Multiple sequence alignment - TraesCS6D01G135900

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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 TraesCS6D01G135900 chr6D 100.000 2798 0 0 1 2798 104145301 104148098 0.000000e+00 5168.0
1 TraesCS6D01G135900 chr6D 98.925 93 1 0 2288 2380 464673704 464673612 1.720000e-37 167.0
2 TraesCS6D01G135900 chr6D 96.939 98 2 1 2284 2380 221219413 221219316 2.230000e-36 163.0
3 TraesCS6D01G135900 chr6D 91.398 93 8 0 80 172 269804444 269804536 8.130000e-26 128.0
4 TraesCS6D01G135900 chr6B 91.478 1854 98 20 111 1935 189276125 189277947 0.000000e+00 2494.0
5 TraesCS6D01G135900 chr6B 91.304 414 35 1 2386 2798 189294796 189295209 5.230000e-157 564.0
6 TraesCS6D01G135900 chr6B 93.421 152 10 0 2125 2276 189294491 189294642 2.800000e-55 226.0
7 TraesCS6D01G135900 chr6B 97.638 127 3 0 1934 2060 189278108 189278234 4.690000e-53 219.0
8 TraesCS6D01G135900 chr6B 97.143 70 2 0 2061 2130 189294364 189294433 4.900000e-23 119.0
9 TraesCS6D01G135900 chr6B 92.453 53 4 0 104 156 714087412 714087360 2.990000e-10 76.8
10 TraesCS6D01G135900 chr6B 95.745 47 1 1 2256 2301 189294749 189294795 1.070000e-09 75.0
11 TraesCS6D01G135900 chr6B 90.566 53 5 0 30 82 66765413 66765465 1.390000e-08 71.3
12 TraesCS6D01G135900 chr6A 90.374 1631 85 24 316 1912 125540781 125542373 0.000000e+00 2076.0
13 TraesCS6D01G135900 chr6A 83.171 410 46 14 2393 2798 125542982 125543372 1.230000e-93 353.0
14 TraesCS6D01G135900 chr6A 86.747 249 22 8 80 328 125540432 125540669 1.650000e-67 267.0
15 TraesCS6D01G135900 chr6A 96.939 98 2 1 2284 2380 262052147 262052050 2.230000e-36 163.0
16 TraesCS6D01G135900 chr6A 84.615 130 20 0 80 209 55266278 55266407 2.260000e-26 130.0
17 TraesCS6D01G135900 chr2B 75.995 829 164 20 996 1799 745724455 745723637 2.020000e-106 396.0
18 TraesCS6D01G135900 chr2D 76.039 818 163 19 1001 1794 610297832 610297024 7.260000e-106 394.0
19 TraesCS6D01G135900 chr2D 84.337 83 11 2 1 83 476912290 476912370 2.310000e-11 80.5
20 TraesCS6D01G135900 chr2D 90.741 54 5 0 26 79 131641424 131641371 3.870000e-09 73.1
21 TraesCS6D01G135900 chr2A 75.850 824 164 20 1001 1799 743114562 743113749 1.220000e-103 387.0
22 TraesCS6D01G135900 chr2A 89.091 55 6 0 25 79 138526191 138526137 5.000000e-08 69.4
23 TraesCS6D01G135900 chr2A 100.000 29 0 0 2034 2062 24975712 24975684 1.000000e-03 54.7
24 TraesCS6D01G135900 chr2A 100.000 29 0 0 2034 2062 83423226 83423198 1.000000e-03 54.7
25 TraesCS6D01G135900 chr7A 92.500 120 9 0 92 211 672645508 672645389 3.710000e-39 172.0
26 TraesCS6D01G135900 chr7A 94.231 104 4 2 2296 2397 257695709 257695606 1.040000e-34 158.0
27 TraesCS6D01G135900 chr4B 96.939 98 2 1 2296 2392 649830815 649830912 2.230000e-36 163.0
28 TraesCS6D01G135900 chr3A 97.872 94 2 0 2296 2389 391475473 391475380 2.230000e-36 163.0
29 TraesCS6D01G135900 chr3A 93.939 99 5 1 2286 2383 368149334 368149236 6.240000e-32 148.0
30 TraesCS6D01G135900 chr1B 96.939 98 2 1 2296 2392 470881317 470881220 2.230000e-36 163.0
31 TraesCS6D01G135900 chr4A 95.050 101 4 1 2296 2396 6801454 6801355 1.040000e-34 158.0
32 TraesCS6D01G135900 chr5A 85.714 133 18 1 78 209 441207195 441207327 3.760000e-29 139.0
33 TraesCS6D01G135900 chr3D 83.333 132 22 0 80 211 615399362 615399493 3.780000e-24 122.0
34 TraesCS6D01G135900 chr3B 84.348 115 18 0 82 196 576617729 576617843 2.280000e-21 113.0
35 TraesCS6D01G135900 chr5B 86.747 83 11 0 1 83 345470998 345471080 2.970000e-15 93.5
36 TraesCS6D01G135900 chr5B 91.379 58 5 0 24 81 704142979 704142922 2.310000e-11 80.5
37 TraesCS6D01G135900 chr4D 93.548 62 3 1 18 79 360488036 360488096 1.070000e-14 91.6


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 TraesCS6D01G135900 chr6D 104145301 104148098 2797 False 5168.000000 5168 100.00000 1 2798 1 chr6D.!!$F1 2797
1 TraesCS6D01G135900 chr6B 189276125 189278234 2109 False 1356.500000 2494 94.55800 111 2060 2 chr6B.!!$F2 1949
2 TraesCS6D01G135900 chr6B 189294364 189295209 845 False 246.000000 564 94.40325 2061 2798 4 chr6B.!!$F3 737
3 TraesCS6D01G135900 chr6A 125540432 125543372 2940 False 898.666667 2076 86.76400 80 2798 3 chr6A.!!$F2 2718
4 TraesCS6D01G135900 chr2B 745723637 745724455 818 True 396.000000 396 75.99500 996 1799 1 chr2B.!!$R1 803
5 TraesCS6D01G135900 chr2D 610297024 610297832 808 True 394.000000 394 76.03900 1001 1794 1 chr2D.!!$R2 793
6 TraesCS6D01G135900 chr2A 743113749 743114562 813 True 387.000000 387 75.85000 1001 1799 1 chr2A.!!$R4 798

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
58 59 0.111446 TTGAAGGGTCGGATTTGCCA 59.889 50.0 0.0 0.0 35.94 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2358 1.727022 GTGATTGCGTGCAGTGTGC 60.727 57.895 0.0 0.0 45.29 4.57 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
22 23 2.643272 GTCCGCAGACACGACTGA 59.357 61.111 11.57 0.00 42.99 3.41
23 24 1.442857 GTCCGCAGACACGACTGAG 60.443 63.158 11.57 8.72 42.99 3.35
24 25 2.807045 CCGCAGACACGACTGAGC 60.807 66.667 11.57 0.00 39.94 4.26
25 26 3.168604 CGCAGACACGACTGAGCG 61.169 66.667 11.57 7.38 39.94 5.03
26 27 3.474034 GCAGACACGACTGAGCGC 61.474 66.667 0.00 0.00 39.94 5.92
27 28 3.168604 CAGACACGACTGAGCGCG 61.169 66.667 0.00 0.00 39.94 6.86
28 29 3.661131 AGACACGACTGAGCGCGT 61.661 61.111 8.43 0.00 42.11 6.01
29 30 3.166630 GACACGACTGAGCGCGTC 61.167 66.667 8.43 2.30 38.92 5.19
30 31 4.702081 ACACGACTGAGCGCGTCC 62.702 66.667 8.43 0.00 38.92 4.79
44 45 4.084888 GTCCGCGGGCGTTTGAAG 62.085 66.667 27.83 0.00 37.81 3.02
48 49 3.733960 GCGGGCGTTTGAAGGGTC 61.734 66.667 0.00 0.00 0.00 4.46
49 50 3.419759 CGGGCGTTTGAAGGGTCG 61.420 66.667 0.00 0.00 0.00 4.79
50 51 3.053896 GGGCGTTTGAAGGGTCGG 61.054 66.667 0.00 0.00 0.00 4.79
51 52 2.031465 GGCGTTTGAAGGGTCGGA 59.969 61.111 0.00 0.00 0.00 4.55
52 53 1.376812 GGCGTTTGAAGGGTCGGAT 60.377 57.895 0.00 0.00 0.00 4.18
53 54 0.958876 GGCGTTTGAAGGGTCGGATT 60.959 55.000 0.00 0.00 0.00 3.01
54 55 0.879090 GCGTTTGAAGGGTCGGATTT 59.121 50.000 0.00 0.00 0.00 2.17
55 56 1.401018 GCGTTTGAAGGGTCGGATTTG 60.401 52.381 0.00 0.00 0.00 2.32
56 57 1.401018 CGTTTGAAGGGTCGGATTTGC 60.401 52.381 0.00 0.00 0.00 3.68
57 58 1.067846 GTTTGAAGGGTCGGATTTGCC 60.068 52.381 0.00 0.00 0.00 4.52
58 59 0.111446 TTGAAGGGTCGGATTTGCCA 59.889 50.000 0.00 0.00 35.94 4.92
59 60 0.111446 TGAAGGGTCGGATTTGCCAA 59.889 50.000 0.00 0.00 35.94 4.52
60 61 0.811281 GAAGGGTCGGATTTGCCAAG 59.189 55.000 0.00 0.00 35.94 3.61
61 62 0.112412 AAGGGTCGGATTTGCCAAGT 59.888 50.000 0.00 0.00 35.94 3.16
62 63 0.112412 AGGGTCGGATTTGCCAAGTT 59.888 50.000 0.00 0.00 35.94 2.66
63 64 0.526211 GGGTCGGATTTGCCAAGTTC 59.474 55.000 0.00 0.00 35.94 3.01
64 65 0.168128 GGTCGGATTTGCCAAGTTCG 59.832 55.000 0.00 0.00 35.94 3.95
65 66 0.168128 GTCGGATTTGCCAAGTTCGG 59.832 55.000 0.49 0.00 35.94 4.30
76 77 3.393089 CCAAGTTCGGCTATAGATGCT 57.607 47.619 3.21 0.00 0.00 3.79
77 78 3.321497 CCAAGTTCGGCTATAGATGCTC 58.679 50.000 3.21 0.00 0.00 4.26
78 79 3.006323 CCAAGTTCGGCTATAGATGCTCT 59.994 47.826 3.21 0.00 0.00 4.09
88 89 7.976175 TCGGCTATAGATGCTCTAAAATACATG 59.024 37.037 3.21 0.00 31.96 3.21
89 90 7.761704 CGGCTATAGATGCTCTAAAATACATGT 59.238 37.037 2.69 2.69 31.96 3.21
103 104 7.435068 AAAATACATGTATTCCTATGCCGAC 57.565 36.000 27.07 0.00 34.90 4.79
146 147 8.564509 AAGTATCGTGTATTACTATCTCCCTC 57.435 38.462 0.00 0.00 0.00 4.30
212 213 0.518636 TCTCGCAAAAGATGTGCAGC 59.481 50.000 0.00 0.00 42.33 5.25
235 236 7.688167 CAGCATAGAGTTAAACAACATAACACG 59.312 37.037 0.00 0.00 36.04 4.49
239 240 7.311364 AGAGTTAAACAACATAACACGTGTT 57.689 32.000 33.99 33.99 40.23 3.32
240 241 7.754625 AGAGTTAAACAACATAACACGTGTTT 58.245 30.769 36.26 21.60 37.69 2.83
241 242 8.881743 AGAGTTAAACAACATAACACGTGTTTA 58.118 29.630 36.26 22.37 37.69 2.01
277 278 8.286800 TCAAAACCACAACACTTATTATCGAAG 58.713 33.333 0.00 0.00 0.00 3.79
283 284 7.010552 CCACAACACTTATTATCGAAGAGAAGG 59.989 40.741 9.59 3.29 42.58 3.46
288 289 9.186837 ACACTTATTATCGAAGAGAAGGAGTAA 57.813 33.333 9.59 0.00 42.58 2.24
314 315 1.315690 CATTACAGGCCATGGCTCAG 58.684 55.000 34.70 25.27 41.60 3.35
348 473 7.141758 AGTTCAAATGCTAGATAGGGATCAA 57.858 36.000 0.00 0.00 34.17 2.57
422 548 7.953158 ATCGAGTGGATATAAACACAATGAG 57.047 36.000 11.34 0.00 39.99 2.90
425 551 6.203530 CGAGTGGATATAAACACAATGAGCAT 59.796 38.462 11.34 0.00 39.99 3.79
429 555 8.620416 GTGGATATAAACACAATGAGCATACAA 58.380 33.333 5.56 0.00 37.54 2.41
434 560 3.407698 ACACAATGAGCATACAACCGAA 58.592 40.909 0.00 0.00 0.00 4.30
435 561 4.009675 ACACAATGAGCATACAACCGAAT 58.990 39.130 0.00 0.00 0.00 3.34
437 563 4.009675 ACAATGAGCATACAACCGAATGT 58.990 39.130 0.00 0.00 37.32 2.71
440 566 3.527533 TGAGCATACAACCGAATGTACC 58.472 45.455 2.91 0.00 38.53 3.34
451 577 2.738846 CCGAATGTACCATGCATAGCTC 59.261 50.000 0.00 0.00 0.00 4.09
456 582 2.289010 TGTACCATGCATAGCTCGGATG 60.289 50.000 0.00 9.75 32.47 3.51
468 594 1.167851 CTCGGATGCACACAACCAAT 58.832 50.000 0.00 0.00 38.63 3.16
469 595 2.355197 CTCGGATGCACACAACCAATA 58.645 47.619 0.00 0.00 38.63 1.90
470 596 2.945008 CTCGGATGCACACAACCAATAT 59.055 45.455 0.00 0.00 38.63 1.28
471 597 4.126437 CTCGGATGCACACAACCAATATA 58.874 43.478 0.00 0.00 38.63 0.86
472 598 4.713553 TCGGATGCACACAACCAATATAT 58.286 39.130 0.00 0.00 38.63 0.86
500 626 2.423892 ACACGCACAAATAAACACACCA 59.576 40.909 0.00 0.00 0.00 4.17
512 638 6.648879 ATAAACACACCAACAAATAGCAGT 57.351 33.333 0.00 0.00 0.00 4.40
529 656 2.233922 GCAGTGTAGGAGACCAAAGCTA 59.766 50.000 0.00 0.00 0.00 3.32
530 657 3.306780 GCAGTGTAGGAGACCAAAGCTAA 60.307 47.826 0.00 0.00 0.00 3.09
531 658 4.802918 GCAGTGTAGGAGACCAAAGCTAAA 60.803 45.833 0.00 0.00 0.00 1.85
559 686 0.370273 ATCGACGCGATGAAAACAGC 59.630 50.000 15.93 0.00 45.24 4.40
646 796 3.279434 GACATAGGCTCAATTCGGGTTT 58.721 45.455 0.00 0.00 0.00 3.27
673 823 5.258841 TGAATGAAGTTGAATCTGAGCCAT 58.741 37.500 0.00 0.00 0.00 4.40
695 849 4.776322 TGCATGGCCGAACGGAGG 62.776 66.667 17.63 0.00 37.50 4.30
776 930 7.982354 GCTACACAAGTCTTAAGATAGTCCAAT 59.018 37.037 8.75 0.00 0.00 3.16
855 1012 0.253044 CCTGAACCATCCCGACACAT 59.747 55.000 0.00 0.00 0.00 3.21
935 1092 7.255451 CCAGATCAAGAAGTATACAGAGTCCTC 60.255 44.444 5.50 0.00 0.00 3.71
936 1093 6.485313 AGATCAAGAAGTATACAGAGTCCTCG 59.515 42.308 5.50 0.00 34.09 4.63
938 1095 3.887352 AGAAGTATACAGAGTCCTCGCA 58.113 45.455 5.50 0.00 34.09 5.10
939 1096 3.880490 AGAAGTATACAGAGTCCTCGCAG 59.120 47.826 5.50 0.00 34.09 5.18
943 1105 3.791973 ATACAGAGTCCTCGCAGAAAG 57.208 47.619 0.00 0.00 34.09 2.62
948 1110 2.029470 AGAGTCCTCGCAGAAAGAAGTG 60.029 50.000 0.00 0.00 34.09 3.16
1159 1321 0.807275 CATCCTCAAGCGCATCGTGA 60.807 55.000 11.47 6.55 0.00 4.35
1672 1855 3.453070 GAGCGCCAGATGGAGTCCC 62.453 68.421 6.74 0.00 37.33 4.46
1819 2002 2.126071 CGTGCTACGGTCACCCTG 60.126 66.667 0.00 0.00 38.08 4.45
1820 2003 2.927580 CGTGCTACGGTCACCCTGT 61.928 63.158 0.00 0.00 38.08 4.00
1825 2008 0.731417 CTACGGTCACCCTGTCTACG 59.269 60.000 0.00 0.00 0.00 3.51
1857 2043 7.908827 ATCACGTATATGAGTACTAGGAGTG 57.091 40.000 0.00 0.95 30.46 3.51
2065 2417 5.596836 TCAAAGCCACAAAGTTTCAGAAT 57.403 34.783 0.00 0.00 0.00 2.40
2198 2832 7.734924 TGGATATAACACAAGATCTTCATGC 57.265 36.000 4.57 0.00 0.00 4.06
2251 2885 8.175069 ACATATAAATACAACGCTTTGTGACTG 58.825 33.333 18.06 8.37 45.91 3.51
2298 3059 8.989980 GTGAGTATTCAGCTTTTGTAAACTACT 58.010 33.333 0.00 0.00 32.98 2.57
2299 3060 9.204570 TGAGTATTCAGCTTTTGTAAACTACTC 57.795 33.333 0.00 0.00 0.00 2.59
2302 3063 5.562298 TCAGCTTTTGTAAACTACTCCCT 57.438 39.130 0.00 0.00 0.00 4.20
2303 3064 5.548406 TCAGCTTTTGTAAACTACTCCCTC 58.452 41.667 0.00 0.00 0.00 4.30
2304 3065 5.307196 TCAGCTTTTGTAAACTACTCCCTCT 59.693 40.000 0.00 0.00 0.00 3.69
2305 3066 5.409826 CAGCTTTTGTAAACTACTCCCTCTG 59.590 44.000 0.00 0.00 0.00 3.35
2306 3067 5.071923 AGCTTTTGTAAACTACTCCCTCTGT 59.928 40.000 0.00 0.00 0.00 3.41
2307 3068 6.269307 AGCTTTTGTAAACTACTCCCTCTGTA 59.731 38.462 0.00 0.00 0.00 2.74
2308 3069 6.932960 GCTTTTGTAAACTACTCCCTCTGTAA 59.067 38.462 0.00 0.00 0.00 2.41
2309 3070 7.443272 GCTTTTGTAAACTACTCCCTCTGTAAA 59.557 37.037 0.00 0.00 0.00 2.01
2310 3071 8.667076 TTTTGTAAACTACTCCCTCTGTAAAC 57.333 34.615 0.00 0.00 0.00 2.01
2311 3072 7.607615 TTGTAAACTACTCCCTCTGTAAACT 57.392 36.000 0.00 0.00 0.00 2.66
2312 3073 8.710749 TTGTAAACTACTCCCTCTGTAAACTA 57.289 34.615 0.00 0.00 0.00 2.24
2313 3074 8.710749 TGTAAACTACTCCCTCTGTAAACTAA 57.289 34.615 0.00 0.00 0.00 2.24
2314 3075 9.317827 TGTAAACTACTCCCTCTGTAAACTAAT 57.682 33.333 0.00 0.00 0.00 1.73
2322 3083 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2323 3084 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2324 3085 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2325 3086 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2326 3087 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2341 3102 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
2342 3103 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
2343 3104 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
2344 3105 9.122779 AGAGCGTTTAGATCACTACTTTAGTAT 57.877 33.333 0.00 0.00 37.82 2.12
2345 3106 9.733219 GAGCGTTTAGATCACTACTTTAGTATT 57.267 33.333 0.00 0.00 37.23 1.89
2346 3107 9.733219 AGCGTTTAGATCACTACTTTAGTATTC 57.267 33.333 0.00 0.00 37.23 1.75
2347 3108 9.733219 GCGTTTAGATCACTACTTTAGTATTCT 57.267 33.333 0.00 0.00 37.23 2.40
2353 3114 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
2354 3115 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
2355 3116 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
2356 3117 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
2357 3118 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
2371 3132 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2372 3133 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2373 3134 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2374 3135 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2375 3136 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2376 3137 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2377 3138 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2378 3139 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2379 3140 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2382 3143 9.812347 TTATATTAGTTTACGGAGGGAGTATCA 57.188 33.333 0.00 0.00 36.25 2.15
2383 3144 5.841957 TTAGTTTACGGAGGGAGTATCAC 57.158 43.478 0.00 0.00 40.51 3.06
2479 3243 9.887406 CGAATAACTTTTTAGTAGCCTTTTTGA 57.113 29.630 0.00 0.00 0.00 2.69
2509 3273 6.009589 TGTTTCTCCTAATGGCAGATGAAAA 58.990 36.000 0.00 0.00 0.00 2.29
2575 3341 4.887748 AGGAAACTGATATGAGTATGGCG 58.112 43.478 0.00 0.00 41.13 5.69
2577 3343 4.503296 GGAAACTGATATGAGTATGGCGGT 60.503 45.833 0.00 0.00 0.00 5.68
2665 3431 9.551734 CATAGAATGTCATTATTTCTCTGTCCA 57.448 33.333 0.00 0.00 0.00 4.02
2676 3442 5.964958 TTTCTCTGTCCATGGAATCAAAC 57.035 39.130 18.20 3.76 0.00 2.93
2677 3443 3.955471 TCTCTGTCCATGGAATCAAACC 58.045 45.455 18.20 2.25 0.00 3.27
2679 3445 3.689347 TCTGTCCATGGAATCAAACCTG 58.311 45.455 18.20 6.42 0.00 4.00
2682 3448 2.493278 GTCCATGGAATCAAACCTGTGG 59.507 50.000 18.20 0.00 36.22 4.17
2698 3464 2.529389 GGGTGTCAGGGGGTGAGT 60.529 66.667 0.00 0.00 35.13 3.41
2699 3465 1.229400 GGGTGTCAGGGGGTGAGTA 60.229 63.158 0.00 0.00 35.13 2.59
2722 3488 2.457598 GGGGAGTCTGTATGTCTGTGA 58.542 52.381 0.00 0.00 0.00 3.58
2730 3496 4.093998 GTCTGTATGTCTGTGATTTGCTGG 59.906 45.833 0.00 0.00 0.00 4.85
2733 3499 1.511850 TGTCTGTGATTTGCTGGTCG 58.488 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.442857 CTCAGTCGTGTCTGCGGAC 60.443 63.158 19.20 19.20 42.42 4.79
6 7 2.954611 CTCAGTCGTGTCTGCGGA 59.045 61.111 0.00 0.00 35.63 5.54
7 8 2.807045 GCTCAGTCGTGTCTGCGG 60.807 66.667 0.00 0.00 35.63 5.69
8 9 3.168604 CGCTCAGTCGTGTCTGCG 61.169 66.667 0.00 0.00 35.63 5.18
9 10 3.474034 GCGCTCAGTCGTGTCTGC 61.474 66.667 0.00 0.00 35.63 4.26
10 11 3.168604 CGCGCTCAGTCGTGTCTG 61.169 66.667 5.56 0.00 35.47 3.51
27 28 4.084888 CTTCAAACGCCCGCGGAC 62.085 66.667 30.73 16.23 44.69 4.79
31 32 3.733960 GACCCTTCAAACGCCCGC 61.734 66.667 0.00 0.00 0.00 6.13
32 33 3.419759 CGACCCTTCAAACGCCCG 61.420 66.667 0.00 0.00 0.00 6.13
33 34 2.814913 ATCCGACCCTTCAAACGCCC 62.815 60.000 0.00 0.00 0.00 6.13
34 35 0.958876 AATCCGACCCTTCAAACGCC 60.959 55.000 0.00 0.00 0.00 5.68
35 36 0.879090 AAATCCGACCCTTCAAACGC 59.121 50.000 0.00 0.00 0.00 4.84
36 37 1.401018 GCAAATCCGACCCTTCAAACG 60.401 52.381 0.00 0.00 0.00 3.60
37 38 1.067846 GGCAAATCCGACCCTTCAAAC 60.068 52.381 0.00 0.00 0.00 2.93
38 39 1.253100 GGCAAATCCGACCCTTCAAA 58.747 50.000 0.00 0.00 0.00 2.69
39 40 0.111446 TGGCAAATCCGACCCTTCAA 59.889 50.000 0.00 0.00 37.80 2.69
40 41 0.111446 TTGGCAAATCCGACCCTTCA 59.889 50.000 0.00 0.00 37.80 3.02
41 42 0.811281 CTTGGCAAATCCGACCCTTC 59.189 55.000 0.00 0.00 37.80 3.46
42 43 0.112412 ACTTGGCAAATCCGACCCTT 59.888 50.000 0.00 0.00 37.80 3.95
43 44 0.112412 AACTTGGCAAATCCGACCCT 59.888 50.000 0.00 0.00 37.80 4.34
44 45 0.526211 GAACTTGGCAAATCCGACCC 59.474 55.000 0.00 0.00 37.80 4.46
45 46 0.168128 CGAACTTGGCAAATCCGACC 59.832 55.000 0.00 0.00 37.80 4.79
46 47 0.168128 CCGAACTTGGCAAATCCGAC 59.832 55.000 13.80 0.00 37.80 4.79
47 48 2.550487 CCGAACTTGGCAAATCCGA 58.450 52.632 13.80 0.00 37.80 4.55
56 57 3.321497 GAGCATCTATAGCCGAACTTGG 58.679 50.000 0.00 0.00 0.00 3.61
73 74 9.219603 GCATAGGAATACATGTATTTTAGAGCA 57.780 33.333 27.48 12.29 36.02 4.26
74 75 8.669243 GGCATAGGAATACATGTATTTTAGAGC 58.331 37.037 27.48 25.14 36.02 4.09
75 76 8.873830 CGGCATAGGAATACATGTATTTTAGAG 58.126 37.037 27.48 19.14 36.02 2.43
76 77 8.590204 TCGGCATAGGAATACATGTATTTTAGA 58.410 33.333 27.48 15.85 36.02 2.10
77 78 8.656849 GTCGGCATAGGAATACATGTATTTTAG 58.343 37.037 27.48 17.77 36.02 1.85
78 79 7.604927 GGTCGGCATAGGAATACATGTATTTTA 59.395 37.037 27.48 22.26 36.02 1.52
88 89 3.074412 CCAATGGTCGGCATAGGAATAC 58.926 50.000 0.00 0.00 0.00 1.89
89 90 2.708861 ACCAATGGTCGGCATAGGAATA 59.291 45.455 0.00 0.00 0.00 1.75
90 91 1.494721 ACCAATGGTCGGCATAGGAAT 59.505 47.619 0.00 0.00 0.00 3.01
146 147 7.344095 AGATCCAAAGCTGATTTTATCTTGG 57.656 36.000 7.02 2.24 31.44 3.61
212 213 8.492748 ACACGTGTTATGTTGTTTAACTCTATG 58.507 33.333 17.22 0.00 37.68 2.23
273 274 8.480643 AATGTGTTAATTACTCCTTCTCTTCG 57.519 34.615 0.00 0.00 0.00 3.79
277 278 9.099454 CCTGTAATGTGTTAATTACTCCTTCTC 57.901 37.037 8.17 0.00 41.58 2.87
283 284 6.995511 TGGCCTGTAATGTGTTAATTACTC 57.004 37.500 3.32 0.03 41.58 2.59
288 289 3.384467 GCCATGGCCTGTAATGTGTTAAT 59.616 43.478 27.24 0.00 34.56 1.40
314 315 7.545362 TCTAGCATTTGAACTATTTGCTCTC 57.455 36.000 0.00 0.00 42.34 3.20
332 457 5.158141 AGTCCATTTGATCCCTATCTAGCA 58.842 41.667 0.00 0.00 32.93 3.49
393 519 9.832445 ATTGTGTTTATATCCACTCGATACTTT 57.168 29.630 0.00 0.00 36.26 2.66
397 523 7.598869 GCTCATTGTGTTTATATCCACTCGATA 59.401 37.037 0.00 0.00 37.85 2.92
401 527 6.925610 TGCTCATTGTGTTTATATCCACTC 57.074 37.500 4.51 0.00 32.76 3.51
410 536 4.998033 TCGGTTGTATGCTCATTGTGTTTA 59.002 37.500 0.00 0.00 0.00 2.01
437 563 2.749280 CATCCGAGCTATGCATGGTA 57.251 50.000 10.16 0.00 0.00 3.25
451 577 6.371271 TGATATATATTGGTTGTGTGCATCCG 59.629 38.462 0.00 0.00 37.30 4.18
456 582 7.643764 GTGTGTTGATATATATTGGTTGTGTGC 59.356 37.037 0.00 0.00 0.00 4.57
468 594 9.923786 GTTTATTTGTGCGTGTGTTGATATATA 57.076 29.630 0.00 0.00 0.00 0.86
469 595 8.454894 TGTTTATTTGTGCGTGTGTTGATATAT 58.545 29.630 0.00 0.00 0.00 0.86
470 596 7.746916 GTGTTTATTTGTGCGTGTGTTGATATA 59.253 33.333 0.00 0.00 0.00 0.86
471 597 6.580791 GTGTTTATTTGTGCGTGTGTTGATAT 59.419 34.615 0.00 0.00 0.00 1.63
472 598 5.910166 GTGTTTATTTGTGCGTGTGTTGATA 59.090 36.000 0.00 0.00 0.00 2.15
500 626 4.286032 TGGTCTCCTACACTGCTATTTGTT 59.714 41.667 0.00 0.00 0.00 2.83
545 672 0.369931 TGATCGCTGTTTTCATCGCG 59.630 50.000 0.00 0.00 42.91 5.87
549 676 3.004629 TGCTTGTTGATCGCTGTTTTCAT 59.995 39.130 0.00 0.00 0.00 2.57
559 686 6.183359 GCTTTCAAACTATTGCTTGTTGATCG 60.183 38.462 0.00 0.00 36.45 3.69
646 796 5.106948 GCTCAGATTCAACTTCATTCAACGA 60.107 40.000 0.00 0.00 0.00 3.85
673 823 0.453793 CCGTTCGGCCATGCATTTTA 59.546 50.000 2.24 0.00 0.00 1.52
695 849 4.184629 CTGAGCTGGTACACAAATAGTCC 58.815 47.826 0.00 0.00 0.00 3.85
817 974 2.301296 AGGAGAAGATGACACACACTGG 59.699 50.000 0.00 0.00 0.00 4.00
855 1012 2.280524 CAAAGGGACACGTCGGCA 60.281 61.111 0.00 0.00 0.00 5.69
935 1092 1.194098 CTCTGTGCACTTCTTTCTGCG 59.806 52.381 19.41 0.00 36.08 5.18
936 1093 1.069364 GCTCTGTGCACTTCTTTCTGC 60.069 52.381 19.41 7.29 42.31 4.26
938 1095 1.141657 TGGCTCTGTGCACTTCTTTCT 59.858 47.619 19.41 0.00 45.15 2.52
939 1096 1.597742 TGGCTCTGTGCACTTCTTTC 58.402 50.000 19.41 4.23 45.15 2.62
943 1105 0.308993 GTGTTGGCTCTGTGCACTTC 59.691 55.000 19.41 4.14 45.15 3.01
948 1110 4.030452 GGCGTGTTGGCTCTGTGC 62.030 66.667 0.00 0.00 40.72 4.57
1008 1170 2.922503 TTCAGCCGCTGTCCCTGA 60.923 61.111 19.77 0.00 34.07 3.86
1295 1457 2.431771 CGATGTTGTCGTGGCGGA 60.432 61.111 0.00 0.00 45.19 5.54
1672 1855 4.570663 CCCGGCGTAGAGCTTCGG 62.571 72.222 6.01 0.00 45.96 4.30
1814 1997 3.677527 CGTCACCGTAGACAGGGT 58.322 61.111 5.50 0.00 43.78 4.34
2006 2358 1.727022 GTGATTGCGTGCAGTGTGC 60.727 57.895 0.00 0.00 45.29 4.57
2065 2417 3.450578 GTTGTTCTACACCGAGTCACAA 58.549 45.455 0.00 0.00 0.00 3.33
2165 2799 7.878547 TCTTGTGTTATATCCATGCAAATGA 57.121 32.000 0.00 0.00 0.00 2.57
2198 2832 2.293399 GCAGGTAGTTTCACTTTGTGGG 59.707 50.000 0.00 0.00 33.87 4.61
2216 2850 6.649436 CGTTGTATTTATATGTCCACAGCAG 58.351 40.000 0.00 0.00 0.00 4.24
2251 2885 4.090066 CACTATAATGTCTATCGCCGTTGC 59.910 45.833 0.00 0.00 0.00 4.17
2298 3059 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2299 3060 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2315 3076 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
2316 3077 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
2317 3078 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
2318 3079 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
2319 3080 9.733219 AATACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
2320 3081 9.733219 GAATACTAAAGTAGTGATCTAAACGCT 57.267 33.333 0.00 0.00 39.81 5.07
2321 3082 9.733219 AGAATACTAAAGTAGTGATCTAAACGC 57.267 33.333 0.00 0.00 39.81 4.84
2327 3088 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
2328 3089 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
2329 3090 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
2330 3091 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
2331 3092 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
2345 3106 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2346 3107 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2347 3108 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2348 3109 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2349 3110 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2350 3111 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2351 3112 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2352 3113 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2353 3114 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2356 3117 9.812347 TGATACTCCCTCCGTAAACTAATATAA 57.188 33.333 0.00 0.00 0.00 0.98
2357 3118 9.236006 GTGATACTCCCTCCGTAAACTAATATA 57.764 37.037 0.00 0.00 0.00 0.86
2358 3119 7.949006 AGTGATACTCCCTCCGTAAACTAATAT 59.051 37.037 0.00 0.00 0.00 1.28
2359 3120 7.293073 AGTGATACTCCCTCCGTAAACTAATA 58.707 38.462 0.00 0.00 0.00 0.98
2360 3121 6.134754 AGTGATACTCCCTCCGTAAACTAAT 58.865 40.000 0.00 0.00 0.00 1.73
2361 3122 5.513233 AGTGATACTCCCTCCGTAAACTAA 58.487 41.667 0.00 0.00 0.00 2.24
2362 3123 5.121380 AGTGATACTCCCTCCGTAAACTA 57.879 43.478 0.00 0.00 0.00 2.24
2363 3124 3.978610 AGTGATACTCCCTCCGTAAACT 58.021 45.455 0.00 0.00 0.00 2.66
2364 3125 4.732672 AAGTGATACTCCCTCCGTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
2365 3126 6.371278 AGATAAGTGATACTCCCTCCGTAAA 58.629 40.000 0.00 0.00 0.00 2.01
2366 3127 5.950023 AGATAAGTGATACTCCCTCCGTAA 58.050 41.667 0.00 0.00 0.00 3.18
2367 3128 5.579753 AGATAAGTGATACTCCCTCCGTA 57.420 43.478 0.00 0.00 0.00 4.02
2368 3129 4.456662 AGATAAGTGATACTCCCTCCGT 57.543 45.455 0.00 0.00 0.00 4.69
2369 3130 5.793030 AAAGATAAGTGATACTCCCTCCG 57.207 43.478 0.00 0.00 0.00 4.63
2439 3203 5.517322 AGTTATTCGTGGATCTCACTACC 57.483 43.478 11.12 0.00 43.94 3.18
2479 3243 7.301868 TCTGCCATTAGGAGAAACAAAAATT 57.698 32.000 0.00 0.00 36.89 1.82
2509 3273 0.552848 ACCCAATCAATCCTCCGCAT 59.447 50.000 0.00 0.00 0.00 4.73
2572 3338 1.442017 GTGTCGCAAAATCACCGCC 60.442 57.895 0.00 0.00 0.00 6.13
2575 3341 2.604614 GGAAGTGTGTCGCAAAATCACC 60.605 50.000 0.00 0.00 0.00 4.02
2577 3343 2.571212 AGGAAGTGTGTCGCAAAATCA 58.429 42.857 0.00 0.00 0.00 2.57
2642 3408 7.501559 CCATGGACAGAGAAATAATGACATTCT 59.498 37.037 5.56 0.00 36.17 2.40
2661 3427 2.493278 CCACAGGTTTGATTCCATGGAC 59.507 50.000 15.91 4.42 36.31 4.02
2677 3443 2.854032 ACCCCCTGACACCCACAG 60.854 66.667 0.00 0.00 35.43 3.66
2679 3445 2.852075 TCACCCCCTGACACCCAC 60.852 66.667 0.00 0.00 0.00 4.61
2682 3448 0.831307 GATACTCACCCCCTGACACC 59.169 60.000 0.00 0.00 0.00 4.16
2698 3464 3.117625 ACAGACATACAGACTCCCCGATA 60.118 47.826 0.00 0.00 0.00 2.92
2699 3465 2.311463 CAGACATACAGACTCCCCGAT 58.689 52.381 0.00 0.00 0.00 4.18
2730 3496 0.815213 TGCTCTAATGGGCATGCGAC 60.815 55.000 12.44 7.88 33.23 5.19
2733 3499 2.428171 TCTTTTGCTCTAATGGGCATGC 59.572 45.455 9.90 9.90 38.30 4.06
2739 3505 5.717119 AGTTGCATTCTTTTGCTCTAATGG 58.283 37.500 0.00 0.00 43.18 3.16


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

AutoCloner maintained by Alex Coulton.