Multiple sequence alignment - TraesCS4D01G164300

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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 TraesCS4D01G164300 chr4D 100.000 4655 0 0 1 4655 264460586 264465240 0.000000e+00 8597.0
1 TraesCS4D01G164300 chr4D 90.909 132 5 5 795 924 4805153 4805279 2.230000e-38 171.0
2 TraesCS4D01G164300 chr4D 95.294 85 4 0 696 780 57032897 57032813 8.120000e-28 135.0
3 TraesCS4D01G164300 chr2D 98.107 3909 68 5 751 4655 575270152 575266246 0.000000e+00 6804.0
4 TraesCS4D01G164300 chr2D 97.638 3980 49 16 693 4655 263424012 263420061 0.000000e+00 6787.0
5 TraesCS4D01G164300 chr2D 97.192 2457 35 7 2205 4655 118381872 118379444 0.000000e+00 4124.0
6 TraesCS4D01G164300 chr2D 96.068 1475 35 3 695 2148 118383340 118381868 0.000000e+00 2381.0
7 TraesCS4D01G164300 chr2D 93.878 98 5 1 696 793 393179966 393180062 3.750000e-31 147.0
8 TraesCS4D01G164300 chr2D 97.619 84 2 0 693 776 7049870 7049953 1.350000e-30 145.0
9 TraesCS4D01G164300 chr2D 87.121 132 7 7 795 924 72591563 72591440 1.750000e-29 141.0
10 TraesCS4D01G164300 chr4A 96.095 3918 130 16 751 4655 359640375 359636468 0.000000e+00 6366.0
11 TraesCS4D01G164300 chr4A 91.398 465 18 2 753 1196 725532214 725532677 6.620000e-173 617.0
12 TraesCS4D01G164300 chr4A 96.000 100 3 1 695 794 712707608 712707510 1.340000e-35 161.0
13 TraesCS4D01G164300 chr2B 96.895 3639 87 11 1022 4655 706585108 706588725 0.000000e+00 6071.0
14 TraesCS4D01G164300 chr2B 93.697 238 13 2 750 987 706584902 706585137 5.730000e-94 355.0
15 TraesCS4D01G164300 chr6A 96.430 2689 69 14 753 3427 526165107 526162432 0.000000e+00 4409.0
16 TraesCS4D01G164300 chr6A 94.161 1610 80 6 3058 4655 393799769 393801376 0.000000e+00 2440.0
17 TraesCS4D01G164300 chr6A 98.204 1225 20 2 3432 4655 526162359 526161136 0.000000e+00 2139.0
18 TraesCS4D01G164300 chr6A 86.284 401 46 6 295 689 554945646 554945249 1.200000e-115 427.0
19 TraesCS4D01G164300 chr6A 86.538 260 31 3 795 1050 54085942 54086201 2.740000e-72 283.0
20 TraesCS4D01G164300 chr6A 91.279 172 13 2 794 963 523829095 523828924 2.800000e-57 233.0
21 TraesCS4D01G164300 chr3B 97.970 2414 46 2 1682 4092 739840915 739843328 0.000000e+00 4183.0
22 TraesCS4D01G164300 chr3B 94.163 1679 56 18 2980 4655 758392218 758393857 0.000000e+00 2519.0
23 TraesCS4D01G164300 chr3B 94.886 1056 31 5 1939 2980 758390654 758391700 0.000000e+00 1629.0
24 TraesCS4D01G164300 chr3B 92.340 966 67 4 3585 4548 749558713 749559673 0.000000e+00 1367.0
25 TraesCS4D01G164300 chr3B 90.029 682 21 13 696 1377 739839630 739840264 0.000000e+00 839.0
26 TraesCS4D01G164300 chr3B 97.464 276 6 1 1370 1645 739840645 739840919 1.960000e-128 470.0
27 TraesCS4D01G164300 chr3B 92.574 202 15 0 1306 1507 758389167 758389368 1.640000e-74 291.0
28 TraesCS4D01G164300 chr3B 88.068 176 11 4 2980 3155 68212897 68213062 2.840000e-47 200.0
29 TraesCS4D01G164300 chr6D 94.048 1680 78 10 2980 4655 249490104 249491765 0.000000e+00 2529.0
30 TraesCS4D01G164300 chr6D 93.530 711 32 2 1 697 292125976 292125266 0.000000e+00 1046.0
31 TraesCS4D01G164300 chr6D 92.340 705 36 9 1 697 258570612 258571306 0.000000e+00 987.0
32 TraesCS4D01G164300 chr6D 91.877 714 38 10 1 697 159500565 159499855 0.000000e+00 979.0
33 TraesCS4D01G164300 chr6D 88.889 594 42 12 138 713 473251614 473252201 0.000000e+00 710.0
34 TraesCS4D01G164300 chr6D 93.963 381 19 4 2602 2980 249489221 249489599 1.450000e-159 573.0
35 TraesCS4D01G164300 chr6D 97.590 83 1 1 696 778 414564743 414564824 1.750000e-29 141.0
36 TraesCS4D01G164300 chr6D 94.118 85 4 1 696 780 289615945 289616028 1.360000e-25 128.0
37 TraesCS4D01G164300 chr6D 96.203 79 2 1 847 924 463918321 463918243 1.360000e-25 128.0
38 TraesCS4D01G164300 chr6D 96.203 79 2 1 847 924 463934550 463934472 1.360000e-25 128.0
39 TraesCS4D01G164300 chr6D 83.871 124 10 3 804 924 315644430 315644314 4.920000e-20 110.0
40 TraesCS4D01G164300 chr6D 95.349 43 1 1 753 794 413771244 413771286 3.010000e-07 67.6
41 TraesCS4D01G164300 chr1D 94.140 802 39 3 3855 4655 209542958 209542164 0.000000e+00 1214.0
42 TraesCS4D01G164300 chr1D 94.708 718 31 5 3151 3861 209571764 209571047 0.000000e+00 1109.0
43 TraesCS4D01G164300 chr1D 93.007 715 28 9 1 697 114428800 114429510 0.000000e+00 1024.0
44 TraesCS4D01G164300 chr1D 92.201 718 33 7 1 697 92328033 92328748 0.000000e+00 994.0
45 TraesCS4D01G164300 chr1D 89.623 636 24 14 94 697 346586590 346585965 0.000000e+00 771.0
46 TraesCS4D01G164300 chr1D 89.785 558 28 3 2219 2774 209572300 209571770 0.000000e+00 688.0
47 TraesCS4D01G164300 chr1D 95.046 323 16 0 1458 1780 209725239 209724917 4.160000e-140 508.0
48 TraesCS4D01G164300 chr1D 92.432 185 11 3 806 989 395800046 395800228 1.280000e-65 261.0
49 TraesCS4D01G164300 chr1D 95.294 85 3 1 696 780 420675758 420675675 2.920000e-27 134.0
50 TraesCS4D01G164300 chr1D 96.250 80 1 1 696 775 193667112 193667189 3.780000e-26 130.0
51 TraesCS4D01G164300 chr1D 94.118 85 5 0 696 780 464631234 464631318 3.780000e-26 130.0
52 TraesCS4D01G164300 chr1D 93.976 83 4 1 695 777 319572470 319572551 1.760000e-24 124.0
53 TraesCS4D01G164300 chr1D 92.771 83 6 0 696 778 360099097 360099179 2.270000e-23 121.0
54 TraesCS4D01G164300 chr1D 90.588 85 8 0 696 780 26566667 26566751 3.810000e-21 113.0
55 TraesCS4D01G164300 chr1D 100.000 45 0 0 1775 1819 209635207 209635163 2.980000e-12 84.2
56 TraesCS4D01G164300 chr1D 97.727 44 1 0 1817 1860 209574746 209574703 4.990000e-10 76.8
57 TraesCS4D01G164300 chr5B 93.890 802 41 3 3855 4655 203450729 203451523 0.000000e+00 1203.0
58 TraesCS4D01G164300 chr5B 93.566 715 39 4 3151 3858 203341435 203342149 0.000000e+00 1059.0
59 TraesCS4D01G164300 chr5B 85.817 557 28 4 2219 2774 203340923 203341429 1.140000e-150 544.0
60 TraesCS4D01G164300 chr5B 92.258 310 24 0 1471 1780 203112650 203112959 1.540000e-119 440.0
61 TraesCS4D01G164300 chr5B 100.000 45 0 0 1775 1819 203295909 203295953 2.980000e-12 84.2
62 TraesCS4D01G164300 chr5B 97.727 44 1 0 1817 1860 203338480 203338523 4.990000e-10 76.8
63 TraesCS4D01G164300 chr5D 93.390 711 28 8 1 697 198333058 198333763 0.000000e+00 1035.0
64 TraesCS4D01G164300 chr5D 93.007 715 31 6 1 697 106965451 106966164 0.000000e+00 1026.0
65 TraesCS4D01G164300 chr5D 94.062 421 12 1 290 697 332841919 332842339 1.100000e-175 627.0
66 TraesCS4D01G164300 chr5D 90.299 134 5 5 795 924 54786346 54786475 8.010000e-38 169.0
67 TraesCS4D01G164300 chr5D 96.386 83 2 1 696 778 114804771 114804852 8.120000e-28 135.0
68 TraesCS4D01G164300 chr5D 89.000 100 10 1 696 794 358626193 358626292 6.330000e-24 122.0
69 TraesCS4D01G164300 chr3D 93.099 710 34 5 1 697 612162804 612162097 0.000000e+00 1026.0
70 TraesCS4D01G164300 chr3D 92.827 711 36 4 1 697 612150502 612149793 0.000000e+00 1016.0
71 TraesCS4D01G164300 chr3D 91.603 131 6 3 795 924 26327437 26327563 4.790000e-40 176.0
72 TraesCS4D01G164300 chr3D 98.795 83 1 0 694 776 140063883 140063801 1.040000e-31 148.0
73 TraesCS4D01G164300 chr3D 96.429 84 3 0 695 778 22068963 22069046 6.280000e-29 139.0
74 TraesCS4D01G164300 chr3D 95.294 85 4 0 696 780 564623362 564623446 8.120000e-28 135.0
75 TraesCS4D01G164300 chr3D 95.000 40 2 0 1673 1712 600410880 600410919 3.890000e-06 63.9
76 TraesCS4D01G164300 chr7D 92.587 715 33 7 1 697 132788174 132787462 0.000000e+00 1009.0
77 TraesCS4D01G164300 chr7D 91.396 616 30 6 95 697 135742468 135743073 0.000000e+00 822.0
78 TraesCS4D01G164300 chr7D 91.883 308 24 1 1771 2077 613624395 613624702 3.330000e-116 429.0
79 TraesCS4D01G164300 chr7D 85.455 385 37 4 1051 1419 613623834 613624215 2.630000e-102 383.0
80 TraesCS4D01G164300 chr7D 94.611 167 6 3 795 959 32506125 32506290 5.980000e-64 255.0
81 TraesCS4D01G164300 chr7D 96.000 100 3 1 695 794 528078423 528078325 1.340000e-35 161.0
82 TraesCS4D01G164300 chr7D 94.949 99 3 1 696 794 64431211 64431115 2.240000e-33 154.0
83 TraesCS4D01G164300 chr7D 97.701 87 1 1 694 780 636066463 636066378 1.040000e-31 148.0
84 TraesCS4D01G164300 chr7D 97.701 87 1 1 694 780 636117115 636117030 1.040000e-31 148.0
85 TraesCS4D01G164300 chr7D 96.512 86 3 0 693 778 310861998 310862083 4.860000e-30 143.0
86 TraesCS4D01G164300 chr7D 96.552 87 2 1 694 780 636160402 636160317 4.860000e-30 143.0
87 TraesCS4D01G164300 chr7D 82.667 150 21 5 883 1031 32506283 32506428 1.360000e-25 128.0
88 TraesCS4D01G164300 chr4B 90.947 729 29 9 753 1480 626780604 626781296 0.000000e+00 946.0
89 TraesCS4D01G164300 chr4B 94.459 379 19 2 818 1196 37100688 37101064 2.410000e-162 582.0
90 TraesCS4D01G164300 chr4B 95.455 66 2 1 754 819 37091977 37092041 2.290000e-18 104.0
91 TraesCS4D01G164300 chr1B 90.409 709 44 17 1 697 255804218 255803522 0.000000e+00 911.0
92 TraesCS4D01G164300 chr1B 95.181 83 4 0 696 778 360520547 360520465 1.050000e-26 132.0
93 TraesCS4D01G164300 chr1B 93.333 90 5 1 692 780 642428009 642427920 1.050000e-26 132.0
94 TraesCS4D01G164300 chr2A 84.500 400 50 8 302 697 120969490 120969099 7.310000e-103 385.0
95 TraesCS4D01G164300 chr7B 78.049 615 95 29 1781 2370 728932660 728933259 7.410000e-93 351.0
96 TraesCS4D01G164300 chr7B 88.889 234 24 2 1846 2077 704287701 704287934 2.120000e-73 287.0
97 TraesCS4D01G164300 chr7B 85.093 161 18 3 1660 1817 704287548 704287705 4.820000e-35 159.0
98 TraesCS4D01G164300 chr7A 77.524 614 100 25 1786 2370 705295436 705296040 7.460000e-88 335.0
99 TraesCS4D01G164300 chr7A 88.931 262 23 5 795 1050 680662007 680661746 7.520000e-83 318.0
100 TraesCS4D01G164300 chr3A 94.000 200 9 3 794 990 648609612 648609413 2.720000e-77 300.0
101 TraesCS4D01G164300 chr6B 96.386 83 3 0 696 778 249503799 249503717 2.260000e-28 137.0
102 TraesCS4D01G164300 chr1A 85.484 124 8 3 804 924 19461368 19461252 2.270000e-23 121.0
103 TraesCS4D01G164300 chr1A 83.871 124 10 3 804 924 19354931 19354815 4.920000e-20 110.0
104 TraesCS4D01G164300 chrUn 93.506 77 5 0 1059 1135 97982513 97982589 1.060000e-21 115.0
105 TraesCS4D01G164300 chrUn 93.590 78 4 1 699 776 317082920 317082844 1.060000e-21 115.0
106 TraesCS4D01G164300 chrUn 92.500 80 5 1 697 776 228436716 228436638 3.810000e-21 113.0
107 TraesCS4D01G164300 chrUn 89.535 86 9 0 695 780 24788361 24788276 4.920000e-20 110.0
108 TraesCS4D01G164300 chrUn 90.000 80 8 0 695 774 249898037 249898116 2.290000e-18 104.0
109 TraesCS4D01G164300 chrUn 88.235 85 10 0 696 780 89868437 89868521 8.240000e-18 102.0
110 TraesCS4D01G164300 chrUn 97.674 43 0 1 753 794 324407831 324407873 6.460000e-09 73.1


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 TraesCS4D01G164300 chr4D 264460586 264465240 4654 False 8597.000000 8597 100.000000 1 4655 1 chr4D.!!$F2 4654
1 TraesCS4D01G164300 chr2D 575266246 575270152 3906 True 6804.000000 6804 98.107000 751 4655 1 chr2D.!!$R3 3904
2 TraesCS4D01G164300 chr2D 263420061 263424012 3951 True 6787.000000 6787 97.638000 693 4655 1 chr2D.!!$R2 3962
3 TraesCS4D01G164300 chr2D 118379444 118383340 3896 True 3252.500000 4124 96.630000 695 4655 2 chr2D.!!$R4 3960
4 TraesCS4D01G164300 chr4A 359636468 359640375 3907 True 6366.000000 6366 96.095000 751 4655 1 chr4A.!!$R1 3904
5 TraesCS4D01G164300 chr2B 706584902 706588725 3823 False 3213.000000 6071 95.296000 750 4655 2 chr2B.!!$F1 3905
6 TraesCS4D01G164300 chr6A 526161136 526165107 3971 True 3274.000000 4409 97.317000 753 4655 2 chr6A.!!$R3 3902
7 TraesCS4D01G164300 chr6A 393799769 393801376 1607 False 2440.000000 2440 94.161000 3058 4655 1 chr6A.!!$F2 1597
8 TraesCS4D01G164300 chr3B 739839630 739843328 3698 False 1830.666667 4183 95.154333 696 4092 3 chr3B.!!$F3 3396
9 TraesCS4D01G164300 chr3B 758389167 758393857 4690 False 1479.666667 2519 93.874333 1306 4655 3 chr3B.!!$F4 3349
10 TraesCS4D01G164300 chr3B 749558713 749559673 960 False 1367.000000 1367 92.340000 3585 4548 1 chr3B.!!$F2 963
11 TraesCS4D01G164300 chr6D 249489221 249491765 2544 False 1551.000000 2529 94.005500 2602 4655 2 chr6D.!!$F6 2053
12 TraesCS4D01G164300 chr6D 292125266 292125976 710 True 1046.000000 1046 93.530000 1 697 1 chr6D.!!$R2 696
13 TraesCS4D01G164300 chr6D 258570612 258571306 694 False 987.000000 987 92.340000 1 697 1 chr6D.!!$F1 696
14 TraesCS4D01G164300 chr6D 159499855 159500565 710 True 979.000000 979 91.877000 1 697 1 chr6D.!!$R1 696
15 TraesCS4D01G164300 chr6D 473251614 473252201 587 False 710.000000 710 88.889000 138 713 1 chr6D.!!$F5 575
16 TraesCS4D01G164300 chr1D 209542164 209542958 794 True 1214.000000 1214 94.140000 3855 4655 1 chr1D.!!$R1 800
17 TraesCS4D01G164300 chr1D 114428800 114429510 710 False 1024.000000 1024 93.007000 1 697 1 chr1D.!!$F3 696
18 TraesCS4D01G164300 chr1D 92328033 92328748 715 False 994.000000 994 92.201000 1 697 1 chr1D.!!$F2 696
19 TraesCS4D01G164300 chr1D 346585965 346586590 625 True 771.000000 771 89.623000 94 697 1 chr1D.!!$R4 603
20 TraesCS4D01G164300 chr1D 209571047 209574746 3699 True 624.600000 1109 94.073333 1817 3861 3 chr1D.!!$R6 2044
21 TraesCS4D01G164300 chr5B 203450729 203451523 794 False 1203.000000 1203 93.890000 3855 4655 1 chr5B.!!$F3 800
22 TraesCS4D01G164300 chr5B 203338480 203342149 3669 False 559.933333 1059 92.370000 1817 3858 3 chr5B.!!$F4 2041
23 TraesCS4D01G164300 chr5D 198333058 198333763 705 False 1035.000000 1035 93.390000 1 697 1 chr5D.!!$F4 696
24 TraesCS4D01G164300 chr5D 106965451 106966164 713 False 1026.000000 1026 93.007000 1 697 1 chr5D.!!$F2 696
25 TraesCS4D01G164300 chr3D 612162097 612162804 707 True 1026.000000 1026 93.099000 1 697 1 chr3D.!!$R3 696
26 TraesCS4D01G164300 chr3D 612149793 612150502 709 True 1016.000000 1016 92.827000 1 697 1 chr3D.!!$R2 696
27 TraesCS4D01G164300 chr7D 132787462 132788174 712 True 1009.000000 1009 92.587000 1 697 1 chr7D.!!$R2 696
28 TraesCS4D01G164300 chr7D 135742468 135743073 605 False 822.000000 822 91.396000 95 697 1 chr7D.!!$F1 602
29 TraesCS4D01G164300 chr7D 613623834 613624702 868 False 406.000000 429 88.669000 1051 2077 2 chr7D.!!$F4 1026
30 TraesCS4D01G164300 chr4B 626780604 626781296 692 False 946.000000 946 90.947000 753 1480 1 chr4B.!!$F3 727
31 TraesCS4D01G164300 chr1B 255803522 255804218 696 True 911.000000 911 90.409000 1 697 1 chr1B.!!$R1 696
32 TraesCS4D01G164300 chr7B 728932660 728933259 599 False 351.000000 351 78.049000 1781 2370 1 chr7B.!!$F1 589
33 TraesCS4D01G164300 chr7A 705295436 705296040 604 False 335.000000 335 77.524000 1786 2370 1 chr7A.!!$F1 584

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
230 247 0.105194 TCCTCACCTCCACTTCACCA 60.105 55.000 0.00 0.00 0.0 4.17 F
819 897 2.044053 CCCCCACGCATGAACCAT 60.044 61.111 0.00 0.00 0.0 3.55 F
1534 2158 1.002366 CCACGATTTCTCTCTTGCGG 58.998 55.000 0.00 0.00 0.0 5.69 F
2498 5748 9.309516 CAAAGCTAATGATATCAAATTTGTGCT 57.690 29.630 17.47 10.69 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1501 0.459899 TGCGCACGATCTACCAATCT 59.540 50.000 5.66 0.0 0.00 2.40 R
2423 5673 2.880890 GGCACTGTCAATGTCTGAACTT 59.119 45.455 0.00 0.0 35.22 2.66 R
2534 5784 4.256920 TGATTTTCTAGGCTCAAGCACTC 58.743 43.478 4.13 0.0 44.36 3.51 R
4251 8134 8.553153 TCCCTTAACAATATGACTGGTTGATAA 58.447 33.333 0.00 0.0 0.00 1.75 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
75 77 1.480789 AGGGAAAAACCAACGCAAGT 58.519 45.000 0.00 0.00 45.14 3.16
88 90 0.716108 CGCAAGTTCAAGAGGTAGCG 59.284 55.000 0.00 0.00 37.91 4.26
142 155 2.902705 ACGCCAAGTCAAGTCAAGTA 57.097 45.000 0.00 0.00 0.00 2.24
195 210 7.936847 TCTTATCCCTCGCATTACATTATTTGT 59.063 33.333 0.00 0.00 42.62 2.83
216 232 2.038426 TCATTTGCCTCTCGTTTCCTCA 59.962 45.455 0.00 0.00 0.00 3.86
219 236 0.832135 TGCCTCTCGTTTCCTCACCT 60.832 55.000 0.00 0.00 0.00 4.00
230 247 0.105194 TCCTCACCTCCACTTCACCA 60.105 55.000 0.00 0.00 0.00 4.17
480 519 5.692115 TTTATGTAGGCATCACTCCTTGA 57.308 39.130 0.00 0.00 39.11 3.02
545 584 5.652014 TGGGTAGCCATACTTTTGATTCTTG 59.348 40.000 10.27 0.00 32.12 3.02
574 613 3.182887 TGATAGGTTTGTTTGGCCCAT 57.817 42.857 0.00 0.00 0.00 4.00
575 614 3.515562 TGATAGGTTTGTTTGGCCCATT 58.484 40.909 0.00 0.00 0.00 3.16
577 616 5.087323 TGATAGGTTTGTTTGGCCCATTAA 58.913 37.500 0.00 0.00 0.00 1.40
580 625 3.906846 AGGTTTGTTTGGCCCATTAATGA 59.093 39.130 17.23 0.00 0.00 2.57
819 897 2.044053 CCCCCACGCATGAACCAT 60.044 61.111 0.00 0.00 0.00 3.55
1301 1501 3.374220 TCGCTTCTTGTTCTTTCGGTA 57.626 42.857 0.00 0.00 0.00 4.02
1534 2158 1.002366 CCACGATTTCTCTCTTGCGG 58.998 55.000 0.00 0.00 0.00 5.69
2498 5748 9.309516 CAAAGCTAATGATATCAAATTTGTGCT 57.690 29.630 17.47 10.69 0.00 4.40
3359 7155 5.045578 AGGCTACTATGGAAGTTGTGAATGT 60.046 40.000 0.00 0.00 39.80 2.71
3929 7811 0.107703 CCGGTAATCAGCTGCTCCAA 60.108 55.000 9.47 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 2.803956 TCCTTCTCGCTACCTCTTGAA 58.196 47.619 0.00 0.00 0.00 2.69
88 90 1.432270 CGGCGCCAGAAATCCTTCTC 61.432 60.000 28.98 0.00 40.05 2.87
142 155 5.013704 TGTGATGGGTACTTGGTATGTCTTT 59.986 40.000 0.00 0.00 0.00 2.52
195 210 2.038426 TGAGGAAACGAGAGGCAAATGA 59.962 45.455 0.00 0.00 0.00 2.57
216 232 0.251341 GGCAATGGTGAAGTGGAGGT 60.251 55.000 0.00 0.00 0.00 3.85
219 236 0.179004 AACGGCAATGGTGAAGTGGA 60.179 50.000 0.00 0.00 0.00 4.02
230 247 2.831526 AGAGGGCAAATAAAACGGCAAT 59.168 40.909 0.00 0.00 0.00 3.56
511 550 4.478686 AGTATGGCTACCCAAGAAATTCCT 59.521 41.667 0.00 0.00 46.14 3.36
545 584 7.704899 GGCCAAACAAACCTATCATAACATTAC 59.295 37.037 0.00 0.00 0.00 1.89
560 599 5.762711 AGTTTCATTAATGGGCCAAACAAAC 59.237 36.000 22.44 18.03 0.00 2.93
577 616 9.206870 CATGCACCAAAGTTAAAATAGTTTCAT 57.793 29.630 0.00 0.00 0.00 2.57
580 625 8.200792 TCACATGCACCAAAGTTAAAATAGTTT 58.799 29.630 0.00 0.00 0.00 2.66
640 692 8.352201 CCAAATTTTCAATCAACTCTACAGTGA 58.648 33.333 0.00 0.00 31.06 3.41
799 877 2.282180 GTTCATGCGTGGGGGTGT 60.282 61.111 5.98 0.00 0.00 4.16
819 897 2.690452 CGAGGAGAGGGAGGGGAA 59.310 66.667 0.00 0.00 0.00 3.97
888 967 3.825160 GACAAGCTCCCGTGTGGCA 62.825 63.158 0.00 0.00 33.76 4.92
1053 1237 3.000819 TCGACCTCCACCGCCATT 61.001 61.111 0.00 0.00 0.00 3.16
1301 1501 0.459899 TGCGCACGATCTACCAATCT 59.540 50.000 5.66 0.00 0.00 2.40
1382 1970 5.537674 AGATTCAAGGCACAATCTTTCTTGT 59.462 36.000 0.00 0.00 36.15 3.16
2423 5673 2.880890 GGCACTGTCAATGTCTGAACTT 59.119 45.455 0.00 0.00 35.22 2.66
2534 5784 4.256920 TGATTTTCTAGGCTCAAGCACTC 58.743 43.478 4.13 0.00 44.36 3.51
2806 6072 8.275758 AGGAGCTCGATATCAGATTACCTTATA 58.724 37.037 7.83 0.00 0.00 0.98
2809 6075 5.329399 AGGAGCTCGATATCAGATTACCTT 58.671 41.667 7.83 0.00 0.00 3.50
4251 8134 8.553153 TCCCTTAACAATATGACTGGTTGATAA 58.447 33.333 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.