Multiple sequence alignment - TraesCS2A01G250000

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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 TraesCS2A01G250000 chr2A 100.000 3351 0 0 1 3351 376754836 376751486 0.000000e+00 6189.0
1 TraesCS2A01G250000 chr2A 90.036 1124 100 10 2231 3351 442137767 442138881 0.000000e+00 1445.0
2 TraesCS2A01G250000 chr2A 92.780 651 40 5 965 1613 385649368 385650013 0.000000e+00 935.0
3 TraesCS2A01G250000 chr2A 90.233 430 34 7 2925 3351 726860923 726861347 3.780000e-154 555.0
4 TraesCS2A01G250000 chr2A 88.889 378 37 4 1634 2007 413902383 413902759 8.470000e-126 460.0
5 TraesCS2A01G250000 chr2A 88.295 393 27 8 1609 1983 726860392 726860783 1.420000e-123 453.0
6 TraesCS2A01G250000 chr2A 91.453 117 10 0 2777 2893 726860810 726860926 9.620000e-36 161.0
7 TraesCS2A01G250000 chr2A 78.616 159 27 7 66 222 544358462 544358615 7.650000e-17 99.0
8 TraesCS2A01G250000 chr3D 95.317 2242 95 8 469 2702 212867114 212869353 0.000000e+00 3550.0
9 TraesCS2A01G250000 chr3D 95.489 665 26 3 2687 3351 212869366 212870026 0.000000e+00 1059.0
10 TraesCS2A01G250000 chr3D 89.242 409 41 2 2278 2684 286532727 286532320 2.980000e-140 508.0
11 TraesCS2A01G250000 chr3D 89.773 88 8 1 272 358 212866672 212866759 9.830000e-21 111.0
12 TraesCS2A01G250000 chr3D 91.304 69 5 1 2159 2227 286534051 286533984 3.560000e-15 93.5
13 TraesCS2A01G250000 chr3D 100.000 40 0 0 425 464 212867113 212867152 1.290000e-09 75.0
14 TraesCS2A01G250000 chr7A 93.949 1223 69 4 445 1662 73888165 73886943 0.000000e+00 1844.0
15 TraesCS2A01G250000 chr7A 85.326 736 83 11 2040 2754 526528600 526529331 0.000000e+00 737.0
16 TraesCS2A01G250000 chr7A 91.628 215 16 2 257 470 73888310 73888097 2.530000e-76 296.0
17 TraesCS2A01G250000 chr7A 90.323 155 15 0 2936 3090 238550909 238550755 1.580000e-48 204.0
18 TraesCS2A01G250000 chr4A 93.713 1193 55 4 445 1634 153048518 153049693 0.000000e+00 1770.0
19 TraesCS2A01G250000 chr4A 85.635 543 72 5 2277 2814 238767501 238766960 1.750000e-157 566.0
20 TraesCS2A01G250000 chr4A 93.365 211 12 2 258 467 153048374 153048583 9.030000e-81 311.0
21 TraesCS2A01G250000 chr6B 89.247 1302 90 22 2069 3351 716082119 716080849 0.000000e+00 1583.0
22 TraesCS2A01G250000 chr6B 88.744 613 62 5 2290 2899 233232104 233231496 0.000000e+00 743.0
23 TraesCS2A01G250000 chr6B 86.380 558 68 6 2278 2828 471136051 471136607 1.330000e-168 603.0
24 TraesCS2A01G250000 chr6B 88.117 446 40 7 1609 2042 703954150 703954594 4.960000e-143 518.0
25 TraesCS2A01G250000 chr6B 90.520 327 27 4 3025 3351 703955646 703955968 2.390000e-116 429.0
26 TraesCS2A01G250000 chr5B 87.602 613 69 5 2290 2899 592100322 592100930 0.000000e+00 704.0
27 TraesCS2A01G250000 chr3A 90.000 430 35 7 2925 3351 573331969 573331545 1.760000e-152 549.0
28 TraesCS2A01G250000 chr3A 90.051 392 21 8 1609 1983 573332499 573332109 3.000000e-135 492.0
29 TraesCS2A01G250000 chr3A 82.759 87 12 3 3 87 259330253 259330168 1.290000e-09 75.0
30 TraesCS2A01G250000 chr6A 89.486 428 41 4 2925 3351 296770593 296771017 3.800000e-149 538.0
31 TraesCS2A01G250000 chr6A 87.563 394 25 7 1609 1983 296770065 296770453 5.130000e-118 435.0
32 TraesCS2A01G250000 chr6A 78.437 371 66 12 2004 2363 169249053 169248686 2.600000e-56 230.0
33 TraesCS2A01G250000 chr6A 89.744 117 12 0 2777 2893 296770480 296770596 2.080000e-32 150.0
34 TraesCS2A01G250000 chr7B 88.117 446 39 8 1609 2042 331037903 331037460 4.960000e-143 518.0
35 TraesCS2A01G250000 chr7B 86.996 446 44 8 1609 2042 296240875 296240432 1.080000e-134 490.0
36 TraesCS2A01G250000 chr7B 90.854 328 24 6 3025 3351 296239349 296239027 5.130000e-118 435.0
37 TraesCS2A01G250000 chr7B 90.549 328 24 6 3025 3351 331036376 331036055 8.590000e-116 427.0
38 TraesCS2A01G250000 chr3B 88.264 409 44 3 2278 2684 358639619 358639213 1.400000e-133 486.0
39 TraesCS2A01G250000 chr3B 78.108 370 70 9 2004 2363 365289950 365289582 1.210000e-54 224.0
40 TraesCS2A01G250000 chr3B 82.895 228 31 6 1389 1613 726080015 726080237 7.330000e-47 198.0
41 TraesCS2A01G250000 chr3B 91.139 79 6 1 88 166 5261059 5261136 4.570000e-19 106.0
42 TraesCS2A01G250000 chr1A 83.094 556 64 17 2004 2541 235353340 235353883 2.340000e-131 479.0
43 TraesCS2A01G250000 chr1A 89.734 263 26 1 2638 2900 235359941 235360202 5.360000e-88 335.0
44 TraesCS2A01G250000 chr6D 85.321 218 31 1 2004 2221 77311529 77311313 1.210000e-54 224.0
45 TraesCS2A01G250000 chr6D 82.969 229 28 8 1389 1613 388434883 388435104 2.640000e-46 196.0
46 TraesCS2A01G250000 chr6D 86.139 101 9 5 4 101 315838508 315838606 1.640000e-18 104.0
47 TraesCS2A01G250000 chr5A 77.686 363 67 11 2004 2356 305752348 305752706 3.390000e-50 209.0
48 TraesCS2A01G250000 chr5A 90.323 155 15 0 2936 3090 116893958 116893804 1.580000e-48 204.0
49 TraesCS2A01G250000 chr2D 89.157 166 18 0 2925 3090 291912016 291912181 1.220000e-49 207.0
50 TraesCS2A01G250000 chr1B 83.854 192 26 4 1049 1237 114987903 114988092 9.550000e-41 178.0
51 TraesCS2A01G250000 chr1B 80.816 245 24 9 1 223 288238462 288238219 1.600000e-38 171.0
52 TraesCS2A01G250000 chr1B 77.907 258 25 13 1 235 537136667 537136915 7.540000e-27 132.0
53 TraesCS2A01G250000 chr1B 89.157 83 8 1 92 174 604643911 604643992 5.910000e-18 102.0
54 TraesCS2A01G250000 chr4B 80.093 216 15 12 4 192 241675912 241675698 5.830000e-28 135.0


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 TraesCS2A01G250000 chr2A 376751486 376754836 3350 True 6189.000000 6189 100.000000 1 3351 1 chr2A.!!$R1 3350
1 TraesCS2A01G250000 chr2A 442137767 442138881 1114 False 1445.000000 1445 90.036000 2231 3351 1 chr2A.!!$F3 1120
2 TraesCS2A01G250000 chr2A 385649368 385650013 645 False 935.000000 935 92.780000 965 1613 1 chr2A.!!$F1 648
3 TraesCS2A01G250000 chr2A 726860392 726861347 955 False 389.666667 555 89.993667 1609 3351 3 chr2A.!!$F5 1742
4 TraesCS2A01G250000 chr3D 212866672 212870026 3354 False 1198.750000 3550 95.144750 272 3351 4 chr3D.!!$F1 3079
5 TraesCS2A01G250000 chr3D 286532320 286534051 1731 True 300.750000 508 90.273000 2159 2684 2 chr3D.!!$R1 525
6 TraesCS2A01G250000 chr7A 73886943 73888310 1367 True 1070.000000 1844 92.788500 257 1662 2 chr7A.!!$R2 1405
7 TraesCS2A01G250000 chr7A 526528600 526529331 731 False 737.000000 737 85.326000 2040 2754 1 chr7A.!!$F1 714
8 TraesCS2A01G250000 chr4A 153048374 153049693 1319 False 1040.500000 1770 93.539000 258 1634 2 chr4A.!!$F1 1376
9 TraesCS2A01G250000 chr4A 238766960 238767501 541 True 566.000000 566 85.635000 2277 2814 1 chr4A.!!$R1 537
10 TraesCS2A01G250000 chr6B 716080849 716082119 1270 True 1583.000000 1583 89.247000 2069 3351 1 chr6B.!!$R2 1282
11 TraesCS2A01G250000 chr6B 233231496 233232104 608 True 743.000000 743 88.744000 2290 2899 1 chr6B.!!$R1 609
12 TraesCS2A01G250000 chr6B 471136051 471136607 556 False 603.000000 603 86.380000 2278 2828 1 chr6B.!!$F1 550
13 TraesCS2A01G250000 chr6B 703954150 703955968 1818 False 473.500000 518 89.318500 1609 3351 2 chr6B.!!$F2 1742
14 TraesCS2A01G250000 chr5B 592100322 592100930 608 False 704.000000 704 87.602000 2290 2899 1 chr5B.!!$F1 609
15 TraesCS2A01G250000 chr3A 573331545 573332499 954 True 520.500000 549 90.025500 1609 3351 2 chr3A.!!$R2 1742
16 TraesCS2A01G250000 chr6A 296770065 296771017 952 False 374.333333 538 88.931000 1609 3351 3 chr6A.!!$F1 1742
17 TraesCS2A01G250000 chr7B 331036055 331037903 1848 True 472.500000 518 89.333000 1609 3351 2 chr7B.!!$R2 1742
18 TraesCS2A01G250000 chr7B 296239027 296240875 1848 True 462.500000 490 88.925000 1609 3351 2 chr7B.!!$R1 1742
19 TraesCS2A01G250000 chr1A 235353340 235353883 543 False 479.000000 479 83.094000 2004 2541 1 chr1A.!!$F1 537

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
597 887 0.248012 CACGTGTAGCCATACCCACA 59.752 55.0 7.58 0.0 0.0 4.17 F
1267 1558 0.178992 CAAGAACAGGGCTGGGACAA 60.179 55.0 0.00 0.0 38.7 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 2378 0.193069 ATAGGCTGGATGGAGCTCCT 59.807 55.0 32.28 18.41 39.11 3.69 R
2893 4940 0.181114 GAGTGCTCCATATGTGGGCA 59.819 55.0 16.83 16.83 46.06 5.36 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
114 115 9.902684 ATATACTACATACTAAGCGTCCATACT 57.097 33.333 0.00 0.00 0.00 2.12
115 116 6.557291 ACTACATACTAAGCGTCCATACTC 57.443 41.667 0.00 0.00 0.00 2.59
116 117 6.297582 ACTACATACTAAGCGTCCATACTCT 58.702 40.000 0.00 0.00 0.00 3.24
117 118 5.692613 ACATACTAAGCGTCCATACTCTC 57.307 43.478 0.00 0.00 0.00 3.20
118 119 4.519730 ACATACTAAGCGTCCATACTCTCC 59.480 45.833 0.00 0.00 0.00 3.71
119 120 3.300239 ACTAAGCGTCCATACTCTCCT 57.700 47.619 0.00 0.00 0.00 3.69
120 121 4.434545 ACTAAGCGTCCATACTCTCCTA 57.565 45.455 0.00 0.00 0.00 2.94
121 122 4.988029 ACTAAGCGTCCATACTCTCCTAT 58.012 43.478 0.00 0.00 0.00 2.57
122 123 5.386924 ACTAAGCGTCCATACTCTCCTATT 58.613 41.667 0.00 0.00 0.00 1.73
123 124 5.834204 ACTAAGCGTCCATACTCTCCTATTT 59.166 40.000 0.00 0.00 0.00 1.40
124 125 4.592485 AGCGTCCATACTCTCCTATTTG 57.408 45.455 0.00 0.00 0.00 2.32
125 126 4.215908 AGCGTCCATACTCTCCTATTTGA 58.784 43.478 0.00 0.00 0.00 2.69
126 127 4.835615 AGCGTCCATACTCTCCTATTTGAT 59.164 41.667 0.00 0.00 0.00 2.57
127 128 6.010850 AGCGTCCATACTCTCCTATTTGATA 58.989 40.000 0.00 0.00 0.00 2.15
128 129 6.151985 AGCGTCCATACTCTCCTATTTGATAG 59.848 42.308 0.00 0.00 0.00 2.08
129 130 6.151312 GCGTCCATACTCTCCTATTTGATAGA 59.849 42.308 0.00 0.00 34.77 1.98
130 131 7.147983 GCGTCCATACTCTCCTATTTGATAGAT 60.148 40.741 0.00 0.00 34.77 1.98
131 132 9.397280 CGTCCATACTCTCCTATTTGATAGATA 57.603 37.037 0.00 0.00 34.77 1.98
164 165 9.023962 ACAACATATACAAACTCAAATGATGGT 57.976 29.630 0.00 0.00 0.00 3.55
172 173 8.862325 ACAAACTCAAATGATGGTAACTATCA 57.138 30.769 0.00 0.00 38.10 2.15
173 174 8.730680 ACAAACTCAAATGATGGTAACTATCAC 58.269 33.333 0.00 0.00 37.08 3.06
174 175 7.865706 AACTCAAATGATGGTAACTATCACC 57.134 36.000 0.00 0.00 37.08 4.02
175 176 6.049149 ACTCAAATGATGGTAACTATCACCG 58.951 40.000 0.00 0.00 39.04 4.94
176 177 6.127168 ACTCAAATGATGGTAACTATCACCGA 60.127 38.462 0.00 0.00 39.04 4.69
177 178 6.826668 TCAAATGATGGTAACTATCACCGAT 58.173 36.000 0.00 0.00 39.04 4.18
178 179 6.705825 TCAAATGATGGTAACTATCACCGATG 59.294 38.462 0.00 0.00 39.04 3.84
179 180 5.808366 ATGATGGTAACTATCACCGATGT 57.192 39.130 0.00 0.00 39.04 3.06
180 181 5.607939 TGATGGTAACTATCACCGATGTT 57.392 39.130 0.00 0.00 39.04 2.71
181 182 6.718522 TGATGGTAACTATCACCGATGTTA 57.281 37.500 0.00 0.00 39.04 2.41
182 183 6.745116 TGATGGTAACTATCACCGATGTTAG 58.255 40.000 0.00 0.00 39.04 2.34
183 184 6.548251 TGATGGTAACTATCACCGATGTTAGA 59.452 38.462 1.74 0.00 39.04 2.10
184 185 6.971726 TGGTAACTATCACCGATGTTAGAT 57.028 37.500 1.74 0.00 39.04 1.98
185 186 8.645814 ATGGTAACTATCACCGATGTTAGATA 57.354 34.615 1.74 0.00 39.04 1.98
186 187 8.467963 TGGTAACTATCACCGATGTTAGATAA 57.532 34.615 1.74 0.00 39.04 1.75
187 188 8.916062 TGGTAACTATCACCGATGTTAGATAAA 58.084 33.333 1.74 0.00 39.04 1.40
188 189 9.754382 GGTAACTATCACCGATGTTAGATAAAA 57.246 33.333 1.74 0.00 33.82 1.52
195 196 9.787532 ATCACCGATGTTAGATAAAATTTGTTG 57.212 29.630 0.00 0.00 0.00 3.33
196 197 8.788806 TCACCGATGTTAGATAAAATTTGTTGT 58.211 29.630 0.00 0.00 0.00 3.32
197 198 8.849490 CACCGATGTTAGATAAAATTTGTTGTG 58.151 33.333 0.00 0.00 0.00 3.33
198 199 8.573035 ACCGATGTTAGATAAAATTTGTTGTGT 58.427 29.630 0.00 0.00 0.00 3.72
199 200 8.849490 CCGATGTTAGATAAAATTTGTTGTGTG 58.151 33.333 0.00 0.00 0.00 3.82
200 201 9.393249 CGATGTTAGATAAAATTTGTTGTGTGT 57.607 29.630 0.00 0.00 0.00 3.72
282 283 7.872993 GGATCAGAATAACTATTTGGATGACGA 59.127 37.037 0.00 0.00 0.00 4.20
287 288 1.135199 ACTATTTGGATGACGACGCGT 60.135 47.619 13.85 13.85 45.10 6.01
296 297 3.601211 GGATGACGACGCGTGTTATATAC 59.399 47.826 20.70 8.47 41.37 1.47
297 298 3.672028 TGACGACGCGTGTTATATACA 57.328 42.857 20.70 5.57 41.37 2.29
330 331 2.202756 CCGAACTCCACTAGCGCC 60.203 66.667 2.29 0.00 0.00 6.53
370 372 1.038130 CCTCGTCATCGTCCTTCCCT 61.038 60.000 0.00 0.00 38.33 4.20
408 412 0.336048 CAATTCCCACCACCCATCCT 59.664 55.000 0.00 0.00 0.00 3.24
474 763 4.785453 CCGCCAGCCTTCCACTCC 62.785 72.222 0.00 0.00 0.00 3.85
475 764 4.785453 CGCCAGCCTTCCACTCCC 62.785 72.222 0.00 0.00 0.00 4.30
476 765 3.334054 GCCAGCCTTCCACTCCCT 61.334 66.667 0.00 0.00 0.00 4.20
477 766 2.673523 CCAGCCTTCCACTCCCTG 59.326 66.667 0.00 0.00 0.00 4.45
478 767 2.673523 CAGCCTTCCACTCCCTGG 59.326 66.667 0.00 0.00 42.29 4.45
479 768 3.334054 AGCCTTCCACTCCCTGGC 61.334 66.667 0.00 0.00 40.39 4.85
480 769 4.785453 GCCTTCCACTCCCTGGCG 62.785 72.222 0.00 0.00 40.39 5.69
481 770 3.003173 CCTTCCACTCCCTGGCGA 61.003 66.667 0.00 0.00 40.39 5.54
482 771 2.581354 CTTCCACTCCCTGGCGAG 59.419 66.667 9.73 9.73 40.39 5.03
483 772 3.672295 CTTCCACTCCCTGGCGAGC 62.672 68.421 10.85 0.00 40.39 5.03
484 773 4.704103 TCCACTCCCTGGCGAGCT 62.704 66.667 10.85 0.00 40.39 4.09
485 774 4.463879 CCACTCCCTGGCGAGCTG 62.464 72.222 10.85 8.79 31.36 4.24
496 785 2.844362 CGAGCTGCCCCATCCCTA 60.844 66.667 0.00 0.00 0.00 3.53
497 786 2.876945 CGAGCTGCCCCATCCCTAG 61.877 68.421 0.00 0.00 0.00 3.02
498 787 3.174265 AGCTGCCCCATCCCTAGC 61.174 66.667 0.00 0.00 34.71 3.42
499 788 4.632974 GCTGCCCCATCCCTAGCG 62.633 72.222 0.00 0.00 0.00 4.26
500 789 4.632974 CTGCCCCATCCCTAGCGC 62.633 72.222 0.00 0.00 0.00 5.92
506 795 4.976925 CATCCCTAGCGCCGCCAG 62.977 72.222 4.98 0.00 0.00 4.85
574 864 1.620739 GCAGCTCCTCCACCAGATCA 61.621 60.000 0.00 0.00 0.00 2.92
582 872 2.048222 CACCAGATCACGCCACGT 60.048 61.111 0.00 0.00 42.36 4.49
597 887 0.248012 CACGTGTAGCCATACCCACA 59.752 55.000 7.58 0.00 0.00 4.17
704 994 4.753662 AGCGGTCGTCCCCTGCTA 62.754 66.667 0.00 0.00 34.25 3.49
771 1061 2.436646 CGCCGCCACCAATCTTCT 60.437 61.111 0.00 0.00 0.00 2.85
821 1111 2.266055 CTTGACCTCCCAGGCGAC 59.734 66.667 0.00 0.00 39.63 5.19
919 1209 3.372730 GCCGCATCAAACTGGCCA 61.373 61.111 4.71 4.71 41.70 5.36
927 1217 3.803021 GCATCAAACTGGCCATTCAACAA 60.803 43.478 5.51 0.00 0.00 2.83
963 1253 2.044053 AATGACGTGGCCCCATGG 60.044 61.111 4.14 4.14 37.27 3.66
992 1282 2.515523 GCAGCGCCTGGATCACAT 60.516 61.111 2.29 0.00 31.21 3.21
1037 1327 6.205464 GCCGAGATATTTCCATTCTTCATTCA 59.795 38.462 0.00 0.00 0.00 2.57
1046 1336 5.673514 TCCATTCTTCATTCATCGACATCA 58.326 37.500 0.00 0.00 0.00 3.07
1148 1439 4.793216 CCGCATTTGTATTTGAACTACAGC 59.207 41.667 0.00 0.00 31.17 4.40
1185 1476 2.552315 GCTTCCCTCTCTCTCTGATACG 59.448 54.545 0.00 0.00 0.00 3.06
1267 1558 0.178992 CAAGAACAGGGCTGGGACAA 60.179 55.000 0.00 0.00 38.70 3.18
1448 1739 8.474025 TCTCAAACAAGAATTATGTGTTGGTTT 58.526 29.630 2.60 0.00 35.70 3.27
1498 1790 6.177610 TGGGGATCTTTGTATGTAAAGTGTC 58.822 40.000 0.00 0.00 38.49 3.67
1622 1915 2.044946 GCACCGATTGAGCCCCTT 60.045 61.111 0.00 0.00 0.00 3.95
1646 1941 6.833041 TCCCAACAGTCTGTTATTTTCTACA 58.167 36.000 17.76 0.00 38.77 2.74
1650 1945 9.003658 CCAACAGTCTGTTATTTTCTACATTCT 57.996 33.333 17.76 0.00 38.77 2.40
1770 2065 4.275689 TCCTGCAAAACAAGTATGTGTGAG 59.724 41.667 0.00 0.00 40.46 3.51
1771 2066 4.036734 CCTGCAAAACAAGTATGTGTGAGT 59.963 41.667 0.00 0.00 40.46 3.41
1816 2112 6.020360 GTCAAGAAAAAGAGTGTTGCATGTTC 60.020 38.462 0.00 0.00 0.00 3.18
1852 2148 6.088016 TGTTATTTGAAGCTGCACATTTCT 57.912 33.333 0.00 0.00 0.00 2.52
2012 2325 3.851128 GGGTGGACGAGCTAGCCC 61.851 72.222 12.13 5.90 39.51 5.19
2064 2378 3.326747 GCAGTTCGGCTAGAAAGAAGAA 58.673 45.455 0.00 0.00 41.10 2.52
2066 2380 3.929610 CAGTTCGGCTAGAAAGAAGAAGG 59.070 47.826 0.00 0.00 41.10 3.46
2067 2381 3.833070 AGTTCGGCTAGAAAGAAGAAGGA 59.167 43.478 0.00 0.00 41.10 3.36
2068 2382 4.081917 AGTTCGGCTAGAAAGAAGAAGGAG 60.082 45.833 0.00 0.00 41.10 3.69
2069 2383 2.166664 TCGGCTAGAAAGAAGAAGGAGC 59.833 50.000 0.00 0.00 0.00 4.70
2070 2384 2.167487 CGGCTAGAAAGAAGAAGGAGCT 59.833 50.000 0.00 0.00 0.00 4.09
2072 2386 3.431626 GGCTAGAAAGAAGAAGGAGCTCC 60.432 52.174 26.22 26.22 0.00 4.70
2073 2387 3.196685 GCTAGAAAGAAGAAGGAGCTCCA 59.803 47.826 33.90 8.17 38.89 3.86
2092 2406 3.523157 TCCATCCAGCCTATGAAGTTCAA 59.477 43.478 10.14 0.00 0.00 2.69
2168 2483 2.595009 TACCGTGTGTGGTGCTTGCA 62.595 55.000 0.00 0.00 43.68 4.08
2178 2493 2.594013 TGCTTGCATGCACACGGA 60.594 55.556 22.58 10.44 38.12 4.69
2304 3825 4.248859 CTGCAGTATCAACTACAACAGCT 58.751 43.478 5.25 0.00 33.48 4.24
2335 3858 0.905357 GTGCTCCTCTCCCTTTGCTA 59.095 55.000 0.00 0.00 0.00 3.49
2390 3958 5.013568 TGTACGAAAAGGTTTGAGTGAGA 57.986 39.130 0.00 0.00 0.00 3.27
2447 4015 4.960938 TCTAATGCGATGGTGCTATTCTT 58.039 39.130 0.00 0.00 35.36 2.52
2543 4312 0.257328 TTGGTCTGACTTGCACCCAA 59.743 50.000 7.85 0.00 32.68 4.12
2550 4321 1.070758 TGACTTGCACCCAACTCTCTC 59.929 52.381 0.00 0.00 0.00 3.20
2594 4365 7.121611 TCACTTATGGACGTACTGAGTAATTCA 59.878 37.037 0.00 0.00 0.00 2.57
2622 4393 0.592637 TGCTGCATCTTGTTTCGGTG 59.407 50.000 0.00 0.00 0.00 4.94
2775 4788 3.409570 TCCGCTATCGCTAGACTAATGT 58.590 45.455 0.00 0.00 0.00 2.71
2850 4863 1.300620 GAGTGTGTGCGTGTGCCTA 60.301 57.895 0.00 0.00 41.78 3.93
2892 4939 3.656651 TGCGAGCGATGACTTTAATTG 57.343 42.857 0.00 0.00 0.00 2.32
2893 4940 3.000041 TGCGAGCGATGACTTTAATTGT 59.000 40.909 0.00 0.00 0.00 2.71
2894 4941 3.181521 TGCGAGCGATGACTTTAATTGTG 60.182 43.478 0.00 0.00 0.00 3.33
2895 4942 3.345714 CGAGCGATGACTTTAATTGTGC 58.654 45.455 0.00 0.00 0.00 4.57
2896 4943 3.685058 GAGCGATGACTTTAATTGTGCC 58.315 45.455 0.00 0.00 0.00 5.01
2897 4944 2.423538 AGCGATGACTTTAATTGTGCCC 59.576 45.455 0.00 0.00 0.00 5.36
2898 4945 2.163412 GCGATGACTTTAATTGTGCCCA 59.837 45.455 0.00 0.00 0.00 5.36
2899 4946 3.758300 CGATGACTTTAATTGTGCCCAC 58.242 45.455 0.00 0.00 0.00 4.61
2900 4947 3.190327 CGATGACTTTAATTGTGCCCACA 59.810 43.478 0.00 0.00 39.98 4.17
2901 4948 4.142403 CGATGACTTTAATTGTGCCCACAT 60.142 41.667 1.46 0.00 41.52 3.21
2902 4949 5.065859 CGATGACTTTAATTGTGCCCACATA 59.934 40.000 1.46 0.00 41.52 2.29
2903 4950 6.238731 CGATGACTTTAATTGTGCCCACATAT 60.239 38.462 1.46 0.00 41.52 1.78
2904 4951 6.206395 TGACTTTAATTGTGCCCACATATG 57.794 37.500 0.00 0.00 41.52 1.78
2905 4952 5.126869 TGACTTTAATTGTGCCCACATATGG 59.873 40.000 7.80 0.00 46.81 2.74
2916 4963 1.575244 CACATATGGAGCACTCACGG 58.425 55.000 7.80 0.00 0.00 4.94
2917 4964 0.465705 ACATATGGAGCACTCACGGG 59.534 55.000 7.80 0.00 0.00 5.28
2928 4975 4.402528 TCACGGGCGGTGGATTGG 62.403 66.667 22.77 0.00 46.96 3.16
3130 5179 9.912634 CCAGAAAATATAGCAACAAAAAGAAGA 57.087 29.630 0.00 0.00 0.00 2.87
3271 5320 3.431912 CGTGTATGCGGCACATATATGTT 59.568 43.478 15.85 3.33 43.11 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 9.902684 AGTATGGACGCTTAGTATGTAGTATAT 57.097 33.333 0.00 0.00 0.00 0.86
89 90 9.376075 GAGTATGGACGCTTAGTATGTAGTATA 57.624 37.037 0.00 0.00 0.00 1.47
90 91 8.102047 AGAGTATGGACGCTTAGTATGTAGTAT 58.898 37.037 0.00 0.00 30.57 2.12
91 92 7.448420 AGAGTATGGACGCTTAGTATGTAGTA 58.552 38.462 0.00 0.00 30.57 1.82
92 93 6.297582 AGAGTATGGACGCTTAGTATGTAGT 58.702 40.000 0.00 0.00 30.57 2.73
93 94 6.128227 GGAGAGTATGGACGCTTAGTATGTAG 60.128 46.154 0.00 0.00 35.63 2.74
94 95 5.704515 GGAGAGTATGGACGCTTAGTATGTA 59.295 44.000 0.00 0.00 35.63 2.29
95 96 4.519730 GGAGAGTATGGACGCTTAGTATGT 59.480 45.833 0.00 0.00 35.63 2.29
96 97 4.762765 AGGAGAGTATGGACGCTTAGTATG 59.237 45.833 0.00 0.00 35.63 2.39
97 98 4.988029 AGGAGAGTATGGACGCTTAGTAT 58.012 43.478 0.00 0.00 35.63 2.12
98 99 4.434545 AGGAGAGTATGGACGCTTAGTA 57.565 45.455 0.00 0.00 35.63 1.82
99 100 3.300239 AGGAGAGTATGGACGCTTAGT 57.700 47.619 0.00 0.00 35.63 2.24
100 101 5.968528 AATAGGAGAGTATGGACGCTTAG 57.031 43.478 0.00 0.00 35.63 2.18
101 102 5.831525 TCAAATAGGAGAGTATGGACGCTTA 59.168 40.000 0.00 0.00 35.63 3.09
102 103 4.649674 TCAAATAGGAGAGTATGGACGCTT 59.350 41.667 0.00 0.00 35.63 4.68
103 104 4.215908 TCAAATAGGAGAGTATGGACGCT 58.784 43.478 0.00 0.00 38.58 5.07
104 105 4.585955 TCAAATAGGAGAGTATGGACGC 57.414 45.455 0.00 0.00 0.00 5.19
105 106 7.689446 TCTATCAAATAGGAGAGTATGGACG 57.311 40.000 0.00 0.00 33.64 4.79
138 139 9.023962 ACCATCATTTGAGTTTGTATATGTTGT 57.976 29.630 0.00 0.00 0.00 3.32
146 147 9.952030 TGATAGTTACCATCATTTGAGTTTGTA 57.048 29.630 0.00 0.00 0.00 2.41
147 148 8.730680 GTGATAGTTACCATCATTTGAGTTTGT 58.269 33.333 0.00 0.00 35.02 2.83
148 149 8.184192 GGTGATAGTTACCATCATTTGAGTTTG 58.816 37.037 0.00 0.00 38.12 2.93
149 150 7.065803 CGGTGATAGTTACCATCATTTGAGTTT 59.934 37.037 0.00 0.00 38.11 2.66
150 151 6.538742 CGGTGATAGTTACCATCATTTGAGTT 59.461 38.462 0.00 0.00 38.11 3.01
151 152 6.049149 CGGTGATAGTTACCATCATTTGAGT 58.951 40.000 0.00 0.00 38.11 3.41
152 153 6.280643 TCGGTGATAGTTACCATCATTTGAG 58.719 40.000 0.00 0.00 38.11 3.02
153 154 6.228616 TCGGTGATAGTTACCATCATTTGA 57.771 37.500 0.00 0.00 38.11 2.69
154 155 6.483307 ACATCGGTGATAGTTACCATCATTTG 59.517 38.462 0.65 0.00 38.11 2.32
155 156 6.591935 ACATCGGTGATAGTTACCATCATTT 58.408 36.000 0.65 0.00 38.11 2.32
156 157 6.174720 ACATCGGTGATAGTTACCATCATT 57.825 37.500 0.65 0.00 38.11 2.57
157 158 5.808366 ACATCGGTGATAGTTACCATCAT 57.192 39.130 0.65 0.00 38.11 2.45
158 159 5.607939 AACATCGGTGATAGTTACCATCA 57.392 39.130 0.65 0.00 38.11 3.07
159 160 6.978338 TCTAACATCGGTGATAGTTACCATC 58.022 40.000 12.15 0.00 38.11 3.51
160 161 6.971726 TCTAACATCGGTGATAGTTACCAT 57.028 37.500 12.15 0.00 38.11 3.55
161 162 6.971726 ATCTAACATCGGTGATAGTTACCA 57.028 37.500 12.15 0.00 38.11 3.25
162 163 9.754382 TTTTATCTAACATCGGTGATAGTTACC 57.246 33.333 12.15 0.00 33.71 2.85
169 170 9.787532 CAACAAATTTTATCTAACATCGGTGAT 57.212 29.630 0.65 0.00 0.00 3.06
170 171 8.788806 ACAACAAATTTTATCTAACATCGGTGA 58.211 29.630 0.65 0.00 0.00 4.02
171 172 8.849490 CACAACAAATTTTATCTAACATCGGTG 58.151 33.333 0.00 0.00 0.00 4.94
172 173 8.573035 ACACAACAAATTTTATCTAACATCGGT 58.427 29.630 0.00 0.00 0.00 4.69
173 174 8.849490 CACACAACAAATTTTATCTAACATCGG 58.151 33.333 0.00 0.00 0.00 4.18
174 175 9.393249 ACACACAACAAATTTTATCTAACATCG 57.607 29.630 0.00 0.00 0.00 3.84
255 256 7.875041 CGTCATCCAAATAGTTATTCTGATCCT 59.125 37.037 0.00 0.00 0.00 3.24
278 279 2.969306 CCTGTATATAACACGCGTCGTC 59.031 50.000 9.86 0.00 38.32 4.20
287 288 2.823747 AGCCGATCGCCTGTATATAACA 59.176 45.455 10.32 0.00 38.78 2.41
296 297 2.892425 GGAACAGCCGATCGCCTG 60.892 66.667 23.25 23.25 38.78 4.85
297 298 4.162690 GGGAACAGCCGATCGCCT 62.163 66.667 10.32 0.00 38.78 5.52
390 394 0.336048 CAGGATGGGTGGTGGGAATT 59.664 55.000 0.00 0.00 0.00 2.17
479 768 2.844362 TAGGGATGGGGCAGCTCG 60.844 66.667 0.00 0.00 0.00 5.03
480 769 3.155750 CTAGGGATGGGGCAGCTC 58.844 66.667 0.00 0.00 0.00 4.09
481 770 3.174265 GCTAGGGATGGGGCAGCT 61.174 66.667 0.00 0.00 0.00 4.24
482 771 4.632974 CGCTAGGGATGGGGCAGC 62.633 72.222 0.00 0.00 0.00 5.25
483 772 4.632974 GCGCTAGGGATGGGGCAG 62.633 72.222 11.61 0.00 40.38 4.85
489 778 4.976925 CTGGCGGCGCTAGGGATG 62.977 72.222 33.85 12.15 33.47 3.51
503 792 3.732849 GAGGTTGGGGGAGGCTGG 61.733 72.222 0.00 0.00 0.00 4.85
504 793 3.732849 GGAGGTTGGGGGAGGCTG 61.733 72.222 0.00 0.00 0.00 4.85
574 864 1.153706 GTATGGCTACACGTGGCGT 60.154 57.895 21.57 9.18 42.36 5.68
582 872 1.200519 GGACTGTGGGTATGGCTACA 58.799 55.000 0.00 0.00 0.00 2.74
584 874 1.046472 CGGGACTGTGGGTATGGCTA 61.046 60.000 0.00 0.00 0.00 3.93
589 879 3.467226 CGGCGGGACTGTGGGTAT 61.467 66.667 0.00 0.00 0.00 2.73
671 961 2.283809 CTCCTGGAGATCCCCGGT 59.716 66.667 19.13 0.00 40.00 5.28
727 1017 3.794475 GCGAAGGTTGTATAGAAGCGCTA 60.794 47.826 12.05 0.00 38.95 4.26
883 1173 3.058160 GCTTGGCTGCGTGGTGAT 61.058 61.111 0.00 0.00 0.00 3.06
919 1209 0.591170 CCAAGACGGCGTTGTTGAAT 59.409 50.000 27.59 0.00 0.00 2.57
1037 1327 5.588958 TCTCAGTTCAATCTGATGTCGAT 57.411 39.130 0.00 0.00 42.47 3.59
1046 1336 4.802248 GCACCTGACTTCTCAGTTCAATCT 60.802 45.833 0.00 0.00 42.36 2.40
1185 1476 0.951558 AACATGACACTTGCGAACCC 59.048 50.000 0.00 0.00 0.00 4.11
1267 1558 7.272037 ACGTGTTTGAGAACAAAAATATCCT 57.728 32.000 0.00 0.00 46.62 3.24
1448 1739 7.759489 AGAATAAGTTTGTTATGGCACTGAA 57.241 32.000 0.00 0.00 0.00 3.02
1498 1790 5.181811 TGCAACACATACCTTCTTGAATGAG 59.818 40.000 0.00 0.00 0.00 2.90
1545 1838 9.454585 CCAGATTATACAAAGTGCATGTTTATG 57.545 33.333 0.00 0.00 37.36 1.90
1569 1862 6.207614 TCACAATGATTTATTTTCGTGGACCA 59.792 34.615 0.00 0.00 0.00 4.02
1622 1915 6.833041 TGTAGAAAATAACAGACTGTTGGGA 58.167 36.000 27.44 11.01 41.30 4.37
1646 1941 6.665680 TCTCCTCTACTTTCAGTAGCAAGAAT 59.334 38.462 6.11 0.00 45.93 2.40
1650 1945 6.437477 TCATTCTCCTCTACTTTCAGTAGCAA 59.563 38.462 6.11 0.00 45.93 3.91
1662 1957 2.034053 CCGAGCAGTCATTCTCCTCTAC 59.966 54.545 0.00 0.00 29.22 2.59
1663 1958 2.092375 TCCGAGCAGTCATTCTCCTCTA 60.092 50.000 0.00 0.00 29.22 2.43
1770 2065 8.709386 TTGACTGAATTCATCTTCTAGCTAAC 57.291 34.615 8.96 0.00 0.00 2.34
1771 2066 8.753133 TCTTGACTGAATTCATCTTCTAGCTAA 58.247 33.333 8.96 0.00 0.00 3.09
1816 2112 6.736853 GCTTCAAATAACAACTACAGTTAGCG 59.263 38.462 0.00 0.00 36.32 4.26
1852 2148 5.353956 ACATAAACACAATCATGCTTCGCTA 59.646 36.000 0.00 0.00 0.00 4.26
2012 2325 2.811317 GAGCAAGACCACGCCTCG 60.811 66.667 0.00 0.00 0.00 4.63
2054 2367 3.199727 GGATGGAGCTCCTTCTTCTTTCT 59.800 47.826 35.00 10.73 39.41 2.52
2064 2378 0.193069 ATAGGCTGGATGGAGCTCCT 59.807 55.000 32.28 18.41 39.11 3.69
2066 2380 1.346062 TCATAGGCTGGATGGAGCTC 58.654 55.000 4.71 4.71 39.11 4.09
2067 2381 1.698532 CTTCATAGGCTGGATGGAGCT 59.301 52.381 0.00 0.00 39.11 4.09
2068 2382 1.419387 ACTTCATAGGCTGGATGGAGC 59.581 52.381 5.61 0.00 33.74 4.70
2069 2383 3.135348 TGAACTTCATAGGCTGGATGGAG 59.865 47.826 4.32 4.32 36.18 3.86
2070 2384 3.114606 TGAACTTCATAGGCTGGATGGA 58.885 45.455 0.00 0.00 0.00 3.41
2072 2386 3.629398 GGTTGAACTTCATAGGCTGGATG 59.371 47.826 0.00 0.00 0.00 3.51
2073 2387 3.682718 CGGTTGAACTTCATAGGCTGGAT 60.683 47.826 0.00 0.00 0.00 3.41
2092 2406 2.359107 CTGCACATGCTCACCGGT 60.359 61.111 0.00 0.00 42.66 5.28
2168 2483 1.074775 ATGTGGGTTCCGTGTGCAT 59.925 52.632 0.00 0.00 0.00 3.96
2288 3809 2.734175 CGCCGAGCTGTTGTAGTTGATA 60.734 50.000 0.00 0.00 0.00 2.15
2447 4015 5.743026 TCACGAGAAACAAATAACTGCAA 57.257 34.783 0.00 0.00 0.00 4.08
2529 4156 1.071385 AGAGAGTTGGGTGCAAGTCAG 59.929 52.381 0.00 0.00 37.07 3.51
2565 4336 4.395542 ACTCAGTACGTCCATAAGTGAGTC 59.604 45.833 16.49 0.00 46.11 3.36
2622 4393 2.200170 GAATCGGTGTTGGGCTGCAC 62.200 60.000 0.50 0.00 35.07 4.57
2729 4742 0.304098 GCTCTTCAGCATTAGCAGCG 59.696 55.000 0.00 0.00 46.06 5.18
2775 4788 3.879998 TGTGTGGTGTTTAGCTCTTCAA 58.120 40.909 0.00 0.00 0.00 2.69
2892 4939 4.984194 TGCTCCATATGTGGGCAC 57.016 55.556 16.83 5.31 46.06 5.01
2893 4940 0.181114 GAGTGCTCCATATGTGGGCA 59.819 55.000 16.83 16.83 46.06 5.36
2894 4941 0.181114 TGAGTGCTCCATATGTGGGC 59.819 55.000 8.84 11.23 46.06 5.36
2895 4942 1.807755 CGTGAGTGCTCCATATGTGGG 60.808 57.143 8.84 0.77 46.06 4.61
2897 4944 1.575244 CCGTGAGTGCTCCATATGTG 58.425 55.000 1.24 0.00 0.00 3.21
2898 4945 0.465705 CCCGTGAGTGCTCCATATGT 59.534 55.000 1.24 0.00 0.00 2.29
2899 4946 0.882042 GCCCGTGAGTGCTCCATATG 60.882 60.000 0.00 0.00 0.00 1.78
2900 4947 1.447643 GCCCGTGAGTGCTCCATAT 59.552 57.895 0.00 0.00 0.00 1.78
2901 4948 2.900273 GCCCGTGAGTGCTCCATA 59.100 61.111 0.00 0.00 0.00 2.74
2902 4949 4.457496 CGCCCGTGAGTGCTCCAT 62.457 66.667 0.00 0.00 0.00 3.41
2908 4955 3.605749 AATCCACCGCCCGTGAGTG 62.606 63.158 0.18 0.00 46.20 3.51
2909 4956 3.319198 AATCCACCGCCCGTGAGT 61.319 61.111 0.18 0.00 46.20 3.41
2910 4957 2.819595 CAATCCACCGCCCGTGAG 60.820 66.667 0.18 0.00 46.20 3.51
2911 4958 4.402528 CCAATCCACCGCCCGTGA 62.403 66.667 0.18 0.00 46.20 4.35
2915 4962 4.839706 ATGCCCAATCCACCGCCC 62.840 66.667 0.00 0.00 0.00 6.13
2916 4963 3.219198 GATGCCCAATCCACCGCC 61.219 66.667 0.00 0.00 0.00 6.13
2984 5031 2.906389 AGTAGATGAACCTTGTCCAGCA 59.094 45.455 0.00 0.00 0.00 4.41
3130 5179 9.020731 TCTAGTTGAACTTCAAGGTTTTTCTTT 57.979 29.630 1.97 0.00 37.00 2.52
3202 5251 0.530650 CACTCAAGACGCACACACCT 60.531 55.000 0.00 0.00 0.00 4.00
3271 5320 5.253330 ACCCTATGATAGACCTAATCGGAGA 59.747 44.000 0.00 0.00 45.75 3.71


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

AutoCloner maintained by Alex Coulton.