Multiple sequence alignment - TraesCS4D01G136400

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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 TraesCS4D01G136400 chr4D 100.000 4139 0 0 1 4139 122288523 122284385 0.000000e+00 7644.0
1 TraesCS4D01G136400 chr4D 84.669 2146 261 39 1102 3218 122275090 122272984 0.000000e+00 2078.0
2 TraesCS4D01G136400 chr4D 100.000 28 0 0 4076 4103 455628530 455628557 7.000000e-03 52.8
3 TraesCS4D01G136400 chr4A 93.846 2665 101 29 861 3495 447791442 447794073 0.000000e+00 3954.0
4 TraesCS4D01G136400 chr4A 84.983 2111 258 31 1103 3185 448092098 448094177 0.000000e+00 2087.0
5 TraesCS4D01G136400 chr4A 85.934 391 21 7 3555 3916 447794078 447794463 1.800000e-103 387.0
6 TraesCS4D01G136400 chr4B 93.408 2412 97 21 841 3224 186593229 186590852 0.000000e+00 3517.0
7 TraesCS4D01G136400 chr4B 84.745 2137 263 32 1109 3218 185911019 185908919 0.000000e+00 2082.0
8 TraesCS4D01G136400 chr4B 88.980 853 77 11 1 838 581178862 581178012 0.000000e+00 1038.0
9 TraesCS4D01G136400 chr4B 92.237 438 17 11 3221 3650 186590741 186590313 4.580000e-169 604.0
10 TraesCS4D01G136400 chr4B 74.131 1036 251 11 2083 3105 186608034 186607003 2.980000e-111 412.0
11 TraesCS4D01G136400 chr4B 87.466 367 22 6 3692 4047 186590219 186589866 6.440000e-108 401.0
12 TraesCS4D01G136400 chr3D 93.083 853 44 7 1 838 551074334 551073482 0.000000e+00 1234.0
13 TraesCS4D01G136400 chr3D 91.646 790 44 10 1 774 397797505 397798288 0.000000e+00 1074.0
14 TraesCS4D01G136400 chr3D 88.772 855 72 14 1 838 135755030 135755877 0.000000e+00 1026.0
15 TraesCS4D01G136400 chr5A 90.931 849 63 13 1 838 404239832 404240677 0.000000e+00 1129.0
16 TraesCS4D01G136400 chr3A 91.226 832 59 11 1 820 81668149 81667320 0.000000e+00 1120.0
17 TraesCS4D01G136400 chr7A 90.369 841 64 16 1 827 1853191 1852354 0.000000e+00 1088.0
18 TraesCS4D01G136400 chr7A 89.357 855 69 18 1 838 726512437 726513286 0.000000e+00 1055.0
19 TraesCS4D01G136400 chr1A 88.530 837 82 8 1 827 99252346 99253178 0.000000e+00 1002.0
20 TraesCS4D01G136400 chr1A 100.000 30 0 0 4074 4103 566135601 566135572 5.780000e-04 56.5
21 TraesCS4D01G136400 chr2A 87.537 674 56 11 182 838 535705269 535704607 0.000000e+00 754.0
22 TraesCS4D01G136400 chr5B 86.022 279 28 8 569 838 243406337 243406061 5.240000e-74 289.0
23 TraesCS4D01G136400 chr2D 90.909 44 2 2 4059 4100 465963976 465963933 1.610000e-04 58.4
24 TraesCS4D01G136400 chr2D 100.000 28 0 0 4076 4103 7646209 7646182 7.000000e-03 52.8
25 TraesCS4D01G136400 chr2D 100.000 28 0 0 4075 4102 605446753 605446780 7.000000e-03 52.8
26 TraesCS4D01G136400 chr6B 100.000 28 0 0 4076 4103 245994494 245994467 7.000000e-03 52.8
27 TraesCS4D01G136400 chr6A 100.000 28 0 0 4076 4103 463531141 463531168 7.000000e-03 52.8
28 TraesCS4D01G136400 chr5D 100.000 28 0 0 4076 4103 499871371 499871398 7.000000e-03 52.8
29 TraesCS4D01G136400 chr1B 100.000 28 0 0 4076 4103 285565147 285565120 7.000000e-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 TraesCS4D01G136400 chr4D 122284385 122288523 4138 True 7644.000000 7644 100.000 1 4139 1 chr4D.!!$R2 4138
1 TraesCS4D01G136400 chr4D 122272984 122275090 2106 True 2078.000000 2078 84.669 1102 3218 1 chr4D.!!$R1 2116
2 TraesCS4D01G136400 chr4A 447791442 447794463 3021 False 2170.500000 3954 89.890 861 3916 2 chr4A.!!$F2 3055
3 TraesCS4D01G136400 chr4A 448092098 448094177 2079 False 2087.000000 2087 84.983 1103 3185 1 chr4A.!!$F1 2082
4 TraesCS4D01G136400 chr4B 185908919 185911019 2100 True 2082.000000 2082 84.745 1109 3218 1 chr4B.!!$R1 2109
5 TraesCS4D01G136400 chr4B 186589866 186593229 3363 True 1507.333333 3517 91.037 841 4047 3 chr4B.!!$R4 3206
6 TraesCS4D01G136400 chr4B 581178012 581178862 850 True 1038.000000 1038 88.980 1 838 1 chr4B.!!$R3 837
7 TraesCS4D01G136400 chr4B 186607003 186608034 1031 True 412.000000 412 74.131 2083 3105 1 chr4B.!!$R2 1022
8 TraesCS4D01G136400 chr3D 551073482 551074334 852 True 1234.000000 1234 93.083 1 838 1 chr3D.!!$R1 837
9 TraesCS4D01G136400 chr3D 397797505 397798288 783 False 1074.000000 1074 91.646 1 774 1 chr3D.!!$F2 773
10 TraesCS4D01G136400 chr3D 135755030 135755877 847 False 1026.000000 1026 88.772 1 838 1 chr3D.!!$F1 837
11 TraesCS4D01G136400 chr5A 404239832 404240677 845 False 1129.000000 1129 90.931 1 838 1 chr5A.!!$F1 837
12 TraesCS4D01G136400 chr3A 81667320 81668149 829 True 1120.000000 1120 91.226 1 820 1 chr3A.!!$R1 819
13 TraesCS4D01G136400 chr7A 1852354 1853191 837 True 1088.000000 1088 90.369 1 827 1 chr7A.!!$R1 826
14 TraesCS4D01G136400 chr7A 726512437 726513286 849 False 1055.000000 1055 89.357 1 838 1 chr7A.!!$F1 837
15 TraesCS4D01G136400 chr1A 99252346 99253178 832 False 1002.000000 1002 88.530 1 827 1 chr1A.!!$F1 826
16 TraesCS4D01G136400 chr2A 535704607 535705269 662 True 754.000000 754 87.537 182 838 1 chr2A.!!$R1 656

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
900 940 0.110295 TTGGTGTACCTGCACTGCAT 59.890 50.000 3.64 0.00 38.13 3.96 F
964 1004 0.971386 TCTCATCTCACTGCACTGCA 59.029 50.000 3.11 3.11 36.92 4.41 F
1958 2080 1.002087 GAAGAACAGCCGGAAGAAGGA 59.998 52.381 5.05 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2318 0.317103 CGACCGAGATGCGACTTAGG 60.317 60.000 0.0 0.0 44.57 2.69 R
2487 2612 2.357517 CGGGCGAAGTTGCTGAGT 60.358 61.111 0.0 0.0 34.52 3.41 R
3292 3548 0.039708 GGTTCAGCAGCAACTCAAGC 60.040 55.000 0.0 0.0 0.00 4.01 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
121 122 3.055719 CGGCCGCTGGTTGTTGAT 61.056 61.111 14.67 0.00 0.00 2.57
266 267 1.153329 TGTCGAACAACTTGCGGGT 60.153 52.632 0.00 0.00 0.00 5.28
268 269 1.144276 TCGAACAACTTGCGGGTGA 59.856 52.632 1.50 0.00 35.89 4.02
605 616 2.281484 GGTTGCTCGTTGGCCTGA 60.281 61.111 3.32 0.00 0.00 3.86
692 731 3.118454 CGCCGACGCAAATCAGGT 61.118 61.111 0.00 0.00 34.03 4.00
694 733 1.579429 GCCGACGCAAATCAGGTTT 59.421 52.632 0.00 0.00 34.03 3.27
734 773 4.394078 GCCCGCGGACGAAAAACC 62.394 66.667 30.73 0.00 43.93 3.27
831 871 1.680338 ATGAGTCGCCCCATTAAAGC 58.320 50.000 0.00 0.00 0.00 3.51
838 878 1.028130 GCCCCATTAAAGCTGCTCTC 58.972 55.000 1.00 0.00 0.00 3.20
839 879 1.685148 CCCCATTAAAGCTGCTCTCC 58.315 55.000 1.00 0.00 0.00 3.71
848 888 2.002505 AGCTGCTCTCCCATACGTAT 57.997 50.000 1.14 1.14 0.00 3.06
861 901 4.496341 CCCATACGTATTCTGCTTTGCTTG 60.496 45.833 5.03 0.00 0.00 4.01
862 902 2.619013 ACGTATTCTGCTTTGCTTGC 57.381 45.000 0.00 0.00 0.00 4.01
863 903 2.154462 ACGTATTCTGCTTTGCTTGCT 58.846 42.857 0.00 0.00 0.00 3.91
864 904 2.554032 ACGTATTCTGCTTTGCTTGCTT 59.446 40.909 0.00 0.00 0.00 3.91
900 940 0.110295 TTGGTGTACCTGCACTGCAT 59.890 50.000 3.64 0.00 38.13 3.96
927 967 2.027837 GGGCCAGCTTCATTCATTTTGT 60.028 45.455 4.39 0.00 0.00 2.83
929 969 3.681417 GGCCAGCTTCATTCATTTTGTTC 59.319 43.478 0.00 0.00 0.00 3.18
956 996 3.710677 CCTCCTCCATTTCTCATCTCACT 59.289 47.826 0.00 0.00 0.00 3.41
957 997 4.443175 CCTCCTCCATTTCTCATCTCACTG 60.443 50.000 0.00 0.00 0.00 3.66
958 998 3.118482 TCCTCCATTTCTCATCTCACTGC 60.118 47.826 0.00 0.00 0.00 4.40
959 999 3.370209 CCTCCATTTCTCATCTCACTGCA 60.370 47.826 0.00 0.00 0.00 4.41
960 1000 3.603532 TCCATTTCTCATCTCACTGCAC 58.396 45.455 0.00 0.00 0.00 4.57
961 1001 3.262660 TCCATTTCTCATCTCACTGCACT 59.737 43.478 0.00 0.00 0.00 4.40
962 1002 3.374367 CCATTTCTCATCTCACTGCACTG 59.626 47.826 0.00 0.00 0.00 3.66
963 1003 2.090400 TTCTCATCTCACTGCACTGC 57.910 50.000 0.00 0.00 0.00 4.40
964 1004 0.971386 TCTCATCTCACTGCACTGCA 59.029 50.000 3.11 3.11 36.92 4.41
965 1005 1.345415 TCTCATCTCACTGCACTGCAA 59.655 47.619 4.99 0.00 38.41 4.08
994 1034 3.310652 GGAACCTTCCCTCCTCCG 58.689 66.667 0.00 0.00 41.62 4.63
1010 1050 2.484062 CCGTGCCCATGCTTCCATC 61.484 63.158 0.00 0.00 38.71 3.51
1047 1087 2.479566 AGAAGAAGAAATGCAGCGGA 57.520 45.000 0.00 0.00 0.00 5.54
1055 1105 2.939103 AGAAATGCAGCGGAGTAATGTC 59.061 45.455 0.00 0.00 0.00 3.06
1079 1140 1.339610 CGCAGCCTTGATAGCTACTCT 59.660 52.381 0.00 0.00 38.95 3.24
1080 1141 2.554462 CGCAGCCTTGATAGCTACTCTA 59.446 50.000 0.00 0.00 38.95 2.43
1081 1142 3.610585 CGCAGCCTTGATAGCTACTCTAC 60.611 52.174 0.00 0.00 38.95 2.59
1082 1143 3.572255 GCAGCCTTGATAGCTACTCTACT 59.428 47.826 0.00 0.00 38.95 2.57
1083 1144 4.320935 GCAGCCTTGATAGCTACTCTACTC 60.321 50.000 0.00 0.00 38.95 2.59
1089 1150 4.720046 TGATAGCTACTCTACTCCAGTGG 58.280 47.826 1.40 1.40 0.00 4.00
1290 1367 2.285368 ATGGAGGAGGGCACGGAA 60.285 61.111 0.00 0.00 0.00 4.30
1667 1771 2.747855 GCTCAACCTGGCCTTCCG 60.748 66.667 3.32 0.00 34.14 4.30
1722 1826 4.783621 GACATCAGCCTGCCGCCA 62.784 66.667 0.00 0.00 38.78 5.69
1789 1899 2.477972 GAAAAAGAGGGCCGCACTGC 62.478 60.000 10.70 0.00 0.00 4.40
1905 2027 3.072184 AGATATGCATGAAGGGGACTCAC 59.928 47.826 10.16 0.00 42.68 3.51
1922 2044 3.869272 CAACCTGATCGCCGCAGC 61.869 66.667 0.00 0.00 32.06 5.25
1958 2080 1.002087 GAAGAACAGCCGGAAGAAGGA 59.998 52.381 5.05 0.00 0.00 3.36
1986 2111 1.341531 AGAAAGGCCGTCGATGATAGG 59.658 52.381 6.11 0.00 0.00 2.57
2193 2318 1.474879 GAGCTGTACCAGTCACTCCTC 59.525 57.143 0.00 0.00 33.43 3.71
2667 2801 0.899717 GCTTTGATGGTCCAAGCCCA 60.900 55.000 0.00 0.00 36.16 5.36
3224 3363 7.571080 AGTAGTAGCACTTATCTCTTGTACC 57.429 40.000 0.00 0.00 0.00 3.34
3225 3364 7.348033 AGTAGTAGCACTTATCTCTTGTACCT 58.652 38.462 0.00 0.00 0.00 3.08
3292 3548 4.237724 TGAAGATGTGCGTGTCTTCTAAG 58.762 43.478 19.14 0.00 46.58 2.18
3296 3552 2.135139 TGTGCGTGTCTTCTAAGCTTG 58.865 47.619 9.86 0.00 0.00 4.01
3308 3564 2.037641 TCTAAGCTTGAGTTGCTGCTGA 59.962 45.455 9.86 0.00 41.03 4.26
3400 3657 0.179023 TGCACTGGTGACTTGCATCA 60.179 50.000 4.79 0.00 42.63 3.07
3403 3661 2.029649 GCACTGGTGACTTGCATCATTT 60.030 45.455 4.79 0.00 36.92 2.32
3405 3663 3.253921 CACTGGTGACTTGCATCATTTGA 59.746 43.478 0.00 0.00 36.92 2.69
3408 3666 3.444742 TGGTGACTTGCATCATTTGATCC 59.555 43.478 0.00 0.00 31.16 3.36
3453 3713 0.323302 TGTGTGTGTGTGTGTGGACT 59.677 50.000 0.00 0.00 0.00 3.85
3454 3714 1.006832 GTGTGTGTGTGTGTGGACTC 58.993 55.000 0.00 0.00 0.00 3.36
3457 3717 1.933853 GTGTGTGTGTGTGGACTCTTC 59.066 52.381 0.00 0.00 0.00 2.87
3775 4108 2.977405 AGCATGAAGTTCAGTTTCGC 57.023 45.000 11.91 8.47 0.00 4.70
3801 4134 4.153475 GCCAGCGTTGTACAGAGAATTAAA 59.847 41.667 0.00 0.00 0.00 1.52
3802 4135 5.671329 GCCAGCGTTGTACAGAGAATTAAAG 60.671 44.000 0.00 0.00 0.00 1.85
3803 4136 5.408604 CCAGCGTTGTACAGAGAATTAAAGT 59.591 40.000 0.00 0.00 0.00 2.66
3804 4137 6.073222 CCAGCGTTGTACAGAGAATTAAAGTT 60.073 38.462 0.00 0.00 0.00 2.66
3805 4138 6.792250 CAGCGTTGTACAGAGAATTAAAGTTG 59.208 38.462 0.00 0.00 0.00 3.16
3806 4139 6.482308 AGCGTTGTACAGAGAATTAAAGTTGT 59.518 34.615 0.00 0.00 0.00 3.32
3807 4140 6.573725 GCGTTGTACAGAGAATTAAAGTTGTG 59.426 38.462 0.00 0.00 0.00 3.33
3808 4141 7.069569 CGTTGTACAGAGAATTAAAGTTGTGG 58.930 38.462 0.00 0.00 0.00 4.17
3809 4142 7.254658 CGTTGTACAGAGAATTAAAGTTGTGGT 60.255 37.037 0.00 0.00 0.00 4.16
3810 4143 7.724305 TGTACAGAGAATTAAAGTTGTGGTC 57.276 36.000 0.00 0.00 0.00 4.02
3849 4193 4.261363 GCTTATTGCCTGGCTGAGTTATTC 60.261 45.833 21.03 0.00 35.15 1.75
3892 4243 3.880490 CGCCACTTATTTAAGCCCATGTA 59.120 43.478 0.00 0.00 36.79 2.29
3896 4247 7.272244 GCCACTTATTTAAGCCCATGTATTTT 58.728 34.615 0.00 0.00 36.79 1.82
3909 4260 8.908903 AGCCCATGTATTTTTATATTTCGAACA 58.091 29.630 0.00 0.00 0.00 3.18
3922 4273 1.081442 CGAACAGGAAAAAGCGCCC 60.081 57.895 2.29 0.00 0.00 6.13
3923 4274 1.289066 GAACAGGAAAAAGCGCCCC 59.711 57.895 2.29 0.00 0.00 5.80
3936 4297 2.105528 GCCCCGAATGCATTGCTG 59.894 61.111 18.59 6.30 0.00 4.41
3942 4303 2.479049 CCCGAATGCATTGCTGAAAGAG 60.479 50.000 18.59 0.00 34.07 2.85
3962 4323 0.313987 GGCAAAGCCCAAGTGTACAC 59.686 55.000 18.56 18.56 44.06 2.90
4008 4370 2.754552 GCCCATGTCAAAGCATTACTCA 59.245 45.455 0.00 0.00 0.00 3.41
4010 4372 4.580167 GCCCATGTCAAAGCATTACTCATA 59.420 41.667 0.00 0.00 0.00 2.15
4019 4381 4.655762 AGCATTACTCATACGAGCTGAA 57.344 40.909 0.00 0.00 43.66 3.02
4028 4390 4.758688 TCATACGAGCTGAATTGACACAT 58.241 39.130 0.00 0.00 0.00 3.21
4030 4392 2.350522 ACGAGCTGAATTGACACATCC 58.649 47.619 0.00 0.00 0.00 3.51
4031 4393 2.289631 ACGAGCTGAATTGACACATCCA 60.290 45.455 0.00 0.00 0.00 3.41
4047 4409 9.330063 TGACACATCCAAAGATATGAAATACTC 57.670 33.333 0.00 0.00 31.05 2.59
4048 4410 8.682936 ACACATCCAAAGATATGAAATACTCC 57.317 34.615 0.00 0.00 31.05 3.85
4049 4411 7.721399 ACACATCCAAAGATATGAAATACTCCC 59.279 37.037 0.00 0.00 31.05 4.30
4050 4412 7.941238 CACATCCAAAGATATGAAATACTCCCT 59.059 37.037 0.00 0.00 27.41 4.20
4051 4413 8.160106 ACATCCAAAGATATGAAATACTCCCTC 58.840 37.037 0.00 0.00 0.00 4.30
4052 4414 7.079451 TCCAAAGATATGAAATACTCCCTCC 57.921 40.000 0.00 0.00 0.00 4.30
4053 4415 5.934625 CCAAAGATATGAAATACTCCCTCCG 59.065 44.000 0.00 0.00 0.00 4.63
4054 4416 5.746990 AAGATATGAAATACTCCCTCCGG 57.253 43.478 0.00 0.00 0.00 5.14
4055 4417 5.011982 AGATATGAAATACTCCCTCCGGA 57.988 43.478 2.93 2.93 36.45 5.14
4056 4418 5.403512 AGATATGAAATACTCCCTCCGGAA 58.596 41.667 5.23 0.00 37.86 4.30
4057 4419 5.482175 AGATATGAAATACTCCCTCCGGAAG 59.518 44.000 5.23 2.16 37.86 3.46
4058 4420 1.485066 TGAAATACTCCCTCCGGAAGC 59.515 52.381 5.23 0.00 37.86 3.86
4059 4421 1.485066 GAAATACTCCCTCCGGAAGCA 59.515 52.381 5.23 0.00 37.86 3.91
4060 4422 1.807814 AATACTCCCTCCGGAAGCAT 58.192 50.000 5.23 0.00 37.86 3.79
4061 4423 2.696526 ATACTCCCTCCGGAAGCATA 57.303 50.000 5.23 0.00 37.86 3.14
4062 4424 2.696526 TACTCCCTCCGGAAGCATAT 57.303 50.000 5.23 0.00 37.86 1.78
4063 4425 1.807814 ACTCCCTCCGGAAGCATATT 58.192 50.000 5.23 0.00 37.86 1.28
4064 4426 1.417890 ACTCCCTCCGGAAGCATATTG 59.582 52.381 5.23 0.00 37.86 1.90
4065 4427 0.764890 TCCCTCCGGAAGCATATTGG 59.235 55.000 5.23 0.00 34.19 3.16
4066 4428 0.764890 CCCTCCGGAAGCATATTGGA 59.235 55.000 5.23 0.00 0.00 3.53
4067 4429 1.142870 CCCTCCGGAAGCATATTGGAA 59.857 52.381 5.23 0.00 0.00 3.53
4068 4430 2.224867 CCCTCCGGAAGCATATTGGAAT 60.225 50.000 5.23 0.00 0.00 3.01
4069 4431 3.009033 CCCTCCGGAAGCATATTGGAATA 59.991 47.826 5.23 0.00 0.00 1.75
4070 4432 4.506625 CCCTCCGGAAGCATATTGGAATAA 60.507 45.833 5.23 0.00 0.00 1.40
4071 4433 5.256474 CCTCCGGAAGCATATTGGAATAAT 58.744 41.667 5.23 0.00 0.00 1.28
4072 4434 6.414732 CCTCCGGAAGCATATTGGAATAATA 58.585 40.000 5.23 0.00 0.00 0.98
4073 4435 6.884295 CCTCCGGAAGCATATTGGAATAATAA 59.116 38.462 5.23 0.00 0.00 1.40
4074 4436 7.393234 CCTCCGGAAGCATATTGGAATAATAAA 59.607 37.037 5.23 0.00 0.00 1.40
4075 4437 8.877864 TCCGGAAGCATATTGGAATAATAAAT 57.122 30.769 0.00 0.00 0.00 1.40
4076 4438 8.956426 TCCGGAAGCATATTGGAATAATAAATC 58.044 33.333 0.00 0.00 0.00 2.17
4077 4439 8.960591 CCGGAAGCATATTGGAATAATAAATCT 58.039 33.333 0.00 0.00 0.00 2.40
4097 4459 8.757307 AAATCTTATATTATGGGACTGAGGGA 57.243 34.615 0.00 0.00 0.00 4.20
4098 4460 7.986553 ATCTTATATTATGGGACTGAGGGAG 57.013 40.000 0.00 0.00 0.00 4.30
4099 4461 6.875469 TCTTATATTATGGGACTGAGGGAGT 58.125 40.000 0.00 0.00 37.76 3.85
4100 4462 8.008104 TCTTATATTATGGGACTGAGGGAGTA 57.992 38.462 0.00 0.00 33.83 2.59
4101 4463 7.894364 TCTTATATTATGGGACTGAGGGAGTAC 59.106 40.741 0.00 0.00 33.83 2.73
4102 4464 4.561254 ATTATGGGACTGAGGGAGTACT 57.439 45.455 0.00 0.00 35.54 2.73
4103 4465 2.463047 ATGGGACTGAGGGAGTACTC 57.537 55.000 14.87 14.87 35.54 2.59
4104 4466 0.034380 TGGGACTGAGGGAGTACTCG 60.034 60.000 16.56 5.07 40.39 4.18
4105 4467 0.752376 GGGACTGAGGGAGTACTCGG 60.752 65.000 16.56 2.04 46.86 4.63
4106 4468 0.752376 GGACTGAGGGAGTACTCGGG 60.752 65.000 16.56 7.11 45.98 5.14
4107 4469 1.380112 ACTGAGGGAGTACTCGGGC 60.380 63.158 16.56 8.41 45.98 6.13
4108 4470 1.379977 CTGAGGGAGTACTCGGGCA 60.380 63.158 16.56 12.23 39.64 5.36
4109 4471 1.668101 CTGAGGGAGTACTCGGGCAC 61.668 65.000 16.56 2.28 39.64 5.01
4110 4472 2.754658 AGGGAGTACTCGGGCACG 60.755 66.667 16.56 0.00 42.74 5.34
4111 4473 3.066814 GGGAGTACTCGGGCACGT 61.067 66.667 16.56 0.00 41.85 4.49
4112 4474 1.750399 GGGAGTACTCGGGCACGTA 60.750 63.158 16.56 0.00 41.85 3.57
4113 4475 1.722636 GGGAGTACTCGGGCACGTAG 61.723 65.000 16.56 7.31 41.85 3.51
4114 4476 0.745845 GGAGTACTCGGGCACGTAGA 60.746 60.000 16.56 0.00 41.85 2.59
4115 4477 0.376502 GAGTACTCGGGCACGTAGAC 59.623 60.000 8.89 4.58 41.85 2.59
4116 4478 1.028868 AGTACTCGGGCACGTAGACC 61.029 60.000 8.89 0.00 41.85 3.85
4117 4479 1.028868 GTACTCGGGCACGTAGACCT 61.029 60.000 8.89 0.00 41.85 3.85
4118 4480 0.322816 TACTCGGGCACGTAGACCTT 60.323 55.000 8.89 0.00 41.85 3.50
4119 4481 0.322816 ACTCGGGCACGTAGACCTTA 60.323 55.000 8.89 0.00 41.85 2.69
4120 4482 0.813184 CTCGGGCACGTAGACCTTAA 59.187 55.000 8.89 0.00 41.85 1.85
4121 4483 0.813184 TCGGGCACGTAGACCTTAAG 59.187 55.000 8.89 0.00 41.85 1.85
4122 4484 0.813184 CGGGCACGTAGACCTTAAGA 59.187 55.000 0.00 0.00 34.81 2.10
4123 4485 1.202268 CGGGCACGTAGACCTTAAGAG 60.202 57.143 0.00 0.00 34.81 2.85
4124 4486 4.405404 CGGGCACGTAGACCTTAAGAGG 62.405 59.091 0.00 0.00 41.31 3.69
4134 4496 2.425143 CCTTAAGAGGCTTGGATGCA 57.575 50.000 3.36 0.00 35.94 3.96
4135 4497 2.726821 CCTTAAGAGGCTTGGATGCAA 58.273 47.619 3.36 0.00 35.94 4.08
4136 4498 3.294214 CCTTAAGAGGCTTGGATGCAAT 58.706 45.455 3.36 0.00 35.94 3.56
4137 4499 3.317430 CCTTAAGAGGCTTGGATGCAATC 59.683 47.826 3.36 0.00 38.37 2.67
4138 4500 5.170301 CCTTAAGAGGCTTGGATGCAATCA 61.170 45.833 3.36 0.00 39.99 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 4.326766 CAACCAGCGGCCGTTGTG 62.327 66.667 35.18 28.22 35.66 3.33
266 267 1.585006 GCCGTCTCCTTCTTCGTCA 59.415 57.895 0.00 0.00 0.00 4.35
268 269 2.971452 GGCCGTCTCCTTCTTCGT 59.029 61.111 0.00 0.00 0.00 3.85
595 606 4.101448 CCCTCCCTCAGGCCAACG 62.101 72.222 5.01 0.00 41.80 4.10
605 616 2.128226 ACATTGGCCTCCCTCCCT 59.872 61.111 3.32 0.00 0.00 4.20
692 731 2.237392 CCATTCCCGGCCCATTTTTAAA 59.763 45.455 0.00 0.00 0.00 1.52
694 733 1.490574 CCATTCCCGGCCCATTTTTA 58.509 50.000 0.00 0.00 0.00 1.52
831 871 3.858877 GCAGAATACGTATGGGAGAGCAG 60.859 52.174 9.24 0.00 0.00 4.24
838 878 3.206150 AGCAAAGCAGAATACGTATGGG 58.794 45.455 9.24 3.06 0.00 4.00
839 879 4.591202 CAAGCAAAGCAGAATACGTATGG 58.409 43.478 9.24 3.42 0.00 2.74
848 888 0.748450 AGCAAGCAAGCAAAGCAGAA 59.252 45.000 3.19 0.00 36.85 3.02
861 901 1.598701 CCCAACCCTAGCAAGCAAGC 61.599 60.000 0.00 0.00 0.00 4.01
862 902 0.251341 ACCCAACCCTAGCAAGCAAG 60.251 55.000 0.00 0.00 0.00 4.01
863 903 0.187361 AACCCAACCCTAGCAAGCAA 59.813 50.000 0.00 0.00 0.00 3.91
864 904 0.539438 CAACCCAACCCTAGCAAGCA 60.539 55.000 0.00 0.00 0.00 3.91
900 940 3.866379 ATGAAGCTGGCCCGTGCAA 62.866 57.895 13.66 1.41 40.13 4.08
927 967 3.246130 TGAGAAATGGAGGAGGAGGAGAA 60.246 47.826 0.00 0.00 0.00 2.87
929 969 2.756907 TGAGAAATGGAGGAGGAGGAG 58.243 52.381 0.00 0.00 0.00 3.69
956 996 1.601759 GAAGGAGCCTTGCAGTGCA 60.602 57.895 15.37 15.37 36.26 4.57
957 997 2.338785 GGAAGGAGCCTTGCAGTGC 61.339 63.158 14.88 8.58 42.71 4.40
958 998 0.959372 CAGGAAGGAGCCTTGCAGTG 60.959 60.000 20.62 9.07 45.06 3.66
959 999 1.377994 CAGGAAGGAGCCTTGCAGT 59.622 57.895 20.62 0.61 45.06 4.40
960 1000 1.378250 CCAGGAAGGAGCCTTGCAG 60.378 63.158 20.62 13.56 45.06 4.41
961 1001 1.847506 TCCAGGAAGGAGCCTTGCA 60.848 57.895 20.62 0.00 45.06 4.08
962 1002 3.081554 TCCAGGAAGGAGCCTTGC 58.918 61.111 12.28 12.28 43.07 4.01
994 1034 2.129785 GGGATGGAAGCATGGGCAC 61.130 63.158 0.00 0.00 44.61 5.01
1010 1050 8.275040 TCTTCTTCTTTAAAAGGATAGGATGGG 58.725 37.037 0.00 0.00 0.00 4.00
1039 1079 0.323302 TTGGACATTACTCCGCTGCA 59.677 50.000 0.00 0.00 32.22 4.41
1047 1087 0.324943 AGGCTGCGTTGGACATTACT 59.675 50.000 0.00 0.00 0.00 2.24
1055 1105 0.745845 AGCTATCAAGGCTGCGTTGG 60.746 55.000 28.27 16.92 38.73 3.77
1079 1140 2.018355 TGGTACTTGCCACTGGAGTA 57.982 50.000 0.00 0.00 32.81 2.59
1080 1141 1.136828 TTGGTACTTGCCACTGGAGT 58.863 50.000 0.00 0.00 38.42 3.85
1081 1142 1.523758 GTTGGTACTTGCCACTGGAG 58.476 55.000 0.00 0.00 38.42 3.86
1082 1143 0.109723 GGTTGGTACTTGCCACTGGA 59.890 55.000 0.00 0.00 38.42 3.86
1083 1144 0.179004 TGGTTGGTACTTGCCACTGG 60.179 55.000 0.00 0.00 38.42 4.00
1089 1150 0.517316 CGCTTCTGGTTGGTACTTGC 59.483 55.000 0.00 0.00 0.00 4.01
1290 1367 3.053470 GGTAGAGGTAGAAGAGGTGGTCT 60.053 52.174 0.00 0.00 36.94 3.85
1395 1472 3.151022 GAGGGCGAGGAGGTGGAG 61.151 72.222 0.00 0.00 0.00 3.86
1622 1720 4.025401 CGCCGGGCAACAAGTGAC 62.025 66.667 20.71 0.00 39.74 3.67
1667 1771 2.421399 GCCTCCTCCATGCCTTTGC 61.421 63.158 0.00 0.00 38.26 3.68
1722 1826 0.324943 CCACTGTCCCCTCGTTGATT 59.675 55.000 0.00 0.00 0.00 2.57
1789 1899 2.124983 CACATCCGGCTCCAGTGG 60.125 66.667 1.40 1.40 0.00 4.00
1905 2027 3.869272 GCTGCGGCGATCAGGTTG 61.869 66.667 12.98 0.00 32.41 3.77
1958 2080 4.065281 CGGCCTTTCTCGACCGGT 62.065 66.667 6.92 6.92 41.95 5.28
1977 2102 2.232452 GTCCACCATCTCCCTATCATCG 59.768 54.545 0.00 0.00 0.00 3.84
1986 2111 1.078143 GTGCAGGTCCACCATCTCC 60.078 63.158 0.00 0.00 38.89 3.71
2193 2318 0.317103 CGACCGAGATGCGACTTAGG 60.317 60.000 0.00 0.00 44.57 2.69
2487 2612 2.357517 CGGGCGAAGTTGCTGAGT 60.358 61.111 0.00 0.00 34.52 3.41
3105 3239 1.752498 GCTGCAATCCATGATGACCAA 59.248 47.619 0.00 0.00 0.00 3.67
3195 3334 9.550406 ACAAGAGATAAGTGCTACTACTACTAG 57.450 37.037 0.00 0.00 0.00 2.57
3201 3340 7.282675 TGAGGTACAAGAGATAAGTGCTACTAC 59.717 40.741 0.00 0.00 0.00 2.73
3224 3363 7.087409 TGTAATATGTGGAATTGCTTGTGAG 57.913 36.000 0.00 0.00 0.00 3.51
3225 3364 7.482474 CATGTAATATGTGGAATTGCTTGTGA 58.518 34.615 0.00 0.00 0.00 3.58
3292 3548 0.039708 GGTTCAGCAGCAACTCAAGC 60.040 55.000 0.00 0.00 0.00 4.01
3296 3552 1.527034 TGATGGTTCAGCAGCAACTC 58.473 50.000 0.00 0.00 36.17 3.01
3308 3564 9.860898 GAAAGCTTATCTAACAATTTGATGGTT 57.139 29.630 0.00 0.00 0.00 3.67
3453 3713 4.792068 ACTTGTGGGAAACATCTTGAAGA 58.208 39.130 0.00 0.00 38.99 2.87
3454 3714 5.520376 AACTTGTGGGAAACATCTTGAAG 57.480 39.130 0.00 0.00 38.99 3.02
3457 3717 5.163519 ACTGAAACTTGTGGGAAACATCTTG 60.164 40.000 0.00 0.00 38.99 3.02
3613 3877 9.926158 TTATTTATGTGTTTGAACTTGCATGAT 57.074 25.926 6.60 0.00 0.00 2.45
3733 4066 6.535150 GCTATACATTCAGCACTTGACTAACA 59.465 38.462 0.00 0.00 37.73 2.41
3775 4108 0.792640 CTCTGTACAACGCTGGCTTG 59.207 55.000 0.00 0.00 0.00 4.01
3784 4117 7.927048 ACCACAACTTTAATTCTCTGTACAAC 58.073 34.615 0.00 0.00 0.00 3.32
3801 4134 2.088104 TCTGACCTCTGACCACAACT 57.912 50.000 0.00 0.00 0.00 3.16
3802 4135 3.764434 TCTATCTGACCTCTGACCACAAC 59.236 47.826 0.00 0.00 0.00 3.32
3803 4136 4.047627 TCTATCTGACCTCTGACCACAA 57.952 45.455 0.00 0.00 0.00 3.33
3804 4137 3.739401 TCTATCTGACCTCTGACCACA 57.261 47.619 0.00 0.00 0.00 4.17
3805 4138 3.243704 GCATCTATCTGACCTCTGACCAC 60.244 52.174 0.00 0.00 0.00 4.16
3806 4139 2.961741 GCATCTATCTGACCTCTGACCA 59.038 50.000 0.00 0.00 0.00 4.02
3807 4140 3.230134 AGCATCTATCTGACCTCTGACC 58.770 50.000 0.00 0.00 0.00 4.02
3808 4141 4.935352 AAGCATCTATCTGACCTCTGAC 57.065 45.455 0.00 0.00 0.00 3.51
3809 4142 6.518032 GCAATAAGCATCTATCTGACCTCTGA 60.518 42.308 0.00 0.00 44.79 3.27
3810 4143 5.638657 GCAATAAGCATCTATCTGACCTCTG 59.361 44.000 0.00 0.00 44.79 3.35
3849 4193 3.120616 CGAATCAAACTTGCAAGCACATG 59.879 43.478 26.27 18.24 0.00 3.21
3896 4247 6.025280 GCGCTTTTTCCTGTTCGAAATATAA 58.975 36.000 0.00 0.00 32.00 0.98
3909 4260 1.304134 ATTCGGGGCGCTTTTTCCT 60.304 52.632 7.64 0.00 0.00 3.36
3922 4273 2.479049 CCTCTTTCAGCAATGCATTCGG 60.479 50.000 9.53 5.89 0.00 4.30
3923 4274 2.479049 CCCTCTTTCAGCAATGCATTCG 60.479 50.000 9.53 6.73 0.00 3.34
3976 4337 2.586079 CATGGGCACTACCTCGCG 60.586 66.667 0.00 0.00 39.10 5.87
4008 4370 4.122776 GGATGTGTCAATTCAGCTCGTAT 58.877 43.478 0.00 0.00 0.00 3.06
4010 4372 2.289631 TGGATGTGTCAATTCAGCTCGT 60.290 45.455 0.00 0.00 0.00 4.18
4028 4390 6.239600 CGGAGGGAGTATTTCATATCTTTGGA 60.240 42.308 0.00 0.00 0.00 3.53
4049 4411 7.921786 TTATTATTCCAATATGCTTCCGGAG 57.078 36.000 3.34 0.00 0.00 4.63
4050 4412 8.877864 ATTTATTATTCCAATATGCTTCCGGA 57.122 30.769 0.00 0.00 0.00 5.14
4051 4413 8.960591 AGATTTATTATTCCAATATGCTTCCGG 58.039 33.333 0.00 0.00 0.00 5.14
4071 4433 9.852784 TCCCTCAGTCCCATAATATAAGATTTA 57.147 33.333 0.00 0.00 0.00 1.40
4072 4434 8.757307 TCCCTCAGTCCCATAATATAAGATTT 57.243 34.615 0.00 0.00 0.00 2.17
4073 4435 7.964293 ACTCCCTCAGTCCCATAATATAAGATT 59.036 37.037 0.00 0.00 0.00 2.40
4074 4436 7.491681 ACTCCCTCAGTCCCATAATATAAGAT 58.508 38.462 0.00 0.00 0.00 2.40
4075 4437 6.875469 ACTCCCTCAGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
4076 4438 7.896496 AGTACTCCCTCAGTCCCATAATATAAG 59.104 40.741 0.00 0.00 36.43 1.73
4077 4439 7.776745 AGTACTCCCTCAGTCCCATAATATAA 58.223 38.462 0.00 0.00 36.43 0.98
4078 4440 7.358255 AGTACTCCCTCAGTCCCATAATATA 57.642 40.000 0.00 0.00 36.43 0.86
4079 4441 6.234404 AGTACTCCCTCAGTCCCATAATAT 57.766 41.667 0.00 0.00 36.43 1.28
4080 4442 5.642165 GAGTACTCCCTCAGTCCCATAATA 58.358 45.833 12.13 0.00 36.43 0.98
4081 4443 4.484912 GAGTACTCCCTCAGTCCCATAAT 58.515 47.826 12.13 0.00 36.43 1.28
4082 4444 3.687551 CGAGTACTCCCTCAGTCCCATAA 60.688 52.174 17.23 0.00 36.43 1.90
4083 4445 2.158652 CGAGTACTCCCTCAGTCCCATA 60.159 54.545 17.23 0.00 36.43 2.74
4084 4446 1.410365 CGAGTACTCCCTCAGTCCCAT 60.410 57.143 17.23 0.00 36.43 4.00
4085 4447 0.034380 CGAGTACTCCCTCAGTCCCA 60.034 60.000 17.23 0.00 36.43 4.37
4086 4448 0.752376 CCGAGTACTCCCTCAGTCCC 60.752 65.000 17.23 0.00 36.43 4.46
4087 4449 0.752376 CCCGAGTACTCCCTCAGTCC 60.752 65.000 17.23 0.00 36.43 3.85
4088 4450 1.385756 GCCCGAGTACTCCCTCAGTC 61.386 65.000 17.23 0.00 36.43 3.51
4089 4451 1.380112 GCCCGAGTACTCCCTCAGT 60.380 63.158 17.23 0.00 39.41 3.41
4090 4452 1.379977 TGCCCGAGTACTCCCTCAG 60.380 63.158 17.23 2.62 0.00 3.35
4091 4453 1.681327 GTGCCCGAGTACTCCCTCA 60.681 63.158 17.23 9.07 0.00 3.86
4092 4454 2.772691 CGTGCCCGAGTACTCCCTC 61.773 68.421 17.23 6.63 35.63 4.30
4093 4455 2.202236 TACGTGCCCGAGTACTCCCT 62.202 60.000 17.23 0.00 37.88 4.20
4094 4456 1.722636 CTACGTGCCCGAGTACTCCC 61.723 65.000 17.23 6.60 37.88 4.30
4095 4457 0.745845 TCTACGTGCCCGAGTACTCC 60.746 60.000 17.23 4.06 37.88 3.85
4096 4458 0.376502 GTCTACGTGCCCGAGTACTC 59.623 60.000 13.18 13.18 37.88 2.59
4097 4459 1.028868 GGTCTACGTGCCCGAGTACT 61.029 60.000 0.00 0.00 37.88 2.73
4098 4460 1.028868 AGGTCTACGTGCCCGAGTAC 61.029 60.000 0.00 0.00 37.88 2.73
4099 4461 0.322816 AAGGTCTACGTGCCCGAGTA 60.323 55.000 0.00 0.00 37.88 2.59
4100 4462 0.322816 TAAGGTCTACGTGCCCGAGT 60.323 55.000 0.00 0.00 37.88 4.18
4101 4463 0.813184 TTAAGGTCTACGTGCCCGAG 59.187 55.000 0.00 0.00 37.88 4.63
4102 4464 0.813184 CTTAAGGTCTACGTGCCCGA 59.187 55.000 0.00 0.00 37.88 5.14
4103 4465 0.813184 TCTTAAGGTCTACGTGCCCG 59.187 55.000 0.00 0.00 40.83 6.13
4104 4466 1.136500 CCTCTTAAGGTCTACGTGCCC 59.864 57.143 0.00 0.00 37.94 5.36
4105 4467 1.471153 GCCTCTTAAGGTCTACGTGCC 60.471 57.143 0.00 0.00 45.34 5.01
4106 4468 1.477295 AGCCTCTTAAGGTCTACGTGC 59.523 52.381 0.00 0.00 45.34 5.34
4107 4469 3.512680 CAAGCCTCTTAAGGTCTACGTG 58.487 50.000 0.00 0.00 45.34 4.49
4108 4470 2.496470 CCAAGCCTCTTAAGGTCTACGT 59.504 50.000 1.85 0.00 45.34 3.57
4109 4471 2.758979 TCCAAGCCTCTTAAGGTCTACG 59.241 50.000 1.85 0.00 45.34 3.51
4110 4472 4.698575 CATCCAAGCCTCTTAAGGTCTAC 58.301 47.826 1.85 0.00 45.34 2.59
4111 4473 3.134804 GCATCCAAGCCTCTTAAGGTCTA 59.865 47.826 1.85 0.00 45.34 2.59
4112 4474 2.092699 GCATCCAAGCCTCTTAAGGTCT 60.093 50.000 1.85 0.00 45.34 3.85
4113 4475 2.293170 GCATCCAAGCCTCTTAAGGTC 58.707 52.381 1.85 0.00 45.34 3.85
4114 4476 1.635487 TGCATCCAAGCCTCTTAAGGT 59.365 47.619 1.85 0.00 45.34 3.50
4115 4477 2.425143 TGCATCCAAGCCTCTTAAGG 57.575 50.000 1.85 0.00 46.44 2.69
4116 4478 3.949754 TGATTGCATCCAAGCCTCTTAAG 59.050 43.478 0.00 0.00 36.55 1.85
4117 4479 3.966979 TGATTGCATCCAAGCCTCTTAA 58.033 40.909 0.00 0.00 36.55 1.85
4118 4480 3.650281 TGATTGCATCCAAGCCTCTTA 57.350 42.857 0.00 0.00 36.55 2.10
4119 4481 2.519771 TGATTGCATCCAAGCCTCTT 57.480 45.000 0.00 0.00 36.55 2.85


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

AutoCloner maintained by Alex Coulton.