Multiple sequence alignment - TraesCS6B01G242700

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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 TraesCS6B01G242700 chr6B 100.000 5135 0 0 1 5135 431698884 431704018 0.000000e+00 9483.0
1 TraesCS6B01G242700 chr6B 94.792 96 5 0 2468 2563 669011488 669011393 3.200000e-32 150.0
2 TraesCS6B01G242700 chr6D 96.892 2220 49 10 1 2212 271004236 271006443 0.000000e+00 3699.0
3 TraesCS6B01G242700 chr6D 96.976 1422 34 6 2559 3974 271006717 271008135 0.000000e+00 2379.0
4 TraesCS6B01G242700 chr6D 97.196 642 13 5 4497 5135 271008614 271009253 0.000000e+00 1081.0
5 TraesCS6B01G242700 chr6D 95.316 491 20 2 3916 4406 271008127 271008614 0.000000e+00 776.0
6 TraesCS6B01G242700 chr6D 83.271 269 7 6 2252 2491 271006427 271006686 4.030000e-51 213.0
7 TraesCS6B01G242700 chr6D 92.222 90 6 1 4405 4493 155253602 155253513 5.400000e-25 126.0
8 TraesCS6B01G242700 chr6D 86.598 97 13 0 4402 4498 348638071 348637975 1.960000e-19 108.0
9 TraesCS6B01G242700 chr6D 91.892 74 4 2 4402 4473 59626114 59626187 9.100000e-18 102.0
10 TraesCS6B01G242700 chr6D 96.429 56 2 0 4403 4458 101231575 101231520 5.470000e-15 93.5
11 TraesCS6B01G242700 chr6D 94.737 57 2 1 4403 4458 14520513 14520569 2.550000e-13 87.9
12 TraesCS6B01G242700 chr6D 93.103 58 3 1 4402 4458 399221447 399221390 3.290000e-12 84.2
13 TraesCS6B01G242700 chr6D 85.714 77 7 4 4402 4476 81224786 81224712 1.530000e-10 78.7
14 TraesCS6B01G242700 chr6A 96.899 1419 37 5 2558 3974 384968465 384967052 0.000000e+00 2370.0
15 TraesCS6B01G242700 chr6A 91.425 1551 73 24 673 2187 384970148 384968622 0.000000e+00 2073.0
16 TraesCS6B01G242700 chr6A 95.742 681 29 0 4 684 384972728 384972048 0.000000e+00 1098.0
17 TraesCS6B01G242700 chr6A 94.058 690 21 14 4460 5135 384966546 384965863 0.000000e+00 1029.0
18 TraesCS6B01G242700 chr6A 95.736 516 16 4 3916 4428 384967060 384966548 0.000000e+00 826.0
19 TraesCS6B01G242700 chr6A 91.339 127 10 1 2344 2470 384968595 384968470 6.840000e-39 172.0
20 TraesCS6B01G242700 chr6A 86.667 135 10 4 2203 2330 189546168 189546035 5.360000e-30 143.0
21 TraesCS6B01G242700 chr6A 93.548 93 4 2 2470 2561 594831610 594831701 2.490000e-28 137.0
22 TraesCS6B01G242700 chr6A 89.216 102 9 2 4402 4501 334046073 334045972 5.400000e-25 126.0
23 TraesCS6B01G242700 chr6A 86.066 122 7 6 2215 2328 603354608 603354489 6.980000e-24 122.0
24 TraesCS6B01G242700 chr2B 75.922 868 159 34 2743 3578 514866844 514867693 2.880000e-107 399.0
25 TraesCS6B01G242700 chr2B 89.503 181 17 2 3672 3851 514867811 514867990 1.440000e-55 228.0
26 TraesCS6B01G242700 chr2B 86.861 137 16 2 2195 2330 132404532 132404397 8.910000e-33 152.0
27 TraesCS6B01G242700 chr2B 95.745 94 4 0 1 94 348440368 348440461 8.910000e-33 152.0
28 TraesCS6B01G242700 chr2B 90.722 97 8 1 2461 2556 503929974 503930070 1.500000e-25 128.0
29 TraesCS6B01G242700 chr2D 85.227 176 26 0 3959 4134 436366612 436366437 1.140000e-41 182.0
30 TraesCS6B01G242700 chr2D 97.727 88 2 0 1 88 162029906 162029819 8.910000e-33 152.0
31 TraesCS6B01G242700 chr2D 91.000 100 8 1 4403 4502 636776350 636776252 3.230000e-27 134.0
32 TraesCS6B01G242700 chr2D 89.130 92 9 1 4403 4493 95416542 95416633 4.200000e-21 113.0
33 TraesCS6B01G242700 chr7D 96.739 92 3 0 2466 2557 185552874 185552783 2.480000e-33 154.0
34 TraesCS6B01G242700 chr7D 95.604 91 4 0 1 91 422063123 422063033 4.140000e-31 147.0
35 TraesCS6B01G242700 chr7D 93.750 96 6 0 1 96 274676610 274676705 1.490000e-30 145.0
36 TraesCS6B01G242700 chr7D 90.476 105 9 1 2470 2573 5068086 5068190 2.490000e-28 137.0
37 TraesCS6B01G242700 chr7D 93.407 91 6 0 2466 2556 485090874 485090964 8.970000e-28 135.0
38 TraesCS6B01G242700 chr7D 87.629 97 10 2 4403 4498 424130403 424130308 1.510000e-20 111.0
39 TraesCS6B01G242700 chr5D 97.753 89 2 0 2469 2557 109535625 109535537 2.480000e-33 154.0
40 TraesCS6B01G242700 chr5D 97.753 89 2 0 2469 2557 112843011 112842923 2.480000e-33 154.0
41 TraesCS6B01G242700 chr5D 97.727 88 2 0 1 88 164849110 164849023 8.910000e-33 152.0
42 TraesCS6B01G242700 chr5D 97.727 88 2 0 1 88 489290678 489290591 8.910000e-33 152.0
43 TraesCS6B01G242700 chr5D 90.099 101 8 2 4403 4502 416422270 416422369 4.170000e-26 130.0
44 TraesCS6B01G242700 chr2A 97.753 89 2 0 2466 2554 498099531 498099443 2.480000e-33 154.0
45 TraesCS6B01G242700 chr2A 87.963 108 10 3 2454 2559 115434401 115434507 1.940000e-24 124.0
46 TraesCS6B01G242700 chr4D 93.878 98 6 0 2461 2558 124628761 124628858 1.150000e-31 148.0
47 TraesCS6B01G242700 chr4D 83.784 148 16 6 2186 2330 83279746 83279888 3.230000e-27 134.0
48 TraesCS6B01G242700 chr4D 88.073 109 12 1 4403 4510 371790999 371791107 1.500000e-25 128.0
49 TraesCS6B01G242700 chr4D 85.870 92 13 0 4402 4493 110076278 110076187 1.180000e-16 99.0
50 TraesCS6B01G242700 chr4D 89.610 77 6 2 4430 4504 220347060 220347136 4.230000e-16 97.1
51 TraesCS6B01G242700 chr1A 84.615 156 16 6 2178 2327 57303628 57303781 1.150000e-31 148.0
52 TraesCS6B01G242700 chr1A 86.765 136 13 4 2197 2330 432985460 432985328 4.140000e-31 147.0
53 TraesCS6B01G242700 chr1A 87.850 107 10 3 4403 4506 520805757 520805651 6.980000e-24 122.0
54 TraesCS6B01G242700 chr3D 92.381 105 5 3 2465 2567 54370501 54370398 4.140000e-31 147.0
55 TraesCS6B01G242700 chr3D 93.750 96 6 0 1 96 402828943 402828848 1.490000e-30 145.0
56 TraesCS6B01G242700 chr3D 90.099 101 10 0 2470 2570 459472523 459472423 1.160000e-26 132.0
57 TraesCS6B01G242700 chr3D 88.119 101 11 1 4403 4502 126955115 126955215 9.030000e-23 119.0
58 TraesCS6B01G242700 chrUn 92.233 103 6 2 2459 2559 461112272 461112374 1.490000e-30 145.0
59 TraesCS6B01G242700 chrUn 86.139 101 13 1 4403 4502 100236700 100236600 1.960000e-19 108.0
60 TraesCS6B01G242700 chr4B 93.684 95 4 2 2466 2559 653746112 653746019 1.930000e-29 141.0
61 TraesCS6B01G242700 chr4B 87.963 108 10 3 2454 2559 438099344 438099450 1.940000e-24 124.0
62 TraesCS6B01G242700 chr1D 92.708 96 6 1 4404 4498 332956527 332956432 2.490000e-28 137.0
63 TraesCS6B01G242700 chr1D 91.000 100 8 1 2469 2568 363804171 363804269 3.230000e-27 134.0
64 TraesCS6B01G242700 chr1D 84.783 138 14 6 2197 2330 335590221 335590087 1.160000e-26 132.0
65 TraesCS6B01G242700 chr1D 87.500 96 12 0 4403 4498 414709787 414709692 1.510000e-20 111.0
66 TraesCS6B01G242700 chr1D 84.848 99 15 0 4400 4498 3184604 3184702 3.270000e-17 100.0
67 TraesCS6B01G242700 chr1D 89.655 58 5 1 4402 4458 192809917 192809974 7.130000e-09 73.1
68 TraesCS6B01G242700 chr1D 89.655 58 4 2 4402 4458 301636363 301636419 7.130000e-09 73.1
69 TraesCS6B01G242700 chr1D 89.655 58 5 1 4402 4458 407351180 407351123 7.130000e-09 73.1
70 TraesCS6B01G242700 chr1D 89.474 57 5 1 4403 4458 47310444 47310388 2.570000e-08 71.3
71 TraesCS6B01G242700 chr1D 97.619 42 0 1 4418 4458 479208795 479208754 2.570000e-08 71.3
72 TraesCS6B01G242700 chr1D 84.722 72 6 5 4389 4458 27855775 27855843 3.320000e-07 67.6
73 TraesCS6B01G242700 chr1D 87.931 58 6 1 4403 4459 318847141 318847084 3.320000e-07 67.6
74 TraesCS6B01G242700 chr1B 89.091 110 8 4 4402 4509 24936405 24936298 3.230000e-27 134.0
75 TraesCS6B01G242700 chr7A 89.320 103 9 2 4402 4503 112799758 112799859 1.500000e-25 128.0
76 TraesCS6B01G242700 chr7A 88.350 103 10 2 4402 4503 112776877 112776978 6.980000e-24 122.0
77 TraesCS6B01G242700 chr3A 83.562 146 14 5 2197 2332 700234086 700234231 1.500000e-25 128.0
78 TraesCS6B01G242700 chr3B 83.168 101 12 2 2227 2327 818302634 818302539 2.550000e-13 87.9


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 TraesCS6B01G242700 chr6B 431698884 431704018 5134 False 9483.000000 9483 100.000000 1 5135 1 chr6B.!!$F1 5134
1 TraesCS6B01G242700 chr6D 271004236 271009253 5017 False 1629.600000 3699 93.930200 1 5135 5 chr6D.!!$F3 5134
2 TraesCS6B01G242700 chr6A 384965863 384972728 6865 True 1261.333333 2370 94.199833 4 5135 6 chr6A.!!$R4 5131
3 TraesCS6B01G242700 chr2B 514866844 514867990 1146 False 313.500000 399 82.712500 2743 3851 2 chr2B.!!$F3 1108

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
250 251 0.889186 AAAGGGCAGCGACGACAAAT 60.889 50.000 0.00 0.0 0.00 2.32 F
1432 3384 1.222115 CGGCCTAGTGCTAATTCGGC 61.222 60.000 0.00 0.0 40.92 5.54 F
1626 3578 0.815213 TGTGTGAGAACTGTGCCTGC 60.815 55.000 0.00 0.0 0.00 4.85 F
2246 4202 0.959553 AGGTCGACTCAACATCGTGT 59.040 50.000 16.46 0.0 40.50 4.49 F
2247 4203 1.068472 AGGTCGACTCAACATCGTGTC 60.068 52.381 16.46 0.0 40.50 3.67 F
2269 4225 1.069159 ACGAGTCACAACTAGTCGCAG 60.069 52.381 0.00 0.0 42.25 5.18 F
3926 6050 0.661020 CCCGTTTCGTTTCTGCTGTT 59.339 50.000 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 3527 0.110486 ACTCCCATTTGCTTCGTGGT 59.890 50.000 0.00 0.0 0.00 4.16 R
2254 4210 0.667487 GCAGCTGCGACTAGTTGTGA 60.667 55.000 25.23 0.0 32.27 3.58 R
2538 4522 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.0 0.00 4.37 R
3735 5809 0.108186 CAGTGCGCACTTCCCTCATA 60.108 55.000 39.13 0.0 40.20 2.15 R
3903 5977 0.454452 GCAGAAACGAAACGGGATGC 60.454 55.000 0.00 0.0 0.00 3.91 R
4015 6139 0.468226 TTTGTCTCCAGAACGCCAGT 59.532 50.000 0.00 0.0 0.00 4.00 R
4843 6971 1.745141 GCTGATTGGAAGCGTGGATCT 60.745 52.381 0.00 0.0 0.00 2.75 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
52 53 1.593006 GGTAGTCATCAATGGCGAACG 59.407 52.381 0.00 0.00 37.51 3.95
143 144 2.506644 TGGACTCAAGATCCATGATGCA 59.493 45.455 0.00 0.00 41.47 3.96
250 251 0.889186 AAAGGGCAGCGACGACAAAT 60.889 50.000 0.00 0.00 0.00 2.32
330 331 8.342634 GTCATATTTCCTTATTGCGCTTCTAAA 58.657 33.333 9.73 0.00 0.00 1.85
343 344 2.351738 GCTTCTAAACTTTGGCATGCGT 60.352 45.455 12.44 0.10 0.00 5.24
426 427 4.575236 GCTAAACTACTAATGCCTTGGACC 59.425 45.833 0.00 0.00 0.00 4.46
595 597 2.409371 CGTTTCGTTGTCGCCTTTACTC 60.409 50.000 0.00 0.00 36.96 2.59
946 2872 2.808321 GAAACTCCCGACGCCGTC 60.808 66.667 7.29 7.29 0.00 4.79
1432 3384 1.222115 CGGCCTAGTGCTAATTCGGC 61.222 60.000 0.00 0.00 40.92 5.54
1575 3527 6.652205 ATAATGTTTACCCTCCTCCAAAGA 57.348 37.500 0.00 0.00 0.00 2.52
1626 3578 0.815213 TGTGTGAGAACTGTGCCTGC 60.815 55.000 0.00 0.00 0.00 4.85
1670 3622 9.035607 GTCAGAACTGTGTCCATTATTAGTATG 57.964 37.037 1.73 0.00 0.00 2.39
1671 3623 7.710907 TCAGAACTGTGTCCATTATTAGTATGC 59.289 37.037 1.73 0.00 0.00 3.14
1672 3624 7.495606 CAGAACTGTGTCCATTATTAGTATGCA 59.504 37.037 0.00 0.00 0.00 3.96
1673 3625 8.046708 AGAACTGTGTCCATTATTAGTATGCAA 58.953 33.333 0.00 0.00 0.00 4.08
1674 3626 8.574251 AACTGTGTCCATTATTAGTATGCAAA 57.426 30.769 0.00 0.00 0.00 3.68
1723 3677 6.541086 CACAATTGAGCATTGAGAAGAGTAC 58.459 40.000 13.59 0.00 44.78 2.73
1752 3706 8.925338 TGAGTATTAAGGAAGGGTAGAATCTTC 58.075 37.037 0.00 0.00 38.79 2.87
1831 3786 1.077357 AGTTTTGTCACCCACGGCA 60.077 52.632 0.00 0.00 0.00 5.69
1929 3885 2.172717 TCCCTATGCTAAGCAACCCTTC 59.827 50.000 0.00 0.00 43.62 3.46
1983 3939 4.703575 AGCTTTGATCTTGCAAATCAGCTA 59.296 37.500 22.22 13.56 36.00 3.32
2055 4011 1.888215 AAGCATCCATATGGTGAGCG 58.112 50.000 21.28 7.75 42.93 5.03
2058 4014 1.943046 GCATCCATATGGTGAGCGGAG 60.943 57.143 21.28 5.19 36.34 4.63
2244 4200 2.814280 AAAGGTCGACTCAACATCGT 57.186 45.000 16.46 0.00 40.50 3.73
2245 4201 2.065993 AAGGTCGACTCAACATCGTG 57.934 50.000 16.46 0.00 40.50 4.35
2246 4202 0.959553 AGGTCGACTCAACATCGTGT 59.040 50.000 16.46 0.00 40.50 4.49
2247 4203 1.068472 AGGTCGACTCAACATCGTGTC 60.068 52.381 16.46 0.00 40.50 3.67
2261 4217 3.546407 GTGTCGACGAGTCACAACT 57.454 52.632 11.62 0.00 38.48 3.16
2262 4218 2.675767 GTGTCGACGAGTCACAACTA 57.324 50.000 11.62 0.00 38.48 2.24
2263 4219 2.572243 GTGTCGACGAGTCACAACTAG 58.428 52.381 11.62 0.00 38.48 2.57
2264 4220 2.032204 GTGTCGACGAGTCACAACTAGT 60.032 50.000 11.62 0.00 43.11 2.57
2269 4225 1.069159 ACGAGTCACAACTAGTCGCAG 60.069 52.381 0.00 0.00 42.25 5.18
2278 4234 4.457496 TAGTCGCAGCTGCAGGGC 62.457 66.667 36.03 23.24 42.21 5.19
2294 4250 1.757699 AGGGCCGTCTATTCAAGAGTC 59.242 52.381 0.00 0.00 33.88 3.36
2346 4302 3.386237 GCTGACCGCCAGACCTCT 61.386 66.667 7.16 0.00 45.78 3.69
2491 4475 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2494 4478 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2495 4479 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2496 4480 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2497 4481 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2498 4482 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2499 4483 5.255687 TCCGTCCCATAATATAAGAGCGTA 58.744 41.667 0.00 0.00 0.00 4.42
2500 4484 5.889853 TCCGTCCCATAATATAAGAGCGTAT 59.110 40.000 0.00 0.00 0.00 3.06
2503 4487 7.010183 CCGTCCCATAATATAAGAGCGTATTTG 59.990 40.741 0.00 0.00 0.00 2.32
2505 4489 8.870879 GTCCCATAATATAAGAGCGTATTTGAC 58.129 37.037 0.00 0.00 0.00 3.18
2506 4490 8.590204 TCCCATAATATAAGAGCGTATTTGACA 58.410 33.333 0.00 0.00 0.00 3.58
2512 4496 9.464714 AATATAAGAGCGTATTTGACACTAGTG 57.535 33.333 21.44 21.44 0.00 2.74
2514 4498 5.892160 AGAGCGTATTTGACACTAGTGTA 57.108 39.130 27.98 13.80 45.05 2.90
2515 4499 5.881447 AGAGCGTATTTGACACTAGTGTAG 58.119 41.667 27.98 13.76 45.05 2.74
2516 4500 5.415077 AGAGCGTATTTGACACTAGTGTAGT 59.585 40.000 27.98 13.07 45.05 2.73
2541 4525 9.659830 GTGTTAAAAACGCTCTTATATTATGGG 57.340 33.333 0.00 0.00 38.81 4.00
2542 4526 9.616156 TGTTAAAAACGCTCTTATATTATGGGA 57.384 29.630 0.00 0.00 0.00 4.37
2543 4527 9.874215 GTTAAAAACGCTCTTATATTATGGGAC 57.126 33.333 0.00 0.00 0.00 4.46
2544 4528 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2545 4529 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2546 4530 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2547 4531 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2548 4532 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2549 4533 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2550 4534 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2551 4535 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2552 4536 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2553 4537 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2556 4540 1.229131 ATGGGACGGAGGGAGTAGTA 58.771 55.000 0.00 0.00 0.00 1.82
2706 4695 6.367969 CGCTGGTGTAAAGTTTGATAAGTACT 59.632 38.462 0.00 0.00 0.00 2.73
2759 4748 5.895636 TGTTTATGAAGAATTGCCGATGT 57.104 34.783 0.00 0.00 0.00 3.06
2894 4883 2.740447 GAGGCCTGGTTAACAAAGTACG 59.260 50.000 12.00 0.00 0.00 3.67
3140 5130 2.107378 TGCCATTTGGAACACCAGAGTA 59.893 45.455 0.00 0.00 39.29 2.59
3225 5222 9.213799 GAGAGAAAGAACAGATTGAAAGTGTAT 57.786 33.333 0.00 0.00 0.00 2.29
3735 5809 5.128827 TCTTCAACCTCATTTCCGCTACTAT 59.871 40.000 0.00 0.00 0.00 2.12
3780 5854 4.444720 GTCTACTCACAGTTTTTGGAGTCG 59.555 45.833 0.00 0.00 37.96 4.18
3795 5869 2.292569 GGAGTCGTACAAGAGTGTGACA 59.707 50.000 0.00 0.00 38.82 3.58
3880 5954 8.335256 GTGAAACAACCGCCTAATTTTATATG 57.665 34.615 0.00 0.00 36.32 1.78
3903 5977 3.760151 CCCATTCCTATGCACCATACATG 59.240 47.826 0.00 0.00 0.00 3.21
3914 5988 2.033299 CACCATACATGCATCCCGTTTC 59.967 50.000 0.00 0.00 0.00 2.78
3926 6050 0.661020 CCCGTTTCGTTTCTGCTGTT 59.339 50.000 0.00 0.00 0.00 3.16
4002 6126 1.321474 CTGGGAAGCTTCACTGCAAA 58.679 50.000 28.18 7.86 34.99 3.68
4015 6139 3.698539 TCACTGCAAAATTGACAAGGTCA 59.301 39.130 0.00 0.00 41.09 4.02
4020 6144 3.383761 CAAAATTGACAAGGTCACTGGC 58.616 45.455 0.00 0.00 42.60 4.85
4047 6171 0.400213 AGACAAACCGGCCTGATGAA 59.600 50.000 0.00 0.00 0.00 2.57
4163 6289 0.603707 TTCTTGTTGGAGCTCTGGCG 60.604 55.000 14.64 0.00 44.37 5.69
4164 6290 2.032528 TTGTTGGAGCTCTGGCGG 59.967 61.111 14.64 0.00 44.37 6.13
4165 6291 4.704833 TGTTGGAGCTCTGGCGGC 62.705 66.667 14.64 0.00 44.37 6.53
4166 6292 4.400961 GTTGGAGCTCTGGCGGCT 62.401 66.667 14.64 0.00 44.37 5.52
4247 6373 1.152694 TGCCTGGCTTTGTTGAGCT 60.153 52.632 21.03 0.00 42.32 4.09
4250 6376 1.035139 CCTGGCTTTGTTGAGCTTGT 58.965 50.000 0.00 0.00 42.32 3.16
4367 6493 4.439700 CCAAGCCTTATCATCTGTGCTTTG 60.440 45.833 0.00 0.00 36.97 2.77
4397 6523 8.124199 GTGAATTTATTTGCTTGGCATATTTGG 58.876 33.333 0.00 0.00 38.76 3.28
4411 6537 2.918712 ATTTGGCAGATACTCCCTCG 57.081 50.000 0.00 0.00 0.00 4.63
4420 6546 2.047830 GATACTCCCTCGGTCCCAAAT 58.952 52.381 0.00 0.00 0.00 2.32
4421 6547 2.852714 TACTCCCTCGGTCCCAAATA 57.147 50.000 0.00 0.00 0.00 1.40
4423 6549 1.838077 ACTCCCTCGGTCCCAAATAAG 59.162 52.381 0.00 0.00 0.00 1.73
4424 6550 1.838077 CTCCCTCGGTCCCAAATAAGT 59.162 52.381 0.00 0.00 0.00 2.24
4425 6551 1.557832 TCCCTCGGTCCCAAATAAGTG 59.442 52.381 0.00 0.00 0.00 3.16
4426 6552 1.280998 CCCTCGGTCCCAAATAAGTGT 59.719 52.381 0.00 0.00 0.00 3.55
4427 6553 2.629051 CCTCGGTCCCAAATAAGTGTC 58.371 52.381 0.00 0.00 0.00 3.67
4428 6554 2.236395 CCTCGGTCCCAAATAAGTGTCT 59.764 50.000 0.00 0.00 0.00 3.41
4429 6555 3.522553 CTCGGTCCCAAATAAGTGTCTC 58.477 50.000 0.00 0.00 0.00 3.36
4430 6556 2.901192 TCGGTCCCAAATAAGTGTCTCA 59.099 45.455 0.00 0.00 0.00 3.27
4433 6559 4.652822 GGTCCCAAATAAGTGTCTCAACT 58.347 43.478 0.00 0.00 0.00 3.16
4434 6560 5.070685 GGTCCCAAATAAGTGTCTCAACTT 58.929 41.667 0.00 0.00 42.89 2.66
4435 6561 5.535030 GGTCCCAAATAAGTGTCTCAACTTT 59.465 40.000 0.00 0.00 40.77 2.66
4438 6564 7.227910 GTCCCAAATAAGTGTCTCAACTTTGTA 59.772 37.037 0.00 0.00 40.77 2.41
4439 6565 7.227910 TCCCAAATAAGTGTCTCAACTTTGTAC 59.772 37.037 0.00 0.00 40.77 2.90
4440 6566 7.228706 CCCAAATAAGTGTCTCAACTTTGTACT 59.771 37.037 0.00 0.00 40.77 2.73
4441 6567 9.268268 CCAAATAAGTGTCTCAACTTTGTACTA 57.732 33.333 0.00 0.00 40.77 1.82
4447 6573 9.880157 AAGTGTCTCAACTTTGTACTAAAGTTA 57.120 29.630 23.56 13.47 45.57 2.24
4448 6574 9.530633 AGTGTCTCAACTTTGTACTAAAGTTAG 57.469 33.333 23.56 20.62 45.57 2.34
4449 6575 9.310716 GTGTCTCAACTTTGTACTAAAGTTAGT 57.689 33.333 23.56 8.67 45.57 2.24
4488 6614 8.934023 AAAGTTGAGATACTTATTTTGGGACA 57.066 30.769 0.00 0.00 37.37 4.02
4498 6624 6.712276 ACTTATTTTGGGACAGAGGAAGTAG 58.288 40.000 0.00 0.00 42.39 2.57
4840 6968 3.849951 CTACAGCCGGCGGTCCAT 61.850 66.667 35.52 14.21 0.00 3.41
4843 6971 4.776322 CAGCCGGCGGTCCATTGA 62.776 66.667 28.82 0.00 0.00 2.57
4943 7085 3.189287 GCTCTGGGAAAACTACATGTGTG 59.811 47.826 9.11 3.79 0.00 3.82
4947 7089 5.654650 TCTGGGAAAACTACATGTGTGTTTT 59.345 36.000 28.42 28.42 39.50 2.43
5029 7171 3.721706 CTTGGAGCGGGGCCTCTT 61.722 66.667 0.00 0.00 32.43 2.85
5060 7202 2.821810 GCTTCTGCTTCGGCCTCC 60.822 66.667 0.00 0.00 40.91 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.029560 CCATCTCACGTGATGATCGGAT 60.030 50.000 20.40 13.88 44.71 4.18
143 144 2.038557 ACTCAATAGCGGGACAACACTT 59.961 45.455 0.00 0.00 0.00 3.16
250 251 8.375506 ACTGACTTCCTACACAAAATCATTCTA 58.624 33.333 0.00 0.00 0.00 2.10
330 331 1.106351 TGTTCCACGCATGCCAAAGT 61.106 50.000 13.15 0.33 0.00 2.66
343 344 3.880490 GCATTGAATACCCGTATGTTCCA 59.120 43.478 0.00 0.00 0.00 3.53
507 509 2.645838 AAGCAACAAGAGGAAGCAGA 57.354 45.000 0.00 0.00 0.00 4.26
595 597 3.617669 CTGAAAAACAAGTACCACGCAG 58.382 45.455 0.00 0.00 0.00 5.18
946 2872 3.361977 CCGGTTGGTTCGCTTGGG 61.362 66.667 0.00 0.00 0.00 4.12
1432 3384 5.857517 GTCTACTTTTGACCACGTCTAGAAG 59.142 44.000 3.94 3.94 33.15 2.85
1575 3527 0.110486 ACTCCCATTTGCTTCGTGGT 59.890 50.000 0.00 0.00 0.00 4.16
1601 3553 3.798337 GGCACAGTTCTCACACAAAATTG 59.202 43.478 0.00 0.00 0.00 2.32
1626 3578 7.482654 TTCTGACAGAAATACAGAACACAAG 57.517 36.000 15.58 0.00 42.91 3.16
1670 3622 6.595716 TCTGAAAGAACTAGCTTCCTATTTGC 59.404 38.462 0.00 0.00 42.31 3.68
1723 3677 9.549078 GATTCTACCCTTCCTTAATACTCAAAG 57.451 37.037 0.00 0.00 0.00 2.77
1831 3786 0.536460 CCCCTGCCGTTGTACAAGTT 60.536 55.000 8.98 0.00 0.00 2.66
2055 4011 3.100862 GATTTGACAGCGCGGCTCC 62.101 63.158 8.83 0.00 36.40 4.70
2058 4014 2.200170 AAAGGATTTGACAGCGCGGC 62.200 55.000 8.83 2.25 36.60 6.53
2069 4025 0.251787 AGCTTCCCCGCAAAGGATTT 60.252 50.000 0.00 0.00 45.00 2.17
2223 4179 3.247648 CACGATGTTGAGTCGACCTTTTT 59.752 43.478 13.01 0.00 41.40 1.94
2224 4180 2.800544 CACGATGTTGAGTCGACCTTTT 59.199 45.455 13.01 0.00 41.40 2.27
2225 4181 2.223971 ACACGATGTTGAGTCGACCTTT 60.224 45.455 13.01 0.00 41.40 3.11
2226 4182 1.340248 ACACGATGTTGAGTCGACCTT 59.660 47.619 13.01 0.00 41.40 3.50
2227 4183 0.959553 ACACGATGTTGAGTCGACCT 59.040 50.000 13.01 0.00 41.40 3.85
2228 4184 1.337821 GACACGATGTTGAGTCGACC 58.662 55.000 13.01 4.42 41.40 4.79
2243 4199 2.032204 ACTAGTTGTGACTCGTCGACAC 60.032 50.000 17.16 6.26 38.51 3.67
2244 4200 2.216046 ACTAGTTGTGACTCGTCGACA 58.784 47.619 17.16 1.87 37.33 4.35
2245 4201 2.837079 GACTAGTTGTGACTCGTCGAC 58.163 52.381 5.18 5.18 38.37 4.20
2248 4204 1.069432 TGCGACTAGTTGTGACTCGTC 60.069 52.381 11.83 2.24 42.25 4.20
2249 4205 0.949397 TGCGACTAGTTGTGACTCGT 59.051 50.000 11.83 0.00 37.33 4.18
2250 4206 1.607713 CTGCGACTAGTTGTGACTCG 58.392 55.000 11.83 2.90 37.33 4.18
2251 4207 1.068194 AGCTGCGACTAGTTGTGACTC 60.068 52.381 11.83 0.00 37.33 3.36
2252 4208 0.962489 AGCTGCGACTAGTTGTGACT 59.038 50.000 11.83 3.91 39.97 3.41
2253 4209 1.063806 CAGCTGCGACTAGTTGTGAC 58.936 55.000 11.83 1.71 0.00 3.67
2254 4210 0.667487 GCAGCTGCGACTAGTTGTGA 60.667 55.000 25.23 0.00 32.27 3.58
2255 4211 0.945743 TGCAGCTGCGACTAGTTGTG 60.946 55.000 32.11 6.46 45.83 3.33
2256 4212 0.668706 CTGCAGCTGCGACTAGTTGT 60.669 55.000 32.11 0.00 45.83 3.32
2257 4213 1.357258 CCTGCAGCTGCGACTAGTTG 61.357 60.000 32.11 14.17 45.83 3.16
2258 4214 1.079543 CCTGCAGCTGCGACTAGTT 60.080 57.895 32.11 0.00 45.83 2.24
2259 4215 2.575993 CCTGCAGCTGCGACTAGT 59.424 61.111 32.11 0.00 45.83 2.57
2260 4216 2.202851 CCCTGCAGCTGCGACTAG 60.203 66.667 32.11 23.15 45.83 2.57
2261 4217 4.457496 GCCCTGCAGCTGCGACTA 62.457 66.667 32.11 15.05 45.83 2.59
2269 4225 1.889573 GAATAGACGGCCCTGCAGC 60.890 63.158 8.66 0.00 0.00 5.25
2278 4234 2.853731 AGCGACTCTTGAATAGACGG 57.146 50.000 4.92 0.00 33.69 4.79
2281 4237 2.957006 GGGGTAGCGACTCTTGAATAGA 59.043 50.000 0.00 0.00 0.00 1.98
2294 4250 1.139095 GAGTCGTTCTGGGGTAGCG 59.861 63.158 0.00 0.00 0.00 4.26
2491 4475 5.135508 ACACTAGTGTCAAATACGCTCTT 57.864 39.130 22.95 0.00 46.05 2.85
2506 4490 6.510536 AGAGCGTTTTTAACACTACACTAGT 58.489 36.000 0.00 0.00 40.28 2.57
2515 4499 9.659830 CCCATAATATAAGAGCGTTTTTAACAC 57.340 33.333 0.00 0.00 0.00 3.32
2516 4500 9.616156 TCCCATAATATAAGAGCGTTTTTAACA 57.384 29.630 0.00 0.00 0.00 2.41
2517 4501 9.874215 GTCCCATAATATAAGAGCGTTTTTAAC 57.126 33.333 0.00 0.00 0.00 2.01
2518 4502 8.767085 CGTCCCATAATATAAGAGCGTTTTTAA 58.233 33.333 0.00 0.00 0.00 1.52
2520 4504 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2521 4505 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2522 4506 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2523 4507 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2524 4508 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2525 4509 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2526 4510 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2527 4511 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2528 4512 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2529 4513 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2530 4514 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2531 4515 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2532 4516 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2533 4517 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2534 4518 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2535 4519 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2536 4520 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2537 4521 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2538 4522 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2539 4523 2.158490 AGATTACTACTCCCTCCGTCCC 60.158 54.545 0.00 0.00 0.00 4.46
2540 4524 3.226682 AGATTACTACTCCCTCCGTCC 57.773 52.381 0.00 0.00 0.00 4.79
2541 4525 4.205587 TCAAGATTACTACTCCCTCCGTC 58.794 47.826 0.00 0.00 0.00 4.79
2542 4526 4.246712 TCAAGATTACTACTCCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
2543 4527 5.793030 ATTCAAGATTACTACTCCCTCCG 57.207 43.478 0.00 0.00 0.00 4.63
2544 4528 6.890293 ACAATTCAAGATTACTACTCCCTCC 58.110 40.000 0.00 0.00 0.00 4.30
2545 4529 8.915036 TCTACAATTCAAGATTACTACTCCCTC 58.085 37.037 0.00 0.00 0.00 4.30
2546 4530 8.697292 GTCTACAATTCAAGATTACTACTCCCT 58.303 37.037 0.00 0.00 0.00 4.20
2547 4531 8.475639 TGTCTACAATTCAAGATTACTACTCCC 58.524 37.037 0.00 0.00 0.00 4.30
2548 4532 9.522804 CTGTCTACAATTCAAGATTACTACTCC 57.477 37.037 0.00 0.00 0.00 3.85
2549 4533 9.522804 CCTGTCTACAATTCAAGATTACTACTC 57.477 37.037 0.00 0.00 0.00 2.59
2550 4534 8.478877 CCCTGTCTACAATTCAAGATTACTACT 58.521 37.037 0.00 0.00 0.00 2.57
2551 4535 8.258708 ACCCTGTCTACAATTCAAGATTACTAC 58.741 37.037 0.00 0.00 0.00 2.73
2552 4536 8.375493 ACCCTGTCTACAATTCAAGATTACTA 57.625 34.615 0.00 0.00 0.00 1.82
2553 4537 7.259088 ACCCTGTCTACAATTCAAGATTACT 57.741 36.000 0.00 0.00 0.00 2.24
2556 4540 7.775561 GGAATACCCTGTCTACAATTCAAGATT 59.224 37.037 7.28 0.00 0.00 2.40
2589 4573 3.364864 CCAACGTGCTTTTCATGATTCGA 60.365 43.478 0.00 0.00 35.66 3.71
2740 4729 6.374053 TCTTCAACATCGGCAATTCTTCATAA 59.626 34.615 0.00 0.00 0.00 1.90
2759 4748 3.244561 ACTCTCGCCCAAATTCTCTTCAA 60.245 43.478 0.00 0.00 0.00 2.69
3225 5222 2.092484 TGCCATGCAGTATAAGCCTTCA 60.092 45.455 0.00 0.00 33.32 3.02
3477 5491 3.696051 TGCTAATCACTGCAAGGATTTCC 59.304 43.478 15.30 9.07 39.30 3.13
3735 5809 0.108186 CAGTGCGCACTTCCCTCATA 60.108 55.000 39.13 0.00 40.20 2.15
3780 5854 4.083802 GCTTCCATTGTCACACTCTTGTAC 60.084 45.833 0.00 0.00 33.30 2.90
3878 5952 0.557238 TGGTGCATAGGAATGGGCAT 59.443 50.000 0.00 0.00 38.68 4.40
3880 5954 2.162681 GTATGGTGCATAGGAATGGGC 58.837 52.381 0.00 0.00 33.38 5.36
3903 5977 0.454452 GCAGAAACGAAACGGGATGC 60.454 55.000 0.00 0.00 0.00 3.91
3914 5988 6.775088 ACATATGAATACAACAGCAGAAACG 58.225 36.000 10.38 0.00 0.00 3.60
4002 6126 1.238439 CGCCAGTGACCTTGTCAATT 58.762 50.000 0.00 0.00 44.49 2.32
4015 6139 0.468226 TTTGTCTCCAGAACGCCAGT 59.532 50.000 0.00 0.00 0.00 4.00
4020 6144 1.566018 GCCGGTTTGTCTCCAGAACG 61.566 60.000 1.90 0.00 35.77 3.95
4047 6171 3.260884 TCGACTGGTAGAAAGCATTCCTT 59.739 43.478 0.00 0.00 36.12 3.36
4163 6289 1.006922 GCACAACCTTTGCTGAGCC 60.007 57.895 0.23 0.00 37.00 4.70
4164 6290 1.006922 GGCACAACCTTTGCTGAGC 60.007 57.895 0.00 0.00 40.07 4.26
4165 6291 1.662044 GGGCACAACCTTTGCTGAG 59.338 57.895 0.00 0.00 40.07 3.35
4166 6292 2.192861 CGGGCACAACCTTTGCTGA 61.193 57.895 0.00 0.00 40.07 4.26
4247 6373 5.306937 TCATACAAGACTTCTTCCTCCACAA 59.693 40.000 0.00 0.00 33.11 3.33
4250 6376 6.627087 ATTCATACAAGACTTCTTCCTCCA 57.373 37.500 0.00 0.00 33.11 3.86
4367 6493 4.754114 TGCCAAGCAAATAAATTCACAACC 59.246 37.500 0.00 0.00 34.76 3.77
4397 6523 1.465200 GGGACCGAGGGAGTATCTGC 61.465 65.000 0.00 0.00 33.73 4.26
4400 6526 1.492764 TTTGGGACCGAGGGAGTATC 58.507 55.000 0.00 0.00 0.00 2.24
4411 6537 4.652822 AGTTGAGACACTTATTTGGGACC 58.347 43.478 0.00 0.00 0.00 4.46
4420 6546 9.880157 AACTTTAGTACAAAGTTGAGACACTTA 57.120 29.630 23.48 0.00 45.58 2.24
4421 6547 8.788325 AACTTTAGTACAAAGTTGAGACACTT 57.212 30.769 23.48 7.33 45.58 3.16
4423 6549 9.310716 ACTAACTTTAGTACAAAGTTGAGACAC 57.689 33.333 27.85 0.00 46.41 3.67
4463 6589 8.934023 TGTCCCAAAATAAGTATCTCAACTTT 57.066 30.769 0.00 0.00 40.20 2.66
4464 6590 8.383175 TCTGTCCCAAAATAAGTATCTCAACTT 58.617 33.333 0.00 0.00 42.31 2.66
4465 6591 7.918076 TCTGTCCCAAAATAAGTATCTCAACT 58.082 34.615 0.00 0.00 0.00 3.16
4466 6592 7.281100 CCTCTGTCCCAAAATAAGTATCTCAAC 59.719 40.741 0.00 0.00 0.00 3.18
4467 6593 7.182026 TCCTCTGTCCCAAAATAAGTATCTCAA 59.818 37.037 0.00 0.00 0.00 3.02
4468 6594 6.672218 TCCTCTGTCCCAAAATAAGTATCTCA 59.328 38.462 0.00 0.00 0.00 3.27
4469 6595 7.125792 TCCTCTGTCCCAAAATAAGTATCTC 57.874 40.000 0.00 0.00 0.00 2.75
4470 6596 7.182930 ACTTCCTCTGTCCCAAAATAAGTATCT 59.817 37.037 0.00 0.00 0.00 1.98
4471 6597 7.339482 ACTTCCTCTGTCCCAAAATAAGTATC 58.661 38.462 0.00 0.00 0.00 2.24
4472 6598 7.272144 ACTTCCTCTGTCCCAAAATAAGTAT 57.728 36.000 0.00 0.00 0.00 2.12
4473 6599 6.697641 ACTTCCTCTGTCCCAAAATAAGTA 57.302 37.500 0.00 0.00 0.00 2.24
4483 6609 6.246919 TGCTATATACTACTTCCTCTGTCCC 58.753 44.000 0.00 0.00 0.00 4.46
4623 6750 9.661187 GAAGATCACAGCTGTATATTGAATTTG 57.339 33.333 21.20 2.36 0.00 2.32
4840 6968 2.027285 TGATTGGAAGCGTGGATCTCAA 60.027 45.455 0.00 0.00 0.00 3.02
4843 6971 1.745141 GCTGATTGGAAGCGTGGATCT 60.745 52.381 0.00 0.00 0.00 2.75
4947 7089 7.253905 AGCAAGGGTTCAGTAAGTAGATAAA 57.746 36.000 0.00 0.00 0.00 1.40
4949 7091 6.351881 CCAAGCAAGGGTTCAGTAAGTAGATA 60.352 42.308 0.00 0.00 0.00 1.98
4950 7092 5.491982 CAAGCAAGGGTTCAGTAAGTAGAT 58.508 41.667 0.00 0.00 0.00 1.98
5029 7171 2.033801 GCAGAAGCAAAAGCAGAAGACA 59.966 45.455 0.00 0.00 41.58 3.41


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

AutoCloner maintained by Alex Coulton.