Multiple sequence alignment - TraesCS5A01G134000

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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 TraesCS5A01G134000 chr5A 100.000 4848 0 0 1 4848 301574558 301569711 0.000000e+00 8953.0
1 TraesCS5A01G134000 chr5D 94.726 2332 74 23 1847 4157 221880270 221882573 0.000000e+00 3579.0
2 TraesCS5A01G134000 chr5D 94.853 1671 54 22 180 1834 221878633 221880287 0.000000e+00 2580.0
3 TraesCS5A01G134000 chr5D 94.915 295 13 2 4142 4435 221883952 221884245 1.230000e-125 460.0
4 TraesCS5A01G134000 chr5D 89.412 340 18 9 4512 4836 221884378 221884714 3.490000e-111 412.0
5 TraesCS5A01G134000 chr5D 87.603 121 15 0 74 194 221876987 221877107 1.820000e-29 141.0
6 TraesCS5A01G134000 chr5B 91.711 1882 88 25 1 1834 244410471 244412332 0.000000e+00 2549.0
7 TraesCS5A01G134000 chr5B 93.277 1190 48 17 1847 3023 244412315 244413485 0.000000e+00 1725.0
8 TraesCS5A01G134000 chr5B 92.088 594 26 8 3734 4321 244414287 244414865 0.000000e+00 817.0
9 TraesCS5A01G134000 chr5B 99.003 301 3 0 3121 3421 244413528 244413828 1.540000e-149 540.0
10 TraesCS5A01G134000 chr5B 95.738 305 9 1 3436 3736 244413880 244414184 5.640000e-134 488.0
11 TraesCS5A01G134000 chr5B 83.262 233 23 11 4615 4832 296374151 296374382 2.960000e-47 200.0
12 TraesCS5A01G134000 chr5B 84.466 206 25 7 4613 4811 243168678 243168883 3.830000e-46 196.0
13 TraesCS5A01G134000 chr5B 92.308 52 2 1 3047 3096 244413481 244413532 6.730000e-09 73.1
14 TraesCS5A01G134000 chr5B 96.970 33 0 1 1996 2028 322129039 322129070 2.000000e-03 54.7
15 TraesCS5A01G134000 chr1B 87.558 217 19 8 4615 4824 196478289 196478074 1.350000e-60 244.0
16 TraesCS5A01G134000 chr1B 94.286 35 1 1 1996 2030 462113168 462113201 9.000000e-03 52.8
17 TraesCS5A01G134000 chr1B 94.286 35 1 1 1996 2030 462481559 462481592 9.000000e-03 52.8
18 TraesCS5A01G134000 chr4D 85.841 226 20 9 4614 4828 254868569 254868345 3.770000e-56 230.0
19 TraesCS5A01G134000 chr4A 85.106 235 22 10 4614 4836 66160737 66160970 1.360000e-55 228.0
20 TraesCS5A01G134000 chr4B 84.375 224 22 8 4613 4824 351127385 351127607 1.770000e-49 207.0
21 TraesCS5A01G134000 chr1D 83.929 224 20 10 4615 4824 126329351 126329130 2.960000e-47 200.0
22 TraesCS5A01G134000 chr6D 83.978 181 24 5 4657 4834 219496255 219496433 8.340000e-38 169.0
23 TraesCS5A01G134000 chr3D 100.000 30 0 0 2003 2032 320635225 320635254 6.780000e-04 56.5
24 TraesCS5A01G134000 chr3D 100.000 30 0 0 2003 2032 341550622 341550651 6.780000e-04 56.5
25 TraesCS5A01G134000 chr3A 78.351 97 10 8 1954 2039 719284751 719284655 9.000000e-03 52.8
26 TraesCS5A01G134000 chr3A 79.762 84 8 6 1954 2028 719327457 719327540 9.000000e-03 52.8


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 TraesCS5A01G134000 chr5A 301569711 301574558 4847 True 8953.000000 8953 100.000000 1 4848 1 chr5A.!!$R1 4847
1 TraesCS5A01G134000 chr5D 221876987 221884714 7727 False 1434.400000 3579 92.301800 74 4836 5 chr5D.!!$F1 4762
2 TraesCS5A01G134000 chr5B 244410471 244414865 4394 False 1032.016667 2549 94.020833 1 4321 6 chr5B.!!$F4 4320

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
129 132 0.176910 TGCTATGCGGACGGATGAAA 59.823 50.000 9.00 0.0 0.00 2.69 F
1357 2946 0.245539 ACGGACGGTTGATTGATCGT 59.754 50.000 0.00 0.0 38.62 3.73 F
2052 3657 0.238817 GCCGCGTTTGGAATACACAA 59.761 50.000 4.92 0.0 0.00 3.33 F
2361 3969 1.134037 ACTTGACAACAAACGGGCCTA 60.134 47.619 0.84 0.0 35.49 3.93 F
3507 5168 0.807667 CGCTCTTCTGGGGAATCACG 60.808 60.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 3501 1.297967 CTCTGTCGCGATCACGAGG 60.298 63.158 14.06 3.10 43.89 4.63 R
2465 4076 0.641275 TCGTCACGTCAACAACAACG 59.359 50.000 0.00 0.00 44.22 4.10 R
3424 5043 0.179045 AGCAAGAAAGCACGGTGACT 60.179 50.000 13.29 5.79 36.85 3.41 R
3799 5569 1.238439 CTTCCACCTGCACAACGAAT 58.762 50.000 0.00 0.00 0.00 3.34 R
4474 7661 0.171903 GCCGTAGCGACCTTTGACTA 59.828 55.000 0.00 0.00 0.00 2.59 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 22 2.747855 GTGGGGCTCCGCTTCTTG 60.748 66.667 9.58 0.00 40.31 3.02
29 32 4.299796 GCTTCTTGGGGTGGGCCA 62.300 66.667 0.00 0.00 36.17 5.36
47 50 1.251355 CAATCGTCTGACGTGTCTCG 58.749 55.000 27.16 9.55 43.14 4.04
60 63 2.075338 GTGTCTCGTCTTCCGACTACT 58.925 52.381 0.00 0.00 41.60 2.57
63 66 0.803117 CTCGTCTTCCGACTACTGCA 59.197 55.000 0.00 0.00 41.60 4.41
77 80 2.335316 ACTGCAAAGTCCCACGTTTA 57.665 45.000 0.00 0.00 0.00 2.01
83 86 3.794564 GCAAAGTCCCACGTTTAGTTTTG 59.205 43.478 0.00 0.00 31.94 2.44
87 90 5.684550 AGTCCCACGTTTAGTTTTGATTC 57.315 39.130 0.00 0.00 0.00 2.52
103 106 3.411446 TGATTCACGGGAATATCATGGC 58.589 45.455 14.07 0.00 43.69 4.40
115 118 1.130054 ATCATGGCCCGGACTGCTAT 61.130 55.000 0.73 0.00 0.00 2.97
117 120 3.482232 ATGGCCCGGACTGCTATGC 62.482 63.158 0.73 0.00 0.00 3.14
122 125 2.655364 CGGACTGCTATGCGGACG 60.655 66.667 5.31 5.76 38.46 4.79
129 132 0.176910 TGCTATGCGGACGGATGAAA 59.823 50.000 9.00 0.00 0.00 2.69
150 153 2.039084 AGTCAGTGTTGGATGTCTTCCC 59.961 50.000 2.43 0.00 44.77 3.97
152 155 1.001974 CAGTGTTGGATGTCTTCCCGA 59.998 52.381 2.43 0.00 44.77 5.14
157 160 1.639722 TGGATGTCTTCCCGAGTTCA 58.360 50.000 2.43 0.00 44.77 3.18
201 1744 2.644555 ATCGATTTGAGGGTCGGCGG 62.645 60.000 7.21 0.00 38.34 6.13
344 1891 2.670148 GCTTCATCCGTCACCCCCT 61.670 63.158 0.00 0.00 0.00 4.79
345 1892 1.522569 CTTCATCCGTCACCCCCTC 59.477 63.158 0.00 0.00 0.00 4.30
495 2074 4.363990 CCACACGAGAGCGCACCT 62.364 66.667 11.47 6.01 42.48 4.00
496 2075 2.356313 CACACGAGAGCGCACCTT 60.356 61.111 11.47 0.00 42.48 3.50
497 2076 1.956170 CACACGAGAGCGCACCTTT 60.956 57.895 11.47 0.00 42.48 3.11
498 2077 1.956170 ACACGAGAGCGCACCTTTG 60.956 57.895 11.47 10.03 42.48 2.77
499 2078 3.044305 ACGAGAGCGCACCTTTGC 61.044 61.111 11.47 0.00 46.21 3.68
615 2198 2.604914 GTGTCCAATATGTGCACTCTCG 59.395 50.000 19.41 2.73 0.00 4.04
658 2242 5.731599 AGACGGTAAGACACGATTAGTAG 57.268 43.478 0.00 0.00 0.00 2.57
924 2510 1.134491 CCCGTCCAACTATCCAAGGAC 60.134 57.143 0.00 0.00 45.46 3.85
953 2540 0.883833 CCACAATCAGCAACTGACCC 59.116 55.000 0.00 0.00 43.63 4.46
975 2562 5.185442 CCCTGTAATACCTTACCTAGCTAGC 59.815 48.000 15.74 6.62 37.09 3.42
977 2564 7.173722 CCTGTAATACCTTACCTAGCTAGCTA 58.826 42.308 22.85 22.85 37.09 3.32
978 2565 7.337436 CCTGTAATACCTTACCTAGCTAGCTAG 59.663 44.444 35.39 35.39 44.07 3.42
989 2576 3.528597 AGCTAGCTAGGTGTAGTTTGC 57.471 47.619 24.15 5.44 38.11 3.68
1236 2823 1.369625 CCGTCTTTGCGGCTTAATCT 58.630 50.000 0.00 0.00 45.47 2.40
1346 2935 1.647545 TATCGAGCGAAACGGACGGT 61.648 55.000 0.00 0.00 43.87 4.83
1347 2936 2.482296 ATCGAGCGAAACGGACGGTT 62.482 55.000 0.00 0.00 41.38 4.44
1348 2937 2.851104 GAGCGAAACGGACGGTTG 59.149 61.111 0.00 0.00 41.38 3.77
1349 2938 1.662446 GAGCGAAACGGACGGTTGA 60.662 57.895 0.00 0.00 41.38 3.18
1355 2944 2.222729 CGAAACGGACGGTTGATTGATC 60.223 50.000 0.00 0.00 39.30 2.92
1357 2946 0.245539 ACGGACGGTTGATTGATCGT 59.754 50.000 0.00 0.00 38.62 3.73
1377 2966 5.957798 TCGTATAGATCGTTTGTTCCACTT 58.042 37.500 0.00 0.00 0.00 3.16
1416 3005 3.369385 CACTTGCTCTGCTTTTGTTCTG 58.631 45.455 0.00 0.00 0.00 3.02
1453 3042 1.262417 TCGTGATGGTGAGGTTAGCA 58.738 50.000 0.00 0.00 0.00 3.49
1488 3078 0.599558 GGTGCTACGGTACAGTGTCA 59.400 55.000 9.06 3.75 0.00 3.58
1615 3215 0.740868 CCACCTCACACGGCAGTATG 60.741 60.000 0.00 0.00 40.87 2.39
1662 3262 0.322322 ATAAGCACCGTGGTTTCCGA 59.678 50.000 20.30 3.83 39.08 4.55
1663 3263 0.322322 TAAGCACCGTGGTTTCCGAT 59.678 50.000 20.30 0.00 39.08 4.18
1664 3264 0.322322 AAGCACCGTGGTTTCCGATA 59.678 50.000 10.18 0.00 33.88 2.92
1689 3289 2.038690 TCCATATGGGACGCGTCTC 58.961 57.895 35.50 33.80 42.15 3.36
1708 3308 6.400091 GCGTCTCGTTGTGATATCAATAATCC 60.400 42.308 7.07 0.00 0.00 3.01
1709 3309 6.183359 CGTCTCGTTGTGATATCAATAATCCG 60.183 42.308 7.07 7.19 0.00 4.18
1813 3413 1.410004 TTAGGTGATGGTCCTAGCCG 58.590 55.000 0.00 0.00 38.55 5.52
1830 3430 1.742750 GCCGCCAACCTAGTTTCCTAG 60.743 57.143 0.00 0.00 40.42 3.02
1831 3431 1.553704 CCGCCAACCTAGTTTCCTAGT 59.446 52.381 0.00 0.00 39.29 2.57
1832 3432 2.027469 CCGCCAACCTAGTTTCCTAGTT 60.027 50.000 0.00 0.00 39.29 2.24
1833 3433 3.558533 CCGCCAACCTAGTTTCCTAGTTT 60.559 47.826 0.00 0.00 39.29 2.66
1834 3434 3.683340 CGCCAACCTAGTTTCCTAGTTTC 59.317 47.826 0.00 0.00 39.29 2.78
1835 3435 4.008330 GCCAACCTAGTTTCCTAGTTTCC 58.992 47.826 0.00 0.00 39.29 3.13
1836 3436 4.586884 CCAACCTAGTTTCCTAGTTTCCC 58.413 47.826 0.00 0.00 39.29 3.97
1837 3437 4.567116 CCAACCTAGTTTCCTAGTTTCCCC 60.567 50.000 0.00 0.00 39.29 4.81
1838 3438 4.157668 ACCTAGTTTCCTAGTTTCCCCT 57.842 45.455 0.00 0.00 39.29 4.79
1839 3439 4.102598 ACCTAGTTTCCTAGTTTCCCCTC 58.897 47.826 0.00 0.00 39.29 4.30
1840 3440 4.101856 CCTAGTTTCCTAGTTTCCCCTCA 58.898 47.826 0.00 0.00 39.29 3.86
1841 3441 4.534897 CCTAGTTTCCTAGTTTCCCCTCAA 59.465 45.833 0.00 0.00 39.29 3.02
1842 3442 5.013808 CCTAGTTTCCTAGTTTCCCCTCAAA 59.986 44.000 0.00 0.00 39.29 2.69
1843 3443 5.397553 AGTTTCCTAGTTTCCCCTCAAAA 57.602 39.130 0.00 0.00 0.00 2.44
1844 3444 5.773091 AGTTTCCTAGTTTCCCCTCAAAAA 58.227 37.500 0.00 0.00 0.00 1.94
1876 3476 6.812160 AGTTTCCTAGTTTATCGCTTGTAGTG 59.188 38.462 0.00 0.00 0.00 2.74
1900 3501 3.188786 CACTGGCCTAGTTCGCGC 61.189 66.667 3.32 0.00 37.60 6.86
1925 3526 3.059800 CGTGATCGCGACAGAGAGTTATA 60.060 47.826 23.89 0.00 0.00 0.98
1977 3581 4.474303 TTACTCCCTCCGTCCCATATAA 57.526 45.455 0.00 0.00 0.00 0.98
1978 3582 2.890814 ACTCCCTCCGTCCCATATAAG 58.109 52.381 0.00 0.00 0.00 1.73
1979 3583 2.179424 ACTCCCTCCGTCCCATATAAGT 59.821 50.000 0.00 0.00 0.00 2.24
1981 3585 1.002087 CCCTCCGTCCCATATAAGTGC 59.998 57.143 0.00 0.00 0.00 4.40
1982 3586 1.691976 CCTCCGTCCCATATAAGTGCA 59.308 52.381 0.00 0.00 0.00 4.57
1983 3587 2.303022 CCTCCGTCCCATATAAGTGCAT 59.697 50.000 0.00 0.00 0.00 3.96
2052 3657 0.238817 GCCGCGTTTGGAATACACAA 59.761 50.000 4.92 0.00 0.00 3.33
2148 3754 1.328279 GGGCCCGGGATATTTTTCAG 58.672 55.000 29.31 0.00 0.00 3.02
2361 3969 1.134037 ACTTGACAACAAACGGGCCTA 60.134 47.619 0.84 0.00 35.49 3.93
2509 4120 7.520798 AGCTTATGGATGAATAAACCATCAGA 58.479 34.615 0.00 0.00 42.44 3.27
2546 4158 8.715191 ACAACATTTGAGCAAACTTGAATTTA 57.285 26.923 16.26 0.00 32.51 1.40
2581 4193 3.152341 AGAGCAAAGATCCTTGTGGTTG 58.848 45.455 5.95 0.00 34.23 3.77
2644 4256 1.889530 GCCGTTGAGGGAGCAGTAGT 61.890 60.000 0.00 0.00 41.48 2.73
2790 4407 1.738908 GGTCTCTTTCGTCTACTCGCT 59.261 52.381 0.00 0.00 0.00 4.93
2905 4522 4.869861 CACCTTTCTGAAACAAGTTTTGGG 59.130 41.667 0.00 0.00 32.11 4.12
2906 4523 4.530553 ACCTTTCTGAAACAAGTTTTGGGT 59.469 37.500 0.00 0.00 32.11 4.51
2907 4524 4.869861 CCTTTCTGAAACAAGTTTTGGGTG 59.130 41.667 0.00 0.00 32.11 4.61
2908 4525 5.476091 TTTCTGAAACAAGTTTTGGGTGT 57.524 34.783 0.00 0.00 32.11 4.16
2909 4526 5.476091 TTCTGAAACAAGTTTTGGGTGTT 57.524 34.783 0.00 0.00 37.07 3.32
2910 4527 5.066968 TCTGAAACAAGTTTTGGGTGTTC 57.933 39.130 0.00 0.00 34.46 3.18
2911 4528 4.770010 TCTGAAACAAGTTTTGGGTGTTCT 59.230 37.500 0.00 0.00 34.46 3.01
2912 4529 5.245075 TCTGAAACAAGTTTTGGGTGTTCTT 59.755 36.000 0.00 0.00 34.46 2.52
2913 4530 5.859495 TGAAACAAGTTTTGGGTGTTCTTT 58.141 33.333 0.00 0.00 34.46 2.52
2914 4531 5.698545 TGAAACAAGTTTTGGGTGTTCTTTG 59.301 36.000 0.00 0.00 34.46 2.77
2964 4581 7.598493 TGCTTTACCTAATTTTGCATTCTCAAC 59.402 33.333 0.00 0.00 0.00 3.18
2998 4615 6.989169 GCTTGTGATGAGTTAGACCATCTATT 59.011 38.462 0.00 0.00 39.75 1.73
2999 4616 8.144478 GCTTGTGATGAGTTAGACCATCTATTA 58.856 37.037 0.00 0.00 39.75 0.98
3100 4719 5.600069 ACTCACTGAGAATGGAGCATGTATA 59.400 40.000 13.25 0.00 33.32 1.47
3424 5043 3.639033 TCCAGCGGGGAGGTTTATA 57.361 52.632 2.05 0.00 42.15 0.98
3430 5049 1.202615 GCGGGGAGGTTTATAGTCACC 60.203 57.143 0.00 0.00 0.00 4.02
3460 5121 6.214191 TCTTGCTAATTTTGTTGGTGTTGA 57.786 33.333 0.00 0.00 0.00 3.18
3507 5168 0.807667 CGCTCTTCTGGGGAATCACG 60.808 60.000 0.00 0.00 0.00 4.35
3757 5527 7.272978 TGTAGCTTGGAAGGAATAATAGTCAC 58.727 38.462 0.00 0.00 0.00 3.67
3780 5550 4.652822 GAGGAAAAGAAGACTTGGGCTAA 58.347 43.478 0.00 0.00 36.39 3.09
3781 5551 5.061721 AGGAAAAGAAGACTTGGGCTAAA 57.938 39.130 0.00 0.00 36.39 1.85
3782 5552 5.645201 AGGAAAAGAAGACTTGGGCTAAAT 58.355 37.500 0.00 0.00 36.39 1.40
3783 5553 6.077993 AGGAAAAGAAGACTTGGGCTAAATT 58.922 36.000 0.00 0.00 36.39 1.82
3799 5569 8.774183 TGGGCTAAATTAACCTATCTGAACTTA 58.226 33.333 0.00 0.00 0.00 2.24
3820 5590 1.227823 CGTTGTGCAGGTGGAAGGA 60.228 57.895 0.00 0.00 0.00 3.36
4063 5835 8.243426 TCTTCAGTTGGATGTAACAATTAATGC 58.757 33.333 0.00 0.00 33.02 3.56
4128 5905 4.046938 TCTCGATCTCTGTTGTTATGCC 57.953 45.455 0.00 0.00 0.00 4.40
4146 5923 1.213296 CCTGTACCATGGGGCTAAGT 58.787 55.000 18.09 0.00 37.90 2.24
4199 7371 2.442413 TCCCTCAAAGCCGGTTAAATG 58.558 47.619 1.90 0.00 0.00 2.32
4257 7429 2.004733 GTCGAACCTTTATCCGGGTTG 58.995 52.381 0.00 0.00 44.69 3.77
4372 7544 6.580788 CATCACATCTCTTCCTAAGTCACAT 58.419 40.000 0.00 0.00 0.00 3.21
4378 7550 5.423015 TCTCTTCCTAAGTCACATTGCATC 58.577 41.667 0.00 0.00 0.00 3.91
4391 7563 2.438254 GCATCGATGTGGGTGCCA 60.438 61.111 25.47 0.00 0.00 4.92
4404 7576 1.293179 GTGCCACCCAAATCAAGCC 59.707 57.895 0.00 0.00 0.00 4.35
4422 7594 2.978010 GGCACCACAACCACCTCG 60.978 66.667 0.00 0.00 0.00 4.63
4453 7640 1.448189 CGGCGTCGTCCCCAAAATA 60.448 57.895 0.00 0.00 0.00 1.40
4465 7652 5.989777 CGTCCCCAAAATAGAAATATCGAGT 59.010 40.000 0.00 0.00 0.00 4.18
4466 7653 7.014518 TCGTCCCCAAAATAGAAATATCGAGTA 59.985 37.037 0.00 0.00 0.00 2.59
4467 7654 7.328737 CGTCCCCAAAATAGAAATATCGAGTAG 59.671 40.741 0.00 0.00 0.00 2.57
4468 7655 8.365647 GTCCCCAAAATAGAAATATCGAGTAGA 58.634 37.037 0.00 0.00 0.00 2.59
4469 7656 9.101325 TCCCCAAAATAGAAATATCGAGTAGAT 57.899 33.333 0.00 0.00 43.19 1.98
4470 7657 9.372369 CCCCAAAATAGAAATATCGAGTAGATC 57.628 37.037 0.00 0.00 40.66 2.75
4488 7675 1.531423 TCGAGTAGTCAAAGGTCGCT 58.469 50.000 0.00 0.00 0.00 4.93
4490 7677 2.417933 TCGAGTAGTCAAAGGTCGCTAC 59.582 50.000 0.00 0.00 35.37 3.58
4491 7678 2.783333 GAGTAGTCAAAGGTCGCTACG 58.217 52.381 0.00 0.00 38.89 3.51
4515 7702 4.698625 AGCCGACCCGAGGAACCT 62.699 66.667 0.00 0.00 0.00 3.50
4517 7704 3.073742 GCCGACCCGAGGAACCTAC 62.074 68.421 0.00 0.00 0.00 3.18
4518 7705 2.421399 CCGACCCGAGGAACCTACC 61.421 68.421 0.00 0.00 0.00 3.18
4519 7706 1.679977 CGACCCGAGGAACCTACCA 60.680 63.158 0.00 0.00 0.00 3.25
4520 7707 1.895966 GACCCGAGGAACCTACCAC 59.104 63.158 0.00 0.00 0.00 4.16
4521 7708 1.611474 GACCCGAGGAACCTACCACC 61.611 65.000 0.00 0.00 0.00 4.61
4522 7709 2.718073 CCCGAGGAACCTACCACCG 61.718 68.421 0.00 0.00 0.00 4.94
4523 7710 1.679977 CCGAGGAACCTACCACCGA 60.680 63.158 0.00 0.00 32.90 4.69
4524 7711 1.664321 CCGAGGAACCTACCACCGAG 61.664 65.000 0.00 0.00 32.90 4.63
4527 7714 0.115745 AGGAACCTACCACCGAGGAA 59.884 55.000 0.00 0.00 41.22 3.36
4570 7804 1.815421 GCAGCAGACATGGGGTACG 60.815 63.158 0.00 0.00 0.00 3.67
4579 7813 2.101249 GACATGGGGTACGTATCGGAAA 59.899 50.000 0.00 0.00 0.00 3.13
4581 7815 3.243975 ACATGGGGTACGTATCGGAAATC 60.244 47.826 0.00 0.00 0.00 2.17
4626 7863 8.307483 CAATACTAGATTAGTGATGTAGGGTGG 58.693 40.741 0.00 0.00 39.81 4.61
4630 7867 5.281314 AGATTAGTGATGTAGGGTGGAACT 58.719 41.667 0.00 0.00 36.74 3.01
4661 7898 2.897326 TGATCTTTTCACACTCGGAGGA 59.103 45.455 10.23 0.00 0.00 3.71
4663 7900 2.594131 TCTTTTCACACTCGGAGGAGA 58.406 47.619 10.23 1.25 43.27 3.71
4669 7906 2.963101 TCACACTCGGAGGAGAAAAAGA 59.037 45.455 10.23 0.00 43.27 2.52
4670 7907 3.386726 TCACACTCGGAGGAGAAAAAGAA 59.613 43.478 10.23 0.00 43.27 2.52
4677 7914 4.036380 TCGGAGGAGAAAAAGAAAGCAAAC 59.964 41.667 0.00 0.00 0.00 2.93
4685 7934 7.926018 GGAGAAAAAGAAAGCAAACCAAAGATA 59.074 33.333 0.00 0.00 0.00 1.98
4689 7938 8.785329 AAAAGAAAGCAAACCAAAGATAAACA 57.215 26.923 0.00 0.00 0.00 2.83
4752 8001 6.931281 CCACATACACATAGAGGGATACAAAG 59.069 42.308 0.00 0.00 39.74 2.77
4774 8023 5.264395 AGGTCCAAATCCAATACAAGAAGG 58.736 41.667 0.00 0.00 0.00 3.46
4783 8032 7.979786 ATCCAATACAAGAAGGTAAGAGAGA 57.020 36.000 0.00 0.00 0.00 3.10
4826 8075 7.846823 TCCTTGAAGGAGAGAGGTCTTAATATT 59.153 37.037 10.46 0.00 40.06 1.28
4836 8085 7.846823 AGAGAGGTCTTAATATTCTTGGAGGAA 59.153 37.037 0.00 0.00 0.00 3.36
4837 8086 8.028652 AGAGGTCTTAATATTCTTGGAGGAAG 57.971 38.462 0.00 0.00 0.00 3.46
4838 8087 7.846823 AGAGGTCTTAATATTCTTGGAGGAAGA 59.153 37.037 0.00 0.00 39.05 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.826265 TTGGCCCACCCCAAGAAGC 62.826 63.158 0.00 0.00 39.85 3.86
19 22 3.728373 AGACGATTGGCCCACCCC 61.728 66.667 0.00 0.00 33.59 4.95
29 32 3.677960 CGAGACACGTCAGACGATT 57.322 52.632 29.53 14.86 46.05 3.34
49 52 2.338500 GGACTTTGCAGTAGTCGGAAG 58.662 52.381 18.97 6.90 42.31 3.46
53 56 1.429463 GTGGGACTTTGCAGTAGTCG 58.571 55.000 18.97 0.00 42.31 4.18
60 63 2.335316 ACTAAACGTGGGACTTTGCA 57.665 45.000 0.00 0.00 0.00 4.08
63 66 6.095720 TGAATCAAAACTAAACGTGGGACTTT 59.904 34.615 0.00 0.00 0.00 2.66
77 80 6.039717 CCATGATATTCCCGTGAATCAAAACT 59.960 38.462 0.00 0.00 41.44 2.66
83 86 2.749621 GGCCATGATATTCCCGTGAATC 59.250 50.000 0.00 0.00 41.44 2.52
87 90 2.946947 GGGCCATGATATTCCCGTG 58.053 57.895 4.39 0.00 0.00 4.94
103 106 3.536917 TCCGCATAGCAGTCCGGG 61.537 66.667 0.00 0.00 41.02 5.73
115 118 0.389817 CTGACTTTCATCCGTCCGCA 60.390 55.000 0.00 0.00 0.00 5.69
117 120 1.336887 ACACTGACTTTCATCCGTCCG 60.337 52.381 0.00 0.00 0.00 4.79
122 125 4.074970 ACATCCAACACTGACTTTCATCC 58.925 43.478 0.00 0.00 0.00 3.51
150 153 3.365465 CCGGATGTAGCTATCTGAACTCG 60.365 52.174 0.00 0.00 35.85 4.18
152 155 3.570550 GTCCGGATGTAGCTATCTGAACT 59.429 47.826 7.81 0.00 35.85 3.01
157 160 1.073444 TCCGTCCGGATGTAGCTATCT 59.927 52.381 22.05 0.00 39.76 1.98
436 2015 0.456312 CGAGGAGAAGAAACGGACGG 60.456 60.000 0.00 0.00 0.00 4.79
727 2311 5.334646 CGGACTTCCTTTTGGTTAAGCTTAC 60.335 44.000 5.45 1.71 41.38 2.34
780 2364 3.060363 CGTACGTATCTTTCCTTGTGTGC 59.940 47.826 7.22 0.00 0.00 4.57
781 2365 3.060363 GCGTACGTATCTTTCCTTGTGTG 59.940 47.826 17.90 0.00 0.00 3.82
924 2510 1.747709 CTGATTGTGGCCTTCCTCAG 58.252 55.000 3.32 7.89 37.20 3.35
953 2540 8.271312 CTAGCTAGCTAGGTAAGGTATTACAG 57.729 42.308 34.95 13.48 42.66 2.74
975 2562 3.003480 GGCTCAAGCAAACTACACCTAG 58.997 50.000 4.13 0.00 44.36 3.02
977 2564 1.142870 TGGCTCAAGCAAACTACACCT 59.857 47.619 4.13 0.00 44.36 4.00
978 2565 1.604604 TGGCTCAAGCAAACTACACC 58.395 50.000 4.13 0.00 44.36 4.16
980 2567 3.207265 TCTTGGCTCAAGCAAACTACA 57.793 42.857 4.13 0.00 44.36 2.74
981 2568 3.503748 ACATCTTGGCTCAAGCAAACTAC 59.496 43.478 4.13 0.00 44.36 2.73
983 2570 2.590821 ACATCTTGGCTCAAGCAAACT 58.409 42.857 4.13 0.00 44.36 2.66
989 2576 1.180029 CCCCAACATCTTGGCTCAAG 58.820 55.000 8.22 8.22 45.32 3.02
1236 2823 1.746220 GAAGCTTGCTCTCTCCGAGTA 59.254 52.381 2.10 0.00 41.98 2.59
1348 2937 7.381408 TGGAACAAACGATCTATACGATCAATC 59.619 37.037 0.00 0.00 41.96 2.67
1349 2938 7.169308 GTGGAACAAACGATCTATACGATCAAT 59.831 37.037 0.00 0.00 44.80 2.57
1355 2944 6.642683 AAAGTGGAACAAACGATCTATACG 57.357 37.500 0.00 0.00 44.16 3.06
1357 2946 7.391620 AGGAAAAGTGGAACAAACGATCTATA 58.608 34.615 0.00 0.00 44.16 1.31
1374 2963 4.822350 GTGGCTCTGTTTCTAAGGAAAAGT 59.178 41.667 0.00 0.00 42.22 2.66
1377 2966 4.706842 AGTGGCTCTGTTTCTAAGGAAA 57.293 40.909 0.00 0.00 38.90 3.13
1416 3005 5.399858 TCACGAAGCTTCATCACTAACTAC 58.600 41.667 25.47 0.00 0.00 2.73
1453 3042 2.683933 CCTGGACCGTGGCTACCT 60.684 66.667 0.00 0.00 0.00 3.08
1462 3051 2.048023 TACCGTAGCACCTGGACCG 61.048 63.158 0.00 0.00 0.00 4.79
1615 3215 5.161943 ACTCCCTCTGTTACAACCAATAC 57.838 43.478 0.00 0.00 0.00 1.89
1689 3289 6.763303 TGTCGGATTATTGATATCACAACG 57.237 37.500 4.48 5.17 32.50 4.10
1708 3308 7.011482 CCTTCTAATAAGGACAGGAAATTGTCG 59.989 40.741 0.00 0.00 46.61 4.35
1709 3309 7.283354 CCCTTCTAATAAGGACAGGAAATTGTC 59.717 40.741 5.35 0.00 45.28 3.18
1843 3443 9.281371 AGCGATAAACTAGGAAACTAAGTTTTT 57.719 29.630 5.15 0.00 43.83 1.94
1844 3444 8.843885 AGCGATAAACTAGGAAACTAAGTTTT 57.156 30.769 5.15 0.00 43.83 2.43
1845 3445 8.718734 CAAGCGATAAACTAGGAAACTAAGTTT 58.281 33.333 5.19 5.19 43.83 2.66
1846 3446 7.876582 ACAAGCGATAAACTAGGAAACTAAGTT 59.123 33.333 0.00 0.00 43.83 2.66
1847 3447 7.384477 ACAAGCGATAAACTAGGAAACTAAGT 58.616 34.615 0.00 0.00 43.83 2.24
1848 3448 7.829378 ACAAGCGATAAACTAGGAAACTAAG 57.171 36.000 0.00 0.00 43.83 2.18
1849 3449 8.526147 ACTACAAGCGATAAACTAGGAAACTAA 58.474 33.333 0.00 0.00 43.83 2.24
1850 3450 7.972277 CACTACAAGCGATAAACTAGGAAACTA 59.028 37.037 0.00 0.00 43.67 2.24
1852 3452 6.035758 CCACTACAAGCGATAAACTAGGAAAC 59.964 42.308 0.00 0.00 0.00 2.78
1853 3453 6.103997 CCACTACAAGCGATAAACTAGGAAA 58.896 40.000 0.00 0.00 0.00 3.13
1854 3454 5.186409 ACCACTACAAGCGATAAACTAGGAA 59.814 40.000 0.00 0.00 0.00 3.36
1855 3455 4.708421 ACCACTACAAGCGATAAACTAGGA 59.292 41.667 0.00 0.00 0.00 2.94
1856 3456 5.007385 ACCACTACAAGCGATAAACTAGG 57.993 43.478 0.00 0.00 0.00 3.02
1857 3457 7.649973 AGATACCACTACAAGCGATAAACTAG 58.350 38.462 0.00 0.00 0.00 2.57
1858 3458 7.283807 TGAGATACCACTACAAGCGATAAACTA 59.716 37.037 0.00 0.00 0.00 2.24
1859 3459 6.096423 TGAGATACCACTACAAGCGATAAACT 59.904 38.462 0.00 0.00 0.00 2.66
1876 3476 2.034812 CGAACTAGGCCAGTGAGATACC 59.965 54.545 5.01 0.00 37.63 2.73
1900 3501 1.297967 CTCTGTCGCGATCACGAGG 60.298 63.158 14.06 3.10 43.89 4.63
1925 3526 2.287915 GGCGAGCAATATTCATCAACGT 59.712 45.455 0.00 0.00 0.00 3.99
1955 3558 3.562108 ATATGGGACGGAGGGAGTAAT 57.438 47.619 0.00 0.00 0.00 1.89
2000 3605 7.905144 ACTCCCTCCATCCCATAATATAAAA 57.095 36.000 0.00 0.00 0.00 1.52
2001 3606 8.191110 ACTACTCCCTCCATCCCATAATATAAA 58.809 37.037 0.00 0.00 0.00 1.40
2052 3657 7.270047 TCCGTGATATCCGAGTAAAAAGAAAT 58.730 34.615 13.18 0.00 0.00 2.17
2100 3705 3.129988 GGAGGCAGGAATTTCATGTTGAG 59.870 47.826 12.19 0.00 29.72 3.02
2131 3737 4.180817 CAAAACTGAAAAATATCCCGGGC 58.819 43.478 18.49 0.00 0.00 6.13
2134 3740 8.028938 AGATGAACAAAACTGAAAAATATCCCG 58.971 33.333 0.00 0.00 0.00 5.14
2148 3754 4.992951 ACACGTAGGGTAGATGAACAAAAC 59.007 41.667 0.00 0.00 0.00 2.43
2214 3822 3.370978 CCAACATAGCAATCGACGTCTTT 59.629 43.478 14.70 4.37 0.00 2.52
2465 4076 0.641275 TCGTCACGTCAACAACAACG 59.359 50.000 0.00 0.00 44.22 4.10
2466 4077 1.591394 GCTCGTCACGTCAACAACAAC 60.591 52.381 0.00 0.00 0.00 3.32
2509 4120 4.260985 TCAAATGTTGTCACTGTCACAGT 58.739 39.130 3.98 3.98 46.51 3.55
2644 4256 1.824230 AGCAACTGACTGCCAAAAACA 59.176 42.857 3.49 0.00 43.73 2.83
2697 4314 3.423749 GGAATCTAAACCGGGTGGAAAA 58.576 45.455 6.32 0.00 39.21 2.29
2790 4407 2.158623 CCAGGCCCTACAAATGATAGCA 60.159 50.000 0.00 0.00 0.00 3.49
2905 4522 8.448615 ACTTAGTACAAAGAACACAAAGAACAC 58.551 33.333 0.00 0.00 0.00 3.32
2906 4523 8.556213 ACTTAGTACAAAGAACACAAAGAACA 57.444 30.769 0.00 0.00 0.00 3.18
2907 4524 7.844653 CGACTTAGTACAAAGAACACAAAGAAC 59.155 37.037 0.00 0.00 0.00 3.01
2908 4525 7.546667 ACGACTTAGTACAAAGAACACAAAGAA 59.453 33.333 0.00 0.00 0.00 2.52
2909 4526 7.037438 ACGACTTAGTACAAAGAACACAAAGA 58.963 34.615 0.00 0.00 0.00 2.52
2910 4527 7.230466 ACGACTTAGTACAAAGAACACAAAG 57.770 36.000 0.00 0.00 0.00 2.77
2911 4528 7.331440 TCAACGACTTAGTACAAAGAACACAAA 59.669 33.333 0.00 0.00 0.00 2.83
2912 4529 6.812656 TCAACGACTTAGTACAAAGAACACAA 59.187 34.615 0.00 0.00 0.00 3.33
2913 4530 6.331845 TCAACGACTTAGTACAAAGAACACA 58.668 36.000 0.00 0.00 0.00 3.72
2914 4531 6.817270 TCAACGACTTAGTACAAAGAACAC 57.183 37.500 0.00 0.00 0.00 3.32
2964 4581 1.395954 CTCATCACAAGCACATGTCCG 59.604 52.381 0.00 0.00 0.00 4.79
3057 4674 8.514594 CAGTGAGTAAAAGCATCCTGAATTTAA 58.485 33.333 0.00 0.00 0.00 1.52
3424 5043 0.179045 AGCAAGAAAGCACGGTGACT 60.179 50.000 13.29 5.79 36.85 3.41
3430 5049 5.332506 CCAACAAAATTAGCAAGAAAGCACG 60.333 40.000 0.00 0.00 36.85 5.34
3460 5121 1.531840 CCTCCGGGTCCTGATCGAT 60.532 63.158 0.00 0.00 0.00 3.59
3681 5342 1.259609 CCATGAAGGTTGCACCACAT 58.740 50.000 0.00 9.10 41.95 3.21
3706 5367 6.839124 AATAAGAATCATCAAAGTGCCACA 57.161 33.333 0.00 0.00 0.00 4.17
3757 5527 1.807142 GCCCAAGTCTTCTTTTCCTCG 59.193 52.381 0.00 0.00 0.00 4.63
3781 5551 9.886132 ACAACGAATAAGTTCAGATAGGTTAAT 57.114 29.630 0.00 0.00 33.86 1.40
3782 5552 9.146984 CACAACGAATAAGTTCAGATAGGTTAA 57.853 33.333 0.00 0.00 33.86 2.01
3783 5553 7.277098 GCACAACGAATAAGTTCAGATAGGTTA 59.723 37.037 0.00 0.00 33.86 2.85
3799 5569 1.238439 CTTCCACCTGCACAACGAAT 58.762 50.000 0.00 0.00 0.00 3.34
3901 5671 5.767665 TGCATTATATTACACCACCACCATC 59.232 40.000 0.00 0.00 0.00 3.51
4063 5835 6.749923 AGGAAGAAAGCTTATTTGCTACTG 57.250 37.500 13.01 0.00 43.24 2.74
4325 7497 1.697291 GGGGGAGGTGGAGATTCATCT 60.697 57.143 0.00 0.00 40.50 2.90
4372 7544 2.045708 GGCACCCACATCGATGCAA 61.046 57.895 25.11 0.00 39.92 4.08
4391 7563 2.117206 TGCCGGCTTGATTTGGGT 59.883 55.556 29.70 0.00 0.00 4.51
4404 7576 2.978010 GAGGTGGTTGTGGTGCCG 60.978 66.667 0.00 0.00 0.00 5.69
4440 7627 6.164417 TCGATATTTCTATTTTGGGGACGA 57.836 37.500 0.00 0.00 0.00 4.20
4465 7652 3.311871 GCGACCTTTGACTACTCGATCTA 59.688 47.826 0.00 0.00 0.00 1.98
4466 7653 2.097791 GCGACCTTTGACTACTCGATCT 59.902 50.000 0.00 0.00 0.00 2.75
4467 7654 2.097791 AGCGACCTTTGACTACTCGATC 59.902 50.000 0.00 0.00 0.00 3.69
4468 7655 2.093106 AGCGACCTTTGACTACTCGAT 58.907 47.619 0.00 0.00 0.00 3.59
4469 7656 1.531423 AGCGACCTTTGACTACTCGA 58.469 50.000 0.00 0.00 0.00 4.04
4470 7657 2.783333 GTAGCGACCTTTGACTACTCG 58.217 52.381 0.00 0.00 33.72 4.18
4471 7658 2.477525 CCGTAGCGACCTTTGACTACTC 60.478 54.545 0.00 0.00 34.23 2.59
4472 7659 1.471684 CCGTAGCGACCTTTGACTACT 59.528 52.381 0.00 0.00 34.23 2.57
4473 7660 1.905449 CCGTAGCGACCTTTGACTAC 58.095 55.000 0.00 0.00 33.27 2.73
4474 7661 0.171903 GCCGTAGCGACCTTTGACTA 59.828 55.000 0.00 0.00 0.00 2.59
4475 7662 1.080025 GCCGTAGCGACCTTTGACT 60.080 57.895 0.00 0.00 0.00 3.41
4497 7684 4.452733 GGTTCCTCGGGTCGGCTG 62.453 72.222 0.00 0.00 0.00 4.85
4500 7687 2.421399 GGTAGGTTCCTCGGGTCGG 61.421 68.421 0.00 0.00 0.00 4.79
4513 7700 1.848652 TCTTCTTCCTCGGTGGTAGG 58.151 55.000 3.39 0.00 34.42 3.18
4515 7702 3.165087 TCTTCTTCTTCCTCGGTGGTA 57.835 47.619 0.00 0.00 37.07 3.25
4517 7704 2.300437 ACTTCTTCTTCTTCCTCGGTGG 59.700 50.000 0.00 0.00 37.10 4.61
4518 7705 3.669251 ACTTCTTCTTCTTCCTCGGTG 57.331 47.619 0.00 0.00 0.00 4.94
4519 7706 3.510753 GGTACTTCTTCTTCTTCCTCGGT 59.489 47.826 0.00 0.00 0.00 4.69
4520 7707 3.510360 TGGTACTTCTTCTTCTTCCTCGG 59.490 47.826 0.00 0.00 0.00 4.63
4521 7708 4.487019 GTGGTACTTCTTCTTCTTCCTCG 58.513 47.826 0.00 0.00 0.00 4.63
4522 7709 4.487019 CGTGGTACTTCTTCTTCTTCCTC 58.513 47.826 0.00 0.00 0.00 3.71
4523 7710 3.258622 CCGTGGTACTTCTTCTTCTTCCT 59.741 47.826 0.00 0.00 0.00 3.36
4524 7711 3.257624 TCCGTGGTACTTCTTCTTCTTCC 59.742 47.826 0.00 0.00 0.00 3.46
4527 7714 3.256136 CACTCCGTGGTACTTCTTCTTCT 59.744 47.826 0.00 0.00 0.00 2.85
4554 7788 1.687123 GATACGTACCCCATGTCTGCT 59.313 52.381 0.00 0.00 0.00 4.24
4570 7804 3.447918 TCGGTCCTTGATTTCCGATAC 57.552 47.619 0.97 0.00 45.49 2.24
4579 7813 1.605058 CCGGTGTCTCGGTCCTTGAT 61.605 60.000 0.00 0.00 44.60 2.57
4581 7815 2.261671 CCGGTGTCTCGGTCCTTG 59.738 66.667 0.00 0.00 44.60 3.61
4630 7867 9.140286 CGAGTGTGAAAAGATCATAAACTTAGA 57.860 33.333 0.00 0.00 40.97 2.10
4638 7875 4.709886 TCCTCCGAGTGTGAAAAGATCATA 59.290 41.667 0.00 0.00 40.97 2.15
4661 7898 9.665719 TTTATCTTTGGTTTGCTTTCTTTTTCT 57.334 25.926 0.00 0.00 0.00 2.52
4663 7900 9.225436 TGTTTATCTTTGGTTTGCTTTCTTTTT 57.775 25.926 0.00 0.00 0.00 1.94
4669 7906 6.872920 TGAGTGTTTATCTTTGGTTTGCTTT 58.127 32.000 0.00 0.00 0.00 3.51
4670 7907 6.463995 TGAGTGTTTATCTTTGGTTTGCTT 57.536 33.333 0.00 0.00 0.00 3.91
4677 7914 9.831737 CTTGTCTATTTGAGTGTTTATCTTTGG 57.168 33.333 0.00 0.00 0.00 3.28
4685 7934 8.641498 ATTGGATCTTGTCTATTTGAGTGTTT 57.359 30.769 0.00 0.00 0.00 2.83
4689 7938 7.335422 GTGTGATTGGATCTTGTCTATTTGAGT 59.665 37.037 0.00 0.00 0.00 3.41
4699 7948 5.443283 AGCATATGTGTGATTGGATCTTGT 58.557 37.500 4.29 0.00 0.00 3.16
4752 8001 5.016831 ACCTTCTTGTATTGGATTTGGACC 58.983 41.667 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.