Multiple sequence alignment - TraesCS3D01G465200

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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 TraesCS3D01G465200 chr3D 100.000 3466 0 0 1 3466 569120605 569117140 0.000000e+00 6401.0
1 TraesCS3D01G465200 chr3D 90.603 2256 170 22 980 3222 567516900 567519126 0.000000e+00 2953.0
2 TraesCS3D01G465200 chr3D 80.676 1273 182 33 950 2173 567664911 567663654 0.000000e+00 929.0
3 TraesCS3D01G465200 chr3D 81.654 1161 176 16 1040 2173 568234906 568236056 0.000000e+00 929.0
4 TraesCS3D01G465200 chr3D 81.629 1105 174 17 1085 2173 58089771 58088680 0.000000e+00 889.0
5 TraesCS3D01G465200 chr3D 81.533 1083 164 12 1083 2138 566954628 566955701 0.000000e+00 859.0
6 TraesCS3D01G465200 chr3D 77.787 1265 202 51 955 2173 567691215 567689984 0.000000e+00 706.0
7 TraesCS3D01G465200 chr3D 85.618 445 60 4 1732 2174 567486234 567486676 6.780000e-127 464.0
8 TraesCS3D01G465200 chr3D 92.742 124 9 0 2825 2948 568020288 568020411 2.750000e-41 180.0
9 TraesCS3D01G465200 chr3A 93.309 2152 123 12 1084 3222 701643452 701645595 0.000000e+00 3157.0
10 TraesCS3D01G465200 chr3A 88.483 877 57 20 1 842 199148527 199149394 0.000000e+00 1020.0
11 TraesCS3D01G465200 chr3A 82.172 1105 168 17 1085 2173 66914196 66913105 0.000000e+00 922.0
12 TraesCS3D01G465200 chr3A 79.170 1133 187 32 1075 2170 701351715 701352835 0.000000e+00 739.0
13 TraesCS3D01G465200 chr3A 98.446 193 3 0 3274 3466 701645577 701645769 1.190000e-89 340.0
14 TraesCS3D01G465200 chr3A 97.143 35 1 0 3144 3178 702412336 702412302 3.740000e-05 60.2
15 TraesCS3D01G465200 chrUn 92.055 1674 108 11 843 2509 287633092 287634747 0.000000e+00 2331.0
16 TraesCS3D01G465200 chrUn 92.055 1674 108 11 843 2509 292972922 292971267 0.000000e+00 2331.0
17 TraesCS3D01G465200 chrUn 93.265 1277 79 2 1233 2509 338767959 338766690 0.000000e+00 1875.0
18 TraesCS3D01G465200 chrUn 92.837 363 24 1 2862 3222 287634894 287635256 3.060000e-145 525.0
19 TraesCS3D01G465200 chrUn 92.837 363 24 1 2862 3222 292971120 292970758 3.060000e-145 525.0
20 TraesCS3D01G465200 chrUn 92.837 363 24 1 2862 3222 338766543 338766181 3.060000e-145 525.0
21 TraesCS3D01G465200 chrUn 86.538 156 19 2 2192 2346 299518414 299518568 1.650000e-38 171.0
22 TraesCS3D01G465200 chrUn 86.538 156 19 2 2192 2346 406080171 406080325 1.650000e-38 171.0
23 TraesCS3D01G465200 chrUn 85.897 156 20 2 2192 2346 217829524 217829678 7.700000e-37 165.0
24 TraesCS3D01G465200 chrUn 85.897 156 20 2 2192 2346 227093792 227093946 7.700000e-37 165.0
25 TraesCS3D01G465200 chrUn 83.333 186 8 4 3274 3459 287635238 287635400 2.150000e-32 150.0
26 TraesCS3D01G465200 chrUn 83.333 186 8 4 3274 3459 292970776 292970614 2.150000e-32 150.0
27 TraesCS3D01G465200 chrUn 83.333 186 8 4 3274 3459 338766199 338766037 2.150000e-32 150.0
28 TraesCS3D01G465200 chr6B 80.769 1066 175 23 1092 2148 685208396 685207352 0.000000e+00 806.0
29 TraesCS3D01G465200 chr6B 93.333 495 29 4 237 728 711314388 711313895 0.000000e+00 728.0
30 TraesCS3D01G465200 chr6B 94.629 391 14 6 340 728 710660435 710660050 1.780000e-167 599.0
31 TraesCS3D01G465200 chr6B 85.201 473 61 6 2591 3055 685206630 685206159 8.700000e-131 477.0
32 TraesCS3D01G465200 chr6B 98.387 124 2 0 719 842 711313870 711313747 5.820000e-53 219.0
33 TraesCS3D01G465200 chr6B 97.581 124 3 0 719 842 710660025 710659902 2.710000e-51 213.0
34 TraesCS3D01G465200 chr6A 80.336 1073 174 24 1092 2148 596777193 596776142 0.000000e+00 778.0
35 TraesCS3D01G465200 chr6A 84.426 488 67 6 2576 3055 596775612 596775126 4.050000e-129 472.0
36 TraesCS3D01G465200 chr6A 81.513 595 73 19 2649 3222 596773810 596773232 4.080000e-124 455.0
37 TraesCS3D01G465200 chr7B 78.346 1076 180 29 1092 2148 747614426 747615467 0.000000e+00 647.0
38 TraesCS3D01G465200 chr7B 94.030 67 4 0 3209 3275 690699606 690699540 6.120000e-18 102.0
39 TraesCS3D01G465200 chr7B 96.667 60 0 2 3216 3275 536117582 536117639 7.920000e-17 99.0
40 TraesCS3D01G465200 chr4B 92.899 338 19 5 1 333 96443024 96442687 1.450000e-133 486.0
41 TraesCS3D01G465200 chr4B 78.679 530 74 25 2 521 460793427 460793927 2.010000e-82 316.0
42 TraesCS3D01G465200 chr4B 88.462 52 6 0 3303 3354 515115831 515115780 2.890000e-06 63.9
43 TraesCS3D01G465200 chr6D 82.125 593 69 17 2649 3222 451116694 451116120 1.130000e-129 473.0
44 TraesCS3D01G465200 chr5B 81.853 529 81 13 2 521 297828578 297829100 6.870000e-117 431.0
45 TraesCS3D01G465200 chr5B 96.667 60 2 0 3216 3275 512980706 512980765 2.200000e-17 100.0
46 TraesCS3D01G465200 chr5B 90.698 43 4 0 3311 3353 280602315 280602357 1.340000e-04 58.4
47 TraesCS3D01G465200 chr2B 78.775 702 106 32 6 683 22551078 22551760 6.870000e-117 431.0
48 TraesCS3D01G465200 chr2B 90.909 77 4 2 3200 3275 331010191 331010265 2.200000e-17 100.0
49 TraesCS3D01G465200 chr2B 93.651 63 4 0 3211 3273 307578401 307578463 1.020000e-15 95.3
50 TraesCS3D01G465200 chr5A 100.000 56 0 0 3220 3275 473631403 473631458 1.700000e-18 104.0
51 TraesCS3D01G465200 chr2D 98.333 60 0 1 3217 3275 155831313 155831372 1.700000e-18 104.0
52 TraesCS3D01G465200 chr2D 88.462 78 8 1 444 521 23075328 23075404 3.680000e-15 93.5
53 TraesCS3D01G465200 chr2D 91.304 46 4 0 3311 3356 530555143 530555098 2.890000e-06 63.9
54 TraesCS3D01G465200 chr1A 100.000 56 0 0 3220 3275 550884838 550884893 1.700000e-18 104.0
55 TraesCS3D01G465200 chr1A 85.897 78 7 3 3391 3466 27330318 27330393 2.870000e-11 80.5
56 TraesCS3D01G465200 chr1B 96.667 60 2 0 3216 3275 402109830 402109889 2.200000e-17 100.0
57 TraesCS3D01G465200 chr1B 84.946 93 9 4 3376 3466 41842397 41842486 4.760000e-14 89.8
58 TraesCS3D01G465200 chr1B 90.385 52 3 2 3305 3355 484715890 484715940 2.230000e-07 67.6
59 TraesCS3D01G465200 chr7D 78.873 142 22 7 2373 2509 41599932 41599794 4.760000e-14 89.8
60 TraesCS3D01G465200 chr7A 82.692 104 14 3 2373 2472 41046909 41046806 4.760000e-14 89.8
61 TraesCS3D01G465200 chr7A 100.000 29 0 0 281 309 602041784 602041756 2.000000e-03 54.7
62 TraesCS3D01G465200 chr4A 83.696 92 11 3 2382 2469 648793425 648793334 2.220000e-12 84.2
63 TraesCS3D01G465200 chr4A 85.000 60 6 2 380 438 690408377 690408434 1.340000e-04 58.4
64 TraesCS3D01G465200 chr1D 84.444 90 9 4 3379 3466 26268365 26268279 2.220000e-12 84.2
65 TraesCS3D01G465200 chr2A 91.489 47 2 2 3309 3354 191635892 191635847 2.890000e-06 63.9


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 TraesCS3D01G465200 chr3D 569117140 569120605 3465 True 6401.000000 6401 100.000000 1 3466 1 chr3D.!!$R4 3465
1 TraesCS3D01G465200 chr3D 567516900 567519126 2226 False 2953.000000 2953 90.603000 980 3222 1 chr3D.!!$F3 2242
2 TraesCS3D01G465200 chr3D 567663654 567664911 1257 True 929.000000 929 80.676000 950 2173 1 chr3D.!!$R2 1223
3 TraesCS3D01G465200 chr3D 568234906 568236056 1150 False 929.000000 929 81.654000 1040 2173 1 chr3D.!!$F5 1133
4 TraesCS3D01G465200 chr3D 58088680 58089771 1091 True 889.000000 889 81.629000 1085 2173 1 chr3D.!!$R1 1088
5 TraesCS3D01G465200 chr3D 566954628 566955701 1073 False 859.000000 859 81.533000 1083 2138 1 chr3D.!!$F1 1055
6 TraesCS3D01G465200 chr3D 567689984 567691215 1231 True 706.000000 706 77.787000 955 2173 1 chr3D.!!$R3 1218
7 TraesCS3D01G465200 chr3A 701643452 701645769 2317 False 1748.500000 3157 95.877500 1084 3466 2 chr3A.!!$F3 2382
8 TraesCS3D01G465200 chr3A 199148527 199149394 867 False 1020.000000 1020 88.483000 1 842 1 chr3A.!!$F1 841
9 TraesCS3D01G465200 chr3A 66913105 66914196 1091 True 922.000000 922 82.172000 1085 2173 1 chr3A.!!$R1 1088
10 TraesCS3D01G465200 chr3A 701351715 701352835 1120 False 739.000000 739 79.170000 1075 2170 1 chr3A.!!$F2 1095
11 TraesCS3D01G465200 chrUn 287633092 287635400 2308 False 1002.000000 2331 89.408333 843 3459 3 chrUn.!!$F5 2616
12 TraesCS3D01G465200 chrUn 292970614 292972922 2308 True 1002.000000 2331 89.408333 843 3459 3 chrUn.!!$R1 2616
13 TraesCS3D01G465200 chrUn 338766037 338767959 1922 True 850.000000 1875 89.811667 1233 3459 3 chrUn.!!$R2 2226
14 TraesCS3D01G465200 chr6B 685206159 685208396 2237 True 641.500000 806 82.985000 1092 3055 2 chr6B.!!$R1 1963
15 TraesCS3D01G465200 chr6B 711313747 711314388 641 True 473.500000 728 95.860000 237 842 2 chr6B.!!$R3 605
16 TraesCS3D01G465200 chr6B 710659902 710660435 533 True 406.000000 599 96.105000 340 842 2 chr6B.!!$R2 502
17 TraesCS3D01G465200 chr6A 596773232 596777193 3961 True 568.333333 778 82.091667 1092 3222 3 chr6A.!!$R1 2130
18 TraesCS3D01G465200 chr7B 747614426 747615467 1041 False 647.000000 647 78.346000 1092 2148 1 chr7B.!!$F2 1056
19 TraesCS3D01G465200 chr4B 460793427 460793927 500 False 316.000000 316 78.679000 2 521 1 chr4B.!!$F1 519
20 TraesCS3D01G465200 chr6D 451116120 451116694 574 True 473.000000 473 82.125000 2649 3222 1 chr6D.!!$R1 573
21 TraesCS3D01G465200 chr5B 297828578 297829100 522 False 431.000000 431 81.853000 2 521 1 chr5B.!!$F2 519
22 TraesCS3D01G465200 chr2B 22551078 22551760 682 False 431.000000 431 78.775000 6 683 1 chr2B.!!$F1 677

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
71 72 1.084289 GGAACTCCAGCGCGTAAAAT 58.916 50.0 8.43 0.0 35.64 1.82 F
1308 1451 0.249657 GGAGATCATCACCTGCGACC 60.250 60.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 1964 0.400213 TGGCCAGAAACAATCGGAGT 59.600 50.0 0.00 0.0 0.0 3.85 R
3264 5850 0.465642 CATTTTAGCTCCCCGGACCC 60.466 60.0 0.73 0.0 0.0 4.46 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
71 72 1.084289 GGAACTCCAGCGCGTAAAAT 58.916 50.000 8.43 0.00 35.64 1.82
73 74 2.870411 GGAACTCCAGCGCGTAAAATAT 59.130 45.455 8.43 0.00 35.64 1.28
74 75 4.053295 GGAACTCCAGCGCGTAAAATATA 58.947 43.478 8.43 0.00 35.64 0.86
117 119 3.029757 CAGATATCGAACTCGTGACGTG 58.970 50.000 4.40 4.96 40.80 4.49
125 127 4.254672 TCGTGACGTGCCGTTCGT 62.255 61.111 4.40 8.70 41.37 3.85
176 179 3.003339 CGTTTTACGTGTCTGTATGCG 57.997 47.619 0.00 0.00 36.74 4.73
290 300 5.682422 ACAAACGCGAACACTATTTAAAACC 59.318 36.000 15.93 0.00 0.00 3.27
329 339 6.822073 AATTTGAACAAACTCCTAAAACGC 57.178 33.333 2.03 0.00 32.51 4.84
695 709 2.989422 ACGAAAAATCAGAAAGCCGG 57.011 45.000 0.00 0.00 0.00 6.13
707 721 2.034685 AGAAAGCCGGCAAAAGAGAAAC 59.965 45.455 31.54 7.33 0.00 2.78
711 725 2.365293 AGCCGGCAAAAGAGAAACAAAT 59.635 40.909 31.54 0.00 0.00 2.32
712 726 3.572255 AGCCGGCAAAAGAGAAACAAATA 59.428 39.130 31.54 0.00 0.00 1.40
713 727 3.920412 GCCGGCAAAAGAGAAACAAATAG 59.080 43.478 24.80 0.00 0.00 1.73
714 728 4.485163 CCGGCAAAAGAGAAACAAATAGG 58.515 43.478 0.00 0.00 0.00 2.57
715 729 4.217550 CCGGCAAAAGAGAAACAAATAGGA 59.782 41.667 0.00 0.00 0.00 2.94
717 731 5.858581 CGGCAAAAGAGAAACAAATAGGAAG 59.141 40.000 0.00 0.00 0.00 3.46
735 781 1.299850 GAAACCGGTTTGCTGGCAC 60.300 57.895 36.17 16.43 45.10 5.01
736 782 1.734388 GAAACCGGTTTGCTGGCACT 61.734 55.000 36.17 9.93 45.10 4.40
737 783 2.015227 AAACCGGTTTGCTGGCACTG 62.015 55.000 31.17 0.00 45.10 3.66
795 841 3.797546 GTGCTCCTGCGCTTCAGC 61.798 66.667 9.73 13.35 45.43 4.26
842 888 1.594331 GCGTCAAATAGGATCCACCC 58.406 55.000 15.82 0.00 40.05 4.61
843 889 1.134220 GCGTCAAATAGGATCCACCCA 60.134 52.381 15.82 0.00 40.05 4.51
844 890 2.838736 CGTCAAATAGGATCCACCCAG 58.161 52.381 15.82 0.57 40.05 4.45
845 891 2.485479 CGTCAAATAGGATCCACCCAGG 60.485 54.545 15.82 0.00 40.05 4.45
861 907 2.435059 GGGAGAACGGAGCTGCAC 60.435 66.667 5.91 0.00 0.00 4.57
874 920 3.134401 CTGCACAGATCAGCTCGTT 57.866 52.632 0.00 0.00 0.00 3.85
876 922 1.802960 CTGCACAGATCAGCTCGTTTT 59.197 47.619 0.00 0.00 0.00 2.43
973 1023 1.153695 ACCTACCCACCTCTCCTCCA 61.154 60.000 0.00 0.00 0.00 3.86
1027 1089 1.064314 TCCTCCTCTACCACTGCTCTC 60.064 57.143 0.00 0.00 0.00 3.20
1028 1090 1.021202 CTCCTCTACCACTGCTCTCG 58.979 60.000 0.00 0.00 0.00 4.04
1030 1092 1.063327 CTCTACCACTGCTCTCGCG 59.937 63.158 0.00 0.00 39.65 5.87
1292 1426 2.430694 TGACGACCTATTGTCCATGGAG 59.569 50.000 16.81 4.59 41.18 3.86
1308 1451 0.249657 GGAGATCATCACCTGCGACC 60.250 60.000 0.00 0.00 0.00 4.79
1419 1570 4.214971 TCCTCGTCTTACGCACCTATAATC 59.785 45.833 0.00 0.00 42.21 1.75
1554 1724 2.359531 GACTACCGACTATTGCTCTGCT 59.640 50.000 0.00 0.00 0.00 4.24
1956 2176 2.409948 AGATCTTGGTAGTTGCTGGC 57.590 50.000 0.00 0.00 0.00 4.85
1957 2177 1.912043 AGATCTTGGTAGTTGCTGGCT 59.088 47.619 0.00 0.00 0.00 4.75
2061 2284 1.261619 GCAAGTTGGTTGACAGTCTCG 59.738 52.381 4.75 0.00 38.60 4.04
2160 2385 3.190535 GGGTTATGTTGTCAATGCTTCGT 59.809 43.478 0.00 0.00 0.00 3.85
2396 2881 3.430333 ACTTGGTTGTTTTGGTTAGCG 57.570 42.857 0.00 0.00 0.00 4.26
2407 2894 5.688176 TGTTTTGGTTAGCGTTTGAAATAGC 59.312 36.000 1.05 1.05 0.00 2.97
2421 2908 7.043391 CGTTTGAAATAGCTGTCGATTGATCTA 60.043 37.037 0.00 0.00 0.00 1.98
2537 3103 1.662629 CTGCGCTCTCGATTTGTTCAT 59.337 47.619 9.73 0.00 38.10 2.57
2563 3135 4.736473 TGCCTTTTCCCCCTTTATATAGC 58.264 43.478 0.00 0.00 0.00 2.97
2752 3588 9.893305 TTCTTTGTTTTATTTTAGCAGACTAGC 57.107 29.630 0.00 0.00 0.00 3.42
2757 3593 9.720769 TGTTTTATTTTAGCAGACTAGCTAGTT 57.279 29.630 26.71 13.81 46.77 2.24
2758 3594 9.974750 GTTTTATTTTAGCAGACTAGCTAGTTG 57.025 33.333 26.71 23.71 46.77 3.16
2759 3595 7.772332 TTATTTTAGCAGACTAGCTAGTTGC 57.228 36.000 31.92 31.92 46.77 4.17
2760 3596 4.801330 TTTAGCAGACTAGCTAGTTGCA 57.199 40.909 35.65 26.71 46.77 4.08
2763 3599 2.499289 AGCAGACTAGCTAGTTGCACAT 59.501 45.455 35.65 24.52 44.50 3.21
2764 3600 2.606725 GCAGACTAGCTAGTTGCACATG 59.393 50.000 32.90 23.21 45.94 3.21
2765 3601 3.677148 GCAGACTAGCTAGTTGCACATGA 60.677 47.826 32.90 1.30 45.94 3.07
2789 3629 4.892788 TCCTTGTTGGCTAGCTAGTTGCT 61.893 47.826 21.62 4.11 45.02 3.91
2829 3670 7.649057 AGCTTGGAACACTAGTAAAATTGAAC 58.351 34.615 0.00 0.00 39.29 3.18
2956 5526 2.229543 GCCTCTGTGTTGCATCATTTGA 59.770 45.455 0.00 0.00 0.00 2.69
3022 5596 7.704271 AGAAATCACAGCTTCATATGATGTTG 58.296 34.615 24.60 24.60 36.80 3.33
3076 5651 0.536724 ATGACGTGCAGAGCCATGTA 59.463 50.000 0.00 0.00 35.22 2.29
3203 5789 9.132521 GATTTGACTTGTGTGAATATCCTTTTG 57.867 33.333 0.00 0.00 0.00 2.44
3204 5790 7.815840 TTGACTTGTGTGAATATCCTTTTGA 57.184 32.000 0.00 0.00 0.00 2.69
3205 5791 7.439157 TGACTTGTGTGAATATCCTTTTGAG 57.561 36.000 0.00 0.00 0.00 3.02
3206 5792 6.072508 TGACTTGTGTGAATATCCTTTTGAGC 60.073 38.462 0.00 0.00 0.00 4.26
3207 5793 6.006449 ACTTGTGTGAATATCCTTTTGAGCT 58.994 36.000 0.00 0.00 0.00 4.09
3208 5794 7.168219 ACTTGTGTGAATATCCTTTTGAGCTA 58.832 34.615 0.00 0.00 0.00 3.32
3209 5795 7.665559 ACTTGTGTGAATATCCTTTTGAGCTAA 59.334 33.333 0.00 0.00 0.00 3.09
3210 5796 7.994425 TGTGTGAATATCCTTTTGAGCTAAA 57.006 32.000 0.00 0.00 0.00 1.85
3211 5797 8.402798 TGTGTGAATATCCTTTTGAGCTAAAA 57.597 30.769 0.00 0.00 36.82 1.52
3212 5798 9.023962 TGTGTGAATATCCTTTTGAGCTAAAAT 57.976 29.630 0.00 0.00 37.61 1.82
3213 5799 9.294030 GTGTGAATATCCTTTTGAGCTAAAATG 57.706 33.333 0.00 0.00 37.61 2.32
3214 5800 8.469200 TGTGAATATCCTTTTGAGCTAAAATGG 58.531 33.333 18.65 18.65 37.61 3.16
3215 5801 7.436376 GTGAATATCCTTTTGAGCTAAAATGGC 59.564 37.037 19.57 8.99 37.61 4.40
3216 5802 7.342799 TGAATATCCTTTTGAGCTAAAATGGCT 59.657 33.333 19.57 14.38 43.26 4.75
3217 5803 8.766994 AATATCCTTTTGAGCTAAAATGGCTA 57.233 30.769 19.57 15.78 40.40 3.93
3218 5804 6.705863 ATCCTTTTGAGCTAAAATGGCTAG 57.294 37.500 19.57 4.75 40.40 3.42
3219 5805 4.399303 TCCTTTTGAGCTAAAATGGCTAGC 59.601 41.667 19.57 6.04 41.80 3.42
3220 5806 4.158394 CCTTTTGAGCTAAAATGGCTAGCA 59.842 41.667 18.24 2.97 43.55 3.49
3221 5807 5.163478 CCTTTTGAGCTAAAATGGCTAGCAT 60.163 40.000 18.24 5.44 43.55 3.79
3222 5808 6.039717 CCTTTTGAGCTAAAATGGCTAGCATA 59.960 38.462 18.24 5.10 43.55 3.14
3223 5809 7.403312 TTTTGAGCTAAAATGGCTAGCATAA 57.597 32.000 18.24 1.28 43.55 1.90
3224 5810 7.403312 TTTGAGCTAAAATGGCTAGCATAAA 57.597 32.000 18.24 0.00 43.55 1.40
3225 5811 7.403312 TTGAGCTAAAATGGCTAGCATAAAA 57.597 32.000 18.24 0.00 43.55 1.52
3226 5812 7.403312 TGAGCTAAAATGGCTAGCATAAAAA 57.597 32.000 18.24 0.00 43.55 1.94
3248 5834 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
3249 5835 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
3250 5836 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
3251 5837 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
3252 5838 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
3258 5844 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3259 5845 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3260 5846 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3261 5847 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3264 5850 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3377 6011 7.654022 AAAGGAGTAGTTTTGGACAAATTCA 57.346 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.011119 ACCGCGTTCATTTTTGGCTATA 58.989 40.909 4.92 0.00 0.00 1.31
73 74 1.068885 CACCGCGTTCATTTTTGGCTA 60.069 47.619 4.92 0.00 0.00 3.93
74 75 0.318614 CACCGCGTTCATTTTTGGCT 60.319 50.000 4.92 0.00 0.00 4.75
117 119 1.984297 GTTCTAGACTTCACGAACGGC 59.016 52.381 0.00 0.00 0.00 5.68
125 127 4.401519 CCGATTGGTAGGTTCTAGACTTCA 59.598 45.833 0.00 0.00 0.00 3.02
170 173 3.538028 TAGAGCTCGCGCCGCATAC 62.538 63.158 19.59 11.54 36.60 2.39
176 179 0.870735 GGTACTTTAGAGCTCGCGCC 60.871 60.000 8.37 1.68 36.60 6.53
243 252 9.936759 TTGTAAAATTTTGTCCAGAGTTTTCTT 57.063 25.926 13.76 0.00 0.00 2.52
250 259 5.108405 CGCGTTTGTAAAATTTTGTCCAGAG 60.108 40.000 13.76 1.52 0.00 3.35
304 314 7.166142 CGCGTTTTAGGAGTTTGTTCAAATTTA 59.834 33.333 0.00 0.00 0.00 1.40
320 330 5.632959 TCCAATAATTGTTCGCGTTTTAGG 58.367 37.500 5.77 0.00 0.00 2.69
321 331 7.535940 TCTTTCCAATAATTGTTCGCGTTTTAG 59.464 33.333 5.77 0.00 0.00 1.85
327 337 5.568482 TCATCTTTCCAATAATTGTTCGCG 58.432 37.500 0.00 0.00 0.00 5.87
329 339 8.236586 TCTGTTCATCTTTCCAATAATTGTTCG 58.763 33.333 0.00 0.00 0.00 3.95
418 431 8.935844 CAGTATGTATCTAAAAACTGTTCAGCA 58.064 33.333 0.00 0.00 31.82 4.41
671 685 5.688176 CCGGCTTTCTGATTTTTCGTTTTTA 59.312 36.000 0.00 0.00 0.00 1.52
672 686 4.506288 CCGGCTTTCTGATTTTTCGTTTTT 59.494 37.500 0.00 0.00 0.00 1.94
673 687 4.048504 CCGGCTTTCTGATTTTTCGTTTT 58.951 39.130 0.00 0.00 0.00 2.43
674 688 3.638484 CCGGCTTTCTGATTTTTCGTTT 58.362 40.909 0.00 0.00 0.00 3.60
675 689 2.607038 GCCGGCTTTCTGATTTTTCGTT 60.607 45.455 22.15 0.00 0.00 3.85
676 690 1.068541 GCCGGCTTTCTGATTTTTCGT 60.069 47.619 22.15 0.00 0.00 3.85
677 691 1.068610 TGCCGGCTTTCTGATTTTTCG 60.069 47.619 29.70 0.00 0.00 3.46
691 705 2.217429 TTTGTTTCTCTTTTGCCGGC 57.783 45.000 22.73 22.73 0.00 6.13
695 709 8.755941 GTTTCTTCCTATTTGTTTCTCTTTTGC 58.244 33.333 0.00 0.00 0.00 3.68
707 721 4.022329 AGCAAACCGGTTTCTTCCTATTTG 60.022 41.667 29.48 15.91 35.24 2.32
711 725 2.500229 CAGCAAACCGGTTTCTTCCTA 58.500 47.619 29.48 0.00 0.00 2.94
712 726 1.318576 CAGCAAACCGGTTTCTTCCT 58.681 50.000 29.48 18.83 0.00 3.36
713 727 0.313987 CCAGCAAACCGGTTTCTTCC 59.686 55.000 29.48 17.02 0.00 3.46
714 728 0.318699 GCCAGCAAACCGGTTTCTTC 60.319 55.000 29.48 19.91 0.00 2.87
715 729 1.040339 TGCCAGCAAACCGGTTTCTT 61.040 50.000 29.48 17.30 0.00 2.52
717 731 1.299850 GTGCCAGCAAACCGGTTTC 60.300 57.895 29.48 22.06 0.00 2.78
735 781 2.069273 CCACTTCGTGAGTTAAGGCAG 58.931 52.381 0.00 0.00 36.10 4.85
736 782 1.270625 CCCACTTCGTGAGTTAAGGCA 60.271 52.381 0.00 0.00 36.10 4.75
737 783 1.439679 CCCACTTCGTGAGTTAAGGC 58.560 55.000 0.00 0.00 36.10 4.35
738 784 1.439679 GCCCACTTCGTGAGTTAAGG 58.560 55.000 0.00 0.00 36.10 2.69
795 841 3.827784 CCACGAGACGCGCTTTCG 61.828 66.667 20.92 20.92 46.04 3.46
842 888 2.125350 GCAGCTCCGTTCTCCCTG 60.125 66.667 0.00 0.00 0.00 4.45
843 889 2.604686 TGCAGCTCCGTTCTCCCT 60.605 61.111 0.00 0.00 0.00 4.20
844 890 2.435059 GTGCAGCTCCGTTCTCCC 60.435 66.667 0.00 0.00 0.00 4.30
845 891 1.739562 CTGTGCAGCTCCGTTCTCC 60.740 63.158 0.00 0.00 0.00 3.71
861 907 3.842820 TCTCTCAAAACGAGCTGATCTG 58.157 45.455 0.00 0.00 41.98 2.90
870 916 5.538118 TCTTATGTGCTTCTCTCAAAACGA 58.462 37.500 0.00 0.00 0.00 3.85
871 917 5.845985 TCTTATGTGCTTCTCTCAAAACG 57.154 39.130 0.00 0.00 0.00 3.60
874 920 5.179368 CCGTTTCTTATGTGCTTCTCTCAAA 59.821 40.000 0.00 0.00 0.00 2.69
876 922 4.245660 CCGTTTCTTATGTGCTTCTCTCA 58.754 43.478 0.00 0.00 0.00 3.27
1030 1092 4.704833 TGGACTGGAGCAAGGCGC 62.705 66.667 0.00 0.00 42.91 6.53
1081 1146 4.200283 GGAGGAGAGGCGTCGCTG 62.200 72.222 18.11 0.00 32.24 5.18
1292 1426 0.811616 GGTGGTCGCAGGTGATGATC 60.812 60.000 0.00 0.00 0.00 2.92
1419 1570 4.154347 GCGCCTCTCACCCCTCTG 62.154 72.222 0.00 0.00 0.00 3.35
1569 1766 4.202461 TGTGAAGACATAGGAGCCACTTTT 60.202 41.667 0.00 0.00 0.00 2.27
1610 1807 3.861797 CCCCTTATGCGCCTCGGT 61.862 66.667 4.18 0.00 0.00 4.69
1618 1815 4.507969 CATCAGGGCCCCTTATGC 57.492 61.111 21.43 0.00 30.01 3.14
1697 1903 7.120579 GTGTCAAATACCATTATCAGGTTGTCA 59.879 37.037 0.00 0.00 40.54 3.58
1752 1964 0.400213 TGGCCAGAAACAATCGGAGT 59.600 50.000 0.00 0.00 0.00 3.85
1813 2029 3.250744 TCTTCGTCATTAAGGCTGAACG 58.749 45.455 0.00 0.00 0.00 3.95
2061 2284 3.306472 AGGATAGAGGAGTCTGTGACC 57.694 52.381 0.00 0.00 33.84 4.02
2160 2385 4.879197 TGAGCTGAAGTCAGATGAAAGA 57.121 40.909 12.54 0.00 43.41 2.52
2396 2881 7.009568 AGATCAATCGACAGCTATTTCAAAC 57.990 36.000 0.00 0.00 0.00 2.93
2407 2894 9.119418 AGATATATGAGGTAGATCAATCGACAG 57.881 37.037 0.00 0.00 34.22 3.51
2537 3103 1.886422 AAAGGGGGAAAAGGCAAACA 58.114 45.000 0.00 0.00 0.00 2.83
2563 3135 6.963049 AACAATTAAGTACTAAGCAGACCG 57.037 37.500 0.00 0.00 0.00 4.79
2749 3585 4.760530 AGGAATCATGTGCAACTAGCTA 57.239 40.909 0.00 0.00 45.94 3.32
2750 3586 3.641434 AGGAATCATGTGCAACTAGCT 57.359 42.857 0.00 0.00 45.94 3.32
2751 3587 3.441572 ACAAGGAATCATGTGCAACTAGC 59.558 43.478 0.00 0.00 45.96 3.42
2752 3588 5.396484 CAACAAGGAATCATGTGCAACTAG 58.604 41.667 0.00 0.00 38.04 2.57
2753 3589 4.218200 CCAACAAGGAATCATGTGCAACTA 59.782 41.667 0.00 0.00 41.22 2.24
2755 3591 3.319755 CCAACAAGGAATCATGTGCAAC 58.680 45.455 0.00 0.00 41.22 4.17
2757 3593 1.273048 GCCAACAAGGAATCATGTGCA 59.727 47.619 0.00 0.00 41.22 4.57
2758 3594 1.547372 AGCCAACAAGGAATCATGTGC 59.453 47.619 0.00 0.00 41.22 4.57
2759 3595 3.181493 GCTAGCCAACAAGGAATCATGTG 60.181 47.826 2.29 0.00 41.22 3.21
2760 3596 3.019564 GCTAGCCAACAAGGAATCATGT 58.980 45.455 2.29 0.00 41.22 3.21
2763 3599 3.519510 ACTAGCTAGCCAACAAGGAATCA 59.480 43.478 20.91 0.00 41.22 2.57
2764 3600 4.143986 ACTAGCTAGCCAACAAGGAATC 57.856 45.455 20.91 0.00 41.22 2.52
2765 3601 4.265073 CAACTAGCTAGCCAACAAGGAAT 58.735 43.478 20.91 0.00 41.22 3.01
2789 3629 3.520721 TCCAAGCTCTTCAGGAATCATGA 59.479 43.478 0.00 0.00 0.00 3.07
2791 3631 4.263639 TGTTCCAAGCTCTTCAGGAATCAT 60.264 41.667 0.00 0.00 41.71 2.45
2797 3637 2.557920 AGTGTTCCAAGCTCTTCAGG 57.442 50.000 0.00 0.00 0.00 3.86
2829 3670 8.177663 ACTTGAAAGTTGACTATAATGCAATCG 58.822 33.333 0.00 0.00 35.21 3.34
3022 5596 8.982685 TCATTTCTCGAGCATATGTTAAGATTC 58.017 33.333 7.81 0.00 0.00 2.52
3103 5678 1.701847 GCCATCTCATAGTGGACCCAT 59.298 52.381 0.00 0.00 37.72 4.00
3105 5682 1.428869 AGCCATCTCATAGTGGACCC 58.571 55.000 0.00 0.00 37.72 4.46
3225 5811 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
3231 5817 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
3232 5818 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
3233 5819 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
3234 5820 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
3235 5821 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
3236 5822 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
3262 5848 1.559065 TTTTAGCTCCCCGGACCCTG 61.559 60.000 0.73 0.00 0.00 4.45
3263 5849 0.623617 ATTTTAGCTCCCCGGACCCT 60.624 55.000 0.73 0.00 0.00 4.34
3264 5850 0.465642 CATTTTAGCTCCCCGGACCC 60.466 60.000 0.73 0.00 0.00 4.46
3265 5851 0.465642 CCATTTTAGCTCCCCGGACC 60.466 60.000 0.73 0.00 0.00 4.46
3266 5852 1.101635 GCCATTTTAGCTCCCCGGAC 61.102 60.000 0.73 0.00 0.00 4.79
3267 5853 1.226262 GCCATTTTAGCTCCCCGGA 59.774 57.895 0.73 0.00 0.00 5.14
3268 5854 0.472471 TAGCCATTTTAGCTCCCCGG 59.528 55.000 0.00 0.00 41.83 5.73
3269 5855 1.884235 CTAGCCATTTTAGCTCCCCG 58.116 55.000 0.00 0.00 41.83 5.73
3270 5856 1.133792 TGCTAGCCATTTTAGCTCCCC 60.134 52.381 13.29 0.00 43.07 4.81
3271 5857 2.348411 TGCTAGCCATTTTAGCTCCC 57.652 50.000 13.29 0.00 43.07 4.30
3272 5858 2.030451 GCATGCTAGCCATTTTAGCTCC 60.030 50.000 13.29 0.00 43.07 4.70
3377 6011 5.876460 GGGCAGATCAATTTGCAACTATTTT 59.124 36.000 0.00 0.00 42.02 1.82


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

AutoCloner maintained by Alex Coulton.