Multiple sequence alignment - TraesCS2A01G079600

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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 TraesCS2A01G079600 chr2A 100.000 4994 0 0 1 4994 36056899 36051906 0.000000e+00 9223.0
1 TraesCS2A01G079600 chr2A 91.879 628 32 3 1 626 44039008 44039618 0.000000e+00 859.0
2 TraesCS2A01G079600 chr2B 93.251 3571 185 26 1 3535 54554261 54550711 0.000000e+00 5208.0
3 TraesCS2A01G079600 chr2B 94.745 609 29 3 3854 4459 54550441 54549833 0.000000e+00 944.0
4 TraesCS2A01G079600 chr2B 95.539 538 23 1 4457 4994 54549752 54549216 0.000000e+00 859.0
5 TraesCS2A01G079600 chr2D 92.776 3502 163 41 1 3474 32807712 32804273 0.000000e+00 4983.0
6 TraesCS2A01G079600 chr2D 91.536 638 37 13 3853 4481 32803792 32803163 0.000000e+00 863.0
7 TraesCS2A01G079600 chr2D 89.231 520 45 8 4477 4994 32803132 32802622 1.520000e-179 640.0
8 TraesCS2A01G079600 chr7B 85.877 439 35 8 3386 3817 19203135 19203553 4.590000e-120 442.0
9 TraesCS2A01G079600 chr5B 74.218 799 165 27 2527 3316 515185778 515186544 3.780000e-76 296.0
10 TraesCS2A01G079600 chr6D 91.795 195 16 0 1267 1461 400556352 400556158 6.370000e-69 272.0
11 TraesCS2A01G079600 chr1B 83.158 95 16 0 1422 1516 561547754 561547848 2.480000e-13 87.9
12 TraesCS2A01G079600 chr1B 82.105 95 17 0 1422 1516 561546680 561546774 1.150000e-11 82.4


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 TraesCS2A01G079600 chr2A 36051906 36056899 4993 True 9223 9223 100.000000 1 4994 1 chr2A.!!$R1 4993
1 TraesCS2A01G079600 chr2A 44039008 44039618 610 False 859 859 91.879000 1 626 1 chr2A.!!$F1 625
2 TraesCS2A01G079600 chr2B 54549216 54554261 5045 True 2337 5208 94.511667 1 4994 3 chr2B.!!$R1 4993
3 TraesCS2A01G079600 chr2D 32802622 32807712 5090 True 2162 4983 91.181000 1 4994 3 chr2D.!!$R1 4993
4 TraesCS2A01G079600 chr5B 515185778 515186544 766 False 296 296 74.218000 2527 3316 1 chr5B.!!$F1 789

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
987 1003 0.038801 TGAGCTTCAGTGAGTGAGCG 60.039 55.0 9.16 0.0 36.21 5.03 F
1962 1981 0.743688 TGCTCAGCTCCTTCGATCTC 59.256 55.0 0.00 0.0 0.00 2.75 F
3410 3458 0.035317 TGAAGACGGTGCAGATGCTT 59.965 50.0 6.35 0.0 42.66 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2160 0.108804 AGCAGTATTGACGGTGTCGG 60.109 55.0 0.0 0.0 41.39 4.79 R
3589 3660 0.250901 AATCACACTGGAGGCACCAC 60.251 55.0 0.0 0.0 44.64 4.16 R
4950 5311 0.402121 ACAAGGAAGTTGAGGAGGGC 59.598 55.0 0.0 0.0 38.60 5.19 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
28 29 4.001248 CGCAATCCTCTTGGGCAA 57.999 55.556 0.00 0.00 34.39 4.52
46 47 2.421775 GCAAGGCTAGCTTCTCCTTTTC 59.578 50.000 15.72 0.12 38.08 2.29
49 50 1.282157 GGCTAGCTTCTCCTTTTCCCA 59.718 52.381 15.72 0.00 0.00 4.37
102 103 0.320374 GATCACCCTCGTTCACACCA 59.680 55.000 0.00 0.00 0.00 4.17
238 239 8.250332 ACAAAATTGCGTTAATGGAGATGTAAT 58.750 29.630 0.00 0.00 0.00 1.89
277 280 5.871524 TCTCAAAACGAGATCAGAATTCAGG 59.128 40.000 8.44 0.00 46.18 3.86
332 336 4.539726 TCCATGGAAATTCTGAGATTGGG 58.460 43.478 13.46 0.00 0.00 4.12
421 427 2.737376 GTGTCCTGGTCGGCGTTC 60.737 66.667 6.85 1.15 0.00 3.95
508 514 3.827898 CTCTCCCACTCGGCGTCC 61.828 72.222 6.85 0.00 0.00 4.79
891 900 2.203437 GTTGGGTTGGGCTCGGTT 60.203 61.111 0.00 0.00 0.00 4.44
897 906 3.897122 TTGGGCTCGGTTTGGGCT 61.897 61.111 0.00 0.00 0.00 5.19
900 909 4.056125 GGCTCGGTTTGGGCTTGC 62.056 66.667 0.00 0.00 0.00 4.01
911 926 2.481471 GGGCTTGCGTATGGGCTTC 61.481 63.158 1.64 0.00 0.00 3.86
931 946 2.281276 GTTCGGCCCAACTCCGTT 60.281 61.111 5.92 0.00 46.49 4.44
987 1003 0.038801 TGAGCTTCAGTGAGTGAGCG 60.039 55.000 9.16 0.00 36.21 5.03
1054 1073 1.700368 CTGGTCCTCCTCCTCCTCA 59.300 63.158 0.00 0.00 34.23 3.86
1234 1253 3.955101 CCTCGCCGCTCTACTCCG 61.955 72.222 0.00 0.00 0.00 4.63
1373 1392 2.820479 CCTCGAGCTCGTCTCCGT 60.820 66.667 33.33 0.00 38.62 4.69
1375 1394 2.815298 CTCGAGCTCGTCTCCGTCC 61.815 68.421 33.33 0.00 38.62 4.79
1465 1484 3.461773 GCCTCCTGCGCCTACTCA 61.462 66.667 4.18 0.00 0.00 3.41
1797 1816 4.147449 CAGGAGATGGCCGACGCA 62.147 66.667 0.00 0.00 36.38 5.24
1800 1819 4.899239 GAGATGGCCGACGCAGGG 62.899 72.222 0.00 0.00 36.38 4.45
1962 1981 0.743688 TGCTCAGCTCCTTCGATCTC 59.256 55.000 0.00 0.00 0.00 2.75
2012 2031 1.701545 TTCGTGGATTTCATCGCCGC 61.702 55.000 0.00 0.00 0.00 6.53
2015 2034 2.895372 GGATTTCATCGCCGCCGT 60.895 61.111 0.00 0.00 35.54 5.68
2082 2101 2.159421 TCTGTCATACTCGAAGCCGAAC 60.159 50.000 0.00 0.00 45.04 3.95
2123 2142 1.960040 ATCATGAAGCTCGGCGACCA 61.960 55.000 4.99 2.00 0.00 4.02
2128 2147 4.742649 AGCTCGGCGACCAGGAGA 62.743 66.667 4.99 0.00 0.00 3.71
2154 2173 2.736995 CGTGCCGACACCGTCAAT 60.737 61.111 0.00 0.00 44.40 2.57
2157 2176 0.389426 GTGCCGACACCGTCAATACT 60.389 55.000 0.00 0.00 41.21 2.12
2162 2181 1.641577 GACACCGTCAATACTGCTCC 58.358 55.000 0.00 0.00 32.09 4.70
2164 2183 0.806102 CACCGTCAATACTGCTCCGG 60.806 60.000 0.00 0.00 41.09 5.14
2166 2185 2.230940 CGTCAATACTGCTCCGGCG 61.231 63.158 0.00 0.00 42.25 6.46
2174 2193 3.466791 CTGCTCCGGCGGGATCAAT 62.467 63.158 27.98 0.00 42.83 2.57
2218 2237 4.858680 TTGTCACCGCCGCAACCA 62.859 61.111 0.00 0.00 0.00 3.67
2257 2276 2.203252 CCATCTGCATCGTGGGGG 60.203 66.667 4.66 0.00 0.00 5.40
2259 2278 3.410628 ATCTGCATCGTGGGGGCA 61.411 61.111 0.00 0.00 35.96 5.36
2277 2296 0.677098 CACTGCTGCTCTTCAGGCAT 60.677 55.000 0.00 0.00 43.06 4.40
2382 2401 3.376935 ATCCAAGGTCTCAGCCGCG 62.377 63.158 0.00 0.00 0.00 6.46
2434 2456 0.394192 CCTCAGCATCGGCCAGATAA 59.606 55.000 2.24 0.00 42.56 1.75
2950 2975 3.725459 CGGCGCATGTGAGCAACA 61.725 61.111 10.83 0.00 42.80 3.33
2951 2976 2.644418 GGCGCATGTGAGCAACAA 59.356 55.556 10.83 0.00 43.61 2.83
3127 3161 3.723235 CTCGTGGACTGGGCGATGG 62.723 68.421 0.00 0.00 34.04 3.51
3128 3162 4.082523 CGTGGACTGGGCGATGGT 62.083 66.667 0.00 0.00 0.00 3.55
3129 3163 2.436646 GTGGACTGGGCGATGGTG 60.437 66.667 0.00 0.00 0.00 4.17
3130 3164 3.716195 TGGACTGGGCGATGGTGG 61.716 66.667 0.00 0.00 0.00 4.61
3133 3167 3.391665 GACTGGGCGATGGTGGAGG 62.392 68.421 0.00 0.00 0.00 4.30
3140 3174 4.176752 GATGGTGGAGGGGCGGAC 62.177 72.222 0.00 0.00 0.00 4.79
3213 3247 4.748679 GCCTCGCTGCGCAAGTTG 62.749 66.667 18.65 0.00 41.68 3.16
3382 3430 1.847968 CAGGGTTCCTCTGGTGGGT 60.848 63.158 0.00 0.00 0.00 4.51
3397 3445 1.745489 GGGTGGCGATGGTGAAGAC 60.745 63.158 0.00 0.00 0.00 3.01
3403 3451 1.374125 CGATGGTGAAGACGGTGCA 60.374 57.895 0.00 0.00 0.00 4.57
3410 3458 0.035317 TGAAGACGGTGCAGATGCTT 59.965 50.000 6.35 0.00 42.66 3.91
3467 3515 4.440808 TCCAAGGGGAAGGTAGATTGTAA 58.559 43.478 0.00 0.00 41.32 2.41
3489 3537 3.145551 GGATGCTGCTGCTTGGGG 61.146 66.667 17.00 0.00 40.48 4.96
3518 3567 5.412594 GCCTGACAATTGACAAATCTGACTA 59.587 40.000 13.59 0.00 0.00 2.59
3519 3568 6.621596 GCCTGACAATTGACAAATCTGACTAC 60.622 42.308 13.59 0.00 0.00 2.73
3525 3577 6.734104 ATTGACAAATCTGACTACTTCTGC 57.266 37.500 0.00 0.00 0.00 4.26
3535 3587 3.057736 TGACTACTTCTGCGGTTCACTAC 60.058 47.826 0.00 0.00 0.00 2.73
3551 3621 4.693283 TCACTACAGGTTCAGTTTGAGTG 58.307 43.478 0.00 0.00 35.48 3.51
3552 3622 4.161565 TCACTACAGGTTCAGTTTGAGTGT 59.838 41.667 0.00 0.00 35.62 3.55
3553 3623 4.508124 CACTACAGGTTCAGTTTGAGTGTC 59.492 45.833 0.00 0.00 0.00 3.67
3589 3660 3.750371 TGGTGTTCTGGTTGTAAGATGG 58.250 45.455 0.00 0.00 0.00 3.51
3592 3663 3.502211 GTGTTCTGGTTGTAAGATGGTGG 59.498 47.826 0.00 0.00 0.00 4.61
3598 3669 2.084546 GTTGTAAGATGGTGGTGCCTC 58.915 52.381 0.00 0.00 38.35 4.70
3599 3670 0.618458 TGTAAGATGGTGGTGCCTCC 59.382 55.000 2.55 2.55 38.35 4.30
3612 3683 2.440409 GTGCCTCCAGTGTGATTGAAT 58.560 47.619 0.00 0.00 0.00 2.57
3613 3684 2.163010 GTGCCTCCAGTGTGATTGAATG 59.837 50.000 0.00 0.00 0.00 2.67
3614 3685 2.040145 TGCCTCCAGTGTGATTGAATGA 59.960 45.455 0.00 0.00 0.00 2.57
3615 3686 2.681848 GCCTCCAGTGTGATTGAATGAG 59.318 50.000 0.00 0.00 0.00 2.90
3616 3687 2.681848 CCTCCAGTGTGATTGAATGAGC 59.318 50.000 0.00 0.00 0.00 4.26
3617 3688 2.349590 TCCAGTGTGATTGAATGAGCG 58.650 47.619 0.00 0.00 0.00 5.03
3618 3689 1.202110 CCAGTGTGATTGAATGAGCGC 60.202 52.381 0.00 0.00 0.00 5.92
3619 3690 1.736126 CAGTGTGATTGAATGAGCGCT 59.264 47.619 11.27 11.27 0.00 5.92
3620 3691 2.161012 CAGTGTGATTGAATGAGCGCTT 59.839 45.455 13.26 0.00 0.00 4.68
3621 3692 2.417933 AGTGTGATTGAATGAGCGCTTC 59.582 45.455 13.26 5.89 0.00 3.86
3622 3693 2.160219 GTGTGATTGAATGAGCGCTTCA 59.840 45.455 13.26 9.14 40.85 3.02
3624 3695 3.181504 TGTGATTGAATGAGCGCTTCATG 60.182 43.478 13.26 0.00 45.82 3.07
3625 3696 3.011818 TGATTGAATGAGCGCTTCATGT 58.988 40.909 13.26 3.48 45.82 3.21
3627 3698 4.818005 TGATTGAATGAGCGCTTCATGTAT 59.182 37.500 13.26 10.44 45.82 2.29
3628 3699 5.297527 TGATTGAATGAGCGCTTCATGTATT 59.702 36.000 13.26 6.04 45.82 1.89
3629 3700 4.801147 TGAATGAGCGCTTCATGTATTC 57.199 40.909 13.26 14.68 45.82 1.75
3644 3742 3.664107 TGTATTCGCTCATATCCTTGCC 58.336 45.455 0.00 0.00 0.00 4.52
3653 3751 3.282021 TCATATCCTTGCCTTCAGTTGC 58.718 45.455 0.00 0.00 0.00 4.17
3668 3766 1.331756 AGTTGCAGCTTGAAACGAGTG 59.668 47.619 0.00 0.00 40.84 3.51
3669 3767 0.662619 TTGCAGCTTGAAACGAGTGG 59.337 50.000 0.00 0.00 0.00 4.00
3673 3771 0.106708 AGCTTGAAACGAGTGGAGCA 59.893 50.000 0.00 0.00 32.78 4.26
3675 3773 1.873903 GCTTGAAACGAGTGGAGCAGA 60.874 52.381 0.00 0.00 0.00 4.26
3677 3775 1.040646 TGAAACGAGTGGAGCAGAGT 58.959 50.000 0.00 0.00 0.00 3.24
3678 3776 1.412710 TGAAACGAGTGGAGCAGAGTT 59.587 47.619 0.00 0.00 0.00 3.01
3679 3777 1.795286 GAAACGAGTGGAGCAGAGTTG 59.205 52.381 0.00 0.00 0.00 3.16
3690 3788 0.595095 GCAGAGTTGCCTTGAGTTGG 59.405 55.000 0.00 0.00 44.74 3.77
3691 3789 1.815408 GCAGAGTTGCCTTGAGTTGGA 60.815 52.381 0.00 0.00 44.74 3.53
3692 3790 2.149578 CAGAGTTGCCTTGAGTTGGAG 58.850 52.381 0.00 0.00 0.00 3.86
3694 3792 2.641815 AGAGTTGCCTTGAGTTGGAGAT 59.358 45.455 0.00 0.00 0.00 2.75
3696 3794 3.416156 AGTTGCCTTGAGTTGGAGATTC 58.584 45.455 0.00 0.00 0.00 2.52
3697 3795 3.149196 GTTGCCTTGAGTTGGAGATTCA 58.851 45.455 0.00 0.00 0.00 2.57
3699 3797 3.831323 TGCCTTGAGTTGGAGATTCAAA 58.169 40.909 0.00 0.00 34.13 2.69
3702 3800 4.065088 CCTTGAGTTGGAGATTCAAACGA 58.935 43.478 0.00 0.00 34.13 3.85
3704 3802 4.336889 TGAGTTGGAGATTCAAACGAGT 57.663 40.909 0.00 0.00 0.00 4.18
3706 3804 4.202212 TGAGTTGGAGATTCAAACGAGTCA 60.202 41.667 0.00 0.00 0.00 3.41
3707 3805 4.703897 AGTTGGAGATTCAAACGAGTCAA 58.296 39.130 0.00 0.00 0.00 3.18
3708 3806 4.752101 AGTTGGAGATTCAAACGAGTCAAG 59.248 41.667 0.00 0.00 0.00 3.02
3709 3807 3.067106 TGGAGATTCAAACGAGTCAAGC 58.933 45.455 0.00 0.00 0.00 4.01
3710 3808 3.067106 GGAGATTCAAACGAGTCAAGCA 58.933 45.455 0.00 0.00 0.00 3.91
3711 3809 3.120511 GGAGATTCAAACGAGTCAAGCAC 60.121 47.826 0.00 0.00 0.00 4.40
3714 3812 1.082756 CAAACGAGTCAAGCACGGC 60.083 57.895 0.00 0.00 35.51 5.68
3715 3813 1.522806 AAACGAGTCAAGCACGGCA 60.523 52.632 0.00 0.00 35.51 5.69
3717 3815 2.356313 CGAGTCAAGCACGGCACT 60.356 61.111 0.00 0.00 0.00 4.40
3719 3817 1.571460 GAGTCAAGCACGGCACTTG 59.429 57.895 7.73 7.73 44.76 3.16
3723 3821 0.380378 TCAAGCACGGCACTTGTTTC 59.620 50.000 12.24 0.00 43.97 2.78
3725 3823 1.734388 AAGCACGGCACTTGTTTCCC 61.734 55.000 0.00 0.00 0.00 3.97
3739 3837 6.313658 CACTTGTTTCCCTCCTTTTTCTTTTG 59.686 38.462 0.00 0.00 0.00 2.44
3740 3838 4.765273 TGTTTCCCTCCTTTTTCTTTTGC 58.235 39.130 0.00 0.00 0.00 3.68
3741 3839 4.469586 TGTTTCCCTCCTTTTTCTTTTGCT 59.530 37.500 0.00 0.00 0.00 3.91
3742 3840 5.659079 TGTTTCCCTCCTTTTTCTTTTGCTA 59.341 36.000 0.00 0.00 0.00 3.49
3743 3841 6.326323 TGTTTCCCTCCTTTTTCTTTTGCTAT 59.674 34.615 0.00 0.00 0.00 2.97
3744 3842 6.994421 TTCCCTCCTTTTTCTTTTGCTATT 57.006 33.333 0.00 0.00 0.00 1.73
3745 3843 6.994421 TCCCTCCTTTTTCTTTTGCTATTT 57.006 33.333 0.00 0.00 0.00 1.40
3746 3844 6.993079 TCCCTCCTTTTTCTTTTGCTATTTC 58.007 36.000 0.00 0.00 0.00 2.17
3747 3845 6.782494 TCCCTCCTTTTTCTTTTGCTATTTCT 59.218 34.615 0.00 0.00 0.00 2.52
3749 3847 6.870439 CCTCCTTTTTCTTTTGCTATTTCTGG 59.130 38.462 0.00 0.00 0.00 3.86
3766 3865 9.237846 CTATTTCTGGAAAACAAGTTCAGAAAC 57.762 33.333 20.82 0.00 37.41 2.78
3772 3871 5.474825 GAAAACAAGTTCAGAAACACCCAA 58.525 37.500 0.00 0.00 37.88 4.12
3792 3891 4.690748 CCAAACGAGCATCAGTTTCTCTTA 59.309 41.667 0.00 0.00 38.86 2.10
3803 3902 7.361542 GCATCAGTTTCTCTTATGAGCTGAAAA 60.362 37.037 14.25 3.55 39.01 2.29
3807 3906 6.658391 AGTTTCTCTTATGAGCTGAAAAGCAT 59.342 34.615 0.00 0.00 40.03 3.79
3808 3907 6.432607 TTCTCTTATGAGCTGAAAAGCATG 57.567 37.500 0.00 0.00 40.03 4.06
3824 3956 7.970061 TGAAAAGCATGTGCAATTTCTATAGAC 59.030 33.333 23.93 0.00 45.16 2.59
3838 3970 0.953471 ATAGACGCACGGCTGCAAAA 60.953 50.000 9.06 0.00 44.50 2.44
3840 3972 1.797537 GACGCACGGCTGCAAAATC 60.798 57.895 0.50 0.00 44.50 2.17
3841 3973 2.254951 CGCACGGCTGCAAAATCA 59.745 55.556 0.50 0.00 44.50 2.57
3843 3975 2.082366 GCACGGCTGCAAAATCACG 61.082 57.895 0.50 0.00 43.62 4.35
3844 3976 1.573932 CACGGCTGCAAAATCACGA 59.426 52.632 0.50 0.00 0.00 4.35
3846 3978 0.665835 ACGGCTGCAAAATCACGAAA 59.334 45.000 0.50 0.00 0.00 3.46
3847 3979 1.330306 CGGCTGCAAAATCACGAAAG 58.670 50.000 0.50 0.00 0.00 2.62
3850 3982 2.126467 GCTGCAAAATCACGAAAGCAA 58.874 42.857 0.00 0.00 0.00 3.91
3851 3983 2.539274 GCTGCAAAATCACGAAAGCAAA 59.461 40.909 0.00 0.00 0.00 3.68
3862 4094 4.270084 TCACGAAAGCAAAACTGTCAGTAG 59.730 41.667 5.77 0.88 31.23 2.57
3967 4200 0.458669 TATTCACGACCTTCGGAGCC 59.541 55.000 0.03 0.00 45.59 4.70
4082 4319 2.490115 TGCGAAGGGTTATTTTTGCGAT 59.510 40.909 0.00 0.00 36.66 4.58
4115 4352 0.618968 AGGGGAACTTGATCGGCTCT 60.619 55.000 0.00 0.00 0.00 4.09
4127 4364 2.338015 CGGCTCTGGTTGCAATGCT 61.338 57.895 6.82 0.00 0.00 3.79
4398 4638 4.025061 CCGAGAGAGAAAAATGCAGCATAG 60.025 45.833 8.75 0.00 0.00 2.23
4475 4834 5.045651 TCAGCTACAAATCAGGATTCAGGAA 60.046 40.000 0.00 0.00 0.00 3.36
4486 4845 0.613012 ATTCAGGAAACCAGCCCAGC 60.613 55.000 0.00 0.00 0.00 4.85
4526 4885 3.569701 ACAAGTGCCAAAACTGACTATGG 59.430 43.478 0.00 0.00 36.00 2.74
4565 4925 9.760077 GCATACTAGTAATAACAATACAGGTGT 57.240 33.333 6.70 0.00 0.00 4.16
4586 4946 2.584492 ACAAAACCAAAGCTCACTGC 57.416 45.000 0.00 0.00 43.29 4.40
4616 4977 1.609208 ATGCCACCACAGACAACTTC 58.391 50.000 0.00 0.00 0.00 3.01
4679 5040 4.211794 CAGGCATTCACAAAAACAATGGAC 59.788 41.667 0.00 0.00 0.00 4.02
4740 5101 3.678965 AGCTCTCTCTGGATAAGGTCA 57.321 47.619 0.00 0.00 0.00 4.02
4863 5224 6.712998 TGACGATTTCAAAAGGGAGTTCATAA 59.287 34.615 0.00 0.00 0.00 1.90
4864 5225 7.393234 TGACGATTTCAAAAGGGAGTTCATAAT 59.607 33.333 0.00 0.00 0.00 1.28
4879 5240 5.182001 AGTTCATAATTGCACTCAACTGGTC 59.818 40.000 0.00 0.00 34.60 4.02
4913 5274 5.934043 GCTTGATTTTGTGCTAAAAGGGAAT 59.066 36.000 5.84 0.00 0.00 3.01
4950 5311 5.296780 AGAACATAATACAAGGCGGTTGATG 59.703 40.000 4.54 1.17 38.60 3.07
4959 5320 2.989639 CGGTTGATGCCCTCCTCA 59.010 61.111 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.562008 GGGAAAAGGAGAAGCTAGCCT 59.438 52.381 12.13 1.38 0.00 4.58
46 47 3.565764 TGAAGCTCATCTTGGTATGGG 57.434 47.619 0.00 0.00 34.56 4.00
277 280 1.755008 CCTCCTCCGACTCTGGGTC 60.755 68.421 0.00 0.00 41.28 4.46
332 336 6.496565 TCCTATCCAGATCTCCTTGAGAATTC 59.503 42.308 0.00 0.00 42.27 2.17
891 900 2.753849 GCCCATACGCAAGCCCAA 60.754 61.111 0.00 0.00 45.62 4.12
897 906 2.124901 CCCGAAGCCCATACGCAA 60.125 61.111 0.00 0.00 0.00 4.85
900 909 1.881252 CGAACCCGAAGCCCATACG 60.881 63.158 0.00 0.00 38.22 3.06
929 944 0.890683 CAATGGGAGCCAGTGGAAAC 59.109 55.000 15.20 2.57 44.60 2.78
931 946 2.079088 TGCAATGGGAGCCAGTGGAA 62.079 55.000 15.20 0.00 45.85 3.53
987 1003 2.550101 GGCCATGGCGCAATCTCTC 61.550 63.158 29.90 9.36 43.06 3.20
1353 1372 1.745864 GGAGACGAGCTCGAGGTCA 60.746 63.158 40.58 0.00 44.91 4.02
1576 1595 0.524862 TTGACGCGGTAGAAGGTCTC 59.475 55.000 12.47 0.00 0.00 3.36
1803 1822 3.283684 TTGAACCGCTGGTTGCCG 61.284 61.111 16.02 0.00 46.95 5.69
2141 2160 0.108804 AGCAGTATTGACGGTGTCGG 60.109 55.000 0.00 0.00 41.39 4.79
2146 2165 1.515954 CCGGAGCAGTATTGACGGT 59.484 57.895 0.00 0.00 34.81 4.83
2149 2168 1.883084 CCGCCGGAGCAGTATTGAC 60.883 63.158 5.05 0.00 39.83 3.18
2154 2173 3.224324 GATCCCGCCGGAGCAGTA 61.224 66.667 5.05 0.00 44.50 2.74
2199 2218 3.276846 GTTGCGGCGGTGACAACT 61.277 61.111 17.11 0.00 40.36 3.16
2239 2258 2.591753 CCCCACGATGCAGATGGT 59.408 61.111 11.55 0.00 0.00 3.55
2259 2278 0.392729 GATGCCTGAAGAGCAGCAGT 60.393 55.000 0.00 0.00 45.72 4.40
2277 2296 0.949105 GTTTCTTGCTCCTTCGGCGA 60.949 55.000 4.99 4.99 0.00 5.54
2283 2302 0.668535 GCCGTTGTTTCTTGCTCCTT 59.331 50.000 0.00 0.00 0.00 3.36
2284 2303 1.507141 CGCCGTTGTTTCTTGCTCCT 61.507 55.000 0.00 0.00 0.00 3.69
2289 2308 1.281656 GGACCGCCGTTGTTTCTTG 59.718 57.895 0.00 0.00 0.00 3.02
2318 2337 4.277552 CTATGGAGGAGGACGGCA 57.722 61.111 0.00 0.00 0.00 5.69
2446 2468 2.257676 GCCCTCGTCGAAGTCGTT 59.742 61.111 0.00 0.00 40.43 3.85
2447 2469 3.745803 GGCCCTCGTCGAAGTCGT 61.746 66.667 0.00 0.00 40.43 4.34
2824 2846 2.280186 GTCCCGGTGGATGATCGC 60.280 66.667 0.00 0.00 44.28 4.58
2873 2895 3.378399 GAGACCTTGGCGGAGAGGC 62.378 68.421 0.00 0.00 46.95 4.70
2939 2964 1.891919 ACCGCGTTGTTGCTCACAT 60.892 52.632 4.92 0.00 34.43 3.21
2940 2965 2.512745 ACCGCGTTGTTGCTCACA 60.513 55.556 4.92 0.00 0.00 3.58
2942 2967 1.369839 TTTCACCGCGTTGTTGCTCA 61.370 50.000 4.92 0.00 0.00 4.26
2943 2968 0.657368 CTTTCACCGCGTTGTTGCTC 60.657 55.000 4.92 0.00 0.00 4.26
2945 2970 1.657181 CCTTTCACCGCGTTGTTGC 60.657 57.895 4.92 0.00 0.00 4.17
2947 2972 2.058829 CTGCCTTTCACCGCGTTGTT 62.059 55.000 4.92 0.00 0.00 2.83
2950 2975 3.660111 GCTGCCTTTCACCGCGTT 61.660 61.111 4.92 0.00 0.00 4.84
2951 2976 4.626081 AGCTGCCTTTCACCGCGT 62.626 61.111 4.92 0.00 0.00 6.01
3149 3183 1.690633 TCCATCACCCTCTCCAGCC 60.691 63.158 0.00 0.00 0.00 4.85
3372 3420 2.124983 CATCGCCACCCACCAGAG 60.125 66.667 0.00 0.00 0.00 3.35
3375 3423 4.343323 CACCATCGCCACCCACCA 62.343 66.667 0.00 0.00 0.00 4.17
3382 3430 2.264480 CCGTCTTCACCATCGCCA 59.736 61.111 0.00 0.00 0.00 5.69
3397 3445 2.360350 ACCCAAGCATCTGCACCG 60.360 61.111 4.79 0.00 45.16 4.94
3403 3451 0.469705 TTGTTGCCACCCAAGCATCT 60.470 50.000 0.00 0.00 40.59 2.90
3410 3458 1.943730 AAGACCCTTGTTGCCACCCA 61.944 55.000 0.00 0.00 0.00 4.51
3430 3478 4.392940 CCCTTGGATCCAATATCTGTGAC 58.607 47.826 27.20 0.00 35.20 3.67
3467 3515 1.076192 AAGCAGCAGCATCCAACCT 59.924 52.632 3.17 0.00 45.49 3.50
3489 3537 0.539438 TGTCAATTGTCAGGCCACCC 60.539 55.000 5.01 0.00 0.00 4.61
3502 3550 5.349817 CGCAGAAGTAGTCAGATTTGTCAAT 59.650 40.000 0.00 0.00 0.00 2.57
3518 3567 1.000955 CCTGTAGTGAACCGCAGAAGT 59.999 52.381 0.00 0.00 0.00 3.01
3519 3568 1.000955 ACCTGTAGTGAACCGCAGAAG 59.999 52.381 0.00 0.00 0.00 2.85
3525 3577 2.814280 ACTGAACCTGTAGTGAACCG 57.186 50.000 0.00 0.00 0.00 4.44
3535 3587 3.806521 CAGAGACACTCAAACTGAACCTG 59.193 47.826 0.00 0.00 32.06 4.00
3551 3621 3.316308 ACACCAGCAATTTCAACAGAGAC 59.684 43.478 0.00 0.00 0.00 3.36
3552 3622 3.554934 ACACCAGCAATTTCAACAGAGA 58.445 40.909 0.00 0.00 0.00 3.10
3553 3623 3.996150 ACACCAGCAATTTCAACAGAG 57.004 42.857 0.00 0.00 0.00 3.35
3589 3660 0.250901 AATCACACTGGAGGCACCAC 60.251 55.000 0.00 0.00 44.64 4.16
3592 3663 1.896220 TTCAATCACACTGGAGGCAC 58.104 50.000 0.00 0.00 0.00 5.01
3598 3669 1.202110 GCGCTCATTCAATCACACTGG 60.202 52.381 0.00 0.00 0.00 4.00
3599 3670 1.736126 AGCGCTCATTCAATCACACTG 59.264 47.619 2.64 0.00 0.00 3.66
3605 3676 3.687572 ACATGAAGCGCTCATTCAATC 57.312 42.857 12.06 2.58 42.46 2.67
3606 3677 5.559608 CGAATACATGAAGCGCTCATTCAAT 60.560 40.000 12.06 6.66 42.46 2.57
3612 3683 0.930310 GCGAATACATGAAGCGCTCA 59.070 50.000 12.06 11.46 43.85 4.26
3613 3684 3.717712 GCGAATACATGAAGCGCTC 57.282 52.632 12.06 4.99 43.85 5.03
3616 3687 4.032217 GGATATGAGCGAATACATGAAGCG 59.968 45.833 0.00 0.00 0.00 4.68
3617 3688 5.174395 AGGATATGAGCGAATACATGAAGC 58.826 41.667 0.00 0.00 0.00 3.86
3618 3689 6.401903 GCAAGGATATGAGCGAATACATGAAG 60.402 42.308 0.00 0.00 0.00 3.02
3619 3690 5.409520 GCAAGGATATGAGCGAATACATGAA 59.590 40.000 0.00 0.00 0.00 2.57
3620 3691 4.931601 GCAAGGATATGAGCGAATACATGA 59.068 41.667 0.00 0.00 0.00 3.07
3621 3692 4.093998 GGCAAGGATATGAGCGAATACATG 59.906 45.833 0.00 0.00 0.00 3.21
3622 3693 4.019860 AGGCAAGGATATGAGCGAATACAT 60.020 41.667 0.00 0.00 0.00 2.29
3624 3695 3.931578 AGGCAAGGATATGAGCGAATAC 58.068 45.455 0.00 0.00 0.00 1.89
3625 3696 4.040339 TGAAGGCAAGGATATGAGCGAATA 59.960 41.667 0.00 0.00 0.00 1.75
3627 3698 2.170397 TGAAGGCAAGGATATGAGCGAA 59.830 45.455 0.00 0.00 0.00 4.70
3628 3699 1.762370 TGAAGGCAAGGATATGAGCGA 59.238 47.619 0.00 0.00 0.00 4.93
3629 3700 2.141517 CTGAAGGCAAGGATATGAGCG 58.858 52.381 0.00 0.00 0.00 5.03
3632 3730 3.282021 GCAACTGAAGGCAAGGATATGA 58.718 45.455 0.00 0.00 0.00 2.15
3644 3742 2.032054 TCGTTTCAAGCTGCAACTGAAG 59.968 45.455 1.02 0.00 0.00 3.02
3653 3751 0.514691 GCTCCACTCGTTTCAAGCTG 59.485 55.000 0.00 0.00 0.00 4.24
3677 3775 3.507162 TGAATCTCCAACTCAAGGCAA 57.493 42.857 0.00 0.00 0.00 4.52
3678 3776 3.507162 TTGAATCTCCAACTCAAGGCA 57.493 42.857 0.00 0.00 0.00 4.75
3679 3777 3.365364 CGTTTGAATCTCCAACTCAAGGC 60.365 47.826 0.00 0.00 31.11 4.35
3680 3778 4.065088 TCGTTTGAATCTCCAACTCAAGG 58.935 43.478 0.00 0.00 31.11 3.61
3681 3779 4.752101 ACTCGTTTGAATCTCCAACTCAAG 59.248 41.667 0.00 0.00 31.11 3.02
3682 3780 4.703897 ACTCGTTTGAATCTCCAACTCAA 58.296 39.130 0.00 0.00 0.00 3.02
3684 3782 4.307432 TGACTCGTTTGAATCTCCAACTC 58.693 43.478 0.00 0.00 0.00 3.01
3685 3783 4.336889 TGACTCGTTTGAATCTCCAACT 57.663 40.909 0.00 0.00 0.00 3.16
3686 3784 4.611581 GCTTGACTCGTTTGAATCTCCAAC 60.612 45.833 0.00 0.00 0.00 3.77
3687 3785 3.498397 GCTTGACTCGTTTGAATCTCCAA 59.502 43.478 0.00 0.00 0.00 3.53
3689 3787 3.067106 TGCTTGACTCGTTTGAATCTCC 58.933 45.455 0.00 0.00 0.00 3.71
3690 3788 3.422343 CGTGCTTGACTCGTTTGAATCTC 60.422 47.826 0.00 0.00 0.00 2.75
3691 3789 2.476619 CGTGCTTGACTCGTTTGAATCT 59.523 45.455 0.00 0.00 0.00 2.40
3692 3790 2.411547 CCGTGCTTGACTCGTTTGAATC 60.412 50.000 0.00 0.00 33.48 2.52
3694 3792 0.934496 CCGTGCTTGACTCGTTTGAA 59.066 50.000 0.00 0.00 33.48 2.69
3696 3794 1.082756 GCCGTGCTTGACTCGTTTG 60.083 57.895 0.00 0.00 33.48 2.93
3697 3795 1.522806 TGCCGTGCTTGACTCGTTT 60.523 52.632 0.00 0.00 33.48 3.60
3699 3797 2.644555 AAGTGCCGTGCTTGACTCGT 62.645 55.000 0.00 0.00 33.48 4.18
3702 3800 0.748005 AACAAGTGCCGTGCTTGACT 60.748 50.000 14.79 1.12 44.29 3.41
3704 3802 0.380378 GAAACAAGTGCCGTGCTTGA 59.620 50.000 14.79 0.00 44.29 3.02
3706 3804 1.733526 GGAAACAAGTGCCGTGCTT 59.266 52.632 0.00 0.00 0.00 3.91
3707 3805 2.193536 GGGAAACAAGTGCCGTGCT 61.194 57.895 0.00 0.00 0.00 4.40
3708 3806 2.130073 GAGGGAAACAAGTGCCGTGC 62.130 60.000 0.00 0.00 33.40 5.34
3709 3807 1.515521 GGAGGGAAACAAGTGCCGTG 61.516 60.000 0.00 0.00 33.40 4.94
3710 3808 1.228154 GGAGGGAAACAAGTGCCGT 60.228 57.895 0.00 0.00 33.40 5.68
3711 3809 0.537371 AAGGAGGGAAACAAGTGCCG 60.537 55.000 0.00 0.00 33.40 5.69
3714 3812 5.598416 AAGAAAAAGGAGGGAAACAAGTG 57.402 39.130 0.00 0.00 0.00 3.16
3715 3813 6.406370 CAAAAGAAAAAGGAGGGAAACAAGT 58.594 36.000 0.00 0.00 0.00 3.16
3717 3815 5.045942 AGCAAAAGAAAAAGGAGGGAAACAA 60.046 36.000 0.00 0.00 0.00 2.83
3719 3817 5.023533 AGCAAAAGAAAAAGGAGGGAAAC 57.976 39.130 0.00 0.00 0.00 2.78
3723 3821 6.870439 CAGAAATAGCAAAAGAAAAAGGAGGG 59.130 38.462 0.00 0.00 0.00 4.30
3725 3823 7.661040 TCCAGAAATAGCAAAAGAAAAAGGAG 58.339 34.615 0.00 0.00 0.00 3.69
3739 3837 6.970484 TCTGAACTTGTTTTCCAGAAATAGC 58.030 36.000 0.00 0.00 0.00 2.97
3740 3838 9.237846 GTTTCTGAACTTGTTTTCCAGAAATAG 57.762 33.333 20.97 0.92 36.35 1.73
3741 3839 8.744652 TGTTTCTGAACTTGTTTTCCAGAAATA 58.255 29.630 20.97 17.95 36.35 1.40
3742 3840 7.545615 GTGTTTCTGAACTTGTTTTCCAGAAAT 59.454 33.333 20.97 0.00 36.35 2.17
3743 3841 6.866248 GTGTTTCTGAACTTGTTTTCCAGAAA 59.134 34.615 17.30 17.30 36.70 2.52
3744 3842 6.386654 GTGTTTCTGAACTTGTTTTCCAGAA 58.613 36.000 10.21 10.21 36.70 3.02
3745 3843 5.105917 GGTGTTTCTGAACTTGTTTTCCAGA 60.106 40.000 0.00 0.00 36.70 3.86
3746 3844 5.102313 GGTGTTTCTGAACTTGTTTTCCAG 58.898 41.667 0.00 0.00 36.70 3.86
3747 3845 4.081917 GGGTGTTTCTGAACTTGTTTTCCA 60.082 41.667 0.00 0.00 36.70 3.53
3749 3847 5.066968 TGGGTGTTTCTGAACTTGTTTTC 57.933 39.130 0.00 0.00 36.70 2.29
3766 3865 1.238439 AACTGATGCTCGTTTGGGTG 58.762 50.000 0.00 0.00 0.00 4.61
3772 3871 5.724328 TCATAAGAGAAACTGATGCTCGTT 58.276 37.500 0.00 0.00 37.38 3.85
3803 3902 4.024556 GCGTCTATAGAAATTGCACATGCT 60.025 41.667 3.40 0.00 42.66 3.79
3808 3907 3.302480 CCGTGCGTCTATAGAAATTGCAC 60.302 47.826 25.60 25.60 45.61 4.57
3838 3970 3.627577 ACTGACAGTTTTGCTTTCGTGAT 59.372 39.130 1.07 0.00 0.00 3.06
3840 3972 3.405170 ACTGACAGTTTTGCTTTCGTG 57.595 42.857 1.07 0.00 0.00 4.35
3841 3973 4.439057 TCTACTGACAGTTTTGCTTTCGT 58.561 39.130 14.50 0.00 0.00 3.85
3843 3975 6.364945 AGTTCTACTGACAGTTTTGCTTTC 57.635 37.500 14.50 0.00 0.00 2.62
3844 3976 6.017852 GCTAGTTCTACTGACAGTTTTGCTTT 60.018 38.462 14.50 0.00 0.00 3.51
3846 3978 4.991687 GCTAGTTCTACTGACAGTTTTGCT 59.008 41.667 14.50 9.96 0.00 3.91
3847 3979 4.750098 TGCTAGTTCTACTGACAGTTTTGC 59.250 41.667 14.50 9.36 0.00 3.68
3850 3982 8.531982 TCATTATGCTAGTTCTACTGACAGTTT 58.468 33.333 14.50 0.00 0.00 2.66
3851 3983 8.067751 TCATTATGCTAGTTCTACTGACAGTT 57.932 34.615 14.50 0.00 0.00 3.16
3862 4094 8.388484 ACATTCCTGAATCATTATGCTAGTTC 57.612 34.615 0.00 0.00 0.00 3.01
3915 4148 1.268079 GAACCTTCTTGCTGTTGAGGC 59.732 52.381 0.00 0.00 0.00 4.70
3967 4200 1.070577 CGTTCTTCTGTGAGGCGTTTG 60.071 52.381 0.00 0.00 0.00 2.93
4115 4352 2.224018 GGTGAAGAAAGCATTGCAACCA 60.224 45.455 11.91 0.00 0.00 3.67
4127 4364 1.048601 AGTCGGAGCTGGTGAAGAAA 58.951 50.000 0.00 0.00 0.00 2.52
4475 4834 4.335647 CACCTCGCTGGGCTGGTT 62.336 66.667 6.52 0.00 41.11 3.67
4565 4925 3.488384 CGCAGTGAGCTTTGGTTTTGTTA 60.488 43.478 0.00 0.00 42.61 2.41
4586 4946 2.094803 TGTGGTGGCATTGCTTATTTCG 60.095 45.455 8.82 0.00 0.00 3.46
4616 4977 1.737793 GTAGTTCCCCTCACATTTGCG 59.262 52.381 0.00 0.00 0.00 4.85
4644 5005 2.290387 TGAATGCCTGCATTTGCCATTT 60.290 40.909 17.66 0.00 45.50 2.32
4645 5006 1.279558 TGAATGCCTGCATTTGCCATT 59.720 42.857 17.66 2.99 45.50 3.16
4679 5040 5.503927 TGAATCCTTCTCCTCAAAATCCAG 58.496 41.667 0.00 0.00 0.00 3.86
4740 5101 3.051880 AGCAACTTTCCCCATTCCCATAT 60.052 43.478 0.00 0.00 0.00 1.78
4863 5224 3.638160 ACAAATGACCAGTTGAGTGCAAT 59.362 39.130 15.75 0.00 38.53 3.56
4864 5225 3.023119 ACAAATGACCAGTTGAGTGCAA 58.977 40.909 15.75 0.00 38.53 4.08
4879 5240 7.181143 AGCACAAAATCAAGCTAAACAAATG 57.819 32.000 0.00 0.00 35.19 2.32
4950 5311 0.402121 ACAAGGAAGTTGAGGAGGGC 59.598 55.000 0.00 0.00 38.60 5.19
4959 5320 3.243975 ACCGTAACGATCACAAGGAAGTT 60.244 43.478 0.00 0.00 35.52 2.66


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

AutoCloner maintained by Alex Coulton.