Multiple sequence alignment - TraesCS1D01G115700

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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 TraesCS1D01G115700 chr1D 100.000 6582 0 0 1 6582 111553380 111546799 0.000000e+00 12155.0
1 TraesCS1D01G115700 chr1A 97.258 3757 51 19 2316 6051 117910291 117906566 0.000000e+00 6320.0
2 TraesCS1D01G115700 chr1A 92.387 1944 81 27 426 2328 117912471 117910554 0.000000e+00 2708.0
3 TraesCS1D01G115700 chr1A 92.754 69 5 0 314 382 117932213 117932145 4.200000e-17 100.0
4 TraesCS1D01G115700 chr1A 100.000 29 0 0 2451 2479 117910237 117910209 3.000000e-03 54.7
5 TraesCS1D01G115700 chr1B 93.544 2401 97 26 2760 5153 170572821 170570472 0.000000e+00 3522.0
6 TraesCS1D01G115700 chr1B 92.714 2100 95 26 181 2237 170576935 170574851 0.000000e+00 2977.0
7 TraesCS1D01G115700 chr1B 97.417 542 14 0 5510 6051 170570095 170569554 0.000000e+00 924.0
8 TraesCS1D01G115700 chr1B 94.896 529 21 4 2223 2750 170573709 170573186 0.000000e+00 822.0
9 TraesCS1D01G115700 chr1B 96.000 325 11 2 5162 5485 170570413 170570090 1.630000e-145 527.0
10 TraesCS1D01G115700 chr7B 95.247 526 17 8 6056 6580 66388657 66389175 0.000000e+00 826.0
11 TraesCS1D01G115700 chr7B 94.184 533 23 8 6051 6580 290090838 290091365 0.000000e+00 806.0
12 TraesCS1D01G115700 chr5B 94.867 526 18 9 6056 6580 398166821 398166304 0.000000e+00 813.0
13 TraesCS1D01G115700 chr3D 94.549 532 19 8 6051 6580 79589116 79588593 0.000000e+00 813.0
14 TraesCS1D01G115700 chr2D 94.497 527 22 7 6056 6580 250451976 250452497 0.000000e+00 806.0
15 TraesCS1D01G115700 chr5A 94.487 526 21 8 6056 6580 642652952 642652434 0.000000e+00 804.0
16 TraesCS1D01G115700 chr5D 94.173 532 21 8 6051 6580 296697917 296697394 0.000000e+00 802.0
17 TraesCS1D01G115700 chr3B 94.487 526 20 9 6056 6580 24546723 24547240 0.000000e+00 802.0
18 TraesCS1D01G115700 chr3B 94.318 528 23 6 6056 6580 325818727 325819250 0.000000e+00 802.0
19 TraesCS1D01G115700 chr6A 90.042 472 31 4 1808 2272 58077224 58076762 1.220000e-166 597.0
20 TraesCS1D01G115700 chr6A 97.590 166 3 1 2316 2481 58076462 58076298 3.890000e-72 283.0
21 TraesCS1D01G115700 chr6A 99.115 113 1 0 2629 2741 58076300 58076188 3.110000e-48 204.0
22 TraesCS1D01G115700 chr7A 89.706 68 6 1 2472 2539 563554892 563554958 1.180000e-12 86.1
23 TraesCS1D01G115700 chr4D 75.127 197 39 10 2092 2283 300861006 300861197 4.230000e-12 84.2


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 TraesCS1D01G115700 chr1D 111546799 111553380 6581 True 12155.000000 12155 100.000000 1 6582 1 chr1D.!!$R1 6581
1 TraesCS1D01G115700 chr1A 117906566 117912471 5905 True 3027.566667 6320 96.548333 426 6051 3 chr1A.!!$R2 5625
2 TraesCS1D01G115700 chr1B 170569554 170576935 7381 True 1754.400000 3522 94.914200 181 6051 5 chr1B.!!$R1 5870
3 TraesCS1D01G115700 chr7B 66388657 66389175 518 False 826.000000 826 95.247000 6056 6580 1 chr7B.!!$F1 524
4 TraesCS1D01G115700 chr7B 290090838 290091365 527 False 806.000000 806 94.184000 6051 6580 1 chr7B.!!$F2 529
5 TraesCS1D01G115700 chr5B 398166304 398166821 517 True 813.000000 813 94.867000 6056 6580 1 chr5B.!!$R1 524
6 TraesCS1D01G115700 chr3D 79588593 79589116 523 True 813.000000 813 94.549000 6051 6580 1 chr3D.!!$R1 529
7 TraesCS1D01G115700 chr2D 250451976 250452497 521 False 806.000000 806 94.497000 6056 6580 1 chr2D.!!$F1 524
8 TraesCS1D01G115700 chr5A 642652434 642652952 518 True 804.000000 804 94.487000 6056 6580 1 chr5A.!!$R1 524
9 TraesCS1D01G115700 chr5D 296697394 296697917 523 True 802.000000 802 94.173000 6051 6580 1 chr5D.!!$R1 529
10 TraesCS1D01G115700 chr3B 24546723 24547240 517 False 802.000000 802 94.487000 6056 6580 1 chr3B.!!$F1 524
11 TraesCS1D01G115700 chr3B 325818727 325819250 523 False 802.000000 802 94.318000 6056 6580 1 chr3B.!!$F2 524
12 TraesCS1D01G115700 chr6A 58076188 58077224 1036 True 361.333333 597 95.582333 1808 2741 3 chr6A.!!$R1 933

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
371 372 0.385098 TTACTGCTCGTCACACGTCG 60.385 55.0 0.0 0.0 43.14 5.12 F
1636 1705 0.251787 GCTTTCAGGTGGATTGGGGT 60.252 55.0 0.0 0.0 0.00 4.95 F
2007 2079 0.751643 ACAACCACACTGAGCCCAAC 60.752 55.0 0.0 0.0 0.00 3.77 F
2116 2200 1.083489 CATGATAAACCACGCACGGT 58.917 50.0 0.0 0.0 42.71 4.83 F
4016 6164 2.350772 CCGTGGTTCATGCTGTCTTTTC 60.351 50.0 0.0 0.0 0.00 2.29 F
4446 6595 1.173043 TAACCTTTTCTGCCGCCATG 58.827 50.0 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 1866 0.399075 AAACAGTACAGGTTCCCCCG 59.601 55.000 0.00 0.0 38.74 5.73 R
2813 4958 1.065854 ACACCAGAGCCATGTAGAAGC 60.066 52.381 0.00 0.0 0.00 3.86 R
3993 6141 0.973632 AGACAGCATGAACCACGGTA 59.026 50.000 0.00 0.0 39.69 4.02 R
4110 6259 1.605202 CCCACAGGAAAACAAATGGCG 60.605 52.381 0.00 0.0 33.47 5.69 R
5110 7266 8.678199 CCATCGATGTAGCTAGATATCAACTTA 58.322 37.037 23.27 0.0 0.00 2.24 R
6190 8406 2.237643 TGAGTTTAGGGTGTGTGTGTGT 59.762 45.455 0.00 0.0 0.00 3.72 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
49 50 5.828299 TTTGATAAATACTCGCCCAAAGG 57.172 39.130 0.00 0.00 0.00 3.11
63 64 4.660789 CCCAAAGGCCATTGAAGATAAG 57.339 45.455 22.03 3.27 31.84 1.73
64 65 3.385755 CCCAAAGGCCATTGAAGATAAGG 59.614 47.826 22.03 8.72 31.84 2.69
65 66 3.181472 CCAAAGGCCATTGAAGATAAGGC 60.181 47.826 22.03 0.00 44.48 4.35
66 67 1.972872 AGGCCATTGAAGATAAGGCG 58.027 50.000 5.01 0.00 46.12 5.52
67 68 0.954452 GGCCATTGAAGATAAGGCGG 59.046 55.000 0.00 0.00 46.12 6.13
68 69 1.476833 GGCCATTGAAGATAAGGCGGA 60.477 52.381 0.00 0.00 46.12 5.54
69 70 2.508526 GCCATTGAAGATAAGGCGGAT 58.491 47.619 0.00 0.00 35.42 4.18
70 71 2.887152 GCCATTGAAGATAAGGCGGATT 59.113 45.455 0.00 0.00 35.42 3.01
71 72 3.304928 GCCATTGAAGATAAGGCGGATTG 60.305 47.826 0.00 0.00 35.42 2.67
72 73 3.885297 CCATTGAAGATAAGGCGGATTGT 59.115 43.478 0.00 0.00 0.00 2.71
73 74 4.023707 CCATTGAAGATAAGGCGGATTGTC 60.024 45.833 0.00 0.00 0.00 3.18
74 75 2.821546 TGAAGATAAGGCGGATTGTCG 58.178 47.619 0.00 0.00 0.00 4.35
75 76 2.135933 GAAGATAAGGCGGATTGTCGG 58.864 52.381 0.00 0.00 0.00 4.79
98 99 2.840102 CCGGCGGGAGGAGAAGAT 60.840 66.667 20.56 0.00 34.06 2.40
99 100 1.530891 CCGGCGGGAGGAGAAGATA 60.531 63.158 20.56 0.00 34.06 1.98
100 101 1.113517 CCGGCGGGAGGAGAAGATAA 61.114 60.000 20.56 0.00 34.06 1.75
101 102 0.750850 CGGCGGGAGGAGAAGATAAA 59.249 55.000 0.00 0.00 0.00 1.40
102 103 1.269831 CGGCGGGAGGAGAAGATAAAG 60.270 57.143 0.00 0.00 0.00 1.85
103 104 1.541452 GGCGGGAGGAGAAGATAAAGC 60.541 57.143 0.00 0.00 0.00 3.51
104 105 1.414550 GCGGGAGGAGAAGATAAAGCT 59.585 52.381 0.00 0.00 0.00 3.74
105 106 2.804933 GCGGGAGGAGAAGATAAAGCTG 60.805 54.545 0.00 0.00 0.00 4.24
106 107 2.695666 CGGGAGGAGAAGATAAAGCTGA 59.304 50.000 0.00 0.00 0.00 4.26
107 108 3.243704 CGGGAGGAGAAGATAAAGCTGAG 60.244 52.174 0.00 0.00 0.00 3.35
108 109 3.070878 GGGAGGAGAAGATAAAGCTGAGG 59.929 52.174 0.00 0.00 0.00 3.86
109 110 3.494223 GGAGGAGAAGATAAAGCTGAGGC 60.494 52.174 0.00 0.00 39.06 4.70
110 111 2.102252 AGGAGAAGATAAAGCTGAGGCG 59.898 50.000 0.00 0.00 44.37 5.52
111 112 2.159028 GGAGAAGATAAAGCTGAGGCGT 60.159 50.000 0.00 0.00 44.37 5.68
112 113 3.526534 GAGAAGATAAAGCTGAGGCGTT 58.473 45.455 0.00 0.00 44.37 4.84
113 114 3.935828 GAGAAGATAAAGCTGAGGCGTTT 59.064 43.478 0.00 0.00 44.37 3.60
114 115 4.327680 AGAAGATAAAGCTGAGGCGTTTT 58.672 39.130 0.00 0.00 44.37 2.43
115 116 4.393371 AGAAGATAAAGCTGAGGCGTTTTC 59.607 41.667 0.00 0.00 44.37 2.29
116 117 3.944087 AGATAAAGCTGAGGCGTTTTCT 58.056 40.909 0.00 4.57 40.72 2.52
117 118 4.327680 AGATAAAGCTGAGGCGTTTTCTT 58.672 39.130 0.00 0.00 41.88 2.52
118 119 2.781945 AAAGCTGAGGCGTTTTCTTG 57.218 45.000 0.00 0.00 44.37 3.02
119 120 1.680338 AAGCTGAGGCGTTTTCTTGT 58.320 45.000 0.00 0.00 44.37 3.16
120 121 1.680338 AGCTGAGGCGTTTTCTTGTT 58.320 45.000 0.00 0.00 44.37 2.83
121 122 1.334869 AGCTGAGGCGTTTTCTTGTTG 59.665 47.619 0.00 0.00 44.37 3.33
122 123 1.333619 GCTGAGGCGTTTTCTTGTTGA 59.666 47.619 0.00 0.00 0.00 3.18
123 124 2.603173 GCTGAGGCGTTTTCTTGTTGAG 60.603 50.000 0.00 0.00 0.00 3.02
124 125 1.946768 TGAGGCGTTTTCTTGTTGAGG 59.053 47.619 0.00 0.00 0.00 3.86
125 126 2.218603 GAGGCGTTTTCTTGTTGAGGA 58.781 47.619 0.00 0.00 0.00 3.71
126 127 2.616842 GAGGCGTTTTCTTGTTGAGGAA 59.383 45.455 0.00 0.00 0.00 3.36
127 128 3.020984 AGGCGTTTTCTTGTTGAGGAAA 58.979 40.909 0.00 0.00 30.13 3.13
128 129 3.066760 AGGCGTTTTCTTGTTGAGGAAAG 59.933 43.478 0.00 0.00 33.46 2.62
129 130 3.066203 GGCGTTTTCTTGTTGAGGAAAGA 59.934 43.478 0.00 0.00 33.46 2.52
130 131 4.282873 GCGTTTTCTTGTTGAGGAAAGAG 58.717 43.478 0.00 0.00 33.46 2.85
131 132 4.282873 CGTTTTCTTGTTGAGGAAAGAGC 58.717 43.478 0.00 0.00 33.46 4.09
132 133 4.035675 CGTTTTCTTGTTGAGGAAAGAGCT 59.964 41.667 0.00 0.00 33.46 4.09
133 134 5.515184 GTTTTCTTGTTGAGGAAAGAGCTC 58.485 41.667 5.27 5.27 33.46 4.09
134 135 3.409026 TCTTGTTGAGGAAAGAGCTCC 57.591 47.619 10.93 0.00 35.51 4.70
136 137 2.847327 TGTTGAGGAAAGAGCTCCTG 57.153 50.000 10.93 0.00 46.33 3.86
137 138 2.329267 TGTTGAGGAAAGAGCTCCTGA 58.671 47.619 10.93 0.00 46.33 3.86
138 139 2.037772 TGTTGAGGAAAGAGCTCCTGAC 59.962 50.000 10.93 3.32 46.33 3.51
139 140 2.301583 GTTGAGGAAAGAGCTCCTGACT 59.698 50.000 10.93 4.07 46.33 3.41
140 141 3.458044 TGAGGAAAGAGCTCCTGACTA 57.542 47.619 10.93 0.00 46.33 2.59
141 142 3.779444 TGAGGAAAGAGCTCCTGACTAA 58.221 45.455 10.93 0.00 46.33 2.24
142 143 4.357325 TGAGGAAAGAGCTCCTGACTAAT 58.643 43.478 10.93 0.00 46.33 1.73
143 144 4.161189 TGAGGAAAGAGCTCCTGACTAATG 59.839 45.833 10.93 0.00 46.33 1.90
144 145 4.100373 AGGAAAGAGCTCCTGACTAATGT 58.900 43.478 10.93 0.00 44.56 2.71
145 146 4.534103 AGGAAAGAGCTCCTGACTAATGTT 59.466 41.667 10.93 0.00 44.56 2.71
146 147 5.013599 AGGAAAGAGCTCCTGACTAATGTTT 59.986 40.000 10.93 0.00 44.56 2.83
147 148 5.707764 GGAAAGAGCTCCTGACTAATGTTTT 59.292 40.000 10.93 0.00 32.21 2.43
148 149 6.128145 GGAAAGAGCTCCTGACTAATGTTTTC 60.128 42.308 10.93 8.87 32.21 2.29
149 150 5.489792 AGAGCTCCTGACTAATGTTTTCA 57.510 39.130 10.93 0.00 0.00 2.69
150 151 6.059787 AGAGCTCCTGACTAATGTTTTCAT 57.940 37.500 10.93 0.00 43.05 2.57
166 167 8.970691 ATGTTTTCATTATGTTGTAGTTGCTC 57.029 30.769 0.00 0.00 37.19 4.26
167 168 8.165239 TGTTTTCATTATGTTGTAGTTGCTCT 57.835 30.769 0.00 0.00 0.00 4.09
168 169 8.075574 TGTTTTCATTATGTTGTAGTTGCTCTG 58.924 33.333 0.00 0.00 0.00 3.35
169 170 7.977789 TTTCATTATGTTGTAGTTGCTCTGA 57.022 32.000 0.00 0.00 0.00 3.27
170 171 7.601073 TTCATTATGTTGTAGTTGCTCTGAG 57.399 36.000 0.00 0.00 0.00 3.35
171 172 6.935167 TCATTATGTTGTAGTTGCTCTGAGA 58.065 36.000 9.28 0.00 0.00 3.27
172 173 6.813649 TCATTATGTTGTAGTTGCTCTGAGAC 59.186 38.462 9.28 0.00 0.00 3.36
173 174 4.607293 ATGTTGTAGTTGCTCTGAGACA 57.393 40.909 9.28 3.27 0.00 3.41
174 175 4.607293 TGTTGTAGTTGCTCTGAGACAT 57.393 40.909 9.28 0.00 0.00 3.06
175 176 4.560128 TGTTGTAGTTGCTCTGAGACATC 58.440 43.478 9.28 5.61 0.00 3.06
176 177 3.494045 TGTAGTTGCTCTGAGACATCG 57.506 47.619 9.28 0.00 0.00 3.84
177 178 2.820197 TGTAGTTGCTCTGAGACATCGT 59.180 45.455 9.28 0.00 0.00 3.73
178 179 2.645730 AGTTGCTCTGAGACATCGTC 57.354 50.000 9.28 0.00 0.00 4.20
179 180 2.166829 AGTTGCTCTGAGACATCGTCT 58.833 47.619 9.28 0.00 46.42 4.18
197 198 8.283291 ACATCGTCTTCTTAATTTGAGAACAAC 58.717 33.333 0.00 1.98 35.63 3.32
236 237 8.800370 TTAAAAGAATGCAAAACTTTTTCCCT 57.200 26.923 23.33 10.07 41.75 4.20
260 261 1.878953 TCTCTTTCTTCCACCGCAAC 58.121 50.000 0.00 0.00 0.00 4.17
264 265 2.103432 TCTTTCTTCCACCGCAACACTA 59.897 45.455 0.00 0.00 0.00 2.74
266 267 2.851263 TCTTCCACCGCAACACTAAT 57.149 45.000 0.00 0.00 0.00 1.73
298 299 7.115663 GTGACACTTGTAAAACAACAACATTGT 59.884 33.333 0.00 0.00 44.72 2.71
299 300 8.297426 TGACACTTGTAAAACAACAACATTGTA 58.703 29.630 0.00 0.00 41.31 2.41
300 301 8.455598 ACACTTGTAAAACAACAACATTGTAC 57.544 30.769 0.00 0.00 41.31 2.90
307 308 9.002080 GTAAAACAACAACATTGTACTACACAC 57.998 33.333 0.00 0.00 41.31 3.82
327 328 1.271488 CCCTTGTACTTTACCGCCCAA 60.271 52.381 0.00 0.00 0.00 4.12
353 354 4.259933 ACACCCCTCTTAAACCAGTTTT 57.740 40.909 0.37 0.00 34.23 2.43
371 372 0.385098 TTACTGCTCGTCACACGTCG 60.385 55.000 0.00 0.00 43.14 5.12
376 377 2.430075 TCGTCACACGTCGCATGG 60.430 61.111 0.00 0.00 43.14 3.66
541 545 2.134630 CTTTGCTGCTCCCTGTCCCT 62.135 60.000 0.00 0.00 0.00 4.20
542 546 2.129555 TTTGCTGCTCCCTGTCCCTC 62.130 60.000 0.00 0.00 0.00 4.30
607 631 3.927163 AACGTGGATCCGCACCGTC 62.927 63.158 24.60 0.37 0.00 4.79
878 927 4.869440 CCGCTCCGCTCTGCTCTG 62.869 72.222 0.00 0.00 0.00 3.35
897 951 4.074526 TCTGCCACGCTCTGCTCC 62.075 66.667 0.00 0.00 0.00 4.70
1095 1150 2.342648 GTCACCGGCGTCTTCCTT 59.657 61.111 6.01 0.00 0.00 3.36
1337 1401 0.531753 GCCCTTCTCGCTTCATCTCC 60.532 60.000 0.00 0.00 0.00 3.71
1392 1456 7.009568 AGCGAATGAGTGAATTAATCTCAAC 57.990 36.000 8.84 6.39 40.73 3.18
1434 1498 1.678728 GCGGATCAGGGTGACAATGAA 60.679 52.381 0.00 0.00 32.24 2.57
1547 1611 0.756903 AACAGCGTCCAGGTTAGTGT 59.243 50.000 0.00 0.00 0.00 3.55
1548 1612 0.317479 ACAGCGTCCAGGTTAGTGTC 59.683 55.000 0.00 0.00 0.00 3.67
1550 1614 1.445582 GCGTCCAGGTTAGTGTCGG 60.446 63.158 0.00 0.00 0.00 4.79
1551 1615 1.870055 GCGTCCAGGTTAGTGTCGGA 61.870 60.000 0.00 0.00 0.00 4.55
1554 1618 0.606604 TCCAGGTTAGTGTCGGAAGC 59.393 55.000 0.00 0.00 0.00 3.86
1568 1637 3.321111 GTCGGAAGCTCCTACCATATGAA 59.679 47.826 3.65 0.00 33.30 2.57
1577 1646 3.068165 TCCTACCATATGAACTCTGCGTG 59.932 47.826 3.65 0.00 0.00 5.34
1590 1659 1.153469 TGCGTGCGATGCTCCATTA 60.153 52.632 0.00 0.00 0.00 1.90
1598 1667 1.606480 CGATGCTCCATTACTGCCGAT 60.606 52.381 0.00 0.00 0.00 4.18
1636 1705 0.251787 GCTTTCAGGTGGATTGGGGT 60.252 55.000 0.00 0.00 0.00 4.95
1805 1875 4.202161 AGATAAGGTCTAACGGGGGAACC 61.202 52.174 0.00 0.00 42.97 3.62
1886 1958 7.617041 AGTAAAGTGGAAAATCTGCTGTATC 57.383 36.000 0.00 0.00 0.00 2.24
1904 1976 6.683861 GCTGTATCATGTCCTGAGATTGTGTA 60.684 42.308 0.00 0.00 37.28 2.90
1905 1977 6.573434 TGTATCATGTCCTGAGATTGTGTAC 58.427 40.000 0.00 0.00 37.28 2.90
1906 1978 4.471904 TCATGTCCTGAGATTGTGTACC 57.528 45.455 0.00 0.00 0.00 3.34
1907 1979 3.197766 TCATGTCCTGAGATTGTGTACCC 59.802 47.826 0.00 0.00 0.00 3.69
1915 1987 4.062293 TGAGATTGTGTACCCGTTTCTTG 58.938 43.478 0.00 0.00 0.00 3.02
1930 2002 4.035792 CGTTTCTTGTGTTGTCCCATGTAA 59.964 41.667 0.00 0.00 0.00 2.41
1940 2012 7.285629 TGTGTTGTCCCATGTAAATTGTCTTAA 59.714 33.333 0.00 0.00 0.00 1.85
1941 2013 7.593644 GTGTTGTCCCATGTAAATTGTCTTAAC 59.406 37.037 0.00 0.00 0.00 2.01
1994 2066 9.772973 AATCGTTATATCAAGCTAATACAACCA 57.227 29.630 0.00 0.00 0.00 3.67
2007 2079 0.751643 ACAACCACACTGAGCCCAAC 60.752 55.000 0.00 0.00 0.00 3.77
2048 2120 1.691976 ACCAACATGTCCGAGAGAACA 59.308 47.619 0.00 0.00 0.00 3.18
2116 2200 1.083489 CATGATAAACCACGCACGGT 58.917 50.000 0.00 0.00 42.71 4.83
2169 2253 8.827177 ACACACGAGATGAAATACTCTTTTTA 57.173 30.769 0.00 0.00 0.00 1.52
2561 4350 5.657302 CCACCTAAACATACTGGTAGACTCT 59.343 44.000 0.00 0.00 0.00 3.24
2778 4923 7.899172 TGGTAATCCACATGTATAGCTATACCT 59.101 37.037 31.61 23.28 39.03 3.08
2813 4958 3.318839 TGGGTCTGTTGCAAATTTGAGAG 59.681 43.478 22.31 9.70 0.00 3.20
3202 5347 3.731652 TTCATGCACCTTGACCTTTTG 57.268 42.857 0.00 0.00 0.00 2.44
3438 5586 8.355913 ACTGATGAAAGAAGAAAGATGGAAAAC 58.644 33.333 0.00 0.00 0.00 2.43
3557 5705 4.829064 TGCTGAAGTTGTGGTTTATGAC 57.171 40.909 0.00 0.00 0.00 3.06
3721 5869 8.405531 TCAAGATAATGGCACTTAAATAGTTGC 58.594 33.333 0.00 0.00 33.85 4.17
3967 6115 5.704053 AGTGAGACCCTTTAACAAAATACCG 59.296 40.000 0.00 0.00 0.00 4.02
3993 6141 7.921041 TCCATCTATTTCTGGAGTATCTTGT 57.079 36.000 0.00 0.00 36.63 3.16
4016 6164 2.350772 CCGTGGTTCATGCTGTCTTTTC 60.351 50.000 0.00 0.00 0.00 2.29
4024 6172 6.369799 GTTCATGCTGTCTTTTCTTCTTCTC 58.630 40.000 0.00 0.00 0.00 2.87
4110 6259 5.934625 ACAGATTAGAGGTTGTGTTCATCAC 59.065 40.000 0.00 0.00 46.31 3.06
4207 6356 2.169561 TGATCCGTGCCTGTATTTGCTA 59.830 45.455 0.00 0.00 0.00 3.49
4226 6375 8.876275 TTTGCTATAATGTTAACTAGTACCCG 57.124 34.615 7.22 0.00 0.00 5.28
4270 6419 6.531594 TGTTTGTTTTCATCAACGTATGCAAA 59.468 30.769 0.00 0.00 0.00 3.68
4404 6553 8.794335 AGTGGAACCAAAGTTAGATTAATCTC 57.206 34.615 21.17 8.52 37.80 2.75
4405 6554 8.383175 AGTGGAACCAAAGTTAGATTAATCTCA 58.617 33.333 21.17 8.28 37.80 3.27
4406 6555 9.178758 GTGGAACCAAAGTTAGATTAATCTCAT 57.821 33.333 21.17 6.24 38.32 2.90
4441 6590 2.487762 TCTGCAATAACCTTTTCTGCCG 59.512 45.455 0.00 0.00 31.92 5.69
4446 6595 1.173043 TAACCTTTTCTGCCGCCATG 58.827 50.000 0.00 0.00 0.00 3.66
4484 6633 6.398234 TGTAGTGAAGCCAAATTTTAAGCA 57.602 33.333 7.22 0.00 0.00 3.91
4494 6643 5.174943 GCCAAATTTTAAGCACGGCATATAC 59.825 40.000 8.21 0.00 37.98 1.47
5110 7266 6.815089 TGTTTTGGTTTGCTGAGTTTGATAT 58.185 32.000 0.00 0.00 0.00 1.63
5278 7484 8.354426 GTTCACTGAGGGTCTATCTCTTTATAC 58.646 40.741 0.00 0.00 32.78 1.47
6001 8209 1.802508 CGAGCGTATGGAACTGCATGA 60.803 52.381 0.00 0.00 32.36 3.07
6016 8224 5.891451 ACTGCATGATTCACATTGATTCAG 58.109 37.500 0.00 0.00 39.28 3.02
6051 8259 8.200120 TGTTGATAATCTAGATGGTCAGAAGTG 58.800 37.037 5.86 0.00 0.00 3.16
6052 8260 7.904558 TGATAATCTAGATGGTCAGAAGTGT 57.095 36.000 5.86 0.00 0.00 3.55
6053 8261 8.311395 TGATAATCTAGATGGTCAGAAGTGTT 57.689 34.615 5.86 0.00 0.00 3.32
6054 8262 8.200120 TGATAATCTAGATGGTCAGAAGTGTTG 58.800 37.037 5.86 0.00 0.00 3.33
6069 8277 7.119699 TCAGAAGTGTTGGAATAGCAACTTATG 59.880 37.037 0.00 0.00 32.91 1.90
6151 8360 4.961730 AGAGGATGCAAGAGACTAGAATGT 59.038 41.667 0.00 0.00 0.00 2.71
6198 8414 9.984190 TTAATATAACTCTAACACACACACACA 57.016 29.630 0.00 0.00 0.00 3.72
6200 8416 3.603158 ACTCTAACACACACACACACA 57.397 42.857 0.00 0.00 0.00 3.72
6201 8417 3.259064 ACTCTAACACACACACACACAC 58.741 45.455 0.00 0.00 0.00 3.82
6203 8419 1.668751 CTAACACACACACACACACCC 59.331 52.381 0.00 0.00 0.00 4.61
6204 8420 0.037590 AACACACACACACACACCCT 59.962 50.000 0.00 0.00 0.00 4.34
6336 8553 3.084039 TGAAGAGCAACAACATGATCCC 58.916 45.455 0.00 0.00 36.40 3.85
6539 8756 1.519234 CATAGCTCGCAACTCGGCA 60.519 57.895 0.00 0.00 37.01 5.69
6580 8797 3.318275 ACTGCAGTCTGTTTCTTCGTCTA 59.682 43.478 15.25 0.00 0.00 2.59
6581 8798 4.202121 ACTGCAGTCTGTTTCTTCGTCTAA 60.202 41.667 15.25 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.626302 CCTTTGGGCGAGTATTTATCAAAAA 58.374 36.000 0.00 0.00 0.00 1.94
26 27 6.202516 CCTTTGGGCGAGTATTTATCAAAA 57.797 37.500 0.00 0.00 0.00 2.44
27 28 5.828299 CCTTTGGGCGAGTATTTATCAAA 57.172 39.130 0.00 0.00 0.00 2.69
42 43 3.385755 CCTTATCTTCAATGGCCTTTGGG 59.614 47.826 26.26 19.74 0.00 4.12
43 44 3.181472 GCCTTATCTTCAATGGCCTTTGG 60.181 47.826 26.26 14.37 37.81 3.28
44 45 3.489738 CGCCTTATCTTCAATGGCCTTTG 60.490 47.826 22.31 22.31 40.40 2.77
45 46 2.689983 CGCCTTATCTTCAATGGCCTTT 59.310 45.455 3.32 0.00 40.40 3.11
46 47 2.301346 CGCCTTATCTTCAATGGCCTT 58.699 47.619 3.32 0.00 40.40 4.35
47 48 1.477558 CCGCCTTATCTTCAATGGCCT 60.478 52.381 3.32 0.00 40.40 5.19
48 49 0.954452 CCGCCTTATCTTCAATGGCC 59.046 55.000 0.00 0.00 40.40 5.36
49 50 1.967319 TCCGCCTTATCTTCAATGGC 58.033 50.000 0.00 0.00 40.14 4.40
50 51 3.885297 ACAATCCGCCTTATCTTCAATGG 59.115 43.478 0.00 0.00 0.00 3.16
51 52 4.319046 CGACAATCCGCCTTATCTTCAATG 60.319 45.833 0.00 0.00 0.00 2.82
52 53 3.809832 CGACAATCCGCCTTATCTTCAAT 59.190 43.478 0.00 0.00 0.00 2.57
53 54 3.194861 CGACAATCCGCCTTATCTTCAA 58.805 45.455 0.00 0.00 0.00 2.69
54 55 2.483013 CCGACAATCCGCCTTATCTTCA 60.483 50.000 0.00 0.00 0.00 3.02
55 56 2.135933 CCGACAATCCGCCTTATCTTC 58.864 52.381 0.00 0.00 0.00 2.87
56 57 1.810412 GCCGACAATCCGCCTTATCTT 60.810 52.381 0.00 0.00 0.00 2.40
57 58 0.249911 GCCGACAATCCGCCTTATCT 60.250 55.000 0.00 0.00 0.00 1.98
58 59 1.557443 CGCCGACAATCCGCCTTATC 61.557 60.000 0.00 0.00 0.00 1.75
59 60 1.594293 CGCCGACAATCCGCCTTAT 60.594 57.895 0.00 0.00 0.00 1.73
60 61 2.202824 CGCCGACAATCCGCCTTA 60.203 61.111 0.00 0.00 0.00 2.69
81 82 1.113517 TTATCTTCTCCTCCCGCCGG 61.114 60.000 0.00 0.00 0.00 6.13
82 83 0.750850 TTTATCTTCTCCTCCCGCCG 59.249 55.000 0.00 0.00 0.00 6.46
83 84 1.541452 GCTTTATCTTCTCCTCCCGCC 60.541 57.143 0.00 0.00 0.00 6.13
84 85 1.414550 AGCTTTATCTTCTCCTCCCGC 59.585 52.381 0.00 0.00 0.00 6.13
85 86 2.695666 TCAGCTTTATCTTCTCCTCCCG 59.304 50.000 0.00 0.00 0.00 5.14
86 87 3.070878 CCTCAGCTTTATCTTCTCCTCCC 59.929 52.174 0.00 0.00 0.00 4.30
87 88 3.494223 GCCTCAGCTTTATCTTCTCCTCC 60.494 52.174 0.00 0.00 35.50 4.30
88 89 3.727726 GCCTCAGCTTTATCTTCTCCTC 58.272 50.000 0.00 0.00 35.50 3.71
89 90 2.102252 CGCCTCAGCTTTATCTTCTCCT 59.898 50.000 0.00 0.00 36.60 3.69
90 91 2.159028 ACGCCTCAGCTTTATCTTCTCC 60.159 50.000 0.00 0.00 36.60 3.71
91 92 3.172229 ACGCCTCAGCTTTATCTTCTC 57.828 47.619 0.00 0.00 36.60 2.87
92 93 3.618690 AACGCCTCAGCTTTATCTTCT 57.381 42.857 0.00 0.00 36.60 2.85
93 94 4.393371 AGAAAACGCCTCAGCTTTATCTTC 59.607 41.667 0.00 0.00 36.60 2.87
94 95 4.327680 AGAAAACGCCTCAGCTTTATCTT 58.672 39.130 0.00 0.00 36.60 2.40
95 96 3.944087 AGAAAACGCCTCAGCTTTATCT 58.056 40.909 0.00 0.00 36.60 1.98
96 97 4.083271 ACAAGAAAACGCCTCAGCTTTATC 60.083 41.667 0.00 0.00 36.60 1.75
97 98 3.821033 ACAAGAAAACGCCTCAGCTTTAT 59.179 39.130 0.00 0.00 36.60 1.40
98 99 3.211045 ACAAGAAAACGCCTCAGCTTTA 58.789 40.909 0.00 0.00 36.60 1.85
99 100 2.024414 ACAAGAAAACGCCTCAGCTTT 58.976 42.857 0.00 0.00 36.60 3.51
100 101 1.680338 ACAAGAAAACGCCTCAGCTT 58.320 45.000 0.00 0.00 36.60 3.74
101 102 1.334869 CAACAAGAAAACGCCTCAGCT 59.665 47.619 0.00 0.00 36.60 4.24
102 103 1.333619 TCAACAAGAAAACGCCTCAGC 59.666 47.619 0.00 0.00 0.00 4.26
103 104 2.031682 CCTCAACAAGAAAACGCCTCAG 60.032 50.000 0.00 0.00 0.00 3.35
104 105 1.946768 CCTCAACAAGAAAACGCCTCA 59.053 47.619 0.00 0.00 0.00 3.86
105 106 2.218603 TCCTCAACAAGAAAACGCCTC 58.781 47.619 0.00 0.00 0.00 4.70
106 107 2.341846 TCCTCAACAAGAAAACGCCT 57.658 45.000 0.00 0.00 0.00 5.52
107 108 3.066203 TCTTTCCTCAACAAGAAAACGCC 59.934 43.478 0.00 0.00 31.91 5.68
108 109 4.282873 CTCTTTCCTCAACAAGAAAACGC 58.717 43.478 0.00 0.00 31.91 4.84
109 110 4.035675 AGCTCTTTCCTCAACAAGAAAACG 59.964 41.667 0.00 0.00 31.91 3.60
110 111 5.506483 GGAGCTCTTTCCTCAACAAGAAAAC 60.506 44.000 14.64 0.00 34.27 2.43
111 112 4.580580 GGAGCTCTTTCCTCAACAAGAAAA 59.419 41.667 14.64 0.00 34.27 2.29
112 113 4.137543 GGAGCTCTTTCCTCAACAAGAAA 58.862 43.478 14.64 0.00 34.27 2.52
113 114 3.392616 AGGAGCTCTTTCCTCAACAAGAA 59.607 43.478 14.64 0.00 44.33 2.52
114 115 2.975489 AGGAGCTCTTTCCTCAACAAGA 59.025 45.455 14.64 0.00 44.33 3.02
115 116 3.072944 CAGGAGCTCTTTCCTCAACAAG 58.927 50.000 14.64 0.00 45.86 3.16
116 117 2.705658 TCAGGAGCTCTTTCCTCAACAA 59.294 45.455 14.64 0.00 45.86 2.83
117 118 2.037772 GTCAGGAGCTCTTTCCTCAACA 59.962 50.000 14.64 0.00 45.86 3.33
118 119 2.301583 AGTCAGGAGCTCTTTCCTCAAC 59.698 50.000 14.64 3.94 45.86 3.18
119 120 2.614259 AGTCAGGAGCTCTTTCCTCAA 58.386 47.619 14.64 0.00 45.86 3.02
120 121 2.317371 AGTCAGGAGCTCTTTCCTCA 57.683 50.000 14.64 0.00 45.86 3.86
121 122 4.161377 ACATTAGTCAGGAGCTCTTTCCTC 59.839 45.833 14.64 0.00 45.86 3.71
123 124 4.479786 ACATTAGTCAGGAGCTCTTTCC 57.520 45.455 14.64 0.00 37.52 3.13
124 125 6.428159 TGAAAACATTAGTCAGGAGCTCTTTC 59.572 38.462 14.64 11.02 0.00 2.62
125 126 6.299141 TGAAAACATTAGTCAGGAGCTCTTT 58.701 36.000 14.64 1.15 0.00 2.52
126 127 5.869579 TGAAAACATTAGTCAGGAGCTCTT 58.130 37.500 14.64 2.08 0.00 2.85
127 128 5.489792 TGAAAACATTAGTCAGGAGCTCT 57.510 39.130 14.64 0.00 0.00 4.09
128 129 6.749923 AATGAAAACATTAGTCAGGAGCTC 57.250 37.500 4.71 4.71 0.00 4.09
129 130 7.831193 ACATAATGAAAACATTAGTCAGGAGCT 59.169 33.333 0.00 0.00 31.47 4.09
130 131 7.989826 ACATAATGAAAACATTAGTCAGGAGC 58.010 34.615 0.00 0.00 31.47 4.70
131 132 9.778993 CAACATAATGAAAACATTAGTCAGGAG 57.221 33.333 0.00 0.00 31.47 3.69
132 133 9.295825 ACAACATAATGAAAACATTAGTCAGGA 57.704 29.630 0.00 0.00 31.47 3.86
140 141 9.410556 GAGCAACTACAACATAATGAAAACATT 57.589 29.630 0.00 0.00 0.00 2.71
141 142 8.796475 AGAGCAACTACAACATAATGAAAACAT 58.204 29.630 0.00 0.00 0.00 2.71
142 143 8.075574 CAGAGCAACTACAACATAATGAAAACA 58.924 33.333 0.00 0.00 0.00 2.83
143 144 8.289618 TCAGAGCAACTACAACATAATGAAAAC 58.710 33.333 0.00 0.00 0.00 2.43
144 145 8.389779 TCAGAGCAACTACAACATAATGAAAA 57.610 30.769 0.00 0.00 0.00 2.29
145 146 7.877612 TCTCAGAGCAACTACAACATAATGAAA 59.122 33.333 0.00 0.00 0.00 2.69
146 147 7.331934 GTCTCAGAGCAACTACAACATAATGAA 59.668 37.037 0.00 0.00 0.00 2.57
147 148 6.813649 GTCTCAGAGCAACTACAACATAATGA 59.186 38.462 0.00 0.00 0.00 2.57
148 149 6.591448 TGTCTCAGAGCAACTACAACATAATG 59.409 38.462 0.00 0.00 0.00 1.90
149 150 6.701340 TGTCTCAGAGCAACTACAACATAAT 58.299 36.000 0.00 0.00 0.00 1.28
150 151 6.096673 TGTCTCAGAGCAACTACAACATAA 57.903 37.500 0.00 0.00 0.00 1.90
151 152 5.722021 TGTCTCAGAGCAACTACAACATA 57.278 39.130 0.00 0.00 0.00 2.29
152 153 4.607293 TGTCTCAGAGCAACTACAACAT 57.393 40.909 0.00 0.00 0.00 2.71
153 154 4.560128 GATGTCTCAGAGCAACTACAACA 58.440 43.478 0.00 0.00 0.00 3.33
154 155 3.610242 CGATGTCTCAGAGCAACTACAAC 59.390 47.826 0.00 0.00 0.00 3.32
155 156 3.255888 ACGATGTCTCAGAGCAACTACAA 59.744 43.478 0.00 0.00 0.00 2.41
156 157 2.820197 ACGATGTCTCAGAGCAACTACA 59.180 45.455 0.00 0.00 0.00 2.74
157 158 3.127895 AGACGATGTCTCAGAGCAACTAC 59.872 47.826 0.00 0.00 38.71 2.73
158 159 3.348119 AGACGATGTCTCAGAGCAACTA 58.652 45.455 0.00 0.00 38.71 2.24
159 160 2.166829 AGACGATGTCTCAGAGCAACT 58.833 47.619 0.00 0.00 38.71 3.16
160 161 2.645730 AGACGATGTCTCAGAGCAAC 57.354 50.000 0.00 0.00 38.71 4.17
161 162 2.822561 AGAAGACGATGTCTCAGAGCAA 59.177 45.455 0.00 0.00 42.59 3.91
162 163 2.441410 AGAAGACGATGTCTCAGAGCA 58.559 47.619 0.00 0.00 42.59 4.26
163 164 3.502191 AAGAAGACGATGTCTCAGAGC 57.498 47.619 0.00 0.00 42.59 4.09
164 165 7.757173 TCAAATTAAGAAGACGATGTCTCAGAG 59.243 37.037 0.00 0.00 42.59 3.35
165 166 7.602753 TCAAATTAAGAAGACGATGTCTCAGA 58.397 34.615 0.00 0.00 42.59 3.27
166 167 7.757173 TCTCAAATTAAGAAGACGATGTCTCAG 59.243 37.037 0.00 0.00 42.59 3.35
167 168 7.602753 TCTCAAATTAAGAAGACGATGTCTCA 58.397 34.615 0.00 0.00 42.59 3.27
168 169 8.376942 GTTCTCAAATTAAGAAGACGATGTCTC 58.623 37.037 0.00 0.00 42.59 3.36
169 170 7.872993 TGTTCTCAAATTAAGAAGACGATGTCT 59.127 33.333 3.98 0.00 45.64 3.41
170 171 8.018677 TGTTCTCAAATTAAGAAGACGATGTC 57.981 34.615 3.98 0.00 33.57 3.06
171 172 7.962964 TGTTCTCAAATTAAGAAGACGATGT 57.037 32.000 3.98 0.00 33.57 3.06
172 173 8.282592 TGTTGTTCTCAAATTAAGAAGACGATG 58.717 33.333 3.98 0.00 33.57 3.84
173 174 8.378172 TGTTGTTCTCAAATTAAGAAGACGAT 57.622 30.769 3.98 0.00 33.57 3.73
174 175 7.780008 TGTTGTTCTCAAATTAAGAAGACGA 57.220 32.000 3.98 0.00 33.57 4.20
175 176 8.282592 TGATGTTGTTCTCAAATTAAGAAGACG 58.717 33.333 3.98 0.00 33.57 4.18
218 219 7.564793 AGAAACTAGGGAAAAAGTTTTGCATT 58.435 30.769 8.61 0.00 43.97 3.56
236 237 3.070446 TGCGGTGGAAGAAAGAGAAACTA 59.930 43.478 0.00 0.00 0.00 2.24
281 282 9.002080 GTGTGTAGTACAATGTTGTTGTTTTAC 57.998 33.333 4.11 3.95 41.89 2.01
298 299 5.048083 CGGTAAAGTACAAGGGTGTGTAGTA 60.048 44.000 0.00 0.00 36.77 1.82
299 300 4.262164 CGGTAAAGTACAAGGGTGTGTAGT 60.262 45.833 0.00 0.00 38.93 2.73
300 301 4.240096 CGGTAAAGTACAAGGGTGTGTAG 58.760 47.826 0.00 0.00 38.82 2.74
307 308 0.325602 TGGGCGGTAAAGTACAAGGG 59.674 55.000 0.00 0.00 0.00 3.95
327 328 5.960704 ACTGGTTTAAGAGGGGTGTAAAAT 58.039 37.500 0.00 0.00 0.00 1.82
353 354 1.205820 CGACGTGTGACGAGCAGTA 59.794 57.895 2.62 0.00 46.05 2.74
371 372 1.982073 GCGTGCTTACTGACCCATGC 61.982 60.000 0.00 0.00 33.69 4.06
376 377 2.730672 CGCAGCGTGCTTACTGACC 61.731 63.158 6.65 0.00 42.25 4.02
769 818 1.455383 GAGGTTGGTGGTGGTTGCAG 61.455 60.000 0.00 0.00 0.00 4.41
875 924 2.993840 AGAGCGTGGCAGAGCAGA 60.994 61.111 15.82 0.00 35.48 4.26
876 925 2.814341 CAGAGCGTGGCAGAGCAG 60.814 66.667 15.82 3.40 35.48 4.24
878 927 4.756458 AGCAGAGCGTGGCAGAGC 62.756 66.667 6.76 6.76 0.00 4.09
879 928 2.508887 GAGCAGAGCGTGGCAGAG 60.509 66.667 0.00 0.00 0.00 3.35
1177 1235 2.722201 GGACCATCGGCTCCTCGTT 61.722 63.158 0.00 0.00 0.00 3.85
1337 1401 0.577269 GAAATCGAGACGGCAATCGG 59.423 55.000 0.00 0.00 44.45 4.18
1374 1438 5.478407 TGCGAGTTGAGATTAATTCACTCA 58.522 37.500 13.39 8.73 38.61 3.41
1377 1441 6.467047 CACAATGCGAGTTGAGATTAATTCAC 59.533 38.462 7.14 0.00 33.37 3.18
1547 1611 3.238788 TCATATGGTAGGAGCTTCCGA 57.761 47.619 2.13 0.00 42.75 4.55
1548 1612 3.322254 AGTTCATATGGTAGGAGCTTCCG 59.678 47.826 2.13 0.00 42.75 4.30
1550 1614 5.537188 CAGAGTTCATATGGTAGGAGCTTC 58.463 45.833 2.13 0.00 30.28 3.86
1551 1615 4.202305 GCAGAGTTCATATGGTAGGAGCTT 60.202 45.833 2.13 0.00 30.28 3.74
1554 1618 3.319405 ACGCAGAGTTCATATGGTAGGAG 59.681 47.826 2.13 0.00 0.00 3.69
1568 1637 2.507992 GAGCATCGCACGCAGAGT 60.508 61.111 0.00 0.00 0.00 3.24
1577 1646 1.835483 CGGCAGTAATGGAGCATCGC 61.835 60.000 0.00 0.00 34.37 4.58
1619 1688 1.075374 CTCACCCCAATCCACCTGAAA 59.925 52.381 0.00 0.00 0.00 2.69
1636 1705 1.361632 CTCGATCATGCTCGCCTCA 59.638 57.895 13.92 0.00 38.52 3.86
1663 1732 1.284198 AGTGCATGGCTGAGAAGGATT 59.716 47.619 0.00 0.00 0.00 3.01
1796 1866 0.399075 AAACAGTACAGGTTCCCCCG 59.601 55.000 0.00 0.00 38.74 5.73
1886 1958 3.535561 GGGTACACAATCTCAGGACATG 58.464 50.000 0.00 0.00 0.00 3.21
1904 1976 1.385528 GGACAACACAAGAAACGGGT 58.614 50.000 0.00 0.00 0.00 5.28
1905 1977 0.666374 GGGACAACACAAGAAACGGG 59.334 55.000 0.00 0.00 0.00 5.28
1906 1978 1.384525 TGGGACAACACAAGAAACGG 58.615 50.000 0.00 0.00 31.92 4.44
1994 2066 1.757306 CAGAGGTTGGGCTCAGTGT 59.243 57.895 0.00 0.00 0.00 3.55
2074 2156 4.201561 GCAAAGGTACGTATCACGAGTTTC 60.202 45.833 8.86 0.00 46.05 2.78
2075 2157 3.676646 GCAAAGGTACGTATCACGAGTTT 59.323 43.478 8.86 0.00 46.05 2.66
2076 2158 3.248266 GCAAAGGTACGTATCACGAGTT 58.752 45.455 8.86 0.00 46.05 3.01
2077 2159 2.229543 TGCAAAGGTACGTATCACGAGT 59.770 45.455 8.86 0.00 46.05 4.18
2078 2160 2.871133 TGCAAAGGTACGTATCACGAG 58.129 47.619 8.86 0.00 46.05 4.18
2081 2163 6.838198 TTATCATGCAAAGGTACGTATCAC 57.162 37.500 8.86 0.00 0.00 3.06
2083 2165 6.259167 TGGTTTATCATGCAAAGGTACGTATC 59.741 38.462 0.00 0.00 0.00 2.24
2084 2166 6.037830 GTGGTTTATCATGCAAAGGTACGTAT 59.962 38.462 0.00 0.00 0.00 3.06
2085 2167 5.352016 GTGGTTTATCATGCAAAGGTACGTA 59.648 40.000 0.00 0.00 0.00 3.57
2116 2200 1.175654 CAGGCATGTACATGTTGGCA 58.824 50.000 31.10 11.37 40.80 4.92
2123 2207 7.065803 GTGTGTAAGTTATTCAGGCATGTACAT 59.934 37.037 1.41 1.41 0.00 2.29
2169 2253 9.439500 CTTTCCATGAATGATGTGGTTTTTAAT 57.561 29.630 0.00 0.00 34.61 1.40
2318 3813 1.818674 GGTCCATTGTTGGGTAGCTTG 59.181 52.381 0.00 0.00 43.81 4.01
2813 4958 1.065854 ACACCAGAGCCATGTAGAAGC 60.066 52.381 0.00 0.00 0.00 3.86
3202 5347 7.478322 CAATATGTTATGCTAGCAATCCATCC 58.522 38.462 23.54 6.25 0.00 3.51
3557 5705 1.167851 ATTCTGGCAACACCACATCG 58.832 50.000 0.00 0.00 46.36 3.84
3886 6034 2.749441 GGGCCTTCTCTGCAGCAC 60.749 66.667 9.47 0.00 0.00 4.40
3967 6115 8.592809 ACAAGATACTCCAGAAATAGATGGATC 58.407 37.037 0.00 0.00 44.45 3.36
3993 6141 0.973632 AGACAGCATGAACCACGGTA 59.026 50.000 0.00 0.00 39.69 4.02
4016 6164 8.321650 AGCTTGAACTATTTTCAGAGAAGAAG 57.678 34.615 0.00 0.00 0.00 2.85
4024 6172 7.706179 TCCAAAACAAGCTTGAACTATTTTCAG 59.294 33.333 32.50 18.41 0.00 3.02
4110 6259 1.605202 CCCACAGGAAAACAAATGGCG 60.605 52.381 0.00 0.00 33.47 5.69
4207 6356 7.422465 TTGGACGGGTACTAGTTAACATTAT 57.578 36.000 8.61 0.00 0.00 1.28
4226 6375 9.786105 AACAAACAAAAATCAATTCATTTGGAC 57.214 25.926 0.00 0.00 37.15 4.02
4441 6590 2.798976 TATACGTACGGGAACATGGC 57.201 50.000 21.06 0.00 0.00 4.40
4446 6595 5.673337 TCACTACATATACGTACGGGAAC 57.327 43.478 21.06 0.00 0.00 3.62
4484 6633 9.530633 CTCTTAAGAAGTTAAAGTATATGCCGT 57.469 33.333 6.63 0.00 0.00 5.68
4512 6661 9.069082 GTAGACATATGAGTAGTGGTTCTATGT 57.931 37.037 10.38 0.00 32.60 2.29
5110 7266 8.678199 CCATCGATGTAGCTAGATATCAACTTA 58.322 37.037 23.27 0.00 0.00 2.24
6053 8261 9.778741 CTCCTAATAACATAAGTTGCTATTCCA 57.221 33.333 0.00 0.00 38.69 3.53
6054 8262 9.220767 CCTCCTAATAACATAAGTTGCTATTCC 57.779 37.037 0.00 0.00 38.69 3.01
6151 8360 7.589958 TTAAGTGATGTCTTTTGGCCTTTTA 57.410 32.000 3.32 0.00 0.00 1.52
6190 8406 2.237643 TGAGTTTAGGGTGTGTGTGTGT 59.762 45.455 0.00 0.00 0.00 3.72
6192 8408 3.476552 CATGAGTTTAGGGTGTGTGTGT 58.523 45.455 0.00 0.00 0.00 3.72
6194 8410 2.441750 ACCATGAGTTTAGGGTGTGTGT 59.558 45.455 0.00 0.00 32.70 3.72
6195 8411 2.813754 CACCATGAGTTTAGGGTGTGTG 59.186 50.000 0.00 0.00 45.00 3.82
6196 8412 3.140325 CACCATGAGTTTAGGGTGTGT 57.860 47.619 0.00 0.00 45.00 3.72
6200 8416 2.509964 GGATCCACCATGAGTTTAGGGT 59.490 50.000 6.95 0.00 38.79 4.34
6201 8417 2.509548 TGGATCCACCATGAGTTTAGGG 59.490 50.000 11.44 0.00 44.64 3.53
6228 8444 5.879763 TGGATTTCATCTCTCCAAACTCAA 58.120 37.500 0.00 0.00 36.15 3.02
6539 8756 2.029828 AGTTTCTCGTTCGAGTGCAGAT 60.030 45.455 19.26 2.92 34.19 2.90


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

AutoCloner maintained by Alex Coulton.