Multiple sequence alignment - TraesCS7A01G521300

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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 TraesCS7A01G521300 chr7A 100.000 7084 0 0 1 7084 705267127 705274210 0.000000e+00 13082.0
1 TraesCS7A01G521300 chr7A 80.812 813 91 30 5 766 705251625 705252423 1.710000e-160 577.0
2 TraesCS7A01G521300 chr7B 94.002 5252 192 44 1725 6904 704267984 704273184 0.000000e+00 7840.0
3 TraesCS7A01G521300 chr7B 86.969 1059 36 38 581 1584 704266740 704267751 0.000000e+00 1098.0
4 TraesCS7A01G521300 chr7B 78.799 283 32 11 1 256 704266185 704266466 1.580000e-36 165.0
5 TraesCS7A01G521300 chr7D 94.206 4056 149 32 3111 7084 613610410 613614461 0.000000e+00 6109.0
6 TraesCS7A01G521300 chr7D 88.857 3177 193 60 1 3115 613607295 613610372 0.000000e+00 3757.0
7 TraesCS7A01G521300 chr7D 80.342 819 90 26 5 767 613598747 613599550 8.030000e-154 555.0
8 TraesCS7A01G521300 chr7D 96.875 32 1 0 3038 3069 613610386 613610417 4.000000e-03 54.7
9 TraesCS7A01G521300 chr2D 76.940 464 67 22 1954 2406 632272092 632272526 1.990000e-55 228.0
10 TraesCS7A01G521300 chr4D 76.674 463 69 21 1957 2409 207780528 207780095 3.330000e-53 220.0


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 TraesCS7A01G521300 chr7A 705267127 705274210 7083 False 13082.000000 13082 100.000000 1 7084 1 chr7A.!!$F2 7083
1 TraesCS7A01G521300 chr7A 705251625 705252423 798 False 577.000000 577 80.812000 5 766 1 chr7A.!!$F1 761
2 TraesCS7A01G521300 chr7B 704266185 704273184 6999 False 3034.333333 7840 86.590000 1 6904 3 chr7B.!!$F1 6903
3 TraesCS7A01G521300 chr7D 613607295 613614461 7166 False 3306.900000 6109 93.312667 1 7084 3 chr7D.!!$F2 7083
4 TraesCS7A01G521300 chr7D 613598747 613599550 803 False 555.000000 555 80.342000 5 767 1 chr7D.!!$F1 762

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
898 1028 0.399806 AGCTCCAATCTCTCCCTCCC 60.400 60.0 0.00 0.00 0.00 4.30 F
1607 1817 0.107945 CCTGAGTGGGCTGTAGCTTC 60.108 60.0 3.63 0.00 41.70 3.86 F
1775 2131 0.400213 TGCCTGTACCCCTGTTTGAG 59.600 55.0 0.00 0.00 0.00 3.02 F
2946 3307 0.179043 TGTTAAAGCCGTGGAGTGCA 60.179 50.0 0.00 0.00 0.00 4.57 F
2951 3312 0.314935 AAGCCGTGGAGTGCATTTTG 59.685 50.0 0.00 0.00 0.00 2.44 F
3543 3971 0.587768 TGTCTTGATTGTGCGTGCTG 59.412 50.0 0.00 0.00 0.00 4.41 F
5363 5816 0.322277 TAGACCTTCTGGCGACGTCT 60.322 55.0 14.70 1.32 34.82 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 2131 0.172803 ACGGTAAGGATGTCTGTCGC 59.827 55.000 0.00 0.0 0.00 5.19 R
2928 3289 1.165270 ATGCACTCCACGGCTTTAAC 58.835 50.000 0.00 0.0 0.00 2.01 R
3696 4124 2.209690 ACCGGGTTTATTTGACTGGG 57.790 50.000 6.32 0.0 0.00 4.45 R
4032 4460 0.609131 CCATCCACACCACTTGGGAC 60.609 60.000 0.00 0.0 41.15 4.46 R
4632 5060 0.764890 TGCTAAGGCACAGGAACAGT 59.235 50.000 0.00 0.0 44.28 3.55 R
5438 5891 1.000938 CTGGAGTTTGACAAAGCAGGC 60.001 52.381 0.00 0.0 0.00 4.85 R
6562 7043 0.462759 AGCTTATCAACAGCTCGGCC 60.463 55.000 0.00 0.0 44.77 6.13 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 202 7.951530 AAGCAAGTATTTGTTGGAATTGAAG 57.048 32.000 0.00 0.00 36.65 3.02
187 217 3.091545 TGGAATTGAAGATTGCCTGTCC 58.908 45.455 0.00 0.00 0.00 4.02
189 219 3.511146 GGAATTGAAGATTGCCTGTCCAA 59.489 43.478 0.00 0.00 0.00 3.53
316 354 1.811025 TAGGACCAGCCACCTCCTCA 61.811 60.000 0.00 0.00 40.02 3.86
354 392 2.126346 GCGCCAAACAGCATCACC 60.126 61.111 0.00 0.00 0.00 4.02
380 420 3.673323 GCTTGGCCTTACATAAGTGCAAC 60.673 47.826 3.32 0.00 33.80 4.17
389 429 3.664107 ACATAAGTGCAACACGAGATGT 58.336 40.909 0.00 8.44 46.42 3.06
409 449 3.388676 TGTATATACCGGTTGGAGTTGGG 59.611 47.826 15.04 0.00 39.21 4.12
422 484 2.290387 GGAGTTGGGGTTCTCTTCTTCC 60.290 54.545 0.00 0.00 0.00 3.46
482 555 3.323758 ATAACTCCAGCGCCGGCAA 62.324 57.895 28.98 4.69 43.41 4.52
522 595 2.768344 ATGTGCGGGGTAGGGAGG 60.768 66.667 0.00 0.00 0.00 4.30
577 650 5.861727 TCCTTTTCTTCTAGGGTTGTGTAC 58.138 41.667 0.00 0.00 32.20 2.90
578 651 5.605488 TCCTTTTCTTCTAGGGTTGTGTACT 59.395 40.000 0.00 0.00 32.20 2.73
579 652 5.701290 CCTTTTCTTCTAGGGTTGTGTACTG 59.299 44.000 0.00 0.00 0.00 2.74
580 653 4.884668 TTCTTCTAGGGTTGTGTACTGG 57.115 45.455 0.00 0.00 0.00 4.00
581 654 3.853207 TCTTCTAGGGTTGTGTACTGGT 58.147 45.455 0.00 0.00 0.00 4.00
582 655 3.576982 TCTTCTAGGGTTGTGTACTGGTG 59.423 47.826 0.00 0.00 0.00 4.17
583 656 2.966915 TCTAGGGTTGTGTACTGGTGT 58.033 47.619 0.00 0.00 0.00 4.16
584 657 3.311091 TCTAGGGTTGTGTACTGGTGTT 58.689 45.455 0.00 0.00 0.00 3.32
598 671 2.554032 CTGGTGTTTGATTTCGGCTCTT 59.446 45.455 0.00 0.00 0.00 2.85
599 672 2.552315 TGGTGTTTGATTTCGGCTCTTC 59.448 45.455 0.00 0.00 0.00 2.87
667 760 2.110213 TGGCGTGTCTGACAACCC 59.890 61.111 21.77 19.29 0.00 4.11
699 792 1.153289 CATCGCCTCCCTGTCCAAG 60.153 63.158 0.00 0.00 0.00 3.61
897 1027 0.758123 CAGCTCCAATCTCTCCCTCC 59.242 60.000 0.00 0.00 0.00 4.30
898 1028 0.399806 AGCTCCAATCTCTCCCTCCC 60.400 60.000 0.00 0.00 0.00 4.30
1192 1357 4.194720 GCGCTCTGATCCGTCCGT 62.195 66.667 0.00 0.00 0.00 4.69
1242 1408 3.036429 GCCGGGTGCTTCTGATCCT 62.036 63.158 2.18 0.00 36.87 3.24
1358 1542 0.666274 TCAGCTCGATTTCGTTGCGT 60.666 50.000 12.16 2.97 41.55 5.24
1485 1669 2.668457 CTGCGGTTACTGATTCAGTGAC 59.332 50.000 25.65 25.65 45.94 3.67
1506 1690 0.613012 AGTGATTTGGAGCTTGCCCC 60.613 55.000 0.00 0.00 0.00 5.80
1508 1692 0.612732 TGATTTGGAGCTTGCCCCAG 60.613 55.000 0.00 0.00 33.43 4.45
1549 1733 8.106247 TCTGAATATCAACAAGTTGGGTTTAC 57.894 34.615 12.54 2.71 40.78 2.01
1561 1745 6.321848 AGTTGGGTTTACGAATTTTACCAG 57.678 37.500 0.00 0.00 0.00 4.00
1564 1748 3.760151 GGGTTTACGAATTTTACCAGCCT 59.240 43.478 0.00 0.00 0.00 4.58
1586 1770 6.208644 CCTGTTGGGCTTATGAATTTTATCG 58.791 40.000 0.00 0.00 0.00 2.92
1593 1803 5.335191 GGCTTATGAATTTTATCGGCCTGAG 60.335 44.000 0.00 0.00 34.86 3.35
1607 1817 0.107945 CCTGAGTGGGCTGTAGCTTC 60.108 60.000 3.63 0.00 41.70 3.86
1610 1820 2.820037 GTGGGCTGTAGCTTCGCC 60.820 66.667 14.61 14.61 43.03 5.54
1612 1822 2.512515 GGGCTGTAGCTTCGCCTG 60.513 66.667 19.58 2.02 43.29 4.85
1614 1824 3.198489 GCTGTAGCTTCGCCTGCC 61.198 66.667 0.00 0.00 38.21 4.85
1623 1833 3.916544 TCGCCTGCCGAGCCTATG 61.917 66.667 0.00 0.00 41.89 2.23
1656 1866 5.567138 GCATTTGAGTGCATAACTAGGTT 57.433 39.130 0.00 0.00 44.43 3.50
1664 1874 8.662781 TGAGTGCATAACTAGGTTAATTCATC 57.337 34.615 0.00 0.00 40.07 2.92
1716 1933 5.839262 TTATTATTCCGAGCGTGCTATTG 57.161 39.130 0.00 0.00 0.00 1.90
1749 2105 1.508088 GCCTGCCTATGTTGTGTGC 59.492 57.895 0.00 0.00 0.00 4.57
1775 2131 0.400213 TGCCTGTACCCCTGTTTGAG 59.600 55.000 0.00 0.00 0.00 3.02
1793 2149 0.456221 AGCGACAGACATCCTTACCG 59.544 55.000 0.00 0.00 0.00 4.02
1846 2202 5.390567 CCAACTGAATAACGCCTTTGTACTC 60.391 44.000 0.00 0.00 0.00 2.59
1874 2230 6.182507 ACACCTTGGTTAATACACTGAGAA 57.817 37.500 0.00 0.00 0.00 2.87
1882 2238 6.049790 GGTTAATACACTGAGAATCCCTGAC 58.950 44.000 0.00 0.00 0.00 3.51
1886 2242 1.912043 CACTGAGAATCCCTGACCCTT 59.088 52.381 0.00 0.00 0.00 3.95
1931 2287 2.279741 CAGTAACGCACCATGCAGTAT 58.720 47.619 1.20 0.00 45.36 2.12
2008 2364 8.147704 CCCAAAAAGGAAAGAAATTAACTGCTA 58.852 33.333 0.00 0.00 41.22 3.49
2021 2377 0.883833 ACTGCTATGCACAACCAAGC 59.116 50.000 0.00 0.00 33.79 4.01
2039 2395 9.360093 CAACCAAGCGGATATTTTGTTTAATTA 57.640 29.630 0.00 0.00 35.59 1.40
2133 2489 2.790433 GCAAAGATGAGGGTGTTACCA 58.210 47.619 0.00 0.00 41.02 3.25
2169 2525 9.462606 TCTGTACATTATCTGAGTCTTCTTACA 57.537 33.333 0.00 0.00 0.00 2.41
2288 2644 1.452145 TTGCTCAAACACCCGAAGCC 61.452 55.000 0.00 0.00 0.00 4.35
2368 2724 6.884280 ACCCTCTTGTTTTTCTCACTTATG 57.116 37.500 0.00 0.00 0.00 1.90
2430 2787 5.066968 TGCAGATAGTAATTGACACGTCA 57.933 39.130 0.00 0.00 37.91 4.35
2432 2789 4.267928 GCAGATAGTAATTGACACGTCACC 59.732 45.833 0.00 0.00 39.66 4.02
2446 2803 6.201425 TGACACGTCACCAGTATTAAAACTTC 59.799 38.462 0.00 0.00 34.14 3.01
2469 2826 6.338146 TCGTGCTATAACAAAATGAGCTAGT 58.662 36.000 0.00 0.00 34.19 2.57
2473 2830 7.065803 GTGCTATAACAAAATGAGCTAGTTGGA 59.934 37.037 0.00 0.00 34.19 3.53
2485 2842 6.711277 TGAGCTAGTTGGAAATACAAGTGAT 58.289 36.000 0.00 0.00 35.70 3.06
2584 2941 6.314896 GGGCTATCTAAGTTCATATCATGTGC 59.685 42.308 0.00 0.00 0.00 4.57
2712 3071 3.942130 AGGCTTAGGACACAAATTTGC 57.058 42.857 18.12 1.99 0.00 3.68
2716 3077 4.501400 GGCTTAGGACACAAATTTGCTTGT 60.501 41.667 18.12 15.16 40.17 3.16
2941 3302 3.998341 GTCTTACATGTTAAAGCCGTGGA 59.002 43.478 2.30 0.00 0.00 4.02
2942 3303 4.092968 GTCTTACATGTTAAAGCCGTGGAG 59.907 45.833 2.30 0.00 0.00 3.86
2943 3304 2.561478 ACATGTTAAAGCCGTGGAGT 57.439 45.000 0.00 0.00 0.00 3.85
2944 3305 2.151202 ACATGTTAAAGCCGTGGAGTG 58.849 47.619 0.00 0.00 0.00 3.51
2945 3306 1.135689 CATGTTAAAGCCGTGGAGTGC 60.136 52.381 0.00 0.00 0.00 4.40
2946 3307 0.179043 TGTTAAAGCCGTGGAGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
2947 3308 1.165270 GTTAAAGCCGTGGAGTGCAT 58.835 50.000 0.00 0.00 0.00 3.96
2948 3309 1.539827 GTTAAAGCCGTGGAGTGCATT 59.460 47.619 0.00 0.00 0.00 3.56
2949 3310 1.904287 TAAAGCCGTGGAGTGCATTT 58.096 45.000 0.00 0.00 0.00 2.32
2950 3311 1.039856 AAAGCCGTGGAGTGCATTTT 58.960 45.000 0.00 0.00 0.00 1.82
2951 3312 0.314935 AAGCCGTGGAGTGCATTTTG 59.685 50.000 0.00 0.00 0.00 2.44
2952 3313 0.823356 AGCCGTGGAGTGCATTTTGT 60.823 50.000 0.00 0.00 0.00 2.83
2953 3314 0.664166 GCCGTGGAGTGCATTTTGTG 60.664 55.000 0.00 0.00 0.00 3.33
3024 3391 1.067516 GTTGGTGCAGTGTCATTTGCT 59.932 47.619 11.93 0.00 40.87 3.91
3030 3397 3.488310 GTGCAGTGTCATTTGCTTTCAAG 59.512 43.478 11.93 0.00 40.87 3.02
3458 3875 4.045636 TGCTTTTCTTGAACTTGAAGCC 57.954 40.909 12.21 0.00 38.88 4.35
3491 3908 5.633117 TCATGTATGTGCATTGGTCCATAT 58.367 37.500 0.00 0.00 0.00 1.78
3530 3958 5.066764 TGTGTATGCATTGATCCATGTCTTG 59.933 40.000 3.54 0.00 0.00 3.02
3543 3971 0.587768 TGTCTTGATTGTGCGTGCTG 59.412 50.000 0.00 0.00 0.00 4.41
3715 4143 1.889262 GCCCAGTCAAATAAACCCGGT 60.889 52.381 0.00 0.00 0.00 5.28
4032 4460 0.848735 ATGGGATGGTCCTGTGGATG 59.151 55.000 0.00 0.00 36.57 3.51
4069 4497 5.939883 TGGATGGACATAGTCAAACAGAAAG 59.060 40.000 0.00 0.00 33.68 2.62
4181 4609 5.643379 TGGTAACCATGCAAAGAAGAATC 57.357 39.130 0.00 0.00 0.00 2.52
4247 4675 5.690464 ATCAGGAAGTAGCAGTCAAAGAT 57.310 39.130 0.00 0.00 0.00 2.40
4324 4752 7.195374 AGTGTAAATCAGGCTCTTGGTATTA 57.805 36.000 0.00 0.00 0.00 0.98
4331 4759 4.721776 TCAGGCTCTTGGTATTACAGGATT 59.278 41.667 0.00 0.00 0.00 3.01
4415 4843 4.868734 GGCCTCGTATAGTTATTATGTGGC 59.131 45.833 0.00 7.23 35.24 5.01
4740 5168 1.269778 CGTGTGGAGTCAGAGAAAGCA 60.270 52.381 0.00 0.00 0.00 3.91
5313 5766 6.293626 TCTTGCAGAAGAACAAGATAACTTGC 60.294 38.462 12.28 0.00 45.48 4.01
5363 5816 0.322277 TAGACCTTCTGGCGACGTCT 60.322 55.000 14.70 1.32 34.82 4.18
5438 5891 4.687483 GGCTGTTTTCATTTGACATGAAGG 59.313 41.667 0.00 0.00 38.98 3.46
5448 5901 1.251251 GACATGAAGGCCTGCTTTGT 58.749 50.000 17.08 17.08 0.00 2.83
5527 5980 2.711009 TCCAGTTGAGAACTTGGACCAT 59.289 45.455 0.00 0.00 40.46 3.55
5681 6134 6.053632 TGATCATGAATGTGTTACCTGTCT 57.946 37.500 0.00 0.00 0.00 3.41
5692 6145 7.470935 TGTGTTACCTGTCTGCTAATTAGTA 57.529 36.000 13.91 8.65 0.00 1.82
5693 6146 7.318141 TGTGTTACCTGTCTGCTAATTAGTAC 58.682 38.462 13.91 10.17 0.00 2.73
5794 6253 5.572896 GGAAAATCCTTGCTTTACGTTGATG 59.427 40.000 0.00 0.00 32.53 3.07
6014 6473 3.255725 CGCTGTAAATACCTCCGTGAAA 58.744 45.455 0.00 0.00 0.00 2.69
6016 6475 4.251268 GCTGTAAATACCTCCGTGAAACT 58.749 43.478 0.00 0.00 31.75 2.66
6137 6605 0.249911 CCCTAGTTATGCGGCCTGAC 60.250 60.000 0.00 0.00 0.00 3.51
6339 6814 4.558178 GGTGCTGAGTGATGATGATAGAG 58.442 47.826 0.00 0.00 0.00 2.43
6345 6820 7.147776 TGCTGAGTGATGATGATAGAGAGAAAA 60.148 37.037 0.00 0.00 0.00 2.29
6346 6821 7.874016 GCTGAGTGATGATGATAGAGAGAAAAT 59.126 37.037 0.00 0.00 0.00 1.82
6387 6867 9.519191 TTTGTGCCATGCTTCTATATATGTAAT 57.481 29.630 0.00 0.00 0.00 1.89
6392 6872 8.461222 GCCATGCTTCTATATATGTAATTGCAA 58.539 33.333 0.00 0.00 0.00 4.08
6410 6890 2.945008 GCAAAGCTGCTGGTATACATGA 59.055 45.455 1.35 0.00 45.74 3.07
6475 6955 3.349006 ACTGCGCAGTTTGCTCCG 61.349 61.111 36.44 11.75 42.25 4.63
6493 6973 2.092968 TCCGGACCAATCTTCTTCCATG 60.093 50.000 0.00 0.00 0.00 3.66
6497 6977 3.054065 GGACCAATCTTCTTCCATGGAGT 60.054 47.826 15.53 5.84 35.16 3.85
6524 7005 4.729458 GCGCTGTTTTGACTTTGTAACTGA 60.729 41.667 0.00 0.00 0.00 3.41
6555 7036 3.262660 TGTGTTCTCTCATGGAGCATTCT 59.737 43.478 6.38 0.00 41.60 2.40
6616 7097 5.744171 TGCTGTGACCAGTTATGAATATGT 58.256 37.500 0.00 0.00 41.02 2.29
6701 7191 7.719483 TGCTCTTGAAATTCTTGAAAGTCATT 58.281 30.769 0.00 0.00 0.00 2.57
6703 7193 8.081025 GCTCTTGAAATTCTTGAAAGTCATTCT 58.919 33.333 0.00 0.00 38.92 2.40
6720 7210 9.512588 AAGTCATTCTAGAATTGAAACTCATGT 57.487 29.630 15.49 0.67 0.00 3.21
6748 7238 0.666913 GCATTCCGCTGCATCTTGAT 59.333 50.000 0.00 0.00 41.87 2.57
6749 7239 1.875514 GCATTCCGCTGCATCTTGATA 59.124 47.619 0.00 0.00 41.87 2.15
6794 7287 6.808829 TGTTTTCTGCTTCATGTGAGAAATT 58.191 32.000 0.00 0.00 35.06 1.82
6848 7341 2.409378 CGCATTTGTGCCTGAAATTCAC 59.591 45.455 0.00 0.00 0.00 3.18
6850 7343 3.641648 CATTTGTGCCTGAAATTCACGT 58.358 40.909 0.00 0.00 33.69 4.49
6910 7407 5.237815 TCATGTTTGCTATTCTTCAGTCGT 58.762 37.500 0.00 0.00 0.00 4.34
6915 7412 4.265904 TGCTATTCTTCAGTCGTTTGGA 57.734 40.909 0.00 0.00 0.00 3.53
6928 7425 4.893524 AGTCGTTTGGAGAAAAATCCCTTT 59.106 37.500 0.00 0.00 38.72 3.11
6943 7440 0.526662 CCTTTAGAGCACCGAGACGT 59.473 55.000 0.00 0.00 0.00 4.34
6946 7443 1.642037 TTAGAGCACCGAGACGTCCG 61.642 60.000 13.01 15.09 0.00 4.79
6954 7451 4.353437 GAGACGTCCGGGCGTGTT 62.353 66.667 42.07 27.03 45.79 3.32
6956 7453 4.651008 GACGTCCGGGCGTGTTGA 62.651 66.667 42.07 0.00 45.79 3.18
6958 7455 4.657824 CGTCCGGGCGTGTTGAGT 62.658 66.667 22.93 0.00 0.00 3.41
6960 7457 1.217244 GTCCGGGCGTGTTGAGTAT 59.783 57.895 0.00 0.00 0.00 2.12
6961 7458 0.804933 GTCCGGGCGTGTTGAGTATC 60.805 60.000 0.00 0.00 0.00 2.24
6962 7459 0.968901 TCCGGGCGTGTTGAGTATCT 60.969 55.000 0.00 0.00 34.92 1.98
6964 7461 0.108804 CGGGCGTGTTGAGTATCTGT 60.109 55.000 0.00 0.00 34.92 3.41
6966 7463 1.067142 GGGCGTGTTGAGTATCTGTGA 60.067 52.381 0.00 0.00 34.92 3.58
6967 7464 2.263077 GGCGTGTTGAGTATCTGTGAG 58.737 52.381 0.00 0.00 34.92 3.51
6968 7465 2.263077 GCGTGTTGAGTATCTGTGAGG 58.737 52.381 0.00 0.00 34.92 3.86
6969 7466 2.094700 GCGTGTTGAGTATCTGTGAGGA 60.095 50.000 0.00 0.00 34.92 3.71
6970 7467 3.763902 CGTGTTGAGTATCTGTGAGGAG 58.236 50.000 0.00 0.00 34.92 3.69
6974 7471 1.062886 TGAGTATCTGTGAGGAGGGGG 60.063 57.143 0.00 0.00 34.92 5.40
6994 7501 4.316823 AGAGGGACAGTCGGGGCA 62.317 66.667 0.00 0.00 0.00 5.36
7027 7541 4.771356 GTGCAGCTACGACGCCGA 62.771 66.667 0.00 0.00 39.50 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 115 2.362736 TGCTTGAACATGATCTCCTGC 58.637 47.619 0.00 1.74 0.00 4.85
176 202 1.133025 CGGTTCATTGGACAGGCAATC 59.867 52.381 0.00 0.00 0.00 2.67
187 217 1.369625 GGGTAGCTGACGGTTCATTG 58.630 55.000 0.00 0.00 0.00 2.82
189 219 1.515954 CGGGTAGCTGACGGTTCAT 59.484 57.895 0.00 0.00 0.00 2.57
260 290 7.596494 ACGTTTGATGATCTTTTCATGTTGAT 58.404 30.769 0.00 0.00 45.29 2.57
300 331 2.665603 GTGAGGAGGTGGCTGGTC 59.334 66.667 0.00 0.00 0.00 4.02
316 354 3.461773 CTGGATGCGGACCTCGGT 61.462 66.667 0.00 0.00 39.69 4.69
380 420 4.216902 TCCAACCGGTATATACATCTCGTG 59.783 45.833 8.00 0.00 0.00 4.35
389 429 2.974099 CCCCAACTCCAACCGGTATATA 59.026 50.000 8.00 0.00 0.00 0.86
409 449 1.139256 GGATCGGGGAAGAAGAGAACC 59.861 57.143 0.00 0.00 0.00 3.62
422 484 1.153823 GCGATATCCACGGATCGGG 60.154 63.158 0.73 0.00 44.03 5.14
490 563 2.645628 CATGTCGATTGCGCGTGC 60.646 61.111 15.48 15.48 43.20 5.34
496 569 2.404789 CCCGCACATGTCGATTGC 59.595 61.111 16.06 7.13 0.00 3.56
522 595 1.036707 CTCCTCGGGAGTCCTTCATC 58.963 60.000 9.58 0.00 44.25 2.92
541 614 7.511959 AGAAGAAAAGGAAAATACAGTCCAC 57.488 36.000 0.00 0.00 36.28 4.02
577 650 2.154462 AGAGCCGAAATCAAACACCAG 58.846 47.619 0.00 0.00 0.00 4.00
578 651 2.270352 AGAGCCGAAATCAAACACCA 57.730 45.000 0.00 0.00 0.00 4.17
579 652 2.814336 AGAAGAGCCGAAATCAAACACC 59.186 45.455 0.00 0.00 0.00 4.16
580 653 3.365364 CCAGAAGAGCCGAAATCAAACAC 60.365 47.826 0.00 0.00 0.00 3.32
581 654 2.813754 CCAGAAGAGCCGAAATCAAACA 59.186 45.455 0.00 0.00 0.00 2.83
582 655 3.074412 TCCAGAAGAGCCGAAATCAAAC 58.926 45.455 0.00 0.00 0.00 2.93
583 656 3.417069 TCCAGAAGAGCCGAAATCAAA 57.583 42.857 0.00 0.00 0.00 2.69
584 657 3.417069 TTCCAGAAGAGCCGAAATCAA 57.583 42.857 0.00 0.00 0.00 2.57
641 716 2.970324 GACACGCCACGCCAAAGA 60.970 61.111 0.00 0.00 0.00 2.52
642 717 2.972505 AGACACGCCACGCCAAAG 60.973 61.111 0.00 0.00 0.00 2.77
643 718 3.276091 CAGACACGCCACGCCAAA 61.276 61.111 0.00 0.00 0.00 3.28
644 719 4.228567 TCAGACACGCCACGCCAA 62.229 61.111 0.00 0.00 0.00 4.52
645 720 4.961511 GTCAGACACGCCACGCCA 62.962 66.667 0.00 0.00 0.00 5.69
646 721 4.961511 TGTCAGACACGCCACGCC 62.962 66.667 0.00 0.00 0.00 5.68
667 760 1.819229 CGATGAGGAGGTGGGACAG 59.181 63.158 0.00 0.00 41.80 3.51
871 995 4.883354 GATTGGAGCTGGGGCGGG 62.883 72.222 0.00 0.00 44.37 6.13
1230 1395 2.124983 GGCGCAGGATCAGAAGCA 60.125 61.111 10.83 0.00 0.00 3.91
1371 1555 1.281899 GACTTAACTAGCTGCTGCCG 58.718 55.000 13.43 6.45 40.80 5.69
1485 1669 2.019984 GGGCAAGCTCCAAATCACTAG 58.980 52.381 0.00 0.00 0.00 2.57
1506 1690 0.827368 GAAGTCTGGACCCTAGCCTG 59.173 60.000 0.00 0.00 0.00 4.85
1508 1692 0.827368 CAGAAGTCTGGACCCTAGCC 59.173 60.000 0.00 0.00 40.20 3.93
1517 1701 7.361542 CCAACTTGTTGATATTCAGAAGTCTGG 60.362 40.741 14.30 0.00 43.91 3.86
1549 1733 2.094752 CCCAACAGGCTGGTAAAATTCG 60.095 50.000 20.34 0.00 34.33 3.34
1564 1748 5.451242 GCCGATAAAATTCATAAGCCCAACA 60.451 40.000 0.00 0.00 0.00 3.33
1610 1820 0.678395 ATCAGACATAGGCTCGGCAG 59.322 55.000 0.00 0.00 0.00 4.85
1612 1822 1.889829 ACTATCAGACATAGGCTCGGC 59.110 52.381 0.00 0.00 0.00 5.54
1614 1824 3.243535 TGCAACTATCAGACATAGGCTCG 60.244 47.826 0.00 0.00 0.00 5.03
1617 1827 5.528690 TCAAATGCAACTATCAGACATAGGC 59.471 40.000 0.00 0.00 0.00 3.93
1623 1833 4.656041 GCACTCAAATGCAACTATCAGAC 58.344 43.478 0.00 0.00 45.39 3.51
1664 1874 5.359194 ACCAAACCTACATCTACCATGAG 57.641 43.478 0.00 0.00 0.00 2.90
1716 1933 2.293170 GCAGGCCTAAGAGGTCAATTC 58.707 52.381 3.98 0.00 44.17 2.17
1749 2105 1.135094 AGGGGTACAGGCATGATCAG 58.865 55.000 4.84 0.00 0.00 2.90
1775 2131 0.172803 ACGGTAAGGATGTCTGTCGC 59.827 55.000 0.00 0.00 0.00 5.19
1793 2149 3.334078 CCATTTCTGGCGAATGCAC 57.666 52.632 0.00 0.00 45.35 4.57
1846 2202 7.484975 TCAGTGTATTAACCAAGGTGTTTTTG 58.515 34.615 0.00 0.00 0.00 2.44
1886 2242 3.830755 GAGGATCGCAACCCCTAGTAATA 59.169 47.826 0.00 0.00 0.00 0.98
1956 2312 5.187687 GGAACAAATTCAATGCATGGGATT 58.812 37.500 1.23 1.23 36.46 3.01
2008 2364 2.057137 ATATCCGCTTGGTTGTGCAT 57.943 45.000 0.00 0.00 0.00 3.96
2039 2395 4.435121 GCGTACGCACTACTAAATTTTGCT 60.435 41.667 33.90 1.46 41.49 3.91
2112 2468 1.737793 GGTAACACCCTCATCTTTGCG 59.262 52.381 0.00 0.00 30.04 4.85
2147 2503 8.972127 AGCTTGTAAGAAGACTCAGATAATGTA 58.028 33.333 0.00 0.00 0.00 2.29
2169 2525 4.261322 CGTGCAGGCAATAAATATGAGCTT 60.261 41.667 0.00 0.00 0.00 3.74
2288 2644 0.603569 AGTTGTCAGAGGCTACACCG 59.396 55.000 0.00 0.00 46.52 4.94
2368 2724 1.891150 TGACTAAACTCCTGGACCGAC 59.109 52.381 0.00 0.00 0.00 4.79
2409 2766 4.267928 GGTGACGTGTCAATTACTATCTGC 59.732 45.833 3.92 0.00 41.85 4.26
2430 2787 8.876790 GTTATAGCACGAAGTTTTAATACTGGT 58.123 33.333 0.00 0.00 41.61 4.00
2446 2803 6.589830 ACTAGCTCATTTTGTTATAGCACG 57.410 37.500 0.00 0.00 35.63 5.34
2544 2901 8.937634 TTAGATAGCCCTTAAGTAAAACTTCG 57.062 34.615 0.97 0.00 39.51 3.79
2608 2965 9.177608 CTTAAATTTAAGTCCATGTCTCCATGA 57.822 33.333 24.06 0.00 41.43 3.07
2712 3071 5.947228 TTTAGATGAAGCAAGACCACAAG 57.053 39.130 0.00 0.00 0.00 3.16
2716 3077 5.415701 GGAACATTTAGATGAAGCAAGACCA 59.584 40.000 0.00 0.00 36.73 4.02
2928 3289 1.165270 ATGCACTCCACGGCTTTAAC 58.835 50.000 0.00 0.00 0.00 2.01
2941 3302 7.436118 ACACTCATAAAATCACAAAATGCACT 58.564 30.769 0.00 0.00 0.00 4.40
2942 3303 7.642071 ACACTCATAAAATCACAAAATGCAC 57.358 32.000 0.00 0.00 0.00 4.57
2943 3304 8.575589 AGTACACTCATAAAATCACAAAATGCA 58.424 29.630 0.00 0.00 0.00 3.96
2944 3305 8.970691 AGTACACTCATAAAATCACAAAATGC 57.029 30.769 0.00 0.00 0.00 3.56
2947 3308 8.708742 CGAGAGTACACTCATAAAATCACAAAA 58.291 33.333 18.62 0.00 45.21 2.44
2948 3309 7.148639 GCGAGAGTACACTCATAAAATCACAAA 60.149 37.037 18.62 0.00 45.21 2.83
2949 3310 6.310467 GCGAGAGTACACTCATAAAATCACAA 59.690 38.462 18.62 0.00 45.21 3.33
2950 3311 5.805486 GCGAGAGTACACTCATAAAATCACA 59.195 40.000 18.62 0.00 45.21 3.58
2951 3312 6.037098 AGCGAGAGTACACTCATAAAATCAC 58.963 40.000 18.62 0.00 45.21 3.06
2952 3313 6.208988 AGCGAGAGTACACTCATAAAATCA 57.791 37.500 18.62 0.00 45.21 2.57
2953 3314 6.975772 AGAAGCGAGAGTACACTCATAAAATC 59.024 38.462 18.62 8.56 45.21 2.17
3024 3391 6.689554 TCAAGAAATATGCATGCACTTGAAA 58.310 32.000 32.10 19.65 39.04 2.69
3030 3397 8.344831 TGTTATACTCAAGAAATATGCATGCAC 58.655 33.333 25.37 10.10 0.00 4.57
3511 3939 5.362717 ACAATCAAGACATGGATCAATGCAT 59.637 36.000 10.19 0.00 39.56 3.96
3530 3958 3.950087 TGATATTCAGCACGCACAATC 57.050 42.857 0.00 0.00 0.00 2.67
3696 4124 2.209690 ACCGGGTTTATTTGACTGGG 57.790 50.000 6.32 0.00 0.00 4.45
3715 4143 4.457949 TCAGACTGATGCTACGAACAAGTA 59.542 41.667 0.00 0.00 0.00 2.24
4012 4440 0.848735 ATCCACAGGACCATCCCATG 59.151 55.000 0.00 0.00 37.19 3.66
4032 4460 0.609131 CCATCCACACCACTTGGGAC 60.609 60.000 0.00 0.00 41.15 4.46
4069 4497 3.797039 TGCATATCTACACCAGCAAGAC 58.203 45.455 0.00 0.00 0.00 3.01
4181 4609 3.181497 CCATATCAGTTTTTGCTGTCCCG 60.181 47.826 0.00 0.00 37.70 5.14
4247 4675 8.934023 AAAGTGATACCTTTGTGGAAAGATAA 57.066 30.769 0.00 0.00 41.12 1.75
4287 4715 9.057089 GCCTGATTTACACTAAAGCATATAAGT 57.943 33.333 0.00 0.00 42.36 2.24
4291 4719 7.512992 AGAGCCTGATTTACACTAAAGCATAT 58.487 34.615 0.00 0.00 42.36 1.78
4324 4752 2.269940 AGACACTTGGCCTAATCCTGT 58.730 47.619 3.32 0.00 0.00 4.00
4331 4759 2.360801 GCAACAAAAGACACTTGGCCTA 59.639 45.455 3.32 0.00 0.00 3.93
4415 4843 5.480772 TCAGTGGAAGGAAAGTACCTAGAAG 59.519 44.000 0.00 0.00 39.62 2.85
4425 4853 4.694509 CAGAAGTCATCAGTGGAAGGAAAG 59.305 45.833 0.00 0.00 0.00 2.62
4632 5060 0.764890 TGCTAAGGCACAGGAACAGT 59.235 50.000 0.00 0.00 44.28 3.55
4740 5168 2.463752 TCTCTATTACCACTGGCGGTT 58.536 47.619 0.00 0.00 40.67 4.44
4989 5417 7.647318 CCGATGTTAAATATTGCTATTGTTGCA 59.353 33.333 0.00 0.00 38.80 4.08
5083 5511 4.525912 AAGGAAACATTGATGAGTTGGC 57.474 40.909 0.00 0.00 0.00 4.52
5117 5568 7.095910 AGAGAGAAACACTGATCACATACAAG 58.904 38.462 0.00 0.00 0.00 3.16
5313 5766 2.165030 GCAAAGATGATGGGTCAACAGG 59.835 50.000 0.00 0.00 38.01 4.00
5363 5816 5.730550 ACAAGAAGGCGTATTCTATTGTCA 58.269 37.500 4.94 0.00 38.59 3.58
5438 5891 1.000938 CTGGAGTTTGACAAAGCAGGC 60.001 52.381 0.00 0.00 0.00 4.85
5468 5921 3.767278 ACGACTTTGGCTTCTATACGAC 58.233 45.455 0.00 0.00 0.00 4.34
5527 5980 6.121776 TCTAATACAAAAGCAGGACTCCAA 57.878 37.500 0.00 0.00 0.00 3.53
5681 6134 6.599356 TGTTCCAGACTGTACTAATTAGCA 57.401 37.500 12.54 2.78 0.00 3.49
5692 6145 0.534877 TTGCGCATGTTCCAGACTGT 60.535 50.000 12.75 0.00 0.00 3.55
5693 6146 0.806868 ATTGCGCATGTTCCAGACTG 59.193 50.000 12.75 0.00 0.00 3.51
5753 6212 7.237471 AGGATTTTCCCCACATTTTAAATCAGT 59.763 33.333 0.00 0.00 37.19 3.41
5794 6253 2.288152 GCTAGATGCTGAGCCTACAGAC 60.288 54.545 0.23 0.85 39.94 3.51
5933 6392 1.478631 TGTCGATGAGCAGGTCAGAT 58.521 50.000 8.56 0.00 39.07 2.90
6014 6473 0.038159 CGGCGTCTTCTTTCTCCAGT 60.038 55.000 0.00 0.00 0.00 4.00
6016 6475 0.038526 GTCGGCGTCTTCTTTCTCCA 60.039 55.000 6.85 0.00 0.00 3.86
6086 6545 4.897076 TCACAAGGATATATACACCGGTGT 59.103 41.667 39.83 39.83 46.87 4.16
6088 6547 6.681729 ATTCACAAGGATATATACACCGGT 57.318 37.500 0.00 0.00 0.00 5.28
6137 6605 7.696035 GCAGTATACTCATCATATCAACTCTCG 59.304 40.741 1.26 0.00 0.00 4.04
6339 6814 7.931407 ACAAAATGGGGACTTGTTTATTTTCTC 59.069 33.333 0.00 0.00 28.99 2.87
6345 6820 4.262851 GGCACAAAATGGGGACTTGTTTAT 60.263 41.667 0.00 0.00 30.99 1.40
6346 6821 3.070302 GGCACAAAATGGGGACTTGTTTA 59.930 43.478 0.00 0.00 30.99 2.01
6350 6825 1.047002 TGGCACAAAATGGGGACTTG 58.953 50.000 0.00 0.00 31.92 3.16
6387 6867 2.789213 TGTATACCAGCAGCTTTGCAA 58.211 42.857 0.00 0.00 37.25 4.08
6392 6872 3.567164 GCAATCATGTATACCAGCAGCTT 59.433 43.478 0.00 0.00 0.00 3.74
6398 6878 8.933807 CAGAGATAAAGCAATCATGTATACCAG 58.066 37.037 0.00 0.00 0.00 4.00
6410 6890 8.671921 CAAACATCTACACAGAGATAAAGCAAT 58.328 33.333 0.00 0.00 34.29 3.56
6475 6955 3.054065 ACTCCATGGAAGAAGATTGGTCC 60.054 47.826 17.00 0.00 0.00 4.46
6493 6973 1.852280 GTCAAAACAGCGCAAAACTCC 59.148 47.619 11.47 0.00 0.00 3.85
6497 6977 3.321497 ACAAAGTCAAAACAGCGCAAAA 58.679 36.364 11.47 0.00 0.00 2.44
6524 7005 6.537355 TCCATGAGAGAACACAATTCTTTCT 58.463 36.000 0.00 0.00 32.69 2.52
6555 7036 3.899981 AACAGCTCGGCCGAATGCA 62.900 57.895 32.92 12.35 43.89 3.96
6562 7043 0.462759 AGCTTATCAACAGCTCGGCC 60.463 55.000 0.00 0.00 44.77 6.13
6616 7097 5.438761 GCTTCTAGCAGGAAACAGAAAAA 57.561 39.130 0.00 0.00 41.89 1.94
6650 7131 5.088739 CGTGAAGTTCATTAGGTTTCATGC 58.911 41.667 9.18 0.00 30.75 4.06
6663 7144 3.266636 TCAAGAGCAAACGTGAAGTTCA 58.733 40.909 0.08 0.08 43.37 3.18
6701 7191 7.712639 GGATGCTACATGAGTTTCAATTCTAGA 59.287 37.037 0.00 0.00 0.00 2.43
6703 7193 7.496920 CAGGATGCTACATGAGTTTCAATTCTA 59.503 37.037 0.00 0.00 0.00 2.10
6738 7228 4.256110 CTGGTCACAAGTATCAAGATGCA 58.744 43.478 0.00 0.00 0.00 3.96
6748 7238 6.530120 ACATATTCACAACTGGTCACAAGTA 58.470 36.000 0.00 0.00 0.00 2.24
6749 7239 5.376625 ACATATTCACAACTGGTCACAAGT 58.623 37.500 0.00 0.00 0.00 3.16
6807 7300 3.354397 CGAATTTCATTAGGCTTCGTGC 58.646 45.455 0.00 0.00 41.94 5.34
6848 7341 9.782028 CACAAAAGAAACATTTCATTTATCACG 57.218 29.630 7.10 0.00 36.35 4.35
6910 7407 6.015434 GTGCTCTAAAGGGATTTTTCTCCAAA 60.015 38.462 0.00 0.00 37.01 3.28
6915 7412 4.010349 CGGTGCTCTAAAGGGATTTTTCT 58.990 43.478 0.00 0.00 0.00 2.52
6928 7425 2.104859 CGGACGTCTCGGTGCTCTA 61.105 63.158 16.46 0.00 0.00 2.43
6943 7440 0.968901 AGATACTCAACACGCCCGGA 60.969 55.000 0.73 0.00 0.00 5.14
6946 7443 1.067142 TCACAGATACTCAACACGCCC 60.067 52.381 0.00 0.00 0.00 6.13
6950 7447 3.118956 CCCTCCTCACAGATACTCAACAC 60.119 52.174 0.00 0.00 0.00 3.32
6951 7448 3.099905 CCCTCCTCACAGATACTCAACA 58.900 50.000 0.00 0.00 0.00 3.33
6952 7449 2.432510 CCCCTCCTCACAGATACTCAAC 59.567 54.545 0.00 0.00 0.00 3.18
6953 7450 2.626950 CCCCCTCCTCACAGATACTCAA 60.627 54.545 0.00 0.00 0.00 3.02
6954 7451 1.062886 CCCCCTCCTCACAGATACTCA 60.063 57.143 0.00 0.00 0.00 3.41
6956 7453 3.957188 CCCCCTCCTCACAGATACT 57.043 57.895 0.00 0.00 0.00 2.12
6974 7471 3.775654 CCCGACTGTCCCTCTGCC 61.776 72.222 1.55 0.00 0.00 4.85
6975 7472 3.775654 CCCCGACTGTCCCTCTGC 61.776 72.222 1.55 0.00 0.00 4.26
6976 7473 3.775654 GCCCCGACTGTCCCTCTG 61.776 72.222 1.55 0.00 0.00 3.35
6978 7475 3.083997 ATGCCCCGACTGTCCCTC 61.084 66.667 1.55 0.00 0.00 4.30
6980 7477 4.530857 CGATGCCCCGACTGTCCC 62.531 72.222 1.55 0.00 0.00 4.46
6981 7478 4.530857 CCGATGCCCCGACTGTCC 62.531 72.222 1.55 0.00 0.00 4.02
7032 7546 3.672503 AGCCAATCCCACCACCCC 61.673 66.667 0.00 0.00 0.00 4.95
7058 7572 3.124921 GTCACCCGCCAATCACCG 61.125 66.667 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.