Multiple sequence alignment - TraesCS1D01G207600

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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 TraesCS1D01G207600 chr1D 100.000 6465 0 0 1 6465 293913173 293906709 0.000000e+00 11939
1 TraesCS1D01G207600 chr1D 91.608 143 9 3 5545 5686 293907490 293907350 1.840000e-45 195
2 TraesCS1D01G207600 chr1D 91.608 143 9 3 5684 5824 293907629 293907488 1.840000e-45 195
3 TraesCS1D01G207600 chr1A 95.325 2738 84 14 3757 6465 366270940 366268218 0.000000e+00 4307
4 TraesCS1D01G207600 chr1A 88.948 2461 124 44 825 3191 366273958 366271552 0.000000e+00 2902
5 TraesCS1D01G207600 chr1A 95.066 527 17 6 3242 3761 366271565 366271041 0.000000e+00 821
6 TraesCS1D01G207600 chr1A 91.400 407 14 9 424 826 366274508 366274119 7.380000e-149 538
7 TraesCS1D01G207600 chr1A 95.046 323 9 4 1 318 366275534 366275214 9.680000e-138 501
8 TraesCS1D01G207600 chr1A 90.411 146 8 4 5545 5686 366268996 366268853 3.080000e-43 187
9 TraesCS1D01G207600 chr1B 95.142 2676 102 17 3800 6465 395248916 395246259 0.000000e+00 4196
10 TraesCS1D01G207600 chr1B 94.924 2423 95 17 4053 6465 395258169 395255765 0.000000e+00 3768
11 TraesCS1D01G207600 chr1B 91.593 2272 85 41 972 3191 395251782 395249565 0.000000e+00 3040
12 TraesCS1D01G207600 chr1B 93.509 647 21 9 318 955 395252705 395252071 0.000000e+00 942
13 TraesCS1D01G207600 chr1B 96.085 562 18 3 3242 3801 395249579 395249020 0.000000e+00 913
14 TraesCS1D01G207600 chr1B 92.923 325 13 5 1 318 395253118 395252797 1.270000e-126 464
15 TraesCS1D01G207600 chr1B 91.608 143 9 3 5545 5686 395247044 395246904 1.840000e-45 195
16 TraesCS1D01G207600 chr1B 91.608 143 9 3 5545 5686 395256550 395256410 1.840000e-45 195
17 TraesCS1D01G207600 chrUn 94.924 2423 95 17 4053 6465 296013112 296010708 0.000000e+00 3768
18 TraesCS1D01G207600 chrUn 91.608 143 9 3 5545 5686 296011493 296011353 1.840000e-45 195
19 TraesCS1D01G207600 chr5B 85.580 319 38 6 3787 4104 603454024 603454335 1.740000e-85 327
20 TraesCS1D01G207600 chr6D 84.768 151 17 4 2464 2608 10811108 10810958 5.220000e-31 147
21 TraesCS1D01G207600 chr6B 80.978 184 28 5 4076 4252 558825495 558825312 8.740000e-29 139
22 TraesCS1D01G207600 chr6B 80.978 184 28 5 4076 4252 558903851 558903668 8.740000e-29 139
23 TraesCS1D01G207600 chr6B 80.435 184 29 5 4076 4252 558742912 558742729 4.070000e-27 134
24 TraesCS1D01G207600 chr2B 78.889 180 31 6 4079 4252 746033783 746033961 1.470000e-21 115


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 TraesCS1D01G207600 chr1D 293906709 293913173 6464 True 11939.000000 11939 100.000000 1 6465 1 chr1D.!!$R1 6464
1 TraesCS1D01G207600 chr1A 366268218 366275534 7316 True 1542.666667 4307 92.699333 1 6465 6 chr1A.!!$R1 6464
2 TraesCS1D01G207600 chr1B 395246259 395258169 11910 True 1714.125000 4196 93.424000 1 6465 8 chr1B.!!$R1 6464
3 TraesCS1D01G207600 chrUn 296010708 296013112 2404 True 1981.500000 3768 93.266000 4053 6465 2 chrUn.!!$R1 2412

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
970 6835 2.018086 AGGAGAGAGGGAGAGGGGG 61.018 68.421 0.00 0.0 0.00 5.40 F
1417 7524 0.468226 TCGTTGGCTTCTTCCTGTGT 59.532 50.000 0.00 0.0 0.00 3.72 F
2911 9099 0.108804 CGCCTCTCTCGCCAACTTTA 60.109 55.000 0.00 0.0 0.00 1.85 F
3455 9650 0.044092 TGGAGATGGCCACCCTTCTA 59.956 55.000 8.16 0.0 43.53 2.10 F
3614 9813 0.176910 GGCTAAGACTCCCAGCTCAC 59.823 60.000 0.00 0.0 35.60 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 7936 0.319900 CACCCAAGACGAGACACTGG 60.320 60.0 0.00 0.0 0.00 4.00 R
3240 9434 0.107017 ACCTGCAGAGCACAAACAGT 60.107 50.0 17.39 0.0 33.79 3.55 R
4340 10694 0.894835 TCACGGTCAGCTGCATAGAA 59.105 50.0 9.47 0.0 0.00 2.10 R
5224 11581 0.538287 ACAAGCCAGGCTGAAACCTC 60.538 55.0 17.05 0.0 39.62 3.85 R
5578 11956 5.647658 CACTATTTGCTGTCCCTATTTGTCA 59.352 40.0 0.00 0.0 0.00 3.58 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
137 5189 3.347216 GGCTAGAAGTGGAATTGCAAGA 58.653 45.455 4.94 0.00 0.00 3.02
297 5356 6.144724 GGAGAGATATCTGTTGCGTTTCATAC 59.855 42.308 10.74 0.00 0.00 2.39
573 6235 4.252073 CCAGACACATCTCTTTCCTTCAG 58.748 47.826 0.00 0.00 30.42 3.02
601 6263 2.799978 CCAAACCGCCTTTCATTTTGTC 59.200 45.455 0.00 0.00 0.00 3.18
720 6388 6.770303 TGTTGATCGGAAATAAATATGCTCCA 59.230 34.615 0.00 0.00 0.00 3.86
726 6394 7.284074 TCGGAAATAAATATGCTCCACCTTTA 58.716 34.615 0.00 0.00 0.00 1.85
727 6395 7.942341 TCGGAAATAAATATGCTCCACCTTTAT 59.058 33.333 0.00 0.00 0.00 1.40
728 6396 8.237267 CGGAAATAAATATGCTCCACCTTTATC 58.763 37.037 0.00 0.00 0.00 1.75
729 6397 8.237267 GGAAATAAATATGCTCCACCTTTATCG 58.763 37.037 0.00 0.00 0.00 2.92
760 6428 2.494059 CTTCTTTTCCTGCCTTGTCGA 58.506 47.619 0.00 0.00 0.00 4.20
783 6451 5.827568 TTTAACCACGTCGATCTTTGTAC 57.172 39.130 0.00 0.00 0.00 2.90
956 6786 3.193267 GCAGCATAGACATAGGAGAGGAG 59.807 52.174 0.00 0.00 0.00 3.69
970 6835 2.018086 AGGAGAGAGGGAGAGGGGG 61.018 68.421 0.00 0.00 0.00 5.40
1216 7317 1.982073 CTCCGCATCCGTTTCTTGGC 61.982 60.000 0.00 0.00 0.00 4.52
1270 7375 1.536073 TTCAGCCGAGTCCAGGTGAG 61.536 60.000 9.04 0.00 0.00 3.51
1271 7376 2.681778 AGCCGAGTCCAGGTGAGG 60.682 66.667 0.00 0.00 0.00 3.86
1272 7377 2.997897 GCCGAGTCCAGGTGAGGT 60.998 66.667 0.00 0.00 0.00 3.85
1273 7378 2.973899 CCGAGTCCAGGTGAGGTG 59.026 66.667 0.00 0.00 0.00 4.00
1274 7379 1.606601 CCGAGTCCAGGTGAGGTGA 60.607 63.158 0.00 0.00 0.00 4.02
1285 7390 1.410882 GGTGAGGTGATCCAGCTAGAC 59.589 57.143 0.00 0.09 42.53 2.59
1333 7438 4.421479 GCTGCTGCTTGCCTGCTG 62.421 66.667 8.53 8.80 42.00 4.41
1365 7472 6.187682 TGTGCTAGGAGATATCGGATCAATA 58.812 40.000 0.00 0.00 0.00 1.90
1396 7503 4.152402 GCCGTATCCTGTATGTTTGCTATG 59.848 45.833 0.00 0.00 0.00 2.23
1412 7519 2.096013 GCTATGTTCGTTGGCTTCTTCC 59.904 50.000 0.00 0.00 0.00 3.46
1414 7521 1.593196 TGTTCGTTGGCTTCTTCCTG 58.407 50.000 0.00 0.00 0.00 3.86
1415 7522 1.134220 TGTTCGTTGGCTTCTTCCTGT 60.134 47.619 0.00 0.00 0.00 4.00
1416 7523 1.264288 GTTCGTTGGCTTCTTCCTGTG 59.736 52.381 0.00 0.00 0.00 3.66
1417 7524 0.468226 TCGTTGGCTTCTTCCTGTGT 59.532 50.000 0.00 0.00 0.00 3.72
1419 7526 1.264288 CGTTGGCTTCTTCCTGTGTTC 59.736 52.381 0.00 0.00 0.00 3.18
1446 7554 0.611062 AGCAGTACGTGAGGCTGGTA 60.611 55.000 0.00 0.00 43.35 3.25
1464 7572 3.097614 GGTAAGACTGTAGGAAGGAGCA 58.902 50.000 0.00 0.00 0.00 4.26
1570 7678 0.671251 CTTCTAGCTAGCCTCCACCG 59.329 60.000 16.35 0.00 0.00 4.94
1628 7743 1.017387 GGAATAGTTGCTTCTGGCCG 58.983 55.000 0.00 0.00 40.92 6.13
1700 7818 2.198827 TTCCGTGAGCCATTGAATGT 57.801 45.000 4.27 0.00 0.00 2.71
1812 7936 1.999024 GACTTTGAGCTAGCAGCAGTC 59.001 52.381 18.83 17.11 45.56 3.51
1813 7937 1.338579 ACTTTGAGCTAGCAGCAGTCC 60.339 52.381 18.83 0.00 45.56 3.85
1814 7938 0.686789 TTTGAGCTAGCAGCAGTCCA 59.313 50.000 18.83 0.00 45.56 4.02
1815 7939 0.248565 TTGAGCTAGCAGCAGTCCAG 59.751 55.000 18.83 0.00 45.56 3.86
1816 7940 0.902048 TGAGCTAGCAGCAGTCCAGT 60.902 55.000 18.83 0.00 45.56 4.00
1817 7941 0.459934 GAGCTAGCAGCAGTCCAGTG 60.460 60.000 18.83 0.00 45.56 3.66
1818 7942 1.190833 AGCTAGCAGCAGTCCAGTGT 61.191 55.000 18.83 0.00 45.56 3.55
1819 7943 0.739112 GCTAGCAGCAGTCCAGTGTC 60.739 60.000 10.63 0.00 41.89 3.67
1820 7944 0.894141 CTAGCAGCAGTCCAGTGTCT 59.106 55.000 0.00 0.00 0.00 3.41
1902 8026 1.618861 CGAGATCTCGCTTTTGTCGT 58.381 50.000 30.41 0.00 46.50 4.34
2093 8256 5.301298 AGAAAAGTCGTTGGTACTGACTACT 59.699 40.000 9.75 6.01 37.25 2.57
2115 8278 6.955364 ACTACTACTACTACCAGTGTCATCA 58.045 40.000 0.00 0.00 0.00 3.07
2116 8279 7.049133 ACTACTACTACTACCAGTGTCATCAG 58.951 42.308 0.00 0.00 0.00 2.90
2153 8317 2.029918 CAGGAAAACTAACCCAAGCAGC 60.030 50.000 0.00 0.00 0.00 5.25
2174 8338 3.131223 GCCCTCATTCTTTAGCCCTTTTC 59.869 47.826 0.00 0.00 0.00 2.29
2175 8339 4.604156 CCCTCATTCTTTAGCCCTTTTCT 58.396 43.478 0.00 0.00 0.00 2.52
2176 8340 5.019470 CCCTCATTCTTTAGCCCTTTTCTT 58.981 41.667 0.00 0.00 0.00 2.52
2182 8348 6.650427 TTCTTTAGCCCTTTTCTTTTCTCC 57.350 37.500 0.00 0.00 0.00 3.71
2292 8458 0.310543 TGTGACGGCACTGAAAATGC 59.689 50.000 24.38 0.00 45.36 3.56
2294 8460 1.797537 GACGGCACTGAAAATGCGC 60.798 57.895 0.00 0.00 44.37 6.09
2492 8665 2.111878 AAGCAGAAGCCAGCGTGT 59.888 55.556 0.00 0.00 43.56 4.49
2493 8666 0.950555 CAAGCAGAAGCCAGCGTGTA 60.951 55.000 0.00 0.00 43.56 2.90
2494 8667 0.951040 AAGCAGAAGCCAGCGTGTAC 60.951 55.000 0.00 0.00 43.56 2.90
2498 8671 0.951040 AGAAGCCAGCGTGTACAAGC 60.951 55.000 23.97 23.97 36.04 4.01
2499 8672 1.227823 AAGCCAGCGTGTACAAGCA 60.228 52.632 30.80 0.00 38.28 3.91
2500 8673 0.606401 AAGCCAGCGTGTACAAGCAT 60.606 50.000 30.80 15.97 38.28 3.79
2505 8692 1.061131 CAGCGTGTACAAGCATACTGC 59.939 52.381 30.80 10.84 45.46 4.40
2724 8911 0.963962 CACAGGCTGCAAGTGGAATT 59.036 50.000 15.89 0.00 35.30 2.17
2743 8930 9.788960 GTGGAATTTAATACTGATCACCTTTTC 57.211 33.333 0.00 0.00 0.00 2.29
2812 8999 3.067742 GCCATACTTCTACGCCTTCTACA 59.932 47.826 0.00 0.00 0.00 2.74
2865 9053 2.242572 CGCCATGATGTGCCTCTCG 61.243 63.158 0.00 0.00 0.00 4.04
2911 9099 0.108804 CGCCTCTCTCGCCAACTTTA 60.109 55.000 0.00 0.00 0.00 1.85
2913 9101 2.003301 GCCTCTCTCGCCAACTTTAAG 58.997 52.381 0.00 0.00 0.00 1.85
2914 9102 2.613223 GCCTCTCTCGCCAACTTTAAGT 60.613 50.000 0.00 0.00 0.00 2.24
2984 9177 3.902881 TGGATTGCTCTCTCTTTCTCC 57.097 47.619 0.00 0.00 0.00 3.71
2990 9183 0.523966 CTCTCTCTTTCTCCGCGTGT 59.476 55.000 4.92 0.00 0.00 4.49
3179 9373 5.707298 CCACATAGGTTGTTTCTTCATCTGT 59.293 40.000 0.00 0.00 36.00 3.41
3180 9374 6.207417 CCACATAGGTTGTTTCTTCATCTGTT 59.793 38.462 0.00 0.00 36.00 3.16
3181 9375 7.255590 CCACATAGGTTGTTTCTTCATCTGTTT 60.256 37.037 0.00 0.00 36.00 2.83
3182 9376 7.592533 CACATAGGTTGTTTCTTCATCTGTTTG 59.407 37.037 0.00 0.00 36.00 2.93
3183 9377 7.285401 ACATAGGTTGTTTCTTCATCTGTTTGT 59.715 33.333 0.00 0.00 33.74 2.83
3184 9378 5.894807 AGGTTGTTTCTTCATCTGTTTGTG 58.105 37.500 0.00 0.00 0.00 3.33
3185 9379 4.504097 GGTTGTTTCTTCATCTGTTTGTGC 59.496 41.667 0.00 0.00 0.00 4.57
3186 9380 5.343249 GTTGTTTCTTCATCTGTTTGTGCT 58.657 37.500 0.00 0.00 0.00 4.40
3187 9381 5.173774 TGTTTCTTCATCTGTTTGTGCTC 57.826 39.130 0.00 0.00 0.00 4.26
3188 9382 4.883585 TGTTTCTTCATCTGTTTGTGCTCT 59.116 37.500 0.00 0.00 0.00 4.09
3189 9383 5.210715 GTTTCTTCATCTGTTTGTGCTCTG 58.789 41.667 0.00 0.00 0.00 3.35
3190 9384 2.810274 TCTTCATCTGTTTGTGCTCTGC 59.190 45.455 0.00 0.00 0.00 4.26
3191 9385 2.556144 TCATCTGTTTGTGCTCTGCT 57.444 45.000 0.00 0.00 0.00 4.24
3192 9386 3.683365 TCATCTGTTTGTGCTCTGCTA 57.317 42.857 0.00 0.00 0.00 3.49
3193 9387 3.329386 TCATCTGTTTGTGCTCTGCTAC 58.671 45.455 0.00 0.00 0.00 3.58
3194 9388 2.169832 TCTGTTTGTGCTCTGCTACC 57.830 50.000 0.00 0.00 0.00 3.18
3195 9389 1.160137 CTGTTTGTGCTCTGCTACCC 58.840 55.000 0.00 0.00 0.00 3.69
3196 9390 0.764890 TGTTTGTGCTCTGCTACCCT 59.235 50.000 0.00 0.00 0.00 4.34
3197 9391 1.270839 TGTTTGTGCTCTGCTACCCTC 60.271 52.381 0.00 0.00 0.00 4.30
3198 9392 1.055849 TTTGTGCTCTGCTACCCTCA 58.944 50.000 0.00 0.00 0.00 3.86
3199 9393 1.055849 TTGTGCTCTGCTACCCTCAA 58.944 50.000 0.00 0.00 0.00 3.02
3200 9394 1.055849 TGTGCTCTGCTACCCTCAAA 58.944 50.000 0.00 0.00 0.00 2.69
3201 9395 1.419762 TGTGCTCTGCTACCCTCAAAA 59.580 47.619 0.00 0.00 0.00 2.44
3202 9396 2.158682 TGTGCTCTGCTACCCTCAAAAA 60.159 45.455 0.00 0.00 0.00 1.94
3226 9420 3.874392 AAAAACTGTTTGTGCTCTGCT 57.126 38.095 6.53 0.00 0.00 4.24
3227 9421 4.981806 AAAAACTGTTTGTGCTCTGCTA 57.018 36.364 6.53 0.00 0.00 3.49
3228 9422 3.971032 AAACTGTTTGTGCTCTGCTAC 57.029 42.857 4.73 0.00 0.00 3.58
3229 9423 1.884235 ACTGTTTGTGCTCTGCTACC 58.116 50.000 0.00 0.00 0.00 3.18
3230 9424 1.160137 CTGTTTGTGCTCTGCTACCC 58.840 55.000 0.00 0.00 0.00 3.69
3231 9425 0.764890 TGTTTGTGCTCTGCTACCCT 59.235 50.000 0.00 0.00 0.00 4.34
3232 9426 1.974957 TGTTTGTGCTCTGCTACCCTA 59.025 47.619 0.00 0.00 0.00 3.53
3233 9427 2.370519 TGTTTGTGCTCTGCTACCCTAA 59.629 45.455 0.00 0.00 0.00 2.69
3234 9428 3.181449 TGTTTGTGCTCTGCTACCCTAAA 60.181 43.478 0.00 0.00 0.00 1.85
3235 9429 3.780804 TTGTGCTCTGCTACCCTAAAA 57.219 42.857 0.00 0.00 0.00 1.52
3236 9430 3.780804 TGTGCTCTGCTACCCTAAAAA 57.219 42.857 0.00 0.00 0.00 1.94
3455 9650 0.044092 TGGAGATGGCCACCCTTCTA 59.956 55.000 8.16 0.00 43.53 2.10
3514 9709 2.634982 TTGCAAAATTAGCCTGCTCG 57.365 45.000 0.00 0.00 37.00 5.03
3575 9772 2.104281 AGTTCAAGTAAGCGAACAGGGT 59.896 45.455 5.21 0.00 43.20 4.34
3610 9809 0.615850 AACAGGCTAAGACTCCCAGC 59.384 55.000 0.00 0.00 34.48 4.85
3614 9813 0.176910 GGCTAAGACTCCCAGCTCAC 59.823 60.000 0.00 0.00 35.60 3.51
3799 10147 6.477901 AGGATAGCTTAGTTCCTCCTATCT 57.522 41.667 0.00 0.00 34.80 1.98
3865 10213 0.601558 CAGCTGAATGCCTGCAAACT 59.398 50.000 8.42 0.00 44.23 2.66
3913 10261 1.199097 GCGGTCGTCACATTTTTCCAT 59.801 47.619 0.00 0.00 0.00 3.41
4074 10422 6.239829 GGGATCATGGACAATCTATCTCTTGT 60.240 42.308 0.00 0.00 38.26 3.16
4190 10544 5.949354 CCAATTCCACTATACCAAGAACCAA 59.051 40.000 0.00 0.00 0.00 3.67
4339 10693 5.571357 CGGCAAAAGCAGTTTACGATTTATT 59.429 36.000 0.00 0.00 33.14 1.40
4340 10694 6.088883 CGGCAAAAGCAGTTTACGATTTATTT 59.911 34.615 0.00 0.00 33.14 1.40
4439 10793 3.099619 CTGCGTGCATGTAAGGGCG 62.100 63.158 7.93 0.00 0.00 6.13
4521 10875 5.220381 CCAATGTGATTTGATCTAGCATGC 58.780 41.667 10.51 10.51 0.00 4.06
4776 11130 9.128107 CATGTAACCATGTCAATAGTTTGTTTC 57.872 33.333 0.00 0.00 42.92 2.78
4894 11248 7.012704 TCCATGACTAAATGAAGCTGCTTATTC 59.987 37.037 15.95 3.70 0.00 1.75
5060 11414 7.870509 AGCATCTGTCATTATCTTTGCTTAA 57.129 32.000 0.00 0.00 35.81 1.85
5108 11462 4.756642 TGTCTTGCATGTCCTTCTTACTTG 59.243 41.667 0.00 0.00 0.00 3.16
5132 11486 1.070127 ATCCCTATGCCACTGCCCAT 61.070 55.000 0.00 0.00 36.33 4.00
5224 11581 1.264288 GACCGCACCTTTCAACTTCAG 59.736 52.381 0.00 0.00 0.00 3.02
5285 11642 4.036852 GGCTCCCTAATTGAACATTGCTAC 59.963 45.833 0.00 0.00 0.00 3.58
5296 11674 7.851387 TTGAACATTGCTACGAATATGGTTA 57.149 32.000 0.00 0.00 0.00 2.85
5576 11954 0.694771 AGCTGTTCCATCCTCTGCAA 59.305 50.000 0.00 0.00 0.00 4.08
5578 11956 2.097825 GCTGTTCCATCCTCTGCAATT 58.902 47.619 0.00 0.00 0.00 2.32
5689 12067 5.979993 TGACACTACAAGTACAAGGTCAAA 58.020 37.500 0.00 0.00 31.75 2.69
5768 12146 9.424319 TGTAAAGTATCAAAAGTAGAAGCAGAG 57.576 33.333 0.00 0.00 0.00 3.35
5790 12168 3.795488 GCCACAGGCTTCAGTTTGTAAAC 60.795 47.826 0.00 0.00 46.69 2.01
6108 12490 6.208599 TCCAATTCTGTAAACCCAAGTTGATC 59.791 38.462 3.87 0.00 35.97 2.92
6109 12491 6.209391 CCAATTCTGTAAACCCAAGTTGATCT 59.791 38.462 3.87 0.00 35.97 2.75
6110 12492 6.824305 ATTCTGTAAACCCAAGTTGATCTG 57.176 37.500 3.87 0.00 35.97 2.90
6111 12493 4.072131 TCTGTAAACCCAAGTTGATCTGC 58.928 43.478 3.87 0.00 35.97 4.26
6112 12494 4.074970 CTGTAAACCCAAGTTGATCTGCT 58.925 43.478 3.87 0.00 35.97 4.24
6113 12495 3.820467 TGTAAACCCAAGTTGATCTGCTG 59.180 43.478 3.87 0.00 35.97 4.41
6286 12675 7.811236 ACAAGCAACAGATATGAATCAAACAAG 59.189 33.333 0.00 0.00 34.28 3.16
6337 12726 4.037923 CCAAACAAGGTTACTCATGCAAGT 59.962 41.667 0.00 0.00 0.00 3.16
6339 12728 3.820557 ACAAGGTTACTCATGCAAGTGT 58.179 40.909 1.14 1.58 0.00 3.55
6453 12845 2.313234 CTGCTCAGTTGCACATTTTCG 58.687 47.619 0.00 0.00 38.12 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 5161 2.254152 TCCACTTCTAGCCCAGTCAT 57.746 50.000 0.00 0.00 0.00 3.06
137 5189 5.815233 AGTCTAGCATGTTGTAGCCATAT 57.185 39.130 0.00 0.00 0.00 1.78
218 5271 4.934797 TCATCTCAGATCTTTGGGGTTT 57.065 40.909 0.00 0.00 0.00 3.27
219 5272 4.290722 ACTTCATCTCAGATCTTTGGGGTT 59.709 41.667 0.00 0.00 0.00 4.11
220 5273 3.848975 ACTTCATCTCAGATCTTTGGGGT 59.151 43.478 0.00 0.00 0.00 4.95
221 5274 4.500499 ACTTCATCTCAGATCTTTGGGG 57.500 45.455 0.00 0.00 0.00 4.96
222 5275 6.017275 GCATAACTTCATCTCAGATCTTTGGG 60.017 42.308 0.00 0.00 0.00 4.12
346 5572 2.823154 CCCAGATCTTTGCGGGTTAAAA 59.177 45.455 7.56 0.00 33.67 1.52
389 5743 0.249955 TCATGCAACTCCGATGCTCA 59.750 50.000 0.00 0.00 44.14 4.26
395 5749 0.684535 TCCAGTTCATGCAACTCCGA 59.315 50.000 0.00 4.76 44.14 4.55
396 5750 1.522668 TTCCAGTTCATGCAACTCCG 58.477 50.000 0.00 3.02 44.14 4.63
439 6098 6.380190 ACGCTACAAATATCTATTCCTCGAC 58.620 40.000 0.00 0.00 0.00 4.20
573 6235 1.744320 AAAGGCGGTTTGGTTGGCTC 61.744 55.000 0.00 0.00 37.56 4.70
720 6388 6.879400 AGAAGCAAAGTAGATCGATAAAGGT 58.121 36.000 0.00 0.00 0.00 3.50
726 6394 6.314896 CAGGAAAAGAAGCAAAGTAGATCGAT 59.685 38.462 0.00 0.00 0.00 3.59
727 6395 5.639506 CAGGAAAAGAAGCAAAGTAGATCGA 59.360 40.000 0.00 0.00 0.00 3.59
728 6396 5.672321 GCAGGAAAAGAAGCAAAGTAGATCG 60.672 44.000 0.00 0.00 0.00 3.69
729 6397 5.392487 GGCAGGAAAAGAAGCAAAGTAGATC 60.392 44.000 0.00 0.00 0.00 2.75
760 6428 5.061311 CGTACAAAGATCGACGTGGTTAAAT 59.939 40.000 0.00 0.00 0.00 1.40
783 6451 2.125912 CAGTGACTTCTCGGGCCG 60.126 66.667 22.51 22.51 0.00 6.13
834 6664 4.378459 GGACATGCACAAAGTACTTACTGC 60.378 45.833 22.19 22.19 36.50 4.40
933 6763 3.164268 CCTCTCCTATGTCTATGCTGCT 58.836 50.000 0.00 0.00 0.00 4.24
970 6835 2.532250 ACCAATGGATGAACCCTTCC 57.468 50.000 6.16 0.00 38.00 3.46
971 6836 4.142160 GCTTTACCAATGGATGAACCCTTC 60.142 45.833 6.16 0.00 38.00 3.46
972 6837 3.769300 GCTTTACCAATGGATGAACCCTT 59.231 43.478 6.16 0.00 38.00 3.95
974 6839 3.131046 CAGCTTTACCAATGGATGAACCC 59.869 47.826 6.16 0.00 38.00 4.11
1032 7133 1.122019 AGAGGAAGGCGAACACCAGT 61.122 55.000 0.00 0.00 0.00 4.00
1216 7317 1.691127 CTGCATGCGTATACGAGGAG 58.309 55.000 28.66 20.97 43.02 3.69
1270 7375 3.723260 GCTAAAGTCTAGCTGGATCACC 58.277 50.000 2.00 0.00 37.56 4.02
1336 7441 2.232452 CGATATCTCCTAGCACAAGGGG 59.768 54.545 0.34 0.00 38.63 4.79
1342 7447 5.590530 ATTGATCCGATATCTCCTAGCAC 57.409 43.478 0.34 0.00 0.00 4.40
1351 7458 4.572389 GCCACACCATATTGATCCGATATC 59.428 45.833 0.00 0.00 0.00 1.63
1365 7472 1.271840 ACAGGATACGGCCACACCAT 61.272 55.000 2.24 0.00 46.39 3.55
1396 7503 1.264288 CACAGGAAGAAGCCAACGAAC 59.736 52.381 0.00 0.00 0.00 3.95
1412 7519 0.788995 CTGCTCAAGCGAGAACACAG 59.211 55.000 0.00 0.00 45.83 3.66
1414 7521 1.721926 GTACTGCTCAAGCGAGAACAC 59.278 52.381 7.97 1.78 45.83 3.32
1415 7522 1.666023 CGTACTGCTCAAGCGAGAACA 60.666 52.381 7.97 0.00 45.83 3.18
1416 7523 0.985549 CGTACTGCTCAAGCGAGAAC 59.014 55.000 7.97 0.00 45.83 3.01
1417 7524 0.596577 ACGTACTGCTCAAGCGAGAA 59.403 50.000 0.00 0.00 45.83 2.87
1419 7526 0.109735 TCACGTACTGCTCAAGCGAG 60.110 55.000 0.00 0.00 45.83 5.03
1446 7554 1.546476 CGTGCTCCTTCCTACAGTCTT 59.454 52.381 0.00 0.00 0.00 3.01
1570 7678 3.526534 GTGGAGGTTAGCTTCATCTGAC 58.473 50.000 0.00 0.00 0.00 3.51
1628 7743 2.406002 TTTCCCAGGTTCCAGACGGC 62.406 60.000 0.00 0.00 0.00 5.68
1678 7793 3.129287 ACATTCAATGGCTCACGGAAATC 59.871 43.478 1.58 0.00 33.60 2.17
1700 7818 5.063438 GCATATGACGAGAGCAAACTTGTTA 59.937 40.000 6.97 0.00 35.00 2.41
1812 7936 0.319900 CACCCAAGACGAGACACTGG 60.320 60.000 0.00 0.00 0.00 4.00
1813 7937 0.946221 GCACCCAAGACGAGACACTG 60.946 60.000 0.00 0.00 0.00 3.66
1814 7938 1.367840 GCACCCAAGACGAGACACT 59.632 57.895 0.00 0.00 0.00 3.55
1815 7939 2.022129 CGCACCCAAGACGAGACAC 61.022 63.158 0.00 0.00 0.00 3.67
1816 7940 1.532604 ATCGCACCCAAGACGAGACA 61.533 55.000 0.00 0.00 39.48 3.41
1817 7941 0.802607 GATCGCACCCAAGACGAGAC 60.803 60.000 0.00 0.00 39.48 3.36
1818 7942 1.511305 GATCGCACCCAAGACGAGA 59.489 57.895 0.00 0.00 39.48 4.04
1819 7943 1.874019 CGATCGCACCCAAGACGAG 60.874 63.158 0.26 0.00 39.48 4.18
1820 7944 1.663379 ATCGATCGCACCCAAGACGA 61.663 55.000 11.09 0.00 40.53 4.20
1857 7981 0.576798 CGTAGTCGTATCGCCGTGTA 59.423 55.000 0.00 0.00 0.00 2.90
2093 8256 7.191593 TCTGATGACACTGGTAGTAGTAGTA 57.808 40.000 0.00 0.00 0.00 1.82
2128 8291 4.103469 TGCTTGGGTTAGTTTTCCTGTCTA 59.897 41.667 0.00 0.00 0.00 2.59
2129 8292 3.117663 TGCTTGGGTTAGTTTTCCTGTCT 60.118 43.478 0.00 0.00 0.00 3.41
2136 8299 1.133167 AGGGCTGCTTGGGTTAGTTTT 60.133 47.619 0.00 0.00 0.00 2.43
2153 8317 4.604156 AGAAAAGGGCTAAAGAATGAGGG 58.396 43.478 0.00 0.00 0.00 4.30
2174 8338 7.016361 TCACGAAGAAGAAAAAGGAGAAAAG 57.984 36.000 0.00 0.00 0.00 2.27
2175 8339 6.995511 TCACGAAGAAGAAAAAGGAGAAAA 57.004 33.333 0.00 0.00 0.00 2.29
2176 8340 6.995511 TTCACGAAGAAGAAAAAGGAGAAA 57.004 33.333 0.00 0.00 0.00 2.52
2268 8434 3.705638 CAGTGCCGTCACACGCAG 61.706 66.667 0.00 0.00 45.49 5.18
2470 8643 1.303155 GCTGGCTTCTGCTTGTCCT 60.303 57.895 0.00 0.00 39.59 3.85
2498 8671 1.815421 GGCCCACACTCGCAGTATG 60.815 63.158 0.00 0.00 40.87 2.39
2499 8672 2.584608 GGCCCACACTCGCAGTAT 59.415 61.111 0.00 0.00 0.00 2.12
2500 8673 4.063967 CGGCCCACACTCGCAGTA 62.064 66.667 0.00 0.00 0.00 2.74
2576 8763 4.388499 ATGACCGGCGTGACCACC 62.388 66.667 6.01 0.00 39.03 4.61
2649 8836 0.391661 CCCAGTGGAACGATGGACAG 60.392 60.000 11.95 0.00 45.86 3.51
2711 8898 7.912250 GTGATCAGTATTAAATTCCACTTGCAG 59.088 37.037 0.00 0.00 0.00 4.41
2724 8911 7.881232 AGGAAACGAAAAGGTGATCAGTATTAA 59.119 33.333 0.00 0.00 0.00 1.40
2743 8930 1.203313 GCCGACACGAAAGGAAACG 59.797 57.895 0.00 0.00 0.00 3.60
2865 9053 1.517913 GGTTACCACGTAGGCGAGC 60.518 63.158 0.00 0.00 43.14 5.03
2934 9122 0.462225 CCAGCTGAGCTCCAGTCATG 60.462 60.000 17.39 9.01 44.71 3.07
2990 9183 4.680237 CCTTGTCGGCCTGCACGA 62.680 66.667 0.00 0.00 38.13 4.35
3063 9256 4.452733 GTGCCGCCTACGAAGCCT 62.453 66.667 0.00 0.00 43.93 4.58
3179 9373 1.055849 TGAGGGTAGCAGAGCACAAA 58.944 50.000 0.00 0.00 0.00 2.83
3180 9374 1.055849 TTGAGGGTAGCAGAGCACAA 58.944 50.000 0.00 0.00 0.00 3.33
3181 9375 1.055849 TTTGAGGGTAGCAGAGCACA 58.944 50.000 0.00 0.00 0.00 4.57
3182 9376 2.185004 TTTTGAGGGTAGCAGAGCAC 57.815 50.000 0.00 0.00 0.00 4.40
3183 9377 2.949177 TTTTTGAGGGTAGCAGAGCA 57.051 45.000 0.00 0.00 0.00 4.26
3206 9400 3.874392 AGCAGAGCACAAACAGTTTTT 57.126 38.095 0.00 0.00 0.00 1.94
3207 9401 3.066760 GGTAGCAGAGCACAAACAGTTTT 59.933 43.478 0.00 0.00 0.00 2.43
3208 9402 2.618709 GGTAGCAGAGCACAAACAGTTT 59.381 45.455 0.00 0.00 0.00 2.66
3209 9403 2.222027 GGTAGCAGAGCACAAACAGTT 58.778 47.619 0.00 0.00 0.00 3.16
3210 9404 1.543429 GGGTAGCAGAGCACAAACAGT 60.543 52.381 0.00 0.00 0.00 3.55
3211 9405 1.160137 GGGTAGCAGAGCACAAACAG 58.840 55.000 0.00 0.00 0.00 3.16
3212 9406 0.764890 AGGGTAGCAGAGCACAAACA 59.235 50.000 0.00 0.00 0.00 2.83
3213 9407 2.762535 TAGGGTAGCAGAGCACAAAC 57.237 50.000 0.00 0.00 0.00 2.93
3214 9408 3.780804 TTTAGGGTAGCAGAGCACAAA 57.219 42.857 0.00 0.00 0.00 2.83
3215 9409 3.780804 TTTTAGGGTAGCAGAGCACAA 57.219 42.857 0.00 0.00 0.00 3.33
3216 9410 3.780804 TTTTTAGGGTAGCAGAGCACA 57.219 42.857 0.00 0.00 0.00 4.57
3236 9430 3.514645 CTGCAGAGCACAAACAGTTTTT 58.485 40.909 8.42 0.00 33.79 1.94
3237 9431 2.159198 CCTGCAGAGCACAAACAGTTTT 60.159 45.455 17.39 0.00 33.79 2.43
3238 9432 1.406539 CCTGCAGAGCACAAACAGTTT 59.593 47.619 17.39 0.00 33.79 2.66
3239 9433 1.027357 CCTGCAGAGCACAAACAGTT 58.973 50.000 17.39 0.00 33.79 3.16
3240 9434 0.107017 ACCTGCAGAGCACAAACAGT 60.107 50.000 17.39 0.00 33.79 3.55
3241 9435 0.309922 CACCTGCAGAGCACAAACAG 59.690 55.000 17.39 0.00 33.79 3.16
3242 9436 1.102809 CCACCTGCAGAGCACAAACA 61.103 55.000 17.39 0.00 33.79 2.83
3243 9437 1.656441 CCACCTGCAGAGCACAAAC 59.344 57.895 17.39 0.00 33.79 2.93
3244 9438 2.195567 GCCACCTGCAGAGCACAAA 61.196 57.895 17.39 0.00 40.77 2.83
3368 9563 2.404750 GGGGCTAGAGGAGGGAGGA 61.405 68.421 0.00 0.00 0.00 3.71
3436 9631 0.044092 TAGAAGGGTGGCCATCTCCA 59.956 55.000 17.44 0.00 0.00 3.86
3455 9650 2.993264 GCATGCCACCTGCTGGTT 60.993 61.111 13.36 0.00 46.05 3.67
3483 9678 6.813152 GGCTAATTTTGCAATCTTTCAAGCTA 59.187 34.615 0.00 0.00 0.00 3.32
3514 9709 1.544691 TCTACTCTCCGTTGAGCCAAC 59.455 52.381 7.71 7.71 40.54 3.77
3610 9809 2.037641 TGGTGATGACAGAACTGGTGAG 59.962 50.000 6.76 0.00 34.19 3.51
3614 9813 3.070018 GAGTTGGTGATGACAGAACTGG 58.930 50.000 6.76 0.00 33.05 4.00
3865 10213 2.543848 CGTGAAAGTTGAGCTGCAAGTA 59.456 45.455 1.02 0.00 39.20 2.24
3913 10261 2.597217 CCTGTTTCGCCAAGGCCA 60.597 61.111 5.01 0.00 37.98 5.36
3997 10345 7.227910 ACCTTCGTGTAGAATTTACAACATTGT 59.772 33.333 2.32 2.32 40.51 2.71
4272 10626 9.616634 GCACATAATCGATCATAAATTGAACAT 57.383 29.630 0.00 0.00 38.03 2.71
4274 10628 9.322776 GAGCACATAATCGATCATAAATTGAAC 57.677 33.333 0.00 0.00 38.03 3.18
4339 10693 1.275010 TCACGGTCAGCTGCATAGAAA 59.725 47.619 9.47 0.00 0.00 2.52
4340 10694 0.894835 TCACGGTCAGCTGCATAGAA 59.105 50.000 9.47 0.00 0.00 2.10
4439 10793 7.568199 AATAACAGGACTATGCCATAACAAC 57.432 36.000 0.00 0.00 0.00 3.32
4521 10875 5.233083 TGTATAGGAATCCCTGCAAGATG 57.767 43.478 0.00 0.00 44.15 2.90
4894 11248 8.881262 ACAAAGGGTATCTAATATCTTAGTGGG 58.119 37.037 0.00 0.00 36.51 4.61
5060 11414 8.939929 CATAATCTGTTGTGAGTTTAGATGTGT 58.060 33.333 0.00 0.00 0.00 3.72
5108 11462 1.678101 GCAGTGGCATAGGGATGAAAC 59.322 52.381 0.00 0.00 40.72 2.78
5132 11486 3.701205 TGACATCTTTGGCTAAGCTCA 57.299 42.857 3.69 2.41 33.66 4.26
5224 11581 0.538287 ACAAGCCAGGCTGAAACCTC 60.538 55.000 17.05 0.00 39.62 3.85
5296 11674 5.789521 ACAAAAAGTGTGCAGTAAGGTTTT 58.210 33.333 0.00 0.00 39.72 2.43
5576 11954 6.891908 ACTATTTGCTGTCCCTATTTGTCAAT 59.108 34.615 0.00 0.00 0.00 2.57
5578 11956 5.647658 CACTATTTGCTGTCCCTATTTGTCA 59.352 40.000 0.00 0.00 0.00 3.58
5768 12146 3.795488 GTTTACAAACTGAAGCCTGTGGC 60.795 47.826 0.00 0.00 41.35 5.01
5790 12168 8.082852 ACTTGTAGTGTCAGTTATTGAGTACAG 58.917 37.037 0.00 0.00 36.21 2.74
6109 12491 7.390440 ACTTACTTAATATTTCACTGTGCAGCA 59.610 33.333 2.12 0.00 0.00 4.41
6110 12492 7.752695 ACTTACTTAATATTTCACTGTGCAGC 58.247 34.615 2.12 0.00 0.00 5.25
6111 12493 9.760660 GAACTTACTTAATATTTCACTGTGCAG 57.239 33.333 2.12 0.00 0.00 4.41
6112 12494 8.440059 CGAACTTACTTAATATTTCACTGTGCA 58.560 33.333 2.12 0.00 0.00 4.57
6113 12495 8.653338 TCGAACTTACTTAATATTTCACTGTGC 58.347 33.333 2.12 0.00 0.00 4.57
6231 12619 7.041107 GCTATAATGGTCTGATGAAGAGGATC 58.959 42.308 0.00 0.00 34.84 3.36
6337 12726 3.213506 CTGTGTTCTTCAATGTCCCACA 58.786 45.455 0.00 0.00 0.00 4.17
6339 12728 2.174639 ACCTGTGTTCTTCAATGTCCCA 59.825 45.455 0.00 0.00 0.00 4.37
6439 12831 5.003804 AGTATCTTCCGAAAATGTGCAACT 58.996 37.500 0.00 0.00 38.04 3.16


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

AutoCloner maintained by Alex Coulton.