Multiple sequence alignment - TraesCS5A01G346600

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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 TraesCS5A01G346600 chr5A 100.000 6856 0 0 1 6856 549323001 549316146 0.000000e+00 12661.0
1 TraesCS5A01G346600 chr5A 99.559 2493 10 1 4365 6856 549298017 549295525 0.000000e+00 4542.0
2 TraesCS5A01G346600 chr5A 96.372 1902 48 8 4628 6510 544226351 544228250 0.000000e+00 3110.0
3 TraesCS5A01G346600 chr5A 96.579 1491 28 9 1915 3389 544223347 544224830 0.000000e+00 2449.0
4 TraesCS5A01G346600 chr5A 94.886 1056 43 4 868 1921 544222274 544223320 0.000000e+00 1640.0
5 TraesCS5A01G346600 chr5A 94.174 944 22 11 3485 4405 544225003 544225936 0.000000e+00 1408.0
6 TraesCS5A01G346600 chr5A 92.808 876 46 6 1 869 29422704 29423569 0.000000e+00 1253.0
7 TraesCS5A01G346600 chr5A 89.145 304 24 1 6548 6851 544228250 544228544 3.020000e-98 370.0
8 TraesCS5A01G346600 chr3D 98.191 2874 44 3 3390 6256 434919506 434916634 0.000000e+00 5012.0
9 TraesCS5A01G346600 chr3D 97.356 1475 24 11 1918 3389 434921017 434919555 0.000000e+00 2494.0
10 TraesCS5A01G346600 chr3D 92.114 875 58 5 1 868 404549059 404548189 0.000000e+00 1223.0
11 TraesCS5A01G346600 chr3D 98.336 601 9 1 1321 1921 434921647 434921048 0.000000e+00 1053.0
12 TraesCS5A01G346600 chr3D 94.021 485 24 4 4257 4739 24753622 24754103 0.000000e+00 730.0
13 TraesCS5A01G346600 chr3D 95.187 187 8 1 6665 6851 434916644 434916459 1.870000e-75 294.0
14 TraesCS5A01G346600 chr3D 78.571 154 16 9 6484 6623 296427073 296426923 1.230000e-12 86.1
15 TraesCS5A01G346600 chr2B 96.078 3060 81 14 3485 6510 622906562 622909616 0.000000e+00 4950.0
16 TraesCS5A01G346600 chr2B 92.840 2067 94 26 894 2942 690776730 690778760 0.000000e+00 2948.0
17 TraesCS5A01G346600 chr2B 95.612 1823 60 6 3387 5192 690779205 690781024 0.000000e+00 2905.0
18 TraesCS5A01G346600 chr2B 96.776 1489 24 10 1915 3389 622904911 622906389 0.000000e+00 2462.0
19 TraesCS5A01G346600 chr2B 94.602 1056 45 5 868 1921 622903839 622904884 0.000000e+00 1624.0
20 TraesCS5A01G346600 chr2B 99.203 878 6 1 1 877 99957722 99958599 0.000000e+00 1581.0
21 TraesCS5A01G346600 chr2B 98.030 406 6 1 2984 3389 690778757 690779160 0.000000e+00 704.0
22 TraesCS5A01G346600 chr2B 90.964 332 28 1 3387 3718 410187359 410187030 4.880000e-121 446.0
23 TraesCS5A01G346600 chr2B 87.171 304 17 2 6548 6851 622909616 622909897 6.630000e-85 326.0
24 TraesCS5A01G346600 chr4A 95.671 3072 75 19 3485 6510 701699532 701696473 0.000000e+00 4883.0
25 TraesCS5A01G346600 chr4A 96.573 1488 28 10 1918 3389 701701185 701699705 0.000000e+00 2444.0
26 TraesCS5A01G346600 chr4A 94.102 1102 45 8 831 1921 701702307 701701215 0.000000e+00 1657.0
27 TraesCS5A01G346600 chr4A 95.455 946 31 3 976 1921 571068302 571067369 0.000000e+00 1498.0
28 TraesCS5A01G346600 chr4A 89.803 304 22 1 6548 6851 701696473 701696179 1.400000e-101 381.0
29 TraesCS5A01G346600 chr4A 77.922 154 27 7 826 974 725392002 725391851 9.470000e-14 89.8
30 TraesCS5A01G346600 chr3B 95.725 2994 72 18 3561 6510 609330805 609327824 0.000000e+00 4769.0
31 TraesCS5A01G346600 chr3B 96.800 2219 56 8 4302 6510 736488600 736490813 0.000000e+00 3690.0
32 TraesCS5A01G346600 chr3B 96.711 1490 26 9 1915 3389 736486201 736487682 0.000000e+00 2459.0
33 TraesCS5A01G346600 chr3B 94.418 1057 42 8 868 1921 736485132 736486174 0.000000e+00 1609.0
34 TraesCS5A01G346600 chr3B 96.577 964 16 7 1918 2868 609334329 609333370 0.000000e+00 1581.0
35 TraesCS5A01G346600 chr3B 99.079 869 8 0 1 869 663969082 663969950 0.000000e+00 1561.0
36 TraesCS5A01G346600 chr3B 95.873 945 30 2 977 1921 609332653 609331718 0.000000e+00 1520.0
37 TraesCS5A01G346600 chr3B 94.282 752 17 7 3485 4213 736487855 736488603 0.000000e+00 1127.0
38 TraesCS5A01G346600 chr3B 97.217 575 9 3 2819 3389 609333377 609332806 0.000000e+00 966.0
39 TraesCS5A01G346600 chr3B 93.982 565 23 4 895 1457 609335234 609334679 0.000000e+00 845.0
40 TraesCS5A01G346600 chr3B 96.138 492 12 2 1918 2402 609331688 609331197 0.000000e+00 797.0
41 TraesCS5A01G346600 chr3B 93.072 332 23 0 3387 3718 466386302 466385971 2.870000e-133 486.0
42 TraesCS5A01G346600 chr3B 80.978 552 59 35 822 1360 818230342 818230860 4.980000e-106 396.0
43 TraesCS5A01G346600 chr3B 90.461 304 20 1 6548 6851 736490813 736491107 6.450000e-105 392.0
44 TraesCS5A01G346600 chr3B 81.086 534 61 29 840 1360 818194610 818195116 2.320000e-104 390.0
45 TraesCS5A01G346600 chr3B 90.132 304 21 1 6548 6851 609327824 609327530 3.000000e-103 387.0
46 TraesCS5A01G346600 chr3B 84.980 253 23 7 840 1091 71887104 71887342 6.870000e-60 243.0
47 TraesCS5A01G346600 chr6B 96.473 2637 74 10 3890 6510 463397585 463400218 0.000000e+00 4337.0
48 TraesCS5A01G346600 chr6B 96.200 1342 29 9 1915 3242 463396252 463397585 0.000000e+00 2176.0
49 TraesCS5A01G346600 chr6B 95.349 946 35 2 976 1921 463395289 463396225 0.000000e+00 1495.0
50 TraesCS5A01G346600 chr6B 87.117 489 29 12 2377 2857 4365670 4366132 2.190000e-144 523.0
51 TraesCS5A01G346600 chr6B 90.461 304 20 1 6548 6851 463400218 463400512 6.450000e-105 392.0
52 TraesCS5A01G346600 chr2D 96.622 1717 45 9 4803 6510 5937025 5935313 0.000000e+00 2837.0
53 TraesCS5A01G346600 chr2D 90.878 296 15 2 6556 6851 5935300 5935017 3.000000e-103 387.0
54 TraesCS5A01G346600 chr4D 93.658 1624 75 13 4223 5839 215155599 215153997 0.000000e+00 2403.0
55 TraesCS5A01G346600 chr4D 91.695 879 58 8 1 871 80713552 80714423 0.000000e+00 1205.0
56 TraesCS5A01G346600 chr6A 92.614 1584 86 11 5204 6760 233347500 233349079 0.000000e+00 2248.0
57 TraesCS5A01G346600 chr6A 95.119 881 39 3 4223 5103 233346625 233347501 0.000000e+00 1386.0
58 TraesCS5A01G346600 chr6A 89.655 87 8 1 2919 3004 170907818 170907904 7.270000e-20 110.0
59 TraesCS5A01G346600 chr3A 99.313 873 5 1 1 872 565349252 565350124 0.000000e+00 1578.0
60 TraesCS5A01G346600 chr5B 99.198 873 6 1 1 872 696754826 696753954 0.000000e+00 1572.0
61 TraesCS5A01G346600 chr5B 92.401 329 25 0 3387 3715 361489767 361490095 2.890000e-128 470.0
62 TraesCS5A01G346600 chr2A 96.091 972 25 12 1 963 173808125 173809092 0.000000e+00 1572.0
63 TraesCS5A01G346600 chr7B 95.773 970 30 11 1 963 315075532 315076497 0.000000e+00 1554.0
64 TraesCS5A01G346600 chr7B 89.165 443 32 9 2470 2906 439933844 439933412 7.820000e-149 538.0
65 TraesCS5A01G346600 chrUn 94.068 944 23 11 3485 4405 394864794 394863861 0.000000e+00 1402.0
66 TraesCS5A01G346600 chrUn 97.938 388 7 1 3002 3389 394865353 394864967 0.000000e+00 671.0
67 TraesCS5A01G346600 chr1B 92.169 332 26 0 3387 3718 289303832 289303501 2.890000e-128 470.0
68 TraesCS5A01G346600 chr1B 91.867 332 27 0 3387 3718 666940442 666940111 1.350000e-126 464.0
69 TraesCS5A01G346600 chr1B 86.829 205 19 7 3715 3912 289302493 289302290 8.950000e-54 222.0
70 TraesCS5A01G346600 chr4B 91.867 332 27 0 3387 3718 145516221 145515890 1.350000e-126 464.0
71 TraesCS5A01G346600 chr4B 78.519 135 23 6 834 962 150986917 150987051 4.410000e-12 84.2
72 TraesCS5A01G346600 chr1A 92.331 326 25 0 3393 3718 375612981 375612656 1.350000e-126 464.0
73 TraesCS5A01G346600 chr1A 88.142 253 23 4 831 1078 244504362 244504112 1.870000e-75 294.0
74 TraesCS5A01G346600 chr7D 90.698 86 5 3 2921 3004 218418389 218418305 2.020000e-20 111.0
75 TraesCS5A01G346600 chr7D 88.172 93 7 4 2918 3008 470204878 470204788 2.610000e-19 108.0
76 TraesCS5A01G346600 chr1D 77.848 158 18 9 6484 6627 321326203 321326049 1.580000e-11 82.4


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 TraesCS5A01G346600 chr5A 549316146 549323001 6855 True 12661.000000 12661 100.00000 1 6856 1 chr5A.!!$R2 6855
1 TraesCS5A01G346600 chr5A 549295525 549298017 2492 True 4542.000000 4542 99.55900 4365 6856 1 chr5A.!!$R1 2491
2 TraesCS5A01G346600 chr5A 544222274 544228544 6270 False 1795.400000 3110 94.23120 868 6851 5 chr5A.!!$F2 5983
3 TraesCS5A01G346600 chr5A 29422704 29423569 865 False 1253.000000 1253 92.80800 1 869 1 chr5A.!!$F1 868
4 TraesCS5A01G346600 chr3D 434916459 434921647 5188 True 2213.250000 5012 97.26750 1321 6851 4 chr3D.!!$R3 5530
5 TraesCS5A01G346600 chr3D 404548189 404549059 870 True 1223.000000 1223 92.11400 1 868 1 chr3D.!!$R2 867
6 TraesCS5A01G346600 chr2B 622903839 622909897 6058 False 2340.500000 4950 93.65675 868 6851 4 chr2B.!!$F2 5983
7 TraesCS5A01G346600 chr2B 690776730 690781024 4294 False 2185.666667 2948 95.49400 894 5192 3 chr2B.!!$F3 4298
8 TraesCS5A01G346600 chr2B 99957722 99958599 877 False 1581.000000 1581 99.20300 1 877 1 chr2B.!!$F1 876
9 TraesCS5A01G346600 chr4A 701696179 701702307 6128 True 2341.250000 4883 94.03725 831 6851 4 chr4A.!!$R3 6020
10 TraesCS5A01G346600 chr4A 571067369 571068302 933 True 1498.000000 1498 95.45500 976 1921 1 chr4A.!!$R1 945
11 TraesCS5A01G346600 chr3B 736485132 736491107 5975 False 1855.400000 3690 94.53440 868 6851 5 chr3B.!!$F5 5983
12 TraesCS5A01G346600 chr3B 663969082 663969950 868 False 1561.000000 1561 99.07900 1 869 1 chr3B.!!$F2 868
13 TraesCS5A01G346600 chr3B 609327530 609335234 7704 True 1552.142857 4769 95.09200 895 6851 7 chr3B.!!$R2 5956
14 TraesCS5A01G346600 chr3B 818230342 818230860 518 False 396.000000 396 80.97800 822 1360 1 chr3B.!!$F4 538
15 TraesCS5A01G346600 chr3B 818194610 818195116 506 False 390.000000 390 81.08600 840 1360 1 chr3B.!!$F3 520
16 TraesCS5A01G346600 chr6B 463395289 463400512 5223 False 2100.000000 4337 94.62075 976 6851 4 chr6B.!!$F2 5875
17 TraesCS5A01G346600 chr2D 5935017 5937025 2008 True 1612.000000 2837 93.75000 4803 6851 2 chr2D.!!$R1 2048
18 TraesCS5A01G346600 chr4D 215153997 215155599 1602 True 2403.000000 2403 93.65800 4223 5839 1 chr4D.!!$R1 1616
19 TraesCS5A01G346600 chr4D 80713552 80714423 871 False 1205.000000 1205 91.69500 1 871 1 chr4D.!!$F1 870
20 TraesCS5A01G346600 chr6A 233346625 233349079 2454 False 1817.000000 2248 93.86650 4223 6760 2 chr6A.!!$F2 2537
21 TraesCS5A01G346600 chr3A 565349252 565350124 872 False 1578.000000 1578 99.31300 1 872 1 chr3A.!!$F1 871
22 TraesCS5A01G346600 chr5B 696753954 696754826 872 True 1572.000000 1572 99.19800 1 872 1 chr5B.!!$R1 871
23 TraesCS5A01G346600 chr2A 173808125 173809092 967 False 1572.000000 1572 96.09100 1 963 1 chr2A.!!$F1 962
24 TraesCS5A01G346600 chr7B 315075532 315076497 965 False 1554.000000 1554 95.77300 1 963 1 chr7B.!!$F1 962
25 TraesCS5A01G346600 chrUn 394863861 394865353 1492 True 1036.500000 1402 96.00300 3002 4405 2 chrUn.!!$R1 1403
26 TraesCS5A01G346600 chr1B 289302290 289303832 1542 True 346.000000 470 89.49900 3387 3912 2 chr1B.!!$R2 525

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
987 1012 0.039798 GAAAAACCGTTTCGAGCCCC 60.040 55.000 0.00 0.0 0.00 5.80 F
1217 1278 1.302033 CTAGCGCCATGGATGTCCC 60.302 63.158 18.40 0.0 34.29 4.46 F
2773 2882 0.877213 GCTTGGCCTGTTGTGCTTTG 60.877 55.000 3.32 0.0 0.00 2.77 F
4208 7228 0.251832 TCCGCTTCCTCTCTGAACCT 60.252 55.000 0.00 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 2332 0.540923 GGAGCTTGAGTCCATCAGCT 59.459 55.000 3.57 3.57 41.86 4.24 R
2811 2920 3.517296 TTCTGGTCCCAACTTGCATTA 57.483 42.857 0.00 0.00 0.00 1.90 R
4210 7230 0.037139 CAGAGAAGCAGCAGCAGACT 60.037 55.000 3.17 0.00 45.49 3.24 R
6516 9875 6.948886 ACTACTTTGTTGAGTGATCTCCTCTA 59.051 38.462 12.30 4.46 39.75 2.43 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
234 235 2.629137 CACCTCCCATGAGATCTCTGAG 59.371 54.545 22.95 19.76 41.42 3.35
304 305 0.595588 TTGGATTCACAAATGCGCGT 59.404 45.000 8.43 0.00 36.09 6.01
627 636 7.386848 TGGTCAGTAATAGCACAACTAAAGTTC 59.613 37.037 0.00 0.00 35.83 3.01
893 917 0.321653 AAACCAGCTACCGCTTCTGG 60.322 55.000 6.01 6.01 46.47 3.86
894 918 2.982130 CCAGCTACCGCTTCTGGT 59.018 61.111 0.00 0.00 46.47 4.00
896 920 1.021390 CCAGCTACCGCTTCTGGTTG 61.021 60.000 0.00 0.00 46.47 3.77
897 921 0.320771 CAGCTACCGCTTCTGGTTGT 60.321 55.000 0.00 0.00 46.47 3.32
898 922 1.067142 CAGCTACCGCTTCTGGTTGTA 60.067 52.381 0.00 0.00 46.47 2.41
899 923 1.067071 AGCTACCGCTTCTGGTTGTAC 60.067 52.381 0.00 0.00 46.47 2.90
900 924 1.625616 CTACCGCTTCTGGTTGTACG 58.374 55.000 0.00 0.00 43.56 3.67
901 925 0.961019 TACCGCTTCTGGTTGTACGT 59.039 50.000 0.00 0.00 43.56 3.57
903 927 1.342082 CCGCTTCTGGTTGTACGTCG 61.342 60.000 0.00 0.00 0.00 5.12
922 946 3.308323 GTCGTGCCAATTTTGCAGAAAAA 59.692 39.130 0.00 0.00 41.88 1.94
974 998 6.020121 GCGGTCCTTTTTAAAGTGAGAAAAAC 60.020 38.462 1.91 0.00 32.56 2.43
987 1012 0.039798 GAAAAACCGTTTCGAGCCCC 60.040 55.000 0.00 0.00 0.00 5.80
1217 1278 1.302033 CTAGCGCCATGGATGTCCC 60.302 63.158 18.40 0.00 34.29 4.46
1278 1339 2.038813 TCCACCAGCCAGATCCGA 59.961 61.111 0.00 0.00 0.00 4.55
1860 1922 8.489489 AGAGATTAGGACTGCTTGATTTATCAA 58.511 33.333 5.16 5.16 43.94 2.57
2293 2396 6.823689 ACGTCTTAATTACATTGGCTCTTGAT 59.176 34.615 0.00 0.00 0.00 2.57
2393 2496 9.476202 GTATGCACATCTACTGATACATACAAA 57.524 33.333 0.00 0.00 39.60 2.83
2773 2882 0.877213 GCTTGGCCTGTTGTGCTTTG 60.877 55.000 3.32 0.00 0.00 2.77
3501 3705 9.877178 TTTGTTATTGTTTGGCTTCTTAAGAAA 57.123 25.926 18.25 1.79 33.07 2.52
3662 5647 5.556355 CACATATGTGCACTCTGAAATGT 57.444 39.130 22.27 14.14 39.39 2.71
3833 6830 1.582968 CATGTTGTGCAGTGGCTCC 59.417 57.895 0.00 0.00 41.91 4.70
3901 6915 0.909610 ACATCGGTGAGGGTGGTCAT 60.910 55.000 0.65 0.00 0.00 3.06
3987 7001 2.106566 GCTCATCTCCAAGACCTCTGA 58.893 52.381 0.00 0.00 0.00 3.27
4008 7022 0.393820 GTCGTGTGTCCCCCAAGTTA 59.606 55.000 0.00 0.00 0.00 2.24
4124 7138 2.203181 GCTCTCTGATGCTGCCCC 60.203 66.667 0.00 0.00 0.00 5.80
4208 7228 0.251832 TCCGCTTCCTCTCTGAACCT 60.252 55.000 0.00 0.00 0.00 3.50
4209 7229 0.174617 CCGCTTCCTCTCTGAACCTC 59.825 60.000 0.00 0.00 0.00 3.85
4210 7230 0.891373 CGCTTCCTCTCTGAACCTCA 59.109 55.000 0.00 0.00 0.00 3.86
4211 7231 1.135141 CGCTTCCTCTCTGAACCTCAG 60.135 57.143 0.00 0.00 45.59 3.35
4212 7232 1.899142 GCTTCCTCTCTGAACCTCAGT 59.101 52.381 3.71 0.00 44.58 3.41
4213 7233 2.094234 GCTTCCTCTCTGAACCTCAGTC 60.094 54.545 3.71 0.00 44.58 3.51
4214 7234 3.430453 CTTCCTCTCTGAACCTCAGTCT 58.570 50.000 3.71 0.00 44.58 3.24
4215 7235 2.801483 TCCTCTCTGAACCTCAGTCTG 58.199 52.381 3.71 0.00 44.58 3.51
4216 7236 1.204467 CCTCTCTGAACCTCAGTCTGC 59.796 57.143 3.71 0.00 44.58 4.26
4217 7237 2.170166 CTCTCTGAACCTCAGTCTGCT 58.830 52.381 3.71 0.00 44.58 4.24
4218 7238 1.891811 TCTCTGAACCTCAGTCTGCTG 59.108 52.381 3.71 0.00 44.58 4.41
4219 7239 0.319728 TCTGAACCTCAGTCTGCTGC 59.680 55.000 3.71 0.00 44.58 5.25
4220 7240 0.321021 CTGAACCTCAGTCTGCTGCT 59.679 55.000 0.00 0.00 42.29 4.24
4221 7241 0.034476 TGAACCTCAGTCTGCTGCTG 59.966 55.000 0.00 0.00 42.29 4.41
4235 7255 1.666700 GCTGCTGCTTCTCTGATTCAG 59.333 52.381 8.53 7.38 36.03 3.02
4258 7278 8.792633 TCAGAGTAAACCAATAAACAGGAATTG 58.207 33.333 0.00 0.00 33.72 2.32
4259 7279 8.576442 CAGAGTAAACCAATAAACAGGAATTGT 58.424 33.333 0.00 0.00 43.45 2.71
4260 7280 9.802039 AGAGTAAACCAATAAACAGGAATTGTA 57.198 29.630 0.00 0.00 39.73 2.41
4263 7283 9.581099 GTAAACCAATAAACAGGAATTGTATGG 57.419 33.333 0.00 0.00 39.73 2.74
4264 7284 8.429237 AAACCAATAAACAGGAATTGTATGGA 57.571 30.769 0.00 0.00 39.73 3.41
4265 7285 7.404671 ACCAATAAACAGGAATTGTATGGAC 57.595 36.000 0.00 0.00 39.73 4.02
4266 7286 7.182060 ACCAATAAACAGGAATTGTATGGACT 58.818 34.615 0.00 0.00 39.73 3.85
4267 7287 7.673926 ACCAATAAACAGGAATTGTATGGACTT 59.326 33.333 0.00 0.00 39.73 3.01
4268 7288 8.190784 CCAATAAACAGGAATTGTATGGACTTC 58.809 37.037 0.00 0.00 39.73 3.01
4269 7289 8.960591 CAATAAACAGGAATTGTATGGACTTCT 58.039 33.333 0.00 0.00 39.73 2.85
4271 7291 9.838339 ATAAACAGGAATTGTATGGACTTCTAG 57.162 33.333 0.00 0.00 39.73 2.43
4272 7292 6.240549 ACAGGAATTGTATGGACTTCTAGG 57.759 41.667 0.00 0.00 38.56 3.02
4273 7293 5.726793 ACAGGAATTGTATGGACTTCTAGGT 59.273 40.000 0.00 0.00 38.56 3.08
4274 7294 6.127026 ACAGGAATTGTATGGACTTCTAGGTC 60.127 42.308 0.00 0.00 38.56 3.85
4275 7295 5.069251 AGGAATTGTATGGACTTCTAGGTCG 59.931 44.000 0.00 0.00 37.12 4.79
4276 7296 5.163437 GGAATTGTATGGACTTCTAGGTCGT 60.163 44.000 0.00 0.00 37.12 4.34
4277 7297 4.713824 TTGTATGGACTTCTAGGTCGTG 57.286 45.455 0.00 0.00 37.12 4.35
4278 7298 3.693807 TGTATGGACTTCTAGGTCGTGT 58.306 45.455 0.00 0.00 37.12 4.49
4279 7299 4.084287 TGTATGGACTTCTAGGTCGTGTT 58.916 43.478 0.00 0.00 37.12 3.32
4280 7300 4.525487 TGTATGGACTTCTAGGTCGTGTTT 59.475 41.667 0.00 0.00 37.12 2.83
4281 7301 3.655276 TGGACTTCTAGGTCGTGTTTC 57.345 47.619 0.00 0.00 37.12 2.78
4282 7302 2.298163 TGGACTTCTAGGTCGTGTTTCC 59.702 50.000 0.00 0.00 37.12 3.13
4283 7303 2.561858 GGACTTCTAGGTCGTGTTTCCT 59.438 50.000 0.00 0.00 37.12 3.36
4284 7304 3.006644 GGACTTCTAGGTCGTGTTTCCTT 59.993 47.826 0.00 0.00 37.12 3.36
4285 7305 4.502777 GGACTTCTAGGTCGTGTTTCCTTT 60.503 45.833 0.00 0.00 37.12 3.11
4286 7306 4.377897 ACTTCTAGGTCGTGTTTCCTTTG 58.622 43.478 0.00 0.00 35.51 2.77
4287 7307 3.396260 TCTAGGTCGTGTTTCCTTTGG 57.604 47.619 0.00 0.00 35.51 3.28
4288 7308 2.701951 TCTAGGTCGTGTTTCCTTTGGT 59.298 45.455 0.00 0.00 35.51 3.67
4289 7309 3.896888 TCTAGGTCGTGTTTCCTTTGGTA 59.103 43.478 0.00 0.00 35.51 3.25
4290 7310 3.564053 AGGTCGTGTTTCCTTTGGTAA 57.436 42.857 0.00 0.00 0.00 2.85
4291 7311 3.208594 AGGTCGTGTTTCCTTTGGTAAC 58.791 45.455 0.00 0.00 34.31 2.50
4292 7312 4.141756 TAGGTCGTGTTTCCTTTGGTAACA 60.142 41.667 4.98 4.98 39.88 2.41
4293 7313 5.969803 TAGGTCGTGTTTCCTTTGGTAACAG 60.970 44.000 8.65 4.85 42.07 3.16
4294 7314 8.312212 TAGGTCGTGTTTCCTTTGGTAACAGT 62.312 42.308 8.65 0.00 42.07 3.55
4295 7315 9.683548 TAGGTCGTGTTTCCTTTGGTAACAGTT 62.684 40.741 8.65 0.00 42.07 3.16
4347 7471 2.041216 ACGATTAGGCTTCCAAGGGTTT 59.959 45.455 0.00 0.00 0.00 3.27
4597 7722 9.143155 GGGATATTTAATGCTCCCTTTTCTTAA 57.857 33.333 15.78 0.00 43.45 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
234 235 5.737290 AGCAAATGTAATATGCGTCGAAAAC 59.263 36.000 0.00 0.00 44.60 2.43
304 305 8.594550 AGAACTAACCTCTACTTGAAAGCATTA 58.405 33.333 0.00 0.00 0.00 1.90
601 610 6.765403 ACTTTAGTTGTGCTATTACTGACCA 58.235 36.000 0.00 0.00 0.00 4.02
602 611 7.411588 CGAACTTTAGTTGTGCTATTACTGACC 60.412 40.741 0.00 0.00 38.56 4.02
603 612 7.115947 ACGAACTTTAGTTGTGCTATTACTGAC 59.884 37.037 0.00 0.00 38.56 3.51
604 613 7.115805 CACGAACTTTAGTTGTGCTATTACTGA 59.884 37.037 0.00 0.00 38.56 3.41
605 614 7.115805 TCACGAACTTTAGTTGTGCTATTACTG 59.884 37.037 14.71 0.00 38.56 2.74
606 615 7.149973 TCACGAACTTTAGTTGTGCTATTACT 58.850 34.615 14.71 0.00 38.56 2.24
627 636 9.172820 CCATTTCATAATGATATGTTGTTCACG 57.827 33.333 6.13 0.00 43.12 4.35
884 907 1.342082 CGACGTACAACCAGAAGCGG 61.342 60.000 0.00 0.00 0.00 5.52
893 917 2.673976 AAATTGGCACGACGTACAAC 57.326 45.000 16.42 2.32 0.00 3.32
894 918 2.855187 GCAAAATTGGCACGACGTACAA 60.855 45.455 16.41 16.41 0.00 2.41
896 920 1.323791 GCAAAATTGGCACGACGTAC 58.676 50.000 0.00 0.00 0.00 3.67
897 921 0.945099 TGCAAAATTGGCACGACGTA 59.055 45.000 0.00 0.00 36.11 3.57
898 922 0.317770 CTGCAAAATTGGCACGACGT 60.318 50.000 0.00 0.00 36.11 4.34
899 923 0.040514 TCTGCAAAATTGGCACGACG 60.041 50.000 0.00 0.00 36.11 5.12
900 924 2.132740 TTCTGCAAAATTGGCACGAC 57.867 45.000 0.00 0.00 36.11 4.34
901 925 2.879002 TTTCTGCAAAATTGGCACGA 57.121 40.000 0.00 0.00 36.11 4.35
903 927 4.320421 GGGATTTTTCTGCAAAATTGGCAC 60.320 41.667 0.00 0.00 43.89 5.01
922 946 7.342026 GGGTTGAATATCAAAAACTACAGGGAT 59.658 37.037 0.00 0.00 38.22 3.85
1200 1261 2.828868 GGGACATCCATGGCGCTA 59.171 61.111 6.96 0.00 44.58 4.26
1201 1262 4.552365 CGGGACATCCATGGCGCT 62.552 66.667 6.96 0.00 45.68 5.92
1202 1263 4.856801 ACGGGACATCCATGGCGC 62.857 66.667 6.96 0.00 44.54 6.53
1203 1264 2.588877 GACGGGACATCCATGGCG 60.589 66.667 6.96 6.23 36.40 5.69
1204 1265 2.203209 GGACGGGACATCCATGGC 60.203 66.667 6.96 0.00 42.28 4.40
1217 1278 2.530497 CGAGGAGAGCTCGAGGACG 61.530 68.421 15.58 8.35 46.06 4.79
1768 1829 3.310193 GGCCAAGACTATACTCCTCCTT 58.690 50.000 0.00 0.00 0.00 3.36
1860 1922 4.042684 AGCTCCAGATCAAGGTTTTCTCTT 59.957 41.667 0.00 0.00 0.00 2.85
1877 1939 1.153765 CTGCATCGACGAAGCTCCA 60.154 57.895 23.62 5.16 0.00 3.86
2233 2332 0.540923 GGAGCTTGAGTCCATCAGCT 59.459 55.000 3.57 3.57 41.86 4.24
2773 2882 6.374333 TGTGTTGAAATATGAAAGCTCTACCC 59.626 38.462 0.00 0.00 0.00 3.69
2805 2914 4.346418 TGGTCCCAACTTGCATTATTGTTT 59.654 37.500 0.00 0.00 0.00 2.83
2809 2918 4.046286 TCTGGTCCCAACTTGCATTATT 57.954 40.909 0.00 0.00 0.00 1.40
2810 2919 3.737559 TCTGGTCCCAACTTGCATTAT 57.262 42.857 0.00 0.00 0.00 1.28
2811 2920 3.517296 TTCTGGTCCCAACTTGCATTA 57.483 42.857 0.00 0.00 0.00 1.90
2993 3149 7.148154 CGGATATCTAGAAACATACTCCCTCTG 60.148 44.444 2.05 0.00 0.00 3.35
2994 3150 6.887545 CGGATATCTAGAAACATACTCCCTCT 59.112 42.308 2.05 0.00 0.00 3.69
3501 3705 3.123621 CGAGTCGTTGCTTGCTAGATTTT 59.876 43.478 3.82 0.00 0.00 1.82
3833 6830 5.004061 GTGTTCAATCACAATGCGATGAATG 59.996 40.000 0.00 0.00 38.12 2.67
3901 6915 5.067283 GTCTGGTGGTTTTAGCTTTTCTTCA 59.933 40.000 0.00 0.00 0.00 3.02
3987 7001 1.374947 CTTGGGGGACACACGACAT 59.625 57.895 0.00 0.00 0.00 3.06
4008 7022 0.105039 GGCGAGGAGATTCGGTGAAT 59.895 55.000 0.00 0.00 40.79 2.57
4124 7138 2.498078 GTTGGAGAAGGAGAGGTACAGG 59.502 54.545 0.00 0.00 0.00 4.00
4210 7230 0.037139 CAGAGAAGCAGCAGCAGACT 60.037 55.000 3.17 0.00 45.49 3.24
4211 7231 0.037512 TCAGAGAAGCAGCAGCAGAC 60.038 55.000 3.17 0.00 45.49 3.51
4212 7232 0.903236 ATCAGAGAAGCAGCAGCAGA 59.097 50.000 3.17 0.00 45.49 4.26
4213 7233 1.666700 GAATCAGAGAAGCAGCAGCAG 59.333 52.381 3.17 0.00 45.49 4.24
4214 7234 1.002773 TGAATCAGAGAAGCAGCAGCA 59.997 47.619 3.17 0.00 45.49 4.41
4215 7235 1.666700 CTGAATCAGAGAAGCAGCAGC 59.333 52.381 3.77 0.00 35.57 5.25
4216 7236 3.248495 TCTGAATCAGAGAAGCAGCAG 57.752 47.619 9.18 0.00 35.39 4.24
4258 7278 4.715527 AACACGACCTAGAAGTCCATAC 57.284 45.455 0.00 0.00 32.91 2.39
4259 7279 4.159135 GGAAACACGACCTAGAAGTCCATA 59.841 45.833 0.00 0.00 32.91 2.74
4260 7280 3.056035 GGAAACACGACCTAGAAGTCCAT 60.056 47.826 0.00 0.00 32.91 3.41
4261 7281 2.298163 GGAAACACGACCTAGAAGTCCA 59.702 50.000 0.00 0.00 32.91 4.02
4262 7282 2.561858 AGGAAACACGACCTAGAAGTCC 59.438 50.000 0.00 0.00 34.47 3.85
4263 7283 3.938289 AGGAAACACGACCTAGAAGTC 57.062 47.619 0.00 0.00 34.47 3.01
4264 7284 4.377897 CAAAGGAAACACGACCTAGAAGT 58.622 43.478 0.00 0.00 35.25 3.01
4265 7285 3.746492 CCAAAGGAAACACGACCTAGAAG 59.254 47.826 0.00 0.00 35.25 2.85
4266 7286 3.135167 ACCAAAGGAAACACGACCTAGAA 59.865 43.478 0.00 0.00 35.25 2.10
4267 7287 2.701951 ACCAAAGGAAACACGACCTAGA 59.298 45.455 0.00 0.00 35.25 2.43
4268 7288 3.121738 ACCAAAGGAAACACGACCTAG 57.878 47.619 0.00 0.00 35.25 3.02
4269 7289 4.141756 TGTTACCAAAGGAAACACGACCTA 60.142 41.667 0.00 0.00 35.25 3.08
4270 7290 3.208594 GTTACCAAAGGAAACACGACCT 58.791 45.455 0.00 0.00 38.23 3.85
4271 7291 2.944349 TGTTACCAAAGGAAACACGACC 59.056 45.455 0.00 0.00 0.00 4.79
4272 7292 3.624410 ACTGTTACCAAAGGAAACACGAC 59.376 43.478 0.00 0.00 0.00 4.34
4273 7293 3.876341 ACTGTTACCAAAGGAAACACGA 58.124 40.909 0.00 0.00 0.00 4.35
4274 7294 4.625972 AACTGTTACCAAAGGAAACACG 57.374 40.909 0.00 0.00 0.00 4.49
4275 7295 7.485810 ACAATAACTGTTACCAAAGGAAACAC 58.514 34.615 1.73 0.00 32.99 3.32
4276 7296 7.648039 ACAATAACTGTTACCAAAGGAAACA 57.352 32.000 1.73 0.00 32.99 2.83
4277 7297 9.673454 CTAACAATAACTGTTACCAAAGGAAAC 57.327 33.333 1.73 0.00 46.75 2.78
4278 7298 9.411189 ACTAACAATAACTGTTACCAAAGGAAA 57.589 29.630 1.73 0.00 46.75 3.13
4279 7299 8.983702 ACTAACAATAACTGTTACCAAAGGAA 57.016 30.769 1.73 0.00 46.75 3.36
4280 7300 8.983702 AACTAACAATAACTGTTACCAAAGGA 57.016 30.769 1.73 0.00 46.75 3.36
4281 7301 9.063615 AGAACTAACAATAACTGTTACCAAAGG 57.936 33.333 1.73 0.00 46.75 3.11
4298 7318 9.296400 GCACTGAAAAATTGTTTAGAACTAACA 57.704 29.630 7.13 0.00 0.00 2.41
4299 7319 8.752254 GGCACTGAAAAATTGTTTAGAACTAAC 58.248 33.333 7.13 0.00 0.00 2.34
4300 7320 8.470805 TGGCACTGAAAAATTGTTTAGAACTAA 58.529 29.630 7.13 0.00 0.00 2.24
5007 8327 1.196127 CAGCCTGCACACATATATGCG 59.804 52.381 12.79 5.89 45.13 4.73
6516 9875 6.948886 ACTACTTTGTTGAGTGATCTCCTCTA 59.051 38.462 12.30 4.46 39.75 2.43


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

AutoCloner maintained by Alex Coulton.