Multiple sequence alignment - TraesCS6B01G250500

Loading Multiple Alignment...

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 TraesCS6B01G250500 chr6B 100.000 3753 0 0 1 3753 450080681 450076929 0.000000e+00 6931.0
1 TraesCS6B01G250500 chr3B 99.108 897 8 0 682 1578 101919640 101920536 0.000000e+00 1613.0
2 TraesCS6B01G250500 chr3B 99.008 504 5 0 1853 2356 201571589 201572092 0.000000e+00 904.0
3 TraesCS6B01G250500 chr3B 100.000 190 0 0 172 361 101913865 101914054 5.960000e-93 351.0
4 TraesCS6B01G250500 chr3B 99.474 190 1 0 172 361 201529714 201529903 2.770000e-91 346.0
5 TraesCS6B01G250500 chr3B 98.276 174 3 0 1 174 101911059 101911232 4.710000e-79 305.0
6 TraesCS6B01G250500 chr1D 98.216 897 14 2 682 1578 254416470 254415576 0.000000e+00 1567.0
7 TraesCS6B01G250500 chr1D 96.990 897 27 0 682 1578 51878666 51879562 0.000000e+00 1507.0
8 TraesCS6B01G250500 chr1D 98.219 786 12 2 2967 3751 254439313 254438529 0.000000e+00 1373.0
9 TraesCS6B01G250500 chr1D 96.447 788 22 4 2967 3753 51867666 51868448 0.000000e+00 1295.0
10 TraesCS6B01G250500 chr1D 96.535 404 6 5 2572 2968 254401992 254402394 0.000000e+00 662.0
11 TraesCS6B01G250500 chr1D 98.678 227 2 1 2355 2581 254473701 254473476 5.840000e-108 401.0
12 TraesCS6B01G250500 chr1D 98.947 190 2 0 172 361 254395422 254395233 1.290000e-89 340.0
13 TraesCS6B01G250500 chr1D 96.739 184 4 2 1 183 254444158 254443976 4.710000e-79 305.0
14 TraesCS6B01G250500 chr1D 100.000 160 0 0 372 531 459901996 459902155 2.830000e-76 296.0
15 TraesCS6B01G250500 chr1D 97.368 152 4 0 530 681 51869699 51869548 3.720000e-65 259.0
16 TraesCS6B01G250500 chr1D 97.345 113 3 0 1576 1688 487312404 487312292 3.830000e-45 193.0
17 TraesCS6B01G250500 chr1D 97.345 113 2 1 1576 1688 254401842 254401953 1.380000e-44 191.0
18 TraesCS6B01G250500 chr1D 100.000 57 0 0 1796 1852 180355852 180355908 5.130000e-19 106.0
19 TraesCS6B01G250500 chr1D 100.000 57 0 0 1796 1852 244201332 244201276 5.130000e-19 106.0
20 TraesCS6B01G250500 chr1D 100.000 57 0 0 1796 1852 254477039 254476983 5.130000e-19 106.0
21 TraesCS6B01G250500 chr1D 91.228 57 4 1 1748 1803 254451910 254451854 4.020000e-10 76.8
22 TraesCS6B01G250500 chr6D 97.882 897 18 1 682 1578 45512158 45513053 0.000000e+00 1550.0
23 TraesCS6B01G250500 chr6D 97.500 400 7 3 2572 2968 45515682 45515283 0.000000e+00 680.0
24 TraesCS6B01G250500 chr6D 100.000 160 0 0 372 531 389243101 389243260 2.830000e-76 296.0
25 TraesCS6B01G250500 chr6D 96.460 113 4 0 1576 1688 45515833 45515721 1.780000e-43 187.0
26 TraesCS6B01G250500 chr6D 98.684 76 1 0 1682 1757 135461436 135461511 6.540000e-28 135.0
27 TraesCS6B01G250500 chr6D 98.667 75 1 0 1683 1757 168260678 168260604 2.350000e-27 134.0
28 TraesCS6B01G250500 chr2A 97.775 899 17 3 682 1578 335831222 335832119 0.000000e+00 1546.0
29 TraesCS6B01G250500 chr2A 99.206 504 4 0 1853 2356 726903257 726903760 0.000000e+00 909.0
30 TraesCS6B01G250500 chr2A 97.250 400 8 3 2572 2968 335834759 335834360 0.000000e+00 675.0
31 TraesCS6B01G250500 chr5D 97.770 897 19 1 682 1578 503286706 503285811 0.000000e+00 1544.0
32 TraesCS6B01G250500 chr5D 97.768 896 17 3 682 1576 6181539 6182432 0.000000e+00 1541.0
33 TraesCS6B01G250500 chr5D 97.244 907 24 1 672 1578 120799286 120798381 0.000000e+00 1535.0
34 TraesCS6B01G250500 chr5D 98.477 788 11 1 2967 3753 512413525 512412738 0.000000e+00 1387.0
35 TraesCS6B01G250500 chr5D 97.595 790 16 2 2967 3753 503296156 503295367 0.000000e+00 1351.0
36 TraesCS6B01G250500 chr5D 97.589 788 16 2 2967 3753 6172654 6173439 0.000000e+00 1347.0
37 TraesCS6B01G250500 chr5D 99.014 507 4 1 1853 2359 503248469 503247964 0.000000e+00 907.0
38 TraesCS6B01G250500 chr5D 99.206 504 3 1 1853 2356 503261579 503262081 0.000000e+00 907.0
39 TraesCS6B01G250500 chr5D 97.270 403 5 3 2572 2968 483807700 483807298 0.000000e+00 678.0
40 TraesCS6B01G250500 chr5D 98.678 227 2 1 2355 2581 6238999 6239224 5.840000e-108 401.0
41 TraesCS6B01G250500 chr5D 98.276 174 3 0 1 174 6167824 6167997 4.710000e-79 305.0
42 TraesCS6B01G250500 chr5D 96.721 183 6 0 1 183 503301026 503300844 4.710000e-79 305.0
43 TraesCS6B01G250500 chr5D 97.701 174 4 0 1 174 6266858 6267031 2.190000e-77 300.0
44 TraesCS6B01G250500 chr5D 98.246 171 3 0 1 171 329158854 329159024 2.190000e-77 300.0
45 TraesCS6B01G250500 chr5D 98.026 152 3 0 530 681 503294119 503294270 7.990000e-67 265.0
46 TraesCS6B01G250500 chr5D 97.345 113 3 0 1576 1688 483807851 483807739 3.830000e-45 193.0
47 TraesCS6B01G250500 chr5D 97.345 113 2 1 1576 1688 503283035 503283146 1.380000e-44 191.0
48 TraesCS6B01G250500 chr5D 91.228 57 4 1 1748 1803 503331394 503331338 4.020000e-10 76.8
49 TraesCS6B01G250500 chr7A 97.550 898 20 2 682 1578 109219825 109220721 0.000000e+00 1535.0
50 TraesCS6B01G250500 chrUn 98.733 789 8 2 2967 3753 425345869 425346657 0.000000e+00 1400.0
51 TraesCS6B01G250500 chrUn 97.744 399 7 2 2572 2968 261573222 261572824 0.000000e+00 686.0
52 TraesCS6B01G250500 chrUn 97.264 402 5 3 2572 2968 458726734 458727134 0.000000e+00 676.0
53 TraesCS6B01G250500 chrUn 99.119 227 1 1 2355 2581 30304131 30304356 1.250000e-109 407.0
54 TraesCS6B01G250500 chrUn 99.474 190 1 0 172 361 421834947 421835136 2.770000e-91 346.0
55 TraesCS6B01G250500 chrUn 98.947 190 2 0 172 361 216515913 216515724 1.290000e-89 340.0
56 TraesCS6B01G250500 chrUn 98.947 190 2 0 172 361 286267470 286267659 1.290000e-89 340.0
57 TraesCS6B01G250500 chrUn 100.000 160 0 0 372 531 414708838 414708679 2.830000e-76 296.0
58 TraesCS6B01G250500 chrUn 100.000 160 0 0 372 531 428084171 428084330 2.830000e-76 296.0
59 TraesCS6B01G250500 chrUn 100.000 160 0 0 372 531 461210923 461211082 2.830000e-76 296.0
60 TraesCS6B01G250500 chrUn 98.684 152 2 0 530 681 381152914 381152763 1.720000e-68 270.0
61 TraesCS6B01G250500 chrUn 97.391 115 2 1 1574 1688 458726582 458726695 1.060000e-45 195.0
62 TraesCS6B01G250500 chrUn 96.460 113 2 1 1576 1688 261573371 261573261 6.400000e-43 185.0
63 TraesCS6B01G250500 chrUn 98.667 75 1 0 1683 1757 216515595 216515669 2.350000e-27 134.0
64 TraesCS6B01G250500 chrUn 98.667 75 1 0 1683 1757 286267788 286267714 2.350000e-27 134.0
65 TraesCS6B01G250500 chrUn 98.667 75 1 0 1683 1757 412653835 412653909 2.350000e-27 134.0
66 TraesCS6B01G250500 chrUn 98.667 75 1 0 1683 1757 421835265 421835191 2.350000e-27 134.0
67 TraesCS6B01G250500 chrUn 100.000 57 0 0 1796 1852 426380344 426380400 5.130000e-19 106.0
68 TraesCS6B01G250500 chrUn 100.000 57 0 0 1796 1852 445362541 445362485 5.130000e-19 106.0
69 TraesCS6B01G250500 chrUn 100.000 57 0 0 1796 1852 447482890 447482946 5.130000e-19 106.0
70 TraesCS6B01G250500 chrUn 100.000 57 0 0 1796 1852 457255091 457255035 5.130000e-19 106.0
71 TraesCS6B01G250500 chrUn 100.000 57 0 0 1796 1852 465171503 465171447 5.130000e-19 106.0
72 TraesCS6B01G250500 chrUn 94.118 51 2 1 1748 1797 387441390 387441440 4.020000e-10 76.8
73 TraesCS6B01G250500 chr2D 97.465 789 18 2 2967 3753 638428786 638427998 0.000000e+00 1345.0
74 TraesCS6B01G250500 chr2D 99.119 227 1 1 2355 2581 33932693 33932918 1.250000e-109 407.0
75 TraesCS6B01G250500 chr2D 99.119 227 1 1 2355 2581 630264166 630263941 1.250000e-109 407.0
76 TraesCS6B01G250500 chr2D 100.000 160 0 0 372 531 272809525 272809684 2.830000e-76 296.0
77 TraesCS6B01G250500 chr2D 100.000 160 0 0 372 531 591987330 591987171 2.830000e-76 296.0
78 TraesCS6B01G250500 chr2D 98.684 152 2 0 530 681 628294582 628294431 1.720000e-68 270.0
79 TraesCS6B01G250500 chr2D 98.026 152 3 0 530 681 638426750 638426901 7.990000e-67 265.0
80 TraesCS6B01G250500 chr2D 94.118 51 2 1 1748 1797 406837379 406837429 4.020000e-10 76.8
81 TraesCS6B01G250500 chr4B 97.335 788 16 4 2967 3753 308675489 308676272 0.000000e+00 1334.0
82 TraesCS6B01G250500 chr5B 96.958 789 21 3 2967 3753 274135492 274134705 0.000000e+00 1321.0
83 TraesCS6B01G250500 chr3A 99.603 504 2 0 1853 2356 66001935 66002438 0.000000e+00 920.0
84 TraesCS6B01G250500 chr3A 99.474 190 1 0 172 361 164861358 164861169 2.770000e-91 346.0
85 TraesCS6B01G250500 chr7D 99.206 504 4 0 1853 2356 231604720 231605223 0.000000e+00 909.0
86 TraesCS6B01G250500 chr7D 96.721 183 6 0 1 183 231528163 231527981 4.710000e-79 305.0
87 TraesCS6B01G250500 chr7D 96.721 183 6 0 1 183 231616555 231616373 4.710000e-79 305.0
88 TraesCS6B01G250500 chr7D 100.000 160 0 0 372 531 231543731 231543572 2.830000e-76 296.0
89 TraesCS6B01G250500 chr7D 100.000 160 0 0 372 531 231551531 231551372 2.830000e-76 296.0
90 TraesCS6B01G250500 chr7D 98.684 152 2 0 530 681 231541452 231541301 1.720000e-68 270.0
91 TraesCS6B01G250500 chr7D 98.026 152 3 0 530 681 231596840 231596991 7.990000e-67 265.0
92 TraesCS6B01G250500 chr7D 97.368 152 4 0 530 681 231623148 231623299 3.720000e-65 259.0
93 TraesCS6B01G250500 chr7D 91.228 57 4 1 1748 1803 231608903 231608847 4.020000e-10 76.8
94 TraesCS6B01G250500 chr3D 99.206 504 4 0 1853 2356 589260329 589260832 0.000000e+00 909.0
95 TraesCS6B01G250500 chr3D 97.022 403 6 3 2572 2968 598874688 598875090 0.000000e+00 673.0
96 TraesCS6B01G250500 chr3D 99.119 227 1 1 2355 2581 24162951 24162726 1.250000e-109 407.0
97 TraesCS6B01G250500 chr3D 98.678 227 2 1 2355 2581 24162467 24162242 5.840000e-108 401.0
98 TraesCS6B01G250500 chr3D 98.667 75 1 0 1683 1757 589273947 589274021 2.350000e-27 134.0
99 TraesCS6B01G250500 chr3D 91.228 57 4 1 1748 1803 527410188 527410132 4.020000e-10 76.8
100 TraesCS6B01G250500 chr4A 99.008 504 5 0 1853 2356 583865708 583866211 0.000000e+00 904.0
101 TraesCS6B01G250500 chr4A 96.460 113 4 0 1576 1688 73815011 73814899 1.780000e-43 187.0
102 TraesCS6B01G250500 chr4A 96.491 114 2 2 1576 1688 309511385 309511273 1.780000e-43 187.0
103 TraesCS6B01G250500 chr4A 96.053 76 3 0 1683 1758 310741590 310741515 1.420000e-24 124.0
104 TraesCS6B01G250500 chr4A 94.118 51 2 1 1748 1797 309451291 309451341 4.020000e-10 76.8
105 TraesCS6B01G250500 chr1B 98.619 507 7 0 1853 2359 421412088 421411582 0.000000e+00 898.0
106 TraesCS6B01G250500 chr1B 98.026 152 3 0 530 681 633709940 633710091 7.990000e-67 265.0
107 TraesCS6B01G250500 chr6A 98.246 399 5 2 2572 2968 215594765 215595163 0.000000e+00 697.0
108 TraesCS6B01G250500 chr6A 97.268 183 5 0 1 183 592504251 592504069 1.010000e-80 311.0
109 TraesCS6B01G250500 chr2B 96.985 398 11 1 2572 2968 657476210 657476607 0.000000e+00 667.0
110 TraesCS6B01G250500 chr2B 100.000 75 0 0 1683 1757 454926896 454926822 5.050000e-29 139.0
111 TraesCS6B01G250500 chr7B 99.119 227 1 1 2355 2581 662740727 662740952 1.250000e-109 407.0
112 TraesCS6B01G250500 chr1A 98.678 227 2 1 2355 2581 554450928 554451153 5.840000e-108 401.0
113 TraesCS6B01G250500 chr1A 98.947 190 2 0 172 361 554514938 554515127 1.290000e-89 340.0
114 TraesCS6B01G250500 chr1A 98.667 75 1 0 1683 1757 554515256 554515182 2.350000e-27 134.0
115 TraesCS6B01G250500 chr1A 100.000 57 0 0 1796 1852 554446097 554446153 5.130000e-19 106.0
116 TraesCS6B01G250500 chr1A 94.118 51 2 1 1748 1797 548024497 548024547 4.020000e-10 76.8
117 TraesCS6B01G250500 chr1A 91.228 57 4 1 1748 1803 554477345 554477289 4.020000e-10 76.8
118 TraesCS6B01G250500 chr5A 99.474 190 1 0 172 361 164646382 164646193 2.770000e-91 346.0


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 TraesCS6B01G250500 chr6B 450076929 450080681 3752 True 6931.0 6931 100.0000 1 3753 1 chr6B.!!$R1 3752
1 TraesCS6B01G250500 chr3B 101919640 101920536 896 False 1613.0 1613 99.1080 682 1578 1 chr3B.!!$F1 896
2 TraesCS6B01G250500 chr3B 201571589 201572092 503 False 904.0 904 99.0080 1853 2356 1 chr3B.!!$F3 503
3 TraesCS6B01G250500 chr3B 101911059 101914054 2995 False 328.0 351 99.1380 1 361 2 chr3B.!!$F4 360
4 TraesCS6B01G250500 chr1D 254415576 254416470 894 True 1567.0 1567 98.2160 682 1578 1 chr1D.!!$R4 896
5 TraesCS6B01G250500 chr1D 51878666 51879562 896 False 1507.0 1507 96.9900 682 1578 1 chr1D.!!$F2 896
6 TraesCS6B01G250500 chr1D 254438529 254439313 784 True 1373.0 1373 98.2190 2967 3751 1 chr1D.!!$R5 784
7 TraesCS6B01G250500 chr1D 51867666 51868448 782 False 1295.0 1295 96.4470 2967 3753 1 chr1D.!!$F1 786
8 TraesCS6B01G250500 chr1D 254401842 254402394 552 False 426.5 662 96.9400 1576 2968 2 chr1D.!!$F5 1392
9 TraesCS6B01G250500 chr1D 254473476 254477039 3563 True 253.5 401 99.3390 1796 2581 2 chr1D.!!$R9 785
10 TraesCS6B01G250500 chr6D 45512158 45513053 895 False 1550.0 1550 97.8820 682 1578 1 chr6D.!!$F1 896
11 TraesCS6B01G250500 chr6D 45515283 45515833 550 True 433.5 680 96.9800 1576 2968 2 chr6D.!!$R2 1392
12 TraesCS6B01G250500 chr2A 335831222 335832119 897 False 1546.0 1546 97.7750 682 1578 1 chr2A.!!$F1 896
13 TraesCS6B01G250500 chr2A 726903257 726903760 503 False 909.0 909 99.2060 1853 2356 1 chr2A.!!$F2 503
14 TraesCS6B01G250500 chr5D 503285811 503286706 895 True 1544.0 1544 97.7700 682 1578 1 chr5D.!!$R3 896
15 TraesCS6B01G250500 chr5D 6181539 6182432 893 False 1541.0 1541 97.7680 682 1576 1 chr5D.!!$F3 894
16 TraesCS6B01G250500 chr5D 120798381 120799286 905 True 1535.0 1535 97.2440 672 1578 1 chr5D.!!$R1 906
17 TraesCS6B01G250500 chr5D 512412738 512413525 787 True 1387.0 1387 98.4770 2967 3753 1 chr5D.!!$R7 786
18 TraesCS6B01G250500 chr5D 503295367 503296156 789 True 1351.0 1351 97.5950 2967 3753 1 chr5D.!!$R4 786
19 TraesCS6B01G250500 chr5D 6172654 6173439 785 False 1347.0 1347 97.5890 2967 3753 1 chr5D.!!$F2 786
20 TraesCS6B01G250500 chr5D 503247964 503248469 505 True 907.0 907 99.0140 1853 2359 1 chr5D.!!$R2 506
21 TraesCS6B01G250500 chr5D 503261579 503262081 502 False 907.0 907 99.2060 1853 2356 1 chr5D.!!$F7 503
22 TraesCS6B01G250500 chr5D 483807298 483807851 553 True 435.5 678 97.3075 1576 2968 2 chr5D.!!$R8 1392
23 TraesCS6B01G250500 chr7A 109219825 109220721 896 False 1535.0 1535 97.5500 682 1578 1 chr7A.!!$F1 896
24 TraesCS6B01G250500 chrUn 425345869 425346657 788 False 1400.0 1400 98.7330 2967 3753 1 chrUn.!!$F7 786
25 TraesCS6B01G250500 chrUn 261572824 261573371 547 True 435.5 686 97.1020 1576 2968 2 chrUn.!!$R9 1392
26 TraesCS6B01G250500 chrUn 458726582 458727134 552 False 435.5 676 97.3275 1574 2968 2 chrUn.!!$F12 1394
27 TraesCS6B01G250500 chr2D 638427998 638428786 788 True 1345.0 1345 97.4650 2967 3753 1 chr2D.!!$R4 786
28 TraesCS6B01G250500 chr4B 308675489 308676272 783 False 1334.0 1334 97.3350 2967 3753 1 chr4B.!!$F1 786
29 TraesCS6B01G250500 chr5B 274134705 274135492 787 True 1321.0 1321 96.9580 2967 3753 1 chr5B.!!$R1 786
30 TraesCS6B01G250500 chr3A 66001935 66002438 503 False 920.0 920 99.6030 1853 2356 1 chr3A.!!$F1 503
31 TraesCS6B01G250500 chr7D 231604720 231605223 503 False 909.0 909 99.2060 1853 2356 1 chr7D.!!$F2 503
32 TraesCS6B01G250500 chr7D 231541301 231543731 2430 True 283.0 296 99.3420 372 681 2 chr7D.!!$R5 309
33 TraesCS6B01G250500 chr3D 589260329 589260832 503 False 909.0 909 99.2060 1853 2356 1 chr3D.!!$F1 503
34 TraesCS6B01G250500 chr3D 24162242 24162951 709 True 404.0 407 98.8985 2355 2581 2 chr3D.!!$R2 226
35 TraesCS6B01G250500 chr4A 583865708 583866211 503 False 904.0 904 99.0080 1853 2356 1 chr4A.!!$F2 503
36 TraesCS6B01G250500 chr1B 421411582 421412088 506 True 898.0 898 98.6190 1853 2359 1 chr1B.!!$R1 506

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
157 158 6.014840 GGATCTGACTAAATCCGGGTATTGTA 60.015 42.308 0.0 0.0 32.62 2.41 F
1786 6546 1.996798 TTCTCTTCACTCGGACCAGT 58.003 50.000 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 6548 0.109272 TTCGTGAAGCAGACTAGGCG 60.109 55.0 0.00 0.0 36.08 5.52 R
3686 11453 2.561733 TTAGTCGACTCGCTCCATTG 57.438 50.0 23.89 0.0 0.00 2.82 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
157 158 6.014840 GGATCTGACTAAATCCGGGTATTGTA 60.015 42.308 0.00 0.00 32.62 2.41
655 5412 6.524586 GTCAGCTTTTCTATTTGAATGGAACG 59.475 38.462 2.49 0.00 35.92 3.95
884 5641 7.908601 AGTCGTCTTTTTCAAACTATGTTTCAC 59.091 33.333 0.00 0.00 0.00 3.18
1039 5796 9.645128 AAACCAATGACTATTCATGATTCCATA 57.355 29.630 0.00 0.00 42.00 2.74
1207 5964 7.118723 TCCATAGTAATGAAAATGCTCTTGGT 58.881 34.615 0.00 0.00 34.84 3.67
1682 6442 9.812347 ACATAATGCATAAGAGGATCCATAAAA 57.188 29.630 15.82 0.00 33.66 1.52
1724 6484 8.588290 ACTAGTAGAGTCTCATCTTTTGTCAT 57.412 34.615 3.59 0.00 29.95 3.06
1725 6485 9.030452 ACTAGTAGAGTCTCATCTTTTGTCATT 57.970 33.333 3.59 0.00 29.95 2.57
1726 6486 9.515020 CTAGTAGAGTCTCATCTTTTGTCATTC 57.485 37.037 0.00 0.00 0.00 2.67
1727 6487 8.133024 AGTAGAGTCTCATCTTTTGTCATTCT 57.867 34.615 0.00 0.00 0.00 2.40
1728 6488 8.592809 AGTAGAGTCTCATCTTTTGTCATTCTT 58.407 33.333 0.00 0.00 0.00 2.52
1729 6489 9.213799 GTAGAGTCTCATCTTTTGTCATTCTTT 57.786 33.333 0.00 0.00 0.00 2.52
1730 6490 8.097078 AGAGTCTCATCTTTTGTCATTCTTTG 57.903 34.615 1.94 0.00 0.00 2.77
1731 6491 6.675987 AGTCTCATCTTTTGTCATTCTTTGC 58.324 36.000 0.00 0.00 0.00 3.68
1732 6492 6.489361 AGTCTCATCTTTTGTCATTCTTTGCT 59.511 34.615 0.00 0.00 0.00 3.91
1733 6493 6.800892 GTCTCATCTTTTGTCATTCTTTGCTC 59.199 38.462 0.00 0.00 0.00 4.26
1734 6494 6.017400 TCATCTTTTGTCATTCTTTGCTCC 57.983 37.500 0.00 0.00 0.00 4.70
1735 6495 5.771666 TCATCTTTTGTCATTCTTTGCTCCT 59.228 36.000 0.00 0.00 0.00 3.69
1736 6496 6.266103 TCATCTTTTGTCATTCTTTGCTCCTT 59.734 34.615 0.00 0.00 0.00 3.36
1737 6497 6.469782 TCTTTTGTCATTCTTTGCTCCTTT 57.530 33.333 0.00 0.00 0.00 3.11
1738 6498 6.877236 TCTTTTGTCATTCTTTGCTCCTTTT 58.123 32.000 0.00 0.00 0.00 2.27
1739 6499 7.330262 TCTTTTGTCATTCTTTGCTCCTTTTT 58.670 30.769 0.00 0.00 0.00 1.94
1740 6500 7.492344 TCTTTTGTCATTCTTTGCTCCTTTTTC 59.508 33.333 0.00 0.00 0.00 2.29
1741 6501 5.850557 TGTCATTCTTTGCTCCTTTTTCA 57.149 34.783 0.00 0.00 0.00 2.69
1742 6502 5.591099 TGTCATTCTTTGCTCCTTTTTCAC 58.409 37.500 0.00 0.00 0.00 3.18
1743 6503 5.360714 TGTCATTCTTTGCTCCTTTTTCACT 59.639 36.000 0.00 0.00 0.00 3.41
1744 6504 5.917447 GTCATTCTTTGCTCCTTTTTCACTC 59.083 40.000 0.00 0.00 0.00 3.51
1745 6505 5.593909 TCATTCTTTGCTCCTTTTTCACTCA 59.406 36.000 0.00 0.00 0.00 3.41
1746 6506 5.913137 TTCTTTGCTCCTTTTTCACTCAA 57.087 34.783 0.00 0.00 0.00 3.02
1747 6507 6.469782 TTCTTTGCTCCTTTTTCACTCAAT 57.530 33.333 0.00 0.00 0.00 2.57
1748 6508 5.835257 TCTTTGCTCCTTTTTCACTCAATG 58.165 37.500 0.00 0.00 0.00 2.82
1749 6509 5.593909 TCTTTGCTCCTTTTTCACTCAATGA 59.406 36.000 0.00 0.00 34.65 2.57
1750 6510 6.266103 TCTTTGCTCCTTTTTCACTCAATGAT 59.734 34.615 0.00 0.00 37.11 2.45
1751 6511 6.409524 TTGCTCCTTTTTCACTCAATGATT 57.590 33.333 0.00 0.00 37.11 2.57
1752 6512 6.017400 TGCTCCTTTTTCACTCAATGATTC 57.983 37.500 0.00 0.00 37.11 2.52
1753 6513 5.047802 TGCTCCTTTTTCACTCAATGATTCC 60.048 40.000 0.00 0.00 37.11 3.01
1754 6514 5.184671 GCTCCTTTTTCACTCAATGATTCCT 59.815 40.000 0.00 0.00 37.11 3.36
1755 6515 6.294955 GCTCCTTTTTCACTCAATGATTCCTT 60.295 38.462 0.00 0.00 37.11 3.36
1756 6516 7.219484 TCCTTTTTCACTCAATGATTCCTTC 57.781 36.000 0.00 0.00 37.11 3.46
1757 6517 7.006509 TCCTTTTTCACTCAATGATTCCTTCT 58.993 34.615 0.00 0.00 37.11 2.85
1758 6518 7.040201 TCCTTTTTCACTCAATGATTCCTTCTG 60.040 37.037 0.00 0.00 37.11 3.02
1759 6519 6.579666 TTTTCACTCAATGATTCCTTCTGG 57.420 37.500 0.00 0.00 37.11 3.86
1760 6520 3.614092 TCACTCAATGATTCCTTCTGGC 58.386 45.455 0.00 0.00 29.99 4.85
1761 6521 3.265221 TCACTCAATGATTCCTTCTGGCT 59.735 43.478 0.00 0.00 29.99 4.75
1762 6522 4.015084 CACTCAATGATTCCTTCTGGCTT 58.985 43.478 0.00 0.00 0.00 4.35
1763 6523 4.461781 CACTCAATGATTCCTTCTGGCTTT 59.538 41.667 0.00 0.00 0.00 3.51
1764 6524 5.047519 CACTCAATGATTCCTTCTGGCTTTT 60.048 40.000 0.00 0.00 0.00 2.27
1765 6525 5.541484 ACTCAATGATTCCTTCTGGCTTTTT 59.459 36.000 0.00 0.00 0.00 1.94
1784 6544 3.830744 TTTTTCTCTTCACTCGGACCA 57.169 42.857 0.00 0.00 0.00 4.02
1785 6545 3.386768 TTTTCTCTTCACTCGGACCAG 57.613 47.619 0.00 0.00 0.00 4.00
1786 6546 1.996798 TTCTCTTCACTCGGACCAGT 58.003 50.000 0.00 0.00 0.00 4.00
1787 6547 1.535833 TCTCTTCACTCGGACCAGTC 58.464 55.000 0.00 0.00 0.00 3.51
1788 6548 0.528470 CTCTTCACTCGGACCAGTCC 59.472 60.000 6.77 6.77 46.18 3.85
3399 11166 2.851195 TCCAACTCTTCTTGGTTCAGC 58.149 47.619 0.00 0.00 41.49 4.26
3686 11453 4.882842 AAGGAGAGAGAGGAAAGTGTTC 57.117 45.455 0.00 0.00 0.00 3.18
3694 11461 3.416156 AGAGGAAAGTGTTCAATGGAGC 58.584 45.455 0.00 0.00 35.25 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 7.798596 AAGATCTAGATCACGAAATTGCATT 57.201 32.000 29.83 11.43 40.22 3.56
56 57 8.912988 TGACAAGTTTCCAACAATTAAAGATCT 58.087 29.630 0.00 0.00 0.00 2.75
157 158 4.570930 GAAAGAGAAACGAGGGAATGTCT 58.429 43.478 0.00 0.00 0.00 3.41
1039 5796 9.950496 GTGGTATAGAGAATTGATCCAATATGT 57.050 33.333 0.00 0.00 32.43 2.29
1207 5964 4.097437 ACGAATAGAACAGGCTATGTCGAA 59.903 41.667 15.68 0.00 43.00 3.71
1615 6375 3.374220 TTCTTGCATCAAAAGGCACTG 57.626 42.857 0.00 0.00 42.83 3.66
1682 6442 5.615925 ACTAGTCTTCACTCTTGTGGTTT 57.384 39.130 0.00 0.00 43.94 3.27
1699 6459 8.588290 ATGACAAAAGATGAGACTCTACTAGT 57.412 34.615 0.00 0.00 42.80 2.57
1700 6460 9.515020 GAATGACAAAAGATGAGACTCTACTAG 57.485 37.037 3.68 0.00 0.00 2.57
1701 6461 9.249053 AGAATGACAAAAGATGAGACTCTACTA 57.751 33.333 3.68 0.00 0.00 1.82
1702 6462 8.133024 AGAATGACAAAAGATGAGACTCTACT 57.867 34.615 3.68 0.36 0.00 2.57
1703 6463 8.770438 AAGAATGACAAAAGATGAGACTCTAC 57.230 34.615 3.68 0.00 0.00 2.59
1704 6464 9.212641 CAAAGAATGACAAAAGATGAGACTCTA 57.787 33.333 3.68 0.00 0.00 2.43
1705 6465 7.308469 GCAAAGAATGACAAAAGATGAGACTCT 60.308 37.037 3.68 0.00 0.00 3.24
1706 6466 6.800892 GCAAAGAATGACAAAAGATGAGACTC 59.199 38.462 0.00 0.00 0.00 3.36
1707 6467 6.489361 AGCAAAGAATGACAAAAGATGAGACT 59.511 34.615 0.00 0.00 0.00 3.24
1708 6468 6.675987 AGCAAAGAATGACAAAAGATGAGAC 58.324 36.000 0.00 0.00 0.00 3.36
1709 6469 6.072286 GGAGCAAAGAATGACAAAAGATGAGA 60.072 38.462 0.00 0.00 0.00 3.27
1710 6470 6.072064 AGGAGCAAAGAATGACAAAAGATGAG 60.072 38.462 0.00 0.00 0.00 2.90
1711 6471 5.771666 AGGAGCAAAGAATGACAAAAGATGA 59.228 36.000 0.00 0.00 0.00 2.92
1712 6472 6.022163 AGGAGCAAAGAATGACAAAAGATG 57.978 37.500 0.00 0.00 0.00 2.90
1713 6473 6.661304 AAGGAGCAAAGAATGACAAAAGAT 57.339 33.333 0.00 0.00 0.00 2.40
1714 6474 6.469782 AAAGGAGCAAAGAATGACAAAAGA 57.530 33.333 0.00 0.00 0.00 2.52
1715 6475 7.278424 TGAAAAAGGAGCAAAGAATGACAAAAG 59.722 33.333 0.00 0.00 0.00 2.27
1716 6476 7.064490 GTGAAAAAGGAGCAAAGAATGACAAAA 59.936 33.333 0.00 0.00 0.00 2.44
1717 6477 6.534793 GTGAAAAAGGAGCAAAGAATGACAAA 59.465 34.615 0.00 0.00 0.00 2.83
1718 6478 6.042143 GTGAAAAAGGAGCAAAGAATGACAA 58.958 36.000 0.00 0.00 0.00 3.18
1719 6479 5.360714 AGTGAAAAAGGAGCAAAGAATGACA 59.639 36.000 0.00 0.00 0.00 3.58
1720 6480 5.836347 AGTGAAAAAGGAGCAAAGAATGAC 58.164 37.500 0.00 0.00 0.00 3.06
1721 6481 5.593909 TGAGTGAAAAAGGAGCAAAGAATGA 59.406 36.000 0.00 0.00 0.00 2.57
1722 6482 5.835257 TGAGTGAAAAAGGAGCAAAGAATG 58.165 37.500 0.00 0.00 0.00 2.67
1723 6483 6.469782 TTGAGTGAAAAAGGAGCAAAGAAT 57.530 33.333 0.00 0.00 0.00 2.40
1724 6484 5.913137 TTGAGTGAAAAAGGAGCAAAGAA 57.087 34.783 0.00 0.00 0.00 2.52
1725 6485 5.593909 TCATTGAGTGAAAAAGGAGCAAAGA 59.406 36.000 0.00 0.00 32.78 2.52
1726 6486 5.835257 TCATTGAGTGAAAAAGGAGCAAAG 58.165 37.500 0.00 0.00 32.78 2.77
1727 6487 5.850557 TCATTGAGTGAAAAAGGAGCAAA 57.149 34.783 0.00 0.00 32.78 3.68
1728 6488 6.409524 AATCATTGAGTGAAAAAGGAGCAA 57.590 33.333 0.00 0.00 40.97 3.91
1729 6489 5.047802 GGAATCATTGAGTGAAAAAGGAGCA 60.048 40.000 0.00 0.00 40.97 4.26
1730 6490 5.184671 AGGAATCATTGAGTGAAAAAGGAGC 59.815 40.000 0.00 0.00 40.97 4.70
1731 6491 6.830873 AGGAATCATTGAGTGAAAAAGGAG 57.169 37.500 0.00 0.00 40.97 3.69
1732 6492 7.006509 AGAAGGAATCATTGAGTGAAAAAGGA 58.993 34.615 0.00 0.00 40.97 3.36
1733 6493 7.088905 CAGAAGGAATCATTGAGTGAAAAAGG 58.911 38.462 0.00 0.00 40.97 3.11
1734 6494 7.088905 CCAGAAGGAATCATTGAGTGAAAAAG 58.911 38.462 0.00 0.00 37.48 2.27
1735 6495 6.517194 GCCAGAAGGAATCATTGAGTGAAAAA 60.517 38.462 0.00 0.00 37.48 1.94
1736 6496 5.047802 GCCAGAAGGAATCATTGAGTGAAAA 60.048 40.000 0.00 0.00 37.48 2.29
1737 6497 4.460382 GCCAGAAGGAATCATTGAGTGAAA 59.540 41.667 0.00 0.00 37.48 2.69
1738 6498 4.012374 GCCAGAAGGAATCATTGAGTGAA 58.988 43.478 0.00 0.00 37.48 3.18
1739 6499 3.265221 AGCCAGAAGGAATCATTGAGTGA 59.735 43.478 0.00 0.00 38.09 3.41
1740 6500 3.618351 AGCCAGAAGGAATCATTGAGTG 58.382 45.455 0.00 0.00 36.89 3.51
1741 6501 4.313020 AAGCCAGAAGGAATCATTGAGT 57.687 40.909 0.00 0.00 36.89 3.41
1742 6502 5.656213 AAAAGCCAGAAGGAATCATTGAG 57.344 39.130 0.00 0.00 36.89 3.02
1764 6524 3.134081 ACTGGTCCGAGTGAAGAGAAAAA 59.866 43.478 0.00 0.00 0.00 1.94
1765 6525 2.698797 ACTGGTCCGAGTGAAGAGAAAA 59.301 45.455 0.00 0.00 0.00 2.29
1766 6526 2.296471 GACTGGTCCGAGTGAAGAGAAA 59.704 50.000 0.00 0.00 0.00 2.52
1767 6527 1.887198 GACTGGTCCGAGTGAAGAGAA 59.113 52.381 0.00 0.00 0.00 2.87
1768 6528 1.535833 GACTGGTCCGAGTGAAGAGA 58.464 55.000 0.00 0.00 0.00 3.10
1769 6529 0.528470 GGACTGGTCCGAGTGAAGAG 59.472 60.000 3.88 0.00 40.36 2.85
1770 6530 2.654802 GGACTGGTCCGAGTGAAGA 58.345 57.895 3.88 0.00 40.36 2.87
1781 6541 2.352032 GCAGACTAGGCGGACTGGT 61.352 63.158 0.00 0.00 44.39 4.00
1782 6542 1.608717 AAGCAGACTAGGCGGACTGG 61.609 60.000 0.00 0.00 36.08 4.00
1783 6543 0.179124 GAAGCAGACTAGGCGGACTG 60.179 60.000 0.00 8.07 36.08 3.51
1784 6544 0.612174 TGAAGCAGACTAGGCGGACT 60.612 55.000 0.00 0.00 36.08 3.85
1785 6545 0.458716 GTGAAGCAGACTAGGCGGAC 60.459 60.000 0.00 0.00 36.08 4.79
1786 6546 1.890894 GTGAAGCAGACTAGGCGGA 59.109 57.895 0.00 0.00 36.08 5.54
1787 6547 1.517257 CGTGAAGCAGACTAGGCGG 60.517 63.158 0.00 0.00 36.08 6.13
1788 6548 0.109272 TTCGTGAAGCAGACTAGGCG 60.109 55.000 0.00 0.00 36.08 5.52
1789 6549 2.301577 ATTCGTGAAGCAGACTAGGC 57.698 50.000 0.00 0.00 0.00 3.93
1790 6550 5.188327 TCATATTCGTGAAGCAGACTAGG 57.812 43.478 0.00 0.00 0.00 3.02
1791 6551 8.978564 AATATCATATTCGTGAAGCAGACTAG 57.021 34.615 0.00 0.00 0.00 2.57
1792 6552 9.764363 AAAATATCATATTCGTGAAGCAGACTA 57.236 29.630 0.00 0.00 0.00 2.59
1793 6553 8.668510 AAAATATCATATTCGTGAAGCAGACT 57.331 30.769 0.00 0.00 0.00 3.24
2793 10549 7.844009 AGATGTTCCATCTTTGCATTTATTGT 58.156 30.769 0.92 0.00 0.00 2.71
2825 10581 4.506625 CCTGGTTCAACTCCTTCAATACCA 60.507 45.833 0.00 0.00 33.69 3.25
3686 11453 2.561733 TTAGTCGACTCGCTCCATTG 57.438 50.000 23.89 0.00 0.00 2.82
3694 11461 4.868450 AAGTCTCTGATTAGTCGACTCG 57.132 45.455 23.89 6.86 35.95 4.18


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

AutoCloner maintained by Alex Coulton.