Multiple sequence alignment - TraesCS5A01G142900

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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 TraesCS5A01G142900 chr5A 100.000 2450 0 0 1 2450 316658243 316660692 0.000000e+00 4525.0
1 TraesCS5A01G142900 chr5A 84.709 327 44 5 400 725 693410238 693409917 3.040000e-84 322.0
2 TraesCS5A01G142900 chr5A 84.146 328 47 5 400 725 693494013 693493689 1.830000e-81 313.0
3 TraesCS5A01G142900 chr5B 93.248 1718 52 20 773 2448 267417202 267418897 0.000000e+00 2471.0
4 TraesCS5A01G142900 chr5D 91.809 1697 61 30 773 2448 238150649 238149010 0.000000e+00 2292.0
5 TraesCS5A01G142900 chr4A 89.030 474 48 2 983 1452 469101957 469102430 3.510000e-163 584.0
6 TraesCS5A01G142900 chr4A 84.564 447 69 0 1004 1450 611278029 611278475 6.220000e-121 444.0
7 TraesCS5A01G142900 chr4D 88.913 460 50 1 1000 1459 106739243 106738785 1.270000e-157 566.0
8 TraesCS5A01G142900 chr4D 84.404 327 42 6 400 725 508101154 508100836 1.830000e-81 313.0
9 TraesCS5A01G142900 chr6B 80.464 604 90 17 132 730 142507209 142507789 1.040000e-118 436.0
10 TraesCS5A01G142900 chr6B 87.622 307 30 5 413 719 50129777 50129479 1.390000e-92 350.0
11 TraesCS5A01G142900 chr6B 93.182 44 3 0 77 120 641759981 641759938 5.650000e-07 65.8
12 TraesCS5A01G142900 chr1D 81.664 529 77 16 203 725 315604993 315605507 2.910000e-114 422.0
13 TraesCS5A01G142900 chr7B 86.579 380 41 5 349 727 333354837 333355207 6.310000e-111 411.0
14 TraesCS5A01G142900 chr2A 85.804 317 40 5 1715 2027 56882048 56881733 5.050000e-87 331.0
15 TraesCS5A01G142900 chr2A 86.174 311 38 5 1715 2021 56885096 56885405 5.050000e-87 331.0
16 TraesCS5A01G142900 chr2A 87.692 65 8 0 1957 2021 56534227 56534291 2.610000e-10 76.8
17 TraesCS5A01G142900 chr2B 79.747 395 59 16 161 549 753918841 753919220 1.440000e-67 267.0
18 TraesCS5A01G142900 chr4B 75.769 520 100 17 213 725 571602576 571602076 3.150000e-59 239.0
19 TraesCS5A01G142900 chr2D 90.244 41 4 0 126 166 570404614 570404654 1.000000e-03 54.7


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 TraesCS5A01G142900 chr5A 316658243 316660692 2449 False 4525 4525 100.000 1 2450 1 chr5A.!!$F1 2449
1 TraesCS5A01G142900 chr5B 267417202 267418897 1695 False 2471 2471 93.248 773 2448 1 chr5B.!!$F1 1675
2 TraesCS5A01G142900 chr5D 238149010 238150649 1639 True 2292 2292 91.809 773 2448 1 chr5D.!!$R1 1675
3 TraesCS5A01G142900 chr6B 142507209 142507789 580 False 436 436 80.464 132 730 1 chr6B.!!$F1 598
4 TraesCS5A01G142900 chr1D 315604993 315605507 514 False 422 422 81.664 203 725 1 chr1D.!!$F1 522
5 TraesCS5A01G142900 chr4B 571602076 571602576 500 True 239 239 75.769 213 725 1 chr4B.!!$R1 512

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
80 81 0.039256 TTGTGCTTCTGGCGATTTGC 60.039 50.0 0.0 0.0 45.43 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 1937 1.306148 TGTCTATACACGAGCCGGAG 58.694 55.0 5.05 0.0 0.0 4.63 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
20 21 3.451141 GTGTGGAACCTTTCATTTGCA 57.549 42.857 0.00 0.00 34.36 4.08
21 22 3.993920 GTGTGGAACCTTTCATTTGCAT 58.006 40.909 0.00 0.00 34.36 3.96
22 23 5.132897 GTGTGGAACCTTTCATTTGCATA 57.867 39.130 0.00 0.00 34.36 3.14
23 24 4.923281 GTGTGGAACCTTTCATTTGCATAC 59.077 41.667 0.00 0.00 34.36 2.39
24 25 4.832266 TGTGGAACCTTTCATTTGCATACT 59.168 37.500 0.00 0.00 34.36 2.12
25 26 5.304101 TGTGGAACCTTTCATTTGCATACTT 59.696 36.000 0.00 0.00 34.36 2.24
26 27 6.183360 TGTGGAACCTTTCATTTGCATACTTT 60.183 34.615 0.00 0.00 34.36 2.66
27 28 6.146021 GTGGAACCTTTCATTTGCATACTTTG 59.854 38.462 0.00 0.00 0.00 2.77
28 29 6.041409 TGGAACCTTTCATTTGCATACTTTGA 59.959 34.615 0.00 0.00 0.00 2.69
29 30 7.099120 GGAACCTTTCATTTGCATACTTTGAT 58.901 34.615 0.00 0.00 0.00 2.57
30 31 7.063780 GGAACCTTTCATTTGCATACTTTGATG 59.936 37.037 0.00 0.00 0.00 3.07
31 32 6.400568 ACCTTTCATTTGCATACTTTGATGG 58.599 36.000 0.00 0.00 0.00 3.51
32 33 5.813672 CCTTTCATTTGCATACTTTGATGGG 59.186 40.000 0.00 0.00 0.00 4.00
33 34 5.341872 TTCATTTGCATACTTTGATGGGG 57.658 39.130 0.00 0.00 0.00 4.96
34 35 4.352009 TCATTTGCATACTTTGATGGGGT 58.648 39.130 0.00 0.00 0.00 4.95
35 36 4.160065 TCATTTGCATACTTTGATGGGGTG 59.840 41.667 0.00 0.00 0.00 4.61
36 37 2.897271 TGCATACTTTGATGGGGTGT 57.103 45.000 0.00 0.00 0.00 4.16
37 38 4.308526 TTGCATACTTTGATGGGGTGTA 57.691 40.909 0.00 0.00 0.00 2.90
38 39 4.518278 TGCATACTTTGATGGGGTGTAT 57.482 40.909 0.00 0.00 0.00 2.29
39 40 5.638530 TGCATACTTTGATGGGGTGTATA 57.361 39.130 0.00 0.00 0.00 1.47
40 41 6.199557 TGCATACTTTGATGGGGTGTATAT 57.800 37.500 0.00 0.00 0.00 0.86
41 42 6.003326 TGCATACTTTGATGGGGTGTATATG 58.997 40.000 0.00 0.00 0.00 1.78
42 43 5.106157 GCATACTTTGATGGGGTGTATATGC 60.106 44.000 0.00 0.00 36.64 3.14
43 44 4.796110 ACTTTGATGGGGTGTATATGCT 57.204 40.909 0.00 0.00 0.00 3.79
44 45 5.904984 ACTTTGATGGGGTGTATATGCTA 57.095 39.130 0.00 0.00 0.00 3.49
45 46 5.621193 ACTTTGATGGGGTGTATATGCTAC 58.379 41.667 0.00 0.00 0.00 3.58
46 47 5.369699 ACTTTGATGGGGTGTATATGCTACT 59.630 40.000 0.00 0.00 0.00 2.57
47 48 5.904984 TTGATGGGGTGTATATGCTACTT 57.095 39.130 0.00 0.00 0.00 2.24
48 49 5.904984 TGATGGGGTGTATATGCTACTTT 57.095 39.130 0.00 0.00 0.00 2.66
49 50 5.620206 TGATGGGGTGTATATGCTACTTTG 58.380 41.667 0.00 0.00 0.00 2.77
50 51 5.131977 TGATGGGGTGTATATGCTACTTTGT 59.868 40.000 0.00 0.00 0.00 2.83
51 52 4.776349 TGGGGTGTATATGCTACTTTGTG 58.224 43.478 0.00 0.00 0.00 3.33
52 53 4.471747 TGGGGTGTATATGCTACTTTGTGA 59.528 41.667 0.00 0.00 0.00 3.58
53 54 5.057149 GGGGTGTATATGCTACTTTGTGAG 58.943 45.833 0.00 0.00 0.00 3.51
54 55 5.163343 GGGGTGTATATGCTACTTTGTGAGA 60.163 44.000 0.00 0.00 0.00 3.27
55 56 5.753921 GGGTGTATATGCTACTTTGTGAGAC 59.246 44.000 0.00 0.00 0.00 3.36
56 57 5.753921 GGTGTATATGCTACTTTGTGAGACC 59.246 44.000 0.00 0.00 0.00 3.85
57 58 6.407074 GGTGTATATGCTACTTTGTGAGACCT 60.407 42.308 0.00 0.00 0.00 3.85
58 59 7.042335 GTGTATATGCTACTTTGTGAGACCTT 58.958 38.462 0.00 0.00 0.00 3.50
59 60 7.010552 GTGTATATGCTACTTTGTGAGACCTTG 59.989 40.741 0.00 0.00 0.00 3.61
60 61 3.838244 TGCTACTTTGTGAGACCTTGT 57.162 42.857 0.00 0.00 0.00 3.16
61 62 4.150897 TGCTACTTTGTGAGACCTTGTT 57.849 40.909 0.00 0.00 0.00 2.83
62 63 4.523083 TGCTACTTTGTGAGACCTTGTTT 58.477 39.130 0.00 0.00 0.00 2.83
63 64 4.335315 TGCTACTTTGTGAGACCTTGTTTG 59.665 41.667 0.00 0.00 0.00 2.93
64 65 4.335594 GCTACTTTGTGAGACCTTGTTTGT 59.664 41.667 0.00 0.00 0.00 2.83
65 66 4.701956 ACTTTGTGAGACCTTGTTTGTG 57.298 40.909 0.00 0.00 0.00 3.33
66 67 3.119495 ACTTTGTGAGACCTTGTTTGTGC 60.119 43.478 0.00 0.00 0.00 4.57
67 68 2.418368 TGTGAGACCTTGTTTGTGCT 57.582 45.000 0.00 0.00 0.00 4.40
68 69 2.722094 TGTGAGACCTTGTTTGTGCTT 58.278 42.857 0.00 0.00 0.00 3.91
69 70 2.682856 TGTGAGACCTTGTTTGTGCTTC 59.317 45.455 0.00 0.00 0.00 3.86
70 71 2.945668 GTGAGACCTTGTTTGTGCTTCT 59.054 45.455 0.00 0.00 0.00 2.85
71 72 2.945008 TGAGACCTTGTTTGTGCTTCTG 59.055 45.455 0.00 0.00 0.00 3.02
72 73 2.291741 GAGACCTTGTTTGTGCTTCTGG 59.708 50.000 0.00 0.00 0.00 3.86
73 74 0.746659 ACCTTGTTTGTGCTTCTGGC 59.253 50.000 0.00 0.00 42.22 4.85
74 75 0.318107 CCTTGTTTGTGCTTCTGGCG 60.318 55.000 0.00 0.00 45.43 5.69
75 76 0.662619 CTTGTTTGTGCTTCTGGCGA 59.337 50.000 0.00 0.00 45.43 5.54
76 77 1.267806 CTTGTTTGTGCTTCTGGCGAT 59.732 47.619 0.00 0.00 45.43 4.58
77 78 1.317613 TGTTTGTGCTTCTGGCGATT 58.682 45.000 0.00 0.00 45.43 3.34
78 79 1.680735 TGTTTGTGCTTCTGGCGATTT 59.319 42.857 0.00 0.00 45.43 2.17
79 80 2.053627 GTTTGTGCTTCTGGCGATTTG 58.946 47.619 0.00 0.00 45.43 2.32
80 81 0.039256 TTGTGCTTCTGGCGATTTGC 60.039 50.000 0.00 0.00 45.43 3.68
81 82 0.890542 TGTGCTTCTGGCGATTTGCT 60.891 50.000 0.00 0.00 45.43 3.91
82 83 0.242017 GTGCTTCTGGCGATTTGCTT 59.758 50.000 0.00 0.00 45.43 3.91
83 84 0.961019 TGCTTCTGGCGATTTGCTTT 59.039 45.000 0.00 0.00 45.43 3.51
84 85 2.095263 GTGCTTCTGGCGATTTGCTTTA 60.095 45.455 0.00 0.00 45.43 1.85
85 86 2.754552 TGCTTCTGGCGATTTGCTTTAT 59.245 40.909 0.00 0.00 45.43 1.40
86 87 3.944650 TGCTTCTGGCGATTTGCTTTATA 59.055 39.130 0.00 0.00 45.43 0.98
87 88 4.580167 TGCTTCTGGCGATTTGCTTTATAT 59.420 37.500 0.00 0.00 45.43 0.86
88 89 5.762711 TGCTTCTGGCGATTTGCTTTATATA 59.237 36.000 0.00 0.00 45.43 0.86
89 90 6.430925 TGCTTCTGGCGATTTGCTTTATATAT 59.569 34.615 0.00 0.00 45.43 0.86
90 91 7.606073 TGCTTCTGGCGATTTGCTTTATATATA 59.394 33.333 0.00 0.00 45.43 0.86
91 92 8.450964 GCTTCTGGCGATTTGCTTTATATATAA 58.549 33.333 0.81 0.81 45.43 0.98
107 108 9.856162 TTTATATATAAAGCGGGAAGAAAACCT 57.144 29.630 12.90 0.00 0.00 3.50
110 111 7.981102 ATATAAAGCGGGAAGAAAACCTATC 57.019 36.000 0.00 0.00 0.00 2.08
111 112 4.302559 AAAGCGGGAAGAAAACCTATCT 57.697 40.909 0.00 0.00 0.00 1.98
112 113 3.545366 AGCGGGAAGAAAACCTATCTC 57.455 47.619 0.00 0.00 0.00 2.75
113 114 2.159085 AGCGGGAAGAAAACCTATCTCG 60.159 50.000 0.00 0.00 0.00 4.04
114 115 2.822764 CGGGAAGAAAACCTATCTCGG 58.177 52.381 0.00 0.00 0.00 4.63
115 116 2.167900 CGGGAAGAAAACCTATCTCGGT 59.832 50.000 0.00 0.00 39.48 4.69
116 117 3.382546 CGGGAAGAAAACCTATCTCGGTA 59.617 47.826 0.00 0.00 35.89 4.02
117 118 4.038883 CGGGAAGAAAACCTATCTCGGTAT 59.961 45.833 0.00 0.00 35.89 2.73
118 119 5.242393 CGGGAAGAAAACCTATCTCGGTATA 59.758 44.000 0.00 0.00 35.89 1.47
119 120 6.071503 CGGGAAGAAAACCTATCTCGGTATAT 60.072 42.308 0.00 0.00 35.89 0.86
120 121 7.321908 GGGAAGAAAACCTATCTCGGTATATC 58.678 42.308 0.00 0.00 35.89 1.63
121 122 7.028361 GGAAGAAAACCTATCTCGGTATATCG 58.972 42.308 0.00 0.00 35.89 2.92
122 123 7.094463 GGAAGAAAACCTATCTCGGTATATCGA 60.094 40.741 8.03 8.03 35.89 3.59
123 124 7.941431 AGAAAACCTATCTCGGTATATCGAT 57.059 36.000 8.85 2.16 38.55 3.59
124 125 9.458727 AAGAAAACCTATCTCGGTATATCGATA 57.541 33.333 8.85 7.75 38.55 2.92
125 126 8.891720 AGAAAACCTATCTCGGTATATCGATAC 58.108 37.037 8.85 0.00 38.55 2.24
177 178 2.509052 TGGCTTCTATTCATCCGTCG 57.491 50.000 0.00 0.00 0.00 5.12
179 180 1.538204 GGCTTCTATTCATCCGTCGCA 60.538 52.381 0.00 0.00 0.00 5.10
181 182 2.809446 CTTCTATTCATCCGTCGCACA 58.191 47.619 0.00 0.00 0.00 4.57
237 238 5.433526 TCAACCCGTATTCCATCTTTAAGG 58.566 41.667 0.00 0.00 0.00 2.69
265 266 8.476925 GTGACGAATTGTTTTTCTCATTTTACC 58.523 33.333 0.00 0.00 0.00 2.85
266 267 8.191446 TGACGAATTGTTTTTCTCATTTTACCA 58.809 29.630 0.00 0.00 0.00 3.25
267 268 8.934507 ACGAATTGTTTTTCTCATTTTACCAA 57.065 26.923 0.00 0.00 0.00 3.67
300 301 7.850982 CCATGACTTTTATACTAATCAACACGC 59.149 37.037 0.00 0.00 0.00 5.34
301 302 8.604035 CATGACTTTTATACTAATCAACACGCT 58.396 33.333 0.00 0.00 0.00 5.07
328 329 5.685511 CCAACTTTAAGTCACAACGAATTGG 59.314 40.000 0.00 0.00 40.42 3.16
333 334 8.460428 ACTTTAAGTCACAACGAATTGGTTTTA 58.540 29.630 2.74 0.00 40.42 1.52
334 335 9.291664 CTTTAAGTCACAACGAATTGGTTTTAA 57.708 29.630 2.74 3.61 40.42 1.52
335 336 9.804758 TTTAAGTCACAACGAATTGGTTTTAAT 57.195 25.926 2.74 0.00 40.42 1.40
336 337 9.804758 TTAAGTCACAACGAATTGGTTTTAATT 57.195 25.926 2.74 1.24 40.42 1.40
373 379 8.116669 TCCCTAATATTTGTGTTAATCAACCCA 58.883 33.333 0.00 0.00 33.41 4.51
381 387 6.320494 TGTGTTAATCAACCCACAATACAC 57.680 37.500 0.00 0.00 33.41 2.90
395 401 8.729047 ACCCACAATACACCTGGAATAAATATA 58.271 33.333 0.00 0.00 0.00 0.86
396 402 9.010029 CCCACAATACACCTGGAATAAATATAC 57.990 37.037 0.00 0.00 0.00 1.47
397 403 9.793259 CCACAATACACCTGGAATAAATATACT 57.207 33.333 0.00 0.00 0.00 2.12
564 572 1.682854 ACCTAAATCAATGGCGCATGG 59.317 47.619 10.83 0.00 0.00 3.66
570 578 2.361104 AATGGCGCATGGTCCGTT 60.361 55.556 10.83 0.00 0.00 4.44
578 586 2.014128 CGCATGGTCCGTTATTCCTTT 58.986 47.619 0.00 0.00 0.00 3.11
583 591 4.895668 TGGTCCGTTATTCCTTTGTACT 57.104 40.909 0.00 0.00 0.00 2.73
587 595 3.008157 TCCGTTATTCCTTTGTACTGGCA 59.992 43.478 0.00 0.00 0.00 4.92
618 626 3.404224 TTGCAAATGAACATGCCACAT 57.596 38.095 0.00 0.00 41.87 3.21
636 644 0.672401 ATGCATTGCTTTGTGCTGCC 60.672 50.000 10.49 0.00 40.71 4.85
709 717 4.240881 AGGCATGTTGTACTTCCATCAT 57.759 40.909 0.00 0.00 0.00 2.45
711 719 3.316308 GGCATGTTGTACTTCCATCATCC 59.684 47.826 0.00 0.00 0.00 3.51
712 720 3.316308 GCATGTTGTACTTCCATCATCCC 59.684 47.826 0.00 0.00 0.00 3.85
725 733 5.471424 TCCATCATCCCTCTCTCTTTGTAT 58.529 41.667 0.00 0.00 0.00 2.29
726 734 6.624297 TCCATCATCCCTCTCTCTTTGTATA 58.376 40.000 0.00 0.00 0.00 1.47
727 735 6.495181 TCCATCATCCCTCTCTCTTTGTATAC 59.505 42.308 0.00 0.00 0.00 1.47
728 736 6.268617 CCATCATCCCTCTCTCTTTGTATACA 59.731 42.308 0.08 0.08 0.00 2.29
729 737 7.038445 CCATCATCCCTCTCTCTTTGTATACAT 60.038 40.741 6.36 0.00 0.00 2.29
730 738 7.921041 TCATCCCTCTCTCTTTGTATACATT 57.079 36.000 6.36 0.00 0.00 2.71
731 739 8.324191 TCATCCCTCTCTCTTTGTATACATTT 57.676 34.615 6.36 0.00 0.00 2.32
732 740 8.772250 TCATCCCTCTCTCTTTGTATACATTTT 58.228 33.333 6.36 0.00 0.00 1.82
733 741 9.401058 CATCCCTCTCTCTTTGTATACATTTTT 57.599 33.333 6.36 0.00 0.00 1.94
759 767 7.807977 TTTTTGAGACAAGCTCTCTTTGTAT 57.192 32.000 3.43 0.00 45.38 2.29
760 768 8.902540 TTTTTGAGACAAGCTCTCTTTGTATA 57.097 30.769 3.43 0.00 45.38 1.47
761 769 7.891183 TTTGAGACAAGCTCTCTTTGTATAC 57.109 36.000 0.00 0.00 45.38 1.47
762 770 6.590234 TGAGACAAGCTCTCTTTGTATACA 57.410 37.500 0.08 0.08 45.38 2.29
763 771 7.175347 TGAGACAAGCTCTCTTTGTATACAT 57.825 36.000 6.36 0.00 45.38 2.29
764 772 7.038048 TGAGACAAGCTCTCTTTGTATACATG 58.962 38.462 6.36 3.36 45.38 3.21
765 773 6.940739 AGACAAGCTCTCTTTGTATACATGT 58.059 36.000 6.36 2.69 0.00 3.21
766 774 7.038659 AGACAAGCTCTCTTTGTATACATGTC 58.961 38.462 16.97 16.97 0.00 3.06
767 775 6.109359 ACAAGCTCTCTTTGTATACATGTCC 58.891 40.000 6.36 0.00 0.00 4.02
768 776 6.070538 ACAAGCTCTCTTTGTATACATGTCCT 60.071 38.462 6.36 0.00 0.00 3.85
769 777 7.124298 ACAAGCTCTCTTTGTATACATGTCCTA 59.876 37.037 6.36 0.00 0.00 2.94
770 778 7.847711 AGCTCTCTTTGTATACATGTCCTAT 57.152 36.000 6.36 0.00 0.00 2.57
771 779 7.665690 AGCTCTCTTTGTATACATGTCCTATG 58.334 38.462 6.36 0.00 0.00 2.23
867 880 1.732809 CATGCAGCTCTTCACTGACTG 59.267 52.381 0.00 0.00 37.32 3.51
868 881 1.043022 TGCAGCTCTTCACTGACTGA 58.957 50.000 0.00 0.00 37.32 3.41
869 882 1.269988 TGCAGCTCTTCACTGACTGAC 60.270 52.381 0.00 0.00 37.32 3.51
870 883 1.938926 GCAGCTCTTCACTGACTGACC 60.939 57.143 0.00 0.00 37.32 4.02
888 901 4.653888 AAACCCCAACGCCTCCGG 62.654 66.667 0.00 0.00 39.22 5.14
1140 1153 1.367471 CATCGAGCTAATCCGCCCA 59.633 57.895 0.00 0.00 0.00 5.36
1263 1276 1.373497 CCAGATCTACGCCATCCGC 60.373 63.158 0.00 0.00 41.76 5.54
1451 1464 4.451629 TCCAGAAGTCTTACCGTTGATC 57.548 45.455 0.00 0.00 0.00 2.92
1602 1616 3.514309 ACTACTGGGTAGTTGCTCGATTT 59.486 43.478 4.72 0.00 45.68 2.17
1686 1705 4.082625 TGCTATGTTTCAGGTTTCATGCTG 60.083 41.667 0.00 0.00 0.00 4.41
1712 1731 5.173664 TGATGTTGTCTGATGACTGATGTC 58.826 41.667 0.00 0.00 43.29 3.06
1743 1762 0.107017 AGCCGGATGAGTTGAATGGG 60.107 55.000 5.05 0.00 0.00 4.00
1765 1784 5.105392 GGGGCAAATACAATCACTTTGATCA 60.105 40.000 0.00 0.00 35.76 2.92
1797 1816 3.696051 TGCCCATGTTGCTCTTTATTCTC 59.304 43.478 6.10 0.00 0.00 2.87
1808 1827 5.121811 GCTCTTTATTCTCTGCATCTTCCA 58.878 41.667 0.00 0.00 0.00 3.53
1890 1911 4.378459 GGTTGATTTCTGTGCTTTACCTCG 60.378 45.833 0.00 0.00 0.00 4.63
1916 1937 7.672738 CAAATTCTAGAATGTTGATGCTTTGC 58.327 34.615 18.61 0.00 0.00 3.68
1929 1950 1.080093 CTTTGCTCCGGCTCGTGTA 60.080 57.895 0.00 0.00 39.59 2.90
1966 1987 6.829229 ATGAATGTGATGTGAGATGTTTGT 57.171 33.333 0.00 0.00 0.00 2.83
1976 1997 4.081142 TGTGAGATGTTTGTGGATATCGGT 60.081 41.667 0.00 0.00 0.00 4.69
2023 2044 7.398618 TGCTTGATACCCAATTTGAGGAATTTA 59.601 33.333 9.92 0.00 35.79 1.40
2052 2073 7.439157 TCATTACCTTGTATTGATGCTATGC 57.561 36.000 0.00 0.00 0.00 3.14
2053 2074 6.430925 TCATTACCTTGTATTGATGCTATGCC 59.569 38.462 0.00 0.00 0.00 4.40
2054 2075 4.169059 ACCTTGTATTGATGCTATGCCA 57.831 40.909 0.00 0.00 0.00 4.92
2055 2076 4.139786 ACCTTGTATTGATGCTATGCCAG 58.860 43.478 0.00 0.00 0.00 4.85
2063 2084 1.268899 GATGCTATGCCAGTTGATGCC 59.731 52.381 0.00 0.00 0.00 4.40
2071 2092 1.547372 GCCAGTTGATGCCATGTTTCT 59.453 47.619 0.00 0.00 0.00 2.52
2128 2149 6.395426 TTGATCAACTATGAATTGCCCATC 57.605 37.500 3.38 0.00 39.49 3.51
2134 2155 3.635373 ACTATGAATTGCCCATCTTGCTG 59.365 43.478 0.00 0.00 0.00 4.41
2141 2162 1.251251 GCCCATCTTGCTGTTGTTCT 58.749 50.000 0.00 0.00 0.00 3.01
2170 2191 4.223032 TCTTTGGTTAGGAGTGATCTGTCC 59.777 45.833 5.93 5.93 0.00 4.02
2205 2226 8.924303 TGTGCTAACTGGTATTCAACTATATCT 58.076 33.333 0.00 0.00 0.00 1.98
2214 2235 4.322080 TTCAACTATATCTGCACTCGGG 57.678 45.455 0.00 0.00 0.00 5.14
2288 2317 4.913335 ATCATCTATGGCAAAAGCACAG 57.087 40.909 0.00 0.00 0.00 3.66
2311 2360 5.531287 AGCGTTTAGTTCATCTTCCTGTTTT 59.469 36.000 0.00 0.00 0.00 2.43
2328 2377 9.444600 TTCCTGTTTTGTTTAACTAGCCTATAG 57.555 33.333 0.00 0.00 0.00 1.31
2379 2428 4.976731 GTGTAGCTCCTTACATACATGTCG 59.023 45.833 0.00 0.00 41.97 4.35
2406 2455 6.712547 AGTATCTGCCTATAGGAAAAACATGC 59.287 38.462 23.61 7.97 37.39 4.06
2409 2458 6.841601 TCTGCCTATAGGAAAAACATGCTAT 58.158 36.000 23.61 0.00 37.64 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.451141 TGCAAATGAAAGGTTCCACAC 57.549 42.857 0.00 0.00 0.00 3.82
1 2 4.832266 AGTATGCAAATGAAAGGTTCCACA 59.168 37.500 0.00 0.00 0.00 4.17
2 3 5.391312 AGTATGCAAATGAAAGGTTCCAC 57.609 39.130 0.00 0.00 0.00 4.02
3 4 6.041409 TCAAAGTATGCAAATGAAAGGTTCCA 59.959 34.615 0.00 0.00 0.00 3.53
4 5 6.454795 TCAAAGTATGCAAATGAAAGGTTCC 58.545 36.000 0.00 0.00 0.00 3.62
5 6 7.063780 CCATCAAAGTATGCAAATGAAAGGTTC 59.936 37.037 0.00 0.00 0.00 3.62
6 7 6.875195 CCATCAAAGTATGCAAATGAAAGGTT 59.125 34.615 0.00 0.00 0.00 3.50
7 8 6.400568 CCATCAAAGTATGCAAATGAAAGGT 58.599 36.000 0.00 0.00 0.00 3.50
8 9 5.813672 CCCATCAAAGTATGCAAATGAAAGG 59.186 40.000 0.00 0.00 0.00 3.11
9 10 5.813672 CCCCATCAAAGTATGCAAATGAAAG 59.186 40.000 0.00 0.00 0.00 2.62
10 11 5.248020 ACCCCATCAAAGTATGCAAATGAAA 59.752 36.000 0.00 0.00 0.00 2.69
11 12 4.776837 ACCCCATCAAAGTATGCAAATGAA 59.223 37.500 0.00 0.00 0.00 2.57
12 13 4.160065 CACCCCATCAAAGTATGCAAATGA 59.840 41.667 0.00 0.00 0.00 2.57
13 14 4.081531 ACACCCCATCAAAGTATGCAAATG 60.082 41.667 0.00 0.00 0.00 2.32
14 15 4.095946 ACACCCCATCAAAGTATGCAAAT 58.904 39.130 0.00 0.00 0.00 2.32
15 16 3.505386 ACACCCCATCAAAGTATGCAAA 58.495 40.909 0.00 0.00 0.00 3.68
16 17 3.168035 ACACCCCATCAAAGTATGCAA 57.832 42.857 0.00 0.00 0.00 4.08
17 18 2.897271 ACACCCCATCAAAGTATGCA 57.103 45.000 0.00 0.00 0.00 3.96
18 19 5.106157 GCATATACACCCCATCAAAGTATGC 60.106 44.000 0.00 0.00 36.34 3.14
19 20 6.240894 AGCATATACACCCCATCAAAGTATG 58.759 40.000 0.00 0.00 0.00 2.39
20 21 6.454223 AGCATATACACCCCATCAAAGTAT 57.546 37.500 0.00 0.00 0.00 2.12
21 22 5.904984 AGCATATACACCCCATCAAAGTA 57.095 39.130 0.00 0.00 0.00 2.24
22 23 4.796110 AGCATATACACCCCATCAAAGT 57.204 40.909 0.00 0.00 0.00 2.66
23 24 5.869579 AGTAGCATATACACCCCATCAAAG 58.130 41.667 0.00 0.00 0.00 2.77
24 25 5.904984 AGTAGCATATACACCCCATCAAA 57.095 39.130 0.00 0.00 0.00 2.69
25 26 5.904984 AAGTAGCATATACACCCCATCAA 57.095 39.130 0.00 0.00 0.00 2.57
26 27 5.131977 ACAAAGTAGCATATACACCCCATCA 59.868 40.000 0.00 0.00 0.00 3.07
27 28 5.470098 CACAAAGTAGCATATACACCCCATC 59.530 44.000 0.00 0.00 0.00 3.51
28 29 5.131977 TCACAAAGTAGCATATACACCCCAT 59.868 40.000 0.00 0.00 0.00 4.00
29 30 4.471747 TCACAAAGTAGCATATACACCCCA 59.528 41.667 0.00 0.00 0.00 4.96
30 31 5.031066 TCACAAAGTAGCATATACACCCC 57.969 43.478 0.00 0.00 0.00 4.95
31 32 5.753921 GTCTCACAAAGTAGCATATACACCC 59.246 44.000 0.00 0.00 0.00 4.61
32 33 5.753921 GGTCTCACAAAGTAGCATATACACC 59.246 44.000 0.00 0.00 0.00 4.16
33 34 6.574350 AGGTCTCACAAAGTAGCATATACAC 58.426 40.000 0.00 0.00 0.00 2.90
34 35 6.791867 AGGTCTCACAAAGTAGCATATACA 57.208 37.500 0.00 0.00 0.00 2.29
35 36 7.042335 ACAAGGTCTCACAAAGTAGCATATAC 58.958 38.462 0.00 0.00 0.00 1.47
36 37 7.182817 ACAAGGTCTCACAAAGTAGCATATA 57.817 36.000 0.00 0.00 0.00 0.86
37 38 6.054860 ACAAGGTCTCACAAAGTAGCATAT 57.945 37.500 0.00 0.00 0.00 1.78
38 39 5.483685 ACAAGGTCTCACAAAGTAGCATA 57.516 39.130 0.00 0.00 0.00 3.14
39 40 4.357918 ACAAGGTCTCACAAAGTAGCAT 57.642 40.909 0.00 0.00 0.00 3.79
40 41 3.838244 ACAAGGTCTCACAAAGTAGCA 57.162 42.857 0.00 0.00 0.00 3.49
41 42 4.335594 ACAAACAAGGTCTCACAAAGTAGC 59.664 41.667 0.00 0.00 0.00 3.58
42 43 5.730568 GCACAAACAAGGTCTCACAAAGTAG 60.731 44.000 0.00 0.00 0.00 2.57
43 44 4.095782 GCACAAACAAGGTCTCACAAAGTA 59.904 41.667 0.00 0.00 0.00 2.24
44 45 3.119495 GCACAAACAAGGTCTCACAAAGT 60.119 43.478 0.00 0.00 0.00 2.66
45 46 3.129287 AGCACAAACAAGGTCTCACAAAG 59.871 43.478 0.00 0.00 0.00 2.77
46 47 3.088532 AGCACAAACAAGGTCTCACAAA 58.911 40.909 0.00 0.00 0.00 2.83
47 48 2.722094 AGCACAAACAAGGTCTCACAA 58.278 42.857 0.00 0.00 0.00 3.33
48 49 2.418368 AGCACAAACAAGGTCTCACA 57.582 45.000 0.00 0.00 0.00 3.58
49 50 2.945668 AGAAGCACAAACAAGGTCTCAC 59.054 45.455 0.00 0.00 0.00 3.51
50 51 2.945008 CAGAAGCACAAACAAGGTCTCA 59.055 45.455 0.00 0.00 0.00 3.27
51 52 2.291741 CCAGAAGCACAAACAAGGTCTC 59.708 50.000 0.00 0.00 0.00 3.36
52 53 2.301346 CCAGAAGCACAAACAAGGTCT 58.699 47.619 0.00 0.00 0.00 3.85
53 54 1.269257 GCCAGAAGCACAAACAAGGTC 60.269 52.381 0.00 0.00 42.97 3.85
54 55 0.746659 GCCAGAAGCACAAACAAGGT 59.253 50.000 0.00 0.00 42.97 3.50
55 56 0.318107 CGCCAGAAGCACAAACAAGG 60.318 55.000 0.00 0.00 44.04 3.61
56 57 0.662619 TCGCCAGAAGCACAAACAAG 59.337 50.000 0.00 0.00 44.04 3.16
57 58 1.317613 ATCGCCAGAAGCACAAACAA 58.682 45.000 0.00 0.00 44.04 2.83
58 59 1.317613 AATCGCCAGAAGCACAAACA 58.682 45.000 0.00 0.00 44.04 2.83
59 60 2.053627 CAAATCGCCAGAAGCACAAAC 58.946 47.619 0.00 0.00 44.04 2.93
60 61 1.602668 GCAAATCGCCAGAAGCACAAA 60.603 47.619 0.00 0.00 44.04 2.83
61 62 0.039256 GCAAATCGCCAGAAGCACAA 60.039 50.000 0.00 0.00 44.04 3.33
62 63 0.890542 AGCAAATCGCCAGAAGCACA 60.891 50.000 0.00 0.00 44.04 4.57
63 64 0.242017 AAGCAAATCGCCAGAAGCAC 59.758 50.000 0.00 0.00 44.04 4.40
64 65 0.961019 AAAGCAAATCGCCAGAAGCA 59.039 45.000 0.00 0.00 44.04 3.91
65 66 2.919666 TAAAGCAAATCGCCAGAAGC 57.080 45.000 0.00 0.00 44.04 3.86
81 82 9.856162 AGGTTTTCTTCCCGCTTTATATATAAA 57.144 29.630 15.47 15.47 0.00 1.40
84 85 9.668497 GATAGGTTTTCTTCCCGCTTTATATAT 57.332 33.333 0.00 0.00 0.00 0.86
85 86 8.877195 AGATAGGTTTTCTTCCCGCTTTATATA 58.123 33.333 0.00 0.00 0.00 0.86
86 87 7.746703 AGATAGGTTTTCTTCCCGCTTTATAT 58.253 34.615 0.00 0.00 0.00 0.86
87 88 7.133133 AGATAGGTTTTCTTCCCGCTTTATA 57.867 36.000 0.00 0.00 0.00 0.98
88 89 6.002653 AGATAGGTTTTCTTCCCGCTTTAT 57.997 37.500 0.00 0.00 0.00 1.40
89 90 5.425630 GAGATAGGTTTTCTTCCCGCTTTA 58.574 41.667 0.00 0.00 0.00 1.85
90 91 4.262617 GAGATAGGTTTTCTTCCCGCTTT 58.737 43.478 0.00 0.00 0.00 3.51
91 92 3.679083 CGAGATAGGTTTTCTTCCCGCTT 60.679 47.826 0.00 0.00 0.00 4.68
92 93 2.159085 CGAGATAGGTTTTCTTCCCGCT 60.159 50.000 0.00 0.00 0.00 5.52
93 94 2.202566 CGAGATAGGTTTTCTTCCCGC 58.797 52.381 0.00 0.00 0.00 6.13
94 95 2.167900 ACCGAGATAGGTTTTCTTCCCG 59.832 50.000 0.00 0.00 43.00 5.14
95 96 3.908643 ACCGAGATAGGTTTTCTTCCC 57.091 47.619 0.00 0.00 43.00 3.97
96 97 7.028361 CGATATACCGAGATAGGTTTTCTTCC 58.972 42.308 0.00 0.00 43.00 3.46
97 98 7.814642 TCGATATACCGAGATAGGTTTTCTTC 58.185 38.462 0.00 0.00 43.00 2.87
98 99 7.756395 TCGATATACCGAGATAGGTTTTCTT 57.244 36.000 0.00 0.00 43.00 2.52
99 100 7.941431 ATCGATATACCGAGATAGGTTTTCT 57.059 36.000 0.00 0.00 43.00 2.52
100 101 8.127954 GGTATCGATATACCGAGATAGGTTTTC 58.872 40.741 8.66 0.00 46.30 2.29
101 102 7.994194 GGTATCGATATACCGAGATAGGTTTT 58.006 38.462 8.66 0.00 46.30 2.43
102 103 7.565323 GGTATCGATATACCGAGATAGGTTT 57.435 40.000 8.66 0.00 46.30 3.27
136 137 9.449719 AGCCATATGTGCTTTATTATTAGGTAC 57.550 33.333 11.55 0.00 34.87 3.34
155 156 4.748892 CGACGGATGAATAGAAGCCATAT 58.251 43.478 0.00 0.00 0.00 1.78
159 160 1.140816 GCGACGGATGAATAGAAGCC 58.859 55.000 0.00 0.00 0.00 4.35
160 161 1.523095 GTGCGACGGATGAATAGAAGC 59.477 52.381 0.00 0.00 0.00 3.86
166 167 3.500982 CAAAAATGTGCGACGGATGAAT 58.499 40.909 0.00 0.00 0.00 2.57
169 170 0.984109 GCAAAAATGTGCGACGGATG 59.016 50.000 0.00 0.00 34.21 3.51
170 171 3.399879 GCAAAAATGTGCGACGGAT 57.600 47.368 0.00 0.00 34.21 4.18
171 172 4.933483 GCAAAAATGTGCGACGGA 57.067 50.000 0.00 0.00 34.21 4.69
177 178 1.866601 AGGCTTTTCGCAAAAATGTGC 59.133 42.857 0.00 0.00 41.67 4.57
179 180 3.733443 AGAGGCTTTTCGCAAAAATGT 57.267 38.095 0.00 0.00 41.67 2.71
181 182 4.278419 ACTGTAGAGGCTTTTCGCAAAAAT 59.722 37.500 0.00 0.00 41.67 1.82
189 190 5.751243 TCAACAAACTGTAGAGGCTTTTC 57.249 39.130 0.00 0.00 0.00 2.29
194 195 5.689383 TGATTTCAACAAACTGTAGAGGC 57.311 39.130 0.00 0.00 0.00 4.70
222 223 4.116961 CGTCACGCCTTAAAGATGGAATA 58.883 43.478 0.00 0.00 0.00 1.75
224 225 2.028839 TCGTCACGCCTTAAAGATGGAA 60.029 45.455 0.00 0.00 0.00 3.53
237 238 3.613563 TGAGAAAAACAATTCGTCACGC 58.386 40.909 0.00 0.00 34.46 5.34
297 298 2.870411 GTGACTTAAAGTTGGACAGCGT 59.130 45.455 0.00 0.00 0.00 5.07
300 301 4.569162 TCGTTGTGACTTAAAGTTGGACAG 59.431 41.667 0.00 0.00 0.00 3.51
301 302 4.505808 TCGTTGTGACTTAAAGTTGGACA 58.494 39.130 0.00 0.00 0.00 4.02
347 348 8.116669 TGGGTTGATTAACACAAATATTAGGGA 58.883 33.333 2.26 0.00 46.69 4.20
462 468 9.140286 TCAAATTCTACACGTTTCTCTAATCAG 57.860 33.333 0.00 0.00 0.00 2.90
471 477 9.988350 ACATCATATTCAAATTCTACACGTTTC 57.012 29.630 0.00 0.00 0.00 2.78
539 547 2.481795 GCGCCATTGATTTAGGTTGCAT 60.482 45.455 0.00 0.00 0.00 3.96
564 572 3.373130 GCCAGTACAAAGGAATAACGGAC 59.627 47.826 0.00 0.00 0.00 4.79
570 578 4.746535 TCGATGCCAGTACAAAGGAATA 57.253 40.909 0.00 0.00 0.00 1.75
578 586 4.048504 CAATACGAATCGATGCCAGTACA 58.951 43.478 10.55 0.00 0.00 2.90
583 591 1.946745 TGCAATACGAATCGATGCCA 58.053 45.000 21.82 12.25 35.25 4.92
587 595 6.117911 TGTTCATTTGCAATACGAATCGAT 57.882 33.333 10.55 0.00 29.15 3.59
627 635 2.913578 CCTTGCCAGGCAGCACAA 60.914 61.111 15.50 0.00 43.97 3.33
636 644 1.079543 CTCACTCGGTCCTTGCCAG 60.080 63.158 0.00 0.00 0.00 4.85
646 654 4.137116 TGTAATCATTTCCCTCACTCGG 57.863 45.455 0.00 0.00 0.00 4.63
741 749 6.940739 ACATGTATACAAAGAGAGCTTGTCT 58.059 36.000 10.14 0.00 38.71 3.41
742 750 6.256757 GGACATGTATACAAAGAGAGCTTGTC 59.743 42.308 10.14 14.29 33.79 3.18
743 751 6.070538 AGGACATGTATACAAAGAGAGCTTGT 60.071 38.462 10.14 6.17 33.79 3.16
744 752 6.344500 AGGACATGTATACAAAGAGAGCTTG 58.656 40.000 10.14 2.81 33.79 4.01
745 753 6.552445 AGGACATGTATACAAAGAGAGCTT 57.448 37.500 10.14 0.00 35.37 3.74
746 754 7.256119 CCATAGGACATGTATACAAAGAGAGCT 60.256 40.741 10.14 0.00 0.00 4.09
747 755 6.870965 CCATAGGACATGTATACAAAGAGAGC 59.129 42.308 10.14 0.00 0.00 4.09
748 756 6.870965 GCCATAGGACATGTATACAAAGAGAG 59.129 42.308 10.14 0.00 0.00 3.20
749 757 6.554982 AGCCATAGGACATGTATACAAAGAGA 59.445 38.462 10.14 0.00 0.00 3.10
750 758 6.763355 AGCCATAGGACATGTATACAAAGAG 58.237 40.000 10.14 3.29 0.00 2.85
751 759 6.747414 AGCCATAGGACATGTATACAAAGA 57.253 37.500 10.14 0.00 0.00 2.52
752 760 6.205464 CCAAGCCATAGGACATGTATACAAAG 59.795 42.308 10.14 8.30 0.00 2.77
753 761 6.061441 CCAAGCCATAGGACATGTATACAAA 58.939 40.000 10.14 0.00 0.00 2.83
754 762 5.620206 CCAAGCCATAGGACATGTATACAA 58.380 41.667 10.14 0.00 0.00 2.41
755 763 4.504864 GCCAAGCCATAGGACATGTATACA 60.505 45.833 8.27 8.27 0.00 2.29
756 764 4.003648 GCCAAGCCATAGGACATGTATAC 58.996 47.826 0.00 0.00 0.00 1.47
757 765 3.306710 CGCCAAGCCATAGGACATGTATA 60.307 47.826 0.00 0.00 0.00 1.47
758 766 2.550855 CGCCAAGCCATAGGACATGTAT 60.551 50.000 0.00 0.00 0.00 2.29
759 767 1.202639 CGCCAAGCCATAGGACATGTA 60.203 52.381 0.00 0.00 0.00 2.29
760 768 0.464373 CGCCAAGCCATAGGACATGT 60.464 55.000 0.00 0.00 0.00 3.21
761 769 1.168407 CCGCCAAGCCATAGGACATG 61.168 60.000 0.00 0.00 0.00 3.21
762 770 1.149174 CCGCCAAGCCATAGGACAT 59.851 57.895 0.00 0.00 0.00 3.06
763 771 2.252072 GACCGCCAAGCCATAGGACA 62.252 60.000 0.00 0.00 0.00 4.02
764 772 1.523938 GACCGCCAAGCCATAGGAC 60.524 63.158 0.00 0.00 0.00 3.85
765 773 2.908015 GACCGCCAAGCCATAGGA 59.092 61.111 0.00 0.00 0.00 2.94
766 774 2.588877 CGACCGCCAAGCCATAGG 60.589 66.667 0.00 0.00 0.00 2.57
767 775 2.588877 CCGACCGCCAAGCCATAG 60.589 66.667 0.00 0.00 0.00 2.23
768 776 3.395702 ACCGACCGCCAAGCCATA 61.396 61.111 0.00 0.00 0.00 2.74
867 880 2.203437 AGGCGTTGGGGTTTGGTC 60.203 61.111 0.00 0.00 0.00 4.02
868 881 2.203437 GAGGCGTTGGGGTTTGGT 60.203 61.111 0.00 0.00 0.00 3.67
869 882 2.989253 GGAGGCGTTGGGGTTTGG 60.989 66.667 0.00 0.00 0.00 3.28
870 883 3.361977 CGGAGGCGTTGGGGTTTG 61.362 66.667 0.00 0.00 0.00 2.93
888 901 2.105993 AGGGGTGGGCGATTTTATACTC 59.894 50.000 0.00 0.00 0.00 2.59
889 902 2.105993 GAGGGGTGGGCGATTTTATACT 59.894 50.000 0.00 0.00 0.00 2.12
1131 1144 1.449353 GAGCATCTCTGGGCGGATT 59.551 57.895 0.00 0.00 34.54 3.01
1287 1300 3.004524 CGACATACTTCTGGTAGTAGGCC 59.995 52.174 0.00 0.00 36.21 5.19
1680 1699 4.957759 TCAGACAACATCATTCAGCATG 57.042 40.909 0.00 0.00 37.54 4.06
1712 1731 3.255725 TCATCCGGCTAACTTAAACACG 58.744 45.455 0.00 0.00 0.00 4.49
1743 1762 7.486647 AGATGATCAAAGTGATTGTATTTGCC 58.513 34.615 0.00 0.00 37.20 4.52
1765 1784 2.961062 GCAACATGGGCATTTCCTAGAT 59.039 45.455 6.74 0.00 34.39 1.98
1797 1816 2.431954 AGACCCAATGGAAGATGCAG 57.568 50.000 0.00 0.00 34.81 4.41
1839 1858 7.849804 TCATCCTAAGCAAATCAGTCTTAAC 57.150 36.000 0.00 0.00 0.00 2.01
1890 1911 7.672738 CAAAGCATCAACATTCTAGAATTTGC 58.327 34.615 15.49 16.94 0.00 3.68
1916 1937 1.306148 TGTCTATACACGAGCCGGAG 58.694 55.000 5.05 0.00 0.00 4.63
1966 1987 3.035363 TCCAGCAACTAACCGATATCCA 58.965 45.455 0.00 0.00 0.00 3.41
1976 1997 4.153475 GCAAAGTCGTATTCCAGCAACTAA 59.847 41.667 0.00 0.00 0.00 2.24
2041 2062 2.359848 GCATCAACTGGCATAGCATCAA 59.640 45.455 0.00 0.00 0.00 2.57
2042 2063 1.951602 GCATCAACTGGCATAGCATCA 59.048 47.619 0.00 0.00 0.00 3.07
2043 2064 2.701073 GCATCAACTGGCATAGCATC 57.299 50.000 0.00 0.00 0.00 3.91
2052 2073 4.012374 ACTAGAAACATGGCATCAACTGG 58.988 43.478 0.00 0.00 0.00 4.00
2053 2074 5.633830 AACTAGAAACATGGCATCAACTG 57.366 39.130 0.00 0.00 0.00 3.16
2054 2075 5.769662 TGAAACTAGAAACATGGCATCAACT 59.230 36.000 0.00 0.00 0.00 3.16
2055 2076 6.012658 TGAAACTAGAAACATGGCATCAAC 57.987 37.500 0.00 0.00 0.00 3.18
2128 2149 2.292569 AGATGTGCAGAACAACAGCAAG 59.707 45.455 0.00 0.00 43.61 4.01
2134 2155 3.715628 ACCAAAGATGTGCAGAACAAC 57.284 42.857 0.00 0.00 43.61 3.32
2141 2162 3.072330 TCACTCCTAACCAAAGATGTGCA 59.928 43.478 0.00 0.00 0.00 4.57
2184 2205 8.924303 AGTGCAGATATAGTTGAATACCAGTTA 58.076 33.333 0.00 0.00 0.00 2.24
2214 2235 9.172820 CATCAATATACACACAATATGCAACAC 57.827 33.333 0.00 0.00 0.00 3.32
2288 2317 5.358298 AAACAGGAAGATGAACTAAACGC 57.642 39.130 0.00 0.00 0.00 4.84
2311 2360 9.484806 AACTTCTACCTATAGGCTAGTTAAACA 57.515 33.333 19.25 1.08 39.32 2.83
2328 2377 6.262273 TGTTTCCATCAGTCAAAACTTCTACC 59.738 38.462 0.00 0.00 31.71 3.18
2342 2391 5.053145 GGAGCTACACTATGTTTCCATCAG 58.947 45.833 0.00 0.00 32.29 2.90
2368 2417 4.827835 AGGCAGATACTACGACATGTATGT 59.172 41.667 0.00 3.08 45.16 2.29
2379 2428 9.209175 CATGTTTTTCCTATAGGCAGATACTAC 57.791 37.037 14.50 4.72 34.44 2.73


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

AutoCloner maintained by Alex Coulton.