Multiple sequence alignment - TraesCS7A01G090800

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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 TraesCS7A01G090800 chr7A 100.000 4378 0 0 1 4378 55354999 55359376 0.000000e+00 8085
1 TraesCS7A01G090800 chr7A 95.712 793 34 0 1 793 96003029 96003821 0.000000e+00 1277
2 TraesCS7A01G090800 chr7A 95.455 792 36 0 1 792 653373135 653372344 0.000000e+00 1264
3 TraesCS7A01G090800 chr7A 94.823 792 41 0 1 792 95997464 95998255 0.000000e+00 1236
4 TraesCS7A01G090800 chr7A 98.198 111 2 0 4268 4378 653013326 653013216 1.240000e-45 195
5 TraesCS7A01G090800 chr4A 93.899 2819 93 23 867 3662 667848823 667851585 0.000000e+00 4180
6 TraesCS7A01G090800 chr4A 94.823 792 41 0 1 792 11783587 11784378 0.000000e+00 1236
7 TraesCS7A01G090800 chr4A 94.710 794 42 0 1 794 33030247 33029454 0.000000e+00 1234
8 TraesCS7A01G090800 chr4A 92.620 542 16 9 3697 4225 667851585 667852115 0.000000e+00 758
9 TraesCS7A01G090800 chr7D 95.525 1944 54 11 2227 4151 52842462 52840533 0.000000e+00 3077
10 TraesCS7A01G090800 chr7D 93.548 1395 55 9 795 2185 52844124 52842761 0.000000e+00 2045
11 TraesCS7A01G090800 chr7D 97.436 78 2 0 4148 4225 52840453 52840376 2.750000e-27 134
12 TraesCS7A01G090800 chr3A 95.859 797 33 0 1 797 701931020 701931816 0.000000e+00 1290
13 TraesCS7A01G090800 chr3A 95.202 792 38 0 1 792 510173001 510173792 0.000000e+00 1253
14 TraesCS7A01G090800 chr3A 94.949 792 40 0 1 792 743944936 743945727 0.000000e+00 1242
15 TraesCS7A01G090800 chr5A 94.697 792 42 0 1 792 379962686 379961895 0.000000e+00 1230
16 TraesCS7A01G090800 chr2D 80.747 1018 170 12 1138 2130 156549213 156550229 0.000000e+00 771
17 TraesCS7A01G090800 chr2D 81.549 607 89 14 2443 3040 156550513 156551105 3.060000e-131 479
18 TraesCS7A01G090800 chr2A 80.255 1018 174 13 1138 2130 166239965 166240980 0.000000e+00 741
19 TraesCS7A01G090800 chr7B 98.261 115 2 0 4264 4378 477974311 477974197 7.420000e-48 202
20 TraesCS7A01G090800 chr3B 98.261 115 2 0 4264 4378 447018225 447018339 7.420000e-48 202
21 TraesCS7A01G090800 chr3B 97.297 111 3 0 4268 4378 685070744 685070634 5.780000e-44 189
22 TraesCS7A01G090800 chr3B 95.690 116 4 1 4264 4378 4304693 4304808 7.480000e-43 185
23 TraesCS7A01G090800 chr3B 96.396 111 4 0 4268 4378 415899672 415899782 2.690000e-42 183
24 TraesCS7A01G090800 chr2B 98.246 114 2 0 4265 4378 677043418 677043531 2.670000e-47 200
25 TraesCS7A01G090800 chr2B 80.952 168 30 2 2579 2745 109875848 109875682 9.880000e-27 132
26 TraesCS7A01G090800 chr1B 98.246 114 2 0 4265 4378 131779215 131779328 2.670000e-47 200
27 TraesCS7A01G090800 chr5B 99.091 110 1 0 4269 4378 692518274 692518383 9.600000e-47 198
28 TraesCS7A01G090800 chrUn 80.952 168 30 2 2579 2745 235538565 235538731 9.880000e-27 132


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 TraesCS7A01G090800 chr7A 55354999 55359376 4377 False 8085 8085 100.0000 1 4378 1 chr7A.!!$F1 4377
1 TraesCS7A01G090800 chr7A 96003029 96003821 792 False 1277 1277 95.7120 1 793 1 chr7A.!!$F3 792
2 TraesCS7A01G090800 chr7A 653372344 653373135 791 True 1264 1264 95.4550 1 792 1 chr7A.!!$R2 791
3 TraesCS7A01G090800 chr7A 95997464 95998255 791 False 1236 1236 94.8230 1 792 1 chr7A.!!$F2 791
4 TraesCS7A01G090800 chr4A 667848823 667852115 3292 False 2469 4180 93.2595 867 4225 2 chr4A.!!$F2 3358
5 TraesCS7A01G090800 chr4A 11783587 11784378 791 False 1236 1236 94.8230 1 792 1 chr4A.!!$F1 791
6 TraesCS7A01G090800 chr4A 33029454 33030247 793 True 1234 1234 94.7100 1 794 1 chr4A.!!$R1 793
7 TraesCS7A01G090800 chr7D 52840376 52844124 3748 True 1752 3077 95.5030 795 4225 3 chr7D.!!$R1 3430
8 TraesCS7A01G090800 chr3A 701931020 701931816 796 False 1290 1290 95.8590 1 797 1 chr3A.!!$F2 796
9 TraesCS7A01G090800 chr3A 510173001 510173792 791 False 1253 1253 95.2020 1 792 1 chr3A.!!$F1 791
10 TraesCS7A01G090800 chr3A 743944936 743945727 791 False 1242 1242 94.9490 1 792 1 chr3A.!!$F3 791
11 TraesCS7A01G090800 chr5A 379961895 379962686 791 True 1230 1230 94.6970 1 792 1 chr5A.!!$R1 791
12 TraesCS7A01G090800 chr2D 156549213 156551105 1892 False 625 771 81.1480 1138 3040 2 chr2D.!!$F1 1902
13 TraesCS7A01G090800 chr2A 166239965 166240980 1015 False 741 741 80.2550 1138 2130 1 chr2A.!!$F1 992

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
910 912 0.317020 GTGCAAGAACTCACCGCAAC 60.317 55.000 0.00 0.0 33.76 4.17 F
1030 1051 0.338814 TTCCTCCTACTCCCAGTCCC 59.661 60.000 0.00 0.0 0.00 4.46 F
1062 1083 0.964358 GCAACCATCTGAAGCAGGCT 60.964 55.000 0.00 0.0 31.51 4.58 F
1721 1745 1.004044 CCCCACATATCATCTGCCTCC 59.996 57.143 0.00 0.0 0.00 4.30 F
2392 2762 1.344065 TTGAGTAGTTTGCCGGGAGA 58.656 50.000 2.18 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 2883 2.095853 CACGGTGAACCTACATGCAATC 59.904 50.000 0.74 0.00 0.0 2.67 R
2989 3367 2.264794 GTGAGTCGGCCGGTGATT 59.735 61.111 27.83 1.78 0.0 2.57 R
2997 3375 2.432628 CGAGGTTGGTGAGTCGGC 60.433 66.667 0.00 0.00 0.0 5.54 R
3251 3630 2.735772 CCTACACGGCAGCCCATCT 61.736 63.158 5.63 0.00 0.0 2.90 R
4255 4733 0.107459 GAGGGCTGGATGTGTTCTCC 60.107 60.000 0.00 0.00 0.0 3.71 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
61 62 1.681264 CGGGAGCTGGAAAGTTTTTGT 59.319 47.619 0.00 0.00 0.00 2.83
223 224 1.141053 ACGCACCAGAACTTCTCCTTT 59.859 47.619 0.00 0.00 0.00 3.11
240 241 1.469335 TTTCTCTCGCCACCGGTTCT 61.469 55.000 2.97 0.00 34.56 3.01
275 276 1.330655 GCTGTCTTCCTCATCCCGGA 61.331 60.000 0.73 0.00 0.00 5.14
281 282 1.334384 TTCCTCATCCCGGATTGCGA 61.334 55.000 0.73 0.00 0.00 5.10
365 366 5.321927 GAGAAGGGTGATAAGGTTTTTGGA 58.678 41.667 0.00 0.00 0.00 3.53
484 485 1.657751 CTCCTCGACGACATGGCTGA 61.658 60.000 0.00 0.00 0.00 4.26
513 514 1.302832 GACCCCAAGTCCAGTGCTG 60.303 63.158 0.00 0.00 39.84 4.41
561 562 8.816894 TGTTCTTCTTTCTGTTAGATATCCTGT 58.183 33.333 0.00 0.00 0.00 4.00
588 589 5.008980 AGTTTCTCGTACTAGTACTTGCCT 58.991 41.667 26.36 13.67 34.04 4.75
657 658 9.686683 TGTCTGCTATAGATATGATAAGCTACA 57.313 33.333 3.21 0.00 37.83 2.74
797 798 5.233957 TGCTCATATTTCCAACATGTTCG 57.766 39.130 8.48 1.70 0.00 3.95
798 799 4.699735 TGCTCATATTTCCAACATGTTCGT 59.300 37.500 8.48 0.00 0.00 3.85
799 800 5.030295 GCTCATATTTCCAACATGTTCGTG 58.970 41.667 8.48 0.00 0.00 4.35
800 801 5.559427 TCATATTTCCAACATGTTCGTGG 57.441 39.130 8.48 8.50 0.00 4.94
801 802 2.723124 ATTTCCAACATGTTCGTGGC 57.277 45.000 8.48 0.00 0.00 5.01
802 803 1.686355 TTTCCAACATGTTCGTGGCT 58.314 45.000 8.48 0.00 0.00 4.75
803 804 1.686355 TTCCAACATGTTCGTGGCTT 58.314 45.000 8.48 0.00 0.00 4.35
804 805 2.552599 TCCAACATGTTCGTGGCTTA 57.447 45.000 8.48 0.00 0.00 3.09
805 806 2.852449 TCCAACATGTTCGTGGCTTAA 58.148 42.857 8.48 0.00 0.00 1.85
806 807 3.215151 TCCAACATGTTCGTGGCTTAAA 58.785 40.909 8.48 0.00 0.00 1.52
807 808 3.632604 TCCAACATGTTCGTGGCTTAAAA 59.367 39.130 8.48 0.00 0.00 1.52
808 809 4.279671 TCCAACATGTTCGTGGCTTAAAAT 59.720 37.500 8.48 0.00 0.00 1.82
809 810 4.987912 CCAACATGTTCGTGGCTTAAAATT 59.012 37.500 8.48 0.00 0.00 1.82
810 811 5.465056 CCAACATGTTCGTGGCTTAAAATTT 59.535 36.000 8.48 0.00 0.00 1.82
811 812 6.642950 CCAACATGTTCGTGGCTTAAAATTTA 59.357 34.615 8.48 0.00 0.00 1.40
812 813 7.358848 CCAACATGTTCGTGGCTTAAAATTTAC 60.359 37.037 8.48 0.00 0.00 2.01
824 825 5.279256 GCTTAAAATTTACCCACTTCTGCCA 60.279 40.000 0.00 0.00 0.00 4.92
832 833 1.067354 CCCACTTCTGCCAAGCATTTC 60.067 52.381 0.00 0.00 38.13 2.17
853 854 2.791253 TCCTGGAGGGAGCAACAAT 58.209 52.632 0.00 0.00 39.58 2.71
854 855 1.075601 TCCTGGAGGGAGCAACAATT 58.924 50.000 0.00 0.00 39.58 2.32
855 856 2.274542 TCCTGGAGGGAGCAACAATTA 58.725 47.619 0.00 0.00 39.58 1.40
856 857 2.647299 TCCTGGAGGGAGCAACAATTAA 59.353 45.455 0.00 0.00 39.58 1.40
910 912 0.317020 GTGCAAGAACTCACCGCAAC 60.317 55.000 0.00 0.00 33.76 4.17
911 913 0.463654 TGCAAGAACTCACCGCAACT 60.464 50.000 0.00 0.00 0.00 3.16
912 914 0.663153 GCAAGAACTCACCGCAACTT 59.337 50.000 0.00 0.00 0.00 2.66
967 977 1.764054 CATCCTCCCTCCGCCTTCT 60.764 63.158 0.00 0.00 0.00 2.85
971 981 1.519719 CTCCCTCCGCCTTCTCTTG 59.480 63.158 0.00 0.00 0.00 3.02
972 982 2.124942 CCCTCCGCCTTCTCTTGC 60.125 66.667 0.00 0.00 0.00 4.01
978 988 2.273776 GCCTTCTCTTGCTCCCCC 59.726 66.667 0.00 0.00 0.00 5.40
999 1009 1.997606 GCAATCTGCAATGCAAACCTC 59.002 47.619 9.92 0.00 44.26 3.85
1016 1037 3.676093 ACCTCCAACGAATTTCTTCCTC 58.324 45.455 0.00 0.00 0.00 3.71
1019 1040 4.081087 CCTCCAACGAATTTCTTCCTCCTA 60.081 45.833 0.00 0.00 0.00 2.94
1020 1041 4.828829 TCCAACGAATTTCTTCCTCCTAC 58.171 43.478 0.00 0.00 0.00 3.18
1021 1042 4.530946 TCCAACGAATTTCTTCCTCCTACT 59.469 41.667 0.00 0.00 0.00 2.57
1022 1043 4.870991 CCAACGAATTTCTTCCTCCTACTC 59.129 45.833 0.00 0.00 0.00 2.59
1023 1044 4.739587 ACGAATTTCTTCCTCCTACTCC 57.260 45.455 0.00 0.00 0.00 3.85
1024 1045 3.451540 ACGAATTTCTTCCTCCTACTCCC 59.548 47.826 0.00 0.00 0.00 4.30
1025 1046 3.451178 CGAATTTCTTCCTCCTACTCCCA 59.549 47.826 0.00 0.00 0.00 4.37
1026 1047 4.442192 CGAATTTCTTCCTCCTACTCCCAG 60.442 50.000 0.00 0.00 0.00 4.45
1027 1048 3.562108 TTTCTTCCTCCTACTCCCAGT 57.438 47.619 0.00 0.00 0.00 4.00
1028 1049 2.830651 TCTTCCTCCTACTCCCAGTC 57.169 55.000 0.00 0.00 0.00 3.51
1029 1050 1.288335 TCTTCCTCCTACTCCCAGTCC 59.712 57.143 0.00 0.00 0.00 3.85
1030 1051 0.338814 TTCCTCCTACTCCCAGTCCC 59.661 60.000 0.00 0.00 0.00 4.46
1062 1083 0.964358 GCAACCATCTGAAGCAGGCT 60.964 55.000 0.00 0.00 31.51 4.58
1064 1085 2.715046 CAACCATCTGAAGCAGGCTAA 58.285 47.619 0.00 0.00 31.51 3.09
1066 1087 1.065126 ACCATCTGAAGCAGGCTAACC 60.065 52.381 0.00 0.00 31.51 2.85
1084 1105 1.680105 CCGTTCGACGAAATGTCCCG 61.680 60.000 12.67 10.21 46.05 5.14
1490 1514 2.715624 GAAATGTGGATCCGCGCC 59.284 61.111 20.16 5.66 0.00 6.53
1592 1616 1.079543 CGTCTCCTGCCACCTCAAG 60.080 63.158 0.00 0.00 0.00 3.02
1721 1745 1.004044 CCCCACATATCATCTGCCTCC 59.996 57.143 0.00 0.00 0.00 4.30
2276 2641 2.985896 TGCACTCTAATACCAACAGCC 58.014 47.619 0.00 0.00 0.00 4.85
2392 2762 1.344065 TTGAGTAGTTTGCCGGGAGA 58.656 50.000 2.18 0.00 0.00 3.71
2497 2869 9.520204 ACTTAATCAGAAACAAACATTCACTTG 57.480 29.630 0.00 0.00 0.00 3.16
2507 2883 5.521010 ACAAACATTCACTTGCAAATGTCTG 59.479 36.000 13.42 12.60 43.45 3.51
2525 2901 3.375299 GTCTGATTGCATGTAGGTTCACC 59.625 47.826 0.00 0.00 0.00 4.02
2587 2963 4.281435 TCACTTGTGTTCCGTATGAAGGTA 59.719 41.667 0.46 0.00 32.37 3.08
2779 3155 5.824904 ACTGCTTATATTTTGAGCTGTGG 57.175 39.130 0.00 0.00 43.76 4.17
2881 3259 1.745087 AGGGTACATCATTTGCTTGCG 59.255 47.619 0.00 0.00 0.00 4.85
2989 3367 5.282055 AGCGATGGAAAAGATATCTGTCA 57.718 39.130 5.86 3.30 0.00 3.58
2997 3375 5.237344 GGAAAAGATATCTGTCAATCACCGG 59.763 44.000 5.86 0.00 0.00 5.28
3031 3409 4.748892 ACCTCGTGAGTCATGTATTCTTG 58.251 43.478 12.07 0.00 0.00 3.02
3192 3571 4.488126 TTGTTTTTCGAGCTTGATCTGG 57.512 40.909 3.98 0.00 0.00 3.86
3251 3630 0.326595 TTCCTTGGCCATAAGACGCA 59.673 50.000 6.09 0.00 0.00 5.24
3301 3680 3.746045 TGGCGGTAAGATCTTACATCC 57.254 47.619 35.10 32.11 45.32 3.51
3340 3719 4.959596 TCTACTGTAACTCTGTAAGGCG 57.040 45.455 0.00 0.00 31.83 5.52
3468 3848 6.426937 TGTGCATCTCCTAAAGTTACACTTTC 59.573 38.462 5.15 0.00 44.47 2.62
3469 3849 6.426937 GTGCATCTCCTAAAGTTACACTTTCA 59.573 38.462 5.15 0.00 44.47 2.69
3470 3850 6.426937 TGCATCTCCTAAAGTTACACTTTCAC 59.573 38.462 5.15 0.00 44.47 3.18
3586 3968 6.256321 CCAAACTGAACAACAAGAAGGAAATG 59.744 38.462 0.00 0.00 0.00 2.32
3592 3974 7.202526 TGAACAACAAGAAGGAAATGATTGAC 58.797 34.615 0.00 0.00 0.00 3.18
3675 4057 4.768968 AGTAAAATCTTCCTGCAGCACATT 59.231 37.500 8.66 0.37 0.00 2.71
3676 4058 5.945784 AGTAAAATCTTCCTGCAGCACATTA 59.054 36.000 8.66 0.00 0.00 1.90
3677 4059 5.927281 AAAATCTTCCTGCAGCACATTAT 57.073 34.783 8.66 0.00 0.00 1.28
3678 4060 5.927281 AAATCTTCCTGCAGCACATTATT 57.073 34.783 8.66 0.00 0.00 1.40
3690 4072 6.204688 TGCAGCACATTATTACTGTTATAGGC 59.795 38.462 0.00 0.00 32.65 3.93
3691 4073 6.348540 GCAGCACATTATTACTGTTATAGGCC 60.349 42.308 0.00 0.00 32.65 5.19
3879 4261 2.749621 GTGTGCCTCTATGAAACCCTTG 59.250 50.000 0.00 0.00 0.00 3.61
3894 4276 2.036089 ACCCTTGAAAGTCGAGACTGTC 59.964 50.000 14.79 14.79 44.18 3.51
4225 4703 3.914426 AGTACCCCATACTTGAGCTTG 57.086 47.619 0.00 0.00 41.71 4.01
4226 4704 3.450904 AGTACCCCATACTTGAGCTTGA 58.549 45.455 0.00 0.00 41.71 3.02
4227 4705 3.452627 AGTACCCCATACTTGAGCTTGAG 59.547 47.826 0.00 0.00 41.71 3.02
4228 4706 1.065126 ACCCCATACTTGAGCTTGAGC 60.065 52.381 0.00 0.00 42.49 4.26
4229 4707 1.065199 CCCCATACTTGAGCTTGAGCA 60.065 52.381 5.70 0.00 45.16 4.26
4230 4708 2.012673 CCCATACTTGAGCTTGAGCAC 58.987 52.381 5.70 0.00 45.16 4.40
4231 4709 2.616256 CCCATACTTGAGCTTGAGCACA 60.616 50.000 5.70 2.18 45.16 4.57
4232 4710 3.276857 CCATACTTGAGCTTGAGCACAT 58.723 45.455 5.70 0.00 45.16 3.21
4233 4711 3.064958 CCATACTTGAGCTTGAGCACATG 59.935 47.826 5.70 9.73 45.16 3.21
4234 4712 0.879765 ACTTGAGCTTGAGCACATGC 59.120 50.000 13.04 13.04 45.16 4.06
4252 4730 7.086376 GCACATGCTTTTGAGGTTATATATGG 58.914 38.462 0.00 0.00 38.21 2.74
4253 4731 7.255590 GCACATGCTTTTGAGGTTATATATGGT 60.256 37.037 0.00 0.00 38.21 3.55
4254 4732 9.283768 CACATGCTTTTGAGGTTATATATGGTA 57.716 33.333 0.00 0.00 0.00 3.25
4255 4733 9.507329 ACATGCTTTTGAGGTTATATATGGTAG 57.493 33.333 0.00 0.00 0.00 3.18
4256 4734 8.950210 CATGCTTTTGAGGTTATATATGGTAGG 58.050 37.037 0.00 0.00 0.00 3.18
4257 4735 8.270137 TGCTTTTGAGGTTATATATGGTAGGA 57.730 34.615 0.00 0.00 0.00 2.94
4258 4736 8.375506 TGCTTTTGAGGTTATATATGGTAGGAG 58.624 37.037 0.00 0.00 0.00 3.69
4259 4737 8.594550 GCTTTTGAGGTTATATATGGTAGGAGA 58.405 37.037 0.00 0.00 0.00 3.71
4262 4740 9.442062 TTTGAGGTTATATATGGTAGGAGAACA 57.558 33.333 0.00 0.00 0.00 3.18
4263 4741 8.418597 TGAGGTTATATATGGTAGGAGAACAC 57.581 38.462 0.00 0.00 0.00 3.32
4264 4742 8.008332 TGAGGTTATATATGGTAGGAGAACACA 58.992 37.037 0.00 0.00 0.00 3.72
4265 4743 8.974292 AGGTTATATATGGTAGGAGAACACAT 57.026 34.615 0.00 0.00 0.00 3.21
4266 4744 9.036980 AGGTTATATATGGTAGGAGAACACATC 57.963 37.037 0.00 0.00 0.00 3.06
4267 4745 8.258708 GGTTATATATGGTAGGAGAACACATCC 58.741 40.741 0.00 0.00 37.07 3.51
4268 4746 8.812972 GTTATATATGGTAGGAGAACACATCCA 58.187 37.037 0.00 0.00 39.47 3.41
4269 4747 5.815233 ATATGGTAGGAGAACACATCCAG 57.185 43.478 0.00 0.00 39.47 3.86
4270 4748 1.555075 TGGTAGGAGAACACATCCAGC 59.445 52.381 0.00 0.00 39.47 4.85
4271 4749 1.134371 GGTAGGAGAACACATCCAGCC 60.134 57.143 0.00 0.00 39.47 4.85
4272 4750 1.134371 GTAGGAGAACACATCCAGCCC 60.134 57.143 0.00 0.00 39.47 5.19
4273 4751 0.548682 AGGAGAACACATCCAGCCCT 60.549 55.000 0.00 0.00 39.47 5.19
4274 4752 0.107459 GGAGAACACATCCAGCCCTC 60.107 60.000 0.00 0.00 36.79 4.30
4275 4753 0.460987 GAGAACACATCCAGCCCTCG 60.461 60.000 0.00 0.00 0.00 4.63
4276 4754 2.045926 AACACATCCAGCCCTCGC 60.046 61.111 0.00 0.00 0.00 5.03
4277 4755 3.958147 AACACATCCAGCCCTCGCG 62.958 63.158 0.00 0.00 41.18 5.87
4278 4756 4.457496 CACATCCAGCCCTCGCGT 62.457 66.667 5.77 0.00 41.18 6.01
4279 4757 4.148825 ACATCCAGCCCTCGCGTC 62.149 66.667 5.77 0.00 41.18 5.19
4280 4758 4.899239 CATCCAGCCCTCGCGTCC 62.899 72.222 5.77 0.00 41.18 4.79
4345 4823 4.329545 GCGCCCTCCTTCCACACA 62.330 66.667 0.00 0.00 0.00 3.72
4346 4824 2.358737 CGCCCTCCTTCCACACAC 60.359 66.667 0.00 0.00 0.00 3.82
4347 4825 2.883828 CGCCCTCCTTCCACACACT 61.884 63.158 0.00 0.00 0.00 3.55
4348 4826 1.003233 GCCCTCCTTCCACACACTC 60.003 63.158 0.00 0.00 0.00 3.51
4349 4827 1.679898 CCCTCCTTCCACACACTCC 59.320 63.158 0.00 0.00 0.00 3.85
4350 4828 1.679898 CCTCCTTCCACACACTCCC 59.320 63.158 0.00 0.00 0.00 4.30
4351 4829 1.679898 CTCCTTCCACACACTCCCC 59.320 63.158 0.00 0.00 0.00 4.81
4352 4830 0.838122 CTCCTTCCACACACTCCCCT 60.838 60.000 0.00 0.00 0.00 4.79
4353 4831 0.836400 TCCTTCCACACACTCCCCTC 60.836 60.000 0.00 0.00 0.00 4.30
4354 4832 1.293498 CTTCCACACACTCCCCTCG 59.707 63.158 0.00 0.00 0.00 4.63
4355 4833 2.788191 CTTCCACACACTCCCCTCGC 62.788 65.000 0.00 0.00 0.00 5.03
4356 4834 4.394712 CCACACACTCCCCTCGCC 62.395 72.222 0.00 0.00 0.00 5.54
4357 4835 4.742201 CACACACTCCCCTCGCCG 62.742 72.222 0.00 0.00 0.00 6.46
4359 4837 4.436998 CACACTCCCCTCGCCGTC 62.437 72.222 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 6.199531 GCGTTCGTATTCAATATCCACTACAA 59.800 38.462 0.00 0.00 0.00 2.41
223 224 0.609957 TTAGAACCGGTGGCGAGAGA 60.610 55.000 8.52 0.00 0.00 3.10
281 282 4.969196 CTGACCTGCGGTGCACGT 62.969 66.667 11.45 1.88 46.52 4.49
297 298 0.252103 TTTCGGAGGCCTACTGTCCT 60.252 55.000 14.69 0.00 34.90 3.85
484 485 1.537889 TTGGGGTCGGTGTCCTCAT 60.538 57.895 0.00 0.00 35.20 2.90
513 514 1.229428 TACAAGACAACAGCAGCAGC 58.771 50.000 0.00 0.00 42.56 5.25
561 562 6.567321 GCAAGTACTAGTACGAGAAACTGTGA 60.567 42.308 23.87 0.00 40.80 3.58
674 675 7.382898 GTTCTGACAGAGAGAAGGAAAATAGT 58.617 38.462 5.10 0.00 30.01 2.12
798 799 5.279256 GCAGAAGTGGGTAAATTTTAAGCCA 60.279 40.000 7.63 7.63 40.82 4.75
799 800 5.168569 GCAGAAGTGGGTAAATTTTAAGCC 58.831 41.667 0.00 0.00 0.00 4.35
800 801 5.168569 GGCAGAAGTGGGTAAATTTTAAGC 58.831 41.667 0.00 0.00 0.00 3.09
801 802 6.339587 TGGCAGAAGTGGGTAAATTTTAAG 57.660 37.500 0.00 0.00 0.00 1.85
802 803 6.732896 TTGGCAGAAGTGGGTAAATTTTAA 57.267 33.333 0.00 0.00 0.00 1.52
803 804 5.279256 GCTTGGCAGAAGTGGGTAAATTTTA 60.279 40.000 0.00 0.00 0.00 1.52
804 805 4.503123 GCTTGGCAGAAGTGGGTAAATTTT 60.503 41.667 0.00 0.00 0.00 1.82
805 806 3.006859 GCTTGGCAGAAGTGGGTAAATTT 59.993 43.478 0.00 0.00 0.00 1.82
806 807 2.562738 GCTTGGCAGAAGTGGGTAAATT 59.437 45.455 0.00 0.00 0.00 1.82
807 808 2.171003 GCTTGGCAGAAGTGGGTAAAT 58.829 47.619 0.00 0.00 0.00 1.40
808 809 1.133637 TGCTTGGCAGAAGTGGGTAAA 60.134 47.619 0.00 0.00 33.32 2.01
809 810 0.476338 TGCTTGGCAGAAGTGGGTAA 59.524 50.000 0.00 0.00 33.32 2.85
810 811 0.698238 ATGCTTGGCAGAAGTGGGTA 59.302 50.000 0.00 0.00 43.65 3.69
811 812 0.178953 AATGCTTGGCAGAAGTGGGT 60.179 50.000 0.00 0.00 43.65 4.51
812 813 0.971386 AAATGCTTGGCAGAAGTGGG 59.029 50.000 0.00 0.00 43.65 4.61
824 825 1.005215 CCCTCCAGGAGTGAAATGCTT 59.995 52.381 15.86 0.00 38.24 3.91
910 912 1.683917 AGGATCGATCGGTGGAAGAAG 59.316 52.381 18.81 0.00 0.00 2.85
911 913 1.776662 AGGATCGATCGGTGGAAGAA 58.223 50.000 18.81 0.00 0.00 2.52
912 914 1.409064 CAAGGATCGATCGGTGGAAGA 59.591 52.381 18.81 0.00 0.00 2.87
954 964 2.660064 GCAAGAGAAGGCGGAGGGA 61.660 63.158 0.00 0.00 0.00 4.20
999 1009 4.833390 AGTAGGAGGAAGAAATTCGTTGG 58.167 43.478 0.00 0.00 0.00 3.77
1016 1037 0.909610 TTGCTGGGACTGGGAGTAGG 60.910 60.000 0.00 0.00 0.00 3.18
1019 1040 1.062488 AGTTTGCTGGGACTGGGAGT 61.062 55.000 0.00 0.00 0.00 3.85
1020 1041 0.322008 GAGTTTGCTGGGACTGGGAG 60.322 60.000 0.00 0.00 0.00 4.30
1021 1042 1.761174 GAGTTTGCTGGGACTGGGA 59.239 57.895 0.00 0.00 0.00 4.37
1022 1043 1.672356 CGAGTTTGCTGGGACTGGG 60.672 63.158 0.00 0.00 0.00 4.45
1023 1044 1.672356 CCGAGTTTGCTGGGACTGG 60.672 63.158 0.00 0.00 42.42 4.00
1024 1045 0.671781 CTCCGAGTTTGCTGGGACTG 60.672 60.000 0.00 0.00 43.36 3.51
1025 1046 1.674057 CTCCGAGTTTGCTGGGACT 59.326 57.895 0.00 0.00 43.36 3.85
1026 1047 2.035442 GCTCCGAGTTTGCTGGGAC 61.035 63.158 0.00 0.00 43.36 4.46
1027 1048 2.050836 TTGCTCCGAGTTTGCTGGGA 62.051 55.000 0.00 0.00 45.53 4.37
1028 1049 1.600636 TTGCTCCGAGTTTGCTGGG 60.601 57.895 0.00 0.00 41.35 4.45
1029 1050 1.576421 GTTGCTCCGAGTTTGCTGG 59.424 57.895 0.00 0.00 0.00 4.85
1030 1051 1.165907 TGGTTGCTCCGAGTTTGCTG 61.166 55.000 0.00 0.00 39.52 4.41
1062 1083 2.327568 GGACATTTCGTCGAACGGTTA 58.672 47.619 7.29 0.00 46.42 2.85
1064 1085 0.668401 GGGACATTTCGTCGAACGGT 60.668 55.000 7.29 8.73 46.42 4.83
1066 1087 1.680105 CCGGGACATTTCGTCGAACG 61.680 60.000 7.29 6.80 46.42 3.95
1084 1105 0.034960 GGCTCTGGGTTTCTTCCTCC 60.035 60.000 0.00 0.00 0.00 4.30
1490 1514 3.887868 GCCCTGCGGTTTATGGCG 61.888 66.667 0.00 0.00 31.55 5.69
1511 1535 1.134189 TGATGGCTGAGCTGGATGAAG 60.134 52.381 3.72 0.00 0.00 3.02
1592 1616 2.821366 CCCGACAGATGCAGGTGC 60.821 66.667 0.00 0.00 42.50 5.01
1721 1745 3.623060 CGACCATGGTCAAAGTGATAAGG 59.377 47.826 37.42 17.37 44.77 2.69
2276 2641 5.407084 TGTTGTGATTGTGAGTATGTAACCG 59.593 40.000 0.00 0.00 0.00 4.44
2362 2732 6.092122 CGGCAAACTACTCAAATTCTATGTGA 59.908 38.462 0.00 0.00 0.00 3.58
2497 2869 4.142315 ACCTACATGCAATCAGACATTTGC 60.142 41.667 0.00 0.87 46.53 3.68
2507 2883 2.095853 CACGGTGAACCTACATGCAATC 59.904 50.000 0.74 0.00 0.00 2.67
2525 2901 7.060174 CGGTCCAAACAAAAGAATAATAACACG 59.940 37.037 0.00 0.00 0.00 4.49
2587 2963 7.504911 CACATCTCCAATTCCCTATTCAGAATT 59.495 37.037 0.00 0.00 42.08 2.17
2989 3367 2.264794 GTGAGTCGGCCGGTGATT 59.735 61.111 27.83 1.78 0.00 2.57
2997 3375 2.432628 CGAGGTTGGTGAGTCGGC 60.433 66.667 0.00 0.00 0.00 5.54
3192 3571 4.953579 TGAGGGGGCAAATAAGTTTACATC 59.046 41.667 0.00 0.00 0.00 3.06
3251 3630 2.735772 CCTACACGGCAGCCCATCT 61.736 63.158 5.63 0.00 0.00 2.90
3301 3680 8.873215 ACAGTAGATGAAAAGATATGTAACCG 57.127 34.615 0.00 0.00 0.00 4.44
3329 3708 3.851976 AGACTTGTACGCCTTACAGAG 57.148 47.619 0.00 0.00 41.86 3.35
3330 3709 5.909621 ATAAGACTTGTACGCCTTACAGA 57.090 39.130 0.00 0.00 41.86 3.41
3331 3710 7.591795 CAGATATAAGACTTGTACGCCTTACAG 59.408 40.741 0.00 0.00 41.86 2.74
3332 3711 7.283807 TCAGATATAAGACTTGTACGCCTTACA 59.716 37.037 0.00 0.00 39.05 2.41
3333 3712 7.646314 TCAGATATAAGACTTGTACGCCTTAC 58.354 38.462 0.00 0.00 0.00 2.34
3334 3713 7.812690 TCAGATATAAGACTTGTACGCCTTA 57.187 36.000 0.00 0.00 0.00 2.69
3335 3714 6.710597 TCAGATATAAGACTTGTACGCCTT 57.289 37.500 0.00 0.00 0.00 4.35
3336 3715 6.710597 TTCAGATATAAGACTTGTACGCCT 57.289 37.500 0.00 0.00 0.00 5.52
3610 3992 4.081198 TGGCATTTTTCACCTTGAACAGTT 60.081 37.500 0.00 0.00 35.89 3.16
3704 4086 5.477291 TGTTCCAAGTTTCAAGGTACACAAA 59.523 36.000 0.00 0.00 29.37 2.83
3720 4102 4.530875 AGATAGCCTTCCATTGTTCCAAG 58.469 43.478 0.00 0.00 0.00 3.61
3879 4261 5.116069 AGAGAAAGACAGTCTCGACTTTC 57.884 43.478 2.72 13.29 45.19 2.62
3894 4276 4.324936 GCTAACTCACAACGCTAGAGAAAG 59.675 45.833 0.00 0.00 33.69 2.62
3940 4322 3.022607 ACTTGTCTAAGGACGAAACCG 57.977 47.619 0.00 0.00 44.83 4.44
4071 4454 0.664224 TCAAAACCGTTTTCCGCTCC 59.336 50.000 6.26 0.00 34.38 4.70
4202 4680 9.978740 GCTCAAGCTCAAGTATGGGGTACTTAG 62.979 48.148 0.60 1.90 43.24 2.18
4227 4705 7.086376 CCATATATAACCTCAAAAGCATGTGC 58.914 38.462 0.00 0.00 42.49 4.57
4228 4706 8.169977 ACCATATATAACCTCAAAAGCATGTG 57.830 34.615 0.00 0.00 0.00 3.21
4229 4707 9.507329 CTACCATATATAACCTCAAAAGCATGT 57.493 33.333 0.00 0.00 0.00 3.21
4230 4708 8.950210 CCTACCATATATAACCTCAAAAGCATG 58.050 37.037 0.00 0.00 0.00 4.06
4231 4709 8.890472 TCCTACCATATATAACCTCAAAAGCAT 58.110 33.333 0.00 0.00 0.00 3.79
4232 4710 8.270137 TCCTACCATATATAACCTCAAAAGCA 57.730 34.615 0.00 0.00 0.00 3.91
4233 4711 8.594550 TCTCCTACCATATATAACCTCAAAAGC 58.405 37.037 0.00 0.00 0.00 3.51
4236 4714 9.442062 TGTTCTCCTACCATATATAACCTCAAA 57.558 33.333 0.00 0.00 0.00 2.69
4237 4715 8.867097 GTGTTCTCCTACCATATATAACCTCAA 58.133 37.037 0.00 0.00 0.00 3.02
4238 4716 8.008332 TGTGTTCTCCTACCATATATAACCTCA 58.992 37.037 0.00 0.00 0.00 3.86
4239 4717 8.418597 TGTGTTCTCCTACCATATATAACCTC 57.581 38.462 0.00 0.00 0.00 3.85
4240 4718 8.974292 ATGTGTTCTCCTACCATATATAACCT 57.026 34.615 0.00 0.00 0.00 3.50
4241 4719 8.258708 GGATGTGTTCTCCTACCATATATAACC 58.741 40.741 0.00 0.00 0.00 2.85
4242 4720 8.812972 TGGATGTGTTCTCCTACCATATATAAC 58.187 37.037 0.00 0.00 33.69 1.89
4243 4721 8.966155 TGGATGTGTTCTCCTACCATATATAA 57.034 34.615 0.00 0.00 33.69 0.98
4244 4722 7.124298 GCTGGATGTGTTCTCCTACCATATATA 59.876 40.741 0.00 0.00 33.69 0.86
4245 4723 6.070538 GCTGGATGTGTTCTCCTACCATATAT 60.071 42.308 0.00 0.00 33.69 0.86
4246 4724 5.246203 GCTGGATGTGTTCTCCTACCATATA 59.754 44.000 0.00 0.00 33.69 0.86
4247 4725 4.040952 GCTGGATGTGTTCTCCTACCATAT 59.959 45.833 0.00 0.00 33.69 1.78
4248 4726 3.388024 GCTGGATGTGTTCTCCTACCATA 59.612 47.826 0.00 0.00 33.69 2.74
4249 4727 2.171448 GCTGGATGTGTTCTCCTACCAT 59.829 50.000 0.00 0.00 33.69 3.55
4250 4728 1.555075 GCTGGATGTGTTCTCCTACCA 59.445 52.381 0.00 0.00 33.69 3.25
4251 4729 1.134371 GGCTGGATGTGTTCTCCTACC 60.134 57.143 0.00 0.00 33.69 3.18
4252 4730 1.134371 GGGCTGGATGTGTTCTCCTAC 60.134 57.143 0.00 0.00 33.69 3.18
4253 4731 1.204146 GGGCTGGATGTGTTCTCCTA 58.796 55.000 0.00 0.00 33.69 2.94
4254 4732 0.548682 AGGGCTGGATGTGTTCTCCT 60.549 55.000 0.00 0.00 33.69 3.69
4255 4733 0.107459 GAGGGCTGGATGTGTTCTCC 60.107 60.000 0.00 0.00 0.00 3.71
4256 4734 0.460987 CGAGGGCTGGATGTGTTCTC 60.461 60.000 0.00 0.00 0.00 2.87
4257 4735 1.599047 CGAGGGCTGGATGTGTTCT 59.401 57.895 0.00 0.00 0.00 3.01
4258 4736 2.109126 GCGAGGGCTGGATGTGTTC 61.109 63.158 0.00 0.00 35.83 3.18
4259 4737 2.045926 GCGAGGGCTGGATGTGTT 60.046 61.111 0.00 0.00 35.83 3.32
4260 4738 4.457496 CGCGAGGGCTGGATGTGT 62.457 66.667 0.00 0.00 36.88 3.72
4261 4739 4.457496 ACGCGAGGGCTGGATGTG 62.457 66.667 15.93 0.00 36.88 3.21
4262 4740 4.148825 GACGCGAGGGCTGGATGT 62.149 66.667 15.93 0.00 36.88 3.06
4263 4741 4.899239 GGACGCGAGGGCTGGATG 62.899 72.222 15.93 0.00 36.88 3.51
4328 4806 4.329545 TGTGTGGAAGGAGGGCGC 62.330 66.667 0.00 0.00 0.00 6.53
4329 4807 2.358737 GTGTGTGGAAGGAGGGCG 60.359 66.667 0.00 0.00 0.00 6.13
4330 4808 1.003233 GAGTGTGTGGAAGGAGGGC 60.003 63.158 0.00 0.00 0.00 5.19
4331 4809 1.679898 GGAGTGTGTGGAAGGAGGG 59.320 63.158 0.00 0.00 0.00 4.30
4332 4810 1.679898 GGGAGTGTGTGGAAGGAGG 59.320 63.158 0.00 0.00 0.00 4.30
4333 4811 0.838122 AGGGGAGTGTGTGGAAGGAG 60.838 60.000 0.00 0.00 0.00 3.69
4334 4812 0.836400 GAGGGGAGTGTGTGGAAGGA 60.836 60.000 0.00 0.00 0.00 3.36
4335 4813 1.679898 GAGGGGAGTGTGTGGAAGG 59.320 63.158 0.00 0.00 0.00 3.46
4336 4814 1.293498 CGAGGGGAGTGTGTGGAAG 59.707 63.158 0.00 0.00 0.00 3.46
4337 4815 2.879233 GCGAGGGGAGTGTGTGGAA 61.879 63.158 0.00 0.00 0.00 3.53
4338 4816 3.311110 GCGAGGGGAGTGTGTGGA 61.311 66.667 0.00 0.00 0.00 4.02
4339 4817 4.394712 GGCGAGGGGAGTGTGTGG 62.395 72.222 0.00 0.00 0.00 4.17
4340 4818 4.742201 CGGCGAGGGGAGTGTGTG 62.742 72.222 0.00 0.00 0.00 3.82
4342 4820 4.436998 GACGGCGAGGGGAGTGTG 62.437 72.222 16.62 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.