Multiple sequence alignment - TraesCS6B01G094300

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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 TraesCS6B01G094300 chr6B 100.000 2811 0 0 1 2811 70624939 70627749 0.000000e+00 5192.0
1 TraesCS6B01G094300 chr6B 89.569 1275 84 16 514 1759 244462667 244461413 0.000000e+00 1572.0
2 TraesCS6B01G094300 chr6B 91.067 1153 81 5 1680 2811 238436860 238435709 0.000000e+00 1539.0
3 TraesCS6B01G094300 chr6B 88.859 377 25 9 1 360 244463447 244463071 5.520000e-122 448.0
4 TraesCS6B01G094300 chr6B 94.079 152 9 0 371 522 244463009 244462858 6.060000e-57 231.0
5 TraesCS6B01G094300 chr5B 91.631 2342 133 14 518 2811 345108239 345110565 0.000000e+00 3181.0
6 TraesCS6B01G094300 chr5B 90.529 1890 132 13 965 2811 291688615 291686730 0.000000e+00 2455.0
7 TraesCS6B01G094300 chr5B 88.052 1473 123 18 524 1970 565309475 565308030 0.000000e+00 1696.0
8 TraesCS6B01G094300 chr5B 87.679 1469 131 12 514 1970 117418616 117420046 0.000000e+00 1664.0
9 TraesCS6B01G094300 chr5B 87.492 1479 133 19 514 1970 639286413 639287861 0.000000e+00 1659.0
10 TraesCS6B01G094300 chr5B 87.406 802 79 14 992 1784 71846527 71847315 0.000000e+00 902.0
11 TraesCS6B01G094300 chr5B 89.777 538 39 2 1 522 345107504 345108041 0.000000e+00 675.0
12 TraesCS6B01G094300 chr5B 85.405 370 30 12 1 360 117417865 117418220 2.060000e-96 363.0
13 TraesCS6B01G094300 chr5B 84.483 290 27 6 1 272 482078146 482078435 1.280000e-68 270.0
14 TraesCS6B01G094300 chr5B 89.706 136 13 1 387 522 62387313 62387179 3.720000e-39 172.0
15 TraesCS6B01G094300 chr5B 96.970 66 2 0 290 355 639286039 639286104 8.230000e-21 111.0
16 TraesCS6B01G094300 chr5B 92.308 39 0 2 263 301 482078441 482078476 5.000000e-03 52.8
17 TraesCS6B01G094300 chr7B 92.355 2119 131 14 55 2145 669508656 669510771 0.000000e+00 2987.0
18 TraesCS6B01G094300 chr7B 85.538 1217 125 32 978 2145 471054623 471055837 0.000000e+00 1225.0
19 TraesCS6B01G094300 chr4B 88.530 2319 179 28 524 2811 288477145 288474883 0.000000e+00 2728.0
20 TraesCS6B01G094300 chr4B 91.070 1299 92 9 1533 2811 200933517 200934811 0.000000e+00 1735.0
21 TraesCS6B01G094300 chr4B 90.468 1154 87 6 1680 2811 343641157 343642309 0.000000e+00 1500.0
22 TraesCS6B01G094300 chr4B 85.627 1468 135 35 514 1970 647882883 647881481 0.000000e+00 1472.0
23 TraesCS6B01G094300 chr4B 90.571 1103 84 5 1728 2811 343788509 343789610 0.000000e+00 1443.0
24 TraesCS6B01G094300 chr4B 89.695 1116 81 15 514 1609 15098076 15096975 0.000000e+00 1393.0
25 TraesCS6B01G094300 chr4B 90.476 1071 80 7 1762 2811 368726016 368727085 0.000000e+00 1393.0
26 TraesCS6B01G094300 chr4B 87.601 371 29 9 1 355 647883680 647883311 5.600000e-112 414.0
27 TraesCS6B01G094300 chr4B 87.003 377 31 10 1 360 288477875 288477500 2.610000e-110 409.0
28 TraesCS6B01G094300 chr4B 94.079 152 9 0 371 522 288477437 288477286 6.060000e-57 231.0
29 TraesCS6B01G094300 chr4B 91.367 139 11 1 135 273 6997260 6997397 3.700000e-44 189.0
30 TraesCS6B01G094300 chr4B 90.647 139 12 1 135 273 113837484 113837621 1.720000e-42 183.0
31 TraesCS6B01G094300 chr4B 88.652 141 16 0 382 522 647883217 647883077 3.720000e-39 172.0
32 TraesCS6B01G094300 chr4B 89.583 96 3 6 569 657 79089511 79089606 6.360000e-22 115.0
33 TraesCS6B01G094300 chr4B 100.000 30 0 0 326 355 15098423 15098394 3.910000e-04 56.5
34 TraesCS6B01G094300 chr3B 89.820 1886 130 15 982 2811 762525682 762523803 0.000000e+00 2362.0
35 TraesCS6B01G094300 chr3B 89.081 1502 95 19 514 1970 142218669 142220146 0.000000e+00 1801.0
36 TraesCS6B01G094300 chr3B 86.698 1496 114 23 514 1970 636098178 636096729 0.000000e+00 1581.0
37 TraesCS6B01G094300 chr3B 86.832 1253 107 23 596 1813 761543403 761542174 0.000000e+00 1347.0
38 TraesCS6B01G094300 chr3B 86.323 1126 106 18 699 1786 318290668 318291783 0.000000e+00 1182.0
39 TraesCS6B01G094300 chr3B 88.629 985 93 10 978 1951 317287062 317288038 0.000000e+00 1181.0
40 TraesCS6B01G094300 chr3B 85.616 292 23 8 1 273 636098995 636098704 3.540000e-74 289.0
41 TraesCS6B01G094300 chr3B 98.214 56 1 0 812 867 632392613 632392558 6.410000e-17 99.0
42 TraesCS6B01G094300 chr3B 88.679 53 4 2 842 894 329534222 329534172 2.340000e-06 63.9
43 TraesCS6B01G094300 chr1B 87.338 1469 136 20 524 1970 681885196 681886636 0.000000e+00 1637.0
44 TraesCS6B01G094300 chr1B 87.364 1290 97 31 514 1759 516774327 516775594 0.000000e+00 1419.0
45 TraesCS6B01G094300 chr4A 88.326 1302 99 26 699 1970 24458412 24459690 0.000000e+00 1513.0
46 TraesCS6B01G094300 chr4A 89.758 537 39 5 2 522 715063984 715064520 0.000000e+00 673.0
47 TraesCS6B01G094300 chr4A 89.443 341 11 7 514 849 29693576 29693256 9.370000e-110 407.0
48 TraesCS6B01G094300 chr4A 93.671 237 10 2 514 746 715064715 715064950 1.600000e-92 350.0
49 TraesCS6B01G094300 chr4A 84.324 370 28 17 1 360 29694325 29693976 4.490000e-88 335.0
50 TraesCS6B01G094300 chr4A 82.185 421 41 22 135 522 326304656 326304237 5.800000e-87 331.0
51 TraesCS6B01G094300 chr4A 83.784 370 32 17 1 360 525187562 525187211 2.700000e-85 326.0
52 TraesCS6B01G094300 chr4A 81.905 420 42 23 135 522 523831822 523832239 9.710000e-85 324.0
53 TraesCS6B01G094300 chr4A 95.610 205 4 2 514 714 525186811 525186608 9.710000e-85 324.0
54 TraesCS6B01G094300 chr4A 81.710 421 43 20 135 522 52482911 52482492 1.260000e-83 320.0
55 TraesCS6B01G094300 chr4A 96.429 168 5 1 514 681 52482428 52482262 2.760000e-70 276.0
56 TraesCS6B01G094300 chr4A 92.086 139 10 1 135 273 713769189 713769326 7.940000e-46 195.0
57 TraesCS6B01G094300 chr4A 90.441 136 13 0 387 522 525187137 525187002 2.220000e-41 180.0
58 TraesCS6B01G094300 chr4A 85.311 177 19 4 346 522 361391176 361391345 2.880000e-40 176.0
59 TraesCS6B01G094300 chr2B 91.107 1102 72 6 514 1609 780643069 780644150 0.000000e+00 1469.0
60 TraesCS6B01G094300 chr2B 88.254 1243 89 18 763 1970 124026935 124025715 0.000000e+00 1434.0
61 TraesCS6B01G094300 chr2B 87.688 999 105 8 964 1951 131501159 131500168 0.000000e+00 1147.0
62 TraesCS6B01G094300 chr2B 89.103 936 72 12 699 1605 149795289 149796223 0.000000e+00 1136.0
63 TraesCS6B01G094300 chr2B 91.493 670 52 5 2146 2811 539878972 539879640 0.000000e+00 917.0
64 TraesCS6B01G094300 chr2B 85.621 153 15 6 760 911 250952863 250952717 1.350000e-33 154.0
65 TraesCS6B01G094300 chr2A 88.111 1228 102 14 514 1733 340637672 340636481 0.000000e+00 1419.0
66 TraesCS6B01G094300 chr2A 85.405 370 27 15 1 360 340638424 340638072 2.660000e-95 359.0
67 TraesCS6B01G094300 chr5A 87.986 1182 99 19 807 1951 501869032 501870207 0.000000e+00 1356.0
68 TraesCS6B01G094300 chr5A 87.769 1022 100 13 943 1951 133818519 133819528 0.000000e+00 1171.0
69 TraesCS6B01G094300 chr5A 80.779 411 45 21 145 522 501868383 501868792 9.850000e-75 291.0
70 TraesCS6B01G094300 chr5A 80.048 421 50 21 135 522 5810064 5809645 5.930000e-72 281.0
71 TraesCS6B01G094300 chr5A 96.154 156 6 0 526 681 501868883 501869038 3.590000e-64 255.0
72 TraesCS6B01G094300 chr5A 86.441 236 20 9 135 360 572300540 572300773 6.010000e-62 248.0
73 TraesCS6B01G094300 chr5A 95.425 153 6 1 514 666 572301070 572301221 2.800000e-60 243.0
74 TraesCS6B01G094300 chr5A 93.023 43 2 1 475 516 5809630 5809588 8.410000e-06 62.1
75 TraesCS6B01G094300 chr5A 97.059 34 0 1 475 507 572301005 572301038 3.910000e-04 56.5
76 TraesCS6B01G094300 chr7D 88.689 999 90 10 985 1969 17944234 17943245 0.000000e+00 1197.0
77 TraesCS6B01G094300 chr7D 87.500 224 19 2 50 264 51246769 51246546 1.670000e-62 250.0
78 TraesCS6B01G094300 chr7D 87.054 224 20 2 50 264 79218474 79218697 7.780000e-61 244.0
79 TraesCS6B01G094300 chr7D 91.489 94 2 5 569 657 581646616 581646708 1.060000e-24 124.0
80 TraesCS6B01G094300 chr7D 89.109 101 4 6 569 662 539400473 539400573 4.920000e-23 119.0
81 TraesCS6B01G094300 chr7D 92.500 80 3 3 290 366 79218768 79218847 8.230000e-21 111.0
82 TraesCS6B01G094300 chr7D 92.647 68 2 3 305 369 51246460 51246393 8.290000e-16 95.3
83 TraesCS6B01G094300 chr1A 87.671 1022 103 13 943 1951 580783841 580784852 0.000000e+00 1168.0
84 TraesCS6B01G094300 chr1A 81.517 422 42 25 135 522 50648515 50648096 5.850000e-82 315.0
85 TraesCS6B01G094300 chr1A 95.238 168 7 1 514 681 50648016 50647850 5.970000e-67 265.0
86 TraesCS6B01G094300 chr1A 86.017 236 21 9 135 360 470995263 470995496 2.800000e-60 243.0
87 TraesCS6B01G094300 chr1A 95.425 153 6 1 514 666 470995793 470995944 2.800000e-60 243.0
88 TraesCS6B01G094300 chr1A 90.517 116 11 0 407 522 470995598 470995713 1.350000e-33 154.0
89 TraesCS6B01G094300 chr1A 97.059 34 0 1 475 507 50648081 50648048 3.910000e-04 56.5
90 TraesCS6B01G094300 chr3D 90.191 836 55 11 1993 2807 571759134 571758305 0.000000e+00 1064.0
91 TraesCS6B01G094300 chr4D 88.038 836 77 11 1995 2811 239800144 239799313 0.000000e+00 968.0
92 TraesCS6B01G094300 chr4D 89.474 133 10 2 148 280 196902777 196902905 6.230000e-37 165.0
93 TraesCS6B01G094300 chr4D 90.805 87 3 4 576 657 279519242 279519328 8.230000e-21 111.0
94 TraesCS6B01G094300 chr4D 92.500 80 1 4 583 657 381522833 381522754 2.960000e-20 110.0
95 TraesCS6B01G094300 chr4D 85.484 62 8 1 50 110 225341753 225341692 2.340000e-06 63.9
96 TraesCS6B01G094300 chr7A 84.324 370 26 15 1 360 56065455 56065802 1.610000e-87 333.0
97 TraesCS6B01G094300 chrUn 87.013 231 21 6 135 357 38464556 38464785 4.650000e-63 252.0
98 TraesCS6B01G094300 chrUn 86.580 231 22 6 135 357 39687953 39688182 2.160000e-61 246.0
99 TraesCS6B01G094300 chrUn 90.625 96 2 6 569 657 30177205 30177300 1.370000e-23 121.0
100 TraesCS6B01G094300 chrUn 90.805 87 3 4 576 657 287761817 287761731 8.230000e-21 111.0
101 TraesCS6B01G094300 chr2D 84.729 203 22 2 50 243 239243518 239243720 7.940000e-46 195.0
102 TraesCS6B01G094300 chr2D 92.500 80 3 3 290 366 239243812 239243891 8.230000e-21 111.0


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 TraesCS6B01G094300 chr6B 70624939 70627749 2810 False 5192.000000 5192 100.000000 1 2811 1 chr6B.!!$F1 2810
1 TraesCS6B01G094300 chr6B 238435709 238436860 1151 True 1539.000000 1539 91.067000 1680 2811 1 chr6B.!!$R1 1131
2 TraesCS6B01G094300 chr6B 244461413 244463447 2034 True 750.333333 1572 90.835667 1 1759 3 chr6B.!!$R2 1758
3 TraesCS6B01G094300 chr5B 291686730 291688615 1885 True 2455.000000 2455 90.529000 965 2811 1 chr5B.!!$R2 1846
4 TraesCS6B01G094300 chr5B 345107504 345110565 3061 False 1928.000000 3181 90.704000 1 2811 2 chr5B.!!$F3 2810
5 TraesCS6B01G094300 chr5B 565308030 565309475 1445 True 1696.000000 1696 88.052000 524 1970 1 chr5B.!!$R3 1446
6 TraesCS6B01G094300 chr5B 117417865 117420046 2181 False 1013.500000 1664 86.542000 1 1970 2 chr5B.!!$F2 1969
7 TraesCS6B01G094300 chr5B 71846527 71847315 788 False 902.000000 902 87.406000 992 1784 1 chr5B.!!$F1 792
8 TraesCS6B01G094300 chr5B 639286039 639287861 1822 False 885.000000 1659 92.231000 290 1970 2 chr5B.!!$F5 1680
9 TraesCS6B01G094300 chr7B 669508656 669510771 2115 False 2987.000000 2987 92.355000 55 2145 1 chr7B.!!$F2 2090
10 TraesCS6B01G094300 chr7B 471054623 471055837 1214 False 1225.000000 1225 85.538000 978 2145 1 chr7B.!!$F1 1167
11 TraesCS6B01G094300 chr4B 200933517 200934811 1294 False 1735.000000 1735 91.070000 1533 2811 1 chr4B.!!$F4 1278
12 TraesCS6B01G094300 chr4B 343641157 343642309 1152 False 1500.000000 1500 90.468000 1680 2811 1 chr4B.!!$F5 1131
13 TraesCS6B01G094300 chr4B 343788509 343789610 1101 False 1443.000000 1443 90.571000 1728 2811 1 chr4B.!!$F6 1083
14 TraesCS6B01G094300 chr4B 368726016 368727085 1069 False 1393.000000 1393 90.476000 1762 2811 1 chr4B.!!$F7 1049
15 TraesCS6B01G094300 chr4B 288474883 288477875 2992 True 1122.666667 2728 89.870667 1 2811 3 chr4B.!!$R2 2810
16 TraesCS6B01G094300 chr4B 15096975 15098423 1448 True 724.750000 1393 94.847500 326 1609 2 chr4B.!!$R1 1283
17 TraesCS6B01G094300 chr4B 647881481 647883680 2199 True 686.000000 1472 87.293333 1 1970 3 chr4B.!!$R3 1969
18 TraesCS6B01G094300 chr3B 762523803 762525682 1879 True 2362.000000 2362 89.820000 982 2811 1 chr3B.!!$R4 1829
19 TraesCS6B01G094300 chr3B 142218669 142220146 1477 False 1801.000000 1801 89.081000 514 1970 1 chr3B.!!$F1 1456
20 TraesCS6B01G094300 chr3B 761542174 761543403 1229 True 1347.000000 1347 86.832000 596 1813 1 chr3B.!!$R3 1217
21 TraesCS6B01G094300 chr3B 318290668 318291783 1115 False 1182.000000 1182 86.323000 699 1786 1 chr3B.!!$F3 1087
22 TraesCS6B01G094300 chr3B 317287062 317288038 976 False 1181.000000 1181 88.629000 978 1951 1 chr3B.!!$F2 973
23 TraesCS6B01G094300 chr3B 636096729 636098995 2266 True 935.000000 1581 86.157000 1 1970 2 chr3B.!!$R5 1969
24 TraesCS6B01G094300 chr1B 681885196 681886636 1440 False 1637.000000 1637 87.338000 524 1970 1 chr1B.!!$F2 1446
25 TraesCS6B01G094300 chr1B 516774327 516775594 1267 False 1419.000000 1419 87.364000 514 1759 1 chr1B.!!$F1 1245
26 TraesCS6B01G094300 chr4A 24458412 24459690 1278 False 1513.000000 1513 88.326000 699 1970 1 chr4A.!!$F1 1271
27 TraesCS6B01G094300 chr4A 715063984 715064950 966 False 511.500000 673 91.714500 2 746 2 chr4A.!!$F5 744
28 TraesCS6B01G094300 chr4A 29693256 29694325 1069 True 371.000000 407 86.883500 1 849 2 chr4A.!!$R2 848
29 TraesCS6B01G094300 chr4A 52482262 52482911 649 True 298.000000 320 89.069500 135 681 2 chr4A.!!$R3 546
30 TraesCS6B01G094300 chr4A 525186608 525187562 954 True 276.666667 326 89.945000 1 714 3 chr4A.!!$R4 713
31 TraesCS6B01G094300 chr2B 780643069 780644150 1081 False 1469.000000 1469 91.107000 514 1609 1 chr2B.!!$F3 1095
32 TraesCS6B01G094300 chr2B 124025715 124026935 1220 True 1434.000000 1434 88.254000 763 1970 1 chr2B.!!$R1 1207
33 TraesCS6B01G094300 chr2B 131500168 131501159 991 True 1147.000000 1147 87.688000 964 1951 1 chr2B.!!$R2 987
34 TraesCS6B01G094300 chr2B 149795289 149796223 934 False 1136.000000 1136 89.103000 699 1605 1 chr2B.!!$F1 906
35 TraesCS6B01G094300 chr2B 539878972 539879640 668 False 917.000000 917 91.493000 2146 2811 1 chr2B.!!$F2 665
36 TraesCS6B01G094300 chr2A 340636481 340638424 1943 True 889.000000 1419 86.758000 1 1733 2 chr2A.!!$R1 1732
37 TraesCS6B01G094300 chr5A 133818519 133819528 1009 False 1171.000000 1171 87.769000 943 1951 1 chr5A.!!$F1 1008
38 TraesCS6B01G094300 chr5A 501868383 501870207 1824 False 634.000000 1356 88.306333 145 1951 3 chr5A.!!$F2 1806
39 TraesCS6B01G094300 chr7D 17943245 17944234 989 True 1197.000000 1197 88.689000 985 1969 1 chr7D.!!$R1 984
40 TraesCS6B01G094300 chr1A 580783841 580784852 1011 False 1168.000000 1168 87.671000 943 1951 1 chr1A.!!$F1 1008
41 TraesCS6B01G094300 chr1A 470995263 470995944 681 False 213.333333 243 90.653000 135 666 3 chr1A.!!$F2 531
42 TraesCS6B01G094300 chr1A 50647850 50648515 665 True 212.166667 315 91.271333 135 681 3 chr1A.!!$R1 546
43 TraesCS6B01G094300 chr3D 571758305 571759134 829 True 1064.000000 1064 90.191000 1993 2807 1 chr3D.!!$R1 814
44 TraesCS6B01G094300 chr4D 239799313 239800144 831 True 968.000000 968 88.038000 1995 2811 1 chr4D.!!$R2 816

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
728 1241 0.801251 GAGTGCACATGCTCAAGTCC 59.199 55.0 21.04 0.0 42.66 3.85 F
1209 1879 0.550914 TGAGCCCCACAAAGTGAAGT 59.449 50.0 0.00 0.0 35.23 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 2274 0.037303 CTGCTCCTCTTCTTGCCCAA 59.963 55.0 0.00 0.0 0.00 4.12 R
2364 3474 0.173481 GCGGAGGCTTCCCATTTTTC 59.827 55.0 9.65 0.0 40.67 2.29 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
44 45 6.880529 CCATTGATTTTATTTGGGTTCTTGCT 59.119 34.615 0.00 0.00 0.00 3.91
47 48 4.953940 TTTTATTTGGGTTCTTGCTGCT 57.046 36.364 0.00 0.00 0.00 4.24
48 58 6.210385 TGATTTTATTTGGGTTCTTGCTGCTA 59.790 34.615 0.00 0.00 0.00 3.49
79 89 5.243954 GGTTTGATTAGGATTGGATTAGGGC 59.756 44.000 0.00 0.00 0.00 5.19
191 211 2.265739 CTTGCCCTACGCTGCTGA 59.734 61.111 0.00 0.00 38.78 4.26
197 217 2.577112 CTACGCTGCTGACGACCG 60.577 66.667 12.66 1.12 0.00 4.79
243 265 2.859992 GCCATCCGCTTCATATCCC 58.140 57.895 0.00 0.00 0.00 3.85
395 618 8.684520 GTGGTAGACTAGTGACAGTGTAATTAT 58.315 37.037 0.00 0.00 0.00 1.28
728 1241 0.801251 GAGTGCACATGCTCAAGTCC 59.199 55.000 21.04 0.00 42.66 3.85
1209 1879 0.550914 TGAGCCCCACAAAGTGAAGT 59.449 50.000 0.00 0.00 35.23 3.01
1386 2056 2.532531 CATGTTCACCGTGAAGATGC 57.467 50.000 28.50 13.42 46.34 3.91
1485 2156 0.615331 TTGGCTTCCTCTACCAGCAG 59.385 55.000 0.00 0.00 35.05 4.24
1562 2274 1.118356 GGGGATGACGAGGAGCAGAT 61.118 60.000 0.00 0.00 0.00 2.90
1667 2497 4.736896 GGTGGCTGACGACGACCC 62.737 72.222 0.00 0.00 0.00 4.46
1689 2573 1.742761 CTATGGTGGTGGCTGACAAG 58.257 55.000 0.00 0.00 0.00 3.16
1693 2577 1.451936 GTGGTGGCTGACAAGGACT 59.548 57.895 0.00 0.00 0.00 3.85
2161 3258 9.848172 GTATGAAACATGTTTGTCAAAAACATC 57.152 29.630 27.85 9.73 45.87 3.06
2162 3259 8.721019 ATGAAACATGTTTGTCAAAAACATCT 57.279 26.923 27.85 0.00 45.87 2.90
2408 3518 2.945008 ACATCATCAAATGTGGCCTACG 59.055 45.455 3.32 0.00 38.43 3.51
2464 3574 5.034797 CGTTTTCTTGAAAAGGTGTTCTCC 58.965 41.667 15.94 0.99 46.24 3.71
2481 3594 2.094390 TCTCCAAAACGACCTACGATGG 60.094 50.000 0.00 0.00 45.77 3.51
2484 3597 2.610976 CCAAAACGACCTACGATGGACA 60.611 50.000 5.55 0.00 45.77 4.02
2495 3608 5.104941 ACCTACGATGGACAAAGATTCATGA 60.105 40.000 0.00 0.00 0.00 3.07
2754 3870 3.538634 AGACCCTATTTTACAGACGGC 57.461 47.619 0.00 0.00 0.00 5.68
2755 3871 3.105283 AGACCCTATTTTACAGACGGCT 58.895 45.455 0.00 0.00 0.00 5.52
2757 3873 2.093128 ACCCTATTTTACAGACGGCTGG 60.093 50.000 24.99 3.15 46.60 4.85
2762 3878 0.948678 TTTACAGACGGCTGGCAAAC 59.051 50.000 24.99 0.00 46.60 2.93
2789 3905 0.460311 ATTTCCGACCCTCGTAGCTG 59.540 55.000 0.00 0.00 38.40 4.24
2794 3910 1.755008 GACCCTCGTAGCTGCTCCT 60.755 63.158 4.91 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.118261 CCTAATCTAGCAGCAAGAACCCA 60.118 47.826 0.00 0.00 0.00 4.51
44 45 7.633018 ATCCTAATCAAACCCTAATCTAGCA 57.367 36.000 0.00 0.00 0.00 3.49
47 48 8.575736 TCCAATCCTAATCAAACCCTAATCTA 57.424 34.615 0.00 0.00 0.00 1.98
48 58 7.465900 TCCAATCCTAATCAAACCCTAATCT 57.534 36.000 0.00 0.00 0.00 2.40
191 211 0.319641 GTCCAAGAAGAAGCGGTCGT 60.320 55.000 0.00 0.00 0.00 4.34
197 217 1.447945 GCCAGAGTCCAAGAAGAAGC 58.552 55.000 0.00 0.00 0.00 3.86
243 265 3.099141 AGAGCAGAAGAGAAAGGAGAGG 58.901 50.000 0.00 0.00 0.00 3.69
395 618 6.071896 CCGCACTATCTACCATAGAATTCAGA 60.072 42.308 8.44 0.68 38.50 3.27
470 693 5.173774 TCAACAGCAACAGAATTCAGTTC 57.826 39.130 12.81 8.59 37.08 3.01
653 1159 9.774742 GAAGAATGTAATGTTTCCATACTTGAC 57.225 33.333 0.00 0.00 0.00 3.18
728 1241 3.240401 GCAAAAACATCAACAGACACACG 59.760 43.478 0.00 0.00 0.00 4.49
886 1452 1.832167 TGTTTGCCAGGGCCTCAAC 60.832 57.895 0.95 5.25 41.09 3.18
1072 1736 6.157645 AGTGATGATAAAGAGATGGGTGAAGT 59.842 38.462 0.00 0.00 0.00 3.01
1273 1943 2.625883 CCAGTCCCTAGGTACATGTGGA 60.626 54.545 9.11 2.00 0.00 4.02
1363 2033 2.513065 CTTCACGGTGAACATGGCGC 62.513 60.000 19.07 0.00 32.21 6.53
1386 2056 1.868997 GGCACATGGTGTTGTCGAG 59.131 57.895 0.00 0.00 35.75 4.04
1485 2156 2.884012 TGTGAACATGGTGTTGTCATCC 59.116 45.455 0.00 0.00 41.28 3.51
1562 2274 0.037303 CTGCTCCTCTTCTTGCCCAA 59.963 55.000 0.00 0.00 0.00 4.12
1667 2497 0.745845 GTCAGCCACCACCATAGCAG 60.746 60.000 0.00 0.00 0.00 4.24
1689 2573 1.787847 CACCACAATCGCGAAGTCC 59.212 57.895 15.24 0.00 0.00 3.85
1693 2577 2.031919 AGGCACCACAATCGCGAA 59.968 55.556 15.24 0.00 0.00 4.70
1907 2931 7.417342 CGTTCTTCTCCTTATTCTCCTTCATCT 60.417 40.741 0.00 0.00 0.00 2.90
1990 3056 4.422840 TCCATAAGCATGCACAAAATTCG 58.577 39.130 21.98 0.00 0.00 3.34
2066 3143 6.293190 GCATGCACAAAATATCAATTCCCATG 60.293 38.462 14.21 0.00 0.00 3.66
2318 3417 2.607631 TCAAAAACCGACCGACTTCT 57.392 45.000 0.00 0.00 0.00 2.85
2322 3421 2.847717 GTGTTTTCAAAAACCGACCGAC 59.152 45.455 14.07 3.15 45.82 4.79
2364 3474 0.173481 GCGGAGGCTTCCCATTTTTC 59.827 55.000 9.65 0.00 40.67 2.29
2375 3485 2.635229 GATGATGTGACGCGGAGGCT 62.635 60.000 12.47 0.00 36.88 4.58
2376 3486 2.202932 ATGATGTGACGCGGAGGC 60.203 61.111 12.47 0.00 0.00 4.70
2464 3574 2.679450 TGTCCATCGTAGGTCGTTTTG 58.321 47.619 0.00 0.00 40.80 2.44
2477 3590 7.149569 TGAAAGTCATGAATCTTTGTCCATC 57.850 36.000 14.21 2.40 34.60 3.51
2481 3594 5.860716 GGCTTGAAAGTCATGAATCTTTGTC 59.139 40.000 14.21 4.14 34.60 3.18
2484 3597 6.409524 TTGGCTTGAAAGTCATGAATCTTT 57.590 33.333 10.25 10.25 40.84 2.52
2495 3608 4.584325 TCATTGCTAGTTTGGCTTGAAAGT 59.416 37.500 0.00 0.00 0.00 2.66
2577 3690 5.697633 GCAACATTGTTTTCCATCACAAGAT 59.302 36.000 0.00 0.00 36.36 2.40
2656 3772 4.520078 TCACGAAAAACGCATGTCTTTAC 58.480 39.130 0.00 0.00 46.94 2.01
2712 3828 7.870445 GGTCTACTTTGAGATAGACATGGAATC 59.130 40.741 12.18 0.00 46.14 2.52
2754 3870 2.933906 GGAAATGCATGATGTTTGCCAG 59.066 45.455 0.00 0.00 39.39 4.85
2755 3871 2.674462 CGGAAATGCATGATGTTTGCCA 60.674 45.455 0.00 0.00 39.39 4.92
2757 3873 2.599973 GTCGGAAATGCATGATGTTTGC 59.400 45.455 0.00 0.00 40.55 3.68
2762 3878 1.605710 GAGGGTCGGAAATGCATGATG 59.394 52.381 0.00 0.00 0.00 3.07
2789 3905 1.452833 GGTCTGAATGGCCAGGAGC 60.453 63.158 13.05 12.37 40.97 4.70


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

AutoCloner maintained by Alex Coulton.