Multiple sequence alignment - TraesCS6D01G012000

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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 TraesCS6D01G012000 chr6D 100.000 4303 0 0 1 4303 4697269 4701571 0.000000e+00 7947.0
1 TraesCS6D01G012000 chr6D 83.908 1392 191 19 1114 2475 4646821 4648209 0.000000e+00 1299.0
2 TraesCS6D01G012000 chr6D 80.464 1121 139 45 2556 3647 4648204 4649273 0.000000e+00 784.0
3 TraesCS6D01G012000 chr6D 85.857 601 67 10 1150 1736 4267517 4266921 1.310000e-174 623.0
4 TraesCS6D01G012000 chr6D 83.059 608 74 17 2559 3157 4266202 4265615 3.810000e-145 525.0
5 TraesCS6D01G012000 chr6D 78.947 247 36 10 880 1123 4056443 4056210 2.070000e-33 154.0
6 TraesCS6D01G012000 chr6D 86.364 110 8 3 8 117 147892406 147892304 3.520000e-21 113.0
7 TraesCS6D01G012000 chr3A 91.593 2391 152 19 1 2353 731445274 731447653 0.000000e+00 3256.0
8 TraesCS6D01G012000 chr3A 94.679 1372 63 8 2689 4054 731404097 731405464 0.000000e+00 2121.0
9 TraesCS6D01G012000 chr3A 94.679 1372 62 9 2689 4054 731447655 731449021 0.000000e+00 2119.0
10 TraesCS6D01G012000 chr3A 94.401 1268 62 5 1089 2353 731402834 731404095 0.000000e+00 1940.0
11 TraesCS6D01G012000 chr3A 90.262 688 53 6 317 990 731401714 731402401 0.000000e+00 887.0
12 TraesCS6D01G012000 chr3A 95.238 168 7 1 4136 4303 731449023 731449189 9.170000e-67 265.0
13 TraesCS6D01G012000 chr6B 88.916 2481 149 55 536 2958 7307995 7305583 0.000000e+00 2942.0
14 TraesCS6D01G012000 chr6B 83.696 1380 192 23 1116 2465 7902259 7900883 0.000000e+00 1271.0
15 TraesCS6D01G012000 chr6B 86.849 1095 94 20 2980 4054 7305591 7304527 0.000000e+00 1179.0
16 TraesCS6D01G012000 chr6B 93.169 688 47 0 1423 2110 7125101 7124414 0.000000e+00 1011.0
17 TraesCS6D01G012000 chr6B 91.740 678 46 5 3387 4054 7124054 7123377 0.000000e+00 933.0
18 TraesCS6D01G012000 chr6B 80.864 1134 153 40 2937 4054 7822656 7821571 0.000000e+00 833.0
19 TraesCS6D01G012000 chr6B 82.323 792 130 6 1693 2475 8423482 8424272 0.000000e+00 678.0
20 TraesCS6D01G012000 chr6B 84.912 570 61 16 2574 3137 7900861 7900311 1.750000e-153 553.0
21 TraesCS6D01G012000 chr6B 88.660 388 25 7 861 1233 7094941 7094558 5.070000e-124 455.0
22 TraesCS6D01G012000 chr6B 85.065 462 41 8 970 1421 7125686 7125243 3.050000e-121 446.0
23 TraesCS6D01G012000 chr6B 81.207 580 43 34 477 1014 7102627 7102072 1.440000e-109 407.0
24 TraesCS6D01G012000 chr6B 80.690 580 47 33 477 1014 7110803 7110247 1.450000e-104 390.0
25 TraesCS6D01G012000 chr6B 78.251 423 34 29 477 857 7095549 7095143 7.240000e-53 219.0
26 TraesCS6D01G012000 chr6B 90.361 166 15 1 4136 4301 7123378 7123214 2.610000e-52 217.0
27 TraesCS6D01G012000 chr6B 89.908 109 9 2 4136 4243 7304528 7304421 5.800000e-29 139.0
28 TraesCS6D01G012000 chrUn 97.556 1391 31 2 1094 2481 71058303 71056913 0.000000e+00 2377.0
29 TraesCS6D01G012000 chrUn 96.736 1103 34 2 2554 3655 71056924 71055823 0.000000e+00 1836.0
30 TraesCS6D01G012000 chrUn 88.078 973 77 8 113 1071 71059352 71058405 0.000000e+00 1118.0
31 TraesCS6D01G012000 chrUn 96.429 168 4 1 4136 4303 71041358 71041193 4.240000e-70 276.0
32 TraesCS6D01G012000 chrUn 97.973 148 3 0 3765 3912 71055576 71055429 1.540000e-64 257.0
33 TraesCS6D01G012000 chrUn 96.454 141 5 0 3914 4054 71041497 71041357 2.590000e-57 233.0
34 TraesCS6D01G012000 chrUn 98.889 90 0 1 4053 4141 226884245 226884334 4.450000e-35 159.0
35 TraesCS6D01G012000 chrUn 96.000 100 1 3 4053 4151 314263420 314263323 4.450000e-35 159.0
36 TraesCS6D01G012000 chrUn 97.753 89 2 0 4049 4137 132121144 132121232 2.070000e-33 154.0
37 TraesCS6D01G012000 chrUn 94.872 78 4 0 3629 3706 71055650 71055573 5.840000e-24 122.0
38 TraesCS6D01G012000 chrUn 82.243 107 11 7 477 577 71076800 71076696 7.670000e-13 86.1
39 TraesCS6D01G012000 chrUn 81.308 107 12 7 477 577 71062138 71062034 3.570000e-11 80.5
40 TraesCS6D01G012000 chrUn 100.000 30 0 0 4274 4303 79850879 79850908 6.010000e-04 56.5
41 TraesCS6D01G012000 chr6A 83.770 1337 185 14 1162 2475 3000812 3002139 0.000000e+00 1238.0
42 TraesCS6D01G012000 chr6A 82.974 1392 204 21 1114 2475 2719201 2717813 0.000000e+00 1227.0
43 TraesCS6D01G012000 chr6A 83.201 1262 200 9 1223 2475 3014857 3016115 0.000000e+00 1146.0
44 TraesCS6D01G012000 chr6A 83.717 608 69 17 2559 3157 2717815 2717229 8.140000e-152 547.0
45 TraesCS6D01G012000 chr6A 84.440 482 52 13 2556 3034 3002134 3002595 1.820000e-123 453.0
46 TraesCS6D01G012000 chr6A 82.243 107 11 7 477 577 2527441 2527337 7.670000e-13 86.1
47 TraesCS6D01G012000 chr3B 81.793 357 60 5 117 469 612303620 612303975 1.170000e-75 294.0
48 TraesCS6D01G012000 chr3B 81.169 308 52 5 171 474 646023586 646023891 4.300000e-60 243.0
49 TraesCS6D01G012000 chr3B 75.263 380 72 14 113 473 425462073 425461697 1.240000e-35 161.0
50 TraesCS6D01G012000 chr5A 80.978 368 63 6 106 469 22612690 22613054 7.040000e-73 285.0
51 TraesCS6D01G012000 chr2B 79.730 370 68 7 110 474 84967988 84968355 1.190000e-65 261.0
52 TraesCS6D01G012000 chr2D 82.331 266 39 7 208 469 391819503 391819764 1.560000e-54 224.0
53 TraesCS6D01G012000 chr2D 77.419 372 76 7 106 474 360270636 360271002 9.370000e-52 215.0
54 TraesCS6D01G012000 chr2D 85.714 105 8 5 1 105 491946259 491946356 2.120000e-18 104.0
55 TraesCS6D01G012000 chr5D 80.000 305 51 8 113 414 388737858 388737561 2.610000e-52 217.0
56 TraesCS6D01G012000 chr5D 100.000 89 0 0 4049 4137 29115694 29115606 9.570000e-37 165.0
57 TraesCS6D01G012000 chr5D 86.486 111 8 4 1 111 384882345 384882242 9.780000e-22 115.0
58 TraesCS6D01G012000 chr2A 96.907 97 2 1 4049 4145 34104432 34104337 1.240000e-35 161.0
59 TraesCS6D01G012000 chr2A 95.918 98 3 1 4051 4148 48468009 48468105 1.600000e-34 158.0
60 TraesCS6D01G012000 chr2A 84.553 123 11 4 1 123 77242270 77242156 9.780000e-22 115.0
61 TraesCS6D01G012000 chr1D 96.000 100 1 3 4053 4151 30049496 30049399 4.450000e-35 159.0
62 TraesCS6D01G012000 chr7D 94.118 102 5 1 4037 4137 481573737 481573838 2.070000e-33 154.0
63 TraesCS6D01G012000 chr7D 83.621 116 12 3 1 116 349638757 349638865 7.610000e-18 102.0
64 TraesCS6D01G012000 chr7B 91.150 113 7 3 4051 4161 389007092 389007203 2.680000e-32 150.0
65 TraesCS6D01G012000 chr3D 87.179 117 8 4 1 117 516073285 516073176 4.520000e-25 126.0
66 TraesCS6D01G012000 chr4A 85.586 111 9 4 1 111 535471086 535470983 4.550000e-20 110.0
67 TraesCS6D01G012000 chr7A 84.483 116 10 6 1 116 500179070 500179177 1.640000e-19 108.0


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 TraesCS6D01G012000 chr6D 4697269 4701571 4302 False 7947.000000 7947 100.000000 1 4303 1 chr6D.!!$F1 4302
1 TraesCS6D01G012000 chr6D 4646821 4649273 2452 False 1041.500000 1299 82.186000 1114 3647 2 chr6D.!!$F2 2533
2 TraesCS6D01G012000 chr6D 4265615 4267517 1902 True 574.000000 623 84.458000 1150 3157 2 chr6D.!!$R3 2007
3 TraesCS6D01G012000 chr3A 731445274 731449189 3915 False 1880.000000 3256 93.836667 1 4303 3 chr3A.!!$F2 4302
4 TraesCS6D01G012000 chr3A 731401714 731405464 3750 False 1649.333333 2121 93.114000 317 4054 3 chr3A.!!$F1 3737
5 TraesCS6D01G012000 chr6B 7304421 7307995 3574 True 1420.000000 2942 88.557667 536 4243 3 chr6B.!!$R6 3707
6 TraesCS6D01G012000 chr6B 7900311 7902259 1948 True 912.000000 1271 84.304000 1116 3137 2 chr6B.!!$R7 2021
7 TraesCS6D01G012000 chr6B 7821571 7822656 1085 True 833.000000 833 80.864000 2937 4054 1 chr6B.!!$R3 1117
8 TraesCS6D01G012000 chr6B 8423482 8424272 790 False 678.000000 678 82.323000 1693 2475 1 chr6B.!!$F1 782
9 TraesCS6D01G012000 chr6B 7123214 7125686 2472 True 651.750000 1011 90.083750 970 4301 4 chr6B.!!$R5 3331
10 TraesCS6D01G012000 chr6B 7102072 7102627 555 True 407.000000 407 81.207000 477 1014 1 chr6B.!!$R1 537
11 TraesCS6D01G012000 chr6B 7110247 7110803 556 True 390.000000 390 80.690000 477 1014 1 chr6B.!!$R2 537
12 TraesCS6D01G012000 chr6B 7094558 7095549 991 True 337.000000 455 83.455500 477 1233 2 chr6B.!!$R4 756
13 TraesCS6D01G012000 chrUn 71055429 71062138 6709 True 965.083333 2377 92.753833 113 3912 6 chrUn.!!$R4 3799
14 TraesCS6D01G012000 chr6A 3014857 3016115 1258 False 1146.000000 1146 83.201000 1223 2475 1 chr6A.!!$F1 1252
15 TraesCS6D01G012000 chr6A 2717229 2719201 1972 True 887.000000 1227 83.345500 1114 3157 2 chr6A.!!$R2 2043
16 TraesCS6D01G012000 chr6A 3000812 3002595 1783 False 845.500000 1238 84.105000 1162 3034 2 chr6A.!!$F2 1872

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
444 3120 0.463295 CTCAGCGGATTGATGCAGGT 60.463 55.000 0.00 0.0 32.78 4.00 F
612 3303 0.953471 GATGGCACCTGCGTACAACA 60.953 55.000 0.00 0.0 43.26 3.33 F
1536 5063 1.302285 CTGCCCAAGAGCACCAGAT 59.698 57.895 0.00 0.0 38.00 2.90 F
1725 5258 0.250081 TGTACTGTGCGTTGATGCCA 60.250 50.000 0.00 0.0 0.00 4.92 F
2080 5648 1.341482 TGCTGGTTTGTTGGACCTGAA 60.341 47.619 4.62 0.0 38.09 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 5063 0.535335 GCTTCATCGGTGTGGTAGGA 59.465 55.000 0.00 0.0 0.00 2.94 R
1725 5258 0.680921 CCATGGACGTGCCCATCTTT 60.681 55.000 5.56 0.0 44.69 2.52 R
2687 6326 1.079612 GGCCAGGCATCAAAGCAAC 60.080 57.895 15.19 0.0 35.83 4.17 R
3222 7136 1.827792 TCTGTCCCTTTCCTCCCAAA 58.172 50.000 0.00 0.0 0.00 3.28 R
3941 8091 1.133869 GCGGCGTACACAATGGAAC 59.866 57.895 9.37 0.0 0.00 3.62 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
46 47 4.451150 GCGGCAGACGGATGGACA 62.451 66.667 0.00 0.00 44.51 4.02
76 77 0.587985 GTGTGCCGTGTCGTTTGAAC 60.588 55.000 0.00 0.00 0.00 3.18
264 2939 1.344438 CTCTAGCCGGGTATGAATGCA 59.656 52.381 14.90 0.00 0.00 3.96
267 2942 2.555547 GCCGGGTATGAATGCAGGC 61.556 63.158 2.18 0.00 36.08 4.85
312 2987 4.941309 AAAACGCGCGGGAGGGTT 62.941 61.111 35.22 15.42 46.95 4.11
320 2995 2.295602 GCGGGAGGGTTGAGGGTTA 61.296 63.158 0.00 0.00 0.00 2.85
347 3023 1.009389 GGTCAGAGCGGTCAGAAACG 61.009 60.000 18.15 0.00 0.00 3.60
377 3053 2.747686 GTCCGGACTCCTGCCAAA 59.252 61.111 27.64 0.00 0.00 3.28
380 3056 1.376037 CCGGACTCCTGCCAAACTC 60.376 63.158 0.00 0.00 0.00 3.01
403 3079 1.400142 CACGTTTGTCTCTGGTTTGCA 59.600 47.619 0.00 0.00 0.00 4.08
424 3100 4.770795 CAGGAGAAAATAAGTCCGGACAT 58.229 43.478 35.00 26.66 35.33 3.06
426 3102 4.717280 AGGAGAAAATAAGTCCGGACATCT 59.283 41.667 35.00 24.62 35.33 2.90
434 3110 1.455773 TCCGGACATCTCAGCGGAT 60.456 57.895 0.00 0.00 28.52 4.18
435 3111 1.043116 TCCGGACATCTCAGCGGATT 61.043 55.000 0.00 0.00 28.52 3.01
444 3120 0.463295 CTCAGCGGATTGATGCAGGT 60.463 55.000 0.00 0.00 32.78 4.00
449 3125 1.153086 GGATTGATGCAGGTCCGCT 60.153 57.895 0.00 0.00 0.00 5.52
469 3145 4.162690 GGATGGCTTCCGCGGTCT 62.163 66.667 27.15 4.25 33.93 3.85
502 3178 3.947834 AGGTTGTTCTCAGTGTTTTCAGG 59.052 43.478 0.00 0.00 0.00 3.86
593 3271 2.980568 TGGGCCAACGTTACATCTTAG 58.019 47.619 2.13 0.00 0.00 2.18
600 3291 4.034048 CCAACGTTACATCTTAGATGGCAC 59.966 45.833 23.94 17.94 0.00 5.01
612 3303 0.953471 GATGGCACCTGCGTACAACA 60.953 55.000 0.00 0.00 43.26 3.33
711 3413 2.032987 AAAACTGCCGTACCCCCG 59.967 61.111 0.00 0.00 0.00 5.73
763 3473 1.482593 GAGAAAGAAGGATCGGAGCCA 59.517 52.381 15.64 0.00 0.00 4.75
872 3807 8.554835 TCTCCATCTAATCTACTAGTGATTCG 57.445 38.462 18.03 14.12 35.90 3.34
957 3892 2.584773 ACCCTAACATCCATCCCCTTT 58.415 47.619 0.00 0.00 0.00 3.11
1108 4480 5.178252 ACTTGCTTTGTATATGCTATCGCTG 59.822 40.000 0.00 0.00 36.97 5.18
1426 4953 1.488705 TTCCTCAAGCACCACCGGAT 61.489 55.000 9.46 0.00 0.00 4.18
1439 4966 1.834378 CCGGATGCCTCCTCTGCTA 60.834 63.158 0.00 0.00 39.65 3.49
1536 5063 1.302285 CTGCCCAAGAGCACCAGAT 59.698 57.895 0.00 0.00 38.00 2.90
1725 5258 0.250081 TGTACTGTGCGTTGATGCCA 60.250 50.000 0.00 0.00 0.00 4.92
1782 5343 5.066593 GCCCATTTAAATTGGTTTTGGTCA 58.933 37.500 17.22 0.00 0.00 4.02
2024 5592 1.670295 GTTACCAACGACCGGTGTTTT 59.330 47.619 14.63 8.67 37.33 2.43
2080 5648 1.341482 TGCTGGTTTGTTGGACCTGAA 60.341 47.619 4.62 0.00 38.09 3.02
2087 5655 3.524095 TTGTTGGACCTGAACATCCAT 57.476 42.857 0.00 0.00 44.49 3.41
2114 5682 6.884472 TGGGATAGGAAATCTAACTGTGAA 57.116 37.500 0.00 0.00 0.00 3.18
2122 5690 5.393461 GGAAATCTAACTGTGAAGGCATTGG 60.393 44.000 0.00 0.00 0.00 3.16
2353 5921 4.514441 CAGGAATTTCTATGCTGCAGGTAG 59.486 45.833 17.12 6.21 29.36 3.18
2404 5976 3.831715 AGTGCAATTAGTTTTCGCTCC 57.168 42.857 0.00 0.00 0.00 4.70
2636 6256 8.691797 TGGTTATCTAATTTCCTATTGTTTGCC 58.308 33.333 0.00 0.00 0.00 4.52
2637 6257 8.914011 GGTTATCTAATTTCCTATTGTTTGCCT 58.086 33.333 0.00 0.00 0.00 4.75
2641 6261 9.700831 ATCTAATTTCCTATTGTTTGCCTAACT 57.299 29.630 0.00 0.00 37.64 2.24
2642 6262 9.528489 TCTAATTTCCTATTGTTTGCCTAACTT 57.472 29.630 0.00 0.00 37.64 2.66
2643 6263 9.573133 CTAATTTCCTATTGTTTGCCTAACTTG 57.427 33.333 0.00 0.00 37.64 3.16
2644 6264 5.975693 TTCCTATTGTTTGCCTAACTTGG 57.024 39.130 1.23 0.00 37.64 3.61
2657 6295 3.711704 CCTAACTTGGCTGATTAGAGGGA 59.288 47.826 0.00 0.00 0.00 4.20
2859 6748 2.349155 CGGTTTAAGGCTTGTCACGTTC 60.349 50.000 10.69 0.00 0.00 3.95
2890 6783 7.149569 TCACTATTCTTCCTTGCAAGAATTG 57.850 36.000 28.05 20.02 46.57 2.32
3042 6940 6.207810 GGTTTCCCATTCCGTGCATATTTATA 59.792 38.462 0.00 0.00 0.00 0.98
3222 7136 3.118261 TCATTTTCTTCTAGGCAGCGGAT 60.118 43.478 0.00 0.00 0.00 4.18
3272 7186 5.181245 CGGAACTTTGAACACACCTGATATT 59.819 40.000 0.00 0.00 0.00 1.28
3306 7220 8.228464 GCTATCTTTGTCAAACAACTTAGGTAC 58.772 37.037 0.00 0.00 37.90 3.34
3425 7355 6.763610 ACTAGCTTGGCATACTAGACATTTTC 59.236 38.462 23.50 0.00 37.44 2.29
3670 7812 4.764823 TCCATTTGTGGTATCAGTTTGTCC 59.235 41.667 0.00 0.00 0.00 4.02
3677 7819 7.624360 TGTGGTATCAGTTTGTCCAATAATC 57.376 36.000 0.00 0.00 0.00 1.75
3904 8054 4.651503 TGTTCCATTTTGTATGGTGTGGTT 59.348 37.500 3.89 0.00 40.06 3.67
3928 8078 3.861840 TGCTCAAAGTGTCCTACTATGC 58.138 45.455 0.00 0.00 39.18 3.14
3954 8104 4.455533 TCTGCAGATTGTTCCATTGTGTAC 59.544 41.667 13.74 0.00 0.00 2.90
4014 8167 3.222173 TGTATTGTGGCCTGTGAAGTT 57.778 42.857 3.32 0.00 0.00 2.66
4057 8210 8.008513 TCATGTGGACTCTTTTATACTACTCC 57.991 38.462 0.00 0.00 0.00 3.85
4058 8211 6.786967 TGTGGACTCTTTTATACTACTCCC 57.213 41.667 0.00 0.00 0.00 4.30
4059 8212 6.500336 TGTGGACTCTTTTATACTACTCCCT 58.500 40.000 0.00 0.00 0.00 4.20
4060 8213 6.606395 TGTGGACTCTTTTATACTACTCCCTC 59.394 42.308 0.00 0.00 0.00 4.30
4061 8214 6.834969 GTGGACTCTTTTATACTACTCCCTCT 59.165 42.308 0.00 0.00 0.00 3.69
4062 8215 6.834451 TGGACTCTTTTATACTACTCCCTCTG 59.166 42.308 0.00 0.00 0.00 3.35
4063 8216 6.834969 GGACTCTTTTATACTACTCCCTCTGT 59.165 42.308 0.00 0.00 0.00 3.41
4064 8217 7.997803 GGACTCTTTTATACTACTCCCTCTGTA 59.002 40.741 0.00 0.00 0.00 2.74
4065 8218 9.406113 GACTCTTTTATACTACTCCCTCTGTAA 57.594 37.037 0.00 0.00 0.00 2.41
4066 8219 9.765295 ACTCTTTTATACTACTCCCTCTGTAAA 57.235 33.333 0.00 0.00 0.00 2.01
4068 8221 9.765295 TCTTTTATACTACTCCCTCTGTAAACT 57.235 33.333 0.00 0.00 0.00 2.66
4079 8232 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
4080 8233 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
4081 8234 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
4082 8235 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
4083 8236 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
4131 8284 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
4132 8285 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
4133 8286 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
4134 8287 7.039923 TGCTCTTATATTAGTTTACGGAGGGAG 60.040 40.741 0.00 0.00 0.00 4.30
4156 8309 7.090808 GGAGTATTATCTAATGTCGACATGCA 58.909 38.462 30.57 19.94 36.56 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.557605 CCCGCATTGATGGCACGC 62.558 66.667 0.00 0.00 0.00 5.34
36 37 4.101448 GGCAGCCTGTCCATCCGT 62.101 66.667 3.29 0.00 0.00 4.69
58 59 1.716760 GTTCAAACGACACGGCACA 59.283 52.632 0.00 0.00 0.00 4.57
112 113 4.873129 CCGTCCGTCCATCTGCCG 62.873 72.222 0.00 0.00 0.00 5.69
287 2962 3.698463 CGCGCGTTTTCGGTCAGT 61.698 61.111 24.19 0.00 44.29 3.41
312 2987 2.041081 CTGACCCACCAAATAACCCTCA 59.959 50.000 0.00 0.00 0.00 3.86
320 2995 1.002134 CCGCTCTGACCCACCAAAT 60.002 57.895 0.00 0.00 0.00 2.32
377 3053 0.393077 CAGAGACAAACGTGGGGAGT 59.607 55.000 0.00 0.00 0.00 3.85
380 3056 0.179029 AACCAGAGACAAACGTGGGG 60.179 55.000 0.00 0.00 33.59 4.96
403 3079 4.717280 AGATGTCCGGACTTATTTTCTCCT 59.283 41.667 33.39 15.54 0.00 3.69
424 3100 0.179065 CCTGCATCAATCCGCTGAGA 60.179 55.000 0.00 0.00 0.00 3.27
426 3102 0.462581 GACCTGCATCAATCCGCTGA 60.463 55.000 0.00 0.00 0.00 4.26
434 3110 1.243342 CCAAAGCGGACCTGCATCAA 61.243 55.000 10.28 0.00 36.56 2.57
435 3111 1.675310 CCAAAGCGGACCTGCATCA 60.675 57.895 10.28 0.00 36.56 3.07
469 3145 2.232941 GAGAACAACCTACATCGGTCCA 59.767 50.000 0.00 0.00 35.89 4.02
539 3217 3.493503 CCTTGTACGTTCCACTGAGAAAC 59.506 47.826 0.00 0.00 0.00 2.78
593 3271 0.953471 TGTTGTACGCAGGTGCCATC 60.953 55.000 0.00 0.00 37.91 3.51
600 3291 1.014044 ACGCTGATGTTGTACGCAGG 61.014 55.000 0.00 0.00 0.00 4.85
649 3343 0.737715 CAGCTGAGTGTAGGAACGCC 60.738 60.000 8.42 0.00 36.76 5.68
711 3413 1.745087 CTGCTGAGAGTGGAGAGACTC 59.255 57.143 0.00 0.00 42.45 3.36
872 3807 7.334671 AGAGGGAAAATAAGATGAGACGAAAAC 59.665 37.037 0.00 0.00 0.00 2.43
1108 4480 1.741706 CACTGCACATCCATCCAGAAC 59.258 52.381 0.00 0.00 0.00 3.01
1439 4966 1.488393 GCATACCCTCTGAAGAAGCCT 59.512 52.381 0.00 0.00 0.00 4.58
1536 5063 0.535335 GCTTCATCGGTGTGGTAGGA 59.465 55.000 0.00 0.00 0.00 2.94
1725 5258 0.680921 CCATGGACGTGCCCATCTTT 60.681 55.000 5.56 0.00 44.69 2.52
1782 5343 3.369892 GCCTGTGTACTGAATCCATCACT 60.370 47.826 0.00 0.00 33.47 3.41
2024 5592 2.124983 GCCATCCGCAAGAGCTGA 60.125 61.111 0.00 0.00 38.38 4.26
2087 5655 8.998814 TCACAGTTAGATTTCCTATCCCATAAA 58.001 33.333 0.00 0.00 0.00 1.40
2114 5682 2.053865 CACCCATTCGCCAATGCCT 61.054 57.895 0.00 0.00 38.53 4.75
2122 5690 2.126346 GCAGCAACACCCATTCGC 60.126 61.111 0.00 0.00 0.00 4.70
2353 5921 2.054799 TCCAATGTAGATAGGGGGCAC 58.945 52.381 0.00 0.00 0.00 5.01
2571 6143 5.409643 ACAGAGAAACGAACAAGACATTG 57.590 39.130 0.00 0.00 42.46 2.82
2583 6201 3.653344 TGACCAGATCAACAGAGAAACG 58.347 45.455 0.00 0.00 33.02 3.60
2635 6255 3.711704 TCCCTCTAATCAGCCAAGTTAGG 59.288 47.826 0.00 0.00 0.00 2.69
2636 6256 5.512232 GGATCCCTCTAATCAGCCAAGTTAG 60.512 48.000 0.00 0.00 0.00 2.34
2637 6257 4.348168 GGATCCCTCTAATCAGCCAAGTTA 59.652 45.833 0.00 0.00 0.00 2.24
2638 6258 3.137360 GGATCCCTCTAATCAGCCAAGTT 59.863 47.826 0.00 0.00 0.00 2.66
2639 6259 2.708325 GGATCCCTCTAATCAGCCAAGT 59.292 50.000 0.00 0.00 0.00 3.16
2640 6260 2.707791 TGGATCCCTCTAATCAGCCAAG 59.292 50.000 9.90 0.00 0.00 3.61
2641 6261 2.775418 TGGATCCCTCTAATCAGCCAA 58.225 47.619 9.90 0.00 0.00 4.52
2642 6262 2.494888 TGGATCCCTCTAATCAGCCA 57.505 50.000 9.90 0.00 0.00 4.75
2643 6263 5.505181 TTAATGGATCCCTCTAATCAGCC 57.495 43.478 9.90 0.00 0.00 4.85
2644 6264 5.414144 GCTTTAATGGATCCCTCTAATCAGC 59.586 44.000 9.90 7.26 0.00 4.26
2645 6265 6.777782 AGCTTTAATGGATCCCTCTAATCAG 58.222 40.000 9.90 1.44 0.00 2.90
2646 6266 6.770286 AGCTTTAATGGATCCCTCTAATCA 57.230 37.500 9.90 0.00 0.00 2.57
2647 6267 8.140112 TCTAGCTTTAATGGATCCCTCTAATC 57.860 38.462 9.90 0.00 0.00 1.75
2657 6295 9.851686 TGTATTCATGTTCTAGCTTTAATGGAT 57.148 29.630 0.00 0.00 0.00 3.41
2687 6326 1.079612 GGCCAGGCATCAAAGCAAC 60.080 57.895 15.19 0.00 35.83 4.17
2859 6748 8.498054 TTGCAAGGAAGAATAGTGAATAAGAG 57.502 34.615 0.00 0.00 0.00 2.85
3042 6940 7.563188 TGTACCAATTATGACCATAAAGCCAAT 59.437 33.333 6.55 0.00 36.90 3.16
3222 7136 1.827792 TCTGTCCCTTTCCTCCCAAA 58.172 50.000 0.00 0.00 0.00 3.28
3272 7186 5.986741 TGTTTGACAAAGATAGCACGTTAGA 59.013 36.000 0.00 0.00 0.00 2.10
3514 7449 2.397754 CGCCGCCAATCATGTGACA 61.398 57.895 0.00 0.00 0.00 3.58
3677 7819 2.105993 TCCAGAGCTCAATCATCCCATG 59.894 50.000 17.77 0.64 0.00 3.66
3904 8054 5.664457 CATAGTAGGACACTTTGAGCATCA 58.336 41.667 0.00 0.00 40.56 3.07
3941 8091 1.133869 GCGGCGTACACAATGGAAC 59.866 57.895 9.37 0.00 0.00 3.62
3954 8104 4.444024 CACAACACATCCGCGGCG 62.444 66.667 23.51 16.78 0.00 6.46
4014 8167 8.591940 TCCACATGATTAAATCCAACAAATTCA 58.408 29.630 0.00 0.00 0.00 2.57
4054 8207 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
4055 8208 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
4056 8209 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
4057 8210 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
4105 8258 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
4106 8259 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
4107 8260 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
4108 8261 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
4109 8262 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4110 8263 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4117 8270 8.953223 AGATAATACTCCCTCCGTAAACTAAT 57.047 34.615 0.00 0.00 0.00 1.73
4118 8271 9.866655 TTAGATAATACTCCCTCCGTAAACTAA 57.133 33.333 0.00 0.00 0.00 2.24
4120 8273 8.804204 CATTAGATAATACTCCCTCCGTAAACT 58.196 37.037 0.00 0.00 0.00 2.66
4121 8274 8.583296 ACATTAGATAATACTCCCTCCGTAAAC 58.417 37.037 0.00 0.00 0.00 2.01
4122 8275 8.716674 ACATTAGATAATACTCCCTCCGTAAA 57.283 34.615 0.00 0.00 0.00 2.01
4123 8276 7.120285 CGACATTAGATAATACTCCCTCCGTAA 59.880 40.741 0.00 0.00 0.00 3.18
4124 8277 6.596888 CGACATTAGATAATACTCCCTCCGTA 59.403 42.308 0.00 0.00 0.00 4.02
4125 8278 5.415077 CGACATTAGATAATACTCCCTCCGT 59.585 44.000 0.00 0.00 0.00 4.69
4126 8279 5.646793 TCGACATTAGATAATACTCCCTCCG 59.353 44.000 0.00 0.00 0.00 4.63
4127 8280 6.433404 TGTCGACATTAGATAATACTCCCTCC 59.567 42.308 15.76 0.00 0.00 4.30
4128 8281 7.450124 TGTCGACATTAGATAATACTCCCTC 57.550 40.000 15.76 0.00 0.00 4.30
4129 8282 7.577807 GCATGTCGACATTAGATAATACTCCCT 60.578 40.741 28.04 0.00 33.61 4.20
4130 8283 6.531948 GCATGTCGACATTAGATAATACTCCC 59.468 42.308 28.04 0.00 33.61 4.30
4131 8284 7.090808 TGCATGTCGACATTAGATAATACTCC 58.909 38.462 28.04 3.39 33.61 3.85
4132 8285 8.590470 CATGCATGTCGACATTAGATAATACTC 58.410 37.037 28.04 4.04 33.61 2.59
4133 8286 7.063898 GCATGCATGTCGACATTAGATAATACT 59.936 37.037 28.04 0.74 33.61 2.12
4134 8287 7.176075 GCATGCATGTCGACATTAGATAATAC 58.824 38.462 28.04 8.31 33.61 1.89
4156 8309 2.642807 ACACTAACCAGTAACCAGGCAT 59.357 45.455 0.00 0.00 32.21 4.40


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

AutoCloner maintained by Alex Coulton.