Multiple sequence alignment - TraesCS3A01G211300

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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 TraesCS3A01G211300 chr3A 100.000 1800 0 0 582 2381 379815251 379817050 0.000000e+00 3325.0
1 TraesCS3A01G211300 chr3A 96.532 1730 60 0 582 2311 379798318 379800047 0.000000e+00 2863.0
2 TraesCS3A01G211300 chr3A 100.000 283 0 0 1 283 379814670 379814952 7.540000e-145 523.0
3 TraesCS3A01G211300 chr3A 95.760 283 11 1 1 283 379797964 379798245 2.790000e-124 455.0
4 TraesCS3A01G211300 chr3A 78.125 768 117 38 1468 2210 509036574 509035833 7.810000e-120 440.0
5 TraesCS3A01G211300 chr3A 91.459 281 24 0 3 283 189085427 189085707 1.030000e-103 387.0
6 TraesCS3A01G211300 chr3A 90.734 259 21 2 1215 1473 509036915 509036660 2.270000e-90 342.0
7 TraesCS3A01G211300 chr3A 90.000 260 22 3 1215 1474 509028870 509028615 1.360000e-87 333.0
8 TraesCS3A01G211300 chr3A 74.558 735 123 53 1614 2311 562596913 562596206 1.810000e-66 263.0
9 TraesCS3A01G211300 chr3A 90.110 182 16 2 582 762 258472714 258472894 3.960000e-58 235.0
10 TraesCS3A01G211300 chr3A 88.824 170 11 4 1468 1637 509028530 509028369 4.010000e-48 202.0
11 TraesCS3A01G211300 chr3A 90.000 60 6 0 1070 1129 316592624 316592565 7.060000e-11 78.7
12 TraesCS3A01G211300 chr6A 95.111 859 31 7 1460 2311 333662058 333662912 0.000000e+00 1343.0
13 TraesCS3A01G211300 chr6A 95.111 859 31 7 1460 2311 333745151 333746005 0.000000e+00 1343.0
14 TraesCS3A01G211300 chr6A 90.895 626 38 15 1694 2311 521579521 521580135 0.000000e+00 822.0
15 TraesCS3A01G211300 chr6A 86.893 412 42 4 582 991 270613999 270614400 3.610000e-123 451.0
16 TraesCS3A01G211300 chr6A 77.378 778 112 44 1468 2210 111684797 111685545 1.020000e-108 403.0
17 TraesCS3A01G211300 chr6A 93.191 235 15 1 6 239 303768694 303768928 6.300000e-91 344.0
18 TraesCS3A01G211300 chr6A 90.698 258 21 2 1215 1472 111692426 111692680 8.150000e-90 340.0
19 TraesCS3A01G211300 chr6A 90.385 260 22 3 1215 1474 111684457 111684713 2.930000e-89 339.0
20 TraesCS3A01G211300 chr6A 92.340 235 17 1 6 239 303760896 303761130 1.360000e-87 333.0
21 TraesCS3A01G211300 chr6A 91.489 235 19 1 6 239 246645867 246646101 2.950000e-84 322.0
22 TraesCS3A01G211300 chr6A 91.489 235 19 1 6 239 246653540 246653774 2.950000e-84 322.0
23 TraesCS3A01G211300 chr6A 93.956 182 11 0 1 182 361410008 361410189 2.330000e-70 276.0
24 TraesCS3A01G211300 chr6A 90.426 188 12 3 1 187 171776683 171776501 2.360000e-60 243.0
25 TraesCS3A01G211300 chr6A 91.429 175 15 0 1 175 361418314 361418488 8.500000e-60 241.0
26 TraesCS3A01G211300 chr6A 89.894 188 13 3 1 187 171784931 171784749 1.100000e-58 237.0
27 TraesCS3A01G211300 chr6A 92.683 164 9 2 1215 1378 266962280 266962120 1.420000e-57 233.0
28 TraesCS3A01G211300 chr6A 92.073 164 10 2 1215 1378 338852163 338852003 6.620000e-56 228.0
29 TraesCS3A01G211300 chr6A 95.714 140 6 0 1 140 258828713 258828574 2.380000e-55 226.0
30 TraesCS3A01G211300 chr6A 95.000 140 7 0 1 140 258835995 258835856 1.110000e-53 220.0
31 TraesCS3A01G211300 chr6A 85.185 216 25 5 4 213 253511577 253511363 5.150000e-52 215.0
32 TraesCS3A01G211300 chr6A 84.722 216 26 5 4 213 253447468 253447254 2.400000e-50 209.0
33 TraesCS3A01G211300 chr6A 85.987 157 19 1 699 855 214216183 214216030 5.270000e-37 165.0
34 TraesCS3A01G211300 chr6A 90.625 96 8 1 1122 1216 236062399 236062304 2.480000e-25 126.0
35 TraesCS3A01G211300 chr6A 91.860 86 7 0 582 667 194912158 194912243 1.160000e-23 121.0
36 TraesCS3A01G211300 chr1A 91.054 816 48 15 1522 2327 196170610 196169810 0.000000e+00 1079.0
37 TraesCS3A01G211300 chr1A 82.722 1227 148 40 1123 2312 121206859 121208058 0.000000e+00 1033.0
38 TraesCS3A01G211300 chr1A 82.524 1236 144 40 1121 2311 121190273 121191481 0.000000e+00 1020.0
39 TraesCS3A01G211300 chr1A 82.339 1223 147 46 1121 2304 121198569 121199761 0.000000e+00 998.0
40 TraesCS3A01G211300 chr1A 92.800 500 35 1 582 1080 311014290 311014789 0.000000e+00 723.0
41 TraesCS3A01G211300 chr1A 91.800 500 37 2 582 1080 343374061 343374557 0.000000e+00 693.0
42 TraesCS3A01G211300 chr1A 91.400 500 39 2 582 1080 132156615 132157111 0.000000e+00 682.0
43 TraesCS3A01G211300 chr1A 90.400 500 43 3 582 1080 343366129 343366624 0.000000e+00 652.0
44 TraesCS3A01G211300 chr1A 95.349 258 12 0 26 283 132156284 132156541 6.130000e-111 411.0
45 TraesCS3A01G211300 chr1A 93.798 258 16 0 26 283 343365799 343366056 2.870000e-104 388.0
46 TraesCS3A01G211300 chr1A 94.298 228 13 0 56 283 343373761 343373988 1.350000e-92 350.0
47 TraesCS3A01G211300 chr1A 88.356 292 23 7 1 283 311013927 311014216 8.150000e-90 340.0
48 TraesCS3A01G211300 chr1A 86.989 269 30 4 1207 1474 203095444 203095180 4.980000e-77 298.0
49 TraesCS3A01G211300 chr1A 90.811 185 15 2 4 187 428019632 428019449 1.830000e-61 246.0
50 TraesCS3A01G211300 chr1A 89.697 165 10 2 119 283 546007576 546007419 1.120000e-48 204.0
51 TraesCS3A01G211300 chr1A 95.238 105 5 0 582 686 545991822 545991718 1.460000e-37 167.0
52 TraesCS3A01G211300 chr1A 94.175 103 6 0 582 684 546007346 546007244 8.810000e-35 158.0
53 TraesCS3A01G211300 chr1A 95.745 47 2 0 203 249 312300283 312300329 2.540000e-10 76.8
54 TraesCS3A01G211300 chr1A 95.349 43 2 0 1516 1558 448784694 448784736 4.250000e-08 69.4
55 TraesCS3A01G211300 chr7A 94.146 632 23 13 1681 2312 200594548 200595165 0.000000e+00 950.0
56 TraesCS3A01G211300 chr7A 95.622 571 22 3 1742 2311 200586625 200587193 0.000000e+00 913.0
57 TraesCS3A01G211300 chr7A 92.000 500 33 3 582 1080 462070934 462070441 0.000000e+00 695.0
58 TraesCS3A01G211300 chr7A 89.563 412 42 1 719 1129 578206638 578206227 2.710000e-144 521.0
59 TraesCS3A01G211300 chr7A 85.591 465 63 3 668 1129 398943920 398943457 3.560000e-133 484.0
60 TraesCS3A01G211300 chr7A 87.136 412 50 3 582 991 575068341 575068751 4.640000e-127 464.0
61 TraesCS3A01G211300 chr7A 95.745 282 12 0 2 283 462071288 462071007 2.790000e-124 455.0
62 TraesCS3A01G211300 chr7A 92.537 268 16 3 1207 1474 207567996 207567733 4.800000e-102 381.0
63 TraesCS3A01G211300 chr7A 90.037 271 21 5 1206 1474 226851389 226851655 1.750000e-91 346.0
64 TraesCS3A01G211300 chr7A 95.187 187 8 1 1468 1654 207559664 207559479 6.440000e-76 294.0
65 TraesCS3A01G211300 chr7A 75.034 741 115 57 1614 2312 150977691 150978403 1.800000e-71 279.0
66 TraesCS3A01G211300 chr7A 94.737 57 1 2 2313 2369 385243433 385243487 1.170000e-13 87.9
67 TraesCS3A01G211300 chr4A 91.318 622 43 9 1693 2311 570857863 570858476 0.000000e+00 839.0
68 TraesCS3A01G211300 chr4A 92.857 322 23 0 808 1129 359298247 359298568 3.580000e-128 468.0
69 TraesCS3A01G211300 chr4A 95.406 283 13 0 1 283 359275677 359275959 3.610000e-123 451.0
70 TraesCS3A01G211300 chr4A 94.700 283 15 0 1 283 359297745 359298027 7.810000e-120 440.0
71 TraesCS3A01G211300 chr4A 91.250 320 28 0 810 1129 359276175 359276494 1.010000e-118 436.0
72 TraesCS3A01G211300 chr4A 94.346 283 16 0 1 283 198179614 198179896 3.630000e-118 435.0
73 TraesCS3A01G211300 chr4A 93.993 283 17 0 1 283 528691891 528692173 1.690000e-116 429.0
74 TraesCS3A01G211300 chr4A 92.580 283 21 0 1 283 198177460 198177742 7.920000e-110 407.0
75 TraesCS3A01G211300 chr4A 92.226 283 22 0 1 283 198175036 198175318 3.690000e-108 401.0
76 TraesCS3A01G211300 chr4A 91.697 277 22 1 1 276 360227382 360227106 1.340000e-102 383.0
77 TraesCS3A01G211300 chr4A 93.617 235 14 1 6 239 499569568 499569802 1.350000e-92 350.0
78 TraesCS3A01G211300 chr4A 91.111 180 15 1 584 763 421000764 421000586 2.360000e-60 243.0
79 TraesCS3A01G211300 chr4A 94.737 152 8 0 582 733 359276033 359276184 1.100000e-58 237.0
80 TraesCS3A01G211300 chr4A 94.737 152 8 0 582 733 359298101 359298252 1.100000e-58 237.0
81 TraesCS3A01G211300 chr4A 98.077 52 1 0 2312 2363 304994991 304995042 9.060000e-15 91.6
82 TraesCS3A01G211300 chr4A 94.643 56 1 2 2312 2367 338550973 338551026 4.220000e-13 86.1
83 TraesCS3A01G211300 chr2A 90.620 629 45 12 1693 2318 505141328 505140711 0.000000e+00 822.0
84 TraesCS3A01G211300 chr2A 90.600 500 43 4 582 1080 194494321 194494817 0.000000e+00 660.0
85 TraesCS3A01G211300 chr2A 90.400 500 40 5 582 1080 194511278 194511770 0.000000e+00 651.0
86 TraesCS3A01G211300 chr2A 86.239 545 71 3 588 1129 286041433 286040890 2.640000e-164 588.0
87 TraesCS3A01G211300 chr2A 86.000 550 73 3 582 1128 286033598 286033050 9.480000e-164 586.0
88 TraesCS3A01G211300 chr2A 92.308 260 17 2 1215 1474 64288703 64288959 1.340000e-97 366.0
89 TraesCS3A01G211300 chr2A 74.728 736 118 55 1614 2311 691985301 691984596 1.400000e-67 267.0
90 TraesCS3A01G211300 chr2A 92.784 97 6 1 1121 1216 271824956 271825052 3.190000e-29 139.0
91 TraesCS3A01G211300 chr2A 90.722 97 8 1 1121 1216 271816946 271817042 6.910000e-26 128.0
92 TraesCS3A01G211300 chr5A 89.753 283 29 0 1 283 192872578 192872860 1.740000e-96 363.0
93 TraesCS3A01G211300 chr5A 88.015 267 26 5 1209 1473 208694706 208694444 6.390000e-81 311.0
94 TraesCS3A01G211300 chr5A 87.308 260 28 4 1215 1473 208693202 208692947 2.310000e-75 292.0
95 TraesCS3A01G211300 chr5A 87.864 206 24 1 649 854 168519780 168519984 8.500000e-60 241.0
96 TraesCS3A01G211300 chr5A 92.784 97 6 1 1121 1216 332241332 332241236 3.190000e-29 139.0
97 TraesCS3A01G211300 chr5A 98.039 51 1 0 2312 2362 217428669 217428719 3.260000e-14 89.8
98 TraesCS3A01G211300 chr6B 95.181 83 4 0 585 667 522795193 522795111 5.340000e-27 132.0
99 TraesCS3A01G211300 chr6B 94.737 57 1 2 2309 2365 380189947 380189893 1.170000e-13 87.9
100 TraesCS3A01G211300 chr1B 93.023 86 6 0 582 667 67647925 67647840 2.480000e-25 126.0
101 TraesCS3A01G211300 chr1B 93.023 86 6 0 582 667 67655747 67655662 2.480000e-25 126.0
102 TraesCS3A01G211300 chr4D 89.109 101 8 3 1118 1216 180126760 180126661 3.210000e-24 122.0
103 TraesCS3A01G211300 chr4D 87.342 79 7 2 600 675 299304524 299304602 1.170000e-13 87.9
104 TraesCS3A01G211300 chr4B 91.860 86 7 0 582 667 439541838 439541923 1.160000e-23 121.0
105 TraesCS3A01G211300 chr4B 93.671 79 5 0 582 660 439534134 439534212 4.160000e-23 119.0
106 TraesCS3A01G211300 chr4B 79.861 144 17 5 20 152 18566253 18566395 7.010000e-16 95.3
107 TraesCS3A01G211300 chr4B 100.000 49 0 0 2312 2360 317421719 317421671 9.060000e-15 91.6
108 TraesCS3A01G211300 chr4B 86.076 79 8 3 600 675 65764900 65764978 5.450000e-12 82.4
109 TraesCS3A01G211300 chr6D 92.647 68 5 0 600 667 232928595 232928528 5.420000e-17 99.0
110 TraesCS3A01G211300 chr6D 90.411 73 4 2 606 675 232957333 232957261 2.520000e-15 93.5
111 TraesCS3A01G211300 chr6D 89.041 73 5 3 606 675 175671506 175671434 1.170000e-13 87.9
112 TraesCS3A01G211300 chr6D 86.842 76 7 2 606 678 178413833 178413758 5.450000e-12 82.4
113 TraesCS3A01G211300 chr7D 98.039 51 1 0 2312 2362 333012000 333012050 3.260000e-14 89.8
114 TraesCS3A01G211300 chrUn 94.643 56 2 1 2312 2366 249704947 249705002 4.220000e-13 86.1
115 TraesCS3A01G211300 chr1D 93.220 59 2 2 2312 2369 178118251 178118194 4.220000e-13 86.1


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 TraesCS3A01G211300 chr3A 379814670 379817050 2380 False 1924.000000 3325 100.000000 1 2381 2 chr3A.!!$F4 2380
1 TraesCS3A01G211300 chr3A 379797964 379800047 2083 False 1659.000000 2863 96.146000 1 2311 2 chr3A.!!$F3 2310
2 TraesCS3A01G211300 chr3A 509035833 509036915 1082 True 391.000000 440 84.429500 1215 2210 2 chr3A.!!$R4 995
3 TraesCS3A01G211300 chr3A 509028369 509028870 501 True 267.500000 333 89.412000 1215 1637 2 chr3A.!!$R3 422
4 TraesCS3A01G211300 chr3A 562596206 562596913 707 True 263.000000 263 74.558000 1614 2311 1 chr3A.!!$R2 697
5 TraesCS3A01G211300 chr6A 333662058 333662912 854 False 1343.000000 1343 95.111000 1460 2311 1 chr6A.!!$F8 851
6 TraesCS3A01G211300 chr6A 333745151 333746005 854 False 1343.000000 1343 95.111000 1460 2311 1 chr6A.!!$F9 851
7 TraesCS3A01G211300 chr6A 521579521 521580135 614 False 822.000000 822 90.895000 1694 2311 1 chr6A.!!$F12 617
8 TraesCS3A01G211300 chr6A 111684457 111685545 1088 False 371.000000 403 83.881500 1215 2210 2 chr6A.!!$F13 995
9 TraesCS3A01G211300 chr1A 196169810 196170610 800 True 1079.000000 1079 91.054000 1522 2327 1 chr1A.!!$R1 805
10 TraesCS3A01G211300 chr1A 121206859 121208058 1199 False 1033.000000 1033 82.722000 1123 2312 1 chr1A.!!$F3 1189
11 TraesCS3A01G211300 chr1A 121190273 121191481 1208 False 1020.000000 1020 82.524000 1121 2311 1 chr1A.!!$F1 1190
12 TraesCS3A01G211300 chr1A 121198569 121199761 1192 False 998.000000 998 82.339000 1121 2304 1 chr1A.!!$F2 1183
13 TraesCS3A01G211300 chr1A 132156284 132157111 827 False 546.500000 682 93.374500 26 1080 2 chr1A.!!$F6 1054
14 TraesCS3A01G211300 chr1A 311013927 311014789 862 False 531.500000 723 90.578000 1 1080 2 chr1A.!!$F7 1079
15 TraesCS3A01G211300 chr1A 343373761 343374557 796 False 521.500000 693 93.049000 56 1080 2 chr1A.!!$F9 1024
16 TraesCS3A01G211300 chr1A 343365799 343366624 825 False 520.000000 652 92.099000 26 1080 2 chr1A.!!$F8 1054
17 TraesCS3A01G211300 chr7A 200594548 200595165 617 False 950.000000 950 94.146000 1681 2312 1 chr7A.!!$F3 631
18 TraesCS3A01G211300 chr7A 200586625 200587193 568 False 913.000000 913 95.622000 1742 2311 1 chr7A.!!$F2 569
19 TraesCS3A01G211300 chr7A 462070441 462071288 847 True 575.000000 695 93.872500 2 1080 2 chr7A.!!$R5 1078
20 TraesCS3A01G211300 chr7A 150977691 150978403 712 False 279.000000 279 75.034000 1614 2312 1 chr7A.!!$F1 698
21 TraesCS3A01G211300 chr4A 570857863 570858476 613 False 839.000000 839 91.318000 1693 2311 1 chr4A.!!$F5 618
22 TraesCS3A01G211300 chr4A 198175036 198179896 4860 False 414.333333 435 93.050667 1 283 3 chr4A.!!$F6 282
23 TraesCS3A01G211300 chr4A 359297745 359298568 823 False 381.666667 468 94.098000 1 1129 3 chr4A.!!$F8 1128
24 TraesCS3A01G211300 chr4A 359275677 359276494 817 False 374.666667 451 93.797667 1 1129 3 chr4A.!!$F7 1128
25 TraesCS3A01G211300 chr2A 505140711 505141328 617 True 822.000000 822 90.620000 1693 2318 1 chr2A.!!$R3 625
26 TraesCS3A01G211300 chr2A 286040890 286041433 543 True 588.000000 588 86.239000 588 1129 1 chr2A.!!$R2 541
27 TraesCS3A01G211300 chr2A 286033050 286033598 548 True 586.000000 586 86.000000 582 1128 1 chr2A.!!$R1 546
28 TraesCS3A01G211300 chr2A 691984596 691985301 705 True 267.000000 267 74.728000 1614 2311 1 chr2A.!!$R4 697
29 TraesCS3A01G211300 chr5A 208692947 208694706 1759 True 301.500000 311 87.661500 1209 1473 2 chr5A.!!$R2 264

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
276 285 0.038892 GCGTTACAAGGTCGGTCTCA 60.039 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 2229 1.617536 AGCCCAGCCAAGATCCAGA 60.618 57.895 0.0 0.0 0.0 3.86 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
249 258 0.745845 GAGTCGCCGGTAGAGGTACA 60.746 60.000 1.90 0.00 0.00 2.90
276 285 0.038892 GCGTTACAAGGTCGGTCTCA 60.039 55.000 0.00 0.00 0.00 3.27
833 864 0.531974 AGCAGCGAAGAAACCGACAA 60.532 50.000 0.00 0.00 0.00 3.18
845 876 4.277239 CGACAACGGCTGGATCAA 57.723 55.556 0.00 0.00 35.72 2.57
852 883 1.153168 CGGCTGGATCAAATCGGGT 60.153 57.895 0.00 0.00 0.00 5.28
896 927 2.640302 GCACAGGCGAGACAGAGGA 61.640 63.158 0.00 0.00 0.00 3.71
900 931 1.416401 ACAGGCGAGACAGAGGAAAAA 59.584 47.619 0.00 0.00 0.00 1.94
986 1020 3.052082 GGAGGACGACCGACGACA 61.052 66.667 0.00 0.00 45.77 4.35
1165 1199 2.093537 GAGCTCGCCGGATCAAGGAT 62.094 60.000 5.05 0.00 0.00 3.24
1197 1232 4.056125 CTGGAGACTGGCGTCGCA 62.056 66.667 20.50 4.36 44.93 5.10
1670 2229 1.915769 AGAAGAGAAGGGGCTGCGT 60.916 57.895 0.00 0.00 0.00 5.24
2315 3189 2.093447 GGTCTTGGGGTGTCACAGATAG 60.093 54.545 5.12 0.00 0.00 2.08
2322 3196 1.210478 GGTGTCACAGATAGCCACCAT 59.790 52.381 5.12 0.00 43.96 3.55
2324 3198 2.169352 GTGTCACAGATAGCCACCATCT 59.831 50.000 0.00 0.00 32.90 2.90
2330 3204 3.713248 ACAGATAGCCACCATCTCATCAA 59.287 43.478 0.00 0.00 30.18 2.57
2332 3206 5.128205 CAGATAGCCACCATCTCATCAAAA 58.872 41.667 0.00 0.00 30.18 2.44
2333 3207 5.238868 CAGATAGCCACCATCTCATCAAAAG 59.761 44.000 0.00 0.00 30.18 2.27
2334 3208 3.726557 AGCCACCATCTCATCAAAAGA 57.273 42.857 0.00 0.00 0.00 2.52
2337 3211 2.679837 CCACCATCTCATCAAAAGACGG 59.320 50.000 0.00 0.00 32.40 4.79
2338 3212 2.679837 CACCATCTCATCAAAAGACGGG 59.320 50.000 0.00 0.00 30.37 5.28
2340 3214 2.939103 CCATCTCATCAAAAGACGGGAC 59.061 50.000 0.00 0.00 0.00 4.46
2341 3215 3.599343 CATCTCATCAAAAGACGGGACA 58.401 45.455 0.00 0.00 0.00 4.02
2342 3216 3.040147 TCTCATCAAAAGACGGGACAC 57.960 47.619 0.00 0.00 0.00 3.67
2343 3217 2.076863 CTCATCAAAAGACGGGACACC 58.923 52.381 0.00 0.00 0.00 4.16
2344 3218 1.697432 TCATCAAAAGACGGGACACCT 59.303 47.619 0.00 0.00 33.28 4.00
2346 3220 2.721425 TCAAAAGACGGGACACCTTT 57.279 45.000 0.00 0.00 32.48 3.11
2347 3221 2.294074 TCAAAAGACGGGACACCTTTG 58.706 47.619 0.00 0.00 31.75 2.77
2348 3222 1.029681 AAAAGACGGGACACCTTTGC 58.970 50.000 0.00 0.00 31.75 3.68
2349 3223 0.822121 AAAGACGGGACACCTTTGCC 60.822 55.000 0.00 0.00 30.55 4.52
2350 3224 1.705997 AAGACGGGACACCTTTGCCT 61.706 55.000 0.00 0.00 33.28 4.75
2357 3640 2.420687 GGGACACCTTTGCCTCTATCAG 60.421 54.545 0.00 0.00 0.00 2.90
2375 3658 7.857456 TCTATCAGAGAGGAGGTAGATGATAC 58.143 42.308 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 1.310933 ATAACCACCGAGACGACGCT 61.311 55.000 0.00 0.0 0.00 5.07
249 258 2.561569 GACCTTGTAACGCTATGCCAT 58.438 47.619 0.00 0.0 0.00 4.40
833 864 1.153168 CCCGATTTGATCCAGCCGT 60.153 57.895 0.00 0.0 0.00 5.68
845 876 1.836999 TAGCACCACAGCACCCGATT 61.837 55.000 0.00 0.0 36.85 3.34
852 883 1.078214 GGAGCATAGCACCACAGCA 60.078 57.895 0.48 0.0 39.08 4.41
896 927 1.241315 CGCCGATGTCCCCTGTTTTT 61.241 55.000 0.00 0.0 0.00 1.94
900 931 3.771160 GACGCCGATGTCCCCTGT 61.771 66.667 0.00 0.0 32.61 4.00
986 1020 2.037208 CCATCCCGGCCAACCTTT 59.963 61.111 2.24 0.0 0.00 3.11
1670 2229 1.617536 AGCCCAGCCAAGATCCAGA 60.618 57.895 0.00 0.0 0.00 3.86
2315 3189 2.096496 CGTCTTTTGATGAGATGGTGGC 59.904 50.000 0.00 0.0 37.65 5.01
2322 3196 2.289444 GGTGTCCCGTCTTTTGATGAGA 60.289 50.000 0.00 0.0 37.65 3.27
2324 3198 1.697432 AGGTGTCCCGTCTTTTGATGA 59.303 47.619 0.00 0.0 37.65 2.92
2330 3204 0.822121 GGCAAAGGTGTCCCGTCTTT 60.822 55.000 0.00 0.0 35.12 2.52
2332 3206 2.113243 GAGGCAAAGGTGTCCCGTCT 62.113 60.000 0.00 0.0 35.12 4.18
2333 3207 1.671379 GAGGCAAAGGTGTCCCGTC 60.671 63.158 0.00 0.0 35.12 4.79
2334 3208 0.834687 TAGAGGCAAAGGTGTCCCGT 60.835 55.000 0.00 0.0 35.12 5.28
2337 3211 2.501723 TCTGATAGAGGCAAAGGTGTCC 59.498 50.000 0.00 0.0 0.00 4.02
2338 3212 3.449018 TCTCTGATAGAGGCAAAGGTGTC 59.551 47.826 6.05 0.0 42.54 3.67
2340 3214 4.057406 CTCTCTGATAGAGGCAAAGGTG 57.943 50.000 6.05 0.0 46.98 4.00
2350 3224 6.968400 ATCATCTACCTCCTCTCTGATAGA 57.032 41.667 0.00 0.0 0.00 1.98


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

AutoCloner maintained by Alex Coulton.