Multiple sequence alignment - TraesCS4A01G099200

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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 TraesCS4A01G099200 chr4A 100.000 4117 0 0 1 4117 111165406 111169522 0.000000e+00 7603.0
1 TraesCS4A01G099200 chr4D 96.723 3326 98 9 795 4117 353699141 353695824 0.000000e+00 5528.0
2 TraesCS4A01G099200 chr4D 95.025 603 20 6 162 764 353699722 353699130 0.000000e+00 939.0
3 TraesCS4A01G099200 chr4D 93.878 49 3 0 3626 3674 353696366 353696318 1.590000e-09 75.0
4 TraesCS4A01G099200 chr4B 97.210 2832 71 6 795 3625 437164270 437161446 0.000000e+00 4785.0
5 TraesCS4A01G099200 chr4B 94.992 619 18 2 156 762 437164878 437164261 0.000000e+00 959.0
6 TraesCS4A01G099200 chr4B 90.284 422 29 10 3625 4039 437161495 437161079 3.620000e-150 542.0
7 TraesCS4A01G099200 chr1D 80.639 1002 191 2 999 2000 410602607 410601609 0.000000e+00 773.0
8 TraesCS4A01G099200 chr1B 80.240 1002 195 2 999 2000 553451923 553450925 0.000000e+00 750.0
9 TraesCS4A01G099200 chr1A 79.341 1002 204 2 999 2000 506855596 506854598 0.000000e+00 701.0
10 TraesCS4A01G099200 chr7D 88.889 144 14 2 2 144 529620353 529620211 4.230000e-40 176.0
11 TraesCS4A01G099200 chr2A 87.500 144 17 1 2 144 678992683 678992540 9.160000e-37 165.0
12 TraesCS4A01G099200 chr2A 96.875 32 1 0 117 148 144028871 144028840 2.000000e-03 54.7
13 TraesCS4A01G099200 chr3B 79.839 124 18 6 25 144 358899466 358899346 2.640000e-12 84.2
14 TraesCS4A01G099200 chr5B 97.059 34 1 0 117 150 670696243 670696210 1.600000e-04 58.4
15 TraesCS4A01G099200 chr5B 92.308 39 1 2 114 151 700435247 700435284 2.000000e-03 54.7
16 TraesCS4A01G099200 chr7B 100.000 29 0 0 118 146 38609341 38609369 2.000000e-03 54.7
17 TraesCS4A01G099200 chr2D 100.000 28 0 0 117 144 487929621 487929648 7.000000e-03 52.8
18 TraesCS4A01G099200 chr2D 100.000 28 0 0 118 145 623761567 623761594 7.000000e-03 52.8


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 TraesCS4A01G099200 chr4A 111165406 111169522 4116 False 7603.000000 7603 100.000000 1 4117 1 chr4A.!!$F1 4116
1 TraesCS4A01G099200 chr4D 353695824 353699722 3898 True 2180.666667 5528 95.208667 162 4117 3 chr4D.!!$R1 3955
2 TraesCS4A01G099200 chr4B 437161079 437164878 3799 True 2095.333333 4785 94.162000 156 4039 3 chr4B.!!$R1 3883
3 TraesCS4A01G099200 chr1D 410601609 410602607 998 True 773.000000 773 80.639000 999 2000 1 chr1D.!!$R1 1001
4 TraesCS4A01G099200 chr1B 553450925 553451923 998 True 750.000000 750 80.240000 999 2000 1 chr1B.!!$R1 1001
5 TraesCS4A01G099200 chr1A 506854598 506855596 998 True 701.000000 701 79.341000 999 2000 1 chr1A.!!$R1 1001

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
216 217 0.035317 CTACTGCTGTGCTGGACCAA 59.965 55.000 6.48 0.0 0.00 3.67 F
226 227 1.135333 TGCTGGACCAAAACGAAAACC 59.865 47.619 0.00 0.0 0.00 3.27 F
726 746 1.170919 CCTGCTGATGGCTATGGTGC 61.171 60.000 0.00 0.0 42.39 5.01 F
2133 2153 1.654954 CTGCAGCCACATCCAAGAGC 61.655 60.000 0.00 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1703 1.446907 AAGCTTCAGCAACATCCTCG 58.553 50.000 0.75 0.0 45.16 4.63 R
2181 2201 3.189606 ACCACCAATCCATCCAGTCTTA 58.810 45.455 0.00 0.0 0.00 2.10 R
2649 2669 5.104360 ACTCTTCCACCTGCATTGTATGTAT 60.104 40.000 0.00 0.0 0.00 2.29 R
3906 3932 0.322997 CCCATGCTTTGTAACCCGGA 60.323 55.000 0.73 0.0 0.00 5.14 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
20 21 2.907910 CAACTTTGCTCCGAGAATGG 57.092 50.000 0.00 0.00 0.00 3.16
21 22 1.470098 CAACTTTGCTCCGAGAATGGG 59.530 52.381 0.00 0.00 33.92 4.00
22 23 0.693049 ACTTTGCTCCGAGAATGGGT 59.307 50.000 0.00 0.00 34.48 4.51
23 24 1.339151 ACTTTGCTCCGAGAATGGGTC 60.339 52.381 0.00 0.00 34.48 4.46
24 25 0.391130 TTTGCTCCGAGAATGGGTCG 60.391 55.000 0.00 0.00 34.48 4.79
25 26 1.254975 TTGCTCCGAGAATGGGTCGA 61.255 55.000 0.00 0.00 39.92 4.20
26 27 1.066587 GCTCCGAGAATGGGTCGAG 59.933 63.158 0.00 0.00 39.92 4.04
27 28 1.736586 CTCCGAGAATGGGTCGAGG 59.263 63.158 0.00 0.00 39.92 4.63
28 29 2.107141 CCGAGAATGGGTCGAGGC 59.893 66.667 0.00 0.00 39.92 4.70
29 30 2.278857 CGAGAATGGGTCGAGGCG 60.279 66.667 0.00 0.00 39.92 5.52
30 31 2.107141 GAGAATGGGTCGAGGCGG 59.893 66.667 0.00 0.00 0.00 6.13
31 32 2.363795 AGAATGGGTCGAGGCGGA 60.364 61.111 0.00 0.00 0.00 5.54
32 33 2.202892 GAATGGGTCGAGGCGGAC 60.203 66.667 3.53 3.53 36.18 4.79
33 34 3.000819 AATGGGTCGAGGCGGACA 61.001 61.111 12.59 0.00 38.70 4.02
34 35 2.515996 GAATGGGTCGAGGCGGACAA 62.516 60.000 12.59 2.48 38.70 3.18
35 36 2.521958 AATGGGTCGAGGCGGACAAG 62.522 60.000 12.59 0.00 38.70 3.16
36 37 3.379445 GGGTCGAGGCGGACAAGA 61.379 66.667 12.59 0.00 38.70 3.02
37 38 2.654877 GGTCGAGGCGGACAAGAA 59.345 61.111 12.59 0.00 38.70 2.52
38 39 1.005394 GGTCGAGGCGGACAAGAAA 60.005 57.895 12.59 0.00 38.70 2.52
39 40 1.289800 GGTCGAGGCGGACAAGAAAC 61.290 60.000 12.59 0.00 38.70 2.78
40 41 1.005394 TCGAGGCGGACAAGAAACC 60.005 57.895 0.00 0.00 0.00 3.27
68 69 3.706600 TTTTAGGACAGGGTTATGCGT 57.293 42.857 0.00 0.00 0.00 5.24
69 70 3.706600 TTTAGGACAGGGTTATGCGTT 57.293 42.857 0.00 0.00 0.00 4.84
70 71 2.684001 TAGGACAGGGTTATGCGTTG 57.316 50.000 0.00 0.00 0.00 4.10
71 72 0.035439 AGGACAGGGTTATGCGTTGG 60.035 55.000 0.00 0.00 0.00 3.77
72 73 1.029947 GGACAGGGTTATGCGTTGGG 61.030 60.000 0.00 0.00 0.00 4.12
73 74 0.035820 GACAGGGTTATGCGTTGGGA 60.036 55.000 0.00 0.00 0.00 4.37
74 75 0.322187 ACAGGGTTATGCGTTGGGAC 60.322 55.000 0.00 0.00 0.00 4.46
85 86 1.421382 CGTTGGGACGTTTCGTATGT 58.579 50.000 0.00 0.00 44.08 2.29
86 87 1.794116 CGTTGGGACGTTTCGTATGTT 59.206 47.619 0.00 0.00 44.08 2.71
87 88 2.159934 CGTTGGGACGTTTCGTATGTTC 60.160 50.000 0.00 0.00 44.08 3.18
88 89 1.700523 TGGGACGTTTCGTATGTTCG 58.299 50.000 0.00 0.00 41.37 3.95
89 90 1.000385 TGGGACGTTTCGTATGTTCGT 60.000 47.619 0.00 0.00 41.37 3.85
90 91 2.061028 GGGACGTTTCGTATGTTCGTT 58.939 47.619 0.00 0.00 41.37 3.85
91 92 2.476241 GGGACGTTTCGTATGTTCGTTT 59.524 45.455 0.00 0.00 41.37 3.60
92 93 3.059665 GGGACGTTTCGTATGTTCGTTTT 60.060 43.478 0.00 0.00 41.37 2.43
93 94 4.149747 GGGACGTTTCGTATGTTCGTTTTA 59.850 41.667 0.00 0.00 41.37 1.52
94 95 5.163963 GGGACGTTTCGTATGTTCGTTTTAT 60.164 40.000 0.00 0.00 41.37 1.40
95 96 5.948085 GGACGTTTCGTATGTTCGTTTTATC 59.052 40.000 0.00 0.00 41.37 1.75
96 97 6.183360 GGACGTTTCGTATGTTCGTTTTATCT 60.183 38.462 0.00 0.00 41.37 1.98
97 98 6.745392 ACGTTTCGTATGTTCGTTTTATCTC 58.255 36.000 0.00 0.00 38.73 2.75
98 99 6.363088 ACGTTTCGTATGTTCGTTTTATCTCA 59.637 34.615 0.00 0.00 38.73 3.27
99 100 7.096106 ACGTTTCGTATGTTCGTTTTATCTCAA 60.096 33.333 0.00 0.00 38.73 3.02
100 101 7.736880 CGTTTCGTATGTTCGTTTTATCTCAAA 59.263 33.333 0.00 0.00 0.00 2.69
101 102 8.824779 GTTTCGTATGTTCGTTTTATCTCAAAC 58.175 33.333 0.00 0.00 33.90 2.93
109 110 4.079665 GTTTTATCTCAAACGGACAGCC 57.920 45.455 0.00 0.00 0.00 4.85
110 111 2.396590 TTATCTCAAACGGACAGCCC 57.603 50.000 0.00 0.00 0.00 5.19
111 112 1.271856 TATCTCAAACGGACAGCCCA 58.728 50.000 0.00 0.00 34.14 5.36
112 113 0.400213 ATCTCAAACGGACAGCCCAA 59.600 50.000 0.00 0.00 34.14 4.12
113 114 0.181587 TCTCAAACGGACAGCCCAAA 59.818 50.000 0.00 0.00 34.14 3.28
114 115 1.202879 TCTCAAACGGACAGCCCAAAT 60.203 47.619 0.00 0.00 34.14 2.32
115 116 2.039216 TCTCAAACGGACAGCCCAAATA 59.961 45.455 0.00 0.00 34.14 1.40
116 117 2.817258 CTCAAACGGACAGCCCAAATAA 59.183 45.455 0.00 0.00 34.14 1.40
117 118 3.426615 TCAAACGGACAGCCCAAATAAT 58.573 40.909 0.00 0.00 34.14 1.28
118 119 3.829601 TCAAACGGACAGCCCAAATAATT 59.170 39.130 0.00 0.00 34.14 1.40
119 120 4.282195 TCAAACGGACAGCCCAAATAATTT 59.718 37.500 0.00 0.00 34.14 1.82
120 121 3.866883 ACGGACAGCCCAAATAATTTG 57.133 42.857 0.00 0.00 40.32 2.32
121 122 3.426615 ACGGACAGCCCAAATAATTTGA 58.573 40.909 0.00 0.00 43.26 2.69
122 123 3.443681 ACGGACAGCCCAAATAATTTGAG 59.556 43.478 0.00 0.00 43.26 3.02
123 124 3.181487 CGGACAGCCCAAATAATTTGAGG 60.181 47.826 0.00 0.00 43.26 3.86
124 125 3.769300 GGACAGCCCAAATAATTTGAGGT 59.231 43.478 0.00 0.00 43.26 3.85
125 126 4.142160 GGACAGCCCAAATAATTTGAGGTC 60.142 45.833 0.00 0.00 43.26 3.85
126 127 3.443681 ACAGCCCAAATAATTTGAGGTCG 59.556 43.478 0.00 0.00 43.26 4.79
127 128 3.443681 CAGCCCAAATAATTTGAGGTCGT 59.556 43.478 0.00 0.00 43.26 4.34
128 129 3.443681 AGCCCAAATAATTTGAGGTCGTG 59.556 43.478 0.00 0.00 43.26 4.35
129 130 3.769536 CCCAAATAATTTGAGGTCGTGC 58.230 45.455 0.00 0.00 43.26 5.34
130 131 3.425404 CCAAATAATTTGAGGTCGTGCG 58.575 45.455 0.00 0.00 43.26 5.34
131 132 3.425404 CAAATAATTTGAGGTCGTGCGG 58.575 45.455 0.00 0.00 43.26 5.69
132 133 2.396590 ATAATTTGAGGTCGTGCGGT 57.603 45.000 0.00 0.00 0.00 5.68
133 134 1.434555 TAATTTGAGGTCGTGCGGTG 58.565 50.000 0.00 0.00 0.00 4.94
134 135 1.234615 AATTTGAGGTCGTGCGGTGG 61.235 55.000 0.00 0.00 0.00 4.61
135 136 2.107041 ATTTGAGGTCGTGCGGTGGA 62.107 55.000 0.00 0.00 0.00 4.02
136 137 2.709125 TTTGAGGTCGTGCGGTGGAG 62.709 60.000 0.00 0.00 0.00 3.86
137 138 3.681835 GAGGTCGTGCGGTGGAGT 61.682 66.667 0.00 0.00 0.00 3.85
138 139 3.222354 GAGGTCGTGCGGTGGAGTT 62.222 63.158 0.00 0.00 0.00 3.01
139 140 3.041940 GGTCGTGCGGTGGAGTTG 61.042 66.667 0.00 0.00 0.00 3.16
140 141 3.041940 GTCGTGCGGTGGAGTTGG 61.042 66.667 0.00 0.00 0.00 3.77
141 142 4.980805 TCGTGCGGTGGAGTTGGC 62.981 66.667 0.00 0.00 0.00 4.52
143 144 4.643387 GTGCGGTGGAGTTGGCCT 62.643 66.667 3.32 0.00 0.00 5.19
144 145 4.329545 TGCGGTGGAGTTGGCCTC 62.330 66.667 3.32 0.00 39.67 4.70
145 146 4.329545 GCGGTGGAGTTGGCCTCA 62.330 66.667 3.32 0.00 42.40 3.86
146 147 2.358737 CGGTGGAGTTGGCCTCAC 60.359 66.667 3.32 0.00 42.40 3.51
147 148 2.358737 GGTGGAGTTGGCCTCACG 60.359 66.667 3.32 0.00 42.40 4.35
148 149 2.358737 GTGGAGTTGGCCTCACGG 60.359 66.667 3.32 0.00 42.40 4.94
149 150 2.847234 TGGAGTTGGCCTCACGGT 60.847 61.111 3.32 0.00 42.40 4.83
150 151 1.534476 TGGAGTTGGCCTCACGGTA 60.534 57.895 3.32 0.00 42.40 4.02
151 152 1.218316 GGAGTTGGCCTCACGGTAG 59.782 63.158 3.32 0.00 42.40 3.18
152 153 1.448013 GAGTTGGCCTCACGGTAGC 60.448 63.158 3.32 0.00 40.17 3.58
216 217 0.035317 CTACTGCTGTGCTGGACCAA 59.965 55.000 6.48 0.00 0.00 3.67
226 227 1.135333 TGCTGGACCAAAACGAAAACC 59.865 47.619 0.00 0.00 0.00 3.27
383 391 1.490574 AGATTCTCCTTCGACCCCTG 58.509 55.000 0.00 0.00 0.00 4.45
437 445 4.637489 CGCGCCAGATCTCCTCCG 62.637 72.222 0.00 0.00 0.00 4.63
493 501 2.606519 CCGGTGAGTCCCCTTCCA 60.607 66.667 0.00 0.00 0.00 3.53
726 746 1.170919 CCTGCTGATGGCTATGGTGC 61.171 60.000 0.00 0.00 42.39 5.01
908 928 3.439440 GGAGGTGCCTTGTTTTCCT 57.561 52.632 0.00 0.00 0.00 3.36
909 929 2.579410 GGAGGTGCCTTGTTTTCCTA 57.421 50.000 0.00 0.00 0.00 2.94
910 930 2.437413 GGAGGTGCCTTGTTTTCCTAG 58.563 52.381 0.00 0.00 0.00 3.02
911 931 2.224793 GGAGGTGCCTTGTTTTCCTAGT 60.225 50.000 0.00 0.00 0.00 2.57
924 944 9.420551 CTTGTTTTCCTAGTAGTAACTTCGATT 57.579 33.333 0.00 0.00 37.15 3.34
1290 1310 5.586243 CCAGACTCATGTGGATAATTCGTTT 59.414 40.000 0.00 0.00 42.06 3.60
2133 2153 1.654954 CTGCAGCCACATCCAAGAGC 61.655 60.000 0.00 0.00 0.00 4.09
2181 2201 7.937394 GCCACCTACAAGTTCTTAATATATGGT 59.063 37.037 0.00 0.00 0.00 3.55
2202 2222 1.673767 AGACTGGATGGATTGGTGGT 58.326 50.000 0.00 0.00 0.00 4.16
2256 2276 7.148069 GGCATACCTTATGAATATGGTAAAGGC 60.148 40.741 15.32 16.88 42.62 4.35
2627 2647 5.551760 AACACATATCCTTTTGCTTCTCG 57.448 39.130 0.00 0.00 0.00 4.04
2885 2906 3.490761 GCATATGGAATTTCACCAACCCG 60.491 47.826 4.56 0.00 40.93 5.28
2939 2960 5.506730 TGTACAAGGAATACATCAACCCA 57.493 39.130 0.00 0.00 0.00 4.51
2996 3017 1.749063 GCCAAGGTTATAGTTGCACCC 59.251 52.381 0.00 0.00 0.00 4.61
3117 3138 8.846211 CAAACAGGAAGGTTTCTACTAATTGAA 58.154 33.333 0.00 0.00 38.86 2.69
3142 3163 2.232208 TCATGTGACACAGGTCTGCTAG 59.768 50.000 18.87 0.00 44.61 3.42
3153 3174 4.141824 ACAGGTCTGCTAGAAGCTATTTCC 60.142 45.833 0.00 0.00 42.97 3.13
3194 3215 0.242017 GTGGCAGCTGTGGTCAATTC 59.758 55.000 16.64 0.00 0.00 2.17
3195 3216 0.895100 TGGCAGCTGTGGTCAATTCC 60.895 55.000 16.64 4.90 0.00 3.01
3259 3280 4.141680 CGCATTACGTTTCACTTGAGAAC 58.858 43.478 0.00 0.00 36.87 3.01
3260 3281 4.318475 CGCATTACGTTTCACTTGAGAACA 60.318 41.667 0.00 0.00 36.87 3.18
3261 3282 5.140177 GCATTACGTTTCACTTGAGAACAG 58.860 41.667 0.00 0.00 0.00 3.16
3262 3283 5.050363 GCATTACGTTTCACTTGAGAACAGA 60.050 40.000 0.00 0.00 0.00 3.41
3263 3284 6.347725 GCATTACGTTTCACTTGAGAACAGAT 60.348 38.462 0.00 0.00 0.00 2.90
3264 3285 6.764877 TTACGTTTCACTTGAGAACAGATC 57.235 37.500 0.00 0.00 0.00 2.75
3265 3286 4.950050 ACGTTTCACTTGAGAACAGATCT 58.050 39.130 0.00 0.00 42.61 2.75
3266 3287 5.360591 ACGTTTCACTTGAGAACAGATCTT 58.639 37.500 0.00 0.00 38.96 2.40
3267 3288 6.513180 ACGTTTCACTTGAGAACAGATCTTA 58.487 36.000 0.00 0.00 38.96 2.10
3268 3289 6.984474 ACGTTTCACTTGAGAACAGATCTTAA 59.016 34.615 0.00 0.00 38.96 1.85
3269 3290 7.494625 ACGTTTCACTTGAGAACAGATCTTAAA 59.505 33.333 0.00 0.00 38.96 1.52
3270 3291 8.335356 CGTTTCACTTGAGAACAGATCTTAAAA 58.665 33.333 0.00 0.00 38.96 1.52
3313 3334 4.584638 TTGTTGGCCTGGTTATCTATGT 57.415 40.909 3.32 0.00 0.00 2.29
3411 3432 6.692232 TTACGTGTTGTTTTTCTTGGTTTG 57.308 33.333 0.00 0.00 0.00 2.93
3487 3508 6.035327 GGTTCATATTTGAAGTTTGCATCAGC 59.965 38.462 0.00 0.00 42.41 4.26
3566 3587 1.153549 CTGTAAGCTCCTGTCGGCC 60.154 63.158 0.00 0.00 0.00 6.13
3572 3593 2.342279 CTCCTGTCGGCCGTCAAA 59.658 61.111 27.15 15.21 0.00 2.69
3573 3594 1.301401 CTCCTGTCGGCCGTCAAAA 60.301 57.895 27.15 14.85 0.00 2.44
3619 3640 6.976925 GCTGAATTATTTGCTTGCAGTAGATT 59.023 34.615 0.00 0.00 0.00 2.40
3684 3705 3.942130 AGATTAGTTTTTGGTGCAGGC 57.058 42.857 0.00 0.00 0.00 4.85
3687 3708 2.356665 TAGTTTTTGGTGCAGGCTGA 57.643 45.000 20.86 0.00 0.00 4.26
3710 3731 0.947244 CGTTGCCAGAGCTTGTCTTT 59.053 50.000 0.00 0.00 40.80 2.52
3713 3734 1.609208 TGCCAGAGCTTGTCTTTTCC 58.391 50.000 0.00 0.00 40.80 3.13
3739 3761 6.262944 TGCTCCACAAACATAATGATCATACC 59.737 38.462 9.04 0.00 0.00 2.73
3838 3860 0.110010 GCGCTTGAAACCTCTCTTGC 60.110 55.000 0.00 0.00 0.00 4.01
3843 3865 0.321671 TGAAACCTCTCTTGCTCGGG 59.678 55.000 0.00 0.00 0.00 5.14
3844 3866 0.391793 GAAACCTCTCTTGCTCGGGG 60.392 60.000 0.00 0.00 0.00 5.73
3846 3868 2.364317 CCTCTCTTGCTCGGGGGA 60.364 66.667 0.00 0.00 0.00 4.81
3847 3869 1.764054 CCTCTCTTGCTCGGGGGAT 60.764 63.158 0.00 0.00 0.00 3.85
3848 3870 0.470080 CCTCTCTTGCTCGGGGGATA 60.470 60.000 0.00 0.00 0.00 2.59
3849 3871 0.676736 CTCTCTTGCTCGGGGGATAC 59.323 60.000 0.00 0.00 0.00 2.24
3891 3917 0.690762 AGTGGGCTATGTTTGGTCGT 59.309 50.000 0.00 0.00 0.00 4.34
3906 3932 1.550976 GGTCGTGTGGGAGAGATTTCT 59.449 52.381 0.00 0.00 36.01 2.52
3990 4016 1.178534 ACACCATTTGGCACTTCGGG 61.179 55.000 0.00 0.00 39.32 5.14
3993 4019 0.684153 CCATTTGGCACTTCGGGGAT 60.684 55.000 0.00 0.00 0.00 3.85
4009 4035 1.119574 GGATTAGGCTGGGCTCCGTA 61.120 60.000 0.00 0.00 0.00 4.02
4020 4046 3.165559 GCTCCGTAGCTGTCGTATG 57.834 57.895 0.00 0.00 45.85 2.39
4051 4078 7.148052 TGGAAAGAGAACTAGATAGAAACGAGG 60.148 40.741 0.00 0.00 0.00 4.63
4070 4097 1.302033 CAGTCTTCAACAGCCGGCT 60.302 57.895 27.08 27.08 0.00 5.52
4073 4100 0.884704 GTCTTCAACAGCCGGCTCAA 60.885 55.000 30.29 15.81 0.00 3.02
4089 4116 2.733227 GCTCAAATTCACCAGGCAATCG 60.733 50.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.470098 CCCATTCTCGGAGCAAAGTTG 59.530 52.381 0.00 0.00 0.00 3.16
2 3 1.073923 ACCCATTCTCGGAGCAAAGTT 59.926 47.619 0.00 0.00 0.00 2.66
3 4 0.693049 ACCCATTCTCGGAGCAAAGT 59.307 50.000 0.00 0.00 0.00 2.66
4 5 1.373570 GACCCATTCTCGGAGCAAAG 58.626 55.000 0.00 0.00 0.00 2.77
5 6 0.391130 CGACCCATTCTCGGAGCAAA 60.391 55.000 0.00 0.00 0.00 3.68
6 7 1.218047 CGACCCATTCTCGGAGCAA 59.782 57.895 0.00 0.00 0.00 3.91
7 8 1.667154 CTCGACCCATTCTCGGAGCA 61.667 60.000 0.00 0.00 0.00 4.26
8 9 1.066587 CTCGACCCATTCTCGGAGC 59.933 63.158 0.00 0.00 0.00 4.70
9 10 1.736586 CCTCGACCCATTCTCGGAG 59.263 63.158 0.00 0.00 0.00 4.63
10 11 2.423898 GCCTCGACCCATTCTCGGA 61.424 63.158 0.00 0.00 0.00 4.55
11 12 2.107141 GCCTCGACCCATTCTCGG 59.893 66.667 0.00 0.00 0.00 4.63
12 13 2.278857 CGCCTCGACCCATTCTCG 60.279 66.667 0.00 0.00 0.00 4.04
13 14 2.107141 CCGCCTCGACCCATTCTC 59.893 66.667 0.00 0.00 0.00 2.87
14 15 2.363795 TCCGCCTCGACCCATTCT 60.364 61.111 0.00 0.00 0.00 2.40
15 16 2.202892 GTCCGCCTCGACCCATTC 60.203 66.667 0.00 0.00 0.00 2.67
16 17 2.521958 CTTGTCCGCCTCGACCCATT 62.522 60.000 0.00 0.00 31.35 3.16
17 18 3.000819 TTGTCCGCCTCGACCCAT 61.001 61.111 0.00 0.00 31.35 4.00
18 19 3.691342 CTTGTCCGCCTCGACCCA 61.691 66.667 0.00 0.00 31.35 4.51
19 20 2.444700 TTTCTTGTCCGCCTCGACCC 62.445 60.000 0.00 0.00 31.35 4.46
20 21 1.005394 TTTCTTGTCCGCCTCGACC 60.005 57.895 0.00 0.00 31.35 4.79
21 22 1.289800 GGTTTCTTGTCCGCCTCGAC 61.290 60.000 0.00 0.00 0.00 4.20
22 23 1.005394 GGTTTCTTGTCCGCCTCGA 60.005 57.895 0.00 0.00 0.00 4.04
23 24 2.380410 CGGTTTCTTGTCCGCCTCG 61.380 63.158 0.00 0.00 40.28 4.63
24 25 1.005394 TCGGTTTCTTGTCCGCCTC 60.005 57.895 0.00 0.00 45.44 4.70
25 26 1.301479 GTCGGTTTCTTGTCCGCCT 60.301 57.895 0.00 0.00 45.44 5.52
26 27 0.953960 ATGTCGGTTTCTTGTCCGCC 60.954 55.000 0.00 0.00 45.44 6.13
27 28 0.872388 AATGTCGGTTTCTTGTCCGC 59.128 50.000 0.00 0.00 45.44 5.54
28 29 3.619233 AAAATGTCGGTTTCTTGTCCG 57.381 42.857 0.00 0.00 46.93 4.79
47 48 4.023726 ACGCATAACCCTGTCCTAAAAA 57.976 40.909 0.00 0.00 0.00 1.94
48 49 3.706600 ACGCATAACCCTGTCCTAAAA 57.293 42.857 0.00 0.00 0.00 1.52
49 50 3.340034 CAACGCATAACCCTGTCCTAAA 58.660 45.455 0.00 0.00 0.00 1.85
50 51 2.355310 CCAACGCATAACCCTGTCCTAA 60.355 50.000 0.00 0.00 0.00 2.69
51 52 1.208535 CCAACGCATAACCCTGTCCTA 59.791 52.381 0.00 0.00 0.00 2.94
52 53 0.035439 CCAACGCATAACCCTGTCCT 60.035 55.000 0.00 0.00 0.00 3.85
53 54 1.029947 CCCAACGCATAACCCTGTCC 61.030 60.000 0.00 0.00 0.00 4.02
54 55 0.035820 TCCCAACGCATAACCCTGTC 60.036 55.000 0.00 0.00 0.00 3.51
55 56 0.322187 GTCCCAACGCATAACCCTGT 60.322 55.000 0.00 0.00 0.00 4.00
56 57 1.366111 CGTCCCAACGCATAACCCTG 61.366 60.000 0.00 0.00 42.82 4.45
57 58 1.078708 CGTCCCAACGCATAACCCT 60.079 57.895 0.00 0.00 42.82 4.34
58 59 3.493213 CGTCCCAACGCATAACCC 58.507 61.111 0.00 0.00 42.82 4.11
66 67 5.505050 CGAACATACGAAACGTCCCAACG 62.505 52.174 0.00 0.00 44.18 4.10
67 68 2.159934 CGAACATACGAAACGTCCCAAC 60.160 50.000 0.00 0.00 41.54 3.77
68 69 2.060284 CGAACATACGAAACGTCCCAA 58.940 47.619 0.00 0.00 41.54 4.12
69 70 1.000385 ACGAACATACGAAACGTCCCA 60.000 47.619 0.00 0.00 41.54 4.37
70 71 1.701704 ACGAACATACGAAACGTCCC 58.298 50.000 0.00 0.00 41.54 4.46
71 72 3.776043 AAACGAACATACGAAACGTCC 57.224 42.857 0.00 0.00 41.54 4.79
72 73 6.745392 AGATAAAACGAACATACGAAACGTC 58.255 36.000 0.00 0.00 41.54 4.34
73 74 6.363088 TGAGATAAAACGAACATACGAAACGT 59.637 34.615 1.91 1.91 44.35 3.99
74 75 6.744418 TGAGATAAAACGAACATACGAAACG 58.256 36.000 0.00 0.00 37.03 3.60
75 76 8.824779 GTTTGAGATAAAACGAACATACGAAAC 58.175 33.333 0.00 0.00 37.03 2.78
76 77 8.922738 GTTTGAGATAAAACGAACATACGAAA 57.077 30.769 0.00 0.00 37.03 3.46
88 89 3.119955 GGGCTGTCCGTTTGAGATAAAAC 60.120 47.826 0.00 0.00 36.81 2.43
89 90 3.078837 GGGCTGTCCGTTTGAGATAAAA 58.921 45.455 0.00 0.00 0.00 1.52
90 91 2.039216 TGGGCTGTCCGTTTGAGATAAA 59.961 45.455 0.00 0.00 38.76 1.40
91 92 1.626321 TGGGCTGTCCGTTTGAGATAA 59.374 47.619 0.00 0.00 38.76 1.75
92 93 1.271856 TGGGCTGTCCGTTTGAGATA 58.728 50.000 0.00 0.00 38.76 1.98
93 94 0.400213 TTGGGCTGTCCGTTTGAGAT 59.600 50.000 0.00 0.00 38.76 2.75
94 95 0.181587 TTTGGGCTGTCCGTTTGAGA 59.818 50.000 0.00 0.00 38.76 3.27
95 96 1.247567 ATTTGGGCTGTCCGTTTGAG 58.752 50.000 0.00 0.00 38.76 3.02
96 97 2.570415 TATTTGGGCTGTCCGTTTGA 57.430 45.000 0.00 0.00 38.76 2.69
97 98 3.866883 ATTATTTGGGCTGTCCGTTTG 57.133 42.857 0.00 0.00 38.76 2.93
98 99 4.282195 TCAAATTATTTGGGCTGTCCGTTT 59.718 37.500 16.42 0.00 40.98 3.60
99 100 3.829601 TCAAATTATTTGGGCTGTCCGTT 59.170 39.130 16.42 0.00 40.98 4.44
100 101 3.426615 TCAAATTATTTGGGCTGTCCGT 58.573 40.909 16.42 0.00 40.98 4.69
101 102 3.181487 CCTCAAATTATTTGGGCTGTCCG 60.181 47.826 16.42 0.00 39.84 4.79
102 103 3.769300 ACCTCAAATTATTTGGGCTGTCC 59.231 43.478 16.42 0.00 39.84 4.02
103 104 4.438744 CGACCTCAAATTATTTGGGCTGTC 60.439 45.833 16.42 14.69 39.84 3.51
104 105 3.443681 CGACCTCAAATTATTTGGGCTGT 59.556 43.478 16.42 8.24 39.84 4.40
105 106 3.443681 ACGACCTCAAATTATTTGGGCTG 59.556 43.478 16.42 13.52 39.84 4.85
106 107 3.443681 CACGACCTCAAATTATTTGGGCT 59.556 43.478 16.42 1.48 39.84 5.19
107 108 3.769536 CACGACCTCAAATTATTTGGGC 58.230 45.455 16.42 4.08 39.84 5.36
108 109 3.730662 CGCACGACCTCAAATTATTTGGG 60.731 47.826 16.42 13.54 40.86 4.12
109 110 3.425404 CGCACGACCTCAAATTATTTGG 58.575 45.455 16.42 5.33 40.98 3.28
110 111 3.119990 ACCGCACGACCTCAAATTATTTG 60.120 43.478 11.12 11.12 41.96 2.32
111 112 3.078837 ACCGCACGACCTCAAATTATTT 58.921 40.909 0.00 0.00 0.00 1.40
112 113 2.418628 CACCGCACGACCTCAAATTATT 59.581 45.455 0.00 0.00 0.00 1.40
113 114 2.006888 CACCGCACGACCTCAAATTAT 58.993 47.619 0.00 0.00 0.00 1.28
114 115 1.434555 CACCGCACGACCTCAAATTA 58.565 50.000 0.00 0.00 0.00 1.40
115 116 1.234615 CCACCGCACGACCTCAAATT 61.235 55.000 0.00 0.00 0.00 1.82
116 117 1.671054 CCACCGCACGACCTCAAAT 60.671 57.895 0.00 0.00 0.00 2.32
117 118 2.280524 CCACCGCACGACCTCAAA 60.281 61.111 0.00 0.00 0.00 2.69
118 119 3.220999 CTCCACCGCACGACCTCAA 62.221 63.158 0.00 0.00 0.00 3.02
119 120 3.680786 CTCCACCGCACGACCTCA 61.681 66.667 0.00 0.00 0.00 3.86
120 121 3.222354 AACTCCACCGCACGACCTC 62.222 63.158 0.00 0.00 0.00 3.85
121 122 3.231736 AACTCCACCGCACGACCT 61.232 61.111 0.00 0.00 0.00 3.85
122 123 3.041940 CAACTCCACCGCACGACC 61.042 66.667 0.00 0.00 0.00 4.79
123 124 3.041940 CCAACTCCACCGCACGAC 61.042 66.667 0.00 0.00 0.00 4.34
124 125 4.980805 GCCAACTCCACCGCACGA 62.981 66.667 0.00 0.00 0.00 4.35
126 127 4.643387 AGGCCAACTCCACCGCAC 62.643 66.667 5.01 0.00 0.00 5.34
127 128 4.329545 GAGGCCAACTCCACCGCA 62.330 66.667 5.01 0.00 40.49 5.69
128 129 4.329545 TGAGGCCAACTCCACCGC 62.330 66.667 5.01 0.00 46.01 5.68
129 130 2.358737 GTGAGGCCAACTCCACCG 60.359 66.667 5.01 0.00 46.01 4.94
130 131 2.358737 CGTGAGGCCAACTCCACC 60.359 66.667 5.01 0.00 46.01 4.61
142 143 1.320344 TGGCTACTGGCTACCGTGAG 61.320 60.000 0.00 0.00 41.46 3.51
143 144 1.304630 TGGCTACTGGCTACCGTGA 60.305 57.895 0.00 0.00 41.46 4.35
144 145 1.141881 CTGGCTACTGGCTACCGTG 59.858 63.158 0.00 0.00 41.46 4.94
145 146 2.058595 CCTGGCTACTGGCTACCGT 61.059 63.158 0.00 0.00 41.46 4.83
146 147 2.017559 GACCTGGCTACTGGCTACCG 62.018 65.000 0.00 0.00 41.46 4.02
147 148 1.823976 GACCTGGCTACTGGCTACC 59.176 63.158 0.00 0.00 41.46 3.18
148 149 1.437986 CGACCTGGCTACTGGCTAC 59.562 63.158 0.00 0.00 41.46 3.58
149 150 2.423898 GCGACCTGGCTACTGGCTA 61.424 63.158 0.00 0.00 41.46 3.93
150 151 3.775654 GCGACCTGGCTACTGGCT 61.776 66.667 0.00 0.00 41.46 4.75
151 152 3.775654 AGCGACCTGGCTACTGGC 61.776 66.667 0.00 0.00 42.62 4.85
152 153 2.185350 CAGCGACCTGGCTACTGG 59.815 66.667 0.00 0.00 42.53 4.00
216 217 2.235891 GTCCCATCCTGGTTTTCGTTT 58.764 47.619 0.00 0.00 35.17 3.60
383 391 2.586357 GTCGCCTTGGAGATCGGC 60.586 66.667 0.00 0.00 40.40 5.54
589 597 4.041723 GTGAAACCACAACCGAATTCTTG 58.958 43.478 3.52 4.97 34.76 3.02
786 806 9.600432 AGGCTATGTAGTAGTAGTAGTAGTAGT 57.400 37.037 5.34 5.34 32.72 2.73
787 807 9.859427 CAGGCTATGTAGTAGTAGTAGTAGTAG 57.141 40.741 0.49 1.45 32.72 2.57
788 808 8.310382 GCAGGCTATGTAGTAGTAGTAGTAGTA 58.690 40.741 0.00 0.00 32.72 1.82
789 809 7.016465 AGCAGGCTATGTAGTAGTAGTAGTAGT 59.984 40.741 0.00 0.00 32.72 2.73
790 810 7.332430 CAGCAGGCTATGTAGTAGTAGTAGTAG 59.668 44.444 0.00 0.00 32.72 2.57
791 811 7.015974 TCAGCAGGCTATGTAGTAGTAGTAGTA 59.984 40.741 0.00 0.00 32.72 1.82
792 812 5.998981 CAGCAGGCTATGTAGTAGTAGTAGT 59.001 44.000 0.00 0.00 32.72 2.73
793 813 6.231951 TCAGCAGGCTATGTAGTAGTAGTAG 58.768 44.000 0.00 0.00 32.72 2.57
794 814 6.183810 TCAGCAGGCTATGTAGTAGTAGTA 57.816 41.667 0.00 0.00 32.72 1.82
795 815 5.050126 TCAGCAGGCTATGTAGTAGTAGT 57.950 43.478 0.00 0.00 32.72 2.73
796 816 5.105957 CCATCAGCAGGCTATGTAGTAGTAG 60.106 48.000 0.00 0.00 32.72 2.57
797 817 4.767409 CCATCAGCAGGCTATGTAGTAGTA 59.233 45.833 0.00 0.00 32.72 1.82
798 818 3.576118 CCATCAGCAGGCTATGTAGTAGT 59.424 47.826 0.00 0.00 32.72 2.73
799 819 4.185467 CCATCAGCAGGCTATGTAGTAG 57.815 50.000 0.00 0.00 0.00 2.57
894 914 6.228995 AGTTACTACTAGGAAAACAAGGCAC 58.771 40.000 0.00 0.00 31.21 5.01
1290 1310 3.295093 TGTGAACTCAAAGGAATTGCCA 58.705 40.909 0.00 0.00 38.98 4.92
1683 1703 1.446907 AAGCTTCAGCAACATCCTCG 58.553 50.000 0.75 0.00 45.16 4.63
1917 1937 3.913799 TCTTCAAACCCTCTTCCCATGTA 59.086 43.478 0.00 0.00 0.00 2.29
2181 2201 3.189606 ACCACCAATCCATCCAGTCTTA 58.810 45.455 0.00 0.00 0.00 2.10
2202 2222 6.183360 GCTTCTCACATATCTTCCCAAGTAGA 60.183 42.308 0.00 0.00 0.00 2.59
2649 2669 5.104360 ACTCTTCCACCTGCATTGTATGTAT 60.104 40.000 0.00 0.00 0.00 2.29
2939 2960 3.199946 TGAAGTTGGTCCACTTGAAGTCT 59.800 43.478 10.35 0.00 37.11 3.24
2996 3017 3.300009 GTCCATTTCGTTGTTGCTTCTG 58.700 45.455 0.00 0.00 0.00 3.02
3117 3138 3.867600 GCAGACCTGTGTCACATGAATCT 60.868 47.826 14.35 8.46 44.33 2.40
3153 3174 9.793252 GCCACCATGAAATATATTAGCTAATTG 57.207 33.333 23.47 12.76 0.00 2.32
3170 3191 2.034532 CCACAGCTGCCACCATGA 59.965 61.111 15.27 0.00 0.00 3.07
3194 3215 2.346766 TGCCTGCTATACCACAATGG 57.653 50.000 0.00 0.00 45.02 3.16
3195 3216 4.388485 TGTATGCCTGCTATACCACAATG 58.612 43.478 0.00 0.00 31.53 2.82
3240 3261 7.155328 AGATCTGTTCTCAAGTGAAACGTAAT 58.845 34.615 0.00 0.00 45.86 1.89
3244 3265 5.914085 AAGATCTGTTCTCAAGTGAAACG 57.086 39.130 0.00 0.00 35.96 3.60
3259 3280 9.265901 CCACCACTACATAGATTTTAAGATCTG 57.734 37.037 16.70 6.30 37.01 2.90
3260 3281 9.213777 TCCACCACTACATAGATTTTAAGATCT 57.786 33.333 12.68 12.68 39.59 2.75
3267 3288 9.920946 AAACATATCCACCACTACATAGATTTT 57.079 29.630 0.00 0.00 0.00 1.82
3268 3289 9.342308 CAAACATATCCACCACTACATAGATTT 57.658 33.333 0.00 0.00 0.00 2.17
3269 3290 8.494433 ACAAACATATCCACCACTACATAGATT 58.506 33.333 0.00 0.00 0.00 2.40
3270 3291 8.034313 ACAAACATATCCACCACTACATAGAT 57.966 34.615 0.00 0.00 0.00 1.98
3411 3432 6.038603 TCTGCCAATACAAACTTCAGATATGC 59.961 38.462 0.00 0.00 0.00 3.14
3487 3508 5.291178 TCTGAATGCACATGTTTTTGGAAG 58.709 37.500 0.00 0.00 0.00 3.46
3572 3593 2.729882 GTGTGATACTCAAACGTCGCTT 59.270 45.455 0.00 0.00 0.00 4.68
3573 3594 2.325761 GTGTGATACTCAAACGTCGCT 58.674 47.619 0.00 0.00 0.00 4.93
3600 3621 9.008965 TCAAACTAATCTACTGCAAGCAAATAA 57.991 29.630 0.00 0.00 37.60 1.40
3619 3640 6.073980 GCGTGTGATACTCAAAAGTCAAACTA 60.074 38.462 0.00 0.00 36.92 2.24
3710 3731 4.661222 TCATTATGTTTGTGGAGCAGGAA 58.339 39.130 0.00 0.00 0.00 3.36
3713 3734 5.823209 TGATCATTATGTTTGTGGAGCAG 57.177 39.130 0.00 0.00 0.00 4.24
3838 3860 0.471971 ACTCCATGGTATCCCCCGAG 60.472 60.000 12.58 0.28 0.00 4.63
3843 3865 1.598130 GCGCACTCCATGGTATCCC 60.598 63.158 12.58 0.00 0.00 3.85
3844 3866 1.956170 CGCGCACTCCATGGTATCC 60.956 63.158 12.58 0.00 0.00 2.59
3846 3868 2.588877 GCGCGCACTCCATGGTAT 60.589 61.111 29.10 0.00 0.00 2.73
3847 3869 3.384275 ATGCGCGCACTCCATGGTA 62.384 57.895 39.05 9.89 0.00 3.25
3848 3870 4.783621 ATGCGCGCACTCCATGGT 62.784 61.111 39.05 15.90 0.00 3.55
3849 3871 4.246206 CATGCGCGCACTCCATGG 62.246 66.667 39.05 15.62 34.26 3.66
3906 3932 0.322997 CCCATGCTTTGTAACCCGGA 60.323 55.000 0.73 0.00 0.00 5.14
3990 4016 1.119574 TACGGAGCCCAGCCTAATCC 61.120 60.000 0.00 0.00 0.00 3.01
3993 4019 2.432300 GCTACGGAGCCCAGCCTAA 61.432 63.158 9.03 0.00 43.49 2.69
4009 4035 2.401583 TCCATTTGCATACGACAGCT 57.598 45.000 0.00 0.00 0.00 4.24
4020 4046 8.723942 TTCTATCTAGTTCTCTTTCCATTTGC 57.276 34.615 0.00 0.00 0.00 3.68
4066 4093 1.243342 TGCCTGGTGAATTTGAGCCG 61.243 55.000 0.00 0.00 0.00 5.52
4070 4097 2.228582 CACGATTGCCTGGTGAATTTGA 59.771 45.455 0.00 0.00 35.75 2.69
4073 4100 1.176527 CCACGATTGCCTGGTGAATT 58.823 50.000 0.00 0.00 35.75 2.17
4089 4116 3.071479 TGAAGCCGAAGTATGTTTCCAC 58.929 45.455 0.00 0.00 0.00 4.02
4095 4122 2.699954 CTTGGTGAAGCCGAAGTATGT 58.300 47.619 0.00 0.00 41.21 2.29


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

AutoCloner maintained by Alex Coulton.