Multiple sequence alignment - TraesCS1B01G349800

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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 TraesCS1B01G349800 chr1B 100.000 2357 0 0 1 2357 580439553 580437197 0.000000e+00 4353.0
1 TraesCS1B01G349800 chr1D 93.081 1402 64 17 692 2083 428613248 428611870 0.000000e+00 2021.0
2 TraesCS1B01G349800 chr1D 88.475 564 40 14 152 694 428618979 428618420 0.000000e+00 658.0
3 TraesCS1B01G349800 chr1D 89.558 249 19 3 2115 2357 428611871 428611624 2.280000e-80 309.0
4 TraesCS1B01G349800 chr1A 92.327 1225 45 12 998 2206 526738240 526737049 0.000000e+00 1696.0
5 TraesCS1B01G349800 chr1A 83.476 702 57 25 274 960 526738898 526738241 1.210000e-167 599.0
6 TraesCS1B01G349800 chr1A 96.875 96 2 1 153 248 526738988 526738894 2.420000e-35 159.0
7 TraesCS1B01G349800 chr1A 89.623 106 11 0 2251 2356 526737048 526736943 4.090000e-28 135.0
8 TraesCS1B01G349800 chr6B 83.019 265 42 3 2095 2357 54899281 54899018 1.090000e-58 237.0
9 TraesCS1B01G349800 chr6B 82.397 267 40 7 2095 2357 54729053 54729316 2.360000e-55 226.0
10 TraesCS1B01G349800 chr6B 82.022 267 41 7 2095 2357 54775553 54775816 1.100000e-53 220.0
11 TraesCS1B01G349800 chr6B 81.250 272 41 7 2092 2357 54697051 54697318 6.600000e-51 211.0
12 TraesCS1B01G349800 chr3B 96.503 143 4 1 1 142 56088140 56088282 3.920000e-58 235.0
13 TraesCS1B01G349800 chr3B 92.908 141 10 0 1 141 334799430 334799570 3.070000e-49 206.0
14 TraesCS1B01G349800 chr6A 81.455 275 41 7 2092 2357 28947755 28948028 1.420000e-52 217.0
15 TraesCS1B01G349800 chr6A 81.159 276 39 8 2092 2356 29022653 29022926 2.370000e-50 209.0
16 TraesCS1B01G349800 chr6A 81.250 224 33 5 2142 2357 29127659 29127437 3.110000e-39 172.0
17 TraesCS1B01G349800 chr3A 93.571 140 8 1 1 140 479780518 479780380 8.540000e-50 207.0
18 TraesCS1B01G349800 chr4A 92.857 140 10 0 1 140 699622693 699622832 1.100000e-48 204.0
19 TraesCS1B01G349800 chr4A 93.182 132 9 0 1 132 618104756 618104625 6.650000e-46 195.0
20 TraesCS1B01G349800 chr5A 90.714 140 13 0 1 140 656682499 656682638 1.110000e-43 187.0
21 TraesCS1B01G349800 chr7A 87.943 141 16 1 1 141 713260716 713260855 5.210000e-37 165.0
22 TraesCS1B01G349800 chr2A 98.039 51 1 0 90 140 713674317 713674267 3.230000e-14 89.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G349800 chr1B 580437197 580439553 2356 True 4353.00 4353 100.00000 1 2357 1 chr1B.!!$R1 2356
1 TraesCS1B01G349800 chr1D 428611624 428613248 1624 True 1165.00 2021 91.31950 692 2357 2 chr1D.!!$R2 1665
2 TraesCS1B01G349800 chr1D 428618420 428618979 559 True 658.00 658 88.47500 152 694 1 chr1D.!!$R1 542
3 TraesCS1B01G349800 chr1A 526736943 526738988 2045 True 647.25 1696 90.57525 153 2356 4 chr1A.!!$R1 2203

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
26 27 0.107410 TGCACGGAAGAGTTGTGGTT 60.107 50.0 0.0 0.0 34.24 3.67 F
94 95 0.174389 TGATTGGCGAGAGAGCAGTC 59.826 55.0 0.0 0.0 39.27 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1076 0.032017 AGCCGGTGAAGTAGGAGGAT 60.032 55.0 1.9 0.0 0.00 3.24 R
1439 1492 0.035598 TTTTCCGCCGAGACATGGAA 59.964 50.0 0.0 0.0 38.67 3.53 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.733236 TTACGGATGCACGGAAGAG 57.267 52.632 1.59 0.00 38.39 2.85
19 20 0.892755 TTACGGATGCACGGAAGAGT 59.107 50.000 1.59 0.00 38.39 3.24
20 21 0.892755 TACGGATGCACGGAAGAGTT 59.107 50.000 1.59 0.00 38.39 3.01
21 22 0.670546 ACGGATGCACGGAAGAGTTG 60.671 55.000 1.59 0.00 38.39 3.16
22 23 0.670546 CGGATGCACGGAAGAGTTGT 60.671 55.000 0.00 0.00 0.00 3.32
23 24 0.798776 GGATGCACGGAAGAGTTGTG 59.201 55.000 0.00 0.00 36.70 3.33
24 25 0.798776 GATGCACGGAAGAGTTGTGG 59.201 55.000 0.00 0.00 34.24 4.17
25 26 0.108585 ATGCACGGAAGAGTTGTGGT 59.891 50.000 0.00 0.00 34.24 4.16
26 27 0.107410 TGCACGGAAGAGTTGTGGTT 60.107 50.000 0.00 0.00 34.24 3.67
27 28 0.307760 GCACGGAAGAGTTGTGGTTG 59.692 55.000 0.00 0.00 34.24 3.77
28 29 0.944386 CACGGAAGAGTTGTGGTTGG 59.056 55.000 0.00 0.00 0.00 3.77
29 30 0.834612 ACGGAAGAGTTGTGGTTGGA 59.165 50.000 0.00 0.00 0.00 3.53
30 31 1.202651 ACGGAAGAGTTGTGGTTGGAG 60.203 52.381 0.00 0.00 0.00 3.86
31 32 1.070134 CGGAAGAGTTGTGGTTGGAGA 59.930 52.381 0.00 0.00 0.00 3.71
32 33 2.484770 CGGAAGAGTTGTGGTTGGAGAA 60.485 50.000 0.00 0.00 0.00 2.87
33 34 3.142174 GGAAGAGTTGTGGTTGGAGAAG 58.858 50.000 0.00 0.00 0.00 2.85
34 35 3.181454 GGAAGAGTTGTGGTTGGAGAAGA 60.181 47.826 0.00 0.00 0.00 2.87
35 36 4.505742 GGAAGAGTTGTGGTTGGAGAAGAT 60.506 45.833 0.00 0.00 0.00 2.40
36 37 4.713792 AGAGTTGTGGTTGGAGAAGATT 57.286 40.909 0.00 0.00 0.00 2.40
37 38 5.825593 AGAGTTGTGGTTGGAGAAGATTA 57.174 39.130 0.00 0.00 0.00 1.75
38 39 6.187727 AGAGTTGTGGTTGGAGAAGATTAA 57.812 37.500 0.00 0.00 0.00 1.40
39 40 6.234177 AGAGTTGTGGTTGGAGAAGATTAAG 58.766 40.000 0.00 0.00 0.00 1.85
40 41 5.316987 AGTTGTGGTTGGAGAAGATTAAGG 58.683 41.667 0.00 0.00 0.00 2.69
41 42 4.993705 TGTGGTTGGAGAAGATTAAGGT 57.006 40.909 0.00 0.00 0.00 3.50
42 43 4.651778 TGTGGTTGGAGAAGATTAAGGTG 58.348 43.478 0.00 0.00 0.00 4.00
43 44 4.010349 GTGGTTGGAGAAGATTAAGGTGG 58.990 47.826 0.00 0.00 0.00 4.61
44 45 3.913799 TGGTTGGAGAAGATTAAGGTGGA 59.086 43.478 0.00 0.00 0.00 4.02
45 46 4.019321 TGGTTGGAGAAGATTAAGGTGGAG 60.019 45.833 0.00 0.00 0.00 3.86
46 47 4.225267 GGTTGGAGAAGATTAAGGTGGAGA 59.775 45.833 0.00 0.00 0.00 3.71
47 48 5.423886 GTTGGAGAAGATTAAGGTGGAGAG 58.576 45.833 0.00 0.00 0.00 3.20
48 49 4.033709 TGGAGAAGATTAAGGTGGAGAGG 58.966 47.826 0.00 0.00 0.00 3.69
49 50 3.181459 GGAGAAGATTAAGGTGGAGAGGC 60.181 52.174 0.00 0.00 0.00 4.70
50 51 2.774809 AGAAGATTAAGGTGGAGAGGCC 59.225 50.000 0.00 0.00 37.10 5.19
51 52 1.512735 AGATTAAGGTGGAGAGGCCC 58.487 55.000 0.00 0.00 34.97 5.80
52 53 0.474614 GATTAAGGTGGAGAGGCCCC 59.525 60.000 0.00 0.00 34.97 5.80
53 54 0.253630 ATTAAGGTGGAGAGGCCCCA 60.254 55.000 0.00 0.00 34.97 4.96
57 58 3.721706 GTGGAGAGGCCCCACCAG 61.722 72.222 16.61 0.00 46.30 4.00
62 63 4.344865 GAGGCCCCACCAGCGAAA 62.345 66.667 0.00 0.00 43.14 3.46
63 64 3.860930 GAGGCCCCACCAGCGAAAA 62.861 63.158 0.00 0.00 43.14 2.29
64 65 2.679996 GGCCCCACCAGCGAAAAT 60.680 61.111 0.00 0.00 38.86 1.82
65 66 2.710902 GGCCCCACCAGCGAAAATC 61.711 63.158 0.00 0.00 38.86 2.17
66 67 1.976474 GCCCCACCAGCGAAAATCA 60.976 57.895 0.00 0.00 0.00 2.57
67 68 1.531739 GCCCCACCAGCGAAAATCAA 61.532 55.000 0.00 0.00 0.00 2.57
68 69 0.527565 CCCCACCAGCGAAAATCAAG 59.472 55.000 0.00 0.00 0.00 3.02
69 70 0.527565 CCCACCAGCGAAAATCAAGG 59.472 55.000 0.00 0.00 0.00 3.61
70 71 0.527565 CCACCAGCGAAAATCAAGGG 59.472 55.000 0.00 0.00 0.00 3.95
71 72 0.527565 CACCAGCGAAAATCAAGGGG 59.472 55.000 0.00 0.00 0.00 4.79
72 73 0.611896 ACCAGCGAAAATCAAGGGGG 60.612 55.000 0.00 0.00 0.00 5.40
86 87 2.674754 GGGGGTTGATTGGCGAGA 59.325 61.111 0.00 0.00 0.00 4.04
87 88 1.452108 GGGGGTTGATTGGCGAGAG 60.452 63.158 0.00 0.00 0.00 3.20
88 89 1.602237 GGGGTTGATTGGCGAGAGA 59.398 57.895 0.00 0.00 0.00 3.10
89 90 0.462759 GGGGTTGATTGGCGAGAGAG 60.463 60.000 0.00 0.00 0.00 3.20
90 91 1.092345 GGGTTGATTGGCGAGAGAGC 61.092 60.000 0.00 0.00 0.00 4.09
91 92 0.391661 GGTTGATTGGCGAGAGAGCA 60.392 55.000 0.00 0.00 39.27 4.26
92 93 1.005340 GTTGATTGGCGAGAGAGCAG 58.995 55.000 0.00 0.00 39.27 4.24
93 94 0.610174 TTGATTGGCGAGAGAGCAGT 59.390 50.000 0.00 0.00 39.27 4.40
94 95 0.174389 TGATTGGCGAGAGAGCAGTC 59.826 55.000 0.00 0.00 39.27 3.51
95 96 0.529555 GATTGGCGAGAGAGCAGTCC 60.530 60.000 0.00 0.00 39.27 3.85
96 97 2.290122 ATTGGCGAGAGAGCAGTCCG 62.290 60.000 0.00 0.00 39.27 4.79
97 98 3.444805 GGCGAGAGAGCAGTCCGT 61.445 66.667 0.00 0.00 39.27 4.69
98 99 2.202544 GCGAGAGAGCAGTCCGTG 60.203 66.667 0.00 0.00 37.05 4.94
99 100 2.691771 GCGAGAGAGCAGTCCGTGA 61.692 63.158 0.00 0.00 37.05 4.35
100 101 1.876664 CGAGAGAGCAGTCCGTGAA 59.123 57.895 0.00 0.00 0.00 3.18
101 102 0.179176 CGAGAGAGCAGTCCGTGAAG 60.179 60.000 0.00 0.00 0.00 3.02
102 103 0.457681 GAGAGAGCAGTCCGTGAAGC 60.458 60.000 0.00 0.00 0.00 3.86
103 104 1.446966 GAGAGCAGTCCGTGAAGCC 60.447 63.158 0.00 0.00 0.00 4.35
104 105 2.159819 GAGAGCAGTCCGTGAAGCCA 62.160 60.000 0.00 0.00 0.00 4.75
105 106 1.739562 GAGCAGTCCGTGAAGCCAG 60.740 63.158 0.00 0.00 0.00 4.85
106 107 2.031163 GCAGTCCGTGAAGCCAGT 59.969 61.111 0.00 0.00 0.00 4.00
107 108 2.029844 GCAGTCCGTGAAGCCAGTC 61.030 63.158 0.00 0.00 0.00 3.51
108 109 1.374758 CAGTCCGTGAAGCCAGTCC 60.375 63.158 0.00 0.00 0.00 3.85
109 110 2.432628 GTCCGTGAAGCCAGTCCG 60.433 66.667 0.00 0.00 0.00 4.79
110 111 2.915659 TCCGTGAAGCCAGTCCGT 60.916 61.111 0.00 0.00 0.00 4.69
111 112 1.604308 TCCGTGAAGCCAGTCCGTA 60.604 57.895 0.00 0.00 0.00 4.02
112 113 1.445582 CCGTGAAGCCAGTCCGTAC 60.446 63.158 0.00 0.00 0.00 3.67
113 114 1.585006 CGTGAAGCCAGTCCGTACT 59.415 57.895 0.00 0.00 35.91 2.73
114 115 0.806868 CGTGAAGCCAGTCCGTACTA 59.193 55.000 0.00 0.00 33.48 1.82
115 116 1.202154 CGTGAAGCCAGTCCGTACTAG 60.202 57.143 0.00 0.00 33.48 2.57
116 117 2.089980 GTGAAGCCAGTCCGTACTAGA 58.910 52.381 0.00 0.00 33.48 2.43
117 118 2.490903 GTGAAGCCAGTCCGTACTAGAA 59.509 50.000 0.00 0.00 33.48 2.10
118 119 3.130693 GTGAAGCCAGTCCGTACTAGAAT 59.869 47.826 0.00 0.00 33.48 2.40
119 120 3.130516 TGAAGCCAGTCCGTACTAGAATG 59.869 47.826 0.00 3.91 33.48 2.67
120 121 3.014304 AGCCAGTCCGTACTAGAATGA 57.986 47.619 10.64 0.00 33.48 2.57
121 122 2.688958 AGCCAGTCCGTACTAGAATGAC 59.311 50.000 10.64 1.25 33.48 3.06
122 123 2.541178 GCCAGTCCGTACTAGAATGACG 60.541 54.545 10.64 0.49 33.48 4.35
123 124 2.681848 CCAGTCCGTACTAGAATGACGT 59.318 50.000 10.64 0.00 33.48 4.34
124 125 3.873361 CCAGTCCGTACTAGAATGACGTA 59.127 47.826 10.64 0.00 33.48 3.57
125 126 4.333649 CCAGTCCGTACTAGAATGACGTAA 59.666 45.833 10.64 0.00 33.48 3.18
126 127 5.499935 CAGTCCGTACTAGAATGACGTAAG 58.500 45.833 0.00 0.00 37.71 2.34
127 128 5.064452 CAGTCCGTACTAGAATGACGTAAGT 59.936 44.000 0.00 0.00 45.20 2.24
128 129 5.064452 AGTCCGTACTAGAATGACGTAAGTG 59.936 44.000 0.00 0.00 43.35 3.16
129 130 7.293731 AGTCCGTACTAGAATGACGTAAGTGT 61.294 42.308 0.00 0.00 43.35 3.55
130 131 8.058698 AGTCCGTACTAGAATGACGTAAGTGTA 61.059 40.741 0.00 0.00 43.35 2.90
187 188 2.639327 GGATGTTGTGGGGCTGTGC 61.639 63.158 0.00 0.00 0.00 4.57
244 245 4.783560 AACTTTAGTGGGTGTAGTTGGT 57.216 40.909 0.00 0.00 0.00 3.67
317 323 0.999406 GCAGCTGTATGTGTACCGTG 59.001 55.000 16.64 0.00 0.00 4.94
323 329 2.429250 CTGTATGTGTACCGTGGGATCA 59.571 50.000 0.00 0.00 0.00 2.92
325 331 1.568504 ATGTGTACCGTGGGATCAGT 58.431 50.000 0.00 0.00 0.00 3.41
326 332 0.892755 TGTGTACCGTGGGATCAGTC 59.107 55.000 0.00 0.00 0.00 3.51
327 333 1.183549 GTGTACCGTGGGATCAGTCT 58.816 55.000 0.00 0.00 0.00 3.24
328 334 1.135083 GTGTACCGTGGGATCAGTCTG 60.135 57.143 0.00 0.00 0.00 3.51
329 335 0.179108 GTACCGTGGGATCAGTCTGC 60.179 60.000 0.00 0.00 0.00 4.26
368 390 3.657634 TGCTAGCAATGATCCTCGATTC 58.342 45.455 16.84 0.00 0.00 2.52
369 391 2.665537 GCTAGCAATGATCCTCGATTCG 59.334 50.000 10.63 0.00 0.00 3.34
370 392 2.898729 AGCAATGATCCTCGATTCGT 57.101 45.000 5.89 0.00 0.00 3.85
371 393 3.185246 AGCAATGATCCTCGATTCGTT 57.815 42.857 5.89 0.00 0.00 3.85
372 394 2.868583 AGCAATGATCCTCGATTCGTTG 59.131 45.455 15.46 15.46 0.00 4.10
373 395 2.600792 GCAATGATCCTCGATTCGTTGC 60.601 50.000 23.00 23.00 32.05 4.17
374 396 2.602257 ATGATCCTCGATTCGTTGCA 57.398 45.000 5.89 0.00 0.00 4.08
375 397 2.378445 TGATCCTCGATTCGTTGCAA 57.622 45.000 5.89 0.00 0.00 4.08
376 398 2.270923 TGATCCTCGATTCGTTGCAAG 58.729 47.619 0.00 0.00 0.00 4.01
377 399 1.594862 GATCCTCGATTCGTTGCAAGG 59.405 52.381 12.91 12.91 0.00 3.61
378 400 1.019278 TCCTCGATTCGTTGCAAGGC 61.019 55.000 14.22 0.01 0.00 4.35
382 404 1.013596 CGATTCGTTGCAAGGCCATA 58.986 50.000 14.22 0.60 0.00 2.74
447 470 1.326852 CTCGTGTCATGATTGCAGCTC 59.673 52.381 0.00 0.00 0.00 4.09
459 482 0.678684 TGCAGCTCATGATGTGGTGG 60.679 55.000 22.84 9.29 39.07 4.61
485 508 1.541169 TCCAGCAAGGAGGCCAAAA 59.459 52.632 5.01 0.00 43.07 2.44
503 526 2.979814 AAAAACAAGTGGCCACCTTC 57.020 45.000 32.29 7.74 0.00 3.46
511 534 0.954452 GTGGCCACCTTCAAGTTCAG 59.046 55.000 26.31 0.00 0.00 3.02
543 570 3.004944 TCATGAGTTAGTACGTGTGCACA 59.995 43.478 17.42 17.42 0.00 4.57
556 583 4.326009 ACGTGTGCACACTTTTGAAAATTC 59.674 37.500 38.81 15.30 44.34 2.17
572 599 6.125029 TGAAAATTCAAATTTGGGCAAGGAA 58.875 32.000 17.90 3.71 38.53 3.36
574 601 7.941238 TGAAAATTCAAATTTGGGCAAGGAATA 59.059 29.630 17.90 0.00 38.53 1.75
591 624 7.750903 GCAAGGAATAGTCACAATACAAAGTTC 59.249 37.037 0.00 0.00 0.00 3.01
595 628 8.946085 GGAATAGTCACAATACAAAGTTCATGA 58.054 33.333 0.00 0.00 0.00 3.07
643 680 9.764363 GATTCACTTTAAAAGAGGTTTCCAATT 57.236 29.630 0.00 0.00 0.00 2.32
652 689 8.887036 AAAAGAGGTTTCCAATTGTGTAATTC 57.113 30.769 4.43 0.00 34.34 2.17
664 702 2.824936 TGTGTAATTCTTGGGGCACATG 59.175 45.455 0.00 0.00 32.79 3.21
685 723 2.415776 GCCCATGGTGAAATTGTTGTG 58.584 47.619 11.73 0.00 0.00 3.33
711 749 2.298163 CCTAGTAAACGTGGACAGTGGT 59.702 50.000 0.00 0.00 0.00 4.16
756 797 4.526650 AGCCGAACCCAAAGACAAAATAAT 59.473 37.500 0.00 0.00 0.00 1.28
758 799 5.699001 GCCGAACCCAAAGACAAAATAATTT 59.301 36.000 0.00 0.00 0.00 1.82
804 845 4.089361 GACAGAAATTTGGAACCATCCCT 58.911 43.478 0.00 0.00 45.95 4.20
850 891 1.141185 CCCTCCTAATCCAACCCTCC 58.859 60.000 0.00 0.00 0.00 4.30
855 896 1.490910 CCTAATCCAACCCTCCCTGAC 59.509 57.143 0.00 0.00 0.00 3.51
861 902 0.478507 CAACCCTCCCTGACACCTTT 59.521 55.000 0.00 0.00 0.00 3.11
862 903 1.133482 CAACCCTCCCTGACACCTTTT 60.133 52.381 0.00 0.00 0.00 2.27
981 1022 1.380403 GCCTCTGTCTCTCGCTAGCA 61.380 60.000 16.45 0.92 0.00 3.49
984 1025 1.063912 CTCTGTCTCTCGCTAGCAGTG 59.936 57.143 16.45 11.77 0.00 3.66
987 1028 1.018148 GTCTCTCGCTAGCAGTGCTA 58.982 55.000 23.14 23.14 40.44 3.49
993 1034 1.066587 GCTAGCAGTGCTACCCGAG 59.933 63.158 21.00 13.70 40.44 4.63
995 1036 0.382515 CTAGCAGTGCTACCCGAGAC 59.617 60.000 21.00 0.00 40.44 3.36
996 1037 1.374343 TAGCAGTGCTACCCGAGACG 61.374 60.000 21.00 0.00 40.44 4.18
1338 1379 3.474570 GGCCAGCTGATCGACCCT 61.475 66.667 17.39 0.00 0.00 4.34
1365 1418 1.411977 CGCCTCAGATGACTCCTTGAT 59.588 52.381 0.00 0.00 0.00 2.57
1366 1419 2.158986 CGCCTCAGATGACTCCTTGATT 60.159 50.000 0.00 0.00 0.00 2.57
1367 1420 3.681034 CGCCTCAGATGACTCCTTGATTT 60.681 47.826 0.00 0.00 0.00 2.17
1368 1421 4.268359 GCCTCAGATGACTCCTTGATTTT 58.732 43.478 0.00 0.00 0.00 1.82
1369 1422 4.335037 GCCTCAGATGACTCCTTGATTTTC 59.665 45.833 0.00 0.00 0.00 2.29
1370 1423 4.880696 CCTCAGATGACTCCTTGATTTTCC 59.119 45.833 0.00 0.00 0.00 3.13
1371 1424 5.339035 CCTCAGATGACTCCTTGATTTTCCT 60.339 44.000 0.00 0.00 0.00 3.36
1372 1425 5.738909 TCAGATGACTCCTTGATTTTCCTC 58.261 41.667 0.00 0.00 0.00 3.71
1373 1426 5.486775 TCAGATGACTCCTTGATTTTCCTCT 59.513 40.000 0.00 0.00 0.00 3.69
1374 1427 5.585445 CAGATGACTCCTTGATTTTCCTCTG 59.415 44.000 0.00 0.00 0.00 3.35
1375 1428 5.486775 AGATGACTCCTTGATTTTCCTCTGA 59.513 40.000 0.00 0.00 0.00 3.27
1439 1492 1.372128 GGTAGTTGCGACGTCGGTT 60.372 57.895 36.13 9.64 40.23 4.44
1495 1548 2.681706 AGATGCAGACTGTTCTTGTCG 58.318 47.619 3.99 0.00 39.24 4.35
1531 1588 2.740668 GAGTCTCGTCTCGTCTCGT 58.259 57.895 0.00 0.00 0.00 4.18
1532 1589 1.906757 GAGTCTCGTCTCGTCTCGTA 58.093 55.000 0.00 0.00 0.00 3.43
1533 1590 2.462889 GAGTCTCGTCTCGTCTCGTAT 58.537 52.381 0.00 0.00 0.00 3.06
1534 1591 2.462889 AGTCTCGTCTCGTCTCGTATC 58.537 52.381 0.00 0.00 0.00 2.24
1546 1603 3.544440 CGTCTCGTATCTCCTTGTCTTCG 60.544 52.174 0.00 0.00 0.00 3.79
1577 1638 1.313835 CGATCGAACGAACGAGTTGTC 59.686 52.381 18.70 1.44 45.22 3.18
1680 1741 0.388134 ACGAATCACAAGGACGGACG 60.388 55.000 0.00 0.00 0.00 4.79
1803 1872 2.158740 GGTAGGGAAGGGAAAGAGATGC 60.159 54.545 0.00 0.00 0.00 3.91
1834 1903 4.115199 GCCGGTGGAGCCAGGAAT 62.115 66.667 1.90 0.00 36.97 3.01
1838 1907 1.597742 CGGTGGAGCCAGGAATAATG 58.402 55.000 0.00 0.00 36.97 1.90
2072 2142 2.966309 GCTTGGGAACTTGCGTCCG 61.966 63.158 0.00 0.00 0.00 4.79
2074 2144 3.835790 TTGGGAACTTGCGTCCGGG 62.836 63.158 0.00 0.00 0.00 5.73
2078 2148 4.572571 AACTTGCGTCCGGGCCAA 62.573 61.111 4.39 5.03 0.00 4.52
2105 2175 0.107508 CGGCAACATGGTCAGATCCT 60.108 55.000 0.00 0.00 0.00 3.24
2167 2241 0.804989 GGCACGAGCAGCTACATTTT 59.195 50.000 7.26 0.00 44.61 1.82
2206 2285 2.394632 TGTAGTGTCAGGTCTGGTTGT 58.605 47.619 0.00 0.00 0.00 3.32
2233 2312 3.570212 ACACAGGTGCCCCCACTC 61.570 66.667 0.00 0.00 41.75 3.51
2258 2337 2.135933 GCATGATGGCTCGGTAACTAC 58.864 52.381 0.00 0.00 0.00 2.73
2261 2340 2.453521 TGATGGCTCGGTAACTACTGT 58.546 47.619 0.00 0.00 34.25 3.55
2270 2349 2.415625 CGGTAACTACTGTCTGCTGGTC 60.416 54.545 0.00 0.00 0.00 4.02
2276 2355 4.344978 ACTACTGTCTGCTGGTCTAATGA 58.655 43.478 0.00 0.00 0.00 2.57
2277 2356 4.772624 ACTACTGTCTGCTGGTCTAATGAA 59.227 41.667 0.00 0.00 0.00 2.57
2279 2358 4.319177 ACTGTCTGCTGGTCTAATGAAAC 58.681 43.478 0.00 0.00 0.00 2.78
2287 2366 4.023536 GCTGGTCTAATGAAACCGTTTGAA 60.024 41.667 0.00 0.00 38.45 2.69
2289 2368 6.007936 TGGTCTAATGAAACCGTTTGAATG 57.992 37.500 0.00 0.00 38.45 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.892755 ACTCTTCCGTGCATCCGTAA 59.107 50.000 0.00 0.00 0.00 3.18
1 2 0.892755 AACTCTTCCGTGCATCCGTA 59.107 50.000 0.00 0.00 0.00 4.02
2 3 0.670546 CAACTCTTCCGTGCATCCGT 60.671 55.000 0.00 0.00 0.00 4.69
3 4 0.670546 ACAACTCTTCCGTGCATCCG 60.671 55.000 0.00 0.00 0.00 4.18
4 5 0.798776 CACAACTCTTCCGTGCATCC 59.201 55.000 0.00 0.00 0.00 3.51
5 6 0.798776 CCACAACTCTTCCGTGCATC 59.201 55.000 0.00 0.00 0.00 3.91
6 7 0.108585 ACCACAACTCTTCCGTGCAT 59.891 50.000 0.00 0.00 0.00 3.96
7 8 0.107410 AACCACAACTCTTCCGTGCA 60.107 50.000 0.00 0.00 0.00 4.57
8 9 0.307760 CAACCACAACTCTTCCGTGC 59.692 55.000 0.00 0.00 0.00 5.34
9 10 0.944386 CCAACCACAACTCTTCCGTG 59.056 55.000 0.00 0.00 0.00 4.94
10 11 0.834612 TCCAACCACAACTCTTCCGT 59.165 50.000 0.00 0.00 0.00 4.69
11 12 1.070134 TCTCCAACCACAACTCTTCCG 59.930 52.381 0.00 0.00 0.00 4.30
12 13 2.930826 TCTCCAACCACAACTCTTCC 57.069 50.000 0.00 0.00 0.00 3.46
13 14 4.073293 TCTTCTCCAACCACAACTCTTC 57.927 45.455 0.00 0.00 0.00 2.87
14 15 4.713792 ATCTTCTCCAACCACAACTCTT 57.286 40.909 0.00 0.00 0.00 2.85
15 16 4.713792 AATCTTCTCCAACCACAACTCT 57.286 40.909 0.00 0.00 0.00 3.24
16 17 5.412904 CCTTAATCTTCTCCAACCACAACTC 59.587 44.000 0.00 0.00 0.00 3.01
17 18 5.163088 ACCTTAATCTTCTCCAACCACAACT 60.163 40.000 0.00 0.00 0.00 3.16
18 19 5.048713 CACCTTAATCTTCTCCAACCACAAC 60.049 44.000 0.00 0.00 0.00 3.32
19 20 5.070001 CACCTTAATCTTCTCCAACCACAA 58.930 41.667 0.00 0.00 0.00 3.33
20 21 4.506625 CCACCTTAATCTTCTCCAACCACA 60.507 45.833 0.00 0.00 0.00 4.17
21 22 4.010349 CCACCTTAATCTTCTCCAACCAC 58.990 47.826 0.00 0.00 0.00 4.16
22 23 3.913799 TCCACCTTAATCTTCTCCAACCA 59.086 43.478 0.00 0.00 0.00 3.67
23 24 4.225267 TCTCCACCTTAATCTTCTCCAACC 59.775 45.833 0.00 0.00 0.00 3.77
24 25 5.422214 TCTCCACCTTAATCTTCTCCAAC 57.578 43.478 0.00 0.00 0.00 3.77
25 26 4.471386 CCTCTCCACCTTAATCTTCTCCAA 59.529 45.833 0.00 0.00 0.00 3.53
26 27 4.033709 CCTCTCCACCTTAATCTTCTCCA 58.966 47.826 0.00 0.00 0.00 3.86
27 28 3.181459 GCCTCTCCACCTTAATCTTCTCC 60.181 52.174 0.00 0.00 0.00 3.71
28 29 3.181459 GGCCTCTCCACCTTAATCTTCTC 60.181 52.174 0.00 0.00 34.01 2.87
29 30 2.774809 GGCCTCTCCACCTTAATCTTCT 59.225 50.000 0.00 0.00 34.01 2.85
30 31 2.158740 GGGCCTCTCCACCTTAATCTTC 60.159 54.545 0.84 0.00 36.21 2.87
31 32 1.847088 GGGCCTCTCCACCTTAATCTT 59.153 52.381 0.84 0.00 36.21 2.40
32 33 1.512735 GGGCCTCTCCACCTTAATCT 58.487 55.000 0.84 0.00 36.21 2.40
33 34 0.474614 GGGGCCTCTCCACCTTAATC 59.525 60.000 0.84 0.00 36.21 1.75
34 35 0.253630 TGGGGCCTCTCCACCTTAAT 60.254 55.000 3.07 0.00 37.50 1.40
35 36 1.162329 TGGGGCCTCTCCACCTTAA 59.838 57.895 3.07 0.00 37.50 1.85
36 37 1.615424 GTGGGGCCTCTCCACCTTA 60.615 63.158 16.61 0.00 46.58 2.69
37 38 2.936032 GTGGGGCCTCTCCACCTT 60.936 66.667 16.61 0.00 46.58 3.50
45 46 3.860930 TTTTCGCTGGTGGGGCCTC 62.861 63.158 0.84 0.00 38.35 4.70
46 47 3.224007 ATTTTCGCTGGTGGGGCCT 62.224 57.895 0.84 0.00 38.35 5.19
47 48 2.679996 ATTTTCGCTGGTGGGGCC 60.680 61.111 0.00 0.00 37.90 5.80
48 49 1.531739 TTGATTTTCGCTGGTGGGGC 61.532 55.000 0.00 0.00 0.00 5.80
49 50 0.527565 CTTGATTTTCGCTGGTGGGG 59.472 55.000 0.00 0.00 0.00 4.96
50 51 0.527565 CCTTGATTTTCGCTGGTGGG 59.472 55.000 0.00 0.00 0.00 4.61
51 52 0.527565 CCCTTGATTTTCGCTGGTGG 59.472 55.000 0.00 0.00 0.00 4.61
52 53 0.527565 CCCCTTGATTTTCGCTGGTG 59.472 55.000 0.00 0.00 0.00 4.17
53 54 0.611896 CCCCCTTGATTTTCGCTGGT 60.612 55.000 0.00 0.00 0.00 4.00
54 55 2.192605 CCCCCTTGATTTTCGCTGG 58.807 57.895 0.00 0.00 0.00 4.85
69 70 1.452108 CTCTCGCCAATCAACCCCC 60.452 63.158 0.00 0.00 0.00 5.40
70 71 0.462759 CTCTCTCGCCAATCAACCCC 60.463 60.000 0.00 0.00 0.00 4.95
71 72 1.092345 GCTCTCTCGCCAATCAACCC 61.092 60.000 0.00 0.00 0.00 4.11
72 73 0.391661 TGCTCTCTCGCCAATCAACC 60.392 55.000 0.00 0.00 0.00 3.77
73 74 1.005340 CTGCTCTCTCGCCAATCAAC 58.995 55.000 0.00 0.00 0.00 3.18
74 75 0.610174 ACTGCTCTCTCGCCAATCAA 59.390 50.000 0.00 0.00 0.00 2.57
75 76 0.174389 GACTGCTCTCTCGCCAATCA 59.826 55.000 0.00 0.00 0.00 2.57
76 77 0.529555 GGACTGCTCTCTCGCCAATC 60.530 60.000 0.00 0.00 0.00 2.67
77 78 1.519719 GGACTGCTCTCTCGCCAAT 59.480 57.895 0.00 0.00 0.00 3.16
78 79 2.973899 GGACTGCTCTCTCGCCAA 59.026 61.111 0.00 0.00 0.00 4.52
79 80 3.443925 CGGACTGCTCTCTCGCCA 61.444 66.667 0.00 0.00 0.00 5.69
80 81 3.444805 ACGGACTGCTCTCTCGCC 61.445 66.667 0.00 0.00 0.00 5.54
81 82 2.201436 TTCACGGACTGCTCTCTCGC 62.201 60.000 0.00 0.00 0.00 5.03
82 83 0.179176 CTTCACGGACTGCTCTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
83 84 0.457681 GCTTCACGGACTGCTCTCTC 60.458 60.000 0.00 0.00 0.00 3.20
84 85 1.589113 GCTTCACGGACTGCTCTCT 59.411 57.895 0.00 0.00 0.00 3.10
85 86 1.446966 GGCTTCACGGACTGCTCTC 60.447 63.158 0.00 0.00 0.00 3.20
86 87 2.164865 CTGGCTTCACGGACTGCTCT 62.165 60.000 0.00 0.00 0.00 4.09
87 88 1.739562 CTGGCTTCACGGACTGCTC 60.740 63.158 0.00 0.00 0.00 4.26
88 89 2.345244 CTGGCTTCACGGACTGCT 59.655 61.111 0.00 0.00 0.00 4.24
89 90 2.029844 GACTGGCTTCACGGACTGC 61.030 63.158 0.00 0.00 0.00 4.40
90 91 1.374758 GGACTGGCTTCACGGACTG 60.375 63.158 0.00 0.00 0.00 3.51
91 92 2.932234 CGGACTGGCTTCACGGACT 61.932 63.158 0.00 0.00 0.00 3.85
92 93 1.870055 TACGGACTGGCTTCACGGAC 61.870 60.000 0.00 0.00 0.00 4.79
93 94 1.604308 TACGGACTGGCTTCACGGA 60.604 57.895 0.00 0.00 0.00 4.69
94 95 1.445582 GTACGGACTGGCTTCACGG 60.446 63.158 0.00 0.00 0.00 4.94
95 96 0.806868 TAGTACGGACTGGCTTCACG 59.193 55.000 11.61 0.00 36.28 4.35
96 97 2.089980 TCTAGTACGGACTGGCTTCAC 58.910 52.381 11.61 0.00 36.28 3.18
97 98 2.502142 TCTAGTACGGACTGGCTTCA 57.498 50.000 11.61 0.00 36.28 3.02
98 99 3.380637 TCATTCTAGTACGGACTGGCTTC 59.619 47.826 11.61 0.00 36.28 3.86
99 100 3.130693 GTCATTCTAGTACGGACTGGCTT 59.869 47.826 11.61 0.00 36.28 4.35
100 101 2.688958 GTCATTCTAGTACGGACTGGCT 59.311 50.000 11.61 0.00 36.28 4.75
101 102 2.541178 CGTCATTCTAGTACGGACTGGC 60.541 54.545 11.61 0.00 36.28 4.85
102 103 2.681848 ACGTCATTCTAGTACGGACTGG 59.318 50.000 11.61 7.94 40.81 4.00
103 104 5.064452 ACTTACGTCATTCTAGTACGGACTG 59.936 44.000 11.61 0.19 40.81 3.51
104 105 5.064452 CACTTACGTCATTCTAGTACGGACT 59.936 44.000 5.18 5.18 40.81 3.85
105 106 5.163814 ACACTTACGTCATTCTAGTACGGAC 60.164 44.000 0.00 0.00 40.81 4.79
106 107 4.937620 ACACTTACGTCATTCTAGTACGGA 59.062 41.667 0.00 3.59 40.81 4.69
107 108 5.227238 ACACTTACGTCATTCTAGTACGG 57.773 43.478 0.00 0.00 40.81 4.02
108 109 5.900789 GCTACACTTACGTCATTCTAGTACG 59.099 44.000 0.00 0.00 42.17 3.67
109 110 6.779117 TGCTACACTTACGTCATTCTAGTAC 58.221 40.000 0.00 0.00 0.00 2.73
110 111 6.990341 TGCTACACTTACGTCATTCTAGTA 57.010 37.500 0.00 0.00 0.00 1.82
111 112 5.892160 TGCTACACTTACGTCATTCTAGT 57.108 39.130 0.00 0.00 0.00 2.57
112 113 7.757097 AAATGCTACACTTACGTCATTCTAG 57.243 36.000 0.00 0.00 0.00 2.43
113 114 8.440059 CAAAAATGCTACACTTACGTCATTCTA 58.560 33.333 0.00 0.00 0.00 2.10
114 115 7.041372 ACAAAAATGCTACACTTACGTCATTCT 60.041 33.333 0.00 0.00 0.00 2.40
115 116 7.075741 ACAAAAATGCTACACTTACGTCATTC 58.924 34.615 0.00 0.00 0.00 2.67
116 117 6.966021 ACAAAAATGCTACACTTACGTCATT 58.034 32.000 0.00 0.00 0.00 2.57
117 118 6.554334 ACAAAAATGCTACACTTACGTCAT 57.446 33.333 0.00 0.00 0.00 3.06
118 119 5.994887 ACAAAAATGCTACACTTACGTCA 57.005 34.783 0.00 0.00 0.00 4.35
119 120 8.944212 ATTAACAAAAATGCTACACTTACGTC 57.056 30.769 0.00 0.00 0.00 4.34
187 188 1.273606 AGAATCACTCGGACACAGGTG 59.726 52.381 0.00 0.00 0.00 4.00
317 323 1.690219 ATCCCACGCAGACTGATCCC 61.690 60.000 6.65 0.00 0.00 3.85
323 329 1.341531 GCATACTATCCCACGCAGACT 59.658 52.381 0.00 0.00 0.00 3.24
325 331 1.408969 TGCATACTATCCCACGCAGA 58.591 50.000 0.00 0.00 0.00 4.26
326 332 1.788258 CTGCATACTATCCCACGCAG 58.212 55.000 0.00 0.00 40.68 5.18
327 333 0.249868 GCTGCATACTATCCCACGCA 60.250 55.000 0.00 0.00 0.00 5.24
328 334 0.034059 AGCTGCATACTATCCCACGC 59.966 55.000 1.02 0.00 0.00 5.34
329 335 1.788258 CAGCTGCATACTATCCCACG 58.212 55.000 0.00 0.00 0.00 4.94
368 390 2.664916 GCAATATATGGCCTTGCAACG 58.335 47.619 18.85 0.00 43.62 4.10
372 394 2.029649 CCACTGCAATATATGGCCTTGC 60.030 50.000 17.38 17.38 44.25 4.01
373 395 3.225104 ACCACTGCAATATATGGCCTTG 58.775 45.455 9.67 6.38 35.49 3.61
374 396 3.490348 GACCACTGCAATATATGGCCTT 58.510 45.455 9.67 0.00 35.49 4.35
375 397 2.224867 GGACCACTGCAATATATGGCCT 60.225 50.000 9.67 0.00 35.49 5.19
376 398 2.162681 GGACCACTGCAATATATGGCC 58.837 52.381 9.67 0.00 35.49 5.36
377 399 3.077359 GAGGACCACTGCAATATATGGC 58.923 50.000 5.02 5.02 35.49 4.40
378 400 4.040829 TGAGAGGACCACTGCAATATATGG 59.959 45.833 0.00 0.00 38.26 2.74
382 404 3.110705 AGTGAGAGGACCACTGCAATAT 58.889 45.455 0.00 0.00 42.68 1.28
447 470 2.048444 AAGCTAGCCACCACATCATG 57.952 50.000 12.13 0.00 0.00 3.07
485 508 1.859302 TGAAGGTGGCCACTTGTTTT 58.141 45.000 33.91 19.79 0.00 2.43
503 526 8.092521 ACTCATGAGTATTTGTTCTGAACTTG 57.907 34.615 26.87 0.00 40.43 3.16
511 534 8.584600 CACGTACTAACTCATGAGTATTTGTTC 58.415 37.037 28.10 16.03 41.58 3.18
556 583 5.170748 GTGACTATTCCTTGCCCAAATTTG 58.829 41.667 11.40 11.40 0.00 2.32
572 599 8.846943 TGTCATGAACTTTGTATTGTGACTAT 57.153 30.769 0.00 0.00 36.57 2.12
574 601 7.566760 TTGTCATGAACTTTGTATTGTGACT 57.433 32.000 0.00 0.00 36.57 3.41
615 651 7.712797 TGGAAACCTCTTTTAAAGTGAATCAC 58.287 34.615 5.02 5.02 34.10 3.06
616 652 7.889873 TGGAAACCTCTTTTAAAGTGAATCA 57.110 32.000 8.16 0.00 0.00 2.57
633 670 5.931724 CCCAAGAATTACACAATTGGAAACC 59.068 40.000 10.83 0.00 42.46 3.27
643 680 2.666272 TGTGCCCCAAGAATTACACA 57.334 45.000 0.00 0.00 35.80 3.72
664 702 1.347378 ACAACAATTTCACCATGGGCC 59.653 47.619 18.09 0.00 0.00 5.80
685 723 2.029649 TGTCCACGTTTACTAGGTGCTC 60.030 50.000 0.00 0.00 40.46 4.26
756 797 9.303537 CACCACTTAAAAATTCGGAAGTTTAAA 57.696 29.630 15.49 5.74 29.73 1.52
758 799 8.130469 GTCACCACTTAAAAATTCGGAAGTTTA 58.870 33.333 15.49 10.05 29.73 2.01
766 807 8.574196 AATTTCTGTCACCACTTAAAAATTCG 57.426 30.769 0.00 0.00 0.00 3.34
804 845 0.413037 AAAGGGGGATGCCATGACAA 59.587 50.000 5.30 0.00 0.00 3.18
864 905 9.856162 GGGGTTTTGATAAGGTTATATACTGAA 57.144 33.333 0.00 0.00 0.00 3.02
865 906 9.232882 AGGGGTTTTGATAAGGTTATATACTGA 57.767 33.333 0.00 0.00 0.00 3.41
866 907 9.503399 GAGGGGTTTTGATAAGGTTATATACTG 57.497 37.037 0.00 0.00 0.00 2.74
917 958 1.068281 CAGAGCTGTGTGTGAGTGAGT 59.932 52.381 1.91 0.00 0.00 3.41
918 959 1.780806 CAGAGCTGTGTGTGAGTGAG 58.219 55.000 1.91 0.00 0.00 3.51
919 960 0.249615 GCAGAGCTGTGTGTGAGTGA 60.250 55.000 13.05 0.00 0.00 3.41
920 961 1.226686 GGCAGAGCTGTGTGTGAGTG 61.227 60.000 13.05 0.00 0.00 3.51
981 1022 0.321919 TGTACGTCTCGGGTAGCACT 60.322 55.000 0.00 0.00 0.00 4.40
984 1025 0.030369 CCATGTACGTCTCGGGTAGC 59.970 60.000 0.00 0.00 0.00 3.58
987 1028 0.034767 TCTCCATGTACGTCTCGGGT 60.035 55.000 0.00 0.00 0.00 5.28
993 1034 2.427453 ACTGTCCATCTCCATGTACGTC 59.573 50.000 0.00 0.00 0.00 4.34
995 1036 2.427095 TCACTGTCCATCTCCATGTACG 59.573 50.000 0.00 0.00 0.00 3.67
996 1037 3.739519 GCTCACTGTCCATCTCCATGTAC 60.740 52.174 0.00 0.00 0.00 2.90
1035 1076 0.032017 AGCCGGTGAAGTAGGAGGAT 60.032 55.000 1.90 0.00 0.00 3.24
1338 1379 4.519437 CATCTGAGGCGCTCGGCA 62.519 66.667 17.74 0.00 46.16 5.69
1365 1418 5.130350 ACGACAAGGAAAATCAGAGGAAAA 58.870 37.500 0.00 0.00 0.00 2.29
1366 1419 4.714632 ACGACAAGGAAAATCAGAGGAAA 58.285 39.130 0.00 0.00 0.00 3.13
1367 1420 4.315803 GACGACAAGGAAAATCAGAGGAA 58.684 43.478 0.00 0.00 0.00 3.36
1368 1421 3.614150 CGACGACAAGGAAAATCAGAGGA 60.614 47.826 0.00 0.00 0.00 3.71
1369 1422 2.668457 CGACGACAAGGAAAATCAGAGG 59.332 50.000 0.00 0.00 0.00 3.69
1370 1423 2.668457 CCGACGACAAGGAAAATCAGAG 59.332 50.000 0.00 0.00 0.00 3.35
1371 1424 2.036733 ACCGACGACAAGGAAAATCAGA 59.963 45.455 0.00 0.00 0.00 3.27
1372 1425 2.413837 ACCGACGACAAGGAAAATCAG 58.586 47.619 0.00 0.00 0.00 2.90
1373 1426 2.536761 ACCGACGACAAGGAAAATCA 57.463 45.000 0.00 0.00 0.00 2.57
1374 1427 2.159881 CGAACCGACGACAAGGAAAATC 60.160 50.000 0.00 0.00 35.09 2.17
1375 1428 1.796459 CGAACCGACGACAAGGAAAAT 59.204 47.619 0.00 0.00 35.09 1.82
1439 1492 0.035598 TTTTCCGCCGAGACATGGAA 59.964 50.000 0.00 0.00 38.67 3.53
1495 1548 2.494073 ACTCGAGAGGGAGTCACATTTC 59.506 50.000 21.68 0.00 43.63 2.17
1530 1587 4.436242 TCACACGAAGACAAGGAGATAC 57.564 45.455 0.00 0.00 0.00 2.24
1531 1588 4.705023 TCATCACACGAAGACAAGGAGATA 59.295 41.667 0.00 0.00 0.00 1.98
1532 1589 3.511540 TCATCACACGAAGACAAGGAGAT 59.488 43.478 0.00 0.00 0.00 2.75
1533 1590 2.890945 TCATCACACGAAGACAAGGAGA 59.109 45.455 0.00 0.00 0.00 3.71
1534 1591 3.303881 TCATCACACGAAGACAAGGAG 57.696 47.619 0.00 0.00 0.00 3.69
1546 1603 1.781429 CGTTCGATCGGATCATCACAC 59.219 52.381 16.41 5.62 0.00 3.82
1606 1667 1.227527 CTGTTCACACGGCCAGTCA 60.228 57.895 2.24 0.00 0.00 3.41
1607 1668 1.227556 ACTGTTCACACGGCCAGTC 60.228 57.895 2.24 0.00 32.97 3.51
1615 1676 2.472816 CAATTTGGCCACTGTTCACAC 58.527 47.619 3.88 0.00 0.00 3.82
1663 1724 0.669318 TGCGTCCGTCCTTGTGATTC 60.669 55.000 0.00 0.00 0.00 2.52
1666 1727 1.080093 GATGCGTCCGTCCTTGTGA 60.080 57.895 0.00 0.00 0.00 3.58
1772 1841 1.000955 CCTTCCCTACCCATCGAATCG 59.999 57.143 0.00 0.00 0.00 3.34
1803 1872 0.738389 ACCGGCCAAATTGATTAGCG 59.262 50.000 0.00 0.00 0.00 4.26
2082 2152 2.359850 TGACCATGTTGCCGAGGC 60.360 61.111 7.26 7.26 42.35 4.70
2083 2153 0.107508 ATCTGACCATGTTGCCGAGG 60.108 55.000 0.00 0.00 0.00 4.63
2084 2154 1.293924 GATCTGACCATGTTGCCGAG 58.706 55.000 0.00 0.00 0.00 4.63
2085 2155 0.107703 GGATCTGACCATGTTGCCGA 60.108 55.000 0.00 0.00 0.00 5.54
2086 2156 0.107508 AGGATCTGACCATGTTGCCG 60.108 55.000 0.00 0.00 0.00 5.69
2098 2168 0.798776 GCCACGTCAACAAGGATCTG 59.201 55.000 0.00 0.00 0.00 2.90
2105 2175 3.115556 GCAAGGCCACGTCAACAA 58.884 55.556 5.01 0.00 0.00 2.83
2139 2213 3.110178 GCTCGTGCCGGTACACAC 61.110 66.667 23.00 11.47 40.73 3.82
2148 2222 0.804989 AAAATGTAGCTGCTCGTGCC 59.195 50.000 4.91 0.00 38.71 5.01
2152 2226 2.483877 TCAACCAAAATGTAGCTGCTCG 59.516 45.455 4.91 0.00 0.00 5.03
2167 2241 7.874016 ACACTACAACGAACTAATAATCAACCA 59.126 33.333 0.00 0.00 0.00 3.67
2189 2268 1.496060 TGACAACCAGACCTGACACT 58.504 50.000 0.00 0.00 0.00 3.55
2190 2269 2.213499 CTTGACAACCAGACCTGACAC 58.787 52.381 0.00 0.00 0.00 3.67
2206 2285 1.543208 GGCACCTGTGTGATCACTTGA 60.543 52.381 25.55 9.24 45.76 3.02
2240 2319 3.031736 ACAGTAGTTACCGAGCCATCAT 58.968 45.455 0.00 0.00 0.00 2.45
2258 2337 3.686726 GGTTTCATTAGACCAGCAGACAG 59.313 47.826 0.00 0.00 35.95 3.51
2261 2340 2.301870 ACGGTTTCATTAGACCAGCAGA 59.698 45.455 0.00 0.00 35.63 4.26
2270 2349 6.237279 CGAATGCATTCAAACGGTTTCATTAG 60.237 38.462 32.72 11.65 36.61 1.73
2276 2355 3.243234 TGACGAATGCATTCAAACGGTTT 60.243 39.130 32.72 9.35 36.61 3.27
2277 2356 2.292016 TGACGAATGCATTCAAACGGTT 59.708 40.909 32.72 9.99 36.61 4.44
2279 2358 2.095768 ACTGACGAATGCATTCAAACGG 60.096 45.455 32.72 27.10 36.61 4.44
2287 2366 1.737029 CGGAGTCACTGACGAATGCAT 60.737 52.381 3.46 0.00 37.67 3.96
2289 2368 0.388649 ACGGAGTCACTGACGAATGC 60.389 55.000 5.56 0.00 29.74 3.56


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

AutoCloner maintained by Alex Coulton.