Multiple sequence alignment - TraesCS1B01G141400

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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 TraesCS1B01G141400 chr1B 100.000 5046 0 0 1 5046 188789873 188794918 0.000000e+00 9319.0
1 TraesCS1B01G141400 chr1A 94.106 2443 64 19 2073 4455 137232920 137235342 0.000000e+00 3640.0
2 TraesCS1B01G141400 chr1A 93.849 1967 68 13 43 1991 137230990 137232921 0.000000e+00 2913.0
3 TraesCS1B01G141400 chr1A 87.349 166 16 3 4853 5013 137235343 137235508 8.630000e-43 185.0
4 TraesCS1B01G141400 chr1D 94.965 2304 60 9 2073 4338 124561376 124563661 0.000000e+00 3561.0
5 TraesCS1B01G141400 chr1D 95.473 1988 63 9 24 1991 124559397 124561377 0.000000e+00 3147.0
6 TraesCS1B01G141400 chr1D 86.612 732 74 13 4336 5045 124565318 124566047 0.000000e+00 787.0
7 TraesCS1B01G141400 chr1D 81.210 463 70 12 4484 4932 148524337 148523878 1.730000e-94 357.0
8 TraesCS1B01G141400 chr1D 97.753 89 2 0 1990 2078 295954300 295954212 2.430000e-33 154.0
9 TraesCS1B01G141400 chr5B 78.351 388 62 17 4505 4879 710668291 710667913 1.090000e-56 231.0
10 TraesCS1B01G141400 chr5B 80.000 240 40 5 4648 4879 618178638 618178399 2.420000e-38 171.0
11 TraesCS1B01G141400 chr4A 79.179 341 54 11 4504 4831 739748610 739748946 2.360000e-53 220.0
12 TraesCS1B01G141400 chr7A 78.750 320 50 11 4484 4793 251837483 251837794 1.110000e-46 198.0
13 TraesCS1B01G141400 chr7A 100.000 32 0 0 4361 4392 134545251 134545282 5.460000e-05 60.2
14 TraesCS1B01G141400 chr6D 95.876 97 3 1 1987 2083 168293842 168293747 6.760000e-34 156.0
15 TraesCS1B01G141400 chr6D 97.778 90 2 0 1986 2075 309072592 309072503 6.760000e-34 156.0
16 TraesCS1B01G141400 chr3B 96.739 92 3 0 1983 2074 723452853 723452944 2.430000e-33 154.0
17 TraesCS1B01G141400 chr3B 76.610 295 57 6 4526 4809 808796223 808796516 8.750000e-33 152.0
18 TraesCS1B01G141400 chr4B 96.739 92 1 2 1988 2078 438099359 438099449 8.750000e-33 152.0
19 TraesCS1B01G141400 chr4B 84.000 100 11 4 4508 4605 606759458 606759362 1.930000e-14 91.6
20 TraesCS1B01G141400 chr2A 96.739 92 1 2 1988 2078 115434416 115434506 8.750000e-33 152.0
21 TraesCS1B01G141400 chr2B 91.429 105 9 0 1989 2093 63783811 63783707 1.460000e-30 145.0
22 TraesCS1B01G141400 chr5D 90.179 112 7 4 1969 2078 461429835 461429726 5.270000e-30 143.0
23 TraesCS1B01G141400 chr5D 74.419 344 69 14 4608 4936 534038962 534038623 4.100000e-26 130.0
24 TraesCS1B01G141400 chr5D 86.869 99 8 4 4294 4392 384349385 384349292 6.910000e-19 106.0
25 TraesCS1B01G141400 chr7D 87.395 119 13 2 1990 2107 519264630 519264513 8.810000e-28 135.0
26 TraesCS1B01G141400 chr7D 91.667 60 4 1 4425 4484 566260434 566260492 1.160000e-11 82.4
27 TraesCS1B01G141400 chrUn 91.176 68 4 2 4720 4786 126733138 126733072 1.930000e-14 91.6
28 TraesCS1B01G141400 chr2D 75.610 205 26 13 4289 4474 301186513 301186712 4.190000e-11 80.5


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 TraesCS1B01G141400 chr1B 188789873 188794918 5045 False 9319.000000 9319 100.000 1 5046 1 chr1B.!!$F1 5045
1 TraesCS1B01G141400 chr1A 137230990 137235508 4518 False 2246.000000 3640 91.768 43 5013 3 chr1A.!!$F1 4970
2 TraesCS1B01G141400 chr1D 124559397 124566047 6650 False 2498.333333 3561 92.350 24 5045 3 chr1D.!!$F1 5021

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
946 967 0.106419 TCCCCTTGTTTCTGCCGTTT 60.106 50.0 0.0 0.0 0.00 3.60 F
1980 2010 0.245539 TTCATCTTCCACGACCGTCC 59.754 55.0 0.0 0.0 0.00 4.79 F
3881 3948 0.808755 CCAGCGTCATGGGGTAAAAC 59.191 55.0 0.0 0.0 36.64 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2250 0.463654 TGTGTGCACAGAGTTCCCAC 60.464 55.000 22.40 5.5 36.21 4.61 R
3937 4004 0.744414 CTGGTATTGTGGCCTCACCG 60.744 60.000 7.09 0.0 43.94 4.94 R
4788 6551 1.265635 TCACCGTCGAAATTGGCAAAG 59.734 47.619 3.01 0.0 0.00 2.77 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
19 20 2.963498 GCCGTGTTGAAGACCTAAAC 57.037 50.000 0.00 0.00 0.00 2.01
20 21 1.193874 GCCGTGTTGAAGACCTAAACG 59.806 52.381 0.00 0.00 0.00 3.60
21 22 2.476821 CCGTGTTGAAGACCTAAACGT 58.523 47.619 0.00 0.00 0.00 3.99
22 23 2.220133 CCGTGTTGAAGACCTAAACGTG 59.780 50.000 0.00 0.00 0.00 4.49
27 28 3.804786 TGAAGACCTAAACGTGTCACA 57.195 42.857 3.42 3.84 33.89 3.58
35 36 3.188460 CCTAAACGTGTCACATTTGGAGG 59.812 47.826 9.17 4.53 0.00 4.30
36 37 2.341846 AACGTGTCACATTTGGAGGT 57.658 45.000 3.42 0.00 0.00 3.85
38 39 1.140052 ACGTGTCACATTTGGAGGTGA 59.860 47.619 3.42 0.00 43.62 4.02
212 225 1.289109 ACGTTTCGTTCCGCCATCAG 61.289 55.000 0.00 0.00 36.35 2.90
262 280 4.497507 GCCGCTCTCCCATTTTACAATTAC 60.498 45.833 0.00 0.00 0.00 1.89
317 335 6.374565 ACGGAAGTAGTACTAGCATTACTG 57.625 41.667 1.87 0.73 46.88 2.74
319 337 5.298777 CGGAAGTAGTACTAGCATTACTGGT 59.701 44.000 1.87 0.00 43.49 4.00
345 363 0.179166 TTGGCGAATTTGCGATCTGC 60.179 50.000 11.57 3.07 46.70 4.26
355 373 2.456000 GCGATCTGCGAAAGAACCA 58.544 52.632 0.00 0.00 44.57 3.67
375 393 1.067776 AGCGAGAAAACGACGGAATCT 60.068 47.619 0.00 0.00 35.09 2.40
497 515 2.554032 CAAGCCAAGACAGAAACGGAAT 59.446 45.455 0.00 0.00 0.00 3.01
516 534 0.533308 TAAACGAGCCGTGCCACTTT 60.533 50.000 0.94 0.00 39.99 2.66
540 558 4.766891 TGAGAGGAAGCTAATTTTGTTGGG 59.233 41.667 0.00 0.00 0.00 4.12
808 829 2.877786 TGCGATTTCTGCAAGTTTCAGA 59.122 40.909 0.68 0.68 39.87 3.27
827 848 0.755686 ACCCTCCTCGCATCAATCTC 59.244 55.000 0.00 0.00 0.00 2.75
850 871 2.943690 GGGTCTAGAGCCCGAAATTTTC 59.056 50.000 27.52 1.00 42.92 2.29
946 967 0.106419 TCCCCTTGTTTCTGCCGTTT 60.106 50.000 0.00 0.00 0.00 3.60
973 994 3.012518 CGGCAGGATTCAGATGTTCTTT 58.987 45.455 0.00 0.00 0.00 2.52
990 1011 2.441750 TCTTTGGCAAGGTAGGTCAAGT 59.558 45.455 9.31 0.00 30.63 3.16
997 1018 4.506095 GGCAAGGTAGGTCAAGTTAAAGGA 60.506 45.833 0.00 0.00 0.00 3.36
1180 1204 0.691413 CCCTCCTCCTTCAGGTACCC 60.691 65.000 8.74 0.00 43.95 3.69
1281 1305 2.744202 CCTCAGTTATGTCTTGTGCACC 59.256 50.000 15.69 0.00 0.00 5.01
1351 1375 6.663953 TCTGCCTCTTCATTTAGTACAGTAGT 59.336 38.462 0.00 0.00 0.00 2.73
1352 1376 7.178628 TCTGCCTCTTCATTTAGTACAGTAGTT 59.821 37.037 0.00 0.00 0.00 2.24
1386 1412 9.138596 ACCACTAAATAAGAAAAACAGGCTAAA 57.861 29.630 0.00 0.00 0.00 1.85
1405 1431 8.313292 AGGCTAAAAAGTGATGCATATTGAAAA 58.687 29.630 0.00 0.00 0.00 2.29
1439 1465 4.642437 TGTTTTGATGTGTTTGTAGAGCCA 59.358 37.500 0.00 0.00 0.00 4.75
1553 1579 6.366877 ACATGATTGCTGTAATTTTTGCACTC 59.633 34.615 0.00 0.00 36.23 3.51
1662 1688 9.829507 ATCAGAAGGTGATACTTAGAATTCTTG 57.170 33.333 14.36 9.69 44.69 3.02
1980 2010 0.245539 TTCATCTTCCACGACCGTCC 59.754 55.000 0.00 0.00 0.00 4.79
1991 2021 3.368843 CCACGACCGTCCTAACAAAATAC 59.631 47.826 0.00 0.00 0.00 1.89
1992 2022 4.240096 CACGACCGTCCTAACAAAATACT 58.760 43.478 0.00 0.00 0.00 2.12
1993 2023 4.325472 CACGACCGTCCTAACAAAATACTC 59.675 45.833 0.00 0.00 0.00 2.59
1994 2024 4.022068 ACGACCGTCCTAACAAAATACTCA 60.022 41.667 0.00 0.00 0.00 3.41
1995 2025 4.325472 CGACCGTCCTAACAAAATACTCAC 59.675 45.833 0.00 0.00 0.00 3.51
1996 2026 5.476614 GACCGTCCTAACAAAATACTCACT 58.523 41.667 0.00 0.00 0.00 3.41
1997 2027 5.476614 ACCGTCCTAACAAAATACTCACTC 58.523 41.667 0.00 0.00 0.00 3.51
1998 2028 5.245526 ACCGTCCTAACAAAATACTCACTCT 59.754 40.000 0.00 0.00 0.00 3.24
1999 2029 5.577164 CCGTCCTAACAAAATACTCACTCTG 59.423 44.000 0.00 0.00 0.00 3.35
2000 2030 6.157211 CGTCCTAACAAAATACTCACTCTGT 58.843 40.000 0.00 0.00 0.00 3.41
2001 2031 6.308282 CGTCCTAACAAAATACTCACTCTGTC 59.692 42.308 0.00 0.00 0.00 3.51
2002 2032 6.590677 GTCCTAACAAAATACTCACTCTGTCC 59.409 42.308 0.00 0.00 0.00 4.02
2003 2033 5.875359 CCTAACAAAATACTCACTCTGTCCC 59.125 44.000 0.00 0.00 0.00 4.46
2004 2034 4.974645 ACAAAATACTCACTCTGTCCCA 57.025 40.909 0.00 0.00 0.00 4.37
2005 2035 5.505181 ACAAAATACTCACTCTGTCCCAT 57.495 39.130 0.00 0.00 0.00 4.00
2006 2036 6.620877 ACAAAATACTCACTCTGTCCCATA 57.379 37.500 0.00 0.00 0.00 2.74
2007 2037 7.016153 ACAAAATACTCACTCTGTCCCATAA 57.984 36.000 0.00 0.00 0.00 1.90
2008 2038 7.633789 ACAAAATACTCACTCTGTCCCATAAT 58.366 34.615 0.00 0.00 0.00 1.28
2009 2039 8.768397 ACAAAATACTCACTCTGTCCCATAATA 58.232 33.333 0.00 0.00 0.00 0.98
2010 2040 9.784531 CAAAATACTCACTCTGTCCCATAATAT 57.215 33.333 0.00 0.00 0.00 1.28
2015 2045 8.415950 ACTCACTCTGTCCCATAATATAAGAG 57.584 38.462 0.00 0.00 36.58 2.85
2016 2046 7.039363 ACTCACTCTGTCCCATAATATAAGAGC 60.039 40.741 0.00 0.00 34.39 4.09
2017 2047 6.071896 TCACTCTGTCCCATAATATAAGAGCG 60.072 42.308 0.00 0.00 34.39 5.03
2018 2048 5.775701 ACTCTGTCCCATAATATAAGAGCGT 59.224 40.000 0.00 0.00 34.39 5.07
2019 2049 6.267928 ACTCTGTCCCATAATATAAGAGCGTT 59.732 38.462 0.00 0.00 34.39 4.84
2020 2050 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
2021 2051 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
2022 2052 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
2064 2094 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2065 2095 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2066 2096 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2067 2097 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2068 2098 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2069 2099 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2070 2100 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2071 2101 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2072 2102 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2073 2103 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2074 2104 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
2075 2105 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
2103 2133 9.255029 ACTTATCCACAAATTAGTTATTGCCTT 57.745 29.630 0.00 0.00 0.00 4.35
2209 2239 2.046892 CAGGAGGACACCAAGGCG 60.047 66.667 0.00 0.00 0.00 5.52
2220 2250 4.438744 GGACACCAAGGCGAAAATAATCAG 60.439 45.833 0.00 0.00 0.00 2.90
2276 2306 3.625897 CCACCACCACTGCCTCGA 61.626 66.667 0.00 0.00 0.00 4.04
2375 2411 6.013898 TGAAATGGTTATGGAAGAATTTGGCA 60.014 34.615 0.00 0.00 0.00 4.92
2381 2417 3.507162 TGGAAGAATTTGGCAGAGACA 57.493 42.857 0.00 0.00 0.00 3.41
2410 2446 4.099170 GCAAGCTCACCTGCAGCG 62.099 66.667 8.66 4.27 42.14 5.18
2577 2613 5.936956 AGCTTGAGAACCAACTGAAGATAAG 59.063 40.000 0.00 0.00 34.07 1.73
2677 2713 6.130058 GTCTGAAAGCTCAAAGTTAACTTCG 58.870 40.000 20.78 10.70 34.61 3.79
2687 2723 3.386768 AGTTAACTTCGCAGCTTGAGA 57.613 42.857 1.12 0.00 0.00 3.27
2785 2821 6.627087 TCCCTTCAGAACATAGTTGATTCT 57.373 37.500 0.00 0.00 32.87 2.40
2794 2830 7.536622 CAGAACATAGTTGATTCTTTTCAGTGC 59.463 37.037 0.00 0.00 30.17 4.40
2821 2857 6.619023 AGGAGATTATTGAGGGAGAAGTTGAT 59.381 38.462 0.00 0.00 0.00 2.57
3005 3041 5.316987 AGGTAAATCTTGACTGTTCTTGGG 58.683 41.667 0.00 0.00 0.00 4.12
3026 3062 3.058914 GGCTGCACTGTAACTAACACTTG 60.059 47.826 0.50 0.00 33.45 3.16
3118 3154 4.870123 TGCCAAACAGAAACTGCATAAT 57.130 36.364 0.00 0.00 34.37 1.28
3195 3253 9.820229 CTGTCACGAATTAAGCAAGTAAAAATA 57.180 29.630 0.00 0.00 0.00 1.40
3561 3619 1.278238 GAACCCGATGACACATCGAC 58.722 55.000 27.74 15.54 43.59 4.20
3565 3623 0.866061 CCGATGACACATCGACCGAC 60.866 60.000 27.74 0.00 43.59 4.79
3751 3809 4.157656 GGAAGAGAGTCGCATGATAGCTAT 59.842 45.833 5.76 5.76 0.00 2.97
3784 3851 1.074405 ACAGAAGGAGCCAATCAGCAA 59.926 47.619 0.00 0.00 34.23 3.91
3839 3906 2.551459 GGCAGCCAAAGATATAGCACAG 59.449 50.000 6.55 0.00 0.00 3.66
3840 3907 2.031333 GCAGCCAAAGATATAGCACAGC 60.031 50.000 0.00 0.00 0.00 4.40
3841 3908 3.474600 CAGCCAAAGATATAGCACAGCT 58.525 45.455 0.00 0.00 43.41 4.24
3881 3948 0.808755 CCAGCGTCATGGGGTAAAAC 59.191 55.000 0.00 0.00 36.64 2.43
3937 4004 5.412594 TGAACATGGTTCTCAGTTTGATAGC 59.587 40.000 10.14 0.00 0.00 2.97
3961 4028 2.027192 TGAGGCCACAATACCAGAAGAC 60.027 50.000 5.01 0.00 0.00 3.01
4156 4235 7.770897 AGATGTTACTGGAATGAAGTATCCAAC 59.229 37.037 0.00 0.00 44.77 3.77
4261 4342 1.581934 TTGTGCTTCTTCACTGTCGG 58.418 50.000 0.00 0.00 37.81 4.79
4262 4343 0.464036 TGTGCTTCTTCACTGTCGGT 59.536 50.000 0.00 0.00 37.81 4.69
4263 4344 1.134521 TGTGCTTCTTCACTGTCGGTT 60.135 47.619 0.00 0.00 37.81 4.44
4264 4345 1.940613 GTGCTTCTTCACTGTCGGTTT 59.059 47.619 0.00 0.00 34.29 3.27
4265 4346 2.354821 GTGCTTCTTCACTGTCGGTTTT 59.645 45.455 0.00 0.00 34.29 2.43
4266 4347 3.013921 TGCTTCTTCACTGTCGGTTTTT 58.986 40.909 0.00 0.00 0.00 1.94
4348 6089 7.559590 AATGTAGCATCAAGTGGATAGAAAC 57.440 36.000 0.00 0.00 33.95 2.78
4363 6104 5.008415 GGATAGAAACCATGATGAGCAACAG 59.992 44.000 0.00 0.00 0.00 3.16
4374 6115 4.487412 GCAACAGCCGGCATCTGC 62.487 66.667 31.54 27.45 41.14 4.26
4379 6120 0.179009 ACAGCCGGCATCTGCATAAT 60.179 50.000 31.54 0.00 44.36 1.28
4385 6126 3.441572 GCCGGCATCTGCATAATTAAGAT 59.558 43.478 24.80 0.00 44.36 2.40
4463 6217 1.001268 ACTGACGCTATGCCTATGTCG 60.001 52.381 0.00 0.00 32.32 4.35
4476 6230 1.672854 TATGTCGAAGGAGGTGGCGG 61.673 60.000 0.00 0.00 0.00 6.13
4483 6237 4.554036 GGAGGTGGCGGGCTGATC 62.554 72.222 0.00 0.00 0.00 2.92
4488 6242 3.089217 TGGCGGGCTGATCATGGA 61.089 61.111 0.00 0.00 0.00 3.41
4492 6246 1.524621 CGGGCTGATCATGGACCAC 60.525 63.158 7.57 0.00 0.00 4.16
4494 6248 2.182842 GGCTGATCATGGACCACGC 61.183 63.158 0.00 0.00 0.00 5.34
4540 6294 5.505181 AAAATAACCTGCAGAGGAGAAGA 57.495 39.130 17.39 0.00 42.93 2.87
4558 6312 8.432013 AGGAGAAGAGTTTTTGCCATTAAAATT 58.568 29.630 0.00 0.00 30.39 1.82
4585 6339 9.462174 CAAATCATTTTTATATAGCCAAAGCGA 57.538 29.630 0.00 0.00 46.67 4.93
4590 6344 8.511321 CATTTTTATATAGCCAAAGCGACCATA 58.489 33.333 0.00 0.00 46.67 2.74
4595 6349 9.727859 TTATATAGCCAAAGCGACCATAATAAA 57.272 29.630 0.00 0.00 46.67 1.40
4617 6371 5.028549 AGCATACACTCTCACCCTTATTG 57.971 43.478 0.00 0.00 0.00 1.90
4620 6374 1.066143 ACACTCTCACCCTTATTGGCG 60.066 52.381 0.00 0.00 0.00 5.69
4624 6378 1.906574 TCTCACCCTTATTGGCGTTCT 59.093 47.619 0.00 0.00 0.00 3.01
4666 6420 9.874205 ACCATCCAAATAATGACAAAAATACTG 57.126 29.630 0.00 0.00 0.00 2.74
4682 6437 1.290203 ACTGACAACACTTGTGAGCG 58.710 50.000 7.83 0.00 46.88 5.03
4693 6448 6.811253 ACACTTGTGAGCGGATAAAAATTA 57.189 33.333 7.83 0.00 0.00 1.40
4696 6451 7.593644 ACACTTGTGAGCGGATAAAAATTAAAC 59.406 33.333 7.83 0.00 0.00 2.01
4697 6452 7.593273 CACTTGTGAGCGGATAAAAATTAAACA 59.407 33.333 0.00 0.00 0.00 2.83
4698 6453 8.138712 ACTTGTGAGCGGATAAAAATTAAACAA 58.861 29.630 0.00 0.00 0.00 2.83
4757 6520 6.183360 GGAAAAAGAGGTGTTTGATTGTCTCA 60.183 38.462 0.00 0.00 0.00 3.27
4762 6525 7.621428 AGAGGTGTTTGATTGTCTCATTATG 57.379 36.000 0.00 0.00 32.72 1.90
4786 6549 9.654663 ATGAGTACAAAATCTACACTTCTTACC 57.345 33.333 0.00 0.00 0.00 2.85
4788 6551 9.356433 GAGTACAAAATCTACACTTCTTACCTC 57.644 37.037 0.00 0.00 0.00 3.85
4789 6552 9.091220 AGTACAAAATCTACACTTCTTACCTCT 57.909 33.333 0.00 0.00 0.00 3.69
4809 6572 1.309950 TTGCCAATTTCGACGGTGAA 58.690 45.000 0.00 0.00 0.00 3.18
4825 6588 3.303791 CGGTGAAGTTGTCTTTGGTTAGC 60.304 47.826 0.00 0.00 33.64 3.09
4827 6590 2.289547 TGAAGTTGTCTTTGGTTAGCGC 59.710 45.455 0.00 0.00 33.64 5.92
4846 6609 4.526262 AGCGCAACTCCTATCAGAAGATAT 59.474 41.667 11.47 0.00 36.21 1.63
4849 6612 6.450545 CGCAACTCCTATCAGAAGATATCAA 58.549 40.000 5.32 0.00 36.21 2.57
4850 6613 6.925718 CGCAACTCCTATCAGAAGATATCAAA 59.074 38.462 5.32 0.00 36.21 2.69
4887 6653 6.408548 CCTTCTAGTGGAATATTTGGCTCAGA 60.409 42.308 0.00 0.00 33.01 3.27
4892 6658 6.870769 AGTGGAATATTTGGCTCAGATTTTG 58.129 36.000 0.00 0.00 0.00 2.44
4923 6689 1.949525 CCAATGGGACCTTAGAATGCG 59.050 52.381 0.00 0.00 35.59 4.73
4928 6694 1.207329 GGGACCTTAGAATGCGTGAGT 59.793 52.381 0.00 0.00 0.00 3.41
5045 6813 5.815581 TGATAATGGTAAACTGCTCCAAGT 58.184 37.500 0.00 0.00 34.80 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.193874 CGTTTAGGTCTTCAACACGGC 59.806 52.381 0.00 0.00 0.00 5.68
1 2 2.220133 CACGTTTAGGTCTTCAACACGG 59.780 50.000 0.00 0.00 0.00 4.94
2 3 2.861935 ACACGTTTAGGTCTTCAACACG 59.138 45.455 0.00 0.00 0.00 4.49
3 4 3.866910 TGACACGTTTAGGTCTTCAACAC 59.133 43.478 5.49 0.00 35.11 3.32
4 5 3.866910 GTGACACGTTTAGGTCTTCAACA 59.133 43.478 5.49 0.00 35.11 3.33
5 6 3.866910 TGTGACACGTTTAGGTCTTCAAC 59.133 43.478 0.22 0.00 35.11 3.18
6 7 4.126208 TGTGACACGTTTAGGTCTTCAA 57.874 40.909 0.22 0.00 35.11 2.69
7 8 3.804786 TGTGACACGTTTAGGTCTTCA 57.195 42.857 0.22 2.89 35.11 3.02
8 9 5.440685 CAAATGTGACACGTTTAGGTCTTC 58.559 41.667 22.18 0.74 35.31 2.87
9 10 4.274950 CCAAATGTGACACGTTTAGGTCTT 59.725 41.667 22.18 0.00 35.31 3.01
10 11 3.813166 CCAAATGTGACACGTTTAGGTCT 59.187 43.478 22.18 0.40 35.31 3.85
11 12 3.810941 TCCAAATGTGACACGTTTAGGTC 59.189 43.478 22.18 0.00 35.31 3.85
12 13 3.811083 TCCAAATGTGACACGTTTAGGT 58.189 40.909 22.18 1.44 35.31 3.08
13 14 3.188460 CCTCCAAATGTGACACGTTTAGG 59.812 47.826 22.18 21.10 35.31 2.69
14 15 3.813166 ACCTCCAAATGTGACACGTTTAG 59.187 43.478 22.18 16.59 35.31 1.85
15 16 3.562141 CACCTCCAAATGTGACACGTTTA 59.438 43.478 22.18 9.80 35.31 2.01
16 17 2.357637 CACCTCCAAATGTGACACGTTT 59.642 45.455 18.11 18.11 37.78 3.60
17 18 1.946768 CACCTCCAAATGTGACACGTT 59.053 47.619 7.24 7.24 34.37 3.99
18 19 1.140052 TCACCTCCAAATGTGACACGT 59.860 47.619 0.22 0.00 36.62 4.49
19 20 1.877637 TCACCTCCAAATGTGACACG 58.122 50.000 0.22 0.00 36.62 4.49
40 41 2.755650 ACAACATCTCCAACGTGACTC 58.244 47.619 0.00 0.00 0.00 3.36
148 150 4.764823 TGATTTCTTCACGCCACCTTTAAT 59.235 37.500 0.00 0.00 0.00 1.40
151 153 2.293399 GTGATTTCTTCACGCCACCTTT 59.707 45.455 0.00 0.00 45.00 3.11
212 225 2.047179 GAGGGTGGCTGAACCGAC 60.047 66.667 0.00 0.00 43.94 4.79
312 330 3.410631 TCGCCAATTCTTCACCAGTAA 57.589 42.857 0.00 0.00 0.00 2.24
317 335 2.667969 GCAAATTCGCCAATTCTTCACC 59.332 45.455 0.00 0.00 30.37 4.02
319 337 2.227626 TCGCAAATTCGCCAATTCTTCA 59.772 40.909 0.00 0.00 30.37 3.02
345 363 2.659291 CGTTTTCTCGCTGGTTCTTTCG 60.659 50.000 0.00 0.00 0.00 3.46
355 373 1.067776 AGATTCCGTCGTTTTCTCGCT 60.068 47.619 0.00 0.00 0.00 4.93
375 393 6.369340 TCGTGTCGCCTTTCTTTATTTATTCA 59.631 34.615 0.00 0.00 0.00 2.57
497 515 0.533308 AAAGTGGCACGGCTCGTTTA 60.533 50.000 12.71 0.00 38.32 2.01
516 534 5.243730 CCCAACAAAATTAGCTTCCTCTCAA 59.756 40.000 0.00 0.00 0.00 3.02
540 558 2.559231 ACGACTGAGGAGGAAGAAGAAC 59.441 50.000 0.00 0.00 0.00 3.01
808 829 0.755686 GAGATTGATGCGAGGAGGGT 59.244 55.000 0.00 0.00 0.00 4.34
973 994 4.394729 CTTTAACTTGACCTACCTTGCCA 58.605 43.478 0.00 0.00 0.00 4.92
1240 1264 7.718753 ACTGAGGCATAATCAATCTTAGAAAGG 59.281 37.037 0.00 0.00 0.00 3.11
1246 1270 9.494271 GACATAACTGAGGCATAATCAATCTTA 57.506 33.333 0.00 0.00 0.00 2.10
1359 1383 9.796180 TTAGCCTGTTTTTCTTATTTAGTGGTA 57.204 29.630 0.00 0.00 0.00 3.25
1407 1433 8.729805 ACAAACACATCAAAACATACCAATTT 57.270 26.923 0.00 0.00 0.00 1.82
1408 1434 9.474920 CTACAAACACATCAAAACATACCAATT 57.525 29.630 0.00 0.00 0.00 2.32
1409 1435 8.855110 TCTACAAACACATCAAAACATACCAAT 58.145 29.630 0.00 0.00 0.00 3.16
1553 1579 5.824624 TCTTAGGTATGGTTACACCTCTACG 59.175 44.000 0.00 0.00 44.17 3.51
1560 1586 7.120923 TCATCCTTCTTAGGTATGGTTACAC 57.879 40.000 0.00 0.00 42.60 2.90
1876 1906 6.412460 CGTGTTACGGCGAATTTGATATAAA 58.588 36.000 16.62 0.00 38.08 1.40
1980 2010 6.464222 TGGGACAGAGTGAGTATTTTGTTAG 58.536 40.000 0.00 0.00 0.00 2.34
2040 2070 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2041 2071 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2042 2072 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2043 2073 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2044 2074 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2045 2075 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2046 2076 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2047 2077 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2048 2078 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2049 2079 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2050 2080 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2051 2081 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2052 2082 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2053 2083 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2054 2084 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2055 2085 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2056 2086 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2057 2087 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2058 2088 1.002069 TTACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2059 2089 1.064091 AGTTACTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
2060 2090 2.433662 AGTTACTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2061 2091 4.518590 GGATAAGTTACTACTCCCTCCGTC 59.481 50.000 2.70 0.00 31.99 4.79
2062 2092 4.079558 TGGATAAGTTACTACTCCCTCCGT 60.080 45.833 9.67 0.00 32.71 4.69
2063 2093 4.277921 GTGGATAAGTTACTACTCCCTCCG 59.722 50.000 9.67 0.00 32.71 4.63
2064 2094 5.206587 TGTGGATAAGTTACTACTCCCTCC 58.793 45.833 9.67 1.09 31.99 4.30
2065 2095 6.786967 TTGTGGATAAGTTACTACTCCCTC 57.213 41.667 9.67 5.23 31.99 4.30
2066 2096 7.750947 ATTTGTGGATAAGTTACTACTCCCT 57.249 36.000 9.67 0.00 31.99 4.20
2067 2097 9.543783 CTAATTTGTGGATAAGTTACTACTCCC 57.456 37.037 9.67 3.88 31.99 4.30
2106 2136 8.585189 TCAACTGATTGAAGAATGATATCGAG 57.415 34.615 0.00 0.00 41.99 4.04
2209 2239 6.623767 GCACAGAGTTCCCACTGATTATTTTC 60.624 42.308 0.00 0.00 37.54 2.29
2220 2250 0.463654 TGTGTGCACAGAGTTCCCAC 60.464 55.000 22.40 5.50 36.21 4.61
2276 2306 1.955208 GCATTTCGGGGGAAGTGACAT 60.955 52.381 3.88 0.00 0.00 3.06
2375 2411 4.564041 CTTGCGATATTGCCTATGTCTCT 58.436 43.478 12.54 0.00 0.00 3.10
2381 2417 3.070018 GTGAGCTTGCGATATTGCCTAT 58.930 45.455 12.54 0.00 0.00 2.57
2410 2446 4.953940 AGATGCATCTTCCCTTACTCTC 57.046 45.455 23.75 0.00 31.97 3.20
2577 2613 1.996292 TAGCTGTGACTCGACATTGC 58.004 50.000 0.00 0.00 0.00 3.56
2677 2713 4.430137 TGATTTTGTCATCTCAAGCTGC 57.570 40.909 0.00 0.00 0.00 5.25
2687 2723 5.761234 ACAGCTTGCATTTTGATTTTGTCAT 59.239 32.000 0.00 0.00 36.54 3.06
2785 2821 6.151648 CCTCAATAATCTCCTTGCACTGAAAA 59.848 38.462 0.00 0.00 0.00 2.29
2794 2830 6.245890 ACTTCTCCCTCAATAATCTCCTTG 57.754 41.667 0.00 0.00 0.00 3.61
2821 2857 3.795688 AATTTCTTCTCAGCCTCACCA 57.204 42.857 0.00 0.00 0.00 4.17
3005 3041 3.807622 TCAAGTGTTAGTTACAGTGCAGC 59.192 43.478 0.00 0.00 39.53 5.25
3195 3253 6.815089 TGTTCTGATGTTTTTACCTGCAATT 58.185 32.000 0.00 0.00 0.00 2.32
3561 3619 3.484065 CGTTGTGATTGATGACATGTCGG 60.484 47.826 20.54 0.00 0.00 4.79
3565 3623 2.478370 GGGCGTTGTGATTGATGACATG 60.478 50.000 0.00 0.00 0.00 3.21
3736 3794 4.815269 AGGAAGAATAGCTATCATGCGAC 58.185 43.478 6.72 0.00 38.13 5.19
3784 3851 2.169789 GCAGCTGCGATCGTCATGT 61.170 57.895 25.23 2.94 0.00 3.21
3839 3906 1.209019 TCTTCCATCTCCTGCTTCAGC 59.791 52.381 0.00 0.00 42.50 4.26
3840 3907 3.842007 ATCTTCCATCTCCTGCTTCAG 57.158 47.619 0.00 0.00 0.00 3.02
3841 3908 3.389329 GGTATCTTCCATCTCCTGCTTCA 59.611 47.826 0.00 0.00 0.00 3.02
3881 3948 2.222678 CGGATCCGAAAGATGCATTCTG 59.777 50.000 30.62 0.00 43.22 3.02
3937 4004 0.744414 CTGGTATTGTGGCCTCACCG 60.744 60.000 7.09 0.00 43.94 4.94
3961 4028 1.005975 GCGAATTTGTGGATCTCGACG 60.006 52.381 2.80 0.00 0.00 5.12
4204 4285 6.916360 TGGCAAAGATTGAGATTAAAGGTT 57.084 33.333 0.00 0.00 0.00 3.50
4239 4320 2.351418 CGACAGTGAAGAAGCACAAACA 59.649 45.455 0.00 0.00 41.19 2.83
4267 4348 9.907576 CAAAAATACTTTGCAAATAACGACAAA 57.092 25.926 13.23 0.00 0.00 2.83
4268 4349 9.302345 TCAAAAATACTTTGCAAATAACGACAA 57.698 25.926 13.23 0.00 0.00 3.18
4269 4350 8.858003 TCAAAAATACTTTGCAAATAACGACA 57.142 26.923 13.23 0.00 0.00 4.35
4315 4396 8.801299 TCCACTTGATGCTACATTTATTTTGAA 58.199 29.630 0.00 0.00 0.00 2.69
4344 6085 2.416431 GGCTGTTGCTCATCATGGTTTC 60.416 50.000 0.00 0.00 39.59 2.78
4348 6089 1.721664 CCGGCTGTTGCTCATCATGG 61.722 60.000 0.00 0.00 39.59 3.66
4363 6104 2.813754 TCTTAATTATGCAGATGCCGGC 59.186 45.455 22.73 22.73 41.18 6.13
4374 6115 6.855836 AGTGTTGGTGTGCATCTTAATTATG 58.144 36.000 0.00 0.00 0.00 1.90
4379 6120 3.814842 CAGAGTGTTGGTGTGCATCTTAA 59.185 43.478 0.00 0.00 0.00 1.85
4385 6126 0.251634 TGTCAGAGTGTTGGTGTGCA 59.748 50.000 0.00 0.00 0.00 4.57
4420 6171 8.608317 CAGTCCTATATGACTCTACATATGTCG 58.392 40.741 12.68 6.31 43.63 4.35
4447 6201 1.000163 CCTTCGACATAGGCATAGCGT 60.000 52.381 0.00 0.00 0.00 5.07
4463 6217 4.785453 CAGCCCGCCACCTCCTTC 62.785 72.222 0.00 0.00 0.00 3.46
4476 6230 2.182842 GCGTGGTCCATGATCAGCC 61.183 63.158 15.72 1.63 0.00 4.85
4479 6233 0.540923 TCATGCGTGGTCCATGATCA 59.459 50.000 15.72 0.00 42.88 2.92
4483 6237 1.430632 GCTTCATGCGTGGTCCATG 59.569 57.895 6.73 6.73 41.03 3.66
4494 6248 1.067693 TGTACGCACTTCGCTTCATG 58.932 50.000 0.00 0.00 43.23 3.07
4504 6258 4.933400 AGGTTATTTTTCGATGTACGCACT 59.067 37.500 0.00 0.00 42.26 4.40
4517 6271 5.880901 TCTTCTCCTCTGCAGGTTATTTTT 58.119 37.500 15.13 0.00 41.28 1.94
4558 6312 9.462174 CGCTTTGGCTATATAAAAATGATTTGA 57.538 29.630 0.00 0.00 36.09 2.69
4585 6339 6.992715 GGTGAGAGTGTATGCTTTATTATGGT 59.007 38.462 0.00 0.00 0.00 3.55
4590 6344 5.700402 AGGGTGAGAGTGTATGCTTTATT 57.300 39.130 0.00 0.00 0.00 1.40
4595 6349 4.141620 CCAATAAGGGTGAGAGTGTATGCT 60.142 45.833 0.00 0.00 0.00 3.79
4617 6371 5.757850 ATTCCAAATAGATTCAGAACGCC 57.242 39.130 0.00 0.00 0.00 5.68
4652 6406 7.701924 CACAAGTGTTGTCAGTATTTTTGTCAT 59.298 33.333 0.00 0.00 43.23 3.06
4662 6416 2.469826 CGCTCACAAGTGTTGTCAGTA 58.530 47.619 0.00 0.00 43.23 2.74
4663 6417 1.290203 CGCTCACAAGTGTTGTCAGT 58.710 50.000 0.00 0.00 43.23 3.41
4664 6418 0.583438 CCGCTCACAAGTGTTGTCAG 59.417 55.000 0.00 0.00 43.23 3.51
4666 6420 1.512926 ATCCGCTCACAAGTGTTGTC 58.487 50.000 0.00 0.00 43.23 3.18
4667 6421 2.831685 TATCCGCTCACAAGTGTTGT 57.168 45.000 0.00 0.00 46.75 3.32
4693 6448 7.798516 CGCGTTCTATTCATGCTAATATTGTTT 59.201 33.333 0.00 0.00 0.00 2.83
4696 6451 5.729883 GCGCGTTCTATTCATGCTAATATTG 59.270 40.000 8.43 0.00 0.00 1.90
4697 6452 5.408299 TGCGCGTTCTATTCATGCTAATATT 59.592 36.000 8.43 0.00 0.00 1.28
4698 6453 4.929211 TGCGCGTTCTATTCATGCTAATAT 59.071 37.500 8.43 0.00 0.00 1.28
4703 6458 1.368641 TTGCGCGTTCTATTCATGCT 58.631 45.000 8.43 0.00 0.00 3.79
4730 6493 4.202111 ACAATCAAACACCTCTTTTTCCGG 60.202 41.667 0.00 0.00 0.00 5.14
4733 6496 6.795399 TGAGACAATCAAACACCTCTTTTTC 58.205 36.000 0.00 0.00 34.02 2.29
4762 6525 9.356433 GAGGTAAGAAGTGTAGATTTTGTACTC 57.644 37.037 0.00 0.00 0.00 2.59
4781 6544 4.669197 CGTCGAAATTGGCAAAGAGGTAAG 60.669 45.833 3.01 0.00 0.00 2.34
4786 6549 1.535462 ACCGTCGAAATTGGCAAAGAG 59.465 47.619 3.01 0.00 0.00 2.85
4788 6551 1.265635 TCACCGTCGAAATTGGCAAAG 59.734 47.619 3.01 0.00 0.00 2.77
4789 6552 1.309950 TCACCGTCGAAATTGGCAAA 58.690 45.000 3.01 0.00 0.00 3.68
4809 6572 1.961793 TGCGCTAACCAAAGACAACT 58.038 45.000 9.73 0.00 0.00 3.16
4825 6588 6.018589 TGATATCTTCTGATAGGAGTTGCG 57.981 41.667 3.98 0.00 38.42 4.85
4827 6590 9.993454 TCATTTGATATCTTCTGATAGGAGTTG 57.007 33.333 3.98 0.00 38.42 3.16
4846 6609 9.231297 CCACTAGAAGGTAAAATCTTCATTTGA 57.769 33.333 0.00 0.00 42.09 2.69
4849 6612 9.981460 ATTCCACTAGAAGGTAAAATCTTCATT 57.019 29.630 0.00 0.00 42.09 2.57
4862 6625 5.684704 TGAGCCAAATATTCCACTAGAAGG 58.315 41.667 0.00 0.00 38.07 3.46
4866 6629 7.814264 AAATCTGAGCCAAATATTCCACTAG 57.186 36.000 0.00 0.00 0.00 2.57
4887 6653 8.264347 GGTCCCATTGGATAATAACAACAAAAT 58.736 33.333 3.62 0.00 44.28 1.82
4892 6658 7.996644 TCTAAGGTCCCATTGGATAATAACAAC 59.003 37.037 3.62 0.00 44.28 3.32
4923 6689 3.820689 TGCAAAATAACGATGCACTCAC 58.179 40.909 0.00 0.00 44.52 3.51
4960 6726 3.730662 CGGTTACCTGCGATTTTTCATGG 60.731 47.826 0.00 0.00 0.00 3.66
4969 6735 1.270412 TGTTTGTCGGTTACCTGCGAT 60.270 47.619 0.00 0.00 0.00 4.58
5020 6788 6.891908 ACTTGGAGCAGTTTACCATTATCAAT 59.108 34.615 0.00 0.00 33.56 2.57
5022 6790 5.815581 ACTTGGAGCAGTTTACCATTATCA 58.184 37.500 0.00 0.00 33.56 2.15


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

AutoCloner maintained by Alex Coulton.