Multiple sequence alignment - TraesCS6D01G281100

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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 TraesCS6D01G281100 chr6D 100.000 4143 0 0 1 4143 388541412 388537270 0.000000e+00 7651.0
1 TraesCS6D01G281100 chr6D 97.143 35 1 0 130 164 316082035 316082069 4.470000e-05 60.2
2 TraesCS6D01G281100 chr6A 93.349 1744 55 28 1745 3460 535153836 535152126 0.000000e+00 2521.0
3 TraesCS6D01G281100 chr6A 94.377 1565 47 13 210 1751 535155424 535153878 0.000000e+00 2364.0
4 TraesCS6D01G281100 chr6A 89.831 354 5 8 3459 3788 535143376 535143030 3.830000e-115 425.0
5 TraesCS6D01G281100 chr6A 88.669 353 22 11 3806 4143 535143041 535142692 8.290000e-112 414.0
6 TraesCS6D01G281100 chr6B 89.201 2102 78 56 1745 3788 581081249 581079239 0.000000e+00 2486.0
7 TraesCS6D01G281100 chr6B 93.176 1612 61 22 166 1751 581083144 581081556 0.000000e+00 2322.0
8 TraesCS6D01G281100 chr6B 89.143 350 18 9 3806 4140 581079250 581078906 6.410000e-113 418.0
9 TraesCS6D01G281100 chr5B 87.940 199 24 0 2898 3096 348448560 348448362 6.920000e-58 235.0
10 TraesCS6D01G281100 chr5B 82.803 157 27 0 1376 1532 348449877 348449721 1.550000e-29 141.0
11 TraesCS6D01G281100 chr5B 86.022 93 11 2 1645 1737 348449619 348449529 9.480000e-17 99.0
12 TraesCS6D01G281100 chr5B 95.652 46 2 0 1847 1892 348449417 348449372 1.600000e-09 75.0
13 TraesCS6D01G281100 chr5D 87.437 199 25 0 2898 3096 303759417 303759219 3.220000e-56 230.0
14 TraesCS6D01G281100 chr5D 82.803 157 27 0 1376 1532 303760733 303760577 1.550000e-29 141.0
15 TraesCS6D01G281100 chr5D 93.750 48 2 1 1847 1894 303760269 303760223 2.070000e-08 71.3
16 TraesCS6D01G281100 chr5A 86.935 199 26 0 2898 3096 394181648 394181450 1.500000e-54 224.0
17 TraesCS6D01G281100 chr5A 84.177 158 25 0 1373 1530 394182970 394182813 1.990000e-33 154.0
18 TraesCS6D01G281100 chr5A 90.141 71 7 0 94 164 427367768 427367698 4.410000e-15 93.5
19 TraesCS6D01G281100 chr5A 93.750 48 2 1 1847 1894 394182517 394182471 2.070000e-08 71.3
20 TraesCS6D01G281100 chr7B 85.185 108 16 0 2219 2326 97973878 97973771 1.220000e-20 111.0
21 TraesCS6D01G281100 chr2D 83.495 103 16 1 1423 1524 112180678 112180576 1.230000e-15 95.3
22 TraesCS6D01G281100 chr3D 100.000 35 0 0 130 164 132154173 132154207 9.610000e-07 65.8
23 TraesCS6D01G281100 chr3A 82.609 69 12 0 96 164 7083657 7083589 1.240000e-05 62.1


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 TraesCS6D01G281100 chr6D 388537270 388541412 4142 True 7651.0 7651 100.000000 1 4143 1 chr6D.!!$R1 4142
1 TraesCS6D01G281100 chr6A 535152126 535155424 3298 True 2442.5 2521 93.863000 210 3460 2 chr6A.!!$R2 3250
2 TraesCS6D01G281100 chr6A 535142692 535143376 684 True 419.5 425 89.250000 3459 4143 2 chr6A.!!$R1 684
3 TraesCS6D01G281100 chr6B 581078906 581083144 4238 True 1742.0 2486 90.506667 166 4140 3 chr6B.!!$R1 3974

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
140 141 0.035739 GCCGACCAAGACCTAACCAA 59.964 55.000 0.0 0.0 0.00 3.67 F
310 314 0.107116 TGTGTTTGGTTACAGCGGGT 60.107 50.000 0.0 0.0 0.00 5.28 F
418 422 0.309922 GCATCAATCATGGACGCCTG 59.690 55.000 0.0 0.0 32.37 4.85 F
801 814 0.859232 GAAGCTACCACACACACACG 59.141 55.000 0.0 0.0 0.00 4.49 F
802 815 1.157870 AAGCTACCACACACACACGC 61.158 55.000 0.0 0.0 0.00 5.34 F
1363 1395 1.538950 CTTTGGCTTCTCTTGTGCTCC 59.461 52.381 0.0 0.0 0.00 4.70 F
2538 2938 0.326264 CCAAGGGAGGAAGGTGAGTG 59.674 60.000 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2360 0.031449 GGCATGAGGCGAGACTAGTC 59.969 60.000 15.41 15.41 46.16 2.59 R
1999 2364 0.179062 GATTGGCATGAGGCGAGACT 60.179 55.000 0.00 0.00 46.16 3.24 R
2001 2366 0.179065 CAGATTGGCATGAGGCGAGA 60.179 55.000 0.00 0.00 46.16 4.04 R
2500 2900 0.322816 GGTGAGCTTCAGCATGGGAA 60.323 55.000 0.75 0.00 43.79 3.97 R
2501 2901 1.300963 GGTGAGCTTCAGCATGGGA 59.699 57.895 0.75 0.00 43.79 4.37 R
2587 2987 1.343465 TCACGAGGGAAAGGTCAACTC 59.657 52.381 0.00 0.00 0.00 3.01 R
3759 4207 0.818296 AGCGACGGATTAGACAAGCT 59.182 50.000 0.00 0.00 0.00 3.74 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
18 19 3.928343 GCGTTTGCACTGGTGTTAA 57.072 47.368 2.64 0.00 42.15 2.01
19 20 2.196295 GCGTTTGCACTGGTGTTAAA 57.804 45.000 2.64 2.76 42.15 1.52
20 21 2.116366 GCGTTTGCACTGGTGTTAAAG 58.884 47.619 2.64 1.88 42.15 1.85
21 22 2.223386 GCGTTTGCACTGGTGTTAAAGA 60.223 45.455 2.64 0.00 42.15 2.52
22 23 3.732471 GCGTTTGCACTGGTGTTAAAGAA 60.732 43.478 2.64 0.00 42.15 2.52
23 24 4.416620 CGTTTGCACTGGTGTTAAAGAAA 58.583 39.130 2.64 0.00 0.00 2.52
24 25 4.859798 CGTTTGCACTGGTGTTAAAGAAAA 59.140 37.500 2.64 0.00 0.00 2.29
25 26 5.346281 CGTTTGCACTGGTGTTAAAGAAAAA 59.654 36.000 2.64 0.00 0.00 1.94
46 47 3.735237 AATATGGCTAGGACACAGTCG 57.265 47.619 0.00 0.00 32.65 4.18
47 48 2.430248 TATGGCTAGGACACAGTCGA 57.570 50.000 0.00 0.00 32.65 4.20
48 49 1.107114 ATGGCTAGGACACAGTCGAG 58.893 55.000 0.00 0.00 32.65 4.04
49 50 0.251209 TGGCTAGGACACAGTCGAGT 60.251 55.000 0.00 0.00 32.65 4.18
50 51 0.171455 GGCTAGGACACAGTCGAGTG 59.829 60.000 18.72 18.72 44.93 3.51
51 52 1.166129 GCTAGGACACAGTCGAGTGA 58.834 55.000 26.62 2.03 42.05 3.41
52 53 1.540267 GCTAGGACACAGTCGAGTGAA 59.460 52.381 26.62 4.07 42.05 3.18
53 54 2.030185 GCTAGGACACAGTCGAGTGAAA 60.030 50.000 26.62 4.40 42.05 2.69
54 55 2.510768 AGGACACAGTCGAGTGAAAC 57.489 50.000 26.62 14.98 42.05 2.78
120 121 8.703604 TTAATGTAAGATCTCACAAGTACAGC 57.296 34.615 1.95 0.00 0.00 4.40
121 122 4.733850 TGTAAGATCTCACAAGTACAGCG 58.266 43.478 0.00 0.00 0.00 5.18
122 123 2.285827 AGATCTCACAAGTACAGCGC 57.714 50.000 0.00 0.00 0.00 5.92
123 124 1.134965 AGATCTCACAAGTACAGCGCC 60.135 52.381 2.29 0.00 0.00 6.53
124 125 0.458543 ATCTCACAAGTACAGCGCCG 60.459 55.000 2.29 0.00 0.00 6.46
125 126 1.080772 CTCACAAGTACAGCGCCGA 60.081 57.895 2.29 0.00 0.00 5.54
126 127 1.344942 CTCACAAGTACAGCGCCGAC 61.345 60.000 2.29 0.00 0.00 4.79
127 128 2.048503 ACAAGTACAGCGCCGACC 60.049 61.111 2.29 0.00 0.00 4.79
128 129 2.048597 CAAGTACAGCGCCGACCA 60.049 61.111 2.29 0.00 0.00 4.02
129 130 1.666553 CAAGTACAGCGCCGACCAA 60.667 57.895 2.29 0.00 0.00 3.67
130 131 1.374252 AAGTACAGCGCCGACCAAG 60.374 57.895 2.29 0.00 0.00 3.61
131 132 1.812686 AAGTACAGCGCCGACCAAGA 61.813 55.000 2.29 0.00 0.00 3.02
132 133 2.092882 GTACAGCGCCGACCAAGAC 61.093 63.158 2.29 0.00 0.00 3.01
133 134 3.291101 TACAGCGCCGACCAAGACC 62.291 63.158 2.29 0.00 0.00 3.85
134 135 4.379243 CAGCGCCGACCAAGACCT 62.379 66.667 2.29 0.00 0.00 3.85
135 136 2.678934 AGCGCCGACCAAGACCTA 60.679 61.111 2.29 0.00 0.00 3.08
136 137 2.263540 GCGCCGACCAAGACCTAA 59.736 61.111 0.00 0.00 0.00 2.69
137 138 2.098831 GCGCCGACCAAGACCTAAC 61.099 63.158 0.00 0.00 0.00 2.34
138 139 1.447314 CGCCGACCAAGACCTAACC 60.447 63.158 0.00 0.00 0.00 2.85
139 140 1.675219 GCCGACCAAGACCTAACCA 59.325 57.895 0.00 0.00 0.00 3.67
140 141 0.035739 GCCGACCAAGACCTAACCAA 59.964 55.000 0.00 0.00 0.00 3.67
141 142 1.944430 GCCGACCAAGACCTAACCAAG 60.944 57.143 0.00 0.00 0.00 3.61
142 143 1.346722 CCGACCAAGACCTAACCAAGT 59.653 52.381 0.00 0.00 0.00 3.16
143 144 2.612221 CCGACCAAGACCTAACCAAGTC 60.612 54.545 0.00 0.00 0.00 3.01
144 145 2.299297 CGACCAAGACCTAACCAAGTCT 59.701 50.000 0.00 0.00 45.18 3.24
151 152 4.660168 AGACCTAACCAAGTCTTAGTCGA 58.340 43.478 0.00 0.00 40.43 4.20
152 153 4.458642 AGACCTAACCAAGTCTTAGTCGAC 59.541 45.833 7.70 7.70 40.43 4.20
153 154 4.405548 ACCTAACCAAGTCTTAGTCGACT 58.594 43.478 23.66 23.66 45.73 4.18
154 155 4.217983 ACCTAACCAAGTCTTAGTCGACTG 59.782 45.833 28.12 12.46 43.14 3.51
155 156 4.458295 CCTAACCAAGTCTTAGTCGACTGA 59.542 45.833 28.12 19.13 43.14 3.41
156 157 4.506886 AACCAAGTCTTAGTCGACTGAG 57.493 45.455 26.80 26.80 43.14 3.35
157 158 3.752665 ACCAAGTCTTAGTCGACTGAGA 58.247 45.455 30.05 30.05 43.14 3.27
158 159 4.337145 ACCAAGTCTTAGTCGACTGAGAT 58.663 43.478 34.18 21.41 43.14 2.75
159 160 4.767928 ACCAAGTCTTAGTCGACTGAGATT 59.232 41.667 34.18 29.10 43.14 2.40
160 161 5.244178 ACCAAGTCTTAGTCGACTGAGATTT 59.756 40.000 34.18 32.05 43.14 2.17
161 162 6.433404 ACCAAGTCTTAGTCGACTGAGATTTA 59.567 38.462 32.94 16.75 43.14 1.40
162 163 6.970043 CCAAGTCTTAGTCGACTGAGATTTAG 59.030 42.308 32.94 26.48 43.14 1.85
163 164 6.126568 AGTCTTAGTCGACTGAGATTTAGC 57.873 41.667 34.18 23.58 42.39 3.09
164 165 4.965158 GTCTTAGTCGACTGAGATTTAGCG 59.035 45.833 34.18 11.89 40.13 4.26
194 195 7.463469 AAATACACAAGTTAGTTTTTGCTGC 57.537 32.000 0.00 0.00 0.00 5.25
220 221 5.712917 TGCCCTAACAAAACATTTAGGTAGG 59.287 40.000 6.64 0.00 42.00 3.18
225 226 9.729281 CCTAACAAAACATTTAGGTAGGAACTA 57.271 33.333 0.00 0.00 39.67 2.24
291 295 0.250513 GCCGTGGATCTTTCTGTCCT 59.749 55.000 0.00 0.00 35.49 3.85
310 314 0.107116 TGTGTTTGGTTACAGCGGGT 60.107 50.000 0.00 0.00 0.00 5.28
395 399 4.070009 GTGTCGAAATTCCACCTACCTTT 58.930 43.478 0.00 0.00 0.00 3.11
418 422 0.309922 GCATCAATCATGGACGCCTG 59.690 55.000 0.00 0.00 32.37 4.85
423 427 2.547640 AATCATGGACGCCTGCTGCT 62.548 55.000 0.00 0.00 38.05 4.24
481 486 9.013229 TGATACAACATGCTAGTTCAAAGATTT 57.987 29.630 0.00 0.00 0.00 2.17
562 567 3.869473 CTTTCGGCCCAACGACGGA 62.869 63.158 0.00 0.00 43.37 4.69
740 753 1.725292 GCCGCTCGAGCTATAAGTACG 60.725 57.143 32.88 15.07 39.32 3.67
798 811 2.035961 TCTGAGAAGCTACCACACACAC 59.964 50.000 0.00 0.00 0.00 3.82
799 812 1.760029 TGAGAAGCTACCACACACACA 59.240 47.619 0.00 0.00 0.00 3.72
800 813 2.135933 GAGAAGCTACCACACACACAC 58.864 52.381 0.00 0.00 0.00 3.82
801 814 0.859232 GAAGCTACCACACACACACG 59.141 55.000 0.00 0.00 0.00 4.49
802 815 1.157870 AAGCTACCACACACACACGC 61.158 55.000 0.00 0.00 0.00 5.34
803 816 2.938823 GCTACCACACACACACGCG 61.939 63.158 3.53 3.53 0.00 6.01
809 822 4.589700 CACACACACGCGCACACC 62.590 66.667 5.73 0.00 0.00 4.16
1363 1395 1.538950 CTTTGGCTTCTCTTGTGCTCC 59.461 52.381 0.00 0.00 0.00 4.70
1518 1550 2.578981 GAGCGACGCGGTAAGTCC 60.579 66.667 15.18 0.00 37.83 3.85
1590 1622 6.204688 CCTGAAAGAAAAATAAAACCAAGGCC 59.795 38.462 0.00 0.00 34.07 5.19
1609 1641 3.365666 GGCCATATTTGCTGATCGATGTG 60.366 47.826 0.54 0.00 0.00 3.21
1610 1642 3.499537 GCCATATTTGCTGATCGATGTGA 59.500 43.478 0.54 0.00 0.00 3.58
1611 1643 4.023792 GCCATATTTGCTGATCGATGTGAA 60.024 41.667 0.54 0.00 0.00 3.18
1612 1644 5.335426 GCCATATTTGCTGATCGATGTGAAT 60.335 40.000 0.54 0.00 0.00 2.57
1619 1651 2.969957 CTGATCGATGTGAATCGTCTCG 59.030 50.000 0.54 0.00 43.85 4.04
1627 1659 3.718210 GAATCGTCTCGCCGGCCTT 62.718 63.158 23.46 2.81 0.00 4.35
1927 2272 2.346529 CATTCCCCTCTCCATCTCCAT 58.653 52.381 0.00 0.00 0.00 3.41
1934 2282 4.166539 CCCTCTCCATCTCCATAACATCT 58.833 47.826 0.00 0.00 0.00 2.90
1935 2283 5.336945 CCCTCTCCATCTCCATAACATCTA 58.663 45.833 0.00 0.00 0.00 1.98
1936 2284 5.421693 CCCTCTCCATCTCCATAACATCTAG 59.578 48.000 0.00 0.00 0.00 2.43
1937 2285 5.105392 CCTCTCCATCTCCATAACATCTAGC 60.105 48.000 0.00 0.00 0.00 3.42
1941 2289 5.717178 TCCATCTCCATAACATCTAGCTACC 59.283 44.000 0.00 0.00 0.00 3.18
1951 2299 3.136077 ACATCTAGCTACCCTCTACGACA 59.864 47.826 0.00 0.00 0.00 4.35
1952 2300 3.920231 TCTAGCTACCCTCTACGACAA 57.080 47.619 0.00 0.00 0.00 3.18
1953 2301 4.434545 TCTAGCTACCCTCTACGACAAT 57.565 45.455 0.00 0.00 0.00 2.71
1954 2302 4.789807 TCTAGCTACCCTCTACGACAATT 58.210 43.478 0.00 0.00 0.00 2.32
1955 2303 5.933617 TCTAGCTACCCTCTACGACAATTA 58.066 41.667 0.00 0.00 0.00 1.40
1956 2304 6.359804 TCTAGCTACCCTCTACGACAATTAA 58.640 40.000 0.00 0.00 0.00 1.40
1957 2305 5.259832 AGCTACCCTCTACGACAATTAAC 57.740 43.478 0.00 0.00 0.00 2.01
1958 2306 4.099113 AGCTACCCTCTACGACAATTAACC 59.901 45.833 0.00 0.00 0.00 2.85
1959 2307 4.142093 GCTACCCTCTACGACAATTAACCA 60.142 45.833 0.00 0.00 0.00 3.67
1960 2308 5.452917 GCTACCCTCTACGACAATTAACCAT 60.453 44.000 0.00 0.00 0.00 3.55
1961 2309 5.019785 ACCCTCTACGACAATTAACCATC 57.980 43.478 0.00 0.00 0.00 3.51
1962 2310 4.141779 ACCCTCTACGACAATTAACCATCC 60.142 45.833 0.00 0.00 0.00 3.51
1972 2320 7.228706 ACGACAATTAACCATCCATCCTTAATC 59.771 37.037 0.00 0.00 0.00 1.75
1978 2326 3.117131 ACCATCCATCCTTAATCAACCCC 60.117 47.826 0.00 0.00 0.00 4.95
1993 2358 4.906618 TCAACCCCTTTGATTACTCTCAC 58.093 43.478 0.00 0.00 39.45 3.51
1994 2359 4.597507 TCAACCCCTTTGATTACTCTCACT 59.402 41.667 0.00 0.00 39.45 3.41
1995 2360 4.559862 ACCCCTTTGATTACTCTCACTG 57.440 45.455 0.00 0.00 0.00 3.66
1996 2361 4.168101 ACCCCTTTGATTACTCTCACTGA 58.832 43.478 0.00 0.00 0.00 3.41
1997 2362 4.020128 ACCCCTTTGATTACTCTCACTGAC 60.020 45.833 0.00 0.00 0.00 3.51
1998 2363 4.223923 CCCCTTTGATTACTCTCACTGACT 59.776 45.833 0.00 0.00 0.00 3.41
1999 2364 5.422331 CCCCTTTGATTACTCTCACTGACTA 59.578 44.000 0.00 0.00 0.00 2.59
2000 2365 6.406400 CCCCTTTGATTACTCTCACTGACTAG 60.406 46.154 0.00 0.00 0.00 2.57
2001 2366 6.153680 CCCTTTGATTACTCTCACTGACTAGT 59.846 42.308 0.00 0.00 37.75 2.57
2002 2367 7.254852 CCTTTGATTACTCTCACTGACTAGTC 58.745 42.308 16.32 16.32 34.07 2.59
2003 2368 7.122055 CCTTTGATTACTCTCACTGACTAGTCT 59.878 40.741 23.01 1.36 34.07 3.24
2004 2369 7.618502 TTGATTACTCTCACTGACTAGTCTC 57.381 40.000 23.01 8.61 34.07 3.36
2005 2370 5.813157 TGATTACTCTCACTGACTAGTCTCG 59.187 44.000 23.01 15.92 34.07 4.04
2149 2525 4.345257 ACCTGTCCATTCGTGCTTATCTAT 59.655 41.667 0.00 0.00 0.00 1.98
2172 2548 1.695788 AGCCGGTGGTGTTTAAGTAGT 59.304 47.619 1.90 0.00 0.00 2.73
2500 2900 2.377136 AGGCCGTGATCAAGGACTT 58.623 52.632 28.44 13.94 46.53 3.01
2501 2901 0.693049 AGGCCGTGATCAAGGACTTT 59.307 50.000 28.44 9.83 46.53 2.66
2538 2938 0.326264 CCAAGGGAGGAAGGTGAGTG 59.674 60.000 0.00 0.00 0.00 3.51
2556 2956 4.176271 GAGTGATTGTTTAATGCCTTGCC 58.824 43.478 0.00 0.00 0.00 4.52
2587 2987 2.476051 GCGACGAACCACAGCATG 59.524 61.111 0.00 0.00 46.00 4.06
2705 3105 3.435186 GCAAGGCGCTGGAGTTCC 61.435 66.667 7.64 0.00 37.77 3.62
2737 3137 1.855213 TAGGTACGCACGCAACGACT 61.855 55.000 0.00 0.00 0.00 4.18
2738 3138 2.713894 GGTACGCACGCAACGACTC 61.714 63.158 0.00 0.00 0.00 3.36
2844 3247 3.804786 TTCACACCACTGTCGTTAAGA 57.195 42.857 0.00 0.00 0.00 2.10
2855 3261 7.486870 ACCACTGTCGTTAAGAAAATGAAAAAC 59.513 33.333 0.00 0.00 0.00 2.43
3082 3488 2.185608 GAGTTCCTGCTCCGGCTC 59.814 66.667 0.00 0.00 39.59 4.70
3107 3513 3.437795 GGAAGCGGAGGTCGTCGA 61.438 66.667 0.00 0.00 41.72 4.20
3171 3577 2.768344 GGCCCACCAGCTAGCCTA 60.768 66.667 12.13 0.00 42.34 3.93
3172 3578 2.812619 GGCCCACCAGCTAGCCTAG 61.813 68.421 12.13 2.60 42.34 3.02
3181 3587 4.434685 CTAGCCTAGCAGCAGCAC 57.565 61.111 3.17 0.00 45.49 4.40
3182 3588 1.519246 CTAGCCTAGCAGCAGCACA 59.481 57.895 3.17 0.00 45.49 4.57
3183 3589 0.530211 CTAGCCTAGCAGCAGCACAG 60.530 60.000 3.17 0.00 45.49 3.66
3187 3593 1.367599 CCTAGCAGCAGCACAGAAGC 61.368 60.000 3.17 0.00 45.49 3.86
3190 3596 3.429141 CAGCAGCACAGAAGCCGG 61.429 66.667 0.00 0.00 34.23 6.13
3191 3597 3.946201 AGCAGCACAGAAGCCGGT 61.946 61.111 1.90 0.00 34.23 5.28
3192 3598 3.426568 GCAGCACAGAAGCCGGTC 61.427 66.667 1.90 0.00 34.23 4.79
3194 3600 4.379243 AGCACAGAAGCCGGTCGG 62.379 66.667 1.90 4.85 38.57 4.79
3197 3603 3.692406 ACAGAAGCCGGTCGGGTC 61.692 66.667 14.61 8.41 46.38 4.46
3384 3790 1.078708 GGAAAACGATCGGAGCCCA 60.079 57.895 20.98 0.00 0.00 5.36
3385 3791 1.366854 GGAAAACGATCGGAGCCCAC 61.367 60.000 20.98 3.94 0.00 4.61
3386 3792 1.693083 GAAAACGATCGGAGCCCACG 61.693 60.000 20.98 0.00 0.00 4.94
3387 3793 4.814294 AACGATCGGAGCCCACGC 62.814 66.667 20.98 0.00 0.00 5.34
3463 3884 2.251642 GGCACAGTGACCAACCGAC 61.252 63.158 4.15 0.00 0.00 4.79
3474 3895 1.214589 CAACCGACCCGTGTCTAGG 59.785 63.158 0.00 0.00 39.47 3.02
3587 4016 4.096003 GCTACCTGCCGCTCCCAA 62.096 66.667 0.00 0.00 35.15 4.12
3667 4112 0.397816 AGCTAGGATCGCCCTCTGTT 60.398 55.000 0.00 0.00 43.31 3.16
3759 4207 0.749091 GCATGCATGGGTGTCAGCTA 60.749 55.000 27.34 0.00 0.00 3.32
3760 4208 1.306148 CATGCATGGGTGTCAGCTAG 58.694 55.000 19.40 0.00 0.00 3.42
3761 4209 0.465097 ATGCATGGGTGTCAGCTAGC 60.465 55.000 6.62 6.62 0.00 3.42
3762 4210 1.222936 GCATGGGTGTCAGCTAGCT 59.777 57.895 12.68 12.68 0.00 3.32
3772 4220 4.116238 GTGTCAGCTAGCTTGTCTAATCC 58.884 47.826 16.46 0.00 0.00 3.01
3777 4225 2.386249 CTAGCTTGTCTAATCCGTCGC 58.614 52.381 0.00 0.00 0.00 5.19
3778 4226 0.818296 AGCTTGTCTAATCCGTCGCT 59.182 50.000 0.00 0.00 0.00 4.93
3779 4227 1.204941 AGCTTGTCTAATCCGTCGCTT 59.795 47.619 0.00 0.00 0.00 4.68
3780 4228 2.000447 GCTTGTCTAATCCGTCGCTTT 59.000 47.619 0.00 0.00 0.00 3.51
3781 4229 2.222819 GCTTGTCTAATCCGTCGCTTTG 60.223 50.000 0.00 0.00 0.00 2.77
3782 4230 3.250744 CTTGTCTAATCCGTCGCTTTGA 58.749 45.455 0.00 0.00 0.00 2.69
3783 4231 3.306917 TGTCTAATCCGTCGCTTTGAA 57.693 42.857 0.00 0.00 0.00 2.69
3784 4232 3.857052 TGTCTAATCCGTCGCTTTGAAT 58.143 40.909 0.00 0.00 0.00 2.57
3785 4233 5.001237 TGTCTAATCCGTCGCTTTGAATA 57.999 39.130 0.00 0.00 0.00 1.75
3786 4234 5.597806 TGTCTAATCCGTCGCTTTGAATAT 58.402 37.500 0.00 0.00 0.00 1.28
3787 4235 5.462068 TGTCTAATCCGTCGCTTTGAATATG 59.538 40.000 0.00 0.00 0.00 1.78
3788 4236 3.609103 AATCCGTCGCTTTGAATATGC 57.391 42.857 0.00 0.00 0.00 3.14
3789 4237 2.309528 TCCGTCGCTTTGAATATGCT 57.690 45.000 0.00 0.00 0.00 3.79
3790 4238 2.627945 TCCGTCGCTTTGAATATGCTT 58.372 42.857 0.00 0.00 0.00 3.91
3791 4239 3.006940 TCCGTCGCTTTGAATATGCTTT 58.993 40.909 0.00 0.00 0.00 3.51
3792 4240 3.438781 TCCGTCGCTTTGAATATGCTTTT 59.561 39.130 0.00 0.00 0.00 2.27
3793 4241 4.083003 TCCGTCGCTTTGAATATGCTTTTT 60.083 37.500 0.00 0.00 0.00 1.94
3824 4272 7.661859 CGAATAGCTTTGAATATGATCTCGTC 58.338 38.462 0.00 0.00 0.00 4.20
3834 4282 0.594602 TGATCTCGTCCGTTCGTTGT 59.405 50.000 0.00 0.00 0.00 3.32
3846 4294 5.349543 GTCCGTTCGTTGTGGTAAAGATATT 59.650 40.000 0.00 0.00 0.00 1.28
3848 4296 6.531240 TCCGTTCGTTGTGGTAAAGATATTAC 59.469 38.462 0.00 0.00 0.00 1.89
3865 4317 8.534954 AGATATTACCTACACACACACATACT 57.465 34.615 0.00 0.00 0.00 2.12
3866 4318 8.630917 AGATATTACCTACACACACACATACTC 58.369 37.037 0.00 0.00 0.00 2.59
3867 4319 3.955650 ACCTACACACACACATACTCC 57.044 47.619 0.00 0.00 0.00 3.85
3868 4320 3.507411 ACCTACACACACACATACTCCT 58.493 45.455 0.00 0.00 0.00 3.69
3870 4322 5.269991 ACCTACACACACACATACTCCTAT 58.730 41.667 0.00 0.00 0.00 2.57
3871 4323 5.127194 ACCTACACACACACATACTCCTATG 59.873 44.000 0.00 0.00 36.54 2.23
3872 4324 5.127194 CCTACACACACACATACTCCTATGT 59.873 44.000 0.00 0.00 43.30 2.29
3875 4327 5.479027 ACACACACACATACTCCTATGTACA 59.521 40.000 0.00 0.00 40.99 2.90
3878 4346 5.985530 CACACACATACTCCTATGTACATGG 59.014 44.000 18.81 15.33 40.99 3.66
3905 4373 2.156310 GTGACCATGAACGAACGGTAAC 59.844 50.000 0.00 0.00 0.00 2.50
3906 4374 2.223994 TGACCATGAACGAACGGTAACA 60.224 45.455 0.00 0.00 0.00 2.41
3907 4375 2.801679 GACCATGAACGAACGGTAACAA 59.198 45.455 0.00 0.00 0.00 2.83
4109 4588 0.893270 TAGTGGCCGCATTGCTTGTT 60.893 50.000 20.59 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.116366 CTTTAACACCAGTGCAAACGC 58.884 47.619 0.00 0.00 0.00 4.84
1 2 3.684103 TCTTTAACACCAGTGCAAACG 57.316 42.857 0.00 0.00 0.00 3.60
2 3 6.713792 TTTTTCTTTAACACCAGTGCAAAC 57.286 33.333 0.00 0.00 0.00 2.93
23 24 4.876107 CGACTGTGTCCTAGCCATATTTTT 59.124 41.667 0.00 0.00 0.00 1.94
24 25 4.161565 TCGACTGTGTCCTAGCCATATTTT 59.838 41.667 0.00 0.00 0.00 1.82
25 26 3.704566 TCGACTGTGTCCTAGCCATATTT 59.295 43.478 0.00 0.00 0.00 1.40
26 27 3.296854 TCGACTGTGTCCTAGCCATATT 58.703 45.455 0.00 0.00 0.00 1.28
27 28 2.887783 CTCGACTGTGTCCTAGCCATAT 59.112 50.000 0.00 0.00 0.00 1.78
28 29 2.298610 CTCGACTGTGTCCTAGCCATA 58.701 52.381 0.00 0.00 0.00 2.74
29 30 1.107114 CTCGACTGTGTCCTAGCCAT 58.893 55.000 0.00 0.00 0.00 4.40
30 31 0.251209 ACTCGACTGTGTCCTAGCCA 60.251 55.000 0.00 0.00 0.00 4.75
31 32 0.171455 CACTCGACTGTGTCCTAGCC 59.829 60.000 0.00 0.00 33.61 3.93
32 33 1.166129 TCACTCGACTGTGTCCTAGC 58.834 55.000 4.89 0.00 38.90 3.42
33 34 3.253677 AGTTTCACTCGACTGTGTCCTAG 59.746 47.826 4.89 0.00 38.90 3.02
34 35 3.220110 AGTTTCACTCGACTGTGTCCTA 58.780 45.455 4.89 0.00 38.90 2.94
35 36 2.032620 AGTTTCACTCGACTGTGTCCT 58.967 47.619 4.89 0.00 38.90 3.85
36 37 2.510768 AGTTTCACTCGACTGTGTCC 57.489 50.000 4.89 0.00 38.90 4.02
37 38 4.802039 TGTTAAGTTTCACTCGACTGTGTC 59.198 41.667 4.89 0.00 38.90 3.67
38 39 4.751060 TGTTAAGTTTCACTCGACTGTGT 58.249 39.130 4.89 0.00 38.90 3.72
39 40 5.712217 TTGTTAAGTTTCACTCGACTGTG 57.288 39.130 0.00 0.00 39.15 3.66
40 41 6.103997 TCTTTGTTAAGTTTCACTCGACTGT 58.896 36.000 0.00 0.00 32.98 3.55
41 42 6.583912 TCTTTGTTAAGTTTCACTCGACTG 57.416 37.500 0.00 0.00 32.98 3.51
42 43 7.605410 TTTCTTTGTTAAGTTTCACTCGACT 57.395 32.000 0.00 0.00 32.98 4.18
43 44 8.663771 TTTTTCTTTGTTAAGTTTCACTCGAC 57.336 30.769 0.00 0.00 32.98 4.20
94 95 8.812329 GCTGTACTTGTGAGATCTTACATTAAG 58.188 37.037 19.85 16.28 37.13 1.85
95 96 7.488150 CGCTGTACTTGTGAGATCTTACATTAA 59.512 37.037 19.85 5.83 0.00 1.40
96 97 6.972901 CGCTGTACTTGTGAGATCTTACATTA 59.027 38.462 19.85 11.94 0.00 1.90
97 98 5.807520 CGCTGTACTTGTGAGATCTTACATT 59.192 40.000 19.85 12.83 0.00 2.71
98 99 5.344066 CGCTGTACTTGTGAGATCTTACAT 58.656 41.667 19.85 9.64 0.00 2.29
99 100 4.733850 CGCTGTACTTGTGAGATCTTACA 58.266 43.478 15.83 15.83 0.00 2.41
100 101 3.548268 GCGCTGTACTTGTGAGATCTTAC 59.452 47.826 10.60 10.60 0.00 2.34
101 102 3.428999 GGCGCTGTACTTGTGAGATCTTA 60.429 47.826 7.64 0.00 0.00 2.10
102 103 2.611518 GCGCTGTACTTGTGAGATCTT 58.388 47.619 0.00 0.00 0.00 2.40
103 104 1.134965 GGCGCTGTACTTGTGAGATCT 60.135 52.381 7.64 0.00 0.00 2.75
104 105 1.281899 GGCGCTGTACTTGTGAGATC 58.718 55.000 7.64 0.00 0.00 2.75
105 106 0.458543 CGGCGCTGTACTTGTGAGAT 60.459 55.000 8.45 0.00 0.00 2.75
106 107 1.080772 CGGCGCTGTACTTGTGAGA 60.081 57.895 8.45 0.00 0.00 3.27
107 108 1.080772 TCGGCGCTGTACTTGTGAG 60.081 57.895 17.37 0.00 0.00 3.51
108 109 1.372499 GTCGGCGCTGTACTTGTGA 60.372 57.895 17.37 0.00 0.00 3.58
109 110 2.380410 GGTCGGCGCTGTACTTGTG 61.380 63.158 17.37 0.00 0.00 3.33
110 111 2.048503 GGTCGGCGCTGTACTTGT 60.049 61.111 17.37 0.00 0.00 3.16
111 112 1.626654 CTTGGTCGGCGCTGTACTTG 61.627 60.000 17.37 1.58 0.00 3.16
112 113 1.374252 CTTGGTCGGCGCTGTACTT 60.374 57.895 17.37 0.00 0.00 2.24
113 114 2.261671 CTTGGTCGGCGCTGTACT 59.738 61.111 17.37 0.00 0.00 2.73
114 115 2.092882 GTCTTGGTCGGCGCTGTAC 61.093 63.158 17.37 12.72 0.00 2.90
115 116 2.260434 GTCTTGGTCGGCGCTGTA 59.740 61.111 17.37 0.00 0.00 2.74
116 117 4.681978 GGTCTTGGTCGGCGCTGT 62.682 66.667 17.37 0.00 0.00 4.40
117 118 2.501223 TTAGGTCTTGGTCGGCGCTG 62.501 60.000 10.86 10.86 0.00 5.18
118 119 2.280552 TTAGGTCTTGGTCGGCGCT 61.281 57.895 7.64 0.00 0.00 5.92
119 120 2.098831 GTTAGGTCTTGGTCGGCGC 61.099 63.158 0.00 0.00 0.00 6.53
120 121 1.447314 GGTTAGGTCTTGGTCGGCG 60.447 63.158 0.00 0.00 0.00 6.46
121 122 0.035739 TTGGTTAGGTCTTGGTCGGC 59.964 55.000 0.00 0.00 0.00 5.54
122 123 1.346722 ACTTGGTTAGGTCTTGGTCGG 59.653 52.381 0.00 0.00 0.00 4.79
123 124 2.299297 AGACTTGGTTAGGTCTTGGTCG 59.701 50.000 0.00 0.00 39.44 4.79
124 125 4.353383 AAGACTTGGTTAGGTCTTGGTC 57.647 45.455 7.42 0.00 46.76 4.02
129 130 4.458642 GTCGACTAAGACTTGGTTAGGTCT 59.541 45.833 8.70 0.00 43.60 3.85
130 131 4.731720 GTCGACTAAGACTTGGTTAGGTC 58.268 47.826 8.70 0.86 38.09 3.85
131 132 4.780275 GTCGACTAAGACTTGGTTAGGT 57.220 45.455 8.70 0.00 38.09 3.08
141 142 4.965158 CGCTAAATCTCAGTCGACTAAGAC 59.035 45.833 20.77 6.87 41.23 3.01
142 143 4.634883 ACGCTAAATCTCAGTCGACTAAGA 59.365 41.667 20.63 20.63 0.00 2.10
143 144 4.911053 ACGCTAAATCTCAGTCGACTAAG 58.089 43.478 19.57 14.47 0.00 2.18
144 145 4.959596 ACGCTAAATCTCAGTCGACTAA 57.040 40.909 19.57 1.94 0.00 2.24
145 146 6.426980 TTTACGCTAAATCTCAGTCGACTA 57.573 37.500 19.57 2.81 0.00 2.59
146 147 4.959596 TTACGCTAAATCTCAGTCGACT 57.040 40.909 13.58 13.58 0.00 4.18
147 148 6.385537 TTTTTACGCTAAATCTCAGTCGAC 57.614 37.500 7.70 7.70 0.00 4.20
192 193 4.348863 AAATGTTTTGTTAGGGCATGCA 57.651 36.364 21.36 0.00 0.00 3.96
193 194 4.869861 CCTAAATGTTTTGTTAGGGCATGC 59.130 41.667 9.90 9.90 41.81 4.06
220 221 8.726870 TTACACATGTAGGGCTAATTTAGTTC 57.273 34.615 0.00 0.00 0.00 3.01
281 285 4.638421 TGTAACCAAACACAGGACAGAAAG 59.362 41.667 0.00 0.00 0.00 2.62
291 295 0.107116 ACCCGCTGTAACCAAACACA 60.107 50.000 0.00 0.00 0.00 3.72
395 399 2.212652 GCGTCCATGATTGATGCAGTA 58.787 47.619 5.90 0.00 42.88 2.74
418 422 1.460743 GCCGATTTTTGGAAAAGCAGC 59.539 47.619 2.88 0.00 0.00 5.25
423 427 5.293560 CAGTTTAGGCCGATTTTTGGAAAA 58.706 37.500 0.00 0.00 0.00 2.29
481 486 2.215196 GTGTACGCAAAGTGAAGGGAA 58.785 47.619 0.39 0.00 0.00 3.97
740 753 2.967615 GGAGTGGGATAAGCGCGC 60.968 66.667 26.66 26.66 39.97 6.86
1363 1395 2.125350 GGGTGCTTCCTCTGCTCG 60.125 66.667 0.00 0.00 36.25 5.03
1420 1452 4.030913 ACATGACGATCTTCTTCCCCTTA 58.969 43.478 0.00 0.00 0.00 2.69
1540 1572 3.408851 GACGGCCGTGGAAACGTC 61.409 66.667 39.65 15.35 46.89 4.34
1609 1641 3.718210 AAGGCCGGCGAGACGATTC 62.718 63.158 22.54 2.36 35.47 2.52
1610 1642 3.771160 AAGGCCGGCGAGACGATT 61.771 61.111 22.54 3.17 35.47 3.34
1611 1643 4.514577 CAAGGCCGGCGAGACGAT 62.515 66.667 22.54 0.00 35.47 3.73
1627 1659 1.952990 CTGCACAAATACACCACCACA 59.047 47.619 0.00 0.00 0.00 4.17
1927 2272 5.163269 TGTCGTAGAGGGTAGCTAGATGTTA 60.163 44.000 0.00 0.00 36.95 2.41
1934 2282 5.300286 GGTTAATTGTCGTAGAGGGTAGCTA 59.700 44.000 0.00 0.00 36.95 3.32
1935 2283 4.099113 GGTTAATTGTCGTAGAGGGTAGCT 59.901 45.833 0.00 0.00 36.95 3.32
1936 2284 4.142093 TGGTTAATTGTCGTAGAGGGTAGC 60.142 45.833 0.00 0.00 36.95 3.58
1937 2285 5.587388 TGGTTAATTGTCGTAGAGGGTAG 57.413 43.478 0.00 0.00 36.95 3.18
1941 2289 5.018539 TGGATGGTTAATTGTCGTAGAGG 57.981 43.478 0.00 0.00 36.95 3.69
1951 2299 7.290014 GGGTTGATTAAGGATGGATGGTTAATT 59.710 37.037 0.00 0.00 0.00 1.40
1952 2300 6.782494 GGGTTGATTAAGGATGGATGGTTAAT 59.218 38.462 0.00 0.00 0.00 1.40
1953 2301 6.133356 GGGTTGATTAAGGATGGATGGTTAA 58.867 40.000 0.00 0.00 0.00 2.01
1954 2302 5.399727 GGGGTTGATTAAGGATGGATGGTTA 60.400 44.000 0.00 0.00 0.00 2.85
1955 2303 4.546674 GGGTTGATTAAGGATGGATGGTT 58.453 43.478 0.00 0.00 0.00 3.67
1956 2304 3.117131 GGGGTTGATTAAGGATGGATGGT 60.117 47.826 0.00 0.00 0.00 3.55
1957 2305 3.140895 AGGGGTTGATTAAGGATGGATGG 59.859 47.826 0.00 0.00 0.00 3.51
1958 2306 4.459852 AGGGGTTGATTAAGGATGGATG 57.540 45.455 0.00 0.00 0.00 3.51
1959 2307 5.043432 TCAAAGGGGTTGATTAAGGATGGAT 60.043 40.000 0.00 0.00 41.47 3.41
1960 2308 4.293634 TCAAAGGGGTTGATTAAGGATGGA 59.706 41.667 0.00 0.00 41.47 3.41
1961 2309 4.609301 TCAAAGGGGTTGATTAAGGATGG 58.391 43.478 0.00 0.00 41.47 3.51
1972 2320 4.697352 CAGTGAGAGTAATCAAAGGGGTTG 59.303 45.833 0.00 0.00 38.71 3.77
1978 2326 8.050778 AGACTAGTCAGTGAGAGTAATCAAAG 57.949 38.462 24.44 0.00 32.20 2.77
1987 2352 1.668751 GGCGAGACTAGTCAGTGAGAG 59.331 57.143 24.44 8.37 34.21 3.20
1993 2358 1.268999 GCATGAGGCGAGACTAGTCAG 60.269 57.143 24.44 17.85 0.00 3.51
1994 2359 0.741326 GCATGAGGCGAGACTAGTCA 59.259 55.000 24.44 3.09 0.00 3.41
1995 2360 0.031449 GGCATGAGGCGAGACTAGTC 59.969 60.000 15.41 15.41 46.16 2.59
1996 2361 0.684479 TGGCATGAGGCGAGACTAGT 60.684 55.000 0.00 0.00 46.16 2.57
1997 2362 0.461548 TTGGCATGAGGCGAGACTAG 59.538 55.000 0.00 0.00 46.16 2.57
1998 2363 1.069204 GATTGGCATGAGGCGAGACTA 59.931 52.381 0.00 0.00 46.16 2.59
1999 2364 0.179062 GATTGGCATGAGGCGAGACT 60.179 55.000 0.00 0.00 46.16 3.24
2000 2365 0.179062 AGATTGGCATGAGGCGAGAC 60.179 55.000 0.00 0.00 46.16 3.36
2001 2366 0.179065 CAGATTGGCATGAGGCGAGA 60.179 55.000 0.00 0.00 46.16 4.04
2002 2367 1.783031 GCAGATTGGCATGAGGCGAG 61.783 60.000 0.00 0.00 46.16 5.03
2003 2368 1.820906 GCAGATTGGCATGAGGCGA 60.821 57.895 0.00 0.00 46.16 5.54
2004 2369 2.060004 CTGCAGATTGGCATGAGGCG 62.060 60.000 8.42 0.00 46.16 5.52
2005 2370 1.734137 CTGCAGATTGGCATGAGGC 59.266 57.895 8.42 0.00 43.97 4.70
2149 2525 1.972795 ACTTAAACACCACCGGCTAGA 59.027 47.619 0.00 0.00 0.00 2.43
2172 2548 1.888436 CTAGCCTCCTCGTGCACCAA 61.888 60.000 12.15 0.00 0.00 3.67
2500 2900 0.322816 GGTGAGCTTCAGCATGGGAA 60.323 55.000 0.75 0.00 43.79 3.97
2501 2901 1.300963 GGTGAGCTTCAGCATGGGA 59.699 57.895 0.75 0.00 43.79 4.37
2538 2938 1.926510 GCGGCAAGGCATTAAACAATC 59.073 47.619 0.00 0.00 0.00 2.67
2587 2987 1.343465 TCACGAGGGAAAGGTCAACTC 59.657 52.381 0.00 0.00 0.00 3.01
2641 3041 5.125739 CCGGAGCTCGAAGACCTATAATATT 59.874 44.000 7.83 0.00 42.43 1.28
2642 3042 4.641094 CCGGAGCTCGAAGACCTATAATAT 59.359 45.833 7.83 0.00 42.43 1.28
2643 3043 4.008330 CCGGAGCTCGAAGACCTATAATA 58.992 47.826 7.83 0.00 42.43 0.98
2644 3044 2.820787 CCGGAGCTCGAAGACCTATAAT 59.179 50.000 7.83 0.00 42.43 1.28
2645 3045 2.228059 CCGGAGCTCGAAGACCTATAA 58.772 52.381 7.83 0.00 42.43 0.98
2705 3105 2.120232 CGTACCTAGCGATTCAAGCAG 58.880 52.381 0.00 0.00 37.01 4.24
2844 3247 3.484393 GCGCACGGTTTGTTTTTCATTTT 60.484 39.130 0.30 0.00 0.00 1.82
3082 3488 2.125912 CTCCGCTTCCACTCCACG 60.126 66.667 0.00 0.00 0.00 4.94
3167 3573 1.367599 CTTCTGTGCTGCTGCTAGGC 61.368 60.000 17.00 3.61 40.48 3.93
3168 3574 1.367599 GCTTCTGTGCTGCTGCTAGG 61.368 60.000 17.00 6.53 40.48 3.02
3169 3575 1.367599 GGCTTCTGTGCTGCTGCTAG 61.368 60.000 17.00 14.13 40.48 3.42
3170 3576 1.376424 GGCTTCTGTGCTGCTGCTA 60.376 57.895 17.00 5.16 40.48 3.49
3171 3577 2.672307 GGCTTCTGTGCTGCTGCT 60.672 61.111 17.00 0.00 40.48 4.24
3172 3578 4.099170 CGGCTTCTGTGCTGCTGC 62.099 66.667 8.89 8.89 40.20 5.25
3173 3579 3.429141 CCGGCTTCTGTGCTGCTG 61.429 66.667 0.00 0.00 37.96 4.41
3174 3580 3.890936 GACCGGCTTCTGTGCTGCT 62.891 63.158 0.00 0.00 37.96 4.24
3175 3581 3.426568 GACCGGCTTCTGTGCTGC 61.427 66.667 0.00 0.00 37.96 5.25
3176 3582 3.114616 CGACCGGCTTCTGTGCTG 61.115 66.667 0.00 0.00 38.94 4.41
3177 3583 4.379243 CCGACCGGCTTCTGTGCT 62.379 66.667 0.00 0.00 0.00 4.40
3179 3585 3.934391 GACCCGACCGGCTTCTGTG 62.934 68.421 0.00 0.00 33.26 3.66
3181 3587 4.796231 CGACCCGACCGGCTTCTG 62.796 72.222 0.00 0.00 33.26 3.02
3335 3741 1.654105 GACCGAAGAACATGCACGTAG 59.346 52.381 0.00 0.00 0.00 3.51
3446 3867 2.251642 GGTCGGTTGGTCACTGTGC 61.252 63.158 2.12 0.00 32.85 4.57
3463 3884 1.480954 ACATTGCTACCTAGACACGGG 59.519 52.381 0.00 0.00 0.00 5.28
3667 4112 7.857734 TTTTACAGAGACAATTGAACACTGA 57.142 32.000 25.92 15.09 0.00 3.41
3759 4207 0.818296 AGCGACGGATTAGACAAGCT 59.182 50.000 0.00 0.00 0.00 3.74
3760 4208 1.641577 AAGCGACGGATTAGACAAGC 58.358 50.000 0.00 0.00 0.00 4.01
3761 4209 3.250744 TCAAAGCGACGGATTAGACAAG 58.749 45.455 0.00 0.00 0.00 3.16
3762 4210 3.306917 TCAAAGCGACGGATTAGACAA 57.693 42.857 0.00 0.00 0.00 3.18
3793 4241 9.236691 GATCATATTCAAAGCTATTCGCAAAAA 57.763 29.630 0.00 0.00 42.61 1.94
3794 4242 8.623903 AGATCATATTCAAAGCTATTCGCAAAA 58.376 29.630 0.00 0.00 42.61 2.44
3795 4243 8.158169 AGATCATATTCAAAGCTATTCGCAAA 57.842 30.769 0.00 0.00 42.61 3.68
3796 4244 7.359514 CGAGATCATATTCAAAGCTATTCGCAA 60.360 37.037 0.00 0.00 42.61 4.85
3797 4245 6.089954 CGAGATCATATTCAAAGCTATTCGCA 59.910 38.462 0.00 0.00 42.61 5.10
3798 4246 6.090088 ACGAGATCATATTCAAAGCTATTCGC 59.910 38.462 0.00 0.00 39.57 4.70
3799 4247 7.201393 GGACGAGATCATATTCAAAGCTATTCG 60.201 40.741 0.00 0.00 0.00 3.34
3800 4248 7.201393 CGGACGAGATCATATTCAAAGCTATTC 60.201 40.741 0.00 0.00 0.00 1.75
3801 4249 6.587990 CGGACGAGATCATATTCAAAGCTATT 59.412 38.462 0.00 0.00 0.00 1.73
3802 4250 6.096036 CGGACGAGATCATATTCAAAGCTAT 58.904 40.000 0.00 0.00 0.00 2.97
3803 4251 5.009710 ACGGACGAGATCATATTCAAAGCTA 59.990 40.000 0.00 0.00 0.00 3.32
3804 4252 4.202161 ACGGACGAGATCATATTCAAAGCT 60.202 41.667 0.00 0.00 0.00 3.74
3805 4253 4.051922 ACGGACGAGATCATATTCAAAGC 58.948 43.478 0.00 0.00 0.00 3.51
3824 4272 5.789710 AATATCTTTACCACAACGAACGG 57.210 39.130 0.00 0.00 0.00 4.44
3834 4282 8.036575 GTGTGTGTGTAGGTAATATCTTTACCA 58.963 37.037 14.99 1.43 45.23 3.25
3846 4294 4.669700 AGGAGTATGTGTGTGTGTAGGTA 58.330 43.478 0.00 0.00 0.00 3.08
3848 4296 5.127194 ACATAGGAGTATGTGTGTGTGTAGG 59.873 44.000 0.00 0.00 46.31 3.18
3865 4317 4.100963 GTCACATCCACCATGTACATAGGA 59.899 45.833 23.07 21.52 44.60 2.94
3866 4318 4.380531 GTCACATCCACCATGTACATAGG 58.619 47.826 8.32 14.25 44.60 2.57
3867 4319 4.141733 TGGTCACATCCACCATGTACATAG 60.142 45.833 8.32 3.52 44.60 2.23
3868 4320 3.777522 TGGTCACATCCACCATGTACATA 59.222 43.478 8.32 0.00 44.60 2.29
3870 4322 1.981495 TGGTCACATCCACCATGTACA 59.019 47.619 0.00 0.00 44.60 2.90
3871 4323 2.779755 TGGTCACATCCACCATGTAC 57.220 50.000 0.00 0.00 44.60 2.90
3878 4346 2.093306 TCGTTCATGGTCACATCCAC 57.907 50.000 0.00 0.00 40.51 4.02
4109 4588 2.181777 GTGGCATCACGAGCTCGA 59.818 61.111 40.58 21.52 43.02 4.04


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

AutoCloner maintained by Alex Coulton.