Multiple sequence alignment - TraesCS7D01G380100

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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 TraesCS7D01G380100 chr7D 100.000 5089 0 0 1 5089 492223607 492218519 0.000000e+00 9398.0
1 TraesCS7D01G380100 chr7D 79.915 234 42 5 237 467 607124464 607124233 3.150000e-37 167.0
2 TraesCS7D01G380100 chr7B 94.410 4562 155 31 577 5089 521619002 521614492 0.000000e+00 6920.0
3 TraesCS7D01G380100 chr7B 89.189 555 51 7 1 550 521667475 521666925 0.000000e+00 684.0
4 TraesCS7D01G380100 chr7B 93.182 44 2 1 140 183 7040453 7040495 4.250000e-06 63.9
5 TraesCS7D01G380100 chr7A 94.827 3847 122 24 535 4356 558758127 558754333 0.000000e+00 5930.0
6 TraesCS7D01G380100 chr7A 92.553 658 33 7 4446 5089 558754318 558753663 0.000000e+00 929.0
7 TraesCS7D01G380100 chr7A 86.174 311 40 3 186 495 558758945 558758637 2.940000e-87 333.0
8 TraesCS7D01G380100 chr7A 91.509 106 8 1 1 105 558759584 558759479 1.480000e-30 145.0
9 TraesCS7D01G380100 chr7A 91.935 62 5 0 4362 4423 87692491 87692430 2.520000e-13 87.9
10 TraesCS7D01G380100 chr4D 82.792 523 81 8 2433 2949 70119277 70119796 4.640000e-125 459.0
11 TraesCS7D01G380100 chr4D 82.990 194 31 2 3606 3798 70120253 70120445 1.880000e-39 174.0
12 TraesCS7D01G380100 chr4D 84.173 139 21 1 242 379 39236161 39236299 3.200000e-27 134.0
13 TraesCS7D01G380100 chr4D 78.010 191 39 3 266 454 341921538 341921727 3.220000e-22 117.0
14 TraesCS7D01G380100 chr4A 82.792 523 81 8 2433 2949 522294309 522294828 4.640000e-125 459.0
15 TraesCS7D01G380100 chr4A 82.990 194 31 2 3606 3798 522295285 522295477 1.880000e-39 174.0
16 TraesCS7D01G380100 chr4A 81.739 115 9 4 4317 4429 37060208 37060104 9.080000e-13 86.1
17 TraesCS7D01G380100 chr4B 84.058 483 68 8 2473 2949 103773177 103773656 1.670000e-124 457.0
18 TraesCS7D01G380100 chr4B 83.511 188 29 2 3606 3792 103774113 103774299 1.880000e-39 174.0
19 TraesCS7D01G380100 chr1D 96.491 228 8 0 1257 1484 42038588 42038815 1.340000e-100 377.0
20 TraesCS7D01G380100 chr1D 94.690 113 4 2 1096 1207 42038495 42038606 1.880000e-39 174.0
21 TraesCS7D01G380100 chr1D 96.739 92 3 0 1597 1688 42038810 42038901 2.450000e-33 154.0
22 TraesCS7D01G380100 chr1D 76.652 227 48 4 242 466 447549387 447549164 2.490000e-23 121.0
23 TraesCS7D01G380100 chr2D 95.175 228 11 0 1257 1484 28963979 28964206 1.350000e-95 361.0
24 TraesCS7D01G380100 chr2D 94.690 113 4 2 1096 1207 28963886 28963997 1.880000e-39 174.0
25 TraesCS7D01G380100 chr2D 94.565 92 5 0 1597 1688 28964201 28964292 5.310000e-30 143.0
26 TraesCS7D01G380100 chr2D 85.047 107 7 1 4318 4424 2476585 2476682 3.240000e-17 100.0
27 TraesCS7D01G380100 chr2D 91.176 68 4 2 4362 4427 290739008 290738941 1.950000e-14 91.6
28 TraesCS7D01G380100 chr5D 79.206 529 100 6 2433 2953 197152404 197151878 4.840000e-95 359.0
29 TraesCS7D01G380100 chr5A 79.800 500 93 5 2433 2925 227923754 227924252 1.740000e-94 357.0
30 TraesCS7D01G380100 chr3A 94.298 228 13 0 1257 1484 13265216 13264989 2.920000e-92 350.0
31 TraesCS7D01G380100 chr3A 80.335 239 42 4 237 472 60660788 60660552 5.240000e-40 176.0
32 TraesCS7D01G380100 chr3A 93.805 113 5 2 1096 1207 13265309 13265198 8.760000e-38 169.0
33 TraesCS7D01G380100 chr3A 88.000 100 6 3 1598 1691 13264993 13264894 4.160000e-21 113.0
34 TraesCS7D01G380100 chr3A 77.465 142 29 3 316 455 223202247 223202107 1.170000e-11 82.4
35 TraesCS7D01G380100 chr3A 95.833 48 2 0 1724 1771 13264840 13264887 1.520000e-10 78.7
36 TraesCS7D01G380100 chr5B 79.125 503 91 9 2433 2925 213250429 213250927 8.160000e-88 335.0
37 TraesCS7D01G380100 chr5B 77.778 216 46 2 241 455 536039842 536040056 1.150000e-26 132.0
38 TraesCS7D01G380100 chr2A 85.075 134 20 0 322 455 621852031 621851898 2.470000e-28 137.0
39 TraesCS7D01G380100 chr2A 92.308 65 3 2 4362 4424 315038017 315038081 1.950000e-14 91.6
40 TraesCS7D01G380100 chr2A 90.769 65 4 2 4362 4424 724414395 724414331 9.080000e-13 86.1
41 TraesCS7D01G380100 chrUn 85.047 107 7 1 4318 4424 15904017 15903920 3.240000e-17 100.0
42 TraesCS7D01G380100 chrUn 93.750 48 2 1 142 189 48220079 48220033 2.540000e-08 71.3
43 TraesCS7D01G380100 chrUn 93.750 48 2 1 142 189 378206971 378207017 2.540000e-08 71.3
44 TraesCS7D01G380100 chrUn 93.750 48 2 1 142 189 431966294 431966340 2.540000e-08 71.3
45 TraesCS7D01G380100 chr1A 83.636 110 6 8 4314 4423 460934573 460934476 5.430000e-15 93.5
46 TraesCS7D01G380100 chr2B 94.118 51 3 0 237 287 711709199 711709249 1.520000e-10 78.7
47 TraesCS7D01G380100 chr2B 94.118 51 3 0 237 287 711715271 711715321 1.520000e-10 78.7


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 TraesCS7D01G380100 chr7D 492218519 492223607 5088 True 9398.00 9398 100.00000 1 5089 1 chr7D.!!$R1 5088
1 TraesCS7D01G380100 chr7B 521614492 521619002 4510 True 6920.00 6920 94.41000 577 5089 1 chr7B.!!$R1 4512
2 TraesCS7D01G380100 chr7B 521666925 521667475 550 True 684.00 684 89.18900 1 550 1 chr7B.!!$R2 549
3 TraesCS7D01G380100 chr7A 558753663 558759584 5921 True 1834.25 5930 91.26575 1 5089 4 chr7A.!!$R2 5088
4 TraesCS7D01G380100 chr4D 70119277 70120445 1168 False 316.50 459 82.89100 2433 3798 2 chr4D.!!$F3 1365
5 TraesCS7D01G380100 chr4A 522294309 522295477 1168 False 316.50 459 82.89100 2433 3798 2 chr4A.!!$F1 1365
6 TraesCS7D01G380100 chr4B 103773177 103774299 1122 False 315.50 457 83.78450 2473 3792 2 chr4B.!!$F1 1319
7 TraesCS7D01G380100 chr5D 197151878 197152404 526 True 359.00 359 79.20600 2433 2953 1 chr5D.!!$R1 520


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
478 977 0.246910 TGGGTGCGCACGTTAATAGA 59.753 50.0 32.35 8.22 0.00 1.98 F
1830 2845 0.324275 AGGAGCAGACAGAGGAGGAC 60.324 60.0 0.00 0.00 0.00 3.85 F
1846 2861 0.459585 GGACCGTAGCAGCGATCAAA 60.460 55.0 1.45 0.00 0.00 2.69 F
3009 4044 0.250553 TGTGAATTCCCACCGTCACC 60.251 55.0 2.27 0.00 39.72 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 3416 1.202639 TCTGCACAAGTCACCATCGTT 60.203 47.619 0.00 0.00 0.00 3.85 R
2991 4026 0.250553 TGGTGACGGTGGGAATTCAC 60.251 55.000 7.93 3.78 38.11 3.18 R
3036 4071 1.078918 TCAGAGCCGTCATTGCTGG 60.079 57.895 0.00 0.00 39.69 4.85 R
4429 5468 1.003580 TCTGCCAACTTGCCTTCTAGG 59.996 52.381 0.00 0.00 38.80 3.02 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
30 31 2.279741 CGCTTTGCAAGGCTATCTGTA 58.720 47.619 28.08 0.00 0.00 2.74
74 76 4.825634 AGAAAGGTTTAGGTTGCTTGGTAC 59.174 41.667 0.00 0.00 0.00 3.34
77 79 1.808343 GTTTAGGTTGCTTGGTACCCG 59.192 52.381 10.07 1.25 34.90 5.28
124 622 6.588204 AGGTTAGTATCACAACACAAACTCA 58.412 36.000 0.00 0.00 0.00 3.41
152 650 7.609760 TTCTCATGTAATTACCATGTGACAC 57.390 36.000 20.23 0.00 31.37 3.67
172 670 7.589954 GTGACACATGTGGTAAGTAATTCAAAC 59.410 37.037 28.64 6.50 34.19 2.93
178 676 9.912634 CATGTGGTAAGTAATTCAAACAATTCT 57.087 29.630 0.00 0.00 0.00 2.40
228 726 7.790823 TGAAGAATGATCAATGAGCGAATTA 57.209 32.000 0.00 0.00 0.00 1.40
270 768 4.524328 AGATTTCTTGTGATGGAACCAACC 59.476 41.667 0.00 0.00 0.00 3.77
286 784 3.573967 ACCAACCCATCAAAGTTCATGTC 59.426 43.478 0.00 0.00 0.00 3.06
287 785 3.828451 CCAACCCATCAAAGTTCATGTCT 59.172 43.478 0.00 0.00 0.00 3.41
309 807 5.246203 TCTTAGACTTGGCACTGATAGTTGT 59.754 40.000 0.00 0.00 0.00 3.32
330 829 6.019779 TGTGTTTTCTGGATTTATTTCCGG 57.980 37.500 0.00 0.00 42.62 5.14
363 862 1.216710 GCGTTCAGTGGGAGGAGAG 59.783 63.158 0.00 0.00 0.00 3.20
420 919 7.703328 ACTTCGTCAATCTTAAAATGTTGTGT 58.297 30.769 0.00 0.00 0.00 3.72
421 920 8.188139 ACTTCGTCAATCTTAAAATGTTGTGTT 58.812 29.630 0.00 0.00 0.00 3.32
423 922 7.698628 TCGTCAATCTTAAAATGTTGTGTTGA 58.301 30.769 0.00 0.00 0.00 3.18
478 977 0.246910 TGGGTGCGCACGTTAATAGA 59.753 50.000 32.35 8.22 0.00 1.98
483 982 2.776225 GTGCGCACGTTAATAGAATTGC 59.224 45.455 26.77 0.00 0.00 3.56
485 984 2.624766 CGCACGTTAATAGAATTGCGG 58.375 47.619 5.89 0.00 46.84 5.69
489 988 4.212636 GCACGTTAATAGAATTGCGGGTAT 59.787 41.667 0.00 0.00 0.00 2.73
490 989 5.675970 CACGTTAATAGAATTGCGGGTATG 58.324 41.667 0.00 0.00 0.00 2.39
505 1004 4.228912 GGGTATGTACGCGTATGTAAGT 57.771 45.455 23.56 7.62 0.00 2.24
520 1019 7.042992 GCGTATGTAAGTATCTGCATTTGTACA 60.043 37.037 0.00 0.00 0.00 2.90
565 1546 3.307674 GACATCAACACGTACGGTTGTA 58.692 45.455 30.77 23.15 44.53 2.41
701 1682 6.869315 AAGAAGTTAAGAAAAGACTGCTCC 57.131 37.500 0.00 0.00 27.79 4.70
702 1683 6.181206 AGAAGTTAAGAAAAGACTGCTCCT 57.819 37.500 0.00 0.00 0.00 3.69
703 1684 6.227522 AGAAGTTAAGAAAAGACTGCTCCTC 58.772 40.000 0.00 0.00 0.00 3.71
977 1986 3.612955 GCACTACCAGCTTAGATCGATCC 60.613 52.174 21.66 6.54 0.00 3.36
1152 2161 1.805945 GGCCTACTTGCTCACGTCG 60.806 63.158 0.00 0.00 0.00 5.12
1830 2845 0.324275 AGGAGCAGACAGAGGAGGAC 60.324 60.000 0.00 0.00 0.00 3.85
1846 2861 0.459585 GGACCGTAGCAGCGATCAAA 60.460 55.000 1.45 0.00 0.00 2.69
1884 2899 2.340809 CGCACGTTGGTGGAGGTA 59.659 61.111 0.00 0.00 44.54 3.08
1932 2947 4.021925 GGGGACGACAAGGCAGCT 62.022 66.667 0.00 0.00 0.00 4.24
1933 2948 2.743928 GGGACGACAAGGCAGCTG 60.744 66.667 10.11 10.11 0.00 4.24
1934 2949 3.426568 GGACGACAAGGCAGCTGC 61.427 66.667 30.88 30.88 41.14 5.25
2307 3322 4.421479 CTCGTCGCGCTCCCAAGT 62.421 66.667 5.56 0.00 0.00 3.16
2401 3416 2.221169 GATTGGTTGCTCACTGACACA 58.779 47.619 0.00 0.00 0.00 3.72
2967 3999 4.469586 TCTGGAAAGGTATGTGCAGACATA 59.530 41.667 0.00 0.00 41.27 2.29
2972 4004 7.998383 TGGAAAGGTATGTGCAGACATAATTAT 59.002 33.333 0.00 0.00 44.85 1.28
2973 4005 8.850156 GGAAAGGTATGTGCAGACATAATTATT 58.150 33.333 0.00 0.00 44.85 1.40
2974 4006 9.884465 GAAAGGTATGTGCAGACATAATTATTC 57.116 33.333 0.00 0.00 44.85 1.75
2995 4030 4.926244 TCGCACTAATTTTTGCTTGTGAA 58.074 34.783 8.77 0.00 36.54 3.18
2999 4034 6.593072 GCACTAATTTTTGCTTGTGAATTCC 58.407 36.000 2.27 0.00 35.74 3.01
3006 4041 0.521735 GCTTGTGAATTCCCACCGTC 59.478 55.000 2.27 0.00 36.26 4.79
3008 4043 1.535462 CTTGTGAATTCCCACCGTCAC 59.465 52.381 2.27 0.00 40.64 3.67
3009 4044 0.250553 TGTGAATTCCCACCGTCACC 60.251 55.000 2.27 0.00 39.72 4.02
3010 4045 0.250553 GTGAATTCCCACCGTCACCA 60.251 55.000 2.27 0.00 35.42 4.17
3011 4046 0.695924 TGAATTCCCACCGTCACCAT 59.304 50.000 2.27 0.00 0.00 3.55
3012 4047 1.094785 GAATTCCCACCGTCACCATG 58.905 55.000 0.00 0.00 0.00 3.66
3013 4048 0.323360 AATTCCCACCGTCACCATGG 60.323 55.000 11.19 11.19 34.34 3.66
3014 4049 1.497309 ATTCCCACCGTCACCATGGT 61.497 55.000 13.00 13.00 43.46 3.55
3015 4050 2.046314 CCCACCGTCACCATGGTC 60.046 66.667 16.53 3.58 40.30 4.02
3026 4061 2.577563 TCACCATGGTCCATGAGTGAAT 59.422 45.455 32.46 14.18 43.81 2.57
3036 4071 5.009410 GGTCCATGAGTGAATGAATCATTCC 59.991 44.000 27.26 19.72 46.65 3.01
3233 4268 4.424566 TACGTCCGCCTGAACGCC 62.425 66.667 0.00 0.00 0.00 5.68
3428 4463 0.316204 ACAAGTCGTACCTCAACGGG 59.684 55.000 0.00 0.00 43.05 5.28
3544 4579 5.906073 GCACCTAGCAATCACCATTAATTT 58.094 37.500 0.00 0.00 44.79 1.82
3545 4580 5.750067 GCACCTAGCAATCACCATTAATTTG 59.250 40.000 0.00 0.00 44.79 2.32
4028 5064 2.544267 CACCTTCTCCAAGAACGACAAC 59.456 50.000 0.00 0.00 29.89 3.32
4114 5150 4.726035 AGCCATCTCCATTCTCATGATT 57.274 40.909 0.00 0.00 31.07 2.57
4132 5168 6.211184 TCATGATTACAAGCAATTTTCACCCT 59.789 34.615 0.00 0.00 0.00 4.34
4133 5169 6.024552 TGATTACAAGCAATTTTCACCCTC 57.975 37.500 0.00 0.00 0.00 4.30
4204 5242 6.618287 TTGGTTAGCATTGATGTAGTATGC 57.382 37.500 0.00 0.00 43.78 3.14
4207 5245 3.751479 AGCATTGATGTAGTATGCGGA 57.249 42.857 0.00 0.00 46.97 5.54
4210 5248 3.809832 GCATTGATGTAGTATGCGGAACT 59.190 43.478 0.00 0.00 35.79 3.01
4211 5249 4.273480 GCATTGATGTAGTATGCGGAACTT 59.727 41.667 0.00 0.00 35.79 2.66
4224 5262 3.834231 TGCGGAACTTACTAACTACCCTT 59.166 43.478 0.00 0.00 0.00 3.95
4241 5279 7.238710 ACTACCCTTCAAATAAGACATGGTTT 58.761 34.615 0.00 0.00 0.00 3.27
4260 5298 8.623903 CATGGTTTTGTAATGCAGTATGTATCT 58.376 33.333 0.00 0.00 41.90 1.98
4284 5322 5.261209 AGACTCATGCATAGAACTGAGAC 57.739 43.478 17.39 12.03 38.74 3.36
4326 5364 6.497259 TGTCAGTTCAAATACTTACTCCCTCT 59.503 38.462 0.00 0.00 0.00 3.69
4336 5374 8.798975 AATACTTACTCCCTCTGATCCATAAA 57.201 34.615 0.00 0.00 0.00 1.40
4343 5381 6.139679 TCCCTCTGATCCATAAAAAGTGTT 57.860 37.500 0.00 0.00 0.00 3.32
4346 5384 5.295431 TCTGATCCATAAAAAGTGTTGCG 57.705 39.130 0.00 0.00 0.00 4.85
4356 5394 3.305398 AAAGTGTTGCGGTTTTGAACA 57.695 38.095 0.00 0.00 0.00 3.18
4358 5396 3.305398 AGTGTTGCGGTTTTGAACAAA 57.695 38.095 0.00 0.00 31.62 2.83
4360 5398 2.347150 GTGTTGCGGTTTTGAACAAAGG 59.653 45.455 0.46 0.00 31.62 3.11
4361 5399 2.028930 TGTTGCGGTTTTGAACAAAGGT 60.029 40.909 0.46 0.00 0.00 3.50
4362 5400 2.997303 GTTGCGGTTTTGAACAAAGGTT 59.003 40.909 0.46 0.00 40.76 3.50
4364 5402 2.231478 TGCGGTTTTGAACAAAGGTTGA 59.769 40.909 0.46 0.00 37.36 3.18
4365 5403 3.254892 GCGGTTTTGAACAAAGGTTGAA 58.745 40.909 0.46 0.00 37.36 2.69
4366 5404 3.061563 GCGGTTTTGAACAAAGGTTGAAC 59.938 43.478 0.46 0.00 37.36 3.18
4367 5405 4.490743 CGGTTTTGAACAAAGGTTGAACT 58.509 39.130 0.00 0.00 37.36 3.01
4368 5406 5.642686 CGGTTTTGAACAAAGGTTGAACTA 58.357 37.500 0.00 0.00 37.36 2.24
4369 5407 6.094061 CGGTTTTGAACAAAGGTTGAACTAA 58.906 36.000 0.00 0.00 37.36 2.24
4370 5408 6.252655 CGGTTTTGAACAAAGGTTGAACTAAG 59.747 38.462 0.00 0.00 37.36 2.18
4371 5409 6.533723 GGTTTTGAACAAAGGTTGAACTAAGG 59.466 38.462 0.00 0.00 37.36 2.69
4372 5410 6.844097 TTTGAACAAAGGTTGAACTAAGGT 57.156 33.333 0.00 0.00 37.36 3.50
4373 5411 6.844097 TTGAACAAAGGTTGAACTAAGGTT 57.156 33.333 0.00 0.00 37.36 3.50
4374 5412 6.202516 TGAACAAAGGTTGAACTAAGGTTG 57.797 37.500 0.00 0.00 37.36 3.77
4375 5413 5.126384 TGAACAAAGGTTGAACTAAGGTTGG 59.874 40.000 0.00 0.00 37.36 3.77
4393 5431 5.006153 GTTGGCAACCTTAGTTCAAAACT 57.994 39.130 19.57 0.00 45.40 2.66
4395 5433 4.020543 TGGCAACCTTAGTTCAAAACTGT 58.979 39.130 2.65 0.00 42.84 3.55
4398 5437 5.034797 GCAACCTTAGTTCAAAACTGTGAC 58.965 41.667 2.65 0.00 42.84 3.67
4401 5440 5.497474 ACCTTAGTTCAAAACTGTGACACT 58.503 37.500 7.20 0.00 42.84 3.55
4421 5460 7.345653 TGACACTTATTATGAATCAGAGGGAGT 59.654 37.037 0.00 0.00 0.00 3.85
4429 5468 9.620259 ATTATGAATCAGAGGGAGTACTTTTTC 57.380 33.333 0.00 0.00 0.00 2.29
4430 5469 5.805728 TGAATCAGAGGGAGTACTTTTTCC 58.194 41.667 0.00 0.00 0.00 3.13
4433 5472 6.800072 ATCAGAGGGAGTACTTTTTCCTAG 57.200 41.667 0.00 0.14 33.85 3.02
4444 5483 5.774498 ACTTTTTCCTAGAAGGCAAGTTG 57.226 39.130 0.00 0.00 34.61 3.16
4448 5487 1.003580 TCCTAGAAGGCAAGTTGGCAG 59.996 52.381 28.85 17.64 46.46 4.85
4462 5501 6.424812 GCAAGTTGGCAGATCAGTTAAATTTT 59.575 34.615 4.75 0.00 0.00 1.82
4463 5502 7.569957 GCAAGTTGGCAGATCAGTTAAATTTTG 60.570 37.037 4.75 0.00 0.00 2.44
4466 5505 8.299570 AGTTGGCAGATCAGTTAAATTTTGTAG 58.700 33.333 0.00 0.00 0.00 2.74
4502 5543 5.016831 TGAGTCCAGCTGTTAGAAGATACA 58.983 41.667 13.81 3.70 0.00 2.29
4537 5581 7.275697 CAGATCGTAATAATGTCTGCAGATC 57.724 40.000 21.47 13.93 34.04 2.75
4645 5691 5.418676 CAAAATCATTTTTGGCCCTCGTAT 58.581 37.500 0.00 0.00 45.18 3.06
4678 5724 2.436646 CCACGACTCATGGTGCCC 60.437 66.667 0.00 0.00 33.44 5.36
5067 6124 5.163513 CACAGTTTCAAATACTCAATGGCC 58.836 41.667 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.641499 TTTCTCGTAATTGTTTTTCATTTGCT 57.359 26.923 0.00 0.00 0.00 3.91
74 76 2.099405 ACATCCATAAAAACCAGCGGG 58.901 47.619 0.00 0.00 41.29 6.13
77 79 7.035612 CCTCTTAAACATCCATAAAAACCAGC 58.964 38.462 0.00 0.00 0.00 4.85
146 644 6.795098 TGAATTACTTACCACATGTGTCAC 57.205 37.500 23.79 0.00 0.00 3.67
152 650 9.912634 AGAATTGTTTGAATTACTTACCACATG 57.087 29.630 0.00 0.00 0.00 3.21
228 726 2.073816 CTAACCATCCGAGTTGCGTTT 58.926 47.619 0.00 0.00 38.67 3.60
233 731 5.643777 ACAAGAAATCTAACCATCCGAGTTG 59.356 40.000 0.00 0.00 0.00 3.16
239 737 6.122277 TCCATCACAAGAAATCTAACCATCC 58.878 40.000 0.00 0.00 0.00 3.51
270 768 7.361542 CCAAGTCTAAGACATGAACTTTGATGG 60.362 40.741 17.38 17.07 33.78 3.51
286 784 5.349817 CACAACTATCAGTGCCAAGTCTAAG 59.650 44.000 0.00 0.00 0.00 2.18
287 785 5.221641 ACACAACTATCAGTGCCAAGTCTAA 60.222 40.000 0.00 0.00 39.30 2.10
309 807 4.081917 GGCCGGAAATAAATCCAGAAAACA 60.082 41.667 5.05 0.00 39.61 2.83
363 862 2.527100 CATTCGTAGTCGACAGGAACC 58.473 52.381 19.50 0.00 46.03 3.62
420 919 3.316588 GCATCTCCGAGATACTCAGTCAA 59.683 47.826 10.65 0.00 32.12 3.18
421 920 2.881513 GCATCTCCGAGATACTCAGTCA 59.118 50.000 10.65 0.00 32.12 3.41
423 922 3.146066 GAGCATCTCCGAGATACTCAGT 58.854 50.000 24.97 1.81 42.21 3.41
483 982 2.967459 TACATACGCGTACATACCCG 57.033 50.000 23.19 6.69 34.00 5.28
485 984 6.740002 CAGATACTTACATACGCGTACATACC 59.260 42.308 23.19 5.05 0.00 2.73
489 988 4.035441 TGCAGATACTTACATACGCGTACA 59.965 41.667 23.19 1.54 0.00 2.90
490 989 4.530388 TGCAGATACTTACATACGCGTAC 58.470 43.478 23.19 5.32 0.00 3.67
495 994 8.347729 TGTACAAATGCAGATACTTACATACG 57.652 34.615 0.00 0.00 0.00 3.06
502 1001 8.615878 TTAACACTGTACAAATGCAGATACTT 57.384 30.769 0.00 0.00 40.79 2.24
540 1521 2.289195 ACCGTACGTGTTGATGTCCATT 60.289 45.455 15.21 0.00 0.00 3.16
578 1559 4.209080 GCATTTCGCTAAACTGCACTTTTT 59.791 37.500 10.86 0.00 37.77 1.94
579 1560 3.735746 GCATTTCGCTAAACTGCACTTTT 59.264 39.130 10.86 0.00 37.77 2.27
580 1561 3.308530 GCATTTCGCTAAACTGCACTTT 58.691 40.909 10.86 0.00 37.77 2.66
581 1562 2.933769 GCATTTCGCTAAACTGCACTT 58.066 42.857 10.86 0.00 37.77 3.16
582 1563 2.619013 GCATTTCGCTAAACTGCACT 57.381 45.000 10.86 0.00 37.77 4.40
598 1579 3.857052 CAATCTTTGCATGAACCAGCAT 58.143 40.909 0.00 0.00 40.94 3.79
701 1682 1.482182 TCCCGTCAACAGGATCATGAG 59.518 52.381 15.42 6.31 0.00 2.90
702 1683 1.482182 CTCCCGTCAACAGGATCATGA 59.518 52.381 15.42 0.00 0.00 3.07
703 1684 1.945387 CTCCCGTCAACAGGATCATG 58.055 55.000 5.68 5.68 0.00 3.07
972 1977 1.004560 CCGATGGATGGGTGGATCG 60.005 63.158 0.00 0.00 37.93 3.69
977 1986 3.182590 ATCGGCCGATGGATGGGTG 62.183 63.158 38.62 0.00 32.98 4.61
1152 2161 3.753070 GATGGACGCGGACGAGGTC 62.753 68.421 12.47 0.00 43.93 3.85
1830 2845 1.631072 CGTTTGATCGCTGCTACGG 59.369 57.895 0.00 0.00 0.00 4.02
1846 2861 3.063084 GTCCTCCTCGACCAGCGT 61.063 66.667 0.00 0.00 41.80 5.07
1917 2932 3.426568 GCAGCTGCCTTGTCGTCC 61.427 66.667 28.76 0.00 34.31 4.79
1932 2947 3.573772 CTTGTGCTCGGACTCGGCA 62.574 63.158 0.00 0.00 39.14 5.69
1933 2948 2.811317 CTTGTGCTCGGACTCGGC 60.811 66.667 0.00 0.00 36.95 5.54
1934 2949 2.125912 CCTTGTGCTCGGACTCGG 60.126 66.667 0.00 0.00 36.95 4.63
1941 2956 1.734477 CGTGTCCTCCTTGTGCTCG 60.734 63.158 0.00 0.00 0.00 5.03
2036 3051 2.992114 ACGCGCTCTGGTCTCCTT 60.992 61.111 5.73 0.00 0.00 3.36
2076 3091 4.452733 CGGTCCTTCTCCCGGTGC 62.453 72.222 0.00 0.00 40.54 5.01
2133 3148 2.505777 CACTCGTGCTGCTCCTCG 60.506 66.667 0.00 1.22 0.00 4.63
2319 3334 4.323477 TTTGGCCACTCGACGGGG 62.323 66.667 3.88 0.00 0.00 5.73
2401 3416 1.202639 TCTGCACAAGTCACCATCGTT 60.203 47.619 0.00 0.00 0.00 3.85
2967 3999 8.434661 CACAAGCAAAAATTAGTGCGAATAATT 58.565 29.630 7.43 0.00 45.62 1.40
2972 4004 4.926244 TCACAAGCAAAAATTAGTGCGAA 58.074 34.783 7.43 0.00 45.62 4.70
2973 4005 4.560136 TCACAAGCAAAAATTAGTGCGA 57.440 36.364 7.43 0.00 45.62 5.10
2974 4006 5.827568 ATTCACAAGCAAAAATTAGTGCG 57.172 34.783 7.43 0.00 45.62 5.34
2991 4026 0.250553 TGGTGACGGTGGGAATTCAC 60.251 55.000 7.93 3.78 38.11 3.18
2995 4030 1.302949 CCATGGTGACGGTGGGAAT 59.697 57.895 2.57 0.00 35.67 3.01
2999 4034 2.046314 GGACCATGGTGACGGTGG 60.046 66.667 25.52 3.69 42.58 4.61
3006 4041 2.495155 TTCACTCATGGACCATGGTG 57.505 50.000 30.83 30.83 41.66 4.17
3008 4043 3.286329 TCATTCACTCATGGACCATGG 57.714 47.619 29.97 22.83 41.66 3.66
3009 4044 4.885325 TGATTCATTCACTCATGGACCATG 59.115 41.667 26.10 26.10 42.60 3.66
3010 4045 5.120054 TGATTCATTCACTCATGGACCAT 57.880 39.130 0.00 0.00 0.00 3.55
3011 4046 4.573021 TGATTCATTCACTCATGGACCA 57.427 40.909 0.00 0.00 0.00 4.02
3012 4047 6.069684 GAATGATTCATTCACTCATGGACC 57.930 41.667 26.99 3.31 46.50 4.46
3013 4048 5.009410 GGGAATGATTCATTCACTCATGGAC 59.991 44.000 30.63 15.73 46.96 4.02
3014 4049 5.135383 GGGAATGATTCATTCACTCATGGA 58.865 41.667 30.63 0.00 46.96 3.41
3015 4050 5.449107 GGGAATGATTCATTCACTCATGG 57.551 43.478 30.63 0.00 46.96 3.66
3026 4061 2.684374 CGTCATTGCTGGGAATGATTCA 59.316 45.455 17.68 0.00 42.78 2.57
3036 4071 1.078918 TCAGAGCCGTCATTGCTGG 60.079 57.895 0.00 0.00 39.69 4.85
3492 4527 2.939103 GGAAGGGTTCTTGTCGATGATG 59.061 50.000 0.00 0.00 32.52 3.07
3497 4532 1.669440 CGGGAAGGGTTCTTGTCGA 59.331 57.895 0.00 0.00 32.52 4.20
3544 4579 1.746615 GCAGGATTTCTCGGCAGCA 60.747 57.895 0.00 0.00 0.00 4.41
3545 4580 1.746615 TGCAGGATTTCTCGGCAGC 60.747 57.895 0.00 0.00 31.32 5.25
3547 4582 1.741401 CGTGCAGGATTTCTCGGCA 60.741 57.895 0.00 0.00 32.13 5.69
3866 4902 4.988598 AACACGGCGCACCTGAGG 62.989 66.667 10.83 0.00 0.00 3.86
3867 4903 3.716006 CAACACGGCGCACCTGAG 61.716 66.667 10.83 0.00 0.00 3.35
3891 4927 1.313812 ATCCTGTCCACCTCGACGAC 61.314 60.000 0.00 0.00 35.40 4.34
4114 5150 3.838565 TGGAGGGTGAAAATTGCTTGTA 58.161 40.909 0.00 0.00 0.00 2.41
4171 5209 7.816031 ACATCAATGCTAACCAAAGAAAGAATG 59.184 33.333 0.00 0.00 0.00 2.67
4204 5242 5.649782 TGAAGGGTAGTTAGTAAGTTCCG 57.350 43.478 7.16 0.00 0.00 4.30
4224 5262 8.363390 TGCATTACAAAACCATGTCTTATTTGA 58.637 29.630 3.81 0.00 35.52 2.69
4241 5279 9.967346 GAGTCTTAGATACATACTGCATTACAA 57.033 33.333 0.00 0.00 0.00 2.41
4260 5298 6.458888 CGTCTCAGTTCTATGCATGAGTCTTA 60.459 42.308 10.16 0.00 40.07 2.10
4284 5322 3.325870 TGACAAACTAATGCTCCACTCG 58.674 45.455 0.00 0.00 0.00 4.18
4318 5356 5.251700 ACACTTTTTATGGATCAGAGGGAGT 59.748 40.000 0.00 0.00 0.00 3.85
4326 5364 3.823873 ACCGCAACACTTTTTATGGATCA 59.176 39.130 0.00 0.00 0.00 2.92
4336 5374 3.305398 TGTTCAAAACCGCAACACTTT 57.695 38.095 0.00 0.00 0.00 2.66
4343 5381 2.231478 TCAACCTTTGTTCAAAACCGCA 59.769 40.909 0.00 0.00 30.42 5.69
4346 5384 6.533723 CCTTAGTTCAACCTTTGTTCAAAACC 59.466 38.462 0.00 0.00 30.42 3.27
4356 5394 3.637769 TGCCAACCTTAGTTCAACCTTT 58.362 40.909 0.00 0.00 32.45 3.11
4358 5396 2.956333 GTTGCCAACCTTAGTTCAACCT 59.044 45.455 0.00 0.00 35.89 3.50
4370 5408 4.142026 AGTTTTGAACTAAGGTTGCCAACC 60.142 41.667 19.12 19.12 45.61 3.77
4371 5409 4.803613 CAGTTTTGAACTAAGGTTGCCAAC 59.196 41.667 0.00 0.00 40.46 3.77
4372 5410 4.464597 ACAGTTTTGAACTAAGGTTGCCAA 59.535 37.500 0.00 0.00 40.46 4.52
4373 5411 4.020543 ACAGTTTTGAACTAAGGTTGCCA 58.979 39.130 0.00 0.00 40.46 4.92
4374 5412 4.097286 TCACAGTTTTGAACTAAGGTTGCC 59.903 41.667 0.00 0.00 40.46 4.52
4375 5413 5.034797 GTCACAGTTTTGAACTAAGGTTGC 58.965 41.667 0.00 0.00 40.46 4.17
4384 5422 9.944663 TTCATAATAAGTGTCACAGTTTTGAAC 57.055 29.630 2.42 0.00 0.00 3.18
4393 5431 7.125659 TCCCTCTGATTCATAATAAGTGTCACA 59.874 37.037 5.62 0.00 0.00 3.58
4395 5433 7.345653 ACTCCCTCTGATTCATAATAAGTGTCA 59.654 37.037 0.00 0.00 0.00 3.58
4398 5437 8.865090 AGTACTCCCTCTGATTCATAATAAGTG 58.135 37.037 0.00 0.00 0.00 3.16
4413 5452 5.722441 CCTTCTAGGAAAAAGTACTCCCTCT 59.278 44.000 0.00 0.00 37.67 3.69
4421 5460 5.768164 CCAACTTGCCTTCTAGGAAAAAGTA 59.232 40.000 0.00 0.00 37.67 2.24
4429 5468 1.003580 TCTGCCAACTTGCCTTCTAGG 59.996 52.381 0.00 0.00 38.80 3.02
4430 5469 2.479566 TCTGCCAACTTGCCTTCTAG 57.520 50.000 0.00 0.00 0.00 2.43
4433 5472 1.471684 CTGATCTGCCAACTTGCCTTC 59.528 52.381 0.00 0.00 0.00 3.46
4444 5483 8.045176 ACTCTACAAAATTTAACTGATCTGCC 57.955 34.615 0.00 0.00 0.00 4.85
4462 5501 5.011635 TGGACTCAACATTGCTAACTCTACA 59.988 40.000 0.00 0.00 0.00 2.74
4463 5502 5.479306 TGGACTCAACATTGCTAACTCTAC 58.521 41.667 0.00 0.00 0.00 2.59
4466 5505 3.126000 GCTGGACTCAACATTGCTAACTC 59.874 47.826 0.00 0.00 0.00 3.01
4502 5543 9.547753 ACATTATTACGATCTGCTATTGAAGTT 57.452 29.630 0.00 0.00 0.00 2.66
4641 5687 6.364165 TCGTGGTTCTGTAAAAGAGAAATACG 59.636 38.462 13.27 13.27 39.70 3.06
4645 5691 5.667466 AGTCGTGGTTCTGTAAAAGAGAAA 58.333 37.500 0.00 0.00 35.91 2.52
4678 5724 3.191078 TCAGCATTTTTGTTTGTGGGG 57.809 42.857 0.00 0.00 0.00 4.96
5067 6124 1.473434 GGTTTAGACCCGGCTGATCTG 60.473 57.143 0.00 0.00 40.25 2.90



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

AutoCloner maintained by Alex Coulton.