Multiple sequence alignment - TraesCS1D01G191000

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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 TraesCS1D01G191000 chr1D 100.000 4210 0 0 1 4210 263070956 263075165 0.000000e+00 7775
1 TraesCS1D01G191000 chr1B 94.430 2675 87 25 664 3307 348861470 348864113 0.000000e+00 4058
2 TraesCS1D01G191000 chr1B 83.540 887 91 26 3329 4210 465383358 465382522 0.000000e+00 778
3 TraesCS1D01G191000 chr1B 86.452 465 29 14 123 581 348860934 348861370 2.940000e-131 479
4 TraesCS1D01G191000 chr1A 93.537 2723 85 34 666 3333 337149863 337152549 0.000000e+00 3969
5 TraesCS1D01G191000 chr1A 91.071 336 18 7 117 451 337149145 337149469 1.070000e-120 444
6 TraesCS1D01G191000 chr1A 96.226 106 4 0 456 561 337149648 337149753 1.560000e-39 174
7 TraesCS1D01G191000 chr6D 87.896 884 89 14 3332 4210 57792452 57793322 0.000000e+00 1024
8 TraesCS1D01G191000 chr6D 87.093 891 82 19 3327 4210 142985417 142984553 0.000000e+00 977
9 TraesCS1D01G191000 chr4B 86.932 880 88 15 3337 4210 650772375 650773233 0.000000e+00 963
10 TraesCS1D01G191000 chr4B 86.986 146 18 1 1831 1975 611853724 611853869 3.370000e-36 163
11 TraesCS1D01G191000 chr4B 89.011 91 10 0 2091 2181 611853947 611854037 3.440000e-21 113
12 TraesCS1D01G191000 chr3A 85.114 880 96 18 3336 4210 711214574 711213725 0.000000e+00 867
13 TraesCS1D01G191000 chr7B 84.555 887 99 19 3330 4210 719365572 719364718 0.000000e+00 845
14 TraesCS1D01G191000 chr4D 84.294 885 93 24 3331 4210 324470293 324471136 0.000000e+00 822
15 TraesCS1D01G191000 chr4D 87.324 142 18 0 1831 1972 482158823 482158964 3.370000e-36 163
16 TraesCS1D01G191000 chr4D 90.110 91 9 0 2091 2181 482159062 482159152 7.390000e-23 119
17 TraesCS1D01G191000 chr3D 85.185 810 89 17 3398 4201 588073343 588074127 0.000000e+00 802
18 TraesCS1D01G191000 chr5B 80.274 877 135 22 3333 4200 609269007 609269854 9.940000e-176 627
19 TraesCS1D01G191000 chr5A 87.075 147 18 1 1831 1977 660442663 660442518 9.360000e-37 165
20 TraesCS1D01G191000 chr5A 90.217 92 9 0 2091 2182 660442427 660442336 2.060000e-23 121


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 TraesCS1D01G191000 chr1D 263070956 263075165 4209 False 7775.0 7775 100.000000 1 4210 1 chr1D.!!$F1 4209
1 TraesCS1D01G191000 chr1B 348860934 348864113 3179 False 2268.5 4058 90.441000 123 3307 2 chr1B.!!$F1 3184
2 TraesCS1D01G191000 chr1B 465382522 465383358 836 True 778.0 778 83.540000 3329 4210 1 chr1B.!!$R1 881
3 TraesCS1D01G191000 chr1A 337149145 337152549 3404 False 1529.0 3969 93.611333 117 3333 3 chr1A.!!$F1 3216
4 TraesCS1D01G191000 chr6D 57792452 57793322 870 False 1024.0 1024 87.896000 3332 4210 1 chr6D.!!$F1 878
5 TraesCS1D01G191000 chr6D 142984553 142985417 864 True 977.0 977 87.093000 3327 4210 1 chr6D.!!$R1 883
6 TraesCS1D01G191000 chr4B 650772375 650773233 858 False 963.0 963 86.932000 3337 4210 1 chr4B.!!$F1 873
7 TraesCS1D01G191000 chr3A 711213725 711214574 849 True 867.0 867 85.114000 3336 4210 1 chr3A.!!$R1 874
8 TraesCS1D01G191000 chr7B 719364718 719365572 854 True 845.0 845 84.555000 3330 4210 1 chr7B.!!$R1 880
9 TraesCS1D01G191000 chr4D 324470293 324471136 843 False 822.0 822 84.294000 3331 4210 1 chr4D.!!$F1 879
10 TraesCS1D01G191000 chr3D 588073343 588074127 784 False 802.0 802 85.185000 3398 4201 1 chr3D.!!$F1 803
11 TraesCS1D01G191000 chr5B 609269007 609269854 847 False 627.0 627 80.274000 3333 4200 1 chr5B.!!$F1 867

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
62 63 0.040781 CGCACCGTTCCGAATTTGTT 60.041 50.0 0.00 0.00 0.0 2.83 F
161 162 0.320247 CCGGATCCTGCTGCATAGTC 60.320 60.0 10.75 1.24 0.0 2.59 F
578 763 0.511221 CAACGACGATCAACACCACC 59.489 55.0 0.00 0.00 0.0 4.61 F
1803 2063 0.463204 CCGAGCTGGACTGACATGAT 59.537 55.0 0.00 0.00 42.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 2037 0.251209 TGTCAGTCCAGCTCGGTAGT 60.251 55.000 2.68 0.0 35.57 2.73 R
1803 2063 0.529773 GGCGCAATCGGAGTGACATA 60.530 55.000 10.83 0.0 35.95 2.29 R
2317 2589 1.134367 GTCGCACTACTCTACATGGCA 59.866 52.381 0.00 0.0 0.00 4.92 R
3703 4035 0.036858 GAGGCGAAGTCAAAGCTCCT 60.037 55.000 0.00 0.0 0.00 3.69 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
17 18 4.464262 CTTCCGAAGCATAGGGCC 57.536 61.111 0.00 0.00 46.50 5.80
18 19 1.595382 CTTCCGAAGCATAGGGCCG 60.595 63.158 0.00 0.00 46.50 6.13
19 20 2.028125 CTTCCGAAGCATAGGGCCGA 62.028 60.000 0.00 0.00 46.50 5.54
20 21 2.280186 CCGAAGCATAGGGCCGAC 60.280 66.667 0.00 0.00 46.50 4.79
21 22 2.280186 CGAAGCATAGGGCCGACC 60.280 66.667 0.00 0.00 46.50 4.79
31 32 3.834799 GGCCGACCCTGAGTACCG 61.835 72.222 0.00 0.00 0.00 4.02
32 33 3.066814 GCCGACCCTGAGTACCGT 61.067 66.667 0.00 0.00 0.00 4.83
33 34 1.750399 GCCGACCCTGAGTACCGTA 60.750 63.158 0.00 0.00 0.00 4.02
34 35 1.315257 GCCGACCCTGAGTACCGTAA 61.315 60.000 0.00 0.00 0.00 3.18
35 36 1.176527 CCGACCCTGAGTACCGTAAA 58.823 55.000 0.00 0.00 0.00 2.01
36 37 1.753073 CCGACCCTGAGTACCGTAAAT 59.247 52.381 0.00 0.00 0.00 1.40
37 38 2.951642 CCGACCCTGAGTACCGTAAATA 59.048 50.000 0.00 0.00 0.00 1.40
38 39 3.004106 CCGACCCTGAGTACCGTAAATAG 59.996 52.174 0.00 0.00 0.00 1.73
39 40 3.629398 CGACCCTGAGTACCGTAAATAGT 59.371 47.826 0.00 0.00 0.00 2.12
40 41 4.816385 CGACCCTGAGTACCGTAAATAGTA 59.184 45.833 0.00 0.00 0.00 1.82
41 42 5.277538 CGACCCTGAGTACCGTAAATAGTAC 60.278 48.000 0.00 0.00 39.31 2.73
47 48 5.162000 AGTACCGTAAATAGTACTCGCAC 57.838 43.478 0.00 0.00 44.54 5.34
48 49 3.427161 ACCGTAAATAGTACTCGCACC 57.573 47.619 0.00 0.00 0.00 5.01
49 50 2.223340 ACCGTAAATAGTACTCGCACCG 60.223 50.000 0.00 0.00 0.00 4.94
50 51 2.223340 CCGTAAATAGTACTCGCACCGT 60.223 50.000 0.00 0.00 0.00 4.83
51 52 3.429085 CGTAAATAGTACTCGCACCGTT 58.571 45.455 0.00 0.00 0.00 4.44
52 53 3.479949 CGTAAATAGTACTCGCACCGTTC 59.520 47.826 0.00 0.00 0.00 3.95
53 54 2.573941 AATAGTACTCGCACCGTTCC 57.426 50.000 0.00 0.00 0.00 3.62
54 55 0.379669 ATAGTACTCGCACCGTTCCG 59.620 55.000 0.00 0.00 0.00 4.30
55 56 0.673333 TAGTACTCGCACCGTTCCGA 60.673 55.000 0.00 0.00 0.00 4.55
56 57 1.081242 GTACTCGCACCGTTCCGAA 60.081 57.895 0.00 0.00 32.56 4.30
57 58 0.457337 GTACTCGCACCGTTCCGAAT 60.457 55.000 0.00 0.00 32.56 3.34
58 59 0.244450 TACTCGCACCGTTCCGAATT 59.756 50.000 0.00 0.00 32.56 2.17
59 60 0.601841 ACTCGCACCGTTCCGAATTT 60.602 50.000 0.00 0.00 32.56 1.82
60 61 0.179225 CTCGCACCGTTCCGAATTTG 60.179 55.000 0.00 0.00 32.56 2.32
61 62 0.881159 TCGCACCGTTCCGAATTTGT 60.881 50.000 0.00 0.00 0.00 2.83
62 63 0.040781 CGCACCGTTCCGAATTTGTT 60.041 50.000 0.00 0.00 0.00 2.83
63 64 1.404477 GCACCGTTCCGAATTTGTTG 58.596 50.000 0.00 0.00 0.00 3.33
64 65 1.268845 GCACCGTTCCGAATTTGTTGT 60.269 47.619 0.00 0.00 0.00 3.32
65 66 2.646250 CACCGTTCCGAATTTGTTGTC 58.354 47.619 0.00 0.00 0.00 3.18
66 67 2.032302 CACCGTTCCGAATTTGTTGTCA 59.968 45.455 0.00 0.00 0.00 3.58
67 68 2.882137 ACCGTTCCGAATTTGTTGTCAT 59.118 40.909 0.00 0.00 0.00 3.06
68 69 4.066490 ACCGTTCCGAATTTGTTGTCATA 58.934 39.130 0.00 0.00 0.00 2.15
69 70 4.153475 ACCGTTCCGAATTTGTTGTCATAG 59.847 41.667 0.00 0.00 0.00 2.23
70 71 4.390603 CCGTTCCGAATTTGTTGTCATAGA 59.609 41.667 0.00 0.00 0.00 1.98
71 72 5.064707 CCGTTCCGAATTTGTTGTCATAGAT 59.935 40.000 0.00 0.00 0.00 1.98
72 73 6.403200 CCGTTCCGAATTTGTTGTCATAGATT 60.403 38.462 0.00 0.00 0.00 2.40
73 74 7.021196 CGTTCCGAATTTGTTGTCATAGATTT 58.979 34.615 0.00 0.00 0.00 2.17
74 75 7.007367 CGTTCCGAATTTGTTGTCATAGATTTG 59.993 37.037 0.00 0.00 0.00 2.32
75 76 7.447374 TCCGAATTTGTTGTCATAGATTTGT 57.553 32.000 0.00 0.00 0.00 2.83
76 77 7.526608 TCCGAATTTGTTGTCATAGATTTGTC 58.473 34.615 0.00 0.00 0.00 3.18
77 78 7.390440 TCCGAATTTGTTGTCATAGATTTGTCT 59.610 33.333 0.00 0.00 0.00 3.41
78 79 8.664798 CCGAATTTGTTGTCATAGATTTGTCTA 58.335 33.333 0.00 0.00 0.00 2.59
79 80 9.694520 CGAATTTGTTGTCATAGATTTGTCTAG 57.305 33.333 0.00 0.00 0.00 2.43
83 84 8.722480 TTGTTGTCATAGATTTGTCTAGATGG 57.278 34.615 0.00 0.00 0.00 3.51
84 85 8.078060 TGTTGTCATAGATTTGTCTAGATGGA 57.922 34.615 0.00 0.00 0.00 3.41
85 86 7.981789 TGTTGTCATAGATTTGTCTAGATGGAC 59.018 37.037 0.00 0.00 36.81 4.02
86 87 7.660030 TGTCATAGATTTGTCTAGATGGACA 57.340 36.000 0.00 0.00 43.41 4.02
101 102 9.542462 TCTAGATGGACAATTAATTTAGAACGG 57.458 33.333 0.00 0.00 0.00 4.44
102 103 7.027778 AGATGGACAATTAATTTAGAACGGC 57.972 36.000 0.00 0.00 0.00 5.68
103 104 5.224562 TGGACAATTAATTTAGAACGGCG 57.775 39.130 4.80 4.80 0.00 6.46
104 105 4.095185 TGGACAATTAATTTAGAACGGCGG 59.905 41.667 13.24 0.00 0.00 6.13
105 106 4.095334 GGACAATTAATTTAGAACGGCGGT 59.905 41.667 13.24 3.35 0.00 5.68
106 107 5.294060 GGACAATTAATTTAGAACGGCGGTA 59.706 40.000 13.24 0.00 0.00 4.02
107 108 6.183360 GGACAATTAATTTAGAACGGCGGTAA 60.183 38.462 13.24 3.00 0.00 2.85
108 109 7.324354 ACAATTAATTTAGAACGGCGGTAAT 57.676 32.000 13.24 0.00 0.00 1.89
109 110 8.436046 ACAATTAATTTAGAACGGCGGTAATA 57.564 30.769 13.24 0.00 0.00 0.98
110 111 8.553696 ACAATTAATTTAGAACGGCGGTAATAG 58.446 33.333 13.24 0.00 0.00 1.73
111 112 8.553696 CAATTAATTTAGAACGGCGGTAATAGT 58.446 33.333 13.24 0.00 0.00 2.12
112 113 9.762933 AATTAATTTAGAACGGCGGTAATAGTA 57.237 29.630 13.24 0.00 0.00 1.82
113 114 9.933723 ATTAATTTAGAACGGCGGTAATAGTAT 57.066 29.630 13.24 0.00 0.00 2.12
115 116 8.748380 AATTTAGAACGGCGGTAATAGTATAC 57.252 34.615 13.24 0.00 0.00 1.47
120 121 6.486657 AGAACGGCGGTAATAGTATACAGTAA 59.513 38.462 13.24 0.00 0.00 2.24
125 126 7.361542 CGGCGGTAATAGTATACAGTAACAGAT 60.362 40.741 5.50 0.00 0.00 2.90
153 154 2.447379 ATCTGGCCGGATCCTGCT 60.447 61.111 25.11 5.03 0.00 4.24
154 155 2.815945 ATCTGGCCGGATCCTGCTG 61.816 63.158 25.11 18.25 0.00 4.41
158 159 2.427320 GCCGGATCCTGCTGCATA 59.573 61.111 19.97 0.00 0.00 3.14
159 160 1.670406 GCCGGATCCTGCTGCATAG 60.670 63.158 19.97 0.00 0.00 2.23
160 161 1.750930 CCGGATCCTGCTGCATAGT 59.249 57.895 10.75 0.00 0.00 2.12
161 162 0.320247 CCGGATCCTGCTGCATAGTC 60.320 60.000 10.75 1.24 0.00 2.59
162 163 0.320247 CGGATCCTGCTGCATAGTCC 60.320 60.000 10.75 9.76 0.00 3.85
163 164 0.761187 GGATCCTGCTGCATAGTCCA 59.239 55.000 17.24 0.00 0.00 4.02
168 169 2.239402 TCCTGCTGCATAGTCCATTTCA 59.761 45.455 1.31 0.00 0.00 2.69
182 183 5.013495 AGTCCATTTCAGACTTGGATCTTGA 59.987 40.000 4.20 0.00 41.87 3.02
230 231 2.852449 TCTTGATAAACCCCCTGCATCT 59.148 45.455 0.00 0.00 0.00 2.90
239 240 2.582636 ACCCCCTGCATCTTTGAAGTAT 59.417 45.455 0.00 0.00 0.00 2.12
519 699 0.837691 ACTGGCCAGTGACTCATCCA 60.838 55.000 37.39 0.00 40.75 3.41
525 705 1.135139 CCAGTGACTCATCCAGTACCG 59.865 57.143 0.00 0.00 34.41 4.02
528 708 1.135083 GTGACTCATCCAGTACCGTGG 60.135 57.143 0.00 0.00 34.41 4.94
563 748 4.319477 CCAACTGTATTCCTCACAACAACG 60.319 45.833 0.00 0.00 0.00 4.10
574 759 2.283086 TCACAACAACGACGATCAACAC 59.717 45.455 0.00 0.00 0.00 3.32
577 762 1.214367 ACAACGACGATCAACACCAC 58.786 50.000 0.00 0.00 0.00 4.16
578 763 0.511221 CAACGACGATCAACACCACC 59.489 55.000 0.00 0.00 0.00 4.61
579 764 0.601841 AACGACGATCAACACCACCC 60.602 55.000 0.00 0.00 0.00 4.61
580 765 1.005512 CGACGATCAACACCACCCA 60.006 57.895 0.00 0.00 0.00 4.51
581 766 1.014044 CGACGATCAACACCACCCAG 61.014 60.000 0.00 0.00 0.00 4.45
582 767 0.673644 GACGATCAACACCACCCAGG 60.674 60.000 0.00 0.00 45.67 4.45
583 768 2.040544 CGATCAACACCACCCAGGC 61.041 63.158 0.00 0.00 43.14 4.85
584 769 1.074775 GATCAACACCACCCAGGCA 59.925 57.895 0.00 0.00 43.14 4.75
585 770 1.228552 ATCAACACCACCCAGGCAC 60.229 57.895 0.00 0.00 43.14 5.01
586 771 2.713531 ATCAACACCACCCAGGCACC 62.714 60.000 0.00 0.00 43.14 5.01
587 772 4.218686 AACACCACCCAGGCACCC 62.219 66.667 0.00 0.00 43.14 4.61
589 774 4.974721 CACCACCCAGGCACCCAC 62.975 72.222 0.00 0.00 43.14 4.61
591 776 4.974721 CCACCCAGGCACCCACAC 62.975 72.222 0.00 0.00 0.00 3.82
594 779 4.033776 CCCAGGCACCCACACGAT 62.034 66.667 0.00 0.00 0.00 3.73
616 801 2.481795 CCCACAGTGGCAAAAACTTCAG 60.482 50.000 14.98 0.00 35.79 3.02
617 802 2.166254 CCACAGTGGCAAAAACTTCAGT 59.834 45.455 6.67 0.00 0.00 3.41
618 803 3.380004 CCACAGTGGCAAAAACTTCAGTA 59.620 43.478 6.67 0.00 0.00 2.74
619 804 4.498009 CCACAGTGGCAAAAACTTCAGTAG 60.498 45.833 6.67 0.00 0.00 2.57
620 805 3.066760 ACAGTGGCAAAAACTTCAGTAGC 59.933 43.478 0.00 0.00 0.00 3.58
621 806 2.290641 AGTGGCAAAAACTTCAGTAGCG 59.709 45.455 0.00 0.00 0.00 4.26
622 807 2.289547 GTGGCAAAAACTTCAGTAGCGA 59.710 45.455 0.00 0.00 0.00 4.93
623 808 2.548057 TGGCAAAAACTTCAGTAGCGAG 59.452 45.455 0.00 0.00 0.00 5.03
624 809 2.548480 GGCAAAAACTTCAGTAGCGAGT 59.452 45.455 0.00 0.00 0.00 4.18
625 810 3.744426 GGCAAAAACTTCAGTAGCGAGTA 59.256 43.478 0.00 0.00 0.00 2.59
626 811 4.143094 GGCAAAAACTTCAGTAGCGAGTAG 60.143 45.833 0.00 0.00 0.00 2.57
627 812 4.448060 GCAAAAACTTCAGTAGCGAGTAGT 59.552 41.667 0.00 0.00 0.00 2.73
628 813 5.632347 GCAAAAACTTCAGTAGCGAGTAGTA 59.368 40.000 0.00 0.00 0.00 1.82
655 841 1.973281 CACCCACCCTGACATGCAC 60.973 63.158 0.00 0.00 0.00 4.57
849 1083 2.093783 GGCCACGCAGCGATTATAATAC 59.906 50.000 24.65 0.00 0.00 1.89
958 1197 1.548973 CCAAGCACACGACACGAGAC 61.549 60.000 0.00 0.00 0.00 3.36
959 1198 1.657487 AAGCACACGACACGAGACG 60.657 57.895 3.08 3.08 38.82 4.18
960 1199 2.051614 GCACACGACACGAGACGA 60.052 61.111 11.70 0.00 36.75 4.20
961 1200 2.075489 GCACACGACACGAGACGAG 61.075 63.158 11.70 6.19 36.75 4.18
962 1201 1.568025 CACACGACACGAGACGAGA 59.432 57.895 11.70 0.00 36.75 4.04
1632 1889 1.004440 GGAGCCGAGCAAGTTCAGT 60.004 57.895 0.00 0.00 0.00 3.41
1803 2063 0.463204 CCGAGCTGGACTGACATGAT 59.537 55.000 0.00 0.00 42.00 2.45
1940 2200 3.314331 CAGACGGAGGCCACCACT 61.314 66.667 20.07 14.22 0.00 4.00
1983 2243 1.276622 ACAGGTACATCCACCAGACC 58.723 55.000 0.00 0.00 41.40 3.85
2096 2368 0.947244 CTTCCTCTTTGTTGCAGCGT 59.053 50.000 0.00 0.00 0.00 5.07
2317 2589 1.834458 GCGTTTGCCCGTTAGTCGTT 61.834 55.000 0.00 0.00 37.94 3.85
2318 2590 0.111001 CGTTTGCCCGTTAGTCGTTG 60.111 55.000 0.00 0.00 37.94 4.10
2516 2788 1.447317 CGCCGGATCCATTTCTTGGG 61.447 60.000 13.41 2.97 46.45 4.12
2517 2789 1.738346 GCCGGATCCATTTCTTGGGC 61.738 60.000 13.41 9.90 46.45 5.36
2518 2790 0.106519 CCGGATCCATTTCTTGGGCT 60.107 55.000 13.41 0.00 46.45 5.19
2579 2861 1.961180 ATCCAAGAAGGCTCCGTCGG 61.961 60.000 4.39 4.39 37.29 4.79
2697 2979 6.930667 TCATCATTCACATCACATTACTGG 57.069 37.500 0.00 0.00 0.00 4.00
2712 2994 3.418687 TGGTGCTGCCATGGATCT 58.581 55.556 18.40 0.00 43.61 2.75
2999 3298 1.522580 GGAGCAGAATGGCGAGTCC 60.523 63.158 0.00 0.00 39.27 3.85
3183 3485 4.277423 TGAATGTTCTTTTCGTTCCTTCCC 59.723 41.667 0.00 0.00 31.97 3.97
3184 3486 3.284793 TGTTCTTTTCGTTCCTTCCCA 57.715 42.857 0.00 0.00 0.00 4.37
3274 3576 6.338146 TCTGTATTGAGTAATGTGTGTAGCC 58.662 40.000 0.00 0.00 0.00 3.93
3300 3602 3.362986 CGGTGTGAAACGACTTTCAGATG 60.363 47.826 1.74 0.00 45.22 2.90
3328 3633 5.568685 TTGATGGAGAAACGTTTGTTGAA 57.431 34.783 20.10 4.62 38.62 2.69
3355 3660 3.189921 GCATCTCCAACATGCGCA 58.810 55.556 14.96 14.96 37.51 6.09
3382 3688 3.022287 CGCCGCGCTGGATAAATT 58.978 55.556 20.06 0.00 42.00 1.82
3464 3781 1.305219 GGCATAAGTGGTTCAGCGCA 61.305 55.000 11.47 0.00 0.00 6.09
3639 3956 2.418910 CGCCGACATCTCCCTCACT 61.419 63.158 0.00 0.00 0.00 3.41
3663 3980 4.371417 TACACCCGCGACCCCTCT 62.371 66.667 8.23 0.00 0.00 3.69
3672 3989 4.459089 GACCCCTCTGCAGCCGTC 62.459 72.222 9.47 7.63 0.00 4.79
3703 4035 4.770874 GCGCAAACCCTAGCCCGA 62.771 66.667 0.30 0.00 0.00 5.14
3713 4045 1.330655 CCTAGCCCGAGGAGCTTTGA 61.331 60.000 9.69 0.00 41.83 2.69
3776 4108 2.929903 GCCTTTTCATGGCGCCACA 61.930 57.895 35.50 19.73 41.03 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.595382 CGGCCCTATGCTTCGGAAG 60.595 63.158 13.39 13.39 40.92 3.46
4 5 2.280186 GGTCGGCCCTATGCTTCG 60.280 66.667 0.00 0.00 40.92 3.79
14 15 3.834799 CGGTACTCAGGGTCGGCC 61.835 72.222 0.00 0.00 0.00 6.13
15 16 1.315257 TTACGGTACTCAGGGTCGGC 61.315 60.000 0.00 0.00 0.00 5.54
16 17 1.176527 TTTACGGTACTCAGGGTCGG 58.823 55.000 0.00 0.00 0.00 4.79
17 18 3.629398 ACTATTTACGGTACTCAGGGTCG 59.371 47.826 0.00 0.00 0.00 4.79
18 19 5.825151 AGTACTATTTACGGTACTCAGGGTC 59.175 44.000 0.00 0.00 43.20 4.46
19 20 5.760131 AGTACTATTTACGGTACTCAGGGT 58.240 41.667 0.00 0.00 43.20 4.34
26 27 4.282873 GGTGCGAGTACTATTTACGGTAC 58.717 47.826 0.00 0.00 38.69 3.34
27 28 3.002246 CGGTGCGAGTACTATTTACGGTA 59.998 47.826 0.00 0.00 0.00 4.02
28 29 2.223340 CGGTGCGAGTACTATTTACGGT 60.223 50.000 0.00 0.00 0.00 4.83
29 30 2.223340 ACGGTGCGAGTACTATTTACGG 60.223 50.000 0.00 0.67 0.00 4.02
30 31 3.056952 ACGGTGCGAGTACTATTTACG 57.943 47.619 0.00 1.11 0.00 3.18
31 32 3.793492 GGAACGGTGCGAGTACTATTTAC 59.207 47.826 0.00 0.00 0.00 2.01
32 33 4.032703 GGAACGGTGCGAGTACTATTTA 57.967 45.455 0.00 0.00 0.00 1.40
33 34 2.884827 GGAACGGTGCGAGTACTATTT 58.115 47.619 0.00 0.00 0.00 1.40
34 35 2.573941 GGAACGGTGCGAGTACTATT 57.426 50.000 0.00 0.00 0.00 1.73
49 50 7.807907 ACAAATCTATGACAACAAATTCGGAAC 59.192 33.333 0.00 0.00 0.00 3.62
50 51 7.881142 ACAAATCTATGACAACAAATTCGGAA 58.119 30.769 0.00 0.00 0.00 4.30
51 52 7.390440 AGACAAATCTATGACAACAAATTCGGA 59.610 33.333 0.00 0.00 31.46 4.55
52 53 7.530010 AGACAAATCTATGACAACAAATTCGG 58.470 34.615 0.00 0.00 31.46 4.30
53 54 9.694520 CTAGACAAATCTATGACAACAAATTCG 57.305 33.333 0.00 0.00 36.81 3.34
57 58 9.166173 CCATCTAGACAAATCTATGACAACAAA 57.834 33.333 0.00 0.00 36.81 2.83
58 59 8.539544 TCCATCTAGACAAATCTATGACAACAA 58.460 33.333 0.00 0.00 36.81 2.83
59 60 7.981789 GTCCATCTAGACAAATCTATGACAACA 59.018 37.037 0.00 0.00 36.81 3.33
60 61 7.981789 TGTCCATCTAGACAAATCTATGACAAC 59.018 37.037 0.00 0.00 43.65 3.32
61 62 8.078060 TGTCCATCTAGACAAATCTATGACAA 57.922 34.615 0.00 0.00 43.65 3.18
62 63 7.660030 TGTCCATCTAGACAAATCTATGACA 57.340 36.000 0.00 0.00 43.65 3.58
75 76 9.542462 CCGTTCTAAATTAATTGTCCATCTAGA 57.458 33.333 0.39 0.00 0.00 2.43
76 77 8.283291 GCCGTTCTAAATTAATTGTCCATCTAG 58.717 37.037 0.39 0.00 0.00 2.43
77 78 7.042321 CGCCGTTCTAAATTAATTGTCCATCTA 60.042 37.037 0.39 0.00 0.00 1.98
78 79 6.238374 CGCCGTTCTAAATTAATTGTCCATCT 60.238 38.462 0.39 0.00 0.00 2.90
79 80 5.907391 CGCCGTTCTAAATTAATTGTCCATC 59.093 40.000 0.39 0.00 0.00 3.51
80 81 5.220970 CCGCCGTTCTAAATTAATTGTCCAT 60.221 40.000 0.39 0.00 0.00 3.41
81 82 4.095185 CCGCCGTTCTAAATTAATTGTCCA 59.905 41.667 0.39 0.00 0.00 4.02
82 83 4.095334 ACCGCCGTTCTAAATTAATTGTCC 59.905 41.667 0.39 0.00 0.00 4.02
83 84 5.225899 ACCGCCGTTCTAAATTAATTGTC 57.774 39.130 0.39 0.00 0.00 3.18
84 85 6.740411 TTACCGCCGTTCTAAATTAATTGT 57.260 33.333 0.39 0.00 0.00 2.71
85 86 8.553696 ACTATTACCGCCGTTCTAAATTAATTG 58.446 33.333 0.39 0.00 0.00 2.32
86 87 8.667076 ACTATTACCGCCGTTCTAAATTAATT 57.333 30.769 0.00 0.00 0.00 1.40
87 88 9.933723 ATACTATTACCGCCGTTCTAAATTAAT 57.066 29.630 0.00 0.00 0.00 1.40
89 90 9.840427 GTATACTATTACCGCCGTTCTAAATTA 57.160 33.333 0.00 0.00 0.00 1.40
90 91 8.359642 TGTATACTATTACCGCCGTTCTAAATT 58.640 33.333 4.17 0.00 0.00 1.82
91 92 7.885297 TGTATACTATTACCGCCGTTCTAAAT 58.115 34.615 4.17 0.00 0.00 1.40
92 93 7.013274 ACTGTATACTATTACCGCCGTTCTAAA 59.987 37.037 4.17 0.00 0.00 1.85
93 94 6.486657 ACTGTATACTATTACCGCCGTTCTAA 59.513 38.462 4.17 0.00 0.00 2.10
94 95 5.997746 ACTGTATACTATTACCGCCGTTCTA 59.002 40.000 4.17 0.00 0.00 2.10
95 96 4.823989 ACTGTATACTATTACCGCCGTTCT 59.176 41.667 4.17 0.00 0.00 3.01
96 97 5.113502 ACTGTATACTATTACCGCCGTTC 57.886 43.478 4.17 0.00 0.00 3.95
97 98 6.039270 TGTTACTGTATACTATTACCGCCGTT 59.961 38.462 4.17 0.00 0.00 4.44
98 99 5.530915 TGTTACTGTATACTATTACCGCCGT 59.469 40.000 4.17 0.00 0.00 5.68
99 100 6.000891 TGTTACTGTATACTATTACCGCCG 57.999 41.667 4.17 0.00 0.00 6.46
100 101 7.206981 TCTGTTACTGTATACTATTACCGCC 57.793 40.000 4.17 0.00 0.00 6.13
107 108 9.589461 ACTGCCTAATCTGTTACTGTATACTAT 57.411 33.333 4.17 0.00 0.00 2.12
108 109 8.991783 ACTGCCTAATCTGTTACTGTATACTA 57.008 34.615 4.17 0.00 0.00 1.82
109 110 7.899648 ACTGCCTAATCTGTTACTGTATACT 57.100 36.000 4.17 0.00 0.00 2.12
110 111 8.627403 TGTACTGCCTAATCTGTTACTGTATAC 58.373 37.037 0.00 0.00 0.00 1.47
111 112 8.756486 TGTACTGCCTAATCTGTTACTGTATA 57.244 34.615 0.00 0.00 0.00 1.47
112 113 7.655521 TGTACTGCCTAATCTGTTACTGTAT 57.344 36.000 0.00 0.00 0.00 2.29
113 114 7.560262 AGATGTACTGCCTAATCTGTTACTGTA 59.440 37.037 0.00 0.00 0.00 2.74
114 115 5.995565 TGTACTGCCTAATCTGTTACTGT 57.004 39.130 0.00 0.00 0.00 3.55
115 116 6.699204 CAGATGTACTGCCTAATCTGTTACTG 59.301 42.308 9.41 0.00 40.64 2.74
120 121 3.181461 GCCAGATGTACTGCCTAATCTGT 60.181 47.826 14.22 0.00 42.88 3.41
125 126 0.464036 CGGCCAGATGTACTGCCTAA 59.536 55.000 2.24 0.00 44.52 2.69
153 154 4.019411 TCCAAGTCTGAAATGGACTATGCA 60.019 41.667 8.22 0.00 42.39 3.96
154 155 4.517285 TCCAAGTCTGAAATGGACTATGC 58.483 43.478 8.22 0.00 42.39 3.14
155 156 6.590068 AGATCCAAGTCTGAAATGGACTATG 58.410 40.000 13.16 0.00 45.47 2.23
156 157 6.821616 AGATCCAAGTCTGAAATGGACTAT 57.178 37.500 13.16 0.88 45.47 2.12
158 159 5.013495 TCAAGATCCAAGTCTGAAATGGACT 59.987 40.000 13.16 10.27 45.47 3.85
159 160 5.248640 TCAAGATCCAAGTCTGAAATGGAC 58.751 41.667 13.16 8.68 45.47 4.02
160 161 5.503634 TCAAGATCCAAGTCTGAAATGGA 57.496 39.130 13.24 13.24 46.60 3.41
161 162 6.770746 AATCAAGATCCAAGTCTGAAATGG 57.229 37.500 4.10 4.10 35.49 3.16
188 189 9.627123 TCAAGATCTCAGAGGTTAAAAGAAAAA 57.373 29.630 0.00 0.00 0.00 1.94
194 195 9.449719 GGTTTATCAAGATCTCAGAGGTTAAAA 57.550 33.333 0.00 0.00 0.00 1.52
195 196 8.047310 GGGTTTATCAAGATCTCAGAGGTTAAA 58.953 37.037 0.00 0.00 0.00 1.52
196 197 7.365652 GGGGTTTATCAAGATCTCAGAGGTTAA 60.366 40.741 0.00 0.00 0.00 2.01
197 198 6.099845 GGGGTTTATCAAGATCTCAGAGGTTA 59.900 42.308 0.00 0.00 0.00 2.85
201 202 4.657969 AGGGGGTTTATCAAGATCTCAGAG 59.342 45.833 0.00 0.00 0.00 3.35
202 203 4.410228 CAGGGGGTTTATCAAGATCTCAGA 59.590 45.833 0.00 0.00 0.00 3.27
204 205 3.117888 GCAGGGGGTTTATCAAGATCTCA 60.118 47.826 0.00 0.00 0.00 3.27
206 207 2.852449 TGCAGGGGGTTTATCAAGATCT 59.148 45.455 0.00 0.00 0.00 2.75
216 217 2.250924 CTTCAAAGATGCAGGGGGTTT 58.749 47.619 0.00 0.00 0.00 3.27
219 220 2.806945 TACTTCAAAGATGCAGGGGG 57.193 50.000 0.00 0.00 0.00 5.40
230 231 2.025037 AGGCATGCTGGGATACTTCAAA 60.025 45.455 18.92 0.00 0.00 2.69
563 748 0.673644 CCTGGGTGGTGTTGATCGTC 60.674 60.000 0.00 0.00 0.00 4.20
574 759 4.974721 GTGTGGGTGCCTGGGTGG 62.975 72.222 0.00 0.00 39.35 4.61
577 762 3.976701 GATCGTGTGGGTGCCTGGG 62.977 68.421 0.00 0.00 0.00 4.45
578 763 2.436646 GATCGTGTGGGTGCCTGG 60.437 66.667 0.00 0.00 0.00 4.45
579 764 2.436646 GGATCGTGTGGGTGCCTG 60.437 66.667 0.00 0.00 0.00 4.85
580 765 3.717294 GGGATCGTGTGGGTGCCT 61.717 66.667 0.00 0.00 0.00 4.75
581 766 4.028490 TGGGATCGTGTGGGTGCC 62.028 66.667 0.00 0.00 0.00 5.01
582 767 2.746277 GTGGGATCGTGTGGGTGC 60.746 66.667 0.00 0.00 0.00 5.01
583 768 1.375908 CTGTGGGATCGTGTGGGTG 60.376 63.158 0.00 0.00 0.00 4.61
584 769 1.841556 ACTGTGGGATCGTGTGGGT 60.842 57.895 0.00 0.00 0.00 4.51
585 770 1.375908 CACTGTGGGATCGTGTGGG 60.376 63.158 0.00 0.00 0.00 4.61
586 771 1.375908 CCACTGTGGGATCGTGTGG 60.376 63.158 19.23 0.00 41.50 4.17
587 772 2.034879 GCCACTGTGGGATCGTGTG 61.035 63.158 27.02 0.00 38.19 3.82
588 773 2.050836 TTGCCACTGTGGGATCGTGT 62.051 55.000 27.02 0.00 37.82 4.49
589 774 0.888736 TTTGCCACTGTGGGATCGTG 60.889 55.000 27.02 1.35 37.82 4.35
590 775 0.179004 TTTTGCCACTGTGGGATCGT 60.179 50.000 27.02 0.00 37.82 3.73
591 776 0.958091 TTTTTGCCACTGTGGGATCG 59.042 50.000 27.02 2.83 37.82 3.69
592 777 1.963515 AGTTTTTGCCACTGTGGGATC 59.036 47.619 27.02 14.85 37.82 3.36
593 778 2.086610 AGTTTTTGCCACTGTGGGAT 57.913 45.000 27.02 7.26 37.82 3.85
594 779 1.754226 GAAGTTTTTGCCACTGTGGGA 59.246 47.619 27.02 22.73 38.19 4.37
616 801 2.474735 GGTCGCTACTACTACTCGCTAC 59.525 54.545 0.00 0.00 0.00 3.58
617 802 2.101415 TGGTCGCTACTACTACTCGCTA 59.899 50.000 0.00 0.00 0.00 4.26
618 803 1.134580 TGGTCGCTACTACTACTCGCT 60.135 52.381 0.00 0.00 0.00 4.93
619 804 1.004079 GTGGTCGCTACTACTACTCGC 60.004 57.143 0.00 0.00 34.45 5.03
620 805 1.596727 GGTGGTCGCTACTACTACTCG 59.403 57.143 4.89 0.00 37.27 4.18
621 806 1.946081 GGGTGGTCGCTACTACTACTC 59.054 57.143 4.89 0.00 37.27 2.59
622 807 1.283029 TGGGTGGTCGCTACTACTACT 59.717 52.381 4.89 0.00 37.27 2.57
623 808 1.403323 GTGGGTGGTCGCTACTACTAC 59.597 57.143 4.89 1.87 37.27 2.73
624 809 1.683011 GGTGGGTGGTCGCTACTACTA 60.683 57.143 4.89 0.00 37.27 1.82
625 810 0.969409 GGTGGGTGGTCGCTACTACT 60.969 60.000 4.89 0.00 37.27 2.57
626 811 1.514553 GGTGGGTGGTCGCTACTAC 59.485 63.158 0.00 0.00 36.42 2.73
627 812 1.683365 GGGTGGGTGGTCGCTACTA 60.683 63.158 0.00 0.00 0.00 1.82
628 813 3.001406 GGGTGGGTGGTCGCTACT 61.001 66.667 0.00 0.00 0.00 2.57
1389 1646 4.899239 CCGCGGCTGTCTCCATCC 62.899 72.222 14.67 0.00 0.00 3.51
1472 1729 2.185608 GGAAGACCTGGCTCTCGC 59.814 66.667 0.00 0.00 0.00 5.03
1632 1889 4.069232 CCGCTGCCGAACTCCAGA 62.069 66.667 0.00 0.00 36.29 3.86
1660 1917 4.207281 CCGCTTCATCTCGGCCGA 62.207 66.667 29.03 29.03 39.14 5.54
1780 2037 0.251209 TGTCAGTCCAGCTCGGTAGT 60.251 55.000 2.68 0.00 35.57 2.73
1803 2063 0.529773 GGCGCAATCGGAGTGACATA 60.530 55.000 10.83 0.00 35.95 2.29
1940 2200 1.590610 GAGTCAGCTGTGCGGAGAGA 61.591 60.000 14.67 0.00 32.90 3.10
2096 2368 4.467084 GCCAGCCCCGACGAATCA 62.467 66.667 0.00 0.00 0.00 2.57
2240 2512 3.449322 ACGAAATCGATGGTTTGAACG 57.551 42.857 10.16 0.00 43.02 3.95
2317 2589 1.134367 GTCGCACTACTCTACATGGCA 59.866 52.381 0.00 0.00 0.00 4.92
2318 2590 1.134367 TGTCGCACTACTCTACATGGC 59.866 52.381 0.00 0.00 0.00 4.40
2516 2788 7.907214 TCTTGTATGGTAGAAAAAGAAGAGC 57.093 36.000 0.00 0.00 0.00 4.09
2579 2861 3.000674 CGACATCGTGACATGAACTAAGC 60.001 47.826 0.00 0.00 34.11 3.09
2618 2900 4.335647 ACTGCCGGCCTCTTGTGG 62.336 66.667 26.77 6.12 0.00 4.17
2697 2979 3.887716 AGATTAAAGATCCATGGCAGCAC 59.112 43.478 6.96 0.00 0.00 4.40
2825 3121 3.602513 CTGCTTCAGGCGCTGGACT 62.603 63.158 7.64 0.00 45.43 3.85
3025 3324 7.598759 TCTAAAAGGACTAGAACTTGAGTGT 57.401 36.000 0.00 0.00 0.00 3.55
3028 3327 9.528018 GATCATCTAAAAGGACTAGAACTTGAG 57.472 37.037 0.00 2.53 0.00 3.02
3154 3456 7.716612 AGGAACGAAAAGAACATTCAGAAAAT 58.283 30.769 0.00 0.00 0.00 1.82
3176 3478 2.692557 CACAATGTGTGTTTGGGAAGGA 59.307 45.455 5.00 0.00 43.08 3.36
3183 3485 1.408340 TCCAGCCACAATGTGTGTTTG 59.592 47.619 12.79 4.92 46.45 2.93
3184 3486 1.774110 TCCAGCCACAATGTGTGTTT 58.226 45.000 12.79 0.00 46.45 2.83
3274 3576 1.567504 AAGTCGTTTCACACCGTGAG 58.432 50.000 5.28 0.00 43.69 3.51
3308 3610 6.918022 AGATTTTCAACAAACGTTTCTCCATC 59.082 34.615 11.37 6.73 0.00 3.51
3309 3611 6.805713 AGATTTTCAACAAACGTTTCTCCAT 58.194 32.000 11.37 0.00 0.00 3.41
3310 3612 6.202516 AGATTTTCAACAAACGTTTCTCCA 57.797 33.333 11.37 0.00 0.00 3.86
3311 3613 8.126700 TCTAAGATTTTCAACAAACGTTTCTCC 58.873 33.333 11.37 0.00 0.00 3.71
3313 3615 7.644157 GCTCTAAGATTTTCAACAAACGTTTCT 59.356 33.333 11.37 0.00 0.00 2.52
3314 3616 7.431084 TGCTCTAAGATTTTCAACAAACGTTTC 59.569 33.333 11.37 0.00 0.00 2.78
3319 3624 7.752686 GGAGATGCTCTAAGATTTTCAACAAAC 59.247 37.037 0.00 0.00 0.00 2.93
3328 3633 5.298777 GCATGTTGGAGATGCTCTAAGATTT 59.701 40.000 3.13 0.00 42.52 2.17
3444 3761 1.715585 CGCTGAACCACTTATGCCG 59.284 57.895 0.00 0.00 0.00 5.69
3445 3762 1.305219 TGCGCTGAACCACTTATGCC 61.305 55.000 9.73 0.00 0.00 4.40
3464 3781 2.324215 CGATGCCATTTCGCTCCAT 58.676 52.632 0.00 0.00 0.00 3.41
3519 3836 2.434185 GTGGGCGCTCGATTGTGA 60.434 61.111 7.64 0.00 0.00 3.58
3631 3948 1.273098 GGTGTAGGAAGGAGTGAGGGA 60.273 57.143 0.00 0.00 0.00 4.20
3639 3956 2.036098 TCGCGGGTGTAGGAAGGA 59.964 61.111 6.13 0.00 0.00 3.36
3703 4035 0.036858 GAGGCGAAGTCAAAGCTCCT 60.037 55.000 0.00 0.00 0.00 3.69
3838 4176 1.709147 CGCATTTGGGAGCTTCGAGG 61.709 60.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.