Multiple sequence alignment - TraesCS1A01G177000

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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 TraesCS1A01G177000 chr1A 100.000 3126 0 0 1 3126 319319087 319322212 0.000000e+00 5773.0
1 TraesCS1A01G177000 chr1D 92.601 2311 91 38 207 2489 249559336 249561594 0.000000e+00 3247.0
2 TraesCS1A01G177000 chr1D 89.835 364 13 12 2604 2947 249561819 249562178 2.210000e-121 446.0
3 TraesCS1A01G177000 chr1D 88.325 197 12 8 2937 3126 249562209 249562401 3.140000e-55 226.0
4 TraesCS1A01G177000 chr1D 96.000 100 4 0 2493 2592 249561673 249561772 2.490000e-36 163.0
5 TraesCS1A01G177000 chr1B 92.314 1236 50 21 1374 2592 364919237 364918030 0.000000e+00 1714.0
6 TraesCS1A01G177000 chr1B 91.069 1254 53 22 129 1372 364920470 364919266 0.000000e+00 1640.0
7 TraesCS1A01G177000 chr1B 89.227 362 7 9 2604 2947 364917659 364917312 1.040000e-114 424.0
8 TraesCS1A01G177000 chr1B 87.245 196 13 10 2937 3126 364917281 364917092 2.440000e-51 213.0
9 TraesCS1A01G177000 chr4B 79.859 566 77 25 1525 2067 670850350 670849799 2.280000e-101 379.0
10 TraesCS1A01G177000 chr4B 84.426 244 24 5 1122 1352 670850698 670850456 8.720000e-56 228.0
11 TraesCS1A01G177000 chrUn 79.174 557 91 17 1525 2067 28674849 28675394 2.290000e-96 363.0
12 TraesCS1A01G177000 chrUn 83.984 256 27 7 1110 1352 28674492 28674746 1.870000e-57 233.0
13 TraesCS1A01G177000 chr5A 79.004 562 85 22 1527 2067 708723262 708722713 1.380000e-93 353.0
14 TraesCS1A01G177000 chr5A 85.246 244 22 5 1122 1352 708723609 708723367 4.030000e-59 239.0
15 TraesCS1A01G177000 chr6D 78.311 438 76 16 1439 1862 313187829 313187397 6.650000e-67 265.0
16 TraesCS1A01G177000 chr6A 78.161 435 82 10 1439 1862 450107901 450107469 6.650000e-67 265.0
17 TraesCS1A01G177000 chr6B 77.910 421 76 12 1439 1846 513135975 513136391 2.410000e-61 246.0
18 TraesCS1A01G177000 chr7B 87.500 72 3 4 3031 3096 717350181 717350110 9.290000e-11 78.7
19 TraesCS1A01G177000 chr2A 93.878 49 3 0 1795 1843 570608626 570608674 1.200000e-09 75.0
20 TraesCS1A01G177000 chr2D 92.000 50 4 0 1797 1846 392526370 392526419 1.560000e-08 71.3


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 TraesCS1A01G177000 chr1A 319319087 319322212 3125 False 5773.00 5773 100.00000 1 3126 1 chr1A.!!$F1 3125
1 TraesCS1A01G177000 chr1D 249559336 249562401 3065 False 1020.50 3247 91.69025 207 3126 4 chr1D.!!$F1 2919
2 TraesCS1A01G177000 chr1B 364917092 364920470 3378 True 997.75 1714 89.96375 129 3126 4 chr1B.!!$R1 2997
3 TraesCS1A01G177000 chr4B 670849799 670850698 899 True 303.50 379 82.14250 1122 2067 2 chr4B.!!$R1 945
4 TraesCS1A01G177000 chrUn 28674492 28675394 902 False 298.00 363 81.57900 1110 2067 2 chrUn.!!$F1 957
5 TraesCS1A01G177000 chr5A 708722713 708723609 896 True 296.00 353 82.12500 1122 2067 2 chr5A.!!$R1 945

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
934 954 0.178975 CACCTCCCTCTATCGGCTCT 60.179 60.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2696 3287 0.17668 ACCCACTAATCTGCTCTGCG 59.823 55.0 0.0 0.0 0.0 5.18 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
22 23 5.560722 TCCCTCAGAGAAAATACACAACA 57.439 39.130 0.00 0.00 0.00 3.33
23 24 5.935945 TCCCTCAGAGAAAATACACAACAA 58.064 37.500 0.00 0.00 0.00 2.83
24 25 5.997746 TCCCTCAGAGAAAATACACAACAAG 59.002 40.000 0.00 0.00 0.00 3.16
25 26 5.182001 CCCTCAGAGAAAATACACAACAAGG 59.818 44.000 0.00 0.00 0.00 3.61
26 27 5.997746 CCTCAGAGAAAATACACAACAAGGA 59.002 40.000 0.00 0.00 0.00 3.36
27 28 6.148480 CCTCAGAGAAAATACACAACAAGGAG 59.852 42.308 0.00 0.00 0.00 3.69
28 29 5.470098 TCAGAGAAAATACACAACAAGGAGC 59.530 40.000 0.00 0.00 0.00 4.70
29 30 5.239306 CAGAGAAAATACACAACAAGGAGCA 59.761 40.000 0.00 0.00 0.00 4.26
30 31 5.827797 AGAGAAAATACACAACAAGGAGCAA 59.172 36.000 0.00 0.00 0.00 3.91
31 32 6.491403 AGAGAAAATACACAACAAGGAGCAAT 59.509 34.615 0.00 0.00 0.00 3.56
32 33 7.014615 AGAGAAAATACACAACAAGGAGCAATT 59.985 33.333 0.00 0.00 0.00 2.32
33 34 8.177119 AGAAAATACACAACAAGGAGCAATTA 57.823 30.769 0.00 0.00 0.00 1.40
34 35 8.806146 AGAAAATACACAACAAGGAGCAATTAT 58.194 29.630 0.00 0.00 0.00 1.28
36 37 9.855021 AAAATACACAACAAGGAGCAATTATAC 57.145 29.630 0.00 0.00 0.00 1.47
37 38 5.897377 ACACAACAAGGAGCAATTATACC 57.103 39.130 0.00 0.00 0.00 2.73
38 39 4.394920 ACACAACAAGGAGCAATTATACCG 59.605 41.667 0.00 0.00 0.00 4.02
39 40 4.394920 CACAACAAGGAGCAATTATACCGT 59.605 41.667 0.00 0.00 0.00 4.83
40 41 4.394920 ACAACAAGGAGCAATTATACCGTG 59.605 41.667 0.00 0.00 37.75 4.94
41 42 2.943033 ACAAGGAGCAATTATACCGTGC 59.057 45.455 0.00 0.00 35.86 5.34
42 43 2.942376 CAAGGAGCAATTATACCGTGCA 59.058 45.455 0.00 0.00 40.83 4.57
43 44 3.275617 AGGAGCAATTATACCGTGCAA 57.724 42.857 0.00 0.00 40.83 4.08
44 45 3.206150 AGGAGCAATTATACCGTGCAAG 58.794 45.455 0.00 0.00 40.83 4.01
45 46 3.118408 AGGAGCAATTATACCGTGCAAGA 60.118 43.478 0.00 0.00 40.83 3.02
46 47 3.002348 GGAGCAATTATACCGTGCAAGAC 59.998 47.826 0.00 0.00 40.83 3.01
47 48 3.605634 AGCAATTATACCGTGCAAGACA 58.394 40.909 0.00 0.00 40.83 3.41
48 49 4.199310 AGCAATTATACCGTGCAAGACAT 58.801 39.130 0.00 0.00 40.83 3.06
49 50 4.035558 AGCAATTATACCGTGCAAGACATG 59.964 41.667 0.00 0.00 40.83 3.21
50 51 4.201910 GCAATTATACCGTGCAAGACATGT 60.202 41.667 0.00 0.00 38.19 3.21
51 52 5.265477 CAATTATACCGTGCAAGACATGTG 58.735 41.667 1.15 0.00 33.01 3.21
52 53 2.472695 ATACCGTGCAAGACATGTGT 57.527 45.000 1.15 0.00 33.01 3.72
53 54 2.248280 TACCGTGCAAGACATGTGTT 57.752 45.000 1.15 1.45 33.01 3.32
54 55 1.388547 ACCGTGCAAGACATGTGTTT 58.611 45.000 1.15 0.00 33.01 2.83
55 56 1.333619 ACCGTGCAAGACATGTGTTTC 59.666 47.619 1.15 0.00 33.01 2.78
56 57 1.334960 CCGTGCAAGACATGTGTTTCC 60.335 52.381 1.15 0.00 33.01 3.13
57 58 1.334960 CGTGCAAGACATGTGTTTCCC 60.335 52.381 1.15 0.00 0.00 3.97
58 59 1.956477 GTGCAAGACATGTGTTTCCCT 59.044 47.619 1.15 0.00 0.00 4.20
59 60 2.030805 GTGCAAGACATGTGTTTCCCTC 60.031 50.000 1.15 0.00 0.00 4.30
60 61 1.541588 GCAAGACATGTGTTTCCCTCC 59.458 52.381 1.15 0.00 0.00 4.30
61 62 2.162681 CAAGACATGTGTTTCCCTCCC 58.837 52.381 1.15 0.00 0.00 4.30
62 63 1.747444 AGACATGTGTTTCCCTCCCT 58.253 50.000 1.15 0.00 0.00 4.20
63 64 2.915869 AGACATGTGTTTCCCTCCCTA 58.084 47.619 1.15 0.00 0.00 3.53
64 65 3.464828 AGACATGTGTTTCCCTCCCTAT 58.535 45.455 1.15 0.00 0.00 2.57
65 66 3.852578 AGACATGTGTTTCCCTCCCTATT 59.147 43.478 1.15 0.00 0.00 1.73
66 67 4.080299 AGACATGTGTTTCCCTCCCTATTC 60.080 45.833 1.15 0.00 0.00 1.75
67 68 3.591527 ACATGTGTTTCCCTCCCTATTCA 59.408 43.478 0.00 0.00 0.00 2.57
68 69 4.230502 ACATGTGTTTCCCTCCCTATTCAT 59.769 41.667 0.00 0.00 0.00 2.57
69 70 4.235079 TGTGTTTCCCTCCCTATTCATG 57.765 45.455 0.00 0.00 0.00 3.07
70 71 3.591527 TGTGTTTCCCTCCCTATTCATGT 59.408 43.478 0.00 0.00 0.00 3.21
71 72 4.200092 GTGTTTCCCTCCCTATTCATGTC 58.800 47.826 0.00 0.00 0.00 3.06
72 73 3.849574 TGTTTCCCTCCCTATTCATGTCA 59.150 43.478 0.00 0.00 0.00 3.58
73 74 4.200092 GTTTCCCTCCCTATTCATGTCAC 58.800 47.826 0.00 0.00 0.00 3.67
74 75 2.408565 TCCCTCCCTATTCATGTCACC 58.591 52.381 0.00 0.00 0.00 4.02
75 76 2.022035 TCCCTCCCTATTCATGTCACCT 60.022 50.000 0.00 0.00 0.00 4.00
76 77 3.208922 TCCCTCCCTATTCATGTCACCTA 59.791 47.826 0.00 0.00 0.00 3.08
77 78 3.580458 CCCTCCCTATTCATGTCACCTAG 59.420 52.174 0.00 0.00 0.00 3.02
78 79 3.007398 CCTCCCTATTCATGTCACCTAGC 59.993 52.174 0.00 0.00 0.00 3.42
79 80 3.643320 CTCCCTATTCATGTCACCTAGCA 59.357 47.826 0.00 0.00 0.00 3.49
80 81 4.037222 TCCCTATTCATGTCACCTAGCAA 58.963 43.478 0.00 0.00 0.00 3.91
81 82 4.473196 TCCCTATTCATGTCACCTAGCAAA 59.527 41.667 0.00 0.00 0.00 3.68
82 83 5.045213 TCCCTATTCATGTCACCTAGCAAAA 60.045 40.000 0.00 0.00 0.00 2.44
83 84 5.066505 CCCTATTCATGTCACCTAGCAAAAC 59.933 44.000 0.00 0.00 0.00 2.43
84 85 5.882557 CCTATTCATGTCACCTAGCAAAACT 59.117 40.000 0.00 0.00 0.00 2.66
85 86 5.633830 ATTCATGTCACCTAGCAAAACTG 57.366 39.130 0.00 0.00 0.00 3.16
86 87 3.411446 TCATGTCACCTAGCAAAACTGG 58.589 45.455 0.00 0.00 0.00 4.00
87 88 3.149196 CATGTCACCTAGCAAAACTGGT 58.851 45.455 0.00 0.00 32.12 4.00
88 89 3.290948 TGTCACCTAGCAAAACTGGTT 57.709 42.857 0.00 0.00 30.26 3.67
89 90 2.948979 TGTCACCTAGCAAAACTGGTTG 59.051 45.455 0.00 0.00 30.26 3.77
115 116 7.993101 CAGAAAATGCAATCCTTATTCTGAGA 58.007 34.615 7.17 0.00 42.92 3.27
116 117 8.630917 CAGAAAATGCAATCCTTATTCTGAGAT 58.369 33.333 7.17 0.00 42.92 2.75
117 118 9.198475 AGAAAATGCAATCCTTATTCTGAGATT 57.802 29.630 0.00 0.00 0.00 2.40
121 122 8.632906 ATGCAATCCTTATTCTGAGATTAAGG 57.367 34.615 26.15 26.15 42.38 2.69
122 123 7.577303 TGCAATCCTTATTCTGAGATTAAGGT 58.423 34.615 28.60 19.20 42.02 3.50
123 124 7.500227 TGCAATCCTTATTCTGAGATTAAGGTG 59.500 37.037 28.60 23.76 42.02 4.00
124 125 7.500559 GCAATCCTTATTCTGAGATTAAGGTGT 59.499 37.037 28.60 20.62 42.02 4.16
135 136 7.710907 TCTGAGATTAAGGTGTATACATTGCAC 59.289 37.037 9.18 0.00 32.39 4.57
178 179 7.446931 ACTTCCAACACAACCAAAAAGAAAATT 59.553 29.630 0.00 0.00 0.00 1.82
241 242 6.146047 TCTCCTATTTGATCTTGATCAGGGA 58.854 40.000 12.31 15.17 31.46 4.20
262 263 3.357166 TCGGCAACCACAAATGTAAAC 57.643 42.857 0.00 0.00 0.00 2.01
312 313 3.134804 AGCATCATCAGGTGTACCTTACC 59.865 47.826 0.00 0.00 46.09 2.85
394 395 4.862823 AGGGTAGGGAGGCTCGGC 62.863 72.222 8.69 0.00 0.00 5.54
395 396 4.862823 GGGTAGGGAGGCTCGGCT 62.863 72.222 8.69 0.00 0.00 5.52
396 397 3.228017 GGTAGGGAGGCTCGGCTC 61.228 72.222 8.69 11.63 0.00 4.70
452 456 3.119990 ACACGCCAATAATCCGTTTTCAG 60.120 43.478 0.00 0.00 32.18 3.02
494 498 2.033747 CGCATGTTATCGTCCATGTGTC 60.034 50.000 0.00 0.00 42.05 3.67
514 518 1.539827 CGATCCAATTATTTCGCCCCC 59.460 52.381 0.00 0.00 0.00 5.40
515 519 2.593026 GATCCAATTATTTCGCCCCCA 58.407 47.619 0.00 0.00 0.00 4.96
519 523 3.196685 TCCAATTATTTCGCCCCCAAAAG 59.803 43.478 0.00 0.00 0.00 2.27
538 542 3.719816 GGACCATTATTCCCGTCCC 57.280 57.895 0.00 0.00 39.13 4.46
541 545 0.466963 ACCATTATTCCCGTCCCGTC 59.533 55.000 0.00 0.00 0.00 4.79
542 546 0.250166 CCATTATTCCCGTCCCGTCC 60.250 60.000 0.00 0.00 0.00 4.79
543 547 0.599204 CATTATTCCCGTCCCGTCCG 60.599 60.000 0.00 0.00 0.00 4.79
544 548 1.751349 ATTATTCCCGTCCCGTCCGG 61.751 60.000 0.00 0.00 45.07 5.14
545 549 3.660422 TATTCCCGTCCCGTCCGGT 62.660 63.158 0.00 0.00 43.98 5.28
549 553 3.372730 CCGTCCCGTCCGGTGTAA 61.373 66.667 0.00 0.00 40.59 2.41
550 554 2.713967 CCGTCCCGTCCGGTGTAAT 61.714 63.158 0.00 0.00 40.59 1.89
551 555 1.226773 CGTCCCGTCCGGTGTAATC 60.227 63.158 0.00 0.00 0.00 1.75
604 610 1.278985 TGAGCCCATCACAGATTTCGT 59.721 47.619 0.00 0.00 31.12 3.85
605 611 1.667724 GAGCCCATCACAGATTTCGTG 59.332 52.381 0.00 0.00 35.63 4.35
606 612 1.003580 AGCCCATCACAGATTTCGTGT 59.996 47.619 0.00 0.00 35.79 4.49
607 613 2.236146 AGCCCATCACAGATTTCGTGTA 59.764 45.455 0.00 0.00 35.79 2.90
608 614 3.118261 AGCCCATCACAGATTTCGTGTAT 60.118 43.478 0.00 0.00 35.79 2.29
609 615 3.002656 GCCCATCACAGATTTCGTGTATG 59.997 47.826 0.00 0.00 35.79 2.39
610 616 4.191544 CCCATCACAGATTTCGTGTATGT 58.808 43.478 0.00 0.00 35.79 2.29
611 617 5.356426 CCCATCACAGATTTCGTGTATGTA 58.644 41.667 0.00 0.00 35.79 2.29
614 620 6.479990 CCATCACAGATTTCGTGTATGTATGT 59.520 38.462 0.00 0.00 35.79 2.29
670 676 2.553028 CCGGATGGAAGGTTATGATGGG 60.553 54.545 0.00 0.00 37.49 4.00
693 699 2.610727 GGTGGTCAGTGAGTGAGTAAGC 60.611 54.545 0.00 0.00 35.13 3.09
733 739 0.250513 AGCGAGATGGTTCTGGTTCC 59.749 55.000 0.00 0.00 30.89 3.62
748 754 0.603065 GTTCCACACTTGCCATTCCC 59.397 55.000 0.00 0.00 0.00 3.97
760 766 4.066139 ATTCCCACCCCTGCCTGC 62.066 66.667 0.00 0.00 0.00 4.85
763 769 3.419580 CCCACCCCTGCCTGCATA 61.420 66.667 0.00 0.00 0.00 3.14
792 799 2.076100 TCTGCTAATGTTGGCACTTCG 58.924 47.619 0.00 0.00 39.85 3.79
861 868 4.143333 CCCCTCTACGCCACACCG 62.143 72.222 0.00 0.00 0.00 4.94
903 913 3.614092 CACAATACACAGAGGAAGCCAT 58.386 45.455 0.00 0.00 0.00 4.40
926 946 0.914417 CCCAAAGCCACCTCCCTCTA 60.914 60.000 0.00 0.00 0.00 2.43
934 954 0.178975 CACCTCCCTCTATCGGCTCT 60.179 60.000 0.00 0.00 0.00 4.09
939 959 1.531739 CCCTCTATCGGCTCTGCTCC 61.532 65.000 0.00 0.00 0.00 4.70
940 960 0.539438 CCTCTATCGGCTCTGCTCCT 60.539 60.000 0.00 0.00 0.00 3.69
947 967 1.037030 CGGCTCTGCTCCTCTCTTCT 61.037 60.000 0.00 0.00 0.00 2.85
976 996 0.927537 TCGTGTGTGTTTGCGAGAAG 59.072 50.000 0.00 0.00 0.00 2.85
1068 1088 2.509336 GACGGCGACATGGAGGTG 60.509 66.667 16.62 0.00 0.00 4.00
1112 1132 4.803908 CAAAGGGGGCGAGGAGGC 62.804 72.222 0.00 0.00 45.91 4.70
1281 1313 2.029964 ATCCACCGCGTGTTTCGT 59.970 55.556 4.92 0.00 42.13 3.85
1386 1445 0.392998 TTCCGGCATTTCTCTGCTCC 60.393 55.000 0.00 0.00 41.95 4.70
1393 1452 2.172483 ATTTCTCTGCTCCGTGCCGT 62.172 55.000 0.00 0.00 42.00 5.68
1406 1474 3.121030 GCCGTCGTGCTGCTGAAT 61.121 61.111 0.00 0.00 0.00 2.57
1407 1475 1.809619 GCCGTCGTGCTGCTGAATA 60.810 57.895 0.00 0.00 0.00 1.75
1423 1491 6.558009 TGCTGAATATGAAGCTGAATTGTTC 58.442 36.000 10.36 0.00 40.21 3.18
1435 1504 4.229096 CTGAATTGTTCGTGGATTTGGTG 58.771 43.478 0.00 0.00 0.00 4.17
1594 1684 2.881352 GAGTACCTGCACGAGCGC 60.881 66.667 0.00 0.00 46.23 5.92
1777 1873 2.106332 GACCCGCACTACATCCGG 59.894 66.667 0.00 0.00 41.60 5.14
2126 2240 2.045536 GCCAGGGGAAGCTGTGAG 60.046 66.667 0.00 0.00 0.00 3.51
2135 2249 0.598562 GAAGCTGTGAGTCACGAGGA 59.401 55.000 18.17 0.00 37.14 3.71
2201 2316 0.741927 TGATGATGGTGTGAGCTGCG 60.742 55.000 0.00 0.00 0.00 5.18
2203 2318 2.743538 GATGGTGTGAGCTGCGCA 60.744 61.111 10.98 10.98 33.90 6.09
2245 2364 4.735132 CCGAGGGCGAGCGAACAA 62.735 66.667 0.00 0.00 40.82 2.83
2246 2365 2.736995 CGAGGGCGAGCGAACAAA 60.737 61.111 0.00 0.00 40.82 2.83
2247 2366 2.861006 GAGGGCGAGCGAACAAAC 59.139 61.111 0.00 0.00 0.00 2.93
2248 2367 2.668550 AGGGCGAGCGAACAAACC 60.669 61.111 0.00 0.00 0.00 3.27
2249 2368 4.084888 GGGCGAGCGAACAAACCG 62.085 66.667 0.00 0.00 0.00 4.44
2279 2398 3.820777 GAGCATATCGAAAAGCCATCC 57.179 47.619 0.00 0.00 0.00 3.51
2314 2435 2.675889 GCGTGGGGAAAAAGAGTCGATA 60.676 50.000 0.00 0.00 0.00 2.92
2359 2486 1.064621 CGCGCTGATGGGGAATTTG 59.935 57.895 5.56 0.00 0.00 2.32
2370 2497 6.383763 TGATGGGGAATTTGGATGACATTAT 58.616 36.000 0.00 0.00 0.00 1.28
2381 2508 6.088016 TGGATGACATTATTATGCCAAAGC 57.912 37.500 0.00 0.00 35.03 3.51
2480 2607 5.988287 AGATTTTGGTGATTGTTTGGTTGT 58.012 33.333 0.00 0.00 0.00 3.32
2482 2609 6.538381 AGATTTTGGTGATTGTTTGGTTGTTC 59.462 34.615 0.00 0.00 0.00 3.18
2521 2723 3.111098 GTGTTCTTGCTGCTGTTCAAAG 58.889 45.455 0.00 0.00 0.00 2.77
2522 2724 2.754552 TGTTCTTGCTGCTGTTCAAAGT 59.245 40.909 0.00 0.00 0.00 2.66
2523 2725 3.193267 TGTTCTTGCTGCTGTTCAAAGTT 59.807 39.130 0.00 0.00 0.00 2.66
2524 2726 3.698029 TCTTGCTGCTGTTCAAAGTTC 57.302 42.857 0.00 0.00 0.00 3.01
2559 2777 2.060326 TTGTGGTTCGAGCTTCTACG 57.940 50.000 0.00 0.00 0.00 3.51
2564 2782 1.337821 GTTCGAGCTTCTACGTGTGG 58.662 55.000 0.00 0.00 0.00 4.17
2577 2795 2.203280 TGTGGCGGGTTTGACAGG 60.203 61.111 0.00 0.00 0.00 4.00
2592 2810 2.631062 TGACAGGCTTTCTCTCCGTAAA 59.369 45.455 1.90 0.00 0.00 2.01
2593 2811 2.994578 GACAGGCTTTCTCTCCGTAAAC 59.005 50.000 0.00 0.00 0.00 2.01
2596 2814 4.003648 CAGGCTTTCTCTCCGTAAACAAT 58.996 43.478 0.00 0.00 0.00 2.71
2597 2815 4.455877 CAGGCTTTCTCTCCGTAAACAATT 59.544 41.667 0.00 0.00 0.00 2.32
2599 2817 5.642491 AGGCTTTCTCTCCGTAAACAATTAC 59.358 40.000 0.00 0.00 38.42 1.89
2608 3185 4.573201 TCCGTAAACAATTACTGCTATGGC 59.427 41.667 0.00 0.00 39.42 4.40
2662 3239 3.004106 CAGTCCAGGTTCAAAAGCAGAAG 59.996 47.826 0.00 0.00 0.00 2.85
2696 3287 1.143969 CGACGTTATTCCGCTGTCCC 61.144 60.000 0.00 0.00 0.00 4.46
2757 3354 2.587194 CCAGAGCGCCAGATTCCG 60.587 66.667 2.29 0.00 0.00 4.30
2766 3364 0.391263 GCCAGATTCCGAAACTCCGT 60.391 55.000 0.00 0.00 0.00 4.69
2804 3402 4.218417 GCACATATTCTCCTCCTCTCTCTC 59.782 50.000 0.00 0.00 0.00 3.20
2805 3403 5.634118 CACATATTCTCCTCCTCTCTCTCT 58.366 45.833 0.00 0.00 0.00 3.10
2806 3404 5.474532 CACATATTCTCCTCCTCTCTCTCTG 59.525 48.000 0.00 0.00 0.00 3.35
2807 3405 5.372363 ACATATTCTCCTCCTCTCTCTCTGA 59.628 44.000 0.00 0.00 0.00 3.27
2843 3441 3.249091 CATGGCGCTCTCTGACATATAC 58.751 50.000 7.64 0.00 0.00 1.47
2844 3442 2.587522 TGGCGCTCTCTGACATATACT 58.412 47.619 7.64 0.00 0.00 2.12
2980 3627 3.853671 CGCTCAAATTGGAATTTTCTCCG 59.146 43.478 0.00 0.00 38.44 4.63
3003 3650 4.286297 AGTAGAAATACCACAGCTGCAA 57.714 40.909 15.27 0.00 0.00 4.08
3007 3654 2.119801 AATACCACAGCTGCAAGAGG 57.880 50.000 15.27 10.70 34.07 3.69
3034 3685 6.786967 AAAAACTATTCCTAGTAGCGGAGA 57.213 37.500 0.00 0.00 37.20 3.71
3035 3686 6.786967 AAAACTATTCCTAGTAGCGGAGAA 57.213 37.500 0.00 0.00 37.20 2.87
3049 3700 3.118038 AGCGGAGAACCCTAATAATGCAA 60.118 43.478 0.00 0.00 0.00 4.08
3051 3702 3.564225 CGGAGAACCCTAATAATGCAACC 59.436 47.826 0.00 0.00 0.00 3.77
3072 3724 3.368323 CCCAAAATGATTAAGCAAGCGGT 60.368 43.478 0.00 0.00 0.00 5.68
3097 3750 1.873591 CAGGGTCTTGACTTTGAACGG 59.126 52.381 0.61 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.560722 TGTTGTGTATTTTCTCTGAGGGA 57.439 39.130 4.59 0.00 0.00 4.20
1 2 5.182001 CCTTGTTGTGTATTTTCTCTGAGGG 59.818 44.000 4.59 0.00 0.00 4.30
2 3 5.997746 TCCTTGTTGTGTATTTTCTCTGAGG 59.002 40.000 4.59 0.00 0.00 3.86
3 4 6.348050 GCTCCTTGTTGTGTATTTTCTCTGAG 60.348 42.308 0.00 0.00 0.00 3.35
4 5 5.470098 GCTCCTTGTTGTGTATTTTCTCTGA 59.530 40.000 0.00 0.00 0.00 3.27
5 6 5.239306 TGCTCCTTGTTGTGTATTTTCTCTG 59.761 40.000 0.00 0.00 0.00 3.35
6 7 5.376625 TGCTCCTTGTTGTGTATTTTCTCT 58.623 37.500 0.00 0.00 0.00 3.10
7 8 5.689383 TGCTCCTTGTTGTGTATTTTCTC 57.311 39.130 0.00 0.00 0.00 2.87
8 9 6.655078 ATTGCTCCTTGTTGTGTATTTTCT 57.345 33.333 0.00 0.00 0.00 2.52
9 10 8.986477 ATAATTGCTCCTTGTTGTGTATTTTC 57.014 30.769 0.00 0.00 0.00 2.29
10 11 9.855021 GTATAATTGCTCCTTGTTGTGTATTTT 57.145 29.630 0.00 0.00 0.00 1.82
11 12 8.466798 GGTATAATTGCTCCTTGTTGTGTATTT 58.533 33.333 0.00 0.00 0.00 1.40
12 13 7.201696 CGGTATAATTGCTCCTTGTTGTGTATT 60.202 37.037 0.00 0.00 0.00 1.89
13 14 6.260050 CGGTATAATTGCTCCTTGTTGTGTAT 59.740 38.462 0.00 0.00 0.00 2.29
14 15 5.583061 CGGTATAATTGCTCCTTGTTGTGTA 59.417 40.000 0.00 0.00 0.00 2.90
15 16 4.394920 CGGTATAATTGCTCCTTGTTGTGT 59.605 41.667 0.00 0.00 0.00 3.72
16 17 4.394920 ACGGTATAATTGCTCCTTGTTGTG 59.605 41.667 0.00 0.00 0.00 3.33
17 18 4.394920 CACGGTATAATTGCTCCTTGTTGT 59.605 41.667 0.00 0.00 0.00 3.32
18 19 4.730613 GCACGGTATAATTGCTCCTTGTTG 60.731 45.833 0.00 0.00 33.26 3.33
19 20 3.377172 GCACGGTATAATTGCTCCTTGTT 59.623 43.478 0.00 0.00 33.26 2.83
20 21 2.943033 GCACGGTATAATTGCTCCTTGT 59.057 45.455 0.00 0.00 33.26 3.16
21 22 2.942376 TGCACGGTATAATTGCTCCTTG 59.058 45.455 0.00 0.00 37.16 3.61
22 23 3.275617 TGCACGGTATAATTGCTCCTT 57.724 42.857 0.00 0.00 37.16 3.36
23 24 3.118408 TCTTGCACGGTATAATTGCTCCT 60.118 43.478 0.00 0.00 37.16 3.69
24 25 3.002348 GTCTTGCACGGTATAATTGCTCC 59.998 47.826 0.00 0.00 37.16 4.70
25 26 3.621268 TGTCTTGCACGGTATAATTGCTC 59.379 43.478 0.00 0.00 37.16 4.26
26 27 3.605634 TGTCTTGCACGGTATAATTGCT 58.394 40.909 0.00 0.00 37.16 3.91
27 28 4.201910 ACATGTCTTGCACGGTATAATTGC 60.202 41.667 0.00 0.00 36.76 3.56
28 29 5.163764 ACACATGTCTTGCACGGTATAATTG 60.164 40.000 0.00 0.00 0.00 2.32
29 30 4.941263 ACACATGTCTTGCACGGTATAATT 59.059 37.500 0.00 0.00 0.00 1.40
30 31 4.513442 ACACATGTCTTGCACGGTATAAT 58.487 39.130 0.00 0.00 0.00 1.28
31 32 3.932822 ACACATGTCTTGCACGGTATAA 58.067 40.909 0.00 0.00 0.00 0.98
32 33 3.603158 ACACATGTCTTGCACGGTATA 57.397 42.857 0.00 0.00 0.00 1.47
33 34 2.472695 ACACATGTCTTGCACGGTAT 57.527 45.000 0.00 0.00 0.00 2.73
34 35 2.248280 AACACATGTCTTGCACGGTA 57.752 45.000 0.00 0.00 0.00 4.02
35 36 1.333619 GAAACACATGTCTTGCACGGT 59.666 47.619 0.00 0.00 0.00 4.83
36 37 1.334960 GGAAACACATGTCTTGCACGG 60.335 52.381 0.00 0.00 0.00 4.94
37 38 1.334960 GGGAAACACATGTCTTGCACG 60.335 52.381 0.00 0.00 0.00 5.34
38 39 1.956477 AGGGAAACACATGTCTTGCAC 59.044 47.619 0.00 0.00 0.00 4.57
39 40 2.229792 GAGGGAAACACATGTCTTGCA 58.770 47.619 0.00 0.00 0.00 4.08
40 41 1.541588 GGAGGGAAACACATGTCTTGC 59.458 52.381 0.00 0.00 0.00 4.01
41 42 2.162681 GGGAGGGAAACACATGTCTTG 58.837 52.381 0.00 0.00 0.00 3.02
42 43 2.065799 AGGGAGGGAAACACATGTCTT 58.934 47.619 0.00 0.00 0.00 3.01
43 44 1.747444 AGGGAGGGAAACACATGTCT 58.253 50.000 0.00 0.00 0.00 3.41
44 45 3.933861 ATAGGGAGGGAAACACATGTC 57.066 47.619 0.00 0.00 0.00 3.06
45 46 3.591527 TGAATAGGGAGGGAAACACATGT 59.408 43.478 0.00 0.00 0.00 3.21
46 47 4.235079 TGAATAGGGAGGGAAACACATG 57.765 45.455 0.00 0.00 0.00 3.21
47 48 4.230502 ACATGAATAGGGAGGGAAACACAT 59.769 41.667 0.00 0.00 0.00 3.21
48 49 3.591527 ACATGAATAGGGAGGGAAACACA 59.408 43.478 0.00 0.00 0.00 3.72
49 50 4.200092 GACATGAATAGGGAGGGAAACAC 58.800 47.826 0.00 0.00 0.00 3.32
50 51 3.849574 TGACATGAATAGGGAGGGAAACA 59.150 43.478 0.00 0.00 0.00 2.83
51 52 4.200092 GTGACATGAATAGGGAGGGAAAC 58.800 47.826 0.00 0.00 0.00 2.78
52 53 3.202151 GGTGACATGAATAGGGAGGGAAA 59.798 47.826 0.00 0.00 0.00 3.13
53 54 2.777692 GGTGACATGAATAGGGAGGGAA 59.222 50.000 0.00 0.00 0.00 3.97
54 55 2.022035 AGGTGACATGAATAGGGAGGGA 60.022 50.000 0.00 0.00 0.00 4.20
55 56 2.412591 AGGTGACATGAATAGGGAGGG 58.587 52.381 0.00 0.00 0.00 4.30
56 57 3.007398 GCTAGGTGACATGAATAGGGAGG 59.993 52.174 0.00 0.00 0.00 4.30
57 58 3.643320 TGCTAGGTGACATGAATAGGGAG 59.357 47.826 0.00 0.00 0.00 4.30
58 59 3.653164 TGCTAGGTGACATGAATAGGGA 58.347 45.455 0.00 0.00 0.00 4.20
59 60 4.422073 TTGCTAGGTGACATGAATAGGG 57.578 45.455 0.00 0.00 0.00 3.53
60 61 5.882557 AGTTTTGCTAGGTGACATGAATAGG 59.117 40.000 0.00 0.00 0.00 2.57
61 62 6.183360 CCAGTTTTGCTAGGTGACATGAATAG 60.183 42.308 0.00 0.00 0.00 1.73
62 63 5.647658 CCAGTTTTGCTAGGTGACATGAATA 59.352 40.000 0.00 0.00 0.00 1.75
63 64 4.460382 CCAGTTTTGCTAGGTGACATGAAT 59.540 41.667 0.00 0.00 0.00 2.57
64 65 3.820467 CCAGTTTTGCTAGGTGACATGAA 59.180 43.478 0.00 0.00 0.00 2.57
65 66 3.181445 ACCAGTTTTGCTAGGTGACATGA 60.181 43.478 0.00 0.00 32.04 3.07
66 67 3.149196 ACCAGTTTTGCTAGGTGACATG 58.851 45.455 0.00 0.00 32.04 3.21
67 68 3.508845 ACCAGTTTTGCTAGGTGACAT 57.491 42.857 0.00 0.00 32.04 3.06
68 69 2.948979 CAACCAGTTTTGCTAGGTGACA 59.051 45.455 0.00 0.00 33.93 3.58
69 70 3.626028 CAACCAGTTTTGCTAGGTGAC 57.374 47.619 0.00 0.00 33.93 3.67
90 91 7.993101 TCTCAGAATAAGGATTGCATTTTCTG 58.007 34.615 11.26 11.26 36.04 3.02
91 92 8.763984 ATCTCAGAATAAGGATTGCATTTTCT 57.236 30.769 0.00 0.00 0.00 2.52
95 96 9.075678 CCTTAATCTCAGAATAAGGATTGCATT 57.924 33.333 20.40 0.00 43.91 3.56
96 97 8.223330 ACCTTAATCTCAGAATAAGGATTGCAT 58.777 33.333 28.68 8.09 43.91 3.96
97 98 7.500227 CACCTTAATCTCAGAATAAGGATTGCA 59.500 37.037 28.68 0.00 43.91 4.08
98 99 7.500559 ACACCTTAATCTCAGAATAAGGATTGC 59.499 37.037 28.68 0.00 43.91 3.56
99 100 8.970859 ACACCTTAATCTCAGAATAAGGATTG 57.029 34.615 28.68 20.80 43.91 2.67
107 108 9.277783 GCAATGTATACACCTTAATCTCAGAAT 57.722 33.333 7.96 0.00 0.00 2.40
108 109 8.264347 TGCAATGTATACACCTTAATCTCAGAA 58.736 33.333 7.96 0.00 0.00 3.02
109 110 7.710907 GTGCAATGTATACACCTTAATCTCAGA 59.289 37.037 7.96 0.00 0.00 3.27
110 111 7.306807 CGTGCAATGTATACACCTTAATCTCAG 60.307 40.741 7.96 0.00 0.00 3.35
111 112 6.478673 CGTGCAATGTATACACCTTAATCTCA 59.521 38.462 7.96 0.00 0.00 3.27
112 113 6.700081 TCGTGCAATGTATACACCTTAATCTC 59.300 38.462 7.96 0.00 0.00 2.75
113 114 6.578944 TCGTGCAATGTATACACCTTAATCT 58.421 36.000 7.96 0.00 0.00 2.40
114 115 6.838198 TCGTGCAATGTATACACCTTAATC 57.162 37.500 7.96 0.00 0.00 1.75
115 116 6.293407 GCATCGTGCAATGTATACACCTTAAT 60.293 38.462 7.96 0.00 44.26 1.40
116 117 5.007234 GCATCGTGCAATGTATACACCTTAA 59.993 40.000 7.96 0.00 44.26 1.85
117 118 4.509970 GCATCGTGCAATGTATACACCTTA 59.490 41.667 7.96 0.00 44.26 2.69
118 119 3.312421 GCATCGTGCAATGTATACACCTT 59.688 43.478 7.96 0.00 44.26 3.50
119 120 2.872245 GCATCGTGCAATGTATACACCT 59.128 45.455 7.96 0.00 44.26 4.00
120 121 3.253371 GCATCGTGCAATGTATACACC 57.747 47.619 7.96 0.47 44.26 4.16
135 136 1.165907 AGTGTTGGGTGTGTGCATCG 61.166 55.000 0.00 0.00 0.00 3.84
206 207 4.998051 TCAAATAGGAGAGCCTGGTTTTT 58.002 39.130 0.00 0.00 46.45 1.94
207 208 4.657814 TCAAATAGGAGAGCCTGGTTTT 57.342 40.909 0.00 0.00 46.45 2.43
208 209 4.476479 AGATCAAATAGGAGAGCCTGGTTT 59.524 41.667 0.00 0.00 46.45 3.27
209 210 4.043596 AGATCAAATAGGAGAGCCTGGTT 58.956 43.478 0.00 0.00 46.45 3.67
210 211 3.663198 AGATCAAATAGGAGAGCCTGGT 58.337 45.455 0.00 0.00 46.45 4.00
215 216 5.933463 CCTGATCAAGATCAAATAGGAGAGC 59.067 44.000 13.25 0.00 46.10 4.09
241 242 3.610585 CGTTTACATTTGTGGTTGCCGAT 60.611 43.478 0.00 0.00 0.00 4.18
312 313 3.711704 ACTACCACTGATATGACTTGGGG 59.288 47.826 0.00 0.00 0.00 4.96
394 395 1.571460 GCCAATTATGCGCGAGGAG 59.429 57.895 12.10 0.00 32.19 3.69
395 396 2.243957 CGCCAATTATGCGCGAGGA 61.244 57.895 12.10 0.00 46.01 3.71
396 397 2.249309 CGCCAATTATGCGCGAGG 59.751 61.111 12.10 0.00 46.01 4.63
494 498 1.539827 GGGGGCGAAATAATTGGATCG 59.460 52.381 0.00 4.76 38.28 3.69
538 542 5.862323 CCAATAGATTAGATTACACCGGACG 59.138 44.000 9.46 0.00 0.00 4.79
541 545 5.869888 GCTCCAATAGATTAGATTACACCGG 59.130 44.000 0.00 0.00 0.00 5.28
542 546 6.692486 AGCTCCAATAGATTAGATTACACCG 58.308 40.000 0.00 0.00 0.00 4.94
543 547 7.100409 GGAGCTCCAATAGATTAGATTACACC 58.900 42.308 28.43 0.00 35.64 4.16
544 548 7.671302 TGGAGCTCCAATAGATTAGATTACAC 58.329 38.462 33.41 0.00 44.35 2.90
545 549 7.038729 CCTGGAGCTCCAATAGATTAGATTACA 60.039 40.741 34.30 7.09 46.97 2.41
546 550 7.327214 CCTGGAGCTCCAATAGATTAGATTAC 58.673 42.308 34.30 2.34 46.97 1.89
547 551 6.441924 CCCTGGAGCTCCAATAGATTAGATTA 59.558 42.308 34.30 8.15 46.97 1.75
548 552 5.250313 CCCTGGAGCTCCAATAGATTAGATT 59.750 44.000 34.30 0.00 46.97 2.40
549 553 4.782156 CCCTGGAGCTCCAATAGATTAGAT 59.218 45.833 34.30 0.00 46.97 1.98
550 554 4.140686 TCCCTGGAGCTCCAATAGATTAGA 60.141 45.833 34.30 18.55 46.97 2.10
551 555 4.020662 GTCCCTGGAGCTCCAATAGATTAG 60.021 50.000 34.30 20.20 46.97 1.73
593 599 8.352752 ACATACATACATACACGAAATCTGTG 57.647 34.615 0.00 4.60 42.99 3.66
647 653 2.184088 TCATAACCTTCCATCCGGGA 57.816 50.000 0.00 0.00 46.61 5.14
648 654 2.553028 CCATCATAACCTTCCATCCGGG 60.553 54.545 0.00 0.00 38.37 5.73
649 655 2.553028 CCCATCATAACCTTCCATCCGG 60.553 54.545 0.00 0.00 0.00 5.14
650 656 2.106511 ACCCATCATAACCTTCCATCCG 59.893 50.000 0.00 0.00 0.00 4.18
670 676 0.753262 ACTCACTCACTGACCACCAC 59.247 55.000 0.00 0.00 0.00 4.16
712 718 0.976641 AACCAGAACCATCTCGCTGA 59.023 50.000 0.00 0.00 32.03 4.26
733 739 1.535204 GGGTGGGAATGGCAAGTGTG 61.535 60.000 0.00 0.00 0.00 3.82
748 754 0.473755 TATGTATGCAGGCAGGGGTG 59.526 55.000 0.00 0.00 0.00 4.61
760 766 7.966753 GCCAACATTAGCAGATCATTATGTATG 59.033 37.037 0.00 0.00 35.45 2.39
761 767 7.666804 TGCCAACATTAGCAGATCATTATGTAT 59.333 33.333 0.00 0.00 33.08 2.29
762 768 6.997476 TGCCAACATTAGCAGATCATTATGTA 59.003 34.615 0.00 0.00 33.08 2.29
763 769 5.829391 TGCCAACATTAGCAGATCATTATGT 59.171 36.000 0.00 0.00 33.08 2.29
792 799 2.597510 GGTGGGGGTGTGAACTGC 60.598 66.667 0.00 0.00 0.00 4.40
861 868 1.153881 GAGAACGGCGGGTGTACTC 60.154 63.158 13.24 6.67 0.00 2.59
903 913 1.771646 GGAGGTGGCTTTGGGGTTA 59.228 57.895 0.00 0.00 0.00 2.85
926 946 0.396974 AAGAGAGGAGCAGAGCCGAT 60.397 55.000 0.00 0.00 0.00 4.18
934 954 1.745232 GAGACGAGAAGAGAGGAGCA 58.255 55.000 0.00 0.00 0.00 4.26
939 959 1.586578 CGAGACGAGACGAGAAGAGAG 59.413 57.143 0.00 0.00 0.00 3.20
940 960 1.067706 ACGAGACGAGACGAGAAGAGA 60.068 52.381 0.00 0.00 0.00 3.10
947 967 1.156034 ACACACACGAGACGAGACGA 61.156 55.000 0.00 0.00 0.00 4.20
976 996 0.529992 CCTCGCCGGTTTCTATGGAC 60.530 60.000 1.90 0.00 0.00 4.02
1005 1025 2.421619 CAGAAGAACCTGAACCTCTGC 58.578 52.381 0.00 0.00 36.29 4.26
1093 1113 4.803908 CTCCTCGCCCCCTTTGCC 62.804 72.222 0.00 0.00 0.00 4.52
1275 1307 0.522180 TCTCGAGCTCCTGACGAAAC 59.478 55.000 7.81 0.00 35.70 2.78
1278 1310 3.892122 GTCTCGAGCTCCTGACGA 58.108 61.111 7.81 0.65 34.90 4.20
1281 1313 2.045829 AGCGTCTCGAGCTCCTGA 60.046 61.111 7.81 3.54 41.83 3.86
1393 1452 1.935873 GCTTCATATTCAGCAGCACGA 59.064 47.619 0.00 0.00 35.95 4.35
1397 1465 4.832590 ATTCAGCTTCATATTCAGCAGC 57.167 40.909 5.82 0.00 38.61 5.25
1398 1466 6.132791 ACAATTCAGCTTCATATTCAGCAG 57.867 37.500 5.82 0.00 38.61 4.24
1404 1472 5.647658 TCCACGAACAATTCAGCTTCATATT 59.352 36.000 0.00 0.00 0.00 1.28
1406 1474 4.574892 TCCACGAACAATTCAGCTTCATA 58.425 39.130 0.00 0.00 0.00 2.15
1407 1475 3.411446 TCCACGAACAATTCAGCTTCAT 58.589 40.909 0.00 0.00 0.00 2.57
1423 1491 0.452987 CTGCATCCACCAAATCCACG 59.547 55.000 0.00 0.00 0.00 4.94
1435 1504 1.890979 CACGCCCTCATCTGCATCC 60.891 63.158 0.00 0.00 0.00 3.51
2135 2249 0.676782 AACGCCTACGGTAGTACGGT 60.677 55.000 23.19 17.86 46.04 4.83
2136 2250 1.295792 TAACGCCTACGGTAGTACGG 58.704 55.000 23.19 6.33 46.04 4.02
2142 2256 1.229428 CGGATCTAACGCCTACGGTA 58.771 55.000 0.00 0.00 46.04 4.02
2201 2316 2.360852 AGGCTCCATGTGTGCTGC 60.361 61.111 0.00 0.00 33.94 5.25
2203 2318 2.267006 CGAGGCTCCATGTGTGCT 59.733 61.111 9.32 0.00 33.94 4.40
2238 2357 1.571215 CCCACTACCGGTTTGTTCGC 61.571 60.000 15.04 0.00 0.00 4.70
2240 2359 1.571215 CGCCCACTACCGGTTTGTTC 61.571 60.000 15.04 3.67 0.00 3.18
2243 2362 1.740296 CTCGCCCACTACCGGTTTG 60.740 63.158 15.04 10.99 0.00 2.93
2244 2363 2.660802 CTCGCCCACTACCGGTTT 59.339 61.111 15.04 0.00 0.00 3.27
2245 2364 4.078516 GCTCGCCCACTACCGGTT 62.079 66.667 15.04 0.00 0.00 4.44
2247 2366 1.816863 ATATGCTCGCCCACTACCGG 61.817 60.000 0.00 0.00 0.00 5.28
2248 2367 0.388649 GATATGCTCGCCCACTACCG 60.389 60.000 0.00 0.00 0.00 4.02
2249 2368 0.388649 CGATATGCTCGCCCACTACC 60.389 60.000 0.00 0.00 41.14 3.18
2292 2413 0.882927 CGACTCTTTTTCCCCACGCA 60.883 55.000 0.00 0.00 0.00 5.24
2314 2435 5.600669 AACCCTACCTTTTTCTCTTCCAT 57.399 39.130 0.00 0.00 0.00 3.41
2359 2486 5.156355 CGCTTTGGCATAATAATGTCATCC 58.844 41.667 0.00 0.00 46.69 3.51
2381 2508 0.888736 TCACACCCAAATCACTGCCG 60.889 55.000 0.00 0.00 0.00 5.69
2480 2607 9.391006 AGAACACTCAATGTACTTTTTACAGAA 57.609 29.630 0.00 0.00 42.31 3.02
2482 2609 9.438291 CAAGAACACTCAATGTACTTTTTACAG 57.562 33.333 0.00 0.00 42.31 2.74
2521 2723 3.599091 ACAAACAAAACGAACGAACGAAC 59.401 39.130 11.97 0.00 37.03 3.95
2522 2724 3.598668 CACAAACAAAACGAACGAACGAA 59.401 39.130 11.97 0.00 37.03 3.85
2523 2725 3.154489 CACAAACAAAACGAACGAACGA 58.846 40.909 11.97 0.00 37.03 3.85
2524 2726 2.274228 CCACAAACAAAACGAACGAACG 59.726 45.455 0.14 0.00 39.31 3.95
2559 2777 2.551912 CCTGTCAAACCCGCCACAC 61.552 63.158 0.00 0.00 0.00 3.82
2564 2782 1.172812 AGAAAGCCTGTCAAACCCGC 61.173 55.000 0.00 0.00 0.00 6.13
2577 2795 6.534934 CAGTAATTGTTTACGGAGAGAAAGC 58.465 40.000 0.00 0.00 42.14 3.51
2662 3239 1.751552 CGTCGTATTAAGAGGACGCC 58.248 55.000 26.07 3.33 46.64 5.68
2696 3287 0.176680 ACCCACTAATCTGCTCTGCG 59.823 55.000 0.00 0.00 0.00 5.18
2804 3402 4.794003 GCCATGGACTGAGTTTTTGTTCAG 60.794 45.833 18.40 0.27 44.93 3.02
2805 3403 3.068024 GCCATGGACTGAGTTTTTGTTCA 59.932 43.478 18.40 0.00 0.00 3.18
2806 3404 3.642705 GCCATGGACTGAGTTTTTGTTC 58.357 45.455 18.40 0.00 0.00 3.18
2807 3405 2.034558 CGCCATGGACTGAGTTTTTGTT 59.965 45.455 18.40 0.00 0.00 2.83
2980 3627 4.755411 TGCAGCTGTGGTATTTCTACTAC 58.245 43.478 16.64 0.00 39.19 2.73
3015 3666 4.143543 GGTTCTCCGCTACTAGGAATAGT 58.856 47.826 0.00 0.00 37.32 2.12
3016 3667 3.506844 GGGTTCTCCGCTACTAGGAATAG 59.493 52.174 0.00 0.00 37.32 1.73
3017 3668 3.139770 AGGGTTCTCCGCTACTAGGAATA 59.860 47.826 0.00 0.00 41.52 1.75
3018 3669 2.091222 AGGGTTCTCCGCTACTAGGAAT 60.091 50.000 0.00 0.00 41.52 3.01
3019 3670 1.287146 AGGGTTCTCCGCTACTAGGAA 59.713 52.381 0.00 0.00 41.52 3.36
3020 3671 0.924823 AGGGTTCTCCGCTACTAGGA 59.075 55.000 0.00 0.00 41.52 2.94
3022 3673 6.622549 CATTATTAGGGTTCTCCGCTACTAG 58.377 44.000 0.00 0.00 38.23 2.57
3023 3674 5.047519 GCATTATTAGGGTTCTCCGCTACTA 60.048 44.000 0.00 0.00 38.23 1.82
3024 3675 4.262506 GCATTATTAGGGTTCTCCGCTACT 60.263 45.833 0.00 0.00 38.23 2.57
3025 3676 3.995048 GCATTATTAGGGTTCTCCGCTAC 59.005 47.826 0.00 0.00 38.23 3.58
3026 3677 3.644265 TGCATTATTAGGGTTCTCCGCTA 59.356 43.478 0.00 0.00 41.52 4.26
3029 3680 3.564225 GGTTGCATTATTAGGGTTCTCCG 59.436 47.826 0.00 0.00 41.52 4.63
3030 3681 3.889538 GGGTTGCATTATTAGGGTTCTCC 59.110 47.826 0.00 0.00 0.00 3.71
3033 3684 5.669164 TTTGGGTTGCATTATTAGGGTTC 57.331 39.130 0.00 0.00 0.00 3.62
3034 3685 6.214412 TCATTTTGGGTTGCATTATTAGGGTT 59.786 34.615 0.00 0.00 0.00 4.11
3035 3686 5.723887 TCATTTTGGGTTGCATTATTAGGGT 59.276 36.000 0.00 0.00 0.00 4.34
3049 3700 3.368323 CCGCTTGCTTAATCATTTTGGGT 60.368 43.478 0.00 0.00 0.00 4.51
3051 3702 3.613737 CACCGCTTGCTTAATCATTTTGG 59.386 43.478 0.00 0.00 0.00 3.28
3072 3724 1.140312 AAAGTCAAGACCCTGGCTCA 58.860 50.000 0.00 0.00 28.77 4.26
3076 3728 1.873591 CGTTCAAAGTCAAGACCCTGG 59.126 52.381 0.00 0.00 0.00 4.45
3077 3729 1.873591 CCGTTCAAAGTCAAGACCCTG 59.126 52.381 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.