Multiple sequence alignment - TraesCS3D01G303500

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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 TraesCS3D01G303500 chr3D 100.000 4441 0 0 1 4441 418384587 418380147 0.000000e+00 8202.0
1 TraesCS3D01G303500 chr3D 90.566 636 58 2 3807 4441 108510336 108509702 0.000000e+00 841.0
2 TraesCS3D01G303500 chr3D 92.857 84 5 1 3440 3522 418381075 418380992 2.170000e-23 121.0
3 TraesCS3D01G303500 chr3D 92.857 84 5 1 3513 3596 418381148 418381066 2.170000e-23 121.0
4 TraesCS3D01G303500 chr7B 93.787 1835 58 5 1088 2884 671264857 671263041 0.000000e+00 2706.0
5 TraesCS3D01G303500 chr7B 94.444 90 4 1 2798 2887 325466367 325466279 2.150000e-28 137.0
6 TraesCS3D01G303500 chr7B 87.037 108 10 3 2774 2879 700869230 700869125 7.800000e-23 119.0
7 TraesCS3D01G303500 chr7B 82.014 139 17 7 3381 3517 616429166 616429298 1.310000e-20 111.0
8 TraesCS3D01G303500 chr5B 93.818 1828 49 10 1088 2875 75081922 75083725 0.000000e+00 2691.0
9 TraesCS3D01G303500 chr5B 93.706 1827 57 7 1088 2875 67027563 67025756 0.000000e+00 2684.0
10 TraesCS3D01G303500 chr5B 96.037 1312 36 2 1088 2399 108858892 108860187 0.000000e+00 2121.0
11 TraesCS3D01G303500 chr5B 96.450 1014 27 4 1 1013 67028560 67027555 0.000000e+00 1664.0
12 TraesCS3D01G303500 chr5B 95.365 1014 36 6 1 1013 75080927 75081930 0.000000e+00 1602.0
13 TraesCS3D01G303500 chr5B 89.564 642 66 1 3801 4441 339453994 339454635 0.000000e+00 813.0
14 TraesCS3D01G303500 chr5B 93.651 63 2 2 2765 2827 629142877 629142937 4.730000e-15 93.5
15 TraesCS3D01G303500 chr3B 93.651 1827 57 8 1088 2877 154422215 154420411 0.000000e+00 2676.0
16 TraesCS3D01G303500 chr3B 93.195 1837 49 13 1088 2882 10051317 10049515 0.000000e+00 2630.0
17 TraesCS3D01G303500 chr3B 93.071 1833 61 11 1088 2878 151116317 151114509 0.000000e+00 2621.0
18 TraesCS3D01G303500 chr3B 96.565 1019 26 8 1 1013 154423222 154422207 0.000000e+00 1679.0
19 TraesCS3D01G303500 chr3B 96.457 1016 27 5 1 1013 10052318 10051309 0.000000e+00 1668.0
20 TraesCS3D01G303500 chr3B 95.957 1014 30 6 1 1013 151117312 151116309 0.000000e+00 1635.0
21 TraesCS3D01G303500 chr3B 95.356 1012 40 6 1 1009 204205753 204206760 0.000000e+00 1602.0
22 TraesCS3D01G303500 chr3B 93.200 500 21 2 2391 2878 204218036 204218534 0.000000e+00 723.0
23 TraesCS3D01G303500 chr3B 92.905 451 23 6 3153 3601 544778646 544778203 0.000000e+00 647.0
24 TraesCS3D01G303500 chr3B 92.219 347 13 5 2877 3223 544778944 544778612 3.110000e-131 479.0
25 TraesCS3D01G303500 chr3B 98.837 86 1 0 1007 1092 752216473 752216558 2.140000e-33 154.0
26 TraesCS3D01G303500 chr3B 97.701 87 2 0 1005 1091 805351692 805351606 2.770000e-32 150.0
27 TraesCS3D01G303500 chr3B 91.667 84 6 1 3440 3522 544778291 544778208 1.010000e-21 115.0
28 TraesCS3D01G303500 chr2B 93.330 1829 60 11 1088 2877 480006965 480008770 0.000000e+00 2645.0
29 TraesCS3D01G303500 chr2B 95.661 1014 32 8 1 1013 480005971 480006973 0.000000e+00 1618.0
30 TraesCS3D01G303500 chr1D 94.509 1730 49 5 1089 2793 492938535 492940243 0.000000e+00 2627.0
31 TraesCS3D01G303500 chr1D 100.000 34 0 0 3767 3800 206072060 206072093 3.710000e-06 63.9
32 TraesCS3D01G303500 chr1B 93.017 1833 62 9 1088 2879 630554025 630552218 0.000000e+00 2615.0
33 TraesCS3D01G303500 chr1B 91.334 1731 94 20 1088 2793 179140427 179138728 0.000000e+00 2314.0
34 TraesCS3D01G303500 chr1B 87.333 150 19 0 3615 3764 672415467 672415616 5.910000e-39 172.0
35 TraesCS3D01G303500 chr1B 94.681 94 5 0 1000 1093 668672140 668672047 3.580000e-31 147.0
36 TraesCS3D01G303500 chr1B 100.000 34 0 0 3767 3800 188809133 188809100 3.710000e-06 63.9
37 TraesCS3D01G303500 chr4B 92.232 1828 56 15 1090 2878 561749588 561747808 0.000000e+00 2510.0
38 TraesCS3D01G303500 chr4B 95.374 1016 40 5 1 1013 561750593 561749582 0.000000e+00 1609.0
39 TraesCS3D01G303500 chr4B 96.667 90 3 0 1005 1094 29271836 29271925 2.770000e-32 150.0
40 TraesCS3D01G303500 chr4B 86.441 118 9 5 2765 2877 277410121 277410006 6.030000e-24 122.0
41 TraesCS3D01G303500 chr4B 100.000 34 0 0 3767 3800 243809212 243809245 3.710000e-06 63.9
42 TraesCS3D01G303500 chr2A 93.125 1731 65 20 1088 2793 191975140 191976841 0.000000e+00 2488.0
43 TraesCS3D01G303500 chr2A 88.816 152 17 0 3615 3766 207411183 207411032 2.110000e-43 187.0
44 TraesCS3D01G303500 chr2A 91.589 107 5 4 1001 1106 628781015 628780912 1.290000e-30 145.0
45 TraesCS3D01G303500 chr6B 95.579 1312 37 2 1088 2399 678822344 678823634 0.000000e+00 2082.0
46 TraesCS3D01G303500 chr6B 95.122 1312 45 3 1088 2399 678841580 678842872 0.000000e+00 2050.0
47 TraesCS3D01G303500 chr6B 96.660 1018 28 5 1 1013 678840572 678841588 0.000000e+00 1687.0
48 TraesCS3D01G303500 chr6B 91.960 597 47 1 3846 4441 179945538 179946134 0.000000e+00 835.0
49 TraesCS3D01G303500 chr6B 88.889 153 17 0 3615 3767 179945361 179945513 5.860000e-44 189.0
50 TraesCS3D01G303500 chr6B 95.699 93 3 1 1007 1098 471127632 471127540 9.950000e-32 148.0
51 TraesCS3D01G303500 chr6B 100.000 34 0 0 3767 3800 22425723 22425690 3.710000e-06 63.9
52 TraesCS3D01G303500 chr6B 100.000 34 0 0 3767 3800 213356960 213356927 3.710000e-06 63.9
53 TraesCS3D01G303500 chr6B 100.000 34 0 0 3767 3800 439930907 439930940 3.710000e-06 63.9
54 TraesCS3D01G303500 chr6D 91.181 703 31 15 2120 2793 429978060 429977360 0.000000e+00 926.0
55 TraesCS3D01G303500 chr6D 88.158 152 17 1 3615 3766 53771025 53770875 3.530000e-41 180.0
56 TraesCS3D01G303500 chr2D 92.356 641 45 3 3804 4441 384835940 384835301 0.000000e+00 909.0
57 TraesCS3D01G303500 chr2D 90.850 153 14 0 3615 3767 384836096 384835944 5.820000e-49 206.0
58 TraesCS3D01G303500 chr2D 89.404 151 16 0 3616 3766 639513356 639513506 1.630000e-44 191.0
59 TraesCS3D01G303500 chr2D 89.362 141 15 0 3627 3767 499718487 499718347 1.270000e-40 178.0
60 TraesCS3D01G303500 chr2D 98.864 88 1 0 1006 1093 476839036 476839123 1.650000e-34 158.0
61 TraesCS3D01G303500 chr2D 97.368 38 0 1 3767 3803 121254133 121254096 3.710000e-06 63.9
62 TraesCS3D01G303500 chr7D 91.108 641 52 5 3804 4441 185195615 185194977 0.000000e+00 863.0
63 TraesCS3D01G303500 chr7D 89.736 643 62 4 3801 4441 121186704 121187344 0.000000e+00 819.0
64 TraesCS3D01G303500 chr7A 89.969 638 60 4 3804 4439 613346295 613345660 0.000000e+00 821.0
65 TraesCS3D01G303500 chr7A 88.571 105 10 2 1007 1111 679814616 679814718 4.660000e-25 126.0
66 TraesCS3D01G303500 chr5D 89.531 640 63 4 3804 4441 249004009 249003372 0.000000e+00 808.0
67 TraesCS3D01G303500 chr5D 100.000 34 0 0 3767 3800 6201500 6201533 3.710000e-06 63.9
68 TraesCS3D01G303500 chr5D 100.000 34 0 0 3767 3800 240137485 240137452 3.710000e-06 63.9
69 TraesCS3D01G303500 chr4D 89.465 636 64 3 3807 4441 488671438 488670805 0.000000e+00 800.0
70 TraesCS3D01G303500 chr4D 92.208 154 12 0 3614 3767 488671598 488671445 7.480000e-53 219.0
71 TraesCS3D01G303500 chr6A 87.500 152 19 0 3615 3766 377726255 377726406 4.570000e-40 176.0
72 TraesCS3D01G303500 chrUn 98.837 86 1 0 1007 1092 335557649 335557734 2.140000e-33 154.0
73 TraesCS3D01G303500 chrUn 87.288 118 10 4 1002 1114 2693320 2693203 3.600000e-26 130.0
74 TraesCS3D01G303500 chr4A 98.837 86 1 0 1007 1092 632934457 632934372 2.140000e-33 154.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G303500 chr3D 418380147 418384587 4440 True 2814.666667 8202 95.238000 1 4441 3 chr3D.!!$R2 4440
1 TraesCS3D01G303500 chr3D 108509702 108510336 634 True 841.000000 841 90.566000 3807 4441 1 chr3D.!!$R1 634
2 TraesCS3D01G303500 chr7B 671263041 671264857 1816 True 2706.000000 2706 93.787000 1088 2884 1 chr7B.!!$R2 1796
3 TraesCS3D01G303500 chr5B 67025756 67028560 2804 True 2174.000000 2684 95.078000 1 2875 2 chr5B.!!$R1 2874
4 TraesCS3D01G303500 chr5B 75080927 75083725 2798 False 2146.500000 2691 94.591500 1 2875 2 chr5B.!!$F4 2874
5 TraesCS3D01G303500 chr5B 108858892 108860187 1295 False 2121.000000 2121 96.037000 1088 2399 1 chr5B.!!$F1 1311
6 TraesCS3D01G303500 chr5B 339453994 339454635 641 False 813.000000 813 89.564000 3801 4441 1 chr5B.!!$F2 640
7 TraesCS3D01G303500 chr3B 154420411 154423222 2811 True 2177.500000 2676 95.108000 1 2877 2 chr3B.!!$R4 2876
8 TraesCS3D01G303500 chr3B 10049515 10052318 2803 True 2149.000000 2630 94.826000 1 2882 2 chr3B.!!$R2 2881
9 TraesCS3D01G303500 chr3B 151114509 151117312 2803 True 2128.000000 2621 94.514000 1 2878 2 chr3B.!!$R3 2877
10 TraesCS3D01G303500 chr3B 204205753 204206760 1007 False 1602.000000 1602 95.356000 1 1009 1 chr3B.!!$F1 1008
11 TraesCS3D01G303500 chr3B 544778203 544778944 741 True 413.666667 647 92.263667 2877 3601 3 chr3B.!!$R5 724
12 TraesCS3D01G303500 chr2B 480005971 480008770 2799 False 2131.500000 2645 94.495500 1 2877 2 chr2B.!!$F1 2876
13 TraesCS3D01G303500 chr1D 492938535 492940243 1708 False 2627.000000 2627 94.509000 1089 2793 1 chr1D.!!$F2 1704
14 TraesCS3D01G303500 chr1B 630552218 630554025 1807 True 2615.000000 2615 93.017000 1088 2879 1 chr1B.!!$R3 1791
15 TraesCS3D01G303500 chr1B 179138728 179140427 1699 True 2314.000000 2314 91.334000 1088 2793 1 chr1B.!!$R1 1705
16 TraesCS3D01G303500 chr4B 561747808 561750593 2785 True 2059.500000 2510 93.803000 1 2878 2 chr4B.!!$R2 2877
17 TraesCS3D01G303500 chr2A 191975140 191976841 1701 False 2488.000000 2488 93.125000 1088 2793 1 chr2A.!!$F1 1705
18 TraesCS3D01G303500 chr6B 678822344 678823634 1290 False 2082.000000 2082 95.579000 1088 2399 1 chr6B.!!$F2 1311
19 TraesCS3D01G303500 chr6B 678840572 678842872 2300 False 1868.500000 2050 95.891000 1 2399 2 chr6B.!!$F4 2398
20 TraesCS3D01G303500 chr6B 179945361 179946134 773 False 512.000000 835 90.424500 3615 4441 2 chr6B.!!$F3 826
21 TraesCS3D01G303500 chr6D 429977360 429978060 700 True 926.000000 926 91.181000 2120 2793 1 chr6D.!!$R2 673
22 TraesCS3D01G303500 chr2D 384835301 384836096 795 True 557.500000 909 91.603000 3615 4441 2 chr2D.!!$R3 826
23 TraesCS3D01G303500 chr7D 185194977 185195615 638 True 863.000000 863 91.108000 3804 4441 1 chr7D.!!$R1 637
24 TraesCS3D01G303500 chr7D 121186704 121187344 640 False 819.000000 819 89.736000 3801 4441 1 chr7D.!!$F1 640
25 TraesCS3D01G303500 chr7A 613345660 613346295 635 True 821.000000 821 89.969000 3804 4439 1 chr7A.!!$R1 635
26 TraesCS3D01G303500 chr5D 249003372 249004009 637 True 808.000000 808 89.531000 3804 4441 1 chr5D.!!$R2 637
27 TraesCS3D01G303500 chr4D 488670805 488671598 793 True 509.500000 800 90.836500 3614 4441 2 chr4D.!!$R1 827

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
32 33 1.482182 AGAGCACATACCTTGATGCGA 59.518 47.619 0.00 0.00 42.98 5.10 F
1005 1031 1.564348 ACCCTGCACCCCTATAAACAG 59.436 52.381 0.00 0.00 0.00 3.16 F
1942 1970 0.322816 GAGTGGATGCTGCCTTCCAA 60.323 55.000 19.26 5.31 44.19 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1085 1111 1.640917 TTGGTCTCTGGGTGTACTCC 58.359 55.0 5.35 5.35 0.00 3.85 R
2742 2804 0.468214 TTGGCCGGACAAATCCAACA 60.468 50.0 23.69 0.00 46.67 3.33 R
3797 3911 0.178944 TCCTCAGTCTCGGGGTGAAA 60.179 55.0 0.00 0.00 0.00 2.69 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
32 33 1.482182 AGAGCACATACCTTGATGCGA 59.518 47.619 0.00 0.00 42.98 5.10
221 222 2.993220 CACACCACGAGATCGAATCAAA 59.007 45.455 9.58 0.00 43.02 2.69
318 320 4.282703 AGGACACAGAACGTAAATACCTGT 59.717 41.667 0.00 0.00 38.48 4.00
382 385 4.737177 GCTCCTTGCTGCCTGCCT 62.737 66.667 0.00 0.00 42.00 4.75
518 521 4.466370 CACCAAGTAGGATCAGTAGTTCCA 59.534 45.833 0.00 0.00 41.22 3.53
1004 1030 1.676248 ACCCTGCACCCCTATAAACA 58.324 50.000 0.00 0.00 0.00 2.83
1005 1031 1.564348 ACCCTGCACCCCTATAAACAG 59.436 52.381 0.00 0.00 0.00 3.16
1006 1032 1.564348 CCCTGCACCCCTATAAACAGT 59.436 52.381 0.00 0.00 0.00 3.55
1007 1033 2.775384 CCCTGCACCCCTATAAACAGTA 59.225 50.000 0.00 0.00 0.00 2.74
1008 1034 3.433173 CCCTGCACCCCTATAAACAGTAC 60.433 52.174 0.00 0.00 0.00 2.73
1009 1035 3.454812 CCTGCACCCCTATAAACAGTACT 59.545 47.826 0.00 0.00 0.00 2.73
1010 1036 4.443034 CCTGCACCCCTATAAACAGTACTC 60.443 50.000 0.00 0.00 0.00 2.59
1011 1037 3.453353 TGCACCCCTATAAACAGTACTCC 59.547 47.826 0.00 0.00 0.00 3.85
1012 1038 3.181457 GCACCCCTATAAACAGTACTCCC 60.181 52.174 0.00 0.00 0.00 4.30
1013 1039 4.296056 CACCCCTATAAACAGTACTCCCT 58.704 47.826 0.00 0.00 0.00 4.20
1014 1040 4.344390 CACCCCTATAAACAGTACTCCCTC 59.656 50.000 0.00 0.00 0.00 4.30
1015 1041 3.902467 CCCCTATAAACAGTACTCCCTCC 59.098 52.174 0.00 0.00 0.00 4.30
1016 1042 3.573110 CCCTATAAACAGTACTCCCTCCG 59.427 52.174 0.00 0.00 0.00 4.63
1017 1043 4.213513 CCTATAAACAGTACTCCCTCCGT 58.786 47.826 0.00 0.00 0.00 4.69
1018 1044 5.380043 CCTATAAACAGTACTCCCTCCGTA 58.620 45.833 0.00 0.00 0.00 4.02
1019 1045 5.829924 CCTATAAACAGTACTCCCTCCGTAA 59.170 44.000 0.00 0.00 0.00 3.18
1020 1046 6.322201 CCTATAAACAGTACTCCCTCCGTAAA 59.678 42.308 0.00 0.00 0.00 2.01
1021 1047 3.949842 AACAGTACTCCCTCCGTAAAC 57.050 47.619 0.00 0.00 0.00 2.01
1022 1048 3.166560 ACAGTACTCCCTCCGTAAACT 57.833 47.619 0.00 0.00 0.00 2.66
1023 1049 4.307032 ACAGTACTCCCTCCGTAAACTA 57.693 45.455 0.00 0.00 0.00 2.24
1024 1050 4.666512 ACAGTACTCCCTCCGTAAACTAA 58.333 43.478 0.00 0.00 0.00 2.24
1025 1051 5.267587 ACAGTACTCCCTCCGTAAACTAAT 58.732 41.667 0.00 0.00 0.00 1.73
1026 1052 6.426587 ACAGTACTCCCTCCGTAAACTAATA 58.573 40.000 0.00 0.00 0.00 0.98
1027 1053 7.065504 ACAGTACTCCCTCCGTAAACTAATAT 58.934 38.462 0.00 0.00 0.00 1.28
1028 1054 8.220559 ACAGTACTCCCTCCGTAAACTAATATA 58.779 37.037 0.00 0.00 0.00 0.86
1029 1055 9.071276 CAGTACTCCCTCCGTAAACTAATATAA 57.929 37.037 0.00 0.00 0.00 0.98
1030 1056 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
1031 1057 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1032 1058 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1033 1059 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
1034 1060 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
1035 1061 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
1036 1062 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
1037 1063 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
1064 1090 8.870879 AGATCACTATTTTAGTTGTCTAAACGC 58.129 33.333 0.00 0.00 43.20 4.84
1065 1091 8.773404 ATCACTATTTTAGTTGTCTAAACGCT 57.227 30.769 0.74 0.00 43.20 5.07
1066 1092 8.597662 TCACTATTTTAGTTGTCTAAACGCTT 57.402 30.769 0.74 0.00 43.20 4.68
1067 1093 9.048446 TCACTATTTTAGTTGTCTAAACGCTTT 57.952 29.630 0.74 0.00 43.20 3.51
1068 1094 9.659830 CACTATTTTAGTTGTCTAAACGCTTTT 57.340 29.630 0.00 0.00 43.20 2.27
1086 1112 8.658499 ACGCTTTTATATTAGTTTACAGAGGG 57.342 34.615 0.00 0.00 0.00 4.30
1853 1881 1.272715 GCGCACCATATTCGTGTCG 59.727 57.895 0.30 9.92 35.39 4.35
1939 1967 1.452833 GGGAGTGGATGCTGCCTTC 60.453 63.158 0.00 0.00 42.73 3.46
1942 1970 0.322816 GAGTGGATGCTGCCTTCCAA 60.323 55.000 19.26 5.31 44.19 3.53
1956 1984 2.511600 CCAAAGGCCGAGGCTACG 60.512 66.667 14.33 0.00 37.50 3.51
2647 2709 8.731605 TGAATTGATTATTGCCTTGTACGTTTA 58.268 29.630 0.00 0.00 0.00 2.01
2761 2823 0.468214 TGTTGGATTTGTCCGGCCAA 60.468 50.000 2.24 0.00 38.02 4.52
2862 2942 2.093973 CGGACTATTCACCAACTGCTCT 60.094 50.000 0.00 0.00 0.00 4.09
2886 2966 9.237187 TCTATTAGGAGTAGAGATTATGCACTG 57.763 37.037 0.00 0.00 0.00 3.66
2975 3055 2.943036 AGGTCGCCTAGGAACAAAAA 57.057 45.000 14.75 0.00 28.47 1.94
3027 3107 1.391577 TTGTGTGTGCAGCAATGTCT 58.608 45.000 0.00 0.00 0.00 3.41
3071 3151 2.483889 GCCCTCTAGTATTGGACACTGC 60.484 54.545 0.00 0.00 0.00 4.40
3096 3176 5.237815 ACGAAGCAGTCTGATTAATGTTCA 58.762 37.500 2.71 0.00 0.00 3.18
3097 3177 5.349817 ACGAAGCAGTCTGATTAATGTTCAG 59.650 40.000 2.71 0.00 41.61 3.02
3098 3178 5.578336 CGAAGCAGTCTGATTAATGTTCAGA 59.422 40.000 2.71 3.61 45.53 3.27
3127 3207 1.482593 ACCTCCGAAGACCTATGCTTG 59.517 52.381 0.00 0.00 0.00 4.01
3244 3357 2.774439 ATGACTTGTTGAACAACGGC 57.226 45.000 6.66 6.54 43.94 5.68
3320 3433 0.527565 ATGTTGCCACAGCCGAAATC 59.472 50.000 0.00 0.00 35.94 2.17
3347 3460 1.018226 CCGTCTCCTTGCAGCTCTTG 61.018 60.000 0.00 0.00 0.00 3.02
3378 3491 1.974957 AGGTTTTACCCCAATTGCCAC 59.025 47.619 0.00 0.00 39.75 5.01
3379 3492 1.337354 GGTTTTACCCCAATTGCCACG 60.337 52.381 0.00 0.00 30.04 4.94
3382 3495 2.715181 TTACCCCAATTGCCACGCCA 62.715 55.000 0.00 0.00 0.00 5.69
3388 3501 1.682854 CCAATTGCCACGCCAGATAAT 59.317 47.619 0.00 0.00 0.00 1.28
3508 3622 6.586082 CCTGATAATTTCGGTTCAGTTTTTGG 59.414 38.462 0.00 0.00 35.01 3.28
3509 3623 6.451393 TGATAATTTCGGTTCAGTTTTTGGG 58.549 36.000 0.00 0.00 0.00 4.12
3559 3673 6.099269 ACTGAAACCTAAGAGTTCTGTTACCA 59.901 38.462 0.00 0.00 0.00 3.25
3570 3684 7.042335 AGAGTTCTGTTACCAGATAATTTCGG 58.958 38.462 0.00 0.00 46.80 4.30
3583 3697 6.586082 CAGATAATTTCGGTTCAGTTTTTGGG 59.414 38.462 0.00 0.00 0.00 4.12
3591 3705 4.096682 CGGTTCAGTTTTTGGGTTAACTCA 59.903 41.667 3.38 3.38 32.50 3.41
3603 3717 9.757227 TTTTGGGTTAACTCAAATTATTGTCAG 57.243 29.630 29.32 0.00 37.79 3.51
3604 3718 8.698973 TTGGGTTAACTCAAATTATTGTCAGA 57.301 30.769 18.59 0.00 37.79 3.27
3605 3719 8.335532 TGGGTTAACTCAAATTATTGTCAGAG 57.664 34.615 5.47 0.00 37.79 3.35
3606 3720 7.942341 TGGGTTAACTCAAATTATTGTCAGAGT 59.058 33.333 5.47 0.00 37.79 3.24
3607 3721 8.793592 GGGTTAACTCAAATTATTGTCAGAGTT 58.206 33.333 5.42 14.72 37.79 3.01
3684 3798 8.547967 TTAGAAATGATTCGAAACTTAGCAGT 57.452 30.769 0.00 0.00 40.63 4.40
3718 3832 8.146412 CCTATGAATGATTCGGATATAGATGCA 58.854 37.037 10.24 0.00 0.00 3.96
3767 3881 1.817099 GCGGATCTTGCACCCTCAG 60.817 63.158 5.74 0.00 0.00 3.35
3768 3882 1.153289 CGGATCTTGCACCCTCAGG 60.153 63.158 0.00 0.00 40.04 3.86
3769 3883 1.617018 CGGATCTTGCACCCTCAGGA 61.617 60.000 0.00 0.00 36.73 3.86
3770 3884 0.842635 GGATCTTGCACCCTCAGGAT 59.157 55.000 0.00 0.00 35.79 3.24
3771 3885 1.202746 GGATCTTGCACCCTCAGGATC 60.203 57.143 0.00 7.16 44.20 3.36
3772 3886 1.487976 GATCTTGCACCCTCAGGATCA 59.512 52.381 0.00 0.00 44.28 2.92
3773 3887 1.361204 TCTTGCACCCTCAGGATCAA 58.639 50.000 0.00 0.00 36.73 2.57
3774 3888 1.704628 TCTTGCACCCTCAGGATCAAA 59.295 47.619 0.00 0.00 36.73 2.69
3775 3889 2.108075 TCTTGCACCCTCAGGATCAAAA 59.892 45.455 0.00 0.00 36.73 2.44
3776 3890 1.909700 TGCACCCTCAGGATCAAAAC 58.090 50.000 0.00 0.00 36.73 2.43
3777 3891 1.177401 GCACCCTCAGGATCAAAACC 58.823 55.000 0.00 0.00 36.73 3.27
3778 3892 1.272147 GCACCCTCAGGATCAAAACCT 60.272 52.381 0.00 0.00 38.40 3.50
3779 3893 2.819348 GCACCCTCAGGATCAAAACCTT 60.819 50.000 0.00 0.00 35.35 3.50
3780 3894 3.084786 CACCCTCAGGATCAAAACCTTC 58.915 50.000 0.00 0.00 35.35 3.46
3781 3895 2.989571 ACCCTCAGGATCAAAACCTTCT 59.010 45.455 0.00 0.00 35.35 2.85
3782 3896 3.245052 ACCCTCAGGATCAAAACCTTCTG 60.245 47.826 0.00 0.00 35.35 3.02
3783 3897 2.751806 CCTCAGGATCAAAACCTTCTGC 59.248 50.000 0.00 0.00 35.35 4.26
3784 3898 3.415212 CTCAGGATCAAAACCTTCTGCA 58.585 45.455 0.00 0.00 35.35 4.41
3785 3899 3.149196 TCAGGATCAAAACCTTCTGCAC 58.851 45.455 0.00 0.00 35.35 4.57
3786 3900 2.229784 CAGGATCAAAACCTTCTGCACC 59.770 50.000 0.00 0.00 35.35 5.01
3787 3901 1.546029 GGATCAAAACCTTCTGCACCC 59.454 52.381 0.00 0.00 0.00 4.61
3788 3902 1.546029 GATCAAAACCTTCTGCACCCC 59.454 52.381 0.00 0.00 0.00 4.95
3789 3903 0.260230 TCAAAACCTTCTGCACCCCA 59.740 50.000 0.00 0.00 0.00 4.96
3790 3904 0.389025 CAAAACCTTCTGCACCCCAC 59.611 55.000 0.00 0.00 0.00 4.61
3791 3905 1.106944 AAAACCTTCTGCACCCCACG 61.107 55.000 0.00 0.00 0.00 4.94
3792 3906 4.643387 ACCTTCTGCACCCCACGC 62.643 66.667 0.00 0.00 0.00 5.34
3793 3907 4.335647 CCTTCTGCACCCCACGCT 62.336 66.667 0.00 0.00 0.00 5.07
3794 3908 3.052082 CTTCTGCACCCCACGCTG 61.052 66.667 0.00 0.00 0.00 5.18
3795 3909 4.641645 TTCTGCACCCCACGCTGG 62.642 66.667 0.00 0.00 37.25 4.85
3797 3911 4.415150 CTGCACCCCACGCTGGAT 62.415 66.667 5.71 0.00 40.96 3.41
3798 3912 3.925630 CTGCACCCCACGCTGGATT 62.926 63.158 5.71 0.00 40.96 3.01
3799 3913 2.676471 GCACCCCACGCTGGATTT 60.676 61.111 5.71 0.00 40.96 2.17
3826 3940 1.408702 GAGACTGAGGAGGATGAGTGC 59.591 57.143 0.00 0.00 0.00 4.40
3828 3942 1.830477 GACTGAGGAGGATGAGTGCTT 59.170 52.381 0.00 0.00 0.00 3.91
3843 3957 2.111792 AGTGCTTTATTTCCCCAAGGGT 59.888 45.455 4.11 0.00 44.74 4.34
3909 4023 1.757340 GTGAGGACCGGGTAGAGGG 60.757 68.421 6.32 0.00 0.00 4.30
4029 4143 9.478238 TGATGAAATATGAAGGGAATCTTTTGA 57.522 29.630 0.00 0.00 35.50 2.69
4175 4290 2.906354 CACTTTATCGGGAGGAGTTGG 58.094 52.381 0.00 0.00 0.00 3.77
4236 4351 5.027460 GGTGGGATTTTACTTGGGGTTAAT 58.973 41.667 0.00 0.00 0.00 1.40
4294 4409 2.122563 TTTTGCGGTTAAGTTTCGGC 57.877 45.000 0.00 0.00 0.00 5.54
4308 4424 0.323629 TTCGGCCAGATCGAAGGTTT 59.676 50.000 2.24 0.00 40.99 3.27
4328 4444 1.560505 ATGGGTTTCAATGGGCACTC 58.439 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
221 222 2.091278 TCCTCCCCGAACTCTATGATGT 60.091 50.000 0.00 0.00 0.00 3.06
318 320 2.671619 GCCACCAGCGCTAAACCA 60.672 61.111 10.99 0.00 0.00 3.67
378 381 2.683465 GGATCCCCAGAGCAAGGCA 61.683 63.158 0.00 0.00 0.00 4.75
382 385 1.402896 CGCTAGGATCCCCAGAGCAA 61.403 60.000 19.77 0.00 41.29 3.91
642 648 8.687824 AGTAAGTCAAGTGTTTTGTCAAAATG 57.312 30.769 13.65 8.24 32.22 2.32
1004 1030 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
1005 1031 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
1006 1032 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1007 1033 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
1008 1034 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
1009 1035 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
1010 1036 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
1011 1037 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
1038 1064 8.870879 GCGTTTAGACAACTAAAATAGTGATCT 58.129 33.333 0.00 8.18 45.97 2.75
1039 1065 8.870879 AGCGTTTAGACAACTAAAATAGTGATC 58.129 33.333 0.00 0.00 45.97 2.92
1040 1066 8.773404 AGCGTTTAGACAACTAAAATAGTGAT 57.227 30.769 0.00 0.00 45.97 3.06
1041 1067 8.597662 AAGCGTTTAGACAACTAAAATAGTGA 57.402 30.769 0.00 0.00 45.97 3.41
1042 1068 9.659830 AAAAGCGTTTAGACAACTAAAATAGTG 57.340 29.630 0.00 0.00 45.97 2.74
1060 1086 9.106070 CCCTCTGTAAACTAATATAAAAGCGTT 57.894 33.333 0.00 0.00 0.00 4.84
1061 1087 8.480501 TCCCTCTGTAAACTAATATAAAAGCGT 58.519 33.333 0.00 0.00 0.00 5.07
1062 1088 8.882415 TCCCTCTGTAAACTAATATAAAAGCG 57.118 34.615 0.00 0.00 0.00 4.68
1063 1089 9.833917 ACTCCCTCTGTAAACTAATATAAAAGC 57.166 33.333 0.00 0.00 0.00 3.51
1068 1094 9.359653 GGTGTACTCCCTCTGTAAACTAATATA 57.640 37.037 2.33 0.00 30.92 0.86
1069 1095 7.289549 GGGTGTACTCCCTCTGTAAACTAATAT 59.710 40.741 23.22 0.00 43.85 1.28
1070 1096 6.608808 GGGTGTACTCCCTCTGTAAACTAATA 59.391 42.308 23.22 0.00 43.85 0.98
1071 1097 5.424573 GGGTGTACTCCCTCTGTAAACTAAT 59.575 44.000 23.22 0.00 43.85 1.73
1072 1098 4.774200 GGGTGTACTCCCTCTGTAAACTAA 59.226 45.833 23.22 0.00 43.85 2.24
1073 1099 4.347607 GGGTGTACTCCCTCTGTAAACTA 58.652 47.826 23.22 0.00 43.85 2.24
1074 1100 3.171528 GGGTGTACTCCCTCTGTAAACT 58.828 50.000 23.22 0.00 43.85 2.66
1075 1101 3.606595 GGGTGTACTCCCTCTGTAAAC 57.393 52.381 23.22 0.00 43.85 2.01
1085 1111 1.640917 TTGGTCTCTGGGTGTACTCC 58.359 55.000 5.35 5.35 0.00 3.85
1086 1112 4.279145 TCTATTGGTCTCTGGGTGTACTC 58.721 47.826 0.00 0.00 0.00 2.59
1939 1967 2.511600 CGTAGCCTCGGCCTTTGG 60.512 66.667 0.00 0.55 43.17 3.28
1942 1970 3.823330 CGACGTAGCCTCGGCCTT 61.823 66.667 0.00 0.00 43.17 4.35
1956 1984 2.023041 GTCTAGCTCGGCGTCGAC 59.977 66.667 8.66 5.18 40.88 4.20
2112 2140 0.674895 GGCGAAACTCCAGCTGATGT 60.675 55.000 17.39 10.57 0.00 3.06
2631 2693 5.068067 ACCAAAACTAAACGTACAAGGCAAT 59.932 36.000 0.00 0.00 0.00 3.56
2742 2804 0.468214 TTGGCCGGACAAATCCAACA 60.468 50.000 23.69 0.00 46.67 3.33
2862 2942 7.093727 GGCAGTGCATAATCTCTACTCCTAATA 60.094 40.741 18.61 0.00 0.00 0.98
2898 2978 8.030692 ACAGTCAACAAGCAAATATACTACGTA 58.969 33.333 0.00 0.00 0.00 3.57
2899 2979 6.872020 ACAGTCAACAAGCAAATATACTACGT 59.128 34.615 0.00 0.00 0.00 3.57
2900 2980 7.290857 ACAGTCAACAAGCAAATATACTACG 57.709 36.000 0.00 0.00 0.00 3.51
2959 3039 5.585820 AAAAACTTTTTGTTCCTAGGCGA 57.414 34.783 2.96 0.00 38.03 5.54
2975 3055 1.963515 CAGCAGCAAGGGGTAAAAACT 59.036 47.619 0.00 0.00 0.00 2.66
3071 3151 3.859961 ACATTAATCAGACTGCTTCGTCG 59.140 43.478 0.00 0.00 38.90 5.12
3096 3176 4.828387 GGTCTTCGGAGGTTAGATACATCT 59.172 45.833 0.00 0.00 37.68 2.90
3097 3177 4.828387 AGGTCTTCGGAGGTTAGATACATC 59.172 45.833 0.00 0.00 36.84 3.06
3098 3178 4.805744 AGGTCTTCGGAGGTTAGATACAT 58.194 43.478 0.00 0.00 0.00 2.29
3099 3179 4.246712 AGGTCTTCGGAGGTTAGATACA 57.753 45.455 0.00 0.00 0.00 2.29
3100 3180 5.335819 GCATAGGTCTTCGGAGGTTAGATAC 60.336 48.000 0.00 0.00 0.00 2.24
3101 3181 4.765856 GCATAGGTCTTCGGAGGTTAGATA 59.234 45.833 0.00 0.00 0.00 1.98
3102 3182 3.574826 GCATAGGTCTTCGGAGGTTAGAT 59.425 47.826 0.00 0.00 0.00 1.98
3103 3183 2.957006 GCATAGGTCTTCGGAGGTTAGA 59.043 50.000 0.00 0.00 0.00 2.10
3104 3184 2.959707 AGCATAGGTCTTCGGAGGTTAG 59.040 50.000 0.00 0.00 0.00 2.34
3105 3185 3.028094 AGCATAGGTCTTCGGAGGTTA 57.972 47.619 0.00 0.00 0.00 2.85
3111 3191 0.830648 TCCCAAGCATAGGTCTTCGG 59.169 55.000 0.00 0.00 0.00 4.30
3127 3207 4.767409 ACTCCACTTATTCTGCTTTTTCCC 59.233 41.667 0.00 0.00 0.00 3.97
3192 3305 8.918202 AATCACTTACAAAGTTCTTACATCCA 57.082 30.769 0.00 0.00 40.46 3.41
3225 3338 2.297701 AGCCGTTGTTCAACAAGTCAT 58.702 42.857 2.26 0.00 39.00 3.06
3244 3357 6.145858 GCTCAAGCACTACTGAATCATCATAG 59.854 42.308 0.00 0.00 41.59 2.23
3285 3398 5.709631 TGGCAACATACATAAGCAGAAGAAA 59.290 36.000 0.00 0.00 46.17 2.52
3300 3413 3.821234 CGATTTCGGCTGTGGCAACATA 61.821 50.000 0.00 0.00 42.44 2.29
3320 3433 1.336517 TGCAAGGAGACGGTAGAAACG 60.337 52.381 0.00 0.00 37.36 3.60
3347 3460 4.100344 TGGGGTAAAACCTGAAAAGAAAGC 59.900 41.667 0.00 0.00 38.64 3.51
3348 3461 5.862678 TGGGGTAAAACCTGAAAAGAAAG 57.137 39.130 0.00 0.00 38.64 2.62
3378 3491 2.680841 TGAAACCCGAAATTATCTGGCG 59.319 45.455 0.00 0.00 35.93 5.69
3379 3492 4.918810 ATGAAACCCGAAATTATCTGGC 57.081 40.909 0.00 0.00 35.93 4.85
3408 3521 6.522625 TCACTGACCAAATCTGTTGAAAAA 57.477 33.333 0.00 0.00 37.39 1.94
3559 3673 6.266786 ACCCAAAAACTGAACCGAAATTATCT 59.733 34.615 0.00 0.00 0.00 1.98
3570 3684 8.487313 AATTTGAGTTAACCCAAAAACTGAAC 57.513 30.769 17.70 0.00 36.10 3.18
3598 3712 9.702253 ATAGAATTAGAGGTCTAAACTCTGACA 57.298 33.333 17.27 5.82 44.57 3.58
3635 3749 2.416547 CACGTTCCGCTTCAAGATCAAT 59.583 45.455 0.00 0.00 0.00 2.57
3684 3798 6.176896 TCCGAATCATTCATAGGTTTGACAA 58.823 36.000 0.00 0.00 0.00 3.18
3718 3832 2.937442 TCAAGTACCCTAACCCCCAAT 58.063 47.619 0.00 0.00 0.00 3.16
3767 3881 1.546029 GGGTGCAGAAGGTTTTGATCC 59.454 52.381 0.00 0.00 0.00 3.36
3768 3882 1.546029 GGGGTGCAGAAGGTTTTGATC 59.454 52.381 0.00 0.00 0.00 2.92
3769 3883 1.133199 TGGGGTGCAGAAGGTTTTGAT 60.133 47.619 0.00 0.00 0.00 2.57
3770 3884 0.260230 TGGGGTGCAGAAGGTTTTGA 59.740 50.000 0.00 0.00 0.00 2.69
3771 3885 0.389025 GTGGGGTGCAGAAGGTTTTG 59.611 55.000 0.00 0.00 0.00 2.44
3772 3886 1.106944 CGTGGGGTGCAGAAGGTTTT 61.107 55.000 0.00 0.00 0.00 2.43
3773 3887 1.528309 CGTGGGGTGCAGAAGGTTT 60.528 57.895 0.00 0.00 0.00 3.27
3774 3888 2.113139 CGTGGGGTGCAGAAGGTT 59.887 61.111 0.00 0.00 0.00 3.50
3775 3889 4.643387 GCGTGGGGTGCAGAAGGT 62.643 66.667 0.00 0.00 0.00 3.50
3776 3890 4.335647 AGCGTGGGGTGCAGAAGG 62.336 66.667 0.00 0.00 33.85 3.46
3777 3891 3.052082 CAGCGTGGGGTGCAGAAG 61.052 66.667 0.00 0.00 34.49 2.85
3778 3892 4.641645 CCAGCGTGGGGTGCAGAA 62.642 66.667 0.00 0.00 40.31 3.02
3780 3894 3.925630 AATCCAGCGTGGGGTGCAG 62.926 63.158 0.00 0.00 40.31 4.41
3781 3895 3.505790 AAATCCAGCGTGGGGTGCA 62.506 57.895 4.52 0.00 40.31 4.57
3782 3896 2.676471 AAATCCAGCGTGGGGTGC 60.676 61.111 4.52 0.00 40.31 5.01
3783 3897 1.303236 TGAAATCCAGCGTGGGGTG 60.303 57.895 4.52 0.00 38.32 4.61
3784 3898 1.303317 GTGAAATCCAGCGTGGGGT 60.303 57.895 4.52 0.00 38.32 4.95
3785 3899 2.046285 GGTGAAATCCAGCGTGGGG 61.046 63.158 4.52 0.00 38.32 4.96
3786 3900 2.046285 GGGTGAAATCCAGCGTGGG 61.046 63.158 4.52 0.00 43.89 4.61
3787 3901 2.046285 GGGGTGAAATCCAGCGTGG 61.046 63.158 0.00 0.00 43.89 4.94
3788 3902 2.398554 CGGGGTGAAATCCAGCGTG 61.399 63.158 0.00 0.00 43.89 5.34
3789 3903 2.046314 CGGGGTGAAATCCAGCGT 60.046 61.111 0.00 0.00 43.89 5.07
3790 3904 1.815421 CTCGGGGTGAAATCCAGCG 60.815 63.158 0.00 0.00 43.89 5.18
3791 3905 0.744771 GTCTCGGGGTGAAATCCAGC 60.745 60.000 0.00 0.00 42.30 4.85
3792 3906 0.905357 AGTCTCGGGGTGAAATCCAG 59.095 55.000 0.00 0.00 0.00 3.86
3793 3907 0.613260 CAGTCTCGGGGTGAAATCCA 59.387 55.000 0.00 0.00 0.00 3.41
3794 3908 0.902531 TCAGTCTCGGGGTGAAATCC 59.097 55.000 0.00 0.00 0.00 3.01
3795 3909 1.134670 CCTCAGTCTCGGGGTGAAATC 60.135 57.143 0.00 0.00 0.00 2.17
3796 3910 0.905357 CCTCAGTCTCGGGGTGAAAT 59.095 55.000 0.00 0.00 0.00 2.17
3797 3911 0.178944 TCCTCAGTCTCGGGGTGAAA 60.179 55.000 0.00 0.00 0.00 2.69
3798 3912 0.612174 CTCCTCAGTCTCGGGGTGAA 60.612 60.000 0.00 0.00 0.00 3.18
3799 3913 1.000771 CTCCTCAGTCTCGGGGTGA 60.001 63.158 0.00 0.00 0.00 4.02
3909 4023 1.008875 GCGCTTAGGCTTGTTTTGGC 61.009 55.000 0.00 0.00 36.09 4.52
4029 4143 8.041919 GCCAAGTTCTTAAGACCTCTACTATTT 58.958 37.037 4.18 0.00 0.00 1.40
4236 4351 1.305201 GGACTTCCAAAGTGTCGCAA 58.695 50.000 0.00 0.00 43.03 4.85
4294 4409 3.560636 ACCCATAAACCTTCGATCTGG 57.439 47.619 0.00 0.00 0.00 3.86
4308 4424 2.733956 GAGTGCCCATTGAAACCCATA 58.266 47.619 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.