Multiple sequence alignment - TraesCS4B01G079700

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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 TraesCS4B01G079700 chr4B 100.000 3049 0 0 1665 4713 77516340 77513292 0.000000e+00 5631
1 TraesCS4B01G079700 chr4B 100.000 1337 0 0 1 1337 77518004 77516668 0.000000e+00 2470
2 TraesCS4B01G079700 chr4B 93.768 706 41 3 1 705 375910430 375911133 0.000000e+00 1057
3 TraesCS4B01G079700 chr4B 93.362 708 43 4 1 705 338392386 338391680 0.000000e+00 1044
4 TraesCS4B01G079700 chr4B 79.469 565 97 16 3860 4413 77003259 77002703 2.660000e-102 383
5 TraesCS4B01G079700 chr4B 86.667 240 23 3 4434 4673 438099921 438099691 1.680000e-64 257
6 TraesCS4B01G079700 chr4D 93.957 1572 88 4 2868 4436 52754919 52753352 0.000000e+00 2370
7 TraesCS4B01G079700 chr4D 92.044 1194 73 11 1679 2869 52756180 52755006 0.000000e+00 1659
8 TraesCS4B01G079700 chr4D 95.986 573 15 5 771 1337 52756810 52756240 0.000000e+00 924
9 TraesCS4B01G079700 chr4D 96.071 280 11 0 4434 4713 52753276 52752997 1.550000e-124 457
10 TraesCS4B01G079700 chr4D 78.445 566 103 16 3860 4413 52496446 52495888 7.500000e-93 351
11 TraesCS4B01G079700 chr4D 90.000 150 13 2 4480 4628 52495556 52495408 4.810000e-45 193
12 TraesCS4B01G079700 chr4A 94.159 1267 70 2 2868 4132 544057439 544058703 0.000000e+00 1927
13 TraesCS4B01G079700 chr4A 92.068 706 41 6 2168 2869 544056662 544057356 0.000000e+00 979
14 TraesCS4B01G079700 chr4A 93.414 577 22 8 771 1335 544055522 544056094 0.000000e+00 841
15 TraesCS4B01G079700 chr4A 91.698 530 37 3 4182 4711 544058796 544059318 0.000000e+00 728
16 TraesCS4B01G079700 chr4A 88.300 453 38 9 1679 2122 544056208 544056654 3.230000e-146 529
17 TraesCS4B01G079700 chr3B 94.193 706 37 4 1 705 59390594 59389892 0.000000e+00 1074
18 TraesCS4B01G079700 chr3B 94.051 706 40 2 1 705 194551367 194550663 0.000000e+00 1070
19 TraesCS4B01G079700 chr3B 93.635 707 41 4 1 705 345797087 345797791 0.000000e+00 1053
20 TraesCS4B01G079700 chr2B 93.909 706 40 3 1 705 431879506 431880209 0.000000e+00 1062
21 TraesCS4B01G079700 chr2B 93.777 707 39 5 1 705 309760846 309760143 0.000000e+00 1057
22 TraesCS4B01G079700 chr5B 93.503 708 40 6 1 706 322320441 322321144 0.000000e+00 1048
23 TraesCS4B01G079700 chr3D 93.352 707 43 4 1 705 540926441 540927145 0.000000e+00 1042
24 TraesCS4B01G079700 chr7D 87.410 278 28 3 4434 4711 511061054 511060784 3.540000e-81 313
25 TraesCS4B01G079700 chr7D 89.167 240 25 1 4434 4673 580124099 580124337 9.910000e-77 298
26 TraesCS4B01G079700 chr1B 90.000 240 23 1 4434 4673 93954867 93954629 4.580000e-80 309
27 TraesCS4B01G079700 chr7A 87.050 278 29 3 4434 4711 611772344 611772074 1.650000e-79 307
28 TraesCS4B01G079700 chr2D 87.446 231 27 2 4434 4663 640356351 640356122 1.010000e-66 265


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 TraesCS4B01G079700 chr4B 77513292 77518004 4712 True 4050.5 5631 100.0000 1 4713 2 chr4B.!!$R4 4712
1 TraesCS4B01G079700 chr4B 375910430 375911133 703 False 1057.0 1057 93.7680 1 705 1 chr4B.!!$F1 704
2 TraesCS4B01G079700 chr4B 338391680 338392386 706 True 1044.0 1044 93.3620 1 705 1 chr4B.!!$R2 704
3 TraesCS4B01G079700 chr4B 77002703 77003259 556 True 383.0 383 79.4690 3860 4413 1 chr4B.!!$R1 553
4 TraesCS4B01G079700 chr4D 52752997 52756810 3813 True 1352.5 2370 94.5145 771 4713 4 chr4D.!!$R2 3942
5 TraesCS4B01G079700 chr4D 52495408 52496446 1038 True 272.0 351 84.2225 3860 4628 2 chr4D.!!$R1 768
6 TraesCS4B01G079700 chr4A 544055522 544059318 3796 False 1000.8 1927 91.9278 771 4711 5 chr4A.!!$F1 3940
7 TraesCS4B01G079700 chr3B 59389892 59390594 702 True 1074.0 1074 94.1930 1 705 1 chr3B.!!$R1 704
8 TraesCS4B01G079700 chr3B 194550663 194551367 704 True 1070.0 1070 94.0510 1 705 1 chr3B.!!$R2 704
9 TraesCS4B01G079700 chr3B 345797087 345797791 704 False 1053.0 1053 93.6350 1 705 1 chr3B.!!$F1 704
10 TraesCS4B01G079700 chr2B 431879506 431880209 703 False 1062.0 1062 93.9090 1 705 1 chr2B.!!$F1 704
11 TraesCS4B01G079700 chr2B 309760143 309760846 703 True 1057.0 1057 93.7770 1 705 1 chr2B.!!$R1 704
12 TraesCS4B01G079700 chr5B 322320441 322321144 703 False 1048.0 1048 93.5030 1 706 1 chr5B.!!$F1 705
13 TraesCS4B01G079700 chr3D 540926441 540927145 704 False 1042.0 1042 93.3520 1 705 1 chr3D.!!$F1 704

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
714 725 0.029834 GGCCGCTACAGCAAATGATG 59.970 55.0 1.61 0.0 42.21 3.07 F
941 956 0.035458 GATCATGGAAGGCCCGGTAG 59.965 60.0 0.00 0.0 37.93 3.18 F
2227 2293 0.439985 CGACTTCCATGCTTCACACG 59.560 55.0 0.00 0.0 0.00 4.49 F
3481 3639 0.179127 ACGATGATGAGCAGGACACG 60.179 55.0 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2274 0.439985 CGTGTGAAGCATGGAAGTCG 59.560 55.000 0.0 0.0 0.00 4.18 R
2766 2835 3.587797 AGGACCACACAAGTATACACG 57.412 47.619 5.5 0.0 0.00 4.49 R
3699 3859 0.179111 GCGTCGGATGTCCAGATTCA 60.179 55.000 0.0 0.0 35.14 2.57 R
4474 4932 1.005340 CGAAGGTGAAGCAGAGATGC 58.995 55.000 0.0 0.0 0.00 3.91 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
44 45 2.967201 TCGAGTCTTGTGGGGAAAAGTA 59.033 45.455 0.00 0.00 0.00 2.24
84 85 8.812972 AGAGTGTACAAACTAATCATGGTTAGA 58.187 33.333 28.50 6.38 35.96 2.10
234 237 5.010516 TCTCAATGTTTAACAACCACCATGG 59.989 40.000 11.19 11.19 45.02 3.66
310 314 8.306761 CAAAACTTTAACCATAGAGCTTTCCAT 58.693 33.333 0.00 0.00 0.00 3.41
317 321 3.548770 CATAGAGCTTTCCATCAGCCAA 58.451 45.455 0.00 0.00 38.09 4.52
326 330 4.859304 TTCCATCAGCCAAATATGCATC 57.141 40.909 0.19 0.00 0.00 3.91
330 334 4.142447 CCATCAGCCAAATATGCATCTAGC 60.142 45.833 0.19 0.29 45.96 3.42
445 453 4.514441 AGACTTTTCAGACGACGAGTAAGA 59.486 41.667 0.00 0.00 0.00 2.10
481 490 3.794028 GTCGTTCACTCAGCTATGTCATC 59.206 47.826 0.00 0.00 0.00 2.92
627 638 9.219603 TGAAACTCTGTTATAAATCCTCAAGTG 57.780 33.333 0.00 0.00 0.00 3.16
651 662 1.006832 GCGTGTCAGCATTACCGATT 58.993 50.000 0.00 0.00 37.05 3.34
658 669 3.799420 GTCAGCATTACCGATTCAGAGAC 59.201 47.826 0.00 0.00 0.00 3.36
697 708 2.300437 ACTAGACTGTTTGAGGTCTGGC 59.700 50.000 0.00 0.00 42.27 4.85
706 717 3.724914 GAGGTCTGGCCGCTACAGC 62.725 68.421 0.00 0.00 43.70 4.40
707 718 4.082523 GGTCTGGCCGCTACAGCA 62.083 66.667 0.00 0.00 42.21 4.41
708 719 2.047274 GTCTGGCCGCTACAGCAA 60.047 61.111 0.00 0.00 42.21 3.91
709 720 1.671054 GTCTGGCCGCTACAGCAAA 60.671 57.895 0.00 0.00 42.21 3.68
710 721 1.026718 GTCTGGCCGCTACAGCAAAT 61.027 55.000 0.00 0.00 42.21 2.32
711 722 1.026182 TCTGGCCGCTACAGCAAATG 61.026 55.000 0.00 0.00 42.21 2.32
712 723 1.002746 TGGCCGCTACAGCAAATGA 60.003 52.632 0.00 0.00 42.21 2.57
713 724 0.394216 TGGCCGCTACAGCAAATGAT 60.394 50.000 0.00 0.00 42.21 2.45
714 725 0.029834 GGCCGCTACAGCAAATGATG 59.970 55.000 1.61 0.00 42.21 3.07
715 726 1.016627 GCCGCTACAGCAAATGATGA 58.983 50.000 5.56 0.00 42.21 2.92
716 727 1.401552 GCCGCTACAGCAAATGATGAA 59.598 47.619 5.56 0.00 42.21 2.57
717 728 2.792542 GCCGCTACAGCAAATGATGAAC 60.793 50.000 5.56 0.00 42.21 3.18
718 729 2.223340 CCGCTACAGCAAATGATGAACC 60.223 50.000 5.56 0.00 42.21 3.62
719 730 2.223340 CGCTACAGCAAATGATGAACCC 60.223 50.000 5.56 0.00 42.21 4.11
720 731 2.223340 GCTACAGCAAATGATGAACCCG 60.223 50.000 5.56 0.00 41.59 5.28
721 732 0.527565 ACAGCAAATGATGAACCCGC 59.472 50.000 5.56 0.00 35.09 6.13
722 733 0.527113 CAGCAAATGATGAACCCGCA 59.473 50.000 0.00 0.00 32.25 5.69
723 734 1.135527 CAGCAAATGATGAACCCGCAT 59.864 47.619 0.00 0.00 32.25 4.73
724 735 1.135527 AGCAAATGATGAACCCGCATG 59.864 47.619 0.00 0.00 0.00 4.06
725 736 1.135024 GCAAATGATGAACCCGCATGT 60.135 47.619 0.00 0.00 0.00 3.21
726 737 2.801063 CAAATGATGAACCCGCATGTC 58.199 47.619 0.00 0.00 0.00 3.06
727 738 2.424601 CAAATGATGAACCCGCATGTCT 59.575 45.455 0.00 0.00 0.00 3.41
728 739 1.671979 ATGATGAACCCGCATGTCTG 58.328 50.000 0.00 0.00 0.00 3.51
729 740 0.324614 TGATGAACCCGCATGTCTGT 59.675 50.000 0.00 0.00 0.00 3.41
730 741 1.009829 GATGAACCCGCATGTCTGTC 58.990 55.000 0.00 0.00 0.00 3.51
731 742 0.324614 ATGAACCCGCATGTCTGTCA 59.675 50.000 0.00 0.00 0.00 3.58
732 743 0.602638 TGAACCCGCATGTCTGTCAC 60.603 55.000 0.00 0.00 0.00 3.67
733 744 0.602638 GAACCCGCATGTCTGTCACA 60.603 55.000 0.00 0.00 40.18 3.58
734 745 0.884704 AACCCGCATGTCTGTCACAC 60.885 55.000 0.00 0.00 38.04 3.82
735 746 1.301637 CCCGCATGTCTGTCACACA 60.302 57.895 0.00 0.00 38.04 3.72
736 747 0.884259 CCCGCATGTCTGTCACACAA 60.884 55.000 0.00 0.00 38.04 3.33
737 748 0.943673 CCGCATGTCTGTCACACAAA 59.056 50.000 0.00 0.00 38.04 2.83
738 749 1.536766 CCGCATGTCTGTCACACAAAT 59.463 47.619 0.00 0.00 38.04 2.32
739 750 2.741517 CCGCATGTCTGTCACACAAATA 59.258 45.455 0.00 0.00 38.04 1.40
740 751 3.181517 CCGCATGTCTGTCACACAAATAG 60.182 47.826 0.00 0.00 38.04 1.73
741 752 3.679502 CGCATGTCTGTCACACAAATAGA 59.320 43.478 0.00 0.00 38.04 1.98
742 753 4.201656 CGCATGTCTGTCACACAAATAGAG 60.202 45.833 0.00 0.00 38.04 2.43
743 754 4.093998 GCATGTCTGTCACACAAATAGAGG 59.906 45.833 0.00 0.00 38.04 3.69
744 755 5.482006 CATGTCTGTCACACAAATAGAGGA 58.518 41.667 0.00 0.00 38.04 3.71
745 756 5.545063 TGTCTGTCACACAAATAGAGGAA 57.455 39.130 0.00 0.00 0.00 3.36
746 757 5.541845 TGTCTGTCACACAAATAGAGGAAG 58.458 41.667 0.00 0.00 0.00 3.46
747 758 5.304357 TGTCTGTCACACAAATAGAGGAAGA 59.696 40.000 0.00 0.00 0.00 2.87
748 759 5.866633 GTCTGTCACACAAATAGAGGAAGAG 59.133 44.000 0.00 0.00 0.00 2.85
749 760 5.775195 TCTGTCACACAAATAGAGGAAGAGA 59.225 40.000 0.00 0.00 0.00 3.10
750 761 6.030548 TGTCACACAAATAGAGGAAGAGAG 57.969 41.667 0.00 0.00 0.00 3.20
751 762 5.775195 TGTCACACAAATAGAGGAAGAGAGA 59.225 40.000 0.00 0.00 0.00 3.10
752 763 6.071672 TGTCACACAAATAGAGGAAGAGAGAG 60.072 42.308 0.00 0.00 0.00 3.20
753 764 5.420421 TCACACAAATAGAGGAAGAGAGAGG 59.580 44.000 0.00 0.00 0.00 3.69
754 765 5.420421 CACACAAATAGAGGAAGAGAGAGGA 59.580 44.000 0.00 0.00 0.00 3.71
755 766 5.656416 ACACAAATAGAGGAAGAGAGAGGAG 59.344 44.000 0.00 0.00 0.00 3.69
756 767 5.656416 CACAAATAGAGGAAGAGAGAGGAGT 59.344 44.000 0.00 0.00 0.00 3.85
757 768 6.154363 CACAAATAGAGGAAGAGAGAGGAGTT 59.846 42.308 0.00 0.00 0.00 3.01
758 769 6.728632 ACAAATAGAGGAAGAGAGAGGAGTTT 59.271 38.462 0.00 0.00 0.00 2.66
759 770 7.236640 ACAAATAGAGGAAGAGAGAGGAGTTTT 59.763 37.037 0.00 0.00 0.00 2.43
760 771 7.806680 AATAGAGGAAGAGAGAGGAGTTTTT 57.193 36.000 0.00 0.00 0.00 1.94
789 800 4.469586 GGAAAGGAAGAGAGAGGAGTTGAT 59.530 45.833 0.00 0.00 0.00 2.57
795 806 7.563906 AGGAAGAGAGAGGAGTTGATATTTTG 58.436 38.462 0.00 0.00 0.00 2.44
796 807 7.181845 AGGAAGAGAGAGGAGTTGATATTTTGT 59.818 37.037 0.00 0.00 0.00 2.83
941 956 0.035458 GATCATGGAAGGCCCGGTAG 59.965 60.000 0.00 0.00 37.93 3.18
983 998 3.399330 TCGCACCTCTAAAAGTCCAAAG 58.601 45.455 0.00 0.00 0.00 2.77
1183 1205 1.940613 GCGCGGAAGAAGGATATTGTT 59.059 47.619 8.83 0.00 0.00 2.83
1194 1216 6.963322 AGAAGGATATTGTTAGCTCCAACTT 58.037 36.000 0.00 0.00 0.00 2.66
1314 1336 2.751913 CCTCGTCCTCGTCGACCTG 61.752 68.421 10.58 2.58 38.33 4.00
1707 1758 1.765314 CCCTCTCTGATCGATTGGGTT 59.235 52.381 0.00 0.00 32.52 4.11
1708 1759 2.965831 CCCTCTCTGATCGATTGGGTTA 59.034 50.000 0.00 0.00 32.52 2.85
1808 1867 8.897752 GCTTCAACTGAGGATTATTTGTTCTAT 58.102 33.333 0.00 0.00 0.00 1.98
1826 1892 8.615878 TGTTCTATACAAACATACAGCTTTGT 57.384 30.769 4.73 4.73 42.09 2.83
1827 1893 8.503196 TGTTCTATACAAACATACAGCTTTGTG 58.497 33.333 9.03 2.43 40.14 3.33
1828 1894 7.609760 TCTATACAAACATACAGCTTTGTGG 57.390 36.000 9.03 1.94 40.14 4.17
1829 1895 7.165485 TCTATACAAACATACAGCTTTGTGGT 58.835 34.615 9.03 0.00 40.14 4.16
1830 1896 4.568152 ACAAACATACAGCTTTGTGGTC 57.432 40.909 1.53 0.00 38.80 4.02
1831 1897 4.207165 ACAAACATACAGCTTTGTGGTCT 58.793 39.130 1.53 0.00 38.80 3.85
1871 1937 4.822026 AGCACAAATGTCTACTGGAGTAC 58.178 43.478 0.00 0.00 0.00 2.73
1876 1942 5.178797 CAAATGTCTACTGGAGTACCAAGG 58.821 45.833 0.00 0.00 46.32 3.61
1880 1946 4.527038 TGTCTACTGGAGTACCAAGGAAAG 59.473 45.833 0.00 0.00 46.32 2.62
1901 1967 8.764287 GGAAAGAAAATTTCATTGTCGAATTGT 58.236 29.630 8.55 0.00 31.65 2.71
1909 1975 2.851263 TTGTCGAATTGTGGTAGGCT 57.149 45.000 0.00 0.00 0.00 4.58
1911 1977 2.422597 TGTCGAATTGTGGTAGGCTTG 58.577 47.619 0.00 0.00 0.00 4.01
1954 2020 8.680903 CAACAGAGCAACCTTCTTATATGAAAT 58.319 33.333 2.99 0.00 0.00 2.17
2040 2106 7.070821 GGATGTTCTTAACTTAGGTCCATCCTA 59.929 40.741 16.03 0.00 46.10 2.94
2122 2188 5.450453 TCCAAAATGTAAACTGGAAGGACA 58.550 37.500 0.00 0.00 39.30 4.02
2124 2190 5.983118 CCAAAATGTAAACTGGAAGGACAAC 59.017 40.000 0.00 0.00 39.30 3.32
2131 2197 3.312736 ACTGGAAGGACAACATTTGGT 57.687 42.857 0.00 0.00 39.30 3.67
2136 2202 5.181748 TGGAAGGACAACATTTGGTTTTTG 58.818 37.500 0.00 0.00 37.72 2.44
2208 2274 3.181516 CGGTATCTTTTGCAGCTTGAGAC 60.182 47.826 0.00 0.00 0.00 3.36
2227 2293 0.439985 CGACTTCCATGCTTCACACG 59.560 55.000 0.00 0.00 0.00 4.49
2306 2372 4.282195 ACTCTAGCTATATCCACCAAGCAC 59.718 45.833 0.00 0.00 37.44 4.40
2322 2391 8.632679 CCACCAAGCACAACATTAATCTAATAT 58.367 33.333 0.00 0.00 0.00 1.28
2348 2417 2.569059 TCATGCTTTCATAGAGCCTGC 58.431 47.619 0.00 0.00 39.38 4.85
2366 2435 7.995488 AGAGCCTGCAAACTTAATTACATCTAT 59.005 33.333 0.00 0.00 0.00 1.98
2553 2622 8.862325 TTGTACATGTATCTGGTTTTCTGAAT 57.138 30.769 9.18 0.00 0.00 2.57
2735 2804 2.700897 CCATTAGTGGTCCTGTCCTAGG 59.299 54.545 0.82 0.82 41.50 3.02
2792 2861 7.031975 GTGTATACTTGTGTGGTCCTAGTTAC 58.968 42.308 4.17 0.00 0.00 2.50
2793 2862 6.950041 TGTATACTTGTGTGGTCCTAGTTACT 59.050 38.462 4.17 0.00 0.00 2.24
2794 2863 6.930068 ATACTTGTGTGGTCCTAGTTACTT 57.070 37.500 0.00 0.00 0.00 2.24
2795 2864 5.211174 ACTTGTGTGGTCCTAGTTACTTC 57.789 43.478 0.00 0.00 0.00 3.01
2796 2865 4.040095 ACTTGTGTGGTCCTAGTTACTTCC 59.960 45.833 0.00 0.00 0.00 3.46
2797 2866 3.578978 TGTGTGGTCCTAGTTACTTCCA 58.421 45.455 0.00 0.00 0.00 3.53
2798 2867 3.576982 TGTGTGGTCCTAGTTACTTCCAG 59.423 47.826 0.00 0.00 0.00 3.86
2799 2868 3.577415 GTGTGGTCCTAGTTACTTCCAGT 59.423 47.826 0.00 0.00 0.00 4.00
2823 2892 9.386122 AGTCTTCCACTATCTTTGACCATATAT 57.614 33.333 0.00 0.00 31.37 0.86
2831 2900 9.392259 ACTATCTTTGACCATATATGATGCATG 57.608 33.333 14.54 0.00 0.00 4.06
2971 3129 8.391075 TCCTAATTCGAAATCCATTATTCCAC 57.609 34.615 0.00 0.00 0.00 4.02
2996 3154 3.138304 TCCACGTCAAGGAACTGAATTG 58.862 45.455 0.00 0.00 40.86 2.32
3032 3190 5.767168 CCAAGAAGCCTAGGAATGATAAAGG 59.233 44.000 14.75 0.00 0.00 3.11
3090 3248 6.585389 AGTACGTTTTTCTCAGTTGACTTC 57.415 37.500 0.00 0.00 0.00 3.01
3101 3259 5.243060 TCTCAGTTGACTTCGTTCATTCCTA 59.757 40.000 0.00 0.00 0.00 2.94
3107 3265 4.870426 TGACTTCGTTCATTCCTATTCTGC 59.130 41.667 0.00 0.00 0.00 4.26
3204 3362 4.955811 TCAAGTACAGAGAAAGGCTTCA 57.044 40.909 0.00 0.00 33.64 3.02
3257 3415 1.001887 TGGTGGGATAACCGGCAAC 60.002 57.895 0.00 0.00 43.73 4.17
3259 3417 0.609681 GGTGGGATAACCGGCAACAA 60.610 55.000 0.00 0.00 44.64 2.83
3334 3492 0.548031 GGCTTCATCCAGATGACCCA 59.452 55.000 9.84 0.00 46.49 4.51
3376 3534 2.910482 CGAATTGATTGACCAGCAAACG 59.090 45.455 0.00 0.00 40.48 3.60
3481 3639 0.179127 ACGATGATGAGCAGGACACG 60.179 55.000 0.00 0.00 0.00 4.49
3547 3705 2.262915 CGGGTCTCCTGCACTGAC 59.737 66.667 0.00 0.00 0.00 3.51
3581 3739 7.051623 ACTGTAAAACTGAATGGAAGTGTGTA 58.948 34.615 0.00 0.00 0.00 2.90
3592 3752 8.704668 TGAATGGAAGTGTGTATGTATAGATGT 58.295 33.333 0.00 0.00 0.00 3.06
3627 3787 2.099263 CACAGGACTCGTCGGATTATGT 59.901 50.000 0.00 0.00 0.00 2.29
3637 3797 4.119862 CGTCGGATTATGTGATTTGGTCT 58.880 43.478 0.00 0.00 0.00 3.85
3650 3810 5.982516 GTGATTTGGTCTTTGTGTGCAAATA 59.017 36.000 0.00 0.00 42.88 1.40
3658 3818 7.013750 TGGTCTTTGTGTGCAAATACTGAATAA 59.986 33.333 0.00 0.00 42.88 1.40
3699 3859 1.816835 CATTCAGTGCTGCAATGGAGT 59.183 47.619 27.09 12.44 29.97 3.85
3716 3876 2.482142 GGAGTGAATCTGGACATCCGAC 60.482 54.545 0.00 0.00 39.43 4.79
3735 3895 6.389091 TCCGACGCACTTTATTAACTCTTAA 58.611 36.000 0.00 0.00 0.00 1.85
3740 3900 4.722447 GCACTTTATTAACTCTTAACGCGC 59.278 41.667 5.73 0.00 0.00 6.86
3746 3906 2.875080 AACTCTTAACGCGCAATGTC 57.125 45.000 5.73 0.00 0.00 3.06
3830 3990 0.321564 TTCCTTGGTCTGTGCATCCG 60.322 55.000 0.00 0.00 0.00 4.18
3939 4099 1.014044 GTCATCGAGAACTTGCGGCA 61.014 55.000 0.00 0.00 0.00 5.69
3981 4141 0.442699 GAACGCGTTGATGTTCTCCC 59.557 55.000 31.89 6.74 40.94 4.30
4093 4253 0.449388 CCATGCTTCTTCGCAACCTC 59.551 55.000 0.00 0.00 44.06 3.85
4117 4277 2.360165 GGTATTCCTTCGTCGCTTCCTA 59.640 50.000 0.00 0.00 0.00 2.94
4120 4280 1.030457 TCCTTCGTCGCTTCCTATCC 58.970 55.000 0.00 0.00 0.00 2.59
4138 4334 3.988379 TCCAAACATCACAACAGAAGC 57.012 42.857 0.00 0.00 0.00 3.86
4142 4338 4.869297 CCAAACATCACAACAGAAGCAAAA 59.131 37.500 0.00 0.00 0.00 2.44
4143 4339 5.005971 CCAAACATCACAACAGAAGCAAAAG 59.994 40.000 0.00 0.00 0.00 2.27
4396 4647 1.005340 GGCAGACTTCAGCAAGATCG 58.995 55.000 0.00 0.00 33.34 3.69
4474 4932 7.664731 ACTGAAAATGAATAGATCTATGGCTGG 59.335 37.037 16.01 4.06 0.00 4.85
4673 5189 8.796475 GGAATTATATACTGGTCTACGGTTACA 58.204 37.037 0.00 0.00 39.94 2.41
4674 5190 9.837525 GAATTATATACTGGTCTACGGTTACAG 57.162 37.037 0.00 0.00 39.94 2.74
4683 5199 6.124340 TGGTCTACGGTTACAGATCTATGAA 58.876 40.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 1.610086 TCCATAACCGGGGACACGT 60.610 57.895 6.32 0.00 0.00 4.49
445 453 0.606604 AACGACAACGACCTAGGCAT 59.393 50.000 9.30 0.00 42.66 4.40
481 490 2.751166 AAGTGAGTCCATCAACTCCG 57.249 50.000 1.88 0.00 44.17 4.63
588 599 7.624360 AACAGAGTTTCAATCACACACTTAA 57.376 32.000 0.00 0.00 0.00 1.85
651 662 1.068264 GTGCATCAGTGTCGTCTCTGA 60.068 52.381 14.93 14.93 44.55 3.27
658 669 1.067985 AGTCTCTGTGCATCAGTGTCG 60.068 52.381 13.59 4.73 43.97 4.35
697 708 2.223340 GGTTCATCATTTGCTGTAGCGG 60.223 50.000 0.00 0.00 45.83 5.52
706 717 2.424601 AGACATGCGGGTTCATCATTTG 59.575 45.455 0.00 0.00 0.00 2.32
707 718 2.424601 CAGACATGCGGGTTCATCATTT 59.575 45.455 0.00 0.00 0.00 2.32
708 719 2.019249 CAGACATGCGGGTTCATCATT 58.981 47.619 0.00 0.00 0.00 2.57
709 720 1.065199 ACAGACATGCGGGTTCATCAT 60.065 47.619 0.00 0.00 0.00 2.45
710 721 0.324614 ACAGACATGCGGGTTCATCA 59.675 50.000 0.00 0.00 0.00 3.07
711 722 1.009829 GACAGACATGCGGGTTCATC 58.990 55.000 0.00 0.00 0.00 2.92
712 723 0.324614 TGACAGACATGCGGGTTCAT 59.675 50.000 0.00 0.00 0.00 2.57
713 724 0.602638 GTGACAGACATGCGGGTTCA 60.603 55.000 0.00 0.00 0.00 3.18
714 725 0.602638 TGTGACAGACATGCGGGTTC 60.603 55.000 0.00 0.00 0.00 3.62
715 726 0.884704 GTGTGACAGACATGCGGGTT 60.885 55.000 0.00 0.00 36.78 4.11
716 727 1.301716 GTGTGACAGACATGCGGGT 60.302 57.895 0.00 0.00 36.78 5.28
717 728 0.884259 TTGTGTGACAGACATGCGGG 60.884 55.000 6.22 0.00 36.78 6.13
718 729 0.943673 TTTGTGTGACAGACATGCGG 59.056 50.000 6.22 0.00 36.78 5.69
719 730 2.975410 ATTTGTGTGACAGACATGCG 57.025 45.000 6.22 0.00 36.78 4.73
720 731 4.093998 CCTCTATTTGTGTGACAGACATGC 59.906 45.833 6.22 0.00 36.78 4.06
721 732 5.482006 TCCTCTATTTGTGTGACAGACATG 58.518 41.667 6.22 0.00 36.78 3.21
722 733 5.745312 TCCTCTATTTGTGTGACAGACAT 57.255 39.130 6.22 0.00 36.78 3.06
723 734 5.304357 TCTTCCTCTATTTGTGTGACAGACA 59.696 40.000 0.41 0.41 0.00 3.41
724 735 5.784177 TCTTCCTCTATTTGTGTGACAGAC 58.216 41.667 0.00 0.00 0.00 3.51
725 736 5.775195 TCTCTTCCTCTATTTGTGTGACAGA 59.225 40.000 0.00 0.00 0.00 3.41
726 737 6.030548 TCTCTTCCTCTATTTGTGTGACAG 57.969 41.667 0.00 0.00 0.00 3.51
727 738 5.775195 TCTCTCTTCCTCTATTTGTGTGACA 59.225 40.000 0.00 0.00 0.00 3.58
728 739 6.274157 TCTCTCTTCCTCTATTTGTGTGAC 57.726 41.667 0.00 0.00 0.00 3.67
729 740 5.420421 CCTCTCTCTTCCTCTATTTGTGTGA 59.580 44.000 0.00 0.00 0.00 3.58
730 741 5.420421 TCCTCTCTCTTCCTCTATTTGTGTG 59.580 44.000 0.00 0.00 0.00 3.82
731 742 5.584913 TCCTCTCTCTTCCTCTATTTGTGT 58.415 41.667 0.00 0.00 0.00 3.72
732 743 5.656416 ACTCCTCTCTCTTCCTCTATTTGTG 59.344 44.000 0.00 0.00 0.00 3.33
733 744 5.837829 ACTCCTCTCTCTTCCTCTATTTGT 58.162 41.667 0.00 0.00 0.00 2.83
734 745 6.790232 AACTCCTCTCTCTTCCTCTATTTG 57.210 41.667 0.00 0.00 0.00 2.32
735 746 7.806680 AAAACTCCTCTCTCTTCCTCTATTT 57.193 36.000 0.00 0.00 0.00 1.40
736 747 7.806680 AAAAACTCCTCTCTCTTCCTCTATT 57.193 36.000 0.00 0.00 0.00 1.73
760 771 6.559157 ACTCCTCTCTCTTCCTTTCCTAAAAA 59.441 38.462 0.00 0.00 0.00 1.94
761 772 6.085416 ACTCCTCTCTCTTCCTTTCCTAAAA 58.915 40.000 0.00 0.00 0.00 1.52
762 773 5.656420 ACTCCTCTCTCTTCCTTTCCTAAA 58.344 41.667 0.00 0.00 0.00 1.85
763 774 5.278127 ACTCCTCTCTCTTCCTTTCCTAA 57.722 43.478 0.00 0.00 0.00 2.69
764 775 4.957606 ACTCCTCTCTCTTCCTTTCCTA 57.042 45.455 0.00 0.00 0.00 2.94
765 776 3.837731 CAACTCCTCTCTCTTCCTTTCCT 59.162 47.826 0.00 0.00 0.00 3.36
766 777 3.835395 TCAACTCCTCTCTCTTCCTTTCC 59.165 47.826 0.00 0.00 0.00 3.13
767 778 5.675684 ATCAACTCCTCTCTCTTCCTTTC 57.324 43.478 0.00 0.00 0.00 2.62
768 779 7.747809 AATATCAACTCCTCTCTCTTCCTTT 57.252 36.000 0.00 0.00 0.00 3.11
769 780 7.747809 AAATATCAACTCCTCTCTCTTCCTT 57.252 36.000 0.00 0.00 0.00 3.36
795 806 4.570772 GGGCCTTTCAGAACAAAGAAAAAC 59.429 41.667 0.84 0.00 35.67 2.43
796 807 4.223923 TGGGCCTTTCAGAACAAAGAAAAA 59.776 37.500 4.53 0.00 35.67 1.94
873 888 2.586648 AAAGAGTGGGCCGAATTCTT 57.413 45.000 9.21 9.21 0.00 2.52
941 956 2.873797 CCTAGTGGGCCTTTTGCTC 58.126 57.895 4.53 0.00 42.61 4.26
967 982 5.122396 CGATTGGTCTTTGGACTTTTAGAGG 59.878 44.000 0.00 0.00 41.82 3.69
983 998 3.841870 GGGAATGCCCGATTGGTC 58.158 61.111 0.00 0.00 46.48 4.02
1240 1262 1.976112 GTCCTCCTCGGAGCTGTTT 59.024 57.895 7.46 0.00 44.20 2.83
1292 1314 2.100603 CGACGAGGACGAGGAAGC 59.899 66.667 0.00 0.00 42.66 3.86
1676 1698 3.776731 TCAGAGAGGGTAATGAAGGGA 57.223 47.619 0.00 0.00 0.00 4.20
1677 1699 3.006323 CGATCAGAGAGGGTAATGAAGGG 59.994 52.174 0.00 0.00 0.00 3.95
1691 1742 9.526713 CAGAATATATAACCCAATCGATCAGAG 57.473 37.037 0.00 0.00 0.00 3.35
1770 1821 6.014584 TCCTCAGTTGAAGCAACAGATAGTAA 60.015 38.462 12.25 0.00 45.66 2.24
1808 1867 5.373222 AGACCACAAAGCTGTATGTTTGTA 58.627 37.500 0.00 0.00 43.43 2.41
1824 1890 2.039746 CCAGGAATACCACAAGACCACA 59.960 50.000 0.00 0.00 38.94 4.17
1825 1891 2.618045 CCCAGGAATACCACAAGACCAC 60.618 54.545 0.00 0.00 38.94 4.16
1826 1892 1.633432 CCCAGGAATACCACAAGACCA 59.367 52.381 0.00 0.00 38.94 4.02
1827 1893 1.633945 ACCCAGGAATACCACAAGACC 59.366 52.381 0.00 0.00 38.94 3.85
1828 1894 3.434940 AACCCAGGAATACCACAAGAC 57.565 47.619 0.00 0.00 38.94 3.01
1829 1895 3.054655 GCTAACCCAGGAATACCACAAGA 60.055 47.826 0.00 0.00 38.94 3.02
1830 1896 3.279434 GCTAACCCAGGAATACCACAAG 58.721 50.000 0.00 0.00 38.94 3.16
1831 1897 2.645297 TGCTAACCCAGGAATACCACAA 59.355 45.455 0.00 0.00 38.94 3.33
1871 1937 6.922957 TCGACAATGAAATTTTCTTTCCTTGG 59.077 34.615 10.33 1.90 37.92 3.61
1876 1942 9.571804 CACAATTCGACAATGAAATTTTCTTTC 57.428 29.630 10.33 0.11 31.22 2.62
1880 1946 7.406799 ACCACAATTCGACAATGAAATTTTC 57.593 32.000 2.05 2.05 31.22 2.29
1909 1975 1.202867 TGTGCCTACATGGAGCAACAA 60.203 47.619 0.00 0.00 38.45 2.83
1911 1977 1.200020 GTTGTGCCTACATGGAGCAAC 59.800 52.381 10.11 10.11 41.19 4.17
1954 2020 7.133133 ACTCTTAGACCTGTGTTTCCTTTTA 57.867 36.000 0.00 0.00 0.00 1.52
2040 2106 3.814005 GCATTGAATTTGCTCCCTGAT 57.186 42.857 0.00 0.00 37.14 2.90
2122 2188 3.643199 AGCCCACAAAAACCAAATGTT 57.357 38.095 0.00 0.00 39.43 2.71
2124 2190 6.048509 GGATATAGCCCACAAAAACCAAATG 58.951 40.000 0.00 0.00 0.00 2.32
2131 2197 6.865834 AACAATGGATATAGCCCACAAAAA 57.134 33.333 4.18 0.00 36.36 1.94
2136 2202 6.490040 ACATACAAACAATGGATATAGCCCAC 59.510 38.462 4.18 0.00 36.36 4.61
2208 2274 0.439985 CGTGTGAAGCATGGAAGTCG 59.560 55.000 0.00 0.00 0.00 4.18
2227 2293 5.580297 TCAAGAGTTGCACAAATTTTTGACC 59.420 36.000 8.51 1.47 40.55 4.02
2322 2391 6.835174 AGGCTCTATGAAAGCATGATCTTTA 58.165 36.000 0.00 0.00 41.66 1.85
2333 2402 6.500684 TTAAGTTTGCAGGCTCTATGAAAG 57.499 37.500 0.00 0.00 0.00 2.62
2432 2501 6.746745 AATTGTTTACACCGTAAGTATGGG 57.253 37.500 1.73 0.00 36.66 4.00
2680 2749 9.300681 ACCAAACTGATCTTCTAAATGATTTCA 57.699 29.630 0.00 0.00 0.00 2.69
2683 2752 9.525826 AGAACCAAACTGATCTTCTAAATGATT 57.474 29.630 0.00 0.00 0.00 2.57
2766 2835 3.587797 AGGACCACACAAGTATACACG 57.412 47.619 5.50 0.00 0.00 4.49
2792 2861 5.872070 GTCAAAGATAGTGGAAGACTGGAAG 59.128 44.000 0.00 0.00 42.29 3.46
2793 2862 5.280011 GGTCAAAGATAGTGGAAGACTGGAA 60.280 44.000 0.00 0.00 35.96 3.53
2794 2863 4.223032 GGTCAAAGATAGTGGAAGACTGGA 59.777 45.833 0.00 0.00 35.96 3.86
2795 2864 4.020218 TGGTCAAAGATAGTGGAAGACTGG 60.020 45.833 0.00 0.00 35.96 4.00
2796 2865 5.152623 TGGTCAAAGATAGTGGAAGACTG 57.847 43.478 0.00 0.00 35.96 3.51
2797 2866 7.682787 ATATGGTCAAAGATAGTGGAAGACT 57.317 36.000 0.00 0.00 38.88 3.24
2798 2867 9.429359 CATATATGGTCAAAGATAGTGGAAGAC 57.571 37.037 4.68 0.00 0.00 3.01
2799 2868 9.379770 TCATATATGGTCAAAGATAGTGGAAGA 57.620 33.333 12.78 0.00 0.00 2.87
2823 2892 6.457355 AGTAGAAACAATTTTGCATGCATCA 58.543 32.000 23.37 11.70 0.00 3.07
2826 2895 6.279123 TGAAGTAGAAACAATTTTGCATGCA 58.721 32.000 18.46 18.46 0.00 3.96
2831 2900 9.255304 TGGTTATTGAAGTAGAAACAATTTTGC 57.745 29.630 0.00 0.00 36.06 3.68
2862 2931 7.589958 ACACAGGGAAACAATTGTTAACATA 57.410 32.000 23.53 1.09 37.25 2.29
2863 2932 6.478512 ACACAGGGAAACAATTGTTAACAT 57.521 33.333 23.53 14.14 37.25 2.71
2864 2933 5.923733 ACACAGGGAAACAATTGTTAACA 57.076 34.783 23.53 3.59 37.25 2.41
2865 2934 5.006261 GCAACACAGGGAAACAATTGTTAAC 59.994 40.000 23.53 18.84 37.25 2.01
2866 2935 5.105146 AGCAACACAGGGAAACAATTGTTAA 60.105 36.000 23.53 0.00 37.25 2.01
2971 3129 2.029020 TCAGTTCCTTGACGTGGATCTG 60.029 50.000 18.70 18.70 45.64 2.90
2996 3154 1.064654 GCTTCTTGGGATCATGAACGC 59.935 52.381 12.40 12.40 34.62 4.84
3032 3190 0.676184 TGATGCTGGATCTACCGAGC 59.324 55.000 10.56 0.00 42.61 5.03
3090 3248 5.490139 ACAATGCAGAATAGGAATGAACG 57.510 39.130 0.00 0.00 0.00 3.95
3101 3259 6.006449 AGACAAAAGGACTACAATGCAGAAT 58.994 36.000 0.00 0.00 0.00 2.40
3204 3362 2.555757 GCAAAGAAGACTTGCCACAGAT 59.444 45.455 0.00 0.00 36.39 2.90
3257 3415 2.058057 GCAACTGGCGTATGGTTTTTG 58.942 47.619 0.00 0.00 0.00 2.44
3259 3417 0.601057 GGCAACTGGCGTATGGTTTT 59.399 50.000 0.00 0.00 46.16 2.43
3334 3492 1.425448 AGCTGCTTTCTTACCCAAGGT 59.575 47.619 0.00 0.00 40.16 3.50
3376 3534 2.125753 CTGCGACCACTCTCTGCC 60.126 66.667 0.00 0.00 0.00 4.85
3481 3639 1.669999 ATCCATTCGCCTGCCTTTGC 61.670 55.000 0.00 0.00 38.26 3.68
3547 3705 7.119699 TCCATTCAGTTTTACAGTCAAGCATAG 59.880 37.037 0.00 0.00 0.00 2.23
3592 3752 5.220873 CGAGTCCTGTGATCGATTTCTCTAA 60.221 44.000 0.00 0.00 38.72 2.10
3607 3767 2.099263 CACATAATCCGACGAGTCCTGT 59.901 50.000 0.00 0.00 0.00 4.00
3610 3770 3.644884 ATCACATAATCCGACGAGTCC 57.355 47.619 0.00 0.00 0.00 3.85
3627 3787 4.462508 TTTGCACACAAAGACCAAATCA 57.537 36.364 0.00 0.00 40.84 2.57
3650 3810 5.642063 CGAGTTACAACCCACATTATTCAGT 59.358 40.000 0.00 0.00 0.00 3.41
3658 3818 2.922740 ACACGAGTTACAACCCACAT 57.077 45.000 0.00 0.00 0.00 3.21
3699 3859 0.179111 GCGTCGGATGTCCAGATTCA 60.179 55.000 0.00 0.00 35.14 2.57
3716 3876 4.947933 CGCGTTAAGAGTTAATAAAGTGCG 59.052 41.667 0.00 0.00 0.00 5.34
3735 3895 0.459899 TCTGGATAGACATTGCGCGT 59.540 50.000 8.43 0.00 0.00 6.01
3746 3906 9.416794 GTCAGTGTATATCATTGTTCTGGATAG 57.583 37.037 0.00 0.00 35.65 2.08
3830 3990 2.672195 GCAAATAACAGCAACCCTCAGC 60.672 50.000 0.00 0.00 0.00 4.26
3970 4130 1.942776 TCAGCTGAGGGAGAACATCA 58.057 50.000 13.74 0.00 0.00 3.07
3981 4141 0.545171 ACCACCATGGATCAGCTGAG 59.455 55.000 22.96 9.67 40.96 3.35
4117 4277 3.890756 TGCTTCTGTTGTGATGTTTGGAT 59.109 39.130 0.00 0.00 0.00 3.41
4120 4280 5.806502 TCTTTTGCTTCTGTTGTGATGTTTG 59.193 36.000 0.00 0.00 0.00 2.93
4202 4453 4.938832 GGCCAAAGTATATACACACACACA 59.061 41.667 15.18 0.00 0.00 3.72
4396 4647 1.112459 CGCTTTGTTTTGTCGCAGTC 58.888 50.000 0.00 0.00 0.00 3.51
4474 4932 1.005340 CGAAGGTGAAGCAGAGATGC 58.995 55.000 0.00 0.00 0.00 3.91
4683 5199 7.175347 TGCAGAAGACAGACAAAGATAGTAT 57.825 36.000 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.