Multiple sequence alignment - TraesCS3B01G292400

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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 TraesCS3B01G292400 chr3B 100.000 3983 0 0 1 3983 470855184 470859166 0.000000e+00 7356
1 TraesCS3B01G292400 chr5B 97.862 2011 31 1 1558 3556 24143650 24141640 0.000000e+00 3465
2 TraesCS3B01G292400 chr5B 91.791 2010 106 26 1577 3556 69032176 69034156 0.000000e+00 2743
3 TraesCS3B01G292400 chr5B 94.833 1529 63 6 1577 3089 621305275 621303747 0.000000e+00 2372
4 TraesCS3B01G292400 chr5B 98.048 461 9 0 3523 3983 24141706 24141246 0.000000e+00 802
5 TraesCS3B01G292400 chr2D 92.231 1995 76 34 1586 3556 7524597 7522658 0.000000e+00 2752
6 TraesCS3B01G292400 chr2D 88.976 1270 49 31 2345 3556 147379741 147378505 0.000000e+00 1485
7 TraesCS3B01G292400 chr2D 91.946 956 42 15 604 1534 513034140 513033195 0.000000e+00 1306
8 TraesCS3B01G292400 chr2D 89.875 958 52 14 604 1544 7525689 7524760 0.000000e+00 1190
9 TraesCS3B01G292400 chr2D 93.213 442 15 10 3128 3556 568355063 568354624 1.560000e-178 636
10 TraesCS3B01G292400 chr4B 96.599 1588 42 1 1558 3133 657804397 657802810 0.000000e+00 2623
11 TraesCS3B01G292400 chr4B 93.835 957 42 7 604 1544 657805506 657804551 0.000000e+00 1424
12 TraesCS3B01G292400 chr4B 92.584 445 12 6 3125 3556 657802777 657802341 1.570000e-173 619
13 TraesCS3B01G292400 chr3D 90.756 2023 80 34 1586 3556 532070175 532068208 0.000000e+00 2601
14 TraesCS3B01G292400 chr3D 94.515 1586 42 7 1586 3133 523401527 523403105 0.000000e+00 2405
15 TraesCS3B01G292400 chr3D 93.614 1425 42 9 1747 3133 160918205 160919618 0.000000e+00 2082
16 TraesCS3B01G292400 chr3D 91.736 968 45 12 601 1544 523400408 523401364 0.000000e+00 1312
17 TraesCS3B01G292400 chr3D 91.478 974 46 15 596 1544 20288611 20289572 0.000000e+00 1304
18 TraesCS3B01G292400 chr3D 91.529 968 45 15 603 1544 160913033 160913989 0.000000e+00 1299
19 TraesCS3B01G292400 chr3D 95.662 461 20 0 3523 3983 160920028 160920488 0.000000e+00 741
20 TraesCS3B01G292400 chr3D 92.986 442 16 10 3128 3556 160919655 160920094 7.260000e-177 630
21 TraesCS3B01G292400 chr3D 92.986 442 16 10 3128 3556 523403142 523403581 7.260000e-177 630
22 TraesCS3B01G292400 chr3D 86.005 393 30 17 1 391 361375309 361375678 8.020000e-107 398
23 TraesCS3B01G292400 chr1B 90.751 2011 97 26 1577 3556 460163078 460161126 0.000000e+00 2601
24 TraesCS3B01G292400 chr1B 90.376 1995 115 36 1577 3556 94935267 94933335 0.000000e+00 2549
25 TraesCS3B01G292400 chr1B 90.064 2023 101 25 1577 3556 544797301 544795336 0.000000e+00 2531
26 TraesCS3B01G292400 chr1B 94.768 1529 64 6 1577 3089 364287239 364285711 0.000000e+00 2366
27 TraesCS3B01G292400 chr1B 94.572 1529 64 8 1577 3089 668658486 668660011 0.000000e+00 2346
28 TraesCS3B01G292400 chr1B 95.329 578 27 0 1577 2154 448520088 448520665 0.000000e+00 918
29 TraesCS3B01G292400 chr4D 90.563 2024 82 33 1586 3556 391456684 391458651 0.000000e+00 2579
30 TraesCS3B01G292400 chr4D 90.853 973 50 18 590 1544 498718583 498717632 0.000000e+00 1267
31 TraesCS3B01G292400 chr4D 90.984 965 49 19 604 1544 391455571 391456521 0.000000e+00 1266
32 TraesCS3B01G292400 chr7D 90.559 2023 80 34 1586 3556 526289337 526291300 0.000000e+00 2575
33 TraesCS3B01G292400 chr7D 95.887 1483 47 3 1558 3026 92233459 92231977 0.000000e+00 2388
34 TraesCS3B01G292400 chr7D 92.037 967 40 17 604 1544 540442133 540443088 0.000000e+00 1325
35 TraesCS3B01G292400 chr7D 91.079 964 49 18 604 1544 526288225 526289174 0.000000e+00 1269
36 TraesCS3B01G292400 chr5D 90.900 1989 75 35 1586 3523 430982892 430980959 0.000000e+00 2573
37 TraesCS3B01G292400 chr5D 93.387 1618 51 14 1558 3133 494244386 494242783 0.000000e+00 2344
38 TraesCS3B01G292400 chr5D 92.179 959 46 13 604 1544 494245452 494244505 0.000000e+00 1328
39 TraesCS3B01G292400 chr4A 95.980 1592 46 5 1558 3133 521946283 521947872 0.000000e+00 2569
40 TraesCS3B01G292400 chr1D 94.641 1586 46 4 1586 3133 30072798 30071214 0.000000e+00 2422
41 TraesCS3B01G292400 chr1D 95.489 1463 49 4 1558 3006 444899400 444900859 0.000000e+00 2320
42 TraesCS3B01G292400 chr1D 90.729 960 45 19 602 1544 30073893 30072961 0.000000e+00 1240
43 TraesCS3B01G292400 chr1D 95.879 461 19 0 3523 3983 30070804 30070344 0.000000e+00 747
44 TraesCS3B01G292400 chr1D 92.760 442 17 10 3128 3556 30071177 30070738 3.380000e-175 625
45 TraesCS3B01G292400 chr6B 95.607 1457 57 3 1577 3029 40797229 40795776 0.000000e+00 2329
46 TraesCS3B01G292400 chr5A 94.828 870 32 3 1558 2414 680754276 680755145 0.000000e+00 1345
47 TraesCS3B01G292400 chr5A 96.963 461 14 0 3523 3983 650153599 650154059 0.000000e+00 774
48 TraesCS3B01G292400 chr6D 91.917 965 41 15 603 1544 175423682 175424632 0.000000e+00 1315
49 TraesCS3B01G292400 chr6D 91.185 658 22 11 918 1544 447818274 447818926 0.000000e+00 861
50 TraesCS3B01G292400 chr6D 95.662 461 20 0 3523 3983 61155550 61155090 0.000000e+00 741
51 TraesCS3B01G292400 chr6D 93.519 432 18 4 3128 3556 61155908 61155484 5.620000e-178 634
52 TraesCS3B01G292400 chr7A 95.547 494 22 0 3490 3983 147917371 147916878 0.000000e+00 791
53 TraesCS3B01G292400 chr3A 96.746 461 15 0 3523 3983 636531026 636530566 0.000000e+00 769
54 TraesCS3B01G292400 chr3A 89.016 610 33 15 1 603 481878418 481879000 0.000000e+00 725
55 TraesCS3B01G292400 chr2A 96.746 461 15 0 3523 3983 769239280 769239740 0.000000e+00 769
56 TraesCS3B01G292400 chr6A 96.312 461 17 0 3523 3983 162657471 162657931 0.000000e+00 758


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 TraesCS3B01G292400 chr3B 470855184 470859166 3982 False 7356.000000 7356 100.000000 1 3983 1 chr3B.!!$F1 3982
1 TraesCS3B01G292400 chr5B 69032176 69034156 1980 False 2743.000000 2743 91.791000 1577 3556 1 chr5B.!!$F1 1979
2 TraesCS3B01G292400 chr5B 621303747 621305275 1528 True 2372.000000 2372 94.833000 1577 3089 1 chr5B.!!$R1 1512
3 TraesCS3B01G292400 chr5B 24141246 24143650 2404 True 2133.500000 3465 97.955000 1558 3983 2 chr5B.!!$R2 2425
4 TraesCS3B01G292400 chr2D 7522658 7525689 3031 True 1971.000000 2752 91.053000 604 3556 2 chr2D.!!$R4 2952
5 TraesCS3B01G292400 chr2D 147378505 147379741 1236 True 1485.000000 1485 88.976000 2345 3556 1 chr2D.!!$R1 1211
6 TraesCS3B01G292400 chr2D 513033195 513034140 945 True 1306.000000 1306 91.946000 604 1534 1 chr2D.!!$R2 930
7 TraesCS3B01G292400 chr4B 657802341 657805506 3165 True 1555.333333 2623 94.339333 604 3556 3 chr4B.!!$R1 2952
8 TraesCS3B01G292400 chr3D 532068208 532070175 1967 True 2601.000000 2601 90.756000 1586 3556 1 chr3D.!!$R1 1970
9 TraesCS3B01G292400 chr3D 523400408 523403581 3173 False 1449.000000 2405 93.079000 601 3556 3 chr3D.!!$F5 2955
10 TraesCS3B01G292400 chr3D 20288611 20289572 961 False 1304.000000 1304 91.478000 596 1544 1 chr3D.!!$F1 948
11 TraesCS3B01G292400 chr3D 160913033 160913989 956 False 1299.000000 1299 91.529000 603 1544 1 chr3D.!!$F2 941
12 TraesCS3B01G292400 chr3D 160918205 160920488 2283 False 1151.000000 2082 94.087333 1747 3983 3 chr3D.!!$F4 2236
13 TraesCS3B01G292400 chr1B 460161126 460163078 1952 True 2601.000000 2601 90.751000 1577 3556 1 chr1B.!!$R3 1979
14 TraesCS3B01G292400 chr1B 94933335 94935267 1932 True 2549.000000 2549 90.376000 1577 3556 1 chr1B.!!$R1 1979
15 TraesCS3B01G292400 chr1B 544795336 544797301 1965 True 2531.000000 2531 90.064000 1577 3556 1 chr1B.!!$R4 1979
16 TraesCS3B01G292400 chr1B 364285711 364287239 1528 True 2366.000000 2366 94.768000 1577 3089 1 chr1B.!!$R2 1512
17 TraesCS3B01G292400 chr1B 668658486 668660011 1525 False 2346.000000 2346 94.572000 1577 3089 1 chr1B.!!$F2 1512
18 TraesCS3B01G292400 chr1B 448520088 448520665 577 False 918.000000 918 95.329000 1577 2154 1 chr1B.!!$F1 577
19 TraesCS3B01G292400 chr4D 391455571 391458651 3080 False 1922.500000 2579 90.773500 604 3556 2 chr4D.!!$F1 2952
20 TraesCS3B01G292400 chr4D 498717632 498718583 951 True 1267.000000 1267 90.853000 590 1544 1 chr4D.!!$R1 954
21 TraesCS3B01G292400 chr7D 92231977 92233459 1482 True 2388.000000 2388 95.887000 1558 3026 1 chr7D.!!$R1 1468
22 TraesCS3B01G292400 chr7D 526288225 526291300 3075 False 1922.000000 2575 90.819000 604 3556 2 chr7D.!!$F2 2952
23 TraesCS3B01G292400 chr7D 540442133 540443088 955 False 1325.000000 1325 92.037000 604 1544 1 chr7D.!!$F1 940
24 TraesCS3B01G292400 chr5D 430980959 430982892 1933 True 2573.000000 2573 90.900000 1586 3523 1 chr5D.!!$R1 1937
25 TraesCS3B01G292400 chr5D 494242783 494245452 2669 True 1836.000000 2344 92.783000 604 3133 2 chr5D.!!$R2 2529
26 TraesCS3B01G292400 chr4A 521946283 521947872 1589 False 2569.000000 2569 95.980000 1558 3133 1 chr4A.!!$F1 1575
27 TraesCS3B01G292400 chr1D 444899400 444900859 1459 False 2320.000000 2320 95.489000 1558 3006 1 chr1D.!!$F1 1448
28 TraesCS3B01G292400 chr1D 30070344 30073893 3549 True 1258.500000 2422 93.502250 602 3983 4 chr1D.!!$R1 3381
29 TraesCS3B01G292400 chr6B 40795776 40797229 1453 True 2329.000000 2329 95.607000 1577 3029 1 chr6B.!!$R1 1452
30 TraesCS3B01G292400 chr5A 680754276 680755145 869 False 1345.000000 1345 94.828000 1558 2414 1 chr5A.!!$F2 856
31 TraesCS3B01G292400 chr6D 175423682 175424632 950 False 1315.000000 1315 91.917000 603 1544 1 chr6D.!!$F1 941
32 TraesCS3B01G292400 chr6D 447818274 447818926 652 False 861.000000 861 91.185000 918 1544 1 chr6D.!!$F2 626
33 TraesCS3B01G292400 chr6D 61155090 61155908 818 True 687.500000 741 94.590500 3128 3983 2 chr6D.!!$R1 855
34 TraesCS3B01G292400 chr3A 481878418 481879000 582 False 725.000000 725 89.016000 1 603 1 chr3A.!!$F1 602

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
47 48 0.178964 CCTTTGGGCTCCTCCAACAA 60.179 55.000 0.00 0.0 45.48 2.83 F
208 213 0.253113 TGGTGGGAGGGACATGATCA 60.253 55.000 0.00 0.0 0.00 2.92 F
209 214 0.918983 GGTGGGAGGGACATGATCAA 59.081 55.000 0.00 0.0 0.00 2.57 F
1014 1065 1.039233 CCGCAATGCCTTCCTGGAAT 61.039 55.000 10.03 0.0 34.85 3.01 F
1800 2024 1.271926 GGAGTTGGCCAAGCTTAGGAA 60.272 52.381 21.21 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 1192 1.074405 ACACTCAGCAACATCCATGGT 59.926 47.619 12.58 0.0 0.0 3.55 R
1886 2110 2.260844 TCCTCCTGCACTTGTTTCTG 57.739 50.000 0.00 0.0 0.0 3.02 R
2177 2437 3.436704 ACCAACATATCACAGCAAGTTCG 59.563 43.478 0.00 0.0 0.0 3.95 R
2733 2998 2.927864 CGCCTCCTCCTCCTCCTA 59.072 66.667 0.00 0.0 0.0 2.94 R
3557 3986 0.550914 TCCAGCAAAGAACACCAGGT 59.449 50.000 0.00 0.0 0.0 4.00 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
47 48 0.178964 CCTTTGGGCTCCTCCAACAA 60.179 55.000 0.00 0.00 45.48 2.83
54 55 2.357569 GGGCTCCTCCAACAAAGATCAT 60.358 50.000 0.00 0.00 36.21 2.45
83 84 1.709760 CTTGTGCACACGCTATCCG 59.290 57.895 21.56 0.00 44.21 4.18
96 97 0.532862 CTATCCGTGTCCCATGCACC 60.533 60.000 0.00 0.00 33.61 5.01
123 124 2.028748 GCAAGGTGTTTGATGGAATGCT 60.029 45.455 0.00 0.00 39.21 3.79
126 127 5.404946 CAAGGTGTTTGATGGAATGCTTAG 58.595 41.667 0.00 0.00 39.21 2.18
132 133 3.845781 TGATGGAATGCTTAGGAGGAC 57.154 47.619 0.00 0.00 0.00 3.85
140 141 5.163301 GGAATGCTTAGGAGGACATGAACTA 60.163 44.000 0.00 0.00 0.00 2.24
171 176 8.806429 TCTTAATGATCAGGTATGCTTTGAAA 57.194 30.769 0.09 0.00 0.00 2.69
187 192 3.608316 TGAAATAATTTGGGCTGGTGC 57.392 42.857 0.00 0.00 38.76 5.01
197 202 4.729918 GCTGGTGCCTGGTGGGAG 62.730 72.222 0.00 0.00 37.23 4.30
198 203 4.039092 CTGGTGCCTGGTGGGAGG 62.039 72.222 0.00 0.00 37.23 4.30
201 206 4.035102 GTGCCTGGTGGGAGGGAC 62.035 72.222 0.00 0.00 45.91 4.46
202 207 4.590553 TGCCTGGTGGGAGGGACA 62.591 66.667 0.00 0.00 37.23 4.02
203 208 3.017581 GCCTGGTGGGAGGGACAT 61.018 66.667 0.00 0.00 37.23 3.06
204 209 3.001514 CCTGGTGGGAGGGACATG 58.998 66.667 0.00 0.00 37.23 3.21
205 210 1.616327 CCTGGTGGGAGGGACATGA 60.616 63.158 0.00 0.00 37.23 3.07
206 211 0.990282 CCTGGTGGGAGGGACATGAT 60.990 60.000 0.00 0.00 37.23 2.45
207 212 0.471617 CTGGTGGGAGGGACATGATC 59.528 60.000 0.00 0.00 0.00 2.92
208 213 0.253113 TGGTGGGAGGGACATGATCA 60.253 55.000 0.00 0.00 0.00 2.92
209 214 0.918983 GGTGGGAGGGACATGATCAA 59.081 55.000 0.00 0.00 0.00 2.57
241 247 4.261447 GCTTCTTTTTGCGAGGGAAAGTTA 60.261 41.667 0.00 0.00 33.32 2.24
252 258 5.800438 GCGAGGGAAAGTTAAAATGCTTTAG 59.200 40.000 0.00 0.00 35.35 1.85
270 276 7.816640 TGCTTTAGTTTCTTATTACTGCCTTG 58.183 34.615 0.00 0.00 0.00 3.61
296 302 3.470709 GCTTAGAGCAGGTGCATATTCA 58.529 45.455 4.48 0.00 45.16 2.57
301 307 2.225963 GAGCAGGTGCATATTCATGAGC 59.774 50.000 4.48 0.00 45.16 4.26
321 327 2.749621 GCACCTCAAACATAGTCTTGGG 59.250 50.000 0.00 0.00 0.00 4.12
338 344 1.879380 TGGGAAAATTGCTGTCTGACG 59.121 47.619 2.98 0.00 0.00 4.35
390 397 8.709308 AGCATGTTTGAAGGAATATCTACTACT 58.291 33.333 0.00 0.00 0.00 2.57
391 398 9.331282 GCATGTTTGAAGGAATATCTACTACTT 57.669 33.333 0.00 0.00 0.00 2.24
410 417 4.524053 ACTTGGTATAGCACTTAAAGCCC 58.476 43.478 3.60 0.00 0.00 5.19
411 418 4.227527 ACTTGGTATAGCACTTAAAGCCCT 59.772 41.667 3.60 0.00 0.00 5.19
466 473 5.046304 ACCTGCTTGCTACTGAGAAATTCTA 60.046 40.000 0.00 0.00 0.00 2.10
468 475 6.018098 CCTGCTTGCTACTGAGAAATTCTATG 60.018 42.308 0.00 0.00 0.00 2.23
470 477 6.051717 GCTTGCTACTGAGAAATTCTATGGA 58.948 40.000 0.00 0.00 0.00 3.41
471 478 6.202570 GCTTGCTACTGAGAAATTCTATGGAG 59.797 42.308 0.00 0.00 0.00 3.86
478 485 8.830915 ACTGAGAAATTCTATGGAGTTCTCTA 57.169 34.615 23.30 14.68 40.82 2.43
510 518 9.883142 CAAGAGAACTAGTCTAAGAAAATGGAT 57.117 33.333 0.00 0.00 36.41 3.41
514 522 9.261035 AGAACTAGTCTAAGAAAATGGATCAGA 57.739 33.333 0.00 0.00 33.56 3.27
526 534 4.751767 ATGGATCAGAGAGACCTGAAAC 57.248 45.455 0.00 0.00 45.22 2.78
546 554 1.289066 CTTGAGAACGCCGGACAGA 59.711 57.895 5.05 0.00 0.00 3.41
593 601 5.435686 TGTTAGACTAGCCACAATTCCAT 57.564 39.130 0.00 0.00 0.00 3.41
742 752 2.884827 GGTGACTAGCGATTTAACCGT 58.115 47.619 0.00 0.00 0.00 4.83
902 917 1.226267 GCTCACTCTCTCGTGCTCG 60.226 63.158 0.81 0.81 34.92 5.03
906 921 1.672682 ACTCTCTCGTGCTCGCTCA 60.673 57.895 2.69 0.00 36.96 4.26
910 925 2.202544 CTCGTGCTCGCTCACTCC 60.203 66.667 2.69 0.00 34.92 3.85
911 926 3.691744 CTCGTGCTCGCTCACTCCC 62.692 68.421 2.69 0.00 34.92 4.30
912 927 4.803426 CGTGCTCGCTCACTCCCC 62.803 72.222 0.00 0.00 34.92 4.81
913 928 3.386237 GTGCTCGCTCACTCCCCT 61.386 66.667 0.53 0.00 34.29 4.79
925 948 1.617839 CTCCCCTTCCCCTGCTCTT 60.618 63.158 0.00 0.00 0.00 2.85
936 987 1.267574 CCTGCTCTTAGTCCCCTGCA 61.268 60.000 0.00 0.00 0.00 4.41
947 998 2.579201 CCCTGCACCAGTACGAGG 59.421 66.667 5.93 5.93 0.00 4.63
1014 1065 1.039233 CCGCAATGCCTTCCTGGAAT 61.039 55.000 10.03 0.00 34.85 3.01
1214 1296 3.181468 GGATTGAGGTAACCTAGGGTTCG 60.181 52.174 14.81 0.00 43.05 3.95
1506 1589 2.398588 CTGCCCAGTCCAGGTTAGATA 58.601 52.381 0.00 0.00 0.00 1.98
1800 2024 1.271926 GGAGTTGGCCAAGCTTAGGAA 60.272 52.381 21.21 0.00 0.00 3.36
1886 2110 1.984288 GCAGGATGGTAGGGTGGACC 61.984 65.000 0.00 0.00 35.86 4.46
1988 2248 4.989279 AAGCTCAAACTTGCAAAAGAGA 57.011 36.364 16.59 6.31 0.00 3.10
2219 2479 5.001232 TGGTGAAGTAAGTACATCCAAAGC 58.999 41.667 0.00 0.00 0.00 3.51
2240 2500 4.665483 AGCCCTTTATATAAGGAAGTGGCT 59.335 41.667 15.07 15.07 39.78 4.75
2733 2998 1.521450 GGACAGCAGCAGCAACACAT 61.521 55.000 3.17 0.00 45.49 3.21
2841 3127 3.327757 AGGTACTGGAGAAGTGCAATGAA 59.672 43.478 0.00 0.00 42.87 2.57
3529 3958 2.093235 GGAGAAGACCTTGATGACCTGG 60.093 54.545 0.00 0.00 0.00 4.45
3530 3959 2.569404 GAGAAGACCTTGATGACCTGGT 59.431 50.000 0.00 0.00 35.23 4.00
3531 3960 2.304180 AGAAGACCTTGATGACCTGGTG 59.696 50.000 2.82 0.00 32.30 4.17
3532 3961 1.734655 AGACCTTGATGACCTGGTGT 58.265 50.000 2.82 0.00 32.30 4.16
3533 3962 2.057922 AGACCTTGATGACCTGGTGTT 58.942 47.619 2.82 0.00 32.30 3.32
3534 3963 2.039084 AGACCTTGATGACCTGGTGTTC 59.961 50.000 2.82 0.93 32.30 3.18
3535 3964 2.039084 GACCTTGATGACCTGGTGTTCT 59.961 50.000 2.82 0.00 32.30 3.01
3536 3965 2.443255 ACCTTGATGACCTGGTGTTCTT 59.557 45.455 2.82 0.00 0.00 2.52
3537 3966 3.117512 ACCTTGATGACCTGGTGTTCTTT 60.118 43.478 2.82 0.00 0.00 2.52
3538 3967 3.254166 CCTTGATGACCTGGTGTTCTTTG 59.746 47.826 2.82 0.00 0.00 2.77
3539 3968 2.229792 TGATGACCTGGTGTTCTTTGC 58.770 47.619 2.82 0.00 0.00 3.68
3540 3969 2.158623 TGATGACCTGGTGTTCTTTGCT 60.159 45.455 2.82 0.00 0.00 3.91
3541 3970 1.679139 TGACCTGGTGTTCTTTGCTG 58.321 50.000 2.82 0.00 0.00 4.41
3542 3971 0.954452 GACCTGGTGTTCTTTGCTGG 59.046 55.000 2.82 0.00 0.00 4.85
3543 3972 0.550914 ACCTGGTGTTCTTTGCTGGA 59.449 50.000 0.00 0.00 0.00 3.86
3544 3973 1.242076 CCTGGTGTTCTTTGCTGGAG 58.758 55.000 0.00 0.00 0.00 3.86
3545 3974 1.202806 CCTGGTGTTCTTTGCTGGAGA 60.203 52.381 0.00 0.00 0.00 3.71
3546 3975 2.575532 CTGGTGTTCTTTGCTGGAGAA 58.424 47.619 0.00 0.00 0.00 2.87
3547 3976 2.551459 CTGGTGTTCTTTGCTGGAGAAG 59.449 50.000 0.00 0.00 34.05 2.85
3548 3977 2.172505 TGGTGTTCTTTGCTGGAGAAGA 59.827 45.455 0.00 0.00 34.05 2.87
3549 3978 2.550180 GGTGTTCTTTGCTGGAGAAGAC 59.450 50.000 12.70 12.70 43.08 3.01
3550 3979 2.550180 GTGTTCTTTGCTGGAGAAGACC 59.450 50.000 11.02 0.00 39.92 3.85
3551 3980 2.439507 TGTTCTTTGCTGGAGAAGACCT 59.560 45.455 0.00 0.00 34.05 3.85
3552 3981 3.117888 TGTTCTTTGCTGGAGAAGACCTT 60.118 43.478 0.00 0.00 34.05 3.50
3553 3982 3.131709 TCTTTGCTGGAGAAGACCTTG 57.868 47.619 0.00 0.00 0.00 3.61
3554 3983 2.705658 TCTTTGCTGGAGAAGACCTTGA 59.294 45.455 0.00 0.00 0.00 3.02
3555 3984 3.328931 TCTTTGCTGGAGAAGACCTTGAT 59.671 43.478 0.00 0.00 0.00 2.57
3556 3985 2.775911 TGCTGGAGAAGACCTTGATG 57.224 50.000 0.00 0.00 0.00 3.07
3557 3986 2.259917 TGCTGGAGAAGACCTTGATGA 58.740 47.619 0.00 0.00 0.00 2.92
3558 3987 2.027745 TGCTGGAGAAGACCTTGATGAC 60.028 50.000 0.00 0.00 0.00 3.06
3559 3988 2.679349 GCTGGAGAAGACCTTGATGACC 60.679 54.545 0.00 0.00 0.00 4.02
3560 3989 2.836981 CTGGAGAAGACCTTGATGACCT 59.163 50.000 0.00 0.00 0.00 3.85
3561 3990 2.568956 TGGAGAAGACCTTGATGACCTG 59.431 50.000 0.00 0.00 0.00 4.00
3686 4115 1.053835 TTGAGAGGTGGTGGTGCTGA 61.054 55.000 0.00 0.00 0.00 4.26
3721 4150 3.055094 TGTTGCCCTCTTCCTTGATCTAC 60.055 47.826 0.00 0.00 0.00 2.59
3760 4189 4.202609 ACTCATTTGTTGTTGGAGGAGGAT 60.203 41.667 0.00 0.00 0.00 3.24
3806 4235 1.457455 CCCTTGGTGGCCTTTGTGT 60.457 57.895 3.32 0.00 0.00 3.72
3814 4243 1.407258 GTGGCCTTTGTGTAGTTGCAA 59.593 47.619 3.32 0.00 0.00 4.08
3847 4276 2.289945 CCAGCCTCAGAGTAGTTTGCTT 60.290 50.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.692475 AGGCGGCAACCACGTACC 62.692 66.667 13.08 0.00 0.00 3.34
43 44 3.094572 CAAGCAGGGGATGATCTTTGTT 58.905 45.455 0.00 0.00 0.00 2.83
47 48 0.924823 AGCAAGCAGGGGATGATCTT 59.075 50.000 0.00 0.00 0.00 2.40
54 55 2.598394 GCACAAGCAAGCAGGGGA 60.598 61.111 0.00 0.00 41.58 4.81
116 117 3.845781 TCATGTCCTCCTAAGCATTCC 57.154 47.619 0.00 0.00 0.00 3.01
123 124 6.846505 AGAATCCATAGTTCATGTCCTCCTAA 59.153 38.462 0.00 0.00 32.21 2.69
126 127 5.559148 AGAATCCATAGTTCATGTCCTCC 57.441 43.478 0.00 0.00 32.21 4.30
140 141 7.696981 AGCATACCTGATCATTAAGAATCCAT 58.303 34.615 0.00 0.00 0.00 3.41
187 192 0.990282 ATCATGTCCCTCCCACCAGG 60.990 60.000 0.00 0.00 0.00 4.45
188 193 0.471617 GATCATGTCCCTCCCACCAG 59.528 60.000 0.00 0.00 0.00 4.00
189 194 0.253113 TGATCATGTCCCTCCCACCA 60.253 55.000 0.00 0.00 0.00 4.17
190 195 0.918983 TTGATCATGTCCCTCCCACC 59.081 55.000 0.00 0.00 0.00 4.61
191 196 1.561542 ACTTGATCATGTCCCTCCCAC 59.438 52.381 8.37 0.00 0.00 4.61
192 197 1.971149 ACTTGATCATGTCCCTCCCA 58.029 50.000 8.37 0.00 0.00 4.37
193 198 4.503714 TTAACTTGATCATGTCCCTCCC 57.496 45.455 14.07 0.00 0.00 4.30
194 199 6.681368 GCATTTTAACTTGATCATGTCCCTCC 60.681 42.308 14.07 0.00 0.00 4.30
195 200 6.096001 AGCATTTTAACTTGATCATGTCCCTC 59.904 38.462 14.07 2.23 0.00 4.30
196 201 5.954150 AGCATTTTAACTTGATCATGTCCCT 59.046 36.000 14.07 2.68 0.00 4.20
197 202 6.212888 AGCATTTTAACTTGATCATGTCCC 57.787 37.500 14.07 0.25 0.00 4.46
198 203 7.542025 AGAAGCATTTTAACTTGATCATGTCC 58.458 34.615 14.07 0.00 0.00 4.02
199 204 8.976986 AAGAAGCATTTTAACTTGATCATGTC 57.023 30.769 14.07 1.28 0.00 3.06
200 205 9.768662 AAAAGAAGCATTTTAACTTGATCATGT 57.231 25.926 8.37 8.37 30.71 3.21
203 208 8.550376 GCAAAAAGAAGCATTTTAACTTGATCA 58.450 29.630 0.00 0.00 32.20 2.92
204 209 7.737311 CGCAAAAAGAAGCATTTTAACTTGATC 59.263 33.333 0.00 0.00 32.20 2.92
205 210 7.437862 TCGCAAAAAGAAGCATTTTAACTTGAT 59.562 29.630 0.00 0.00 32.20 2.57
206 211 6.754209 TCGCAAAAAGAAGCATTTTAACTTGA 59.246 30.769 0.00 0.00 32.20 3.02
207 212 6.932051 TCGCAAAAAGAAGCATTTTAACTTG 58.068 32.000 0.00 0.00 32.20 3.16
208 213 6.200854 CCTCGCAAAAAGAAGCATTTTAACTT 59.799 34.615 0.00 0.00 32.20 2.66
209 214 5.691754 CCTCGCAAAAAGAAGCATTTTAACT 59.308 36.000 0.00 0.00 32.20 2.24
241 247 9.639601 GGCAGTAATAAGAAACTAAAGCATTTT 57.360 29.630 0.00 0.00 40.09 1.82
270 276 0.523519 GCACCTGCTCTAAGCCAAAC 59.476 55.000 0.00 0.00 41.51 2.93
296 302 4.833478 AGACTATGTTTGAGGTGCTCAT 57.167 40.909 0.00 0.00 40.39 2.90
301 307 4.286297 TCCCAAGACTATGTTTGAGGTG 57.714 45.455 0.00 0.00 0.00 4.00
306 312 6.366877 CAGCAATTTTCCCAAGACTATGTTTG 59.633 38.462 0.00 0.00 0.00 2.93
321 327 3.609103 ACACGTCAGACAGCAATTTTC 57.391 42.857 0.41 0.00 0.00 2.29
349 355 8.229253 TCAAACATGCTTTCAGAATGCTATAT 57.771 30.769 18.99 4.95 34.47 0.86
350 356 7.628769 TCAAACATGCTTTCAGAATGCTATA 57.371 32.000 18.99 2.97 34.47 1.31
351 357 6.519679 TCAAACATGCTTTCAGAATGCTAT 57.480 33.333 18.99 10.05 34.47 2.97
352 358 5.963176 TCAAACATGCTTTCAGAATGCTA 57.037 34.783 18.99 8.49 34.47 3.49
390 397 4.226394 TGAGGGCTTTAAGTGCTATACCAA 59.774 41.667 0.00 0.00 0.00 3.67
391 398 3.778075 TGAGGGCTTTAAGTGCTATACCA 59.222 43.478 0.00 0.00 0.00 3.25
392 399 4.141688 ACTGAGGGCTTTAAGTGCTATACC 60.142 45.833 0.00 0.00 0.00 2.73
410 417 7.010923 GCATCCAACTACTTTCATAGAACTGAG 59.989 40.741 0.00 0.00 0.00 3.35
411 418 6.818644 GCATCCAACTACTTTCATAGAACTGA 59.181 38.462 0.00 0.00 0.00 3.41
466 473 5.954752 TCTCTTGTCACATAGAGAACTCCAT 59.045 40.000 13.97 0.00 42.82 3.41
468 475 5.906113 TCTCTTGTCACATAGAGAACTCC 57.094 43.478 13.97 0.00 42.82 3.85
478 485 8.410673 TTCTTAGACTAGTTCTCTTGTCACAT 57.589 34.615 0.00 0.00 44.54 3.21
510 518 3.960755 TCAAGTGTTTCAGGTCTCTCTGA 59.039 43.478 0.00 0.00 41.51 3.27
514 522 4.698575 GTTCTCAAGTGTTTCAGGTCTCT 58.301 43.478 0.00 0.00 0.00 3.10
526 534 1.284982 CTGTCCGGCGTTCTCAAGTG 61.285 60.000 6.01 0.00 0.00 3.16
546 554 7.349412 ACTTATTCTCGGCTTGTATTCTAGT 57.651 36.000 0.00 0.00 0.00 2.57
712 722 0.606604 GCTAGTCACCGAGGGTTTGA 59.393 55.000 0.00 0.00 31.02 2.69
720 730 2.478370 CGGTTAAATCGCTAGTCACCGA 60.478 50.000 1.57 0.00 46.95 4.69
741 751 0.446616 GCCCGATCCGTCAGAAAAAC 59.553 55.000 0.00 0.00 0.00 2.43
742 752 0.675522 GGCCCGATCCGTCAGAAAAA 60.676 55.000 0.00 0.00 0.00 1.94
794 804 2.339556 GCCATTAACAGCCACGCCA 61.340 57.895 0.00 0.00 0.00 5.69
902 917 2.285743 AGGGGAAGGGGAGTGAGC 60.286 66.667 0.00 0.00 0.00 4.26
906 921 2.285743 GAGCAGGGGAAGGGGAGT 60.286 66.667 0.00 0.00 0.00 3.85
910 925 0.833949 GACTAAGAGCAGGGGAAGGG 59.166 60.000 0.00 0.00 0.00 3.95
911 926 0.833949 GGACTAAGAGCAGGGGAAGG 59.166 60.000 0.00 0.00 0.00 3.46
912 927 0.833949 GGGACTAAGAGCAGGGGAAG 59.166 60.000 0.00 0.00 0.00 3.46
913 928 0.620700 GGGGACTAAGAGCAGGGGAA 60.621 60.000 0.00 0.00 0.00 3.97
925 948 0.968901 CGTACTGGTGCAGGGGACTA 60.969 60.000 0.00 0.00 40.21 2.59
936 987 3.437795 CGGCGACCTCGTACTGGT 61.438 66.667 0.00 7.07 42.22 4.00
1014 1065 1.289066 CGAGCTGGTTTCCTCGTCA 59.711 57.895 0.00 0.00 44.25 4.35
1129 1192 1.074405 ACACTCAGCAACATCCATGGT 59.926 47.619 12.58 0.00 0.00 3.55
1214 1296 5.354792 CCCTAACACTGTACAGAGAGAGTAC 59.645 48.000 29.30 0.00 41.63 2.73
1520 1603 8.978874 ATAACATAACTGAACATCCATAGCAA 57.021 30.769 0.00 0.00 0.00 3.91
1800 2024 5.992829 TCAATGCAAAGCTTGTCATTTTCAT 59.007 32.000 18.39 0.00 36.20 2.57
1886 2110 2.260844 TCCTCCTGCACTTGTTTCTG 57.739 50.000 0.00 0.00 0.00 3.02
2177 2437 3.436704 ACCAACATATCACAGCAAGTTCG 59.563 43.478 0.00 0.00 0.00 3.95
2219 2479 5.770162 CCAAGCCACTTCCTTATATAAAGGG 59.230 44.000 4.05 0.00 37.99 3.95
2733 2998 2.927864 CGCCTCCTCCTCCTCCTA 59.072 66.667 0.00 0.00 0.00 2.94
2841 3127 5.071115 AGTGAAAACCAGCTCTAGTTCTTCT 59.929 40.000 0.00 0.00 0.00 2.85
3484 3913 0.839946 AAGAACACCAGGTCAGCTGT 59.160 50.000 14.67 0.00 0.00 4.40
3529 3958 2.550180 GGTCTTCTCCAGCAAAGAACAC 59.450 50.000 0.00 0.00 38.74 3.32
3530 3959 2.439507 AGGTCTTCTCCAGCAAAGAACA 59.560 45.455 3.29 0.00 40.86 3.18
3531 3960 3.133141 AGGTCTTCTCCAGCAAAGAAC 57.867 47.619 0.00 0.00 39.10 3.01
3532 3961 3.136443 TCAAGGTCTTCTCCAGCAAAGAA 59.864 43.478 0.00 0.00 33.53 2.52
3533 3962 2.705658 TCAAGGTCTTCTCCAGCAAAGA 59.294 45.455 0.00 0.00 0.00 2.52
3534 3963 3.131709 TCAAGGTCTTCTCCAGCAAAG 57.868 47.619 0.00 0.00 0.00 2.77
3535 3964 3.072915 TCATCAAGGTCTTCTCCAGCAAA 59.927 43.478 0.00 0.00 0.00 3.68
3536 3965 2.639347 TCATCAAGGTCTTCTCCAGCAA 59.361 45.455 0.00 0.00 0.00 3.91
3537 3966 2.027745 GTCATCAAGGTCTTCTCCAGCA 60.028 50.000 0.00 0.00 0.00 4.41
3538 3967 2.626840 GTCATCAAGGTCTTCTCCAGC 58.373 52.381 0.00 0.00 0.00 4.85
3539 3968 2.836981 AGGTCATCAAGGTCTTCTCCAG 59.163 50.000 0.00 0.00 0.00 3.86
3540 3969 2.568956 CAGGTCATCAAGGTCTTCTCCA 59.431 50.000 0.00 0.00 0.00 3.86
3541 3970 2.093235 CCAGGTCATCAAGGTCTTCTCC 60.093 54.545 0.00 0.00 0.00 3.71
3542 3971 2.569404 ACCAGGTCATCAAGGTCTTCTC 59.431 50.000 0.00 0.00 0.00 2.87
3543 3972 2.304180 CACCAGGTCATCAAGGTCTTCT 59.696 50.000 0.00 0.00 30.44 2.85
3544 3973 2.039084 ACACCAGGTCATCAAGGTCTTC 59.961 50.000 0.00 0.00 30.44 2.87
3545 3974 2.057922 ACACCAGGTCATCAAGGTCTT 58.942 47.619 0.00 0.00 30.44 3.01
3546 3975 1.734655 ACACCAGGTCATCAAGGTCT 58.265 50.000 0.00 0.00 30.44 3.85
3547 3976 2.039084 AGAACACCAGGTCATCAAGGTC 59.961 50.000 0.00 0.00 30.44 3.85
3548 3977 2.057922 AGAACACCAGGTCATCAAGGT 58.942 47.619 0.00 0.00 33.91 3.50
3549 3978 2.867109 AGAACACCAGGTCATCAAGG 57.133 50.000 0.00 0.00 0.00 3.61
3550 3979 3.304928 GCAAAGAACACCAGGTCATCAAG 60.305 47.826 0.00 0.00 0.00 3.02
3551 3980 2.622942 GCAAAGAACACCAGGTCATCAA 59.377 45.455 0.00 0.00 0.00 2.57
3552 3981 2.158623 AGCAAAGAACACCAGGTCATCA 60.159 45.455 0.00 0.00 0.00 3.07
3553 3982 2.227388 CAGCAAAGAACACCAGGTCATC 59.773 50.000 0.00 0.00 0.00 2.92
3554 3983 2.233271 CAGCAAAGAACACCAGGTCAT 58.767 47.619 0.00 0.00 0.00 3.06
3555 3984 1.679139 CAGCAAAGAACACCAGGTCA 58.321 50.000 0.00 0.00 0.00 4.02
3556 3985 0.954452 CCAGCAAAGAACACCAGGTC 59.046 55.000 0.00 0.00 0.00 3.85
3557 3986 0.550914 TCCAGCAAAGAACACCAGGT 59.449 50.000 0.00 0.00 0.00 4.00
3558 3987 1.202806 TCTCCAGCAAAGAACACCAGG 60.203 52.381 0.00 0.00 0.00 4.45
3559 3988 2.260844 TCTCCAGCAAAGAACACCAG 57.739 50.000 0.00 0.00 0.00 4.00
3560 3989 2.172505 TCTTCTCCAGCAAAGAACACCA 59.827 45.455 0.00 0.00 0.00 4.17
3561 3990 2.550180 GTCTTCTCCAGCAAAGAACACC 59.450 50.000 0.00 0.00 33.53 4.16
3686 4115 2.305927 AGGGCAACACTAGCTACAACAT 59.694 45.455 0.00 0.00 39.74 2.71
3721 4150 2.554142 TGAGTCAACACAGACAGCTTG 58.446 47.619 0.00 0.00 40.98 4.01
3806 4235 4.211125 TGGTTCTTCAATGGTTGCAACTA 58.789 39.130 27.64 23.36 0.00 2.24
3814 4243 1.425066 TGAGGCTGGTTCTTCAATGGT 59.575 47.619 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.