Multiple sequence alignment - TraesCS3A01G271800

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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 TraesCS3A01G271800 chr3A 100.000 4734 0 0 1 4734 500983911 500988644 0.000000e+00 8743.0
1 TraesCS3A01G271800 chr3D 91.332 2215 96 27 717 2865 376261546 376263730 0.000000e+00 2939.0
2 TraesCS3A01G271800 chr3D 93.154 1227 55 22 2859 4077 376263763 376264968 0.000000e+00 1773.0
3 TraesCS3A01G271800 chr3D 88.704 602 33 10 4136 4734 376265347 376265916 0.000000e+00 702.0
4 TraesCS3A01G271800 chr3D 85.299 653 83 5 4 654 376260771 376261412 0.000000e+00 662.0
5 TraesCS3A01G271800 chr3D 90.683 161 12 3 1439 1599 322435291 322435448 1.330000e-50 211.0
6 TraesCS3A01G271800 chr3D 90.968 155 13 1 1440 1594 288550611 288550458 1.730000e-49 207.0
7 TraesCS3A01G271800 chr3B 89.707 2079 106 35 819 2865 490883732 490885734 0.000000e+00 2555.0
8 TraesCS3A01G271800 chr3B 94.169 1269 34 19 2874 4119 490885845 490887096 0.000000e+00 1897.0
9 TraesCS3A01G271800 chr3B 92.634 448 22 8 4125 4562 490887190 490887636 6.680000e-178 634.0
10 TraesCS3A01G271800 chr3B 82.314 605 65 23 3 599 490882381 490882951 1.980000e-133 486.0
11 TraesCS3A01G271800 chr3B 91.053 190 13 3 4547 4734 490887657 490887844 2.190000e-63 254.0
12 TraesCS3A01G271800 chr3B 90.683 161 12 3 1439 1599 396271878 396272035 1.330000e-50 211.0
13 TraesCS3A01G271800 chr3B 95.192 104 5 0 717 820 490883603 490883706 1.050000e-36 165.0
14 TraesCS3A01G271800 chr4D 92.258 155 11 1 1448 1602 74079359 74079512 7.980000e-53 219.0
15 TraesCS3A01G271800 chr7D 93.706 143 7 2 1454 1596 34757004 34756864 3.710000e-51 213.0
16 TraesCS3A01G271800 chr6D 89.571 163 15 2 1432 1594 410398439 410398279 6.210000e-49 206.0
17 TraesCS3A01G271800 chr2D 90.385 156 13 2 1439 1594 79056166 79056319 2.230000e-48 204.0
18 TraesCS3A01G271800 chr7B 78.744 207 27 14 184 380 634159386 634159187 6.430000e-24 122.0
19 TraesCS3A01G271800 chr7B 79.275 193 27 12 196 380 634258115 634257928 6.430000e-24 122.0
20 TraesCS3A01G271800 chr1B 77.000 200 38 8 3070 3265 643590164 643590359 1.800000e-19 108.0
21 TraesCS3A01G271800 chr1D 76.500 200 39 8 3070 3265 467033657 467033852 8.380000e-18 102.0
22 TraesCS3A01G271800 chr7A 81.579 114 17 1 271 380 664179270 664179157 1.810000e-14 91.6
23 TraesCS3A01G271800 chr1A 75.124 201 40 9 3070 3265 558978562 558978757 8.440000e-13 86.1


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 TraesCS3A01G271800 chr3A 500983911 500988644 4733 False 8743.0 8743 100.000000 1 4734 1 chr3A.!!$F1 4733
1 TraesCS3A01G271800 chr3D 376260771 376265916 5145 False 1519.0 2939 89.622250 4 4734 4 chr3D.!!$F2 4730
2 TraesCS3A01G271800 chr3B 490882381 490887844 5463 False 998.5 2555 90.844833 3 4734 6 chr3B.!!$F2 4731

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
482 488 0.830648 CCTATGCTTCGGGTCAGGAA 59.169 55.0 0.00 0.00 0.00 3.36 F
1146 1730 0.108520 TTCCGCGTGGTTGGATCTAC 60.109 55.0 16.01 0.00 33.42 2.59 F
1217 1802 0.391927 CTGCGGTTTCGGGTGGATAA 60.392 55.0 0.00 0.00 36.79 1.75 F
1446 2034 0.461516 GGGCTTGGAAGGTACTACGC 60.462 60.0 0.00 0.00 38.49 4.42 F
1718 2307 1.188871 TCTGGTGATGTGGCCGTGTA 61.189 55.0 0.00 0.00 0.00 2.90 F
3011 3749 0.373716 ATAAAACTGCGCGCTGCTAC 59.626 50.0 33.78 4.96 46.63 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 2171 1.687123 GCTAATTGCTACTCCCTCCGA 59.313 52.381 0.00 0.0 38.95 4.55 R
2178 2767 1.739067 ATGTAAGAAAGCCGGTCAGC 58.261 50.000 1.90 0.0 0.00 4.26 R
2263 2852 2.032681 GGGGCAGCCATCGGATAC 59.967 66.667 15.19 0.0 0.00 2.24 R
2357 2973 2.147150 GCCAAAGAGGAAGTCACACTC 58.853 52.381 0.00 0.0 41.22 3.51 R
3064 3802 2.500098 TCAGAAACCTAACCTGCGCTAT 59.500 45.455 9.73 0.0 0.00 2.97 R
4176 5297 0.034863 TTGGTCCGGCTAAACCATCC 60.035 55.000 13.13 0.0 44.72 3.51 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
133 136 3.955471 AGAATCATCAACCGTTCCACAT 58.045 40.909 0.00 0.00 0.00 3.21
143 146 4.301637 ACCGTTCCACATCTTTTGTTTC 57.698 40.909 0.00 0.00 36.00 2.78
145 148 3.067461 CCGTTCCACATCTTTTGTTTCCA 59.933 43.478 0.00 0.00 36.00 3.53
148 151 5.507149 CGTTCCACATCTTTTGTTTCCATCA 60.507 40.000 0.00 0.00 36.00 3.07
149 152 6.458210 GTTCCACATCTTTTGTTTCCATCAT 58.542 36.000 0.00 0.00 36.00 2.45
163 166 6.368791 TGTTTCCATCATACTCTTTTCTGACG 59.631 38.462 0.00 0.00 0.00 4.35
172 175 3.187700 CTCTTTTCTGACGATTACGGGG 58.812 50.000 0.00 0.00 44.46 5.73
177 180 1.066716 TCTGACGATTACGGGGTTTGG 60.067 52.381 0.00 0.00 44.46 3.28
202 205 5.844004 CGTAAGGGTACTTCTAATGCTGAT 58.156 41.667 0.00 0.00 38.14 2.90
228 231 4.812476 TGCTCCCGCATCCGTTCG 62.812 66.667 0.00 0.00 42.25 3.95
238 241 1.669604 CATCCGTTCGGAGAGAGAGA 58.330 55.000 18.54 0.00 38.43 3.10
249 252 3.496692 CGGAGAGAGAGAGATCAGTCCAT 60.497 52.174 0.00 0.00 0.00 3.41
250 253 3.822735 GGAGAGAGAGAGATCAGTCCATG 59.177 52.174 0.00 0.00 0.00 3.66
251 254 4.464008 GAGAGAGAGAGATCAGTCCATGT 58.536 47.826 0.00 0.00 0.00 3.21
260 263 6.722328 AGAGATCAGTCCATGTATACGGATA 58.278 40.000 3.20 0.00 31.88 2.59
268 271 6.928348 TCCATGTATACGGATATGGAAACT 57.072 37.500 16.46 0.00 44.38 2.66
270 273 6.495526 TCCATGTATACGGATATGGAAACTGA 59.504 38.462 16.46 0.00 44.38 3.41
285 288 4.504858 GAAACTGACCATCCAACGATACT 58.495 43.478 0.00 0.00 0.00 2.12
335 338 2.353579 GTCCGCACGTTTAAATAGCCAT 59.646 45.455 0.00 0.00 0.00 4.40
380 384 4.691860 ATGTTCAAATGCAGCAGTAGTC 57.308 40.909 0.00 0.00 0.00 2.59
393 399 5.622460 GCAGCAGTAGTCCGCATATATAGTT 60.622 44.000 0.00 0.00 0.00 2.24
403 409 9.362539 AGTCCGCATATATAGTTTAAAATACCG 57.637 33.333 0.00 0.00 0.00 4.02
418 424 0.961019 TACCGACGTTTAGCACTGGT 59.039 50.000 0.00 0.00 0.00 4.00
423 429 1.194772 GACGTTTAGCACTGGTCAAGC 59.805 52.381 0.00 0.00 0.00 4.01
482 488 0.830648 CCTATGCTTCGGGTCAGGAA 59.169 55.000 0.00 0.00 0.00 3.36
504 510 2.970324 GCACGCGTTCTTGACCCA 60.970 61.111 10.22 0.00 0.00 4.51
511 517 1.670674 GCGTTCTTGACCCATGTCGTA 60.671 52.381 0.00 0.00 44.86 3.43
568 574 4.778415 CGCGAGGTGAGACCCACG 62.778 72.222 0.00 0.00 46.62 4.94
582 588 3.353029 CACGTGCCGGCATGACAA 61.353 61.111 46.38 17.26 36.80 3.18
583 589 2.359850 ACGTGCCGGCATGACAAT 60.360 55.556 46.38 26.97 36.80 2.71
584 590 1.971167 ACGTGCCGGCATGACAATT 60.971 52.632 46.38 26.60 36.80 2.32
587 593 1.349234 GTGCCGGCATGACAATTTTC 58.651 50.000 35.23 11.91 0.00 2.29
627 633 5.912892 TCTTTTTGAACATCCCAAAAGGTC 58.087 37.500 0.00 0.00 42.28 3.85
666 1111 2.959507 AAATGGCAAAATACCGAGGC 57.040 45.000 0.00 0.00 0.00 4.70
667 1112 1.846007 AATGGCAAAATACCGAGGCA 58.154 45.000 0.00 0.00 40.91 4.75
671 1116 2.004808 GCAAAATACCGAGGCAGCCC 62.005 60.000 8.22 0.00 0.00 5.19
672 1117 1.451387 AAAATACCGAGGCAGCCCG 60.451 57.895 8.22 11.63 35.76 6.13
687 1195 2.095768 CAGCCCGTTTAGTTCATGTGTG 60.096 50.000 0.00 0.00 0.00 3.82
700 1208 4.684134 GTGTGGTGCCTGGGCCAT 62.684 66.667 6.72 0.00 41.09 4.40
706 1214 1.302949 GTGCCTGGGCCATAAGACA 59.697 57.895 6.72 0.00 41.09 3.41
734 1286 2.686816 CGTGCCAGGCCCTTTTACG 61.687 63.158 9.64 7.20 0.00 3.18
796 1349 1.743394 CCGGGATAAAACTTGAGCACC 59.257 52.381 0.00 0.00 0.00 5.01
820 1373 5.465935 GTGGAATGGAATAAAGCAACGAAA 58.534 37.500 0.00 0.00 0.00 3.46
821 1374 5.923684 GTGGAATGGAATAAAGCAACGAAAA 59.076 36.000 0.00 0.00 0.00 2.29
822 1375 6.422400 GTGGAATGGAATAAAGCAACGAAAAA 59.578 34.615 0.00 0.00 0.00 1.94
1020 1600 2.644992 GCCAACAGCAACCTTCCG 59.355 61.111 0.00 0.00 42.97 4.30
1040 1620 1.590238 GCGACGAATCATCAAGGTGAG 59.410 52.381 0.00 0.00 0.00 3.51
1081 1661 1.408702 GCACAGATCTCTCCACTCCTC 59.591 57.143 0.00 0.00 0.00 3.71
1100 1680 1.131883 TCCGATCCGACTCGTCTTTTC 59.868 52.381 0.00 0.00 36.93 2.29
1125 1709 1.883926 CCCGTGTCTAACTTTTTGGGG 59.116 52.381 0.00 0.00 0.00 4.96
1146 1730 0.108520 TTCCGCGTGGTTGGATCTAC 60.109 55.000 16.01 0.00 33.42 2.59
1216 1801 1.219664 CTGCGGTTTCGGGTGGATA 59.780 57.895 0.00 0.00 36.79 2.59
1217 1802 0.391927 CTGCGGTTTCGGGTGGATAA 60.392 55.000 0.00 0.00 36.79 1.75
1230 1815 2.365582 GTGGATAATGGCGAGGTGTTT 58.634 47.619 0.00 0.00 0.00 2.83
1242 1827 2.226437 CGAGGTGTTTCATTTCTGGGTG 59.774 50.000 0.00 0.00 0.00 4.61
1243 1828 1.963515 AGGTGTTTCATTTCTGGGTGC 59.036 47.619 0.00 0.00 0.00 5.01
1264 1849 2.420022 CGATTTCCGCTCTTTGAATGGT 59.580 45.455 0.00 0.00 0.00 3.55
1265 1850 3.119849 CGATTTCCGCTCTTTGAATGGTT 60.120 43.478 0.00 0.00 0.00 3.67
1318 1903 1.880340 CTCGGAGGAGAACATGCGC 60.880 63.158 0.00 0.00 43.27 6.09
1373 1958 2.983402 GCCCTACGAAGGTTTTGTTC 57.017 50.000 0.00 0.00 41.89 3.18
1374 1959 2.501261 GCCCTACGAAGGTTTTGTTCT 58.499 47.619 0.00 0.00 41.89 3.01
1375 1960 2.882761 GCCCTACGAAGGTTTTGTTCTT 59.117 45.455 0.00 0.00 41.89 2.52
1376 1961 3.058432 GCCCTACGAAGGTTTTGTTCTTC 60.058 47.826 0.00 0.00 41.89 2.87
1377 1962 3.501062 CCCTACGAAGGTTTTGTTCTTCC 59.499 47.826 0.00 0.00 41.89 3.46
1378 1963 4.386711 CCTACGAAGGTTTTGTTCTTCCT 58.613 43.478 0.00 0.00 38.19 3.36
1379 1964 4.820173 CCTACGAAGGTTTTGTTCTTCCTT 59.180 41.667 0.00 0.00 42.10 3.36
1446 2034 0.461516 GGGCTTGGAAGGTACTACGC 60.462 60.000 0.00 0.00 38.49 4.42
1494 2083 5.869753 ACTTTTTCTCTGAATCGGATGTG 57.130 39.130 0.00 0.00 0.00 3.21
1538 2127 2.128035 GTTCACTCACTTCAGTCCGTG 58.872 52.381 0.00 0.00 0.00 4.94
1546 2135 2.293677 CACTTCAGTCCGTGTGTACTCT 59.706 50.000 0.00 0.00 0.00 3.24
1629 2218 3.121944 CGAGATGACTCTGTTCAAAACCG 59.878 47.826 0.00 0.00 40.65 4.44
1678 2267 4.671831 TGTGTTGGAATTATGGATGGTGT 58.328 39.130 0.00 0.00 0.00 4.16
1718 2307 1.188871 TCTGGTGATGTGGCCGTGTA 61.189 55.000 0.00 0.00 0.00 2.90
1726 2315 3.749088 TGATGTGGCCGTGTAAGTTTTAG 59.251 43.478 0.00 0.00 0.00 1.85
1839 2428 5.581126 TGCTCCAAGCTTATTTGTAATGG 57.419 39.130 0.00 0.00 42.97 3.16
1861 2450 5.047660 TGGCACACTTATTTCCATGGTTAAC 60.048 40.000 12.58 0.00 0.00 2.01
1883 2472 6.579666 ACATTGTATTGATATGGATGCCAC 57.420 37.500 0.00 0.00 35.80 5.01
1902 2491 8.634335 ATGCCACATATTATGCATAGTGTTAA 57.366 30.769 17.65 2.17 42.30 2.01
1903 2492 8.457238 TGCCACATATTATGCATAGTGTTAAA 57.543 30.769 17.65 1.54 0.00 1.52
1904 2493 8.349245 TGCCACATATTATGCATAGTGTTAAAC 58.651 33.333 17.65 9.67 0.00 2.01
1905 2494 8.567948 GCCACATATTATGCATAGTGTTAAACT 58.432 33.333 17.65 0.00 43.40 2.66
1906 2495 9.882996 CCACATATTATGCATAGTGTTAAACTG 57.117 33.333 17.65 8.11 40.26 3.16
1944 2533 4.219725 TGCTTAAGCCCTTTGGTGTTATTC 59.780 41.667 24.30 0.00 41.18 1.75
1953 2542 2.380081 GGTGTTATTCGAGCCACCG 58.620 57.895 8.48 0.00 38.14 4.94
2132 2721 9.381033 GCTTATCTTCTGCATGATATATCTGTT 57.619 33.333 13.79 0.00 0.00 3.16
2180 2769 8.525290 AAGTGTTAGCATTCTATTTTATGGCT 57.475 30.769 0.00 0.00 0.00 4.75
2263 2852 3.007614 TGGAACTCTTTTTACCCGAGGAG 59.992 47.826 0.00 0.00 0.00 3.69
2365 2981 8.436200 GTTGTATTCAGAATTGTAGAGTGTGAC 58.564 37.037 0.00 0.00 0.00 3.67
2378 2994 1.771255 AGTGTGACTTCCTCTTTGGCT 59.229 47.619 0.00 0.00 35.26 4.75
2411 3027 7.201857 GCTGATTTCTTCTTTGGCTAATATGGT 60.202 37.037 0.00 0.00 0.00 3.55
2428 3044 3.059634 TGGTTTCGACTTTCTTTTGCG 57.940 42.857 0.00 0.00 0.00 4.85
2462 3078 0.467290 TGTTCAAGGGCTGGTCAACC 60.467 55.000 0.00 0.00 0.00 3.77
2484 3100 3.247648 CGCATTTAGATTACTTCGGTGGG 59.752 47.826 0.00 0.00 0.00 4.61
2601 3217 6.819146 TGTTGTGTTACTGTTGACATTCACTA 59.181 34.615 0.00 0.00 0.00 2.74
2643 3259 9.414295 TGTTGTGGTAGTATATTATTGTATCGC 57.586 33.333 0.00 0.00 0.00 4.58
2666 3282 5.407407 TCTCATTTCCCTGTCTAGACAAC 57.593 43.478 25.14 0.00 41.33 3.32
2678 3294 4.991056 TGTCTAGACAACTTTAGCTGCTTG 59.009 41.667 23.24 1.50 38.56 4.01
2705 3337 4.818546 GGACATAGAAATGATGGAGTGTGG 59.181 45.833 0.00 0.00 36.54 4.17
2794 3426 6.064846 TCAGAGAAATTTTCACTTGCACTC 57.935 37.500 11.53 0.00 0.00 3.51
2799 3431 7.014038 AGAGAAATTTTCACTTGCACTCAGATT 59.986 33.333 11.53 0.00 0.00 2.40
2865 3497 7.992033 AGTCTAGTATAGTTGTCGTGGTTCTAT 59.008 37.037 0.00 0.00 40.38 1.98
2867 3499 9.486497 TCTAGTATAGTTGTCGTGGTTCTATAG 57.514 37.037 0.00 0.00 40.38 1.31
2946 3681 8.950208 AAGGATGAATAAGTAGCACTTAAGTC 57.050 34.615 4.77 1.12 43.16 3.01
3011 3749 0.373716 ATAAAACTGCGCGCTGCTAC 59.626 50.000 33.78 4.96 46.63 3.58
3064 3802 6.580791 GCGAACATTTATACTTTGCTTGTTGA 59.419 34.615 0.00 0.00 0.00 3.18
3283 4023 3.041946 GGTCCTCTCTCTCTCTCTCTCT 58.958 54.545 0.00 0.00 0.00 3.10
3284 4024 3.070302 GGTCCTCTCTCTCTCTCTCTCTC 59.930 56.522 0.00 0.00 0.00 3.20
3302 4042 4.952957 TCTCTCATTCTGGGTCTCTGTAAG 59.047 45.833 0.00 0.00 0.00 2.34
3303 4043 3.449018 TCTCATTCTGGGTCTCTGTAAGC 59.551 47.826 0.00 0.00 0.00 3.09
3320 4060 6.986817 TCTGTAAGCTAGCATTTCATAACCTC 59.013 38.462 18.83 0.00 0.00 3.85
3359 4099 6.723298 TCCTTTGCTATGTTTCTCCAAAAA 57.277 33.333 0.00 0.00 0.00 1.94
3453 4229 2.362397 TCCGGCACAGTATCTGATTCTC 59.638 50.000 0.00 0.00 35.18 2.87
3661 4437 0.690411 CCATTTGCCCTTGGGCCATA 60.690 55.000 26.03 12.62 0.00 2.74
3903 4681 1.946267 CGTTGGTTGGTTCCCTTCG 59.054 57.895 0.00 0.00 0.00 3.79
4018 4796 5.068855 TCCACATTGTTGAAATTGAAGCTGA 59.931 36.000 0.00 0.00 0.00 4.26
4086 4864 0.463654 GGTTGCATCTGATACGCCCA 60.464 55.000 0.00 0.00 0.00 5.36
4105 4883 4.098501 GCCCAAATATTTTCTCAGTCCCTG 59.901 45.833 0.00 0.00 0.00 4.45
4106 4884 4.098501 CCCAAATATTTTCTCAGTCCCTGC 59.901 45.833 0.00 0.00 0.00 4.85
4112 4890 0.768221 TTCTCAGTCCCTGCCCTGTT 60.768 55.000 0.00 0.00 0.00 3.16
4143 5264 1.330080 GCAGTGACGCGTTGAATTGC 61.330 55.000 15.53 16.79 0.00 3.56
4176 5297 3.429085 GCTCAAACACAGCCAAATATCG 58.571 45.455 0.00 0.00 0.00 2.92
4201 5322 2.433436 GTTTAGCCGGACCAATCTTGT 58.567 47.619 5.05 0.00 0.00 3.16
4211 5336 3.191371 GGACCAATCTTGTTTACTGCCAG 59.809 47.826 0.00 0.00 0.00 4.85
4228 5353 2.355716 GCCAGTACAGGAGCCAATACAA 60.356 50.000 8.77 0.00 0.00 2.41
4233 5358 2.514803 ACAGGAGCCAATACAACAACC 58.485 47.619 0.00 0.00 0.00 3.77
4239 5364 0.808755 CCAATACAACAACCGAGCCC 59.191 55.000 0.00 0.00 0.00 5.19
4383 5508 1.415672 TTTCCACCCACGAGAAGGCT 61.416 55.000 0.00 0.00 0.00 4.58
4390 5515 1.364626 CCACGAGAAGGCTGATGTGC 61.365 60.000 0.00 0.00 0.00 4.57
4393 5518 2.806856 GAGAAGGCTGATGTGCGCG 61.807 63.158 0.00 0.00 0.00 6.86
4509 5640 2.358615 GCAGGGCGACACACATCA 60.359 61.111 0.00 0.00 0.00 3.07
4512 5643 2.358615 GGGCGACACACATCAGCA 60.359 61.111 0.00 0.00 0.00 4.41
4631 5798 2.943033 CGTTATGGGAGGGTGACAATTC 59.057 50.000 0.00 0.00 0.00 2.17
4635 5802 1.354368 TGGGAGGGTGACAATTCCTTC 59.646 52.381 0.00 0.00 0.00 3.46
4642 5809 3.058224 GGGTGACAATTCCTTCAGAAACG 60.058 47.826 0.00 0.00 38.21 3.60
4659 5826 1.538047 ACGCATGGCAACTTCTGAAT 58.462 45.000 0.00 0.00 37.61 2.57
4660 5827 1.200716 ACGCATGGCAACTTCTGAATG 59.799 47.619 0.00 0.00 37.61 2.67
4661 5828 1.469703 CGCATGGCAACTTCTGAATGA 59.530 47.619 0.00 0.00 37.61 2.57
4662 5829 2.095110 CGCATGGCAACTTCTGAATGAA 60.095 45.455 0.00 0.00 37.61 2.57
4666 5833 5.107220 GCATGGCAACTTCTGAATGAAAAAG 60.107 40.000 0.00 0.00 33.79 2.27
4668 5835 6.219417 TGGCAACTTCTGAATGAAAAAGAA 57.781 33.333 0.00 0.00 33.79 2.52
4700 5870 6.436843 TTTCTGCGATAAAGGAAGGATTTC 57.563 37.500 0.00 0.00 0.00 2.17
4729 5899 3.741249 TCACCACGTAAACTTGCCATAA 58.259 40.909 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.067425 CGTGGATTTACCTGACGTCCA 60.067 52.381 14.12 0.00 39.86 4.02
1 2 1.203052 TCGTGGATTTACCTGACGTCC 59.797 52.381 14.12 0.00 38.59 4.79
16 17 4.135153 CCTCACTCCCGCTCGTGG 62.135 72.222 0.00 0.00 0.00 4.94
91 94 2.325583 TGCCAACTTGAACGAAGACT 57.674 45.000 0.00 0.00 35.42 3.24
143 146 7.096436 CGTAATCGTCAGAAAAGAGTATGATGG 60.096 40.741 0.00 0.00 28.32 3.51
145 148 6.918569 CCGTAATCGTCAGAAAAGAGTATGAT 59.081 38.462 0.00 0.00 35.01 2.45
148 151 5.451520 CCCCGTAATCGTCAGAAAAGAGTAT 60.452 44.000 0.00 0.00 35.01 2.12
149 152 4.142315 CCCCGTAATCGTCAGAAAAGAGTA 60.142 45.833 0.00 0.00 35.01 2.59
163 166 3.504927 CGGCCAAACCCCGTAATC 58.495 61.111 2.24 0.00 40.84 1.75
172 175 2.079158 GAAGTACCCTTACGGCCAAAC 58.921 52.381 2.24 0.00 32.93 2.93
177 180 3.129109 GCATTAGAAGTACCCTTACGGC 58.871 50.000 0.00 0.00 32.93 5.68
187 190 8.335356 GCAAATTTACGATCAGCATTAGAAGTA 58.665 33.333 0.00 0.00 0.00 2.24
189 192 7.412853 AGCAAATTTACGATCAGCATTAGAAG 58.587 34.615 0.00 0.00 0.00 2.85
190 193 7.320443 AGCAAATTTACGATCAGCATTAGAA 57.680 32.000 0.00 0.00 0.00 2.10
228 231 3.576078 TGGACTGATCTCTCTCTCTCC 57.424 52.381 0.00 0.00 0.00 3.71
229 232 4.464008 ACATGGACTGATCTCTCTCTCTC 58.536 47.826 0.00 0.00 0.00 3.20
230 233 4.524802 ACATGGACTGATCTCTCTCTCT 57.475 45.455 0.00 0.00 0.00 3.10
238 241 6.322456 CCATATCCGTATACATGGACTGATCT 59.678 42.308 12.53 0.00 42.80 2.75
249 252 5.599242 TGGTCAGTTTCCATATCCGTATACA 59.401 40.000 3.32 0.00 0.00 2.29
250 253 6.092955 TGGTCAGTTTCCATATCCGTATAC 57.907 41.667 0.00 0.00 0.00 1.47
251 254 6.070995 GGATGGTCAGTTTCCATATCCGTATA 60.071 42.308 0.00 0.00 44.52 1.47
260 263 2.039746 TCGTTGGATGGTCAGTTTCCAT 59.960 45.455 0.00 0.00 46.78 3.41
266 269 3.802948 GAGTATCGTTGGATGGTCAGT 57.197 47.619 0.00 0.00 34.00 3.41
380 384 8.316046 CGTCGGTATTTTAAACTATATATGCGG 58.684 37.037 0.00 0.00 0.00 5.69
393 399 5.120519 CCAGTGCTAAACGTCGGTATTTTAA 59.879 40.000 0.00 0.00 0.00 1.52
399 405 0.961019 ACCAGTGCTAAACGTCGGTA 59.039 50.000 0.00 0.00 31.37 4.02
403 409 1.194772 GCTTGACCAGTGCTAAACGTC 59.805 52.381 0.00 0.00 0.00 4.34
466 472 1.604378 CCTTCCTGACCCGAAGCAT 59.396 57.895 0.00 0.00 36.26 3.79
478 484 3.591254 GAACGCGTGCTCCCTTCCT 62.591 63.158 14.98 0.00 0.00 3.36
482 488 2.357517 CAAGAACGCGTGCTCCCT 60.358 61.111 22.59 1.09 0.00 4.20
504 510 2.363276 TCGGGCCAGGTACGACAT 60.363 61.111 4.39 0.00 0.00 3.06
568 574 1.067635 AGAAAATTGTCATGCCGGCAC 60.068 47.619 35.50 20.76 0.00 5.01
650 656 1.312371 GCTGCCTCGGTATTTTGCCA 61.312 55.000 0.00 0.00 0.00 4.92
654 1099 1.451387 CGGGCTGCCTCGGTATTTT 60.451 57.895 19.68 0.00 0.00 1.82
655 1100 2.189521 CGGGCTGCCTCGGTATTT 59.810 61.111 19.68 0.00 0.00 1.40
660 1105 2.511600 CTAAACGGGCTGCCTCGG 60.512 66.667 25.72 15.87 0.00 4.63
663 1108 0.328258 ATGAACTAAACGGGCTGCCT 59.672 50.000 19.68 0.28 0.00 4.75
664 1109 0.451783 CATGAACTAAACGGGCTGCC 59.548 55.000 11.05 11.05 0.00 4.85
665 1110 1.135689 CACATGAACTAAACGGGCTGC 60.136 52.381 0.00 0.00 0.00 5.25
666 1111 2.095768 CACACATGAACTAAACGGGCTG 60.096 50.000 0.00 0.00 0.00 4.85
667 1112 2.151202 CACACATGAACTAAACGGGCT 58.849 47.619 0.00 0.00 0.00 5.19
671 1116 2.350388 GGCACCACACATGAACTAAACG 60.350 50.000 0.00 0.00 0.00 3.60
672 1117 2.884639 AGGCACCACACATGAACTAAAC 59.115 45.455 0.00 0.00 0.00 2.01
687 1195 1.453928 GTCTTATGGCCCAGGCACC 60.454 63.158 11.50 0.40 41.84 5.01
757 1310 0.603975 GTGAGTCAGACCTGGCCAAC 60.604 60.000 7.01 0.00 35.39 3.77
796 1349 3.126171 TCGTTGCTTTATTCCATTCCACG 59.874 43.478 0.00 0.00 0.00 4.94
822 1375 3.687200 CTTACACGTCCGTTTGCTTTTT 58.313 40.909 0.00 0.00 0.00 1.94
823 1376 2.540157 GCTTACACGTCCGTTTGCTTTT 60.540 45.455 0.00 0.00 0.00 2.27
824 1377 1.003223 GCTTACACGTCCGTTTGCTTT 60.003 47.619 0.00 0.00 0.00 3.51
825 1378 0.584876 GCTTACACGTCCGTTTGCTT 59.415 50.000 0.00 0.00 0.00 3.91
826 1379 0.249741 AGCTTACACGTCCGTTTGCT 60.250 50.000 0.00 0.00 0.00 3.91
827 1380 0.163146 GAGCTTACACGTCCGTTTGC 59.837 55.000 0.00 0.00 0.00 3.68
829 1382 0.390124 TGGAGCTTACACGTCCGTTT 59.610 50.000 0.00 0.00 32.51 3.60
1020 1600 1.590238 CTCACCTTGATGATTCGTCGC 59.410 52.381 1.59 0.00 0.00 5.19
1040 1620 1.270826 TCGGATGATCAGATCGGAAGC 59.729 52.381 0.09 0.00 30.97 3.86
1081 1661 1.132643 AGAAAAGACGAGTCGGATCGG 59.867 52.381 18.30 0.00 46.91 4.18
1100 1680 5.278604 CCAAAAAGTTAGACACGGGAAAAG 58.721 41.667 0.00 0.00 0.00 2.27
1125 1709 0.953960 AGATCCAACCACGCGGAAAC 60.954 55.000 12.47 0.00 34.22 2.78
1146 1730 3.443925 TCTCTGCGTCTCCTGCGG 61.444 66.667 0.00 0.00 40.13 5.69
1192 1777 0.953960 ACCCGAAACCGCAGATTGAC 60.954 55.000 0.00 0.00 0.00 3.18
1216 1801 3.057315 CAGAAATGAAACACCTCGCCATT 60.057 43.478 0.00 0.00 0.00 3.16
1217 1802 2.489329 CAGAAATGAAACACCTCGCCAT 59.511 45.455 0.00 0.00 0.00 4.40
1230 1815 2.091541 GGAAATCGCACCCAGAAATGA 58.908 47.619 0.00 0.00 0.00 2.57
1243 1828 2.420022 ACCATTCAAAGAGCGGAAATCG 59.580 45.455 0.00 0.00 42.76 3.34
1264 1849 0.459237 CCGGTGCTGCACAAACAAAA 60.459 50.000 31.35 0.00 35.86 2.44
1265 1850 1.140589 CCGGTGCTGCACAAACAAA 59.859 52.632 31.35 0.00 35.86 2.83
1318 1903 4.568359 CCAAGGATCATGACGTTGAAGTAG 59.432 45.833 21.63 9.16 35.89 2.57
1370 1955 9.362539 TCACTATCGTGTATTAAAAGGAAGAAC 57.637 33.333 0.00 0.00 41.89 3.01
1372 1957 9.529325 CATCACTATCGTGTATTAAAAGGAAGA 57.471 33.333 0.00 0.00 41.89 2.87
1373 1958 9.314321 ACATCACTATCGTGTATTAAAAGGAAG 57.686 33.333 0.00 0.00 41.89 3.46
1374 1959 9.661563 AACATCACTATCGTGTATTAAAAGGAA 57.338 29.630 0.00 0.00 41.89 3.36
1375 1960 9.093970 CAACATCACTATCGTGTATTAAAAGGA 57.906 33.333 0.00 0.00 41.89 3.36
1376 1961 8.879759 ACAACATCACTATCGTGTATTAAAAGG 58.120 33.333 0.00 0.00 41.89 3.11
1446 2034 7.553881 AGAACATCTTATATTTGTGAACGGG 57.446 36.000 0.00 0.00 0.00 5.28
1479 2067 6.319141 TGTCTATACACATCCGATTCAGAG 57.681 41.667 0.00 0.00 0.00 3.35
1494 2083 8.374327 ACAAACACACTAAAAGGTGTCTATAC 57.626 34.615 0.00 0.00 46.82 1.47
1504 2093 6.842163 AGTGAGTGAACAAACACACTAAAAG 58.158 36.000 5.75 0.00 46.06 2.27
1582 2171 1.687123 GCTAATTGCTACTCCCTCCGA 59.313 52.381 0.00 0.00 38.95 4.55
1655 2244 4.706476 ACACCATCCATAATTCCAACACAG 59.294 41.667 0.00 0.00 0.00 3.66
1678 2267 4.065088 GACTGATCAAACAGCACAACCTA 58.935 43.478 0.00 0.00 41.06 3.08
1718 2307 8.523658 GCCATGAAGAGGAATAAACTAAAACTT 58.476 33.333 0.00 0.00 0.00 2.66
1726 2315 5.904362 AACTGCCATGAAGAGGAATAAAC 57.096 39.130 0.00 0.00 0.00 2.01
1839 2428 6.019779 TGTTAACCATGGAAATAAGTGTGC 57.980 37.500 21.47 3.59 0.00 4.57
1861 2450 6.578163 TGTGGCATCCATATCAATACAATG 57.422 37.500 0.00 0.00 35.28 2.82
1902 2491 9.410556 CTTAAGCAAGCAAATATGTTAACAGTT 57.589 29.630 14.65 8.62 0.00 3.16
1903 2492 8.970691 CTTAAGCAAGCAAATATGTTAACAGT 57.029 30.769 14.65 2.46 0.00 3.55
2178 2767 1.739067 ATGTAAGAAAGCCGGTCAGC 58.261 50.000 1.90 0.00 0.00 4.26
2180 2769 3.134574 ACAATGTAAGAAAGCCGGTCA 57.865 42.857 1.90 0.00 0.00 4.02
2263 2852 2.032681 GGGGCAGCCATCGGATAC 59.967 66.667 15.19 0.00 0.00 2.24
2357 2973 2.147150 GCCAAAGAGGAAGTCACACTC 58.853 52.381 0.00 0.00 41.22 3.51
2365 2981 4.518211 CAGCCATATTAGCCAAAGAGGAAG 59.482 45.833 0.00 0.00 41.22 3.46
2378 2994 6.835488 AGCCAAAGAAGAAATCAGCCATATTA 59.165 34.615 0.00 0.00 0.00 0.98
2411 3027 4.609691 ACTTCGCAAAAGAAAGTCGAAA 57.390 36.364 3.02 0.00 38.45 3.46
2428 3044 7.606839 AGCCCTTGAACATAAGTACTTAACTTC 59.393 37.037 18.88 19.29 45.64 3.01
2462 3078 3.247648 CCCACCGAAGTAATCTAAATGCG 59.752 47.826 0.00 0.00 0.00 4.73
2601 3217 4.400251 CCACAACAGGACATATGAAAGCAT 59.600 41.667 10.38 0.00 38.54 3.79
2642 3258 3.449018 TGTCTAGACAGGGAAATGAGAGC 59.551 47.826 21.74 0.00 36.21 4.09
2643 3259 5.186797 AGTTGTCTAGACAGGGAAATGAGAG 59.813 44.000 23.97 0.00 42.94 3.20
2666 3282 4.978083 ATGTCCAATCAAGCAGCTAAAG 57.022 40.909 0.00 0.00 0.00 1.85
2678 3294 6.769822 ACACTCCATCATTTCTATGTCCAATC 59.230 38.462 0.00 0.00 33.34 2.67
2705 3337 4.292977 GGCATTTAGGCTGTACATGTTC 57.707 45.455 2.30 0.00 40.24 3.18
2776 3408 7.144000 AGAATCTGAGTGCAAGTGAAAATTTC 58.856 34.615 0.00 0.00 0.00 2.17
2782 3414 6.095300 TCAAAAAGAATCTGAGTGCAAGTGAA 59.905 34.615 0.00 0.00 0.00 3.18
2794 3426 9.748708 TTGACATAAACCTTCAAAAAGAATCTG 57.251 29.630 0.00 0.00 35.25 2.90
2847 3479 6.570692 CAACCTATAGAACCACGACAACTAT 58.429 40.000 0.00 0.00 0.00 2.12
2848 3480 5.622914 GCAACCTATAGAACCACGACAACTA 60.623 44.000 0.00 0.00 0.00 2.24
2849 3481 4.817517 CAACCTATAGAACCACGACAACT 58.182 43.478 0.00 0.00 0.00 3.16
2865 3497 9.474313 AAATACAAAATCAGAATAGGCAACCTA 57.526 29.630 0.00 0.00 40.71 3.08
2867 3499 7.706607 GGAAATACAAAATCAGAATAGGCAACC 59.293 37.037 0.00 0.00 37.17 3.77
2946 3681 4.093998 CTGTACTCCAGTAGCAATTGCTTG 59.906 45.833 35.99 27.48 41.66 4.01
2974 3712 4.772886 TTATAGAGACCAAAGGAAGGGC 57.227 45.455 0.00 0.00 0.00 5.19
3064 3802 2.500098 TCAGAAACCTAACCTGCGCTAT 59.500 45.455 9.73 0.00 0.00 2.97
3283 4023 3.445008 AGCTTACAGAGACCCAGAATGA 58.555 45.455 0.00 0.00 39.69 2.57
3284 4024 3.902881 AGCTTACAGAGACCCAGAATG 57.097 47.619 0.00 0.00 0.00 2.67
3302 4042 7.699812 CAGAAAAAGAGGTTATGAAATGCTAGC 59.300 37.037 8.10 8.10 0.00 3.42
3303 4043 8.950210 TCAGAAAAAGAGGTTATGAAATGCTAG 58.050 33.333 0.00 0.00 0.00 3.42
3320 4060 4.505556 GCAAAGGAAACAGCTCAGAAAAAG 59.494 41.667 0.00 0.00 0.00 2.27
3384 4124 5.149973 TGCTACAAACAGGTTATTCGGTA 57.850 39.130 0.00 0.00 0.00 4.02
3414 4154 2.675317 CGGAAACTGAGACAGGGTGATC 60.675 54.545 0.00 0.00 35.51 2.92
3661 4437 9.384764 GCCAGAACAGAACTTAGTTAAGATATT 57.615 33.333 0.00 0.00 37.08 1.28
4018 4796 7.547227 ACAAGAGCAAGAACAAATTAACAAGT 58.453 30.769 0.00 0.00 0.00 3.16
4117 4895 0.242825 AACGCGTCACTGCTAGCTAA 59.757 50.000 14.44 0.00 0.00 3.09
4119 4897 1.734477 CAACGCGTCACTGCTAGCT 60.734 57.895 14.44 0.00 0.00 3.32
4120 4898 1.282248 TTCAACGCGTCACTGCTAGC 61.282 55.000 14.44 8.10 0.00 3.42
4121 4899 1.350193 ATTCAACGCGTCACTGCTAG 58.650 50.000 14.44 0.00 0.00 3.42
4123 4901 0.235665 CAATTCAACGCGTCACTGCT 59.764 50.000 14.44 0.00 0.00 4.24
4176 5297 0.034863 TTGGTCCGGCTAAACCATCC 60.035 55.000 13.13 0.00 44.72 3.51
4201 5322 1.278127 GGCTCCTGTACTGGCAGTAAA 59.722 52.381 27.75 22.01 31.62 2.01
4211 5336 3.439129 GGTTGTTGTATTGGCTCCTGTAC 59.561 47.826 0.00 0.00 0.00 2.90
4239 5364 3.117171 GCCACACTCGAGCAGCAG 61.117 66.667 13.61 1.84 0.00 4.24
4324 5449 1.665169 CAAGCAGGTTTTGTTGCAACC 59.335 47.619 26.14 11.85 43.73 3.77
4402 5527 2.047844 CCGTCTGTGACAGGGCAG 60.048 66.667 13.33 2.01 32.09 4.85
4501 5626 0.870393 GTCCTGTGTGCTGATGTGTG 59.130 55.000 0.00 0.00 0.00 3.82
4509 5640 0.392193 GCATGCTAGTCCTGTGTGCT 60.392 55.000 11.37 0.00 0.00 4.40
4512 5643 0.979665 ACTGCATGCTAGTCCTGTGT 59.020 50.000 20.33 1.26 0.00 3.72
4549 5680 4.028131 TCGCAAGATAAGAGGGTCCTTTA 58.972 43.478 0.00 0.00 45.01 1.85
4631 5798 0.597568 TTGCCATGCGTTTCTGAAGG 59.402 50.000 0.00 0.00 0.00 3.46
4635 5802 1.267806 AGAAGTTGCCATGCGTTTCTG 59.732 47.619 0.00 0.00 0.00 3.02
4642 5809 3.581024 TTCATTCAGAAGTTGCCATGC 57.419 42.857 0.00 0.00 0.00 4.06
4669 5836 7.433425 CCTTCCTTTATCGCAGAAATCATTTTC 59.567 37.037 0.00 0.00 43.58 2.29
4674 5844 5.097742 TCCTTCCTTTATCGCAGAAATCA 57.902 39.130 0.00 0.00 43.58 2.57
4675 5845 6.625873 AATCCTTCCTTTATCGCAGAAATC 57.374 37.500 0.00 0.00 43.58 2.17
4676 5846 6.039829 GGAAATCCTTCCTTTATCGCAGAAAT 59.960 38.462 0.00 0.00 46.80 2.17
4679 5849 4.451900 GGAAATCCTTCCTTTATCGCAGA 58.548 43.478 0.00 0.00 46.80 4.26
4700 5870 3.408634 AGTTTACGTGGTGAAAGATGGG 58.591 45.455 0.00 0.00 0.00 4.00
4708 5878 2.264005 ATGGCAAGTTTACGTGGTGA 57.736 45.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.