Multiple sequence alignment - TraesCS5D01G325500

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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 TraesCS5D01G325500 chr5D 100.000 2900 0 0 1 2900 417606859 417609758 0.000000e+00 5356.0
1 TraesCS5D01G325500 chr5A 92.914 2399 131 15 524 2897 531018736 531021120 0.000000e+00 3452.0
2 TraesCS5D01G325500 chr5A 94.947 475 22 2 1064 1536 502229989 502230463 0.000000e+00 743.0
3 TraesCS5D01G325500 chr5B 91.042 2054 118 19 160 2162 504774482 504776520 0.000000e+00 2713.0
4 TraesCS5D01G325500 chr6B 89.276 718 66 9 2188 2900 127393702 127392991 0.000000e+00 889.0
5 TraesCS5D01G325500 chr6B 79.545 220 35 9 262 477 702884001 702884214 6.470000e-32 148.0
6 TraesCS5D01G325500 chr6B 79.545 220 35 9 262 477 702892874 702893087 6.470000e-32 148.0
7 TraesCS5D01G325500 chr2D 89.481 713 62 7 2199 2900 373748692 373747982 0.000000e+00 889.0
8 TraesCS5D01G325500 chr2D 88.227 705 75 7 2200 2900 401290741 401291441 0.000000e+00 835.0
9 TraesCS5D01G325500 chr2D 77.148 547 104 17 1109 1643 14380258 14380795 6.080000e-77 298.0
10 TraesCS5D01G325500 chr4B 89.341 713 62 7 2199 2900 75535331 75536040 0.000000e+00 883.0
11 TraesCS5D01G325500 chr4B 75.000 832 183 21 1026 1843 191079622 191080442 7.640000e-96 361.0
12 TraesCS5D01G325500 chr7B 89.216 714 63 7 2198 2900 581380042 581380752 0.000000e+00 880.0
13 TraesCS5D01G325500 chr7B 77.542 236 48 5 242 476 167012436 167012667 1.400000e-28 137.0
14 TraesCS5D01G325500 chr6D 88.796 714 64 12 2199 2900 412058028 412057319 0.000000e+00 861.0
15 TraesCS5D01G325500 chr6D 80.488 205 34 4 262 464 86658608 86658808 5.010000e-33 152.0
16 TraesCS5D01G325500 chr1B 88.511 705 69 9 2198 2900 515051501 515052195 0.000000e+00 843.0
17 TraesCS5D01G325500 chr1B 74.589 791 158 33 1088 1849 598844484 598843708 1.010000e-79 307.0
18 TraesCS5D01G325500 chr1B 75.460 163 32 8 1678 1836 598836845 598836687 4.010000e-09 73.1
19 TraesCS5D01G325500 chr6A 88.119 707 75 8 2198 2899 224609834 224609132 0.000000e+00 832.0
20 TraesCS5D01G325500 chr4A 91.554 296 25 0 1351 1646 24242917 24243212 2.690000e-110 409.0
21 TraesCS5D01G325500 chr4A 74.791 837 188 20 1026 1849 441944859 441944033 3.550000e-94 355.0
22 TraesCS5D01G325500 chr1A 74.904 785 158 30 1079 1836 536974442 536975214 3.600000e-84 322.0
23 TraesCS5D01G325500 chr2A 77.037 540 105 15 1115 1643 16607907 16607376 2.830000e-75 292.0
24 TraesCS5D01G325500 chr2A 76.580 538 111 11 1115 1643 16622472 16621941 6.120000e-72 281.0
25 TraesCS5D01G325500 chr2B 79.302 401 76 5 1109 1507 26135732 26136127 1.020000e-69 274.0
26 TraesCS5D01G325500 chr2B 82.427 239 37 4 245 480 45740931 45740695 1.360000e-48 204.0
27 TraesCS5D01G325500 chr3D 84.314 204 29 3 262 464 67054877 67055078 2.280000e-46 196.0
28 TraesCS5D01G325500 chr7D 80.478 251 42 7 228 475 611352751 611352505 4.930000e-43 185.0
29 TraesCS5D01G325500 chr3B 83.957 187 27 3 263 448 719881171 719880987 2.970000e-40 176.0
30 TraesCS5D01G325500 chr7A 100.000 28 0 0 2196 2223 15255005 15255032 5.000000e-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 TraesCS5D01G325500 chr5D 417606859 417609758 2899 False 5356 5356 100.000 1 2900 1 chr5D.!!$F1 2899
1 TraesCS5D01G325500 chr5A 531018736 531021120 2384 False 3452 3452 92.914 524 2897 1 chr5A.!!$F2 2373
2 TraesCS5D01G325500 chr5B 504774482 504776520 2038 False 2713 2713 91.042 160 2162 1 chr5B.!!$F1 2002
3 TraesCS5D01G325500 chr6B 127392991 127393702 711 True 889 889 89.276 2188 2900 1 chr6B.!!$R1 712
4 TraesCS5D01G325500 chr2D 373747982 373748692 710 True 889 889 89.481 2199 2900 1 chr2D.!!$R1 701
5 TraesCS5D01G325500 chr2D 401290741 401291441 700 False 835 835 88.227 2200 2900 1 chr2D.!!$F2 700
6 TraesCS5D01G325500 chr2D 14380258 14380795 537 False 298 298 77.148 1109 1643 1 chr2D.!!$F1 534
7 TraesCS5D01G325500 chr4B 75535331 75536040 709 False 883 883 89.341 2199 2900 1 chr4B.!!$F1 701
8 TraesCS5D01G325500 chr4B 191079622 191080442 820 False 361 361 75.000 1026 1843 1 chr4B.!!$F2 817
9 TraesCS5D01G325500 chr7B 581380042 581380752 710 False 880 880 89.216 2198 2900 1 chr7B.!!$F2 702
10 TraesCS5D01G325500 chr6D 412057319 412058028 709 True 861 861 88.796 2199 2900 1 chr6D.!!$R1 701
11 TraesCS5D01G325500 chr1B 515051501 515052195 694 False 843 843 88.511 2198 2900 1 chr1B.!!$F1 702
12 TraesCS5D01G325500 chr1B 598843708 598844484 776 True 307 307 74.589 1088 1849 1 chr1B.!!$R2 761
13 TraesCS5D01G325500 chr6A 224609132 224609834 702 True 832 832 88.119 2198 2899 1 chr6A.!!$R1 701
14 TraesCS5D01G325500 chr4A 441944033 441944859 826 True 355 355 74.791 1026 1849 1 chr4A.!!$R1 823
15 TraesCS5D01G325500 chr1A 536974442 536975214 772 False 322 322 74.904 1079 1836 1 chr1A.!!$F1 757
16 TraesCS5D01G325500 chr2A 16607376 16607907 531 True 292 292 77.037 1115 1643 1 chr2A.!!$R1 528
17 TraesCS5D01G325500 chr2A 16621941 16622472 531 True 281 281 76.580 1115 1643 1 chr2A.!!$R2 528

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
919 961 0.098376 ATCTCGACTCGCACCGTAAC 59.902 55.000 0.0 0.0 0.00 2.50 F
1024 1071 2.034532 TGACACGCCGGAGTCCTA 59.965 61.111 8.3 0.0 33.42 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 1924 0.109412 GTAGTGGTCCTGGACGTTCG 60.109 60.0 19.98 0.0 32.65 3.95 R
1914 1985 0.742281 CAAGGTGATGCGTGGAGGAG 60.742 60.0 0.00 0.0 0.00 3.69 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
29 30 7.906199 ATGGTGAGAAAGCTACTATAGAGTT 57.094 36.000 6.78 0.00 37.10 3.01
30 31 7.719871 TGGTGAGAAAGCTACTATAGAGTTT 57.280 36.000 6.78 1.55 37.10 2.66
31 32 8.135382 TGGTGAGAAAGCTACTATAGAGTTTT 57.865 34.615 6.78 9.66 37.10 2.43
32 33 9.251440 TGGTGAGAAAGCTACTATAGAGTTTTA 57.749 33.333 6.78 0.00 37.10 1.52
49 50 8.794335 AGAGTTTTATAGTTTCCTTGACATCC 57.206 34.615 0.00 0.00 0.00 3.51
50 51 8.383175 AGAGTTTTATAGTTTCCTTGACATCCA 58.617 33.333 0.00 0.00 0.00 3.41
51 52 8.934023 AGTTTTATAGTTTCCTTGACATCCAA 57.066 30.769 0.00 0.00 0.00 3.53
52 53 8.793592 AGTTTTATAGTTTCCTTGACATCCAAC 58.206 33.333 0.00 0.00 0.00 3.77
53 54 8.573035 GTTTTATAGTTTCCTTGACATCCAACA 58.427 33.333 0.00 0.00 0.00 3.33
54 55 8.877864 TTTATAGTTTCCTTGACATCCAACAT 57.122 30.769 0.00 0.00 0.00 2.71
55 56 8.877864 TTATAGTTTCCTTGACATCCAACATT 57.122 30.769 0.00 0.00 0.00 2.71
56 57 9.967451 TTATAGTTTCCTTGACATCCAACATTA 57.033 29.630 0.00 0.00 0.00 1.90
57 58 8.877864 ATAGTTTCCTTGACATCCAACATTAA 57.122 30.769 0.00 0.00 0.00 1.40
58 59 7.781324 AGTTTCCTTGACATCCAACATTAAT 57.219 32.000 0.00 0.00 0.00 1.40
59 60 8.193953 AGTTTCCTTGACATCCAACATTAATT 57.806 30.769 0.00 0.00 0.00 1.40
60 61 8.650490 AGTTTCCTTGACATCCAACATTAATTT 58.350 29.630 0.00 0.00 0.00 1.82
61 62 8.925700 GTTTCCTTGACATCCAACATTAATTTC 58.074 33.333 0.00 0.00 0.00 2.17
62 63 8.421249 TTCCTTGACATCCAACATTAATTTCT 57.579 30.769 0.00 0.00 0.00 2.52
63 64 8.421249 TCCTTGACATCCAACATTAATTTCTT 57.579 30.769 0.00 0.00 0.00 2.52
64 65 9.527157 TCCTTGACATCCAACATTAATTTCTTA 57.473 29.630 0.00 0.00 0.00 2.10
102 103 9.905713 AATCAAAATAGGTAGAAGTTGATAGCA 57.094 29.630 0.00 0.00 35.28 3.49
103 104 9.905713 ATCAAAATAGGTAGAAGTTGATAGCAA 57.094 29.630 0.00 0.00 34.74 3.91
104 105 9.733556 TCAAAATAGGTAGAAGTTGATAGCAAA 57.266 29.630 0.00 0.00 35.42 3.68
107 108 8.594881 AATAGGTAGAAGTTGATAGCAAATCG 57.405 34.615 0.00 0.00 35.42 3.34
108 109 4.811557 AGGTAGAAGTTGATAGCAAATCGC 59.188 41.667 0.00 0.00 42.91 4.58
109 110 4.570772 GGTAGAAGTTGATAGCAAATCGCA 59.429 41.667 0.00 0.00 46.13 5.10
110 111 4.606457 AGAAGTTGATAGCAAATCGCAC 57.394 40.909 0.00 0.00 46.13 5.34
111 112 4.256920 AGAAGTTGATAGCAAATCGCACT 58.743 39.130 0.00 0.00 46.13 4.40
112 113 4.697352 AGAAGTTGATAGCAAATCGCACTT 59.303 37.500 0.00 12.52 46.13 3.16
113 114 5.874810 AGAAGTTGATAGCAAATCGCACTTA 59.125 36.000 0.00 0.00 46.13 2.24
114 115 6.371548 AGAAGTTGATAGCAAATCGCACTTAA 59.628 34.615 0.00 0.00 46.13 1.85
115 116 6.683974 AGTTGATAGCAAATCGCACTTAAT 57.316 33.333 0.00 0.00 46.13 1.40
116 117 6.719365 AGTTGATAGCAAATCGCACTTAATC 58.281 36.000 0.00 0.00 46.13 1.75
117 118 5.328886 TGATAGCAAATCGCACTTAATCG 57.671 39.130 0.00 0.00 46.13 3.34
118 119 4.211164 TGATAGCAAATCGCACTTAATCGG 59.789 41.667 0.00 0.00 46.13 4.18
119 120 1.064060 AGCAAATCGCACTTAATCGGC 59.936 47.619 0.00 0.00 46.13 5.54
120 121 1.202132 GCAAATCGCACTTAATCGGCA 60.202 47.619 0.00 0.00 41.79 5.69
121 122 2.541588 GCAAATCGCACTTAATCGGCAT 60.542 45.455 0.00 0.00 41.79 4.40
122 123 3.694734 CAAATCGCACTTAATCGGCATT 58.305 40.909 0.00 0.00 0.00 3.56
123 124 4.788201 GCAAATCGCACTTAATCGGCATTA 60.788 41.667 0.00 0.00 41.79 1.90
124 125 5.270083 CAAATCGCACTTAATCGGCATTAA 58.730 37.500 0.00 0.00 34.03 1.40
125 126 5.493133 AATCGCACTTAATCGGCATTAAA 57.507 34.783 0.00 0.00 34.64 1.52
126 127 5.689383 ATCGCACTTAATCGGCATTAAAT 57.311 34.783 0.00 0.00 34.64 1.40
127 128 4.843147 TCGCACTTAATCGGCATTAAATG 58.157 39.130 6.54 6.54 35.62 2.32
128 129 3.974401 CGCACTTAATCGGCATTAAATGG 59.026 43.478 10.54 2.01 33.90 3.16
129 130 4.497340 CGCACTTAATCGGCATTAAATGGT 60.497 41.667 10.54 2.43 33.90 3.55
130 131 5.348164 GCACTTAATCGGCATTAAATGGTT 58.652 37.500 10.54 0.00 33.90 3.67
131 132 6.500041 GCACTTAATCGGCATTAAATGGTTA 58.500 36.000 10.54 0.00 33.90 2.85
132 133 6.416750 GCACTTAATCGGCATTAAATGGTTAC 59.583 38.462 10.54 0.00 33.90 2.50
133 134 7.681065 GCACTTAATCGGCATTAAATGGTTACT 60.681 37.037 10.54 0.00 33.90 2.24
134 135 7.855904 CACTTAATCGGCATTAAATGGTTACTC 59.144 37.037 0.00 0.00 34.64 2.59
135 136 5.418310 AATCGGCATTAAATGGTTACTCG 57.582 39.130 0.00 0.00 0.00 4.18
136 137 2.610374 TCGGCATTAAATGGTTACTCGC 59.390 45.455 0.00 0.00 0.00 5.03
137 138 2.353269 CGGCATTAAATGGTTACTCGCA 59.647 45.455 0.00 0.00 0.00 5.10
138 139 3.181505 CGGCATTAAATGGTTACTCGCAA 60.182 43.478 0.00 0.00 0.00 4.85
139 140 4.673061 CGGCATTAAATGGTTACTCGCAAA 60.673 41.667 0.00 0.00 0.00 3.68
140 141 5.164954 GGCATTAAATGGTTACTCGCAAAA 58.835 37.500 0.00 0.00 0.00 2.44
141 142 5.810074 GGCATTAAATGGTTACTCGCAAAAT 59.190 36.000 0.00 0.00 0.00 1.82
142 143 6.975772 GGCATTAAATGGTTACTCGCAAAATA 59.024 34.615 0.00 0.00 0.00 1.40
143 144 7.489757 GGCATTAAATGGTTACTCGCAAAATAA 59.510 33.333 0.00 0.00 0.00 1.40
144 145 9.030301 GCATTAAATGGTTACTCGCAAAATAAT 57.970 29.630 0.00 0.00 0.00 1.28
148 149 8.920509 AAATGGTTACTCGCAAAATAATAACC 57.079 30.769 4.39 4.39 41.21 2.85
149 150 7.875327 ATGGTTACTCGCAAAATAATAACCT 57.125 32.000 11.20 0.00 41.34 3.50
150 151 7.690952 TGGTTACTCGCAAAATAATAACCTT 57.309 32.000 11.20 0.00 41.34 3.50
151 152 8.789825 TGGTTACTCGCAAAATAATAACCTTA 57.210 30.769 11.20 0.00 41.34 2.69
152 153 9.228949 TGGTTACTCGCAAAATAATAACCTTAA 57.771 29.630 11.20 0.00 41.34 1.85
153 154 9.494479 GGTTACTCGCAAAATAATAACCTTAAC 57.506 33.333 0.00 0.00 38.89 2.01
156 157 7.758495 ACTCGCAAAATAATAACCTTAACTGG 58.242 34.615 0.00 0.00 0.00 4.00
157 158 7.392393 ACTCGCAAAATAATAACCTTAACTGGT 59.608 33.333 0.00 0.00 43.11 4.00
173 174 0.689080 TGGTTTGCCCTTGCTTCCAA 60.689 50.000 0.00 0.00 38.71 3.53
231 232 3.726557 TCAGGCAATTGATCTTGGACT 57.273 42.857 10.34 0.00 0.00 3.85
255 257 6.951643 TGAATATTCAGCGAATGTCTGATTG 58.048 36.000 14.23 0.00 39.96 2.67
275 277 2.163412 TGTTAGGCATGGCAAATCGAAC 59.837 45.455 22.64 14.20 0.00 3.95
281 283 4.081752 AGGCATGGCAAATCGAACATTTTA 60.082 37.500 22.64 0.00 0.00 1.52
287 289 5.167845 GGCAAATCGAACATTTTACATGGT 58.832 37.500 0.00 0.00 0.00 3.55
307 309 9.818270 ACATGGTGAATTATATTCATTGAGGAT 57.182 29.630 5.49 0.00 0.00 3.24
330 332 4.211164 TGACAAGTTTAGTTGACGAGCATG 59.789 41.667 4.40 0.00 0.00 4.06
331 333 4.377021 ACAAGTTTAGTTGACGAGCATGA 58.623 39.130 0.00 0.00 0.00 3.07
337 339 6.649141 AGTTTAGTTGACGAGCATGACAAATA 59.351 34.615 0.00 0.00 0.00 1.40
340 342 4.937620 AGTTGACGAGCATGACAAATATGT 59.062 37.500 0.00 0.00 44.25 2.29
354 356 8.554835 TGACAAATATGTTCGGTTCATCTTTA 57.445 30.769 0.00 0.00 40.74 1.85
358 360 8.840321 CAAATATGTTCGGTTCATCTTTAGGAT 58.160 33.333 0.00 0.00 34.51 3.24
361 363 6.785337 TGTTCGGTTCATCTTTAGGATAGA 57.215 37.500 0.00 0.00 32.64 1.98
368 370 7.857885 CGGTTCATCTTTAGGATAGAAAATTGC 59.142 37.037 0.00 0.00 32.64 3.56
372 374 6.677781 TCTTTAGGATAGAAAATTGCCGTG 57.322 37.500 0.00 0.00 0.00 4.94
378 380 2.611974 AGAAAATTGCCGTGCTTACG 57.388 45.000 0.00 0.00 0.00 3.18
390 392 4.399978 CCGTGCTTACGAACTAAATTTGG 58.600 43.478 0.00 0.00 34.64 3.28
491 516 1.480954 TCCGTTGATCCTTAGGTGCTC 59.519 52.381 0.00 0.00 0.00 4.26
493 518 1.473434 CGTTGATCCTTAGGTGCTCCC 60.473 57.143 0.00 0.00 0.00 4.30
497 522 3.309296 TGATCCTTAGGTGCTCCCTTAG 58.691 50.000 0.00 1.83 42.73 2.18
511 536 6.092807 GTGCTCCCTTAGTTTTAAGAGACATG 59.907 42.308 0.00 0.00 38.88 3.21
519 544 9.856488 CTTAGTTTTAAGAGACATGCAGTACTA 57.144 33.333 0.00 0.00 38.88 1.82
845 871 0.322008 GGCAAGCCAGCTAAGTGAGT 60.322 55.000 6.14 0.00 35.81 3.41
853 879 2.159170 CCAGCTAAGTGAGTCCAGCTAC 60.159 54.545 5.61 0.00 42.33 3.58
856 882 3.053544 AGCTAAGTGAGTCCAGCTACCTA 60.054 47.826 4.39 0.00 42.41 3.08
857 883 3.892588 GCTAAGTGAGTCCAGCTACCTAT 59.107 47.826 0.00 0.00 0.00 2.57
859 885 2.672098 AGTGAGTCCAGCTACCTATGG 58.328 52.381 0.00 0.00 37.97 2.74
861 887 0.682292 GAGTCCAGCTACCTATGGCC 59.318 60.000 0.00 0.00 36.47 5.36
862 888 1.115930 AGTCCAGCTACCTATGGCCG 61.116 60.000 0.00 0.00 36.47 6.13
872 905 2.437537 TATGGCCGCGCAACACAT 60.438 55.556 8.75 8.62 0.00 3.21
873 906 2.378945 CTATGGCCGCGCAACACATC 62.379 60.000 8.75 0.00 0.00 3.06
917 959 1.022982 ACATCTCGACTCGCACCGTA 61.023 55.000 0.00 0.00 0.00 4.02
919 961 0.098376 ATCTCGACTCGCACCGTAAC 59.902 55.000 0.00 0.00 0.00 2.50
927 969 3.602483 ACTCGCACCGTAACCAATAATT 58.398 40.909 0.00 0.00 0.00 1.40
976 1023 3.056891 AGCCAGCTAGCTAATTCGATCTC 60.057 47.826 18.86 0.00 42.70 2.75
978 1025 3.367910 CCAGCTAGCTAATTCGATCTCCC 60.368 52.174 18.86 0.00 0.00 4.30
979 1026 3.509575 CAGCTAGCTAATTCGATCTCCCT 59.490 47.826 18.86 0.00 0.00 4.20
980 1027 4.021544 CAGCTAGCTAATTCGATCTCCCTT 60.022 45.833 18.86 0.00 0.00 3.95
986 1033 5.010213 AGCTAATTCGATCTCCCTTGAGTAC 59.990 44.000 0.00 0.00 39.75 2.73
1009 1056 3.266510 AGTAATCAGAAATGGCGCTGA 57.733 42.857 7.64 1.46 44.43 4.26
1023 1070 3.374402 CTGACACGCCGGAGTCCT 61.374 66.667 8.30 0.00 33.42 3.85
1024 1071 2.034532 TGACACGCCGGAGTCCTA 59.965 61.111 8.30 0.00 33.42 2.94
1587 1658 4.699522 GCGTTCCCGGACAGGCTT 62.700 66.667 0.73 0.00 39.21 4.35
1632 1703 2.792290 CTTCGAGCGCATCCACGTG 61.792 63.158 11.47 9.08 34.88 4.49
1853 1924 2.100991 CCGGTACTACGACGTGGC 59.899 66.667 11.56 0.00 35.47 5.01
1912 1983 3.790437 CCTGAGCTCCGGCCATGT 61.790 66.667 11.59 0.00 39.73 3.21
1913 1984 2.202987 CTGAGCTCCGGCCATGTC 60.203 66.667 12.15 0.00 39.73 3.06
1914 1985 3.746949 CTGAGCTCCGGCCATGTCC 62.747 68.421 12.15 0.00 39.73 4.02
1928 1999 0.977627 ATGTCCTCCTCCACGCATCA 60.978 55.000 0.00 0.00 0.00 3.07
2011 2082 8.869897 TGTAAATCGAAAGTAATCTGCTGTTAG 58.130 33.333 0.00 0.00 0.00 2.34
2050 2123 2.343101 TGCAAGAATAAAGGGACGACG 58.657 47.619 0.00 0.00 0.00 5.12
2061 2134 1.443872 GGACGACGGTGCAGTACAG 60.444 63.158 0.00 0.00 34.18 2.74
2079 2152 7.626452 GCAGTACAGGGATAAACAGTTCATTTC 60.626 40.741 0.00 0.00 0.00 2.17
2162 2235 9.767684 CTGCTTGATTACGTTTTGAAATGTATA 57.232 29.630 8.81 2.82 39.40 1.47
2173 2246 6.489127 TTTGAAATGTATACCTCAACCACG 57.511 37.500 10.18 0.00 0.00 4.94
2195 2268 3.365832 GGTGCGTGCAATCAATAATCAG 58.634 45.455 0.00 0.00 0.00 2.90
2318 2399 1.921573 GCTGCAAATTATAGCGCACGG 60.922 52.381 11.47 0.00 33.03 4.94
2495 2580 9.767684 TTATCTTGCAATACAACAAATAGTTCG 57.232 29.630 0.00 0.00 38.74 3.95
2535 2620 9.491675 AAACATACAAATCATGATGCTTTTTGA 57.508 25.926 20.26 8.60 32.88 2.69
2593 2678 4.025061 CCTTCTGAAGATCATCATGCGTTC 60.025 45.833 18.68 0.00 0.00 3.95
2750 2836 1.900245 TGTGCATGATCACACAAGCT 58.100 45.000 14.82 0.00 43.48 3.74
2831 2918 0.249955 ATTGGGCTTGCAAAATCCCG 59.750 50.000 19.96 2.38 40.46 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.906199 AACTCTATAGTAGCTTTCTCACCAT 57.094 36.000 0.00 0.00 33.75 3.55
23 24 9.886132 GGATGTCAAGGAAACTATAAAACTCTA 57.114 33.333 0.00 0.00 42.68 2.43
24 25 8.383175 TGGATGTCAAGGAAACTATAAAACTCT 58.617 33.333 0.00 0.00 42.68 3.24
25 26 8.561738 TGGATGTCAAGGAAACTATAAAACTC 57.438 34.615 0.00 0.00 42.68 3.01
26 27 8.793592 GTTGGATGTCAAGGAAACTATAAAACT 58.206 33.333 0.00 0.00 42.68 2.66
27 28 8.573035 TGTTGGATGTCAAGGAAACTATAAAAC 58.427 33.333 0.00 0.00 42.68 2.43
28 29 8.698973 TGTTGGATGTCAAGGAAACTATAAAA 57.301 30.769 0.00 0.00 42.68 1.52
29 30 8.877864 ATGTTGGATGTCAAGGAAACTATAAA 57.122 30.769 0.00 0.00 42.68 1.40
30 31 8.877864 AATGTTGGATGTCAAGGAAACTATAA 57.122 30.769 0.00 0.00 42.68 0.98
31 32 9.967451 TTAATGTTGGATGTCAAGGAAACTATA 57.033 29.630 0.00 0.00 42.68 1.31
32 33 8.877864 TTAATGTTGGATGTCAAGGAAACTAT 57.122 30.769 0.00 0.00 42.68 2.12
33 34 8.877864 ATTAATGTTGGATGTCAAGGAAACTA 57.122 30.769 0.00 0.00 42.68 2.24
35 36 8.831715 AAATTAATGTTGGATGTCAAGGAAAC 57.168 30.769 0.00 0.00 35.80 2.78
36 37 8.869109 AGAAATTAATGTTGGATGTCAAGGAAA 58.131 29.630 0.00 0.00 35.80 3.13
37 38 8.421249 AGAAATTAATGTTGGATGTCAAGGAA 57.579 30.769 0.00 0.00 35.80 3.36
38 39 8.421249 AAGAAATTAATGTTGGATGTCAAGGA 57.579 30.769 0.00 0.00 35.80 3.36
76 77 9.905713 TGCTATCAACTTCTACCTATTTTGATT 57.094 29.630 0.00 0.00 35.73 2.57
77 78 9.905713 TTGCTATCAACTTCTACCTATTTTGAT 57.094 29.630 0.00 0.00 37.44 2.57
78 79 9.733556 TTTGCTATCAACTTCTACCTATTTTGA 57.266 29.630 0.00 0.00 30.75 2.69
81 82 9.046296 CGATTTGCTATCAACTTCTACCTATTT 57.954 33.333 0.00 0.00 30.75 1.40
82 83 7.171678 GCGATTTGCTATCAACTTCTACCTATT 59.828 37.037 0.00 0.00 41.73 1.73
83 84 6.647067 GCGATTTGCTATCAACTTCTACCTAT 59.353 38.462 0.00 0.00 41.73 2.57
84 85 5.983720 GCGATTTGCTATCAACTTCTACCTA 59.016 40.000 0.00 0.00 41.73 3.08
85 86 4.811557 GCGATTTGCTATCAACTTCTACCT 59.188 41.667 0.00 0.00 41.73 3.08
86 87 4.570772 TGCGATTTGCTATCAACTTCTACC 59.429 41.667 0.00 0.00 46.63 3.18
87 88 5.292101 AGTGCGATTTGCTATCAACTTCTAC 59.708 40.000 0.00 0.00 46.63 2.59
88 89 5.419542 AGTGCGATTTGCTATCAACTTCTA 58.580 37.500 0.00 0.00 46.63 2.10
89 90 4.256920 AGTGCGATTTGCTATCAACTTCT 58.743 39.130 0.00 0.00 46.63 2.85
90 91 4.606457 AGTGCGATTTGCTATCAACTTC 57.394 40.909 0.00 0.00 46.63 3.01
91 92 6.494893 TTAAGTGCGATTTGCTATCAACTT 57.505 33.333 15.26 15.26 46.63 2.66
92 93 6.510157 CGATTAAGTGCGATTTGCTATCAACT 60.510 38.462 0.00 0.00 46.63 3.16
93 94 5.617187 CGATTAAGTGCGATTTGCTATCAAC 59.383 40.000 0.00 0.00 46.63 3.18
94 95 5.277297 CCGATTAAGTGCGATTTGCTATCAA 60.277 40.000 0.00 0.00 46.63 2.57
95 96 4.211164 CCGATTAAGTGCGATTTGCTATCA 59.789 41.667 0.00 0.00 46.63 2.15
96 97 4.702392 CCGATTAAGTGCGATTTGCTATC 58.298 43.478 0.00 0.00 46.63 2.08
97 98 3.058914 GCCGATTAAGTGCGATTTGCTAT 60.059 43.478 0.00 0.00 46.63 2.97
98 99 2.286833 GCCGATTAAGTGCGATTTGCTA 59.713 45.455 0.00 0.00 46.63 3.49
99 100 1.064060 GCCGATTAAGTGCGATTTGCT 59.936 47.619 0.00 0.00 46.63 3.91
100 101 1.202132 TGCCGATTAAGTGCGATTTGC 60.202 47.619 0.00 0.00 46.70 3.68
101 102 2.823196 TGCCGATTAAGTGCGATTTG 57.177 45.000 0.00 0.00 0.00 2.32
102 103 5.493133 TTAATGCCGATTAAGTGCGATTT 57.507 34.783 0.00 0.00 31.60 2.17
103 104 5.493133 TTTAATGCCGATTAAGTGCGATT 57.507 34.783 0.00 0.00 35.81 3.34
104 105 5.451908 CATTTAATGCCGATTAAGTGCGAT 58.548 37.500 0.00 0.00 35.92 4.58
105 106 4.260990 CCATTTAATGCCGATTAAGTGCGA 60.261 41.667 0.00 0.00 39.06 5.10
106 107 3.974401 CCATTTAATGCCGATTAAGTGCG 59.026 43.478 0.00 0.00 39.06 5.34
107 108 4.932146 ACCATTTAATGCCGATTAAGTGC 58.068 39.130 0.00 0.00 39.06 4.40
108 109 7.703328 AGTAACCATTTAATGCCGATTAAGTG 58.297 34.615 0.00 0.00 39.63 3.16
109 110 7.254658 CGAGTAACCATTTAATGCCGATTAAGT 60.255 37.037 0.00 0.00 35.81 2.24
110 111 7.069569 CGAGTAACCATTTAATGCCGATTAAG 58.930 38.462 0.00 0.00 35.81 1.85
111 112 6.512091 GCGAGTAACCATTTAATGCCGATTAA 60.512 38.462 0.00 0.00 33.09 1.40
112 113 5.049954 GCGAGTAACCATTTAATGCCGATTA 60.050 40.000 0.00 0.00 0.00 1.75
113 114 4.261031 GCGAGTAACCATTTAATGCCGATT 60.261 41.667 0.00 0.00 0.00 3.34
114 115 3.250040 GCGAGTAACCATTTAATGCCGAT 59.750 43.478 0.00 0.00 0.00 4.18
115 116 2.610374 GCGAGTAACCATTTAATGCCGA 59.390 45.455 0.00 0.00 0.00 5.54
116 117 2.353269 TGCGAGTAACCATTTAATGCCG 59.647 45.455 0.00 0.00 0.00 5.69
117 118 4.364415 TTGCGAGTAACCATTTAATGCC 57.636 40.909 0.00 0.00 0.00 4.40
118 119 6.885735 ATTTTGCGAGTAACCATTTAATGC 57.114 33.333 0.00 0.00 0.00 3.56
123 124 8.745590 AGGTTATTATTTTGCGAGTAACCATTT 58.254 29.630 12.88 0.00 42.05 2.32
124 125 8.288689 AGGTTATTATTTTGCGAGTAACCATT 57.711 30.769 12.88 0.00 42.05 3.16
125 126 7.875327 AGGTTATTATTTTGCGAGTAACCAT 57.125 32.000 12.88 0.00 42.05 3.55
126 127 7.690952 AAGGTTATTATTTTGCGAGTAACCA 57.309 32.000 12.88 0.00 42.05 3.67
127 128 9.494479 GTTAAGGTTATTATTTTGCGAGTAACC 57.506 33.333 0.00 0.00 40.68 2.85
130 131 8.885722 CCAGTTAAGGTTATTATTTTGCGAGTA 58.114 33.333 0.00 0.00 0.00 2.59
131 132 7.392393 ACCAGTTAAGGTTATTATTTTGCGAGT 59.608 33.333 0.00 0.00 39.34 4.18
132 133 7.758495 ACCAGTTAAGGTTATTATTTTGCGAG 58.242 34.615 0.00 0.00 39.34 5.03
133 134 7.690952 ACCAGTTAAGGTTATTATTTTGCGA 57.309 32.000 0.00 0.00 39.34 5.10
144 145 7.924153 AGCAAGGGCAAACCAGTTAAGGTTA 62.924 44.000 0.00 0.00 46.03 2.85
146 147 2.316108 CAAGGGCAAACCAGTTAAGGT 58.684 47.619 0.00 0.00 45.91 3.50
147 148 1.000843 GCAAGGGCAAACCAGTTAAGG 59.999 52.381 0.00 0.00 43.89 2.69
148 149 1.963515 AGCAAGGGCAAACCAGTTAAG 59.036 47.619 0.00 0.00 44.61 1.85
149 150 2.080654 AGCAAGGGCAAACCAGTTAA 57.919 45.000 0.00 0.00 44.61 2.01
150 151 1.960689 GAAGCAAGGGCAAACCAGTTA 59.039 47.619 0.00 0.00 44.61 2.24
151 152 0.752658 GAAGCAAGGGCAAACCAGTT 59.247 50.000 0.00 0.00 44.61 3.16
152 153 1.115326 GGAAGCAAGGGCAAACCAGT 61.115 55.000 0.00 0.00 44.61 4.00
153 154 1.114722 TGGAAGCAAGGGCAAACCAG 61.115 55.000 0.00 0.00 44.61 4.00
154 155 0.689080 TTGGAAGCAAGGGCAAACCA 60.689 50.000 0.00 0.00 44.61 3.67
155 156 0.249868 GTTGGAAGCAAGGGCAAACC 60.250 55.000 0.00 0.00 44.61 3.27
156 157 0.463620 TGTTGGAAGCAAGGGCAAAC 59.536 50.000 0.00 0.00 44.61 2.93
157 158 0.752054 CTGTTGGAAGCAAGGGCAAA 59.248 50.000 0.00 0.00 44.61 3.68
158 159 0.396974 ACTGTTGGAAGCAAGGGCAA 60.397 50.000 0.00 0.00 44.61 4.52
195 196 9.925268 CAATTGCCTGATATTTTTATTTGCTTC 57.075 29.630 0.00 0.00 0.00 3.86
210 211 3.952323 CAGTCCAAGATCAATTGCCTGAT 59.048 43.478 0.00 0.00 38.79 2.90
231 232 6.539826 ACAATCAGACATTCGCTGAATATTCA 59.460 34.615 17.07 17.07 44.71 2.57
243 245 4.498682 GCCATGCCTAACAATCAGACATTC 60.499 45.833 0.00 0.00 0.00 2.67
250 252 3.181488 CGATTTGCCATGCCTAACAATCA 60.181 43.478 0.00 0.00 0.00 2.57
255 257 2.163412 TGTTCGATTTGCCATGCCTAAC 59.837 45.455 0.00 0.00 0.00 2.34
281 283 9.818270 ATCCTCAATGAATATAATTCACCATGT 57.182 29.630 4.54 0.00 0.00 3.21
298 300 7.301054 GTCAACTAAACTTGTCATCCTCAATG 58.699 38.462 0.00 0.00 36.65 2.82
307 309 3.787785 TGCTCGTCAACTAAACTTGTCA 58.212 40.909 0.00 0.00 0.00 3.58
308 310 4.447724 TCATGCTCGTCAACTAAACTTGTC 59.552 41.667 0.00 0.00 0.00 3.18
330 332 8.122952 CCTAAAGATGAACCGAACATATTTGTC 58.877 37.037 14.30 0.00 38.81 3.18
331 333 7.827236 TCCTAAAGATGAACCGAACATATTTGT 59.173 33.333 14.30 0.00 38.81 2.83
337 339 7.361457 TCTATCCTAAAGATGAACCGAACAT 57.639 36.000 0.00 0.00 36.33 2.71
340 342 9.681062 AATTTTCTATCCTAAAGATGAACCGAA 57.319 29.630 0.00 0.00 36.33 4.30
343 345 8.138074 GGCAATTTTCTATCCTAAAGATGAACC 58.862 37.037 0.00 0.00 36.33 3.62
354 356 3.004752 AGCACGGCAATTTTCTATCCT 57.995 42.857 0.00 0.00 0.00 3.24
358 360 3.733024 CGTAAGCACGGCAATTTTCTA 57.267 42.857 0.00 0.00 44.59 2.10
372 374 5.636837 TGATGCCAAATTTAGTTCGTAAGC 58.363 37.500 0.00 0.00 37.18 3.09
378 380 7.247728 TGACGTAATGATGCCAAATTTAGTTC 58.752 34.615 0.00 0.00 0.00 3.01
390 392 8.161754 GGCAATTTATATTGACGTAATGATGC 57.838 34.615 9.76 0.00 43.12 3.91
491 516 5.940470 ACTGCATGTCTCTTAAAACTAAGGG 59.060 40.000 0.00 0.00 0.00 3.95
493 518 8.764524 AGTACTGCATGTCTCTTAAAACTAAG 57.235 34.615 0.00 0.00 0.00 2.18
511 536 7.610509 CGTTTTGCTCTACTAAATAGTACTGC 58.389 38.462 5.39 10.62 37.73 4.40
519 544 6.554334 TTTCTGCGTTTTGCTCTACTAAAT 57.446 33.333 0.00 0.00 46.63 1.40
527 552 2.125461 AGCTTTTCTGCGTTTTGCTC 57.875 45.000 0.00 0.00 46.63 4.26
845 871 2.507854 GCGGCCATAGGTAGCTGGA 61.508 63.158 2.24 0.00 35.84 3.86
853 879 3.876198 GTGTTGCGCGGCCATAGG 61.876 66.667 8.83 0.00 0.00 2.57
856 882 3.814268 GATGTGTTGCGCGGCCAT 61.814 61.111 8.83 1.74 0.00 4.40
872 905 0.246360 TGGCTTTTGATCTCTCGCGA 59.754 50.000 9.26 9.26 0.00 5.87
873 906 0.371645 GTGGCTTTTGATCTCTCGCG 59.628 55.000 0.00 0.00 0.00 5.87
880 913 1.177401 GTGGGAGGTGGCTTTTGATC 58.823 55.000 0.00 0.00 0.00 2.92
884 917 0.779997 AGATGTGGGAGGTGGCTTTT 59.220 50.000 0.00 0.00 0.00 2.27
957 1004 3.509575 AGGGAGATCGAATTAGCTAGCTG 59.490 47.826 27.68 10.14 0.00 4.24
976 1023 6.446781 TTCTGATTACTACGTACTCAAGGG 57.553 41.667 0.00 0.00 29.74 3.95
978 1025 7.043325 GCCATTTCTGATTACTACGTACTCAAG 60.043 40.741 0.00 0.00 29.74 3.02
979 1026 6.755141 GCCATTTCTGATTACTACGTACTCAA 59.245 38.462 0.00 0.00 29.74 3.02
980 1027 6.270815 GCCATTTCTGATTACTACGTACTCA 58.729 40.000 0.00 0.00 0.00 3.41
986 1033 3.060272 CAGCGCCATTTCTGATTACTACG 60.060 47.826 2.29 0.00 32.26 3.51
1009 1056 3.066814 GGTAGGACTCCGGCGTGT 61.067 66.667 0.00 4.04 0.00 4.49
1023 1070 0.106167 CGATGACCAGGAGGGAGGTA 60.106 60.000 0.00 0.00 38.50 3.08
1024 1071 1.381872 CGATGACCAGGAGGGAGGT 60.382 63.158 0.00 0.00 41.83 3.85
1294 1350 0.684805 ATGGAGAGGGAGACGGTGAC 60.685 60.000 0.00 0.00 0.00 3.67
1443 1499 3.680338 GAAGAGGTCGACGCCGTCC 62.680 68.421 12.26 0.00 42.87 4.79
1632 1703 1.020437 CCGGGTAGTCGTAGAACCTC 58.980 60.000 0.00 0.00 37.55 3.85
1853 1924 0.109412 GTAGTGGTCCTGGACGTTCG 60.109 60.000 19.98 0.00 32.65 3.95
1910 1981 1.609210 TGATGCGTGGAGGAGGACA 60.609 57.895 0.00 0.00 0.00 4.02
1911 1982 1.153549 GTGATGCGTGGAGGAGGAC 60.154 63.158 0.00 0.00 0.00 3.85
1912 1983 2.359169 GGTGATGCGTGGAGGAGGA 61.359 63.158 0.00 0.00 0.00 3.71
1913 1984 1.903877 AAGGTGATGCGTGGAGGAGG 61.904 60.000 0.00 0.00 0.00 4.30
1914 1985 0.742281 CAAGGTGATGCGTGGAGGAG 60.742 60.000 0.00 0.00 0.00 3.69
1928 1999 4.021925 GGGAGGAGCACGCAAGGT 62.022 66.667 0.00 0.00 46.39 3.50
2050 2123 3.270877 CTGTTTATCCCTGTACTGCACC 58.729 50.000 0.00 0.00 0.00 5.01
2061 2134 5.946377 ACCTCTGAAATGAACTGTTTATCCC 59.054 40.000 0.00 0.00 0.00 3.85
2079 2152 5.221303 ACAACATGATTGAACCAAACCTCTG 60.221 40.000 0.00 0.00 0.00 3.35
2162 2235 4.619227 CGCACCCGTGGTTGAGGT 62.619 66.667 0.00 0.00 31.02 3.85
2173 2246 2.098934 TGATTATTGATTGCACGCACCC 59.901 45.455 0.00 0.00 0.00 4.61
2195 2268 1.210478 TGTTGGAGATGCTCTAAGGGC 59.790 52.381 0.00 0.00 31.92 5.19
2495 2580 7.748031 TTTGTATGTTTGATGTTGTGTTGTC 57.252 32.000 0.00 0.00 0.00 3.18
2593 2678 3.186047 GGACATTCGACGTGCCGG 61.186 66.667 0.00 0.00 0.00 6.13
2608 2693 3.334691 CGTTTTGTTGCTCCTATCAGGA 58.665 45.455 0.00 0.00 43.43 3.86
2610 2695 2.420022 CCCGTTTTGTTGCTCCTATCAG 59.580 50.000 0.00 0.00 0.00 2.90
2712 2798 5.410439 TGCACAATATGATCATCGAGAATGG 59.590 40.000 12.53 0.00 35.94 3.16
2750 2836 4.018490 AGATGCTTTGGTACATCATGCAA 58.982 39.130 5.84 0.00 44.16 4.08
2831 2918 3.938334 GGAAAGATGTGGAGAGAGCTTTC 59.062 47.826 0.00 0.00 40.04 2.62


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

AutoCloner maintained by Alex Coulton.