Multiple sequence alignment - TraesCS7A01G069900

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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 TraesCS7A01G069900 chr7A 100.000 3916 0 0 1 3916 35693424 35689509 0.000000e+00 7232
1 TraesCS7A01G069900 chr7A 93.443 122 7 1 632 752 35692673 35692552 3.110000e-41 180
2 TraesCS7A01G069900 chr7A 93.443 122 7 1 752 873 35692793 35692673 3.110000e-41 180
3 TraesCS7A01G069900 chr7D 94.554 1524 68 8 1441 2959 36048890 36050403 0.000000e+00 2340
4 TraesCS7A01G069900 chr7D 92.027 878 57 13 3042 3916 43138020 43138887 0.000000e+00 1221
5 TraesCS7A01G069900 chr7D 89.180 878 83 10 3042 3916 277559171 277560039 0.000000e+00 1085
6 TraesCS7A01G069900 chr7D 89.643 589 41 8 872 1444 36048210 36048794 0.000000e+00 732
7 TraesCS7A01G069900 chr7D 88.767 454 21 8 237 662 36047762 36048213 2.680000e-146 529
8 TraesCS7A01G069900 chr7D 85.019 514 65 7 2535 3039 35818091 35818601 2.700000e-141 512
9 TraesCS7A01G069900 chr7D 83.099 568 81 11 1971 2529 35817460 35818021 1.620000e-138 503
10 TraesCS7A01G069900 chr7D 81.979 566 43 32 141 653 35815698 35816257 3.620000e-115 425
11 TraesCS7A01G069900 chr7D 81.871 513 77 6 872 1369 35816263 35816774 6.050000e-113 418
12 TraesCS7A01G069900 chr7D 80.201 596 62 32 95 653 35856045 35856621 2.840000e-106 396
13 TraesCS7A01G069900 chr7D 95.726 234 8 1 1 232 36047485 36047718 3.690000e-100 375
14 TraesCS7A01G069900 chr7D 80.190 525 74 20 1155 1675 35857114 35857612 2.220000e-97 366
15 TraesCS7A01G069900 chr7D 83.660 306 47 1 872 1177 35856627 35856929 6.400000e-73 285
16 TraesCS7A01G069900 chr7D 97.895 95 2 0 2949 3043 36051191 36051285 8.700000e-37 165
17 TraesCS7A01G069900 chr7D 97.727 88 2 0 779 866 22260880 22260967 6.780000e-33 152
18 TraesCS7A01G069900 chr7D 93.182 88 6 0 659 746 22260880 22260967 3.180000e-26 130
19 TraesCS7A01G069900 chr4A 89.072 1153 104 15 1393 2531 687809863 687808719 0.000000e+00 1411
20 TraesCS7A01G069900 chr4A 92.593 810 55 2 3042 3851 346285691 346286495 0.000000e+00 1158
21 TraesCS7A01G069900 chr4A 86.266 881 104 13 3039 3916 30813195 30814061 0.000000e+00 941
22 TraesCS7A01G069900 chr4A 89.642 531 38 9 868 1382 687810373 687809844 0.000000e+00 660
23 TraesCS7A01G069900 chr4A 88.330 437 21 10 251 662 687810798 687810367 7.560000e-137 497
24 TraesCS7A01G069900 chr5A 90.557 879 69 13 3045 3916 37085078 37085949 0.000000e+00 1151
25 TraesCS7A01G069900 chr5A 95.789 95 4 0 779 873 47955841 47955747 1.880000e-33 154
26 TraesCS7A01G069900 chr6B 89.294 878 80 11 3043 3916 662251842 662252709 0.000000e+00 1088
27 TraesCS7A01G069900 chr6B 95.652 92 4 0 779 870 716607870 716607779 8.770000e-32 148
28 TraesCS7A01G069900 chr6B 94.186 86 5 0 659 744 9358054 9358139 8.830000e-27 132
29 TraesCS7A01G069900 chr6B 94.186 86 4 1 659 744 286774938 286775022 3.180000e-26 130
30 TraesCS7A01G069900 chr5D 87.955 880 93 11 3043 3916 43011603 43012475 0.000000e+00 1026
31 TraesCS7A01G069900 chr2A 87.955 880 80 22 3043 3916 235311803 235312662 0.000000e+00 1014
32 TraesCS7A01G069900 chr3D 86.674 878 94 17 3043 3916 267264620 267263762 0.000000e+00 952
33 TraesCS7A01G069900 chr5B 97.753 89 2 0 776 864 582585230 582585142 1.880000e-33 154
34 TraesCS7A01G069900 chr5B 96.629 89 3 0 779 867 664669496 664669408 8.770000e-32 148
35 TraesCS7A01G069900 chr5B 93.258 89 6 0 656 744 582585230 582585142 8.830000e-27 132
36 TraesCS7A01G069900 chr1A 97.727 88 2 0 778 865 578474307 578474394 6.780000e-33 152
37 TraesCS7A01G069900 chr6A 96.629 89 3 0 779 867 26975971 26976059 8.770000e-32 148
38 TraesCS7A01G069900 chr2B 96.629 89 3 0 777 865 774106558 774106646 8.770000e-32 148
39 TraesCS7A01G069900 chr1D 87.023 131 14 1 1229 1359 486905614 486905741 1.130000e-30 145
40 TraesCS7A01G069900 chr1D 93.103 87 6 0 659 745 120019101 120019015 1.140000e-25 128
41 TraesCS7A01G069900 chr3A 91.089 101 8 1 646 746 19445919 19446018 6.830000e-28 135
42 TraesCS7A01G069900 chr4D 93.258 89 6 0 659 747 80976542 80976630 8.830000e-27 132
43 TraesCS7A01G069900 chr1B 92.222 90 7 0 656 745 172000770 172000859 1.140000e-25 128


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 TraesCS7A01G069900 chr7A 35689509 35693424 3915 True 2530.666667 7232 95.628667 1 3916 3 chr7A.!!$R1 3915
1 TraesCS7A01G069900 chr7D 43138020 43138887 867 False 1221.000000 1221 92.027000 3042 3916 1 chr7D.!!$F1 874
2 TraesCS7A01G069900 chr7D 277559171 277560039 868 False 1085.000000 1085 89.180000 3042 3916 1 chr7D.!!$F2 874
3 TraesCS7A01G069900 chr7D 36047485 36051285 3800 False 828.200000 2340 93.317000 1 3043 5 chr7D.!!$F6 3042
4 TraesCS7A01G069900 chr7D 35815698 35818601 2903 False 464.500000 512 82.992000 141 3039 4 chr7D.!!$F4 2898
5 TraesCS7A01G069900 chr7D 35856045 35857612 1567 False 349.000000 396 81.350333 95 1675 3 chr7D.!!$F5 1580
6 TraesCS7A01G069900 chr4A 346285691 346286495 804 False 1158.000000 1158 92.593000 3042 3851 1 chr4A.!!$F2 809
7 TraesCS7A01G069900 chr4A 30813195 30814061 866 False 941.000000 941 86.266000 3039 3916 1 chr4A.!!$F1 877
8 TraesCS7A01G069900 chr4A 687808719 687810798 2079 True 856.000000 1411 89.014667 251 2531 3 chr4A.!!$R1 2280
9 TraesCS7A01G069900 chr5A 37085078 37085949 871 False 1151.000000 1151 90.557000 3045 3916 1 chr5A.!!$F1 871
10 TraesCS7A01G069900 chr6B 662251842 662252709 867 False 1088.000000 1088 89.294000 3043 3916 1 chr6B.!!$F3 873
11 TraesCS7A01G069900 chr5D 43011603 43012475 872 False 1026.000000 1026 87.955000 3043 3916 1 chr5D.!!$F1 873
12 TraesCS7A01G069900 chr2A 235311803 235312662 859 False 1014.000000 1014 87.955000 3043 3916 1 chr2A.!!$F1 873
13 TraesCS7A01G069900 chr3D 267263762 267264620 858 True 952.000000 952 86.674000 3043 3916 1 chr3D.!!$R1 873

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
669 786 0.042131 TTGGGTGATACTCCCTCCGT 59.958 55.0 9.72 0.0 44.84 4.69 F
790 907 0.107066 TGCGTGATACTCCCTCCGTA 60.107 55.0 0.00 0.0 0.00 4.02 F
1732 2191 0.466189 CCCGGCCTCTGCATTAACAT 60.466 55.0 0.00 0.0 40.13 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 2302 0.179004 ATTGAGCCCACCGTTCAACA 60.179 50.0 0.00 0.00 43.47 3.33 R
1855 2321 0.179032 CATAGTTGGCGCCCCACATA 60.179 55.0 26.77 14.21 41.97 2.29 R
3704 5249 0.175760 AATGGATCCGTGGACGACTG 59.824 55.0 7.39 0.00 43.02 3.51 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
22 23 2.246469 TGCACATGCCCTTGTATTTGT 58.754 42.857 0.49 0.00 41.18 2.83
39 40 0.834687 TGTAGGACAGAAGGCGGGTT 60.835 55.000 0.00 0.00 0.00 4.11
47 48 5.131475 AGGACAGAAGGCGGGTTTAATTATA 59.869 40.000 0.00 0.00 0.00 0.98
92 93 3.181500 GGGTTTTAACGAGGCAGCATAAG 60.181 47.826 0.00 0.00 0.00 1.73
132 133 1.476488 ACACACTGCCTTTGTTTGGAC 59.524 47.619 0.00 0.00 0.00 4.02
258 300 2.033662 GTGAGCTCTGACGTGTTCAAAC 60.034 50.000 16.19 0.00 32.21 2.93
303 368 0.600255 CTGACTTTTGAGGCGACCGT 60.600 55.000 0.00 0.00 0.00 4.83
312 377 1.200716 TGAGGCGACCGTACTTAGTTG 59.799 52.381 0.00 0.00 0.00 3.16
327 392 8.926710 CGTACTTAGTTGTGAAGATTTCAGATT 58.073 33.333 0.00 0.00 41.01 2.40
375 440 8.435187 AGGCATATCATCTCAAGATTTGACTTA 58.565 33.333 0.00 0.00 38.96 2.24
477 569 7.228507 GCTACTCTCTATCTCTTCAGTTCATCA 59.771 40.741 0.00 0.00 0.00 3.07
515 607 0.732880 CCTGCACGTACAAGTCTCCG 60.733 60.000 0.00 0.00 0.00 4.63
597 706 2.139118 GCACCGGAGAATCTTATGAGC 58.861 52.381 9.46 0.00 33.73 4.26
606 715 2.810439 ATCTTATGAGCTGCCGACTC 57.190 50.000 0.00 0.00 34.62 3.36
662 779 8.964476 TCTTGATTAAATCTTGGGTGATACTC 57.036 34.615 0.00 0.00 0.00 2.59
663 780 7.993183 TCTTGATTAAATCTTGGGTGATACTCC 59.007 37.037 0.00 0.00 0.00 3.85
664 781 6.601332 TGATTAAATCTTGGGTGATACTCCC 58.399 40.000 0.00 0.00 44.81 4.30
665 782 6.389869 TGATTAAATCTTGGGTGATACTCCCT 59.610 38.462 9.72 0.00 44.84 4.20
666 783 4.779993 AAATCTTGGGTGATACTCCCTC 57.220 45.455 9.72 0.00 44.84 4.30
667 784 2.176247 TCTTGGGTGATACTCCCTCC 57.824 55.000 9.72 0.00 44.84 4.30
668 785 0.753262 CTTGGGTGATACTCCCTCCG 59.247 60.000 9.72 0.00 44.84 4.63
669 786 0.042131 TTGGGTGATACTCCCTCCGT 59.958 55.000 9.72 0.00 44.84 4.69
670 787 0.928505 TGGGTGATACTCCCTCCGTA 59.071 55.000 9.72 0.00 44.84 4.02
671 788 1.288633 TGGGTGATACTCCCTCCGTAA 59.711 52.381 9.72 0.00 44.84 3.18
672 789 2.292389 TGGGTGATACTCCCTCCGTAAA 60.292 50.000 9.72 0.00 44.84 2.01
673 790 2.102084 GGGTGATACTCCCTCCGTAAAC 59.898 54.545 0.00 0.00 41.58 2.01
674 791 3.029570 GGTGATACTCCCTCCGTAAACT 58.970 50.000 0.00 0.00 0.00 2.66
675 792 4.210331 GGTGATACTCCCTCCGTAAACTA 58.790 47.826 0.00 0.00 0.00 2.24
676 793 4.646492 GGTGATACTCCCTCCGTAAACTAA 59.354 45.833 0.00 0.00 0.00 2.24
677 794 5.303845 GGTGATACTCCCTCCGTAAACTAAT 59.696 44.000 0.00 0.00 0.00 1.73
678 795 6.491403 GGTGATACTCCCTCCGTAAACTAATA 59.509 42.308 0.00 0.00 0.00 0.98
679 796 7.178097 GGTGATACTCCCTCCGTAAACTAATAT 59.822 40.741 0.00 0.00 0.00 1.28
680 797 9.236006 GTGATACTCCCTCCGTAAACTAATATA 57.764 37.037 0.00 0.00 0.00 0.86
681 798 9.812347 TGATACTCCCTCCGTAAACTAATATAA 57.188 33.333 0.00 0.00 0.00 0.98
684 801 8.773033 ACTCCCTCCGTAAACTAATATAAGAA 57.227 34.615 0.00 0.00 0.00 2.52
685 802 8.637099 ACTCCCTCCGTAAACTAATATAAGAAC 58.363 37.037 0.00 0.00 0.00 3.01
686 803 7.651808 TCCCTCCGTAAACTAATATAAGAACG 58.348 38.462 0.00 0.00 0.00 3.95
687 804 7.285401 TCCCTCCGTAAACTAATATAAGAACGT 59.715 37.037 0.00 0.00 0.00 3.99
688 805 7.922811 CCCTCCGTAAACTAATATAAGAACGTT 59.077 37.037 0.00 0.00 0.00 3.99
689 806 9.305925 CCTCCGTAAACTAATATAAGAACGTTT 57.694 33.333 0.46 0.00 0.00 3.60
749 866 8.792831 TTAGTTTACAAAGAGAGTACTTGTCG 57.207 34.615 0.00 0.00 0.00 4.35
750 867 6.803642 AGTTTACAAAGAGAGTACTTGTCGT 58.196 36.000 0.00 0.00 0.00 4.34
751 868 7.934457 AGTTTACAAAGAGAGTACTTGTCGTA 58.066 34.615 0.00 0.00 0.00 3.43
752 869 8.074972 AGTTTACAAAGAGAGTACTTGTCGTAG 58.925 37.037 0.00 0.00 0.00 3.51
753 870 7.734924 TTACAAAGAGAGTACTTGTCGTAGA 57.265 36.000 0.00 0.00 0.00 2.59
754 871 6.243811 ACAAAGAGAGTACTTGTCGTAGAG 57.756 41.667 0.00 0.00 36.95 2.43
755 872 5.764192 ACAAAGAGAGTACTTGTCGTAGAGT 59.236 40.000 0.00 0.00 36.95 3.24
756 873 6.933521 ACAAAGAGAGTACTTGTCGTAGAGTA 59.066 38.462 0.00 0.00 36.95 2.59
757 874 7.607223 ACAAAGAGAGTACTTGTCGTAGAGTAT 59.393 37.037 0.00 0.00 36.95 2.12
758 875 7.775397 AAGAGAGTACTTGTCGTAGAGTATC 57.225 40.000 0.00 0.00 36.95 2.24
777 894 8.131455 GAGTATCTTGATTAAATCTTGCGTGA 57.869 34.615 0.00 0.00 0.00 4.35
778 895 8.668510 AGTATCTTGATTAAATCTTGCGTGAT 57.331 30.769 0.00 0.00 0.00 3.06
779 896 9.764363 AGTATCTTGATTAAATCTTGCGTGATA 57.236 29.630 0.00 0.00 0.00 2.15
780 897 9.798885 GTATCTTGATTAAATCTTGCGTGATAC 57.201 33.333 0.00 0.00 0.00 2.24
781 898 8.668510 ATCTTGATTAAATCTTGCGTGATACT 57.331 30.769 0.00 0.00 0.00 2.12
782 899 8.131455 TCTTGATTAAATCTTGCGTGATACTC 57.869 34.615 0.00 0.00 0.00 2.59
783 900 6.844696 TGATTAAATCTTGCGTGATACTCC 57.155 37.500 0.00 0.00 0.00 3.85
784 901 5.758296 TGATTAAATCTTGCGTGATACTCCC 59.242 40.000 0.00 0.00 0.00 4.30
785 902 3.914426 AAATCTTGCGTGATACTCCCT 57.086 42.857 0.00 0.00 0.00 4.20
786 903 3.460857 AATCTTGCGTGATACTCCCTC 57.539 47.619 0.00 0.00 0.00 4.30
787 904 1.112113 TCTTGCGTGATACTCCCTCC 58.888 55.000 0.00 0.00 0.00 4.30
788 905 0.249073 CTTGCGTGATACTCCCTCCG 60.249 60.000 0.00 0.00 0.00 4.63
789 906 0.968901 TTGCGTGATACTCCCTCCGT 60.969 55.000 0.00 0.00 0.00 4.69
790 907 0.107066 TGCGTGATACTCCCTCCGTA 60.107 55.000 0.00 0.00 0.00 4.02
791 908 1.027357 GCGTGATACTCCCTCCGTAA 58.973 55.000 0.00 0.00 0.00 3.18
792 909 1.406539 GCGTGATACTCCCTCCGTAAA 59.593 52.381 0.00 0.00 0.00 2.01
793 910 2.797439 GCGTGATACTCCCTCCGTAAAC 60.797 54.545 0.00 0.00 0.00 2.01
794 911 2.686915 CGTGATACTCCCTCCGTAAACT 59.313 50.000 0.00 0.00 0.00 2.66
795 912 3.879295 CGTGATACTCCCTCCGTAAACTA 59.121 47.826 0.00 0.00 0.00 2.24
796 913 4.336433 CGTGATACTCCCTCCGTAAACTAA 59.664 45.833 0.00 0.00 0.00 2.24
797 914 5.009410 CGTGATACTCCCTCCGTAAACTAAT 59.991 44.000 0.00 0.00 0.00 1.73
798 915 6.205464 CGTGATACTCCCTCCGTAAACTAATA 59.795 42.308 0.00 0.00 0.00 0.98
799 916 7.094463 CGTGATACTCCCTCCGTAAACTAATAT 60.094 40.741 0.00 0.00 0.00 1.28
800 917 9.236006 GTGATACTCCCTCCGTAAACTAATATA 57.764 37.037 0.00 0.00 0.00 0.86
801 918 9.812347 TGATACTCCCTCCGTAAACTAATATAA 57.188 33.333 0.00 0.00 0.00 0.98
805 922 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
806 923 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
807 924 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
808 925 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
809 926 8.606602 CCTCCGTAAACTAATATAAAAGCGTTT 58.393 33.333 2.53 2.53 0.00 3.60
827 944 9.918630 AAAGCGTTTAGAATACTAAAGTAGTGA 57.081 29.630 0.00 0.00 45.42 3.41
829 946 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
830 947 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
868 985 8.843885 ATTAGTTTACAAAGGGAGTACTTGTC 57.156 34.615 0.00 0.00 0.00 3.18
869 986 6.243216 AGTTTACAAAGGGAGTACTTGTCA 57.757 37.500 0.00 0.00 0.00 3.58
870 987 6.289064 AGTTTACAAAGGGAGTACTTGTCAG 58.711 40.000 0.00 0.00 0.00 3.51
871 988 5.881923 TTACAAAGGGAGTACTTGTCAGT 57.118 39.130 0.00 0.00 36.99 3.41
872 989 6.982160 TTACAAAGGGAGTACTTGTCAGTA 57.018 37.500 0.00 0.00 34.06 2.74
915 1032 0.740868 TCGGCTACTCACATTGCTGC 60.741 55.000 0.00 0.00 0.00 5.25
959 1076 0.819582 CCATTAACCCAGCTTGCTGG 59.180 55.000 29.11 29.11 43.86 4.85
966 1093 1.001641 CCAGCTTGCTGGCTAACCT 60.002 57.895 25.97 0.00 41.00 3.50
977 1107 7.117956 GCTTGCTGGCTAACCTTAGTATATAAC 59.882 40.741 0.00 0.00 36.63 1.89
998 1128 1.673808 ATACCCTTGAGGCCGTCGAC 61.674 60.000 5.18 5.18 40.58 4.20
1147 1287 2.202703 GCGCAATACCCGTCGTCT 60.203 61.111 0.30 0.00 0.00 4.18
1152 1292 1.673626 GCAATACCCGTCGTCTCCAAA 60.674 52.381 0.00 0.00 0.00 3.28
1180 1428 1.152819 CTCGTATCCGTCCCCAGGA 60.153 63.158 0.00 0.00 42.69 3.86
1302 1649 4.742201 CACGAGCACCTGTCCCGG 62.742 72.222 0.00 0.00 0.00 5.73
1580 2036 2.458006 CTTGCCCAAGGTCGAAACGC 62.458 60.000 0.06 0.00 34.87 4.84
1686 2142 2.159572 GCGTGACAAACCCATGATACAC 60.160 50.000 0.00 0.00 0.00 2.90
1732 2191 0.466189 CCCGGCCTCTGCATTAACAT 60.466 55.000 0.00 0.00 40.13 2.71
1748 2214 6.020599 GCATTAACATATCATACGGCTACTCG 60.021 42.308 0.00 0.00 0.00 4.18
1774 2240 2.105306 TCATCCATGATTGATCCGCTGT 59.895 45.455 0.00 0.00 0.00 4.40
1777 2243 2.945008 TCCATGATTGATCCGCTGTTTC 59.055 45.455 0.00 0.00 0.00 2.78
1836 2302 0.995024 AGCCCTCCAGCTTACATGTT 59.005 50.000 2.30 0.00 41.41 2.71
1855 2321 0.179004 TGTTGAACGGTGGGCTCAAT 60.179 50.000 0.00 0.00 32.08 2.57
1926 2392 2.884012 CTGTAAGTCAACCCATTGCACA 59.116 45.455 0.00 0.00 35.63 4.57
2066 2705 4.641645 CCAAGCTGGGTGGCGACA 62.642 66.667 0.00 0.00 37.29 4.35
2293 2932 2.359975 AAGCCGCAGCCCTACAAC 60.360 61.111 0.00 0.00 41.25 3.32
2318 2957 1.821753 ACTATGTCTGCGACAAGAGCT 59.178 47.619 13.81 0.00 45.96 4.09
2404 3043 1.876546 AACCGGGGCTCTCCTACTCT 61.877 60.000 6.32 0.00 35.33 3.24
2456 3095 1.937546 CTTCGCCCACCCAGCAAATC 61.938 60.000 0.00 0.00 0.00 2.17
2694 3406 1.553704 GACGGTTACTGGTTCTGGGAT 59.446 52.381 0.00 0.00 0.00 3.85
2795 3507 2.586648 ACCTTTAAGGCTCTGTTGGG 57.413 50.000 11.45 0.00 39.63 4.12
2850 3567 4.240096 AGTACGTATTTGTTTCCACTCCG 58.760 43.478 0.00 0.00 0.00 4.63
3013 4530 1.000938 CTTTGTGCCCTGTGCTTCTTC 60.001 52.381 0.00 0.00 42.00 2.87
3048 4565 8.438676 AAGAAAGTTATCTTGATGATTACCGG 57.561 34.615 0.00 0.00 38.22 5.28
3086 4603 5.579119 CCCGTTTCATAAATAAAGCAAACCC 59.421 40.000 0.00 0.00 0.00 4.11
3096 4613 0.178924 AAGCAAACCCCCAAGAGCAT 60.179 50.000 0.00 0.00 0.00 3.79
3329 4871 1.899437 GAAGGTGGAGATGGCGTCCA 61.899 60.000 2.37 0.62 42.06 4.02
3337 4879 0.397675 AGATGGCGTCCAGATCCTGA 60.398 55.000 2.37 0.00 36.75 3.86
3373 4915 1.233285 CGCCAGAGCTGCAAGAAACT 61.233 55.000 1.02 0.00 34.07 2.66
3403 4945 1.681793 GAATAGAGCGTCAGTAGCCCA 59.318 52.381 0.00 0.00 34.64 5.36
3707 5252 4.954118 TCCACCCCAGACGGCAGT 62.954 66.667 0.00 0.00 0.00 4.40
3808 5353 3.148279 GGACGAGGGAGCGATGGT 61.148 66.667 0.00 0.00 34.83 3.55
3871 5416 2.978824 CCACCGAACCTCATCCGT 59.021 61.111 0.00 0.00 0.00 4.69
3872 5417 1.447838 CCACCGAACCTCATCCGTG 60.448 63.158 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.941377 TAAACCCGCCTTCTGTCCTA 58.059 50.000 0.00 0.00 0.00 2.94
72 73 3.119990 TGCTTATGCTGCCTCGTTAAAAC 60.120 43.478 0.00 0.00 40.48 2.43
79 80 4.498241 TCTATATTGCTTATGCTGCCTCG 58.502 43.478 0.00 0.00 40.48 4.63
92 93 7.810282 AGTGTGTTCGACTATCATCTATATTGC 59.190 37.037 0.00 0.00 0.00 3.56
132 133 1.588082 GCTGGGTGCATCTTGGTTG 59.412 57.895 0.00 0.00 42.31 3.77
258 300 8.931905 AGCGCACAATTTTTGTATTTTATTTG 57.068 26.923 11.47 0.00 43.23 2.32
312 377 7.811236 TCATGCTTGAAAATCTGAAATCTTCAC 59.189 33.333 0.00 0.00 35.46 3.18
327 392 0.040157 GCACGTGCTCATGCTTGAAA 60.040 50.000 32.55 0.00 38.84 2.69
346 411 3.949842 TCTTGAGATGATATGCCTCCG 57.050 47.619 0.00 0.00 0.00 4.63
375 440 1.768870 ACTACGGAATGCAGGCCTTAT 59.231 47.619 0.00 0.00 0.00 1.73
597 706 1.444553 GAACAGGTCGAGTCGGCAG 60.445 63.158 20.23 13.13 30.88 4.85
606 715 6.802608 TGGAATACAAGTATAGAACAGGTCG 58.197 40.000 0.00 0.00 0.00 4.79
653 770 3.029570 AGTTTACGGAGGGAGTATCACC 58.970 50.000 0.00 0.00 41.89 4.02
654 771 5.841957 TTAGTTTACGGAGGGAGTATCAC 57.158 43.478 0.00 0.00 40.51 3.06
660 777 7.806960 CGTTCTTATATTAGTTTACGGAGGGAG 59.193 40.741 0.00 0.00 0.00 4.30
661 778 7.285401 ACGTTCTTATATTAGTTTACGGAGGGA 59.715 37.037 13.71 0.00 32.54 4.20
662 779 7.428826 ACGTTCTTATATTAGTTTACGGAGGG 58.571 38.462 13.71 0.00 32.54 4.30
663 780 8.862550 AACGTTCTTATATTAGTTTACGGAGG 57.137 34.615 0.00 0.00 32.54 4.30
723 840 9.408069 CGACAAGTACTCTCTTTGTAAACTAAT 57.592 33.333 0.00 0.00 0.00 1.73
724 841 8.408601 ACGACAAGTACTCTCTTTGTAAACTAA 58.591 33.333 0.00 0.00 0.00 2.24
725 842 7.934457 ACGACAAGTACTCTCTTTGTAAACTA 58.066 34.615 0.00 0.00 0.00 2.24
726 843 6.803642 ACGACAAGTACTCTCTTTGTAAACT 58.196 36.000 0.00 0.00 0.00 2.66
727 844 8.072567 TCTACGACAAGTACTCTCTTTGTAAAC 58.927 37.037 0.00 0.00 0.00 2.01
728 845 8.158169 TCTACGACAAGTACTCTCTTTGTAAA 57.842 34.615 0.00 0.00 0.00 2.01
729 846 7.443575 ACTCTACGACAAGTACTCTCTTTGTAA 59.556 37.037 0.00 0.00 0.00 2.41
730 847 6.933521 ACTCTACGACAAGTACTCTCTTTGTA 59.066 38.462 0.00 0.00 0.00 2.41
731 848 5.764192 ACTCTACGACAAGTACTCTCTTTGT 59.236 40.000 0.00 0.00 0.00 2.83
732 849 6.243811 ACTCTACGACAAGTACTCTCTTTG 57.756 41.667 0.00 0.00 0.00 2.77
733 850 8.042515 AGATACTCTACGACAAGTACTCTCTTT 58.957 37.037 0.00 0.00 31.15 2.52
734 851 7.558604 AGATACTCTACGACAAGTACTCTCTT 58.441 38.462 0.00 0.00 31.15 2.85
735 852 7.116075 AGATACTCTACGACAAGTACTCTCT 57.884 40.000 0.00 0.00 31.15 3.10
736 853 7.492020 TCAAGATACTCTACGACAAGTACTCTC 59.508 40.741 0.00 0.00 31.15 3.20
737 854 7.329499 TCAAGATACTCTACGACAAGTACTCT 58.671 38.462 0.00 0.00 31.15 3.24
738 855 7.536895 TCAAGATACTCTACGACAAGTACTC 57.463 40.000 0.00 0.00 31.15 2.59
739 856 8.508883 AATCAAGATACTCTACGACAAGTACT 57.491 34.615 0.00 0.00 31.15 2.73
747 864 9.464714 GCAAGATTTAATCAAGATACTCTACGA 57.535 33.333 7.74 0.00 0.00 3.43
748 865 8.420945 CGCAAGATTTAATCAAGATACTCTACG 58.579 37.037 7.74 0.00 43.02 3.51
749 866 9.250624 ACGCAAGATTTAATCAAGATACTCTAC 57.749 33.333 7.74 0.00 43.62 2.59
750 867 9.249457 CACGCAAGATTTAATCAAGATACTCTA 57.751 33.333 7.74 0.00 43.62 2.43
751 868 7.981789 TCACGCAAGATTTAATCAAGATACTCT 59.018 33.333 7.74 0.00 43.62 3.24
752 869 8.131455 TCACGCAAGATTTAATCAAGATACTC 57.869 34.615 7.74 0.00 43.62 2.59
753 870 8.668510 ATCACGCAAGATTTAATCAAGATACT 57.331 30.769 7.74 0.00 43.62 2.12
754 871 9.798885 GTATCACGCAAGATTTAATCAAGATAC 57.201 33.333 7.74 10.19 43.62 2.24
755 872 9.764363 AGTATCACGCAAGATTTAATCAAGATA 57.236 29.630 7.74 3.30 43.62 1.98
756 873 8.668510 AGTATCACGCAAGATTTAATCAAGAT 57.331 30.769 7.74 4.10 43.62 2.40
757 874 7.224753 GGAGTATCACGCAAGATTTAATCAAGA 59.775 37.037 7.74 0.00 43.62 3.02
758 875 7.348201 GGAGTATCACGCAAGATTTAATCAAG 58.652 38.462 7.74 0.45 43.62 3.02
759 876 6.260050 GGGAGTATCACGCAAGATTTAATCAA 59.740 38.462 7.74 0.00 43.62 2.57
760 877 5.758296 GGGAGTATCACGCAAGATTTAATCA 59.242 40.000 7.74 0.00 43.62 2.57
761 878 6.229561 GGGAGTATCACGCAAGATTTAATC 57.770 41.667 0.00 0.00 43.62 1.75
774 891 5.841957 TTAGTTTACGGAGGGAGTATCAC 57.158 43.478 0.00 0.00 40.51 3.06
775 892 9.812347 TTATATTAGTTTACGGAGGGAGTATCA 57.188 33.333 0.00 0.00 36.25 2.15
779 896 7.930325 GCTTTTATATTAGTTTACGGAGGGAGT 59.070 37.037 0.00 0.00 0.00 3.85
780 897 7.115947 CGCTTTTATATTAGTTTACGGAGGGAG 59.884 40.741 0.00 0.00 0.00 4.30
781 898 6.925165 CGCTTTTATATTAGTTTACGGAGGGA 59.075 38.462 0.00 0.00 0.00 4.20
782 899 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
783 900 7.704789 ACGCTTTTATATTAGTTTACGGAGG 57.295 36.000 0.00 0.00 0.00 4.30
801 918 9.918630 TCACTACTTTAGTATTCTAAACGCTTT 57.081 29.630 0.76 0.00 40.05 3.51
803 920 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
804 921 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
842 959 9.933723 GACAAGTACTCCCTTTGTAAACTAATA 57.066 33.333 0.00 0.00 35.35 0.98
843 960 8.434392 TGACAAGTACTCCCTTTGTAAACTAAT 58.566 33.333 0.00 0.00 35.35 1.73
844 961 7.794041 TGACAAGTACTCCCTTTGTAAACTAA 58.206 34.615 0.00 0.00 35.35 2.24
845 962 7.070322 ACTGACAAGTACTCCCTTTGTAAACTA 59.930 37.037 0.00 0.00 35.35 2.24
846 963 6.126854 ACTGACAAGTACTCCCTTTGTAAACT 60.127 38.462 0.00 0.00 35.35 2.66
847 964 6.053650 ACTGACAAGTACTCCCTTTGTAAAC 58.946 40.000 0.00 0.00 35.35 2.01
848 965 6.243216 ACTGACAAGTACTCCCTTTGTAAA 57.757 37.500 0.00 0.00 35.35 2.01
849 966 5.881923 ACTGACAAGTACTCCCTTTGTAA 57.118 39.130 0.00 0.00 35.35 2.41
861 978 3.561310 ACGACGACAAGTACTGACAAGTA 59.439 43.478 0.00 0.00 37.88 2.24
862 979 2.357009 ACGACGACAAGTACTGACAAGT 59.643 45.455 0.00 0.00 40.67 3.16
863 980 2.996155 ACGACGACAAGTACTGACAAG 58.004 47.619 0.00 0.00 0.00 3.16
864 981 3.181498 TGAACGACGACAAGTACTGACAA 60.181 43.478 0.00 0.00 0.00 3.18
865 982 2.355444 TGAACGACGACAAGTACTGACA 59.645 45.455 0.00 0.00 0.00 3.58
866 983 2.990941 TGAACGACGACAAGTACTGAC 58.009 47.619 0.00 0.00 0.00 3.51
867 984 3.909776 ATGAACGACGACAAGTACTGA 57.090 42.857 0.00 0.00 0.00 3.41
868 985 5.283247 GTCTTATGAACGACGACAAGTACTG 59.717 44.000 0.00 0.00 0.00 2.74
869 986 5.049198 TGTCTTATGAACGACGACAAGTACT 60.049 40.000 0.00 0.00 32.26 2.73
870 987 5.149273 TGTCTTATGAACGACGACAAGTAC 58.851 41.667 0.00 0.00 32.26 2.73
871 988 5.049198 ACTGTCTTATGAACGACGACAAGTA 60.049 40.000 0.00 0.00 34.59 2.24
872 989 4.227538 CTGTCTTATGAACGACGACAAGT 58.772 43.478 0.00 0.00 34.59 3.16
915 1032 1.026718 GTTGACCCAGATTGCCGGAG 61.027 60.000 5.05 0.00 0.00 4.63
959 1076 9.183368 AGGGTATCGTTATATACTAAGGTTAGC 57.817 37.037 0.00 0.00 33.62 3.09
966 1093 7.123247 GGCCTCAAGGGTATCGTTATATACTAA 59.877 40.741 0.00 0.00 37.43 2.24
977 1107 1.067582 GACGGCCTCAAGGGTATCG 59.932 63.158 0.00 0.00 37.43 2.92
1027 1157 2.190325 AGCTAATCGACGGAAAGACG 57.810 50.000 0.00 0.00 39.26 4.18
1078 1212 1.068083 CACCACGAGCACACTCACT 59.932 57.895 0.00 0.00 43.66 3.41
1147 1287 2.280552 CGAGTCCGGGGAGTTTGGA 61.281 63.158 0.00 0.00 0.00 3.53
1152 1292 1.152798 GGATACGAGTCCGGGGAGT 60.153 63.158 0.00 0.00 40.78 3.85
1237 1584 1.966451 GCAGGTGACGTTCCTTGGG 60.966 63.158 9.96 2.45 32.37 4.12
1455 1908 4.143389 CGTCGTCTATTTTCACCAGAACAC 60.143 45.833 0.00 0.00 32.39 3.32
1594 2050 2.685388 GCTAGATTGGGAAACTTGAGGC 59.315 50.000 0.00 0.00 0.00 4.70
1603 2059 1.153168 GCCGCTGCTAGATTGGGAA 60.153 57.895 0.00 0.00 33.53 3.97
1670 2126 3.825908 AAGGGTGTATCATGGGTTTGT 57.174 42.857 0.00 0.00 0.00 2.83
1695 2151 3.515901 CCGGGGATATCCTCCTTTTCTAG 59.484 52.174 21.18 1.95 44.28 2.43
1732 2191 3.030668 TCGACGAGTAGCCGTATGATA 57.969 47.619 0.00 0.00 43.49 2.15
1748 2214 3.615937 CGGATCAATCATGGATGATCGAC 59.384 47.826 23.50 15.40 46.22 4.20
1774 2240 8.145134 ATGTTGCTGGACACCATGAAATGAAA 62.145 38.462 0.00 0.00 46.28 2.69
1777 2243 2.296752 TGTTGCTGGACACCATGAAATG 59.703 45.455 0.00 0.00 46.21 2.32
1836 2302 0.179004 ATTGAGCCCACCGTTCAACA 60.179 50.000 0.00 0.00 43.47 3.33
1855 2321 0.179032 CATAGTTGGCGCCCCACATA 60.179 55.000 26.77 14.21 41.97 2.29
1936 2402 7.159437 TCAAATGTTTGTAATTTCGCACAAG 57.841 32.000 5.48 0.00 39.18 3.16
2066 2705 2.690778 GGAGCTCGCGCAATTTGGT 61.691 57.895 8.75 0.00 39.10 3.67
2086 2725 2.261729 AGGAGGAAGAAGGACTTGGAC 58.738 52.381 0.00 0.00 39.13 4.02
2143 2782 1.407618 CGTGGATATCCGGACTCAACA 59.592 52.381 17.04 8.42 39.43 3.33
2318 2957 1.352404 CGGTGGCGTTTTCGTTCAA 59.648 52.632 0.00 0.00 46.03 2.69
2345 2984 3.011517 GAGGGGCTTGAGGGCAGA 61.012 66.667 0.00 0.00 42.84 4.26
2404 3043 1.617322 AGCCATAGAAGTCGCCGATA 58.383 50.000 0.00 0.00 0.00 2.92
2694 3406 4.426971 TCCGTCATGAACTCCGGA 57.573 55.556 18.30 18.30 46.44 5.14
2850 3567 2.991190 CAGTTGCTCCAATTGCACAATC 59.009 45.455 0.00 0.35 40.40 2.67
3013 4530 4.324267 AGATAACTTTCTTGGTCCGTTGG 58.676 43.478 0.00 0.00 0.00 3.77
3066 4583 6.688073 TGGGGGTTTGCTTTATTTATGAAA 57.312 33.333 0.00 0.00 0.00 2.69
3069 4586 6.293004 TCTTGGGGGTTTGCTTTATTTATG 57.707 37.500 0.00 0.00 0.00 1.90
3086 4603 3.018856 TCTTTGTATGCATGCTCTTGGG 58.981 45.455 20.33 4.15 0.00 4.12
3096 4613 6.423905 GTGTTCTGAACTAGTCTTTGTATGCA 59.576 38.462 20.18 0.00 0.00 3.96
3231 4772 1.038130 AGAGCCTGATTAGACGCCGT 61.038 55.000 0.00 0.00 0.00 5.68
3329 4871 2.605535 TTAGCCGCCCCTCAGGATCT 62.606 60.000 0.00 0.00 38.24 2.75
3373 4915 6.631016 ACTGACGCTCTATTCAAATTGTCTA 58.369 36.000 0.00 0.00 0.00 2.59
3403 4945 5.010012 GTGATTCAACATGTTCCTCTTTGGT 59.990 40.000 8.48 0.00 37.07 3.67
3555 5100 2.203998 AGAGGTGGTGGGAGGTGG 60.204 66.667 0.00 0.00 0.00 4.61
3623 5168 1.282738 GGTACCCCCGAAGATTCCAAA 59.717 52.381 0.00 0.00 0.00 3.28
3704 5249 0.175760 AATGGATCCGTGGACGACTG 59.824 55.000 7.39 0.00 43.02 3.51
3707 5252 1.153449 GCAATGGATCCGTGGACGA 60.153 57.895 13.02 0.00 43.02 4.20
3808 5353 2.314852 TCCACCAAGTCCCTCTATCTGA 59.685 50.000 0.00 0.00 0.00 3.27
3852 5397 2.668632 GGATGAGGTTCGGTGGCA 59.331 61.111 0.00 0.00 0.00 4.92
3871 5416 0.888736 CGGTTGTGGATTCTGGCACA 60.889 55.000 0.00 0.00 0.00 4.57
3872 5417 1.586154 CCGGTTGTGGATTCTGGCAC 61.586 60.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.