Multiple sequence alignment - TraesCS2D01G421500

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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 TraesCS2D01G421500 chr2D 100.000 3458 0 0 1 3458 535095637 535099094 0.000000e+00 6386.0
1 TraesCS2D01G421500 chr2D 100.000 48 0 0 2731 2778 535098321 535098368 4.750000e-14 89.8
2 TraesCS2D01G421500 chr2D 100.000 48 0 0 2685 2732 535098367 535098414 4.750000e-14 89.8
3 TraesCS2D01G421500 chr2A 97.125 1287 32 5 1451 2732 678361220 678362506 0.000000e+00 2167.0
4 TraesCS2D01G421500 chr2A 89.013 1256 64 25 192 1444 678359987 678361171 0.000000e+00 1487.0
5 TraesCS2D01G421500 chr2A 90.909 385 13 5 2731 3093 678362459 678362843 6.660000e-137 497.0
6 TraesCS2D01G421500 chr2A 88.150 346 27 7 3114 3458 678363174 678363506 1.930000e-107 399.0
7 TraesCS2D01G421500 chr2B 95.257 1286 36 11 1451 2732 636462049 636463313 0.000000e+00 2013.0
8 TraesCS2D01G421500 chr2B 92.741 799 41 10 654 1446 636461215 636462002 0.000000e+00 1138.0
9 TraesCS2D01G421500 chr2B 96.186 472 13 4 2731 3199 636463267 636463736 0.000000e+00 767.0
10 TraesCS2D01G421500 chr2B 92.830 265 18 1 3194 3458 636467188 636467451 1.950000e-102 383.0
11 TraesCS2D01G421500 chr2B 100.000 28 0 0 3273 3300 231633284 231633257 6.000000e-03 52.8
12 TraesCS2D01G421500 chr3B 93.023 43 3 0 988 1030 642217911 642217869 2.880000e-06 63.9
13 TraesCS2D01G421500 chr6B 96.875 32 0 1 3269 3300 585997474 585997504 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G421500 chr2D 535095637 535099094 3457 False 2188.533333 6386 100.00000 1 3458 3 chr2D.!!$F1 3457
1 TraesCS2D01G421500 chr2A 678359987 678363506 3519 False 1137.500000 2167 91.29925 192 3458 4 chr2A.!!$F1 3266
2 TraesCS2D01G421500 chr2B 636461215 636467451 6236 False 1075.250000 2013 94.25350 654 3458 4 chr2B.!!$F1 2804

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
821 822 0.038744 CTCCCATCCCACACAAGCTT 59.961 55.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2753 2806 2.039879 GGAGCAGAGTTTTCCTAACCCA 59.96 50.0 0.0 0.0 0.0 4.51 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
31 32 8.961294 AATCCATGTTTCTTTTGAATCAAACA 57.039 26.923 8.06 3.95 41.64 2.83
32 33 8.961294 ATCCATGTTTCTTTTGAATCAAACAA 57.039 26.923 8.06 1.81 40.97 2.83
33 34 8.783833 TCCATGTTTCTTTTGAATCAAACAAA 57.216 26.923 8.06 7.75 40.97 2.83
34 35 9.393512 TCCATGTTTCTTTTGAATCAAACAAAT 57.606 25.926 8.06 0.00 40.97 2.32
35 36 9.440784 CCATGTTTCTTTTGAATCAAACAAATG 57.559 29.630 8.06 6.86 40.97 2.32
45 46 9.474920 TTTGAATCAAACAAATGAATAGTGTCC 57.525 29.630 4.03 0.00 33.25 4.02
46 47 8.175925 TGAATCAAACAAATGAATAGTGTCCA 57.824 30.769 0.00 0.00 32.06 4.02
47 48 8.081633 TGAATCAAACAAATGAATAGTGTCCAC 58.918 33.333 0.00 0.00 32.06 4.02
48 49 6.951062 TCAAACAAATGAATAGTGTCCACA 57.049 33.333 0.00 0.00 0.00 4.17
49 50 6.969366 TCAAACAAATGAATAGTGTCCACAG 58.031 36.000 0.00 0.00 0.00 3.66
50 51 6.770303 TCAAACAAATGAATAGTGTCCACAGA 59.230 34.615 0.00 0.00 0.00 3.41
51 52 6.808008 AACAAATGAATAGTGTCCACAGAG 57.192 37.500 0.00 0.00 0.00 3.35
52 53 6.114187 ACAAATGAATAGTGTCCACAGAGA 57.886 37.500 0.00 0.00 0.00 3.10
53 54 6.533730 ACAAATGAATAGTGTCCACAGAGAA 58.466 36.000 0.00 0.00 0.00 2.87
54 55 6.998074 ACAAATGAATAGTGTCCACAGAGAAA 59.002 34.615 0.00 0.00 0.00 2.52
55 56 7.502226 ACAAATGAATAGTGTCCACAGAGAAAA 59.498 33.333 0.00 0.00 0.00 2.29
56 57 7.678947 AATGAATAGTGTCCACAGAGAAAAG 57.321 36.000 0.00 0.00 0.00 2.27
57 58 6.419484 TGAATAGTGTCCACAGAGAAAAGA 57.581 37.500 0.00 0.00 0.00 2.52
58 59 6.459066 TGAATAGTGTCCACAGAGAAAAGAG 58.541 40.000 0.00 0.00 0.00 2.85
59 60 3.118905 AGTGTCCACAGAGAAAAGAGC 57.881 47.619 0.00 0.00 0.00 4.09
60 61 2.147150 GTGTCCACAGAGAAAAGAGCC 58.853 52.381 0.00 0.00 0.00 4.70
61 62 1.768275 TGTCCACAGAGAAAAGAGCCA 59.232 47.619 0.00 0.00 0.00 4.75
62 63 2.147150 GTCCACAGAGAAAAGAGCCAC 58.853 52.381 0.00 0.00 0.00 5.01
63 64 2.050144 TCCACAGAGAAAAGAGCCACT 58.950 47.619 0.00 0.00 0.00 4.00
64 65 3.006967 GTCCACAGAGAAAAGAGCCACTA 59.993 47.826 0.00 0.00 0.00 2.74
65 66 3.259374 TCCACAGAGAAAAGAGCCACTAG 59.741 47.826 0.00 0.00 0.00 2.57
66 67 3.259374 CCACAGAGAAAAGAGCCACTAGA 59.741 47.826 0.00 0.00 0.00 2.43
67 68 4.081198 CCACAGAGAAAAGAGCCACTAGAT 60.081 45.833 0.00 0.00 0.00 1.98
68 69 4.869297 CACAGAGAAAAGAGCCACTAGATG 59.131 45.833 0.00 0.00 0.00 2.90
83 84 7.361457 CCACTAGATGGTAGGATTCTAAACA 57.639 40.000 0.00 0.00 44.46 2.83
84 85 7.437748 CCACTAGATGGTAGGATTCTAAACAG 58.562 42.308 0.00 0.00 44.46 3.16
85 86 7.287927 CCACTAGATGGTAGGATTCTAAACAGA 59.712 40.741 0.00 0.00 44.46 3.41
86 87 8.696374 CACTAGATGGTAGGATTCTAAACAGAA 58.304 37.037 0.00 0.00 0.00 3.02
87 88 9.268282 ACTAGATGGTAGGATTCTAAACAGAAA 57.732 33.333 0.00 0.00 0.00 2.52
90 91 8.214364 AGATGGTAGGATTCTAAACAGAAATCC 58.786 37.037 5.42 5.42 0.00 3.01
91 92 7.510675 TGGTAGGATTCTAAACAGAAATCCT 57.489 36.000 17.32 17.32 38.33 3.24
92 93 7.928873 TGGTAGGATTCTAAACAGAAATCCTT 58.071 34.615 18.13 6.06 37.22 3.36
93 94 8.390921 TGGTAGGATTCTAAACAGAAATCCTTT 58.609 33.333 18.13 1.86 37.22 3.11
94 95 8.678199 GGTAGGATTCTAAACAGAAATCCTTTG 58.322 37.037 18.13 0.00 37.22 2.77
95 96 7.709149 AGGATTCTAAACAGAAATCCTTTGG 57.291 36.000 9.51 0.00 34.89 3.28
96 97 7.241628 AGGATTCTAAACAGAAATCCTTTGGT 58.758 34.615 9.51 0.00 34.89 3.67
97 98 7.177392 AGGATTCTAAACAGAAATCCTTTGGTG 59.823 37.037 9.51 0.00 34.89 4.17
98 99 5.705609 TCTAAACAGAAATCCTTTGGTGC 57.294 39.130 0.00 0.00 0.00 5.01
99 100 3.751479 AAACAGAAATCCTTTGGTGCC 57.249 42.857 0.00 0.00 0.00 5.01
100 101 2.380064 ACAGAAATCCTTTGGTGCCA 57.620 45.000 0.00 0.00 0.00 4.92
101 102 2.893424 ACAGAAATCCTTTGGTGCCAT 58.107 42.857 0.00 0.00 0.00 4.40
102 103 3.242011 ACAGAAATCCTTTGGTGCCATT 58.758 40.909 0.00 0.00 0.00 3.16
103 104 3.647590 ACAGAAATCCTTTGGTGCCATTT 59.352 39.130 0.00 0.00 0.00 2.32
104 105 3.998341 CAGAAATCCTTTGGTGCCATTTG 59.002 43.478 0.00 0.00 0.00 2.32
105 106 3.008266 AGAAATCCTTTGGTGCCATTTGG 59.992 43.478 0.00 0.00 38.53 3.28
106 107 2.028561 ATCCTTTGGTGCCATTTGGT 57.971 45.000 0.00 0.00 37.57 3.67
107 108 1.047002 TCCTTTGGTGCCATTTGGTG 58.953 50.000 0.00 0.00 37.57 4.17
108 109 0.603439 CCTTTGGTGCCATTTGGTGC 60.603 55.000 0.00 0.00 37.57 5.01
109 110 0.106335 CTTTGGTGCCATTTGGTGCA 59.894 50.000 0.00 0.00 37.57 4.57
110 111 0.543277 TTTGGTGCCATTTGGTGCAA 59.457 45.000 0.00 0.00 39.57 4.08
111 112 0.543277 TTGGTGCCATTTGGTGCAAA 59.457 45.000 0.00 0.00 39.57 3.68
112 113 0.106335 TGGTGCCATTTGGTGCAAAG 59.894 50.000 0.00 0.00 39.57 2.77
113 114 0.603439 GGTGCCATTTGGTGCAAAGG 60.603 55.000 0.00 0.00 39.57 3.11
114 115 0.392336 GTGCCATTTGGTGCAAAGGA 59.608 50.000 0.00 0.00 37.32 3.36
115 116 1.126488 TGCCATTTGGTGCAAAGGAA 58.874 45.000 0.00 0.00 37.32 3.36
116 117 1.698532 TGCCATTTGGTGCAAAGGAAT 59.301 42.857 0.00 0.00 37.32 3.01
117 118 2.289569 TGCCATTTGGTGCAAAGGAATC 60.290 45.455 0.00 0.00 37.32 2.52
118 119 2.609350 CCATTTGGTGCAAAGGAATCG 58.391 47.619 0.00 0.00 37.32 3.34
119 120 2.230992 CCATTTGGTGCAAAGGAATCGA 59.769 45.455 0.00 0.00 37.32 3.59
120 121 3.119029 CCATTTGGTGCAAAGGAATCGAT 60.119 43.478 0.00 0.00 37.32 3.59
121 122 3.574284 TTTGGTGCAAAGGAATCGATG 57.426 42.857 0.00 0.00 0.00 3.84
122 123 2.198827 TGGTGCAAAGGAATCGATGT 57.801 45.000 0.00 0.00 0.00 3.06
123 124 2.513753 TGGTGCAAAGGAATCGATGTT 58.486 42.857 0.00 0.00 0.00 2.71
124 125 2.487762 TGGTGCAAAGGAATCGATGTTC 59.512 45.455 0.00 0.00 0.00 3.18
125 126 2.749621 GGTGCAAAGGAATCGATGTTCT 59.250 45.455 0.00 0.00 0.00 3.01
126 127 3.938963 GGTGCAAAGGAATCGATGTTCTA 59.061 43.478 0.00 0.00 0.00 2.10
127 128 4.201822 GGTGCAAAGGAATCGATGTTCTAC 60.202 45.833 0.00 0.00 0.00 2.59
128 129 4.391830 GTGCAAAGGAATCGATGTTCTACA 59.608 41.667 0.00 0.00 0.00 2.74
129 130 5.065218 GTGCAAAGGAATCGATGTTCTACAT 59.935 40.000 0.00 0.00 42.43 2.29
130 131 5.647658 TGCAAAGGAATCGATGTTCTACATT 59.352 36.000 0.00 0.00 39.27 2.71
131 132 6.150976 TGCAAAGGAATCGATGTTCTACATTT 59.849 34.615 0.00 0.00 39.27 2.32
132 133 6.470235 GCAAAGGAATCGATGTTCTACATTTG 59.530 38.462 0.00 8.30 39.27 2.32
133 134 5.741388 AGGAATCGATGTTCTACATTTGC 57.259 39.130 0.00 0.00 39.27 3.68
134 135 5.431765 AGGAATCGATGTTCTACATTTGCT 58.568 37.500 0.00 0.00 39.27 3.91
135 136 5.882557 AGGAATCGATGTTCTACATTTGCTT 59.117 36.000 0.00 0.00 39.27 3.91
136 137 7.047891 AGGAATCGATGTTCTACATTTGCTTA 58.952 34.615 0.00 0.00 39.27 3.09
137 138 7.716998 AGGAATCGATGTTCTACATTTGCTTAT 59.283 33.333 0.00 0.00 39.27 1.73
138 139 8.988934 GGAATCGATGTTCTACATTTGCTTATA 58.011 33.333 0.00 0.00 39.27 0.98
152 153 9.432982 ACATTTGCTTATAATATTCCCAAGGAA 57.567 29.630 0.00 0.00 46.39 3.36
153 154 9.696917 CATTTGCTTATAATATTCCCAAGGAAC 57.303 33.333 0.00 0.00 45.07 3.62
154 155 7.504924 TTGCTTATAATATTCCCAAGGAACG 57.495 36.000 0.00 0.00 45.07 3.95
155 156 6.833041 TGCTTATAATATTCCCAAGGAACGA 58.167 36.000 0.00 0.00 45.07 3.85
156 157 6.934645 TGCTTATAATATTCCCAAGGAACGAG 59.065 38.462 0.00 0.00 45.07 4.18
157 158 6.128254 GCTTATAATATTCCCAAGGAACGAGC 60.128 42.308 0.00 0.00 45.07 5.03
158 159 3.644966 AATATTCCCAAGGAACGAGCA 57.355 42.857 0.00 0.00 45.07 4.26
159 160 3.864789 ATATTCCCAAGGAACGAGCAT 57.135 42.857 0.00 0.00 45.07 3.79
160 161 2.514458 ATTCCCAAGGAACGAGCATT 57.486 45.000 0.00 0.00 45.07 3.56
161 162 3.644966 ATTCCCAAGGAACGAGCATTA 57.355 42.857 0.00 0.00 45.07 1.90
162 163 2.396590 TCCCAAGGAACGAGCATTAC 57.603 50.000 0.00 0.00 0.00 1.89
163 164 1.626321 TCCCAAGGAACGAGCATTACA 59.374 47.619 0.00 0.00 0.00 2.41
164 165 2.238646 TCCCAAGGAACGAGCATTACAT 59.761 45.455 0.00 0.00 0.00 2.29
165 166 3.452990 TCCCAAGGAACGAGCATTACATA 59.547 43.478 0.00 0.00 0.00 2.29
166 167 4.102524 TCCCAAGGAACGAGCATTACATAT 59.897 41.667 0.00 0.00 0.00 1.78
167 168 4.214119 CCCAAGGAACGAGCATTACATATG 59.786 45.833 0.00 0.00 0.00 1.78
168 169 5.056480 CCAAGGAACGAGCATTACATATGA 58.944 41.667 10.38 0.00 0.00 2.15
169 170 5.527214 CCAAGGAACGAGCATTACATATGAA 59.473 40.000 10.38 0.00 0.00 2.57
170 171 6.205464 CCAAGGAACGAGCATTACATATGAAT 59.795 38.462 10.38 2.33 0.00 2.57
171 172 7.255242 CCAAGGAACGAGCATTACATATGAATT 60.255 37.037 10.38 0.00 0.00 2.17
172 173 7.807977 AGGAACGAGCATTACATATGAATTT 57.192 32.000 10.38 0.00 0.00 1.82
173 174 8.225603 AGGAACGAGCATTACATATGAATTTT 57.774 30.769 10.38 0.00 0.00 1.82
174 175 8.131100 AGGAACGAGCATTACATATGAATTTTG 58.869 33.333 10.38 1.13 0.00 2.44
175 176 7.379529 GGAACGAGCATTACATATGAATTTTGG 59.620 37.037 10.38 0.94 0.00 3.28
176 177 7.566760 ACGAGCATTACATATGAATTTTGGA 57.433 32.000 10.38 0.00 0.00 3.53
177 178 7.642669 ACGAGCATTACATATGAATTTTGGAG 58.357 34.615 10.38 0.00 0.00 3.86
178 179 7.498900 ACGAGCATTACATATGAATTTTGGAGA 59.501 33.333 10.38 0.00 0.00 3.71
179 180 8.344831 CGAGCATTACATATGAATTTTGGAGAA 58.655 33.333 10.38 0.00 0.00 2.87
217 218 7.708998 GGTTCTACCTAACATTCAAACAAACA 58.291 34.615 0.00 0.00 34.73 2.83
218 219 8.192110 GGTTCTACCTAACATTCAAACAAACAA 58.808 33.333 0.00 0.00 34.73 2.83
312 313 9.962809 AAGCTAATACGACCTCTCTAACTATAT 57.037 33.333 0.00 0.00 0.00 0.86
314 315 9.165035 GCTAATACGACCTCTCTAACTATATGT 57.835 37.037 0.00 0.00 0.00 2.29
332 333 3.878086 TGTCATCAAAACTTCGAGCAC 57.122 42.857 0.00 0.00 0.00 4.40
353 354 6.030849 GCACGCACACAACCAAATTATTATA 58.969 36.000 0.00 0.00 0.00 0.98
354 355 6.528423 GCACGCACACAACCAAATTATTATAA 59.472 34.615 0.00 0.00 0.00 0.98
357 358 9.134734 ACGCACACAACCAAATTATTATAAAAG 57.865 29.630 0.00 0.00 0.00 2.27
371 372 5.789710 TTATAAAAGAAACTCCCGAAGCG 57.210 39.130 0.00 0.00 0.00 4.68
372 373 2.249844 AAAAGAAACTCCCGAAGCGA 57.750 45.000 0.00 0.00 0.00 4.93
373 374 2.474410 AAAGAAACTCCCGAAGCGAT 57.526 45.000 0.00 0.00 0.00 4.58
374 375 2.011540 AAGAAACTCCCGAAGCGATC 57.988 50.000 0.00 0.00 0.00 3.69
375 376 0.895530 AGAAACTCCCGAAGCGATCA 59.104 50.000 0.00 0.00 0.00 2.92
376 377 1.275291 AGAAACTCCCGAAGCGATCAA 59.725 47.619 0.00 0.00 0.00 2.57
377 378 1.393883 GAAACTCCCGAAGCGATCAAC 59.606 52.381 0.00 0.00 0.00 3.18
405 406 0.538118 ATGGCATGCAACAATGACCC 59.462 50.000 21.36 0.00 34.38 4.46
406 407 1.218854 GGCATGCAACAATGACCCC 59.781 57.895 21.36 0.00 28.36 4.95
415 416 2.285368 AATGACCCCTGGCTCCGA 60.285 61.111 0.00 0.00 0.00 4.55
436 437 4.284123 TCGCAATCGAAAGCAGCT 57.716 50.000 12.14 0.00 42.44 4.24
443 444 0.933097 ATCGAAAGCAGCTGCATACG 59.067 50.000 38.24 33.62 45.16 3.06
451 452 0.859882 CAGCTGCATACGCTCATGAG 59.140 55.000 18.84 18.84 39.64 2.90
497 498 3.389687 GTGAGTAATGTCACGCCAATG 57.610 47.619 0.00 0.00 37.69 2.82
503 504 4.574828 AGTAATGTCACGCCAATGATAACC 59.425 41.667 0.00 0.00 0.00 2.85
504 505 2.481289 TGTCACGCCAATGATAACCA 57.519 45.000 0.00 0.00 0.00 3.67
505 506 2.997980 TGTCACGCCAATGATAACCAT 58.002 42.857 0.00 0.00 36.99 3.55
506 507 2.682352 TGTCACGCCAATGATAACCATG 59.318 45.455 0.00 0.00 35.24 3.66
507 508 1.675483 TCACGCCAATGATAACCATGC 59.325 47.619 0.00 0.00 35.24 4.06
508 509 1.677576 CACGCCAATGATAACCATGCT 59.322 47.619 0.00 0.00 35.24 3.79
509 510 2.099592 CACGCCAATGATAACCATGCTT 59.900 45.455 0.00 0.00 35.24 3.91
510 511 2.099592 ACGCCAATGATAACCATGCTTG 59.900 45.455 0.00 0.00 35.24 4.01
523 524 3.186909 CCATGCTTGCATGACATTTCAG 58.813 45.455 30.12 11.96 34.35 3.02
550 551 2.093972 TTTTTAGAACACACACGCGC 57.906 45.000 5.73 0.00 0.00 6.86
551 552 0.042880 TTTTAGAACACACACGCGCG 60.043 50.000 30.96 30.96 0.00 6.86
564 565 1.725625 CGCGCGCACATTTCAGTTT 60.726 52.632 32.61 0.00 0.00 2.66
577 578 5.997746 ACATTTCAGTTTAGTTCTAGCAGCA 59.002 36.000 0.00 0.00 0.00 4.41
584 585 6.423905 CAGTTTAGTTCTAGCAGCAACAAGTA 59.576 38.462 0.00 0.00 0.00 2.24
585 586 7.118390 CAGTTTAGTTCTAGCAGCAACAAGTAT 59.882 37.037 0.00 0.00 0.00 2.12
706 707 4.629523 TTCGGGTCCAACGCCACC 62.630 66.667 0.00 0.00 0.00 4.61
791 792 1.317611 CGCATTCAGTGTAACGTCTCG 59.682 52.381 0.00 0.00 45.86 4.04
817 818 1.203300 TCTCTCTCCCATCCCACACAA 60.203 52.381 0.00 0.00 0.00 3.33
821 822 0.038744 CTCCCATCCCACACAAGCTT 59.961 55.000 0.00 0.00 0.00 3.74
867 868 2.669569 GCCCTGCTTTCTCGCACA 60.670 61.111 0.00 0.00 35.74 4.57
958 959 1.604755 GTAGACATCGAGATCAGCCGT 59.395 52.381 0.00 0.00 0.00 5.68
1066 1067 3.322466 CGCCCACTCCTCCCAAGT 61.322 66.667 0.00 0.00 0.00 3.16
1217 1218 3.827898 GTCCGCGGAGACCAGGAG 61.828 72.222 31.97 0.00 32.19 3.69
1377 1381 0.038890 GAGCAGGCCTTCCCTTTTCT 59.961 55.000 0.00 0.00 43.06 2.52
1430 1435 9.109393 TCTTTCTTTCGAGAATATTAATGGTGG 57.891 33.333 0.00 0.00 0.00 4.61
1439 1444 7.095695 AGAATATTAATGGTGGGTTTTGTCG 57.904 36.000 0.00 0.00 0.00 4.35
1446 1451 0.519961 GTGGGTTTTGTCGGATTCGG 59.480 55.000 0.00 0.00 36.95 4.30
1449 1454 2.224475 TGGGTTTTGTCGGATTCGGTAA 60.224 45.455 0.00 0.00 36.95 2.85
1631 1679 6.318648 GTGATAGGCATTTGTTCTGTTATCCA 59.681 38.462 0.00 0.00 0.00 3.41
1706 1755 7.177216 TGAATCAATTGATGAACTGGCTTAACT 59.823 33.333 21.39 0.52 42.54 2.24
1721 1770 9.833917 ACTGGCTTAACTAATTTATAAGAGGTC 57.166 33.333 8.11 0.00 0.00 3.85
1730 1779 4.919774 TTTATAAGAGGTCAAGGCCACA 57.080 40.909 5.01 0.00 0.00 4.17
1744 1795 3.639099 CCACAAGAGGCAGTGACAT 57.361 52.632 0.00 0.00 37.97 3.06
1834 1885 3.181465 CCGAGTATGGTTCTGGTTATGCT 60.181 47.826 0.00 0.00 0.00 3.79
1891 1942 6.086222 TCATTTCTTGCAAACTTCTATTCGC 58.914 36.000 0.00 0.00 0.00 4.70
2322 2373 3.411517 CCACCGAGCCCCAATCCT 61.412 66.667 0.00 0.00 0.00 3.24
2415 2466 1.112113 TAGAGCGGGAAGGTGACATC 58.888 55.000 0.00 0.00 0.00 3.06
2728 2781 2.039879 TGGGTTAGGAAAACTCTGCTCC 59.960 50.000 0.00 0.00 0.00 4.70
2729 2782 2.618302 GGGTTAGGAAAACTCTGCTCCC 60.618 54.545 0.00 0.00 0.00 4.30
2730 2783 2.306219 GGTTAGGAAAACTCTGCTCCCT 59.694 50.000 0.00 0.00 0.00 4.20
2731 2784 3.518303 GGTTAGGAAAACTCTGCTCCCTA 59.482 47.826 0.00 0.00 0.00 3.53
2732 2785 4.505808 GTTAGGAAAACTCTGCTCCCTAC 58.494 47.826 0.00 0.00 0.00 3.18
2733 2786 2.621070 AGGAAAACTCTGCTCCCTACA 58.379 47.619 0.00 0.00 0.00 2.74
2734 2787 2.979678 AGGAAAACTCTGCTCCCTACAA 59.020 45.455 0.00 0.00 0.00 2.41
2735 2788 3.394606 AGGAAAACTCTGCTCCCTACAAA 59.605 43.478 0.00 0.00 0.00 2.83
2736 2789 4.141251 AGGAAAACTCTGCTCCCTACAAAA 60.141 41.667 0.00 0.00 0.00 2.44
2737 2790 4.216472 GGAAAACTCTGCTCCCTACAAAAG 59.784 45.833 0.00 0.00 0.00 2.27
2738 2791 4.439253 AAACTCTGCTCCCTACAAAAGT 57.561 40.909 0.00 0.00 0.00 2.66
2739 2792 4.439253 AACTCTGCTCCCTACAAAAGTT 57.561 40.909 0.00 0.00 0.00 2.66
2740 2793 3.744660 ACTCTGCTCCCTACAAAAGTTG 58.255 45.455 0.00 0.00 0.00 3.16
2742 2795 4.347000 ACTCTGCTCCCTACAAAAGTTGTA 59.653 41.667 1.22 1.22 43.27 2.41
2756 2809 7.661040 ACAAAAGTTGTAGATTTTCTCATGGG 58.339 34.615 0.00 0.00 43.27 4.00
2757 2810 7.287696 ACAAAAGTTGTAGATTTTCTCATGGGT 59.712 33.333 0.00 0.00 43.27 4.51
2758 2811 7.839680 AAAGTTGTAGATTTTCTCATGGGTT 57.160 32.000 0.00 0.00 0.00 4.11
2759 2812 8.934023 AAAGTTGTAGATTTTCTCATGGGTTA 57.066 30.769 0.00 0.00 0.00 2.85
2760 2813 8.567285 AAGTTGTAGATTTTCTCATGGGTTAG 57.433 34.615 0.00 0.00 0.00 2.34
2761 2814 7.112779 AGTTGTAGATTTTCTCATGGGTTAGG 58.887 38.462 0.00 0.00 0.00 2.69
2762 2815 6.884472 TGTAGATTTTCTCATGGGTTAGGA 57.116 37.500 0.00 0.00 0.00 2.94
2763 2816 7.265599 TGTAGATTTTCTCATGGGTTAGGAA 57.734 36.000 0.00 0.00 0.00 3.36
2764 2817 7.695055 TGTAGATTTTCTCATGGGTTAGGAAA 58.305 34.615 0.00 0.00 0.00 3.13
2765 2818 8.167392 TGTAGATTTTCTCATGGGTTAGGAAAA 58.833 33.333 0.00 0.00 39.23 2.29
2766 2819 7.468141 AGATTTTCTCATGGGTTAGGAAAAC 57.532 36.000 0.00 0.00 38.25 2.43
2767 2820 7.241628 AGATTTTCTCATGGGTTAGGAAAACT 58.758 34.615 0.00 0.00 38.25 2.66
2768 2821 6.894339 TTTTCTCATGGGTTAGGAAAACTC 57.106 37.500 0.00 0.00 33.04 3.01
2769 2822 5.843019 TTCTCATGGGTTAGGAAAACTCT 57.157 39.130 0.00 0.00 0.00 3.24
2770 2823 5.165961 TCTCATGGGTTAGGAAAACTCTG 57.834 43.478 0.00 0.00 0.00 3.35
2771 2824 3.686016 TCATGGGTTAGGAAAACTCTGC 58.314 45.455 0.00 0.00 0.00 4.26
2772 2825 3.330701 TCATGGGTTAGGAAAACTCTGCT 59.669 43.478 0.00 0.00 0.00 4.24
2773 2826 3.418684 TGGGTTAGGAAAACTCTGCTC 57.581 47.619 0.00 0.00 0.00 4.26
3072 3147 1.898472 ACCTGGAGAGTCATGTGTCAG 59.102 52.381 0.00 0.00 0.00 3.51
3128 3522 1.075536 ACAAATCCCCTGTCCTTCACC 59.924 52.381 0.00 0.00 0.00 4.02
3159 3553 5.829924 ACCTTCTTATAATCCTTGTGCCATG 59.170 40.000 0.00 0.00 0.00 3.66
3228 7079 7.607991 ACAAAGTATCACCAAGATAAGGACTTG 59.392 37.037 0.00 0.00 40.76 3.16
3268 7119 7.280356 AGCGTTCAGTAAATAACTATCCCAAT 58.720 34.615 0.00 0.00 35.76 3.16
3269 7120 7.226720 AGCGTTCAGTAAATAACTATCCCAATG 59.773 37.037 0.00 0.00 35.76 2.82
3270 7121 7.519970 GCGTTCAGTAAATAACTATCCCAATGG 60.520 40.741 0.00 0.00 35.76 3.16
3271 7122 7.519970 CGTTCAGTAAATAACTATCCCAATGGC 60.520 40.741 0.00 0.00 35.76 4.40
3272 7123 7.149202 TCAGTAAATAACTATCCCAATGGCT 57.851 36.000 0.00 0.00 35.76 4.75
3273 7124 6.998074 TCAGTAAATAACTATCCCAATGGCTG 59.002 38.462 0.00 0.00 35.76 4.85
3274 7125 6.207417 CAGTAAATAACTATCCCAATGGCTGG 59.793 42.308 0.00 0.00 39.95 4.85
3275 7126 2.656947 TAACTATCCCAATGGCTGGC 57.343 50.000 0.00 0.00 44.90 4.85
3276 7127 0.106015 AACTATCCCAATGGCTGGCC 60.106 55.000 4.43 4.43 44.90 5.36
3277 7128 1.601759 CTATCCCAATGGCTGGCCG 60.602 63.158 7.14 0.00 44.90 6.13
3278 7129 3.132029 TATCCCAATGGCTGGCCGG 62.132 63.158 7.41 7.41 44.90 6.13
3306 7169 3.459063 GGCCGGCCGACTACTTCT 61.459 66.667 33.60 0.00 0.00 2.85
3369 7232 1.471119 CCAAGCCATCATGAAGCACT 58.529 50.000 19.75 5.15 0.00 4.40
3388 7251 3.764434 CACTTCCTACTCTCTTGCACCTA 59.236 47.826 0.00 0.00 0.00 3.08
3405 7268 2.245028 ACCTATCTCCTACTCTGTGCCA 59.755 50.000 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.393512 TGTTTGATTCAAAAGAAACATGGATTT 57.606 25.926 13.21 0.00 35.03 2.17
6 7 8.961294 TGTTTGATTCAAAAGAAACATGGATT 57.039 26.923 13.21 0.00 35.03 3.01
7 8 8.961294 TTGTTTGATTCAAAAGAAACATGGAT 57.039 26.923 13.21 0.00 37.94 3.41
8 9 8.783833 TTTGTTTGATTCAAAAGAAACATGGA 57.216 26.923 13.21 0.00 37.94 3.41
9 10 9.440784 CATTTGTTTGATTCAAAAGAAACATGG 57.559 29.630 13.21 4.35 37.94 3.66
19 20 9.474920 GGACACTATTCATTTGTTTGATTCAAA 57.525 29.630 7.74 7.74 38.77 2.69
20 21 8.637099 TGGACACTATTCATTTGTTTGATTCAA 58.363 29.630 0.00 0.00 0.00 2.69
21 22 8.081633 GTGGACACTATTCATTTGTTTGATTCA 58.918 33.333 0.00 0.00 0.00 2.57
22 23 8.081633 TGTGGACACTATTCATTTGTTTGATTC 58.918 33.333 3.91 0.00 0.00 2.52
23 24 7.950512 TGTGGACACTATTCATTTGTTTGATT 58.049 30.769 3.91 0.00 0.00 2.57
24 25 7.448161 TCTGTGGACACTATTCATTTGTTTGAT 59.552 33.333 3.91 0.00 0.00 2.57
25 26 6.770303 TCTGTGGACACTATTCATTTGTTTGA 59.230 34.615 3.91 0.00 0.00 2.69
26 27 6.969366 TCTGTGGACACTATTCATTTGTTTG 58.031 36.000 3.91 0.00 0.00 2.93
27 28 6.998074 TCTCTGTGGACACTATTCATTTGTTT 59.002 34.615 3.91 0.00 0.00 2.83
28 29 6.533730 TCTCTGTGGACACTATTCATTTGTT 58.466 36.000 3.91 0.00 0.00 2.83
29 30 6.114187 TCTCTGTGGACACTATTCATTTGT 57.886 37.500 3.91 0.00 0.00 2.83
30 31 7.439157 TTTCTCTGTGGACACTATTCATTTG 57.561 36.000 3.91 0.00 0.00 2.32
31 32 7.939039 TCTTTTCTCTGTGGACACTATTCATTT 59.061 33.333 3.91 0.00 0.00 2.32
32 33 7.453393 TCTTTTCTCTGTGGACACTATTCATT 58.547 34.615 3.91 0.00 0.00 2.57
33 34 7.009179 TCTTTTCTCTGTGGACACTATTCAT 57.991 36.000 3.91 0.00 0.00 2.57
34 35 6.419484 TCTTTTCTCTGTGGACACTATTCA 57.581 37.500 3.91 0.00 0.00 2.57
35 36 5.350091 GCTCTTTTCTCTGTGGACACTATTC 59.650 44.000 3.91 0.00 0.00 1.75
36 37 5.241662 GCTCTTTTCTCTGTGGACACTATT 58.758 41.667 3.91 0.00 0.00 1.73
37 38 4.323104 GGCTCTTTTCTCTGTGGACACTAT 60.323 45.833 3.91 0.00 0.00 2.12
38 39 3.006967 GGCTCTTTTCTCTGTGGACACTA 59.993 47.826 3.91 0.00 0.00 2.74
39 40 2.224402 GGCTCTTTTCTCTGTGGACACT 60.224 50.000 3.91 0.00 0.00 3.55
40 41 2.147150 GGCTCTTTTCTCTGTGGACAC 58.853 52.381 0.00 0.00 0.00 3.67
41 42 1.768275 TGGCTCTTTTCTCTGTGGACA 59.232 47.619 0.00 0.00 0.00 4.02
42 43 2.147150 GTGGCTCTTTTCTCTGTGGAC 58.853 52.381 0.00 0.00 0.00 4.02
43 44 2.050144 AGTGGCTCTTTTCTCTGTGGA 58.950 47.619 0.00 0.00 0.00 4.02
44 45 2.557920 AGTGGCTCTTTTCTCTGTGG 57.442 50.000 0.00 0.00 0.00 4.17
45 46 4.527509 TCTAGTGGCTCTTTTCTCTGTG 57.472 45.455 0.00 0.00 0.00 3.66
46 47 4.081198 CCATCTAGTGGCTCTTTTCTCTGT 60.081 45.833 0.00 0.00 42.12 3.41
47 48 4.440880 CCATCTAGTGGCTCTTTTCTCTG 58.559 47.826 0.00 0.00 42.12 3.35
48 49 4.751767 CCATCTAGTGGCTCTTTTCTCT 57.248 45.455 0.00 0.00 42.12 3.10
60 61 8.239038 TCTGTTTAGAATCCTACCATCTAGTG 57.761 38.462 0.00 0.00 0.00 2.74
61 62 8.840200 TTCTGTTTAGAATCCTACCATCTAGT 57.160 34.615 0.00 0.00 37.99 2.57
64 65 8.214364 GGATTTCTGTTTAGAATCCTACCATCT 58.786 37.037 7.01 0.00 42.25 2.90
65 66 8.214364 AGGATTTCTGTTTAGAATCCTACCATC 58.786 37.037 13.58 1.38 42.56 3.51
66 67 8.107196 AGGATTTCTGTTTAGAATCCTACCAT 57.893 34.615 13.58 0.00 42.56 3.55
67 68 7.510675 AGGATTTCTGTTTAGAATCCTACCA 57.489 36.000 13.58 0.00 42.56 3.25
68 69 8.678199 CAAAGGATTTCTGTTTAGAATCCTACC 58.322 37.037 15.07 3.79 43.00 3.18
69 70 8.678199 CCAAAGGATTTCTGTTTAGAATCCTAC 58.322 37.037 15.07 0.00 43.00 3.18
70 71 8.390921 ACCAAAGGATTTCTGTTTAGAATCCTA 58.609 33.333 15.07 0.00 43.00 2.94
71 72 7.177392 CACCAAAGGATTTCTGTTTAGAATCCT 59.823 37.037 10.27 10.27 44.18 3.24
72 73 7.315890 CACCAAAGGATTTCTGTTTAGAATCC 58.684 38.462 6.29 6.29 42.25 3.01
73 74 6.808704 GCACCAAAGGATTTCTGTTTAGAATC 59.191 38.462 0.00 0.00 42.25 2.52
74 75 6.295292 GGCACCAAAGGATTTCTGTTTAGAAT 60.295 38.462 0.00 0.00 42.25 2.40
75 76 5.010617 GGCACCAAAGGATTTCTGTTTAGAA 59.989 40.000 0.00 0.00 41.06 2.10
76 77 4.522789 GGCACCAAAGGATTTCTGTTTAGA 59.477 41.667 0.00 0.00 35.03 2.10
77 78 4.280677 TGGCACCAAAGGATTTCTGTTTAG 59.719 41.667 0.00 0.00 35.03 1.85
78 79 4.219115 TGGCACCAAAGGATTTCTGTTTA 58.781 39.130 0.00 0.00 35.03 2.01
79 80 3.037549 TGGCACCAAAGGATTTCTGTTT 58.962 40.909 0.00 0.00 35.03 2.83
80 81 2.676748 TGGCACCAAAGGATTTCTGTT 58.323 42.857 0.00 0.00 35.03 3.16
81 82 2.380064 TGGCACCAAAGGATTTCTGT 57.620 45.000 0.00 0.00 35.03 3.41
82 83 3.967332 AATGGCACCAAAGGATTTCTG 57.033 42.857 0.00 0.00 35.03 3.02
83 84 3.008266 CCAAATGGCACCAAAGGATTTCT 59.992 43.478 0.00 0.00 35.03 2.52
84 85 3.244526 ACCAAATGGCACCAAAGGATTTC 60.245 43.478 11.10 0.00 35.35 2.17
85 86 2.710471 ACCAAATGGCACCAAAGGATTT 59.290 40.909 11.10 0.00 37.52 2.17
86 87 2.038820 CACCAAATGGCACCAAAGGATT 59.961 45.455 11.10 0.00 39.32 3.01
87 88 1.624813 CACCAAATGGCACCAAAGGAT 59.375 47.619 11.10 0.00 39.32 3.24
88 89 1.047002 CACCAAATGGCACCAAAGGA 58.953 50.000 11.10 0.00 39.32 3.36
89 90 0.603439 GCACCAAATGGCACCAAAGG 60.603 55.000 0.00 0.00 39.32 3.11
90 91 0.106335 TGCACCAAATGGCACCAAAG 59.894 50.000 0.00 0.00 39.32 2.77
91 92 0.543277 TTGCACCAAATGGCACCAAA 59.457 45.000 0.00 0.00 40.23 3.28
92 93 0.543277 TTTGCACCAAATGGCACCAA 59.457 45.000 0.00 0.00 40.23 3.67
93 94 0.106335 CTTTGCACCAAATGGCACCA 59.894 50.000 0.00 0.00 40.23 4.17
94 95 0.603439 CCTTTGCACCAAATGGCACC 60.603 55.000 0.00 0.00 40.23 5.01
95 96 0.392336 TCCTTTGCACCAAATGGCAC 59.608 50.000 0.00 0.00 40.23 5.01
96 97 1.126488 TTCCTTTGCACCAAATGGCA 58.874 45.000 0.00 0.00 39.32 4.92
97 98 2.349590 GATTCCTTTGCACCAAATGGC 58.650 47.619 0.00 0.00 39.32 4.40
98 99 2.230992 TCGATTCCTTTGCACCAAATGG 59.769 45.455 0.00 0.00 42.17 3.16
99 100 3.574284 TCGATTCCTTTGCACCAAATG 57.426 42.857 0.00 0.00 32.70 2.32
100 101 3.511146 ACATCGATTCCTTTGCACCAAAT 59.489 39.130 0.00 0.00 32.70 2.32
101 102 2.890311 ACATCGATTCCTTTGCACCAAA 59.110 40.909 0.00 0.00 0.00 3.28
102 103 2.513753 ACATCGATTCCTTTGCACCAA 58.486 42.857 0.00 0.00 0.00 3.67
103 104 2.198827 ACATCGATTCCTTTGCACCA 57.801 45.000 0.00 0.00 0.00 4.17
104 105 2.749621 AGAACATCGATTCCTTTGCACC 59.250 45.455 0.00 0.00 0.00 5.01
105 106 4.391830 TGTAGAACATCGATTCCTTTGCAC 59.608 41.667 0.00 0.00 0.00 4.57
106 107 4.574892 TGTAGAACATCGATTCCTTTGCA 58.425 39.130 0.00 0.00 0.00 4.08
107 108 5.741388 ATGTAGAACATCGATTCCTTTGC 57.259 39.130 0.00 0.00 32.38 3.68
108 109 6.470235 GCAAATGTAGAACATCGATTCCTTTG 59.530 38.462 0.00 3.00 37.97 2.77
109 110 6.375455 AGCAAATGTAGAACATCGATTCCTTT 59.625 34.615 0.00 0.00 37.97 3.11
110 111 5.882557 AGCAAATGTAGAACATCGATTCCTT 59.117 36.000 0.00 0.00 37.97 3.36
111 112 5.431765 AGCAAATGTAGAACATCGATTCCT 58.568 37.500 0.00 0.00 37.97 3.36
112 113 5.741388 AGCAAATGTAGAACATCGATTCC 57.259 39.130 0.00 0.00 37.97 3.01
126 127 9.432982 TTCCTTGGGAATATTATAAGCAAATGT 57.567 29.630 0.00 0.00 36.71 2.71
127 128 9.696917 GTTCCTTGGGAATATTATAAGCAAATG 57.303 33.333 2.20 0.00 44.04 2.32
128 129 8.576442 CGTTCCTTGGGAATATTATAAGCAAAT 58.424 33.333 2.20 0.00 44.04 2.32
129 130 7.776030 TCGTTCCTTGGGAATATTATAAGCAAA 59.224 33.333 2.20 0.00 44.04 3.68
130 131 7.284074 TCGTTCCTTGGGAATATTATAAGCAA 58.716 34.615 2.20 0.00 44.04 3.91
131 132 6.833041 TCGTTCCTTGGGAATATTATAAGCA 58.167 36.000 2.20 0.00 44.04 3.91
132 133 6.128254 GCTCGTTCCTTGGGAATATTATAAGC 60.128 42.308 2.20 2.02 44.04 3.09
133 134 6.934645 TGCTCGTTCCTTGGGAATATTATAAG 59.065 38.462 2.20 0.00 44.04 1.73
134 135 6.833041 TGCTCGTTCCTTGGGAATATTATAA 58.167 36.000 2.20 0.00 44.04 0.98
135 136 6.428083 TGCTCGTTCCTTGGGAATATTATA 57.572 37.500 2.20 0.00 44.04 0.98
136 137 5.304686 TGCTCGTTCCTTGGGAATATTAT 57.695 39.130 2.20 0.00 44.04 1.28
137 138 4.764050 TGCTCGTTCCTTGGGAATATTA 57.236 40.909 2.20 0.00 44.04 0.98
138 139 3.644966 TGCTCGTTCCTTGGGAATATT 57.355 42.857 2.20 0.00 44.04 1.28
139 140 3.864789 ATGCTCGTTCCTTGGGAATAT 57.135 42.857 2.20 0.00 44.04 1.28
140 141 3.644966 AATGCTCGTTCCTTGGGAATA 57.355 42.857 2.20 0.00 44.04 1.75
141 142 2.514458 AATGCTCGTTCCTTGGGAAT 57.486 45.000 2.20 0.00 44.04 3.01
142 143 2.039216 TGTAATGCTCGTTCCTTGGGAA 59.961 45.455 0.00 0.00 39.66 3.97
143 144 1.626321 TGTAATGCTCGTTCCTTGGGA 59.374 47.619 0.00 0.00 0.00 4.37
144 145 2.107950 TGTAATGCTCGTTCCTTGGG 57.892 50.000 0.00 0.00 0.00 4.12
145 146 5.056480 TCATATGTAATGCTCGTTCCTTGG 58.944 41.667 1.90 0.00 0.00 3.61
146 147 6.603237 TTCATATGTAATGCTCGTTCCTTG 57.397 37.500 1.90 0.00 0.00 3.61
147 148 7.807977 AATTCATATGTAATGCTCGTTCCTT 57.192 32.000 1.90 0.00 0.00 3.36
148 149 7.807977 AAATTCATATGTAATGCTCGTTCCT 57.192 32.000 1.90 0.00 0.00 3.36
149 150 7.379529 CCAAAATTCATATGTAATGCTCGTTCC 59.620 37.037 1.90 0.00 0.00 3.62
150 151 8.128582 TCCAAAATTCATATGTAATGCTCGTTC 58.871 33.333 1.90 0.00 0.00 3.95
151 152 7.995289 TCCAAAATTCATATGTAATGCTCGTT 58.005 30.769 1.90 0.00 0.00 3.85
152 153 7.498900 TCTCCAAAATTCATATGTAATGCTCGT 59.501 33.333 1.90 0.00 0.00 4.18
153 154 7.864686 TCTCCAAAATTCATATGTAATGCTCG 58.135 34.615 1.90 0.00 0.00 5.03
165 166 9.781633 TCATGTTTGATTTTCTCCAAAATTCAT 57.218 25.926 0.00 0.00 41.47 2.57
166 167 9.263538 CTCATGTTTGATTTTCTCCAAAATTCA 57.736 29.630 0.00 0.00 41.47 2.57
167 168 8.715088 CCTCATGTTTGATTTTCTCCAAAATTC 58.285 33.333 0.00 0.00 41.47 2.17
168 169 8.212995 ACCTCATGTTTGATTTTCTCCAAAATT 58.787 29.630 0.00 0.00 41.47 1.82
169 170 7.738847 ACCTCATGTTTGATTTTCTCCAAAAT 58.261 30.769 0.00 0.00 43.64 1.82
170 171 7.123355 ACCTCATGTTTGATTTTCTCCAAAA 57.877 32.000 0.00 0.00 34.52 2.44
171 172 6.729690 ACCTCATGTTTGATTTTCTCCAAA 57.270 33.333 0.00 0.00 0.00 3.28
172 173 6.550854 AGAACCTCATGTTTGATTTTCTCCAA 59.449 34.615 0.00 0.00 37.29 3.53
173 174 6.070656 AGAACCTCATGTTTGATTTTCTCCA 58.929 36.000 0.00 0.00 37.29 3.86
174 175 6.581171 AGAACCTCATGTTTGATTTTCTCC 57.419 37.500 0.00 0.00 37.29 3.71
175 176 7.530863 GGTAGAACCTCATGTTTGATTTTCTC 58.469 38.462 0.00 0.00 37.29 2.87
176 177 7.454260 GGTAGAACCTCATGTTTGATTTTCT 57.546 36.000 0.00 0.00 37.29 2.52
215 216 8.700973 ACCACATAAAAACTCTAAAATGGTTGT 58.299 29.630 0.00 0.00 32.90 3.32
216 217 9.541143 AACCACATAAAAACTCTAAAATGGTTG 57.459 29.630 0.00 0.00 43.30 3.77
236 237 4.039245 TCAACAAAAGGTGTCAAAACCACA 59.961 37.500 0.00 0.00 43.20 4.17
275 276 9.640963 GAGGTCGTATTAGCTTGTGATATTAAT 57.359 33.333 0.00 0.00 0.00 1.40
276 277 8.857098 AGAGGTCGTATTAGCTTGTGATATTAA 58.143 33.333 0.00 0.00 0.00 1.40
277 278 8.405418 AGAGGTCGTATTAGCTTGTGATATTA 57.595 34.615 0.00 0.00 0.00 0.98
278 279 7.231722 AGAGAGGTCGTATTAGCTTGTGATATT 59.768 37.037 0.00 0.00 0.00 1.28
279 280 6.717540 AGAGAGGTCGTATTAGCTTGTGATAT 59.282 38.462 0.00 0.00 0.00 1.63
280 281 6.062749 AGAGAGGTCGTATTAGCTTGTGATA 58.937 40.000 0.00 0.00 0.00 2.15
281 282 4.890581 AGAGAGGTCGTATTAGCTTGTGAT 59.109 41.667 0.00 0.00 0.00 3.06
282 283 4.270834 AGAGAGGTCGTATTAGCTTGTGA 58.729 43.478 0.00 0.00 0.00 3.58
283 284 4.640789 AGAGAGGTCGTATTAGCTTGTG 57.359 45.455 0.00 0.00 0.00 3.33
284 285 5.887035 AGTTAGAGAGGTCGTATTAGCTTGT 59.113 40.000 0.00 0.00 0.00 3.16
285 286 6.380095 AGTTAGAGAGGTCGTATTAGCTTG 57.620 41.667 0.00 0.00 0.00 4.01
286 287 9.962809 ATATAGTTAGAGAGGTCGTATTAGCTT 57.037 33.333 0.00 0.00 0.00 3.74
287 288 9.386010 CATATAGTTAGAGAGGTCGTATTAGCT 57.614 37.037 0.00 0.00 0.00 3.32
288 289 9.165035 ACATATAGTTAGAGAGGTCGTATTAGC 57.835 37.037 0.00 0.00 0.00 3.09
291 292 9.742144 ATGACATATAGTTAGAGAGGTCGTATT 57.258 33.333 0.00 0.00 0.00 1.89
312 313 2.220824 CGTGCTCGAAGTTTTGATGACA 59.779 45.455 1.00 0.00 39.71 3.58
314 315 1.194547 GCGTGCTCGAAGTTTTGATGA 59.805 47.619 13.13 0.00 39.71 2.92
332 333 9.347934 TCTTTTATAATAATTTGGTTGTGTGCG 57.652 29.630 0.00 0.00 0.00 5.34
353 354 2.249844 TCGCTTCGGGAGTTTCTTTT 57.750 45.000 0.00 0.00 0.00 2.27
354 355 2.289444 TGATCGCTTCGGGAGTTTCTTT 60.289 45.455 0.00 0.00 0.00 2.52
357 358 1.393883 GTTGATCGCTTCGGGAGTTTC 59.606 52.381 0.00 0.00 0.00 2.78
360 361 0.320374 TTGTTGATCGCTTCGGGAGT 59.680 50.000 0.00 0.00 0.00 3.85
362 363 1.066502 TCATTGTTGATCGCTTCGGGA 60.067 47.619 0.00 0.00 0.00 5.14
363 364 1.368641 TCATTGTTGATCGCTTCGGG 58.631 50.000 0.00 0.00 0.00 5.14
364 365 3.244670 GATCATTGTTGATCGCTTCGG 57.755 47.619 0.60 0.00 46.46 4.30
372 373 4.141824 TGCATGCCATTGATCATTGTTGAT 60.142 37.500 16.68 3.22 45.39 2.57
373 374 3.195825 TGCATGCCATTGATCATTGTTGA 59.804 39.130 16.68 1.28 36.00 3.18
374 375 3.526534 TGCATGCCATTGATCATTGTTG 58.473 40.909 16.68 10.69 0.00 3.33
375 376 3.897141 TGCATGCCATTGATCATTGTT 57.103 38.095 16.68 0.00 0.00 2.83
376 377 3.055747 TGTTGCATGCCATTGATCATTGT 60.056 39.130 16.68 0.00 0.00 2.71
377 378 3.526534 TGTTGCATGCCATTGATCATTG 58.473 40.909 16.68 10.09 0.00 2.82
387 388 1.543065 GGGGTCATTGTTGCATGCCA 61.543 55.000 16.68 0.00 0.00 4.92
389 390 0.108520 CAGGGGTCATTGTTGCATGC 60.109 55.000 11.82 11.82 0.00 4.06
393 394 1.598701 GAGCCAGGGGTCATTGTTGC 61.599 60.000 12.42 0.00 41.72 4.17
405 406 4.899239 GCGATGGTCGGAGCCAGG 62.899 72.222 4.54 1.52 42.47 4.45
406 407 2.930385 ATTGCGATGGTCGGAGCCAG 62.930 60.000 4.54 0.00 42.14 4.85
451 452 2.484889 GACCATGAGACGATAAAGGGC 58.515 52.381 0.00 0.00 0.00 5.19
477 478 3.000041 TCATTGGCGTGACATTACTCAC 59.000 45.455 0.00 0.00 37.75 3.51
504 505 4.530710 AACTGAAATGTCATGCAAGCAT 57.469 36.364 0.86 0.86 37.08 3.79
505 506 4.202131 TGAAACTGAAATGTCATGCAAGCA 60.202 37.500 0.00 0.00 31.85 3.91
506 507 4.300803 TGAAACTGAAATGTCATGCAAGC 58.699 39.130 0.00 0.00 31.85 4.01
507 508 7.416154 AAATGAAACTGAAATGTCATGCAAG 57.584 32.000 0.00 0.00 31.85 4.01
508 509 7.789273 AAAATGAAACTGAAATGTCATGCAA 57.211 28.000 0.00 0.00 31.85 4.08
509 510 7.789273 AAAAATGAAACTGAAATGTCATGCA 57.211 28.000 0.00 0.00 31.85 3.96
535 536 3.399770 GCGCGCGTGTGTGTTCTA 61.400 61.111 32.35 0.00 0.00 2.10
547 548 1.250476 CTAAACTGAAATGTGCGCGC 58.750 50.000 27.26 27.26 0.00 6.86
549 550 4.147219 AGAACTAAACTGAAATGTGCGC 57.853 40.909 0.00 0.00 0.00 6.09
550 551 5.107104 TGCTAGAACTAAACTGAAATGTGCG 60.107 40.000 0.00 0.00 0.00 5.34
551 552 6.241207 TGCTAGAACTAAACTGAAATGTGC 57.759 37.500 0.00 0.00 0.00 4.57
564 565 7.979444 AAAATACTTGTTGCTGCTAGAACTA 57.021 32.000 0.00 0.00 0.00 2.24
592 593 5.682943 ATTACTTGTCGCTGTTTTTGCTA 57.317 34.783 0.00 0.00 0.00 3.49
706 707 2.072298 CTGGCTTTTCTTCCGAGACAG 58.928 52.381 0.00 0.00 39.92 3.51
791 792 2.444895 ATGGGAGAGAGACGGCCC 60.445 66.667 0.00 0.00 38.09 5.80
817 818 2.360100 CAGAGGCTGCAGCAAGCT 60.360 61.111 37.63 26.23 45.94 3.74
867 868 6.265196 TGTTCCATGTAGAAGCTTCAAATTGT 59.735 34.615 27.57 8.95 0.00 2.71
958 959 2.903784 TGTCCCCTCGATTTTTCTCTCA 59.096 45.455 0.00 0.00 0.00 3.27
1055 1056 1.614824 AGCTGGGACTTGGGAGGAG 60.615 63.158 0.00 0.00 0.00 3.69
1059 1060 3.003173 CCGAGCTGGGACTTGGGA 61.003 66.667 9.58 0.00 37.54 4.37
1061 1062 4.785453 GGCCGAGCTGGGACTTGG 62.785 72.222 20.35 0.00 43.30 3.61
1411 1415 7.394923 ACAAAACCCACCATTAATATTCTCGAA 59.605 33.333 0.00 0.00 0.00 3.71
1413 1417 7.095695 ACAAAACCCACCATTAATATTCTCG 57.904 36.000 0.00 0.00 0.00 4.04
1414 1418 7.193595 CGACAAAACCCACCATTAATATTCTC 58.806 38.462 0.00 0.00 0.00 2.87
1416 1420 6.095720 TCCGACAAAACCCACCATTAATATTC 59.904 38.462 0.00 0.00 0.00 1.75
1424 1429 2.167662 GAATCCGACAAAACCCACCAT 58.832 47.619 0.00 0.00 0.00 3.55
1430 1435 2.160219 GGTTACCGAATCCGACAAAACC 59.840 50.000 0.00 0.00 38.22 3.27
1439 1444 3.246936 GCTACGATTTGGTTACCGAATCC 59.753 47.826 28.92 16.62 46.43 3.01
1446 1451 1.591619 GCCGAGCTACGATTTGGTTAC 59.408 52.381 7.07 0.00 45.77 2.50
1449 1454 0.460284 CTGCCGAGCTACGATTTGGT 60.460 55.000 7.07 0.00 45.77 3.67
1631 1679 8.817092 TTAGCAGTTAATAAAGGGCTAATGTT 57.183 30.769 0.00 0.00 38.49 2.71
1706 1755 6.964464 TGTGGCCTTGACCTCTTATAAATTA 58.036 36.000 3.32 0.00 0.00 1.40
1713 1762 2.303022 CTCTTGTGGCCTTGACCTCTTA 59.697 50.000 3.32 0.00 0.00 2.10
1730 1779 2.105477 ACTGTCAATGTCACTGCCTCTT 59.895 45.455 0.00 0.00 0.00 2.85
1744 1795 3.421919 TTGCTGATGATGGACTGTCAA 57.578 42.857 10.38 0.00 0.00 3.18
1834 1885 2.936919 AGCATTCCTGTCAGTGTCAA 57.063 45.000 0.00 0.00 0.00 3.18
1891 1942 2.094026 TGTGCCTACAGTGCATCTACAG 60.094 50.000 0.00 0.00 41.46 2.74
2322 2373 2.041081 CCCAACCACATCCCAGAAAGTA 59.959 50.000 0.00 0.00 0.00 2.24
2415 2466 3.463585 ATGCAAATGCCTGCGGGG 61.464 61.111 15.02 1.86 45.74 5.73
2730 2783 8.792633 CCCATGAGAAAATCTACAACTTTTGTA 58.207 33.333 0.00 0.00 43.27 2.41
2732 2785 7.661040 ACCCATGAGAAAATCTACAACTTTTG 58.339 34.615 0.00 0.00 0.00 2.44
2733 2786 7.839680 ACCCATGAGAAAATCTACAACTTTT 57.160 32.000 0.00 0.00 0.00 2.27
2734 2787 7.839680 AACCCATGAGAAAATCTACAACTTT 57.160 32.000 0.00 0.00 0.00 2.66
2735 2788 7.611855 CCTAACCCATGAGAAAATCTACAACTT 59.388 37.037 0.00 0.00 0.00 2.66
2736 2789 7.037586 TCCTAACCCATGAGAAAATCTACAACT 60.038 37.037 0.00 0.00 0.00 3.16
2737 2790 7.110155 TCCTAACCCATGAGAAAATCTACAAC 58.890 38.462 0.00 0.00 0.00 3.32
2738 2791 7.265599 TCCTAACCCATGAGAAAATCTACAA 57.734 36.000 0.00 0.00 0.00 2.41
2739 2792 6.884472 TCCTAACCCATGAGAAAATCTACA 57.116 37.500 0.00 0.00 0.00 2.74
2740 2793 8.459635 GTTTTCCTAACCCATGAGAAAATCTAC 58.540 37.037 0.00 0.00 38.34 2.59
2741 2794 8.390921 AGTTTTCCTAACCCATGAGAAAATCTA 58.609 33.333 0.00 0.00 38.34 1.98
2742 2795 7.241628 AGTTTTCCTAACCCATGAGAAAATCT 58.758 34.615 0.00 0.00 38.34 2.40
2743 2796 7.394641 AGAGTTTTCCTAACCCATGAGAAAATC 59.605 37.037 0.00 0.00 38.34 2.17
2744 2797 7.177392 CAGAGTTTTCCTAACCCATGAGAAAAT 59.823 37.037 0.00 0.00 38.34 1.82
2745 2798 6.490040 CAGAGTTTTCCTAACCCATGAGAAAA 59.510 38.462 0.00 0.00 34.87 2.29
2746 2799 6.003950 CAGAGTTTTCCTAACCCATGAGAAA 58.996 40.000 0.00 0.00 0.00 2.52
2747 2800 5.560724 CAGAGTTTTCCTAACCCATGAGAA 58.439 41.667 0.00 0.00 0.00 2.87
2748 2801 4.565652 GCAGAGTTTTCCTAACCCATGAGA 60.566 45.833 0.00 0.00 0.00 3.27
2749 2802 3.691609 GCAGAGTTTTCCTAACCCATGAG 59.308 47.826 0.00 0.00 0.00 2.90
2750 2803 3.330701 AGCAGAGTTTTCCTAACCCATGA 59.669 43.478 0.00 0.00 0.00 3.07
2751 2804 3.690460 AGCAGAGTTTTCCTAACCCATG 58.310 45.455 0.00 0.00 0.00 3.66
2752 2805 3.308473 GGAGCAGAGTTTTCCTAACCCAT 60.308 47.826 0.00 0.00 0.00 4.00
2753 2806 2.039879 GGAGCAGAGTTTTCCTAACCCA 59.960 50.000 0.00 0.00 0.00 4.51
2754 2807 2.618302 GGGAGCAGAGTTTTCCTAACCC 60.618 54.545 0.00 0.00 0.00 4.11
2755 2808 2.306219 AGGGAGCAGAGTTTTCCTAACC 59.694 50.000 0.00 0.00 0.00 2.85
2756 2809 3.704800 AGGGAGCAGAGTTTTCCTAAC 57.295 47.619 0.00 0.00 0.00 2.34
2757 2810 5.836024 TTTAGGGAGCAGAGTTTTCCTAA 57.164 39.130 0.00 0.00 35.73 2.69
2758 2811 6.388619 AATTTAGGGAGCAGAGTTTTCCTA 57.611 37.500 0.00 0.00 0.00 2.94
2759 2812 4.936685 ATTTAGGGAGCAGAGTTTTCCT 57.063 40.909 0.00 0.00 0.00 3.36
2760 2813 7.646548 AATAATTTAGGGAGCAGAGTTTTCC 57.353 36.000 0.00 0.00 0.00 3.13
2763 2816 9.975218 TCTTAAATAATTTAGGGAGCAGAGTTT 57.025 29.630 0.00 0.00 0.00 2.66
2764 2817 9.975218 TTCTTAAATAATTTAGGGAGCAGAGTT 57.025 29.630 0.00 0.00 0.00 3.01
2765 2818 9.975218 TTTCTTAAATAATTTAGGGAGCAGAGT 57.025 29.630 0.00 0.00 0.00 3.24
2798 2851 7.756395 ACATCACAAATGTTCTTTGAGATCT 57.244 32.000 0.00 0.00 37.53 2.75
3039 3114 2.368875 TCTCCAGGTTTCCAGTCTGAAC 59.631 50.000 0.00 0.00 0.00 3.18
3159 3553 5.452302 GCAAGCATACAAATGTACATTCGAC 59.548 40.000 21.02 8.34 35.38 4.20
3228 7079 5.178809 ACTGAACGCTTCAAACCAAGTATAC 59.821 40.000 0.00 0.00 39.58 1.47
3292 7155 2.225963 CCTATACAGAAGTAGTCGGCCG 59.774 54.545 22.12 22.12 32.86 6.13
3306 7169 7.797062 TGCACCACAGAATATAAACCTATACA 58.203 34.615 0.00 0.00 0.00 2.29
3369 7232 4.873010 AGATAGGTGCAAGAGAGTAGGAA 58.127 43.478 0.00 0.00 0.00 3.36
3405 7268 2.261671 GCTCACCGGTGTGACGAT 59.738 61.111 34.54 0.00 46.40 3.73
3427 7290 1.911293 TTCAGCTTCACGCCGAATGC 61.911 55.000 0.00 0.00 40.39 3.56


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

AutoCloner maintained by Alex Coulton.