Multiple sequence alignment - TraesCS6B01G081000

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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 TraesCS6B01G081000 chr6B 100.000 3071 0 0 1 3071 57451654 57454724 0.000000e+00 5672.0
1 TraesCS6B01G081000 chr6B 93.472 720 46 1 39 758 579103398 579102680 0.000000e+00 1068.0
2 TraesCS6B01G081000 chr6B 85.335 866 95 22 2197 3042 57902676 57901823 0.000000e+00 867.0
3 TraesCS6B01G081000 chr6B 79.029 1092 184 27 1033 2111 81008066 81009125 0.000000e+00 706.0
4 TraesCS6B01G081000 chr6B 78.763 970 161 25 1189 2136 57726567 57725621 2.620000e-170 608.0
5 TraesCS6B01G081000 chr6B 76.171 1217 228 35 993 2190 80207441 80208614 4.410000e-163 584.0
6 TraesCS6B01G081000 chr6B 75.738 1220 236 34 993 2190 81668094 81666913 2.670000e-155 558.0
7 TraesCS6B01G081000 chr6B 81.013 632 74 23 2437 3041 81665271 81664659 7.760000e-126 460.0
8 TraesCS6B01G081000 chr6B 80.505 436 77 5 1560 1990 56393678 56393246 8.210000e-86 327.0
9 TraesCS6B01G081000 chr6B 83.152 184 21 5 2458 2632 57724420 57724238 3.170000e-35 159.0
10 TraesCS6B01G081000 chr6D 95.628 892 27 8 2184 3071 30077208 30076325 0.000000e+00 1421.0
11 TraesCS6B01G081000 chr6D 90.677 783 38 15 800 1556 30079320 30078547 0.000000e+00 1009.0
12 TraesCS6B01G081000 chr6D 79.080 1109 186 25 1041 2135 29875229 29876305 0.000000e+00 721.0
13 TraesCS6B01G081000 chr6D 84.463 708 101 5 1477 2181 31266544 31265843 0.000000e+00 689.0
14 TraesCS6B01G081000 chr6D 78.858 946 151 30 1237 2161 29932722 29933639 7.330000e-166 593.0
15 TraesCS6B01G081000 chr6D 92.112 393 21 4 1802 2187 30078547 30078158 2.080000e-151 545.0
16 TraesCS6B01G081000 chr6D 91.159 328 24 5 2427 2751 29877547 29877872 1.010000e-119 440.0
17 TraesCS6B01G081000 chr6D 79.909 438 48 18 2437 2847 29934887 29935311 5.010000e-73 285.0
18 TraesCS6B01G081000 chr6D 81.028 253 41 6 2176 2423 29934148 29934398 8.690000e-46 195.0
19 TraesCS6B01G081000 chr6D 100.000 38 0 0 1 38 102357177 102357140 1.530000e-08 71.3
20 TraesCS6B01G081000 chr2D 94.715 719 37 1 41 759 638865363 638864646 0.000000e+00 1116.0
21 TraesCS6B01G081000 chr2D 93.370 724 43 5 39 761 589512917 589512198 0.000000e+00 1066.0
22 TraesCS6B01G081000 chr2D 100.000 38 0 0 1 38 521301770 521301807 1.530000e-08 71.3
23 TraesCS6B01G081000 chr3D 94.313 721 40 1 39 759 547514967 547514248 0.000000e+00 1103.0
24 TraesCS6B01G081000 chr3D 79.897 388 66 11 1025 1403 497810857 497810473 1.080000e-69 274.0
25 TraesCS6B01G081000 chr5D 94.274 716 40 1 42 757 8436979 8436265 0.000000e+00 1094.0
26 TraesCS6B01G081000 chr5D 93.759 721 44 1 39 759 353646160 353645441 0.000000e+00 1081.0
27 TraesCS6B01G081000 chr5D 93.602 719 43 3 41 758 430918678 430917962 0.000000e+00 1070.0
28 TraesCS6B01G081000 chr5D 79.897 388 66 11 1025 1403 533536307 533535923 1.080000e-69 274.0
29 TraesCS6B01G081000 chrUn 93.750 720 45 0 39 758 42146286 42145567 0.000000e+00 1081.0
30 TraesCS6B01G081000 chrUn 78.258 1458 234 54 998 2426 27038602 27040005 0.000000e+00 859.0
31 TraesCS6B01G081000 chrUn 76.194 1214 226 38 993 2185 27285223 27284052 1.590000e-162 582.0
32 TraesCS6B01G081000 chrUn 82.627 236 39 2 2197 2431 27040792 27041026 1.120000e-49 207.0
33 TraesCS6B01G081000 chrUn 100.000 38 0 0 1 38 441343712 441343749 1.530000e-08 71.3
34 TraesCS6B01G081000 chrUn 100.000 28 0 0 1710 1737 34662391 34662364 6.000000e-03 52.8
35 TraesCS6B01G081000 chr4D 94.093 711 41 1 49 759 39302923 39302214 0.000000e+00 1079.0
36 TraesCS6B01G081000 chr5B 89.835 728 59 7 44 768 345850935 345850220 0.000000e+00 920.0
37 TraesCS6B01G081000 chr5B 100.000 38 0 0 1 38 127838265 127838302 1.530000e-08 71.3
38 TraesCS6B01G081000 chr2B 89.722 720 68 6 46 763 39318064 39318779 0.000000e+00 915.0
39 TraesCS6B01G081000 chr6A 89.510 572 50 7 2184 2751 32821115 32820550 0.000000e+00 715.0
40 TraesCS6B01G081000 chr6A 78.571 1134 187 35 998 2112 47139803 47140899 0.000000e+00 697.0
41 TraesCS6B01G081000 chr6A 79.601 902 141 26 1230 2111 32796690 32795812 9.420000e-170 606.0
42 TraesCS6B01G081000 chr6A 88.248 451 48 4 1740 2187 32328135 32328583 4.510000e-148 534.0
43 TraesCS6B01G081000 chr6A 78.992 714 119 10 1044 1749 32326084 32326774 2.790000e-125 459.0
44 TraesCS6B01G081000 chr6A 80.478 251 43 5 2176 2421 32795219 32794970 1.450000e-43 187.0
45 TraesCS6B01G081000 chr6A 71.687 498 118 21 1701 2187 40542581 40542096 1.930000e-22 117.0
46 TraesCS6B01G081000 chr1D 87.850 428 50 1 2201 2628 478062483 478062908 4.570000e-138 501.0
47 TraesCS6B01G081000 chr1D 90.741 108 7 3 2870 2976 478063312 478063417 1.150000e-29 141.0
48 TraesCS6B01G081000 chr1D 100.000 38 0 0 1 38 351088462 351088425 1.530000e-08 71.3
49 TraesCS6B01G081000 chr1A 77.718 745 134 22 1450 2182 574317571 574318295 7.870000e-116 427.0
50 TraesCS6B01G081000 chr1A 91.667 120 7 3 2858 2976 574318520 574318637 2.450000e-36 163.0
51 TraesCS6B01G081000 chr1A 100.000 38 0 0 1 38 278510428 278510391 1.530000e-08 71.3
52 TraesCS6B01G081000 chr1B 100.000 38 0 0 1 38 135080552 135080515 1.530000e-08 71.3
53 TraesCS6B01G081000 chr1B 100.000 38 0 0 1 38 338940010 338939973 1.530000e-08 71.3
54 TraesCS6B01G081000 chr1B 100.000 38 0 0 1 38 339015707 339015670 1.530000e-08 71.3
55 TraesCS6B01G081000 chr4A 100.000 31 0 0 2013 2043 657518883 657518853 1.190000e-04 58.4
56 TraesCS6B01G081000 chr3A 100.000 28 0 0 1710 1737 11350643 11350670 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G081000 chr6B 57451654 57454724 3070 False 5672.000000 5672 100.000000 1 3071 1 chr6B.!!$F1 3070
1 TraesCS6B01G081000 chr6B 579102680 579103398 718 True 1068.000000 1068 93.472000 39 758 1 chr6B.!!$R3 719
2 TraesCS6B01G081000 chr6B 57901823 57902676 853 True 867.000000 867 85.335000 2197 3042 1 chr6B.!!$R2 845
3 TraesCS6B01G081000 chr6B 81008066 81009125 1059 False 706.000000 706 79.029000 1033 2111 1 chr6B.!!$F3 1078
4 TraesCS6B01G081000 chr6B 80207441 80208614 1173 False 584.000000 584 76.171000 993 2190 1 chr6B.!!$F2 1197
5 TraesCS6B01G081000 chr6B 81664659 81668094 3435 True 509.000000 558 78.375500 993 3041 2 chr6B.!!$R5 2048
6 TraesCS6B01G081000 chr6B 57724238 57726567 2329 True 383.500000 608 80.957500 1189 2632 2 chr6B.!!$R4 1443
7 TraesCS6B01G081000 chr6D 30076325 30079320 2995 True 991.666667 1421 92.805667 800 3071 3 chr6D.!!$R3 2271
8 TraesCS6B01G081000 chr6D 31265843 31266544 701 True 689.000000 689 84.463000 1477 2181 1 chr6D.!!$R1 704
9 TraesCS6B01G081000 chr6D 29875229 29877872 2643 False 580.500000 721 85.119500 1041 2751 2 chr6D.!!$F1 1710
10 TraesCS6B01G081000 chr6D 29932722 29935311 2589 False 357.666667 593 79.931667 1237 2847 3 chr6D.!!$F2 1610
11 TraesCS6B01G081000 chr2D 638864646 638865363 717 True 1116.000000 1116 94.715000 41 759 1 chr2D.!!$R2 718
12 TraesCS6B01G081000 chr2D 589512198 589512917 719 True 1066.000000 1066 93.370000 39 761 1 chr2D.!!$R1 722
13 TraesCS6B01G081000 chr3D 547514248 547514967 719 True 1103.000000 1103 94.313000 39 759 1 chr3D.!!$R2 720
14 TraesCS6B01G081000 chr5D 8436265 8436979 714 True 1094.000000 1094 94.274000 42 757 1 chr5D.!!$R1 715
15 TraesCS6B01G081000 chr5D 353645441 353646160 719 True 1081.000000 1081 93.759000 39 759 1 chr5D.!!$R2 720
16 TraesCS6B01G081000 chr5D 430917962 430918678 716 True 1070.000000 1070 93.602000 41 758 1 chr5D.!!$R3 717
17 TraesCS6B01G081000 chrUn 42145567 42146286 719 True 1081.000000 1081 93.750000 39 758 1 chrUn.!!$R3 719
18 TraesCS6B01G081000 chrUn 27284052 27285223 1171 True 582.000000 582 76.194000 993 2185 1 chrUn.!!$R1 1192
19 TraesCS6B01G081000 chrUn 27038602 27041026 2424 False 533.000000 859 80.442500 998 2431 2 chrUn.!!$F2 1433
20 TraesCS6B01G081000 chr4D 39302214 39302923 709 True 1079.000000 1079 94.093000 49 759 1 chr4D.!!$R1 710
21 TraesCS6B01G081000 chr5B 345850220 345850935 715 True 920.000000 920 89.835000 44 768 1 chr5B.!!$R1 724
22 TraesCS6B01G081000 chr2B 39318064 39318779 715 False 915.000000 915 89.722000 46 763 1 chr2B.!!$F1 717
23 TraesCS6B01G081000 chr6A 32820550 32821115 565 True 715.000000 715 89.510000 2184 2751 1 chr6A.!!$R1 567
24 TraesCS6B01G081000 chr6A 47139803 47140899 1096 False 697.000000 697 78.571000 998 2112 1 chr6A.!!$F1 1114
25 TraesCS6B01G081000 chr6A 32326084 32328583 2499 False 496.500000 534 83.620000 1044 2187 2 chr6A.!!$F2 1143
26 TraesCS6B01G081000 chr6A 32794970 32796690 1720 True 396.500000 606 80.039500 1230 2421 2 chr6A.!!$R3 1191
27 TraesCS6B01G081000 chr1D 478062483 478063417 934 False 321.000000 501 89.295500 2201 2976 2 chr1D.!!$F1 775
28 TraesCS6B01G081000 chr1A 574317571 574318637 1066 False 295.000000 427 84.692500 1450 2976 2 chr1A.!!$F1 1526

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
944 946 0.034186 TGCGGGCTTCAATCAATCCT 60.034 50.0 0.0 0.00 0.00 3.24 F
1553 1602 0.179124 CCTACAAGAGTGCTCGCCTC 60.179 60.0 0.0 0.87 34.09 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 3673 2.435693 CCCATCCGACCACCCTCTC 61.436 68.421 0.0 0.00 0.0 3.2 R
2388 5705 2.522185 ACCTCAACTTGCATGCAGAAT 58.478 42.857 21.5 7.55 0.0 2.4 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.841443 CTTTGCTGAACAGATGTATAGAGG 57.159 41.667 5.97 0.00 0.00 3.69
24 25 6.544928 TTTGCTGAACAGATGTATAGAGGA 57.455 37.500 5.97 0.00 0.00 3.71
25 26 6.544928 TTGCTGAACAGATGTATAGAGGAA 57.455 37.500 5.97 0.00 0.00 3.36
26 27 6.544928 TGCTGAACAGATGTATAGAGGAAA 57.455 37.500 5.97 0.00 0.00 3.13
27 28 6.946340 TGCTGAACAGATGTATAGAGGAAAA 58.054 36.000 5.97 0.00 0.00 2.29
28 29 7.044181 TGCTGAACAGATGTATAGAGGAAAAG 58.956 38.462 5.97 0.00 0.00 2.27
29 30 6.481644 GCTGAACAGATGTATAGAGGAAAAGG 59.518 42.308 5.97 0.00 0.00 3.11
30 31 6.889198 TGAACAGATGTATAGAGGAAAAGGG 58.111 40.000 0.00 0.00 0.00 3.95
31 32 6.443849 TGAACAGATGTATAGAGGAAAAGGGT 59.556 38.462 0.00 0.00 0.00 4.34
32 33 6.240549 ACAGATGTATAGAGGAAAAGGGTG 57.759 41.667 0.00 0.00 0.00 4.61
33 34 5.964477 ACAGATGTATAGAGGAAAAGGGTGA 59.036 40.000 0.00 0.00 0.00 4.02
34 35 6.127026 ACAGATGTATAGAGGAAAAGGGTGAC 60.127 42.308 0.00 0.00 0.00 3.67
76 77 5.622233 GCACAAGGTTCAACTTCAAACTCTT 60.622 40.000 0.00 0.00 0.00 2.85
77 78 6.389906 CACAAGGTTCAACTTCAAACTCTTT 58.610 36.000 0.00 0.00 0.00 2.52
149 150 0.819259 ACCGCGGCATAGCAATCAAT 60.819 50.000 28.58 0.00 36.85 2.57
365 366 2.586079 CGGCCGATGAAGATGCGT 60.586 61.111 24.07 0.00 0.00 5.24
439 440 0.744771 GAGAATGGTGGCGGGAGTTC 60.745 60.000 0.00 0.00 0.00 3.01
477 478 2.037144 GCTAAATAGGGGTGGACTCGA 58.963 52.381 0.00 0.00 0.00 4.04
701 703 3.989787 GCAGGCAACCAAACGGGG 61.990 66.667 0.00 0.00 42.91 5.73
717 719 2.668550 GGCAAGTTCTTCCCGCGT 60.669 61.111 4.92 0.00 0.00 6.01
763 765 0.179001 ACCAAACACGCCCTTAGCTT 60.179 50.000 0.00 0.00 40.39 3.74
764 766 1.072648 ACCAAACACGCCCTTAGCTTA 59.927 47.619 0.00 0.00 40.39 3.09
765 767 1.737793 CCAAACACGCCCTTAGCTTAG 59.262 52.381 0.00 0.00 40.39 2.18
766 768 2.614481 CCAAACACGCCCTTAGCTTAGA 60.614 50.000 0.16 0.00 40.39 2.10
767 769 2.381725 AACACGCCCTTAGCTTAGAC 57.618 50.000 0.16 0.00 40.39 2.59
768 770 1.263356 ACACGCCCTTAGCTTAGACA 58.737 50.000 0.16 0.00 40.39 3.41
769 771 1.621814 ACACGCCCTTAGCTTAGACAA 59.378 47.619 0.16 0.00 40.39 3.18
770 772 2.236395 ACACGCCCTTAGCTTAGACAAT 59.764 45.455 0.16 0.00 40.39 2.71
771 773 3.270877 CACGCCCTTAGCTTAGACAATT 58.729 45.455 0.16 0.00 40.39 2.32
772 774 3.063997 CACGCCCTTAGCTTAGACAATTG 59.936 47.826 3.24 3.24 40.39 2.32
773 775 2.614057 CGCCCTTAGCTTAGACAATTGG 59.386 50.000 10.83 0.00 40.39 3.16
774 776 2.359214 GCCCTTAGCTTAGACAATTGGC 59.641 50.000 10.83 6.83 38.99 4.52
775 777 3.620488 CCCTTAGCTTAGACAATTGGCA 58.380 45.455 15.18 0.00 0.00 4.92
776 778 4.210331 CCCTTAGCTTAGACAATTGGCAT 58.790 43.478 15.18 1.05 0.00 4.40
777 779 4.037208 CCCTTAGCTTAGACAATTGGCATG 59.963 45.833 15.18 3.94 0.00 4.06
778 780 4.883585 CCTTAGCTTAGACAATTGGCATGA 59.116 41.667 15.18 0.00 0.00 3.07
779 781 5.220931 CCTTAGCTTAGACAATTGGCATGAC 60.221 44.000 15.18 0.00 0.00 3.06
780 782 3.689347 AGCTTAGACAATTGGCATGACA 58.311 40.909 15.18 0.00 0.00 3.58
781 783 3.693085 AGCTTAGACAATTGGCATGACAG 59.307 43.478 15.18 2.60 0.00 3.51
782 784 3.733077 GCTTAGACAATTGGCATGACAGC 60.733 47.826 15.18 9.05 0.00 4.40
783 785 2.211250 AGACAATTGGCATGACAGCT 57.789 45.000 15.18 0.00 34.17 4.24
784 786 2.522185 AGACAATTGGCATGACAGCTT 58.478 42.857 15.18 0.00 34.17 3.74
785 787 2.895404 AGACAATTGGCATGACAGCTTT 59.105 40.909 15.18 0.00 34.17 3.51
786 788 2.991190 GACAATTGGCATGACAGCTTTG 59.009 45.455 6.36 15.53 34.17 2.77
787 789 2.366266 ACAATTGGCATGACAGCTTTGT 59.634 40.909 16.54 16.54 31.95 2.83
788 790 2.991190 CAATTGGCATGACAGCTTTGTC 59.009 45.455 0.00 0.00 39.15 3.18
789 791 1.985473 TTGGCATGACAGCTTTGTCT 58.015 45.000 0.00 0.00 39.41 3.41
790 792 1.527034 TGGCATGACAGCTTTGTCTC 58.473 50.000 0.00 0.00 39.41 3.36
791 793 1.202794 TGGCATGACAGCTTTGTCTCA 60.203 47.619 0.00 0.00 39.41 3.27
792 794 2.089980 GGCATGACAGCTTTGTCTCAT 58.910 47.619 7.52 0.00 39.41 2.90
793 795 2.490903 GGCATGACAGCTTTGTCTCATT 59.509 45.455 7.52 0.00 39.41 2.57
794 796 3.057033 GGCATGACAGCTTTGTCTCATTT 60.057 43.478 7.52 0.00 39.41 2.32
795 797 4.553323 GCATGACAGCTTTGTCTCATTTT 58.447 39.130 7.52 0.00 39.41 1.82
796 798 4.986659 GCATGACAGCTTTGTCTCATTTTT 59.013 37.500 7.52 0.00 39.41 1.94
820 822 0.813821 GGCATGACAGCTCCTTTTCC 59.186 55.000 0.00 0.00 34.17 3.13
821 823 1.615384 GGCATGACAGCTCCTTTTCCT 60.615 52.381 0.00 0.00 34.17 3.36
824 826 0.250901 TGACAGCTCCTTTTCCTGCC 60.251 55.000 0.00 0.00 0.00 4.85
836 838 6.935167 TCCTTTTCCTGCCTTTGATTATTTC 58.065 36.000 0.00 0.00 0.00 2.17
866 868 2.862530 GCTTTTCCCGCCTTTGAGTTTC 60.863 50.000 0.00 0.00 0.00 2.78
871 873 3.822940 TCCCGCCTTTGAGTTTCTTTTA 58.177 40.909 0.00 0.00 0.00 1.52
872 874 4.403734 TCCCGCCTTTGAGTTTCTTTTAT 58.596 39.130 0.00 0.00 0.00 1.40
873 875 4.830600 TCCCGCCTTTGAGTTTCTTTTATT 59.169 37.500 0.00 0.00 0.00 1.40
874 876 5.303333 TCCCGCCTTTGAGTTTCTTTTATTT 59.697 36.000 0.00 0.00 0.00 1.40
895 897 3.641437 TTTTGAGTGGATTCCGCTTTG 57.359 42.857 19.49 0.00 45.19 2.77
896 898 2.559698 TTGAGTGGATTCCGCTTTGA 57.440 45.000 19.49 6.64 45.19 2.69
897 899 2.099141 TGAGTGGATTCCGCTTTGAG 57.901 50.000 19.49 0.00 45.19 3.02
898 900 1.339055 TGAGTGGATTCCGCTTTGAGG 60.339 52.381 19.49 0.00 45.19 3.86
899 901 0.035056 AGTGGATTCCGCTTTGAGGG 60.035 55.000 13.12 0.00 42.24 4.30
900 902 0.035439 GTGGATTCCGCTTTGAGGGA 60.035 55.000 9.06 0.00 0.00 4.20
939 941 2.334946 GCACTGCGGGCTTCAATCA 61.335 57.895 0.00 0.00 0.00 2.57
940 942 1.865788 GCACTGCGGGCTTCAATCAA 61.866 55.000 0.00 0.00 0.00 2.57
941 943 0.813184 CACTGCGGGCTTCAATCAAT 59.187 50.000 0.00 0.00 0.00 2.57
942 944 1.098050 ACTGCGGGCTTCAATCAATC 58.902 50.000 0.00 0.00 0.00 2.67
943 945 0.383231 CTGCGGGCTTCAATCAATCC 59.617 55.000 0.00 0.00 0.00 3.01
944 946 0.034186 TGCGGGCTTCAATCAATCCT 60.034 50.000 0.00 0.00 0.00 3.24
985 987 0.596577 TAGTCACTGACCTCACACGC 59.403 55.000 5.51 0.00 32.18 5.34
989 991 4.662961 CTGACCTCACACGCCGCA 62.663 66.667 0.00 0.00 0.00 5.69
990 992 4.961511 TGACCTCACACGCCGCAC 62.962 66.667 0.00 0.00 0.00 5.34
1086 1101 2.560119 CGAGATCCTCCTCCGCCTG 61.560 68.421 0.00 0.00 0.00 4.85
1217 1235 2.042843 TCCCCTCCTCGGCTTCTC 60.043 66.667 0.00 0.00 0.00 2.87
1351 1375 3.251043 GCCTCGCGCTCTTCTTCG 61.251 66.667 5.56 0.00 0.00 3.79
1553 1602 0.179124 CCTACAAGAGTGCTCGCCTC 60.179 60.000 0.00 0.87 34.09 4.70
1602 1651 1.592669 CGATTTCATCTCGGCGCCT 60.593 57.895 26.68 1.35 32.58 5.52
1620 1669 3.491267 CGCCTATTTCATCCGAGACTTTC 59.509 47.826 0.00 0.00 0.00 2.62
1689 1742 4.966787 GTTGCCGCCCCAGGTTCA 62.967 66.667 0.00 0.00 0.00 3.18
1690 1743 4.659172 TTGCCGCCCCAGGTTCAG 62.659 66.667 0.00 0.00 0.00 3.02
1822 3696 1.683441 GGTGGTCGGATGGGTTTCT 59.317 57.895 0.00 0.00 0.00 2.52
1960 3837 1.352352 AGAAAGATCCCCCGCATATGG 59.648 52.381 4.56 0.00 0.00 2.74
1965 3842 0.118346 ATCCCCCGCATATGGTAGGA 59.882 55.000 4.56 3.89 34.92 2.94
2083 3963 5.512749 GCCACCATCTGATCTCACTATCATT 60.513 44.000 0.00 0.00 35.40 2.57
2190 4174 5.001237 TGGCTGATTAAATGCTGTTGATG 57.999 39.130 0.00 0.00 0.00 3.07
2195 5463 4.705991 TGATTAAATGCTGTTGATGCCTCA 59.294 37.500 0.00 0.00 0.00 3.86
2375 5691 4.154737 GCTGTTGTGATGTATTGCTTGAGA 59.845 41.667 0.00 0.00 0.00 3.27
2582 6427 8.477419 TTTCTGAATGGACCAAATAATATCCC 57.523 34.615 0.00 0.00 0.00 3.85
2818 6758 2.340210 TCTGCTTGCAAACTGTACCA 57.660 45.000 0.00 0.00 0.00 3.25
2888 6837 9.101325 ACTGCCTACTAGCATTATTATTCCTTA 57.899 33.333 0.00 0.00 43.09 2.69
2923 6974 8.759481 AATTGGTTTGGTGATGGTAAATTTTT 57.241 26.923 0.00 0.00 0.00 1.94
3041 7098 1.177401 CAGTAAGCCTTTCTTGCCCC 58.823 55.000 0.00 0.00 38.03 5.80
3045 7102 0.906282 AAGCCTTTCTTGCCCCATGG 60.906 55.000 4.14 4.14 32.79 3.66
3046 7103 4.887258 TAAGCCTTTCTTGCCCCATGGG 62.887 54.545 25.30 25.30 39.98 4.00
3056 7113 2.813726 CCCCATGGGCCATGCATTG 61.814 63.158 35.99 23.58 40.20 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.577103 TCCTCTATACATCTGTTCAGCAAAG 58.423 40.000 0.00 0.00 0.00 2.77
1 2 6.544928 TCCTCTATACATCTGTTCAGCAAA 57.455 37.500 0.00 0.00 0.00 3.68
2 3 6.544928 TTCCTCTATACATCTGTTCAGCAA 57.455 37.500 0.00 0.00 0.00 3.91
3 4 6.544928 TTTCCTCTATACATCTGTTCAGCA 57.455 37.500 0.00 0.00 0.00 4.41
4 5 6.481644 CCTTTTCCTCTATACATCTGTTCAGC 59.518 42.308 0.00 0.00 0.00 4.26
5 6 6.989169 CCCTTTTCCTCTATACATCTGTTCAG 59.011 42.308 0.00 0.00 0.00 3.02
6 7 6.443849 ACCCTTTTCCTCTATACATCTGTTCA 59.556 38.462 0.00 0.00 0.00 3.18
7 8 6.763610 CACCCTTTTCCTCTATACATCTGTTC 59.236 42.308 0.00 0.00 0.00 3.18
8 9 6.443849 TCACCCTTTTCCTCTATACATCTGTT 59.556 38.462 0.00 0.00 0.00 3.16
9 10 5.964477 TCACCCTTTTCCTCTATACATCTGT 59.036 40.000 0.00 0.00 0.00 3.41
10 11 6.284459 GTCACCCTTTTCCTCTATACATCTG 58.716 44.000 0.00 0.00 0.00 2.90
11 12 5.367060 GGTCACCCTTTTCCTCTATACATCT 59.633 44.000 0.00 0.00 0.00 2.90
12 13 5.454897 GGGTCACCCTTTTCCTCTATACATC 60.455 48.000 5.22 0.00 41.34 3.06
13 14 4.412528 GGGTCACCCTTTTCCTCTATACAT 59.587 45.833 5.22 0.00 41.34 2.29
14 15 3.778629 GGGTCACCCTTTTCCTCTATACA 59.221 47.826 5.22 0.00 41.34 2.29
15 16 3.778629 TGGGTCACCCTTTTCCTCTATAC 59.221 47.826 16.04 0.00 45.70 1.47
16 17 4.083080 TGGGTCACCCTTTTCCTCTATA 57.917 45.455 16.04 0.00 45.70 1.31
17 18 2.929301 TGGGTCACCCTTTTCCTCTAT 58.071 47.619 16.04 0.00 45.70 1.98
18 19 2.374170 GTTGGGTCACCCTTTTCCTCTA 59.626 50.000 16.04 0.00 45.70 2.43
19 20 1.145119 GTTGGGTCACCCTTTTCCTCT 59.855 52.381 16.04 0.00 45.70 3.69
20 21 1.617322 GTTGGGTCACCCTTTTCCTC 58.383 55.000 16.04 0.00 45.70 3.71
21 22 0.179001 CGTTGGGTCACCCTTTTCCT 60.179 55.000 16.04 0.00 45.70 3.36
22 23 0.179012 TCGTTGGGTCACCCTTTTCC 60.179 55.000 16.04 0.00 45.70 3.13
23 24 1.682740 TTCGTTGGGTCACCCTTTTC 58.317 50.000 16.04 0.70 45.70 2.29
24 25 2.235891 GATTCGTTGGGTCACCCTTTT 58.764 47.619 16.04 0.00 45.70 2.27
25 26 1.144093 TGATTCGTTGGGTCACCCTTT 59.856 47.619 16.04 0.00 45.70 3.11
26 27 0.768622 TGATTCGTTGGGTCACCCTT 59.231 50.000 16.04 0.00 45.70 3.95
27 28 0.768622 TTGATTCGTTGGGTCACCCT 59.231 50.000 16.04 0.00 45.70 4.34
28 29 0.879090 GTTGATTCGTTGGGTCACCC 59.121 55.000 5.63 5.63 45.71 4.61
29 30 1.265905 GTGTTGATTCGTTGGGTCACC 59.734 52.381 0.00 0.00 37.24 4.02
30 31 1.944024 TGTGTTGATTCGTTGGGTCAC 59.056 47.619 0.00 0.00 0.00 3.67
31 32 2.333688 TGTGTTGATTCGTTGGGTCA 57.666 45.000 0.00 0.00 0.00 4.02
32 33 2.604614 GCTTGTGTTGATTCGTTGGGTC 60.605 50.000 0.00 0.00 0.00 4.46
33 34 1.336755 GCTTGTGTTGATTCGTTGGGT 59.663 47.619 0.00 0.00 0.00 4.51
34 35 1.336440 TGCTTGTGTTGATTCGTTGGG 59.664 47.619 0.00 0.00 0.00 4.12
35 36 2.223456 TGTGCTTGTGTTGATTCGTTGG 60.223 45.455 0.00 0.00 0.00 3.77
36 37 3.063670 TGTGCTTGTGTTGATTCGTTG 57.936 42.857 0.00 0.00 0.00 4.10
37 38 3.489059 CCTTGTGCTTGTGTTGATTCGTT 60.489 43.478 0.00 0.00 0.00 3.85
76 77 6.326583 AGCATGTGGTAGGCTAGATTAGTAAA 59.673 38.462 0.00 0.00 46.08 2.01
77 78 5.839063 AGCATGTGGTAGGCTAGATTAGTAA 59.161 40.000 0.00 0.00 46.08 2.24
149 150 4.280425 GGTCTGATCTGTGAGCTCATATGA 59.720 45.833 21.47 17.64 0.00 2.15
288 289 0.258194 ATCTTCTACGACCGTCCCCT 59.742 55.000 0.00 0.00 0.00 4.79
365 366 2.483745 CGACGAGCAGGTAAGCGA 59.516 61.111 0.00 0.00 40.15 4.93
477 478 2.240162 GATTTCGGCTCACCTCCCGT 62.240 60.000 0.00 0.00 44.63 5.28
701 703 2.556287 CACGCGGGAAGAACTTGC 59.444 61.111 12.47 0.00 0.00 4.01
730 732 3.255642 GTGTTTGGTTGTCTGCATATGGT 59.744 43.478 4.56 0.00 0.00 3.55
741 743 1.314730 CTAAGGGCGTGTTTGGTTGT 58.685 50.000 0.00 0.00 0.00 3.32
763 765 3.354948 AGCTGTCATGCCAATTGTCTA 57.645 42.857 4.43 0.00 0.00 2.59
764 766 2.211250 AGCTGTCATGCCAATTGTCT 57.789 45.000 4.43 0.00 0.00 3.41
765 767 2.991190 CAAAGCTGTCATGCCAATTGTC 59.009 45.455 4.43 0.00 0.00 3.18
766 768 2.366266 ACAAAGCTGTCATGCCAATTGT 59.634 40.909 4.43 0.00 33.24 2.71
767 769 3.034721 ACAAAGCTGTCATGCCAATTG 57.965 42.857 0.00 0.00 0.00 2.32
796 798 1.999648 AGGAGCTGTCATGCCAAAAA 58.000 45.000 0.00 0.00 0.00 1.94
797 799 1.999648 AAGGAGCTGTCATGCCAAAA 58.000 45.000 0.00 0.00 0.00 2.44
798 800 1.999648 AAAGGAGCTGTCATGCCAAA 58.000 45.000 0.00 0.00 0.00 3.28
811 813 6.535963 AATAATCAAAGGCAGGAAAAGGAG 57.464 37.500 0.00 0.00 0.00 3.69
820 822 7.650903 GCATCTAAAGGAAATAATCAAAGGCAG 59.349 37.037 0.00 0.00 0.00 4.85
821 823 7.342799 AGCATCTAAAGGAAATAATCAAAGGCA 59.657 33.333 0.00 0.00 0.00 4.75
836 838 1.405463 GGCGGGAAAAGCATCTAAAGG 59.595 52.381 0.00 0.00 36.08 3.11
874 876 3.634448 TCAAAGCGGAATCCACTCAAAAA 59.366 39.130 0.00 0.00 0.00 1.94
879 881 1.373570 CCTCAAAGCGGAATCCACTC 58.626 55.000 0.00 0.00 0.00 3.51
887 889 1.374947 CCACTTCCCTCAAAGCGGA 59.625 57.895 0.00 0.00 31.36 5.54
892 894 0.772124 AGCCTCCCACTTCCCTCAAA 60.772 55.000 0.00 0.00 0.00 2.69
895 897 2.993853 CAGCCTCCCACTTCCCTC 59.006 66.667 0.00 0.00 0.00 4.30
896 898 3.334054 GCAGCCTCCCACTTCCCT 61.334 66.667 0.00 0.00 0.00 4.20
897 899 3.635268 CTGCAGCCTCCCACTTCCC 62.635 68.421 0.00 0.00 0.00 3.97
898 900 2.045536 CTGCAGCCTCCCACTTCC 60.046 66.667 0.00 0.00 0.00 3.46
899 901 1.078567 CTCTGCAGCCTCCCACTTC 60.079 63.158 9.47 0.00 0.00 3.01
900 902 3.076092 CTCTGCAGCCTCCCACTT 58.924 61.111 9.47 0.00 0.00 3.16
985 987 1.002134 ACATTTCTCCCTGGTGCGG 60.002 57.895 0.00 0.00 0.00 5.69
989 991 1.271379 CCGTTGACATTTCTCCCTGGT 60.271 52.381 0.00 0.00 0.00 4.00
990 992 1.453155 CCGTTGACATTTCTCCCTGG 58.547 55.000 0.00 0.00 0.00 4.45
1217 1235 2.863346 TTCCTGTGGTGGTCGTCGG 61.863 63.158 0.00 0.00 0.00 4.79
1276 1300 4.168291 CAGGGAGAAGAGGCCGCC 62.168 72.222 1.49 0.00 0.00 6.13
1351 1375 3.827898 CTGGAGCGAGACCGGGAC 61.828 72.222 6.32 0.00 36.06 4.46
1680 1733 2.508526 CTTCTTGAACCTGAACCTGGG 58.491 52.381 0.00 0.00 0.00 4.45
1688 1741 3.063510 TGAGGATGCTTCTTGAACCTG 57.936 47.619 0.00 0.00 0.00 4.00
1689 1742 3.073650 ACTTGAGGATGCTTCTTGAACCT 59.926 43.478 0.00 0.00 0.00 3.50
1690 1743 3.416156 ACTTGAGGATGCTTCTTGAACC 58.584 45.455 0.00 0.00 0.00 3.62
1691 1744 5.009010 TCAAACTTGAGGATGCTTCTTGAAC 59.991 40.000 0.00 0.00 32.50 3.18
1692 1745 5.132502 TCAAACTTGAGGATGCTTCTTGAA 58.867 37.500 0.00 0.00 32.50 2.69
1799 3673 2.435693 CCCATCCGACCACCCTCTC 61.436 68.421 0.00 0.00 0.00 3.20
1822 3696 4.932146 GCAGTAAAGCCTGACAAGAAAAA 58.068 39.130 0.00 0.00 34.23 1.94
1960 3837 6.543831 ACATTGTTTTCCTCAGCATATCCTAC 59.456 38.462 0.00 0.00 0.00 3.18
1965 3842 5.018809 ACCACATTGTTTTCCTCAGCATAT 58.981 37.500 0.00 0.00 0.00 1.78
2083 3963 6.183360 CCTGGAGTATAGACAGTTTCGAATGA 60.183 42.308 5.78 0.00 0.00 2.57
2190 4174 9.875691 AAAGAAAAGGTCAAATAAATATGAGGC 57.124 29.630 0.00 0.00 0.00 4.70
2375 5691 6.064060 TGCATGCAGAATATAAGCTTACCTT 58.936 36.000 18.46 5.20 37.57 3.50
2388 5705 2.522185 ACCTCAACTTGCATGCAGAAT 58.478 42.857 21.50 7.55 0.00 2.40
2582 6427 7.951530 ATGCCAAAAGAAATTTCAGTACAAG 57.048 32.000 19.99 4.06 0.00 3.16
2707 6636 9.941664 CATGAAGATTTGTTAATCCAGATGTAC 57.058 33.333 0.00 0.00 40.91 2.90
2818 6758 7.439056 CAGAATTGCCTTTGTTGTACTTCAAAT 59.561 33.333 13.32 2.40 37.81 2.32
2850 6790 8.985315 TGCTAGTAGGCAGTAGTACTATTTAA 57.015 34.615 5.75 0.00 37.29 1.52
2888 6837 3.327464 CACCAAACCAATTTCAGGGGAAT 59.673 43.478 0.00 0.00 31.93 3.01
2923 6974 9.094578 AGATTTGTTAGCTAGATGAGGCTATAA 57.905 33.333 0.00 0.00 40.16 0.98
2980 7032 3.056607 AGTGTATTTGAAGCCATGTTGCC 60.057 43.478 0.00 0.00 0.00 4.52
3048 7105 3.930229 CCACAGATTTTCACCAATGCATG 59.070 43.478 0.00 0.00 0.00 4.06
3049 7106 4.196626 CCACAGATTTTCACCAATGCAT 57.803 40.909 0.00 0.00 0.00 3.96
3050 7107 3.663995 CCACAGATTTTCACCAATGCA 57.336 42.857 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.