Multiple sequence alignment - TraesCS5D01G003000

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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 TraesCS5D01G003000 chr5D 100.000 3395 0 0 1 3395 2796228 2799622 0.000000e+00 6270.0
1 TraesCS5D01G003000 chr5D 84.531 1280 108 45 1088 2304 3012529 3013781 0.000000e+00 1184.0
2 TraesCS5D01G003000 chr5D 85.646 836 75 27 1476 2298 3071058 3071861 0.000000e+00 837.0
3 TraesCS5D01G003000 chr5D 90.808 631 48 6 2762 3385 294597291 294597918 0.000000e+00 835.0
4 TraesCS5D01G003000 chr5D 89.580 643 55 7 2760 3395 112713660 112714297 0.000000e+00 806.0
5 TraesCS5D01G003000 chr5D 83.054 537 49 19 932 1441 3070466 3070987 1.860000e-122 449.0
6 TraesCS5D01G003000 chr5D 89.179 268 23 1 71 338 279292870 279293131 2.530000e-86 329.0
7 TraesCS5D01G003000 chr5D 89.503 181 16 1 580 760 3070226 3070403 3.410000e-55 226.0
8 TraesCS5D01G003000 chr5D 90.196 102 7 2 2394 2495 3016341 3016439 2.750000e-26 130.0
9 TraesCS5D01G003000 chr5D 100.000 43 0 0 2339 2381 3013859 3013901 2.810000e-11 80.5
10 TraesCS5D01G003000 chr5B 91.446 1473 88 20 898 2341 2805391 2806854 0.000000e+00 1988.0
11 TraesCS5D01G003000 chr5B 81.983 1432 161 52 932 2298 2883416 2884815 0.000000e+00 1125.0
12 TraesCS5D01G003000 chr5B 85.208 818 67 29 1492 2297 2613864 2613089 0.000000e+00 791.0
13 TraesCS5D01G003000 chr5B 92.023 514 28 5 335 846 2804582 2805084 0.000000e+00 710.0
14 TraesCS5D01G003000 chr5B 87.547 265 31 2 2496 2760 2612792 2612530 4.260000e-79 305.0
15 TraesCS5D01G003000 chr5B 89.840 187 15 4 581 764 2883166 2883351 1.570000e-58 237.0
16 TraesCS5D01G003000 chr5A 91.114 1463 90 16 898 2326 1835030 1833574 0.000000e+00 1945.0
17 TraesCS5D01G003000 chr5A 83.114 1291 114 58 1088 2298 1714348 1713082 0.000000e+00 1081.0
18 TraesCS5D01G003000 chr5A 85.763 878 72 28 1441 2296 1759121 1758275 0.000000e+00 880.0
19 TraesCS5D01G003000 chr5A 91.132 530 27 7 335 844 1835875 1835346 0.000000e+00 701.0
20 TraesCS5D01G003000 chr5A 93.750 384 23 1 1952 2335 1803139 1802757 2.940000e-160 575.0
21 TraesCS5D01G003000 chr5A 92.000 350 24 2 2394 2743 1833253 1832908 3.940000e-134 488.0
22 TraesCS5D01G003000 chr5A 84.198 405 37 12 1052 1441 1759546 1759154 5.350000e-98 368.0
23 TraesCS5D01G003000 chr5A 90.500 200 18 1 583 782 1803409 1803211 2.600000e-66 263.0
24 TraesCS5D01G003000 chr5A 86.475 244 15 11 1088 1316 1336413 1336653 5.620000e-63 252.0
25 TraesCS5D01G003000 chr5A 89.418 189 15 3 2396 2580 1802522 1802335 2.040000e-57 233.0
26 TraesCS5D01G003000 chr5A 88.172 186 11 3 583 762 1760179 1759999 9.540000e-51 211.0
27 TraesCS5D01G003000 chr5A 85.149 101 14 1 433 533 1760273 1760174 5.990000e-18 102.0
28 TraesCS5D01G003000 chr5A 93.846 65 3 1 613 677 1714502 1714439 2.790000e-16 97.1
29 TraesCS5D01G003000 chr5A 100.000 40 0 0 2339 2378 1833524 1833485 1.310000e-09 75.0
30 TraesCS5D01G003000 chr5A 100.000 37 0 0 2347 2383 1802623 1802587 6.080000e-08 69.4
31 TraesCS5D01G003000 chr5A 93.478 46 2 1 2343 2387 1757901 1757856 2.190000e-07 67.6
32 TraesCS5D01G003000 chr2D 90.781 640 48 6 2763 3395 239067534 239066899 0.000000e+00 845.0
33 TraesCS5D01G003000 chr2D 89.591 269 22 3 70 338 558801621 558801359 1.510000e-88 337.0
34 TraesCS5D01G003000 chr2D 88.971 272 24 1 71 342 315859249 315858984 7.020000e-87 331.0
35 TraesCS5D01G003000 chr1D 90.723 636 49 5 2763 3391 397983758 397984390 0.000000e+00 839.0
36 TraesCS5D01G003000 chr3D 90.709 635 48 7 2763 3390 326536142 326536772 0.000000e+00 835.0
37 TraesCS5D01G003000 chr3D 90.110 637 51 7 2761 3390 473730062 473730693 0.000000e+00 817.0
38 TraesCS5D01G003000 chr3D 89.482 637 56 7 2762 3391 90495156 90494524 0.000000e+00 795.0
39 TraesCS5D01G003000 chr2A 90.328 641 51 7 2763 3395 1118077 1118714 0.000000e+00 830.0
40 TraesCS5D01G003000 chr6D 88.974 653 61 9 2751 3395 94826999 94827648 0.000000e+00 797.0
41 TraesCS5D01G003000 chr7A 89.259 270 23 4 72 341 672041119 672041382 1.950000e-87 333.0
42 TraesCS5D01G003000 chr7A 88.848 269 24 4 70 338 730827244 730826982 3.270000e-85 326.0
43 TraesCS5D01G003000 chr6A 89.299 271 21 6 70 339 614646499 614646762 1.950000e-87 333.0
44 TraesCS5D01G003000 chr4B 88.930 271 24 2 71 341 15428369 15428105 2.530000e-86 329.0
45 TraesCS5D01G003000 chr3A 88.603 272 25 4 67 338 399898171 399898436 3.270000e-85 326.0
46 TraesCS5D01G003000 chr1A 88.603 272 23 5 72 342 539684260 539683996 1.180000e-84 324.0


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 TraesCS5D01G003000 chr5D 2796228 2799622 3394 False 6270.000000 6270 100.000000 1 3395 1 chr5D.!!$F1 3394
1 TraesCS5D01G003000 chr5D 294597291 294597918 627 False 835.000000 835 90.808000 2762 3385 1 chr5D.!!$F4 623
2 TraesCS5D01G003000 chr5D 112713660 112714297 637 False 806.000000 806 89.580000 2760 3395 1 chr5D.!!$F2 635
3 TraesCS5D01G003000 chr5D 3070226 3071861 1635 False 504.000000 837 86.067667 580 2298 3 chr5D.!!$F6 1718
4 TraesCS5D01G003000 chr5D 3012529 3016439 3910 False 464.833333 1184 91.575667 1088 2495 3 chr5D.!!$F5 1407
5 TraesCS5D01G003000 chr5B 2804582 2806854 2272 False 1349.000000 1988 91.734500 335 2341 2 chr5B.!!$F1 2006
6 TraesCS5D01G003000 chr5B 2883166 2884815 1649 False 681.000000 1125 85.911500 581 2298 2 chr5B.!!$F2 1717
7 TraesCS5D01G003000 chr5B 2612530 2613864 1334 True 548.000000 791 86.377500 1492 2760 2 chr5B.!!$R1 1268
8 TraesCS5D01G003000 chr5A 1832908 1835875 2967 True 802.250000 1945 93.561500 335 2743 4 chr5A.!!$R4 2408
9 TraesCS5D01G003000 chr5A 1713082 1714502 1420 True 589.050000 1081 88.480000 613 2298 2 chr5A.!!$R1 1685
10 TraesCS5D01G003000 chr5A 1757856 1760273 2417 True 325.720000 880 87.352000 433 2387 5 chr5A.!!$R2 1954
11 TraesCS5D01G003000 chr5A 1802335 1803409 1074 True 285.100000 575 93.417000 583 2580 4 chr5A.!!$R3 1997
12 TraesCS5D01G003000 chr2D 239066899 239067534 635 True 845.000000 845 90.781000 2763 3395 1 chr2D.!!$R1 632
13 TraesCS5D01G003000 chr1D 397983758 397984390 632 False 839.000000 839 90.723000 2763 3391 1 chr1D.!!$F1 628
14 TraesCS5D01G003000 chr3D 326536142 326536772 630 False 835.000000 835 90.709000 2763 3390 1 chr3D.!!$F1 627
15 TraesCS5D01G003000 chr3D 473730062 473730693 631 False 817.000000 817 90.110000 2761 3390 1 chr3D.!!$F2 629
16 TraesCS5D01G003000 chr3D 90494524 90495156 632 True 795.000000 795 89.482000 2762 3391 1 chr3D.!!$R1 629
17 TraesCS5D01G003000 chr2A 1118077 1118714 637 False 830.000000 830 90.328000 2763 3395 1 chr2A.!!$F1 632
18 TraesCS5D01G003000 chr6D 94826999 94827648 649 False 797.000000 797 88.974000 2751 3395 1 chr6D.!!$F1 644

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
81 82 0.106619 ACTAGGCAGTACTCCCTCCG 60.107 60.0 9.19 4.55 31.45 4.63 F
82 83 0.106619 CTAGGCAGTACTCCCTCCGT 60.107 60.0 9.19 0.00 32.65 4.69 F
1032 1660 0.034896 CTCACTACACAACCCCGCTT 59.965 55.0 0.00 0.00 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1660 0.250234 CGGTGGAGATGAAGCTTCCA 59.750 55.0 23.42 12.02 0.00 3.53 R
1869 2676 0.332632 CCACCACCTCCACCATCATT 59.667 55.0 0.00 0.00 0.00 2.57 R
2656 6558 0.179045 GCCACGAGCATCATAGGGTT 60.179 55.0 0.00 0.00 42.97 4.11 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
25 26 7.618019 ATGAAGGCTAGATATTACCAGACAA 57.382 36.000 0.00 0.00 0.00 3.18
26 27 7.618019 TGAAGGCTAGATATTACCAGACAAT 57.382 36.000 0.00 0.00 0.00 2.71
27 28 8.721133 TGAAGGCTAGATATTACCAGACAATA 57.279 34.615 0.00 0.00 0.00 1.90
28 29 9.154632 TGAAGGCTAGATATTACCAGACAATAA 57.845 33.333 0.00 0.00 0.00 1.40
29 30 9.646427 GAAGGCTAGATATTACCAGACAATAAG 57.354 37.037 0.00 0.00 0.00 1.73
30 31 8.958060 AGGCTAGATATTACCAGACAATAAGA 57.042 34.615 0.00 0.00 0.00 2.10
31 32 9.381038 AGGCTAGATATTACCAGACAATAAGAA 57.619 33.333 0.00 0.00 0.00 2.52
59 60 9.933240 ACCAATTACTAGTAGTATCCAAGTACT 57.067 33.333 10.82 0.00 44.81 2.73
61 62 9.680315 CAATTACTAGTAGTATCCAAGTACTGC 57.320 37.037 10.82 0.00 43.03 4.40
62 63 8.991783 ATTACTAGTAGTATCCAAGTACTGCA 57.008 34.615 10.82 0.00 43.03 4.41
63 64 6.696441 ACTAGTAGTATCCAAGTACTGCAC 57.304 41.667 0.00 0.00 43.03 4.57
64 65 6.424883 ACTAGTAGTATCCAAGTACTGCACT 58.575 40.000 0.00 0.00 43.03 4.40
65 66 7.571919 ACTAGTAGTATCCAAGTACTGCACTA 58.428 38.462 0.00 0.00 43.03 2.74
66 67 6.945938 AGTAGTATCCAAGTACTGCACTAG 57.054 41.667 0.00 0.00 41.84 2.57
67 68 5.828859 AGTAGTATCCAAGTACTGCACTAGG 59.171 44.000 0.00 0.00 41.84 3.02
68 69 2.990066 ATCCAAGTACTGCACTAGGC 57.010 50.000 0.00 0.00 45.13 3.93
78 79 2.903404 GCACTAGGCAGTACTCCCT 58.097 57.895 10.99 10.99 43.97 4.20
79 80 0.747852 GCACTAGGCAGTACTCCCTC 59.252 60.000 9.19 0.00 43.97 4.30
80 81 1.404843 CACTAGGCAGTACTCCCTCC 58.595 60.000 9.19 0.12 32.21 4.30
81 82 0.106619 ACTAGGCAGTACTCCCTCCG 60.107 60.000 9.19 4.55 31.45 4.63
82 83 0.106619 CTAGGCAGTACTCCCTCCGT 60.107 60.000 9.19 0.00 32.65 4.69
83 84 0.333993 TAGGCAGTACTCCCTCCGTT 59.666 55.000 9.19 0.00 32.65 4.44
84 85 0.544595 AGGCAGTACTCCCTCCGTTT 60.545 55.000 0.00 0.00 0.00 3.60
85 86 0.323957 GGCAGTACTCCCTCCGTTTT 59.676 55.000 0.00 0.00 0.00 2.43
86 87 1.271217 GGCAGTACTCCCTCCGTTTTT 60.271 52.381 0.00 0.00 0.00 1.94
87 88 2.027837 GGCAGTACTCCCTCCGTTTTTA 60.028 50.000 0.00 0.00 0.00 1.52
88 89 3.370209 GGCAGTACTCCCTCCGTTTTTAT 60.370 47.826 0.00 0.00 0.00 1.40
89 90 4.259356 GCAGTACTCCCTCCGTTTTTATT 58.741 43.478 0.00 0.00 0.00 1.40
90 91 4.698780 GCAGTACTCCCTCCGTTTTTATTT 59.301 41.667 0.00 0.00 0.00 1.40
91 92 5.876460 GCAGTACTCCCTCCGTTTTTATTTA 59.124 40.000 0.00 0.00 0.00 1.40
92 93 6.036844 GCAGTACTCCCTCCGTTTTTATTTAG 59.963 42.308 0.00 0.00 0.00 1.85
93 94 7.101700 CAGTACTCCCTCCGTTTTTATTTAGT 58.898 38.462 0.00 0.00 0.00 2.24
94 95 7.605309 CAGTACTCCCTCCGTTTTTATTTAGTT 59.395 37.037 0.00 0.00 0.00 2.24
95 96 7.821359 AGTACTCCCTCCGTTTTTATTTAGTTC 59.179 37.037 0.00 0.00 0.00 3.01
96 97 5.640783 ACTCCCTCCGTTTTTATTTAGTTCG 59.359 40.000 0.00 0.00 0.00 3.95
97 98 4.392754 TCCCTCCGTTTTTATTTAGTTCGC 59.607 41.667 0.00 0.00 0.00 4.70
98 99 4.328667 CCTCCGTTTTTATTTAGTTCGCG 58.671 43.478 0.00 0.00 0.00 5.87
99 100 4.143052 CCTCCGTTTTTATTTAGTTCGCGT 60.143 41.667 5.77 0.00 0.00 6.01
100 101 5.062058 CCTCCGTTTTTATTTAGTTCGCGTA 59.938 40.000 5.77 0.00 0.00 4.42
101 102 6.237915 CCTCCGTTTTTATTTAGTTCGCGTAT 60.238 38.462 5.77 0.00 0.00 3.06
102 103 7.059448 TCCGTTTTTATTTAGTTCGCGTATT 57.941 32.000 5.77 0.00 0.00 1.89
103 104 8.179148 TCCGTTTTTATTTAGTTCGCGTATTA 57.821 30.769 5.77 0.00 0.00 0.98
104 105 8.320295 TCCGTTTTTATTTAGTTCGCGTATTAG 58.680 33.333 5.77 0.00 0.00 1.73
105 106 7.109259 CCGTTTTTATTTAGTTCGCGTATTAGC 59.891 37.037 5.77 0.00 0.00 3.09
106 107 7.842721 CGTTTTTATTTAGTTCGCGTATTAGCT 59.157 33.333 5.77 0.00 34.40 3.32
107 108 9.481800 GTTTTTATTTAGTTCGCGTATTAGCTT 57.518 29.630 5.77 0.00 34.40 3.74
109 110 9.480538 TTTTATTTAGTTCGCGTATTAGCTTTG 57.519 29.630 5.77 0.00 34.40 2.77
110 111 5.459110 TTTAGTTCGCGTATTAGCTTTGG 57.541 39.130 5.77 0.00 34.40 3.28
111 112 2.968675 AGTTCGCGTATTAGCTTTGGT 58.031 42.857 5.77 0.00 34.40 3.67
112 113 2.928116 AGTTCGCGTATTAGCTTTGGTC 59.072 45.455 5.77 0.00 34.40 4.02
113 114 2.658373 TCGCGTATTAGCTTTGGTCA 57.342 45.000 5.77 0.00 34.40 4.02
114 115 2.962125 TCGCGTATTAGCTTTGGTCAA 58.038 42.857 5.77 0.00 34.40 3.18
115 116 3.327626 TCGCGTATTAGCTTTGGTCAAA 58.672 40.909 5.77 0.00 34.40 2.69
130 131 8.099364 CTTTGGTCAAAGTCAAGCTTTATAGA 57.901 34.615 13.58 0.00 44.95 1.98
131 132 7.435068 TTGGTCAAAGTCAAGCTTTATAGAC 57.565 36.000 0.00 0.75 44.95 2.59
132 133 6.769512 TGGTCAAAGTCAAGCTTTATAGACT 58.230 36.000 10.53 10.53 44.95 3.24
139 140 8.854614 AAGTCAAGCTTTATAGACTTTGACAT 57.145 30.769 19.06 2.76 46.02 3.06
140 141 9.944376 AAGTCAAGCTTTATAGACTTTGACATA 57.056 29.630 19.06 0.00 46.02 2.29
141 142 9.593134 AGTCAAGCTTTATAGACTTTGACATAG 57.407 33.333 10.53 0.00 38.08 2.23
142 143 9.372369 GTCAAGCTTTATAGACTTTGACATAGT 57.628 33.333 0.00 0.00 0.00 2.12
143 144 9.944376 TCAAGCTTTATAGACTTTGACATAGTT 57.056 29.630 0.00 0.00 0.00 2.24
175 176 9.486497 ACAAAAATATGAACACATGCAATAACA 57.514 25.926 0.00 0.00 0.00 2.41
180 181 9.872721 AATATGAACACATGCAATAACAAATCA 57.127 25.926 0.00 0.00 0.00 2.57
181 182 9.872721 ATATGAACACATGCAATAACAAATCAA 57.127 25.926 0.00 0.00 0.00 2.57
182 183 8.780846 ATGAACACATGCAATAACAAATCAAT 57.219 26.923 0.00 0.00 0.00 2.57
183 184 9.872721 ATGAACACATGCAATAACAAATCAATA 57.127 25.926 0.00 0.00 0.00 1.90
184 185 9.138062 TGAACACATGCAATAACAAATCAATAC 57.862 29.630 0.00 0.00 0.00 1.89
185 186 8.477984 AACACATGCAATAACAAATCAATACC 57.522 30.769 0.00 0.00 0.00 2.73
186 187 7.609960 ACACATGCAATAACAAATCAATACCA 58.390 30.769 0.00 0.00 0.00 3.25
187 188 8.259411 ACACATGCAATAACAAATCAATACCAT 58.741 29.630 0.00 0.00 0.00 3.55
188 189 9.100554 CACATGCAATAACAAATCAATACCATT 57.899 29.630 0.00 0.00 0.00 3.16
302 303 9.788960 ACTTTAAGAAGTTTGATTTCAGTCAAC 57.211 29.630 0.00 0.00 43.48 3.18
305 306 7.872113 AAGAAGTTTGATTTCAGTCAACTCT 57.128 32.000 0.00 0.00 37.80 3.24
306 307 8.964476 AAGAAGTTTGATTTCAGTCAACTCTA 57.036 30.769 0.00 0.00 37.80 2.43
307 308 8.964476 AGAAGTTTGATTTCAGTCAACTCTAA 57.036 30.769 0.00 0.00 37.80 2.10
308 309 9.566432 AGAAGTTTGATTTCAGTCAACTCTAAT 57.434 29.630 0.00 0.00 37.80 1.73
312 313 9.495754 GTTTGATTTCAGTCAACTCTAATATGC 57.504 33.333 0.00 0.00 37.80 3.14
313 314 8.791327 TTGATTTCAGTCAACTCTAATATGCA 57.209 30.769 0.00 0.00 33.41 3.96
314 315 8.429493 TGATTTCAGTCAACTCTAATATGCAG 57.571 34.615 0.00 0.00 0.00 4.41
315 316 8.260114 TGATTTCAGTCAACTCTAATATGCAGA 58.740 33.333 0.00 0.00 0.00 4.26
316 317 8.659925 ATTTCAGTCAACTCTAATATGCAGAG 57.340 34.615 11.37 11.37 44.28 3.35
332 333 9.515226 AATATGCAGAGTAAGTAAAAACCAAGA 57.485 29.630 0.00 0.00 0.00 3.02
333 334 6.861065 TGCAGAGTAAGTAAAAACCAAGAG 57.139 37.500 0.00 0.00 0.00 2.85
338 339 9.930693 CAGAGTAAGTAAAAACCAAGAGAGTAT 57.069 33.333 0.00 0.00 0.00 2.12
357 358 6.493458 AGAGTATTACAAGTTTGCAAATGGGT 59.507 34.615 16.21 15.00 0.00 4.51
417 437 5.474825 TCCCTCAACAACAACAAAAAGAAC 58.525 37.500 0.00 0.00 0.00 3.01
463 483 4.939509 TCTGGCGTAAACTTTGCTAATC 57.060 40.909 0.00 0.00 0.00 1.75
468 488 4.438744 GGCGTAAACTTTGCTAATCTGCAT 60.439 41.667 0.00 0.00 42.96 3.96
534 555 3.325716 TGTAGGTGACTAGAAACCCAACC 59.674 47.826 12.98 3.15 45.49 3.77
594 615 4.599041 AGGATGCAACACCTAATAAAGCA 58.401 39.130 8.38 0.00 34.47 3.91
788 820 1.352114 TGCAAACGTACTACATCGCC 58.648 50.000 0.00 0.00 0.00 5.54
830 862 5.738619 TTGCTCCTAGATGAACAGTAACA 57.261 39.130 0.00 0.00 0.00 2.41
836 868 7.041372 GCTCCTAGATGAACAGTAACACAAAAA 60.041 37.037 0.00 0.00 0.00 1.94
881 928 7.499321 TTTTATGGATGTTCGTGTTAGTGTT 57.501 32.000 0.00 0.00 0.00 3.32
882 929 7.499321 TTTATGGATGTTCGTGTTAGTGTTT 57.501 32.000 0.00 0.00 0.00 2.83
993 1618 1.843376 CTCACCCCCACTCACCACT 60.843 63.158 0.00 0.00 0.00 4.00
1032 1660 0.034896 CTCACTACACAACCCCGCTT 59.965 55.000 0.00 0.00 0.00 4.68
1086 1717 1.074752 GTCTTCTTCTTGCGCTCTGG 58.925 55.000 9.73 0.00 0.00 3.86
1119 1755 1.215647 GTTCGAGATGACGGTGGCT 59.784 57.895 0.00 0.00 0.00 4.75
1323 2010 1.521010 CATGAGCCACGAGAGCCTG 60.521 63.158 0.00 0.00 0.00 4.85
1766 2567 2.337532 GCAACAGCAACAGCCAGG 59.662 61.111 0.00 0.00 0.00 4.45
1815 2616 2.855963 TGTTGAAGAAGTTGTCGACGAC 59.144 45.455 25.65 25.65 31.72 4.34
1841 2648 1.127343 GATGAAGTGGAGGAGGAGGG 58.873 60.000 0.00 0.00 0.00 4.30
1869 2676 2.203938 GAGGTGGTGGACAGGGGA 60.204 66.667 0.00 0.00 0.00 4.81
1873 2680 1.497309 GGTGGTGGACAGGGGAATGA 61.497 60.000 0.00 0.00 0.00 2.57
1941 2748 3.060895 GGATCGTCATCAACAAGTTCGTC 59.939 47.826 0.00 0.00 0.00 4.20
2297 3131 5.116180 CGCCTGATCATTACTCCAAACTAA 58.884 41.667 0.00 0.00 0.00 2.24
2498 6396 3.125316 CGAGAGTGAAGTTATGTTTGCCC 59.875 47.826 0.00 0.00 0.00 5.36
2520 6418 3.634397 TGGTCTCCAAATCATGTCTCC 57.366 47.619 0.00 0.00 0.00 3.71
2527 6427 3.070159 TCCAAATCATGTCTCCGATCTCC 59.930 47.826 0.00 0.00 0.00 3.71
2555 6455 5.817296 ACCAAAAATTTGAAGAGGAAAGCAC 59.183 36.000 7.44 0.00 40.55 4.40
2574 6476 8.630054 AAAGCACCACTTGTTAGATATAAACA 57.370 30.769 0.13 0.13 39.09 2.83
2634 6536 8.363390 TGCTCAGAACACCTCATTAGATAATAG 58.637 37.037 0.00 0.00 0.00 1.73
2746 6648 1.208535 CGGTGGAGCCAAGGTTATGTA 59.791 52.381 0.00 0.00 36.97 2.29
2747 6649 2.640184 GGTGGAGCCAAGGTTATGTAC 58.360 52.381 0.00 0.00 37.17 2.90
2750 6652 2.026636 TGGAGCCAAGGTTATGTACACC 60.027 50.000 0.00 0.00 34.06 4.16
2769 6671 4.265056 GCAGGGGTGGTGTCGGTT 62.265 66.667 0.00 0.00 0.00 4.44
2840 6744 4.508662 GATCAAGGGTAACAGGAGACAAG 58.491 47.826 0.00 0.00 39.74 3.16
2844 6748 1.652947 GGTAACAGGAGACAAGGGGA 58.347 55.000 0.00 0.00 0.00 4.81
2972 6876 2.791347 TCGCAATGGCTAAACCCTAA 57.209 45.000 0.00 0.00 37.83 2.69
3180 7088 1.612146 TTCTCGGCCCATCAGTCCA 60.612 57.895 0.00 0.00 0.00 4.02
3190 7098 3.411114 ATCAGTCCAGCCCATGCCG 62.411 63.158 0.00 0.00 38.69 5.69
3229 7137 3.913163 GAGGATCCCATAATCCAGGACTT 59.087 47.826 8.55 0.00 46.56 3.01
3239 7147 3.767309 ATCCAGGACTTCCTCAGTAGT 57.233 47.619 0.00 0.00 46.65 2.73
3268 7181 7.793888 CCGAACTTCAATGACGATGTAATATTG 59.206 37.037 0.00 0.00 0.00 1.90
3309 7222 2.009774 CAAGGCGGGTTCTTCACTATG 58.990 52.381 0.00 0.00 0.00 2.23
3359 7272 9.387123 GATAATCTTGATGCCTTTTTACGATTC 57.613 33.333 0.00 0.00 0.00 2.52
3392 7306 0.519175 CTTCGATTTCCGTGCGCTTG 60.519 55.000 9.73 0.00 39.75 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.721133 TTGTCTGGTAATATCTAGCCTTCATA 57.279 34.615 0.00 0.00 0.00 2.15
1 2 7.618019 TTGTCTGGTAATATCTAGCCTTCAT 57.382 36.000 0.00 0.00 0.00 2.57
2 3 7.618019 ATTGTCTGGTAATATCTAGCCTTCA 57.382 36.000 0.00 0.00 0.00 3.02
33 34 9.933240 AGTACTTGGATACTACTAGTAATTGGT 57.067 33.333 3.76 1.10 33.89 3.67
35 36 9.680315 GCAGTACTTGGATACTACTAGTAATTG 57.320 37.037 3.76 0.00 33.89 2.32
36 37 9.417561 TGCAGTACTTGGATACTACTAGTAATT 57.582 33.333 3.76 0.00 33.89 1.40
37 38 8.848182 GTGCAGTACTTGGATACTACTAGTAAT 58.152 37.037 3.76 0.00 33.89 1.89
38 39 8.051535 AGTGCAGTACTTGGATACTACTAGTAA 58.948 37.037 3.76 0.00 35.67 2.24
39 40 7.571919 AGTGCAGTACTTGGATACTACTAGTA 58.428 38.462 1.89 1.89 35.67 1.82
40 41 6.424883 AGTGCAGTACTTGGATACTACTAGT 58.575 40.000 0.00 0.00 35.67 2.57
41 42 6.945938 AGTGCAGTACTTGGATACTACTAG 57.054 41.667 0.00 0.00 35.67 2.57
43 44 6.945938 CTAGTGCAGTACTTGGATACTACT 57.054 41.667 0.00 0.00 40.89 2.57
66 67 0.323957 AAAACGGAGGGAGTACTGCC 59.676 55.000 24.99 24.99 41.91 4.85
67 68 2.180432 AAAAACGGAGGGAGTACTGC 57.820 50.000 5.70 5.70 0.00 4.40
68 69 7.101700 ACTAAATAAAAACGGAGGGAGTACTG 58.898 38.462 0.00 0.00 0.00 2.74
69 70 7.250032 ACTAAATAAAAACGGAGGGAGTACT 57.750 36.000 0.00 0.00 0.00 2.73
70 71 7.201470 CGAACTAAATAAAAACGGAGGGAGTAC 60.201 40.741 0.00 0.00 0.00 2.73
71 72 6.813152 CGAACTAAATAAAAACGGAGGGAGTA 59.187 38.462 0.00 0.00 0.00 2.59
72 73 5.640783 CGAACTAAATAAAAACGGAGGGAGT 59.359 40.000 0.00 0.00 0.00 3.85
73 74 5.446875 GCGAACTAAATAAAAACGGAGGGAG 60.447 44.000 0.00 0.00 0.00 4.30
74 75 4.392754 GCGAACTAAATAAAAACGGAGGGA 59.607 41.667 0.00 0.00 0.00 4.20
75 76 4.655027 GCGAACTAAATAAAAACGGAGGG 58.345 43.478 0.00 0.00 0.00 4.30
76 77 4.143052 ACGCGAACTAAATAAAAACGGAGG 60.143 41.667 15.93 0.00 0.00 4.30
77 78 4.949756 ACGCGAACTAAATAAAAACGGAG 58.050 39.130 15.93 0.00 0.00 4.63
78 79 4.988708 ACGCGAACTAAATAAAAACGGA 57.011 36.364 15.93 0.00 0.00 4.69
79 80 7.109259 GCTAATACGCGAACTAAATAAAAACGG 59.891 37.037 15.93 0.00 0.00 4.44
80 81 7.842721 AGCTAATACGCGAACTAAATAAAAACG 59.157 33.333 15.93 0.00 34.40 3.60
81 82 9.481800 AAGCTAATACGCGAACTAAATAAAAAC 57.518 29.630 15.93 0.00 34.40 2.43
83 84 9.480538 CAAAGCTAATACGCGAACTAAATAAAA 57.519 29.630 15.93 0.00 34.40 1.52
84 85 8.117988 CCAAAGCTAATACGCGAACTAAATAAA 58.882 33.333 15.93 0.00 34.40 1.40
85 86 7.278424 ACCAAAGCTAATACGCGAACTAAATAA 59.722 33.333 15.93 0.00 34.40 1.40
86 87 6.757947 ACCAAAGCTAATACGCGAACTAAATA 59.242 34.615 15.93 0.00 34.40 1.40
87 88 5.583457 ACCAAAGCTAATACGCGAACTAAAT 59.417 36.000 15.93 0.00 34.40 1.40
88 89 4.931002 ACCAAAGCTAATACGCGAACTAAA 59.069 37.500 15.93 0.00 34.40 1.85
89 90 4.497300 ACCAAAGCTAATACGCGAACTAA 58.503 39.130 15.93 0.00 34.40 2.24
90 91 4.107622 GACCAAAGCTAATACGCGAACTA 58.892 43.478 15.93 0.00 34.40 2.24
91 92 2.928116 GACCAAAGCTAATACGCGAACT 59.072 45.455 15.93 0.00 34.40 3.01
92 93 2.669434 TGACCAAAGCTAATACGCGAAC 59.331 45.455 15.93 0.00 34.40 3.95
93 94 2.962125 TGACCAAAGCTAATACGCGAA 58.038 42.857 15.93 0.00 34.40 4.70
94 95 2.658373 TGACCAAAGCTAATACGCGA 57.342 45.000 15.93 0.00 34.40 5.87
95 96 3.670203 CTTTGACCAAAGCTAATACGCG 58.330 45.455 3.53 3.53 40.94 6.01
115 116 9.593134 CTATGTCAAAGTCTATAAAGCTTGACT 57.407 33.333 10.53 10.53 40.95 3.41
116 117 9.372369 ACTATGTCAAAGTCTATAAAGCTTGAC 57.628 33.333 0.00 2.80 0.00 3.18
117 118 9.944376 AACTATGTCAAAGTCTATAAAGCTTGA 57.056 29.630 0.00 0.00 0.00 3.02
149 150 9.486497 TGTTATTGCATGTGTTCATATTTTTGT 57.514 25.926 0.00 0.00 32.47 2.83
154 155 9.872721 TGATTTGTTATTGCATGTGTTCATATT 57.127 25.926 0.00 0.00 32.47 1.28
155 156 9.872721 TTGATTTGTTATTGCATGTGTTCATAT 57.127 25.926 0.00 0.00 32.47 1.78
156 157 9.872721 ATTGATTTGTTATTGCATGTGTTCATA 57.127 25.926 0.00 0.00 32.47 2.15
157 158 8.780846 ATTGATTTGTTATTGCATGTGTTCAT 57.219 26.923 0.00 0.00 34.21 2.57
158 159 9.138062 GTATTGATTTGTTATTGCATGTGTTCA 57.862 29.630 0.00 0.00 0.00 3.18
159 160 8.594687 GGTATTGATTTGTTATTGCATGTGTTC 58.405 33.333 0.00 0.00 0.00 3.18
160 161 8.093307 TGGTATTGATTTGTTATTGCATGTGTT 58.907 29.630 0.00 0.00 0.00 3.32
161 162 7.609960 TGGTATTGATTTGTTATTGCATGTGT 58.390 30.769 0.00 0.00 0.00 3.72
162 163 8.651391 ATGGTATTGATTTGTTATTGCATGTG 57.349 30.769 0.00 0.00 0.00 3.21
279 280 9.396022 AGAGTTGACTGAAATCAAACTTCTTAA 57.604 29.630 1.69 0.00 40.22 1.85
280 281 8.964476 AGAGTTGACTGAAATCAAACTTCTTA 57.036 30.769 1.69 0.00 40.22 2.10
281 282 7.872113 AGAGTTGACTGAAATCAAACTTCTT 57.128 32.000 1.69 0.00 40.22 2.52
282 283 8.964476 TTAGAGTTGACTGAAATCAAACTTCT 57.036 30.769 1.69 0.00 40.22 2.85
286 287 9.495754 GCATATTAGAGTTGACTGAAATCAAAC 57.504 33.333 0.00 0.00 40.22 2.93
287 288 9.230122 TGCATATTAGAGTTGACTGAAATCAAA 57.770 29.630 0.00 0.00 40.22 2.69
288 289 8.791327 TGCATATTAGAGTTGACTGAAATCAA 57.209 30.769 0.00 0.00 36.23 2.57
289 290 8.260114 TCTGCATATTAGAGTTGACTGAAATCA 58.740 33.333 0.00 0.00 30.70 2.57
290 291 8.654230 TCTGCATATTAGAGTTGACTGAAATC 57.346 34.615 0.00 0.00 0.00 2.17
291 292 8.659925 CTCTGCATATTAGAGTTGACTGAAAT 57.340 34.615 5.84 0.00 37.48 2.17
306 307 9.515226 TCTTGGTTTTTACTTACTCTGCATATT 57.485 29.630 0.00 0.00 0.00 1.28
307 308 9.167311 CTCTTGGTTTTTACTTACTCTGCATAT 57.833 33.333 0.00 0.00 0.00 1.78
308 309 8.372459 TCTCTTGGTTTTTACTTACTCTGCATA 58.628 33.333 0.00 0.00 0.00 3.14
309 310 7.224297 TCTCTTGGTTTTTACTTACTCTGCAT 58.776 34.615 0.00 0.00 0.00 3.96
310 311 6.588204 TCTCTTGGTTTTTACTTACTCTGCA 58.412 36.000 0.00 0.00 0.00 4.41
311 312 6.706716 ACTCTCTTGGTTTTTACTTACTCTGC 59.293 38.462 0.00 0.00 0.00 4.26
312 313 9.930693 ATACTCTCTTGGTTTTTACTTACTCTG 57.069 33.333 0.00 0.00 0.00 3.35
323 324 8.135529 GCAAACTTGTAATACTCTCTTGGTTTT 58.864 33.333 0.00 0.00 0.00 2.43
324 325 7.284489 TGCAAACTTGTAATACTCTCTTGGTTT 59.716 33.333 0.00 0.00 0.00 3.27
325 326 6.770785 TGCAAACTTGTAATACTCTCTTGGTT 59.229 34.615 0.00 0.00 0.00 3.67
326 327 6.296026 TGCAAACTTGTAATACTCTCTTGGT 58.704 36.000 0.00 0.00 0.00 3.67
327 328 6.801539 TGCAAACTTGTAATACTCTCTTGG 57.198 37.500 0.00 0.00 0.00 3.61
328 329 9.121517 CATTTGCAAACTTGTAATACTCTCTTG 57.878 33.333 15.41 0.00 32.91 3.02
329 330 8.299570 CCATTTGCAAACTTGTAATACTCTCTT 58.700 33.333 15.41 0.00 32.91 2.85
330 331 7.094205 CCCATTTGCAAACTTGTAATACTCTCT 60.094 37.037 15.41 0.00 32.91 3.10
331 332 7.029563 CCCATTTGCAAACTTGTAATACTCTC 58.970 38.462 15.41 0.00 32.91 3.20
332 333 6.493458 ACCCATTTGCAAACTTGTAATACTCT 59.507 34.615 15.41 0.00 32.91 3.24
333 334 6.687604 ACCCATTTGCAAACTTGTAATACTC 58.312 36.000 15.41 0.00 32.91 2.59
476 497 6.251376 CGGCAACTAGAAATAATTTGCACTTC 59.749 38.462 12.36 0.00 43.54 3.01
534 555 0.386352 CAAGCATCAAGTGTGCCGTG 60.386 55.000 0.00 0.00 43.50 4.94
864 911 4.904154 GCTTGAAACACTAACACGAACATC 59.096 41.667 0.00 0.00 0.00 3.06
993 1618 4.342092 TGAGATTGTGAGTGAGTGAGTGAA 59.658 41.667 0.00 0.00 0.00 3.18
1032 1660 0.250234 CGGTGGAGATGAAGCTTCCA 59.750 55.000 23.42 12.02 0.00 3.53
1067 1695 1.074752 CCAGAGCGCAAGAAGAAGAC 58.925 55.000 11.47 0.00 43.02 3.01
1086 1717 5.219226 TCTCGAACGATCTACAGAAAGAC 57.781 43.478 0.00 0.00 0.00 3.01
1323 2010 2.493973 CTCTCCGTGCAGAGGCTC 59.506 66.667 6.34 6.34 41.91 4.70
1409 2099 3.680786 CGCTCTGGTGGGACGACA 61.681 66.667 0.00 0.00 0.00 4.35
1766 2567 0.599558 TTGCAGCATCTGTTCTTGGC 59.400 50.000 0.00 0.00 33.43 4.52
1815 2616 3.430098 CCTCCTCCACTTCATCTTCTTCG 60.430 52.174 0.00 0.00 0.00 3.79
1841 2648 3.391382 CCACCTCCACCTCGTCCC 61.391 72.222 0.00 0.00 0.00 4.46
1869 2676 0.332632 CCACCACCTCCACCATCATT 59.667 55.000 0.00 0.00 0.00 2.57
1873 2680 4.033776 CGCCACCACCTCCACCAT 62.034 66.667 0.00 0.00 0.00 3.55
2297 3131 1.392589 AAATTGGCGGCGATGAAGAT 58.607 45.000 12.98 0.00 0.00 2.40
2393 3829 7.148755 GCGTGACATGCTAAAAGAATGAAAATT 60.149 33.333 12.54 0.00 32.78 1.82
2483 6352 3.763897 AGACCATGGGCAAACATAACTTC 59.236 43.478 22.78 0.72 0.00 3.01
2498 6396 3.881688 GGAGACATGATTTGGAGACCATG 59.118 47.826 0.00 0.00 41.40 3.66
2520 6418 5.953183 TCAAATTTTTGGTCATGGAGATCG 58.047 37.500 3.38 0.00 38.66 3.69
2527 6427 7.307573 GCTTTCCTCTTCAAATTTTTGGTCATG 60.308 37.037 3.38 0.00 38.66 3.07
2602 6504 2.036475 TGAGGTGTTCTGAGCAAGAGAC 59.964 50.000 0.00 0.00 35.91 3.36
2656 6558 0.179045 GCCACGAGCATCATAGGGTT 60.179 55.000 0.00 0.00 42.97 4.11
2668 6570 2.040544 GGTGTCCAATGGCCACGAG 61.041 63.158 8.16 0.00 0.00 4.18
2718 6620 0.321564 TTGGCTCCACCGTTCATCAG 60.322 55.000 0.00 0.00 43.94 2.90
2750 6652 4.704833 CCGACACCACCCCTGCAG 62.705 72.222 6.78 6.78 0.00 4.41
2769 6671 0.878416 CAAGATCGGCCGGTTTTGAA 59.122 50.000 32.03 9.52 0.00 2.69
2822 6724 1.985895 CCCTTGTCTCCTGTTACCCTT 59.014 52.381 0.00 0.00 0.00 3.95
2824 6726 0.618981 CCCCTTGTCTCCTGTTACCC 59.381 60.000 0.00 0.00 0.00 3.69
2840 6744 3.023832 CTGGGTAAACATCATGTTCCCC 58.976 50.000 23.06 23.06 44.91 4.81
2844 6748 3.756434 CGAACCTGGGTAAACATCATGTT 59.244 43.478 0.00 0.00 43.41 2.71
2889 6793 3.840666 AGTCAATCAAGCAGGAAGTAGGA 59.159 43.478 0.00 0.00 0.00 2.94
2956 6860 6.238759 GCTAGACATTTAGGGTTTAGCCATTG 60.239 42.308 0.00 0.00 40.90 2.82
2997 6902 5.322754 CGGAGGGTTTAGTCCATAGAGATA 58.677 45.833 0.00 0.00 32.55 1.98
3180 7088 4.489771 GGCTGTACGGCATGGGCT 62.490 66.667 27.29 0.00 40.87 5.19
3212 7120 3.438131 AGGAAGTCCTGGATTATGGGA 57.562 47.619 0.00 0.00 46.55 4.37
3229 7137 0.702902 AGTTCGGGGACTACTGAGGA 59.297 55.000 0.00 0.00 0.00 3.71
3239 7147 0.970640 TCGTCATTGAAGTTCGGGGA 59.029 50.000 0.00 0.00 0.00 4.81
3268 7181 3.591254 AAGCCGAAGACGTGAGCCC 62.591 63.158 0.00 0.00 37.88 5.19
3309 7222 1.341531 AGATTGTCATCGGTCCGGATC 59.658 52.381 7.81 5.81 34.17 3.36


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

AutoCloner maintained by Alex Coulton.