Multiple sequence alignment - TraesCS4D01G149200

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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 TraesCS4D01G149200 chr4D 100.000 4417 0 0 1 4417 152920268 152915852 0.000000e+00 8157.0
1 TraesCS4D01G149200 chr4D 86.105 842 110 7 1 837 463332546 463333385 0.000000e+00 900.0
2 TraesCS4D01G149200 chr4D 77.198 364 63 12 3228 3577 74408498 74408855 1.250000e-45 195.0
3 TraesCS4D01G149200 chr4A 95.203 1626 64 6 999 2611 250425614 250427238 0.000000e+00 2558.0
4 TraesCS4D01G149200 chr4A 93.810 1034 52 6 2608 3634 250427623 250428651 0.000000e+00 1544.0
5 TraesCS4D01G149200 chr4A 92.509 801 44 6 3626 4417 250428929 250429722 0.000000e+00 1133.0
6 TraesCS4D01G149200 chr4A 84.524 84 9 4 4102 4183 476837892 476837973 3.660000e-11 80.5
7 TraesCS4D01G149200 chr4A 94.595 37 1 1 3229 3265 734958848 734958813 6.170000e-04 56.5
8 TraesCS4D01G149200 chr7B 91.510 1331 79 17 998 2299 483531170 483532495 0.000000e+00 1801.0
9 TraesCS4D01G149200 chr7B 92.448 384 26 3 2629 3010 483533495 483533877 3.000000e-151 545.0
10 TraesCS4D01G149200 chr7B 89.333 225 15 3 2345 2569 483533263 483533478 1.570000e-69 274.0
11 TraesCS4D01G149200 chr7D 91.298 1333 80 16 997 2299 461089108 461090434 0.000000e+00 1786.0
12 TraesCS4D01G149200 chr7D 87.277 841 94 11 1 834 428037386 428038220 0.000000e+00 948.0
13 TraesCS4D01G149200 chr7D 89.260 689 66 8 1 685 630509370 630508686 0.000000e+00 856.0
14 TraesCS4D01G149200 chr7D 93.750 384 21 3 2629 3010 461091951 461092333 1.380000e-159 573.0
15 TraesCS4D01G149200 chr7D 90.667 225 12 3 2345 2569 461091719 461091934 1.550000e-74 291.0
16 TraesCS4D01G149200 chr7D 81.712 257 31 12 3237 3479 64473878 64473624 2.690000e-47 200.0
17 TraesCS4D01G149200 chr1D 86.417 854 94 19 1 837 63920322 63919474 0.000000e+00 915.0
18 TraesCS4D01G149200 chr4B 86.342 842 105 8 3 837 578667685 578668523 0.000000e+00 909.0
19 TraesCS4D01G149200 chr1A 85.514 856 102 17 1 838 62977800 62976949 0.000000e+00 874.0
20 TraesCS4D01G149200 chr1A 80.912 351 47 13 3237 3571 47213006 47212660 4.380000e-65 259.0
21 TraesCS4D01G149200 chr3B 87.047 772 84 10 1 769 377434960 377435718 0.000000e+00 857.0
22 TraesCS4D01G149200 chr3B 78.992 357 57 11 3234 3576 404620021 404620373 1.240000e-55 228.0
23 TraesCS4D01G149200 chr3D 85.082 858 94 16 1 838 554943575 554942732 0.000000e+00 845.0
24 TraesCS4D01G149200 chr2D 88.937 687 67 8 15 696 170818292 170818974 0.000000e+00 839.0
25 TraesCS4D01G149200 chr5B 85.733 771 93 11 1 767 368492230 368491473 0.000000e+00 798.0
26 TraesCS4D01G149200 chr5B 80.738 244 32 11 3271 3501 540321303 540321062 4.540000e-40 176.0
27 TraesCS4D01G149200 chr5B 89.431 123 10 1 719 838 679576913 679576791 7.650000e-33 152.0
28 TraesCS4D01G149200 chr5B 92.857 56 4 0 858 913 47095421 47095476 1.020000e-11 82.4
29 TraesCS4D01G149200 chr5B 86.957 69 8 1 845 913 368491440 368491373 4.740000e-10 76.8
30 TraesCS4D01G149200 chr3A 80.839 715 95 22 133 838 370395311 370395992 1.410000e-144 523.0
31 TraesCS4D01G149200 chr5D 78.892 379 61 13 3213 3575 409571965 409571590 5.710000e-59 239.0
32 TraesCS4D01G149200 chr5D 78.592 355 57 16 3237 3575 6446480 6446831 2.680000e-52 217.0
33 TraesCS4D01G149200 chr5D 94.643 56 3 0 859 914 424779933 424779988 2.190000e-13 87.9
34 TraesCS4D01G149200 chr5A 78.310 355 58 16 3237 3575 3217263 3216912 1.240000e-50 211.0
35 TraesCS4D01G149200 chr2B 85.235 149 19 2 693 838 225812866 225812718 2.750000e-32 150.0


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 TraesCS4D01G149200 chr4D 152915852 152920268 4416 True 8157.000000 8157 100.000000 1 4417 1 chr4D.!!$R1 4416
1 TraesCS4D01G149200 chr4D 463332546 463333385 839 False 900.000000 900 86.105000 1 837 1 chr4D.!!$F2 836
2 TraesCS4D01G149200 chr4A 250425614 250429722 4108 False 1745.000000 2558 93.840667 999 4417 3 chr4A.!!$F2 3418
3 TraesCS4D01G149200 chr7B 483531170 483533877 2707 False 873.333333 1801 91.097000 998 3010 3 chr7B.!!$F1 2012
4 TraesCS4D01G149200 chr7D 428037386 428038220 834 False 948.000000 948 87.277000 1 834 1 chr7D.!!$F1 833
5 TraesCS4D01G149200 chr7D 461089108 461092333 3225 False 883.333333 1786 91.905000 997 3010 3 chr7D.!!$F2 2013
6 TraesCS4D01G149200 chr7D 630508686 630509370 684 True 856.000000 856 89.260000 1 685 1 chr7D.!!$R2 684
7 TraesCS4D01G149200 chr1D 63919474 63920322 848 True 915.000000 915 86.417000 1 837 1 chr1D.!!$R1 836
8 TraesCS4D01G149200 chr4B 578667685 578668523 838 False 909.000000 909 86.342000 3 837 1 chr4B.!!$F1 834
9 TraesCS4D01G149200 chr1A 62976949 62977800 851 True 874.000000 874 85.514000 1 838 1 chr1A.!!$R2 837
10 TraesCS4D01G149200 chr3B 377434960 377435718 758 False 857.000000 857 87.047000 1 769 1 chr3B.!!$F1 768
11 TraesCS4D01G149200 chr3D 554942732 554943575 843 True 845.000000 845 85.082000 1 838 1 chr3D.!!$R1 837
12 TraesCS4D01G149200 chr2D 170818292 170818974 682 False 839.000000 839 88.937000 15 696 1 chr2D.!!$F1 681
13 TraesCS4D01G149200 chr5B 368491373 368492230 857 True 437.400000 798 86.345000 1 913 2 chr5B.!!$R3 912
14 TraesCS4D01G149200 chr3A 370395311 370395992 681 False 523.000000 523 80.839000 133 838 1 chr3A.!!$F1 705

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
934 981 0.036765 TGCGCGACCTTAATCCTGTT 60.037 50.0 12.1 0.0 0.0 3.16 F
935 982 0.651031 GCGCGACCTTAATCCTGTTC 59.349 55.0 12.1 0.0 0.0 3.18 F
2384 4092 0.036765 TTATTCCCGTGCGTGCTTCT 60.037 50.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2042 0.103026 TCTCCATGCGGTCATTCTCG 59.897 55.000 0.00 0.00 0.00 4.04 R
2386 4094 3.812053 GCTAGCCCAAAGTCACATATCTG 59.188 47.826 2.29 0.00 0.00 2.90 R
4128 6529 0.036010 CACTACCAGGCCAGGTTGAG 60.036 60.000 30.23 22.26 43.08 3.02 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
90 91 1.671261 GCAAATGGCCGCACATACAAA 60.671 47.619 0.00 0.00 36.11 2.83
141 142 2.224450 CCCGAGGTGGAGTACTTTTGTT 60.224 50.000 0.00 0.00 42.00 2.83
155 157 7.044798 AGTACTTTTGTTAAGCCAATTGCAAA 58.955 30.769 1.71 1.38 44.83 3.68
225 227 3.452627 GCTAGGAAAGATGTTGAGAGGGA 59.547 47.826 0.00 0.00 0.00 4.20
238 242 4.051661 TGAGAGGGATTTGGATTTTGCT 57.948 40.909 0.00 0.00 0.00 3.91
363 368 5.063880 AGAATGGGCGTGGATAGAATTTAC 58.936 41.667 0.00 0.00 0.00 2.01
385 390 5.109903 ACATTACACCTTCTATCGCTTGAC 58.890 41.667 0.00 0.00 0.00 3.18
404 409 0.461339 CGGGTGTACGCTTTATGCCT 60.461 55.000 6.35 0.00 38.78 4.75
471 476 7.774157 ACAATGAAATTAGAGACTCTGATGCAT 59.226 33.333 15.55 15.10 32.46 3.96
472 477 7.731882 ATGAAATTAGAGACTCTGATGCATG 57.268 36.000 15.55 0.00 0.00 4.06
473 478 6.881570 TGAAATTAGAGACTCTGATGCATGA 58.118 36.000 15.55 0.00 0.00 3.07
548 554 4.816925 AGAGCCGCCTAGTTTCATTATTTC 59.183 41.667 0.00 0.00 0.00 2.17
781 823 5.895636 TTACATCTCCGTTTTGCATCATT 57.104 34.783 0.00 0.00 0.00 2.57
883 930 9.624697 TTTTTACATCTCATGTTTTACATCTGC 57.375 29.630 0.00 0.00 41.63 4.26
884 931 5.475273 ACATCTCATGTTTTACATCTGCG 57.525 39.130 0.00 0.00 41.63 5.18
918 965 7.633621 TCTTTTATTGAAGATGCTCTTATGCG 58.366 34.615 0.00 0.00 36.73 4.73
919 966 3.892918 ATTGAAGATGCTCTTATGCGC 57.107 42.857 0.00 0.00 36.73 6.09
920 967 1.211743 TGAAGATGCTCTTATGCGCG 58.788 50.000 0.00 0.00 36.73 6.86
921 968 1.202405 TGAAGATGCTCTTATGCGCGA 60.202 47.619 12.10 0.00 36.73 5.87
922 969 1.191204 GAAGATGCTCTTATGCGCGAC 59.809 52.381 12.10 0.88 36.73 5.19
923 970 0.598680 AGATGCTCTTATGCGCGACC 60.599 55.000 12.10 0.00 35.36 4.79
924 971 0.598680 GATGCTCTTATGCGCGACCT 60.599 55.000 12.10 0.00 35.36 3.85
925 972 0.179073 ATGCTCTTATGCGCGACCTT 60.179 50.000 12.10 0.00 35.36 3.50
926 973 0.458260 TGCTCTTATGCGCGACCTTA 59.542 50.000 12.10 0.00 35.36 2.69
927 974 1.134936 TGCTCTTATGCGCGACCTTAA 60.135 47.619 12.10 0.92 35.36 1.85
928 975 2.135933 GCTCTTATGCGCGACCTTAAT 58.864 47.619 12.10 0.00 0.00 1.40
929 976 2.155924 GCTCTTATGCGCGACCTTAATC 59.844 50.000 12.10 0.00 0.00 1.75
930 977 2.731976 CTCTTATGCGCGACCTTAATCC 59.268 50.000 12.10 0.00 0.00 3.01
931 978 2.364324 TCTTATGCGCGACCTTAATCCT 59.636 45.455 12.10 0.00 0.00 3.24
932 979 2.148916 TATGCGCGACCTTAATCCTG 57.851 50.000 12.10 0.00 0.00 3.86
933 980 0.178068 ATGCGCGACCTTAATCCTGT 59.822 50.000 12.10 0.00 0.00 4.00
934 981 0.036765 TGCGCGACCTTAATCCTGTT 60.037 50.000 12.10 0.00 0.00 3.16
935 982 0.651031 GCGCGACCTTAATCCTGTTC 59.349 55.000 12.10 0.00 0.00 3.18
936 983 1.287425 CGCGACCTTAATCCTGTTCC 58.713 55.000 0.00 0.00 0.00 3.62
937 984 1.404986 CGCGACCTTAATCCTGTTCCA 60.405 52.381 0.00 0.00 0.00 3.53
938 985 2.280628 GCGACCTTAATCCTGTTCCAG 58.719 52.381 0.00 0.00 0.00 3.86
939 986 2.354805 GCGACCTTAATCCTGTTCCAGT 60.355 50.000 0.00 0.00 0.00 4.00
940 987 3.868754 GCGACCTTAATCCTGTTCCAGTT 60.869 47.826 0.00 0.00 0.00 3.16
941 988 3.684788 CGACCTTAATCCTGTTCCAGTTG 59.315 47.826 0.00 0.00 0.00 3.16
942 989 4.652822 GACCTTAATCCTGTTCCAGTTGT 58.347 43.478 0.00 0.00 0.00 3.32
943 990 5.061721 ACCTTAATCCTGTTCCAGTTGTT 57.938 39.130 0.00 0.00 0.00 2.83
944 991 5.454966 ACCTTAATCCTGTTCCAGTTGTTT 58.545 37.500 0.00 0.00 0.00 2.83
945 992 5.535030 ACCTTAATCCTGTTCCAGTTGTTTC 59.465 40.000 0.00 0.00 0.00 2.78
946 993 5.334879 CCTTAATCCTGTTCCAGTTGTTTCG 60.335 44.000 0.00 0.00 0.00 3.46
947 994 2.992124 TCCTGTTCCAGTTGTTTCGA 57.008 45.000 0.00 0.00 0.00 3.71
948 995 3.269538 TCCTGTTCCAGTTGTTTCGAA 57.730 42.857 0.00 0.00 0.00 3.71
949 996 3.611970 TCCTGTTCCAGTTGTTTCGAAA 58.388 40.909 6.47 6.47 0.00 3.46
950 997 4.011023 TCCTGTTCCAGTTGTTTCGAAAA 58.989 39.130 13.10 0.34 0.00 2.29
951 998 4.095782 TCCTGTTCCAGTTGTTTCGAAAAG 59.904 41.667 13.10 2.11 0.00 2.27
952 999 3.765026 TGTTCCAGTTGTTTCGAAAAGC 58.235 40.909 13.10 5.87 0.00 3.51
953 1000 3.191581 TGTTCCAGTTGTTTCGAAAAGCA 59.808 39.130 13.10 4.52 0.00 3.91
954 1001 4.170256 GTTCCAGTTGTTTCGAAAAGCAA 58.830 39.130 13.10 10.81 33.78 3.91
955 1002 4.442375 TCCAGTTGTTTCGAAAAGCAAA 57.558 36.364 13.10 2.51 37.34 3.68
956 1003 4.170256 TCCAGTTGTTTCGAAAAGCAAAC 58.830 39.130 13.10 13.95 37.34 2.93
957 1004 3.923461 CCAGTTGTTTCGAAAAGCAAACA 59.077 39.130 13.10 2.81 40.05 2.83
958 1005 4.201580 CCAGTTGTTTCGAAAAGCAAACAC 60.202 41.667 13.10 3.28 41.18 3.32
959 1006 3.924073 AGTTGTTTCGAAAAGCAAACACC 59.076 39.130 13.10 0.00 41.18 4.16
960 1007 3.859411 TGTTTCGAAAAGCAAACACCT 57.141 38.095 13.10 0.00 37.54 4.00
961 1008 4.181309 TGTTTCGAAAAGCAAACACCTT 57.819 36.364 13.10 0.00 37.54 3.50
962 1009 4.561105 TGTTTCGAAAAGCAAACACCTTT 58.439 34.783 13.10 0.00 37.54 3.11
963 1010 4.623595 TGTTTCGAAAAGCAAACACCTTTC 59.376 37.500 13.10 0.00 37.54 2.62
964 1011 4.442375 TTCGAAAAGCAAACACCTTTCA 57.558 36.364 0.00 0.00 31.69 2.69
965 1012 3.765026 TCGAAAAGCAAACACCTTTCAC 58.235 40.909 0.00 0.00 31.69 3.18
966 1013 3.442273 TCGAAAAGCAAACACCTTTCACT 59.558 39.130 0.00 0.00 31.69 3.41
967 1014 3.547468 CGAAAAGCAAACACCTTTCACTG 59.453 43.478 0.00 0.00 31.69 3.66
968 1015 4.494484 GAAAAGCAAACACCTTTCACTGT 58.506 39.130 0.00 0.00 31.69 3.55
969 1016 5.646606 GAAAAGCAAACACCTTTCACTGTA 58.353 37.500 0.00 0.00 31.69 2.74
970 1017 5.852282 AAAGCAAACACCTTTCACTGTAT 57.148 34.783 0.00 0.00 0.00 2.29
971 1018 6.952773 AAAGCAAACACCTTTCACTGTATA 57.047 33.333 0.00 0.00 0.00 1.47
972 1019 6.952773 AAGCAAACACCTTTCACTGTATAA 57.047 33.333 0.00 0.00 0.00 0.98
973 1020 6.952773 AGCAAACACCTTTCACTGTATAAA 57.047 33.333 0.00 0.00 0.00 1.40
974 1021 7.341445 AGCAAACACCTTTCACTGTATAAAA 57.659 32.000 0.00 0.00 0.00 1.52
975 1022 7.777095 AGCAAACACCTTTCACTGTATAAAAA 58.223 30.769 0.00 0.00 0.00 1.94
992 1039 3.840890 AAAAACGTGTGTGCTTTCTGA 57.159 38.095 0.00 0.00 0.00 3.27
993 1040 4.370364 AAAAACGTGTGTGCTTTCTGAT 57.630 36.364 0.00 0.00 0.00 2.90
994 1041 3.609103 AAACGTGTGTGCTTTCTGATC 57.391 42.857 0.00 0.00 0.00 2.92
995 1042 2.238942 ACGTGTGTGCTTTCTGATCA 57.761 45.000 0.00 0.00 0.00 2.92
1153 1200 1.599171 CGCCATCGTTTGCAAGAAACA 60.599 47.619 0.00 0.00 0.00 2.83
1154 1201 2.468831 GCCATCGTTTGCAAGAAACAA 58.531 42.857 0.00 0.00 0.00 2.83
1155 1202 3.059166 GCCATCGTTTGCAAGAAACAAT 58.941 40.909 0.00 0.00 0.00 2.71
1159 1207 6.580476 CCATCGTTTGCAAGAAACAATAAAC 58.420 36.000 0.00 0.00 0.00 2.01
1287 1335 7.530426 AGACAAAGCAAGTAAAAGATCCAAT 57.470 32.000 0.00 0.00 0.00 3.16
1297 1345 8.362639 CAAGTAAAAGATCCAATATTCCATGGG 58.637 37.037 13.02 0.00 37.31 4.00
1398 1453 3.181462 CCATGGATTTGACCTCTCGATGA 60.181 47.826 5.56 0.00 29.64 2.92
1826 1899 1.745264 GCGCTGAGGCTATCCTTCT 59.255 57.895 0.00 0.00 44.46 2.85
2003 2076 0.251634 GGAGAGCTTCCTGTTGGAGG 59.748 60.000 7.46 0.00 44.24 4.30
2175 2248 1.684734 GGGAGGCGAGGTACAAGGA 60.685 63.158 0.00 0.00 0.00 3.36
2332 2503 4.466567 TTTGCATTACGTCTTGTCTGTG 57.533 40.909 0.00 0.00 0.00 3.66
2384 4092 0.036765 TTATTCCCGTGCGTGCTTCT 60.037 50.000 0.00 0.00 0.00 2.85
2385 4093 0.036765 TATTCCCGTGCGTGCTTCTT 60.037 50.000 0.00 0.00 0.00 2.52
2386 4094 1.298859 ATTCCCGTGCGTGCTTCTTC 61.299 55.000 0.00 0.00 0.00 2.87
2485 4193 1.666872 GGGTCGGTCGGTCTGTTTG 60.667 63.158 0.00 0.00 0.00 2.93
2489 4197 1.267806 GTCGGTCGGTCTGTTTGTCTA 59.732 52.381 0.00 0.00 0.00 2.59
2519 4227 3.302434 CACAATCACGCTGATGCAATTTC 59.698 43.478 0.00 0.00 37.15 2.17
2570 4278 4.488879 GGATCGAGTTTAAGTAACACGGT 58.511 43.478 7.43 1.06 44.93 4.83
2590 4298 5.943416 ACGGTCAGGTGAATGAATGAATTAA 59.057 36.000 0.00 0.00 0.00 1.40
2597 4305 9.655769 CAGGTGAATGAATGAATTAAATCGTAG 57.344 33.333 0.00 0.00 0.00 3.51
2598 4306 9.396022 AGGTGAATGAATGAATTAAATCGTAGT 57.604 29.630 0.00 0.00 0.00 2.73
2756 4856 0.591170 CATCGACGGCAAAAACCACT 59.409 50.000 0.00 0.00 0.00 4.00
2796 4896 3.123050 GCTTGTTTCCAGCGTTCAAAAT 58.877 40.909 0.00 0.00 0.00 1.82
3033 5135 6.074698 TCCCTCCTTTCTTTCCGATTTATT 57.925 37.500 0.00 0.00 0.00 1.40
3170 5272 2.607499 ACATCAAGTGAATTTGGGCCA 58.393 42.857 0.00 0.00 0.00 5.36
3190 5292 5.630680 GGCCATTTATTTATGTGATTCAGCG 59.369 40.000 0.00 0.00 0.00 5.18
3211 5313 5.538813 AGCGACCCAGATGTCATAATACTAA 59.461 40.000 0.00 0.00 34.88 2.24
3224 5326 8.952278 TGTCATAATACTAAAGCAAAATTCGGT 58.048 29.630 0.00 0.00 0.00 4.69
3252 5359 1.171308 TAGTAGATGATACCCCGCGC 58.829 55.000 0.00 0.00 0.00 6.86
3260 5367 4.799824 TACCCCGCGCGTTGCTAC 62.800 66.667 29.95 0.00 43.27 3.58
3273 5380 0.885196 TTGCTACGGGAATTGGTTGC 59.115 50.000 0.00 0.00 35.84 4.17
3275 5382 0.885196 GCTACGGGAATTGGTTGCAA 59.115 50.000 0.00 0.00 35.47 4.08
3276 5383 1.476488 GCTACGGGAATTGGTTGCAAT 59.524 47.619 0.59 0.00 35.47 3.56
3288 5395 8.284693 GGAATTGGTTGCAATATATTTCAATGC 58.715 33.333 12.65 6.60 37.52 3.56
3456 5565 1.780309 TGTGGTGATGGGTCTTTTCCT 59.220 47.619 0.00 0.00 0.00 3.36
3463 5572 5.376625 GTGATGGGTCTTTTCCTATGCATA 58.623 41.667 6.20 6.20 0.00 3.14
3489 5598 8.308931 AGTTGCATGTTGAGATGTGATTTATTT 58.691 29.630 0.00 0.00 0.00 1.40
3520 5629 3.362870 TGTATGGTGATGTGGCAATGA 57.637 42.857 0.00 0.00 0.00 2.57
3530 5639 5.517411 GTGATGTGGCAATGATTACATGTTG 59.483 40.000 2.30 0.00 36.79 3.33
3532 5641 5.918426 TGTGGCAATGATTACATGTTGAT 57.082 34.783 2.30 0.00 36.79 2.57
3624 5733 4.479786 ACAGCCTCTTATCTTCAACTCC 57.520 45.455 0.00 0.00 0.00 3.85
3630 5739 8.087750 CAGCCTCTTATCTTCAACTCCTTATAG 58.912 40.741 0.00 0.00 0.00 1.31
3652 6046 2.604046 ATCACATCTCTAACGGTGGC 57.396 50.000 0.00 0.00 32.29 5.01
3693 6087 9.685828 TCCTTAAATTTAACTCAAACGAATTGG 57.314 29.630 6.54 2.78 39.62 3.16
3699 6093 0.243636 CTCAAACGAATTGGCCCCAC 59.756 55.000 0.00 0.00 39.62 4.61
3718 6112 4.331168 CCCACGTGAAAATCTCTCTTCATC 59.669 45.833 19.30 0.00 34.26 2.92
3724 6118 7.659390 ACGTGAAAATCTCTCTTCATCTTCTTT 59.341 33.333 0.00 0.00 34.26 2.52
3772 6173 0.378962 CGACCAGCTAGAGTTCTCCG 59.621 60.000 0.00 0.00 0.00 4.63
3797 6198 1.657594 CAGCAACAGCGAGTGATGTAG 59.342 52.381 0.00 0.00 45.67 2.74
3850 6251 1.667724 CAACGACAAGGATGAGGATGC 59.332 52.381 0.00 0.00 0.00 3.91
3861 6262 5.153675 AGGATGAGGATGCAGAAGAAGATA 58.846 41.667 0.00 0.00 0.00 1.98
3936 6337 2.282462 CTGGTCCTTGGTGGTGGC 60.282 66.667 0.00 0.00 37.07 5.01
3960 6361 4.678269 CGCACACACAGCAGCAGC 62.678 66.667 0.00 0.00 42.56 5.25
3964 6365 1.527611 ACACACAGCAGCAGCACAT 60.528 52.632 3.17 0.00 45.49 3.21
3966 6367 0.167470 CACACAGCAGCAGCACATAC 59.833 55.000 3.17 0.00 45.49 2.39
3997 6398 1.004560 ACACGCAGCAGTAGCACAT 60.005 52.632 0.00 0.00 45.49 3.21
4015 6416 4.096311 CACATACACGTAGCAGTAGACAC 58.904 47.826 0.00 0.00 0.00 3.67
4028 6429 4.677250 GCAGTAGACACCTACACCATGTAC 60.677 50.000 0.00 0.00 45.95 2.90
4040 6441 0.744057 CCATGTACGATGCCTGCACA 60.744 55.000 0.00 0.00 0.00 4.57
4062 6463 0.179215 GTTGCATCTTTCGAGCCACG 60.179 55.000 0.00 0.00 44.09 4.94
4128 6529 1.177401 GGCCATTCAGTTGTTCCTCC 58.823 55.000 0.00 0.00 0.00 4.30
4134 6535 2.930826 TCAGTTGTTCCTCCTCAACC 57.069 50.000 0.00 0.00 43.10 3.77
4136 6537 2.104792 TCAGTTGTTCCTCCTCAACCTG 59.895 50.000 0.00 0.00 43.10 4.00
4137 6538 1.421646 AGTTGTTCCTCCTCAACCTGG 59.578 52.381 0.00 0.00 43.10 4.45
4138 6539 0.110486 TTGTTCCTCCTCAACCTGGC 59.890 55.000 0.00 0.00 0.00 4.85
4139 6540 1.002011 GTTCCTCCTCAACCTGGCC 60.002 63.158 0.00 0.00 0.00 5.36
4141 6542 1.492133 TTCCTCCTCAACCTGGCCTG 61.492 60.000 3.32 2.54 0.00 4.85
4142 6543 2.673523 CTCCTCAACCTGGCCTGG 59.326 66.667 26.14 26.14 0.00 4.45
4158 6561 3.128764 GGCCTGGTAGTGCTTTAAACATC 59.871 47.826 0.00 0.00 0.00 3.06
4175 6578 1.674441 CATCGTGCATGCCAAGATTCT 59.326 47.619 16.68 0.00 40.07 2.40
4211 6614 5.576774 GCCTACTAAACATCCAATTTTGCAC 59.423 40.000 0.00 0.00 0.00 4.57
4226 6629 4.636435 CACCGCCCGGACTTGGTT 62.636 66.667 14.44 0.00 38.96 3.67
4227 6630 4.636435 ACCGCCCGGACTTGGTTG 62.636 66.667 14.44 0.00 38.96 3.77
4303 6706 1.212616 GCGTACATGAGCTAGCTTGG 58.787 55.000 20.42 13.64 0.00 3.61
4353 6756 1.608590 ACGCACAAGGGAAAACTCATG 59.391 47.619 0.00 0.00 0.00 3.07
4361 6764 3.950397 AGGGAAAACTCATGTATGCGAA 58.050 40.909 0.00 0.00 0.00 4.70
4381 6784 2.457366 ACATTGGAGTGACGGAGAAC 57.543 50.000 0.00 0.00 0.00 3.01
4405 6808 2.068519 CAGAGCTGCAAATGTACACGA 58.931 47.619 0.00 0.00 0.00 4.35
4406 6809 2.674852 CAGAGCTGCAAATGTACACGAT 59.325 45.455 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 4.162320 CCATCCGCAAGATAGTACCCATAT 59.838 45.833 0.00 0.00 43.02 1.78
141 142 2.439507 TGGGGTTTTTGCAATTGGCTTA 59.560 40.909 7.72 0.00 45.15 3.09
155 157 5.138276 GAGTTCTTTCTTACCTTGGGGTTT 58.862 41.667 0.00 0.00 44.73 3.27
238 242 2.805671 CGCACGATAGCAAATTGGGATA 59.194 45.455 0.00 0.00 42.67 2.59
321 326 5.469373 TTCTCAATGATCACGTTATGCAC 57.531 39.130 0.00 0.00 0.00 4.57
330 335 2.032550 CACGCCCATTCTCAATGATCAC 59.967 50.000 0.00 0.00 41.46 3.06
363 368 4.207224 CGTCAAGCGATAGAAGGTGTAATG 59.793 45.833 0.00 0.00 44.77 1.90
379 384 1.226030 AAAGCGTACACCCGTCAAGC 61.226 55.000 0.00 0.00 0.00 4.01
385 390 2.547218 ATAGGCATAAAGCGTACACCCG 60.547 50.000 0.00 0.00 45.35 5.28
404 409 4.464947 TGATTCGCTCCTCTCTTCTCATA 58.535 43.478 0.00 0.00 0.00 2.15
434 439 8.336235 TCTCTAATTTCATTGTACCCCTTCATT 58.664 33.333 0.00 0.00 0.00 2.57
442 447 9.039870 CATCAGAGTCTCTAATTTCATTGTACC 57.960 37.037 0.94 0.00 0.00 3.34
471 476 6.772605 TCAAATCCTTCTGAAGTTGATCTCA 58.227 36.000 15.72 0.00 30.34 3.27
472 477 7.201714 CCATCAAATCCTTCTGAAGTTGATCTC 60.202 40.741 22.01 0.00 38.64 2.75
473 478 6.602406 CCATCAAATCCTTCTGAAGTTGATCT 59.398 38.462 22.01 9.26 38.64 2.75
548 554 8.351495 ACATAGTTTTGCACAATACAACAAAG 57.649 30.769 6.71 0.00 33.87 2.77
630 657 6.795399 ACTTAAAAGTTTCACATGTCCACAG 58.205 36.000 0.00 0.00 35.21 3.66
659 686 9.410556 ACAGAAATTGAAATAAAACAATCGGAG 57.589 29.630 0.00 0.00 35.99 4.63
682 709 2.242113 GGCTGCTGTTCAGTCACAG 58.758 57.895 0.00 0.00 46.44 3.66
728 770 5.263599 ACTCCAATAGGTGATGCAAAATGA 58.736 37.500 0.00 0.00 35.89 2.57
857 904 9.624697 GCAGATGTAAAACATGAGATGTAAAAA 57.375 29.630 0.00 0.00 44.07 1.94
869 916 5.468592 TGCAAATTCGCAGATGTAAAACAT 58.531 33.333 0.00 0.00 38.12 2.71
875 922 5.565592 AAAGATGCAAATTCGCAGATGTA 57.434 34.783 0.00 0.00 46.99 2.29
882 929 7.510428 TCTTCAATAAAAGATGCAAATTCGC 57.490 32.000 0.00 0.00 30.38 4.70
913 960 1.411246 ACAGGATTAAGGTCGCGCATA 59.589 47.619 8.75 0.00 0.00 3.14
914 961 0.178068 ACAGGATTAAGGTCGCGCAT 59.822 50.000 8.75 0.00 0.00 4.73
915 962 0.036765 AACAGGATTAAGGTCGCGCA 60.037 50.000 8.75 0.00 0.00 6.09
916 963 0.651031 GAACAGGATTAAGGTCGCGC 59.349 55.000 0.00 0.00 0.00 6.86
917 964 1.287425 GGAACAGGATTAAGGTCGCG 58.713 55.000 0.00 0.00 0.00 5.87
918 965 2.396590 TGGAACAGGATTAAGGTCGC 57.603 50.000 0.00 0.00 0.00 5.19
930 977 9.439539 GTTTGCTTTTCGAAACAACTGGAACAG 62.440 40.741 10.79 2.35 45.22 3.16
931 978 3.191581 TGCTTTTCGAAACAACTGGAACA 59.808 39.130 10.79 0.00 0.00 3.18
932 979 3.765026 TGCTTTTCGAAACAACTGGAAC 58.235 40.909 10.79 0.00 0.00 3.62
933 980 4.442375 TTGCTTTTCGAAACAACTGGAA 57.558 36.364 10.79 3.85 0.00 3.53
934 981 4.170256 GTTTGCTTTTCGAAACAACTGGA 58.830 39.130 10.79 0.00 33.16 3.86
935 982 3.923461 TGTTTGCTTTTCGAAACAACTGG 59.077 39.130 10.79 0.00 38.73 4.00
936 983 4.201580 GGTGTTTGCTTTTCGAAACAACTG 60.202 41.667 10.79 0.33 43.48 3.16
937 984 3.924073 GGTGTTTGCTTTTCGAAACAACT 59.076 39.130 10.79 0.00 43.48 3.16
938 985 3.924073 AGGTGTTTGCTTTTCGAAACAAC 59.076 39.130 10.79 7.73 45.97 3.32
939 986 4.181309 AGGTGTTTGCTTTTCGAAACAA 57.819 36.364 10.79 9.85 42.23 2.83
940 987 3.859411 AGGTGTTTGCTTTTCGAAACA 57.141 38.095 10.79 3.39 39.24 2.83
941 988 4.623595 TGAAAGGTGTTTGCTTTTCGAAAC 59.376 37.500 10.79 0.36 33.40 2.78
942 989 4.623595 GTGAAAGGTGTTTGCTTTTCGAAA 59.376 37.500 6.47 6.47 33.40 3.46
943 990 4.082463 AGTGAAAGGTGTTTGCTTTTCGAA 60.082 37.500 0.00 0.00 33.40 3.71
944 991 3.442273 AGTGAAAGGTGTTTGCTTTTCGA 59.558 39.130 0.00 0.00 33.40 3.71
945 992 3.547468 CAGTGAAAGGTGTTTGCTTTTCG 59.453 43.478 0.00 0.00 33.40 3.46
946 993 4.494484 ACAGTGAAAGGTGTTTGCTTTTC 58.506 39.130 0.00 0.00 0.00 2.29
947 994 4.535526 ACAGTGAAAGGTGTTTGCTTTT 57.464 36.364 0.00 0.00 0.00 2.27
948 995 5.852282 ATACAGTGAAAGGTGTTTGCTTT 57.148 34.783 0.00 0.00 0.00 3.51
949 996 6.952773 TTATACAGTGAAAGGTGTTTGCTT 57.047 33.333 0.00 0.00 0.00 3.91
950 997 6.952773 TTTATACAGTGAAAGGTGTTTGCT 57.047 33.333 0.00 0.00 0.00 3.91
951 998 7.995463 TTTTTATACAGTGAAAGGTGTTTGC 57.005 32.000 0.00 0.00 0.00 3.68
972 1019 3.840890 TCAGAAAGCACACACGTTTTT 57.159 38.095 0.00 0.00 0.00 1.94
973 1020 3.376859 TGATCAGAAAGCACACACGTTTT 59.623 39.130 0.00 0.00 0.00 2.43
974 1021 2.942376 TGATCAGAAAGCACACACGTTT 59.058 40.909 0.00 0.00 0.00 3.60
975 1022 2.560504 TGATCAGAAAGCACACACGTT 58.439 42.857 0.00 0.00 0.00 3.99
976 1023 2.238942 TGATCAGAAAGCACACACGT 57.761 45.000 0.00 0.00 0.00 4.49
977 1024 3.607422 TTTGATCAGAAAGCACACACG 57.393 42.857 0.00 0.00 0.00 4.49
1153 1200 9.961264 CTTCTTTTTCTAGTCCCTAGGTTTATT 57.039 33.333 8.29 0.00 35.03 1.40
1154 1201 9.335211 TCTTCTTTTTCTAGTCCCTAGGTTTAT 57.665 33.333 8.29 0.00 35.03 1.40
1155 1202 8.731591 TCTTCTTTTTCTAGTCCCTAGGTTTA 57.268 34.615 8.29 0.00 35.03 2.01
1287 1335 1.415672 GGCTCCGTCCCCATGGAATA 61.416 60.000 15.22 0.00 44.07 1.75
1297 1345 3.564027 CATTTCGCGGCTCCGTCC 61.564 66.667 6.13 0.00 42.09 4.79
1571 1635 3.969802 AACGCCCGTCTTCGTCGT 61.970 61.111 0.00 0.00 38.03 4.34
1826 1899 2.636412 CCGACAGCGAGAAGGTCCA 61.636 63.158 0.00 0.00 40.82 4.02
1900 1973 1.374505 GCGGTACACCTTGGCGTTA 60.375 57.895 0.00 0.00 0.00 3.18
1901 1974 2.667199 GCGGTACACCTTGGCGTT 60.667 61.111 0.00 0.00 0.00 4.84
1969 2042 0.103026 TCTCCATGCGGTCATTCTCG 59.897 55.000 0.00 0.00 0.00 4.04
2384 4092 4.574674 AGCCCAAAGTCACATATCTGAA 57.425 40.909 0.00 0.00 0.00 3.02
2385 4093 4.443457 GCTAGCCCAAAGTCACATATCTGA 60.443 45.833 2.29 0.00 0.00 3.27
2386 4094 3.812053 GCTAGCCCAAAGTCACATATCTG 59.188 47.826 2.29 0.00 0.00 2.90
2485 4193 5.046529 AGCGTGATTGTGAATGAGATAGAC 58.953 41.667 0.00 0.00 0.00 2.59
2489 4197 3.865446 TCAGCGTGATTGTGAATGAGAT 58.135 40.909 0.00 0.00 0.00 2.75
2570 4278 8.279970 ACGATTTAATTCATTCATTCACCTGA 57.720 30.769 0.00 0.00 0.00 3.86
2571 4279 9.655769 CTACGATTTAATTCATTCATTCACCTG 57.344 33.333 0.00 0.00 0.00 4.00
3167 5269 6.360681 GTCGCTGAATCACATAAATAAATGGC 59.639 38.462 0.00 0.00 0.00 4.40
3170 5272 6.545666 TGGGTCGCTGAATCACATAAATAAAT 59.454 34.615 0.00 0.00 0.00 1.40
3190 5292 7.217200 TGCTTTAGTATTATGACATCTGGGTC 58.783 38.462 0.00 0.00 38.29 4.46
3226 5328 7.523380 GCGCGGGGTATCATCTACTAATATAAT 60.523 40.741 8.83 0.00 0.00 1.28
3235 5337 1.443872 CGCGCGGGGTATCATCTAC 60.444 63.158 24.84 0.00 0.00 2.59
3260 5367 6.511416 TGAAATATATTGCAACCAATTCCCG 58.489 36.000 0.00 0.00 41.68 5.14
3263 5370 9.048446 AGCATTGAAATATATTGCAACCAATTC 57.952 29.630 19.23 4.17 38.09 2.17
3275 5382 9.480053 GCACAACCAAATAGCATTGAAATATAT 57.520 29.630 0.00 0.00 31.84 0.86
3276 5383 7.647318 CGCACAACCAAATAGCATTGAAATATA 59.353 33.333 0.00 0.00 31.84 0.86
3433 5542 2.978156 AAAGACCCATCACCACATGT 57.022 45.000 0.00 0.00 0.00 3.21
3442 5551 5.625150 ACTATGCATAGGAAAAGACCCATC 58.375 41.667 31.87 0.00 34.69 3.51
3463 5572 5.717078 AAATCACATCTCAACATGCAACT 57.283 34.783 0.00 0.00 0.00 3.16
3489 5598 8.575589 GCCACATCACCATACAATTATAAATGA 58.424 33.333 7.53 0.00 0.00 2.57
3507 5616 5.418209 TCAACATGTAATCATTGCCACATCA 59.582 36.000 0.00 0.00 31.15 3.07
3538 5647 6.954352 AAGAGGGTCATTCCTACTAACTTT 57.046 37.500 0.00 0.00 37.25 2.66
3543 5652 5.745988 ACCTAAGAGGGTCATTCCTACTA 57.254 43.478 0.00 0.00 40.58 1.82
3548 5657 7.420029 TCCTATATACCTAAGAGGGTCATTCC 58.580 42.308 0.00 0.00 40.58 3.01
3554 5663 7.185304 TCGGTTATCCTATATACCTAAGAGGGT 59.815 40.741 0.00 0.00 40.58 4.34
3556 5665 9.643735 AATCGGTTATCCTATATACCTAAGAGG 57.356 37.037 0.00 0.00 42.49 3.69
3605 5714 7.787424 ACTATAAGGAGTTGAAGATAAGAGGCT 59.213 37.037 0.00 0.00 0.00 4.58
3624 5733 9.613957 CACCGTTAGAGATGTGATTACTATAAG 57.386 37.037 0.00 0.00 0.00 1.73
3630 5739 3.802685 GCCACCGTTAGAGATGTGATTAC 59.197 47.826 0.00 0.00 0.00 1.89
3693 6087 1.087501 GAGAGATTTTCACGTGGGGC 58.912 55.000 17.00 1.29 0.00 5.80
3699 6093 7.593875 AAGAAGATGAAGAGAGATTTTCACG 57.406 36.000 0.00 0.00 36.26 4.35
3724 6118 7.491048 CCGGAAGAAAGAACAAAAAGAATGAAA 59.509 33.333 0.00 0.00 0.00 2.69
3737 6131 2.025418 TCGCGCCGGAAGAAAGAAC 61.025 57.895 5.05 0.00 0.00 3.01
3748 6149 4.914420 CTCTAGCTGGTCGCGCCG 62.914 72.222 0.00 4.28 45.59 6.46
3772 6173 1.063806 CACTCGCTGTTGCTGTAGAC 58.936 55.000 0.00 0.00 36.97 2.59
3797 6198 2.860062 CGTATGTATACACCGCCTAGC 58.140 52.381 7.96 0.00 32.87 3.42
3850 6251 7.821359 TCTCTTCCACACAATTATCTTCTTCTG 59.179 37.037 0.00 0.00 0.00 3.02
3861 6262 2.489329 CGCCATTCTCTTCCACACAATT 59.511 45.455 0.00 0.00 0.00 2.32
3950 6351 1.092348 CATGTATGTGCTGCTGCTGT 58.908 50.000 17.00 5.31 40.48 4.40
3953 6354 0.384309 ATGCATGTATGTGCTGCTGC 59.616 50.000 8.89 8.89 45.27 5.25
3997 6398 3.063510 AGGTGTCTACTGCTACGTGTA 57.936 47.619 0.00 0.00 0.00 2.90
4015 6416 1.412710 AGGCATCGTACATGGTGTAGG 59.587 52.381 0.00 4.01 39.36 3.18
4040 6441 1.168714 GGCTCGAAAGATGCAACCTT 58.831 50.000 0.00 0.00 40.84 3.50
4082 6483 2.330041 GAGCTAGGCTCGAGCGAC 59.670 66.667 29.81 17.77 45.85 5.19
4128 6529 0.036010 CACTACCAGGCCAGGTTGAG 60.036 60.000 30.23 22.26 43.08 3.02
4134 6535 2.488153 GTTTAAAGCACTACCAGGCCAG 59.512 50.000 5.01 0.00 0.00 4.85
4136 6537 2.510613 TGTTTAAAGCACTACCAGGCC 58.489 47.619 0.00 0.00 0.00 5.19
4137 6538 3.181510 CGATGTTTAAAGCACTACCAGGC 60.182 47.826 0.00 0.00 0.00 4.85
4138 6539 4.000988 ACGATGTTTAAAGCACTACCAGG 58.999 43.478 0.00 0.00 0.00 4.45
4139 6540 4.669197 GCACGATGTTTAAAGCACTACCAG 60.669 45.833 0.00 0.00 0.00 4.00
4141 6542 3.187637 TGCACGATGTTTAAAGCACTACC 59.812 43.478 0.00 0.00 0.00 3.18
4142 6543 4.398549 TGCACGATGTTTAAAGCACTAC 57.601 40.909 0.00 0.00 0.00 2.73
4158 6561 0.099968 CCAGAATCTTGGCATGCACG 59.900 55.000 21.36 6.90 0.00 5.34
4175 6578 4.033776 GTAGGCTGGGCTGCACCA 62.034 66.667 0.00 4.49 42.05 4.17
4223 6626 3.650950 TCTGCAGGAGGCCCAACC 61.651 66.667 15.13 0.09 43.89 3.77
4224 6627 1.553690 TAGTCTGCAGGAGGCCCAAC 61.554 60.000 15.13 1.46 43.89 3.77
4225 6628 1.229496 TAGTCTGCAGGAGGCCCAA 60.229 57.895 15.13 0.00 43.89 4.12
4226 6629 1.990060 GTAGTCTGCAGGAGGCCCA 60.990 63.158 15.13 0.00 43.89 5.36
4227 6630 2.736826 GGTAGTCTGCAGGAGGCCC 61.737 68.421 15.13 4.28 43.89 5.80
4353 6756 3.483574 CGTCACTCCAATGTTTCGCATAC 60.484 47.826 0.00 0.00 36.67 2.39
4361 6764 2.368875 AGTTCTCCGTCACTCCAATGTT 59.631 45.455 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.