Multiple sequence alignment - TraesCS3A01G368600

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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 TraesCS3A01G368600 chr3A 100.000 3539 0 0 1 3539 617531500 617535038 0.000000e+00 6536.0
1 TraesCS3A01G368600 chr3A 97.872 47 1 0 10 56 531905305 531905259 8.140000e-12 82.4
2 TraesCS3A01G368600 chr3D 93.696 3236 117 26 361 3539 475121502 475124707 0.000000e+00 4765.0
3 TraesCS3A01G368600 chr3B 95.157 2643 81 18 633 3245 631661099 631663724 0.000000e+00 4128.0
4 TraesCS3A01G368600 chr3B 86.972 284 17 8 361 641 631660800 631661066 5.740000e-78 302.0
5 TraesCS3A01G368600 chr3B 88.166 169 10 7 199 364 631660603 631660764 3.610000e-45 193.0
6 TraesCS3A01G368600 chr3B 86.957 92 7 3 8 96 589541931 589542020 8.090000e-17 99.0
7 TraesCS3A01G368600 chr3B 83.036 112 13 3 7 112 790492186 790492297 2.910000e-16 97.1
8 TraesCS3A01G368600 chr1B 75.374 1336 247 57 1249 2545 499593382 499592090 1.430000e-158 569.0
9 TraesCS3A01G368600 chr1D 74.820 1390 245 69 1198 2545 375205607 375204281 6.730000e-147 531.0
10 TraesCS3A01G368600 chr1A 74.747 1386 241 72 1198 2545 474293259 474291945 1.460000e-143 520.0
11 TraesCS3A01G368600 chr6B 80.571 175 32 2 1415 1587 526337551 526337725 2.220000e-27 134.0
12 TraesCS3A01G368600 chr7B 83.019 106 13 2 12 112 646487814 646487709 1.350000e-14 91.6
13 TraesCS3A01G368600 chr7B 83.871 93 12 1 7 96 692347410 692347502 6.290000e-13 86.1
14 TraesCS3A01G368600 chrUn 87.879 66 8 0 6 71 382796656 382796721 1.050000e-10 78.7
15 TraesCS3A01G368600 chrUn 86.957 69 9 0 6 74 382885238 382885170 1.050000e-10 78.7


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 TraesCS3A01G368600 chr3A 617531500 617535038 3538 False 6536 6536 100.000000 1 3539 1 chr3A.!!$F1 3538
1 TraesCS3A01G368600 chr3D 475121502 475124707 3205 False 4765 4765 93.696000 361 3539 1 chr3D.!!$F1 3178
2 TraesCS3A01G368600 chr3B 631660603 631663724 3121 False 1541 4128 90.098333 199 3245 3 chr3B.!!$F3 3046
3 TraesCS3A01G368600 chr1B 499592090 499593382 1292 True 569 569 75.374000 1249 2545 1 chr1B.!!$R1 1296
4 TraesCS3A01G368600 chr1D 375204281 375205607 1326 True 531 531 74.820000 1198 2545 1 chr1D.!!$R1 1347
5 TraesCS3A01G368600 chr1A 474291945 474293259 1314 True 520 520 74.747000 1198 2545 1 chr1A.!!$R1 1347

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
69 70 0.029834 GAATGCCGATGTGGACATGC 59.970 55.0 0.0 0.0 42.00 4.06 F
169 170 0.034863 TGGGGGTCCATTTAAGTCGC 60.035 55.0 0.0 0.0 38.32 5.19 F
521 575 0.169009 GATTCTTTGAGCACACCCGC 59.831 55.0 0.0 0.0 0.00 6.13 F
2095 2264 0.175989 GAAGATGGACACGGAGGACC 59.824 60.0 0.0 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1186 1298 0.336737 AGGAACTCCTCGTCATCCCT 59.663 55.000 0.00 0.0 44.77 4.20 R
2111 2283 1.777030 CGCGTATCTCTGCTCCGTCT 61.777 60.000 0.00 0.0 0.00 4.18 R
2319 2508 1.669760 CACCGCCCGCTTGAAGTAA 60.670 57.895 0.00 0.0 0.00 2.24 R
2984 3197 0.028637 GACACGTACGGCTACTAGGC 59.971 60.000 21.06 0.0 37.44 3.93 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
47 48 4.308458 CGCCCACCAGGTGTTCGA 62.308 66.667 18.82 0.00 41.64 3.71
48 49 2.668550 GCCCACCAGGTGTTCGAC 60.669 66.667 18.82 0.00 38.26 4.20
49 50 3.148084 CCCACCAGGTGTTCGACT 58.852 61.111 18.82 0.00 0.00 4.18
50 51 1.301716 CCCACCAGGTGTTCGACTG 60.302 63.158 18.82 0.80 34.54 3.51
51 52 1.745890 CCACCAGGTGTTCGACTGA 59.254 57.895 18.82 0.00 36.86 3.41
52 53 0.105964 CCACCAGGTGTTCGACTGAA 59.894 55.000 18.82 0.00 36.86 3.02
53 54 1.270839 CCACCAGGTGTTCGACTGAAT 60.271 52.381 18.82 0.00 36.86 2.57
54 55 1.800586 CACCAGGTGTTCGACTGAATG 59.199 52.381 11.99 0.00 36.86 2.67
55 56 0.798776 CCAGGTGTTCGACTGAATGC 59.201 55.000 2.52 0.00 36.86 3.56
56 57 0.798776 CAGGTGTTCGACTGAATGCC 59.201 55.000 0.00 0.00 36.86 4.40
57 58 0.670546 AGGTGTTCGACTGAATGCCG 60.671 55.000 0.00 0.00 36.48 5.69
58 59 0.669318 GGTGTTCGACTGAATGCCGA 60.669 55.000 0.00 0.00 36.29 5.54
59 60 1.359848 GTGTTCGACTGAATGCCGAT 58.640 50.000 0.00 0.00 36.29 4.18
60 61 1.061131 GTGTTCGACTGAATGCCGATG 59.939 52.381 0.00 0.00 36.29 3.84
61 62 1.337728 TGTTCGACTGAATGCCGATGT 60.338 47.619 0.00 0.00 36.29 3.06
62 63 1.061131 GTTCGACTGAATGCCGATGTG 59.939 52.381 0.00 0.00 36.29 3.21
63 64 0.460109 TCGACTGAATGCCGATGTGG 60.460 55.000 0.00 0.00 42.50 4.17
64 65 0.460109 CGACTGAATGCCGATGTGGA 60.460 55.000 0.00 0.00 42.00 4.02
65 66 1.009829 GACTGAATGCCGATGTGGAC 58.990 55.000 0.00 0.00 42.00 4.02
66 67 0.324614 ACTGAATGCCGATGTGGACA 59.675 50.000 0.00 0.00 42.00 4.02
67 68 1.065199 ACTGAATGCCGATGTGGACAT 60.065 47.619 0.00 0.00 42.00 3.06
68 69 1.332686 CTGAATGCCGATGTGGACATG 59.667 52.381 0.00 0.00 42.00 3.21
69 70 0.029834 GAATGCCGATGTGGACATGC 59.970 55.000 0.00 0.00 42.00 4.06
70 71 0.680601 AATGCCGATGTGGACATGCA 60.681 50.000 7.10 7.10 42.00 3.96
71 72 1.378882 ATGCCGATGTGGACATGCAC 61.379 55.000 6.86 0.00 42.00 4.57
72 73 2.039974 GCCGATGTGGACATGCACA 61.040 57.895 8.75 8.75 42.00 4.57
73 74 1.585267 GCCGATGTGGACATGCACAA 61.585 55.000 10.39 0.00 42.00 3.33
74 75 0.448990 CCGATGTGGACATGCACAAG 59.551 55.000 10.39 7.66 42.00 3.16
75 76 0.179181 CGATGTGGACATGCACAAGC 60.179 55.000 10.39 5.20 36.57 4.01
76 77 0.179181 GATGTGGACATGCACAAGCG 60.179 55.000 10.39 0.00 46.23 4.68
77 78 0.890542 ATGTGGACATGCACAAGCGT 60.891 50.000 10.39 0.00 46.23 5.07
78 79 1.207593 GTGGACATGCACAAGCGTC 59.792 57.895 0.00 0.00 46.23 5.19
79 80 1.071299 TGGACATGCACAAGCGTCT 59.929 52.632 0.00 0.00 46.23 4.18
80 81 1.229975 TGGACATGCACAAGCGTCTG 61.230 55.000 0.00 0.00 46.23 3.51
81 82 1.154338 GACATGCACAAGCGTCTGC 60.154 57.895 0.00 0.00 46.23 4.26
82 83 2.177531 CATGCACAAGCGTCTGCC 59.822 61.111 0.00 0.00 46.23 4.85
83 84 2.033141 ATGCACAAGCGTCTGCCT 59.967 55.556 0.00 0.00 46.23 4.75
84 85 2.037136 ATGCACAAGCGTCTGCCTC 61.037 57.895 0.00 0.00 46.23 4.70
85 86 3.426568 GCACAAGCGTCTGCCTCC 61.427 66.667 0.00 0.00 44.31 4.30
86 87 2.743928 CACAAGCGTCTGCCTCCC 60.744 66.667 0.00 0.00 44.31 4.30
87 88 4.379243 ACAAGCGTCTGCCTCCCG 62.379 66.667 0.00 0.00 44.31 5.14
88 89 4.379243 CAAGCGTCTGCCTCCCGT 62.379 66.667 0.00 0.00 44.31 5.28
89 90 3.626924 AAGCGTCTGCCTCCCGTT 61.627 61.111 0.00 0.00 44.31 4.44
90 91 3.883744 AAGCGTCTGCCTCCCGTTG 62.884 63.158 0.00 0.00 44.31 4.10
92 93 3.691342 CGTCTGCCTCCCGTTGGA 61.691 66.667 0.00 0.00 38.75 3.53
93 94 2.047179 GTCTGCCTCCCGTTGGAC 60.047 66.667 0.00 0.00 35.03 4.02
94 95 3.691342 TCTGCCTCCCGTTGGACG 61.691 66.667 0.00 0.00 42.11 4.79
107 108 4.440127 GGACGCGGGCCGAACTAA 62.440 66.667 33.44 0.00 41.02 2.24
108 109 2.432972 GACGCGGGCCGAACTAAA 60.433 61.111 33.44 0.00 41.02 1.85
109 110 2.733671 GACGCGGGCCGAACTAAAC 61.734 63.158 33.44 8.98 41.02 2.01
110 111 3.845472 CGCGGGCCGAACTAAACG 61.845 66.667 33.44 18.12 40.02 3.60
111 112 2.432972 GCGGGCCGAACTAAACGA 60.433 61.111 33.44 0.00 0.00 3.85
112 113 2.450345 GCGGGCCGAACTAAACGAG 61.450 63.158 33.44 0.00 0.00 4.18
113 114 2.450345 CGGGCCGAACTAAACGAGC 61.450 63.158 24.41 0.00 0.00 5.03
114 115 1.375013 GGGCCGAACTAAACGAGCA 60.375 57.895 0.00 0.00 0.00 4.26
115 116 1.359459 GGGCCGAACTAAACGAGCAG 61.359 60.000 0.00 0.00 0.00 4.24
116 117 0.389426 GGCCGAACTAAACGAGCAGA 60.389 55.000 0.00 0.00 0.00 4.26
117 118 0.714439 GCCGAACTAAACGAGCAGAC 59.286 55.000 0.00 0.00 0.00 3.51
118 119 1.933500 GCCGAACTAAACGAGCAGACA 60.934 52.381 0.00 0.00 0.00 3.41
119 120 1.986378 CCGAACTAAACGAGCAGACAG 59.014 52.381 0.00 0.00 0.00 3.51
120 121 2.351447 CCGAACTAAACGAGCAGACAGA 60.351 50.000 0.00 0.00 0.00 3.41
121 122 2.657372 CGAACTAAACGAGCAGACAGAC 59.343 50.000 0.00 0.00 0.00 3.51
122 123 2.333389 ACTAAACGAGCAGACAGACG 57.667 50.000 0.00 0.00 0.00 4.18
123 124 1.878088 ACTAAACGAGCAGACAGACGA 59.122 47.619 0.00 0.00 0.00 4.20
124 125 2.488545 ACTAAACGAGCAGACAGACGAT 59.511 45.455 0.00 0.00 0.00 3.73
125 126 2.440539 AAACGAGCAGACAGACGATT 57.559 45.000 0.00 0.00 0.00 3.34
126 127 1.983972 AACGAGCAGACAGACGATTC 58.016 50.000 0.00 0.00 0.00 2.52
127 128 0.881796 ACGAGCAGACAGACGATTCA 59.118 50.000 0.00 0.00 0.00 2.57
128 129 1.269723 ACGAGCAGACAGACGATTCAA 59.730 47.619 0.00 0.00 0.00 2.69
129 130 2.288213 ACGAGCAGACAGACGATTCAAA 60.288 45.455 0.00 0.00 0.00 2.69
130 131 2.091277 CGAGCAGACAGACGATTCAAAC 59.909 50.000 0.00 0.00 0.00 2.93
131 132 3.321497 GAGCAGACAGACGATTCAAACT 58.679 45.455 0.00 0.00 0.00 2.66
132 133 4.486090 GAGCAGACAGACGATTCAAACTA 58.514 43.478 0.00 0.00 0.00 2.24
133 134 4.883083 AGCAGACAGACGATTCAAACTAA 58.117 39.130 0.00 0.00 0.00 2.24
134 135 4.926238 AGCAGACAGACGATTCAAACTAAG 59.074 41.667 0.00 0.00 0.00 2.18
135 136 4.923871 GCAGACAGACGATTCAAACTAAGA 59.076 41.667 0.00 0.00 0.00 2.10
136 137 5.405571 GCAGACAGACGATTCAAACTAAGAA 59.594 40.000 0.00 0.00 0.00 2.52
137 138 6.073765 GCAGACAGACGATTCAAACTAAGAAA 60.074 38.462 0.00 0.00 0.00 2.52
138 139 7.518370 GCAGACAGACGATTCAAACTAAGAAAA 60.518 37.037 0.00 0.00 0.00 2.29
139 140 8.335356 CAGACAGACGATTCAAACTAAGAAAAA 58.665 33.333 0.00 0.00 0.00 1.94
158 159 4.431416 AAAAAGAACAAAATGGGGGTCC 57.569 40.909 0.00 0.00 0.00 4.46
169 170 0.034863 TGGGGGTCCATTTAAGTCGC 60.035 55.000 0.00 0.00 38.32 5.19
170 171 0.255033 GGGGGTCCATTTAAGTCGCT 59.745 55.000 0.00 0.00 0.00 4.93
171 172 1.379527 GGGGTCCATTTAAGTCGCTG 58.620 55.000 0.00 0.00 0.00 5.18
172 173 1.339727 GGGGTCCATTTAAGTCGCTGT 60.340 52.381 0.00 0.00 0.00 4.40
173 174 2.433436 GGGTCCATTTAAGTCGCTGTT 58.567 47.619 0.00 0.00 0.00 3.16
174 175 2.161609 GGGTCCATTTAAGTCGCTGTTG 59.838 50.000 0.00 0.00 0.00 3.33
175 176 2.414161 GGTCCATTTAAGTCGCTGTTGC 60.414 50.000 0.00 0.00 0.00 4.17
176 177 1.810151 TCCATTTAAGTCGCTGTTGCC 59.190 47.619 0.00 0.00 35.36 4.52
177 178 1.812571 CCATTTAAGTCGCTGTTGCCT 59.187 47.619 0.00 0.00 35.36 4.75
178 179 2.228822 CCATTTAAGTCGCTGTTGCCTT 59.771 45.455 0.00 0.00 35.36 4.35
179 180 3.236816 CATTTAAGTCGCTGTTGCCTTG 58.763 45.455 0.00 0.00 35.36 3.61
180 181 1.234821 TTAAGTCGCTGTTGCCTTGG 58.765 50.000 0.00 0.00 35.36 3.61
181 182 0.394938 TAAGTCGCTGTTGCCTTGGA 59.605 50.000 0.00 0.00 35.36 3.53
182 183 0.886490 AAGTCGCTGTTGCCTTGGAG 60.886 55.000 0.00 0.00 35.36 3.86
183 184 1.598130 GTCGCTGTTGCCTTGGAGT 60.598 57.895 0.00 0.00 35.36 3.85
184 185 1.148273 TCGCTGTTGCCTTGGAGTT 59.852 52.632 0.00 0.00 35.36 3.01
185 186 1.165907 TCGCTGTTGCCTTGGAGTTG 61.166 55.000 0.00 0.00 35.36 3.16
186 187 1.006922 GCTGTTGCCTTGGAGTTGC 60.007 57.895 0.00 0.00 0.00 4.17
187 188 1.458639 GCTGTTGCCTTGGAGTTGCT 61.459 55.000 0.00 0.00 0.00 3.91
188 189 0.595095 CTGTTGCCTTGGAGTTGCTC 59.405 55.000 0.00 0.00 0.00 4.26
189 190 0.183492 TGTTGCCTTGGAGTTGCTCT 59.817 50.000 0.00 0.00 0.00 4.09
190 191 1.322442 GTTGCCTTGGAGTTGCTCTT 58.678 50.000 0.00 0.00 0.00 2.85
191 192 2.158682 TGTTGCCTTGGAGTTGCTCTTA 60.159 45.455 0.00 0.00 0.00 2.10
192 193 3.084786 GTTGCCTTGGAGTTGCTCTTAT 58.915 45.455 0.00 0.00 0.00 1.73
193 194 4.261801 GTTGCCTTGGAGTTGCTCTTATA 58.738 43.478 0.00 0.00 0.00 0.98
194 195 4.568072 TGCCTTGGAGTTGCTCTTATAA 57.432 40.909 0.00 0.00 0.00 0.98
195 196 4.917385 TGCCTTGGAGTTGCTCTTATAAA 58.083 39.130 0.00 0.00 0.00 1.40
196 197 5.509498 TGCCTTGGAGTTGCTCTTATAAAT 58.491 37.500 0.00 0.00 0.00 1.40
197 198 5.951747 TGCCTTGGAGTTGCTCTTATAAATT 59.048 36.000 0.00 0.00 0.00 1.82
259 261 1.823169 TAAGGTGTCACCGCTCCCAC 61.823 60.000 16.44 0.00 44.90 4.61
273 275 1.205893 CTCCCACCTAACTGCAGTCTC 59.794 57.143 21.95 0.00 0.00 3.36
336 340 5.943416 TGATAACCATGGAAAAGACGATTGT 59.057 36.000 21.47 0.00 0.00 2.71
348 352 7.113544 GGAAAAGACGATTGTGAGAAATTTCAC 59.886 37.037 19.99 14.20 46.02 3.18
350 354 6.233430 AGACGATTGTGAGAAATTTCACTG 57.767 37.500 19.99 6.06 46.00 3.66
351 355 5.760253 AGACGATTGTGAGAAATTTCACTGT 59.240 36.000 19.99 8.72 46.00 3.55
352 356 6.260936 AGACGATTGTGAGAAATTTCACTGTT 59.739 34.615 19.99 0.00 46.00 3.16
354 358 7.352739 ACGATTGTGAGAAATTTCACTGTTAC 58.647 34.615 19.99 8.54 46.00 2.50
355 359 7.011950 ACGATTGTGAGAAATTTCACTGTTACA 59.988 33.333 19.99 10.81 46.00 2.41
356 360 8.017373 CGATTGTGAGAAATTTCACTGTTACAT 58.983 33.333 19.99 5.21 46.00 2.29
359 363 7.864686 TGTGAGAAATTTCACTGTTACATGAG 58.135 34.615 19.99 0.00 46.00 2.90
429 477 6.773200 TGTAAACATGACTACAACCCATGAAA 59.227 34.615 0.00 0.00 39.86 2.69
432 480 4.215399 ACATGACTACAACCCATGAAAACG 59.785 41.667 0.00 0.00 39.86 3.60
439 487 3.190535 ACAACCCATGAAAACGCATAGAC 59.809 43.478 0.00 0.00 0.00 2.59
476 524 2.879907 CGGCCGTACGGAAGAGAA 59.120 61.111 37.62 0.00 37.50 2.87
477 525 1.213537 CGGCCGTACGGAAGAGAAA 59.786 57.895 37.62 0.00 37.50 2.52
478 526 0.801067 CGGCCGTACGGAAGAGAAAG 60.801 60.000 37.62 13.79 37.50 2.62
479 527 0.529378 GGCCGTACGGAAGAGAAAGA 59.471 55.000 37.62 0.00 37.50 2.52
480 528 1.469423 GGCCGTACGGAAGAGAAAGAG 60.469 57.143 37.62 6.94 37.50 2.85
481 529 1.471684 GCCGTACGGAAGAGAAAGAGA 59.528 52.381 37.62 0.00 37.50 3.10
484 532 3.064271 CCGTACGGAAGAGAAAGAGAGAG 59.936 52.174 30.64 0.00 37.50 3.20
520 574 1.466167 CAGATTCTTTGAGCACACCCG 59.534 52.381 0.00 0.00 0.00 5.28
521 575 0.169009 GATTCTTTGAGCACACCCGC 59.831 55.000 0.00 0.00 0.00 6.13
522 576 1.577328 ATTCTTTGAGCACACCCGCG 61.577 55.000 0.00 0.00 36.85 6.46
523 577 2.652382 TTCTTTGAGCACACCCGCGA 62.652 55.000 8.23 0.00 36.85 5.87
524 578 2.954753 CTTTGAGCACACCCGCGAC 61.955 63.158 8.23 0.00 36.85 5.19
525 579 4.980805 TTGAGCACACCCGCGACC 62.981 66.667 8.23 0.00 36.85 4.79
665 760 2.017782 TCTTCGTCTTCCATCCTCGAG 58.982 52.381 5.13 5.13 32.39 4.04
681 776 1.141591 CGAGCCATTTCCATTTGCGC 61.142 55.000 0.00 0.00 0.00 6.09
883 990 1.670083 CACCGTTCGTTTCCCCTCC 60.670 63.158 0.00 0.00 0.00 4.30
884 991 2.046604 CCGTTCGTTTCCCCTCCC 60.047 66.667 0.00 0.00 0.00 4.30
885 992 2.745037 CGTTCGTTTCCCCTCCCA 59.255 61.111 0.00 0.00 0.00 4.37
886 993 1.298667 CGTTCGTTTCCCCTCCCAT 59.701 57.895 0.00 0.00 0.00 4.00
1335 1447 0.523072 GGATGCTCAAGCGCAAGAAA 59.477 50.000 11.47 0.00 44.06 2.52
1347 1459 2.985847 AAGAAACGGCAGCAGGGC 60.986 61.111 0.00 0.00 39.06 5.19
2051 2220 4.176752 GGACCCGGACATCCTGGC 62.177 72.222 0.73 2.08 43.39 4.85
2095 2264 0.175989 GAAGATGGACACGGAGGACC 59.824 60.000 0.00 0.00 0.00 4.46
2445 2634 1.201429 AGACGTTCCAGGAGGCCATT 61.201 55.000 5.01 0.00 33.74 3.16
2712 2902 1.402325 GCCAACCACGAAGCAAATACC 60.402 52.381 0.00 0.00 0.00 2.73
2718 2908 2.347452 CCACGAAGCAAATACCAGTACG 59.653 50.000 0.00 0.00 0.00 3.67
2758 2948 1.942657 GCTCATACATTCACACGGCAT 59.057 47.619 0.00 0.00 0.00 4.40
2759 2949 2.032549 GCTCATACATTCACACGGCATC 60.033 50.000 0.00 0.00 0.00 3.91
2760 2950 3.197265 CTCATACATTCACACGGCATCA 58.803 45.455 0.00 0.00 0.00 3.07
2762 2952 2.464157 TACATTCACACGGCATCACA 57.536 45.000 0.00 0.00 0.00 3.58
2793 2983 5.864628 ATCTCTCGTTTTACTTTGGCTTC 57.135 39.130 0.00 0.00 0.00 3.86
2842 3055 2.050714 GCATGCCGCGATGAATGG 60.051 61.111 8.23 0.00 0.00 3.16
2852 3065 2.514592 ATGAATGGTCGGCGGCTG 60.515 61.111 12.73 1.35 0.00 4.85
3093 3306 2.770164 AAGTGGTGATGTGAGGCTAC 57.230 50.000 0.00 0.00 0.00 3.58
3160 3380 0.893270 TACAGCAGCAATTTGGCCGT 60.893 50.000 0.00 0.00 0.00 5.68
3169 3389 3.128589 AGCAATTTGGCCGTATGTAACTG 59.871 43.478 0.00 0.00 0.00 3.16
3208 3428 6.687393 GCAATGAGAATATCTCCAGTTCTCCA 60.687 42.308 10.72 2.02 44.46 3.86
3247 3468 2.896243 GCAACAAGCATCTCTCTGTG 57.104 50.000 0.00 0.00 44.79 3.66
3251 3472 1.973515 ACAAGCATCTCTCTGTGTCCA 59.026 47.619 0.00 0.00 0.00 4.02
3252 3473 2.028294 ACAAGCATCTCTCTGTGTCCAG 60.028 50.000 0.00 0.00 40.25 3.86
3253 3474 2.228545 AGCATCTCTCTGTGTCCAGA 57.771 50.000 0.00 0.00 45.44 3.86
3254 3475 2.749600 AGCATCTCTCTGTGTCCAGAT 58.250 47.619 0.00 0.00 46.38 2.90
3255 3476 2.431419 AGCATCTCTCTGTGTCCAGATG 59.569 50.000 3.81 3.81 46.38 2.90
3267 3488 5.491070 TGTGTCCAGATGTGAAGAAATAGG 58.509 41.667 0.00 0.00 0.00 2.57
3272 3493 4.212847 CCAGATGTGAAGAAATAGGATGCG 59.787 45.833 0.00 0.00 0.00 4.73
3298 3519 6.938596 TCAGCATGAATTTCATATCGAGGAAT 59.061 34.615 11.44 0.00 45.97 3.01
3307 3528 9.790344 AATTTCATATCGAGGAATGATTCTTCT 57.210 29.630 14.19 0.15 33.98 2.85
3333 3554 5.444176 AGGCTCATTTTCCTAGAGAAATGG 58.556 41.667 20.84 15.58 43.93 3.16
3335 3556 4.886489 GCTCATTTTCCTAGAGAAATGGCT 59.114 41.667 20.84 0.00 43.93 4.75
3337 3558 6.065976 TCATTTTCCTAGAGAAATGGCTGA 57.934 37.500 20.84 12.81 43.93 4.26
3340 3561 7.284034 TCATTTTCCTAGAGAAATGGCTGAATC 59.716 37.037 20.84 0.00 43.93 2.52
3342 3563 5.287674 TCCTAGAGAAATGGCTGAATCAG 57.712 43.478 5.78 5.78 34.12 2.90
3344 3565 5.605908 TCCTAGAGAAATGGCTGAATCAGAT 59.394 40.000 15.38 0.00 32.44 2.90
3350 3572 7.236019 AGAGAAATGGCTGAATCAGATAGATCT 59.764 37.037 15.38 10.69 35.39 2.75
3359 3581 9.008965 GCTGAATCAGATAGATCTACTTCAGTA 57.991 37.037 25.57 7.88 45.17 2.74
3370 3592 6.975772 AGATCTACTTCAGTAATCTGCGTTTC 59.024 38.462 0.00 0.00 41.10 2.78
3433 3658 7.201530 GCTGCTCGACTTTTAGCTTAATTTCTA 60.202 37.037 0.00 0.00 39.53 2.10
3434 3659 8.718102 TGCTCGACTTTTAGCTTAATTTCTAT 57.282 30.769 0.00 0.00 39.53 1.98
3440 3665 9.709600 GACTTTTAGCTTAATTTCTATGTCTGC 57.290 33.333 0.00 0.00 0.00 4.26
3466 3691 4.134563 TGGCTTTTCAGGTGTCTTTAGTC 58.865 43.478 0.00 0.00 0.00 2.59
3467 3692 4.134563 GGCTTTTCAGGTGTCTTTAGTCA 58.865 43.478 0.00 0.00 0.00 3.41
3468 3693 4.214332 GGCTTTTCAGGTGTCTTTAGTCAG 59.786 45.833 0.00 0.00 0.00 3.51
3469 3694 4.816925 GCTTTTCAGGTGTCTTTAGTCAGT 59.183 41.667 0.00 0.00 0.00 3.41
3470 3695 5.989777 GCTTTTCAGGTGTCTTTAGTCAGTA 59.010 40.000 0.00 0.00 0.00 2.74
3498 3723 2.315925 ACGCCATGTTCCATACTCTG 57.684 50.000 0.00 0.00 0.00 3.35
3505 3730 5.734720 CCATGTTCCATACTCTGTTGTACT 58.265 41.667 0.00 0.00 0.00 2.73
3509 3734 5.169295 GTTCCATACTCTGTTGTACTGACC 58.831 45.833 0.00 0.00 0.00 4.02
3533 3758 6.701400 CCTTTGAAAAGTTGGTTGTCCTTATG 59.299 38.462 2.33 0.00 34.20 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.767255 CACCTGGTGGGCGAGCTC 62.767 72.222 19.23 2.73 39.10 4.09
27 28 4.643387 AACACCTGGTGGGCGAGC 62.643 66.667 29.05 0.00 37.94 5.03
28 29 2.358737 GAACACCTGGTGGGCGAG 60.359 66.667 29.05 4.91 37.94 5.03
29 30 4.308458 CGAACACCTGGTGGGCGA 62.308 66.667 29.05 0.00 37.94 5.54
30 31 4.308458 TCGAACACCTGGTGGGCG 62.308 66.667 29.05 27.86 37.94 6.13
31 32 2.668550 GTCGAACACCTGGTGGGC 60.669 66.667 29.05 18.99 37.94 5.36
32 33 1.301716 CAGTCGAACACCTGGTGGG 60.302 63.158 29.05 17.90 37.94 4.61
33 34 0.105964 TTCAGTCGAACACCTGGTGG 59.894 55.000 29.05 12.92 37.94 4.61
34 35 1.800586 CATTCAGTCGAACACCTGGTG 59.199 52.381 24.80 24.80 39.75 4.17
35 36 1.878102 GCATTCAGTCGAACACCTGGT 60.878 52.381 0.00 0.00 32.81 4.00
36 37 0.798776 GCATTCAGTCGAACACCTGG 59.201 55.000 1.40 0.00 32.81 4.45
37 38 0.798776 GGCATTCAGTCGAACACCTG 59.201 55.000 0.00 0.00 32.81 4.00
38 39 3.233355 GGCATTCAGTCGAACACCT 57.767 52.632 0.00 0.00 32.81 4.00
46 47 1.009829 GTCCACATCGGCATTCAGTC 58.990 55.000 0.00 0.00 33.14 3.51
47 48 0.324614 TGTCCACATCGGCATTCAGT 59.675 50.000 0.00 0.00 33.14 3.41
48 49 1.332686 CATGTCCACATCGGCATTCAG 59.667 52.381 0.00 0.00 33.61 3.02
49 50 1.381522 CATGTCCACATCGGCATTCA 58.618 50.000 0.00 0.00 33.61 2.57
50 51 0.029834 GCATGTCCACATCGGCATTC 59.970 55.000 0.00 0.00 33.61 2.67
51 52 0.680601 TGCATGTCCACATCGGCATT 60.681 50.000 0.00 0.00 32.54 3.56
52 53 1.077572 TGCATGTCCACATCGGCAT 60.078 52.632 0.00 0.00 32.54 4.40
53 54 2.039974 GTGCATGTCCACATCGGCA 61.040 57.895 0.00 1.57 34.30 5.69
54 55 1.585267 TTGTGCATGTCCACATCGGC 61.585 55.000 6.94 0.00 44.44 5.54
55 56 0.448990 CTTGTGCATGTCCACATCGG 59.551 55.000 6.94 0.00 44.44 4.18
56 57 0.179181 GCTTGTGCATGTCCACATCG 60.179 55.000 6.94 3.84 44.44 3.84
57 58 0.179181 CGCTTGTGCATGTCCACATC 60.179 55.000 6.94 2.81 44.44 3.06
58 59 0.890542 ACGCTTGTGCATGTCCACAT 60.891 50.000 6.94 0.00 44.44 3.21
59 60 1.506309 GACGCTTGTGCATGTCCACA 61.506 55.000 2.41 2.41 43.48 4.17
60 61 1.207593 GACGCTTGTGCATGTCCAC 59.792 57.895 0.00 0.00 39.64 4.02
61 62 1.071299 AGACGCTTGTGCATGTCCA 59.929 52.632 0.00 0.00 39.64 4.02
62 63 1.499056 CAGACGCTTGTGCATGTCC 59.501 57.895 0.00 0.00 39.64 4.02
63 64 1.154338 GCAGACGCTTGTGCATGTC 60.154 57.895 7.50 0.00 41.73 3.06
64 65 2.620112 GGCAGACGCTTGTGCATGT 61.620 57.895 14.37 0.00 43.95 3.21
65 66 2.177531 GGCAGACGCTTGTGCATG 59.822 61.111 14.37 0.00 43.95 4.06
66 67 2.033141 AGGCAGACGCTTGTGCAT 59.967 55.556 14.37 3.93 43.95 3.96
67 68 2.666190 GAGGCAGACGCTTGTGCA 60.666 61.111 14.37 0.00 43.95 4.57
68 69 3.426568 GGAGGCAGACGCTTGTGC 61.427 66.667 3.46 3.46 41.38 4.57
69 70 2.743928 GGGAGGCAGACGCTTGTG 60.744 66.667 0.00 0.00 38.60 3.33
70 71 4.379243 CGGGAGGCAGACGCTTGT 62.379 66.667 0.00 0.00 38.60 3.16
71 72 3.883744 AACGGGAGGCAGACGCTTG 62.884 63.158 0.00 0.00 38.60 4.01
72 73 3.626924 AACGGGAGGCAGACGCTT 61.627 61.111 0.00 0.00 38.60 4.68
73 74 4.379243 CAACGGGAGGCAGACGCT 62.379 66.667 0.00 0.00 38.60 5.07
75 76 3.691342 TCCAACGGGAGGCAGACG 61.691 66.667 0.00 0.00 38.64 4.18
76 77 2.047179 GTCCAACGGGAGGCAGAC 60.047 66.667 0.00 0.00 46.12 3.51
77 78 3.691342 CGTCCAACGGGAGGCAGA 61.691 66.667 0.00 0.00 46.12 4.26
90 91 3.938019 TTTAGTTCGGCCCGCGTCC 62.938 63.158 4.92 4.80 0.00 4.79
91 92 2.432972 TTTAGTTCGGCCCGCGTC 60.433 61.111 4.92 0.00 0.00 5.19
92 93 2.739671 GTTTAGTTCGGCCCGCGT 60.740 61.111 4.92 0.00 0.00 6.01
93 94 3.845472 CGTTTAGTTCGGCCCGCG 61.845 66.667 0.00 0.00 0.00 6.46
94 95 2.432972 TCGTTTAGTTCGGCCCGC 60.433 61.111 0.00 0.00 0.00 6.13
95 96 2.450345 GCTCGTTTAGTTCGGCCCG 61.450 63.158 0.00 0.00 0.00 6.13
96 97 1.359459 CTGCTCGTTTAGTTCGGCCC 61.359 60.000 0.00 0.00 0.00 5.80
97 98 0.389426 TCTGCTCGTTTAGTTCGGCC 60.389 55.000 0.00 0.00 0.00 6.13
98 99 0.714439 GTCTGCTCGTTTAGTTCGGC 59.286 55.000 0.00 0.00 0.00 5.54
99 100 1.986378 CTGTCTGCTCGTTTAGTTCGG 59.014 52.381 0.00 0.00 0.00 4.30
100 101 2.657372 GTCTGTCTGCTCGTTTAGTTCG 59.343 50.000 0.00 0.00 0.00 3.95
101 102 2.657372 CGTCTGTCTGCTCGTTTAGTTC 59.343 50.000 0.00 0.00 0.00 3.01
102 103 2.292569 TCGTCTGTCTGCTCGTTTAGTT 59.707 45.455 0.00 0.00 0.00 2.24
103 104 1.878088 TCGTCTGTCTGCTCGTTTAGT 59.122 47.619 0.00 0.00 0.00 2.24
104 105 2.613730 TCGTCTGTCTGCTCGTTTAG 57.386 50.000 0.00 0.00 0.00 1.85
105 106 3.057806 TGAATCGTCTGTCTGCTCGTTTA 60.058 43.478 0.00 0.00 0.00 2.01
106 107 2.288213 TGAATCGTCTGTCTGCTCGTTT 60.288 45.455 0.00 0.00 0.00 3.60
107 108 1.269723 TGAATCGTCTGTCTGCTCGTT 59.730 47.619 0.00 0.00 0.00 3.85
108 109 0.881796 TGAATCGTCTGTCTGCTCGT 59.118 50.000 0.00 0.00 0.00 4.18
109 110 1.982612 TTGAATCGTCTGTCTGCTCG 58.017 50.000 0.00 0.00 0.00 5.03
110 111 3.321497 AGTTTGAATCGTCTGTCTGCTC 58.679 45.455 0.00 0.00 0.00 4.26
111 112 3.393089 AGTTTGAATCGTCTGTCTGCT 57.607 42.857 0.00 0.00 0.00 4.24
112 113 4.923871 TCTTAGTTTGAATCGTCTGTCTGC 59.076 41.667 0.00 0.00 0.00 4.26
113 114 7.408132 TTTCTTAGTTTGAATCGTCTGTCTG 57.592 36.000 0.00 0.00 0.00 3.51
114 115 8.433421 TTTTTCTTAGTTTGAATCGTCTGTCT 57.567 30.769 0.00 0.00 0.00 3.41
137 138 3.783082 TGGACCCCCATTTTGTTCTTTTT 59.217 39.130 0.00 0.00 37.58 1.94
138 139 3.388913 TGGACCCCCATTTTGTTCTTTT 58.611 40.909 0.00 0.00 37.58 2.27
139 140 3.053359 TGGACCCCCATTTTGTTCTTT 57.947 42.857 0.00 0.00 37.58 2.52
140 141 2.785357 TGGACCCCCATTTTGTTCTT 57.215 45.000 0.00 0.00 37.58 2.52
151 152 0.255033 AGCGACTTAAATGGACCCCC 59.745 55.000 0.00 0.00 0.00 5.40
152 153 1.339727 ACAGCGACTTAAATGGACCCC 60.340 52.381 0.00 0.00 0.00 4.95
153 154 2.109425 ACAGCGACTTAAATGGACCC 57.891 50.000 0.00 0.00 0.00 4.46
154 155 2.414161 GCAACAGCGACTTAAATGGACC 60.414 50.000 0.00 0.00 0.00 4.46
155 156 2.414161 GGCAACAGCGACTTAAATGGAC 60.414 50.000 0.00 0.00 0.00 4.02
156 157 1.810151 GGCAACAGCGACTTAAATGGA 59.190 47.619 0.00 0.00 0.00 3.41
157 158 1.812571 AGGCAACAGCGACTTAAATGG 59.187 47.619 0.00 0.00 41.41 3.16
158 159 3.236816 CAAGGCAACAGCGACTTAAATG 58.763 45.455 0.00 0.00 41.41 2.32
159 160 2.228822 CCAAGGCAACAGCGACTTAAAT 59.771 45.455 0.00 0.00 41.41 1.40
160 161 1.606668 CCAAGGCAACAGCGACTTAAA 59.393 47.619 0.00 0.00 41.41 1.52
161 162 1.202710 TCCAAGGCAACAGCGACTTAA 60.203 47.619 0.00 0.00 41.41 1.85
162 163 0.394938 TCCAAGGCAACAGCGACTTA 59.605 50.000 0.00 0.00 41.41 2.24
163 164 0.886490 CTCCAAGGCAACAGCGACTT 60.886 55.000 0.00 0.00 41.41 3.01
164 165 1.302033 CTCCAAGGCAACAGCGACT 60.302 57.895 0.00 0.00 41.41 4.18
165 166 1.166531 AACTCCAAGGCAACAGCGAC 61.167 55.000 0.00 0.00 41.41 5.19
166 167 1.148273 AACTCCAAGGCAACAGCGA 59.852 52.632 0.00 0.00 41.41 4.93
167 168 1.283793 CAACTCCAAGGCAACAGCG 59.716 57.895 0.00 0.00 41.41 5.18
168 169 1.006922 GCAACTCCAAGGCAACAGC 60.007 57.895 0.00 0.00 41.41 4.40
169 170 0.595095 GAGCAACTCCAAGGCAACAG 59.405 55.000 0.00 0.00 41.41 3.16
170 171 0.183492 AGAGCAACTCCAAGGCAACA 59.817 50.000 0.00 0.00 41.41 3.33
171 172 1.322442 AAGAGCAACTCCAAGGCAAC 58.678 50.000 0.00 0.00 0.00 4.17
172 173 2.949177 TAAGAGCAACTCCAAGGCAA 57.051 45.000 0.00 0.00 0.00 4.52
173 174 4.568072 TTATAAGAGCAACTCCAAGGCA 57.432 40.909 0.00 0.00 0.00 4.75
174 175 6.456795 AATTTATAAGAGCAACTCCAAGGC 57.543 37.500 0.00 0.00 0.00 4.35
239 240 1.079336 GGGAGCGGTGACACCTTAC 60.079 63.158 22.14 10.89 35.66 2.34
244 246 1.823169 TTAGGTGGGAGCGGTGACAC 61.823 60.000 9.15 9.15 0.00 3.67
251 253 1.448540 CTGCAGTTAGGTGGGAGCG 60.449 63.158 5.25 0.00 0.00 5.03
259 261 5.392767 TCAGTAAAGAGACTGCAGTTAGG 57.607 43.478 22.65 4.50 45.44 2.69
318 320 4.002982 TCTCACAATCGTCTTTTCCATGG 58.997 43.478 4.97 4.97 0.00 3.66
320 322 6.824305 ATTTCTCACAATCGTCTTTTCCAT 57.176 33.333 0.00 0.00 0.00 3.41
321 323 6.633500 AATTTCTCACAATCGTCTTTTCCA 57.367 33.333 0.00 0.00 0.00 3.53
322 324 7.113544 GTGAAATTTCTCACAATCGTCTTTTCC 59.886 37.037 18.64 0.00 44.32 3.13
336 340 8.853077 ATCTCATGTAACAGTGAAATTTCTCA 57.147 30.769 18.64 0.00 0.00 3.27
354 358 9.254133 ACTCGACAAAATTACTGATATCTCATG 57.746 33.333 3.98 0.00 0.00 3.07
355 359 9.823647 AACTCGACAAAATTACTGATATCTCAT 57.176 29.630 3.98 0.00 0.00 2.90
356 360 9.653287 AAACTCGACAAAATTACTGATATCTCA 57.347 29.630 3.98 0.00 0.00 3.27
397 438 9.174166 GGGTTGTAGTCATGTTTACAGAATTAT 57.826 33.333 10.42 0.00 31.95 1.28
406 453 7.520776 CGTTTTCATGGGTTGTAGTCATGTTTA 60.521 37.037 0.00 0.00 39.25 2.01
429 477 0.800631 TCAGTCGTCGTCTATGCGTT 59.199 50.000 0.00 0.00 0.00 4.84
432 480 2.288186 TCTCATCAGTCGTCGTCTATGC 59.712 50.000 0.00 0.00 0.00 3.14
439 487 0.660488 CCCTCTCTCATCAGTCGTCG 59.340 60.000 0.00 0.00 0.00 5.12
468 516 4.332819 CGTCTCTCTCTCTCTTTCTCTTCC 59.667 50.000 0.00 0.00 0.00 3.46
476 524 0.746563 CCGCCGTCTCTCTCTCTCTT 60.747 60.000 0.00 0.00 0.00 2.85
477 525 1.153249 CCGCCGTCTCTCTCTCTCT 60.153 63.158 0.00 0.00 0.00 3.10
478 526 1.433837 GACCGCCGTCTCTCTCTCTC 61.434 65.000 0.00 0.00 35.99 3.20
479 527 1.450669 GACCGCCGTCTCTCTCTCT 60.451 63.158 0.00 0.00 35.99 3.10
480 528 1.450669 AGACCGCCGTCTCTCTCTC 60.451 63.158 1.51 0.00 46.90 3.20
481 529 1.747367 CAGACCGCCGTCTCTCTCT 60.747 63.158 4.61 0.00 46.90 3.10
484 532 3.691744 CTGCAGACCGCCGTCTCTC 62.692 68.421 8.42 1.55 46.90 3.20
521 575 4.415332 AGTGCGTAGGCGTGGTCG 62.415 66.667 2.53 0.00 44.10 4.79
522 576 2.809601 CAGTGCGTAGGCGTGGTC 60.810 66.667 2.53 0.00 44.10 4.02
523 577 4.373116 CCAGTGCGTAGGCGTGGT 62.373 66.667 16.66 0.00 44.10 4.16
525 579 4.373116 ACCCAGTGCGTAGGCGTG 62.373 66.667 2.53 2.95 44.10 5.34
531 585 4.015406 CCTGCCACCCAGTGCGTA 62.015 66.667 0.00 0.00 40.06 4.42
665 760 2.166579 CGGCGCAAATGGAAATGGC 61.167 57.895 10.83 0.00 0.00 4.40
681 776 1.062587 CCAAAATTAGCGCTCACTCGG 59.937 52.381 16.34 5.09 0.00 4.63
883 990 1.772156 GAGGGGAAGGGAGGGATGG 60.772 68.421 0.00 0.00 0.00 3.51
884 991 1.772156 GGAGGGGAAGGGAGGGATG 60.772 68.421 0.00 0.00 0.00 3.51
885 992 2.712746 GGAGGGGAAGGGAGGGAT 59.287 66.667 0.00 0.00 0.00 3.85
886 993 3.707189 GGGAGGGGAAGGGAGGGA 61.707 72.222 0.00 0.00 0.00 4.20
1027 1139 4.779733 GCCCAGAGAGGACGGGGA 62.780 72.222 7.99 0.00 45.73 4.81
1150 1262 3.558411 GTCGATGCTGGCGCTGAC 61.558 66.667 7.64 0.00 36.97 3.51
1186 1298 0.336737 AGGAACTCCTCGTCATCCCT 59.663 55.000 0.00 0.00 44.77 4.20
1905 2056 2.920645 CGCCTGTGACTCGTCCTGT 61.921 63.158 0.00 0.00 0.00 4.00
1965 2134 3.750130 CGGCTATCCTTTTCCAGATGATG 59.250 47.826 0.00 0.00 0.00 3.07
1966 2135 3.648067 TCGGCTATCCTTTTCCAGATGAT 59.352 43.478 0.00 0.00 0.00 2.45
2104 2276 3.175240 CTGCTCCGTCTTCGCGTG 61.175 66.667 5.77 0.00 35.54 5.34
2111 2283 1.777030 CGCGTATCTCTGCTCCGTCT 61.777 60.000 0.00 0.00 0.00 4.18
2319 2508 1.669760 CACCGCCCGCTTGAAGTAA 60.670 57.895 0.00 0.00 0.00 2.24
2712 2902 2.251869 TGCAAGCGTAGTACGTACTG 57.748 50.000 33.23 20.77 44.73 2.74
2718 2908 3.949313 GCACTTGCAAGCGTAGTAC 57.051 52.632 26.27 0.00 41.59 2.73
2741 2931 2.677337 TGTGATGCCGTGTGAATGTATG 59.323 45.455 0.00 0.00 0.00 2.39
2758 2948 2.297315 ACGAGAGATTCTTGCACTGTGA 59.703 45.455 12.86 0.00 30.88 3.58
2759 2949 2.681706 ACGAGAGATTCTTGCACTGTG 58.318 47.619 2.76 2.76 30.88 3.66
2760 2950 3.393089 AACGAGAGATTCTTGCACTGT 57.607 42.857 0.00 0.00 30.88 3.55
2762 2952 5.542779 AGTAAAACGAGAGATTCTTGCACT 58.457 37.500 0.00 0.00 30.88 4.40
2793 2983 1.510844 GCCATTGCACCCCGTAAAG 59.489 57.895 0.00 0.00 37.47 1.85
2852 3065 0.995803 AGAAAGGGGAAGAGGAAGCC 59.004 55.000 0.00 0.00 0.00 4.35
2919 3132 1.065928 CGATCTACCACACCCTCGC 59.934 63.158 0.00 0.00 0.00 5.03
2920 3133 1.734137 CCGATCTACCACACCCTCG 59.266 63.158 0.00 0.00 0.00 4.63
2921 3134 2.029307 GCCCGATCTACCACACCCTC 62.029 65.000 0.00 0.00 0.00 4.30
2984 3197 0.028637 GACACGTACGGCTACTAGGC 59.971 60.000 21.06 0.00 37.44 3.93
3160 3380 3.330267 TGTTCATGCGCACAGTTACATA 58.670 40.909 14.90 0.00 0.00 2.29
3169 3389 0.711670 CATTGCTTGTTCATGCGCAC 59.288 50.000 14.90 0.00 31.24 5.34
3208 3428 4.184079 GCTTGATGCAGGATTTTTCAGT 57.816 40.909 0.00 0.00 42.31 3.41
3245 3466 5.734720 TCCTATTTCTTCACATCTGGACAC 58.265 41.667 0.00 0.00 0.00 3.67
3247 3468 5.238214 GCATCCTATTTCTTCACATCTGGAC 59.762 44.000 0.00 0.00 0.00 4.02
3251 3472 5.028549 ACGCATCCTATTTCTTCACATCT 57.971 39.130 0.00 0.00 0.00 2.90
3252 3473 4.811024 TGACGCATCCTATTTCTTCACATC 59.189 41.667 0.00 0.00 0.00 3.06
3253 3474 4.769688 TGACGCATCCTATTTCTTCACAT 58.230 39.130 0.00 0.00 0.00 3.21
3254 3475 4.183865 CTGACGCATCCTATTTCTTCACA 58.816 43.478 0.00 0.00 0.00 3.58
3255 3476 3.001736 GCTGACGCATCCTATTTCTTCAC 59.998 47.826 0.00 0.00 35.78 3.18
3272 3493 5.698089 TCCTCGATATGAAATTCATGCTGAC 59.302 40.000 17.93 4.69 37.70 3.51
3281 3502 9.790344 AGAAGAATCATTCCTCGATATGAAATT 57.210 29.630 8.49 5.16 34.69 1.82
3291 3512 3.559242 GCCTTCAGAAGAATCATTCCTCG 59.441 47.826 12.14 0.00 32.31 4.63
3298 3519 5.416952 GGAAAATGAGCCTTCAGAAGAATCA 59.583 40.000 12.14 14.27 36.61 2.57
3307 3528 5.762179 TTCTCTAGGAAAATGAGCCTTCA 57.238 39.130 0.00 0.00 37.81 3.02
3340 3561 7.962373 CGCAGATTACTGAAGTAGATCTATCTG 59.038 40.741 16.74 16.74 46.03 2.90
3342 3563 7.812648 ACGCAGATTACTGAAGTAGATCTATC 58.187 38.462 5.57 0.95 46.03 2.08
3344 3565 7.569639 AACGCAGATTACTGAAGTAGATCTA 57.430 36.000 0.00 0.00 46.03 1.98
3350 3572 6.312918 GGATTGAAACGCAGATTACTGAAGTA 59.687 38.462 0.00 0.00 46.03 2.24
3359 3581 6.949352 AGATAATGGATTGAAACGCAGATT 57.051 33.333 0.00 0.00 0.00 2.40
3361 3583 7.857734 TTAAGATAATGGATTGAAACGCAGA 57.142 32.000 0.00 0.00 0.00 4.26
3388 3613 4.321750 GCAGCTCCCGTACATTAGCTATTA 60.322 45.833 11.28 0.00 43.26 0.98
3389 3614 3.555168 GCAGCTCCCGTACATTAGCTATT 60.555 47.826 11.28 0.00 43.26 1.73
3390 3615 2.028930 GCAGCTCCCGTACATTAGCTAT 60.029 50.000 11.28 0.00 43.26 2.97
3391 3616 1.340248 GCAGCTCCCGTACATTAGCTA 59.660 52.381 11.28 0.00 43.26 3.32
3392 3617 0.105039 GCAGCTCCCGTACATTAGCT 59.895 55.000 6.95 6.95 45.94 3.32
3405 3630 2.003196 AGCTAAAAGTCGAGCAGCTC 57.997 50.000 12.94 12.94 38.12 4.09
3414 3639 9.709600 GCAGACATAGAAATTAAGCTAAAAGTC 57.290 33.333 0.00 0.00 0.00 3.01
3440 3665 0.595095 GACACCTGAAAAGCCAGCAG 59.405 55.000 0.00 0.00 32.97 4.24
3498 3723 6.033966 CCAACTTTTCAAAGGTCAGTACAAC 58.966 40.000 4.36 0.00 40.31 3.32
3505 3730 4.081917 GGACAACCAACTTTTCAAAGGTCA 60.082 41.667 4.36 0.00 32.57 4.02
3509 3734 7.488322 TCATAAGGACAACCAACTTTTCAAAG 58.512 34.615 0.00 0.00 39.15 2.77


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

AutoCloner maintained by Alex Coulton.