Multiple sequence alignment - TraesCS5D01G504500

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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 TraesCS5D01G504500 chr5D 100.000 2756 0 0 1 2756 530853187 530850432 0.000000e+00 5090.0
1 TraesCS5D01G504500 chr5D 83.650 263 31 8 1561 1820 530839546 530839293 1.280000e-58 237.0
2 TraesCS5D01G504500 chr5D 88.601 193 20 2 618 808 530840540 530840348 1.650000e-57 233.0
3 TraesCS5D01G504500 chr5D 91.057 123 10 1 1152 1273 530839777 530839655 6.110000e-37 165.0
4 TraesCS5D01G504500 chr5D 91.176 68 6 0 1410 1477 530839646 530839579 2.920000e-15 93.5
5 TraesCS5D01G504500 chr5D 88.406 69 5 2 205 270 474811227 474811295 2.280000e-11 80.5
6 TraesCS5D01G504500 chr4A 86.117 1880 135 55 1 1815 641415836 641417654 0.000000e+00 1910.0
7 TraesCS5D01G504500 chr4A 83.196 363 33 13 1422 1781 641425611 641425948 9.590000e-80 307.0
8 TraesCS5D01G504500 chr4A 85.632 174 18 5 1821 1988 641417711 641417883 2.820000e-40 176.0
9 TraesCS5D01G504500 chr5B 86.477 1686 124 40 1 1646 670083421 670081800 0.000000e+00 1755.0
10 TraesCS5D01G504500 chr5B 84.010 838 69 31 959 1778 670099301 670098511 0.000000e+00 745.0
11 TraesCS5D01G504500 chr5B 86.500 600 51 14 324 911 670099886 670099305 1.390000e-177 632.0
12 TraesCS5D01G504500 chr5B 91.537 449 11 2 1583 2004 670081722 670081274 6.570000e-166 593.0
13 TraesCS5D01G504500 chr5B 95.238 147 4 2 1 144 670100125 670099979 2.130000e-56 230.0
14 TraesCS5D01G504500 chr5B 93.590 78 2 3 1762 1836 670098498 670098421 2.240000e-21 113.0
15 TraesCS5D01G504500 chr5B 94.444 54 3 0 1410 1463 670081063 670081010 1.760000e-12 84.2
16 TraesCS5D01G504500 chr5B 84.146 82 13 0 220 301 491865687 491865606 2.280000e-11 80.5
17 TraesCS5D01G504500 chr2A 92.265 543 42 0 2214 2756 749526092 749525550 0.000000e+00 771.0
18 TraesCS5D01G504500 chr2A 91.344 543 47 0 2214 2756 532077928 532077386 0.000000e+00 743.0
19 TraesCS5D01G504500 chr2A 82.353 85 15 0 217 301 707030630 707030546 1.060000e-09 75.0
20 TraesCS5D01G504500 chr5A 92.265 543 41 1 2214 2756 654559550 654559009 0.000000e+00 769.0
21 TraesCS5D01G504500 chr5A 90.323 62 6 0 220 281 368176418 368176479 6.330000e-12 82.4
22 TraesCS5D01G504500 chr5A 82.927 82 14 0 220 301 698461557 698461476 1.060000e-09 75.0
23 TraesCS5D01G504500 chr3A 91.897 543 44 0 2214 2756 581627753 581628295 0.000000e+00 760.0
24 TraesCS5D01G504500 chr3B 89.687 543 54 2 2214 2756 694177921 694178461 0.000000e+00 691.0
25 TraesCS5D01G504500 chr3B 89.134 543 58 1 2214 2756 576019475 576020016 0.000000e+00 675.0
26 TraesCS5D01G504500 chr3B 84.337 83 9 1 219 301 594555771 594555849 8.180000e-11 78.7
27 TraesCS5D01G504500 chr4B 88.483 547 56 7 2214 2756 428486675 428487218 0.000000e+00 654.0
28 TraesCS5D01G504500 chr6D 88.029 543 63 2 2214 2756 97771634 97771094 2.310000e-180 641.0
29 TraesCS5D01G504500 chr2B 87.684 544 63 4 2214 2756 349932884 349932344 5.010000e-177 630.0
30 TraesCS5D01G504500 chr2B 90.164 122 12 0 1152 1273 784764883 784765004 2.840000e-35 159.0
31 TraesCS5D01G504500 chr1A 80.583 103 16 2 203 301 524275740 524275638 2.940000e-10 76.8


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 TraesCS5D01G504500 chr5D 530850432 530853187 2755 True 5090.000000 5090 100.000000 1 2756 1 chr5D.!!$R1 2755
1 TraesCS5D01G504500 chr4A 641415836 641417883 2047 False 1043.000000 1910 85.874500 1 1988 2 chr4A.!!$F2 1987
2 TraesCS5D01G504500 chr5B 670081010 670083421 2411 True 810.733333 1755 90.819333 1 2004 3 chr5B.!!$R2 2003
3 TraesCS5D01G504500 chr5B 670098421 670100125 1704 True 430.000000 745 89.834500 1 1836 4 chr5B.!!$R3 1835
4 TraesCS5D01G504500 chr2A 749525550 749526092 542 True 771.000000 771 92.265000 2214 2756 1 chr2A.!!$R3 542
5 TraesCS5D01G504500 chr2A 532077386 532077928 542 True 743.000000 743 91.344000 2214 2756 1 chr2A.!!$R1 542
6 TraesCS5D01G504500 chr5A 654559009 654559550 541 True 769.000000 769 92.265000 2214 2756 1 chr5A.!!$R1 542
7 TraesCS5D01G504500 chr3A 581627753 581628295 542 False 760.000000 760 91.897000 2214 2756 1 chr3A.!!$F1 542
8 TraesCS5D01G504500 chr3B 694177921 694178461 540 False 691.000000 691 89.687000 2214 2756 1 chr3B.!!$F3 542
9 TraesCS5D01G504500 chr3B 576019475 576020016 541 False 675.000000 675 89.134000 2214 2756 1 chr3B.!!$F1 542
10 TraesCS5D01G504500 chr4B 428486675 428487218 543 False 654.000000 654 88.483000 2214 2756 1 chr4B.!!$F1 542
11 TraesCS5D01G504500 chr6D 97771094 97771634 540 True 641.000000 641 88.029000 2214 2756 1 chr6D.!!$R1 542
12 TraesCS5D01G504500 chr2B 349932344 349932884 540 True 630.000000 630 87.684000 2214 2756 1 chr2B.!!$R1 542

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
581 619 0.974383 ATCCCCTCTGTTTTCGTCGT 59.026 50.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2451 0.459585 TCGAGCTCAAATACACCCGC 60.46 55.0 15.4 0.0 0.0 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
190 196 3.500680 GCCTTCCGTCATTTTGAGTGTTA 59.499 43.478 0.00 0.00 0.00 2.41
201 207 8.011106 GTCATTTTGAGTGTTATGCCATTTTTG 58.989 33.333 0.00 0.00 0.00 2.44
270 279 3.460857 AAGATCTCGGCGCTAGAAATT 57.539 42.857 15.25 10.74 0.00 1.82
274 283 4.745620 AGATCTCGGCGCTAGAAATTTAAC 59.254 41.667 15.25 4.21 0.00 2.01
276 285 1.928503 TCGGCGCTAGAAATTTAACGG 59.071 47.619 7.64 0.00 0.00 4.44
281 290 4.201881 GGCGCTAGAAATTTAACGGTGAAT 60.202 41.667 7.64 0.00 0.00 2.57
306 315 9.730420 ATACAATTAATAATTTGGACGTCTTGC 57.270 29.630 16.46 0.00 0.00 4.01
314 323 1.371558 GGACGTCTTGCTCAAGGGT 59.628 57.895 16.46 8.02 38.88 4.34
321 351 4.036380 ACGTCTTGCTCAAGGGTTAAAAAG 59.964 41.667 9.48 0.00 38.88 2.27
372 404 3.128589 ACGGGTTGTGATAAATGATGCAC 59.871 43.478 0.00 0.00 0.00 4.57
408 440 4.096732 GCAGTGGCGAAATGAAAGTAAT 57.903 40.909 0.00 0.00 0.00 1.89
485 517 2.052782 ACTTCGGGTGAAAGCTTGTT 57.947 45.000 0.00 0.00 32.66 2.83
581 619 0.974383 ATCCCCTCTGTTTTCGTCGT 59.026 50.000 0.00 0.00 0.00 4.34
582 620 1.619654 TCCCCTCTGTTTTCGTCGTA 58.380 50.000 0.00 0.00 0.00 3.43
583 621 2.173519 TCCCCTCTGTTTTCGTCGTAT 58.826 47.619 0.00 0.00 0.00 3.06
584 622 3.355378 TCCCCTCTGTTTTCGTCGTATA 58.645 45.455 0.00 0.00 0.00 1.47
605 647 3.037249 GTTCGTGCCGCGGTAACA 61.037 61.111 28.70 13.99 41.72 2.41
672 714 2.025898 TGCCGATAACGATGACCTACA 58.974 47.619 0.00 0.00 42.66 2.74
679 721 5.122554 CGATAACGATGACCTACAGCTCTAT 59.877 44.000 0.00 0.00 42.66 1.98
689 731 3.754323 CCTACAGCTCTATTAGAGACCGG 59.246 52.174 22.23 0.00 45.07 5.28
718 760 1.380524 GAACAGGACGATCGAGAGGA 58.619 55.000 24.34 0.00 0.00 3.71
723 765 1.134068 AGGACGATCGAGAGGATGACA 60.134 52.381 24.34 0.00 34.82 3.58
726 768 1.064208 ACGATCGAGAGGATGACAACG 59.936 52.381 24.34 0.00 34.82 4.10
729 771 3.549019 CGATCGAGAGGATGACAACGAAT 60.549 47.826 10.26 0.00 34.82 3.34
825 875 1.225827 GCGACGACGATGTGTACGA 60.226 57.895 12.29 0.00 42.66 3.43
912 963 1.592669 CCGCTGAGGCTTATCACCG 60.593 63.158 0.00 0.00 36.09 4.94
945 996 1.300931 ACTCGTGTGCATGCTCGTT 60.301 52.632 20.33 9.63 0.00 3.85
947 998 2.174107 CGTGTGCATGCTCGTTGG 59.826 61.111 20.33 2.24 0.00 3.77
951 1002 1.207593 GTGCATGCTCGTTGGTCAC 59.792 57.895 20.33 0.83 0.00 3.67
987 1039 7.386851 TCTTTCCAGATAAAGATCGAGTTTGT 58.613 34.615 5.93 0.00 39.86 2.83
996 1048 3.589988 AGATCGAGTTTGTTGCTAGGTG 58.410 45.455 0.00 0.00 0.00 4.00
1082 1145 0.604243 GCCGTGTACAACCATCCACA 60.604 55.000 0.00 0.00 0.00 4.17
1100 1163 3.119065 CCACAATCCATAGTGCATGCAAA 60.119 43.478 24.58 14.49 34.48 3.68
1132 1195 7.031226 TGCAAGATTCATAATTAGCCTTGTC 57.969 36.000 0.00 0.00 33.94 3.18
1144 1217 1.322442 GCCTTGTCTTATGGCATCCC 58.678 55.000 1.65 0.00 46.20 3.85
1195 1268 1.901085 GTCGCTGACCAAGGAGGAT 59.099 57.895 0.00 0.00 41.22 3.24
1296 1369 2.576847 CCGCGTACGTAACCGGTC 60.577 66.667 19.73 0.00 37.24 4.79
1328 1405 2.324477 CGTCGGATTTGCATCGGC 59.676 61.111 0.00 0.00 41.68 5.54
1347 1424 3.681594 CGGCCTCCTTAATCAAGCTTGTA 60.682 47.826 25.19 12.97 0.00 2.41
1540 1624 2.179018 GCCGCGACTGGTACGTAA 59.821 61.111 8.23 0.00 0.00 3.18
1542 1626 1.864750 CCGCGACTGGTACGTAACG 60.865 63.158 8.23 3.60 0.00 3.18
1588 1807 6.127810 TGAGCTTCTTGATTTCATACATGC 57.872 37.500 0.00 0.00 0.00 4.06
1636 1859 2.295070 TGGGTACATGTATCGATCACGG 59.705 50.000 9.18 0.00 40.21 4.94
1901 2235 3.758023 TGGCATGTCACTTTCTGTATTGG 59.242 43.478 0.00 0.00 0.00 3.16
1986 2320 8.293867 TCAGATAGTACCAAAAACAAAATTCGG 58.706 33.333 0.00 0.00 0.00 4.30
2004 2338 3.950397 TCGGGACTAAAACAAGATGCAT 58.050 40.909 0.00 0.00 0.00 3.96
2005 2339 4.331968 TCGGGACTAAAACAAGATGCATT 58.668 39.130 0.00 0.00 0.00 3.56
2006 2340 4.764823 TCGGGACTAAAACAAGATGCATTT 59.235 37.500 0.00 0.00 0.00 2.32
2007 2341 5.242838 TCGGGACTAAAACAAGATGCATTTT 59.757 36.000 0.00 0.00 0.00 1.82
2008 2342 5.345741 CGGGACTAAAACAAGATGCATTTTG 59.654 40.000 24.20 24.20 0.00 2.44
2009 2343 5.639082 GGGACTAAAACAAGATGCATTTTGG 59.361 40.000 27.82 16.56 32.05 3.28
2010 2344 6.454795 GGACTAAAACAAGATGCATTTTGGA 58.545 36.000 27.82 13.01 30.78 3.53
2011 2345 6.587608 GGACTAAAACAAGATGCATTTTGGAG 59.412 38.462 27.82 20.98 30.78 3.86
2012 2346 5.928264 ACTAAAACAAGATGCATTTTGGAGC 59.072 36.000 27.82 3.26 30.78 4.70
2013 2347 4.339872 AAACAAGATGCATTTTGGAGCA 57.660 36.364 27.82 0.00 45.92 4.26
2046 2380 5.755409 TTTACACACACCTCTATGGATGT 57.245 39.130 0.00 0.00 38.54 3.06
2047 2381 5.755409 TTACACACACCTCTATGGATGTT 57.245 39.130 0.00 0.00 36.85 2.71
2049 2383 5.344743 ACACACACCTCTATGGATGTTAG 57.655 43.478 0.00 0.00 36.85 2.34
2051 2385 5.483937 ACACACACCTCTATGGATGTTAGAA 59.516 40.000 0.00 0.00 36.85 2.10
2052 2386 6.013725 ACACACACCTCTATGGATGTTAGAAA 60.014 38.462 0.00 0.00 36.85 2.52
2053 2387 6.313905 CACACACCTCTATGGATGTTAGAAAC 59.686 42.308 0.00 0.00 36.85 2.78
2054 2388 6.213600 ACACACCTCTATGGATGTTAGAAACT 59.786 38.462 0.00 0.00 35.99 2.66
2055 2389 7.106239 CACACCTCTATGGATGTTAGAAACTT 58.894 38.462 0.00 0.00 39.71 2.66
2056 2390 7.065085 CACACCTCTATGGATGTTAGAAACTTG 59.935 40.741 0.00 0.00 39.71 3.16
2057 2391 7.106239 CACCTCTATGGATGTTAGAAACTTGT 58.894 38.462 0.00 0.00 39.71 3.16
2058 2392 7.607991 CACCTCTATGGATGTTAGAAACTTGTT 59.392 37.037 0.00 0.00 39.71 2.83
2060 2394 7.824289 CCTCTATGGATGTTAGAAACTTGTTGA 59.176 37.037 0.00 0.00 38.35 3.18
2061 2395 9.388506 CTCTATGGATGTTAGAAACTTGTTGAT 57.611 33.333 0.00 0.00 0.00 2.57
2062 2396 9.166173 TCTATGGATGTTAGAAACTTGTTGATG 57.834 33.333 0.00 0.00 0.00 3.07
2063 2397 7.765695 ATGGATGTTAGAAACTTGTTGATGT 57.234 32.000 0.00 0.00 0.00 3.06
2064 2398 7.581213 TGGATGTTAGAAACTTGTTGATGTT 57.419 32.000 0.00 0.00 0.00 2.71
2065 2399 7.424803 TGGATGTTAGAAACTTGTTGATGTTG 58.575 34.615 0.00 0.00 0.00 3.33
2066 2400 7.284261 TGGATGTTAGAAACTTGTTGATGTTGA 59.716 33.333 0.00 0.00 0.00 3.18
2067 2401 8.299570 GGATGTTAGAAACTTGTTGATGTTGAT 58.700 33.333 0.00 0.00 0.00 2.57
2068 2402 9.334693 GATGTTAGAAACTTGTTGATGTTGATC 57.665 33.333 0.00 0.00 0.00 2.92
2069 2403 7.648142 TGTTAGAAACTTGTTGATGTTGATCC 58.352 34.615 0.00 0.00 0.00 3.36
2070 2404 7.284261 TGTTAGAAACTTGTTGATGTTGATCCA 59.716 33.333 0.00 0.00 0.00 3.41
2071 2405 6.076981 AGAAACTTGTTGATGTTGATCCAC 57.923 37.500 0.00 0.00 0.00 4.02
2073 2407 5.850557 AACTTGTTGATGTTGATCCACAA 57.149 34.783 3.42 0.00 40.29 3.33
2074 2408 5.850557 ACTTGTTGATGTTGATCCACAAA 57.149 34.783 3.42 0.00 41.35 2.83
2076 2410 6.638610 ACTTGTTGATGTTGATCCACAAAAA 58.361 32.000 3.42 0.00 41.35 1.94
2119 2453 9.430838 CTTTATTCAGAATTTACTCTTCATGCG 57.569 33.333 0.00 0.00 0.00 4.73
2120 2454 5.801350 TTCAGAATTTACTCTTCATGCGG 57.199 39.130 0.00 0.00 0.00 5.69
2121 2455 4.191544 TCAGAATTTACTCTTCATGCGGG 58.808 43.478 0.00 0.00 0.00 6.13
2122 2456 3.941483 CAGAATTTACTCTTCATGCGGGT 59.059 43.478 0.00 0.00 0.00 5.28
2123 2457 3.941483 AGAATTTACTCTTCATGCGGGTG 59.059 43.478 0.00 0.00 0.00 4.61
2124 2458 2.851263 TTTACTCTTCATGCGGGTGT 57.149 45.000 0.00 0.00 0.00 4.16
2125 2459 3.965379 TTTACTCTTCATGCGGGTGTA 57.035 42.857 0.00 0.00 0.00 2.90
2126 2460 4.481368 TTTACTCTTCATGCGGGTGTAT 57.519 40.909 0.00 0.00 0.00 2.29
2127 2461 4.481368 TTACTCTTCATGCGGGTGTATT 57.519 40.909 0.00 0.00 0.00 1.89
2128 2462 3.350219 ACTCTTCATGCGGGTGTATTT 57.650 42.857 0.00 0.00 0.00 1.40
2129 2463 3.009723 ACTCTTCATGCGGGTGTATTTG 58.990 45.455 0.00 0.00 0.00 2.32
2130 2464 3.270027 CTCTTCATGCGGGTGTATTTGA 58.730 45.455 0.00 0.00 0.00 2.69
2131 2465 3.270027 TCTTCATGCGGGTGTATTTGAG 58.730 45.455 0.00 0.00 0.00 3.02
2132 2466 1.378531 TCATGCGGGTGTATTTGAGC 58.621 50.000 0.00 0.00 0.00 4.26
2133 2467 1.065491 TCATGCGGGTGTATTTGAGCT 60.065 47.619 0.00 0.00 0.00 4.09
2134 2468 1.331756 CATGCGGGTGTATTTGAGCTC 59.668 52.381 6.82 6.82 0.00 4.09
2135 2469 0.739462 TGCGGGTGTATTTGAGCTCG 60.739 55.000 9.64 0.00 0.00 5.03
2136 2470 0.459585 GCGGGTGTATTTGAGCTCGA 60.460 55.000 9.64 3.88 0.00 4.04
2137 2471 1.560923 CGGGTGTATTTGAGCTCGAG 58.439 55.000 8.45 8.45 0.00 4.04
2138 2472 1.134367 CGGGTGTATTTGAGCTCGAGA 59.866 52.381 18.75 0.00 0.00 4.04
2139 2473 2.223829 CGGGTGTATTTGAGCTCGAGAT 60.224 50.000 18.75 10.84 0.00 2.75
2140 2474 3.738281 CGGGTGTATTTGAGCTCGAGATT 60.738 47.826 18.75 2.53 0.00 2.40
2141 2475 4.499188 CGGGTGTATTTGAGCTCGAGATTA 60.499 45.833 18.75 3.00 0.00 1.75
2142 2476 4.985409 GGGTGTATTTGAGCTCGAGATTAG 59.015 45.833 18.75 0.00 0.00 1.73
2143 2477 5.221263 GGGTGTATTTGAGCTCGAGATTAGA 60.221 44.000 18.75 1.47 0.00 2.10
2144 2478 6.273825 GGTGTATTTGAGCTCGAGATTAGAA 58.726 40.000 18.75 6.70 0.00 2.10
2145 2479 6.419413 GGTGTATTTGAGCTCGAGATTAGAAG 59.581 42.308 18.75 0.00 0.00 2.85
2146 2480 7.197017 GTGTATTTGAGCTCGAGATTAGAAGA 58.803 38.462 18.75 0.66 0.00 2.87
2147 2481 7.865385 GTGTATTTGAGCTCGAGATTAGAAGAT 59.135 37.037 18.75 2.64 0.00 2.40
2148 2482 8.079203 TGTATTTGAGCTCGAGATTAGAAGATC 58.921 37.037 18.75 0.00 0.00 2.75
2149 2483 6.456795 TTTGAGCTCGAGATTAGAAGATCA 57.543 37.500 18.75 0.00 0.00 2.92
2150 2484 5.431420 TGAGCTCGAGATTAGAAGATCAC 57.569 43.478 18.75 0.00 0.00 3.06
2151 2485 5.129634 TGAGCTCGAGATTAGAAGATCACT 58.870 41.667 18.75 0.00 0.00 3.41
2152 2486 5.592282 TGAGCTCGAGATTAGAAGATCACTT 59.408 40.000 18.75 0.00 39.24 3.16
2166 2500 7.787725 GAAGATCACTTCCGTTAATAATGGT 57.212 36.000 10.74 0.00 44.60 3.55
2167 2501 8.882415 GAAGATCACTTCCGTTAATAATGGTA 57.118 34.615 10.74 1.14 44.60 3.25
2174 2508 9.367444 CACTTCCGTTAATAATGGTATCTATCC 57.633 37.037 10.74 0.00 38.73 2.59
2178 2512 9.042450 TCCGTTAATAATGGTATCTATCCATGT 57.958 33.333 10.74 0.00 43.85 3.21
2194 2528 3.447229 TCCATGTAGCTCGTTTCATGAGA 59.553 43.478 13.42 0.00 39.68 3.27
2206 2540 2.455674 TCATGAGAAACCGGTCACTG 57.544 50.000 8.04 0.05 0.00 3.66
2209 2543 1.116308 TGAGAAACCGGTCACTGACA 58.884 50.000 8.04 2.98 33.68 3.58
2212 2546 2.940410 GAGAAACCGGTCACTGACAAAA 59.060 45.455 8.04 0.00 33.68 2.44
2334 2668 0.965363 ATTGGACGGTGTTGCCCATC 60.965 55.000 0.00 0.00 0.00 3.51
2534 2873 0.251121 TGTTGGATCGGCACATTGGT 60.251 50.000 0.00 0.00 0.00 3.67
2574 2913 1.876156 CTCTGTTGGGAGCTTTGTGTC 59.124 52.381 0.00 0.00 0.00 3.67
2649 2997 3.497031 GGTCCTTTGCGGCGCTAC 61.497 66.667 33.26 20.52 0.00 3.58
2704 3052 4.679372 GCTTCTCTTAGATCGGAGCAAGTT 60.679 45.833 0.00 0.00 0.00 2.66
2736 3084 1.597461 GCCACTTCCTCTTAGGCGT 59.403 57.895 0.00 0.00 34.61 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 182 7.714377 ACAAAAATGGCATAACACTCAAAATGA 59.286 29.630 0.00 0.00 0.00 2.57
249 258 2.961526 TTTCTAGCGCCGAGATCTTT 57.038 45.000 2.29 0.00 0.00 2.52
258 267 2.674357 TCACCGTTAAATTTCTAGCGCC 59.326 45.455 2.29 0.00 0.00 6.53
274 283 9.165014 CGTCCAAATTATTAATTGTATTCACCG 57.835 33.333 2.48 0.00 0.00 4.94
281 290 8.952278 AGCAAGACGTCCAAATTATTAATTGTA 58.048 29.630 13.01 0.00 0.00 2.41
372 404 1.657594 CACTGCTGATAAGTGACGCAG 59.342 52.381 7.90 7.90 46.55 5.18
485 517 1.217916 TGAAAACAGAGGGGGTGTCA 58.782 50.000 0.00 0.00 0.00 3.58
553 587 2.030027 ACAGAGGGGATGTCACAAGA 57.970 50.000 0.00 0.00 0.00 3.02
605 647 2.158559 TGCACTGCATTCCGTACATTT 58.841 42.857 0.00 0.00 31.71 2.32
697 739 0.028242 CTCTCGATCGTCCTGTTCGG 59.972 60.000 15.94 0.00 39.65 4.30
699 741 1.380524 TCCTCTCGATCGTCCTGTTC 58.619 55.000 15.94 0.00 0.00 3.18
700 742 1.678627 CATCCTCTCGATCGTCCTGTT 59.321 52.381 15.94 0.00 0.00 3.16
701 743 1.134068 TCATCCTCTCGATCGTCCTGT 60.134 52.381 15.94 0.00 0.00 4.00
702 744 1.265635 GTCATCCTCTCGATCGTCCTG 59.734 57.143 15.94 5.87 0.00 3.86
703 745 1.134068 TGTCATCCTCTCGATCGTCCT 60.134 52.381 15.94 0.00 0.00 3.85
705 747 2.722071 GTTGTCATCCTCTCGATCGTC 58.278 52.381 15.94 0.00 0.00 4.20
706 748 1.064208 CGTTGTCATCCTCTCGATCGT 59.936 52.381 15.94 0.00 0.00 3.73
718 760 1.369091 GCGGCTCCATTCGTTGTCAT 61.369 55.000 0.00 0.00 0.00 3.06
723 765 3.118454 CGTGCGGCTCCATTCGTT 61.118 61.111 0.00 0.00 0.00 3.85
726 768 1.887242 TATGCGTGCGGCTCCATTC 60.887 57.895 0.00 0.00 44.05 2.67
933 984 1.207593 GTGACCAACGAGCATGCAC 59.792 57.895 21.98 13.43 0.00 4.57
945 996 5.765677 TGGAAAGATGAAATTAACGTGACCA 59.234 36.000 0.00 0.00 0.00 4.02
947 998 7.129109 TCTGGAAAGATGAAATTAACGTGAC 57.871 36.000 0.00 0.00 0.00 3.67
987 1039 1.699634 GAGCCCATATCCACCTAGCAA 59.300 52.381 0.00 0.00 0.00 3.91
996 1048 1.065564 GCCATGAGAGAGCCCATATCC 60.066 57.143 0.00 0.00 0.00 2.59
1082 1145 5.353938 GTGAATTTGCATGCACTATGGATT 58.646 37.500 22.58 13.11 36.12 3.01
1100 1163 7.645340 GCTAATTATGAATCTTGCAACGTGAAT 59.355 33.333 0.00 0.00 0.00 2.57
1132 1195 5.121811 GCATACATAGAGGGATGCCATAAG 58.878 45.833 5.86 0.00 39.00 1.73
1144 1217 8.352752 TCATAAAACGAACTGCATACATAGAG 57.647 34.615 0.00 0.00 0.00 2.43
1195 1268 1.920325 CCTCCAGAAGGCCTCCACA 60.920 63.158 5.23 0.00 38.67 4.17
1328 1405 7.630242 TTTGATACAAGCTTGATTAAGGAGG 57.370 36.000 32.50 2.31 34.40 4.30
1540 1624 7.067496 TGCTACTATACTAGGTAAGGTACGT 57.933 40.000 0.00 0.00 0.00 3.57
1542 1626 9.165035 CTCATGCTACTATACTAGGTAAGGTAC 57.835 40.741 0.00 0.00 0.00 3.34
1545 1629 7.090953 GCTCATGCTACTATACTAGGTAAGG 57.909 44.000 0.00 0.00 36.03 2.69
1577 1756 8.393671 TGCTATGAATATGTGCATGTATGAAA 57.606 30.769 0.00 0.00 0.00 2.69
1588 1807 5.890424 TCCATGCATGCTATGAATATGTG 57.110 39.130 21.69 2.87 0.00 3.21
1617 1836 3.562505 GTCCGTGATCGATACATGTACC 58.437 50.000 7.96 0.00 39.71 3.34
1636 1859 2.260869 ATGCACACAACCAGCCGTC 61.261 57.895 0.00 0.00 0.00 4.79
1743 1972 1.752358 ATGATGATCAGACGGCGGCT 61.752 55.000 10.88 10.88 0.00 5.52
1901 2235 1.009829 CTCCAAGGTTACATGAGCGC 58.990 55.000 0.00 0.00 0.00 5.92
1986 2320 6.454795 TCCAAAATGCATCTTGTTTTAGTCC 58.545 36.000 11.67 0.00 0.00 3.85
2022 2356 6.539173 ACATCCATAGAGGTGTGTGTAAAAA 58.461 36.000 0.00 0.00 35.24 1.94
2024 2358 5.755409 ACATCCATAGAGGTGTGTGTAAA 57.245 39.130 0.00 0.00 35.24 2.01
2025 2359 5.755409 AACATCCATAGAGGTGTGTGTAA 57.245 39.130 0.00 0.00 37.04 2.41
2026 2360 6.192044 TCTAACATCCATAGAGGTGTGTGTA 58.808 40.000 0.00 0.00 37.04 2.90
2027 2361 5.023452 TCTAACATCCATAGAGGTGTGTGT 58.977 41.667 0.00 0.00 37.04 3.72
2028 2362 5.598416 TCTAACATCCATAGAGGTGTGTG 57.402 43.478 0.00 0.00 37.04 3.82
2029 2363 6.213600 AGTTTCTAACATCCATAGAGGTGTGT 59.786 38.462 0.00 0.00 37.04 3.72
2032 2366 7.106239 ACAAGTTTCTAACATCCATAGAGGTG 58.894 38.462 0.00 0.00 37.04 4.00
2033 2367 7.259088 ACAAGTTTCTAACATCCATAGAGGT 57.741 36.000 0.00 0.00 39.08 3.85
2035 2369 8.777865 TCAACAAGTTTCTAACATCCATAGAG 57.222 34.615 0.00 0.00 31.41 2.43
2036 2370 9.166173 CATCAACAAGTTTCTAACATCCATAGA 57.834 33.333 0.00 0.00 0.00 1.98
2037 2371 8.950210 ACATCAACAAGTTTCTAACATCCATAG 58.050 33.333 0.00 0.00 0.00 2.23
2039 2373 7.765695 ACATCAACAAGTTTCTAACATCCAT 57.234 32.000 0.00 0.00 0.00 3.41
2040 2374 7.284261 TCAACATCAACAAGTTTCTAACATCCA 59.716 33.333 0.00 0.00 0.00 3.41
2041 2375 7.648142 TCAACATCAACAAGTTTCTAACATCC 58.352 34.615 0.00 0.00 0.00 3.51
2042 2376 9.334693 GATCAACATCAACAAGTTTCTAACATC 57.665 33.333 0.00 0.00 0.00 3.06
2043 2377 8.299570 GGATCAACATCAACAAGTTTCTAACAT 58.700 33.333 0.00 0.00 0.00 2.71
2044 2378 7.284261 TGGATCAACATCAACAAGTTTCTAACA 59.716 33.333 0.00 0.00 0.00 2.41
2045 2379 7.591426 GTGGATCAACATCAACAAGTTTCTAAC 59.409 37.037 0.00 0.00 33.48 2.34
2046 2380 7.284261 TGTGGATCAACATCAACAAGTTTCTAA 59.716 33.333 0.00 0.00 39.66 2.10
2047 2381 6.770303 TGTGGATCAACATCAACAAGTTTCTA 59.230 34.615 0.00 0.00 39.66 2.10
2049 2383 5.830912 TGTGGATCAACATCAACAAGTTTC 58.169 37.500 0.00 0.00 39.66 2.78
2051 2385 5.850557 TTGTGGATCAACATCAACAAGTT 57.149 34.783 3.10 0.00 44.83 2.66
2093 2427 9.430838 CGCATGAAGAGTAAATTCTGAATAAAG 57.569 33.333 2.85 0.00 0.00 1.85
2094 2428 8.397906 CCGCATGAAGAGTAAATTCTGAATAAA 58.602 33.333 2.85 0.00 0.00 1.40
2095 2429 7.012327 CCCGCATGAAGAGTAAATTCTGAATAA 59.988 37.037 2.85 0.00 0.00 1.40
2096 2430 6.483307 CCCGCATGAAGAGTAAATTCTGAATA 59.517 38.462 2.85 0.00 0.00 1.75
2097 2431 5.297776 CCCGCATGAAGAGTAAATTCTGAAT 59.702 40.000 0.00 0.00 0.00 2.57
2098 2432 4.635765 CCCGCATGAAGAGTAAATTCTGAA 59.364 41.667 0.00 0.00 0.00 3.02
2099 2433 4.191544 CCCGCATGAAGAGTAAATTCTGA 58.808 43.478 0.00 0.00 0.00 3.27
2100 2434 3.941483 ACCCGCATGAAGAGTAAATTCTG 59.059 43.478 0.00 0.00 0.00 3.02
2101 2435 3.941483 CACCCGCATGAAGAGTAAATTCT 59.059 43.478 0.00 0.00 0.00 2.40
2102 2436 3.689649 ACACCCGCATGAAGAGTAAATTC 59.310 43.478 0.00 0.00 0.00 2.17
2103 2437 3.686016 ACACCCGCATGAAGAGTAAATT 58.314 40.909 0.00 0.00 0.00 1.82
2104 2438 3.350219 ACACCCGCATGAAGAGTAAAT 57.650 42.857 0.00 0.00 0.00 1.40
2105 2439 2.851263 ACACCCGCATGAAGAGTAAA 57.149 45.000 0.00 0.00 0.00 2.01
2106 2440 4.481368 AATACACCCGCATGAAGAGTAA 57.519 40.909 0.00 0.00 0.00 2.24
2107 2441 4.081365 TCAAATACACCCGCATGAAGAGTA 60.081 41.667 0.00 0.00 0.00 2.59
2108 2442 3.009723 CAAATACACCCGCATGAAGAGT 58.990 45.455 0.00 0.00 0.00 3.24
2109 2443 3.270027 TCAAATACACCCGCATGAAGAG 58.730 45.455 0.00 0.00 0.00 2.85
2110 2444 3.270027 CTCAAATACACCCGCATGAAGA 58.730 45.455 0.00 0.00 0.00 2.87
2111 2445 2.223340 GCTCAAATACACCCGCATGAAG 60.223 50.000 0.00 0.00 0.00 3.02
2112 2446 1.742831 GCTCAAATACACCCGCATGAA 59.257 47.619 0.00 0.00 0.00 2.57
2113 2447 1.065491 AGCTCAAATACACCCGCATGA 60.065 47.619 0.00 0.00 0.00 3.07
2114 2448 1.331756 GAGCTCAAATACACCCGCATG 59.668 52.381 9.40 0.00 0.00 4.06
2115 2449 1.668419 GAGCTCAAATACACCCGCAT 58.332 50.000 9.40 0.00 0.00 4.73
2116 2450 0.739462 CGAGCTCAAATACACCCGCA 60.739 55.000 15.40 0.00 0.00 5.69
2117 2451 0.459585 TCGAGCTCAAATACACCCGC 60.460 55.000 15.40 0.00 0.00 6.13
2118 2452 1.134367 TCTCGAGCTCAAATACACCCG 59.866 52.381 15.40 0.00 0.00 5.28
2119 2453 2.961526 TCTCGAGCTCAAATACACCC 57.038 50.000 15.40 0.00 0.00 4.61
2120 2454 5.833082 TCTAATCTCGAGCTCAAATACACC 58.167 41.667 15.40 0.00 0.00 4.16
2121 2455 7.197017 TCTTCTAATCTCGAGCTCAAATACAC 58.803 38.462 15.40 0.00 0.00 2.90
2122 2456 7.334844 TCTTCTAATCTCGAGCTCAAATACA 57.665 36.000 15.40 0.00 0.00 2.29
2123 2457 8.079203 TGATCTTCTAATCTCGAGCTCAAATAC 58.921 37.037 15.40 0.00 0.00 1.89
2124 2458 8.079203 GTGATCTTCTAATCTCGAGCTCAAATA 58.921 37.037 15.40 0.00 0.00 1.40
2125 2459 6.922957 GTGATCTTCTAATCTCGAGCTCAAAT 59.077 38.462 15.40 0.33 0.00 2.32
2126 2460 6.096141 AGTGATCTTCTAATCTCGAGCTCAAA 59.904 38.462 15.40 0.00 0.00 2.69
2127 2461 5.592282 AGTGATCTTCTAATCTCGAGCTCAA 59.408 40.000 15.40 0.00 0.00 3.02
2128 2462 5.129634 AGTGATCTTCTAATCTCGAGCTCA 58.870 41.667 15.40 0.00 0.00 4.26
2129 2463 5.689383 AGTGATCTTCTAATCTCGAGCTC 57.311 43.478 7.81 2.73 0.00 4.09
2130 2464 5.009610 GGAAGTGATCTTCTAATCTCGAGCT 59.990 44.000 7.81 0.00 46.47 4.09
2131 2465 5.219633 GGAAGTGATCTTCTAATCTCGAGC 58.780 45.833 7.81 0.00 46.47 5.03
2132 2466 5.008217 ACGGAAGTGATCTTCTAATCTCGAG 59.992 44.000 5.93 5.93 46.47 4.04
2133 2467 4.882427 ACGGAAGTGATCTTCTAATCTCGA 59.118 41.667 7.69 0.00 46.47 4.04
2134 2468 5.176407 ACGGAAGTGATCTTCTAATCTCG 57.824 43.478 7.69 4.83 46.47 4.04
2149 2483 9.096823 TGGATAGATACCATTATTAACGGAAGT 57.903 33.333 0.00 0.00 38.15 3.01
2151 2485 9.884636 CATGGATAGATACCATTATTAACGGAA 57.115 33.333 0.00 0.00 44.51 4.30
2152 2486 9.042450 ACATGGATAGATACCATTATTAACGGA 57.958 33.333 0.00 0.00 44.51 4.69
2158 2492 8.417106 CGAGCTACATGGATAGATACCATTATT 58.583 37.037 0.00 0.00 44.51 1.40
2159 2493 7.561722 ACGAGCTACATGGATAGATACCATTAT 59.438 37.037 0.00 0.00 44.51 1.28
2160 2494 6.890268 ACGAGCTACATGGATAGATACCATTA 59.110 38.462 0.00 0.00 44.51 1.90
2161 2495 5.717178 ACGAGCTACATGGATAGATACCATT 59.283 40.000 0.00 0.00 44.51 3.16
2163 2497 4.663334 ACGAGCTACATGGATAGATACCA 58.337 43.478 0.00 0.00 41.83 3.25
2164 2498 5.646577 AACGAGCTACATGGATAGATACC 57.353 43.478 0.00 0.00 0.00 2.73
2165 2499 6.678878 TGAAACGAGCTACATGGATAGATAC 58.321 40.000 0.00 0.00 0.00 2.24
2166 2500 6.894339 TGAAACGAGCTACATGGATAGATA 57.106 37.500 0.00 0.00 0.00 1.98
2167 2501 5.791336 TGAAACGAGCTACATGGATAGAT 57.209 39.130 0.00 0.00 0.00 1.98
2173 2507 3.785486 TCTCATGAAACGAGCTACATGG 58.215 45.455 0.00 0.00 40.00 3.66
2174 2508 5.784750 TTTCTCATGAAACGAGCTACATG 57.215 39.130 0.00 0.00 37.27 3.21
2194 2528 3.181480 CCAATTTTGTCAGTGACCGGTTT 60.181 43.478 20.43 6.78 0.00 3.27
2202 2536 1.066908 ACCGCACCAATTTTGTCAGTG 59.933 47.619 0.00 0.00 0.00 3.66
2203 2537 1.066908 CACCGCACCAATTTTGTCAGT 59.933 47.619 0.00 0.00 0.00 3.41
2206 2540 0.943835 GCCACCGCACCAATTTTGTC 60.944 55.000 0.00 0.00 34.03 3.18
2209 2543 2.740438 GGCCACCGCACCAATTTT 59.260 55.556 0.00 0.00 36.38 1.82
2234 2568 3.136123 CCGGCTGCATGACCAAGG 61.136 66.667 0.50 0.00 0.00 3.61
2334 2668 0.742281 CATCACCACGCCTCCTGAAG 60.742 60.000 0.00 0.00 0.00 3.02
2358 2695 0.652592 AAGATTTTCATCCGCGCGAG 59.347 50.000 34.63 21.63 0.00 5.03
2427 2764 2.358247 GGCGACGCCTCCAAGAAA 60.358 61.111 31.30 0.00 46.69 2.52
2574 2913 2.412591 AGGACCCAACCATATCTCCAG 58.587 52.381 0.00 0.00 0.00 3.86
2624 2963 0.250295 CCGCAAAGGACCAACAGAGA 60.250 55.000 0.00 0.00 45.00 3.10
2704 3052 1.228245 GTGGCAAGTGGAAGGCAGA 60.228 57.895 0.00 0.00 41.21 4.26
2736 3084 0.037326 GACGCACCATCCACTCTGAA 60.037 55.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.