Multiple sequence alignment - TraesCS7B01G182100

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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 TraesCS7B01G182100 chr7B 100.000 5844 0 0 1 5844 282328065 282333908 0.000000e+00 10792.0
1 TraesCS7B01G182100 chr7B 95.339 236 11 0 5609 5844 575889885 575889650 5.530000e-100 375.0
2 TraesCS7B01G182100 chr7B 95.339 236 11 0 5609 5844 686727363 686727128 5.530000e-100 375.0
3 TraesCS7B01G182100 chr7B 91.566 83 5 2 4060 4141 282332205 282332124 4.790000e-21 113.0
4 TraesCS7B01G182100 chr7D 97.197 4495 82 14 768 5234 306462060 306457582 0.000000e+00 7563.0
5 TraesCS7B01G182100 chr7D 89.053 475 42 4 195 661 306477172 306476700 1.090000e-161 580.0
6 TraesCS7B01G182100 chr7D 97.059 340 10 0 5271 5610 306457431 306457092 1.830000e-159 573.0
7 TraesCS7B01G182100 chr7D 95.161 124 6 0 654 777 306462433 306462310 4.620000e-46 196.0
8 TraesCS7B01G182100 chr7D 90.351 114 10 1 18 131 306477300 306477188 1.310000e-31 148.0
9 TraesCS7B01G182100 chr7D 91.566 83 5 2 4060 4141 306458668 306458749 4.790000e-21 113.0
10 TraesCS7B01G182100 chr7D 98.039 51 1 0 2539 2589 306460235 306460285 8.070000e-14 89.8
11 TraesCS7B01G182100 chr7D 100.000 30 0 0 5235 5264 306457502 306457473 8.180000e-04 56.5
12 TraesCS7B01G182100 chr7D 100.000 29 0 0 2538 2566 47416219 47416191 3.000000e-03 54.7
13 TraesCS7B01G182100 chr7A 96.709 4497 99 16 768 5234 359048857 359053334 0.000000e+00 7439.0
14 TraesCS7B01G182100 chr7A 87.925 588 60 6 195 773 359048031 359048616 0.000000e+00 682.0
15 TraesCS7B01G182100 chr7A 96.765 340 11 0 5271 5610 359053485 359053824 8.500000e-158 568.0
16 TraesCS7B01G182100 chr7A 87.719 114 13 1 18 131 359047903 359048015 1.320000e-26 132.0
17 TraesCS7B01G182100 chr7A 91.566 83 5 2 4060 4141 359052251 359052170 4.790000e-21 113.0
18 TraesCS7B01G182100 chr4B 95.816 239 10 0 5606 5844 624379485 624379723 2.550000e-103 387.0
19 TraesCS7B01G182100 chr4B 95.082 244 10 2 5601 5844 495310803 495310562 3.300000e-102 383.0
20 TraesCS7B01G182100 chr4B 95.763 236 10 0 5609 5844 50839401 50839636 1.190000e-101 381.0
21 TraesCS7B01G182100 chr5B 95.798 238 10 0 5607 5844 693263194 693263431 9.190000e-103 385.0
22 TraesCS7B01G182100 chr5B 95.339 236 11 0 5609 5844 379254456 379254221 5.530000e-100 375.0
23 TraesCS7B01G182100 chr5B 92.308 78 4 2 4062 4139 355601227 355601152 6.190000e-20 110.0
24 TraesCS7B01G182100 chr5B 90.278 72 7 0 2282 2353 637466160 637466089 1.730000e-15 95.3
25 TraesCS7B01G182100 chr5B 96.774 31 1 0 2539 2569 706166243 706166213 1.100000e-02 52.8
26 TraesCS7B01G182100 chr3B 95.763 236 10 0 5609 5844 140316217 140315982 1.190000e-101 381.0
27 TraesCS7B01G182100 chr2B 95.339 236 11 0 5609 5844 541199873 541200108 5.530000e-100 375.0
28 TraesCS7B01G182100 chr2B 92.683 82 1 5 4061 4139 693753288 693753367 4.790000e-21 113.0
29 TraesCS7B01G182100 chr5D 82.386 176 23 2 2284 2451 72221927 72222102 4.720000e-31 147.0
30 TraesCS7B01G182100 chr5D 100.000 28 0 0 2539 2566 175781921 175781948 1.100000e-02 52.8
31 TraesCS7B01G182100 chr5D 96.774 31 1 0 2560 2590 563756000 563756030 1.100000e-02 52.8
32 TraesCS7B01G182100 chr3A 93.827 81 1 4 4063 4141 430526505 430526427 1.030000e-22 119.0
33 TraesCS7B01G182100 chr6D 87.368 95 4 8 4061 4152 309955221 309955310 1.040000e-17 102.0
34 TraesCS7B01G182100 chr6D 100.000 28 0 0 2539 2566 363033206 363033179 1.100000e-02 52.8
35 TraesCS7B01G182100 chr6A 87.500 56 1 1 2539 2594 529567108 529567059 6.320000e-05 60.2
36 TraesCS7B01G182100 chr6B 100.000 29 0 0 2563 2591 16341376 16341348 3.000000e-03 54.7
37 TraesCS7B01G182100 chr3D 100.000 28 0 0 2539 2566 99872699 99872726 1.100000e-02 52.8
38 TraesCS7B01G182100 chr3D 100.000 28 0 0 2539 2566 209619460 209619433 1.100000e-02 52.8
39 TraesCS7B01G182100 chr1D 100.000 28 0 0 2539 2566 331917699 331917672 1.100000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G182100 chr7B 282328065 282333908 5843 False 10792.000 10792 100.00000 1 5844 1 chr7B.!!$F1 5843
1 TraesCS7B01G182100 chr7D 306457092 306462433 5341 True 2097.125 7563 97.35425 654 5610 4 chr7D.!!$R2 4956
2 TraesCS7B01G182100 chr7D 306476700 306477300 600 True 364.000 580 89.70200 18 661 2 chr7D.!!$R3 643
3 TraesCS7B01G182100 chr7A 359047903 359053824 5921 False 2205.250 7439 92.27950 18 5610 4 chr7A.!!$F1 5592

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
325 329 0.034337 GCTGCATAAATGGGGCATGG 59.966 55.000 0.00 0.00 36.87 3.66 F
484 488 0.099968 TGATCTTTCGACCTACGCCG 59.900 55.000 0.00 0.00 42.26 6.46 F
622 627 0.107410 TCACCCAACTGCAACGAACT 60.107 50.000 0.00 0.00 0.00 3.01 F
853 1124 0.314418 CTCTTCGTCTCGCGTACTCG 60.314 60.000 5.77 7.67 42.13 4.18 F
1419 1691 0.328258 ATTGCCCCTACTCGTTGCTT 59.672 50.000 0.00 0.00 0.00 3.91 F
2147 2422 1.357137 TGTCTACCAGCCCAATGTGA 58.643 50.000 0.00 0.00 0.00 3.58 F
2389 2665 2.100749 CTGGAAACAAAACCACCAGTCC 59.899 50.000 0.00 0.00 41.91 3.85 F
3298 3579 1.299316 CGGCAACACAACCAAGCAG 60.299 57.895 0.00 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1674 0.248289 GTAAGCAACGAGTAGGGGCA 59.752 55.000 0.00 0.00 0.00 5.36 R
2151 2426 0.679505 GACTGTCTGTGGCTGTGGTA 59.320 55.000 0.00 0.00 0.00 3.25 R
2389 2665 0.872881 CGGTTTAGGATACACGCCCG 60.873 60.000 0.00 0.00 41.41 6.13 R
2445 2721 5.806654 ACAATGCAAACTTGACCCTTTAT 57.193 34.783 5.55 0.00 0.00 1.40 R
2938 3219 1.059584 TGGCCCTCTCCAACAGTTGA 61.060 55.000 15.36 0.37 32.18 3.18 R
3298 3579 1.318576 CCCAAATAATCCCGGAGCAC 58.681 55.000 0.73 0.00 0.00 4.40 R
4267 4578 0.535780 TCCACTTGTCTTGCTGCCAG 60.536 55.000 0.00 0.00 0.00 4.85 R
5264 5662 1.191647 CGAATATTACGAAGCGGGCAC 59.808 52.381 0.00 0.00 0.00 5.01 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
30 31 2.274542 TCTGAGATAGTTTTGGGGGCA 58.725 47.619 0.00 0.00 0.00 5.36
116 117 8.280909 ACGACATGACAACAAATTAAACAATC 57.719 30.769 0.00 0.00 0.00 2.67
175 176 9.553418 AAATTTTTGCATTGAACAAACAAGTAC 57.447 25.926 0.00 0.00 36.77 2.73
176 177 7.658179 TTTTTGCATTGAACAAACAAGTACA 57.342 28.000 0.00 0.00 36.77 2.90
177 178 7.840342 TTTTGCATTGAACAAACAAGTACAT 57.160 28.000 0.00 0.00 36.77 2.29
178 179 8.932945 TTTTGCATTGAACAAACAAGTACATA 57.067 26.923 0.00 0.00 36.77 2.29
179 180 9.539825 TTTTGCATTGAACAAACAAGTACATAT 57.460 25.926 0.00 0.00 36.77 1.78
182 183 9.786105 TGCATTGAACAAACAAGTACATATATG 57.214 29.630 11.29 11.29 33.22 1.78
193 194 9.665719 AACAAGTACATATATGACAACATGACA 57.334 29.630 19.63 0.00 37.87 3.58
305 309 7.544217 ACACTTGAAAATGACAAAAGTAACCAC 59.456 33.333 0.00 0.00 30.20 4.16
315 319 4.036971 ACAAAAGTAACCACGCTGCATAAA 59.963 37.500 0.00 0.00 0.00 1.40
325 329 0.034337 GCTGCATAAATGGGGCATGG 59.966 55.000 0.00 0.00 36.87 3.66
327 331 0.690077 TGCATAAATGGGGCATGGCA 60.690 50.000 22.06 0.94 31.58 4.92
351 355 0.259065 TTGCAAACACCCACACCCTA 59.741 50.000 0.00 0.00 0.00 3.53
366 370 4.021192 CACACCCTAGACATGGCAAAAATT 60.021 41.667 0.00 0.00 0.00 1.82
397 401 0.239347 CAAGCAAAAGGAGGAGCACG 59.761 55.000 0.00 0.00 0.00 5.34
403 407 2.554032 CAAAAGGAGGAGCACGACAAAT 59.446 45.455 0.00 0.00 0.00 2.32
404 408 2.568623 AAGGAGGAGCACGACAAATT 57.431 45.000 0.00 0.00 0.00 1.82
409 413 3.067106 GAGGAGCACGACAAATTTGAGA 58.933 45.455 24.64 0.00 0.00 3.27
422 426 1.937191 TTTGAGAGGAAATTGCCCCC 58.063 50.000 0.00 0.00 0.00 5.40
463 467 1.383456 GCCGCCAAATGCCTCATGTA 61.383 55.000 0.00 0.00 36.24 2.29
484 488 0.099968 TGATCTTTCGACCTACGCCG 59.900 55.000 0.00 0.00 42.26 6.46
488 492 3.951655 TTTCGACCTACGCCGCGAC 62.952 63.158 21.79 0.00 42.26 5.19
542 547 1.752198 CTGTTGTGTCCTTCCCCGA 59.248 57.895 0.00 0.00 0.00 5.14
612 617 3.965258 TGCCGGCATCACCCAACT 61.965 61.111 29.03 0.00 33.26 3.16
613 618 3.443045 GCCGGCATCACCCAACTG 61.443 66.667 24.80 0.00 33.26 3.16
622 627 0.107410 TCACCCAACTGCAACGAACT 60.107 50.000 0.00 0.00 0.00 3.01
625 630 1.134340 ACCCAACTGCAACGAACTACA 60.134 47.619 0.00 0.00 0.00 2.74
627 632 2.286772 CCCAACTGCAACGAACTACAAC 60.287 50.000 0.00 0.00 0.00 3.32
629 634 2.212869 ACTGCAACGAACTACAACGA 57.787 45.000 0.00 0.00 0.00 3.85
632 637 3.371591 ACTGCAACGAACTACAACGAAAA 59.628 39.130 0.00 0.00 0.00 2.29
633 638 4.142859 ACTGCAACGAACTACAACGAAAAA 60.143 37.500 0.00 0.00 0.00 1.94
668 678 4.699735 CCAACATTTTTCTTTATTGGGGGC 59.300 41.667 0.00 0.00 34.25 5.80
713 723 6.838198 TTCGTTTGGTACATATACATGAGC 57.162 37.500 0.00 0.00 39.30 4.26
715 725 4.149922 CGTTTGGTACATATACATGAGCGG 59.850 45.833 0.00 0.00 39.30 5.52
745 755 4.554723 CGAGGCAGGTTTTACTTTCACAAG 60.555 45.833 0.00 0.00 35.92 3.16
853 1124 0.314418 CTCTTCGTCTCGCGTACTCG 60.314 60.000 5.77 7.67 42.13 4.18
867 1138 2.775032 TACTCGCCAGCGTCAAACCC 62.775 60.000 12.32 0.00 40.74 4.11
1125 1397 5.374071 AGGACGAATTTACACTCCTGTTTT 58.626 37.500 0.00 0.00 29.74 2.43
1259 1531 2.928396 ACCTACCGCTGCAAGGGT 60.928 61.111 12.51 12.51 46.92 4.34
1335 1607 0.619255 TGCAGGGGTCCGGAGATTAA 60.619 55.000 3.06 0.00 0.00 1.40
1339 1611 0.765510 GGGGTCCGGAGATTAATGCT 59.234 55.000 3.06 0.00 0.00 3.79
1402 1674 9.640963 GTTATAGGATGTATTAGCTCGACAATT 57.359 33.333 0.00 0.00 0.00 2.32
1406 1678 3.202906 TGTATTAGCTCGACAATTGCCC 58.797 45.455 5.05 0.00 0.00 5.36
1419 1691 0.328258 ATTGCCCCTACTCGTTGCTT 59.672 50.000 0.00 0.00 0.00 3.91
1426 1698 3.635373 CCCCTACTCGTTGCTTACAGATA 59.365 47.826 0.00 0.00 0.00 1.98
1481 1753 3.674410 GCCTGCCTGAAATTTGAGTTAGC 60.674 47.826 3.91 1.21 0.00 3.09
1746 2021 3.996825 GCTTTAGCATGTTGGTCGG 57.003 52.632 0.00 0.00 41.59 4.79
1773 2048 7.040617 ACAATTCTCTGGCTTATATGATGCAAG 60.041 37.037 0.00 0.00 31.67 4.01
1808 2083 4.692155 CCATGGCAAAACTTTCTGGAAATC 59.308 41.667 0.00 0.00 0.00 2.17
1832 2107 3.568538 CCTTTTCAGCTTATGTGTGCAC 58.431 45.455 10.75 10.75 0.00 4.57
1862 2137 7.442062 CCTTCCTTTTTGTAGATTGCACAATTT 59.558 33.333 0.00 0.00 35.89 1.82
2075 2350 4.382147 GCTCTACCTCCTTAAAGTCACCAG 60.382 50.000 0.00 0.00 0.00 4.00
2138 2413 2.990066 ACAGCCTTATGTCTACCAGC 57.010 50.000 0.00 0.00 0.00 4.85
2147 2422 1.357137 TGTCTACCAGCCCAATGTGA 58.643 50.000 0.00 0.00 0.00 3.58
2151 2426 2.308570 TCTACCAGCCCAATGTGAATGT 59.691 45.455 0.00 0.00 0.00 2.71
2186 2461 5.068460 CAGACAGTCTATTCTGGAGGTTAGG 59.932 48.000 1.67 0.00 39.48 2.69
2389 2665 2.100749 CTGGAAACAAAACCACCAGTCC 59.899 50.000 0.00 0.00 41.91 3.85
2445 2721 2.124320 GCTAATCCAAGCGGGGCA 60.124 61.111 0.00 0.00 37.22 5.36
2568 2847 9.881529 CCTCTGTAACTAAATATAAGACGTCTC 57.118 37.037 20.33 1.63 0.00 3.36
2636 2915 9.529325 TGTTATATCTTGATTCTTACGAGGTTG 57.471 33.333 0.00 0.00 0.00 3.77
3157 3438 5.707298 CCATTTGAGTCATACAACAGAGGTT 59.293 40.000 0.00 0.00 37.87 3.50
3158 3439 6.128172 CCATTTGAGTCATACAACAGAGGTTC 60.128 42.308 0.00 0.00 34.21 3.62
3298 3579 1.299316 CGGCAACACAACCAAGCAG 60.299 57.895 0.00 0.00 0.00 4.24
3467 3778 2.084546 GTGCCCTGAAATGTCCAGTAC 58.915 52.381 0.00 0.00 0.00 2.73
3557 3868 5.368989 ACAAGCTAGTAAATATGGAGGCAC 58.631 41.667 0.00 0.00 0.00 5.01
3989 4300 2.561419 TGTTCTTCTCGGTAAGACCAGG 59.439 50.000 0.56 0.00 38.47 4.45
4046 4357 4.774124 TGTAAAGATGAGGCTGAGAATGG 58.226 43.478 0.00 0.00 0.00 3.16
4534 4845 5.632118 AGCATATTCAAGAATCATGAGGCT 58.368 37.500 0.09 0.00 32.50 4.58
4663 4974 0.535797 ACGCTAAGGCTGTAGGGAAC 59.464 55.000 19.70 1.10 37.45 3.62
4805 5116 0.667993 CAAGGCCGAAGAAAGCAACA 59.332 50.000 0.00 0.00 0.00 3.33
4877 5188 4.009675 CCATTTACTAGTTTGGAGCAGCA 58.990 43.478 0.00 0.00 0.00 4.41
4878 5189 4.095483 CCATTTACTAGTTTGGAGCAGCAG 59.905 45.833 0.00 0.00 0.00 4.24
4879 5190 4.351874 TTTACTAGTTTGGAGCAGCAGT 57.648 40.909 0.00 0.00 0.00 4.40
4880 5191 2.938956 ACTAGTTTGGAGCAGCAGTT 57.061 45.000 0.00 0.00 0.00 3.16
4881 5192 2.498167 ACTAGTTTGGAGCAGCAGTTG 58.502 47.619 0.00 0.00 0.00 3.16
4882 5193 1.808945 CTAGTTTGGAGCAGCAGTTGG 59.191 52.381 0.00 0.00 0.00 3.77
4883 5194 0.183492 AGTTTGGAGCAGCAGTTGGA 59.817 50.000 0.00 0.00 0.00 3.53
4884 5195 1.202976 AGTTTGGAGCAGCAGTTGGAT 60.203 47.619 0.00 0.00 0.00 3.41
4885 5196 1.200948 GTTTGGAGCAGCAGTTGGATC 59.799 52.381 0.00 0.00 0.00 3.36
4886 5197 0.322816 TTGGAGCAGCAGTTGGATCC 60.323 55.000 4.20 4.20 0.00 3.36
4887 5198 1.300963 GGAGCAGCAGTTGGATCCA 59.699 57.895 11.44 11.44 0.00 3.41
4944 5256 1.107114 AGATGCCGATTCGAGTCAGT 58.893 50.000 7.83 0.00 0.00 3.41
4986 5298 5.934043 TCAGTTGTGAACATCATAGTCCTTG 59.066 40.000 0.00 0.00 0.00 3.61
4990 5302 7.285401 AGTTGTGAACATCATAGTCCTTGTTTT 59.715 33.333 0.00 0.00 32.73 2.43
5083 5398 8.854312 GTGTTCTTTCTTGTTTTCTTCTCTTTG 58.146 33.333 0.00 0.00 0.00 2.77
5103 5420 6.864165 TCTTTGTTTTTACTTGTGTTGTGTCC 59.136 34.615 0.00 0.00 0.00 4.02
5157 5474 2.812011 CTCCTTTTGGTTTACCCGTCTG 59.188 50.000 0.00 0.00 41.38 3.51
5217 5536 5.181245 CGTGTTGTGAAATGTTCCCTTCTAT 59.819 40.000 0.00 0.00 0.00 1.98
5268 5666 7.690228 TCATTACGTTATAATCTTGTTGTGCC 58.310 34.615 0.00 0.00 0.00 5.01
5275 5708 1.577328 ATCTTGTTGTGCCCGCTTCG 61.577 55.000 0.00 0.00 0.00 3.79
5291 5724 5.277154 CCCGCTTCGTAATATTCGTTGAAAT 60.277 40.000 0.00 0.00 0.00 2.17
5340 5773 5.028549 AGATGAGATTTTCATACACGGCT 57.971 39.130 0.00 0.00 46.51 5.52
5564 5997 8.479313 TGATACACTAATAAGTTCTTGTGCAG 57.521 34.615 0.00 0.00 31.97 4.41
5587 6020 6.262496 CAGCATCAAGGATTCATGTTGTCTAT 59.738 38.462 0.00 0.00 33.41 1.98
5610 6043 7.976135 ATGGCTTCATTCTCAATATGAGTAC 57.024 36.000 7.21 0.00 44.58 2.73
5611 6044 7.129457 TGGCTTCATTCTCAATATGAGTACT 57.871 36.000 0.00 0.00 44.58 2.73
5612 6045 7.212976 TGGCTTCATTCTCAATATGAGTACTC 58.787 38.462 16.32 16.32 44.58 2.59
5613 6046 6.648725 GGCTTCATTCTCAATATGAGTACTCC 59.351 42.308 20.11 3.06 44.58 3.85
5614 6047 7.441017 GCTTCATTCTCAATATGAGTACTCCT 58.559 38.462 20.11 12.93 44.58 3.69
5615 6048 7.930865 GCTTCATTCTCAATATGAGTACTCCTT 59.069 37.037 20.11 10.18 44.58 3.36
5616 6049 9.474920 CTTCATTCTCAATATGAGTACTCCTTC 57.525 37.037 20.11 0.00 44.58 3.46
5617 6050 7.957002 TCATTCTCAATATGAGTACTCCTTCC 58.043 38.462 20.11 0.00 44.58 3.46
5618 6051 7.786943 TCATTCTCAATATGAGTACTCCTTCCT 59.213 37.037 20.11 2.82 44.58 3.36
5619 6052 7.979786 TTCTCAATATGAGTACTCCTTCCTT 57.020 36.000 20.11 4.26 44.58 3.36
5620 6053 7.979786 TCTCAATATGAGTACTCCTTCCTTT 57.020 36.000 20.11 3.10 44.58 3.11
5621 6054 8.012957 TCTCAATATGAGTACTCCTTCCTTTC 57.987 38.462 20.11 0.00 44.58 2.62
5622 6055 7.070074 TCTCAATATGAGTACTCCTTCCTTTCC 59.930 40.741 20.11 0.00 44.58 3.13
5623 6056 5.793030 ATATGAGTACTCCTTCCTTTCCG 57.207 43.478 20.11 0.00 0.00 4.30
5624 6057 2.176889 TGAGTACTCCTTCCTTTCCGG 58.823 52.381 20.11 0.00 0.00 5.14
5625 6058 2.177734 GAGTACTCCTTCCTTTCCGGT 58.822 52.381 12.13 0.00 0.00 5.28
5626 6059 2.566279 GAGTACTCCTTCCTTTCCGGTT 59.434 50.000 12.13 0.00 0.00 4.44
5627 6060 2.977580 AGTACTCCTTCCTTTCCGGTTT 59.022 45.455 0.00 0.00 0.00 3.27
5628 6061 4.162651 AGTACTCCTTCCTTTCCGGTTTA 58.837 43.478 0.00 0.00 0.00 2.01
5629 6062 4.781621 AGTACTCCTTCCTTTCCGGTTTAT 59.218 41.667 0.00 0.00 0.00 1.40
5630 6063 5.960202 AGTACTCCTTCCTTTCCGGTTTATA 59.040 40.000 0.00 0.00 0.00 0.98
5631 6064 5.354842 ACTCCTTCCTTTCCGGTTTATAG 57.645 43.478 0.00 0.00 0.00 1.31
5632 6065 4.163649 ACTCCTTCCTTTCCGGTTTATAGG 59.836 45.833 0.00 3.14 0.00 2.57
5633 6066 3.457012 TCCTTCCTTTCCGGTTTATAGGG 59.543 47.826 0.00 0.00 0.00 3.53
5634 6067 3.211865 CTTCCTTTCCGGTTTATAGGGC 58.788 50.000 0.00 0.00 0.00 5.19
5635 6068 2.484602 TCCTTTCCGGTTTATAGGGCT 58.515 47.619 0.00 0.00 0.00 5.19
5636 6069 2.848071 TCCTTTCCGGTTTATAGGGCTT 59.152 45.455 0.00 0.00 0.00 4.35
5637 6070 4.039339 TCCTTTCCGGTTTATAGGGCTTA 58.961 43.478 0.00 0.00 0.00 3.09
5638 6071 4.661709 TCCTTTCCGGTTTATAGGGCTTAT 59.338 41.667 0.00 0.00 0.00 1.73
5639 6072 5.001874 CCTTTCCGGTTTATAGGGCTTATC 58.998 45.833 0.00 0.00 0.00 1.75
5640 6073 5.221864 CCTTTCCGGTTTATAGGGCTTATCT 60.222 44.000 0.00 0.00 0.00 1.98
5641 6074 5.479124 TTCCGGTTTATAGGGCTTATCTC 57.521 43.478 0.00 0.00 0.00 2.75
5642 6075 4.485875 TCCGGTTTATAGGGCTTATCTCA 58.514 43.478 0.00 0.00 0.00 3.27
5643 6076 4.903049 TCCGGTTTATAGGGCTTATCTCAA 59.097 41.667 0.00 0.00 0.00 3.02
5644 6077 5.367352 TCCGGTTTATAGGGCTTATCTCAAA 59.633 40.000 0.00 0.00 0.00 2.69
5645 6078 6.059484 CCGGTTTATAGGGCTTATCTCAAAA 58.941 40.000 0.00 0.00 0.00 2.44
5646 6079 6.715264 CCGGTTTATAGGGCTTATCTCAAAAT 59.285 38.462 0.00 0.00 0.00 1.82
5647 6080 7.230712 CCGGTTTATAGGGCTTATCTCAAAATT 59.769 37.037 0.00 0.00 0.00 1.82
5648 6081 8.630037 CGGTTTATAGGGCTTATCTCAAAATTT 58.370 33.333 0.00 0.00 0.00 1.82
5687 6120 9.713713 TTTATAAGGCTTAATTTGGTTGTTTCC 57.286 29.630 11.59 0.00 0.00 3.13
5688 6121 4.617253 AGGCTTAATTTGGTTGTTTCCC 57.383 40.909 0.00 0.00 0.00 3.97
5689 6122 3.970640 AGGCTTAATTTGGTTGTTTCCCA 59.029 39.130 0.00 0.00 0.00 4.37
5690 6123 4.597075 AGGCTTAATTTGGTTGTTTCCCAT 59.403 37.500 0.00 0.00 0.00 4.00
5691 6124 4.935205 GGCTTAATTTGGTTGTTTCCCATC 59.065 41.667 0.00 0.00 0.00 3.51
5692 6125 5.512232 GGCTTAATTTGGTTGTTTCCCATCA 60.512 40.000 0.00 0.00 0.00 3.07
5693 6126 5.408299 GCTTAATTTGGTTGTTTCCCATCAC 59.592 40.000 0.00 0.00 0.00 3.06
5694 6127 6.485830 TTAATTTGGTTGTTTCCCATCACA 57.514 33.333 0.00 0.00 0.00 3.58
5695 6128 5.565455 AATTTGGTTGTTTCCCATCACAT 57.435 34.783 0.00 0.00 0.00 3.21
5696 6129 4.333913 TTTGGTTGTTTCCCATCACATG 57.666 40.909 0.00 0.00 0.00 3.21
5697 6130 2.956132 TGGTTGTTTCCCATCACATGT 58.044 42.857 0.00 0.00 0.00 3.21
5698 6131 3.303938 TGGTTGTTTCCCATCACATGTT 58.696 40.909 0.00 0.00 0.00 2.71
5699 6132 3.320541 TGGTTGTTTCCCATCACATGTTC 59.679 43.478 0.00 0.00 0.00 3.18
5700 6133 3.320541 GGTTGTTTCCCATCACATGTTCA 59.679 43.478 0.00 0.00 0.00 3.18
5701 6134 4.549458 GTTGTTTCCCATCACATGTTCAG 58.451 43.478 0.00 0.00 0.00 3.02
5702 6135 4.097551 TGTTTCCCATCACATGTTCAGA 57.902 40.909 0.00 0.00 0.00 3.27
5703 6136 4.665451 TGTTTCCCATCACATGTTCAGAT 58.335 39.130 0.00 0.00 0.00 2.90
5704 6137 5.078949 TGTTTCCCATCACATGTTCAGATT 58.921 37.500 0.00 0.00 0.00 2.40
5705 6138 5.539574 TGTTTCCCATCACATGTTCAGATTT 59.460 36.000 0.00 0.00 0.00 2.17
5706 6139 5.902613 TTCCCATCACATGTTCAGATTTC 57.097 39.130 0.00 0.00 0.00 2.17
5707 6140 4.920999 TCCCATCACATGTTCAGATTTCA 58.079 39.130 0.00 0.00 0.00 2.69
5708 6141 5.323581 TCCCATCACATGTTCAGATTTCAA 58.676 37.500 0.00 0.00 0.00 2.69
5709 6142 5.416639 TCCCATCACATGTTCAGATTTCAAG 59.583 40.000 0.00 0.00 0.00 3.02
5710 6143 5.416639 CCCATCACATGTTCAGATTTCAAGA 59.583 40.000 0.00 0.00 0.00 3.02
5711 6144 6.096423 CCCATCACATGTTCAGATTTCAAGAT 59.904 38.462 0.00 0.00 0.00 2.40
5712 6145 7.363530 CCCATCACATGTTCAGATTTCAAGATT 60.364 37.037 0.00 0.00 0.00 2.40
5713 6146 7.701078 CCATCACATGTTCAGATTTCAAGATTC 59.299 37.037 0.00 0.00 0.00 2.52
5714 6147 7.748691 TCACATGTTCAGATTTCAAGATTCA 57.251 32.000 0.00 0.00 0.00 2.57
5715 6148 8.344446 TCACATGTTCAGATTTCAAGATTCAT 57.656 30.769 0.00 0.00 0.00 2.57
5716 6149 8.799367 TCACATGTTCAGATTTCAAGATTCATT 58.201 29.630 0.00 0.00 0.00 2.57
5730 6163 8.360325 TCAAGATTCATTAAATCATTGCATGC 57.640 30.769 11.82 11.82 45.34 4.06
5731 6164 7.982354 TCAAGATTCATTAAATCATTGCATGCA 59.018 29.630 18.46 18.46 45.34 3.96
5732 6165 8.608317 CAAGATTCATTAAATCATTGCATGCAA 58.392 29.630 33.57 33.57 45.34 4.08
5733 6166 8.365399 AGATTCATTAAATCATTGCATGCAAG 57.635 30.769 34.15 25.40 45.34 4.01
5734 6167 7.985184 AGATTCATTAAATCATTGCATGCAAGT 59.015 29.630 34.15 21.32 45.34 3.16
5735 6168 9.251792 GATTCATTAAATCATTGCATGCAAGTA 57.748 29.630 34.15 25.25 42.89 2.24
5736 6169 9.772973 ATTCATTAAATCATTGCATGCAAGTAT 57.227 25.926 34.15 26.18 39.47 2.12
5737 6170 9.602568 TTCATTAAATCATTGCATGCAAGTATT 57.397 25.926 34.15 29.40 39.47 1.89
5832 6265 8.994429 TTGTTTGAGAAAAACAAGAGCATTAA 57.006 26.923 11.29 0.00 42.96 1.40
5833 6266 9.598517 TTGTTTGAGAAAAACAAGAGCATTAAT 57.401 25.926 11.29 0.00 42.96 1.40
5834 6267 9.598517 TGTTTGAGAAAAACAAGAGCATTAATT 57.401 25.926 1.33 0.00 37.22 1.40
5837 6270 9.912634 TTGAGAAAAACAAGAGCATTAATTAGG 57.087 29.630 0.00 0.00 0.00 2.69
5838 6271 9.077885 TGAGAAAAACAAGAGCATTAATTAGGT 57.922 29.630 0.00 0.00 0.00 3.08
5839 6272 9.346725 GAGAAAAACAAGAGCATTAATTAGGTG 57.653 33.333 0.00 0.00 0.00 4.00
5840 6273 7.814587 AGAAAAACAAGAGCATTAATTAGGTGC 59.185 33.333 13.92 13.92 39.10 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.382488 CCCAAAACTATCTCAGATACGTACATG 59.618 40.741 0.00 0.00 0.00 3.21
2 3 6.183360 CCCCAAAACTATCTCAGATACGTACA 60.183 42.308 0.00 0.00 0.00 2.90
3 4 6.214399 CCCCAAAACTATCTCAGATACGTAC 58.786 44.000 0.00 0.00 0.00 3.67
5 6 4.101119 CCCCCAAAACTATCTCAGATACGT 59.899 45.833 0.00 0.00 0.00 3.57
6 7 4.632153 CCCCCAAAACTATCTCAGATACG 58.368 47.826 0.00 0.00 0.00 3.06
7 8 4.141482 TGCCCCCAAAACTATCTCAGATAC 60.141 45.833 0.00 0.00 0.00 2.24
8 9 4.044308 TGCCCCCAAAACTATCTCAGATA 58.956 43.478 0.00 0.00 0.00 1.98
9 10 2.852449 TGCCCCCAAAACTATCTCAGAT 59.148 45.455 0.00 0.00 0.00 2.90
10 11 2.026262 GTGCCCCCAAAACTATCTCAGA 60.026 50.000 0.00 0.00 0.00 3.27
11 12 2.369394 GTGCCCCCAAAACTATCTCAG 58.631 52.381 0.00 0.00 0.00 3.35
12 13 1.339631 CGTGCCCCCAAAACTATCTCA 60.340 52.381 0.00 0.00 0.00 3.27
13 14 1.379527 CGTGCCCCCAAAACTATCTC 58.620 55.000 0.00 0.00 0.00 2.75
14 15 0.034477 CCGTGCCCCCAAAACTATCT 60.034 55.000 0.00 0.00 0.00 1.98
15 16 1.035385 CCCGTGCCCCCAAAACTATC 61.035 60.000 0.00 0.00 0.00 2.08
16 17 1.000145 CCCGTGCCCCCAAAACTAT 60.000 57.895 0.00 0.00 0.00 2.12
17 18 2.437002 CCCGTGCCCCCAAAACTA 59.563 61.111 0.00 0.00 0.00 2.24
18 19 4.614036 CCCCGTGCCCCCAAAACT 62.614 66.667 0.00 0.00 0.00 2.66
59 60 2.335712 GCTTTCAAGCCCGGTCCTG 61.336 63.158 0.00 0.00 46.20 3.86
70 71 7.815549 TGTCGTAATGAATGTAGTAGCTTTCAA 59.184 33.333 0.00 0.00 36.55 2.69
81 82 7.659652 TTGTTGTCATGTCGTAATGAATGTA 57.340 32.000 4.69 0.00 38.28 2.29
149 150 9.553418 GTACTTGTTTGTTCAATGCAAAAATTT 57.447 25.926 0.00 0.00 37.54 1.82
150 151 8.725148 TGTACTTGTTTGTTCAATGCAAAAATT 58.275 25.926 0.00 0.00 37.54 1.82
151 152 8.261492 TGTACTTGTTTGTTCAATGCAAAAAT 57.739 26.923 0.00 0.00 37.54 1.82
152 153 7.658179 TGTACTTGTTTGTTCAATGCAAAAA 57.342 28.000 0.00 0.00 37.54 1.94
153 154 7.840342 ATGTACTTGTTTGTTCAATGCAAAA 57.160 28.000 0.00 0.00 37.54 2.44
156 157 9.786105 CATATATGTACTTGTTTGTTCAATGCA 57.214 29.630 4.43 0.00 0.00 3.96
167 168 9.665719 TGTCATGTTGTCATATATGTACTTGTT 57.334 29.630 12.42 0.00 32.47 2.83
168 169 9.665719 TTGTCATGTTGTCATATATGTACTTGT 57.334 29.630 12.42 0.00 32.47 3.16
180 181 8.192774 GGATGTGATATTTTGTCATGTTGTCAT 58.807 33.333 0.00 0.00 34.21 3.06
181 182 7.176340 TGGATGTGATATTTTGTCATGTTGTCA 59.824 33.333 0.00 0.00 0.00 3.58
182 183 7.537715 TGGATGTGATATTTTGTCATGTTGTC 58.462 34.615 0.00 0.00 0.00 3.18
183 184 7.465353 TGGATGTGATATTTTGTCATGTTGT 57.535 32.000 0.00 0.00 0.00 3.32
184 185 8.760103 TTTGGATGTGATATTTTGTCATGTTG 57.240 30.769 0.00 0.00 0.00 3.33
185 186 9.947433 ATTTTGGATGTGATATTTTGTCATGTT 57.053 25.926 0.00 0.00 0.00 2.71
186 187 9.373603 CATTTTGGATGTGATATTTTGTCATGT 57.626 29.630 0.00 0.00 0.00 3.21
187 188 9.589111 TCATTTTGGATGTGATATTTTGTCATG 57.411 29.630 0.00 0.00 0.00 3.07
188 189 9.590451 GTCATTTTGGATGTGATATTTTGTCAT 57.410 29.630 0.00 0.00 0.00 3.06
189 190 8.805175 AGTCATTTTGGATGTGATATTTTGTCA 58.195 29.630 0.00 0.00 0.00 3.58
305 309 0.319211 CATGCCCCATTTATGCAGCG 60.319 55.000 0.00 0.00 38.58 5.18
315 319 0.834612 CAATTCTTGCCATGCCCCAT 59.165 50.000 0.00 0.00 0.00 4.00
327 331 2.158971 GGTGTGGGTGTTTGCAATTCTT 60.159 45.455 0.00 0.00 0.00 2.52
334 338 0.109723 TCTAGGGTGTGGGTGTTTGC 59.890 55.000 0.00 0.00 0.00 3.68
351 355 5.716228 TCCATGTAGAATTTTTGCCATGTCT 59.284 36.000 0.00 0.00 0.00 3.41
366 370 3.820467 CCTTTTGCTTGTGTCCATGTAGA 59.180 43.478 0.00 0.00 0.00 2.59
397 401 4.931601 GGGCAATTTCCTCTCAAATTTGTC 59.068 41.667 17.47 0.00 34.37 3.18
403 407 1.148867 TGGGGGCAATTTCCTCTCAAA 59.851 47.619 0.00 0.00 0.00 2.69
404 408 0.783206 TGGGGGCAATTTCCTCTCAA 59.217 50.000 0.00 0.00 0.00 3.02
409 413 4.073425 TCTTTATTGGGGGCAATTTCCT 57.927 40.909 0.00 0.00 0.00 3.36
436 440 2.094675 GGCATTTGGCGGCTATGATAT 58.905 47.619 22.30 0.00 46.16 1.63
438 442 0.178981 AGGCATTTGGCGGCTATGAT 60.179 50.000 22.30 11.00 46.16 2.45
439 443 0.819259 GAGGCATTTGGCGGCTATGA 60.819 55.000 22.30 3.32 46.16 2.15
440 444 1.102809 TGAGGCATTTGGCGGCTATG 61.103 55.000 11.43 14.62 46.16 2.23
441 445 0.178981 ATGAGGCATTTGGCGGCTAT 60.179 50.000 11.43 0.38 46.16 2.97
442 446 1.102809 CATGAGGCATTTGGCGGCTA 61.103 55.000 11.43 0.00 46.16 3.93
443 447 2.043652 ATGAGGCATTTGGCGGCT 60.044 55.556 11.43 0.00 46.16 5.52
463 467 2.798499 CGGCGTAGGTCGAAAGATCATT 60.798 50.000 2.72 0.00 46.20 2.57
475 479 3.677648 AAGTGTCGCGGCGTAGGT 61.678 61.111 22.90 3.25 0.00 3.08
484 488 2.477176 TTGTGGTGGCAAGTGTCGC 61.477 57.895 0.00 0.00 0.00 5.19
488 492 1.437160 GGTGTTGTGGTGGCAAGTG 59.563 57.895 0.00 0.00 0.00 3.16
489 493 2.118404 CGGTGTTGTGGTGGCAAGT 61.118 57.895 0.00 0.00 0.00 3.16
499 503 1.944024 TCTGCGATTTTTCGGTGTTGT 59.056 42.857 0.00 0.00 0.00 3.32
542 547 4.986645 TGCATGCAGTCACCGCGT 62.987 61.111 18.46 0.00 0.00 6.01
553 558 1.339711 GTTTCGATGTGGTTGCATGC 58.660 50.000 11.82 11.82 0.00 4.06
612 617 4.337985 TTTTTCGTTGTAGTTCGTTGCA 57.662 36.364 0.00 0.00 0.00 4.08
633 638 3.535280 AAATGTTGGGCGTCACTTTTT 57.465 38.095 0.00 0.00 0.00 1.94
647 657 4.041075 ACGCCCCCAATAAAGAAAAATGTT 59.959 37.500 0.00 0.00 0.00 2.71
668 678 8.060090 ACGAAAAATGTGAAAAGACTACTTACG 58.940 33.333 0.00 0.00 35.05 3.18
853 1124 3.723348 GTCGGGTTTGACGCTGGC 61.723 66.667 0.00 0.00 0.00 4.85
867 1138 0.669625 GAGGTTTCCTTCCACCGTCG 60.670 60.000 0.00 0.00 38.21 5.12
941 1212 2.486370 GGAGAGAAAAGATGGGCTAGCC 60.486 54.545 26.55 26.55 0.00 3.93
1071 1343 3.470888 CGAGGGAAGCACGGGGAT 61.471 66.667 0.00 0.00 0.00 3.85
1125 1397 1.356124 AGCAGAAGAAGGCTCCAGAA 58.644 50.000 0.00 0.00 34.76 3.02
1318 1590 1.543429 GCATTAATCTCCGGACCCCTG 60.543 57.143 0.00 0.00 0.00 4.45
1402 1674 0.248289 GTAAGCAACGAGTAGGGGCA 59.752 55.000 0.00 0.00 0.00 5.36
1406 1678 6.199154 CACATTATCTGTAAGCAACGAGTAGG 59.801 42.308 0.00 0.00 35.91 3.18
1419 1691 6.070481 TGAGCCTTTACCACACATTATCTGTA 60.070 38.462 0.00 0.00 35.91 2.74
1426 1698 5.570320 ACTTATGAGCCTTTACCACACATT 58.430 37.500 0.00 0.00 0.00 2.71
1481 1753 8.915654 GCAAAACTAATTAATTCAGTGAACCAG 58.084 33.333 7.96 2.23 0.00 4.00
1746 2021 6.429078 TGCATCATATAAGCCAGAGAATTGTC 59.571 38.462 0.00 0.00 0.00 3.18
1808 2083 2.493278 CACACATAAGCTGAAAAGGGGG 59.507 50.000 0.00 0.00 0.00 5.40
1832 2107 4.475944 CAATCTACAAAAAGGAAGGTGCG 58.524 43.478 0.00 0.00 0.00 5.34
1862 2137 5.617529 CGACTACAATTTCTGATTGCAGCAA 60.618 40.000 11.07 11.07 42.01 3.91
1893 2168 2.808906 ATTTACACTCTTGGAGGGGC 57.191 50.000 1.82 0.00 37.40 5.80
2075 2350 0.807496 GCCTTCTCATGTGCACCTTC 59.193 55.000 15.69 0.00 0.00 3.46
2138 2413 2.164219 GCTGTGGTACATTCACATTGGG 59.836 50.000 4.23 0.00 44.52 4.12
2147 2422 1.419762 TGTCTGTGGCTGTGGTACATT 59.580 47.619 0.00 0.00 44.52 2.71
2151 2426 0.679505 GACTGTCTGTGGCTGTGGTA 59.320 55.000 0.00 0.00 0.00 3.25
2338 2614 9.227777 GGAAATTAGCTATGACCGGTAATTTAT 57.772 33.333 10.53 1.50 46.47 1.40
2363 2639 1.365999 GGTTTTGTTTCCAGGCGGG 59.634 57.895 0.00 0.00 38.37 6.13
2389 2665 0.872881 CGGTTTAGGATACACGCCCG 60.873 60.000 0.00 0.00 41.41 6.13
2445 2721 5.806654 ACAATGCAAACTTGACCCTTTAT 57.193 34.783 5.55 0.00 0.00 1.40
2696 2977 7.271511 GGATTGATGTATCCTACAGATGATCC 58.728 42.308 0.00 0.00 42.77 3.36
2938 3219 1.059584 TGGCCCTCTCCAACAGTTGA 61.060 55.000 15.36 0.37 32.18 3.18
3157 3438 3.255149 GGAGACTGAAAGGTACAGAACGA 59.745 47.826 0.00 0.00 39.30 3.85
3158 3439 3.576648 GGAGACTGAAAGGTACAGAACG 58.423 50.000 0.00 0.00 39.30 3.95
3208 3489 5.068329 TCACAACAACACATATTGCTTCCAA 59.932 36.000 0.00 0.00 32.47 3.53
3298 3579 1.318576 CCCAAATAATCCCGGAGCAC 58.681 55.000 0.73 0.00 0.00 4.40
3557 3868 3.456277 AGCAGAACCCCAATTAGGAGTAG 59.544 47.826 0.78 0.00 41.22 2.57
3657 3968 6.218746 GTTTTGCTCATTCAGAAACTCCAAT 58.781 36.000 0.00 0.00 0.00 3.16
3658 3969 5.451798 GGTTTTGCTCATTCAGAAACTCCAA 60.452 40.000 0.00 0.00 32.39 3.53
4046 4357 4.040952 AGGGAGTACATAGATCCAATGCAC 59.959 45.833 0.00 3.89 34.62 4.57
4267 4578 0.535780 TCCACTTGTCTTGCTGCCAG 60.536 55.000 0.00 0.00 0.00 4.85
4410 4721 7.948034 ATTCCCCATAAAAACTCGATTGTTA 57.052 32.000 0.00 0.00 0.00 2.41
4534 4845 1.699083 TCCTCCACAATGCTTGTCTCA 59.301 47.619 0.00 0.00 43.23 3.27
4663 4974 3.251245 AGTCCGCGATATGAGTAACAGAG 59.749 47.826 8.23 0.00 0.00 3.35
4805 5116 5.105513 CCACAGGACCTTTAGTTTTGTTTGT 60.106 40.000 0.00 0.00 0.00 2.83
4877 5188 6.312529 AGCATCAAATCATATGGATCCAACT 58.687 36.000 20.67 5.70 34.28 3.16
4878 5189 6.585695 AGCATCAAATCATATGGATCCAAC 57.414 37.500 20.67 0.00 34.28 3.77
4879 5190 5.413523 CGAGCATCAAATCATATGGATCCAA 59.586 40.000 20.67 8.82 31.73 3.53
4880 5191 4.939439 CGAGCATCAAATCATATGGATCCA 59.061 41.667 18.88 18.88 31.73 3.41
4881 5192 4.940046 ACGAGCATCAAATCATATGGATCC 59.060 41.667 4.20 4.20 31.73 3.36
4882 5193 5.873712 AGACGAGCATCAAATCATATGGATC 59.126 40.000 2.13 0.00 31.73 3.36
4883 5194 5.642491 CAGACGAGCATCAAATCATATGGAT 59.358 40.000 2.13 0.00 33.79 3.41
4884 5195 4.992951 CAGACGAGCATCAAATCATATGGA 59.007 41.667 2.13 0.00 33.17 3.41
4885 5196 4.153655 CCAGACGAGCATCAAATCATATGG 59.846 45.833 2.13 0.00 33.17 2.74
4886 5197 4.992951 TCCAGACGAGCATCAAATCATATG 59.007 41.667 0.00 0.00 33.17 1.78
4887 5198 5.219343 TCCAGACGAGCATCAAATCATAT 57.781 39.130 0.00 0.00 33.17 1.78
4986 5298 6.178324 ACTATAACCTAAGTGGAGGCAAAAC 58.822 40.000 0.00 0.00 40.65 2.43
4990 5302 5.486063 TGAAACTATAACCTAAGTGGAGGCA 59.514 40.000 0.00 0.00 40.65 4.75
5083 5398 5.945155 TCAGGACACAACACAAGTAAAAAC 58.055 37.500 0.00 0.00 0.00 2.43
5157 5474 6.955963 CACTAAAACTCGACAGCATTTATGAC 59.044 38.462 0.00 0.00 0.00 3.06
5217 5536 8.038944 AGAATGAGAATACGGCTAAAACACTAA 58.961 33.333 0.00 0.00 0.00 2.24
5264 5662 1.191647 CGAATATTACGAAGCGGGCAC 59.808 52.381 0.00 0.00 0.00 5.01
5266 5664 1.494824 ACGAATATTACGAAGCGGGC 58.505 50.000 12.27 0.00 34.70 6.13
5268 5666 4.765281 TTCAACGAATATTACGAAGCGG 57.235 40.909 12.27 1.11 34.70 5.52
5313 5746 6.142480 CCGTGTATGAAAATCTCATCTCGTAC 59.858 42.308 0.00 0.00 44.05 3.67
5316 5749 4.084849 GCCGTGTATGAAAATCTCATCTCG 60.085 45.833 0.00 0.00 44.05 4.04
5516 5949 8.193953 TCATGACATACTGAGATAATTAGGCA 57.806 34.615 0.00 0.00 0.00 4.75
5564 5997 4.978083 AGACAACATGAATCCTTGATGC 57.022 40.909 0.00 0.00 0.00 3.91
5610 6043 4.444449 CCCTATAAACCGGAAAGGAAGGAG 60.444 50.000 9.46 0.00 45.00 3.69
5611 6044 3.457012 CCCTATAAACCGGAAAGGAAGGA 59.543 47.826 9.46 0.00 45.00 3.36
5612 6045 3.816994 CCCTATAAACCGGAAAGGAAGG 58.183 50.000 9.46 7.50 45.00 3.46
5613 6046 3.118000 AGCCCTATAAACCGGAAAGGAAG 60.118 47.826 9.46 0.00 45.00 3.46
5614 6047 2.848071 AGCCCTATAAACCGGAAAGGAA 59.152 45.455 9.46 0.00 45.00 3.36
5615 6048 2.484602 AGCCCTATAAACCGGAAAGGA 58.515 47.619 9.46 0.00 45.00 3.36
5617 6050 5.866207 AGATAAGCCCTATAAACCGGAAAG 58.134 41.667 9.46 0.00 0.00 2.62
5618 6051 5.367352 TGAGATAAGCCCTATAAACCGGAAA 59.633 40.000 9.46 0.00 0.00 3.13
5619 6052 4.903049 TGAGATAAGCCCTATAAACCGGAA 59.097 41.667 9.46 0.00 0.00 4.30
5620 6053 4.485875 TGAGATAAGCCCTATAAACCGGA 58.514 43.478 9.46 0.00 0.00 5.14
5621 6054 4.884668 TGAGATAAGCCCTATAAACCGG 57.115 45.455 0.00 0.00 0.00 5.28
5622 6055 7.745620 ATTTTGAGATAAGCCCTATAAACCG 57.254 36.000 0.00 0.00 0.00 4.44
5661 6094 9.713713 GGAAACAACCAAATTAAGCCTTATAAA 57.286 29.630 0.00 0.00 0.00 1.40
5662 6095 8.315482 GGGAAACAACCAAATTAAGCCTTATAA 58.685 33.333 0.00 0.00 0.00 0.98
5663 6096 7.455008 TGGGAAACAACCAAATTAAGCCTTATA 59.545 33.333 0.00 0.00 34.44 0.98
5664 6097 6.271159 TGGGAAACAACCAAATTAAGCCTTAT 59.729 34.615 0.00 0.00 34.44 1.73
5665 6098 5.602978 TGGGAAACAACCAAATTAAGCCTTA 59.397 36.000 0.00 0.00 34.44 2.69
5666 6099 4.410555 TGGGAAACAACCAAATTAAGCCTT 59.589 37.500 0.00 0.00 34.44 4.35
5667 6100 3.970640 TGGGAAACAACCAAATTAAGCCT 59.029 39.130 0.00 0.00 34.44 4.58
5668 6101 4.344359 TGGGAAACAACCAAATTAAGCC 57.656 40.909 0.00 0.00 34.44 4.35
5669 6102 5.408299 GTGATGGGAAACAACCAAATTAAGC 59.592 40.000 0.00 0.00 42.17 3.09
5670 6103 6.520272 TGTGATGGGAAACAACCAAATTAAG 58.480 36.000 0.00 0.00 42.17 1.85
5671 6104 6.485830 TGTGATGGGAAACAACCAAATTAA 57.514 33.333 0.00 0.00 42.17 1.40
5672 6105 6.042552 ACATGTGATGGGAAACAACCAAATTA 59.957 34.615 0.00 0.00 42.17 1.40
5673 6106 5.163216 ACATGTGATGGGAAACAACCAAATT 60.163 36.000 0.00 0.00 42.17 1.82
5674 6107 4.347583 ACATGTGATGGGAAACAACCAAAT 59.652 37.500 0.00 0.00 42.17 2.32
5675 6108 3.708631 ACATGTGATGGGAAACAACCAAA 59.291 39.130 0.00 0.00 42.17 3.28
5676 6109 3.303938 ACATGTGATGGGAAACAACCAA 58.696 40.909 0.00 0.00 42.17 3.67
5677 6110 2.956132 ACATGTGATGGGAAACAACCA 58.044 42.857 0.00 0.00 43.22 3.67
5678 6111 3.320541 TGAACATGTGATGGGAAACAACC 59.679 43.478 0.00 0.00 33.60 3.77
5679 6112 4.278170 TCTGAACATGTGATGGGAAACAAC 59.722 41.667 0.00 0.00 33.60 3.32
5680 6113 4.468713 TCTGAACATGTGATGGGAAACAA 58.531 39.130 0.00 0.00 33.60 2.83
5681 6114 4.097551 TCTGAACATGTGATGGGAAACA 57.902 40.909 0.00 0.00 33.60 2.83
5682 6115 5.649782 AATCTGAACATGTGATGGGAAAC 57.350 39.130 0.00 0.00 33.60 2.78
5683 6116 5.774184 TGAAATCTGAACATGTGATGGGAAA 59.226 36.000 0.00 0.00 33.60 3.13
5684 6117 5.323581 TGAAATCTGAACATGTGATGGGAA 58.676 37.500 0.00 0.00 33.60 3.97
5685 6118 4.920999 TGAAATCTGAACATGTGATGGGA 58.079 39.130 0.00 0.00 33.60 4.37
5686 6119 5.416639 TCTTGAAATCTGAACATGTGATGGG 59.583 40.000 0.00 0.00 33.60 4.00
5687 6120 6.505044 TCTTGAAATCTGAACATGTGATGG 57.495 37.500 0.00 0.00 33.60 3.51
5688 6121 8.241367 TGAATCTTGAAATCTGAACATGTGATG 58.759 33.333 0.00 0.00 0.00 3.07
5689 6122 8.344446 TGAATCTTGAAATCTGAACATGTGAT 57.656 30.769 0.00 0.00 0.00 3.06
5690 6123 7.748691 TGAATCTTGAAATCTGAACATGTGA 57.251 32.000 0.00 0.00 0.00 3.58
5691 6124 8.981724 AATGAATCTTGAAATCTGAACATGTG 57.018 30.769 0.00 0.00 0.00 3.21
5744 6177 8.984764 GCATAATGTACATGCATTGATCAATTT 58.015 29.630 18.41 9.39 46.47 1.82
5745 6178 8.528917 GCATAATGTACATGCATTGATCAATT 57.471 30.769 18.41 6.51 46.47 2.32
5801 6234 9.034544 GCTCTTGTTTTTCTCAAACAATTATGT 57.965 29.630 12.10 0.00 45.56 2.29
5802 6235 9.033481 TGCTCTTGTTTTTCTCAAACAATTATG 57.967 29.630 12.10 3.11 45.56 1.90
5803 6236 9.768662 ATGCTCTTGTTTTTCTCAAACAATTAT 57.231 25.926 12.10 4.13 45.56 1.28
5804 6237 9.598517 AATGCTCTTGTTTTTCTCAAACAATTA 57.401 25.926 12.10 4.89 45.56 1.40
5805 6238 8.496707 AATGCTCTTGTTTTTCTCAAACAATT 57.503 26.923 12.10 2.83 45.56 2.32
5806 6239 9.598517 TTAATGCTCTTGTTTTTCTCAAACAAT 57.401 25.926 12.10 1.55 45.56 2.71
5807 6240 8.994429 TTAATGCTCTTGTTTTTCTCAAACAA 57.006 26.923 11.36 11.36 44.85 2.83
5808 6241 9.598517 AATTAATGCTCTTGTTTTTCTCAAACA 57.401 25.926 0.00 0.00 38.26 2.83
5811 6244 9.912634 CCTAATTAATGCTCTTGTTTTTCTCAA 57.087 29.630 0.00 0.00 0.00 3.02
5812 6245 9.077885 ACCTAATTAATGCTCTTGTTTTTCTCA 57.922 29.630 0.00 0.00 0.00 3.27
5813 6246 9.346725 CACCTAATTAATGCTCTTGTTTTTCTC 57.653 33.333 0.00 0.00 0.00 2.87
5814 6247 7.814587 GCACCTAATTAATGCTCTTGTTTTTCT 59.185 33.333 12.17 0.00 36.40 2.52
5815 6248 7.814587 AGCACCTAATTAATGCTCTTGTTTTTC 59.185 33.333 15.10 0.00 46.68 2.29
5816 6249 7.670364 AGCACCTAATTAATGCTCTTGTTTTT 58.330 30.769 15.10 0.00 46.68 1.94
5817 6250 7.232118 AGCACCTAATTAATGCTCTTGTTTT 57.768 32.000 15.10 0.00 46.68 2.43
5818 6251 6.840780 AGCACCTAATTAATGCTCTTGTTT 57.159 33.333 15.10 0.00 46.68 2.83


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

AutoCloner maintained by Alex Coulton.