Multiple sequence alignment - TraesCS2D01G124200

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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 TraesCS2D01G124200 chr2D 100.000 4946 0 0 1 4946 72703247 72698302 0.000000e+00 9134.0
1 TraesCS2D01G124200 chr2D 95.374 3956 98 32 415 4335 72442963 72439058 0.000000e+00 6213.0
2 TraesCS2D01G124200 chr2D 85.771 1251 118 31 3091 4322 72660204 72658995 0.000000e+00 1269.0
3 TraesCS2D01G124200 chr2D 98.699 615 8 0 4332 4946 72439032 72438418 0.000000e+00 1092.0
4 TraesCS2D01G124200 chr2D 84.615 728 67 25 3603 4326 72379042 72378356 0.000000e+00 682.0
5 TraesCS2D01G124200 chr2D 91.404 349 22 2 3 349 459856016 459856358 5.800000e-129 472.0
6 TraesCS2D01G124200 chr2D 81.239 565 88 13 3098 3649 72373899 72373340 1.630000e-119 440.0
7 TraesCS2D01G124200 chr2A 92.367 3734 187 30 659 4326 71350765 71347064 0.000000e+00 5227.0
8 TraesCS2D01G124200 chr2A 85.011 1341 116 38 3003 4323 71268044 71266769 0.000000e+00 1284.0
9 TraesCS2D01G124200 chr2A 84.948 1342 115 40 3003 4323 71165588 71164313 0.000000e+00 1279.0
10 TraesCS2D01G124200 chr2A 84.937 1341 117 41 3003 4323 71218371 71217096 0.000000e+00 1279.0
11 TraesCS2D01G124200 chr2A 81.020 980 156 18 980 1935 71155706 71154733 0.000000e+00 752.0
12 TraesCS2D01G124200 chr2A 82.388 846 134 11 1078 1911 71261771 71260929 0.000000e+00 723.0
13 TraesCS2D01G124200 chr2A 86.214 486 44 10 1976 2443 71124383 71123903 5.710000e-139 505.0
14 TraesCS2D01G124200 chr2A 86.128 483 49 7 1976 2443 71166318 71165839 5.710000e-139 505.0
15 TraesCS2D01G124200 chr2A 82.405 449 72 6 914 1360 71269768 71269325 7.770000e-103 385.0
16 TraesCS2D01G124200 chr2A 81.960 449 74 6 914 1360 71220095 71219652 1.680000e-99 374.0
17 TraesCS2D01G124200 chr2A 88.686 274 29 2 4351 4623 71312344 71312072 2.850000e-87 333.0
18 TraesCS2D01G124200 chr2A 85.000 200 21 4 4683 4877 71157304 71157109 1.400000e-45 195.0
19 TraesCS2D01G124200 chr2A 80.000 195 23 8 4683 4877 71210062 71209884 4.020000e-26 130.0
20 TraesCS2D01G124200 chr2A 80.000 195 23 8 4683 4877 71262692 71262514 4.020000e-26 130.0
21 TraesCS2D01G124200 chr2A 87.736 106 12 1 2532 2637 71165813 71165709 6.720000e-24 122.0
22 TraesCS2D01G124200 chr2A 87.736 106 12 1 2532 2637 71218596 71218492 6.720000e-24 122.0
23 TraesCS2D01G124200 chr2B 92.646 2706 117 24 381 3041 109937185 109934517 0.000000e+00 3819.0
24 TraesCS2D01G124200 chr2B 93.535 2181 108 12 875 3041 109983309 109981148 0.000000e+00 3216.0
25 TraesCS2D01G124200 chr2B 94.828 1334 45 10 2995 4326 109934531 109933220 0.000000e+00 2060.0
26 TraesCS2D01G124200 chr2B 92.580 1415 74 13 3058 4453 109976428 109975026 0.000000e+00 2002.0
27 TraesCS2D01G124200 chr2B 85.460 1348 115 41 3003 4326 109760088 109758798 0.000000e+00 1328.0
28 TraesCS2D01G124200 chr2B 85.586 1332 114 39 3003 4313 109875975 109874701 0.000000e+00 1325.0
29 TraesCS2D01G124200 chr2B 80.402 1393 174 57 433 1810 110067144 110068452 0.000000e+00 968.0
30 TraesCS2D01G124200 chr2B 82.157 992 164 8 914 1903 109877698 109876718 0.000000e+00 839.0
31 TraesCS2D01G124200 chr2B 81.864 998 156 22 958 1935 109931485 109930493 0.000000e+00 817.0
32 TraesCS2D01G124200 chr2B 91.091 449 28 5 4332 4773 109933176 109932733 9.160000e-167 597.0
33 TraesCS2D01G124200 chr2B 91.146 384 30 3 3 384 631605772 631606153 7.340000e-143 518.0
34 TraesCS2D01G124200 chr2B 86.056 502 45 13 1966 2443 109876724 109876224 2.640000e-142 516.0
35 TraesCS2D01G124200 chr2B 86.177 463 46 9 4332 4785 109095220 109094767 7.440000e-133 484.0
36 TraesCS2D01G124200 chr2B 85.961 463 48 8 4332 4785 109874623 109874169 3.460000e-131 479.0
37 TraesCS2D01G124200 chr2B 76.496 936 164 38 3013 3921 109929555 109928649 4.510000e-125 459.0
38 TraesCS2D01G124200 chr2B 88.329 377 39 4 4332 4706 109193689 109193316 9.770000e-122 448.0
39 TraesCS2D01G124200 chr2B 91.321 265 23 0 118 382 765076319 765076583 3.640000e-96 363.0
40 TraesCS2D01G124200 chr2B 86.364 264 36 0 914 1177 109204392 109204129 6.260000e-74 289.0
41 TraesCS2D01G124200 chr2B 85.062 241 16 10 415 644 109994697 109994466 1.390000e-55 228.0
42 TraesCS2D01G124200 chr2B 84.656 189 20 9 2532 2713 109195275 109195089 3.930000e-41 180.0
43 TraesCS2D01G124200 chr2B 95.604 91 4 0 3 93 765073940 765074030 3.990000e-31 147.0
44 TraesCS2D01G124200 chr2B 80.978 184 7 7 659 842 109983469 109983314 2.420000e-23 121.0
45 TraesCS2D01G124200 chr2B 95.946 74 2 1 2995 3068 109981162 109981090 8.700000e-23 119.0
46 TraesCS2D01G124200 chr2B 86.458 96 12 1 2532 2627 109876198 109876104 2.440000e-18 104.0
47 TraesCS2D01G124200 chr2B 87.059 85 9 2 2630 2713 109760242 109760159 1.470000e-15 95.3
48 TraesCS2D01G124200 chr2B 84.706 85 12 1 2630 2713 109096706 109096622 3.170000e-12 84.2
49 TraesCS2D01G124200 chrUn 93.860 1645 75 9 1225 2867 289939069 289940689 0.000000e+00 2455.0
50 TraesCS2D01G124200 chrUn 95.277 1334 57 4 2995 4326 289940899 289942228 0.000000e+00 2109.0
51 TraesCS2D01G124200 chrUn 82.012 1123 166 15 787 1903 235536603 235537695 0.000000e+00 922.0
52 TraesCS2D01G124200 chrUn 100.000 384 0 0 3342 3725 480865901 480866284 0.000000e+00 710.0
53 TraesCS2D01G124200 chrUn 86.255 502 44 11 1966 2443 235537689 235538189 5.670000e-144 521.0
54 TraesCS2D01G124200 chrUn 85.313 463 50 9 4332 4785 235539791 235540244 3.490000e-126 462.0
55 TraesCS2D01G124200 chrUn 85.648 432 45 7 4505 4930 261752386 261752806 5.880000e-119 438.0
56 TraesCS2D01G124200 chrUn 80.708 565 91 13 3098 3649 289660414 289659855 1.650000e-114 424.0
57 TraesCS2D01G124200 chrUn 98.214 224 4 0 2818 3041 289940690 289940913 4.640000e-105 392.0
58 TraesCS2D01G124200 chrUn 86.170 282 29 3 4351 4623 289659153 289658873 3.740000e-76 296.0
59 TraesCS2D01G124200 chrUn 91.489 188 16 0 4332 4519 289942276 289942463 4.910000e-65 259.0
60 TraesCS2D01G124200 chrUn 89.840 187 16 3 4142 4326 289507970 289508155 2.300000e-58 237.0
61 TraesCS2D01G124200 chrUn 89.623 106 10 1 2532 2637 235538215 235538319 3.110000e-27 134.0
62 TraesCS2D01G124200 chrUn 90.909 99 2 3 415 513 352890243 352890334 5.200000e-25 126.0
63 TraesCS2D01G124200 chrUn 94.000 50 3 0 2664 2713 235538322 235538371 5.310000e-10 76.8
64 TraesCS2D01G124200 chr7A 97.043 372 11 0 7 378 13062022 13061651 1.170000e-175 627.0
65 TraesCS2D01G124200 chr1A 96.053 380 15 0 3 382 124354052 124354431 1.960000e-173 619.0
66 TraesCS2D01G124200 chr5B 92.911 395 21 4 3 393 412665203 412664812 7.190000e-158 568.0
67 TraesCS2D01G124200 chr6B 89.610 385 28 5 3 386 715416167 715415794 3.460000e-131 479.0
68 TraesCS2D01G124200 chr1D 85.714 315 42 2 70 384 250411319 250411008 3.690000e-86 329.0
69 TraesCS2D01G124200 chr4D 84.641 306 42 3 79 384 474382175 474382475 2.890000e-77 300.0
70 TraesCS2D01G124200 chr4B 86.617 269 32 4 2727 2994 464159012 464159277 1.350000e-75 294.0
71 TraesCS2D01G124200 chr3A 85.560 277 30 6 2727 2996 523754956 523754683 1.050000e-71 281.0
72 TraesCS2D01G124200 chr3B 84.838 277 34 5 2727 2996 528639797 528639522 6.310000e-69 272.0


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 TraesCS2D01G124200 chr2D 72698302 72703247 4945 True 9134.000000 9134 100.000000 1 4946 1 chr2D.!!$R4 4945
1 TraesCS2D01G124200 chr2D 72438418 72442963 4545 True 3652.500000 6213 97.036500 415 4946 2 chr2D.!!$R5 4531
2 TraesCS2D01G124200 chr2D 72658995 72660204 1209 True 1269.000000 1269 85.771000 3091 4322 1 chr2D.!!$R3 1231
3 TraesCS2D01G124200 chr2D 72378356 72379042 686 True 682.000000 682 84.615000 3603 4326 1 chr2D.!!$R2 723
4 TraesCS2D01G124200 chr2D 72373340 72373899 559 True 440.000000 440 81.239000 3098 3649 1 chr2D.!!$R1 551
5 TraesCS2D01G124200 chr2A 71347064 71350765 3701 True 5227.000000 5227 92.367000 659 4326 1 chr2A.!!$R4 3667
6 TraesCS2D01G124200 chr2A 71266769 71269768 2999 True 834.500000 1284 83.708000 914 4323 2 chr2A.!!$R9 3409
7 TraesCS2D01G124200 chr2A 71164313 71166318 2005 True 635.333333 1279 86.270667 1976 4323 3 chr2A.!!$R6 2347
8 TraesCS2D01G124200 chr2A 71217096 71220095 2999 True 591.666667 1279 84.877667 914 4323 3 chr2A.!!$R7 3409
9 TraesCS2D01G124200 chr2A 71154733 71157304 2571 True 473.500000 752 83.010000 980 4877 2 chr2A.!!$R5 3897
10 TraesCS2D01G124200 chr2A 71260929 71262692 1763 True 426.500000 723 81.194000 1078 4877 2 chr2A.!!$R8 3799
11 TraesCS2D01G124200 chr2B 109975026 109976428 1402 True 2002.000000 2002 92.580000 3058 4453 1 chr2B.!!$R2 1395
12 TraesCS2D01G124200 chr2B 109928649 109937185 8536 True 1550.400000 3819 87.385000 381 4773 5 chr2B.!!$R8 4392
13 TraesCS2D01G124200 chr2B 109981090 109983469 2379 True 1152.000000 3216 90.153000 659 3068 3 chr2B.!!$R9 2409
14 TraesCS2D01G124200 chr2B 110067144 110068452 1308 False 968.000000 968 80.402000 433 1810 1 chr2B.!!$F1 1377
15 TraesCS2D01G124200 chr2B 109758798 109760242 1444 True 711.650000 1328 86.259500 2630 4326 2 chr2B.!!$R6 1696
16 TraesCS2D01G124200 chr2B 109874169 109877698 3529 True 652.600000 1325 85.243600 914 4785 5 chr2B.!!$R7 3871
17 TraesCS2D01G124200 chr2B 109193316 109195275 1959 True 314.000000 448 86.492500 2532 4706 2 chr2B.!!$R5 2174
18 TraesCS2D01G124200 chr2B 109094767 109096706 1939 True 284.100000 484 85.441500 2630 4785 2 chr2B.!!$R4 2155
19 TraesCS2D01G124200 chr2B 765073940 765076583 2643 False 255.000000 363 93.462500 3 382 2 chr2B.!!$F3 379
20 TraesCS2D01G124200 chrUn 289939069 289942463 3394 False 1303.750000 2455 94.710000 1225 4519 4 chrUn.!!$F6 3294
21 TraesCS2D01G124200 chrUn 235536603 235540244 3641 False 423.160000 922 87.440600 787 4785 5 chrUn.!!$F5 3998
22 TraesCS2D01G124200 chrUn 289658873 289660414 1541 True 360.000000 424 83.439000 3098 4623 2 chrUn.!!$R1 1525

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
109 110 0.474184 GCCAAGGGCTAGCCAATCTA 59.526 55.0 34.09 0.0 46.69 1.98 F
154 155 0.892358 CATCACACAACAGGCCAGCT 60.892 55.0 5.01 0.0 0.00 4.24 F
256 257 1.028905 TGCTGTAACCAAACACCTGC 58.971 50.0 0.00 0.0 0.00 4.85 F
1366 1998 0.038526 GGGCTTCGACGAGAAAGACA 60.039 55.0 3.43 0.0 38.57 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1880 0.178958 AGTCACAGAACTCCTCCGGT 60.179 55.000 0.00 0.00 0.00 5.28 R
1366 1998 2.047274 CCTGATCCACGCGTTGGT 60.047 61.111 10.22 0.44 46.97 3.67 R
1963 2640 3.996150 ATCAAAATCGCCATCATCACC 57.004 42.857 0.00 0.00 0.00 4.02 R
4212 6546 5.541098 AATTTCGTTTCTGATCCGGTAAC 57.459 39.130 0.00 0.00 0.00 2.50 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
27 28 0.819259 GTGCTGCAGGTGGACTTTCA 60.819 55.000 17.12 0.00 0.00 2.69
91 92 3.871006 TCAGTTCATATGGACGTGAATGC 59.129 43.478 8.54 0.00 36.79 3.56
95 96 3.205338 TCATATGGACGTGAATGCCAAG 58.795 45.455 2.13 0.00 34.95 3.61
96 97 2.036958 TATGGACGTGAATGCCAAGG 57.963 50.000 0.00 0.00 34.95 3.61
97 98 0.680921 ATGGACGTGAATGCCAAGGG 60.681 55.000 0.00 0.00 34.95 3.95
107 108 3.847621 GCCAAGGGCTAGCCAATC 58.152 61.111 34.09 17.75 46.69 2.67
109 110 0.474184 GCCAAGGGCTAGCCAATCTA 59.526 55.000 34.09 0.00 46.69 1.98
114 115 2.896039 AGGGCTAGCCAATCTACCTAG 58.104 52.381 34.09 0.00 37.98 3.02
139 140 4.002982 AGATTAGCGCAACAGAAACATCA 58.997 39.130 11.47 0.00 0.00 3.07
142 143 1.002468 AGCGCAACAGAAACATCACAC 60.002 47.619 11.47 0.00 0.00 3.82
144 145 2.794282 GCGCAACAGAAACATCACACAA 60.794 45.455 0.30 0.00 0.00 3.33
146 147 3.730362 CGCAACAGAAACATCACACAACA 60.730 43.478 0.00 0.00 0.00 3.33
150 151 1.956477 AGAAACATCACACAACAGGCC 59.044 47.619 0.00 0.00 0.00 5.19
152 153 1.321474 AACATCACACAACAGGCCAG 58.679 50.000 5.01 0.00 0.00 4.85
154 155 0.892358 CATCACACAACAGGCCAGCT 60.892 55.000 5.01 0.00 0.00 4.24
155 156 0.892358 ATCACACAACAGGCCAGCTG 60.892 55.000 6.78 6.78 0.00 4.24
157 158 1.825191 ACACAACAGGCCAGCTGTG 60.825 57.895 25.13 25.13 43.81 3.66
158 159 2.908940 ACAACAGGCCAGCTGTGC 60.909 61.111 13.81 15.21 34.97 4.57
165 166 1.117142 AGGCCAGCTGTGCATGTTTT 61.117 50.000 23.05 4.49 0.00 2.43
181 182 4.597404 TGTTTTTGCATTGCTACCATGA 57.403 36.364 10.49 0.00 0.00 3.07
183 184 4.930405 TGTTTTTGCATTGCTACCATGATG 59.070 37.500 10.49 0.00 0.00 3.07
184 185 3.804786 TTTGCATTGCTACCATGATGG 57.195 42.857 10.53 10.53 45.02 3.51
186 187 1.325355 GCATTGCTACCATGATGGCT 58.675 50.000 12.25 1.49 42.67 4.75
188 189 2.486982 GCATTGCTACCATGATGGCTAG 59.513 50.000 12.25 12.97 42.67 3.42
193 194 2.828520 GCTACCATGATGGCTAGCTAGA 59.171 50.000 25.15 4.63 42.67 2.43
194 195 3.450457 GCTACCATGATGGCTAGCTAGAT 59.550 47.826 25.15 9.82 42.67 1.98
195 196 3.977134 ACCATGATGGCTAGCTAGATG 57.023 47.619 25.15 16.89 42.67 2.90
196 197 2.027377 ACCATGATGGCTAGCTAGATGC 60.027 50.000 25.15 9.96 42.67 3.91
198 199 3.558533 CCATGATGGCTAGCTAGATGCAA 60.559 47.826 25.15 3.76 45.94 4.08
200 201 2.702478 TGATGGCTAGCTAGATGCAACT 59.298 45.455 25.15 0.86 45.94 3.16
201 202 2.609427 TGGCTAGCTAGATGCAACTG 57.391 50.000 25.15 0.00 45.94 3.16
203 204 1.224965 GCTAGCTAGATGCAACTGCC 58.775 55.000 25.15 0.00 45.94 4.85
204 205 1.202627 GCTAGCTAGATGCAACTGCCT 60.203 52.381 25.15 5.23 45.94 4.75
206 207 3.493350 GCTAGCTAGATGCAACTGCCTAA 60.493 47.826 25.15 0.00 45.94 2.69
207 208 3.191078 AGCTAGATGCAACTGCCTAAG 57.809 47.619 6.76 0.00 45.94 2.18
208 209 2.158842 AGCTAGATGCAACTGCCTAAGG 60.159 50.000 6.76 0.00 45.94 2.69
238 239 9.577110 AGTCAGCAAATTTTACATCATTATGTG 57.423 29.630 2.68 0.00 45.99 3.21
239 240 8.323140 GTCAGCAAATTTTACATCATTATGTGC 58.677 33.333 2.68 0.00 45.99 4.57
240 241 8.252417 TCAGCAAATTTTACATCATTATGTGCT 58.748 29.630 2.68 0.00 45.99 4.40
242 243 8.036575 AGCAAATTTTACATCATTATGTGCTGT 58.963 29.630 2.68 2.29 45.99 4.40
246 247 9.801873 AATTTTACATCATTATGTGCTGTAACC 57.198 29.630 2.68 0.00 44.57 2.85
247 248 7.929941 TTTACATCATTATGTGCTGTAACCA 57.070 32.000 2.68 3.36 44.57 3.67
248 249 7.929941 TTACATCATTATGTGCTGTAACCAA 57.070 32.000 2.68 0.00 45.99 3.67
250 251 6.620678 ACATCATTATGTGCTGTAACCAAAC 58.379 36.000 0.00 0.00 44.79 2.93
251 252 6.208402 ACATCATTATGTGCTGTAACCAAACA 59.792 34.615 0.00 0.00 44.79 2.83
252 253 6.007936 TCATTATGTGCTGTAACCAAACAC 57.992 37.500 0.00 0.00 0.00 3.32
253 254 4.839668 TTATGTGCTGTAACCAAACACC 57.160 40.909 0.00 0.00 30.39 4.16
254 255 2.428544 TGTGCTGTAACCAAACACCT 57.571 45.000 0.00 0.00 30.39 4.00
256 257 1.028905 TGCTGTAACCAAACACCTGC 58.971 50.000 0.00 0.00 0.00 4.85
257 258 1.318576 GCTGTAACCAAACACCTGCT 58.681 50.000 0.00 0.00 0.00 4.24
258 259 1.266989 GCTGTAACCAAACACCTGCTC 59.733 52.381 0.00 0.00 0.00 4.26
259 260 2.851195 CTGTAACCAAACACCTGCTCT 58.149 47.619 0.00 0.00 0.00 4.09
260 261 2.549754 CTGTAACCAAACACCTGCTCTG 59.450 50.000 0.00 0.00 0.00 3.35
261 262 2.092646 TGTAACCAAACACCTGCTCTGT 60.093 45.455 0.00 0.00 0.00 3.41
262 263 3.134985 TGTAACCAAACACCTGCTCTGTA 59.865 43.478 0.00 0.00 0.00 2.74
266 267 4.215109 ACCAAACACCTGCTCTGTATTTT 58.785 39.130 0.00 0.00 0.00 1.82
268 269 4.278170 CCAAACACCTGCTCTGTATTTTGA 59.722 41.667 0.00 0.00 0.00 2.69
270 271 6.449698 CAAACACCTGCTCTGTATTTTGAAT 58.550 36.000 0.00 0.00 0.00 2.57
275 276 6.037610 CACCTGCTCTGTATTTTGAATACTCC 59.962 42.308 10.98 0.66 0.00 3.85
276 277 5.235186 CCTGCTCTGTATTTTGAATACTCCG 59.765 44.000 10.98 2.45 0.00 4.63
277 278 5.972935 TGCTCTGTATTTTGAATACTCCGA 58.027 37.500 10.98 5.62 0.00 4.55
279 280 6.876789 TGCTCTGTATTTTGAATACTCCGAAA 59.123 34.615 10.98 0.00 0.00 3.46
281 282 8.234546 GCTCTGTATTTTGAATACTCCGAAAAA 58.765 33.333 10.98 0.00 0.00 1.94
282 283 9.543018 CTCTGTATTTTGAATACTCCGAAAAAC 57.457 33.333 10.98 0.00 0.00 2.43
283 284 9.280174 TCTGTATTTTGAATACTCCGAAAAACT 57.720 29.630 10.98 0.00 0.00 2.66
284 285 9.543018 CTGTATTTTGAATACTCCGAAAAACTC 57.457 33.333 10.98 0.00 0.00 3.01
286 287 9.543018 GTATTTTGAATACTCCGAAAAACTCTG 57.457 33.333 4.09 0.00 0.00 3.35
289 290 8.665643 TTTGAATACTCCGAAAAACTCTGTTA 57.334 30.769 0.00 0.00 0.00 2.41
291 292 8.665643 TGAATACTCCGAAAAACTCTGTTAAA 57.334 30.769 0.00 0.00 0.00 1.52
299 300 9.518906 TCCGAAAAACTCTGTTAAATAAAAACC 57.481 29.630 0.00 0.00 0.00 3.27
300 301 9.303537 CCGAAAAACTCTGTTAAATAAAAACCA 57.696 29.630 0.00 0.00 0.00 3.67
323 324 9.705103 ACCATTGTTTAGTATACCTACTGACTA 57.295 33.333 0.00 0.00 38.65 2.59
335 336 6.607004 ACCTACTGACTAAATTACTGCAGT 57.393 37.500 25.12 25.12 39.61 4.40
337 338 7.450903 ACCTACTGACTAAATTACTGCAGTTT 58.549 34.615 27.06 15.98 37.69 2.66
338 339 7.937394 ACCTACTGACTAAATTACTGCAGTTTT 59.063 33.333 27.06 21.63 37.69 2.43
340 341 9.599322 CTACTGACTAAATTACTGCAGTTTTTG 57.401 33.333 27.06 21.37 37.69 2.44
342 343 8.850156 ACTGACTAAATTACTGCAGTTTTTGAT 58.150 29.630 27.06 16.03 33.19 2.57
349 350 8.816640 AATTACTGCAGTTTTTGATACTTTGG 57.183 30.769 27.06 0.00 0.00 3.28
350 351 5.852282 ACTGCAGTTTTTGATACTTTGGT 57.148 34.783 15.25 0.00 0.00 3.67
351 352 6.220726 ACTGCAGTTTTTGATACTTTGGTT 57.779 33.333 15.25 0.00 0.00 3.67
352 353 6.639563 ACTGCAGTTTTTGATACTTTGGTTT 58.360 32.000 15.25 0.00 0.00 3.27
354 355 7.606073 ACTGCAGTTTTTGATACTTTGGTTTTT 59.394 29.630 15.25 0.00 0.00 1.94
355 356 7.969314 TGCAGTTTTTGATACTTTGGTTTTTC 58.031 30.769 0.00 0.00 0.00 2.29
356 357 7.821846 TGCAGTTTTTGATACTTTGGTTTTTCT 59.178 29.630 0.00 0.00 0.00 2.52
357 358 8.116136 GCAGTTTTTGATACTTTGGTTTTTCTG 58.884 33.333 0.00 0.00 0.00 3.02
358 359 9.364989 CAGTTTTTGATACTTTGGTTTTTCTGA 57.635 29.630 0.00 0.00 0.00 3.27
368 369 8.232913 ACTTTGGTTTTTCTGATACTTTGCTA 57.767 30.769 0.00 0.00 0.00 3.49
369 370 8.860088 ACTTTGGTTTTTCTGATACTTTGCTAT 58.140 29.630 0.00 0.00 0.00 2.97
371 372 7.994425 TGGTTTTTCTGATACTTTGCTATCA 57.006 32.000 0.00 0.00 33.08 2.15
373 374 8.855110 TGGTTTTTCTGATACTTTGCTATCAAA 58.145 29.630 0.00 0.00 39.67 2.69
374 375 9.129209 GGTTTTTCTGATACTTTGCTATCAAAC 57.871 33.333 0.00 0.00 37.28 2.93
375 376 9.677567 GTTTTTCTGATACTTTGCTATCAAACA 57.322 29.630 0.00 0.00 37.28 2.83
390 391 7.996066 TGCTATCAAACATACCCTAAATGCTTA 59.004 33.333 0.00 0.00 0.00 3.09
484 489 2.362077 GTGTGCATCTGGTCCAAGTTTT 59.638 45.455 0.00 0.00 0.00 2.43
485 490 3.030291 TGTGCATCTGGTCCAAGTTTTT 58.970 40.909 0.00 0.00 0.00 1.94
872 955 3.055385 TCCGTAAGTTGGATCCTTTCCTG 60.055 47.826 14.23 0.00 45.68 3.86
903 986 1.924731 CATACGCCCCTCTAGATCCA 58.075 55.000 0.00 0.00 0.00 3.41
956 1040 7.266922 TGGATTTTCCTGCGTAATATTTACC 57.733 36.000 0.00 0.00 37.46 2.85
1013 1633 2.177654 GACGAAATGCGCCGGACAAA 62.178 55.000 5.05 0.00 46.04 2.83
1121 1753 2.393768 CGCTCCTGCACCACATCAC 61.394 63.158 0.00 0.00 39.64 3.06
1248 1880 4.337177 TTCCGCGATGCCAACCCA 62.337 61.111 8.23 0.00 0.00 4.51
1366 1998 0.038526 GGGCTTCGACGAGAAAGACA 60.039 55.000 3.43 0.00 38.57 3.41
2149 2837 1.979155 GGGGCCAAGCTTTCCAGTC 60.979 63.158 4.39 0.00 0.00 3.51
2172 3330 6.828785 GTCAAGATGGTAAGTATGGTGGAAAT 59.171 38.462 0.00 0.00 0.00 2.17
4212 6546 5.295787 TGTGGTCTGTAGTAACTTTGCTTTG 59.704 40.000 0.00 0.00 0.00 2.77
4388 6886 6.851222 AGAATATTGACGTAAGCTTCATGG 57.149 37.500 0.00 0.00 45.62 3.66
4640 7150 7.996066 AGTTTAACCCAATTTAACAATTTGCCT 59.004 29.630 0.00 0.00 33.19 4.75
4810 7328 4.080807 TGGCAAATCTAGTTCCGGTTATCA 60.081 41.667 0.00 0.00 0.00 2.15
4843 7361 0.890683 GTTCATCTTTGCCCCACTGG 59.109 55.000 0.00 0.00 37.09 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.819259 TGAAAGTCCACCTGCAGCAC 60.819 55.000 8.66 1.61 0.00 4.40
91 92 1.202818 GGTAGATTGGCTAGCCCTTGG 60.203 57.143 30.81 0.00 40.82 3.61
95 96 1.276705 GCTAGGTAGATTGGCTAGCCC 59.723 57.143 30.81 15.68 46.36 5.19
96 97 2.252714 AGCTAGGTAGATTGGCTAGCC 58.747 52.381 27.71 27.71 46.36 3.93
97 98 4.337145 TCTAGCTAGGTAGATTGGCTAGC 58.663 47.826 24.39 6.04 46.76 3.42
120 121 2.875317 TGTGATGTTTCTGTTGCGCTAA 59.125 40.909 9.73 0.00 0.00 3.09
125 126 3.768406 TGTTGTGTGATGTTTCTGTTGC 58.232 40.909 0.00 0.00 0.00 4.17
126 127 4.353737 CCTGTTGTGTGATGTTTCTGTTG 58.646 43.478 0.00 0.00 0.00 3.33
131 132 1.680735 TGGCCTGTTGTGTGATGTTTC 59.319 47.619 3.32 0.00 0.00 2.78
132 133 1.682854 CTGGCCTGTTGTGTGATGTTT 59.317 47.619 3.32 0.00 0.00 2.83
133 134 1.321474 CTGGCCTGTTGTGTGATGTT 58.679 50.000 3.32 0.00 0.00 2.71
134 135 1.174712 GCTGGCCTGTTGTGTGATGT 61.175 55.000 11.69 0.00 0.00 3.06
146 147 1.117142 AAAACATGCACAGCTGGCCT 61.117 50.000 19.93 8.79 0.00 5.19
157 158 3.065655 TGGTAGCAATGCAAAAACATGC 58.934 40.909 8.35 0.00 46.58 4.06
158 159 4.930405 TCATGGTAGCAATGCAAAAACATG 59.070 37.500 20.11 20.11 35.77 3.21
165 166 1.409790 GCCATCATGGTAGCAATGCAA 59.590 47.619 8.35 0.00 40.46 4.08
169 170 2.374504 AGCTAGCCATCATGGTAGCAAT 59.625 45.455 26.83 13.61 43.35 3.56
170 171 1.770658 AGCTAGCCATCATGGTAGCAA 59.229 47.619 26.83 4.09 43.35 3.91
171 172 1.427809 AGCTAGCCATCATGGTAGCA 58.572 50.000 26.83 0.00 43.35 3.49
172 173 2.828520 TCTAGCTAGCCATCATGGTAGC 59.171 50.000 21.68 21.68 42.32 3.58
173 174 4.680172 GCATCTAGCTAGCCATCATGGTAG 60.680 50.000 16.35 7.18 39.15 3.18
181 182 2.809665 GCAGTTGCATCTAGCTAGCCAT 60.810 50.000 16.35 2.36 45.94 4.40
183 184 1.224965 GCAGTTGCATCTAGCTAGCC 58.775 55.000 16.35 7.33 45.94 3.93
184 185 1.202627 AGGCAGTTGCATCTAGCTAGC 60.203 52.381 16.35 6.62 45.94 3.42
186 187 3.070159 CCTTAGGCAGTTGCATCTAGCTA 59.930 47.826 6.43 0.00 45.94 3.32
188 189 2.216898 CCTTAGGCAGTTGCATCTAGC 58.783 52.381 6.43 4.15 44.36 3.42
214 215 8.252417 AGCACATAATGATGTAAAATTTGCTGA 58.748 29.630 0.00 0.00 44.82 4.26
215 216 8.325282 CAGCACATAATGATGTAAAATTTGCTG 58.675 33.333 12.63 12.63 44.82 4.41
216 217 8.415192 CAGCACATAATGATGTAAAATTTGCT 57.585 30.769 0.00 0.00 44.82 3.91
228 229 6.350110 GGTGTTTGGTTACAGCACATAATGAT 60.350 38.462 0.00 0.00 43.96 2.45
229 230 5.048364 GGTGTTTGGTTACAGCACATAATGA 60.048 40.000 0.00 0.00 43.96 2.57
230 231 5.048083 AGGTGTTTGGTTACAGCACATAATG 60.048 40.000 8.43 0.00 46.24 1.90
231 232 5.048083 CAGGTGTTTGGTTACAGCACATAAT 60.048 40.000 8.43 0.00 46.24 1.28
234 235 2.622942 CAGGTGTTTGGTTACAGCACAT 59.377 45.455 8.43 0.00 46.24 3.21
238 239 1.266989 GAGCAGGTGTTTGGTTACAGC 59.733 52.381 0.00 0.00 44.66 4.40
239 240 2.549754 CAGAGCAGGTGTTTGGTTACAG 59.450 50.000 0.00 0.00 0.00 2.74
240 241 2.092646 ACAGAGCAGGTGTTTGGTTACA 60.093 45.455 0.00 0.00 0.00 2.41
242 243 4.634012 ATACAGAGCAGGTGTTTGGTTA 57.366 40.909 0.00 0.00 0.00 2.85
246 247 5.437289 TCAAAATACAGAGCAGGTGTTTG 57.563 39.130 0.00 0.00 31.28 2.93
247 248 6.655078 ATTCAAAATACAGAGCAGGTGTTT 57.345 33.333 0.00 0.00 32.01 2.83
248 249 6.942576 AGTATTCAAAATACAGAGCAGGTGTT 59.057 34.615 11.30 0.00 0.00 3.32
250 251 6.037610 GGAGTATTCAAAATACAGAGCAGGTG 59.962 42.308 11.30 0.00 0.00 4.00
251 252 6.116126 GGAGTATTCAAAATACAGAGCAGGT 58.884 40.000 11.30 0.00 0.00 4.00
252 253 5.235186 CGGAGTATTCAAAATACAGAGCAGG 59.765 44.000 11.30 0.00 0.00 4.85
253 254 6.042777 TCGGAGTATTCAAAATACAGAGCAG 58.957 40.000 11.30 1.48 0.00 4.24
254 255 5.972935 TCGGAGTATTCAAAATACAGAGCA 58.027 37.500 11.30 0.00 0.00 4.26
256 257 9.543018 GTTTTTCGGAGTATTCAAAATACAGAG 57.457 33.333 11.30 3.54 0.00 3.35
257 258 9.280174 AGTTTTTCGGAGTATTCAAAATACAGA 57.720 29.630 11.30 5.89 0.00 3.41
258 259 9.543018 GAGTTTTTCGGAGTATTCAAAATACAG 57.457 33.333 11.30 4.09 0.00 2.74
259 260 9.280174 AGAGTTTTTCGGAGTATTCAAAATACA 57.720 29.630 11.30 0.00 0.00 2.29
260 261 9.543018 CAGAGTTTTTCGGAGTATTCAAAATAC 57.457 33.333 2.32 2.32 0.00 1.89
261 262 9.280174 ACAGAGTTTTTCGGAGTATTCAAAATA 57.720 29.630 0.00 0.00 0.00 1.40
262 263 8.166422 ACAGAGTTTTTCGGAGTATTCAAAAT 57.834 30.769 0.00 0.00 0.00 1.82
266 267 8.665643 TTTAACAGAGTTTTTCGGAGTATTCA 57.334 30.769 0.00 0.00 0.00 2.57
296 297 9.043548 AGTCAGTAGGTATACTAAACAATGGTT 57.956 33.333 2.25 0.00 40.38 3.67
308 309 9.680315 CTGCAGTAATTTAGTCAGTAGGTATAC 57.320 37.037 5.25 0.00 0.00 1.47
311 312 7.713734 ACTGCAGTAATTTAGTCAGTAGGTA 57.286 36.000 20.16 0.00 33.56 3.08
312 313 6.607004 ACTGCAGTAATTTAGTCAGTAGGT 57.393 37.500 20.16 0.00 33.56 3.08
315 316 9.332502 TCAAAAACTGCAGTAATTTAGTCAGTA 57.667 29.630 22.01 3.10 34.14 2.74
323 324 9.260002 CCAAAGTATCAAAAACTGCAGTAATTT 57.740 29.630 22.01 20.42 0.00 1.82
326 327 7.341445 ACCAAAGTATCAAAAACTGCAGTAA 57.659 32.000 22.01 4.02 0.00 2.24
327 328 6.952773 ACCAAAGTATCAAAAACTGCAGTA 57.047 33.333 22.01 3.84 0.00 2.74
340 341 9.129209 GCAAAGTATCAGAAAAACCAAAGTATC 57.871 33.333 0.00 0.00 0.00 2.24
342 343 8.232913 AGCAAAGTATCAGAAAAACCAAAGTA 57.767 30.769 0.00 0.00 0.00 2.24
343 344 7.112452 AGCAAAGTATCAGAAAAACCAAAGT 57.888 32.000 0.00 0.00 0.00 2.66
345 346 8.855110 TGATAGCAAAGTATCAGAAAAACCAAA 58.145 29.630 0.00 0.00 35.01 3.28
346 347 8.402798 TGATAGCAAAGTATCAGAAAAACCAA 57.597 30.769 0.00 0.00 35.01 3.67
347 348 7.994425 TGATAGCAAAGTATCAGAAAAACCA 57.006 32.000 0.00 0.00 35.01 3.67
349 350 9.677567 TGTTTGATAGCAAAGTATCAGAAAAAC 57.322 29.630 6.36 0.00 44.12 2.43
354 355 7.715249 GGGTATGTTTGATAGCAAAGTATCAGA 59.285 37.037 6.36 0.00 44.12 3.27
355 356 7.716998 AGGGTATGTTTGATAGCAAAGTATCAG 59.283 37.037 6.36 0.00 44.12 2.90
356 357 7.573710 AGGGTATGTTTGATAGCAAAGTATCA 58.426 34.615 6.36 1.61 44.12 2.15
357 358 9.555727 TTAGGGTATGTTTGATAGCAAAGTATC 57.444 33.333 6.36 3.74 44.12 2.24
358 359 9.914834 TTTAGGGTATGTTTGATAGCAAAGTAT 57.085 29.630 6.36 7.30 44.12 2.12
359 360 9.914834 ATTTAGGGTATGTTTGATAGCAAAGTA 57.085 29.630 6.36 0.00 44.12 2.24
360 361 8.686334 CATTTAGGGTATGTTTGATAGCAAAGT 58.314 33.333 6.36 1.58 44.12 2.66
362 363 7.341769 AGCATTTAGGGTATGTTTGATAGCAAA 59.658 33.333 1.13 1.13 41.47 3.68
363 364 6.833416 AGCATTTAGGGTATGTTTGATAGCAA 59.167 34.615 0.00 0.00 0.00 3.91
364 365 6.364701 AGCATTTAGGGTATGTTTGATAGCA 58.635 36.000 0.00 0.00 0.00 3.49
365 366 6.884280 AGCATTTAGGGTATGTTTGATAGC 57.116 37.500 0.00 0.00 0.00 2.97
484 489 1.351017 GTCCCACTGGTCCAGATCAAA 59.649 52.381 26.18 3.94 35.18 2.69
485 490 0.984230 GTCCCACTGGTCCAGATCAA 59.016 55.000 26.18 5.36 35.18 2.57
487 492 1.207791 ATGTCCCACTGGTCCAGATC 58.792 55.000 26.18 10.41 35.18 2.75
489 494 1.444933 AAATGTCCCACTGGTCCAGA 58.555 50.000 26.18 1.63 35.18 3.86
490 495 2.292828 AAAATGTCCCACTGGTCCAG 57.707 50.000 17.88 17.88 37.52 3.86
626 636 9.659830 CTCCAACAAAAATGTACTACTACAAAC 57.340 33.333 0.00 0.00 36.43 2.93
741 789 0.178947 TTCTCCCCCGCACCAAATTT 60.179 50.000 0.00 0.00 0.00 1.82
872 955 1.095807 GGCGTATGCAGGGAGGAAAC 61.096 60.000 9.59 0.00 45.35 2.78
903 986 0.106708 ACGCGTATGGAGATGGCATT 59.893 50.000 11.67 0.00 0.00 3.56
1021 1641 2.228480 GGTGGTAAGGTCCCCAGCA 61.228 63.158 9.30 0.00 46.13 4.41
1029 1649 4.388499 CCAGCGCGGTGGTAAGGT 62.388 66.667 41.41 0.00 32.32 3.50
1121 1753 2.049433 ACGCCTTCAGGAACGACG 60.049 61.111 0.00 0.00 37.39 5.12
1248 1880 0.178958 AGTCACAGAACTCCTCCGGT 60.179 55.000 0.00 0.00 0.00 5.28
1366 1998 2.047274 CCTGATCCACGCGTTGGT 60.047 61.111 10.22 0.44 46.97 3.67
1963 2640 3.996150 ATCAAAATCGCCATCATCACC 57.004 42.857 0.00 0.00 0.00 4.02
2149 2837 7.993183 ACTATTTCCACCATACTTACCATCTTG 59.007 37.037 0.00 0.00 0.00 3.02
4212 6546 5.541098 AATTTCGTTTCTGATCCGGTAAC 57.459 39.130 0.00 0.00 0.00 2.50
4388 6886 1.171308 AGGCACACATGATTGCAGAC 58.829 50.000 20.04 7.45 40.75 3.51
4640 7150 6.074648 AGTGGACCCAACAGATTAAAATCAA 58.925 36.000 5.55 0.00 37.89 2.57
4810 7328 0.827507 ATGAACAAAGGGCGGCAAGT 60.828 50.000 12.47 0.00 0.00 3.16
4843 7361 1.446907 CCACTCCATGAGACTGCAAC 58.553 55.000 0.00 0.00 33.32 4.17


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

AutoCloner maintained by Alex Coulton.