Multiple sequence alignment - TraesCS5D01G437000

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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 TraesCS5D01G437000 chr5D 100.000 4997 0 0 1 4997 491094643 491099639 0.000000e+00 9228.0
1 TraesCS5D01G437000 chr5B 92.801 4084 185 44 128 4169 605821506 605825522 0.000000e+00 5812.0
2 TraesCS5D01G437000 chr5B 91.429 595 28 6 4308 4899 605825768 605826342 0.000000e+00 795.0
3 TraesCS5D01G437000 chr5B 99.000 100 1 0 4898 4997 605826425 605826524 3.970000e-41 180.0
4 TraesCS5D01G437000 chr5A 93.131 3625 180 32 705 4273 613539745 613543356 0.000000e+00 5251.0
5 TraesCS5D01G437000 chr5A 94.302 702 33 5 4303 4997 613543355 613544056 0.000000e+00 1068.0
6 TraesCS5D01G437000 chr5A 82.822 489 39 17 128 595 613539188 613539652 3.630000e-106 396.0
7 TraesCS5D01G437000 chr6D 83.406 687 86 13 2781 3444 358395810 358396491 3.310000e-171 612.0
8 TraesCS5D01G437000 chr6D 88.811 143 15 1 2569 2710 358394763 358394905 1.850000e-39 174.0
9 TraesCS5D01G437000 chr6A 81.259 715 104 15 2754 3444 500270475 500271183 7.310000e-153 551.0
10 TraesCS5D01G437000 chr2B 76.216 1110 217 33 1071 2149 368339437 368338344 1.220000e-150 544.0
11 TraesCS5D01G437000 chr2D 75.612 1103 215 35 1071 2149 291955988 291954916 9.660000e-137 497.0
12 TraesCS5D01G437000 chr2A 75.458 1092 218 34 1077 2149 342546421 342545361 2.090000e-133 486.0
13 TraesCS5D01G437000 chr4A 100.000 28 0 0 1970 1997 532793172 532793199 9.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G437000 chr5D 491094643 491099639 4996 False 9228.000000 9228 100.0000 1 4997 1 chr5D.!!$F1 4996
1 TraesCS5D01G437000 chr5B 605821506 605826524 5018 False 2262.333333 5812 94.4100 128 4997 3 chr5B.!!$F1 4869
2 TraesCS5D01G437000 chr5A 613539188 613544056 4868 False 2238.333333 5251 90.0850 128 4997 3 chr5A.!!$F1 4869
3 TraesCS5D01G437000 chr6D 358394763 358396491 1728 False 393.000000 612 86.1085 2569 3444 2 chr6D.!!$F1 875
4 TraesCS5D01G437000 chr6A 500270475 500271183 708 False 551.000000 551 81.2590 2754 3444 1 chr6A.!!$F1 690
5 TraesCS5D01G437000 chr2B 368338344 368339437 1093 True 544.000000 544 76.2160 1071 2149 1 chr2B.!!$R1 1078
6 TraesCS5D01G437000 chr2D 291954916 291955988 1072 True 497.000000 497 75.6120 1071 2149 1 chr2D.!!$R1 1078
7 TraesCS5D01G437000 chr2A 342545361 342546421 1060 True 486.000000 486 75.4580 1077 2149 1 chr2A.!!$R1 1072

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
533 559 0.030638 TGTTTCTTTTCGCCAGCTGC 59.969 50.000 8.66 2.87 0.00 5.25 F
956 1012 0.579156 GGTTCTTGCTGATCGATCGC 59.421 55.000 25.28 25.28 0.00 4.58 F
2493 2577 0.324614 CCCTTTTGGCATTTGGGACC 59.675 55.000 12.15 0.00 40.23 4.46 F
2666 2751 1.062880 GTCGTCGATCTCTCCACTGAC 59.937 57.143 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1877 0.463620 CCAGCAGGTAGAAGGAGCTC 59.536 60.000 4.71 4.71 32.35 4.09 R
2897 3818 4.828939 TCATATTCAAAGCAATGCCCTAGG 59.171 41.667 0.00 0.06 0.00 3.02 R
3703 4657 0.109735 CACAGCAGCTGCATCACAAG 60.110 55.000 38.24 20.33 45.16 3.16 R
4060 5018 0.179137 TAACTCGGTCATCTGCAGCG 60.179 55.000 9.47 6.59 36.08 5.18 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.905637 AACCGGTGGAGACCAAAATC 58.094 50.000 8.52 0.00 43.33 2.17
20 21 1.064825 ACCGGTGGAGACCAAAATCT 58.935 50.000 6.12 0.00 43.33 2.40
21 22 1.271379 ACCGGTGGAGACCAAAATCTG 60.271 52.381 6.12 0.00 43.33 2.90
22 23 1.271379 CCGGTGGAGACCAAAATCTGT 60.271 52.381 0.00 0.00 43.33 3.41
23 24 2.027561 CCGGTGGAGACCAAAATCTGTA 60.028 50.000 0.00 0.00 43.33 2.74
24 25 3.370527 CCGGTGGAGACCAAAATCTGTAT 60.371 47.826 0.00 0.00 43.33 2.29
25 26 4.141801 CCGGTGGAGACCAAAATCTGTATA 60.142 45.833 0.00 0.00 43.33 1.47
26 27 5.424757 CGGTGGAGACCAAAATCTGTATAA 58.575 41.667 0.00 0.00 43.33 0.98
27 28 6.055588 CGGTGGAGACCAAAATCTGTATAAT 58.944 40.000 0.00 0.00 43.33 1.28
28 29 6.202954 CGGTGGAGACCAAAATCTGTATAATC 59.797 42.308 0.00 0.00 43.33 1.75
29 30 6.486993 GGTGGAGACCAAAATCTGTATAATCC 59.513 42.308 0.00 0.00 42.59 3.01
30 31 6.486993 GTGGAGACCAAAATCTGTATAATCCC 59.513 42.308 0.00 0.00 34.18 3.85
31 32 6.159575 TGGAGACCAAAATCTGTATAATCCCA 59.840 38.462 0.00 0.00 0.00 4.37
32 33 7.060421 GGAGACCAAAATCTGTATAATCCCAA 58.940 38.462 0.00 0.00 0.00 4.12
33 34 7.229506 GGAGACCAAAATCTGTATAATCCCAAG 59.770 40.741 0.00 0.00 0.00 3.61
34 35 7.872138 AGACCAAAATCTGTATAATCCCAAGA 58.128 34.615 0.00 0.00 0.00 3.02
35 36 8.336235 AGACCAAAATCTGTATAATCCCAAGAA 58.664 33.333 0.00 0.00 0.00 2.52
36 37 8.893563 ACCAAAATCTGTATAATCCCAAGAAA 57.106 30.769 0.00 0.00 0.00 2.52
37 38 8.971073 ACCAAAATCTGTATAATCCCAAGAAAG 58.029 33.333 0.00 0.00 0.00 2.62
38 39 7.922811 CCAAAATCTGTATAATCCCAAGAAAGC 59.077 37.037 0.00 0.00 0.00 3.51
39 40 8.469200 CAAAATCTGTATAATCCCAAGAAAGCA 58.531 33.333 0.00 0.00 0.00 3.91
40 41 8.593945 AAATCTGTATAATCCCAAGAAAGCAA 57.406 30.769 0.00 0.00 0.00 3.91
41 42 8.773033 AATCTGTATAATCCCAAGAAAGCAAT 57.227 30.769 0.00 0.00 0.00 3.56
42 43 7.572523 TCTGTATAATCCCAAGAAAGCAATG 57.427 36.000 0.00 0.00 0.00 2.82
43 44 7.345691 TCTGTATAATCCCAAGAAAGCAATGA 58.654 34.615 0.00 0.00 0.00 2.57
44 45 7.833682 TCTGTATAATCCCAAGAAAGCAATGAA 59.166 33.333 0.00 0.00 0.00 2.57
45 46 7.999679 TGTATAATCCCAAGAAAGCAATGAAG 58.000 34.615 0.00 0.00 0.00 3.02
46 47 4.813750 AATCCCAAGAAAGCAATGAAGG 57.186 40.909 0.00 0.00 0.00 3.46
47 48 3.524095 TCCCAAGAAAGCAATGAAGGA 57.476 42.857 0.00 0.00 0.00 3.36
48 49 4.051661 TCCCAAGAAAGCAATGAAGGAT 57.948 40.909 0.00 0.00 0.00 3.24
49 50 4.419282 TCCCAAGAAAGCAATGAAGGATT 58.581 39.130 0.00 0.00 0.00 3.01
50 51 5.579047 TCCCAAGAAAGCAATGAAGGATTA 58.421 37.500 0.00 0.00 0.00 1.75
51 52 6.197168 TCCCAAGAAAGCAATGAAGGATTAT 58.803 36.000 0.00 0.00 0.00 1.28
52 53 7.353525 TCCCAAGAAAGCAATGAAGGATTATA 58.646 34.615 0.00 0.00 0.00 0.98
53 54 7.285401 TCCCAAGAAAGCAATGAAGGATTATAC 59.715 37.037 0.00 0.00 0.00 1.47
54 55 7.286316 CCCAAGAAAGCAATGAAGGATTATACT 59.714 37.037 0.00 0.00 0.00 2.12
55 56 9.342308 CCAAGAAAGCAATGAAGGATTATACTA 57.658 33.333 0.00 0.00 0.00 1.82
57 58 9.905713 AAGAAAGCAATGAAGGATTATACTACA 57.094 29.630 0.00 0.00 0.00 2.74
58 59 9.553064 AGAAAGCAATGAAGGATTATACTACAG 57.447 33.333 0.00 0.00 0.00 2.74
59 60 9.331282 GAAAGCAATGAAGGATTATACTACAGT 57.669 33.333 0.00 0.00 0.00 3.55
61 62 9.988815 AAGCAATGAAGGATTATACTACAGTAG 57.011 33.333 6.00 6.00 33.52 2.57
62 63 8.091449 AGCAATGAAGGATTATACTACAGTAGC 58.909 37.037 7.57 0.00 33.52 3.58
63 64 8.091449 GCAATGAAGGATTATACTACAGTAGCT 58.909 37.037 7.57 0.00 33.52 3.32
64 65 9.416794 CAATGAAGGATTATACTACAGTAGCTG 57.583 37.037 7.57 0.00 37.52 4.24
65 66 7.526142 TGAAGGATTATACTACAGTAGCTGG 57.474 40.000 7.57 0.00 35.51 4.85
66 67 7.067421 TGAAGGATTATACTACAGTAGCTGGT 58.933 38.462 7.57 0.00 35.51 4.00
67 68 8.222637 TGAAGGATTATACTACAGTAGCTGGTA 58.777 37.037 7.57 0.00 35.51 3.25
68 69 7.999450 AGGATTATACTACAGTAGCTGGTAC 57.001 40.000 7.57 8.91 35.51 3.34
69 70 6.654161 AGGATTATACTACAGTAGCTGGTACG 59.346 42.308 7.57 8.80 36.66 3.67
70 71 6.128063 GGATTATACTACAGTAGCTGGTACGG 60.128 46.154 14.13 14.13 36.66 4.02
71 72 2.503895 ACTACAGTAGCTGGTACGGT 57.496 50.000 22.38 22.38 42.10 4.83
72 73 3.634397 ACTACAGTAGCTGGTACGGTA 57.366 47.619 22.25 22.25 40.19 4.02
73 74 4.162040 ACTACAGTAGCTGGTACGGTAT 57.838 45.455 23.31 14.27 40.28 2.73
74 75 5.296151 ACTACAGTAGCTGGTACGGTATA 57.704 43.478 23.31 10.26 40.28 1.47
75 76 5.874093 ACTACAGTAGCTGGTACGGTATAT 58.126 41.667 23.31 15.19 40.28 0.86
76 77 7.009179 ACTACAGTAGCTGGTACGGTATATA 57.991 40.000 23.31 9.41 40.28 0.86
77 78 7.453393 ACTACAGTAGCTGGTACGGTATATAA 58.547 38.462 23.31 9.12 40.28 0.98
78 79 7.939039 ACTACAGTAGCTGGTACGGTATATAAA 59.061 37.037 23.31 8.55 40.28 1.40
79 80 7.771927 ACAGTAGCTGGTACGGTATATAAAT 57.228 36.000 18.65 0.00 38.17 1.40
80 81 8.868522 ACAGTAGCTGGTACGGTATATAAATA 57.131 34.615 18.65 0.00 38.17 1.40
81 82 8.954350 ACAGTAGCTGGTACGGTATATAAATAG 58.046 37.037 18.65 0.00 38.17 1.73
82 83 9.170734 CAGTAGCTGGTACGGTATATAAATAGA 57.829 37.037 10.98 0.00 36.66 1.98
83 84 9.171877 AGTAGCTGGTACGGTATATAAATAGAC 57.828 37.037 10.98 0.00 36.66 2.59
84 85 8.950210 GTAGCTGGTACGGTATATAAATAGACA 58.050 37.037 0.00 0.00 36.83 3.41
85 86 8.053026 AGCTGGTACGGTATATAAATAGACAG 57.947 38.462 0.00 0.00 36.83 3.51
86 87 7.886970 AGCTGGTACGGTATATAAATAGACAGA 59.113 37.037 2.60 0.00 36.83 3.41
87 88 8.182881 GCTGGTACGGTATATAAATAGACAGAG 58.817 40.741 2.60 0.00 36.83 3.35
88 89 8.571461 TGGTACGGTATATAAATAGACAGAGG 57.429 38.462 2.60 0.00 0.00 3.69
89 90 8.385491 TGGTACGGTATATAAATAGACAGAGGA 58.615 37.037 2.60 0.00 0.00 3.71
90 91 9.236006 GGTACGGTATATAAATAGACAGAGGAA 57.764 37.037 2.60 0.00 0.00 3.36
93 94 9.233649 ACGGTATATAAATAGACAGAGGAAGAG 57.766 37.037 2.60 0.00 0.00 2.85
94 95 8.679100 CGGTATATAAATAGACAGAGGAAGAGG 58.321 40.741 0.00 0.00 0.00 3.69
95 96 8.973182 GGTATATAAATAGACAGAGGAAGAGGG 58.027 40.741 0.00 0.00 0.00 4.30
96 97 5.816955 ATAAATAGACAGAGGAAGAGGGC 57.183 43.478 0.00 0.00 0.00 5.19
97 98 1.698506 ATAGACAGAGGAAGAGGGCG 58.301 55.000 0.00 0.00 0.00 6.13
98 99 0.331954 TAGACAGAGGAAGAGGGCGT 59.668 55.000 0.00 0.00 0.00 5.68
99 100 0.968393 AGACAGAGGAAGAGGGCGTC 60.968 60.000 0.00 0.00 0.00 5.19
100 101 1.228894 ACAGAGGAAGAGGGCGTCA 60.229 57.895 10.15 0.00 0.00 4.35
101 102 1.254284 ACAGAGGAAGAGGGCGTCAG 61.254 60.000 10.15 0.00 0.00 3.51
102 103 0.967887 CAGAGGAAGAGGGCGTCAGA 60.968 60.000 10.15 0.00 0.00 3.27
103 104 0.682855 AGAGGAAGAGGGCGTCAGAG 60.683 60.000 10.15 0.00 0.00 3.35
104 105 0.681564 GAGGAAGAGGGCGTCAGAGA 60.682 60.000 10.15 0.00 0.00 3.10
105 106 0.682855 AGGAAGAGGGCGTCAGAGAG 60.683 60.000 10.15 0.00 0.00 3.20
106 107 0.968393 GGAAGAGGGCGTCAGAGAGT 60.968 60.000 10.15 0.00 0.00 3.24
107 108 1.682394 GGAAGAGGGCGTCAGAGAGTA 60.682 57.143 10.15 0.00 0.00 2.59
108 109 2.093106 GAAGAGGGCGTCAGAGAGTAA 58.907 52.381 10.15 0.00 0.00 2.24
109 110 2.217510 AGAGGGCGTCAGAGAGTAAA 57.782 50.000 10.15 0.00 0.00 2.01
110 111 2.096248 AGAGGGCGTCAGAGAGTAAAG 58.904 52.381 10.15 0.00 0.00 1.85
111 112 1.135333 GAGGGCGTCAGAGAGTAAAGG 59.865 57.143 1.64 0.00 0.00 3.11
112 113 1.183549 GGGCGTCAGAGAGTAAAGGA 58.816 55.000 0.00 0.00 0.00 3.36
113 114 1.135333 GGGCGTCAGAGAGTAAAGGAG 59.865 57.143 0.00 0.00 0.00 3.69
114 115 2.093106 GGCGTCAGAGAGTAAAGGAGA 58.907 52.381 0.00 0.00 0.00 3.71
115 116 2.098443 GGCGTCAGAGAGTAAAGGAGAG 59.902 54.545 0.00 0.00 0.00 3.20
116 117 2.478879 GCGTCAGAGAGTAAAGGAGAGC 60.479 54.545 0.00 0.00 0.00 4.09
117 118 2.223157 CGTCAGAGAGTAAAGGAGAGCG 60.223 54.545 0.00 0.00 0.00 5.03
118 119 1.746220 TCAGAGAGTAAAGGAGAGCGC 59.254 52.381 0.00 0.00 0.00 5.92
119 120 1.107945 AGAGAGTAAAGGAGAGCGCC 58.892 55.000 2.29 0.00 0.00 6.53
120 121 0.248702 GAGAGTAAAGGAGAGCGCCG 60.249 60.000 2.29 0.00 0.00 6.46
121 122 1.227002 GAGTAAAGGAGAGCGCCGG 60.227 63.158 2.29 0.00 0.00 6.13
122 123 1.664321 GAGTAAAGGAGAGCGCCGGA 61.664 60.000 5.05 0.00 0.00 5.14
123 124 1.518792 GTAAAGGAGAGCGCCGGAC 60.519 63.158 5.05 0.00 0.00 4.79
124 125 1.681327 TAAAGGAGAGCGCCGGACT 60.681 57.895 5.05 0.00 0.00 3.85
125 126 1.945354 TAAAGGAGAGCGCCGGACTG 61.945 60.000 5.05 0.00 0.00 3.51
126 127 4.742649 AGGAGAGCGCCGGACTGA 62.743 66.667 5.05 0.00 0.00 3.41
277 283 1.137872 CCATAGCTCACAGGACACTCC 59.862 57.143 0.00 0.00 36.58 3.85
291 298 0.397816 CACTCCCTCCCTCCACTAGG 60.398 65.000 0.00 0.00 46.09 3.02
311 318 3.349006 CCACAGTGCACCACGAGC 61.349 66.667 14.63 0.00 39.64 5.03
314 321 2.049526 CAGTGCACCACGAGCGTA 60.050 61.111 14.63 0.00 39.64 4.42
317 324 2.813474 TGCACCACGAGCGTATGC 60.813 61.111 18.81 18.81 38.86 3.14
319 326 2.173669 GCACCACGAGCGTATGCAT 61.174 57.895 20.01 3.79 46.23 3.96
321 328 2.173669 ACCACGAGCGTATGCATGC 61.174 57.895 11.82 11.82 46.23 4.06
322 329 2.173020 CCACGAGCGTATGCATGCA 61.173 57.895 25.04 25.04 46.23 3.96
324 331 0.383860 CACGAGCGTATGCATGCATG 60.384 55.000 37.43 24.94 46.23 4.06
325 332 0.811219 ACGAGCGTATGCATGCATGT 60.811 50.000 37.43 24.51 46.23 3.21
326 333 0.383860 CGAGCGTATGCATGCATGTG 60.384 55.000 37.43 29.31 46.23 3.21
350 357 2.987413 TGACAGCCAAAACGCAATAG 57.013 45.000 0.00 0.00 0.00 1.73
386 397 1.067295 TCCTGCCCATCACAACTTCT 58.933 50.000 0.00 0.00 0.00 2.85
403 414 0.914644 TCTCTTGGCCTCTTCCATGG 59.085 55.000 4.97 4.97 35.77 3.66
411 422 1.077644 CTCTTCCATGGCTGCTGCT 60.078 57.895 15.64 0.00 39.59 4.24
412 423 1.077930 TCTTCCATGGCTGCTGCTC 60.078 57.895 15.64 6.34 39.59 4.26
418 435 3.341202 ATGGCTGCTGCTCCTCCAC 62.341 63.158 15.64 0.00 39.59 4.02
420 437 2.362369 GGCTGCTGCTCCTCCACTA 61.362 63.158 15.64 0.00 39.59 2.74
423 440 0.901124 CTGCTGCTCCTCCACTAACT 59.099 55.000 0.00 0.00 0.00 2.24
424 441 2.103373 CTGCTGCTCCTCCACTAACTA 58.897 52.381 0.00 0.00 0.00 2.24
426 443 1.825474 GCTGCTCCTCCACTAACTACA 59.175 52.381 0.00 0.00 0.00 2.74
435 452 6.762333 TCCTCCACTAACTACAAGGTAAAAC 58.238 40.000 0.00 0.00 0.00 2.43
530 556 4.295051 TGTTTATGTTTCTTTTCGCCAGC 58.705 39.130 0.00 0.00 0.00 4.85
533 559 0.030638 TGTTTCTTTTCGCCAGCTGC 59.969 50.000 8.66 2.87 0.00 5.25
557 583 6.533367 GCTGAGCAAGTATATACTCTAATGCC 59.467 42.308 24.09 18.33 37.15 4.40
596 622 2.328819 CAGGCTTCTCTGCTAATGCT 57.671 50.000 0.00 0.00 40.48 3.79
598 624 0.662085 GGCTTCTCTGCTAATGCTGC 59.338 55.000 0.00 0.00 40.48 5.25
599 625 1.666054 GCTTCTCTGCTAATGCTGCT 58.334 50.000 0.00 0.00 40.48 4.24
600 626 1.331138 GCTTCTCTGCTAATGCTGCTG 59.669 52.381 0.00 0.00 40.48 4.41
603 629 1.445716 CTCTGCTAATGCTGCTGGGC 61.446 60.000 0.00 1.04 40.48 5.36
605 631 3.589881 GCTAATGCTGCTGGGCGG 61.590 66.667 0.00 0.00 38.08 6.13
606 632 2.903855 CTAATGCTGCTGGGCGGG 60.904 66.667 0.00 0.00 35.15 6.13
615 641 3.221389 CTGGGCGGGGATGCATTG 61.221 66.667 0.00 0.00 36.28 2.82
616 642 4.837797 TGGGCGGGGATGCATTGG 62.838 66.667 0.00 0.00 36.28 3.16
617 643 4.521292 GGGCGGGGATGCATTGGA 62.521 66.667 0.00 0.00 36.28 3.53
621 647 1.394266 GCGGGGATGCATTGGACATT 61.394 55.000 0.00 0.00 34.15 2.71
631 657 2.731572 CATTGGACATTGGAGGAAGCT 58.268 47.619 0.00 0.00 0.00 3.74
632 658 3.889815 CATTGGACATTGGAGGAAGCTA 58.110 45.455 0.00 0.00 0.00 3.32
651 677 5.942961 AGCTATAGTCTAGTCTAGTGCCAA 58.057 41.667 15.08 0.00 0.00 4.52
674 700 5.862845 ACATCTTTGTGACTTGTGAGAGAT 58.137 37.500 0.00 0.00 33.85 2.75
697 723 0.597568 TTTGGACGCCATTCTGCTTG 59.402 50.000 0.00 0.00 31.53 4.01
789 841 0.735471 GCGAGGCCTCTGAAATTTCC 59.265 55.000 29.73 0.55 0.00 3.13
922 974 4.982916 AGTACACATTCTTAATCCGATCGC 59.017 41.667 10.32 0.00 0.00 4.58
955 1011 0.848942 CGGTTCTTGCTGATCGATCG 59.151 55.000 20.03 9.36 0.00 3.69
956 1012 0.579156 GGTTCTTGCTGATCGATCGC 59.421 55.000 25.28 25.28 0.00 4.58
957 1013 1.565305 GTTCTTGCTGATCGATCGCT 58.435 50.000 28.97 0.00 0.00 4.93
958 1014 1.520590 GTTCTTGCTGATCGATCGCTC 59.479 52.381 28.97 11.54 0.00 5.03
1038 1097 3.259425 CTGCTTGCTGGCGTTGGTC 62.259 63.158 0.00 0.00 34.52 4.02
1042 1101 1.856265 CTTGCTGGCGTTGGTCTTCC 61.856 60.000 0.00 0.00 0.00 3.46
1251 1310 3.550431 CTCCACATCGCCGGGGAT 61.550 66.667 27.11 27.11 0.00 3.85
1788 1856 3.650369 CGGAACAAGTTCACCGGG 58.350 61.111 6.32 0.00 41.20 5.73
2176 2259 7.915397 GTCACAATGAAAAGAAGAAAGTTAGCA 59.085 33.333 0.00 0.00 0.00 3.49
2369 2452 2.009625 CTGTTCGCCGATGCACGTAC 62.010 60.000 0.00 0.00 40.78 3.67
2391 2474 5.836347 ACGATCGATCTCTGAATTTCATCA 58.164 37.500 24.34 0.00 0.00 3.07
2393 2476 6.585702 ACGATCGATCTCTGAATTTCATCATC 59.414 38.462 24.34 1.81 0.00 2.92
2493 2577 0.324614 CCCTTTTGGCATTTGGGACC 59.675 55.000 12.15 0.00 40.23 4.46
2666 2751 1.062880 GTCGTCGATCTCTCCACTGAC 59.937 57.143 0.00 0.00 0.00 3.51
2701 2841 2.887152 GTTCTGAGTTGGGCAAGTGATT 59.113 45.455 0.00 0.00 0.00 2.57
2741 2882 5.292834 CGACTTGTTCAGTTATGCTCATGAT 59.707 40.000 0.00 0.00 35.01 2.45
3097 4019 6.431198 TGTTTGAACTGTTCTTTACCAGAC 57.569 37.500 20.18 6.71 0.00 3.51
3148 4070 1.194781 AGAGGATATCGGCCGCCATT 61.195 55.000 23.51 7.65 0.00 3.16
3173 4095 2.115291 GCGAAGGGCATCCAGTTCC 61.115 63.158 0.00 0.00 42.87 3.62
3274 4198 4.787598 CCAAAATCGGCAGCTACAATATC 58.212 43.478 0.00 0.00 0.00 1.63
3328 4252 7.360361 AGGTAATTCAGCGAAAAACTAACTTG 58.640 34.615 0.00 0.00 0.00 3.16
3329 4253 7.227910 AGGTAATTCAGCGAAAAACTAACTTGA 59.772 33.333 0.00 0.00 0.00 3.02
3331 4255 6.619801 ATTCAGCGAAAAACTAACTTGAGT 57.380 33.333 0.00 0.00 0.00 3.41
3334 4258 5.583061 TCAGCGAAAAACTAACTTGAGTGAA 59.417 36.000 0.00 0.00 0.00 3.18
3426 4376 4.444306 GCAGGCACCAAACTGATAGGTATA 60.444 45.833 0.00 0.00 36.86 1.47
3437 4387 9.193133 CAAACTGATAGGTATATACAAGGTTCG 57.807 37.037 14.70 0.55 0.00 3.95
3453 4403 2.605366 GGTTCGAGCTTCAGATGCTTAC 59.395 50.000 11.93 10.23 41.30 2.34
3468 4422 1.859080 GCTTACCATCTAGCGGTTTCG 59.141 52.381 8.75 1.03 37.99 3.46
3487 4441 3.450578 TCGACCGGCACAACTAATATTC 58.549 45.455 0.00 0.00 0.00 1.75
3521 4475 5.129634 TCCTTGTTCTGCAATGTCACTTTA 58.870 37.500 0.00 0.00 36.36 1.85
3612 4566 4.631813 GGAAAGCCGATCACATCCATATAC 59.368 45.833 0.00 0.00 0.00 1.47
3660 4614 5.106237 GGTATGTATGATCGGTCACCTAGTC 60.106 48.000 0.00 0.00 37.14 2.59
3703 4657 3.311871 CAGCACAGATACCTGAATCTTGC 59.688 47.826 0.00 0.00 43.02 4.01
3709 4663 5.181009 CAGATACCTGAATCTTGCTTGTGA 58.819 41.667 0.00 0.00 43.02 3.58
3771 4725 1.985116 GAGGAGCTTCGTGGACCCT 60.985 63.158 0.00 0.00 0.00 4.34
4002 4956 4.022503 TCCAGATTCAGCAGATAGACGATG 60.023 45.833 0.00 0.00 0.00 3.84
4027 4984 0.591659 GCTGTTTCTCCCGTCCAAAC 59.408 55.000 0.00 0.00 0.00 2.93
4028 4985 1.235724 CTGTTTCTCCCGTCCAAACC 58.764 55.000 0.00 0.00 30.32 3.27
4029 4986 0.533308 TGTTTCTCCCGTCCAAACCG 60.533 55.000 0.00 0.00 30.32 4.44
4030 4987 0.533531 GTTTCTCCCGTCCAAACCGT 60.534 55.000 0.00 0.00 0.00 4.83
4031 4988 0.533308 TTTCTCCCGTCCAAACCGTG 60.533 55.000 0.00 0.00 0.00 4.94
4060 5018 1.144503 AGGAGGATGGATGAACATGCC 59.855 52.381 4.06 1.34 39.68 4.40
4102 5074 0.343372 TCCAGGGAGGCTCCAACTAT 59.657 55.000 33.27 11.75 38.64 2.12
4105 5077 2.370189 CCAGGGAGGCTCCAACTATTAG 59.630 54.545 33.27 13.38 38.64 1.73
4171 5178 4.508405 CCAATCCCCCTGTTGTTTCTCTAA 60.508 45.833 0.00 0.00 0.00 2.10
4174 5181 3.326880 TCCCCCTGTTGTTTCTCTAACTC 59.673 47.826 0.00 0.00 37.64 3.01
4189 5196 5.481824 TCTCTAACTCAAGCCTTCATCTCAA 59.518 40.000 0.00 0.00 0.00 3.02
4196 5203 3.648507 AGCCTTCATCTCAAGAGCAAT 57.351 42.857 0.00 0.00 0.00 3.56
4198 5205 4.342359 AGCCTTCATCTCAAGAGCAATTT 58.658 39.130 0.00 0.00 0.00 1.82
4206 5213 9.685276 TTCATCTCAAGAGCAATTTTTCCTATA 57.315 29.630 0.00 0.00 0.00 1.31
4278 5285 3.806949 TCCTGTTTCTACCAATGCCTT 57.193 42.857 0.00 0.00 0.00 4.35
4287 5294 7.094377 TGTTTCTACCAATGCCTTGAGAATTAC 60.094 37.037 2.97 3.14 34.04 1.89
4289 5296 2.423538 ACCAATGCCTTGAGAATTACGC 59.576 45.455 2.97 0.00 34.04 4.42
4291 5298 1.299541 ATGCCTTGAGAATTACGCCG 58.700 50.000 0.00 0.00 0.00 6.46
4327 5430 4.517285 ACAGCACAAATACCATCTGTAGG 58.483 43.478 0.00 0.00 33.56 3.18
4329 5432 5.185454 CAGCACAAATACCATCTGTAGGAA 58.815 41.667 0.00 0.00 31.61 3.36
4354 5458 1.594331 AGGGTTCAAAGACTCGCAAC 58.406 50.000 0.00 0.00 0.00 4.17
4360 5464 0.662619 CAAAGACTCGCAACCAGCAA 59.337 50.000 0.00 0.00 46.13 3.91
4495 5602 4.694982 GCCATGGGGTTTTCAATGTTTTAG 59.305 41.667 15.13 0.00 36.17 1.85
4501 5608 4.446385 GGGTTTTCAATGTTTTAGTTCGGC 59.554 41.667 0.00 0.00 0.00 5.54
4564 5671 1.683943 GCTTATTGCAGGATCTGGCA 58.316 50.000 7.59 7.59 42.31 4.92
4793 5900 2.338500 CCAGGTCACTACTTTCGAAGC 58.662 52.381 0.00 0.00 0.00 3.86
4798 5905 2.800544 GTCACTACTTTCGAAGCAAGCA 59.199 45.455 0.00 0.00 0.00 3.91
4887 5994 5.300969 TGATCAAACTTTAGCATGCTGTC 57.699 39.130 30.42 12.96 0.00 3.51
4888 5995 4.761227 TGATCAAACTTTAGCATGCTGTCA 59.239 37.500 30.42 7.62 0.00 3.58
4890 5997 4.136796 TCAAACTTTAGCATGCTGTCACT 58.863 39.130 30.42 8.96 0.00 3.41
4891 5998 4.023792 TCAAACTTTAGCATGCTGTCACTG 60.024 41.667 30.42 18.32 0.00 3.66
4892 5999 2.430465 ACTTTAGCATGCTGTCACTGG 58.570 47.619 30.42 14.16 0.00 4.00
4893 6000 2.224621 ACTTTAGCATGCTGTCACTGGT 60.225 45.455 30.42 14.75 0.00 4.00
4894 6001 3.007940 ACTTTAGCATGCTGTCACTGGTA 59.992 43.478 30.42 3.38 0.00 3.25
4895 6002 3.694043 TTAGCATGCTGTCACTGGTAA 57.306 42.857 30.42 10.07 32.26 2.85
4896 6003 1.813513 AGCATGCTGTCACTGGTAAC 58.186 50.000 21.98 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.486993 GGATTATACAGATTTTGGTCTCCACC 59.513 42.308 0.00 0.00 44.10 4.61
5 6 6.486993 GGGATTATACAGATTTTGGTCTCCAC 59.513 42.308 0.00 0.00 30.78 4.02
6 7 6.159575 TGGGATTATACAGATTTTGGTCTCCA 59.840 38.462 0.00 0.00 0.00 3.86
7 8 6.601332 TGGGATTATACAGATTTTGGTCTCC 58.399 40.000 0.00 0.00 0.00 3.71
8 9 7.993183 TCTTGGGATTATACAGATTTTGGTCTC 59.007 37.037 0.00 0.00 0.00 3.36
9 10 7.872138 TCTTGGGATTATACAGATTTTGGTCT 58.128 34.615 0.00 0.00 0.00 3.85
10 11 8.519799 TTCTTGGGATTATACAGATTTTGGTC 57.480 34.615 0.00 0.00 0.00 4.02
11 12 8.893563 TTTCTTGGGATTATACAGATTTTGGT 57.106 30.769 0.00 0.00 0.00 3.67
12 13 7.922811 GCTTTCTTGGGATTATACAGATTTTGG 59.077 37.037 0.00 0.00 0.00 3.28
13 14 8.469200 TGCTTTCTTGGGATTATACAGATTTTG 58.531 33.333 0.00 0.00 0.00 2.44
14 15 8.593945 TGCTTTCTTGGGATTATACAGATTTT 57.406 30.769 0.00 0.00 0.00 1.82
15 16 8.593945 TTGCTTTCTTGGGATTATACAGATTT 57.406 30.769 0.00 0.00 0.00 2.17
16 17 8.636213 CATTGCTTTCTTGGGATTATACAGATT 58.364 33.333 0.00 0.00 0.00 2.40
17 18 8.000709 TCATTGCTTTCTTGGGATTATACAGAT 58.999 33.333 0.00 0.00 0.00 2.90
18 19 7.345691 TCATTGCTTTCTTGGGATTATACAGA 58.654 34.615 0.00 0.00 0.00 3.41
19 20 7.572523 TCATTGCTTTCTTGGGATTATACAG 57.427 36.000 0.00 0.00 0.00 2.74
20 21 7.068593 CCTTCATTGCTTTCTTGGGATTATACA 59.931 37.037 0.00 0.00 0.00 2.29
21 22 7.285401 TCCTTCATTGCTTTCTTGGGATTATAC 59.715 37.037 0.00 0.00 0.00 1.47
22 23 7.353525 TCCTTCATTGCTTTCTTGGGATTATA 58.646 34.615 0.00 0.00 0.00 0.98
23 24 6.197168 TCCTTCATTGCTTTCTTGGGATTAT 58.803 36.000 0.00 0.00 0.00 1.28
24 25 5.579047 TCCTTCATTGCTTTCTTGGGATTA 58.421 37.500 0.00 0.00 0.00 1.75
25 26 4.419282 TCCTTCATTGCTTTCTTGGGATT 58.581 39.130 0.00 0.00 0.00 3.01
26 27 4.051661 TCCTTCATTGCTTTCTTGGGAT 57.948 40.909 0.00 0.00 0.00 3.85
27 28 3.524095 TCCTTCATTGCTTTCTTGGGA 57.476 42.857 0.00 0.00 0.00 4.37
28 29 4.813750 AATCCTTCATTGCTTTCTTGGG 57.186 40.909 0.00 0.00 0.00 4.12
29 30 8.230472 AGTATAATCCTTCATTGCTTTCTTGG 57.770 34.615 0.00 0.00 0.00 3.61
31 32 9.905713 TGTAGTATAATCCTTCATTGCTTTCTT 57.094 29.630 0.00 0.00 0.00 2.52
32 33 9.553064 CTGTAGTATAATCCTTCATTGCTTTCT 57.447 33.333 0.00 0.00 0.00 2.52
33 34 9.331282 ACTGTAGTATAATCCTTCATTGCTTTC 57.669 33.333 0.00 0.00 0.00 2.62
35 36 9.988815 CTACTGTAGTATAATCCTTCATTGCTT 57.011 33.333 6.67 0.00 0.00 3.91
36 37 8.091449 GCTACTGTAGTATAATCCTTCATTGCT 58.909 37.037 15.71 0.00 0.00 3.91
37 38 8.091449 AGCTACTGTAGTATAATCCTTCATTGC 58.909 37.037 15.71 0.00 0.00 3.56
38 39 9.416794 CAGCTACTGTAGTATAATCCTTCATTG 57.583 37.037 15.71 0.00 0.00 2.82
39 40 8.589338 CCAGCTACTGTAGTATAATCCTTCATT 58.411 37.037 15.71 0.00 0.00 2.57
40 41 7.730784 ACCAGCTACTGTAGTATAATCCTTCAT 59.269 37.037 15.71 0.00 0.00 2.57
41 42 7.067421 ACCAGCTACTGTAGTATAATCCTTCA 58.933 38.462 15.71 0.00 0.00 3.02
42 43 7.527568 ACCAGCTACTGTAGTATAATCCTTC 57.472 40.000 15.71 0.00 0.00 3.46
43 44 7.174599 CGTACCAGCTACTGTAGTATAATCCTT 59.825 40.741 15.71 0.00 0.00 3.36
44 45 6.654161 CGTACCAGCTACTGTAGTATAATCCT 59.346 42.308 15.71 0.54 0.00 3.24
45 46 6.128063 CCGTACCAGCTACTGTAGTATAATCC 60.128 46.154 15.71 0.00 0.00 3.01
46 47 6.429385 ACCGTACCAGCTACTGTAGTATAATC 59.571 42.308 15.71 0.00 0.00 1.75
47 48 6.302269 ACCGTACCAGCTACTGTAGTATAAT 58.698 40.000 15.71 2.25 0.00 1.28
48 49 5.684704 ACCGTACCAGCTACTGTAGTATAA 58.315 41.667 15.71 0.00 0.00 0.98
49 50 5.296151 ACCGTACCAGCTACTGTAGTATA 57.704 43.478 15.71 2.02 0.00 1.47
50 51 4.162040 ACCGTACCAGCTACTGTAGTAT 57.838 45.455 15.71 3.16 0.00 2.12
51 52 3.634397 ACCGTACCAGCTACTGTAGTA 57.366 47.619 15.71 0.00 0.00 1.82
52 53 2.503895 ACCGTACCAGCTACTGTAGT 57.496 50.000 15.71 0.15 0.00 2.73
53 54 7.912056 TTATATACCGTACCAGCTACTGTAG 57.088 40.000 10.48 10.48 30.97 2.74
54 55 8.868522 ATTTATATACCGTACCAGCTACTGTA 57.131 34.615 0.00 0.00 31.73 2.74
55 56 7.771927 ATTTATATACCGTACCAGCTACTGT 57.228 36.000 0.00 0.00 0.00 3.55
56 57 9.170734 TCTATTTATATACCGTACCAGCTACTG 57.829 37.037 0.00 0.00 0.00 2.74
57 58 9.171877 GTCTATTTATATACCGTACCAGCTACT 57.828 37.037 0.00 0.00 0.00 2.57
58 59 8.950210 TGTCTATTTATATACCGTACCAGCTAC 58.050 37.037 0.00 0.00 0.00 3.58
59 60 9.170734 CTGTCTATTTATATACCGTACCAGCTA 57.829 37.037 0.00 0.00 0.00 3.32
60 61 7.886970 TCTGTCTATTTATATACCGTACCAGCT 59.113 37.037 0.00 0.00 0.00 4.24
61 62 8.048534 TCTGTCTATTTATATACCGTACCAGC 57.951 38.462 0.00 0.00 0.00 4.85
62 63 8.675504 CCTCTGTCTATTTATATACCGTACCAG 58.324 40.741 0.00 0.00 0.00 4.00
63 64 8.385491 TCCTCTGTCTATTTATATACCGTACCA 58.615 37.037 0.00 0.00 0.00 3.25
64 65 8.798859 TCCTCTGTCTATTTATATACCGTACC 57.201 38.462 0.00 0.00 0.00 3.34
67 68 9.233649 CTCTTCCTCTGTCTATTTATATACCGT 57.766 37.037 0.00 0.00 0.00 4.83
68 69 8.679100 CCTCTTCCTCTGTCTATTTATATACCG 58.321 40.741 0.00 0.00 0.00 4.02
69 70 8.973182 CCCTCTTCCTCTGTCTATTTATATACC 58.027 40.741 0.00 0.00 0.00 2.73
70 71 8.471609 GCCCTCTTCCTCTGTCTATTTATATAC 58.528 40.741 0.00 0.00 0.00 1.47
71 72 7.339721 CGCCCTCTTCCTCTGTCTATTTATATA 59.660 40.741 0.00 0.00 0.00 0.86
72 73 6.153680 CGCCCTCTTCCTCTGTCTATTTATAT 59.846 42.308 0.00 0.00 0.00 0.86
73 74 5.477291 CGCCCTCTTCCTCTGTCTATTTATA 59.523 44.000 0.00 0.00 0.00 0.98
74 75 4.282195 CGCCCTCTTCCTCTGTCTATTTAT 59.718 45.833 0.00 0.00 0.00 1.40
75 76 3.637229 CGCCCTCTTCCTCTGTCTATTTA 59.363 47.826 0.00 0.00 0.00 1.40
76 77 2.432510 CGCCCTCTTCCTCTGTCTATTT 59.567 50.000 0.00 0.00 0.00 1.40
77 78 2.035632 CGCCCTCTTCCTCTGTCTATT 58.964 52.381 0.00 0.00 0.00 1.73
78 79 1.063567 ACGCCCTCTTCCTCTGTCTAT 60.064 52.381 0.00 0.00 0.00 1.98
79 80 0.331954 ACGCCCTCTTCCTCTGTCTA 59.668 55.000 0.00 0.00 0.00 2.59
80 81 0.968393 GACGCCCTCTTCCTCTGTCT 60.968 60.000 0.00 0.00 0.00 3.41
81 82 1.251527 TGACGCCCTCTTCCTCTGTC 61.252 60.000 0.00 0.00 0.00 3.51
82 83 1.228894 TGACGCCCTCTTCCTCTGT 60.229 57.895 0.00 0.00 0.00 3.41
83 84 0.967887 TCTGACGCCCTCTTCCTCTG 60.968 60.000 0.00 0.00 0.00 3.35
84 85 0.682855 CTCTGACGCCCTCTTCCTCT 60.683 60.000 0.00 0.00 0.00 3.69
85 86 0.681564 TCTCTGACGCCCTCTTCCTC 60.682 60.000 0.00 0.00 0.00 3.71
86 87 0.682855 CTCTCTGACGCCCTCTTCCT 60.683 60.000 0.00 0.00 0.00 3.36
87 88 0.968393 ACTCTCTGACGCCCTCTTCC 60.968 60.000 0.00 0.00 0.00 3.46
88 89 1.752683 TACTCTCTGACGCCCTCTTC 58.247 55.000 0.00 0.00 0.00 2.87
89 90 2.217510 TTACTCTCTGACGCCCTCTT 57.782 50.000 0.00 0.00 0.00 2.85
90 91 2.096248 CTTTACTCTCTGACGCCCTCT 58.904 52.381 0.00 0.00 0.00 3.69
91 92 1.135333 CCTTTACTCTCTGACGCCCTC 59.865 57.143 0.00 0.00 0.00 4.30
92 93 1.187087 CCTTTACTCTCTGACGCCCT 58.813 55.000 0.00 0.00 0.00 5.19
93 94 1.135333 CTCCTTTACTCTCTGACGCCC 59.865 57.143 0.00 0.00 0.00 6.13
94 95 2.093106 TCTCCTTTACTCTCTGACGCC 58.907 52.381 0.00 0.00 0.00 5.68
95 96 2.478879 GCTCTCCTTTACTCTCTGACGC 60.479 54.545 0.00 0.00 0.00 5.19
96 97 2.223157 CGCTCTCCTTTACTCTCTGACG 60.223 54.545 0.00 0.00 0.00 4.35
97 98 2.478879 GCGCTCTCCTTTACTCTCTGAC 60.479 54.545 0.00 0.00 0.00 3.51
98 99 1.746220 GCGCTCTCCTTTACTCTCTGA 59.254 52.381 0.00 0.00 0.00 3.27
99 100 1.202359 GGCGCTCTCCTTTACTCTCTG 60.202 57.143 7.64 0.00 0.00 3.35
100 101 1.107945 GGCGCTCTCCTTTACTCTCT 58.892 55.000 7.64 0.00 0.00 3.10
101 102 0.248702 CGGCGCTCTCCTTTACTCTC 60.249 60.000 7.64 0.00 0.00 3.20
102 103 1.668101 CCGGCGCTCTCCTTTACTCT 61.668 60.000 7.64 0.00 0.00 3.24
103 104 1.227002 CCGGCGCTCTCCTTTACTC 60.227 63.158 7.64 0.00 0.00 2.59
104 105 1.681327 TCCGGCGCTCTCCTTTACT 60.681 57.895 7.64 0.00 0.00 2.24
105 106 1.518792 GTCCGGCGCTCTCCTTTAC 60.519 63.158 7.64 0.00 0.00 2.01
106 107 1.681327 AGTCCGGCGCTCTCCTTTA 60.681 57.895 7.64 0.00 0.00 1.85
107 108 2.997897 AGTCCGGCGCTCTCCTTT 60.998 61.111 7.64 0.00 0.00 3.11
108 109 3.764466 CAGTCCGGCGCTCTCCTT 61.764 66.667 7.64 0.00 0.00 3.36
109 110 4.742649 TCAGTCCGGCGCTCTCCT 62.743 66.667 7.64 0.00 0.00 3.69
110 111 3.532155 ATCAGTCCGGCGCTCTCC 61.532 66.667 7.64 0.00 0.00 3.71
111 112 2.279120 CATCAGTCCGGCGCTCTC 60.279 66.667 7.64 0.00 0.00 3.20
112 113 4.521062 GCATCAGTCCGGCGCTCT 62.521 66.667 7.64 0.00 0.00 4.09
134 135 2.438075 CTGAGCTGGAAGGCTGGC 60.438 66.667 0.00 0.00 43.20 4.85
311 318 3.248125 TCATACACACATGCATGCATACG 59.752 43.478 31.73 25.65 34.91 3.06
314 321 3.018149 TGTCATACACACATGCATGCAT 58.982 40.909 27.46 27.46 37.08 3.96
317 324 2.223409 GGCTGTCATACACACATGCATG 60.223 50.000 25.09 25.09 31.62 4.06
319 326 1.271271 TGGCTGTCATACACACATGCA 60.271 47.619 0.00 0.00 0.00 3.96
321 328 4.229096 GTTTTGGCTGTCATACACACATG 58.771 43.478 0.00 0.00 0.00 3.21
322 329 3.058293 CGTTTTGGCTGTCATACACACAT 60.058 43.478 0.00 0.00 0.00 3.21
324 331 2.916111 CGTTTTGGCTGTCATACACAC 58.084 47.619 0.00 0.00 0.00 3.82
325 332 1.265635 GCGTTTTGGCTGTCATACACA 59.734 47.619 0.00 0.00 0.00 3.72
326 333 1.265635 TGCGTTTTGGCTGTCATACAC 59.734 47.619 0.00 0.00 0.00 2.90
350 357 1.205893 AGGACGATGAGCTCTGTTTCC 59.794 52.381 16.19 14.81 0.00 3.13
386 397 1.304282 GCCATGGAAGAGGCCAAGA 59.696 57.895 18.40 0.00 45.18 3.02
403 414 0.742635 GTTAGTGGAGGAGCAGCAGC 60.743 60.000 0.00 0.00 42.56 5.25
411 422 6.556116 AGTTTTACCTTGTAGTTAGTGGAGGA 59.444 38.462 0.00 0.00 0.00 3.71
412 423 6.766429 AGTTTTACCTTGTAGTTAGTGGAGG 58.234 40.000 0.00 0.00 0.00 4.30
435 452 9.933723 AGGAAACCATTCAGAAAATAAAATGAG 57.066 29.630 0.00 0.00 37.29 2.90
442 459 7.523709 GCTTGACAGGAAACCATTCAGAAAATA 60.524 37.037 0.00 0.00 37.29 1.40
444 461 5.451798 GCTTGACAGGAAACCATTCAGAAAA 60.452 40.000 0.00 0.00 37.29 2.29
530 556 7.275341 GCATTAGAGTATATACTTGCTCAGCAG 59.725 40.741 21.94 0.00 40.61 4.24
533 559 6.749578 CGGCATTAGAGTATATACTTGCTCAG 59.250 42.308 25.52 17.56 36.85 3.35
598 624 3.221389 CAATGCATCCCCGCCCAG 61.221 66.667 0.00 0.00 0.00 4.45
599 625 4.837797 CCAATGCATCCCCGCCCA 62.838 66.667 0.00 0.00 0.00 5.36
600 626 4.521292 TCCAATGCATCCCCGCCC 62.521 66.667 0.00 0.00 0.00 6.13
603 629 0.386476 CAATGTCCAATGCATCCCCG 59.614 55.000 0.00 0.00 0.00 5.73
605 631 1.684983 CTCCAATGTCCAATGCATCCC 59.315 52.381 0.00 0.00 0.00 3.85
606 632 1.684983 CCTCCAATGTCCAATGCATCC 59.315 52.381 0.00 0.00 0.00 3.51
608 634 2.832643 TCCTCCAATGTCCAATGCAT 57.167 45.000 0.00 0.00 0.00 3.96
609 635 2.449464 CTTCCTCCAATGTCCAATGCA 58.551 47.619 0.00 0.00 0.00 3.96
610 636 1.135721 GCTTCCTCCAATGTCCAATGC 59.864 52.381 0.00 0.00 0.00 3.56
611 637 2.731572 AGCTTCCTCCAATGTCCAATG 58.268 47.619 0.00 0.00 0.00 2.82
612 638 4.803329 ATAGCTTCCTCCAATGTCCAAT 57.197 40.909 0.00 0.00 0.00 3.16
613 639 4.721776 ACTATAGCTTCCTCCAATGTCCAA 59.278 41.667 0.00 0.00 0.00 3.53
614 640 4.298626 ACTATAGCTTCCTCCAATGTCCA 58.701 43.478 0.00 0.00 0.00 4.02
615 641 4.591072 AGACTATAGCTTCCTCCAATGTCC 59.409 45.833 0.00 0.00 0.00 4.02
616 642 5.799827 AGACTATAGCTTCCTCCAATGTC 57.200 43.478 0.00 0.00 0.00 3.06
617 643 6.377912 ACTAGACTATAGCTTCCTCCAATGT 58.622 40.000 0.00 0.00 0.00 2.71
621 647 5.915744 AGACTAGACTATAGCTTCCTCCA 57.084 43.478 0.00 0.00 0.00 3.86
631 657 7.519057 AGATGTTGGCACTAGACTAGACTATA 58.481 38.462 16.55 2.65 0.00 1.31
632 658 6.369629 AGATGTTGGCACTAGACTAGACTAT 58.630 40.000 16.55 1.24 0.00 2.12
651 677 5.282055 TCTCTCACAAGTCACAAAGATGT 57.718 39.130 0.00 0.00 41.61 3.06
674 700 3.088532 AGCAGAATGGCGTCCAAATTAA 58.911 40.909 2.68 0.00 36.95 1.40
697 723 2.159254 ACCAGACAACAACAATGTGCAC 60.159 45.455 10.75 10.75 40.46 4.57
789 841 0.183971 TTGTGGGTTGTGGGTACAGG 59.816 55.000 0.00 0.00 38.23 4.00
838 890 2.008329 GTGATCGAGGACTGTACGTCT 58.992 52.381 14.50 4.55 42.44 4.18
839 891 1.063764 GGTGATCGAGGACTGTACGTC 59.936 57.143 0.00 8.69 42.07 4.34
916 968 1.060937 CGGAGCAAAAAGGCGATCG 59.939 57.895 11.69 11.69 39.27 3.69
956 1012 3.610791 TTCGGCGTCACTGCTCGAG 62.611 63.158 8.45 8.45 38.26 4.04
957 1013 3.610791 CTTCGGCGTCACTGCTCGA 62.611 63.158 6.85 0.00 36.34 4.04
958 1014 3.175240 CTTCGGCGTCACTGCTCG 61.175 66.667 6.85 0.00 34.52 5.03
1038 1097 4.711949 AGCAGCACCGCCAGGAAG 62.712 66.667 0.00 0.00 41.02 3.46
1809 1877 0.463620 CCAGCAGGTAGAAGGAGCTC 59.536 60.000 4.71 4.71 32.35 4.09
2369 2452 6.807720 AGATGATGAAATTCAGAGATCGATCG 59.192 38.462 19.33 9.36 0.00 3.69
2391 2474 9.868277 CTCTTAGACTAATTTCACAAGTCAGAT 57.132 33.333 7.80 0.00 41.69 2.90
2393 2476 9.134734 GTCTCTTAGACTAATTTCACAAGTCAG 57.865 37.037 7.80 0.00 41.88 3.51
2666 2751 6.238320 CCAACTCAGAACAGACTGAAGAAAAG 60.238 42.308 10.08 2.15 44.62 2.27
2701 2841 5.127491 ACAAGTCGTGGTAAAATTTCAGGA 58.873 37.500 0.00 0.00 0.00 3.86
2897 3818 4.828939 TCATATTCAAAGCAATGCCCTAGG 59.171 41.667 0.00 0.06 0.00 3.02
2906 3827 5.348164 TCGTCGAGATCATATTCAAAGCAA 58.652 37.500 0.00 0.00 0.00 3.91
3051 3972 7.092716 ACAAGAAACATAACATTCAGCCATTC 58.907 34.615 0.00 0.00 0.00 2.67
3148 4070 3.950794 GATGCCCTTCGCGACACCA 62.951 63.158 9.15 4.14 42.08 4.17
3173 4095 1.983691 AGGTATGATCCCTCCATGCAG 59.016 52.381 0.00 0.00 0.00 4.41
3274 4198 1.055040 CAGCCTCTCCTAGGATTGGG 58.945 60.000 23.64 19.97 43.19 4.12
3328 4252 6.969473 GCAATAGCCATAGAAAAACTTCACTC 59.031 38.462 0.00 0.00 33.58 3.51
3329 4253 6.660949 AGCAATAGCCATAGAAAAACTTCACT 59.339 34.615 0.00 0.00 43.56 3.41
3331 4255 6.658816 TCAGCAATAGCCATAGAAAAACTTCA 59.341 34.615 0.00 0.00 43.56 3.02
3334 4258 5.358160 GGTCAGCAATAGCCATAGAAAAACT 59.642 40.000 0.00 0.00 43.56 2.66
3336 4260 5.260424 TGGTCAGCAATAGCCATAGAAAAA 58.740 37.500 0.00 0.00 43.56 1.94
3337 4261 4.854173 TGGTCAGCAATAGCCATAGAAAA 58.146 39.130 0.00 0.00 43.56 2.29
3341 4289 3.544684 TGTTGGTCAGCAATAGCCATAG 58.455 45.455 0.00 0.00 43.56 2.23
3426 4376 4.437239 CATCTGAAGCTCGAACCTTGTAT 58.563 43.478 3.00 0.00 0.00 2.29
3437 4387 4.070630 AGATGGTAAGCATCTGAAGCTC 57.929 45.455 7.95 0.00 42.53 4.09
3453 4403 2.973420 GGTCGAAACCGCTAGATGG 58.027 57.895 0.00 0.00 35.36 3.51
3462 4416 0.600782 TAGTTGTGCCGGTCGAAACC 60.601 55.000 1.90 0.00 42.66 3.27
3468 4422 4.694339 AGAGAATATTAGTTGTGCCGGTC 58.306 43.478 1.90 0.00 0.00 4.79
3487 4441 4.758674 TGCAGAACAAGGAAAGATGAAGAG 59.241 41.667 0.00 0.00 0.00 2.85
3549 4503 6.237901 CAGGATCACCCCGAAATCAAATATA 58.762 40.000 0.00 0.00 36.73 0.86
3612 4566 4.100189 AGTTCCTTCATTATCTCCACCTCG 59.900 45.833 0.00 0.00 0.00 4.63
3660 4614 1.917955 CGTTGTGCACTACCATCTACG 59.082 52.381 22.80 12.72 0.00 3.51
3683 4637 3.539604 AGCAAGATTCAGGTATCTGTGC 58.460 45.455 2.20 5.17 41.59 4.57
3703 4657 0.109735 CACAGCAGCTGCATCACAAG 60.110 55.000 38.24 20.33 45.16 3.16
4002 4956 0.250338 ACGGGAGAAACAGCTGGTTC 60.250 55.000 32.84 32.84 41.89 3.62
4027 4984 4.463879 CTCCTGGGAGCTGCACGG 62.464 72.222 7.79 6.63 35.31 4.94
4028 4985 4.463879 CCTCCTGGGAGCTGCACG 62.464 72.222 7.79 0.00 40.69 5.34
4029 4986 3.005539 TCCTCCTGGGAGCTGCAC 61.006 66.667 7.79 0.00 39.58 4.57
4060 5018 0.179137 TAACTCGGTCATCTGCAGCG 60.179 55.000 9.47 6.59 36.08 5.18
4072 5030 1.333177 CTCCCTGGAGGATAACTCGG 58.667 60.000 5.22 0.00 46.33 4.63
4102 5074 6.094881 CACTGACAGAAGAAAAACAACCCTAA 59.905 38.462 10.08 0.00 0.00 2.69
4105 5077 4.157840 ACACTGACAGAAGAAAAACAACCC 59.842 41.667 10.08 0.00 0.00 4.11
4145 5117 2.309136 AACAACAGGGGGATTGGAAG 57.691 50.000 0.00 0.00 0.00 3.46
4148 5120 2.171003 GAGAAACAACAGGGGGATTGG 58.829 52.381 0.00 0.00 0.00 3.16
4156 5163 4.214332 GGCTTGAGTTAGAGAAACAACAGG 59.786 45.833 0.00 0.00 40.83 4.00
4171 5178 3.619487 GCTCTTGAGATGAAGGCTTGAGT 60.619 47.826 3.46 0.00 0.00 3.41
4174 5181 2.708051 TGCTCTTGAGATGAAGGCTTG 58.292 47.619 3.46 0.00 0.00 4.01
4234 5241 4.584325 ACGATATGCTTGCCCAACATTATT 59.416 37.500 0.00 0.00 0.00 1.40
4235 5242 4.144297 ACGATATGCTTGCCCAACATTAT 58.856 39.130 0.00 0.00 0.00 1.28
4236 5243 3.550820 ACGATATGCTTGCCCAACATTA 58.449 40.909 0.00 0.00 0.00 1.90
4237 5244 2.378038 ACGATATGCTTGCCCAACATT 58.622 42.857 0.00 0.00 0.00 2.71
4238 5245 2.057137 ACGATATGCTTGCCCAACAT 57.943 45.000 0.00 0.00 0.00 2.71
4239 5246 1.742831 GAACGATATGCTTGCCCAACA 59.257 47.619 0.00 0.00 0.00 3.33
4253 5260 3.689649 GCATTGGTAGAAACAGGAACGAT 59.310 43.478 0.00 0.00 0.00 3.73
4254 5261 3.071479 GCATTGGTAGAAACAGGAACGA 58.929 45.455 0.00 0.00 0.00 3.85
4278 5285 4.848562 ATACTGATCGGCGTAATTCTCA 57.151 40.909 6.85 1.24 0.00 3.27
4305 5312 4.225042 TCCTACAGATGGTATTTGTGCTGT 59.775 41.667 0.00 0.00 39.61 4.40
4306 5313 4.769688 TCCTACAGATGGTATTTGTGCTG 58.230 43.478 0.00 0.00 0.00 4.41
4321 5424 2.224523 TGAACCCTTGTGCTTCCTACAG 60.225 50.000 0.00 0.00 0.00 2.74
4327 5430 2.952310 AGTCTTTGAACCCTTGTGCTTC 59.048 45.455 0.00 0.00 0.00 3.86
4329 5432 2.576615 GAGTCTTTGAACCCTTGTGCT 58.423 47.619 0.00 0.00 0.00 4.40
4341 5445 0.662619 TTGCTGGTTGCGAGTCTTTG 59.337 50.000 0.00 0.00 46.63 2.77
4354 5458 6.371548 TGTTATAGCTAAGAAGTTGTTGCTGG 59.628 38.462 15.23 0.00 32.72 4.85
4564 5671 2.214181 CTGGACAGCGGACTAGCGTT 62.214 60.000 0.00 0.00 43.00 4.84
4778 5885 3.106242 TGCTTGCTTCGAAAGTAGTGA 57.894 42.857 0.00 0.00 0.00 3.41
4793 5900 9.305925 GGATGTAAAGATTATTTTCCTTGCTTG 57.694 33.333 0.00 0.00 0.00 4.01
4881 5988 6.597672 CCAATAAATAGTTACCAGTGACAGCA 59.402 38.462 0.00 0.00 0.00 4.41
4887 5994 5.583061 TGCGACCAATAAATAGTTACCAGTG 59.417 40.000 0.00 0.00 0.00 3.66
4888 5995 5.736813 TGCGACCAATAAATAGTTACCAGT 58.263 37.500 0.00 0.00 0.00 4.00
4890 5997 6.116806 ACATGCGACCAATAAATAGTTACCA 58.883 36.000 0.00 0.00 0.00 3.25
4891 5998 6.613755 ACATGCGACCAATAAATAGTTACC 57.386 37.500 0.00 0.00 0.00 2.85
4892 5999 8.066000 GGTAACATGCGACCAATAAATAGTTAC 58.934 37.037 10.97 0.00 37.76 2.50
4893 6000 7.988599 AGGTAACATGCGACCAATAAATAGTTA 59.011 33.333 16.73 0.00 38.27 2.24
4894 6001 6.826741 AGGTAACATGCGACCAATAAATAGTT 59.173 34.615 16.73 0.00 38.27 2.24
4895 6002 6.354130 AGGTAACATGCGACCAATAAATAGT 58.646 36.000 16.73 0.00 38.27 2.12
4896 6003 6.861065 AGGTAACATGCGACCAATAAATAG 57.139 37.500 16.73 0.00 38.27 1.73


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

AutoCloner maintained by Alex Coulton.