Multiple sequence alignment - TraesCS1A01G160300

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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 TraesCS1A01G160300 chr1A 100.000 4184 0 0 1 4184 287685614 287689797 0.000000e+00 7727.0
1 TraesCS1A01G160300 chr1D 93.363 4023 139 57 196 4184 222015104 222019032 0.000000e+00 5832.0
2 TraesCS1A01G160300 chr1D 96.154 52 0 2 115 165 222015057 222015107 2.680000e-12 84.2
3 TraesCS1A01G160300 chr1B 97.598 2165 41 4 2022 4184 317586244 317584089 0.000000e+00 3699.0
4 TraesCS1A01G160300 chr1B 89.362 1222 78 20 196 1384 317588021 317586819 0.000000e+00 1489.0
5 TraesCS1A01G160300 chr1B 86.978 599 42 8 1405 1978 317586830 317586243 3.530000e-180 641.0
6 TraesCS1A01G160300 chr1B 91.358 81 7 0 1986 2066 482179915 482179995 1.230000e-20 111.0
7 TraesCS1A01G160300 chr6D 89.247 93 8 2 1980 2071 437953759 437953668 9.510000e-22 115.0
8 TraesCS1A01G160300 chr7B 88.764 89 8 2 1985 2071 622269328 622269416 1.590000e-19 108.0
9 TraesCS1A01G160300 chr6B 90.244 82 8 0 1984 2065 171703710 171703791 1.590000e-19 108.0
10 TraesCS1A01G160300 chr7A 88.506 87 10 0 1985 2071 654796953 654797039 5.720000e-19 106.0
11 TraesCS1A01G160300 chr6A 88.506 87 10 0 1979 2065 145129811 145129725 5.720000e-19 106.0
12 TraesCS1A01G160300 chr7D 86.170 94 13 0 1976 2069 119896988 119897081 7.400000e-18 102.0


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 TraesCS1A01G160300 chr1A 287685614 287689797 4183 False 7727.0 7727 100.000000 1 4184 1 chr1A.!!$F1 4183
1 TraesCS1A01G160300 chr1D 222015057 222019032 3975 False 2958.1 5832 94.758500 115 4184 2 chr1D.!!$F1 4069
2 TraesCS1A01G160300 chr1B 317584089 317588021 3932 True 1943.0 3699 91.312667 196 4184 3 chr1B.!!$R1 3988

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
45 46 0.033601 GTGGGAGCCTCTCTCTCTCA 60.034 60.000 0.00 0.00 42.94 3.27 F
286 288 0.039256 CAAACAGGTGGCGATGTTGG 60.039 55.000 3.05 0.00 39.50 3.77 F
1119 1154 0.393537 GATGTCTGGCCTTGGTGGAG 60.394 60.000 3.32 0.00 38.35 3.86 F
1235 1270 0.970937 TACCCCAGGAGAAGCTCGTG 60.971 60.000 9.49 9.49 43.38 4.35 F
2899 2967 1.202818 ACAGGCTGGAGGTTTGTCTTC 60.203 52.381 20.34 0.00 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 1805 0.108138 AGCGGTCAATGACTGTAGGC 60.108 55.000 21.73 13.01 40.69 3.93 R
1992 2060 6.056884 ACTAAAACCACGTCACTTATTTCCA 58.943 36.000 0.00 0.00 0.00 3.53 R
2307 2375 1.421646 AGGTGGGTAATATCAGCTGCC 59.578 52.381 9.47 2.68 39.81 4.85 R
3076 3144 1.940613 GTTAATGCCCCGAACTAGCAG 59.059 52.381 0.00 0.00 40.40 4.24 R
3979 4049 1.609841 GGTTTAGTCGAGGGGTTGGTG 60.610 57.143 0.00 0.00 0.00 4.17 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
21 22 3.876274 TGTTTTGCAACCAGTAAAGCA 57.124 38.095 0.00 0.00 39.80 3.91
22 23 4.399004 TGTTTTGCAACCAGTAAAGCAT 57.601 36.364 0.00 0.00 37.91 3.79
23 24 5.521906 TGTTTTGCAACCAGTAAAGCATA 57.478 34.783 0.00 0.00 37.91 3.14
24 25 5.285651 TGTTTTGCAACCAGTAAAGCATAC 58.714 37.500 0.00 0.00 37.91 2.39
25 26 4.513198 TTTGCAACCAGTAAAGCATACC 57.487 40.909 0.00 0.00 36.80 2.73
26 27 2.080693 TGCAACCAGTAAAGCATACCG 58.919 47.619 0.00 0.00 31.05 4.02
27 28 2.081462 GCAACCAGTAAAGCATACCGT 58.919 47.619 0.00 0.00 0.00 4.83
28 29 2.159572 GCAACCAGTAAAGCATACCGTG 60.160 50.000 0.00 0.00 0.00 4.94
29 30 2.396590 ACCAGTAAAGCATACCGTGG 57.603 50.000 6.48 6.48 0.00 4.94
30 31 1.065709 ACCAGTAAAGCATACCGTGGG 60.066 52.381 10.65 0.00 0.00 4.61
31 32 1.208535 CCAGTAAAGCATACCGTGGGA 59.791 52.381 0.00 0.00 0.00 4.37
32 33 2.550978 CAGTAAAGCATACCGTGGGAG 58.449 52.381 0.00 0.00 0.00 4.30
33 34 1.134491 AGTAAAGCATACCGTGGGAGC 60.134 52.381 0.00 0.00 0.00 4.70
34 35 0.179468 TAAAGCATACCGTGGGAGCC 59.821 55.000 0.00 0.00 0.00 4.70
35 36 1.562672 AAAGCATACCGTGGGAGCCT 61.563 55.000 0.00 0.00 0.00 4.58
36 37 1.972660 AAGCATACCGTGGGAGCCTC 61.973 60.000 0.00 0.00 0.00 4.70
37 38 2.435693 GCATACCGTGGGAGCCTCT 61.436 63.158 0.00 0.00 0.00 3.69
38 39 1.742768 CATACCGTGGGAGCCTCTC 59.257 63.158 0.00 0.00 0.00 3.20
39 40 0.757188 CATACCGTGGGAGCCTCTCT 60.757 60.000 0.00 0.00 0.00 3.10
40 41 0.468400 ATACCGTGGGAGCCTCTCTC 60.468 60.000 0.00 0.00 41.15 3.20
41 42 1.572689 TACCGTGGGAGCCTCTCTCT 61.573 60.000 0.00 0.00 41.60 3.10
42 43 2.124693 CCGTGGGAGCCTCTCTCTC 61.125 68.421 0.00 0.00 42.82 3.20
43 44 1.077068 CGTGGGAGCCTCTCTCTCT 60.077 63.158 0.00 0.00 42.94 3.10
44 45 1.101049 CGTGGGAGCCTCTCTCTCTC 61.101 65.000 0.00 0.00 42.94 3.20
45 46 0.033601 GTGGGAGCCTCTCTCTCTCA 60.034 60.000 0.00 0.00 42.94 3.27
46 47 0.707024 TGGGAGCCTCTCTCTCTCAA 59.293 55.000 0.00 0.00 42.94 3.02
47 48 1.077828 TGGGAGCCTCTCTCTCTCAAA 59.922 52.381 0.00 0.00 42.94 2.69
48 49 2.183679 GGGAGCCTCTCTCTCTCAAAA 58.816 52.381 0.00 0.00 39.29 2.44
49 50 2.569404 GGGAGCCTCTCTCTCTCAAAAA 59.431 50.000 0.00 0.00 39.29 1.94
74 75 8.916628 AAAAAGAAGAAGAAGAAGCTAGACAT 57.083 30.769 0.00 0.00 0.00 3.06
75 76 8.546597 AAAAGAAGAAGAAGAAGCTAGACATC 57.453 34.615 0.00 0.00 0.00 3.06
76 77 6.220726 AGAAGAAGAAGAAGCTAGACATCC 57.779 41.667 0.00 0.00 0.00 3.51
77 78 5.128663 AGAAGAAGAAGAAGCTAGACATCCC 59.871 44.000 0.00 0.00 0.00 3.85
78 79 3.709141 AGAAGAAGAAGCTAGACATCCCC 59.291 47.826 0.00 0.00 0.00 4.81
79 80 2.035632 AGAAGAAGCTAGACATCCCCG 58.964 52.381 0.00 0.00 0.00 5.73
80 81 1.069358 GAAGAAGCTAGACATCCCCGG 59.931 57.143 0.00 0.00 0.00 5.73
81 82 0.760945 AGAAGCTAGACATCCCCGGG 60.761 60.000 15.80 15.80 0.00 5.73
82 83 0.759436 GAAGCTAGACATCCCCGGGA 60.759 60.000 26.32 9.16 35.55 5.14
83 84 0.760945 AAGCTAGACATCCCCGGGAG 60.761 60.000 26.32 14.42 34.05 4.30
84 85 1.457831 GCTAGACATCCCCGGGAGT 60.458 63.158 26.32 18.02 34.05 3.85
85 86 0.178970 GCTAGACATCCCCGGGAGTA 60.179 60.000 26.32 7.45 34.05 2.59
86 87 1.912417 CTAGACATCCCCGGGAGTAG 58.088 60.000 26.32 11.55 34.05 2.57
87 88 0.178970 TAGACATCCCCGGGAGTAGC 60.179 60.000 26.32 8.41 34.05 3.58
88 89 1.760875 GACATCCCCGGGAGTAGCA 60.761 63.158 26.32 0.00 34.05 3.49
89 90 1.074471 ACATCCCCGGGAGTAGCAT 60.074 57.895 26.32 0.13 34.05 3.79
90 91 1.372683 CATCCCCGGGAGTAGCATG 59.627 63.158 26.32 9.91 34.05 4.06
91 92 1.074471 ATCCCCGGGAGTAGCATGT 60.074 57.895 26.32 0.00 34.05 3.21
92 93 0.694444 ATCCCCGGGAGTAGCATGTT 60.694 55.000 26.32 0.00 34.05 2.71
93 94 0.912487 TCCCCGGGAGTAGCATGTTT 60.912 55.000 26.32 0.00 0.00 2.83
94 95 0.834612 CCCCGGGAGTAGCATGTTTA 59.165 55.000 26.32 0.00 0.00 2.01
95 96 1.202651 CCCCGGGAGTAGCATGTTTAG 60.203 57.143 26.32 0.00 0.00 1.85
96 97 1.485066 CCCGGGAGTAGCATGTTTAGT 59.515 52.381 18.48 0.00 0.00 2.24
97 98 2.483188 CCCGGGAGTAGCATGTTTAGTC 60.483 54.545 18.48 0.45 0.00 2.59
98 99 2.483188 CCGGGAGTAGCATGTTTAGTCC 60.483 54.545 18.00 18.00 39.09 3.85
99 100 2.798499 CGGGAGTAGCATGTTTAGTCCG 60.798 54.545 18.86 12.06 40.20 4.79
100 101 2.429610 GGGAGTAGCATGTTTAGTCCGA 59.570 50.000 18.86 0.00 40.20 4.55
101 102 3.445857 GGAGTAGCATGTTTAGTCCGAC 58.554 50.000 13.88 0.00 32.53 4.79
102 103 3.119245 GGAGTAGCATGTTTAGTCCGACA 60.119 47.826 13.88 0.00 32.53 4.35
103 104 4.106197 GAGTAGCATGTTTAGTCCGACAG 58.894 47.826 0.40 0.00 0.00 3.51
104 105 1.726853 AGCATGTTTAGTCCGACAGC 58.273 50.000 0.40 0.00 0.00 4.40
105 106 0.727398 GCATGTTTAGTCCGACAGCC 59.273 55.000 0.40 0.00 0.00 4.85
106 107 1.369625 CATGTTTAGTCCGACAGCCC 58.630 55.000 0.40 0.00 0.00 5.19
107 108 0.252197 ATGTTTAGTCCGACAGCCCC 59.748 55.000 0.40 0.00 0.00 5.80
108 109 0.834687 TGTTTAGTCCGACAGCCCCT 60.835 55.000 0.40 0.00 0.00 4.79
109 110 0.391263 GTTTAGTCCGACAGCCCCTG 60.391 60.000 0.40 0.00 37.52 4.45
111 112 0.834687 TTAGTCCGACAGCCCCTGTT 60.835 55.000 0.40 0.00 45.44 3.16
112 113 1.255667 TAGTCCGACAGCCCCTGTTC 61.256 60.000 0.40 0.00 45.44 3.18
113 114 2.203788 TCCGACAGCCCCTGTTCT 60.204 61.111 0.00 0.00 45.44 3.01
114 115 1.841556 TCCGACAGCCCCTGTTCTT 60.842 57.895 0.00 0.00 45.44 2.52
115 116 1.376037 CCGACAGCCCCTGTTCTTC 60.376 63.158 0.00 0.00 45.44 2.87
116 117 1.371183 CGACAGCCCCTGTTCTTCA 59.629 57.895 0.00 0.00 45.44 3.02
117 118 0.951040 CGACAGCCCCTGTTCTTCAC 60.951 60.000 0.00 0.00 45.44 3.18
118 119 0.606673 GACAGCCCCTGTTCTTCACC 60.607 60.000 0.00 0.00 45.44 4.02
119 120 1.303643 CAGCCCCTGTTCTTCACCC 60.304 63.158 0.00 0.00 0.00 4.61
164 166 2.480555 GAGCAAACCGGCGATGTG 59.519 61.111 9.30 0.00 39.27 3.21
165 167 2.031919 AGCAAACCGGCGATGTGA 59.968 55.556 9.30 0.00 39.27 3.58
166 168 1.970917 GAGCAAACCGGCGATGTGAG 61.971 60.000 9.30 0.00 39.27 3.51
167 169 3.039202 GCAAACCGGCGATGTGAGG 62.039 63.158 9.30 0.00 0.00 3.86
168 170 2.746277 AAACCGGCGATGTGAGGC 60.746 61.111 9.30 0.00 0.00 4.70
169 171 3.254024 AAACCGGCGATGTGAGGCT 62.254 57.895 9.30 0.00 0.00 4.58
170 172 1.895020 AAACCGGCGATGTGAGGCTA 61.895 55.000 9.30 0.00 0.00 3.93
171 173 2.279517 CCGGCGATGTGAGGCTAC 60.280 66.667 9.30 0.00 0.00 3.58
172 174 2.655364 CGGCGATGTGAGGCTACG 60.655 66.667 0.00 0.00 0.00 3.51
173 175 2.962253 GGCGATGTGAGGCTACGC 60.962 66.667 0.00 0.00 46.79 4.42
174 176 2.202743 GCGATGTGAGGCTACGCA 60.203 61.111 0.00 9.24 46.75 5.24
175 177 1.592669 GCGATGTGAGGCTACGCAT 60.593 57.895 11.15 11.15 46.75 4.73
176 178 1.154205 GCGATGTGAGGCTACGCATT 61.154 55.000 12.17 0.80 46.75 3.56
177 179 0.578683 CGATGTGAGGCTACGCATTG 59.421 55.000 12.17 11.55 40.40 2.82
178 180 1.656652 GATGTGAGGCTACGCATTGT 58.343 50.000 12.17 0.00 40.40 2.71
179 181 1.594862 GATGTGAGGCTACGCATTGTC 59.405 52.381 12.17 1.25 40.40 3.18
180 182 0.608130 TGTGAGGCTACGCATTGTCT 59.392 50.000 0.00 0.00 0.00 3.41
181 183 1.002366 GTGAGGCTACGCATTGTCTG 58.998 55.000 0.00 0.00 0.00 3.51
182 184 0.608130 TGAGGCTACGCATTGTCTGT 59.392 50.000 0.00 0.00 0.00 3.41
183 185 1.822371 TGAGGCTACGCATTGTCTGTA 59.178 47.619 0.00 0.00 0.00 2.74
184 186 2.159240 TGAGGCTACGCATTGTCTGTAG 60.159 50.000 0.00 7.88 38.83 2.74
185 187 2.099263 GAGGCTACGCATTGTCTGTAGA 59.901 50.000 13.48 0.00 38.23 2.59
186 188 2.496070 AGGCTACGCATTGTCTGTAGAA 59.504 45.455 13.48 0.00 38.23 2.10
187 189 2.860735 GGCTACGCATTGTCTGTAGAAG 59.139 50.000 13.48 0.00 38.23 2.85
188 190 3.428999 GGCTACGCATTGTCTGTAGAAGA 60.429 47.826 13.48 0.00 38.23 2.87
218 220 0.987715 CAACAGATGCTCACGACGAG 59.012 55.000 0.00 0.00 45.37 4.18
219 221 0.598562 AACAGATGCTCACGACGAGT 59.401 50.000 0.00 0.00 44.33 4.18
227 229 2.608090 TGCTCACGACGAGTATACAGAG 59.392 50.000 0.00 0.00 44.33 3.35
235 237 3.736720 ACGAGTATACAGAGTATCGCCA 58.263 45.455 5.50 0.00 42.67 5.69
243 245 8.516234 AGTATACAGAGTATCGCCAAAGATAAG 58.484 37.037 5.50 0.00 42.67 1.73
260 262 0.242017 AAGAAACGGAAGCATGCAGC 59.758 50.000 21.98 10.95 46.19 5.25
275 277 1.450531 GCAGCTGCAGTCAAACAGGT 61.451 55.000 33.36 0.00 45.01 4.00
286 288 0.039256 CAAACAGGTGGCGATGTTGG 60.039 55.000 3.05 0.00 39.50 3.77
295 297 2.100631 GCGATGTTGGGAGTGACCG 61.101 63.158 0.00 0.00 40.11 4.79
305 307 2.901192 TGGGAGTGACCGAACAATTCTA 59.099 45.455 0.00 0.00 40.11 2.10
310 312 2.921754 GTGACCGAACAATTCTACCTCG 59.078 50.000 0.00 0.00 0.00 4.63
317 319 3.611766 ACAATTCTACCTCGTCTTGGG 57.388 47.619 0.00 0.00 0.00 4.12
318 320 2.280628 CAATTCTACCTCGTCTTGGGC 58.719 52.381 0.00 0.00 0.00 5.36
319 321 1.568504 ATTCTACCTCGTCTTGGGCA 58.431 50.000 0.00 0.00 0.00 5.36
320 322 0.895530 TTCTACCTCGTCTTGGGCAG 59.104 55.000 0.00 0.00 0.00 4.85
326 328 1.001378 CCTCGTCTTGGGCAGTTTTTG 60.001 52.381 0.00 0.00 0.00 2.44
354 356 3.365291 CTAGCCGTGCCGCTTGGTA 62.365 63.158 3.83 0.00 40.39 3.25
367 369 1.471119 CTTGGTACAGGCCGTCTAGA 58.529 55.000 0.00 0.00 42.39 2.43
368 370 1.405821 CTTGGTACAGGCCGTCTAGAG 59.594 57.143 0.00 0.00 42.39 2.43
369 371 0.622136 TGGTACAGGCCGTCTAGAGA 59.378 55.000 0.00 0.00 0.00 3.10
370 372 1.310904 GGTACAGGCCGTCTAGAGAG 58.689 60.000 0.00 0.00 0.00 3.20
395 397 2.040544 CACGGTGTGGGCAAGGATC 61.041 63.158 0.00 0.00 0.00 3.36
396 398 2.819595 CGGTGTGGGCAAGGATCG 60.820 66.667 0.00 0.00 0.00 3.69
491 522 3.649986 ACAAGTTGCGCGCAGACC 61.650 61.111 34.25 24.32 0.00 3.85
556 587 1.202806 CCAGGTTTCAGCTCCAGAACA 60.203 52.381 0.00 0.00 0.00 3.18
557 588 2.575532 CAGGTTTCAGCTCCAGAACAA 58.424 47.619 0.00 0.00 0.00 2.83
558 589 2.291741 CAGGTTTCAGCTCCAGAACAAC 59.708 50.000 0.00 0.00 0.00 3.32
609 640 3.055675 TCCAAGAAACAGTATACCCACCG 60.056 47.826 0.00 0.00 0.00 4.94
625 656 2.297597 CCACCGAAGAGAAGTGAAGAGT 59.702 50.000 0.00 0.00 33.21 3.24
640 675 5.826601 TGAAGAGTCACTGCTCATACTAG 57.173 43.478 0.00 0.00 37.94 2.57
730 765 4.264380 CGTTTCAGGTAAACAAACAAGCAC 59.736 41.667 0.00 0.00 46.59 4.40
753 788 4.546570 GAGACATTTTTACAACAGGGCAC 58.453 43.478 0.00 0.00 0.00 5.01
823 858 1.460699 GAGCCAAAGAAGGGGGTGT 59.539 57.895 0.00 0.00 34.46 4.16
884 919 4.177537 TGGAAGAAAACCAGATGACCAA 57.822 40.909 0.00 0.00 33.22 3.67
1074 1109 2.178912 TGTAAACCTGAAGCGGAAGG 57.821 50.000 0.62 0.62 39.65 3.46
1119 1154 0.393537 GATGTCTGGCCTTGGTGGAG 60.394 60.000 3.32 0.00 38.35 3.86
1130 1165 1.488705 TTGGTGGAGTCGGGAGCATT 61.489 55.000 0.00 0.00 0.00 3.56
1235 1270 0.970937 TACCCCAGGAGAAGCTCGTG 60.971 60.000 9.49 9.49 43.38 4.35
1438 1473 7.112452 TGATTCTCCGTAAAGAGATCATTGA 57.888 36.000 0.00 0.00 42.38 2.57
1441 1476 5.651530 TCTCCGTAAAGAGATCATTGACAC 58.348 41.667 0.00 0.00 37.98 3.67
1442 1477 5.419155 TCTCCGTAAAGAGATCATTGACACT 59.581 40.000 0.00 0.00 37.98 3.55
1454 1489 7.542890 AGATCATTGACACTAGTGAGTTGTAG 58.457 38.462 29.30 11.93 31.73 2.74
1458 1493 8.803235 TCATTGACACTAGTGAGTTGTAGTAAT 58.197 33.333 29.30 11.52 31.73 1.89
1474 1509 4.718940 AGTAATACTGCCATTTGGTTGC 57.281 40.909 0.00 0.00 37.57 4.17
1571 1631 9.675464 AATCTCCACTCGGTAAATAAAATGTTA 57.325 29.630 0.00 0.00 0.00 2.41
1645 1705 9.650714 TCAGCAGTACCTAACCTATTTTATAGA 57.349 33.333 0.00 0.00 0.00 1.98
1646 1706 9.915629 CAGCAGTACCTAACCTATTTTATAGAG 57.084 37.037 0.00 0.00 0.00 2.43
1743 1805 6.258068 ACAAGAAAAGACTGTAGGAAAACTCG 59.742 38.462 0.00 0.00 0.00 4.18
1764 1826 1.471676 CCTACAGTCATTGACCGCTCC 60.472 57.143 13.14 0.00 32.18 4.70
1855 1923 5.407407 TTTGCTCTAGGAGAAACACTAGG 57.593 43.478 0.00 0.00 37.77 3.02
1856 1924 4.317530 TGCTCTAGGAGAAACACTAGGA 57.682 45.455 0.00 0.00 37.77 2.94
1857 1925 4.017808 TGCTCTAGGAGAAACACTAGGAC 58.982 47.826 0.00 0.00 37.77 3.85
1858 1926 4.017808 GCTCTAGGAGAAACACTAGGACA 58.982 47.826 0.00 0.00 37.77 4.02
1992 2060 8.810990 TTATTTGTTATGTATTCCCTCCGTTT 57.189 30.769 0.00 0.00 0.00 3.60
2006 2074 3.124636 CCTCCGTTTGGAAATAAGTGACG 59.875 47.826 0.00 0.00 45.87 4.35
2718 2786 4.832266 ACAGACAAGGTAATTGATGGCAAA 59.168 37.500 0.00 0.00 41.83 3.68
2899 2967 1.202818 ACAGGCTGGAGGTTTGTCTTC 60.203 52.381 20.34 0.00 0.00 2.87
2964 3032 3.264193 TGAACTATGGGAATGTGAGCAGT 59.736 43.478 0.00 0.00 0.00 4.40
3076 3144 2.165030 CCAGGCATCACATTTGAAGGAC 59.835 50.000 0.00 0.00 34.61 3.85
3169 3237 2.704725 AACAAGCTTTACATGGCACG 57.295 45.000 0.00 0.00 0.00 5.34
3417 3486 5.605564 TGTACAATGTACAAGTGCATGAC 57.394 39.130 22.36 6.61 36.07 3.06
3425 3494 4.754618 TGTACAAGTGCATGACCAAACTAG 59.245 41.667 0.00 0.00 0.00 2.57
3633 3703 4.460731 AGGCAACAAAATAGAAGAAGCTCC 59.539 41.667 0.00 0.00 41.41 4.70
3659 3729 5.163519 ACAGAAAAGGGATTATGAAATGGCG 60.164 40.000 0.00 0.00 0.00 5.69
3979 4049 1.613630 TGCAGACCTCCCTCCCTTC 60.614 63.158 0.00 0.00 0.00 3.46
4084 4154 2.977914 TCATCAAGCCTTTCCTTCTCG 58.022 47.619 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.399004 TGCTTTACTGGTTGCAAAACAT 57.601 36.364 0.00 0.00 46.27 2.71
1 2 3.876274 TGCTTTACTGGTTGCAAAACA 57.124 38.095 0.00 2.42 44.52 2.83
2 3 4.684242 GGTATGCTTTACTGGTTGCAAAAC 59.316 41.667 0.00 0.00 38.96 2.43
3 4 4.557695 CGGTATGCTTTACTGGTTGCAAAA 60.558 41.667 0.00 0.00 38.96 2.44
4 5 3.057876 CGGTATGCTTTACTGGTTGCAAA 60.058 43.478 0.00 0.00 38.96 3.68
5 6 2.486203 CGGTATGCTTTACTGGTTGCAA 59.514 45.455 0.00 0.00 38.96 4.08
6 7 2.080693 CGGTATGCTTTACTGGTTGCA 58.919 47.619 0.00 0.00 39.83 4.08
7 8 2.081462 ACGGTATGCTTTACTGGTTGC 58.919 47.619 9.92 0.00 0.00 4.17
8 9 2.418628 CCACGGTATGCTTTACTGGTTG 59.581 50.000 9.92 2.32 0.00 3.77
9 10 2.617021 CCCACGGTATGCTTTACTGGTT 60.617 50.000 9.92 0.00 0.00 3.67
10 11 1.065709 CCCACGGTATGCTTTACTGGT 60.066 52.381 9.92 1.91 0.00 4.00
11 12 1.208535 TCCCACGGTATGCTTTACTGG 59.791 52.381 9.92 5.43 0.00 4.00
12 13 2.550978 CTCCCACGGTATGCTTTACTG 58.449 52.381 5.10 5.10 0.00 2.74
13 14 1.134491 GCTCCCACGGTATGCTTTACT 60.134 52.381 0.00 0.00 0.00 2.24
14 15 1.296727 GCTCCCACGGTATGCTTTAC 58.703 55.000 0.00 0.00 0.00 2.01
15 16 0.179468 GGCTCCCACGGTATGCTTTA 59.821 55.000 0.00 0.00 0.00 1.85
16 17 1.077716 GGCTCCCACGGTATGCTTT 60.078 57.895 0.00 0.00 0.00 3.51
17 18 1.972660 GAGGCTCCCACGGTATGCTT 61.973 60.000 2.15 0.00 0.00 3.91
18 19 2.365635 AGGCTCCCACGGTATGCT 60.366 61.111 0.00 0.00 0.00 3.79
19 20 2.109181 GAGGCTCCCACGGTATGC 59.891 66.667 2.15 0.00 0.00 3.14
20 21 0.757188 AGAGAGGCTCCCACGGTATG 60.757 60.000 11.71 0.00 0.00 2.39
21 22 0.468400 GAGAGAGGCTCCCACGGTAT 60.468 60.000 11.71 0.00 37.69 2.73
22 23 1.076923 GAGAGAGGCTCCCACGGTA 60.077 63.158 11.71 0.00 37.69 4.02
23 24 2.363147 GAGAGAGGCTCCCACGGT 60.363 66.667 11.71 0.00 37.69 4.83
24 25 2.043450 AGAGAGAGGCTCCCACGG 60.043 66.667 11.71 0.00 45.10 4.94
25 26 1.077068 AGAGAGAGAGGCTCCCACG 60.077 63.158 11.71 0.00 45.10 4.94
26 27 0.033601 TGAGAGAGAGAGGCTCCCAC 60.034 60.000 11.71 0.00 45.10 4.61
27 28 0.707024 TTGAGAGAGAGAGGCTCCCA 59.293 55.000 11.71 0.00 45.10 4.37
28 29 1.859302 TTTGAGAGAGAGAGGCTCCC 58.141 55.000 11.71 0.00 45.10 4.30
29 30 3.971245 TTTTTGAGAGAGAGAGGCTCC 57.029 47.619 11.71 2.69 45.10 4.70
49 50 8.916628 ATGTCTAGCTTCTTCTTCTTCTTTTT 57.083 30.769 0.00 0.00 0.00 1.94
50 51 7.606073 GGATGTCTAGCTTCTTCTTCTTCTTTT 59.394 37.037 0.00 0.00 0.00 2.27
51 52 7.102993 GGATGTCTAGCTTCTTCTTCTTCTTT 58.897 38.462 0.00 0.00 0.00 2.52
52 53 6.351796 GGGATGTCTAGCTTCTTCTTCTTCTT 60.352 42.308 0.00 0.00 0.00 2.52
53 54 5.128663 GGGATGTCTAGCTTCTTCTTCTTCT 59.871 44.000 0.00 0.00 0.00 2.85
54 55 5.356426 GGGATGTCTAGCTTCTTCTTCTTC 58.644 45.833 0.00 0.00 0.00 2.87
55 56 4.163268 GGGGATGTCTAGCTTCTTCTTCTT 59.837 45.833 0.00 0.00 0.00 2.52
56 57 3.709141 GGGGATGTCTAGCTTCTTCTTCT 59.291 47.826 0.00 0.00 0.00 2.85
57 58 3.491792 CGGGGATGTCTAGCTTCTTCTTC 60.492 52.174 0.00 0.00 0.00 2.87
58 59 2.432510 CGGGGATGTCTAGCTTCTTCTT 59.567 50.000 0.00 0.00 0.00 2.52
59 60 2.035632 CGGGGATGTCTAGCTTCTTCT 58.964 52.381 0.00 0.00 0.00 2.85
60 61 1.069358 CCGGGGATGTCTAGCTTCTTC 59.931 57.143 0.00 0.00 0.00 2.87
61 62 1.123928 CCGGGGATGTCTAGCTTCTT 58.876 55.000 0.00 0.00 0.00 2.52
62 63 0.760945 CCCGGGGATGTCTAGCTTCT 60.761 60.000 14.71 0.00 0.00 2.85
63 64 0.759436 TCCCGGGGATGTCTAGCTTC 60.759 60.000 23.50 0.00 0.00 3.86
64 65 0.760945 CTCCCGGGGATGTCTAGCTT 60.761 60.000 23.50 0.00 0.00 3.74
65 66 1.152440 CTCCCGGGGATGTCTAGCT 60.152 63.158 23.50 0.00 0.00 3.32
66 67 0.178970 TACTCCCGGGGATGTCTAGC 60.179 60.000 23.50 0.00 0.00 3.42
67 68 1.912417 CTACTCCCGGGGATGTCTAG 58.088 60.000 23.50 11.46 0.00 2.43
68 69 0.178970 GCTACTCCCGGGGATGTCTA 60.179 60.000 23.50 0.00 0.00 2.59
69 70 1.457831 GCTACTCCCGGGGATGTCT 60.458 63.158 23.50 2.10 0.00 3.41
70 71 1.122019 ATGCTACTCCCGGGGATGTC 61.122 60.000 23.50 8.35 0.00 3.06
71 72 1.074471 ATGCTACTCCCGGGGATGT 60.074 57.895 23.50 19.17 0.00 3.06
72 73 1.372683 CATGCTACTCCCGGGGATG 59.627 63.158 23.50 14.01 0.00 3.51
73 74 0.694444 AACATGCTACTCCCGGGGAT 60.694 55.000 23.50 12.03 0.00 3.85
74 75 0.912487 AAACATGCTACTCCCGGGGA 60.912 55.000 23.50 16.55 0.00 4.81
75 76 0.834612 TAAACATGCTACTCCCGGGG 59.165 55.000 23.50 14.41 0.00 5.73
76 77 1.485066 ACTAAACATGCTACTCCCGGG 59.515 52.381 16.85 16.85 0.00 5.73
77 78 2.483188 GGACTAAACATGCTACTCCCGG 60.483 54.545 0.00 0.00 0.00 5.73
78 79 2.798499 CGGACTAAACATGCTACTCCCG 60.798 54.545 0.00 0.00 0.00 5.14
79 80 2.429610 TCGGACTAAACATGCTACTCCC 59.570 50.000 0.00 0.00 0.00 4.30
80 81 3.119245 TGTCGGACTAAACATGCTACTCC 60.119 47.826 9.88 0.00 0.00 3.85
81 82 4.106029 TGTCGGACTAAACATGCTACTC 57.894 45.455 9.88 0.00 0.00 2.59
82 83 3.676324 GCTGTCGGACTAAACATGCTACT 60.676 47.826 9.88 0.00 0.00 2.57
83 84 2.603560 GCTGTCGGACTAAACATGCTAC 59.396 50.000 9.88 0.00 0.00 3.58
84 85 2.418197 GGCTGTCGGACTAAACATGCTA 60.418 50.000 9.88 0.00 0.00 3.49
85 86 1.676014 GGCTGTCGGACTAAACATGCT 60.676 52.381 9.88 0.00 0.00 3.79
86 87 0.727398 GGCTGTCGGACTAAACATGC 59.273 55.000 9.88 2.86 0.00 4.06
87 88 1.369625 GGGCTGTCGGACTAAACATG 58.630 55.000 9.88 0.00 0.00 3.21
88 89 0.252197 GGGGCTGTCGGACTAAACAT 59.748 55.000 9.88 0.00 0.00 2.71
89 90 0.834687 AGGGGCTGTCGGACTAAACA 60.835 55.000 9.88 0.00 0.00 2.83
90 91 0.391263 CAGGGGCTGTCGGACTAAAC 60.391 60.000 9.88 0.00 0.00 2.01
91 92 0.834687 ACAGGGGCTGTCGGACTAAA 60.835 55.000 9.88 0.00 41.21 1.85
92 93 0.834687 AACAGGGGCTGTCGGACTAA 60.835 55.000 9.88 0.00 44.62 2.24
93 94 1.229082 AACAGGGGCTGTCGGACTA 60.229 57.895 9.88 0.00 44.62 2.59
94 95 2.526873 AACAGGGGCTGTCGGACT 60.527 61.111 9.88 0.00 44.62 3.85
95 96 2.047179 GAACAGGGGCTGTCGGAC 60.047 66.667 0.00 0.00 44.62 4.79
96 97 1.827399 GAAGAACAGGGGCTGTCGGA 61.827 60.000 0.00 0.00 44.62 4.55
97 98 1.376037 GAAGAACAGGGGCTGTCGG 60.376 63.158 0.00 0.00 44.62 4.79
98 99 0.951040 GTGAAGAACAGGGGCTGTCG 60.951 60.000 0.00 0.00 44.62 4.35
99 100 0.606673 GGTGAAGAACAGGGGCTGTC 60.607 60.000 0.00 0.00 44.62 3.51
101 102 1.303643 GGGTGAAGAACAGGGGCTG 60.304 63.158 0.00 0.00 37.52 4.85
102 103 1.774217 TGGGTGAAGAACAGGGGCT 60.774 57.895 0.00 0.00 0.00 5.19
103 104 1.603739 GTGGGTGAAGAACAGGGGC 60.604 63.158 0.00 0.00 0.00 5.80
104 105 0.184933 TTGTGGGTGAAGAACAGGGG 59.815 55.000 0.00 0.00 0.00 4.79
105 106 1.318576 GTTGTGGGTGAAGAACAGGG 58.681 55.000 0.00 0.00 0.00 4.45
106 107 1.318576 GGTTGTGGGTGAAGAACAGG 58.681 55.000 0.00 0.00 0.00 4.00
107 108 0.944386 CGGTTGTGGGTGAAGAACAG 59.056 55.000 0.00 0.00 0.00 3.16
108 109 0.464735 CCGGTTGTGGGTGAAGAACA 60.465 55.000 0.00 0.00 0.00 3.18
109 110 1.170290 CCCGGTTGTGGGTGAAGAAC 61.170 60.000 0.00 0.00 44.76 3.01
110 111 1.149627 CCCGGTTGTGGGTGAAGAA 59.850 57.895 0.00 0.00 44.76 2.52
111 112 2.833227 CCCGGTTGTGGGTGAAGA 59.167 61.111 0.00 0.00 44.76 2.87
178 180 2.288457 GCACACAGCAGTCTTCTACAGA 60.288 50.000 0.00 0.00 44.79 3.41
179 181 2.064762 GCACACAGCAGTCTTCTACAG 58.935 52.381 0.00 0.00 44.79 2.74
180 182 2.154854 GCACACAGCAGTCTTCTACA 57.845 50.000 0.00 0.00 44.79 2.74
215 217 4.744136 TTGGCGATACTCTGTATACTCG 57.256 45.455 4.17 5.11 0.00 4.18
216 218 6.315091 TCTTTGGCGATACTCTGTATACTC 57.685 41.667 4.17 0.00 0.00 2.59
218 220 8.512956 TCTTATCTTTGGCGATACTCTGTATAC 58.487 37.037 0.00 0.00 0.00 1.47
219 221 8.631480 TCTTATCTTTGGCGATACTCTGTATA 57.369 34.615 0.00 0.00 0.00 1.47
227 229 4.807304 TCCGTTTCTTATCTTTGGCGATAC 59.193 41.667 0.00 0.00 0.00 2.24
235 237 4.458989 TGCATGCTTCCGTTTCTTATCTTT 59.541 37.500 20.33 0.00 0.00 2.52
243 245 4.465413 GCTGCATGCTTCCGTTTC 57.535 55.556 20.33 0.00 38.95 2.78
260 262 1.656441 GCCACCTGTTTGACTGCAG 59.344 57.895 13.48 13.48 0.00 4.41
267 269 0.039256 CCAACATCGCCACCTGTTTG 60.039 55.000 0.00 0.00 33.45 2.93
268 270 1.178534 CCCAACATCGCCACCTGTTT 61.179 55.000 0.00 0.00 33.45 2.83
275 277 1.003839 GTCACTCCCAACATCGCCA 60.004 57.895 0.00 0.00 0.00 5.69
286 288 3.056035 AGGTAGAATTGTTCGGTCACTCC 60.056 47.826 0.00 0.00 34.02 3.85
295 297 3.933332 CCCAAGACGAGGTAGAATTGTTC 59.067 47.826 0.00 0.00 0.00 3.18
305 307 0.182775 AAAACTGCCCAAGACGAGGT 59.817 50.000 0.00 0.00 0.00 3.85
310 312 2.473816 GCTTCAAAAACTGCCCAAGAC 58.526 47.619 0.00 0.00 0.00 3.01
317 319 2.955607 GCATTGGCTTCAAAAACTGC 57.044 45.000 0.00 0.00 36.96 4.40
354 356 2.115911 CGCTCTCTAGACGGCCTGT 61.116 63.158 0.00 0.00 0.00 4.00
360 362 2.649349 GCGTGCGCTCTCTAGACG 60.649 66.667 9.73 9.60 38.26 4.18
361 363 1.870016 GTGCGTGCGCTCTCTAGAC 60.870 63.158 17.49 1.93 42.51 2.59
362 364 2.485582 GTGCGTGCGCTCTCTAGA 59.514 61.111 17.49 0.00 42.51 2.43
363 365 2.946597 CGTGCGTGCGCTCTCTAG 60.947 66.667 17.49 0.00 42.51 2.43
364 366 4.476410 CCGTGCGTGCGCTCTCTA 62.476 66.667 17.49 0.00 42.51 2.43
426 429 3.936203 ACTCGGCGCCCAACTCAA 61.936 61.111 23.46 0.00 0.00 3.02
427 430 4.680237 CACTCGGCGCCCAACTCA 62.680 66.667 23.46 0.00 0.00 3.41
429 432 4.988598 CACACTCGGCGCCCAACT 62.989 66.667 23.46 0.00 0.00 3.16
475 506 4.724697 CGGTCTGCGCGCAACTTG 62.725 66.667 35.50 23.09 0.00 3.16
485 516 2.300787 CGCCTAATACGCGGTCTGC 61.301 63.158 12.47 4.19 45.80 4.26
494 525 0.532196 GTGCCTGGGACGCCTAATAC 60.532 60.000 1.54 0.00 0.00 1.89
556 587 6.601613 TCAGTTTTCAACATCACTACAAGGTT 59.398 34.615 0.00 0.00 0.00 3.50
557 588 6.038271 GTCAGTTTTCAACATCACTACAAGGT 59.962 38.462 0.00 0.00 0.00 3.50
558 589 6.038161 TGTCAGTTTTCAACATCACTACAAGG 59.962 38.462 0.00 0.00 0.00 3.61
589 620 4.196626 TCGGTGGGTATACTGTTTCTTG 57.803 45.455 2.25 0.00 0.00 3.02
625 656 7.090808 CAGTTTGTTACTAGTATGAGCAGTGA 58.909 38.462 2.79 0.00 34.56 3.41
640 675 6.412653 CGTGAAATGTGGTTACAGTTTGTTAC 59.587 38.462 0.00 0.00 44.28 2.50
730 765 3.252215 TGCCCTGTTGTAAAAATGTCTCG 59.748 43.478 0.00 0.00 0.00 4.04
884 919 4.044065 TGAAAAGGATGGTAGGTTGTGGAT 59.956 41.667 0.00 0.00 0.00 3.41
1023 1058 0.587768 CTGTGATTTCGCTGTGTGCA 59.412 50.000 0.00 0.00 43.06 4.57
1074 1109 0.319900 TCACAGTCGCTCCTTGCTTC 60.320 55.000 0.00 0.00 40.11 3.86
1119 1154 4.467084 TCCGCCAATGCTCCCGAC 62.467 66.667 0.00 0.00 34.43 4.79
1199 1234 2.638363 GGGTAGAACTTGTTCAGGGAGT 59.362 50.000 14.80 0.00 0.00 3.85
1343 1378 3.080121 CTCTCAGCCCGGGAAGCT 61.080 66.667 29.31 12.12 42.70 3.74
1349 1384 2.474410 ACTTAAAACTCTCAGCCCGG 57.526 50.000 0.00 0.00 0.00 5.73
1438 1473 7.362747 GGCAGTATTACTACAACTCACTAGTGT 60.363 40.741 21.99 5.49 35.62 3.55
1441 1476 7.096884 TGGCAGTATTACTACAACTCACTAG 57.903 40.000 0.00 0.00 0.00 2.57
1442 1477 7.655521 ATGGCAGTATTACTACAACTCACTA 57.344 36.000 0.00 0.00 0.00 2.74
1454 1489 4.448537 TGCAACCAAATGGCAGTATTAC 57.551 40.909 0.00 0.00 39.32 1.89
1474 1509 7.981789 TGGTAGATTCTGTAAACTAAGATGCTG 59.018 37.037 0.00 0.00 0.00 4.41
1541 1576 7.605410 TTTATTTACCGAGTGGAGATTTGTC 57.395 36.000 0.00 0.00 39.21 3.18
1544 1579 8.575649 ACATTTTATTTACCGAGTGGAGATTT 57.424 30.769 0.00 0.00 39.21 2.17
1571 1631 9.354673 CTGGGATTTAGTAATAATGACCATGTT 57.645 33.333 0.00 0.00 0.00 2.71
1654 1714 9.859427 CATCACACTAATTCCATTTTACACAAT 57.141 29.630 0.00 0.00 0.00 2.71
1655 1715 9.072375 TCATCACACTAATTCCATTTTACACAA 57.928 29.630 0.00 0.00 0.00 3.33
1743 1805 0.108138 AGCGGTCAATGACTGTAGGC 60.108 55.000 21.73 13.01 40.69 3.93
1992 2060 6.056884 ACTAAAACCACGTCACTTATTTCCA 58.943 36.000 0.00 0.00 0.00 3.53
2307 2375 1.421646 AGGTGGGTAATATCAGCTGCC 59.578 52.381 9.47 2.68 39.81 4.85
2718 2786 6.445139 TGAAGTTAATCCCTTCCTCTGAGATT 59.555 38.462 6.17 0.00 38.00 2.40
2899 2967 5.947228 TTGAGTTTATCTGGCTCAAGTTG 57.053 39.130 0.00 0.00 42.24 3.16
2964 3032 4.526650 TCCAGCACATAGAAGACTGTGTTA 59.473 41.667 4.78 0.00 43.93 2.41
3076 3144 1.940613 GTTAATGCCCCGAACTAGCAG 59.059 52.381 0.00 0.00 40.40 4.24
3135 3203 4.469657 AGCTTGTTTGTGACCTTTCCATA 58.530 39.130 0.00 0.00 0.00 2.74
3144 3212 3.735746 GCCATGTAAAGCTTGTTTGTGAC 59.264 43.478 0.00 0.00 0.00 3.67
3460 3529 0.514691 GCCTCAGTTGTTCTGCTTCG 59.485 55.000 0.00 0.00 43.32 3.79
3517 3586 5.721876 TCACTGTAACCGTTTGTTTAGTG 57.278 39.130 12.22 12.22 44.22 2.74
3563 3633 4.469657 ACATTTGTTGAAGTGCTAAGGGA 58.530 39.130 0.00 0.00 0.00 4.20
3633 3703 7.428826 GCCATTTCATAATCCCTTTTCTGTAG 58.571 38.462 0.00 0.00 0.00 2.74
3659 3729 4.039730 TCTCTATAAGGCAGAATGGTCAGC 59.960 45.833 0.00 0.00 35.86 4.26
3979 4049 1.609841 GGTTTAGTCGAGGGGTTGGTG 60.610 57.143 0.00 0.00 0.00 4.17
4084 4154 4.023963 GTCCTGCTGTTTAAGAGTTTGGTC 60.024 45.833 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.