Multiple sequence alignment - TraesCS6B01G041100

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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 TraesCS6B01G041100 chr6B 100.000 2687 0 0 1 2687 25552673 25549987 0.000000e+00 4963.0
1 TraesCS6B01G041100 chr6B 96.835 632 17 3 2057 2687 21430271 21429642 0.000000e+00 1053.0
2 TraesCS6B01G041100 chr6D 88.095 1302 64 45 605 1890 13990327 13991553 0.000000e+00 1461.0
3 TraesCS6B01G041100 chr6D 86.400 250 33 1 2 250 13989682 13989931 3.410000e-69 272.0
4 TraesCS6B01G041100 chr6D 97.619 42 1 0 449 490 86961686 86961727 3.710000e-09 73.1
5 TraesCS6B01G041100 chr6D 97.619 42 1 0 449 490 120224042 120224001 3.710000e-09 73.1
6 TraesCS6B01G041100 chr6A 90.298 907 55 16 999 1878 14603952 14603052 0.000000e+00 1157.0
7 TraesCS6B01G041100 chr6A 92.506 387 29 0 1235 1621 14582818 14582432 3.020000e-154 555.0
8 TraesCS6B01G041100 chr6A 82.636 478 52 15 5 460 14604813 14604345 6.970000e-106 394.0
9 TraesCS6B01G041100 chr6A 89.732 224 13 6 665 884 14604213 14603996 7.330000e-71 278.0
10 TraesCS6B01G041100 chr6A 90.909 143 13 0 1899 2041 611108792 611108934 2.730000e-45 193.0
11 TraesCS6B01G041100 chr6A 84.358 179 16 9 1631 1798 14580705 14580528 5.950000e-37 165.0
12 TraesCS6B01G041100 chr5A 97.222 648 15 3 2040 2687 484820698 484820054 0.000000e+00 1094.0
13 TraesCS6B01G041100 chr5A 92.029 138 9 1 1905 2040 442308670 442308533 2.730000e-45 193.0
14 TraesCS6B01G041100 chr1B 96.989 631 17 2 2057 2687 555050379 555051007 0.000000e+00 1059.0
15 TraesCS6B01G041100 chr1B 96.513 631 20 2 2057 2687 554998040 554998668 0.000000e+00 1042.0
16 TraesCS6B01G041100 chr1B 94.615 130 7 0 1911 2040 662240150 662240279 4.540000e-48 202.0
17 TraesCS6B01G041100 chr7D 94.118 646 31 5 2042 2687 400158630 400159268 0.000000e+00 976.0
18 TraesCS6B01G041100 chr7D 93.385 650 36 5 2038 2687 585298800 585298158 0.000000e+00 955.0
19 TraesCS6B01G041100 chr7D 100.000 38 0 0 453 490 355125081 355125044 1.330000e-08 71.3
20 TraesCS6B01G041100 chr4D 93.529 649 35 5 2039 2687 407787190 407787831 0.000000e+00 959.0
21 TraesCS6B01G041100 chr3A 96.071 560 21 1 2128 2687 26574890 26574332 0.000000e+00 911.0
22 TraesCS6B01G041100 chr3A 93.846 130 8 0 1911 2040 455786639 455786510 2.110000e-46 196.0
23 TraesCS6B01G041100 chr7A 86.614 635 77 7 2057 2687 729124252 729124882 0.000000e+00 695.0
24 TraesCS6B01G041100 chr7A 92.199 141 9 2 1900 2038 727826925 727827065 5.870000e-47 198.0
25 TraesCS6B01G041100 chr2B 94.615 130 7 0 1911 2040 680572877 680573006 4.540000e-48 202.0
26 TraesCS6B01G041100 chr2B 92.000 50 3 1 442 490 168616322 168616371 4.800000e-08 69.4
27 TraesCS6B01G041100 chr4B 93.382 136 7 1 1905 2038 519387932 519387797 1.630000e-47 200.0
28 TraesCS6B01G041100 chr4B 92.086 139 11 0 1902 2040 286183023 286183161 2.110000e-46 196.0
29 TraesCS6B01G041100 chr2D 92.199 141 9 1 1902 2040 15019067 15019207 5.870000e-47 198.0
30 TraesCS6B01G041100 chr5D 97.727 44 1 0 447 490 267365483 267365440 2.870000e-10 76.8
31 TraesCS6B01G041100 chr5B 94.118 51 2 1 441 490 69132101 69132051 2.870000e-10 76.8
32 TraesCS6B01G041100 chr1D 95.556 45 2 0 446 490 465049385 465049429 3.710000e-09 73.1
33 TraesCS6B01G041100 chrUn 93.878 49 0 3 443 490 279936315 279936269 1.330000e-08 71.3
34 TraesCS6B01G041100 chrUn 93.878 49 0 3 443 490 395541702 395541656 1.330000e-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 TraesCS6B01G041100 chr6B 25549987 25552673 2686 True 4963.000000 4963 100.000000 1 2687 1 chr6B.!!$R2 2686
1 TraesCS6B01G041100 chr6B 21429642 21430271 629 True 1053.000000 1053 96.835000 2057 2687 1 chr6B.!!$R1 630
2 TraesCS6B01G041100 chr6D 13989682 13991553 1871 False 866.500000 1461 87.247500 2 1890 2 chr6D.!!$F2 1888
3 TraesCS6B01G041100 chr6A 14603052 14604813 1761 True 609.666667 1157 87.555333 5 1878 3 chr6A.!!$R2 1873
4 TraesCS6B01G041100 chr6A 14580528 14582818 2290 True 360.000000 555 88.432000 1235 1798 2 chr6A.!!$R1 563
5 TraesCS6B01G041100 chr5A 484820054 484820698 644 True 1094.000000 1094 97.222000 2040 2687 1 chr5A.!!$R2 647
6 TraesCS6B01G041100 chr1B 555050379 555051007 628 False 1059.000000 1059 96.989000 2057 2687 1 chr1B.!!$F2 630
7 TraesCS6B01G041100 chr1B 554998040 554998668 628 False 1042.000000 1042 96.513000 2057 2687 1 chr1B.!!$F1 630
8 TraesCS6B01G041100 chr7D 400158630 400159268 638 False 976.000000 976 94.118000 2042 2687 1 chr7D.!!$F1 645
9 TraesCS6B01G041100 chr7D 585298158 585298800 642 True 955.000000 955 93.385000 2038 2687 1 chr7D.!!$R2 649
10 TraesCS6B01G041100 chr4D 407787190 407787831 641 False 959.000000 959 93.529000 2039 2687 1 chr4D.!!$F1 648
11 TraesCS6B01G041100 chr3A 26574332 26574890 558 True 911.000000 911 96.071000 2128 2687 1 chr3A.!!$R1 559
12 TraesCS6B01G041100 chr7A 729124252 729124882 630 False 695.000000 695 86.614000 2057 2687 1 chr7A.!!$F2 630

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
656 849 0.035439 GGACGCCTGGAAATCTGGAA 60.035 55.0 0.0 0.0 36.68 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1702 3628 0.43883 GCCAGCAACGAACGAAGTAG 59.561 55.0 0.14 0.0 45.0 2.57 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
64 67 2.173669 GGATCGTCACCATGCACCG 61.174 63.158 0.00 0.00 0.00 4.94
67 70 4.088762 CGTCACCATGCACCGTGC 62.089 66.667 16.93 16.93 45.29 5.34
68 71 2.669569 GTCACCATGCACCGTGCT 60.670 61.111 23.52 7.30 45.31 4.40
72 75 2.290287 ACCATGCACCGTGCTCCTA 61.290 57.895 23.52 4.37 45.31 2.94
74 77 1.219124 CATGCACCGTGCTCCTACT 59.781 57.895 23.52 0.07 45.31 2.57
75 78 0.391661 CATGCACCGTGCTCCTACTT 60.392 55.000 23.52 0.00 45.31 2.24
83 86 1.464997 CGTGCTCCTACTTCTTTTGGC 59.535 52.381 0.00 0.00 0.00 4.52
96 99 4.715534 TCTTTTGGCCCCGAATATATCA 57.284 40.909 0.00 0.00 0.00 2.15
97 100 5.255397 TCTTTTGGCCCCGAATATATCAT 57.745 39.130 0.00 0.00 0.00 2.45
99 102 6.785076 TCTTTTGGCCCCGAATATATCATTA 58.215 36.000 0.00 0.00 0.00 1.90
109 112 6.310467 CCCGAATATATCATTAACACGACAGG 59.690 42.308 0.00 0.00 0.00 4.00
133 167 8.883731 AGGTTGTTGAAGAATCTACATATTTCG 58.116 33.333 0.00 0.00 40.23 3.46
149 183 7.021196 ACATATTTCGTCAATGTGTTTGCTAC 58.979 34.615 6.64 0.00 42.85 3.58
165 199 3.374764 TGCTACTCATATGGTGACTGGT 58.625 45.455 2.13 0.00 32.22 4.00
191 226 0.669318 TCGCCGTGTCAGTTGATTCC 60.669 55.000 0.00 0.00 0.00 3.01
195 230 2.341257 CCGTGTCAGTTGATTCCTGAG 58.659 52.381 0.00 0.00 39.51 3.35
205 240 2.257409 GATTCCTGAGGAAGGCGGCA 62.257 60.000 19.92 0.00 45.48 5.69
228 263 1.965930 GCAGTTGCCCACGATGTCA 60.966 57.895 0.00 0.00 34.31 3.58
231 266 0.108585 AGTTGCCCACGATGTCAACT 59.891 50.000 10.37 10.37 42.80 3.16
242 277 0.172803 ATGTCAACTACGAGGCCGAC 59.827 55.000 0.00 0.00 39.50 4.79
261 304 1.273838 ACCCAGGAGAGTGCCATAGAA 60.274 52.381 0.00 0.00 0.00 2.10
262 305 1.139853 CCCAGGAGAGTGCCATAGAAC 59.860 57.143 0.00 0.00 0.00 3.01
270 313 4.211986 GCCATAGAACGGGCGAAA 57.788 55.556 0.00 0.00 40.93 3.46
273 316 1.734163 CCATAGAACGGGCGAAACTT 58.266 50.000 0.00 0.00 0.00 2.66
298 341 1.003718 CAGAGGGTTGACGGGTTCC 60.004 63.158 0.00 0.00 0.00 3.62
449 626 2.880963 TGGTGCGATGTCGATGATTA 57.119 45.000 6.60 0.00 43.02 1.75
460 637 6.575572 CGATGTCGATGATTACAGAGAAGTAC 59.424 42.308 0.00 0.00 43.02 2.73
461 638 7.519168 CGATGTCGATGATTACAGAGAAGTACT 60.519 40.741 0.00 0.00 43.02 2.73
462 639 7.017498 TGTCGATGATTACAGAGAAGTACTC 57.983 40.000 0.00 0.00 45.22 2.59
463 640 6.038382 TGTCGATGATTACAGAGAAGTACTCC 59.962 42.308 0.00 0.00 45.96 3.85
464 641 5.531659 TCGATGATTACAGAGAAGTACTCCC 59.468 44.000 0.00 0.00 45.96 4.30
465 642 5.533154 CGATGATTACAGAGAAGTACTCCCT 59.467 44.000 0.00 0.00 45.96 4.20
466 643 6.293735 CGATGATTACAGAGAAGTACTCCCTC 60.294 46.154 14.19 14.19 45.96 4.30
467 644 5.202004 TGATTACAGAGAAGTACTCCCTCC 58.798 45.833 16.95 6.06 45.96 4.30
468 645 2.131776 ACAGAGAAGTACTCCCTCCG 57.868 55.000 16.95 11.93 45.96 4.63
469 646 1.355043 ACAGAGAAGTACTCCCTCCGT 59.645 52.381 16.95 12.42 45.96 4.69
470 647 2.225066 ACAGAGAAGTACTCCCTCCGTT 60.225 50.000 16.95 4.33 45.96 4.44
471 648 2.424246 CAGAGAAGTACTCCCTCCGTTC 59.576 54.545 16.95 1.23 45.96 3.95
472 649 1.750206 GAGAAGTACTCCCTCCGTTCC 59.250 57.143 12.00 0.00 39.53 3.62
473 650 1.076677 AGAAGTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.00 0.00 3.53
474 651 1.897802 GAAGTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 0.00 3.53
475 652 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
476 653 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
477 654 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
478 655 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
479 656 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
480 657 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
481 658 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
482 659 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
483 660 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
484 661 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
485 662 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
486 663 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
487 664 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
488 665 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
489 666 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
490 667 5.445939 CCGTTCCAAAATAGATGACTCAACG 60.446 44.000 0.00 0.00 34.21 4.10
491 668 5.445939 CGTTCCAAAATAGATGACTCAACGG 60.446 44.000 0.00 0.00 31.56 4.44
492 669 3.938963 TCCAAAATAGATGACTCAACGGC 59.061 43.478 0.00 0.00 0.00 5.68
493 670 3.065371 CCAAAATAGATGACTCAACGGCC 59.935 47.826 0.00 0.00 0.00 6.13
510 687 2.694305 CGGGTAAGGAGGAGGGGA 59.306 66.667 0.00 0.00 0.00 4.81
550 743 4.646572 AGCGGGAGATGAAGAATAAATCC 58.353 43.478 0.00 0.00 0.00 3.01
551 744 4.349342 AGCGGGAGATGAAGAATAAATCCT 59.651 41.667 0.00 0.00 0.00 3.24
570 763 4.957296 TCCTAGCCGTTAGATTTCAATCC 58.043 43.478 0.00 0.00 36.04 3.01
574 767 5.310720 AGCCGTTAGATTTCAATCCAAAC 57.689 39.130 0.00 1.72 36.04 2.93
578 771 6.569610 GCCGTTAGATTTCAATCCAAACTCAA 60.570 38.462 11.03 0.00 36.04 3.02
635 828 0.404040 AATTCAGTCGCCCCCTTTCA 59.596 50.000 0.00 0.00 0.00 2.69
642 835 3.140814 GCCCCCTTTCATGGACGC 61.141 66.667 0.00 0.00 0.00 5.19
649 842 1.533625 CTTTCATGGACGCCTGGAAA 58.466 50.000 0.00 11.60 0.00 3.13
650 843 2.094675 CTTTCATGGACGCCTGGAAAT 58.905 47.619 0.00 0.00 30.58 2.17
652 845 0.911769 TCATGGACGCCTGGAAATCT 59.088 50.000 0.00 0.00 0.00 2.40
653 846 1.019673 CATGGACGCCTGGAAATCTG 58.980 55.000 0.00 0.00 0.00 2.90
654 847 0.107017 ATGGACGCCTGGAAATCTGG 60.107 55.000 0.00 0.00 37.51 3.86
655 848 1.198094 TGGACGCCTGGAAATCTGGA 61.198 55.000 0.00 0.00 36.68 3.86
656 849 0.035439 GGACGCCTGGAAATCTGGAA 60.035 55.000 0.00 0.00 36.68 3.53
657 850 1.408822 GGACGCCTGGAAATCTGGAAT 60.409 52.381 0.00 0.00 36.68 3.01
658 851 2.158813 GGACGCCTGGAAATCTGGAATA 60.159 50.000 0.00 0.00 36.68 1.75
659 852 2.872858 GACGCCTGGAAATCTGGAATAC 59.127 50.000 0.00 0.00 36.68 1.89
662 855 3.491964 CGCCTGGAAATCTGGAATACGTA 60.492 47.826 0.00 0.00 36.68 3.57
663 856 3.808174 GCCTGGAAATCTGGAATACGTAC 59.192 47.826 0.00 0.00 36.68 3.67
665 858 5.221382 GCCTGGAAATCTGGAATACGTACTA 60.221 44.000 0.00 0.00 36.68 1.82
666 859 6.214399 CCTGGAAATCTGGAATACGTACTAC 58.786 44.000 0.00 0.00 36.68 2.73
668 861 7.230108 CCTGGAAATCTGGAATACGTACTACTA 59.770 40.741 0.00 0.00 36.68 1.82
669 862 8.701908 TGGAAATCTGGAATACGTACTACTAT 57.298 34.615 0.00 0.00 0.00 2.12
670 863 9.139734 TGGAAATCTGGAATACGTACTACTATT 57.860 33.333 0.00 0.00 0.00 1.73
671 864 9.978044 GGAAATCTGGAATACGTACTACTATTT 57.022 33.333 0.00 0.00 0.00 1.40
673 866 9.978044 AAATCTGGAATACGTACTACTATTTCC 57.022 33.333 12.78 12.78 0.00 3.13
674 867 8.937207 ATCTGGAATACGTACTACTATTTCCT 57.063 34.615 18.03 1.55 0.00 3.36
675 868 8.162878 TCTGGAATACGTACTACTATTTCCTG 57.837 38.462 18.03 17.24 0.00 3.86
758 951 2.034878 TCTCATGGCCTACAGCTACAG 58.965 52.381 3.32 0.00 43.05 2.74
759 952 0.465705 TCATGGCCTACAGCTACAGC 59.534 55.000 3.32 0.00 43.05 4.40
788 981 1.429463 CACTACGTGCTTCCAGGAAC 58.571 55.000 0.00 0.00 0.00 3.62
811 1004 3.186119 TGCAAAAGCTTCCGTTCAAAAG 58.814 40.909 0.00 0.00 0.00 2.27
884 1082 2.603473 ACACCACTAGCGCCCAGA 60.603 61.111 13.16 0.00 0.00 3.86
885 1083 1.990060 ACACCACTAGCGCCCAGAT 60.990 57.895 13.16 0.00 0.00 2.90
888 1086 0.464452 ACCACTAGCGCCCAGATAAC 59.536 55.000 13.16 0.00 0.00 1.89
896 1094 0.664761 CGCCCAGATAACAATGCAGG 59.335 55.000 0.00 0.00 0.00 4.85
903 1101 1.714899 ATAACAATGCAGGCCGTCGC 61.715 55.000 7.79 7.79 0.00 5.19
910 1108 3.043419 CAGGCCGTCGCTAGCTAT 58.957 61.111 13.93 0.00 34.44 2.97
911 1109 1.081108 CAGGCCGTCGCTAGCTATC 60.081 63.158 13.93 2.00 34.44 2.08
912 1110 1.528542 AGGCCGTCGCTAGCTATCA 60.529 57.895 13.93 0.00 34.44 2.15
926 1127 3.535561 AGCTATCATCCAAAGACCAACG 58.464 45.455 0.00 0.00 0.00 4.10
933 1134 0.788391 CCAAAGACCAACGAGTACGC 59.212 55.000 0.00 0.00 43.96 4.42
966 1171 1.445754 CACCGAGCTGAGCAGTGAG 60.446 63.158 14.57 0.00 31.33 3.51
967 1172 1.905843 ACCGAGCTGAGCAGTGAGT 60.906 57.895 7.39 0.00 0.00 3.41
968 1173 1.445754 CCGAGCTGAGCAGTGAGTG 60.446 63.158 7.39 0.00 0.00 3.51
969 1174 1.583477 CGAGCTGAGCAGTGAGTGA 59.417 57.895 7.39 0.00 0.00 3.41
970 1175 0.456482 CGAGCTGAGCAGTGAGTGAG 60.456 60.000 7.39 0.00 0.00 3.51
971 1176 0.737019 GAGCTGAGCAGTGAGTGAGC 60.737 60.000 7.39 0.00 0.00 4.26
972 1177 2.093473 GCTGAGCAGTGAGTGAGCG 61.093 63.158 0.00 0.00 0.00 5.03
973 1178 1.445754 CTGAGCAGTGAGTGAGCGG 60.446 63.158 0.00 0.00 0.00 5.52
974 1179 2.813042 GAGCAGTGAGTGAGCGGC 60.813 66.667 0.00 0.00 0.00 6.53
975 1180 4.385405 AGCAGTGAGTGAGCGGCC 62.385 66.667 0.00 0.00 0.00 6.13
1157 1366 2.656069 GCTCCTACCCGTGCAGGAA 61.656 63.158 8.24 0.00 45.00 3.36
1694 3620 5.278561 CCGAGCTGGAGGACTAGTTAATTAG 60.279 48.000 0.00 3.60 42.00 1.73
1695 3621 5.299782 CGAGCTGGAGGACTAGTTAATTAGT 59.700 44.000 10.17 10.17 36.61 2.24
1696 3622 6.183360 CGAGCTGGAGGACTAGTTAATTAGTT 60.183 42.308 11.50 0.00 34.13 2.24
1697 3623 7.497773 AGCTGGAGGACTAGTTAATTAGTTT 57.502 36.000 11.50 4.43 34.13 2.66
1698 3624 8.605325 AGCTGGAGGACTAGTTAATTAGTTTA 57.395 34.615 11.50 0.00 34.13 2.01
1699 3625 9.214962 AGCTGGAGGACTAGTTAATTAGTTTAT 57.785 33.333 11.50 2.20 34.13 1.40
1857 3826 1.523938 GTTGGTAGGGCTCATCCGC 60.524 63.158 0.00 0.00 34.94 5.54
1867 3836 1.993370 GGCTCATCCGCGTAATGATAC 59.007 52.381 18.25 14.11 32.91 2.24
1891 3860 8.836268 ACGAAAAGTGTAAGGTATACAAATGA 57.164 30.769 5.01 0.00 0.00 2.57
1892 3861 9.444600 ACGAAAAGTGTAAGGTATACAAATGAT 57.555 29.630 5.01 0.00 0.00 2.45
1895 3864 9.855021 AAAAGTGTAAGGTATACAAATGATTGC 57.145 29.630 5.01 0.00 40.34 3.56
1896 3865 7.246674 AGTGTAAGGTATACAAATGATTGCG 57.753 36.000 5.01 0.00 40.34 4.85
1897 3866 7.045416 AGTGTAAGGTATACAAATGATTGCGA 58.955 34.615 5.01 0.00 40.34 5.10
1898 3867 7.224753 AGTGTAAGGTATACAAATGATTGCGAG 59.775 37.037 5.01 0.00 40.34 5.03
1899 3868 7.011109 GTGTAAGGTATACAAATGATTGCGAGT 59.989 37.037 5.01 0.00 40.34 4.18
1900 3869 8.198778 TGTAAGGTATACAAATGATTGCGAGTA 58.801 33.333 5.01 0.00 40.34 2.59
1901 3870 9.204570 GTAAGGTATACAAATGATTGCGAGTAT 57.795 33.333 5.01 0.00 40.34 2.12
1903 3872 9.944376 AAGGTATACAAATGATTGCGAGTATAT 57.056 29.630 5.01 0.00 40.34 0.86
1904 3873 9.944376 AGGTATACAAATGATTGCGAGTATATT 57.056 29.630 5.01 0.00 40.34 1.28
1915 3884 9.232473 TGATTGCGAGTATATTATACTCTCTGT 57.768 33.333 28.59 18.78 41.19 3.41
1931 3900 7.724305 ACTCTCTGTTTTTATTTAGTTCGCA 57.276 32.000 0.00 0.00 0.00 5.10
1932 3901 8.324163 ACTCTCTGTTTTTATTTAGTTCGCAT 57.676 30.769 0.00 0.00 0.00 4.73
1933 3902 9.431887 ACTCTCTGTTTTTATTTAGTTCGCATA 57.568 29.630 0.00 0.00 0.00 3.14
1946 3915 7.908827 TTAGTTCGCATATTAGTTTTGGTCA 57.091 32.000 0.00 0.00 0.00 4.02
1947 3916 6.811253 AGTTCGCATATTAGTTTTGGTCAA 57.189 33.333 0.00 0.00 0.00 3.18
1948 3917 7.209471 AGTTCGCATATTAGTTTTGGTCAAA 57.791 32.000 0.00 0.00 0.00 2.69
1949 3918 7.653647 AGTTCGCATATTAGTTTTGGTCAAAA 58.346 30.769 4.92 4.92 37.90 2.44
1950 3919 8.303876 AGTTCGCATATTAGTTTTGGTCAAAAT 58.696 29.630 11.37 4.86 41.64 1.82
1951 3920 9.562583 GTTCGCATATTAGTTTTGGTCAAAATA 57.437 29.630 11.37 2.01 41.64 1.40
1976 3945 8.528917 AAAGTTTTACAAACTTTGACCAAGTC 57.471 30.769 21.10 0.00 45.77 3.01
1977 3946 7.462571 AGTTTTACAAACTTTGACCAAGTCT 57.537 32.000 8.55 0.00 45.77 3.24
1978 3947 8.570068 AGTTTTACAAACTTTGACCAAGTCTA 57.430 30.769 8.55 0.00 45.77 2.59
1979 3948 9.185680 AGTTTTACAAACTTTGACCAAGTCTAT 57.814 29.630 8.55 0.00 45.77 1.98
1984 3953 8.514330 ACAAACTTTGACCAAGTCTATAAACA 57.486 30.769 8.55 0.00 45.77 2.83
1985 3954 8.962679 ACAAACTTTGACCAAGTCTATAAACAA 58.037 29.630 8.55 0.00 45.77 2.83
1986 3955 9.796120 CAAACTTTGACCAAGTCTATAAACAAA 57.204 29.630 0.00 0.00 45.77 2.83
2067 4036 8.352752 TGTAAAGTATATGCGAGAGACAATTG 57.647 34.615 3.24 3.24 0.00 2.32
2162 4131 3.066233 GAGGGACGCGAAGGGAGAC 62.066 68.421 15.93 0.00 46.37 3.36
2645 4619 1.307084 AGGAAGGTACTCCCCCTGC 60.307 63.158 0.00 0.00 25.57 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 67 1.813178 GGCCAAAAGAAGTAGGAGCAC 59.187 52.381 0.00 0.00 0.00 4.40
67 70 1.679032 CGGGGCCAAAAGAAGTAGGAG 60.679 57.143 4.39 0.00 0.00 3.69
68 71 0.326927 CGGGGCCAAAAGAAGTAGGA 59.673 55.000 4.39 0.00 0.00 2.94
72 75 2.891191 TATTCGGGGCCAAAAGAAGT 57.109 45.000 4.39 0.00 0.00 3.01
74 77 5.055265 TGATATATTCGGGGCCAAAAGAA 57.945 39.130 4.39 5.63 0.00 2.52
75 78 4.715534 TGATATATTCGGGGCCAAAAGA 57.284 40.909 4.39 0.00 0.00 2.52
83 86 6.160684 TGTCGTGTTAATGATATATTCGGGG 58.839 40.000 0.00 0.00 0.00 5.73
96 99 5.120399 TCTTCAACAACCTGTCGTGTTAAT 58.880 37.500 0.00 0.00 0.00 1.40
97 100 4.505808 TCTTCAACAACCTGTCGTGTTAA 58.494 39.130 0.00 0.00 0.00 2.01
99 102 2.980568 TCTTCAACAACCTGTCGTGTT 58.019 42.857 0.00 0.00 0.00 3.32
109 112 9.690434 GACGAAATATGTAGATTCTTCAACAAC 57.310 33.333 0.00 0.00 0.00 3.32
133 167 6.094048 ACCATATGAGTAGCAAACACATTGAC 59.906 38.462 3.65 0.00 41.85 3.18
178 213 4.277515 CTTCCTCAGGAATCAACTGACA 57.722 45.455 6.60 0.00 41.23 3.58
191 226 1.078214 TTCATGCCGCCTTCCTCAG 60.078 57.895 0.00 0.00 0.00 3.35
195 230 2.751436 TGCTTCATGCCGCCTTCC 60.751 61.111 4.02 0.00 42.00 3.46
205 240 0.322816 ATCGTGGGCAACTGCTTCAT 60.323 50.000 1.06 0.00 41.70 2.57
217 252 1.469251 CCTCGTAGTTGACATCGTGGG 60.469 57.143 9.47 5.50 34.66 4.61
228 263 2.283388 TGGGTCGGCCTCGTAGTT 60.283 61.111 5.77 0.00 37.69 2.24
231 266 4.051167 TCCTGGGTCGGCCTCGTA 62.051 66.667 5.77 0.00 37.69 3.43
242 277 1.139853 GTTCTATGGCACTCTCCTGGG 59.860 57.143 0.00 0.00 0.00 4.45
261 304 2.184167 CCACACAAGTTTCGCCCGT 61.184 57.895 0.00 0.00 0.00 5.28
262 305 2.637025 CCACACAAGTTTCGCCCG 59.363 61.111 0.00 0.00 0.00 6.13
270 313 0.466189 CAACCCTCTGCCACACAAGT 60.466 55.000 0.00 0.00 0.00 3.16
273 316 1.148273 GTCAACCCTCTGCCACACA 59.852 57.895 0.00 0.00 0.00 3.72
449 626 1.355043 ACGGAGGGAGTACTTCTCTGT 59.645 52.381 24.26 24.26 36.51 3.41
460 637 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
461 638 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
462 639 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
463 640 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
464 641 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
465 642 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
466 643 5.445939 CGTTGAGTCATCTATTTTGGAACGG 60.446 44.000 0.00 0.00 31.31 4.44
467 644 5.445939 CCGTTGAGTCATCTATTTTGGAACG 60.446 44.000 0.00 0.00 33.93 3.95
468 645 5.673818 GCCGTTGAGTCATCTATTTTGGAAC 60.674 44.000 0.00 0.00 0.00 3.62
469 646 4.394920 GCCGTTGAGTCATCTATTTTGGAA 59.605 41.667 0.00 0.00 0.00 3.53
470 647 3.938963 GCCGTTGAGTCATCTATTTTGGA 59.061 43.478 0.00 0.00 0.00 3.53
471 648 3.065371 GGCCGTTGAGTCATCTATTTTGG 59.935 47.826 0.00 0.00 0.00 3.28
472 649 3.242413 CGGCCGTTGAGTCATCTATTTTG 60.242 47.826 19.50 0.00 0.00 2.44
473 650 2.936498 CGGCCGTTGAGTCATCTATTTT 59.064 45.455 19.50 0.00 0.00 1.82
474 651 2.550978 CGGCCGTTGAGTCATCTATTT 58.449 47.619 19.50 0.00 0.00 1.40
475 652 1.202533 CCGGCCGTTGAGTCATCTATT 60.203 52.381 26.12 0.00 0.00 1.73
476 653 0.389391 CCGGCCGTTGAGTCATCTAT 59.611 55.000 26.12 0.00 0.00 1.98
477 654 1.672854 CCCGGCCGTTGAGTCATCTA 61.673 60.000 26.12 0.00 0.00 1.98
478 655 2.579201 CCGGCCGTTGAGTCATCT 59.421 61.111 26.12 0.00 0.00 2.90
479 656 1.952102 TACCCGGCCGTTGAGTCATC 61.952 60.000 26.12 0.00 0.00 2.92
480 657 1.546589 TTACCCGGCCGTTGAGTCAT 61.547 55.000 26.12 2.17 0.00 3.06
481 658 2.162338 CTTACCCGGCCGTTGAGTCA 62.162 60.000 26.12 6.49 0.00 3.41
482 659 1.447314 CTTACCCGGCCGTTGAGTC 60.447 63.158 26.12 0.00 0.00 3.36
483 660 2.660802 CTTACCCGGCCGTTGAGT 59.339 61.111 26.12 17.57 0.00 3.41
484 661 2.125269 CCTTACCCGGCCGTTGAG 60.125 66.667 26.12 15.94 0.00 3.02
485 662 2.604079 TCCTTACCCGGCCGTTGA 60.604 61.111 26.12 6.33 0.00 3.18
486 663 2.125269 CTCCTTACCCGGCCGTTG 60.125 66.667 26.12 17.46 0.00 4.10
487 664 3.396570 CCTCCTTACCCGGCCGTT 61.397 66.667 26.12 13.41 0.00 4.44
488 665 4.387343 TCCTCCTTACCCGGCCGT 62.387 66.667 26.12 9.29 0.00 5.68
489 666 3.537874 CTCCTCCTTACCCGGCCG 61.538 72.222 21.04 21.04 0.00 6.13
490 667 3.162154 CCTCCTCCTTACCCGGCC 61.162 72.222 0.00 0.00 0.00 6.13
491 668 3.162154 CCCTCCTCCTTACCCGGC 61.162 72.222 0.00 0.00 0.00 6.13
492 669 2.446036 CCCCTCCTCCTTACCCGG 60.446 72.222 0.00 0.00 0.00 5.73
493 670 1.002533 TTCCCCTCCTCCTTACCCG 59.997 63.158 0.00 0.00 0.00 5.28
510 687 0.618981 CTCCTACCCTTTTCGCCCTT 59.381 55.000 0.00 0.00 0.00 3.95
550 743 6.316390 AGTTTGGATTGAAATCTAACGGCTAG 59.684 38.462 1.73 0.00 35.92 3.42
551 744 6.177610 AGTTTGGATTGAAATCTAACGGCTA 58.822 36.000 1.73 0.00 35.92 3.93
607 800 5.897250 AGGGGGCGACTGAATTTTATTTTAT 59.103 36.000 0.00 0.00 0.00 1.40
626 819 2.440247 GGCGTCCATGAAAGGGGG 60.440 66.667 0.00 0.00 39.14 5.40
635 828 0.107017 CCAGATTTCCAGGCGTCCAT 60.107 55.000 0.00 0.00 0.00 3.41
642 835 5.277857 AGTACGTATTCCAGATTTCCAGG 57.722 43.478 0.00 0.00 0.00 4.45
649 842 8.794553 CAGGAAATAGTAGTACGTATTCCAGAT 58.205 37.037 23.84 10.31 0.00 2.90
650 843 7.230108 CCAGGAAATAGTAGTACGTATTCCAGA 59.770 40.741 23.84 0.00 0.00 3.86
652 845 7.062322 TCCAGGAAATAGTAGTACGTATTCCA 58.938 38.462 23.84 10.31 0.00 3.53
653 846 7.516198 TCCAGGAAATAGTAGTACGTATTCC 57.484 40.000 18.59 18.59 0.00 3.01
654 847 9.460906 CTTTCCAGGAAATAGTAGTACGTATTC 57.539 37.037 15.38 0.00 30.85 1.75
655 848 8.975295 ACTTTCCAGGAAATAGTAGTACGTATT 58.025 33.333 15.38 0.00 30.85 1.89
656 849 8.530804 ACTTTCCAGGAAATAGTAGTACGTAT 57.469 34.615 15.38 0.00 30.85 3.06
657 850 7.831193 AGACTTTCCAGGAAATAGTAGTACGTA 59.169 37.037 15.38 0.00 30.85 3.57
658 851 6.662663 AGACTTTCCAGGAAATAGTAGTACGT 59.337 38.462 15.38 6.26 30.85 3.57
659 852 7.098074 AGACTTTCCAGGAAATAGTAGTACG 57.902 40.000 15.38 3.04 30.85 3.67
662 855 7.974504 TCAAAGACTTTCCAGGAAATAGTAGT 58.025 34.615 15.38 9.06 30.85 2.73
663 856 7.065204 GCTCAAAGACTTTCCAGGAAATAGTAG 59.935 40.741 15.38 5.71 30.85 2.57
665 858 5.707764 GCTCAAAGACTTTCCAGGAAATAGT 59.292 40.000 15.38 10.57 30.85 2.12
666 859 5.163814 CGCTCAAAGACTTTCCAGGAAATAG 60.164 44.000 15.38 7.20 30.85 1.73
668 861 3.503748 CGCTCAAAGACTTTCCAGGAAAT 59.496 43.478 15.38 5.89 30.85 2.17
669 862 2.878406 CGCTCAAAGACTTTCCAGGAAA 59.122 45.455 14.28 14.28 0.00 3.13
670 863 2.104111 TCGCTCAAAGACTTTCCAGGAA 59.896 45.455 0.00 0.00 0.00 3.36
671 864 1.691976 TCGCTCAAAGACTTTCCAGGA 59.308 47.619 0.00 0.00 0.00 3.86
672 865 1.801178 GTCGCTCAAAGACTTTCCAGG 59.199 52.381 0.00 0.00 35.84 4.45
673 866 2.760374 AGTCGCTCAAAGACTTTCCAG 58.240 47.619 0.00 0.00 45.74 3.86
674 867 2.910688 AGTCGCTCAAAGACTTTCCA 57.089 45.000 0.00 0.00 45.74 3.53
758 951 1.878775 ACGTAGTGGTCCGTGTAGC 59.121 57.895 0.00 0.00 42.51 3.58
857 1053 3.061697 GCGCTAGTGGTGTGTTTATGTAC 59.938 47.826 0.00 0.00 0.00 2.90
884 1082 1.714899 GCGACGGCCTGCATTGTTAT 61.715 55.000 0.00 0.00 0.00 1.89
885 1083 2.395360 GCGACGGCCTGCATTGTTA 61.395 57.895 0.00 0.00 0.00 2.41
888 1086 2.511373 TAGCGACGGCCTGCATTG 60.511 61.111 13.09 0.00 41.24 2.82
896 1094 0.456995 GGATGATAGCTAGCGACGGC 60.457 60.000 9.55 0.00 40.37 5.68
903 1101 4.747108 CGTTGGTCTTTGGATGATAGCTAG 59.253 45.833 0.00 0.00 0.00 3.42
908 1106 4.819105 ACTCGTTGGTCTTTGGATGATA 57.181 40.909 0.00 0.00 0.00 2.15
910 1108 3.613193 CGTACTCGTTGGTCTTTGGATGA 60.613 47.826 0.00 0.00 0.00 2.92
911 1109 2.666508 CGTACTCGTTGGTCTTTGGATG 59.333 50.000 0.00 0.00 0.00 3.51
912 1110 2.929592 GCGTACTCGTTGGTCTTTGGAT 60.930 50.000 0.00 0.00 39.49 3.41
926 1127 2.221055 CACTTCACTTGTTGGCGTACTC 59.779 50.000 0.00 0.00 0.00 2.59
933 1134 0.029300 CGGTGCACTTCACTTGTTGG 59.971 55.000 17.98 0.00 44.98 3.77
950 1151 1.445754 CACTCACTGCTCAGCTCGG 60.446 63.158 0.00 0.00 0.00 4.63
995 1201 2.324330 TGGTGCGTCGCCATTCTTG 61.324 57.895 15.88 0.00 39.28 3.02
1016 1222 1.675720 GAGCAGGAGGAGGAGAGCAC 61.676 65.000 0.00 0.00 0.00 4.40
1020 1226 2.441164 GCGAGCAGGAGGAGGAGA 60.441 66.667 0.00 0.00 0.00 3.71
1021 1227 3.535962 GGCGAGCAGGAGGAGGAG 61.536 72.222 0.00 0.00 0.00 3.69
1119 1328 0.107459 GGATGAGGTTGAGCTCCACC 60.107 60.000 25.91 25.91 0.00 4.61
1694 3620 6.946584 CAGCAACGAACGAAGTAGTAATAAAC 59.053 38.462 0.14 0.00 45.00 2.01
1695 3621 6.089820 CCAGCAACGAACGAAGTAGTAATAAA 59.910 38.462 0.14 0.00 45.00 1.40
1696 3622 5.574055 CCAGCAACGAACGAAGTAGTAATAA 59.426 40.000 0.14 0.00 45.00 1.40
1697 3623 5.097529 CCAGCAACGAACGAAGTAGTAATA 58.902 41.667 0.14 0.00 45.00 0.98
1698 3624 3.924686 CCAGCAACGAACGAAGTAGTAAT 59.075 43.478 0.14 0.00 45.00 1.89
1699 3625 3.311106 CCAGCAACGAACGAAGTAGTAA 58.689 45.455 0.14 0.00 45.00 2.24
1702 3628 0.438830 GCCAGCAACGAACGAAGTAG 59.561 55.000 0.14 0.00 45.00 2.57
1738 3684 4.504461 GTCTACCTGTCAACTAATCATGCG 59.496 45.833 0.00 0.00 0.00 4.73
1813 3772 9.793259 CCACCACTATAAATCCACAAGTATATT 57.207 33.333 0.00 0.00 0.00 1.28
1905 3874 9.431887 TGCGAACTAAATAAAAACAGAGAGTAT 57.568 29.630 0.00 0.00 0.00 2.12
1906 3875 8.821147 TGCGAACTAAATAAAAACAGAGAGTA 57.179 30.769 0.00 0.00 0.00 2.59
1907 3876 7.724305 TGCGAACTAAATAAAAACAGAGAGT 57.276 32.000 0.00 0.00 0.00 3.24
1920 3889 8.952278 TGACCAAAACTAATATGCGAACTAAAT 58.048 29.630 0.00 0.00 0.00 1.40
1921 3890 8.325421 TGACCAAAACTAATATGCGAACTAAA 57.675 30.769 0.00 0.00 0.00 1.85
1922 3891 7.908827 TGACCAAAACTAATATGCGAACTAA 57.091 32.000 0.00 0.00 0.00 2.24
1923 3892 7.908827 TTGACCAAAACTAATATGCGAACTA 57.091 32.000 0.00 0.00 0.00 2.24
1924 3893 6.811253 TTGACCAAAACTAATATGCGAACT 57.189 33.333 0.00 0.00 0.00 3.01
1925 3894 7.861176 TTTTGACCAAAACTAATATGCGAAC 57.139 32.000 4.00 0.00 35.57 3.95
2029 3998 9.619316 GCATATACTTTACAACACATTCAACAA 57.381 29.630 0.00 0.00 0.00 2.83
2030 3999 7.960195 CGCATATACTTTACAACACATTCAACA 59.040 33.333 0.00 0.00 0.00 3.33
2031 4000 8.172484 TCGCATATACTTTACAACACATTCAAC 58.828 33.333 0.00 0.00 0.00 3.18
2032 4001 8.257830 TCGCATATACTTTACAACACATTCAA 57.742 30.769 0.00 0.00 0.00 2.69
2033 4002 7.762159 TCTCGCATATACTTTACAACACATTCA 59.238 33.333 0.00 0.00 0.00 2.57
2034 4003 8.126871 TCTCGCATATACTTTACAACACATTC 57.873 34.615 0.00 0.00 0.00 2.67
2035 4004 7.979537 TCTCTCGCATATACTTTACAACACATT 59.020 33.333 0.00 0.00 0.00 2.71
2036 4005 7.435488 GTCTCTCGCATATACTTTACAACACAT 59.565 37.037 0.00 0.00 0.00 3.21
2067 4036 2.271800 CAGCGATTCCACTACTTGTCC 58.728 52.381 0.00 0.00 0.00 4.02
2490 4462 0.774908 TTCTGTTTTCCCCACCGGAT 59.225 50.000 9.46 0.00 41.63 4.18
2491 4463 0.551879 TTTCTGTTTTCCCCACCGGA 59.448 50.000 9.46 0.00 39.68 5.14
2617 4591 4.019231 GGGAGTACCTTCCTGAATTGTTCT 60.019 45.833 1.52 0.00 37.40 3.01
2645 4619 2.030007 TGGCTTCGGAATTTGCAAGAAG 60.030 45.455 16.88 16.88 40.69 2.85


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

AutoCloner maintained by Alex Coulton.