Multiple sequence alignment - TraesCS1D01G165500

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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 TraesCS1D01G165500 chr1D 100.000 3992 0 0 1 3992 236499926 236503917 0.000000e+00 7372
1 TraesCS1D01G165500 chr1D 94.905 687 31 1 68 750 414247077 414247763 0.000000e+00 1072
2 TraesCS1D01G165500 chr1D 91.346 104 5 3 749 851 320727771 320727871 5.380000e-29 139
3 TraesCS1D01G165500 chr1D 92.222 90 5 2 1 89 123341534 123341446 4.190000e-25 126
4 TraesCS1D01G165500 chr1B 93.716 2610 80 18 909 3471 342085777 342088349 0.000000e+00 3834
5 TraesCS1D01G165500 chr1B 93.431 411 7 2 3601 3992 342088347 342088756 3.440000e-165 592
6 TraesCS1D01G165500 chr1B 88.235 119 9 5 745 861 300581238 300581353 1.930000e-28 137
7 TraesCS1D01G165500 chr1B 86.923 130 8 8 765 890 447815448 447815324 1.930000e-28 137
8 TraesCS1D01G165500 chr1A 93.878 2336 91 23 888 3190 308953180 308950864 0.000000e+00 3474
9 TraesCS1D01G165500 chr1A 88.760 516 34 4 3489 3992 308950144 308949641 9.480000e-171 610
10 TraesCS1D01G165500 chr1A 97.674 215 5 0 3276 3490 308950441 308950227 1.750000e-98 370
11 TraesCS1D01G165500 chr1A 96.117 103 4 0 3176 3278 308950848 308950746 6.860000e-38 169
12 TraesCS1D01G165500 chr1A 92.157 102 5 3 764 864 133417548 133417449 1.500000e-29 141
13 TraesCS1D01G165500 chr1A 90.654 107 7 3 752 857 168394373 168394477 5.380000e-29 139
14 TraesCS1D01G165500 chr7D 94.883 684 31 1 68 747 552168659 552169342 0.000000e+00 1066
15 TraesCS1D01G165500 chr7D 93.506 693 38 4 68 755 552276376 552275686 0.000000e+00 1024
16 TraesCS1D01G165500 chr7D 93.182 88 2 3 1 85 194185511 194185597 4.190000e-25 126
17 TraesCS1D01G165500 chr7D 90.426 94 6 3 1 92 532503200 532503108 1.950000e-23 121
18 TraesCS1D01G165500 chr5D 94.477 688 33 2 68 750 29587079 29586392 0.000000e+00 1055
19 TraesCS1D01G165500 chr5D 96.386 83 3 0 1 83 298495012 298495094 1.930000e-28 137
20 TraesCS1D01G165500 chr5D 95.181 83 2 2 1 82 415674923 415675004 3.240000e-26 130
21 TraesCS1D01G165500 chr5D 96.203 79 0 2 1 79 160428970 160429045 4.190000e-25 126
22 TraesCS1D01G165500 chr4A 94.032 687 31 2 68 750 701572893 701573573 0.000000e+00 1033
23 TraesCS1D01G165500 chr3D 93.786 692 36 3 68 754 594521627 594520938 0.000000e+00 1033
24 TraesCS1D01G165500 chr3A 92.722 687 44 3 68 749 127863831 127863146 0.000000e+00 987
25 TraesCS1D01G165500 chr7A 92.442 688 46 3 68 750 102043655 102042969 0.000000e+00 977
26 TraesCS1D01G165500 chr2B 91.001 689 56 3 68 750 132806235 132805547 0.000000e+00 924
27 TraesCS1D01G165500 chr5B 92.157 102 6 2 760 860 521983142 521983042 4.160000e-30 143
28 TraesCS1D01G165500 chr5B 92.929 99 4 3 764 861 331307404 331307500 1.500000e-29 141
29 TraesCS1D01G165500 chr7B 91.429 105 6 3 750 853 43510195 43510297 1.500000e-29 141
30 TraesCS1D01G165500 chr4B 91.262 103 7 2 757 858 565213369 565213470 5.380000e-29 139
31 TraesCS1D01G165500 chr4D 91.000 100 5 3 1 98 434517307 434517404 9.000000e-27 132
32 TraesCS1D01G165500 chr2D 95.122 82 2 2 1 81 301311679 301311759 1.160000e-25 128
33 TraesCS1D01G165500 chr6D 87.037 108 8 6 1 106 388482056 388482159 2.520000e-22 117


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 TraesCS1D01G165500 chr1D 236499926 236503917 3991 False 7372.00 7372 100.00000 1 3992 1 chr1D.!!$F1 3991
1 TraesCS1D01G165500 chr1D 414247077 414247763 686 False 1072.00 1072 94.90500 68 750 1 chr1D.!!$F3 682
2 TraesCS1D01G165500 chr1B 342085777 342088756 2979 False 2213.00 3834 93.57350 909 3992 2 chr1B.!!$F2 3083
3 TraesCS1D01G165500 chr1A 308949641 308953180 3539 True 1155.75 3474 94.10725 888 3992 4 chr1A.!!$R2 3104
4 TraesCS1D01G165500 chr7D 552168659 552169342 683 False 1066.00 1066 94.88300 68 747 1 chr7D.!!$F2 679
5 TraesCS1D01G165500 chr7D 552275686 552276376 690 True 1024.00 1024 93.50600 68 755 1 chr7D.!!$R2 687
6 TraesCS1D01G165500 chr5D 29586392 29587079 687 True 1055.00 1055 94.47700 68 750 1 chr5D.!!$R1 682
7 TraesCS1D01G165500 chr4A 701572893 701573573 680 False 1033.00 1033 94.03200 68 750 1 chr4A.!!$F1 682
8 TraesCS1D01G165500 chr3D 594520938 594521627 689 True 1033.00 1033 93.78600 68 754 1 chr3D.!!$R1 686
9 TraesCS1D01G165500 chr3A 127863146 127863831 685 True 987.00 987 92.72200 68 749 1 chr3A.!!$R1 681
10 TraesCS1D01G165500 chr7A 102042969 102043655 686 True 977.00 977 92.44200 68 750 1 chr7A.!!$R1 682
11 TraesCS1D01G165500 chr2B 132805547 132806235 688 True 924.00 924 91.00100 68 750 1 chr2B.!!$R1 682

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
33 34 0.233590 GTCGTACACATTTGCGTGCA 59.766 50.0 0.0 0.00 40.73 4.57 F
58 59 0.248289 AGTGTACGGTCAAATCGGGG 59.752 55.0 0.0 0.00 0.00 5.73 F
750 757 0.305922 GCGCGATTCAGAATTCAGGG 59.694 55.0 12.1 2.62 0.00 4.45 F
1159 1173 0.467659 ACTCGGTATCTCGGGGAAGG 60.468 60.0 0.0 0.00 34.44 3.46 F
1563 1578 0.544697 GGTCGATTTCCTTAGCCCCA 59.455 55.0 0.0 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1146 1160 0.635009 ACTCACCCTTCCCCGAGATA 59.365 55.000 0.00 0.0 0.00 1.98 R
1207 1221 1.183549 TCAGGCTACGAAGGAAGTCC 58.816 55.000 0.00 0.0 0.00 3.85 R
2317 2336 1.284198 AGCCTCAAGCCATCAACTCAT 59.716 47.619 0.00 0.0 45.47 2.90 R
2890 2937 0.251787 ATGGGCCCTGTTCCTTTGAC 60.252 55.000 25.70 0.0 0.00 3.18 R
3535 4014 2.603021 ACTCATCGATGTAGCCTGGAT 58.397 47.619 24.09 0.0 0.00 3.41 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
18 19 3.383162 AGTCCCTGATCTTGGTCGT 57.617 52.632 0.00 0.00 0.00 4.34
19 20 2.526888 AGTCCCTGATCTTGGTCGTA 57.473 50.000 0.00 0.00 0.00 3.43
20 21 2.100989 AGTCCCTGATCTTGGTCGTAC 58.899 52.381 0.00 0.00 0.00 3.67
21 22 1.822990 GTCCCTGATCTTGGTCGTACA 59.177 52.381 0.00 0.00 0.00 2.90
22 23 1.822990 TCCCTGATCTTGGTCGTACAC 59.177 52.381 0.00 0.00 0.00 2.90
23 24 1.548719 CCCTGATCTTGGTCGTACACA 59.451 52.381 0.00 0.00 0.00 3.72
24 25 2.168521 CCCTGATCTTGGTCGTACACAT 59.831 50.000 0.00 0.00 0.00 3.21
25 26 3.369471 CCCTGATCTTGGTCGTACACATT 60.369 47.826 0.00 0.00 0.00 2.71
26 27 4.253685 CCTGATCTTGGTCGTACACATTT 58.746 43.478 0.00 0.00 0.00 2.32
27 28 4.093408 CCTGATCTTGGTCGTACACATTTG 59.907 45.833 0.00 0.00 0.00 2.32
28 29 3.435327 TGATCTTGGTCGTACACATTTGC 59.565 43.478 0.00 0.00 0.00 3.68
29 30 1.795872 TCTTGGTCGTACACATTTGCG 59.204 47.619 0.00 0.00 0.00 4.85
30 31 1.529438 CTTGGTCGTACACATTTGCGT 59.471 47.619 0.00 0.00 0.00 5.24
31 32 0.862490 TGGTCGTACACATTTGCGTG 59.138 50.000 0.00 0.00 42.81 5.34
32 33 0.452122 GGTCGTACACATTTGCGTGC 60.452 55.000 0.00 0.00 40.73 5.34
33 34 0.233590 GTCGTACACATTTGCGTGCA 59.766 50.000 0.00 0.00 40.73 4.57
34 35 1.136085 GTCGTACACATTTGCGTGCAT 60.136 47.619 0.00 0.00 40.73 3.96
35 36 1.136113 TCGTACACATTTGCGTGCATG 60.136 47.619 0.09 0.09 40.73 4.06
36 37 1.136113 CGTACACATTTGCGTGCATGA 60.136 47.619 10.93 0.00 40.73 3.07
37 38 2.476018 CGTACACATTTGCGTGCATGAT 60.476 45.455 10.93 0.00 40.73 2.45
38 39 2.728690 ACACATTTGCGTGCATGATT 57.271 40.000 10.93 0.00 40.73 2.57
39 40 3.846423 ACACATTTGCGTGCATGATTA 57.154 38.095 10.93 0.00 40.73 1.75
40 41 3.761657 ACACATTTGCGTGCATGATTAG 58.238 40.909 10.93 0.00 40.73 1.73
41 42 3.191162 ACACATTTGCGTGCATGATTAGT 59.809 39.130 10.93 0.00 40.73 2.24
42 43 3.544682 CACATTTGCGTGCATGATTAGTG 59.455 43.478 10.93 7.27 0.00 2.74
43 44 3.191162 ACATTTGCGTGCATGATTAGTGT 59.809 39.130 10.93 4.47 0.00 3.55
44 45 4.394610 ACATTTGCGTGCATGATTAGTGTA 59.605 37.500 10.93 0.00 0.00 2.90
45 46 4.335082 TTTGCGTGCATGATTAGTGTAC 57.665 40.909 10.93 0.00 0.00 2.90
48 49 2.536365 CGTGCATGATTAGTGTACGGT 58.464 47.619 0.00 0.00 46.91 4.83
49 50 2.534349 CGTGCATGATTAGTGTACGGTC 59.466 50.000 0.00 0.00 46.91 4.79
50 51 3.517602 GTGCATGATTAGTGTACGGTCA 58.482 45.455 0.00 0.00 0.00 4.02
51 52 3.930229 GTGCATGATTAGTGTACGGTCAA 59.070 43.478 0.00 0.00 0.00 3.18
52 53 4.390603 GTGCATGATTAGTGTACGGTCAAA 59.609 41.667 0.00 0.00 0.00 2.69
53 54 5.064707 GTGCATGATTAGTGTACGGTCAAAT 59.935 40.000 0.00 0.00 0.00 2.32
54 55 5.293324 TGCATGATTAGTGTACGGTCAAATC 59.707 40.000 0.00 0.00 0.00 2.17
55 56 5.556382 GCATGATTAGTGTACGGTCAAATCG 60.556 44.000 0.00 0.00 0.00 3.34
56 57 4.426416 TGATTAGTGTACGGTCAAATCGG 58.574 43.478 0.00 0.00 0.00 4.18
57 58 2.945447 TAGTGTACGGTCAAATCGGG 57.055 50.000 0.00 0.00 0.00 5.14
58 59 0.248289 AGTGTACGGTCAAATCGGGG 59.752 55.000 0.00 0.00 0.00 5.73
59 60 0.741927 GTGTACGGTCAAATCGGGGG 60.742 60.000 0.00 0.00 0.00 5.40
60 61 1.816679 GTACGGTCAAATCGGGGGC 60.817 63.158 0.00 0.00 0.00 5.80
61 62 3.374012 TACGGTCAAATCGGGGGCG 62.374 63.158 0.00 0.00 0.00 6.13
62 63 4.770874 CGGTCAAATCGGGGGCGT 62.771 66.667 0.00 0.00 0.00 5.68
63 64 2.822701 GGTCAAATCGGGGGCGTC 60.823 66.667 0.00 0.00 0.00 5.19
64 65 2.046700 GTCAAATCGGGGGCGTCA 60.047 61.111 0.00 0.00 0.00 4.35
65 66 2.046700 TCAAATCGGGGGCGTCAC 60.047 61.111 0.00 0.00 0.00 3.67
66 67 2.359354 CAAATCGGGGGCGTCACA 60.359 61.111 0.00 0.00 0.00 3.58
142 147 6.813152 CCAAAAAGTATTGCAACTAAGGATGG 59.187 38.462 0.00 2.63 0.00 3.51
296 301 9.509956 CTAGTTAACTAGATAGTCATGGTAGCT 57.490 37.037 30.84 0.00 46.80 3.32
400 405 1.812571 CCGTAGCATCCAAAGTTGCTT 59.187 47.619 2.43 0.00 44.83 3.91
480 486 6.016943 CACGATTAACCTAAGGGTGAAAACAA 60.017 38.462 0.00 0.00 46.67 2.83
482 488 7.068470 ACGATTAACCTAAGGGTGAAAACAAAA 59.932 33.333 0.00 0.00 46.67 2.44
551 557 6.884096 TGAAAACGCTAATTAAATGCATGG 57.116 33.333 0.00 0.00 0.00 3.66
625 631 0.320374 TCCCTTTCGCTTGTCGTGAT 59.680 50.000 0.00 0.00 39.67 3.06
626 632 1.546923 TCCCTTTCGCTTGTCGTGATA 59.453 47.619 0.00 0.00 39.67 2.15
750 757 0.305922 GCGCGATTCAGAATTCAGGG 59.694 55.000 12.10 2.62 0.00 4.45
754 761 3.313526 CGCGATTCAGAATTCAGGGAAAT 59.686 43.478 0.00 0.00 0.00 2.17
755 762 4.201950 CGCGATTCAGAATTCAGGGAAATT 60.202 41.667 0.00 0.00 0.00 1.82
756 763 5.007626 CGCGATTCAGAATTCAGGGAAATTA 59.992 40.000 0.00 0.00 0.00 1.40
757 764 6.458206 CGCGATTCAGAATTCAGGGAAATTAA 60.458 38.462 0.00 0.00 0.00 1.40
758 765 7.257722 GCGATTCAGAATTCAGGGAAATTAAA 58.742 34.615 8.44 0.00 0.00 1.52
759 766 7.759433 GCGATTCAGAATTCAGGGAAATTAAAA 59.241 33.333 8.44 0.00 0.00 1.52
760 767 9.076596 CGATTCAGAATTCAGGGAAATTAAAAC 57.923 33.333 8.44 0.00 0.00 2.43
761 768 9.927668 GATTCAGAATTCAGGGAAATTAAAACA 57.072 29.630 8.44 0.00 0.00 2.83
770 777 8.990163 TCAGGGAAATTAAAACATATACTCCC 57.010 34.615 0.00 0.00 40.34 4.30
772 779 9.067986 CAGGGAAATTAAAACATATACTCCCTC 57.932 37.037 2.79 0.00 45.88 4.30
773 780 9.015146 AGGGAAATTAAAACATATACTCCCTCT 57.985 33.333 0.00 0.00 45.88 3.69
774 781 9.067986 GGGAAATTAAAACATATACTCCCTCTG 57.932 37.037 0.00 0.00 37.57 3.35
775 782 9.628500 GGAAATTAAAACATATACTCCCTCTGT 57.372 33.333 0.00 0.00 0.00 3.41
790 797 8.431910 ACTCCCTCTGTAAACTAAATGTAAGA 57.568 34.615 0.00 0.00 0.00 2.10
791 798 8.532819 ACTCCCTCTGTAAACTAAATGTAAGAG 58.467 37.037 0.00 0.00 0.00 2.85
792 799 7.328737 TCCCTCTGTAAACTAAATGTAAGAGC 58.671 38.462 0.00 0.00 30.78 4.09
793 800 6.255887 CCCTCTGTAAACTAAATGTAAGAGCG 59.744 42.308 0.00 0.00 30.78 5.03
794 801 6.812160 CCTCTGTAAACTAAATGTAAGAGCGT 59.188 38.462 0.00 0.00 30.78 5.07
795 802 7.331193 CCTCTGTAAACTAAATGTAAGAGCGTT 59.669 37.037 0.00 0.00 30.78 4.84
796 803 8.597662 TCTGTAAACTAAATGTAAGAGCGTTT 57.402 30.769 0.00 0.00 0.00 3.60
797 804 9.695526 TCTGTAAACTAAATGTAAGAGCGTTTA 57.304 29.630 0.00 0.00 0.00 2.01
798 805 9.953825 CTGTAAACTAAATGTAAGAGCGTTTAG 57.046 33.333 13.19 13.19 45.92 1.85
799 806 9.695526 TGTAAACTAAATGTAAGAGCGTTTAGA 57.304 29.630 18.75 0.00 44.51 2.10
802 809 8.997621 AACTAAATGTAAGAGCGTTTAGATCA 57.002 30.769 18.75 0.00 44.51 2.92
803 810 8.408743 ACTAAATGTAAGAGCGTTTAGATCAC 57.591 34.615 18.75 0.00 44.51 3.06
804 811 8.251721 ACTAAATGTAAGAGCGTTTAGATCACT 58.748 33.333 18.75 0.00 44.51 3.41
805 812 9.731819 CTAAATGTAAGAGCGTTTAGATCACTA 57.268 33.333 10.56 0.00 44.51 2.74
843 850 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
844 851 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
845 852 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
846 853 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
847 854 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
855 862 9.710818 ATTAGTTTACAGAGGGAGTACTTATCA 57.289 33.333 0.00 0.00 0.00 2.15
856 863 9.537852 TTAGTTTACAGAGGGAGTACTTATCAA 57.462 33.333 0.00 0.00 0.00 2.57
857 864 8.431910 AGTTTACAGAGGGAGTACTTATCAAA 57.568 34.615 0.00 0.00 0.00 2.69
858 865 8.877195 AGTTTACAGAGGGAGTACTTATCAAAA 58.123 33.333 0.00 0.00 0.00 2.44
859 866 9.498176 GTTTACAGAGGGAGTACTTATCAAAAA 57.502 33.333 0.00 0.00 0.00 1.94
1159 1173 0.467659 ACTCGGTATCTCGGGGAAGG 60.468 60.000 0.00 0.00 34.44 3.46
1207 1221 3.180984 GGATCCGATCCTCGTTTCG 57.819 57.895 18.84 0.00 46.19 3.46
1563 1578 0.544697 GGTCGATTTCCTTAGCCCCA 59.455 55.000 0.00 0.00 0.00 4.96
1620 1635 4.763073 TGAATTCAGACTATCAGCTGTGG 58.237 43.478 14.67 5.89 33.90 4.17
1659 1674 2.544267 CCTTCAGAACTCGGTTGTGAAC 59.456 50.000 18.63 0.00 45.96 3.18
1660 1675 3.458189 CTTCAGAACTCGGTTGTGAACT 58.542 45.455 18.63 0.00 45.96 3.01
1661 1676 3.536956 TCAGAACTCGGTTGTGAACTT 57.463 42.857 12.13 0.00 41.60 2.66
1662 1677 3.194861 TCAGAACTCGGTTGTGAACTTG 58.805 45.455 12.13 0.00 41.60 3.16
1663 1678 2.936498 CAGAACTCGGTTGTGAACTTGT 59.064 45.455 7.78 0.00 38.79 3.16
1664 1679 2.936498 AGAACTCGGTTGTGAACTTGTG 59.064 45.455 0.00 0.00 0.00 3.33
1665 1680 2.684001 ACTCGGTTGTGAACTTGTGA 57.316 45.000 0.00 0.00 0.00 3.58
1787 1802 3.448660 GCCTAAACCTGGAAGCAAATGAT 59.551 43.478 0.00 0.00 0.00 2.45
1819 1834 9.953565 CTTCTATGCTAGGTCTAGTAGTATTCT 57.046 37.037 6.84 0.00 35.65 2.40
1871 1887 9.736023 GAAATAATTCGAAGGCAGTATTTTGAT 57.264 29.630 3.35 0.00 27.51 2.57
2181 2197 4.321899 CCGATGTGGGTTCAATTGTTCAAT 60.322 41.667 5.13 0.00 0.00 2.57
2299 2318 6.991485 AAATGCGATCACAAGTTAACAAAG 57.009 33.333 8.61 0.00 0.00 2.77
2347 2366 1.347817 GCTTGAGGCTCGTGAGAACG 61.348 60.000 10.42 0.00 41.32 3.95
2435 2454 3.753272 GCATCAGCAAGGTTAGAACTTCA 59.247 43.478 0.00 0.00 41.58 3.02
2482 2503 8.573035 GGTGATTTGTTCTTTATGGACTGTAAA 58.427 33.333 0.00 0.00 0.00 2.01
2569 2590 6.223852 ACAGTAAGATAACGCATATCCCTTG 58.776 40.000 5.46 3.40 41.23 3.61
2641 2662 7.678837 ACCTTTTGCCATCAAAGATGAAATTA 58.321 30.769 8.49 0.00 42.50 1.40
2709 2756 5.117584 TGATTTGTGCTTTGCAGAATGTTT 58.882 33.333 3.10 0.00 41.24 2.83
2888 2935 5.122396 CCAGCAAGTATGTGAAAGTAGGAAC 59.878 44.000 0.00 0.00 0.00 3.62
2890 2937 4.092968 GCAAGTATGTGAAAGTAGGAACCG 59.907 45.833 0.00 0.00 0.00 4.44
2904 2951 1.235724 GAACCGTCAAAGGAACAGGG 58.764 55.000 0.00 0.00 34.73 4.45
2914 2961 0.919710 AGGAACAGGGCCCATAGAAC 59.080 55.000 27.56 9.55 0.00 3.01
3094 3142 1.769026 CCTCCTAGCTGCTACAGTGA 58.231 55.000 5.02 0.00 33.43 3.41
3299 3690 7.699709 TCCATGTTATTAGTTGGATCCCTTA 57.300 36.000 9.90 0.00 33.40 2.69
3451 3846 6.892310 AACTGACATGAAAAGAAAAACAGC 57.108 33.333 0.00 0.00 0.00 4.40
3514 3993 8.948401 AGATATGAAATCTAGAAGCTCAGGTA 57.052 34.615 0.00 0.00 0.00 3.08
3528 4007 2.791560 CTCAGGTATTCGATGCACTTCG 59.208 50.000 3.28 3.28 40.46 3.79
3535 4014 0.173255 TCGATGCACTTCGATGAGCA 59.827 50.000 21.89 21.89 42.81 4.26
3542 4021 0.179062 ACTTCGATGAGCATCCAGGC 60.179 55.000 5.16 0.00 34.40 4.85
3554 4033 2.930023 GCATCCAGGCTACATCGATGAG 60.930 54.545 31.33 22.39 33.66 2.90
3562 4041 4.036971 AGGCTACATCGATGAGTACTCAAC 59.963 45.833 31.33 24.00 43.58 3.18
3612 4091 0.608130 TGCTATCTGTCAAGTGCCGT 59.392 50.000 0.00 0.00 0.00 5.68
3675 4154 4.898861 ACTTTTTGTTAATCCCAGCCTCAA 59.101 37.500 0.00 0.00 0.00 3.02
3676 4155 5.011023 ACTTTTTGTTAATCCCAGCCTCAAG 59.989 40.000 0.00 0.00 0.00 3.02
3776 4274 4.047142 CAGCTTGTCTTTTGCCTTTTCTC 58.953 43.478 0.00 0.00 0.00 2.87
3777 4275 3.701040 AGCTTGTCTTTTGCCTTTTCTCA 59.299 39.130 0.00 0.00 0.00 3.27
3778 4276 4.343239 AGCTTGTCTTTTGCCTTTTCTCAT 59.657 37.500 0.00 0.00 0.00 2.90
3779 4277 4.446719 GCTTGTCTTTTGCCTTTTCTCATG 59.553 41.667 0.00 0.00 0.00 3.07
3780 4278 4.589216 TGTCTTTTGCCTTTTCTCATGG 57.411 40.909 0.00 0.00 0.00 3.66
3781 4279 3.243839 TGTCTTTTGCCTTTTCTCATGGC 60.244 43.478 0.00 0.00 44.61 4.40
3782 4280 2.299867 TCTTTTGCCTTTTCTCATGGCC 59.700 45.455 0.00 0.00 43.88 5.36
3783 4281 2.014010 TTTGCCTTTTCTCATGGCCT 57.986 45.000 3.32 0.00 43.88 5.19
3784 4282 2.014010 TTGCCTTTTCTCATGGCCTT 57.986 45.000 3.32 0.00 43.88 4.35
3785 4283 1.549203 TGCCTTTTCTCATGGCCTTC 58.451 50.000 3.32 0.00 43.88 3.46
3786 4284 1.076024 TGCCTTTTCTCATGGCCTTCT 59.924 47.619 3.32 0.00 43.88 2.85
3959 4480 5.816777 CCGGGATTTTGCATGATTTAACATT 59.183 36.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.100989 GTACGACCAAGATCAGGGACT 58.899 52.381 9.43 0.00 43.88 3.85
1 2 1.822990 TGTACGACCAAGATCAGGGAC 59.177 52.381 9.43 2.88 0.00 4.46
3 4 1.548719 TGTGTACGACCAAGATCAGGG 59.451 52.381 8.82 5.29 0.00 4.45
4 5 3.526931 ATGTGTACGACCAAGATCAGG 57.473 47.619 0.00 0.00 0.00 3.86
5 6 4.436050 GCAAATGTGTACGACCAAGATCAG 60.436 45.833 0.00 0.00 0.00 2.90
6 7 3.435327 GCAAATGTGTACGACCAAGATCA 59.565 43.478 0.00 0.00 0.00 2.92
7 8 3.483574 CGCAAATGTGTACGACCAAGATC 60.484 47.826 0.00 0.00 0.00 2.75
8 9 2.415168 CGCAAATGTGTACGACCAAGAT 59.585 45.455 0.00 0.00 0.00 2.40
9 10 1.795872 CGCAAATGTGTACGACCAAGA 59.204 47.619 0.00 0.00 0.00 3.02
10 11 1.529438 ACGCAAATGTGTACGACCAAG 59.471 47.619 0.00 0.00 36.94 3.61
11 12 1.261885 CACGCAAATGTGTACGACCAA 59.738 47.619 0.00 0.00 36.94 3.67
12 13 0.862490 CACGCAAATGTGTACGACCA 59.138 50.000 0.00 0.00 36.94 4.02
13 14 0.452122 GCACGCAAATGTGTACGACC 60.452 55.000 0.00 0.00 41.94 4.79
14 15 0.233590 TGCACGCAAATGTGTACGAC 59.766 50.000 0.00 0.00 41.94 4.34
15 16 1.136113 CATGCACGCAAATGTGTACGA 60.136 47.619 0.00 0.00 41.94 3.43
16 17 1.136113 TCATGCACGCAAATGTGTACG 60.136 47.619 0.00 0.00 41.94 3.67
17 18 2.610219 TCATGCACGCAAATGTGTAC 57.390 45.000 0.00 0.00 41.94 2.90
18 19 3.846423 AATCATGCACGCAAATGTGTA 57.154 38.095 0.00 0.00 41.94 2.90
19 20 2.728690 AATCATGCACGCAAATGTGT 57.271 40.000 0.00 0.00 41.94 3.72
20 21 3.544682 CACTAATCATGCACGCAAATGTG 59.455 43.478 0.00 0.00 42.81 3.21
21 22 3.191162 ACACTAATCATGCACGCAAATGT 59.809 39.130 0.00 0.00 0.00 2.71
22 23 3.761657 ACACTAATCATGCACGCAAATG 58.238 40.909 0.00 0.00 0.00 2.32
23 24 4.494035 CGTACACTAATCATGCACGCAAAT 60.494 41.667 0.00 0.00 30.70 2.32
24 25 3.181525 CGTACACTAATCATGCACGCAAA 60.182 43.478 0.00 0.00 30.70 3.68
25 26 2.347150 CGTACACTAATCATGCACGCAA 59.653 45.455 0.00 0.00 30.70 4.85
26 27 1.923864 CGTACACTAATCATGCACGCA 59.076 47.619 0.00 0.00 30.70 5.24
27 28 1.257936 CCGTACACTAATCATGCACGC 59.742 52.381 0.00 0.00 35.86 5.34
28 29 2.534349 GACCGTACACTAATCATGCACG 59.466 50.000 0.00 0.00 36.74 5.34
29 30 3.517602 TGACCGTACACTAATCATGCAC 58.482 45.455 0.00 0.00 0.00 4.57
30 31 3.878160 TGACCGTACACTAATCATGCA 57.122 42.857 0.00 0.00 0.00 3.96
31 32 5.556382 CGATTTGACCGTACACTAATCATGC 60.556 44.000 13.93 0.00 32.03 4.06
32 33 5.051039 CCGATTTGACCGTACACTAATCATG 60.051 44.000 13.93 0.00 32.03 3.07
33 34 5.047847 CCGATTTGACCGTACACTAATCAT 58.952 41.667 13.93 0.00 32.03 2.45
34 35 4.426416 CCGATTTGACCGTACACTAATCA 58.574 43.478 13.93 0.90 32.03 2.57
35 36 3.800506 CCCGATTTGACCGTACACTAATC 59.199 47.826 0.00 2.04 0.00 1.75
36 37 3.431207 CCCCGATTTGACCGTACACTAAT 60.431 47.826 0.00 0.00 0.00 1.73
37 38 2.094078 CCCCGATTTGACCGTACACTAA 60.094 50.000 0.00 0.00 0.00 2.24
38 39 1.477700 CCCCGATTTGACCGTACACTA 59.522 52.381 0.00 0.00 0.00 2.74
39 40 0.248289 CCCCGATTTGACCGTACACT 59.752 55.000 0.00 0.00 0.00 3.55
40 41 0.741927 CCCCCGATTTGACCGTACAC 60.742 60.000 0.00 0.00 0.00 2.90
41 42 1.597989 CCCCCGATTTGACCGTACA 59.402 57.895 0.00 0.00 0.00 2.90
42 43 1.816679 GCCCCCGATTTGACCGTAC 60.817 63.158 0.00 0.00 0.00 3.67
43 44 2.585698 GCCCCCGATTTGACCGTA 59.414 61.111 0.00 0.00 0.00 4.02
44 45 4.770874 CGCCCCCGATTTGACCGT 62.771 66.667 0.00 0.00 36.29 4.83
45 46 4.770874 ACGCCCCCGATTTGACCG 62.771 66.667 0.00 0.00 38.29 4.79
46 47 2.822701 GACGCCCCCGATTTGACC 60.823 66.667 0.00 0.00 38.29 4.02
47 48 2.046700 TGACGCCCCCGATTTGAC 60.047 61.111 0.00 0.00 38.29 3.18
48 49 2.046700 GTGACGCCCCCGATTTGA 60.047 61.111 0.00 0.00 38.29 2.69
49 50 2.359354 TGTGACGCCCCCGATTTG 60.359 61.111 0.00 0.00 38.29 2.32
50 51 2.359478 GTGTGACGCCCCCGATTT 60.359 61.111 0.00 0.00 38.29 2.17
51 52 4.404098 GGTGTGACGCCCCCGATT 62.404 66.667 3.20 0.00 38.29 3.34
55 56 2.837031 AATGATGGTGTGACGCCCCC 62.837 60.000 13.34 4.87 32.22 5.40
56 57 1.378514 AATGATGGTGTGACGCCCC 60.379 57.895 13.34 5.25 32.22 5.80
57 58 0.960364 ACAATGATGGTGTGACGCCC 60.960 55.000 13.34 0.00 32.22 6.13
58 59 0.881118 AACAATGATGGTGTGACGCC 59.119 50.000 8.52 8.52 34.12 5.68
59 60 2.742053 ACTAACAATGATGGTGTGACGC 59.258 45.455 0.00 0.00 0.00 5.19
60 61 5.637810 ACTTACTAACAATGATGGTGTGACG 59.362 40.000 0.00 0.00 0.00 4.35
61 62 7.298122 CAACTTACTAACAATGATGGTGTGAC 58.702 38.462 0.00 0.00 0.00 3.67
62 63 6.072728 GCAACTTACTAACAATGATGGTGTGA 60.073 38.462 0.00 0.00 0.00 3.58
63 64 6.086222 GCAACTTACTAACAATGATGGTGTG 58.914 40.000 0.00 0.00 0.00 3.82
64 65 5.183140 GGCAACTTACTAACAATGATGGTGT 59.817 40.000 0.00 0.00 0.00 4.16
65 66 5.640732 GGCAACTTACTAACAATGATGGTG 58.359 41.667 0.00 0.00 0.00 4.17
66 67 5.897377 GGCAACTTACTAACAATGATGGT 57.103 39.130 0.00 0.00 0.00 3.55
337 342 7.170393 AGGAAAGCAACTTCTTGTTAGTTTT 57.830 32.000 0.00 0.00 37.07 2.43
480 486 6.575162 AGACCAAGCATCGAAATTAAGTTT 57.425 33.333 0.00 0.00 0.00 2.66
482 488 7.681939 TTTAGACCAAGCATCGAAATTAAGT 57.318 32.000 0.00 0.00 0.00 2.24
551 557 6.052360 GGGATTCAGTTGGAACTTAGATCTC 58.948 44.000 0.00 0.00 38.60 2.75
612 618 0.821517 ACCCATATCACGACAAGCGA 59.178 50.000 0.00 0.00 44.57 4.93
625 631 6.099990 TCCGACCAGAACAATAATAACCCATA 59.900 38.462 0.00 0.00 0.00 2.74
626 632 5.104277 TCCGACCAGAACAATAATAACCCAT 60.104 40.000 0.00 0.00 0.00 4.00
764 771 9.537852 TCTTACATTTAGTTTACAGAGGGAGTA 57.462 33.333 0.00 0.00 0.00 2.59
765 772 8.431910 TCTTACATTTAGTTTACAGAGGGAGT 57.568 34.615 0.00 0.00 0.00 3.85
766 773 7.492994 GCTCTTACATTTAGTTTACAGAGGGAG 59.507 40.741 0.00 0.00 0.00 4.30
767 774 7.328737 GCTCTTACATTTAGTTTACAGAGGGA 58.671 38.462 0.00 0.00 0.00 4.20
768 775 6.255887 CGCTCTTACATTTAGTTTACAGAGGG 59.744 42.308 0.00 0.00 0.00 4.30
769 776 6.812160 ACGCTCTTACATTTAGTTTACAGAGG 59.188 38.462 0.00 0.00 0.00 3.69
770 777 7.813852 ACGCTCTTACATTTAGTTTACAGAG 57.186 36.000 0.00 0.00 0.00 3.35
771 778 8.597662 AAACGCTCTTACATTTAGTTTACAGA 57.402 30.769 0.00 0.00 0.00 3.41
772 779 9.953825 CTAAACGCTCTTACATTTAGTTTACAG 57.046 33.333 0.00 0.00 32.40 2.74
773 780 9.695526 TCTAAACGCTCTTACATTTAGTTTACA 57.304 29.630 0.00 0.00 36.47 2.41
776 783 9.431887 TGATCTAAACGCTCTTACATTTAGTTT 57.568 29.630 0.00 0.00 36.47 2.66
777 784 8.870879 GTGATCTAAACGCTCTTACATTTAGTT 58.129 33.333 0.00 0.00 36.47 2.24
778 785 8.251721 AGTGATCTAAACGCTCTTACATTTAGT 58.748 33.333 0.00 0.00 36.47 2.24
779 786 8.635877 AGTGATCTAAACGCTCTTACATTTAG 57.364 34.615 0.00 0.00 36.42 1.85
817 824 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
818 825 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
819 826 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
820 827 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
821 828 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
829 836 9.710818 TGATAAGTACTCCCTCTGTAAACTAAT 57.289 33.333 0.00 0.00 0.00 1.73
830 837 9.537852 TTGATAAGTACTCCCTCTGTAAACTAA 57.462 33.333 0.00 0.00 0.00 2.24
831 838 9.537852 TTTGATAAGTACTCCCTCTGTAAACTA 57.462 33.333 0.00 0.00 0.00 2.24
832 839 8.431910 TTTGATAAGTACTCCCTCTGTAAACT 57.568 34.615 0.00 0.00 0.00 2.66
833 840 9.498176 TTTTTGATAAGTACTCCCTCTGTAAAC 57.502 33.333 0.00 0.00 0.00 2.01
890 897 9.458374 CTGGTCAAATTAACACGTAATTTTCTT 57.542 29.630 5.05 0.00 45.96 2.52
891 898 7.593644 GCTGGTCAAATTAACACGTAATTTTCT 59.406 33.333 5.05 0.00 45.96 2.52
892 899 7.593644 AGCTGGTCAAATTAACACGTAATTTTC 59.406 33.333 5.05 3.01 45.96 2.29
893 900 7.381139 CAGCTGGTCAAATTAACACGTAATTTT 59.619 33.333 5.57 0.00 45.96 1.82
900 907 3.498397 AGTCAGCTGGTCAAATTAACACG 59.502 43.478 15.13 0.00 0.00 4.49
1146 1160 0.635009 ACTCACCCTTCCCCGAGATA 59.365 55.000 0.00 0.00 0.00 1.98
1159 1173 3.718815 ACTCGAAAACAGAGAACTCACC 58.281 45.455 4.64 0.00 38.97 4.02
1207 1221 1.183549 TCAGGCTACGAAGGAAGTCC 58.816 55.000 0.00 0.00 0.00 3.85
1331 1346 1.445582 GACGCCACCTTGTAGACCG 60.446 63.158 0.00 0.00 0.00 4.79
1380 1395 2.680352 ACCTCCTGCCATCGTCGT 60.680 61.111 0.00 0.00 0.00 4.34
1431 1446 2.204136 ATCTCCCCCACCTGCACA 60.204 61.111 0.00 0.00 0.00 4.57
1563 1578 5.569630 GCCGAATTGGAGGTGTATATGAGAT 60.570 44.000 0.00 0.00 42.00 2.75
1620 1635 4.462483 TGAAGGAGTAATTGATTTGGTGGC 59.538 41.667 0.00 0.00 0.00 5.01
1718 1733 8.964476 AAGAATGTTTTCACTTCAGAGAGTAA 57.036 30.769 0.00 0.00 34.08 2.24
1787 1802 7.719871 ACTAGACCTAGCATAGAAGAACAAA 57.280 36.000 0.00 0.00 42.77 2.83
1819 1834 8.332464 CGCACAATTTCCTACGATTCTTATTTA 58.668 33.333 0.00 0.00 0.00 1.40
1830 1845 7.363589 GAATTATTTCGCACAATTTCCTACG 57.636 36.000 0.00 0.00 0.00 3.51
1855 1870 6.690194 ATGACTCATCAAAATACTGCCTTC 57.310 37.500 0.00 0.00 38.69 3.46
1871 1887 1.347378 TGCACAACTGCCTATGACTCA 59.653 47.619 0.00 0.00 43.51 3.41
1901 1917 6.427853 TCAACTCAGGTCAATGTGTTCATTAG 59.572 38.462 0.00 0.00 41.66 1.73
1906 1922 6.992063 ATATCAACTCAGGTCAATGTGTTC 57.008 37.500 0.00 0.00 35.36 3.18
2181 2197 8.367911 CCTCTAAATACACCATGTAGATTAGCA 58.632 37.037 13.96 7.29 36.80 3.49
2274 2293 6.746104 TTGTTAACTTGTGATCGCATTTTG 57.254 33.333 10.29 3.95 0.00 2.44
2317 2336 1.284198 AGCCTCAAGCCATCAACTCAT 59.716 47.619 0.00 0.00 45.47 2.90
2387 2406 8.345565 CACTGCAAAAATATAGTCCAGGTAATC 58.654 37.037 0.00 0.00 0.00 1.75
2596 2617 9.733556 AAAAGGTTGAGTTAAAAACTTTGGATT 57.266 25.926 2.88 0.00 42.32 3.01
2709 2756 1.542628 TGGTCCACCAGGCCCATAA 60.543 57.895 0.00 0.00 42.01 1.90
2888 2935 1.971695 GGCCCTGTTCCTTTGACGG 60.972 63.158 0.00 0.00 0.00 4.79
2890 2937 0.251787 ATGGGCCCTGTTCCTTTGAC 60.252 55.000 25.70 0.00 0.00 3.18
3150 3201 5.403246 ACATTACACTTCAGCTTCTAGTCG 58.597 41.667 0.00 0.00 0.00 4.18
3205 3286 4.682787 CAACAACGAGGCATCATACTCTA 58.317 43.478 0.00 0.00 0.00 2.43
3299 3690 8.362639 ACTTGTTTTGATTGAGCATTGACTATT 58.637 29.630 0.00 0.00 0.00 1.73
3451 3846 7.525688 ACAGAACATGTACGTTATCATTGAG 57.474 36.000 0.00 0.00 41.60 3.02
3528 4007 2.697654 GATGTAGCCTGGATGCTCATC 58.302 52.381 0.00 4.49 41.68 2.92
3535 4014 2.603021 ACTCATCGATGTAGCCTGGAT 58.397 47.619 24.09 0.00 0.00 3.41
3554 4033 3.585862 TGGCTGATTCTTCGTTGAGTAC 58.414 45.455 0.00 0.00 0.00 2.73
3562 4041 2.687842 GCTCCTGGCTGATTCTTCG 58.312 57.895 0.00 0.00 38.06 3.79
3612 4091 3.676172 CCACGCGTTGTCTAACTGAAATA 59.324 43.478 10.22 0.00 34.60 1.40
3675 4154 1.544691 ACTCGTTCGTGACATAAGCCT 59.455 47.619 1.45 0.00 0.00 4.58
3676 4155 1.992170 ACTCGTTCGTGACATAAGCC 58.008 50.000 1.45 0.00 0.00 4.35
3776 4274 1.830279 TCTCAGCAAAGAAGGCCATG 58.170 50.000 5.01 0.00 0.00 3.66
3777 4275 2.025605 TCATCTCAGCAAAGAAGGCCAT 60.026 45.455 5.01 0.00 0.00 4.40
3778 4276 1.352017 TCATCTCAGCAAAGAAGGCCA 59.648 47.619 5.01 0.00 0.00 5.36
3779 4277 2.015587 CTCATCTCAGCAAAGAAGGCC 58.984 52.381 0.00 0.00 0.00 5.19
3780 4278 2.015587 CCTCATCTCAGCAAAGAAGGC 58.984 52.381 0.00 0.00 0.00 4.35
3781 4279 2.015587 GCCTCATCTCAGCAAAGAAGG 58.984 52.381 0.00 0.00 0.00 3.46
3782 4280 2.708051 TGCCTCATCTCAGCAAAGAAG 58.292 47.619 0.00 0.00 32.56 2.85
3783 4281 2.865119 TGCCTCATCTCAGCAAAGAA 57.135 45.000 0.00 0.00 32.56 2.52
3784 4282 2.237893 TCATGCCTCATCTCAGCAAAGA 59.762 45.455 0.00 0.00 40.46 2.52
3785 4283 2.355132 GTCATGCCTCATCTCAGCAAAG 59.645 50.000 0.00 0.00 40.46 2.77
3786 4284 2.290450 TGTCATGCCTCATCTCAGCAAA 60.290 45.455 0.00 0.00 40.46 3.68
3959 4480 5.766174 ACGTTTCTCCAAATTTACTGCCTTA 59.234 36.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.