Multiple sequence alignment - TraesCS1D01G329000

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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 TraesCS1D01G329000 chr1D 100.000 4211 0 0 750 4960 420536138 420540348 0.000000e+00 7777
1 TraesCS1D01G329000 chr1D 100.000 349 0 0 1 349 420535389 420535737 0.000000e+00 645
2 TraesCS1D01G329000 chr1A 91.987 4268 220 52 750 4960 516769636 516773838 0.000000e+00 5875
3 TraesCS1D01G329000 chr1A 84.177 158 19 6 4563 4716 574571055 574571210 1.110000e-31 148
4 TraesCS1D01G329000 chr1B 92.322 2149 115 23 750 2882 568522007 568524121 0.000000e+00 3009
5 TraesCS1D01G329000 chr1B 86.139 2121 180 51 2881 4954 568524203 568526256 0.000000e+00 2183
6 TraesCS1D01G329000 chr1B 90.230 174 16 1 176 349 568521662 568521834 5.000000e-55 226
7 TraesCS1D01G329000 chr1B 81.646 158 19 7 4563 4716 666249286 666249437 6.740000e-24 122
8 TraesCS1D01G329000 chr7A 84.049 163 20 4 4560 4716 701493468 701493630 8.600000e-33 152


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 TraesCS1D01G329000 chr1D 420535389 420540348 4959 False 4211 7777 100.000000 1 4960 2 chr1D.!!$F1 4959
1 TraesCS1D01G329000 chr1A 516769636 516773838 4202 False 5875 5875 91.987000 750 4960 1 chr1A.!!$F1 4210
2 TraesCS1D01G329000 chr1B 568521662 568526256 4594 False 1806 3009 89.563667 176 4954 3 chr1B.!!$F2 4778

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
52 53 0.032678 ATCGAGGTTGATGCTAGCGG 59.967 55.0 10.77 0.00 0.00 5.52 F
214 215 0.036875 AATGGGCTAATCGGGCTAGC 59.963 55.0 6.04 6.04 40.93 3.42 F
853 855 0.249398 CACGGGTTACTTCTCCAGGG 59.751 60.0 0.00 0.00 0.00 4.45 F
2216 2227 0.599558 TGCATTCAAAGCTGGAGCAC 59.400 50.0 0.65 0.00 45.16 4.40 F
2986 3092 0.249911 ACCTTCTGCTCGTGTGTTCC 60.250 55.0 0.00 0.00 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1257 1.102154 CTGGCCCATTGCAATAACGA 58.898 50.000 12.53 1.08 43.89 3.85 R
1516 1520 1.801332 CTGCTGCTGTGCAAGATCC 59.199 57.895 0.00 0.00 42.83 3.36 R
2708 2721 1.538950 CTTGCTCAGAGGGAAGTTTGC 59.461 52.381 0.00 0.00 31.49 3.68 R
3476 3590 1.073284 ACTACGGCAACATTCCACCTT 59.927 47.619 0.00 0.00 0.00 3.50 R
4478 4644 0.457853 GCGACGAGTGCAATGAGGTA 60.458 55.000 0.00 0.00 0.00 3.08 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
19 20 0.798776 GACATTGAGGTTGACGCTGG 59.201 55.000 0.00 0.00 0.00 4.85
20 21 0.108585 ACATTGAGGTTGACGCTGGT 59.891 50.000 0.00 0.00 0.00 4.00
21 22 0.518636 CATTGAGGTTGACGCTGGTG 59.481 55.000 0.00 0.00 0.00 4.17
22 23 0.606401 ATTGAGGTTGACGCTGGTGG 60.606 55.000 0.00 0.00 0.00 4.61
23 24 3.050275 GAGGTTGACGCTGGTGGC 61.050 66.667 0.00 0.00 37.64 5.01
35 36 4.832608 GGTGGCGACCCGGACATC 62.833 72.222 6.63 0.00 36.03 3.06
38 39 4.570663 GGCGACCCGGACATCGAG 62.571 72.222 21.98 0.00 40.86 4.04
39 40 4.570663 GCGACCCGGACATCGAGG 62.571 72.222 21.98 0.00 40.86 4.63
40 41 3.138798 CGACCCGGACATCGAGGT 61.139 66.667 15.16 0.50 42.32 3.85
41 42 2.707849 CGACCCGGACATCGAGGTT 61.708 63.158 15.16 0.00 40.66 3.50
42 43 1.153628 GACCCGGACATCGAGGTTG 60.154 63.158 3.38 0.00 40.66 3.77
43 44 1.601419 GACCCGGACATCGAGGTTGA 61.601 60.000 3.38 0.00 40.66 3.18
44 45 0.976073 ACCCGGACATCGAGGTTGAT 60.976 55.000 3.38 0.00 42.43 2.57
51 52 1.135046 CATCGAGGTTGATGCTAGCG 58.865 55.000 10.77 0.00 39.33 4.26
52 53 0.032678 ATCGAGGTTGATGCTAGCGG 59.967 55.000 10.77 0.00 0.00 5.52
53 54 1.141881 CGAGGTTGATGCTAGCGGT 59.858 57.895 10.77 0.41 0.00 5.68
54 55 1.148157 CGAGGTTGATGCTAGCGGTG 61.148 60.000 10.77 0.00 0.00 4.94
55 56 0.175760 GAGGTTGATGCTAGCGGTGA 59.824 55.000 10.77 0.00 0.00 4.02
56 57 0.108138 AGGTTGATGCTAGCGGTGAC 60.108 55.000 10.77 6.41 0.00 3.67
57 58 1.090052 GGTTGATGCTAGCGGTGACC 61.090 60.000 10.77 11.79 0.00 4.02
58 59 0.108138 GTTGATGCTAGCGGTGACCT 60.108 55.000 10.77 0.00 0.00 3.85
59 60 0.108186 TTGATGCTAGCGGTGACCTG 60.108 55.000 10.77 0.00 0.00 4.00
60 61 1.227380 GATGCTAGCGGTGACCTGG 60.227 63.158 10.77 0.00 0.00 4.45
61 62 3.391665 ATGCTAGCGGTGACCTGGC 62.392 63.158 10.77 0.00 36.27 4.85
62 63 4.840005 GCTAGCGGTGACCTGGCC 62.840 72.222 0.00 0.00 31.91 5.36
63 64 3.390521 CTAGCGGTGACCTGGCCA 61.391 66.667 4.71 4.71 0.00 5.36
64 65 2.687200 TAGCGGTGACCTGGCCAT 60.687 61.111 5.51 0.00 0.00 4.40
65 66 2.650813 CTAGCGGTGACCTGGCCATC 62.651 65.000 5.51 1.61 0.00 3.51
71 72 4.778143 GACCTGGCCATCGCGGTT 62.778 66.667 15.13 0.35 36.97 4.44
73 74 4.776322 CCTGGCCATCGCGGTTGA 62.776 66.667 5.51 0.00 36.97 3.18
74 75 3.197790 CTGGCCATCGCGGTTGAG 61.198 66.667 5.51 0.53 36.97 3.02
75 76 4.776322 TGGCCATCGCGGTTGAGG 62.776 66.667 0.00 0.00 36.97 3.86
77 78 4.467084 GCCATCGCGGTTGAGGGA 62.467 66.667 6.13 0.00 42.34 4.20
78 79 2.202932 CCATCGCGGTTGAGGGAG 60.203 66.667 6.13 0.00 42.34 4.30
79 80 2.202932 CATCGCGGTTGAGGGAGG 60.203 66.667 6.13 0.00 36.53 4.30
80 81 2.363795 ATCGCGGTTGAGGGAGGA 60.364 61.111 6.13 0.00 36.53 3.71
81 82 2.427245 ATCGCGGTTGAGGGAGGAG 61.427 63.158 6.13 0.00 36.53 3.69
82 83 2.856039 ATCGCGGTTGAGGGAGGAGA 62.856 60.000 6.13 0.00 36.53 3.71
83 84 2.646175 CGCGGTTGAGGGAGGAGAA 61.646 63.158 0.00 0.00 0.00 2.87
84 85 1.219393 GCGGTTGAGGGAGGAGAAG 59.781 63.158 0.00 0.00 0.00 2.85
85 86 1.219393 CGGTTGAGGGAGGAGAAGC 59.781 63.158 0.00 0.00 0.00 3.86
86 87 1.544825 CGGTTGAGGGAGGAGAAGCA 61.545 60.000 0.00 0.00 0.00 3.91
87 88 0.251634 GGTTGAGGGAGGAGAAGCAG 59.748 60.000 0.00 0.00 0.00 4.24
88 89 0.980423 GTTGAGGGAGGAGAAGCAGT 59.020 55.000 0.00 0.00 0.00 4.40
89 90 0.979665 TTGAGGGAGGAGAAGCAGTG 59.020 55.000 0.00 0.00 0.00 3.66
90 91 0.115152 TGAGGGAGGAGAAGCAGTGA 59.885 55.000 0.00 0.00 0.00 3.41
91 92 0.823460 GAGGGAGGAGAAGCAGTGAG 59.177 60.000 0.00 0.00 0.00 3.51
92 93 0.617249 AGGGAGGAGAAGCAGTGAGG 60.617 60.000 0.00 0.00 0.00 3.86
93 94 1.220477 GGAGGAGAAGCAGTGAGGC 59.780 63.158 0.00 0.00 0.00 4.70
94 95 1.153667 GAGGAGAAGCAGTGAGGCG 60.154 63.158 0.00 0.00 39.27 5.52
95 96 2.125350 GGAGAAGCAGTGAGGCGG 60.125 66.667 0.00 0.00 39.27 6.13
96 97 2.817396 GAGAAGCAGTGAGGCGGC 60.817 66.667 0.00 0.00 39.27 6.53
97 98 3.596066 GAGAAGCAGTGAGGCGGCA 62.596 63.158 13.08 0.00 40.81 5.69
98 99 3.123620 GAAGCAGTGAGGCGGCAG 61.124 66.667 13.08 0.00 40.81 4.85
99 100 3.890936 GAAGCAGTGAGGCGGCAGT 62.891 63.158 13.08 0.00 40.81 4.40
100 101 4.694233 AGCAGTGAGGCGGCAGTG 62.694 66.667 13.08 5.70 40.81 3.66
104 105 4.767255 GTGAGGCGGCAGTGGGAG 62.767 72.222 13.08 0.00 0.00 4.30
106 107 4.767255 GAGGCGGCAGTGGGAGTG 62.767 72.222 13.08 0.00 0.00 3.51
137 138 4.329545 GCGCCCTCCTGTGTCCAA 62.330 66.667 0.00 0.00 0.00 3.53
138 139 2.046892 CGCCCTCCTGTGTCCAAG 60.047 66.667 0.00 0.00 0.00 3.61
139 140 2.583441 CGCCCTCCTGTGTCCAAGA 61.583 63.158 0.00 0.00 0.00 3.02
140 141 1.298014 GCCCTCCTGTGTCCAAGAG 59.702 63.158 0.00 0.00 0.00 2.85
141 142 1.194781 GCCCTCCTGTGTCCAAGAGA 61.195 60.000 0.00 0.00 31.84 3.10
142 143 0.901124 CCCTCCTGTGTCCAAGAGAG 59.099 60.000 0.00 0.00 31.84 3.20
143 144 0.901124 CCTCCTGTGTCCAAGAGAGG 59.099 60.000 0.00 0.00 31.84 3.69
144 145 1.551099 CCTCCTGTGTCCAAGAGAGGA 60.551 57.143 0.00 0.00 42.93 3.71
145 146 1.824230 CTCCTGTGTCCAAGAGAGGAG 59.176 57.143 3.38 3.38 42.93 3.69
146 147 1.148027 TCCTGTGTCCAAGAGAGGAGT 59.852 52.381 0.00 0.00 38.64 3.85
147 148 1.548269 CCTGTGTCCAAGAGAGGAGTC 59.452 57.143 0.00 0.00 38.64 3.36
148 149 2.524306 CTGTGTCCAAGAGAGGAGTCT 58.476 52.381 0.00 0.00 38.64 3.24
149 150 2.230992 CTGTGTCCAAGAGAGGAGTCTG 59.769 54.545 0.00 0.00 38.64 3.51
150 151 1.548269 GTGTCCAAGAGAGGAGTCTGG 59.452 57.143 0.00 0.00 38.64 3.86
151 152 1.148027 TGTCCAAGAGAGGAGTCTGGT 59.852 52.381 0.00 0.00 38.64 4.00
152 153 1.822371 GTCCAAGAGAGGAGTCTGGTC 59.178 57.143 0.00 0.00 38.64 4.02
153 154 1.713647 TCCAAGAGAGGAGTCTGGTCT 59.286 52.381 0.00 0.00 30.97 3.85
154 155 2.110899 TCCAAGAGAGGAGTCTGGTCTT 59.889 50.000 0.00 0.00 30.97 3.01
155 156 2.903135 CCAAGAGAGGAGTCTGGTCTTT 59.097 50.000 0.00 0.00 30.97 2.52
156 157 3.326297 CCAAGAGAGGAGTCTGGTCTTTT 59.674 47.826 0.00 0.00 30.97 2.27
157 158 4.202409 CCAAGAGAGGAGTCTGGTCTTTTT 60.202 45.833 0.00 0.00 30.97 1.94
211 212 1.456287 GGAATGGGCTAATCGGGCT 59.544 57.895 0.00 0.00 0.00 5.19
214 215 0.036875 AATGGGCTAATCGGGCTAGC 59.963 55.000 6.04 6.04 40.93 3.42
260 261 2.603075 TGGAAGCCCAGTAAAGCAAT 57.397 45.000 0.00 0.00 37.58 3.56
288 289 0.458025 GACGTGCCCGGTAAGAAGAG 60.458 60.000 0.00 0.00 38.78 2.85
320 321 1.711060 GGAGGTCTCTCTCGCAGTCG 61.711 65.000 0.00 0.00 39.86 4.18
767 769 4.875713 CCCCTCCATTTCGCCCCG 62.876 72.222 0.00 0.00 0.00 5.73
853 855 0.249398 CACGGGTTACTTCTCCAGGG 59.751 60.000 0.00 0.00 0.00 4.45
920 922 1.135373 TCCGCTCGTCTGATCTGTTTC 60.135 52.381 0.00 0.00 0.00 2.78
928 930 4.223964 GATCTGTTTCGCCGCCGC 62.224 66.667 0.00 0.00 0.00 6.53
954 956 7.219154 CCGACGATTGAGCTAGATTTATATGTC 59.781 40.741 0.00 0.00 0.00 3.06
1022 1024 1.752198 CGTGGGAGTTCACCAAGGA 59.248 57.895 0.00 0.00 40.24 3.36
1127 1130 7.912250 GCTGGATTTGAAATAACTGTGACATAG 59.088 37.037 0.00 0.00 0.00 2.23
1155 1158 3.818961 AATTGTGTGCTCAGATGTTCG 57.181 42.857 0.00 0.00 0.00 3.95
1247 1250 8.738645 AATGATAGTCTTCAGTTTAACATCCC 57.261 34.615 0.00 0.00 0.00 3.85
1303 1306 9.489084 TGTTAATATCGTTTATTCCTGATCCTG 57.511 33.333 0.00 0.00 0.00 3.86
1322 1325 7.665145 TGATCCTGAATGAACAATTGTAACAGA 59.335 33.333 12.39 8.76 0.00 3.41
1333 1336 6.539173 ACAATTGTAACAGAACTATGGGTCA 58.461 36.000 9.97 0.00 0.00 4.02
1347 1351 5.997746 ACTATGGGTCATAATGTTCCATTCG 59.002 40.000 9.46 5.65 38.87 3.34
1367 1371 3.516300 TCGTACAGGAGAAATGGGCTTAA 59.484 43.478 0.00 0.00 0.00 1.85
1438 1442 9.490663 GTTTGTTATCATCTGGACTAATTTTCG 57.509 33.333 0.00 0.00 0.00 3.46
1516 1520 6.015688 AGCAATCTGGTATTATTCCAATGCTG 60.016 38.462 17.76 5.26 42.36 4.41
1584 1588 6.364976 GCAATGGACGCTGTAAGTTAAAATTT 59.635 34.615 0.00 0.00 35.30 1.82
1589 1593 5.827666 ACGCTGTAAGTTAAAATTTGTGCT 58.172 33.333 0.00 0.00 35.30 4.40
1592 1596 7.589954 ACGCTGTAAGTTAAAATTTGTGCTAAG 59.410 33.333 0.00 0.00 35.30 2.18
1634 1638 6.819146 TCAGCATGTTATGTTGTATTCCGTTA 59.181 34.615 5.72 0.00 41.52 3.18
1709 1713 9.623000 AAAACTTGTATCTTACCTGTACTTGTT 57.377 29.630 0.00 0.00 0.00 2.83
1713 1717 9.268268 CTTGTATCTTACCTGTACTTGTTGAAA 57.732 33.333 0.00 0.00 0.00 2.69
1714 1718 8.597662 TGTATCTTACCTGTACTTGTTGAAAC 57.402 34.615 0.00 0.00 0.00 2.78
1715 1719 8.426489 TGTATCTTACCTGTACTTGTTGAAACT 58.574 33.333 0.00 0.00 0.00 2.66
1716 1720 9.918630 GTATCTTACCTGTACTTGTTGAAACTA 57.081 33.333 0.00 0.00 0.00 2.24
1718 1722 8.827177 TCTTACCTGTACTTGTTGAAACTATG 57.173 34.615 0.00 0.00 0.00 2.23
1719 1723 5.941948 ACCTGTACTTGTTGAAACTATGC 57.058 39.130 0.00 0.00 0.00 3.14
1720 1724 5.373222 ACCTGTACTTGTTGAAACTATGCA 58.627 37.500 0.00 0.00 0.00 3.96
1733 1737 9.040939 GTTGAAACTATGCAAAAACCTTATTGT 57.959 29.630 0.00 0.00 0.00 2.71
1745 1749 9.554395 CAAAAACCTTATTGTCCCTTGTTTATT 57.446 29.630 0.00 0.00 0.00 1.40
1756 1760 9.521841 TTGTCCCTTGTTTATTGTTGTATATGA 57.478 29.630 0.00 0.00 0.00 2.15
1760 1764 9.950680 CCCTTGTTTATTGTTGTATATGATGTC 57.049 33.333 0.00 0.00 0.00 3.06
1794 1798 4.764172 ACTCTTCTGTCCATTCACTATGC 58.236 43.478 0.00 0.00 32.60 3.14
1802 1806 1.942657 CCATTCACTATGCCTGGAACG 59.057 52.381 0.00 0.00 32.60 3.95
1837 1841 3.804325 CCGTATAGGTGCACAGAAAGATG 59.196 47.826 20.43 3.28 34.51 2.90
1857 1861 5.699915 AGATGTCATGTGCATATTGAGTAGC 59.300 40.000 0.00 0.00 0.00 3.58
1911 1915 8.739461 CGTTGGTCTTTAATTTTGACACTTTAC 58.261 33.333 0.00 0.00 32.84 2.01
1930 1938 9.385902 CACTTTACAATCAAGTTACATCTTGTG 57.614 33.333 6.38 2.20 43.44 3.33
1958 1966 3.434309 AGCATTTGGAAGTGGCAGTTAT 58.566 40.909 7.71 0.00 0.00 1.89
2092 2100 9.224058 GTCGACATACTAGTTGAAATCTCTTAC 57.776 37.037 11.55 0.00 33.86 2.34
2105 2113 9.825972 TTGAAATCTCTTACGATCATGTTTTTC 57.174 29.630 0.00 0.00 0.00 2.29
2150 2158 6.111382 TGAAGCTGATTTGATGGAAGTCTAG 58.889 40.000 0.00 0.00 0.00 2.43
2152 2160 5.426504 AGCTGATTTGATGGAAGTCTAGTG 58.573 41.667 0.00 0.00 0.00 2.74
2216 2227 0.599558 TGCATTCAAAGCTGGAGCAC 59.400 50.000 0.65 0.00 45.16 4.40
2231 2242 1.736681 GAGCACATCCTTTCTCAGCAC 59.263 52.381 0.00 0.00 0.00 4.40
2235 2246 1.620819 ACATCCTTTCTCAGCACGACT 59.379 47.619 0.00 0.00 0.00 4.18
2253 2264 7.040686 AGCACGACTATTAGGTTCACAATTTTT 60.041 33.333 0.00 0.00 0.00 1.94
2375 2386 4.637276 ACACTTCACATATTCGGTGTTCA 58.363 39.130 0.00 0.00 37.52 3.18
2377 2388 6.403049 ACACTTCACATATTCGGTGTTCATA 58.597 36.000 0.00 0.00 37.52 2.15
2525 2538 7.892241 ACTCTGTACTCATTACTACCACCTTTA 59.108 37.037 0.00 0.00 0.00 1.85
2527 2540 8.910944 TCTGTACTCATTACTACCACCTTTATC 58.089 37.037 0.00 0.00 0.00 1.75
2542 2555 5.520288 CACCTTTATCTACCATGAAGTCGTG 59.480 44.000 0.00 0.00 0.00 4.35
2613 2626 4.635765 CACCTTGTATGATTCGTGGTTCAT 59.364 41.667 0.00 0.00 36.57 2.57
2621 2634 7.714813 TGTATGATTCGTGGTTCATGTGATATT 59.285 33.333 0.00 0.00 34.52 1.28
2633 2646 5.698104 TCATGTGATATTGAAGATGCCCTT 58.302 37.500 0.00 0.00 37.93 3.95
2668 2681 4.036971 TGGAGTTAAACGGAATGGTTTGTG 59.963 41.667 1.24 0.00 40.18 3.33
2674 2687 5.523438 AAACGGAATGGTTTGTGTATTGT 57.477 34.783 0.00 0.00 38.61 2.71
2708 2721 9.529325 TTCTGATATCTGTAGATTTGTTAACCG 57.471 33.333 2.48 0.00 36.05 4.44
2716 2729 6.432107 TGTAGATTTGTTAACCGCAAACTTC 58.568 36.000 2.48 0.00 38.44 3.01
2919 3025 8.542497 TGGTCTGTAGTATGTTTGTAATGAAC 57.458 34.615 0.00 0.00 0.00 3.18
2937 3043 7.940178 AATGAACGGTTTTAAATCTTTGGTC 57.060 32.000 0.00 0.00 0.00 4.02
2986 3092 0.249911 ACCTTCTGCTCGTGTGTTCC 60.250 55.000 0.00 0.00 0.00 3.62
3161 3267 0.667993 GTGCTTGCACTTGCTGGTAA 59.332 50.000 17.36 0.00 42.66 2.85
3171 3277 4.567159 GCACTTGCTGGTAATAGTCAGTAC 59.433 45.833 0.00 0.00 38.21 2.73
3201 3307 1.405872 ATGCTGGCATAATGTGGTGG 58.594 50.000 6.25 0.00 34.49 4.61
3236 3342 7.404985 CAGAAACAGCATGACACATCTTATAC 58.595 38.462 0.00 0.00 39.69 1.47
3250 3356 7.064609 ACACATCTTATACGACAATTGGTTCAG 59.935 37.037 10.83 0.00 0.00 3.02
3268 3381 5.218139 GTTCAGCCTGATCAGAAACAAAAG 58.782 41.667 24.62 5.66 0.00 2.27
3273 3386 4.037923 GCCTGATCAGAAACAAAAGTTGGA 59.962 41.667 24.62 0.00 34.12 3.53
3282 3395 7.015487 TCAGAAACAAAAGTTGGATGATGGAAT 59.985 33.333 0.00 0.00 34.12 3.01
3332 3445 5.009631 TGTTAGGAAAGGGTTGATGTGATG 58.990 41.667 0.00 0.00 0.00 3.07
3337 3450 4.280677 GGAAAGGGTTGATGTGATGACAAA 59.719 41.667 0.00 0.00 35.11 2.83
3365 3479 5.105752 TGCATGTTTGAACAGTTGTTTACC 58.894 37.500 2.77 0.00 43.04 2.85
3473 3587 5.536497 ACCTTCTTCTTTGGGGACATTAT 57.464 39.130 0.00 0.00 42.32 1.28
3476 3590 6.447084 ACCTTCTTCTTTGGGGACATTATAGA 59.553 38.462 0.00 0.00 42.32 1.98
3481 3595 6.001449 TCTTTGGGGACATTATAGAAGGTG 57.999 41.667 0.00 0.00 42.32 4.00
3504 3618 5.123186 TGGAATGTTGCCGTAGTTATCTTTG 59.877 40.000 0.00 0.00 0.00 2.77
3570 3684 0.912486 AAGTTGCTAGCCTACCAGGG 59.088 55.000 13.29 0.00 35.37 4.45
3613 3727 3.316588 GCCTTTTGCTAATAGAAGAGGCC 59.683 47.826 16.07 0.00 41.90 5.19
3618 3732 5.435686 TTGCTAATAGAAGAGGCCTTGAA 57.564 39.130 6.77 0.00 31.62 2.69
3721 3835 2.349817 CGTTGAGCTCGTTGAAATGCTT 60.350 45.455 9.64 0.00 35.76 3.91
4210 4335 4.223144 TGCCCACTGATAAGATAGTGCTA 58.777 43.478 0.00 0.00 42.21 3.49
4256 4381 2.106511 GGCATAAGAATCTGGGGCACTA 59.893 50.000 0.00 0.00 0.00 2.74
4345 4470 1.024579 CACGGACCTGGTACATTGCC 61.025 60.000 10.24 0.00 38.20 4.52
4478 4644 2.370189 GCTCTTCCCAGTACCTATGCAT 59.630 50.000 3.79 3.79 0.00 3.96
4485 4651 3.840666 CCCAGTACCTATGCATACCTCAT 59.159 47.826 1.16 0.00 0.00 2.90
4493 4659 1.655484 TGCATACCTCATTGCACTCG 58.345 50.000 0.00 0.00 43.54 4.18
4495 4661 1.594862 GCATACCTCATTGCACTCGTC 59.405 52.381 0.00 0.00 38.72 4.20
4612 4780 3.897505 CCTCCAACCCTCTTTTGTTCAAT 59.102 43.478 0.00 0.00 0.00 2.57
4686 4857 2.297698 TTGAACAGTAGGTCGGAGGA 57.702 50.000 0.00 0.00 0.00 3.71
4715 4890 4.347583 TGAAGGTTTCAAATTTGCATCCCT 59.652 37.500 13.54 11.85 36.59 4.20
4716 4891 4.276058 AGGTTTCAAATTTGCATCCCTG 57.724 40.909 13.54 0.00 0.00 4.45
4720 4895 2.886913 TCAAATTTGCATCCCTGACCA 58.113 42.857 13.54 0.00 0.00 4.02
4722 4897 2.299582 CAAATTTGCATCCCTGACCACA 59.700 45.455 5.01 0.00 0.00 4.17
4723 4898 2.537633 ATTTGCATCCCTGACCACAT 57.462 45.000 0.00 0.00 0.00 3.21
4724 4899 3.668141 ATTTGCATCCCTGACCACATA 57.332 42.857 0.00 0.00 0.00 2.29
4725 4900 3.448093 TTTGCATCCCTGACCACATAA 57.552 42.857 0.00 0.00 0.00 1.90
4726 4901 3.668141 TTGCATCCCTGACCACATAAT 57.332 42.857 0.00 0.00 0.00 1.28
4727 4902 3.668141 TGCATCCCTGACCACATAATT 57.332 42.857 0.00 0.00 0.00 1.40
4774 4949 7.770433 CAGGTGATGATCCTTATTAACACTTCA 59.230 37.037 0.00 0.00 32.37 3.02
4800 4975 0.545646 ATGAGCCCTTGAGCCTTCTC 59.454 55.000 0.00 0.00 39.78 2.87
4846 5022 1.069775 AACCGGGTTTCCATGGTAGT 58.930 50.000 12.58 0.00 33.61 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.798776 CCAGCGTCAACCTCAATGTC 59.201 55.000 0.00 0.00 0.00 3.06
1 2 0.108585 ACCAGCGTCAACCTCAATGT 59.891 50.000 0.00 0.00 0.00 2.71
3 4 0.606401 CCACCAGCGTCAACCTCAAT 60.606 55.000 0.00 0.00 0.00 2.57
6 7 3.050275 GCCACCAGCGTCAACCTC 61.050 66.667 0.00 0.00 0.00 3.85
18 19 4.832608 GATGTCCGGGTCGCCACC 62.833 72.222 0.00 0.00 42.90 4.61
21 22 4.570663 CTCGATGTCCGGGTCGCC 62.571 72.222 16.49 0.00 37.74 5.54
22 23 4.570663 CCTCGATGTCCGGGTCGC 62.571 72.222 16.49 0.65 36.93 5.19
23 24 2.707849 AACCTCGATGTCCGGGTCG 61.708 63.158 15.56 15.56 39.68 4.79
24 25 1.153628 CAACCTCGATGTCCGGGTC 60.154 63.158 0.00 0.00 39.68 4.46
25 26 0.976073 ATCAACCTCGATGTCCGGGT 60.976 55.000 0.00 0.00 41.42 5.28
26 27 0.530650 CATCAACCTCGATGTCCGGG 60.531 60.000 0.00 0.00 38.38 5.73
27 28 1.154205 GCATCAACCTCGATGTCCGG 61.154 60.000 0.00 0.00 43.92 5.14
28 29 0.179100 AGCATCAACCTCGATGTCCG 60.179 55.000 0.00 0.00 43.92 4.79
29 30 2.748605 CTAGCATCAACCTCGATGTCC 58.251 52.381 0.00 0.00 43.92 4.02
30 31 2.131183 GCTAGCATCAACCTCGATGTC 58.869 52.381 10.63 0.00 43.92 3.06
31 32 1.536922 CGCTAGCATCAACCTCGATGT 60.537 52.381 16.45 0.00 43.92 3.06
32 33 1.135046 CGCTAGCATCAACCTCGATG 58.865 55.000 16.45 0.00 44.69 3.84
33 34 0.032678 CCGCTAGCATCAACCTCGAT 59.967 55.000 16.45 0.00 0.00 3.59
34 35 1.320344 ACCGCTAGCATCAACCTCGA 61.320 55.000 16.45 0.00 0.00 4.04
35 36 1.141881 ACCGCTAGCATCAACCTCG 59.858 57.895 16.45 0.00 0.00 4.63
36 37 0.175760 TCACCGCTAGCATCAACCTC 59.824 55.000 16.45 0.00 0.00 3.85
37 38 0.108138 GTCACCGCTAGCATCAACCT 60.108 55.000 16.45 0.00 0.00 3.50
38 39 1.090052 GGTCACCGCTAGCATCAACC 61.090 60.000 16.45 12.50 0.00 3.77
39 40 0.108138 AGGTCACCGCTAGCATCAAC 60.108 55.000 16.45 7.12 0.00 3.18
40 41 0.108186 CAGGTCACCGCTAGCATCAA 60.108 55.000 16.45 0.00 0.00 2.57
41 42 1.517361 CAGGTCACCGCTAGCATCA 59.483 57.895 16.45 0.00 0.00 3.07
42 43 1.227380 CCAGGTCACCGCTAGCATC 60.227 63.158 16.45 0.00 0.00 3.91
43 44 2.903357 CCAGGTCACCGCTAGCAT 59.097 61.111 16.45 0.00 0.00 3.79
44 45 4.082523 GCCAGGTCACCGCTAGCA 62.083 66.667 16.45 0.00 0.00 3.49
45 46 4.840005 GGCCAGGTCACCGCTAGC 62.840 72.222 4.06 4.06 0.00 3.42
46 47 2.650813 GATGGCCAGGTCACCGCTAG 62.651 65.000 13.05 0.00 0.00 3.42
47 48 2.687200 ATGGCCAGGTCACCGCTA 60.687 61.111 13.05 0.00 0.00 4.26
48 49 4.101448 GATGGCCAGGTCACCGCT 62.101 66.667 13.05 0.00 0.00 5.52
54 55 4.778143 AACCGCGATGGCCAGGTC 62.778 66.667 13.05 3.44 43.94 3.85
56 57 4.776322 TCAACCGCGATGGCCAGG 62.776 66.667 13.05 9.74 43.94 4.45
57 58 3.197790 CTCAACCGCGATGGCCAG 61.198 66.667 13.05 0.00 43.94 4.85
58 59 4.776322 CCTCAACCGCGATGGCCA 62.776 66.667 8.56 8.56 43.94 5.36
60 61 4.467084 TCCCTCAACCGCGATGGC 62.467 66.667 8.23 0.00 43.94 4.40
61 62 2.202932 CTCCCTCAACCGCGATGG 60.203 66.667 8.23 1.44 46.41 3.51
62 63 2.202932 CCTCCCTCAACCGCGATG 60.203 66.667 8.23 6.60 0.00 3.84
63 64 2.363795 TCCTCCCTCAACCGCGAT 60.364 61.111 8.23 0.00 0.00 4.58
64 65 3.068691 CTCCTCCCTCAACCGCGA 61.069 66.667 8.23 0.00 0.00 5.87
65 66 2.564553 CTTCTCCTCCCTCAACCGCG 62.565 65.000 0.00 0.00 0.00 6.46
66 67 1.219393 CTTCTCCTCCCTCAACCGC 59.781 63.158 0.00 0.00 0.00 5.68
67 68 1.219393 GCTTCTCCTCCCTCAACCG 59.781 63.158 0.00 0.00 0.00 4.44
68 69 0.251634 CTGCTTCTCCTCCCTCAACC 59.748 60.000 0.00 0.00 0.00 3.77
69 70 0.980423 ACTGCTTCTCCTCCCTCAAC 59.020 55.000 0.00 0.00 0.00 3.18
70 71 0.979665 CACTGCTTCTCCTCCCTCAA 59.020 55.000 0.00 0.00 0.00 3.02
71 72 0.115152 TCACTGCTTCTCCTCCCTCA 59.885 55.000 0.00 0.00 0.00 3.86
72 73 0.823460 CTCACTGCTTCTCCTCCCTC 59.177 60.000 0.00 0.00 0.00 4.30
73 74 0.617249 CCTCACTGCTTCTCCTCCCT 60.617 60.000 0.00 0.00 0.00 4.20
74 75 1.904032 CCTCACTGCTTCTCCTCCC 59.096 63.158 0.00 0.00 0.00 4.30
75 76 1.220477 GCCTCACTGCTTCTCCTCC 59.780 63.158 0.00 0.00 0.00 4.30
76 77 1.153667 CGCCTCACTGCTTCTCCTC 60.154 63.158 0.00 0.00 0.00 3.71
77 78 2.654079 CCGCCTCACTGCTTCTCCT 61.654 63.158 0.00 0.00 0.00 3.69
78 79 2.125350 CCGCCTCACTGCTTCTCC 60.125 66.667 0.00 0.00 0.00 3.71
79 80 2.817396 GCCGCCTCACTGCTTCTC 60.817 66.667 0.00 0.00 0.00 2.87
80 81 3.602513 CTGCCGCCTCACTGCTTCT 62.603 63.158 0.00 0.00 0.00 2.85
81 82 3.123620 CTGCCGCCTCACTGCTTC 61.124 66.667 0.00 0.00 0.00 3.86
82 83 3.946201 ACTGCCGCCTCACTGCTT 61.946 61.111 0.00 0.00 0.00 3.91
83 84 4.694233 CACTGCCGCCTCACTGCT 62.694 66.667 0.00 0.00 0.00 4.24
87 88 4.767255 CTCCCACTGCCGCCTCAC 62.767 72.222 0.00 0.00 0.00 3.51
89 90 4.767255 CACTCCCACTGCCGCCTC 62.767 72.222 0.00 0.00 0.00 4.70
120 121 4.329545 TTGGACACAGGAGGGCGC 62.330 66.667 0.00 0.00 0.00 6.53
121 122 2.046892 CTTGGACACAGGAGGGCG 60.047 66.667 0.00 0.00 0.00 6.13
122 123 1.298014 CTCTTGGACACAGGAGGGC 59.702 63.158 0.00 0.00 44.53 5.19
126 127 1.148027 ACTCCTCTCTTGGACACAGGA 59.852 52.381 0.00 0.00 31.94 3.86
127 128 1.548269 GACTCCTCTCTTGGACACAGG 59.452 57.143 0.00 0.00 31.94 4.00
128 129 2.230992 CAGACTCCTCTCTTGGACACAG 59.769 54.545 0.00 0.00 31.94 3.66
129 130 2.242926 CAGACTCCTCTCTTGGACACA 58.757 52.381 0.00 0.00 31.94 3.72
130 131 1.548269 CCAGACTCCTCTCTTGGACAC 59.452 57.143 0.00 0.00 31.94 3.67
131 132 1.148027 ACCAGACTCCTCTCTTGGACA 59.852 52.381 0.00 0.00 31.94 4.02
132 133 1.822371 GACCAGACTCCTCTCTTGGAC 59.178 57.143 0.00 0.00 31.94 4.02
133 134 1.713647 AGACCAGACTCCTCTCTTGGA 59.286 52.381 0.00 0.00 34.52 3.53
134 135 2.230130 AGACCAGACTCCTCTCTTGG 57.770 55.000 0.00 0.00 0.00 3.61
135 136 4.615588 AAAAGACCAGACTCCTCTCTTG 57.384 45.455 0.00 0.00 0.00 3.02
168 169 7.381408 CCCCGTTCTAAAGAAAAGATGTTTTTC 59.619 37.037 1.67 3.38 35.94 2.29
169 170 7.068962 TCCCCGTTCTAAAGAAAAGATGTTTTT 59.931 33.333 1.67 0.00 35.94 1.94
170 171 6.548251 TCCCCGTTCTAAAGAAAAGATGTTTT 59.452 34.615 0.00 0.00 38.65 2.43
171 172 6.066032 TCCCCGTTCTAAAGAAAAGATGTTT 58.934 36.000 0.00 0.00 35.58 2.83
172 173 5.627135 TCCCCGTTCTAAAGAAAAGATGTT 58.373 37.500 0.00 0.00 35.58 2.71
173 174 5.237236 TCCCCGTTCTAAAGAAAAGATGT 57.763 39.130 0.00 0.00 35.58 3.06
174 175 6.404734 CCATTCCCCGTTCTAAAGAAAAGATG 60.405 42.308 0.00 0.00 35.58 2.90
175 176 5.652452 CCATTCCCCGTTCTAAAGAAAAGAT 59.348 40.000 0.00 0.00 35.58 2.40
176 177 5.007682 CCATTCCCCGTTCTAAAGAAAAGA 58.992 41.667 0.00 0.00 35.58 2.52
177 178 4.157840 CCCATTCCCCGTTCTAAAGAAAAG 59.842 45.833 0.00 0.00 35.58 2.27
178 179 4.083565 CCCATTCCCCGTTCTAAAGAAAA 58.916 43.478 0.00 0.00 35.58 2.29
179 180 3.692690 CCCATTCCCCGTTCTAAAGAAA 58.307 45.455 0.00 0.00 35.58 2.52
180 181 2.619590 GCCCATTCCCCGTTCTAAAGAA 60.620 50.000 0.00 0.00 0.00 2.52
181 182 1.064979 GCCCATTCCCCGTTCTAAAGA 60.065 52.381 0.00 0.00 0.00 2.52
182 183 1.064685 AGCCCATTCCCCGTTCTAAAG 60.065 52.381 0.00 0.00 0.00 1.85
224 225 1.505538 TCCATTGGACAGGGGGAAAAA 59.494 47.619 0.00 0.00 0.00 1.94
225 226 1.162505 TCCATTGGACAGGGGGAAAA 58.837 50.000 0.00 0.00 0.00 2.29
226 227 1.077005 CTTCCATTGGACAGGGGGAAA 59.923 52.381 4.45 0.00 37.20 3.13
227 228 0.704076 CTTCCATTGGACAGGGGGAA 59.296 55.000 4.45 0.00 36.31 3.97
228 229 1.863155 GCTTCCATTGGACAGGGGGA 61.863 60.000 4.45 0.00 0.00 4.81
229 230 1.380380 GCTTCCATTGGACAGGGGG 60.380 63.158 4.45 0.00 0.00 5.40
230 231 1.380380 GGCTTCCATTGGACAGGGG 60.380 63.158 4.45 0.00 0.00 4.79
231 232 1.380380 GGGCTTCCATTGGACAGGG 60.380 63.158 4.45 0.00 0.00 4.45
241 242 2.603075 ATTGCTTTACTGGGCTTCCA 57.397 45.000 0.00 0.00 39.08 3.53
260 261 1.373246 CGGGCACGTCGACCTAAAA 60.373 57.895 10.58 0.00 34.81 1.52
288 289 0.963225 GACCTCCTATTCCTCGCTCC 59.037 60.000 0.00 0.00 0.00 4.70
320 321 2.641559 GCTTGTGTGTGAGCCTGC 59.358 61.111 0.00 0.00 32.80 4.85
853 855 0.739813 TTAAGCGCGGAAGAGAAGGC 60.740 55.000 8.83 0.00 0.00 4.35
928 930 7.030165 ACATATAAATCTAGCTCAATCGTCGG 58.970 38.462 0.00 0.00 0.00 4.79
954 956 4.211164 TCGATGTGCTACAGAAACAACAAG 59.789 41.667 0.00 0.00 0.00 3.16
1127 1130 4.858935 TCTGAGCACACAATTTAACAAGC 58.141 39.130 0.00 0.00 0.00 4.01
1155 1158 5.763876 ATGCTACCCTAAGAACCATATCC 57.236 43.478 0.00 0.00 0.00 2.59
1254 1257 1.102154 CTGGCCCATTGCAATAACGA 58.898 50.000 12.53 1.08 43.89 3.85
1257 1260 2.496871 CAAGACTGGCCCATTGCAATAA 59.503 45.455 12.53 0.00 43.89 1.40
1266 1269 3.199071 ACGATATTAACAAGACTGGCCCA 59.801 43.478 0.00 0.00 0.00 5.36
1270 1273 9.326413 AGGAATAAACGATATTAACAAGACTGG 57.674 33.333 0.00 0.00 0.00 4.00
1298 1301 8.299570 GTTCTGTTACAATTGTTCATTCAGGAT 58.700 33.333 17.78 0.00 0.00 3.24
1299 1302 7.502226 AGTTCTGTTACAATTGTTCATTCAGGA 59.498 33.333 17.78 10.00 0.00 3.86
1300 1303 7.651808 AGTTCTGTTACAATTGTTCATTCAGG 58.348 34.615 17.78 5.16 0.00 3.86
1303 1306 9.559958 CCATAGTTCTGTTACAATTGTTCATTC 57.440 33.333 17.78 9.45 0.00 2.67
1347 1351 5.437060 TCATTAAGCCCATTTCTCCTGTAC 58.563 41.667 0.00 0.00 0.00 2.90
1367 1371 6.152323 GGATGAGCCATATTAACTGCATTCAT 59.848 38.462 0.00 0.00 36.34 2.57
1516 1520 1.801332 CTGCTGCTGTGCAAGATCC 59.199 57.895 0.00 0.00 42.83 3.36
1584 1588 2.171659 TGGAAGGTCACAACTTAGCACA 59.828 45.455 0.00 0.00 0.00 4.57
1589 1593 5.042463 TGATGTTGGAAGGTCACAACTTA 57.958 39.130 8.71 0.00 45.36 2.24
1592 1596 2.030805 GCTGATGTTGGAAGGTCACAAC 60.031 50.000 0.00 0.00 45.35 3.32
1634 1638 8.653191 TCGTAACAATTTCACCCTATATATGGT 58.347 33.333 3.99 3.99 34.40 3.55
1642 1646 7.879160 ACATTAACTCGTAACAATTTCACCCTA 59.121 33.333 0.00 0.00 0.00 3.53
1699 1703 8.531530 GTTTTTGCATAGTTTCAACAAGTACAG 58.468 33.333 0.00 0.00 0.00 2.74
1705 1709 9.606631 AATAAGGTTTTTGCATAGTTTCAACAA 57.393 25.926 0.00 0.00 0.00 2.83
1709 1713 7.870445 GGACAATAAGGTTTTTGCATAGTTTCA 59.130 33.333 0.00 0.00 0.00 2.69
1713 1717 6.016555 AGGGACAATAAGGTTTTTGCATAGT 58.983 36.000 0.00 0.00 0.00 2.12
1714 1718 6.530019 AGGGACAATAAGGTTTTTGCATAG 57.470 37.500 0.00 0.00 0.00 2.23
1715 1719 6.268847 ACAAGGGACAATAAGGTTTTTGCATA 59.731 34.615 0.00 0.00 0.00 3.14
1716 1720 5.071653 ACAAGGGACAATAAGGTTTTTGCAT 59.928 36.000 0.00 0.00 0.00 3.96
1717 1721 4.407296 ACAAGGGACAATAAGGTTTTTGCA 59.593 37.500 0.00 0.00 0.00 4.08
1718 1722 4.956085 ACAAGGGACAATAAGGTTTTTGC 58.044 39.130 0.00 0.00 0.00 3.68
1719 1723 9.554395 AATAAACAAGGGACAATAAGGTTTTTG 57.446 29.630 0.00 0.00 0.00 2.44
1720 1724 9.554395 CAATAAACAAGGGACAATAAGGTTTTT 57.446 29.630 0.00 0.00 0.00 1.94
1733 1737 9.693739 ACATCATATACAACAATAAACAAGGGA 57.306 29.630 0.00 0.00 0.00 4.20
1745 1749 6.883756 TGCAGAAAAGGACATCATATACAACA 59.116 34.615 0.00 0.00 0.00 3.33
1756 1760 5.879223 CAGAAGAGTATGCAGAAAAGGACAT 59.121 40.000 0.00 0.00 0.00 3.06
1760 1764 4.633565 GGACAGAAGAGTATGCAGAAAAGG 59.366 45.833 0.00 0.00 0.00 3.11
1794 1798 4.201783 CGGACTTTAATTAAGCGTTCCAGG 60.202 45.833 12.96 0.00 37.37 4.45
1802 1806 6.480981 TGCACCTATACGGACTTTAATTAAGC 59.519 38.462 0.00 0.00 35.09 3.09
1837 1841 3.185188 CGGCTACTCAATATGCACATGAC 59.815 47.826 0.00 0.00 0.00 3.06
1857 1861 3.006940 TGCAAGTCATAAGCTAAACCGG 58.993 45.455 0.00 0.00 0.00 5.28
1911 1915 6.969366 TGTTCCACAAGATGTAACTTGATTG 58.031 36.000 14.00 4.37 46.85 2.67
1930 1938 3.392882 CCACTTCCAAATGCTTTGTTCC 58.607 45.455 7.53 0.00 38.98 3.62
1938 1946 3.874392 ATAACTGCCACTTCCAAATGC 57.126 42.857 0.00 0.00 0.00 3.56
2044 2052 8.349245 TCGACAAACAAACATGTTCTTTCATAT 58.651 29.630 12.39 0.00 0.00 1.78
2047 2055 5.797934 GTCGACAAACAAACATGTTCTTTCA 59.202 36.000 12.39 0.00 0.00 2.69
2105 2113 9.964253 GCTTCAGAAAAGAAAAGAAAAGAAAAG 57.036 29.630 0.00 0.00 0.00 2.27
2150 2158 7.388776 TCAATAATATGAGCTGCCAGATTACAC 59.611 37.037 15.42 0.00 34.36 2.90
2152 2160 7.912056 TCAATAATATGAGCTGCCAGATTAC 57.088 36.000 15.42 0.00 34.36 1.89
2216 2227 2.376808 AGTCGTGCTGAGAAAGGATG 57.623 50.000 0.00 0.00 34.65 3.51
2231 2242 9.543018 GAAGAAAAATTGTGAACCTAATAGTCG 57.457 33.333 0.00 0.00 0.00 4.18
2315 2326 4.358214 AGAGGGGGAAAACAACAGAAAAA 58.642 39.130 0.00 0.00 0.00 1.94
2334 2345 7.442364 TGAAGTGTTCACTTTTCCAAGATAGAG 59.558 37.037 17.44 0.00 34.08 2.43
2364 2375 8.506168 AGACATTATTGTTATGAACACCGAAT 57.494 30.769 0.00 0.00 41.97 3.34
2525 2538 4.686972 CATGACACGACTTCATGGTAGAT 58.313 43.478 14.11 0.00 44.52 1.98
2542 2555 3.838244 TTCCCACCTACATAGCATGAC 57.162 47.619 0.00 0.00 0.00 3.06
2613 2626 7.953005 TTAAAAGGGCATCTTCAATATCACA 57.047 32.000 0.00 0.00 33.94 3.58
2621 2634 4.898861 AGGTGTTTTAAAAGGGCATCTTCA 59.101 37.500 0.00 0.00 33.94 3.02
2633 2646 6.376581 TCCGTTTAACTCCAAGGTGTTTTAAA 59.623 34.615 11.31 5.23 34.34 1.52
2696 2709 3.985279 GGGAAGTTTGCGGTTAACAAATC 59.015 43.478 8.10 0.00 39.09 2.17
2708 2721 1.538950 CTTGCTCAGAGGGAAGTTTGC 59.461 52.381 0.00 0.00 31.49 3.68
2895 3001 7.201496 CCGTTCATTACAAACATACTACAGACC 60.201 40.741 0.00 0.00 0.00 3.85
2919 3025 7.538575 AGATCATGACCAAAGATTTAAAACCG 58.461 34.615 0.00 0.00 0.00 4.44
2930 3036 8.624776 GGTTTTAAGGATAGATCATGACCAAAG 58.375 37.037 0.00 0.00 0.00 2.77
2986 3092 0.599558 CATTCACACAGCAACCCTGG 59.400 55.000 0.00 0.00 46.14 4.45
3096 3202 8.524870 AACAGAATAGTGAAATGTTGAATTGC 57.475 30.769 0.00 0.00 33.09 3.56
3171 3277 5.518848 TTATGCCAGCATAAAGTCATTGG 57.481 39.130 19.95 0.00 43.40 3.16
3201 3307 1.340889 TGCTGTTTCTGGCACAATTCC 59.659 47.619 0.00 0.00 38.70 3.01
3236 3342 1.522668 TCAGGCTGAACCAATTGTCG 58.477 50.000 16.28 0.00 43.14 4.35
3250 3356 4.037923 TCCAACTTTTGTTTCTGATCAGGC 59.962 41.667 22.42 13.15 41.35 4.85
3268 3381 9.071276 AGTGATTATGTTATTCCATCATCCAAC 57.929 33.333 0.00 0.00 28.61 3.77
3322 3435 4.038883 TGCAACCATTTGTCATCACATCAA 59.961 37.500 0.00 0.00 34.90 2.57
3332 3445 4.569966 TGTTCAAACATGCAACCATTTGTC 59.430 37.500 12.31 9.07 32.65 3.18
3337 3450 4.121317 CAACTGTTCAAACATGCAACCAT 58.879 39.130 0.00 0.00 38.41 3.55
3473 3587 1.349688 ACGGCAACATTCCACCTTCTA 59.650 47.619 0.00 0.00 0.00 2.10
3476 3590 1.073284 ACTACGGCAACATTCCACCTT 59.927 47.619 0.00 0.00 0.00 3.50
3481 3595 5.353123 TCAAAGATAACTACGGCAACATTCC 59.647 40.000 0.00 0.00 0.00 3.01
3518 3632 8.918116 TCTAGTGATGCAGTAGTTCTATTGAAT 58.082 33.333 8.63 1.81 38.24 2.57
3570 3684 2.766970 TGCGAGTTTTAACAAGCCAC 57.233 45.000 8.92 0.00 34.28 5.01
3613 3727 7.011828 TCAGACGGAAAAGTTTACTTTCAAG 57.988 36.000 8.21 5.64 44.69 3.02
3618 3732 7.713942 AGTTACATCAGACGGAAAAGTTTACTT 59.286 33.333 0.00 0.00 37.91 2.24
3721 3835 1.192428 GGGGCGTTTCTCCTCTTCTA 58.808 55.000 0.00 0.00 0.00 2.10
4082 4205 6.969366 ACAACAACAAGATCAATCAAATCGA 58.031 32.000 0.00 0.00 0.00 3.59
4256 4381 5.207110 AGTAGCATAACAGCAATCGATCT 57.793 39.130 0.00 0.00 36.85 2.75
4345 4470 4.499037 AAAAGTTTCTCCCCGAAAATCG 57.501 40.909 0.00 0.00 42.87 3.34
4478 4644 0.457853 GCGACGAGTGCAATGAGGTA 60.458 55.000 0.00 0.00 0.00 3.08
4485 4651 1.080772 CCACTAGCGACGAGTGCAA 60.081 57.895 10.38 0.00 42.52 4.08
4493 4659 3.064207 TCAAACAATGTCCACTAGCGAC 58.936 45.455 4.03 4.03 0.00 5.19
4495 4661 3.067106 AGTCAAACAATGTCCACTAGCG 58.933 45.455 0.00 0.00 0.00 4.26
4673 4841 1.145325 CAGGGTATCCTCCGACCTACT 59.855 57.143 0.00 0.00 42.67 2.57
4674 4842 1.144503 TCAGGGTATCCTCCGACCTAC 59.855 57.143 0.00 0.00 42.67 3.18
4675 4843 1.526315 TCAGGGTATCCTCCGACCTA 58.474 55.000 0.00 0.00 42.67 3.08
4676 4844 0.635009 TTCAGGGTATCCTCCGACCT 59.365 55.000 0.00 0.00 42.67 3.85
4715 4890 3.075283 ACAAGGACCCAATTATGTGGTCA 59.925 43.478 13.19 0.00 43.30 4.02
4716 4891 3.443681 CACAAGGACCCAATTATGTGGTC 59.556 47.826 5.21 5.21 41.99 4.02
4720 4895 2.825532 GCACACAAGGACCCAATTATGT 59.174 45.455 0.00 0.00 0.00 2.29
4722 4897 3.356290 GAGCACACAAGGACCCAATTAT 58.644 45.455 0.00 0.00 0.00 1.28
4723 4898 2.790433 GAGCACACAAGGACCCAATTA 58.210 47.619 0.00 0.00 0.00 1.40
4724 4899 1.620822 GAGCACACAAGGACCCAATT 58.379 50.000 0.00 0.00 0.00 2.32
4725 4900 0.606401 CGAGCACACAAGGACCCAAT 60.606 55.000 0.00 0.00 0.00 3.16
4726 4901 1.227823 CGAGCACACAAGGACCCAA 60.228 57.895 0.00 0.00 0.00 4.12
4727 4902 2.425592 CGAGCACACAAGGACCCA 59.574 61.111 0.00 0.00 0.00 4.51
4774 4949 1.202330 CTCAAGGGCTCATCTGAGGT 58.798 55.000 9.15 0.00 42.29 3.85
4800 4975 2.361757 TCCAACATGCACTTTCAACAGG 59.638 45.455 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.