Multiple sequence alignment - TraesCS6B01G015900

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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 TraesCS6B01G015900 chr6B 100.000 3073 0 0 1 3073 9476940 9480012 0.000000e+00 5675.0
1 TraesCS6B01G015900 chr6B 96.093 1331 27 4 838 2166 11112024 11110717 0.000000e+00 2146.0
2 TraesCS6B01G015900 chr6B 96.529 893 17 6 2181 3073 11110667 11109789 0.000000e+00 1465.0
3 TraesCS6B01G015900 chr6B 90.018 571 36 4 347 899 11141591 11141024 0.000000e+00 719.0
4 TraesCS6B01G015900 chr6B 89.624 559 45 8 347 899 11119041 11118490 0.000000e+00 699.0
5 TraesCS6B01G015900 chr6B 88.946 389 39 4 2449 2835 554815921 554816307 7.710000e-131 477.0
6 TraesCS6B01G015900 chr6B 89.433 388 20 4 479 847 11116616 11116231 1.290000e-128 470.0
7 TraesCS6B01G015900 chr6B 92.647 68 2 3 1 68 11119099 11119035 9.070000e-16 95.3
8 TraesCS6B01G015900 chr6B 92.647 68 2 3 1 68 11141649 11141585 9.070000e-16 95.3
9 TraesCS6B01G015900 chr6B 96.429 56 2 0 1 56 11116740 11116685 3.260000e-15 93.5
10 TraesCS6B01G015900 chr7D 85.736 673 89 4 1433 2099 629599290 629598619 0.000000e+00 704.0
11 TraesCS6B01G015900 chr7D 90.104 384 37 1 2453 2835 262115226 262115609 5.920000e-137 497.0
12 TraesCS6B01G015900 chr7A 82.345 776 114 13 1184 1948 725613964 725613201 0.000000e+00 652.0
13 TraesCS6B01G015900 chr7A 89.062 384 40 2 2453 2835 76262945 76263327 2.770000e-130 475.0
14 TraesCS6B01G015900 chr7A 94.558 294 14 2 60 351 104653365 104653658 1.300000e-123 453.0
15 TraesCS6B01G015900 chr7A 87.324 142 16 2 1941 2080 725612518 725612377 8.820000e-36 161.0
16 TraesCS6B01G015900 chr3B 83.529 680 97 7 1367 2043 505287806 505287139 3.370000e-174 621.0
17 TraesCS6B01G015900 chr3D 82.941 680 101 7 1367 2043 388450605 388449938 1.580000e-167 599.0
18 TraesCS6B01G015900 chr3D 94.257 296 14 3 59 353 151791647 151791940 1.680000e-122 449.0
19 TraesCS6B01G015900 chr3A 82.941 680 101 7 1367 2043 509548869 509548202 1.580000e-167 599.0
20 TraesCS6B01G015900 chr3A 93.939 297 16 2 59 353 365236065 365235769 6.040000e-122 448.0
21 TraesCS6B01G015900 chr6D 90.104 384 37 1 2453 2835 278678136 278678519 5.920000e-137 497.0
22 TraesCS6B01G015900 chr5D 90.026 381 37 1 2456 2835 542432343 542431963 2.750000e-135 492.0
23 TraesCS6B01G015900 chr1D 90.026 381 37 1 2456 2835 4773246 4772866 2.750000e-135 492.0
24 TraesCS6B01G015900 chr5B 97.849 279 5 1 76 353 237079943 237080221 5.960000e-132 481.0
25 TraesCS6B01G015900 chr5B 94.218 294 15 2 59 351 616030338 616030630 6.040000e-122 448.0
26 TraesCS6B01G015900 chr4A 88.802 384 42 1 2453 2835 686512206 686512589 1.290000e-128 470.0
27 TraesCS6B01G015900 chr4A 94.218 294 15 2 59 351 620356770 620356478 6.040000e-122 448.0
28 TraesCS6B01G015900 chr4A 94.198 293 15 2 59 351 609445225 609444935 2.170000e-121 446.0
29 TraesCS6B01G015900 chr2B 88.976 381 41 1 2456 2835 22999833 22999453 1.290000e-128 470.0
30 TraesCS6B01G015900 chr1B 94.218 294 16 1 59 351 19078727 19078434 6.040000e-122 448.0
31 TraesCS6B01G015900 chr1B 94.237 295 14 3 59 351 670857934 670858227 6.040000e-122 448.0


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 TraesCS6B01G015900 chr6B 9476940 9480012 3072 False 5675.00 5675 100.00000 1 3073 1 chr6B.!!$F1 3072
1 TraesCS6B01G015900 chr6B 11109789 11112024 2235 True 1805.50 2146 96.31100 838 3073 2 chr6B.!!$R1 2235
2 TraesCS6B01G015900 chr6B 11141024 11141649 625 True 407.15 719 91.33250 1 899 2 chr6B.!!$R3 898
3 TraesCS6B01G015900 chr6B 11116231 11119099 2868 True 339.45 699 92.03325 1 899 4 chr6B.!!$R2 898
4 TraesCS6B01G015900 chr7D 629598619 629599290 671 True 704.00 704 85.73600 1433 2099 1 chr7D.!!$R1 666
5 TraesCS6B01G015900 chr7A 725612377 725613964 1587 True 406.50 652 84.83450 1184 2080 2 chr7A.!!$R1 896
6 TraesCS6B01G015900 chr3B 505287139 505287806 667 True 621.00 621 83.52900 1367 2043 1 chr3B.!!$R1 676
7 TraesCS6B01G015900 chr3D 388449938 388450605 667 True 599.00 599 82.94100 1367 2043 1 chr3D.!!$R1 676
8 TraesCS6B01G015900 chr3A 509548202 509548869 667 True 599.00 599 82.94100 1367 2043 1 chr3A.!!$R2 676

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
171 172 0.601558 AACCGAGAGTATGCACGTGT 59.398 50.0 18.38 0.0 0.00 4.49 F
1530 2171 0.247736 CCCGTTCTCCTCTGACAAGG 59.752 60.0 0.00 0.0 37.81 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 2179 0.106967 GGGAGAAGTGGCCAAGGATC 60.107 60.000 7.24 3.57 0.0 3.36 R
2914 4902 1.535028 TGTTAGCGATGCCACTGTTTG 59.465 47.619 0.00 0.00 0.0 2.93 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 9.749996 AAATATCACCTCCCCTCATATATATGT 57.250 33.333 19.78 1.91 35.26 2.29
69 70 9.830186 ATATCACCTCCCCTCATATATATGTAC 57.170 37.037 19.78 0.00 35.26 2.90
70 71 7.051696 TCACCTCCCCTCATATATATGTACA 57.948 40.000 19.78 0.00 35.26 2.90
71 72 7.483881 TCACCTCCCCTCATATATATGTACAA 58.516 38.462 19.78 2.75 35.26 2.41
72 73 7.959152 TCACCTCCCCTCATATATATGTACAAA 59.041 37.037 19.78 2.41 35.26 2.83
73 74 8.602424 CACCTCCCCTCATATATATGTACAAAA 58.398 37.037 19.78 1.77 35.26 2.44
74 75 9.177927 ACCTCCCCTCATATATATGTACAAAAA 57.822 33.333 19.78 1.13 35.26 1.94
98 99 9.927668 AAAATATGGACAAATGTTTCCTACAAG 57.072 29.630 0.00 0.00 40.89 3.16
99 100 4.846779 TGGACAAATGTTTCCTACAAGC 57.153 40.909 0.00 0.00 40.89 4.01
100 101 4.211125 TGGACAAATGTTTCCTACAAGCA 58.789 39.130 0.00 0.00 40.89 3.91
101 102 4.278170 TGGACAAATGTTTCCTACAAGCAG 59.722 41.667 0.00 0.00 40.89 4.24
102 103 4.278419 GGACAAATGTTTCCTACAAGCAGT 59.722 41.667 0.00 0.00 40.89 4.40
103 104 5.186996 ACAAATGTTTCCTACAAGCAGTG 57.813 39.130 0.00 0.00 40.89 3.66
104 105 4.037923 ACAAATGTTTCCTACAAGCAGTGG 59.962 41.667 0.00 0.00 40.89 4.00
105 106 3.508845 ATGTTTCCTACAAGCAGTGGT 57.491 42.857 0.00 0.00 40.89 4.16
106 107 4.634012 ATGTTTCCTACAAGCAGTGGTA 57.366 40.909 0.00 0.00 40.89 3.25
107 108 4.002906 TGTTTCCTACAAGCAGTGGTAG 57.997 45.455 0.00 0.00 37.36 3.18
108 109 3.389983 TGTTTCCTACAAGCAGTGGTAGT 59.610 43.478 0.00 0.00 36.17 2.73
109 110 4.141574 TGTTTCCTACAAGCAGTGGTAGTT 60.142 41.667 0.00 0.00 36.17 2.24
110 111 5.070714 TGTTTCCTACAAGCAGTGGTAGTTA 59.929 40.000 0.00 0.00 36.17 2.24
111 112 4.796038 TCCTACAAGCAGTGGTAGTTAC 57.204 45.455 0.00 0.00 36.17 2.50
112 113 4.413760 TCCTACAAGCAGTGGTAGTTACT 58.586 43.478 0.00 0.00 36.17 2.24
113 114 5.573219 TCCTACAAGCAGTGGTAGTTACTA 58.427 41.667 0.00 0.00 36.17 1.82
114 115 5.416952 TCCTACAAGCAGTGGTAGTTACTAC 59.583 44.000 13.66 13.66 36.17 2.73
126 127 5.912360 GTAGTTACTACCACTTGCGTTTT 57.088 39.130 11.19 0.00 31.38 2.43
127 128 4.806342 AGTTACTACCACTTGCGTTTTG 57.194 40.909 0.00 0.00 0.00 2.44
128 129 4.193865 AGTTACTACCACTTGCGTTTTGT 58.806 39.130 0.00 0.00 0.00 2.83
129 130 5.358922 AGTTACTACCACTTGCGTTTTGTA 58.641 37.500 0.00 0.00 0.00 2.41
130 131 5.993441 AGTTACTACCACTTGCGTTTTGTAT 59.007 36.000 0.00 0.00 0.00 2.29
131 132 4.742438 ACTACCACTTGCGTTTTGTATG 57.258 40.909 0.00 0.00 0.00 2.39
132 133 4.131596 ACTACCACTTGCGTTTTGTATGT 58.868 39.130 0.00 0.00 0.00 2.29
133 134 4.577283 ACTACCACTTGCGTTTTGTATGTT 59.423 37.500 0.00 0.00 0.00 2.71
134 135 3.701241 ACCACTTGCGTTTTGTATGTTG 58.299 40.909 0.00 0.00 0.00 3.33
135 136 3.129638 ACCACTTGCGTTTTGTATGTTGT 59.870 39.130 0.00 0.00 0.00 3.32
136 137 4.335874 ACCACTTGCGTTTTGTATGTTGTA 59.664 37.500 0.00 0.00 0.00 2.41
137 138 5.009210 ACCACTTGCGTTTTGTATGTTGTAT 59.991 36.000 0.00 0.00 0.00 2.29
138 139 5.341993 CCACTTGCGTTTTGTATGTTGTATG 59.658 40.000 0.00 0.00 0.00 2.39
139 140 5.912396 CACTTGCGTTTTGTATGTTGTATGT 59.088 36.000 0.00 0.00 0.00 2.29
140 141 7.072647 CACTTGCGTTTTGTATGTTGTATGTA 58.927 34.615 0.00 0.00 0.00 2.29
141 142 7.268235 CACTTGCGTTTTGTATGTTGTATGTAG 59.732 37.037 0.00 0.00 0.00 2.74
142 143 6.788684 TGCGTTTTGTATGTTGTATGTAGT 57.211 33.333 0.00 0.00 0.00 2.73
143 144 7.886405 TGCGTTTTGTATGTTGTATGTAGTA 57.114 32.000 0.00 0.00 0.00 1.82
144 145 8.481974 TGCGTTTTGTATGTTGTATGTAGTAT 57.518 30.769 0.00 0.00 0.00 2.12
145 146 8.597227 TGCGTTTTGTATGTTGTATGTAGTATC 58.403 33.333 0.00 0.00 0.00 2.24
146 147 8.814235 GCGTTTTGTATGTTGTATGTAGTATCT 58.186 33.333 0.00 0.00 0.00 1.98
156 157 9.524106 TGTTGTATGTAGTATCTATTGAAACCG 57.476 33.333 0.00 0.00 0.00 4.44
157 158 9.740239 GTTGTATGTAGTATCTATTGAAACCGA 57.260 33.333 0.00 0.00 0.00 4.69
158 159 9.961265 TTGTATGTAGTATCTATTGAAACCGAG 57.039 33.333 0.00 0.00 0.00 4.63
159 160 9.346005 TGTATGTAGTATCTATTGAAACCGAGA 57.654 33.333 0.00 0.00 0.00 4.04
160 161 9.828852 GTATGTAGTATCTATTGAAACCGAGAG 57.171 37.037 0.00 0.00 0.00 3.20
161 162 7.876936 TGTAGTATCTATTGAAACCGAGAGT 57.123 36.000 0.00 0.00 0.00 3.24
162 163 8.969260 TGTAGTATCTATTGAAACCGAGAGTA 57.031 34.615 0.00 0.00 0.00 2.59
163 164 9.570468 TGTAGTATCTATTGAAACCGAGAGTAT 57.430 33.333 0.00 0.00 0.00 2.12
164 165 9.828852 GTAGTATCTATTGAAACCGAGAGTATG 57.171 37.037 0.00 0.00 0.00 2.39
165 166 7.371936 AGTATCTATTGAAACCGAGAGTATGC 58.628 38.462 0.00 0.00 0.00 3.14
166 167 5.592104 TCTATTGAAACCGAGAGTATGCA 57.408 39.130 0.00 0.00 0.00 3.96
167 168 5.348986 TCTATTGAAACCGAGAGTATGCAC 58.651 41.667 0.00 0.00 0.00 4.57
168 169 1.990799 TGAAACCGAGAGTATGCACG 58.009 50.000 0.00 0.00 0.00 5.34
169 170 1.271379 TGAAACCGAGAGTATGCACGT 59.729 47.619 0.00 0.00 0.00 4.49
170 171 1.654105 GAAACCGAGAGTATGCACGTG 59.346 52.381 12.28 12.28 0.00 4.49
171 172 0.601558 AACCGAGAGTATGCACGTGT 59.398 50.000 18.38 0.00 0.00 4.49
172 173 1.456296 ACCGAGAGTATGCACGTGTA 58.544 50.000 18.38 14.09 0.00 2.90
173 174 1.400846 ACCGAGAGTATGCACGTGTAG 59.599 52.381 18.38 0.35 0.00 2.74
174 175 1.400846 CCGAGAGTATGCACGTGTAGT 59.599 52.381 18.38 5.29 0.00 2.73
175 176 2.610833 CCGAGAGTATGCACGTGTAGTA 59.389 50.000 18.38 5.06 0.00 1.82
176 177 3.250280 CCGAGAGTATGCACGTGTAGTAT 59.750 47.826 18.38 9.34 0.00 2.12
177 178 4.212150 CGAGAGTATGCACGTGTAGTATG 58.788 47.826 18.38 0.00 0.00 2.39
178 179 4.260661 CGAGAGTATGCACGTGTAGTATGT 60.261 45.833 18.38 0.00 0.00 2.29
179 180 5.050567 CGAGAGTATGCACGTGTAGTATGTA 60.051 44.000 18.38 0.00 0.00 2.29
180 181 6.301687 AGAGTATGCACGTGTAGTATGTAG 57.698 41.667 18.38 0.00 0.00 2.74
181 182 5.821470 AGAGTATGCACGTGTAGTATGTAGT 59.179 40.000 18.38 4.36 0.00 2.73
182 183 6.988580 AGAGTATGCACGTGTAGTATGTAGTA 59.011 38.462 18.38 0.00 0.00 1.82
183 184 7.660617 AGAGTATGCACGTGTAGTATGTAGTAT 59.339 37.037 18.38 0.00 0.00 2.12
184 185 8.837788 AGTATGCACGTGTAGTATGTAGTATA 57.162 34.615 18.38 0.00 0.00 1.47
185 186 9.445878 AGTATGCACGTGTAGTATGTAGTATAT 57.554 33.333 18.38 0.00 0.00 0.86
189 190 9.054922 TGCACGTGTAGTATGTAGTATATAACA 57.945 33.333 18.38 0.00 0.00 2.41
190 191 9.882996 GCACGTGTAGTATGTAGTATATAACAA 57.117 33.333 18.38 0.00 0.00 2.83
311 312 6.528537 ACAAAAACTATTGGCTCATATGCA 57.471 33.333 0.00 0.00 34.56 3.96
312 313 6.934056 ACAAAAACTATTGGCTCATATGCAA 58.066 32.000 0.00 0.00 34.56 4.08
313 314 7.558604 ACAAAAACTATTGGCTCATATGCAAT 58.441 30.769 10.61 10.61 34.56 3.56
314 315 8.042515 ACAAAAACTATTGGCTCATATGCAATT 58.957 29.630 10.93 0.00 34.56 2.32
315 316 8.885722 CAAAAACTATTGGCTCATATGCAATTT 58.114 29.630 10.93 1.06 34.04 1.82
316 317 9.452287 AAAAACTATTGGCTCATATGCAATTTT 57.548 25.926 10.93 5.76 34.04 1.82
317 318 9.452287 AAAACTATTGGCTCATATGCAATTTTT 57.548 25.926 10.93 9.89 34.04 1.94
338 339 7.820044 TTTTTCACGTAACTTGCTTTCAAAT 57.180 28.000 0.00 0.00 0.00 2.32
339 340 8.912787 TTTTTCACGTAACTTGCTTTCAAATA 57.087 26.923 0.00 0.00 0.00 1.40
340 341 9.522804 TTTTTCACGTAACTTGCTTTCAAATAT 57.477 25.926 0.00 0.00 0.00 1.28
341 342 8.722342 TTTCACGTAACTTGCTTTCAAATATC 57.278 30.769 0.00 0.00 0.00 1.63
342 343 7.667043 TCACGTAACTTGCTTTCAAATATCT 57.333 32.000 0.00 0.00 0.00 1.98
343 344 8.094798 TCACGTAACTTGCTTTCAAATATCTT 57.905 30.769 0.00 0.00 0.00 2.40
344 345 9.210329 TCACGTAACTTGCTTTCAAATATCTTA 57.790 29.630 0.00 0.00 0.00 2.10
345 346 9.478019 CACGTAACTTGCTTTCAAATATCTTAG 57.522 33.333 0.00 0.00 0.00 2.18
407 408 9.143631 TCATTTGTCTATGAATATGCTATCACG 57.856 33.333 0.00 0.00 31.82 4.35
422 423 7.428282 TGCTATCACGTTGAGAAATACAAAA 57.572 32.000 0.00 0.00 0.00 2.44
432 433 9.345517 CGTTGAGAAATACAAAATCAATCACAT 57.654 29.630 0.00 0.00 32.93 3.21
448 449 8.242085 TCAATCACATTATTTGTTTGCATCAC 57.758 30.769 0.00 0.00 36.00 3.06
507 508 8.232913 AGTTTTCTTTATGTAGTGGCTTGAAA 57.767 30.769 0.00 0.00 0.00 2.69
508 509 8.691797 AGTTTTCTTTATGTAGTGGCTTGAAAA 58.308 29.630 0.00 0.00 0.00 2.29
526 527 7.653311 GCTTGAAAATGAAAGTTGGTTCTACAT 59.347 33.333 0.00 0.00 0.00 2.29
533 534 5.298276 TGAAAGTTGGTTCTACATCCACAAC 59.702 40.000 0.00 0.00 38.67 3.32
553 554 4.503714 ACATTACTCCCACCTTACCATG 57.496 45.455 0.00 0.00 0.00 3.66
570 571 2.323599 CATGGTGGATGGCTCTCTCTA 58.676 52.381 0.00 0.00 0.00 2.43
571 572 1.781786 TGGTGGATGGCTCTCTCTAC 58.218 55.000 0.00 0.00 0.00 2.59
612 613 3.150767 CACCGAAACATAAAACAGGGGA 58.849 45.455 0.00 0.00 0.00 4.81
616 617 5.221362 ACCGAAACATAAAACAGGGGAAAAG 60.221 40.000 0.00 0.00 0.00 2.27
646 647 5.504755 CGAAACATCACGAAGCAAGATTAAC 59.495 40.000 0.00 0.00 0.00 2.01
659 660 7.073342 AGCAAGATTAACTTTGATAACGACC 57.927 36.000 0.00 0.00 36.61 4.79
662 663 7.464358 CAAGATTAACTTTGATAACGACCCAG 58.536 38.462 0.00 0.00 36.61 4.45
806 829 1.906574 ACCCTTACATCATGGTGTCGT 59.093 47.619 16.57 5.09 33.62 4.34
815 838 6.596309 ACATCATGGTGTCGTATATGAGAT 57.404 37.500 5.56 0.00 33.53 2.75
827 850 1.768684 TATGAGATTCCCAGCCCCGC 61.769 60.000 0.00 0.00 0.00 6.13
866 889 1.274416 ACTTCCCCTGCTCCCTTGATA 60.274 52.381 0.00 0.00 0.00 2.15
885 908 1.617947 ATTGACCAGCTCCCTCCGTC 61.618 60.000 0.00 0.00 0.00 4.79
888 911 2.765807 CCAGCTCCCTCCGTCCAT 60.766 66.667 0.00 0.00 0.00 3.41
915 938 4.231273 TGATCTGGGGCTAGCTGTATAAA 58.769 43.478 15.72 0.00 0.00 1.40
975 998 4.409574 ACATCAATCATCTCCTCTGCTTCT 59.590 41.667 0.00 0.00 0.00 2.85
1008 1031 1.953559 TGCTCTCAATAATGGGTCGC 58.046 50.000 0.00 0.00 0.00 5.19
1023 1046 3.535962 CGCCTCCTCTCCAGCCTC 61.536 72.222 0.00 0.00 0.00 4.70
1186 1215 0.915364 GGGGCTTCCATTCTGACTCT 59.085 55.000 0.00 0.00 35.00 3.24
1337 1372 4.853924 ATCCCATGTGTTTTTCAGTGTC 57.146 40.909 0.00 0.00 0.00 3.67
1522 2163 2.107141 CGCCATCCCGTTCTCCTC 59.893 66.667 0.00 0.00 0.00 3.71
1523 2164 2.427245 CGCCATCCCGTTCTCCTCT 61.427 63.158 0.00 0.00 0.00 3.69
1524 2165 1.144936 GCCATCCCGTTCTCCTCTG 59.855 63.158 0.00 0.00 0.00 3.35
1525 2166 1.330655 GCCATCCCGTTCTCCTCTGA 61.331 60.000 0.00 0.00 0.00 3.27
1526 2167 0.461961 CCATCCCGTTCTCCTCTGAC 59.538 60.000 0.00 0.00 0.00 3.51
1527 2168 1.186200 CATCCCGTTCTCCTCTGACA 58.814 55.000 0.00 0.00 0.00 3.58
1528 2169 1.550524 CATCCCGTTCTCCTCTGACAA 59.449 52.381 0.00 0.00 0.00 3.18
1529 2170 1.257743 TCCCGTTCTCCTCTGACAAG 58.742 55.000 0.00 0.00 0.00 3.16
1530 2171 0.247736 CCCGTTCTCCTCTGACAAGG 59.752 60.000 0.00 0.00 37.81 3.61
1531 2172 0.969894 CCGTTCTCCTCTGACAAGGT 59.030 55.000 4.31 0.00 37.69 3.50
1532 2173 1.067495 CCGTTCTCCTCTGACAAGGTC 60.067 57.143 4.31 0.00 37.69 3.85
1533 2174 1.067495 CGTTCTCCTCTGACAAGGTCC 60.067 57.143 0.00 0.00 37.69 4.46
1534 2175 1.276705 GTTCTCCTCTGACAAGGTCCC 59.723 57.143 0.00 0.00 37.69 4.46
1535 2176 0.787084 TCTCCTCTGACAAGGTCCCT 59.213 55.000 0.00 0.00 37.69 4.20
1536 2177 0.901124 CTCCTCTGACAAGGTCCCTG 59.099 60.000 0.00 0.00 37.69 4.45
1537 2178 0.487325 TCCTCTGACAAGGTCCCTGA 59.513 55.000 0.00 0.00 37.69 3.86
1538 2179 0.901124 CCTCTGACAAGGTCCCTGAG 59.099 60.000 0.00 0.00 0.00 3.35
1539 2180 1.551099 CCTCTGACAAGGTCCCTGAGA 60.551 57.143 0.00 0.00 30.84 3.27
1540 2181 2.465813 CTCTGACAAGGTCCCTGAGAT 58.534 52.381 0.00 0.00 30.84 2.75
1541 2182 2.430332 CTCTGACAAGGTCCCTGAGATC 59.570 54.545 0.00 0.00 30.84 2.75
1542 2183 1.484240 CTGACAAGGTCCCTGAGATCC 59.516 57.143 0.00 0.00 0.00 3.36
1543 2184 1.079490 TGACAAGGTCCCTGAGATCCT 59.921 52.381 0.00 0.00 0.00 3.24
1754 2507 1.603739 GGGAACACCAAGGCAGGAC 60.604 63.158 2.81 0.00 39.85 3.85
2062 4015 1.398390 CCGTGAGTTTGCCAGCTATTC 59.602 52.381 0.00 0.00 0.00 1.75
2069 4022 1.667236 TTGCCAGCTATTCGGATGTG 58.333 50.000 0.00 0.00 0.00 3.21
2116 4069 2.559231 TGTGGTCTGTGTACGCAGATAA 59.441 45.455 34.76 24.82 45.81 1.75
2130 4083 4.083431 ACGCAGATAATGGTACTAGTAGCG 60.083 45.833 23.27 21.24 44.98 4.26
2193 4181 7.804843 TTTAGATTTCGTCTGGTTTTGGTAA 57.195 32.000 0.00 0.00 37.83 2.85
2253 4241 6.459923 TCGGTTTTCCCTTATTTCAAATTGG 58.540 36.000 0.00 0.00 36.42 3.16
2260 4248 8.606754 TTCCCTTATTTCAAATTGGATCATCA 57.393 30.769 0.00 0.00 0.00 3.07
2261 4249 8.786710 TCCCTTATTTCAAATTGGATCATCAT 57.213 30.769 0.00 0.00 0.00 2.45
2262 4250 8.644216 TCCCTTATTTCAAATTGGATCATCATG 58.356 33.333 0.00 0.00 0.00 3.07
2263 4251 7.386848 CCCTTATTTCAAATTGGATCATCATGC 59.613 37.037 0.00 0.00 0.00 4.06
2264 4252 7.929245 CCTTATTTCAAATTGGATCATCATGCA 59.071 33.333 0.00 0.00 0.00 3.96
2281 4269 1.966493 GCATGTTCCACAGCGTACCG 61.966 60.000 0.00 0.00 0.00 4.02
2319 4307 7.696992 TGTTATGTCTTTTTACTGGATTCCC 57.303 36.000 0.00 0.00 0.00 3.97
2401 4389 2.499896 CGTTCTTGTCTACGTCGGTAC 58.500 52.381 0.00 0.00 33.33 3.34
2528 4516 3.782523 TGGAAGCCATAGTCAAGGAGAAT 59.217 43.478 0.00 0.00 0.00 2.40
2529 4517 4.133078 GGAAGCCATAGTCAAGGAGAATG 58.867 47.826 0.00 0.00 0.00 2.67
2530 4518 4.384647 GGAAGCCATAGTCAAGGAGAATGT 60.385 45.833 0.00 0.00 0.00 2.71
2532 4520 4.521146 AGCCATAGTCAAGGAGAATGTTG 58.479 43.478 0.00 0.00 0.00 3.33
2533 4521 4.225942 AGCCATAGTCAAGGAGAATGTTGA 59.774 41.667 0.00 0.00 0.00 3.18
2695 4683 1.128321 CCAATTTGCCGCAATTTTCCG 59.872 47.619 6.64 0.00 0.00 4.30
2914 4902 3.876589 TTTCGTCCTCCGCCACTGC 62.877 63.158 0.00 0.00 36.19 4.40
2937 4925 2.009774 ACAGTGGCATCGCTAACATTC 58.990 47.619 0.00 0.00 31.63 2.67
2952 4940 5.004916 GCTAACATTCGTAGAGCTTGAAGTC 59.995 44.000 0.00 0.00 38.43 3.01
3045 5033 5.011943 AGGAGTCCAGATCTATCTCAATTGC 59.988 44.000 12.86 5.40 34.22 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.034544 TGTTTCATTCGTCATGATATTCTGTAG 57.965 33.333 0.00 0.00 41.82 2.74
72 73 9.927668 CTTGTAGGAAACATTTGTCCATATTTT 57.072 29.630 0.00 0.00 38.10 1.82
73 74 8.034804 GCTTGTAGGAAACATTTGTCCATATTT 58.965 33.333 0.00 0.00 38.10 1.40
74 75 7.178274 TGCTTGTAGGAAACATTTGTCCATATT 59.822 33.333 0.00 0.00 38.10 1.28
75 76 6.663093 TGCTTGTAGGAAACATTTGTCCATAT 59.337 34.615 0.00 0.00 38.10 1.78
76 77 6.007076 TGCTTGTAGGAAACATTTGTCCATA 58.993 36.000 0.00 0.00 38.10 2.74
77 78 4.832266 TGCTTGTAGGAAACATTTGTCCAT 59.168 37.500 0.00 0.00 38.10 3.41
78 79 4.211125 TGCTTGTAGGAAACATTTGTCCA 58.789 39.130 0.00 0.00 38.10 4.02
79 80 4.278419 ACTGCTTGTAGGAAACATTTGTCC 59.722 41.667 0.00 0.00 38.10 4.02
80 81 5.215160 CACTGCTTGTAGGAAACATTTGTC 58.785 41.667 0.00 0.00 38.10 3.18
81 82 4.037923 CCACTGCTTGTAGGAAACATTTGT 59.962 41.667 0.00 0.00 38.10 2.83
82 83 4.037923 ACCACTGCTTGTAGGAAACATTTG 59.962 41.667 0.00 0.00 38.10 2.32
83 84 4.215109 ACCACTGCTTGTAGGAAACATTT 58.785 39.130 0.00 0.00 38.10 2.32
84 85 3.832527 ACCACTGCTTGTAGGAAACATT 58.167 40.909 0.00 0.00 38.10 2.71
85 86 3.508845 ACCACTGCTTGTAGGAAACAT 57.491 42.857 0.00 0.00 38.10 2.71
86 87 3.389983 ACTACCACTGCTTGTAGGAAACA 59.610 43.478 0.00 0.00 38.98 2.83
87 88 4.004196 ACTACCACTGCTTGTAGGAAAC 57.996 45.455 0.00 0.00 38.98 2.78
88 89 4.699925 AACTACCACTGCTTGTAGGAAA 57.300 40.909 0.00 0.00 38.98 3.13
89 90 4.836736 AGTAACTACCACTGCTTGTAGGAA 59.163 41.667 0.00 0.00 38.98 3.36
90 91 4.413760 AGTAACTACCACTGCTTGTAGGA 58.586 43.478 0.00 0.00 38.98 2.94
91 92 4.803098 AGTAACTACCACTGCTTGTAGG 57.197 45.455 0.00 0.00 38.98 3.18
118 119 7.192148 ACTACATACAACATACAAAACGCAA 57.808 32.000 0.00 0.00 0.00 4.85
119 120 6.788684 ACTACATACAACATACAAAACGCA 57.211 33.333 0.00 0.00 0.00 5.24
120 121 8.814235 AGATACTACATACAACATACAAAACGC 58.186 33.333 0.00 0.00 0.00 4.84
130 131 9.524106 CGGTTTCAATAGATACTACATACAACA 57.476 33.333 0.00 0.00 0.00 3.33
131 132 9.740239 TCGGTTTCAATAGATACTACATACAAC 57.260 33.333 0.00 0.00 0.00 3.32
132 133 9.961265 CTCGGTTTCAATAGATACTACATACAA 57.039 33.333 0.00 0.00 0.00 2.41
133 134 9.346005 TCTCGGTTTCAATAGATACTACATACA 57.654 33.333 0.00 0.00 0.00 2.29
134 135 9.828852 CTCTCGGTTTCAATAGATACTACATAC 57.171 37.037 0.00 0.00 0.00 2.39
135 136 9.570468 ACTCTCGGTTTCAATAGATACTACATA 57.430 33.333 0.00 0.00 0.00 2.29
136 137 8.466617 ACTCTCGGTTTCAATAGATACTACAT 57.533 34.615 0.00 0.00 0.00 2.29
137 138 7.876936 ACTCTCGGTTTCAATAGATACTACA 57.123 36.000 0.00 0.00 0.00 2.74
138 139 9.828852 CATACTCTCGGTTTCAATAGATACTAC 57.171 37.037 0.00 0.00 0.00 2.73
139 140 8.512956 GCATACTCTCGGTTTCAATAGATACTA 58.487 37.037 0.00 0.00 0.00 1.82
140 141 7.014326 TGCATACTCTCGGTTTCAATAGATACT 59.986 37.037 0.00 0.00 0.00 2.12
141 142 7.115095 GTGCATACTCTCGGTTTCAATAGATAC 59.885 40.741 0.00 0.00 0.00 2.24
142 143 7.145985 GTGCATACTCTCGGTTTCAATAGATA 58.854 38.462 0.00 0.00 0.00 1.98
143 144 5.986135 GTGCATACTCTCGGTTTCAATAGAT 59.014 40.000 0.00 0.00 0.00 1.98
144 145 5.348986 GTGCATACTCTCGGTTTCAATAGA 58.651 41.667 0.00 0.00 0.00 1.98
145 146 4.207224 CGTGCATACTCTCGGTTTCAATAG 59.793 45.833 0.00 0.00 0.00 1.73
146 147 4.109766 CGTGCATACTCTCGGTTTCAATA 58.890 43.478 0.00 0.00 0.00 1.90
147 148 2.930040 CGTGCATACTCTCGGTTTCAAT 59.070 45.455 0.00 0.00 0.00 2.57
148 149 2.288579 ACGTGCATACTCTCGGTTTCAA 60.289 45.455 0.00 0.00 0.00 2.69
149 150 1.271379 ACGTGCATACTCTCGGTTTCA 59.729 47.619 0.00 0.00 0.00 2.69
150 151 1.654105 CACGTGCATACTCTCGGTTTC 59.346 52.381 0.82 0.00 0.00 2.78
151 152 1.000506 ACACGTGCATACTCTCGGTTT 59.999 47.619 17.22 0.00 0.00 3.27
152 153 0.601558 ACACGTGCATACTCTCGGTT 59.398 50.000 17.22 0.00 0.00 4.44
153 154 1.400846 CTACACGTGCATACTCTCGGT 59.599 52.381 17.22 0.00 0.00 4.69
154 155 1.400846 ACTACACGTGCATACTCTCGG 59.599 52.381 17.22 0.00 0.00 4.63
155 156 2.826979 ACTACACGTGCATACTCTCG 57.173 50.000 17.22 0.00 0.00 4.04
156 157 5.171147 ACATACTACACGTGCATACTCTC 57.829 43.478 17.22 0.00 0.00 3.20
157 158 5.821470 ACTACATACTACACGTGCATACTCT 59.179 40.000 17.22 0.00 0.00 3.24
158 159 6.057627 ACTACATACTACACGTGCATACTC 57.942 41.667 17.22 0.00 0.00 2.59
159 160 7.741027 ATACTACATACTACACGTGCATACT 57.259 36.000 17.22 0.00 0.00 2.12
163 164 9.054922 TGTTATATACTACATACTACACGTGCA 57.945 33.333 17.22 0.49 0.00 4.57
164 165 9.882996 TTGTTATATACTACATACTACACGTGC 57.117 33.333 17.22 0.00 0.00 5.34
285 286 8.694540 TGCATATGAGCCAATAGTTTTTGTTAT 58.305 29.630 6.97 0.00 0.00 1.89
286 287 8.060931 TGCATATGAGCCAATAGTTTTTGTTA 57.939 30.769 6.97 0.00 0.00 2.41
287 288 6.934056 TGCATATGAGCCAATAGTTTTTGTT 58.066 32.000 6.97 0.00 0.00 2.83
288 289 6.528537 TGCATATGAGCCAATAGTTTTTGT 57.471 33.333 6.97 0.00 0.00 2.83
289 290 8.428186 AATTGCATATGAGCCAATAGTTTTTG 57.572 30.769 6.97 0.00 0.00 2.44
290 291 9.452287 AAAATTGCATATGAGCCAATAGTTTTT 57.548 25.926 6.97 3.09 0.00 1.94
291 292 9.452287 AAAAATTGCATATGAGCCAATAGTTTT 57.548 25.926 6.97 8.46 0.00 2.43
314 315 7.820044 ATTTGAAAGCAAGTTACGTGAAAAA 57.180 28.000 1.88 0.00 35.04 1.94
315 316 9.176181 GATATTTGAAAGCAAGTTACGTGAAAA 57.824 29.630 1.88 0.00 35.04 2.29
316 317 8.564574 AGATATTTGAAAGCAAGTTACGTGAAA 58.435 29.630 1.88 0.00 35.04 2.69
317 318 8.094798 AGATATTTGAAAGCAAGTTACGTGAA 57.905 30.769 1.88 0.00 35.04 3.18
318 319 7.667043 AGATATTTGAAAGCAAGTTACGTGA 57.333 32.000 1.88 0.00 35.04 4.35
319 320 9.478019 CTAAGATATTTGAAAGCAAGTTACGTG 57.522 33.333 0.00 0.00 35.04 4.49
320 321 9.431887 TCTAAGATATTTGAAAGCAAGTTACGT 57.568 29.630 0.00 0.00 35.04 3.57
393 394 8.978539 TGTATTTCTCAACGTGATAGCATATTC 58.021 33.333 0.00 0.00 0.00 1.75
422 423 8.875803 GTGATGCAAACAAATAATGTGATTGAT 58.124 29.630 0.00 0.00 42.99 2.57
432 433 6.577103 TCCTTGTTGTGATGCAAACAAATAA 58.423 32.000 17.12 14.25 39.14 1.40
507 508 6.068010 TGTGGATGTAGAACCAACTTTCATT 58.932 36.000 0.00 0.00 37.94 2.57
508 509 5.630121 TGTGGATGTAGAACCAACTTTCAT 58.370 37.500 0.00 0.00 37.94 2.57
526 527 2.344592 AGGTGGGAGTAATGTTGTGGA 58.655 47.619 0.00 0.00 0.00 4.02
533 534 3.202151 ACCATGGTAAGGTGGGAGTAATG 59.798 47.826 18.10 0.00 39.86 1.90
553 554 1.781786 TGTAGAGAGAGCCATCCACC 58.218 55.000 0.00 0.00 0.00 4.61
556 557 3.386078 TGAACATGTAGAGAGAGCCATCC 59.614 47.826 0.00 0.00 0.00 3.51
558 559 5.454471 GGATTGAACATGTAGAGAGAGCCAT 60.454 44.000 0.00 0.00 0.00 4.40
565 566 4.454678 GCATGGGATTGAACATGTAGAGA 58.545 43.478 0.00 0.00 44.74 3.10
570 571 1.826720 GTGGCATGGGATTGAACATGT 59.173 47.619 0.00 0.00 44.74 3.21
571 572 1.137479 GGTGGCATGGGATTGAACATG 59.863 52.381 0.00 0.00 45.49 3.21
612 613 2.601266 CGTGATGTTTCGTTCGGCTTTT 60.601 45.455 0.00 0.00 0.00 2.27
616 617 0.509499 TTCGTGATGTTTCGTTCGGC 59.491 50.000 0.00 0.00 0.00 5.54
792 797 6.596309 ATCTCATATACGACACCATGATGT 57.404 37.500 0.00 0.00 34.78 3.06
806 829 2.187958 CGGGGCTGGGAATCTCATATA 58.812 52.381 0.00 0.00 0.00 0.86
866 889 1.613630 ACGGAGGGAGCTGGTCAAT 60.614 57.895 9.30 0.00 0.00 2.57
885 908 2.376695 AGCCCCAGATCAATTCATGG 57.623 50.000 0.00 0.00 0.00 3.66
888 911 2.130193 AGCTAGCCCCAGATCAATTCA 58.870 47.619 12.13 0.00 0.00 2.57
915 938 3.055530 GCTAGCTAGGCACACATGGATAT 60.056 47.826 22.10 0.00 0.00 1.63
975 998 2.224597 TGAGAGCAACAATGAGGAGCAA 60.225 45.455 0.00 0.00 0.00 3.91
1008 1031 1.002792 AAGGAGGCTGGAGAGGAGG 59.997 63.158 0.00 0.00 0.00 4.30
1023 1046 2.945668 GCATACCAGTAGAAAGCCAAGG 59.054 50.000 0.00 0.00 0.00 3.61
1079 1102 9.296400 CCCAAAATTATTTAGTGATAACAACCG 57.704 33.333 0.00 0.00 0.00 4.44
1179 1208 0.962855 TGCTCGGGAGTCAGAGTCAG 60.963 60.000 7.59 1.10 36.88 3.51
1186 1215 0.965866 CCAGTACTGCTCGGGAGTCA 60.966 60.000 17.86 0.00 0.00 3.41
1337 1372 1.983224 CCCCTCCACTGTGGTGTAG 59.017 63.158 25.15 15.59 41.53 2.74
1522 2163 1.484240 GGATCTCAGGGACCTTGTCAG 59.516 57.143 3.17 0.00 33.68 3.51
1523 2164 1.079490 AGGATCTCAGGGACCTTGTCA 59.921 52.381 3.17 0.00 33.68 3.58
1524 2165 1.872773 AGGATCTCAGGGACCTTGTC 58.127 55.000 3.17 0.00 0.00 3.18
1525 2166 2.350863 AAGGATCTCAGGGACCTTGT 57.649 50.000 3.17 0.00 40.59 3.16
1527 2168 1.589414 CCAAGGATCTCAGGGACCTT 58.411 55.000 0.00 0.00 42.49 3.50
1528 2169 0.985490 GCCAAGGATCTCAGGGACCT 60.985 60.000 0.00 0.00 0.00 3.85
1529 2170 1.529309 GCCAAGGATCTCAGGGACC 59.471 63.158 0.00 0.00 0.00 4.46
1530 2171 1.274703 TGGCCAAGGATCTCAGGGAC 61.275 60.000 0.61 0.00 0.00 4.46
1531 2172 1.082766 TGGCCAAGGATCTCAGGGA 59.917 57.895 0.61 0.00 0.00 4.20
1532 2173 1.225704 GTGGCCAAGGATCTCAGGG 59.774 63.158 7.24 0.00 0.00 4.45
1533 2174 0.622665 AAGTGGCCAAGGATCTCAGG 59.377 55.000 7.24 0.00 0.00 3.86
1534 2175 1.558756 AGAAGTGGCCAAGGATCTCAG 59.441 52.381 7.24 0.00 0.00 3.35
1535 2176 1.556911 GAGAAGTGGCCAAGGATCTCA 59.443 52.381 23.27 0.00 34.78 3.27
1536 2177 1.134250 GGAGAAGTGGCCAAGGATCTC 60.134 57.143 21.43 21.43 34.08 2.75
1537 2178 0.915364 GGAGAAGTGGCCAAGGATCT 59.085 55.000 7.24 8.93 0.00 2.75
1538 2179 0.106967 GGGAGAAGTGGCCAAGGATC 60.107 60.000 7.24 3.57 0.00 3.36
1539 2180 0.551131 AGGGAGAAGTGGCCAAGGAT 60.551 55.000 7.24 0.00 0.00 3.24
1540 2181 1.151810 AGGGAGAAGTGGCCAAGGA 60.152 57.895 7.24 0.00 0.00 3.36
1541 2182 1.001641 CAGGGAGAAGTGGCCAAGG 60.002 63.158 7.24 0.00 0.00 3.61
1542 2183 0.401738 TTCAGGGAGAAGTGGCCAAG 59.598 55.000 7.24 0.00 0.00 3.61
1543 2184 0.850100 TTTCAGGGAGAAGTGGCCAA 59.150 50.000 7.24 0.00 37.57 4.52
1754 2507 1.167851 TTACGTCGGTCAGGGTGTAG 58.832 55.000 0.00 0.00 0.00 2.74
2062 4015 3.334691 ACATAACCAACTCACACATCCG 58.665 45.455 0.00 0.00 0.00 4.18
2069 4022 4.833390 AGGCTAGAACATAACCAACTCAC 58.167 43.478 0.00 0.00 0.00 3.51
2116 4069 5.221263 CCATTTCTCACGCTACTAGTACCAT 60.221 44.000 0.00 0.00 0.00 3.55
2173 4151 4.517832 ACCTTACCAAAACCAGACGAAATC 59.482 41.667 0.00 0.00 0.00 2.17
2193 4181 4.929211 GCACTGAAAAACAAAGACAAACCT 59.071 37.500 0.00 0.00 0.00 3.50
2281 4269 3.877508 GACATAACAACCCAGTATCTGCC 59.122 47.826 0.00 0.00 0.00 4.85
2407 4395 3.749064 TGTGGACTCTCGCTCGGC 61.749 66.667 0.00 0.00 0.00 5.54
2528 4516 5.964477 ACCTTCATATCCTAGAACCTCAACA 59.036 40.000 0.00 0.00 0.00 3.33
2529 4517 6.487299 ACCTTCATATCCTAGAACCTCAAC 57.513 41.667 0.00 0.00 0.00 3.18
2530 4518 8.010697 TCATACCTTCATATCCTAGAACCTCAA 58.989 37.037 0.00 0.00 0.00 3.02
2532 4520 7.093684 GGTCATACCTTCATATCCTAGAACCTC 60.094 44.444 0.00 0.00 34.73 3.85
2533 4521 6.726764 GGTCATACCTTCATATCCTAGAACCT 59.273 42.308 0.00 0.00 34.73 3.50
2579 4567 9.823647 TGAAATGTGAAGTCTAGATAATCCTTC 57.176 33.333 11.33 11.33 33.74 3.46
2695 4683 4.897140 AGCATCTTTCATCTCTATCTGGC 58.103 43.478 0.00 0.00 0.00 4.85
2801 4789 4.316645 TCGTCCATTCGGTCATGTTTAAA 58.683 39.130 0.00 0.00 0.00 1.52
2802 4790 3.927854 TCGTCCATTCGGTCATGTTTAA 58.072 40.909 0.00 0.00 0.00 1.52
2803 4791 3.596310 TCGTCCATTCGGTCATGTTTA 57.404 42.857 0.00 0.00 0.00 2.01
2914 4902 1.535028 TGTTAGCGATGCCACTGTTTG 59.465 47.619 0.00 0.00 0.00 2.93
2927 4915 3.435566 TCAAGCTCTACGAATGTTAGCG 58.564 45.455 0.00 0.00 39.54 4.26
2937 4925 5.403246 ACTAACATGACTTCAAGCTCTACG 58.597 41.667 0.00 0.00 0.00 3.51
2952 4940 8.290325 TCTTCAGCTACGTATCATACTAACATG 58.710 37.037 0.00 0.00 0.00 3.21
3045 5033 4.664150 TTGGTTTTGCCTAGTTTCCTTG 57.336 40.909 0.00 0.00 38.35 3.61


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

AutoCloner maintained by Alex Coulton.