Multiple sequence alignment - TraesCS4A01G441600

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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 TraesCS4A01G441600 chr4A 100.000 4535 0 0 1 4535 709980475 709975941 0.000000e+00 8375.0
1 TraesCS4A01G441600 chr4A 92.704 233 17 0 1 233 727152184 727151952 2.020000e-88 337.0
2 TraesCS4A01G441600 chr7D 95.856 3740 101 25 232 3950 25525396 25521690 0.000000e+00 5999.0
3 TraesCS4A01G441600 chr7D 90.598 585 40 6 3951 4530 25517312 25516738 0.000000e+00 761.0
4 TraesCS4A01G441600 chr7A 94.910 3831 118 33 546 4353 26451369 26447593 0.000000e+00 5923.0
5 TraesCS4A01G441600 chr7A 89.175 194 15 5 4344 4535 26446460 26446271 2.110000e-58 237.0
6 TraesCS4A01G441600 chr3B 78.819 779 149 13 2617 3387 236496339 236495569 1.130000e-140 510.0
7 TraesCS4A01G441600 chr3B 93.162 234 15 1 1 233 11879335 11879568 4.340000e-90 342.0
8 TraesCS4A01G441600 chr3D 78.562 779 151 14 2617 3387 159786675 159785905 2.440000e-137 499.0
9 TraesCS4A01G441600 chr3A 78.306 779 153 15 2617 3387 186041028 186040258 5.270000e-134 488.0
10 TraesCS4A01G441600 chr5B 78.077 780 149 19 2617 3388 515185775 515186540 1.480000e-129 473.0
11 TraesCS4A01G441600 chr5B 71.309 359 86 15 4127 4476 10413658 10413308 4.860000e-10 76.8
12 TraesCS4A01G441600 chr5D 77.564 780 153 19 2617 3388 425840604 425841369 6.920000e-123 451.0
13 TraesCS4A01G441600 chr5A 77.506 778 157 15 2617 3388 540053662 540054427 6.920000e-123 451.0
14 TraesCS4A01G441600 chr5A 82.131 291 42 8 2666 2951 678083107 678082822 1.630000e-59 241.0
15 TraesCS4A01G441600 chr5A 90.000 80 7 1 330 408 513909243 513909164 8.030000e-18 102.0
16 TraesCS4A01G441600 chr4B 77.308 780 156 17 2617 3387 1244490 1243723 1.500000e-119 440.0
17 TraesCS4A01G441600 chr4D 77.051 780 158 17 2617 3387 630233 631000 3.240000e-116 429.0
18 TraesCS4A01G441600 chr4D 82.313 294 36 13 2666 2951 497666784 497667069 1.630000e-59 241.0
19 TraesCS4A01G441600 chr4D 78.042 378 67 16 3019 3388 497667164 497667533 1.640000e-54 224.0
20 TraesCS4A01G441600 chr6B 95.708 233 8 2 1 233 132417674 132417904 1.540000e-99 374.0
21 TraesCS4A01G441600 chr6B 73.463 309 71 9 4182 4484 62625775 62626078 6.200000e-19 106.0
22 TraesCS4A01G441600 chr1B 95.671 231 10 0 1 231 68729557 68729327 5.540000e-99 372.0
23 TraesCS4A01G441600 chr2B 94.850 233 12 0 1 233 29245304 29245536 9.270000e-97 364.0
24 TraesCS4A01G441600 chr2B 93.991 233 14 0 1 233 44166568 44166800 2.010000e-93 353.0
25 TraesCS4A01G441600 chr7B 96.744 215 7 0 19 233 29060308 29060094 4.310000e-95 359.0
26 TraesCS4A01G441600 chrUn 92.275 233 17 1 1 233 299573685 299573454 3.380000e-86 329.0
27 TraesCS4A01G441600 chrUn 92.275 233 17 1 1 233 350810631 350810400 3.380000e-86 329.0


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 TraesCS4A01G441600 chr4A 709975941 709980475 4534 True 8375.0 8375 100.0000 1 4535 1 chr4A.!!$R1 4534
1 TraesCS4A01G441600 chr7D 25521690 25525396 3706 True 5999.0 5999 95.8560 232 3950 1 chr7D.!!$R2 3718
2 TraesCS4A01G441600 chr7D 25516738 25517312 574 True 761.0 761 90.5980 3951 4530 1 chr7D.!!$R1 579
3 TraesCS4A01G441600 chr7A 26446271 26451369 5098 True 3080.0 5923 92.0425 546 4535 2 chr7A.!!$R1 3989
4 TraesCS4A01G441600 chr3B 236495569 236496339 770 True 510.0 510 78.8190 2617 3387 1 chr3B.!!$R1 770
5 TraesCS4A01G441600 chr3D 159785905 159786675 770 True 499.0 499 78.5620 2617 3387 1 chr3D.!!$R1 770
6 TraesCS4A01G441600 chr3A 186040258 186041028 770 True 488.0 488 78.3060 2617 3387 1 chr3A.!!$R1 770
7 TraesCS4A01G441600 chr5B 515185775 515186540 765 False 473.0 473 78.0770 2617 3388 1 chr5B.!!$F1 771
8 TraesCS4A01G441600 chr5D 425840604 425841369 765 False 451.0 451 77.5640 2617 3388 1 chr5D.!!$F1 771
9 TraesCS4A01G441600 chr5A 540053662 540054427 765 False 451.0 451 77.5060 2617 3388 1 chr5A.!!$F1 771
10 TraesCS4A01G441600 chr4B 1243723 1244490 767 True 440.0 440 77.3080 2617 3387 1 chr4B.!!$R1 770
11 TraesCS4A01G441600 chr4D 630233 631000 767 False 429.0 429 77.0510 2617 3387 1 chr4D.!!$F1 770
12 TraesCS4A01G441600 chr4D 497666784 497667533 749 False 232.5 241 80.1775 2666 3388 2 chr4D.!!$F2 722

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
138 139 0.036294 GACCCTAGTGCTCCACAACC 60.036 60.0 0.00 0.0 36.74 3.77 F
150 151 0.108615 CCACAACCGACTAGGAGCAG 60.109 60.0 0.00 0.0 45.00 4.24 F
223 224 0.036294 GGCGCCTCTTTGGTAGAACT 60.036 55.0 22.15 0.0 38.35 3.01 F
1489 1508 0.527817 GGCGGTCATGAAGGAGTACG 60.528 60.0 0.00 0.0 0.00 3.67 F
2124 2143 0.179094 TCAATACCGACGGCCACATC 60.179 55.0 15.39 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1453 0.250513 AGCCATGGAGAAGGACGTTC 59.749 55.000 18.40 0.00 35.08 3.95 R
1639 1658 1.260538 TGGTAGGCAGCCTCTGACAG 61.261 60.000 20.38 0.00 42.99 3.51 R
2124 2143 2.658593 GGCCCGACGTCGATGATG 60.659 66.667 37.65 20.57 43.02 3.07 R
2952 2974 0.817634 CCTTGGCCACGAACTTGTCA 60.818 55.000 11.54 0.00 0.00 3.58 R
3560 3612 1.344438 GACGCATGGAGGTATGGATCA 59.656 52.381 0.00 0.00 0.00 2.92 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
39 40 2.893398 GGTCCACCCTCGCACTAG 59.107 66.667 0.00 0.00 0.00 2.57
40 41 2.722201 GGTCCACCCTCGCACTAGG 61.722 68.421 0.00 0.00 36.30 3.02
41 42 1.982938 GTCCACCCTCGCACTAGGT 60.983 63.158 0.00 0.00 34.56 3.08
43 44 3.377656 CACCCTCGCACTAGGTGT 58.622 61.111 0.18 0.00 44.95 4.16
44 45 2.575108 CACCCTCGCACTAGGTGTA 58.425 57.895 0.18 0.00 44.95 2.90
45 46 0.456221 CACCCTCGCACTAGGTGTAG 59.544 60.000 0.18 0.00 44.95 2.74
46 47 0.330604 ACCCTCGCACTAGGTGTAGA 59.669 55.000 0.00 0.07 35.75 2.59
47 48 0.739561 CCCTCGCACTAGGTGTAGAC 59.260 60.000 0.00 0.00 35.75 2.59
48 49 1.682394 CCCTCGCACTAGGTGTAGACT 60.682 57.143 0.00 0.00 35.75 3.24
49 50 1.671845 CCTCGCACTAGGTGTAGACTC 59.328 57.143 0.00 0.00 35.75 3.36
50 51 1.671845 CTCGCACTAGGTGTAGACTCC 59.328 57.143 0.00 0.00 35.75 3.85
51 52 0.377554 CGCACTAGGTGTAGACTCCG 59.622 60.000 0.00 0.00 35.75 4.63
52 53 0.100861 GCACTAGGTGTAGACTCCGC 59.899 60.000 0.00 0.00 35.75 5.54
53 54 0.377554 CACTAGGTGTAGACTCCGCG 59.622 60.000 0.00 0.00 34.85 6.46
54 55 0.747283 ACTAGGTGTAGACTCCGCGG 60.747 60.000 22.12 22.12 34.85 6.46
55 56 0.747283 CTAGGTGTAGACTCCGCGGT 60.747 60.000 27.15 6.47 34.85 5.68
56 57 0.745845 TAGGTGTAGACTCCGCGGTC 60.746 60.000 27.15 16.88 34.85 4.79
57 58 2.099831 GTGTAGACTCCGCGGTCG 59.900 66.667 27.15 19.65 40.76 4.79
58 59 2.359107 TGTAGACTCCGCGGTCGT 60.359 61.111 27.15 22.88 40.76 4.34
59 60 2.393768 TGTAGACTCCGCGGTCGTC 61.394 63.158 29.76 29.76 40.76 4.20
60 61 2.046988 TAGACTCCGCGGTCGTCA 60.047 61.111 34.32 23.85 40.76 4.35
61 62 2.393768 TAGACTCCGCGGTCGTCAC 61.394 63.158 34.32 20.00 40.76 3.67
62 63 4.773117 GACTCCGCGGTCGTCACC 62.773 72.222 30.99 14.93 39.69 4.02
64 65 4.477975 CTCCGCGGTCGTCACCTC 62.478 72.222 27.15 0.00 41.17 3.85
66 67 4.477975 CCGCGGTCGTCACCTCTC 62.478 72.222 19.50 0.00 41.17 3.20
67 68 4.477975 CGCGGTCGTCACCTCTCC 62.478 72.222 0.00 0.00 41.17 3.71
68 69 4.477975 GCGGTCGTCACCTCTCCG 62.478 72.222 0.00 0.00 41.17 4.63
69 70 3.812019 CGGTCGTCACCTCTCCGG 61.812 72.222 0.00 0.00 41.17 5.14
70 71 4.131088 GGTCGTCACCTCTCCGGC 62.131 72.222 0.00 0.00 40.00 6.13
71 72 3.371063 GTCGTCACCTCTCCGGCA 61.371 66.667 0.00 0.00 35.61 5.69
72 73 2.599281 TCGTCACCTCTCCGGCAA 60.599 61.111 0.00 0.00 35.61 4.52
73 74 2.125912 CGTCACCTCTCCGGCAAG 60.126 66.667 0.00 0.00 35.61 4.01
74 75 2.636412 CGTCACCTCTCCGGCAAGA 61.636 63.158 0.00 0.00 35.61 3.02
75 76 1.079750 GTCACCTCTCCGGCAAGAC 60.080 63.158 0.00 0.00 35.61 3.01
76 77 1.228894 TCACCTCTCCGGCAAGACT 60.229 57.895 0.00 0.00 35.61 3.24
77 78 1.216710 CACCTCTCCGGCAAGACTC 59.783 63.158 0.00 0.00 35.61 3.36
78 79 2.344203 ACCTCTCCGGCAAGACTCG 61.344 63.158 0.00 0.00 35.61 4.18
79 80 2.046864 CCTCTCCGGCAAGACTCGA 61.047 63.158 0.00 0.00 0.00 4.04
80 81 1.137825 CTCTCCGGCAAGACTCGAC 59.862 63.158 0.00 0.00 0.00 4.20
81 82 1.587043 CTCTCCGGCAAGACTCGACA 61.587 60.000 0.00 0.00 0.00 4.35
82 83 1.444553 CTCCGGCAAGACTCGACAC 60.445 63.158 0.00 0.00 0.00 3.67
83 84 1.867919 CTCCGGCAAGACTCGACACT 61.868 60.000 0.00 0.00 0.00 3.55
84 85 1.734477 CCGGCAAGACTCGACACTG 60.734 63.158 0.00 0.00 0.00 3.66
85 86 1.734477 CGGCAAGACTCGACACTGG 60.734 63.158 0.00 0.00 0.00 4.00
86 87 1.367840 GGCAAGACTCGACACTGGT 59.632 57.895 0.00 0.00 0.00 4.00
87 88 0.946221 GGCAAGACTCGACACTGGTG 60.946 60.000 0.00 0.00 0.00 4.17
88 89 0.946221 GCAAGACTCGACACTGGTGG 60.946 60.000 5.70 0.00 34.19 4.61
89 90 0.389391 CAAGACTCGACACTGGTGGT 59.611 55.000 5.70 0.00 34.19 4.16
90 91 1.611977 CAAGACTCGACACTGGTGGTA 59.388 52.381 5.70 0.00 34.19 3.25
91 92 1.535833 AGACTCGACACTGGTGGTAG 58.464 55.000 5.70 2.51 34.19 3.18
92 93 0.109226 GACTCGACACTGGTGGTAGC 60.109 60.000 5.70 0.00 34.19 3.58
93 94 0.539901 ACTCGACACTGGTGGTAGCT 60.540 55.000 5.70 0.00 34.19 3.32
94 95 0.171455 CTCGACACTGGTGGTAGCTC 59.829 60.000 5.70 0.00 34.19 4.09
95 96 0.538746 TCGACACTGGTGGTAGCTCA 60.539 55.000 5.70 0.00 34.19 4.26
96 97 0.317160 CGACACTGGTGGTAGCTCAA 59.683 55.000 5.70 0.00 34.19 3.02
97 98 1.670087 CGACACTGGTGGTAGCTCAAG 60.670 57.143 5.70 0.00 34.19 3.02
98 99 1.344763 GACACTGGTGGTAGCTCAAGT 59.655 52.381 5.70 0.00 34.19 3.16
99 100 1.768870 ACACTGGTGGTAGCTCAAGTT 59.231 47.619 1.26 0.00 34.19 2.66
100 101 2.224305 ACACTGGTGGTAGCTCAAGTTC 60.224 50.000 1.26 0.00 34.19 3.01
101 102 1.348036 ACTGGTGGTAGCTCAAGTTCC 59.652 52.381 0.00 0.00 0.00 3.62
102 103 0.320374 TGGTGGTAGCTCAAGTTCCG 59.680 55.000 0.00 0.00 0.00 4.30
103 104 1.019805 GGTGGTAGCTCAAGTTCCGC 61.020 60.000 0.00 0.00 0.00 5.54
104 105 1.019805 GTGGTAGCTCAAGTTCCGCC 61.020 60.000 0.00 0.00 0.00 6.13
105 106 1.810030 GGTAGCTCAAGTTCCGCCG 60.810 63.158 0.00 0.00 0.00 6.46
106 107 1.810030 GTAGCTCAAGTTCCGCCGG 60.810 63.158 0.00 0.00 0.00 6.13
107 108 3.014085 TAGCTCAAGTTCCGCCGGG 62.014 63.158 1.90 0.00 0.00 5.73
108 109 4.699522 GCTCAAGTTCCGCCGGGT 62.700 66.667 1.90 0.00 33.83 5.28
109 110 2.434359 CTCAAGTTCCGCCGGGTC 60.434 66.667 1.90 0.00 33.83 4.46
110 111 4.367023 TCAAGTTCCGCCGGGTCG 62.367 66.667 1.90 0.00 33.83 4.79
111 112 4.675029 CAAGTTCCGCCGGGTCGT 62.675 66.667 1.90 0.00 33.83 4.34
112 113 4.368543 AAGTTCCGCCGGGTCGTC 62.369 66.667 1.90 0.00 33.83 4.20
125 126 2.672908 TCGTCTGCCTCGACCCTA 59.327 61.111 0.00 0.00 32.30 3.53
126 127 1.451567 TCGTCTGCCTCGACCCTAG 60.452 63.158 0.00 0.00 32.30 3.02
127 128 1.749638 CGTCTGCCTCGACCCTAGT 60.750 63.158 0.00 0.00 0.00 2.57
128 129 1.810532 GTCTGCCTCGACCCTAGTG 59.189 63.158 0.00 0.00 0.00 2.74
129 130 2.052690 TCTGCCTCGACCCTAGTGC 61.053 63.158 0.00 0.00 0.00 4.40
130 131 2.037367 TGCCTCGACCCTAGTGCT 59.963 61.111 0.00 0.00 0.00 4.40
131 132 2.010582 CTGCCTCGACCCTAGTGCTC 62.011 65.000 0.00 0.00 0.00 4.26
132 133 2.787567 GCCTCGACCCTAGTGCTCC 61.788 68.421 0.00 0.00 0.00 4.70
133 134 1.379977 CCTCGACCCTAGTGCTCCA 60.380 63.158 0.00 0.00 0.00 3.86
134 135 1.668101 CCTCGACCCTAGTGCTCCAC 61.668 65.000 0.00 0.00 34.10 4.02
135 136 0.965866 CTCGACCCTAGTGCTCCACA 60.966 60.000 0.00 0.00 36.74 4.17
136 137 0.541063 TCGACCCTAGTGCTCCACAA 60.541 55.000 0.00 0.00 36.74 3.33
137 138 0.389948 CGACCCTAGTGCTCCACAAC 60.390 60.000 0.00 0.00 36.74 3.32
138 139 0.036294 GACCCTAGTGCTCCACAACC 60.036 60.000 0.00 0.00 36.74 3.77
139 140 1.079127 CCCTAGTGCTCCACAACCG 60.079 63.158 0.00 0.00 36.74 4.44
140 141 1.541310 CCCTAGTGCTCCACAACCGA 61.541 60.000 0.00 0.00 36.74 4.69
141 142 0.389948 CCTAGTGCTCCACAACCGAC 60.390 60.000 0.00 0.00 36.74 4.79
142 143 0.603569 CTAGTGCTCCACAACCGACT 59.396 55.000 0.00 0.00 36.74 4.18
143 144 1.816835 CTAGTGCTCCACAACCGACTA 59.183 52.381 0.00 0.00 36.74 2.59
144 145 0.603569 AGTGCTCCACAACCGACTAG 59.396 55.000 0.00 0.00 36.74 2.57
145 146 0.389948 GTGCTCCACAACCGACTAGG 60.390 60.000 0.00 0.00 39.13 3.02
146 147 0.541063 TGCTCCACAACCGACTAGGA 60.541 55.000 0.00 0.00 45.00 2.94
147 148 0.173708 GCTCCACAACCGACTAGGAG 59.826 60.000 0.00 0.00 46.71 3.69
148 149 0.173708 CTCCACAACCGACTAGGAGC 59.826 60.000 0.00 0.00 45.00 4.70
149 150 0.541063 TCCACAACCGACTAGGAGCA 60.541 55.000 0.00 0.00 45.00 4.26
150 151 0.108615 CCACAACCGACTAGGAGCAG 60.109 60.000 0.00 0.00 45.00 4.24
151 152 0.888619 CACAACCGACTAGGAGCAGA 59.111 55.000 0.00 0.00 45.00 4.26
152 153 0.889306 ACAACCGACTAGGAGCAGAC 59.111 55.000 0.00 0.00 45.00 3.51
153 154 0.173708 CAACCGACTAGGAGCAGACC 59.826 60.000 0.00 0.00 45.00 3.85
154 155 0.971447 AACCGACTAGGAGCAGACCC 60.971 60.000 0.00 0.00 45.00 4.46
155 156 2.128507 CCGACTAGGAGCAGACCCC 61.129 68.421 0.00 0.00 45.00 4.95
156 157 2.482333 CGACTAGGAGCAGACCCCG 61.482 68.421 0.00 0.00 0.00 5.73
157 158 2.042843 ACTAGGAGCAGACCCCGG 60.043 66.667 0.00 0.00 0.00 5.73
158 159 2.042843 CTAGGAGCAGACCCCGGT 60.043 66.667 0.00 0.00 0.00 5.28
159 160 2.363795 TAGGAGCAGACCCCGGTG 60.364 66.667 0.00 0.00 0.00 4.94
162 163 4.329545 GAGCAGACCCCGGTGCAA 62.330 66.667 16.21 0.00 42.47 4.08
163 164 3.842925 GAGCAGACCCCGGTGCAAA 62.843 63.158 16.21 0.00 42.47 3.68
164 165 3.365265 GCAGACCCCGGTGCAAAG 61.365 66.667 9.73 0.00 39.62 2.77
165 166 2.672996 CAGACCCCGGTGCAAAGG 60.673 66.667 0.00 0.00 0.00 3.11
166 167 2.852075 AGACCCCGGTGCAAAGGA 60.852 61.111 10.05 0.00 0.00 3.36
167 168 2.359975 GACCCCGGTGCAAAGGAG 60.360 66.667 10.05 0.00 0.00 3.69
168 169 4.660938 ACCCCGGTGCAAAGGAGC 62.661 66.667 10.05 0.00 0.00 4.70
170 171 4.659172 CCCGGTGCAAAGGAGCCA 62.659 66.667 10.05 0.00 0.00 4.75
171 172 2.597217 CCGGTGCAAAGGAGCCAA 60.597 61.111 2.72 0.00 0.00 4.52
172 173 2.199652 CCGGTGCAAAGGAGCCAAA 61.200 57.895 2.72 0.00 0.00 3.28
173 174 1.739049 CGGTGCAAAGGAGCCAAAA 59.261 52.632 0.00 0.00 0.00 2.44
174 175 0.597377 CGGTGCAAAGGAGCCAAAAC 60.597 55.000 0.00 0.00 0.00 2.43
175 176 0.597377 GGTGCAAAGGAGCCAAAACG 60.597 55.000 0.00 0.00 0.00 3.60
176 177 0.383949 GTGCAAAGGAGCCAAAACGA 59.616 50.000 0.00 0.00 0.00 3.85
177 178 1.107114 TGCAAAGGAGCCAAAACGAA 58.893 45.000 0.00 0.00 0.00 3.85
178 179 1.066908 TGCAAAGGAGCCAAAACGAAG 59.933 47.619 0.00 0.00 0.00 3.79
179 180 1.770957 CAAAGGAGCCAAAACGAAGC 58.229 50.000 0.00 0.00 0.00 3.86
180 181 0.310854 AAAGGAGCCAAAACGAAGCG 59.689 50.000 0.00 0.00 0.00 4.68
181 182 0.534203 AAGGAGCCAAAACGAAGCGA 60.534 50.000 0.00 0.00 0.00 4.93
182 183 0.951040 AGGAGCCAAAACGAAGCGAG 60.951 55.000 0.00 0.00 0.00 5.03
183 184 1.228657 GGAGCCAAAACGAAGCGAGT 61.229 55.000 0.00 0.00 0.00 4.18
184 185 0.586802 GAGCCAAAACGAAGCGAGTT 59.413 50.000 0.00 0.00 0.00 3.01
185 186 0.586802 AGCCAAAACGAAGCGAGTTC 59.413 50.000 0.00 0.00 0.00 3.01
186 187 0.306533 GCCAAAACGAAGCGAGTTCA 59.693 50.000 0.00 0.00 34.44 3.18
187 188 1.069227 GCCAAAACGAAGCGAGTTCAT 60.069 47.619 0.00 0.00 34.44 2.57
188 189 2.839474 CCAAAACGAAGCGAGTTCATC 58.161 47.619 0.00 0.00 34.44 2.92
200 201 3.423996 GAGTTCATCGGAGTAGTGGAC 57.576 52.381 0.00 0.00 0.00 4.02
201 202 1.743958 AGTTCATCGGAGTAGTGGACG 59.256 52.381 0.00 0.00 0.00 4.79
202 203 1.100510 TTCATCGGAGTAGTGGACGG 58.899 55.000 0.00 0.00 0.00 4.79
203 204 0.750546 TCATCGGAGTAGTGGACGGG 60.751 60.000 0.00 0.00 0.00 5.28
204 205 1.455217 ATCGGAGTAGTGGACGGGG 60.455 63.158 0.00 0.00 0.00 5.73
205 206 2.923634 ATCGGAGTAGTGGACGGGGG 62.924 65.000 0.00 0.00 0.00 5.40
206 207 3.468140 GGAGTAGTGGACGGGGGC 61.468 72.222 0.00 0.00 0.00 5.80
207 208 3.834799 GAGTAGTGGACGGGGGCG 61.835 72.222 0.00 0.00 0.00 6.13
218 219 3.723922 GGGGGCGCCTCTTTGGTA 61.724 66.667 28.78 0.00 38.35 3.25
219 220 2.124695 GGGGCGCCTCTTTGGTAG 60.125 66.667 28.56 0.00 38.35 3.18
220 221 2.666098 GGGGCGCCTCTTTGGTAGA 61.666 63.158 28.56 0.00 38.35 2.59
221 222 1.298667 GGGCGCCTCTTTGGTAGAA 59.701 57.895 28.56 0.00 38.35 2.10
222 223 1.025113 GGGCGCCTCTTTGGTAGAAC 61.025 60.000 28.56 0.00 38.35 3.01
223 224 0.036294 GGCGCCTCTTTGGTAGAACT 60.036 55.000 22.15 0.00 38.35 3.01
224 225 1.206371 GGCGCCTCTTTGGTAGAACTA 59.794 52.381 22.15 0.00 38.35 2.24
225 226 2.158943 GGCGCCTCTTTGGTAGAACTAT 60.159 50.000 22.15 0.00 38.35 2.12
226 227 3.124560 GCGCCTCTTTGGTAGAACTATC 58.875 50.000 0.00 0.00 38.35 2.08
227 228 3.181474 GCGCCTCTTTGGTAGAACTATCT 60.181 47.826 0.00 0.00 38.35 1.98
228 229 4.037684 GCGCCTCTTTGGTAGAACTATCTA 59.962 45.833 0.00 0.00 38.35 1.98
266 267 5.784177 AGATTCTCAAGCGAACAAGAGTTA 58.216 37.500 0.00 0.00 38.30 2.24
274 275 5.708877 AGCGAACAAGAGTTAGTAAGACT 57.291 39.130 0.00 0.00 38.30 3.24
307 308 5.453567 ACAGTTTTTCTTAATCCCTGCAC 57.546 39.130 0.00 0.00 0.00 4.57
308 309 4.280929 ACAGTTTTTCTTAATCCCTGCACC 59.719 41.667 0.00 0.00 0.00 5.01
351 355 4.739195 AGTCTTGCTAAATCTCTGTCGAC 58.261 43.478 9.11 9.11 0.00 4.20
352 356 3.860536 GTCTTGCTAAATCTCTGTCGACC 59.139 47.826 14.12 0.00 0.00 4.79
353 357 3.509967 TCTTGCTAAATCTCTGTCGACCA 59.490 43.478 14.12 0.00 0.00 4.02
354 358 3.953712 TGCTAAATCTCTGTCGACCAA 57.046 42.857 14.12 0.00 0.00 3.67
355 359 3.849911 TGCTAAATCTCTGTCGACCAAG 58.150 45.455 14.12 10.42 0.00 3.61
356 360 3.258372 TGCTAAATCTCTGTCGACCAAGT 59.742 43.478 14.12 0.00 0.00 3.16
372 376 3.504906 ACCAAGTCTTCGTTATGTCTCGA 59.495 43.478 0.00 0.00 0.00 4.04
384 388 5.325494 GTTATGTCTCGACCGATGCTATAG 58.675 45.833 0.00 0.00 0.00 1.31
398 402 6.037720 CCGATGCTATAGTCGTGAGATCTTAT 59.962 42.308 10.73 0.00 45.19 1.73
427 432 9.281371 TGAGATCATGCTAAATTATCCTTTCAG 57.719 33.333 0.00 0.00 0.00 3.02
428 433 9.282569 GAGATCATGCTAAATTATCCTTTCAGT 57.717 33.333 0.00 0.00 0.00 3.41
429 434 9.638176 AGATCATGCTAAATTATCCTTTCAGTT 57.362 29.630 0.00 0.00 0.00 3.16
463 468 9.619316 TTTGTTTATACATGTTATGTCACTTGC 57.381 29.630 2.30 0.00 43.67 4.01
464 469 8.329203 TGTTTATACATGTTATGTCACTTGCA 57.671 30.769 2.30 0.00 43.67 4.08
465 470 8.450180 TGTTTATACATGTTATGTCACTTGCAG 58.550 33.333 2.30 0.00 43.67 4.41
466 471 8.450964 GTTTATACATGTTATGTCACTTGCAGT 58.549 33.333 2.30 0.00 43.67 4.40
467 472 6.668541 ATACATGTTATGTCACTTGCAGTC 57.331 37.500 2.30 0.00 43.67 3.51
472 477 1.788258 ATGTCACTTGCAGTCGACTG 58.212 50.000 35.80 35.80 46.40 3.51
473 478 0.744281 TGTCACTTGCAGTCGACTGA 59.256 50.000 42.03 26.44 46.59 3.41
474 479 1.136110 TGTCACTTGCAGTCGACTGAA 59.864 47.619 42.03 33.56 46.59 3.02
476 481 2.033662 GTCACTTGCAGTCGACTGAAAC 60.034 50.000 42.03 26.08 46.59 2.78
477 482 1.261619 CACTTGCAGTCGACTGAAACC 59.738 52.381 42.03 26.85 46.59 3.27
478 483 1.139058 ACTTGCAGTCGACTGAAACCT 59.861 47.619 42.03 23.71 46.59 3.50
479 484 2.213499 CTTGCAGTCGACTGAAACCTT 58.787 47.619 42.03 6.81 46.59 3.50
480 485 1.581934 TGCAGTCGACTGAAACCTTG 58.418 50.000 42.03 19.52 46.59 3.61
481 486 1.138069 TGCAGTCGACTGAAACCTTGA 59.862 47.619 42.03 15.83 46.59 3.02
483 488 3.006430 TGCAGTCGACTGAAACCTTGATA 59.994 43.478 42.03 15.34 46.59 2.15
485 490 4.556233 CAGTCGACTGAAACCTTGATACA 58.444 43.478 36.73 0.00 46.59 2.29
486 491 4.386049 CAGTCGACTGAAACCTTGATACAC 59.614 45.833 36.73 0.00 46.59 2.90
487 492 4.281182 AGTCGACTGAAACCTTGATACACT 59.719 41.667 19.30 0.00 0.00 3.55
488 493 4.989168 GTCGACTGAAACCTTGATACACTT 59.011 41.667 8.70 0.00 0.00 3.16
489 494 5.465724 GTCGACTGAAACCTTGATACACTTT 59.534 40.000 8.70 0.00 0.00 2.66
490 495 5.694910 TCGACTGAAACCTTGATACACTTTC 59.305 40.000 0.00 0.00 0.00 2.62
568 578 3.340727 GCACAAGCTCCAATCATGC 57.659 52.632 0.00 0.00 37.91 4.06
569 579 0.528924 GCACAAGCTCCAATCATGCA 59.471 50.000 0.00 0.00 37.91 3.96
591 601 0.797249 GTCACCGTCGATCGTTCAGG 60.797 60.000 15.94 15.54 37.94 3.86
1291 1310 4.111016 CGTCGCACCTCTACCGCA 62.111 66.667 0.00 0.00 0.00 5.69
1292 1311 2.202623 GTCGCACCTCTACCGCAG 60.203 66.667 0.00 0.00 0.00 5.18
1459 1478 0.745845 CCTTCTCCATGGCTTCACCG 60.746 60.000 6.96 0.00 43.94 4.94
1489 1508 0.527817 GGCGGTCATGAAGGAGTACG 60.528 60.000 0.00 0.00 0.00 3.67
1581 1600 3.692406 GAGGTCGTCAACGCCCCT 61.692 66.667 11.70 11.70 38.28 4.79
1653 1672 4.792804 GGGCTGTCAGAGGCTGCC 62.793 72.222 11.65 11.65 46.72 4.85
1992 2011 2.985282 ACGTCCGCCAACGACCTA 60.985 61.111 11.99 0.00 45.37 3.08
2124 2143 0.179094 TCAATACCGACGGCCACATC 60.179 55.000 15.39 0.00 0.00 3.06
2204 2223 1.086634 GCGGAGGTGCTCAAGATGAC 61.087 60.000 0.00 0.00 31.08 3.06
2355 2374 1.252904 GCATGGTGGTGAAGTGGCAT 61.253 55.000 0.00 0.00 0.00 4.40
2454 2476 2.032681 GGCAAGTCCAAGAGCGGT 59.967 61.111 0.00 0.00 34.01 5.68
2952 2974 0.833287 CCACCAACATCCTCCTCGAT 59.167 55.000 0.00 0.00 0.00 3.59
3111 3163 1.802960 GACAAGTCCGACGTCTACTCA 59.197 52.381 17.52 0.00 0.00 3.41
3396 3448 3.160585 CTGCAGGAGTCCAACCCA 58.839 61.111 12.86 1.56 0.00 4.51
3528 3580 2.892425 CTCGCCGACATGAAGGGC 60.892 66.667 13.85 13.85 43.42 5.19
3531 3583 2.825836 GCCGACATGAAGGGCAGG 60.826 66.667 17.40 4.26 46.13 4.85
3534 3586 1.296392 CGACATGAAGGGCAGGTGA 59.704 57.895 0.00 0.00 42.39 4.02
3535 3587 0.107508 CGACATGAAGGGCAGGTGAT 60.108 55.000 0.00 0.00 42.39 3.06
3536 3588 1.673168 GACATGAAGGGCAGGTGATC 58.327 55.000 0.00 0.00 42.39 2.92
3537 3589 0.257039 ACATGAAGGGCAGGTGATCC 59.743 55.000 0.00 0.00 40.52 3.36
3545 3597 0.769873 GGCAGGTGATCCATCCATCT 59.230 55.000 0.00 0.00 35.89 2.90
3550 3602 2.106166 AGGTGATCCATCCATCTTCTGC 59.894 50.000 0.00 0.00 35.89 4.26
3557 3609 2.742589 CCATCCATCTTCTGCATCGATG 59.257 50.000 21.27 21.27 35.48 3.84
3661 3713 3.884350 CGCGCCTTCTGCATGCAT 61.884 61.111 22.97 0.00 41.33 3.96
3796 3850 3.612423 TGTCTCAATCGCGTTTACTGATG 59.388 43.478 5.77 0.00 0.00 3.07
3899 3953 3.770263 TTGTTAGCATGCATTCAGCTC 57.230 42.857 21.98 1.97 45.94 4.09
3912 3967 3.977134 TTCAGCTCAGCTCATTTCTCT 57.023 42.857 0.00 0.00 36.40 3.10
4017 4076 9.577110 TCTTGTTATCGAATTTTCTATGTACGT 57.423 29.630 0.00 0.00 0.00 3.57
4070 4130 5.167303 ACAAAATAAGAGTCCTGGTCCTC 57.833 43.478 7.71 7.71 0.00 3.71
4071 4131 4.019231 ACAAAATAAGAGTCCTGGTCCTCC 60.019 45.833 10.96 0.00 0.00 4.30
4072 4132 3.786213 AATAAGAGTCCTGGTCCTCCT 57.214 47.619 10.96 3.52 34.23 3.69
4092 4152 2.558359 CTGGTGGTTTCCCATTGAGTTC 59.442 50.000 0.00 0.00 44.35 3.01
4106 4166 7.512402 TCCCATTGAGTTCTACCACATATGATA 59.488 37.037 10.38 0.00 0.00 2.15
4107 4167 8.156820 CCCATTGAGTTCTACCACATATGATAA 58.843 37.037 10.38 0.00 0.00 1.75
4108 4168 9.212641 CCATTGAGTTCTACCACATATGATAAG 57.787 37.037 10.38 1.58 0.00 1.73
4157 4217 9.803507 AAGCTATGATTGATGATTTCCATAGAA 57.196 29.630 0.00 0.00 36.98 2.10
4244 4308 6.541641 TGCTAAACAAATTCAAAATTGCTGGT 59.458 30.769 0.00 0.00 0.00 4.00
4246 4310 6.998968 AAACAAATTCAAAATTGCTGGTCA 57.001 29.167 0.00 0.00 0.00 4.02
4259 4323 2.892852 TGCTGGTCAATTTTCCTCTTGG 59.107 45.455 0.00 0.00 0.00 3.61
4333 4399 4.844085 TGGTGAGTCCTCCAATTTCTCTTA 59.156 41.667 2.24 0.00 33.40 2.10
4334 4400 5.046304 TGGTGAGTCCTCCAATTTCTCTTAG 60.046 44.000 2.24 0.00 33.40 2.18
4362 5570 9.836076 CAAACTGCTTTTATTAAAGGTAGGTAC 57.164 33.333 16.70 0.00 40.90 3.34
4393 5602 4.832492 AGGGTCCATATCCTACATGAAGT 58.168 43.478 0.00 0.00 32.91 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.722201 CCTAGTGCGAGGGTGGACC 61.722 68.421 0.00 0.00 40.67 4.46
23 24 1.982938 ACCTAGTGCGAGGGTGGAC 60.983 63.158 3.53 0.00 41.36 4.02
24 25 1.982395 CACCTAGTGCGAGGGTGGA 60.982 63.158 9.22 0.00 44.63 4.02
25 26 2.579201 CACCTAGTGCGAGGGTGG 59.421 66.667 9.22 0.00 44.63 4.61
27 28 0.330604 TCTACACCTAGTGCGAGGGT 59.669 55.000 3.53 1.73 41.36 4.34
28 29 0.739561 GTCTACACCTAGTGCGAGGG 59.260 60.000 3.53 0.00 41.36 4.30
29 30 1.671845 GAGTCTACACCTAGTGCGAGG 59.328 57.143 0.00 0.00 42.89 4.63
30 31 1.671845 GGAGTCTACACCTAGTGCGAG 59.328 57.143 0.00 0.00 36.98 5.03
31 32 1.747709 GGAGTCTACACCTAGTGCGA 58.252 55.000 0.00 0.00 36.98 5.10
32 33 0.377554 CGGAGTCTACACCTAGTGCG 59.622 60.000 0.00 0.00 36.98 5.34
33 34 0.100861 GCGGAGTCTACACCTAGTGC 59.899 60.000 0.00 0.00 36.98 4.40
34 35 0.377554 CGCGGAGTCTACACCTAGTG 59.622 60.000 0.00 0.00 39.75 2.74
35 36 0.747283 CCGCGGAGTCTACACCTAGT 60.747 60.000 24.07 0.00 0.00 2.57
36 37 0.747283 ACCGCGGAGTCTACACCTAG 60.747 60.000 35.90 0.00 0.00 3.02
37 38 0.745845 GACCGCGGAGTCTACACCTA 60.746 60.000 35.90 0.00 33.79 3.08
38 39 2.035312 ACCGCGGAGTCTACACCT 59.965 61.111 35.90 0.68 0.00 4.00
39 40 2.488820 GACCGCGGAGTCTACACC 59.511 66.667 35.90 4.89 33.79 4.16
40 41 2.099831 CGACCGCGGAGTCTACAC 59.900 66.667 35.90 10.71 34.46 2.90
41 42 2.359107 ACGACCGCGGAGTCTACA 60.359 61.111 35.90 0.00 43.17 2.74
42 43 2.393768 TGACGACCGCGGAGTCTAC 61.394 63.158 37.16 23.92 43.17 2.59
43 44 2.046988 TGACGACCGCGGAGTCTA 60.047 61.111 37.16 27.55 43.17 2.59
44 45 3.735029 GTGACGACCGCGGAGTCT 61.735 66.667 37.16 19.98 43.17 3.24
45 46 4.773117 GGTGACGACCGCGGAGTC 62.773 72.222 34.31 34.31 43.17 3.36
53 54 4.131088 GCCGGAGAGGTGACGACC 62.131 72.222 5.05 0.00 43.70 4.79
54 55 2.820767 CTTGCCGGAGAGGTGACGAC 62.821 65.000 5.05 0.00 43.70 4.34
55 56 2.599281 TTGCCGGAGAGGTGACGA 60.599 61.111 5.05 0.00 43.70 4.20
56 57 2.125912 CTTGCCGGAGAGGTGACG 60.126 66.667 5.05 0.00 43.70 4.35
57 58 1.079750 GTCTTGCCGGAGAGGTGAC 60.080 63.158 5.05 0.00 43.70 3.67
58 59 1.228894 AGTCTTGCCGGAGAGGTGA 60.229 57.895 5.05 0.00 43.70 4.02
59 60 1.216710 GAGTCTTGCCGGAGAGGTG 59.783 63.158 5.05 0.00 43.70 4.00
60 61 2.344203 CGAGTCTTGCCGGAGAGGT 61.344 63.158 5.05 0.00 43.70 3.85
61 62 2.046864 TCGAGTCTTGCCGGAGAGG 61.047 63.158 5.05 0.00 44.97 3.69
62 63 1.137825 GTCGAGTCTTGCCGGAGAG 59.862 63.158 5.05 0.90 0.00 3.20
63 64 1.602605 TGTCGAGTCTTGCCGGAGA 60.603 57.895 5.05 0.00 0.00 3.71
64 65 1.444553 GTGTCGAGTCTTGCCGGAG 60.445 63.158 5.05 0.00 0.00 4.63
65 66 1.901948 AGTGTCGAGTCTTGCCGGA 60.902 57.895 5.05 0.00 0.00 5.14
66 67 1.734477 CAGTGTCGAGTCTTGCCGG 60.734 63.158 0.00 0.00 0.00 6.13
67 68 1.734477 CCAGTGTCGAGTCTTGCCG 60.734 63.158 0.00 0.00 0.00 5.69
68 69 0.946221 CACCAGTGTCGAGTCTTGCC 60.946 60.000 0.00 0.00 0.00 4.52
69 70 0.946221 CCACCAGTGTCGAGTCTTGC 60.946 60.000 0.00 0.00 0.00 4.01
70 71 0.389391 ACCACCAGTGTCGAGTCTTG 59.611 55.000 0.00 0.00 0.00 3.02
71 72 1.887198 CTACCACCAGTGTCGAGTCTT 59.113 52.381 0.00 0.00 0.00 3.01
72 73 1.535833 CTACCACCAGTGTCGAGTCT 58.464 55.000 0.00 0.00 0.00 3.24
73 74 0.109226 GCTACCACCAGTGTCGAGTC 60.109 60.000 0.00 0.00 0.00 3.36
74 75 0.539901 AGCTACCACCAGTGTCGAGT 60.540 55.000 0.00 0.00 0.00 4.18
75 76 0.171455 GAGCTACCACCAGTGTCGAG 59.829 60.000 0.00 0.00 0.00 4.04
76 77 0.538746 TGAGCTACCACCAGTGTCGA 60.539 55.000 0.00 0.00 0.00 4.20
77 78 0.317160 TTGAGCTACCACCAGTGTCG 59.683 55.000 0.00 0.00 0.00 4.35
78 79 1.344763 ACTTGAGCTACCACCAGTGTC 59.655 52.381 0.00 0.00 0.00 3.67
79 80 1.424638 ACTTGAGCTACCACCAGTGT 58.575 50.000 0.00 0.00 0.00 3.55
80 81 2.417719 GAACTTGAGCTACCACCAGTG 58.582 52.381 0.00 0.00 0.00 3.66
81 82 1.348036 GGAACTTGAGCTACCACCAGT 59.652 52.381 0.00 0.00 0.00 4.00
82 83 1.673033 CGGAACTTGAGCTACCACCAG 60.673 57.143 0.00 0.00 0.00 4.00
83 84 0.320374 CGGAACTTGAGCTACCACCA 59.680 55.000 0.00 0.00 0.00 4.17
84 85 1.019805 GCGGAACTTGAGCTACCACC 61.020 60.000 0.00 0.00 0.00 4.61
85 86 1.019805 GGCGGAACTTGAGCTACCAC 61.020 60.000 0.00 0.00 0.00 4.16
86 87 1.295423 GGCGGAACTTGAGCTACCA 59.705 57.895 0.00 0.00 0.00 3.25
87 88 1.810030 CGGCGGAACTTGAGCTACC 60.810 63.158 0.00 0.00 0.00 3.18
88 89 1.810030 CCGGCGGAACTTGAGCTAC 60.810 63.158 24.41 0.00 0.00 3.58
89 90 2.577059 CCGGCGGAACTTGAGCTA 59.423 61.111 24.41 0.00 0.00 3.32
90 91 4.394712 CCCGGCGGAACTTGAGCT 62.395 66.667 30.79 0.00 0.00 4.09
91 92 4.699522 ACCCGGCGGAACTTGAGC 62.700 66.667 30.79 0.00 0.00 4.26
92 93 2.434359 GACCCGGCGGAACTTGAG 60.434 66.667 30.79 11.41 0.00 3.02
93 94 4.367023 CGACCCGGCGGAACTTGA 62.367 66.667 30.79 0.00 0.00 3.02
94 95 4.675029 ACGACCCGGCGGAACTTG 62.675 66.667 30.79 13.10 35.12 3.16
95 96 4.368543 GACGACCCGGCGGAACTT 62.369 66.667 30.79 14.22 35.12 2.66
108 109 1.451567 CTAGGGTCGAGGCAGACGA 60.452 63.158 6.97 2.77 41.81 4.20
109 110 1.749638 ACTAGGGTCGAGGCAGACG 60.750 63.158 6.97 0.50 41.81 4.18
110 111 1.810532 CACTAGGGTCGAGGCAGAC 59.189 63.158 4.80 4.80 40.25 3.51
111 112 2.052690 GCACTAGGGTCGAGGCAGA 61.053 63.158 0.00 0.00 0.00 4.26
112 113 2.010582 GAGCACTAGGGTCGAGGCAG 62.011 65.000 0.00 0.00 33.78 4.85
113 114 2.037367 AGCACTAGGGTCGAGGCA 59.963 61.111 0.00 0.00 0.00 4.75
114 115 2.787567 GGAGCACTAGGGTCGAGGC 61.788 68.421 0.00 0.00 45.03 4.70
115 116 1.379977 TGGAGCACTAGGGTCGAGG 60.380 63.158 0.00 0.00 45.03 4.63
116 117 0.965866 TGTGGAGCACTAGGGTCGAG 60.966 60.000 0.00 0.00 45.03 4.04
117 118 0.541063 TTGTGGAGCACTAGGGTCGA 60.541 55.000 0.00 0.00 45.03 4.20
118 119 0.389948 GTTGTGGAGCACTAGGGTCG 60.390 60.000 0.00 0.00 45.03 4.79
119 120 0.036294 GGTTGTGGAGCACTAGGGTC 60.036 60.000 0.00 0.00 43.35 4.46
120 121 1.827399 CGGTTGTGGAGCACTAGGGT 61.827 60.000 0.00 0.00 35.11 4.34
121 122 1.079127 CGGTTGTGGAGCACTAGGG 60.079 63.158 0.00 0.00 35.11 3.53
122 123 0.389948 GTCGGTTGTGGAGCACTAGG 60.390 60.000 0.00 0.00 35.11 3.02
123 124 0.603569 AGTCGGTTGTGGAGCACTAG 59.396 55.000 0.00 0.00 35.11 2.57
124 125 1.816835 CTAGTCGGTTGTGGAGCACTA 59.183 52.381 0.00 0.00 35.11 2.74
125 126 0.603569 CTAGTCGGTTGTGGAGCACT 59.396 55.000 0.00 0.00 35.11 4.40
126 127 0.389948 CCTAGTCGGTTGTGGAGCAC 60.390 60.000 0.00 0.00 34.56 4.40
127 128 0.541063 TCCTAGTCGGTTGTGGAGCA 60.541 55.000 0.00 0.00 0.00 4.26
128 129 0.173708 CTCCTAGTCGGTTGTGGAGC 59.826 60.000 0.00 0.00 37.98 4.70
129 130 0.173708 GCTCCTAGTCGGTTGTGGAG 59.826 60.000 0.00 0.00 45.05 3.86
130 131 0.541063 TGCTCCTAGTCGGTTGTGGA 60.541 55.000 0.00 0.00 0.00 4.02
131 132 0.108615 CTGCTCCTAGTCGGTTGTGG 60.109 60.000 0.00 0.00 0.00 4.17
132 133 0.888619 TCTGCTCCTAGTCGGTTGTG 59.111 55.000 0.00 0.00 0.00 3.33
133 134 0.889306 GTCTGCTCCTAGTCGGTTGT 59.111 55.000 0.00 0.00 0.00 3.32
134 135 0.173708 GGTCTGCTCCTAGTCGGTTG 59.826 60.000 0.00 0.00 0.00 3.77
135 136 0.971447 GGGTCTGCTCCTAGTCGGTT 60.971 60.000 0.00 0.00 0.00 4.44
136 137 1.380112 GGGTCTGCTCCTAGTCGGT 60.380 63.158 0.00 0.00 0.00 4.69
137 138 2.128507 GGGGTCTGCTCCTAGTCGG 61.129 68.421 0.00 0.00 30.72 4.79
138 139 2.482333 CGGGGTCTGCTCCTAGTCG 61.482 68.421 0.00 0.00 31.37 4.18
139 140 2.128507 CCGGGGTCTGCTCCTAGTC 61.129 68.421 0.00 0.00 31.37 2.59
140 141 2.042843 CCGGGGTCTGCTCCTAGT 60.043 66.667 0.00 0.00 31.37 2.57
141 142 2.042843 ACCGGGGTCTGCTCCTAG 60.043 66.667 6.32 0.00 31.37 3.02
142 143 2.363795 CACCGGGGTCTGCTCCTA 60.364 66.667 6.32 0.00 31.37 2.94
145 146 3.842925 TTTGCACCGGGGTCTGCTC 62.843 63.158 15.00 0.00 0.00 4.26
146 147 3.850098 CTTTGCACCGGGGTCTGCT 62.850 63.158 15.00 0.00 0.00 4.24
147 148 3.365265 CTTTGCACCGGGGTCTGC 61.365 66.667 5.12 6.71 0.00 4.26
148 149 2.672996 CCTTTGCACCGGGGTCTG 60.673 66.667 5.12 0.00 0.00 3.51
149 150 2.852075 TCCTTTGCACCGGGGTCT 60.852 61.111 5.12 0.00 0.00 3.85
150 151 2.359975 CTCCTTTGCACCGGGGTC 60.360 66.667 5.12 0.00 0.00 4.46
151 152 4.660938 GCTCCTTTGCACCGGGGT 62.661 66.667 5.12 0.00 0.00 4.95
153 154 4.659172 TGGCTCCTTTGCACCGGG 62.659 66.667 6.32 0.00 34.04 5.73
154 155 1.743321 TTTTGGCTCCTTTGCACCGG 61.743 55.000 0.00 0.00 34.04 5.28
155 156 0.597377 GTTTTGGCTCCTTTGCACCG 60.597 55.000 0.00 0.00 34.04 4.94
156 157 0.597377 CGTTTTGGCTCCTTTGCACC 60.597 55.000 0.00 0.00 34.04 5.01
157 158 0.383949 TCGTTTTGGCTCCTTTGCAC 59.616 50.000 0.00 0.00 34.04 4.57
158 159 1.066908 CTTCGTTTTGGCTCCTTTGCA 59.933 47.619 0.00 0.00 34.04 4.08
159 160 1.770957 CTTCGTTTTGGCTCCTTTGC 58.229 50.000 0.00 0.00 0.00 3.68
160 161 1.770957 GCTTCGTTTTGGCTCCTTTG 58.229 50.000 0.00 0.00 0.00 2.77
161 162 0.310854 CGCTTCGTTTTGGCTCCTTT 59.689 50.000 0.00 0.00 0.00 3.11
162 163 0.534203 TCGCTTCGTTTTGGCTCCTT 60.534 50.000 0.00 0.00 0.00 3.36
163 164 0.951040 CTCGCTTCGTTTTGGCTCCT 60.951 55.000 0.00 0.00 0.00 3.69
164 165 1.228657 ACTCGCTTCGTTTTGGCTCC 61.229 55.000 0.00 0.00 0.00 4.70
165 166 0.586802 AACTCGCTTCGTTTTGGCTC 59.413 50.000 0.00 0.00 0.00 4.70
166 167 0.586802 GAACTCGCTTCGTTTTGGCT 59.413 50.000 0.00 0.00 0.00 4.75
167 168 0.306533 TGAACTCGCTTCGTTTTGGC 59.693 50.000 0.00 0.00 0.00 4.52
168 169 2.721797 CGATGAACTCGCTTCGTTTTGG 60.722 50.000 0.00 0.00 41.14 3.28
169 170 2.486128 CGATGAACTCGCTTCGTTTTG 58.514 47.619 0.00 0.00 41.14 2.44
170 171 1.459592 CCGATGAACTCGCTTCGTTTT 59.540 47.619 0.00 0.00 46.25 2.43
171 172 1.068474 CCGATGAACTCGCTTCGTTT 58.932 50.000 0.00 0.00 46.25 3.60
172 173 0.242825 TCCGATGAACTCGCTTCGTT 59.757 50.000 0.00 0.00 46.25 3.85
173 174 0.179161 CTCCGATGAACTCGCTTCGT 60.179 55.000 0.00 0.00 46.25 3.85
174 175 0.179161 ACTCCGATGAACTCGCTTCG 60.179 55.000 0.00 0.00 46.25 3.79
175 176 2.097791 ACTACTCCGATGAACTCGCTTC 59.902 50.000 0.00 0.00 46.25 3.86
176 177 2.093106 ACTACTCCGATGAACTCGCTT 58.907 47.619 0.00 0.00 46.25 4.68
177 178 1.402259 CACTACTCCGATGAACTCGCT 59.598 52.381 0.00 0.00 46.25 4.93
178 179 1.534175 CCACTACTCCGATGAACTCGC 60.534 57.143 0.00 0.00 46.25 5.03
180 181 2.223294 CGTCCACTACTCCGATGAACTC 60.223 54.545 0.00 0.00 0.00 3.01
181 182 1.743958 CGTCCACTACTCCGATGAACT 59.256 52.381 0.00 0.00 0.00 3.01
182 183 1.202268 CCGTCCACTACTCCGATGAAC 60.202 57.143 0.00 0.00 0.00 3.18
183 184 1.100510 CCGTCCACTACTCCGATGAA 58.899 55.000 0.00 0.00 0.00 2.57
184 185 0.750546 CCCGTCCACTACTCCGATGA 60.751 60.000 0.00 0.00 0.00 2.92
185 186 1.734137 CCCGTCCACTACTCCGATG 59.266 63.158 0.00 0.00 0.00 3.84
186 187 1.455217 CCCCGTCCACTACTCCGAT 60.455 63.158 0.00 0.00 0.00 4.18
187 188 2.044650 CCCCGTCCACTACTCCGA 60.045 66.667 0.00 0.00 0.00 4.55
188 189 3.145551 CCCCCGTCCACTACTCCG 61.146 72.222 0.00 0.00 0.00 4.63
189 190 3.468140 GCCCCCGTCCACTACTCC 61.468 72.222 0.00 0.00 0.00 3.85
190 191 3.834799 CGCCCCCGTCCACTACTC 61.835 72.222 0.00 0.00 0.00 2.59
201 202 3.699134 CTACCAAAGAGGCGCCCCC 62.699 68.421 26.15 16.22 43.14 5.40
202 203 2.124695 CTACCAAAGAGGCGCCCC 60.125 66.667 26.15 12.96 43.14 5.80
203 204 1.025113 GTTCTACCAAAGAGGCGCCC 61.025 60.000 26.15 15.34 43.14 6.13
204 205 0.036294 AGTTCTACCAAAGAGGCGCC 60.036 55.000 21.89 21.89 43.14 6.53
205 206 2.667473 TAGTTCTACCAAAGAGGCGC 57.333 50.000 0.00 0.00 43.14 6.53
206 207 4.657436 AGATAGTTCTACCAAAGAGGCG 57.343 45.455 0.00 0.00 43.14 5.52
217 218 8.508601 TCTTGGTATTCAGGGTAGATAGTTCTA 58.491 37.037 0.00 0.00 33.17 2.10
218 219 7.363031 TCTTGGTATTCAGGGTAGATAGTTCT 58.637 38.462 0.00 0.00 35.90 3.01
219 220 7.506261 TCTCTTGGTATTCAGGGTAGATAGTTC 59.494 40.741 0.00 0.00 0.00 3.01
220 221 7.363031 TCTCTTGGTATTCAGGGTAGATAGTT 58.637 38.462 0.00 0.00 0.00 2.24
221 222 6.923670 TCTCTTGGTATTCAGGGTAGATAGT 58.076 40.000 0.00 0.00 0.00 2.12
222 223 8.429237 AATCTCTTGGTATTCAGGGTAGATAG 57.571 38.462 0.00 0.00 0.00 2.08
223 224 8.235230 AGAATCTCTTGGTATTCAGGGTAGATA 58.765 37.037 0.00 0.00 35.07 1.98
224 225 7.079048 AGAATCTCTTGGTATTCAGGGTAGAT 58.921 38.462 0.00 0.00 35.07 1.98
225 226 6.444704 AGAATCTCTTGGTATTCAGGGTAGA 58.555 40.000 0.00 0.00 35.07 2.59
226 227 6.325028 TGAGAATCTCTTGGTATTCAGGGTAG 59.675 42.308 11.92 0.00 35.07 3.18
227 228 6.202331 TGAGAATCTCTTGGTATTCAGGGTA 58.798 40.000 11.92 0.00 35.07 3.69
228 229 5.032846 TGAGAATCTCTTGGTATTCAGGGT 58.967 41.667 11.92 0.00 35.07 4.34
229 230 5.620738 TGAGAATCTCTTGGTATTCAGGG 57.379 43.478 11.92 0.00 35.07 4.45
230 231 5.526846 GCTTGAGAATCTCTTGGTATTCAGG 59.473 44.000 11.92 0.00 35.07 3.86
235 236 5.112686 GTTCGCTTGAGAATCTCTTGGTAT 58.887 41.667 11.92 0.00 34.92 2.73
266 267 9.780186 AAAACTGTTAGAAATAGCAGTCTTACT 57.220 29.630 5.42 0.00 39.95 2.24
329 333 4.381079 GGTCGACAGAGATTTAGCAAGACT 60.381 45.833 18.91 0.00 0.00 3.24
340 344 2.162608 CGAAGACTTGGTCGACAGAGAT 59.837 50.000 18.91 6.07 39.64 2.75
342 346 1.267261 ACGAAGACTTGGTCGACAGAG 59.733 52.381 18.91 15.95 39.64 3.35
343 347 1.315690 ACGAAGACTTGGTCGACAGA 58.684 50.000 18.91 3.80 39.64 3.41
344 348 2.135664 AACGAAGACTTGGTCGACAG 57.864 50.000 18.91 9.69 39.64 3.51
346 350 3.572584 ACATAACGAAGACTTGGTCGAC 58.427 45.455 7.13 7.13 39.64 4.20
347 351 3.504906 AGACATAACGAAGACTTGGTCGA 59.495 43.478 3.11 0.00 39.64 4.20
348 352 3.834610 AGACATAACGAAGACTTGGTCG 58.165 45.455 3.11 0.00 42.91 4.79
351 355 3.852536 GTCGAGACATAACGAAGACTTGG 59.147 47.826 0.00 0.00 40.12 3.61
352 356 3.852536 GGTCGAGACATAACGAAGACTTG 59.147 47.826 5.55 0.00 40.12 3.16
353 357 3.425892 CGGTCGAGACATAACGAAGACTT 60.426 47.826 5.55 0.00 40.12 3.01
354 358 2.095532 CGGTCGAGACATAACGAAGACT 59.904 50.000 5.55 0.00 40.12 3.24
355 359 2.094894 TCGGTCGAGACATAACGAAGAC 59.905 50.000 5.55 0.00 40.12 3.01
356 360 2.349590 TCGGTCGAGACATAACGAAGA 58.650 47.619 5.55 0.00 40.12 2.87
372 376 2.847441 TCTCACGACTATAGCATCGGT 58.153 47.619 14.94 1.56 42.67 4.69
384 388 9.288124 CATGATCTCAATATAAGATCTCACGAC 57.712 37.037 20.48 3.33 46.14 4.34
440 445 8.826546 CTGCAAGTGACATAACATGTATAAAC 57.173 34.615 0.00 0.00 45.03 2.01
461 466 1.138069 TCAAGGTTTCAGTCGACTGCA 59.862 47.619 35.48 25.88 43.46 4.41
463 468 4.386049 GTGTATCAAGGTTTCAGTCGACTG 59.614 45.833 34.76 34.76 45.08 3.51
464 469 4.281182 AGTGTATCAAGGTTTCAGTCGACT 59.719 41.667 13.58 13.58 0.00 4.18
465 470 4.557205 AGTGTATCAAGGTTTCAGTCGAC 58.443 43.478 7.70 7.70 0.00 4.20
466 471 4.866508 AGTGTATCAAGGTTTCAGTCGA 57.133 40.909 0.00 0.00 0.00 4.20
467 472 5.696724 AGAAAGTGTATCAAGGTTTCAGTCG 59.303 40.000 0.00 0.00 30.92 4.18
472 477 9.803315 AAGAAAAAGAAAGTGTATCAAGGTTTC 57.197 29.630 0.00 0.00 0.00 2.78
504 514 3.136260 ACCCATTGTGAAACCAGCAATTT 59.864 39.130 0.00 0.00 34.36 1.82
508 518 3.529948 ACCCATTGTGAAACCAGCA 57.470 47.368 0.00 0.00 34.36 4.41
536 546 4.307443 GCTTGTGCTAGTTTTGAGGTTT 57.693 40.909 0.00 0.00 36.03 3.27
566 576 1.153647 GATCGACGGTGACCATGCA 60.154 57.895 1.11 0.00 0.00 3.96
567 577 2.230940 CGATCGACGGTGACCATGC 61.231 63.158 10.26 0.00 38.46 4.06
568 578 2.382624 GAACGATCGACGGTGACCATG 61.383 57.143 24.34 0.00 44.13 3.66
569 579 0.179145 GAACGATCGACGGTGACCAT 60.179 55.000 24.34 0.00 44.13 3.55
591 601 1.484356 CTTGTCTTTGTTGCTGCTGC 58.516 50.000 8.89 8.89 40.20 5.25
1434 1453 0.250513 AGCCATGGAGAAGGACGTTC 59.749 55.000 18.40 0.00 35.08 3.95
1581 1600 2.096013 CGTCTTACTGATGAGCTCGTCA 59.904 50.000 31.50 31.50 39.38 4.35
1639 1658 1.260538 TGGTAGGCAGCCTCTGACAG 61.261 60.000 20.38 0.00 42.99 3.51
1992 2011 4.624024 CCGTTGATGTACACGTTGAAGTAT 59.376 41.667 0.00 0.00 0.00 2.12
2124 2143 2.658593 GGCCCGACGTCGATGATG 60.659 66.667 37.65 20.57 43.02 3.07
2409 2428 2.125106 GACTGGCCCGTGTGGATC 60.125 66.667 3.79 0.00 37.49 3.36
2454 2476 1.263356 CGGTGGAGGAGAAGGTGTAA 58.737 55.000 0.00 0.00 0.00 2.41
2531 2553 2.732468 CGATGATGGCGCTCTCGG 60.732 66.667 7.64 0.00 35.95 4.63
2607 2629 1.225704 GGCCACCTTGATCCTGGAG 59.774 63.158 1.52 0.72 0.00 3.86
2952 2974 0.817634 CCTTGGCCACGAACTTGTCA 60.818 55.000 11.54 0.00 0.00 3.58
3111 3163 3.650950 AGCAGCACCACCCCGAAT 61.651 61.111 0.00 0.00 0.00 3.34
3477 3529 2.933287 TTGGCGGAGGTGGTGGAT 60.933 61.111 0.00 0.00 0.00 3.41
3528 3580 3.741249 CAGAAGATGGATGGATCACCTG 58.259 50.000 0.00 0.00 37.04 4.00
3531 3583 3.204306 TGCAGAAGATGGATGGATCAC 57.796 47.619 0.00 0.00 0.00 3.06
3534 3586 2.636403 TCGATGCAGAAGATGGATGGAT 59.364 45.455 0.00 0.00 40.55 3.41
3535 3587 2.041701 TCGATGCAGAAGATGGATGGA 58.958 47.619 0.00 0.00 40.55 3.41
3536 3588 2.538512 TCGATGCAGAAGATGGATGG 57.461 50.000 0.00 0.00 40.55 3.51
3550 3602 3.869832 GAGGTATGGATCATGCATCGATG 59.130 47.826 21.27 21.27 32.51 3.84
3558 3610 2.289882 ACGCATGGAGGTATGGATCATG 60.290 50.000 0.00 0.00 38.46 3.07
3559 3611 1.980765 ACGCATGGAGGTATGGATCAT 59.019 47.619 0.00 0.00 0.00 2.45
3560 3612 1.344438 GACGCATGGAGGTATGGATCA 59.656 52.381 0.00 0.00 0.00 2.92
3561 3613 1.670087 CGACGCATGGAGGTATGGATC 60.670 57.143 0.00 0.00 0.00 3.36
3565 3617 1.956170 GGCGACGCATGGAGGTATG 60.956 63.158 23.09 0.00 0.00 2.39
3566 3618 2.421739 GGCGACGCATGGAGGTAT 59.578 61.111 23.09 0.00 0.00 2.73
3661 3713 1.601166 GATGCATGCATGGACTAGCA 58.399 50.000 36.73 18.11 45.92 3.49
3696 3748 4.550076 ATGATGATCGGATCCTTCCTTC 57.450 45.455 15.06 7.27 40.17 3.46
3713 3765 5.768164 ACCTCGTTTGGTTTTGAGTTATGAT 59.232 36.000 0.00 0.00 36.89 2.45
3714 3766 5.127491 ACCTCGTTTGGTTTTGAGTTATGA 58.873 37.500 0.00 0.00 36.89 2.15
3715 3767 5.432885 ACCTCGTTTGGTTTTGAGTTATG 57.567 39.130 0.00 0.00 36.89 1.90
3796 3850 6.475402 CGGTATACATTTTGGAATTTTCTGCC 59.525 38.462 5.01 0.00 0.00 4.85
4108 4168 9.129209 GCTTTTAGACACCATTTAATCAAACTC 57.871 33.333 0.00 0.00 0.00 3.01
4157 4217 8.512138 GTTCAAGGTAGCAATGTTAATGTTACT 58.488 33.333 0.00 0.00 35.56 2.24
4288 4353 6.828785 ACCACCCACTCAATCTATTCATAAAC 59.171 38.462 0.00 0.00 0.00 2.01
4333 4399 8.793592 CCTACCTTTAATAAAAGCAGTTTGTCT 58.206 33.333 0.00 0.00 40.73 3.41
4334 4400 8.573885 ACCTACCTTTAATAAAAGCAGTTTGTC 58.426 33.333 0.00 0.00 40.73 3.18
4356 5564 2.841881 GGACCCTTCCACAATGTACCTA 59.158 50.000 0.00 0.00 42.30 3.08
4419 5628 7.014134 TCCACTTTGAAAATCATAGCACTTTGA 59.986 33.333 0.00 0.00 30.07 2.69
4422 5631 6.491403 AGTCCACTTTGAAAATCATAGCACTT 59.509 34.615 0.00 0.00 30.07 3.16


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

AutoCloner maintained by Alex Coulton.