.00 0.00 0.00 2.75
610 640 1.589196 GACGCCTAGCCACACGATC 60.589 63.158 0.00 0.00 0.00 3.69
654 976 9.716531 ACAACCATATTAGTGACATGATATCAG 57.283 33.333 11.78 6.15 0.00 2.90
700 1022 4.314440 TGCGACCTGCTCACCCAC 62.314 66.667 0.00 0.00 46.63 4.61
771 1093 4.081322 ACCATAGTTCGGCCGATTAAAT 57.919 40.909 31.56 16.58 0.00 1.40
971 1330 5.014228 CCTTCCCTTCTTCCTTTCTTTCCTA 59.986 44.000 0.00 0.00 0.00 2.94
983 1342 1.004745 TCATGTGCCCTTCCCTTCTTC 59.995 52.381 0.00 0.00 0.00 2.87
1839 2673 2.113774 CAGTTGAGCACCAGCCCA 59.886 61.111 0.00 0.00 43.56 5.36
1952 2786 2.660552 CGCCCACGTCGACAGTTT 60.661 61.111 17.16 0.00 33.53 2.66
2193 3165 9.277565 CGCGTGTTAATTAAACTCTTACTACTA 57.722 33.333 0.00 0.00 38.99 1.82
2266 3241 3.252701 AGACGACGTCAAAAAGCTCTCTA 59.747 43.478 28.31 0.00 34.60 2.43
2267 3242 2.034812 AGACGACGTCAAAAAGCTCTCT 59.965 45.455 28.31 1.48 34.60 3.10
2312 3308 2.214216 TTACAGACACCGGCAGCCT 61.214 57.895 10.54 0.00 0.00 4.58
2319 3315 4.377431 GCTTGATCTTTGTTACAGACACCG 60.377 45.833 0.00 0.00 38.18 4.94
2324 3320 5.368145 ACAGTGCTTGATCTTTGTTACAGA 58.632 37.500 0.00 0.00 0.00 3.41
2374 3378 0.926293 TCCCAGGGTGATGGAAATCC 59.074 55.000 5.01 0.00 43.57 3.01
2381 3385 0.108138 GTTCTCGTCCCAGGGTGATG 60.108 60.000 5.01 0.00 0.00 3.07
2396 3400 8.947115 CCCTTTTAACTGAAGATTTATCGTTCT 58.053 33.333 0.00 0.00 0.00 3.01
2400 3404 7.065803 TCTGCCCTTTTAACTGAAGATTTATCG 59.934 37.037 0.00 0.00 0.00 2.92
2401 3405 8.281212 TCTGCCCTTTTAACTGAAGATTTATC 57.719 34.615 0.00 0.00 0.00 1.75
2402 3406 8.109634 TCTCTGCCCTTTTAACTGAAGATTTAT 58.890 33.333 0.00 0.00 0.00 1.40
2403 3407 7.458397 TCTCTGCCCTTTTAACTGAAGATTTA 58.542 34.615 0.00 0.00 0.00 1.40
2451 4055 2.882761 TCCGAGAGTATACCCATGAACG 59.117 50.000 0.00 0.00 0.00 3.95
2458 4062 2.941480 TCCAACTCCGAGAGTATACCC 58.059 52.381 1.33 0.00 42.59 3.69
2459 4063 4.583489 TCATTCCAACTCCGAGAGTATACC 59.417 45.833 1.33 0.00 42.59 2.73
2485 4089 2.807906 TTGCACTGTCGCACGTGTG 61.808 57.895 22.93 22.93 42.87 3.82
2486 4090 2.510464 TTGCACTGTCGCACGTGT 60.510 55.556 18.38 0.00 42.87 4.49
2487 4091 2.053116 GTTGCACTGTCGCACGTG 60.053 61.111 12.28 12.28 42.87 4.49
2488 4092 2.510464 TGTTGCACTGTCGCACGT 60.510 55.556 4.75 0.00 42.87 4.49
2489 4093 2.053116 GTGTTGCACTGTCGCACG 60.053 61.111 4.75 0.00 42.87 5.34
2490 4094 1.297598 GTGTGTTGCACTGTCGCAC 60.298 57.895 4.75 0.00 42.87 5.34
2491 4095 2.807906 CGTGTGTTGCACTGTCGCA 61.808 57.895 0.00 1.65 45.57 5.10
2492 4096 2.053116 CGTGTGTTGCACTGTCGC 60.053 61.111 0.00 0.00 45.57 5.19
2493 4097 2.053116 GCGTGTGTTGCACTGTCG 60.053 61.111 0.00 4.80 45.57 4.35
2494 4098 0.179176 TTTGCGTGTGTTGCACTGTC 60.179 50.000 0.00 0.00 45.57 3.51
2495 4099 0.179166 CTTTGCGTGTGTTGCACTGT 60.179 50.000 0.00 0.00 45.57 3.55
2536 4546 6.855914 TCGTATGTTTCGTACTACTTTCGTTT 59.144 34.615 0.00 0.00 0.00 3.60
2540 4550 7.324616 AGTTGTCGTATGTTTCGTACTACTTTC 59.675 37.037 0.00 0.00 0.00 2.62
2646 4656 2.332312 TTACACGGCCCACTTGTGCT 62.332 55.000 7.54 0.00 37.11 4.40
2647 4657 1.448922 TTTACACGGCCCACTTGTGC 61.449 55.000 7.54 0.00 37.11 4.57
2648 4658 0.309612 GTTTACACGGCCCACTTGTG 59.690 55.000 0.00 0.84 39.47 3.33
2649 4659 0.820482 GGTTTACACGGCCCACTTGT 60.820 55.000 0.00 0.00 0.00 3.16
2656 4666 1.886886 TTCTTCTGGTTTACACGGCC 58.113 50.000 0.00 0.00 0.00 6.13
2686 4696 5.163652 CCGGGAATAAAATCCAAGACTGAAC 60.164 44.000 0.00 0.00 41.55 3.18
2747 4757 3.756933 ATTGTGGCATTGAGCTGTTTT 57.243 38.095 0.00 0.00 44.79 2.43
2748 4758 3.756933 AATTGTGGCATTGAGCTGTTT 57.243 38.095 0.00 0.00 44.79 2.83
2749 4759 3.756933 AAATTGTGGCATTGAGCTGTT 57.243 38.095 0.00 0.00 44.79 3.16
2750 4760 3.181463 ACAAAATTGTGGCATTGAGCTGT 60.181 39.130 0.00 0.00 40.49 4.40
2751 4761 3.395639 ACAAAATTGTGGCATTGAGCTG 58.604 40.909 0.00 0.00 40.49 4.24
2752 4762 3.756933 ACAAAATTGTGGCATTGAGCT 57.243 38.095 0.00 0.00 40.49 4.09
2753 4763 4.060205 AGAACAAAATTGTGGCATTGAGC 58.940 39.130 0.00 0.00 41.31 4.26
2754 4764 4.449743 CCAGAACAAAATTGTGGCATTGAG 59.550 41.667 0.00 0.00 41.31 3.02
2756 4766 4.378774 TCCAGAACAAAATTGTGGCATTG 58.621 39.130 0.00 0.00 41.31 2.82
2758 4768 4.379652 GTTCCAGAACAAAATTGTGGCAT 58.620 39.130 5.66 0.00 41.31 4.40
2759 4769 3.791245 GTTCCAGAACAAAATTGTGGCA 58.209 40.909 5.66 0.00 41.31 4.92
2872 4885 1.399343 CGCATGTGAGTGCTCAGTTTG 60.399 52.381 0.00 2.58 42.88 2.93
2887 4900 2.892425 GGAGGAACCTCGCGCATG 60.892 66.667 8.75 0.00 43.59 4.06
2904 4917 3.661648 CTGGGGTGGGAGGGTTGG 61.662 72.222 0.00 0.00 0.00 3.77
2913 4926 4.785453 GAAGAGCGGCTGGGGTGG 62.785 72.222 7.50 0.00 0.00 4.61
2914 4927 4.785453 GGAAGAGCGGCTGGGGTG 62.785 72.222 7.50 0.00 0.00 4.61
2917 4930 4.168291 GGAGGAAGAGCGGCTGGG 62.168 72.222 7.50 0.00 0.00 4.45
2918 4931 4.168291 GGGAGGAAGAGCGGCTGG 62.168 72.222 7.50 0.00 0.00 4.85
2920 4933 2.607750 TTGGGAGGAAGAGCGGCT 60.608 61.111 0.00 0.00 0.00 5.52
2921 4934 2.436824 GTTGGGAGGAAGAGCGGC 60.437 66.667 0.00 0.00 0.00 6.53
2922 4935 2.269241 GGTTGGGAGGAAGAGCGG 59.731 66.667 0.00 0.00 0.00 5.52
2923 4936 0.976073 TAGGGTTGGGAGGAAGAGCG 60.976 60.000 0.00 0.00 0.00 5.03
2925 4938 0.833949 GCTAGGGTTGGGAGGAAGAG 59.166 60.000 0.00 0.00 0.00 2.85
2926 4939 0.620700 GGCTAGGGTTGGGAGGAAGA 60.621 60.000 0.00 0.00 0.00 2.87
2927 4940 1.915983 GGCTAGGGTTGGGAGGAAG 59.084 63.158 0.00 0.00 0.00 3.46
2928 4941 1.993391 CGGCTAGGGTTGGGAGGAA 60.993 63.158 0.00 0.00 0.00 3.36
2929 4942 2.365105 CGGCTAGGGTTGGGAGGA 60.365 66.667 0.00 0.00 0.00 3.71
2930 4943 4.176752 GCGGCTAGGGTTGGGAGG 62.177 72.222 0.00 0.00 0.00 4.30
2931 4944 4.176752 GGCGGCTAGGGTTGGGAG 62.177 72.222 0.00 0.00 0.00 4.30
2935 4948 4.176752 GAGGGGCGGCTAGGGTTG 62.177 72.222 9.56 0.00 0.00 3.77
2940 4953 4.548513 AGGAGGAGGGGCGGCTAG 62.549 72.222 9.56 0.00 0.00 3.42
2941 4954 4.541648 GAGGAGGAGGGGCGGCTA 62.542 72.222 9.56 0.00 0.00 3.93
2947 4960 4.825679 GGGGGTGAGGAGGAGGGG 62.826 77.778 0.00 0.00 0.00 4.79
2968 4981 2.066999 CGAGGAAGGGAAGAGGGGG 61.067 68.421 0.00 0.00 0.00 5.40
2969 4982 2.736826 GCGAGGAAGGGAAGAGGGG 61.737 68.421 0.00 0.00 0.00 4.79
2970 4983 2.736826 GGCGAGGAAGGGAAGAGGG 61.737 68.421 0.00 0.00 0.00 4.30
2971 4984 2.904131 GGCGAGGAAGGGAAGAGG 59.096 66.667 0.00 0.00 0.00 3.69
2972 4985 2.496817 CGGCGAGGAAGGGAAGAG 59.503 66.667 0.00 0.00 0.00 2.85
2973 4986 3.771160 GCGGCGAGGAAGGGAAGA 61.771 66.667 12.98 0.00 0.00 2.87
2974 4987 4.840005 GGCGGCGAGGAAGGGAAG 62.840 72.222 12.98 0.00 0.00 3.46
3015 5028 2.751436 CCGCCACCACCATCCTTG 60.751 66.667 0.00 0.00 0.00 3.61
3016 5029 4.047125 CCCGCCACCACCATCCTT 62.047 66.667 0.00 0.00 0.00 3.36
3040 5053 3.058160 ACGCAGATGCAGGGCAAC 61.058 61.111 5.55 0.00 43.62 4.17
3041 5054 3.057548 CACGCAGATGCAGGGCAA 61.058 61.111 5.55 0.00 43.62 4.52
3045 5058 3.626996 TTCCCCACGCAGATGCAGG 62.627 63.158 5.55 6.01 42.21 4.85
3046 5059 2.046023 TTCCCCACGCAGATGCAG 60.046 61.111 5.55 0.69 42.21 4.41
3047 5060 2.359850 GTTCCCCACGCAGATGCA 60.360 61.111 5.55 0.00 42.21 3.96
3048 5061 3.134127 GGTTCCCCACGCAGATGC 61.134 66.667 0.00 0.00 37.78 3.91
3049 5062 2.438434 GGGTTCCCCACGCAGATG 60.438 66.667 0.00 0.00 44.65 2.90
3058 5071 3.489513 CCTGATCCGGGGTTCCCC 61.490 72.222 16.52 16.52 41.57 4.81
3059 5072 2.366435 TCCTGATCCGGGGTTCCC 60.366 66.667 0.00 0.00 41.09 3.97
3060 5073 3.108288 GCTCCTGATCCGGGGTTCC 62.108 68.421 0.00 0.00 0.00 3.62
3061 5074 2.506472 GCTCCTGATCCGGGGTTC 59.494 66.667 0.00 0.00 0.00 3.62
3062 5075 3.470888 CGCTCCTGATCCGGGGTT 61.471 66.667 0.00 0.00 0.00 4.11
3078 5091 3.688475 CTTGCCAATTGAGCCGCCG 62.688 63.158 7.12 0.00 0.00 6.46
3079 5092 2.182537 CTTGCCAATTGAGCCGCC 59.817 61.111 7.12 0.00 0.00 6.13
3080 5093 2.182537 CCTTGCCAATTGAGCCGC 59.817 61.111 7.12 1.96 0.00 6.53
3081 5094 2.182537 GCCTTGCCAATTGAGCCG 59.817 61.111 7.12 3.21 0.00 5.52
3082 5095 1.079612 GTGCCTTGCCAATTGAGCC 60.080 57.895 7.12 0.00 0.00 4.70
3083 5096 0.033781 TTGTGCCTTGCCAATTGAGC 59.966 50.000 7.12 9.39 0.00 4.26
3084 5097 1.606224 GGTTGTGCCTTGCCAATTGAG 60.606 52.381 7.12 0.00 0.00 3.02
3085 5098 0.392336 GGTTGTGCCTTGCCAATTGA 59.608 50.000 7.12 0.00 0.00 2.57
3086 5099 0.945265 CGGTTGTGCCTTGCCAATTG 60.945 55.000 0.00 0.00 34.25 2.32
3087 5100 1.367102 CGGTTGTGCCTTGCCAATT 59.633 52.632 0.00 0.00 34.25 2.32
3088 5101 2.573083 CCGGTTGTGCCTTGCCAAT 61.573 57.895 0.00 0.00 34.25 3.16
3089 5102 3.222855 CCGGTTGTGCCTTGCCAA 61.223 61.111 0.00 0.00 34.25 4.52
3092 5105 2.671619 TAGCCGGTTGTGCCTTGC 60.672 61.111 1.90 0.00 34.20 4.01
3093 5106 2.690778 GCTAGCCGGTTGTGCCTTG 61.691 63.158 2.29 0.00 34.25 3.61
3094 5107 2.359975 GCTAGCCGGTTGTGCCTT 60.360 61.111 2.29 0.00 34.25 4.35
3095 5108 3.612247 CTGCTAGCCGGTTGTGCCT 62.612 63.158 13.29 0.00 34.25 4.75
3096 5109 3.127533 CTGCTAGCCGGTTGTGCC 61.128 66.667 13.29 0.00 0.00 5.01
3097 5110 3.804193 GCTGCTAGCCGGTTGTGC 61.804 66.667 13.29 7.26 34.48 4.57
3119 5132 4.838152 CACCAGATCCACCGCCCG 62.838 72.222 0.00 0.00 0.00 6.13
3120 5133 3.682292 GACACCAGATCCACCGCCC 62.682 68.421 0.00 0.00 0.00 6.13
3121 5134 2.125106 GACACCAGATCCACCGCC 60.125 66.667 0.00 0.00 0.00 6.13
3122 5135 2.125106 GGACACCAGATCCACCGC 60.125 66.667 0.00 0.00 36.15 5.68
3123 5136 2.584608 GGGACACCAGATCCACCG 59.415 66.667 0.00 0.00 38.06 4.94
3124 5137 2.584608 CGGGACACCAGATCCACC 59.415 66.667 0.00 0.00 38.06 4.61
3125 5138 2.584608 CCGGGACACCAGATCCAC 59.415 66.667 0.00 0.00 38.06 4.02
3126 5139 3.399181 GCCGGGACACCAGATCCA 61.399 66.667 2.18 0.00 38.06 3.41
3127 5140 4.176752 GGCCGGGACACCAGATCC 62.177 72.222 2.18 0.00 36.13 3.36
3128 5141 4.530857 CGGCCGGGACACCAGATC 62.531 72.222 20.10 0.00 36.13 2.75


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

AutoCloner maintained by Alex Coulton.