Multiple sequence alignment - TraesCS5A01G519800

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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 TraesCS5A01G519800 chr5A 100.000 2489 0 0 1 2489 680977427 680974939 0.000000e+00 4597.0
1 TraesCS5A01G519800 chr5A 77.753 899 125 40 1051 1919 680887564 680886711 1.340000e-132 483.0
2 TraesCS5A01G519800 chr5A 90.850 153 11 3 1975 2127 680886712 680886563 4.200000e-48 202.0
3 TraesCS5A01G519800 chr4D 81.497 1443 173 47 1042 2451 500285939 500284558 0.000000e+00 1099.0
4 TraesCS5A01G519800 chr4D 92.966 327 14 4 1 326 500297636 500297318 3.750000e-128 468.0
5 TraesCS5A01G519800 chr4D 88.014 292 23 8 900 1183 500271331 500271044 3.970000e-88 335.0
6 TraesCS5A01G519800 chr4D 87.770 278 15 10 328 599 500297268 500297004 8.650000e-80 307.0
7 TraesCS5A01G519800 chr4D 86.667 285 20 7 632 911 500292708 500292437 1.450000e-77 300.0
8 TraesCS5A01G519800 chr4D 92.056 214 10 5 903 1110 500292404 500292192 6.730000e-76 294.0
9 TraesCS5A01G519800 chr4D 83.612 299 24 12 628 911 500286421 500286133 8.830000e-65 257.0
10 TraesCS5A01G519800 chr4D 84.583 240 17 8 679 911 500271579 500271353 1.160000e-53 220.0
11 TraesCS5A01G519800 chr4D 87.261 157 15 4 444 599 500286708 500286556 9.150000e-40 174.0
12 TraesCS5A01G519800 chr4D 97.674 43 1 0 595 637 500292831 500292789 9.550000e-10 75.0
13 TraesCS5A01G519800 chr4D 100.000 29 0 0 442 470 500297197 500297169 1.000000e-03 54.7
14 TraesCS5A01G519800 chrUn 90.402 771 64 8 1682 2446 60375115 60375881 0.000000e+00 1005.0
15 TraesCS5A01G519800 chrUn 89.909 773 64 11 1682 2446 60463848 60464614 0.000000e+00 983.0
16 TraesCS5A01G519800 chrUn 84.384 1063 93 36 629 1627 60374063 60375116 0.000000e+00 976.0
17 TraesCS5A01G519800 chrUn 85.734 743 69 13 903 1610 60456902 60457642 0.000000e+00 750.0
18 TraesCS5A01G519800 chrUn 86.634 202 15 5 714 911 60456684 60456877 1.940000e-51 213.0
19 TraesCS5A01G519800 chrUn 93.431 137 9 0 1004 1140 332275199 332275063 1.170000e-48 204.0
20 TraesCS5A01G519800 chrUn 93.431 137 9 0 1004 1140 381972073 381971937 1.170000e-48 204.0
21 TraesCS5A01G519800 chrUn 85.714 161 16 4 444 599 60373769 60373927 1.980000e-36 163.0
22 TraesCS5A01G519800 chrUn 100.000 28 0 0 163 190 473838466 473838493 4.000000e-03 52.8
23 TraesCS5A01G519800 chr4B 89.683 756 64 11 1682 2428 643491443 643490693 0.000000e+00 952.0
24 TraesCS5A01G519800 chr4B 84.953 638 59 15 1027 1627 643492079 643491442 1.640000e-171 612.0
25 TraesCS5A01G519800 chr4B 93.030 330 18 3 1 326 643625971 643625643 6.230000e-131 477.0
26 TraesCS5A01G519800 chr4B 91.165 249 11 6 902 1140 643576168 643575921 6.640000e-86 327.0
27 TraesCS5A01G519800 chr4B 81.338 284 23 12 632 911 643492501 643492244 1.170000e-48 204.0
28 TraesCS5A01G519800 chr4B 84.834 211 10 6 629 837 643625206 643625016 2.530000e-45 193.0
29 TraesCS5A01G519800 chr4B 88.961 154 12 4 448 599 643492790 643492640 4.230000e-43 185.0
30 TraesCS5A01G519800 chr4B 80.625 160 10 9 440 599 643625479 643625341 1.220000e-18 104.0
31 TraesCS5A01G519800 chr6D 100.000 28 0 0 163 190 429815066 429815039 4.000000e-03 52.8
32 TraesCS5A01G519800 chr5D 100.000 28 0 0 163 190 6248074 6248047 4.000000e-03 52.8
33 TraesCS5A01G519800 chr5D 100.000 28 0 0 163 190 329196837 329196864 4.000000e-03 52.8
34 TraesCS5A01G519800 chr1D 100.000 28 0 0 163 190 51826772 51826745 4.000000e-03 52.8
35 TraesCS5A01G519800 chr1D 100.000 28 0 0 163 190 254464608 254464635 4.000000e-03 52.8
36 TraesCS5A01G519800 chr1A 100.000 28 0 0 163 190 554487227 554487254 4.000000e-03 52.8


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 TraesCS5A01G519800 chr5A 680974939 680977427 2488 True 4597.000000 4597 100.000000 1 2489 1 chr5A.!!$R1 2488
1 TraesCS5A01G519800 chr5A 680886563 680887564 1001 True 342.500000 483 84.301500 1051 2127 2 chr5A.!!$R2 1076
2 TraesCS5A01G519800 chr4D 500284558 500286708 2150 True 510.000000 1099 84.123333 444 2451 3 chr4D.!!$R2 2007
3 TraesCS5A01G519800 chr4D 500271044 500271579 535 True 277.500000 335 86.298500 679 1183 2 chr4D.!!$R1 504
4 TraesCS5A01G519800 chr4D 500297004 500297636 632 True 276.566667 468 93.578667 1 599 3 chr4D.!!$R4 598
5 TraesCS5A01G519800 chr4D 500292192 500292831 639 True 223.000000 300 92.132333 595 1110 3 chr4D.!!$R3 515
6 TraesCS5A01G519800 chrUn 60463848 60464614 766 False 983.000000 983 89.909000 1682 2446 1 chrUn.!!$F1 764
7 TraesCS5A01G519800 chrUn 60373769 60375881 2112 False 714.666667 1005 86.833333 444 2446 3 chrUn.!!$F3 2002
8 TraesCS5A01G519800 chrUn 60456684 60457642 958 False 481.500000 750 86.184000 714 1610 2 chrUn.!!$F4 896
9 TraesCS5A01G519800 chr4B 643490693 643492790 2097 True 488.250000 952 86.233750 448 2428 4 chr4B.!!$R2 1980
10 TraesCS5A01G519800 chr4B 643625016 643625971 955 True 258.000000 477 86.163000 1 837 3 chr4B.!!$R3 836

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
669 893 0.320421 CCGATCAACTGTCCGTGGTT 60.32 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 2068 0.89553 GGACCACTCGAACCTCATCA 59.104 55.0 0.0 0.0 0.0 3.07 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
38 39 4.208686 GCGGTACAGGAGCCTCCG 62.209 72.222 4.80 9.97 42.75 4.63
41 42 1.516423 GGTACAGGAGCCTCCGAAC 59.484 63.158 4.80 4.93 42.75 3.95
58 59 4.451096 TCCGAACTCAGTTTGTTATTCAGC 59.549 41.667 3.99 0.00 0.00 4.26
141 142 8.529424 TTAGATAACGACCTCCAAGAAATCTA 57.471 34.615 0.00 0.00 0.00 1.98
193 194 9.725019 ATATAGGTTCGATCAAGATTTGCAATA 57.275 29.630 0.00 0.00 0.00 1.90
203 204 3.624777 AGATTTGCAATACTGTCAGGGG 58.375 45.455 0.00 0.00 0.00 4.79
204 205 2.969821 TTTGCAATACTGTCAGGGGT 57.030 45.000 0.00 0.00 0.00 4.95
205 206 2.489938 TTGCAATACTGTCAGGGGTC 57.510 50.000 4.53 0.00 0.00 4.46
206 207 1.357137 TGCAATACTGTCAGGGGTCA 58.643 50.000 4.53 0.00 0.00 4.02
207 208 1.915489 TGCAATACTGTCAGGGGTCAT 59.085 47.619 4.53 0.00 0.00 3.06
208 209 2.092968 TGCAATACTGTCAGGGGTCATC 60.093 50.000 4.53 0.00 0.00 2.92
233 234 2.044946 GCAAGTTCCTGGCCCGAT 60.045 61.111 0.00 0.00 0.00 4.18
304 309 9.763465 CGTCTAAACGGACAAATTTATAAATGT 57.237 29.630 11.42 7.72 45.21 2.71
326 331 9.829507 AATGTTACAATCCTGATTTTGACAAAA 57.170 25.926 15.39 15.39 33.02 2.44
328 333 9.829507 TGTTACAATCCTGATTTTGACAAAAAT 57.170 25.926 16.85 6.14 46.37 1.82
365 454 2.805099 CAAGTCTTTCAGAGGTGTCAGC 59.195 50.000 0.00 0.00 0.00 4.26
377 466 1.802960 GGTGTCAGCTGTGTTCTCATG 59.197 52.381 14.67 0.00 0.00 3.07
378 467 2.548707 GGTGTCAGCTGTGTTCTCATGA 60.549 50.000 14.67 0.00 0.00 3.07
390 479 7.201522 GCTGTGTTCTCATGATTAACATAACGA 60.202 37.037 20.47 0.00 37.46 3.85
391 480 8.185003 TGTGTTCTCATGATTAACATAACGAG 57.815 34.615 20.47 0.00 37.46 4.18
392 481 7.817478 TGTGTTCTCATGATTAACATAACGAGT 59.183 33.333 20.47 0.00 37.46 4.18
393 482 8.656849 GTGTTCTCATGATTAACATAACGAGTT 58.343 33.333 20.47 0.00 37.46 3.01
394 483 9.214957 TGTTCTCATGATTAACATAACGAGTTT 57.785 29.630 15.97 0.00 37.46 2.66
398 487 9.916397 CTCATGATTAACATAACGAGTTTAACC 57.084 33.333 0.00 0.00 37.46 2.85
399 488 9.661563 TCATGATTAACATAACGAGTTTAACCT 57.338 29.630 0.00 0.00 37.46 3.50
400 489 9.702726 CATGATTAACATAACGAGTTTAACCTG 57.297 33.333 0.00 0.00 37.46 4.00
412 508 1.036707 TTAACCTGCAGGCACCAAAC 58.963 50.000 33.06 0.00 39.32 2.93
505 601 5.304871 GGTAAAACCATGAGTTAAACCCCAA 59.695 40.000 0.00 0.00 37.88 4.12
506 602 5.959583 AAAACCATGAGTTAAACCCCAAA 57.040 34.783 0.00 0.00 37.88 3.28
543 642 9.319143 GATACTCATGTAAATTAGCAACACTCT 57.681 33.333 0.00 0.00 31.80 3.24
548 656 7.661437 TCATGTAAATTAGCAACACTCTGTCTT 59.339 33.333 0.00 0.00 0.00 3.01
549 657 8.935844 CATGTAAATTAGCAACACTCTGTCTTA 58.064 33.333 0.00 0.00 0.00 2.10
550 658 9.672673 ATGTAAATTAGCAACACTCTGTCTTAT 57.327 29.630 0.00 0.00 0.00 1.73
656 877 3.745912 CGAGATCCGTCCCGATCA 58.254 61.111 0.00 0.00 41.03 2.92
662 884 0.460311 ATCCGTCCCGATCAACTGTC 59.540 55.000 0.00 0.00 0.00 3.51
669 893 0.320421 CCGATCAACTGTCCGTGGTT 60.320 55.000 0.00 0.00 0.00 3.67
705 937 3.803778 GGCCACAATTTTTGTCTGAAGTG 59.196 43.478 0.00 0.00 43.23 3.16
731 967 7.432252 GCATATGGTCGTCTTTTTATTCTTTGG 59.568 37.037 4.56 0.00 0.00 3.28
732 968 6.894339 ATGGTCGTCTTTTTATTCTTTGGT 57.106 33.333 0.00 0.00 0.00 3.67
733 969 6.702716 TGGTCGTCTTTTTATTCTTTGGTT 57.297 33.333 0.00 0.00 0.00 3.67
734 970 6.500041 TGGTCGTCTTTTTATTCTTTGGTTG 58.500 36.000 0.00 0.00 0.00 3.77
744 981 0.542333 TCTTTGGTTGACGGGTGTGA 59.458 50.000 0.00 0.00 0.00 3.58
808 1050 1.136305 CCGCGTATTCCTCTCCTTCAA 59.864 52.381 4.92 0.00 0.00 2.69
862 1111 5.849081 GTCATTTTCGCTCGACAATTAAACA 59.151 36.000 1.42 0.00 0.00 2.83
864 1113 4.797693 TTTCGCTCGACAATTAAACACA 57.202 36.364 0.00 0.00 0.00 3.72
865 1114 3.781341 TCGCTCGACAATTAAACACAC 57.219 42.857 0.00 0.00 0.00 3.82
866 1115 2.154198 TCGCTCGACAATTAAACACACG 59.846 45.455 0.00 0.00 0.00 4.49
867 1116 2.097104 CGCTCGACAATTAAACACACGT 60.097 45.455 0.00 0.00 0.00 4.49
875 1124 3.781341 ATTAAACACACGTACGCAGTG 57.219 42.857 28.92 28.92 45.73 3.66
892 1141 1.556911 AGTGCTCGGTGAGATTTGGAT 59.443 47.619 0.00 0.00 0.00 3.41
924 1214 4.377839 TCGACACATCAATCTCCTCTTC 57.622 45.455 0.00 0.00 0.00 2.87
931 1223 5.581479 CACATCAATCTCCTCTTCACAGAAG 59.419 44.000 0.39 0.39 0.00 2.85
1010 1323 0.109153 TGAGGATCAATGGCATCCCG 59.891 55.000 0.00 0.00 45.97 5.14
1106 1443 1.964223 GCAGATTCCTGATCCTACCGA 59.036 52.381 0.00 0.00 43.02 4.69
1116 1453 1.746220 GATCCTACCGATGATCCTCCG 59.254 57.143 0.00 0.00 32.92 4.63
1127 1464 1.749334 GATCCTCCGGCCGATCAAGT 61.749 60.000 30.73 7.76 35.88 3.16
1149 1504 4.083862 GACACTCCACCCGCTCCC 62.084 72.222 0.00 0.00 0.00 4.30
1185 1568 5.067273 TCAGCTACTTATCTACTCTCAGCC 58.933 45.833 0.00 0.00 0.00 4.85
1201 1584 3.756963 CTCAGCCTGCATGCATACATTAT 59.243 43.478 22.97 0.23 32.87 1.28
1202 1585 3.754850 TCAGCCTGCATGCATACATTATC 59.245 43.478 22.97 4.39 32.87 1.75
1206 1589 3.822167 CCTGCATGCATACATTATCCACA 59.178 43.478 22.97 0.00 32.87 4.17
1213 1598 7.327761 GCATGCATACATTATCCACATCTTTTC 59.672 37.037 14.21 0.00 32.87 2.29
1315 1709 1.171308 CCTTGATGGTGCAGTTGAGG 58.829 55.000 0.00 0.00 0.00 3.86
1359 1753 1.756538 CTTGGCAGTTCCACCAGTTTT 59.243 47.619 0.00 0.00 46.55 2.43
1386 1780 5.090757 CGACACAAAATTCATGATCCTGTG 58.909 41.667 18.67 18.67 36.78 3.66
1425 1819 0.678048 AAGGATCACGAAGGCTTGCC 60.678 55.000 3.46 2.97 0.00 4.52
1509 1941 2.615493 GGGTTTCTTCGGATGCTTCTCA 60.615 50.000 0.00 0.00 0.00 3.27
1531 1963 4.343526 CAGCCGAGGCCTTCATCTATATAT 59.656 45.833 6.77 0.00 43.17 0.86
1536 1968 7.472100 GCCGAGGCCTTCATCTATATATAACAT 60.472 40.741 6.77 0.00 34.56 2.71
1580 2013 5.652014 AGAAATATTGTTTCTTCGCCATCCA 59.348 36.000 2.84 0.00 35.39 3.41
1582 2015 2.270352 TTGTTTCTTCGCCATCCAGT 57.730 45.000 0.00 0.00 0.00 4.00
1603 2036 1.678101 CGAAGGAGGAATTCATTGCCC 59.322 52.381 7.93 0.00 28.22 5.36
1620 2053 4.981806 TGCCCAACTTTAGCAATATCAC 57.018 40.909 0.00 0.00 32.56 3.06
1626 2059 6.460123 CCCAACTTTAGCAATATCACCATCAC 60.460 42.308 0.00 0.00 0.00 3.06
1628 2061 5.133221 ACTTTAGCAATATCACCATCACCC 58.867 41.667 0.00 0.00 0.00 4.61
1632 2065 3.716353 AGCAATATCACCATCACCCTGTA 59.284 43.478 0.00 0.00 0.00 2.74
1635 2068 2.270434 ATCACCATCACCCTGTACCT 57.730 50.000 0.00 0.00 0.00 3.08
1642 2075 1.866015 TCACCCTGTACCTGATGAGG 58.134 55.000 0.00 0.00 46.21 3.86
1685 2122 6.721208 CCCGGACTATGGGTTTATAGTACTAA 59.279 42.308 0.73 0.00 42.38 2.24
1749 2188 4.263435 TCATGTGAGCTGCAACATATGAA 58.737 39.130 24.19 14.59 39.99 2.57
1872 2317 7.866898 TGATTGTAAGATTGGTTTGTCAATGTG 59.133 33.333 0.00 0.00 37.47 3.21
1887 2332 4.877823 GTCAATGTGTATTGGATCTCTGCA 59.122 41.667 0.00 0.00 43.11 4.41
1945 2390 8.917088 AGGGGATAATAATGAGAACAATGTTTG 58.083 33.333 0.00 0.00 0.00 2.93
2001 2448 2.111384 GATGAAGTAGACAGAGGGGCA 58.889 52.381 0.00 0.00 0.00 5.36
2022 2469 4.941263 GCAGTATGATTAACCTGGTGACAA 59.059 41.667 0.00 0.00 38.29 3.18
2046 2493 7.526142 AAGAAGATTAAAGAACTTGTTCCCC 57.474 36.000 9.58 0.00 0.00 4.81
2148 2595 5.639506 AGATTTACTCTCAACAATGTGTCCG 59.360 40.000 0.00 0.00 0.00 4.79
2203 2652 1.917872 TTACTTGGGTGTTCATGGGC 58.082 50.000 0.00 0.00 0.00 5.36
2241 2692 7.497909 CGTGGAATATTACCCAAGTGATTTACT 59.502 37.037 0.00 0.00 42.89 2.24
2271 2722 5.215845 TGGGATCTTAGATGTATGGACACA 58.784 41.667 0.00 0.00 38.76 3.72
2277 2728 9.330063 GATCTTAGATGTATGGACACAATGAAA 57.670 33.333 0.00 0.00 38.76 2.69
2306 2758 9.472361 GACGTACAATTATTGGTATGACTATGT 57.528 33.333 9.88 2.62 32.25 2.29
2308 2760 8.221100 CGTACAATTATTGGTATGACTATGTGC 58.779 37.037 9.88 0.00 34.12 4.57
2395 2847 2.926778 ATGGACTAGCAAGATCTGGC 57.073 50.000 14.77 14.77 0.00 4.85
2399 2851 2.035832 GGACTAGCAAGATCTGGCTCTC 59.964 54.545 28.16 21.32 41.41 3.20
2428 2880 0.611896 ATGGTTCCGCTCCAAAAGGG 60.612 55.000 0.00 0.00 38.52 3.95
2446 2898 2.695585 GGGTCTCCCATAAGACAGGAT 58.304 52.381 6.40 0.00 46.15 3.24
2448 2900 3.309296 GGTCTCCCATAAGACAGGATGA 58.691 50.000 6.40 0.00 46.15 2.92
2449 2901 3.323403 GGTCTCCCATAAGACAGGATGAG 59.677 52.174 6.40 0.00 46.15 2.90
2450 2902 3.964031 GTCTCCCATAAGACAGGATGAGT 59.036 47.826 0.00 0.00 44.20 3.41
2451 2903 3.963374 TCTCCCATAAGACAGGATGAGTG 59.037 47.826 0.00 0.00 39.69 3.51
2452 2904 3.708631 CTCCCATAAGACAGGATGAGTGT 59.291 47.826 0.00 0.00 39.69 3.55
2453 2905 3.706594 TCCCATAAGACAGGATGAGTGTC 59.293 47.826 0.00 0.00 44.02 3.67
2457 2909 3.425578 GACAGGATGAGTGTCGGTG 57.574 57.895 0.00 0.00 39.69 4.94
2458 2910 0.888619 GACAGGATGAGTGTCGGTGA 59.111 55.000 0.00 0.00 39.69 4.02
2459 2911 1.478510 GACAGGATGAGTGTCGGTGAT 59.521 52.381 0.00 0.00 39.69 3.06
2460 2912 2.688446 GACAGGATGAGTGTCGGTGATA 59.312 50.000 0.00 0.00 39.69 2.15
2461 2913 3.300388 ACAGGATGAGTGTCGGTGATAT 58.700 45.455 0.00 0.00 39.69 1.63
2462 2914 4.470602 ACAGGATGAGTGTCGGTGATATA 58.529 43.478 0.00 0.00 39.69 0.86
2463 2915 5.080337 ACAGGATGAGTGTCGGTGATATAT 58.920 41.667 0.00 0.00 39.69 0.86
2464 2916 6.246163 ACAGGATGAGTGTCGGTGATATATA 58.754 40.000 0.00 0.00 39.69 0.86
2465 2917 6.719829 ACAGGATGAGTGTCGGTGATATATAA 59.280 38.462 0.00 0.00 39.69 0.98
2466 2918 7.094162 ACAGGATGAGTGTCGGTGATATATAAG 60.094 40.741 0.00 0.00 39.69 1.73
2467 2919 6.948886 AGGATGAGTGTCGGTGATATATAAGT 59.051 38.462 0.00 0.00 0.00 2.24
2468 2920 7.121463 AGGATGAGTGTCGGTGATATATAAGTC 59.879 40.741 0.00 0.00 0.00 3.01
2469 2921 7.094334 GGATGAGTGTCGGTGATATATAAGTCA 60.094 40.741 0.00 0.00 0.00 3.41
2470 2922 7.576861 TGAGTGTCGGTGATATATAAGTCAA 57.423 36.000 0.00 0.00 0.00 3.18
2471 2923 8.002984 TGAGTGTCGGTGATATATAAGTCAAA 57.997 34.615 0.00 0.00 0.00 2.69
2472 2924 8.638873 TGAGTGTCGGTGATATATAAGTCAAAT 58.361 33.333 0.00 0.00 0.00 2.32
2473 2925 9.477484 GAGTGTCGGTGATATATAAGTCAAATT 57.523 33.333 0.00 0.00 0.00 1.82
2476 2928 9.701098 TGTCGGTGATATATAAGTCAAATTACC 57.299 33.333 0.00 0.00 0.00 2.85
2477 2929 9.924650 GTCGGTGATATATAAGTCAAATTACCT 57.075 33.333 0.00 0.00 0.00 3.08
2485 2937 4.772886 AAGTCAAATTACCTATCGGCCT 57.227 40.909 0.00 0.00 0.00 5.19
2486 2938 4.073293 AGTCAAATTACCTATCGGCCTG 57.927 45.455 0.00 0.00 0.00 4.85
2487 2939 2.548480 GTCAAATTACCTATCGGCCTGC 59.452 50.000 0.00 0.00 0.00 4.85
2488 2940 2.438021 TCAAATTACCTATCGGCCTGCT 59.562 45.455 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.082733 GGGGCTGAATAACAAACTGAGTTC 60.083 45.833 0.00 0.00 0.00 3.01
41 42 2.420022 CGGGGCTGAATAACAAACTGAG 59.580 50.000 0.00 0.00 0.00 3.35
58 59 2.373540 TAGAACGAAACATCACGGGG 57.626 50.000 0.00 0.00 0.00 5.73
141 142 0.257039 CTTGTGGGAAGGCTGGCTAT 59.743 55.000 3.41 0.00 0.00 2.97
193 194 2.472029 CTTAGGATGACCCCTGACAGT 58.528 52.381 0.93 0.00 37.10 3.55
203 204 2.680339 GGAACTTGCAGCTTAGGATGAC 59.320 50.000 0.00 0.00 0.00 3.06
204 205 2.573462 AGGAACTTGCAGCTTAGGATGA 59.427 45.455 0.00 0.00 27.25 2.92
205 206 2.681848 CAGGAACTTGCAGCTTAGGATG 59.318 50.000 0.00 0.00 34.60 3.51
206 207 2.356535 CCAGGAACTTGCAGCTTAGGAT 60.357 50.000 0.00 0.00 34.60 3.24
207 208 1.003580 CCAGGAACTTGCAGCTTAGGA 59.996 52.381 0.00 0.00 34.60 2.94
208 209 1.457346 CCAGGAACTTGCAGCTTAGG 58.543 55.000 0.00 0.00 34.60 2.69
233 234 1.340889 GCAATGGGCAGAAGTTGTTGA 59.659 47.619 0.00 0.00 43.97 3.18
299 304 9.829507 TTTGTCAAAATCAGGATTGTAACATTT 57.170 25.926 0.00 0.00 0.00 2.32
326 331 7.823745 AGACTTGTTTCTTGGTATGTTGATT 57.176 32.000 0.00 0.00 0.00 2.57
328 333 7.338196 TGAAAGACTTGTTTCTTGGTATGTTGA 59.662 33.333 1.10 0.00 35.92 3.18
329 334 7.479980 TGAAAGACTTGTTTCTTGGTATGTTG 58.520 34.615 1.10 0.00 35.92 3.33
339 428 5.104259 ACACCTCTGAAAGACTTGTTTCT 57.896 39.130 1.10 0.00 38.67 2.52
365 454 8.185003 TCGTTATGTTAATCATGAGAACACAG 57.815 34.615 21.86 15.14 35.99 3.66
377 466 7.745015 TGCAGGTTAAACTCGTTATGTTAATC 58.255 34.615 0.00 0.00 0.00 1.75
378 467 7.148306 CCTGCAGGTTAAACTCGTTATGTTAAT 60.148 37.037 25.53 0.00 0.00 1.40
390 479 0.184933 TGGTGCCTGCAGGTTAAACT 59.815 50.000 32.81 0.00 37.57 2.66
391 480 1.036707 TTGGTGCCTGCAGGTTAAAC 58.963 50.000 32.81 23.61 37.57 2.01
392 481 1.410882 GTTTGGTGCCTGCAGGTTAAA 59.589 47.619 32.81 23.17 37.57 1.52
393 482 1.036707 GTTTGGTGCCTGCAGGTTAA 58.963 50.000 32.81 19.22 37.57 2.01
394 483 0.825840 GGTTTGGTGCCTGCAGGTTA 60.826 55.000 32.81 20.00 37.57 2.85
396 485 2.521708 GGTTTGGTGCCTGCAGGT 60.522 61.111 32.81 0.00 37.57 4.00
397 486 1.833934 AAGGTTTGGTGCCTGCAGG 60.834 57.895 29.34 29.34 36.30 4.85
398 487 1.108727 TCAAGGTTTGGTGCCTGCAG 61.109 55.000 6.78 6.78 36.30 4.41
399 488 0.685785 TTCAAGGTTTGGTGCCTGCA 60.686 50.000 0.00 0.00 36.30 4.41
400 489 0.681175 ATTCAAGGTTTGGTGCCTGC 59.319 50.000 0.00 0.00 36.30 4.85
412 508 4.155826 TGTTCTAACGATGGCAATTCAAGG 59.844 41.667 0.00 0.00 0.00 3.61
534 633 8.879342 AGTTCATATATAAGACAGAGTGTTGC 57.121 34.615 0.00 0.00 0.00 4.17
543 642 9.961265 CGAGTGGTTAAGTTCATATATAAGACA 57.039 33.333 0.00 0.00 0.00 3.41
548 656 9.304335 TCATCCGAGTGGTTAAGTTCATATATA 57.696 33.333 0.00 0.00 36.30 0.86
549 657 8.190326 TCATCCGAGTGGTTAAGTTCATATAT 57.810 34.615 0.00 0.00 36.30 0.86
550 658 7.255836 CCTCATCCGAGTGGTTAAGTTCATATA 60.256 40.741 0.00 0.00 37.59 0.86
551 659 6.463049 CCTCATCCGAGTGGTTAAGTTCATAT 60.463 42.308 0.00 0.00 37.59 1.78
656 877 1.070289 GGAGAGAAACCACGGACAGTT 59.930 52.381 0.00 0.00 0.00 3.16
662 884 2.434359 GGCGGAGAGAAACCACGG 60.434 66.667 0.00 0.00 0.00 4.94
705 937 7.432252 CCAAAGAATAAAAAGACGACCATATGC 59.568 37.037 0.00 0.00 0.00 3.14
731 967 2.069273 CTTCAGATCACACCCGTCAAC 58.931 52.381 0.00 0.00 0.00 3.18
732 968 1.608025 GCTTCAGATCACACCCGTCAA 60.608 52.381 0.00 0.00 0.00 3.18
733 969 0.037326 GCTTCAGATCACACCCGTCA 60.037 55.000 0.00 0.00 0.00 4.35
734 970 1.078759 CGCTTCAGATCACACCCGTC 61.079 60.000 0.00 0.00 0.00 4.79
744 981 0.174389 ACGATGACTGCGCTTCAGAT 59.826 50.000 9.73 0.00 45.72 2.90
847 1096 3.515071 ACGTGTGTTTAATTGTCGAGC 57.485 42.857 0.00 0.00 0.00 5.03
862 1111 2.428569 CGAGCACTGCGTACGTGT 60.429 61.111 17.90 13.18 34.91 4.49
864 1113 3.667282 ACCGAGCACTGCGTACGT 61.667 61.111 17.90 0.00 0.00 3.57
865 1114 3.172575 CACCGAGCACTGCGTACG 61.173 66.667 11.84 11.84 0.00 3.67
866 1115 1.801913 CTCACCGAGCACTGCGTAC 60.802 63.158 0.00 0.00 0.00 3.67
867 1116 1.313091 ATCTCACCGAGCACTGCGTA 61.313 55.000 0.00 0.00 0.00 4.42
875 1124 7.819900 ACTTATAATATCCAAATCTCACCGAGC 59.180 37.037 0.00 0.00 0.00 5.03
924 1214 4.079970 TCACTAGTGTACCTCCTTCTGTG 58.920 47.826 21.99 0.00 0.00 3.66
931 1223 6.770746 TTAGTTGATCACTAGTGTACCTCC 57.229 41.667 21.99 7.72 39.28 4.30
1010 1323 2.011046 GCTTCATGAGTGACTCCAGCC 61.011 57.143 10.52 0.00 31.37 4.85
1149 1504 3.722147 AGTAGCTGATTGCATACCTTCG 58.278 45.455 0.00 0.00 45.94 3.79
1161 1537 5.710099 GGCTGAGAGTAGATAAGTAGCTGAT 59.290 44.000 0.00 0.00 0.00 2.90
1185 1568 5.414765 AGATGTGGATAATGTATGCATGCAG 59.585 40.000 26.69 0.00 38.77 4.41
1201 1584 1.001393 GGGGGCGAAAAGATGTGGA 60.001 57.895 0.00 0.00 0.00 4.02
1202 1585 3.603365 GGGGGCGAAAAGATGTGG 58.397 61.111 0.00 0.00 0.00 4.17
1225 1619 3.181469 ACGCCACGGATTATTATCACACT 60.181 43.478 0.00 0.00 32.09 3.55
1359 1753 4.635765 GGATCATGAATTTTGTGTCGAGGA 59.364 41.667 0.00 0.00 0.00 3.71
1386 1780 0.676736 CCTGAGAGGAGTAATCGCCC 59.323 60.000 0.00 0.00 37.67 6.13
1509 1941 2.310779 TATAGATGAAGGCCTCGGCT 57.689 50.000 5.23 4.00 41.24 5.52
1559 1992 4.949856 ACTGGATGGCGAAGAAACAATATT 59.050 37.500 0.00 0.00 0.00 1.28
1574 2007 1.195115 TTCCTCCTTCGACTGGATGG 58.805 55.000 6.78 9.98 40.49 3.51
1580 2013 3.274288 GCAATGAATTCCTCCTTCGACT 58.726 45.455 2.27 0.00 0.00 4.18
1582 2015 2.643551 GGCAATGAATTCCTCCTTCGA 58.356 47.619 2.27 0.00 0.00 3.71
1603 2036 6.460123 GGGTGATGGTGATATTGCTAAAGTTG 60.460 42.308 0.00 0.00 0.00 3.16
1620 2053 2.103771 CTCATCAGGTACAGGGTGATGG 59.896 54.545 18.84 10.86 45.13 3.51
1635 2068 0.895530 GGACCACTCGAACCTCATCA 59.104 55.000 0.00 0.00 0.00 3.07
1642 2075 1.292541 GAGGTGGGACCACTCGAAC 59.707 63.158 19.94 4.23 45.52 3.95
1715 2152 6.991531 TGCAGCTCACATGATGTATACATAAA 59.008 34.615 18.28 10.34 36.57 1.40
1716 2153 6.523840 TGCAGCTCACATGATGTATACATAA 58.476 36.000 18.28 11.93 36.57 1.90
1728 2167 4.625972 TTCATATGTTGCAGCTCACATG 57.374 40.909 16.95 10.61 0.00 3.21
1872 2317 6.488683 AGACTAGTAGTGCAGAGATCCAATAC 59.511 42.308 7.76 0.00 33.95 1.89
1966 2411 9.640963 GTCTACTTCATCTAATACACACTGTTT 57.359 33.333 0.00 0.00 0.00 2.83
1971 2418 8.132362 CCTCTGTCTACTTCATCTAATACACAC 58.868 40.741 0.00 0.00 0.00 3.82
2001 2448 7.016153 TCTTTGTCACCAGGTTAATCATACT 57.984 36.000 0.00 0.00 0.00 2.12
2022 2469 7.298374 AGGGGAACAAGTTCTTTAATCTTCTT 58.702 34.615 12.22 0.00 39.45 2.52
2046 2493 4.504858 ACGAGCCAAGAAAGTATACCAAG 58.495 43.478 0.00 0.00 0.00 3.61
2148 2595 5.803020 ACCGAGAACTGCAATAAGAATTC 57.197 39.130 0.00 0.00 0.00 2.17
2203 2652 7.298122 GGTAATATTCCACGTTATGCAGAATG 58.702 38.462 11.67 11.67 40.87 2.67
2213 2662 5.168647 TCACTTGGGTAATATTCCACGTT 57.831 39.130 3.37 0.00 33.97 3.99
2221 2672 8.107095 ACACACAGTAAATCACTTGGGTAATAT 58.893 33.333 0.00 0.00 34.26 1.28
2241 2692 4.908601 ACATCTAAGATCCCAACACACA 57.091 40.909 0.00 0.00 0.00 3.72
2271 2722 7.981142 ACCAATAATTGTACGTCGATTTCATT 58.019 30.769 0.00 0.00 32.85 2.57
2277 2728 7.431249 AGTCATACCAATAATTGTACGTCGAT 58.569 34.615 0.00 0.00 0.00 3.59
2306 2758 2.583024 TTGATCAACCCAGTGATGCA 57.417 45.000 3.38 0.00 38.38 3.96
2308 2760 6.947644 TGATATTTGATCAACCCAGTGATG 57.052 37.500 7.89 0.00 38.38 3.07
2391 2843 2.806818 CCATCATGAATTCGAGAGCCAG 59.193 50.000 0.00 0.00 0.00 4.85
2395 2847 3.492383 CGGAACCATCATGAATTCGAGAG 59.508 47.826 0.00 0.00 0.00 3.20
2399 2851 1.942657 AGCGGAACCATCATGAATTCG 59.057 47.619 0.00 0.00 0.00 3.34
2428 2880 3.964031 ACTCATCCTGTCTTATGGGAGAC 59.036 47.826 0.00 0.00 44.97 3.36
2446 2898 7.576861 TTGACTTATATATCACCGACACTCA 57.423 36.000 0.00 0.00 0.00 3.41
2450 2902 9.701098 GGTAATTTGACTTATATATCACCGACA 57.299 33.333 0.00 0.00 0.00 4.35
2451 2903 9.924650 AGGTAATTTGACTTATATATCACCGAC 57.075 33.333 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.