Multiple sequence alignment - TraesCS5D01G496900

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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 TraesCS5D01G496900 chr5D 100.000 1870 0 0 1 1870 527195495 527197364 0.000000e+00 3454.0
1 TraesCS5D01G496900 chr5D 100.000 694 0 0 2048 2741 527197542 527198235 0.000000e+00 1282.0
2 TraesCS5D01G496900 chr5D 90.980 255 21 2 2092 2345 527430922 527431175 2.610000e-90 342.0
3 TraesCS5D01G496900 chr5D 90.449 178 15 2 2092 2268 54191181 54191005 1.640000e-57 233.0
4 TraesCS5D01G496900 chr5D 85.185 54 7 1 435 487 515404676 515404623 1.000000e-03 54.7
5 TraesCS5D01G496900 chr5A 92.105 874 48 12 884 1754 619371062 619370207 0.000000e+00 1212.0
6 TraesCS5D01G496900 chr5A 93.797 661 26 7 2087 2741 654406736 654407387 0.000000e+00 979.0
7 TraesCS5D01G496900 chr5A 93.069 606 39 1 1152 1754 632591122 632590517 0.000000e+00 883.0
8 TraesCS5D01G496900 chr5A 93.182 264 15 1 1494 1754 609811330 609811593 4.280000e-103 385.0
9 TraesCS5D01G496900 chr5A 93.443 244 9 5 2 238 282590666 282590423 3.360000e-94 355.0
10 TraesCS5D01G496900 chr5A 90.588 255 22 2 2092 2345 654560631 654560884 1.220000e-88 337.0
11 TraesCS5D01G496900 chr5A 90.152 132 10 1 239 367 654405214 654405345 4.690000e-38 169.0
12 TraesCS5D01G496900 chr5A 80.531 113 16 3 2369 2475 654560946 654561058 6.290000e-12 82.4
13 TraesCS5D01G496900 chr5A 91.667 48 4 0 448 495 199228991 199229038 1.760000e-07 67.6
14 TraesCS5D01G496900 chr5B 85.901 688 54 22 236 887 663516536 663517216 0.000000e+00 693.0
15 TraesCS5D01G496900 chr5B 95.249 421 13 4 2061 2475 663520435 663520854 0.000000e+00 660.0
16 TraesCS5D01G496900 chr5B 92.157 255 18 1 2487 2741 663520971 663521223 2.600000e-95 359.0
17 TraesCS5D01G496900 chr5B 90.726 248 21 2 2092 2338 663796172 663796418 2.030000e-86 329.0
18 TraesCS5D01G496900 chr4B 96.063 254 9 1 2 254 322646321 322646068 1.960000e-111 412.0
19 TraesCS5D01G496900 chr4D 97.479 238 6 0 1 238 339059691 339059928 9.140000e-110 407.0
20 TraesCS5D01G496900 chr1D 97.059 238 7 0 1 238 80297059 80296822 4.250000e-108 401.0
21 TraesCS5D01G496900 chr1D 96.682 211 7 0 28 238 155712213 155712003 4.340000e-93 351.0
22 TraesCS5D01G496900 chr6B 96.624 237 8 0 2 238 637404829 637404593 7.110000e-106 394.0
23 TraesCS5D01G496900 chr6B 95.781 237 10 0 2 238 637399822 637399586 1.540000e-102 383.0
24 TraesCS5D01G496900 chr7A 93.776 241 11 3 2 238 11230920 11230680 2.600000e-95 359.0
25 TraesCS5D01G496900 chr7A 92.653 245 12 4 2 240 696841220 696840976 5.620000e-92 348.0
26 TraesCS5D01G496900 chr6D 91.892 185 12 1 1573 1754 331187367 331187551 3.500000e-64 255.0
27 TraesCS5D01G496900 chr3B 89.730 185 16 1 1573 1754 246060218 246060402 1.640000e-57 233.0
28 TraesCS5D01G496900 chr2A 89.730 185 15 2 1573 1754 375716907 375717090 1.640000e-57 233.0
29 TraesCS5D01G496900 chr2B 88.649 185 18 1 1573 1754 415321678 415321862 3.550000e-54 222.0
30 TraesCS5D01G496900 chr2B 88.649 185 18 1 1573 1754 415329545 415329729 3.550000e-54 222.0
31 TraesCS5D01G496900 chr2B 91.667 48 4 0 447 494 132580966 132580919 1.760000e-07 67.6
32 TraesCS5D01G496900 chr2B 100.000 32 0 0 448 479 416664929 416664898 2.950000e-05 60.2
33 TraesCS5D01G496900 chr1B 89.516 124 13 0 1594 1717 267570587 267570710 1.020000e-34 158.0
34 TraesCS5D01G496900 chr1B 89.362 47 4 1 441 486 547528091 547528137 1.060000e-04 58.4
35 TraesCS5D01G496900 chr1A 89.796 49 3 2 448 495 80567988 80567941 8.200000e-06 62.1
36 TraesCS5D01G496900 chr1A 92.683 41 2 1 447 487 502818406 502818445 1.060000e-04 58.4


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 TraesCS5D01G496900 chr5D 527195495 527198235 2740 False 2368.000000 3454 100.000000 1 2741 2 chr5D.!!$F2 2740
1 TraesCS5D01G496900 chr5A 619370207 619371062 855 True 1212.000000 1212 92.105000 884 1754 1 chr5A.!!$R2 870
2 TraesCS5D01G496900 chr5A 632590517 632591122 605 True 883.000000 883 93.069000 1152 1754 1 chr5A.!!$R3 602
3 TraesCS5D01G496900 chr5A 654405214 654407387 2173 False 574.000000 979 91.974500 239 2741 2 chr5A.!!$F3 2502
4 TraesCS5D01G496900 chr5B 663516536 663521223 4687 False 570.666667 693 91.102333 236 2741 3 chr5B.!!$F2 2505

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
46 47 0.040336 CGATCGGGATGTACAGACGG 60.04 60.0 7.38 8.27 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 4969 0.324368 TCACGATAGGACCAGGTGCT 60.324 55.0 18.99 18.99 43.77 4.4 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
17 18 3.849064 AAGAGGAGATCGAGCGGG 58.151 61.111 0.00 0.00 0.00 6.13
18 19 1.830408 AAGAGGAGATCGAGCGGGG 60.830 63.158 0.00 0.00 0.00 5.73
19 20 2.519780 GAGGAGATCGAGCGGGGT 60.520 66.667 0.00 0.00 0.00 4.95
20 21 2.042843 AGGAGATCGAGCGGGGTT 60.043 61.111 0.00 0.00 0.00 4.11
21 22 2.107141 GGAGATCGAGCGGGGTTG 59.893 66.667 0.00 0.00 0.00 3.77
22 23 2.107141 GAGATCGAGCGGGGTTGG 59.893 66.667 0.00 0.00 0.00 3.77
23 24 2.363795 AGATCGAGCGGGGTTGGA 60.364 61.111 0.00 0.00 0.00 3.53
24 25 2.107141 GATCGAGCGGGGTTGGAG 59.893 66.667 0.00 0.00 0.00 3.86
25 26 2.363795 ATCGAGCGGGGTTGGAGA 60.364 61.111 0.00 0.00 0.00 3.71
26 27 1.749334 GATCGAGCGGGGTTGGAGAT 61.749 60.000 0.00 0.00 0.00 2.75
27 28 1.749334 ATCGAGCGGGGTTGGAGATC 61.749 60.000 0.00 0.00 0.00 2.75
28 29 2.107141 GAGCGGGGTTGGAGATCG 59.893 66.667 0.00 0.00 0.00 3.69
29 30 2.363795 AGCGGGGTTGGAGATCGA 60.364 61.111 0.00 0.00 0.00 3.59
30 31 1.749334 GAGCGGGGTTGGAGATCGAT 61.749 60.000 0.00 0.00 0.00 3.59
31 32 1.301009 GCGGGGTTGGAGATCGATC 60.301 63.158 17.91 17.91 0.00 3.69
32 33 1.007271 CGGGGTTGGAGATCGATCG 60.007 63.158 19.33 9.36 0.00 3.69
33 34 1.367840 GGGGTTGGAGATCGATCGG 59.632 63.158 19.33 0.00 0.00 4.18
34 35 1.367840 GGGTTGGAGATCGATCGGG 59.632 63.158 19.33 0.00 0.00 5.14
35 36 1.113517 GGGTTGGAGATCGATCGGGA 61.114 60.000 19.33 4.60 0.00 5.14
36 37 0.969894 GGTTGGAGATCGATCGGGAT 59.030 55.000 19.33 1.47 0.00 3.85
37 38 1.337260 GGTTGGAGATCGATCGGGATG 60.337 57.143 19.33 0.00 0.00 3.51
38 39 1.341531 GTTGGAGATCGATCGGGATGT 59.658 52.381 19.33 0.04 0.00 3.06
39 40 2.557056 GTTGGAGATCGATCGGGATGTA 59.443 50.000 19.33 0.00 0.00 2.29
40 41 2.160205 TGGAGATCGATCGGGATGTAC 58.840 52.381 19.33 2.09 0.00 2.90
41 42 2.160205 GGAGATCGATCGGGATGTACA 58.840 52.381 19.33 0.00 0.00 2.90
42 43 2.162608 GGAGATCGATCGGGATGTACAG 59.837 54.545 19.33 0.00 0.00 2.74
43 44 3.075148 GAGATCGATCGGGATGTACAGA 58.925 50.000 19.33 0.00 0.00 3.41
44 45 2.814919 AGATCGATCGGGATGTACAGAC 59.185 50.000 19.33 0.00 0.00 3.51
45 46 0.942252 TCGATCGGGATGTACAGACG 59.058 55.000 16.41 6.01 0.00 4.18
46 47 0.040336 CGATCGGGATGTACAGACGG 60.040 60.000 7.38 8.27 0.00 4.79
47 48 1.315690 GATCGGGATGTACAGACGGA 58.684 55.000 14.11 12.41 0.00 4.69
48 49 1.887198 GATCGGGATGTACAGACGGAT 59.113 52.381 17.05 17.05 0.00 4.18
49 50 1.315690 TCGGGATGTACAGACGGATC 58.684 55.000 14.11 0.90 0.00 3.36
50 51 1.029681 CGGGATGTACAGACGGATCA 58.970 55.000 0.33 0.00 0.00 2.92
51 52 1.407618 CGGGATGTACAGACGGATCAA 59.592 52.381 0.33 0.00 0.00 2.57
52 53 2.159156 CGGGATGTACAGACGGATCAAA 60.159 50.000 0.33 0.00 0.00 2.69
53 54 3.195661 GGGATGTACAGACGGATCAAAC 58.804 50.000 0.33 0.00 0.00 2.93
54 55 3.369052 GGGATGTACAGACGGATCAAACA 60.369 47.826 0.33 0.00 0.00 2.83
55 56 3.617263 GGATGTACAGACGGATCAAACAC 59.383 47.826 0.33 0.00 0.00 3.32
56 57 3.737032 TGTACAGACGGATCAAACACA 57.263 42.857 0.00 0.00 0.00 3.72
57 58 3.386486 TGTACAGACGGATCAAACACAC 58.614 45.455 0.00 0.00 0.00 3.82
58 59 1.497991 ACAGACGGATCAAACACACG 58.502 50.000 0.00 0.00 0.00 4.49
59 60 1.067974 ACAGACGGATCAAACACACGA 59.932 47.619 0.00 0.00 0.00 4.35
60 61 1.721389 CAGACGGATCAAACACACGAG 59.279 52.381 0.00 0.00 0.00 4.18
61 62 1.340248 AGACGGATCAAACACACGAGT 59.660 47.619 0.00 0.00 0.00 4.18
62 63 2.132762 GACGGATCAAACACACGAGTT 58.867 47.619 0.00 0.00 0.00 3.01
63 64 1.864711 ACGGATCAAACACACGAGTTG 59.135 47.619 0.00 0.00 0.00 3.16
64 65 1.398451 CGGATCAAACACACGAGTTGC 60.398 52.381 0.00 0.00 0.00 4.17
65 66 1.601903 GGATCAAACACACGAGTTGCA 59.398 47.619 0.00 0.00 0.00 4.08
66 67 2.349817 GGATCAAACACACGAGTTGCAG 60.350 50.000 0.00 0.00 0.00 4.41
67 68 0.376852 TCAAACACACGAGTTGCAGC 59.623 50.000 0.00 0.00 0.00 5.25
68 69 0.925267 CAAACACACGAGTTGCAGCG 60.925 55.000 0.00 0.00 0.00 5.18
69 70 1.366111 AAACACACGAGTTGCAGCGT 61.366 50.000 5.66 5.66 42.11 5.07
99 100 8.682936 AAAATTGACCTAGCTCTAATACCATG 57.317 34.615 0.00 0.00 0.00 3.66
100 101 7.380423 AATTGACCTAGCTCTAATACCATGT 57.620 36.000 0.00 0.00 0.00 3.21
101 102 6.808321 TTGACCTAGCTCTAATACCATGTT 57.192 37.500 0.00 0.00 0.00 2.71
102 103 7.907841 TTGACCTAGCTCTAATACCATGTTA 57.092 36.000 0.00 0.00 0.00 2.41
103 104 7.526142 TGACCTAGCTCTAATACCATGTTAG 57.474 40.000 0.00 0.00 0.00 2.34
104 105 6.493802 TGACCTAGCTCTAATACCATGTTAGG 59.506 42.308 0.00 0.00 31.59 2.69
105 106 6.621394 ACCTAGCTCTAATACCATGTTAGGA 58.379 40.000 0.00 0.00 31.59 2.94
106 107 7.073854 ACCTAGCTCTAATACCATGTTAGGAA 58.926 38.462 0.00 0.00 31.59 3.36
107 108 7.735321 ACCTAGCTCTAATACCATGTTAGGAAT 59.265 37.037 0.00 0.00 31.59 3.01
108 109 9.256228 CCTAGCTCTAATACCATGTTAGGAATA 57.744 37.037 0.00 0.00 31.59 1.75
111 112 8.097662 AGCTCTAATACCATGTTAGGAATAAGC 58.902 37.037 0.00 0.00 31.59 3.09
112 113 7.878127 GCTCTAATACCATGTTAGGAATAAGCA 59.122 37.037 0.00 0.00 31.59 3.91
113 114 9.778741 CTCTAATACCATGTTAGGAATAAGCAA 57.221 33.333 0.00 0.00 31.59 3.91
114 115 9.555727 TCTAATACCATGTTAGGAATAAGCAAC 57.444 33.333 0.00 0.00 31.59 4.17
115 116 9.561069 CTAATACCATGTTAGGAATAAGCAACT 57.439 33.333 0.00 0.00 0.00 3.16
116 117 8.823220 AATACCATGTTAGGAATAAGCAACTT 57.177 30.769 0.00 0.00 0.00 2.66
117 118 6.515272 ACCATGTTAGGAATAAGCAACTTG 57.485 37.500 0.00 0.00 0.00 3.16
118 119 6.010219 ACCATGTTAGGAATAAGCAACTTGT 58.990 36.000 0.00 0.00 0.00 3.16
119 120 7.172342 ACCATGTTAGGAATAAGCAACTTGTA 58.828 34.615 0.00 0.00 0.00 2.41
120 121 7.834181 ACCATGTTAGGAATAAGCAACTTGTAT 59.166 33.333 0.00 0.00 0.00 2.29
121 122 8.686334 CCATGTTAGGAATAAGCAACTTGTATT 58.314 33.333 0.00 0.00 0.00 1.89
122 123 9.722056 CATGTTAGGAATAAGCAACTTGTATTC 57.278 33.333 0.00 4.57 34.75 1.75
126 127 6.715347 GGAATAAGCAACTTGTATTCCCAT 57.285 37.500 14.79 0.00 43.89 4.00
127 128 6.507023 GGAATAAGCAACTTGTATTCCCATG 58.493 40.000 14.79 0.00 43.89 3.66
128 129 6.321181 GGAATAAGCAACTTGTATTCCCATGA 59.679 38.462 14.79 0.00 43.89 3.07
129 130 6.949352 ATAAGCAACTTGTATTCCCATGAG 57.051 37.500 0.00 0.00 0.00 2.90
130 131 3.624777 AGCAACTTGTATTCCCATGAGG 58.375 45.455 0.00 0.00 0.00 3.86
131 132 2.099756 GCAACTTGTATTCCCATGAGGC 59.900 50.000 0.00 0.00 34.51 4.70
132 133 2.689983 CAACTTGTATTCCCATGAGGCC 59.310 50.000 0.00 0.00 34.51 5.19
133 134 1.922447 ACTTGTATTCCCATGAGGCCA 59.078 47.619 5.01 0.00 34.51 5.36
134 135 2.515429 ACTTGTATTCCCATGAGGCCAT 59.485 45.455 5.01 0.00 34.51 4.40
135 136 3.721575 ACTTGTATTCCCATGAGGCCATA 59.278 43.478 5.01 0.00 34.51 2.74
136 137 4.202503 ACTTGTATTCCCATGAGGCCATAG 60.203 45.833 5.01 0.00 34.51 2.23
137 138 2.644299 TGTATTCCCATGAGGCCATAGG 59.356 50.000 5.01 0.21 33.55 2.57
154 155 6.936279 GCCATAGGCCGATATATATACATGT 58.064 40.000 2.69 2.69 44.06 3.21
155 156 8.063200 GCCATAGGCCGATATATATACATGTA 57.937 38.462 8.27 8.27 44.06 2.29
156 157 7.974501 GCCATAGGCCGATATATATACATGTAC 59.025 40.741 7.96 0.00 44.06 2.90
157 158 9.020731 CCATAGGCCGATATATATACATGTACA 57.979 37.037 7.96 0.00 0.00 2.90
160 161 8.534954 AGGCCGATATATATACATGTACAAGT 57.465 34.615 7.96 8.98 0.00 3.16
161 162 8.414003 AGGCCGATATATATACATGTACAAGTG 58.586 37.037 13.80 4.46 0.00 3.16
162 163 8.195436 GGCCGATATATATACATGTACAAGTGT 58.805 37.037 13.80 10.36 0.00 3.55
163 164 9.020813 GCCGATATATATACATGTACAAGTGTG 57.979 37.037 13.80 3.34 0.00 3.82
164 165 9.516314 CCGATATATATACATGTACAAGTGTGG 57.484 37.037 13.80 1.15 0.00 4.17
181 182 3.088532 TGTGGAACATATGCAGGAAACC 58.911 45.455 1.58 0.00 45.67 3.27
182 183 3.245229 TGTGGAACATATGCAGGAAACCT 60.245 43.478 1.58 0.00 45.67 3.50
183 184 3.378427 GTGGAACATATGCAGGAAACCTC 59.622 47.826 1.58 0.00 44.52 3.85
184 185 3.266772 TGGAACATATGCAGGAAACCTCT 59.733 43.478 1.58 0.00 0.00 3.69
185 186 4.263905 TGGAACATATGCAGGAAACCTCTT 60.264 41.667 1.58 0.00 0.00 2.85
186 187 5.045213 TGGAACATATGCAGGAAACCTCTTA 60.045 40.000 1.58 0.00 0.00 2.10
187 188 6.064717 GGAACATATGCAGGAAACCTCTTAT 58.935 40.000 1.58 0.00 0.00 1.73
188 189 7.147391 TGGAACATATGCAGGAAACCTCTTATA 60.147 37.037 1.58 0.00 0.00 0.98
189 190 7.173390 GGAACATATGCAGGAAACCTCTTATAC 59.827 40.741 1.58 0.00 0.00 1.47
190 191 7.136822 ACATATGCAGGAAACCTCTTATACA 57.863 36.000 1.58 0.00 0.00 2.29
191 192 7.573710 ACATATGCAGGAAACCTCTTATACAA 58.426 34.615 1.58 0.00 0.00 2.41
192 193 7.499232 ACATATGCAGGAAACCTCTTATACAAC 59.501 37.037 1.58 0.00 0.00 3.32
193 194 5.235850 TGCAGGAAACCTCTTATACAACA 57.764 39.130 0.00 0.00 0.00 3.33
194 195 5.245531 TGCAGGAAACCTCTTATACAACAG 58.754 41.667 0.00 0.00 0.00 3.16
195 196 4.636206 GCAGGAAACCTCTTATACAACAGG 59.364 45.833 0.00 0.00 0.00 4.00
196 197 5.570844 GCAGGAAACCTCTTATACAACAGGA 60.571 44.000 0.00 0.00 0.00 3.86
197 198 6.653989 CAGGAAACCTCTTATACAACAGGAT 58.346 40.000 0.00 0.00 0.00 3.24
198 199 7.635089 GCAGGAAACCTCTTATACAACAGGATA 60.635 40.741 0.00 0.00 0.00 2.59
199 200 8.265055 CAGGAAACCTCTTATACAACAGGATAA 58.735 37.037 0.00 0.00 0.00 1.75
200 201 8.832735 AGGAAACCTCTTATACAACAGGATAAA 58.167 33.333 0.00 0.00 0.00 1.40
201 202 9.628500 GGAAACCTCTTATACAACAGGATAAAT 57.372 33.333 0.00 0.00 0.00 1.40
210 211 9.635404 TTATACAACAGGATAAATACAAAGGGG 57.365 33.333 0.00 0.00 0.00 4.79
211 212 5.899278 ACAACAGGATAAATACAAAGGGGT 58.101 37.500 0.00 0.00 0.00 4.95
212 213 7.034967 ACAACAGGATAAATACAAAGGGGTA 57.965 36.000 0.00 0.00 0.00 3.69
213 214 6.888088 ACAACAGGATAAATACAAAGGGGTAC 59.112 38.462 0.00 0.00 0.00 3.34
214 215 6.645884 ACAGGATAAATACAAAGGGGTACA 57.354 37.500 0.00 0.00 0.00 2.90
215 216 7.220890 ACAGGATAAATACAAAGGGGTACAT 57.779 36.000 0.00 0.00 0.00 2.29
216 217 7.060421 ACAGGATAAATACAAAGGGGTACATG 58.940 38.462 0.00 0.00 0.00 3.21
217 218 7.092174 ACAGGATAAATACAAAGGGGTACATGA 60.092 37.037 0.00 0.00 0.00 3.07
218 219 7.228706 CAGGATAAATACAAAGGGGTACATGAC 59.771 40.741 0.00 0.00 0.00 3.06
219 220 7.128883 AGGATAAATACAAAGGGGTACATGACT 59.871 37.037 0.00 0.00 0.00 3.41
220 221 7.778382 GGATAAATACAAAGGGGTACATGACTT 59.222 37.037 0.00 0.00 0.00 3.01
221 222 9.841295 GATAAATACAAAGGGGTACATGACTTA 57.159 33.333 0.00 0.00 0.00 2.24
329 333 9.135189 TGAATAGCAATAAGAAATAATGTGGCT 57.865 29.630 0.00 0.00 0.00 4.75
354 358 1.375908 GCCTGGAGCGTCATCAACA 60.376 57.895 0.00 0.00 0.00 3.33
399 456 4.751600 TGACATCAGTTGCTTGAGTACTTG 59.248 41.667 0.00 0.00 0.00 3.16
765 1637 4.696877 ACACACACATACACATGGATGAAG 59.303 41.667 11.15 5.58 36.39 3.02
768 1640 6.371271 CACACACATACACATGGATGAAGTAA 59.629 38.462 11.15 0.00 36.39 2.24
782 1656 4.383774 TGAAGTAAGTTTTGACGATGCG 57.616 40.909 0.00 0.00 0.00 4.73
784 1658 4.084745 TGAAGTAAGTTTTGACGATGCGAC 60.085 41.667 0.00 0.00 0.00 5.19
791 1665 1.493772 TTGACGATGCGACGACTTTT 58.506 45.000 0.00 0.00 37.03 2.27
818 1694 6.494893 TTAATCTGTGGCTCACATACAAAC 57.505 37.500 8.23 0.00 43.71 2.93
831 1707 9.177304 GCTCACATACAAACATATTTCATCATG 57.823 33.333 0.00 0.00 0.00 3.07
850 1726 7.595875 TCATCATGCAACTTTACAAACATGAAG 59.404 33.333 0.00 4.04 44.84 3.02
887 1766 5.978814 TCTCTCAGTCCTAAAATAAGTGCC 58.021 41.667 0.00 0.00 0.00 5.01
888 1767 5.099042 TCTCAGTCCTAAAATAAGTGCCC 57.901 43.478 0.00 0.00 0.00 5.36
966 1845 4.267349 TGTAGTAAGGAAAGTGTGGAGC 57.733 45.455 0.00 0.00 0.00 4.70
974 1853 1.003580 GAAAGTGTGGAGCCTGATGGA 59.996 52.381 0.00 0.00 34.57 3.41
978 1857 1.747355 GTGTGGAGCCTGATGGAATTG 59.253 52.381 0.00 0.00 34.57 2.32
983 1862 2.692041 GGAGCCTGATGGAATTGGAAAG 59.308 50.000 0.00 0.00 34.57 2.62
985 1864 1.202336 GCCTGATGGAATTGGAAAGCG 60.202 52.381 0.00 0.00 34.57 4.68
1028 2642 6.904626 ACCTAACTGATCCAAAGCAGATTAT 58.095 36.000 0.00 0.00 41.56 1.28
1035 2649 7.497249 ACTGATCCAAAGCAGATTATCTGTTAC 59.503 37.037 21.46 7.08 45.94 2.50
1099 3308 0.843309 TCTGCTTTGGAACTGGTGGA 59.157 50.000 0.00 0.00 0.00 4.02
1107 3316 2.684943 TGGAACTGGTGGAAGTGTAGA 58.315 47.619 0.00 0.00 0.00 2.59
1186 3395 4.264253 TGGTTCTGATGCAAAGGAGTATG 58.736 43.478 0.00 0.00 0.00 2.39
1217 3426 1.334054 GCACAGCGCAAAGATTCAAG 58.666 50.000 11.47 0.00 41.79 3.02
1226 3435 4.318050 GCGCAAAGATTCAAGTCCAAAAAC 60.318 41.667 0.30 0.00 0.00 2.43
1227 3436 4.803088 CGCAAAGATTCAAGTCCAAAAACA 59.197 37.500 0.00 0.00 0.00 2.83
1234 3443 4.108699 TCAAGTCCAAAAACAGTGCAAG 57.891 40.909 0.00 0.00 0.00 4.01
1274 3483 7.571428 GCCACAGGATATTCTAAAGATTAACGC 60.571 40.741 0.00 0.00 0.00 4.84
1347 3576 2.031870 CGAGACCACATGGGAGATGTA 58.968 52.381 0.00 0.00 41.15 2.29
1481 3971 0.100682 GTAGAGACGGATGCGCAGAA 59.899 55.000 18.32 0.00 0.00 3.02
1488 3978 0.248215 CGGATGCGCAGAATTTGGTC 60.248 55.000 18.32 5.42 0.00 4.02
1501 3991 6.115446 CAGAATTTGGTCCAAGCTATCACTA 58.885 40.000 4.09 0.00 0.00 2.74
1504 3994 4.901197 TTGGTCCAAGCTATCACTAACA 57.099 40.909 0.00 0.00 0.00 2.41
1551 4041 7.398904 CCAAATGGAGTCCTTTTTAGGGAAATA 59.601 37.037 18.03 0.00 37.39 1.40
1553 4043 9.560860 AAATGGAGTCCTTTTTAGGGAAATAAT 57.439 29.630 15.53 0.00 34.35 1.28
1575 4079 3.095332 TGCCCTTGCTATGTTGCATTTA 58.905 40.909 0.00 0.00 42.96 1.40
1607 4770 0.404040 ATCTCTTTTTGCCCACGGGA 59.596 50.000 6.21 0.00 37.50 5.14
1644 4807 4.175489 GCTCTAGCGACGCACGGA 62.175 66.667 23.70 14.83 42.83 4.69
1718 4881 0.824109 ATCCGAGACTTGATTGCCGA 59.176 50.000 0.00 0.00 0.00 5.54
1723 4886 1.855360 GAGACTTGATTGCCGACGATC 59.145 52.381 0.00 0.00 37.23 3.69
1729 4892 1.999735 TGATTGCCGACGATCTTGTTC 59.000 47.619 0.00 0.00 37.55 3.18
1754 4920 6.528423 CGGCGTGGTTAATTGAAATGAAATTA 59.472 34.615 0.00 0.00 33.67 1.40
1755 4921 7.062371 CGGCGTGGTTAATTGAAATGAAATTAA 59.938 33.333 0.00 0.00 33.67 1.40
1782 4948 5.514500 AAAACCCTGGTAAGCTATCTCAA 57.486 39.130 0.00 0.00 0.00 3.02
1783 4949 5.514500 AAACCCTGGTAAGCTATCTCAAA 57.486 39.130 0.00 0.00 0.00 2.69
1784 4950 5.514500 AACCCTGGTAAGCTATCTCAAAA 57.486 39.130 0.00 0.00 0.00 2.44
1785 4951 5.514500 ACCCTGGTAAGCTATCTCAAAAA 57.486 39.130 0.00 0.00 0.00 1.94
1805 4971 6.978343 AAAAACAAAAACCCTTAGTCAAGC 57.022 33.333 0.00 0.00 0.00 4.01
1806 4972 5.669164 AAACAAAAACCCTTAGTCAAGCA 57.331 34.783 0.00 0.00 0.00 3.91
1807 4973 4.649088 ACAAAAACCCTTAGTCAAGCAC 57.351 40.909 0.00 0.00 0.00 4.40
1808 4974 3.383505 ACAAAAACCCTTAGTCAAGCACC 59.616 43.478 0.00 0.00 0.00 5.01
1809 4975 3.595190 AAAACCCTTAGTCAAGCACCT 57.405 42.857 0.00 0.00 0.00 4.00
1810 4976 2.568623 AACCCTTAGTCAAGCACCTG 57.431 50.000 0.00 0.00 0.00 4.00
1811 4977 0.693049 ACCCTTAGTCAAGCACCTGG 59.307 55.000 0.00 0.00 0.00 4.45
1812 4978 0.693049 CCCTTAGTCAAGCACCTGGT 59.307 55.000 0.00 0.00 0.00 4.00
1813 4979 1.339151 CCCTTAGTCAAGCACCTGGTC 60.339 57.143 0.00 0.00 0.00 4.02
1814 4980 1.339151 CCTTAGTCAAGCACCTGGTCC 60.339 57.143 0.00 0.00 0.00 4.46
1817 4983 1.958288 AGTCAAGCACCTGGTCCTAT 58.042 50.000 0.00 0.00 0.00 2.57
1818 4984 1.834263 AGTCAAGCACCTGGTCCTATC 59.166 52.381 0.00 0.00 0.00 2.08
1821 4987 0.537188 AAGCACCTGGTCCTATCGTG 59.463 55.000 0.00 0.00 0.00 4.35
1822 4988 0.324368 AGCACCTGGTCCTATCGTGA 60.324 55.000 0.00 0.00 0.00 4.35
1849 5031 1.831652 AAACCCTCCACTCCTGCTCG 61.832 60.000 0.00 0.00 0.00 5.03
2568 5913 6.697395 TCGTCTTATGATCTTCAGTTTCCAA 58.303 36.000 0.00 0.00 0.00 3.53
2569 5914 7.158697 TCGTCTTATGATCTTCAGTTTCCAAA 58.841 34.615 0.00 0.00 0.00 3.28
2570 5915 7.659799 TCGTCTTATGATCTTCAGTTTCCAAAA 59.340 33.333 0.00 0.00 0.00 2.44
2598 5943 6.669278 CATCCAGCAATCAACTTGATAGATG 58.331 40.000 4.65 8.67 40.94 2.90
2691 6036 1.106285 GGTGATTTCATGCCTGTCCC 58.894 55.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.203422 CCCCGCTCGATCTCCTCT 60.203 66.667 0.00 0.00 0.00 3.69
3 4 2.042843 AACCCCGCTCGATCTCCT 60.043 61.111 0.00 0.00 0.00 3.69
4 5 2.107141 CAACCCCGCTCGATCTCC 59.893 66.667 0.00 0.00 0.00 3.71
5 6 2.107141 CCAACCCCGCTCGATCTC 59.893 66.667 0.00 0.00 0.00 2.75
6 7 2.363795 TCCAACCCCGCTCGATCT 60.364 61.111 0.00 0.00 0.00 2.75
7 8 1.749334 ATCTCCAACCCCGCTCGATC 61.749 60.000 0.00 0.00 0.00 3.69
8 9 1.749334 GATCTCCAACCCCGCTCGAT 61.749 60.000 0.00 0.00 0.00 3.59
9 10 2.363795 ATCTCCAACCCCGCTCGA 60.364 61.111 0.00 0.00 0.00 4.04
10 11 2.107141 GATCTCCAACCCCGCTCG 59.893 66.667 0.00 0.00 0.00 5.03
11 12 1.749334 ATCGATCTCCAACCCCGCTC 61.749 60.000 0.00 0.00 0.00 5.03
12 13 1.749334 GATCGATCTCCAACCCCGCT 61.749 60.000 18.29 0.00 0.00 5.52
13 14 1.301009 GATCGATCTCCAACCCCGC 60.301 63.158 18.29 0.00 0.00 6.13
14 15 1.007271 CGATCGATCTCCAACCCCG 60.007 63.158 22.43 3.48 0.00 5.73
15 16 1.367840 CCGATCGATCTCCAACCCC 59.632 63.158 22.43 0.00 0.00 4.95
16 17 1.113517 TCCCGATCGATCTCCAACCC 61.114 60.000 22.43 0.00 0.00 4.11
17 18 0.969894 ATCCCGATCGATCTCCAACC 59.030 55.000 22.43 0.00 0.00 3.77
18 19 1.341531 ACATCCCGATCGATCTCCAAC 59.658 52.381 22.43 0.00 0.00 3.77
19 20 1.704641 ACATCCCGATCGATCTCCAA 58.295 50.000 22.43 6.49 0.00 3.53
20 21 2.160205 GTACATCCCGATCGATCTCCA 58.840 52.381 22.43 6.67 0.00 3.86
21 22 2.160205 TGTACATCCCGATCGATCTCC 58.840 52.381 22.43 0.00 0.00 3.71
22 23 3.075148 TCTGTACATCCCGATCGATCTC 58.925 50.000 22.43 0.00 0.00 2.75
23 24 2.814919 GTCTGTACATCCCGATCGATCT 59.185 50.000 22.43 5.87 0.00 2.75
24 25 2.412977 CGTCTGTACATCCCGATCGATC 60.413 54.545 18.66 15.68 0.00 3.69
25 26 1.535896 CGTCTGTACATCCCGATCGAT 59.464 52.381 18.66 0.00 0.00 3.59
26 27 0.942252 CGTCTGTACATCCCGATCGA 59.058 55.000 18.66 0.00 0.00 3.59
27 28 0.040336 CCGTCTGTACATCCCGATCG 60.040 60.000 8.51 8.51 0.00 3.69
28 29 1.315690 TCCGTCTGTACATCCCGATC 58.684 55.000 0.00 0.00 0.00 3.69
29 30 1.887198 GATCCGTCTGTACATCCCGAT 59.113 52.381 0.00 0.00 0.00 4.18
30 31 1.315690 GATCCGTCTGTACATCCCGA 58.684 55.000 0.00 0.00 0.00 5.14
31 32 1.029681 TGATCCGTCTGTACATCCCG 58.970 55.000 0.00 0.00 0.00 5.14
32 33 3.195661 GTTTGATCCGTCTGTACATCCC 58.804 50.000 0.00 0.00 0.00 3.85
33 34 3.617263 GTGTTTGATCCGTCTGTACATCC 59.383 47.826 0.00 0.00 0.00 3.51
34 35 4.091509 GTGTGTTTGATCCGTCTGTACATC 59.908 45.833 0.00 0.00 0.00 3.06
35 36 3.994392 GTGTGTTTGATCCGTCTGTACAT 59.006 43.478 0.00 0.00 0.00 2.29
36 37 3.386486 GTGTGTTTGATCCGTCTGTACA 58.614 45.455 0.00 0.00 0.00 2.90
37 38 2.407361 CGTGTGTTTGATCCGTCTGTAC 59.593 50.000 0.00 0.00 0.00 2.90
38 39 2.293955 TCGTGTGTTTGATCCGTCTGTA 59.706 45.455 0.00 0.00 0.00 2.74
39 40 1.067974 TCGTGTGTTTGATCCGTCTGT 59.932 47.619 0.00 0.00 0.00 3.41
40 41 1.721389 CTCGTGTGTTTGATCCGTCTG 59.279 52.381 0.00 0.00 0.00 3.51
41 42 1.340248 ACTCGTGTGTTTGATCCGTCT 59.660 47.619 0.00 0.00 0.00 4.18
42 43 1.779569 ACTCGTGTGTTTGATCCGTC 58.220 50.000 0.00 0.00 0.00 4.79
43 44 1.864711 CAACTCGTGTGTTTGATCCGT 59.135 47.619 0.00 0.00 0.00 4.69
44 45 1.398451 GCAACTCGTGTGTTTGATCCG 60.398 52.381 0.00 0.00 0.00 4.18
45 46 1.601903 TGCAACTCGTGTGTTTGATCC 59.398 47.619 0.00 0.00 0.00 3.36
46 47 2.908634 CTGCAACTCGTGTGTTTGATC 58.091 47.619 0.00 0.00 0.00 2.92
47 48 1.002468 GCTGCAACTCGTGTGTTTGAT 60.002 47.619 0.00 0.00 0.00 2.57
48 49 0.376852 GCTGCAACTCGTGTGTTTGA 59.623 50.000 0.00 0.00 0.00 2.69
49 50 0.925267 CGCTGCAACTCGTGTGTTTG 60.925 55.000 0.00 0.00 0.00 2.93
50 51 1.351707 CGCTGCAACTCGTGTGTTT 59.648 52.632 0.00 0.00 0.00 2.83
51 52 1.813753 ACGCTGCAACTCGTGTGTT 60.814 52.632 7.40 0.00 37.55 3.32
52 53 2.202878 ACGCTGCAACTCGTGTGT 60.203 55.556 7.40 0.00 37.55 3.72
73 74 9.125026 CATGGTATTAGAGCTAGGTCAATTTTT 57.875 33.333 23.18 4.64 0.00 1.94
74 75 8.275040 ACATGGTATTAGAGCTAGGTCAATTTT 58.725 33.333 23.18 5.36 0.00 1.82
75 76 7.806180 ACATGGTATTAGAGCTAGGTCAATTT 58.194 34.615 23.18 5.73 0.00 1.82
76 77 7.380423 ACATGGTATTAGAGCTAGGTCAATT 57.620 36.000 23.18 9.70 0.00 2.32
77 78 7.380423 AACATGGTATTAGAGCTAGGTCAAT 57.620 36.000 23.18 19.82 0.00 2.57
78 79 6.808321 AACATGGTATTAGAGCTAGGTCAA 57.192 37.500 23.18 15.02 0.00 3.18
79 80 6.493802 CCTAACATGGTATTAGAGCTAGGTCA 59.506 42.308 23.18 4.56 32.31 4.02
80 81 6.720288 TCCTAACATGGTATTAGAGCTAGGTC 59.280 42.308 14.19 14.19 32.31 3.85
81 82 6.621394 TCCTAACATGGTATTAGAGCTAGGT 58.379 40.000 0.00 0.00 32.31 3.08
82 83 7.540474 TTCCTAACATGGTATTAGAGCTAGG 57.460 40.000 0.00 0.00 32.31 3.02
85 86 8.097662 GCTTATTCCTAACATGGTATTAGAGCT 58.902 37.037 0.00 0.00 32.31 4.09
86 87 7.878127 TGCTTATTCCTAACATGGTATTAGAGC 59.122 37.037 0.00 1.28 32.31 4.09
87 88 9.778741 TTGCTTATTCCTAACATGGTATTAGAG 57.221 33.333 0.00 0.00 32.31 2.43
88 89 9.555727 GTTGCTTATTCCTAACATGGTATTAGA 57.444 33.333 0.00 0.00 32.31 2.10
89 90 9.561069 AGTTGCTTATTCCTAACATGGTATTAG 57.439 33.333 0.00 0.00 0.00 1.73
90 91 9.914834 AAGTTGCTTATTCCTAACATGGTATTA 57.085 29.630 0.00 0.00 0.00 0.98
91 92 8.686334 CAAGTTGCTTATTCCTAACATGGTATT 58.314 33.333 0.00 0.00 0.00 1.89
92 93 7.834181 ACAAGTTGCTTATTCCTAACATGGTAT 59.166 33.333 1.81 0.00 0.00 2.73
93 94 7.172342 ACAAGTTGCTTATTCCTAACATGGTA 58.828 34.615 1.81 0.00 0.00 3.25
94 95 6.010219 ACAAGTTGCTTATTCCTAACATGGT 58.990 36.000 1.81 0.00 0.00 3.55
95 96 6.515272 ACAAGTTGCTTATTCCTAACATGG 57.485 37.500 1.81 0.00 0.00 3.66
96 97 9.722056 GAATACAAGTTGCTTATTCCTAACATG 57.278 33.333 1.81 0.00 0.00 3.21
97 98 8.903820 GGAATACAAGTTGCTTATTCCTAACAT 58.096 33.333 24.74 0.00 41.60 2.71
98 99 7.338449 GGGAATACAAGTTGCTTATTCCTAACA 59.662 37.037 27.77 0.00 43.33 2.41
99 100 7.338449 TGGGAATACAAGTTGCTTATTCCTAAC 59.662 37.037 27.77 19.00 43.33 2.34
100 101 7.406916 TGGGAATACAAGTTGCTTATTCCTAA 58.593 34.615 27.77 19.95 43.33 2.69
101 102 6.964464 TGGGAATACAAGTTGCTTATTCCTA 58.036 36.000 27.77 23.73 43.33 2.94
102 103 5.826643 TGGGAATACAAGTTGCTTATTCCT 58.173 37.500 27.77 4.94 43.33 3.36
103 104 6.321181 TCATGGGAATACAAGTTGCTTATTCC 59.679 38.462 24.35 24.35 43.17 3.01
104 105 7.333528 TCATGGGAATACAAGTTGCTTATTC 57.666 36.000 13.88 13.88 0.00 1.75
105 106 6.322201 CCTCATGGGAATACAAGTTGCTTATT 59.678 38.462 1.81 0.58 37.23 1.40
106 107 5.829924 CCTCATGGGAATACAAGTTGCTTAT 59.170 40.000 1.81 0.00 37.23 1.73
107 108 5.192927 CCTCATGGGAATACAAGTTGCTTA 58.807 41.667 1.81 0.00 37.23 3.09
108 109 4.019174 CCTCATGGGAATACAAGTTGCTT 58.981 43.478 1.81 0.00 37.23 3.91
109 110 3.624777 CCTCATGGGAATACAAGTTGCT 58.375 45.455 1.81 0.00 37.23 3.91
110 111 2.099756 GCCTCATGGGAATACAAGTTGC 59.900 50.000 1.81 0.00 37.23 4.17
111 112 2.689983 GGCCTCATGGGAATACAAGTTG 59.310 50.000 0.00 0.00 37.23 3.16
112 113 2.311542 TGGCCTCATGGGAATACAAGTT 59.688 45.455 3.32 0.00 37.23 2.66
113 114 1.922447 TGGCCTCATGGGAATACAAGT 59.078 47.619 3.32 0.00 37.23 3.16
114 115 2.734755 TGGCCTCATGGGAATACAAG 57.265 50.000 3.32 0.00 37.23 3.16
115 116 4.371624 CTATGGCCTCATGGGAATACAA 57.628 45.455 3.32 0.00 37.23 2.41
131 132 9.020731 TGTACATGTATATATATCGGCCTATGG 57.979 37.037 9.18 0.00 0.00 2.74
134 135 9.636789 ACTTGTACATGTATATATATCGGCCTA 57.363 33.333 12.39 0.00 0.00 3.93
135 136 8.414003 CACTTGTACATGTATATATATCGGCCT 58.586 37.037 13.51 0.00 0.00 5.19
136 137 8.195436 ACACTTGTACATGTATATATATCGGCC 58.805 37.037 13.51 0.00 0.00 6.13
137 138 9.020813 CACACTTGTACATGTATATATATCGGC 57.979 37.037 13.51 0.00 0.00 5.54
138 139 9.516314 CCACACTTGTACATGTATATATATCGG 57.484 37.037 13.51 1.07 0.00 4.18
146 147 9.541143 CATATGTTCCACACTTGTACATGTATA 57.459 33.333 13.51 3.08 31.83 1.47
147 148 7.012327 GCATATGTTCCACACTTGTACATGTAT 59.988 37.037 13.51 0.23 31.83 2.29
148 149 6.315144 GCATATGTTCCACACTTGTACATGTA 59.685 38.462 13.51 0.08 31.83 2.29
149 150 5.123820 GCATATGTTCCACACTTGTACATGT 59.876 40.000 8.51 8.51 31.83 3.21
150 151 5.123661 TGCATATGTTCCACACTTGTACATG 59.876 40.000 4.29 7.18 31.83 3.21
151 152 5.252547 TGCATATGTTCCACACTTGTACAT 58.747 37.500 4.29 0.00 33.23 2.29
152 153 4.646572 TGCATATGTTCCACACTTGTACA 58.353 39.130 4.29 0.00 0.00 2.90
153 154 4.094887 CCTGCATATGTTCCACACTTGTAC 59.905 45.833 4.29 0.00 0.00 2.90
154 155 4.019771 TCCTGCATATGTTCCACACTTGTA 60.020 41.667 4.29 0.00 0.00 2.41
155 156 3.084039 CCTGCATATGTTCCACACTTGT 58.916 45.455 4.29 0.00 0.00 3.16
156 157 3.346315 TCCTGCATATGTTCCACACTTG 58.654 45.455 4.29 0.00 0.00 3.16
157 158 3.719268 TCCTGCATATGTTCCACACTT 57.281 42.857 4.29 0.00 0.00 3.16
158 159 3.719268 TTCCTGCATATGTTCCACACT 57.281 42.857 4.29 0.00 0.00 3.55
159 160 3.119495 GGTTTCCTGCATATGTTCCACAC 60.119 47.826 4.29 0.00 0.00 3.82
160 161 3.088532 GGTTTCCTGCATATGTTCCACA 58.911 45.455 4.29 0.00 0.00 4.17
161 162 3.356290 AGGTTTCCTGCATATGTTCCAC 58.644 45.455 4.29 0.00 29.57 4.02
162 163 3.266772 AGAGGTTTCCTGCATATGTTCCA 59.733 43.478 4.29 0.00 31.76 3.53
163 164 3.891049 AGAGGTTTCCTGCATATGTTCC 58.109 45.455 4.29 0.00 31.76 3.62
164 165 7.715249 TGTATAAGAGGTTTCCTGCATATGTTC 59.285 37.037 4.29 0.00 31.76 3.18
165 166 7.573710 TGTATAAGAGGTTTCCTGCATATGTT 58.426 34.615 4.29 0.00 31.76 2.71
166 167 7.136822 TGTATAAGAGGTTTCCTGCATATGT 57.863 36.000 4.29 0.00 31.76 2.29
167 168 7.498900 TGTTGTATAAGAGGTTTCCTGCATATG 59.501 37.037 0.00 0.00 31.76 1.78
168 169 7.573710 TGTTGTATAAGAGGTTTCCTGCATAT 58.426 34.615 0.00 0.00 31.76 1.78
169 170 6.953101 TGTTGTATAAGAGGTTTCCTGCATA 58.047 36.000 0.00 0.00 31.76 3.14
170 171 5.815581 TGTTGTATAAGAGGTTTCCTGCAT 58.184 37.500 0.00 0.00 31.76 3.96
171 172 5.235850 TGTTGTATAAGAGGTTTCCTGCA 57.764 39.130 0.00 0.00 31.76 4.41
172 173 4.636206 CCTGTTGTATAAGAGGTTTCCTGC 59.364 45.833 7.20 0.00 41.28 4.85
173 174 6.049955 TCCTGTTGTATAAGAGGTTTCCTG 57.950 41.667 14.03 0.00 45.23 3.86
174 175 6.893020 ATCCTGTTGTATAAGAGGTTTCCT 57.107 37.500 14.03 0.00 45.23 3.36
175 176 9.628500 ATTTATCCTGTTGTATAAGAGGTTTCC 57.372 33.333 14.03 0.00 45.23 3.13
184 185 9.635404 CCCCTTTGTATTTATCCTGTTGTATAA 57.365 33.333 0.00 0.00 0.00 0.98
185 186 8.783903 ACCCCTTTGTATTTATCCTGTTGTATA 58.216 33.333 0.00 0.00 0.00 1.47
186 187 7.648770 ACCCCTTTGTATTTATCCTGTTGTAT 58.351 34.615 0.00 0.00 0.00 2.29
187 188 7.034967 ACCCCTTTGTATTTATCCTGTTGTA 57.965 36.000 0.00 0.00 0.00 2.41
188 189 5.899278 ACCCCTTTGTATTTATCCTGTTGT 58.101 37.500 0.00 0.00 0.00 3.32
189 190 6.887545 TGTACCCCTTTGTATTTATCCTGTTG 59.112 38.462 0.00 0.00 0.00 3.33
190 191 7.034967 TGTACCCCTTTGTATTTATCCTGTT 57.965 36.000 0.00 0.00 0.00 3.16
191 192 6.645884 TGTACCCCTTTGTATTTATCCTGT 57.354 37.500 0.00 0.00 0.00 4.00
192 193 7.228706 GTCATGTACCCCTTTGTATTTATCCTG 59.771 40.741 0.00 0.00 0.00 3.86
193 194 7.128883 AGTCATGTACCCCTTTGTATTTATCCT 59.871 37.037 0.00 0.00 0.00 3.24
194 195 7.287810 AGTCATGTACCCCTTTGTATTTATCC 58.712 38.462 0.00 0.00 0.00 2.59
195 196 8.747538 AAGTCATGTACCCCTTTGTATTTATC 57.252 34.615 0.00 0.00 0.00 1.75
329 333 4.753662 ACGCTCCAGGCCTCCGTA 62.754 66.667 0.00 0.00 37.74 4.02
354 358 9.944376 TGTCACTAGCTGAAACTTATTTAAGAT 57.056 29.630 0.00 0.00 37.08 2.40
390 447 3.701542 CAGAGTATGCCCTCAAGTACTCA 59.298 47.826 12.31 0.00 43.33 3.41
399 456 1.068250 GGCGTCAGAGTATGCCCTC 59.932 63.158 0.00 0.00 44.44 4.30
621 1489 4.870426 CAGACACTACCATACCATCACAAC 59.130 45.833 0.00 0.00 0.00 3.32
737 1605 7.392953 TCATCCATGTGTATGTGTGTGTATTTT 59.607 33.333 0.00 0.00 32.21 1.82
739 1607 6.413892 TCATCCATGTGTATGTGTGTGTATT 58.586 36.000 0.00 0.00 32.21 1.89
741 1609 5.413309 TCATCCATGTGTATGTGTGTGTA 57.587 39.130 0.00 0.00 32.21 2.90
751 1623 7.095397 CGTCAAAACTTACTTCATCCATGTGTA 60.095 37.037 0.00 0.00 0.00 2.90
765 1637 2.406024 TCGTCGCATCGTCAAAACTTAC 59.594 45.455 0.00 0.00 0.00 2.34
768 1640 0.782384 GTCGTCGCATCGTCAAAACT 59.218 50.000 0.00 0.00 0.00 2.66
802 1676 6.851609 TGAAATATGTTTGTATGTGAGCCAC 58.148 36.000 0.00 0.00 34.56 5.01
805 1679 9.177304 CATGATGAAATATGTTTGTATGTGAGC 57.823 33.333 0.00 0.00 0.00 4.26
806 1680 9.177304 GCATGATGAAATATGTTTGTATGTGAG 57.823 33.333 0.00 0.00 0.00 3.51
807 1681 8.684520 TGCATGATGAAATATGTTTGTATGTGA 58.315 29.630 0.00 0.00 0.00 3.58
809 1683 9.304731 GTTGCATGATGAAATATGTTTGTATGT 57.695 29.630 0.00 0.00 0.00 2.29
810 1684 9.524106 AGTTGCATGATGAAATATGTTTGTATG 57.476 29.630 0.00 0.00 0.00 2.39
831 1707 8.970691 ATATGACTTCATGTTTGTAAAGTTGC 57.029 30.769 1.77 0.00 37.15 4.17
865 1744 5.119694 GGGCACTTATTTTAGGACTGAGAG 58.880 45.833 0.00 0.00 0.00 3.20
869 1748 3.869065 TCGGGCACTTATTTTAGGACTG 58.131 45.455 0.00 0.00 0.00 3.51
870 1749 4.080526 ACATCGGGCACTTATTTTAGGACT 60.081 41.667 0.00 0.00 0.00 3.85
871 1750 4.035208 CACATCGGGCACTTATTTTAGGAC 59.965 45.833 0.00 0.00 0.00 3.85
875 1754 2.685897 GGCACATCGGGCACTTATTTTA 59.314 45.455 0.00 0.00 0.00 1.52
945 1824 3.007614 GGCTCCACACTTTCCTTACTACA 59.992 47.826 0.00 0.00 0.00 2.74
946 1825 3.261137 AGGCTCCACACTTTCCTTACTAC 59.739 47.826 0.00 0.00 0.00 2.73
947 1826 3.260884 CAGGCTCCACACTTTCCTTACTA 59.739 47.826 0.00 0.00 0.00 1.82
948 1827 2.039084 CAGGCTCCACACTTTCCTTACT 59.961 50.000 0.00 0.00 0.00 2.24
966 1845 2.094675 ACGCTTTCCAATTCCATCAGG 58.905 47.619 0.00 0.00 0.00 3.86
974 1853 1.156736 CTGTCGGACGCTTTCCAATT 58.843 50.000 3.34 0.00 46.29 2.32
978 1857 1.298859 ATTGCTGTCGGACGCTTTCC 61.299 55.000 19.88 0.00 41.75 3.13
983 1862 0.301687 CATACATTGCTGTCGGACGC 59.698 55.000 14.91 14.91 36.79 5.19
985 1864 2.351726 GGTTCATACATTGCTGTCGGAC 59.648 50.000 0.00 0.00 36.79 4.79
1099 3308 8.062065 TCAAAATTCACCTTGTTTCTACACTT 57.938 30.769 0.00 0.00 32.98 3.16
1107 3316 5.948742 TTCCCTCAAAATTCACCTTGTTT 57.051 34.783 0.00 0.00 0.00 2.83
1139 3348 4.327087 CCTGAAAAACAACTGAGTTGCAAC 59.673 41.667 24.08 22.17 46.20 4.17
1149 3358 3.131046 CAGAACCAGCCTGAAAAACAACT 59.869 43.478 0.00 0.00 33.65 3.16
1186 3395 1.136224 GCGCTGTGCAAAGAACTCTAC 60.136 52.381 8.49 0.00 45.45 2.59
1217 3426 1.480545 ACCCTTGCACTGTTTTTGGAC 59.519 47.619 0.00 0.00 0.00 4.02
1226 3435 2.270986 GGCTTCCACCCTTGCACTG 61.271 63.158 0.00 0.00 0.00 3.66
1227 3436 2.116125 GGCTTCCACCCTTGCACT 59.884 61.111 0.00 0.00 0.00 4.40
1254 3463 8.660373 CCATCAGCGTTAATCTTTAGAATATCC 58.340 37.037 0.00 0.00 0.00 2.59
1347 3576 2.283388 CCAGCACCTGCACCCATT 60.283 61.111 0.00 0.00 45.16 3.16
1365 3594 2.521958 CTTGGGCGTACTCCACCCTG 62.522 65.000 3.91 0.00 44.56 4.45
1422 3912 2.636830 CACTCCTGGGCATAGTTCAAG 58.363 52.381 0.00 0.00 0.00 3.02
1451 3941 3.427573 TCCGTCTCTACCAAGATGTTGA 58.572 45.455 3.74 0.00 35.46 3.18
1481 3971 5.648092 GTGTTAGTGATAGCTTGGACCAAAT 59.352 40.000 8.59 0.00 0.00 2.32
1488 3978 4.744570 TCTTCGTGTTAGTGATAGCTTGG 58.255 43.478 0.00 0.00 0.00 3.61
1501 3991 4.660105 GCTAGATCGTAGTTCTTCGTGTT 58.340 43.478 0.00 0.00 0.00 3.32
1504 3994 2.286301 GCGCTAGATCGTAGTTCTTCGT 60.286 50.000 0.00 0.00 0.00 3.85
1551 4041 1.901159 TGCAACATAGCAAGGGCAATT 59.099 42.857 0.00 0.00 42.46 2.32
1553 4043 3.048563 TGCAACATAGCAAGGGCAA 57.951 47.368 0.00 0.00 42.46 4.52
1575 4079 8.144478 GGGCAAAAAGAGATAGAAAAAGAACTT 58.856 33.333 0.00 0.00 0.00 2.66
1607 4770 5.532406 AGAGCATCCGCAACATTATTACAAT 59.468 36.000 0.00 0.00 42.27 2.71
1644 4807 2.283298 GACACATGCACCATCTTCGAT 58.717 47.619 0.00 0.00 0.00 3.59
1694 4857 3.561725 GGCAATCAAGTCTCGGATAAAGG 59.438 47.826 0.00 0.00 0.00 3.11
1718 4881 1.736645 CCACGCCGAACAAGATCGT 60.737 57.895 0.00 0.00 41.16 3.73
1723 4886 2.224549 TCAATTAACCACGCCGAACAAG 59.775 45.455 0.00 0.00 0.00 3.16
1729 4892 3.479505 TCATTTCAATTAACCACGCCG 57.520 42.857 0.00 0.00 0.00 6.46
1759 4925 5.514500 TGAGATAGCTTACCAGGGTTTTT 57.486 39.130 0.00 0.00 0.00 1.94
1761 4927 5.514500 TTTGAGATAGCTTACCAGGGTTT 57.486 39.130 0.00 0.00 0.00 3.27
1762 4928 5.514500 TTTTGAGATAGCTTACCAGGGTT 57.486 39.130 0.00 0.00 0.00 4.11
1782 4948 6.370442 GTGCTTGACTAAGGGTTTTTGTTTTT 59.630 34.615 0.00 0.00 34.40 1.94
1783 4949 5.872617 GTGCTTGACTAAGGGTTTTTGTTTT 59.127 36.000 0.00 0.00 34.40 2.43
1784 4950 5.416083 GTGCTTGACTAAGGGTTTTTGTTT 58.584 37.500 0.00 0.00 34.40 2.83
1785 4951 4.142026 GGTGCTTGACTAAGGGTTTTTGTT 60.142 41.667 0.00 0.00 34.40 2.83
1786 4952 3.383505 GGTGCTTGACTAAGGGTTTTTGT 59.616 43.478 0.00 0.00 34.40 2.83
1787 4953 3.636764 AGGTGCTTGACTAAGGGTTTTTG 59.363 43.478 0.00 0.00 34.40 2.44
1788 4954 3.636764 CAGGTGCTTGACTAAGGGTTTTT 59.363 43.478 0.00 0.00 34.40 1.94
1790 4956 2.489073 CCAGGTGCTTGACTAAGGGTTT 60.489 50.000 0.00 0.00 34.40 3.27
1791 4957 1.073923 CCAGGTGCTTGACTAAGGGTT 59.926 52.381 0.00 0.00 34.40 4.11
1793 4959 0.693049 ACCAGGTGCTTGACTAAGGG 59.307 55.000 0.00 0.00 34.40 3.95
1794 4960 1.339151 GGACCAGGTGCTTGACTAAGG 60.339 57.143 3.25 0.00 34.40 2.69
1795 4961 1.625818 AGGACCAGGTGCTTGACTAAG 59.374 52.381 8.06 0.00 36.97 2.18
1796 4962 1.729586 AGGACCAGGTGCTTGACTAA 58.270 50.000 8.06 0.00 27.37 2.24
1797 4963 2.615986 TAGGACCAGGTGCTTGACTA 57.384 50.000 20.29 0.00 35.47 2.59
1798 4964 1.834263 GATAGGACCAGGTGCTTGACT 59.166 52.381 20.29 1.91 35.47 3.41
1799 4965 1.471676 CGATAGGACCAGGTGCTTGAC 60.472 57.143 20.29 9.92 35.47 3.18
1800 4966 0.824109 CGATAGGACCAGGTGCTTGA 59.176 55.000 20.29 1.90 35.47 3.02
1803 4969 0.324368 TCACGATAGGACCAGGTGCT 60.324 55.000 18.99 18.99 43.77 4.40
1804 4970 0.535335 TTCACGATAGGACCAGGTGC 59.465 55.000 1.97 1.97 43.77 5.01
1805 4971 3.328382 TTTTCACGATAGGACCAGGTG 57.672 47.619 0.00 0.00 43.77 4.00
2363 5591 3.326006 ACAATCACACATGACTCCAGAGT 59.674 43.478 0.00 0.00 45.84 3.24
2364 5592 3.683340 CACAATCACACATGACTCCAGAG 59.317 47.826 0.00 0.00 37.79 3.35
2365 5593 3.667360 CACAATCACACATGACTCCAGA 58.333 45.455 0.00 0.00 37.79 3.86
2366 5594 2.161012 GCACAATCACACATGACTCCAG 59.839 50.000 0.00 0.00 37.79 3.86
2367 5595 2.153645 GCACAATCACACATGACTCCA 58.846 47.619 0.00 0.00 37.79 3.86
2368 5596 1.129251 CGCACAATCACACATGACTCC 59.871 52.381 0.00 0.00 37.79 3.85
2568 5913 2.835764 AGTTGATTGCTGGATGCCATTT 59.164 40.909 0.00 0.00 42.00 2.32
2569 5914 2.463752 AGTTGATTGCTGGATGCCATT 58.536 42.857 0.00 0.00 42.00 3.16
2570 5915 2.154567 AGTTGATTGCTGGATGCCAT 57.845 45.000 0.00 0.00 42.00 4.40
2616 5961 9.512588 AGAAGACTGAACATTCAATTTATGAGT 57.487 29.630 4.70 0.00 39.77 3.41
2638 5983 6.149973 TGAATTTGACCTGCAGATACAAGAAG 59.850 38.462 17.39 0.00 0.00 2.85
2648 5993 5.319140 TCAATCATGAATTTGACCTGCAG 57.681 39.130 6.78 6.78 30.99 4.41
2691 6036 5.424757 TGGTGTATCTTACGATTTTCCCTG 58.575 41.667 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.