Multiple sequence alignment - TraesCS3D01G338800

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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 TraesCS3D01G338800 chr3D 100.000 3626 0 0 1 3626 452022192 452025817 0.000000e+00 6697.0
1 TraesCS3D01G338800 chr3D 93.082 1113 47 11 667 1768 452171671 452172764 0.000000e+00 1602.0
2 TraesCS3D01G338800 chr3D 91.477 1056 64 17 2081 3123 452173271 452174313 0.000000e+00 1428.0
3 TraesCS3D01G338800 chr3D 84.058 1104 98 41 2090 3123 452016005 452017100 0.000000e+00 992.0
4 TraesCS3D01G338800 chr3D 89.145 608 58 7 1310 1912 452014907 452015511 0.000000e+00 750.0
5 TraesCS3D01G338800 chr3D 89.041 584 48 9 730 1306 452006511 452007085 0.000000e+00 710.0
6 TraesCS3D01G338800 chr3D 87.266 267 25 7 309 574 452170805 452171063 2.740000e-76 296.0
7 TraesCS3D01G338800 chr3D 89.116 147 13 1 3154 3300 452174319 452174462 2.880000e-41 180.0
8 TraesCS3D01G338800 chr3D 94.068 118 5 1 1933 2048 452173087 452173204 1.030000e-40 178.0
9 TraesCS3D01G338800 chr3D 90.076 131 10 3 3315 3444 452174777 452174905 2.240000e-37 167.0
10 TraesCS3D01G338800 chr3D 87.500 128 14 2 738 864 452005214 452005340 2.920000e-31 147.0
11 TraesCS3D01G338800 chr3D 84.177 158 14 4 1758 1915 447895055 447895201 3.770000e-30 143.0
12 TraesCS3D01G338800 chr3D 90.816 98 4 4 566 661 452171537 452171631 3.800000e-25 126.0
13 TraesCS3D01G338800 chr3D 81.651 109 11 8 1756 1864 452172823 452172922 8.340000e-12 82.4
14 TraesCS3D01G338800 chr3B 93.369 1327 70 11 592 1915 593553176 593554487 0.000000e+00 1947.0
15 TraesCS3D01G338800 chr3B 88.716 1090 38 17 2089 3123 593556940 593557999 0.000000e+00 1253.0
16 TraesCS3D01G338800 chr3B 87.640 267 24 7 309 574 593552192 593552450 5.880000e-78 302.0
17 TraesCS3D01G338800 chr3B 86.972 284 18 9 1936 2200 593554566 593554849 5.880000e-78 302.0
18 TraesCS3D01G338800 chr3B 91.860 172 11 3 3298 3468 593558545 593558714 1.680000e-58 237.0
19 TraesCS3D01G338800 chr3B 88.199 161 16 1 3135 3295 593557980 593558137 4.780000e-44 189.0
20 TraesCS3D01G338800 chr3B 97.980 99 2 0 1950 2048 593556765 593556863 4.810000e-39 172.0
21 TraesCS3D01G338800 chr3B 85.625 160 12 3 1756 1915 587425372 587425520 1.350000e-34 158.0
22 TraesCS3D01G338800 chr3B 93.333 75 2 1 2217 2288 593556578 593556652 1.380000e-19 108.0
23 TraesCS3D01G338800 chr3B 75.620 242 33 15 787 1017 593548424 593548650 2.980000e-16 97.1
24 TraesCS3D01G338800 chr3A 87.702 1236 53 15 689 1915 594514399 594515544 0.000000e+00 1349.0
25 TraesCS3D01G338800 chr3A 84.802 658 53 13 2513 3123 594518810 594519467 5.140000e-173 617.0
26 TraesCS3D01G338800 chr3A 92.260 323 8 3 3315 3626 594504982 594505298 3.320000e-120 442.0
27 TraesCS3D01G338800 chr3A 81.132 636 46 21 1936 2517 594515623 594516238 3.320000e-120 442.0
28 TraesCS3D01G338800 chr3A 85.806 310 38 5 1 309 613498034 613497730 1.260000e-84 324.0
29 TraesCS3D01G338800 chr3A 86.891 267 25 7 309 574 594512307 594512564 1.270000e-74 291.0
30 TraesCS3D01G338800 chr3A 94.798 173 7 2 3297 3468 594520001 594520172 5.970000e-68 268.0
31 TraesCS3D01G338800 chr3A 88.820 161 15 1 3135 3295 594519448 594519605 1.030000e-45 195.0
32 TraesCS3D01G338800 chr3A 85.024 207 12 1 2934 3121 594504322 594504528 3.690000e-45 193.0
33 TraesCS3D01G338800 chr3A 77.431 288 36 18 2668 2943 594498790 594499060 1.050000e-30 145.0
34 TraesCS3D01G338800 chr3A 81.818 121 21 1 1270 1390 594497093 594497212 2.300000e-17 100.0
35 TraesCS3D01G338800 chr3A 95.122 41 2 0 613 653 594514366 594514406 8.400000e-07 65.8
36 TraesCS3D01G338800 chr7D 92.038 314 23 2 1 312 589242233 589242546 1.200000e-119 440.0
37 TraesCS3D01G338800 chr7D 89.308 159 12 2 3468 3626 239733395 239733242 1.030000e-45 195.0
38 TraesCS3D01G338800 chr4D 87.013 308 35 5 5 310 51290225 51289921 3.470000e-90 342.0
39 TraesCS3D01G338800 chr4D 90.323 155 12 1 3472 3626 93144530 93144379 2.210000e-47 200.0
40 TraesCS3D01G338800 chrUn 86.174 311 38 5 1 309 281651319 281651626 7.500000e-87 331.0
41 TraesCS3D01G338800 chrUn 86.557 305 36 5 7 309 333801710 333801409 7.500000e-87 331.0
42 TraesCS3D01G338800 chrUn 86.557 305 36 5 7 309 433723384 433723083 7.500000e-87 331.0
43 TraesCS3D01G338800 chr6A 85.266 319 39 7 1 315 2938166 2937852 4.520000e-84 322.0
44 TraesCS3D01G338800 chr6A 91.333 150 10 1 3476 3625 183267999 183268145 6.140000e-48 202.0
45 TraesCS3D01G338800 chr6D 85.489 317 34 9 1 316 418458731 418458426 1.620000e-83 320.0
46 TraesCS3D01G338800 chr2A 85.577 312 37 8 1 309 754045683 754045377 1.620000e-83 320.0
47 TraesCS3D01G338800 chr1D 91.503 153 10 1 3473 3625 169064845 169064696 1.320000e-49 207.0
48 TraesCS3D01G338800 chr1A 91.503 153 10 1 3473 3625 225514061 225513912 1.320000e-49 207.0
49 TraesCS3D01G338800 chr4A 90.850 153 11 1 3473 3625 279772315 279772166 6.140000e-48 202.0
50 TraesCS3D01G338800 chr2D 88.889 162 15 1 3465 3626 561229104 561228946 2.860000e-46 196.0
51 TraesCS3D01G338800 chr6B 88.415 164 14 4 3465 3626 692335983 692335823 3.690000e-45 193.0
52 TraesCS3D01G338800 chr5D 87.879 99 12 0 1093 1191 519793218 519793316 2.290000e-22 117.0
53 TraesCS3D01G338800 chr5A 87.879 99 12 0 1093 1191 646347898 646347996 2.290000e-22 117.0


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 TraesCS3D01G338800 chr3D 452022192 452025817 3625 False 6697.000000 6697 100.000000 1 3626 1 chr3D.!!$F2 3625
1 TraesCS3D01G338800 chr3D 452014907 452017100 2193 False 871.000000 992 86.601500 1310 3123 2 chr3D.!!$F4 1813
2 TraesCS3D01G338800 chr3D 452170805 452174905 4100 False 507.425000 1602 89.694000 309 3444 8 chr3D.!!$F5 3135
3 TraesCS3D01G338800 chr3D 452005214 452007085 1871 False 428.500000 710 88.270500 730 1306 2 chr3D.!!$F3 576
4 TraesCS3D01G338800 chr3B 593548424 593558714 10290 False 511.900000 1947 89.298778 309 3468 9 chr3B.!!$F2 3159
5 TraesCS3D01G338800 chr3A 594512307 594520172 7865 False 461.114286 1349 88.466714 309 3468 7 chr3A.!!$F3 3159
6 TraesCS3D01G338800 chr3A 594504322 594505298 976 False 317.500000 442 88.642000 2934 3626 2 chr3A.!!$F2 692

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
306 307 0.109723 AAAGTGCGCCCAACCTTCTA 59.890 50.0 4.18 0.0 0.0 2.10 F
1042 7891 0.035458 CTTTCACCTCAACTCCGGCT 59.965 55.0 0.00 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1484 8362 0.103937 GGATCAGAGAAGAGGTGCGG 59.896 60.0 0.0 0.0 0.0 5.69 R
2958 15262 0.663153 AACAAGAGCAAACGGTGAGC 59.337 50.0 0.0 0.0 0.0 4.26 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
163 164 8.924511 ACCAATTTGATATTATGGATTCTCGT 57.075 30.769 0.00 0.00 35.16 4.18
212 213 9.990360 AAACTTAAAAGGTTTGACTTTTCAGAA 57.010 25.926 15.47 3.51 44.90 3.02
213 214 9.990360 AACTTAAAAGGTTTGACTTTTCAGAAA 57.010 25.926 15.47 0.00 44.90 2.52
277 278 9.945904 AATTTTTAAGAAACCTAACAACACCAA 57.054 25.926 0.00 0.00 0.00 3.67
278 279 9.945904 ATTTTTAAGAAACCTAACAACACCAAA 57.054 25.926 0.00 0.00 0.00 3.28
279 280 8.989653 TTTTAAGAAACCTAACAACACCAAAG 57.010 30.769 0.00 0.00 0.00 2.77
280 281 5.592104 AAGAAACCTAACAACACCAAAGG 57.408 39.130 0.00 0.00 0.00 3.11
281 282 4.606210 AGAAACCTAACAACACCAAAGGT 58.394 39.130 0.00 0.00 42.35 3.50
292 293 2.671130 ACCAAAGGTGCAACAAAGTG 57.329 45.000 3.64 0.00 39.98 3.16
293 294 1.289276 CCAAAGGTGCAACAAAGTGC 58.711 50.000 3.64 0.00 45.15 4.40
300 301 2.237066 GCAACAAAGTGCGCCCAAC 61.237 57.895 4.18 0.00 34.21 3.77
303 304 1.326951 AACAAAGTGCGCCCAACCTT 61.327 50.000 4.18 0.00 0.00 3.50
304 305 1.007387 CAAAGTGCGCCCAACCTTC 60.007 57.895 4.18 0.00 0.00 3.46
305 306 1.152756 AAAGTGCGCCCAACCTTCT 60.153 52.632 4.18 0.00 0.00 2.85
306 307 0.109723 AAAGTGCGCCCAACCTTCTA 59.890 50.000 4.18 0.00 0.00 2.10
357 3818 6.581171 AAATAAGGAGAAAACTCAAGCTGG 57.419 37.500 0.00 0.00 0.00 4.85
364 3825 3.378427 AGAAAACTCAAGCTGGTGACAAC 59.622 43.478 0.00 0.00 42.06 3.32
366 3827 2.645838 ACTCAAGCTGGTGACAACAT 57.354 45.000 0.00 0.00 42.06 2.71
375 3836 4.584325 AGCTGGTGACAACATTTACAACAT 59.416 37.500 0.00 0.00 42.06 2.71
379 3840 7.062138 GCTGGTGACAACATTTACAACATATTG 59.938 37.037 0.00 0.00 42.06 1.90
501 3963 9.285770 GTTTGAAGTTCCTAACACAAAACTAAG 57.714 33.333 0.00 0.00 39.54 2.18
518 3980 1.238439 AAGTTCTGGCACACGATTGG 58.762 50.000 0.00 0.00 0.00 3.16
526 3988 1.019673 GCACACGATTGGAGCATCAT 58.980 50.000 0.00 0.00 36.25 2.45
529 3991 3.251729 GCACACGATTGGAGCATCATATT 59.748 43.478 0.00 0.00 36.25 1.28
530 3992 4.261322 GCACACGATTGGAGCATCATATTT 60.261 41.667 0.00 0.00 36.25 1.40
545 4007 7.919091 AGCATCATATTTCATTGTCACATGAAC 59.081 33.333 0.00 0.00 36.62 3.18
663 6165 3.744559 TGCCAACGCAGAGAAACC 58.255 55.556 0.00 0.00 41.12 3.27
665 6167 1.165907 TGCCAACGCAGAGAAACCAG 61.166 55.000 0.00 0.00 41.12 4.00
666 6168 1.166531 GCCAACGCAGAGAAACCAGT 61.167 55.000 0.00 0.00 34.03 4.00
672 6174 0.871057 GCAGAGAAACCAGTGACAGC 59.129 55.000 0.00 0.00 0.00 4.40
783 7623 0.613260 AGGCAGTGAATACGCCTTCA 59.387 50.000 0.00 0.00 46.91 3.02
877 7717 4.020485 GGTCCCGCCACTCACTATATAAAT 60.020 45.833 0.00 0.00 37.17 1.40
1042 7891 0.035458 CTTTCACCTCAACTCCGGCT 59.965 55.000 0.00 0.00 0.00 5.52
1210 8066 1.723870 GTTGGATCATGCCGCTGTC 59.276 57.895 0.00 0.00 0.00 3.51
1211 8067 1.026182 GTTGGATCATGCCGCTGTCA 61.026 55.000 0.00 0.00 0.00 3.58
1231 8087 5.721480 TGTCATCCAAAACTCTCTCCTCATA 59.279 40.000 0.00 0.00 0.00 2.15
1352 8218 1.186200 AGGCATCAGCTACTTCACGA 58.814 50.000 0.00 0.00 41.70 4.35
1378 8244 4.681978 GTCCTTGACGGTGCGGCT 62.682 66.667 0.00 0.00 35.04 5.52
1380 8246 2.978010 CCTTGACGGTGCGGCTTT 60.978 61.111 0.00 0.00 35.04 3.51
1381 8247 2.252260 CTTGACGGTGCGGCTTTG 59.748 61.111 0.00 0.00 35.04 2.77
1382 8248 3.254014 CTTGACGGTGCGGCTTTGG 62.254 63.158 0.00 0.00 35.04 3.28
1383 8249 4.555709 TGACGGTGCGGCTTTGGT 62.556 61.111 0.00 0.00 35.04 3.67
1384 8250 3.284449 GACGGTGCGGCTTTGGTT 61.284 61.111 0.00 0.00 0.00 3.67
1385 8251 3.249973 GACGGTGCGGCTTTGGTTC 62.250 63.158 0.00 0.00 0.00 3.62
1386 8252 4.038080 CGGTGCGGCTTTGGTTCC 62.038 66.667 0.00 0.00 0.00 3.62
1387 8253 2.597510 GGTGCGGCTTTGGTTCCT 60.598 61.111 0.00 0.00 0.00 3.36
1388 8254 2.626780 GGTGCGGCTTTGGTTCCTC 61.627 63.158 0.00 0.00 0.00 3.71
1408 8286 8.417106 GTTCCTCCTTTGATTTCTTCTTCTTTT 58.583 33.333 0.00 0.00 0.00 2.27
1427 8305 7.553881 TCTTTTCTGTTCTTAACTGTTGGAG 57.446 36.000 2.69 1.60 0.00 3.86
1429 8307 4.415881 TCTGTTCTTAACTGTTGGAGCA 57.584 40.909 2.69 8.57 0.00 4.26
1484 8362 4.651994 CTGCGACATGGAAATTTCAGTAC 58.348 43.478 19.49 10.46 0.00 2.73
1595 8477 3.018423 ACCATCTGCCCAAGATTTACC 57.982 47.619 0.00 0.00 43.52 2.85
1871 8859 6.182039 TGTGAACTGCTGAATATTACTTGC 57.818 37.500 0.00 0.00 0.00 4.01
1892 8880 6.057627 TGCCAAGCATGTTGTTTTATTTTG 57.942 33.333 0.00 0.00 31.71 2.44
1915 8903 3.681897 GTGAGAAGTAACTGACATGCCTG 59.318 47.826 0.00 0.00 0.00 4.85
1918 8906 2.770164 AGTAACTGACATGCCTGGAC 57.230 50.000 0.00 0.00 0.00 4.02
2034 11540 3.763897 AGGGGTTTGTATGCAGTGAATTC 59.236 43.478 0.00 0.00 0.00 2.17
2051 11564 5.874810 GTGAATTCTTCATGCTAGTGGTGTA 59.125 40.000 7.05 0.00 42.47 2.90
2054 11567 4.456280 TCTTCATGCTAGTGGTGTACTG 57.544 45.455 0.00 0.00 40.65 2.74
2062 11575 0.763035 AGTGGTGTACTGGTGTTCCC 59.237 55.000 0.00 0.00 38.49 3.97
2064 11577 1.053424 TGGTGTACTGGTGTTCCCTC 58.947 55.000 0.00 0.00 0.00 4.30
2080 11593 2.887151 CCTCACAGGGGTCTGAATTT 57.113 50.000 0.00 0.00 43.49 1.82
2081 11594 3.160679 CCTCACAGGGGTCTGAATTTT 57.839 47.619 0.00 0.00 43.49 1.82
2082 11595 3.500343 CCTCACAGGGGTCTGAATTTTT 58.500 45.455 0.00 0.00 43.49 1.94
2083 11596 3.256631 CCTCACAGGGGTCTGAATTTTTG 59.743 47.826 0.00 0.00 43.49 2.44
2084 11597 3.891366 CTCACAGGGGTCTGAATTTTTGT 59.109 43.478 0.00 0.00 43.49 2.83
2086 11599 3.636300 CACAGGGGTCTGAATTTTTGTGA 59.364 43.478 0.00 0.00 43.49 3.58
2125 11667 5.865085 TGTTGTACTTGAAGGCTGAAGTAT 58.135 37.500 17.68 0.67 37.10 2.12
2128 11670 6.222038 TGTACTTGAAGGCTGAAGTATAGG 57.778 41.667 17.68 0.00 37.10 2.57
2145 11687 7.687941 AGTATAGGTTGTTTTCTGTCAATGG 57.312 36.000 0.00 0.00 0.00 3.16
2203 11747 1.733912 TCTCGCTGTTGCATTGATGTC 59.266 47.619 0.00 0.00 39.64 3.06
2214 11758 3.228749 GCATTGATGTCTGAAACACACG 58.771 45.455 0.00 0.00 41.75 4.49
2413 12007 2.634940 TCTACCATCTGGCCTAATGCTC 59.365 50.000 3.32 0.00 40.92 4.26
2534 14731 2.666812 CGGGGGTTCTGGTGGTAC 59.333 66.667 0.00 0.00 0.00 3.34
2535 14732 2.963101 CGGGGGTTCTGGTGGTACC 61.963 68.421 4.43 4.43 39.22 3.34
2536 14733 2.666812 GGGGTTCTGGTGGTACCG 59.333 66.667 7.57 0.00 42.58 4.02
2537 14734 2.666812 GGGTTCTGGTGGTACCGG 59.333 66.667 7.57 0.00 46.14 5.28
2538 14735 2.046604 GGTTCTGGTGGTACCGGC 60.047 66.667 7.57 2.35 44.40 6.13
2539 14736 2.433664 GTTCTGGTGGTACCGGCG 60.434 66.667 7.57 0.00 44.40 6.46
2540 14737 3.697747 TTCTGGTGGTACCGGCGG 61.698 66.667 27.06 27.06 44.40 6.13
2542 14739 4.752879 CTGGTGGTACCGGCGGTG 62.753 72.222 39.80 18.70 42.58 4.94
2545 14742 4.692475 GTGGTACCGGCGGTGCTT 62.692 66.667 38.67 18.75 38.37 3.91
2546 14743 3.943691 TGGTACCGGCGGTGCTTT 61.944 61.111 38.67 18.37 38.37 3.51
2547 14744 3.122971 GGTACCGGCGGTGCTTTC 61.123 66.667 38.67 23.31 38.37 2.62
2548 14745 3.484547 GTACCGGCGGTGCTTTCG 61.485 66.667 39.80 8.00 36.19 3.46
2549 14746 4.745751 TACCGGCGGTGCTTTCGG 62.746 66.667 39.80 7.18 46.95 4.30
2648 14911 3.601443 TCCTAGAGTGCTCTGCTTTTC 57.399 47.619 11.63 0.00 40.71 2.29
2659 14922 5.353678 GTGCTCTGCTTTTCATCAGTCTATT 59.646 40.000 0.00 0.00 0.00 1.73
2675 14938 9.814899 ATCAGTCTATTGTAATATCTAGCATGC 57.185 33.333 10.51 10.51 0.00 4.06
2980 15284 0.030638 CACCGTTTGCTCTTGTTGGG 59.969 55.000 0.00 0.00 0.00 4.12
3058 15382 2.794103 TCAGTTACCATGCACTGCAAT 58.206 42.857 8.03 0.00 43.62 3.56
3123 15448 4.743348 GCAATCCAAATTGTTGTCCACCTT 60.743 41.667 0.00 0.00 43.54 3.50
3124 15449 5.367302 CAATCCAAATTGTTGTCCACCTTT 58.633 37.500 0.00 0.00 37.97 3.11
3126 15451 5.428184 TCCAAATTGTTGTCCACCTTTTT 57.572 34.783 0.00 0.00 32.40 1.94
3152 15477 7.897575 TTTGGCATCAAAATTGTTATACACC 57.102 32.000 0.00 0.00 39.64 4.16
3188 15513 0.607217 CTGCTCATCACCAGGTGCAA 60.607 55.000 15.64 0.00 32.98 4.08
3189 15514 0.178995 TGCTCATCACCAGGTGCAAA 60.179 50.000 15.64 0.00 32.98 3.68
3228 15554 3.093057 TGCCCTGTACTGTTTTTGTTGT 58.907 40.909 0.00 0.00 0.00 3.32
3229 15555 4.270834 TGCCCTGTACTGTTTTTGTTGTA 58.729 39.130 0.00 0.00 0.00 2.41
3230 15556 4.096682 TGCCCTGTACTGTTTTTGTTGTAC 59.903 41.667 0.00 0.00 36.69 2.90
3231 15557 4.337274 GCCCTGTACTGTTTTTGTTGTACT 59.663 41.667 0.00 0.00 36.98 2.73
3255 15581 4.991153 TGTCAAGGTGTTGTGCATTTTA 57.009 36.364 0.00 0.00 34.98 1.52
3273 15599 6.258947 GCATTTTACTCTGACTCTTACCCATC 59.741 42.308 0.00 0.00 0.00 3.51
3302 15730 9.965902 ATCCAAATCTAGTCAAGTATCTTTTGT 57.034 29.630 0.00 0.00 0.00 2.83
3303 15731 9.793259 TCCAAATCTAGTCAAGTATCTTTTGTT 57.207 29.630 0.00 0.00 0.00 2.83
3305 15733 9.831737 CAAATCTAGTCAAGTATCTTTTGTTGG 57.168 33.333 0.00 0.00 0.00 3.77
3306 15734 9.793259 AAATCTAGTCAAGTATCTTTTGTTGGA 57.207 29.630 0.00 0.00 0.00 3.53
3308 15736 9.965902 ATCTAGTCAAGTATCTTTTGTTGGAAT 57.034 29.630 0.00 0.00 0.00 3.01
3309 15737 9.793259 TCTAGTCAAGTATCTTTTGTTGGAATT 57.207 29.630 0.00 0.00 0.00 2.17
3488 16241 0.173255 AATTAGCAATGTGCCCGTGC 59.827 50.000 0.00 0.00 46.52 5.34
3500 16253 3.361158 CCGTGCGTTGCCATGGAA 61.361 61.111 18.40 0.00 43.20 3.53
3523 16276 9.899226 GGAACCAAAGTAGAATAATGCATATTC 57.101 33.333 0.00 9.79 46.92 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 8.924511 ACGAGAATCCATAATATCAAATTGGT 57.075 30.769 0.00 0.00 0.00 3.67
186 187 9.990360 TTCTGAAAAGTCAAACCTTTTAAGTTT 57.010 25.926 9.49 0.00 42.98 2.66
187 188 9.990360 TTTCTGAAAAGTCAAACCTTTTAAGTT 57.010 25.926 0.00 0.00 42.98 2.66
188 189 9.990360 TTTTCTGAAAAGTCAAACCTTTTAAGT 57.010 25.926 11.33 0.00 42.98 2.24
251 252 9.945904 TTGGTGTTGTTAGGTTTCTTAAAAATT 57.054 25.926 0.00 0.00 0.00 1.82
252 253 9.945904 TTTGGTGTTGTTAGGTTTCTTAAAAAT 57.054 25.926 0.00 0.00 0.00 1.82
253 254 9.425577 CTTTGGTGTTGTTAGGTTTCTTAAAAA 57.574 29.630 0.00 0.00 0.00 1.94
254 255 8.035984 CCTTTGGTGTTGTTAGGTTTCTTAAAA 58.964 33.333 0.00 0.00 0.00 1.52
255 256 7.178805 ACCTTTGGTGTTGTTAGGTTTCTTAAA 59.821 33.333 0.00 0.00 35.77 1.52
256 257 6.664384 ACCTTTGGTGTTGTTAGGTTTCTTAA 59.336 34.615 0.00 0.00 35.77 1.85
258 259 5.020795 ACCTTTGGTGTTGTTAGGTTTCTT 58.979 37.500 0.00 0.00 35.77 2.52
259 260 4.606210 ACCTTTGGTGTTGTTAGGTTTCT 58.394 39.130 0.00 0.00 35.77 2.52
260 261 4.994907 ACCTTTGGTGTTGTTAGGTTTC 57.005 40.909 0.00 0.00 35.77 2.78
273 274 1.405391 GCACTTTGTTGCACCTTTGGT 60.405 47.619 0.00 0.00 42.49 3.67
274 275 1.289276 GCACTTTGTTGCACCTTTGG 58.711 50.000 0.00 0.00 42.49 3.28
276 277 0.805711 GCGCACTTTGTTGCACCTTT 60.806 50.000 0.30 0.00 43.15 3.11
277 278 1.226945 GCGCACTTTGTTGCACCTT 60.227 52.632 0.30 0.00 43.15 3.50
278 279 2.412937 GCGCACTTTGTTGCACCT 59.587 55.556 0.30 0.00 43.15 4.00
279 280 2.658268 GGCGCACTTTGTTGCACC 60.658 61.111 10.83 0.00 43.15 5.01
280 281 2.658268 GGGCGCACTTTGTTGCAC 60.658 61.111 10.83 0.00 43.15 4.57
281 282 2.714991 TTGGGCGCACTTTGTTGCA 61.715 52.632 12.74 0.00 43.15 4.08
284 285 1.326951 AAGGTTGGGCGCACTTTGTT 61.327 50.000 12.74 0.00 0.00 2.83
285 286 1.734388 GAAGGTTGGGCGCACTTTGT 61.734 55.000 12.74 0.00 0.00 2.83
287 288 0.109723 TAGAAGGTTGGGCGCACTTT 59.890 50.000 12.74 1.56 0.00 2.66
289 290 1.296715 CTAGAAGGTTGGGCGCACT 59.703 57.895 12.74 0.00 0.00 4.40
290 291 0.605589 AACTAGAAGGTTGGGCGCAC 60.606 55.000 10.83 6.04 0.00 5.34
291 292 0.605319 CAACTAGAAGGTTGGGCGCA 60.605 55.000 10.83 0.00 41.78 6.09
292 293 0.321298 TCAACTAGAAGGTTGGGCGC 60.321 55.000 0.00 0.00 44.52 6.53
293 294 2.403252 ATCAACTAGAAGGTTGGGCG 57.597 50.000 0.00 0.00 44.52 6.13
294 295 6.072452 GCATAATATCAACTAGAAGGTTGGGC 60.072 42.308 0.00 0.00 44.52 5.36
295 296 7.227156 AGCATAATATCAACTAGAAGGTTGGG 58.773 38.462 0.00 0.00 44.52 4.12
328 3789 9.186323 GCTTGAGTTTTCTCCTTATTTTCTTTC 57.814 33.333 0.00 0.00 45.63 2.62
331 3792 7.040132 CCAGCTTGAGTTTTCTCCTTATTTTCT 60.040 37.037 0.00 0.00 45.63 2.52
332 3793 7.087007 CCAGCTTGAGTTTTCTCCTTATTTTC 58.913 38.462 0.00 0.00 45.63 2.29
344 3805 3.088532 TGTTGTCACCAGCTTGAGTTTT 58.911 40.909 0.00 0.00 0.00 2.43
366 3827 9.278978 TGCAAGTTCTACTCAATATGTTGTAAA 57.721 29.630 1.86 0.00 36.69 2.01
474 3936 7.222000 AGTTTTGTGTTAGGAACTTCAAACA 57.778 32.000 5.32 5.32 41.75 2.83
475 3937 9.285770 CTTAGTTTTGTGTTAGGAACTTCAAAC 57.714 33.333 10.38 7.31 41.75 2.93
479 3941 8.890718 AGAACTTAGTTTTGTGTTAGGAACTTC 58.109 33.333 0.00 0.00 41.75 3.01
483 3945 6.038936 GCCAGAACTTAGTTTTGTGTTAGGAA 59.961 38.462 13.37 0.00 0.00 3.36
501 3963 0.798776 CTCCAATCGTGTGCCAGAAC 59.201 55.000 0.00 0.00 0.00 3.01
518 3980 7.645402 TCATGTGACAATGAAATATGATGCTC 58.355 34.615 0.00 0.00 33.63 4.26
608 6082 4.002797 GCACACTTGGGCCTAAGG 57.997 61.111 30.00 21.08 38.87 2.69
783 7623 0.543749 GGCAGCAGATGGGTCTAGTT 59.456 55.000 0.00 0.00 32.09 2.24
815 7655 1.226603 GTTCCTGGATCGACGGTCG 60.227 63.158 23.73 23.73 42.10 4.79
877 7717 3.138798 GCCAGCCGTCCTCGAGTA 61.139 66.667 12.31 0.00 39.71 2.59
1042 7891 1.971167 GACCTGCATTGGGTCGCAA 60.971 57.895 7.77 4.63 42.84 4.85
1210 8066 5.814705 GTGTATGAGGAGAGAGTTTTGGATG 59.185 44.000 0.00 0.00 0.00 3.51
1211 8067 5.394663 CGTGTATGAGGAGAGAGTTTTGGAT 60.395 44.000 0.00 0.00 0.00 3.41
1352 8218 2.342648 GTCAAGGACGGACGCCTT 59.657 61.111 12.42 12.42 46.36 4.35
1377 8243 6.266330 AGAAGAAATCAAAGGAGGAACCAAAG 59.734 38.462 0.00 0.00 42.04 2.77
1378 8244 6.136155 AGAAGAAATCAAAGGAGGAACCAAA 58.864 36.000 0.00 0.00 42.04 3.28
1380 8246 5.324832 AGAAGAAATCAAAGGAGGAACCA 57.675 39.130 0.00 0.00 42.04 3.67
1381 8247 6.007076 AGAAGAAGAAATCAAAGGAGGAACC 58.993 40.000 0.00 0.00 39.35 3.62
1382 8248 7.517614 AAGAAGAAGAAATCAAAGGAGGAAC 57.482 36.000 0.00 0.00 0.00 3.62
1383 8249 8.539117 AAAAGAAGAAGAAATCAAAGGAGGAA 57.461 30.769 0.00 0.00 0.00 3.36
1384 8250 8.001292 AGAAAAGAAGAAGAAATCAAAGGAGGA 58.999 33.333 0.00 0.00 0.00 3.71
1385 8251 8.081025 CAGAAAAGAAGAAGAAATCAAAGGAGG 58.919 37.037 0.00 0.00 0.00 4.30
1386 8252 8.628280 ACAGAAAAGAAGAAGAAATCAAAGGAG 58.372 33.333 0.00 0.00 0.00 3.69
1387 8253 8.525290 ACAGAAAAGAAGAAGAAATCAAAGGA 57.475 30.769 0.00 0.00 0.00 3.36
1388 8254 9.242477 GAACAGAAAAGAAGAAGAAATCAAAGG 57.758 33.333 0.00 0.00 0.00 3.11
1408 8286 4.380531 CTGCTCCAACAGTTAAGAACAGA 58.619 43.478 9.05 0.00 32.78 3.41
1427 8305 2.032634 TTTGATCCGCGACCACTGC 61.033 57.895 8.23 0.00 0.00 4.40
1429 8307 0.670546 CAGTTTGATCCGCGACCACT 60.671 55.000 8.23 0.00 0.00 4.00
1433 8311 1.421485 CAGCAGTTTGATCCGCGAC 59.579 57.895 8.23 0.00 0.00 5.19
1466 8344 3.438781 TGCGGTACTGAAATTTCCATGTC 59.561 43.478 15.48 2.46 0.00 3.06
1469 8347 2.752903 GGTGCGGTACTGAAATTTCCAT 59.247 45.455 15.48 6.17 0.00 3.41
1484 8362 0.103937 GGATCAGAGAAGAGGTGCGG 59.896 60.000 0.00 0.00 0.00 5.69
1595 8477 3.123620 GCACCAGCGCTCCTTGAG 61.124 66.667 7.13 0.00 0.00 3.02
1741 8623 8.357402 ACTAACTACCAATTGAACATGGAAAAC 58.643 33.333 7.12 0.00 39.12 2.43
1871 8859 6.259608 TCACCAAAATAAAACAACATGCTTGG 59.740 34.615 4.44 0.00 37.42 3.61
1892 8880 3.003480 GGCATGTCAGTTACTTCTCACC 58.997 50.000 0.00 0.00 0.00 4.02
2034 11540 3.055819 ACCAGTACACCACTAGCATGAAG 60.056 47.826 0.00 0.00 34.98 3.02
2051 11564 2.145865 CCTGTGAGGGAACACCAGT 58.854 57.895 0.00 0.00 43.89 4.00
2062 11575 3.891366 ACAAAAATTCAGACCCCTGTGAG 59.109 43.478 0.00 0.00 41.16 3.51
2064 11577 3.636300 TCACAAAAATTCAGACCCCTGTG 59.364 43.478 0.00 0.00 41.16 3.66
2098 11640 3.820467 TCAGCCTTCAAGTACAACATTGG 59.180 43.478 0.00 0.00 0.00 3.16
2125 11667 5.068460 CCAACCATTGACAGAAAACAACCTA 59.932 40.000 0.00 0.00 0.00 3.08
2128 11670 4.754322 ACCAACCATTGACAGAAAACAAC 58.246 39.130 0.00 0.00 0.00 3.32
2145 11687 5.246307 ACAAGGAATAGCTAGACAACCAAC 58.754 41.667 0.00 0.00 0.00 3.77
2203 11747 1.487482 TCGAAGCTCGTGTGTTTCAG 58.513 50.000 0.00 0.00 41.35 3.02
2214 11758 3.988819 AGCTAAAGGATCATCGAAGCTC 58.011 45.455 5.53 0.00 33.78 4.09
2413 12007 3.603532 AGTATCAGCCACATGACACAAG 58.396 45.455 0.00 0.00 28.73 3.16
2675 14938 3.668447 AGACAGAACAACATACTGGCAG 58.332 45.455 14.16 14.16 41.55 4.85
2952 15256 2.591311 GCAAACGGTGAGCGACGAA 61.591 57.895 12.27 0.00 0.00 3.85
2958 15262 0.663153 AACAAGAGCAAACGGTGAGC 59.337 50.000 0.00 0.00 0.00 4.26
2980 15284 8.398665 ACAAGCGATGAGGAAAATAGATAAAAC 58.601 33.333 0.00 0.00 0.00 2.43
3058 15382 6.723977 ACCAAAAACTAGAATCTGGCCAAATA 59.276 34.615 7.01 0.00 0.00 1.40
3128 15453 7.675062 AGGTGTATAACAATTTTGATGCCAAA 58.325 30.769 0.00 0.00 40.24 3.28
3129 15454 7.238486 AGGTGTATAACAATTTTGATGCCAA 57.762 32.000 0.00 0.00 0.00 4.52
3130 15455 6.849085 AGGTGTATAACAATTTTGATGCCA 57.151 33.333 0.00 0.00 0.00 4.92
3131 15456 7.996385 ACTAGGTGTATAACAATTTTGATGCC 58.004 34.615 0.00 0.00 0.00 4.40
3134 15459 9.847224 CCCTACTAGGTGTATAACAATTTTGAT 57.153 33.333 1.25 0.00 31.93 2.57
3135 15460 7.771826 GCCCTACTAGGTGTATAACAATTTTGA 59.228 37.037 1.25 0.00 31.93 2.69
3136 15461 7.554835 TGCCCTACTAGGTGTATAACAATTTTG 59.445 37.037 1.25 0.00 31.93 2.44
3137 15462 7.635648 TGCCCTACTAGGTGTATAACAATTTT 58.364 34.615 1.25 0.00 31.93 1.82
3138 15463 7.202972 TGCCCTACTAGGTGTATAACAATTT 57.797 36.000 1.25 0.00 31.93 1.82
3139 15464 6.688156 GCTGCCCTACTAGGTGTATAACAATT 60.688 42.308 1.25 0.00 31.93 2.32
3140 15465 5.221661 GCTGCCCTACTAGGTGTATAACAAT 60.222 44.000 1.25 0.00 31.93 2.71
3141 15466 4.100498 GCTGCCCTACTAGGTGTATAACAA 59.900 45.833 1.25 0.00 31.93 2.83
3142 15467 3.640029 GCTGCCCTACTAGGTGTATAACA 59.360 47.826 1.25 0.00 31.93 2.41
3143 15468 3.006644 GGCTGCCCTACTAGGTGTATAAC 59.993 52.174 7.66 0.00 31.93 1.89
3144 15469 3.116862 AGGCTGCCCTACTAGGTGTATAA 60.117 47.826 16.57 0.00 40.58 0.98
3145 15470 2.449730 AGGCTGCCCTACTAGGTGTATA 59.550 50.000 16.57 0.00 40.58 1.47
3146 15471 1.220750 AGGCTGCCCTACTAGGTGTAT 59.779 52.381 16.57 0.00 40.58 2.29
3147 15472 0.635009 AGGCTGCCCTACTAGGTGTA 59.365 55.000 16.57 0.00 40.58 2.90
3148 15473 0.978146 CAGGCTGCCCTACTAGGTGT 60.978 60.000 16.57 0.00 40.33 4.16
3149 15474 0.978146 ACAGGCTGCCCTACTAGGTG 60.978 60.000 16.57 6.91 40.33 4.00
3150 15475 0.688087 GACAGGCTGCCCTACTAGGT 60.688 60.000 16.57 2.37 40.33 3.08
3151 15476 0.397816 AGACAGGCTGCCCTACTAGG 60.398 60.000 16.57 0.00 40.33 3.02
3152 15477 0.749649 CAGACAGGCTGCCCTACTAG 59.250 60.000 16.57 1.20 40.33 2.57
3188 15513 2.616510 GCAGACAAGCTCCCACAGTATT 60.617 50.000 0.00 0.00 0.00 1.89
3189 15514 1.065854 GCAGACAAGCTCCCACAGTAT 60.066 52.381 0.00 0.00 0.00 2.12
3228 15554 4.709250 TGCACAACACCTTGACAATAGTA 58.291 39.130 0.00 0.00 0.00 1.82
3229 15555 3.550820 TGCACAACACCTTGACAATAGT 58.449 40.909 0.00 0.00 0.00 2.12
3230 15556 4.771590 ATGCACAACACCTTGACAATAG 57.228 40.909 0.00 0.00 0.00 1.73
3231 15557 5.528043 AAATGCACAACACCTTGACAATA 57.472 34.783 0.00 0.00 0.00 1.90
3255 15581 3.474798 TGGATGGGTAAGAGTCAGAGT 57.525 47.619 0.00 0.00 0.00 3.24
3273 15599 8.970859 AAGATACTTGACTAGATTTGGATTGG 57.029 34.615 0.00 0.00 0.00 3.16
3300 15728 4.085733 CTCCACCCATACAAATTCCAACA 58.914 43.478 0.00 0.00 0.00 3.33
3301 15729 4.086457 ACTCCACCCATACAAATTCCAAC 58.914 43.478 0.00 0.00 0.00 3.77
3302 15730 4.340617 GACTCCACCCATACAAATTCCAA 58.659 43.478 0.00 0.00 0.00 3.53
3303 15731 3.308832 GGACTCCACCCATACAAATTCCA 60.309 47.826 0.00 0.00 0.00 3.53
3305 15733 2.943033 CGGACTCCACCCATACAAATTC 59.057 50.000 0.00 0.00 0.00 2.17
3306 15734 2.307686 ACGGACTCCACCCATACAAATT 59.692 45.455 0.00 0.00 0.00 1.82
3308 15736 1.002659 CACGGACTCCACCCATACAAA 59.997 52.381 0.00 0.00 0.00 2.83
3309 15737 0.611200 CACGGACTCCACCCATACAA 59.389 55.000 0.00 0.00 0.00 2.41
3310 15738 1.261938 CCACGGACTCCACCCATACA 61.262 60.000 0.00 0.00 0.00 2.29
3311 15739 1.520666 CCACGGACTCCACCCATAC 59.479 63.158 0.00 0.00 0.00 2.39
3488 16241 0.673437 ACTTTGGTTCCATGGCAACG 59.327 50.000 6.96 6.21 42.51 4.10
3494 16247 7.099266 TGCATTATTCTACTTTGGTTCCATG 57.901 36.000 0.00 0.00 0.00 3.66
3500 16253 9.407380 TGTGAATATGCATTATTCTACTTTGGT 57.593 29.630 20.11 0.00 44.43 3.67


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

AutoCloner maintained by Alex Coulton.