Multiple sequence alignment - TraesCS5B01G521300

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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 TraesCS5B01G521300 chr5B 100.000 5558 0 0 1 5558 683339169 683344726 0.000000e+00 10264.0
1 TraesCS5B01G521300 chr5B 78.186 408 63 19 203 603 231263975 231263587 2.590000e-58 237.0
2 TraesCS5B01G521300 chr5D 95.600 3682 137 11 1222 4894 542664457 542660792 0.000000e+00 5879.0
3 TraesCS5B01G521300 chr5D 87.310 197 24 1 2 197 444472350 444472546 2.010000e-54 224.0
4 TraesCS5B01G521300 chr4A 94.397 3855 136 33 859 4693 626337968 626341762 0.000000e+00 5849.0
5 TraesCS5B01G521300 chr4A 77.116 1997 392 36 2286 4271 531075865 531073923 0.000000e+00 1096.0
6 TraesCS5B01G521300 chr4A 90.774 672 41 8 4895 5558 235648075 235647417 0.000000e+00 878.0
7 TraesCS5B01G521300 chr4A 81.515 779 105 14 63 830 626336817 626337567 6.160000e-169 604.0
8 TraesCS5B01G521300 chr4A 93.197 147 7 1 4751 4894 626341785 626341931 4.360000e-51 213.0
9 TraesCS5B01G521300 chr4B 88.821 653 46 13 4901 5546 324972665 324972033 0.000000e+00 776.0
10 TraesCS5B01G521300 chr4D 77.504 1178 246 15 2286 3457 65114100 65112936 0.000000e+00 689.0
11 TraesCS5B01G521300 chr4D 90.541 148 10 3 4896 5043 230471072 230470929 5.680000e-45 193.0
12 TraesCS5B01G521300 chr7D 76.774 620 86 27 210 810 294010492 294011072 1.510000e-75 294.0
13 TraesCS5B01G521300 chr1A 75.069 722 131 26 203 901 132261113 132261808 1.960000e-74 291.0
14 TraesCS5B01G521300 chr2D 89.340 197 17 4 6 200 136984716 136984522 1.550000e-60 244.0
15 TraesCS5B01G521300 chr2D 86.869 198 25 1 7 203 607666051 607665854 2.610000e-53 220.0
16 TraesCS5B01G521300 chr3B 78.462 390 62 9 203 578 748626946 748626565 9.310000e-58 235.0
17 TraesCS5B01G521300 chr1D 85.981 214 27 3 2 213 111493221 111493009 5.600000e-55 226.0
18 TraesCS5B01G521300 chr1D 78.341 217 37 5 205 421 211419114 211419320 1.260000e-26 132.0
19 TraesCS5B01G521300 chr1D 80.892 157 15 9 268 421 263203609 263203753 5.890000e-20 110.0
20 TraesCS5B01G521300 chr2B 87.629 194 21 2 8 200 195541172 195540981 7.250000e-54 222.0
21 TraesCS5B01G521300 chr2B 87.310 197 22 3 2 197 270202763 270202569 7.250000e-54 222.0
22 TraesCS5B01G521300 chr2B 77.219 338 66 9 342 677 768407322 768406994 2.640000e-43 187.0
23 TraesCS5B01G521300 chr2B 78.409 176 27 4 203 378 754886411 754886247 2.740000e-18 104.0
24 TraesCS5B01G521300 chrUn 85.446 213 29 2 2 213 50078801 50079012 2.610000e-53 220.0
25 TraesCS5B01G521300 chrUn 85.990 207 27 2 8 213 50128564 50128359 2.610000e-53 220.0
26 TraesCS5B01G521300 chr6D 76.535 456 69 23 226 671 355884932 355884505 1.210000e-51 215.0
27 TraesCS5B01G521300 chr6D 82.243 214 25 8 203 415 48871555 48871354 7.400000e-39 172.0
28 TraesCS5B01G521300 chr1B 79.928 279 45 6 220 497 183250775 183251043 1.580000e-45 195.0
29 TraesCS5B01G521300 chr1B 96.970 33 1 0 4701 4733 685275441 685275409 7.780000e-04 56.5
30 TraesCS5B01G521300 chr6B 74.610 449 85 17 229 671 536861406 536860981 2.660000e-38 171.0
31 TraesCS5B01G521300 chr3D 76.033 363 59 16 205 564 447552489 447552152 4.460000e-36 163.0
32 TraesCS5B01G521300 chr3D 75.429 350 69 10 203 548 272938009 272938345 2.680000e-33 154.0
33 TraesCS5B01G521300 chr2A 96.970 33 1 0 4701 4733 38931630 38931598 7.780000e-04 56.5
34 TraesCS5B01G521300 chr3A 100.000 28 0 0 4702 4729 41222343 41222316 1.000000e-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 TraesCS5B01G521300 chr5B 683339169 683344726 5557 False 10264 10264 100.000 1 5558 1 chr5B.!!$F1 5557
1 TraesCS5B01G521300 chr5D 542660792 542664457 3665 True 5879 5879 95.600 1222 4894 1 chr5D.!!$R1 3672
2 TraesCS5B01G521300 chr4A 626336817 626341931 5114 False 2222 5849 89.703 63 4894 3 chr4A.!!$F1 4831
3 TraesCS5B01G521300 chr4A 531073923 531075865 1942 True 1096 1096 77.116 2286 4271 1 chr4A.!!$R2 1985
4 TraesCS5B01G521300 chr4A 235647417 235648075 658 True 878 878 90.774 4895 5558 1 chr4A.!!$R1 663
5 TraesCS5B01G521300 chr4B 324972033 324972665 632 True 776 776 88.821 4901 5546 1 chr4B.!!$R1 645
6 TraesCS5B01G521300 chr4D 65112936 65114100 1164 True 689 689 77.504 2286 3457 1 chr4D.!!$R1 1171
7 TraesCS5B01G521300 chr7D 294010492 294011072 580 False 294 294 76.774 210 810 1 chr7D.!!$F1 600
8 TraesCS5B01G521300 chr1A 132261113 132261808 695 False 291 291 75.069 203 901 1 chr1A.!!$F1 698

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
420 427 0.250553 CTTCCCCGTACAGGCAACAA 60.251 55.000 0.00 0.00 39.21 2.83 F
984 1397 0.323908 AAGAGGCGTACTGGAGAGCT 60.324 55.000 0.00 0.00 0.00 4.09 F
2527 2949 1.059098 TCTCTGAGAAAGCTTGCCCA 58.941 50.000 4.57 0.00 0.00 5.36 F
2779 3201 1.335689 GCTCTCAAAGCCTGCTTGTTG 60.336 52.381 4.95 1.25 45.92 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2341 2762 0.667993 TTCTTTTCCACTGCGCTTGG 59.332 50.000 19.34 19.34 35.18 3.61 R
2545 2967 2.105649 TGCTGTTGTATCAGGTTGGTCA 59.894 45.455 0.00 0.00 36.12 4.02 R
3782 4204 1.507140 TAGCAGGGTCCTTGTATGGG 58.493 55.000 2.53 0.00 0.00 4.00 R
4636 5062 0.037605 CTTCGACACCTAAAGCCCGT 60.038 55.000 0.00 0.00 0.00 5.28 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.378013 CATCGCGCATTCCATGATG 57.622 52.632 8.75 6.50 0.00 3.07
19 20 0.869730 CATCGCGCATTCCATGATGA 59.130 50.000 8.75 0.00 38.93 2.92
20 21 1.264826 CATCGCGCATTCCATGATGAA 59.735 47.619 8.75 0.00 38.93 2.57
21 22 1.377536 TCGCGCATTCCATGATGAAA 58.622 45.000 8.75 0.00 0.00 2.69
22 23 1.948834 TCGCGCATTCCATGATGAAAT 59.051 42.857 8.75 0.00 0.00 2.17
23 24 2.358582 TCGCGCATTCCATGATGAAATT 59.641 40.909 8.75 0.00 0.00 1.82
24 25 2.469886 CGCGCATTCCATGATGAAATTG 59.530 45.455 8.75 0.00 0.00 2.32
25 26 2.798283 GCGCATTCCATGATGAAATTGG 59.202 45.455 0.30 0.00 0.00 3.16
26 27 3.386486 CGCATTCCATGATGAAATTGGG 58.614 45.455 0.00 0.00 0.00 4.12
27 28 3.181473 CGCATTCCATGATGAAATTGGGT 60.181 43.478 0.00 0.00 0.00 4.51
28 29 4.124238 GCATTCCATGATGAAATTGGGTG 58.876 43.478 0.00 0.00 0.00 4.61
29 30 4.141892 GCATTCCATGATGAAATTGGGTGA 60.142 41.667 0.00 0.00 0.00 4.02
30 31 5.627272 GCATTCCATGATGAAATTGGGTGAA 60.627 40.000 0.00 0.00 0.00 3.18
31 32 6.588204 CATTCCATGATGAAATTGGGTGAAT 58.412 36.000 0.00 0.00 0.00 2.57
32 33 6.623979 TTCCATGATGAAATTGGGTGAATT 57.376 33.333 0.00 0.00 35.65 2.17
33 34 5.979993 TCCATGATGAAATTGGGTGAATTG 58.020 37.500 0.00 0.00 34.30 2.32
34 35 5.484644 TCCATGATGAAATTGGGTGAATTGT 59.515 36.000 0.00 0.00 34.30 2.71
35 36 6.013553 TCCATGATGAAATTGGGTGAATTGTT 60.014 34.615 0.00 0.00 34.30 2.83
36 37 7.179872 TCCATGATGAAATTGGGTGAATTGTTA 59.820 33.333 0.00 0.00 34.30 2.41
37 38 7.823310 CCATGATGAAATTGGGTGAATTGTTAA 59.177 33.333 0.00 0.00 34.30 2.01
38 39 9.217278 CATGATGAAATTGGGTGAATTGTTAAA 57.783 29.630 0.00 0.00 34.30 1.52
39 40 8.600449 TGATGAAATTGGGTGAATTGTTAAAC 57.400 30.769 0.00 0.00 34.30 2.01
40 41 7.383572 TGATGAAATTGGGTGAATTGTTAAACG 59.616 33.333 0.00 0.00 34.30 3.60
41 42 6.574350 TGAAATTGGGTGAATTGTTAAACGT 58.426 32.000 0.00 0.00 34.30 3.99
42 43 7.042335 TGAAATTGGGTGAATTGTTAAACGTT 58.958 30.769 0.00 0.00 34.30 3.99
43 44 6.836577 AATTGGGTGAATTGTTAAACGTTG 57.163 33.333 0.00 0.00 32.69 4.10
44 45 3.707793 TGGGTGAATTGTTAAACGTTGC 58.292 40.909 0.00 0.00 0.00 4.17
45 46 3.054166 GGGTGAATTGTTAAACGTTGCC 58.946 45.455 0.00 0.00 0.00 4.52
46 47 2.722116 GGTGAATTGTTAAACGTTGCCG 59.278 45.455 0.00 0.00 40.83 5.69
47 48 2.722116 GTGAATTGTTAAACGTTGCCGG 59.278 45.455 0.00 0.00 38.78 6.13
48 49 2.358267 TGAATTGTTAAACGTTGCCGGT 59.642 40.909 0.00 0.00 38.78 5.28
50 51 2.471862 TTGTTAAACGTTGCCGGTTC 57.528 45.000 0.00 0.00 40.81 3.62
51 52 1.666054 TGTTAAACGTTGCCGGTTCT 58.334 45.000 0.00 0.00 40.81 3.01
52 53 2.015587 TGTTAAACGTTGCCGGTTCTT 58.984 42.857 0.00 0.00 40.81 2.52
53 54 2.223294 TGTTAAACGTTGCCGGTTCTTG 60.223 45.455 0.00 0.00 40.81 3.02
54 55 0.945813 TAAACGTTGCCGGTTCTTGG 59.054 50.000 0.00 0.00 40.81 3.61
55 56 1.033202 AAACGTTGCCGGTTCTTGGT 61.033 50.000 0.00 0.00 40.81 3.67
56 57 1.720694 AACGTTGCCGGTTCTTGGTG 61.721 55.000 1.90 0.00 38.78 4.17
57 58 2.335011 GTTGCCGGTTCTTGGTGC 59.665 61.111 1.90 0.00 0.00 5.01
58 59 2.193536 GTTGCCGGTTCTTGGTGCT 61.194 57.895 1.90 0.00 0.00 4.40
59 60 1.896660 TTGCCGGTTCTTGGTGCTC 60.897 57.895 1.90 0.00 0.00 4.26
60 61 3.423154 GCCGGTTCTTGGTGCTCG 61.423 66.667 1.90 0.00 0.00 5.03
61 62 2.342279 CCGGTTCTTGGTGCTCGA 59.658 61.111 0.00 0.00 0.00 4.04
84 85 5.018809 AGCACAACATTTTCACCCTGATAT 58.981 37.500 0.00 0.00 0.00 1.63
99 100 3.627577 CCTGATATTCAAACCCTTGGTCG 59.372 47.826 0.00 0.00 33.12 4.79
101 102 5.423704 TGATATTCAAACCCTTGGTCGTA 57.576 39.130 0.00 0.00 33.12 3.43
105 106 5.687166 ATTCAAACCCTTGGTCGTAGATA 57.313 39.130 0.00 0.00 40.67 1.98
106 107 5.687166 TTCAAACCCTTGGTCGTAGATAT 57.313 39.130 0.00 0.00 40.67 1.63
114 115 6.325545 ACCCTTGGTCGTAGATATTGTTATCA 59.674 38.462 0.00 0.00 40.67 2.15
115 116 7.016268 ACCCTTGGTCGTAGATATTGTTATCAT 59.984 37.037 0.00 0.00 40.67 2.45
116 117 7.331934 CCCTTGGTCGTAGATATTGTTATCATG 59.668 40.741 0.00 0.00 40.67 3.07
126 127 7.040494 AGATATTGTTATCATGCTCATCCTCG 58.960 38.462 0.00 0.00 37.31 4.63
128 129 4.879197 TGTTATCATGCTCATCCTCGAT 57.121 40.909 0.00 0.00 0.00 3.59
135 136 3.314541 TGCTCATCCTCGATGATCATG 57.685 47.619 14.30 5.89 46.16 3.07
139 140 4.629092 CTCATCCTCGATGATCATGTTGT 58.371 43.478 14.30 0.00 46.16 3.32
158 159 0.524414 TGCATGATCACACAAGCAGC 59.476 50.000 0.00 0.00 31.53 5.25
168 169 0.322277 CACAAGCAGCCATCACCTCT 60.322 55.000 0.00 0.00 0.00 3.69
200 201 1.550524 GGTGCTCCATGTCAGTGTAGA 59.449 52.381 0.00 0.00 0.00 2.59
207 208 2.760650 CCATGTCAGTGTAGAGTGCCTA 59.239 50.000 0.00 0.00 0.00 3.93
320 321 0.966920 ATTACTCGGCCCCACTATCG 59.033 55.000 0.00 0.00 0.00 2.92
334 335 4.503123 CCCACTATCGATGATACCTTGCAA 60.503 45.833 8.54 0.00 0.00 4.08
381 388 4.338539 GTCGTGGTGGAGACGCGT 62.339 66.667 13.85 13.85 43.50 6.01
395 402 2.125512 GCGTCCGGTGAAGAGCAT 60.126 61.111 0.00 0.00 0.00 3.79
420 427 0.250553 CTTCCCCGTACAGGCAACAA 60.251 55.000 0.00 0.00 39.21 2.83
434 441 1.671850 GCAACAAGCCTGTAGTAGCGA 60.672 52.381 0.00 0.00 33.45 4.93
440 447 0.450983 GCCTGTAGTAGCGAAGACGT 59.549 55.000 0.00 0.00 41.98 4.34
477 484 1.897423 CAGCATGAGGTGGACGGTA 59.103 57.895 0.00 0.00 39.69 4.02
482 489 1.484653 CATGAGGTGGACGGTATTGGA 59.515 52.381 0.00 0.00 0.00 3.53
485 492 2.040178 GAGGTGGACGGTATTGGATCT 58.960 52.381 0.00 0.00 0.00 2.75
497 504 1.613317 TTGGATCTGATGGGCGTCGT 61.613 55.000 0.00 0.00 0.00 4.34
525 532 1.815003 CGTGGTTTCTCTAGTACCGGT 59.185 52.381 13.98 13.98 34.62 5.28
551 558 2.544267 GCGAAGTAAGCTCACAAACACT 59.456 45.455 0.00 0.00 0.00 3.55
568 575 3.547567 CTGGCAAGAACTCCTCCAG 57.452 57.895 0.00 0.00 38.41 3.86
603 611 0.523335 GGGAATTTGTGTCGATGCGC 60.523 55.000 0.00 0.00 0.00 6.09
694 706 2.084930 GGGTGGGGGATAGGTGCAT 61.085 63.158 0.00 0.00 0.00 3.96
698 710 2.281761 GGGGATAGGTGCATGCCG 60.282 66.667 16.68 0.00 37.29 5.69
699 711 2.980233 GGGATAGGTGCATGCCGC 60.980 66.667 16.68 8.07 42.89 6.53
729 744 1.210967 GGGGTATGTTTCACCGATGGA 59.789 52.381 0.00 0.00 36.89 3.41
749 764 2.626467 GGGCCAGGGGAGGACAAAT 61.626 63.158 4.39 0.00 38.98 2.32
751 766 0.629058 GGCCAGGGGAGGACAAATAA 59.371 55.000 0.00 0.00 36.38 1.40
757 772 2.100197 GGGGAGGACAAATAAAGTGCC 58.900 52.381 0.00 0.00 0.00 5.01
760 785 2.433436 GAGGACAAATAAAGTGCCCGT 58.567 47.619 0.00 0.00 0.00 5.28
784 809 3.885297 CCCTATCCATTTCGATGCAAACT 59.115 43.478 0.00 0.00 0.00 2.66
810 835 3.958147 CCTAATTTTAGGCCGGAAATGGT 59.042 43.478 5.05 7.77 43.43 3.55
823 849 4.303282 CGGAAATGGTTTGGACGAAAAAT 58.697 39.130 0.00 0.00 0.00 1.82
842 868 1.209127 GAACACCCGTCCATTTGCG 59.791 57.895 0.00 0.00 0.00 4.85
847 873 4.114997 CCGTCCATTTGCGGGCAC 62.115 66.667 0.00 0.00 43.85 5.01
871 1269 2.955660 GTTGGGTTCTGATTTGTGTCCA 59.044 45.455 0.00 0.00 0.00 4.02
874 1272 3.826157 TGGGTTCTGATTTGTGTCCATTC 59.174 43.478 0.00 0.00 0.00 2.67
884 1282 4.387026 TTGTGTCCATTCCTCTCCAAAT 57.613 40.909 0.00 0.00 0.00 2.32
902 1300 2.852495 ATTGACGCGAGCGGACCAAT 62.852 55.000 21.69 20.81 44.69 3.16
903 1301 2.103538 GACGCGAGCGGACCAATA 59.896 61.111 21.69 0.00 44.69 1.90
958 1358 2.358247 CTTCGGTCAACCACGGGG 60.358 66.667 0.00 0.00 41.29 5.73
972 1372 2.280186 GGGGCGATACAAGAGGCG 60.280 66.667 0.00 0.00 0.00 5.52
984 1397 0.323908 AAGAGGCGTACTGGAGAGCT 60.324 55.000 0.00 0.00 0.00 4.09
1091 1504 1.621301 CGAAGCTCTTGTCGCTGGTG 61.621 60.000 0.00 0.00 37.87 4.17
1193 1606 2.792290 CGACATGGAGCTCAACGCG 61.792 63.158 17.19 3.53 45.59 6.01
1465 1878 2.187946 CCAGACCTCCGGTGATGC 59.812 66.667 4.76 0.00 35.25 3.91
1634 2050 1.852626 CTGGGGGTTGGGGAAGACT 60.853 63.158 0.00 0.00 0.00 3.24
1829 2245 4.314961 TGTGCGTACAAGTCAGAAATCAT 58.685 39.130 3.02 0.00 32.88 2.45
1851 2272 5.715434 TTTGGCCAACAAGAGGTATTTAC 57.285 39.130 20.35 0.00 40.82 2.01
1880 2301 6.321435 TCTCTGCTTTACTTCTCGGATTCATA 59.679 38.462 0.00 0.00 0.00 2.15
2163 2584 6.074994 CGAAAGATATACGTACTTGAACCTGC 60.075 42.308 0.00 0.00 0.00 4.85
2173 2594 5.637810 CGTACTTGAACCTGCTAATTTCTCA 59.362 40.000 0.00 0.00 0.00 3.27
2211 2632 1.074775 TGAGAAATTGCGGCCCTGT 59.925 52.632 0.00 0.00 0.00 4.00
2213 2634 2.125952 GAAATTGCGGCCCTGTGC 60.126 61.111 0.00 0.00 40.16 4.57
2229 2650 1.143889 TGTGCCCACAGGTGTAATTGA 59.856 47.619 0.00 0.00 36.21 2.57
2232 2653 3.377172 GTGCCCACAGGTGTAATTGATAC 59.623 47.826 0.00 0.00 34.57 2.24
2233 2654 3.265737 TGCCCACAGGTGTAATTGATACT 59.734 43.478 0.00 0.00 35.42 2.12
2234 2655 3.627577 GCCCACAGGTGTAATTGATACTG 59.372 47.826 0.00 0.00 35.42 2.74
2341 2762 7.471721 TCATTGTAATCGATGACATTCAAACC 58.528 34.615 16.48 0.00 38.95 3.27
2512 2934 3.717400 TGCTCGAAGCGATTATTCTCT 57.283 42.857 0.00 0.00 46.26 3.10
2527 2949 1.059098 TCTCTGAGAAAGCTTGCCCA 58.941 50.000 4.57 0.00 0.00 5.36
2545 2967 7.012610 GCTTGCCCAAAGAAATATTTGCATTAT 59.987 33.333 5.17 0.00 38.57 1.28
2551 2973 9.381033 CCAAAGAAATATTTGCATTATGACCAA 57.619 29.630 5.17 0.00 38.57 3.67
2779 3201 1.335689 GCTCTCAAAGCCTGCTTGTTG 60.336 52.381 4.95 1.25 45.92 3.33
3193 3615 5.648092 GGAGGCATGTAAAACTGTACTCAAT 59.352 40.000 0.00 0.00 0.00 2.57
3409 3831 2.351706 TACTGCCGGTGGAAGTTTTT 57.648 45.000 1.90 0.00 38.75 1.94
3466 3888 8.834749 AGTTTAGGATTTCAGACAAAGTCTAC 57.165 34.615 0.00 0.00 41.37 2.59
3496 3918 5.880341 AGTGTTTTCCTCAAAAAGAAGACG 58.120 37.500 0.00 0.00 37.52 4.18
3499 3921 3.570912 TTCCTCAAAAAGAAGACGGGT 57.429 42.857 0.00 0.00 0.00 5.28
3508 3930 5.941948 AAAAGAAGACGGGTAATGAAGTG 57.058 39.130 0.00 0.00 0.00 3.16
3510 3932 1.659098 GAAGACGGGTAATGAAGTGCG 59.341 52.381 0.00 0.00 0.00 5.34
3681 4103 3.381908 ACTGACTGGTCCGATCTTATGAC 59.618 47.826 0.00 0.00 0.00 3.06
3754 4176 5.997385 ACACGTTCTTTATCGCTTCATTTT 58.003 33.333 0.00 0.00 0.00 1.82
3782 4204 2.437281 TGCTCTGGAGATTTCCTGGATC 59.563 50.000 9.00 0.00 44.36 3.36
3802 4224 2.057922 CCCATACAAGGACCCTGCTAT 58.942 52.381 0.00 0.00 0.00 2.97
3919 4341 6.436843 AAACTTACAACTGGTGTTCTTGAG 57.563 37.500 2.56 0.00 41.98 3.02
4116 4538 8.192774 CCAGCTTCTTTGCAAAGATATAAATGA 58.807 33.333 35.66 20.52 43.92 2.57
4287 4709 7.556635 TGATGAAGCAGAGAATTCAAATGATCT 59.443 33.333 8.44 0.00 38.80 2.75
4336 4758 4.398319 GGATTTCTGAAGTTTGTCCTCCA 58.602 43.478 0.00 0.00 0.00 3.86
4357 4779 0.530744 TAAATGAGTCGGCGAGCAGT 59.469 50.000 11.20 8.48 0.00 4.40
4380 4802 7.607991 CAGTATTGTGGTGTCTTAAGAAGGATT 59.392 37.037 6.78 0.00 0.00 3.01
4438 4860 9.622004 TTTTCGATTACTTCTCTGTAGTGTTAG 57.378 33.333 0.00 0.00 0.00 2.34
4483 4909 2.110188 ACCTTCCTCTGGAGTGTAGACA 59.890 50.000 0.00 0.00 31.21 3.41
4535 4961 3.243401 GGAACGTCCTTTGTGCTGATTTT 60.243 43.478 0.00 0.00 32.53 1.82
4626 5052 4.767409 TCAGTTAGCTCGATGTATATGGCT 59.233 41.667 0.00 0.00 0.00 4.75
4627 5053 5.243954 TCAGTTAGCTCGATGTATATGGCTT 59.756 40.000 0.00 0.00 0.00 4.35
4635 5061 6.565999 GCTCGATGTATATGGCTTTTGTTACC 60.566 42.308 0.00 0.00 0.00 2.85
4636 5062 6.350103 TCGATGTATATGGCTTTTGTTACCA 58.650 36.000 0.00 0.00 37.99 3.25
4638 5064 5.804692 TGTATATGGCTTTTGTTACCACG 57.195 39.130 0.00 0.00 35.99 4.94
4661 5091 2.889852 CTTTAGGTGTCGAAGTAGGCC 58.110 52.381 0.00 0.00 0.00 5.19
4674 5104 7.389884 TGTCGAAGTAGGCCTATATGTACTTAG 59.610 40.741 17.38 15.56 36.16 2.18
4676 5106 6.658391 CGAAGTAGGCCTATATGTACTTAGGT 59.342 42.308 17.38 0.00 36.16 3.08
4720 5150 5.740290 TGGTACTCCCTCTGTAAAGAAAG 57.260 43.478 0.00 0.00 0.00 2.62
4730 5160 7.455008 TCCCTCTGTAAAGAAAGATAAGAGTGT 59.545 37.037 0.00 0.00 0.00 3.55
4771 5201 4.316645 GAGGGAGTACTTGTTTTGAGGAC 58.683 47.826 0.00 0.00 0.00 3.85
4772 5202 3.072622 AGGGAGTACTTGTTTTGAGGACC 59.927 47.826 0.00 0.00 0.00 4.46
4834 5267 5.815740 GCTTTTCGTAATGAGGAGACCATTA 59.184 40.000 0.00 0.00 35.94 1.90
4874 5307 4.202121 TGACGGCATTAGGATCACTTACTC 60.202 45.833 0.00 0.00 0.00 2.59
4894 5329 4.705023 ACTCTTGTTGGTGTTAGTGCTTTT 59.295 37.500 0.00 0.00 0.00 2.27
4895 5330 5.185056 ACTCTTGTTGGTGTTAGTGCTTTTT 59.815 36.000 0.00 0.00 0.00 1.94
4932 5367 5.845103 TGCAAATCAAGAGCTTTGATTCAA 58.155 33.333 24.38 15.87 45.36 2.69
4963 5398 4.269183 TGGGATTACAATCGTTCAGCAAT 58.731 39.130 0.00 0.00 36.27 3.56
5091 5526 4.944317 AGCAAAGGTTAACTGGAATAGCTC 59.056 41.667 5.42 0.00 0.00 4.09
5131 5567 6.825721 GCTCTTCTATTTCTTGAAGGATGGAA 59.174 38.462 0.00 0.98 39.85 3.53
5154 5590 3.491619 GCAATCTCTGATCTACCTTCGCA 60.492 47.826 0.00 0.00 0.00 5.10
5182 5618 2.619074 CCTCCAAAGATTGACCACCTCC 60.619 54.545 0.00 0.00 0.00 4.30
5191 5628 0.904865 TGACCACCTCCTTCGCATCT 60.905 55.000 0.00 0.00 0.00 2.90
5238 5675 6.037172 AGACCAATATCACACGCTAATTTGAC 59.963 38.462 0.00 0.00 0.00 3.18
5246 5683 1.933853 ACGCTAATTTGACGCCATCTC 59.066 47.619 0.00 0.00 0.00 2.75
5251 5690 2.332063 ATTTGACGCCATCTCGGATT 57.668 45.000 0.00 0.00 36.56 3.01
5268 5707 3.192466 GGATTGCAAATGCTTCCATGAC 58.808 45.455 17.49 0.00 40.96 3.06
5278 5717 1.735386 CTTCCATGACCAGAGCACTG 58.265 55.000 3.89 3.89 43.12 3.66
5312 5751 0.555769 CCAAATAGCCTGGCCCCTTA 59.444 55.000 16.57 0.79 0.00 2.69
5359 5806 3.009115 GCCCCTGTAGCACCCTCA 61.009 66.667 0.00 0.00 0.00 3.86
5412 5859 1.909700 ATTTTCAGCAAGCCTTCCGA 58.090 45.000 0.00 0.00 0.00 4.55
5419 5866 2.030562 AAGCCTTCCGACGGTGTG 59.969 61.111 14.79 4.40 0.00 3.82
5447 5894 1.089920 CTCCCGTTTCTTCCATGCAG 58.910 55.000 0.00 0.00 0.00 4.41
5449 5896 0.804989 CCCGTTTCTTCCATGCAGTC 59.195 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.596603 TTCATCATGGAATGCGCGAT 58.403 45.000 12.10 0.00 46.21 4.58
4 5 2.798283 CCAATTTCATCATGGAATGCGC 59.202 45.455 0.00 0.00 46.21 6.09
5 6 3.181473 ACCCAATTTCATCATGGAATGCG 60.181 43.478 0.00 0.00 46.21 4.73
8 9 6.818281 ATTCACCCAATTTCATCATGGAAT 57.182 33.333 0.00 0.00 36.27 3.01
9 10 6.013553 ACAATTCACCCAATTTCATCATGGAA 60.014 34.615 0.00 0.00 36.27 3.53
10 11 5.484644 ACAATTCACCCAATTTCATCATGGA 59.515 36.000 0.00 0.00 36.27 3.41
11 12 5.736813 ACAATTCACCCAATTTCATCATGG 58.263 37.500 0.00 0.00 31.79 3.66
12 13 8.774890 TTAACAATTCACCCAATTTCATCATG 57.225 30.769 0.00 0.00 31.79 3.07
13 14 9.218440 GTTTAACAATTCACCCAATTTCATCAT 57.782 29.630 0.00 0.00 31.79 2.45
14 15 7.383572 CGTTTAACAATTCACCCAATTTCATCA 59.616 33.333 0.00 0.00 31.79 3.07
15 16 7.383843 ACGTTTAACAATTCACCCAATTTCATC 59.616 33.333 0.00 0.00 31.79 2.92
16 17 7.213678 ACGTTTAACAATTCACCCAATTTCAT 58.786 30.769 0.00 0.00 31.79 2.57
17 18 6.574350 ACGTTTAACAATTCACCCAATTTCA 58.426 32.000 0.00 0.00 31.79 2.69
18 19 7.341446 CAACGTTTAACAATTCACCCAATTTC 58.659 34.615 0.00 0.00 31.79 2.17
19 20 6.238239 GCAACGTTTAACAATTCACCCAATTT 60.238 34.615 0.00 0.00 31.79 1.82
20 21 5.235401 GCAACGTTTAACAATTCACCCAATT 59.765 36.000 0.00 0.00 34.79 2.32
21 22 4.747605 GCAACGTTTAACAATTCACCCAAT 59.252 37.500 0.00 0.00 0.00 3.16
22 23 4.113354 GCAACGTTTAACAATTCACCCAA 58.887 39.130 0.00 0.00 0.00 4.12
23 24 3.491104 GGCAACGTTTAACAATTCACCCA 60.491 43.478 0.00 0.00 0.00 4.51
24 25 3.054166 GGCAACGTTTAACAATTCACCC 58.946 45.455 0.00 0.00 0.00 4.61
40 41 2.130073 GAGCACCAAGAACCGGCAAC 62.130 60.000 0.00 0.00 0.00 4.17
41 42 1.896660 GAGCACCAAGAACCGGCAA 60.897 57.895 0.00 0.00 0.00 4.52
42 43 2.281484 GAGCACCAAGAACCGGCA 60.281 61.111 0.00 0.00 0.00 5.69
43 44 3.423154 CGAGCACCAAGAACCGGC 61.423 66.667 0.00 0.00 0.00 6.13
44 45 1.738099 CTCGAGCACCAAGAACCGG 60.738 63.158 0.00 0.00 0.00 5.28
45 46 2.383527 GCTCGAGCACCAAGAACCG 61.384 63.158 31.91 0.00 41.59 4.44
46 47 3.567473 GCTCGAGCACCAAGAACC 58.433 61.111 31.91 0.00 41.59 3.62
56 57 2.310577 GTGAAAATGTTGTGCTCGAGC 58.689 47.619 30.42 30.42 42.50 5.03
57 58 2.350772 GGGTGAAAATGTTGTGCTCGAG 60.351 50.000 8.45 8.45 0.00 4.04
58 59 1.606668 GGGTGAAAATGTTGTGCTCGA 59.393 47.619 0.00 0.00 0.00 4.04
59 60 1.608590 AGGGTGAAAATGTTGTGCTCG 59.391 47.619 0.00 0.00 0.00 5.03
60 61 2.622942 TCAGGGTGAAAATGTTGTGCTC 59.377 45.455 0.00 0.00 0.00 4.26
61 62 2.665165 TCAGGGTGAAAATGTTGTGCT 58.335 42.857 0.00 0.00 0.00 4.40
84 85 5.687166 ATATCTACGACCAAGGGTTTGAA 57.313 39.130 0.00 0.00 35.25 2.69
99 100 9.311916 GAGGATGAGCATGATAACAATATCTAC 57.688 37.037 0.00 0.00 38.99 2.59
101 102 7.040494 CGAGGATGAGCATGATAACAATATCT 58.960 38.462 0.00 0.00 38.99 1.98
105 106 5.219343 TCGAGGATGAGCATGATAACAAT 57.781 39.130 0.00 0.00 0.00 2.71
106 107 4.670896 TCGAGGATGAGCATGATAACAA 57.329 40.909 0.00 0.00 0.00 2.83
139 140 0.524414 GCTGCTTGTGTGATCATGCA 59.476 50.000 0.00 4.59 42.97 3.96
147 148 0.892358 AGGTGATGGCTGCTTGTGTG 60.892 55.000 0.00 0.00 0.00 3.82
158 159 3.269178 GAGAAGCTTTGAGAGGTGATGG 58.731 50.000 0.00 0.00 35.94 3.51
168 169 0.320771 GGAGCACCGAGAAGCTTTGA 60.321 55.000 0.00 0.00 42.04 2.69
200 201 2.949177 TGACCACATTGTTAGGCACT 57.051 45.000 0.00 0.00 46.37 4.40
254 255 1.154282 GATGACTCGTCGTCGCACA 60.154 57.895 3.74 0.00 45.87 4.57
300 301 1.343465 CGATAGTGGGGCCGAGTAATT 59.657 52.381 7.21 0.00 0.00 1.40
302 303 0.106569 TCGATAGTGGGGCCGAGTAA 60.107 55.000 7.21 0.00 37.40 2.24
309 310 2.180276 AGGTATCATCGATAGTGGGGC 58.820 52.381 0.00 0.00 37.40 5.80
334 335 1.378531 TCGACACTTTGCTTGCAAGT 58.621 45.000 26.55 5.15 34.67 3.16
381 388 0.820226 CTGAGATGCTCTTCACCGGA 59.180 55.000 9.46 0.00 0.00 5.14
395 402 0.970937 CCTGTACGGGGAAGCTGAGA 60.971 60.000 13.47 0.00 0.00 3.27
399 406 2.221299 TTGCCTGTACGGGGAAGCT 61.221 57.895 22.66 0.00 32.95 3.74
402 409 0.250553 CTTGTTGCCTGTACGGGGAA 60.251 55.000 22.66 22.66 34.36 3.97
420 427 0.733729 CGTCTTCGCTACTACAGGCT 59.266 55.000 0.00 0.00 0.00 4.58
477 484 0.250038 CGACGCCCATCAGATCCAAT 60.250 55.000 0.00 0.00 0.00 3.16
482 489 2.413351 CGACGACGCCCATCAGAT 59.587 61.111 0.00 0.00 0.00 2.90
502 509 1.823610 GGTACTAGAGAAACCACGGCT 59.176 52.381 0.00 0.00 33.28 5.52
525 532 2.125673 GAGCTTACTTCGCCGCCA 60.126 61.111 0.00 0.00 0.00 5.69
536 543 2.340210 TGCCAGTGTTTGTGAGCTTA 57.660 45.000 0.00 0.00 0.00 3.09
551 558 1.349026 CTTCTGGAGGAGTTCTTGCCA 59.651 52.381 0.00 0.00 0.00 4.92
581 588 0.732571 CATCGACACAAATTCCCCGG 59.267 55.000 0.00 0.00 0.00 5.73
583 590 0.098728 CGCATCGACACAAATTCCCC 59.901 55.000 0.00 0.00 0.00 4.81
587 595 1.134487 CGGCGCATCGACACAAATT 59.866 52.632 10.83 0.00 32.52 1.82
694 706 4.738998 CCCCTTCCATGTGCGGCA 62.739 66.667 0.00 0.00 0.00 5.69
698 710 0.258774 ACATACCCCCTTCCATGTGC 59.741 55.000 0.00 0.00 30.64 4.57
699 711 2.826674 AACATACCCCCTTCCATGTG 57.173 50.000 0.00 0.00 32.15 3.21
700 712 2.652348 TGAAACATACCCCCTTCCATGT 59.348 45.455 0.00 0.00 33.12 3.21
701 713 3.023832 GTGAAACATACCCCCTTCCATG 58.976 50.000 0.00 0.00 36.32 3.66
703 715 1.356398 GGTGAAACATACCCCCTTCCA 59.644 52.381 0.00 0.00 39.98 3.53
757 772 0.105964 TCGAAATGGATAGGGCACGG 59.894 55.000 0.00 0.00 0.00 4.94
760 785 1.142667 TGCATCGAAATGGATAGGGCA 59.857 47.619 0.00 0.00 33.19 5.36
810 835 3.489398 CGGGTGTTCATTTTTCGTCCAAA 60.489 43.478 0.00 0.00 0.00 3.28
823 849 1.511318 CGCAAATGGACGGGTGTTCA 61.511 55.000 0.00 0.00 38.19 3.18
847 873 0.591170 ACAAATCAGAACCCAACGCG 59.409 50.000 3.53 3.53 0.00 6.01
856 882 5.246981 AGAGGAATGGACACAAATCAGAA 57.753 39.130 0.00 0.00 0.00 3.02
857 883 4.323792 GGAGAGGAATGGACACAAATCAGA 60.324 45.833 0.00 0.00 0.00 3.27
871 1269 2.009774 CGCGTCAATTTGGAGAGGAAT 58.990 47.619 0.00 0.00 0.00 3.01
874 1272 1.002366 CTCGCGTCAATTTGGAGAGG 58.998 55.000 5.77 0.00 0.00 3.69
884 1282 2.215465 TATTGGTCCGCTCGCGTCAA 62.215 55.000 5.77 11.37 37.81 3.18
958 1358 1.478137 CAGTACGCCTCTTGTATCGC 58.522 55.000 0.00 0.00 0.00 4.58
972 1372 0.031449 GATCCGCAGCTCTCCAGTAC 59.969 60.000 0.00 0.00 0.00 2.73
984 1397 2.332869 CTGCTCGATCGATCCGCA 59.667 61.111 26.03 26.03 0.00 5.69
1012 1425 2.957006 TCCATCTCCGTTTCCTAGCTAC 59.043 50.000 0.00 0.00 0.00 3.58
1013 1426 3.223435 CTCCATCTCCGTTTCCTAGCTA 58.777 50.000 0.00 0.00 0.00 3.32
1091 1504 3.055530 TGCTCAGATTCCAACTCTTCTCC 60.056 47.826 0.00 0.00 0.00 3.71
1193 1606 0.033228 CTCCATGATCCTGTCTCGGC 59.967 60.000 0.00 0.00 0.00 5.54
1476 1889 0.757188 GGATCCGAAGCAGAGGAGGA 60.757 60.000 0.00 0.00 40.26 3.71
1477 1890 1.745264 GGATCCGAAGCAGAGGAGG 59.255 63.158 0.00 0.00 40.26 4.30
1478 1891 1.361993 CGGATCCGAAGCAGAGGAG 59.638 63.158 30.62 0.00 42.83 3.69
1511 1927 2.510918 TCGACGCCGACGAGATCT 60.511 61.111 7.70 0.00 43.93 2.75
1634 2050 4.393155 ACATCGGCGGCAAGAGCA 62.393 61.111 10.53 0.00 44.61 4.26
1679 2095 4.134187 CACGCGCGCTTGTCGAAT 62.134 61.111 32.58 3.21 41.67 3.34
1737 2153 2.780595 CGAATTCCCGGAGCATGTT 58.219 52.632 0.73 0.00 0.00 2.71
1829 2245 5.141182 TGTAAATACCTCTTGTTGGCCAAA 58.859 37.500 22.47 4.38 31.20 3.28
1851 2272 3.923461 CCGAGAAGTAAAGCAGAGAGTTG 59.077 47.826 0.00 0.00 0.00 3.16
1880 2301 9.676861 TCTCTGAATCAATAAGTCAAATGTGAT 57.323 29.630 0.00 0.00 35.80 3.06
1997 2418 7.173218 CAGCACAGAGTAATTAAGGAAACTGAA 59.827 37.037 0.00 0.00 42.68 3.02
2146 2567 7.328737 AGAAATTAGCAGGTTCAAGTACGTAT 58.671 34.615 0.00 0.00 0.00 3.06
2147 2568 6.694447 AGAAATTAGCAGGTTCAAGTACGTA 58.306 36.000 0.00 0.00 0.00 3.57
2148 2569 5.548406 AGAAATTAGCAGGTTCAAGTACGT 58.452 37.500 0.00 0.00 0.00 3.57
2149 2570 5.637810 TGAGAAATTAGCAGGTTCAAGTACG 59.362 40.000 0.00 0.00 0.00 3.67
2211 2632 2.897271 ATCAATTACACCTGTGGGCA 57.103 45.000 1.91 0.00 35.63 5.36
2213 2634 4.199310 CCAGTATCAATTACACCTGTGGG 58.801 47.826 1.91 0.00 38.88 4.61
2229 2650 8.378565 AGCTATACATAATGACTTTGCCAGTAT 58.621 33.333 0.00 0.00 35.01 2.12
2232 2653 6.072838 CCAGCTATACATAATGACTTTGCCAG 60.073 42.308 0.00 0.00 0.00 4.85
2233 2654 5.764686 CCAGCTATACATAATGACTTTGCCA 59.235 40.000 0.00 0.00 0.00 4.92
2234 2655 5.335191 GCCAGCTATACATAATGACTTTGCC 60.335 44.000 0.00 0.00 0.00 4.52
2341 2762 0.667993 TTCTTTTCCACTGCGCTTGG 59.332 50.000 19.34 19.34 35.18 3.61
2512 2934 2.363306 TCTTTGGGCAAGCTTTCTCA 57.637 45.000 0.00 0.00 31.70 3.27
2527 2949 9.382275 GGTTGGTCATAATGCAAATATTTCTTT 57.618 29.630 0.00 1.94 0.00 2.52
2545 2967 2.105649 TGCTGTTGTATCAGGTTGGTCA 59.894 45.455 0.00 0.00 36.12 4.02
2551 2973 4.910195 TCAGAATTGCTGTTGTATCAGGT 58.090 39.130 0.00 0.00 45.14 4.00
2779 3201 2.752903 ACTCGGGAACATGGCAAAATAC 59.247 45.455 0.00 0.00 0.00 1.89
3409 3831 3.118629 TGTGCATTAAACAGGGCAACAAA 60.119 39.130 0.00 0.00 38.10 2.83
3466 3888 8.532977 TCTTTTTGAGGAAAACACTCTTTTTG 57.467 30.769 0.00 0.00 35.98 2.44
3496 3918 2.109425 ACTTCCGCACTTCATTACCC 57.891 50.000 0.00 0.00 0.00 3.69
3499 3921 5.048991 GGAAAGAAACTTCCGCACTTCATTA 60.049 40.000 0.00 0.00 35.79 1.90
3541 3963 6.349300 GGTGATAAATCCTGCTAGAGTTTCA 58.651 40.000 0.00 0.00 0.00 2.69
3681 4103 2.228582 TGAATGAACTGTTGAATGGCCG 59.771 45.455 0.00 0.00 0.00 6.13
3754 4176 4.165565 AGGAAATCTCCAGAGCATTCATCA 59.834 41.667 11.72 0.00 45.24 3.07
3782 4204 1.507140 TAGCAGGGTCCTTGTATGGG 58.493 55.000 2.53 0.00 0.00 4.00
4116 4538 8.118976 ACATTCAATGTTGATGACAGAAAGAT 57.881 30.769 0.00 0.00 41.63 2.40
4336 4758 2.205074 CTGCTCGCCGACTCATTTAAT 58.795 47.619 0.00 0.00 0.00 1.40
4357 4779 7.333423 CGAAATCCTTCTTAAGACACCACAATA 59.667 37.037 4.18 0.00 0.00 1.90
4380 4802 2.615447 GCATGCTGAATCAAGGATCGAA 59.385 45.455 11.37 0.00 0.00 3.71
4415 4837 7.918536 ACTAACACTACAGAGAAGTAATCGA 57.081 36.000 0.00 0.00 0.00 3.59
4438 4860 9.712359 GGTTCGAAATTAAGGTGATACATAAAC 57.288 33.333 0.00 0.00 0.00 2.01
4483 4909 7.201785 CCATTGACTTAACGCCAATAATAGGTT 60.202 37.037 0.00 0.00 0.00 3.50
4535 4961 6.575267 TCATTATTAAGCTGCACGGTAGTTA 58.425 36.000 1.02 0.00 0.00 2.24
4635 5061 0.320073 TTCGACACCTAAAGCCCGTG 60.320 55.000 0.00 0.00 0.00 4.94
4636 5062 0.037605 CTTCGACACCTAAAGCCCGT 60.038 55.000 0.00 0.00 0.00 5.28
4638 5064 2.418334 CCTACTTCGACACCTAAAGCCC 60.418 54.545 0.00 0.00 0.00 5.19
4674 5104 5.216614 AGTTTGACTTTGAGAGGAGTACC 57.783 43.478 0.00 0.00 0.00 3.34
4676 5106 6.497259 ACCATAGTTTGACTTTGAGAGGAGTA 59.503 38.462 0.95 0.00 30.18 2.59
4730 5160 8.836735 ACTCCCTCCATAAAGAAAGATAAGAAA 58.163 33.333 0.00 0.00 0.00 2.52
4738 5168 6.712276 ACAAGTACTCCCTCCATAAAGAAAG 58.288 40.000 0.00 0.00 0.00 2.62
4747 5177 3.072476 CCTCAAAACAAGTACTCCCTCCA 59.928 47.826 0.00 0.00 0.00 3.86
4748 5178 3.326880 TCCTCAAAACAAGTACTCCCTCC 59.673 47.826 0.00 0.00 0.00 4.30
4771 5201 3.027412 TCCAGTTCTGCTTAGCTAGAGG 58.973 50.000 5.60 5.22 0.00 3.69
4772 5202 4.727507 TTCCAGTTCTGCTTAGCTAGAG 57.272 45.455 5.60 0.00 0.00 2.43
4834 5267 4.156008 GCCGTCAGTTAAGGAATGACAATT 59.844 41.667 7.29 0.00 42.76 2.32
4932 5367 8.744652 TGAACGATTGTAATCCCATTGTTTAAT 58.255 29.630 0.00 0.00 31.68 1.40
4963 5398 5.367352 TGTACCAAACTTCTTAGTTCCCTGA 59.633 40.000 0.00 0.00 43.74 3.86
5003 5438 4.280677 AGCCTCGGAGAATAGAAGAAGATG 59.719 45.833 6.58 0.00 34.09 2.90
5005 5440 3.904717 AGCCTCGGAGAATAGAAGAAGA 58.095 45.455 6.58 0.00 34.09 2.87
5006 5441 4.367450 CAAGCCTCGGAGAATAGAAGAAG 58.633 47.826 6.58 0.00 34.09 2.85
5007 5442 3.430929 GCAAGCCTCGGAGAATAGAAGAA 60.431 47.826 6.58 0.00 34.09 2.52
5063 5498 1.535462 CCAGTTAACCTTTGCTGGTCG 59.465 52.381 0.88 0.00 42.47 4.79
5088 5523 0.882484 GCTTAGCGGGAATCTGGAGC 60.882 60.000 0.00 0.00 0.00 4.70
5091 5526 0.755686 AGAGCTTAGCGGGAATCTGG 59.244 55.000 0.00 0.00 0.00 3.86
5131 5567 3.243704 GCGAAGGTAGATCAGAGATTGCT 60.244 47.826 0.00 0.00 0.00 3.91
5154 5590 4.043310 TGGTCAATCTTTGGAGGAACAGAT 59.957 41.667 0.00 0.00 0.00 2.90
5182 5618 7.036829 AGATCATCATAGAATCAGATGCGAAG 58.963 38.462 0.00 0.00 39.12 3.79
5191 5628 7.935755 GGTCTTTCCAAGATCATCATAGAATCA 59.064 37.037 0.00 0.00 38.54 2.57
5227 5664 1.071239 CGAGATGGCGTCAAATTAGCG 60.071 52.381 9.78 0.00 0.00 4.26
5238 5675 0.664761 ATTTGCAATCCGAGATGGCG 59.335 50.000 0.00 0.00 37.80 5.69
5246 5683 2.159212 TCATGGAAGCATTTGCAATCCG 60.159 45.455 17.29 8.48 46.09 4.18
5251 5690 1.546923 CTGGTCATGGAAGCATTTGCA 59.453 47.619 5.20 0.00 45.16 4.08
5312 5751 9.887862 AATAAGGAACCATCAAGGAATTATGAT 57.112 29.630 0.00 0.00 41.22 2.45
5341 5780 2.689034 GAGGGTGCTACAGGGGCT 60.689 66.667 0.00 0.00 0.00 5.19
5359 5806 4.022849 GCAAGCTTCAGTTCCAATACAACT 60.023 41.667 0.00 0.00 34.24 3.16
5412 5859 1.302511 GAGCAATGGACCACACCGT 60.303 57.895 0.00 0.00 0.00 4.83
5419 5866 0.322546 AGAAACGGGAGCAATGGACC 60.323 55.000 0.00 0.00 0.00 4.46
5447 5894 1.403679 AGCTCACGCATCTACAGAGAC 59.596 52.381 0.00 0.00 39.10 3.36
5449 5896 1.403323 TCAGCTCACGCATCTACAGAG 59.597 52.381 0.00 0.00 39.10 3.35


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

AutoCloner maintained by Alex Coulton.