Multiple sequence alignment - TraesCS1D01G344500

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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 TraesCS1D01G344500 chr1D 100.000 3324 0 0 1 3324 433091641 433094964 0.000000e+00 6139.0
1 TraesCS1D01G344500 chr1D 91.459 1487 83 15 1461 2939 433143196 433144646 0.000000e+00 2002.0
2 TraesCS1D01G344500 chr1D 86.742 1780 125 55 639 2401 433060266 433061951 0.000000e+00 1877.0
3 TraesCS1D01G344500 chr1D 86.667 285 32 1 3040 3324 433144656 433144934 8.950000e-81 311.0
4 TraesCS1D01G344500 chr1D 90.972 144 8 2 180 323 433059721 433059859 4.380000e-44 189.0
5 TraesCS1D01G344500 chr1D 87.179 117 6 4 664 773 433140787 433140901 1.250000e-24 124.0
6 TraesCS1D01G344500 chr1D 80.769 182 10 2 96 254 433127196 433127375 5.830000e-23 119.0
7 TraesCS1D01G344500 chr1D 92.308 78 4 2 262 337 433129493 433129570 3.510000e-20 110.0
8 TraesCS1D01G344500 chr1B 90.336 2173 117 34 393 2539 584761445 584763550 0.000000e+00 2763.0
9 TraesCS1D01G344500 chr1B 90.588 2008 105 31 393 2376 584778732 584780679 0.000000e+00 2584.0
10 TraesCS1D01G344500 chr1B 88.986 2052 135 43 379 2384 584619810 584621816 0.000000e+00 2453.0
11 TraesCS1D01G344500 chr1B 88.889 2052 137 46 379 2384 584574449 584576455 0.000000e+00 2442.0
12 TraesCS1D01G344500 chr1B 89.263 1574 93 29 829 2376 584797948 584799471 0.000000e+00 1901.0
13 TraesCS1D01G344500 chr1B 86.114 1714 139 32 700 2384 584603540 584605183 0.000000e+00 1757.0
14 TraesCS1D01G344500 chr1B 87.816 870 69 13 1526 2384 584566230 584567073 0.000000e+00 985.0
15 TraesCS1D01G344500 chr1B 95.759 448 15 3 393 839 584797095 584797539 0.000000e+00 719.0
16 TraesCS1D01G344500 chr1B 91.525 295 21 4 92 383 584574116 584574409 1.440000e-108 403.0
17 TraesCS1D01G344500 chr1B 91.525 295 21 4 92 383 584619477 584619770 1.440000e-108 403.0
18 TraesCS1D01G344500 chr1B 80.905 199 13 2 96 271 584874761 584874957 2.080000e-27 134.0
19 TraesCS1D01G344500 chr1B 87.395 119 11 2 422 537 584875083 584875200 2.080000e-27 134.0
20 TraesCS1D01G344500 chr1B 80.905 199 13 2 96 271 584901164 584901360 2.080000e-27 134.0
21 TraesCS1D01G344500 chr1B 87.395 119 11 2 422 537 584901486 584901603 2.080000e-27 134.0
22 TraesCS1D01G344500 chr1A 90.482 1576 106 21 978 2539 531513133 531514678 0.000000e+00 2039.0
23 TraesCS1D01G344500 chr1A 89.530 1576 121 24 978 2539 531561962 531563507 0.000000e+00 1956.0
24 TraesCS1D01G344500 chr1A 91.955 1243 68 12 966 2191 531366994 531368221 0.000000e+00 1712.0
25 TraesCS1D01G344500 chr1A 95.833 288 12 0 96 383 531501652 531501939 1.810000e-127 466.0
26 TraesCS1D01G344500 chr1A 95.439 285 10 3 379 662 531501979 531502261 5.060000e-123 451.0
27 TraesCS1D01G344500 chr1A 86.073 438 33 17 379 808 531561460 531561877 2.350000e-121 446.0
28 TraesCS1D01G344500 chr1A 91.216 296 19 6 92 383 531561128 531561420 2.400000e-106 396.0
29 TraesCS1D01G344500 chr1A 94.355 248 13 1 623 870 531502261 531502507 2.420000e-101 379.0
30 TraesCS1D01G344500 chr1A 87.013 231 16 8 704 927 531512910 531513133 7.120000e-62 248.0
31 TraesCS1D01G344500 chr1A 91.724 145 8 4 180 323 531366137 531366278 7.270000e-47 198.0
32 TraesCS1D01G344500 chr1A 76.657 347 44 19 218 543 531509821 531510151 1.230000e-34 158.0
33 TraesCS1D01G344500 chr1A 92.000 75 2 2 857 927 531561888 531561962 5.870000e-18 102.0
34 TraesCS1D01G344500 chr1A 89.552 67 5 2 111 177 531366040 531366104 2.130000e-12 84.2
35 TraesCS1D01G344500 chr1A 87.013 77 7 2 539 613 531510309 531510384 2.130000e-12 84.2
36 TraesCS1D01G344500 chr1A 100.000 33 0 0 180 212 531509696 531509728 9.960000e-06 62.1
37 TraesCS1D01G344500 chr3D 84.976 1644 140 60 715 2333 485232666 485231105 0.000000e+00 1568.0
38 TraesCS1D01G344500 chr3D 83.189 577 67 15 2756 3316 532235118 532234556 4.950000e-138 501.0
39 TraesCS1D01G344500 chr3D 80.000 495 58 22 2728 3194 315745403 315745884 8.890000e-86 327.0
40 TraesCS1D01G344500 chr3D 87.179 195 20 5 2538 2730 26296739 26296548 2.010000e-52 217.0
41 TraesCS1D01G344500 chr3B 87.527 1379 115 33 958 2314 647943952 647942609 0.000000e+00 1541.0
42 TraesCS1D01G344500 chr3B 87.956 548 41 16 958 1500 647969359 647968832 1.010000e-174 623.0
43 TraesCS1D01G344500 chr3B 81.868 364 44 13 2963 3317 573365193 573364843 1.510000e-73 287.0
44 TraesCS1D01G344500 chr3B 85.204 196 22 5 2538 2731 44000194 44000004 9.410000e-46 195.0
45 TraesCS1D01G344500 chr3B 84.694 196 23 5 2538 2731 43893749 43893559 4.380000e-44 189.0
46 TraesCS1D01G344500 chr3A 87.136 1407 108 34 958 2333 628220252 628218888 0.000000e+00 1528.0
47 TraesCS1D01G344500 chr3A 83.366 517 66 11 2756 3257 667496163 667495652 8.400000e-126 460.0
48 TraesCS1D01G344500 chr3A 77.383 535 74 24 2808 3315 364450595 364450081 1.170000e-69 274.0
49 TraesCS1D01G344500 chr2B 84.833 600 81 7 2728 3324 183263913 183264505 2.210000e-166 595.0
50 TraesCS1D01G344500 chr2B 82.886 298 44 3 3028 3324 383065745 383065454 9.150000e-66 261.0
51 TraesCS1D01G344500 chr5A 82.372 624 73 24 2728 3317 407932257 407932877 2.960000e-140 508.0
52 TraesCS1D01G344500 chr4B 81.728 602 86 10 2728 3324 539502183 539501601 6.450000e-132 481.0
53 TraesCS1D01G344500 chr4D 80.880 591 83 20 2730 3317 421510841 421510278 3.940000e-119 438.0
54 TraesCS1D01G344500 chr4D 79.365 504 61 22 2757 3248 478234489 478234961 6.920000e-82 315.0
55 TraesCS1D01G344500 chr4D 85.020 247 31 5 2728 2973 478034971 478034730 2.560000e-61 246.0
56 TraesCS1D01G344500 chr7D 80.214 561 65 23 2775 3320 205727806 205727277 2.420000e-101 379.0
57 TraesCS1D01G344500 chr6B 79.576 519 72 19 2823 3324 233084957 233085458 1.140000e-89 340.0
58 TraesCS1D01G344500 chr6B 79.684 443 70 16 2736 3164 624805741 624805305 5.390000e-78 302.0
59 TraesCS1D01G344500 chr2D 79.515 454 72 17 2728 3177 8300179 8300615 1.500000e-78 303.0
60 TraesCS1D01G344500 chr2D 84.656 189 24 5 2546 2731 131631259 131631073 2.040000e-42 183.0
61 TraesCS1D01G344500 chr5D 86.842 190 24 1 2541 2729 247504627 247504438 9.340000e-51 211.0
62 TraesCS1D01G344500 chr5D 83.246 191 24 8 2541 2728 555074794 555074609 5.700000e-38 169.0
63 TraesCS1D01G344500 chr4A 86.294 197 22 5 2541 2735 255336727 255336534 3.360000e-50 209.0
64 TraesCS1D01G344500 chr5B 83.673 196 29 3 2538 2731 281250092 281250286 7.330000e-42 182.0
65 TraesCS1D01G344500 chr6A 96.296 81 3 0 801 881 616689246 616689166 2.080000e-27 134.0


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 TraesCS1D01G344500 chr1D 433091641 433094964 3323 False 6139.000000 6139 100.00000 1 3324 1 chr1D.!!$F1 3323
1 TraesCS1D01G344500 chr1D 433059721 433061951 2230 False 1033.000000 1877 88.85700 180 2401 2 chr1D.!!$F2 2221
2 TraesCS1D01G344500 chr1D 433140787 433144934 4147 False 812.333333 2002 88.43500 664 3324 3 chr1D.!!$F4 2660
3 TraesCS1D01G344500 chr1B 584761445 584763550 2105 False 2763.000000 2763 90.33600 393 2539 1 chr1B.!!$F3 2146
4 TraesCS1D01G344500 chr1B 584778732 584780679 1947 False 2584.000000 2584 90.58800 393 2376 1 chr1B.!!$F4 1983
5 TraesCS1D01G344500 chr1B 584603540 584605183 1643 False 1757.000000 1757 86.11400 700 2384 1 chr1B.!!$F2 1684
6 TraesCS1D01G344500 chr1B 584619477 584621816 2339 False 1428.000000 2453 90.25550 92 2384 2 chr1B.!!$F6 2292
7 TraesCS1D01G344500 chr1B 584574116 584576455 2339 False 1422.500000 2442 90.20700 92 2384 2 chr1B.!!$F5 2292
8 TraesCS1D01G344500 chr1B 584797095 584799471 2376 False 1310.000000 1901 92.51100 393 2376 2 chr1B.!!$F7 1983
9 TraesCS1D01G344500 chr1B 584566230 584567073 843 False 985.000000 985 87.81600 1526 2384 1 chr1B.!!$F1 858
10 TraesCS1D01G344500 chr1A 531561128 531563507 2379 False 725.000000 1956 89.70475 92 2539 4 chr1A.!!$F4 2447
11 TraesCS1D01G344500 chr1A 531366040 531368221 2181 False 664.733333 1712 91.07700 111 2191 3 chr1A.!!$F1 2080
12 TraesCS1D01G344500 chr1A 531509696 531514678 4982 False 518.260000 2039 88.23300 180 2539 5 chr1A.!!$F3 2359
13 TraesCS1D01G344500 chr1A 531501652 531502507 855 False 432.000000 466 95.20900 96 870 3 chr1A.!!$F2 774
14 TraesCS1D01G344500 chr3D 485231105 485232666 1561 True 1568.000000 1568 84.97600 715 2333 1 chr3D.!!$R2 1618
15 TraesCS1D01G344500 chr3D 532234556 532235118 562 True 501.000000 501 83.18900 2756 3316 1 chr3D.!!$R3 560
16 TraesCS1D01G344500 chr3B 647942609 647943952 1343 True 1541.000000 1541 87.52700 958 2314 1 chr3B.!!$R4 1356
17 TraesCS1D01G344500 chr3B 647968832 647969359 527 True 623.000000 623 87.95600 958 1500 1 chr3B.!!$R5 542
18 TraesCS1D01G344500 chr3A 628218888 628220252 1364 True 1528.000000 1528 87.13600 958 2333 1 chr3A.!!$R2 1375
19 TraesCS1D01G344500 chr3A 667495652 667496163 511 True 460.000000 460 83.36600 2756 3257 1 chr3A.!!$R3 501
20 TraesCS1D01G344500 chr3A 364450081 364450595 514 True 274.000000 274 77.38300 2808 3315 1 chr3A.!!$R1 507
21 TraesCS1D01G344500 chr2B 183263913 183264505 592 False 595.000000 595 84.83300 2728 3324 1 chr2B.!!$F1 596
22 TraesCS1D01G344500 chr5A 407932257 407932877 620 False 508.000000 508 82.37200 2728 3317 1 chr5A.!!$F1 589
23 TraesCS1D01G344500 chr4B 539501601 539502183 582 True 481.000000 481 81.72800 2728 3324 1 chr4B.!!$R1 596
24 TraesCS1D01G344500 chr4D 421510278 421510841 563 True 438.000000 438 80.88000 2730 3317 1 chr4D.!!$R1 587
25 TraesCS1D01G344500 chr7D 205727277 205727806 529 True 379.000000 379 80.21400 2775 3320 1 chr7D.!!$R1 545
26 TraesCS1D01G344500 chr6B 233084957 233085458 501 False 340.000000 340 79.57600 2823 3324 1 chr6B.!!$F1 501

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
740 3644 0.035176 GGCAACAACCCGGTGTAGTA 59.965 55.0 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 7737 0.10212 TTTTGCCACTTGTGGAAGCG 59.898 50.0 22.52 0.0 31.68 4.68 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
20 21 2.450476 GATGGATCCTTGTTGCTTGGT 58.550 47.619 14.23 0.00 0.00 3.67
21 22 2.380064 TGGATCCTTGTTGCTTGGTT 57.620 45.000 14.23 0.00 0.00 3.67
22 23 2.676748 TGGATCCTTGTTGCTTGGTTT 58.323 42.857 14.23 0.00 0.00 3.27
23 24 2.364970 TGGATCCTTGTTGCTTGGTTTG 59.635 45.455 14.23 0.00 0.00 2.93
24 25 2.289010 GGATCCTTGTTGCTTGGTTTGG 60.289 50.000 3.84 0.00 0.00 3.28
25 26 0.463620 TCCTTGTTGCTTGGTTTGGC 59.536 50.000 0.00 0.00 0.00 4.52
26 27 0.177604 CCTTGTTGCTTGGTTTGGCA 59.822 50.000 0.00 0.00 36.62 4.92
27 28 1.202675 CCTTGTTGCTTGGTTTGGCAT 60.203 47.619 0.00 0.00 38.30 4.40
28 29 2.563702 CTTGTTGCTTGGTTTGGCATT 58.436 42.857 0.00 0.00 38.30 3.56
29 30 2.706339 TGTTGCTTGGTTTGGCATTT 57.294 40.000 0.00 0.00 38.30 2.32
30 31 3.827008 TGTTGCTTGGTTTGGCATTTA 57.173 38.095 0.00 0.00 38.30 1.40
31 32 3.726607 TGTTGCTTGGTTTGGCATTTAG 58.273 40.909 0.00 0.00 38.30 1.85
32 33 3.386078 TGTTGCTTGGTTTGGCATTTAGA 59.614 39.130 0.00 0.00 38.30 2.10
33 34 3.940209 TGCTTGGTTTGGCATTTAGAG 57.060 42.857 0.00 0.00 33.23 2.43
34 35 2.562298 TGCTTGGTTTGGCATTTAGAGG 59.438 45.455 0.00 0.00 33.23 3.69
35 36 2.825532 GCTTGGTTTGGCATTTAGAGGA 59.174 45.455 0.00 0.00 0.00 3.71
36 37 3.258123 GCTTGGTTTGGCATTTAGAGGAA 59.742 43.478 0.00 0.00 0.00 3.36
37 38 4.081476 GCTTGGTTTGGCATTTAGAGGAAT 60.081 41.667 0.00 0.00 0.00 3.01
38 39 5.127031 GCTTGGTTTGGCATTTAGAGGAATA 59.873 40.000 0.00 0.00 0.00 1.75
39 40 6.524101 TTGGTTTGGCATTTAGAGGAATAC 57.476 37.500 0.00 0.00 0.00 1.89
40 41 5.826643 TGGTTTGGCATTTAGAGGAATACT 58.173 37.500 0.00 0.00 0.00 2.12
41 42 6.964464 TGGTTTGGCATTTAGAGGAATACTA 58.036 36.000 0.00 0.00 0.00 1.82
42 43 6.826741 TGGTTTGGCATTTAGAGGAATACTAC 59.173 38.462 0.00 0.00 0.00 2.73
43 44 7.054751 GGTTTGGCATTTAGAGGAATACTACT 58.945 38.462 0.00 0.00 0.00 2.57
44 45 8.208903 GGTTTGGCATTTAGAGGAATACTACTA 58.791 37.037 0.00 0.00 0.00 1.82
45 46 9.043079 GTTTGGCATTTAGAGGAATACTACTAC 57.957 37.037 0.00 0.00 0.00 2.73
46 47 7.907841 TGGCATTTAGAGGAATACTACTACA 57.092 36.000 0.00 0.00 0.00 2.74
47 48 8.313944 TGGCATTTAGAGGAATACTACTACAA 57.686 34.615 0.00 0.00 0.00 2.41
48 49 8.421784 TGGCATTTAGAGGAATACTACTACAAG 58.578 37.037 0.00 0.00 0.00 3.16
49 50 8.639761 GGCATTTAGAGGAATACTACTACAAGA 58.360 37.037 0.00 0.00 0.00 3.02
50 51 9.465985 GCATTTAGAGGAATACTACTACAAGAC 57.534 37.037 0.00 0.00 0.00 3.01
56 57 9.398538 AGAGGAATACTACTACAAGACTACAAG 57.601 37.037 0.00 0.00 0.00 3.16
57 58 9.176460 GAGGAATACTACTACAAGACTACAAGT 57.824 37.037 0.00 0.00 0.00 3.16
58 59 8.958506 AGGAATACTACTACAAGACTACAAGTG 58.041 37.037 0.00 0.00 0.00 3.16
59 60 8.189460 GGAATACTACTACAAGACTACAAGTGG 58.811 40.741 0.00 0.00 0.00 4.00
60 61 5.388408 ACTACTACAAGACTACAAGTGGC 57.612 43.478 0.00 0.00 0.00 5.01
61 62 5.078256 ACTACTACAAGACTACAAGTGGCT 58.922 41.667 0.00 0.00 0.00 4.75
62 63 4.957684 ACTACAAGACTACAAGTGGCTT 57.042 40.909 0.00 0.00 0.00 4.35
63 64 4.884247 ACTACAAGACTACAAGTGGCTTC 58.116 43.478 0.00 0.00 0.00 3.86
64 65 3.838244 ACAAGACTACAAGTGGCTTCA 57.162 42.857 0.00 0.00 0.00 3.02
65 66 4.150897 ACAAGACTACAAGTGGCTTCAA 57.849 40.909 0.00 0.00 0.00 2.69
66 67 3.877508 ACAAGACTACAAGTGGCTTCAAC 59.122 43.478 0.00 0.00 0.00 3.18
67 68 3.838244 AGACTACAAGTGGCTTCAACA 57.162 42.857 0.00 0.00 0.00 3.33
68 69 4.357918 AGACTACAAGTGGCTTCAACAT 57.642 40.909 0.00 0.00 0.00 2.71
69 70 4.718961 AGACTACAAGTGGCTTCAACATT 58.281 39.130 0.00 0.00 0.00 2.71
70 71 4.516698 AGACTACAAGTGGCTTCAACATTG 59.483 41.667 0.00 0.00 0.00 2.82
71 72 4.207165 ACTACAAGTGGCTTCAACATTGT 58.793 39.130 0.00 0.00 35.28 2.71
72 73 4.644685 ACTACAAGTGGCTTCAACATTGTT 59.355 37.500 0.00 0.00 33.31 2.83
73 74 3.784338 ACAAGTGGCTTCAACATTGTTG 58.216 40.909 21.04 21.04 0.00 3.33
74 75 3.446873 ACAAGTGGCTTCAACATTGTTGA 59.553 39.130 24.66 24.66 0.00 3.18
75 76 3.715628 AGTGGCTTCAACATTGTTGAC 57.284 42.857 27.43 18.30 0.00 3.18
76 77 3.023119 AGTGGCTTCAACATTGTTGACA 58.977 40.909 27.43 20.20 0.00 3.58
77 78 3.115554 GTGGCTTCAACATTGTTGACAC 58.884 45.455 27.43 25.52 35.10 3.67
78 79 2.100584 TGGCTTCAACATTGTTGACACC 59.899 45.455 27.43 27.65 0.00 4.16
79 80 2.100584 GGCTTCAACATTGTTGACACCA 59.899 45.455 28.71 17.66 0.00 4.17
80 81 3.243839 GGCTTCAACATTGTTGACACCAT 60.244 43.478 28.71 0.00 0.00 3.55
81 82 4.370917 GCTTCAACATTGTTGACACCATT 58.629 39.130 27.43 0.00 0.00 3.16
82 83 5.508825 GGCTTCAACATTGTTGACACCATTA 60.509 40.000 28.71 16.35 0.00 1.90
83 84 5.630680 GCTTCAACATTGTTGACACCATTAG 59.369 40.000 27.43 20.90 0.00 1.73
84 85 6.707440 TTCAACATTGTTGACACCATTAGT 57.293 33.333 27.43 0.00 0.00 2.24
85 86 7.521423 GCTTCAACATTGTTGACACCATTAGTA 60.521 37.037 27.43 11.21 0.00 1.82
86 87 7.433708 TCAACATTGTTGACACCATTAGTAG 57.566 36.000 24.66 0.00 0.00 2.57
87 88 5.880054 ACATTGTTGACACCATTAGTAGC 57.120 39.130 0.00 0.00 0.00 3.58
88 89 5.560724 ACATTGTTGACACCATTAGTAGCT 58.439 37.500 0.00 0.00 0.00 3.32
89 90 5.643777 ACATTGTTGACACCATTAGTAGCTC 59.356 40.000 0.00 0.00 0.00 4.09
90 91 4.882842 TGTTGACACCATTAGTAGCTCA 57.117 40.909 0.00 0.00 0.00 4.26
94 95 5.675684 TGACACCATTAGTAGCTCATTCA 57.324 39.130 0.00 0.00 0.00 2.57
122 124 5.714806 TCAGGGAAAGTGAAAAAGAGTTTGT 59.285 36.000 0.00 0.00 0.00 2.83
211 246 7.440255 AGCTTTAACGTCTCAGCTAACTAAAAA 59.560 33.333 12.32 0.00 40.92 1.94
212 247 7.529854 GCTTTAACGTCTCAGCTAACTAAAAAC 59.470 37.037 5.74 0.00 0.00 2.43
213 248 5.919272 AACGTCTCAGCTAACTAAAAACC 57.081 39.130 0.00 0.00 0.00 3.27
246 368 3.312421 CAGACGTGACAAATGAACTGGTT 59.688 43.478 0.00 0.00 0.00 3.67
254 376 7.307989 CGTGACAAATGAACTGGTTAAAGAGAT 60.308 37.037 0.00 0.00 0.00 2.75
443 672 8.185003 TCTTTCATTAACGTATGTGACATCTG 57.815 34.615 0.00 0.00 0.00 2.90
461 690 2.159071 TCTGAACGACCGGAAAAACAGA 60.159 45.455 9.46 14.29 0.00 3.41
628 1071 4.688413 GCTTCATATAGTGAACAGCTAGCC 59.312 45.833 12.13 0.00 41.79 3.93
649 3529 6.661669 AGCCGTTTGTTTACTATTTGTGTAC 58.338 36.000 0.00 0.00 0.00 2.90
740 3644 0.035176 GGCAACAACCCGGTGTAGTA 59.965 55.000 0.00 0.00 0.00 1.82
839 3896 0.328592 AGCTAGGTCCTCGAGTGTCA 59.671 55.000 12.31 0.00 0.00 3.58
946 4432 1.405821 CCTATATCCACCGATCGAGGC 59.594 57.143 18.66 0.00 33.69 4.70
1239 6182 2.108514 CGTCGAGGTACGGGCACTA 61.109 63.158 0.00 0.00 42.82 2.74
1307 6550 4.440250 CCGGACTTGACTAATCTCGTTGAT 60.440 45.833 0.00 0.00 36.89 2.57
1355 6599 3.596799 TCCTCCTGGACCCGACCA 61.597 66.667 0.00 0.00 37.46 4.02
1606 6882 2.032528 CCGCTCAAGTTCCTGGCA 59.967 61.111 0.00 0.00 0.00 4.92
1786 7062 4.116328 CTCGCCGCGTTCCTGAGA 62.116 66.667 13.39 0.00 0.00 3.27
1798 7074 1.611851 CCTGAGAGGACAGTGCCCT 60.612 63.158 0.00 0.00 37.67 5.19
2068 7344 1.134159 CAGGGCCAGATCAGGAAGAAG 60.134 57.143 8.61 0.00 0.00 2.85
2218 7547 2.796304 TCTTTCACTGCGCACTTTTTG 58.204 42.857 5.66 0.00 0.00 2.44
2319 7655 2.445427 TGGGGTTGTGCATGTCTAATG 58.555 47.619 0.00 0.00 0.00 1.90
2378 7722 2.730069 CACGCAGCTTGTTTTGATCAA 58.270 42.857 3.38 3.38 0.00 2.57
2401 7745 5.864628 AGAAAGATTTTAGACGCTTCCAC 57.135 39.130 0.00 0.00 0.00 4.02
2441 7785 4.893424 TTTGTTTCCTCAACTCTTTCCG 57.107 40.909 0.00 0.00 36.21 4.30
2481 7825 2.071778 AACCACACAAACTGCTCCAT 57.928 45.000 0.00 0.00 0.00 3.41
2505 7849 6.748132 TGAATTCTCCAAACCAGTCATTTTC 58.252 36.000 7.05 0.00 0.00 2.29
2506 7850 6.323482 TGAATTCTCCAAACCAGTCATTTTCA 59.677 34.615 7.05 0.00 0.00 2.69
2517 7862 4.082571 CCAGTCATTTTCATCCTTGTGGAC 60.083 45.833 0.00 0.00 46.51 4.02
2523 7868 1.746615 CATCCTTGTGGACAGGCGG 60.747 63.158 0.00 0.00 46.51 6.13
2544 7889 3.309954 GGCATTGTTTCGCTACTAAGAGG 59.690 47.826 0.00 0.00 0.00 3.69
2560 7905 0.594110 GAGGATCTCTAGCCGTTCGG 59.406 60.000 6.90 6.90 35.82 4.30
2582 7927 0.916809 CCCCCGGGAACAGAAATAGT 59.083 55.000 26.32 0.00 37.50 2.12
2585 7930 1.339631 CCCGGGAACAGAAATAGTGCA 60.340 52.381 18.48 0.00 0.00 4.57
2602 7947 2.040884 ATTCTGGGGGCTAGCCGA 60.041 61.111 27.24 15.91 36.85 5.54
2608 7953 3.534056 GGGGCTAGCCGACGCTAA 61.534 66.667 27.24 0.00 46.89 3.09
2619 7964 2.435938 ACGCTAATGTGGCCGTGG 60.436 61.111 0.00 0.00 0.00 4.94
2653 7998 2.847234 AACCACGGCCTCAGGTCA 60.847 61.111 10.57 0.00 33.74 4.02
2694 8040 9.751542 TTTTGAATTGAAGTTCGGCTAAAATTA 57.248 25.926 0.00 0.00 0.00 1.40
2715 8061 4.370620 AGACGAAAAAGACACGAATTCG 57.629 40.909 25.64 25.64 45.98 3.34
2726 8072 5.597806 AGACACGAATTCGGCTAATATTCA 58.402 37.500 29.79 0.00 44.95 2.57
2912 8274 2.867472 CCATGGTTGCGGTTCGAC 59.133 61.111 2.57 0.00 0.00 4.20
2951 8323 2.250646 TCGGCGTCGAAGAAGAGAA 58.749 52.632 10.97 0.00 43.03 2.87
2953 8328 0.386858 CGGCGTCGAAGAAGAGAACA 60.387 55.000 1.44 0.00 38.59 3.18
2956 8331 2.596452 GCGTCGAAGAAGAGAACATCA 58.404 47.619 1.37 0.00 38.59 3.07
2990 8388 0.882927 GTTGTAGAGTGTGCGGCCAA 60.883 55.000 2.24 0.00 0.00 4.52
3002 8401 3.706373 GGCCAACAGCGAGGGAGA 61.706 66.667 0.00 0.00 45.17 3.71
3006 8406 2.604686 AACAGCGAGGGAGAGGCA 60.605 61.111 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.450476 ACCAAGCAACAAGGATCCATC 58.550 47.619 15.82 0.00 0.00 3.51
1 2 2.610438 ACCAAGCAACAAGGATCCAT 57.390 45.000 15.82 0.00 0.00 3.41
2 3 2.364970 CAAACCAAGCAACAAGGATCCA 59.635 45.455 15.82 0.00 0.00 3.41
3 4 2.289010 CCAAACCAAGCAACAAGGATCC 60.289 50.000 2.48 2.48 0.00 3.36
4 5 2.867647 GCCAAACCAAGCAACAAGGATC 60.868 50.000 0.00 0.00 0.00 3.36
5 6 1.070601 GCCAAACCAAGCAACAAGGAT 59.929 47.619 0.00 0.00 0.00 3.24
6 7 0.463620 GCCAAACCAAGCAACAAGGA 59.536 50.000 0.00 0.00 0.00 3.36
7 8 0.177604 TGCCAAACCAAGCAACAAGG 59.822 50.000 0.00 0.00 35.69 3.61
8 9 2.243602 ATGCCAAACCAAGCAACAAG 57.756 45.000 0.00 0.00 43.36 3.16
9 10 2.706339 AATGCCAAACCAAGCAACAA 57.294 40.000 0.00 0.00 43.36 2.83
10 11 2.706339 AAATGCCAAACCAAGCAACA 57.294 40.000 0.00 0.00 43.36 3.33
11 12 3.988819 TCTAAATGCCAAACCAAGCAAC 58.011 40.909 0.00 0.00 43.36 4.17
12 13 3.006752 CCTCTAAATGCCAAACCAAGCAA 59.993 43.478 0.00 0.00 43.36 3.91
13 14 2.562298 CCTCTAAATGCCAAACCAAGCA 59.438 45.455 0.00 0.00 44.45 3.91
14 15 2.825532 TCCTCTAAATGCCAAACCAAGC 59.174 45.455 0.00 0.00 0.00 4.01
15 16 5.665916 ATTCCTCTAAATGCCAAACCAAG 57.334 39.130 0.00 0.00 0.00 3.61
16 17 6.252995 AGTATTCCTCTAAATGCCAAACCAA 58.747 36.000 0.00 0.00 0.00 3.67
17 18 5.826643 AGTATTCCTCTAAATGCCAAACCA 58.173 37.500 0.00 0.00 0.00 3.67
18 19 7.054751 AGTAGTATTCCTCTAAATGCCAAACC 58.945 38.462 0.00 0.00 0.00 3.27
19 20 9.043079 GTAGTAGTATTCCTCTAAATGCCAAAC 57.957 37.037 0.00 0.00 0.00 2.93
20 21 8.764558 TGTAGTAGTATTCCTCTAAATGCCAAA 58.235 33.333 0.00 0.00 0.00 3.28
21 22 8.313944 TGTAGTAGTATTCCTCTAAATGCCAA 57.686 34.615 0.00 0.00 0.00 4.52
22 23 7.907841 TGTAGTAGTATTCCTCTAAATGCCA 57.092 36.000 0.00 0.00 0.00 4.92
23 24 8.639761 TCTTGTAGTAGTATTCCTCTAAATGCC 58.360 37.037 0.00 0.00 0.00 4.40
24 25 9.465985 GTCTTGTAGTAGTATTCCTCTAAATGC 57.534 37.037 0.00 0.00 0.00 3.56
30 31 9.398538 CTTGTAGTCTTGTAGTAGTATTCCTCT 57.601 37.037 0.00 0.00 0.00 3.69
31 32 9.176460 ACTTGTAGTCTTGTAGTAGTATTCCTC 57.824 37.037 0.00 0.00 0.00 3.71
32 33 8.958506 CACTTGTAGTCTTGTAGTAGTATTCCT 58.041 37.037 0.00 0.00 0.00 3.36
33 34 8.189460 CCACTTGTAGTCTTGTAGTAGTATTCC 58.811 40.741 0.00 0.00 0.00 3.01
34 35 7.701501 GCCACTTGTAGTCTTGTAGTAGTATTC 59.298 40.741 0.00 0.00 0.00 1.75
35 36 7.396623 AGCCACTTGTAGTCTTGTAGTAGTATT 59.603 37.037 0.00 0.00 0.00 1.89
36 37 6.890814 AGCCACTTGTAGTCTTGTAGTAGTAT 59.109 38.462 0.00 0.00 0.00 2.12
37 38 6.243900 AGCCACTTGTAGTCTTGTAGTAGTA 58.756 40.000 0.00 0.00 0.00 1.82
38 39 5.078256 AGCCACTTGTAGTCTTGTAGTAGT 58.922 41.667 0.00 0.00 0.00 2.73
39 40 5.646577 AGCCACTTGTAGTCTTGTAGTAG 57.353 43.478 0.00 0.00 0.00 2.57
40 41 5.537295 TGAAGCCACTTGTAGTCTTGTAGTA 59.463 40.000 0.00 0.00 0.00 1.82
41 42 4.344102 TGAAGCCACTTGTAGTCTTGTAGT 59.656 41.667 0.00 0.00 0.00 2.73
42 43 4.883083 TGAAGCCACTTGTAGTCTTGTAG 58.117 43.478 0.00 0.00 0.00 2.74
43 44 4.948341 TGAAGCCACTTGTAGTCTTGTA 57.052 40.909 0.00 0.00 0.00 2.41
44 45 3.838244 TGAAGCCACTTGTAGTCTTGT 57.162 42.857 0.00 0.00 0.00 3.16
45 46 3.876914 TGTTGAAGCCACTTGTAGTCTTG 59.123 43.478 0.00 0.00 0.00 3.02
46 47 4.150897 TGTTGAAGCCACTTGTAGTCTT 57.849 40.909 0.00 0.00 0.00 3.01
47 48 3.838244 TGTTGAAGCCACTTGTAGTCT 57.162 42.857 0.00 0.00 0.00 3.24
48 49 4.275936 ACAATGTTGAAGCCACTTGTAGTC 59.724 41.667 0.00 0.00 0.00 2.59
49 50 4.207165 ACAATGTTGAAGCCACTTGTAGT 58.793 39.130 0.00 0.00 0.00 2.73
50 51 4.836125 ACAATGTTGAAGCCACTTGTAG 57.164 40.909 0.00 0.00 0.00 2.74
51 52 4.642437 TCAACAATGTTGAAGCCACTTGTA 59.358 37.500 24.63 0.00 0.00 2.41
52 53 3.446873 TCAACAATGTTGAAGCCACTTGT 59.553 39.130 24.63 0.00 0.00 3.16
53 54 3.798337 GTCAACAATGTTGAAGCCACTTG 59.202 43.478 27.77 0.00 0.00 3.16
54 55 3.446873 TGTCAACAATGTTGAAGCCACTT 59.553 39.130 27.77 0.00 0.00 3.16
55 56 3.023119 TGTCAACAATGTTGAAGCCACT 58.977 40.909 27.77 0.00 0.00 4.00
56 57 3.115554 GTGTCAACAATGTTGAAGCCAC 58.884 45.455 27.77 25.08 0.00 5.01
57 58 2.100584 GGTGTCAACAATGTTGAAGCCA 59.899 45.455 27.77 19.31 0.00 4.75
58 59 2.100584 TGGTGTCAACAATGTTGAAGCC 59.899 45.455 27.77 27.91 0.00 4.35
59 60 3.435105 TGGTGTCAACAATGTTGAAGC 57.565 42.857 27.77 24.05 0.00 3.86
60 61 6.738114 ACTAATGGTGTCAACAATGTTGAAG 58.262 36.000 27.77 21.05 0.00 3.02
61 62 6.707440 ACTAATGGTGTCAACAATGTTGAA 57.293 33.333 27.77 14.54 0.00 2.69
62 63 6.072728 GCTACTAATGGTGTCAACAATGTTGA 60.073 38.462 23.28 23.28 0.00 3.18
63 64 6.072508 AGCTACTAATGGTGTCAACAATGTTG 60.073 38.462 19.23 19.23 0.00 3.33
64 65 6.003950 AGCTACTAATGGTGTCAACAATGTT 58.996 36.000 0.00 0.00 0.00 2.71
65 66 5.560724 AGCTACTAATGGTGTCAACAATGT 58.439 37.500 0.00 0.00 0.00 2.71
66 67 5.643348 TGAGCTACTAATGGTGTCAACAATG 59.357 40.000 0.00 0.00 0.00 2.82
67 68 5.804639 TGAGCTACTAATGGTGTCAACAAT 58.195 37.500 0.00 0.00 0.00 2.71
68 69 5.222079 TGAGCTACTAATGGTGTCAACAA 57.778 39.130 0.00 0.00 0.00 2.83
69 70 4.882842 TGAGCTACTAATGGTGTCAACA 57.117 40.909 0.00 0.00 0.00 3.33
70 71 5.874810 TGAATGAGCTACTAATGGTGTCAAC 59.125 40.000 0.00 0.00 0.00 3.18
71 72 6.048732 TGAATGAGCTACTAATGGTGTCAA 57.951 37.500 0.00 0.00 0.00 3.18
72 73 5.675684 TGAATGAGCTACTAATGGTGTCA 57.324 39.130 0.00 0.00 0.00 3.58
73 74 7.559590 AAATGAATGAGCTACTAATGGTGTC 57.440 36.000 0.00 0.00 0.00 3.67
74 75 7.611467 TGAAAATGAATGAGCTACTAATGGTGT 59.389 33.333 0.00 0.00 0.00 4.16
75 76 7.988737 TGAAAATGAATGAGCTACTAATGGTG 58.011 34.615 0.00 0.00 0.00 4.17
76 77 7.284034 CCTGAAAATGAATGAGCTACTAATGGT 59.716 37.037 0.00 0.00 0.00 3.55
77 78 7.255381 CCCTGAAAATGAATGAGCTACTAATGG 60.255 40.741 0.00 0.00 0.00 3.16
78 79 7.500227 TCCCTGAAAATGAATGAGCTACTAATG 59.500 37.037 0.00 0.00 0.00 1.90
79 80 7.577303 TCCCTGAAAATGAATGAGCTACTAAT 58.423 34.615 0.00 0.00 0.00 1.73
80 81 6.957631 TCCCTGAAAATGAATGAGCTACTAA 58.042 36.000 0.00 0.00 0.00 2.24
81 82 6.560003 TCCCTGAAAATGAATGAGCTACTA 57.440 37.500 0.00 0.00 0.00 1.82
82 83 5.441718 TCCCTGAAAATGAATGAGCTACT 57.558 39.130 0.00 0.00 0.00 2.57
83 84 6.151817 ACTTTCCCTGAAAATGAATGAGCTAC 59.848 38.462 0.00 0.00 30.84 3.58
84 85 6.151648 CACTTTCCCTGAAAATGAATGAGCTA 59.848 38.462 0.00 0.00 31.56 3.32
85 86 5.047519 CACTTTCCCTGAAAATGAATGAGCT 60.048 40.000 0.00 0.00 31.56 4.09
86 87 5.047802 TCACTTTCCCTGAAAATGAATGAGC 60.048 40.000 0.00 0.00 35.38 4.26
87 88 6.579666 TCACTTTCCCTGAAAATGAATGAG 57.420 37.500 0.00 0.00 35.38 2.90
88 89 6.975196 TTCACTTTCCCTGAAAATGAATGA 57.025 33.333 8.79 0.00 40.92 2.57
89 90 8.436046 TTTTTCACTTTCCCTGAAAATGAATG 57.564 30.769 12.45 0.00 43.68 2.67
90 91 8.485392 TCTTTTTCACTTTCCCTGAAAATGAAT 58.515 29.630 12.45 0.00 43.68 2.57
94 95 7.423844 ACTCTTTTTCACTTTCCCTGAAAAT 57.576 32.000 7.05 0.00 43.66 1.82
122 124 2.416296 CCGACAGTTAGCGTGTGGAATA 60.416 50.000 0.00 0.00 0.00 1.75
211 246 2.760650 TCACGTCTGATCATTAGCTGGT 59.239 45.455 0.00 0.00 0.00 4.00
212 247 3.119291 GTCACGTCTGATCATTAGCTGG 58.881 50.000 0.00 0.00 0.00 4.85
213 248 3.774066 TGTCACGTCTGATCATTAGCTG 58.226 45.455 0.00 0.00 0.00 4.24
246 368 7.667043 ACACTTTAATTGCGTCATCTCTTTA 57.333 32.000 0.00 0.00 0.00 1.85
254 376 6.034150 CGTCATAGTACACTTTAATTGCGTCA 59.966 38.462 0.00 0.00 0.00 4.35
443 672 1.071041 CGTCTGTTTTTCCGGTCGTTC 60.071 52.381 0.00 0.00 0.00 3.95
461 690 2.607750 AGTGGCAGATGGGGACGT 60.608 61.111 0.00 0.00 0.00 4.34
649 3529 4.156915 GTCTTCGGTCCGTAATGATATCG 58.843 47.826 11.88 0.00 0.00 2.92
839 3896 8.973182 GCAGGAAGCTATCTACTTATATAGGTT 58.027 37.037 2.49 6.51 44.73 3.50
946 4432 6.279123 TGCTTGACTAAGATGAAGCTATCTG 58.721 40.000 0.00 0.00 41.19 2.90
1239 6182 9.723601 ATATATGTTTGCAAATTGGTTTCTTGT 57.276 25.926 16.21 0.36 0.00 3.16
1273 6502 0.815615 CAAGTCCGGGCAGGCTAATC 60.816 60.000 9.71 0.00 40.77 1.75
1307 6550 5.114764 TCACAGCCCTAATCATCATCAAA 57.885 39.130 0.00 0.00 0.00 2.69
1822 7098 4.077184 TGCATCACCGTCGGGTCC 62.077 66.667 17.28 0.00 46.01 4.46
1853 7129 1.228245 GCCTGTCCAGCTTGTTGGA 60.228 57.895 2.02 2.02 44.84 3.53
2068 7344 4.036804 TGGTTGATTGCGCGGCAC 62.037 61.111 8.83 0.00 38.71 5.01
2218 7547 2.241722 CGACAACGATGAATGCCAAAC 58.758 47.619 0.00 0.00 42.66 2.93
2319 7655 7.489574 TTTCAACAAGGAACATTTATTTGCC 57.510 32.000 0.00 0.00 0.00 4.52
2378 7722 5.763204 TGTGGAAGCGTCTAAAATCTTTCTT 59.237 36.000 0.00 0.00 0.00 2.52
2393 7737 0.102120 TTTTGCCACTTGTGGAAGCG 59.898 50.000 22.52 0.00 31.68 4.68
2401 7745 3.525268 AAACTGGACTTTTGCCACTTG 57.475 42.857 0.00 0.00 0.00 3.16
2441 7785 0.108567 GAGAGTCGAGGGACCAAAGC 60.109 60.000 0.00 0.00 44.54 3.51
2481 7825 6.323482 TGAAAATGACTGGTTTGGAGAATTCA 59.677 34.615 8.44 0.00 0.00 2.57
2517 7862 2.504681 GCGAAACAATGCCGCCTG 60.505 61.111 0.00 0.00 42.77 4.85
2523 7868 4.181578 TCCTCTTAGTAGCGAAACAATGC 58.818 43.478 0.00 0.00 0.00 3.56
2568 7913 4.096984 CCAGAATGCACTATTTCTGTTCCC 59.903 45.833 20.75 0.00 31.97 3.97
2582 7927 2.597340 GCTAGCCCCCAGAATGCA 59.403 61.111 2.29 0.00 31.97 3.96
2585 7930 2.040884 TCGGCTAGCCCCCAGAAT 60.041 61.111 28.09 0.00 0.00 2.40
2602 7947 2.435938 CCACGGCCACATTAGCGT 60.436 61.111 2.24 0.00 0.00 5.07
2604 7949 2.828549 CCCCACGGCCACATTAGC 60.829 66.667 2.24 0.00 0.00 3.09
2653 7998 2.931921 AAAAAGGCGTCTGGGGGT 59.068 55.556 0.00 0.00 0.00 4.95
2672 8018 7.425595 CGTCTAATTTTAGCCGAACTTCAATTC 59.574 37.037 0.00 0.00 34.38 2.17
2686 8032 9.807386 ATTCGTGTCTTTTTCGTCTAATTTTAG 57.193 29.630 0.00 0.00 0.00 1.85
2694 8040 3.183775 CCGAATTCGTGTCTTTTTCGTCT 59.816 43.478 25.10 0.00 37.94 4.18
2715 8061 0.602905 ACCGCCGCTGAATATTAGCC 60.603 55.000 9.76 0.38 37.90 3.93
2754 8100 4.074526 GCTCGTGGAGGCTCAGCA 62.075 66.667 17.69 2.80 0.00 4.41
2887 8233 4.440127 GCAACCATGGCCAAGCGG 62.440 66.667 10.96 14.04 0.00 5.52
2912 8274 1.101049 GCCCTCTCTCTCCTCGTCTG 61.101 65.000 0.00 0.00 0.00 3.51
2939 8303 2.416027 CCGCTGATGTTCTCTTCTTCGA 60.416 50.000 0.00 0.00 0.00 3.71
2951 8323 1.723608 CTCTCTCTCGCCGCTGATGT 61.724 60.000 0.00 0.00 0.00 3.06
2953 8328 2.192861 CCTCTCTCTCGCCGCTGAT 61.193 63.158 0.00 0.00 0.00 2.90
2956 8331 2.361865 AACCTCTCTCTCGCCGCT 60.362 61.111 0.00 0.00 0.00 5.52
2990 8388 3.073735 CTGCCTCTCCCTCGCTGT 61.074 66.667 0.00 0.00 0.00 4.40
3036 8436 2.125310 TCCACACTATTGCCGCCG 60.125 61.111 0.00 0.00 0.00 6.46
3164 8575 3.987547 TCTTCATCATCCTCATCGCTTC 58.012 45.455 0.00 0.00 0.00 3.86
3205 8617 1.149288 TGGTGGACCCTTCTAGTCAGT 59.851 52.381 0.00 0.00 35.89 3.41


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

AutoCloner maintained by Alex Coulton.