Multiple sequence alignment - TraesCS3D01G379600

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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 TraesCS3D01G379600 chr3D 100.000 5135 0 0 1 5135 496503183 496508317 0.000000e+00 9483.0
1 TraesCS3D01G379600 chr3B 94.969 4393 147 33 197 4559 655435091 655439439 0.000000e+00 6820.0
2 TraesCS3D01G379600 chr3B 89.247 93 10 0 202 294 811143725 811143633 3.250000e-22 117.0
3 TraesCS3D01G379600 chr3B 82.222 135 22 1 8 140 811460502 811460636 1.170000e-21 115.0
4 TraesCS3D01G379600 chr3B 81.897 116 16 5 193 307 224430366 224430477 5.470000e-15 93.5
5 TraesCS3D01G379600 chr3B 95.349 43 2 0 160 202 741566410 741566452 9.230000e-08 69.4
6 TraesCS3D01G379600 chr3A 94.428 4289 141 43 299 4558 638329559 638325340 0.000000e+00 6506.0
7 TraesCS3D01G379600 chr3A 94.118 153 4 4 160 307 638329748 638329596 1.440000e-55 228.0
8 TraesCS3D01G379600 chr3A 75.460 163 38 1 1 163 610386769 610386609 1.530000e-10 78.7
9 TraesCS3D01G379600 chr3A 95.556 45 2 0 4993 5037 638325343 638325299 7.130000e-09 73.1
10 TraesCS3D01G379600 chr7A 92.763 304 22 0 4696 4999 128018087 128018390 1.700000e-119 440.0
11 TraesCS3D01G379600 chr7A 91.096 146 12 1 4556 4701 128017863 128018007 4.060000e-46 196.0
12 TraesCS3D01G379600 chr2B 92.079 303 24 0 4696 4998 772533613 772533311 1.320000e-115 427.0
13 TraesCS3D01G379600 chr2B 90.759 303 26 1 4696 4996 132353092 132352790 2.230000e-108 403.0
14 TraesCS3D01G379600 chr2B 91.096 146 12 1 4556 4701 772533837 772533693 4.060000e-46 196.0
15 TraesCS3D01G379600 chr2B 84.733 131 18 2 15 144 23870416 23870545 4.170000e-26 130.0
16 TraesCS3D01G379600 chr2B 100.000 38 0 0 165 202 160671319 160671282 2.570000e-08 71.3
17 TraesCS3D01G379600 chr2B 95.238 42 2 0 160 201 87921867 87921908 3.320000e-07 67.6
18 TraesCS3D01G379600 chrUn 91.639 299 25 0 4696 4994 10328136 10327838 1.030000e-111 414.0
19 TraesCS3D01G379600 chr1B 91.611 298 25 0 4696 4993 524347716 524348013 3.700000e-111 412.0
20 TraesCS3D01G379600 chr1B 92.568 148 9 2 4554 4701 524347491 524347636 1.450000e-50 211.0
21 TraesCS3D01G379600 chr4B 90.635 299 28 0 4696 4994 649612720 649613018 1.040000e-106 398.0
22 TraesCS3D01G379600 chr4B 93.056 144 9 1 4558 4701 649612497 649612639 5.210000e-50 209.0
23 TraesCS3D01G379600 chr7B 90.099 303 30 0 4696 4998 221875214 221875516 1.340000e-105 394.0
24 TraesCS3D01G379600 chr7B 92.361 144 10 1 4558 4701 221874991 221875133 2.420000e-48 204.0
25 TraesCS3D01G379600 chr7B 97.436 39 1 0 163 201 504191018 504190980 3.320000e-07 67.6
26 TraesCS3D01G379600 chr5D 98.295 176 3 0 4822 4997 497133723 497133898 4.990000e-80 309.0
27 TraesCS3D01G379600 chr5D 97.159 176 5 0 4822 4997 497401699 497401524 1.080000e-76 298.0
28 TraesCS3D01G379600 chr5D 97.945 146 3 0 4556 4701 497402914 497402769 2.370000e-63 254.0
29 TraesCS3D01G379600 chr5D 97.260 146 4 0 4556 4701 497132324 497132469 1.100000e-61 248.0
30 TraesCS3D01G379600 chr5D 93.373 166 11 0 4 169 375282626 375282461 3.970000e-61 246.0
31 TraesCS3D01G379600 chr5D 97.241 145 4 0 4556 4700 497435716 497435572 3.970000e-61 246.0
32 TraesCS3D01G379600 chr5D 96.575 146 5 0 4556 4701 497215136 497215281 5.140000e-60 243.0
33 TraesCS3D01G379600 chr5D 91.667 132 7 1 4697 4828 497132553 497132680 4.080000e-41 180.0
34 TraesCS3D01G379600 chr5D 91.111 135 8 1 4696 4830 497435120 497434990 4.080000e-41 180.0
35 TraesCS3D01G379600 chr5D 78.621 145 29 1 15 159 101750049 101750191 1.520000e-15 95.3
36 TraesCS3D01G379600 chr1D 84.733 131 16 3 3 133 49607862 49607736 1.500000e-25 128.0
37 TraesCS3D01G379600 chr6D 82.394 142 24 1 1 142 13036405 13036545 6.980000e-24 122.0
38 TraesCS3D01G379600 chr4D 89.691 97 9 1 212 308 497923024 497922929 6.980000e-24 122.0
39 TraesCS3D01G379600 chr2D 78.750 160 31 3 3 161 450915664 450915507 2.530000e-18 104.0
40 TraesCS3D01G379600 chr2D 94.595 37 2 0 166 202 21052350 21052314 2.000000e-04 58.4
41 TraesCS3D01G379600 chr5A 82.645 121 16 5 193 312 67318544 67318428 9.100000e-18 102.0
42 TraesCS3D01G379600 chr5A 100.000 38 0 0 165 202 559822624 559822661 2.570000e-08 71.3
43 TraesCS3D01G379600 chr2A 82.051 117 17 4 4 118 598653703 598653817 4.230000e-16 97.1
44 TraesCS3D01G379600 chr6B 92.308 39 3 0 164 202 88872819 88872781 7.180000e-04 56.5


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 TraesCS3D01G379600 chr3D 496503183 496508317 5134 False 9483.000000 9483 100.000000 1 5135 1 chr3D.!!$F1 5134
1 TraesCS3D01G379600 chr3B 655435091 655439439 4348 False 6820.000000 6820 94.969000 197 4559 1 chr3B.!!$F2 4362
2 TraesCS3D01G379600 chr3A 638325299 638329748 4449 True 2269.033333 6506 94.700667 160 5037 3 chr3A.!!$R2 4877
3 TraesCS3D01G379600 chr7A 128017863 128018390 527 False 318.000000 440 91.929500 4556 4999 2 chr7A.!!$F1 443
4 TraesCS3D01G379600 chr2B 772533311 772533837 526 True 311.500000 427 91.587500 4556 4998 2 chr2B.!!$R3 442
5 TraesCS3D01G379600 chr1B 524347491 524348013 522 False 311.500000 412 92.089500 4554 4993 2 chr1B.!!$F1 439
6 TraesCS3D01G379600 chr4B 649612497 649613018 521 False 303.500000 398 91.845500 4558 4994 2 chr4B.!!$F1 436
7 TraesCS3D01G379600 chr7B 221874991 221875516 525 False 299.000000 394 91.230000 4558 4998 2 chr7B.!!$F1 440
8 TraesCS3D01G379600 chr5D 497401524 497402914 1390 True 276.000000 298 97.552000 4556 4997 2 chr5D.!!$R2 441
9 TraesCS3D01G379600 chr5D 497132324 497133898 1574 False 245.666667 309 95.740667 4556 4997 3 chr5D.!!$F3 441
10 TraesCS3D01G379600 chr5D 497434990 497435716 726 True 213.000000 246 94.176000 4556 4830 2 chr5D.!!$R3 274

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
345 405 0.036732 CGCAGGGTGGGTGCATATAT 59.963 55.0 0.0 0.0 41.26 0.86 F
710 782 0.692419 TGGCCCCTCTCCTGAAGATC 60.692 60.0 0.0 0.0 32.19 2.75 F
1866 1954 0.729116 CGATGCACATTGGACAGGAC 59.271 55.0 0.0 0.0 0.00 3.85 F
2517 2605 0.798776 GACATTCTCCACAACGGCAG 59.201 55.0 0.0 0.0 33.14 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1400 0.848942 CTGAAATCGACCGCAGATCG 59.151 55.0 4.70 0.0 38.08 3.69 R
1876 1964 1.067295 TCTGCAGGTCCCAAAGTCAT 58.933 50.0 15.13 0.0 0.00 3.06 R
3670 3758 0.733909 CGTTGAGCAGCACGATCAGA 60.734 55.0 0.00 0.0 42.01 3.27 R
4488 4589 0.249741 GGTGGTGGCGCGTATAAGAT 60.250 55.0 8.43 0.0 0.00 2.40 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 2.361643 ACATAGACCCTCCGTAGACC 57.638 55.000 0.00 0.00 0.00 3.85
20 21 1.567649 ACATAGACCCTCCGTAGACCA 59.432 52.381 0.00 0.00 0.00 4.02
21 22 2.177233 ACATAGACCCTCCGTAGACCAT 59.823 50.000 0.00 0.00 0.00 3.55
22 23 3.231818 CATAGACCCTCCGTAGACCATT 58.768 50.000 0.00 0.00 0.00 3.16
23 24 1.486211 AGACCCTCCGTAGACCATTG 58.514 55.000 0.00 0.00 0.00 2.82
24 25 0.179081 GACCCTCCGTAGACCATTGC 60.179 60.000 0.00 0.00 0.00 3.56
25 26 0.907704 ACCCTCCGTAGACCATTGCA 60.908 55.000 0.00 0.00 0.00 4.08
26 27 0.251916 CCCTCCGTAGACCATTGCAA 59.748 55.000 0.00 0.00 0.00 4.08
27 28 1.369625 CCTCCGTAGACCATTGCAAC 58.630 55.000 0.00 0.00 0.00 4.17
28 29 1.338674 CCTCCGTAGACCATTGCAACA 60.339 52.381 0.00 0.00 0.00 3.33
29 30 1.732259 CTCCGTAGACCATTGCAACAC 59.268 52.381 0.00 0.00 0.00 3.32
30 31 0.802494 CCGTAGACCATTGCAACACC 59.198 55.000 0.00 0.00 0.00 4.16
31 32 0.442310 CGTAGACCATTGCAACACCG 59.558 55.000 0.00 0.00 0.00 4.94
32 33 0.168128 GTAGACCATTGCAACACCGC 59.832 55.000 0.00 0.00 0.00 5.68
33 34 0.250510 TAGACCATTGCAACACCGCA 60.251 50.000 0.00 0.00 41.03 5.69
34 35 0.895100 AGACCATTGCAACACCGCAT 60.895 50.000 0.00 0.00 42.62 4.73
35 36 0.808125 GACCATTGCAACACCGCATA 59.192 50.000 0.00 0.00 42.62 3.14
36 37 1.405105 GACCATTGCAACACCGCATAT 59.595 47.619 0.00 0.00 42.62 1.78
37 38 1.134753 ACCATTGCAACACCGCATATG 59.865 47.619 0.00 0.00 42.62 1.78
38 39 1.134753 CCATTGCAACACCGCATATGT 59.865 47.619 0.00 0.00 42.62 2.29
39 40 2.417107 CCATTGCAACACCGCATATGTT 60.417 45.455 0.00 0.00 42.62 2.71
40 41 3.252400 CATTGCAACACCGCATATGTTT 58.748 40.909 0.00 0.00 42.62 2.83
41 42 2.627863 TGCAACACCGCATATGTTTC 57.372 45.000 4.29 0.00 38.22 2.78
42 43 1.882623 TGCAACACCGCATATGTTTCA 59.117 42.857 4.29 0.00 38.22 2.69
43 44 2.095314 TGCAACACCGCATATGTTTCAG 60.095 45.455 4.29 0.00 38.22 3.02
44 45 2.161410 GCAACACCGCATATGTTTCAGA 59.839 45.455 4.29 0.00 38.22 3.27
45 46 3.365868 GCAACACCGCATATGTTTCAGAA 60.366 43.478 4.29 0.00 38.22 3.02
46 47 4.406069 CAACACCGCATATGTTTCAGAAG 58.594 43.478 4.29 0.00 38.22 2.85
47 48 2.420022 ACACCGCATATGTTTCAGAAGC 59.580 45.455 4.29 0.00 0.00 3.86
48 49 2.419673 CACCGCATATGTTTCAGAAGCA 59.580 45.455 1.71 1.71 0.00 3.91
49 50 3.065786 CACCGCATATGTTTCAGAAGCAT 59.934 43.478 15.93 15.93 0.00 3.79
50 51 4.273235 CACCGCATATGTTTCAGAAGCATA 59.727 41.667 18.82 18.82 0.00 3.14
51 52 4.512944 ACCGCATATGTTTCAGAAGCATAG 59.487 41.667 20.50 14.68 0.00 2.23
52 53 4.461405 CGCATATGTTTCAGAAGCATAGC 58.539 43.478 20.50 20.11 0.00 2.97
53 54 4.212847 CGCATATGTTTCAGAAGCATAGCT 59.787 41.667 20.50 6.58 42.56 3.32
64 65 2.775911 AGCATAGCTTCAGTTGCAGA 57.224 45.000 0.00 0.00 33.89 4.26
65 66 3.063510 AGCATAGCTTCAGTTGCAGAA 57.936 42.857 0.00 0.00 33.89 3.02
66 67 2.746362 AGCATAGCTTCAGTTGCAGAAC 59.254 45.455 0.00 0.00 33.89 3.01
67 68 2.159462 GCATAGCTTCAGTTGCAGAACC 60.159 50.000 0.00 0.00 35.22 3.62
68 69 1.795768 TAGCTTCAGTTGCAGAACCG 58.204 50.000 0.00 0.00 31.81 4.44
69 70 0.106708 AGCTTCAGTTGCAGAACCGA 59.893 50.000 0.00 0.00 31.81 4.69
70 71 0.514691 GCTTCAGTTGCAGAACCGAG 59.485 55.000 0.00 0.00 31.81 4.63
71 72 1.871080 CTTCAGTTGCAGAACCGAGT 58.129 50.000 0.00 0.00 31.81 4.18
72 73 2.213499 CTTCAGTTGCAGAACCGAGTT 58.787 47.619 0.00 0.00 31.81 3.01
73 74 1.865865 TCAGTTGCAGAACCGAGTTC 58.134 50.000 8.26 8.26 42.25 3.01
74 75 0.508641 CAGTTGCAGAACCGAGTTCG 59.491 55.000 9.99 0.00 45.96 3.95
75 76 0.387929 AGTTGCAGAACCGAGTTCGA 59.612 50.000 2.59 0.00 45.96 3.71
76 77 1.000955 AGTTGCAGAACCGAGTTCGAT 59.999 47.619 2.59 0.00 45.96 3.59
77 78 1.126846 GTTGCAGAACCGAGTTCGATG 59.873 52.381 2.59 6.46 45.96 3.84
78 79 0.601057 TGCAGAACCGAGTTCGATGA 59.399 50.000 2.59 0.00 45.96 2.92
79 80 1.000394 TGCAGAACCGAGTTCGATGAA 60.000 47.619 2.59 0.00 45.96 2.57
80 81 2.271800 GCAGAACCGAGTTCGATGAAT 58.728 47.619 2.59 0.00 45.96 2.57
81 82 2.029728 GCAGAACCGAGTTCGATGAATG 59.970 50.000 2.59 4.85 45.96 2.67
82 83 3.511699 CAGAACCGAGTTCGATGAATGA 58.488 45.455 2.59 0.00 45.96 2.57
83 84 4.115516 CAGAACCGAGTTCGATGAATGAT 58.884 43.478 2.59 0.00 45.96 2.45
84 85 4.026228 CAGAACCGAGTTCGATGAATGATG 60.026 45.833 2.59 0.00 45.96 3.07
85 86 2.826428 ACCGAGTTCGATGAATGATGG 58.174 47.619 2.59 0.00 43.02 3.51
86 87 2.168521 ACCGAGTTCGATGAATGATGGT 59.831 45.455 2.59 0.00 43.02 3.55
87 88 3.383505 ACCGAGTTCGATGAATGATGGTA 59.616 43.478 2.59 0.00 43.02 3.25
88 89 4.039245 ACCGAGTTCGATGAATGATGGTAT 59.961 41.667 2.59 0.00 43.02 2.73
89 90 4.386954 CCGAGTTCGATGAATGATGGTATG 59.613 45.833 2.59 0.00 43.02 2.39
90 91 4.143242 CGAGTTCGATGAATGATGGTATGC 60.143 45.833 0.00 0.00 43.02 3.14
91 92 3.742882 AGTTCGATGAATGATGGTATGCG 59.257 43.478 0.00 0.00 0.00 4.73
92 93 2.687370 TCGATGAATGATGGTATGCGG 58.313 47.619 0.00 0.00 0.00 5.69
93 94 1.733912 CGATGAATGATGGTATGCGGG 59.266 52.381 0.00 0.00 0.00 6.13
94 95 1.470098 GATGAATGATGGTATGCGGGC 59.530 52.381 0.00 0.00 0.00 6.13
95 96 0.537143 TGAATGATGGTATGCGGGCC 60.537 55.000 0.00 0.00 0.00 5.80
96 97 0.250901 GAATGATGGTATGCGGGCCT 60.251 55.000 0.84 0.00 0.00 5.19
97 98 0.185901 AATGATGGTATGCGGGCCTT 59.814 50.000 0.84 0.00 0.00 4.35
98 99 0.250901 ATGATGGTATGCGGGCCTTC 60.251 55.000 0.84 0.00 0.00 3.46
99 100 1.148273 GATGGTATGCGGGCCTTCA 59.852 57.895 0.84 0.44 0.00 3.02
100 101 1.152963 ATGGTATGCGGGCCTTCAC 60.153 57.895 0.84 0.00 0.00 3.18
101 102 1.635817 ATGGTATGCGGGCCTTCACT 61.636 55.000 0.84 0.00 0.00 3.41
102 103 1.077716 GGTATGCGGGCCTTCACTT 60.078 57.895 0.84 0.00 0.00 3.16
103 104 0.179468 GGTATGCGGGCCTTCACTTA 59.821 55.000 0.84 0.00 0.00 2.24
104 105 1.583054 GTATGCGGGCCTTCACTTAG 58.417 55.000 0.84 0.00 0.00 2.18
105 106 1.138266 GTATGCGGGCCTTCACTTAGA 59.862 52.381 0.84 0.00 0.00 2.10
106 107 0.107654 ATGCGGGCCTTCACTTAGAC 60.108 55.000 0.84 0.00 0.00 2.59
107 108 1.295423 GCGGGCCTTCACTTAGACA 59.705 57.895 0.84 0.00 0.00 3.41
108 109 1.019805 GCGGGCCTTCACTTAGACAC 61.020 60.000 0.84 0.00 0.00 3.67
109 110 0.736325 CGGGCCTTCACTTAGACACG 60.736 60.000 0.84 0.00 0.00 4.49
110 111 0.320697 GGGCCTTCACTTAGACACGT 59.679 55.000 0.84 0.00 0.00 4.49
111 112 1.429463 GGCCTTCACTTAGACACGTG 58.571 55.000 15.48 15.48 0.00 4.49
112 113 1.270147 GGCCTTCACTTAGACACGTGT 60.270 52.381 23.64 23.64 33.07 4.49
113 114 2.059541 GCCTTCACTTAGACACGTGTC 58.940 52.381 35.83 35.83 45.08 3.67
125 126 4.883026 CGTGTCACGTAGGGAAGG 57.117 61.111 17.30 0.00 36.74 3.46
126 127 1.962144 CGTGTCACGTAGGGAAGGT 59.038 57.895 17.30 0.00 36.74 3.50
127 128 0.388134 CGTGTCACGTAGGGAAGGTG 60.388 60.000 17.30 0.00 43.79 4.00
128 129 0.037605 GTGTCACGTAGGGAAGGTGG 60.038 60.000 0.00 0.00 42.88 4.61
129 130 1.079336 GTCACGTAGGGAAGGTGGC 60.079 63.158 0.00 0.00 42.88 5.01
130 131 2.125673 CACGTAGGGAAGGTGGCG 60.126 66.667 0.00 0.00 39.73 5.69
131 132 3.387947 ACGTAGGGAAGGTGGCGG 61.388 66.667 0.00 0.00 0.00 6.13
132 133 3.072468 CGTAGGGAAGGTGGCGGA 61.072 66.667 0.00 0.00 0.00 5.54
133 134 2.582978 GTAGGGAAGGTGGCGGAC 59.417 66.667 0.00 0.00 0.00 4.79
134 135 3.072468 TAGGGAAGGTGGCGGACG 61.072 66.667 0.00 0.00 0.00 4.79
150 151 2.125552 CGCAGCCGTTGAGATCCA 60.126 61.111 0.00 0.00 0.00 3.41
151 152 2.456119 CGCAGCCGTTGAGATCCAC 61.456 63.158 0.00 0.00 0.00 4.02
152 153 1.375908 GCAGCCGTTGAGATCCACA 60.376 57.895 0.00 0.00 0.00 4.17
153 154 1.364626 GCAGCCGTTGAGATCCACAG 61.365 60.000 0.00 0.00 0.00 3.66
154 155 0.742281 CAGCCGTTGAGATCCACAGG 60.742 60.000 0.00 0.00 0.00 4.00
155 156 1.450312 GCCGTTGAGATCCACAGGG 60.450 63.158 0.00 0.00 0.00 4.45
156 157 1.983224 CCGTTGAGATCCACAGGGT 59.017 57.895 0.00 0.00 34.93 4.34
157 158 0.391661 CCGTTGAGATCCACAGGGTG 60.392 60.000 0.00 0.00 34.93 4.61
158 159 0.608130 CGTTGAGATCCACAGGGTGA 59.392 55.000 0.00 0.00 35.23 4.02
159 160 1.208052 CGTTGAGATCCACAGGGTGAT 59.792 52.381 0.00 0.00 35.23 3.06
160 161 2.636830 GTTGAGATCCACAGGGTGATG 58.363 52.381 0.00 0.00 35.23 3.07
161 162 1.206878 TGAGATCCACAGGGTGATGG 58.793 55.000 0.00 0.00 35.23 3.51
162 163 1.207791 GAGATCCACAGGGTGATGGT 58.792 55.000 0.00 0.00 37.27 3.55
163 164 0.914644 AGATCCACAGGGTGATGGTG 59.085 55.000 0.00 0.00 37.27 4.17
170 171 3.308402 CCACAGGGTGATGGTGAAAGTAT 60.308 47.826 0.00 0.00 35.23 2.12
176 177 8.333235 ACAGGGTGATGGTGAAAGTATATAAAA 58.667 33.333 0.00 0.00 0.00 1.52
344 404 1.341913 ACGCAGGGTGGGTGCATATA 61.342 55.000 0.00 0.00 42.20 0.86
345 405 0.036732 CGCAGGGTGGGTGCATATAT 59.963 55.000 0.00 0.00 41.26 0.86
373 435 1.130561 GAAGCCATAGCCACGTTCAAC 59.869 52.381 0.00 0.00 41.25 3.18
694 765 1.589716 AAAGATTCACAGGCGCTGGC 61.590 55.000 7.64 0.00 35.51 4.85
708 780 1.306482 CTGGCCCCTCTCCTGAAGA 60.306 63.158 0.00 0.00 0.00 2.87
709 781 0.693767 CTGGCCCCTCTCCTGAAGAT 60.694 60.000 0.00 0.00 32.19 2.40
710 782 0.692419 TGGCCCCTCTCCTGAAGATC 60.692 60.000 0.00 0.00 32.19 2.75
800 872 4.515567 CGTTTGAATTCCTAGCCTTATCCC 59.484 45.833 2.27 0.00 0.00 3.85
816 888 2.304069 CCCTTAGGCGGTTAGGGTT 58.696 57.895 0.00 0.00 43.07 4.11
817 889 1.499368 CCCTTAGGCGGTTAGGGTTA 58.501 55.000 0.00 0.00 43.07 2.85
819 891 2.158856 CCCTTAGGCGGTTAGGGTTAAG 60.159 54.545 0.00 0.00 43.07 1.85
842 914 1.221414 CATTCCGCGAGATCCTTTCC 58.779 55.000 8.23 0.00 0.00 3.13
898 976 1.832366 TGTCGTTTATCCCATTCCCGA 59.168 47.619 0.00 0.00 0.00 5.14
934 1012 1.514003 TACGTTTTGCAGATTCGGCA 58.486 45.000 7.42 7.42 40.00 5.69
980 1058 5.667175 CGCGTTTGATTAGATTAGGTTAGC 58.333 41.667 0.00 0.00 0.00 3.09
990 1068 3.778629 AGATTAGGTTAGCCTCGGGAAAA 59.221 43.478 0.00 0.00 45.64 2.29
991 1069 3.339253 TTAGGTTAGCCTCGGGAAAAC 57.661 47.619 0.00 0.00 45.64 2.43
1025 1103 2.017049 CATGGCTAAACGGGAGAAAGG 58.983 52.381 0.00 0.00 0.00 3.11
1122 1209 3.948086 GACGTCTGCGAGGTCGGTG 62.948 68.421 8.70 0.00 37.62 4.94
1280 1367 4.292643 GTGTCCCTAAACCCTATCTACCA 58.707 47.826 0.00 0.00 0.00 3.25
1309 1396 6.014499 TCCTCAGAAGTTCGTCCTAAATTCTT 60.014 38.462 0.00 0.00 39.93 2.52
1313 1400 7.601508 TCAGAAGTTCGTCCTAAATTCTTTACC 59.398 37.037 0.00 0.00 39.93 2.85
1314 1401 6.589139 AGAAGTTCGTCCTAAATTCTTTACCG 59.411 38.462 0.00 0.00 39.93 4.02
1405 1493 2.169352 CCAGATCTTCCAGTACCAGGTG 59.831 54.545 0.76 0.00 0.00 4.00
1444 1532 1.141881 CCTCGTGGGATCCTTCGTG 59.858 63.158 21.38 19.32 37.23 4.35
1538 1626 1.472082 TCATGCGGCAAAACAGGTATG 59.528 47.619 6.82 0.00 0.00 2.39
1600 1688 1.178534 AGACCCAAACAATGCACGGG 61.179 55.000 0.00 0.00 43.02 5.28
1866 1954 0.729116 CGATGCACATTGGACAGGAC 59.271 55.000 0.00 0.00 0.00 3.85
1876 1964 4.102524 ACATTGGACAGGACTAAGTTGTGA 59.897 41.667 0.00 0.00 0.00 3.58
1877 1965 4.974645 TTGGACAGGACTAAGTTGTGAT 57.025 40.909 0.00 0.00 0.00 3.06
1878 1966 4.271696 TGGACAGGACTAAGTTGTGATG 57.728 45.455 0.00 0.00 0.00 3.07
2014 2102 4.157120 GGGTCGCGCAGGTATGGT 62.157 66.667 8.75 0.00 0.00 3.55
2256 2344 8.074370 CGCATAGAACTGCTACTAGTGTTTATA 58.926 37.037 5.39 0.00 40.06 0.98
2283 2371 3.244526 GGGAAAGTGCAATTTCACCCAAT 60.245 43.478 33.00 2.58 40.29 3.16
2381 2469 6.680810 TCACATTGAACTGTGGAATGAAATC 58.319 36.000 15.28 0.00 45.29 2.17
2384 2472 7.752239 CACATTGAACTGTGGAATGAAATCTAC 59.248 37.037 15.28 0.00 42.26 2.59
2385 2473 6.480524 TTGAACTGTGGAATGAAATCTACG 57.519 37.500 0.00 0.00 33.87 3.51
2390 2478 2.933906 GTGGAATGAAATCTACGGCGAA 59.066 45.455 16.62 0.00 0.00 4.70
2394 2482 4.970003 GGAATGAAATCTACGGCGAATTTG 59.030 41.667 16.62 0.00 0.00 2.32
2395 2483 3.398954 TGAAATCTACGGCGAATTTGC 57.601 42.857 16.62 9.36 0.00 3.68
2418 2506 3.439895 TTGTTTTTCAAACCGGGCTAC 57.560 42.857 6.32 0.00 32.64 3.58
2421 2509 2.882761 GTTTTTCAAACCGGGCTACTCT 59.117 45.455 6.32 0.00 0.00 3.24
2422 2510 2.178912 TTTCAAACCGGGCTACTCTG 57.821 50.000 6.32 0.00 0.00 3.35
2435 2523 3.118223 GGCTACTCTGCTCCCATTACTTT 60.118 47.826 0.00 0.00 0.00 2.66
2439 2527 5.957771 ACTCTGCTCCCATTACTTTCATA 57.042 39.130 0.00 0.00 0.00 2.15
2466 2554 3.565902 CAGAAACCCTTTGTCCTTCTGAC 59.434 47.826 4.49 0.00 41.37 3.51
2517 2605 0.798776 GACATTCTCCACAACGGCAG 59.201 55.000 0.00 0.00 33.14 4.85
2713 2801 1.260561 CTTCAACCACTTTGTCGACCG 59.739 52.381 14.12 4.04 36.49 4.79
2779 2867 6.770785 TCCGAATTAACCTCATTATGAAAGGG 59.229 38.462 5.64 2.15 34.31 3.95
2790 2878 7.104043 TCATTATGAAAGGGAAGCATTTCTG 57.896 36.000 0.00 0.00 36.57 3.02
2842 2930 2.837532 TTTGAATTTGCAGGAAGGGC 57.162 45.000 0.00 0.00 0.00 5.19
3058 3146 1.563111 TCTTCAACACCAACGACGAC 58.437 50.000 0.00 0.00 0.00 4.34
3142 3230 0.885879 TCTTCATCGGCGTGTACACT 59.114 50.000 23.01 1.46 0.00 3.55
3400 3488 1.176619 TCGTCCTGCTCGTCTCCAAA 61.177 55.000 0.00 0.00 0.00 3.28
3670 3758 4.415150 CTGGTGCTGCGGTCCCAT 62.415 66.667 5.86 0.00 0.00 4.00
3751 3839 1.166531 AGGTGTTCCGCAAGCTCAAC 61.167 55.000 0.00 0.00 39.05 3.18
3881 3969 4.487412 GGTCGCCCTACACCGTCG 62.487 72.222 0.00 0.00 0.00 5.12
4136 4224 0.877071 AACGTCCTTCGCGAGTAGAA 59.123 50.000 9.59 0.00 44.19 2.10
4148 4237 1.334239 CGAGTAGAAGAAGATCGCCGG 60.334 57.143 0.00 0.00 0.00 6.13
4149 4238 1.001158 GAGTAGAAGAAGATCGCCGGG 60.001 57.143 2.18 0.00 0.00 5.73
4183 4275 7.425915 TGCATATATTTTACGCACGTTTTTC 57.574 32.000 0.00 0.00 0.00 2.29
4184 4276 6.469595 TGCATATATTTTACGCACGTTTTTCC 59.530 34.615 0.00 0.00 0.00 3.13
4326 4427 1.553704 ACCGACCCTGAATTAGTGGAC 59.446 52.381 0.00 0.00 0.00 4.02
4406 4507 7.833786 ACTATTTTATTGGCATGCCTGATATG 58.166 34.615 35.53 18.97 36.94 1.78
4483 4584 2.095969 TCATTGTCGCCACGATTTTCAC 60.096 45.455 0.00 0.00 38.42 3.18
4484 4585 1.588674 TTGTCGCCACGATTTTCACT 58.411 45.000 0.00 0.00 38.42 3.41
4485 4586 2.442212 TGTCGCCACGATTTTCACTA 57.558 45.000 0.00 0.00 38.42 2.74
4486 4587 2.063266 TGTCGCCACGATTTTCACTAC 58.937 47.619 0.00 0.00 38.42 2.73
4487 4588 1.058695 GTCGCCACGATTTTCACTACG 59.941 52.381 0.00 0.00 38.42 3.51
4488 4589 1.068402 TCGCCACGATTTTCACTACGA 60.068 47.619 0.00 0.00 0.00 3.43
4489 4590 1.924524 CGCCACGATTTTCACTACGAT 59.075 47.619 0.00 0.00 0.00 3.73
4490 4591 2.034842 CGCCACGATTTTCACTACGATC 60.035 50.000 0.00 0.00 0.00 3.69
4491 4592 3.187700 GCCACGATTTTCACTACGATCT 58.812 45.455 0.00 0.00 0.00 2.75
4537 4638 0.320508 GTCGGTGGGAGAAACTGTCC 60.321 60.000 0.00 0.00 0.00 4.02
4584 4685 1.275573 GTTCGGTACTCCTCCAGCTTT 59.724 52.381 0.00 0.00 0.00 3.51
4697 4798 2.032681 GGAGCGGTGTTTCTGGCT 59.967 61.111 0.00 0.00 38.70 4.75
4715 5273 6.843208 TCTGGCTATCTTCGTTATATTCTCG 58.157 40.000 0.00 0.00 0.00 4.04
4728 5286 6.600350 GTTATATTCTCGTGATGAGCTACGA 58.400 40.000 8.99 8.99 45.87 3.43
4762 5320 1.151668 CTTTCACTCTGAACTGGGCG 58.848 55.000 0.00 0.00 35.89 6.13
4796 5354 2.997315 CTCCTGTGTCCGGCTGGA 60.997 66.667 11.27 11.27 43.88 3.86
4877 6485 0.450583 CTGGCACGTACGAGAAGCTA 59.549 55.000 24.41 15.82 0.00 3.32
4913 6521 1.393539 ACGGTTTTTCATCGATCGCAG 59.606 47.619 11.09 5.20 0.00 5.18
5031 6639 0.597568 TGAATTGCTTGCTTCCCACG 59.402 50.000 0.00 0.00 0.00 4.94
5053 6661 2.562912 CACGCATGCACAGAACCC 59.437 61.111 19.57 0.00 0.00 4.11
5054 6662 1.968017 CACGCATGCACAGAACCCT 60.968 57.895 19.57 0.00 0.00 4.34
5055 6663 1.228245 ACGCATGCACAGAACCCTT 60.228 52.632 19.57 0.00 0.00 3.95
5056 6664 1.210931 CGCATGCACAGAACCCTTG 59.789 57.895 19.57 0.00 0.00 3.61
5057 6665 1.236616 CGCATGCACAGAACCCTTGA 61.237 55.000 19.57 0.00 0.00 3.02
5058 6666 0.242017 GCATGCACAGAACCCTTGAC 59.758 55.000 14.21 0.00 0.00 3.18
5059 6667 1.901591 CATGCACAGAACCCTTGACT 58.098 50.000 0.00 0.00 0.00 3.41
5060 6668 2.233271 CATGCACAGAACCCTTGACTT 58.767 47.619 0.00 0.00 0.00 3.01
5061 6669 3.411446 CATGCACAGAACCCTTGACTTA 58.589 45.455 0.00 0.00 0.00 2.24
5062 6670 3.569194 TGCACAGAACCCTTGACTTAA 57.431 42.857 0.00 0.00 0.00 1.85
5063 6671 4.098914 TGCACAGAACCCTTGACTTAAT 57.901 40.909 0.00 0.00 0.00 1.40
5064 6672 4.469657 TGCACAGAACCCTTGACTTAATT 58.530 39.130 0.00 0.00 0.00 1.40
5065 6673 4.892934 TGCACAGAACCCTTGACTTAATTT 59.107 37.500 0.00 0.00 0.00 1.82
5066 6674 5.221224 TGCACAGAACCCTTGACTTAATTTG 60.221 40.000 0.00 0.00 0.00 2.32
5067 6675 5.221244 GCACAGAACCCTTGACTTAATTTGT 60.221 40.000 0.00 0.00 0.00 2.83
5068 6676 6.682861 GCACAGAACCCTTGACTTAATTTGTT 60.683 38.462 0.00 0.00 0.00 2.83
5069 6677 7.469456 GCACAGAACCCTTGACTTAATTTGTTA 60.469 37.037 0.00 0.00 0.00 2.41
5070 6678 8.076178 CACAGAACCCTTGACTTAATTTGTTAG 58.924 37.037 0.00 0.00 0.00 2.34
5071 6679 7.778382 ACAGAACCCTTGACTTAATTTGTTAGT 59.222 33.333 0.00 0.00 0.00 2.24
5072 6680 9.280174 CAGAACCCTTGACTTAATTTGTTAGTA 57.720 33.333 0.00 0.00 0.00 1.82
5093 6701 9.640952 TTAGTATTATCAAAGGGAAGGATTTGG 57.359 33.333 0.00 0.00 37.09 3.28
5094 6702 7.882755 AGTATTATCAAAGGGAAGGATTTGGA 58.117 34.615 0.00 0.00 37.09 3.53
5095 6703 8.343787 AGTATTATCAAAGGGAAGGATTTGGAA 58.656 33.333 0.00 0.00 37.09 3.53
5096 6704 8.977412 GTATTATCAAAGGGAAGGATTTGGAAA 58.023 33.333 0.00 0.00 37.09 3.13
5097 6705 7.480760 TTATCAAAGGGAAGGATTTGGAAAG 57.519 36.000 0.00 0.00 37.09 2.62
5098 6706 4.814967 TCAAAGGGAAGGATTTGGAAAGT 58.185 39.130 0.00 0.00 37.09 2.66
5099 6707 4.588528 TCAAAGGGAAGGATTTGGAAAGTG 59.411 41.667 0.00 0.00 37.09 3.16
5100 6708 4.469469 AAGGGAAGGATTTGGAAAGTGA 57.531 40.909 0.00 0.00 0.00 3.41
5101 6709 4.682021 AGGGAAGGATTTGGAAAGTGAT 57.318 40.909 0.00 0.00 0.00 3.06
5102 6710 5.015813 AGGGAAGGATTTGGAAAGTGATT 57.984 39.130 0.00 0.00 0.00 2.57
5103 6711 5.406163 AGGGAAGGATTTGGAAAGTGATTT 58.594 37.500 0.00 0.00 0.00 2.17
5104 6712 5.481824 AGGGAAGGATTTGGAAAGTGATTTC 59.518 40.000 0.00 0.00 0.00 2.17
5116 6724 7.161773 GGAAAGTGATTTCCTTGATTGATCA 57.838 36.000 11.62 0.00 45.37 2.92
5117 6725 7.605449 GGAAAGTGATTTCCTTGATTGATCAA 58.395 34.615 11.26 11.26 45.37 2.57
5118 6726 8.090214 GGAAAGTGATTTCCTTGATTGATCAAA 58.910 33.333 13.09 0.00 45.26 2.69
5119 6727 9.480053 GAAAGTGATTTCCTTGATTGATCAAAA 57.520 29.630 13.09 2.16 45.26 2.44
5120 6728 8.822652 AAGTGATTTCCTTGATTGATCAAAAC 57.177 30.769 13.09 10.29 45.26 2.43
5121 6729 8.186709 AGTGATTTCCTTGATTGATCAAAACT 57.813 30.769 13.09 0.00 45.26 2.66
5122 6730 9.300681 AGTGATTTCCTTGATTGATCAAAACTA 57.699 29.630 13.09 6.16 45.26 2.24
5123 6731 9.912634 GTGATTTCCTTGATTGATCAAAACTAA 57.087 29.630 13.09 4.79 45.26 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.567649 TGGTCTACGGAGGGTCTATGT 59.432 52.381 0.00 0.00 0.00 2.29
2 3 3.231818 CAATGGTCTACGGAGGGTCTAT 58.768 50.000 0.00 0.00 0.00 1.98
4 5 1.486211 CAATGGTCTACGGAGGGTCT 58.514 55.000 0.00 0.00 0.00 3.85
6 7 0.907704 TGCAATGGTCTACGGAGGGT 60.908 55.000 0.00 0.00 0.00 4.34
7 8 0.251916 TTGCAATGGTCTACGGAGGG 59.748 55.000 0.00 0.00 0.00 4.30
8 9 1.338674 TGTTGCAATGGTCTACGGAGG 60.339 52.381 0.59 0.00 0.00 4.30
9 10 1.732259 GTGTTGCAATGGTCTACGGAG 59.268 52.381 0.59 0.00 0.00 4.63
10 11 1.609580 GGTGTTGCAATGGTCTACGGA 60.610 52.381 0.59 0.00 0.00 4.69
11 12 0.802494 GGTGTTGCAATGGTCTACGG 59.198 55.000 0.59 0.00 0.00 4.02
12 13 0.442310 CGGTGTTGCAATGGTCTACG 59.558 55.000 0.59 0.00 0.00 3.51
13 14 0.168128 GCGGTGTTGCAATGGTCTAC 59.832 55.000 0.59 0.00 34.15 2.59
14 15 0.250510 TGCGGTGTTGCAATGGTCTA 60.251 50.000 0.59 0.00 43.02 2.59
15 16 1.528076 TGCGGTGTTGCAATGGTCT 60.528 52.632 0.59 0.00 43.02 3.85
16 17 3.038280 TGCGGTGTTGCAATGGTC 58.962 55.556 0.59 0.00 43.02 4.02
23 24 2.161410 TCTGAAACATATGCGGTGTTGC 59.839 45.455 1.58 1.70 39.57 4.17
24 25 4.406069 CTTCTGAAACATATGCGGTGTTG 58.594 43.478 1.58 0.00 39.57 3.33
25 26 3.119849 GCTTCTGAAACATATGCGGTGTT 60.120 43.478 1.58 0.00 41.28 3.32
26 27 2.420022 GCTTCTGAAACATATGCGGTGT 59.580 45.455 1.58 0.00 0.00 4.16
27 28 2.419673 TGCTTCTGAAACATATGCGGTG 59.580 45.455 1.58 0.00 0.00 4.94
28 29 2.710377 TGCTTCTGAAACATATGCGGT 58.290 42.857 1.58 0.00 0.00 5.68
29 30 3.976793 ATGCTTCTGAAACATATGCGG 57.023 42.857 4.55 0.00 0.00 5.69
30 31 4.212847 AGCTATGCTTCTGAAACATATGCG 59.787 41.667 12.45 4.71 33.89 4.73
31 32 5.686159 AGCTATGCTTCTGAAACATATGC 57.314 39.130 12.45 15.57 33.89 3.14
44 45 5.872383 GGTTCTGCAACTGAAGCTATGCTT 61.872 45.833 4.35 4.35 41.01 3.91
45 46 2.746362 GTTCTGCAACTGAAGCTATGCT 59.254 45.455 8.97 0.00 42.56 3.79
46 47 2.159462 GGTTCTGCAACTGAAGCTATGC 60.159 50.000 8.62 0.00 37.04 3.14
47 48 2.094894 CGGTTCTGCAACTGAAGCTATG 59.905 50.000 12.69 0.00 40.95 2.23
48 49 2.028112 TCGGTTCTGCAACTGAAGCTAT 60.028 45.455 12.69 0.00 43.71 2.97
49 50 1.343142 TCGGTTCTGCAACTGAAGCTA 59.657 47.619 12.69 1.77 43.71 3.32
50 51 0.106708 TCGGTTCTGCAACTGAAGCT 59.893 50.000 12.69 0.00 43.71 3.74
51 52 0.514691 CTCGGTTCTGCAACTGAAGC 59.485 55.000 6.36 6.36 45.54 3.86
52 53 1.871080 ACTCGGTTCTGCAACTGAAG 58.129 50.000 1.86 0.09 45.54 3.02
53 54 2.210116 GAACTCGGTTCTGCAACTGAA 58.790 47.619 1.86 0.00 45.54 3.02
54 55 1.865865 GAACTCGGTTCTGCAACTGA 58.134 50.000 8.87 0.28 44.34 3.41
55 56 0.508641 CGAACTCGGTTCTGCAACTG 59.491 55.000 12.80 0.00 40.05 3.16
56 57 0.387929 TCGAACTCGGTTCTGCAACT 59.612 50.000 12.80 0.00 40.05 3.16
57 58 1.126846 CATCGAACTCGGTTCTGCAAC 59.873 52.381 12.80 0.00 40.05 4.17
58 59 1.000394 TCATCGAACTCGGTTCTGCAA 60.000 47.619 12.80 0.45 40.05 4.08
59 60 0.601057 TCATCGAACTCGGTTCTGCA 59.399 50.000 12.80 0.00 40.05 4.41
60 61 1.710013 TTCATCGAACTCGGTTCTGC 58.290 50.000 12.80 0.00 40.05 4.26
61 62 3.511699 TCATTCATCGAACTCGGTTCTG 58.488 45.455 12.80 7.19 40.05 3.02
62 63 3.868757 TCATTCATCGAACTCGGTTCT 57.131 42.857 12.80 0.00 40.05 3.01
63 64 3.246226 CCATCATTCATCGAACTCGGTTC 59.754 47.826 0.00 6.68 38.97 3.62
64 65 3.198068 CCATCATTCATCGAACTCGGTT 58.802 45.455 0.00 0.00 40.29 4.44
65 66 2.168521 ACCATCATTCATCGAACTCGGT 59.831 45.455 0.00 0.00 40.29 4.69
66 67 2.826428 ACCATCATTCATCGAACTCGG 58.174 47.619 0.00 0.00 40.29 4.63
67 68 4.143242 GCATACCATCATTCATCGAACTCG 60.143 45.833 0.00 0.00 41.45 4.18
68 69 4.143242 CGCATACCATCATTCATCGAACTC 60.143 45.833 0.00 0.00 0.00 3.01
69 70 3.742882 CGCATACCATCATTCATCGAACT 59.257 43.478 0.00 0.00 0.00 3.01
70 71 3.120546 CCGCATACCATCATTCATCGAAC 60.121 47.826 0.00 0.00 0.00 3.95
71 72 3.066380 CCGCATACCATCATTCATCGAA 58.934 45.455 0.00 0.00 0.00 3.71
72 73 2.612721 CCCGCATACCATCATTCATCGA 60.613 50.000 0.00 0.00 0.00 3.59
73 74 1.733912 CCCGCATACCATCATTCATCG 59.266 52.381 0.00 0.00 0.00 3.84
74 75 1.470098 GCCCGCATACCATCATTCATC 59.530 52.381 0.00 0.00 0.00 2.92
75 76 1.538047 GCCCGCATACCATCATTCAT 58.462 50.000 0.00 0.00 0.00 2.57
76 77 0.537143 GGCCCGCATACCATCATTCA 60.537 55.000 0.00 0.00 0.00 2.57
77 78 0.250901 AGGCCCGCATACCATCATTC 60.251 55.000 0.00 0.00 0.00 2.67
78 79 0.185901 AAGGCCCGCATACCATCATT 59.814 50.000 0.00 0.00 0.00 2.57
79 80 0.250901 GAAGGCCCGCATACCATCAT 60.251 55.000 0.00 0.00 0.00 2.45
80 81 1.148273 GAAGGCCCGCATACCATCA 59.852 57.895 0.00 0.00 0.00 3.07
81 82 1.148273 TGAAGGCCCGCATACCATC 59.852 57.895 0.00 0.00 0.00 3.51
82 83 1.152963 GTGAAGGCCCGCATACCAT 60.153 57.895 0.00 0.00 0.00 3.55
83 84 1.847798 AAGTGAAGGCCCGCATACCA 61.848 55.000 0.00 0.00 0.00 3.25
84 85 0.179468 TAAGTGAAGGCCCGCATACC 59.821 55.000 0.00 0.00 0.00 2.73
85 86 1.138266 TCTAAGTGAAGGCCCGCATAC 59.862 52.381 0.00 0.00 0.00 2.39
86 87 1.138266 GTCTAAGTGAAGGCCCGCATA 59.862 52.381 0.00 0.00 0.00 3.14
87 88 0.107654 GTCTAAGTGAAGGCCCGCAT 60.108 55.000 0.00 0.00 0.00 4.73
88 89 1.295423 GTCTAAGTGAAGGCCCGCA 59.705 57.895 0.00 0.00 0.00 5.69
89 90 1.019805 GTGTCTAAGTGAAGGCCCGC 61.020 60.000 0.00 0.00 0.00 6.13
90 91 0.736325 CGTGTCTAAGTGAAGGCCCG 60.736 60.000 0.00 0.00 0.00 6.13
91 92 0.320697 ACGTGTCTAAGTGAAGGCCC 59.679 55.000 0.00 0.00 0.00 5.80
92 93 1.270147 ACACGTGTCTAAGTGAAGGCC 60.270 52.381 17.22 0.00 38.37 5.19
93 94 2.059541 GACACGTGTCTAAGTGAAGGC 58.940 52.381 35.51 10.35 41.65 4.35
94 95 3.050619 GTGACACGTGTCTAAGTGAAGG 58.949 50.000 39.62 4.72 44.99 3.46
95 96 2.719556 CGTGACACGTGTCTAAGTGAAG 59.280 50.000 39.62 22.12 44.99 3.02
96 97 2.723209 CGTGACACGTGTCTAAGTGAA 58.277 47.619 39.62 21.49 44.99 3.18
97 98 2.394545 CGTGACACGTGTCTAAGTGA 57.605 50.000 39.62 22.16 44.99 3.41
109 110 0.037605 CCACCTTCCCTACGTGACAC 60.038 60.000 0.00 0.00 0.00 3.67
110 111 1.823169 GCCACCTTCCCTACGTGACA 61.823 60.000 0.00 0.00 0.00 3.58
111 112 1.079336 GCCACCTTCCCTACGTGAC 60.079 63.158 0.00 0.00 0.00 3.67
112 113 2.642254 CGCCACCTTCCCTACGTGA 61.642 63.158 0.00 0.00 0.00 4.35
113 114 2.125673 CGCCACCTTCCCTACGTG 60.126 66.667 0.00 0.00 0.00 4.49
114 115 3.387947 CCGCCACCTTCCCTACGT 61.388 66.667 0.00 0.00 0.00 3.57
115 116 3.072468 TCCGCCACCTTCCCTACG 61.072 66.667 0.00 0.00 0.00 3.51
116 117 2.582978 GTCCGCCACCTTCCCTAC 59.417 66.667 0.00 0.00 0.00 3.18
117 118 3.072468 CGTCCGCCACCTTCCCTA 61.072 66.667 0.00 0.00 0.00 3.53
130 131 2.125512 ATCTCAACGGCTGCGTCC 60.126 61.111 0.00 0.00 0.00 4.79
131 132 2.167861 GGATCTCAACGGCTGCGTC 61.168 63.158 0.00 0.00 0.00 5.19
132 133 2.125512 GGATCTCAACGGCTGCGT 60.126 61.111 0.00 0.00 0.00 5.24
133 134 2.125552 TGGATCTCAACGGCTGCG 60.126 61.111 0.00 0.00 0.00 5.18
134 135 1.364626 CTGTGGATCTCAACGGCTGC 61.365 60.000 0.00 0.00 0.00 5.25
135 136 0.742281 CCTGTGGATCTCAACGGCTG 60.742 60.000 0.00 0.00 0.00 4.85
136 137 1.599047 CCTGTGGATCTCAACGGCT 59.401 57.895 0.00 0.00 0.00 5.52
137 138 1.450312 CCCTGTGGATCTCAACGGC 60.450 63.158 0.00 0.00 0.00 5.68
138 139 0.391661 CACCCTGTGGATCTCAACGG 60.392 60.000 0.00 0.00 34.81 4.44
139 140 0.608130 TCACCCTGTGGATCTCAACG 59.392 55.000 0.00 0.00 33.87 4.10
140 141 2.636830 CATCACCCTGTGGATCTCAAC 58.363 52.381 0.00 0.00 33.87 3.18
141 142 1.561076 CCATCACCCTGTGGATCTCAA 59.439 52.381 0.00 0.00 37.72 3.02
142 143 1.206878 CCATCACCCTGTGGATCTCA 58.793 55.000 0.00 0.00 37.72 3.27
143 144 1.134280 CACCATCACCCTGTGGATCTC 60.134 57.143 0.00 0.00 38.86 2.75
144 145 0.914644 CACCATCACCCTGTGGATCT 59.085 55.000 0.00 0.00 38.86 2.75
145 146 0.911769 TCACCATCACCCTGTGGATC 59.088 55.000 0.00 0.00 38.86 3.36
146 147 1.371467 TTCACCATCACCCTGTGGAT 58.629 50.000 0.00 0.00 38.86 3.41
147 148 1.073763 CTTTCACCATCACCCTGTGGA 59.926 52.381 0.00 0.00 38.86 4.02
148 149 1.202927 ACTTTCACCATCACCCTGTGG 60.203 52.381 0.00 0.00 41.35 4.17
149 150 2.276732 ACTTTCACCATCACCCTGTG 57.723 50.000 0.00 0.00 34.45 3.66
150 151 5.975988 ATATACTTTCACCATCACCCTGT 57.024 39.130 0.00 0.00 0.00 4.00
151 152 8.746052 TTTTATATACTTTCACCATCACCCTG 57.254 34.615 0.00 0.00 0.00 4.45
152 153 9.936329 AATTTTATATACTTTCACCATCACCCT 57.064 29.630 0.00 0.00 0.00 4.34
307 367 1.197492 CGTGCAATACAGCTGAAGCAA 59.803 47.619 23.35 6.60 45.16 3.91
320 380 4.284550 ACCCACCCTGCGTGCAAT 62.285 61.111 0.00 0.00 41.53 3.56
344 404 2.154462 GGCTATGGCTTCGCAACATAT 58.846 47.619 0.00 0.00 38.73 1.78
345 405 1.134250 TGGCTATGGCTTCGCAACATA 60.134 47.619 0.00 0.00 38.73 2.29
373 435 1.177256 GGATGCATGCAGGGCTTAGG 61.177 60.000 26.69 0.00 0.00 2.69
694 765 1.977129 GGATGATCTTCAGGAGAGGGG 59.023 57.143 10.48 0.00 37.93 4.79
697 768 4.439305 GATCGGATGATCTTCAGGAGAG 57.561 50.000 10.48 0.00 46.22 3.20
800 872 3.736126 CGACTTAACCCTAACCGCCTAAG 60.736 52.174 0.00 0.00 0.00 2.18
842 914 4.421948 ACGTATCTGGCTTCGTTTAAGAG 58.578 43.478 0.00 0.00 37.38 2.85
898 976 3.075884 ACGTAAACACGGGCATTATTGT 58.924 40.909 1.97 0.00 37.45 2.71
934 1012 1.513586 GCGTTCTTCGATCGTCCGT 60.514 57.895 15.94 0.00 42.86 4.69
980 1058 1.003118 TGGATCTGTGTTTTCCCGAGG 59.997 52.381 0.00 0.00 0.00 4.63
990 1068 3.507675 CATGGCCATGGATCTGTGT 57.492 52.632 34.31 0.00 35.24 3.72
1110 1197 2.338620 CACTTCACCGACCTCGCA 59.661 61.111 0.00 0.00 38.18 5.10
1122 1209 3.358076 CTCGAGGTCGCCCCACTTC 62.358 68.421 3.91 0.00 39.60 3.01
1280 1367 1.473278 GGACGAACTTCTGAGGATCGT 59.527 52.381 21.42 21.42 45.79 3.73
1313 1400 0.848942 CTGAAATCGACCGCAGATCG 59.151 55.000 4.70 0.00 38.08 3.69
1314 1401 1.202417 TCCTGAAATCGACCGCAGATC 60.202 52.381 10.73 0.00 0.00 2.75
1405 1493 1.065273 CGCCATGAGCCATTTGAGC 59.935 57.895 0.00 0.00 38.78 4.26
1444 1532 1.153147 GAAGAATCCCACGAGGCCC 60.153 63.158 0.00 0.00 34.51 5.80
1538 1626 2.362120 ATGTCTGGCAGGCAAGGC 60.362 61.111 27.32 0.00 31.33 4.35
1600 1688 2.550423 CCACAGAGATGGAGATGATGCC 60.550 54.545 0.00 0.00 43.02 4.40
1866 1954 4.455877 GGTCCCAAAGTCATCACAACTTAG 59.544 45.833 0.00 0.00 35.96 2.18
1876 1964 1.067295 TCTGCAGGTCCCAAAGTCAT 58.933 50.000 15.13 0.00 0.00 3.06
1877 1965 1.067295 ATCTGCAGGTCCCAAAGTCA 58.933 50.000 15.13 0.00 0.00 3.41
1878 1966 2.206576 AATCTGCAGGTCCCAAAGTC 57.793 50.000 15.13 0.00 0.00 3.01
2007 2095 1.549170 AGTTCCACGTGAGACCATACC 59.451 52.381 19.30 0.00 0.00 2.73
2014 2102 1.546029 CTGATCCAGTTCCACGTGAGA 59.454 52.381 19.30 9.99 0.00 3.27
2179 2267 5.627499 TTGGAAATAGAACATGCACAGTC 57.373 39.130 0.00 0.00 0.00 3.51
2241 2329 6.475596 TCCCAAGGTATAAACACTAGTAGC 57.524 41.667 0.00 0.00 0.00 3.58
2256 2344 3.037549 TGAAATTGCACTTTCCCAAGGT 58.962 40.909 22.36 0.00 34.83 3.50
2283 2371 9.246670 AGATGATGAATTTATCTGAAACCAACA 57.753 29.630 11.13 0.00 30.41 3.33
2384 2472 7.415770 TTGAAAAACAAAGGCAAATTCGCCG 62.416 40.000 0.72 0.00 44.38 6.46
2385 2473 4.201861 TTGAAAAACAAAGGCAAATTCGCC 60.202 37.500 0.00 0.00 42.05 5.54
2400 2488 2.882761 AGAGTAGCCCGGTTTGAAAAAC 59.117 45.455 0.00 0.00 0.00 2.43
2401 2489 2.882137 CAGAGTAGCCCGGTTTGAAAAA 59.118 45.455 0.00 0.00 0.00 1.94
2418 2506 8.778358 GTTATTATGAAAGTAATGGGAGCAGAG 58.222 37.037 0.00 0.00 0.00 3.35
2421 2509 8.271458 TCTGTTATTATGAAAGTAATGGGAGCA 58.729 33.333 0.00 0.00 0.00 4.26
2422 2510 8.677148 TCTGTTATTATGAAAGTAATGGGAGC 57.323 34.615 0.00 0.00 0.00 4.70
2435 2523 7.466804 AGGACAAAGGGTTTCTGTTATTATGA 58.533 34.615 0.00 0.00 0.00 2.15
2439 2527 6.265422 CAGAAGGACAAAGGGTTTCTGTTATT 59.735 38.462 4.77 0.00 39.71 1.40
2466 2554 2.681778 ACTCCGCCACCTGAGAGG 60.682 66.667 0.00 0.00 42.49 3.69
2517 2605 2.517450 GCAGCACTATCGCCGACAC 61.517 63.158 0.00 0.00 0.00 3.67
2779 2867 4.863152 GAAGCTCTCTCAGAAATGCTTC 57.137 45.455 15.66 15.66 45.72 3.86
2790 2878 2.564947 TCCAACTTCCTGAAGCTCTCTC 59.435 50.000 6.81 0.00 41.99 3.20
2842 2930 1.944676 GAGGATCTTGTACGGCGCG 60.945 63.158 6.90 0.00 0.00 6.86
3142 3230 0.824109 CGTAGGTGATCAGGCCAAGA 59.176 55.000 5.01 2.09 0.00 3.02
3400 3488 4.250305 AAGCAGTCCGCCACCGTT 62.250 61.111 0.00 0.00 44.04 4.44
3664 3752 1.156645 GCAGCACGATCAGATGGGAC 61.157 60.000 0.00 0.00 0.00 4.46
3670 3758 0.733909 CGTTGAGCAGCACGATCAGA 60.734 55.000 0.00 0.00 42.01 3.27
3751 3839 1.741770 CTTGGCGAAGTCGAAGGGG 60.742 63.158 4.59 0.00 43.02 4.79
3881 3969 1.639298 GCCAGCGACATGTTCTCCAC 61.639 60.000 0.00 0.00 0.00 4.02
4136 4224 0.394352 AAAATGCCCGGCGATCTTCT 60.394 50.000 9.30 0.00 0.00 2.85
4146 4235 7.481275 AAAATATATGCAAAGAAAATGCCCG 57.519 32.000 0.00 0.00 43.16 6.13
4148 4237 8.003784 GCGTAAAATATATGCAAAGAAAATGCC 58.996 33.333 0.00 0.00 43.16 4.40
4149 4238 8.538856 TGCGTAAAATATATGCAAAGAAAATGC 58.461 29.630 0.00 0.00 44.08 3.56
4343 4444 7.712639 AGTCAGCACTAATTATCGATGATTTGT 59.287 33.333 19.13 19.17 0.00 2.83
4378 4479 6.600388 TCAGGCATGCCAATAAAATAGTCTA 58.400 36.000 37.18 1.39 38.92 2.59
4379 4480 5.448654 TCAGGCATGCCAATAAAATAGTCT 58.551 37.500 37.18 10.08 38.92 3.24
4380 4481 5.772825 TCAGGCATGCCAATAAAATAGTC 57.227 39.130 37.18 6.57 38.92 2.59
4381 4482 7.093640 CCATATCAGGCATGCCAATAAAATAGT 60.094 37.037 37.18 15.17 38.92 2.12
4382 4483 7.123098 TCCATATCAGGCATGCCAATAAAATAG 59.877 37.037 37.18 17.78 38.92 1.73
4383 4484 6.952938 TCCATATCAGGCATGCCAATAAAATA 59.047 34.615 37.18 22.46 38.92 1.40
4384 4485 5.781306 TCCATATCAGGCATGCCAATAAAAT 59.219 36.000 37.18 21.21 38.92 1.82
4385 4486 5.146298 TCCATATCAGGCATGCCAATAAAA 58.854 37.500 37.18 17.92 38.92 1.52
4386 4487 4.738685 TCCATATCAGGCATGCCAATAAA 58.261 39.130 37.18 18.99 38.92 1.40
4387 4488 4.385478 TCCATATCAGGCATGCCAATAA 57.615 40.909 37.18 20.43 38.92 1.40
4388 4489 4.596354 ATCCATATCAGGCATGCCAATA 57.404 40.909 37.18 30.38 38.92 1.90
4389 4490 2.984435 TCCATATCAGGCATGCCAAT 57.016 45.000 37.18 29.36 38.92 3.16
4390 4491 2.894765 CAATCCATATCAGGCATGCCAA 59.105 45.455 37.18 25.18 38.92 4.52
4391 4492 2.108601 TCAATCCATATCAGGCATGCCA 59.891 45.455 37.18 19.62 38.92 4.92
4483 4584 2.240040 GTGGCGCGTATAAGATCGTAG 58.760 52.381 8.43 0.00 0.00 3.51
4484 4585 1.069022 GGTGGCGCGTATAAGATCGTA 60.069 52.381 8.43 0.00 0.00 3.43
4485 4586 0.318445 GGTGGCGCGTATAAGATCGT 60.318 55.000 8.43 0.00 0.00 3.73
4486 4587 0.318360 TGGTGGCGCGTATAAGATCG 60.318 55.000 8.43 0.00 0.00 3.69
4487 4588 1.137513 GTGGTGGCGCGTATAAGATC 58.862 55.000 8.43 0.00 0.00 2.75
4488 4589 0.249741 GGTGGTGGCGCGTATAAGAT 60.250 55.000 8.43 0.00 0.00 2.40
4489 4590 1.142314 GGTGGTGGCGCGTATAAGA 59.858 57.895 8.43 0.00 0.00 2.10
4490 4591 0.531974 ATGGTGGTGGCGCGTATAAG 60.532 55.000 8.43 0.00 0.00 1.73
4491 4592 0.812014 CATGGTGGTGGCGCGTATAA 60.812 55.000 8.43 0.00 0.00 0.98
4517 4618 0.666577 GACAGTTTCTCCCACCGACG 60.667 60.000 0.00 0.00 0.00 5.12
4518 4619 0.320508 GGACAGTTTCTCCCACCGAC 60.321 60.000 0.00 0.00 0.00 4.79
4519 4620 0.761323 TGGACAGTTTCTCCCACCGA 60.761 55.000 0.00 0.00 0.00 4.69
4520 4621 0.320771 CTGGACAGTTTCTCCCACCG 60.321 60.000 0.00 0.00 0.00 4.94
4521 4622 0.765510 ACTGGACAGTTTCTCCCACC 59.234 55.000 0.00 0.00 38.83 4.61
4522 4623 2.367567 TGTACTGGACAGTTTCTCCCAC 59.632 50.000 10.57 1.63 42.54 4.61
4537 4638 4.755123 CCCTTAGACACCAAAACTGTACTG 59.245 45.833 0.00 0.00 0.00 2.74
4697 4798 7.963465 GCTCATCACGAGAATATAACGAAGATA 59.037 37.037 0.00 0.00 45.45 1.98
4715 5273 0.031449 GCCTCCTCGTAGCTCATCAC 59.969 60.000 0.00 0.00 0.00 3.06
4728 5286 1.274416 TGAAAGGTAGGGATGCCTCCT 60.274 52.381 10.00 13.56 41.74 3.69
4762 5320 0.750249 GAGGAGAGTAGCTGGGCTTC 59.250 60.000 0.00 0.00 40.44 3.86
4796 5354 2.345560 ACAGTTAAGGTGGCCTTAGGT 58.654 47.619 3.32 5.75 45.40 3.08
4913 6521 0.322816 TGCTGGCTTCTTCCATGGAC 60.323 55.000 15.91 1.74 35.22 4.02
5037 6645 1.228245 AAGGGTTCTGTGCATGCGT 60.228 52.632 14.09 0.00 0.00 5.24
5038 6646 1.210931 CAAGGGTTCTGTGCATGCG 59.789 57.895 14.09 0.00 0.00 4.73
5039 6647 0.242017 GTCAAGGGTTCTGTGCATGC 59.758 55.000 11.82 11.82 0.00 4.06
5040 6648 1.901591 AGTCAAGGGTTCTGTGCATG 58.098 50.000 0.00 0.00 0.00 4.06
5041 6649 2.664402 AAGTCAAGGGTTCTGTGCAT 57.336 45.000 0.00 0.00 0.00 3.96
5042 6650 3.569194 TTAAGTCAAGGGTTCTGTGCA 57.431 42.857 0.00 0.00 0.00 4.57
5043 6651 5.221244 ACAAATTAAGTCAAGGGTTCTGTGC 60.221 40.000 0.00 0.00 0.00 4.57
5044 6652 6.391227 ACAAATTAAGTCAAGGGTTCTGTG 57.609 37.500 0.00 0.00 0.00 3.66
5045 6653 7.778382 ACTAACAAATTAAGTCAAGGGTTCTGT 59.222 33.333 0.00 0.00 0.00 3.41
5046 6654 8.166422 ACTAACAAATTAAGTCAAGGGTTCTG 57.834 34.615 0.00 0.00 0.00 3.02
5067 6675 9.640952 CCAAATCCTTCCCTTTGATAATACTAA 57.359 33.333 0.00 0.00 34.93 2.24
5068 6676 9.009675 TCCAAATCCTTCCCTTTGATAATACTA 57.990 33.333 0.00 0.00 34.93 1.82
5069 6677 7.882755 TCCAAATCCTTCCCTTTGATAATACT 58.117 34.615 0.00 0.00 34.93 2.12
5070 6678 8.533569 TTCCAAATCCTTCCCTTTGATAATAC 57.466 34.615 0.00 0.00 34.93 1.89
5071 6679 9.200817 CTTTCCAAATCCTTCCCTTTGATAATA 57.799 33.333 0.00 0.00 34.93 0.98
5072 6680 7.679881 ACTTTCCAAATCCTTCCCTTTGATAAT 59.320 33.333 0.00 0.00 34.93 1.28
5073 6681 7.016296 ACTTTCCAAATCCTTCCCTTTGATAA 58.984 34.615 0.00 0.00 34.93 1.75
5074 6682 6.437162 CACTTTCCAAATCCTTCCCTTTGATA 59.563 38.462 0.00 0.00 34.93 2.15
5075 6683 5.246883 CACTTTCCAAATCCTTCCCTTTGAT 59.753 40.000 0.00 0.00 34.93 2.57
5076 6684 4.588528 CACTTTCCAAATCCTTCCCTTTGA 59.411 41.667 0.00 0.00 34.93 2.69
5077 6685 4.588528 TCACTTTCCAAATCCTTCCCTTTG 59.411 41.667 0.00 0.00 33.20 2.77
5078 6686 4.814967 TCACTTTCCAAATCCTTCCCTTT 58.185 39.130 0.00 0.00 0.00 3.11
5079 6687 4.469469 TCACTTTCCAAATCCTTCCCTT 57.531 40.909 0.00 0.00 0.00 3.95
5080 6688 4.682021 ATCACTTTCCAAATCCTTCCCT 57.318 40.909 0.00 0.00 0.00 4.20
5081 6689 5.724328 GAAATCACTTTCCAAATCCTTCCC 58.276 41.667 0.00 0.00 35.69 3.97
5092 6700 7.605449 TTGATCAATCAAGGAAATCACTTTCC 58.395 34.615 3.38 8.71 45.19 3.13
5093 6701 9.480053 TTTTGATCAATCAAGGAAATCACTTTC 57.520 29.630 9.40 0.00 46.34 2.62
5094 6702 9.264719 GTTTTGATCAATCAAGGAAATCACTTT 57.735 29.630 9.40 0.00 46.34 2.66
5095 6703 8.645110 AGTTTTGATCAATCAAGGAAATCACTT 58.355 29.630 9.40 0.00 46.34 3.16
5096 6704 8.186709 AGTTTTGATCAATCAAGGAAATCACT 57.813 30.769 9.40 0.00 46.34 3.41
5097 6705 9.912634 TTAGTTTTGATCAATCAAGGAAATCAC 57.087 29.630 9.40 0.00 46.34 3.06


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

AutoCloner maintained by Alex Coulton.