Multiple sequence alignment - TraesCS5B01G211000

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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 TraesCS5B01G211000 chr5B 100.000 3106 0 0 1 3106 381841773 381844878 0.000000e+00 5736
1 TraesCS5B01G211000 chr5A 90.984 1952 110 25 363 2281 427895999 427894081 0.000000e+00 2569
2 TraesCS5B01G211000 chr5A 92.386 788 50 7 2320 3106 427894081 427893303 0.000000e+00 1114
3 TraesCS5B01G211000 chr5A 83.424 368 50 6 12 373 427896486 427896124 6.420000e-87 331
4 TraesCS5B01G211000 chr5A 77.957 186 39 2 2915 3098 368779277 368779092 7.040000e-22 115
5 TraesCS5B01G211000 chr5D 91.222 1800 81 34 504 2278 328608207 328609954 0.000000e+00 2377
6 TraesCS5B01G211000 chr5D 88.235 170 11 2 2320 2480 328609958 328610127 8.790000e-46 195
7 TraesCS5B01G211000 chr5D 90.625 96 6 3 355 449 328607996 328608089 1.170000e-24 124
8 TraesCS5B01G211000 chr4B 86.387 191 20 4 2887 3073 86473906 86474094 1.460000e-48 204
9 TraesCS5B01G211000 chr4B 79.487 195 35 4 2902 3093 37221458 37221650 1.940000e-27 134
10 TraesCS5B01G211000 chr4A 83.636 220 30 4 2887 3102 538838443 538838226 5.250000e-48 202
11 TraesCS5B01G211000 chr1D 78.744 207 39 4 2900 3103 328861492 328861696 1.940000e-27 134
12 TraesCS5B01G211000 chr3B 78.652 178 28 5 2900 3074 447970799 447970969 3.270000e-20 110
13 TraesCS5B01G211000 chr1A 79.042 167 30 4 2900 3063 425708675 425708839 3.270000e-20 110
14 TraesCS5B01G211000 chr6D 77.157 197 35 9 2912 3103 380558630 380558821 4.240000e-19 106


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 TraesCS5B01G211000 chr5B 381841773 381844878 3105 False 5736.000000 5736 100.000000 1 3106 1 chr5B.!!$F1 3105
1 TraesCS5B01G211000 chr5A 427893303 427896486 3183 True 1338.000000 2569 88.931333 12 3106 3 chr5A.!!$R2 3094
2 TraesCS5B01G211000 chr5D 328607996 328610127 2131 False 898.666667 2377 90.027333 355 2480 3 chr5D.!!$F1 2125

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
189 194 0.106708 TTGAGTTGCAGACGCTTCCT 59.893 50.0 0.0 0.0 39.64 3.36 F
777 988 0.244994 AGAACCTAGTGAGCTGCGTG 59.755 55.0 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1205 1417 0.968901 TCACGGCGTACCTCCTTCAT 60.969 55.0 14.22 0.0 0.00 2.57 R
2571 2816 0.392193 ATCTCAAACTGAGCAGCCCG 60.392 55.0 0.00 0.0 43.95 6.13 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
39 44 1.490621 AGTTACAAAACCGACGGTCG 58.509 50.000 22.00 22.88 40.07 4.79
47 52 4.065281 CCGACGGTCGCCTTCCTT 62.065 66.667 24.26 0.00 38.82 3.36
50 55 1.153804 GACGGTCGCCTTCCTTCTC 60.154 63.158 0.00 0.00 0.00 2.87
52 57 2.646175 CGGTCGCCTTCCTTCTCCA 61.646 63.158 0.00 0.00 0.00 3.86
53 58 1.908483 GGTCGCCTTCCTTCTCCAT 59.092 57.895 0.00 0.00 0.00 3.41
54 59 0.253327 GGTCGCCTTCCTTCTCCATT 59.747 55.000 0.00 0.00 0.00 3.16
55 60 1.373570 GTCGCCTTCCTTCTCCATTG 58.626 55.000 0.00 0.00 0.00 2.82
56 61 0.392998 TCGCCTTCCTTCTCCATTGC 60.393 55.000 0.00 0.00 0.00 3.56
57 62 0.393537 CGCCTTCCTTCTCCATTGCT 60.394 55.000 0.00 0.00 0.00 3.91
61 66 3.424703 CCTTCCTTCTCCATTGCTTTCA 58.575 45.455 0.00 0.00 0.00 2.69
62 67 4.021916 CCTTCCTTCTCCATTGCTTTCAT 58.978 43.478 0.00 0.00 0.00 2.57
63 68 4.465305 CCTTCCTTCTCCATTGCTTTCATT 59.535 41.667 0.00 0.00 0.00 2.57
88 93 1.032657 TCGTCCCTCACTCTGCTAGC 61.033 60.000 8.10 8.10 0.00 3.42
116 121 0.456221 CGAGGCGCCCTATACTATGG 59.544 60.000 26.15 0.00 31.76 2.74
123 128 3.432378 CGCCCTATACTATGGAGAGGTT 58.568 50.000 0.00 0.00 0.00 3.50
129 134 4.857509 ATACTATGGAGAGGTTTCGAGC 57.142 45.455 0.00 0.00 0.00 5.03
135 140 2.070028 GGAGAGGTTTCGAGCTTCAAC 58.930 52.381 0.00 0.00 0.00 3.18
136 141 2.289133 GGAGAGGTTTCGAGCTTCAACT 60.289 50.000 0.00 0.00 0.00 3.16
139 144 3.561725 AGAGGTTTCGAGCTTCAACTTTG 59.438 43.478 0.00 0.00 0.00 2.77
145 150 1.322442 GAGCTTCAACTTTGTGGGCT 58.678 50.000 0.00 0.00 33.82 5.19
160 165 0.759060 GGGCTTTTGTTCCCACACCT 60.759 55.000 0.00 0.00 42.18 4.00
168 173 0.818040 GTTCCCACACCTCACCACAC 60.818 60.000 0.00 0.00 0.00 3.82
170 175 2.452064 CCCACACCTCACCACACCT 61.452 63.158 0.00 0.00 0.00 4.00
183 188 0.583438 CACACCTTGAGTTGCAGACG 59.417 55.000 0.00 0.00 0.00 4.18
186 191 0.179045 ACCTTGAGTTGCAGACGCTT 60.179 50.000 0.00 0.00 39.64 4.68
189 194 0.106708 TTGAGTTGCAGACGCTTCCT 59.893 50.000 0.00 0.00 39.64 3.36
195 200 1.807573 GCAGACGCTTCCTTCTCGG 60.808 63.158 0.00 0.00 34.30 4.63
249 254 3.325870 TGGTTGTAATTCAGCGAGACAG 58.674 45.455 0.00 0.00 0.00 3.51
251 256 3.746492 GGTTGTAATTCAGCGAGACAGTT 59.254 43.478 0.00 0.00 0.00 3.16
269 274 2.197465 GTTGTCTCCAATACCCCCTCT 58.803 52.381 0.00 0.00 32.11 3.69
271 276 3.042059 TGTCTCCAATACCCCCTCTAC 57.958 52.381 0.00 0.00 0.00 2.59
276 281 2.047830 CCAATACCCCCTCTACTGGTC 58.952 57.143 0.00 0.00 33.55 4.02
293 298 9.760926 TCTACTGGTCAGAATAGCTATCATAAT 57.239 33.333 6.72 0.00 0.00 1.28
298 303 7.108847 GGTCAGAATAGCTATCATAATGGCTT 58.891 38.462 6.72 0.00 46.53 4.35
300 305 7.605691 GTCAGAATAGCTATCATAATGGCTTGT 59.394 37.037 6.72 0.00 46.53 3.16
302 307 7.823310 CAGAATAGCTATCATAATGGCTTGTCT 59.177 37.037 6.72 0.00 46.53 3.41
303 308 9.040259 AGAATAGCTATCATAATGGCTTGTCTA 57.960 33.333 6.72 0.00 46.53 2.59
313 318 9.625747 TCATAATGGCTTGTCTATTTGAATACA 57.374 29.630 0.00 0.00 0.00 2.29
347 353 4.668576 TTGCGCTTTTCTAGATCAACTG 57.331 40.909 9.73 0.00 0.00 3.16
348 354 3.925379 TGCGCTTTTCTAGATCAACTGA 58.075 40.909 9.73 0.00 0.00 3.41
354 360 7.030165 CGCTTTTCTAGATCAACTGAGACTTA 58.970 38.462 0.00 0.00 0.00 2.24
361 367 8.470805 TCTAGATCAACTGAGACTTAATGAACC 58.529 37.037 0.00 0.00 0.00 3.62
364 370 4.010349 CAACTGAGACTTAATGAACCCCC 58.990 47.826 0.00 0.00 0.00 5.40
365 371 3.256704 ACTGAGACTTAATGAACCCCCA 58.743 45.455 0.00 0.00 0.00 4.96
373 379 0.701731 AATGAACCCCCATCGGTTGA 59.298 50.000 0.00 0.00 46.35 3.18
374 380 0.255890 ATGAACCCCCATCGGTTGAG 59.744 55.000 0.00 0.00 46.35 3.02
375 381 0.838554 TGAACCCCCATCGGTTGAGA 60.839 55.000 0.00 0.00 46.35 3.27
376 382 0.392595 GAACCCCCATCGGTTGAGAC 60.393 60.000 0.00 0.00 46.35 3.36
408 548 2.223272 CGTCGTCATAGAGCAACAGCTA 60.223 50.000 0.00 0.00 39.10 3.32
413 553 2.501316 TCATAGAGCAACAGCTAAGCCA 59.499 45.455 0.00 0.00 39.10 4.75
452 592 7.312154 TCACCAAATGTAAATCAGCACATTAC 58.688 34.615 0.76 0.00 42.93 1.89
456 596 6.832520 AATGTAAATCAGCACATTACCACA 57.167 33.333 0.00 0.00 42.17 4.17
457 597 7.408756 AATGTAAATCAGCACATTACCACAT 57.591 32.000 0.00 0.00 42.17 3.21
485 626 0.320421 GCCAAACGTACTGCTCCTCA 60.320 55.000 0.00 0.00 0.00 3.86
511 714 2.048222 CATGCCCGTCACACGTCT 60.048 61.111 0.00 0.00 40.58 4.18
512 715 1.667830 CATGCCCGTCACACGTCTT 60.668 57.895 0.00 0.00 40.58 3.01
551 754 1.386485 CCTCCCATCCCATCCACCT 60.386 63.158 0.00 0.00 0.00 4.00
570 773 5.811100 CCACCTAAAAATAACCGAGAGAGAC 59.189 44.000 0.00 0.00 0.00 3.36
571 774 5.811100 CACCTAAAAATAACCGAGAGAGACC 59.189 44.000 0.00 0.00 0.00 3.85
572 775 5.041940 CCTAAAAATAACCGAGAGAGACCG 58.958 45.833 0.00 0.00 0.00 4.79
573 776 4.796038 AAAAATAACCGAGAGAGACCGA 57.204 40.909 0.00 0.00 0.00 4.69
574 777 3.779271 AAATAACCGAGAGAGACCGAC 57.221 47.619 0.00 0.00 0.00 4.79
692 903 1.129058 ACACTCCACGACCTTTTCCT 58.871 50.000 0.00 0.00 0.00 3.36
775 986 1.634702 GAAGAACCTAGTGAGCTGCG 58.365 55.000 0.00 0.00 0.00 5.18
776 987 0.969894 AAGAACCTAGTGAGCTGCGT 59.030 50.000 0.00 0.00 0.00 5.24
777 988 0.244994 AGAACCTAGTGAGCTGCGTG 59.755 55.000 0.00 0.00 0.00 5.34
778 989 1.355066 GAACCTAGTGAGCTGCGTGC 61.355 60.000 0.00 0.00 43.29 5.34
1093 1305 3.717294 GGGCGGCCAAGGAGAAGA 61.717 66.667 25.33 0.00 0.00 2.87
1211 1423 1.874019 CTGCCGTCGTCGATGAAGG 60.874 63.158 28.84 28.84 40.07 3.46
1284 1496 4.019321 TCTTGTAGAAAGAACAGGGGATGG 60.019 45.833 0.00 0.00 0.00 3.51
1287 1499 3.903530 AGAAAGAACAGGGGATGGTTT 57.096 42.857 0.00 0.00 0.00 3.27
1291 1503 3.903530 AGAACAGGGGATGGTTTTCTT 57.096 42.857 0.00 0.00 0.00 2.52
1299 1511 3.084786 GGGATGGTTTTCTTCTGACTGG 58.915 50.000 0.00 0.00 0.00 4.00
1308 1520 3.667497 TCTTCTGACTGGTCATGTGTC 57.333 47.619 3.80 0.00 39.13 3.67
1397 1630 0.540365 CCACCACCATGAACCTGCTT 60.540 55.000 0.00 0.00 0.00 3.91
1406 1639 1.298667 GAACCTGCTTTCGGGGCTA 59.701 57.895 0.00 0.00 43.28 3.93
1497 1730 1.955778 CAACTGACAACCAAGATGCCA 59.044 47.619 0.00 0.00 0.00 4.92
1656 1889 4.361429 AGAGCCCTCCCCAGCCTT 62.361 66.667 0.00 0.00 0.00 4.35
1690 1923 4.345257 TCTCCCTGGTACTAATTCTCATGC 59.655 45.833 0.00 0.00 0.00 4.06
1702 1935 5.717078 AATTCTCATGCTCTCTTTTGCAA 57.283 34.783 0.00 0.00 42.74 4.08
1703 1936 4.494350 TTCTCATGCTCTCTTTTGCAAC 57.506 40.909 0.00 0.00 42.74 4.17
1732 1965 7.639039 ACCGTGAAAATATACAATACATGCAG 58.361 34.615 0.00 0.00 0.00 4.41
1742 1975 4.603131 ACAATACATGCAGACAAAGGGAT 58.397 39.130 0.00 0.00 0.00 3.85
1765 1998 4.060900 TGTTTCAGTTCAGAGTCTCATGC 58.939 43.478 1.94 0.00 0.00 4.06
1801 2034 6.042777 TGAAATCCTTATCGCTAACAGAGTG 58.957 40.000 0.00 0.00 36.98 3.51
1894 2127 0.541863 AAAGGGCAGGTACCTGATCG 59.458 55.000 40.26 18.46 46.30 3.69
1898 2131 1.395826 GGCAGGTACCTGATCGAGCT 61.396 60.000 40.26 1.96 46.30 4.09
1900 2133 0.387202 CAGGTACCTGATCGAGCTGG 59.613 60.000 34.54 23.14 46.30 4.85
1901 2134 0.757188 AGGTACCTGATCGAGCTGGG 60.757 60.000 27.21 18.85 0.00 4.45
1903 2136 0.824759 GTACCTGATCGAGCTGGGTT 59.175 55.000 27.21 12.34 0.00 4.11
1905 2138 0.693049 ACCTGATCGAGCTGGGTTTT 59.307 50.000 27.21 6.58 0.00 2.43
1906 2139 1.073923 ACCTGATCGAGCTGGGTTTTT 59.926 47.619 27.21 6.22 0.00 1.94
2031 2264 2.780993 CGCCTTACCAAATTAACAGCG 58.219 47.619 0.00 0.00 34.70 5.18
2120 2353 4.809426 ACAAACTGACGGTACAAGAAAGAG 59.191 41.667 0.00 0.00 0.00 2.85
2140 2375 3.755378 GAGGCATGATGAACACTTGACTT 59.245 43.478 0.00 0.00 32.26 3.01
2141 2376 3.504906 AGGCATGATGAACACTTGACTTG 59.495 43.478 0.00 0.00 28.52 3.16
2163 2398 3.436470 GGGCTCCAAATCTATAGGGCAAA 60.436 47.826 0.00 0.00 0.00 3.68
2243 2478 1.295792 TGAAGCGACAATAATCGGGC 58.704 50.000 0.00 0.00 42.49 6.13
2266 2501 7.184779 GGCGTTGGTTATTCATTTCTAGTAAC 58.815 38.462 0.00 0.00 0.00 2.50
2285 2520 9.837525 CTAGTAACAATTAGTAGTAATAGCCGG 57.162 37.037 0.00 0.00 35.41 6.13
2286 2521 8.242729 AGTAACAATTAGTAGTAATAGCCGGT 57.757 34.615 1.90 0.00 0.00 5.28
2287 2522 8.139989 AGTAACAATTAGTAGTAATAGCCGGTG 58.860 37.037 1.90 0.51 0.00 4.94
2288 2523 5.850614 ACAATTAGTAGTAATAGCCGGTGG 58.149 41.667 1.90 0.00 0.00 4.61
2289 2524 5.364735 ACAATTAGTAGTAATAGCCGGTGGT 59.635 40.000 1.90 0.00 0.00 4.16
2290 2525 6.126968 ACAATTAGTAGTAATAGCCGGTGGTT 60.127 38.462 1.90 0.00 0.00 3.67
2291 2526 3.814005 AGTAGTAATAGCCGGTGGTTG 57.186 47.619 1.90 0.00 0.00 3.77
2292 2527 3.368248 AGTAGTAATAGCCGGTGGTTGA 58.632 45.455 1.90 0.00 0.00 3.18
2293 2528 3.965347 AGTAGTAATAGCCGGTGGTTGAT 59.035 43.478 1.90 0.00 0.00 2.57
2294 2529 3.926058 AGTAATAGCCGGTGGTTGATT 57.074 42.857 1.90 0.00 0.00 2.57
2295 2530 3.805207 AGTAATAGCCGGTGGTTGATTC 58.195 45.455 1.90 0.00 0.00 2.52
2296 2531 3.454812 AGTAATAGCCGGTGGTTGATTCT 59.545 43.478 1.90 0.00 0.00 2.40
2297 2532 2.332063 ATAGCCGGTGGTTGATTCTG 57.668 50.000 1.90 0.00 0.00 3.02
2298 2533 1.271856 TAGCCGGTGGTTGATTCTGA 58.728 50.000 1.90 0.00 0.00 3.27
2299 2534 0.620556 AGCCGGTGGTTGATTCTGAT 59.379 50.000 1.90 0.00 0.00 2.90
2300 2535 1.004745 AGCCGGTGGTTGATTCTGATT 59.995 47.619 1.90 0.00 0.00 2.57
2301 2536 1.133025 GCCGGTGGTTGATTCTGATTG 59.867 52.381 1.90 0.00 0.00 2.67
2302 2537 2.710377 CCGGTGGTTGATTCTGATTGA 58.290 47.619 0.00 0.00 0.00 2.57
2303 2538 3.081061 CCGGTGGTTGATTCTGATTGAA 58.919 45.455 0.00 0.00 39.24 2.69
2304 2539 3.119849 CCGGTGGTTGATTCTGATTGAAC 60.120 47.826 0.00 0.00 37.52 3.18
2305 2540 3.501828 CGGTGGTTGATTCTGATTGAACA 59.498 43.478 4.72 0.00 37.52 3.18
2306 2541 4.156556 CGGTGGTTGATTCTGATTGAACAT 59.843 41.667 4.72 0.00 37.52 2.71
2307 2542 5.644644 GGTGGTTGATTCTGATTGAACATC 58.355 41.667 4.72 0.00 37.52 3.06
2308 2543 5.327091 GTGGTTGATTCTGATTGAACATCG 58.673 41.667 4.72 0.00 37.52 3.84
2309 2544 4.395854 TGGTTGATTCTGATTGAACATCGG 59.604 41.667 4.72 0.00 37.52 4.18
2310 2545 4.346129 GTTGATTCTGATTGAACATCGGC 58.654 43.478 0.00 0.00 37.52 5.54
2311 2546 3.608796 TGATTCTGATTGAACATCGGCA 58.391 40.909 0.00 0.00 37.52 5.69
2312 2547 4.201657 TGATTCTGATTGAACATCGGCAT 58.798 39.130 0.00 0.00 37.52 4.40
2313 2548 5.367302 TGATTCTGATTGAACATCGGCATA 58.633 37.500 0.00 0.00 37.52 3.14
2314 2549 5.999600 TGATTCTGATTGAACATCGGCATAT 59.000 36.000 0.00 0.00 37.52 1.78
2315 2550 7.160726 TGATTCTGATTGAACATCGGCATATA 58.839 34.615 0.00 0.00 37.52 0.86
2316 2551 7.825761 TGATTCTGATTGAACATCGGCATATAT 59.174 33.333 0.00 0.00 37.52 0.86
2317 2552 9.317936 GATTCTGATTGAACATCGGCATATATA 57.682 33.333 0.00 0.00 37.52 0.86
2318 2553 8.707938 TTCTGATTGAACATCGGCATATATAG 57.292 34.615 0.00 0.00 0.00 1.31
2322 2557 9.750125 TGATTGAACATCGGCATATATAGATAC 57.250 33.333 0.00 0.00 0.00 2.24
2327 2562 9.331106 GAACATCGGCATATATAGATACGTATG 57.669 37.037 13.97 0.00 0.00 2.39
2334 2569 9.395707 GGCATATATAGATACGTATGTAAGCAC 57.604 37.037 13.97 3.10 33.44 4.40
2347 2582 1.535462 GTAAGCACATGCCGTCTGTTT 59.465 47.619 0.00 0.00 43.38 2.83
2349 2584 1.730547 GCACATGCCGTCTGTTTGC 60.731 57.895 0.00 0.00 34.31 3.68
2429 2669 6.412362 ACTAGGACTATTGTCATGGTCATC 57.588 41.667 9.51 0.00 43.30 2.92
2473 2717 1.089920 CAGATGGTTTGCCTTCCTCG 58.910 55.000 0.00 0.00 39.12 4.63
2493 2737 2.226200 CGACATGTCATGGAAAGTTGCA 59.774 45.455 24.93 0.00 33.60 4.08
2494 2738 3.568538 GACATGTCATGGAAAGTTGCAC 58.431 45.455 21.07 0.00 33.60 4.57
2518 2762 6.130723 CGCGCGTTCCTTGATTATTTTATTA 58.869 36.000 24.19 0.00 0.00 0.98
2520 2764 7.953173 CGCGCGTTCCTTGATTATTTTATTATA 59.047 33.333 24.19 0.00 0.00 0.98
2552 2796 1.064906 AGTCCCCTGATTCATGCAGTG 60.065 52.381 0.00 0.00 0.00 3.66
2556 2800 1.680860 CCCTGATTCATGCAGTGCTCA 60.681 52.381 17.60 10.13 0.00 4.26
2561 2805 5.163591 CCTGATTCATGCAGTGCTCATTTTA 60.164 40.000 17.60 0.00 0.00 1.52
2562 2806 6.270156 TGATTCATGCAGTGCTCATTTTAA 57.730 33.333 17.60 1.74 0.00 1.52
2571 2816 7.083858 TGCAGTGCTCATTTTAATTCTTACAC 58.916 34.615 17.60 0.00 0.00 2.90
2632 2877 2.711547 ACTTCTGCTACCCCTCAAAAGT 59.288 45.455 0.00 0.00 0.00 2.66
2705 2950 6.092122 CGGATCTAATGTTCAGCAAAACTACA 59.908 38.462 0.00 0.00 0.00 2.74
2715 2960 6.729391 TCAGCAAAACTACAACGCATTATA 57.271 33.333 0.00 0.00 0.00 0.98
2723 2968 7.661127 AACTACAACGCATTATAGAACACAA 57.339 32.000 0.00 0.00 0.00 3.33
2724 2969 7.290857 ACTACAACGCATTATAGAACACAAG 57.709 36.000 0.00 0.00 0.00 3.16
2761 3006 2.649129 GGCAACTCCAATGTGGGGC 61.649 63.158 0.00 0.00 43.56 5.80
2798 3043 3.016031 AGGCATCAAATGTATGTTCGCA 58.984 40.909 0.00 0.00 0.00 5.10
2802 3047 5.277974 GGCATCAAATGTATGTTCGCATAGT 60.278 40.000 0.00 0.00 40.41 2.12
2803 3048 6.073276 GGCATCAAATGTATGTTCGCATAGTA 60.073 38.462 0.00 0.00 40.41 1.82
2804 3049 7.361201 GGCATCAAATGTATGTTCGCATAGTAT 60.361 37.037 0.00 0.00 40.41 2.12
2834 3079 9.959749 TTTTTCTGTGCTCGAAGTATTAAAAAT 57.040 25.926 0.00 0.00 0.00 1.82
3011 3256 7.542534 TTTATTGACACGTGTTCTAGTTGTT 57.457 32.000 24.26 0.00 0.00 2.83
3019 3264 6.926826 ACACGTGTTCTAGTTGTTCATATGAA 59.073 34.615 17.22 14.23 0.00 2.57
3022 3267 7.439955 ACGTGTTCTAGTTGTTCATATGAAACA 59.560 33.333 19.55 15.89 35.58 2.83
3041 3286 1.534163 CACCCGCATATGCTCAATCAG 59.466 52.381 24.56 7.74 39.32 2.90
3045 3290 3.620374 CCCGCATATGCTCAATCAGATAC 59.380 47.826 24.56 0.00 39.32 2.24
3046 3291 4.502016 CCGCATATGCTCAATCAGATACT 58.498 43.478 24.56 0.00 39.32 2.12
3054 3299 7.934855 ATGCTCAATCAGATACTTTTGAAGT 57.065 32.000 0.00 0.00 45.40 3.01
3076 3321 2.697229 TGCTCATGAGTTCCTCGATCAT 59.303 45.455 23.38 0.00 34.02 2.45
3103 3348 4.502171 TGCTGATGCATTTCGAGAAAAA 57.498 36.364 0.00 0.00 45.31 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.079809 CGGTTTTGTAACTTGTGGATTTAAGAT 58.920 33.333 0.00 0.00 34.59 2.40
7 8 7.282675 TCGGTTTTGTAACTTGTGGATTTAAGA 59.717 33.333 0.00 0.00 34.59 2.10
8 9 7.377662 GTCGGTTTTGTAACTTGTGGATTTAAG 59.622 37.037 0.00 0.00 34.59 1.85
9 10 7.194962 GTCGGTTTTGTAACTTGTGGATTTAA 58.805 34.615 0.00 0.00 34.59 1.52
10 11 6.511444 CGTCGGTTTTGTAACTTGTGGATTTA 60.511 38.462 0.00 0.00 34.59 1.40
14 15 2.608546 CGTCGGTTTTGTAACTTGTGGA 59.391 45.455 0.00 0.00 34.59 4.02
39 44 1.844687 AAGCAATGGAGAAGGAAGGC 58.155 50.000 0.00 0.00 0.00 4.35
72 77 1.326213 GCAGCTAGCAGAGTGAGGGA 61.326 60.000 18.83 0.00 44.79 4.20
98 103 1.751924 CTCCATAGTATAGGGCGCCTC 59.248 57.143 28.56 16.85 43.55 4.70
108 113 4.475345 AGCTCGAAACCTCTCCATAGTAT 58.525 43.478 0.00 0.00 0.00 2.12
116 121 3.033368 AGTTGAAGCTCGAAACCTCTC 57.967 47.619 0.00 0.00 0.00 3.20
123 128 1.946768 CCCACAAAGTTGAAGCTCGAA 59.053 47.619 0.00 0.00 0.00 3.71
129 134 3.860641 ACAAAAGCCCACAAAGTTGAAG 58.139 40.909 0.00 0.00 0.00 3.02
135 140 2.238942 GGGAACAAAAGCCCACAAAG 57.761 50.000 0.00 0.00 44.07 2.77
145 150 1.006043 TGGTGAGGTGTGGGAACAAAA 59.994 47.619 0.00 0.00 46.06 2.44
160 165 0.254462 TGCAACTCAAGGTGTGGTGA 59.746 50.000 0.00 0.00 30.71 4.02
168 173 0.514691 GAAGCGTCTGCAACTCAAGG 59.485 55.000 0.00 0.00 46.23 3.61
170 175 0.106708 AGGAAGCGTCTGCAACTCAA 59.893 50.000 0.00 0.00 46.23 3.02
183 188 1.585006 TCGTCACCGAGAAGGAAGC 59.415 57.895 0.00 0.00 45.00 3.86
201 206 2.559698 TCAACAACGGTGATGGTGAT 57.440 45.000 7.88 0.00 39.49 3.06
206 211 3.073678 TGAGGAATCAACAACGGTGATG 58.926 45.455 7.88 5.71 0.00 3.07
210 215 2.224769 ACCATGAGGAATCAACAACGGT 60.225 45.455 0.00 0.00 38.69 4.83
251 256 2.590611 AGTAGAGGGGGTATTGGAGACA 59.409 50.000 0.00 0.00 39.83 3.41
259 264 2.224077 TCTGACCAGTAGAGGGGGTAT 58.776 52.381 0.00 0.00 34.39 2.73
269 274 8.753133 CCATTATGATAGCTATTCTGACCAGTA 58.247 37.037 7.87 0.00 0.00 2.74
271 276 6.538021 GCCATTATGATAGCTATTCTGACCAG 59.462 42.308 7.87 0.00 0.00 4.00
276 281 7.823310 AGACAAGCCATTATGATAGCTATTCTG 59.177 37.037 7.87 1.99 34.49 3.02
314 319 6.544038 AGAAAAGCGCAAATTTAGCAAATT 57.456 29.167 11.47 9.94 42.62 1.82
317 322 6.007936 TCTAGAAAAGCGCAAATTTAGCAA 57.992 33.333 11.47 0.00 0.00 3.91
324 329 5.412594 TCAGTTGATCTAGAAAAGCGCAAAT 59.587 36.000 11.47 0.00 0.00 2.32
328 333 4.032331 GTCTCAGTTGATCTAGAAAAGCGC 59.968 45.833 0.00 0.00 0.00 5.92
329 334 5.406649 AGTCTCAGTTGATCTAGAAAAGCG 58.593 41.667 0.00 0.00 0.00 4.68
330 335 8.764524 TTAAGTCTCAGTTGATCTAGAAAAGC 57.235 34.615 0.00 0.00 0.00 3.51
347 353 3.467803 CGATGGGGGTTCATTAAGTCTC 58.532 50.000 0.00 0.00 0.00 3.36
348 354 2.172717 CCGATGGGGGTTCATTAAGTCT 59.827 50.000 0.00 0.00 0.00 3.24
361 367 1.762957 ACTATGTCTCAACCGATGGGG 59.237 52.381 0.00 0.00 43.62 4.96
364 370 6.345920 GGTTTTACTATGTCTCAACCGATG 57.654 41.667 0.00 0.00 0.00 3.84
373 379 4.771590 TGACGACGGTTTTACTATGTCT 57.228 40.909 0.00 0.00 0.00 3.41
374 380 6.489675 TCTATGACGACGGTTTTACTATGTC 58.510 40.000 0.00 0.00 0.00 3.06
375 381 6.441093 TCTATGACGACGGTTTTACTATGT 57.559 37.500 0.00 0.00 0.00 2.29
376 382 5.398711 GCTCTATGACGACGGTTTTACTATG 59.601 44.000 0.00 0.00 0.00 2.23
408 548 2.158784 TGATTTTTGGCTTGCTTGGCTT 60.159 40.909 4.95 0.00 0.00 4.35
413 553 3.557228 TTGGTGATTTTTGGCTTGCTT 57.443 38.095 0.00 0.00 0.00 3.91
452 592 3.244770 ACGTTTGGCCCCTATATATGTGG 60.245 47.826 0.00 0.00 0.00 4.17
456 596 4.323257 GCAGTACGTTTGGCCCCTATATAT 60.323 45.833 0.00 0.00 0.00 0.86
457 597 3.007182 GCAGTACGTTTGGCCCCTATATA 59.993 47.826 0.00 0.00 0.00 0.86
485 626 4.314440 ACGGGCATGTGTCGTGCT 62.314 61.111 12.56 0.00 44.78 4.40
511 714 1.675219 GTACGGGGCAAGGAGACAA 59.325 57.895 0.00 0.00 0.00 3.18
512 715 2.642254 CGTACGGGGCAAGGAGACA 61.642 63.158 7.57 0.00 0.00 3.41
551 754 5.393461 GGTCGGTCTCTCTCGGTTATTTTTA 60.393 44.000 0.00 0.00 0.00 1.52
692 903 4.485834 CGCGACGGTCCCATCGAA 62.486 66.667 5.92 0.00 40.86 3.71
775 986 4.143301 GGGGAATGGGAGGGGCAC 62.143 72.222 0.00 0.00 0.00 5.01
778 989 3.429580 GTGGGGGAATGGGAGGGG 61.430 72.222 0.00 0.00 0.00 4.79
867 1078 3.699038 CTCCGCCCTTTTAAAATGGATCA 59.301 43.478 22.18 6.80 0.00 2.92
900 1111 1.490490 ACTCCAGTGCACTTTTCCTCA 59.510 47.619 18.94 0.00 0.00 3.86
942 1153 1.298014 CTCGCTCCTTCCTTGGCTT 59.702 57.895 0.00 0.00 0.00 4.35
971 1182 3.382832 AAGTCGCCTCTCCACCGG 61.383 66.667 0.00 0.00 0.00 5.28
1076 1288 3.717294 TCTTCTCCTTGGCCGCCC 61.717 66.667 7.03 0.00 0.00 6.13
1194 1406 2.180769 CCTTCATCGACGACGGCA 59.819 61.111 7.55 0.00 40.21 5.69
1205 1417 0.968901 TCACGGCGTACCTCCTTCAT 60.969 55.000 14.22 0.00 0.00 2.57
1211 1423 2.503375 CACGTCACGGCGTACCTC 60.503 66.667 14.22 2.45 43.83 3.85
1284 1496 4.576463 ACACATGACCAGTCAGAAGAAAAC 59.424 41.667 6.63 0.00 43.61 2.43
1287 1499 3.643320 AGACACATGACCAGTCAGAAGAA 59.357 43.478 6.63 0.00 43.61 2.52
1291 1503 2.597455 TGAGACACATGACCAGTCAGA 58.403 47.619 6.63 0.00 43.61 3.27
1308 1520 7.086376 ACTTTGTTGCTAACTAAATGCATGAG 58.914 34.615 0.00 3.37 36.55 2.90
1425 1658 3.775654 GAGGGGGAGCTCCACGTG 61.776 72.222 33.99 9.08 45.91 4.49
1497 1730 2.898738 CTGGTGCGCATCCTCTCT 59.101 61.111 19.88 0.00 0.00 3.10
1656 1889 1.342074 CCAGGGAGAGTGTTCTGTGA 58.658 55.000 0.00 0.00 32.53 3.58
1690 1923 3.430218 CACGGTAGAGTTGCAAAAGAGAG 59.570 47.826 0.00 0.00 0.00 3.20
1739 1972 5.300752 TGAGACTCTGAACTGAAACAATCC 58.699 41.667 3.68 0.00 0.00 3.01
1742 1975 4.512944 GCATGAGACTCTGAACTGAAACAA 59.487 41.667 3.68 0.00 0.00 2.83
2120 2353 3.366679 CCAAGTCAAGTGTTCATCATGCC 60.367 47.826 0.00 0.00 0.00 4.40
2140 2375 1.705186 GCCCTATAGATTTGGAGCCCA 59.295 52.381 0.00 0.00 0.00 5.36
2141 2376 1.705186 TGCCCTATAGATTTGGAGCCC 59.295 52.381 0.00 0.00 0.00 5.19
2266 2501 5.850614 ACCACCGGCTATTACTACTAATTG 58.149 41.667 0.00 0.00 0.00 2.32
2272 2507 3.806625 TCAACCACCGGCTATTACTAC 57.193 47.619 0.00 0.00 0.00 2.73
2278 2513 1.837439 TCAGAATCAACCACCGGCTAT 59.163 47.619 0.00 0.00 0.00 2.97
2279 2514 1.271856 TCAGAATCAACCACCGGCTA 58.728 50.000 0.00 0.00 0.00 3.93
2281 2516 1.133025 CAATCAGAATCAACCACCGGC 59.867 52.381 0.00 0.00 0.00 6.13
2282 2517 2.710377 TCAATCAGAATCAACCACCGG 58.290 47.619 0.00 0.00 0.00 5.28
2283 2518 3.501828 TGTTCAATCAGAATCAACCACCG 59.498 43.478 0.00 0.00 38.76 4.94
2284 2519 5.644644 GATGTTCAATCAGAATCAACCACC 58.355 41.667 0.00 0.00 38.76 4.61
2285 2520 5.327091 CGATGTTCAATCAGAATCAACCAC 58.673 41.667 0.00 0.00 38.76 4.16
2286 2521 4.395854 CCGATGTTCAATCAGAATCAACCA 59.604 41.667 0.00 0.00 38.76 3.67
2287 2522 4.731773 GCCGATGTTCAATCAGAATCAACC 60.732 45.833 0.00 0.00 38.76 3.77
2288 2523 4.142622 TGCCGATGTTCAATCAGAATCAAC 60.143 41.667 0.00 0.00 38.76 3.18
2289 2524 4.009002 TGCCGATGTTCAATCAGAATCAA 58.991 39.130 0.00 0.00 38.76 2.57
2290 2525 3.608796 TGCCGATGTTCAATCAGAATCA 58.391 40.909 0.00 0.00 38.76 2.57
2291 2526 4.825546 ATGCCGATGTTCAATCAGAATC 57.174 40.909 0.00 0.00 38.76 2.52
2292 2527 9.322773 CTATATATGCCGATGTTCAATCAGAAT 57.677 33.333 0.00 0.00 38.76 2.40
2293 2528 8.531146 TCTATATATGCCGATGTTCAATCAGAA 58.469 33.333 0.00 0.00 0.00 3.02
2294 2529 8.066612 TCTATATATGCCGATGTTCAATCAGA 57.933 34.615 0.00 0.00 0.00 3.27
2295 2530 8.883954 ATCTATATATGCCGATGTTCAATCAG 57.116 34.615 0.00 0.00 0.00 2.90
2296 2531 9.750125 GTATCTATATATGCCGATGTTCAATCA 57.250 33.333 0.00 0.00 0.00 2.57
2297 2532 8.906693 CGTATCTATATATGCCGATGTTCAATC 58.093 37.037 0.00 0.00 0.00 2.67
2298 2533 8.414003 ACGTATCTATATATGCCGATGTTCAAT 58.586 33.333 0.00 0.00 0.00 2.57
2299 2534 7.768240 ACGTATCTATATATGCCGATGTTCAA 58.232 34.615 0.00 0.00 0.00 2.69
2300 2535 7.329588 ACGTATCTATATATGCCGATGTTCA 57.670 36.000 0.00 0.00 0.00 3.18
2301 2536 9.331106 CATACGTATCTATATATGCCGATGTTC 57.669 37.037 4.74 0.00 0.00 3.18
2302 2537 8.847196 ACATACGTATCTATATATGCCGATGTT 58.153 33.333 4.74 0.00 29.76 2.71
2303 2538 8.392372 ACATACGTATCTATATATGCCGATGT 57.608 34.615 4.74 0.00 0.00 3.06
2306 2541 8.501580 GCTTACATACGTATCTATATATGCCGA 58.498 37.037 4.74 0.00 0.00 5.54
2307 2542 8.287503 TGCTTACATACGTATCTATATATGCCG 58.712 37.037 4.74 0.00 0.00 5.69
2308 2543 9.395707 GTGCTTACATACGTATCTATATATGCC 57.604 37.037 4.74 0.42 0.00 4.40
2309 2544 9.946165 TGTGCTTACATACGTATCTATATATGC 57.054 33.333 4.74 7.81 0.00 3.14
2312 2547 9.946165 GCATGTGCTTACATACGTATCTATATA 57.054 33.333 4.74 0.00 38.21 0.86
2313 2548 7.921214 GGCATGTGCTTACATACGTATCTATAT 59.079 37.037 4.74 0.00 41.70 0.86
2314 2549 7.255569 GGCATGTGCTTACATACGTATCTATA 58.744 38.462 4.74 0.00 41.70 1.31
2315 2550 6.100004 GGCATGTGCTTACATACGTATCTAT 58.900 40.000 4.74 0.00 41.70 1.98
2316 2551 5.466819 GGCATGTGCTTACATACGTATCTA 58.533 41.667 4.74 0.00 41.70 1.98
2317 2552 4.307432 GGCATGTGCTTACATACGTATCT 58.693 43.478 4.74 0.00 41.70 1.98
2318 2553 3.121279 CGGCATGTGCTTACATACGTATC 59.879 47.826 4.74 0.00 41.70 2.24
2322 2557 1.257936 GACGGCATGTGCTTACATACG 59.742 52.381 4.84 12.16 41.70 3.06
2327 2562 1.156736 AACAGACGGCATGTGCTTAC 58.843 50.000 4.84 0.00 41.70 2.34
2334 2569 1.081242 GGTGCAAACAGACGGCATG 60.081 57.895 0.00 0.00 40.05 4.06
2473 2717 3.568538 GTGCAACTTTCCATGACATGTC 58.431 45.455 19.27 19.27 0.00 3.06
2493 2737 1.365699 AATAATCAAGGAACGCGCGT 58.634 45.000 32.73 32.73 0.00 6.01
2494 2738 2.452006 AAATAATCAAGGAACGCGCG 57.548 45.000 30.96 30.96 0.00 6.86
2522 2766 7.449704 GCATGAATCAGGGGACTATCTAAAAAT 59.550 37.037 0.00 0.00 40.21 1.82
2527 2771 4.492646 TGCATGAATCAGGGGACTATCTA 58.507 43.478 0.00 0.00 40.21 1.98
2530 2774 3.051581 ACTGCATGAATCAGGGGACTAT 58.948 45.455 0.00 0.00 40.21 2.12
2552 2796 5.034797 GCCCGTGTAAGAATTAAAATGAGC 58.965 41.667 0.00 0.00 28.70 4.26
2556 2800 4.705023 AGCAGCCCGTGTAAGAATTAAAAT 59.295 37.500 0.00 0.00 28.70 1.82
2561 2805 1.003118 TGAGCAGCCCGTGTAAGAATT 59.997 47.619 0.00 0.00 0.00 2.17
2562 2806 0.613260 TGAGCAGCCCGTGTAAGAAT 59.387 50.000 0.00 0.00 0.00 2.40
2571 2816 0.392193 ATCTCAAACTGAGCAGCCCG 60.392 55.000 0.00 0.00 43.95 6.13
2604 2849 4.534500 TGAGGGGTAGCAGAAGTTCAATTA 59.466 41.667 5.50 0.00 0.00 1.40
2891 3136 8.375717 TGTTGCGTTGAAATATTTATCTTTCG 57.624 30.769 0.00 2.75 34.76 3.46
2985 3230 8.821147 ACAACTAGAACACGTGTCAATAAATA 57.179 30.769 23.61 6.47 0.00 1.40
2987 3232 7.278203 TGAACAACTAGAACACGTGTCAATAAA 59.722 33.333 23.61 3.93 0.00 1.40
2994 3239 6.452242 TCATATGAACAACTAGAACACGTGT 58.548 36.000 17.22 17.22 0.00 4.49
3011 3256 3.501828 GCATATGCGGGTGTTTCATATGA 59.498 43.478 12.82 0.00 46.34 2.15
3041 3286 7.138692 ACTCATGAGCAACTTCAAAAGTATC 57.861 36.000 22.83 0.00 41.91 2.24
3045 3290 5.009410 AGGAACTCATGAGCAACTTCAAAAG 59.991 40.000 22.83 0.00 0.00 2.27
3046 3291 4.889409 AGGAACTCATGAGCAACTTCAAAA 59.111 37.500 22.83 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.