Multiple sequence alignment - TraesCS6D01G240000

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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 TraesCS6D01G240000 chr6D 100.000 2835 0 0 1 2835 341118534 341115700 0.000000e+00 5236.0
1 TraesCS6D01G240000 chr6D 90.288 659 61 3 1 657 58437828 58437171 0.000000e+00 859.0
2 TraesCS6D01G240000 chr6D 98.387 62 0 1 2344 2405 341116129 341116069 1.070000e-19 108.0
3 TraesCS6D01G240000 chr6D 98.387 62 0 1 2406 2466 341116191 341116130 1.070000e-19 108.0
4 TraesCS6D01G240000 chr6B 93.203 1736 55 32 693 2405 479299319 479301014 0.000000e+00 2494.0
5 TraesCS6D01G240000 chr6B 94.432 431 21 3 2406 2835 479300954 479301382 0.000000e+00 660.0
6 TraesCS6D01G240000 chr6A 90.730 1575 57 27 691 2231 481083480 481081961 0.000000e+00 2017.0
7 TraesCS6D01G240000 chr6A 86.577 298 28 10 2541 2833 481080805 481080515 4.560000e-83 318.0
8 TraesCS6D01G240000 chr6A 81.481 135 8 5 2230 2359 481081935 481081813 8.360000e-16 95.3
9 TraesCS6D01G240000 chr5D 91.463 656 52 3 1 655 382082420 382081768 0.000000e+00 898.0
10 TraesCS6D01G240000 chr1D 91.258 652 55 2 1 650 461760067 461759416 0.000000e+00 887.0
11 TraesCS6D01G240000 chr7D 90.937 651 57 2 1 650 509531623 509530974 0.000000e+00 874.0
12 TraesCS6D01G240000 chr7D 90.578 658 59 3 1 655 583073251 583072594 0.000000e+00 869.0
13 TraesCS6D01G240000 chr3D 90.854 656 54 4 1 655 397538671 397539321 0.000000e+00 874.0
14 TraesCS6D01G240000 chr3D 90.687 655 55 3 1 650 578148450 578149103 0.000000e+00 867.0
15 TraesCS6D01G240000 chr4D 90.798 652 57 3 1 650 19346721 19347371 0.000000e+00 869.0
16 TraesCS6D01G240000 chr2D 90.783 651 58 2 1 650 399427993 399427344 0.000000e+00 869.0
17 TraesCS6D01G240000 chr2D 78.626 655 86 36 1099 1727 502929837 502930463 4.430000e-103 385.0
18 TraesCS6D01G240000 chr2B 78.053 647 89 35 1102 1727 590918855 590919469 2.690000e-95 359.0
19 TraesCS6D01G240000 chr2A 77.150 407 61 26 1092 1494 648341584 648341962 1.030000e-49 207.0


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 TraesCS6D01G240000 chr6D 341115700 341118534 2834 True 1817.333333 5236 98.924667 1 2835 3 chr6D.!!$R2 2834
1 TraesCS6D01G240000 chr6D 58437171 58437828 657 True 859.000000 859 90.288000 1 657 1 chr6D.!!$R1 656
2 TraesCS6D01G240000 chr6B 479299319 479301382 2063 False 1577.000000 2494 93.817500 693 2835 2 chr6B.!!$F1 2142
3 TraesCS6D01G240000 chr6A 481080515 481083480 2965 True 810.100000 2017 86.262667 691 2833 3 chr6A.!!$R1 2142
4 TraesCS6D01G240000 chr5D 382081768 382082420 652 True 898.000000 898 91.463000 1 655 1 chr5D.!!$R1 654
5 TraesCS6D01G240000 chr1D 461759416 461760067 651 True 887.000000 887 91.258000 1 650 1 chr1D.!!$R1 649
6 TraesCS6D01G240000 chr7D 509530974 509531623 649 True 874.000000 874 90.937000 1 650 1 chr7D.!!$R1 649
7 TraesCS6D01G240000 chr7D 583072594 583073251 657 True 869.000000 869 90.578000 1 655 1 chr7D.!!$R2 654
8 TraesCS6D01G240000 chr3D 397538671 397539321 650 False 874.000000 874 90.854000 1 655 1 chr3D.!!$F1 654
9 TraesCS6D01G240000 chr3D 578148450 578149103 653 False 867.000000 867 90.687000 1 650 1 chr3D.!!$F2 649
10 TraesCS6D01G240000 chr4D 19346721 19347371 650 False 869.000000 869 90.798000 1 650 1 chr4D.!!$F1 649
11 TraesCS6D01G240000 chr2D 399427344 399427993 649 True 869.000000 869 90.783000 1 650 1 chr2D.!!$R1 649
12 TraesCS6D01G240000 chr2D 502929837 502930463 626 False 385.000000 385 78.626000 1099 1727 1 chr2D.!!$F1 628
13 TraesCS6D01G240000 chr2B 590918855 590919469 614 False 359.000000 359 78.053000 1102 1727 1 chr2B.!!$F1 625

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
117 121 0.041312 GACGACAACTGCAATTGCGT 60.041 50.0 23.08 23.08 45.83 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2097 0.179065 TGCGCGCTAGTACTCCTAGA 60.179 55.0 33.29 3.26 45.21 2.43 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
111 115 2.232756 TTGCTAGACGACAACTGCAA 57.767 45.000 0.00 0.00 37.96 4.08
117 121 0.041312 GACGACAACTGCAATTGCGT 60.041 50.000 23.08 23.08 45.83 5.24
133 137 2.314647 CGTGTACGTGGCAACCAGG 61.315 63.158 0.00 4.83 44.01 4.45
146 152 2.621055 GCAACCAGGTAAACACACATGA 59.379 45.455 0.00 0.00 32.01 3.07
214 226 3.818773 GGCAACTAGGTAAACACACATGT 59.181 43.478 0.00 0.00 42.46 3.21
221 233 7.676947 ACTAGGTAAACACACATGTCAACTAT 58.323 34.615 0.00 0.00 38.45 2.12
316 328 8.454106 CCATAAATTAGACATGGCAACTATAGC 58.546 37.037 0.00 0.00 33.29 2.97
362 374 5.530915 TCATGCTTTTACAACTACACTTGCT 59.469 36.000 0.00 0.00 0.00 3.91
374 386 4.838986 ACTACACTTGCTATCCCGGATAAT 59.161 41.667 0.73 0.00 0.00 1.28
387 399 4.042809 TCCCGGATAATTACATCTGCCAAT 59.957 41.667 0.73 0.00 31.05 3.16
407 419 2.288666 TCAGGATGGCAACTAAATCGC 58.711 47.619 0.00 0.00 36.16 4.58
463 476 1.866601 GTGTGGGCATTTTTGCTTCAC 59.133 47.619 13.68 13.68 38.41 3.18
491 505 1.948104 CGCGGGGTGAAGATGAATAA 58.052 50.000 0.00 0.00 0.00 1.40
551 565 3.057596 CACGTGTGGGCAATTCTAATGTT 60.058 43.478 7.58 0.00 0.00 2.71
553 567 4.762765 ACGTGTGGGCAATTCTAATGTTTA 59.237 37.500 0.00 0.00 0.00 2.01
585 599 1.070786 CGTGTGGGTTGCCTACTGT 59.929 57.895 3.47 0.00 35.94 3.55
587 601 1.687563 GTGTGGGTTGCCTACTGTTT 58.312 50.000 3.47 0.00 35.94 2.83
593 607 2.224695 GGGTTGCCTACTGTTTACACCT 60.225 50.000 0.00 0.00 0.00 4.00
607 621 7.039293 ACTGTTTACACCTCACACAGTATATGA 60.039 37.037 1.44 0.00 44.91 2.15
627 641 8.877808 ATATGAACGCATGTCGAATATATCAT 57.122 30.769 14.88 13.89 41.67 2.45
657 671 5.589855 TGATGGATATCTGCGTCAAAAACAT 59.410 36.000 2.05 0.00 36.00 2.71
658 672 5.895636 TGGATATCTGCGTCAAAAACATT 57.104 34.783 2.05 0.00 0.00 2.71
659 673 6.993786 TGGATATCTGCGTCAAAAACATTA 57.006 33.333 2.05 0.00 0.00 1.90
660 674 6.781138 TGGATATCTGCGTCAAAAACATTAC 58.219 36.000 2.05 0.00 0.00 1.89
661 675 6.183360 TGGATATCTGCGTCAAAAACATTACC 60.183 38.462 2.05 0.00 0.00 2.85
662 676 3.907894 TCTGCGTCAAAAACATTACCC 57.092 42.857 0.00 0.00 0.00 3.69
663 677 2.224549 TCTGCGTCAAAAACATTACCCG 59.775 45.455 0.00 0.00 0.00 5.28
664 678 2.219458 TGCGTCAAAAACATTACCCGA 58.781 42.857 0.00 0.00 0.00 5.14
665 679 2.224549 TGCGTCAAAAACATTACCCGAG 59.775 45.455 0.00 0.00 0.00 4.63
666 680 2.413634 GCGTCAAAAACATTACCCGAGG 60.414 50.000 0.00 0.00 0.00 4.63
667 681 3.068560 CGTCAAAAACATTACCCGAGGA 58.931 45.455 0.00 0.00 0.00 3.71
668 682 3.687698 CGTCAAAAACATTACCCGAGGAT 59.312 43.478 0.00 0.00 0.00 3.24
669 683 4.436852 CGTCAAAAACATTACCCGAGGATG 60.437 45.833 0.00 0.00 0.00 3.51
670 684 3.442273 TCAAAAACATTACCCGAGGATGC 59.558 43.478 0.00 0.00 0.00 3.91
671 685 2.799126 AAACATTACCCGAGGATGCA 57.201 45.000 0.00 0.00 0.00 3.96
672 686 3.297134 AAACATTACCCGAGGATGCAT 57.703 42.857 0.00 0.00 0.00 3.96
673 687 2.260844 ACATTACCCGAGGATGCATG 57.739 50.000 2.46 0.00 0.00 4.06
674 688 1.768275 ACATTACCCGAGGATGCATGA 59.232 47.619 2.46 0.00 0.00 3.07
675 689 2.373169 ACATTACCCGAGGATGCATGAT 59.627 45.455 2.46 0.00 0.00 2.45
676 690 3.582647 ACATTACCCGAGGATGCATGATA 59.417 43.478 2.46 0.00 0.00 2.15
677 691 4.225942 ACATTACCCGAGGATGCATGATAT 59.774 41.667 2.46 0.00 0.00 1.63
678 692 4.908601 TTACCCGAGGATGCATGATATT 57.091 40.909 2.46 0.00 0.00 1.28
679 693 6.070251 ACATTACCCGAGGATGCATGATATTA 60.070 38.462 2.46 0.00 0.00 0.98
680 694 4.207891 ACCCGAGGATGCATGATATTAC 57.792 45.455 2.46 0.00 0.00 1.89
681 695 3.055094 ACCCGAGGATGCATGATATTACC 60.055 47.826 2.46 0.00 0.00 2.85
682 696 3.055167 CCCGAGGATGCATGATATTACCA 60.055 47.826 2.46 0.00 0.00 3.25
683 697 4.384537 CCCGAGGATGCATGATATTACCAT 60.385 45.833 2.46 0.00 0.00 3.55
684 698 5.163311 CCCGAGGATGCATGATATTACCATA 60.163 44.000 2.46 0.00 0.00 2.74
685 699 5.755375 CCGAGGATGCATGATATTACCATAC 59.245 44.000 2.46 0.00 0.00 2.39
686 700 5.460091 CGAGGATGCATGATATTACCATACG 59.540 44.000 2.46 1.49 0.00 3.06
687 701 6.544928 AGGATGCATGATATTACCATACGA 57.455 37.500 2.46 0.00 0.00 3.43
688 702 6.577103 AGGATGCATGATATTACCATACGAG 58.423 40.000 2.46 0.00 0.00 4.18
689 703 6.155221 AGGATGCATGATATTACCATACGAGT 59.845 38.462 2.46 0.00 0.00 4.18
740 755 0.664466 GCCAGAACGAAAGCAAAGCC 60.664 55.000 0.00 0.00 0.00 4.35
865 882 0.604511 CACGTCCCAACCAACTACCC 60.605 60.000 0.00 0.00 0.00 3.69
934 969 2.760385 CCCACTCGTCTCCCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
935 970 2.360980 CCACTCGTCTCCCTCCCT 59.639 66.667 0.00 0.00 0.00 4.20
936 971 1.755008 CCACTCGTCTCCCTCCCTC 60.755 68.421 0.00 0.00 0.00 4.30
937 972 1.755008 CACTCGTCTCCCTCCCTCC 60.755 68.421 0.00 0.00 0.00 4.30
938 973 2.123640 CTCGTCTCCCTCCCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
939 974 2.617538 TCGTCTCCCTCCCTCCCT 60.618 66.667 0.00 0.00 0.00 4.20
940 975 2.123640 CGTCTCCCTCCCTCCCTC 60.124 72.222 0.00 0.00 0.00 4.30
941 976 2.284151 GTCTCCCTCCCTCCCTCC 59.716 72.222 0.00 0.00 0.00 4.30
1079 1125 4.112341 CTGGACGGACGGACGGAC 62.112 72.222 6.00 0.00 38.39 4.79
1082 1128 4.410743 GACGGACGGACGGACCAC 62.411 72.222 6.00 0.00 38.90 4.16
1212 1279 1.695597 CCTCCTCTGGGCCTTCCAT 60.696 63.158 4.53 0.00 46.01 3.41
1713 1816 4.379243 CTGCTCAACGGCCTCGGT 62.379 66.667 0.00 0.00 41.39 4.69
1953 2069 2.100631 GCCACATTCGGGTCGTCTG 61.101 63.158 0.00 0.00 0.00 3.51
1954 2070 1.589630 CCACATTCGGGTCGTCTGA 59.410 57.895 0.00 0.00 0.00 3.27
1955 2071 0.175760 CCACATTCGGGTCGTCTGAT 59.824 55.000 0.00 0.00 0.00 2.90
1957 2073 0.460311 ACATTCGGGTCGTCTGATCC 59.540 55.000 0.00 0.00 42.45 3.36
1958 2074 0.747255 CATTCGGGTCGTCTGATCCT 59.253 55.000 0.00 0.00 43.82 3.24
1959 2075 1.033574 ATTCGGGTCGTCTGATCCTC 58.966 55.000 0.00 0.00 43.82 3.71
1969 2085 1.342819 GTCTGATCCTCCCCGATCTTG 59.657 57.143 0.00 0.00 39.57 3.02
1977 2093 1.529244 CCCCGATCTTGCCATTCCC 60.529 63.158 0.00 0.00 0.00 3.97
1978 2094 1.529244 CCCGATCTTGCCATTCCCC 60.529 63.158 0.00 0.00 0.00 4.81
1979 2095 1.533711 CCGATCTTGCCATTCCCCT 59.466 57.895 0.00 0.00 0.00 4.79
1980 2096 0.106519 CCGATCTTGCCATTCCCCTT 60.107 55.000 0.00 0.00 0.00 3.95
1981 2097 1.686115 CCGATCTTGCCATTCCCCTTT 60.686 52.381 0.00 0.00 0.00 3.11
1984 2100 3.433598 CGATCTTGCCATTCCCCTTTCTA 60.434 47.826 0.00 0.00 0.00 2.10
1985 2101 3.652057 TCTTGCCATTCCCCTTTCTAG 57.348 47.619 0.00 0.00 0.00 2.43
1986 2102 2.242196 TCTTGCCATTCCCCTTTCTAGG 59.758 50.000 0.00 0.00 41.60 3.02
1987 2103 1.979809 TGCCATTCCCCTTTCTAGGA 58.020 50.000 0.00 0.00 45.05 2.94
1988 2104 1.846439 TGCCATTCCCCTTTCTAGGAG 59.154 52.381 0.00 0.00 45.05 3.69
1989 2105 1.847088 GCCATTCCCCTTTCTAGGAGT 59.153 52.381 0.00 0.00 45.05 3.85
1990 2106 3.046374 GCCATTCCCCTTTCTAGGAGTA 58.954 50.000 0.00 0.00 45.05 2.59
2172 2302 1.947013 TCGGTCTCGACAGTGACAC 59.053 57.895 0.00 0.00 41.28 3.67
2243 2400 2.963854 CAGGTAGCTGCGCCGATG 60.964 66.667 9.34 0.00 0.00 3.84
2299 2461 3.636043 CACCGTGTCCGTGTGTGC 61.636 66.667 0.00 0.00 33.43 4.57
2366 2535 1.609208 TCCTGCTTCACTGCTTTTCC 58.391 50.000 0.00 0.00 0.00 3.13
2367 2536 1.133823 TCCTGCTTCACTGCTTTTCCA 60.134 47.619 0.00 0.00 0.00 3.53
2368 2537 1.000938 CCTGCTTCACTGCTTTTCCAC 60.001 52.381 0.00 0.00 0.00 4.02
2369 2538 0.662619 TGCTTCACTGCTTTTCCACG 59.337 50.000 0.00 0.00 0.00 4.94
2370 2539 0.944386 GCTTCACTGCTTTTCCACGA 59.056 50.000 0.00 0.00 0.00 4.35
2371 2540 1.069636 GCTTCACTGCTTTTCCACGAG 60.070 52.381 0.00 0.00 0.00 4.18
2372 2541 2.483876 CTTCACTGCTTTTCCACGAGA 58.516 47.619 0.00 0.00 0.00 4.04
2373 2542 1.865865 TCACTGCTTTTCCACGAGAC 58.134 50.000 0.00 0.00 0.00 3.36
2374 2543 0.508641 CACTGCTTTTCCACGAGACG 59.491 55.000 0.00 0.00 0.00 4.18
2375 2544 0.600255 ACTGCTTTTCCACGAGACGG 60.600 55.000 0.00 0.00 0.00 4.79
2376 2545 1.291877 CTGCTTTTCCACGAGACGGG 61.292 60.000 0.00 0.00 0.00 5.28
2377 2546 1.005394 GCTTTTCCACGAGACGGGA 60.005 57.895 0.00 0.00 28.17 5.14
2378 2547 1.289800 GCTTTTCCACGAGACGGGAC 61.290 60.000 0.00 0.00 31.59 4.46
2392 2561 3.754766 GGGACGGGCTAGTAACAAG 57.245 57.895 0.00 0.00 0.00 3.16
2393 2562 0.461516 GGGACGGGCTAGTAACAAGC 60.462 60.000 0.00 0.00 39.33 4.01
2401 2570 3.053831 GCTAGTAACAAGCCAAGGTCA 57.946 47.619 0.00 0.00 33.73 4.02
2402 2571 3.408634 GCTAGTAACAAGCCAAGGTCAA 58.591 45.455 0.00 0.00 33.73 3.18
2403 2572 4.010349 GCTAGTAACAAGCCAAGGTCAAT 58.990 43.478 0.00 0.00 33.73 2.57
2404 2573 4.095036 GCTAGTAACAAGCCAAGGTCAATC 59.905 45.833 0.00 0.00 33.73 2.67
2405 2574 4.373156 AGTAACAAGCCAAGGTCAATCT 57.627 40.909 0.00 0.00 0.00 2.40
2406 2575 4.327680 AGTAACAAGCCAAGGTCAATCTC 58.672 43.478 0.00 0.00 0.00 2.75
2407 2576 2.206576 ACAAGCCAAGGTCAATCTCC 57.793 50.000 0.00 0.00 0.00 3.71
2408 2577 1.707427 ACAAGCCAAGGTCAATCTCCT 59.293 47.619 0.00 0.00 36.81 3.69
2409 2578 2.108952 ACAAGCCAAGGTCAATCTCCTT 59.891 45.455 0.00 0.00 44.93 3.36
2410 2579 2.751806 CAAGCCAAGGTCAATCTCCTTC 59.248 50.000 0.00 0.00 42.57 3.46
2411 2580 1.283321 AGCCAAGGTCAATCTCCTTCC 59.717 52.381 0.00 0.00 42.57 3.46
2412 2581 1.283321 GCCAAGGTCAATCTCCTTCCT 59.717 52.381 0.00 0.00 42.57 3.36
2413 2582 2.943199 GCCAAGGTCAATCTCCTTCCTG 60.943 54.545 0.00 0.00 42.57 3.86
2414 2583 2.363683 CAAGGTCAATCTCCTTCCTGC 58.636 52.381 0.00 0.00 42.57 4.85
2415 2584 1.963985 AGGTCAATCTCCTTCCTGCT 58.036 50.000 0.00 0.00 30.18 4.24
2416 2585 2.273619 AGGTCAATCTCCTTCCTGCTT 58.726 47.619 0.00 0.00 30.18 3.91
2417 2586 2.238395 AGGTCAATCTCCTTCCTGCTTC 59.762 50.000 0.00 0.00 30.18 3.86
2418 2587 2.026822 GGTCAATCTCCTTCCTGCTTCA 60.027 50.000 0.00 0.00 0.00 3.02
2419 2588 3.006247 GTCAATCTCCTTCCTGCTTCAC 58.994 50.000 0.00 0.00 0.00 3.18
2420 2589 2.909006 TCAATCTCCTTCCTGCTTCACT 59.091 45.455 0.00 0.00 0.00 3.41
2421 2590 3.008330 CAATCTCCTTCCTGCTTCACTG 58.992 50.000 0.00 0.00 0.00 3.66
2422 2591 0.322975 TCTCCTTCCTGCTTCACTGC 59.677 55.000 0.00 0.00 0.00 4.40
2423 2592 0.324285 CTCCTTCCTGCTTCACTGCT 59.676 55.000 0.00 0.00 0.00 4.24
2424 2593 0.767375 TCCTTCCTGCTTCACTGCTT 59.233 50.000 0.00 0.00 0.00 3.91
2425 2594 1.143684 TCCTTCCTGCTTCACTGCTTT 59.856 47.619 0.00 0.00 0.00 3.51
2426 2595 1.959282 CCTTCCTGCTTCACTGCTTTT 59.041 47.619 0.00 0.00 0.00 2.27
2427 2596 2.030451 CCTTCCTGCTTCACTGCTTTTC 60.030 50.000 0.00 0.00 0.00 2.29
2477 2646 2.165167 AGGTCAATCACAATGCCACAG 58.835 47.619 0.00 0.00 0.00 3.66
2515 2690 5.607119 TTGGAAACGAGTGAGCTTATTTC 57.393 39.130 0.00 0.00 32.56 2.17
2539 3600 0.942962 GGATGGAAATGAGCGAGCTG 59.057 55.000 0.84 0.00 0.00 4.24
2546 3607 4.274214 TGGAAATGAGCGAGCTGATTATTG 59.726 41.667 9.98 0.00 30.08 1.90
2577 3638 2.106683 GCTCCGAATGAACCGGGTG 61.107 63.158 6.32 0.00 46.47 4.61
2582 3643 1.077716 GAATGAACCGGGTGGAGGG 60.078 63.158 6.32 0.00 39.21 4.30
2584 3645 2.137177 AATGAACCGGGTGGAGGGTG 62.137 60.000 6.32 0.00 39.21 4.61
2603 3664 0.680061 GGGCGAACGGGAATAGAGAT 59.320 55.000 0.00 0.00 0.00 2.75
2624 3685 1.280421 GAGAAGCCTTGAGGTCCACAT 59.720 52.381 0.00 0.00 37.57 3.21
2687 3748 1.722464 CATGCTTTTGACGTGCCATTG 59.278 47.619 0.00 0.00 0.00 2.82
2762 3823 5.691305 CCGCATGATTTTGTTTTCTGAAAGA 59.309 36.000 0.00 0.00 44.68 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 115 1.572447 GTTGCCACGTACACGCAAT 59.428 52.632 12.66 0.00 43.78 3.56
117 121 0.757512 TTACCTGGTTGCCACGTACA 59.242 50.000 3.84 0.00 27.95 2.90
133 137 5.478233 TCACAGTTGTCATGTGTGTTTAC 57.522 39.130 11.76 0.00 46.49 2.01
137 141 5.008613 GGTTAATCACAGTTGTCATGTGTGT 59.991 40.000 11.76 0.00 46.49 3.72
138 142 5.008514 TGGTTAATCACAGTTGTCATGTGTG 59.991 40.000 6.99 6.99 46.49 3.82
146 152 6.757897 CCATGTATGGTTAATCACAGTTGT 57.242 37.500 2.66 0.00 43.05 3.32
185 197 3.069300 TGTTTACCTAGTTGCCACGTGTA 59.931 43.478 15.65 0.00 0.00 2.90
214 226 7.389803 CCACATATGGTCAAACAATAGTTGA 57.610 36.000 7.80 0.00 41.64 3.18
316 328 7.962964 TGACAACTCTATCTGTTTTGGTTAG 57.037 36.000 0.00 0.00 0.00 2.34
362 374 4.780554 TGGCAGATGTAATTATCCGGGATA 59.219 41.667 12.75 12.75 0.00 2.59
387 399 2.288666 GCGATTTAGTTGCCATCCTGA 58.711 47.619 0.00 0.00 0.00 3.86
407 419 0.529119 GTTAGGTACCCGCGTGATGG 60.529 60.000 8.74 0.45 0.00 3.51
412 424 1.993369 GCTACGTTAGGTACCCGCGT 61.993 60.000 23.11 23.11 36.04 6.01
491 505 2.289547 GTGCCACACGTTCAACAAGTAT 59.710 45.455 0.00 0.00 0.00 2.12
551 565 0.464013 CACGGGTTGTGTGTGGGTAA 60.464 55.000 0.00 0.00 43.88 2.85
553 567 2.124487 CACGGGTTGTGTGTGGGT 60.124 61.111 0.00 0.00 43.88 4.51
575 589 3.134985 TGTGAGGTGTAAACAGTAGGCAA 59.865 43.478 0.00 0.00 0.00 4.52
581 595 3.906720 ACTGTGTGAGGTGTAAACAGT 57.093 42.857 1.08 1.08 44.94 3.55
585 599 6.809689 CGTTCATATACTGTGTGAGGTGTAAA 59.190 38.462 0.00 0.00 0.00 2.01
587 601 5.677852 GCGTTCATATACTGTGTGAGGTGTA 60.678 44.000 0.00 0.00 0.00 2.90
593 607 4.754322 ACATGCGTTCATATACTGTGTGA 58.246 39.130 0.00 0.00 0.00 3.58
607 621 6.554700 CGTATGATATATTCGACATGCGTT 57.445 37.500 11.80 2.60 41.28 4.84
627 641 2.621526 ACGCAGATATCCATCACACGTA 59.378 45.455 0.00 0.00 35.68 3.57
644 658 2.219458 TCGGGTAATGTTTTTGACGCA 58.781 42.857 0.00 0.00 0.00 5.24
657 671 4.908601 AATATCATGCATCCTCGGGTAA 57.091 40.909 0.00 0.00 0.00 2.85
658 672 4.161565 GGTAATATCATGCATCCTCGGGTA 59.838 45.833 0.00 0.00 0.00 3.69
659 673 3.055094 GGTAATATCATGCATCCTCGGGT 60.055 47.826 0.00 0.00 0.00 5.28
660 674 3.055167 TGGTAATATCATGCATCCTCGGG 60.055 47.826 0.00 0.00 0.00 5.14
661 675 4.206477 TGGTAATATCATGCATCCTCGG 57.794 45.455 0.00 0.00 0.00 4.63
662 676 5.460091 CGTATGGTAATATCATGCATCCTCG 59.540 44.000 0.00 0.00 0.00 4.63
663 677 6.573434 TCGTATGGTAATATCATGCATCCTC 58.427 40.000 0.00 0.00 0.00 3.71
664 678 6.155221 ACTCGTATGGTAATATCATGCATCCT 59.845 38.462 0.00 0.00 0.00 3.24
665 679 6.341316 ACTCGTATGGTAATATCATGCATCC 58.659 40.000 0.00 0.00 0.00 3.51
666 680 7.435488 GGTACTCGTATGGTAATATCATGCATC 59.565 40.741 0.00 0.00 0.00 3.91
667 681 7.265673 GGTACTCGTATGGTAATATCATGCAT 58.734 38.462 0.00 0.00 0.00 3.96
668 682 6.350696 GGGTACTCGTATGGTAATATCATGCA 60.351 42.308 2.73 0.00 0.00 3.96
669 683 6.040878 GGGTACTCGTATGGTAATATCATGC 58.959 44.000 0.00 0.00 0.00 4.06
670 684 6.570692 GGGGTACTCGTATGGTAATATCATG 58.429 44.000 0.00 0.00 0.00 3.07
671 685 5.359009 CGGGGTACTCGTATGGTAATATCAT 59.641 44.000 0.00 0.00 0.00 2.45
672 686 4.701651 CGGGGTACTCGTATGGTAATATCA 59.298 45.833 0.00 0.00 0.00 2.15
673 687 4.439289 GCGGGGTACTCGTATGGTAATATC 60.439 50.000 9.94 0.00 0.00 1.63
674 688 3.445096 GCGGGGTACTCGTATGGTAATAT 59.555 47.826 9.94 0.00 0.00 1.28
675 689 2.819608 GCGGGGTACTCGTATGGTAATA 59.180 50.000 9.94 0.00 0.00 0.98
676 690 1.615392 GCGGGGTACTCGTATGGTAAT 59.385 52.381 9.94 0.00 0.00 1.89
677 691 1.032014 GCGGGGTACTCGTATGGTAA 58.968 55.000 9.94 0.00 0.00 2.85
678 692 0.183492 AGCGGGGTACTCGTATGGTA 59.817 55.000 9.94 0.00 0.00 3.25
679 693 1.076485 AGCGGGGTACTCGTATGGT 60.076 57.895 9.94 0.00 0.00 3.55
680 694 1.362717 CAGCGGGGTACTCGTATGG 59.637 63.158 9.94 0.00 0.00 2.74
681 695 1.299926 GCAGCGGGGTACTCGTATG 60.300 63.158 9.94 9.90 0.00 2.39
682 696 2.842256 CGCAGCGGGGTACTCGTAT 61.842 63.158 7.00 0.00 0.00 3.06
683 697 3.511595 CGCAGCGGGGTACTCGTA 61.512 66.667 7.00 0.00 0.00 3.43
740 755 2.355837 ACTGTGGCGTGCTACGTG 60.356 61.111 0.00 2.32 44.73 4.49
789 806 2.203112 TGATGCTCCATCGGCTGC 60.203 61.111 0.00 0.00 43.14 5.25
934 969 1.382420 CAGTCAGGGGAGGAGGGAG 60.382 68.421 0.00 0.00 0.00 4.30
935 970 2.780693 CAGTCAGGGGAGGAGGGA 59.219 66.667 0.00 0.00 0.00 4.20
936 971 2.366167 CCAGTCAGGGGAGGAGGG 60.366 72.222 0.00 0.00 0.00 4.30
937 972 3.086600 GCCAGTCAGGGGAGGAGG 61.087 72.222 0.00 0.00 38.09 4.30
938 973 2.040278 AGCCAGTCAGGGGAGGAG 59.960 66.667 0.00 0.00 38.09 3.69
939 974 2.284921 CAGCCAGTCAGGGGAGGA 60.285 66.667 0.00 0.00 38.09 3.71
940 975 2.284921 TCAGCCAGTCAGGGGAGG 60.285 66.667 0.00 0.00 38.09 4.30
941 976 2.664081 GGTCAGCCAGTCAGGGGAG 61.664 68.421 0.00 0.00 38.09 4.30
1062 1108 4.112341 GTCCGTCCGTCCGTCCAG 62.112 72.222 0.00 0.00 0.00 3.86
1065 1111 4.410743 GTGGTCCGTCCGTCCGTC 62.411 72.222 0.00 0.00 39.52 4.79
1713 1816 2.596851 GCCTCCTCACTGGAAGCCA 61.597 63.158 0.00 0.00 44.52 4.75
1760 1863 1.591594 CCGTGGCGCCTATGTACAG 60.592 63.158 29.70 12.49 0.00 2.74
1953 2069 1.373059 GGCAAGATCGGGGAGGATC 59.627 63.158 0.00 0.00 42.52 3.36
1954 2070 0.769776 ATGGCAAGATCGGGGAGGAT 60.770 55.000 0.00 0.00 0.00 3.24
1955 2071 0.988145 AATGGCAAGATCGGGGAGGA 60.988 55.000 0.00 0.00 0.00 3.71
1957 2073 0.536006 GGAATGGCAAGATCGGGGAG 60.536 60.000 0.00 0.00 0.00 4.30
1958 2074 1.531748 GGAATGGCAAGATCGGGGA 59.468 57.895 0.00 0.00 0.00 4.81
1959 2075 1.529244 GGGAATGGCAAGATCGGGG 60.529 63.158 0.00 0.00 0.00 5.73
1977 2093 2.031857 CGCGCTAGTACTCCTAGAAAGG 60.032 54.545 5.56 0.00 45.21 3.11
1978 2094 2.602694 GCGCGCTAGTACTCCTAGAAAG 60.603 54.545 26.67 0.00 45.21 2.62
1979 2095 1.332997 GCGCGCTAGTACTCCTAGAAA 59.667 52.381 26.67 0.00 45.21 2.52
1980 2096 0.942962 GCGCGCTAGTACTCCTAGAA 59.057 55.000 26.67 0.00 45.21 2.10
1981 2097 0.179065 TGCGCGCTAGTACTCCTAGA 60.179 55.000 33.29 3.26 45.21 2.43
1984 2100 3.111939 CTGCGCGCTAGTACTCCT 58.888 61.111 33.29 0.00 0.00 3.69
1985 2101 2.655685 GCTGCGCGCTAGTACTCC 60.656 66.667 33.29 10.44 35.14 3.85
1986 2102 2.655685 GGCTGCGCGCTAGTACTC 60.656 66.667 33.29 13.64 39.13 2.59
1987 2103 3.417275 CTGGCTGCGCGCTAGTACT 62.417 63.158 33.29 0.00 41.82 2.73
1988 2104 2.956964 CTGGCTGCGCGCTAGTAC 60.957 66.667 33.29 21.65 41.82 2.73
1989 2105 3.126074 CTCTGGCTGCGCGCTAGTA 62.126 63.158 33.29 17.82 46.33 1.82
1990 2106 4.504916 CTCTGGCTGCGCGCTAGT 62.505 66.667 33.29 0.00 46.33 2.57
2005 2121 2.279120 CTCGCCGCATCCTGACTC 60.279 66.667 0.00 0.00 0.00 3.36
2006 2122 2.755876 TCTCGCCGCATCCTGACT 60.756 61.111 0.00 0.00 0.00 3.41
2007 2123 2.583593 GTCTCGCCGCATCCTGAC 60.584 66.667 0.00 0.00 0.00 3.51
2010 2126 3.376935 CTTGGTCTCGCCGCATCCT 62.377 63.158 0.00 0.00 41.21 3.24
2243 2400 2.030457 CCACTGCATCCGTTTACGAATC 59.970 50.000 3.46 0.00 43.02 2.52
2296 2458 2.490993 CTTTGTTCATGGGGGCGCAC 62.491 60.000 10.83 4.83 0.00 5.34
2299 2461 1.814772 TTGCTTTGTTCATGGGGGCG 61.815 55.000 0.00 0.00 0.00 6.13
2367 2536 4.415150 TAGCCCGTCCCGTCTCGT 62.415 66.667 0.00 0.00 0.00 4.18
2368 2537 2.930385 TACTAGCCCGTCCCGTCTCG 62.930 65.000 0.00 0.00 0.00 4.04
2369 2538 0.749454 TTACTAGCCCGTCCCGTCTC 60.749 60.000 0.00 0.00 0.00 3.36
2370 2539 1.034292 GTTACTAGCCCGTCCCGTCT 61.034 60.000 0.00 0.00 0.00 4.18
2371 2540 1.315257 TGTTACTAGCCCGTCCCGTC 61.315 60.000 0.00 0.00 0.00 4.79
2372 2541 0.899717 TTGTTACTAGCCCGTCCCGT 60.900 55.000 0.00 0.00 0.00 5.28
2373 2542 0.179119 CTTGTTACTAGCCCGTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
2374 2543 0.461516 GCTTGTTACTAGCCCGTCCC 60.462 60.000 7.53 0.00 32.45 4.46
2375 2544 3.061093 GCTTGTTACTAGCCCGTCC 57.939 57.895 7.53 0.00 32.45 4.79
2381 2550 3.053831 TGACCTTGGCTTGTTACTAGC 57.946 47.619 10.15 10.15 37.91 3.42
2382 2551 5.491982 AGATTGACCTTGGCTTGTTACTAG 58.508 41.667 0.00 0.00 0.00 2.57
2383 2552 5.488341 GAGATTGACCTTGGCTTGTTACTA 58.512 41.667 0.00 0.00 0.00 1.82
2384 2553 4.327680 GAGATTGACCTTGGCTTGTTACT 58.672 43.478 0.00 0.00 0.00 2.24
2385 2554 3.440522 GGAGATTGACCTTGGCTTGTTAC 59.559 47.826 0.00 0.00 0.00 2.50
2386 2555 3.330701 AGGAGATTGACCTTGGCTTGTTA 59.669 43.478 0.00 0.00 33.55 2.41
2387 2556 2.108952 AGGAGATTGACCTTGGCTTGTT 59.891 45.455 0.00 0.00 33.55 2.83
2388 2557 1.707427 AGGAGATTGACCTTGGCTTGT 59.293 47.619 0.00 0.00 33.55 3.16
2389 2558 2.503895 AGGAGATTGACCTTGGCTTG 57.496 50.000 0.00 0.00 33.55 4.01
2390 2559 2.291217 GGAAGGAGATTGACCTTGGCTT 60.291 50.000 0.00 0.00 46.14 4.35
2391 2560 1.283321 GGAAGGAGATTGACCTTGGCT 59.717 52.381 0.00 0.00 46.14 4.75
2392 2561 1.283321 AGGAAGGAGATTGACCTTGGC 59.717 52.381 0.00 0.00 46.14 4.52
2393 2562 2.943199 GCAGGAAGGAGATTGACCTTGG 60.943 54.545 0.00 0.00 46.14 3.61
2394 2563 2.026449 AGCAGGAAGGAGATTGACCTTG 60.026 50.000 0.00 0.00 46.14 3.61
2396 2565 1.963985 AGCAGGAAGGAGATTGACCT 58.036 50.000 0.00 0.00 39.69 3.85
2397 2566 2.026822 TGAAGCAGGAAGGAGATTGACC 60.027 50.000 0.00 0.00 0.00 4.02
2398 2567 3.006247 GTGAAGCAGGAAGGAGATTGAC 58.994 50.000 0.00 0.00 0.00 3.18
2399 2568 2.909006 AGTGAAGCAGGAAGGAGATTGA 59.091 45.455 0.00 0.00 0.00 2.57
2400 2569 3.008330 CAGTGAAGCAGGAAGGAGATTG 58.992 50.000 0.00 0.00 0.00 2.67
2401 2570 2.617532 GCAGTGAAGCAGGAAGGAGATT 60.618 50.000 0.00 0.00 0.00 2.40
2402 2571 1.065564 GCAGTGAAGCAGGAAGGAGAT 60.066 52.381 0.00 0.00 0.00 2.75
2403 2572 0.322975 GCAGTGAAGCAGGAAGGAGA 59.677 55.000 0.00 0.00 0.00 3.71
2404 2573 0.324285 AGCAGTGAAGCAGGAAGGAG 59.676 55.000 0.00 0.00 36.85 3.69
2405 2574 0.767375 AAGCAGTGAAGCAGGAAGGA 59.233 50.000 0.00 0.00 36.85 3.36
2406 2575 1.613836 AAAGCAGTGAAGCAGGAAGG 58.386 50.000 0.00 0.00 36.85 3.46
2407 2576 2.030451 GGAAAAGCAGTGAAGCAGGAAG 60.030 50.000 0.00 0.00 36.85 3.46
2408 2577 1.956477 GGAAAAGCAGTGAAGCAGGAA 59.044 47.619 0.00 0.00 36.85 3.36
2409 2578 1.133823 TGGAAAAGCAGTGAAGCAGGA 60.134 47.619 0.00 0.00 36.85 3.86
2410 2579 1.000938 GTGGAAAAGCAGTGAAGCAGG 60.001 52.381 0.00 0.00 36.85 4.85
2411 2580 1.334419 CGTGGAAAAGCAGTGAAGCAG 60.334 52.381 0.00 0.00 36.85 4.24
2412 2581 0.662619 CGTGGAAAAGCAGTGAAGCA 59.337 50.000 0.00 0.00 36.85 3.91
2413 2582 0.944386 TCGTGGAAAAGCAGTGAAGC 59.056 50.000 0.00 0.00 0.00 3.86
2414 2583 2.221981 GTCTCGTGGAAAAGCAGTGAAG 59.778 50.000 0.00 0.00 0.00 3.02
2415 2584 2.210116 GTCTCGTGGAAAAGCAGTGAA 58.790 47.619 0.00 0.00 0.00 3.18
2416 2585 1.865865 GTCTCGTGGAAAAGCAGTGA 58.134 50.000 0.00 0.00 0.00 3.41
2417 2586 0.508641 CGTCTCGTGGAAAAGCAGTG 59.491 55.000 0.00 0.00 0.00 3.66
2418 2587 0.600255 CCGTCTCGTGGAAAAGCAGT 60.600 55.000 0.00 0.00 0.00 4.40
2419 2588 1.291877 CCCGTCTCGTGGAAAAGCAG 61.292 60.000 0.00 0.00 0.00 4.24
2420 2589 1.301401 CCCGTCTCGTGGAAAAGCA 60.301 57.895 0.00 0.00 0.00 3.91
2421 2590 1.005394 TCCCGTCTCGTGGAAAAGC 60.005 57.895 0.00 0.00 0.00 3.51
2422 2591 1.007336 CGTCCCGTCTCGTGGAAAAG 61.007 60.000 0.00 0.00 30.73 2.27
2423 2592 1.007038 CGTCCCGTCTCGTGGAAAA 60.007 57.895 0.00 0.00 30.73 2.29
2424 2593 2.646719 CGTCCCGTCTCGTGGAAA 59.353 61.111 0.00 0.00 30.73 3.13
2425 2594 3.367743 CCGTCCCGTCTCGTGGAA 61.368 66.667 0.00 0.00 30.73 3.53
2443 2612 2.762535 TGACCTTGGCTGTTACTAGC 57.237 50.000 0.00 0.00 42.94 3.42
2460 2629 1.548081 CCCTGTGGCATTGTGATTGA 58.452 50.000 0.00 0.00 0.00 2.57
2477 2646 0.750249 CCAAACAAGTCACAACCCCC 59.250 55.000 0.00 0.00 0.00 5.40
2515 2690 1.694150 TCGCTCATTTCCATCCCCTAG 59.306 52.381 0.00 0.00 0.00 3.02
2582 3643 0.529992 CTCTATTCCCGTTCGCCCAC 60.530 60.000 0.00 0.00 0.00 4.61
2584 3645 0.680061 ATCTCTATTCCCGTTCGCCC 59.320 55.000 0.00 0.00 0.00 6.13
2603 3664 0.687354 GTGGACCTCAAGGCTTCTCA 59.313 55.000 0.00 0.00 39.32 3.27
2624 3685 2.336667 CATGTATGCGATGGCGATACA 58.663 47.619 19.20 19.20 42.12 2.29


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

AutoCloner maintained by Alex Coulton.