Multiple sequence alignment - TraesCS3D01G292300

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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 TraesCS3D01G292300 chr3D 100.000 3353 0 0 1 3353 402495152 402491800 0.000000e+00 6192.0
1 TraesCS3D01G292300 chr3D 93.282 521 34 1 1 521 547932151 547932670 0.000000e+00 767.0
2 TraesCS3D01G292300 chr3D 78.873 213 37 8 1026 1234 142473953 142474161 1.620000e-28 137.0
3 TraesCS3D01G292300 chr3B 91.411 1630 74 17 1768 3344 528077973 528076357 0.000000e+00 2174.0
4 TraesCS3D01G292300 chr3B 90.349 974 41 32 566 1496 528079233 528078270 0.000000e+00 1229.0
5 TraesCS3D01G292300 chr3B 79.535 215 32 10 1026 1234 204279328 204279536 3.490000e-30 143.0
6 TraesCS3D01G292300 chr3A 94.118 1071 47 8 1805 2866 523333122 523332059 0.000000e+00 1615.0
7 TraesCS3D01G292300 chr3A 95.793 618 13 10 573 1185 523334548 523333939 0.000000e+00 985.0
8 TraesCS3D01G292300 chr3A 89.451 455 17 12 2916 3350 523331993 523331550 2.270000e-151 545.0
9 TraesCS3D01G292300 chr3A 79.343 213 36 8 1026 1234 161443809 161444017 3.490000e-30 143.0
10 TraesCS3D01G292300 chr1D 94.434 521 28 1 1 521 236079876 236080395 0.000000e+00 800.0
11 TraesCS3D01G292300 chr1D 94.242 521 27 1 7 527 433908223 433907706 0.000000e+00 793.0
12 TraesCS3D01G292300 chr5D 94.050 521 30 1 1 521 525594775 525595294 0.000000e+00 789.0
13 TraesCS3D01G292300 chr5D 93.605 516 30 1 6 521 135516446 135516958 0.000000e+00 767.0
14 TraesCS3D01G292300 chr5D 90.909 88 8 0 3125 3212 447765269 447765182 5.880000e-23 119.0
15 TraesCS3D01G292300 chr5D 87.342 79 9 1 3225 3302 330100271 330100349 4.610000e-14 89.8
16 TraesCS3D01G292300 chr7D 93.666 521 32 1 1 521 397377584 397378103 0.000000e+00 778.0
17 TraesCS3D01G292300 chr7D 92.710 535 34 4 1 534 511939517 511940047 0.000000e+00 767.0
18 TraesCS3D01G292300 chr7D 78.818 203 16 9 3122 3298 621640450 621640651 9.830000e-21 111.0
19 TraesCS3D01G292300 chr2D 93.474 521 31 1 1 521 549506293 549506810 0.000000e+00 771.0
20 TraesCS3D01G292300 chr2D 93.282 521 31 2 1 521 549981742 549982258 0.000000e+00 765.0
21 TraesCS3D01G292300 chr2D 78.534 191 17 8 3127 3293 67787338 67787148 1.650000e-18 104.0
22 TraesCS3D01G292300 chr2D 85.567 97 14 0 3125 3221 332482732 332482636 5.920000e-18 102.0
23 TraesCS3D01G292300 chr4A 77.500 200 18 10 3125 3299 33567621 33567818 9.900000e-16 95.3
24 TraesCS3D01G292300 chr7B 87.654 81 9 1 3225 3304 200900172 200900252 3.560000e-15 93.5
25 TraesCS3D01G292300 chr7B 88.462 78 8 1 3226 3302 697289133 697289210 3.560000e-15 93.5
26 TraesCS3D01G292300 chr2B 84.270 89 13 1 3122 3209 754662155 754662243 5.960000e-13 86.1
27 TraesCS3D01G292300 chr2B 95.455 44 2 0 3122 3165 549512344 549512387 1.670000e-08 71.3


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 TraesCS3D01G292300 chr3D 402491800 402495152 3352 True 6192.000000 6192 100.000000 1 3353 1 chr3D.!!$R1 3352
1 TraesCS3D01G292300 chr3D 547932151 547932670 519 False 767.000000 767 93.282000 1 521 1 chr3D.!!$F2 520
2 TraesCS3D01G292300 chr3B 528076357 528079233 2876 True 1701.500000 2174 90.880000 566 3344 2 chr3B.!!$R1 2778
3 TraesCS3D01G292300 chr3A 523331550 523334548 2998 True 1048.333333 1615 93.120667 573 3350 3 chr3A.!!$R1 2777
4 TraesCS3D01G292300 chr1D 236079876 236080395 519 False 800.000000 800 94.434000 1 521 1 chr1D.!!$F1 520
5 TraesCS3D01G292300 chr1D 433907706 433908223 517 True 793.000000 793 94.242000 7 527 1 chr1D.!!$R1 520
6 TraesCS3D01G292300 chr5D 525594775 525595294 519 False 789.000000 789 94.050000 1 521 1 chr5D.!!$F3 520
7 TraesCS3D01G292300 chr5D 135516446 135516958 512 False 767.000000 767 93.605000 6 521 1 chr5D.!!$F1 515
8 TraesCS3D01G292300 chr7D 397377584 397378103 519 False 778.000000 778 93.666000 1 521 1 chr7D.!!$F1 520
9 TraesCS3D01G292300 chr7D 511939517 511940047 530 False 767.000000 767 92.710000 1 534 1 chr7D.!!$F2 533
10 TraesCS3D01G292300 chr2D 549506293 549506810 517 False 771.000000 771 93.474000 1 521 1 chr2D.!!$F1 520
11 TraesCS3D01G292300 chr2D 549981742 549982258 516 False 765.000000 765 93.282000 1 521 1 chr2D.!!$F2 520

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
678 683 0.382515 AGCGTACTACTGCTAGCTGC 59.617 55.0 20.35 9.03 40.28 5.25 F
1328 1491 0.248621 GCGCATACAACCTGGATTGC 60.249 55.0 0.30 0.00 32.47 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1947 0.035739 GGGTAAACTTCGGGAGCACA 59.964 55.0 0.0 0.0 0.0 4.57 R
3041 3386 0.677731 CGCCCTTGTGATGATGGTGT 60.678 55.0 0.0 0.0 0.0 4.16 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
24 25 1.971505 GAGCATGATGACCGGGGTGA 61.972 60.000 6.32 0.00 0.00 4.02
28 29 0.541863 ATGATGACCGGGGTGAAGAC 59.458 55.000 6.32 0.00 0.00 3.01
176 177 2.751436 GTGTGCCGGCATGACCAT 60.751 61.111 35.23 0.00 39.03 3.55
213 214 2.034812 GTGGTCGAACTCAAGTCTCACT 59.965 50.000 0.33 0.00 0.00 3.41
339 340 2.124570 ACATGAGACATGGCCGCC 60.125 61.111 14.70 1.04 0.00 6.13
428 429 1.743623 CGCACTGCCGACCCAAATA 60.744 57.895 0.00 0.00 0.00 1.40
490 492 1.202359 ACAAAAAGCGGACAAATGCGT 60.202 42.857 0.00 0.00 42.52 5.24
492 494 0.665835 AAAAGCGGACAAATGCGTCA 59.334 45.000 0.00 0.00 42.52 4.35
501 503 1.876799 ACAAATGCGTCATCCGTTTGA 59.123 42.857 11.66 0.00 40.09 2.69
521 523 3.423154 CGGCTCGTTGGAGTTGCC 61.423 66.667 0.00 0.00 42.53 4.52
533 535 4.142609 TGGAGTTGCCATAAGACATCTC 57.857 45.455 0.00 0.00 43.33 2.75
534 536 3.776969 TGGAGTTGCCATAAGACATCTCT 59.223 43.478 0.00 0.00 43.33 3.10
535 537 4.141846 TGGAGTTGCCATAAGACATCTCTC 60.142 45.833 0.00 0.00 43.33 3.20
536 538 4.141846 GGAGTTGCCATAAGACATCTCTCA 60.142 45.833 0.00 0.00 34.49 3.27
537 539 5.454471 GGAGTTGCCATAAGACATCTCTCAT 60.454 44.000 0.00 0.00 34.49 2.90
538 540 5.999044 AGTTGCCATAAGACATCTCTCATT 58.001 37.500 0.00 0.00 0.00 2.57
539 541 6.421485 AGTTGCCATAAGACATCTCTCATTT 58.579 36.000 0.00 0.00 0.00 2.32
540 542 6.318144 AGTTGCCATAAGACATCTCTCATTTG 59.682 38.462 0.00 0.00 0.00 2.32
541 543 5.748402 TGCCATAAGACATCTCTCATTTGT 58.252 37.500 0.00 0.00 0.00 2.83
542 544 6.182627 TGCCATAAGACATCTCTCATTTGTT 58.817 36.000 0.00 0.00 0.00 2.83
543 545 6.660521 TGCCATAAGACATCTCTCATTTGTTT 59.339 34.615 0.00 0.00 0.00 2.83
544 546 7.177216 TGCCATAAGACATCTCTCATTTGTTTT 59.823 33.333 0.00 0.00 0.00 2.43
545 547 8.031277 GCCATAAGACATCTCTCATTTGTTTTT 58.969 33.333 0.00 0.00 0.00 1.94
546 548 9.350357 CCATAAGACATCTCTCATTTGTTTTTG 57.650 33.333 0.00 0.00 0.00 2.44
547 549 9.903682 CATAAGACATCTCTCATTTGTTTTTGT 57.096 29.630 0.00 0.00 0.00 2.83
550 552 8.682936 AGACATCTCTCATTTGTTTTTGTACT 57.317 30.769 0.00 0.00 0.00 2.73
551 553 9.778741 AGACATCTCTCATTTGTTTTTGTACTA 57.221 29.630 0.00 0.00 0.00 1.82
552 554 9.813080 GACATCTCTCATTTGTTTTTGTACTAC 57.187 33.333 0.00 0.00 0.00 2.73
553 555 8.784043 ACATCTCTCATTTGTTTTTGTACTACC 58.216 33.333 0.00 0.00 0.00 3.18
554 556 8.783093 CATCTCTCATTTGTTTTTGTACTACCA 58.217 33.333 0.00 0.00 0.00 3.25
555 557 8.740123 TCTCTCATTTGTTTTTGTACTACCAA 57.260 30.769 0.00 0.00 0.00 3.67
556 558 9.179909 TCTCTCATTTGTTTTTGTACTACCAAA 57.820 29.630 0.00 0.00 32.70 3.28
557 559 9.233232 CTCTCATTTGTTTTTGTACTACCAAAC 57.767 33.333 0.00 0.00 34.23 2.93
558 560 8.740906 TCTCATTTGTTTTTGTACTACCAAACA 58.259 29.630 8.67 8.67 37.35 2.83
559 561 9.528018 CTCATTTGTTTTTGTACTACCAAACAT 57.472 29.630 11.76 0.92 38.56 2.71
560 562 9.307121 TCATTTGTTTTTGTACTACCAAACATG 57.693 29.630 11.76 0.00 38.56 3.21
561 563 8.547069 CATTTGTTTTTGTACTACCAAACATGG 58.453 33.333 11.76 0.00 38.56 3.66
562 564 6.777213 TGTTTTTGTACTACCAAACATGGT 57.223 33.333 5.73 5.73 45.46 3.55
563 565 6.565234 TGTTTTTGTACTACCAAACATGGTG 58.435 36.000 10.68 3.82 43.03 4.17
564 566 4.839668 TTTGTACTACCAAACATGGTGC 57.160 40.909 10.68 0.01 43.03 5.01
608 610 0.384725 CAGACGAAACGCAAGCCAAG 60.385 55.000 0.00 0.00 45.62 3.61
654 659 5.046910 TGAAAGAAAAGAAATGCGGCTAG 57.953 39.130 0.00 0.00 0.00 3.42
665 670 4.610844 CGGCTAGTAGCAGCGTAC 57.389 61.111 23.24 4.26 44.75 3.67
666 671 2.023318 CGGCTAGTAGCAGCGTACT 58.977 57.895 23.24 8.87 44.75 2.73
667 672 1.224075 CGGCTAGTAGCAGCGTACTA 58.776 55.000 23.24 9.87 44.75 1.82
668 673 1.070041 CGGCTAGTAGCAGCGTACTAC 60.070 57.143 23.24 2.14 44.75 2.73
677 682 2.112475 CAGCGTACTACTGCTAGCTG 57.888 55.000 19.01 19.01 44.51 4.24
678 683 0.382515 AGCGTACTACTGCTAGCTGC 59.617 55.000 20.35 9.03 40.28 5.25
811 820 2.113351 GCTATTCGCCCTTCCCCC 59.887 66.667 0.00 0.00 0.00 5.40
812 821 2.452937 GCTATTCGCCCTTCCCCCT 61.453 63.158 0.00 0.00 0.00 4.79
813 822 1.755384 CTATTCGCCCTTCCCCCTC 59.245 63.158 0.00 0.00 0.00 4.30
814 823 2.100879 CTATTCGCCCTTCCCCCTCG 62.101 65.000 0.00 0.00 0.00 4.63
815 824 2.884179 TATTCGCCCTTCCCCCTCGT 62.884 60.000 0.00 0.00 0.00 4.18
817 826 3.078836 CGCCCTTCCCCCTCGTAA 61.079 66.667 0.00 0.00 0.00 3.18
1241 1252 2.019249 CAACGACCAGGGTACGATCTA 58.981 52.381 14.27 0.00 0.00 1.98
1242 1253 1.673168 ACGACCAGGGTACGATCTAC 58.327 55.000 14.27 0.00 0.00 2.59
1318 1481 0.527600 AGATTCTCGCGCGCATACAA 60.528 50.000 32.61 17.49 0.00 2.41
1328 1491 0.248621 GCGCATACAACCTGGATTGC 60.249 55.000 0.30 0.00 32.47 3.56
1334 1497 1.549203 ACAACCTGGATTGCCACATC 58.451 50.000 0.00 0.00 39.92 3.06
1400 1567 2.276201 GTGTATGCGGCAGAACACATA 58.724 47.619 30.74 9.18 41.43 2.29
1401 1568 2.285220 GTGTATGCGGCAGAACACATAG 59.715 50.000 30.74 0.00 41.43 2.23
1403 1570 2.401583 ATGCGGCAGAACACATAGAA 57.598 45.000 9.25 0.00 0.00 2.10
1439 1607 5.350365 TCCTAGAATCGGATTGTGAAAAACG 59.650 40.000 8.18 0.00 0.00 3.60
1446 1614 4.083537 TCGGATTGTGAAAAACGGAAGATG 60.084 41.667 0.00 0.00 0.00 2.90
1452 1620 8.934507 ATTGTGAAAAACGGAAGATGTAAAAA 57.065 26.923 0.00 0.00 0.00 1.94
1462 1630 7.712797 ACGGAAGATGTAAAAACAAATTCAGT 58.287 30.769 0.00 7.00 0.00 3.41
1488 1657 4.623932 ATCCAAGTAGCAAGTGAACTGA 57.376 40.909 0.00 0.00 0.00 3.41
1496 1665 4.622701 AGCAAGTGAACTGAAAAGTGTC 57.377 40.909 0.00 0.00 0.00 3.67
1497 1666 3.063997 AGCAAGTGAACTGAAAAGTGTCG 59.936 43.478 0.00 0.00 0.00 4.35
1501 1670 3.248602 AGTGAACTGAAAAGTGTCGATGC 59.751 43.478 0.00 0.00 0.00 3.91
1502 1671 2.548057 TGAACTGAAAAGTGTCGATGCC 59.452 45.455 0.00 0.00 0.00 4.40
1503 1672 2.550830 ACTGAAAAGTGTCGATGCCT 57.449 45.000 0.00 0.00 0.00 4.75
1511 1680 4.749245 AAGTGTCGATGCCTTGTAAAAG 57.251 40.909 0.00 0.00 0.00 2.27
1515 1693 2.418976 GTCGATGCCTTGTAAAAGGTCC 59.581 50.000 13.46 0.00 42.00 4.46
1518 1696 3.421844 GATGCCTTGTAAAAGGTCCTGT 58.578 45.455 13.46 0.00 42.00 4.00
1525 1703 7.038160 TGCCTTGTAAAAGGTCCTGTAGTATAA 60.038 37.037 13.46 0.00 42.00 0.98
1556 1840 6.287107 ACTATATATTTGTGCAAGTGCGTC 57.713 37.500 0.00 0.00 45.83 5.19
1598 1886 5.008217 GGTTGGCTGGTTTTTGTTAAATTCC 59.992 40.000 0.00 0.00 0.00 3.01
1599 1887 4.372656 TGGCTGGTTTTTGTTAAATTCCG 58.627 39.130 0.00 0.00 0.00 4.30
1603 1891 5.344933 GCTGGTTTTTGTTAAATTCCGCTAG 59.655 40.000 0.00 0.00 0.00 3.42
1604 1892 6.394025 TGGTTTTTGTTAAATTCCGCTAGT 57.606 33.333 0.00 0.00 0.00 2.57
1605 1893 7.507733 TGGTTTTTGTTAAATTCCGCTAGTA 57.492 32.000 0.00 0.00 0.00 1.82
1606 1894 7.586747 TGGTTTTTGTTAAATTCCGCTAGTAG 58.413 34.615 0.00 0.00 0.00 2.57
1607 1895 7.229106 TGGTTTTTGTTAAATTCCGCTAGTAGT 59.771 33.333 0.00 0.00 0.00 2.73
1608 1896 8.720562 GGTTTTTGTTAAATTCCGCTAGTAGTA 58.279 33.333 0.00 0.00 0.00 1.82
1609 1897 9.750882 GTTTTTGTTAAATTCCGCTAGTAGTAG 57.249 33.333 0.00 0.00 0.00 2.57
1611 1899 6.780457 TGTTAAATTCCGCTAGTAGTAGGT 57.220 37.500 6.73 0.00 0.00 3.08
1612 1900 6.567050 TGTTAAATTCCGCTAGTAGTAGGTG 58.433 40.000 6.73 0.00 0.00 4.00
1613 1901 6.153340 TGTTAAATTCCGCTAGTAGTAGGTGT 59.847 38.462 6.73 2.54 0.00 4.16
1614 1902 7.339212 TGTTAAATTCCGCTAGTAGTAGGTGTA 59.661 37.037 6.73 2.86 0.00 2.90
1615 1903 6.973460 AAATTCCGCTAGTAGTAGGTGTAT 57.027 37.500 6.73 4.48 0.00 2.29
1631 1921 9.780186 AGTAGGTGTATTATCTTATTGAAAGGC 57.220 33.333 0.00 0.00 0.00 4.35
1632 1922 9.780186 GTAGGTGTATTATCTTATTGAAAGGCT 57.220 33.333 0.00 0.00 0.00 4.58
1633 1923 8.910351 AGGTGTATTATCTTATTGAAAGGCTC 57.090 34.615 0.00 0.00 0.00 4.70
1634 1924 8.718656 AGGTGTATTATCTTATTGAAAGGCTCT 58.281 33.333 0.00 0.00 0.00 4.09
1654 1944 0.961019 TGTGCACTGAAAATGGAGCC 59.039 50.000 19.41 0.00 0.00 4.70
1657 1947 1.260544 GCACTGAAAATGGAGCCCTT 58.739 50.000 0.00 0.00 0.00 3.95
1658 1948 1.067354 GCACTGAAAATGGAGCCCTTG 60.067 52.381 0.00 0.00 0.00 3.61
1659 1949 2.242043 CACTGAAAATGGAGCCCTTGT 58.758 47.619 0.00 0.00 0.00 3.16
1660 1950 2.029649 CACTGAAAATGGAGCCCTTGTG 60.030 50.000 0.00 0.00 0.00 3.33
1661 1951 0.968405 TGAAAATGGAGCCCTTGTGC 59.032 50.000 0.00 0.00 0.00 4.57
1672 1962 0.537371 CCCTTGTGCTCCCGAAGTTT 60.537 55.000 0.00 0.00 0.00 2.66
1677 1967 0.035739 GTGCTCCCGAAGTTTACCCA 59.964 55.000 0.00 0.00 0.00 4.51
1679 1969 1.025113 GCTCCCGAAGTTTACCCAGC 61.025 60.000 0.00 0.00 0.00 4.85
1681 1971 1.378119 CCCGAAGTTTACCCAGCCC 60.378 63.158 0.00 0.00 0.00 5.19
1682 1972 1.377229 CCGAAGTTTACCCAGCCCA 59.623 57.895 0.00 0.00 0.00 5.36
1685 1977 1.472480 CGAAGTTTACCCAGCCCATTG 59.528 52.381 0.00 0.00 0.00 2.82
1698 1990 2.093341 AGCCCATTGCCAATCAATTGTC 60.093 45.455 5.13 0.00 42.48 3.18
1701 1993 3.874543 CCCATTGCCAATCAATTGTCATG 59.125 43.478 5.13 3.43 42.48 3.07
1705 1999 2.496871 TGCCAATCAATTGTCATGGGTC 59.503 45.455 20.52 10.78 36.06 4.46
1717 2011 3.209410 GTCATGGGTCTCATTAGCTTGG 58.791 50.000 0.00 0.00 32.92 3.61
1720 2014 4.660303 TCATGGGTCTCATTAGCTTGGTAT 59.340 41.667 0.00 0.00 32.92 2.73
1730 2024 6.525629 TCATTAGCTTGGTATAGAGGCTTTC 58.474 40.000 0.00 0.00 34.88 2.62
1739 2033 1.055849 TAGAGGCTTTCAGGCACACA 58.944 50.000 0.00 0.00 44.19 3.72
1740 2034 0.536006 AGAGGCTTTCAGGCACACAC 60.536 55.000 0.00 0.00 44.19 3.82
1741 2035 0.819259 GAGGCTTTCAGGCACACACA 60.819 55.000 0.00 0.00 44.19 3.72
1742 2036 1.103398 AGGCTTTCAGGCACACACAC 61.103 55.000 0.00 0.00 44.19 3.82
1743 2037 1.360192 GCTTTCAGGCACACACACC 59.640 57.895 0.00 0.00 0.00 4.16
1744 2038 1.103398 GCTTTCAGGCACACACACCT 61.103 55.000 0.00 0.00 36.45 4.00
1748 2042 2.510906 AGGCACACACACCTGGTC 59.489 61.111 0.00 0.00 34.07 4.02
1749 2043 2.191908 GGCACACACACCTGGTCA 59.808 61.111 0.00 0.00 0.00 4.02
1750 2044 1.453015 GGCACACACACCTGGTCAA 60.453 57.895 0.00 0.00 0.00 3.18
1751 2045 1.447317 GGCACACACACCTGGTCAAG 61.447 60.000 0.00 0.00 0.00 3.02
1752 2046 0.748005 GCACACACACCTGGTCAAGT 60.748 55.000 0.00 0.00 0.00 3.16
1753 2047 1.750193 CACACACACCTGGTCAAGTT 58.250 50.000 0.00 0.00 0.00 2.66
1754 2048 2.091541 CACACACACCTGGTCAAGTTT 58.908 47.619 0.00 0.00 0.00 2.66
1755 2049 2.091541 ACACACACCTGGTCAAGTTTG 58.908 47.619 0.00 0.00 0.00 2.93
1756 2050 2.091541 CACACACCTGGTCAAGTTTGT 58.908 47.619 0.00 0.00 0.00 2.83
1757 2051 2.097466 CACACACCTGGTCAAGTTTGTC 59.903 50.000 0.00 0.00 0.00 3.18
1758 2052 2.026262 ACACACCTGGTCAAGTTTGTCT 60.026 45.455 0.00 0.00 0.00 3.41
1759 2053 3.199071 ACACACCTGGTCAAGTTTGTCTA 59.801 43.478 0.00 0.00 0.00 2.59
1760 2054 4.196193 CACACCTGGTCAAGTTTGTCTAA 58.804 43.478 0.00 0.00 0.00 2.10
1761 2055 4.638421 CACACCTGGTCAAGTTTGTCTAAA 59.362 41.667 0.00 0.00 0.00 1.85
1762 2056 5.124776 CACACCTGGTCAAGTTTGTCTAAAA 59.875 40.000 0.00 0.00 0.00 1.52
1763 2057 5.712917 ACACCTGGTCAAGTTTGTCTAAAAA 59.287 36.000 0.00 0.00 0.00 1.94
1815 2109 9.640952 ATTGTTGTTACATTATATGGTTAGGCT 57.359 29.630 0.00 0.00 33.44 4.58
1817 2111 7.500892 TGTTGTTACATTATATGGTTAGGCTGG 59.499 37.037 0.00 0.00 33.60 4.85
1819 2113 6.995686 TGTTACATTATATGGTTAGGCTGGTG 59.004 38.462 0.00 0.00 33.60 4.17
1824 2118 0.106519 ATGGTTAGGCTGGTGATGGC 60.107 55.000 0.00 0.00 0.00 4.40
1835 2129 3.152341 CTGGTGATGGCTCAAAAGAGTT 58.848 45.455 0.00 0.00 31.85 3.01
1840 2134 5.920840 GGTGATGGCTCAAAAGAGTTTAAAC 59.079 40.000 10.47 10.47 31.85 2.01
1845 2139 7.164230 TGGCTCAAAAGAGTTTAAACTTGAA 57.836 32.000 21.40 4.77 39.88 2.69
1898 2192 6.542005 TCGTATTATGTGCATCATGTTTTCCT 59.458 34.615 10.77 0.00 37.91 3.36
1907 2201 6.473455 GTGCATCATGTTTTCCTGCTTATTAC 59.527 38.462 0.00 0.00 34.02 1.89
1914 2208 9.507280 CATGTTTTCCTGCTTATTACATTAGTG 57.493 33.333 0.00 0.00 0.00 2.74
1915 2209 8.630054 TGTTTTCCTGCTTATTACATTAGTGT 57.370 30.769 0.00 0.00 42.39 3.55
1995 2290 7.817418 ACTTTGTATGCTTAGGAACAAGAAA 57.183 32.000 0.00 0.00 33.70 2.52
1996 2291 8.232913 ACTTTGTATGCTTAGGAACAAGAAAA 57.767 30.769 0.00 0.00 33.70 2.29
2068 2363 4.824479 TTGATCCTCAACTCATGTGCTA 57.176 40.909 0.00 0.00 30.26 3.49
2102 2397 5.479027 TGCTCTGCCATAAATGCATGATTAT 59.521 36.000 0.00 0.00 38.22 1.28
2103 2398 5.805486 GCTCTGCCATAAATGCATGATTATG 59.195 40.000 18.37 18.37 38.22 1.90
2110 2405 7.522562 GCCATAAATGCATGATTATGTGACTGA 60.523 37.037 21.44 0.00 37.66 3.41
2115 2410 5.584442 TGCATGATTATGTGACTGATTTGC 58.416 37.500 0.00 0.00 36.65 3.68
2160 2455 8.512138 GGCGATATAACAAGCATATACCTTTTT 58.488 33.333 0.00 0.00 0.00 1.94
2161 2456 9.329913 GCGATATAACAAGCATATACCTTTTTG 57.670 33.333 0.00 0.00 0.00 2.44
2199 2494 3.054434 AGCCTGGCAACACTGTCATTATA 60.054 43.478 22.65 0.00 46.17 0.98
2693 2998 2.573462 ACACTGATGTTGGATAGTGGCT 59.427 45.455 0.00 0.00 43.56 4.75
2729 3034 6.438763 CACAAAAGGAGGATTGTTGAGTTAC 58.561 40.000 0.00 0.00 37.66 2.50
2814 3119 6.839820 AACCACTTGTTTTCTACGAACTAG 57.160 37.500 0.00 0.00 36.42 2.57
2999 3342 6.240894 ACCACATCTTACTTCACATCACATT 58.759 36.000 0.00 0.00 0.00 2.71
3013 3356 6.988580 TCACATCACATTCATTAGATGGAGAC 59.011 38.462 0.00 0.00 41.55 3.36
3040 3385 1.197721 GTCAAAAGTGTCCGATGGCAG 59.802 52.381 0.00 0.00 0.00 4.85
3041 3386 1.071542 TCAAAAGTGTCCGATGGCAGA 59.928 47.619 0.00 0.00 0.00 4.26
3175 3521 2.784347 AGCTGCCTCTTTCCAGTTTAC 58.216 47.619 0.00 0.00 0.00 2.01
3182 3528 7.577616 GCTGCCTCTTTCCAGTTTACAAAATAT 60.578 37.037 0.00 0.00 0.00 1.28
3346 3708 3.775261 ATTTTGTTTGCCTGCATCCTT 57.225 38.095 0.00 0.00 0.00 3.36
3349 3711 0.899717 TGTTTGCCTGCATCCTTCCC 60.900 55.000 0.00 0.00 0.00 3.97
3350 3712 0.899717 GTTTGCCTGCATCCTTCCCA 60.900 55.000 0.00 0.00 0.00 4.37
3351 3713 0.041535 TTTGCCTGCATCCTTCCCAT 59.958 50.000 0.00 0.00 0.00 4.00
3352 3714 0.685131 TTGCCTGCATCCTTCCCATG 60.685 55.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.012518 GTGTTGAGATCCACCTTCATGG 58.987 50.000 0.00 0.00 41.57 3.66
51 52 1.202582 CGACCTCTTCCTTGACGACAT 59.797 52.381 0.00 0.00 0.00 3.06
428 429 1.890510 GGCGTCCGTCCAGTTTTGT 60.891 57.895 0.00 0.00 0.00 2.83
454 456 4.629523 GTCCGTTTGGGTCGGCCA 62.630 66.667 9.07 0.00 46.49 5.36
501 503 1.006102 CAACTCCAACGAGCCGACT 60.006 57.895 1.50 0.00 40.03 4.18
521 523 9.903682 ACAAAAACAAATGAGAGATGTCTTATG 57.096 29.630 0.00 0.00 29.62 1.90
528 530 8.783093 TGGTAGTACAAAAACAAATGAGAGATG 58.217 33.333 2.06 0.00 0.00 2.90
529 531 8.918202 TGGTAGTACAAAAACAAATGAGAGAT 57.082 30.769 2.06 0.00 0.00 2.75
530 532 8.740123 TTGGTAGTACAAAAACAAATGAGAGA 57.260 30.769 2.06 0.00 0.00 3.10
531 533 9.233232 GTTTGGTAGTACAAAAACAAATGAGAG 57.767 33.333 18.73 0.00 41.53 3.20
532 534 8.740906 TGTTTGGTAGTACAAAAACAAATGAGA 58.259 29.630 21.84 6.12 41.53 3.27
533 535 8.918961 TGTTTGGTAGTACAAAAACAAATGAG 57.081 30.769 21.84 0.00 41.53 2.90
534 536 9.307121 CATGTTTGGTAGTACAAAAACAAATGA 57.693 29.630 25.17 11.23 43.49 2.57
535 537 8.547069 CCATGTTTGGTAGTACAAAAACAAATG 58.453 33.333 25.17 21.02 43.49 2.32
536 538 8.655651 CCATGTTTGGTAGTACAAAAACAAAT 57.344 30.769 25.17 14.50 43.49 2.32
552 554 6.238157 GCATATAAAATGTGCACCATGTTTGG 60.238 38.462 15.69 0.00 45.37 3.28
553 555 6.707711 GCATATAAAATGTGCACCATGTTTG 58.292 36.000 15.69 6.27 45.37 2.93
554 556 6.907206 GCATATAAAATGTGCACCATGTTT 57.093 33.333 15.69 11.23 45.37 2.83
563 565 8.382875 GGTTTTCTTCAAGCATATAAAATGTGC 58.617 33.333 0.85 0.85 46.26 4.57
564 566 9.421806 TGGTTTTCTTCAAGCATATAAAATGTG 57.578 29.630 0.00 0.00 0.00 3.21
608 610 1.134670 ACAAATCCCTGCTCTAGACGC 60.135 52.381 7.10 7.10 0.00 5.19
665 670 0.318275 GCCTACGCAGCTAGCAGTAG 60.318 60.000 25.32 25.32 46.13 2.57
666 671 1.035385 TGCCTACGCAGCTAGCAGTA 61.035 55.000 18.83 15.97 46.13 2.74
667 672 2.351244 TGCCTACGCAGCTAGCAGT 61.351 57.895 18.83 15.68 46.13 4.40
668 673 2.496341 TGCCTACGCAGCTAGCAG 59.504 61.111 18.83 10.62 46.13 4.24
676 681 2.817834 GCCGTGATTGCCTACGCA 60.818 61.111 0.00 0.00 45.49 5.24
677 682 2.309764 CTTGCCGTGATTGCCTACGC 62.310 60.000 0.00 0.00 38.87 4.42
678 683 1.715585 CTTGCCGTGATTGCCTACG 59.284 57.895 0.00 0.00 39.83 3.51
811 820 3.772060 AGGCGTTACTTACCTTACGAG 57.228 47.619 0.00 0.00 36.16 4.18
812 821 5.835113 ATTAGGCGTTACTTACCTTACGA 57.165 39.130 0.00 0.00 36.16 3.43
813 822 6.892310 AAATTAGGCGTTACTTACCTTACG 57.108 37.500 0.00 0.00 34.92 3.18
814 823 8.321005 CGTTAAATTAGGCGTTACTTACCTTAC 58.679 37.037 0.00 0.00 34.92 2.34
815 824 8.247562 TCGTTAAATTAGGCGTTACTTACCTTA 58.752 33.333 0.00 0.00 34.92 2.69
817 826 6.531594 GTCGTTAAATTAGGCGTTACTTACCT 59.468 38.462 0.00 0.00 37.61 3.08
1241 1252 2.154462 CATGACGCCAAAAAGGAGAGT 58.846 47.619 0.00 0.00 40.01 3.24
1242 1253 1.135575 GCATGACGCCAAAAAGGAGAG 60.136 52.381 0.00 0.00 40.01 3.20
1318 1481 2.173519 CTTTGATGTGGCAATCCAGGT 58.826 47.619 0.00 0.00 44.48 4.00
1328 1491 7.548196 AACATAATACGGTACTTTGATGTGG 57.452 36.000 0.00 0.00 0.00 4.17
1359 1524 3.711704 ACAGTCCTTCCATGATAACGGAT 59.288 43.478 0.00 0.00 0.00 4.18
1360 1525 3.104512 ACAGTCCTTCCATGATAACGGA 58.895 45.455 0.00 0.00 0.00 4.69
1361 1526 3.198068 CACAGTCCTTCCATGATAACGG 58.802 50.000 0.00 0.00 0.00 4.44
1362 1527 3.861840 ACACAGTCCTTCCATGATAACG 58.138 45.455 0.00 0.00 0.00 3.18
1363 1528 5.237344 GCATACACAGTCCTTCCATGATAAC 59.763 44.000 0.00 0.00 0.00 1.89
1365 1530 4.501400 CGCATACACAGTCCTTCCATGATA 60.501 45.833 0.00 0.00 0.00 2.15
1366 1531 3.742327 CGCATACACAGTCCTTCCATGAT 60.742 47.826 0.00 0.00 0.00 2.45
1368 1533 1.935873 CGCATACACAGTCCTTCCATG 59.064 52.381 0.00 0.00 0.00 3.66
1371 1536 1.090052 GCCGCATACACAGTCCTTCC 61.090 60.000 0.00 0.00 0.00 3.46
1372 1537 0.391130 TGCCGCATACACAGTCCTTC 60.391 55.000 0.00 0.00 0.00 3.46
1373 1538 0.391661 CTGCCGCATACACAGTCCTT 60.392 55.000 0.00 0.00 0.00 3.36
1377 1544 0.034756 TGTTCTGCCGCATACACAGT 59.965 50.000 0.00 0.00 33.12 3.55
1400 1567 8.361139 CCGATTCTAGGATTGTAATACACTTCT 58.639 37.037 0.00 0.00 0.00 2.85
1401 1568 8.358148 TCCGATTCTAGGATTGTAATACACTTC 58.642 37.037 0.00 0.00 31.86 3.01
1403 1570 7.834881 TCCGATTCTAGGATTGTAATACACT 57.165 36.000 0.00 0.00 31.86 3.55
1458 1626 8.706322 TCACTTGCTACTTGGATATATACTGA 57.294 34.615 0.00 0.00 0.00 3.41
1462 1630 9.143155 TCAGTTCACTTGCTACTTGGATATATA 57.857 33.333 0.00 0.00 0.00 0.86
1466 1634 5.738619 TCAGTTCACTTGCTACTTGGATA 57.261 39.130 0.00 0.00 0.00 2.59
1475 1644 3.063997 CGACACTTTTCAGTTCACTTGCT 59.936 43.478 0.00 0.00 0.00 3.91
1488 1657 5.507315 CCTTTTACAAGGCATCGACACTTTT 60.507 40.000 0.00 0.00 43.55 2.27
1528 1706 7.042725 CGCACTTGCACAAATATATAGTACACT 60.043 37.037 1.48 0.00 42.21 3.55
1529 1707 7.063456 CGCACTTGCACAAATATATAGTACAC 58.937 38.462 1.48 0.00 42.21 2.90
1530 1708 6.759356 ACGCACTTGCACAAATATATAGTACA 59.241 34.615 1.48 0.00 42.21 2.90
1531 1709 7.169308 AGACGCACTTGCACAAATATATAGTAC 59.831 37.037 1.48 0.00 42.21 2.73
1532 1710 7.169140 CAGACGCACTTGCACAAATATATAGTA 59.831 37.037 1.48 0.00 42.21 1.82
1533 1711 6.018751 CAGACGCACTTGCACAAATATATAGT 60.019 38.462 1.48 0.00 42.21 2.12
1556 1840 0.245539 CCAGGGCATTGCTGTTTCAG 59.754 55.000 8.82 0.00 34.12 3.02
1583 1867 9.750882 CTACTACTAGCGGAATTTAACAAAAAC 57.249 33.333 0.00 0.00 0.00 2.43
1605 1893 9.780186 GCCTTTCAATAAGATAATACACCTACT 57.220 33.333 0.00 0.00 0.00 2.57
1606 1894 9.780186 AGCCTTTCAATAAGATAATACACCTAC 57.220 33.333 0.00 0.00 0.00 3.18
1607 1895 9.998106 GAGCCTTTCAATAAGATAATACACCTA 57.002 33.333 0.00 0.00 0.00 3.08
1608 1896 8.718656 AGAGCCTTTCAATAAGATAATACACCT 58.281 33.333 0.00 0.00 0.00 4.00
1609 1897 8.910351 AGAGCCTTTCAATAAGATAATACACC 57.090 34.615 0.00 0.00 0.00 4.16
1611 1899 9.905713 ACAAGAGCCTTTCAATAAGATAATACA 57.094 29.630 0.00 0.00 0.00 2.29
1613 1901 8.840321 GCACAAGAGCCTTTCAATAAGATAATA 58.160 33.333 0.00 0.00 0.00 0.98
1614 1902 7.340232 TGCACAAGAGCCTTTCAATAAGATAAT 59.660 33.333 0.00 0.00 0.00 1.28
1615 1903 6.658816 TGCACAAGAGCCTTTCAATAAGATAA 59.341 34.615 0.00 0.00 0.00 1.75
1630 1920 2.294233 TCCATTTTCAGTGCACAAGAGC 59.706 45.455 21.04 0.00 0.00 4.09
1631 1921 3.611057 GCTCCATTTTCAGTGCACAAGAG 60.611 47.826 21.04 12.63 0.00 2.85
1632 1922 2.294233 GCTCCATTTTCAGTGCACAAGA 59.706 45.455 21.04 13.78 0.00 3.02
1633 1923 2.608752 GGCTCCATTTTCAGTGCACAAG 60.609 50.000 21.04 11.41 0.00 3.16
1634 1924 1.340889 GGCTCCATTTTCAGTGCACAA 59.659 47.619 21.04 4.51 0.00 3.33
1654 1944 1.804748 GTAAACTTCGGGAGCACAAGG 59.195 52.381 0.00 0.00 0.00 3.61
1657 1947 0.035739 GGGTAAACTTCGGGAGCACA 59.964 55.000 0.00 0.00 0.00 4.57
1658 1948 0.035739 TGGGTAAACTTCGGGAGCAC 59.964 55.000 0.00 0.00 0.00 4.40
1659 1949 0.323629 CTGGGTAAACTTCGGGAGCA 59.676 55.000 0.00 0.00 0.00 4.26
1660 1950 1.025113 GCTGGGTAAACTTCGGGAGC 61.025 60.000 0.00 0.00 0.00 4.70
1661 1951 0.392595 GGCTGGGTAAACTTCGGGAG 60.393 60.000 0.00 0.00 0.00 4.30
1666 1956 1.204704 GCAATGGGCTGGGTAAACTTC 59.795 52.381 0.00 0.00 40.25 3.01
1672 1962 0.396974 GATTGGCAATGGGCTGGGTA 60.397 55.000 19.07 0.00 44.01 3.69
1677 1967 1.910671 ACAATTGATTGGCAATGGGCT 59.089 42.857 19.07 0.00 46.25 5.19
1685 1977 2.762327 AGACCCATGACAATTGATTGGC 59.238 45.455 13.59 5.69 46.03 4.52
1698 1990 3.287867 ACCAAGCTAATGAGACCCATG 57.712 47.619 0.00 0.00 35.24 3.66
1701 1993 5.046950 CCTCTATACCAAGCTAATGAGACCC 60.047 48.000 0.00 0.00 0.00 4.46
1705 1999 5.736951 AGCCTCTATACCAAGCTAATGAG 57.263 43.478 0.00 0.00 30.46 2.90
1717 2011 3.198872 GTGTGCCTGAAAGCCTCTATAC 58.801 50.000 0.00 0.00 0.00 1.47
1720 2014 1.055849 TGTGTGCCTGAAAGCCTCTA 58.944 50.000 0.00 0.00 0.00 2.43
1739 2033 4.497291 TTAGACAAACTTGACCAGGTGT 57.503 40.909 0.00 0.00 0.00 4.16
1740 2034 5.828299 TTTTAGACAAACTTGACCAGGTG 57.172 39.130 0.00 0.00 0.00 4.00
1763 2057 3.317993 CCAATCGACTTGACCAGGTTTTT 59.682 43.478 0.00 0.00 36.97 1.94
1764 2058 2.884639 CCAATCGACTTGACCAGGTTTT 59.115 45.455 0.00 0.00 36.97 2.43
1765 2059 2.158667 ACCAATCGACTTGACCAGGTTT 60.159 45.455 0.00 0.00 36.97 3.27
1766 2060 1.420138 ACCAATCGACTTGACCAGGTT 59.580 47.619 0.00 0.00 36.97 3.50
1767 2061 1.056660 ACCAATCGACTTGACCAGGT 58.943 50.000 0.00 0.00 36.97 4.00
1768 2062 2.496070 TCTACCAATCGACTTGACCAGG 59.504 50.000 8.56 0.00 36.97 4.45
1813 2107 1.471684 CTCTTTTGAGCCATCACCAGC 59.528 52.381 0.00 0.00 39.99 4.85
1840 2134 7.144722 TGGTAAAAGCATAGTGTGATTCAAG 57.855 36.000 0.00 0.00 34.86 3.02
1874 2168 6.634035 CAGGAAAACATGATGCACATAATACG 59.366 38.462 0.00 0.00 37.46 3.06
1898 2192 7.106890 TGCCAGTAACACTAATGTAATAAGCA 58.893 34.615 0.00 0.00 38.45 3.91
1907 2201 6.435430 TGCTTATTGCCAGTAACACTAATG 57.565 37.500 0.00 0.00 42.00 1.90
1911 2205 7.339212 TGAATTATGCTTATTGCCAGTAACACT 59.661 33.333 0.00 0.00 42.00 3.55
1912 2206 7.479980 TGAATTATGCTTATTGCCAGTAACAC 58.520 34.615 0.00 0.00 42.00 3.32
1914 2208 9.533253 AAATGAATTATGCTTATTGCCAGTAAC 57.467 29.630 0.00 0.00 42.00 2.50
1917 2211 7.011669 GCAAAATGAATTATGCTTATTGCCAGT 59.988 33.333 0.00 0.00 42.00 4.00
1918 2212 7.011576 TGCAAAATGAATTATGCTTATTGCCAG 59.988 33.333 0.00 0.00 39.75 4.85
2015 2310 9.515226 TTCAGTAAAGCATAAAAGGAACATAGT 57.485 29.630 0.00 0.00 0.00 2.12
2020 2315 8.968242 CAAGTTTCAGTAAAGCATAAAAGGAAC 58.032 33.333 0.00 0.00 0.00 3.62
2068 2363 3.690745 GCAGAGCATTTGTGCCCT 58.309 55.556 0.00 0.00 40.05 5.19
2084 2379 6.584942 CAGTCACATAATCATGCATTTATGGC 59.415 38.462 24.75 17.45 39.19 4.40
2102 2397 5.301551 ACCAATGTTTAGCAAATCAGTCACA 59.698 36.000 0.00 0.00 0.00 3.58
2103 2398 5.772521 ACCAATGTTTAGCAAATCAGTCAC 58.227 37.500 0.00 0.00 0.00 3.67
2110 2405 6.934083 CCCAAGTAAACCAATGTTTAGCAAAT 59.066 34.615 0.00 0.00 45.16 2.32
2115 2410 4.216687 TCGCCCAAGTAAACCAATGTTTAG 59.783 41.667 0.00 0.00 45.16 1.85
2160 2455 2.694628 AGGCTTCAAAACATCAACTGCA 59.305 40.909 0.00 0.00 0.00 4.41
2161 2456 3.054878 CAGGCTTCAAAACATCAACTGC 58.945 45.455 0.00 0.00 0.00 4.40
2199 2494 5.252969 ACATATCAATCTTTGCATTGCGT 57.747 34.783 3.84 0.00 34.26 5.24
2363 2658 5.649395 TGGGAAAGCACTTCTGATTAAGATG 59.351 40.000 0.00 0.00 33.93 2.90
2693 2998 5.311121 TCCTCCTTTTGTGGGTAGTATCAAA 59.689 40.000 0.00 0.00 0.00 2.69
2729 3034 2.423538 GGTTCTTTCCATCACCCAATCG 59.576 50.000 0.00 0.00 0.00 3.34
2797 3102 6.711579 CACTTTGCTAGTTCGTAGAAAACAA 58.288 36.000 0.00 0.00 45.90 2.83
2814 3119 1.562575 GCAAGCCACATGCACTTTGC 61.563 55.000 9.02 9.02 44.83 3.68
2999 3342 3.967326 ACCATTCGGTCTCCATCTAATGA 59.033 43.478 0.00 0.00 44.71 2.57
3013 3356 1.196808 CGGACACTTTTGACCATTCGG 59.803 52.381 0.00 0.00 37.41 4.30
3040 3385 1.098050 GCCCTTGTGATGATGGTGTC 58.902 55.000 0.00 0.00 0.00 3.67
3041 3386 0.677731 CGCCCTTGTGATGATGGTGT 60.678 55.000 0.00 0.00 0.00 4.16
3175 3521 6.378280 ACAAACTTAGAGGGAGGCATATTTTG 59.622 38.462 0.00 0.00 0.00 2.44
3182 3528 2.708861 TCAACAAACTTAGAGGGAGGCA 59.291 45.455 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.