Multiple sequence alignment - TraesCS3D01G446900

Loading Multiple Alignment...

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 TraesCS3D01G446900 chr3D 100.000 2993 0 0 1 2993 555531103 555534095 0.000000e+00 5528.0
1 TraesCS3D01G446900 chr3D 92.581 310 17 3 2667 2975 206173118 206172814 9.850000e-120 440.0
2 TraesCS3D01G446900 chr3D 82.639 288 23 9 2445 2713 206174084 206173805 2.320000e-56 230.0
3 TraesCS3D01G446900 chr3D 80.085 236 43 4 998 1231 612263738 612263971 3.970000e-39 172.0
4 TraesCS3D01G446900 chr3D 76.705 176 27 12 2453 2619 546262025 546262195 5.320000e-13 86.1
5 TraesCS3D01G446900 chr3B 93.985 2211 109 12 247 2452 738716155 738718346 0.000000e+00 3325.0
6 TraesCS3D01G446900 chr3B 77.709 1624 243 66 737 2302 617439571 617438009 0.000000e+00 883.0
7 TraesCS3D01G446900 chr3B 86.765 204 22 3 49 251 738705673 738705872 3.880000e-54 222.0
8 TraesCS3D01G446900 chr3A 94.196 2033 105 6 173 2199 692676800 692678825 0.000000e+00 3088.0
9 TraesCS3D01G446900 chr3A 81.456 1030 185 5 1003 2028 607234405 607233378 0.000000e+00 839.0
10 TraesCS3D01G446900 chr3A 80.927 928 169 5 1003 1923 607146282 607145356 0.000000e+00 726.0
11 TraesCS3D01G446900 chr3A 94.562 331 17 1 2664 2993 748847319 748846989 7.400000e-141 510.0
12 TraesCS3D01G446900 chr3A 94.961 258 11 2 2196 2452 692693836 692694092 1.290000e-108 403.0
13 TraesCS3D01G446900 chr3A 90.541 148 7 1 2453 2593 748847469 748847322 3.940000e-44 189.0
14 TraesCS3D01G446900 chr3A 89.922 129 10 3 49 175 692628679 692628806 2.390000e-36 163.0
15 TraesCS3D01G446900 chr3A 79.386 228 47 0 1298 1525 746901037 746901264 8.590000e-36 161.0
16 TraesCS3D01G446900 chr3A 77.528 178 26 12 2451 2619 716904042 716904214 8.830000e-16 95.3
17 TraesCS3D01G446900 chr3A 91.667 60 5 0 2600 2659 748847340 748847281 1.910000e-12 84.2
18 TraesCS3D01G446900 chr5D 81.087 1877 276 39 614 2452 8594120 8592285 0.000000e+00 1426.0
19 TraesCS3D01G446900 chr5A 80.109 1830 295 36 655 2452 6774559 6772767 0.000000e+00 1299.0
20 TraesCS3D01G446900 chr5A 92.523 321 18 3 2656 2975 25130625 25130310 3.520000e-124 455.0
21 TraesCS3D01G446900 chr5A 79.261 352 51 6 2110 2452 14854807 14854469 3.000000e-55 226.0
22 TraesCS3D01G446900 chr5A 82.796 279 23 7 2453 2713 25130979 25130708 3.000000e-55 226.0
23 TraesCS3D01G446900 chr5A 76.836 177 27 12 2452 2619 268039981 268040152 1.480000e-13 87.9
24 TraesCS3D01G446900 chr4D 92.523 321 18 3 2656 2975 490888109 490887794 3.520000e-124 455.0
25 TraesCS3D01G446900 chr4D 82.796 279 23 7 2453 2713 490888463 490888192 3.000000e-55 226.0
26 TraesCS3D01G446900 chr4D 100.000 30 0 0 2016 2045 3717804 3717775 4.170000e-04 56.5
27 TraesCS3D01G446900 chr6D 90.517 348 21 5 2622 2968 378803906 378804242 1.640000e-122 449.0
28 TraesCS3D01G446900 chr6D 82.971 276 22 7 2453 2710 378803578 378803846 3.000000e-55 226.0
29 TraesCS3D01G446900 chr6D 73.889 540 112 21 1001 1515 427170924 427171459 3.940000e-44 189.0
30 TraesCS3D01G446900 chrUn 92.581 310 17 3 2667 2975 345163865 345163561 9.850000e-120 440.0
31 TraesCS3D01G446900 chrUn 90.984 122 10 1 54 175 264502424 264502304 2.390000e-36 163.0
32 TraesCS3D01G446900 chr1A 92.903 155 11 0 2839 2993 63755190 63755036 3.000000e-55 226.0
33 TraesCS3D01G446900 chr1A 84.659 176 11 8 2656 2815 63755359 63755184 8.590000e-36 161.0
34 TraesCS3D01G446900 chr1A 77.095 179 27 12 2450 2619 536686508 536686335 1.140000e-14 91.6
35 TraesCS3D01G446900 chr1A 86.792 53 5 2 2708 2758 536686081 536686029 1.160000e-04 58.4
36 TraesCS3D01G446900 chr6B 74.535 538 112 16 1001 1515 643131464 643131999 8.410000e-51 211.0
37 TraesCS3D01G446900 chr6B 74.109 533 117 17 1001 1515 642989559 642990088 1.820000e-47 200.0
38 TraesCS3D01G446900 chr6B 77.273 176 26 12 2453 2619 48068897 48068727 1.140000e-14 91.6
39 TraesCS3D01G446900 chr6A 73.308 532 123 14 1001 1515 571881423 571881952 8.530000e-41 178.0
40 TraesCS3D01G446900 chr6A 77.273 176 26 12 2453 2619 545334028 545334198 1.140000e-14 91.6
41 TraesCS3D01G446900 chr2B 77.273 176 26 12 2453 2619 576574644 576574474 1.140000e-14 91.6
42 TraesCS3D01G446900 chr7D 87.719 57 6 1 2699 2754 629589209 629589265 6.930000e-07 65.8


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 TraesCS3D01G446900 chr3D 555531103 555534095 2992 False 5528.0 5528 100.0000 1 2993 1 chr3D.!!$F2 2992
1 TraesCS3D01G446900 chr3D 206172814 206174084 1270 True 335.0 440 87.6100 2445 2975 2 chr3D.!!$R1 530
2 TraesCS3D01G446900 chr3B 738716155 738718346 2191 False 3325.0 3325 93.9850 247 2452 1 chr3B.!!$F2 2205
3 TraesCS3D01G446900 chr3B 617438009 617439571 1562 True 883.0 883 77.7090 737 2302 1 chr3B.!!$R1 1565
4 TraesCS3D01G446900 chr3A 692676800 692678825 2025 False 3088.0 3088 94.1960 173 2199 1 chr3A.!!$F2 2026
5 TraesCS3D01G446900 chr3A 607233378 607234405 1027 True 839.0 839 81.4560 1003 2028 1 chr3A.!!$R2 1025
6 TraesCS3D01G446900 chr3A 607145356 607146282 926 True 726.0 726 80.9270 1003 1923 1 chr3A.!!$R1 920
7 TraesCS3D01G446900 chr5D 8592285 8594120 1835 True 1426.0 1426 81.0870 614 2452 1 chr5D.!!$R1 1838
8 TraesCS3D01G446900 chr5A 6772767 6774559 1792 True 1299.0 1299 80.1090 655 2452 1 chr5A.!!$R1 1797
9 TraesCS3D01G446900 chr5A 25130310 25130979 669 True 340.5 455 87.6595 2453 2975 2 chr5A.!!$R3 522
10 TraesCS3D01G446900 chr4D 490887794 490888463 669 True 340.5 455 87.6595 2453 2975 2 chr4D.!!$R2 522
11 TraesCS3D01G446900 chr6D 378803578 378804242 664 False 337.5 449 86.7440 2453 2968 2 chr6D.!!$F2 515
12 TraesCS3D01G446900 chr6B 643131464 643131999 535 False 211.0 211 74.5350 1001 1515 1 chr6B.!!$F2 514

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
126 127 0.038892 CATGCAACCAACAGAGGTGC 60.039 55.0 0.00 0.0 42.25 5.01 F
127 128 0.178981 ATGCAACCAACAGAGGTGCT 60.179 50.0 2.15 0.0 42.25 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2054 2.672908 CCCTGCTGCACCATCTCA 59.327 61.111 0.0 0.0 0.0 3.27 R
2107 2225 6.992063 AACTAGAGTGGCAATGAACTAATG 57.008 37.500 0.0 0.0 0.0 1.90 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 3.935993 CTGTTCGACCACTCCCAAT 57.064 52.632 0.00 0.00 0.00 3.16
19 20 1.726853 CTGTTCGACCACTCCCAATC 58.273 55.000 0.00 0.00 0.00 2.67
20 21 0.323629 TGTTCGACCACTCCCAATCC 59.676 55.000 0.00 0.00 0.00 3.01
21 22 0.323629 GTTCGACCACTCCCAATCCA 59.676 55.000 0.00 0.00 0.00 3.41
22 23 0.323629 TTCGACCACTCCCAATCCAC 59.676 55.000 0.00 0.00 0.00 4.02
23 24 1.447838 CGACCACTCCCAATCCACG 60.448 63.158 0.00 0.00 0.00 4.94
24 25 1.884075 CGACCACTCCCAATCCACGA 61.884 60.000 0.00 0.00 0.00 4.35
25 26 0.541863 GACCACTCCCAATCCACGAT 59.458 55.000 0.00 0.00 0.00 3.73
26 27 0.253044 ACCACTCCCAATCCACGATG 59.747 55.000 0.00 0.00 0.00 3.84
27 28 0.253044 CCACTCCCAATCCACGATGT 59.747 55.000 0.00 0.00 0.00 3.06
28 29 1.656652 CACTCCCAATCCACGATGTC 58.343 55.000 0.00 0.00 0.00 3.06
29 30 1.066215 CACTCCCAATCCACGATGTCA 60.066 52.381 0.00 0.00 0.00 3.58
30 31 1.839994 ACTCCCAATCCACGATGTCAT 59.160 47.619 0.00 0.00 0.00 3.06
31 32 3.038280 ACTCCCAATCCACGATGTCATA 58.962 45.455 0.00 0.00 0.00 2.15
32 33 3.648067 ACTCCCAATCCACGATGTCATAT 59.352 43.478 0.00 0.00 0.00 1.78
33 34 4.248859 CTCCCAATCCACGATGTCATATC 58.751 47.826 0.00 0.00 0.00 1.63
34 35 3.645687 TCCCAATCCACGATGTCATATCA 59.354 43.478 0.00 0.00 0.00 2.15
35 36 4.102367 TCCCAATCCACGATGTCATATCAA 59.898 41.667 0.00 0.00 0.00 2.57
36 37 4.214119 CCCAATCCACGATGTCATATCAAC 59.786 45.833 0.00 0.00 0.00 3.18
37 38 4.214119 CCAATCCACGATGTCATATCAACC 59.786 45.833 0.00 0.00 0.00 3.77
38 39 4.687901 ATCCACGATGTCATATCAACCA 57.312 40.909 0.00 0.00 0.00 3.67
39 40 4.687901 TCCACGATGTCATATCAACCAT 57.312 40.909 0.00 0.00 0.00 3.55
40 41 4.631131 TCCACGATGTCATATCAACCATC 58.369 43.478 0.00 0.00 0.00 3.51
41 42 3.748048 CCACGATGTCATATCAACCATCC 59.252 47.826 0.00 0.00 32.03 3.51
42 43 4.379652 CACGATGTCATATCAACCATCCA 58.620 43.478 0.00 0.00 32.03 3.41
43 44 4.815846 CACGATGTCATATCAACCATCCAA 59.184 41.667 0.00 0.00 32.03 3.53
44 45 5.296531 CACGATGTCATATCAACCATCCAAA 59.703 40.000 0.00 0.00 32.03 3.28
45 46 5.885352 ACGATGTCATATCAACCATCCAAAA 59.115 36.000 0.00 0.00 32.03 2.44
46 47 6.547141 ACGATGTCATATCAACCATCCAAAAT 59.453 34.615 0.00 0.00 32.03 1.82
47 48 7.068593 ACGATGTCATATCAACCATCCAAAATT 59.931 33.333 0.00 0.00 32.03 1.82
48 49 7.380333 CGATGTCATATCAACCATCCAAAATTG 59.620 37.037 0.00 0.00 32.03 2.32
60 61 0.461135 CAAAATTGGATCCAGGCGGG 59.539 55.000 15.53 0.00 38.37 6.13
68 69 3.948719 TCCAGGCGGGAACACCAC 61.949 66.667 3.10 0.00 44.80 4.16
70 71 4.308458 CAGGCGGGAACACCACGA 62.308 66.667 0.00 0.00 40.22 4.35
71 72 4.003788 AGGCGGGAACACCACGAG 62.004 66.667 0.00 0.00 40.22 4.18
74 75 4.308458 CGGGAACACCACGAGGCA 62.308 66.667 0.00 0.00 40.22 4.75
75 76 2.112297 GGGAACACCACGAGGCAA 59.888 61.111 0.00 0.00 39.85 4.52
76 77 1.303317 GGGAACACCACGAGGCAAT 60.303 57.895 0.00 0.00 39.85 3.56
77 78 1.586154 GGGAACACCACGAGGCAATG 61.586 60.000 0.00 0.00 39.85 2.82
78 79 1.586154 GGAACACCACGAGGCAATGG 61.586 60.000 0.00 0.61 42.13 3.16
79 80 1.586154 GAACACCACGAGGCAATGGG 61.586 60.000 0.00 0.00 40.59 4.00
80 81 2.034066 CACCACGAGGCAATGGGT 59.966 61.111 0.00 0.00 40.59 4.51
81 82 2.034066 ACCACGAGGCAATGGGTG 59.966 61.111 0.00 0.00 40.59 4.61
82 83 2.034066 CCACGAGGCAATGGGTGT 59.966 61.111 0.00 0.00 31.83 4.16
83 84 2.040544 CCACGAGGCAATGGGTGTC 61.041 63.158 0.00 0.00 31.83 3.67
84 85 1.302431 CACGAGGCAATGGGTGTCA 60.302 57.895 0.00 0.00 32.63 3.58
85 86 1.003355 ACGAGGCAATGGGTGTCAG 60.003 57.895 0.00 0.00 32.63 3.51
86 87 1.296392 CGAGGCAATGGGTGTCAGA 59.704 57.895 0.00 0.00 32.63 3.27
87 88 0.321564 CGAGGCAATGGGTGTCAGAA 60.322 55.000 0.00 0.00 32.63 3.02
88 89 1.168714 GAGGCAATGGGTGTCAGAAC 58.831 55.000 0.00 0.00 32.63 3.01
89 90 0.478072 AGGCAATGGGTGTCAGAACA 59.522 50.000 0.00 0.00 32.63 3.18
90 91 1.076024 AGGCAATGGGTGTCAGAACAT 59.924 47.619 0.00 0.00 37.81 2.71
91 92 1.895131 GGCAATGGGTGTCAGAACATT 59.105 47.619 0.00 0.00 37.81 2.71
93 94 2.353011 GCAATGGGTGTCAGAACATTGG 60.353 50.000 18.35 7.24 46.20 3.16
94 95 3.156293 CAATGGGTGTCAGAACATTGGA 58.844 45.455 12.77 0.00 43.81 3.53
95 96 3.524095 ATGGGTGTCAGAACATTGGAA 57.476 42.857 0.00 0.00 37.81 3.53
96 97 3.304911 TGGGTGTCAGAACATTGGAAA 57.695 42.857 0.00 0.00 37.81 3.13
97 98 3.221771 TGGGTGTCAGAACATTGGAAAG 58.778 45.455 0.00 0.00 37.81 2.62
98 99 2.558359 GGGTGTCAGAACATTGGAAAGG 59.442 50.000 0.00 0.00 37.81 3.11
99 100 2.029918 GGTGTCAGAACATTGGAAAGGC 60.030 50.000 0.00 0.00 37.81 4.35
100 101 2.622942 GTGTCAGAACATTGGAAAGGCA 59.377 45.455 0.00 0.00 37.81 4.75
101 102 3.068024 GTGTCAGAACATTGGAAAGGCAA 59.932 43.478 0.00 0.00 37.81 4.52
102 103 3.068024 TGTCAGAACATTGGAAAGGCAAC 59.932 43.478 0.00 0.00 0.00 4.17
103 104 3.068024 GTCAGAACATTGGAAAGGCAACA 59.932 43.478 0.00 0.00 41.41 3.33
104 105 3.703556 TCAGAACATTGGAAAGGCAACAA 59.296 39.130 0.00 0.00 41.41 2.83
105 106 3.803778 CAGAACATTGGAAAGGCAACAAC 59.196 43.478 0.00 0.00 41.41 3.32
106 107 3.450457 AGAACATTGGAAAGGCAACAACA 59.550 39.130 0.00 0.00 41.41 3.33
107 108 3.177997 ACATTGGAAAGGCAACAACAC 57.822 42.857 0.00 0.00 41.41 3.32
108 109 2.499289 ACATTGGAAAGGCAACAACACA 59.501 40.909 0.00 0.00 41.41 3.72
109 110 3.134442 ACATTGGAAAGGCAACAACACAT 59.866 39.130 0.00 0.00 41.41 3.21
110 111 2.886862 TGGAAAGGCAACAACACATG 57.113 45.000 0.00 0.00 41.41 3.21
111 112 1.202510 TGGAAAGGCAACAACACATGC 60.203 47.619 0.00 0.00 41.82 4.06
112 113 1.202510 GGAAAGGCAACAACACATGCA 60.203 47.619 0.00 0.00 44.32 3.96
113 114 2.548875 GAAAGGCAACAACACATGCAA 58.451 42.857 0.00 0.00 44.32 4.08
114 115 1.938625 AAGGCAACAACACATGCAAC 58.061 45.000 0.00 0.00 44.32 4.17
115 116 0.104671 AGGCAACAACACATGCAACC 59.895 50.000 0.00 0.00 44.32 3.77
116 117 0.179089 GGCAACAACACATGCAACCA 60.179 50.000 0.00 0.00 44.32 3.67
117 118 1.649664 GCAACAACACATGCAACCAA 58.350 45.000 0.00 0.00 42.12 3.67
118 119 1.327156 GCAACAACACATGCAACCAAC 59.673 47.619 0.00 0.00 42.12 3.77
119 120 2.614779 CAACAACACATGCAACCAACA 58.385 42.857 0.00 0.00 0.00 3.33
120 121 2.582728 ACAACACATGCAACCAACAG 57.417 45.000 0.00 0.00 0.00 3.16
121 122 2.098614 ACAACACATGCAACCAACAGA 58.901 42.857 0.00 0.00 0.00 3.41
122 123 2.099592 ACAACACATGCAACCAACAGAG 59.900 45.455 0.00 0.00 0.00 3.35
123 124 1.321474 ACACATGCAACCAACAGAGG 58.679 50.000 0.00 0.00 0.00 3.69
124 125 1.321474 CACATGCAACCAACAGAGGT 58.679 50.000 0.00 0.00 45.91 3.85
125 126 1.001048 CACATGCAACCAACAGAGGTG 60.001 52.381 0.00 0.00 42.25 4.00
126 127 0.038892 CATGCAACCAACAGAGGTGC 60.039 55.000 0.00 0.00 42.25 5.01
127 128 0.178981 ATGCAACCAACAGAGGTGCT 60.179 50.000 2.15 0.00 42.25 4.40
128 129 0.472044 TGCAACCAACAGAGGTGCTA 59.528 50.000 2.15 0.00 42.25 3.49
129 130 1.073763 TGCAACCAACAGAGGTGCTAT 59.926 47.619 2.15 0.00 42.25 2.97
130 131 2.304470 TGCAACCAACAGAGGTGCTATA 59.696 45.455 2.15 0.00 42.25 1.31
131 132 3.054434 TGCAACCAACAGAGGTGCTATAT 60.054 43.478 2.15 0.00 42.25 0.86
132 133 3.313526 GCAACCAACAGAGGTGCTATATG 59.686 47.826 0.00 0.00 42.25 1.78
133 134 4.517285 CAACCAACAGAGGTGCTATATGT 58.483 43.478 0.00 0.00 42.25 2.29
134 135 4.408182 ACCAACAGAGGTGCTATATGTC 57.592 45.455 0.00 0.00 41.30 3.06
135 136 3.134804 ACCAACAGAGGTGCTATATGTCC 59.865 47.826 0.00 0.00 41.30 4.02
136 137 3.389329 CCAACAGAGGTGCTATATGTCCT 59.611 47.826 0.00 0.00 0.00 3.85
137 138 4.588951 CCAACAGAGGTGCTATATGTCCTA 59.411 45.833 0.00 0.00 0.00 2.94
138 139 5.247110 CCAACAGAGGTGCTATATGTCCTAT 59.753 44.000 0.00 0.00 0.00 2.57
139 140 6.393990 CAACAGAGGTGCTATATGTCCTATC 58.606 44.000 0.00 0.00 0.00 2.08
140 141 5.020132 ACAGAGGTGCTATATGTCCTATCC 58.980 45.833 0.00 0.00 0.00 2.59
141 142 4.404073 CAGAGGTGCTATATGTCCTATCCC 59.596 50.000 0.00 0.00 0.00 3.85
142 143 4.045974 AGAGGTGCTATATGTCCTATCCCA 59.954 45.833 0.00 0.00 0.00 4.37
143 144 4.097418 AGGTGCTATATGTCCTATCCCAC 58.903 47.826 0.00 0.00 0.00 4.61
144 145 3.119101 GGTGCTATATGTCCTATCCCACG 60.119 52.174 0.00 0.00 0.00 4.94
145 146 3.762288 GTGCTATATGTCCTATCCCACGA 59.238 47.826 0.00 0.00 0.00 4.35
146 147 3.762288 TGCTATATGTCCTATCCCACGAC 59.238 47.826 0.00 0.00 0.00 4.34
147 148 3.762288 GCTATATGTCCTATCCCACGACA 59.238 47.826 0.00 0.00 40.58 4.35
148 149 4.219944 GCTATATGTCCTATCCCACGACAA 59.780 45.833 0.00 0.00 39.78 3.18
149 150 2.981859 ATGTCCTATCCCACGACAAC 57.018 50.000 0.00 0.00 39.78 3.32
150 151 1.634960 TGTCCTATCCCACGACAACA 58.365 50.000 0.00 0.00 33.72 3.33
151 152 2.184533 TGTCCTATCCCACGACAACAT 58.815 47.619 0.00 0.00 33.72 2.71
152 153 3.367321 TGTCCTATCCCACGACAACATA 58.633 45.455 0.00 0.00 33.72 2.29
153 154 3.964688 TGTCCTATCCCACGACAACATAT 59.035 43.478 0.00 0.00 33.72 1.78
154 155 5.141910 TGTCCTATCCCACGACAACATATA 58.858 41.667 0.00 0.00 33.72 0.86
155 156 5.778241 TGTCCTATCCCACGACAACATATAT 59.222 40.000 0.00 0.00 33.72 0.86
156 157 6.269077 TGTCCTATCCCACGACAACATATATT 59.731 38.462 0.00 0.00 33.72 1.28
157 158 7.452189 TGTCCTATCCCACGACAACATATATTA 59.548 37.037 0.00 0.00 33.72 0.98
158 159 7.974501 GTCCTATCCCACGACAACATATATTAG 59.025 40.741 0.00 0.00 0.00 1.73
159 160 7.672660 TCCTATCCCACGACAACATATATTAGT 59.327 37.037 0.00 0.00 0.00 2.24
160 161 8.963725 CCTATCCCACGACAACATATATTAGTA 58.036 37.037 0.00 0.00 0.00 1.82
206 207 9.656040 AGATGCAATTTTCTTACATATGCAAAA 57.344 25.926 1.58 4.08 44.39 2.44
420 421 2.295909 CCGAGGAAAGTGGCATGAAAAA 59.704 45.455 0.00 0.00 0.00 1.94
438 443 1.987807 AATGGATCAGGCCACTCCCG 61.988 60.000 5.01 0.00 41.56 5.14
492 499 3.367327 CGTCTGTCGTATATCTAGGTCGG 59.633 52.174 0.00 0.00 34.52 4.79
538 545 0.409876 TAGTGGAGGAGGAGCACACT 59.590 55.000 0.00 0.00 43.95 3.55
574 581 2.613739 CTTCGCCGCCTCGAGATCAA 62.614 60.000 15.71 0.00 39.82 2.57
584 591 3.994392 GCCTCGAGATCAAAAGTGTAACA 59.006 43.478 15.71 0.00 41.43 2.41
588 595 6.018262 CCTCGAGATCAAAAGTGTAACAAACA 60.018 38.462 15.71 0.00 41.43 2.83
652 659 7.095270 ACATCGATTCGTTTCCTACTAAAACT 58.905 34.615 5.89 0.00 35.04 2.66
821 835 7.591421 TGGACAGAGAATACCGAATAATACA 57.409 36.000 0.00 0.00 0.00 2.29
936 951 0.617820 AGCACCTACAACCCCGAGAT 60.618 55.000 0.00 0.00 0.00 2.75
994 1047 2.659016 CTGAGCCAGCCAACGAGA 59.341 61.111 0.00 0.00 0.00 4.04
1166 1219 2.027751 GGTAGCCATCGTCGCCTC 59.972 66.667 0.00 0.00 0.00 4.70
1234 1311 0.670546 CGTCATTGACCGCTTCCTGT 60.671 55.000 11.12 0.00 0.00 4.00
1890 2000 1.319614 TGGCGATGTCTCCGATGTCA 61.320 55.000 0.00 0.00 0.00 3.58
1896 2006 3.443037 GATGTCTCCGATGTCAGAGTTG 58.557 50.000 0.00 0.00 0.00 3.16
1944 2054 4.185286 GGAATAGCCGCGGGGGTT 62.185 66.667 28.94 11.93 42.78 4.11
2107 2225 1.669115 CATGGATGGACGCCGATCC 60.669 63.158 5.80 5.80 38.98 3.36
2228 2357 1.112113 ATCTTCGTATCGGTGGCACT 58.888 50.000 18.45 0.00 0.00 4.40
2334 2463 3.909430 TGTAGTCGTGAATCTTGACCAC 58.091 45.455 2.69 0.98 33.09 4.16
2373 2502 8.490355 CAATTTATATCCCCGTCGTACTTAAAC 58.510 37.037 0.00 0.00 0.00 2.01
2374 2503 6.707440 TTATATCCCCGTCGTACTTAAACA 57.293 37.500 0.00 0.00 0.00 2.83
2472 2601 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2497 2626 2.030562 CTGGCGACCTTGTTCCGT 59.969 61.111 0.00 0.00 0.00 4.69
2522 2651 2.293399 GGTGAAATCGTGCAAAAGGACT 59.707 45.455 0.00 0.00 0.00 3.85
2523 2652 3.555518 GTGAAATCGTGCAAAAGGACTC 58.444 45.455 0.00 0.00 0.00 3.36
2535 2664 2.850695 AAGGACTCTACTACCCCCAG 57.149 55.000 0.00 0.00 0.00 4.45
2539 2668 3.599698 AGGACTCTACTACCCCCAGTTTA 59.400 47.826 0.00 0.00 0.00 2.01
2542 2671 5.337894 GGACTCTACTACCCCCAGTTTAAAC 60.338 48.000 10.47 10.47 0.00 2.01
2543 2672 5.157395 ACTCTACTACCCCCAGTTTAAACA 58.843 41.667 20.06 0.00 0.00 2.83
2548 2677 5.899278 ACTACCCCCAGTTTAAACATGAAT 58.101 37.500 20.06 4.08 0.00 2.57
2554 2683 4.463891 CCCAGTTTAAACATGAATCCTGCT 59.536 41.667 20.06 0.00 0.00 4.24
2616 2757 3.775654 CTCCACCTCCGCCCTCAC 61.776 72.222 0.00 0.00 0.00 3.51
2619 2760 3.322466 CACCTCCGCCCTCACCTT 61.322 66.667 0.00 0.00 0.00 3.50
2620 2761 3.322466 ACCTCCGCCCTCACCTTG 61.322 66.667 0.00 0.00 0.00 3.61
2622 2763 4.785453 CTCCGCCCTCACCTTGCC 62.785 72.222 0.00 0.00 0.00 4.52
2634 2781 4.047125 CTTGCCCCCACATCCGGT 62.047 66.667 0.00 0.00 0.00 5.28
2644 2791 2.514592 CATCCGGTGAATGCGCCT 60.515 61.111 4.18 0.00 42.66 5.52
2650 2797 1.523938 GGTGAATGCGCCTAGGTCC 60.524 63.158 11.31 2.10 41.58 4.46
2651 2798 1.220749 GTGAATGCGCCTAGGTCCA 59.779 57.895 11.31 8.28 0.00 4.02
2652 2799 0.811616 GTGAATGCGCCTAGGTCCAG 60.812 60.000 11.31 1.02 0.00 3.86
2653 2800 1.889573 GAATGCGCCTAGGTCCAGC 60.890 63.158 11.31 11.62 0.00 4.85
2654 2801 3.406595 AATGCGCCTAGGTCCAGCC 62.407 63.158 11.31 0.00 37.58 4.85
2791 3671 2.770748 AGGCTCTTCCTCAAGCTGT 58.229 52.632 0.00 0.00 43.20 4.40
2854 3735 3.512329 AGATGTTGCCTGCATTTGATTCA 59.488 39.130 0.00 0.00 0.00 2.57
2855 3736 3.306917 TGTTGCCTGCATTTGATTCAG 57.693 42.857 0.00 0.00 0.00 3.02
2866 3747 4.565564 GCATTTGATTCAGGAGATGTTTGC 59.434 41.667 0.00 0.00 0.00 3.68
2873 3754 0.254178 AGGAGATGTTTGCTGCCGAT 59.746 50.000 0.00 0.00 0.00 4.18
2911 3792 8.450578 AATGTGAACAAGTTAACTGAATCTGA 57.549 30.769 9.34 0.09 0.00 3.27
2933 3814 9.201989 TCTGACAGTACTGATGGAGTATAATTT 57.798 33.333 29.30 0.94 39.44 1.82
2976 3857 7.810658 TGAACTGATAATTTGAAGACAAGAGC 58.189 34.615 0.00 0.00 37.32 4.09
2977 3858 7.445096 TGAACTGATAATTTGAAGACAAGAGCA 59.555 33.333 0.00 0.00 37.32 4.26
2978 3859 7.138692 ACTGATAATTTGAAGACAAGAGCAC 57.861 36.000 0.00 0.00 37.32 4.40
2979 3860 6.939163 ACTGATAATTTGAAGACAAGAGCACT 59.061 34.615 0.00 0.00 37.32 4.40
2980 3861 7.118971 ACTGATAATTTGAAGACAAGAGCACTC 59.881 37.037 0.00 0.00 37.32 3.51
2981 3862 6.372659 TGATAATTTGAAGACAAGAGCACTCC 59.627 38.462 0.00 0.00 37.32 3.85
2982 3863 2.550830 TTGAAGACAAGAGCACTCCC 57.449 50.000 0.00 0.00 0.00 4.30
2983 3864 1.722034 TGAAGACAAGAGCACTCCCT 58.278 50.000 0.00 0.00 0.00 4.20
2984 3865 1.620819 TGAAGACAAGAGCACTCCCTC 59.379 52.381 0.00 0.00 0.00 4.30
2985 3866 1.620819 GAAGACAAGAGCACTCCCTCA 59.379 52.381 0.00 0.00 34.26 3.86
2986 3867 1.265236 AGACAAGAGCACTCCCTCAG 58.735 55.000 0.00 0.00 34.26 3.35
2987 3868 0.972883 GACAAGAGCACTCCCTCAGT 59.027 55.000 0.00 0.00 34.26 3.41
2988 3869 2.171840 GACAAGAGCACTCCCTCAGTA 58.828 52.381 0.00 0.00 32.21 2.74
2989 3870 2.763448 GACAAGAGCACTCCCTCAGTAT 59.237 50.000 0.00 0.00 32.21 2.12
2990 3871 2.763448 ACAAGAGCACTCCCTCAGTATC 59.237 50.000 0.00 0.00 32.21 2.24
2991 3872 2.762887 CAAGAGCACTCCCTCAGTATCA 59.237 50.000 0.00 0.00 32.21 2.15
2992 3873 2.383855 AGAGCACTCCCTCAGTATCAC 58.616 52.381 0.00 0.00 32.21 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.676014 GGATTGGGAGTGGTCGAACAG 60.676 57.143 1.63 0.00 0.00 3.16
4 5 1.884075 CGTGGATTGGGAGTGGTCGA 61.884 60.000 0.00 0.00 0.00 4.20
5 6 1.447838 CGTGGATTGGGAGTGGTCG 60.448 63.158 0.00 0.00 0.00 4.79
6 7 0.541863 ATCGTGGATTGGGAGTGGTC 59.458 55.000 0.00 0.00 0.00 4.02
7 8 0.253044 CATCGTGGATTGGGAGTGGT 59.747 55.000 0.00 0.00 0.00 4.16
8 9 0.253044 ACATCGTGGATTGGGAGTGG 59.747 55.000 0.00 0.00 0.00 4.00
9 10 1.066215 TGACATCGTGGATTGGGAGTG 60.066 52.381 0.00 0.00 0.00 3.51
10 11 1.275666 TGACATCGTGGATTGGGAGT 58.724 50.000 0.00 0.00 0.00 3.85
11 12 2.627515 ATGACATCGTGGATTGGGAG 57.372 50.000 0.00 0.00 0.00 4.30
12 13 3.645687 TGATATGACATCGTGGATTGGGA 59.354 43.478 0.00 0.00 0.00 4.37
13 14 4.006780 TGATATGACATCGTGGATTGGG 57.993 45.455 0.00 0.00 0.00 4.12
14 15 4.214119 GGTTGATATGACATCGTGGATTGG 59.786 45.833 0.00 0.00 0.00 3.16
15 16 4.815846 TGGTTGATATGACATCGTGGATTG 59.184 41.667 0.00 0.00 0.00 2.67
16 17 5.034852 TGGTTGATATGACATCGTGGATT 57.965 39.130 0.00 0.00 0.00 3.01
17 18 4.687901 TGGTTGATATGACATCGTGGAT 57.312 40.909 0.00 0.00 0.00 3.41
18 19 4.503123 GGATGGTTGATATGACATCGTGGA 60.503 45.833 0.00 0.00 40.36 4.02
19 20 3.748048 GGATGGTTGATATGACATCGTGG 59.252 47.826 0.00 0.00 40.36 4.94
20 21 4.379652 TGGATGGTTGATATGACATCGTG 58.620 43.478 0.00 0.00 40.36 4.35
21 22 4.687901 TGGATGGTTGATATGACATCGT 57.312 40.909 0.00 0.00 40.36 3.73
22 23 6.375945 TTTTGGATGGTTGATATGACATCG 57.624 37.500 0.00 0.00 40.36 3.84
23 24 8.583810 CAATTTTGGATGGTTGATATGACATC 57.416 34.615 0.00 0.00 39.11 3.06
40 41 0.461135 CCGCCTGGATCCAATTTTGG 59.539 55.000 17.00 14.04 43.68 3.28
41 42 0.461135 CCCGCCTGGATCCAATTTTG 59.539 55.000 17.00 3.21 37.49 2.44
42 43 0.334676 TCCCGCCTGGATCCAATTTT 59.665 50.000 17.00 0.00 38.61 1.82
43 44 0.334676 TTCCCGCCTGGATCCAATTT 59.665 50.000 17.00 0.00 44.66 1.82
44 45 0.395724 GTTCCCGCCTGGATCCAATT 60.396 55.000 17.00 0.00 44.66 2.32
45 46 1.227383 GTTCCCGCCTGGATCCAAT 59.773 57.895 17.00 0.00 44.66 3.16
46 47 2.227757 TGTTCCCGCCTGGATCCAA 61.228 57.895 17.00 0.00 44.66 3.53
47 48 2.609299 TGTTCCCGCCTGGATCCA 60.609 61.111 15.27 15.27 44.66 3.41
48 49 2.124695 GTGTTCCCGCCTGGATCC 60.125 66.667 4.20 4.20 44.66 3.36
49 50 2.124695 GGTGTTCCCGCCTGGATC 60.125 66.667 0.00 0.00 44.66 3.36
50 51 2.933287 TGGTGTTCCCGCCTGGAT 60.933 61.111 0.00 0.00 44.66 3.41
51 52 3.948719 GTGGTGTTCCCGCCTGGA 61.949 66.667 0.00 0.00 42.08 3.86
53 54 4.308458 TCGTGGTGTTCCCGCCTG 62.308 66.667 0.00 0.00 42.08 4.85
54 55 4.003788 CTCGTGGTGTTCCCGCCT 62.004 66.667 0.00 0.00 42.08 5.52
57 58 3.818121 TTGCCTCGTGGTGTTCCCG 62.818 63.158 5.26 0.00 35.15 5.14
58 59 1.303317 ATTGCCTCGTGGTGTTCCC 60.303 57.895 5.26 0.00 35.27 3.97
59 60 1.586154 CCATTGCCTCGTGGTGTTCC 61.586 60.000 5.26 0.00 35.27 3.62
60 61 1.586154 CCCATTGCCTCGTGGTGTTC 61.586 60.000 5.26 0.00 33.55 3.18
61 62 1.603455 CCCATTGCCTCGTGGTGTT 60.603 57.895 5.26 0.00 33.55 3.32
62 63 2.034066 CCCATTGCCTCGTGGTGT 59.966 61.111 5.26 0.00 33.55 4.16
63 64 2.034066 ACCCATTGCCTCGTGGTG 59.966 61.111 5.26 0.00 33.55 4.17
64 65 2.034066 CACCCATTGCCTCGTGGT 59.966 61.111 5.26 0.00 33.55 4.16
65 66 2.034066 ACACCCATTGCCTCGTGG 59.966 61.111 0.00 0.00 35.22 4.94
66 67 1.300971 CTGACACCCATTGCCTCGTG 61.301 60.000 0.00 0.00 0.00 4.35
67 68 1.003355 CTGACACCCATTGCCTCGT 60.003 57.895 0.00 0.00 0.00 4.18
68 69 0.321564 TTCTGACACCCATTGCCTCG 60.322 55.000 0.00 0.00 0.00 4.63
69 70 1.168714 GTTCTGACACCCATTGCCTC 58.831 55.000 0.00 0.00 0.00 4.70
70 71 0.478072 TGTTCTGACACCCATTGCCT 59.522 50.000 0.00 0.00 0.00 4.75
71 72 1.549203 ATGTTCTGACACCCATTGCC 58.451 50.000 0.00 0.00 38.91 4.52
72 73 2.353011 CCAATGTTCTGACACCCATTGC 60.353 50.000 0.00 0.00 41.64 3.56
73 74 3.156293 TCCAATGTTCTGACACCCATTG 58.844 45.455 0.00 0.00 42.28 2.82
74 75 3.524095 TCCAATGTTCTGACACCCATT 57.476 42.857 0.00 0.00 38.91 3.16
75 76 3.524095 TTCCAATGTTCTGACACCCAT 57.476 42.857 0.00 0.00 38.91 4.00
76 77 3.221771 CTTTCCAATGTTCTGACACCCA 58.778 45.455 0.00 0.00 38.91 4.51
77 78 2.558359 CCTTTCCAATGTTCTGACACCC 59.442 50.000 0.00 0.00 38.91 4.61
78 79 2.029918 GCCTTTCCAATGTTCTGACACC 60.030 50.000 0.00 0.00 38.91 4.16
79 80 2.622942 TGCCTTTCCAATGTTCTGACAC 59.377 45.455 0.00 0.00 38.91 3.67
80 81 2.942804 TGCCTTTCCAATGTTCTGACA 58.057 42.857 0.00 0.00 40.71 3.58
81 82 3.068024 TGTTGCCTTTCCAATGTTCTGAC 59.932 43.478 0.00 0.00 0.00 3.51
82 83 3.295093 TGTTGCCTTTCCAATGTTCTGA 58.705 40.909 0.00 0.00 0.00 3.27
83 84 3.731652 TGTTGCCTTTCCAATGTTCTG 57.268 42.857 0.00 0.00 0.00 3.02
84 85 3.450457 TGTTGTTGCCTTTCCAATGTTCT 59.550 39.130 0.00 0.00 0.00 3.01
85 86 3.555547 GTGTTGTTGCCTTTCCAATGTTC 59.444 43.478 0.00 0.00 0.00 3.18
86 87 3.055530 TGTGTTGTTGCCTTTCCAATGTT 60.056 39.130 0.00 0.00 0.00 2.71
87 88 2.499289 TGTGTTGTTGCCTTTCCAATGT 59.501 40.909 0.00 0.00 0.00 2.71
88 89 3.176552 TGTGTTGTTGCCTTTCCAATG 57.823 42.857 0.00 0.00 0.00 2.82
89 90 3.731089 CATGTGTTGTTGCCTTTCCAAT 58.269 40.909 0.00 0.00 0.00 3.16
90 91 2.741228 GCATGTGTTGTTGCCTTTCCAA 60.741 45.455 0.00 0.00 32.66 3.53
91 92 1.202510 GCATGTGTTGTTGCCTTTCCA 60.203 47.619 0.00 0.00 32.66 3.53
92 93 1.202510 TGCATGTGTTGTTGCCTTTCC 60.203 47.619 0.00 0.00 38.08 3.13
93 94 2.222007 TGCATGTGTTGTTGCCTTTC 57.778 45.000 0.00 0.00 38.08 2.62
94 95 2.278854 GTTGCATGTGTTGTTGCCTTT 58.721 42.857 0.00 0.00 38.08 3.11
95 96 1.473080 GGTTGCATGTGTTGTTGCCTT 60.473 47.619 0.00 0.00 38.08 4.35
96 97 0.104671 GGTTGCATGTGTTGTTGCCT 59.895 50.000 0.00 0.00 38.08 4.75
97 98 0.179089 TGGTTGCATGTGTTGTTGCC 60.179 50.000 0.00 0.00 38.08 4.52
98 99 1.327156 GTTGGTTGCATGTGTTGTTGC 59.673 47.619 0.00 0.00 39.33 4.17
99 100 2.604011 CTGTTGGTTGCATGTGTTGTTG 59.396 45.455 0.00 0.00 0.00 3.33
100 101 2.495270 TCTGTTGGTTGCATGTGTTGTT 59.505 40.909 0.00 0.00 0.00 2.83
101 102 2.098614 TCTGTTGGTTGCATGTGTTGT 58.901 42.857 0.00 0.00 0.00 3.32
102 103 2.544277 CCTCTGTTGGTTGCATGTGTTG 60.544 50.000 0.00 0.00 0.00 3.33
103 104 1.682854 CCTCTGTTGGTTGCATGTGTT 59.317 47.619 0.00 0.00 0.00 3.32
104 105 1.321474 CCTCTGTTGGTTGCATGTGT 58.679 50.000 0.00 0.00 0.00 3.72
105 106 1.001048 CACCTCTGTTGGTTGCATGTG 60.001 52.381 0.00 0.00 38.45 3.21
106 107 1.321474 CACCTCTGTTGGTTGCATGT 58.679 50.000 0.00 0.00 38.45 3.21
107 108 0.038892 GCACCTCTGTTGGTTGCATG 60.039 55.000 0.00 0.00 38.45 4.06
108 109 0.178981 AGCACCTCTGTTGGTTGCAT 60.179 50.000 0.00 0.00 38.45 3.96
109 110 0.472044 TAGCACCTCTGTTGGTTGCA 59.528 50.000 0.00 0.00 38.45 4.08
110 111 1.826385 ATAGCACCTCTGTTGGTTGC 58.174 50.000 0.00 0.00 38.45 4.17
111 112 4.517285 ACATATAGCACCTCTGTTGGTTG 58.483 43.478 0.00 0.00 38.45 3.77
112 113 4.384208 GGACATATAGCACCTCTGTTGGTT 60.384 45.833 0.00 0.00 38.45 3.67
113 114 3.134804 GGACATATAGCACCTCTGTTGGT 59.865 47.826 0.00 0.00 41.77 3.67
114 115 3.389329 AGGACATATAGCACCTCTGTTGG 59.611 47.826 0.00 0.00 0.00 3.77
115 116 4.679373 AGGACATATAGCACCTCTGTTG 57.321 45.455 0.00 0.00 0.00 3.33
116 117 5.482175 GGATAGGACATATAGCACCTCTGTT 59.518 44.000 0.00 0.00 34.42 3.16
117 118 5.020132 GGATAGGACATATAGCACCTCTGT 58.980 45.833 0.00 0.00 34.42 3.41
118 119 4.404073 GGGATAGGACATATAGCACCTCTG 59.596 50.000 0.00 0.00 34.42 3.35
119 120 4.045974 TGGGATAGGACATATAGCACCTCT 59.954 45.833 0.00 0.00 34.42 3.69
120 121 4.160626 GTGGGATAGGACATATAGCACCTC 59.839 50.000 0.00 0.00 34.42 3.85
121 122 4.097418 GTGGGATAGGACATATAGCACCT 58.903 47.826 0.00 0.00 36.65 4.00
122 123 3.119101 CGTGGGATAGGACATATAGCACC 60.119 52.174 0.00 0.00 0.00 5.01
123 124 3.762288 TCGTGGGATAGGACATATAGCAC 59.238 47.826 0.00 0.00 0.00 4.40
124 125 3.762288 GTCGTGGGATAGGACATATAGCA 59.238 47.826 0.00 0.00 42.34 3.49
125 126 3.762288 TGTCGTGGGATAGGACATATAGC 59.238 47.826 0.00 0.00 46.11 2.97
132 133 2.981859 ATGTTGTCGTGGGATAGGAC 57.018 50.000 0.00 0.00 42.92 3.85
133 134 6.928348 AATATATGTTGTCGTGGGATAGGA 57.072 37.500 0.00 0.00 0.00 2.94
134 135 7.837863 ACTAATATATGTTGTCGTGGGATAGG 58.162 38.462 0.00 0.00 0.00 2.57
208 209 6.878389 TGCTTTCCTCAGAAAACACAATTTTT 59.122 30.769 0.00 0.00 41.40 1.94
209 210 6.405538 TGCTTTCCTCAGAAAACACAATTTT 58.594 32.000 0.00 0.00 41.40 1.82
210 211 5.976458 TGCTTTCCTCAGAAAACACAATTT 58.024 33.333 0.00 0.00 41.40 1.82
211 212 5.596836 TGCTTTCCTCAGAAAACACAATT 57.403 34.783 0.00 0.00 41.40 2.32
212 213 5.535333 CATGCTTTCCTCAGAAAACACAAT 58.465 37.500 0.00 0.00 40.03 2.71
215 216 3.243501 TGCATGCTTTCCTCAGAAAACAC 60.244 43.478 20.33 0.00 40.03 3.32
218 219 3.575256 ACATGCATGCTTTCCTCAGAAAA 59.425 39.130 26.53 0.00 41.40 2.29
224 225 3.881688 ACTCATACATGCATGCTTTCCTC 59.118 43.478 26.53 0.00 0.00 3.71
281 282 4.982241 TGACATTCTCCTGTTTTCCTCT 57.018 40.909 0.00 0.00 0.00 3.69
290 291 0.449388 GCCGCTTTGACATTCTCCTG 59.551 55.000 0.00 0.00 0.00 3.86
320 321 4.232221 CAATGACAAAGAGGTGATTGCAC 58.768 43.478 0.00 0.00 44.39 4.57
389 390 3.370953 CCACTTTCCTCGGATTGGATCTT 60.371 47.826 0.00 0.00 33.09 2.40
420 421 2.446848 CGGGAGTGGCCTGATCCAT 61.447 63.158 19.11 0.00 46.81 3.41
438 443 0.249911 GTGAGGGTGAGTGTGTGGAC 60.250 60.000 0.00 0.00 0.00 4.02
469 474 4.233005 CGACCTAGATATACGACAGACGA 58.767 47.826 0.00 0.00 45.77 4.20
492 499 4.228912 CCACACATTTGGTTCTCTTCAC 57.771 45.455 0.00 0.00 0.00 3.18
538 545 1.819288 GAAGACCATGACTCTCCGACA 59.181 52.381 0.00 0.00 0.00 4.35
574 581 3.716601 GCTGGCATGTTTGTTACACTTT 58.283 40.909 0.00 0.00 40.19 2.66
584 591 2.977456 TCGCACGCTGGCATGTTT 60.977 55.556 0.00 0.00 0.00 2.83
588 595 4.377708 TCTGTCGCACGCTGGCAT 62.378 61.111 0.00 0.00 0.00 4.40
704 713 0.885596 CACTCCGCCCCGTGTTTTTA 60.886 55.000 0.00 0.00 0.00 1.52
705 714 2.190841 CACTCCGCCCCGTGTTTTT 61.191 57.895 0.00 0.00 0.00 1.94
706 715 2.593436 CACTCCGCCCCGTGTTTT 60.593 61.111 0.00 0.00 0.00 2.43
710 719 3.047877 GTTTCACTCCGCCCCGTG 61.048 66.667 0.00 0.00 0.00 4.94
743 754 7.088905 GGCTAGTGCGCTCTAGTATTTAAATA 58.911 38.462 34.43 3.71 39.44 1.40
744 755 5.927115 GGCTAGTGCGCTCTAGTATTTAAAT 59.073 40.000 34.43 5.89 39.44 1.40
765 779 1.067776 GCGTATAGGCATAACTCGGCT 60.068 52.381 12.42 0.00 42.68 5.52
821 835 5.003160 TGACAACTCATGATTGGAAACGAT 58.997 37.500 16.89 1.20 37.06 3.73
936 951 5.185249 GGAGGTAGATTTGTGTCTGTCTACA 59.815 44.000 11.95 0.00 42.91 2.74
994 1047 2.998279 GCTTTGGCGCCATTGCTCT 61.998 57.895 33.10 0.00 34.43 4.09
1890 2000 2.683933 ATCCCGGCGGACAACTCT 60.684 61.111 30.79 0.00 42.48 3.24
1896 2006 3.234730 ATCTCCATCCCGGCGGAC 61.235 66.667 30.79 0.00 42.48 4.79
1944 2054 2.672908 CCCTGCTGCACCATCTCA 59.327 61.111 0.00 0.00 0.00 3.27
2107 2225 6.992063 AACTAGAGTGGCAATGAACTAATG 57.008 37.500 0.00 0.00 0.00 1.90
2497 2626 1.974265 TTTGCACGATTTCACCTGGA 58.026 45.000 0.00 0.00 0.00 3.86
2522 2651 5.786457 TCATGTTTAAACTGGGGGTAGTAGA 59.214 40.000 18.72 0.00 0.00 2.59
2523 2652 6.057321 TCATGTTTAAACTGGGGGTAGTAG 57.943 41.667 18.72 0.00 0.00 2.57
2535 2664 5.699839 ACGAAGCAGGATTCATGTTTAAAC 58.300 37.500 11.54 11.54 0.00 2.01
2539 2668 3.679389 AGACGAAGCAGGATTCATGTTT 58.321 40.909 0.00 0.00 0.00 2.83
2542 2671 3.529533 AGAAGACGAAGCAGGATTCATG 58.470 45.455 0.00 0.00 0.00 3.07
2543 2672 3.902881 AGAAGACGAAGCAGGATTCAT 57.097 42.857 0.00 0.00 0.00 2.57
2548 2677 2.217510 AGGTAGAAGACGAAGCAGGA 57.782 50.000 0.00 0.00 0.00 3.86
2554 2683 1.549170 GGGCTGAAGGTAGAAGACGAA 59.451 52.381 0.00 0.00 0.00 3.85
2615 2756 4.047125 CGGATGTGGGGGCAAGGT 62.047 66.667 0.00 0.00 0.00 3.50
2616 2757 4.820744 CCGGATGTGGGGGCAAGG 62.821 72.222 0.00 0.00 0.00 3.61
2617 2758 4.047125 ACCGGATGTGGGGGCAAG 62.047 66.667 9.46 0.00 0.00 4.01
2618 2759 4.358841 CACCGGATGTGGGGGCAA 62.359 66.667 9.46 0.00 41.52 4.52
2620 2761 3.358932 ATTCACCGGATGTGGGGGC 62.359 63.158 9.46 0.00 45.48 5.80
2622 2763 2.120909 GCATTCACCGGATGTGGGG 61.121 63.158 9.46 0.00 45.48 4.96
2634 2781 1.522092 CTGGACCTAGGCGCATTCA 59.478 57.895 10.83 0.00 0.00 2.57
2637 2784 3.866582 GGCTGGACCTAGGCGCAT 61.867 66.667 10.83 3.98 33.36 4.73
2644 2791 2.363795 CCTGGACGGCTGGACCTA 60.364 66.667 11.34 0.00 35.61 3.08
2693 2840 4.392166 TGGAGGTGGAGGCGCCTA 62.392 66.667 32.97 13.11 37.63 3.93
2785 3665 2.670934 CGAGCCCAGCAACAGCTT 60.671 61.111 0.00 0.00 36.87 3.74
2805 3685 0.913451 AGGAGATGAACCTGGCAGCT 60.913 55.000 9.56 0.00 36.30 4.24
2808 3688 1.003580 GTTGAGGAGATGAACCTGGCA 59.996 52.381 0.00 0.00 37.93 4.92
2830 3711 2.516906 TCAAATGCAGGCAACATCTCA 58.483 42.857 0.00 0.00 41.41 3.27
2834 3715 3.369052 CCTGAATCAAATGCAGGCAACAT 60.369 43.478 0.95 0.00 42.30 2.71
2837 3718 2.494471 CTCCTGAATCAAATGCAGGCAA 59.506 45.455 8.86 0.00 46.82 4.52
2854 3735 0.254178 ATCGGCAGCAAACATCTCCT 59.746 50.000 0.00 0.00 0.00 3.69
2855 3736 1.953559 TATCGGCAGCAAACATCTCC 58.046 50.000 0.00 0.00 0.00 3.71
2856 3737 4.035558 TGAATTATCGGCAGCAAACATCTC 59.964 41.667 0.00 0.00 0.00 2.75
2866 3747 7.914871 TCACATTATTTGTTGAATTATCGGCAG 59.085 33.333 0.00 0.00 36.00 4.85
2968 3849 0.972883 ACTGAGGGAGTGCTCTTGTC 59.027 55.000 0.00 0.00 31.75 3.18
2970 3851 2.762887 TGATACTGAGGGAGTGCTCTTG 59.237 50.000 0.00 0.00 35.96 3.02
2971 3852 2.763448 GTGATACTGAGGGAGTGCTCTT 59.237 50.000 0.00 0.00 35.96 2.85
2973 3854 2.880963 GTGATACTGAGGGAGTGCTC 57.119 55.000 0.00 0.00 35.96 4.26


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

AutoCloner maintained by Alex Coulton.