Multiple sequence alignment - TraesCS6D01G169900

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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 TraesCS6D01G169900 chr6D 100.000 5450 0 0 1 5450 156442827 156448276 0.000000e+00 10065.0
1 TraesCS6D01G169900 chr6D 100.000 2459 0 0 6309 8767 156449135 156451593 0.000000e+00 4542.0
2 TraesCS6D01G169900 chr6D 85.054 368 47 5 114 477 464465640 464466003 1.390000e-97 368.0
3 TraesCS6D01G169900 chr6D 86.096 187 20 6 5182 5366 427749569 427749387 6.940000e-46 196.0
4 TraesCS6D01G169900 chr6A 96.037 4340 126 18 872 5184 209893717 209898037 0.000000e+00 7020.0
5 TraesCS6D01G169900 chr6A 95.395 1216 35 13 6752 7957 209898035 209899239 0.000000e+00 1916.0
6 TraesCS6D01G169900 chr6A 85.697 832 80 13 8 810 209892826 209893647 0.000000e+00 841.0
7 TraesCS6D01G169900 chr6A 95.202 396 14 5 8001 8394 209900918 209901310 9.670000e-174 621.0
8 TraesCS6D01G169900 chr6A 88.235 255 15 4 8426 8667 209901306 209901558 3.100000e-74 291.0
9 TraesCS6D01G169900 chr6A 100.000 66 0 0 7951 8016 209900206 209900271 1.200000e-23 122.0
10 TraesCS6D01G169900 chr6A 94.805 77 4 0 8661 8737 209902977 209903053 4.300000e-23 121.0
11 TraesCS6D01G169900 chr6B 95.652 2852 86 16 829 3656 279044670 279047507 0.000000e+00 4545.0
12 TraesCS6D01G169900 chr6B 97.466 1539 29 6 3586 5122 279047508 279049038 0.000000e+00 2617.0
13 TraesCS6D01G169900 chr6B 95.596 1635 49 13 6752 8380 279049193 279050810 0.000000e+00 2599.0
14 TraesCS6D01G169900 chr6B 90.076 393 36 2 1 390 279035392 279035784 2.820000e-139 507.0
15 TraesCS6D01G169900 chr6B 92.199 282 13 4 512 787 279035824 279036102 2.970000e-104 390.0
16 TraesCS6D01G169900 chr6B 90.476 273 14 4 8397 8665 279064722 279064986 5.040000e-92 350.0
17 TraesCS6D01G169900 chr6B 95.575 113 4 1 8653 8764 279066350 279066462 6.990000e-41 180.0
18 TraesCS6D01G169900 chr6B 93.846 65 4 0 5120 5184 279049131 279049195 2.010000e-16 99.0
19 TraesCS6D01G169900 chr3B 87.822 427 50 2 6330 6754 791667362 791667788 4.730000e-137 499.0
20 TraesCS6D01G169900 chr3B 86.667 165 16 2 7525 7688 404830477 404830318 2.520000e-40 178.0
21 TraesCS6D01G169900 chr3B 89.855 69 7 0 8 76 754389900 754389832 1.210000e-13 89.8
22 TraesCS6D01G169900 chr5D 86.682 443 54 4 6314 6754 473514402 473513963 3.680000e-133 486.0
23 TraesCS6D01G169900 chr5D 89.571 163 15 2 5180 5341 473515287 473515126 1.150000e-48 206.0
24 TraesCS6D01G169900 chr5D 89.937 159 13 3 5184 5341 557425176 557425020 1.490000e-47 202.0
25 TraesCS6D01G169900 chr7B 86.936 421 41 12 6343 6752 16132311 16131894 2.230000e-125 460.0
26 TraesCS6D01G169900 chr7B 86.723 354 42 3 114 464 339619201 339619552 1.070000e-103 388.0
27 TraesCS6D01G169900 chr7B 84.492 374 50 5 114 484 693252990 693252622 6.470000e-96 363.0
28 TraesCS6D01G169900 chr1B 85.811 444 50 9 6310 6752 605267678 605268109 8.020000e-125 459.0
29 TraesCS6D01G169900 chr1B 84.472 161 19 2 7529 7689 136627525 136627371 4.240000e-33 154.0
30 TraesCS6D01G169900 chr1B 84.024 169 15 8 7522 7689 632021084 632020927 1.520000e-32 152.0
31 TraesCS6D01G169900 chr1B 89.474 76 8 0 1 76 46372512 46372437 7.240000e-16 97.1
32 TraesCS6D01G169900 chr2B 88.828 367 39 2 6388 6752 626918274 626918640 4.830000e-122 449.0
33 TraesCS6D01G169900 chr2B 85.366 369 49 4 114 478 570063699 570064066 2.310000e-100 377.0
34 TraesCS6D01G169900 chr2B 84.865 370 48 7 114 479 646129935 646130300 5.000000e-97 366.0
35 TraesCS6D01G169900 chr2B 81.287 171 30 2 3284 3453 42619506 42619337 4.270000e-28 137.0
36 TraesCS6D01G169900 chr2B 77.075 253 49 5 3284 3535 42759824 42759580 4.270000e-28 137.0
37 TraesCS6D01G169900 chr2B 76.680 253 50 5 3284 3535 42828317 42828073 1.990000e-26 132.0
38 TraesCS6D01G169900 chr2B 88.406 69 8 0 8 76 391843026 391842958 5.640000e-12 84.2
39 TraesCS6D01G169900 chr2B 85.000 80 12 0 1 80 369008676 369008755 2.030000e-11 82.4
40 TraesCS6D01G169900 chr2D 85.919 419 50 4 6332 6750 623760627 623760218 1.040000e-118 438.0
41 TraesCS6D01G169900 chr2D 87.228 368 44 2 6386 6752 283768429 283768064 4.900000e-112 416.0
42 TraesCS6D01G169900 chr2D 90.728 151 13 1 5184 5334 30427818 30427967 5.370000e-47 200.0
43 TraesCS6D01G169900 chr4A 88.732 355 37 2 6400 6752 531102970 531103323 1.750000e-116 431.0
44 TraesCS6D01G169900 chr4A 85.443 158 16 4 7533 7689 48905839 48905990 3.280000e-34 158.0
45 TraesCS6D01G169900 chr4A 85.057 87 9 3 4926 5012 331467509 331467591 1.570000e-12 86.1
46 TraesCS6D01G169900 chr4A 87.143 70 8 1 4926 4994 38715198 38715267 2.620000e-10 78.7
47 TraesCS6D01G169900 chr2A 85.856 403 54 2 6356 6755 748894414 748894012 8.130000e-115 425.0
48 TraesCS6D01G169900 chr2A 86.061 165 15 2 7525 7689 79316001 79316157 4.210000e-38 171.0
49 TraesCS6D01G169900 chr2A 82.581 155 22 5 7829 7981 5378792 5378943 1.990000e-26 132.0
50 TraesCS6D01G169900 chr4D 84.906 371 50 5 114 480 504283648 504283280 3.870000e-98 370.0
51 TraesCS6D01G169900 chrUn 84.824 369 48 5 114 478 83928773 83928409 1.800000e-96 364.0
52 TraesCS6D01G169900 chrUn 76.140 285 55 7 3256 3535 364972353 364972629 4.270000e-28 137.0
53 TraesCS6D01G169900 chr1D 93.878 147 9 0 5184 5330 335404146 335404292 1.150000e-53 222.0
54 TraesCS6D01G169900 chr5A 92.053 151 11 1 5184 5334 111106646 111106497 2.480000e-50 211.0
55 TraesCS6D01G169900 chr5A 86.842 76 10 0 1 76 82285572 82285497 1.570000e-12 86.1
56 TraesCS6D01G169900 chr5A 85.057 87 9 3 4926 5012 398259142 398259060 1.570000e-12 86.1
57 TraesCS6D01G169900 chr5A 82.609 92 15 1 8576 8667 104582231 104582141 7.300000e-11 80.5
58 TraesCS6D01G169900 chr3A 90.968 155 13 1 5180 5334 18546091 18546244 3.210000e-49 207.0
59 TraesCS6D01G169900 chr3A 90.968 155 13 1 5180 5334 18593240 18593393 3.210000e-49 207.0
60 TraesCS6D01G169900 chr3A 84.848 165 19 2 7525 7688 414818208 414818049 2.530000e-35 161.0
61 TraesCS6D01G169900 chr3A 83.908 87 10 4 4926 5012 714570387 714570305 7.300000e-11 80.5
62 TraesCS6D01G169900 chr7D 89.937 159 14 2 5184 5341 395074928 395075085 4.150000e-48 204.0
63 TraesCS6D01G169900 chr7D 83.721 86 10 4 4927 5012 38012248 38012167 2.620000e-10 78.7
64 TraesCS6D01G169900 chr3D 87.273 165 14 4 7525 7688 315480420 315480578 1.940000e-41 182.0
65 TraesCS6D01G169900 chr4B 89.706 68 7 0 9 76 639960106 639960173 4.360000e-13 87.9
66 TraesCS6D01G169900 chr4B 86.842 76 10 0 1 76 635514298 635514373 1.570000e-12 86.1
67 TraesCS6D01G169900 chr4B 88.406 69 8 0 8 76 586233008 586232940 5.640000e-12 84.2
68 TraesCS6D01G169900 chr7A 83.908 87 10 4 4926 5012 145452839 145452921 7.300000e-11 80.5
69 TraesCS6D01G169900 chr5B 84.146 82 9 4 4931 5012 576798571 576798648 9.440000e-10 76.8


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 TraesCS6D01G169900 chr6D 156442827 156451593 8766 False 7303.500000 10065 100.000000 1 8767 2 chr6D.!!$F2 8766
1 TraesCS6D01G169900 chr6A 209892826 209903053 10227 False 1561.714286 7020 93.624429 8 8737 7 chr6A.!!$F1 8729
2 TraesCS6D01G169900 chr6B 279044670 279050810 6140 False 2465.000000 4545 95.640000 829 8380 4 chr6B.!!$F2 7551
3 TraesCS6D01G169900 chr6B 279035392 279036102 710 False 448.500000 507 91.137500 1 787 2 chr6B.!!$F1 786
4 TraesCS6D01G169900 chr6B 279064722 279066462 1740 False 265.000000 350 93.025500 8397 8764 2 chr6B.!!$F3 367
5 TraesCS6D01G169900 chr5D 473513963 473515287 1324 True 346.000000 486 88.126500 5180 6754 2 chr5D.!!$R2 1574

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
232 246 1.442017 GTTCAATGTCGGCGGTTGC 60.442 57.895 7.21 0.0 41.71 4.17 F
1117 1182 2.025155 TCGCTGTATGTTCCTCCTCTC 58.975 52.381 0.00 0.0 0.00 3.20 F
1118 1183 2.028130 CGCTGTATGTTCCTCCTCTCT 58.972 52.381 0.00 0.0 0.00 3.10 F
2803 2891 1.801178 GCAAACCTGTCACTAGCAGTC 59.199 52.381 0.00 0.0 32.41 3.51 F
2937 3025 1.019805 GCGGGTTCTTGAGTGGTAGC 61.020 60.000 0.00 0.0 0.00 3.58 F
3354 3443 1.595993 ATGTACGTGCAGAGTCGCCT 61.596 55.000 12.93 0.0 0.00 5.52 F
4761 4919 1.869767 GGCAGTGCTATGTGCTGATAC 59.130 52.381 16.11 0.0 43.37 2.24 F
5237 5493 0.168128 CGTTTTGCCCGGATTCTGTC 59.832 55.000 0.73 0.0 0.00 3.51 F
5238 5494 0.526211 GTTTTGCCCGGATTCTGTCC 59.474 55.000 0.73 0.0 44.10 4.02 F
6641 7000 0.329596 GGATGGGTCCAAAGCAGACT 59.670 55.000 0.00 0.0 44.42 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1690 3.146066 TGTGTGGATAAACTCTGCAACC 58.854 45.455 0.00 0.00 0.00 3.77 R
2803 2891 2.092753 ACATACTGATCAACCTGCAGGG 60.093 50.000 35.42 19.57 40.27 4.45 R
2927 3015 3.492656 GGATATCAAAGCGCTACCACTCA 60.493 47.826 12.05 0.00 0.00 3.41 R
4723 4881 3.865224 GCCACAGCAATTGAACAAAAG 57.135 42.857 10.34 0.00 39.53 2.27 R
4795 4953 4.098654 GCTAGCCTATGAACTCTCTCAACA 59.901 45.833 2.29 0.00 0.00 3.33 R
5219 5475 0.526211 GGACAGAATCCGGGCAAAAC 59.474 55.000 0.00 0.00 37.88 2.43 R
6582 6941 0.106419 TTTTGGGGTCAAAGCGGACT 60.106 50.000 6.25 0.00 42.93 3.85 R
6590 6949 0.631753 TGGTCTGGTTTTGGGGTCAA 59.368 50.000 0.00 0.00 0.00 3.18 R
6711 7070 1.077501 CCATTCTGTCCGGGTGCAT 60.078 57.895 0.00 0.00 0.00 3.96 R
7949 9296 1.338389 GCAAGCATGGCAAATCCTTGT 60.338 47.619 15.93 0.00 40.93 3.16 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
29 30 3.187700 CGAGTTTAACGAGCCAAGCTAT 58.812 45.455 0.00 0.00 39.88 2.97
49 50 5.686397 GCTATCGAGTGTTTATTAAGCTCGT 59.314 40.000 17.96 12.19 46.08 4.18
220 234 5.196341 TCCGATCTACGCTATTGTTCAAT 57.804 39.130 3.55 3.55 41.07 2.57
232 246 1.442017 GTTCAATGTCGGCGGTTGC 60.442 57.895 7.21 0.00 41.71 4.17
278 292 3.335579 GGCCTTAACACGATGACTTTCT 58.664 45.455 0.00 0.00 0.00 2.52
291 305 6.092944 ACGATGACTTTCTGAGTGTCTACTAG 59.907 42.308 11.44 0.00 39.19 2.57
293 307 7.465379 CGATGACTTTCTGAGTGTCTACTAGAG 60.465 44.444 0.00 0.00 39.19 2.43
350 364 3.426568 GCAGCGCGCCTTCTTCTT 61.427 61.111 30.33 2.66 32.94 2.52
369 383 9.772973 TTCTTCTTAATTCAGTGCTTGTACTTA 57.227 29.630 0.00 0.00 0.00 2.24
390 404 7.445945 ACTTATTGCTAGGTTGTCTATGGATC 58.554 38.462 0.00 0.00 0.00 3.36
454 468 7.827729 TGCCATGATTGAAGATGGATAGATTAG 59.172 37.037 9.55 0.00 41.63 1.73
470 484 9.262358 GGATAGATTAGAAGTATTTCCACACAC 57.738 37.037 0.00 0.00 33.64 3.82
471 485 9.817809 GATAGATTAGAAGTATTTCCACACACA 57.182 33.333 0.00 0.00 33.64 3.72
499 513 5.560148 ACATGACGATTTATCTGTTTTCGC 58.440 37.500 0.00 0.00 33.30 4.70
501 515 5.203358 TGACGATTTATCTGTTTTCGCAG 57.797 39.130 0.00 0.00 37.81 5.18
502 516 4.092821 TGACGATTTATCTGTTTTCGCAGG 59.907 41.667 0.00 0.00 37.12 4.85
585 601 6.417635 TCTGTTAAAGTTACTACGTTGAACCG 59.582 38.462 3.44 0.00 0.00 4.44
820 885 4.142315 CGGAACAAGTTCTCGTATCCCTTA 60.142 45.833 12.22 0.00 39.45 2.69
830 895 4.058817 CTCGTATCCCTTAGTGCATTTCC 58.941 47.826 0.00 0.00 0.00 3.13
886 951 3.776340 ACCAAAACCTTAAGCACAAACG 58.224 40.909 0.00 0.00 0.00 3.60
910 975 2.210144 TACAGGGCCCAGCAACATCC 62.210 60.000 27.56 0.00 0.00 3.51
1107 1172 2.738643 CGTCTTCCCAATCGCTGTATGT 60.739 50.000 0.00 0.00 0.00 2.29
1116 1181 2.145397 TCGCTGTATGTTCCTCCTCT 57.855 50.000 0.00 0.00 0.00 3.69
1117 1182 2.025155 TCGCTGTATGTTCCTCCTCTC 58.975 52.381 0.00 0.00 0.00 3.20
1118 1183 2.028130 CGCTGTATGTTCCTCCTCTCT 58.972 52.381 0.00 0.00 0.00 3.10
1119 1184 2.034053 CGCTGTATGTTCCTCCTCTCTC 59.966 54.545 0.00 0.00 0.00 3.20
1120 1185 3.295973 GCTGTATGTTCCTCCTCTCTCT 58.704 50.000 0.00 0.00 0.00 3.10
1121 1186 3.317993 GCTGTATGTTCCTCCTCTCTCTC 59.682 52.174 0.00 0.00 0.00 3.20
1122 1187 4.792068 CTGTATGTTCCTCCTCTCTCTCT 58.208 47.826 0.00 0.00 0.00 3.10
1301 1366 4.284490 TGAGAAGTTGAGCCACACTAATCT 59.716 41.667 0.00 0.00 0.00 2.40
1359 1424 8.322906 TGGAAAATCGATATAGCTTTGGTATG 57.677 34.615 0.00 0.00 0.00 2.39
1370 1435 5.266733 AGCTTTGGTATGCCACATTTATG 57.733 39.130 0.24 0.00 46.01 1.90
1576 1641 6.655003 GGTCTGGATCTTGTGAAATTAGAACA 59.345 38.462 0.00 0.00 0.00 3.18
1625 1690 7.546316 TCATGTTTGACCTCATGCATTAAATTG 59.454 33.333 0.00 0.00 40.54 2.32
1627 1692 5.999205 TTGACCTCATGCATTAAATTGGT 57.001 34.783 0.00 0.00 0.00 3.67
1650 1715 4.910195 TGCAGAGTTTATCCACACATCTT 58.090 39.130 0.00 0.00 0.00 2.40
1655 1720 4.655963 AGTTTATCCACACATCTTGCAGT 58.344 39.130 0.00 0.00 0.00 4.40
1753 1818 9.819267 GTAAGCACTATGAATTTAAGTACTCCT 57.181 33.333 0.00 0.00 0.00 3.69
1757 1822 9.685828 GCACTATGAATTTAAGTACTCCTCTAG 57.314 37.037 0.00 0.00 0.00 2.43
2265 2349 3.347216 TCTCATGCTTTAGGAAGGTTGC 58.653 45.455 0.00 0.00 33.34 4.17
2352 2436 8.416329 AGGTAATTTGGCTTATATTTGCTTCAG 58.584 33.333 0.00 0.00 0.00 3.02
2424 2508 7.012327 CACACTCATTTTGGTGTCTTCTTCTTA 59.988 37.037 0.00 0.00 43.65 2.10
2756 2844 5.076873 ACTAAAGCCTAAAATTCAGCACCA 58.923 37.500 0.00 0.00 0.00 4.17
2803 2891 1.801178 GCAAACCTGTCACTAGCAGTC 59.199 52.381 0.00 0.00 32.41 3.51
2927 3015 1.813513 CACAGAGATTGCGGGTTCTT 58.186 50.000 0.00 0.00 0.00 2.52
2937 3025 1.019805 GCGGGTTCTTGAGTGGTAGC 61.020 60.000 0.00 0.00 0.00 3.58
2956 3044 4.607293 AGCGCTTTGATATCCATGAGTA 57.393 40.909 2.64 0.00 0.00 2.59
2977 3065 8.786898 TGAGTATTTCTGTCTTTCTTTTGATGG 58.213 33.333 0.00 0.00 0.00 3.51
3189 3277 6.631016 TCCTTATACAGTGAGTGAATGTGTC 58.369 40.000 0.00 0.00 0.00 3.67
3354 3443 1.595993 ATGTACGTGCAGAGTCGCCT 61.596 55.000 12.93 0.00 0.00 5.52
3546 3635 6.820152 GGATTATTTGTAAACCCTACGTCAGT 59.180 38.462 0.00 0.00 0.00 3.41
4093 4251 5.462405 GTCATGTCTCCTACCGTTGATATC 58.538 45.833 0.00 0.00 0.00 1.63
4217 4375 9.185680 GGGTTTCTTAGAAATCCTAAAGCATTA 57.814 33.333 25.17 0.00 36.95 1.90
4311 4469 5.302059 CCATTGGATTCAGCAATCAGATCTT 59.698 40.000 0.00 0.00 40.41 2.40
4568 4726 4.019321 TGCTGGCAGGTAATAAAGTTCTCT 60.019 41.667 17.64 0.00 0.00 3.10
4761 4919 1.869767 GGCAGTGCTATGTGCTGATAC 59.130 52.381 16.11 0.00 43.37 2.24
4822 4980 4.662278 AGAGAGTTCATAGGCTAGCTAGG 58.338 47.826 22.10 7.06 0.00 3.02
4889 5048 3.311322 TCGTGTTGTGACTTAGCCTTTTG 59.689 43.478 0.00 0.00 0.00 2.44
4900 5059 7.803659 GTGACTTAGCCTTTTGATTAAGAACAC 59.196 37.037 0.00 0.00 32.97 3.32
5148 5404 6.154203 TGCAACTGACATTACATTTTTGGA 57.846 33.333 0.00 0.00 0.00 3.53
5152 5408 8.011106 GCAACTGACATTACATTTTTGGAATTG 58.989 33.333 0.00 0.00 0.00 2.32
5195 5451 3.515901 AGAAGTAGTTAGGCCAACTCCAG 59.484 47.826 19.64 0.00 44.48 3.86
5213 5469 4.973055 CGCACGACCCCAAACGGA 62.973 66.667 0.00 0.00 0.00 4.69
5237 5493 0.168128 CGTTTTGCCCGGATTCTGTC 59.832 55.000 0.73 0.00 0.00 3.51
5238 5494 0.526211 GTTTTGCCCGGATTCTGTCC 59.474 55.000 0.73 0.00 44.10 4.02
5283 5539 4.388499 GGACATGCACGTCCGGGT 62.388 66.667 17.32 0.00 45.77 5.28
5284 5540 2.358247 GACATGCACGTCCGGGTT 60.358 61.111 0.29 0.00 0.00 4.11
6403 6760 4.899239 CACTCGCATCTCCCCGCC 62.899 72.222 0.00 0.00 0.00 6.13
6477 6836 2.499693 GGGTGAAAAGGAGGAGAGAGAG 59.500 54.545 0.00 0.00 0.00 3.20
6478 6837 3.436243 GGTGAAAAGGAGGAGAGAGAGA 58.564 50.000 0.00 0.00 0.00 3.10
6503 6862 2.015726 TGGGTGGTGGGTCCCTTTT 61.016 57.895 10.00 0.00 43.74 2.27
6509 6868 2.237643 GTGGTGGGTCCCTTTTTGTTTT 59.762 45.455 10.00 0.00 34.77 2.43
6511 6870 2.502130 GGTGGGTCCCTTTTTGTTTTGA 59.498 45.455 10.00 0.00 0.00 2.69
6590 6949 1.741770 GTCCGCATTCAGTCCGCTT 60.742 57.895 0.00 0.00 0.00 4.68
6604 6963 1.395826 CCGCTTTGACCCCAAAACCA 61.396 55.000 0.00 0.00 41.28 3.67
6641 7000 0.329596 GGATGGGTCCAAAGCAGACT 59.670 55.000 0.00 0.00 44.42 3.24
6642 7001 1.457346 GATGGGTCCAAAGCAGACTG 58.543 55.000 0.00 0.00 34.56 3.51
6645 7004 1.425066 TGGGTCCAAAGCAGACTGAAT 59.575 47.619 6.65 0.00 34.56 2.57
6655 7014 4.002906 AGCAGACTGAATACGGACAAAA 57.997 40.909 6.65 0.00 0.00 2.44
6700 7059 2.674747 GCCGTCTGGTATGTCCGTTTTA 60.675 50.000 0.00 0.00 39.52 1.52
6704 7063 2.236893 TCTGGTATGTCCGTTTTACCCC 59.763 50.000 0.00 0.00 39.52 4.95
6707 7066 3.181436 TGGTATGTCCGTTTTACCCCAAA 60.181 43.478 0.00 0.00 39.52 3.28
6708 7067 3.191162 GGTATGTCCGTTTTACCCCAAAC 59.809 47.826 0.00 0.00 33.90 2.93
7509 7872 4.566070 CCCCATTGATTTCTTGCCATTGTT 60.566 41.667 0.00 0.00 0.00 2.83
7545 7909 1.763968 TGTACTCCCTCCGATCACAG 58.236 55.000 0.00 0.00 0.00 3.66
7618 7982 6.862944 AACATGTTTTAGTGTGTTTGTTCG 57.137 33.333 4.92 0.00 31.20 3.95
7794 8160 4.612259 CGGAACTTGCACTCTTTTCTGATG 60.612 45.833 0.00 0.00 0.00 3.07
7834 8202 7.558807 TGGAATGCTAAAAATCTGACATCTGAT 59.441 33.333 0.00 0.00 36.31 2.90
7866 8234 0.607489 AGGCATGGCATATCGAAGGC 60.607 55.000 22.64 0.00 0.00 4.35
7934 8303 7.686438 TTTAGCTAGCATGACAATTTCTGAA 57.314 32.000 18.83 0.00 0.00 3.02
7937 8309 6.618811 AGCTAGCATGACAATTTCTGAAAAG 58.381 36.000 18.83 5.75 0.00 2.27
8054 10063 1.134128 TCGTGGTGGAATCCATGATGG 60.134 52.381 4.81 4.74 45.20 3.51
8249 10260 6.762661 ACTGTGTTTTGAAAATAGCAAAGCAT 59.237 30.769 8.42 0.00 44.31 3.79
8412 10424 5.515797 TTGACTCCTAAGTGATCCATACG 57.484 43.478 0.00 0.00 35.28 3.06
8604 10620 8.089597 TGCAATAGTTCACATTCAAAATCATGT 58.910 29.630 0.00 0.00 33.72 3.21
8702 12212 6.847289 GTGTTGCAGCATGACAATTTTTAAAG 59.153 34.615 6.50 0.00 39.69 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.079961 GGATGGGGGCAAGGGCTT 62.080 66.667 0.00 0.00 40.87 4.35
178 189 0.756294 AGGATCCAACGTGACACACA 59.244 50.000 15.82 0.00 33.40 3.72
220 234 2.933878 AAGAACAGCAACCGCCGACA 62.934 55.000 0.00 0.00 39.83 4.35
232 246 1.009829 GGACCAGCGCATAAGAACAG 58.990 55.000 11.47 0.00 0.00 3.16
278 292 6.216569 CAAAACTTGCTCTAGTAGACACTCA 58.783 40.000 0.00 0.00 36.14 3.41
340 354 5.048434 ACAAGCACTGAATTAAGAAGAAGGC 60.048 40.000 0.00 0.00 0.00 4.35
350 364 7.921786 AGCAATAAGTACAAGCACTGAATTA 57.078 32.000 0.00 0.00 0.00 1.40
369 383 5.221803 CCAGATCCATAGACAACCTAGCAAT 60.222 44.000 0.00 0.00 0.00 3.56
371 385 3.643320 CCAGATCCATAGACAACCTAGCA 59.357 47.826 0.00 0.00 0.00 3.49
407 421 4.772434 CAGTACAACGAACACCAGAAATG 58.228 43.478 0.00 0.00 0.00 2.32
420 434 3.684305 TCTTCAATCATGGCAGTACAACG 59.316 43.478 0.00 0.00 0.00 4.10
472 486 8.901748 CGAAAACAGATAAATCGTCATGTTTTT 58.098 29.630 15.86 6.30 45.64 1.94
483 497 3.128589 TGCCCTGCGAAAACAGATAAATC 59.871 43.478 0.00 0.00 40.25 2.17
495 509 1.004560 CTCAGAACTGCCCTGCGAA 60.005 57.895 0.00 0.00 0.00 4.70
499 513 1.093159 GAATGCTCAGAACTGCCCTG 58.907 55.000 0.00 0.00 0.00 4.45
501 515 1.986575 GCGAATGCTCAGAACTGCCC 61.987 60.000 0.00 0.00 38.39 5.36
502 516 1.427020 GCGAATGCTCAGAACTGCC 59.573 57.895 0.00 0.00 38.39 4.85
585 601 2.640184 ACCCCTGCGTTTTATTCTAGC 58.360 47.619 0.00 0.00 0.00 3.42
820 885 4.980339 AATTTTTGGAGGGAAATGCACT 57.020 36.364 0.00 0.00 0.00 4.40
830 895 7.492344 GCATAAACTCATGGTAATTTTTGGAGG 59.508 37.037 0.00 0.00 0.00 4.30
886 951 1.257055 TTGCTGGGCCCTGTATTTGC 61.257 55.000 27.68 17.12 0.00 3.68
1107 1172 3.711704 GAGAGAGAGAGAGAGAGGAGGAA 59.288 52.174 0.00 0.00 0.00 3.36
1116 1181 5.485353 ACAGAAAGAGAGAGAGAGAGAGAGA 59.515 44.000 0.00 0.00 0.00 3.10
1117 1182 5.583854 CACAGAAAGAGAGAGAGAGAGAGAG 59.416 48.000 0.00 0.00 0.00 3.20
1118 1183 5.491070 CACAGAAAGAGAGAGAGAGAGAGA 58.509 45.833 0.00 0.00 0.00 3.10
1119 1184 4.637534 CCACAGAAAGAGAGAGAGAGAGAG 59.362 50.000 0.00 0.00 0.00 3.20
1120 1185 4.042809 ACCACAGAAAGAGAGAGAGAGAGA 59.957 45.833 0.00 0.00 0.00 3.10
1121 1186 4.156556 CACCACAGAAAGAGAGAGAGAGAG 59.843 50.000 0.00 0.00 0.00 3.20
1122 1187 4.078537 CACCACAGAAAGAGAGAGAGAGA 58.921 47.826 0.00 0.00 0.00 3.10
1301 1366 9.847706 GAAGCAGAAAACTATATCGATCTGATA 57.152 33.333 0.00 8.88 43.54 2.15
1414 1479 7.882791 TGCTCTGAGAAGGTTAAAATTGTCATA 59.117 33.333 9.28 0.00 29.52 2.15
1576 1641 5.382618 ACTAGTTTTATCACGGTTCGACT 57.617 39.130 0.00 0.00 0.00 4.18
1625 1690 3.146066 TGTGTGGATAAACTCTGCAACC 58.854 45.455 0.00 0.00 0.00 3.77
1627 1692 4.910195 AGATGTGTGGATAAACTCTGCAA 58.090 39.130 0.00 0.00 0.00 4.08
1650 1715 5.794726 TGTACCTAACTTTACTGACTGCA 57.205 39.130 0.00 0.00 0.00 4.41
1655 1720 5.247564 ACAGGCATGTACCTAACTTTACTGA 59.752 40.000 0.06 0.00 38.26 3.41
1702 1767 9.173021 ACATGAAATATTATCAAGTTGTTCGGA 57.827 29.630 0.00 0.00 0.00 4.55
1733 1798 9.422681 TGCTAGAGGAGTACTTAAATTCATAGT 57.577 33.333 0.00 0.00 0.00 2.12
1757 1822 9.923143 AACCTAAGGTAGAAAATTTGTATTTGC 57.077 29.630 0.00 0.00 33.12 3.68
2116 2200 7.022055 TGCTGAAATTCTTTAGTTTCGACAA 57.978 32.000 0.00 0.00 37.19 3.18
2265 2349 5.535333 ACTTGAAACAATTCTGCAAGATGG 58.465 37.500 10.56 0.00 46.36 3.51
2352 2436 5.786401 AGATAACAGCTTCGATGTGAAAC 57.214 39.130 0.00 0.00 35.79 2.78
2424 2508 3.275999 AGCACGTAAACAAACAGGAGTT 58.724 40.909 0.00 0.00 40.40 3.01
2608 2692 8.090214 AGATAGTGACCAAATCAAAACCAAATG 58.910 33.333 0.00 0.00 39.72 2.32
2609 2693 8.193953 AGATAGTGACCAAATCAAAACCAAAT 57.806 30.769 0.00 0.00 39.72 2.32
2618 2702 4.937620 GCAGTTGAGATAGTGACCAAATCA 59.062 41.667 0.00 0.00 33.79 2.57
2756 2844 7.994911 TCTGCAGTTTATTCTTCCATGACATAT 59.005 33.333 14.67 0.00 0.00 1.78
2803 2891 2.092753 ACATACTGATCAACCTGCAGGG 60.093 50.000 35.42 19.57 40.27 4.45
2927 3015 3.492656 GGATATCAAAGCGCTACCACTCA 60.493 47.826 12.05 0.00 0.00 3.41
2937 3025 7.172190 ACAGAAATACTCATGGATATCAAAGCG 59.828 37.037 4.83 0.00 0.00 4.68
2956 3044 5.541484 AGGCCATCAAAAGAAAGACAGAAAT 59.459 36.000 5.01 0.00 0.00 2.17
2977 3065 4.301628 CACCAAGAAAAACATCAGAAGGC 58.698 43.478 0.00 0.00 0.00 4.35
3546 3635 9.613428 CCAATTAATAAGTACCATCACTTCTCA 57.387 33.333 0.00 0.00 39.45 3.27
4217 4375 8.486210 TCTATGACAGCTTTAATCACCATTAGT 58.514 33.333 0.00 0.00 0.00 2.24
4568 4726 7.873719 TCAGAAACTTGGTCACTGAAAAATA 57.126 32.000 0.00 0.00 35.20 1.40
4723 4881 3.865224 GCCACAGCAATTGAACAAAAG 57.135 42.857 10.34 0.00 39.53 2.27
4795 4953 4.098654 GCTAGCCTATGAACTCTCTCAACA 59.901 45.833 2.29 0.00 0.00 3.33
4803 4961 5.771165 ACTTACCTAGCTAGCCTATGAACTC 59.229 44.000 15.74 0.00 0.00 3.01
4822 4980 7.425595 GCGTTATTTCTTTGAGTATGCACTTAC 59.574 37.037 0.00 0.00 34.21 2.34
5052 5213 9.520204 AATATTCCTTATTTTTCATTGTGCTCG 57.480 29.630 0.00 0.00 0.00 5.03
5152 5408 9.232473 ACTTCTATCTTGTTACCAAAAAGGATC 57.768 33.333 0.00 0.00 41.22 3.36
5163 5419 7.779073 TGGCCTAACTACTTCTATCTTGTTAC 58.221 38.462 3.32 0.00 0.00 2.50
5219 5475 0.526211 GGACAGAATCCGGGCAAAAC 59.474 55.000 0.00 0.00 37.88 2.43
5237 5493 2.656055 CATTGCCACCCCAAACGG 59.344 61.111 0.00 0.00 0.00 4.44
5238 5494 2.656055 CCATTGCCACCCCAAACG 59.344 61.111 0.00 0.00 0.00 3.60
5283 5539 1.456726 TTGGGCGCCTCCAACTAAA 59.543 52.632 28.56 5.40 41.44 1.85
5284 5540 3.162529 TTGGGCGCCTCCAACTAA 58.837 55.556 28.56 7.56 41.44 2.24
5307 5563 2.280321 ACGTTTTGGGGACGGACG 60.280 61.111 1.64 0.00 44.34 4.79
5308 5564 1.962822 GGACGTTTTGGGGACGGAC 60.963 63.158 0.00 0.00 44.34 4.79
5309 5565 2.426887 GGACGTTTTGGGGACGGA 59.573 61.111 0.00 0.00 44.34 4.69
5313 5569 4.646877 GGGCGGACGTTTTGGGGA 62.647 66.667 0.00 0.00 0.00 4.81
6446 6805 2.070654 CTTTTCACCCACCGCACCAC 62.071 60.000 0.00 0.00 0.00 4.16
6477 6836 2.677228 CCACCACCCACCCATCTC 59.323 66.667 0.00 0.00 0.00 2.75
6478 6837 2.941025 CCCACCACCCACCCATCT 60.941 66.667 0.00 0.00 0.00 2.90
6499 6858 5.697633 CCCCATCTGTCATCAAAACAAAAAG 59.302 40.000 0.00 0.00 0.00 2.27
6503 6862 2.562298 GCCCCATCTGTCATCAAAACAA 59.438 45.455 0.00 0.00 0.00 2.83
6509 6868 0.475475 GATGGCCCCATCTGTCATCA 59.525 55.000 17.90 0.00 46.67 3.07
6554 6913 2.943653 GTTTTCCTCGCCCGTGTG 59.056 61.111 0.00 0.00 0.00 3.82
6555 6914 2.663852 CGTTTTCCTCGCCCGTGT 60.664 61.111 0.00 0.00 0.00 4.49
6582 6941 0.106419 TTTTGGGGTCAAAGCGGACT 60.106 50.000 6.25 0.00 42.93 3.85
6590 6949 0.631753 TGGTCTGGTTTTGGGGTCAA 59.368 50.000 0.00 0.00 0.00 3.18
6616 6975 2.552231 CTTTGGACCCATCCCCGACC 62.552 65.000 0.00 0.00 45.59 4.79
6631 6990 3.325870 TGTCCGTATTCAGTCTGCTTTG 58.674 45.455 0.00 0.00 0.00 2.77
6655 7014 3.036084 CGCGAGTGCAAACGGACT 61.036 61.111 0.00 0.00 42.97 3.85
6680 7039 2.088950 AAAACGGACATACCAGACGG 57.911 50.000 0.00 0.00 38.90 4.79
6683 7042 2.236893 GGGGTAAAACGGACATACCAGA 59.763 50.000 9.99 0.00 40.71 3.86
6684 7043 2.027007 TGGGGTAAAACGGACATACCAG 60.027 50.000 9.99 0.00 40.71 4.00
6700 7059 2.282887 GGTGCATCCGTTTGGGGT 60.283 61.111 0.00 0.00 36.01 4.95
6710 7069 1.097547 CCATTCTGTCCGGGTGCATC 61.098 60.000 0.00 0.00 0.00 3.91
6711 7070 1.077501 CCATTCTGTCCGGGTGCAT 60.078 57.895 0.00 0.00 0.00 3.96
6713 7072 2.438434 CCCATTCTGTCCGGGTGC 60.438 66.667 0.00 0.00 35.03 5.01
6739 7098 1.893137 GGGTTTTAAGGCCAACTCCAG 59.107 52.381 5.01 0.00 0.00 3.86
7291 7654 6.071320 ACTCTCAGCCTTCCTAAAACAAAAT 58.929 36.000 0.00 0.00 0.00 1.82
7292 7655 5.445964 ACTCTCAGCCTTCCTAAAACAAAA 58.554 37.500 0.00 0.00 0.00 2.44
7293 7656 5.048846 ACTCTCAGCCTTCCTAAAACAAA 57.951 39.130 0.00 0.00 0.00 2.83
7294 7657 4.706842 ACTCTCAGCCTTCCTAAAACAA 57.293 40.909 0.00 0.00 0.00 2.83
7328 7691 4.954202 CCCATCCTGGAATGATATCAATGG 59.046 45.833 17.86 17.86 40.96 3.16
7509 7872 5.339008 AGTACATATTTCAGTGCTCCGAA 57.661 39.130 0.00 0.00 0.00 4.30
7618 7982 4.734917 ACTACATACAGAGTGAAACGAGC 58.265 43.478 0.00 0.00 45.86 5.03
7676 8040 1.386533 TGATCGTTACTCCCTCCGTC 58.613 55.000 0.00 0.00 0.00 4.79
7754 8119 1.957177 TCCGCTGCCAAAAATGTGTAA 59.043 42.857 0.00 0.00 0.00 2.41
7766 8131 2.970974 GAGTGCAAGTTCCGCTGCC 61.971 63.158 0.00 0.00 0.00 4.85
7794 8160 3.323243 GCATTCCATCATTTATGCTGCC 58.677 45.455 0.00 0.00 40.08 4.85
7834 8202 3.282021 GCCATGCCTAAAAGATCTGACA 58.718 45.455 0.00 0.00 0.00 3.58
7842 8210 4.083110 CCTTCGATATGCCATGCCTAAAAG 60.083 45.833 0.00 0.00 0.00 2.27
7884 8253 1.368345 TTGCCATCCTCGCGACAATG 61.368 55.000 3.71 11.80 0.00 2.82
7949 9296 1.338389 GCAAGCATGGCAAATCCTTGT 60.338 47.619 15.93 0.00 40.93 3.16
8054 10063 2.227388 CCCAAGCTCAGTGACACATTTC 59.773 50.000 8.59 0.00 0.00 2.17
8121 10130 8.935844 GGAATTTGTTCAGATATTTTGGAAACC 58.064 33.333 0.00 0.00 0.00 3.27
8249 10260 7.921786 ACTTTAGCATATGAGTAGCAAACAA 57.078 32.000 6.97 0.00 0.00 2.83
8389 10401 5.421056 ACGTATGGATCACTTAGGAGTCAAA 59.579 40.000 0.00 0.00 32.54 2.69
8390 10402 4.954202 ACGTATGGATCACTTAGGAGTCAA 59.046 41.667 0.00 0.00 32.54 3.18
8391 10403 4.533815 ACGTATGGATCACTTAGGAGTCA 58.466 43.478 0.00 0.00 32.54 3.41
8392 10404 5.163540 ACAACGTATGGATCACTTAGGAGTC 60.164 44.000 0.00 0.00 32.54 3.36
8393 10405 4.710375 ACAACGTATGGATCACTTAGGAGT 59.290 41.667 0.00 0.00 36.25 3.85
8394 10406 5.263968 ACAACGTATGGATCACTTAGGAG 57.736 43.478 0.00 0.00 0.00 3.69
8395 10407 5.653330 TGTACAACGTATGGATCACTTAGGA 59.347 40.000 0.00 0.00 0.00 2.94
8406 10418 6.475727 CCTCAAAGTAGATGTACAACGTATGG 59.524 42.308 0.00 0.00 0.00 2.74
8412 10424 4.833390 AGGCCTCAAAGTAGATGTACAAC 58.167 43.478 0.00 0.00 0.00 3.32
8515 10527 6.827727 TCTGCTAGAGGTTTAAAGAGTGTTT 58.172 36.000 0.00 0.00 0.00 2.83
8632 10657 2.224314 TGTTTGATTGCGCATTCGTACA 59.776 40.909 23.63 23.63 38.14 2.90
8633 10658 2.845486 TGTTTGATTGCGCATTCGTAC 58.155 42.857 23.00 21.61 38.14 3.67
8741 12251 3.731216 CGTATGACATGCTGTAGTAGTGC 59.269 47.826 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.