Multiple sequence alignment - TraesCS4A01G385800

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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 TraesCS4A01G385800 chr4A 100.000 2810 0 0 1 2810 662961914 662959105 0.000000e+00 5190
1 TraesCS4A01G385800 chr4A 91.823 746 45 9 1 739 523974674 523973938 0.000000e+00 1026
2 TraesCS4A01G385800 chr4A 82.779 331 43 12 1930 2249 662952646 662952319 1.650000e-72 283
3 TraesCS4A01G385800 chr7D 89.250 1386 96 20 932 2273 47820407 47819031 0.000000e+00 1685
4 TraesCS4A01G385800 chr7D 85.997 657 60 5 1069 1712 78315686 78315049 0.000000e+00 675
5 TraesCS4A01G385800 chr7D 88.136 531 51 6 2289 2810 528047787 528048314 3.070000e-174 621
6 TraesCS4A01G385800 chr7D 82.510 749 67 24 1283 1996 47848533 47847814 1.440000e-167 599
7 TraesCS4A01G385800 chr7D 90.200 449 34 7 791 1237 47848971 47848531 6.750000e-161 577
8 TraesCS4A01G385800 chr7D 82.749 371 43 8 1839 2188 47818727 47818357 7.560000e-81 311
9 TraesCS4A01G385800 chr7D 84.321 287 42 1 1990 2273 47847422 47847136 7.670000e-71 278
10 TraesCS4A01G385800 chr7A 87.046 1212 98 12 932 2100 50629291 50628096 0.000000e+00 1314
11 TraesCS4A01G385800 chr7A 85.124 1331 106 31 995 2273 50597871 50596581 0.000000e+00 1277
12 TraesCS4A01G385800 chr7A 91.935 744 42 12 1 736 273433713 273434446 0.000000e+00 1026
13 TraesCS4A01G385800 chr7A 85.194 412 37 4 1208 1604 81782306 81781904 4.360000e-108 401
14 TraesCS4A01G385800 chr7A 87.556 225 16 7 791 1010 50598107 50597890 1.670000e-62 250
15 TraesCS4A01G385800 chr7A 85.366 246 21 10 1839 2070 50596276 50596032 1.010000e-59 241
16 TraesCS4A01G385800 chrUn 90.010 1021 65 15 1283 2273 49641773 49640760 0.000000e+00 1286
17 TraesCS4A01G385800 chrUn 87.061 626 49 4 1283 1876 48707842 48707217 0.000000e+00 678
18 TraesCS4A01G385800 chrUn 86.422 626 53 4 1283 1876 48673671 48673046 0.000000e+00 656
19 TraesCS4A01G385800 chrUn 86.422 626 53 4 1283 1876 48731009 48730384 0.000000e+00 656
20 TraesCS4A01G385800 chrUn 86.422 626 53 4 1283 1876 188907146 188906521 0.000000e+00 656
21 TraesCS4A01G385800 chrUn 84.010 419 36 17 836 1237 48674073 48673669 9.500000e-100 374
22 TraesCS4A01G385800 chrUn 84.010 419 36 17 836 1237 48731411 48731007 9.500000e-100 374
23 TraesCS4A01G385800 chrUn 84.010 419 36 17 836 1237 188907548 188907144 9.500000e-100 374
24 TraesCS4A01G385800 chrUn 83.532 419 38 17 836 1237 48708244 48707840 2.060000e-96 363
25 TraesCS4A01G385800 chrUn 82.624 282 28 13 1839 2100 49640458 49640178 2.180000e-56 230
26 TraesCS4A01G385800 chrUn 80.488 164 14 9 1873 2031 48676811 48676661 2.960000e-20 110
27 TraesCS4A01G385800 chr3A 92.627 746 39 10 1 737 24544114 24543376 0.000000e+00 1059
28 TraesCS4A01G385800 chr3A 90.092 545 42 7 2274 2810 40592545 40593085 0.000000e+00 697
29 TraesCS4A01G385800 chr2A 90.698 731 51 11 12 736 396396518 396397237 0.000000e+00 957
30 TraesCS4A01G385800 chr2A 90.646 727 51 9 12 732 404686005 404685290 0.000000e+00 950
31 TraesCS4A01G385800 chr3B 90.450 733 53 9 12 739 186534116 186533396 0.000000e+00 950
32 TraesCS4A01G385800 chr3B 90.450 733 53 9 12 739 186542749 186542029 0.000000e+00 950
33 TraesCS4A01G385800 chr2B 93.528 618 24 6 126 736 27940173 27940781 0.000000e+00 905
34 TraesCS4A01G385800 chr2B 87.004 554 55 11 2269 2810 666737600 666737052 2.390000e-170 608
35 TraesCS4A01G385800 chr6B 89.315 730 60 11 12 736 70266151 70266867 0.000000e+00 900
36 TraesCS4A01G385800 chr2D 92.976 541 32 2 2274 2810 639541086 639540548 0.000000e+00 784
37 TraesCS4A01G385800 chr5D 91.667 528 34 5 2289 2810 7079276 7078753 0.000000e+00 723
38 TraesCS4A01G385800 chr5D 88.300 547 48 12 2274 2810 543430513 543431053 2.360000e-180 641
39 TraesCS4A01G385800 chr6A 88.826 528 50 4 2289 2810 74369717 74369193 8.490000e-180 640
40 TraesCS4A01G385800 chr4B 86.957 529 60 8 2285 2808 24054463 24054987 1.120000e-163 586
41 TraesCS4A01G385800 chr3D 86.447 546 61 8 2274 2810 549755564 549755023 1.120000e-163 586


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 TraesCS4A01G385800 chr4A 662959105 662961914 2809 True 5190.000000 5190 100.000000 1 2810 1 chr4A.!!$R3 2809
1 TraesCS4A01G385800 chr4A 523973938 523974674 736 True 1026.000000 1026 91.823000 1 739 1 chr4A.!!$R1 738
2 TraesCS4A01G385800 chr7D 47818357 47820407 2050 True 998.000000 1685 85.999500 932 2273 2 chr7D.!!$R2 1341
3 TraesCS4A01G385800 chr7D 78315049 78315686 637 True 675.000000 675 85.997000 1069 1712 1 chr7D.!!$R1 643
4 TraesCS4A01G385800 chr7D 528047787 528048314 527 False 621.000000 621 88.136000 2289 2810 1 chr7D.!!$F1 521
5 TraesCS4A01G385800 chr7D 47847136 47848971 1835 True 484.666667 599 85.677000 791 2273 3 chr7D.!!$R3 1482
6 TraesCS4A01G385800 chr7A 50628096 50629291 1195 True 1314.000000 1314 87.046000 932 2100 1 chr7A.!!$R1 1168
7 TraesCS4A01G385800 chr7A 273433713 273434446 733 False 1026.000000 1026 91.935000 1 736 1 chr7A.!!$F1 735
8 TraesCS4A01G385800 chr7A 50596032 50598107 2075 True 589.333333 1277 86.015333 791 2273 3 chr7A.!!$R3 1482
9 TraesCS4A01G385800 chrUn 49640178 49641773 1595 True 758.000000 1286 86.317000 1283 2273 2 chrUn.!!$R4 990
10 TraesCS4A01G385800 chrUn 48707217 48708244 1027 True 520.500000 678 85.296500 836 1876 2 chrUn.!!$R2 1040
11 TraesCS4A01G385800 chrUn 48730384 48731411 1027 True 515.000000 656 85.216000 836 1876 2 chrUn.!!$R3 1040
12 TraesCS4A01G385800 chrUn 188906521 188907548 1027 True 515.000000 656 85.216000 836 1876 2 chrUn.!!$R5 1040
13 TraesCS4A01G385800 chrUn 48673046 48676811 3765 True 380.000000 656 83.640000 836 2031 3 chrUn.!!$R1 1195
14 TraesCS4A01G385800 chr3A 24543376 24544114 738 True 1059.000000 1059 92.627000 1 737 1 chr3A.!!$R1 736
15 TraesCS4A01G385800 chr3A 40592545 40593085 540 False 697.000000 697 90.092000 2274 2810 1 chr3A.!!$F1 536
16 TraesCS4A01G385800 chr2A 396396518 396397237 719 False 957.000000 957 90.698000 12 736 1 chr2A.!!$F1 724
17 TraesCS4A01G385800 chr2A 404685290 404686005 715 True 950.000000 950 90.646000 12 732 1 chr2A.!!$R1 720
18 TraesCS4A01G385800 chr3B 186533396 186534116 720 True 950.000000 950 90.450000 12 739 1 chr3B.!!$R1 727
19 TraesCS4A01G385800 chr3B 186542029 186542749 720 True 950.000000 950 90.450000 12 739 1 chr3B.!!$R2 727
20 TraesCS4A01G385800 chr2B 27940173 27940781 608 False 905.000000 905 93.528000 126 736 1 chr2B.!!$F1 610
21 TraesCS4A01G385800 chr2B 666737052 666737600 548 True 608.000000 608 87.004000 2269 2810 1 chr2B.!!$R1 541
22 TraesCS4A01G385800 chr6B 70266151 70266867 716 False 900.000000 900 89.315000 12 736 1 chr6B.!!$F1 724
23 TraesCS4A01G385800 chr2D 639540548 639541086 538 True 784.000000 784 92.976000 2274 2810 1 chr2D.!!$R1 536
24 TraesCS4A01G385800 chr5D 7078753 7079276 523 True 723.000000 723 91.667000 2289 2810 1 chr5D.!!$R1 521
25 TraesCS4A01G385800 chr5D 543430513 543431053 540 False 641.000000 641 88.300000 2274 2810 1 chr5D.!!$F1 536
26 TraesCS4A01G385800 chr6A 74369193 74369717 524 True 640.000000 640 88.826000 2289 2810 1 chr6A.!!$R1 521
27 TraesCS4A01G385800 chr4B 24054463 24054987 524 False 586.000000 586 86.957000 2285 2808 1 chr4B.!!$F1 523
28 TraesCS4A01G385800 chr3D 549755023 549755564 541 True 586.000000 586 86.447000 2274 2810 1 chr3D.!!$R1 536

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
759 781 0.179092 GCTGGCATTTGAATCCTGGC 60.179 55.0 0.0 0.0 36.12 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 5273 1.001378 GAACGGCATATCCAATGCACC 60.001 52.381 11.69 0.0 46.21 5.01 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
29 33 7.147655 TGGCAGATTAGTAGCATATCTAATCCC 60.148 40.741 16.28 13.15 46.35 3.85
78 82 7.699391 CCTTGTGTAACTGAAAATGCTATCATG 59.301 37.037 0.00 0.00 38.04 3.07
103 107 8.849168 TGATTCAACAAACTGACAACAATCTAT 58.151 29.630 0.00 0.00 0.00 1.98
234 242 1.224069 CTCCACCAGCACAACTCACG 61.224 60.000 0.00 0.00 0.00 4.35
235 243 2.253758 CCACCAGCACAACTCACGG 61.254 63.158 0.00 0.00 0.00 4.94
332 343 3.568443 ACGCTTCCCCCTTTTTCTTTTA 58.432 40.909 0.00 0.00 0.00 1.52
509 524 8.150945 GCAAGAGATAGGTTGAGATTTACCATA 58.849 37.037 0.00 0.00 36.87 2.74
698 720 5.655974 TGGAACATTTGCATTTAGCTATCCA 59.344 36.000 0.00 0.00 45.94 3.41
732 754 6.318648 AGTTGATGCTCAAAACTGACAGTAAA 59.681 34.615 8.91 0.00 38.22 2.01
733 755 6.060028 TGATGCTCAAAACTGACAGTAAAC 57.940 37.500 8.91 0.00 0.00 2.01
734 756 5.588246 TGATGCTCAAAACTGACAGTAAACA 59.412 36.000 8.91 2.64 0.00 2.83
735 757 5.484173 TGCTCAAAACTGACAGTAAACAG 57.516 39.130 8.91 4.54 39.65 3.16
737 759 4.201910 GCTCAAAACTGACAGTAAACAGCA 60.202 41.667 8.91 0.00 37.61 4.41
738 760 5.484173 TCAAAACTGACAGTAAACAGCAG 57.516 39.130 8.91 0.00 37.61 4.24
740 762 2.550830 ACTGACAGTAAACAGCAGGG 57.449 50.000 6.24 0.00 37.61 4.45
741 763 1.160137 CTGACAGTAAACAGCAGGGC 58.840 55.000 0.00 0.00 0.00 5.19
742 764 0.764890 TGACAGTAAACAGCAGGGCT 59.235 50.000 0.00 0.00 40.77 5.19
751 773 2.441959 AGCAGGGCTGGCATTTGA 59.558 55.556 2.88 0.00 37.57 2.69
752 774 1.228956 AGCAGGGCTGGCATTTGAA 60.229 52.632 2.88 0.00 37.57 2.69
753 775 0.616679 AGCAGGGCTGGCATTTGAAT 60.617 50.000 2.88 0.00 37.57 2.57
755 777 0.462789 CAGGGCTGGCATTTGAATCC 59.537 55.000 2.88 0.00 0.00 3.01
756 778 0.337428 AGGGCTGGCATTTGAATCCT 59.663 50.000 2.88 0.00 0.00 3.24
757 779 0.462789 GGGCTGGCATTTGAATCCTG 59.537 55.000 2.88 0.00 0.00 3.86
758 780 0.462789 GGCTGGCATTTGAATCCTGG 59.537 55.000 0.00 0.00 0.00 4.45
759 781 0.179092 GCTGGCATTTGAATCCTGGC 60.179 55.000 0.00 0.00 36.12 4.85
761 783 0.977108 TGGCATTTGAATCCTGGCCC 60.977 55.000 0.00 0.00 40.64 5.80
762 784 1.689243 GGCATTTGAATCCTGGCCCC 61.689 60.000 0.00 0.00 35.42 5.80
763 785 0.688749 GCATTTGAATCCTGGCCCCT 60.689 55.000 0.00 0.00 0.00 4.79
764 786 1.406903 CATTTGAATCCTGGCCCCTC 58.593 55.000 0.00 0.00 0.00 4.30
765 787 0.262876 ATTTGAATCCTGGCCCCTCC 59.737 55.000 0.00 0.00 0.00 4.30
766 788 0.850883 TTTGAATCCTGGCCCCTCCT 60.851 55.000 0.00 0.00 35.26 3.69
767 789 1.574526 TTGAATCCTGGCCCCTCCTG 61.575 60.000 0.00 0.00 35.26 3.86
772 794 2.935481 CTGGCCCCTCCTGGACAA 60.935 66.667 0.00 0.00 44.80 3.18
773 795 2.451493 TGGCCCCTCCTGGACAAA 60.451 61.111 0.00 0.00 41.70 2.83
774 796 1.856873 TGGCCCCTCCTGGACAAAT 60.857 57.895 0.00 0.00 41.70 2.32
777 799 1.615262 CCCCTCCTGGACAAATCCC 59.385 63.158 0.00 0.00 45.59 3.85
780 802 1.224592 CTCCTGGACAAATCCCGGG 59.775 63.158 16.85 16.85 46.87 5.73
781 803 1.540367 TCCTGGACAAATCCCGGGT 60.540 57.895 22.86 4.84 46.87 5.28
782 804 1.137594 TCCTGGACAAATCCCGGGTT 61.138 55.000 22.86 9.98 46.87 4.11
783 805 0.251608 CCTGGACAAATCCCGGGTTT 60.252 55.000 22.86 16.72 43.96 3.27
784 806 1.004979 CCTGGACAAATCCCGGGTTTA 59.995 52.381 22.86 0.06 43.96 2.01
785 807 2.555670 CCTGGACAAATCCCGGGTTTAA 60.556 50.000 22.86 0.00 43.96 1.52
786 808 3.158676 CTGGACAAATCCCGGGTTTAAA 58.841 45.455 22.86 0.00 45.59 1.52
787 809 3.573695 TGGACAAATCCCGGGTTTAAAA 58.426 40.909 22.86 0.00 45.59 1.52
788 810 3.321396 TGGACAAATCCCGGGTTTAAAAC 59.679 43.478 22.86 10.68 45.59 2.43
789 811 3.306225 GGACAAATCCCGGGTTTAAAACC 60.306 47.826 22.86 12.63 44.32 3.27
843 2747 1.296715 CGGAACTTGGTAGCCTGCT 59.703 57.895 0.00 0.00 0.00 4.24
850 2754 1.026182 TTGGTAGCCTGCTTGCATCG 61.026 55.000 0.00 0.00 0.00 3.84
851 2755 1.153369 GGTAGCCTGCTTGCATCGA 60.153 57.895 0.00 0.00 0.00 3.59
852 2756 0.744414 GGTAGCCTGCTTGCATCGAA 60.744 55.000 0.00 0.00 0.00 3.71
854 2758 0.462581 TAGCCTGCTTGCATCGAAGG 60.463 55.000 6.24 6.24 0.00 3.46
855 2759 2.796651 CCTGCTTGCATCGAAGGC 59.203 61.111 5.56 5.56 0.00 4.35
859 2766 0.672091 TGCTTGCATCGAAGGCGTTA 60.672 50.000 7.77 0.00 38.98 3.18
884 2791 6.262273 ACGTATTCAGTTTCCAACAGAACAAT 59.738 34.615 0.00 0.00 39.28 2.71
916 2831 3.732219 CGTAGCAGTAGTCACGTGAAAAA 59.268 43.478 21.95 5.69 0.00 1.94
951 2874 0.321564 AGCACGCACCTAGATTGCAA 60.322 50.000 0.00 0.00 40.20 4.08
952 2875 0.521291 GCACGCACCTAGATTGCAAA 59.479 50.000 1.71 0.00 40.20 3.68
978 2901 6.128282 CGATGCCATTATAAATGTACTCACCC 60.128 42.308 0.00 0.00 0.00 4.61
1033 2989 1.081513 TCCCTAGCTTCCCCCAAACTA 59.918 52.381 0.00 0.00 0.00 2.24
1034 2990 1.490910 CCCTAGCTTCCCCCAAACTAG 59.509 57.143 0.00 0.00 0.00 2.57
1140 3102 3.545481 GTCGCCGTCGCATGTCAG 61.545 66.667 0.00 0.00 35.26 3.51
1149 3117 2.821366 GCATGTCAGGGACAGCGG 60.821 66.667 5.25 0.00 46.04 5.52
1239 3207 1.066430 ACAATACATCGCCCAAGACGT 60.066 47.619 0.00 0.00 0.00 4.34
1251 3219 0.770590 CAAGACGTCGACGACAACAG 59.229 55.000 41.52 22.03 43.02 3.16
1281 3249 1.727467 GACAACAGCAACCGCAACT 59.273 52.632 0.00 0.00 42.27 3.16
1289 3257 3.000041 CAGCAACCGCAACTAGAATACA 59.000 45.455 0.00 0.00 42.27 2.29
1297 3265 2.190981 CAACTAGAATACACCGACGCC 58.809 52.381 0.00 0.00 0.00 5.68
1317 3285 0.093705 CTGTTTCGCGAGCTTACTGC 59.906 55.000 9.59 0.00 43.29 4.40
1339 3307 4.209703 GCCGTCGATTTTAATTCCGATGTA 59.790 41.667 0.00 0.00 36.61 2.29
1453 3436 0.605589 GCCCGATCTGTATGGAGGAG 59.394 60.000 0.00 0.00 0.00 3.69
1458 3441 1.271102 GATCTGTATGGAGGAGGACGC 59.729 57.143 0.00 0.00 0.00 5.19
1465 3448 2.423898 GGAGGAGGACGCCGATGAA 61.424 63.158 0.00 0.00 0.00 2.57
1672 3664 2.502295 GGACTTGAGGATGCCATCATC 58.498 52.381 12.23 12.23 46.46 2.92
1716 3721 6.931281 GCATCTTATGATAGGTCTTAGTTGCA 59.069 38.462 0.00 0.00 0.00 4.08
1775 3797 4.997395 TGTTGGATGTTTGCTCTTAGTCTC 59.003 41.667 0.00 0.00 0.00 3.36
1821 3847 4.098349 TCAGCAAACAAATCATATGCTCCC 59.902 41.667 0.00 0.00 44.97 4.30
1849 4626 9.860898 CCTGATGTCTCGAAATGTAATCATATA 57.139 33.333 0.00 0.00 33.49 0.86
1886 4672 9.739276 TGTTCCTCATCATGTTTAATTACTCTT 57.261 29.630 0.00 0.00 0.00 2.85
1913 4699 5.075493 ACTGAGATGCTTTGAACCTTTGAT 58.925 37.500 0.00 0.00 0.00 2.57
1914 4700 5.048224 ACTGAGATGCTTTGAACCTTTGATG 60.048 40.000 0.00 0.00 0.00 3.07
1919 4705 8.757982 AGATGCTTTGAACCTTTGATGTATAT 57.242 30.769 0.00 0.00 0.00 0.86
2061 5248 7.777440 AGAATCCATAGGAAGAAATTCCAACTC 59.223 37.037 9.55 0.00 43.54 3.01
2064 5251 7.470192 TCCATAGGAAGAAATTCCAACTCTTT 58.530 34.615 9.55 0.00 43.54 2.52
2068 5255 5.600069 AGGAAGAAATTCCAACTCTTTTGCT 59.400 36.000 9.55 0.00 43.54 3.91
2071 5258 8.090831 GGAAGAAATTCCAACTCTTTTGCTTAT 58.909 33.333 2.14 0.00 40.79 1.73
2086 5273 8.671921 TCTTTTGCTTATAGAAAAGAGCATCAG 58.328 33.333 0.00 4.49 43.83 2.90
2101 5288 3.570926 CATCAGGTGCATTGGATATGC 57.429 47.619 2.90 2.90 44.76 3.14
2102 5289 1.985473 TCAGGTGCATTGGATATGCC 58.015 50.000 7.23 0.00 43.94 4.40
2129 5316 3.003275 TGAATCGACCAAAAGCACTTGAC 59.997 43.478 0.00 0.00 0.00 3.18
2142 5329 2.610374 GCACTTGACCTTGACACGTTTA 59.390 45.455 0.00 0.00 0.00 2.01
2147 5334 5.011329 ACTTGACCTTGACACGTTTATCCTA 59.989 40.000 0.00 0.00 0.00 2.94
2153 5340 3.592059 TGACACGTTTATCCTACCTTGC 58.408 45.455 0.00 0.00 0.00 4.01
2183 5370 2.406024 CAGCTGTAAAACAATTGCGCAG 59.594 45.455 11.31 0.87 0.00 5.18
2213 5400 2.642154 TCCTTGCCCGTAAAAACAGA 57.358 45.000 0.00 0.00 0.00 3.41
2238 5425 2.641815 GAGAGATGCATACCTCCCCAAT 59.358 50.000 13.91 0.00 0.00 3.16
2239 5426 3.840666 GAGAGATGCATACCTCCCCAATA 59.159 47.826 13.91 0.00 0.00 1.90
2454 5752 1.194781 TCAGAGCCACCTCTTCCCAC 61.195 60.000 0.00 0.00 46.16 4.61
2468 5774 0.613260 TCCCACACATCTAGCCACAC 59.387 55.000 0.00 0.00 0.00 3.82
2469 5775 0.392998 CCCACACATCTAGCCACACC 60.393 60.000 0.00 0.00 0.00 4.16
2470 5776 0.392998 CCACACATCTAGCCACACCC 60.393 60.000 0.00 0.00 0.00 4.61
2471 5777 0.392998 CACACATCTAGCCACACCCC 60.393 60.000 0.00 0.00 0.00 4.95
2495 5802 4.396166 CCAAAACCCTAGATCACACATCAC 59.604 45.833 0.00 0.00 0.00 3.06
2595 5902 1.216710 CCTCTGGAAGACGCAGGTC 59.783 63.158 0.00 0.00 38.67 3.85
2647 5954 1.816863 GCTCCGGGACAACTCTGACA 61.817 60.000 0.00 0.00 0.00 3.58
2698 6005 4.308458 CGGACAAGACCACGGCCA 62.308 66.667 2.24 0.00 0.00 5.36
2719 6026 1.053424 AGAGCCGAACCCTTTGTACA 58.947 50.000 0.00 0.00 0.00 2.90
2761 6268 4.293494 TCAGCAGGTCCTTTCATATCTCT 58.707 43.478 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.607600 AGATGCGGGATTAGATATGCTACTAA 59.392 38.462 0.00 0.00 33.97 2.24
29 33 1.303799 ACTTCAGCCTTGCAGATGCG 61.304 55.000 0.00 0.00 45.83 4.73
109 115 8.316946 TCATGGAGCTATCTGATTTATTAGTGG 58.683 37.037 0.00 0.00 0.00 4.00
201 209 5.880332 TGCTGGTGGAGACTTGAAAATATAC 59.120 40.000 0.00 0.00 0.00 1.47
234 242 6.581712 ACATTGGAATGCCATTATTTGTACC 58.418 36.000 0.00 0.00 45.46 3.34
235 243 8.413229 AGTACATTGGAATGCCATTATTTGTAC 58.587 33.333 16.62 16.62 45.46 2.90
281 291 1.542915 CTCCTGGACCAGCATTTTGTG 59.457 52.381 16.72 0.00 0.00 3.33
456 471 1.207089 CGTTCCTGATCTGGCAACCTA 59.793 52.381 13.60 0.00 0.00 3.08
624 646 5.699458 ACGACGTTCCTTCTGTAATGAATTT 59.301 36.000 0.00 0.00 0.00 1.82
625 647 5.120208 CACGACGTTCCTTCTGTAATGAATT 59.880 40.000 0.00 0.00 0.00 2.17
626 648 4.625742 CACGACGTTCCTTCTGTAATGAAT 59.374 41.667 0.00 0.00 0.00 2.57
724 746 3.633361 AGCCCTGCTGTTTACTGTC 57.367 52.632 0.00 0.00 37.57 3.51
734 756 0.616679 ATTCAAATGCCAGCCCTGCT 60.617 50.000 0.00 0.00 40.77 4.24
735 757 0.179092 GATTCAAATGCCAGCCCTGC 60.179 55.000 0.00 0.00 0.00 4.85
737 759 0.337428 AGGATTCAAATGCCAGCCCT 59.663 50.000 0.00 0.00 0.00 5.19
738 760 0.462789 CAGGATTCAAATGCCAGCCC 59.537 55.000 0.00 0.00 0.00 5.19
740 762 0.179092 GCCAGGATTCAAATGCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
741 763 0.462789 GGCCAGGATTCAAATGCCAG 59.537 55.000 0.00 0.00 38.73 4.85
742 764 0.977108 GGGCCAGGATTCAAATGCCA 60.977 55.000 4.39 0.00 40.64 4.92
743 765 1.689243 GGGGCCAGGATTCAAATGCC 61.689 60.000 4.39 0.00 38.16 4.40
744 766 0.688749 AGGGGCCAGGATTCAAATGC 60.689 55.000 4.39 0.00 0.00 3.56
745 767 1.406903 GAGGGGCCAGGATTCAAATG 58.593 55.000 4.39 0.00 0.00 2.32
747 769 0.850883 AGGAGGGGCCAGGATTCAAA 60.851 55.000 4.39 0.00 40.02 2.69
749 771 2.002977 CAGGAGGGGCCAGGATTCA 61.003 63.158 4.39 0.00 40.02 2.57
751 773 2.697644 CCAGGAGGGGCCAGGATT 60.698 66.667 4.39 0.00 45.96 3.01
752 774 3.710631 TCCAGGAGGGGCCAGGAT 61.711 66.667 4.39 0.00 46.52 3.24
755 777 1.867595 ATTTGTCCAGGAGGGGCCAG 61.868 60.000 4.39 0.00 42.20 4.85
756 778 1.856873 ATTTGTCCAGGAGGGGCCA 60.857 57.895 4.39 0.00 42.20 5.36
757 779 1.076705 GATTTGTCCAGGAGGGGCC 60.077 63.158 0.00 0.00 42.20 5.80
758 780 1.076705 GGATTTGTCCAGGAGGGGC 60.077 63.158 0.00 0.00 43.63 5.80
759 781 1.615262 GGGATTTGTCCAGGAGGGG 59.385 63.158 0.00 0.00 37.22 4.79
761 783 1.224592 CCGGGATTTGTCCAGGAGG 59.775 63.158 7.75 0.00 46.19 4.30
762 784 1.224592 CCCGGGATTTGTCCAGGAG 59.775 63.158 18.48 2.38 46.19 3.69
763 785 1.137594 AACCCGGGATTTGTCCAGGA 61.138 55.000 32.02 0.00 46.19 3.86
764 786 0.251608 AAACCCGGGATTTGTCCAGG 60.252 55.000 32.02 6.66 43.48 4.45
765 787 2.500392 TAAACCCGGGATTTGTCCAG 57.500 50.000 32.02 0.00 0.00 3.86
766 788 2.973983 TTAAACCCGGGATTTGTCCA 57.026 45.000 32.02 2.43 0.00 4.02
767 789 3.306225 GGTTTTAAACCCGGGATTTGTCC 60.306 47.826 32.02 17.56 46.12 4.02
768 790 3.916761 GGTTTTAAACCCGGGATTTGTC 58.083 45.455 32.02 12.64 46.12 3.18
780 802 6.635166 TTTTTCACGCTCTTGGTTTTAAAC 57.365 33.333 0.00 0.00 0.00 2.01
800 822 1.183030 GGGCCGGCCTACAACTTTTT 61.183 55.000 42.70 0.00 36.10 1.94
806 828 1.529796 CTATTGGGCCGGCCTACAA 59.470 57.895 42.70 36.36 36.10 2.41
817 839 2.561569 CTACCAAGTTCCGCTATTGGG 58.438 52.381 7.98 0.00 46.33 4.12
843 2747 0.668096 ACGTAACGCCTTCGATGCAA 60.668 50.000 8.02 0.00 39.41 4.08
850 2754 4.201656 GGAAACTGAATACGTAACGCCTTC 60.202 45.833 0.00 0.00 0.00 3.46
851 2755 3.681417 GGAAACTGAATACGTAACGCCTT 59.319 43.478 0.00 0.00 0.00 4.35
852 2756 3.256558 GGAAACTGAATACGTAACGCCT 58.743 45.455 0.00 0.00 0.00 5.52
854 2758 4.388790 GTTGGAAACTGAATACGTAACGC 58.611 43.478 0.00 0.00 45.32 4.84
884 2791 2.210961 CTACTGCTACGATCGAGTCCA 58.789 52.381 24.34 11.63 0.00 4.02
916 2831 2.857744 GCTAGTGGCGGCGTAGGAT 61.858 63.158 9.37 0.00 0.00 3.24
951 2874 7.041372 GGTGAGTACATTTATAATGGCATCGTT 60.041 37.037 0.00 0.00 0.00 3.85
952 2875 6.426937 GGTGAGTACATTTATAATGGCATCGT 59.573 38.462 0.00 0.00 0.00 3.73
1001 2924 1.528542 CTAGGGACGGGAGCGATCA 60.529 63.158 1.84 0.00 0.00 2.92
1034 2990 1.223763 GATTGGAACGGGAGGGGAC 59.776 63.158 0.00 0.00 0.00 4.46
1130 3092 2.265739 GCTGTCCCTGACATGCGA 59.734 61.111 0.00 0.00 41.94 5.10
1149 3117 1.443194 TAGAACAAGTCGTCGGCGC 60.443 57.895 3.52 0.00 38.14 6.53
1239 3207 2.028484 GGTGCCTGTTGTCGTCGA 59.972 61.111 0.00 0.00 0.00 4.20
1281 3249 0.742505 CAGGGCGTCGGTGTATTCTA 59.257 55.000 0.00 0.00 0.00 2.10
1297 3265 0.716108 CAGTAAGCTCGCGAAACAGG 59.284 55.000 11.33 0.00 0.00 4.00
1317 3285 4.789095 ACATCGGAATTAAAATCGACGG 57.211 40.909 0.00 0.00 34.40 4.79
1339 3307 3.321648 TCTGTGTCCGCCATGGCT 61.322 61.111 33.07 0.00 39.32 4.75
1396 3367 2.932234 CGCCTCCACGGTCTTCAGT 61.932 63.158 0.00 0.00 34.25 3.41
1444 3427 1.153061 ATCGGCGTCCTCCTCCATA 59.847 57.895 6.85 0.00 0.00 2.74
1453 3436 3.255379 GCGTCTTCATCGGCGTCC 61.255 66.667 6.85 0.00 0.00 4.79
1458 3441 2.202610 TCGCTGCGTCTTCATCGG 60.203 61.111 22.48 0.00 0.00 4.18
1655 3647 2.224233 ACTCGATGATGGCATCCTCAAG 60.224 50.000 25.67 21.14 46.55 3.02
1672 3664 1.267235 GCAATCTCACGCATGAACTCG 60.267 52.381 0.00 0.00 33.30 4.18
1716 3721 5.360591 CACAACCCTAATTTCGCTAGAGAT 58.639 41.667 0.00 0.00 0.00 2.75
1821 3847 5.812127 TGATTACATTTCGAGACATCAGGTG 59.188 40.000 0.00 0.00 0.00 4.00
1849 4626 7.520451 CATGATGAGGAACATGTGGATAAAT 57.480 36.000 0.00 0.00 39.56 1.40
1886 4672 6.959639 AAGGTTCAAAGCATCTCAGTTTTA 57.040 33.333 0.00 0.00 0.00 1.52
1919 4705 7.541783 CAGAACATCTCACACTCAAAAACAAAA 59.458 33.333 0.00 0.00 0.00 2.44
2061 5248 7.914346 CCTGATGCTCTTTTCTATAAGCAAAAG 59.086 37.037 0.00 2.76 46.80 2.27
2064 5251 6.317140 CACCTGATGCTCTTTTCTATAAGCAA 59.683 38.462 0.00 0.00 46.80 3.91
2086 5273 1.001378 GAACGGCATATCCAATGCACC 60.001 52.381 11.69 0.00 46.21 5.01
2101 5288 2.412847 GCTTTTGGTCGATTCAGAACGG 60.413 50.000 0.00 0.00 0.00 4.44
2102 5289 2.223144 TGCTTTTGGTCGATTCAGAACG 59.777 45.455 0.00 0.00 0.00 3.95
2129 5316 4.467198 AGGTAGGATAAACGTGTCAAGG 57.533 45.455 0.00 0.00 0.00 3.61
2142 5329 4.335594 GCTGATTTTTACGCAAGGTAGGAT 59.664 41.667 0.00 0.00 46.39 3.24
2147 5334 2.884639 ACAGCTGATTTTTACGCAAGGT 59.115 40.909 23.35 0.00 46.39 3.50
2153 5340 7.735586 GCAATTGTTTTACAGCTGATTTTTACG 59.264 33.333 23.35 1.17 0.00 3.18
2183 5370 2.202349 GCAAGGATGCGCGTGTTC 60.202 61.111 6.97 1.95 43.83 3.18
2213 5400 2.564947 GGGAGGTATGCATCTCTCGATT 59.435 50.000 0.19 0.00 0.00 3.34
2222 5409 4.041691 GTGTAGTATTGGGGAGGTATGCAT 59.958 45.833 3.79 3.79 0.00 3.96
2238 5425 2.832643 TCCCGGGAAGATGTGTAGTA 57.167 50.000 24.50 0.00 0.00 1.82
2239 5426 1.946984 TTCCCGGGAAGATGTGTAGT 58.053 50.000 32.53 0.00 0.00 2.73
2265 5452 7.473511 GCAATGGTATATTCTAACAGTCTCCCT 60.474 40.741 0.00 0.00 0.00 4.20
2454 5752 1.224592 GGGGGTGTGGCTAGATGTG 59.775 63.158 0.00 0.00 0.00 3.21
2469 5775 1.638589 TGTGATCTAGGGTTTTGGGGG 59.361 52.381 0.00 0.00 0.00 5.40
2470 5776 2.041081 TGTGTGATCTAGGGTTTTGGGG 59.959 50.000 0.00 0.00 0.00 4.96
2471 5777 3.433306 TGTGTGATCTAGGGTTTTGGG 57.567 47.619 0.00 0.00 0.00 4.12
2495 5802 1.135915 CTGAGGAAGACATGGAGACGG 59.864 57.143 0.00 0.00 0.00 4.79
2615 5922 3.712907 GGAGCCCGGTAACCTGCA 61.713 66.667 0.00 0.00 0.00 4.41
2698 6005 2.835764 TGTACAAAGGGTTCGGCTCTAT 59.164 45.455 0.00 0.00 0.00 1.98
2761 6268 3.510459 TCTCTGGAGACATGGAGTTGAA 58.490 45.455 0.00 0.00 41.51 2.69


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

AutoCloner maintained by Alex Coulton.