Multiple sequence alignment - TraesCS1B01G432100

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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 TraesCS1B01G432100 chr1B 100.000 2468 0 0 1 2468 656663778 656666245 0.000000e+00 4558.0
1 TraesCS1B01G432100 chr1A 86.815 1661 128 35 749 2355 566390304 566391927 0.000000e+00 1770.0
2 TraesCS1B01G432100 chr1A 85.311 177 16 5 108 278 566389692 566389864 9.070000e-40 174.0
3 TraesCS1B01G432100 chr1A 89.109 101 7 1 2368 2468 566392343 566392439 3.330000e-24 122.0
4 TraesCS1B01G432100 chr1D 88.169 1420 92 22 744 2122 472402232 472403616 0.000000e+00 1622.0
5 TraesCS1B01G432100 chr1D 81.296 540 46 23 103 624 472401641 472402143 1.070000e-103 387.0
6 TraesCS1B01G432100 chr1D 85.656 244 25 4 2109 2351 472403633 472403867 5.270000e-62 248.0
7 TraesCS1B01G432100 chr1D 94.872 78 4 0 2368 2445 472404297 472404374 3.330000e-24 122.0
8 TraesCS1B01G432100 chr3B 89.181 684 46 11 567 1236 4650850 4650181 0.000000e+00 828.0
9 TraesCS1B01G432100 chr3B 87.717 692 48 15 567 1244 3750330 3749662 0.000000e+00 773.0
10 TraesCS1B01G432100 chr4B 93.137 102 7 0 1 102 609362757 609362858 1.530000e-32 150.0
11 TraesCS1B01G432100 chr7B 91.589 107 9 0 5 111 624165502 624165396 5.500000e-32 148.0
12 TraesCS1B01G432100 chrUn 86.585 82 10 1 2 83 183984541 183984621 3.380000e-14 89.8


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 TraesCS1B01G432100 chr1B 656663778 656666245 2467 False 4558.000000 4558 100.000000 1 2468 1 chr1B.!!$F1 2467
1 TraesCS1B01G432100 chr1A 566389692 566392439 2747 False 688.666667 1770 87.078333 108 2468 3 chr1A.!!$F1 2360
2 TraesCS1B01G432100 chr1D 472401641 472404374 2733 False 594.750000 1622 87.498250 103 2445 4 chr1D.!!$F1 2342
3 TraesCS1B01G432100 chr3B 4650181 4650850 669 True 828.000000 828 89.181000 567 1236 1 chr3B.!!$R2 669
4 TraesCS1B01G432100 chr3B 3749662 3750330 668 True 773.000000 773 87.717000 567 1244 1 chr3B.!!$R1 677

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
73 74 0.109781 CAGACCGGCCAAAACATTCG 60.110 55.0 0.0 0.0 0.00 3.34 F
327 339 0.184211 AACCCACCTTTTGGCTACGT 59.816 50.0 0.0 0.0 45.37 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1413 0.736325 CTGCCGGTACTGTTTCCTCG 60.736 60.0 1.9 0.0 0.00 4.63 R
2299 2481 0.108424 GCAGTCTCCATCTTGCGACT 60.108 55.0 0.0 0.0 37.22 4.18 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
23 24 2.957491 AGAGGAGCTTGAATCTGACG 57.043 50.000 0.00 0.00 0.00 4.35
24 25 1.480137 AGAGGAGCTTGAATCTGACGG 59.520 52.381 0.00 0.00 0.00 4.79
25 26 1.205893 GAGGAGCTTGAATCTGACGGT 59.794 52.381 0.00 0.00 0.00 4.83
26 27 1.066573 AGGAGCTTGAATCTGACGGTG 60.067 52.381 0.00 0.00 0.00 4.94
27 28 1.338200 GGAGCTTGAATCTGACGGTGT 60.338 52.381 0.00 0.00 0.00 4.16
28 29 2.417719 GAGCTTGAATCTGACGGTGTT 58.582 47.619 0.00 0.00 0.00 3.32
29 30 2.146342 AGCTTGAATCTGACGGTGTTG 58.854 47.619 0.00 0.00 0.00 3.33
30 31 1.400242 GCTTGAATCTGACGGTGTTGC 60.400 52.381 0.00 0.00 0.00 4.17
31 32 1.872952 CTTGAATCTGACGGTGTTGCA 59.127 47.619 0.00 0.00 0.00 4.08
32 33 1.225855 TGAATCTGACGGTGTTGCAC 58.774 50.000 0.00 0.00 0.00 4.57
33 34 1.225855 GAATCTGACGGTGTTGCACA 58.774 50.000 1.61 0.00 35.86 4.57
34 35 1.601903 GAATCTGACGGTGTTGCACAA 59.398 47.619 1.61 0.00 35.86 3.33
35 36 0.944386 ATCTGACGGTGTTGCACAAC 59.056 50.000 6.57 6.57 41.50 3.32
43 44 2.627791 TGTTGCACAACAGATCGGG 58.372 52.632 12.02 0.00 45.42 5.14
44 45 1.210155 GTTGCACAACAGATCGGGC 59.790 57.895 8.61 0.00 40.84 6.13
45 46 2.324330 TTGCACAACAGATCGGGCG 61.324 57.895 0.00 0.00 0.00 6.13
46 47 3.499737 GCACAACAGATCGGGCGG 61.500 66.667 0.00 0.00 0.00 6.13
47 48 3.499737 CACAACAGATCGGGCGGC 61.500 66.667 0.00 0.00 0.00 6.53
48 49 3.706373 ACAACAGATCGGGCGGCT 61.706 61.111 9.56 0.00 0.00 5.52
49 50 3.197790 CAACAGATCGGGCGGCTG 61.198 66.667 12.43 12.43 35.81 4.85
67 68 2.668212 CGAGCAGACCGGCCAAAA 60.668 61.111 0.00 0.00 0.00 2.44
68 69 2.954611 GAGCAGACCGGCCAAAAC 59.045 61.111 0.00 0.00 0.00 2.43
69 70 1.896660 GAGCAGACCGGCCAAAACA 60.897 57.895 0.00 0.00 0.00 2.83
70 71 1.228552 AGCAGACCGGCCAAAACAT 60.229 52.632 0.00 0.00 0.00 2.71
71 72 0.827507 AGCAGACCGGCCAAAACATT 60.828 50.000 0.00 0.00 0.00 2.71
72 73 0.388520 GCAGACCGGCCAAAACATTC 60.389 55.000 0.00 0.00 0.00 2.67
73 74 0.109781 CAGACCGGCCAAAACATTCG 60.110 55.000 0.00 0.00 0.00 3.34
74 75 1.211709 GACCGGCCAAAACATTCGG 59.788 57.895 0.00 0.00 45.42 4.30
75 76 2.126110 CCGGCCAAAACATTCGGC 60.126 61.111 2.24 0.00 45.47 5.54
78 79 2.126110 GCCAAAACATTCGGCCGG 60.126 61.111 27.83 12.37 40.07 6.13
79 80 2.926420 GCCAAAACATTCGGCCGGT 61.926 57.895 27.83 13.15 40.07 5.28
80 81 1.080839 CCAAAACATTCGGCCGGTG 60.081 57.895 27.83 25.41 0.00 4.94
81 82 1.732683 CAAAACATTCGGCCGGTGC 60.733 57.895 27.83 0.00 0.00 5.01
82 83 3.262142 AAAACATTCGGCCGGTGCG 62.262 57.895 27.83 14.10 38.85 5.34
114 115 2.506444 CGGTGCCCTAAGTTTTAACCA 58.494 47.619 0.00 0.00 0.00 3.67
119 120 4.521256 GTGCCCTAAGTTTTAACCATGTCA 59.479 41.667 0.00 0.00 0.00 3.58
128 129 6.872920 AGTTTTAACCATGTCACATTTGTGT 58.127 32.000 10.30 0.00 45.76 3.72
133 134 3.817084 ACCATGTCACATTTGTGTCTGAG 59.183 43.478 10.30 2.00 45.76 3.35
143 144 1.239347 TGTGTCTGAGACTCTCGTGG 58.761 55.000 14.42 0.00 32.35 4.94
153 154 1.226156 CTCTCGTGGTCTCTTCGCG 60.226 63.158 0.00 0.00 39.20 5.87
156 157 1.913451 CTCGTGGTCTCTTCGCGTCT 61.913 60.000 5.77 0.00 38.95 4.18
169 170 4.079850 CGTCTCCTGCTGCTGGCT 62.080 66.667 19.55 0.00 42.39 4.75
170 171 2.436292 GTCTCCTGCTGCTGGCTG 60.436 66.667 19.55 14.38 42.39 4.85
171 172 4.405671 TCTCCTGCTGCTGGCTGC 62.406 66.667 19.55 15.66 42.39 5.25
197 201 2.036346 GCAGTTTGAAATGCTTGGGAGT 59.964 45.455 8.72 0.00 45.65 3.85
283 290 3.895232 ACCACTGCTCCTGTACTTATG 57.105 47.619 0.00 0.00 0.00 1.90
295 302 4.023878 CCTGTACTTATGAGCGTACTCTCC 60.024 50.000 10.28 0.00 43.85 3.71
296 303 4.778579 TGTACTTATGAGCGTACTCTCCT 58.221 43.478 10.28 3.30 43.85 3.69
298 305 3.215975 ACTTATGAGCGTACTCTCCTCC 58.784 50.000 10.28 0.00 43.85 4.30
314 326 1.473434 CCTCCGCTATCTTCAACCCAC 60.473 57.143 0.00 0.00 0.00 4.61
324 336 2.175931 TCTTCAACCCACCTTTTGGCTA 59.824 45.455 0.00 0.00 45.37 3.93
326 338 0.596082 CAACCCACCTTTTGGCTACG 59.404 55.000 0.00 0.00 45.37 3.51
327 339 0.184211 AACCCACCTTTTGGCTACGT 59.816 50.000 0.00 0.00 45.37 3.57
329 341 1.271001 ACCCACCTTTTGGCTACGTAC 60.271 52.381 0.00 0.00 45.37 3.67
331 343 2.234414 CCCACCTTTTGGCTACGTACTA 59.766 50.000 0.00 0.00 45.37 1.82
332 344 3.256558 CCACCTTTTGGCTACGTACTAC 58.743 50.000 0.00 0.00 45.59 2.73
333 345 3.306225 CCACCTTTTGGCTACGTACTACA 60.306 47.826 0.00 0.00 45.59 2.74
334 346 4.309099 CACCTTTTGGCTACGTACTACAA 58.691 43.478 0.00 0.00 45.59 2.41
335 347 4.387862 CACCTTTTGGCTACGTACTACAAG 59.612 45.833 0.00 0.00 45.59 3.16
336 348 3.370061 CCTTTTGGCTACGTACTACAAGC 59.630 47.826 0.00 0.00 0.00 4.01
349 361 4.013267 ACTACAAGCTGTGCAAGATCTT 57.987 40.909 0.88 0.88 0.00 2.40
404 437 1.931841 CAGTGCCGTCAGATTCAGATG 59.068 52.381 0.00 0.00 0.00 2.90
405 438 0.654683 GTGCCGTCAGATTCAGATGC 59.345 55.000 0.00 0.00 0.00 3.91
406 439 0.807275 TGCCGTCAGATTCAGATGCG 60.807 55.000 0.00 0.00 0.00 4.73
407 440 1.930100 CCGTCAGATTCAGATGCGC 59.070 57.895 0.00 0.00 0.00 6.09
408 441 1.493950 CCGTCAGATTCAGATGCGCC 61.494 60.000 4.18 0.00 0.00 6.53
409 442 1.493950 CGTCAGATTCAGATGCGCCC 61.494 60.000 4.18 0.00 0.00 6.13
412 445 1.147824 AGATTCAGATGCGCCCTGG 59.852 57.895 21.62 3.82 32.73 4.45
441 476 1.596727 GCTCAGAATCGCCATCTTCAC 59.403 52.381 0.00 0.00 0.00 3.18
452 487 1.467734 CCATCTTCACAAGCTCAGCAC 59.532 52.381 0.00 0.00 0.00 4.40
457 492 0.815213 TCACAAGCTCAGCACCACAC 60.815 55.000 0.00 0.00 0.00 3.82
458 493 1.096967 CACAAGCTCAGCACCACACA 61.097 55.000 0.00 0.00 0.00 3.72
459 494 0.394216 ACAAGCTCAGCACCACACAA 60.394 50.000 0.00 0.00 0.00 3.33
460 495 0.740149 CAAGCTCAGCACCACACAAA 59.260 50.000 0.00 0.00 0.00 2.83
461 496 1.338973 CAAGCTCAGCACCACACAAAT 59.661 47.619 0.00 0.00 0.00 2.32
466 501 3.853307 GCTCAGCACCACACAAATGTAAC 60.853 47.826 0.00 0.00 36.72 2.50
470 505 3.249080 AGCACCACACAAATGTAACGTAC 59.751 43.478 0.00 0.00 36.72 3.67
584 625 4.038080 CCAACGAAACCTGCCCGC 62.038 66.667 0.00 0.00 0.00 6.13
585 626 2.978010 CAACGAAACCTGCCCGCT 60.978 61.111 0.00 0.00 0.00 5.52
586 627 2.203294 AACGAAACCTGCCCGCTT 60.203 55.556 0.00 0.00 0.00 4.68
587 628 2.551912 AACGAAACCTGCCCGCTTG 61.552 57.895 0.00 0.00 0.00 4.01
588 629 4.404654 CGAAACCTGCCCGCTTGC 62.405 66.667 0.00 0.00 0.00 4.01
723 764 2.743928 CCACCGCCTGCTCTGTTC 60.744 66.667 0.00 0.00 0.00 3.18
724 765 3.114616 CACCGCCTGCTCTGTTCG 61.115 66.667 0.00 0.00 0.00 3.95
725 766 4.379243 ACCGCCTGCTCTGTTCGG 62.379 66.667 0.00 0.00 45.04 4.30
730 771 4.379243 CTGCTCTGTTCGGCCGGT 62.379 66.667 27.83 0.00 0.00 5.28
1132 1223 1.452833 GGGAGCAAGATGCCAGTCC 60.453 63.158 0.00 0.00 46.52 3.85
1182 1285 1.142778 CTAAGAAGAGGCGCTGCGAC 61.143 60.000 28.07 25.36 33.59 5.19
1420 1523 1.585668 CTAGCGTGATCGTGAAGCTTG 59.414 52.381 2.10 0.00 39.14 4.01
1470 1576 1.377536 GGAACCAGCAGAGATGAAGC 58.622 55.000 0.00 0.00 0.00 3.86
1496 1606 1.547820 TGATCTCTGAACTCGCTTGCT 59.452 47.619 0.00 0.00 0.00 3.91
1501 1611 2.341257 TCTGAACTCGCTTGCTGAATC 58.659 47.619 0.00 0.00 0.00 2.52
1505 1615 2.462456 ACTCGCTTGCTGAATCTCAA 57.538 45.000 0.00 0.00 0.00 3.02
1508 1618 3.755378 ACTCGCTTGCTGAATCTCAATTT 59.245 39.130 0.00 0.00 0.00 1.82
1558 1674 7.713507 CAGTGTGTTCTAGCTAGATAGAGTAGT 59.286 40.741 23.81 8.97 33.44 2.73
1569 1685 9.245481 AGCTAGATAGAGTAGTTGTAGTTTGTT 57.755 33.333 0.00 0.00 0.00 2.83
1575 1691 7.527568 AGAGTAGTTGTAGTTTGTTCTAGCT 57.472 36.000 0.00 0.00 0.00 3.32
1576 1692 8.632906 AGAGTAGTTGTAGTTTGTTCTAGCTA 57.367 34.615 0.00 0.00 0.00 3.32
1577 1693 8.732531 AGAGTAGTTGTAGTTTGTTCTAGCTAG 58.267 37.037 15.01 15.01 0.00 3.42
1635 1758 4.916041 AATCAGGTGATTGGACTTGAGA 57.084 40.909 4.37 0.00 42.66 3.27
1660 1783 4.142609 CTTGGCTATCTCAAGGCTAACA 57.857 45.455 0.00 0.00 42.33 2.41
1670 1793 2.938451 TCAAGGCTAACAGAATGCATCG 59.062 45.455 0.00 0.00 42.53 3.84
1682 1805 4.975502 CAGAATGCATCGAGTCTACTTCTC 59.024 45.833 0.00 0.00 0.00 2.87
1694 1817 6.349777 CGAGTCTACTTCTCCTTCTGTTTGAT 60.350 42.308 0.00 0.00 0.00 2.57
1740 1863 4.344359 AACAGAGGAGAGTGGTTTCTTC 57.656 45.455 0.00 0.00 0.00 2.87
1751 1874 3.578716 AGTGGTTTCTTCTGGATCGAGAA 59.421 43.478 17.88 17.88 0.00 2.87
1787 1910 1.153706 CTACCCGGTGTGCTTACGG 60.154 63.158 0.00 0.00 46.79 4.02
1802 1925 6.260493 TGTGCTTACGGTTTACAAACATACTT 59.740 34.615 7.12 0.00 40.63 2.24
1806 1929 8.019094 GCTTACGGTTTACAAACATACTTTCAT 58.981 33.333 7.12 0.00 40.63 2.57
1825 1948 9.553064 ACTTTCATTGAGATGTTATGGATCTAC 57.447 33.333 0.00 0.00 34.77 2.59
1834 1957 9.553064 GAGATGTTATGGATCTACAAAACAGAT 57.447 33.333 8.68 0.00 35.43 2.90
1837 1960 8.722480 TGTTATGGATCTACAAAACAGATGAG 57.278 34.615 0.00 0.00 32.86 2.90
1856 1979 3.243535 TGAGGATGGATTCTTGTCGATCG 60.244 47.826 9.36 9.36 35.09 3.69
1860 1983 3.699779 TGGATTCTTGTCGATCGAGAG 57.300 47.619 20.09 18.75 37.79 3.20
1876 1999 3.829026 TCGAGAGAGTGGGGAATGATATG 59.171 47.826 0.00 0.00 34.84 1.78
1880 2003 6.323482 CGAGAGAGTGGGGAATGATATGATAT 59.677 42.308 0.00 0.00 0.00 1.63
1882 2005 9.206690 GAGAGAGTGGGGAATGATATGATATTA 57.793 37.037 0.00 0.00 0.00 0.98
1895 2018 9.666191 ATGATATGATATTACTAGGATGGCTGA 57.334 33.333 0.00 0.00 0.00 4.26
1896 2019 8.918116 TGATATGATATTACTAGGATGGCTGAC 58.082 37.037 0.00 0.00 0.00 3.51
1897 2020 8.844865 ATATGATATTACTAGGATGGCTGACA 57.155 34.615 0.00 0.00 0.00 3.58
1898 2021 6.346477 TGATATTACTAGGATGGCTGACAC 57.654 41.667 0.00 0.00 0.00 3.67
1899 2022 5.246203 TGATATTACTAGGATGGCTGACACC 59.754 44.000 0.00 0.00 0.00 4.16
1900 2023 2.848678 TACTAGGATGGCTGACACCT 57.151 50.000 9.17 9.17 35.61 4.00
1901 2024 1.490574 ACTAGGATGGCTGACACCTC 58.509 55.000 7.74 0.00 34.11 3.85
1902 2025 1.007721 ACTAGGATGGCTGACACCTCT 59.992 52.381 7.74 0.00 34.11 3.69
1903 2026 1.686052 CTAGGATGGCTGACACCTCTC 59.314 57.143 7.74 0.00 34.11 3.20
1904 2027 0.252421 AGGATGGCTGACACCTCTCA 60.252 55.000 0.00 0.00 0.00 3.27
1905 2028 0.835941 GGATGGCTGACACCTCTCAT 59.164 55.000 0.00 0.00 0.00 2.90
1906 2029 1.474677 GGATGGCTGACACCTCTCATG 60.475 57.143 0.00 0.00 0.00 3.07
1907 2030 1.209019 GATGGCTGACACCTCTCATGT 59.791 52.381 0.00 0.00 0.00 3.21
1908 2031 0.322648 TGGCTGACACCTCTCATGTG 59.677 55.000 0.00 0.00 39.63 3.21
1909 2032 0.392193 GGCTGACACCTCTCATGTGG 60.392 60.000 0.00 0.00 38.05 4.17
1910 2033 0.322975 GCTGACACCTCTCATGTGGT 59.677 55.000 0.00 0.00 40.33 4.16
1911 2034 1.674221 GCTGACACCTCTCATGTGGTC 60.674 57.143 5.16 0.00 37.92 4.02
1912 2035 1.898472 CTGACACCTCTCATGTGGTCT 59.102 52.381 5.16 0.00 37.92 3.85
1913 2036 1.620323 TGACACCTCTCATGTGGTCTG 59.380 52.381 5.16 0.21 37.92 3.51
1914 2037 1.620819 GACACCTCTCATGTGGTCTGT 59.379 52.381 5.16 2.79 37.92 3.41
1940 2063 1.549203 AACATGGTGGCATTCAGGTC 58.451 50.000 10.52 0.00 0.00 3.85
1998 2121 1.142667 TCTCAACCATGGCTTGTGACA 59.857 47.619 13.04 0.00 34.57 3.58
2018 2144 7.390996 TGTGACAAAGGTTTAAGACACTAACAA 59.609 33.333 0.00 0.00 0.00 2.83
2025 2151 7.107542 AGGTTTAAGACACTAACAACACTTGA 58.892 34.615 0.00 0.00 0.00 3.02
2028 2154 4.481368 AGACACTAACAACACTTGACCA 57.519 40.909 0.00 0.00 0.00 4.02
2030 2156 3.541632 ACACTAACAACACTTGACCAGG 58.458 45.455 0.00 0.00 0.00 4.45
2035 2161 1.682854 ACAACACTTGACCAGGCATTG 59.317 47.619 0.00 0.00 0.00 2.82
2040 2166 1.423541 ACTTGACCAGGCATTGTACCA 59.576 47.619 0.00 0.00 0.00 3.25
2061 2201 7.553881 ACCAATTGTATTACTCTGTGTATGC 57.446 36.000 4.43 0.00 0.00 3.14
2075 2222 4.650734 TGTGTATGCCAAGAATGAACTCA 58.349 39.130 0.00 0.00 0.00 3.41
2080 2227 9.224267 GTGTATGCCAAGAATGAACTCATATAT 57.776 33.333 0.00 0.00 35.10 0.86
2125 2307 4.828829 ACCACTCTTCGGTTTATAACTGG 58.171 43.478 0.00 0.00 38.33 4.00
2152 2334 4.702131 ACAGATCAAGTTGCAGGTTATTCC 59.298 41.667 0.00 0.00 0.00 3.01
2154 2336 3.517296 TCAAGTTGCAGGTTATTCCCA 57.483 42.857 0.00 0.00 36.75 4.37
2159 2341 0.403655 TGCAGGTTATTCCCACAGCA 59.596 50.000 0.00 0.00 36.75 4.41
2237 2419 8.335532 TGACAAGAGAACCAAAATATTGTAGG 57.664 34.615 0.00 0.00 34.60 3.18
2248 2430 6.211515 CAAAATATTGTAGGGCTCAAGCATC 58.788 40.000 4.13 0.00 44.36 3.91
2272 2454 5.319043 TCCCAAGAGTTACCAAATCAACT 57.681 39.130 0.00 0.00 37.69 3.16
2295 2477 4.391830 TCAATTCATTCAGCAAGTACCGAC 59.608 41.667 0.00 0.00 0.00 4.79
2296 2478 1.990799 TCATTCAGCAAGTACCGACG 58.009 50.000 0.00 0.00 0.00 5.12
2297 2479 0.370273 CATTCAGCAAGTACCGACGC 59.630 55.000 0.00 0.00 0.00 5.19
2298 2480 0.037697 ATTCAGCAAGTACCGACGCA 60.038 50.000 0.00 0.00 0.00 5.24
2299 2481 0.249531 TTCAGCAAGTACCGACGCAA 60.250 50.000 0.00 0.00 0.00 4.85
2320 2502 0.321346 TCGCAAGATGGAGACTGCAA 59.679 50.000 0.00 0.00 45.01 4.08
2332 2514 5.129634 TGGAGACTGCAAACTGAAAACATA 58.870 37.500 0.00 0.00 0.00 2.29
2338 2520 6.265577 ACTGCAAACTGAAAACATAACTGAC 58.734 36.000 0.00 0.00 0.00 3.51
2343 2525 9.243637 GCAAACTGAAAACATAACTGACATTTA 57.756 29.630 0.00 0.00 0.00 1.40
2355 2537 6.524101 AACTGACATTTAACACAACCTGTT 57.476 33.333 0.00 0.00 45.57 3.16
2356 2538 6.524101 ACTGACATTTAACACAACCTGTTT 57.476 33.333 0.00 0.00 40.45 2.83
2357 2539 6.930731 ACTGACATTTAACACAACCTGTTTT 58.069 32.000 0.00 0.00 40.45 2.43
2358 2540 7.382898 ACTGACATTTAACACAACCTGTTTTT 58.617 30.769 0.00 0.00 40.45 1.94
2424 3030 0.590481 CATCGTGGCATTGATGTGCG 60.590 55.000 18.96 4.41 45.97 5.34
2425 3031 0.744057 ATCGTGGCATTGATGTGCGA 60.744 50.000 4.62 0.09 45.97 5.10
2445 3051 4.775440 GAAGAGCAGATTCTTCGATGTG 57.225 45.455 0.55 0.00 42.44 3.21
2446 3052 2.548875 AGAGCAGATTCTTCGATGTGC 58.451 47.619 0.00 0.00 44.19 4.57
2455 3061 2.621338 TCTTCGATGTGCTCATGTTCC 58.379 47.619 5.89 0.00 34.06 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.490078 CCGTCAGATTCAAGCTCCTCTAC 60.490 52.174 0.00 0.00 0.00 2.59
3 4 2.690497 CCGTCAGATTCAAGCTCCTCTA 59.310 50.000 0.00 0.00 0.00 2.43
4 5 1.480137 CCGTCAGATTCAAGCTCCTCT 59.520 52.381 0.00 0.00 0.00 3.69
5 6 1.205893 ACCGTCAGATTCAAGCTCCTC 59.794 52.381 0.00 0.00 0.00 3.71
6 7 1.066573 CACCGTCAGATTCAAGCTCCT 60.067 52.381 0.00 0.00 0.00 3.69
7 8 1.338200 ACACCGTCAGATTCAAGCTCC 60.338 52.381 0.00 0.00 0.00 4.70
8 9 2.086054 ACACCGTCAGATTCAAGCTC 57.914 50.000 0.00 0.00 0.00 4.09
9 10 2.146342 CAACACCGTCAGATTCAAGCT 58.854 47.619 0.00 0.00 0.00 3.74
10 11 1.400242 GCAACACCGTCAGATTCAAGC 60.400 52.381 0.00 0.00 0.00 4.01
11 12 1.872952 TGCAACACCGTCAGATTCAAG 59.127 47.619 0.00 0.00 0.00 3.02
12 13 1.601903 GTGCAACACCGTCAGATTCAA 59.398 47.619 0.00 0.00 36.32 2.69
13 14 1.225855 GTGCAACACCGTCAGATTCA 58.774 50.000 0.00 0.00 36.32 2.57
14 15 1.225855 TGTGCAACACCGTCAGATTC 58.774 50.000 0.00 0.00 45.67 2.52
15 16 3.395210 TGTGCAACACCGTCAGATT 57.605 47.368 0.00 0.00 45.67 2.40
26 27 1.210155 GCCCGATCTGTTGTGCAAC 59.790 57.895 8.01 8.01 41.50 4.17
27 28 2.324330 CGCCCGATCTGTTGTGCAA 61.324 57.895 0.00 0.00 0.00 4.08
28 29 2.741985 CGCCCGATCTGTTGTGCA 60.742 61.111 0.00 0.00 0.00 4.57
29 30 3.499737 CCGCCCGATCTGTTGTGC 61.500 66.667 0.00 0.00 0.00 4.57
30 31 3.499737 GCCGCCCGATCTGTTGTG 61.500 66.667 0.00 0.00 0.00 3.33
31 32 3.706373 AGCCGCCCGATCTGTTGT 61.706 61.111 0.00 0.00 0.00 3.32
32 33 3.197790 CAGCCGCCCGATCTGTTG 61.198 66.667 0.00 0.00 0.00 3.33
50 51 2.668212 TTTTGGCCGGTCTGCTCG 60.668 61.111 7.97 0.00 0.00 5.03
51 52 1.244019 ATGTTTTGGCCGGTCTGCTC 61.244 55.000 7.97 0.00 0.00 4.26
52 53 0.827507 AATGTTTTGGCCGGTCTGCT 60.828 50.000 7.97 0.00 0.00 4.24
53 54 0.388520 GAATGTTTTGGCCGGTCTGC 60.389 55.000 7.97 0.00 0.00 4.26
54 55 0.109781 CGAATGTTTTGGCCGGTCTG 60.110 55.000 7.97 0.00 0.00 3.51
55 56 1.241315 CCGAATGTTTTGGCCGGTCT 61.241 55.000 7.97 0.00 35.83 3.85
56 57 1.211709 CCGAATGTTTTGGCCGGTC 59.788 57.895 0.00 0.00 35.83 4.79
57 58 3.361174 CCGAATGTTTTGGCCGGT 58.639 55.556 1.90 0.00 35.83 5.28
62 63 1.080839 CACCGGCCGAATGTTTTGG 60.081 57.895 30.73 8.96 37.26 3.28
63 64 1.732683 GCACCGGCCGAATGTTTTG 60.733 57.895 30.73 9.82 0.00 2.44
64 65 2.648454 GCACCGGCCGAATGTTTT 59.352 55.556 30.73 0.00 0.00 2.43
65 66 3.732892 CGCACCGGCCGAATGTTT 61.733 61.111 30.73 0.00 36.38 2.83
96 97 4.521256 TGACATGGTTAAAACTTAGGGCAC 59.479 41.667 0.00 0.00 0.00 5.01
97 98 4.521256 GTGACATGGTTAAAACTTAGGGCA 59.479 41.667 0.00 0.00 0.00 5.36
98 99 4.521256 TGTGACATGGTTAAAACTTAGGGC 59.479 41.667 0.00 0.00 0.00 5.19
99 100 6.834168 ATGTGACATGGTTAAAACTTAGGG 57.166 37.500 0.00 0.00 0.00 3.53
100 101 8.141268 ACAAATGTGACATGGTTAAAACTTAGG 58.859 33.333 0.00 0.00 0.00 2.69
119 120 3.319405 ACGAGAGTCTCAGACACAAATGT 59.681 43.478 19.99 2.87 44.19 2.71
143 144 1.515304 GCAGGAGACGCGAAGAGAC 60.515 63.158 15.93 0.00 0.00 3.36
148 149 3.684990 AGCAGCAGGAGACGCGAA 61.685 61.111 15.93 0.00 35.50 4.70
170 171 1.142474 GCATTTCAAACTGCCTGTGC 58.858 50.000 0.00 0.00 38.26 4.57
171 172 2.798283 CAAGCATTTCAAACTGCCTGTG 59.202 45.455 1.91 0.00 39.22 3.66
172 173 2.224113 CCAAGCATTTCAAACTGCCTGT 60.224 45.455 1.91 0.00 39.22 4.00
173 174 2.409975 CCAAGCATTTCAAACTGCCTG 58.590 47.619 1.91 0.12 39.22 4.85
174 175 1.345415 CCCAAGCATTTCAAACTGCCT 59.655 47.619 1.91 0.00 39.22 4.75
175 176 1.344114 TCCCAAGCATTTCAAACTGCC 59.656 47.619 1.91 0.00 39.22 4.85
176 177 2.036346 ACTCCCAAGCATTTCAAACTGC 59.964 45.455 0.00 0.00 38.69 4.40
177 178 4.520492 AGTACTCCCAAGCATTTCAAACTG 59.480 41.667 0.00 0.00 0.00 3.16
178 179 4.729868 AGTACTCCCAAGCATTTCAAACT 58.270 39.130 0.00 0.00 0.00 2.66
179 180 5.472137 TGTAGTACTCCCAAGCATTTCAAAC 59.528 40.000 0.00 0.00 0.00 2.93
182 186 4.286032 ACTGTAGTACTCCCAAGCATTTCA 59.714 41.667 0.00 0.00 0.00 2.69
191 195 2.865119 TCGTGACTGTAGTACTCCCA 57.135 50.000 0.00 0.00 0.00 4.37
197 201 2.943690 GCCTCTCATCGTGACTGTAGTA 59.056 50.000 0.00 0.00 0.00 1.82
295 302 1.473434 GGTGGGTTGAAGATAGCGGAG 60.473 57.143 0.00 0.00 0.00 4.63
296 303 0.539986 GGTGGGTTGAAGATAGCGGA 59.460 55.000 0.00 0.00 0.00 5.54
298 305 2.403252 AAGGTGGGTTGAAGATAGCG 57.597 50.000 0.00 0.00 0.00 4.26
314 326 3.370061 GCTTGTAGTACGTAGCCAAAAGG 59.630 47.826 13.51 0.00 0.00 3.11
324 336 2.035449 TCTTGCACAGCTTGTAGTACGT 59.965 45.455 0.00 0.00 0.00 3.57
326 338 4.499183 AGATCTTGCACAGCTTGTAGTAC 58.501 43.478 0.00 0.00 0.00 2.73
327 339 4.808414 AGATCTTGCACAGCTTGTAGTA 57.192 40.909 0.00 0.00 0.00 1.82
329 341 4.337985 CAAGATCTTGCACAGCTTGTAG 57.662 45.455 21.96 0.00 33.45 2.74
349 361 1.684450 TCCAAGTTGTAGTCGACAGCA 59.316 47.619 19.50 12.95 41.51 4.41
351 363 3.917329 TCTCCAAGTTGTAGTCGACAG 57.083 47.619 19.50 1.95 39.88 3.51
359 371 3.843619 TCCATGTCCATCTCCAAGTTGTA 59.156 43.478 1.45 0.00 0.00 2.41
393 426 1.164662 CCAGGGCGCATCTGAATCTG 61.165 60.000 25.14 11.91 34.36 2.90
415 448 3.567797 GCGATTCTGAGCACGCCC 61.568 66.667 11.82 0.00 44.27 6.13
441 476 0.740149 TTTGTGTGGTGCTGAGCTTG 59.260 50.000 5.83 0.00 0.00 4.01
452 487 5.412526 AACAGTACGTTACATTTGTGTGG 57.587 39.130 0.00 0.00 35.52 4.17
457 492 3.903644 CGCCAAACAGTACGTTACATTTG 59.096 43.478 0.00 0.54 36.59 2.32
458 493 3.607542 GCGCCAAACAGTACGTTACATTT 60.608 43.478 0.00 0.00 36.59 2.32
459 494 2.096119 GCGCCAAACAGTACGTTACATT 60.096 45.455 0.00 0.00 36.59 2.71
460 495 1.461897 GCGCCAAACAGTACGTTACAT 59.538 47.619 0.00 0.00 36.59 2.29
461 496 0.860533 GCGCCAAACAGTACGTTACA 59.139 50.000 0.00 0.00 36.59 2.41
466 501 0.720173 GTTTCGCGCCAAACAGTACG 60.720 55.000 23.14 0.00 36.44 3.67
470 505 2.426752 CGGTTTCGCGCCAAACAG 60.427 61.111 27.68 21.62 37.91 3.16
584 625 2.747855 GGACGGAGGCAAGGCAAG 60.748 66.667 0.00 0.00 0.00 4.01
585 626 3.565214 TGGACGGAGGCAAGGCAA 61.565 61.111 0.00 0.00 0.00 4.52
586 627 4.329545 GTGGACGGAGGCAAGGCA 62.330 66.667 0.00 0.00 0.00 4.75
587 628 3.959991 GAGTGGACGGAGGCAAGGC 62.960 68.421 0.00 0.00 0.00 4.35
588 629 2.266055 GAGTGGACGGAGGCAAGG 59.734 66.667 0.00 0.00 0.00 3.61
598 639 4.408821 TGGCCATGGCGAGTGGAC 62.409 66.667 29.90 14.85 45.44 4.02
627 668 2.041405 GGAGGTGGAGGAGGAGGG 60.041 72.222 0.00 0.00 0.00 4.30
628 669 2.443016 CGGAGGTGGAGGAGGAGG 60.443 72.222 0.00 0.00 0.00 4.30
714 755 4.680237 CACCGGCCGAACAGAGCA 62.680 66.667 30.73 0.00 0.00 4.26
1310 1413 0.736325 CTGCCGGTACTGTTTCCTCG 60.736 60.000 1.90 0.00 0.00 4.63
1376 1479 4.821589 CCTTGCTCCCGTCCTCGC 62.822 72.222 0.00 0.00 35.54 5.03
1420 1523 2.493547 GGCCATGGTTGCCTCTAAC 58.506 57.895 14.67 0.00 45.70 2.34
1459 1562 4.505808 AGATCACAGTTGCTTCATCTCTG 58.494 43.478 0.00 0.00 0.00 3.35
1470 1576 2.665537 GCGAGTTCAGAGATCACAGTTG 59.334 50.000 0.00 0.00 0.00 3.16
1496 1606 3.827876 TCAGGCTGCAAAATTGAGATTCA 59.172 39.130 10.34 0.00 0.00 2.57
1501 1611 3.678072 CACATTCAGGCTGCAAAATTGAG 59.322 43.478 10.34 0.00 0.00 3.02
1505 1615 5.597806 CATATCACATTCAGGCTGCAAAAT 58.402 37.500 10.34 1.48 0.00 1.82
1508 1618 2.359848 GCATATCACATTCAGGCTGCAA 59.640 45.455 10.34 5.74 0.00 4.08
1558 1674 9.682465 TCTCTATCTAGCTAGAACAAACTACAA 57.318 33.333 26.62 0.04 35.69 2.41
1580 1703 8.797350 TGAACATGATGACAATAAACATCTCT 57.203 30.769 0.00 0.00 42.05 3.10
1660 1783 4.037446 GGAGAAGTAGACTCGATGCATTCT 59.963 45.833 0.00 1.79 35.49 2.40
1670 1793 6.334102 TCAAACAGAAGGAGAAGTAGACTC 57.666 41.667 0.00 0.00 0.00 3.36
1682 1805 2.076863 GTCGACCCATCAAACAGAAGG 58.923 52.381 3.51 0.00 34.85 3.46
1694 1817 1.124780 TTCAGTTCAAGGTCGACCCA 58.875 50.000 30.82 12.72 36.42 4.51
1740 1863 4.399618 TCAACCTCTACTTTCTCGATCCAG 59.600 45.833 0.00 0.00 0.00 3.86
1802 1925 9.904198 TTTGTAGATCCATAACATCTCAATGAA 57.096 29.630 0.00 0.00 36.67 2.57
1806 1929 9.166173 CTGTTTTGTAGATCCATAACATCTCAA 57.834 33.333 7.89 0.00 36.27 3.02
1815 1938 7.675161 TCCTCATCTGTTTTGTAGATCCATA 57.325 36.000 0.00 0.00 32.75 2.74
1825 1948 6.152323 ACAAGAATCCATCCTCATCTGTTTTG 59.848 38.462 0.00 0.00 0.00 2.44
1834 1957 3.243535 CGATCGACAAGAATCCATCCTCA 60.244 47.826 10.26 0.00 0.00 3.86
1837 1960 3.004839 TCTCGATCGACAAGAATCCATCC 59.995 47.826 15.15 0.00 0.00 3.51
1856 1979 7.673641 ATATCATATCATTCCCCACTCTCTC 57.326 40.000 0.00 0.00 0.00 3.20
1872 1995 8.700051 GTGTCAGCCATCCTAGTAATATCATAT 58.300 37.037 0.00 0.00 0.00 1.78
1876 1999 5.482175 AGGTGTCAGCCATCCTAGTAATATC 59.518 44.000 0.00 0.00 0.00 1.63
1880 2003 3.031736 GAGGTGTCAGCCATCCTAGTAA 58.968 50.000 0.00 0.00 0.00 2.24
1882 2005 1.007721 AGAGGTGTCAGCCATCCTAGT 59.992 52.381 0.00 0.00 0.00 2.57
1886 2009 0.835941 ATGAGAGGTGTCAGCCATCC 59.164 55.000 0.00 0.00 0.00 3.51
1895 2018 1.722034 ACAGACCACATGAGAGGTGT 58.278 50.000 12.64 7.15 38.95 4.16
1896 2019 2.847327 AACAGACCACATGAGAGGTG 57.153 50.000 12.64 4.11 38.95 4.00
1897 2020 4.974645 TTAAACAGACCACATGAGAGGT 57.025 40.909 0.00 4.13 41.74 3.85
1898 2021 7.390440 TGTTTATTAAACAGACCACATGAGAGG 59.610 37.037 16.17 0.35 45.79 3.69
1899 2022 8.322906 TGTTTATTAAACAGACCACATGAGAG 57.677 34.615 16.17 0.00 45.79 3.20
1913 2036 6.534793 CCTGAATGCCACCATGTTTATTAAAC 59.465 38.462 11.57 11.57 41.73 2.01
1914 2037 6.212388 ACCTGAATGCCACCATGTTTATTAAA 59.788 34.615 0.00 0.00 0.00 1.52
1940 2063 2.250939 TTTGTCGCCGCAACCTGAG 61.251 57.895 0.00 0.00 0.00 3.35
1991 2114 7.390996 TGTTAGTGTCTTAAACCTTTGTCACAA 59.609 33.333 0.00 0.00 0.00 3.33
1998 2121 7.933215 AGTGTTGTTAGTGTCTTAAACCTTT 57.067 32.000 0.00 0.00 0.00 3.11
2018 2144 2.504367 GTACAATGCCTGGTCAAGTGT 58.496 47.619 0.00 5.95 0.00 3.55
2035 2161 8.548721 GCATACACAGAGTAATACAATTGGTAC 58.451 37.037 10.83 8.93 36.05 3.34
2040 2166 8.046708 TCTTGGCATACACAGAGTAATACAATT 58.953 33.333 0.00 0.00 36.05 2.32
2075 2222 7.406620 TGAATGGGGTCCTTTCAGAATATAT 57.593 36.000 10.10 0.00 40.93 0.86
2080 2227 3.893753 TTGAATGGGGTCCTTTCAGAA 57.106 42.857 12.76 1.05 44.52 3.02
2091 2241 3.627577 CGAAGAGTGGTATTTGAATGGGG 59.372 47.826 0.00 0.00 0.00 4.96
2125 2307 1.467734 CCTGCAACTTGATCTGTCAGC 59.532 52.381 0.00 2.71 35.39 4.26
2152 2334 1.889105 CCCGGATTCGATGCTGTGG 60.889 63.158 0.73 0.00 39.00 4.17
2154 2336 2.203070 GCCCGGATTCGATGCTGT 60.203 61.111 0.73 0.00 39.00 4.40
2159 2341 1.227263 CTCGTTGCCCGGATTCGAT 60.227 57.895 0.73 0.00 39.00 3.59
2176 2358 1.811266 CCGTGCTCATAGCGTTGCT 60.811 57.895 0.00 0.00 46.26 3.91
2181 2363 1.431488 ATGTTGCCGTGCTCATAGCG 61.431 55.000 0.00 0.00 46.26 4.26
2237 2419 1.101331 CTTGGGAAGATGCTTGAGCC 58.899 55.000 0.00 0.00 41.18 4.70
2248 2430 5.770162 AGTTGATTTGGTAACTCTTGGGAAG 59.230 40.000 0.00 0.00 31.88 3.46
2272 2454 4.391830 GTCGGTACTTGCTGAATGAATTGA 59.608 41.667 0.00 0.00 0.00 2.57
2296 2478 0.723981 GTCTCCATCTTGCGACTTGC 59.276 55.000 0.00 0.00 46.70 4.01
2297 2479 1.998315 CAGTCTCCATCTTGCGACTTG 59.002 52.381 0.00 0.00 34.72 3.16
2298 2480 1.674221 GCAGTCTCCATCTTGCGACTT 60.674 52.381 0.00 0.00 34.72 3.01
2299 2481 0.108424 GCAGTCTCCATCTTGCGACT 60.108 55.000 0.00 0.00 37.22 4.18
2300 2482 0.390340 TGCAGTCTCCATCTTGCGAC 60.390 55.000 0.00 0.00 0.00 5.19
2301 2483 0.321346 TTGCAGTCTCCATCTTGCGA 59.679 50.000 0.00 0.00 0.00 5.10
2414 3020 2.391616 TCTGCTCTTCGCACATCAAT 57.608 45.000 0.00 0.00 45.47 2.57
2424 3030 3.001127 GCACATCGAAGAATCTGCTCTTC 59.999 47.826 0.00 3.87 45.30 2.87
2425 3031 2.935201 GCACATCGAAGAATCTGCTCTT 59.065 45.455 0.00 0.00 43.58 2.85
2445 3051 2.681848 CCTCAATGACTGGAACATGAGC 59.318 50.000 0.00 0.00 38.20 4.26
2446 3052 4.212143 TCCTCAATGACTGGAACATGAG 57.788 45.455 0.00 0.00 38.20 2.90


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

AutoCloner maintained by Alex Coulton.