Multiple sequence alignment - TraesCS6A01G398400

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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 TraesCS6A01G398400 chr6A 100.000 2756 0 0 1 2756 609108591 609105836 0.000000e+00 5090.0
1 TraesCS6A01G398400 chr6D 85.540 2137 145 81 716 2756 462273386 462271318 0.000000e+00 2084.0
2 TraesCS6A01G398400 chr6D 80.607 593 21 25 41 590 462273926 462273385 3.350000e-99 372.0
3 TraesCS6A01G398400 chr6D 88.281 128 15 0 588 715 295604183 295604310 1.320000e-33 154.0
4 TraesCS6A01G398400 chr6B 87.458 1475 94 41 712 2122 704751007 704752454 0.000000e+00 1615.0
5 TraesCS6A01G398400 chr6B 90.134 598 29 7 2177 2752 704752457 704753046 0.000000e+00 750.0
6 TraesCS6A01G398400 chr6B 92.500 200 12 3 163 359 704743032 704743231 1.620000e-72 283.0
7 TraesCS6A01G398400 chr6B 80.156 257 21 12 360 590 704750758 704751010 6.110000e-37 165.0
8 TraesCS6A01G398400 chr6B 86.567 134 18 0 586 719 55561882 55561749 6.150000e-32 148.0
9 TraesCS6A01G398400 chr6B 86.567 134 18 0 586 719 607980139 607980272 6.150000e-32 148.0
10 TraesCS6A01G398400 chr4D 87.407 270 34 0 1040 1309 478999194 478998925 7.410000e-81 311.0
11 TraesCS6A01G398400 chr4D 83.333 282 44 3 1028 1308 382737997 382738276 9.790000e-65 257.0
12 TraesCS6A01G398400 chr4B 87.085 271 35 0 1039 1309 605693090 605692820 9.590000e-80 307.0
13 TraesCS6A01G398400 chr4B 88.060 134 16 0 586 719 483398903 483399036 2.840000e-35 159.0
14 TraesCS6A01G398400 chr4B 87.313 134 17 0 586 719 446222069 446222202 1.320000e-33 154.0
15 TraesCS6A01G398400 chr4B 76.894 264 48 12 1043 1301 77651297 77651552 1.330000e-28 137.0
16 TraesCS6A01G398400 chr4A 83.688 282 43 3 1028 1308 64956707 64956986 2.100000e-66 263.0
17 TraesCS6A01G398400 chr1B 87.027 185 15 6 2565 2748 654917092 654916916 1.670000e-47 200.0
18 TraesCS6A01G398400 chr1B 87.313 134 17 0 586 719 271366867 271367000 1.320000e-33 154.0
19 TraesCS6A01G398400 chr1B 74.216 287 45 23 1038 1311 475470116 475469846 2.920000e-15 93.5
20 TraesCS6A01G398400 chr2B 88.406 138 13 3 583 718 75678640 75678776 2.200000e-36 163.0
21 TraesCS6A01G398400 chr2D 88.462 130 15 0 586 715 351287794 351287923 1.020000e-34 158.0
22 TraesCS6A01G398400 chr7B 85.926 135 19 0 584 718 742402687 742402553 7.950000e-31 145.0
23 TraesCS6A01G398400 chr1D 73.868 287 46 23 1038 1311 353557691 353557421 1.360000e-13 87.9


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 TraesCS6A01G398400 chr6A 609105836 609108591 2755 True 5090.000000 5090 100.0000 1 2756 1 chr6A.!!$R1 2755
1 TraesCS6A01G398400 chr6D 462271318 462273926 2608 True 1228.000000 2084 83.0735 41 2756 2 chr6D.!!$R1 2715
2 TraesCS6A01G398400 chr6B 704750758 704753046 2288 False 843.333333 1615 85.9160 360 2752 3 chr6B.!!$F3 2392

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
554 602 0.171903 AGCAGCGCCATGAACATTTC 59.828 50.0 2.29 0.0 0.0 2.17 F
556 604 0.179129 CAGCGCCATGAACATTTCCC 60.179 55.0 2.29 0.0 0.0 3.97 F
1396 1514 0.322816 TCAATCAGCTGGCCACTTCC 60.323 55.0 15.13 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 1517 0.249955 TCATCAGCTTGCGTCCATGA 59.750 50.000 0.00 0.0 0.00 3.07 R
1431 1549 0.947244 GGATCGCCACCTGCAATAAG 59.053 55.000 0.00 0.0 41.33 1.73 R
2458 2656 1.002900 CAAACTTGCGCCGAAAAGAGA 60.003 47.619 11.71 0.0 0.00 3.10 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
17 18 2.696893 AGATACAGAGGCCGGGGT 59.303 61.111 2.18 0.00 0.00 4.95
18 19 1.457831 AGATACAGAGGCCGGGGTC 60.458 63.158 2.18 0.00 0.00 4.46
19 20 1.760875 GATACAGAGGCCGGGGTCA 60.761 63.158 2.18 0.00 0.00 4.02
20 21 1.074471 ATACAGAGGCCGGGGTCAT 60.074 57.895 2.18 0.00 0.00 3.06
21 22 1.122019 ATACAGAGGCCGGGGTCATC 61.122 60.000 2.18 0.00 0.00 2.92
22 23 3.866582 CAGAGGCCGGGGTCATCC 61.867 72.222 2.18 0.00 0.00 3.51
23 24 4.095400 AGAGGCCGGGGTCATCCT 62.095 66.667 2.18 0.00 35.33 3.24
24 25 3.551407 GAGGCCGGGGTCATCCTC 61.551 72.222 2.18 5.59 38.40 3.71
27 28 3.171388 GCCGGGGTCATCCTCCAT 61.171 66.667 2.18 0.00 35.33 3.41
28 29 2.757124 GCCGGGGTCATCCTCCATT 61.757 63.158 2.18 0.00 35.33 3.16
29 30 1.922821 CCGGGGTCATCCTCCATTT 59.077 57.895 0.00 0.00 35.33 2.32
30 31 0.179018 CCGGGGTCATCCTCCATTTC 60.179 60.000 0.00 0.00 35.33 2.17
31 32 0.839946 CGGGGTCATCCTCCATTTCT 59.160 55.000 0.00 0.00 35.33 2.52
32 33 2.047061 CGGGGTCATCCTCCATTTCTA 58.953 52.381 0.00 0.00 35.33 2.10
33 34 2.438021 CGGGGTCATCCTCCATTTCTAA 59.562 50.000 0.00 0.00 35.33 2.10
34 35 3.744530 CGGGGTCATCCTCCATTTCTAAC 60.745 52.174 0.00 0.00 35.33 2.34
35 36 3.202151 GGGGTCATCCTCCATTTCTAACA 59.798 47.826 0.00 0.00 35.33 2.41
36 37 4.325030 GGGGTCATCCTCCATTTCTAACAA 60.325 45.833 0.00 0.00 35.33 2.83
37 38 5.261216 GGGTCATCCTCCATTTCTAACAAA 58.739 41.667 0.00 0.00 0.00 2.83
38 39 5.714806 GGGTCATCCTCCATTTCTAACAAAA 59.285 40.000 0.00 0.00 0.00 2.44
39 40 6.210584 GGGTCATCCTCCATTTCTAACAAAAA 59.789 38.462 0.00 0.00 0.00 1.94
98 99 6.985188 GTGCTATACACTGATTGGAAGAAA 57.015 37.500 0.00 0.00 46.41 2.52
139 140 1.043673 GGGAGGAGCGGTGTCACTAT 61.044 60.000 2.35 0.00 0.00 2.12
140 141 0.386113 GGAGGAGCGGTGTCACTATC 59.614 60.000 2.35 0.00 0.00 2.08
141 142 1.103803 GAGGAGCGGTGTCACTATCA 58.896 55.000 2.35 0.00 0.00 2.15
142 143 1.066303 GAGGAGCGGTGTCACTATCAG 59.934 57.143 2.35 0.00 0.00 2.90
143 144 0.818296 GGAGCGGTGTCACTATCAGT 59.182 55.000 2.35 0.00 0.00 3.41
171 172 3.550275 CGTAGCAGTATTTGTATGCACGT 59.450 43.478 0.00 0.00 42.45 4.49
253 270 2.120909 CCATTCGGCGGGAAATGCT 61.121 57.895 7.21 0.00 38.36 3.79
278 295 5.158141 TCTTTATCCATCTGTCTATGCCCT 58.842 41.667 0.00 0.00 0.00 5.19
307 324 4.054455 CACGTACGTGCGCACACC 62.054 66.667 37.03 23.03 44.40 4.16
354 376 1.358877 TTCAGATGCGATGTTGACCG 58.641 50.000 0.00 0.00 0.00 4.79
355 377 0.460109 TCAGATGCGATGTTGACCGG 60.460 55.000 0.00 0.00 0.00 5.28
356 378 1.815421 AGATGCGATGTTGACCGGC 60.815 57.895 0.00 0.00 0.00 6.13
357 379 2.823829 GATGCGATGTTGACCGGCC 61.824 63.158 0.00 0.00 0.00 6.13
358 380 3.620419 ATGCGATGTTGACCGGCCA 62.620 57.895 0.00 0.00 0.00 5.36
361 383 3.799755 GATGTTGACCGGCCACGC 61.800 66.667 0.00 0.00 39.22 5.34
404 426 2.156310 CCTTTGTACGTACGTTTCAGCC 59.844 50.000 27.92 8.36 0.00 4.85
416 438 0.250901 TTTCAGCCTCTCCTGCAACC 60.251 55.000 0.00 0.00 32.87 3.77
421 443 1.904032 CCTCTCCTGCAACCCTCTC 59.096 63.158 0.00 0.00 0.00 3.20
480 509 5.021458 ACAAAGATGGGATGAGAAGCATTT 58.979 37.500 0.00 0.00 37.34 2.32
488 517 5.481122 TGGGATGAGAAGCATTTTCATTTCA 59.519 36.000 0.00 0.00 37.34 2.69
503 532 2.980317 TTTCACATGCACGCACGCAC 62.980 55.000 0.00 0.00 46.56 5.34
527 571 3.133464 CGCATTCCACATGCCCGT 61.133 61.111 0.00 0.00 41.71 5.28
547 595 2.036571 CAGTTGAGCAGCGCCATGA 61.037 57.895 2.29 0.00 0.00 3.07
554 602 0.171903 AGCAGCGCCATGAACATTTC 59.828 50.000 2.29 0.00 0.00 2.17
556 604 0.179129 CAGCGCCATGAACATTTCCC 60.179 55.000 2.29 0.00 0.00 3.97
597 648 8.803397 ATTGGTTGTAAATTAGTACTCCTTCC 57.197 34.615 0.00 0.00 0.00 3.46
598 649 6.400568 TGGTTGTAAATTAGTACTCCTTCCG 58.599 40.000 0.00 0.00 0.00 4.30
599 650 6.014327 TGGTTGTAAATTAGTACTCCTTCCGT 60.014 38.462 0.00 0.00 0.00 4.69
600 651 6.875726 GGTTGTAAATTAGTACTCCTTCCGTT 59.124 38.462 0.00 0.00 0.00 4.44
601 652 7.063898 GGTTGTAAATTAGTACTCCTTCCGTTC 59.936 40.741 0.00 0.00 0.00 3.95
602 653 7.472334 TGTAAATTAGTACTCCTTCCGTTCT 57.528 36.000 0.00 0.00 0.00 3.01
603 654 8.579850 TGTAAATTAGTACTCCTTCCGTTCTA 57.420 34.615 0.00 0.00 0.00 2.10
604 655 9.023962 TGTAAATTAGTACTCCTTCCGTTCTAA 57.976 33.333 0.00 0.00 31.75 2.10
605 656 9.860898 GTAAATTAGTACTCCTTCCGTTCTAAA 57.139 33.333 0.00 0.00 31.24 1.85
607 658 9.955102 AAATTAGTACTCCTTCCGTTCTAAAAT 57.045 29.630 0.00 0.00 31.24 1.82
608 659 9.955102 AATTAGTACTCCTTCCGTTCTAAAATT 57.045 29.630 0.00 0.00 31.24 1.82
609 660 8.992835 TTAGTACTCCTTCCGTTCTAAAATTC 57.007 34.615 0.00 0.00 0.00 2.17
610 661 7.242322 AGTACTCCTTCCGTTCTAAAATTCT 57.758 36.000 0.00 0.00 0.00 2.40
611 662 7.677892 AGTACTCCTTCCGTTCTAAAATTCTT 58.322 34.615 0.00 0.00 0.00 2.52
612 663 6.803154 ACTCCTTCCGTTCTAAAATTCTTG 57.197 37.500 0.00 0.00 0.00 3.02
613 664 6.296803 ACTCCTTCCGTTCTAAAATTCTTGT 58.703 36.000 0.00 0.00 0.00 3.16
614 665 6.427242 ACTCCTTCCGTTCTAAAATTCTTGTC 59.573 38.462 0.00 0.00 0.00 3.18
615 666 6.531021 TCCTTCCGTTCTAAAATTCTTGTCT 58.469 36.000 0.00 0.00 0.00 3.41
616 667 6.996282 TCCTTCCGTTCTAAAATTCTTGTCTT 59.004 34.615 0.00 0.00 0.00 3.01
617 668 8.152246 TCCTTCCGTTCTAAAATTCTTGTCTTA 58.848 33.333 0.00 0.00 0.00 2.10
618 669 8.443937 CCTTCCGTTCTAAAATTCTTGTCTTAG 58.556 37.037 0.00 0.00 0.00 2.18
619 670 9.204570 CTTCCGTTCTAAAATTCTTGTCTTAGA 57.795 33.333 0.00 0.00 0.00 2.10
620 671 9.720769 TTCCGTTCTAAAATTCTTGTCTTAGAT 57.279 29.630 0.00 0.00 32.07 1.98
621 672 9.720769 TCCGTTCTAAAATTCTTGTCTTAGATT 57.279 29.630 0.00 0.00 32.07 2.40
654 705 9.692749 AATACGGATGTATCTAACACTACAATG 57.307 33.333 0.00 0.00 42.09 2.82
655 706 7.108841 ACGGATGTATCTAACACTACAATGT 57.891 36.000 0.00 0.00 42.09 2.71
656 707 8.229253 ACGGATGTATCTAACACTACAATGTA 57.771 34.615 0.00 0.00 42.09 2.29
657 708 8.689061 ACGGATGTATCTAACACTACAATGTAA 58.311 33.333 0.00 0.00 42.09 2.41
658 709 9.692749 CGGATGTATCTAACACTACAATGTAAT 57.307 33.333 0.00 0.00 42.09 1.89
710 761 6.683974 AGACAAGAATTTTGATACGGATGG 57.316 37.500 0.00 0.00 0.00 3.51
758 809 1.006832 CGGGCTCCTTGTATTCAACG 58.993 55.000 0.00 0.00 0.00 4.10
860 927 2.046314 CTTCGCCACCGTCCCATT 60.046 61.111 0.00 0.00 35.54 3.16
864 931 4.815108 GCCACCGTCCCATTCCCC 62.815 72.222 0.00 0.00 0.00 4.81
865 932 4.483243 CCACCGTCCCATTCCCCG 62.483 72.222 0.00 0.00 0.00 5.73
896 966 3.519913 CCAGCTCCCCTCTATAAATACCC 59.480 52.174 0.00 0.00 0.00 3.69
1281 1384 4.771356 GTCTACGGCTGCGTCGCA 62.771 66.667 20.44 20.44 32.11 5.10
1313 1416 4.767255 CCAGCAGCAGGTCCGTCC 62.767 72.222 0.00 0.00 0.00 4.79
1375 1489 1.676529 GATCACTCCTTCGGTCGATCA 59.323 52.381 0.00 0.00 31.64 2.92
1377 1491 2.100197 TCACTCCTTCGGTCGATCAAT 58.900 47.619 0.00 0.00 0.00 2.57
1384 1502 3.492383 CCTTCGGTCGATCAATCAATCAG 59.508 47.826 0.00 0.00 0.00 2.90
1391 1509 2.304092 GATCAATCAATCAGCTGGCCA 58.696 47.619 15.13 4.71 0.00 5.36
1393 1511 1.005097 TCAATCAATCAGCTGGCCACT 59.995 47.619 15.13 0.75 0.00 4.00
1394 1512 1.822990 CAATCAATCAGCTGGCCACTT 59.177 47.619 15.13 0.00 0.00 3.16
1395 1513 1.760192 ATCAATCAGCTGGCCACTTC 58.240 50.000 15.13 0.00 0.00 3.01
1396 1514 0.322816 TCAATCAGCTGGCCACTTCC 60.323 55.000 15.13 0.00 0.00 3.46
1397 1515 1.000396 AATCAGCTGGCCACTTCCC 60.000 57.895 15.13 0.00 0.00 3.97
1398 1516 2.826777 AATCAGCTGGCCACTTCCCG 62.827 60.000 15.13 0.00 0.00 5.14
1399 1517 4.335647 CAGCTGGCCACTTCCCGT 62.336 66.667 0.00 0.00 0.00 5.28
1422 1540 1.469703 TGGACGCAAGCTGATGATTTG 59.530 47.619 0.00 0.00 45.62 2.32
1423 1541 1.739466 GGACGCAAGCTGATGATTTGA 59.261 47.619 0.00 0.00 45.62 2.69
1424 1542 2.357009 GGACGCAAGCTGATGATTTGAT 59.643 45.455 0.00 0.00 45.62 2.57
1425 1543 3.181493 GGACGCAAGCTGATGATTTGATT 60.181 43.478 0.00 0.00 45.62 2.57
1426 1544 4.418392 GACGCAAGCTGATGATTTGATTT 58.582 39.130 0.00 0.00 45.62 2.17
1431 1549 5.220416 GCAAGCTGATGATTTGATTTCTTGC 60.220 40.000 7.26 7.26 44.23 4.01
1434 1552 7.400599 AGCTGATGATTTGATTTCTTGCTTA 57.599 32.000 0.00 0.00 0.00 3.09
1820 1951 0.963225 TCCAACAACCTCATCGACGA 59.037 50.000 0.00 0.00 0.00 4.20
1821 1952 1.548719 TCCAACAACCTCATCGACGAT 59.451 47.619 4.05 4.05 0.00 3.73
1822 1953 1.927174 CCAACAACCTCATCGACGATC 59.073 52.381 7.54 0.00 0.00 3.69
1823 1954 2.417379 CCAACAACCTCATCGACGATCT 60.417 50.000 7.54 0.00 0.00 2.75
1843 1978 0.464870 ATCAGAGTGCTGCTAGCTGG 59.535 55.000 21.46 12.77 42.97 4.85
1856 1991 0.172578 TAGCTGGTGGAATCGTGTCG 59.827 55.000 0.00 0.00 0.00 4.35
1857 1992 2.100631 GCTGGTGGAATCGTGTCGG 61.101 63.158 0.00 0.00 0.00 4.79
1858 1993 2.047655 TGGTGGAATCGTGTCGGC 60.048 61.111 0.00 0.00 0.00 5.54
1890 2027 0.452184 TCGAGCTAGAAGAACGCAGG 59.548 55.000 0.00 0.00 0.00 4.85
1891 2028 0.452184 CGAGCTAGAAGAACGCAGGA 59.548 55.000 0.00 0.00 0.00 3.86
2029 2172 3.603532 TGAGTGGCTCAGTTGATGAATC 58.396 45.455 0.00 0.00 37.52 2.52
2030 2173 3.262660 TGAGTGGCTCAGTTGATGAATCT 59.737 43.478 0.00 0.00 37.52 2.40
2031 2174 4.467438 TGAGTGGCTCAGTTGATGAATCTA 59.533 41.667 0.00 0.00 37.52 1.98
2032 2175 5.129980 TGAGTGGCTCAGTTGATGAATCTAT 59.870 40.000 0.00 0.00 37.52 1.98
2034 2177 6.520272 AGTGGCTCAGTTGATGAATCTATAC 58.480 40.000 0.00 0.00 37.52 1.47
2063 2224 6.656270 CAGCTTATATATTGCAAGATCACCCA 59.344 38.462 10.37 0.00 0.00 4.51
2072 2233 2.808543 GCAAGATCACCCATTATCGGAC 59.191 50.000 0.00 0.00 0.00 4.79
2090 2254 5.997385 TCGGACTTTTATTTTGCAAGTCTC 58.003 37.500 11.20 2.91 44.00 3.36
2113 2277 8.034804 TCTCGATAATGACATCACTGAAAAAGA 58.965 33.333 0.00 0.00 0.00 2.52
2114 2278 8.722480 TCGATAATGACATCACTGAAAAAGAT 57.278 30.769 0.00 0.00 0.00 2.40
2115 2279 9.816354 TCGATAATGACATCACTGAAAAAGATA 57.184 29.630 0.00 0.00 0.00 1.98
2122 2286 8.615211 TGACATCACTGAAAAAGATATGTATGC 58.385 33.333 0.00 0.00 35.97 3.14
2123 2287 7.633621 ACATCACTGAAAAAGATATGTATGCG 58.366 34.615 0.00 0.00 34.89 4.73
2124 2288 6.603237 TCACTGAAAAAGATATGTATGCGG 57.397 37.500 0.00 0.00 0.00 5.69
2125 2289 6.345298 TCACTGAAAAAGATATGTATGCGGA 58.655 36.000 0.00 0.00 0.00 5.54
2126 2290 6.821160 TCACTGAAAAAGATATGTATGCGGAA 59.179 34.615 0.00 0.00 0.00 4.30
2127 2291 7.011389 TCACTGAAAAAGATATGTATGCGGAAG 59.989 37.037 0.00 0.00 0.00 3.46
2128 2292 6.823689 ACTGAAAAAGATATGTATGCGGAAGT 59.176 34.615 0.00 0.00 0.00 3.01
2129 2293 7.985184 ACTGAAAAAGATATGTATGCGGAAGTA 59.015 33.333 0.00 0.00 0.00 2.24
2142 2306 8.464404 TGTATGCGGAAGTAGTATATGTAATCC 58.536 37.037 0.00 0.00 0.00 3.01
2144 2308 7.534723 TGCGGAAGTAGTATATGTAATCCTT 57.465 36.000 0.00 0.00 0.00 3.36
2153 2321 6.951971 AGTATATGTAATCCTTCTGATGGCC 58.048 40.000 0.00 0.00 32.68 5.36
2168 2336 1.367346 TGGCCTAGTGAACCCAATCA 58.633 50.000 3.32 0.00 0.00 2.57
2171 2339 1.678101 GCCTAGTGAACCCAATCATGC 59.322 52.381 0.00 0.00 0.00 4.06
2180 2348 1.064463 ACCCAATCATGCGGAACAGAT 60.064 47.619 0.00 0.00 0.00 2.90
2222 2402 5.234757 GCAAGATGCATGAAACAAAGTTCAA 59.765 36.000 2.46 0.00 44.26 2.69
2299 2479 4.141892 TGAACCAAAACTCTACCGTCTGAA 60.142 41.667 0.00 0.00 0.00 3.02
2313 2493 3.251571 CGTCTGAAGCTACCCTTTGTAC 58.748 50.000 0.00 0.00 32.78 2.90
2318 2498 3.810941 TGAAGCTACCCTTTGTACGTTTG 59.189 43.478 0.00 0.00 32.78 2.93
2357 2542 9.890629 ATAGTTTAGAAGTTTGATAGTGCATCA 57.109 29.630 0.00 0.00 42.07 3.07
2458 2656 4.806342 AAACTGTCAGTTTTACGCGAAT 57.194 36.364 22.62 0.42 45.38 3.34
2525 2739 5.046910 CCAAAGTTTGGTACTAGTGCATG 57.953 43.478 24.17 0.00 45.93 4.06
2526 2740 4.475944 CAAAGTTTGGTACTAGTGCATGC 58.524 43.478 11.82 11.82 35.54 4.06
2527 2741 3.417069 AGTTTGGTACTAGTGCATGCA 57.583 42.857 18.46 18.46 34.56 3.96
2528 2742 3.955471 AGTTTGGTACTAGTGCATGCAT 58.045 40.909 25.64 15.04 34.56 3.96
2543 2757 3.056607 GCATGCATACCAAAAGTCCAAGT 60.057 43.478 14.21 0.00 0.00 3.16
2553 2767 6.060136 ACCAAAAGTCCAAGTAAGAGTTACC 58.940 40.000 0.00 0.00 36.81 2.85
2555 2769 6.017357 CCAAAAGTCCAAGTAAGAGTTACCAC 60.017 42.308 0.00 0.00 36.81 4.16
2556 2770 5.881923 AAGTCCAAGTAAGAGTTACCACA 57.118 39.130 0.00 0.00 36.81 4.17
2643 2858 8.304596 TGTATACATTCATAGCTAGGCTTGTAC 58.695 37.037 16.97 11.56 40.44 2.90
2644 2859 4.621991 ACATTCATAGCTAGGCTTGTACG 58.378 43.478 10.15 0.00 40.44 3.67
2648 2863 1.179152 TAGCTAGGCTTGTACGCACA 58.821 50.000 0.00 0.00 40.44 4.57
2649 2864 0.389948 AGCTAGGCTTGTACGCACAC 60.390 55.000 0.00 0.00 33.89 3.82
2701 2921 3.495331 TCCTAGTTTTTCATGCCAAGCA 58.505 40.909 0.00 0.00 44.86 3.91
2752 2972 3.984193 GAACTGCCCAGCCGCTCAT 62.984 63.158 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.457831 GACCCCGGCCTCTGTATCT 60.458 63.158 0.00 0.00 0.00 1.98
1 2 1.122019 ATGACCCCGGCCTCTGTATC 61.122 60.000 0.00 0.00 0.00 2.24
2 3 1.074471 ATGACCCCGGCCTCTGTAT 60.074 57.895 0.00 0.00 0.00 2.29
3 4 1.760875 GATGACCCCGGCCTCTGTA 60.761 63.158 0.00 0.00 0.00 2.74
4 5 3.083997 GATGACCCCGGCCTCTGT 61.084 66.667 0.00 0.00 0.00 3.41
5 6 3.866582 GGATGACCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
6 7 4.095400 AGGATGACCCCGGCCTCT 62.095 66.667 0.00 0.00 36.73 3.69
7 8 3.551407 GAGGATGACCCCGGCCTC 61.551 72.222 7.66 7.66 40.04 4.70
10 11 2.284515 AAATGGAGGATGACCCCGGC 62.285 60.000 0.00 0.00 36.73 6.13
11 12 0.179018 GAAATGGAGGATGACCCCGG 60.179 60.000 0.00 0.00 36.73 5.73
12 13 0.839946 AGAAATGGAGGATGACCCCG 59.160 55.000 0.00 0.00 36.73 5.73
13 14 3.202151 TGTTAGAAATGGAGGATGACCCC 59.798 47.826 0.00 0.00 36.73 4.95
14 15 4.503714 TGTTAGAAATGGAGGATGACCC 57.496 45.455 0.00 0.00 36.73 4.46
15 16 6.834168 TTTTGTTAGAAATGGAGGATGACC 57.166 37.500 0.00 0.00 0.00 4.02
37 38 9.765795 AATAGTAGCAGCGAGACTAATATTTTT 57.234 29.630 8.42 0.00 36.68 1.94
38 39 9.765795 AAATAGTAGCAGCGAGACTAATATTTT 57.234 29.630 13.76 3.63 42.45 1.82
39 40 9.413048 GAAATAGTAGCAGCGAGACTAATATTT 57.587 33.333 16.96 16.96 45.22 1.40
45 46 6.766944 AGTAAGAAATAGTAGCAGCGAGACTA 59.233 38.462 7.17 7.17 0.00 2.59
52 53 5.582665 ACTTGCAGTAAGAAATAGTAGCAGC 59.417 40.000 5.10 0.00 39.76 5.25
57 58 9.745880 GTATAGCACTTGCAGTAAGAAATAGTA 57.254 33.333 5.10 0.00 45.16 1.82
139 140 6.218019 ACAAATACTGCTACGTACAAACTGA 58.782 36.000 0.00 0.00 0.00 3.41
140 141 6.462073 ACAAATACTGCTACGTACAAACTG 57.538 37.500 0.00 0.00 0.00 3.16
141 142 7.201496 GCATACAAATACTGCTACGTACAAACT 60.201 37.037 0.00 0.00 33.15 2.66
142 143 6.898189 GCATACAAATACTGCTACGTACAAAC 59.102 38.462 0.00 0.00 33.15 2.93
143 144 6.590677 TGCATACAAATACTGCTACGTACAAA 59.409 34.615 0.00 0.00 36.84 2.83
171 172 2.047213 GCCCCGTGGATTTATCCCGA 62.047 60.000 16.28 0.00 46.59 5.14
221 238 0.248094 GAATGGCCGCGCTTTAGTTC 60.248 55.000 5.56 0.71 0.00 3.01
253 270 6.101734 AGGGCATAGACAGATGGATAAAGAAA 59.898 38.462 0.00 0.00 0.00 2.52
290 307 4.054455 GGTGTGCGCACGTACGTG 62.054 66.667 37.44 37.44 46.13 4.49
293 310 3.110178 GAGGGTGTGCGCACGTAC 61.110 66.667 33.22 26.12 46.13 3.67
294 311 3.607661 TGAGGGTGTGCGCACGTA 61.608 61.111 33.22 16.38 46.13 3.57
297 314 4.626081 AGGTGAGGGTGTGCGCAC 62.626 66.667 33.11 33.11 44.53 5.34
298 315 4.624364 CAGGTGAGGGTGTGCGCA 62.624 66.667 5.66 5.66 0.00 6.09
300 317 2.958578 AAACCAGGTGAGGGTGTGCG 62.959 60.000 0.00 0.00 39.01 5.34
301 318 0.755327 AAAACCAGGTGAGGGTGTGC 60.755 55.000 0.00 0.00 39.01 4.57
302 319 1.775385 AAAAACCAGGTGAGGGTGTG 58.225 50.000 0.00 0.00 39.01 3.82
323 340 6.750501 ACATCGCATCTGAAAAATGAATTGAG 59.249 34.615 0.00 0.00 0.00 3.02
324 341 6.623486 ACATCGCATCTGAAAAATGAATTGA 58.377 32.000 0.00 0.00 0.00 2.57
325 342 6.880822 ACATCGCATCTGAAAAATGAATTG 57.119 33.333 0.00 0.00 0.00 2.32
326 343 7.062605 GTCAACATCGCATCTGAAAAATGAATT 59.937 33.333 0.00 0.00 0.00 2.17
341 363 4.321966 TGGCCGGTCAACATCGCA 62.322 61.111 6.10 0.00 0.00 5.10
343 365 3.487202 CGTGGCCGGTCAACATCG 61.487 66.667 12.16 6.30 0.00 3.84
361 383 0.178767 TCGATCAATCAGCCACTGGG 59.821 55.000 0.00 0.00 31.51 4.45
370 392 4.142026 ACGTACAAAGGGATCGATCAATCA 60.142 41.667 25.93 2.37 0.00 2.57
371 393 4.369182 ACGTACAAAGGGATCGATCAATC 58.631 43.478 25.93 14.63 0.00 2.67
372 394 4.402056 ACGTACAAAGGGATCGATCAAT 57.598 40.909 25.93 11.44 0.00 2.57
373 395 3.880047 ACGTACAAAGGGATCGATCAA 57.120 42.857 25.93 0.49 0.00 2.57
378 400 2.549633 ACGTACGTACAAAGGGATCG 57.450 50.000 21.41 10.29 0.00 3.69
404 426 1.621672 GGGAGAGGGTTGCAGGAGAG 61.622 65.000 0.00 0.00 0.00 3.20
416 438 1.379977 TACAGGTCGCAGGGAGAGG 60.380 63.158 0.00 0.00 0.00 3.69
421 443 4.143333 CCGGTACAGGTCGCAGGG 62.143 72.222 3.54 0.00 0.00 4.45
480 509 1.662592 CGTGCGTGCATGTGAAATGAA 60.663 47.619 7.93 0.00 0.00 2.57
504 533 1.758319 GCATGTGGAATGCGCAATGC 61.758 55.000 22.34 22.34 46.70 3.56
505 534 1.149361 GGCATGTGGAATGCGCAATG 61.149 55.000 17.11 14.00 45.41 2.82
506 535 1.142314 GGCATGTGGAATGCGCAAT 59.858 52.632 17.11 5.60 45.41 3.56
507 536 2.572812 GGCATGTGGAATGCGCAA 59.427 55.556 17.11 0.00 45.41 4.85
510 539 3.112126 GACGGGCATGTGGAATGCG 62.112 63.158 4.37 0.00 45.41 4.73
512 541 1.378382 TGGACGGGCATGTGGAATG 60.378 57.895 0.00 0.00 0.00 2.67
514 543 2.063015 AACTGGACGGGCATGTGGAA 62.063 55.000 0.00 0.00 0.00 3.53
515 544 2.525124 AACTGGACGGGCATGTGGA 61.525 57.895 0.00 0.00 0.00 4.02
527 571 3.258228 ATGGCGCTGCTCAACTGGA 62.258 57.895 7.64 0.00 0.00 3.86
586 637 7.242322 AGAATTTTAGAACGGAAGGAGTACT 57.758 36.000 0.00 0.00 0.00 2.73
587 638 7.387122 ACAAGAATTTTAGAACGGAAGGAGTAC 59.613 37.037 0.00 0.00 0.00 2.73
588 639 7.447594 ACAAGAATTTTAGAACGGAAGGAGTA 58.552 34.615 0.00 0.00 0.00 2.59
589 640 6.296803 ACAAGAATTTTAGAACGGAAGGAGT 58.703 36.000 0.00 0.00 0.00 3.85
590 641 6.651225 AGACAAGAATTTTAGAACGGAAGGAG 59.349 38.462 0.00 0.00 0.00 3.69
591 642 6.531021 AGACAAGAATTTTAGAACGGAAGGA 58.469 36.000 0.00 0.00 0.00 3.36
592 643 6.803154 AGACAAGAATTTTAGAACGGAAGG 57.197 37.500 0.00 0.00 0.00 3.46
593 644 9.204570 TCTAAGACAAGAATTTTAGAACGGAAG 57.795 33.333 0.00 0.00 31.26 3.46
594 645 9.720769 ATCTAAGACAAGAATTTTAGAACGGAA 57.279 29.630 0.45 0.00 36.18 4.30
595 646 9.720769 AATCTAAGACAAGAATTTTAGAACGGA 57.279 29.630 0.45 0.00 36.18 4.69
628 679 9.692749 CATTGTAGTGTTAGATACATCCGTATT 57.307 33.333 0.00 0.00 38.48 1.89
629 680 8.857098 ACATTGTAGTGTTAGATACATCCGTAT 58.143 33.333 0.00 0.00 41.16 3.06
630 681 8.229253 ACATTGTAGTGTTAGATACATCCGTA 57.771 34.615 0.00 0.00 39.39 4.02
631 682 7.108841 ACATTGTAGTGTTAGATACATCCGT 57.891 36.000 0.00 0.00 39.39 4.69
632 683 9.692749 ATTACATTGTAGTGTTAGATACATCCG 57.307 33.333 0.00 0.00 39.39 4.18
684 735 8.673711 CCATCCGTATCAAAATTCTTGTCTTAA 58.326 33.333 0.00 0.00 0.00 1.85
685 736 8.044309 TCCATCCGTATCAAAATTCTTGTCTTA 58.956 33.333 0.00 0.00 0.00 2.10
686 737 6.884295 TCCATCCGTATCAAAATTCTTGTCTT 59.116 34.615 0.00 0.00 0.00 3.01
687 738 6.414732 TCCATCCGTATCAAAATTCTTGTCT 58.585 36.000 0.00 0.00 0.00 3.41
688 739 6.316390 ACTCCATCCGTATCAAAATTCTTGTC 59.684 38.462 0.00 0.00 0.00 3.18
689 740 6.180472 ACTCCATCCGTATCAAAATTCTTGT 58.820 36.000 0.00 0.00 0.00 3.16
690 741 6.683974 ACTCCATCCGTATCAAAATTCTTG 57.316 37.500 0.00 0.00 0.00 3.02
697 748 9.938280 CCTAATTTATACTCCATCCGTATCAAA 57.062 33.333 0.00 0.00 0.00 2.69
698 749 8.537016 CCCTAATTTATACTCCATCCGTATCAA 58.463 37.037 0.00 0.00 0.00 2.57
699 750 7.676893 ACCCTAATTTATACTCCATCCGTATCA 59.323 37.037 0.00 0.00 0.00 2.15
700 751 8.075761 ACCCTAATTTATACTCCATCCGTATC 57.924 38.462 0.00 0.00 0.00 2.24
701 752 9.551339 TTACCCTAATTTATACTCCATCCGTAT 57.449 33.333 0.00 0.00 0.00 3.06
702 753 8.954834 TTACCCTAATTTATACTCCATCCGTA 57.045 34.615 0.00 0.00 0.00 4.02
703 754 7.860649 TTACCCTAATTTATACTCCATCCGT 57.139 36.000 0.00 0.00 0.00 4.69
704 755 9.216117 CTTTTACCCTAATTTATACTCCATCCG 57.784 37.037 0.00 0.00 0.00 4.18
708 759 9.623000 GCTTCTTTTACCCTAATTTATACTCCA 57.377 33.333 0.00 0.00 0.00 3.86
709 760 9.064706 GGCTTCTTTTACCCTAATTTATACTCC 57.935 37.037 0.00 0.00 0.00 3.85
710 761 8.771766 CGGCTTCTTTTACCCTAATTTATACTC 58.228 37.037 0.00 0.00 0.00 2.59
744 795 2.177394 TGCTGCGTTGAATACAAGGA 57.823 45.000 0.00 0.00 42.27 3.36
758 809 2.050477 AGCAAACGTGTAAATGCTGC 57.950 45.000 10.85 0.00 46.66 5.25
875 945 3.195825 CGGGTATTTATAGAGGGGAGCTG 59.804 52.174 0.00 0.00 0.00 4.24
896 966 1.227823 TGCAGGTTGAGGTTGGACG 60.228 57.895 0.00 0.00 0.00 4.79
1281 1384 1.965754 GCTGGAGGGCGAAGATCTGT 61.966 60.000 0.00 0.00 0.00 3.41
1313 1416 1.475441 GAAGAATGAGACGAGCGCCG 61.475 60.000 15.25 15.25 45.44 6.46
1314 1417 0.179124 AGAAGAATGAGACGAGCGCC 60.179 55.000 2.29 0.00 0.00 6.53
1315 1418 1.586123 GAAGAAGAATGAGACGAGCGC 59.414 52.381 0.00 0.00 0.00 5.92
1317 1420 3.862845 GGAAGAAGAAGAATGAGACGAGC 59.137 47.826 0.00 0.00 0.00 5.03
1321 1424 7.330262 AGAAGATGGAAGAAGAAGAATGAGAC 58.670 38.462 0.00 0.00 0.00 3.36
1322 1425 7.493499 AGAAGATGGAAGAAGAAGAATGAGA 57.507 36.000 0.00 0.00 0.00 3.27
1323 1426 7.280652 GGAAGAAGATGGAAGAAGAAGAATGAG 59.719 40.741 0.00 0.00 0.00 2.90
1368 1480 2.032204 GCCAGCTGATTGATTGATCGAC 60.032 50.000 17.39 0.00 0.00 4.20
1375 1489 2.097825 GAAGTGGCCAGCTGATTGATT 58.902 47.619 17.39 4.12 0.00 2.57
1377 1491 0.322816 GGAAGTGGCCAGCTGATTGA 60.323 55.000 17.39 0.00 0.00 2.57
1384 1502 3.628646 ATGACGGGAAGTGGCCAGC 62.629 63.158 5.11 0.39 0.00 4.85
1398 1516 0.376152 CATCAGCTTGCGTCCATGAC 59.624 55.000 0.00 0.00 0.00 3.06
1399 1517 0.249955 TCATCAGCTTGCGTCCATGA 59.750 50.000 0.00 0.00 0.00 3.07
1431 1549 0.947244 GGATCGCCACCTGCAATAAG 59.053 55.000 0.00 0.00 41.33 1.73
1434 1552 1.452651 CAGGATCGCCACCTGCAAT 60.453 57.895 0.00 0.00 46.30 3.56
1524 1642 4.007644 CTGCTGTCCGGCCACTGA 62.008 66.667 2.24 0.00 0.00 3.41
1609 1733 2.511145 GAGCTCTGGCAGAAGCGG 60.511 66.667 19.29 7.89 43.41 5.52
1732 1856 2.183679 CAGGGAGTAGTTGGAGCTTCT 58.816 52.381 0.00 0.00 0.00 2.85
1823 1954 1.685517 CCAGCTAGCAGCACTCTGATA 59.314 52.381 18.83 0.00 45.56 2.15
1843 1978 3.186047 CCGCCGACACGATTCCAC 61.186 66.667 0.00 0.00 34.06 4.02
1890 2027 5.995446 ACAGGTTAATCAATTCCCTCTCTC 58.005 41.667 0.00 0.00 0.00 3.20
1891 2028 6.674419 AGTACAGGTTAATCAATTCCCTCTCT 59.326 38.462 0.00 0.00 0.00 3.10
2030 2173 9.942850 TCTTGCAATATATAAGCTGCTTGTATA 57.057 29.630 29.00 29.00 35.58 1.47
2031 2174 8.853077 TCTTGCAATATATAAGCTGCTTGTAT 57.147 30.769 27.21 27.21 35.78 2.29
2032 2175 8.853077 ATCTTGCAATATATAAGCTGCTTGTA 57.147 30.769 24.35 21.51 35.78 2.41
2034 2177 7.749570 GTGATCTTGCAATATATAAGCTGCTTG 59.250 37.037 24.35 7.98 35.78 4.01
2063 2224 8.911247 GACTTGCAAAATAAAAGTCCGATAAT 57.089 30.769 0.00 0.00 42.52 1.28
2072 2233 9.773328 TCATTATCGAGACTTGCAAAATAAAAG 57.227 29.630 0.00 0.00 0.00 2.27
2116 2280 8.464404 GGATTACATATACTACTTCCGCATACA 58.536 37.037 0.00 0.00 0.00 2.29
2117 2281 8.684520 AGGATTACATATACTACTTCCGCATAC 58.315 37.037 0.00 0.00 0.00 2.39
2118 2282 8.818622 AGGATTACATATACTACTTCCGCATA 57.181 34.615 0.00 0.00 0.00 3.14
2119 2283 7.719871 AGGATTACATATACTACTTCCGCAT 57.280 36.000 0.00 0.00 0.00 4.73
2120 2284 7.450634 AGAAGGATTACATATACTACTTCCGCA 59.549 37.037 0.00 0.00 35.04 5.69
2121 2285 7.755822 CAGAAGGATTACATATACTACTTCCGC 59.244 40.741 0.00 0.00 35.04 5.54
2122 2286 9.011095 TCAGAAGGATTACATATACTACTTCCG 57.989 37.037 0.00 0.00 35.04 4.30
2126 2290 8.754080 GCCATCAGAAGGATTACATATACTACT 58.246 37.037 0.00 0.00 32.57 2.57
2127 2291 7.982354 GGCCATCAGAAGGATTACATATACTAC 59.018 40.741 0.00 0.00 32.57 2.73
2128 2292 7.901322 AGGCCATCAGAAGGATTACATATACTA 59.099 37.037 5.01 0.00 32.57 1.82
2129 2293 6.732862 AGGCCATCAGAAGGATTACATATACT 59.267 38.462 5.01 0.00 32.57 2.12
2142 2306 2.420687 GGGTTCACTAGGCCATCAGAAG 60.421 54.545 5.01 0.00 0.00 2.85
2144 2308 1.204146 GGGTTCACTAGGCCATCAGA 58.796 55.000 5.01 0.00 0.00 3.27
2153 2321 1.942657 CCGCATGATTGGGTTCACTAG 59.057 52.381 0.00 0.00 34.12 2.57
2168 2336 2.309528 TCGCTTAATCTGTTCCGCAT 57.690 45.000 0.00 0.00 0.00 4.73
2171 2339 4.369182 ACCTAATCGCTTAATCTGTTCCG 58.631 43.478 0.00 0.00 0.00 4.30
2180 2348 2.705730 TGCTGCAACCTAATCGCTTAA 58.294 42.857 0.00 0.00 0.00 1.85
2269 2449 5.183969 GGTAGAGTTTTGGTTCATCCTACC 58.816 45.833 0.00 0.00 38.40 3.18
2299 2479 3.480505 ACAAACGTACAAAGGGTAGCT 57.519 42.857 0.00 0.00 31.13 3.32
2313 2493 6.879188 AACTATTTCCAACACAAACAAACG 57.121 33.333 0.00 0.00 0.00 3.60
2318 2498 9.797556 AACTTCTAAACTATTTCCAACACAAAC 57.202 29.630 0.00 0.00 0.00 2.93
2357 2542 9.554395 TTTTTCAAACTCTTCCTTGAACTTTTT 57.446 25.926 0.00 0.00 40.36 1.94
2458 2656 1.002900 CAAACTTGCGCCGAAAAGAGA 60.003 47.619 11.71 0.00 0.00 3.10
2525 2739 5.705905 ACTCTTACTTGGACTTTTGGTATGC 59.294 40.000 0.00 0.00 0.00 3.14
2526 2740 7.745620 AACTCTTACTTGGACTTTTGGTATG 57.254 36.000 0.00 0.00 0.00 2.39
2527 2741 7.881751 GGTAACTCTTACTTGGACTTTTGGTAT 59.118 37.037 0.00 0.00 36.39 2.73
2528 2742 7.147514 TGGTAACTCTTACTTGGACTTTTGGTA 60.148 37.037 0.00 0.00 36.39 3.25
2543 2757 6.104146 TGTGTGCTATTGTGGTAACTCTTA 57.896 37.500 0.00 0.00 37.61 2.10
2553 2767 5.173774 ACTCAAAGTTGTGTGCTATTGTG 57.826 39.130 0.00 0.00 34.04 3.33
2581 2796 3.336997 TCTCTAGAGAGGGGGAAACTTGA 59.663 47.826 18.76 0.00 42.30 3.02
2643 2858 5.629849 GCCTATGAGTTTATACTAGTGTGCG 59.370 44.000 5.39 0.00 33.84 5.34
2644 2859 6.642950 CAGCCTATGAGTTTATACTAGTGTGC 59.357 42.308 5.39 0.00 33.84 4.57
2648 2863 6.517529 GCAGCAGCCTATGAGTTTATACTAGT 60.518 42.308 0.00 0.00 31.93 2.57
2649 2864 5.866633 GCAGCAGCCTATGAGTTTATACTAG 59.133 44.000 0.00 0.00 31.93 2.57
2701 2921 1.630878 GATCAGGGGGACAGTCTTTGT 59.369 52.381 0.00 0.00 44.55 2.83


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

AutoCloner maintained by Alex Coulton.