Multiple sequence alignment - TraesCS1D01G214100

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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 TraesCS1D01G214100 chr1D 100.000 8120 0 0 1 8120 299263460 299271579 0.000000e+00 14995.0
1 TraesCS1D01G214100 chr1A 96.668 2641 45 13 5077 7678 373317656 373320292 0.000000e+00 4349.0
2 TraesCS1D01G214100 chr1A 92.881 2964 119 28 168 3074 373312768 373315696 0.000000e+00 4220.0
3 TraesCS1D01G214100 chr1A 96.679 1656 45 8 3323 4969 373315937 373317591 0.000000e+00 2745.0
4 TraesCS1D01G214100 chr1A 94.647 411 19 3 7709 8118 373320382 373320790 1.150000e-177 634.0
5 TraesCS1D01G214100 chr1A 85.714 112 5 6 74 184 373312626 373312727 3.100000e-19 108.0
6 TraesCS1D01G214100 chr1A 94.643 56 3 0 1 56 373312498 373312553 4.040000e-13 87.9
7 TraesCS1D01G214100 chr1B 94.812 2506 93 20 5087 7576 403416020 403418504 0.000000e+00 3873.0
8 TraesCS1D01G214100 chr1B 94.444 1656 62 9 3323 4963 403414382 403416022 0.000000e+00 2521.0
9 TraesCS1D01G214100 chr1B 94.084 1589 60 16 1495 3074 403412574 403414137 0.000000e+00 2383.0
10 TraesCS1D01G214100 chr1B 93.878 1323 50 12 127 1430 403411255 403412565 0.000000e+00 1965.0
11 TraesCS1D01G214100 chr1B 88.382 241 16 8 3107 3339 403414129 403414365 6.210000e-71 279.0
12 TraesCS1D01G214100 chr1B 84.043 188 18 3 7686 7870 403418538 403418716 3.900000e-38 171.0
13 TraesCS1D01G214100 chr1B 95.652 46 2 0 62 107 403396934 403396979 3.140000e-09 75.0
14 TraesCS1D01G214100 chr5D 98.462 130 2 0 4961 5090 269087868 269087739 6.340000e-56 230.0
15 TraesCS1D01G214100 chr2D 97.761 134 2 1 4961 5094 451958898 451959030 6.340000e-56 230.0
16 TraesCS1D01G214100 chr2D 96.350 137 5 0 4952 5088 147350363 147350499 8.200000e-55 226.0
17 TraesCS1D01G214100 chr2D 93.750 144 8 1 4956 5099 410405495 410405353 1.770000e-51 215.0
18 TraesCS1D01G214100 chr2B 95.775 142 6 0 4960 5101 291611721 291611862 6.340000e-56 230.0
19 TraesCS1D01G214100 chr7D 97.037 135 4 0 4955 5089 635616349 635616483 2.280000e-55 228.0
20 TraesCS1D01G214100 chr5B 95.070 142 6 1 4951 5092 711094177 711094317 1.060000e-53 222.0
21 TraesCS1D01G214100 chr5B 96.970 33 0 1 7655 7687 621341106 621341075 4.000000e-03 54.7
22 TraesCS1D01G214100 chr3B 96.324 136 3 2 4954 5088 262425115 262424981 1.060000e-53 222.0
23 TraesCS1D01G214100 chr6D 94.444 144 7 1 4954 5096 464487025 464487168 3.810000e-53 220.0
24 TraesCS1D01G214100 chr7A 100.000 30 0 0 7659 7688 491487406 491487377 1.000000e-03 56.5
25 TraesCS1D01G214100 chr2A 100.000 28 0 0 7661 7688 765054713 765054740 1.500000e-02 52.8


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 TraesCS1D01G214100 chr1D 299263460 299271579 8119 False 14995.000000 14995 100.000000 1 8120 1 chr1D.!!$F1 8119
1 TraesCS1D01G214100 chr1A 373312498 373320790 8292 False 2023.983333 4349 93.538667 1 8118 6 chr1A.!!$F1 8117
2 TraesCS1D01G214100 chr1B 403411255 403418716 7461 False 1865.333333 3873 91.607167 127 7870 6 chr1B.!!$F2 7743

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
226 336 0.323999 ATTGGGTTTCCGGTTAGGCC 60.324 55.0 0.00 0.0 40.77 5.19 F
1460 1647 0.108992 TAGCGAAACATCGAGCGGTT 60.109 50.0 1.91 0.0 35.91 4.44 F
2072 2267 0.307760 GTGAGTTTGCTGGGAACGTG 59.692 55.0 0.00 0.0 32.38 4.49 F
2649 2846 0.509929 GTTGCGTTAAGGACCGTGTC 59.490 55.0 0.00 0.0 0.00 3.67 F
3507 3750 0.260230 TTGTTTGGAGTCTGGCCCAA 59.740 50.0 0.00 0.0 40.38 4.12 F
4446 4703 0.830444 ACGGTGTGGCTAGTCCTGAA 60.830 55.0 0.00 0.0 35.26 3.02 F
5229 5486 0.107456 ATGCTTCCACAGATAGCCGG 59.893 55.0 0.00 0.0 34.03 6.13 F
5724 5981 1.656587 TCCAGTGGAGCAAGGTACAT 58.343 50.0 8.12 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 2382 0.249911 ATCATCTAAAGGACCGGCGC 60.250 55.000 0.00 0.00 0.00 6.53 R
3035 3232 1.282157 AGGGCTCCGCAAGTTCTTAAT 59.718 47.619 0.00 0.00 0.00 1.40 R
3485 3728 0.310854 GGCCAGACTCCAAACAAACG 59.689 55.000 0.00 0.00 0.00 3.60 R
3929 4183 1.202698 AGTCACAGGTGCTTGGAGAAC 60.203 52.381 0.00 0.00 0.00 3.01 R
5229 5486 1.338105 GGATTGAAAGGTTTGCAGGGC 60.338 52.381 0.00 0.00 0.00 5.19 R
6181 6439 0.379669 GGCGAGGATTACGTTCGAGA 59.620 55.000 10.57 0.00 0.00 4.04 R
6385 6643 5.055144 TGATGTGAAATATGAGAGCTCAGC 58.945 41.667 17.77 8.11 43.61 4.26 R
7337 7619 1.463375 TCTCACCGGAGACAAGGGA 59.537 57.895 9.46 0.00 45.12 4.20 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
67 81 2.037251 AGTCGCTAGCCACAAAAAGAGA 59.963 45.455 15.13 0.00 0.00 3.10
68 82 3.003480 GTCGCTAGCCACAAAAAGAGAT 58.997 45.455 9.66 0.00 0.00 2.75
69 83 4.081642 AGTCGCTAGCCACAAAAAGAGATA 60.082 41.667 15.13 0.00 0.00 1.98
71 85 5.294552 GTCGCTAGCCACAAAAAGAGATAAT 59.705 40.000 9.66 0.00 0.00 1.28
72 86 5.523916 TCGCTAGCCACAAAAAGAGATAATC 59.476 40.000 9.66 0.00 0.00 1.75
74 88 6.510799 CGCTAGCCACAAAAAGAGATAATCAG 60.511 42.308 9.66 0.00 0.00 2.90
76 90 7.228308 GCTAGCCACAAAAAGAGATAATCAGAT 59.772 37.037 2.29 0.00 0.00 2.90
77 91 9.770097 CTAGCCACAAAAAGAGATAATCAGATA 57.230 33.333 0.00 0.00 0.00 1.98
79 93 9.466497 AGCCACAAAAAGAGATAATCAGATAAA 57.534 29.630 0.00 0.00 0.00 1.40
91 148 1.201414 TCAGATAAACGCAGCGAGTGA 59.799 47.619 24.65 11.12 0.00 3.41
110 167 1.403323 GATTTGTTCAGCCAGCTAGCC 59.597 52.381 12.13 0.00 0.00 3.93
119 176 4.227134 CAGCTAGCCCGCCATCGT 62.227 66.667 12.13 0.00 0.00 3.73
120 177 4.227134 AGCTAGCCCGCCATCGTG 62.227 66.667 12.13 0.00 0.00 4.35
226 336 0.323999 ATTGGGTTTCCGGTTAGGCC 60.324 55.000 0.00 0.00 40.77 5.19
269 379 1.078143 CCACCAGGTTGGAGCTAGC 60.078 63.158 6.62 6.62 40.96 3.42
364 499 1.226888 GGTCCGTCATCGTAGCCAC 60.227 63.158 0.00 0.00 35.01 5.01
382 517 2.512515 GGTGCTGGAGGATGACGC 60.513 66.667 0.00 0.00 0.00 5.19
504 658 3.195698 CGGGCTCCTGTTAAGCGC 61.196 66.667 0.00 0.00 46.06 5.92
517 671 3.181505 TGTTAAGCGCAATTAACGATGGG 60.182 43.478 20.66 0.00 44.85 4.00
562 716 1.805945 GTCAAGCGAGCCTACCGTG 60.806 63.158 0.00 0.00 0.00 4.94
724 887 1.075896 GGGAGAGGGACACGAGGAT 60.076 63.158 0.00 0.00 0.00 3.24
761 924 0.890683 AAAGATGCCGCTCCAAAAGG 59.109 50.000 0.00 0.00 0.00 3.11
891 1064 4.393155 TCTGCTCGCCACCGCAAT 62.393 61.111 0.00 0.00 35.46 3.56
904 1077 0.724549 CCGCAATCGAACGAATCCAA 59.275 50.000 7.35 0.00 38.10 3.53
1355 1542 2.014857 CGTCCATCTCAAGGTCTCGTA 58.985 52.381 0.00 0.00 0.00 3.43
1356 1543 2.223294 CGTCCATCTCAAGGTCTCGTAC 60.223 54.545 0.00 0.00 0.00 3.67
1388 1575 2.507769 CCGTTTCCCGTCCGCTAC 60.508 66.667 0.00 0.00 33.66 3.58
1435 1622 1.661112 GATAGCTTCCACACAACTCGC 59.339 52.381 0.00 0.00 0.00 5.03
1460 1647 0.108992 TAGCGAAACATCGAGCGGTT 60.109 50.000 1.91 0.00 35.91 4.44
1493 1680 1.065273 CAGCGCATTTCATCTGGCC 59.935 57.895 11.47 0.00 0.00 5.36
1673 1868 2.916423 GCACATCGTCGCGATCTG 59.084 61.111 14.06 12.88 45.19 2.90
1730 1925 3.427638 CGCTTGTGTCGGATAAAGAGAGA 60.428 47.826 2.61 0.00 0.00 3.10
1731 1926 4.109050 GCTTGTGTCGGATAAAGAGAGAG 58.891 47.826 2.61 0.00 0.00 3.20
1965 2160 0.749649 TTTGTTCAAATGGCACGGCT 59.250 45.000 0.00 0.00 0.00 5.52
1990 2185 5.236478 CCGGCCTATCTGTATTTTGTACAAG 59.764 44.000 8.56 0.00 0.00 3.16
1991 2186 5.236478 CGGCCTATCTGTATTTTGTACAAGG 59.764 44.000 8.56 3.56 0.00 3.61
1992 2187 5.531287 GGCCTATCTGTATTTTGTACAAGGG 59.469 44.000 8.56 1.86 0.00 3.95
1993 2188 6.354130 GCCTATCTGTATTTTGTACAAGGGA 58.646 40.000 8.56 0.00 0.00 4.20
1994 2189 6.483640 GCCTATCTGTATTTTGTACAAGGGAG 59.516 42.308 8.56 2.70 0.00 4.30
1995 2190 7.635089 GCCTATCTGTATTTTGTACAAGGGAGA 60.635 40.741 8.56 7.66 0.00 3.71
1996 2191 8.265055 CCTATCTGTATTTTGTACAAGGGAGAA 58.735 37.037 8.56 0.10 0.00 2.87
1997 2192 9.838339 CTATCTGTATTTTGTACAAGGGAGAAT 57.162 33.333 8.56 7.90 0.00 2.40
2072 2267 0.307760 GTGAGTTTGCTGGGAACGTG 59.692 55.000 0.00 0.00 32.38 4.49
2108 2303 5.319453 AGCATCTGTCCATATACCCATTTG 58.681 41.667 0.00 0.00 0.00 2.32
2122 2317 1.259609 CATTTGAAGGAGCCTTGCCA 58.740 50.000 6.49 0.00 36.26 4.92
2152 2347 0.534412 CCTGATGAGCGGTCTCTTGT 59.466 55.000 16.64 0.00 40.03 3.16
2187 2382 2.959516 TGAGTCAGCGTCCTTTATGTG 58.040 47.619 0.00 0.00 0.00 3.21
2188 2383 1.661112 GAGTCAGCGTCCTTTATGTGC 59.339 52.381 0.00 0.00 0.00 4.57
2192 2387 2.701006 CGTCCTTTATGTGCGCCG 59.299 61.111 4.18 0.00 0.00 6.46
2220 2415 9.823647 TCCTTTAGATGATAACTGATCAAGTTC 57.176 33.333 12.05 1.95 46.60 3.01
2278 2473 1.067295 ACAGTGCTGGGAGGATTCAA 58.933 50.000 4.11 0.00 34.19 2.69
2281 2476 3.266772 ACAGTGCTGGGAGGATTCAATAA 59.733 43.478 4.11 0.00 34.19 1.40
2377 2572 5.305585 TGTGTTGGAAGGAACTGAAGTATC 58.694 41.667 0.00 0.00 40.86 2.24
2397 2592 4.445452 TCTGTTGTCGTTGGTCTATACC 57.555 45.455 0.00 0.00 46.98 2.73
2449 2645 1.404583 GCATGGGGCATCACTGTTTTC 60.405 52.381 0.00 0.00 43.97 2.29
2562 2759 9.950496 AACTGTTTGTAGATCTCATCATTTAGT 57.050 29.630 0.00 0.60 0.00 2.24
2649 2846 0.509929 GTTGCGTTAAGGACCGTGTC 59.490 55.000 0.00 0.00 0.00 3.67
3035 3232 5.603596 ACCAACTTTAGTGACGAATGTACA 58.396 37.500 0.00 0.00 0.00 2.90
3164 3361 7.416664 GCCAAAAGATGACTGGATATTTTGCTA 60.417 37.037 12.56 0.00 40.67 3.49
3165 3362 8.636213 CCAAAAGATGACTGGATATTTTGCTAT 58.364 33.333 12.56 0.00 40.67 2.97
3240 3443 6.569226 GCACTTGCTAGCAATATTATCCCAAG 60.569 42.308 29.40 15.69 38.21 3.61
3262 3465 0.621082 TGGTGTCAAACAGGACCACA 59.379 50.000 0.00 0.00 36.97 4.17
3275 3478 2.087646 GGACCACAATCTCAGCCTTTC 58.912 52.381 0.00 0.00 0.00 2.62
3277 3480 1.072331 ACCACAATCTCAGCCTTTCGT 59.928 47.619 0.00 0.00 0.00 3.85
3283 3486 5.235186 CACAATCTCAGCCTTTCGTAATAGG 59.765 44.000 0.00 0.00 34.54 2.57
3290 3493 7.494625 TCTCAGCCTTTCGTAATAGGTTTAATG 59.505 37.037 0.00 0.00 33.91 1.90
3297 3501 9.902196 CTTTCGTAATAGGTTTAATGGTTTTGT 57.098 29.630 0.00 0.00 0.00 2.83
3360 3598 8.749026 AAGTAAAGATGAAGATACTCGACCTA 57.251 34.615 0.00 0.00 0.00 3.08
3408 3646 5.389520 TGTGGTCCAAACATTTCCTCATAA 58.610 37.500 0.00 0.00 0.00 1.90
3409 3647 6.015918 TGTGGTCCAAACATTTCCTCATAAT 58.984 36.000 0.00 0.00 0.00 1.28
3507 3750 0.260230 TTGTTTGGAGTCTGGCCCAA 59.740 50.000 0.00 0.00 40.38 4.12
3510 3753 2.166907 TTTGGAGTCTGGCCCAAAAA 57.833 45.000 0.00 0.00 46.07 1.94
3777 4020 8.770438 TTTCATGCATAATTTTTCCTTACCAC 57.230 30.769 0.00 0.00 0.00 4.16
3873 4118 3.181445 ACAGGTGTGAAGGTGCTAATTCA 60.181 43.478 0.00 0.00 33.16 2.57
4089 4346 4.042398 CCATCATACGTAGTTGAGAACGG 58.958 47.826 0.08 0.00 37.78 4.44
4274 4531 3.316029 TCACTGCAAACACTTCTTCCATG 59.684 43.478 0.00 0.00 0.00 3.66
4373 4630 5.253330 TGCTGGTAAACAAGAAATAGGGAG 58.747 41.667 0.00 0.00 0.00 4.30
4446 4703 0.830444 ACGGTGTGGCTAGTCCTGAA 60.830 55.000 0.00 0.00 35.26 3.02
4525 4782 1.466167 CTGCCGACAAGACCAATGAAG 59.534 52.381 0.00 0.00 0.00 3.02
4972 5229 8.953223 ATATCTAAAATACTACTCCCTCCGTT 57.047 34.615 0.00 0.00 0.00 4.44
4973 5230 6.705863 TCTAAAATACTACTCCCTCCGTTC 57.294 41.667 0.00 0.00 0.00 3.95
4974 5231 4.750021 AAAATACTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
4975 5232 3.393426 AATACTACTCCCTCCGTTCCA 57.607 47.619 0.00 0.00 0.00 3.53
4976 5233 2.905415 TACTACTCCCTCCGTTCCAA 57.095 50.000 0.00 0.00 0.00 3.53
4981 5238 3.345508 ACTCCCTCCGTTCCAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
4982 5239 2.910977 ACTCCCTCCGTTCCAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
4983 5240 3.329814 ACTCCCTCCGTTCCAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
4986 5243 3.439129 CCCTCCGTTCCAAAATACTTGAC 59.561 47.826 0.00 0.00 0.00 3.18
4988 5245 4.760204 CCTCCGTTCCAAAATACTTGACTT 59.240 41.667 0.00 0.00 0.00 3.01
4989 5246 5.106673 CCTCCGTTCCAAAATACTTGACTTC 60.107 44.000 0.00 0.00 0.00 3.01
4990 5247 4.758165 TCCGTTCCAAAATACTTGACTTCC 59.242 41.667 0.00 0.00 0.00 3.46
4991 5248 4.517453 CCGTTCCAAAATACTTGACTTCCA 59.483 41.667 0.00 0.00 0.00 3.53
4992 5249 5.183140 CCGTTCCAAAATACTTGACTTCCAT 59.817 40.000 0.00 0.00 0.00 3.41
4993 5250 6.294508 CCGTTCCAAAATACTTGACTTCCATT 60.295 38.462 0.00 0.00 0.00 3.16
4994 5251 7.145323 CGTTCCAAAATACTTGACTTCCATTT 58.855 34.615 0.00 0.00 0.00 2.32
4995 5252 7.114811 CGTTCCAAAATACTTGACTTCCATTTG 59.885 37.037 0.00 0.00 0.00 2.32
4996 5253 7.595819 TCCAAAATACTTGACTTCCATTTGT 57.404 32.000 0.00 0.00 0.00 2.83
4997 5254 8.017418 TCCAAAATACTTGACTTCCATTTGTT 57.983 30.769 0.00 0.00 0.00 2.83
4999 5256 7.925483 CCAAAATACTTGACTTCCATTTGTTCA 59.075 33.333 0.00 0.00 0.00 3.18
5005 5262 8.200364 ACTTGACTTCCATTTGTTCAAAAATG 57.800 30.769 2.11 3.25 43.94 2.32
5016 5273 9.874205 CATTTGTTCAAAAATGGATGTACCTAT 57.126 29.630 2.11 0.00 41.71 2.57
5063 5320 8.416329 ACATCTATATTTTGACAAATGGAAGGC 58.584 33.333 0.50 0.00 34.29 4.35
5064 5321 7.953005 TCTATATTTTGACAAATGGAAGGCA 57.047 32.000 0.50 0.00 34.29 4.75
5065 5322 8.537728 TCTATATTTTGACAAATGGAAGGCAT 57.462 30.769 0.50 0.00 34.29 4.40
5066 5323 8.415553 TCTATATTTTGACAAATGGAAGGCATG 58.584 33.333 0.50 0.00 34.29 4.06
5067 5324 4.686191 TTTTGACAAATGGAAGGCATGT 57.314 36.364 0.50 0.00 0.00 3.21
5068 5325 5.798125 TTTTGACAAATGGAAGGCATGTA 57.202 34.783 0.50 0.00 0.00 2.29
5069 5326 5.999205 TTTGACAAATGGAAGGCATGTAT 57.001 34.783 0.00 0.00 0.00 2.29
5070 5327 5.999205 TTGACAAATGGAAGGCATGTATT 57.001 34.783 0.00 0.00 0.00 1.89
5071 5328 5.327616 TGACAAATGGAAGGCATGTATTG 57.672 39.130 0.00 0.00 0.00 1.90
5072 5329 4.771577 TGACAAATGGAAGGCATGTATTGT 59.228 37.500 0.00 0.00 32.89 2.71
5073 5330 5.948758 TGACAAATGGAAGGCATGTATTGTA 59.051 36.000 0.00 0.00 30.58 2.41
5074 5331 6.095300 TGACAAATGGAAGGCATGTATTGTAG 59.905 38.462 0.00 0.00 30.58 2.74
5075 5332 6.186957 ACAAATGGAAGGCATGTATTGTAGA 58.813 36.000 0.00 0.00 0.00 2.59
5229 5486 0.107456 ATGCTTCCACAGATAGCCGG 59.893 55.000 0.00 0.00 34.03 6.13
5724 5981 1.656587 TCCAGTGGAGCAAGGTACAT 58.343 50.000 8.12 0.00 0.00 2.29
5753 6010 6.553953 TCACCAAAGGCACTCATACTATTA 57.446 37.500 0.00 0.00 38.49 0.98
6000 6258 2.355132 CTCACATGAAGCTTGGAGATGC 59.645 50.000 2.10 0.00 0.00 3.91
6385 6643 6.700020 CGTTGTTAGTGATGATGCTTCTAAG 58.300 40.000 0.88 0.00 0.00 2.18
6753 7012 9.719433 ATACCCTAGTTGTTTATACTGTCCTAA 57.281 33.333 0.00 0.00 0.00 2.69
6754 7013 7.845037 ACCCTAGTTGTTTATACTGTCCTAAC 58.155 38.462 0.00 0.00 0.00 2.34
6755 7014 7.455638 ACCCTAGTTGTTTATACTGTCCTAACA 59.544 37.037 0.00 0.00 0.00 2.41
6756 7015 8.483758 CCCTAGTTGTTTATACTGTCCTAACAT 58.516 37.037 0.00 0.00 34.13 2.71
6763 7022 9.226606 TGTTTATACTGTCCTAACATTTTCCTG 57.773 33.333 0.00 0.00 34.13 3.86
7350 7634 2.717639 ATCATTTCCCTTGTCTCCGG 57.282 50.000 0.00 0.00 0.00 5.14
7514 7798 7.528996 AGATCTCATCTCAATCTTAGTCCTG 57.471 40.000 0.00 0.00 33.42 3.86
7516 7800 5.523588 TCTCATCTCAATCTTAGTCCTGGT 58.476 41.667 0.00 0.00 0.00 4.00
7517 7801 6.673583 TCTCATCTCAATCTTAGTCCTGGTA 58.326 40.000 0.00 0.00 0.00 3.25
7518 7802 6.547880 TCTCATCTCAATCTTAGTCCTGGTAC 59.452 42.308 0.00 0.00 0.00 3.34
7581 7879 9.522804 GTAACTGATATGGTTTCTCTGTAGAAG 57.477 37.037 0.00 0.00 42.60 2.85
7738 8097 8.996651 AATCCTCTTCAACCTCTTAAAAAGAA 57.003 30.769 0.00 0.00 37.02 2.52
7739 8098 9.593565 AATCCTCTTCAACCTCTTAAAAAGAAT 57.406 29.630 0.00 0.00 37.02 2.40
7775 8136 9.734620 TTCTTTTGATGTTTATCACAAACTCAG 57.265 29.630 0.00 0.00 42.79 3.35
7784 8145 8.106462 TGTTTATCACAAACTCAGATCCCATAA 58.894 33.333 2.00 0.00 29.87 1.90
7790 8151 6.377996 CACAAACTCAGATCCCATAAAATCCA 59.622 38.462 0.00 0.00 0.00 3.41
7909 8271 1.594331 GGCGCTAATACAGGGGAAAG 58.406 55.000 7.64 0.00 37.67 2.62
7918 8280 6.433093 GCTAATACAGGGGAAAGAAACAAAGA 59.567 38.462 0.00 0.00 0.00 2.52
7925 8287 8.544622 ACAGGGGAAAGAAACAAAGAATTTTAA 58.455 29.630 0.00 0.00 35.03 1.52
7971 8333 1.136169 CGACGATGGGGTTCGAAAAAC 60.136 52.381 0.00 0.00 41.62 2.43
7985 8347 3.743886 CGAAAAACGAACCCTAATCAGC 58.256 45.455 0.00 0.00 45.77 4.26
7999 8361 4.436998 CAGCCACCGGGACTCGAC 62.437 72.222 6.32 0.00 42.43 4.20
8008 8370 0.531090 CGGGACTCGACAAACCAACA 60.531 55.000 0.00 0.00 42.43 3.33
8029 8391 4.079787 ACAGCTAATTGGCCAGGAATCTTA 60.080 41.667 10.54 0.00 0.00 2.10
8059 8421 1.217001 CATGCTAAGCGTCCGCATTA 58.783 50.000 14.70 8.51 42.03 1.90
8118 8481 4.075682 CAGTGCTTATCTCTATCGGAGGA 58.924 47.826 0.00 0.00 42.10 3.71
8119 8482 4.704540 CAGTGCTTATCTCTATCGGAGGAT 59.295 45.833 0.00 0.00 42.10 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.730949 TCCGGTATTCACAACCTTCTAG 57.269 45.455 0.00 0.00 34.66 2.43
11 12 4.561105 GCCAATTTTTCCGGTATTCACAA 58.439 39.130 0.00 0.00 0.00 3.33
67 81 4.445718 CACTCGCTGCGTTTATCTGATTAT 59.554 41.667 22.48 0.00 0.00 1.28
68 82 3.796717 CACTCGCTGCGTTTATCTGATTA 59.203 43.478 22.48 0.00 0.00 1.75
69 83 2.604914 CACTCGCTGCGTTTATCTGATT 59.395 45.455 22.48 0.00 0.00 2.57
71 85 1.201414 TCACTCGCTGCGTTTATCTGA 59.799 47.619 22.48 11.03 0.00 3.27
72 86 1.629013 TCACTCGCTGCGTTTATCTG 58.371 50.000 22.48 9.03 0.00 2.90
74 88 3.181520 ACAAATCACTCGCTGCGTTTATC 60.182 43.478 22.48 0.00 0.00 1.75
76 90 2.139917 ACAAATCACTCGCTGCGTTTA 58.860 42.857 22.48 6.76 0.00 2.01
77 91 0.944386 ACAAATCACTCGCTGCGTTT 59.056 45.000 22.48 11.61 0.00 3.60
78 92 0.944386 AACAAATCACTCGCTGCGTT 59.056 45.000 22.48 7.53 0.00 4.84
79 93 0.512952 GAACAAATCACTCGCTGCGT 59.487 50.000 22.48 0.00 0.00 5.24
91 148 1.467920 GGCTAGCTGGCTGAACAAAT 58.532 50.000 22.23 0.00 38.32 2.32
116 173 3.273654 ACTCCCTCTCCCCCACGA 61.274 66.667 0.00 0.00 0.00 4.35
119 176 4.075793 CGGACTCCCTCTCCCCCA 62.076 72.222 0.00 0.00 0.00 4.96
120 177 4.862823 CCGGACTCCCTCTCCCCC 62.863 77.778 0.00 0.00 0.00 5.40
156 213 1.121240 CCACGAGATATCGCACGAAC 58.879 55.000 10.14 0.00 36.44 3.95
269 379 5.292765 CATGTCTTGTACCAGTGGCTATAG 58.707 45.833 9.78 2.26 0.00 1.31
338 473 3.740128 GATGACGGACCAGCGGCAT 62.740 63.158 1.45 0.00 0.00 4.40
364 499 2.202797 CGTCATCCTCCAGCACCG 60.203 66.667 0.00 0.00 0.00 4.94
382 517 0.321653 CGAACCTTCCTTGGACCAGG 60.322 60.000 5.98 5.98 34.86 4.45
504 658 3.192422 TGTGCTTTCCCCATCGTTAATTG 59.808 43.478 0.00 0.00 0.00 2.32
517 671 5.181748 ACTCTAGATGTCAATGTGCTTTCC 58.818 41.667 0.00 0.00 0.00 3.13
706 869 1.075896 ATCCTCGTGTCCCTCTCCC 60.076 63.158 0.00 0.00 0.00 4.30
724 887 4.873129 GAGCGCGCGATCCTTCCA 62.873 66.667 35.80 0.00 0.00 3.53
761 924 1.633852 CGCTCACTTCTGCTGCTTCC 61.634 60.000 0.00 0.00 0.00 3.46
891 1064 1.470285 GGGTCGATTGGATTCGTTCGA 60.470 52.381 0.00 0.00 40.03 3.71
1077 1258 4.477975 GAGCAGTCCCCGTCGTCG 62.478 72.222 0.00 0.00 0.00 5.12
1360 1547 4.468689 GAAACGGAGGGGGCGGAG 62.469 72.222 0.00 0.00 0.00 4.63
1388 1575 0.877071 GCAATGGGATCATGGTAGCG 59.123 55.000 0.00 0.00 33.18 4.26
1435 1622 1.920574 CTCGATGTTTCGCTACTGGTG 59.079 52.381 0.00 0.00 45.10 4.17
1493 1680 6.468000 GGAAACTAAAAATAGTTGAATCGCCG 59.532 38.462 2.27 0.00 39.93 6.46
1544 1731 5.468746 CCAACTCGTTTTGGTAATGAGAAGA 59.531 40.000 12.33 0.00 41.18 2.87
1673 1868 1.226407 GCAAGAAAATCTCCGCCGC 60.226 57.895 0.00 0.00 0.00 6.53
1730 1925 0.990374 AGTCCAAGCAAGGCATCTCT 59.010 50.000 0.00 0.00 0.00 3.10
1731 1926 1.093159 CAGTCCAAGCAAGGCATCTC 58.907 55.000 0.00 0.00 0.00 2.75
1965 2160 4.406326 TGTACAAAATACAGATAGGCCGGA 59.594 41.667 5.05 0.00 0.00 5.14
1990 2185 1.603739 GCCCGGCCATTATTCTCCC 60.604 63.158 2.24 0.00 0.00 4.30
1991 2186 4.081050 GCCCGGCCATTATTCTCC 57.919 61.111 2.24 0.00 0.00 3.71
2072 2267 3.087906 ATGCTCCGTACCACCCCC 61.088 66.667 0.00 0.00 0.00 5.40
2108 2303 2.354103 GGAAAAATGGCAAGGCTCCTTC 60.354 50.000 0.00 0.00 33.42 3.46
2122 2317 3.019564 CGCTCATCAGGGAAGGAAAAAT 58.980 45.455 0.00 0.00 34.38 1.82
2152 2347 1.303074 CTCAAGCAGCAGCCAAGGA 60.303 57.895 0.00 0.00 43.56 3.36
2187 2382 0.249911 ATCATCTAAAGGACCGGCGC 60.250 55.000 0.00 0.00 0.00 6.53
2188 2383 3.057734 GTTATCATCTAAAGGACCGGCG 58.942 50.000 0.00 0.00 0.00 6.46
2192 2387 8.207545 ACTTGATCAGTTATCATCTAAAGGACC 58.792 37.037 0.00 0.00 44.13 4.46
2220 2415 8.877808 TTCACACTGTTGCATCTATAGATAAG 57.122 34.615 14.92 5.41 32.63 1.73
2397 2592 1.729517 TCATGCGGTGATTACACGTTG 59.270 47.619 0.00 0.00 46.77 4.10
2409 2604 5.405935 TGCTATCTACATATTCATGCGGT 57.594 39.130 0.00 0.00 35.39 5.68
2449 2645 7.114811 GTGTTCAAGGCACACAAATTATAGTTG 59.885 37.037 1.36 0.00 43.52 3.16
2562 2759 6.485313 ACCGTTTGTCATCTGATTTACTTTCA 59.515 34.615 0.00 0.00 0.00 2.69
3035 3232 1.282157 AGGGCTCCGCAAGTTCTTAAT 59.718 47.619 0.00 0.00 0.00 1.40
3111 3308 9.066892 ACAACTAAGAACATCAATTGTGTGTAT 57.933 29.630 15.89 10.17 38.99 2.29
3112 3309 8.341903 CACAACTAAGAACATCAATTGTGTGTA 58.658 33.333 15.89 8.40 40.19 2.90
3113 3310 7.195646 CACAACTAAGAACATCAATTGTGTGT 58.804 34.615 5.13 9.11 40.19 3.72
3114 3311 6.142798 GCACAACTAAGAACATCAATTGTGTG 59.857 38.462 13.81 8.85 44.53 3.82
3115 3312 6.208644 GCACAACTAAGAACATCAATTGTGT 58.791 36.000 13.81 6.59 44.53 3.72
3116 3313 5.630680 GGCACAACTAAGAACATCAATTGTG 59.369 40.000 5.13 9.29 45.15 3.33
3117 3314 5.301551 TGGCACAACTAAGAACATCAATTGT 59.698 36.000 5.13 0.00 35.68 2.71
3164 3361 5.748402 TGCTGAATACAAGGAAGACATGAT 58.252 37.500 0.00 0.00 0.00 2.45
3165 3362 5.164620 TGCTGAATACAAGGAAGACATGA 57.835 39.130 0.00 0.00 0.00 3.07
3262 3465 5.615925 ACCTATTACGAAAGGCTGAGATT 57.384 39.130 0.00 0.00 36.24 2.40
3283 3486 8.192110 TGTCACCTTCTAACAAAACCATTAAAC 58.808 33.333 0.00 0.00 0.00 2.01
3290 3493 3.949113 TGGTGTCACCTTCTAACAAAACC 59.051 43.478 22.56 0.00 39.58 3.27
3360 3598 9.889128 CAATTGGGTTTCCTTGTCATTTATAAT 57.111 29.630 0.00 0.00 0.00 1.28
3485 3728 0.310854 GGCCAGACTCCAAACAAACG 59.689 55.000 0.00 0.00 0.00 3.60
3532 3775 9.914131 TTCACGATACCAGAATTTCAGATATAG 57.086 33.333 0.00 0.00 0.00 1.31
3541 3784 7.467811 GCAGATGATTTCACGATACCAGAATTT 60.468 37.037 0.00 0.00 0.00 1.82
3542 3785 6.017605 GCAGATGATTTCACGATACCAGAATT 60.018 38.462 0.00 0.00 0.00 2.17
3770 4013 6.293571 CCAAAGTAAAGGTTTACCGTGGTAAG 60.294 42.308 16.90 0.00 43.03 2.34
3777 4020 9.917129 AAAATAATCCAAAGTAAAGGTTTACCG 57.083 29.630 8.66 0.00 43.03 4.02
3844 4089 2.027745 CACCTTCACACCTGTGCTCTAT 60.028 50.000 0.17 0.00 45.25 1.98
3873 4118 6.594788 ACATCAGCAGTCCAATAAAAATGT 57.405 33.333 0.00 0.00 0.00 2.71
3881 4126 4.511527 CAGTCTAACATCAGCAGTCCAAT 58.488 43.478 0.00 0.00 0.00 3.16
3929 4183 1.202698 AGTCACAGGTGCTTGGAGAAC 60.203 52.381 0.00 0.00 0.00 3.01
4089 4346 2.746277 CACTGCCCCGCTGGTAAC 60.746 66.667 0.00 0.00 36.04 2.50
4373 4630 7.606858 TGAAACTCATCTTCATCTGACATTC 57.393 36.000 0.00 0.00 0.00 2.67
4745 5002 8.483758 AGGAAAGGTATATAAATAGGCATACCG 58.516 37.037 0.00 0.00 45.01 4.02
4969 5226 5.682943 TGGAAGTCAAGTATTTTGGAACG 57.317 39.130 0.00 0.00 0.00 3.95
4972 5229 7.595819 ACAAATGGAAGTCAAGTATTTTGGA 57.404 32.000 0.00 0.00 29.41 3.53
4973 5230 7.925483 TGAACAAATGGAAGTCAAGTATTTTGG 59.075 33.333 0.00 0.00 29.41 3.28
4974 5231 8.870160 TGAACAAATGGAAGTCAAGTATTTTG 57.130 30.769 0.00 0.00 0.00 2.44
4975 5232 9.883142 TTTGAACAAATGGAAGTCAAGTATTTT 57.117 25.926 0.00 0.00 0.00 1.82
4976 5233 9.883142 TTTTGAACAAATGGAAGTCAAGTATTT 57.117 25.926 0.82 0.00 0.00 1.40
4990 5247 9.874205 ATAGGTACATCCATTTTTGAACAAATG 57.126 29.630 0.00 0.04 41.86 2.32
5037 5294 8.416329 GCCTTCCATTTGTCAAAATATAGATGT 58.584 33.333 1.31 0.00 34.14 3.06
5038 5295 8.415553 TGCCTTCCATTTGTCAAAATATAGATG 58.584 33.333 1.31 0.00 34.14 2.90
5039 5296 8.537728 TGCCTTCCATTTGTCAAAATATAGAT 57.462 30.769 1.31 0.00 34.14 1.98
5040 5297 7.953005 TGCCTTCCATTTGTCAAAATATAGA 57.047 32.000 1.31 0.00 34.14 1.98
5041 5298 8.199449 ACATGCCTTCCATTTGTCAAAATATAG 58.801 33.333 1.31 0.00 34.14 1.31
5042 5299 8.076910 ACATGCCTTCCATTTGTCAAAATATA 57.923 30.769 1.31 0.00 34.14 0.86
5043 5300 6.949715 ACATGCCTTCCATTTGTCAAAATAT 58.050 32.000 1.31 0.00 34.14 1.28
5044 5301 6.357579 ACATGCCTTCCATTTGTCAAAATA 57.642 33.333 1.31 0.00 34.14 1.40
5045 5302 5.231702 ACATGCCTTCCATTTGTCAAAAT 57.768 34.783 1.31 0.00 36.39 1.82
5046 5303 4.686191 ACATGCCTTCCATTTGTCAAAA 57.314 36.364 1.31 0.00 29.71 2.44
5047 5304 5.999205 ATACATGCCTTCCATTTGTCAAA 57.001 34.783 0.00 0.00 29.71 2.69
5048 5305 5.245751 ACAATACATGCCTTCCATTTGTCAA 59.754 36.000 0.00 0.00 30.42 3.18
5049 5306 4.771577 ACAATACATGCCTTCCATTTGTCA 59.228 37.500 0.00 0.00 30.42 3.58
5050 5307 5.329035 ACAATACATGCCTTCCATTTGTC 57.671 39.130 0.00 0.00 30.42 3.18
5051 5308 6.186957 TCTACAATACATGCCTTCCATTTGT 58.813 36.000 0.00 0.00 36.71 2.83
5052 5309 6.698008 TCTACAATACATGCCTTCCATTTG 57.302 37.500 0.00 0.00 29.71 2.32
5053 5310 6.183360 CGTTCTACAATACATGCCTTCCATTT 60.183 38.462 0.00 0.00 29.71 2.32
5054 5311 5.296780 CGTTCTACAATACATGCCTTCCATT 59.703 40.000 0.00 0.00 29.71 3.16
5055 5312 4.816385 CGTTCTACAATACATGCCTTCCAT 59.184 41.667 0.00 0.00 33.39 3.41
5056 5313 4.188462 CGTTCTACAATACATGCCTTCCA 58.812 43.478 0.00 0.00 0.00 3.53
5057 5314 3.560068 CCGTTCTACAATACATGCCTTCC 59.440 47.826 0.00 0.00 0.00 3.46
5058 5315 4.439057 TCCGTTCTACAATACATGCCTTC 58.561 43.478 0.00 0.00 0.00 3.46
5059 5316 4.442706 CTCCGTTCTACAATACATGCCTT 58.557 43.478 0.00 0.00 0.00 4.35
5060 5317 3.181465 CCTCCGTTCTACAATACATGCCT 60.181 47.826 0.00 0.00 0.00 4.75
5061 5318 3.131396 CCTCCGTTCTACAATACATGCC 58.869 50.000 0.00 0.00 0.00 4.40
5062 5319 3.131396 CCCTCCGTTCTACAATACATGC 58.869 50.000 0.00 0.00 0.00 4.06
5063 5320 4.099573 ACTCCCTCCGTTCTACAATACATG 59.900 45.833 0.00 0.00 0.00 3.21
5064 5321 4.287552 ACTCCCTCCGTTCTACAATACAT 58.712 43.478 0.00 0.00 0.00 2.29
5065 5322 3.705051 ACTCCCTCCGTTCTACAATACA 58.295 45.455 0.00 0.00 0.00 2.29
5066 5323 4.641989 TGTACTCCCTCCGTTCTACAATAC 59.358 45.833 0.00 0.00 0.00 1.89
5067 5324 4.858850 TGTACTCCCTCCGTTCTACAATA 58.141 43.478 0.00 0.00 0.00 1.90
5068 5325 3.705051 TGTACTCCCTCCGTTCTACAAT 58.295 45.455 0.00 0.00 0.00 2.71
5069 5326 3.159213 TGTACTCCCTCCGTTCTACAA 57.841 47.619 0.00 0.00 0.00 2.41
5070 5327 2.885135 TGTACTCCCTCCGTTCTACA 57.115 50.000 0.00 0.00 0.00 2.74
5071 5328 4.275443 CACTATGTACTCCCTCCGTTCTAC 59.725 50.000 0.00 0.00 0.00 2.59
5072 5329 4.458397 CACTATGTACTCCCTCCGTTCTA 58.542 47.826 0.00 0.00 0.00 2.10
5073 5330 3.288964 CACTATGTACTCCCTCCGTTCT 58.711 50.000 0.00 0.00 0.00 3.01
5074 5331 2.361438 CCACTATGTACTCCCTCCGTTC 59.639 54.545 0.00 0.00 0.00 3.95
5075 5332 2.292061 ACCACTATGTACTCCCTCCGTT 60.292 50.000 0.00 0.00 0.00 4.44
5229 5486 1.338105 GGATTGAAAGGTTTGCAGGGC 60.338 52.381 0.00 0.00 0.00 5.19
5724 5981 4.365514 TGAGTGCCTTTGGTGAAGAATA 57.634 40.909 0.00 0.00 37.57 1.75
5753 6010 6.652481 CGAGAATGGTAATCATGGAAAGCTAT 59.348 38.462 0.00 0.00 35.99 2.97
5966 6224 3.161866 TCATGTGAGTAGTGGCAGTGTA 58.838 45.455 4.76 0.00 0.00 2.90
6000 6258 9.345517 TCAAAAAGATATTCAATTCTTCTTGCG 57.654 29.630 4.65 0.00 32.47 4.85
6181 6439 0.379669 GGCGAGGATTACGTTCGAGA 59.620 55.000 10.57 0.00 0.00 4.04
6385 6643 5.055144 TGATGTGAAATATGAGAGCTCAGC 58.945 41.667 17.77 8.11 43.61 4.26
6421 6679 6.460953 GCTCATTTTTCTTCCACAACAAGGTA 60.461 38.462 0.00 0.00 0.00 3.08
6738 6997 9.227777 ACAGGAAAATGTTAGGACAGTATAAAC 57.772 33.333 0.00 0.00 39.58 2.01
6753 7012 9.855021 GCAATATGTAGTTTTACAGGAAAATGT 57.145 29.630 0.00 0.00 42.72 2.71
6843 7103 6.826741 AGGTACTTCTTCAGTGTAAGCAAAAA 59.173 34.615 0.00 0.00 35.97 1.94
6844 7104 6.260050 CAGGTACTTCTTCAGTGTAAGCAAAA 59.740 38.462 0.00 0.00 34.60 2.44
7289 7571 6.250527 GCAACAATGTTAGCAAAAGTATACCG 59.749 38.462 13.02 0.00 0.00 4.02
7337 7619 1.463375 TCTCACCGGAGACAAGGGA 59.537 57.895 9.46 0.00 45.12 4.20
7350 7634 4.579869 ACATACTTGTCACCCATTCTCAC 58.420 43.478 0.00 0.00 0.00 3.51
7581 7879 3.065925 GCTCACCAGCCAAATATCTTCAC 59.934 47.826 0.00 0.00 40.14 3.18
7713 8072 8.996651 TTCTTTTTAAGAGGTTGAAGAGGATT 57.003 30.769 0.00 0.00 39.03 3.01
7784 8145 4.847990 AATGTCATGCCCATTTGGATTT 57.152 36.364 0.00 0.00 37.39 2.17
7790 8151 5.667466 GAGATTGAAATGTCATGCCCATTT 58.333 37.500 17.71 17.71 43.33 2.32
7909 8271 8.289618 GGGATGCCTTTTAAAATTCTTTGTTTC 58.710 33.333 0.09 0.00 0.00 2.78
7918 8280 3.054434 GCCAGGGGATGCCTTTTAAAATT 60.054 43.478 2.19 0.00 0.00 1.82
7925 8287 2.097978 AACTGCCAGGGGATGCCTTT 62.098 55.000 2.19 0.00 0.00 3.11
7971 8333 0.810031 CGGTGGCTGATTAGGGTTCG 60.810 60.000 0.00 0.00 0.00 3.95
7981 8343 4.671590 TCGAGTCCCGGTGGCTGA 62.672 66.667 0.00 0.00 39.14 4.26
7985 8347 1.666872 GTTTGTCGAGTCCCGGTGG 60.667 63.158 0.00 0.00 39.14 4.61
7999 8361 2.036992 TGGCCAATTAGCTGTTGGTTTG 59.963 45.455 24.85 8.92 46.21 2.93
8008 8370 3.677156 AAGATTCCTGGCCAATTAGCT 57.323 42.857 7.01 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.