Multiple sequence alignment - TraesCS2A01G412600

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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 TraesCS2A01G412600 chr2A 100.000 3792 0 0 1 3792 670218045 670221836 0.000000e+00 7003
1 TraesCS2A01G412600 chr2D 92.756 1629 65 24 624 2237 524563399 524564989 0.000000e+00 2305
2 TraesCS2A01G412600 chr2D 93.169 1537 62 16 2273 3792 524565056 524566566 0.000000e+00 2217
3 TraesCS2A01G412600 chr2D 89.080 348 13 11 165 508 524562694 524563020 3.530000e-110 409
4 TraesCS2A01G412600 chr2B 90.737 1641 87 31 634 2238 620643555 620641944 0.000000e+00 2128
5 TraesCS2A01G412600 chr2B 93.527 1066 32 11 2248 3288 620641899 620640846 0.000000e+00 1552
6 TraesCS2A01G412600 chr2B 93.353 331 14 2 3461 3791 620640387 620640065 2.050000e-132 483
7 TraesCS2A01G412600 chr2B 86.480 392 21 16 180 566 620644247 620643883 5.900000e-108 401
8 TraesCS2A01G412600 chr2B 95.161 186 6 3 3284 3469 620640725 620640543 1.330000e-74 291
9 TraesCS2A01G412600 chr7D 84.211 171 22 5 2056 2224 403645306 403645139 1.090000e-35 161
10 TraesCS2A01G412600 chr7B 83.041 171 24 5 2056 2224 412903061 412902894 2.360000e-32 150
11 TraesCS2A01G412600 chr7A 83.041 171 24 5 2056 2224 462301470 462301303 2.360000e-32 150


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 TraesCS2A01G412600 chr2A 670218045 670221836 3791 False 7003.000000 7003 100.000000 1 3792 1 chr2A.!!$F1 3791
1 TraesCS2A01G412600 chr2D 524562694 524566566 3872 False 1643.666667 2305 91.668333 165 3792 3 chr2D.!!$F1 3627
2 TraesCS2A01G412600 chr2B 620640065 620644247 4182 True 971.000000 2128 91.851600 180 3791 5 chr2B.!!$R1 3611

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
606 855 0.03759 TAATGCCCGTTGCTCAACCT 59.962 50.0 7.12 0.0 42.00 3.5 F
995 1287 0.38359 CGCAGGAGATCGACACTGAT 59.616 55.0 10.52 0.0 32.86 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1863 0.037975 GTACGTTCATGGACCACCGT 60.038 55.0 0.0 5.95 39.42 4.83 R
2956 3341 0.592637 TGTGCCTGTGCTTTCGAATG 59.407 50.0 0.0 2.02 38.71 2.67 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
21 22 2.681848 GTCTGCATGTGGAAGAAGATGG 59.318 50.000 0.00 0.00 0.00 3.51
22 23 1.404391 CTGCATGTGGAAGAAGATGGC 59.596 52.381 0.00 0.00 0.00 4.40
23 24 0.743097 GCATGTGGAAGAAGATGGCC 59.257 55.000 0.00 0.00 0.00 5.36
24 25 1.684248 GCATGTGGAAGAAGATGGCCT 60.684 52.381 3.32 0.00 0.00 5.19
25 26 2.295885 CATGTGGAAGAAGATGGCCTC 58.704 52.381 3.32 0.00 0.00 4.70
26 27 0.620556 TGTGGAAGAAGATGGCCTCC 59.379 55.000 3.32 0.16 0.00 4.30
27 28 0.915364 GTGGAAGAAGATGGCCTCCT 59.085 55.000 3.32 0.00 0.00 3.69
28 29 1.134250 GTGGAAGAAGATGGCCTCCTC 60.134 57.143 3.32 0.00 0.00 3.71
29 30 0.105778 GGAAGAAGATGGCCTCCTCG 59.894 60.000 3.32 0.00 0.00 4.63
30 31 0.531753 GAAGAAGATGGCCTCCTCGC 60.532 60.000 3.32 0.00 0.00 5.03
31 32 0.980231 AAGAAGATGGCCTCCTCGCT 60.980 55.000 3.32 0.00 0.00 4.93
32 33 1.068921 GAAGATGGCCTCCTCGCTC 59.931 63.158 3.32 0.00 0.00 5.03
33 34 2.691674 GAAGATGGCCTCCTCGCTCG 62.692 65.000 3.32 0.00 0.00 5.03
34 35 3.532155 GATGGCCTCCTCGCTCGT 61.532 66.667 3.32 0.00 0.00 4.18
35 36 3.492311 GATGGCCTCCTCGCTCGTC 62.492 68.421 3.32 0.00 0.00 4.20
39 40 2.902846 CCTCCTCGCTCGTCGGAT 60.903 66.667 0.00 0.00 39.05 4.18
40 41 1.597302 CCTCCTCGCTCGTCGGATA 60.597 63.158 0.00 0.00 39.05 2.59
41 42 0.956410 CCTCCTCGCTCGTCGGATAT 60.956 60.000 0.00 0.00 39.05 1.63
42 43 1.675116 CCTCCTCGCTCGTCGGATATA 60.675 57.143 0.00 0.00 39.05 0.86
43 44 2.074576 CTCCTCGCTCGTCGGATATAA 58.925 52.381 0.00 0.00 39.05 0.98
44 45 2.483106 CTCCTCGCTCGTCGGATATAAA 59.517 50.000 0.00 0.00 39.05 1.40
45 46 3.079578 TCCTCGCTCGTCGGATATAAAT 58.920 45.455 0.00 0.00 39.05 1.40
46 47 3.126514 TCCTCGCTCGTCGGATATAAATC 59.873 47.826 0.00 0.00 39.05 2.17
47 48 3.119955 CCTCGCTCGTCGGATATAAATCA 60.120 47.826 0.00 0.00 39.05 2.57
48 49 4.079665 TCGCTCGTCGGATATAAATCAG 57.920 45.455 0.00 0.00 39.05 2.90
49 50 3.749609 TCGCTCGTCGGATATAAATCAGA 59.250 43.478 0.00 0.00 39.05 3.27
50 51 4.395231 TCGCTCGTCGGATATAAATCAGAT 59.605 41.667 0.00 0.00 38.37 2.90
51 52 4.497251 CGCTCGTCGGATATAAATCAGATG 59.503 45.833 0.00 2.50 41.82 2.90
52 53 4.800993 GCTCGTCGGATATAAATCAGATGG 59.199 45.833 7.55 2.03 41.20 3.51
53 54 5.622460 GCTCGTCGGATATAAATCAGATGGT 60.622 44.000 7.55 0.00 41.20 3.55
54 55 5.709966 TCGTCGGATATAAATCAGATGGTG 58.290 41.667 7.55 0.00 41.20 4.17
55 56 5.475564 TCGTCGGATATAAATCAGATGGTGA 59.524 40.000 7.55 0.00 41.20 4.02
56 57 6.015772 TCGTCGGATATAAATCAGATGGTGAA 60.016 38.462 7.55 0.00 41.20 3.18
57 58 6.309009 CGTCGGATATAAATCAGATGGTGAAG 59.691 42.308 1.28 0.00 38.76 3.02
58 59 7.378966 GTCGGATATAAATCAGATGGTGAAGA 58.621 38.462 0.00 0.00 38.37 2.87
59 60 7.872993 GTCGGATATAAATCAGATGGTGAAGAA 59.127 37.037 0.00 0.00 38.37 2.52
60 61 8.428852 TCGGATATAAATCAGATGGTGAAGAAA 58.571 33.333 0.00 0.00 39.19 2.52
61 62 9.056005 CGGATATAAATCAGATGGTGAAGAAAA 57.944 33.333 0.00 0.00 39.19 2.29
84 85 8.477419 AAAAAGGTGACTGGAATAGAAAATCA 57.523 30.769 0.00 0.00 42.68 2.57
85 86 7.693969 AAAGGTGACTGGAATAGAAAATCAG 57.306 36.000 0.00 0.00 42.68 2.90
86 87 6.380079 AGGTGACTGGAATAGAAAATCAGT 57.620 37.500 0.00 0.00 41.13 3.41
90 91 6.576551 GACTGGAATAGAAAATCAGTCGAC 57.423 41.667 7.70 7.70 42.85 4.20
91 92 6.287589 ACTGGAATAGAAAATCAGTCGACT 57.712 37.500 13.58 13.58 34.00 4.18
92 93 7.406031 ACTGGAATAGAAAATCAGTCGACTA 57.594 36.000 19.57 7.46 34.00 2.59
93 94 7.837863 ACTGGAATAGAAAATCAGTCGACTAA 58.162 34.615 19.57 3.55 34.00 2.24
94 95 7.760340 ACTGGAATAGAAAATCAGTCGACTAAC 59.240 37.037 19.57 6.27 34.00 2.34
95 96 7.608153 TGGAATAGAAAATCAGTCGACTAACA 58.392 34.615 19.57 5.58 0.00 2.41
96 97 8.092068 TGGAATAGAAAATCAGTCGACTAACAA 58.908 33.333 19.57 4.65 0.00 2.83
97 98 8.932791 GGAATAGAAAATCAGTCGACTAACAAA 58.067 33.333 19.57 2.00 0.00 2.83
100 101 7.133891 AGAAAATCAGTCGACTAACAAATGG 57.866 36.000 19.57 3.12 0.00 3.16
101 102 6.710744 AGAAAATCAGTCGACTAACAAATGGT 59.289 34.615 19.57 0.00 0.00 3.55
102 103 6.481954 AAATCAGTCGACTAACAAATGGTC 57.518 37.500 19.57 0.00 36.26 4.02
107 108 2.109425 GACTAACAAATGGTCGGCCT 57.891 50.000 7.97 0.00 35.27 5.19
108 109 2.007608 GACTAACAAATGGTCGGCCTC 58.992 52.381 7.97 0.00 35.27 4.70
109 110 1.628846 ACTAACAAATGGTCGGCCTCT 59.371 47.619 7.97 0.00 35.27 3.69
110 111 2.039879 ACTAACAAATGGTCGGCCTCTT 59.960 45.455 7.97 0.00 35.27 2.85
111 112 2.871096 AACAAATGGTCGGCCTCTTA 57.129 45.000 7.97 0.00 35.27 2.10
112 113 2.403252 ACAAATGGTCGGCCTCTTAG 57.597 50.000 7.97 0.00 35.27 2.18
113 114 1.628846 ACAAATGGTCGGCCTCTTAGT 59.371 47.619 7.97 0.00 35.27 2.24
114 115 2.039879 ACAAATGGTCGGCCTCTTAGTT 59.960 45.455 7.97 0.00 35.27 2.24
115 116 2.678336 CAAATGGTCGGCCTCTTAGTTC 59.322 50.000 7.97 0.00 35.27 3.01
116 117 1.568504 ATGGTCGGCCTCTTAGTTCA 58.431 50.000 7.97 0.00 35.27 3.18
117 118 0.895530 TGGTCGGCCTCTTAGTTCAG 59.104 55.000 7.97 0.00 35.27 3.02
118 119 0.460459 GGTCGGCCTCTTAGTTCAGC 60.460 60.000 0.00 0.00 0.00 4.26
119 120 0.460459 GTCGGCCTCTTAGTTCAGCC 60.460 60.000 0.00 0.00 40.33 4.85
120 121 1.153349 CGGCCTCTTAGTTCAGCCC 60.153 63.158 0.00 0.00 40.65 5.19
121 122 1.617947 CGGCCTCTTAGTTCAGCCCT 61.618 60.000 0.00 0.00 40.65 5.19
122 123 1.497161 GGCCTCTTAGTTCAGCCCTA 58.503 55.000 0.00 0.00 37.66 3.53
123 124 2.050918 GGCCTCTTAGTTCAGCCCTAT 58.949 52.381 0.00 0.00 37.66 2.57
124 125 2.439880 GGCCTCTTAGTTCAGCCCTATT 59.560 50.000 0.00 0.00 37.66 1.73
125 126 3.117851 GGCCTCTTAGTTCAGCCCTATTT 60.118 47.826 0.00 0.00 37.66 1.40
126 127 3.879892 GCCTCTTAGTTCAGCCCTATTTG 59.120 47.826 0.00 0.00 0.00 2.32
127 128 4.384208 GCCTCTTAGTTCAGCCCTATTTGA 60.384 45.833 0.00 0.00 0.00 2.69
128 129 5.745227 CCTCTTAGTTCAGCCCTATTTGAA 58.255 41.667 0.00 0.00 0.00 2.69
129 130 6.360618 CCTCTTAGTTCAGCCCTATTTGAAT 58.639 40.000 0.00 0.00 35.91 2.57
130 131 6.830838 CCTCTTAGTTCAGCCCTATTTGAATT 59.169 38.462 0.00 0.00 35.91 2.17
131 132 7.201767 CCTCTTAGTTCAGCCCTATTTGAATTG 60.202 40.741 0.00 0.00 35.91 2.32
132 133 4.725790 AGTTCAGCCCTATTTGAATTGC 57.274 40.909 0.00 0.00 35.91 3.56
133 134 4.088634 AGTTCAGCCCTATTTGAATTGCA 58.911 39.130 0.00 0.00 35.91 4.08
134 135 4.159135 AGTTCAGCCCTATTTGAATTGCAG 59.841 41.667 0.00 0.00 35.91 4.41
135 136 3.700538 TCAGCCCTATTTGAATTGCAGT 58.299 40.909 0.00 0.00 0.00 4.40
136 137 3.444742 TCAGCCCTATTTGAATTGCAGTG 59.555 43.478 0.00 0.00 0.00 3.66
137 138 3.194116 CAGCCCTATTTGAATTGCAGTGT 59.806 43.478 0.00 0.00 0.00 3.55
138 139 3.834231 AGCCCTATTTGAATTGCAGTGTT 59.166 39.130 0.00 0.00 0.00 3.32
139 140 4.284234 AGCCCTATTTGAATTGCAGTGTTT 59.716 37.500 0.00 0.00 0.00 2.83
140 141 4.627035 GCCCTATTTGAATTGCAGTGTTTC 59.373 41.667 0.00 0.00 0.00 2.78
141 142 5.782047 CCCTATTTGAATTGCAGTGTTTCA 58.218 37.500 0.00 0.00 0.00 2.69
142 143 5.865552 CCCTATTTGAATTGCAGTGTTTCAG 59.134 40.000 0.00 0.00 31.54 3.02
143 144 5.346822 CCTATTTGAATTGCAGTGTTTCAGC 59.653 40.000 0.00 0.00 31.54 4.26
144 145 4.389890 TTTGAATTGCAGTGTTTCAGCT 57.610 36.364 0.00 0.00 31.54 4.24
145 146 4.389890 TTGAATTGCAGTGTTTCAGCTT 57.610 36.364 0.00 0.00 31.54 3.74
146 147 3.968649 TGAATTGCAGTGTTTCAGCTTC 58.031 40.909 0.00 0.00 0.00 3.86
147 148 3.243501 TGAATTGCAGTGTTTCAGCTTCC 60.244 43.478 0.00 0.00 0.00 3.46
148 149 1.761449 TTGCAGTGTTTCAGCTTCCA 58.239 45.000 0.00 0.00 0.00 3.53
149 150 1.985473 TGCAGTGTTTCAGCTTCCAT 58.015 45.000 0.00 0.00 0.00 3.41
150 151 1.610038 TGCAGTGTTTCAGCTTCCATG 59.390 47.619 0.00 0.00 0.00 3.66
151 152 1.668047 GCAGTGTTTCAGCTTCCATGC 60.668 52.381 0.00 0.00 0.00 4.06
152 153 1.610038 CAGTGTTTCAGCTTCCATGCA 59.390 47.619 0.00 0.00 34.99 3.96
153 154 1.610522 AGTGTTTCAGCTTCCATGCAC 59.389 47.619 0.00 0.00 34.99 4.57
154 155 1.610522 GTGTTTCAGCTTCCATGCACT 59.389 47.619 0.00 0.00 34.99 4.40
155 156 2.035066 GTGTTTCAGCTTCCATGCACTT 59.965 45.455 0.00 0.00 34.99 3.16
156 157 2.294233 TGTTTCAGCTTCCATGCACTTC 59.706 45.455 0.00 0.00 34.99 3.01
157 158 2.555757 GTTTCAGCTTCCATGCACTTCT 59.444 45.455 0.00 0.00 34.99 2.85
158 159 2.574006 TCAGCTTCCATGCACTTCTT 57.426 45.000 0.00 0.00 34.99 2.52
159 160 2.867624 TCAGCTTCCATGCACTTCTTT 58.132 42.857 0.00 0.00 34.99 2.52
160 161 2.555325 TCAGCTTCCATGCACTTCTTTG 59.445 45.455 0.00 0.00 34.99 2.77
161 162 1.271656 AGCTTCCATGCACTTCTTTGC 59.728 47.619 0.00 0.00 43.31 3.68
172 173 5.999483 GCACTTCTTTGCACTAATTTAGC 57.001 39.130 3.28 0.00 42.49 3.09
173 174 5.460646 GCACTTCTTTGCACTAATTTAGCA 58.539 37.500 3.28 0.00 42.49 3.49
174 175 5.570589 GCACTTCTTTGCACTAATTTAGCAG 59.429 40.000 3.28 0.00 42.49 4.24
175 176 5.570589 CACTTCTTTGCACTAATTTAGCAGC 59.429 40.000 12.19 12.19 39.72 5.25
176 177 4.340894 TCTTTGCACTAATTTAGCAGCG 57.659 40.909 13.50 4.02 39.72 5.18
177 178 3.126858 TCTTTGCACTAATTTAGCAGCGG 59.873 43.478 13.50 8.55 39.72 5.52
310 311 1.095228 AATGGGCAGTAATCGGTGCG 61.095 55.000 0.00 0.00 40.82 5.34
329 330 0.598158 GTGCATGTTGCTGTTGGTGG 60.598 55.000 0.00 0.00 45.31 4.61
330 331 1.665599 GCATGTTGCTGTTGGTGGC 60.666 57.895 0.00 0.00 40.96 5.01
331 332 2.043625 CATGTTGCTGTTGGTGGCT 58.956 52.632 0.00 0.00 0.00 4.75
332 333 0.390124 CATGTTGCTGTTGGTGGCTT 59.610 50.000 0.00 0.00 0.00 4.35
335 336 0.459489 GTTGCTGTTGGTGGCTTTGA 59.541 50.000 0.00 0.00 0.00 2.69
336 337 1.069049 GTTGCTGTTGGTGGCTTTGAT 59.931 47.619 0.00 0.00 0.00 2.57
337 338 0.675083 TGCTGTTGGTGGCTTTGATG 59.325 50.000 0.00 0.00 0.00 3.07
338 339 0.668401 GCTGTTGGTGGCTTTGATGC 60.668 55.000 0.00 0.00 0.00 3.91
340 341 0.961019 TGTTGGTGGCTTTGATGCTC 59.039 50.000 0.00 0.00 0.00 4.26
341 342 0.961019 GTTGGTGGCTTTGATGCTCA 59.039 50.000 0.00 0.00 0.00 4.26
342 343 1.547372 GTTGGTGGCTTTGATGCTCAT 59.453 47.619 0.00 0.00 0.00 2.90
343 344 2.754552 GTTGGTGGCTTTGATGCTCATA 59.245 45.455 0.00 0.00 0.00 2.15
344 345 3.301794 TGGTGGCTTTGATGCTCATAT 57.698 42.857 0.00 0.00 0.00 1.78
345 346 3.216800 TGGTGGCTTTGATGCTCATATC 58.783 45.455 0.00 0.00 0.00 1.63
346 347 3.216800 GGTGGCTTTGATGCTCATATCA 58.783 45.455 0.00 0.00 35.38 2.15
347 348 3.633525 GGTGGCTTTGATGCTCATATCAA 59.366 43.478 0.00 0.00 43.32 2.57
348 349 4.498682 GGTGGCTTTGATGCTCATATCAAC 60.499 45.833 0.00 0.00 44.33 3.18
349 350 3.313249 TGGCTTTGATGCTCATATCAACG 59.687 43.478 0.00 0.00 44.33 4.10
351 352 4.541085 CTTTGATGCTCATATCAACGCA 57.459 40.909 0.00 0.00 44.33 5.24
365 366 1.215655 AACGCACACGCTCTTGTCTC 61.216 55.000 0.00 0.00 45.53 3.36
456 462 0.991920 AGGGATCCGGAAAAGCTGAA 59.008 50.000 9.01 0.00 0.00 3.02
457 463 1.354368 AGGGATCCGGAAAAGCTGAAA 59.646 47.619 9.01 0.00 0.00 2.69
458 464 2.024941 AGGGATCCGGAAAAGCTGAAAT 60.025 45.455 9.01 0.00 0.00 2.17
459 465 2.099756 GGGATCCGGAAAAGCTGAAATG 59.900 50.000 9.01 0.00 0.00 2.32
460 466 2.480244 GGATCCGGAAAAGCTGAAATGC 60.480 50.000 9.01 0.00 0.00 3.56
461 467 0.887933 TCCGGAAAAGCTGAAATGCC 59.112 50.000 0.00 0.00 0.00 4.40
462 468 0.602562 CCGGAAAAGCTGAAATGCCA 59.397 50.000 0.00 0.00 0.00 4.92
463 469 1.000731 CCGGAAAAGCTGAAATGCCAA 59.999 47.619 0.00 0.00 0.00 4.52
480 486 0.657312 CAATGCCACGCACGTCATAT 59.343 50.000 0.00 0.00 43.04 1.78
481 487 0.657312 AATGCCACGCACGTCATATG 59.343 50.000 0.00 0.00 43.04 1.78
504 510 1.851658 ACATGCGTTTTCAGTTTGGC 58.148 45.000 0.00 0.00 0.00 4.52
507 513 0.814457 TGCGTTTTCAGTTTGGCACT 59.186 45.000 0.00 0.00 35.35 4.40
520 526 6.280643 CAGTTTGGCACTGCTATATGTACTA 58.719 40.000 0.00 0.00 46.70 1.82
530 536 7.757173 CACTGCTATATGTACTAATCGAGCATT 59.243 37.037 7.76 1.98 37.98 3.56
543 558 1.318251 GAGCATTCGACGTGCAAAAC 58.682 50.000 20.36 8.11 44.87 2.43
544 559 0.660488 AGCATTCGACGTGCAAAACA 59.340 45.000 20.36 0.00 44.87 2.83
571 586 3.740764 GCTGATGAGCAGTTTAGAGGGAG 60.741 52.174 0.00 0.00 46.62 4.30
573 588 1.573108 TGAGCAGTTTAGAGGGAGGG 58.427 55.000 0.00 0.00 0.00 4.30
579 828 2.688958 CAGTTTAGAGGGAGGGAGTACG 59.311 54.545 0.00 0.00 0.00 3.67
603 852 2.352388 GTACTAATGCCCGTTGCTCAA 58.648 47.619 0.00 0.00 42.00 3.02
604 853 1.165270 ACTAATGCCCGTTGCTCAAC 58.835 50.000 2.80 2.80 42.00 3.18
605 854 0.451783 CTAATGCCCGTTGCTCAACC 59.548 55.000 7.12 0.00 42.00 3.77
606 855 0.037590 TAATGCCCGTTGCTCAACCT 59.962 50.000 7.12 0.00 42.00 3.50
607 856 0.037590 AATGCCCGTTGCTCAACCTA 59.962 50.000 7.12 0.00 42.00 3.08
609 858 1.745489 GCCCGTTGCTCAACCTAGG 60.745 63.158 7.41 7.41 38.03 3.02
610 859 1.745489 CCCGTTGCTCAACCTAGGC 60.745 63.158 9.30 0.00 38.03 3.93
612 861 2.740714 CGTTGCTCAACCTAGGCGC 61.741 63.158 9.30 0.00 38.03 6.53
613 862 2.434185 TTGCTCAACCTAGGCGCG 60.434 61.111 9.30 0.00 0.00 6.86
619 868 4.814294 AACCTAGGCGCGCGGAAG 62.814 66.667 33.06 21.39 0.00 3.46
710 992 0.465460 TGGACTTTGGTGCACTCCAC 60.465 55.000 18.12 2.50 43.90 4.02
713 995 1.103398 ACTTTGGTGCACTCCACAGC 61.103 55.000 17.98 0.00 46.50 4.40
790 1073 6.809196 CACGTCTATATATTTCAAGCCTCTCC 59.191 42.308 0.00 0.00 0.00 3.71
829 1115 2.167487 ACCTAGCTAGCTTTGCTCTCAC 59.833 50.000 24.88 0.00 40.44 3.51
832 1118 1.700600 GCTAGCTTTGCTCTCACGGC 61.701 60.000 7.70 0.00 40.44 5.68
842 1128 0.387202 CTCTCACGGCCTCACCATAG 59.613 60.000 0.00 0.00 39.03 2.23
874 1160 2.189594 TGCATGTGAAGAAGGTGAGG 57.810 50.000 0.00 0.00 0.00 3.86
876 1162 1.457346 CATGTGAAGAAGGTGAGGGC 58.543 55.000 0.00 0.00 0.00 5.19
929 1219 2.167861 GCTAGCTAGGCACACACGC 61.168 63.158 22.10 1.41 0.00 5.34
930 1220 1.215382 CTAGCTAGGCACACACGCA 59.785 57.895 13.32 0.00 0.00 5.24
932 1222 2.812542 TAGCTAGGCACACACGCACG 62.813 60.000 0.00 0.00 0.00 5.34
949 1241 2.851386 GCACGCACAGATAGAGTACTCG 60.851 54.545 17.07 5.27 34.09 4.18
973 1265 0.993251 CATTGTCACACAAGCACGCG 60.993 55.000 3.53 3.53 41.94 6.01
990 1282 2.181777 GCACGCAGGAGATCGACA 59.818 61.111 0.00 0.00 0.00 4.35
995 1287 0.383590 CGCAGGAGATCGACACTGAT 59.616 55.000 10.52 0.00 32.86 2.90
1236 1528 2.480102 GTGCGCGTCATCATGCAA 59.520 55.556 8.43 0.00 39.34 4.08
1250 1542 1.947597 ATGCAAATCAACGCCGGCAT 61.948 50.000 28.98 8.91 37.17 4.40
1280 1575 2.128367 GCTCTAGCTTTCGAGTAGCC 57.872 55.000 15.48 0.18 39.47 3.93
1285 1580 1.848652 AGCTTTCGAGTAGCCACCTA 58.151 50.000 15.48 0.00 39.47 3.08
1290 1585 1.103803 TCGAGTAGCCACCTAGCTTG 58.896 55.000 0.00 0.00 41.41 4.01
1565 1862 2.383527 GCTTCAAGGTGAGTCGCCG 61.384 63.158 16.97 4.21 39.30 6.46
1566 1863 1.289066 CTTCAAGGTGAGTCGCCGA 59.711 57.895 16.97 6.65 39.30 5.54
1567 1864 1.006571 TTCAAGGTGAGTCGCCGAC 60.007 57.895 16.97 9.71 39.30 4.79
1568 1865 2.742710 TTCAAGGTGAGTCGCCGACG 62.743 60.000 16.97 9.55 39.30 5.12
1648 1945 4.039092 CCCCCTGTCCCTGTGCTG 62.039 72.222 0.00 0.00 0.00 4.41
1649 1946 4.729918 CCCCTGTCCCTGTGCTGC 62.730 72.222 0.00 0.00 0.00 5.25
1650 1947 3.957586 CCCTGTCCCTGTGCTGCA 61.958 66.667 0.00 0.00 0.00 4.41
1794 2099 0.247460 TCTCTGTGCATCCCTGTTCG 59.753 55.000 0.00 0.00 0.00 3.95
1815 2128 7.584847 TGTTCGTTTGAGATTTTGAATTCGTAC 59.415 33.333 0.04 0.00 0.00 3.67
1818 2131 9.146984 TCGTTTGAGATTTTGAATTCGTACTAT 57.853 29.630 0.04 0.00 0.00 2.12
1903 2223 2.355126 CCGGCGAGATGGACGATG 60.355 66.667 9.30 0.00 42.31 3.84
1915 2235 4.479993 ACGATGGCTGGCTGGAGC 62.480 66.667 2.00 0.00 38.34 4.70
2233 2555 0.108615 CTCCCTCTACAAGGTGCGTG 60.109 60.000 0.00 0.00 44.56 5.34
2239 2561 1.904852 CTACAAGGTGCGTGCTGCTG 61.905 60.000 0.00 0.00 46.63 4.41
2271 2631 3.811722 ACATATGTGTGTTGCGTTGAG 57.188 42.857 7.78 0.00 37.14 3.02
2571 2943 7.473366 CATGTAACTACTACACCACTACTCTG 58.527 42.308 0.00 0.00 43.35 3.35
2594 2966 4.318333 GCTGCATACATATTCAGACACACG 60.318 45.833 3.12 0.00 30.04 4.49
2799 3184 2.038952 CACCAGATGTCTGAACTCCCAA 59.961 50.000 11.47 0.00 46.59 4.12
2802 3187 3.244700 CCAGATGTCTGAACTCCCAAACT 60.245 47.826 11.47 0.00 46.59 2.66
2826 3211 0.322277 CCAGCACCACAGATTCAGCT 60.322 55.000 0.00 0.00 0.00 4.24
2834 3219 3.008813 ACCACAGATTCAGCTGACAAGAT 59.991 43.478 18.03 7.18 39.20 2.40
2835 3220 4.223700 ACCACAGATTCAGCTGACAAGATA 59.776 41.667 18.03 0.00 39.20 1.98
2836 3221 4.809958 CCACAGATTCAGCTGACAAGATAG 59.190 45.833 18.03 6.24 39.20 2.08
2889 3274 8.079211 ACAAGAGTAGCACAGATATAAAGGAA 57.921 34.615 0.00 0.00 0.00 3.36
2890 3275 7.982354 ACAAGAGTAGCACAGATATAAAGGAAC 59.018 37.037 0.00 0.00 0.00 3.62
2956 3341 5.178797 TCCCAGTGTAGTTACTACGTAGTC 58.821 45.833 30.53 17.75 43.93 2.59
3009 3394 5.964958 ACCAGACCAAATTGTTCATGTAG 57.035 39.130 0.00 0.00 0.00 2.74
3011 3396 6.539173 ACCAGACCAAATTGTTCATGTAGTA 58.461 36.000 0.00 0.00 0.00 1.82
3012 3397 7.001674 ACCAGACCAAATTGTTCATGTAGTAA 58.998 34.615 0.00 0.00 0.00 2.24
3015 3400 8.950210 CAGACCAAATTGTTCATGTAGTAATCT 58.050 33.333 0.00 0.00 0.00 2.40
3016 3401 9.520515 AGACCAAATTGTTCATGTAGTAATCTT 57.479 29.630 0.00 0.00 0.00 2.40
3017 3402 9.774742 GACCAAATTGTTCATGTAGTAATCTTC 57.225 33.333 0.00 0.00 0.00 2.87
3042 3427 8.203485 TCAAAACTAAACAGCAAGGATGAATTT 58.797 29.630 0.00 0.00 0.00 1.82
3059 3444 4.573201 TGAATTTGTTATACGCCTGCCTAC 59.427 41.667 0.00 0.00 0.00 3.18
3083 3468 0.450983 GATGCTTTGCAGAGGACAGC 59.549 55.000 6.36 0.00 43.65 4.40
3101 3486 1.901650 GCAACTCTTTCGAGGGTGCG 61.902 60.000 4.58 0.00 40.35 5.34
3209 3594 1.611673 CCCAGTAGACCTGCAAAGGTG 60.612 57.143 1.69 0.00 43.24 4.00
3282 3667 5.178623 GCAAAGCGCATACACCTATTATACA 59.821 40.000 11.47 0.00 41.79 2.29
3480 4156 3.386726 TCAAGTTATATAGCAGGCACCGT 59.613 43.478 0.00 0.00 0.00 4.83
3567 4243 6.473778 CCACTGTACATATCTTGAAGACTTCG 59.526 42.308 10.56 0.00 0.00 3.79
3570 4246 8.470805 ACTGTACATATCTTGAAGACTTCGATT 58.529 33.333 10.56 2.67 0.00 3.34
3596 4272 5.497474 AGGCTATGTGTCCGTTTTTCTAAT 58.503 37.500 0.00 0.00 0.00 1.73
3597 4273 5.944007 AGGCTATGTGTCCGTTTTTCTAATT 59.056 36.000 0.00 0.00 0.00 1.40
3598 4274 6.093633 AGGCTATGTGTCCGTTTTTCTAATTC 59.906 38.462 0.00 0.00 0.00 2.17
3599 4275 6.093633 GGCTATGTGTCCGTTTTTCTAATTCT 59.906 38.462 0.00 0.00 0.00 2.40
3600 4276 7.279313 GGCTATGTGTCCGTTTTTCTAATTCTA 59.721 37.037 0.00 0.00 0.00 2.10
3601 4277 8.662141 GCTATGTGTCCGTTTTTCTAATTCTAA 58.338 33.333 0.00 0.00 0.00 2.10
3602 4278 9.968743 CTATGTGTCCGTTTTTCTAATTCTAAC 57.031 33.333 0.00 0.00 0.00 2.34
3603 4279 7.193377 TGTGTCCGTTTTTCTAATTCTAACC 57.807 36.000 0.00 0.00 0.00 2.85
3604 4280 6.766944 TGTGTCCGTTTTTCTAATTCTAACCA 59.233 34.615 0.00 0.00 0.00 3.67
3605 4281 7.446013 TGTGTCCGTTTTTCTAATTCTAACCAT 59.554 33.333 0.00 0.00 0.00 3.55
3626 4303 9.566432 AACCATTTAAACAAGGCAATGATTTAA 57.434 25.926 0.00 3.25 0.00 1.52
3655 4332 1.274167 CAGCCTTCAACACCATGCATT 59.726 47.619 0.00 0.00 0.00 3.56
3656 4333 1.274167 AGCCTTCAACACCATGCATTG 59.726 47.619 0.00 0.00 0.00 2.82
3671 4348 3.354467 TGCATTGCATGAACCATCACTA 58.646 40.909 7.38 0.00 38.69 2.74
3746 4423 2.258748 GAGCTGTGTTAGGCTCCCCC 62.259 65.000 0.00 0.00 46.32 5.40
3763 4440 1.152567 CCCACCAAAGTCCCAGCAA 60.153 57.895 0.00 0.00 0.00 3.91
3768 4445 1.242076 CCAAAGTCCCAGCAAGACAG 58.758 55.000 3.98 0.00 36.68 3.51
3785 4462 6.566187 GCAAGACAGCAGAAGCATTATGATAG 60.566 42.308 0.00 0.00 40.36 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.681848 CCATCTTCTTCCACATGCAGAC 59.318 50.000 0.00 0.00 0.00 3.51
1 2 2.942752 GCCATCTTCTTCCACATGCAGA 60.943 50.000 0.00 0.00 0.00 4.26
2 3 1.404391 GCCATCTTCTTCCACATGCAG 59.596 52.381 0.00 0.00 0.00 4.41
4 5 0.743097 GGCCATCTTCTTCCACATGC 59.257 55.000 0.00 0.00 0.00 4.06
5 6 2.295885 GAGGCCATCTTCTTCCACATG 58.704 52.381 5.01 0.00 0.00 3.21
7 8 0.620556 GGAGGCCATCTTCTTCCACA 59.379 55.000 5.01 0.00 0.00 4.17
9 10 1.207791 GAGGAGGCCATCTTCTTCCA 58.792 55.000 5.01 0.00 29.49 3.53
10 11 0.105778 CGAGGAGGCCATCTTCTTCC 59.894 60.000 5.01 0.00 29.49 3.46
11 12 0.531753 GCGAGGAGGCCATCTTCTTC 60.532 60.000 5.01 0.00 29.49 2.87
12 13 0.980231 AGCGAGGAGGCCATCTTCTT 60.980 55.000 5.01 0.00 29.49 2.52
13 14 1.382420 AGCGAGGAGGCCATCTTCT 60.382 57.895 5.01 0.62 32.88 2.85
14 15 1.068921 GAGCGAGGAGGCCATCTTC 59.931 63.158 5.01 4.87 0.00 2.87
15 16 2.790791 CGAGCGAGGAGGCCATCTT 61.791 63.158 5.01 0.00 0.00 2.40
16 17 3.222855 CGAGCGAGGAGGCCATCT 61.223 66.667 5.01 0.31 0.00 2.90
17 18 3.492311 GACGAGCGAGGAGGCCATC 62.492 68.421 5.01 0.00 0.00 3.51
18 19 3.532155 GACGAGCGAGGAGGCCAT 61.532 66.667 5.01 0.00 0.00 4.40
22 23 0.956410 ATATCCGACGAGCGAGGAGG 60.956 60.000 14.37 5.21 44.57 4.30
23 24 1.723220 TATATCCGACGAGCGAGGAG 58.277 55.000 14.37 0.00 44.57 3.69
24 25 2.174363 TTATATCCGACGAGCGAGGA 57.826 50.000 12.29 12.29 44.57 3.71
25 26 2.983402 TTTATATCCGACGAGCGAGG 57.017 50.000 0.00 0.00 44.57 4.63
26 27 4.079665 TGATTTATATCCGACGAGCGAG 57.920 45.455 0.00 0.00 44.57 5.03
27 28 3.749609 TCTGATTTATATCCGACGAGCGA 59.250 43.478 0.00 0.00 44.57 4.93
28 29 4.079665 TCTGATTTATATCCGACGAGCG 57.920 45.455 0.00 0.00 40.47 5.03
29 30 4.800993 CCATCTGATTTATATCCGACGAGC 59.199 45.833 0.00 0.00 28.50 5.03
30 31 5.802451 CACCATCTGATTTATATCCGACGAG 59.198 44.000 0.00 0.00 28.50 4.18
31 32 5.475564 TCACCATCTGATTTATATCCGACGA 59.524 40.000 0.00 0.00 28.50 4.20
32 33 5.709966 TCACCATCTGATTTATATCCGACG 58.290 41.667 0.00 0.00 28.50 5.12
33 34 7.378966 TCTTCACCATCTGATTTATATCCGAC 58.621 38.462 0.00 0.00 28.50 4.79
34 35 7.539034 TCTTCACCATCTGATTTATATCCGA 57.461 36.000 0.00 0.00 0.00 4.55
35 36 8.607441 TTTCTTCACCATCTGATTTATATCCG 57.393 34.615 0.00 0.00 0.00 4.18
59 60 8.477419 TGATTTTCTATTCCAGTCACCTTTTT 57.523 30.769 0.00 0.00 0.00 1.94
60 61 7.725844 ACTGATTTTCTATTCCAGTCACCTTTT 59.274 33.333 0.00 0.00 33.27 2.27
61 62 7.234355 ACTGATTTTCTATTCCAGTCACCTTT 58.766 34.615 0.00 0.00 33.27 3.11
62 63 6.784031 ACTGATTTTCTATTCCAGTCACCTT 58.216 36.000 0.00 0.00 33.27 3.50
63 64 6.380079 ACTGATTTTCTATTCCAGTCACCT 57.620 37.500 0.00 0.00 33.27 4.00
67 68 6.334202 AGTCGACTGATTTTCTATTCCAGTC 58.666 40.000 19.30 0.00 46.00 3.51
68 69 6.287589 AGTCGACTGATTTTCTATTCCAGT 57.712 37.500 19.30 0.00 40.37 4.00
69 70 7.759886 TGTTAGTCGACTGATTTTCTATTCCAG 59.240 37.037 28.12 0.00 0.00 3.86
70 71 7.608153 TGTTAGTCGACTGATTTTCTATTCCA 58.392 34.615 28.12 7.06 0.00 3.53
71 72 8.475331 TTGTTAGTCGACTGATTTTCTATTCC 57.525 34.615 28.12 4.46 0.00 3.01
74 75 8.883731 CCATTTGTTAGTCGACTGATTTTCTAT 58.116 33.333 28.12 8.11 0.00 1.98
75 76 7.876068 ACCATTTGTTAGTCGACTGATTTTCTA 59.124 33.333 28.12 1.88 0.00 2.10
76 77 6.710744 ACCATTTGTTAGTCGACTGATTTTCT 59.289 34.615 28.12 1.25 0.00 2.52
77 78 6.899114 ACCATTTGTTAGTCGACTGATTTTC 58.101 36.000 28.12 8.45 0.00 2.29
78 79 6.877611 ACCATTTGTTAGTCGACTGATTTT 57.122 33.333 28.12 2.87 0.00 1.82
79 80 6.481954 GACCATTTGTTAGTCGACTGATTT 57.518 37.500 28.12 3.68 0.00 2.17
88 89 2.007608 GAGGCCGACCATTTGTTAGTC 58.992 52.381 0.00 0.00 39.06 2.59
89 90 1.628846 AGAGGCCGACCATTTGTTAGT 59.371 47.619 0.00 0.00 39.06 2.24
90 91 2.403252 AGAGGCCGACCATTTGTTAG 57.597 50.000 0.00 0.00 39.06 2.34
91 92 2.871096 AAGAGGCCGACCATTTGTTA 57.129 45.000 0.00 0.00 39.06 2.41
92 93 2.039879 ACTAAGAGGCCGACCATTTGTT 59.960 45.455 0.00 0.00 39.06 2.83
93 94 1.628846 ACTAAGAGGCCGACCATTTGT 59.371 47.619 0.00 0.00 39.06 2.83
94 95 2.403252 ACTAAGAGGCCGACCATTTG 57.597 50.000 0.00 0.00 39.06 2.32
95 96 2.304761 TGAACTAAGAGGCCGACCATTT 59.695 45.455 0.00 0.00 39.06 2.32
96 97 1.906574 TGAACTAAGAGGCCGACCATT 59.093 47.619 0.00 0.00 39.06 3.16
97 98 1.482593 CTGAACTAAGAGGCCGACCAT 59.517 52.381 0.00 0.00 39.06 3.55
98 99 0.895530 CTGAACTAAGAGGCCGACCA 59.104 55.000 0.00 0.00 39.06 4.02
99 100 0.460459 GCTGAACTAAGAGGCCGACC 60.460 60.000 0.00 0.00 0.00 4.79
100 101 0.460459 GGCTGAACTAAGAGGCCGAC 60.460 60.000 0.00 0.00 33.30 4.79
101 102 1.614241 GGGCTGAACTAAGAGGCCGA 61.614 60.000 0.00 0.00 44.23 5.54
102 103 1.153349 GGGCTGAACTAAGAGGCCG 60.153 63.158 0.00 0.00 44.23 6.13
103 104 4.966123 GGGCTGAACTAAGAGGCC 57.034 61.111 0.00 0.00 46.57 5.19
104 105 3.847671 AATAGGGCTGAACTAAGAGGC 57.152 47.619 0.00 0.00 0.00 4.70
105 106 5.359194 TCAAATAGGGCTGAACTAAGAGG 57.641 43.478 0.00 0.00 0.00 3.69
106 107 7.680588 GCAATTCAAATAGGGCTGAACTAAGAG 60.681 40.741 0.00 0.00 34.52 2.85
107 108 6.095440 GCAATTCAAATAGGGCTGAACTAAGA 59.905 38.462 0.00 0.00 34.52 2.10
108 109 6.127647 TGCAATTCAAATAGGGCTGAACTAAG 60.128 38.462 0.00 0.00 34.52 2.18
109 110 5.714333 TGCAATTCAAATAGGGCTGAACTAA 59.286 36.000 0.00 0.00 34.52 2.24
110 111 5.260424 TGCAATTCAAATAGGGCTGAACTA 58.740 37.500 0.00 0.00 34.52 2.24
111 112 4.088634 TGCAATTCAAATAGGGCTGAACT 58.911 39.130 0.00 0.00 34.52 3.01
112 113 4.082026 ACTGCAATTCAAATAGGGCTGAAC 60.082 41.667 0.00 0.00 34.52 3.18
113 114 4.082081 CACTGCAATTCAAATAGGGCTGAA 60.082 41.667 0.00 0.00 36.08 3.02
114 115 3.444742 CACTGCAATTCAAATAGGGCTGA 59.555 43.478 0.00 0.00 0.00 4.26
115 116 3.194116 ACACTGCAATTCAAATAGGGCTG 59.806 43.478 0.00 0.00 0.00 4.85
116 117 3.434309 ACACTGCAATTCAAATAGGGCT 58.566 40.909 0.00 0.00 0.00 5.19
117 118 3.874392 ACACTGCAATTCAAATAGGGC 57.126 42.857 0.00 0.00 0.00 5.19
118 119 5.782047 TGAAACACTGCAATTCAAATAGGG 58.218 37.500 0.00 0.00 30.60 3.53
119 120 5.346822 GCTGAAACACTGCAATTCAAATAGG 59.653 40.000 0.00 0.00 41.89 2.57
120 121 6.154445 AGCTGAAACACTGCAATTCAAATAG 58.846 36.000 0.00 0.00 44.13 1.73
121 122 6.088016 AGCTGAAACACTGCAATTCAAATA 57.912 33.333 0.00 0.00 44.13 1.40
122 123 4.952460 AGCTGAAACACTGCAATTCAAAT 58.048 34.783 0.00 0.00 44.13 2.32
123 124 4.389890 AGCTGAAACACTGCAATTCAAA 57.610 36.364 0.00 0.00 44.13 2.69
124 125 4.362279 GAAGCTGAAACACTGCAATTCAA 58.638 39.130 0.00 0.00 44.13 2.69
125 126 3.243501 GGAAGCTGAAACACTGCAATTCA 60.244 43.478 0.00 0.00 44.13 2.57
126 127 3.243501 TGGAAGCTGAAACACTGCAATTC 60.244 43.478 0.00 0.00 44.13 2.17
127 128 2.694628 TGGAAGCTGAAACACTGCAATT 59.305 40.909 0.00 0.00 44.13 2.32
128 129 2.309613 TGGAAGCTGAAACACTGCAAT 58.690 42.857 0.00 0.00 44.13 3.56
129 130 1.761449 TGGAAGCTGAAACACTGCAA 58.239 45.000 0.00 0.00 44.13 4.08
130 131 1.610038 CATGGAAGCTGAAACACTGCA 59.390 47.619 0.00 0.00 44.13 4.41
131 132 1.668047 GCATGGAAGCTGAAACACTGC 60.668 52.381 0.00 0.00 42.46 4.40
132 133 1.610038 TGCATGGAAGCTGAAACACTG 59.390 47.619 0.00 0.00 34.99 3.66
133 134 1.610522 GTGCATGGAAGCTGAAACACT 59.389 47.619 0.00 0.00 34.99 3.55
134 135 1.610522 AGTGCATGGAAGCTGAAACAC 59.389 47.619 0.00 0.00 34.99 3.32
135 136 1.985473 AGTGCATGGAAGCTGAAACA 58.015 45.000 0.00 0.00 34.99 2.83
136 137 2.555757 AGAAGTGCATGGAAGCTGAAAC 59.444 45.455 0.00 0.00 34.99 2.78
137 138 2.867624 AGAAGTGCATGGAAGCTGAAA 58.132 42.857 0.00 0.00 34.99 2.69
138 139 2.574006 AGAAGTGCATGGAAGCTGAA 57.426 45.000 0.00 0.00 34.99 3.02
139 140 2.555325 CAAAGAAGTGCATGGAAGCTGA 59.445 45.455 0.00 0.00 34.99 4.26
140 141 2.925306 GCAAAGAAGTGCATGGAAGCTG 60.925 50.000 0.00 0.00 44.29 4.24
141 142 1.271656 GCAAAGAAGTGCATGGAAGCT 59.728 47.619 0.00 0.00 44.29 3.74
142 143 1.706443 GCAAAGAAGTGCATGGAAGC 58.294 50.000 0.00 0.00 44.29 3.86
150 151 5.460646 TGCTAAATTAGTGCAAAGAAGTGC 58.539 37.500 1.68 0.00 45.15 4.40
151 152 5.570589 GCTGCTAAATTAGTGCAAAGAAGTG 59.429 40.000 12.53 0.00 36.22 3.16
152 153 5.617751 CGCTGCTAAATTAGTGCAAAGAAGT 60.618 40.000 15.79 0.00 36.22 3.01
153 154 4.790140 CGCTGCTAAATTAGTGCAAAGAAG 59.210 41.667 15.79 0.00 36.22 2.85
154 155 4.379394 CCGCTGCTAAATTAGTGCAAAGAA 60.379 41.667 15.79 0.00 36.22 2.52
155 156 3.126858 CCGCTGCTAAATTAGTGCAAAGA 59.873 43.478 15.79 0.00 36.22 2.52
156 157 3.119849 ACCGCTGCTAAATTAGTGCAAAG 60.120 43.478 15.79 9.07 36.22 2.77
157 158 2.817258 ACCGCTGCTAAATTAGTGCAAA 59.183 40.909 15.79 0.00 36.22 3.68
158 159 2.161410 CACCGCTGCTAAATTAGTGCAA 59.839 45.455 15.79 0.00 36.22 4.08
159 160 1.737236 CACCGCTGCTAAATTAGTGCA 59.263 47.619 15.79 4.49 35.30 4.57
160 161 1.531883 GCACCGCTGCTAAATTAGTGC 60.532 52.381 1.68 6.08 41.86 4.40
161 162 1.064060 GGCACCGCTGCTAAATTAGTG 59.936 52.381 2.19 0.00 43.66 2.74
162 163 1.065418 AGGCACCGCTGCTAAATTAGT 60.065 47.619 2.19 0.00 43.66 2.24
163 164 1.668419 AGGCACCGCTGCTAAATTAG 58.332 50.000 2.19 0.00 43.66 1.73
164 165 1.742831 CAAGGCACCGCTGCTAAATTA 59.257 47.619 2.19 0.00 43.66 1.40
165 166 0.527565 CAAGGCACCGCTGCTAAATT 59.472 50.000 2.19 0.00 43.66 1.82
166 167 1.315257 CCAAGGCACCGCTGCTAAAT 61.315 55.000 2.19 0.00 43.66 1.40
167 168 1.971167 CCAAGGCACCGCTGCTAAA 60.971 57.895 2.19 0.00 43.66 1.85
168 169 2.359850 CCAAGGCACCGCTGCTAA 60.360 61.111 2.19 0.00 43.66 3.09
176 177 3.440415 GCTTACGGCCAAGGCACC 61.440 66.667 13.87 0.00 44.11 5.01
187 188 3.705043 AGTATCCGTTACAGGCTTACG 57.295 47.619 6.60 6.60 32.87 3.18
289 290 1.065551 GCACCGATTACTGCCCATTTC 59.934 52.381 0.00 0.00 0.00 2.17
335 336 1.594397 CGTGTGCGTTGATATGAGCAT 59.406 47.619 0.00 0.00 41.88 3.79
336 337 0.998669 CGTGTGCGTTGATATGAGCA 59.001 50.000 0.00 0.00 37.26 4.26
337 338 0.315382 GCGTGTGCGTTGATATGAGC 60.315 55.000 0.00 0.00 40.81 4.26
338 339 3.786955 GCGTGTGCGTTGATATGAG 57.213 52.632 0.00 0.00 40.81 2.90
349 350 1.300931 TGGAGACAAGAGCGTGTGC 60.301 57.895 0.00 0.00 38.59 4.57
365 366 3.206150 CCTGAAACGGTAGATTGGATGG 58.794 50.000 0.00 0.00 0.00 3.51
456 462 2.262292 GTGCGTGGCATTGGCATT 59.738 55.556 16.56 0.00 41.91 3.56
457 463 4.118995 CGTGCGTGGCATTGGCAT 62.119 61.111 16.56 0.00 41.91 4.40
459 465 4.759096 GACGTGCGTGGCATTGGC 62.759 66.667 0.67 2.73 41.91 4.52
460 466 1.365368 TATGACGTGCGTGGCATTGG 61.365 55.000 0.67 0.00 41.91 3.16
461 467 0.657312 ATATGACGTGCGTGGCATTG 59.343 50.000 0.67 0.00 41.91 2.82
462 468 0.657312 CATATGACGTGCGTGGCATT 59.343 50.000 0.67 0.00 41.91 3.56
463 469 1.775039 GCATATGACGTGCGTGGCAT 61.775 55.000 6.97 1.64 41.91 4.40
497 503 5.359194 AGTACATATAGCAGTGCCAAACT 57.641 39.130 12.58 3.40 40.93 2.66
504 510 6.612306 TGCTCGATTAGTACATATAGCAGTG 58.388 40.000 0.00 0.00 34.05 3.66
538 553 2.658285 GCTCATCAGCTGTGTGTTTTG 58.342 47.619 14.67 7.71 43.09 2.44
566 581 1.134371 GTACGTACGTACTCCCTCCCT 60.134 57.143 38.40 10.95 45.30 4.20
579 828 1.589779 GCAACGGGCATTAGTACGTAC 59.410 52.381 18.10 18.10 43.97 3.67
591 840 1.745489 CCTAGGTTGAGCAACGGGC 60.745 63.158 0.00 0.00 42.02 6.13
593 842 2.100631 CGCCTAGGTTGAGCAACGG 61.101 63.158 11.31 4.70 42.02 4.44
612 861 2.023741 GTCATGCATGCTTCCGCG 59.976 61.111 22.25 0.00 39.65 6.46
613 862 2.410469 GGTCATGCATGCTTCCGC 59.590 61.111 22.25 7.14 0.00 5.54
614 863 1.647545 AACGGTCATGCATGCTTCCG 61.648 55.000 33.77 33.77 39.79 4.30
615 864 0.179156 CAACGGTCATGCATGCTTCC 60.179 55.000 22.25 20.07 0.00 3.46
616 865 0.179156 CCAACGGTCATGCATGCTTC 60.179 55.000 22.25 13.63 0.00 3.86
617 866 1.885157 CCAACGGTCATGCATGCTT 59.115 52.632 22.25 10.16 0.00 3.91
618 867 2.703798 GCCAACGGTCATGCATGCT 61.704 57.895 22.25 1.07 0.00 3.79
619 868 2.202650 GCCAACGGTCATGCATGC 60.203 61.111 22.25 11.82 0.00 4.06
620 869 2.100797 CGCCAACGGTCATGCATG 59.899 61.111 21.07 21.07 34.97 4.06
622 871 3.047280 GACGCCAACGGTCATGCA 61.047 61.111 0.00 0.00 46.04 3.96
678 960 4.884164 ACCAAAGTCCAAATGCTATAGCTC 59.116 41.667 24.61 7.30 42.66 4.09
710 992 1.042559 GGAGGAGAGAGTCTGGGCTG 61.043 65.000 0.00 0.00 0.00 4.85
713 995 2.173126 AATGGAGGAGAGAGTCTGGG 57.827 55.000 0.00 0.00 0.00 4.45
799 1082 2.871453 AGCTAGCTAGGTAGGCTCTTC 58.129 52.381 23.58 11.35 40.74 2.87
829 1115 0.179100 CAGTGTCTATGGTGAGGCCG 60.179 60.000 0.00 0.00 41.21 6.13
832 1118 2.996249 ATGCAGTGTCTATGGTGAGG 57.004 50.000 0.00 0.00 0.00 3.86
876 1162 1.090728 TCACTCGCAGTGCTCTCTAG 58.909 55.000 14.33 5.28 45.54 2.43
929 1219 2.608090 TCGAGTACTCTATCTGTGCGTG 59.392 50.000 20.34 0.87 0.00 5.34
930 1220 2.867368 CTCGAGTACTCTATCTGTGCGT 59.133 50.000 20.34 0.00 0.00 5.24
932 1222 4.333095 TGTTCTCGAGTACTCTATCTGTGC 59.667 45.833 20.87 4.42 0.00 4.57
949 1241 3.621794 GTGCTTGTGTGACAATGTTCTC 58.378 45.455 0.00 0.00 37.48 2.87
973 1265 2.161486 GTGTCGATCTCCTGCGTGC 61.161 63.158 0.00 0.00 0.00 5.34
990 1282 0.179062 GGCGAGCCATCTGAATCAGT 60.179 55.000 10.36 0.00 35.81 3.41
995 1287 4.838152 GCGGGCGAGCCATCTGAA 62.838 66.667 16.65 0.00 37.98 3.02
1072 1364 3.767230 CTCGCACGTTGTCGCCTG 61.767 66.667 0.00 0.00 41.18 4.85
1107 1399 2.942796 CGGCTGCCTGTACTGGTGA 61.943 63.158 17.92 6.57 0.00 4.02
1236 1528 0.107897 TGTAGATGCCGGCGTTGATT 60.108 50.000 24.75 11.52 0.00 2.57
1280 1575 4.269603 CGAAGAATGATGACAAGCTAGGTG 59.730 45.833 0.00 0.00 0.00 4.00
1285 1580 3.434641 CACACGAAGAATGATGACAAGCT 59.565 43.478 0.00 0.00 0.00 3.74
1290 1585 2.480037 TGCACACACGAAGAATGATGAC 59.520 45.455 0.00 0.00 0.00 3.06
1565 1862 0.244450 TACGTTCATGGACCACCGTC 59.756 55.000 12.03 0.00 39.42 4.79
1566 1863 0.037975 GTACGTTCATGGACCACCGT 60.038 55.000 0.00 5.95 39.42 4.83
1567 1864 1.074319 CGTACGTTCATGGACCACCG 61.074 60.000 7.22 0.00 39.42 4.94
1568 1865 0.244450 TCGTACGTTCATGGACCACC 59.756 55.000 16.05 0.00 0.00 4.61
1700 1997 4.269523 TTTGTCTGCGCCCCTGCT 62.270 61.111 4.18 0.00 35.36 4.24
1708 2006 2.111756 GCTTTTGTCACTTTGTCTGCG 58.888 47.619 0.00 0.00 0.00 5.18
1768 2073 1.405256 GGGATGCACAGAGACAGACAG 60.405 57.143 0.00 0.00 0.00 3.51
1769 2074 0.610174 GGGATGCACAGAGACAGACA 59.390 55.000 0.00 0.00 0.00 3.41
1770 2075 0.901124 AGGGATGCACAGAGACAGAC 59.099 55.000 0.00 0.00 0.00 3.51
1771 2076 0.900421 CAGGGATGCACAGAGACAGA 59.100 55.000 0.00 0.00 0.00 3.41
1818 2131 8.510243 AACTCAAAACACATCTATCATGCATA 57.490 30.769 0.00 0.00 0.00 3.14
1828 2141 5.105392 TCCAAGCAAAACTCAAAACACATCT 60.105 36.000 0.00 0.00 0.00 2.90
1829 2142 5.108517 TCCAAGCAAAACTCAAAACACATC 58.891 37.500 0.00 0.00 0.00 3.06
1830 2143 5.083533 TCCAAGCAAAACTCAAAACACAT 57.916 34.783 0.00 0.00 0.00 3.21
1831 2144 4.493547 CTCCAAGCAAAACTCAAAACACA 58.506 39.130 0.00 0.00 0.00 3.72
1915 2235 1.823899 GTATTTGCTCGGCCCAGGG 60.824 63.158 0.00 0.00 0.00 4.45
1979 2301 5.223382 AGATAGAAACACAACGTCAGTCAG 58.777 41.667 0.00 0.00 0.00 3.51
2239 2561 4.094294 ACACACATATGTAATGGTGAACGC 59.906 41.667 23.48 0.00 36.72 4.84
2241 2563 5.799936 GCAACACACATATGTAATGGTGAAC 59.200 40.000 28.82 15.54 36.72 3.18
2242 2564 5.391416 CGCAACACACATATGTAATGGTGAA 60.391 40.000 28.82 0.00 36.72 3.18
2243 2565 4.094146 CGCAACACACATATGTAATGGTGA 59.906 41.667 28.82 0.00 36.72 4.02
2244 2566 4.142708 ACGCAACACACATATGTAATGGTG 60.143 41.667 23.74 23.74 36.72 4.17
2245 2567 4.006989 ACGCAACACACATATGTAATGGT 58.993 39.130 18.65 12.33 36.72 3.55
2292 2661 1.454653 GTCCTGCTCGTACGTGTTTTC 59.545 52.381 16.05 0.53 0.00 2.29
2293 2662 1.068127 AGTCCTGCTCGTACGTGTTTT 59.932 47.619 16.05 0.00 0.00 2.43
2571 2943 4.318333 CGTGTGTCTGAATATGTATGCAGC 60.318 45.833 3.51 0.00 38.90 5.25
2594 2966 8.060090 GTGCTCAATTTATTTTATTCATGCTGC 58.940 33.333 0.00 0.00 0.00 5.25
2743 3128 1.221466 CGTTGACGAAGCTCTTGCCA 61.221 55.000 0.00 0.00 43.02 4.92
2802 3187 2.229792 GAATCTGTGGTGCTGGAAACA 58.770 47.619 0.00 0.00 39.59 2.83
2835 3220 9.698309 GCTTGTGATGTATAGTATGAATGTACT 57.302 33.333 0.00 0.00 38.42 2.73
2836 3221 9.476202 TGCTTGTGATGTATAGTATGAATGTAC 57.524 33.333 0.00 0.00 0.00 2.90
2930 3315 3.192212 ACGTAGTAACTACACTGGGAAGC 59.808 47.826 0.00 0.00 41.94 3.86
2956 3341 0.592637 TGTGCCTGTGCTTTCGAATG 59.407 50.000 0.00 2.02 38.71 2.67
3009 3394 8.349983 TCCTTGCTGTTTAGTTTTGAAGATTAC 58.650 33.333 0.00 0.00 0.00 1.89
3011 3396 7.346751 TCCTTGCTGTTTAGTTTTGAAGATT 57.653 32.000 0.00 0.00 0.00 2.40
3012 3397 6.959639 TCCTTGCTGTTTAGTTTTGAAGAT 57.040 33.333 0.00 0.00 0.00 2.40
3015 3400 6.707440 TCATCCTTGCTGTTTAGTTTTGAA 57.293 33.333 0.00 0.00 0.00 2.69
3016 3401 6.707440 TTCATCCTTGCTGTTTAGTTTTGA 57.293 33.333 0.00 0.00 0.00 2.69
3017 3402 7.951530 AATTCATCCTTGCTGTTTAGTTTTG 57.048 32.000 0.00 0.00 0.00 2.44
3042 3427 4.525100 TCATATGTAGGCAGGCGTATAACA 59.475 41.667 1.90 0.00 0.00 2.41
3059 3444 3.881089 TGTCCTCTGCAAAGCATCATATG 59.119 43.478 0.00 0.00 38.13 1.78
3209 3594 5.878406 TTTGACTTCATAGGATCTCCTCC 57.122 43.478 1.00 0.00 44.77 4.30
3223 3608 6.145535 CACCTTTTGCAGTAGATTTGACTTC 58.854 40.000 0.00 0.00 0.00 3.01
3263 3648 5.710984 ACTCTGTATAATAGGTGTATGCGC 58.289 41.667 0.00 0.00 0.00 6.09
3264 3649 8.041829 ACTACTCTGTATAATAGGTGTATGCG 57.958 38.462 0.00 0.00 0.00 4.73
3302 3814 8.774183 TCTTGGTACCTTATTAACCACATATGT 58.226 33.333 14.36 1.41 42.84 2.29
3303 3815 9.793259 ATCTTGGTACCTTATTAACCACATATG 57.207 33.333 14.36 0.00 42.84 1.78
3417 3929 2.161855 TGCATGCTTACCAAGAACAGG 58.838 47.619 20.33 0.00 0.00 4.00
3480 4156 3.610114 GCTGTCGTTAGTAAGTCAACGGA 60.610 47.826 6.97 0.00 45.70 4.69
3567 4243 2.906354 ACGGACACATAGCCTTCAATC 58.094 47.619 0.00 0.00 0.00 2.67
3570 4246 2.851263 AAACGGACACATAGCCTTCA 57.149 45.000 0.00 0.00 0.00 3.02
3580 4256 7.193377 TGGTTAGAATTAGAAAAACGGACAC 57.807 36.000 0.00 0.00 0.00 3.67
3596 4272 7.957002 TCATTGCCTTGTTTAAATGGTTAGAA 58.043 30.769 0.00 0.00 32.17 2.10
3597 4273 7.531857 TCATTGCCTTGTTTAAATGGTTAGA 57.468 32.000 0.00 0.00 32.17 2.10
3598 4274 8.776376 AATCATTGCCTTGTTTAAATGGTTAG 57.224 30.769 0.00 0.00 32.88 2.34
3600 4276 9.566432 TTAAATCATTGCCTTGTTTAAATGGTT 57.434 25.926 0.00 0.00 35.42 3.67
3601 4277 8.998377 GTTAAATCATTGCCTTGTTTAAATGGT 58.002 29.630 0.00 0.00 32.17 3.55
3602 4278 9.218440 AGTTAAATCATTGCCTTGTTTAAATGG 57.782 29.630 0.00 0.00 32.17 3.16
3608 4284 8.637986 TCTTGTAGTTAAATCATTGCCTTGTTT 58.362 29.630 0.00 0.00 0.00 2.83
3626 4303 3.467803 GTGTTGAAGGCTGTCTTGTAGT 58.532 45.455 0.00 0.00 35.50 2.73
3655 4332 7.512130 AGATCTTAATAGTGATGGTTCATGCA 58.488 34.615 0.00 0.00 33.56 3.96
3656 4333 7.976135 AGATCTTAATAGTGATGGTTCATGC 57.024 36.000 0.00 0.00 33.56 4.06
3671 4348 8.090831 TCTGTAATGCAAGCGATAGATCTTAAT 58.909 33.333 0.00 0.00 39.76 1.40
3684 4361 5.922544 ACTTGAACAAATCTGTAATGCAAGC 59.077 36.000 0.00 0.00 35.82 4.01
3746 4423 0.178992 TCTTGCTGGGACTTTGGTGG 60.179 55.000 0.00 0.00 0.00 4.61
3747 4424 0.954452 GTCTTGCTGGGACTTTGGTG 59.046 55.000 0.00 0.00 0.00 4.17
3763 4440 5.071519 ACCTATCATAATGCTTCTGCTGTCT 59.928 40.000 0.00 0.00 40.48 3.41


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

AutoCloner maintained by Alex Coulton.