Multiple sequence alignment - TraesCS7B01G286500

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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 TraesCS7B01G286500 chr7B 100.000 4545 0 0 538 5082 521619026 521614482 0.000000e+00 8394.0
1 TraesCS7B01G286500 chr7B 100.000 219 0 0 1 219 521619563 521619345 6.130000e-109 405.0
2 TraesCS7B01G286500 chr7D 94.423 4572 155 31 562 5082 492223031 492218509 0.000000e+00 6938.0
3 TraesCS7B01G286500 chr7A 94.616 3826 122 28 547 4337 558758110 558754334 0.000000e+00 5847.0
4 TraesCS7B01G286500 chr7A 94.205 673 32 5 4412 5082 558754320 558753653 0.000000e+00 1020.0
5 TraesCS7B01G286500 chr4D 83.644 483 70 8 2476 2952 70119317 70119796 3.610000e-121 446.0
6 TraesCS7B01G286500 chr4D 81.443 194 34 2 3598 3790 70120253 70120445 1.890000e-34 158.0
7 TraesCS7B01G286500 chr4B 83.644 483 70 8 2476 2952 103773177 103773656 3.610000e-121 446.0
8 TraesCS7B01G286500 chr4B 81.915 188 32 2 3598 3784 103774113 103774299 1.890000e-34 158.0
9 TraesCS7B01G286500 chr4A 83.644 483 70 8 2476 2952 522294349 522294828 3.610000e-121 446.0
10 TraesCS7B01G286500 chr4A 91.705 217 16 2 1 216 185746748 185746963 2.970000e-77 300.0
11 TraesCS7B01G286500 chr4A 81.443 194 34 2 3598 3790 522295285 522295477 1.890000e-34 158.0
12 TraesCS7B01G286500 chr1D 94.737 228 12 0 1257 1484 42038588 42038815 6.260000e-94 355.0
13 TraesCS7B01G286500 chr1D 92.920 113 6 2 1096 1207 42038495 42038606 4.070000e-36 163.0
14 TraesCS7B01G286500 chr1D 97.826 92 2 0 1603 1694 42038810 42038901 5.270000e-35 159.0
15 TraesCS7B01G286500 chr2D 93.421 228 15 0 1257 1484 28963979 28964206 6.300000e-89 339.0
16 TraesCS7B01G286500 chr2D 92.920 113 6 2 1096 1207 28963886 28963997 4.070000e-36 163.0
17 TraesCS7B01G286500 chr2D 95.652 92 4 0 1603 1694 28964201 28964292 1.140000e-31 148.0
18 TraesCS7B01G286500 chr3B 94.884 215 10 1 2 216 787453746 787453533 8.150000e-88 335.0
19 TraesCS7B01G286500 chr3B 94.419 215 11 1 2 216 787443623 787443410 3.790000e-86 329.0
20 TraesCS7B01G286500 chr3B 94.419 215 11 1 2 216 787448685 787448472 3.790000e-86 329.0
21 TraesCS7B01G286500 chr3B 94.419 215 11 1 2 216 787458809 787458596 3.790000e-86 329.0
22 TraesCS7B01G286500 chr3B 92.558 215 13 2 2 216 191259832 191259621 6.390000e-79 305.0
23 TraesCS7B01G286500 chr3B 91.388 209 15 2 8 216 191264869 191264664 3.000000e-72 283.0
24 TraesCS7B01G286500 chr5D 78.343 531 101 9 2436 2956 197152404 197151878 1.050000e-86 331.0
25 TraesCS7B01G286500 chrUn 94.419 215 11 1 2 216 416511022 416510809 3.790000e-86 329.0
26 TraesCS7B01G286500 chr5B 78.842 501 96 6 2436 2928 213250429 213250927 3.790000e-86 329.0
27 TraesCS7B01G286500 chr5A 78.884 502 94 8 2436 2928 227923754 227924252 3.790000e-86 329.0
28 TraesCS7B01G286500 chr5A 91.667 216 16 2 2 216 427094040 427094254 1.070000e-76 298.0
29 TraesCS7B01G286500 chr3A 92.544 228 17 0 1257 1484 13265216 13264989 1.360000e-85 327.0
30 TraesCS7B01G286500 chr3A 92.035 113 7 2 1096 1207 13265309 13265198 1.890000e-34 158.0
31 TraesCS7B01G286500 chr3A 89.000 100 5 3 1604 1697 13264993 13264894 8.940000e-23 119.0
32 TraesCS7B01G286500 chr3A 93.750 48 3 0 1730 1777 13264840 13264887 7.060000e-09 73.1


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 TraesCS7B01G286500 chr7B 521614482 521619563 5081 True 4399.5 8394 100.0000 1 5082 2 chr7B.!!$R1 5081
1 TraesCS7B01G286500 chr7D 492218509 492223031 4522 True 6938.0 6938 94.4230 562 5082 1 chr7D.!!$R1 4520
2 TraesCS7B01G286500 chr7A 558753653 558758110 4457 True 3433.5 5847 94.4105 547 5082 2 chr7A.!!$R1 4535
3 TraesCS7B01G286500 chr4D 70119317 70120445 1128 False 302.0 446 82.5435 2476 3790 2 chr4D.!!$F1 1314
4 TraesCS7B01G286500 chr4B 103773177 103774299 1122 False 302.0 446 82.7795 2476 3784 2 chr4B.!!$F1 1308
5 TraesCS7B01G286500 chr4A 522294349 522295477 1128 False 302.0 446 82.5435 2476 3790 2 chr4A.!!$F2 1314
6 TraesCS7B01G286500 chr5D 197151878 197152404 526 True 331.0 331 78.3430 2436 2956 1 chr5D.!!$R1 520

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
187 188 0.031817 CCCCTTTCCTCCATGGCAAT 60.032 55.000 6.96 0.0 35.26 3.56 F
832 841 0.179034 GTCATCCCCACATCCTGCTC 60.179 60.000 0.00 0.0 0.00 4.26 F
1263 1276 0.471211 ACGAGGTGACCAGGGAGAAA 60.471 55.000 3.63 0.0 0.00 2.52 F
2936 2969 1.204941 GTGTACCAGAAGCTCACCGAT 59.795 52.381 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1807 1.354705 TCGGGTCTATCCTCATCCGAT 59.645 52.381 0.00 0.0 41.11 4.18 R
2444 2468 1.069765 CTGGACCAGCTTCGTGTGT 59.930 57.895 8.99 0.0 0.00 3.72 R
3030 3075 0.390340 GTCAGAGCCGTCATTGCTGA 60.390 55.000 0.00 0.0 39.69 4.26 R
4353 4426 1.073177 ACGTATCGCCCGTTTTGAAG 58.927 50.000 0.00 0.0 34.28 3.02 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
24 25 3.827782 CGATACGCATCAGACGAGT 57.172 52.632 0.00 0.00 0.00 4.18
25 26 1.389853 CGATACGCATCAGACGAGTG 58.610 55.000 0.00 0.00 0.00 3.51
26 27 1.759994 GATACGCATCAGACGAGTGG 58.240 55.000 0.00 0.00 0.00 4.00
27 28 0.385751 ATACGCATCAGACGAGTGGG 59.614 55.000 0.00 0.00 0.00 4.61
28 29 0.963856 TACGCATCAGACGAGTGGGT 60.964 55.000 0.00 0.00 41.17 4.51
29 30 1.517257 CGCATCAGACGAGTGGGTC 60.517 63.158 0.00 0.00 37.19 4.46
30 31 1.591703 GCATCAGACGAGTGGGTCA 59.408 57.895 0.00 0.00 39.42 4.02
31 32 0.037326 GCATCAGACGAGTGGGTCAA 60.037 55.000 0.00 0.00 39.42 3.18
32 33 2.001812 CATCAGACGAGTGGGTCAAG 57.998 55.000 0.00 0.00 39.42 3.02
33 34 1.273606 CATCAGACGAGTGGGTCAAGT 59.726 52.381 0.00 0.00 39.42 3.16
34 35 0.673985 TCAGACGAGTGGGTCAAGTG 59.326 55.000 0.00 0.00 39.42 3.16
35 36 0.673985 CAGACGAGTGGGTCAAGTGA 59.326 55.000 0.00 0.00 39.42 3.41
36 37 1.068588 CAGACGAGTGGGTCAAGTGAA 59.931 52.381 0.00 0.00 39.42 3.18
37 38 1.068741 AGACGAGTGGGTCAAGTGAAC 59.931 52.381 0.00 0.00 39.42 3.18
38 39 1.068741 GACGAGTGGGTCAAGTGAACT 59.931 52.381 0.00 0.00 36.91 3.01
39 40 2.295349 GACGAGTGGGTCAAGTGAACTA 59.705 50.000 0.00 0.00 36.91 2.24
40 41 2.897969 ACGAGTGGGTCAAGTGAACTAT 59.102 45.455 0.00 0.00 31.02 2.12
41 42 4.084287 ACGAGTGGGTCAAGTGAACTATA 58.916 43.478 0.00 0.00 31.02 1.31
42 43 4.710375 ACGAGTGGGTCAAGTGAACTATAT 59.290 41.667 0.00 0.00 31.02 0.86
43 44 5.889853 ACGAGTGGGTCAAGTGAACTATATA 59.110 40.000 0.00 0.00 31.02 0.86
44 45 6.550108 ACGAGTGGGTCAAGTGAACTATATAT 59.450 38.462 0.00 0.00 31.02 0.86
45 46 7.085116 CGAGTGGGTCAAGTGAACTATATATC 58.915 42.308 0.00 0.00 31.02 1.63
46 47 6.982852 AGTGGGTCAAGTGAACTATATATCG 58.017 40.000 0.00 0.00 31.02 2.92
47 48 6.776116 AGTGGGTCAAGTGAACTATATATCGA 59.224 38.462 0.00 0.00 31.02 3.59
48 49 6.862090 GTGGGTCAAGTGAACTATATATCGAC 59.138 42.308 0.00 0.00 31.02 4.20
49 50 6.084925 GGGTCAAGTGAACTATATATCGACG 58.915 44.000 0.00 0.00 31.02 5.12
50 51 6.293845 GGGTCAAGTGAACTATATATCGACGT 60.294 42.308 0.00 0.00 31.02 4.34
51 52 6.577800 GGTCAAGTGAACTATATATCGACGTG 59.422 42.308 0.00 0.00 0.00 4.49
52 53 7.130917 GTCAAGTGAACTATATATCGACGTGT 58.869 38.462 0.00 0.00 0.00 4.49
53 54 7.320797 GTCAAGTGAACTATATATCGACGTGTC 59.679 40.741 0.00 0.00 0.00 3.67
54 55 6.238610 AGTGAACTATATATCGACGTGTCC 57.761 41.667 0.00 0.00 0.00 4.02
55 56 5.180868 AGTGAACTATATATCGACGTGTCCC 59.819 44.000 0.00 0.00 0.00 4.46
56 57 5.049198 GTGAACTATATATCGACGTGTCCCA 60.049 44.000 0.00 0.00 0.00 4.37
57 58 5.180680 TGAACTATATATCGACGTGTCCCAG 59.819 44.000 0.00 0.00 0.00 4.45
58 59 3.439476 ACTATATATCGACGTGTCCCAGC 59.561 47.826 0.00 0.00 0.00 4.85
59 60 1.977056 TATATCGACGTGTCCCAGCT 58.023 50.000 0.00 0.00 0.00 4.24
60 61 1.977056 ATATCGACGTGTCCCAGCTA 58.023 50.000 0.00 0.00 0.00 3.32
61 62 1.019673 TATCGACGTGTCCCAGCTAC 58.980 55.000 0.00 0.00 0.00 3.58
62 63 1.664321 ATCGACGTGTCCCAGCTACC 61.664 60.000 0.00 0.00 0.00 3.18
63 64 2.181021 GACGTGTCCCAGCTACCG 59.819 66.667 0.00 0.00 0.00 4.02
64 65 2.599578 ACGTGTCCCAGCTACCGT 60.600 61.111 0.00 0.00 0.00 4.83
65 66 2.126071 CGTGTCCCAGCTACCGTG 60.126 66.667 0.00 0.00 0.00 4.94
66 67 2.927580 CGTGTCCCAGCTACCGTGT 61.928 63.158 0.00 0.00 0.00 4.49
67 68 1.080025 GTGTCCCAGCTACCGTGTC 60.080 63.158 0.00 0.00 0.00 3.67
68 69 1.532078 TGTCCCAGCTACCGTGTCA 60.532 57.895 0.00 0.00 0.00 3.58
69 70 0.902984 TGTCCCAGCTACCGTGTCAT 60.903 55.000 0.00 0.00 0.00 3.06
70 71 0.249398 GTCCCAGCTACCGTGTCATT 59.751 55.000 0.00 0.00 0.00 2.57
71 72 0.535335 TCCCAGCTACCGTGTCATTC 59.465 55.000 0.00 0.00 0.00 2.67
72 73 0.806102 CCCAGCTACCGTGTCATTCG 60.806 60.000 0.00 0.00 0.00 3.34
78 79 3.903783 CCGTGTCATTCGGCCATT 58.096 55.556 2.24 0.00 41.48 3.16
79 80 1.429021 CCGTGTCATTCGGCCATTG 59.571 57.895 2.24 0.00 41.48 2.82
80 81 1.429021 CGTGTCATTCGGCCATTGG 59.571 57.895 2.24 0.00 0.00 3.16
81 82 1.305219 CGTGTCATTCGGCCATTGGT 61.305 55.000 2.24 0.00 0.00 3.67
82 83 0.887933 GTGTCATTCGGCCATTGGTT 59.112 50.000 2.24 0.00 0.00 3.67
83 84 0.887247 TGTCATTCGGCCATTGGTTG 59.113 50.000 2.24 0.00 0.00 3.77
84 85 1.173043 GTCATTCGGCCATTGGTTGA 58.827 50.000 2.24 0.00 0.00 3.18
85 86 1.543802 GTCATTCGGCCATTGGTTGAA 59.456 47.619 2.24 12.22 0.00 2.69
86 87 1.543802 TCATTCGGCCATTGGTTGAAC 59.456 47.619 2.24 0.00 0.00 3.18
87 88 0.525761 ATTCGGCCATTGGTTGAACG 59.474 50.000 2.24 6.69 0.00 3.95
88 89 1.519751 TTCGGCCATTGGTTGAACGG 61.520 55.000 2.24 0.00 0.00 4.44
89 90 2.261361 GGCCATTGGTTGAACGGC 59.739 61.111 4.26 3.73 42.21 5.68
90 91 2.275380 GGCCATTGGTTGAACGGCT 61.275 57.895 10.90 0.00 42.56 5.52
91 92 1.212751 GCCATTGGTTGAACGGCTC 59.787 57.895 4.26 0.00 39.73 4.70
92 93 1.244019 GCCATTGGTTGAACGGCTCT 61.244 55.000 4.26 0.00 39.73 4.09
93 94 0.523072 CCATTGGTTGAACGGCTCTG 59.477 55.000 0.00 0.00 0.00 3.35
94 95 1.238439 CATTGGTTGAACGGCTCTGT 58.762 50.000 0.00 0.00 0.00 3.41
95 96 1.608590 CATTGGTTGAACGGCTCTGTT 59.391 47.619 0.00 0.00 34.02 3.16
96 97 1.305201 TTGGTTGAACGGCTCTGTTC 58.695 50.000 13.21 13.21 46.63 3.18
102 103 2.823628 AACGGCTCTGTTCGTTAGC 58.176 52.632 0.00 0.00 45.97 3.09
103 104 0.317479 AACGGCTCTGTTCGTTAGCT 59.683 50.000 0.00 0.00 45.97 3.32
104 105 0.317479 ACGGCTCTGTTCGTTAGCTT 59.683 50.000 0.00 0.00 36.04 3.74
105 106 0.716108 CGGCTCTGTTCGTTAGCTTG 59.284 55.000 0.00 0.00 36.48 4.01
106 107 1.797025 GGCTCTGTTCGTTAGCTTGT 58.203 50.000 0.00 0.00 36.48 3.16
107 108 2.670229 CGGCTCTGTTCGTTAGCTTGTA 60.670 50.000 0.00 0.00 36.48 2.41
108 109 3.323243 GGCTCTGTTCGTTAGCTTGTAA 58.677 45.455 0.00 0.00 36.48 2.41
109 110 3.368236 GGCTCTGTTCGTTAGCTTGTAAG 59.632 47.826 0.00 0.00 36.48 2.34
110 111 4.235360 GCTCTGTTCGTTAGCTTGTAAGA 58.765 43.478 0.00 0.00 33.40 2.10
111 112 4.324936 GCTCTGTTCGTTAGCTTGTAAGAG 59.675 45.833 0.00 0.00 33.40 2.85
112 113 4.806330 TCTGTTCGTTAGCTTGTAAGAGG 58.194 43.478 0.00 0.00 0.00 3.69
113 114 4.521639 TCTGTTCGTTAGCTTGTAAGAGGA 59.478 41.667 0.00 0.00 0.00 3.71
114 115 4.806330 TGTTCGTTAGCTTGTAAGAGGAG 58.194 43.478 0.00 0.00 0.00 3.69
115 116 4.521639 TGTTCGTTAGCTTGTAAGAGGAGA 59.478 41.667 0.00 0.00 0.00 3.71
116 117 5.010314 TGTTCGTTAGCTTGTAAGAGGAGAA 59.990 40.000 0.00 0.00 0.00 2.87
117 118 5.717078 TCGTTAGCTTGTAAGAGGAGAAA 57.283 39.130 0.00 0.00 0.00 2.52
118 119 5.467705 TCGTTAGCTTGTAAGAGGAGAAAC 58.532 41.667 0.00 0.00 0.00 2.78
119 120 4.626172 CGTTAGCTTGTAAGAGGAGAAACC 59.374 45.833 0.00 0.00 39.35 3.27
133 134 5.918426 GGAGAAACCTGTAACTAGCTACT 57.082 43.478 4.98 0.00 35.41 2.57
134 135 5.652518 GGAGAAACCTGTAACTAGCTACTG 58.347 45.833 4.98 4.36 35.41 2.74
135 136 5.074584 AGAAACCTGTAACTAGCTACTGC 57.925 43.478 4.98 0.00 40.05 4.40
136 137 4.527038 AGAAACCTGTAACTAGCTACTGCA 59.473 41.667 4.98 0.00 42.74 4.41
137 138 4.884668 AACCTGTAACTAGCTACTGCAA 57.115 40.909 4.98 0.00 42.74 4.08
138 139 5.422214 AACCTGTAACTAGCTACTGCAAT 57.578 39.130 4.98 0.00 42.74 3.56
139 140 5.422214 ACCTGTAACTAGCTACTGCAATT 57.578 39.130 4.98 0.00 42.74 2.32
140 141 5.420409 ACCTGTAACTAGCTACTGCAATTC 58.580 41.667 4.98 0.00 42.74 2.17
141 142 4.504461 CCTGTAACTAGCTACTGCAATTCG 59.496 45.833 4.98 0.00 42.74 3.34
142 143 5.319140 TGTAACTAGCTACTGCAATTCGA 57.681 39.130 4.98 0.00 42.74 3.71
143 144 5.716094 TGTAACTAGCTACTGCAATTCGAA 58.284 37.500 0.00 0.00 42.74 3.71
144 145 6.338146 TGTAACTAGCTACTGCAATTCGAAT 58.662 36.000 4.39 4.39 42.74 3.34
145 146 7.485810 TGTAACTAGCTACTGCAATTCGAATA 58.514 34.615 11.83 0.00 42.74 1.75
146 147 6.830114 AACTAGCTACTGCAATTCGAATAC 57.170 37.500 11.83 7.59 42.74 1.89
147 148 6.150396 ACTAGCTACTGCAATTCGAATACT 57.850 37.500 11.83 0.00 42.74 2.12
148 149 5.980116 ACTAGCTACTGCAATTCGAATACTG 59.020 40.000 11.83 12.69 42.74 2.74
149 150 5.011090 AGCTACTGCAATTCGAATACTGA 57.989 39.130 11.83 0.00 42.74 3.41
150 151 5.419542 AGCTACTGCAATTCGAATACTGAA 58.580 37.500 11.83 0.35 42.74 3.02
151 152 5.874810 AGCTACTGCAATTCGAATACTGAAA 59.125 36.000 11.83 0.00 42.74 2.69
152 153 6.540189 AGCTACTGCAATTCGAATACTGAAAT 59.460 34.615 11.83 0.00 42.74 2.17
153 154 7.710907 AGCTACTGCAATTCGAATACTGAAATA 59.289 33.333 11.83 0.00 42.74 1.40
154 155 8.335356 GCTACTGCAATTCGAATACTGAAATAA 58.665 33.333 11.83 0.00 39.41 1.40
157 158 9.722056 ACTGCAATTCGAATACTGAAATAATTC 57.278 29.630 11.83 0.00 36.04 2.17
158 159 9.173939 CTGCAATTCGAATACTGAAATAATTCC 57.826 33.333 11.83 0.00 34.49 3.01
159 160 8.902806 TGCAATTCGAATACTGAAATAATTCCT 58.097 29.630 11.83 0.00 34.49 3.36
160 161 9.387123 GCAATTCGAATACTGAAATAATTCCTC 57.613 33.333 11.83 0.00 34.49 3.71
164 165 9.751542 TTCGAATACTGAAATAATTCCTCTCTC 57.248 33.333 0.00 0.00 34.49 3.20
165 166 8.076781 TCGAATACTGAAATAATTCCTCTCTCG 58.923 37.037 0.00 0.00 34.49 4.04
166 167 8.076781 CGAATACTGAAATAATTCCTCTCTCGA 58.923 37.037 0.00 0.00 34.49 4.04
167 168 9.921637 GAATACTGAAATAATTCCTCTCTCGAT 57.078 33.333 0.00 0.00 34.49 3.59
168 169 9.921637 AATACTGAAATAATTCCTCTCTCGATC 57.078 33.333 0.00 0.00 34.49 3.69
169 170 6.754193 ACTGAAATAATTCCTCTCTCGATCC 58.246 40.000 0.00 0.00 34.49 3.36
170 171 6.102897 TGAAATAATTCCTCTCTCGATCCC 57.897 41.667 0.00 0.00 34.49 3.85
171 172 5.012148 TGAAATAATTCCTCTCTCGATCCCC 59.988 44.000 0.00 0.00 34.49 4.81
172 173 2.785357 AATTCCTCTCTCGATCCCCT 57.215 50.000 0.00 0.00 0.00 4.79
173 174 2.785357 ATTCCTCTCTCGATCCCCTT 57.215 50.000 0.00 0.00 0.00 3.95
174 175 2.552093 TTCCTCTCTCGATCCCCTTT 57.448 50.000 0.00 0.00 0.00 3.11
175 176 2.074729 TCCTCTCTCGATCCCCTTTC 57.925 55.000 0.00 0.00 0.00 2.62
176 177 1.044611 CCTCTCTCGATCCCCTTTCC 58.955 60.000 0.00 0.00 0.00 3.13
177 178 1.412361 CCTCTCTCGATCCCCTTTCCT 60.412 57.143 0.00 0.00 0.00 3.36
178 179 1.960689 CTCTCTCGATCCCCTTTCCTC 59.039 57.143 0.00 0.00 0.00 3.71
179 180 1.044611 CTCTCGATCCCCTTTCCTCC 58.955 60.000 0.00 0.00 0.00 4.30
180 181 0.338467 TCTCGATCCCCTTTCCTCCA 59.662 55.000 0.00 0.00 0.00 3.86
181 182 1.062121 TCTCGATCCCCTTTCCTCCAT 60.062 52.381 0.00 0.00 0.00 3.41
182 183 1.071385 CTCGATCCCCTTTCCTCCATG 59.929 57.143 0.00 0.00 0.00 3.66
183 184 0.109342 CGATCCCCTTTCCTCCATGG 59.891 60.000 4.97 4.97 37.10 3.66
184 185 0.178978 GATCCCCTTTCCTCCATGGC 60.179 60.000 6.96 0.00 35.26 4.40
185 186 0.925720 ATCCCCTTTCCTCCATGGCA 60.926 55.000 6.96 0.00 35.26 4.92
186 187 1.145900 TCCCCTTTCCTCCATGGCAA 61.146 55.000 6.96 0.00 35.26 4.52
187 188 0.031817 CCCCTTTCCTCCATGGCAAT 60.032 55.000 6.96 0.00 35.26 3.56
188 189 1.406903 CCCTTTCCTCCATGGCAATC 58.593 55.000 6.96 0.00 35.26 2.67
189 190 1.406903 CCTTTCCTCCATGGCAATCC 58.593 55.000 6.96 0.00 35.26 3.01
190 191 1.406903 CTTTCCTCCATGGCAATCCC 58.593 55.000 6.96 0.00 35.26 3.85
191 192 1.009997 TTTCCTCCATGGCAATCCCT 58.990 50.000 6.96 0.00 35.26 4.20
192 193 1.009997 TTCCTCCATGGCAATCCCTT 58.990 50.000 6.96 0.00 35.26 3.95
193 194 0.259647 TCCTCCATGGCAATCCCTTG 59.740 55.000 6.96 0.00 38.24 3.61
194 195 0.259647 CCTCCATGGCAATCCCTTGA 59.740 55.000 6.96 0.00 40.33 3.02
195 196 1.688772 CTCCATGGCAATCCCTTGAG 58.311 55.000 6.96 0.00 40.33 3.02
196 197 1.213678 CTCCATGGCAATCCCTTGAGA 59.786 52.381 6.96 0.00 40.33 3.27
197 198 1.854939 TCCATGGCAATCCCTTGAGAT 59.145 47.619 6.96 0.00 40.33 2.75
198 199 2.245546 TCCATGGCAATCCCTTGAGATT 59.754 45.455 6.96 0.00 40.33 2.40
199 200 2.626743 CCATGGCAATCCCTTGAGATTC 59.373 50.000 0.00 0.00 40.33 2.52
200 201 2.042686 TGGCAATCCCTTGAGATTCG 57.957 50.000 0.00 0.00 34.19 3.34
201 202 1.281867 TGGCAATCCCTTGAGATTCGT 59.718 47.619 0.00 0.00 34.19 3.85
202 203 2.503765 TGGCAATCCCTTGAGATTCGTA 59.496 45.455 0.00 0.00 34.19 3.43
203 204 3.134458 GGCAATCCCTTGAGATTCGTAG 58.866 50.000 0.00 0.00 34.19 3.51
204 205 2.545946 GCAATCCCTTGAGATTCGTAGC 59.454 50.000 0.00 0.00 34.19 3.58
205 206 3.742640 GCAATCCCTTGAGATTCGTAGCT 60.743 47.826 0.00 0.00 34.19 3.32
206 207 4.501571 GCAATCCCTTGAGATTCGTAGCTA 60.502 45.833 0.00 0.00 34.19 3.32
207 208 5.226396 CAATCCCTTGAGATTCGTAGCTAG 58.774 45.833 0.00 0.00 34.19 3.42
208 209 3.899726 TCCCTTGAGATTCGTAGCTAGT 58.100 45.455 0.00 0.00 0.00 2.57
209 210 4.279145 TCCCTTGAGATTCGTAGCTAGTT 58.721 43.478 0.00 0.00 0.00 2.24
210 211 4.098044 TCCCTTGAGATTCGTAGCTAGTTG 59.902 45.833 0.00 0.00 0.00 3.16
211 212 4.142138 CCCTTGAGATTCGTAGCTAGTTGT 60.142 45.833 0.00 0.00 0.00 3.32
212 213 5.411781 CCTTGAGATTCGTAGCTAGTTGTT 58.588 41.667 0.00 0.00 0.00 2.83
213 214 6.405508 CCCTTGAGATTCGTAGCTAGTTGTTA 60.406 42.308 0.00 0.00 0.00 2.41
214 215 7.033791 CCTTGAGATTCGTAGCTAGTTGTTAA 58.966 38.462 0.00 0.00 0.00 2.01
215 216 7.009357 CCTTGAGATTCGTAGCTAGTTGTTAAC 59.991 40.741 0.00 0.00 0.00 2.01
216 217 6.327934 TGAGATTCGTAGCTAGTTGTTAACC 58.672 40.000 2.48 0.00 0.00 2.85
217 218 5.658468 AGATTCGTAGCTAGTTGTTAACCC 58.342 41.667 2.48 0.00 0.00 4.11
218 219 4.870123 TTCGTAGCTAGTTGTTAACCCA 57.130 40.909 2.48 0.00 0.00 4.51
814 823 3.941188 CCTGCTGACCCCACACGT 61.941 66.667 0.00 0.00 0.00 4.49
816 825 3.157949 TGCTGACCCCACACGTCA 61.158 61.111 0.00 0.00 37.91 4.35
817 826 2.347490 GCTGACCCCACACGTCAT 59.653 61.111 0.00 0.00 39.43 3.06
818 827 1.741770 GCTGACCCCACACGTCATC 60.742 63.158 0.00 0.00 39.43 2.92
820 829 2.267961 GACCCCACACGTCATCCC 59.732 66.667 0.00 0.00 0.00 3.85
821 830 3.325201 GACCCCACACGTCATCCCC 62.325 68.421 0.00 0.00 0.00 4.81
822 831 3.326578 CCCCACACGTCATCCCCA 61.327 66.667 0.00 0.00 0.00 4.96
823 832 2.046314 CCCACACGTCATCCCCAC 60.046 66.667 0.00 0.00 0.00 4.61
824 833 2.747022 CCACACGTCATCCCCACA 59.253 61.111 0.00 0.00 0.00 4.17
825 834 1.299648 CCACACGTCATCCCCACAT 59.700 57.895 0.00 0.00 0.00 3.21
826 835 0.744414 CCACACGTCATCCCCACATC 60.744 60.000 0.00 0.00 0.00 3.06
827 836 0.744414 CACACGTCATCCCCACATCC 60.744 60.000 0.00 0.00 0.00 3.51
828 837 0.909610 ACACGTCATCCCCACATCCT 60.910 55.000 0.00 0.00 0.00 3.24
829 838 0.462581 CACGTCATCCCCACATCCTG 60.463 60.000 0.00 0.00 0.00 3.86
830 839 1.524621 CGTCATCCCCACATCCTGC 60.525 63.158 0.00 0.00 0.00 4.85
831 840 1.918253 GTCATCCCCACATCCTGCT 59.082 57.895 0.00 0.00 0.00 4.24
832 841 0.179034 GTCATCCCCACATCCTGCTC 60.179 60.000 0.00 0.00 0.00 4.26
833 842 1.227764 CATCCCCACATCCTGCTCG 60.228 63.158 0.00 0.00 0.00 5.03
834 843 3.112205 ATCCCCACATCCTGCTCGC 62.112 63.158 0.00 0.00 0.00 5.03
1143 1156 4.197498 GTCGCCGGCGCCTACTTA 62.197 66.667 42.78 22.47 39.59 2.24
1263 1276 0.471211 ACGAGGTGACCAGGGAGAAA 60.471 55.000 3.63 0.00 0.00 2.52
1457 1470 1.303398 AGGACTCCAAGAGCGACGA 60.303 57.895 0.00 0.00 32.04 4.20
1541 1554 3.462678 GGAGGAGGAGGACGCCAC 61.463 72.222 0.00 0.00 42.23 5.01
1542 1555 3.827898 GAGGAGGAGGACGCCACG 61.828 72.222 0.00 0.00 42.23 4.94
1872 1885 2.182030 CTGGTCGAAGAGGACGGC 59.818 66.667 0.00 0.00 36.95 5.68
1914 1927 2.269241 GACCCCGGGCAAGAAGAG 59.731 66.667 17.73 0.15 0.00 2.85
2309 2325 4.735132 CCTCGTCGCGCTCCCAAA 62.735 66.667 5.56 0.00 0.00 3.28
2389 2405 3.118884 ACATTCTTCTTGCCATGGATTGC 60.119 43.478 18.40 0.00 0.00 3.56
2391 2407 3.650281 TCTTCTTGCCATGGATTGCTA 57.350 42.857 18.40 0.00 0.00 3.49
2392 2408 3.966979 TCTTCTTGCCATGGATTGCTAA 58.033 40.909 18.40 0.15 0.00 3.09
2411 2427 1.235724 ACTCACTGACACGACGATGA 58.764 50.000 0.00 0.00 0.00 2.92
2471 2495 2.224159 GCTGGTCCAGGTGAAGGGA 61.224 63.158 20.72 0.00 31.21 4.20
2504 2534 1.264749 TGAAGGTGAGCGGGCAGTAT 61.265 55.000 0.00 0.00 0.00 2.12
2540 2573 3.909662 GGCACGCAGTTCATCCAT 58.090 55.556 0.00 0.00 41.61 3.41
2660 2693 1.683441 CTTCGGGGGCTACCTGTTT 59.317 57.895 6.69 0.00 46.44 2.83
2936 2969 1.204941 GTGTACCAGAAGCTCACCGAT 59.795 52.381 0.00 0.00 0.00 4.18
2978 3016 3.957671 ATGTGCAGACATGATTAAGCG 57.042 42.857 0.00 0.00 41.52 4.68
3030 3075 4.511527 AGCATGAGTGAACGAATCATTCT 58.488 39.130 15.27 1.24 43.29 2.40
3070 3115 0.685458 AAATCCATGTGCTGGGAGCC 60.685 55.000 0.00 0.00 45.98 4.70
3492 3537 2.496470 GCCTACGGAGGGTAATATCAGG 59.504 54.545 17.58 0.00 43.97 3.86
3537 3583 4.864247 GCACCTAGCAAACACCATTAATTG 59.136 41.667 0.00 0.00 44.79 2.32
3538 3584 4.864247 CACCTAGCAAACACCATTAATTGC 59.136 41.667 1.31 1.31 46.43 3.56
3689 3736 4.208686 ATCTTCGACCGCGGGCTC 62.209 66.667 31.71 17.99 38.28 4.70
3802 3849 0.676184 GACAGGTCAGTCACTGCTCA 59.324 55.000 0.00 0.00 38.25 4.26
3804 3851 0.678395 CAGGTCAGTCACTGCTCAGT 59.322 55.000 0.00 0.00 43.61 3.41
3807 3854 1.342819 GGTCAGTCACTGCTCAGTTCT 59.657 52.381 0.00 0.00 40.20 3.01
3808 3855 2.558795 GGTCAGTCACTGCTCAGTTCTA 59.441 50.000 0.00 0.00 40.20 2.10
3982 4029 0.530288 AGAAGCTCTTGAGGTCGCTC 59.470 55.000 2.69 0.00 31.30 5.03
4000 4047 2.047844 CACTGGGACGTGAGGCTG 60.048 66.667 0.00 0.00 40.87 4.85
4104 4151 4.082665 TCAAGCCATCTCCATTCTCATC 57.917 45.455 0.00 0.00 0.00 2.92
4304 4364 6.543831 AGTTTGTCAGTTCAAATACTTGCTCT 59.456 34.615 0.00 0.00 39.09 4.09
4306 4366 5.610398 TGTCAGTTCAAATACTTGCTCTCA 58.390 37.500 0.00 0.00 32.14 3.27
4317 4377 2.968574 ACTTGCTCTCACCGATCCATAT 59.031 45.455 0.00 0.00 0.00 1.78
4337 4397 6.742718 CCATATTAAGTGTCGCAGTTTTGAAG 59.257 38.462 5.46 0.00 0.00 3.02
4338 4398 4.545823 TTAAGTGTCGCAGTTTTGAAGG 57.454 40.909 5.46 0.00 0.00 3.46
4339 4399 2.038387 AGTGTCGCAGTTTTGAAGGT 57.962 45.000 0.00 0.00 0.00 3.50
4340 4400 2.365582 AGTGTCGCAGTTTTGAAGGTT 58.634 42.857 0.00 0.00 0.00 3.50
4342 4402 2.096819 GTGTCGCAGTTTTGAAGGTTGA 59.903 45.455 0.00 0.00 0.00 3.18
4343 4403 2.750166 TGTCGCAGTTTTGAAGGTTGAA 59.250 40.909 0.00 0.00 0.00 2.69
4344 4404 3.105937 GTCGCAGTTTTGAAGGTTGAAC 58.894 45.455 0.00 0.00 0.00 3.18
4362 4435 5.238006 TGAACCAACCTTACTTCAAAACG 57.762 39.130 0.00 0.00 0.00 3.60
4364 4437 2.953648 ACCAACCTTACTTCAAAACGGG 59.046 45.455 0.00 0.00 0.00 5.28
4365 4438 2.287970 CCAACCTTACTTCAAAACGGGC 60.288 50.000 0.00 0.00 0.00 6.13
4368 4441 2.081462 CCTTACTTCAAAACGGGCGAT 58.919 47.619 0.00 0.00 0.00 4.58
4371 4444 1.073177 ACTTCAAAACGGGCGATACG 58.927 50.000 0.00 0.00 37.36 3.06
4383 4456 3.481028 CGGGCGATACGTATTATGAATCG 59.519 47.826 9.92 9.75 41.69 3.34
4391 4464 3.056749 ACGTATTATGAATCGGAGGGAGC 60.057 47.826 0.00 0.00 0.00 4.70
4430 4505 9.418045 GGCAAGTTAGCAAATCAGTTAAATTTA 57.582 29.630 0.00 0.00 35.83 1.40
4464 4539 3.365364 GCAATGTTGAGTCCAGCTGTTAC 60.365 47.826 13.81 10.56 0.00 2.50
4476 4551 7.117397 AGTCCAGCTGTTACAAGATACTACTA 58.883 38.462 13.81 0.00 0.00 1.82
4478 4553 7.067251 GTCCAGCTGTTACAAGATACTACTACT 59.933 40.741 13.81 0.00 0.00 2.57
4479 4554 8.270030 TCCAGCTGTTACAAGATACTACTACTA 58.730 37.037 13.81 0.00 0.00 1.82
4480 4555 8.900781 CCAGCTGTTACAAGATACTACTACTAA 58.099 37.037 13.81 0.00 0.00 2.24
4509 4584 6.442112 TCAGATCGTAATAATGTCTGCAGAG 58.558 40.000 18.89 1.64 36.97 3.35
4719 4797 7.885399 ACTGATATTAGATATTTGGTGCCTTCC 59.115 37.037 0.78 0.00 0.00 3.46
4814 4892 1.234615 TGCAGCTAGCCCGTTTGAAC 61.235 55.000 12.13 0.00 44.83 3.18
4852 4930 4.390129 AGAGGTCTGGTCTCTGTAAAGA 57.610 45.455 0.00 0.00 39.83 2.52
4880 4958 1.374758 CCGCCGAGTTCTTTCAGCT 60.375 57.895 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.389853 CACTCGTCTGATGCGTATCG 58.610 55.000 9.02 4.27 36.04 2.92
7 8 1.600663 CCCACTCGTCTGATGCGTATC 60.601 57.143 6.54 6.54 0.00 2.24
8 9 0.385751 CCCACTCGTCTGATGCGTAT 59.614 55.000 0.00 0.00 0.00 3.06
9 10 0.963856 ACCCACTCGTCTGATGCGTA 60.964 55.000 0.00 0.00 0.00 4.42
10 11 2.214181 GACCCACTCGTCTGATGCGT 62.214 60.000 0.00 0.00 0.00 5.24
11 12 1.517257 GACCCACTCGTCTGATGCG 60.517 63.158 0.00 0.00 0.00 4.73
12 13 0.037326 TTGACCCACTCGTCTGATGC 60.037 55.000 0.00 0.00 33.70 3.91
13 14 1.273606 ACTTGACCCACTCGTCTGATG 59.726 52.381 0.00 0.00 33.70 3.07
14 15 1.273606 CACTTGACCCACTCGTCTGAT 59.726 52.381 0.00 0.00 33.70 2.90
15 16 0.673985 CACTTGACCCACTCGTCTGA 59.326 55.000 0.00 0.00 33.70 3.27
16 17 0.673985 TCACTTGACCCACTCGTCTG 59.326 55.000 0.00 0.00 33.70 3.51
17 18 1.068741 GTTCACTTGACCCACTCGTCT 59.931 52.381 0.00 0.00 33.70 4.18
18 19 1.068741 AGTTCACTTGACCCACTCGTC 59.931 52.381 0.00 0.00 0.00 4.20
19 20 1.120530 AGTTCACTTGACCCACTCGT 58.879 50.000 0.00 0.00 0.00 4.18
20 21 3.594603 ATAGTTCACTTGACCCACTCG 57.405 47.619 0.00 0.00 0.00 4.18
21 22 7.040617 TCGATATATAGTTCACTTGACCCACTC 60.041 40.741 0.00 0.00 0.00 3.51
22 23 6.776116 TCGATATATAGTTCACTTGACCCACT 59.224 38.462 0.00 0.00 0.00 4.00
23 24 6.862090 GTCGATATATAGTTCACTTGACCCAC 59.138 42.308 0.00 0.00 0.00 4.61
24 25 6.293790 CGTCGATATATAGTTCACTTGACCCA 60.294 42.308 0.00 0.00 0.00 4.51
25 26 6.084925 CGTCGATATATAGTTCACTTGACCC 58.915 44.000 0.00 0.00 0.00 4.46
26 27 6.577800 CACGTCGATATATAGTTCACTTGACC 59.422 42.308 0.00 0.00 0.00 4.02
27 28 7.130917 ACACGTCGATATATAGTTCACTTGAC 58.869 38.462 0.00 0.00 0.00 3.18
28 29 7.255491 ACACGTCGATATATAGTTCACTTGA 57.745 36.000 0.00 0.00 0.00 3.02
29 30 6.577800 GGACACGTCGATATATAGTTCACTTG 59.422 42.308 0.00 0.00 0.00 3.16
30 31 6.293845 GGGACACGTCGATATATAGTTCACTT 60.294 42.308 0.00 0.00 0.00 3.16
31 32 5.180868 GGGACACGTCGATATATAGTTCACT 59.819 44.000 0.00 0.00 0.00 3.41
32 33 5.049198 TGGGACACGTCGATATATAGTTCAC 60.049 44.000 0.00 0.00 0.00 3.18
33 34 5.065235 TGGGACACGTCGATATATAGTTCA 58.935 41.667 0.00 0.00 0.00 3.18
34 35 5.618056 TGGGACACGTCGATATATAGTTC 57.382 43.478 0.00 0.00 0.00 3.01
35 36 4.082895 GCTGGGACACGTCGATATATAGTT 60.083 45.833 0.00 0.00 0.00 2.24
36 37 3.439476 GCTGGGACACGTCGATATATAGT 59.561 47.826 0.00 0.00 0.00 2.12
37 38 3.690139 AGCTGGGACACGTCGATATATAG 59.310 47.826 0.00 0.00 0.00 1.31
38 39 3.682696 AGCTGGGACACGTCGATATATA 58.317 45.455 0.00 0.00 0.00 0.86
39 40 2.515854 AGCTGGGACACGTCGATATAT 58.484 47.619 0.00 0.00 0.00 0.86
40 41 1.977056 AGCTGGGACACGTCGATATA 58.023 50.000 0.00 0.00 0.00 0.86
41 42 1.607628 GTAGCTGGGACACGTCGATAT 59.392 52.381 0.00 0.00 0.00 1.63
42 43 1.019673 GTAGCTGGGACACGTCGATA 58.980 55.000 0.00 0.00 0.00 2.92
43 44 1.664321 GGTAGCTGGGACACGTCGAT 61.664 60.000 0.00 0.00 0.00 3.59
44 45 2.338015 GGTAGCTGGGACACGTCGA 61.338 63.158 0.00 0.00 0.00 4.20
45 46 2.181021 GGTAGCTGGGACACGTCG 59.819 66.667 0.00 0.00 0.00 5.12
46 47 2.181021 CGGTAGCTGGGACACGTC 59.819 66.667 0.00 0.00 0.00 4.34
47 48 2.599578 ACGGTAGCTGGGACACGT 60.600 61.111 0.00 0.00 0.00 4.49
48 49 2.126071 CACGGTAGCTGGGACACG 60.126 66.667 0.00 0.00 0.00 4.49
49 50 1.080025 GACACGGTAGCTGGGACAC 60.080 63.158 0.00 0.00 0.00 3.67
50 51 0.902984 ATGACACGGTAGCTGGGACA 60.903 55.000 0.00 0.00 0.00 4.02
51 52 0.249398 AATGACACGGTAGCTGGGAC 59.751 55.000 0.00 0.00 0.00 4.46
52 53 0.535335 GAATGACACGGTAGCTGGGA 59.465 55.000 0.00 0.00 0.00 4.37
53 54 0.806102 CGAATGACACGGTAGCTGGG 60.806 60.000 0.00 0.00 0.00 4.45
54 55 0.806102 CCGAATGACACGGTAGCTGG 60.806 60.000 0.00 0.00 44.57 4.85
55 56 2.665777 CCGAATGACACGGTAGCTG 58.334 57.895 0.00 0.00 44.57 4.24
62 63 1.305219 ACCAATGGCCGAATGACACG 61.305 55.000 0.00 0.00 0.00 4.49
63 64 0.887933 AACCAATGGCCGAATGACAC 59.112 50.000 0.00 0.00 0.00 3.67
64 65 0.887247 CAACCAATGGCCGAATGACA 59.113 50.000 0.00 0.00 0.00 3.58
65 66 1.173043 TCAACCAATGGCCGAATGAC 58.827 50.000 0.00 0.00 0.00 3.06
66 67 1.543802 GTTCAACCAATGGCCGAATGA 59.456 47.619 0.00 0.00 0.00 2.57
67 68 1.732077 CGTTCAACCAATGGCCGAATG 60.732 52.381 0.00 4.14 0.00 2.67
68 69 0.525761 CGTTCAACCAATGGCCGAAT 59.474 50.000 0.00 0.00 0.00 3.34
69 70 1.519751 CCGTTCAACCAATGGCCGAA 61.520 55.000 0.00 0.00 34.19 4.30
70 71 1.969064 CCGTTCAACCAATGGCCGA 60.969 57.895 0.00 0.00 34.19 5.54
71 72 2.566010 CCGTTCAACCAATGGCCG 59.434 61.111 0.00 0.00 34.19 6.13
74 75 0.523072 CAGAGCCGTTCAACCAATGG 59.477 55.000 0.00 0.00 43.51 3.16
75 76 1.238439 ACAGAGCCGTTCAACCAATG 58.762 50.000 0.00 0.00 0.00 2.82
76 77 1.880027 GAACAGAGCCGTTCAACCAAT 59.120 47.619 6.43 0.00 43.89 3.16
77 78 1.305201 GAACAGAGCCGTTCAACCAA 58.695 50.000 6.43 0.00 43.89 3.67
78 79 0.878523 CGAACAGAGCCGTTCAACCA 60.879 55.000 10.72 0.00 44.54 3.67
79 80 0.878961 ACGAACAGAGCCGTTCAACC 60.879 55.000 10.72 0.00 44.54 3.77
80 81 0.935196 AACGAACAGAGCCGTTCAAC 59.065 50.000 10.72 0.00 44.46 3.18
81 82 2.400399 CTAACGAACAGAGCCGTTCAA 58.600 47.619 0.00 0.00 44.46 2.69
82 83 1.933500 GCTAACGAACAGAGCCGTTCA 60.934 52.381 0.00 0.00 44.46 3.18
83 84 0.714439 GCTAACGAACAGAGCCGTTC 59.286 55.000 0.00 0.85 44.46 3.95
85 86 0.317479 AAGCTAACGAACAGAGCCGT 59.683 50.000 0.00 0.00 41.14 5.68
86 87 0.716108 CAAGCTAACGAACAGAGCCG 59.284 55.000 0.00 0.00 36.87 5.52
87 88 1.797025 ACAAGCTAACGAACAGAGCC 58.203 50.000 0.00 0.00 36.87 4.70
88 89 4.235360 TCTTACAAGCTAACGAACAGAGC 58.765 43.478 0.00 0.00 36.42 4.09
89 90 4.859798 CCTCTTACAAGCTAACGAACAGAG 59.140 45.833 0.00 0.00 0.00 3.35
90 91 4.521639 TCCTCTTACAAGCTAACGAACAGA 59.478 41.667 0.00 0.00 0.00 3.41
91 92 4.806330 TCCTCTTACAAGCTAACGAACAG 58.194 43.478 0.00 0.00 0.00 3.16
92 93 4.521639 TCTCCTCTTACAAGCTAACGAACA 59.478 41.667 0.00 0.00 0.00 3.18
93 94 5.056894 TCTCCTCTTACAAGCTAACGAAC 57.943 43.478 0.00 0.00 0.00 3.95
94 95 5.717078 TTCTCCTCTTACAAGCTAACGAA 57.283 39.130 0.00 0.00 0.00 3.85
95 96 5.467705 GTTTCTCCTCTTACAAGCTAACGA 58.532 41.667 0.00 0.00 0.00 3.85
96 97 4.626172 GGTTTCTCCTCTTACAAGCTAACG 59.374 45.833 0.00 0.00 0.00 3.18
97 98 5.639931 CAGGTTTCTCCTCTTACAAGCTAAC 59.360 44.000 0.00 0.00 46.24 2.34
98 99 5.307196 ACAGGTTTCTCCTCTTACAAGCTAA 59.693 40.000 0.00 0.00 46.24 3.09
99 100 4.838986 ACAGGTTTCTCCTCTTACAAGCTA 59.161 41.667 0.00 0.00 46.24 3.32
100 101 3.648545 ACAGGTTTCTCCTCTTACAAGCT 59.351 43.478 0.00 0.00 46.24 3.74
101 102 4.009370 ACAGGTTTCTCCTCTTACAAGC 57.991 45.455 0.00 0.00 46.24 4.01
102 103 6.760291 AGTTACAGGTTTCTCCTCTTACAAG 58.240 40.000 0.00 0.00 46.24 3.16
103 104 6.742559 AGTTACAGGTTTCTCCTCTTACAA 57.257 37.500 0.00 0.00 46.24 2.41
104 105 6.071503 GCTAGTTACAGGTTTCTCCTCTTACA 60.072 42.308 0.00 0.00 46.24 2.41
105 106 6.153170 AGCTAGTTACAGGTTTCTCCTCTTAC 59.847 42.308 0.00 0.00 46.24 2.34
106 107 6.254522 AGCTAGTTACAGGTTTCTCCTCTTA 58.745 40.000 0.00 0.00 46.24 2.10
107 108 5.088026 AGCTAGTTACAGGTTTCTCCTCTT 58.912 41.667 0.00 0.00 46.24 2.85
108 109 4.679331 AGCTAGTTACAGGTTTCTCCTCT 58.321 43.478 0.00 0.00 46.24 3.69
109 110 5.653330 AGTAGCTAGTTACAGGTTTCTCCTC 59.347 44.000 17.72 0.00 46.24 3.71
110 111 8.025906 GCAGTAGCTAGTTACAGGTTTCTCCT 62.026 46.154 17.72 0.00 42.14 3.69
111 112 5.652518 CAGTAGCTAGTTACAGGTTTCTCC 58.347 45.833 17.72 0.00 0.00 3.71
112 113 5.103687 GCAGTAGCTAGTTACAGGTTTCTC 58.896 45.833 17.72 0.00 37.91 2.87
113 114 4.527038 TGCAGTAGCTAGTTACAGGTTTCT 59.473 41.667 17.72 0.00 42.74 2.52
114 115 4.817517 TGCAGTAGCTAGTTACAGGTTTC 58.182 43.478 17.72 0.00 42.74 2.78
115 116 4.884668 TGCAGTAGCTAGTTACAGGTTT 57.115 40.909 17.72 0.00 42.74 3.27
116 117 4.884668 TTGCAGTAGCTAGTTACAGGTT 57.115 40.909 17.72 0.00 42.74 3.50
117 118 5.420409 GAATTGCAGTAGCTAGTTACAGGT 58.580 41.667 17.72 0.00 42.74 4.00
118 119 4.504461 CGAATTGCAGTAGCTAGTTACAGG 59.496 45.833 17.72 10.77 42.74 4.00
119 120 5.340803 TCGAATTGCAGTAGCTAGTTACAG 58.659 41.667 17.72 11.44 42.74 2.74
120 121 5.319140 TCGAATTGCAGTAGCTAGTTACA 57.681 39.130 17.72 0.00 42.74 2.41
121 122 6.830114 ATTCGAATTGCAGTAGCTAGTTAC 57.170 37.500 4.39 8.59 42.74 2.50
122 123 7.648112 CAGTATTCGAATTGCAGTAGCTAGTTA 59.352 37.037 17.19 0.00 42.74 2.24
123 124 6.477033 CAGTATTCGAATTGCAGTAGCTAGTT 59.523 38.462 17.19 0.00 42.74 2.24
124 125 5.980116 CAGTATTCGAATTGCAGTAGCTAGT 59.020 40.000 17.19 0.00 42.74 2.57
125 126 6.209361 TCAGTATTCGAATTGCAGTAGCTAG 58.791 40.000 17.19 0.00 42.74 3.42
126 127 6.144078 TCAGTATTCGAATTGCAGTAGCTA 57.856 37.500 17.19 0.00 42.74 3.32
127 128 5.011090 TCAGTATTCGAATTGCAGTAGCT 57.989 39.130 17.19 0.00 42.74 3.32
128 129 5.718649 TTCAGTATTCGAATTGCAGTAGC 57.281 39.130 17.19 0.00 42.57 3.58
131 132 9.722056 GAATTATTTCAGTATTCGAATTGCAGT 57.278 29.630 17.19 0.00 0.00 4.40
132 133 9.173939 GGAATTATTTCAGTATTCGAATTGCAG 57.826 33.333 17.19 7.15 33.23 4.41
133 134 8.902806 AGGAATTATTTCAGTATTCGAATTGCA 58.097 29.630 17.19 0.00 33.23 4.08
134 135 9.387123 GAGGAATTATTTCAGTATTCGAATTGC 57.613 33.333 17.19 9.89 33.23 3.56
138 139 9.751542 GAGAGAGGAATTATTTCAGTATTCGAA 57.248 33.333 0.00 0.00 33.23 3.71
139 140 8.076781 CGAGAGAGGAATTATTTCAGTATTCGA 58.923 37.037 0.20 0.00 33.23 3.71
140 141 8.076781 TCGAGAGAGGAATTATTTCAGTATTCG 58.923 37.037 0.20 4.04 31.51 3.34
160 161 1.044611 GGAGGAAAGGGGATCGAGAG 58.955 60.000 0.00 0.00 0.00 3.20
161 162 0.338467 TGGAGGAAAGGGGATCGAGA 59.662 55.000 0.00 0.00 0.00 4.04
162 163 1.071385 CATGGAGGAAAGGGGATCGAG 59.929 57.143 0.00 0.00 0.00 4.04
163 164 1.131638 CATGGAGGAAAGGGGATCGA 58.868 55.000 0.00 0.00 0.00 3.59
164 165 0.109342 CCATGGAGGAAAGGGGATCG 59.891 60.000 5.56 0.00 41.22 3.69
165 166 0.178978 GCCATGGAGGAAAGGGGATC 60.179 60.000 18.40 0.00 41.22 3.36
166 167 0.925720 TGCCATGGAGGAAAGGGGAT 60.926 55.000 18.40 0.00 41.22 3.85
167 168 1.145900 TTGCCATGGAGGAAAGGGGA 61.146 55.000 18.40 0.00 41.22 4.81
168 169 0.031817 ATTGCCATGGAGGAAAGGGG 60.032 55.000 18.40 0.00 38.72 4.79
169 170 1.406903 GATTGCCATGGAGGAAAGGG 58.593 55.000 18.40 0.00 38.72 3.95
170 171 1.406903 GGATTGCCATGGAGGAAAGG 58.593 55.000 18.40 0.00 38.72 3.11
171 172 1.063417 AGGGATTGCCATGGAGGAAAG 60.063 52.381 18.40 0.00 38.72 2.62
172 173 1.009997 AGGGATTGCCATGGAGGAAA 58.990 50.000 18.40 3.87 40.03 3.13
173 174 1.009997 AAGGGATTGCCATGGAGGAA 58.990 50.000 18.40 4.71 41.22 3.36
174 175 0.259647 CAAGGGATTGCCATGGAGGA 59.740 55.000 18.40 0.00 41.22 3.71
175 176 0.259647 TCAAGGGATTGCCATGGAGG 59.740 55.000 18.40 0.00 41.84 4.30
176 177 1.213678 TCTCAAGGGATTGCCATGGAG 59.786 52.381 18.40 0.00 45.49 3.86
177 178 1.297968 TCTCAAGGGATTGCCATGGA 58.702 50.000 18.40 0.00 35.15 3.41
178 179 2.376695 ATCTCAAGGGATTGCCATGG 57.623 50.000 7.63 7.63 35.15 3.66
179 180 2.292569 CGAATCTCAAGGGATTGCCATG 59.707 50.000 0.00 0.00 36.24 3.66
180 181 2.092212 ACGAATCTCAAGGGATTGCCAT 60.092 45.455 0.00 0.00 36.24 4.40
181 182 1.281867 ACGAATCTCAAGGGATTGCCA 59.718 47.619 0.00 0.00 36.24 4.92
182 183 2.044123 ACGAATCTCAAGGGATTGCC 57.956 50.000 0.00 0.00 36.24 4.52
183 184 2.545946 GCTACGAATCTCAAGGGATTGC 59.454 50.000 0.00 0.00 36.24 3.56
184 185 4.065321 AGCTACGAATCTCAAGGGATTG 57.935 45.455 0.00 0.00 36.24 2.67
185 186 4.896482 ACTAGCTACGAATCTCAAGGGATT 59.104 41.667 0.00 0.00 38.47 3.01
186 187 4.475345 ACTAGCTACGAATCTCAAGGGAT 58.525 43.478 0.00 0.00 0.00 3.85
187 188 3.899726 ACTAGCTACGAATCTCAAGGGA 58.100 45.455 0.00 0.00 0.00 4.20
188 189 4.142138 ACAACTAGCTACGAATCTCAAGGG 60.142 45.833 0.00 0.00 0.00 3.95
189 190 5.000012 ACAACTAGCTACGAATCTCAAGG 58.000 43.478 0.00 0.00 0.00 3.61
190 191 7.009357 GGTTAACAACTAGCTACGAATCTCAAG 59.991 40.741 8.10 0.00 0.00 3.02
191 192 6.810182 GGTTAACAACTAGCTACGAATCTCAA 59.190 38.462 8.10 0.00 0.00 3.02
192 193 6.327934 GGTTAACAACTAGCTACGAATCTCA 58.672 40.000 8.10 0.00 0.00 3.27
193 194 5.747675 GGGTTAACAACTAGCTACGAATCTC 59.252 44.000 8.10 0.00 0.00 2.75
194 195 5.186409 TGGGTTAACAACTAGCTACGAATCT 59.814 40.000 8.10 0.00 0.00 2.40
195 196 5.413499 TGGGTTAACAACTAGCTACGAATC 58.587 41.667 8.10 0.00 0.00 2.52
196 197 5.410355 TGGGTTAACAACTAGCTACGAAT 57.590 39.130 8.10 0.00 0.00 3.34
197 198 4.870123 TGGGTTAACAACTAGCTACGAA 57.130 40.909 8.10 0.00 0.00 3.85
537 538 4.619973 ACAACCGTACGTGTATTCTCAAA 58.380 39.130 15.21 0.00 0.00 2.69
538 539 4.241590 ACAACCGTACGTGTATTCTCAA 57.758 40.909 15.21 0.00 0.00 3.02
539 540 3.921119 ACAACCGTACGTGTATTCTCA 57.079 42.857 15.21 0.00 0.00 3.27
540 541 6.689178 TTTAACAACCGTACGTGTATTCTC 57.311 37.500 15.21 0.00 0.00 2.87
541 542 7.475771 TTTTTAACAACCGTACGTGTATTCT 57.524 32.000 15.21 0.72 0.00 2.40
812 821 1.524621 GCAGGATGTGGGGATGACG 60.525 63.158 0.00 0.00 39.31 4.35
813 822 0.179034 GAGCAGGATGTGGGGATGAC 60.179 60.000 0.00 0.00 39.31 3.06
814 823 1.689243 CGAGCAGGATGTGGGGATGA 61.689 60.000 0.00 0.00 39.31 2.92
816 825 3.112205 GCGAGCAGGATGTGGGGAT 62.112 63.158 0.00 0.00 39.31 3.85
817 826 3.785859 GCGAGCAGGATGTGGGGA 61.786 66.667 0.00 0.00 39.31 4.81
818 827 4.864334 GGCGAGCAGGATGTGGGG 62.864 72.222 0.00 0.00 39.31 4.96
820 829 4.864334 GGGGCGAGCAGGATGTGG 62.864 72.222 0.00 0.00 39.31 4.17
821 830 4.864334 GGGGGCGAGCAGGATGTG 62.864 72.222 0.00 0.00 39.31 3.21
1312 1325 4.400961 GCCAGCGTCCTCCTTGCT 62.401 66.667 0.00 0.00 40.16 3.91
1473 1486 2.259818 CGCTCGTTGCTCTGGTCT 59.740 61.111 2.29 0.00 40.11 3.85
1704 1717 1.448119 CGCTCATACGCTCCTCCTCA 61.448 60.000 0.00 0.00 0.00 3.86
1794 1807 1.354705 TCGGGTCTATCCTCATCCGAT 59.645 52.381 0.00 0.00 41.11 4.18
1872 1885 4.619227 ACCTCCACCAACGTGCGG 62.619 66.667 2.77 2.77 38.79 5.69
2175 2191 3.845259 GGGATGTAGTCGGCGCCA 61.845 66.667 28.98 11.20 0.00 5.69
2378 2394 2.357009 CAGTGAGTTAGCAATCCATGGC 59.643 50.000 6.96 0.00 0.00 4.40
2389 2405 2.963498 TCGTCGTGTCAGTGAGTTAG 57.037 50.000 0.00 0.00 0.00 2.34
2391 2407 1.607148 TCATCGTCGTGTCAGTGAGTT 59.393 47.619 0.00 0.00 0.00 3.01
2392 2408 1.235724 TCATCGTCGTGTCAGTGAGT 58.764 50.000 0.00 0.00 0.00 3.41
2411 2427 2.230508 CAGCCAAATCTGCACAAGTCAT 59.769 45.455 0.00 0.00 0.00 3.06
2444 2468 1.069765 CTGGACCAGCTTCGTGTGT 59.930 57.895 8.99 0.00 0.00 3.72
2540 2573 4.758251 ATGTAGTGCAGCGCGCCA 62.758 61.111 30.33 17.61 40.23 5.69
2660 2693 3.986006 GTCACCACGTCCCGCTCA 61.986 66.667 0.00 0.00 0.00 4.26
2936 2969 1.472878 CCTTTCCAGATCTCGACGTCA 59.527 52.381 17.16 1.87 0.00 4.35
2978 3016 7.486232 GGTGAGAACTCATAAGCAAAAATTAGC 59.514 37.037 7.77 0.00 42.18 3.09
3030 3075 0.390340 GTCAGAGCCGTCATTGCTGA 60.390 55.000 0.00 0.00 39.69 4.26
3070 3115 1.993370 GGTCTTTCTTGATCGTCACCG 59.007 52.381 0.00 0.00 0.00 4.94
3492 3537 1.079057 GGCGAGAGGGTTCTTGTCC 60.079 63.158 0.00 0.00 37.20 4.02
3505 3550 3.414272 GCTAGGTGCAATGGCGAG 58.586 61.111 0.00 0.00 45.35 5.03
3525 3571 0.678366 TCGGCGGCAATTAATGGTGT 60.678 50.000 10.53 0.00 0.00 4.16
3537 3583 3.577313 GCAGGATTTCTCGGCGGC 61.577 66.667 7.21 0.00 0.00 6.53
3538 3584 2.125147 TGCAGGATTTCTCGGCGG 60.125 61.111 7.21 0.00 0.00 6.13
3602 3649 1.603236 CCTTCTGGTCTCTCAGCGCT 61.603 60.000 2.64 2.64 34.91 5.92
3802 3849 5.686124 GCCATGGCTGAAGTAGAATAGAACT 60.686 44.000 29.98 0.00 38.26 3.01
3804 3851 4.708177 GCCATGGCTGAAGTAGAATAGAA 58.292 43.478 29.98 0.00 38.26 2.10
3982 4029 3.314331 AGCCTCACGTCCCAGTGG 61.314 66.667 0.63 0.63 42.10 4.00
4000 4047 2.814280 TGTCGTTCTTGGAGAAGGTC 57.186 50.000 9.40 5.77 40.08 3.85
4104 4151 3.991773 CTGGGTGAAAATTGCTTGTGATG 59.008 43.478 0.00 0.00 0.00 3.07
4166 4213 7.147976 ACATCAATGCTAACCAAAGAAAGAAC 58.852 34.615 0.00 0.00 0.00 3.01
4242 4301 4.952335 TCTCAGTTCTATGCATGAGTCTCA 59.048 41.667 10.16 4.68 40.07 3.27
4243 4302 5.512753 TCTCAGTTCTATGCATGAGTCTC 57.487 43.478 10.16 0.00 40.07 3.36
4304 4364 4.794981 GCGACACTTAATATGGATCGGTGA 60.795 45.833 0.00 0.00 0.00 4.02
4306 4366 3.069016 TGCGACACTTAATATGGATCGGT 59.931 43.478 0.00 0.00 0.00 4.69
4317 4377 3.942748 ACCTTCAAAACTGCGACACTTAA 59.057 39.130 0.00 0.00 0.00 1.85
4338 4398 5.513849 CGTTTTGAAGTAAGGTTGGTTCAAC 59.486 40.000 2.46 2.46 42.89 3.18
4339 4399 5.393243 CCGTTTTGAAGTAAGGTTGGTTCAA 60.393 40.000 0.00 0.00 37.18 2.69
4340 4400 4.096682 CCGTTTTGAAGTAAGGTTGGTTCA 59.903 41.667 0.00 0.00 0.00 3.18
4342 4402 3.382227 CCCGTTTTGAAGTAAGGTTGGTT 59.618 43.478 0.00 0.00 0.00 3.67
4343 4403 2.953648 CCCGTTTTGAAGTAAGGTTGGT 59.046 45.455 0.00 0.00 0.00 3.67
4344 4404 2.287970 GCCCGTTTTGAAGTAAGGTTGG 60.288 50.000 0.00 0.00 0.00 3.77
4353 4426 1.073177 ACGTATCGCCCGTTTTGAAG 58.927 50.000 0.00 0.00 34.28 3.02
4362 4435 3.795101 CCGATTCATAATACGTATCGCCC 59.205 47.826 8.86 0.00 37.39 6.13
4364 4437 4.733887 CCTCCGATTCATAATACGTATCGC 59.266 45.833 8.86 0.00 37.39 4.58
4365 4438 5.065602 TCCCTCCGATTCATAATACGTATCG 59.934 44.000 8.86 8.05 38.19 2.92
4368 4441 4.157289 GCTCCCTCCGATTCATAATACGTA 59.843 45.833 0.00 0.00 0.00 3.57
4371 4444 4.021016 AGTGCTCCCTCCGATTCATAATAC 60.021 45.833 0.00 0.00 0.00 1.89
4401 4476 4.510038 ACTGATTTGCTAACTTGCCTTG 57.490 40.909 0.00 0.00 0.00 3.61
4430 4505 8.637986 TGGACTCAACATTGCTTTAACTTTATT 58.362 29.630 0.00 0.00 0.00 1.40
4431 4506 8.177119 TGGACTCAACATTGCTTTAACTTTAT 57.823 30.769 0.00 0.00 0.00 1.40
4480 4555 9.710900 TGCAGACATTATTACGATCTGATATTT 57.289 29.630 3.80 0.00 39.33 1.40
4485 4560 6.391227 TCTGCAGACATTATTACGATCTGA 57.609 37.500 13.74 0.00 39.33 3.27
4509 4584 4.615949 TGTTGTAACAATTGATGTGCACC 58.384 39.130 15.69 0.00 42.99 5.01
4615 4692 6.362820 GTCGTGGTTCTGTAAAAGAGAACTAG 59.637 42.308 14.32 8.03 45.82 2.57
4719 4797 3.939592 GGAGGGAAACTAAAGATGAACCG 59.060 47.826 0.00 0.00 0.00 4.44
4814 4892 4.315803 ACCTCTTTACAGTCACAAATCGG 58.684 43.478 0.00 0.00 0.00 4.18
4880 4958 4.892934 GGGGTTGCATGATATGGTAAAGAA 59.107 41.667 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.