Multiple sequence alignment - TraesCS7B01G079200

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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 TraesCS7B01G079200 chr7B 100.000 2591 0 0 1 2591 89207703 89210293 0.000000e+00 4785.0
1 TraesCS7B01G079200 chr7B 93.656 867 47 5 992 1857 88880497 88879638 0.000000e+00 1290.0
2 TraesCS7B01G079200 chr7B 90.252 318 24 1 625 942 88970416 88970106 2.400000e-110 409.0
3 TraesCS7B01G079200 chr7B 90.476 189 14 4 403 587 88970602 88970414 1.990000e-61 246.0
4 TraesCS7B01G079200 chr7B 88.482 191 16 3 32 216 88971297 88971107 2.590000e-55 226.0
5 TraesCS7B01G079200 chr7B 85.882 170 12 2 251 408 88970794 88970625 1.230000e-38 171.0
6 TraesCS7B01G079200 chr7D 91.061 1980 105 39 624 2550 127420606 127422566 0.000000e+00 2610.0
7 TraesCS7B01G079200 chr7D 92.147 191 8 7 403 587 127282696 127282507 1.980000e-66 263.0
8 TraesCS7B01G079200 chr7D 91.667 192 12 4 404 592 127420420 127420610 1.980000e-66 263.0
9 TraesCS7B01G079200 chr7D 88.073 218 24 2 1 216 127419665 127419882 9.200000e-65 257.0
10 TraesCS7B01G079200 chr7D 91.228 171 10 4 422 587 127278791 127278621 7.210000e-56 228.0
11 TraesCS7B01G079200 chr7D 84.746 177 7 5 251 408 127420221 127420396 2.670000e-35 159.0
12 TraesCS7B01G079200 chr7D 95.455 66 2 1 344 408 127282784 127282719 1.270000e-18 104.0
13 TraesCS7B01G079200 chr7D 94.545 55 1 2 2537 2590 540413456 540413403 1.650000e-12 84.2
14 TraesCS7B01G079200 chr7D 86.154 65 6 3 583 647 355125031 355125092 1.660000e-07 67.6
15 TraesCS7B01G079200 chr7D 100.000 31 0 0 1875 1905 16208013 16207983 1.000000e-04 58.4
16 TraesCS7B01G079200 chr7A 90.518 1023 70 13 856 1857 127907525 127906509 0.000000e+00 1327.0
17 TraesCS7B01G079200 chr7A 90.654 856 55 12 941 1786 128153914 128154754 0.000000e+00 1114.0
18 TraesCS7B01G079200 chr7A 92.542 295 15 1 625 919 128152396 128152683 1.430000e-112 416.0
19 TraesCS7B01G079200 chr7A 84.450 373 19 18 251 584 128152023 128152395 5.340000e-87 331.0
20 TraesCS7B01G079200 chr7A 94.444 54 2 1 2538 2590 20698545 20698598 5.940000e-12 82.4
21 TraesCS7B01G079200 chr6D 96.078 51 2 0 2541 2591 230928103 230928053 1.650000e-12 84.2
22 TraesCS7B01G079200 chr5B 92.982 57 2 2 2536 2590 612333410 612333466 5.940000e-12 82.4
23 TraesCS7B01G079200 chr5B 92.727 55 4 0 2536 2590 38359475 38359421 2.140000e-11 80.5
24 TraesCS7B01G079200 chr1D 90.323 62 4 2 2530 2590 478431308 478431248 2.140000e-11 80.5
25 TraesCS7B01G079200 chr2B 91.379 58 3 2 2535 2591 54766006 54765950 7.690000e-11 78.7
26 TraesCS7B01G079200 chr1B 90.164 61 4 2 2532 2590 544492685 544492625 7.690000e-11 78.7
27 TraesCS7B01G079200 chr1B 97.619 42 1 0 1872 1913 292341691 292341650 3.580000e-09 73.1
28 TraesCS7B01G079200 chr1B 97.619 42 1 0 1872 1913 292413178 292413137 3.580000e-09 73.1
29 TraesCS7B01G079200 chr1B 96.970 33 1 0 1872 1904 470696438 470696470 3.600000e-04 56.5
30 TraesCS7B01G079200 chr6B 88.889 63 4 3 2529 2589 3836050 3836111 9.940000e-10 75.0
31 TraesCS7B01G079200 chr6B 94.737 38 2 0 1872 1909 643609634 643609671 2.780000e-05 60.2
32 TraesCS7B01G079200 chr3A 92.157 51 4 0 582 632 19865503 19865553 3.580000e-09 73.1
33 TraesCS7B01G079200 chr4A 100.000 38 0 0 1872 1909 668932492 668932455 1.290000e-08 71.3
34 TraesCS7B01G079200 chr5D 92.000 50 2 2 588 637 279315265 279315218 4.630000e-08 69.4
35 TraesCS7B01G079200 chr5D 100.000 37 0 0 1874 1910 396448861 396448825 4.630000e-08 69.4
36 TraesCS7B01G079200 chr1A 92.000 50 3 1 588 637 202071883 202071835 4.630000e-08 69.4
37 TraesCS7B01G079200 chr3D 87.097 62 5 3 582 642 465372273 465372214 1.660000e-07 67.6
38 TraesCS7B01G079200 chr3D 93.182 44 3 0 588 631 16318111 16318154 5.980000e-07 65.8
39 TraesCS7B01G079200 chr3D 100.000 34 0 0 1872 1905 584678906 584678939 2.150000e-06 63.9
40 TraesCS7B01G079200 chr2A 84.848 66 7 3 588 652 775020234 775020171 2.150000e-06 63.9
41 TraesCS7B01G079200 chr2A 100.000 33 0 0 588 620 482370479 482370511 7.740000e-06 62.1
42 TraesCS7B01G079200 chr4B 85.484 62 5 4 585 645 167393873 167393815 7.740000e-06 62.1


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 TraesCS7B01G079200 chr7B 89207703 89210293 2590 False 4785.000000 4785 100.000000 1 2591 1 chr7B.!!$F1 2590
1 TraesCS7B01G079200 chr7B 88879638 88880497 859 True 1290.000000 1290 93.656000 992 1857 1 chr7B.!!$R1 865
2 TraesCS7B01G079200 chr7B 88970106 88971297 1191 True 263.000000 409 88.773000 32 942 4 chr7B.!!$R2 910
3 TraesCS7B01G079200 chr7D 127419665 127422566 2901 False 822.250000 2610 88.886750 1 2550 4 chr7D.!!$F2 2549
4 TraesCS7B01G079200 chr7A 127906509 127907525 1016 True 1327.000000 1327 90.518000 856 1857 1 chr7A.!!$R1 1001
5 TraesCS7B01G079200 chr7A 128152023 128154754 2731 False 620.333333 1114 89.215333 251 1786 3 chr7A.!!$F2 1535

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
184 191 0.043485 GACCCTTCCTCTCCCTTCCT 59.957 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 3539 0.871722 CATCCAGGTTCGACGCAAAA 59.128 50.0 0.0 0.0 0.0 2.44 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
40 42 7.868906 ATCTTGCATTTTGAAAATAATGGGG 57.131 32.000 2.42 0.00 33.41 4.96
68 75 3.516300 AGGAAGCAAAATCAATGGCATCA 59.484 39.130 0.00 0.00 0.00 3.07
70 77 4.879545 GGAAGCAAAATCAATGGCATCATT 59.120 37.500 0.00 0.00 43.79 2.57
71 78 5.007332 GGAAGCAAAATCAATGGCATCATTC 59.993 40.000 0.00 0.00 41.29 2.67
100 107 3.895041 ACTTGGTCGGAAATCAAATTGGT 59.105 39.130 0.00 0.00 0.00 3.67
134 141 8.744008 ATATTTCTTATACCGACACGAGATTG 57.256 34.615 0.00 0.00 0.00 2.67
165 172 0.249120 TAGGATCACACCCAACGCTG 59.751 55.000 0.00 0.00 0.00 5.18
184 191 0.043485 GACCCTTCCTCTCCCTTCCT 59.957 60.000 0.00 0.00 0.00 3.36
208 216 6.806751 TCAACCCTCTATCTTGTCTTATTCG 58.193 40.000 0.00 0.00 0.00 3.34
240 260 4.561735 CCTCAAGGTTTCGCTTAAAACA 57.438 40.909 8.03 0.00 40.22 2.83
242 262 3.942739 TCAAGGTTTCGCTTAAAACACG 58.057 40.909 8.03 0.00 40.22 4.49
243 263 3.374678 TCAAGGTTTCGCTTAAAACACGT 59.625 39.130 8.03 0.00 40.22 4.49
244 264 3.597377 AGGTTTCGCTTAAAACACGTC 57.403 42.857 8.03 0.00 40.22 4.34
245 265 3.200483 AGGTTTCGCTTAAAACACGTCT 58.800 40.909 8.03 0.00 40.22 4.18
246 266 4.370917 AGGTTTCGCTTAAAACACGTCTA 58.629 39.130 8.03 0.00 40.22 2.59
247 267 4.810491 AGGTTTCGCTTAAAACACGTCTAA 59.190 37.500 8.03 0.00 40.22 2.10
248 268 5.294060 AGGTTTCGCTTAAAACACGTCTAAA 59.706 36.000 8.03 0.00 40.22 1.85
286 613 4.759516 AATCGGCAAACACGTCTAAAAT 57.240 36.364 0.00 0.00 0.00 1.82
325 671 2.499685 GGCCTCACGAACGCCTAT 59.500 61.111 0.00 0.00 39.70 2.57
488 864 6.066054 TCGTCAAGTTGATGTATTTGCAAA 57.934 33.333 21.61 15.44 35.03 3.68
499 875 8.795786 TGATGTATTTGCAAACTTCTACAAAC 57.204 30.769 21.08 18.14 35.06 2.93
506 882 5.636837 TGCAAACTTCTACAAACTGTTGAC 58.363 37.500 0.00 0.00 38.20 3.18
563 939 5.614324 TCCGTGATCATTTACTTCATCCT 57.386 39.130 0.00 0.00 0.00 3.24
564 940 5.359756 TCCGTGATCATTTACTTCATCCTG 58.640 41.667 0.00 0.00 0.00 3.86
565 941 5.104941 TCCGTGATCATTTACTTCATCCTGT 60.105 40.000 0.00 0.00 0.00 4.00
566 942 5.235186 CCGTGATCATTTACTTCATCCTGTC 59.765 44.000 0.00 0.00 0.00 3.51
568 944 6.019237 CGTGATCATTTACTTCATCCTGTCTG 60.019 42.308 0.00 0.00 0.00 3.51
584 963 5.068987 TCCTGTCTGTTTTTAAGCTGCAATT 59.931 36.000 1.02 0.00 0.00 2.32
587 966 7.437862 CCTGTCTGTTTTTAAGCTGCAATTTAA 59.562 33.333 1.02 0.00 0.00 1.52
588 967 8.351495 TGTCTGTTTTTAAGCTGCAATTTAAG 57.649 30.769 1.02 0.00 0.00 1.85
589 968 7.978975 TGTCTGTTTTTAAGCTGCAATTTAAGT 59.021 29.630 1.02 0.00 0.00 2.24
590 969 9.458374 GTCTGTTTTTAAGCTGCAATTTAAGTA 57.542 29.630 1.02 0.00 0.00 2.24
591 970 9.458374 TCTGTTTTTAAGCTGCAATTTAAGTAC 57.542 29.630 1.02 1.99 0.00 2.73
592 971 9.243637 CTGTTTTTAAGCTGCAATTTAAGTACA 57.756 29.630 1.02 5.90 0.00 2.90
593 972 9.587772 TGTTTTTAAGCTGCAATTTAAGTACAA 57.412 25.926 1.02 0.00 0.00 2.41
596 975 9.810545 TTTTAAGCTGCAATTTAAGTACAAAGT 57.189 25.926 1.02 0.00 0.00 2.66
597 976 9.810545 TTTAAGCTGCAATTTAAGTACAAAGTT 57.189 25.926 1.02 0.00 0.00 2.66
598 977 7.698836 AAGCTGCAATTTAAGTACAAAGTTG 57.301 32.000 1.02 10.14 0.00 3.16
599 978 7.038154 AGCTGCAATTTAAGTACAAAGTTGA 57.962 32.000 15.70 5.18 0.00 3.18
600 979 7.141363 AGCTGCAATTTAAGTACAAAGTTGAG 58.859 34.615 15.70 11.91 0.00 3.02
601 980 6.918022 GCTGCAATTTAAGTACAAAGTTGAGT 59.082 34.615 15.70 0.00 0.00 3.41
602 981 7.113544 GCTGCAATTTAAGTACAAAGTTGAGTC 59.886 37.037 15.70 0.00 0.00 3.36
603 982 7.990917 TGCAATTTAAGTACAAAGTTGAGTCA 58.009 30.769 15.70 0.00 0.00 3.41
604 983 8.629158 TGCAATTTAAGTACAAAGTTGAGTCAT 58.371 29.630 15.70 0.00 0.00 3.06
605 984 9.118236 GCAATTTAAGTACAAAGTTGAGTCATC 57.882 33.333 15.70 0.00 0.00 2.92
613 992 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
614 993 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
615 994 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
616 995 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
617 996 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
618 997 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
619 998 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
620 999 5.800296 TGAGTCATCTATTTTGGAACGGAA 58.200 37.500 0.00 0.00 0.00 4.30
621 1000 6.414732 TGAGTCATCTATTTTGGAACGGAAT 58.585 36.000 0.00 0.00 0.00 3.01
622 1001 7.561251 TGAGTCATCTATTTTGGAACGGAATA 58.439 34.615 0.00 0.00 0.00 1.75
623 1002 8.044309 TGAGTCATCTATTTTGGAACGGAATAA 58.956 33.333 0.00 0.00 0.00 1.40
673 1052 4.097741 TGTTGTGGAATGTTTGAGACTTGG 59.902 41.667 0.00 0.00 0.00 3.61
695 1074 2.034939 TGTGCTCCTGTTGCTCATTTTG 59.965 45.455 0.00 0.00 0.00 2.44
698 1077 4.081406 TGCTCCTGTTGCTCATTTTGTAT 58.919 39.130 0.00 0.00 0.00 2.29
699 1078 5.123820 GTGCTCCTGTTGCTCATTTTGTATA 59.876 40.000 0.00 0.00 0.00 1.47
731 1110 5.717178 AGTAGATGGTTGTTCTGAGCTCTTA 59.283 40.000 16.19 0.00 0.00 2.10
752 1131 2.031012 CTGGCTGGCTGAACGACA 59.969 61.111 2.00 0.00 0.00 4.35
766 1145 1.514228 CGACAGGACGGTGATCACG 60.514 63.158 19.33 16.15 37.36 4.35
786 1165 1.025113 GCGGGGAAAGTTACTCTGCC 61.025 60.000 0.00 0.00 34.41 4.85
839 1218 4.044390 AGGGCTGGGACCTGGGAT 62.044 66.667 0.00 0.00 41.17 3.85
840 1219 3.813724 GGGCTGGGACCTGGGATG 61.814 72.222 0.00 0.00 0.00 3.51
939 2505 4.389077 CGTTACCATCTTGAGTTCTTGACC 59.611 45.833 0.00 0.00 0.00 4.02
958 2546 6.510879 TGACCTCCATATACATATCGACAC 57.489 41.667 0.00 0.00 0.00 3.67
965 2553 8.873186 TCCATATACATATCGACACCTTCTAA 57.127 34.615 0.00 0.00 0.00 2.10
973 2561 4.298103 TCGACACCTTCTAACTAGGAGT 57.702 45.455 0.00 0.00 38.97 3.85
974 2562 4.660168 TCGACACCTTCTAACTAGGAGTT 58.340 43.478 0.00 0.00 41.97 3.01
976 2564 4.380655 CGACACCTTCTAACTAGGAGTTGG 60.381 50.000 2.09 0.00 39.11 3.77
977 2565 4.748701 ACACCTTCTAACTAGGAGTTGGA 58.251 43.478 1.69 1.69 42.72 3.53
978 2566 4.773149 ACACCTTCTAACTAGGAGTTGGAG 59.227 45.833 5.69 0.00 44.58 3.86
979 2567 4.773149 CACCTTCTAACTAGGAGTTGGAGT 59.227 45.833 5.69 0.22 44.58 3.85
984 2572 6.639590 TCTAACTAGGAGTTGGAGTAGAGT 57.360 41.667 1.69 0.00 40.15 3.24
985 2573 6.652053 TCTAACTAGGAGTTGGAGTAGAGTC 58.348 44.000 1.69 0.00 40.15 3.36
990 2578 4.083565 AGGAGTTGGAGTAGAGTCAGTTC 58.916 47.826 0.00 0.00 0.00 3.01
1027 2615 1.477558 CCAGCACTGGGAAGTTCACTT 60.478 52.381 8.93 0.00 46.81 3.16
1176 2771 2.450502 ACCAACCAGCTCCAGGGT 60.451 61.111 0.00 0.00 39.65 4.34
1484 3087 2.359975 GGCCCAAGTCCGGTTCAG 60.360 66.667 0.00 0.00 0.00 3.02
1503 3106 4.208686 GTCGGGCTGGCCTACTCG 62.209 72.222 18.81 11.16 36.10 4.18
1601 3204 3.076621 GTGTTGCCTGACAGATTGATCA 58.923 45.455 3.32 0.00 0.00 2.92
1859 3465 3.409026 AGAAATGCAGAGAGTTTCGGT 57.591 42.857 0.00 0.00 37.04 4.69
1860 3466 4.537135 AGAAATGCAGAGAGTTTCGGTA 57.463 40.909 0.00 0.00 37.04 4.02
1879 3485 4.154717 GGTACGTTTAGAAGTCAGTCGAC 58.845 47.826 7.70 7.70 42.95 4.20
1933 3539 2.093447 CCAGACCTCCTATTTGACGCTT 60.093 50.000 0.00 0.00 0.00 4.68
1957 3589 2.158959 GTCGAACCTGGATGCGTCG 61.159 63.158 0.00 1.59 0.00 5.12
1971 3603 3.723348 GTCGGCAAACGGGTGAGC 61.723 66.667 0.00 0.00 44.45 4.26
1974 3606 3.365265 GGCAAACGGGTGAGCAGG 61.365 66.667 0.00 0.00 0.00 4.85
1975 3607 2.281484 GCAAACGGGTGAGCAGGA 60.281 61.111 0.00 0.00 0.00 3.86
1976 3608 2.328099 GCAAACGGGTGAGCAGGAG 61.328 63.158 0.00 0.00 0.00 3.69
1980 3612 0.250513 AACGGGTGAGCAGGAGAATC 59.749 55.000 0.00 0.00 0.00 2.52
2017 3649 6.019075 CGAGCCGAATGTATTTTATCAAGTCA 60.019 38.462 0.00 0.00 0.00 3.41
2202 3835 8.958175 AAAATTCCGAAAACTTTTTGAAAACC 57.042 26.923 3.35 0.00 0.00 3.27
2203 3836 7.674471 AATTCCGAAAACTTTTTGAAAACCA 57.326 28.000 3.35 0.00 0.00 3.67
2204 3837 7.857734 ATTCCGAAAACTTTTTGAAAACCAT 57.142 28.000 3.35 0.00 0.00 3.55
2205 3838 6.654793 TCCGAAAACTTTTTGAAAACCATG 57.345 33.333 3.35 0.00 0.00 3.66
2207 3840 6.874134 TCCGAAAACTTTTTGAAAACCATGAA 59.126 30.769 0.00 0.00 0.00 2.57
2208 3841 6.958752 CCGAAAACTTTTTGAAAACCATGAAC 59.041 34.615 0.00 0.00 0.00 3.18
2209 3842 7.360438 CCGAAAACTTTTTGAAAACCATGAACA 60.360 33.333 0.00 0.00 0.00 3.18
2313 3948 8.613613 TCGAAAACATGAACATTTATACATGC 57.386 30.769 0.00 0.00 42.28 4.06
2389 4024 9.535270 TTTGAAAAGCGAATGTTTTTGTAAAAG 57.465 25.926 0.00 0.00 38.43 2.27
2441 4077 8.870160 TGTCATTCGAACATTTTCAGAATTTT 57.130 26.923 0.00 0.00 35.06 1.82
2554 4196 5.945144 TTTAGTGGTATGTTCCTACTCCC 57.055 43.478 0.00 0.00 0.00 4.30
2555 4197 3.778622 AGTGGTATGTTCCTACTCCCT 57.221 47.619 0.00 0.00 0.00 4.20
2556 4198 4.076175 AGTGGTATGTTCCTACTCCCTT 57.924 45.455 0.00 0.00 0.00 3.95
2557 4199 4.031611 AGTGGTATGTTCCTACTCCCTTC 58.968 47.826 0.00 0.00 0.00 3.46
2558 4200 3.028850 TGGTATGTTCCTACTCCCTTCG 58.971 50.000 0.00 0.00 0.00 3.79
2559 4201 3.029570 GGTATGTTCCTACTCCCTTCGT 58.970 50.000 0.00 0.00 0.00 3.85
2560 4202 3.450096 GGTATGTTCCTACTCCCTTCGTT 59.550 47.826 0.00 0.00 0.00 3.85
2561 4203 3.889520 ATGTTCCTACTCCCTTCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
2562 4204 1.897802 TGTTCCTACTCCCTTCGTTCC 59.102 52.381 0.00 0.00 0.00 3.62
2563 4205 1.897802 GTTCCTACTCCCTTCGTTCCA 59.102 52.381 0.00 0.00 0.00 3.53
2564 4206 2.301009 GTTCCTACTCCCTTCGTTCCAA 59.699 50.000 0.00 0.00 0.00 3.53
2565 4207 2.612000 TCCTACTCCCTTCGTTCCAAA 58.388 47.619 0.00 0.00 0.00 3.28
2566 4208 2.974099 TCCTACTCCCTTCGTTCCAAAA 59.026 45.455 0.00 0.00 0.00 2.44
2567 4209 3.585732 TCCTACTCCCTTCGTTCCAAAAT 59.414 43.478 0.00 0.00 0.00 1.82
2568 4210 4.778958 TCCTACTCCCTTCGTTCCAAAATA 59.221 41.667 0.00 0.00 0.00 1.40
2569 4211 5.105064 TCCTACTCCCTTCGTTCCAAAATAG 60.105 44.000 0.00 0.00 0.00 1.73
2570 4212 4.903045 ACTCCCTTCGTTCCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
2571 4213 5.437191 ACTCCCTTCGTTCCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
2572 4214 5.186198 ACTCCCTTCGTTCCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
2573 4215 5.045869 ACTCCCTTCGTTCCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
2574 4216 5.183228 TCCCTTCGTTCCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
2575 4217 5.045869 TCCCTTCGTTCCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
2576 4218 5.294552 CCCTTCGTTCCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
2577 4219 5.874810 CCTTCGTTCCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
2578 4220 6.371548 CCTTCGTTCCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
2579 4221 6.721571 TCGTTCCAAAATAGATGACTCAAC 57.278 37.500 0.00 0.00 0.00 3.18
2580 4222 6.464222 TCGTTCCAAAATAGATGACTCAACT 58.536 36.000 0.00 0.00 0.00 3.16
2581 4223 6.934645 TCGTTCCAAAATAGATGACTCAACTT 59.065 34.615 0.00 0.00 0.00 2.66
2582 4224 7.444183 TCGTTCCAAAATAGATGACTCAACTTT 59.556 33.333 0.00 0.00 0.00 2.66
2583 4225 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2584 4226 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2585 4227 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2586 4228 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2587 4229 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 15 8.948145 CCCATTATTTTCAAAATGCAAGATTCA 58.052 29.630 5.56 0.00 32.79 2.57
38 40 4.335400 TGATTTTGCTTCCTTTGTTCCC 57.665 40.909 0.00 0.00 0.00 3.97
40 42 5.334337 GCCATTGATTTTGCTTCCTTTGTTC 60.334 40.000 0.00 0.00 0.00 3.18
68 75 1.616865 TCCGACCAAGTCTTGACGAAT 59.383 47.619 23.43 4.19 34.27 3.34
70 77 1.034356 TTCCGACCAAGTCTTGACGA 58.966 50.000 23.43 12.82 34.27 4.20
71 78 1.860676 TTTCCGACCAAGTCTTGACG 58.139 50.000 14.42 16.86 0.00 4.35
110 117 7.933396 TCAATCTCGTGTCGGTATAAGAAATA 58.067 34.615 0.00 0.00 0.00 1.40
119 126 4.811908 TCAATTTCAATCTCGTGTCGGTA 58.188 39.130 0.00 0.00 0.00 4.02
123 130 4.095483 AGCCATCAATTTCAATCTCGTGTC 59.905 41.667 0.00 0.00 0.00 3.67
134 141 4.276926 GGTGTGATCCTAGCCATCAATTTC 59.723 45.833 4.59 0.00 31.98 2.17
165 172 0.043485 AGGAAGGGAGAGGAAGGGTC 59.957 60.000 0.00 0.00 0.00 4.46
184 191 6.605995 TCGAATAAGACAAGATAGAGGGTTGA 59.394 38.462 0.00 0.00 0.00 3.18
219 239 4.287720 GTGTTTTAAGCGAAACCTTGAGG 58.712 43.478 9.74 0.00 38.45 3.86
246 266 9.868277 TGCCGATTTCTAATTGACATAAATTTT 57.132 25.926 0.00 0.00 32.16 1.82
247 267 9.868277 TTGCCGATTTCTAATTGACATAAATTT 57.132 25.926 0.00 0.00 32.16 1.82
248 268 9.868277 TTTGCCGATTTCTAATTGACATAAATT 57.132 25.926 0.00 0.00 34.24 1.82
260 586 3.395639 AGACGTGTTTGCCGATTTCTAA 58.604 40.909 0.00 0.00 0.00 2.10
268 594 3.879427 TCAATTTTAGACGTGTTTGCCG 58.121 40.909 0.00 0.00 0.00 5.69
286 613 1.573829 GCCGCATCCACTCGTTTCAA 61.574 55.000 0.00 0.00 0.00 2.69
408 755 2.359107 CCTCCCGCGCATGCATAT 60.359 61.111 19.57 0.00 42.97 1.78
488 864 5.007385 ACGAGTCAACAGTTTGTAGAAGT 57.993 39.130 0.00 0.00 34.02 3.01
499 875 3.785505 GCACTCAAACAACGAGTCAACAG 60.786 47.826 0.00 0.00 41.80 3.16
506 882 2.480037 TGCATAGCACTCAAACAACGAG 59.520 45.455 0.00 0.00 31.71 4.18
563 939 7.978975 ACTTAAATTGCAGCTTAAAAACAGACA 59.021 29.630 0.00 0.00 0.00 3.41
564 940 8.352752 ACTTAAATTGCAGCTTAAAAACAGAC 57.647 30.769 0.00 0.00 0.00 3.51
565 941 9.458374 GTACTTAAATTGCAGCTTAAAAACAGA 57.542 29.630 0.00 0.00 0.00 3.41
566 942 9.243637 TGTACTTAAATTGCAGCTTAAAAACAG 57.756 29.630 0.00 0.00 0.00 3.16
587 966 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
588 967 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
589 968 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
590 969 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
591 970 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
592 971 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
593 972 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
594 973 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
595 974 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
596 975 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
597 976 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
598 977 6.927294 ATTCCGTTCCAAAATAGATGACTC 57.073 37.500 0.00 0.00 0.00 3.36
599 978 8.047310 ACTTATTCCGTTCCAAAATAGATGACT 58.953 33.333 0.00 0.00 0.00 3.41
600 979 8.209917 ACTTATTCCGTTCCAAAATAGATGAC 57.790 34.615 0.00 0.00 0.00 3.06
601 980 9.321562 GTACTTATTCCGTTCCAAAATAGATGA 57.678 33.333 0.00 0.00 0.00 2.92
602 981 9.326413 AGTACTTATTCCGTTCCAAAATAGATG 57.674 33.333 0.00 0.00 0.00 2.90
606 985 9.048446 GCATAGTACTTATTCCGTTCCAAAATA 57.952 33.333 0.00 0.00 0.00 1.40
607 986 7.773690 AGCATAGTACTTATTCCGTTCCAAAAT 59.226 33.333 0.00 0.00 0.00 1.82
608 987 7.107542 AGCATAGTACTTATTCCGTTCCAAAA 58.892 34.615 0.00 0.00 0.00 2.44
609 988 6.646267 AGCATAGTACTTATTCCGTTCCAAA 58.354 36.000 0.00 0.00 0.00 3.28
610 989 6.127281 TGAGCATAGTACTTATTCCGTTCCAA 60.127 38.462 0.00 0.00 0.00 3.53
611 990 5.361571 TGAGCATAGTACTTATTCCGTTCCA 59.638 40.000 0.00 0.00 0.00 3.53
612 991 5.839621 TGAGCATAGTACTTATTCCGTTCC 58.160 41.667 0.00 0.00 0.00 3.62
613 992 7.145985 TGATGAGCATAGTACTTATTCCGTTC 58.854 38.462 0.00 0.00 0.00 3.95
614 993 7.050970 TGATGAGCATAGTACTTATTCCGTT 57.949 36.000 0.00 0.00 0.00 4.44
615 994 6.650427 TGATGAGCATAGTACTTATTCCGT 57.350 37.500 0.00 0.00 0.00 4.69
616 995 6.923508 TGTTGATGAGCATAGTACTTATTCCG 59.076 38.462 0.00 0.00 0.00 4.30
617 996 8.662781 TTGTTGATGAGCATAGTACTTATTCC 57.337 34.615 0.00 0.00 0.00 3.01
618 997 9.319143 ACTTGTTGATGAGCATAGTACTTATTC 57.681 33.333 0.00 0.00 0.00 1.75
619 998 9.672673 AACTTGTTGATGAGCATAGTACTTATT 57.327 29.630 0.00 0.00 0.00 1.40
622 1001 9.102757 CATAACTTGTTGATGAGCATAGTACTT 57.897 33.333 0.00 0.00 0.00 2.24
623 1002 8.478066 TCATAACTTGTTGATGAGCATAGTACT 58.522 33.333 0.00 0.00 0.00 2.73
673 1052 1.242076 AATGAGCAACAGGAGCACAC 58.758 50.000 0.00 0.00 35.50 3.82
695 1074 2.555757 ACCATCTACTCGCCGGTTATAC 59.444 50.000 1.90 0.00 0.00 1.47
698 1077 1.135527 CAACCATCTACTCGCCGGTTA 59.864 52.381 1.90 0.00 37.87 2.85
699 1078 0.108329 CAACCATCTACTCGCCGGTT 60.108 55.000 1.90 0.00 40.57 4.44
752 1131 4.129737 CGCCGTGATCACCGTCCT 62.130 66.667 20.03 0.00 0.00 3.85
766 1145 1.025113 GCAGAGTAACTTTCCCCGCC 61.025 60.000 0.00 0.00 0.00 6.13
786 1165 3.282157 AGCACAACGCACAGCAGG 61.282 61.111 0.00 0.00 46.13 4.85
836 1215 4.626081 CGCGGGGATCCCACATCC 62.626 72.222 32.07 13.36 45.83 3.51
837 1216 4.626081 CCGCGGGGATCCCACATC 62.626 72.222 32.07 13.75 45.83 3.06
907 1286 3.009695 TCAAGATGGTAACGGGGTGAAAT 59.990 43.478 0.00 0.00 42.51 2.17
939 2505 7.397892 AGAAGGTGTCGATATGTATATGGAG 57.602 40.000 0.00 0.00 29.87 3.86
958 2546 6.424883 TCTACTCCAACTCCTAGTTAGAAGG 58.575 44.000 0.00 0.00 36.03 3.46
965 2553 4.290196 ACTGACTCTACTCCAACTCCTAGT 59.710 45.833 0.00 0.00 0.00 2.57
973 2561 7.309867 GGACAATAAGAACTGACTCTACTCCAA 60.310 40.741 0.00 0.00 0.00 3.53
974 2562 6.153000 GGACAATAAGAACTGACTCTACTCCA 59.847 42.308 0.00 0.00 0.00 3.86
976 2564 7.159322 TGGACAATAAGAACTGACTCTACTC 57.841 40.000 0.00 0.00 0.00 2.59
977 2565 7.364232 CCATGGACAATAAGAACTGACTCTACT 60.364 40.741 5.56 0.00 0.00 2.57
978 2566 6.758886 CCATGGACAATAAGAACTGACTCTAC 59.241 42.308 5.56 0.00 0.00 2.59
979 2567 6.630413 GCCATGGACAATAAGAACTGACTCTA 60.630 42.308 18.40 0.00 0.00 2.43
984 2572 3.055458 TCGCCATGGACAATAAGAACTGA 60.055 43.478 18.40 0.00 0.00 3.41
985 2573 3.063997 GTCGCCATGGACAATAAGAACTG 59.936 47.826 18.40 0.00 36.91 3.16
990 2578 1.942657 CTGGTCGCCATGGACAATAAG 59.057 52.381 18.40 0.89 38.70 1.73
1104 2692 1.142748 GCTGAGGATGACGGAGGTG 59.857 63.158 0.00 0.00 0.00 4.00
1176 2771 2.173758 TTAGGATCAACACCGGCGCA 62.174 55.000 10.83 0.00 0.00 6.09
1230 2825 3.782443 CTGTACTCCACCCCCGCC 61.782 72.222 0.00 0.00 0.00 6.13
1374 2976 3.181967 CGCAGGTCGAAGAAGGCG 61.182 66.667 0.00 0.00 43.55 5.52
1601 3204 4.848357 ACACAAACAGCTAGGCATAGATT 58.152 39.130 10.11 0.00 0.00 2.40
1914 3520 3.983044 AAAGCGTCAAATAGGAGGTCT 57.017 42.857 0.00 0.00 0.00 3.85
1933 3539 0.871722 CATCCAGGTTCGACGCAAAA 59.128 50.000 0.00 0.00 0.00 2.44
1939 3545 2.158959 CGACGCATCCAGGTTCGAC 61.159 63.158 5.09 0.00 0.00 4.20
1941 3547 2.885644 CCGACGCATCCAGGTTCG 60.886 66.667 0.00 0.00 0.00 3.95
1946 3552 2.480555 GTTTGCCGACGCATCCAG 59.519 61.111 0.00 0.00 46.67 3.86
1957 3589 3.365265 CCTGCTCACCCGTTTGCC 61.365 66.667 0.00 0.00 0.00 4.52
1971 3603 4.520874 TCGCTAGATTACCTGATTCTCCTG 59.479 45.833 0.00 0.00 0.00 3.86
1974 3606 4.481463 GCTCGCTAGATTACCTGATTCTC 58.519 47.826 0.00 0.00 0.00 2.87
1975 3607 3.257127 GGCTCGCTAGATTACCTGATTCT 59.743 47.826 0.00 0.00 0.00 2.40
1976 3608 3.580731 GGCTCGCTAGATTACCTGATTC 58.419 50.000 0.00 0.00 0.00 2.52
1980 3612 0.952280 TCGGCTCGCTAGATTACCTG 59.048 55.000 0.00 0.00 0.00 4.00
2056 3688 3.439825 TGTAGTACATCGGTTCGCTGTAA 59.560 43.478 0.00 0.00 39.50 2.41
2061 3693 1.197910 GCTGTAGTACATCGGTTCGC 58.802 55.000 2.82 0.00 0.00 4.70
2178 3811 8.100508 TGGTTTTCAAAAAGTTTTCGGAATTT 57.899 26.923 13.17 0.00 0.00 1.82
2183 3816 6.654793 TCATGGTTTTCAAAAAGTTTTCGG 57.345 33.333 0.32 0.00 0.00 4.30
2185 3818 9.838975 AATGTTCATGGTTTTCAAAAAGTTTTC 57.161 25.926 0.32 0.00 0.00 2.29
2230 3863 6.997655 TCCAAAATATGTTTGTGTTGCCATA 58.002 32.000 0.00 0.00 0.00 2.74
2288 3922 8.458052 AGCATGTATAAATGTTCATGTTTTCGA 58.542 29.630 4.80 0.00 39.54 3.71
2289 3923 8.525876 CAGCATGTATAAATGTTCATGTTTTCG 58.474 33.333 4.80 0.00 39.54 3.46
2372 4007 5.746245 TGTCCTGCTTTTACAAAAACATTCG 59.254 36.000 0.00 0.00 0.00 3.34
2497 4133 8.251026 GGGGACATTTTAGAAGGTTTTTCTATG 58.749 37.037 0.00 0.00 31.78 2.23
2508 4149 8.637196 AAAAACTCTAGGGGACATTTTAGAAG 57.363 34.615 0.00 0.00 0.00 2.85
2545 4187 2.314071 TTGGAACGAAGGGAGTAGGA 57.686 50.000 0.00 0.00 0.00 2.94
2550 4192 5.294552 GTCATCTATTTTGGAACGAAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
2551 4193 5.045869 AGTCATCTATTTTGGAACGAAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
2552 4194 5.186198 AGTCATCTATTTTGGAACGAAGGG 58.814 41.667 0.00 0.00 0.00 3.95
2553 4195 5.874810 TGAGTCATCTATTTTGGAACGAAGG 59.125 40.000 0.00 0.00 0.00 3.46
2554 4196 6.968131 TGAGTCATCTATTTTGGAACGAAG 57.032 37.500 0.00 0.00 0.00 3.79
2555 4197 6.934645 AGTTGAGTCATCTATTTTGGAACGAA 59.065 34.615 1.70 0.00 0.00 3.85
2556 4198 6.464222 AGTTGAGTCATCTATTTTGGAACGA 58.536 36.000 1.70 0.00 0.00 3.85
2557 4199 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2558 4200 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2559 4201 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2560 4202 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2561 4203 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28


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

AutoCloner maintained by Alex Coulton.