Multiple sequence alignment - TraesCS4B01G080500

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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 TraesCS4B01G080500 chr4B 100.000 3377 0 0 1 3377 78488098 78484722 0.000000e+00 6237
1 TraesCS4B01G080500 chr4D 94.705 2304 70 18 897 3154 53496177 53493880 0.000000e+00 3531
2 TraesCS4B01G080500 chr4D 91.519 283 12 5 584 857 53496896 53496617 2.460000e-101 379
3 TraesCS4B01G080500 chr4A 91.365 2652 116 44 804 3377 543608435 543611051 0.000000e+00 3524
4 TraesCS4B01G080500 chr4A 94.298 228 8 3 586 812 543607988 543608211 8.970000e-91 344
5 TraesCS4B01G080500 chr1D 93.583 374 24 0 150 523 254417022 254417395 2.940000e-155 558
6 TraesCS4B01G080500 chr1A 93.583 374 24 0 150 523 554456162 554456535 2.940000e-155 558
7 TraesCS4B01G080500 chr1A 93.583 374 24 0 150 523 554458424 554458797 2.940000e-155 558
8 TraesCS4B01G080500 chr3B 93.316 374 25 0 150 523 101919088 101918715 1.370000e-153 553
9 TraesCS4B01G080500 chr6D 93.067 375 25 1 150 523 45511614 45511240 6.370000e-152 547
10 TraesCS4B01G080500 chr5D 93.048 374 26 0 150 523 6180989 6180616 6.370000e-152 547
11 TraesCS4B01G080500 chr5D 92.781 374 27 0 150 523 503287256 503287629 2.960000e-150 542
12 TraesCS4B01G080500 chr2D 93.048 374 26 0 150 523 9785100 9785473 6.370000e-152 547
13 TraesCS4B01G080500 chr2B 92.819 376 26 1 150 525 474900299 474900673 8.240000e-151 544


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 TraesCS4B01G080500 chr4B 78484722 78488098 3376 True 6237 6237 100.0000 1 3377 1 chr4B.!!$R1 3376
1 TraesCS4B01G080500 chr4D 53493880 53496896 3016 True 1955 3531 93.1120 584 3154 2 chr4D.!!$R1 2570
2 TraesCS4B01G080500 chr4A 543607988 543611051 3063 False 1934 3524 92.8315 586 3377 2 chr4A.!!$F1 2791
3 TraesCS4B01G080500 chr1A 554456162 554458797 2635 False 558 558 93.5830 150 523 2 chr1A.!!$F1 373

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
130 131 0.035725 CCCCGGGGTTTCAGTTCTAC 60.036 60.0 33.25 0.00 0.00 2.59 F
568 1226 0.108138 ACGAAATCCCAGAGGCTTCG 60.108 55.0 11.99 11.99 45.95 3.79 F
569 1227 0.175760 CGAAATCCCAGAGGCTTCGA 59.824 55.0 9.30 0.00 44.56 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 2814 0.386858 TCTCCGCGTCGTTCAAGAAG 60.387 55.0 4.92 0.0 0.0 2.85 R
2277 3592 0.382873 CCAGGCGTGCGTATGTACTA 59.617 55.0 0.00 0.0 0.0 1.82 R
2447 3762 0.458543 CTGCTGCGACGACCAACTAT 60.459 55.0 0.00 0.0 0.0 2.12 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
32 33 7.687941 TCCAGAGGAATTTTAACATTCACTC 57.312 36.000 14.60 15.90 35.18 3.51
33 34 7.230747 TCCAGAGGAATTTTAACATTCACTCA 58.769 34.615 21.76 9.31 35.27 3.41
34 35 7.890127 TCCAGAGGAATTTTAACATTCACTCAT 59.110 33.333 21.76 12.18 35.27 2.90
35 36 9.177608 CCAGAGGAATTTTAACATTCACTCATA 57.822 33.333 21.76 0.00 35.27 2.15
36 37 9.994432 CAGAGGAATTTTAACATTCACTCATAC 57.006 33.333 21.76 6.22 35.27 2.39
37 38 9.178758 AGAGGAATTTTAACATTCACTCATACC 57.821 33.333 21.76 6.19 35.27 2.73
38 39 9.178758 GAGGAATTTTAACATTCACTCATACCT 57.821 33.333 14.60 2.60 35.18 3.08
39 40 9.178758 AGGAATTTTAACATTCACTCATACCTC 57.821 33.333 14.60 0.00 35.18 3.85
40 41 9.178758 GGAATTTTAACATTCACTCATACCTCT 57.821 33.333 14.60 0.00 35.18 3.69
43 44 7.921786 TTTAACATTCACTCATACCTCTTGG 57.078 36.000 0.00 0.00 39.83 3.61
44 45 5.762179 AACATTCACTCATACCTCTTGGA 57.238 39.130 0.00 0.00 37.04 3.53
45 46 5.762179 ACATTCACTCATACCTCTTGGAA 57.238 39.130 0.00 0.00 37.04 3.53
46 47 5.738909 ACATTCACTCATACCTCTTGGAAG 58.261 41.667 0.00 0.00 37.04 3.46
47 48 5.485353 ACATTCACTCATACCTCTTGGAAGA 59.515 40.000 0.00 0.00 37.04 2.87
48 49 6.013379 ACATTCACTCATACCTCTTGGAAGAA 60.013 38.462 0.00 0.00 34.03 2.52
49 50 6.627087 TTCACTCATACCTCTTGGAAGAAT 57.373 37.500 0.00 0.00 34.03 2.40
50 51 6.227298 TCACTCATACCTCTTGGAAGAATC 57.773 41.667 0.00 0.00 34.03 2.52
51 52 5.721480 TCACTCATACCTCTTGGAAGAATCA 59.279 40.000 0.00 0.00 34.03 2.57
52 53 6.385176 TCACTCATACCTCTTGGAAGAATCAT 59.615 38.462 0.00 0.00 34.03 2.45
53 54 6.482641 CACTCATACCTCTTGGAAGAATCATG 59.517 42.308 0.00 0.00 34.03 3.07
54 55 6.157645 ACTCATACCTCTTGGAAGAATCATGT 59.842 38.462 0.00 0.00 34.03 3.21
55 56 6.351711 TCATACCTCTTGGAAGAATCATGTG 58.648 40.000 0.00 0.00 34.03 3.21
56 57 4.916041 ACCTCTTGGAAGAATCATGTGA 57.084 40.909 0.00 0.00 34.03 3.58
57 58 4.583871 ACCTCTTGGAAGAATCATGTGAC 58.416 43.478 0.00 0.00 34.03 3.67
58 59 3.620374 CCTCTTGGAAGAATCATGTGACG 59.380 47.826 0.00 0.00 34.03 4.35
59 60 3.002791 TCTTGGAAGAATCATGTGACGC 58.997 45.455 0.00 0.00 30.73 5.19
60 61 2.470983 TGGAAGAATCATGTGACGCA 57.529 45.000 0.00 0.00 0.00 5.24
61 62 2.777094 TGGAAGAATCATGTGACGCAA 58.223 42.857 0.00 0.00 0.00 4.85
62 63 3.346315 TGGAAGAATCATGTGACGCAAT 58.654 40.909 0.00 0.00 0.00 3.56
63 64 3.758023 TGGAAGAATCATGTGACGCAATT 59.242 39.130 0.00 0.00 0.00 2.32
64 65 4.940654 TGGAAGAATCATGTGACGCAATTA 59.059 37.500 0.00 0.00 0.00 1.40
65 66 5.065090 TGGAAGAATCATGTGACGCAATTAG 59.935 40.000 0.00 0.00 0.00 1.73
66 67 5.294306 GGAAGAATCATGTGACGCAATTAGA 59.706 40.000 0.00 0.00 0.00 2.10
67 68 5.725110 AGAATCATGTGACGCAATTAGAC 57.275 39.130 0.00 0.00 0.00 2.59
68 69 5.178061 AGAATCATGTGACGCAATTAGACA 58.822 37.500 0.00 0.00 0.00 3.41
69 70 5.643348 AGAATCATGTGACGCAATTAGACAA 59.357 36.000 0.00 0.00 0.00 3.18
70 71 4.661993 TCATGTGACGCAATTAGACAAC 57.338 40.909 0.00 0.00 0.00 3.32
71 72 4.061596 TCATGTGACGCAATTAGACAACA 58.938 39.130 0.00 0.00 0.00 3.33
72 73 4.152223 TCATGTGACGCAATTAGACAACAG 59.848 41.667 0.00 0.00 0.00 3.16
73 74 3.723260 TGTGACGCAATTAGACAACAGA 58.277 40.909 0.00 0.00 0.00 3.41
74 75 4.123506 TGTGACGCAATTAGACAACAGAA 58.876 39.130 0.00 0.00 0.00 3.02
75 76 4.572795 TGTGACGCAATTAGACAACAGAAA 59.427 37.500 0.00 0.00 0.00 2.52
76 77 5.065346 TGTGACGCAATTAGACAACAGAAAA 59.935 36.000 0.00 0.00 0.00 2.29
77 78 6.142817 GTGACGCAATTAGACAACAGAAAAT 58.857 36.000 0.00 0.00 0.00 1.82
78 79 7.041712 TGTGACGCAATTAGACAACAGAAAATA 60.042 33.333 0.00 0.00 0.00 1.40
79 80 7.478667 GTGACGCAATTAGACAACAGAAAATAG 59.521 37.037 0.00 0.00 0.00 1.73
80 81 7.172532 TGACGCAATTAGACAACAGAAAATAGT 59.827 33.333 0.00 0.00 0.00 2.12
81 82 7.871853 ACGCAATTAGACAACAGAAAATAGTT 58.128 30.769 0.00 0.00 0.00 2.24
82 83 8.995220 ACGCAATTAGACAACAGAAAATAGTTA 58.005 29.630 0.00 0.00 0.00 2.24
83 84 9.262472 CGCAATTAGACAACAGAAAATAGTTAC 57.738 33.333 0.00 0.00 0.00 2.50
84 85 9.262472 GCAATTAGACAACAGAAAATAGTTACG 57.738 33.333 0.00 0.00 0.00 3.18
85 86 9.755064 CAATTAGACAACAGAAAATAGTTACGG 57.245 33.333 0.00 0.00 0.00 4.02
86 87 9.498176 AATTAGACAACAGAAAATAGTTACGGT 57.502 29.630 0.00 0.00 0.00 4.83
87 88 8.891671 TTAGACAACAGAAAATAGTTACGGTT 57.108 30.769 0.00 0.00 0.00 4.44
88 89 7.797038 AGACAACAGAAAATAGTTACGGTTT 57.203 32.000 0.00 0.00 0.00 3.27
89 90 7.636326 AGACAACAGAAAATAGTTACGGTTTG 58.364 34.615 0.00 0.00 0.00 2.93
90 91 7.496591 AGACAACAGAAAATAGTTACGGTTTGA 59.503 33.333 0.00 0.00 0.00 2.69
91 92 7.987649 ACAACAGAAAATAGTTACGGTTTGAA 58.012 30.769 0.00 0.00 0.00 2.69
92 93 8.626526 ACAACAGAAAATAGTTACGGTTTGAAT 58.373 29.630 0.00 0.00 0.00 2.57
93 94 9.458374 CAACAGAAAATAGTTACGGTTTGAATT 57.542 29.630 0.00 0.00 0.00 2.17
94 95 9.458374 AACAGAAAATAGTTACGGTTTGAATTG 57.542 29.630 0.00 0.00 0.00 2.32
95 96 8.079809 ACAGAAAATAGTTACGGTTTGAATTGG 58.920 33.333 0.00 0.00 0.00 3.16
96 97 7.061789 CAGAAAATAGTTACGGTTTGAATTGGC 59.938 37.037 0.00 0.00 0.00 4.52
97 98 5.968528 AATAGTTACGGTTTGAATTGGCA 57.031 34.783 0.00 0.00 0.00 4.92
98 99 5.968528 ATAGTTACGGTTTGAATTGGCAA 57.031 34.783 0.68 0.68 0.00 4.52
99 100 4.657436 AGTTACGGTTTGAATTGGCAAA 57.343 36.364 3.01 0.00 35.54 3.68
106 107 4.436365 GTTTGAATTGGCAAACGACTTG 57.564 40.909 3.01 0.00 45.40 3.16
107 108 4.109050 GTTTGAATTGGCAAACGACTTGA 58.891 39.130 3.01 0.00 45.40 3.02
108 109 4.377839 TTGAATTGGCAAACGACTTGAA 57.622 36.364 3.01 0.00 37.17 2.69
109 110 4.582701 TGAATTGGCAAACGACTTGAAT 57.417 36.364 3.01 0.00 37.17 2.57
110 111 4.545610 TGAATTGGCAAACGACTTGAATC 58.454 39.130 3.01 0.00 37.17 2.52
111 112 3.575965 ATTGGCAAACGACTTGAATCC 57.424 42.857 3.01 0.03 37.17 3.01
112 113 1.243902 TGGCAAACGACTTGAATCCC 58.756 50.000 6.25 0.00 37.17 3.85
113 114 0.526211 GGCAAACGACTTGAATCCCC 59.474 55.000 6.25 0.00 37.17 4.81
114 115 0.526211 GCAAACGACTTGAATCCCCC 59.474 55.000 6.25 0.00 37.17 5.40
115 116 0.802494 CAAACGACTTGAATCCCCCG 59.198 55.000 0.00 0.00 37.17 5.73
116 117 0.322187 AAACGACTTGAATCCCCCGG 60.322 55.000 0.00 0.00 0.00 5.73
117 118 2.189521 CGACTTGAATCCCCCGGG 59.810 66.667 15.80 15.80 0.00 5.73
118 119 2.595655 GACTTGAATCCCCCGGGG 59.404 66.667 34.65 34.65 46.11 5.73
119 120 2.204244 ACTTGAATCCCCCGGGGT 60.204 61.111 37.66 20.94 44.74 4.95
120 121 1.855451 ACTTGAATCCCCCGGGGTT 60.855 57.895 37.66 26.64 44.74 4.11
121 122 1.386550 CTTGAATCCCCCGGGGTTT 59.613 57.895 37.66 29.18 44.74 3.27
122 123 0.683179 CTTGAATCCCCCGGGGTTTC 60.683 60.000 37.66 34.14 46.35 2.78
123 124 3.092624 GAATCCCCCGGGGTTTCA 58.907 61.111 37.66 19.00 45.79 2.69
124 125 1.076995 GAATCCCCCGGGGTTTCAG 60.077 63.158 37.66 22.25 45.79 3.02
125 126 1.855451 AATCCCCCGGGGTTTCAGT 60.855 57.895 37.66 15.22 44.74 3.41
126 127 1.440362 AATCCCCCGGGGTTTCAGTT 61.440 55.000 37.66 18.77 44.74 3.16
127 128 1.859841 ATCCCCCGGGGTTTCAGTTC 61.860 60.000 37.66 0.00 44.74 3.01
128 129 2.535331 CCCCCGGGGTTTCAGTTCT 61.535 63.158 37.66 0.00 38.25 3.01
129 130 1.202769 CCCCCGGGGTTTCAGTTCTA 61.203 60.000 37.66 0.00 38.25 2.10
130 131 0.035725 CCCCGGGGTTTCAGTTCTAC 60.036 60.000 33.25 0.00 0.00 2.59
131 132 0.390735 CCCGGGGTTTCAGTTCTACG 60.391 60.000 14.71 0.00 0.00 3.51
132 133 0.604578 CCGGGGTTTCAGTTCTACGA 59.395 55.000 0.00 0.00 0.00 3.43
133 134 1.001181 CCGGGGTTTCAGTTCTACGAA 59.999 52.381 0.00 0.00 0.00 3.85
134 135 2.354403 CCGGGGTTTCAGTTCTACGAAT 60.354 50.000 0.00 0.00 0.00 3.34
135 136 2.928116 CGGGGTTTCAGTTCTACGAATC 59.072 50.000 0.00 0.00 0.00 2.52
136 137 3.615592 CGGGGTTTCAGTTCTACGAATCA 60.616 47.826 0.00 0.00 0.00 2.57
137 138 4.320870 GGGGTTTCAGTTCTACGAATCAA 58.679 43.478 0.00 0.00 0.00 2.57
138 139 4.758165 GGGGTTTCAGTTCTACGAATCAAA 59.242 41.667 0.00 0.00 0.00 2.69
139 140 5.106673 GGGGTTTCAGTTCTACGAATCAAAG 60.107 44.000 0.00 0.00 0.00 2.77
140 141 5.699458 GGGTTTCAGTTCTACGAATCAAAGA 59.301 40.000 0.00 0.00 0.00 2.52
141 142 6.128526 GGGTTTCAGTTCTACGAATCAAAGAG 60.129 42.308 0.00 0.00 0.00 2.85
142 143 6.645415 GGTTTCAGTTCTACGAATCAAAGAGA 59.355 38.462 0.00 0.00 0.00 3.10
143 144 7.359347 GGTTTCAGTTCTACGAATCAAAGAGAC 60.359 40.741 0.00 0.00 0.00 3.36
144 145 5.710984 TCAGTTCTACGAATCAAAGAGACC 58.289 41.667 0.00 0.00 0.00 3.85
145 146 4.865365 CAGTTCTACGAATCAAAGAGACCC 59.135 45.833 0.00 0.00 0.00 4.46
146 147 4.773149 AGTTCTACGAATCAAAGAGACCCT 59.227 41.667 0.00 0.00 0.00 4.34
147 148 4.985538 TCTACGAATCAAAGAGACCCTC 57.014 45.455 0.00 0.00 0.00 4.30
148 149 4.341487 TCTACGAATCAAAGAGACCCTCA 58.659 43.478 0.00 0.00 32.06 3.86
155 156 6.457934 CGAATCAAAGAGACCCTCAATCATTG 60.458 42.308 0.00 0.00 32.06 2.82
167 168 5.289595 CCTCAATCATTGCATGGAATTCTG 58.710 41.667 10.07 7.84 0.00 3.02
256 257 2.938838 TGTGTTTGGGAAAGTCCGAAT 58.061 42.857 0.00 0.00 37.43 3.34
262 263 6.419710 GTGTTTGGGAAAGTCCGAATAAAAAG 59.580 38.462 0.00 0.00 37.43 2.27
365 366 8.792633 TGAAATGCTTGTTATGCCTAATATACC 58.207 33.333 0.00 0.00 0.00 2.73
444 445 0.746659 AATTGCCCGAAGCTTATGCC 59.253 50.000 0.00 0.00 44.23 4.40
458 459 5.422145 AGCTTATGCCATTTTCAATCCAAC 58.578 37.500 0.00 0.00 40.80 3.77
459 460 4.268405 GCTTATGCCATTTTCAATCCAACG 59.732 41.667 0.00 0.00 0.00 4.10
461 462 1.337635 TGCCATTTTCAATCCAACGGC 60.338 47.619 0.00 0.00 38.79 5.68
470 471 3.659786 TCAATCCAACGGCGGATATTAG 58.340 45.455 13.24 0.00 45.39 1.73
490 491 6.585695 TTAGGCCTGTTATACCTCTATTCG 57.414 41.667 17.99 0.00 34.92 3.34
523 524 1.473788 CCTTTGTTTGGCAAGCTGCTT 60.474 47.619 15.19 9.53 44.28 3.91
524 525 1.595794 CTTTGTTTGGCAAGCTGCTTG 59.404 47.619 32.35 32.35 44.28 4.01
527 528 1.413445 TGTTTGGCAAGCTGCTTGAAT 59.587 42.857 38.49 6.13 43.42 2.57
529 530 2.443887 TTGGCAAGCTGCTTGAATTC 57.556 45.000 38.49 24.87 43.42 2.17
530 531 0.241749 TGGCAAGCTGCTTGAATTCG 59.758 50.000 38.49 17.02 43.42 3.34
532 533 1.334054 GCAAGCTGCTTGAATTCGTG 58.666 50.000 38.49 16.58 43.42 4.35
533 534 1.335324 GCAAGCTGCTTGAATTCGTGT 60.335 47.619 38.49 1.74 43.42 4.49
534 535 2.313234 CAAGCTGCTTGAATTCGTGTG 58.687 47.619 32.99 6.40 43.42 3.82
535 536 1.882912 AGCTGCTTGAATTCGTGTGA 58.117 45.000 0.00 0.00 0.00 3.58
536 537 1.532868 AGCTGCTTGAATTCGTGTGAC 59.467 47.619 0.00 0.00 0.00 3.67
537 538 1.722751 GCTGCTTGAATTCGTGTGACG 60.723 52.381 0.04 0.00 44.19 4.35
538 539 0.234625 TGCTTGAATTCGTGTGACGC 59.765 50.000 0.04 0.00 42.21 5.19
542 1200 2.873170 TGAATTCGTGTGACGCAATC 57.127 45.000 0.04 0.00 42.21 2.67
552 1210 2.096013 TGTGACGCAATCAAACAAACGA 59.904 40.909 0.00 0.00 39.72 3.85
553 1211 3.102276 GTGACGCAATCAAACAAACGAA 58.898 40.909 0.00 0.00 39.72 3.85
554 1212 3.544285 GTGACGCAATCAAACAAACGAAA 59.456 39.130 0.00 0.00 39.72 3.46
555 1213 4.206200 GTGACGCAATCAAACAAACGAAAT 59.794 37.500 0.00 0.00 39.72 2.17
556 1214 4.439449 TGACGCAATCAAACAAACGAAATC 59.561 37.500 0.00 0.00 33.02 2.17
557 1215 3.733727 ACGCAATCAAACAAACGAAATCC 59.266 39.130 0.00 0.00 0.00 3.01
558 1216 3.121113 CGCAATCAAACAAACGAAATCCC 59.879 43.478 0.00 0.00 0.00 3.85
559 1217 4.054671 GCAATCAAACAAACGAAATCCCA 58.945 39.130 0.00 0.00 0.00 4.37
560 1218 4.150451 GCAATCAAACAAACGAAATCCCAG 59.850 41.667 0.00 0.00 0.00 4.45
561 1219 5.527951 CAATCAAACAAACGAAATCCCAGA 58.472 37.500 0.00 0.00 0.00 3.86
562 1220 4.829064 TCAAACAAACGAAATCCCAGAG 57.171 40.909 0.00 0.00 0.00 3.35
563 1221 3.568007 TCAAACAAACGAAATCCCAGAGG 59.432 43.478 0.00 0.00 0.00 3.69
564 1222 1.534729 ACAAACGAAATCCCAGAGGC 58.465 50.000 0.00 0.00 0.00 4.70
565 1223 1.073923 ACAAACGAAATCCCAGAGGCT 59.926 47.619 0.00 0.00 0.00 4.58
567 1225 2.115343 AACGAAATCCCAGAGGCTTC 57.885 50.000 0.00 0.00 0.00 3.86
568 1226 0.108138 ACGAAATCCCAGAGGCTTCG 60.108 55.000 11.99 11.99 45.95 3.79
569 1227 0.175760 CGAAATCCCAGAGGCTTCGA 59.824 55.000 9.30 0.00 44.56 3.71
570 1228 1.405526 CGAAATCCCAGAGGCTTCGAA 60.406 52.381 0.00 0.00 44.56 3.71
574 1232 1.738099 CCCAGAGGCTTCGAACGTG 60.738 63.158 0.00 0.00 0.00 4.49
576 1234 1.664649 CAGAGGCTTCGAACGTGCA 60.665 57.895 9.71 0.00 0.00 4.57
577 1235 1.664965 AGAGGCTTCGAACGTGCAC 60.665 57.895 6.82 6.82 0.00 4.57
582 1240 1.886861 GCTTCGAACGTGCACGACAT 61.887 55.000 42.94 27.88 43.02 3.06
583 1241 0.506932 CTTCGAACGTGCACGACATT 59.493 50.000 42.94 27.81 43.02 2.71
584 1242 0.231024 TTCGAACGTGCACGACATTG 59.769 50.000 42.94 28.86 43.02 2.82
642 1308 0.953960 CACCTACCGGGAAAGTGCAC 60.954 60.000 9.40 9.40 38.76 4.57
649 1315 1.352156 CGGGAAAGTGCACGCTAGTC 61.352 60.000 12.01 5.54 0.00 2.59
650 1316 0.320421 GGGAAAGTGCACGCTAGTCA 60.320 55.000 12.01 0.00 0.00 3.41
651 1317 0.790814 GGAAAGTGCACGCTAGTCAC 59.209 55.000 12.01 0.00 0.00 3.67
918 2217 1.119574 CATACCCCGTCCGGATCCTT 61.120 60.000 7.81 0.00 37.50 3.36
989 2288 2.029200 TGTACATAACGGAAGCACGGAA 60.029 45.455 0.00 0.00 38.39 4.30
1005 2304 2.141535 GGAACGGATCGAGAATGGAG 57.858 55.000 0.00 0.00 0.00 3.86
1115 2414 0.388134 GGCAAGCTGCTGTTGATGTG 60.388 55.000 1.35 0.00 44.28 3.21
1162 2464 0.324091 GGAAGACGAGGAGGGGTACA 60.324 60.000 0.00 0.00 0.00 2.90
1325 2631 8.671921 GTCTATATATCTGCATCCATTGGTTTG 58.328 37.037 1.86 3.53 0.00 2.93
1353 2660 1.204146 GGAACAGAGCCCCTGACATA 58.796 55.000 10.30 0.00 45.78 2.29
1476 2783 1.004785 TGACGTACGTGCACAATCGG 61.005 55.000 28.16 2.02 0.00 4.18
1507 2814 0.467804 CCCCTCTTAGCTTCCTCTGC 59.532 60.000 0.00 0.00 0.00 4.26
1517 2824 1.462670 GCTTCCTCTGCTTCTTGAACG 59.537 52.381 0.00 0.00 0.00 3.95
1532 2843 3.553437 AACGACGCGGAGACTGGTG 62.553 63.158 12.47 0.00 0.00 4.17
1558 2873 0.965866 TTTTTGGTGCGTGTGGGTGA 60.966 50.000 0.00 0.00 0.00 4.02
1876 3191 2.656651 CTCATCTTCTCCGCCGCG 60.657 66.667 5.59 5.59 0.00 6.46
1907 3222 5.305585 AGTTACTTGACAACCACATCGATT 58.694 37.500 0.00 0.00 0.00 3.34
1911 3226 5.487433 ACTTGACAACCACATCGATTCATA 58.513 37.500 0.00 0.00 0.00 2.15
1927 3242 1.550524 TCATAGACCGTGCTCTGCTTT 59.449 47.619 0.00 0.00 0.00 3.51
1933 3248 2.349886 GACCGTGCTCTGCTTTTATCAG 59.650 50.000 0.00 0.00 0.00 2.90
1958 3273 1.578423 GTGCTCTGTTCTTGCAGCC 59.422 57.895 0.00 0.00 37.39 4.85
2160 3475 1.523758 GTCAAACCAGTTCGCCTGAT 58.476 50.000 3.77 0.00 44.49 2.90
2177 3492 2.291465 CTGATGGCCGATGTTATTGTGG 59.709 50.000 0.00 0.00 0.00 4.17
2178 3493 2.297701 GATGGCCGATGTTATTGTGGT 58.702 47.619 0.00 0.00 0.00 4.16
2223 3538 2.109593 ATGATGCTGCGCGATCCA 59.890 55.556 12.10 2.24 0.00 3.41
2389 3704 4.115199 GGTGATCCAAGCCCGCCT 62.115 66.667 0.00 0.00 0.00 5.52
2444 3759 2.203015 GCGGCCGGAGCTTCATTA 60.203 61.111 29.38 0.00 39.73 1.90
2445 3760 2.247437 GCGGCCGGAGCTTCATTAG 61.247 63.158 29.38 0.00 39.73 1.73
2447 3762 0.387929 CGGCCGGAGCTTCATTAGTA 59.612 55.000 20.10 0.00 39.73 1.82
2762 4467 0.246635 CACGTCGGATTCCACTTCCT 59.753 55.000 3.09 0.00 0.00 3.36
2765 4470 0.107654 GTCGGATTCCACTTCCTGGG 60.108 60.000 3.09 0.00 41.06 4.45
2806 4517 1.557099 CTGGCTGGTGTAGTGTAGGA 58.443 55.000 0.00 0.00 0.00 2.94
2856 4570 2.505407 TGGAGGATGTAGAATGGTGGTG 59.495 50.000 0.00 0.00 0.00 4.17
3005 4727 2.390288 GACGCGCACACATGTACG 59.610 61.111 5.73 4.26 37.82 3.67
3029 4757 1.460497 TGGTGGTGGTGGCTACTCA 60.460 57.895 0.00 0.00 0.00 3.41
3040 4768 3.047752 GCTACTCACAGAGCAGCAG 57.952 57.895 13.00 0.00 45.44 4.24
3041 4769 1.083242 GCTACTCACAGAGCAGCAGC 61.083 60.000 13.00 0.00 45.44 5.25
3097 4825 2.416296 CGGTTCATTCTGCCACGTACTA 60.416 50.000 0.00 0.00 0.00 1.82
3188 4953 6.264744 GTGTAGCTCTACATCTTGTATACCCA 59.735 42.308 12.29 0.00 46.36 4.51
3195 4960 5.680594 ACATCTTGTATACCCACCGTTTA 57.319 39.130 0.00 0.00 0.00 2.01
3197 4962 6.053005 ACATCTTGTATACCCACCGTTTATG 58.947 40.000 0.00 0.00 0.00 1.90
3227 4993 2.099263 AGGATGTATCAACGACACGGAG 59.901 50.000 0.00 0.00 0.00 4.63
3234 5000 1.006102 AACGACACGGAGCCTGAAG 60.006 57.895 0.00 0.00 0.00 3.02
3264 5030 4.207019 GCAGTTCGAAAACCACATTTCAAG 59.793 41.667 0.00 0.00 38.87 3.02
3302 5068 6.567687 TGGAAAAATACACATGTACACAGG 57.432 37.500 0.00 0.00 32.72 4.00
3322 5098 5.600484 ACAGGGATGGTGTGTAAATTTTCAA 59.400 36.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.723616 TGAGTGAATGTTAAAATTCCTCTGGAA 59.276 33.333 23.37 1.24 46.39 3.53
8 9 7.230747 TGAGTGAATGTTAAAATTCCTCTGGA 58.769 34.615 23.37 11.28 36.21 3.86
9 10 7.452880 TGAGTGAATGTTAAAATTCCTCTGG 57.547 36.000 23.37 0.00 36.21 3.86
10 11 9.994432 GTATGAGTGAATGTTAAAATTCCTCTG 57.006 33.333 23.37 0.00 36.21 3.35
11 12 9.178758 GGTATGAGTGAATGTTAAAATTCCTCT 57.821 33.333 23.37 17.88 36.21 3.69
12 13 9.178758 AGGTATGAGTGAATGTTAAAATTCCTC 57.821 33.333 19.77 19.77 35.98 3.71
13 14 9.178758 GAGGTATGAGTGAATGTTAAAATTCCT 57.821 33.333 14.54 11.16 35.98 3.36
14 15 9.178758 AGAGGTATGAGTGAATGTTAAAATTCC 57.821 33.333 14.54 7.17 35.98 3.01
17 18 8.960591 CCAAGAGGTATGAGTGAATGTTAAAAT 58.039 33.333 0.00 0.00 0.00 1.82
18 19 8.160765 TCCAAGAGGTATGAGTGAATGTTAAAA 58.839 33.333 0.00 0.00 35.89 1.52
19 20 7.685481 TCCAAGAGGTATGAGTGAATGTTAAA 58.315 34.615 0.00 0.00 35.89 1.52
20 21 7.252612 TCCAAGAGGTATGAGTGAATGTTAA 57.747 36.000 0.00 0.00 35.89 2.01
21 22 6.867519 TCCAAGAGGTATGAGTGAATGTTA 57.132 37.500 0.00 0.00 35.89 2.41
22 23 5.762179 TCCAAGAGGTATGAGTGAATGTT 57.238 39.130 0.00 0.00 35.89 2.71
23 24 5.485353 TCTTCCAAGAGGTATGAGTGAATGT 59.515 40.000 0.00 0.00 35.89 2.71
24 25 5.982356 TCTTCCAAGAGGTATGAGTGAATG 58.018 41.667 0.00 0.00 35.89 2.67
25 26 6.627087 TTCTTCCAAGAGGTATGAGTGAAT 57.373 37.500 0.00 0.00 36.22 2.57
26 27 6.213397 TGATTCTTCCAAGAGGTATGAGTGAA 59.787 38.462 0.00 0.00 36.22 3.18
27 28 5.721480 TGATTCTTCCAAGAGGTATGAGTGA 59.279 40.000 0.00 0.00 36.22 3.41
28 29 5.982356 TGATTCTTCCAAGAGGTATGAGTG 58.018 41.667 0.00 0.00 36.22 3.51
29 30 6.157645 ACATGATTCTTCCAAGAGGTATGAGT 59.842 38.462 0.00 0.00 36.22 3.41
30 31 6.482641 CACATGATTCTTCCAAGAGGTATGAG 59.517 42.308 0.00 4.87 36.22 2.90
31 32 6.156775 TCACATGATTCTTCCAAGAGGTATGA 59.843 38.462 0.00 2.86 36.22 2.15
32 33 6.259608 GTCACATGATTCTTCCAAGAGGTATG 59.740 42.308 0.00 0.00 36.22 2.39
33 34 6.352516 GTCACATGATTCTTCCAAGAGGTAT 58.647 40.000 0.00 0.00 36.22 2.73
34 35 5.624509 CGTCACATGATTCTTCCAAGAGGTA 60.625 44.000 0.00 0.00 36.22 3.08
35 36 4.583871 GTCACATGATTCTTCCAAGAGGT 58.416 43.478 0.00 0.00 36.22 3.85
36 37 3.620374 CGTCACATGATTCTTCCAAGAGG 59.380 47.826 0.00 0.00 36.22 3.69
37 38 3.063180 GCGTCACATGATTCTTCCAAGAG 59.937 47.826 0.00 0.00 36.22 2.85
38 39 3.002791 GCGTCACATGATTCTTCCAAGA 58.997 45.455 0.00 0.00 0.00 3.02
39 40 2.743664 TGCGTCACATGATTCTTCCAAG 59.256 45.455 0.00 0.00 0.00 3.61
40 41 2.777094 TGCGTCACATGATTCTTCCAA 58.223 42.857 0.00 0.00 0.00 3.53
41 42 2.470983 TGCGTCACATGATTCTTCCA 57.529 45.000 0.00 0.00 0.00 3.53
42 43 4.361451 AATTGCGTCACATGATTCTTCC 57.639 40.909 0.00 0.00 0.00 3.46
43 44 6.183360 TGTCTAATTGCGTCACATGATTCTTC 60.183 38.462 0.00 0.00 0.00 2.87
44 45 5.643348 TGTCTAATTGCGTCACATGATTCTT 59.357 36.000 0.00 0.00 0.00 2.52
45 46 5.178061 TGTCTAATTGCGTCACATGATTCT 58.822 37.500 0.00 0.00 0.00 2.40
46 47 5.469373 TGTCTAATTGCGTCACATGATTC 57.531 39.130 0.00 0.00 0.00 2.52
47 48 5.181056 TGTTGTCTAATTGCGTCACATGATT 59.819 36.000 0.00 0.00 0.00 2.57
48 49 4.694982 TGTTGTCTAATTGCGTCACATGAT 59.305 37.500 0.00 0.00 0.00 2.45
49 50 4.061596 TGTTGTCTAATTGCGTCACATGA 58.938 39.130 0.00 0.00 0.00 3.07
50 51 4.152223 TCTGTTGTCTAATTGCGTCACATG 59.848 41.667 0.00 0.00 0.00 3.21
51 52 4.314961 TCTGTTGTCTAATTGCGTCACAT 58.685 39.130 0.00 0.00 0.00 3.21
52 53 3.723260 TCTGTTGTCTAATTGCGTCACA 58.277 40.909 0.00 0.00 0.00 3.58
53 54 4.725556 TTCTGTTGTCTAATTGCGTCAC 57.274 40.909 0.00 0.00 0.00 3.67
54 55 5.743026 TTTTCTGTTGTCTAATTGCGTCA 57.257 34.783 0.00 0.00 0.00 4.35
55 56 7.519002 ACTATTTTCTGTTGTCTAATTGCGTC 58.481 34.615 0.00 0.00 0.00 5.19
56 57 7.435068 ACTATTTTCTGTTGTCTAATTGCGT 57.565 32.000 0.00 0.00 0.00 5.24
57 58 9.262472 GTAACTATTTTCTGTTGTCTAATTGCG 57.738 33.333 0.00 0.00 0.00 4.85
58 59 9.262472 CGTAACTATTTTCTGTTGTCTAATTGC 57.738 33.333 0.00 0.00 0.00 3.56
59 60 9.755064 CCGTAACTATTTTCTGTTGTCTAATTG 57.245 33.333 0.00 0.00 0.00 2.32
60 61 9.498176 ACCGTAACTATTTTCTGTTGTCTAATT 57.502 29.630 0.00 0.00 0.00 1.40
61 62 9.498176 AACCGTAACTATTTTCTGTTGTCTAAT 57.502 29.630 0.00 0.00 0.00 1.73
62 63 8.891671 AACCGTAACTATTTTCTGTTGTCTAA 57.108 30.769 0.00 0.00 0.00 2.10
63 64 8.767085 CAAACCGTAACTATTTTCTGTTGTCTA 58.233 33.333 0.00 0.00 0.00 2.59
64 65 7.496591 TCAAACCGTAACTATTTTCTGTTGTCT 59.503 33.333 0.00 0.00 0.00 3.41
65 66 7.632721 TCAAACCGTAACTATTTTCTGTTGTC 58.367 34.615 0.00 0.00 0.00 3.18
66 67 7.556733 TCAAACCGTAACTATTTTCTGTTGT 57.443 32.000 0.00 0.00 0.00 3.32
67 68 9.458374 AATTCAAACCGTAACTATTTTCTGTTG 57.542 29.630 0.00 0.00 0.00 3.33
68 69 9.458374 CAATTCAAACCGTAACTATTTTCTGTT 57.542 29.630 0.00 0.00 0.00 3.16
69 70 8.079809 CCAATTCAAACCGTAACTATTTTCTGT 58.920 33.333 0.00 0.00 0.00 3.41
70 71 7.061789 GCCAATTCAAACCGTAACTATTTTCTG 59.938 37.037 0.00 0.00 0.00 3.02
71 72 7.088272 GCCAATTCAAACCGTAACTATTTTCT 58.912 34.615 0.00 0.00 0.00 2.52
72 73 6.864165 TGCCAATTCAAACCGTAACTATTTTC 59.136 34.615 0.00 0.00 0.00 2.29
73 74 6.750148 TGCCAATTCAAACCGTAACTATTTT 58.250 32.000 0.00 0.00 0.00 1.82
74 75 6.334102 TGCCAATTCAAACCGTAACTATTT 57.666 33.333 0.00 0.00 0.00 1.40
75 76 5.968528 TGCCAATTCAAACCGTAACTATT 57.031 34.783 0.00 0.00 0.00 1.73
76 77 5.968528 TTGCCAATTCAAACCGTAACTAT 57.031 34.783 0.00 0.00 0.00 2.12
77 78 5.521544 GTTTGCCAATTCAAACCGTAACTA 58.478 37.500 10.28 0.00 46.02 2.24
78 79 4.364860 GTTTGCCAATTCAAACCGTAACT 58.635 39.130 10.28 0.00 46.02 2.24
79 80 4.702247 GTTTGCCAATTCAAACCGTAAC 57.298 40.909 10.28 0.00 46.02 2.50
86 87 4.377839 TCAAGTCGTTTGCCAATTCAAA 57.622 36.364 0.00 0.00 36.70 2.69
87 88 4.377839 TTCAAGTCGTTTGCCAATTCAA 57.622 36.364 0.00 0.00 36.70 2.69
88 89 4.545610 GATTCAAGTCGTTTGCCAATTCA 58.454 39.130 0.00 0.00 36.70 2.57
89 90 3.920412 GGATTCAAGTCGTTTGCCAATTC 59.080 43.478 0.00 0.00 36.70 2.17
90 91 3.306019 GGGATTCAAGTCGTTTGCCAATT 60.306 43.478 0.00 0.00 36.70 2.32
91 92 2.231235 GGGATTCAAGTCGTTTGCCAAT 59.769 45.455 0.00 0.00 36.70 3.16
92 93 1.611491 GGGATTCAAGTCGTTTGCCAA 59.389 47.619 0.00 0.00 36.70 4.52
93 94 1.243902 GGGATTCAAGTCGTTTGCCA 58.756 50.000 0.00 0.00 36.70 4.92
94 95 0.526211 GGGGATTCAAGTCGTTTGCC 59.474 55.000 0.00 0.00 36.70 4.52
95 96 0.526211 GGGGGATTCAAGTCGTTTGC 59.474 55.000 0.00 0.00 36.70 3.68
96 97 0.802494 CGGGGGATTCAAGTCGTTTG 59.198 55.000 0.00 0.00 38.17 2.93
97 98 0.322187 CCGGGGGATTCAAGTCGTTT 60.322 55.000 0.00 0.00 0.00 3.60
98 99 1.298667 CCGGGGGATTCAAGTCGTT 59.701 57.895 0.00 0.00 0.00 3.85
99 100 2.666098 CCCGGGGGATTCAAGTCGT 61.666 63.158 14.71 0.00 37.50 4.34
100 101 2.189521 CCCGGGGGATTCAAGTCG 59.810 66.667 14.71 0.00 37.50 4.18
111 112 0.035725 GTAGAACTGAAACCCCGGGG 60.036 60.000 39.18 39.18 42.03 5.73
112 113 0.390735 CGTAGAACTGAAACCCCGGG 60.391 60.000 15.80 15.80 0.00 5.73
113 114 0.604578 TCGTAGAACTGAAACCCCGG 59.395 55.000 0.00 0.00 0.00 5.73
114 115 2.443887 TTCGTAGAACTGAAACCCCG 57.556 50.000 0.00 0.00 45.90 5.73
115 116 3.934068 TGATTCGTAGAACTGAAACCCC 58.066 45.455 0.00 0.00 45.90 4.95
116 117 5.699458 TCTTTGATTCGTAGAACTGAAACCC 59.301 40.000 0.00 0.00 45.90 4.11
117 118 6.645415 TCTCTTTGATTCGTAGAACTGAAACC 59.355 38.462 0.00 0.00 45.90 3.27
118 119 7.359347 GGTCTCTTTGATTCGTAGAACTGAAAC 60.359 40.741 0.00 0.00 45.90 2.78
119 120 6.645415 GGTCTCTTTGATTCGTAGAACTGAAA 59.355 38.462 0.00 0.00 45.90 2.69
120 121 6.157211 GGTCTCTTTGATTCGTAGAACTGAA 58.843 40.000 0.00 0.00 45.90 3.02
121 122 5.336531 GGGTCTCTTTGATTCGTAGAACTGA 60.337 44.000 0.00 0.00 45.90 3.41
122 123 4.865365 GGGTCTCTTTGATTCGTAGAACTG 59.135 45.833 0.00 0.00 45.90 3.16
123 124 4.773149 AGGGTCTCTTTGATTCGTAGAACT 59.227 41.667 0.00 0.00 45.90 3.01
124 125 5.074584 AGGGTCTCTTTGATTCGTAGAAC 57.925 43.478 0.00 0.00 45.90 3.01
125 126 4.770531 TGAGGGTCTCTTTGATTCGTAGAA 59.229 41.667 0.00 0.00 45.90 2.10
126 127 4.341487 TGAGGGTCTCTTTGATTCGTAGA 58.659 43.478 0.00 0.00 0.00 2.59
127 128 4.720649 TGAGGGTCTCTTTGATTCGTAG 57.279 45.455 0.00 0.00 0.00 3.51
128 129 5.186992 TGATTGAGGGTCTCTTTGATTCGTA 59.813 40.000 0.00 0.00 0.00 3.43
129 130 4.020218 TGATTGAGGGTCTCTTTGATTCGT 60.020 41.667 0.00 0.00 0.00 3.85
130 131 4.507710 TGATTGAGGGTCTCTTTGATTCG 58.492 43.478 0.00 0.00 0.00 3.34
131 132 6.679884 GCAATGATTGAGGGTCTCTTTGATTC 60.680 42.308 9.76 0.00 0.00 2.52
132 133 5.126707 GCAATGATTGAGGGTCTCTTTGATT 59.873 40.000 9.76 0.00 0.00 2.57
133 134 4.643784 GCAATGATTGAGGGTCTCTTTGAT 59.356 41.667 9.76 0.00 0.00 2.57
134 135 4.012374 GCAATGATTGAGGGTCTCTTTGA 58.988 43.478 9.76 0.00 0.00 2.69
135 136 3.760151 TGCAATGATTGAGGGTCTCTTTG 59.240 43.478 9.76 0.00 0.00 2.77
136 137 4.038271 TGCAATGATTGAGGGTCTCTTT 57.962 40.909 9.76 0.00 0.00 2.52
137 138 3.726557 TGCAATGATTGAGGGTCTCTT 57.273 42.857 9.76 0.00 0.00 2.85
138 139 3.947612 ATGCAATGATTGAGGGTCTCT 57.052 42.857 9.76 0.00 0.00 3.10
148 149 8.701895 ATCTTAACAGAATTCCATGCAATGATT 58.298 29.630 0.65 0.00 38.65 2.57
256 257 9.157104 GAAAACACAGGTTCAAAATCCTTTTTA 57.843 29.630 0.00 0.00 35.82 1.52
262 263 5.276461 AGGAAAACACAGGTTCAAAATCC 57.724 39.130 0.00 0.00 35.82 3.01
272 273 3.566351 AGGGAAAGAAGGAAAACACAGG 58.434 45.455 0.00 0.00 0.00 4.00
420 421 0.318120 AAGCTTCGGGCAATTTGGTG 59.682 50.000 0.00 0.00 44.79 4.17
421 422 1.917872 TAAGCTTCGGGCAATTTGGT 58.082 45.000 0.00 0.00 44.79 3.67
429 430 0.746659 AAATGGCATAAGCTTCGGGC 59.253 50.000 0.00 9.66 41.70 6.13
444 445 1.201181 TCCGCCGTTGGATTGAAAATG 59.799 47.619 0.00 0.00 31.53 2.32
459 460 3.629142 ATAACAGGCCTAATATCCGCC 57.371 47.619 3.98 0.00 43.35 6.13
461 462 5.657302 AGAGGTATAACAGGCCTAATATCCG 59.343 44.000 3.98 0.00 31.89 4.18
470 471 4.868314 ACGAATAGAGGTATAACAGGCC 57.132 45.455 0.00 0.00 0.00 5.19
523 524 2.139118 TGATTGCGTCACACGAATTCA 58.861 42.857 6.22 0.00 46.05 2.57
524 525 2.873170 TGATTGCGTCACACGAATTC 57.127 45.000 0.00 0.00 46.05 2.17
527 528 1.666189 TGTTTGATTGCGTCACACGAA 59.334 42.857 0.00 0.00 46.05 3.85
529 530 2.098215 TTGTTTGATTGCGTCACACG 57.902 45.000 4.43 0.00 45.88 4.49
530 531 2.213131 CGTTTGTTTGATTGCGTCACAC 59.787 45.455 2.30 2.30 37.89 3.82
532 533 2.710760 TCGTTTGTTTGATTGCGTCAC 58.289 42.857 0.00 0.00 36.32 3.67
533 534 3.406728 TTCGTTTGTTTGATTGCGTCA 57.593 38.095 0.00 0.00 34.25 4.35
534 535 4.143618 GGATTTCGTTTGTTTGATTGCGTC 60.144 41.667 0.00 0.00 0.00 5.19
535 536 3.733727 GGATTTCGTTTGTTTGATTGCGT 59.266 39.130 0.00 0.00 0.00 5.24
536 537 3.121113 GGGATTTCGTTTGTTTGATTGCG 59.879 43.478 0.00 0.00 0.00 4.85
537 538 4.054671 TGGGATTTCGTTTGTTTGATTGC 58.945 39.130 0.00 0.00 0.00 3.56
538 539 5.527951 TCTGGGATTTCGTTTGTTTGATTG 58.472 37.500 0.00 0.00 0.00 2.67
542 1200 3.857010 GCCTCTGGGATTTCGTTTGTTTG 60.857 47.826 0.00 0.00 33.58 2.93
552 1210 1.676014 CGTTCGAAGCCTCTGGGATTT 60.676 52.381 0.00 0.00 41.79 2.17
553 1211 0.108138 CGTTCGAAGCCTCTGGGATT 60.108 55.000 0.00 0.00 44.73 3.01
554 1212 1.258445 ACGTTCGAAGCCTCTGGGAT 61.258 55.000 0.00 0.00 33.58 3.85
555 1213 1.906824 ACGTTCGAAGCCTCTGGGA 60.907 57.895 0.00 0.00 33.58 4.37
556 1214 1.738099 CACGTTCGAAGCCTCTGGG 60.738 63.158 0.00 0.00 0.00 4.45
557 1215 2.383527 GCACGTTCGAAGCCTCTGG 61.384 63.158 0.00 0.00 0.00 3.86
558 1216 1.664649 TGCACGTTCGAAGCCTCTG 60.665 57.895 0.00 0.00 0.00 3.35
559 1217 1.664965 GTGCACGTTCGAAGCCTCT 60.665 57.895 0.00 0.00 0.00 3.69
560 1218 2.853914 GTGCACGTTCGAAGCCTC 59.146 61.111 0.00 0.00 0.00 4.70
561 1219 3.036084 CGTGCACGTTCGAAGCCT 61.036 61.111 30.50 0.00 34.11 4.58
562 1220 3.033764 TCGTGCACGTTCGAAGCC 61.034 61.111 35.74 0.00 40.80 4.35
563 1221 1.886861 ATGTCGTGCACGTTCGAAGC 61.887 55.000 35.74 18.63 40.80 3.86
564 1222 0.506932 AATGTCGTGCACGTTCGAAG 59.493 50.000 35.74 9.23 40.80 3.79
565 1223 0.231024 CAATGTCGTGCACGTTCGAA 59.769 50.000 35.74 16.27 40.80 3.71
567 1225 0.231024 TTCAATGTCGTGCACGTTCG 59.769 50.000 35.74 21.17 40.80 3.95
568 1226 2.594529 ATTCAATGTCGTGCACGTTC 57.405 45.000 35.74 28.15 40.80 3.95
569 1227 3.296628 GAAATTCAATGTCGTGCACGTT 58.703 40.909 35.74 21.94 40.80 3.99
570 1228 2.350388 GGAAATTCAATGTCGTGCACGT 60.350 45.455 35.74 17.06 40.80 4.49
574 1232 2.611974 ACGGAAATTCAATGTCGTGC 57.388 45.000 0.00 0.00 0.00 5.34
576 1234 3.331150 TGCTACGGAAATTCAATGTCGT 58.669 40.909 0.00 0.00 35.07 4.34
577 1235 4.334443 CTTGCTACGGAAATTCAATGTCG 58.666 43.478 0.00 0.00 0.00 4.35
582 1240 2.487762 CAGGCTTGCTACGGAAATTCAA 59.512 45.455 0.00 0.00 0.00 2.69
583 1241 2.083774 CAGGCTTGCTACGGAAATTCA 58.916 47.619 0.00 0.00 0.00 2.57
584 1242 2.084546 ACAGGCTTGCTACGGAAATTC 58.915 47.619 0.00 0.00 0.00 2.17
649 1315 2.448926 TTCATACTGTCACCGTGGTG 57.551 50.000 12.91 12.91 46.64 4.17
650 1316 3.695830 AATTCATACTGTCACCGTGGT 57.304 42.857 0.00 0.00 0.00 4.16
651 1317 3.426159 GCAAATTCATACTGTCACCGTGG 60.426 47.826 0.00 0.00 0.00 4.94
662 1328 6.258727 TCCTCAAGATTCGAGCAAATTCATAC 59.741 38.462 0.00 0.00 0.00 2.39
871 1769 2.930019 TGGCAGTGGGAGTGGAGG 60.930 66.667 0.00 0.00 0.00 4.30
900 2198 0.484212 TAAGGATCCGGACGGGGTAT 59.516 55.000 6.12 0.00 36.01 2.73
918 2217 6.033707 GCTTTGTCAAAGTACCATGAGGGTA 61.034 44.000 23.07 0.00 43.87 3.69
989 2288 1.742768 GCCTCCATTCTCGATCCGT 59.257 57.895 0.00 0.00 0.00 4.69
1094 2393 2.986306 ATCAACAGCAGCTTGCCGC 61.986 57.895 0.00 0.00 46.52 6.53
1325 2631 2.019984 GGGCTCTGTTCCATCATCAAC 58.980 52.381 0.00 0.00 0.00 3.18
1457 2764 1.004785 CCGATTGTGCACGTACGTCA 61.005 55.000 19.94 16.28 0.00 4.35
1476 2783 2.671896 AAGAGGGGATCAATGGATGC 57.328 50.000 0.00 0.00 40.80 3.91
1507 2814 0.386858 TCTCCGCGTCGTTCAAGAAG 60.387 55.000 4.92 0.00 0.00 2.85
1517 2824 2.126424 GTCACCAGTCTCCGCGTC 60.126 66.667 4.92 0.00 0.00 5.19
1554 2869 2.262915 CCGACCTCTGCACTCACC 59.737 66.667 0.00 0.00 0.00 4.02
1558 2873 1.593787 CATCACCGACCTCTGCACT 59.406 57.895 0.00 0.00 0.00 4.40
1618 2933 1.227350 CTCATCCATCTTCGCCGCA 60.227 57.895 0.00 0.00 0.00 5.69
1876 3191 5.237996 GTGGTTGTCAAGTAACTAACCTTCC 59.762 44.000 0.00 0.00 40.99 3.46
1884 3199 4.330944 TCGATGTGGTTGTCAAGTAACT 57.669 40.909 0.00 0.00 0.00 2.24
1907 3222 1.186200 AAGCAGAGCACGGTCTATGA 58.814 50.000 0.00 0.00 0.00 2.15
1911 3226 2.028112 TGATAAAAGCAGAGCACGGTCT 60.028 45.455 0.00 0.00 0.00 3.85
1927 3242 1.134995 CAGAGCACGGTCAGCTGATAA 60.135 52.381 21.47 0.00 43.58 1.75
1933 3248 0.601311 AAGAACAGAGCACGGTCAGC 60.601 55.000 0.00 0.00 0.00 4.26
1958 3273 3.561213 TAGTCGAGGACGCTCGCG 61.561 66.667 10.06 10.06 45.45 5.87
1967 3282 3.885521 GACGGCCGGTAGTCGAGG 61.886 72.222 31.76 0.00 42.43 4.63
2160 3475 1.003696 TGACCACAATAACATCGGCCA 59.996 47.619 2.24 0.00 0.00 5.36
2171 3486 5.513788 GCATATACATCCTCCTGACCACAAT 60.514 44.000 0.00 0.00 0.00 2.71
2177 3492 3.618507 GCAGGCATATACATCCTCCTGAC 60.619 52.174 9.98 0.00 42.64 3.51
2178 3493 2.568956 GCAGGCATATACATCCTCCTGA 59.431 50.000 9.98 0.00 42.64 3.86
2277 3592 0.382873 CCAGGCGTGCGTATGTACTA 59.617 55.000 0.00 0.00 0.00 1.82
2389 3704 1.658686 AAAAACAAGCGTGCCGTGGA 61.659 50.000 0.00 0.00 0.00 4.02
2443 3758 2.032550 GCTGCGACGACCAACTATACTA 59.967 50.000 0.00 0.00 0.00 1.82
2444 3759 1.202268 GCTGCGACGACCAACTATACT 60.202 52.381 0.00 0.00 0.00 2.12
2445 3760 1.197910 GCTGCGACGACCAACTATAC 58.802 55.000 0.00 0.00 0.00 1.47
2447 3762 0.458543 CTGCTGCGACGACCAACTAT 60.459 55.000 0.00 0.00 0.00 2.12
2551 3870 1.743623 CCGCACTGCCAATAACCGA 60.744 57.895 0.00 0.00 0.00 4.69
2702 4403 0.909610 TTTCCCTCCGATCCTGTGCT 60.910 55.000 0.00 0.00 0.00 4.40
2705 4406 0.618968 AGCTTTCCCTCCGATCCTGT 60.619 55.000 0.00 0.00 0.00 4.00
3005 4727 2.113139 CCACCACCACCACCACTC 59.887 66.667 0.00 0.00 0.00 3.51
3039 4767 3.352222 GCAGTGAAGTGCAGCGCT 61.352 61.111 2.64 2.64 43.41 5.92
3097 4825 4.315803 CAACGAACAGGGATTCAGTAAGT 58.684 43.478 0.00 0.00 0.00 2.24
3164 4929 6.264744 GTGGGTATACAAGATGTAGAGCTACA 59.735 42.308 19.11 12.28 46.18 2.74
3188 4953 4.345859 TCCTGTTGTCTTCATAAACGGT 57.654 40.909 0.00 0.00 0.00 4.83
3195 4960 5.582269 CGTTGATACATCCTGTTGTCTTCAT 59.418 40.000 0.00 0.00 0.00 2.57
3197 4962 5.062308 GTCGTTGATACATCCTGTTGTCTTC 59.938 44.000 0.00 0.00 0.00 2.87
3216 4982 1.006102 CTTCAGGCTCCGTGTCGTT 60.006 57.895 0.00 0.00 0.00 3.85
3227 4993 1.195674 GAACTGCTCGAAACTTCAGGC 59.804 52.381 0.00 0.00 0.00 4.85
3298 5064 5.144100 TGAAAATTTACACACCATCCCTGT 58.856 37.500 0.00 0.00 0.00 4.00
3299 5065 5.720371 TGAAAATTTACACACCATCCCTG 57.280 39.130 0.00 0.00 0.00 4.45
3302 5068 9.868277 TTCATATTGAAAATTTACACACCATCC 57.132 29.630 0.00 0.00 32.71 3.51


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

AutoCloner maintained by Alex Coulton.