Multiple sequence alignment - TraesCS5B01G464800

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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 TraesCS5B01G464800 chr5B 100.000 3274 0 0 1 3274 639622359 639619086 0.000000e+00 6047.0
1 TraesCS5B01G464800 chr5B 95.244 778 35 2 1 778 535220866 535220091 0.000000e+00 1230.0
2 TraesCS5B01G464800 chr5B 81.903 862 108 31 1459 2276 639676989 639677846 0.000000e+00 684.0
3 TraesCS5B01G464800 chr5B 83.595 573 56 15 778 1350 639676325 639676859 1.360000e-138 503.0
4 TraesCS5B01G464800 chr5B 87.261 157 8 2 1723 1878 639669713 639669568 5.620000e-38 169.0
5 TraesCS5B01G464800 chr5B 79.904 209 27 7 1501 1709 639670000 639669807 4.410000e-29 139.0
6 TraesCS5B01G464800 chr5B 94.118 34 2 0 1909 1942 639669569 639669536 6.000000e-03 52.8
7 TraesCS5B01G464800 chr5D 89.739 1608 81 31 778 2336 509021806 509020234 0.000000e+00 1978.0
8 TraesCS5B01G464800 chr5D 82.973 787 98 16 2345 3106 271456294 271455519 0.000000e+00 678.0
9 TraesCS5B01G464800 chr5D 80.685 818 92 31 2345 3108 20755564 20754759 2.830000e-160 575.0
10 TraesCS5B01G464800 chr5D 80.048 827 92 30 2382 3186 277619526 277618751 2.220000e-151 545.0
11 TraesCS5B01G464800 chr5D 82.906 585 53 21 778 1350 509135367 509135916 1.770000e-132 483.0
12 TraesCS5B01G464800 chr5D 88.164 414 34 7 2423 2823 65751650 65751239 2.290000e-131 479.0
13 TraesCS5B01G464800 chr5D 77.107 878 122 36 2333 3175 425018253 425019086 5.020000e-118 435.0
14 TraesCS5B01G464800 chr5D 91.367 278 24 0 1999 2276 509136641 509136918 6.630000e-102 381.0
15 TraesCS5B01G464800 chr5D 83.226 310 28 12 1634 1919 509023277 509022968 2.510000e-66 263.0
16 TraesCS5B01G464800 chr5D 89.583 192 17 3 1478 1666 509136066 509136257 1.170000e-59 241.0
17 TraesCS5B01G464800 chr5D 82.576 264 34 6 2896 3153 557768852 557769109 4.250000e-54 222.0
18 TraesCS5B01G464800 chr5D 90.400 125 12 0 2212 2336 509019528 509019404 7.270000e-37 165.0
19 TraesCS5B01G464800 chr5D 96.703 91 3 0 3175 3265 519207150 519207060 5.660000e-33 152.0
20 TraesCS5B01G464800 chr5D 77.857 280 28 19 2923 3175 20754997 20754725 3.410000e-30 143.0
21 TraesCS5B01G464800 chr5D 94.505 91 5 0 3175 3265 425019652 425019742 1.220000e-29 141.0
22 TraesCS5B01G464800 chr5D 91.753 97 8 0 3178 3274 20754196 20754100 5.700000e-28 135.0
23 TraesCS5B01G464800 chr5D 93.407 91 6 0 3175 3265 277618222 277618132 5.700000e-28 135.0
24 TraesCS5B01G464800 chr3B 97.044 778 22 1 1 778 10291961 10291185 0.000000e+00 1308.0
25 TraesCS5B01G464800 chr3B 95.624 777 21 3 1 777 780540910 780541673 0.000000e+00 1234.0
26 TraesCS5B01G464800 chr3B 91.829 771 52 5 2345 3108 706727027 706726261 0.000000e+00 1064.0
27 TraesCS5B01G464800 chr3B 87.578 483 42 12 2345 2812 116060495 116060974 7.990000e-151 544.0
28 TraesCS5B01G464800 chr3B 85.450 378 36 5 2345 2711 252872158 252871789 3.080000e-100 375.0
29 TraesCS5B01G464800 chr3B 96.000 100 4 0 3175 3274 70317849 70317750 2.610000e-36 163.0
30 TraesCS5B01G464800 chr3B 84.354 147 21 2 613 758 821859252 821859107 3.410000e-30 143.0
31 TraesCS5B01G464800 chr5A 92.140 916 51 13 1428 2336 636306802 636305901 0.000000e+00 1273.0
32 TraesCS5B01G464800 chr5A 93.228 694 45 2 1 694 704992493 704993184 0.000000e+00 1020.0
33 TraesCS5B01G464800 chr5A 90.854 656 34 16 778 1423 636307486 636306847 0.000000e+00 856.0
34 TraesCS5B01G464800 chr5A 84.337 581 51 18 778 1350 636412347 636412895 1.730000e-147 532.0
35 TraesCS5B01G464800 chr5A 81.569 510 63 22 1453 1936 636413016 636413520 3.060000e-105 392.0
36 TraesCS5B01G464800 chr5A 90.071 282 28 0 1995 2276 636413604 636413885 1.860000e-97 366.0
37 TraesCS5B01G464800 chr1A 93.742 783 46 3 1 782 579725599 579724819 0.000000e+00 1171.0
38 TraesCS5B01G464800 chr1A 81.863 204 30 5 2348 2548 17323153 17322954 7.270000e-37 165.0
39 TraesCS5B01G464800 chr4B 95.129 739 34 2 2 739 667270678 667269941 0.000000e+00 1164.0
40 TraesCS5B01G464800 chr4B 87.251 502 38 10 2345 2823 591927092 591927590 1.720000e-152 549.0
41 TraesCS5B01G464800 chr3A 93.445 778 46 3 1 778 578999579 578998807 0.000000e+00 1149.0
42 TraesCS5B01G464800 chr3A 93.133 699 42 4 1 699 579002703 579002011 0.000000e+00 1020.0
43 TraesCS5B01G464800 chr3A 94.969 636 30 2 1 636 673861713 673862346 0.000000e+00 996.0
44 TraesCS5B01G464800 chr3A 91.489 564 31 5 2551 3108 100724831 100724279 0.000000e+00 760.0
45 TraesCS5B01G464800 chr2A 89.364 865 64 14 2345 3186 657058867 657058008 0.000000e+00 1062.0
46 TraesCS5B01G464800 chr2A 89.373 781 58 17 2345 3108 678728401 678729173 0.000000e+00 959.0
47 TraesCS5B01G464800 chr2A 84.021 194 21 6 2337 2524 615692093 615692282 9.330000e-41 178.0
48 TraesCS5B01G464800 chr2A 96.000 100 4 0 3175 3274 195742035 195741936 2.610000e-36 163.0
49 TraesCS5B01G464800 chr6D 88.498 852 73 14 2344 3186 371299847 371299012 0.000000e+00 1007.0
50 TraesCS5B01G464800 chr6D 80.952 882 114 33 2345 3186 31803448 31804315 0.000000e+00 649.0
51 TraesCS5B01G464800 chr6D 78.309 816 107 40 2390 3186 397363476 397362712 2.300000e-126 462.0
52 TraesCS5B01G464800 chr6D 81.443 388 43 16 2823 3186 409649459 409649841 1.150000e-74 291.0
53 TraesCS5B01G464800 chr6D 82.704 318 35 8 2863 3175 131697045 131697347 6.970000e-67 265.0
54 TraesCS5B01G464800 chr6D 83.333 264 32 6 2896 3153 397363027 397362770 1.960000e-57 233.0
55 TraesCS5B01G464800 chr6D 95.000 100 5 0 3175 3274 409650352 409650451 1.220000e-34 158.0
56 TraesCS5B01G464800 chr6D 94.898 98 5 0 3175 3272 371298481 371298384 1.570000e-33 154.0
57 TraesCS5B01G464800 chr6D 77.689 251 30 12 2923 3150 31803995 31804242 2.650000e-26 130.0
58 TraesCS5B01G464800 chr6D 76.172 256 32 13 2923 3153 409649508 409649759 1.240000e-19 108.0
59 TraesCS5B01G464800 chr6D 96.667 60 2 0 3094 3153 371299129 371299070 2.080000e-17 100.0
60 TraesCS5B01G464800 chr6D 93.443 61 4 0 2932 2992 93633734 93633794 1.250000e-14 91.6
61 TraesCS5B01G464800 chr6D 83.505 97 14 2 3013 3108 157158561 157158466 4.500000e-14 89.8
62 TraesCS5B01G464800 chr6D 83.750 80 10 2 2907 2986 237785285 237785361 4.530000e-09 73.1
63 TraesCS5B01G464800 chr2D 87.921 861 71 14 2345 3186 535624477 535625323 0.000000e+00 983.0
64 TraesCS5B01G464800 chr2D 89.554 785 44 10 2345 3105 386513721 386514491 0.000000e+00 961.0
65 TraesCS5B01G464800 chr2D 81.890 635 87 19 2345 2962 613222031 613221408 8.100000e-141 510.0
66 TraesCS5B01G464800 chr2D 83.725 553 59 18 2429 2962 15786388 15786928 8.160000e-136 494.0
67 TraesCS5B01G464800 chr2D 84.615 286 32 6 2896 3175 15786829 15787108 1.160000e-69 274.0
68 TraesCS5B01G464800 chr2D 98.000 100 2 0 3175 3274 535625777 535625876 1.210000e-39 174.0
69 TraesCS5B01G464800 chr2D 94.059 101 5 1 3175 3274 386514817 386514917 5.660000e-33 152.0
70 TraesCS5B01G464800 chr6A 88.847 789 62 13 2345 3111 133505969 133505185 0.000000e+00 946.0
71 TraesCS5B01G464800 chr6A 95.000 100 5 0 3175 3274 133421222 133421123 1.220000e-34 158.0
72 TraesCS5B01G464800 chr1D 91.857 614 37 5 2466 3070 51044081 51044690 0.000000e+00 845.0
73 TraesCS5B01G464800 chr1D 80.303 858 105 30 2345 3186 16969820 16969011 1.010000e-164 590.0
74 TraesCS5B01G464800 chr1D 80.093 859 105 33 2345 3186 260983718 260982909 2.190000e-161 579.0
75 TraesCS5B01G464800 chr1D 79.840 873 105 30 2345 3186 119304373 119303541 3.660000e-159 571.0
76 TraesCS5B01G464800 chr1D 87.841 477 48 9 2345 2816 79106916 79107387 4.770000e-153 551.0
77 TraesCS5B01G464800 chr1D 78.888 881 130 32 2346 3186 430430663 430431527 2.220000e-151 545.0
78 TraesCS5B01G464800 chr1D 81.173 648 74 28 2336 2962 440411818 440412438 8.220000e-131 477.0
79 TraesCS5B01G464800 chr1D 80.344 524 74 14 2678 3175 493701166 493700646 1.430000e-98 370.0
80 TraesCS5B01G464800 chr1D 84.068 295 28 9 2896 3186 440412339 440412618 1.940000e-67 267.0
81 TraesCS5B01G464800 chr1D 87.931 174 19 2 2345 2517 324352536 324352364 1.540000e-48 204.0
82 TraesCS5B01G464800 chr1D 82.447 188 28 2 2345 2527 450742189 450742002 3.380000e-35 159.0
83 TraesCS5B01G464800 chr1D 95.604 91 4 0 3175 3265 493700081 493699991 2.630000e-31 147.0
84 TraesCS5B01G464800 chr1D 92.308 91 5 1 3175 3265 430432059 430432147 9.540000e-26 128.0
85 TraesCS5B01G464800 chr1D 91.489 94 7 1 3094 3186 458884913 458885006 9.540000e-26 128.0
86 TraesCS5B01G464800 chr1D 84.211 114 15 1 2878 2991 221923131 221923241 1.240000e-19 108.0
87 TraesCS5B01G464800 chr1D 89.286 56 6 0 3047 3102 493774534 493774479 1.630000e-08 71.3
88 TraesCS5B01G464800 chr3D 91.667 564 29 8 2545 3102 84474681 84474130 0.000000e+00 765.0
89 TraesCS5B01G464800 chr3D 78.990 871 128 29 2345 3186 397771418 397772262 7.990000e-151 544.0
90 TraesCS5B01G464800 chr3D 87.097 341 32 4 2630 2961 98597011 98596674 3.080000e-100 375.0
91 TraesCS5B01G464800 chr3D 87.143 280 24 7 2896 3175 98596772 98596505 1.140000e-79 307.0
92 TraesCS5B01G464800 chr3D 81.818 385 41 13 2475 2839 428600011 428600386 2.470000e-76 296.0
93 TraesCS5B01G464800 chr3D 95.699 93 4 0 3175 3267 98595987 98595895 2.040000e-32 150.0
94 TraesCS5B01G464800 chr4A 82.832 897 106 24 2345 3204 573376700 573375815 0.000000e+00 760.0
95 TraesCS5B01G464800 chr4A 92.488 213 13 1 2896 3108 585609941 585609732 5.310000e-78 302.0
96 TraesCS5B01G464800 chr4A 97.000 100 3 0 3175 3274 585593606 585593507 5.620000e-38 169.0
97 TraesCS5B01G464800 chr4A 94.000 100 5 1 3175 3274 573370371 573370273 2.040000e-32 150.0
98 TraesCS5B01G464800 chr7A 87.868 544 46 9 2345 2870 522926185 522926726 3.590000e-174 621.0
99 TraesCS5B01G464800 chr7A 84.228 298 34 7 2896 3186 78105924 78105633 8.950000e-71 278.0
100 TraesCS5B01G464800 chr7A 83.712 264 41 2 2012 2274 89835456 89835718 7.020000e-62 248.0
101 TraesCS5B01G464800 chr4D 84.746 413 39 10 2345 2740 494853816 494854221 3.060000e-105 392.0
102 TraesCS5B01G464800 chr4D 95.604 91 4 0 3175 3265 439787196 439787106 2.630000e-31 147.0
103 TraesCS5B01G464800 chr4D 94.505 91 5 0 3175 3265 94416737 94416827 1.220000e-29 141.0
104 TraesCS5B01G464800 chr4D 83.784 148 12 10 2540 2686 84237393 84237257 2.650000e-26 130.0
105 TraesCS5B01G464800 chr7B 83.582 268 42 2 2012 2278 37091074 37091340 1.950000e-62 250.0
106 TraesCS5B01G464800 chr7D 83.712 264 41 2 2012 2274 88149595 88149857 7.020000e-62 248.0
107 TraesCS5B01G464800 chr7D 87.037 216 20 5 2345 2554 79615480 79615267 1.520000e-58 237.0
108 TraesCS5B01G464800 chr7D 85.106 141 17 3 2381 2518 51412438 51412299 1.220000e-29 141.0
109 TraesCS5B01G464800 chr2B 85.981 214 25 4 2345 2554 382458982 382458770 1.180000e-54 224.0
110 TraesCS5B01G464800 chr1B 84.058 207 27 4 2345 2548 15345021 15345224 9.270000e-46 195.0
111 TraesCS5B01G464800 chr1B 83.182 220 29 6 2345 2559 567201498 567201282 9.270000e-46 195.0
112 TraesCS5B01G464800 chr6B 96.000 100 3 1 3175 3274 532194692 532194594 9.400000e-36 161.0


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 TraesCS5B01G464800 chr5B 639619086 639622359 3273 True 6047.000000 6047 100.000000 1 3274 1 chr5B.!!$R2 3273
1 TraesCS5B01G464800 chr5B 535220091 535220866 775 True 1230.000000 1230 95.244000 1 778 1 chr5B.!!$R1 777
2 TraesCS5B01G464800 chr5B 639676325 639677846 1521 False 593.500000 684 82.749000 778 2276 2 chr5B.!!$F1 1498
3 TraesCS5B01G464800 chr5D 509019404 509023277 3873 True 802.000000 1978 87.788333 778 2336 3 chr5D.!!$R6 1558
4 TraesCS5B01G464800 chr5D 271455519 271456294 775 True 678.000000 678 82.973000 2345 3106 1 chr5D.!!$R2 761
5 TraesCS5B01G464800 chr5D 509135367 509136918 1551 False 368.333333 483 87.952000 778 2276 3 chr5D.!!$F3 1498
6 TraesCS5B01G464800 chr5D 277618132 277619526 1394 True 340.000000 545 86.727500 2382 3265 2 chr5D.!!$R5 883
7 TraesCS5B01G464800 chr5D 425018253 425019742 1489 False 288.000000 435 85.806000 2333 3265 2 chr5D.!!$F2 932
8 TraesCS5B01G464800 chr5D 20754100 20755564 1464 True 284.333333 575 83.431667 2345 3274 3 chr5D.!!$R4 929
9 TraesCS5B01G464800 chr3B 10291185 10291961 776 True 1308.000000 1308 97.044000 1 778 1 chr3B.!!$R1 777
10 TraesCS5B01G464800 chr3B 780540910 780541673 763 False 1234.000000 1234 95.624000 1 777 1 chr3B.!!$F2 776
11 TraesCS5B01G464800 chr3B 706726261 706727027 766 True 1064.000000 1064 91.829000 2345 3108 1 chr3B.!!$R4 763
12 TraesCS5B01G464800 chr5A 636305901 636307486 1585 True 1064.500000 1273 91.497000 778 2336 2 chr5A.!!$R1 1558
13 TraesCS5B01G464800 chr5A 704992493 704993184 691 False 1020.000000 1020 93.228000 1 694 1 chr5A.!!$F1 693
14 TraesCS5B01G464800 chr5A 636412347 636413885 1538 False 430.000000 532 85.325667 778 2276 3 chr5A.!!$F2 1498
15 TraesCS5B01G464800 chr1A 579724819 579725599 780 True 1171.000000 1171 93.742000 1 782 1 chr1A.!!$R2 781
16 TraesCS5B01G464800 chr4B 667269941 667270678 737 True 1164.000000 1164 95.129000 2 739 1 chr4B.!!$R1 737
17 TraesCS5B01G464800 chr3A 578998807 579002703 3896 True 1084.500000 1149 93.289000 1 778 2 chr3A.!!$R2 777
18 TraesCS5B01G464800 chr3A 673861713 673862346 633 False 996.000000 996 94.969000 1 636 1 chr3A.!!$F1 635
19 TraesCS5B01G464800 chr3A 100724279 100724831 552 True 760.000000 760 91.489000 2551 3108 1 chr3A.!!$R1 557
20 TraesCS5B01G464800 chr2A 657058008 657058867 859 True 1062.000000 1062 89.364000 2345 3186 1 chr2A.!!$R2 841
21 TraesCS5B01G464800 chr2A 678728401 678729173 772 False 959.000000 959 89.373000 2345 3108 1 chr2A.!!$F2 763
22 TraesCS5B01G464800 chr6D 371298384 371299847 1463 True 420.333333 1007 93.354333 2344 3272 3 chr6D.!!$R2 928
23 TraesCS5B01G464800 chr6D 31803448 31804315 867 False 389.500000 649 79.320500 2345 3186 2 chr6D.!!$F4 841
24 TraesCS5B01G464800 chr6D 397362712 397363476 764 True 347.500000 462 80.821000 2390 3186 2 chr6D.!!$R3 796
25 TraesCS5B01G464800 chr2D 535624477 535625876 1399 False 578.500000 983 92.960500 2345 3274 2 chr2D.!!$F3 929
26 TraesCS5B01G464800 chr2D 386513721 386514917 1196 False 556.500000 961 91.806500 2345 3274 2 chr2D.!!$F2 929
27 TraesCS5B01G464800 chr2D 613221408 613222031 623 True 510.000000 510 81.890000 2345 2962 1 chr2D.!!$R1 617
28 TraesCS5B01G464800 chr2D 15786388 15787108 720 False 384.000000 494 84.170000 2429 3175 2 chr2D.!!$F1 746
29 TraesCS5B01G464800 chr6A 133505185 133505969 784 True 946.000000 946 88.847000 2345 3111 1 chr6A.!!$R2 766
30 TraesCS5B01G464800 chr1D 51044081 51044690 609 False 845.000000 845 91.857000 2466 3070 1 chr1D.!!$F1 604
31 TraesCS5B01G464800 chr1D 16969011 16969820 809 True 590.000000 590 80.303000 2345 3186 1 chr1D.!!$R1 841
32 TraesCS5B01G464800 chr1D 260982909 260983718 809 True 579.000000 579 80.093000 2345 3186 1 chr1D.!!$R3 841
33 TraesCS5B01G464800 chr1D 119303541 119304373 832 True 571.000000 571 79.840000 2345 3186 1 chr1D.!!$R2 841
34 TraesCS5B01G464800 chr1D 440411818 440412618 800 False 372.000000 477 82.620500 2336 3186 2 chr1D.!!$F6 850
35 TraesCS5B01G464800 chr1D 430430663 430432147 1484 False 336.500000 545 85.598000 2346 3265 2 chr1D.!!$F5 919
36 TraesCS5B01G464800 chr1D 493699991 493701166 1175 True 258.500000 370 87.974000 2678 3265 2 chr1D.!!$R7 587
37 TraesCS5B01G464800 chr3D 84474130 84474681 551 True 765.000000 765 91.667000 2545 3102 1 chr3D.!!$R1 557
38 TraesCS5B01G464800 chr3D 397771418 397772262 844 False 544.000000 544 78.990000 2345 3186 1 chr3D.!!$F1 841
39 TraesCS5B01G464800 chr3D 98595895 98597011 1116 True 277.333333 375 89.979667 2630 3267 3 chr3D.!!$R2 637
40 TraesCS5B01G464800 chr4A 573375815 573376700 885 True 760.000000 760 82.832000 2345 3204 1 chr4A.!!$R2 859
41 TraesCS5B01G464800 chr7A 522926185 522926726 541 False 621.000000 621 87.868000 2345 2870 1 chr7A.!!$F2 525

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
990 4130 0.174845 GCAGGTACGATGTGCTGGTA 59.825 55.0 0.0 0.0 34.23 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2480 5855 0.106149 GGACCGTCTGTTGGAGTTGT 59.894 55.0 0.0 0.0 0.0 3.32 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
388 3331 2.818274 GGTTGTCCCACGGATCGC 60.818 66.667 0.00 0.00 32.73 4.58
636 3760 1.141019 GCTTGGTCTATGCCGACGA 59.859 57.895 0.00 0.00 34.75 4.20
915 4039 4.396166 CACAATTACACATCCTCAACCTCC 59.604 45.833 0.00 0.00 0.00 4.30
959 4093 0.465287 TGCACAGTCTCACAGCTCAA 59.535 50.000 0.00 0.00 0.00 3.02
967 4101 5.046735 ACAGTCTCACAGCTCAATTGATACT 60.047 40.000 8.96 6.95 29.40 2.12
990 4130 0.174845 GCAGGTACGATGTGCTGGTA 59.825 55.000 0.00 0.00 34.23 3.25
1052 4192 1.379576 GGCTGATGGGCAAGCTTCT 60.380 57.895 0.00 0.00 40.53 2.85
1248 4406 4.683832 CCGATAAAGATGAAGACGAAGGT 58.316 43.478 0.00 0.00 0.00 3.50
1356 4514 2.549611 CTTCCCAGAGAGGTCGCACG 62.550 65.000 0.00 0.00 34.66 5.34
1476 4721 0.837260 ATTGGTTTGGGCATGCAGGT 60.837 50.000 21.36 0.00 0.00 4.00
1641 4895 1.592223 CCCTCTTGGACTCGGACAC 59.408 63.158 0.00 0.00 35.39 3.67
1697 5009 1.885871 GCAACAGACCCATTGCTCC 59.114 57.895 1.80 0.00 46.21 4.70
1713 5025 6.038603 CCATTGCTCCGAATTTCTGAATTCTA 59.961 38.462 7.05 0.00 45.78 2.10
1721 5033 8.450964 TCCGAATTTCTGAATTCTAAACATGAC 58.549 33.333 7.05 0.00 45.78 3.06
1736 5048 1.745087 CATGACCCCATTGTTCTTCCG 59.255 52.381 0.00 0.00 0.00 4.30
1829 5142 1.276138 TCAGACAACATGGTGATCGCT 59.724 47.619 19.90 6.07 0.00 4.93
1931 5244 3.228188 ACCAAAGACAAGCTCATGGAA 57.772 42.857 0.00 0.00 37.11 3.53
1942 5255 1.303236 TCATGGAAAGGTGCCACGG 60.303 57.895 0.00 0.00 38.44 4.94
1964 5305 0.034089 ACCTGCAGCTTGGAATACCC 60.034 55.000 8.66 0.00 34.81 3.69
1981 5322 6.407074 GGAATACCCGAGAATTCCGATCATAT 60.407 42.308 15.21 6.76 41.20 1.78
1982 5323 7.201884 GGAATACCCGAGAATTCCGATCATATA 60.202 40.741 15.21 2.71 41.20 0.86
1983 5324 7.841282 ATACCCGAGAATTCCGATCATATAT 57.159 36.000 15.21 0.00 0.00 0.86
1984 5325 8.935614 ATACCCGAGAATTCCGATCATATATA 57.064 34.615 15.21 0.00 0.00 0.86
1985 5326 7.655521 ACCCGAGAATTCCGATCATATATAA 57.344 36.000 15.21 0.00 0.00 0.98
1987 5328 7.123697 ACCCGAGAATTCCGATCATATATAACA 59.876 37.037 15.21 0.00 0.00 2.41
1989 5330 8.191446 CCGAGAATTCCGATCATATATAACAGT 58.809 37.037 15.21 0.00 0.00 3.55
1990 5331 9.574458 CGAGAATTCCGATCATATATAACAGTT 57.426 33.333 0.65 0.00 0.00 3.16
2147 5488 3.712907 GCCAAGGGGACGCTGGTA 61.713 66.667 0.62 0.00 39.58 3.25
2168 5509 0.173029 CATCAGTCGTGCAGAGAGCT 59.827 55.000 0.00 0.00 45.94 4.09
2170 5511 1.175347 TCAGTCGTGCAGAGAGCTGT 61.175 55.000 0.00 0.00 45.94 4.40
2171 5512 0.319383 CAGTCGTGCAGAGAGCTGTT 60.319 55.000 0.00 0.00 45.94 3.16
2258 5599 9.449719 AAGAACTTCTATTTCCATGATTACGTT 57.550 29.630 0.00 0.00 0.00 3.99
2282 5623 7.776933 TCATGCTTACAAGTGAAGACATATC 57.223 36.000 0.00 0.00 0.00 1.63
2308 5649 2.086869 CCGTGCCATTCAGTCAAAGAT 58.913 47.619 0.00 0.00 0.00 2.40
2313 5654 5.740569 CGTGCCATTCAGTCAAAGATAAATG 59.259 40.000 0.00 0.00 0.00 2.32
2317 5658 7.124599 TGCCATTCAGTCAAAGATAAATGGATT 59.875 33.333 14.40 0.00 43.70 3.01
2378 5719 9.158233 CCAATGGATGATTATATTTTTGATGCC 57.842 33.333 0.00 0.00 0.00 4.40
2405 5748 9.534565 TCAAATCGGTGATGTAAAAATTTGAAA 57.465 25.926 5.42 0.00 38.18 2.69
2439 5782 8.897872 AGTACTTTTTACATCTCCGAAAAAGA 57.102 30.769 20.17 6.60 46.17 2.52
2448 5791 4.939052 TCTCCGAAAAAGACTCAACTCT 57.061 40.909 0.00 0.00 0.00 3.24
2480 5855 6.319152 TGGTTCAAAACGGAGATGTAAAAGAA 59.681 34.615 0.00 0.00 0.00 2.52
2784 6204 3.057526 GGTACGATCATCATCATCACCGA 60.058 47.826 0.00 0.00 0.00 4.69
2857 6292 0.032813 ACCTTCATTGCCTCCCATGG 60.033 55.000 4.14 4.14 0.00 3.66
2894 6329 1.764571 AAGCTACCTCCAACGCCACA 61.765 55.000 0.00 0.00 0.00 4.17
2965 6540 3.402681 CACCTCCCATGCCGGTCT 61.403 66.667 1.90 0.00 0.00 3.85
2990 6565 2.285368 TCCGAAGCCACCTCCCAT 60.285 61.111 0.00 0.00 0.00 4.00
2991 6566 1.915078 CTCCGAAGCCACCTCCCATT 61.915 60.000 0.00 0.00 0.00 3.16
2992 6567 1.000896 CCGAAGCCACCTCCCATTT 60.001 57.895 0.00 0.00 0.00 2.32
3023 6620 0.827089 CCACCTTCCATGTTGCCACA 60.827 55.000 0.00 0.00 37.31 4.17
3111 6830 0.826256 CCATGGCACCTCCCATCATG 60.826 60.000 0.00 0.00 43.63 3.07
3113 6832 0.632835 ATGGCACCTCCCATCATGTT 59.367 50.000 0.00 0.00 41.75 2.71
3114 6833 0.034186 TGGCACCTCCCATCATGTTC 60.034 55.000 0.00 0.00 0.00 3.18
3115 6834 0.034186 GGCACCTCCCATCATGTTCA 60.034 55.000 0.00 0.00 0.00 3.18
3116 6835 1.410648 GGCACCTCCCATCATGTTCAT 60.411 52.381 0.00 0.00 0.00 2.57
3117 6836 1.679680 GCACCTCCCATCATGTTCATG 59.320 52.381 6.46 6.46 0.00 3.07
3118 6837 2.947243 GCACCTCCCATCATGTTCATGT 60.947 50.000 11.73 0.00 0.00 3.21
3119 6838 3.685265 GCACCTCCCATCATGTTCATGTA 60.685 47.826 11.73 1.31 0.00 2.29
3123 6845 2.509131 TCCCATCATGTTCATGTAGCCA 59.491 45.455 11.73 0.00 0.00 4.75
3127 6849 1.016627 CATGTTCATGTAGCCACCCG 58.983 55.000 4.80 0.00 0.00 5.28
3163 6957 1.878088 CTCCTCCCATCATCATTTGCG 59.122 52.381 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 226 1.645034 CTTCGCCACGTCATTGATCT 58.355 50.000 0.00 0.00 0.00 2.75
411 3535 4.007644 CCCTCTGCCACGTCAGCA 62.008 66.667 9.30 9.30 38.82 4.41
459 3583 0.390492 CGGCATATCTGTGGCAGAGA 59.610 55.000 17.33 17.33 44.08 3.10
544 3668 4.127744 GCATAGCCAGGGCCCACA 62.128 66.667 27.56 3.59 43.17 4.17
636 3760 1.046472 TTCATCTATGCCGACGGGGT 61.046 55.000 17.22 0.00 38.44 4.95
896 4020 6.770286 ATATGGAGGTTGAGGATGTGTAAT 57.230 37.500 0.00 0.00 0.00 1.89
897 4021 7.679783 CATATATGGAGGTTGAGGATGTGTAA 58.320 38.462 4.68 0.00 0.00 2.41
915 4039 0.745845 GGGAGGCAGCCGCATATATG 60.746 60.000 17.96 8.45 41.24 1.78
959 4093 5.163405 ACATCGTACCTGCAAGAGTATCAAT 60.163 40.000 0.00 0.00 37.82 2.57
967 4101 0.608130 AGCACATCGTACCTGCAAGA 59.392 50.000 0.00 0.00 34.07 3.02
990 4130 1.577736 CAGGGTCCATGAGGTTCTCT 58.422 55.000 0.00 0.00 35.89 3.10
1155 4313 6.624423 ACAATTGAATCAGCACTTGTATTCC 58.376 36.000 13.59 0.00 39.09 3.01
1476 4721 1.774254 TGAACTGGGGCTTCTTCTTCA 59.226 47.619 0.00 0.00 0.00 3.02
1573 4827 1.641577 GTATGACCTTGTCGAGCCAC 58.358 55.000 0.00 0.00 34.95 5.01
1641 4895 1.703438 CTCGACGTGGAGGAGGTACG 61.703 65.000 18.85 0.00 42.98 3.67
1713 5025 3.578282 GGAAGAACAATGGGGTCATGTTT 59.422 43.478 0.00 0.00 33.18 2.83
1721 5033 0.321298 ACGACGGAAGAACAATGGGG 60.321 55.000 0.00 0.00 0.00 4.96
1736 5048 1.204312 GTTGCGCTCCTGAAACGAC 59.796 57.895 9.73 0.00 0.00 4.34
1771 5084 1.576421 GCTTTGTGCCAGTTCTCGG 59.424 57.895 0.00 0.00 35.15 4.63
1811 5124 2.479566 AAGCGATCACCATGTTGTCT 57.520 45.000 0.00 0.00 0.00 3.41
1950 5291 2.691409 TTCTCGGGTATTCCAAGCTG 57.309 50.000 0.00 0.00 34.36 4.24
1964 5305 9.574458 AACTGTTATATATGATCGGAATTCTCG 57.426 33.333 5.23 7.63 0.00 4.04
1981 5322 7.040132 TGCCATCACAACATCAAAACTGTTATA 60.040 33.333 0.00 0.00 35.15 0.98
1982 5323 6.158598 GCCATCACAACATCAAAACTGTTAT 58.841 36.000 0.00 0.00 35.15 1.89
1983 5324 5.068329 TGCCATCACAACATCAAAACTGTTA 59.932 36.000 0.00 0.00 35.15 2.41
1984 5325 4.141981 TGCCATCACAACATCAAAACTGTT 60.142 37.500 0.00 0.00 37.31 3.16
1985 5326 3.384146 TGCCATCACAACATCAAAACTGT 59.616 39.130 0.00 0.00 0.00 3.55
1987 5328 4.322198 GGATGCCATCACAACATCAAAACT 60.322 41.667 7.06 0.00 41.58 2.66
1989 5330 3.577415 TGGATGCCATCACAACATCAAAA 59.423 39.130 7.06 0.00 41.58 2.44
1990 5331 3.056678 GTGGATGCCATCACAACATCAAA 60.057 43.478 7.06 0.00 41.58 2.69
2147 5488 1.671261 GCTCTCTGCACGACTGATGTT 60.671 52.381 0.00 0.00 42.31 2.71
2153 5494 0.319383 CAACAGCTCTCTGCACGACT 60.319 55.000 0.00 0.00 44.10 4.18
2168 5509 1.380403 CGGCCAAGGACACAACAACA 61.380 55.000 2.24 0.00 0.00 3.33
2170 5511 1.077357 ACGGCCAAGGACACAACAA 60.077 52.632 2.24 0.00 0.00 2.83
2171 5512 1.821759 CACGGCCAAGGACACAACA 60.822 57.895 2.24 0.00 0.00 3.33
2258 5599 6.763135 GGATATGTCTTCACTTGTAAGCATGA 59.237 38.462 0.00 0.00 0.00 3.07
2297 5638 6.404623 CGGCAAATCCATTTATCTTTGACTGA 60.405 38.462 0.00 0.00 35.03 3.41
2300 5641 5.890334 TCGGCAAATCCATTTATCTTTGAC 58.110 37.500 0.00 0.00 34.07 3.18
2308 5649 3.454447 TCCTCTCTCGGCAAATCCATTTA 59.546 43.478 0.00 0.00 34.01 1.40
2313 5654 0.827368 AGTCCTCTCTCGGCAAATCC 59.173 55.000 0.00 0.00 0.00 3.01
2317 5658 2.244695 TGTAAAGTCCTCTCTCGGCAA 58.755 47.619 0.00 0.00 0.00 4.52
2378 5719 8.741101 TCAAATTTTTACATCACCGATTTGAG 57.259 30.769 0.00 0.00 37.21 3.02
2439 5782 7.639113 TTTGAACCATTTGTTAGAGTTGAGT 57.361 32.000 0.00 0.00 37.29 3.41
2448 5791 6.039941 ACATCTCCGTTTTGAACCATTTGTTA 59.960 34.615 0.00 0.00 37.29 2.41
2480 5855 0.106149 GGACCGTCTGTTGGAGTTGT 59.894 55.000 0.00 0.00 0.00 3.32
2784 6204 4.201822 GCTTCACAAACTCGACAAAGAAGT 60.202 41.667 0.00 0.00 35.07 3.01
2797 6217 1.940613 AGACTTCACCGCTTCACAAAC 59.059 47.619 0.00 0.00 0.00 2.93
2894 6329 2.120909 GGCTATGGCGGCAACATGT 61.121 57.895 18.31 0.38 39.81 3.21
2990 6565 0.980231 AGGTGGCTTTGGTGGCAAAA 60.980 50.000 0.00 0.00 44.02 2.44
2991 6566 0.980231 AAGGTGGCTTTGGTGGCAAA 60.980 50.000 0.00 0.00 44.02 3.68
2992 6567 1.382420 AAGGTGGCTTTGGTGGCAA 60.382 52.632 0.00 0.00 44.02 4.52
3023 6620 3.054802 CAGAAACATGGGAGGTAGCTTCT 60.055 47.826 0.00 0.00 0.00 2.85
3070 6669 3.544684 GTGGCTACATGAACATGATGGA 58.455 45.455 19.56 0.00 41.20 3.41
3111 6830 1.024579 CCACGGGTGGCTACATGAAC 61.025 60.000 4.68 0.00 44.73 3.18
3113 6832 2.986290 CCACGGGTGGCTACATGA 59.014 61.111 4.68 0.00 44.73 3.07
3163 6957 1.739466 TGAAAGGCGAATGCTCATGAC 59.261 47.619 0.00 0.00 42.25 3.06
3236 8168 7.700022 TCCACATTTTGATGATGATGTGTTA 57.300 32.000 12.59 0.80 44.79 2.41


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

AutoCloner maintained by Alex Coulton.