Multiple sequence alignment - TraesCS1D01G346500

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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 TraesCS1D01G346500 chr1D 100.000 4178 0 0 1 4178 434037492 434033315 0.000000e+00 7716.0
1 TraesCS1D01G346500 chr1D 99.665 2389 8 0 699 3087 433981808 433979420 0.000000e+00 4368.0
2 TraesCS1D01G346500 chr1D 97.810 1096 12 3 3083 4178 433969086 433968003 0.000000e+00 1881.0
3 TraesCS1D01G346500 chr1D 94.843 543 23 3 3637 4178 460916856 460916318 0.000000e+00 843.0
4 TraesCS1D01G346500 chr1D 82.287 621 58 30 2643 3238 355430782 355431375 1.350000e-134 490.0
5 TraesCS1D01G346500 chr1D 81.094 640 71 34 1740 2361 355430173 355430780 2.270000e-127 466.0
6 TraesCS1D01G346500 chr1D 80.053 376 40 18 1339 1708 355429826 355430172 3.230000e-61 246.0
7 TraesCS1D01G346500 chr1D 92.053 151 12 0 3498 3648 40434301 40434451 3.270000e-51 213.0
8 TraesCS1D01G346500 chr1D 88.068 176 13 4 1165 1340 198055684 198055851 7.080000e-48 202.0
9 TraesCS1D01G346500 chr1D 76.667 150 21 10 61 204 1858317 1858176 2.080000e-08 71.3
10 TraesCS1D01G346500 chr1D 91.837 49 1 3 2611 2659 144763 144808 9.700000e-07 65.8
11 TraesCS1D01G346500 chr1D 91.837 49 1 3 2611 2659 176051 176096 9.700000e-07 65.8
12 TraesCS1D01G346500 chr1D 91.837 49 1 3 2611 2659 188269 188314 9.700000e-07 65.8
13 TraesCS1D01G346500 chr1B 86.695 947 87 26 2125 3045 587527449 587526516 0.000000e+00 1014.0
14 TraesCS1D01G346500 chr1B 86.660 937 75 23 167 1084 587048652 587047747 0.000000e+00 992.0
15 TraesCS1D01G346500 chr1B 86.660 937 75 23 167 1084 587070529 587069624 0.000000e+00 992.0
16 TraesCS1D01G346500 chr1B 88.532 654 48 12 2227 2871 587039538 587038903 0.000000e+00 767.0
17 TraesCS1D01G346500 chr1B 85.490 765 65 22 1316 2076 587040976 587040254 0.000000e+00 756.0
18 TraesCS1D01G346500 chr1B 81.107 614 68 27 2643 3234 478055103 478055690 8.240000e-122 448.0
19 TraesCS1D01G346500 chr1B 91.411 326 17 7 2869 3192 587035793 587035477 1.780000e-118 436.0
20 TraesCS1D01G346500 chr1B 78.616 636 63 35 1740 2343 478054489 478055083 1.850000e-93 353.0
21 TraesCS1D01G346500 chr1B 76.319 739 79 42 422 1139 478053419 478054082 1.460000e-79 307.0
22 TraesCS1D01G346500 chr1B 80.208 384 42 19 1335 1702 478054117 478054482 1.490000e-64 257.0
23 TraesCS1D01G346500 chr1B 86.458 192 18 4 3306 3497 587031382 587031199 1.970000e-48 204.0
24 TraesCS1D01G346500 chr1B 96.703 91 3 0 2125 2215 587039762 587039672 7.230000e-33 152.0
25 TraesCS1D01G346500 chr1B 84.076 157 16 5 3342 3497 587527639 587527491 4.350000e-30 143.0
26 TraesCS1D01G346500 chr1B 89.381 113 9 3 1073 1183 587041146 587041035 5.630000e-29 139.0
27 TraesCS1D01G346500 chr1B 95.082 61 1 1 3240 3300 587035476 587035418 1.240000e-15 95.3
28 TraesCS1D01G346500 chr6D 94.454 595 30 2 3585 4178 455680291 455680883 0.000000e+00 913.0
29 TraesCS1D01G346500 chr3D 96.488 541 16 2 3637 4177 611707449 611707986 0.000000e+00 891.0
30 TraesCS1D01G346500 chr3D 95.203 542 23 2 3637 4178 600900771 600901309 0.000000e+00 854.0
31 TraesCS1D01G346500 chr3D 92.053 151 11 1 3498 3648 30249039 30249188 1.180000e-50 211.0
32 TraesCS1D01G346500 chr3D 88.108 185 13 4 1162 1345 217587557 217587733 1.180000e-50 211.0
33 TraesCS1D01G346500 chr3D 88.571 175 13 3 1162 1336 4171114 4171281 5.480000e-49 206.0
34 TraesCS1D01G346500 chr3D 89.937 159 15 1 3498 3656 611707242 611707399 1.970000e-48 204.0
35 TraesCS1D01G346500 chr3D 88.125 160 17 2 3498 3656 588782508 588782350 5.510000e-44 189.0
36 TraesCS1D01G346500 chr3D 100.000 40 0 0 2606 2645 6067490 6067451 1.610000e-09 75.0
37 TraesCS1D01G346500 chr3D 94.872 39 2 0 2605 2643 78915550 78915588 1.250000e-05 62.1
38 TraesCS1D01G346500 chr7D 96.303 541 18 1 3638 4178 611201978 611201440 0.000000e+00 887.0
39 TraesCS1D01G346500 chr7D 95.018 542 24 2 3637 4178 634552698 634553236 0.000000e+00 848.0
40 TraesCS1D01G346500 chr7D 94.834 542 26 1 3637 4178 76526981 76526442 0.000000e+00 845.0
41 TraesCS1D01G346500 chr7D 89.279 541 22 5 3638 4178 27563599 27564103 0.000000e+00 645.0
42 TraesCS1D01G346500 chr7D 92.715 151 10 1 3498 3648 17323872 17324021 2.530000e-52 217.0
43 TraesCS1D01G346500 chr7D 92.053 151 11 1 3498 3648 92767604 92767753 1.180000e-50 211.0
44 TraesCS1D01G346500 chr7D 92.053 151 11 1 3498 3648 154614043 154613894 1.180000e-50 211.0
45 TraesCS1D01G346500 chr7D 88.372 172 12 5 1165 1336 462612755 462612918 2.550000e-47 200.0
46 TraesCS1D01G346500 chr7D 83.333 96 15 1 63 158 92126836 92126742 2.070000e-13 87.9
47 TraesCS1D01G346500 chr7D 94.737 38 2 0 2606 2643 623066223 623066186 4.510000e-05 60.2
48 TraesCS1D01G346500 chr2D 95.212 543 24 2 3637 4178 490606660 490607201 0.000000e+00 857.0
49 TraesCS1D01G346500 chr2D 93.377 151 9 1 3498 3648 95273769 95273620 5.440000e-54 222.0
50 TraesCS1D01G346500 chr2D 86.243 189 17 5 1156 1343 309971593 309971413 3.300000e-46 196.0
51 TraesCS1D01G346500 chrUn 100.000 399 0 0 699 1097 478884579 478884181 0.000000e+00 737.0
52 TraesCS1D01G346500 chrUn 97.368 38 0 1 2612 2649 89342752 89342716 3.490000e-06 63.9
53 TraesCS1D01G346500 chrUn 100.000 33 0 0 2611 2643 28823563 28823531 1.250000e-05 62.1
54 TraesCS1D01G346500 chr1A 81.922 614 72 22 1753 2361 455605806 455606385 2.260000e-132 483.0
55 TraesCS1D01G346500 chr1A 81.129 620 67 25 2643 3242 455606387 455606976 6.370000e-123 451.0
56 TraesCS1D01G346500 chr1A 85.915 426 28 13 2886 3300 532264517 532264113 3.860000e-115 425.0
57 TraesCS1D01G346500 chr1A 80.000 460 53 19 698 1140 455605048 455605485 1.890000e-78 303.0
58 TraesCS1D01G346500 chr1A 85.417 192 18 5 3306 3495 532263740 532263557 1.530000e-44 191.0
59 TraesCS1D01G346500 chr1A 79.085 306 31 18 1338 1626 455605511 455605800 3.320000e-41 180.0
60 TraesCS1D01G346500 chr5D 92.715 151 10 1 3498 3648 57376771 57376920 2.530000e-52 217.0
61 TraesCS1D01G346500 chr5D 92.053 151 11 1 3498 3648 483858833 483858982 1.180000e-50 211.0
62 TraesCS1D01G346500 chr5D 89.375 160 16 1 3498 3657 15129893 15130051 2.550000e-47 200.0
63 TraesCS1D01G346500 chr5B 88.636 176 13 3 1161 1336 540367882 540367714 1.520000e-49 207.0
64 TraesCS1D01G346500 chr5B 81.592 201 27 9 2 198 469292697 469292503 1.550000e-34 158.0
65 TraesCS1D01G346500 chr5B 80.667 150 22 6 60 205 698461395 698461249 4.420000e-20 110.0
66 TraesCS1D01G346500 chr3B 88.439 173 13 4 1164 1336 592650138 592649973 7.080000e-48 202.0
67 TraesCS1D01G346500 chr4A 88.372 172 13 3 1165 1336 680405226 680405390 2.550000e-47 200.0
68 TraesCS1D01G346500 chr4A 97.368 38 1 0 2606 2643 741428986 741428949 9.700000e-07 65.8
69 TraesCS1D01G346500 chr4D 88.125 160 16 3 3498 3656 481908810 481908653 1.980000e-43 187.0
70 TraesCS1D01G346500 chr4D 76.829 164 29 7 46 204 68463027 68463186 2.680000e-12 84.2
71 TraesCS1D01G346500 chr4B 78.049 205 40 5 3 204 100916168 100916370 1.580000e-24 124.0
72 TraesCS1D01G346500 chr4B 78.571 154 28 5 54 204 72658613 72658462 3.440000e-16 97.1
73 TraesCS1D01G346500 chr7B 82.787 122 19 2 60 180 44233142 44233022 1.590000e-19 108.0
74 TraesCS1D01G346500 chr7B 91.111 45 4 0 2606 2650 14876913 14876869 1.250000e-05 62.1
75 TraesCS1D01G346500 chr3A 79.268 164 27 4 45 204 620586725 620586565 1.590000e-19 108.0
76 TraesCS1D01G346500 chr3A 100.000 40 0 0 2606 2645 14925912 14925951 1.610000e-09 75.0
77 TraesCS1D01G346500 chr2B 97.368 38 1 0 2606 2643 796835006 796835043 9.700000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G346500 chr1D 434033315 434037492 4177 True 7716.000000 7716 100.000000 1 4178 1 chr1D.!!$R4 4177
1 TraesCS1D01G346500 chr1D 433979420 433981808 2388 True 4368.000000 4368 99.665000 699 3087 1 chr1D.!!$R3 2388
2 TraesCS1D01G346500 chr1D 433968003 433969086 1083 True 1881.000000 1881 97.810000 3083 4178 1 chr1D.!!$R2 1095
3 TraesCS1D01G346500 chr1D 460916318 460916856 538 True 843.000000 843 94.843000 3637 4178 1 chr1D.!!$R5 541
4 TraesCS1D01G346500 chr1D 355429826 355431375 1549 False 400.666667 490 81.144667 1339 3238 3 chr1D.!!$F6 1899
5 TraesCS1D01G346500 chr1B 587047747 587048652 905 True 992.000000 992 86.660000 167 1084 1 chr1B.!!$R2 917
6 TraesCS1D01G346500 chr1B 587069624 587070529 905 True 992.000000 992 86.660000 167 1084 1 chr1B.!!$R3 917
7 TraesCS1D01G346500 chr1B 587526516 587527639 1123 True 578.500000 1014 85.385500 2125 3497 2 chr1B.!!$R5 1372
8 TraesCS1D01G346500 chr1B 587035418 587041146 5728 True 390.883333 767 91.099833 1073 3300 6 chr1B.!!$R4 2227
9 TraesCS1D01G346500 chr1B 478053419 478055690 2271 False 341.250000 448 79.062500 422 3234 4 chr1B.!!$F1 2812
10 TraesCS1D01G346500 chr6D 455680291 455680883 592 False 913.000000 913 94.454000 3585 4178 1 chr6D.!!$F1 593
11 TraesCS1D01G346500 chr3D 600900771 600901309 538 False 854.000000 854 95.203000 3637 4178 1 chr3D.!!$F5 541
12 TraesCS1D01G346500 chr3D 611707242 611707986 744 False 547.500000 891 93.212500 3498 4177 2 chr3D.!!$F6 679
13 TraesCS1D01G346500 chr7D 611201440 611201978 538 True 887.000000 887 96.303000 3638 4178 1 chr7D.!!$R4 540
14 TraesCS1D01G346500 chr7D 634552698 634553236 538 False 848.000000 848 95.018000 3637 4178 1 chr7D.!!$F5 541
15 TraesCS1D01G346500 chr7D 76526442 76526981 539 True 845.000000 845 94.834000 3637 4178 1 chr7D.!!$R1 541
16 TraesCS1D01G346500 chr7D 27563599 27564103 504 False 645.000000 645 89.279000 3638 4178 1 chr7D.!!$F2 540
17 TraesCS1D01G346500 chr2D 490606660 490607201 541 False 857.000000 857 95.212000 3637 4178 1 chr2D.!!$F1 541
18 TraesCS1D01G346500 chr1A 455605048 455606976 1928 False 354.250000 483 80.534000 698 3242 4 chr1A.!!$F1 2544
19 TraesCS1D01G346500 chr1A 532263557 532264517 960 True 308.000000 425 85.666000 2886 3495 2 chr1A.!!$R1 609

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
22 23 0.036732 ACTACTCCGTCACCACCGTA 59.963 55.0 0.0 0.0 0.0 4.02 F
24 25 0.324614 TACTCCGTCACCACCGTAGA 59.675 55.0 0.0 0.0 0.0 2.59 F
76 77 0.458716 GTGAGGAGTGGTCGCTTAGC 60.459 60.0 0.0 0.0 0.0 3.09 F
591 609 0.470341 GTAGATCCCTGGACCCTTGC 59.530 60.0 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2521 3242 1.501169 GGCCTGACAAACAATGCAAC 58.499 50.000 0.00 0.0 0.0 4.17 R
3125 7003 3.268023 AGAGAATAAAGCTGGGGAACG 57.732 47.619 0.00 0.0 0.0 3.95 R
3127 7005 3.458487 GGGTAGAGAATAAAGCTGGGGAA 59.542 47.826 0.00 0.0 0.0 3.97 R
3370 7622 0.540830 TAAACCCTGCGGCCATTTGT 60.541 50.000 2.24 0.0 0.0 2.83 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 1.505353 CCGACTACTCCGTCACCAC 59.495 63.158 0.00 0.00 33.54 4.16
20 21 1.505353 GACTACTCCGTCACCACCG 59.495 63.158 0.00 0.00 34.11 4.94
21 22 1.228367 ACTACTCCGTCACCACCGT 60.228 57.895 0.00 0.00 0.00 4.83
22 23 0.036732 ACTACTCCGTCACCACCGTA 59.963 55.000 0.00 0.00 0.00 4.02
23 24 0.731417 CTACTCCGTCACCACCGTAG 59.269 60.000 0.00 0.00 0.00 3.51
24 25 0.324614 TACTCCGTCACCACCGTAGA 59.675 55.000 0.00 0.00 0.00 2.59
25 26 1.239968 ACTCCGTCACCACCGTAGAC 61.240 60.000 0.00 0.00 0.00 2.59
26 27 1.228215 TCCGTCACCACCGTAGACA 60.228 57.895 0.00 0.00 32.68 3.41
29 30 1.656441 GTCACCACCGTAGACACGT 59.344 57.895 0.00 0.00 46.96 4.49
31 32 0.535780 TCACCACCGTAGACACGTCT 60.536 55.000 4.87 4.87 46.96 4.18
39 40 4.718064 AGACACGTCTACGAGGCT 57.282 55.556 9.86 5.95 43.30 4.58
40 41 1.736681 GTAGACACGTCTACGAGGCTT 59.263 52.381 18.76 0.00 45.78 4.35
42 43 2.859933 AGACACGTCTACGAGGCTTCG 61.860 57.143 17.51 17.51 45.78 3.79
69 70 1.065854 CCTTGATGGTGAGGAGTGGTC 60.066 57.143 0.00 0.00 34.91 4.02
71 72 1.153549 GATGGTGAGGAGTGGTCGC 60.154 63.158 0.00 0.00 0.00 5.19
72 73 1.608717 GATGGTGAGGAGTGGTCGCT 61.609 60.000 0.00 0.00 0.00 4.93
73 74 1.194781 ATGGTGAGGAGTGGTCGCTT 61.195 55.000 0.00 0.00 0.00 4.68
74 75 0.541063 TGGTGAGGAGTGGTCGCTTA 60.541 55.000 0.00 0.00 0.00 3.09
76 77 0.458716 GTGAGGAGTGGTCGCTTAGC 60.459 60.000 0.00 0.00 0.00 3.09
92 93 2.892425 GCGACTCCTCCGCCAATG 60.892 66.667 0.00 0.00 46.22 2.82
93 94 2.892425 CGACTCCTCCGCCAATGC 60.892 66.667 0.00 0.00 0.00 3.56
94 95 2.586792 GACTCCTCCGCCAATGCT 59.413 61.111 0.00 0.00 34.43 3.79
95 96 1.817099 GACTCCTCCGCCAATGCTG 60.817 63.158 0.00 0.00 34.43 4.41
96 97 2.515523 CTCCTCCGCCAATGCTGG 60.516 66.667 0.00 0.00 46.65 4.85
105 106 2.998480 CAATGCTGGCAGGGGCAA 60.998 61.111 17.64 0.00 43.71 4.52
106 107 2.203818 AATGCTGGCAGGGGCAAA 60.204 55.556 17.64 0.00 43.71 3.68
119 120 4.002797 GCAAAGGCCACTACCAGG 57.997 61.111 5.01 0.00 0.00 4.45
126 127 2.990479 CCACTACCAGGGCTCCAC 59.010 66.667 0.00 0.00 0.00 4.02
127 128 2.579201 CACTACCAGGGCTCCACG 59.421 66.667 0.00 0.00 0.00 4.94
128 129 1.982395 CACTACCAGGGCTCCACGA 60.982 63.158 0.00 0.00 0.00 4.35
129 130 1.682684 ACTACCAGGGCTCCACGAG 60.683 63.158 0.00 0.00 0.00 4.18
138 139 2.202797 CTCCACGAGCACCATCGG 60.203 66.667 0.91 0.00 46.91 4.18
139 140 4.451150 TCCACGAGCACCATCGGC 62.451 66.667 0.91 0.00 46.91 5.54
140 141 4.758251 CCACGAGCACCATCGGCA 62.758 66.667 0.91 0.00 46.91 5.69
141 142 2.512286 CACGAGCACCATCGGCAT 60.512 61.111 0.91 0.00 46.91 4.40
142 143 2.108514 CACGAGCACCATCGGCATT 61.109 57.895 0.91 0.00 46.91 3.56
143 144 2.108514 ACGAGCACCATCGGCATTG 61.109 57.895 0.91 0.00 46.91 2.82
145 146 3.129913 GAGCACCATCGGCATTGGC 62.130 63.158 0.00 0.00 37.81 4.52
177 178 1.001641 ACCATGCACAGGAGGAAGC 60.002 57.895 13.62 0.00 0.00 3.86
218 220 4.095932 GCGCCAGGCTATAAACTTTAGTTT 59.904 41.667 10.54 12.10 43.70 2.66
245 256 4.839121 TCAGTTATACGGCCAAAACATCT 58.161 39.130 2.24 0.00 0.00 2.90
250 261 1.154225 CGGCCAAAACATCTGTCGC 60.154 57.895 2.24 0.00 0.00 5.19
272 284 9.737025 GTCGCTTTATGTAAATTATATCCGAAC 57.263 33.333 0.00 0.00 0.00 3.95
288 300 4.450976 TCCGAACATGAATGAAATCCGAT 58.549 39.130 0.00 0.00 0.00 4.18
310 322 4.355437 TGTGTTTGCTGAAATTTGTACCG 58.645 39.130 0.00 0.00 0.00 4.02
323 335 9.032420 TGAAATTTGTACCGTTTGTTTAAATCC 57.968 29.630 0.00 0.00 0.00 3.01
340 352 5.398603 AAATCCGGTTTGAATTGTATGCA 57.601 34.783 0.00 0.00 0.00 3.96
341 353 5.398603 AATCCGGTTTGAATTGTATGCAA 57.601 34.783 0.00 0.00 39.16 4.08
342 354 4.167554 TCCGGTTTGAATTGTATGCAAC 57.832 40.909 0.00 0.00 37.44 4.17
351 363 9.243637 GTTTGAATTGTATGCAACTAGTTTTGA 57.756 29.630 5.07 0.00 37.44 2.69
355 367 8.761575 AATTGTATGCAACTAGTTTTGAATGG 57.238 30.769 5.07 0.00 37.44 3.16
356 368 6.892658 TGTATGCAACTAGTTTTGAATGGT 57.107 33.333 5.07 0.00 0.00 3.55
370 382 1.091771 AATGGTCGGCTTCTGCATCG 61.092 55.000 0.00 0.00 41.91 3.84
395 407 4.129737 CGGACGGATGCGGTGTCT 62.130 66.667 12.44 0.00 35.75 3.41
396 408 2.767445 CGGACGGATGCGGTGTCTA 61.767 63.158 12.44 0.00 35.75 2.59
397 409 1.065928 GGACGGATGCGGTGTCTAG 59.934 63.158 12.44 0.00 33.21 2.43
406 418 1.338674 TGCGGTGTCTAGTTTGGGATG 60.339 52.381 0.00 0.00 0.00 3.51
410 422 2.271800 GTGTCTAGTTTGGGATGAGCG 58.728 52.381 0.00 0.00 0.00 5.03
426 438 2.342279 CGTTGGAGACGCCCTTGA 59.658 61.111 0.00 0.00 45.86 3.02
436 448 4.452455 GGAGACGCCCTTGATATATGTTTG 59.548 45.833 0.00 0.00 0.00 2.93
493 505 1.265568 GCGATCTTGTTTGCATGCAG 58.734 50.000 21.50 9.09 0.00 4.41
494 506 1.904144 CGATCTTGTTTGCATGCAGG 58.096 50.000 21.50 9.94 0.00 4.85
495 507 1.200716 CGATCTTGTTTGCATGCAGGT 59.799 47.619 21.50 4.72 0.00 4.00
496 508 2.730090 CGATCTTGTTTGCATGCAGGTC 60.730 50.000 21.50 13.35 0.00 3.85
497 509 1.689984 TCTTGTTTGCATGCAGGTCA 58.310 45.000 21.50 17.24 0.00 4.02
530 544 1.268539 CCTTCCGTGTCTTGTTGTTGC 60.269 52.381 0.00 0.00 0.00 4.17
532 546 1.098712 TCCGTGTCTTGTTGTTGCCC 61.099 55.000 0.00 0.00 0.00 5.36
552 566 3.198068 CCGTACTGCAATATTCTGTGCT 58.802 45.455 0.00 0.00 41.48 4.40
566 581 1.528586 CTGTGCTACACTTGTGTCAGC 59.471 52.381 9.85 15.77 35.11 4.26
591 609 0.470341 GTAGATCCCTGGACCCTTGC 59.530 60.000 0.00 0.00 0.00 4.01
619 638 5.515184 TGCACGCGCATAAAATATAATGTT 58.485 33.333 5.73 0.00 45.36 2.71
678 702 1.202359 GCTCGAAGCTAGTCCTGGAAG 60.202 57.143 0.00 0.00 38.45 3.46
681 705 2.952978 TCGAAGCTAGTCCTGGAAGATC 59.047 50.000 0.00 0.00 34.07 2.75
687 711 4.078863 AGCTAGTCCTGGAAGATCCTACTT 60.079 45.833 0.00 0.00 37.46 2.24
1097 1137 5.582665 CCACATGTAAGAACTTCTAGCTTCC 59.417 44.000 0.00 0.00 0.00 3.46
3370 7622 3.009033 CAGTTTCCCCATCTACCAGTCAA 59.991 47.826 0.00 0.00 0.00 3.18
3459 7711 1.531739 GCCGATTGGGAGTTTTGCCA 61.532 55.000 0.00 0.00 43.87 4.92
3492 7744 3.695060 TGCAACCAAACGAGACCTTAAAA 59.305 39.130 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.228215 TGTCTACGGTGGTGACGGA 60.228 57.895 0.00 0.00 33.81 4.69
9 10 1.080974 GTGTCTACGGTGGTGACGG 60.081 63.158 0.00 0.00 33.81 4.79
10 11 1.441515 CGTGTCTACGGTGGTGACG 60.442 63.158 0.00 0.00 46.23 4.35
11 12 4.546637 CGTGTCTACGGTGGTGAC 57.453 61.111 0.00 0.00 46.23 3.67
21 22 2.005451 GAAGCCTCGTAGACGTGTCTA 58.995 52.381 5.64 5.64 40.93 2.59
22 23 0.803740 GAAGCCTCGTAGACGTGTCT 59.196 55.000 7.77 7.77 43.40 3.41
23 24 0.520827 CGAAGCCTCGTAGACGTGTC 60.521 60.000 0.00 0.00 40.33 3.67
24 25 1.500844 CGAAGCCTCGTAGACGTGT 59.499 57.895 0.00 0.00 40.33 4.49
25 26 4.361827 CGAAGCCTCGTAGACGTG 57.638 61.111 0.00 0.00 40.33 4.49
43 44 4.776322 TCACCATCAAGGCGGCGG 62.776 66.667 9.78 0.00 43.14 6.13
44 45 3.197790 CTCACCATCAAGGCGGCG 61.198 66.667 0.51 0.51 43.14 6.46
46 47 1.153289 CTCCTCACCATCAAGGCGG 60.153 63.158 0.00 0.00 43.14 6.13
47 48 0.742281 CACTCCTCACCATCAAGGCG 60.742 60.000 0.00 0.00 43.14 5.52
48 49 0.393537 CCACTCCTCACCATCAAGGC 60.394 60.000 0.00 0.00 43.14 4.35
49 50 0.987294 ACCACTCCTCACCATCAAGG 59.013 55.000 0.00 0.00 45.67 3.61
50 51 1.404717 CGACCACTCCTCACCATCAAG 60.405 57.143 0.00 0.00 0.00 3.02
51 52 0.608130 CGACCACTCCTCACCATCAA 59.392 55.000 0.00 0.00 0.00 2.57
52 53 1.888436 GCGACCACTCCTCACCATCA 61.888 60.000 0.00 0.00 0.00 3.07
53 54 1.153549 GCGACCACTCCTCACCATC 60.154 63.158 0.00 0.00 0.00 3.51
54 55 1.194781 AAGCGACCACTCCTCACCAT 61.195 55.000 0.00 0.00 0.00 3.55
55 56 0.541063 TAAGCGACCACTCCTCACCA 60.541 55.000 0.00 0.00 0.00 4.17
56 57 0.173708 CTAAGCGACCACTCCTCACC 59.826 60.000 0.00 0.00 0.00 4.02
57 58 0.458716 GCTAAGCGACCACTCCTCAC 60.459 60.000 0.00 0.00 0.00 3.51
59 60 4.816990 GCTAAGCGACCACTCCTC 57.183 61.111 0.00 0.00 0.00 3.71
76 77 2.892425 GCATTGGCGGAGGAGTCG 60.892 66.667 0.00 0.00 0.00 4.18
89 90 2.203818 TTTGCCCCTGCCAGCATT 60.204 55.556 0.00 0.00 39.11 3.56
90 91 2.682494 CTTTGCCCCTGCCAGCAT 60.682 61.111 0.00 0.00 39.11 3.79
102 103 1.678970 CCCTGGTAGTGGCCTTTGC 60.679 63.158 3.32 0.00 0.00 3.68
103 104 1.678970 GCCCTGGTAGTGGCCTTTG 60.679 63.158 3.32 0.00 41.97 2.77
109 110 2.990479 GTGGAGCCCTGGTAGTGG 59.010 66.667 0.00 0.00 0.00 4.00
110 111 1.949847 CTCGTGGAGCCCTGGTAGTG 61.950 65.000 0.00 0.00 0.00 2.74
111 112 1.682684 CTCGTGGAGCCCTGGTAGT 60.683 63.158 0.00 0.00 0.00 2.73
112 113 3.211288 CTCGTGGAGCCCTGGTAG 58.789 66.667 0.00 0.00 0.00 3.18
121 122 2.202797 CCGATGGTGCTCGTGGAG 60.203 66.667 0.00 0.00 36.93 3.86
123 124 4.758251 TGCCGATGGTGCTCGTGG 62.758 66.667 0.00 0.00 36.93 4.94
126 127 2.711311 CAATGCCGATGGTGCTCG 59.289 61.111 0.00 0.00 38.37 5.03
127 128 3.113745 CCAATGCCGATGGTGCTC 58.886 61.111 0.00 0.00 33.08 4.26
128 129 3.142838 GCCAATGCCGATGGTGCT 61.143 61.111 2.04 0.00 40.23 4.40
151 152 4.720902 TGTGCATGGTGAGGGCCG 62.721 66.667 0.00 0.00 0.00 6.13
152 153 2.753043 CTGTGCATGGTGAGGGCC 60.753 66.667 0.00 0.00 0.00 5.80
153 154 2.753043 CCTGTGCATGGTGAGGGC 60.753 66.667 0.00 0.00 0.00 5.19
154 155 1.077930 CTCCTGTGCATGGTGAGGG 60.078 63.158 8.29 0.00 0.00 4.30
155 156 1.077930 CCTCCTGTGCATGGTGAGG 60.078 63.158 10.92 10.10 36.92 3.86
157 158 0.325933 CTTCCTCCTGTGCATGGTGA 59.674 55.000 10.92 6.15 0.00 4.02
159 160 1.001641 GCTTCCTCCTGTGCATGGT 60.002 57.895 8.29 0.00 0.00 3.55
162 163 0.252479 CTCAGCTTCCTCCTGTGCAT 59.748 55.000 0.00 0.00 0.00 3.96
163 164 1.675801 CTCAGCTTCCTCCTGTGCA 59.324 57.895 0.00 0.00 0.00 4.57
164 165 1.744741 GCTCAGCTTCCTCCTGTGC 60.745 63.158 0.00 0.00 40.94 4.57
165 166 1.447489 CGCTCAGCTTCCTCCTGTG 60.447 63.158 0.00 0.00 0.00 3.66
177 178 1.449246 CTCCAAAGGAGCCGCTCAG 60.449 63.158 21.76 5.79 43.29 3.35
230 241 1.434555 CGACAGATGTTTTGGCCGTA 58.565 50.000 0.00 0.00 0.00 4.02
245 256 9.478768 TTCGGATATAATTTACATAAAGCGACA 57.521 29.630 0.00 0.00 0.00 4.35
265 277 4.450976 TCGGATTTCATTCATGTTCGGAT 58.549 39.130 0.00 0.00 0.00 4.18
268 280 4.965762 CACATCGGATTTCATTCATGTTCG 59.034 41.667 0.00 0.00 0.00 3.95
272 284 5.005012 GCAAACACATCGGATTTCATTCATG 59.995 40.000 0.00 0.00 0.00 3.07
288 300 4.142359 ACGGTACAAATTTCAGCAAACACA 60.142 37.500 0.00 0.00 0.00 3.72
310 322 7.911343 ACAATTCAAACCGGATTTAAACAAAC 58.089 30.769 9.46 0.00 0.00 2.93
323 335 5.938322 ACTAGTTGCATACAATTCAAACCG 58.062 37.500 0.00 0.00 38.27 4.44
340 352 3.751518 AGCCGACCATTCAAAACTAGTT 58.248 40.909 1.12 1.12 0.00 2.24
341 353 3.418684 AGCCGACCATTCAAAACTAGT 57.581 42.857 0.00 0.00 0.00 2.57
342 354 4.003648 AGAAGCCGACCATTCAAAACTAG 58.996 43.478 0.00 0.00 0.00 2.57
351 363 1.091771 CGATGCAGAAGCCGACCATT 61.092 55.000 0.00 0.00 41.13 3.16
355 367 1.880340 CTCCGATGCAGAAGCCGAC 60.880 63.158 0.00 0.00 41.13 4.79
356 368 2.284798 GACTCCGATGCAGAAGCCGA 62.285 60.000 0.00 0.00 41.13 5.54
370 382 2.105128 CATCCGTCCGCAGACTCC 59.895 66.667 0.00 0.00 41.16 3.85
390 402 2.271800 CGCTCATCCCAAACTAGACAC 58.728 52.381 0.00 0.00 0.00 3.67
391 403 1.899814 ACGCTCATCCCAAACTAGACA 59.100 47.619 0.00 0.00 0.00 3.41
392 404 2.673368 CAACGCTCATCCCAAACTAGAC 59.327 50.000 0.00 0.00 0.00 2.59
393 405 2.354704 CCAACGCTCATCCCAAACTAGA 60.355 50.000 0.00 0.00 0.00 2.43
394 406 2.009774 CCAACGCTCATCCCAAACTAG 58.990 52.381 0.00 0.00 0.00 2.57
395 407 1.626321 TCCAACGCTCATCCCAAACTA 59.374 47.619 0.00 0.00 0.00 2.24
396 408 0.400213 TCCAACGCTCATCCCAAACT 59.600 50.000 0.00 0.00 0.00 2.66
397 409 0.804989 CTCCAACGCTCATCCCAAAC 59.195 55.000 0.00 0.00 0.00 2.93
410 422 2.622064 ATATCAAGGGCGTCTCCAAC 57.378 50.000 0.00 0.00 36.21 3.77
425 437 8.611757 TCAGTATGCAACACACAAACATATATC 58.388 33.333 0.00 0.00 34.76 1.63
426 438 8.504812 TCAGTATGCAACACACAAACATATAT 57.495 30.769 0.00 0.00 34.76 0.86
436 448 4.572389 CCCTCTTATCAGTATGCAACACAC 59.428 45.833 0.00 0.00 34.76 3.82
530 544 2.287915 GCACAGAATATTGCAGTACGGG 59.712 50.000 0.00 0.00 38.68 5.28
532 546 4.803613 TGTAGCACAGAATATTGCAGTACG 59.196 41.667 0.00 0.00 41.48 3.67
566 581 1.341531 GGTCCAGGGATCTACGTCATG 59.658 57.143 0.00 0.00 0.00 3.07
610 629 9.165057 AGGAGCTAGAAGAAGGAAACATTATAT 57.835 33.333 0.00 0.00 0.00 0.86
615 634 5.338789 GGAAGGAGCTAGAAGAAGGAAACAT 60.339 44.000 0.00 0.00 0.00 2.71
616 635 4.020128 GGAAGGAGCTAGAAGAAGGAAACA 60.020 45.833 0.00 0.00 0.00 2.83
619 638 3.108376 GGGAAGGAGCTAGAAGAAGGAA 58.892 50.000 0.00 0.00 0.00 3.36
661 683 2.035321 GGATCTTCCAGGACTAGCTTCG 59.965 54.545 0.00 0.00 36.28 3.79
678 702 8.184304 AGATGGATAGTGTGTAAAGTAGGATC 57.816 38.462 0.00 0.00 0.00 3.36
681 705 7.504238 AGAGAGATGGATAGTGTGTAAAGTAGG 59.496 40.741 0.00 0.00 0.00 3.18
687 711 7.119387 TGAAGAGAGAGATGGATAGTGTGTAA 58.881 38.462 0.00 0.00 0.00 2.41
2521 3242 1.501169 GGCCTGACAAACAATGCAAC 58.499 50.000 0.00 0.00 0.00 4.17
3125 7003 3.268023 AGAGAATAAAGCTGGGGAACG 57.732 47.619 0.00 0.00 0.00 3.95
3126 7004 4.452825 GGTAGAGAATAAAGCTGGGGAAC 58.547 47.826 0.00 0.00 0.00 3.62
3127 7005 3.458487 GGGTAGAGAATAAAGCTGGGGAA 59.542 47.826 0.00 0.00 0.00 3.97
3370 7622 0.540830 TAAACCCTGCGGCCATTTGT 60.541 50.000 2.24 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.