Multiple sequence alignment - TraesCS5D01G024100

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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 TraesCS5D01G024100 chr5D 100.000 8129 0 0 1 8129 20957435 20965563 0.000000e+00 15012.0
1 TraesCS5D01G024100 chr5D 99.220 7436 33 6 299 7731 17245044 17237631 0.000000e+00 13387.0
2 TraesCS5D01G024100 chr5D 97.460 315 7 1 1 314 17246133 17245819 3.340000e-148 536.0
3 TraesCS5D01G024100 chr5D 97.959 245 5 0 7784 8028 17237644 17237400 7.540000e-115 425.0
4 TraesCS5D01G024100 chr5D 90.964 166 14 1 1 166 563942649 563942813 1.060000e-53 222.0
5 TraesCS5D01G024100 chr5D 90.361 166 16 0 1 166 188851366 188851531 1.370000e-52 219.0
6 TraesCS5D01G024100 chr5D 97.248 109 3 0 8021 8129 75415149 75415257 1.390000e-42 185.0
7 TraesCS5D01G024100 chr1B 91.507 3768 224 32 1972 5714 80919958 80923654 0.000000e+00 5097.0
8 TraesCS5D01G024100 chr1B 93.710 2655 119 11 3067 5714 80952843 80955456 0.000000e+00 3934.0
9 TraesCS5D01G024100 chr1B 90.536 1680 120 25 5711 7381 80923792 80925441 0.000000e+00 2185.0
10 TraesCS5D01G024100 chr1B 90.578 1677 118 25 5711 7376 80955594 80957241 0.000000e+00 2185.0
11 TraesCS5D01G024100 chr1B 85.215 629 75 6 1972 2585 80952086 80952711 1.490000e-176 630.0
12 TraesCS5D01G024100 chr1B 83.245 567 71 9 1476 2039 80951920 80952465 4.380000e-137 499.0
13 TraesCS5D01G024100 chr1B 83.708 534 63 9 1509 2039 80919825 80920337 4.410000e-132 483.0
14 TraesCS5D01G024100 chr1B 84.286 420 34 14 7390 7778 80958420 80958838 1.660000e-101 381.0
15 TraesCS5D01G024100 chr1B 84.507 142 16 3 3294 3429 80920194 80920335 1.420000e-27 135.0
16 TraesCS5D01G024100 chr1B 84.507 142 16 3 3294 3429 80952322 80952463 1.420000e-27 135.0
17 TraesCS5D01G024100 chr7D 90.361 166 16 0 1 166 159573971 159573806 1.370000e-52 219.0
18 TraesCS5D01G024100 chr7D 90.361 166 16 0 1 166 191373185 191373350 1.370000e-52 219.0
19 TraesCS5D01G024100 chr5A 90.361 166 16 0 1 166 271246093 271246258 1.370000e-52 219.0
20 TraesCS5D01G024100 chr4D 90.361 166 16 0 1 166 96240280 96240115 1.370000e-52 219.0
21 TraesCS5D01G024100 chr4D 98.039 102 2 0 8028 8129 118575261 118575160 2.330000e-40 178.0
22 TraesCS5D01G024100 chr3A 90.361 166 16 0 1 166 682707552 682707387 1.370000e-52 219.0
23 TraesCS5D01G024100 chr2D 90.361 166 16 0 1 166 541324561 541324396 1.370000e-52 219.0
24 TraesCS5D01G024100 chr2D 95.575 113 3 2 8018 8129 56075045 56074934 6.480000e-41 180.0
25 TraesCS5D01G024100 chr2D 96.296 108 4 0 8022 8129 275231531 275231424 2.330000e-40 178.0
26 TraesCS5D01G024100 chr2D 96.296 108 4 0 8022 8129 458715799 458715906 2.330000e-40 178.0
27 TraesCS5D01G024100 chr3D 99.000 100 1 0 8028 8127 518545625 518545526 6.480000e-41 180.0
28 TraesCS5D01G024100 chr7B 98.039 102 2 0 8028 8129 493505050 493504949 2.330000e-40 178.0
29 TraesCS5D01G024100 chr6D 98.039 102 2 0 8028 8129 470655222 470655323 2.330000e-40 178.0
30 TraesCS5D01G024100 chr6D 91.667 60 4 1 7140 7198 370852999 370852940 1.880000e-11 82.4
31 TraesCS5D01G024100 chr2A 93.913 115 7 0 8015 8129 779886557 779886671 3.020000e-39 174.0
32 TraesCS5D01G024100 chr6B 85.714 112 10 2 7140 7251 555959888 555959783 6.670000e-21 113.0


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 TraesCS5D01G024100 chr5D 20957435 20965563 8128 False 15012.000000 15012 100.0000 1 8129 1 chr5D.!!$F1 8128
1 TraesCS5D01G024100 chr5D 17237400 17246133 8733 True 4782.666667 13387 98.2130 1 8028 3 chr5D.!!$R1 8027
2 TraesCS5D01G024100 chr1B 80919825 80925441 5616 False 1975.000000 5097 87.5645 1509 7381 4 chr1B.!!$F1 5872
3 TraesCS5D01G024100 chr1B 80951920 80958838 6918 False 1294.000000 3934 86.9235 1476 7778 6 chr1B.!!$F2 6302

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
513 1305 0.031585 TTCAAAAGCAGCAGCAGCAG 59.968 50.000 12.92 0.0 45.49 4.24 F
539 1331 2.125952 GCATTTGAACTGGGCCGC 60.126 61.111 0.00 0.0 0.00 6.53 F
1670 2465 1.621672 GGAGCAGGAGGAGAAGGTGG 61.622 65.000 0.00 0.0 0.00 4.61 F
2016 2814 1.273495 ACAGAAGAGGAGGATGGAGCA 60.273 52.381 0.00 0.0 0.00 4.26 F
3263 4064 0.905357 TACCTTGGAGGAAGAGCAGC 59.095 55.000 0.07 0.0 37.67 5.25 F
3987 4791 3.584848 AGGAAACTATCTGGCAAGTCACT 59.415 43.478 0.00 0.0 40.61 3.41 F
6331 7278 1.587034 GTCTATTTGCGTCGGTGCTAC 59.413 52.381 0.00 0.0 35.36 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 2406 0.615331 GGAGGCACAAGGAGATGACA 59.385 55.000 0.00 0.0 0.00 3.58 R
2016 2814 1.078848 GAGTTGTCGGATGGCTGCT 60.079 57.895 0.00 0.0 0.00 4.24 R
3263 4064 2.765807 AGTCATGGCCTCCTCCCG 60.766 66.667 3.32 0.0 0.00 5.14 R
3987 4791 2.378038 GGCTGGAGTCAAATGGCAATA 58.622 47.619 0.00 0.0 0.00 1.90 R
6331 7278 5.819379 ACATGACCATAGAGTATGCTGTTTG 59.181 40.000 0.00 0.0 34.85 2.93 R
6674 7621 1.474879 AGCCTCTTCGTGCTAGAGTTC 59.525 52.381 0.00 0.0 37.93 3.01 R
8082 10236 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.0 34.77 3.62 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
49 50 0.106619 ATCTTCGTCCTACGCCTCCT 60.107 55.000 0.00 0.00 42.21 3.69
58 59 1.341531 CCTACGCCTCCTACAGATTGG 59.658 57.143 0.00 0.00 0.00 3.16
75 76 8.706322 ACAGATTGGTAAACTTTAGGTCATTT 57.294 30.769 0.00 0.00 0.00 2.32
185 186 1.070289 ACAGTGGACCGAGGAAGAAAC 59.930 52.381 0.00 0.00 0.00 2.78
287 289 4.373116 GCAACGGACGCCCTGAGA 62.373 66.667 0.00 0.00 0.00 3.27
302 304 5.394883 CGCCCTGAGATACCTAAAGTTGTAA 60.395 44.000 0.00 0.00 0.00 2.41
419 1211 4.213906 TGATATGCGCCATGAACACATTAG 59.786 41.667 4.18 0.00 0.00 1.73
512 1304 0.460722 TTTCAAAAGCAGCAGCAGCA 59.539 45.000 12.92 0.00 45.49 4.41
513 1305 0.031585 TTCAAAAGCAGCAGCAGCAG 59.968 50.000 12.92 0.00 45.49 4.24
539 1331 2.125952 GCATTTGAACTGGGCCGC 60.126 61.111 0.00 0.00 0.00 6.53
585 1377 4.712122 TGTGTGTGAATCGCTATGTCTA 57.288 40.909 0.00 0.00 0.00 2.59
965 1760 4.333926 GCTTTTCTCTCCTCGTAAATGCAT 59.666 41.667 0.00 0.00 34.16 3.96
1670 2465 1.621672 GGAGCAGGAGGAGAAGGTGG 61.622 65.000 0.00 0.00 0.00 4.61
2016 2814 1.273495 ACAGAAGAGGAGGATGGAGCA 60.273 52.381 0.00 0.00 0.00 4.26
3263 4064 0.905357 TACCTTGGAGGAAGAGCAGC 59.095 55.000 0.07 0.00 37.67 5.25
3987 4791 3.584848 AGGAAACTATCTGGCAAGTCACT 59.415 43.478 0.00 0.00 40.61 3.41
6178 7124 6.797540 AGGATGATTATTATGTTGTAGGGGGA 59.202 38.462 0.00 0.00 0.00 4.81
6331 7278 1.587034 GTCTATTTGCGTCGGTGCTAC 59.413 52.381 0.00 0.00 35.36 3.58
6379 7326 6.018832 GTGTGTTGCATGCTAATTTGAGTTTT 60.019 34.615 20.33 0.00 0.00 2.43
6674 7621 2.825264 GGCTCCTCCCCTGAATCG 59.175 66.667 0.00 0.00 0.00 3.34
6927 7877 1.338107 TGCGGATCCCTCGATAACAT 58.662 50.000 6.06 0.00 0.00 2.71
7059 8011 7.643528 ACATCAATGCTATATTGTCGTACTG 57.356 36.000 0.00 0.00 0.00 2.74
7060 8012 7.433680 ACATCAATGCTATATTGTCGTACTGA 58.566 34.615 0.00 0.00 0.00 3.41
7061 8013 7.926018 ACATCAATGCTATATTGTCGTACTGAA 59.074 33.333 0.00 0.00 0.00 3.02
7062 8014 8.929746 CATCAATGCTATATTGTCGTACTGAAT 58.070 33.333 0.00 0.00 0.00 2.57
7742 9896 3.403057 CAACAGCGTCGTCCGTGG 61.403 66.667 0.00 0.00 39.32 4.94
7767 9921 0.318762 AGTCTGAGGCTTGACGGTTC 59.681 55.000 13.34 0.00 38.16 3.62
7778 9932 4.715523 ACGGTTCATGGTGCGGGG 62.716 66.667 0.00 0.00 0.00 5.73
7779 9933 4.715523 CGGTTCATGGTGCGGGGT 62.716 66.667 0.00 0.00 0.00 4.95
7780 9934 2.282887 GGTTCATGGTGCGGGGTT 60.283 61.111 0.00 0.00 0.00 4.11
7781 9935 2.635443 GGTTCATGGTGCGGGGTTG 61.635 63.158 0.00 0.00 0.00 3.77
7782 9936 2.988684 TTCATGGTGCGGGGTTGC 60.989 61.111 0.00 0.00 0.00 4.17
7792 9946 4.424711 GGGGTTGCCGATGCTGGA 62.425 66.667 0.00 0.00 38.71 3.86
7793 9947 2.124151 GGGTTGCCGATGCTGGAT 60.124 61.111 0.00 0.00 38.71 3.41
7794 9948 2.189499 GGGTTGCCGATGCTGGATC 61.189 63.158 0.00 0.00 38.71 3.36
7795 9949 1.451927 GGTTGCCGATGCTGGATCA 60.452 57.895 9.85 0.00 38.71 2.92
7796 9950 1.442526 GGTTGCCGATGCTGGATCAG 61.443 60.000 9.85 0.00 38.71 2.90
7943 10097 2.270434 AGGCCCCTTAGAATGACAGA 57.730 50.000 0.00 0.00 0.00 3.41
8031 10185 9.667607 AATATAGATAGGAGTATGAATCAGGGG 57.332 37.037 0.00 0.00 0.00 4.79
8032 10186 4.693420 AGATAGGAGTATGAATCAGGGGG 58.307 47.826 0.00 0.00 0.00 5.40
8033 10187 2.897823 AGGAGTATGAATCAGGGGGT 57.102 50.000 0.00 0.00 0.00 4.95
8034 10188 2.412591 AGGAGTATGAATCAGGGGGTG 58.587 52.381 0.00 0.00 0.00 4.61
8035 10189 2.127708 GGAGTATGAATCAGGGGGTGT 58.872 52.381 0.00 0.00 0.00 4.16
8036 10190 2.509964 GGAGTATGAATCAGGGGGTGTT 59.490 50.000 0.00 0.00 0.00 3.32
8037 10191 3.053619 GGAGTATGAATCAGGGGGTGTTT 60.054 47.826 0.00 0.00 0.00 2.83
8038 10192 3.947834 GAGTATGAATCAGGGGGTGTTTG 59.052 47.826 0.00 0.00 0.00 2.93
8039 10193 2.236489 ATGAATCAGGGGGTGTTTGG 57.764 50.000 0.00 0.00 0.00 3.28
8040 10194 0.856982 TGAATCAGGGGGTGTTTGGT 59.143 50.000 0.00 0.00 0.00 3.67
8041 10195 1.219213 TGAATCAGGGGGTGTTTGGTT 59.781 47.619 0.00 0.00 0.00 3.67
8042 10196 1.893137 GAATCAGGGGGTGTTTGGTTC 59.107 52.381 0.00 0.00 0.00 3.62
8043 10197 0.856982 ATCAGGGGGTGTTTGGTTCA 59.143 50.000 0.00 0.00 0.00 3.18
8044 10198 0.184933 TCAGGGGGTGTTTGGTTCAG 59.815 55.000 0.00 0.00 0.00 3.02
8045 10199 0.827507 CAGGGGGTGTTTGGTTCAGG 60.828 60.000 0.00 0.00 0.00 3.86
8046 10200 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
8047 10201 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
8048 10202 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
8049 10203 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
8050 10204 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
8051 10205 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
8052 10206 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
8053 10207 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
8054 10208 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
8055 10209 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
8056 10210 4.098807 TGTTTGGTTCAGGGACTTTTTAGC 59.901 41.667 0.00 0.00 34.60 3.09
8057 10211 2.871453 TGGTTCAGGGACTTTTTAGCC 58.129 47.619 0.00 0.00 34.60 3.93
8058 10212 2.168496 GGTTCAGGGACTTTTTAGCCC 58.832 52.381 0.00 0.00 42.37 5.19
8059 10213 2.168496 GTTCAGGGACTTTTTAGCCCC 58.832 52.381 0.00 0.00 43.08 5.80
8060 10214 1.451449 TCAGGGACTTTTTAGCCCCA 58.549 50.000 0.00 0.00 43.08 4.96
8061 10215 1.354368 TCAGGGACTTTTTAGCCCCAG 59.646 52.381 0.00 0.00 43.08 4.45
8062 10216 1.354368 CAGGGACTTTTTAGCCCCAGA 59.646 52.381 0.00 0.00 43.08 3.86
8063 10217 1.636003 AGGGACTTTTTAGCCCCAGAG 59.364 52.381 0.00 0.00 43.08 3.35
8064 10218 1.633945 GGGACTTTTTAGCCCCAGAGA 59.366 52.381 0.00 0.00 38.69 3.10
8065 10219 2.618302 GGGACTTTTTAGCCCCAGAGAC 60.618 54.545 0.00 0.00 38.69 3.36
8066 10220 2.306219 GGACTTTTTAGCCCCAGAGACT 59.694 50.000 0.00 0.00 0.00 3.24
8067 10221 3.518303 GGACTTTTTAGCCCCAGAGACTA 59.482 47.826 0.00 0.00 0.00 2.59
8068 10222 4.383226 GGACTTTTTAGCCCCAGAGACTAG 60.383 50.000 0.00 0.00 0.00 2.57
8069 10223 4.426704 ACTTTTTAGCCCCAGAGACTAGA 58.573 43.478 0.00 0.00 0.00 2.43
8070 10224 4.844655 ACTTTTTAGCCCCAGAGACTAGAA 59.155 41.667 0.00 0.00 0.00 2.10
8071 10225 5.309806 ACTTTTTAGCCCCAGAGACTAGAAA 59.690 40.000 0.00 0.00 0.00 2.52
8072 10226 5.836024 TTTTAGCCCCAGAGACTAGAAAA 57.164 39.130 0.00 0.00 0.00 2.29
8073 10227 5.836024 TTTAGCCCCAGAGACTAGAAAAA 57.164 39.130 0.00 0.00 0.00 1.94
8074 10228 3.990959 AGCCCCAGAGACTAGAAAAAG 57.009 47.619 0.00 0.00 0.00 2.27
8075 10229 3.252351 AGCCCCAGAGACTAGAAAAAGT 58.748 45.455 0.00 0.00 0.00 2.66
8076 10230 3.653352 AGCCCCAGAGACTAGAAAAAGTT 59.347 43.478 0.00 0.00 0.00 2.66
8077 10231 4.004314 GCCCCAGAGACTAGAAAAAGTTC 58.996 47.826 0.00 0.00 0.00 3.01
8078 10232 4.580868 CCCCAGAGACTAGAAAAAGTTCC 58.419 47.826 0.00 0.00 33.92 3.62
8079 10233 4.287326 CCCCAGAGACTAGAAAAAGTTCCT 59.713 45.833 0.00 0.00 33.92 3.36
8080 10234 5.484290 CCCCAGAGACTAGAAAAAGTTCCTA 59.516 44.000 0.00 0.00 33.92 2.94
8081 10235 6.351456 CCCCAGAGACTAGAAAAAGTTCCTAG 60.351 46.154 0.00 0.00 33.92 3.02
8082 10236 6.351456 CCCAGAGACTAGAAAAAGTTCCTAGG 60.351 46.154 0.82 0.82 33.92 3.02
8083 10237 6.437793 CCAGAGACTAGAAAAAGTTCCTAGGA 59.562 42.308 7.62 7.62 33.92 2.94
8084 10238 7.038941 CCAGAGACTAGAAAAAGTTCCTAGGAA 60.039 40.741 20.72 20.72 33.92 3.36
8093 10247 1.817357 GTTCCTAGGAACCAAACGGG 58.183 55.000 35.48 0.00 46.21 5.28
8094 10248 1.348696 GTTCCTAGGAACCAAACGGGA 59.651 52.381 35.48 5.90 46.21 5.14
8095 10249 1.272807 TCCTAGGAACCAAACGGGAG 58.727 55.000 9.71 0.00 41.15 4.30
8096 10250 0.252197 CCTAGGAACCAAACGGGAGG 59.748 60.000 1.05 0.00 41.15 4.30
8097 10251 0.252197 CTAGGAACCAAACGGGAGGG 59.748 60.000 0.00 0.00 41.15 4.30
8098 10252 0.178897 TAGGAACCAAACGGGAGGGA 60.179 55.000 0.00 0.00 41.15 4.20
8099 10253 1.303074 GGAACCAAACGGGAGGGAC 60.303 63.158 0.00 0.00 41.15 4.46
8101 10255 0.109913 GAACCAAACGGGAGGGACTT 59.890 55.000 0.00 0.00 41.55 3.01
8102 10256 0.554305 AACCAAACGGGAGGGACTTT 59.446 50.000 0.00 0.00 41.55 2.66
8103 10257 0.554305 ACCAAACGGGAGGGACTTTT 59.446 50.000 0.00 0.00 41.55 2.27
8104 10258 1.063492 ACCAAACGGGAGGGACTTTTT 60.063 47.619 0.00 0.00 41.55 1.94
8105 10259 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
8106 10260 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
8107 10261 3.497227 CCAAACGGGAGGGACTTTTTCTA 60.497 47.826 0.00 0.00 41.55 2.10
8108 10262 3.413846 AACGGGAGGGACTTTTTCTAC 57.586 47.619 0.00 0.00 41.55 2.59
8109 10263 2.332117 ACGGGAGGGACTTTTTCTACA 58.668 47.619 0.00 0.00 41.55 2.74
8110 10264 2.302157 ACGGGAGGGACTTTTTCTACAG 59.698 50.000 0.00 0.00 41.55 2.74
8111 10265 2.354805 CGGGAGGGACTTTTTCTACAGG 60.355 54.545 0.00 0.00 41.55 4.00
8112 10266 2.026169 GGGAGGGACTTTTTCTACAGGG 60.026 54.545 0.00 0.00 41.55 4.45
8113 10267 2.910977 GGAGGGACTTTTTCTACAGGGA 59.089 50.000 0.00 0.00 41.55 4.20
8114 10268 3.307550 GGAGGGACTTTTTCTACAGGGAC 60.308 52.174 0.00 0.00 41.55 4.46
8115 10269 3.583526 GAGGGACTTTTTCTACAGGGACT 59.416 47.826 0.00 0.00 41.55 3.85
8116 10270 4.759953 AGGGACTTTTTCTACAGGGACTA 58.240 43.478 0.00 0.00 28.08 2.59
8117 10271 4.778427 AGGGACTTTTTCTACAGGGACTAG 59.222 45.833 0.00 0.00 28.08 2.57
8118 10272 4.776308 GGGACTTTTTCTACAGGGACTAGA 59.224 45.833 0.00 0.00 36.02 2.43
8119 10273 5.247792 GGGACTTTTTCTACAGGGACTAGAA 59.752 44.000 0.00 0.00 36.02 2.10
8120 10274 6.239800 GGGACTTTTTCTACAGGGACTAGAAA 60.240 42.308 0.00 0.00 38.08 2.52
8121 10275 7.222161 GGACTTTTTCTACAGGGACTAGAAAA 58.778 38.462 0.00 8.58 43.60 2.29
8125 10279 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
8126 10280 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
8127 10281 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
8128 10282 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.802039 AAATGACCTAAAGTTTACCAATCTGTA 57.198 29.630 0.00 0.00 0.00 2.74
58 59 9.498176 TCCTCAAGTAAATGACCTAAAGTTTAC 57.502 33.333 0.00 0.00 37.32 2.01
75 76 9.959721 AGAATAGTAGCAATTTTTCCTCAAGTA 57.040 29.630 0.00 0.00 0.00 2.24
185 186 3.498397 GGCCTTGGATAACATGACATACG 59.502 47.826 0.00 0.00 0.00 3.06
287 289 4.141779 CCCTCGGCTTACAACTTTAGGTAT 60.142 45.833 0.00 0.00 0.00 2.73
302 304 2.770048 CCCTCCATTCCCTCGGCT 60.770 66.667 0.00 0.00 0.00 5.52
516 1308 1.532437 GCCCAGTTCAAATGCTTTTGC 59.468 47.619 17.79 7.23 41.66 3.68
517 1309 2.145536 GGCCCAGTTCAAATGCTTTTG 58.854 47.619 16.77 16.77 42.98 2.44
835 1630 0.937699 TAATTGTAGCTAGCGCGGCG 60.938 55.000 19.62 19.62 42.32 6.46
965 1760 2.023015 TCATAGGCAAGGAGAGGAAGGA 60.023 50.000 0.00 0.00 0.00 3.36
1611 2406 0.615331 GGAGGCACAAGGAGATGACA 59.385 55.000 0.00 0.00 0.00 3.58
1670 2465 1.269723 CCTCCTTTTCCGTTTCCTTGC 59.730 52.381 0.00 0.00 0.00 4.01
1963 2761 1.661463 TCACCTCCTGCTCCTGAATT 58.339 50.000 0.00 0.00 0.00 2.17
2016 2814 1.078848 GAGTTGTCGGATGGCTGCT 60.079 57.895 0.00 0.00 0.00 4.24
3263 4064 2.765807 AGTCATGGCCTCCTCCCG 60.766 66.667 3.32 0.00 0.00 5.14
3987 4791 2.378038 GGCTGGAGTCAAATGGCAATA 58.622 47.619 0.00 0.00 0.00 1.90
6331 7278 5.819379 ACATGACCATAGAGTATGCTGTTTG 59.181 40.000 0.00 0.00 34.85 2.93
6379 7326 4.399934 TCATATACCACTGCTTCACGTACA 59.600 41.667 0.00 0.00 0.00 2.90
6674 7621 1.474879 AGCCTCTTCGTGCTAGAGTTC 59.525 52.381 0.00 0.00 37.93 3.01
6834 7781 4.158579 GGAGCTTTGGTCCCTAATTTGAAG 59.841 45.833 4.60 0.00 43.62 3.02
6927 7877 3.945346 TGCTAATTTCCGCTGAACCTTA 58.055 40.909 0.00 0.00 0.00 2.69
7059 8011 4.635765 TCAAGTAACCATGCTGCACTATTC 59.364 41.667 3.57 0.00 0.00 1.75
7060 8012 4.396166 GTCAAGTAACCATGCTGCACTATT 59.604 41.667 3.57 1.70 0.00 1.73
7061 8013 3.941483 GTCAAGTAACCATGCTGCACTAT 59.059 43.478 3.57 0.00 0.00 2.12
7062 8014 3.244387 TGTCAAGTAACCATGCTGCACTA 60.244 43.478 3.57 0.00 0.00 2.74
7063 8015 2.154462 GTCAAGTAACCATGCTGCACT 58.846 47.619 3.57 0.00 0.00 4.40
7236 8193 1.972075 TCCAAGGTACATGAACCACGA 59.028 47.619 0.00 0.00 42.40 4.35
7382 8339 2.650322 ACCAACCTTTGAACATGACGT 58.350 42.857 0.00 0.00 0.00 4.34
7506 9631 1.703411 ACACATGTTTTCACCCCCAG 58.297 50.000 0.00 0.00 0.00 4.45
7734 9888 3.450115 GACTCCCCTCCACGGACG 61.450 72.222 0.00 0.00 33.16 4.79
7738 9892 2.055042 CCTCAGACTCCCCTCCACG 61.055 68.421 0.00 0.00 0.00 4.94
7742 9896 0.616111 TCAAGCCTCAGACTCCCCTC 60.616 60.000 0.00 0.00 0.00 4.30
7778 9932 0.745845 ACTGATCCAGCATCGGCAAC 60.746 55.000 0.00 0.00 41.24 4.17
7779 9933 0.462581 GACTGATCCAGCATCGGCAA 60.463 55.000 0.00 0.00 41.24 4.52
7780 9934 1.144716 GACTGATCCAGCATCGGCA 59.855 57.895 0.00 0.00 41.24 5.69
7781 9935 0.879400 CAGACTGATCCAGCATCGGC 60.879 60.000 0.00 0.00 41.24 5.54
7782 9936 0.249784 CCAGACTGATCCAGCATCGG 60.250 60.000 3.32 0.00 43.02 4.18
7783 9937 0.463204 ACCAGACTGATCCAGCATCG 59.537 55.000 3.32 0.00 34.37 3.84
7784 9938 1.474677 CCACCAGACTGATCCAGCATC 60.475 57.143 3.32 0.00 34.37 3.91
7785 9939 0.545171 CCACCAGACTGATCCAGCAT 59.455 55.000 3.32 0.00 34.37 3.79
7786 9940 0.545071 TCCACCAGACTGATCCAGCA 60.545 55.000 3.32 0.00 34.37 4.41
7787 9941 0.615331 TTCCACCAGACTGATCCAGC 59.385 55.000 3.32 0.00 34.37 4.85
7788 9942 1.209019 CCTTCCACCAGACTGATCCAG 59.791 57.143 3.32 0.00 37.52 3.86
7789 9943 1.203300 TCCTTCCACCAGACTGATCCA 60.203 52.381 3.32 0.00 0.00 3.41
7790 9944 1.484240 CTCCTTCCACCAGACTGATCC 59.516 57.143 3.32 0.00 0.00 3.36
7791 9945 1.484240 CCTCCTTCCACCAGACTGATC 59.516 57.143 3.32 0.00 0.00 2.92
7792 9946 1.203364 ACCTCCTTCCACCAGACTGAT 60.203 52.381 3.32 0.00 0.00 2.90
7793 9947 0.191064 ACCTCCTTCCACCAGACTGA 59.809 55.000 3.32 0.00 0.00 3.41
7794 9948 1.059913 AACCTCCTTCCACCAGACTG 58.940 55.000 0.00 0.00 0.00 3.51
7795 9949 1.821088 AAACCTCCTTCCACCAGACT 58.179 50.000 0.00 0.00 0.00 3.24
7796 9950 2.904434 TCTAAACCTCCTTCCACCAGAC 59.096 50.000 0.00 0.00 0.00 3.51
7927 10081 6.678568 ATATCTGTCTGTCATTCTAAGGGG 57.321 41.667 0.00 0.00 0.00 4.79
7943 10097 5.665701 TCCCTCCCTGCTAATAATATCTGT 58.334 41.667 0.00 0.00 0.00 3.41
8028 10182 1.533033 CCCTGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
8029 10183 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
8030 10184 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
8031 10185 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
8032 10186 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
8033 10187 4.098807 GCTAAAAAGTCCCTGAACCAAACA 59.901 41.667 0.00 0.00 0.00 2.83
8034 10188 4.500887 GGCTAAAAAGTCCCTGAACCAAAC 60.501 45.833 0.00 0.00 0.00 2.93
8035 10189 3.639561 GGCTAAAAAGTCCCTGAACCAAA 59.360 43.478 0.00 0.00 0.00 3.28
8036 10190 3.227614 GGCTAAAAAGTCCCTGAACCAA 58.772 45.455 0.00 0.00 0.00 3.67
8037 10191 2.490168 GGGCTAAAAAGTCCCTGAACCA 60.490 50.000 0.00 0.00 37.08 3.67
8038 10192 2.168496 GGGCTAAAAAGTCCCTGAACC 58.832 52.381 0.00 0.00 37.08 3.62
8045 10199 2.306219 AGTCTCTGGGGCTAAAAAGTCC 59.694 50.000 0.00 0.00 0.00 3.85
8046 10200 3.704800 AGTCTCTGGGGCTAAAAAGTC 57.295 47.619 0.00 0.00 0.00 3.01
8047 10201 4.426704 TCTAGTCTCTGGGGCTAAAAAGT 58.573 43.478 0.00 0.00 0.00 2.66
8048 10202 5.422214 TTCTAGTCTCTGGGGCTAAAAAG 57.578 43.478 0.00 0.00 0.00 2.27
8049 10203 5.836024 TTTCTAGTCTCTGGGGCTAAAAA 57.164 39.130 0.00 0.00 0.00 1.94
8050 10204 5.836024 TTTTCTAGTCTCTGGGGCTAAAA 57.164 39.130 0.00 0.00 0.00 1.52
8051 10205 5.309806 ACTTTTTCTAGTCTCTGGGGCTAAA 59.690 40.000 0.00 0.00 0.00 1.85
8052 10206 4.844655 ACTTTTTCTAGTCTCTGGGGCTAA 59.155 41.667 0.00 0.00 0.00 3.09
8053 10207 4.426704 ACTTTTTCTAGTCTCTGGGGCTA 58.573 43.478 0.00 0.00 0.00 3.93
8054 10208 3.252351 ACTTTTTCTAGTCTCTGGGGCT 58.748 45.455 0.00 0.00 0.00 5.19
8055 10209 3.704800 ACTTTTTCTAGTCTCTGGGGC 57.295 47.619 0.00 0.00 0.00 5.80
8056 10210 4.287326 AGGAACTTTTTCTAGTCTCTGGGG 59.713 45.833 0.00 0.00 27.25 4.96
8057 10211 5.491323 AGGAACTTTTTCTAGTCTCTGGG 57.509 43.478 0.00 0.00 27.25 4.45
8058 10212 6.437793 TCCTAGGAACTTTTTCTAGTCTCTGG 59.562 42.308 9.71 0.00 41.75 3.86
8059 10213 7.469537 TCCTAGGAACTTTTTCTAGTCTCTG 57.530 40.000 9.71 0.00 41.75 3.35
8075 10229 1.626825 CTCCCGTTTGGTTCCTAGGAA 59.373 52.381 20.72 20.72 34.77 3.36
8076 10230 1.272807 CTCCCGTTTGGTTCCTAGGA 58.727 55.000 7.62 7.62 34.77 2.94
8077 10231 0.252197 CCTCCCGTTTGGTTCCTAGG 59.748 60.000 0.82 0.82 34.77 3.02
8078 10232 0.252197 CCCTCCCGTTTGGTTCCTAG 59.748 60.000 0.00 0.00 34.77 3.02
8079 10233 0.178897 TCCCTCCCGTTTGGTTCCTA 60.179 55.000 0.00 0.00 34.77 2.94
8080 10234 1.462627 TCCCTCCCGTTTGGTTCCT 60.463 57.895 0.00 0.00 34.77 3.36
8081 10235 1.303074 GTCCCTCCCGTTTGGTTCC 60.303 63.158 0.00 0.00 34.77 3.62
8082 10236 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.00 34.77 3.62
8083 10237 0.554305 AAAGTCCCTCCCGTTTGGTT 59.446 50.000 0.00 0.00 34.77 3.67
8084 10238 0.554305 AAAAGTCCCTCCCGTTTGGT 59.446 50.000 0.00 0.00 34.77 3.67
8085 10239 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
8086 10240 2.583143 AGAAAAAGTCCCTCCCGTTTG 58.417 47.619 0.00 0.00 0.00 2.93
8087 10241 3.136992 TGTAGAAAAAGTCCCTCCCGTTT 59.863 43.478 0.00 0.00 0.00 3.60
8088 10242 2.707257 TGTAGAAAAAGTCCCTCCCGTT 59.293 45.455 0.00 0.00 0.00 4.44
8089 10243 2.302157 CTGTAGAAAAAGTCCCTCCCGT 59.698 50.000 0.00 0.00 0.00 5.28
8090 10244 2.354805 CCTGTAGAAAAAGTCCCTCCCG 60.355 54.545 0.00 0.00 0.00 5.14
8091 10245 2.026169 CCCTGTAGAAAAAGTCCCTCCC 60.026 54.545 0.00 0.00 0.00 4.30
8092 10246 2.910977 TCCCTGTAGAAAAAGTCCCTCC 59.089 50.000 0.00 0.00 0.00 4.30
8093 10247 3.583526 AGTCCCTGTAGAAAAAGTCCCTC 59.416 47.826 0.00 0.00 0.00 4.30
8094 10248 3.599348 AGTCCCTGTAGAAAAAGTCCCT 58.401 45.455 0.00 0.00 0.00 4.20
8095 10249 4.776308 TCTAGTCCCTGTAGAAAAAGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
8096 10250 5.997384 TCTAGTCCCTGTAGAAAAAGTCC 57.003 43.478 0.00 0.00 0.00 3.85
8102 10256 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
8103 10257 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
8104 10258 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
8105 10259 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.