Multiple sequence alignment - TraesCS7A01G415900

Loading Multiple Alignment...

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 TraesCS7A01G415900 chr7A 100.000 2822 0 0 1 2822 608237680 608234859 0.000000e+00 5212
1 TraesCS7A01G415900 chr7A 98.775 1959 14 4 1 1958 232344915 232346864 0.000000e+00 3476
2 TraesCS7A01G415900 chr7A 93.487 737 30 9 1 722 511550537 511549804 0.000000e+00 1079
3 TraesCS7A01G415900 chr7A 96.525 518 16 1 1435 1952 661879526 661880041 0.000000e+00 856
4 TraesCS7A01G415900 chr7A 95.677 532 22 1 2291 2822 733225378 733225908 0.000000e+00 854
5 TraesCS7A01G415900 chr3A 99.130 1953 15 2 1 1953 747647744 747649694 0.000000e+00 3511
6 TraesCS7A01G415900 chr3A 98.446 1866 27 1 86 1951 337496905 337498768 0.000000e+00 3284
7 TraesCS7A01G415900 chr3A 96.395 527 18 1 2296 2822 641473751 641474276 0.000000e+00 867
8 TraesCS7A01G415900 chr3A 88.904 721 54 19 1245 1956 265372477 265373180 0.000000e+00 865
9 TraesCS7A01G415900 chr3A 95.336 536 24 1 2287 2822 127996965 127996431 0.000000e+00 850
10 TraesCS7A01G415900 chr1B 98.618 1954 18 3 1 1954 4986643 4984699 0.000000e+00 3450
11 TraesCS7A01G415900 chr1B 89.559 1973 137 34 1 1951 65108495 65106570 0.000000e+00 2438
12 TraesCS7A01G415900 chr3B 95.472 1038 43 4 921 1958 35475123 35474090 0.000000e+00 1653
13 TraesCS7A01G415900 chr3B 94.190 895 35 9 1 895 35475980 35475103 0.000000e+00 1349
14 TraesCS7A01G415900 chr2B 87.138 933 79 21 1034 1939 90632557 90633475 0.000000e+00 1020
15 TraesCS7A01G415900 chr2B 91.980 399 27 3 1562 1958 771167971 771168366 3.180000e-154 555
16 TraesCS7A01G415900 chr2A 96.219 529 19 1 2294 2822 429438243 429438770 0.000000e+00 865
17 TraesCS7A01G415900 chr2A 95.531 537 23 1 2286 2822 42725645 42726180 0.000000e+00 857
18 TraesCS7A01G415900 chr2A 80.418 766 107 36 1 733 14925197 14924442 6.880000e-151 544
19 TraesCS7A01G415900 chr2A 80.919 718 101 28 1 691 14926110 14925402 4.140000e-148 534
20 TraesCS7A01G415900 chr5D 96.015 527 20 1 2296 2822 368064271 368063746 0.000000e+00 856
21 TraesCS7A01G415900 chr5B 96.015 527 20 1 2296 2822 450747955 450747430 0.000000e+00 856
22 TraesCS7A01G415900 chr3D 96.015 527 20 1 2296 2822 300809592 300809067 0.000000e+00 856
23 TraesCS7A01G415900 chr1A 96.015 527 20 1 2296 2822 314417321 314416796 0.000000e+00 856
24 TraesCS7A01G415900 chr1A 91.980 399 28 3 1562 1958 446716610 446717006 8.830000e-155 556
25 TraesCS7A01G415900 chr6B 86.243 756 73 16 944 1674 243235412 243234663 0.000000e+00 791
26 TraesCS7A01G415900 chr4A 81.846 986 105 44 1008 1958 727254067 727253121 0.000000e+00 761
27 TraesCS7A01G415900 chr6A 92.583 391 25 2 1562 1951 317608909 317609296 2.460000e-155 558
28 TraesCS7A01G415900 chr6A 80.161 746 108 35 8 733 249211076 249211801 3.220000e-144 521
29 TraesCS7A01G415900 chr4B 78.273 695 94 40 21 691 16226459 16227120 7.330000e-106 394
30 TraesCS7A01G415900 chrUn 89.143 175 12 4 1951 2121 475767087 475766916 7.920000e-51 211
31 TraesCS7A01G415900 chr7B 89.143 175 12 4 1951 2121 565092570 565092399 7.920000e-51 211
32 TraesCS7A01G415900 chr7B 89.143 175 12 4 1951 2121 565093021 565092850 7.920000e-51 211


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 TraesCS7A01G415900 chr7A 608234859 608237680 2821 True 5212 5212 100.0000 1 2822 1 chr7A.!!$R2 2821
1 TraesCS7A01G415900 chr7A 232344915 232346864 1949 False 3476 3476 98.7750 1 1958 1 chr7A.!!$F1 1957
2 TraesCS7A01G415900 chr7A 511549804 511550537 733 True 1079 1079 93.4870 1 722 1 chr7A.!!$R1 721
3 TraesCS7A01G415900 chr7A 661879526 661880041 515 False 856 856 96.5250 1435 1952 1 chr7A.!!$F2 517
4 TraesCS7A01G415900 chr7A 733225378 733225908 530 False 854 854 95.6770 2291 2822 1 chr7A.!!$F3 531
5 TraesCS7A01G415900 chr3A 747647744 747649694 1950 False 3511 3511 99.1300 1 1953 1 chr3A.!!$F4 1952
6 TraesCS7A01G415900 chr3A 337496905 337498768 1863 False 3284 3284 98.4460 86 1951 1 chr3A.!!$F2 1865
7 TraesCS7A01G415900 chr3A 641473751 641474276 525 False 867 867 96.3950 2296 2822 1 chr3A.!!$F3 526
8 TraesCS7A01G415900 chr3A 265372477 265373180 703 False 865 865 88.9040 1245 1956 1 chr3A.!!$F1 711
9 TraesCS7A01G415900 chr3A 127996431 127996965 534 True 850 850 95.3360 2287 2822 1 chr3A.!!$R1 535
10 TraesCS7A01G415900 chr1B 4984699 4986643 1944 True 3450 3450 98.6180 1 1954 1 chr1B.!!$R1 1953
11 TraesCS7A01G415900 chr1B 65106570 65108495 1925 True 2438 2438 89.5590 1 1951 1 chr1B.!!$R2 1950
12 TraesCS7A01G415900 chr3B 35474090 35475980 1890 True 1501 1653 94.8310 1 1958 2 chr3B.!!$R1 1957
13 TraesCS7A01G415900 chr2B 90632557 90633475 918 False 1020 1020 87.1380 1034 1939 1 chr2B.!!$F1 905
14 TraesCS7A01G415900 chr2A 429438243 429438770 527 False 865 865 96.2190 2294 2822 1 chr2A.!!$F2 528
15 TraesCS7A01G415900 chr2A 42725645 42726180 535 False 857 857 95.5310 2286 2822 1 chr2A.!!$F1 536
16 TraesCS7A01G415900 chr2A 14924442 14926110 1668 True 539 544 80.6685 1 733 2 chr2A.!!$R1 732
17 TraesCS7A01G415900 chr5D 368063746 368064271 525 True 856 856 96.0150 2296 2822 1 chr5D.!!$R1 526
18 TraesCS7A01G415900 chr5B 450747430 450747955 525 True 856 856 96.0150 2296 2822 1 chr5B.!!$R1 526
19 TraesCS7A01G415900 chr3D 300809067 300809592 525 True 856 856 96.0150 2296 2822 1 chr3D.!!$R1 526
20 TraesCS7A01G415900 chr1A 314416796 314417321 525 True 856 856 96.0150 2296 2822 1 chr1A.!!$R1 526
21 TraesCS7A01G415900 chr6B 243234663 243235412 749 True 791 791 86.2430 944 1674 1 chr6B.!!$R1 730
22 TraesCS7A01G415900 chr4A 727253121 727254067 946 True 761 761 81.8460 1008 1958 1 chr4A.!!$R1 950
23 TraesCS7A01G415900 chr6A 249211076 249211801 725 False 521 521 80.1610 8 733 1 chr6A.!!$F1 725
24 TraesCS7A01G415900 chr4B 16226459 16227120 661 False 394 394 78.2730 21 691 1 chr4B.!!$F1 670
25 TraesCS7A01G415900 chr7B 565092399 565093021 622 True 211 211 89.1430 1951 2121 2 chr7B.!!$R1 170

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
426 470 8.597662 TTAGCGGGATATACAGACAAAATAAC 57.402 34.615 0.0 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 3706 0.031994 GGAGAAAAAGGCAAAGCGCA 59.968 50.0 11.47 0.0 45.17 6.09 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
426 470 8.597662 TTAGCGGGATATACAGACAAAATAAC 57.402 34.615 0.00 0.00 0.00 1.89
1969 3045 9.869844 GGAAAGATTTAATATCACATGTTCGAG 57.130 33.333 0.00 0.00 0.00 4.04
1978 3502 7.721286 ATATCACATGTTCGAGGATTTCTTC 57.279 36.000 0.00 0.00 0.00 2.87
1989 3513 3.201363 AGGATTTCTTCATCCCCCAAGA 58.799 45.455 0.00 0.00 43.68 3.02
2001 3525 0.106217 CCCCAAGACCCAAACACAGT 60.106 55.000 0.00 0.00 0.00 3.55
2013 3537 0.320771 AACACAGTGAGCCATCCGAC 60.321 55.000 7.81 0.00 0.00 4.79
2016 3540 1.448540 CAGTGAGCCATCCGACACC 60.449 63.158 0.00 0.00 34.33 4.16
2018 3542 2.606213 TGAGCCATCCGACACCCA 60.606 61.111 0.00 0.00 0.00 4.51
2029 3553 3.605634 TCCGACACCCAAATAATGAGTG 58.394 45.455 0.00 0.00 42.97 3.51
2037 3561 5.066893 CACCCAAATAATGAGTGTCTCCATG 59.933 44.000 0.00 0.00 33.40 3.66
2039 3563 5.066893 CCCAAATAATGAGTGTCTCCATGTG 59.933 44.000 0.00 0.00 0.00 3.21
2040 3564 5.449588 CCAAATAATGAGTGTCTCCATGTGC 60.450 44.000 0.00 0.00 0.00 4.57
2064 3592 5.914635 CCGATGCATTACATATGGAACAAAC 59.085 40.000 1.41 0.00 40.55 2.93
2121 3649 6.388619 ACTTCCTGTTGGTAAGGATGTATT 57.611 37.500 8.73 0.00 45.50 1.89
2122 3650 6.415573 ACTTCCTGTTGGTAAGGATGTATTC 58.584 40.000 8.73 0.00 45.50 1.75
2123 3651 5.367945 TCCTGTTGGTAAGGATGTATTCC 57.632 43.478 0.00 0.00 38.96 3.01
2124 3652 4.165372 TCCTGTTGGTAAGGATGTATTCCC 59.835 45.833 0.00 0.00 38.96 3.97
2125 3653 4.166144 CCTGTTGGTAAGGATGTATTCCCT 59.834 45.833 0.00 0.00 46.81 4.20
2126 3654 5.367945 TGTTGGTAAGGATGTATTCCCTC 57.632 43.478 0.00 0.00 46.81 4.30
2127 3655 5.036916 TGTTGGTAAGGATGTATTCCCTCT 58.963 41.667 0.00 0.00 46.81 3.69
2128 3656 5.104527 TGTTGGTAAGGATGTATTCCCTCTG 60.105 44.000 0.00 0.00 46.81 3.35
2129 3657 4.631234 TGGTAAGGATGTATTCCCTCTGT 58.369 43.478 0.00 0.00 46.81 3.41
2130 3658 5.036916 TGGTAAGGATGTATTCCCTCTGTT 58.963 41.667 0.00 0.00 46.81 3.16
2131 3659 5.130477 TGGTAAGGATGTATTCCCTCTGTTC 59.870 44.000 0.00 0.00 46.81 3.18
2132 3660 4.779993 AAGGATGTATTCCCTCTGTTCC 57.220 45.455 0.00 0.00 46.81 3.62
2133 3661 3.049344 AGGATGTATTCCCTCTGTTCCC 58.951 50.000 0.00 0.00 46.81 3.97
2134 3662 3.049344 GGATGTATTCCCTCTGTTCCCT 58.951 50.000 0.00 0.00 38.75 4.20
2135 3663 3.459969 GGATGTATTCCCTCTGTTCCCTT 59.540 47.826 0.00 0.00 38.75 3.95
2136 3664 4.079730 GGATGTATTCCCTCTGTTCCCTTT 60.080 45.833 0.00 0.00 38.75 3.11
2137 3665 5.510430 GATGTATTCCCTCTGTTCCCTTTT 58.490 41.667 0.00 0.00 0.00 2.27
2138 3666 5.333566 TGTATTCCCTCTGTTCCCTTTTT 57.666 39.130 0.00 0.00 0.00 1.94
2139 3667 5.321927 TGTATTCCCTCTGTTCCCTTTTTC 58.678 41.667 0.00 0.00 0.00 2.29
2140 3668 4.749048 ATTCCCTCTGTTCCCTTTTTCT 57.251 40.909 0.00 0.00 0.00 2.52
2141 3669 3.790089 TCCCTCTGTTCCCTTTTTCTC 57.210 47.619 0.00 0.00 0.00 2.87
2142 3670 3.327439 TCCCTCTGTTCCCTTTTTCTCT 58.673 45.455 0.00 0.00 0.00 3.10
2143 3671 3.073062 TCCCTCTGTTCCCTTTTTCTCTG 59.927 47.826 0.00 0.00 0.00 3.35
2144 3672 2.816672 CCTCTGTTCCCTTTTTCTCTGC 59.183 50.000 0.00 0.00 0.00 4.26
2145 3673 2.481952 CTCTGTTCCCTTTTTCTCTGCG 59.518 50.000 0.00 0.00 0.00 5.18
2146 3674 0.951558 TGTTCCCTTTTTCTCTGCGC 59.048 50.000 0.00 0.00 0.00 6.09
2147 3675 0.951558 GTTCCCTTTTTCTCTGCGCA 59.048 50.000 10.98 10.98 0.00 6.09
2148 3676 1.541588 GTTCCCTTTTTCTCTGCGCAT 59.458 47.619 12.24 0.00 0.00 4.73
2149 3677 2.747446 GTTCCCTTTTTCTCTGCGCATA 59.253 45.455 12.24 1.74 0.00 3.14
2150 3678 3.066291 TCCCTTTTTCTCTGCGCATAA 57.934 42.857 12.24 2.77 0.00 1.90
2151 3679 3.009723 TCCCTTTTTCTCTGCGCATAAG 58.990 45.455 12.24 12.37 0.00 1.73
2152 3680 3.009723 CCCTTTTTCTCTGCGCATAAGA 58.990 45.455 12.24 14.79 0.00 2.10
2153 3681 3.629398 CCCTTTTTCTCTGCGCATAAGAT 59.371 43.478 19.64 0.00 0.00 2.40
2154 3682 4.096984 CCCTTTTTCTCTGCGCATAAGATT 59.903 41.667 19.64 0.00 0.00 2.40
2155 3683 5.393461 CCCTTTTTCTCTGCGCATAAGATTT 60.393 40.000 19.64 0.00 0.00 2.17
2156 3684 6.095377 CCTTTTTCTCTGCGCATAAGATTTT 58.905 36.000 19.64 0.00 0.00 1.82
2157 3685 6.587608 CCTTTTTCTCTGCGCATAAGATTTTT 59.412 34.615 19.64 0.00 0.00 1.94
2158 3686 7.201384 CCTTTTTCTCTGCGCATAAGATTTTTC 60.201 37.037 19.64 0.00 0.00 2.29
2159 3687 4.882671 TCTCTGCGCATAAGATTTTTCC 57.117 40.909 12.24 0.00 0.00 3.13
2160 3688 3.309682 TCTCTGCGCATAAGATTTTTCCG 59.690 43.478 12.24 0.00 0.00 4.30
2161 3689 3.006940 TCTGCGCATAAGATTTTTCCGT 58.993 40.909 12.24 0.00 0.00 4.69
2162 3690 3.438781 TCTGCGCATAAGATTTTTCCGTT 59.561 39.130 12.24 0.00 0.00 4.44
2163 3691 4.083003 TCTGCGCATAAGATTTTTCCGTTT 60.083 37.500 12.24 0.00 0.00 3.60
2164 3692 4.551388 TGCGCATAAGATTTTTCCGTTTT 58.449 34.783 5.66 0.00 0.00 2.43
2165 3693 4.985409 TGCGCATAAGATTTTTCCGTTTTT 59.015 33.333 5.66 0.00 0.00 1.94
2183 3711 4.846779 TTTTTCCTGAATAGTTTGCGCT 57.153 36.364 9.73 0.00 0.00 5.92
2184 3712 4.846779 TTTTCCTGAATAGTTTGCGCTT 57.153 36.364 9.73 0.00 0.00 4.68
2185 3713 4.846779 TTTCCTGAATAGTTTGCGCTTT 57.153 36.364 9.73 0.00 0.00 3.51
2186 3714 3.829886 TCCTGAATAGTTTGCGCTTTG 57.170 42.857 9.73 0.00 0.00 2.77
2187 3715 2.095263 TCCTGAATAGTTTGCGCTTTGC 60.095 45.455 9.73 0.00 46.70 3.68
2188 3716 2.253603 CTGAATAGTTTGCGCTTTGCC 58.746 47.619 9.73 0.00 45.60 4.52
2189 3717 1.885887 TGAATAGTTTGCGCTTTGCCT 59.114 42.857 9.73 0.00 45.60 4.75
2190 3718 2.295909 TGAATAGTTTGCGCTTTGCCTT 59.704 40.909 9.73 0.00 45.60 4.35
2191 3719 3.243704 TGAATAGTTTGCGCTTTGCCTTT 60.244 39.130 9.73 0.00 45.60 3.11
2192 3720 2.880963 TAGTTTGCGCTTTGCCTTTT 57.119 40.000 9.73 0.00 45.60 2.27
2193 3721 2.022764 AGTTTGCGCTTTGCCTTTTT 57.977 40.000 9.73 0.00 45.60 1.94
2194 3722 1.933181 AGTTTGCGCTTTGCCTTTTTC 59.067 42.857 9.73 0.00 45.60 2.29
2195 3723 1.933181 GTTTGCGCTTTGCCTTTTTCT 59.067 42.857 9.73 0.00 45.60 2.52
2196 3724 1.851658 TTGCGCTTTGCCTTTTTCTC 58.148 45.000 9.73 0.00 45.60 2.87
2197 3725 0.031994 TGCGCTTTGCCTTTTTCTCC 59.968 50.000 9.73 0.00 45.60 3.71
2198 3726 0.667487 GCGCTTTGCCTTTTTCTCCC 60.667 55.000 0.00 0.00 37.76 4.30
2199 3727 0.673437 CGCTTTGCCTTTTTCTCCCA 59.327 50.000 0.00 0.00 0.00 4.37
2200 3728 1.602920 CGCTTTGCCTTTTTCTCCCAC 60.603 52.381 0.00 0.00 0.00 4.61
2201 3729 1.270305 GCTTTGCCTTTTTCTCCCACC 60.270 52.381 0.00 0.00 0.00 4.61
2202 3730 2.319844 CTTTGCCTTTTTCTCCCACCT 58.680 47.619 0.00 0.00 0.00 4.00
2203 3731 1.703411 TTGCCTTTTTCTCCCACCTG 58.297 50.000 0.00 0.00 0.00 4.00
2204 3732 0.555769 TGCCTTTTTCTCCCACCTGT 59.444 50.000 0.00 0.00 0.00 4.00
2205 3733 1.063266 TGCCTTTTTCTCCCACCTGTT 60.063 47.619 0.00 0.00 0.00 3.16
2206 3734 2.039418 GCCTTTTTCTCCCACCTGTTT 58.961 47.619 0.00 0.00 0.00 2.83
2207 3735 2.035961 GCCTTTTTCTCCCACCTGTTTC 59.964 50.000 0.00 0.00 0.00 2.78
2208 3736 2.628178 CCTTTTTCTCCCACCTGTTTCC 59.372 50.000 0.00 0.00 0.00 3.13
2209 3737 3.295973 CTTTTTCTCCCACCTGTTTCCA 58.704 45.455 0.00 0.00 0.00 3.53
2210 3738 3.390175 TTTTCTCCCACCTGTTTCCAA 57.610 42.857 0.00 0.00 0.00 3.53
2211 3739 3.611025 TTTCTCCCACCTGTTTCCAAT 57.389 42.857 0.00 0.00 0.00 3.16
2212 3740 2.584835 TCTCCCACCTGTTTCCAATG 57.415 50.000 0.00 0.00 0.00 2.82
2213 3741 1.075374 TCTCCCACCTGTTTCCAATGG 59.925 52.381 0.00 0.00 0.00 3.16
2214 3742 0.856982 TCCCACCTGTTTCCAATGGT 59.143 50.000 0.00 0.00 0.00 3.55
2215 3743 2.041081 CTCCCACCTGTTTCCAATGGTA 59.959 50.000 0.00 0.00 0.00 3.25
2216 3744 2.167662 CCCACCTGTTTCCAATGGTAC 58.832 52.381 0.00 0.00 0.00 3.34
2217 3745 2.167662 CCACCTGTTTCCAATGGTACC 58.832 52.381 4.43 4.43 0.00 3.34
2218 3746 2.167662 CACCTGTTTCCAATGGTACCC 58.832 52.381 10.07 0.00 0.00 3.69
2219 3747 1.076513 ACCTGTTTCCAATGGTACCCC 59.923 52.381 10.07 0.00 0.00 4.95
2220 3748 1.459450 CTGTTTCCAATGGTACCCCG 58.541 55.000 10.07 0.00 0.00 5.73
2221 3749 0.609681 TGTTTCCAATGGTACCCCGC 60.610 55.000 10.07 0.00 0.00 6.13
2222 3750 1.377463 TTTCCAATGGTACCCCGCG 60.377 57.895 10.07 0.00 0.00 6.46
2223 3751 2.127027 TTTCCAATGGTACCCCGCGT 62.127 55.000 10.07 0.00 0.00 6.01
2224 3752 2.512974 CCAATGGTACCCCGCGTC 60.513 66.667 10.07 0.00 0.00 5.19
2225 3753 2.582436 CAATGGTACCCCGCGTCT 59.418 61.111 10.07 0.00 0.00 4.18
2226 3754 1.813753 CAATGGTACCCCGCGTCTG 60.814 63.158 10.07 0.00 0.00 3.51
2227 3755 2.288025 AATGGTACCCCGCGTCTGT 61.288 57.895 10.07 1.00 0.00 3.41
2228 3756 2.234913 AATGGTACCCCGCGTCTGTC 62.235 60.000 10.07 0.00 0.00 3.51
2229 3757 4.487412 GGTACCCCGCGTCTGTCG 62.487 72.222 4.92 0.00 43.12 4.35
2252 3780 3.282557 CGTATGCGTTATCCTGGCA 57.717 52.632 0.00 0.00 41.48 4.92
2253 3781 1.139989 CGTATGCGTTATCCTGGCAG 58.860 55.000 7.75 7.75 40.44 4.85
2254 3782 0.868406 GTATGCGTTATCCTGGCAGC 59.132 55.000 9.56 0.00 40.44 5.25
2255 3783 0.599991 TATGCGTTATCCTGGCAGCG 60.600 55.000 9.56 8.08 40.44 5.18
2256 3784 3.272334 GCGTTATCCTGGCAGCGG 61.272 66.667 9.56 0.00 0.00 5.52
2257 3785 3.272334 CGTTATCCTGGCAGCGGC 61.272 66.667 9.56 0.00 40.13 6.53
2258 3786 2.124736 GTTATCCTGGCAGCGGCA 60.125 61.111 11.88 7.89 43.71 5.69
2265 3793 3.286751 TGGCAGCGGCAGAAACAC 61.287 61.111 11.88 0.00 43.71 3.32
2266 3794 2.980233 GGCAGCGGCAGAAACACT 60.980 61.111 11.88 0.00 43.71 3.55
2267 3795 2.558313 GCAGCGGCAGAAACACTC 59.442 61.111 3.18 0.00 40.72 3.51
2268 3796 2.970974 GCAGCGGCAGAAACACTCC 61.971 63.158 3.18 0.00 40.72 3.85
2269 3797 1.597854 CAGCGGCAGAAACACTCCA 60.598 57.895 1.45 0.00 0.00 3.86
2270 3798 1.148273 AGCGGCAGAAACACTCCAA 59.852 52.632 1.45 0.00 0.00 3.53
2271 3799 1.166531 AGCGGCAGAAACACTCCAAC 61.167 55.000 1.45 0.00 0.00 3.77
2272 3800 1.949257 CGGCAGAAACACTCCAACC 59.051 57.895 0.00 0.00 0.00 3.77
2273 3801 0.817634 CGGCAGAAACACTCCAACCA 60.818 55.000 0.00 0.00 0.00 3.67
2274 3802 1.398692 GGCAGAAACACTCCAACCAA 58.601 50.000 0.00 0.00 0.00 3.67
2275 3803 1.963515 GGCAGAAACACTCCAACCAAT 59.036 47.619 0.00 0.00 0.00 3.16
2276 3804 2.029918 GGCAGAAACACTCCAACCAATC 60.030 50.000 0.00 0.00 0.00 2.67
2277 3805 2.622942 GCAGAAACACTCCAACCAATCA 59.377 45.455 0.00 0.00 0.00 2.57
2278 3806 3.068024 GCAGAAACACTCCAACCAATCAA 59.932 43.478 0.00 0.00 0.00 2.57
2279 3807 4.441356 GCAGAAACACTCCAACCAATCAAA 60.441 41.667 0.00 0.00 0.00 2.69
2280 3808 5.739935 GCAGAAACACTCCAACCAATCAAAT 60.740 40.000 0.00 0.00 0.00 2.32
2281 3809 5.922544 CAGAAACACTCCAACCAATCAAATC 59.077 40.000 0.00 0.00 0.00 2.17
2282 3810 4.503741 AACACTCCAACCAATCAAATCG 57.496 40.909 0.00 0.00 0.00 3.34
2283 3811 2.228822 ACACTCCAACCAATCAAATCGC 59.771 45.455 0.00 0.00 0.00 4.58
2284 3812 1.818674 ACTCCAACCAATCAAATCGCC 59.181 47.619 0.00 0.00 0.00 5.54
2305 3833 4.382901 GCCATGCAAATGGTGAAGGAAATA 60.383 41.667 8.13 0.00 43.53 1.40
2318 3846 4.726825 TGAAGGAAATAATGCCCTAGAGGT 59.273 41.667 0.00 0.00 38.26 3.85
2392 3920 8.902540 ATTCATGCTAGAATTGTATTAACCGA 57.097 30.769 0.00 0.00 34.70 4.69
2471 3999 8.467598 TCTACTTGACTAGCTCGTTAATCAAAT 58.532 33.333 0.00 0.00 0.00 2.32
2739 4267 2.703536 TGCTCTACAGGTGTCTCCAAAA 59.296 45.455 0.00 0.00 39.02 2.44
2740 4268 3.327757 TGCTCTACAGGTGTCTCCAAAAT 59.672 43.478 0.00 0.00 39.02 1.82
2766 4294 2.693591 TGTTGGGTTGGCGTATTTTGAA 59.306 40.909 0.00 0.00 0.00 2.69
2772 4300 7.406031 TGGGTTGGCGTATTTTGAAATTATA 57.594 32.000 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1820 2887 7.661847 AGTGGATCTGAGAAACTATTCGTTTTT 59.338 33.333 0.00 0.00 45.48 1.94
1836 2903 5.511373 CGCAATCCCTATTAAGTGGATCTGA 60.511 44.000 4.25 0.00 37.92 3.27
1969 3045 3.291584 GTCTTGGGGGATGAAGAAATCC 58.708 50.000 0.00 0.00 44.76 3.01
1978 3502 0.114168 TGTTTGGGTCTTGGGGGATG 59.886 55.000 0.00 0.00 0.00 3.51
1989 3513 0.185901 ATGGCTCACTGTGTTTGGGT 59.814 50.000 7.79 0.00 0.00 4.51
2001 3525 1.773856 TTTGGGTGTCGGATGGCTCA 61.774 55.000 0.00 0.00 0.00 4.26
2029 3553 3.414272 GCATCGGCACATGGAGAC 58.586 61.111 0.00 0.00 40.72 3.36
2039 3563 3.501828 TGTTCCATATGTAATGCATCGGC 59.498 43.478 0.00 0.00 38.94 5.54
2040 3564 5.687770 TTGTTCCATATGTAATGCATCGG 57.312 39.130 0.00 0.00 38.94 4.18
2121 3649 3.073062 CAGAGAAAAAGGGAACAGAGGGA 59.927 47.826 0.00 0.00 0.00 4.20
2122 3650 3.416156 CAGAGAAAAAGGGAACAGAGGG 58.584 50.000 0.00 0.00 0.00 4.30
2123 3651 2.816672 GCAGAGAAAAAGGGAACAGAGG 59.183 50.000 0.00 0.00 0.00 3.69
2124 3652 2.481952 CGCAGAGAAAAAGGGAACAGAG 59.518 50.000 0.00 0.00 0.00 3.35
2125 3653 2.494059 CGCAGAGAAAAAGGGAACAGA 58.506 47.619 0.00 0.00 0.00 3.41
2126 3654 1.068954 GCGCAGAGAAAAAGGGAACAG 60.069 52.381 0.30 0.00 0.00 3.16
2127 3655 0.951558 GCGCAGAGAAAAAGGGAACA 59.048 50.000 0.30 0.00 0.00 3.18
2128 3656 0.951558 TGCGCAGAGAAAAAGGGAAC 59.048 50.000 5.66 0.00 0.00 3.62
2129 3657 1.909700 ATGCGCAGAGAAAAAGGGAA 58.090 45.000 18.32 0.00 0.00 3.97
2130 3658 2.779755 TATGCGCAGAGAAAAAGGGA 57.220 45.000 18.32 0.00 0.00 4.20
2131 3659 3.009723 TCTTATGCGCAGAGAAAAAGGG 58.990 45.455 18.32 0.00 0.00 3.95
2132 3660 4.889832 ATCTTATGCGCAGAGAAAAAGG 57.110 40.909 24.43 5.54 0.00 3.11
2133 3661 7.201384 GGAAAAATCTTATGCGCAGAGAAAAAG 60.201 37.037 24.43 16.02 0.00 2.27
2134 3662 6.586082 GGAAAAATCTTATGCGCAGAGAAAAA 59.414 34.615 24.43 7.52 0.00 1.94
2135 3663 6.092748 GGAAAAATCTTATGCGCAGAGAAAA 58.907 36.000 24.43 10.10 0.00 2.29
2136 3664 5.640732 GGAAAAATCTTATGCGCAGAGAAA 58.359 37.500 24.43 12.24 0.00 2.52
2137 3665 4.201812 CGGAAAAATCTTATGCGCAGAGAA 60.202 41.667 24.43 14.28 0.00 2.87
2138 3666 3.309682 CGGAAAAATCTTATGCGCAGAGA 59.690 43.478 23.32 23.32 0.00 3.10
2139 3667 3.063997 ACGGAAAAATCTTATGCGCAGAG 59.936 43.478 18.32 16.54 0.00 3.35
2140 3668 3.006940 ACGGAAAAATCTTATGCGCAGA 58.993 40.909 18.32 9.06 0.00 4.26
2141 3669 3.405170 ACGGAAAAATCTTATGCGCAG 57.595 42.857 18.32 1.66 0.00 5.18
2142 3670 3.840890 AACGGAAAAATCTTATGCGCA 57.159 38.095 14.96 14.96 0.00 6.09
2143 3671 5.509605 AAAAACGGAAAAATCTTATGCGC 57.490 34.783 0.00 0.00 0.00 6.09
2162 3690 4.846779 AGCGCAAACTATTCAGGAAAAA 57.153 36.364 11.47 0.00 0.00 1.94
2163 3691 4.846779 AAGCGCAAACTATTCAGGAAAA 57.153 36.364 11.47 0.00 0.00 2.29
2164 3692 4.545610 CAAAGCGCAAACTATTCAGGAAA 58.454 39.130 11.47 0.00 0.00 3.13
2165 3693 3.611530 GCAAAGCGCAAACTATTCAGGAA 60.612 43.478 11.47 0.00 41.79 3.36
2166 3694 2.095263 GCAAAGCGCAAACTATTCAGGA 60.095 45.455 11.47 0.00 41.79 3.86
2167 3695 2.253603 GCAAAGCGCAAACTATTCAGG 58.746 47.619 11.47 0.00 41.79 3.86
2168 3696 2.095059 AGGCAAAGCGCAAACTATTCAG 60.095 45.455 11.47 0.00 45.17 3.02
2169 3697 1.885887 AGGCAAAGCGCAAACTATTCA 59.114 42.857 11.47 0.00 45.17 2.57
2170 3698 2.636768 AGGCAAAGCGCAAACTATTC 57.363 45.000 11.47 0.00 45.17 1.75
2171 3699 3.385193 AAAGGCAAAGCGCAAACTATT 57.615 38.095 11.47 0.00 45.17 1.73
2172 3700 3.385193 AAAAGGCAAAGCGCAAACTAT 57.615 38.095 11.47 0.00 45.17 2.12
2173 3701 2.880963 AAAAGGCAAAGCGCAAACTA 57.119 40.000 11.47 0.00 45.17 2.24
2174 3702 1.933181 GAAAAAGGCAAAGCGCAAACT 59.067 42.857 11.47 0.00 45.17 2.66
2175 3703 1.933181 AGAAAAAGGCAAAGCGCAAAC 59.067 42.857 11.47 0.00 45.17 2.93
2176 3704 2.200899 GAGAAAAAGGCAAAGCGCAAA 58.799 42.857 11.47 0.00 45.17 3.68
2177 3705 1.537990 GGAGAAAAAGGCAAAGCGCAA 60.538 47.619 11.47 0.00 45.17 4.85
2178 3706 0.031994 GGAGAAAAAGGCAAAGCGCA 59.968 50.000 11.47 0.00 45.17 6.09
2179 3707 0.667487 GGGAGAAAAAGGCAAAGCGC 60.667 55.000 0.00 0.00 41.28 5.92
2180 3708 0.673437 TGGGAGAAAAAGGCAAAGCG 59.327 50.000 0.00 0.00 0.00 4.68
2181 3709 1.270305 GGTGGGAGAAAAAGGCAAAGC 60.270 52.381 0.00 0.00 0.00 3.51
2182 3710 2.036346 CAGGTGGGAGAAAAAGGCAAAG 59.964 50.000 0.00 0.00 0.00 2.77
2183 3711 2.038659 CAGGTGGGAGAAAAAGGCAAA 58.961 47.619 0.00 0.00 0.00 3.68
2184 3712 1.063266 ACAGGTGGGAGAAAAAGGCAA 60.063 47.619 0.00 0.00 0.00 4.52
2185 3713 0.555769 ACAGGTGGGAGAAAAAGGCA 59.444 50.000 0.00 0.00 0.00 4.75
2186 3714 1.704641 AACAGGTGGGAGAAAAAGGC 58.295 50.000 0.00 0.00 0.00 4.35
2187 3715 2.628178 GGAAACAGGTGGGAGAAAAAGG 59.372 50.000 0.00 0.00 0.00 3.11
2188 3716 3.295973 TGGAAACAGGTGGGAGAAAAAG 58.704 45.455 0.00 0.00 35.01 2.27
2189 3717 3.390175 TGGAAACAGGTGGGAGAAAAA 57.610 42.857 0.00 0.00 35.01 1.94
2190 3718 3.390175 TTGGAAACAGGTGGGAGAAAA 57.610 42.857 0.00 0.00 44.54 2.29
2191 3719 3.230134 CATTGGAAACAGGTGGGAGAAA 58.770 45.455 0.00 0.00 44.54 2.52
2192 3720 2.490718 CCATTGGAAACAGGTGGGAGAA 60.491 50.000 0.00 0.00 44.54 2.87
2193 3721 1.075374 CCATTGGAAACAGGTGGGAGA 59.925 52.381 0.00 0.00 44.54 3.71
2194 3722 1.203050 ACCATTGGAAACAGGTGGGAG 60.203 52.381 10.37 0.00 46.44 4.30
2195 3723 0.856982 ACCATTGGAAACAGGTGGGA 59.143 50.000 10.37 0.00 46.44 4.37
2196 3724 2.167662 GTACCATTGGAAACAGGTGGG 58.832 52.381 10.37 0.00 46.44 4.61
2212 3740 4.487412 CGACAGACGCGGGGTACC 62.487 72.222 12.47 2.17 41.72 3.34
2235 3763 0.868406 GCTGCCAGGATAACGCATAC 59.132 55.000 0.00 0.00 0.00 2.39
2236 3764 0.599991 CGCTGCCAGGATAACGCATA 60.600 55.000 0.00 0.00 0.00 3.14
2237 3765 1.889105 CGCTGCCAGGATAACGCAT 60.889 57.895 0.00 0.00 0.00 4.73
2238 3766 2.511373 CGCTGCCAGGATAACGCA 60.511 61.111 0.00 0.00 0.00 5.24
2239 3767 3.272334 CCGCTGCCAGGATAACGC 61.272 66.667 0.00 0.00 0.00 4.84
2240 3768 3.272334 GCCGCTGCCAGGATAACG 61.272 66.667 0.00 0.00 0.00 3.18
2241 3769 2.124736 TGCCGCTGCCAGGATAAC 60.125 61.111 0.00 0.00 36.33 1.89
2242 3770 1.909459 TTCTGCCGCTGCCAGGATAA 61.909 55.000 0.00 0.00 36.33 1.75
2243 3771 1.909459 TTTCTGCCGCTGCCAGGATA 61.909 55.000 0.00 0.00 36.33 2.59
2244 3772 3.272364 TTTCTGCCGCTGCCAGGAT 62.272 57.895 0.00 0.00 36.33 3.24
2245 3773 3.952508 TTTCTGCCGCTGCCAGGA 61.953 61.111 0.00 0.00 36.33 3.86
2246 3774 3.741476 GTTTCTGCCGCTGCCAGG 61.741 66.667 0.00 0.00 36.33 4.45
2247 3775 2.979676 TGTTTCTGCCGCTGCCAG 60.980 61.111 0.00 0.00 36.33 4.85
2248 3776 3.286751 GTGTTTCTGCCGCTGCCA 61.287 61.111 0.00 0.00 36.33 4.92
2249 3777 2.970974 GAGTGTTTCTGCCGCTGCC 61.971 63.158 0.00 0.00 36.33 4.85
2250 3778 2.558313 GAGTGTTTCTGCCGCTGC 59.442 61.111 0.00 0.00 38.26 5.25
2251 3779 1.165907 TTGGAGTGTTTCTGCCGCTG 61.166 55.000 0.00 0.00 33.42 5.18
2252 3780 1.148273 TTGGAGTGTTTCTGCCGCT 59.852 52.632 0.00 0.00 33.42 5.52
2253 3781 1.282875 GTTGGAGTGTTTCTGCCGC 59.717 57.895 0.00 0.00 33.42 6.53
2254 3782 0.817634 TGGTTGGAGTGTTTCTGCCG 60.818 55.000 0.00 0.00 33.42 5.69
2255 3783 1.398692 TTGGTTGGAGTGTTTCTGCC 58.601 50.000 0.00 0.00 33.42 4.85
2256 3784 2.622942 TGATTGGTTGGAGTGTTTCTGC 59.377 45.455 0.00 0.00 35.00 4.26
2257 3785 4.916983 TTGATTGGTTGGAGTGTTTCTG 57.083 40.909 0.00 0.00 0.00 3.02
2258 3786 5.278463 CGATTTGATTGGTTGGAGTGTTTCT 60.278 40.000 0.00 0.00 0.00 2.52
2259 3787 4.917415 CGATTTGATTGGTTGGAGTGTTTC 59.083 41.667 0.00 0.00 0.00 2.78
2260 3788 4.795962 GCGATTTGATTGGTTGGAGTGTTT 60.796 41.667 0.00 0.00 0.00 2.83
2261 3789 3.305335 GCGATTTGATTGGTTGGAGTGTT 60.305 43.478 0.00 0.00 0.00 3.32
2262 3790 2.228822 GCGATTTGATTGGTTGGAGTGT 59.771 45.455 0.00 0.00 0.00 3.55
2263 3791 2.415893 GGCGATTTGATTGGTTGGAGTG 60.416 50.000 0.00 0.00 0.00 3.51
2264 3792 1.818674 GGCGATTTGATTGGTTGGAGT 59.181 47.619 0.00 0.00 0.00 3.85
2265 3793 1.818060 TGGCGATTTGATTGGTTGGAG 59.182 47.619 0.00 0.00 0.00 3.86
2266 3794 1.916506 TGGCGATTTGATTGGTTGGA 58.083 45.000 0.00 0.00 0.00 3.53
2267 3795 2.542597 CATGGCGATTTGATTGGTTGG 58.457 47.619 0.00 0.00 0.00 3.77
2268 3796 1.928503 GCATGGCGATTTGATTGGTTG 59.071 47.619 0.00 0.00 0.00 3.77
2269 3797 1.549620 TGCATGGCGATTTGATTGGTT 59.450 42.857 0.00 0.00 0.00 3.67
2270 3798 1.184431 TGCATGGCGATTTGATTGGT 58.816 45.000 0.00 0.00 0.00 3.67
2271 3799 2.296831 TTGCATGGCGATTTGATTGG 57.703 45.000 0.00 0.00 0.00 3.16
2272 3800 3.001838 CCATTTGCATGGCGATTTGATTG 59.998 43.478 0.00 0.00 43.95 2.67
2273 3801 3.199677 CCATTTGCATGGCGATTTGATT 58.800 40.909 0.00 0.00 43.95 2.57
2274 3802 2.828877 CCATTTGCATGGCGATTTGAT 58.171 42.857 0.00 0.00 43.95 2.57
2275 3803 2.296831 CCATTTGCATGGCGATTTGA 57.703 45.000 0.00 0.00 43.95 2.69
2284 3812 6.238266 GCATTATTTCCTTCACCATTTGCATG 60.238 38.462 0.00 0.00 0.00 4.06
2471 3999 7.291416 TGTCTATGGCTAGGAAACATAACCATA 59.709 37.037 0.00 0.00 37.58 2.74
2739 4267 1.989706 ACGCCAACCCAACAAGTAAT 58.010 45.000 0.00 0.00 0.00 1.89
2740 4268 2.634815 TACGCCAACCCAACAAGTAA 57.365 45.000 0.00 0.00 0.00 2.24
2766 4294 8.335356 CGACAATCGGAGTGACAAATTATAATT 58.665 33.333 12.93 4.81 36.00 1.40


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

AutoCloner maintained by Alex Coulton.