Multiple sequence alignment - TraesCS6D01G113600

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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 TraesCS6D01G113600 chr6D 100.000 6341 0 0 1 6341 80526379 80520039 0.000000e+00 11710.0
1 TraesCS6D01G113600 chr6D 85.185 189 8 6 5721 5909 80513055 80512887 6.530000e-40 176.0
2 TraesCS6D01G113600 chr6D 78.626 131 12 10 5573 5702 80520752 80520637 8.820000e-09 73.1
3 TraesCS6D01G113600 chr6D 78.626 131 12 10 5628 5743 80520807 80520678 8.820000e-09 73.1
4 TraesCS6D01G113600 chr6A 94.338 4274 165 38 2077 6308 96988471 96984233 0.000000e+00 6481.0
5 TraesCS6D01G113600 chr6A 84.892 2138 160 68 1 2078 96990632 96988598 0.000000e+00 2008.0
6 TraesCS6D01G113600 chr6A 89.499 1038 96 1 3652 4689 20768829 20769853 0.000000e+00 1301.0
7 TraesCS6D01G113600 chr6A 89.403 1038 97 1 3652 4689 20801546 20802570 0.000000e+00 1295.0
8 TraesCS6D01G113600 chr6A 89.347 995 84 12 2264 3254 20767344 20768320 0.000000e+00 1230.0
9 TraesCS6D01G113600 chr6A 89.347 995 84 12 2264 3254 20800061 20801037 0.000000e+00 1230.0
10 TraesCS6D01G113600 chr6A 82.670 352 38 11 1647 1976 20766939 20767289 2.240000e-74 291.0
11 TraesCS6D01G113600 chr6A 82.486 354 37 10 1647 1976 20799654 20800006 2.890000e-73 287.0
12 TraesCS6D01G113600 chr6A 88.199 161 13 3 3406 3563 20768652 20768809 3.020000e-43 187.0
13 TraesCS6D01G113600 chr6A 88.199 161 13 3 3406 3563 20801369 20801526 3.020000e-43 187.0
14 TraesCS6D01G113600 chr6A 76.404 267 40 20 5311 5574 96820792 96820546 8.630000e-24 122.0
15 TraesCS6D01G113600 chr6A 91.304 46 3 1 3592 3637 20768786 20768830 1.910000e-05 62.1
16 TraesCS6D01G113600 chr6A 91.304 46 3 1 3592 3637 20801503 20801547 1.910000e-05 62.1
17 TraesCS6D01G113600 chr6B 97.735 2252 39 6 3562 5810 153958372 153956130 0.000000e+00 3866.0
18 TraesCS6D01G113600 chr6B 94.340 1696 72 12 2027 3702 153960243 153958552 0.000000e+00 2579.0
19 TraesCS6D01G113600 chr6B 88.910 2092 137 29 1 2028 153962440 153960380 0.000000e+00 2490.0
20 TraesCS6D01G113600 chr6B 83.700 1135 129 30 2027 3111 73892102 73893230 0.000000e+00 1020.0
21 TraesCS6D01G113600 chr6B 83.855 1022 118 26 1931 2914 73587786 73588798 0.000000e+00 929.0
22 TraesCS6D01G113600 chr6B 83.710 1019 119 25 1934 2914 73656565 73657574 0.000000e+00 918.0
23 TraesCS6D01G113600 chr6B 83.611 1019 116 27 1934 2914 73628012 73629017 0.000000e+00 909.0
24 TraesCS6D01G113600 chr6B 83.784 925 108 22 2027 2914 73732047 73732966 0.000000e+00 839.0
25 TraesCS6D01G113600 chr6B 87.225 454 43 7 2662 3111 73745518 73745960 2.640000e-138 503.0
26 TraesCS6D01G113600 chr6B 81.416 678 70 31 5693 6341 153685823 153685173 2.640000e-138 503.0
27 TraesCS6D01G113600 chr6B 86.013 479 53 6 2637 3111 73738483 73738951 9.490000e-138 501.0
28 TraesCS6D01G113600 chr6B 81.213 676 71 24 5695 6341 153757425 153756777 1.590000e-135 494.0
29 TraesCS6D01G113600 chr6B 92.336 274 19 1 6070 6341 153955874 153955601 7.710000e-104 388.0
30 TraesCS6D01G113600 chr6B 98.104 211 4 0 5851 6061 153956123 153955913 1.000000e-97 368.0
31 TraesCS6D01G113600 chr6B 86.486 296 22 11 5723 6018 153530010 153529733 6.170000e-80 309.0
32 TraesCS6D01G113600 chr6B 93.750 160 9 1 3532 3691 153958558 153958400 8.220000e-59 239.0
33 TraesCS6D01G113600 chr6B 88.889 189 5 9 5721 5909 153676477 153676305 1.070000e-52 219.0
34 TraesCS6D01G113600 chr6B 88.360 189 6 9 5721 5909 153747789 153747617 4.980000e-51 213.0
35 TraesCS6D01G113600 chr6B 93.333 135 7 2 5693 5826 153401550 153401417 1.390000e-46 198.0
36 TraesCS6D01G113600 chr6B 85.987 157 12 3 6108 6257 153365463 153365310 6.580000e-35 159.0
37 TraesCS6D01G113600 chr6B 85.621 153 14 2 6110 6257 153907814 153907665 3.060000e-33 154.0
38 TraesCS6D01G113600 chr6B 86.260 131 14 3 5903 6033 153400980 153400854 8.570000e-29 139.0
39 TraesCS6D01G113600 chr6B 90.099 101 8 1 6108 6206 153453365 153453265 5.160000e-26 130.0
40 TraesCS6D01G113600 chr6B 84.884 86 7 3 594 679 155233876 155233797 1.470000e-11 82.4
41 TraesCS6D01G113600 chr6B 91.071 56 5 0 2048 2103 73656626 73656681 6.820000e-10 76.8
42 TraesCS6D01G113600 chr6B 95.238 42 2 0 5661 5702 153685815 153685774 4.100000e-07 67.6
43 TraesCS6D01G113600 chr6B 93.182 44 3 0 5851 5894 153359123 153359080 1.480000e-06 65.8
44 TraesCS6D01G113600 chr6B 93.182 44 1 2 5661 5702 153956240 153956197 5.310000e-06 63.9
45 TraesCS6D01G113600 chr6B 90.909 44 4 0 5851 5894 153357079 153357036 6.870000e-05 60.2
46 TraesCS6D01G113600 chrUn 85.804 479 54 6 2637 3111 300243341 300243809 4.420000e-136 496.0
47 TraesCS6D01G113600 chrUn 85.595 479 55 6 2637 3111 300248053 300248521 2.050000e-134 490.0


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 TraesCS6D01G113600 chr6D 80520039 80526379 6340 True 11710.00 11710 100.0000 1 6341 1 chr6D.!!$R2 6340
1 TraesCS6D01G113600 chr6A 96984233 96990632 6399 True 4244.50 6481 89.6150 1 6308 2 chr6A.!!$R2 6307
2 TraesCS6D01G113600 chr6A 20766939 20769853 2914 False 614.22 1301 88.2038 1647 4689 5 chr6A.!!$F1 3042
3 TraesCS6D01G113600 chr6A 20799654 20802570 2916 False 612.22 1295 88.1478 1647 4689 5 chr6A.!!$F2 3042
4 TraesCS6D01G113600 chr6B 153955601 153962440 6839 True 1427.70 3866 94.0510 1 6341 7 chr6B.!!$R12 6340
5 TraesCS6D01G113600 chr6B 73892102 73893230 1128 False 1020.00 1020 83.7000 2027 3111 1 chr6B.!!$F6 1084
6 TraesCS6D01G113600 chr6B 73587786 73588798 1012 False 929.00 929 83.8550 1931 2914 1 chr6B.!!$F1 983
7 TraesCS6D01G113600 chr6B 73628012 73629017 1005 False 909.00 909 83.6110 1934 2914 1 chr6B.!!$F2 980
8 TraesCS6D01G113600 chr6B 73732047 73732966 919 False 839.00 839 83.7840 2027 2914 1 chr6B.!!$F3 887
9 TraesCS6D01G113600 chr6B 73656565 73657574 1009 False 497.40 918 87.3905 1934 2914 2 chr6B.!!$F7 980
10 TraesCS6D01G113600 chr6B 153756777 153757425 648 True 494.00 494 81.2130 5695 6341 1 chr6B.!!$R6 646
11 TraesCS6D01G113600 chr6B 153685173 153685823 650 True 285.30 503 88.3270 5661 6341 2 chr6B.!!$R11 680

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
24 25 0.108662 GCATTACAAGCCAACCCTGC 60.109 55.0 0.0 0.0 0.00 4.85 F
1055 1103 0.395311 TCCCGATTCCTACGCTGTCT 60.395 55.0 0.0 0.0 0.00 3.41 F
1738 1851 0.255890 TTAGGATTCAGCAGGGTGGC 59.744 55.0 0.0 0.0 0.00 5.01 F
2149 2559 0.405198 TGGGTGGTCTTGTGCATGAT 59.595 50.0 0.0 0.0 0.00 2.45 F
3206 3653 0.671781 ACTGTCGGAAGCAGCATGAC 60.672 55.0 0.0 0.0 39.69 3.06 F
4482 5532 1.692411 ACAGGAGCCCAAAGACAAAC 58.308 50.0 0.0 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1794 0.105039 GCTAACCCCAGTCATCCTCG 59.895 60.0 0.00 0.00 0.00 4.63 R
2516 2951 0.417841 TAGCTCCTGGAGGAAAGGGT 59.582 55.0 24.43 7.04 44.91 4.34 R
3185 3632 0.167470 CATGCTGCTTCCGACAGTTG 59.833 55.0 0.00 0.00 37.47 3.16 R
3747 4797 1.257750 ATATATCCAGCCGCCGAGCA 61.258 55.0 0.70 0.00 34.23 4.26 R
4674 5724 0.708209 TGACCTCTGGTACCCTAGCA 59.292 55.0 10.07 0.00 35.25 3.49 R
6073 7155 0.949105 GCTGCGAGTTCTCGGGAAAA 60.949 55.0 20.97 0.00 32.81 2.29 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
24 25 0.108662 GCATTACAAGCCAACCCTGC 60.109 55.000 0.00 0.00 0.00 4.85
86 88 0.622665 CTCAATCCTTCTGGCTGGGT 59.377 55.000 0.00 0.00 0.00 4.51
123 125 2.787994 CAATCACTCTGGCAACCTTCT 58.212 47.619 0.00 0.00 0.00 2.85
127 129 1.071385 CACTCTGGCAACCTTCTGACT 59.929 52.381 0.00 0.00 0.00 3.41
128 130 2.300152 CACTCTGGCAACCTTCTGACTA 59.700 50.000 0.00 0.00 0.00 2.59
136 138 5.189180 GGCAACCTTCTGACTATGAGATTT 58.811 41.667 0.00 0.00 0.00 2.17
154 156 5.730550 AGATTTGAGCGAACCTTGTACATA 58.269 37.500 0.00 0.00 0.00 2.29
157 159 5.339008 TTGAGCGAACCTTGTACATAGAT 57.661 39.130 0.00 0.00 0.00 1.98
158 160 4.682787 TGAGCGAACCTTGTACATAGATG 58.317 43.478 0.00 0.00 0.00 2.90
159 161 4.159693 TGAGCGAACCTTGTACATAGATGT 59.840 41.667 0.00 0.08 44.48 3.06
162 164 4.679639 GCGAACCTTGTACATAGATGTGGA 60.680 45.833 5.39 0.00 41.89 4.02
167 169 4.499865 CCTTGTACATAGATGTGGACGGAG 60.500 50.000 5.39 0.30 41.89 4.63
168 170 2.956333 TGTACATAGATGTGGACGGAGG 59.044 50.000 5.39 0.00 41.89 4.30
169 171 0.753262 ACATAGATGTGGACGGAGGC 59.247 55.000 0.00 0.00 40.03 4.70
188 190 1.067635 GCTCATCACCGCCAAAACAAT 60.068 47.619 0.00 0.00 0.00 2.71
202 204 6.260936 CGCCAAAACAATCTAGAGGATAACAT 59.739 38.462 0.00 0.00 33.71 2.71
203 205 7.420800 GCCAAAACAATCTAGAGGATAACATG 58.579 38.462 0.00 0.00 33.71 3.21
205 207 9.177608 CCAAAACAATCTAGAGGATAACATGAA 57.822 33.333 0.00 0.00 33.71 2.57
207 209 9.965902 AAAACAATCTAGAGGATAACATGAAGT 57.034 29.630 0.00 0.00 33.71 3.01
208 210 9.606631 AAACAATCTAGAGGATAACATGAAGTC 57.393 33.333 0.00 0.00 33.71 3.01
209 211 8.311395 ACAATCTAGAGGATAACATGAAGTCA 57.689 34.615 0.00 0.00 33.71 3.41
210 212 8.200792 ACAATCTAGAGGATAACATGAAGTCAC 58.799 37.037 0.00 0.00 33.71 3.67
211 213 6.716934 TCTAGAGGATAACATGAAGTCACC 57.283 41.667 0.00 0.00 0.00 4.02
217 219 4.209288 GGATAACATGAAGTCACCGAATCG 59.791 45.833 0.00 0.00 0.00 3.34
237 239 3.120792 CGGAAACCAACGATGACGATAT 58.879 45.455 0.00 0.00 42.66 1.63
279 289 8.924511 TCCTTCTCTTTCAAACATATGAACTT 57.075 30.769 10.38 0.00 38.95 2.66
285 295 9.599322 CTCTTTCAAACATATGAACTTGTACAC 57.401 33.333 10.38 0.00 38.95 2.90
345 355 5.281693 GCAATGCGCATCACATATAACTA 57.718 39.130 25.53 0.00 41.79 2.24
346 356 5.082059 GCAATGCGCATCACATATAACTAC 58.918 41.667 25.53 0.00 41.79 2.73
347 357 5.621422 CAATGCGCATCACATATAACTACC 58.379 41.667 25.53 0.00 0.00 3.18
348 358 4.329462 TGCGCATCACATATAACTACCA 57.671 40.909 5.66 0.00 0.00 3.25
349 359 4.893608 TGCGCATCACATATAACTACCAT 58.106 39.130 5.66 0.00 0.00 3.55
401 414 6.906157 AATTCACACATCAACCTTTCATCT 57.094 33.333 0.00 0.00 0.00 2.90
412 425 7.687941 TCAACCTTTCATCTTCTATTCAACC 57.312 36.000 0.00 0.00 0.00 3.77
434 447 9.168451 CAACCGATCTATCATAGTATAGACACT 57.832 37.037 0.00 0.00 40.40 3.55
446 459 2.913777 TAGACACTCATCGACGGTTG 57.086 50.000 0.00 0.00 0.00 3.77
466 479 5.415701 GGTTGGATGAGTAACACACAATGAT 59.584 40.000 0.00 0.00 32.80 2.45
470 483 6.539826 TGGATGAGTAACACACAATGATGATC 59.460 38.462 0.00 0.00 0.00 2.92
471 484 6.539826 GGATGAGTAACACACAATGATGATCA 59.460 38.462 0.00 0.00 0.00 2.92
521 538 6.899114 GTGGAAGGTTACACAAACTTATCAG 58.101 40.000 0.00 0.00 41.87 2.90
551 568 5.468072 GTGACAATAGACATAGATTGCCCTG 59.532 44.000 0.00 0.00 36.67 4.45
639 670 3.629142 ACCAGCTAACACCATCTAACC 57.371 47.619 0.00 0.00 0.00 2.85
762 793 4.700365 GTGGGACGCAAAAGCGGC 62.700 66.667 14.62 11.25 41.01 6.53
846 888 2.601868 GGCGGGGGTAGAGAGAGA 59.398 66.667 0.00 0.00 0.00 3.10
847 889 1.076192 GGCGGGGGTAGAGAGAGAA 60.076 63.158 0.00 0.00 0.00 2.87
848 890 0.686769 GGCGGGGGTAGAGAGAGAAA 60.687 60.000 0.00 0.00 0.00 2.52
849 891 1.192428 GCGGGGGTAGAGAGAGAAAA 58.808 55.000 0.00 0.00 0.00 2.29
886 928 3.051803 AGAGGAGGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
888 930 3.051803 AGGAGGAGAGAGAGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
947 994 4.154347 GTGAGCCCAGCGGAGGAG 62.154 72.222 0.00 0.00 0.00 3.69
952 999 4.465446 CCCAGCGGAGGAGGAGGA 62.465 72.222 0.00 0.00 0.00 3.71
1055 1103 0.395311 TCCCGATTCCTACGCTGTCT 60.395 55.000 0.00 0.00 0.00 3.41
1361 1454 4.367023 GCGTGGCTGTACCGGTGA 62.367 66.667 19.93 2.06 43.94 4.02
1519 1614 4.309950 GTCCGCCGGGAACAGTGT 62.310 66.667 1.90 0.00 46.08 3.55
1525 1620 2.432628 CGGGAACAGTGTCTCCGC 60.433 66.667 19.59 9.72 34.17 5.54
1683 1791 6.385649 TGGTCTTATCTGTTTTGTGGTTTC 57.614 37.500 0.00 0.00 0.00 2.78
1686 1794 5.915196 GTCTTATCTGTTTTGTGGTTTCTGC 59.085 40.000 0.00 0.00 0.00 4.26
1687 1795 2.842208 TCTGTTTTGTGGTTTCTGCG 57.158 45.000 0.00 0.00 0.00 5.18
1696 1804 0.976641 TGGTTTCTGCGAGGATGACT 59.023 50.000 0.00 0.00 0.00 3.41
1738 1851 0.255890 TTAGGATTCAGCAGGGTGGC 59.744 55.000 0.00 0.00 0.00 5.01
1772 1891 2.426522 GTTCCATGTCAAGCTGCTGTA 58.573 47.619 1.35 0.00 0.00 2.74
1797 1923 1.448985 GCGCAAGTAGATGGTTTCCA 58.551 50.000 0.30 0.00 37.61 3.53
1814 1940 1.360852 TCCATATGCCAACCCTGGTTT 59.639 47.619 0.00 0.00 45.53 3.27
1816 1942 1.756538 CATATGCCAACCCTGGTTTCC 59.243 52.381 0.00 0.00 45.53 3.13
1824 1950 1.964373 CCCTGGTTTCCGGTGTTCG 60.964 63.158 0.00 0.00 38.88 3.95
1867 2000 6.023435 GTGTATGTACAATGCACATGTCTTG 58.977 40.000 9.23 3.07 37.22 3.02
1998 2131 4.154015 TCTGGTGCATTTCGAGTTTGTATG 59.846 41.667 0.00 0.00 0.00 2.39
2123 2533 1.743252 GTAGTCAGTGCCAGCAGCC 60.743 63.158 0.00 0.00 42.71 4.85
2138 2548 1.152546 AGCCTTTGGTTGGGTGGTC 60.153 57.895 0.00 0.00 33.62 4.02
2149 2559 0.405198 TGGGTGGTCTTGTGCATGAT 59.595 50.000 0.00 0.00 0.00 2.45
2169 2579 3.600717 TTGCACTTGTTATGTCGTGTG 57.399 42.857 0.00 0.00 0.00 3.82
2261 2692 7.087639 GCATGTGTTATGCTTTTTAGTACCAA 58.912 34.615 4.73 0.00 41.52 3.67
2343 2775 5.212934 GGAATTTTCGGTTCTCAAGTTGTC 58.787 41.667 2.11 0.00 0.00 3.18
2358 2790 5.355071 TCAAGTTGTCCATTGCTGATACATC 59.645 40.000 2.11 0.00 0.00 3.06
2359 2791 3.873361 AGTTGTCCATTGCTGATACATCG 59.127 43.478 0.00 0.00 0.00 3.84
2426 2860 1.242076 ACTTCTGGATGTGCAAGCAC 58.758 50.000 17.76 17.76 46.33 4.40
2481 2916 6.183360 GCACAAGATTGATTGCACTGTTTATG 60.183 38.462 0.00 0.00 32.38 1.90
2486 2921 9.715121 AAGATTGATTGCACTGTTTATGAATTT 57.285 25.926 0.00 0.00 0.00 1.82
2603 3042 7.331026 AGAAGGATCTTGTTCGTGAATTATCA 58.669 34.615 0.00 0.00 29.15 2.15
2799 3241 1.682854 TGCAAGAAAAGGAGCCAACTG 59.317 47.619 0.00 0.00 0.00 3.16
2831 3273 2.026636 TGCAAGTAACCATCAGTACCCC 60.027 50.000 0.00 0.00 0.00 4.95
3068 3515 4.862902 ATCCTGTAGTTCAGATCATCCG 57.137 45.455 0.00 0.00 46.27 4.18
3185 3632 2.230660 GATGGTGCTTATTACTGCCCC 58.769 52.381 0.00 0.00 0.00 5.80
3206 3653 0.671781 ACTGTCGGAAGCAGCATGAC 60.672 55.000 0.00 0.00 39.69 3.06
3240 3687 4.892433 TGTATTCTGGGGCATTGTTTTTG 58.108 39.130 0.00 0.00 0.00 2.44
3354 3801 8.685838 TTCACTGCCTTAGTTTGTTTATTACT 57.314 30.769 0.00 0.00 37.60 2.24
3357 3804 6.488683 ACTGCCTTAGTTTGTTTATTACTGCA 59.511 34.615 0.00 0.00 35.67 4.41
3429 4152 4.927425 GCACGTCTGTTAACAAGAATCCTA 59.073 41.667 10.03 0.00 0.00 2.94
3527 4256 8.788806 CAACCCAGTACAATGTACTTTTATCAA 58.211 33.333 22.14 0.00 0.00 2.57
3560 4289 6.817765 TTCATCAAGTTTACCAGTCCATTC 57.182 37.500 0.00 0.00 0.00 2.67
3581 4474 7.255035 CCATTCTCCATACAATAGCAACTCTTG 60.255 40.741 0.00 0.00 0.00 3.02
3637 4530 5.421277 TCTGTTTCCTCTTGTTTGAACGTA 58.579 37.500 0.00 0.00 0.00 3.57
3643 4536 7.504924 TTCCTCTTGTTTGAACGTATGAATT 57.495 32.000 0.00 0.00 0.00 2.17
3726 4776 3.406764 CTTGTTCAGGTCCTGGAAGAAG 58.593 50.000 19.11 18.47 34.07 2.85
3747 4797 9.454859 AAGAAGCAACTAATGTTAGCTAAAGAT 57.545 29.630 7.99 0.45 38.55 2.40
3780 4830 6.351541 GGCTGGATATATTGTGTTACCGGATA 60.352 42.308 9.46 0.00 0.00 2.59
3801 4851 6.500751 GGATATTTCTGGGTCATAAGGTCCTA 59.499 42.308 0.00 0.00 0.00 2.94
3807 4857 4.890988 TGGGTCATAAGGTCCTATTCTCA 58.109 43.478 0.00 0.00 0.00 3.27
4005 5055 4.168101 AGTTCCCTGTTGAATCTCCTACA 58.832 43.478 0.00 0.00 0.00 2.74
4168 5218 5.008811 ACGCCTACATCTATCACTGTAGTTC 59.991 44.000 8.44 1.11 42.04 3.01
4239 5289 2.283143 TATGGCACCAGGTGGATGGC 62.283 60.000 21.77 8.05 44.80 4.40
4257 5307 3.071479 TGGCACAGGATTTTACTCGTTC 58.929 45.455 0.00 0.00 0.00 3.95
4482 5532 1.692411 ACAGGAGCCCAAAGACAAAC 58.308 50.000 0.00 0.00 0.00 2.93
5014 6064 1.479368 GCCTGATAGAGAGCCAGGGG 61.479 65.000 9.37 0.00 45.67 4.79
5118 6168 2.829384 GGTGGTGAGGTGGCTGGAA 61.829 63.158 0.00 0.00 0.00 3.53
5374 6424 2.125512 CACCGCCTTCTCTTCCCG 60.126 66.667 0.00 0.00 0.00 5.14
5664 6719 2.269940 ACCTTGGTAGCATGAGGAGTT 58.730 47.619 17.56 0.00 33.47 3.01
5665 6720 2.026822 ACCTTGGTAGCATGAGGAGTTG 60.027 50.000 17.56 0.00 33.47 3.16
5666 6721 2.012673 CTTGGTAGCATGAGGAGTTGC 58.987 52.381 0.00 0.00 39.17 4.17
5667 6722 0.108186 TGGTAGCATGAGGAGTTGCG 60.108 55.000 0.00 0.00 43.61 4.85
5811 6872 4.379918 GCTGAATCTGGCTGAGTTTTTACC 60.380 45.833 0.00 0.00 0.00 2.85
5821 6882 3.460103 TGAGTTTTTACCGTGTCCTGTC 58.540 45.455 0.00 0.00 0.00 3.51
5826 6887 6.056884 AGTTTTTACCGTGTCCTGTCATTAA 58.943 36.000 0.00 0.00 0.00 1.40
5827 6888 6.204108 AGTTTTTACCGTGTCCTGTCATTAAG 59.796 38.462 0.00 0.00 0.00 1.85
5828 6889 5.471556 TTTACCGTGTCCTGTCATTAAGA 57.528 39.130 0.00 0.00 0.00 2.10
5829 6890 5.670792 TTACCGTGTCCTGTCATTAAGAT 57.329 39.130 0.00 0.00 0.00 2.40
5830 6891 3.861840 ACCGTGTCCTGTCATTAAGATG 58.138 45.455 0.00 0.00 34.46 2.90
5831 6892 3.513912 ACCGTGTCCTGTCATTAAGATGA 59.486 43.478 0.00 0.00 39.92 2.92
5833 6894 4.509230 CCGTGTCCTGTCATTAAGATGATG 59.491 45.833 0.00 0.00 43.76 3.07
5834 6895 4.509230 CGTGTCCTGTCATTAAGATGATGG 59.491 45.833 0.00 0.00 43.76 3.51
5835 6896 5.431765 GTGTCCTGTCATTAAGATGATGGT 58.568 41.667 9.53 0.00 43.76 3.55
5836 6897 5.882557 GTGTCCTGTCATTAAGATGATGGTT 59.117 40.000 9.53 0.00 43.76 3.67
5837 6898 6.375455 GTGTCCTGTCATTAAGATGATGGTTT 59.625 38.462 9.53 0.00 43.76 3.27
5838 6899 6.947733 TGTCCTGTCATTAAGATGATGGTTTT 59.052 34.615 9.53 0.00 43.76 2.43
5839 6900 8.106462 TGTCCTGTCATTAAGATGATGGTTTTA 58.894 33.333 9.53 0.00 43.76 1.52
5840 6901 9.125026 GTCCTGTCATTAAGATGATGGTTTTAT 57.875 33.333 9.53 0.00 43.76 1.40
5945 7012 2.829741 AGTCTGTCTGTTCTTCCAGC 57.170 50.000 0.00 0.00 32.32 4.85
6064 7146 1.477553 CAGGGGATGGAACCATTGTG 58.522 55.000 7.79 0.73 36.70 3.33
6067 7149 1.329913 GGGATGGAACCATTGTGGCC 61.330 60.000 7.79 0.00 42.67 5.36
6073 7155 0.251341 GAACCATTGTGGCCCACTCT 60.251 55.000 16.23 0.00 42.67 3.24
6074 7156 0.188342 AACCATTGTGGCCCACTCTT 59.812 50.000 16.23 0.00 42.67 2.85
6077 7193 1.273327 CCATTGTGGCCCACTCTTTTC 59.727 52.381 16.23 0.00 35.11 2.29
6118 7238 2.722094 TGCCCTGCAAATCTCGTTATT 58.278 42.857 0.00 0.00 34.76 1.40
6198 7319 5.220548 CGTTCTTCAGATAAACCTCATGCAG 60.221 44.000 0.00 0.00 0.00 4.41
6210 7331 0.036105 TCATGCAGCGAGTCCAACAT 60.036 50.000 0.00 0.00 0.00 2.71
6217 7338 2.485426 CAGCGAGTCCAACATGTTCATT 59.515 45.455 8.48 0.00 0.00 2.57
6264 7385 3.635373 CCAAGAGGATACATTGCTGCATT 59.365 43.478 1.84 0.00 41.41 3.56
6265 7386 4.098960 CCAAGAGGATACATTGCTGCATTT 59.901 41.667 1.84 0.00 41.41 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.781786 TTTGCAGGGTTGGCTTGTAA 58.218 45.000 0.00 0.00 0.00 2.41
43 45 0.105913 GAGACTCCCTAGGGACCTGG 60.106 65.000 27.73 19.12 39.76 4.45
101 103 0.111061 AGGTTGCCAGAGTGATTGCA 59.889 50.000 0.00 0.00 0.00 4.08
106 108 1.070758 GTCAGAAGGTTGCCAGAGTGA 59.929 52.381 0.00 0.00 0.00 3.41
123 125 4.160439 AGGTTCGCTCAAATCTCATAGTCA 59.840 41.667 0.00 0.00 0.00 3.41
127 129 4.832248 ACAAGGTTCGCTCAAATCTCATA 58.168 39.130 0.00 0.00 0.00 2.15
128 130 3.679389 ACAAGGTTCGCTCAAATCTCAT 58.321 40.909 0.00 0.00 0.00 2.90
136 138 4.159693 ACATCTATGTACAAGGTTCGCTCA 59.840 41.667 0.00 0.00 39.68 4.26
154 156 0.689080 ATGAGCCTCCGTCCACATCT 60.689 55.000 0.00 0.00 0.00 2.90
157 159 1.609210 TGATGAGCCTCCGTCCACA 60.609 57.895 0.00 0.00 0.00 4.17
158 160 1.153549 GTGATGAGCCTCCGTCCAC 60.154 63.158 0.00 0.00 0.00 4.02
159 161 2.359169 GGTGATGAGCCTCCGTCCA 61.359 63.158 0.00 0.00 0.00 4.02
162 164 4.148825 GCGGTGATGAGCCTCCGT 62.149 66.667 0.00 0.00 42.99 4.69
168 170 0.313672 TTGTTTTGGCGGTGATGAGC 59.686 50.000 0.00 0.00 0.00 4.26
169 171 2.489329 AGATTGTTTTGGCGGTGATGAG 59.511 45.455 0.00 0.00 0.00 2.90
188 190 5.299531 CGGTGACTTCATGTTATCCTCTAGA 59.700 44.000 0.00 0.00 0.00 2.43
211 213 1.996898 TCATCGTTGGTTTCCGATTCG 59.003 47.619 0.00 0.00 41.54 3.34
217 219 4.331717 ACAATATCGTCATCGTTGGTTTCC 59.668 41.667 0.00 0.00 38.33 3.13
223 225 7.566858 TCATATCACAATATCGTCATCGTTG 57.433 36.000 0.00 0.00 38.33 4.10
330 340 8.153479 TGTCAAATGGTAGTTATATGTGATGC 57.847 34.615 0.00 0.00 0.00 3.91
374 384 9.643693 GATGAAAGGTTGATGTGTGAATTATTT 57.356 29.630 0.00 0.00 0.00 1.40
385 395 8.734386 GTTGAATAGAAGATGAAAGGTTGATGT 58.266 33.333 0.00 0.00 0.00 3.06
393 403 9.703892 ATAGATCGGTTGAATAGAAGATGAAAG 57.296 33.333 0.00 0.00 0.00 2.62
434 447 1.182667 ACTCATCCAACCGTCGATGA 58.817 50.000 6.11 9.68 41.94 2.92
446 459 6.539826 TGATCATCATTGTGTGTTACTCATCC 59.460 38.462 0.00 0.00 0.00 3.51
466 479 2.836372 AGGCATGAGAGACTGTTGATCA 59.164 45.455 0.00 0.00 0.00 2.92
470 483 3.567164 ACAAAAGGCATGAGAGACTGTTG 59.433 43.478 0.00 0.00 34.97 3.33
471 484 3.567164 CACAAAAGGCATGAGAGACTGTT 59.433 43.478 0.00 0.00 0.00 3.16
513 530 7.931407 TGTCTATTGTCACACAAACTGATAAGT 59.069 33.333 0.00 0.00 41.96 2.24
519 536 7.889589 TCTATGTCTATTGTCACACAAACTG 57.110 36.000 0.00 0.00 41.96 3.16
521 538 7.693951 GCAATCTATGTCTATTGTCACACAAAC 59.306 37.037 0.00 0.00 41.96 2.93
524 541 5.817296 GGCAATCTATGTCTATTGTCACACA 59.183 40.000 0.00 0.00 37.58 3.72
531 548 6.949352 AAACAGGGCAATCTATGTCTATTG 57.051 37.500 0.00 0.00 36.40 1.90
551 568 4.514066 ACTTTGGACGTAGACATGGAAAAC 59.486 41.667 0.00 0.00 0.00 2.43
639 670 4.065281 ACGGGGAAACGGAGAGCG 62.065 66.667 0.00 0.00 38.39 5.03
848 890 2.894126 TCCTCTGCGTCTCTCTCTTTTT 59.106 45.455 0.00 0.00 0.00 1.94
849 891 2.491693 CTCCTCTGCGTCTCTCTCTTTT 59.508 50.000 0.00 0.00 0.00 2.27
886 928 0.396974 CCTCTGCTGCTACCCTCTCT 60.397 60.000 0.00 0.00 0.00 3.10
888 930 0.396974 CTCCTCTGCTGCTACCCTCT 60.397 60.000 0.00 0.00 0.00 3.69
947 994 4.144727 TCCTCCTCCGCCTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
948 995 2.520741 CTCCTCCTCCGCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
949 996 4.851214 GCTCCTCCTCCGCCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
1055 1103 3.640498 CCAGATGGCAGAGAGACAGATAA 59.360 47.826 0.00 0.00 39.86 1.75
1361 1454 2.353573 GTACCGCCCACCAACCAT 59.646 61.111 0.00 0.00 0.00 3.55
1519 1614 2.180017 GACGTAAAGCCGCGGAGA 59.820 61.111 33.48 7.02 0.00 3.71
1525 1620 1.136446 CAGGAAAACGACGTAAAGCCG 60.136 52.381 0.00 0.00 0.00 5.52
1634 1742 1.444895 GCATGCAAACAGAAGGCCG 60.445 57.895 14.21 0.00 0.00 6.13
1637 1745 2.333926 CACATGCATGCAAACAGAAGG 58.666 47.619 26.68 2.90 0.00 3.46
1683 1791 1.903877 AACCCCAGTCATCCTCGCAG 61.904 60.000 0.00 0.00 0.00 5.18
1686 1794 0.105039 GCTAACCCCAGTCATCCTCG 59.895 60.000 0.00 0.00 0.00 4.63
1687 1795 1.139853 CTGCTAACCCCAGTCATCCTC 59.860 57.143 0.00 0.00 0.00 3.71
1696 1804 4.229582 ACAGATTTAATCCTGCTAACCCCA 59.770 41.667 0.78 0.00 33.90 4.96
1738 1851 2.383527 GGAACGCAAGAGACTGCCG 61.384 63.158 0.00 0.00 39.26 5.69
1772 1891 1.699634 ACCATCTACTTGCGCCCATAT 59.300 47.619 4.18 0.00 0.00 1.78
1814 1940 2.172851 AAAATAGCACGAACACCGGA 57.827 45.000 9.46 0.00 43.93 5.14
1816 1942 3.262135 ACAAAAATAGCACGAACACCG 57.738 42.857 0.00 0.00 45.44 4.94
1824 1950 3.181470 ACACCACCCAACAAAAATAGCAC 60.181 43.478 0.00 0.00 0.00 4.40
1867 2000 2.744202 CCAGACACAGGCACATTAAGTC 59.256 50.000 0.00 0.00 0.00 3.01
1998 2131 2.372264 TCAGGAAGATCTTGCAATGCC 58.628 47.619 26.36 13.98 33.04 4.40
2123 2533 1.408702 CACAAGACCACCCAACCAAAG 59.591 52.381 0.00 0.00 0.00 2.77
2149 2559 3.600717 CACACGACATAACAAGTGCAA 57.399 42.857 0.00 0.00 38.08 4.08
2169 2579 9.769093 CATTATACCACAGTTAAGTTAGTTTGC 57.231 33.333 0.00 0.00 0.00 3.68
2261 2692 7.065563 GTCAAGAATAGCATGACAAATGAGAGT 59.934 37.037 0.00 0.00 43.01 3.24
2290 2722 3.366052 ACAACCCAATATCCCACAGAC 57.634 47.619 0.00 0.00 0.00 3.51
2343 2775 3.622612 TGACAACGATGTATCAGCAATGG 59.377 43.478 0.00 0.00 40.74 3.16
2358 2790 2.525750 AAGCACGCATATTGACAACG 57.474 45.000 0.00 0.00 0.00 4.10
2359 2791 4.335082 TGTAAGCACGCATATTGACAAC 57.665 40.909 0.00 0.00 0.00 3.32
2407 2841 1.242076 GTGCTTGCACATCCAGAAGT 58.758 50.000 19.36 0.00 0.00 3.01
2426 2860 9.438228 AGTAGATTTGAGATGCATAATCAGATG 57.562 33.333 17.32 0.00 37.81 2.90
2432 2866 6.206243 GCACCAGTAGATTTGAGATGCATAAT 59.794 38.462 0.00 0.00 0.00 1.28
2516 2951 0.417841 TAGCTCCTGGAGGAAAGGGT 59.582 55.000 24.43 7.04 44.91 4.34
2517 2952 1.813102 ATAGCTCCTGGAGGAAAGGG 58.187 55.000 24.43 0.00 44.91 3.95
2603 3042 1.322442 GAGCAGTTTGTGGCCTCTTT 58.678 50.000 3.32 0.00 0.00 2.52
2735 3174 1.380302 GCCAGTCACCACCCTGAAT 59.620 57.895 0.00 0.00 0.00 2.57
2799 3241 2.354821 GGTTACTTGCATTGGGATCGAC 59.645 50.000 0.00 0.00 0.00 4.20
2879 3321 1.577328 CGGTTTGCGGATTGCTGACT 61.577 55.000 0.00 0.00 46.63 3.41
3047 3494 4.474394 TCGGATGATCTGAACTACAGGAT 58.526 43.478 0.51 0.00 45.76 3.24
3185 3632 0.167470 CATGCTGCTTCCGACAGTTG 59.833 55.000 0.00 0.00 37.47 3.16
3206 3653 4.384056 CCCAGAATACATACCTGAGCAAG 58.616 47.826 0.00 0.00 0.00 4.01
3240 3687 4.574599 AGAACAGAAAACCTGCATGAAC 57.425 40.909 0.00 0.00 46.81 3.18
3282 3729 9.476202 GGAAAACAAGCAAAGTAACAATCTAAT 57.524 29.630 0.00 0.00 0.00 1.73
3322 3769 3.601443 ACTAAGGCAGTGAAGCAGTAG 57.399 47.619 0.00 0.00 35.62 2.57
3560 4289 6.577103 TCTCAAGAGTTGCTATTGTATGGAG 58.423 40.000 3.87 0.00 34.71 3.86
3581 4474 7.192232 GCAGTGTAAAATGGATCAGAAATCTC 58.808 38.462 0.00 0.00 0.00 2.75
3726 4776 7.020914 AGCATCTTTAGCTAACATTAGTTGC 57.979 36.000 21.12 21.12 41.32 4.17
3747 4797 1.257750 ATATATCCAGCCGCCGAGCA 61.258 55.000 0.70 0.00 34.23 4.26
3780 4830 6.621514 AGAATAGGACCTTATGACCCAGAAAT 59.378 38.462 0.00 0.00 0.00 2.17
3807 4857 2.197283 AGACCGAGTACTTCTCCGTT 57.803 50.000 0.00 0.00 39.84 4.44
4101 5151 2.417933 GCTCGATGGCATCATATTGGAC 59.582 50.000 25.88 6.50 32.98 4.02
4168 5218 2.636830 AGGACATCGAGCCAAATCAAG 58.363 47.619 4.80 0.00 0.00 3.02
4239 5289 5.411361 TGGATTGAACGAGTAAAATCCTGTG 59.589 40.000 20.80 0.00 45.52 3.66
4257 5307 0.802494 GTACGGTGCCAGTTGGATTG 59.198 55.000 1.45 0.00 37.39 2.67
4482 5532 2.274437 CGATCAGATTGACCACCACTG 58.726 52.381 0.00 0.00 0.00 3.66
4674 5724 0.708209 TGACCTCTGGTACCCTAGCA 59.292 55.000 10.07 0.00 35.25 3.49
5014 6064 4.083484 ACCCGATCTTTTGTTTGACGAATC 60.083 41.667 0.00 0.00 0.00 2.52
5118 6168 2.237392 GGTCTCAATGTAGCCCTCAGTT 59.763 50.000 0.00 0.00 0.00 3.16
5664 6719 4.379143 CGACCGACGACTCACGCA 62.379 66.667 0.00 0.00 46.94 5.24
5666 6721 4.456253 CCCGACCGACGACTCACG 62.456 72.222 0.00 0.00 45.77 4.35
5667 6722 1.577328 TAACCCGACCGACGACTCAC 61.577 60.000 0.00 0.00 45.77 3.51
5811 6872 4.509230 CCATCATCTTAATGACAGGACACG 59.491 45.833 3.76 0.00 44.51 4.49
5837 6898 9.645059 GAGCTGCAAACTCAGATATACATATAA 57.355 33.333 10.73 0.00 36.19 0.98
5838 6899 8.253810 GGAGCTGCAAACTCAGATATACATATA 58.746 37.037 16.04 0.00 36.19 0.86
5839 6900 7.102346 GGAGCTGCAAACTCAGATATACATAT 58.898 38.462 16.04 0.00 36.19 1.78
5840 6901 6.041979 TGGAGCTGCAAACTCAGATATACATA 59.958 38.462 5.01 0.00 36.19 2.29
5841 6902 5.163269 TGGAGCTGCAAACTCAGATATACAT 60.163 40.000 5.01 0.00 36.19 2.29
5842 6903 4.162131 TGGAGCTGCAAACTCAGATATACA 59.838 41.667 5.01 3.01 36.19 2.29
5843 6904 4.697514 TGGAGCTGCAAACTCAGATATAC 58.302 43.478 5.01 0.82 36.19 1.47
5844 6905 5.557576 ATGGAGCTGCAAACTCAGATATA 57.442 39.130 13.45 0.00 36.19 0.86
5845 6906 3.920231 TGGAGCTGCAAACTCAGATAT 57.080 42.857 5.01 0.00 36.19 1.63
5846 6907 3.920231 ATGGAGCTGCAAACTCAGATA 57.080 42.857 13.45 2.80 36.19 1.98
5847 6908 2.753452 CAATGGAGCTGCAAACTCAGAT 59.247 45.455 13.45 6.56 36.19 2.90
5848 6909 2.156917 CAATGGAGCTGCAAACTCAGA 58.843 47.619 13.45 4.78 36.19 3.27
5849 6910 2.156917 TCAATGGAGCTGCAAACTCAG 58.843 47.619 13.45 0.00 35.79 3.35
5945 7012 3.599730 TGACCTTCATACACTGCAGAG 57.400 47.619 23.35 16.23 0.00 3.35
6064 7146 1.377333 CTCGGGAAAAGAGTGGGCC 60.377 63.158 0.00 0.00 0.00 5.80
6067 7149 2.689646 GAGTTCTCGGGAAAAGAGTGG 58.310 52.381 0.00 0.00 37.07 4.00
6073 7155 0.949105 GCTGCGAGTTCTCGGGAAAA 60.949 55.000 20.97 0.00 32.81 2.29
6074 7156 1.374252 GCTGCGAGTTCTCGGGAAA 60.374 57.895 20.97 0.00 32.81 3.13
6077 7193 2.811317 GTGCTGCGAGTTCTCGGG 60.811 66.667 20.97 0.00 0.00 5.14
6106 7224 7.308408 CCAGATGATGATGCAATAACGAGATTT 60.308 37.037 0.00 0.00 0.00 2.17
6112 7232 3.817084 ACCCAGATGATGATGCAATAACG 59.183 43.478 0.00 0.00 0.00 3.18
6118 7238 3.216800 GCTTTACCCAGATGATGATGCA 58.783 45.455 0.00 0.00 0.00 3.96
6198 7319 3.559238 AAATGAACATGTTGGACTCGC 57.441 42.857 17.58 0.00 0.00 5.03
6210 7331 3.505680 CGGATGGGTGAAGAAAATGAACA 59.494 43.478 0.00 0.00 0.00 3.18
6217 7338 1.974957 TGAGACGGATGGGTGAAGAAA 59.025 47.619 0.00 0.00 0.00 2.52
6264 7385 2.102588 GCGGCAATCCTACCTCTTCTAA 59.897 50.000 0.00 0.00 0.00 2.10
6265 7386 1.687123 GCGGCAATCCTACCTCTTCTA 59.313 52.381 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.