Multiple sequence alignment - TraesCS5D01G269700

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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 TraesCS5D01G269700 chr5D 100.000 4770 0 0 1 4770 373213345 373218114 0.000000e+00 8809.0
1 TraesCS5D01G269700 chr5D 91.941 1824 127 14 2079 3897 384143049 384144857 0.000000e+00 2536.0
2 TraesCS5D01G269700 chr5D 84.728 1840 233 20 2079 3891 384153738 384155556 0.000000e+00 1797.0
3 TraesCS5D01G269700 chr5D 84.973 1637 209 11 2078 3686 404880869 404882496 0.000000e+00 1626.0
4 TraesCS5D01G269700 chr5D 76.960 1263 261 24 2524 3771 384019216 384017969 0.000000e+00 693.0
5 TraesCS5D01G269700 chr5D 91.635 263 18 3 1742 2003 384152629 384152888 1.260000e-95 361.0
6 TraesCS5D01G269700 chr5D 94.667 225 10 1 1742 1966 404879029 404879251 9.820000e-92 348.0
7 TraesCS5D01G269700 chr5D 88.686 274 20 4 1737 2009 384141316 384141579 1.660000e-84 324.0
8 TraesCS5D01G269700 chr5D 84.431 334 26 6 919 1228 384151776 384152107 6.000000e-79 305.0
9 TraesCS5D01G269700 chr5D 84.211 285 28 9 1459 1743 384140903 384141170 1.320000e-65 261.0
10 TraesCS5D01G269700 chr5D 86.818 220 18 6 1516 1735 404878663 404878871 7.980000e-58 235.0
11 TraesCS5D01G269700 chr5D 92.308 117 8 1 997 1112 404878076 404878192 1.060000e-36 165.0
12 TraesCS5D01G269700 chr5D 92.857 98 5 2 1367 1463 342698117 342698213 1.790000e-29 141.0
13 TraesCS5D01G269700 chr5D 83.333 96 4 7 768 857 384151685 384151774 1.420000e-10 78.7
14 TraesCS5D01G269700 chr5B 97.453 3298 41 6 1508 4770 443289468 443292757 0.000000e+00 5585.0
15 TraesCS5D01G269700 chr5B 85.353 1700 214 12 2077 3750 460942530 460944220 0.000000e+00 1727.0
16 TraesCS5D01G269700 chr5B 95.914 979 34 4 256 1229 443288212 443289189 0.000000e+00 1581.0
17 TraesCS5D01G269700 chr5B 92.118 609 39 5 1 607 22046924 22047525 0.000000e+00 850.0
18 TraesCS5D01G269700 chr5B 77.053 1242 254 28 2524 3748 460494942 460493715 0.000000e+00 686.0
19 TraesCS5D01G269700 chr5B 87.751 449 32 14 3481 3921 460938434 460938867 1.980000e-138 503.0
20 TraesCS5D01G269700 chr5B 92.419 277 16 4 1735 2009 460941418 460941691 1.610000e-104 390.0
21 TraesCS5D01G269700 chr5B 85.970 335 20 8 919 1228 460940539 460940871 2.750000e-87 333.0
22 TraesCS5D01G269700 chr5B 90.265 113 6 3 1271 1379 460940872 460940983 4.980000e-30 143.0
23 TraesCS5D01G269700 chr5B 90.816 98 7 2 1367 1463 402737533 402737629 3.870000e-26 130.0
24 TraesCS5D01G269700 chr5B 90.816 98 7 2 1367 1463 411517284 411517380 3.870000e-26 130.0
25 TraesCS5D01G269700 chr5B 98.000 50 1 0 1460 1509 443289260 443289309 2.360000e-13 87.9
26 TraesCS5D01G269700 chr5B 79.231 130 14 7 703 829 460940378 460940497 1.420000e-10 78.7
27 TraesCS5D01G269700 chr5A 88.715 2490 194 44 1459 3897 484833142 484835595 0.000000e+00 2961.0
28 TraesCS5D01G269700 chr5A 90.443 1852 150 20 2079 3921 484589237 484591070 0.000000e+00 2414.0
29 TraesCS5D01G269700 chr5A 84.982 1698 216 15 2078 3746 509126602 509124915 0.000000e+00 1687.0
30 TraesCS5D01G269700 chr5A 83.646 1278 177 7 2077 3330 484839522 484840791 0.000000e+00 1173.0
31 TraesCS5D01G269700 chr5A 94.444 270 11 3 1742 2009 509128327 509128060 3.440000e-111 412.0
32 TraesCS5D01G269700 chr5A 89.051 274 19 4 1737 2009 484587554 484587817 3.560000e-86 329.0
33 TraesCS5D01G269700 chr5A 86.942 291 17 6 924 1197 509137597 509137311 1.670000e-79 307.0
34 TraesCS5D01G269700 chr5A 84.561 285 27 11 1459 1743 484587144 484587411 2.830000e-67 267.0
35 TraesCS5D01G269700 chr5A 91.848 184 11 2 1742 1925 484838484 484838663 2.200000e-63 254.0
36 TraesCS5D01G269700 chr5A 82.895 228 25 2 879 1103 484837725 484837941 4.870000e-45 193.0
37 TraesCS5D01G269700 chr5A 85.827 127 15 2 1612 1738 509128606 509128483 1.080000e-26 132.0
38 TraesCS5D01G269700 chr5A 87.156 109 7 4 1478 1583 484838083 484838187 3.020000e-22 117.0
39 TraesCS5D01G269700 chr5A 100.000 29 0 0 771 799 484837666 484837694 2.000000e-03 54.7
40 TraesCS5D01G269700 chr6D 94.737 608 27 3 4 607 277054911 277054305 0.000000e+00 941.0
41 TraesCS5D01G269700 chr1D 94.127 613 31 4 1 609 458395508 458396119 0.000000e+00 928.0
42 TraesCS5D01G269700 chr1D 92.453 106 5 3 1228 1330 301353589 301353484 1.070000e-31 148.0
43 TraesCS5D01G269700 chr2D 93.388 605 38 2 1 603 638873126 638873730 0.000000e+00 894.0
44 TraesCS5D01G269700 chr2D 96.809 94 3 0 1219 1312 636386040 636385947 1.780000e-34 158.0
45 TraesCS5D01G269700 chr2D 98.851 87 1 0 1227 1313 15192881 15192967 6.390000e-34 156.0
46 TraesCS5D01G269700 chr2D 90.625 96 7 2 1370 1463 208540137 208540232 5.010000e-25 126.0
47 TraesCS5D01G269700 chr6A 92.397 605 44 2 4 607 24235942 24235339 0.000000e+00 861.0
48 TraesCS5D01G269700 chr3B 91.776 608 47 3 1 607 467879647 467880252 0.000000e+00 843.0
49 TraesCS5D01G269700 chr3B 88.360 189 21 1 4583 4770 727260403 727260591 4.800000e-55 226.0
50 TraesCS5D01G269700 chr3B 93.103 87 6 0 1377 1463 671380776 671380690 1.390000e-25 128.0
51 TraesCS5D01G269700 chr6B 90.984 610 48 6 1 607 169240230 169240835 0.000000e+00 815.0
52 TraesCS5D01G269700 chr7B 90.805 609 53 3 1 607 629546492 629547099 0.000000e+00 811.0
53 TraesCS5D01G269700 chr1A 87.530 417 37 12 4183 4599 372220037 372219636 7.230000e-128 468.0
54 TraesCS5D01G269700 chr1A 83.173 416 36 20 4357 4770 372219814 372219431 2.730000e-92 350.0
55 TraesCS5D01G269700 chr1A 94.309 123 4 3 4065 4185 372220120 372219999 8.150000e-43 185.0
56 TraesCS5D01G269700 chr7D 95.876 97 3 1 1228 1324 22964341 22964246 6.390000e-34 156.0
57 TraesCS5D01G269700 chr7D 94.845 97 5 0 1219 1315 41837670 41837766 8.270000e-33 152.0
58 TraesCS5D01G269700 chr7D 92.391 92 7 0 1372 1463 6744876 6744967 1.080000e-26 132.0
59 TraesCS5D01G269700 chr7D 91.209 91 8 0 1372 1462 6744970 6744880 1.800000e-24 124.0
60 TraesCS5D01G269700 chr4D 95.876 97 2 1 1228 1322 434161698 434161602 6.390000e-34 156.0
61 TraesCS5D01G269700 chr4D 92.135 89 7 0 1374 1462 64347448 64347360 5.010000e-25 126.0
62 TraesCS5D01G269700 chr4D 86.486 111 12 2 1353 1462 39411295 39411187 8.390000e-23 119.0
63 TraesCS5D01G269700 chr3D 95.789 95 4 0 1227 1321 436459712 436459806 2.300000e-33 154.0
64 TraesCS5D01G269700 chr3D 96.739 92 3 0 1224 1315 545547791 545547882 2.300000e-33 154.0
65 TraesCS5D01G269700 chr1B 97.701 87 2 0 1228 1314 320588050 320588136 2.970000e-32 150.0


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 TraesCS5D01G269700 chr5D 373213345 373218114 4769 False 8809.000000 8809 100.000000 1 4770 1 chr5D.!!$F2 4769
1 TraesCS5D01G269700 chr5D 384140903 384144857 3954 False 1040.333333 2536 88.279333 1459 3897 3 chr5D.!!$F3 2438
2 TraesCS5D01G269700 chr5D 384017969 384019216 1247 True 693.000000 693 76.960000 2524 3771 1 chr5D.!!$R1 1247
3 TraesCS5D01G269700 chr5D 384151685 384155556 3871 False 635.425000 1797 86.031750 768 3891 4 chr5D.!!$F4 3123
4 TraesCS5D01G269700 chr5D 404878076 404882496 4420 False 593.500000 1626 89.691500 997 3686 4 chr5D.!!$F5 2689
5 TraesCS5D01G269700 chr5B 443288212 443292757 4545 False 2417.966667 5585 97.122333 256 4770 3 chr5B.!!$F4 4514
6 TraesCS5D01G269700 chr5B 22046924 22047525 601 False 850.000000 850 92.118000 1 607 1 chr5B.!!$F1 606
7 TraesCS5D01G269700 chr5B 460493715 460494942 1227 True 686.000000 686 77.053000 2524 3748 1 chr5B.!!$R1 1224
8 TraesCS5D01G269700 chr5B 460938434 460944220 5786 False 529.116667 1727 86.831500 703 3921 6 chr5B.!!$F5 3218
9 TraesCS5D01G269700 chr5A 484587144 484591070 3926 False 1003.333333 2414 88.018333 1459 3921 3 chr5A.!!$F1 2462
10 TraesCS5D01G269700 chr5A 484833142 484840791 7649 False 792.116667 2961 89.043333 771 3897 6 chr5A.!!$F2 3126
11 TraesCS5D01G269700 chr5A 509124915 509128606 3691 True 743.666667 1687 88.417667 1612 3746 3 chr5A.!!$R2 2134
12 TraesCS5D01G269700 chr6D 277054305 277054911 606 True 941.000000 941 94.737000 4 607 1 chr6D.!!$R1 603
13 TraesCS5D01G269700 chr1D 458395508 458396119 611 False 928.000000 928 94.127000 1 609 1 chr1D.!!$F1 608
14 TraesCS5D01G269700 chr2D 638873126 638873730 604 False 894.000000 894 93.388000 1 603 1 chr2D.!!$F3 602
15 TraesCS5D01G269700 chr6A 24235339 24235942 603 True 861.000000 861 92.397000 4 607 1 chr6A.!!$R1 603
16 TraesCS5D01G269700 chr3B 467879647 467880252 605 False 843.000000 843 91.776000 1 607 1 chr3B.!!$F1 606
17 TraesCS5D01G269700 chr6B 169240230 169240835 605 False 815.000000 815 90.984000 1 607 1 chr6B.!!$F1 606
18 TraesCS5D01G269700 chr7B 629546492 629547099 607 False 811.000000 811 90.805000 1 607 1 chr7B.!!$F1 606
19 TraesCS5D01G269700 chr1A 372219431 372220120 689 True 334.333333 468 88.337333 4065 4770 3 chr1A.!!$R1 705

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
738 1981 0.398696 TAGCAAAACAGGCCCGAGAA 59.601 50.0 0.00 0.0 0.0 2.87 F
1241 2650 0.186873 TATGGTACTCCCTCCGTCCC 59.813 60.0 0.00 0.0 0.0 4.46 F
1607 3190 0.339859 AGGCTGTATGGGGTCTGAGA 59.660 55.0 0.00 0.0 0.0 3.27 F
2455 5943 0.457166 CATGCATTGCCACCAAGACG 60.457 55.0 6.12 0.0 33.8 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 3179 0.041238 AAGGATCGTCTCAGACCCCA 59.959 55.000 0.00 0.00 0.00 4.96 R
2455 5943 3.678548 AGTAACGGAAAACAATCTCGAGC 59.321 43.478 7.81 0.00 0.00 5.03 R
3419 6933 2.798499 GCATCTGCCTCAAATGTGATGC 60.798 50.000 6.22 6.22 45.97 3.91 R
4053 7590 1.134788 AGCACGCGCCTTAACTTATCT 60.135 47.619 5.73 0.00 39.83 1.98 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
338 347 3.504906 TCGACGTTTGATGTACTCCTTCT 59.495 43.478 0.00 0.00 0.00 2.85
412 425 0.669318 GAACTGTGGCACCGAATCGA 60.669 55.000 16.26 0.00 0.00 3.59
455 468 4.165779 CTGTTTGTTGTTTCTTTGAGCGT 58.834 39.130 0.00 0.00 0.00 5.07
635 652 1.002315 GGCACAAACCTAGTTCCCGTA 59.998 52.381 0.00 0.00 0.00 4.02
738 1981 0.398696 TAGCAAAACAGGCCCGAGAA 59.601 50.000 0.00 0.00 0.00 2.87
1226 2635 3.199946 TGGGTGAGCTAAGGTTTCTATGG 59.800 47.826 0.00 0.00 0.00 2.74
1227 2636 3.200165 GGGTGAGCTAAGGTTTCTATGGT 59.800 47.826 0.00 0.00 0.00 3.55
1228 2637 4.407945 GGGTGAGCTAAGGTTTCTATGGTA 59.592 45.833 0.00 0.00 0.00 3.25
1229 2638 5.358090 GGTGAGCTAAGGTTTCTATGGTAC 58.642 45.833 0.00 0.00 0.00 3.34
1230 2639 5.128991 GGTGAGCTAAGGTTTCTATGGTACT 59.871 44.000 0.00 0.00 0.00 2.73
1231 2640 6.274579 GTGAGCTAAGGTTTCTATGGTACTC 58.725 44.000 0.00 0.00 0.00 2.59
1232 2641 5.363005 TGAGCTAAGGTTTCTATGGTACTCC 59.637 44.000 0.00 0.00 0.00 3.85
1233 2642 4.654724 AGCTAAGGTTTCTATGGTACTCCC 59.345 45.833 0.00 0.00 0.00 4.30
1234 2643 4.654724 GCTAAGGTTTCTATGGTACTCCCT 59.345 45.833 0.00 0.00 0.00 4.20
1235 2644 5.221481 GCTAAGGTTTCTATGGTACTCCCTC 60.221 48.000 0.00 0.00 0.00 4.30
1236 2645 3.655384 AGGTTTCTATGGTACTCCCTCC 58.345 50.000 0.00 0.00 0.00 4.30
1237 2646 2.364647 GGTTTCTATGGTACTCCCTCCG 59.635 54.545 0.00 0.00 0.00 4.63
1238 2647 3.029570 GTTTCTATGGTACTCCCTCCGT 58.970 50.000 0.00 0.00 0.00 4.69
1239 2648 2.653234 TCTATGGTACTCCCTCCGTC 57.347 55.000 0.00 0.00 0.00 4.79
1240 2649 1.144503 TCTATGGTACTCCCTCCGTCC 59.855 57.143 0.00 0.00 0.00 4.79
1241 2650 0.186873 TATGGTACTCCCTCCGTCCC 59.813 60.000 0.00 0.00 0.00 4.46
1242 2651 1.882189 ATGGTACTCCCTCCGTCCCA 61.882 60.000 0.00 0.00 0.00 4.37
1243 2652 1.075450 GGTACTCCCTCCGTCCCAT 60.075 63.158 0.00 0.00 0.00 4.00
1244 2653 0.186873 GGTACTCCCTCCGTCCCATA 59.813 60.000 0.00 0.00 0.00 2.74
1245 2654 1.412074 GGTACTCCCTCCGTCCCATAA 60.412 57.143 0.00 0.00 0.00 1.90
1246 2655 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
1247 2656 3.501019 GGTACTCCCTCCGTCCCATAATA 60.501 52.174 0.00 0.00 0.00 0.98
1248 2657 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1249 2658 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1250 2659 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1251 2660 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1252 2661 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1253 2662 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
1254 2663 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
1255 2664 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
1256 2665 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
1257 2666 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
1258 2667 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
1259 2668 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
1260 2669 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
1261 2670 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
1262 2671 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
1263 2672 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
1264 2673 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
1265 2674 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
1266 2675 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
1269 2678 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
1382 2794 5.121768 GTGTGTGTTGTTCATATGTACTCCC 59.878 44.000 12.92 2.88 0.00 4.30
1383 2795 5.012664 TGTGTGTTGTTCATATGTACTCCCT 59.987 40.000 12.92 0.00 0.00 4.20
1385 2797 5.483937 TGTGTTGTTCATATGTACTCCCTCT 59.516 40.000 12.92 0.00 0.00 3.69
1386 2798 5.812642 GTGTTGTTCATATGTACTCCCTCTG 59.187 44.000 12.92 0.00 0.00 3.35
1387 2799 5.483937 TGTTGTTCATATGTACTCCCTCTGT 59.516 40.000 12.92 0.00 0.00 3.41
1388 2800 6.666113 TGTTGTTCATATGTACTCCCTCTGTA 59.334 38.462 12.92 0.00 0.00 2.74
1389 2801 7.179516 TGTTGTTCATATGTACTCCCTCTGTAA 59.820 37.037 12.92 0.00 0.00 2.41
1390 2802 7.727578 TGTTCATATGTACTCCCTCTGTAAA 57.272 36.000 12.92 0.00 0.00 2.01
1391 2803 7.782049 TGTTCATATGTACTCCCTCTGTAAAG 58.218 38.462 12.92 0.00 0.00 1.85
1392 2804 7.618117 TGTTCATATGTACTCCCTCTGTAAAGA 59.382 37.037 12.92 0.00 0.00 2.52
1393 2805 8.475639 GTTCATATGTACTCCCTCTGTAAAGAA 58.524 37.037 1.90 0.00 0.00 2.52
1394 2806 8.603898 TCATATGTACTCCCTCTGTAAAGAAA 57.396 34.615 1.90 0.00 0.00 2.52
1395 2807 9.213777 TCATATGTACTCCCTCTGTAAAGAAAT 57.786 33.333 1.90 0.00 0.00 2.17
1427 2839 9.632807 ATCATTTAGATCACTACTTTAGCGATC 57.367 33.333 0.00 3.88 42.08 3.69
1434 2846 8.851145 AGATCACTACTTTAGCGATCTAAATGA 58.149 33.333 10.63 0.00 46.98 2.57
1435 2847 9.632807 GATCACTACTTTAGCGATCTAAATGAT 57.367 33.333 9.52 9.52 42.15 2.45
1436 2848 9.632807 ATCACTACTTTAGCGATCTAAATGATC 57.367 33.333 0.00 0.00 46.07 2.92
1458 2870 9.967346 TGATCTTATATTTCTTTACTGACGGAG 57.033 33.333 0.00 0.00 0.00 4.63
1536 3111 8.978874 ACATAGTAAGCATACATTGGATTTGA 57.021 30.769 1.44 0.00 34.29 2.69
1588 3171 3.636231 AGGTGGCTGCCGTGCTTA 61.636 61.111 14.98 0.00 0.00 3.09
1589 3172 3.127533 GGTGGCTGCCGTGCTTAG 61.128 66.667 14.98 0.00 0.00 2.18
1590 3173 3.127533 GTGGCTGCCGTGCTTAGG 61.128 66.667 14.98 0.00 0.00 2.69
1598 3181 2.992089 CCGTGCTTAGGCTGTATGG 58.008 57.895 0.00 0.00 39.59 2.74
1599 3182 0.532862 CCGTGCTTAGGCTGTATGGG 60.533 60.000 0.00 0.00 39.59 4.00
1600 3183 0.532862 CGTGCTTAGGCTGTATGGGG 60.533 60.000 0.00 0.00 39.59 4.96
1601 3184 0.546598 GTGCTTAGGCTGTATGGGGT 59.453 55.000 0.00 0.00 39.59 4.95
1602 3185 0.837272 TGCTTAGGCTGTATGGGGTC 59.163 55.000 0.00 0.00 39.59 4.46
1603 3186 1.132500 GCTTAGGCTGTATGGGGTCT 58.868 55.000 0.00 0.00 35.22 3.85
1604 3187 1.202698 GCTTAGGCTGTATGGGGTCTG 60.203 57.143 0.00 0.00 35.22 3.51
1605 3188 2.398588 CTTAGGCTGTATGGGGTCTGA 58.601 52.381 0.00 0.00 0.00 3.27
1606 3189 2.088104 TAGGCTGTATGGGGTCTGAG 57.912 55.000 0.00 0.00 0.00 3.35
1607 3190 0.339859 AGGCTGTATGGGGTCTGAGA 59.660 55.000 0.00 0.00 0.00 3.27
1617 3227 1.475403 GGGTCTGAGACGATCCTTGA 58.525 55.000 6.50 0.00 31.25 3.02
2455 5943 0.457166 CATGCATTGCCACCAAGACG 60.457 55.000 6.12 0.00 33.80 4.18
3419 6933 1.845266 CGAGTCAATCGTGGGAGATG 58.155 55.000 0.00 0.00 46.62 2.90
3794 7330 2.875933 CTGTGTAAAAGTTCCCGCAAGA 59.124 45.455 0.00 0.00 43.02 3.02
3921 7458 1.336887 ACTAGTAGGCTGTGTGTTGCG 60.337 52.381 0.00 0.00 0.00 4.85
3997 7534 9.365311 CTATTATAACAGCCGTTTTTAACATCG 57.635 33.333 0.00 0.00 36.52 3.84
4155 7695 4.832608 GCGGCCGTTCGATCCCTT 62.833 66.667 28.70 0.00 0.00 3.95
4156 7696 2.585247 CGGCCGTTCGATCCCTTC 60.585 66.667 19.50 0.00 0.00 3.46
4158 7698 1.227292 GGCCGTTCGATCCCTTCTC 60.227 63.158 0.00 0.00 0.00 2.87
4203 7743 4.727507 TTTCGATCCCTTCTCTCTTCTG 57.272 45.455 0.00 0.00 0.00 3.02
4567 10534 4.760047 CACCAACGCTCCCTCCCG 62.760 72.222 0.00 0.00 0.00 5.14
4638 10637 2.224523 TGACAGGTCACAGATTCCCAAC 60.225 50.000 0.00 0.00 34.14 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 3.040414 CTTCTCGTCGCCGCTCTGA 62.040 63.158 0.00 0.00 0.00 3.27
338 347 2.762745 GTACAGAAAAGGAAGGACGCA 58.237 47.619 0.00 0.00 0.00 5.24
455 468 4.368315 CCATATTCGAACTCCATCGTTCA 58.632 43.478 0.00 0.00 42.57 3.18
649 666 1.901650 GCACGCACACAAGCCTCTAC 61.902 60.000 0.00 0.00 0.00 2.59
1226 2635 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
1227 2636 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
1228 2637 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1229 2638 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
1230 2639 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
1231 2640 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
1232 2641 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
1233 2642 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
1234 2643 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
1235 2644 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
1236 2645 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
1237 2646 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
1238 2647 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
1239 2648 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
1240 2649 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
1243 2652 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
1244 2653 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
1245 2654 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
1246 2655 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
1247 2656 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
1248 2657 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
1249 2658 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
1250 2659 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
1251 2660 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
1283 2692 5.105310 CCCTCCGTCCCATAATATAAGAGTG 60.105 48.000 0.00 0.00 0.00 3.51
1284 2693 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
1285 2694 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
1291 2700 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
1432 2844 9.967346 CTCCGTCAGTAAAGAAATATAAGATCA 57.033 33.333 0.00 0.00 0.00 2.92
1433 2845 9.968870 ACTCCGTCAGTAAAGAAATATAAGATC 57.031 33.333 0.00 0.00 31.37 2.75
1436 2848 9.460906 GGTACTCCGTCAGTAAAGAAATATAAG 57.539 37.037 0.00 0.00 39.44 1.73
1437 2849 8.416329 GGGTACTCCGTCAGTAAAGAAATATAA 58.584 37.037 0.00 0.00 39.44 0.98
1438 2850 7.945134 GGGTACTCCGTCAGTAAAGAAATATA 58.055 38.462 0.00 0.00 39.44 0.86
1439 2851 6.814043 GGGTACTCCGTCAGTAAAGAAATAT 58.186 40.000 0.00 0.00 39.44 1.28
1440 2852 6.212888 GGGTACTCCGTCAGTAAAGAAATA 57.787 41.667 0.00 0.00 39.44 1.40
1441 2853 5.082251 GGGTACTCCGTCAGTAAAGAAAT 57.918 43.478 0.00 0.00 39.44 2.17
1442 2854 4.525912 GGGTACTCCGTCAGTAAAGAAA 57.474 45.455 0.00 0.00 39.44 2.52
1455 2867 6.997239 AATTTTTCATAACTCGGGTACTCC 57.003 37.500 0.00 0.00 0.00 3.85
1456 2868 6.745907 GCAAATTTTTCATAACTCGGGTACTC 59.254 38.462 0.00 0.00 0.00 2.59
1457 2869 6.433093 AGCAAATTTTTCATAACTCGGGTACT 59.567 34.615 0.00 0.00 0.00 2.73
1458 2870 6.617879 AGCAAATTTTTCATAACTCGGGTAC 58.382 36.000 0.00 0.00 0.00 3.34
1459 2871 6.827586 AGCAAATTTTTCATAACTCGGGTA 57.172 33.333 0.00 0.00 0.00 3.69
1460 2872 5.722021 AGCAAATTTTTCATAACTCGGGT 57.278 34.783 0.00 0.00 0.00 5.28
1461 2873 9.233232 GTTATAGCAAATTTTTCATAACTCGGG 57.767 33.333 13.40 0.00 0.00 5.14
1462 2874 9.781834 TGTTATAGCAAATTTTTCATAACTCGG 57.218 29.630 17.76 0.00 32.60 4.63
1511 2923 8.978874 TCAAATCCAATGTATGCTTACTATGT 57.021 30.769 10.74 0.00 0.00 2.29
1536 3111 1.272704 GGAAGACAAATGGGGCCTCTT 60.273 52.381 3.07 1.85 0.00 2.85
1587 3170 1.573857 TCTCAGACCCCATACAGCCTA 59.426 52.381 0.00 0.00 0.00 3.93
1588 3171 0.339859 TCTCAGACCCCATACAGCCT 59.660 55.000 0.00 0.00 0.00 4.58
1589 3172 0.466124 GTCTCAGACCCCATACAGCC 59.534 60.000 0.00 0.00 0.00 4.85
1590 3173 0.103208 CGTCTCAGACCCCATACAGC 59.897 60.000 0.00 0.00 0.00 4.40
1591 3174 1.763968 TCGTCTCAGACCCCATACAG 58.236 55.000 0.00 0.00 0.00 2.74
1592 3175 2.307768 GATCGTCTCAGACCCCATACA 58.692 52.381 0.00 0.00 0.00 2.29
1593 3176 1.614413 GGATCGTCTCAGACCCCATAC 59.386 57.143 0.00 0.00 0.00 2.39
1594 3177 1.499438 AGGATCGTCTCAGACCCCATA 59.501 52.381 0.00 0.00 0.00 2.74
1595 3178 0.263172 AGGATCGTCTCAGACCCCAT 59.737 55.000 0.00 0.00 0.00 4.00
1596 3179 0.041238 AAGGATCGTCTCAGACCCCA 59.959 55.000 0.00 0.00 0.00 4.96
1597 3180 0.461961 CAAGGATCGTCTCAGACCCC 59.538 60.000 0.00 0.00 0.00 4.95
1598 3181 1.135333 GTCAAGGATCGTCTCAGACCC 59.865 57.143 0.00 0.00 0.00 4.46
1599 3182 1.819288 TGTCAAGGATCGTCTCAGACC 59.181 52.381 0.00 0.00 0.00 3.85
1600 3183 3.577649 TTGTCAAGGATCGTCTCAGAC 57.422 47.619 0.00 0.00 0.00 3.51
1601 3184 4.705023 TGTATTGTCAAGGATCGTCTCAGA 59.295 41.667 0.00 0.00 0.00 3.27
1602 3185 4.998788 TGTATTGTCAAGGATCGTCTCAG 58.001 43.478 0.00 0.00 0.00 3.35
1603 3186 5.168569 GTTGTATTGTCAAGGATCGTCTCA 58.831 41.667 0.00 0.00 0.00 3.27
1604 3187 5.168569 TGTTGTATTGTCAAGGATCGTCTC 58.831 41.667 0.00 0.00 0.00 3.36
1605 3188 5.047306 TCTGTTGTATTGTCAAGGATCGTCT 60.047 40.000 0.00 0.00 0.00 4.18
1606 3189 5.168569 TCTGTTGTATTGTCAAGGATCGTC 58.831 41.667 0.00 0.00 0.00 4.20
1607 3190 5.147330 TCTGTTGTATTGTCAAGGATCGT 57.853 39.130 0.00 0.00 0.00 3.73
1617 3227 3.650942 TGAGTTCCCCTCTGTTGTATTGT 59.349 43.478 0.00 0.00 41.11 2.71
1778 3592 2.425143 TTGAATCAGCTGGTCCATCC 57.575 50.000 15.13 0.00 0.00 3.51
2455 5943 3.678548 AGTAACGGAAAACAATCTCGAGC 59.321 43.478 7.81 0.00 0.00 5.03
3419 6933 2.798499 GCATCTGCCTCAAATGTGATGC 60.798 50.000 6.22 6.22 45.97 3.91
3794 7330 7.514127 ACAGGAATCATAGGGTACTTATGATGT 59.486 37.037 22.60 17.76 39.88 3.06
3915 7452 1.500512 GCAAAGGGTACGTCGCAACA 61.501 55.000 0.00 0.00 0.00 3.33
3921 7458 1.265905 CCAAACAGCAAAGGGTACGTC 59.734 52.381 0.00 0.00 0.00 4.34
4053 7590 1.134788 AGCACGCGCCTTAACTTATCT 60.135 47.619 5.73 0.00 39.83 1.98
4113 7653 2.233654 GCGCATCAGACGGCTGTAG 61.234 63.158 19.93 13.18 42.84 2.74
4154 7694 3.801638 GCAGTGTGCAGAAGAAGAGAGAA 60.802 47.826 0.00 0.00 44.26 2.87
4155 7695 2.288702 GCAGTGTGCAGAAGAAGAGAGA 60.289 50.000 0.00 0.00 44.26 3.10
4156 7696 2.067766 GCAGTGTGCAGAAGAAGAGAG 58.932 52.381 0.00 0.00 44.26 3.20
4534 10501 2.167861 GTGCTCGTCGGAAGCATCC 61.168 63.158 11.29 0.00 40.84 3.51
4638 10637 3.853330 CGGTTGCTGCGATGGTCG 61.853 66.667 0.00 0.00 43.89 4.79


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

AutoCloner maintained by Alex Coulton.