Multiple sequence alignment - TraesCS5D01G029900

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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 TraesCS5D01G029900 chr5D 100.000 2528 0 0 1 2528 27681020 27683547 0.000000e+00 4669.0
1 TraesCS5D01G029900 chr5D 88.834 1218 88 13 796 1969 27691290 27692503 0.000000e+00 1452.0
2 TraesCS5D01G029900 chr5D 88.579 788 49 14 1767 2522 27692234 27693012 0.000000e+00 918.0
3 TraesCS5D01G029900 chr5D 91.463 246 9 3 1824 2059 27682729 27682972 6.740000e-86 327.0
4 TraesCS5D01G029900 chr5D 91.463 246 9 3 1710 1953 27682843 27683078 6.740000e-86 327.0
5 TraesCS5D01G029900 chr5D 90.551 254 14 2 1710 1953 27692291 27692544 6.740000e-86 327.0
6 TraesCS5D01G029900 chr5D 87.500 256 10 5 1824 2059 27692234 27692487 2.480000e-70 276.0
7 TraesCS5D01G029900 chr5D 93.750 160 6 2 174 333 27690914 27691069 1.170000e-58 237.0
8 TraesCS5D01G029900 chr5B 91.384 2356 102 27 174 2492 20036752 20034461 0.000000e+00 3133.0
9 TraesCS5D01G029900 chr5B 88.378 1480 95 19 638 2059 20066306 20064846 0.000000e+00 1709.0
10 TraesCS5D01G029900 chr5B 87.500 1104 97 10 797 1865 20013381 20012284 0.000000e+00 1236.0
11 TraesCS5D01G029900 chr5B 87.106 1078 97 20 797 1837 20688673 20689745 0.000000e+00 1182.0
12 TraesCS5D01G029900 chr5B 87.008 1016 89 20 797 1774 20672463 20673473 0.000000e+00 1105.0
13 TraesCS5D01G029900 chr5B 87.070 843 64 20 1710 2517 20065041 20064209 0.000000e+00 911.0
14 TraesCS5D01G029900 chr5B 90.575 626 27 14 1907 2528 20067722 20067125 0.000000e+00 800.0
15 TraesCS5D01G029900 chr5B 87.305 449 32 10 1930 2358 20689620 20690063 8.130000e-135 490.0
16 TraesCS5D01G029900 chr5B 88.378 370 20 8 1710 2059 20065098 20064732 8.360000e-115 424.0
17 TraesCS5D01G029900 chr5B 88.410 371 18 6 1710 2059 20065155 20064789 8.360000e-115 424.0
18 TraesCS5D01G029900 chr5B 89.610 308 17 6 1981 2279 20012234 20011933 6.600000e-101 377.0
19 TraesCS5D01G029900 chr5B 91.481 270 12 6 1710 1969 20064984 20064716 6.650000e-96 361.0
20 TraesCS5D01G029900 chr5B 92.181 243 8 3 1710 1942 20064927 20064686 1.450000e-87 333.0
21 TraesCS5D01G029900 chr5B 88.934 244 17 2 1710 1953 20035113 20034880 2.460000e-75 292.0
22 TraesCS5D01G029900 chr5B 93.889 180 9 2 2351 2528 20690613 20690792 1.150000e-68 270.0
23 TraesCS5D01G029900 chr5B 96.026 151 6 0 1803 1953 20067722 20067572 1.940000e-61 246.0
24 TraesCS5D01G029900 chr5B 88.667 150 7 4 1830 1969 20012433 20012284 9.300000e-40 174.0
25 TraesCS5D01G029900 chr5B 87.582 153 12 4 174 319 20671842 20671994 1.200000e-38 171.0
26 TraesCS5D01G029900 chr5B 87.582 153 12 4 174 319 20688052 20688204 1.200000e-38 171.0
27 TraesCS5D01G029900 chr5B 90.000 60 5 1 261 319 20013792 20013733 2.700000e-10 76.8
28 TraesCS5D01G029900 chr5A 86.496 1096 102 13 796 1849 18950667 18951758 0.000000e+00 1162.0
29 TraesCS5D01G029900 chr5A 93.291 477 32 0 1316 1792 18920700 18921176 0.000000e+00 704.0
30 TraesCS5D01G029900 chr5A 85.037 675 52 21 1871 2522 18951618 18952266 2.120000e-180 641.0
31 TraesCS5D01G029900 chr5A 95.210 334 9 5 1975 2306 18921094 18921422 2.880000e-144 521.0
32 TraesCS5D01G029900 chr5A 95.928 221 8 1 2308 2528 18940378 18940597 8.600000e-95 357.0
33 TraesCS5D01G029900 chr5A 87.425 167 6 6 1928 2083 18951618 18951780 7.190000e-41 178.0
34 TraesCS5D01G029900 chr5A 84.337 166 12 6 174 333 18950262 18950419 1.570000e-32 150.0
35 TraesCS5D01G029900 chr4A 97.727 176 2 2 3 176 717456822 717456647 4.090000e-78 302.0
36 TraesCS5D01G029900 chr3B 97.727 176 3 1 3 177 434725297 434725472 4.090000e-78 302.0
37 TraesCS5D01G029900 chr6B 98.256 172 2 1 3 173 261696314 261696143 1.470000e-77 300.0
38 TraesCS5D01G029900 chr6B 98.256 172 2 1 3 173 391080753 391080582 1.470000e-77 300.0
39 TraesCS5D01G029900 chr2B 98.256 172 2 1 3 173 47196583 47196412 1.470000e-77 300.0
40 TraesCS5D01G029900 chr2B 97.143 175 4 1 3 176 47191563 47191389 6.840000e-76 294.0
41 TraesCS5D01G029900 chr1B 98.235 170 2 1 5 173 669344027 669344196 1.900000e-76 296.0
42 TraesCS5D01G029900 chr7B 97.674 172 3 1 3 173 192778721 192778892 6.840000e-76 294.0
43 TraesCS5D01G029900 chr1A 97.674 172 3 1 3 173 12679200 12679371 6.840000e-76 294.0


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 TraesCS5D01G029900 chr5D 27681020 27683547 2527 False 1774.333333 4669 94.308667 1 2528 3 chr5D.!!$F1 2527
1 TraesCS5D01G029900 chr5D 27690914 27693012 2098 False 642.000000 1452 89.842800 174 2522 5 chr5D.!!$F2 2348
2 TraesCS5D01G029900 chr5B 20034461 20036752 2291 True 1712.500000 3133 90.159000 174 2492 2 chr5B.!!$R2 2318
3 TraesCS5D01G029900 chr5B 20064209 20067722 3513 True 651.000000 1709 90.312375 638 2528 8 chr5B.!!$R3 1890
4 TraesCS5D01G029900 chr5B 20671842 20673473 1631 False 638.000000 1105 87.295000 174 1774 2 chr5B.!!$F1 1600
5 TraesCS5D01G029900 chr5B 20688052 20690792 2740 False 528.250000 1182 88.970500 174 2528 4 chr5B.!!$F2 2354
6 TraesCS5D01G029900 chr5B 20011933 20013792 1859 True 465.950000 1236 88.944250 261 2279 4 chr5B.!!$R1 2018
7 TraesCS5D01G029900 chr5A 18920700 18921422 722 False 612.500000 704 94.250500 1316 2306 2 chr5A.!!$F2 990
8 TraesCS5D01G029900 chr5A 18950262 18952266 2004 False 532.750000 1162 85.823750 174 2522 4 chr5A.!!$F3 2348

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
70 71 0.254747 TCATTTCCTACCTTGCCCCG 59.745 55.000 0.00 0.0 0.00 5.73 F
146 147 0.322008 TGCGTGTATGCACCCAATCA 60.322 50.000 8.45 0.0 42.39 2.57 F
147 148 0.808125 GCGTGTATGCACCCAATCAA 59.192 50.000 8.45 0.0 42.39 2.57 F
1278 2425 1.003839 GGACACGGATGCCAAGACA 60.004 57.895 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 2518 0.325671 CTGCCTCCTCCTTCCCTGTA 60.326 60.000 0.00 0.0 0.0 2.74 R
1416 2563 0.673333 TCACAAAGGCATCGTCGCAT 60.673 50.000 1.52 0.0 0.0 4.73 R
1497 2644 1.555075 AGGTTAGTGATGGTCGTGCAT 59.445 47.619 0.00 0.0 0.0 3.96 R
2097 3814 3.275617 TGGATCGGTCTTATTGGGTTG 57.724 47.619 0.00 0.0 0.0 3.77 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
27 28 8.880244 AGGTGTTGAATATATTCTGTATAGGCA 58.120 33.333 22.77 9.57 37.67 4.75
28 29 9.155975 GGTGTTGAATATATTCTGTATAGGCAG 57.844 37.037 22.77 0.00 37.67 4.85
37 38 6.775594 ATTCTGTATAGGCAGTATATCGCA 57.224 37.500 0.00 0.00 37.70 5.10
39 40 6.136541 TCTGTATAGGCAGTATATCGCATG 57.863 41.667 0.00 0.00 37.70 4.06
43 44 8.685838 TGTATAGGCAGTATATCGCATGTATA 57.314 34.615 0.00 0.00 0.00 1.47
45 46 9.561270 GTATAGGCAGTATATCGCATGTATATG 57.439 37.037 11.02 0.00 37.36 1.78
47 48 7.582667 AGGCAGTATATCGCATGTATATGTA 57.417 36.000 11.02 0.00 36.65 2.29
48 49 7.652727 AGGCAGTATATCGCATGTATATGTAG 58.347 38.462 11.02 0.00 36.65 2.74
49 50 6.863645 GGCAGTATATCGCATGTATATGTAGG 59.136 42.308 11.02 0.00 36.65 3.18
50 51 7.255486 GGCAGTATATCGCATGTATATGTAGGA 60.255 40.741 11.02 0.00 36.65 2.94
51 52 8.300286 GCAGTATATCGCATGTATATGTAGGAT 58.700 37.037 11.02 5.08 36.65 3.24
52 53 9.833182 CAGTATATCGCATGTATATGTAGGATC 57.167 37.037 11.02 0.00 36.65 3.36
53 54 9.574516 AGTATATCGCATGTATATGTAGGATCA 57.425 33.333 11.02 0.00 36.65 2.92
57 58 8.654230 ATCGCATGTATATGTAGGATCATTTC 57.346 34.615 1.14 0.00 36.65 2.17
58 59 7.041721 TCGCATGTATATGTAGGATCATTTCC 58.958 38.462 1.14 0.00 39.51 3.13
59 60 7.044181 CGCATGTATATGTAGGATCATTTCCT 58.956 38.462 1.14 0.00 44.71 3.36
60 61 8.197439 CGCATGTATATGTAGGATCATTTCCTA 58.803 37.037 1.14 0.00 43.60 2.94
68 69 2.587522 GGATCATTTCCTACCTTGCCC 58.412 52.381 0.00 0.00 41.78 5.36
69 70 2.587522 GATCATTTCCTACCTTGCCCC 58.412 52.381 0.00 0.00 0.00 5.80
70 71 0.254747 TCATTTCCTACCTTGCCCCG 59.745 55.000 0.00 0.00 0.00 5.73
73 74 4.733725 TCCTACCTTGCCCCGCCT 62.734 66.667 0.00 0.00 0.00 5.52
74 75 4.176752 CCTACCTTGCCCCGCCTC 62.177 72.222 0.00 0.00 0.00 4.70
75 76 4.176752 CTACCTTGCCCCGCCTCC 62.177 72.222 0.00 0.00 0.00 4.30
77 78 3.320411 TACCTTGCCCCGCCTCCTA 62.320 63.158 0.00 0.00 0.00 2.94
78 79 3.866582 CCTTGCCCCGCCTCCTAG 61.867 72.222 0.00 0.00 0.00 3.02
79 80 3.083997 CTTGCCCCGCCTCCTAGT 61.084 66.667 0.00 0.00 0.00 2.57
81 82 1.306312 TTGCCCCGCCTCCTAGTTA 60.306 57.895 0.00 0.00 0.00 2.24
82 83 1.619807 TTGCCCCGCCTCCTAGTTAC 61.620 60.000 0.00 0.00 0.00 2.50
83 84 2.804912 GCCCCGCCTCCTAGTTACC 61.805 68.421 0.00 0.00 0.00 2.85
84 85 1.382146 CCCCGCCTCCTAGTTACCA 60.382 63.158 0.00 0.00 0.00 3.25
86 87 0.393077 CCCGCCTCCTAGTTACCATG 59.607 60.000 0.00 0.00 0.00 3.66
90 91 4.084287 CCGCCTCCTAGTTACCATGTATA 58.916 47.826 0.00 0.00 0.00 1.47
91 92 4.158025 CCGCCTCCTAGTTACCATGTATAG 59.842 50.000 0.00 0.00 0.00 1.31
92 93 4.765856 CGCCTCCTAGTTACCATGTATAGT 59.234 45.833 0.00 0.00 0.00 2.12
93 94 5.106237 CGCCTCCTAGTTACCATGTATAGTC 60.106 48.000 0.00 0.00 0.00 2.59
94 95 5.106237 GCCTCCTAGTTACCATGTATAGTCG 60.106 48.000 0.00 0.00 0.00 4.18
95 96 6.236409 CCTCCTAGTTACCATGTATAGTCGA 58.764 44.000 0.00 0.00 0.00 4.20
96 97 6.372103 CCTCCTAGTTACCATGTATAGTCGAG 59.628 46.154 0.00 0.00 0.00 4.04
99 100 3.573110 AGTTACCATGTATAGTCGAGGCC 59.427 47.826 0.00 0.00 0.00 5.19
100 101 0.959553 ACCATGTATAGTCGAGGCCG 59.040 55.000 0.00 0.00 37.07 6.13
101 102 0.959553 CCATGTATAGTCGAGGCCGT 59.040 55.000 0.00 0.00 37.05 5.68
102 103 1.335964 CCATGTATAGTCGAGGCCGTG 60.336 57.143 0.00 0.00 37.05 4.94
103 104 0.959553 ATGTATAGTCGAGGCCGTGG 59.040 55.000 0.00 0.00 37.05 4.94
104 105 1.105167 TGTATAGTCGAGGCCGTGGG 61.105 60.000 0.00 0.00 37.05 4.61
114 115 3.818787 GCCGTGGGCTGCTCATTG 61.819 66.667 5.08 1.07 46.69 2.82
115 116 2.360350 CCGTGGGCTGCTCATTGT 60.360 61.111 5.08 0.00 0.00 2.71
118 119 1.164411 CGTGGGCTGCTCATTGTAAA 58.836 50.000 5.08 0.00 0.00 2.01
120 121 2.942376 CGTGGGCTGCTCATTGTAAATA 59.058 45.455 5.08 0.00 0.00 1.40
122 123 4.754618 CGTGGGCTGCTCATTGTAAATATA 59.245 41.667 5.08 0.00 0.00 0.86
124 125 6.593770 CGTGGGCTGCTCATTGTAAATATATA 59.406 38.462 5.08 0.00 0.00 0.86
125 126 7.413000 CGTGGGCTGCTCATTGTAAATATATAC 60.413 40.741 5.08 0.00 0.00 1.47
126 127 6.593770 TGGGCTGCTCATTGTAAATATATACG 59.406 38.462 0.00 0.00 0.00 3.06
127 128 6.594159 GGGCTGCTCATTGTAAATATATACGT 59.406 38.462 0.00 0.00 0.00 3.57
128 129 7.413000 GGGCTGCTCATTGTAAATATATACGTG 60.413 40.741 0.00 0.00 0.00 4.49
130 131 7.044589 TGCTCATTGTAAATATATACGTGCG 57.955 36.000 0.00 0.00 0.00 5.34
132 133 6.948228 GCTCATTGTAAATATATACGTGCGTG 59.052 38.462 7.55 0.00 0.00 5.34
134 135 9.120422 CTCATTGTAAATATATACGTGCGTGTA 57.880 33.333 7.55 5.58 0.00 2.90
135 136 9.628746 TCATTGTAAATATATACGTGCGTGTAT 57.371 29.630 15.86 15.86 38.54 2.29
136 137 9.670180 CATTGTAAATATATACGTGCGTGTATG 57.330 33.333 19.27 3.49 35.85 2.39
137 138 7.268186 TGTAAATATATACGTGCGTGTATGC 57.732 36.000 19.27 3.63 35.85 3.14
138 139 6.862090 TGTAAATATATACGTGCGTGTATGCA 59.138 34.615 19.27 0.00 43.95 3.96
144 145 4.732568 TGCGTGTATGCACCCAAT 57.267 50.000 8.45 0.00 42.39 3.16
145 146 2.476772 TGCGTGTATGCACCCAATC 58.523 52.632 8.45 0.00 42.39 2.67
146 147 0.322008 TGCGTGTATGCACCCAATCA 60.322 50.000 8.45 0.00 42.39 2.57
147 148 0.808125 GCGTGTATGCACCCAATCAA 59.192 50.000 8.45 0.00 42.39 2.57
149 150 2.159254 GCGTGTATGCACCCAATCAATT 60.159 45.455 8.45 0.00 42.39 2.32
150 151 3.437428 CGTGTATGCACCCAATCAATTG 58.563 45.455 8.45 0.00 42.39 2.32
152 153 4.675510 GTGTATGCACCCAATCAATTGAG 58.324 43.478 14.54 2.58 38.54 3.02
153 154 4.398988 GTGTATGCACCCAATCAATTGAGA 59.601 41.667 14.54 0.00 38.54 3.27
154 155 4.641541 TGTATGCACCCAATCAATTGAGAG 59.358 41.667 14.54 8.46 40.14 3.20
155 156 3.159213 TGCACCCAATCAATTGAGAGT 57.841 42.857 14.54 5.56 40.14 3.24
156 157 3.499338 TGCACCCAATCAATTGAGAGTT 58.501 40.909 14.54 0.40 40.14 3.01
157 158 3.256383 TGCACCCAATCAATTGAGAGTTG 59.744 43.478 14.54 12.87 40.14 3.16
158 159 3.841643 CACCCAATCAATTGAGAGTTGC 58.158 45.455 14.54 0.00 40.14 4.17
160 161 4.081862 CACCCAATCAATTGAGAGTTGCAT 60.082 41.667 14.54 2.25 40.14 3.96
161 162 4.529377 ACCCAATCAATTGAGAGTTGCATT 59.471 37.500 14.54 0.00 40.14 3.56
162 163 4.868171 CCCAATCAATTGAGAGTTGCATTG 59.132 41.667 14.54 10.17 40.14 2.82
163 164 4.328983 CCAATCAATTGAGAGTTGCATTGC 59.671 41.667 14.54 0.46 40.14 3.56
164 165 3.581024 TCAATTGAGAGTTGCATTGCC 57.419 42.857 3.38 0.00 0.00 4.52
166 167 3.321396 TCAATTGAGAGTTGCATTGCCAA 59.679 39.130 3.38 2.29 0.00 4.52
168 169 2.798976 TGAGAGTTGCATTGCCAAAC 57.201 45.000 6.12 5.00 0.00 2.93
169 170 2.030371 TGAGAGTTGCATTGCCAAACA 58.970 42.857 6.12 0.00 0.00 2.83
316 329 2.613026 TGCAATCCATGGGTACGTAG 57.387 50.000 13.02 0.00 0.00 3.51
317 330 1.226746 GCAATCCATGGGTACGTAGC 58.773 55.000 16.33 16.33 0.00 3.58
379 396 2.232208 CTGGAGGCTGTTGGGATTTTTC 59.768 50.000 0.00 0.00 0.00 2.29
405 424 8.025243 TCTGAACCAAATACAGTAACGAAATC 57.975 34.615 0.00 0.00 33.93 2.17
588 624 5.294799 CGAGTGCTGACTACTTACTGAGTAT 59.705 44.000 0.00 0.00 40.01 2.12
676 1670 1.971357 ACGCCAGCCTAGCAATAGTAT 59.029 47.619 0.00 0.00 0.00 2.12
678 1672 2.738846 CGCCAGCCTAGCAATAGTATTG 59.261 50.000 17.09 17.09 0.00 1.90
776 1850 7.794683 TCTGACAGTTAATATCCTAATTCCCCT 59.205 37.037 1.59 0.00 0.00 4.79
777 1851 9.101325 CTGACAGTTAATATCCTAATTCCCCTA 57.899 37.037 0.00 0.00 0.00 3.53
778 1852 9.455144 TGACAGTTAATATCCTAATTCCCCTAA 57.545 33.333 0.00 0.00 0.00 2.69
992 2127 2.029470 GCTTACCATCTCTCTCCATCCG 60.029 54.545 0.00 0.00 0.00 4.18
1119 2266 5.549347 GACAAGGATGCTCATGTCATCTAT 58.451 41.667 21.20 12.80 41.35 1.98
1278 2425 1.003839 GGACACGGATGCCAAGACA 60.004 57.895 0.00 0.00 0.00 3.41
1371 2518 2.104253 CAACGGCCGGAATTACGCT 61.104 57.895 31.76 0.57 0.00 5.07
1588 2735 1.659098 GTCGGATCAAACTTGTAGCGG 59.341 52.381 0.00 0.00 0.00 5.52
1602 2751 5.010415 ACTTGTAGCGGTTACTACTTGAACT 59.990 40.000 0.00 0.00 42.53 3.01
1688 2837 7.095271 GCCTAATAGAGTTCTCAATGCATCTTC 60.095 40.741 0.00 0.00 0.00 2.87
1695 2870 2.028876 CTCAATGCATCTTCATGGGCA 58.971 47.619 0.00 0.00 41.00 5.36
1706 2881 6.316890 GCATCTTCATGGGCACATTAAATTTT 59.683 34.615 0.00 0.00 34.35 1.82
1761 3051 4.851558 GCTTGTAACGTAGCCAAAGAATTG 59.148 41.667 0.00 0.00 36.25 2.32
1773 3063 6.122964 AGCCAAAGAATTGTCTTATACCCTC 58.877 40.000 0.00 0.00 43.59 4.30
1779 3069 8.970859 AAGAATTGTCTTATACCCTCTCAATG 57.029 34.615 0.00 0.00 42.53 2.82
1785 3075 6.382859 TGTCTTATACCCTCTCAATGTGCTAA 59.617 38.462 0.00 0.00 0.00 3.09
1828 3346 6.537301 CGTAGCCAAAGAATTGTCTTATACCA 59.463 38.462 0.00 0.00 43.59 3.25
1965 3682 9.497030 TGTGCTATATTTATTTTGCTTGTAACG 57.503 29.630 0.00 0.00 0.00 3.18
1966 3683 9.498307 GTGCTATATTTATTTTGCTTGTAACGT 57.502 29.630 0.00 0.00 0.00 3.99
1987 3704 7.605410 ACGTAGTTTGTATACCCTTTCAATG 57.395 36.000 0.00 0.00 37.78 2.82
1988 3705 7.163441 ACGTAGTTTGTATACCCTTTCAATGT 58.837 34.615 0.00 0.00 37.78 2.71
1989 3706 7.118680 ACGTAGTTTGTATACCCTTTCAATGTG 59.881 37.037 0.00 0.00 37.78 3.21
1990 3707 6.267496 AGTTTGTATACCCTTTCAATGTGC 57.733 37.500 0.00 0.00 0.00 4.57
1991 3708 6.010219 AGTTTGTATACCCTTTCAATGTGCT 58.990 36.000 0.00 0.00 0.00 4.40
1992 3709 7.172342 AGTTTGTATACCCTTTCAATGTGCTA 58.828 34.615 0.00 0.00 0.00 3.49
1993 3710 7.834181 AGTTTGTATACCCTTTCAATGTGCTAT 59.166 33.333 0.00 0.00 0.00 2.97
1994 3711 9.116067 GTTTGTATACCCTTTCAATGTGCTATA 57.884 33.333 0.00 0.00 0.00 1.31
1995 3712 9.860650 TTTGTATACCCTTTCAATGTGCTATAT 57.139 29.630 0.00 0.00 0.00 0.86
2097 3814 4.001618 AGAGTTGAGCAAAGAAGAGGTC 57.998 45.455 0.00 0.00 0.00 3.85
2117 3835 2.841266 TCAACCCAATAAGACCGATCCA 59.159 45.455 0.00 0.00 0.00 3.41
2118 3836 3.264706 TCAACCCAATAAGACCGATCCAA 59.735 43.478 0.00 0.00 0.00 3.53
2306 4038 2.688446 TGCACATGGACGTAACCAAAAA 59.312 40.909 0.00 0.00 43.47 1.94
2524 4817 1.153823 CGGGTCAAGAACGATCGCT 60.154 57.895 16.60 1.61 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.372369 GCCTATACAGAATATATTCAACACCTC 57.628 37.037 24.00 6.38 39.23 3.85
1 2 8.880244 TGCCTATACAGAATATATTCAACACCT 58.120 33.333 24.00 8.68 39.23 4.00
3 4 9.712305 ACTGCCTATACAGAATATATTCAACAC 57.288 33.333 24.00 8.23 40.25 3.32
11 12 9.569122 TGCGATATACTGCCTATACAGAATATA 57.431 33.333 0.00 0.00 40.25 0.86
13 14 7.875327 TGCGATATACTGCCTATACAGAATA 57.125 36.000 0.00 0.00 40.25 1.75
14 15 6.775594 TGCGATATACTGCCTATACAGAAT 57.224 37.500 0.00 0.00 40.25 2.40
16 17 5.652452 ACATGCGATATACTGCCTATACAGA 59.348 40.000 0.00 0.00 40.25 3.41
17 18 5.895928 ACATGCGATATACTGCCTATACAG 58.104 41.667 0.00 0.00 43.59 2.74
18 19 5.914898 ACATGCGATATACTGCCTATACA 57.085 39.130 0.00 0.00 0.00 2.29
19 20 9.561270 CATATACATGCGATATACTGCCTATAC 57.439 37.037 0.00 0.00 0.00 1.47
24 25 6.863645 CCTACATATACATGCGATATACTGCC 59.136 42.308 0.00 0.00 35.39 4.85
25 26 7.649057 TCCTACATATACATGCGATATACTGC 58.351 38.462 0.00 0.00 35.39 4.40
27 28 9.574516 TGATCCTACATATACATGCGATATACT 57.425 33.333 0.00 0.00 35.39 2.12
31 32 9.750125 GAAATGATCCTACATATACATGCGATA 57.250 33.333 0.00 0.00 35.39 2.92
34 35 7.239166 GGAAATGATCCTACATATACATGCG 57.761 40.000 0.00 0.00 45.56 4.73
49 50 2.587522 GGGGCAAGGTAGGAAATGATC 58.412 52.381 0.00 0.00 0.00 2.92
50 51 1.133792 CGGGGCAAGGTAGGAAATGAT 60.134 52.381 0.00 0.00 0.00 2.45
51 52 0.254747 CGGGGCAAGGTAGGAAATGA 59.745 55.000 0.00 0.00 0.00 2.57
52 53 1.384222 GCGGGGCAAGGTAGGAAATG 61.384 60.000 0.00 0.00 0.00 2.32
53 54 1.076995 GCGGGGCAAGGTAGGAAAT 60.077 57.895 0.00 0.00 0.00 2.17
54 55 2.353573 GCGGGGCAAGGTAGGAAA 59.646 61.111 0.00 0.00 0.00 3.13
56 57 4.733725 AGGCGGGGCAAGGTAGGA 62.734 66.667 0.00 0.00 0.00 2.94
57 58 4.176752 GAGGCGGGGCAAGGTAGG 62.177 72.222 0.00 0.00 0.00 3.18
58 59 4.176752 GGAGGCGGGGCAAGGTAG 62.177 72.222 0.00 0.00 0.00 3.18
59 60 3.320411 TAGGAGGCGGGGCAAGGTA 62.320 63.158 0.00 0.00 0.00 3.08
60 61 4.733725 TAGGAGGCGGGGCAAGGT 62.734 66.667 0.00 0.00 0.00 3.50
61 62 3.866582 CTAGGAGGCGGGGCAAGG 61.867 72.222 0.00 0.00 0.00 3.61
62 63 1.335132 TAACTAGGAGGCGGGGCAAG 61.335 60.000 0.00 0.00 0.00 4.01
64 65 2.062177 GTAACTAGGAGGCGGGGCA 61.062 63.158 0.00 0.00 0.00 5.36
65 66 2.804912 GGTAACTAGGAGGCGGGGC 61.805 68.421 0.00 0.00 0.00 5.80
66 67 0.763223 ATGGTAACTAGGAGGCGGGG 60.763 60.000 0.00 0.00 37.61 5.73
67 68 0.393077 CATGGTAACTAGGAGGCGGG 59.607 60.000 0.00 0.00 37.61 6.13
68 69 1.120530 ACATGGTAACTAGGAGGCGG 58.879 55.000 0.00 0.00 37.61 6.13
69 70 4.765856 ACTATACATGGTAACTAGGAGGCG 59.234 45.833 0.00 0.00 37.61 5.52
70 71 5.106237 CGACTATACATGGTAACTAGGAGGC 60.106 48.000 0.00 0.00 37.61 4.70
73 74 6.236409 CCTCGACTATACATGGTAACTAGGA 58.764 44.000 0.00 0.00 37.61 2.94
74 75 5.106237 GCCTCGACTATACATGGTAACTAGG 60.106 48.000 0.00 0.00 37.61 3.02
75 76 5.106237 GGCCTCGACTATACATGGTAACTAG 60.106 48.000 0.00 0.00 37.61 2.57
77 78 3.573110 GGCCTCGACTATACATGGTAACT 59.427 47.826 0.00 0.00 37.61 2.24
78 79 3.611057 CGGCCTCGACTATACATGGTAAC 60.611 52.174 0.00 0.00 39.00 2.50
79 80 2.555325 CGGCCTCGACTATACATGGTAA 59.445 50.000 0.00 0.00 39.00 2.85
81 82 0.959553 CGGCCTCGACTATACATGGT 59.040 55.000 0.00 0.00 39.00 3.55
82 83 0.959553 ACGGCCTCGACTATACATGG 59.040 55.000 0.00 0.00 40.11 3.66
83 84 1.335964 CCACGGCCTCGACTATACATG 60.336 57.143 0.00 0.00 40.11 3.21
84 85 0.959553 CCACGGCCTCGACTATACAT 59.040 55.000 0.00 0.00 40.11 2.29
86 87 1.658673 CCCACGGCCTCGACTATAC 59.341 63.158 0.00 0.00 40.11 1.47
99 100 1.164411 TTTACAATGAGCAGCCCACG 58.836 50.000 0.00 0.00 0.00 4.94
100 101 6.824305 ATATATTTACAATGAGCAGCCCAC 57.176 37.500 0.00 0.00 0.00 4.61
101 102 6.593770 CGTATATATTTACAATGAGCAGCCCA 59.406 38.462 4.52 0.00 0.00 5.36
102 103 6.594159 ACGTATATATTTACAATGAGCAGCCC 59.406 38.462 4.52 0.00 0.00 5.19
103 104 7.456253 CACGTATATATTTACAATGAGCAGCC 58.544 38.462 4.52 0.00 0.00 4.85
104 105 6.955963 GCACGTATATATTTACAATGAGCAGC 59.044 38.462 4.52 0.00 0.00 5.25
105 106 7.148804 ACGCACGTATATATTTACAATGAGCAG 60.149 37.037 0.00 0.00 0.00 4.24
106 107 6.643360 ACGCACGTATATATTTACAATGAGCA 59.357 34.615 0.00 0.00 0.00 4.26
107 108 6.948228 CACGCACGTATATATTTACAATGAGC 59.052 38.462 0.00 0.00 0.00 4.26
108 109 8.003508 ACACGCACGTATATATTTACAATGAG 57.996 34.615 0.00 5.78 0.00 2.90
109 110 7.933728 ACACGCACGTATATATTTACAATGA 57.066 32.000 0.00 0.00 0.00 2.57
111 112 8.377681 GCATACACGCACGTATATATTTACAAT 58.622 33.333 0.00 0.00 30.83 2.71
112 113 7.381678 TGCATACACGCACGTATATATTTACAA 59.618 33.333 0.00 0.00 36.86 2.41
113 114 6.862090 TGCATACACGCACGTATATATTTACA 59.138 34.615 0.00 0.00 36.86 2.41
114 115 7.268186 TGCATACACGCACGTATATATTTAC 57.732 36.000 0.00 0.00 36.86 2.01
130 131 4.398988 TCTCAATTGATTGGGTGCATACAC 59.601 41.667 8.96 0.00 39.29 2.90
132 133 4.641989 ACTCTCAATTGATTGGGTGCATAC 59.358 41.667 8.96 0.00 39.29 2.39
134 135 3.705051 ACTCTCAATTGATTGGGTGCAT 58.295 40.909 8.96 0.00 39.29 3.96
135 136 3.159213 ACTCTCAATTGATTGGGTGCA 57.841 42.857 8.96 0.00 39.29 4.57
136 137 3.841643 CAACTCTCAATTGATTGGGTGC 58.158 45.455 8.96 0.00 39.29 5.01
137 138 3.256383 TGCAACTCTCAATTGATTGGGTG 59.744 43.478 17.64 15.24 39.29 4.61
138 139 3.499338 TGCAACTCTCAATTGATTGGGT 58.501 40.909 17.64 8.08 39.29 4.51
139 140 4.730949 ATGCAACTCTCAATTGATTGGG 57.269 40.909 17.64 7.51 39.62 4.12
140 141 4.328983 GCAATGCAACTCTCAATTGATTGG 59.671 41.667 17.64 10.26 38.30 3.16
142 143 4.020928 TGGCAATGCAACTCTCAATTGATT 60.021 37.500 8.96 0.00 0.00 2.57
144 145 2.892215 TGGCAATGCAACTCTCAATTGA 59.108 40.909 7.79 8.12 0.00 2.57
145 146 3.306917 TGGCAATGCAACTCTCAATTG 57.693 42.857 7.79 0.00 0.00 2.32
146 147 4.060205 GTTTGGCAATGCAACTCTCAATT 58.940 39.130 7.79 0.00 0.00 2.32
147 148 3.069872 TGTTTGGCAATGCAACTCTCAAT 59.930 39.130 7.79 0.00 0.00 2.57
149 150 2.030371 TGTTTGGCAATGCAACTCTCA 58.970 42.857 7.79 0.00 0.00 3.27
150 151 2.798976 TGTTTGGCAATGCAACTCTC 57.201 45.000 7.79 0.00 0.00 3.20
152 153 4.559153 ACTATTGTTTGGCAATGCAACTC 58.441 39.130 16.35 0.00 46.40 3.01
153 154 4.605640 ACTATTGTTTGGCAATGCAACT 57.394 36.364 16.35 10.38 46.40 3.16
154 155 4.749099 TGAACTATTGTTTGGCAATGCAAC 59.251 37.500 16.35 4.43 46.40 4.17
155 156 4.953667 TGAACTATTGTTTGGCAATGCAA 58.046 34.783 16.35 16.35 46.40 4.08
156 157 4.597404 TGAACTATTGTTTGGCAATGCA 57.403 36.364 7.79 0.33 46.40 3.96
157 158 6.484818 AAATGAACTATTGTTTGGCAATGC 57.515 33.333 0.00 0.00 46.40 3.56
158 159 7.331440 TGCTAAATGAACTATTGTTTGGCAATG 59.669 33.333 0.00 0.00 46.40 2.82
160 161 6.644592 GTGCTAAATGAACTATTGTTTGGCAA 59.355 34.615 8.84 0.00 45.24 4.52
161 162 6.155827 GTGCTAAATGAACTATTGTTTGGCA 58.844 36.000 4.06 4.06 42.88 4.92
162 163 5.286082 CGTGCTAAATGAACTATTGTTTGGC 59.714 40.000 0.00 0.00 38.17 4.52
163 164 5.286082 GCGTGCTAAATGAACTATTGTTTGG 59.714 40.000 0.00 0.00 36.39 3.28
164 165 5.286082 GGCGTGCTAAATGAACTATTGTTTG 59.714 40.000 0.00 0.00 36.39 2.93
166 167 4.436852 CGGCGTGCTAAATGAACTATTGTT 60.437 41.667 0.00 0.00 39.42 2.83
168 169 3.546020 CCGGCGTGCTAAATGAACTATTG 60.546 47.826 6.01 0.00 0.00 1.90
169 170 2.612212 CCGGCGTGCTAAATGAACTATT 59.388 45.455 6.01 0.00 0.00 1.73
171 172 1.647346 CCGGCGTGCTAAATGAACTA 58.353 50.000 6.01 0.00 0.00 2.24
172 173 1.644786 GCCGGCGTGCTAAATGAACT 61.645 55.000 12.58 0.00 0.00 3.01
379 396 7.416154 TTTCGTTACTGTATTTGGTTCAGAG 57.584 36.000 0.00 0.00 33.93 3.35
538 557 2.438434 GGAGTTGGGTCATGGCCG 60.438 66.667 10.95 0.00 0.00 6.13
588 624 3.711704 AGGGCTTCCTCGAATAGATTTCA 59.288 43.478 0.00 0.00 35.60 2.69
676 1670 7.151308 ACCAAATTAATTTCATCGTCTTGCAA 58.849 30.769 10.53 0.00 0.00 4.08
678 1672 6.253512 GGACCAAATTAATTTCATCGTCTTGC 59.746 38.462 10.53 0.35 0.00 4.01
862 1990 2.231478 TGAGCACAGCTAGTTACAGGTC 59.769 50.000 0.00 0.00 39.88 3.85
992 2127 0.034059 CGGTGGCCTCATGGATCTAC 59.966 60.000 3.32 0.00 34.57 2.59
1119 2266 2.734606 CAACTCCGACACGCAGAAATTA 59.265 45.455 0.00 0.00 0.00 1.40
1259 2406 1.003839 GTCTTGGCATCCGTGTCCA 60.004 57.895 0.00 0.00 32.23 4.02
1371 2518 0.325671 CTGCCTCCTCCTTCCCTGTA 60.326 60.000 0.00 0.00 0.00 2.74
1416 2563 0.673333 TCACAAAGGCATCGTCGCAT 60.673 50.000 1.52 0.00 0.00 4.73
1497 2644 1.555075 AGGTTAGTGATGGTCGTGCAT 59.445 47.619 0.00 0.00 0.00 3.96
1504 2651 6.620877 TCACTTGATAAGGTTAGTGATGGT 57.379 37.500 0.00 0.00 41.34 3.55
1565 2712 3.335579 GCTACAAGTTTGATCCGACCTT 58.664 45.455 0.00 0.00 0.00 3.50
1602 2751 6.909550 ATTCCTTGCATGTACCTTACAAAA 57.090 33.333 0.00 0.00 42.76 2.44
1688 2837 5.821516 ATGCAAAATTTAATGTGCCCATG 57.178 34.783 9.48 0.00 36.12 3.66
1695 2870 9.737844 ATTGAAAGGGTATGCAAAATTTAATGT 57.262 25.926 0.00 0.00 0.00 2.71
1706 2881 2.806434 AGCACATTGAAAGGGTATGCA 58.194 42.857 0.00 0.00 34.03 3.96
1761 3051 5.283457 AGCACATTGAGAGGGTATAAGAC 57.717 43.478 0.00 0.00 0.00 3.01
1773 3063 9.749490 CAAGCAAAATAAATTTAGCACATTGAG 57.251 29.630 3.94 0.00 31.57 3.02
1779 3069 8.696175 ACGTTACAAGCAAAATAAATTTAGCAC 58.304 29.630 3.94 0.00 31.57 4.40
1785 3075 7.371936 TGGCTACGTTACAAGCAAAATAAATT 58.628 30.769 10.05 0.00 40.61 1.82
1965 3682 7.120726 AGCACATTGAAAGGGTATACAAACTAC 59.879 37.037 5.01 0.00 0.00 2.73
1966 3683 7.172342 AGCACATTGAAAGGGTATACAAACTA 58.828 34.615 5.01 0.00 0.00 2.24
1967 3684 6.010219 AGCACATTGAAAGGGTATACAAACT 58.990 36.000 5.01 0.00 0.00 2.66
1968 3685 6.267496 AGCACATTGAAAGGGTATACAAAC 57.733 37.500 5.01 0.00 0.00 2.93
1969 3686 9.860650 ATATAGCACATTGAAAGGGTATACAAA 57.139 29.630 5.01 0.00 31.41 2.83
1994 3711 8.679100 TGGCTACGTTACAAGCAAAATAAATAT 58.321 29.630 10.05 0.00 40.61 1.28
1995 3712 8.041829 TGGCTACGTTACAAGCAAAATAAATA 57.958 30.769 10.05 0.00 40.61 1.40
1996 3713 6.915349 TGGCTACGTTACAAGCAAAATAAAT 58.085 32.000 10.05 0.00 40.61 1.40
1997 3714 6.315091 TGGCTACGTTACAAGCAAAATAAA 57.685 33.333 10.05 0.00 40.61 1.40
1998 3715 5.943706 TGGCTACGTTACAAGCAAAATAA 57.056 34.783 10.05 0.00 40.61 1.40
1999 3716 5.943706 TTGGCTACGTTACAAGCAAAATA 57.056 34.783 10.05 0.00 40.61 1.40
2000 3717 4.839668 TTGGCTACGTTACAAGCAAAAT 57.160 36.364 10.05 0.00 40.61 1.82
2001 3718 4.335874 TCTTTGGCTACGTTACAAGCAAAA 59.664 37.500 9.63 9.63 38.91 2.44
2002 3719 3.878103 TCTTTGGCTACGTTACAAGCAAA 59.122 39.130 10.05 2.20 40.61 3.68
2003 3720 3.468770 TCTTTGGCTACGTTACAAGCAA 58.531 40.909 10.05 0.00 40.61 3.91
2004 3721 3.114668 TCTTTGGCTACGTTACAAGCA 57.885 42.857 10.05 0.00 40.61 3.91
2005 3722 4.680171 ATTCTTTGGCTACGTTACAAGC 57.320 40.909 0.00 0.00 38.03 4.01
2006 3723 5.997385 ACAATTCTTTGGCTACGTTACAAG 58.003 37.500 0.00 0.00 37.15 3.16
2007 3724 5.992729 GACAATTCTTTGGCTACGTTACAA 58.007 37.500 0.00 0.00 37.91 2.41
2008 3725 5.600908 GACAATTCTTTGGCTACGTTACA 57.399 39.130 0.00 0.00 37.91 2.41
2097 3814 3.275617 TGGATCGGTCTTATTGGGTTG 57.724 47.619 0.00 0.00 0.00 3.77
2128 3849 4.833478 AGTGCCATTATGTTGAGAGAGT 57.167 40.909 0.00 0.00 0.00 3.24
2306 4038 9.407380 TGTGATGACTAGCACCATAAAAATATT 57.593 29.630 0.00 0.00 42.40 1.28


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

AutoCloner maintained by Alex Coulton.