Multiple sequence alignment - TraesCS2B01G169700

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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 TraesCS2B01G169700 chr2B 100.000 4450 0 0 1 4450 142862492 142866941 0.000000e+00 8218
1 TraesCS2B01G169700 chr2B 93.939 99 5 1 2027 2124 78868105 78868007 9.970000e-32 148
2 TraesCS2B01G169700 chr2A 91.954 2088 98 36 3 2040 89765509 89767576 0.000000e+00 2861
3 TraesCS2B01G169700 chr2A 94.619 1115 39 10 2135 3246 89767593 89768689 0.000000e+00 1707
4 TraesCS2B01G169700 chr2A 86.258 1077 81 45 3287 4331 89768690 89769731 0.000000e+00 1107
5 TraesCS2B01G169700 chr2A 88.158 456 33 15 3 443 89763007 89763456 1.420000e-144 523
6 TraesCS2B01G169700 chr2A 83.297 455 53 13 3719 4157 89918221 89918668 8.970000e-107 398
7 TraesCS2B01G169700 chr2A 85.427 398 29 11 4058 4450 89920377 89920750 1.940000e-103 387
8 TraesCS2B01G169700 chr2A 83.794 253 23 8 3 248 89764315 89764556 1.610000e-54 224
9 TraesCS2B01G169700 chr2A 85.455 165 13 5 4286 4450 89769738 89769891 1.280000e-35 161
10 TraesCS2B01G169700 chr2A 95.789 95 3 1 2030 2123 227632603 227632697 7.710000e-33 152
11 TraesCS2B01G169700 chr2D 89.286 2352 151 52 2151 4450 90242703 90245005 0.000000e+00 2854
12 TraesCS2B01G169700 chr2D 94.121 1616 26 16 462 2040 90241093 90242676 0.000000e+00 2394
13 TraesCS2B01G169700 chr2D 88.286 461 30 13 3 442 90240298 90240755 8.480000e-147 531
14 TraesCS2B01G169700 chr2D 95.699 93 4 0 2037 2129 33786908 33786816 2.770000e-32 150
15 TraesCS2B01G169700 chr4B 100.000 88 0 0 2037 2124 11912401 11912314 3.560000e-36 163
16 TraesCS2B01G169700 chr4B 94.737 95 3 2 2037 2129 255382697 255382791 3.590000e-31 147
17 TraesCS2B01G169700 chr5D 93.814 97 6 0 2028 2124 107238565 107238661 3.590000e-31 147
18 TraesCS2B01G169700 chr5B 92.308 104 4 3 2023 2123 82872449 82872347 1.290000e-30 145
19 TraesCS2B01G169700 chr1A 90.566 106 9 1 2031 2135 33232748 33232853 6.000000e-29 139
20 TraesCS2B01G169700 chr6B 88.034 117 8 6 2031 2145 187052334 187052222 2.790000e-27 134


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 TraesCS2B01G169700 chr2B 142862492 142866941 4449 False 8218.000000 8218 100.000000 1 4450 1 chr2B.!!$F1 4449
1 TraesCS2B01G169700 chr2A 89763007 89769891 6884 False 1097.166667 2861 88.373000 3 4450 6 chr2A.!!$F2 4447
2 TraesCS2B01G169700 chr2A 89918221 89920750 2529 False 392.500000 398 84.362000 3719 4450 2 chr2A.!!$F3 731
3 TraesCS2B01G169700 chr2D 90240298 90245005 4707 False 1926.333333 2854 90.564333 3 4450 3 chr2D.!!$F1 4447

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
741 3608 0.175760 CGTGAGATTGGTGGACGGAT 59.824 55.000 0.0 0.0 0.00 4.18 F
970 3850 0.544120 TTTTGATTGGGGGCTGGTCC 60.544 55.000 0.0 0.0 0.00 4.46 F
2052 4955 1.204231 GTCTTGTACTCCCTCCGTTCC 59.796 57.143 0.0 0.0 0.00 3.62 F
2357 5260 0.320771 AATCAACCGCTTCACGCTCT 60.321 50.000 0.0 0.0 41.76 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 4789 0.039256 CACACGAAACATGCCAAGGG 60.039 55.0 0.00 0.0 0.00 3.95 R
2297 5200 0.179089 CTGAGAGCCGGATGGAAGTG 60.179 60.0 5.05 0.0 37.49 3.16 R
2911 5822 0.245539 CAGGGCAGGCACAGAATTTG 59.754 55.0 0.00 0.0 0.00 2.32 R
4169 8949 0.536687 AGGTCACTCGTCTCGTTCCA 60.537 55.0 0.00 0.0 0.00 3.53 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
62 1368 6.509656 AGCAAAACACATATATGCTTGGATG 58.490 36.000 12.79 5.07 44.43 3.51
67 1373 6.624352 ACACATATATGCTTGGATGACAAC 57.376 37.500 12.79 0.00 34.76 3.32
76 1382 4.576873 TGCTTGGATGACAACGTAGAAAAA 59.423 37.500 0.00 0.00 34.76 1.94
80 1386 6.869315 TGGATGACAACGTAGAAAAATCAA 57.131 33.333 0.00 0.00 0.00 2.57
143 2658 4.500477 CACGCAAAGAAAGAAGGTGAAAAG 59.500 41.667 0.00 0.00 0.00 2.27
179 2695 6.040166 AGAGAAACACAAATGCTCAATCAAGT 59.960 34.615 0.00 0.00 0.00 3.16
255 2771 1.860078 GAGAAACCTGTCGTTGCGG 59.140 57.895 0.00 0.00 34.81 5.69
325 2841 3.470888 CACACGGCCCCCTCCTAG 61.471 72.222 0.00 0.00 0.00 3.02
326 2842 4.007323 ACACGGCCCCCTCCTAGT 62.007 66.667 0.00 0.00 0.00 2.57
327 2843 3.155167 CACGGCCCCCTCCTAGTC 61.155 72.222 0.00 0.00 0.00 2.59
340 2856 1.012302 TCCTAGTCCTACCCCTCTCCT 59.988 57.143 0.00 0.00 0.00 3.69
341 2857 1.146152 CCTAGTCCTACCCCTCTCCTG 59.854 61.905 0.00 0.00 0.00 3.86
423 2958 1.154282 GCATCGCATCGCATCCATG 60.154 57.895 0.00 0.00 0.00 3.66
619 3480 0.324943 CCGAGGAGGAAGGAAAGCAA 59.675 55.000 0.00 0.00 45.00 3.91
680 3541 4.666253 TTCCTCCCGTCCGTCCGT 62.666 66.667 0.00 0.00 0.00 4.69
738 3605 2.100631 GCCGTGAGATTGGTGGACG 61.101 63.158 0.00 0.00 0.00 4.79
739 3606 1.447838 CCGTGAGATTGGTGGACGG 60.448 63.158 0.00 0.00 43.22 4.79
740 3607 1.589630 CGTGAGATTGGTGGACGGA 59.410 57.895 0.00 0.00 0.00 4.69
741 3608 0.175760 CGTGAGATTGGTGGACGGAT 59.824 55.000 0.00 0.00 0.00 4.18
782 3649 2.058001 GGTAATGCCAACCCCCTGC 61.058 63.158 0.00 0.00 37.17 4.85
783 3650 2.044451 TAATGCCAACCCCCTGCG 60.044 61.111 0.00 0.00 0.00 5.18
869 3745 5.052304 CGTGTTCGTCTTGTATCTATCTTGC 60.052 44.000 0.00 0.00 0.00 4.01
872 3748 4.215908 TCGTCTTGTATCTATCTTGCCCT 58.784 43.478 0.00 0.00 0.00 5.19
969 3849 0.608130 GTTTTGATTGGGGGCTGGTC 59.392 55.000 0.00 0.00 0.00 4.02
970 3850 0.544120 TTTTGATTGGGGGCTGGTCC 60.544 55.000 0.00 0.00 0.00 4.46
1433 4335 1.617947 AAGGTCACGCTCATCCCCTC 61.618 60.000 0.00 0.00 0.00 4.30
1689 4592 1.874019 CTCACGCGGATTCGTCCTG 60.874 63.158 12.47 0.00 41.21 3.86
1722 4625 1.863155 ATTGGGAAGACCGTGGGCAT 61.863 55.000 0.00 0.00 44.64 4.40
1826 4729 7.275560 CGTCCAAACCATTTCCAGAAAATTATC 59.724 37.037 0.00 0.00 35.32 1.75
1831 4734 9.933723 AAACCATTTCCAGAAAATTATCTTCTG 57.066 29.630 10.26 10.26 46.22 3.02
2041 4944 9.991906 TTACTTAAGTAATGCTTGTCTTGTACT 57.008 29.630 21.52 0.00 38.05 2.73
2043 4946 7.603024 ACTTAAGTAATGCTTGTCTTGTACTCC 59.397 37.037 6.26 0.00 38.05 3.85
2044 4947 4.833390 AGTAATGCTTGTCTTGTACTCCC 58.167 43.478 0.00 0.00 0.00 4.30
2045 4948 4.532521 AGTAATGCTTGTCTTGTACTCCCT 59.467 41.667 0.00 0.00 0.00 4.20
2046 4949 3.618690 ATGCTTGTCTTGTACTCCCTC 57.381 47.619 0.00 0.00 0.00 4.30
2047 4950 1.623811 TGCTTGTCTTGTACTCCCTCC 59.376 52.381 0.00 0.00 0.00 4.30
2048 4951 1.404315 GCTTGTCTTGTACTCCCTCCG 60.404 57.143 0.00 0.00 0.00 4.63
2050 4953 2.005370 TGTCTTGTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
2051 4954 1.891150 TGTCTTGTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
2052 4955 1.204231 GTCTTGTACTCCCTCCGTTCC 59.796 57.143 0.00 0.00 0.00 3.62
2054 4957 1.621814 CTTGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
2055 4958 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2056 4959 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
2057 4960 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
2058 4961 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
2059 4962 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2060 4963 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2061 4964 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2062 4965 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2063 4966 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2064 4967 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2065 4968 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2066 4969 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2067 4970 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2068 4971 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2069 4972 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2070 4973 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2071 4974 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2072 4975 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2073 4976 8.717821 CGTTCCAAAATAGATGACTCAACTTTA 58.282 33.333 0.00 0.00 0.00 1.85
2110 5013 9.739276 ATACAAAGTTGACTCATCTATTTTGGA 57.261 29.630 0.00 3.92 39.71 3.53
2111 5014 8.463930 ACAAAGTTGACTCATCTATTTTGGAA 57.536 30.769 0.00 0.00 39.71 3.53
2112 5015 8.352942 ACAAAGTTGACTCATCTATTTTGGAAC 58.647 33.333 0.00 0.00 39.71 3.62
2113 5016 6.727824 AGTTGACTCATCTATTTTGGAACG 57.272 37.500 0.00 0.00 0.00 3.95
2114 5017 5.643777 AGTTGACTCATCTATTTTGGAACGG 59.356 40.000 0.00 0.00 0.00 4.44
2115 5018 5.414789 TGACTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2116 5019 5.419542 TGACTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2117 5020 4.770795 ACTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2118 5021 4.130118 CTCATCTATTTTGGAACGGAGGG 58.870 47.826 0.00 0.00 0.00 4.30
2119 5022 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2120 5023 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2121 5024 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2122 5025 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2123 5026 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
2124 5027 6.138263 TCTATTTTGGAACGGAGGGAGTATA 58.862 40.000 0.00 0.00 0.00 1.47
2125 5028 5.703730 ATTTTGGAACGGAGGGAGTATAA 57.296 39.130 0.00 0.00 0.00 0.98
2126 5029 4.748277 TTTGGAACGGAGGGAGTATAAG 57.252 45.455 0.00 0.00 0.00 1.73
2127 5030 2.037144 TGGAACGGAGGGAGTATAAGC 58.963 52.381 0.00 0.00 0.00 3.09
2128 5031 2.317973 GGAACGGAGGGAGTATAAGCT 58.682 52.381 0.00 0.00 0.00 3.74
2129 5032 3.117398 TGGAACGGAGGGAGTATAAGCTA 60.117 47.826 0.00 0.00 0.00 3.32
2130 5033 3.255395 GGAACGGAGGGAGTATAAGCTAC 59.745 52.174 0.00 0.00 0.00 3.58
2131 5034 3.880168 ACGGAGGGAGTATAAGCTACT 57.120 47.619 0.00 0.00 0.00 2.57
2132 5035 4.989875 ACGGAGGGAGTATAAGCTACTA 57.010 45.455 0.00 0.00 0.00 1.82
2133 5036 4.909001 ACGGAGGGAGTATAAGCTACTAG 58.091 47.826 0.00 0.00 0.00 2.57
2148 5051 6.542574 AGCTACTAGTAGTTATGTGCTACG 57.457 41.667 26.76 2.71 42.49 3.51
2297 5200 2.811317 CTCTTCGCCACACCGAGC 60.811 66.667 0.00 0.00 38.60 5.03
2333 5236 6.823689 GGCTCTCAGAGGTAATTGAATTTACA 59.176 38.462 3.18 0.00 34.42 2.41
2334 5237 7.201652 GGCTCTCAGAGGTAATTGAATTTACAC 60.202 40.741 3.18 0.00 34.42 2.90
2336 5239 9.388506 CTCTCAGAGGTAATTGAATTTACACAT 57.611 33.333 0.00 0.00 34.42 3.21
2349 5252 7.598278 TGAATTTACACATAAATCAACCGCTT 58.402 30.769 0.00 0.00 39.61 4.68
2350 5253 7.753132 TGAATTTACACATAAATCAACCGCTTC 59.247 33.333 0.00 0.00 39.61 3.86
2351 5254 6.561737 TTTACACATAAATCAACCGCTTCA 57.438 33.333 0.00 0.00 0.00 3.02
2353 5256 3.120338 ACACATAAATCAACCGCTTCACG 60.120 43.478 0.00 0.00 43.15 4.35
2354 5257 2.159572 ACATAAATCAACCGCTTCACGC 60.160 45.455 0.00 0.00 41.76 5.34
2355 5258 1.803334 TAAATCAACCGCTTCACGCT 58.197 45.000 0.00 0.00 41.76 5.07
2356 5259 0.517316 AAATCAACCGCTTCACGCTC 59.483 50.000 0.00 0.00 41.76 5.03
2357 5260 0.320771 AATCAACCGCTTCACGCTCT 60.321 50.000 0.00 0.00 41.76 4.09
2358 5261 1.016130 ATCAACCGCTTCACGCTCTG 61.016 55.000 0.00 0.00 41.76 3.35
2359 5262 1.956170 CAACCGCTTCACGCTCTGT 60.956 57.895 0.00 0.00 41.76 3.41
2360 5263 0.666274 CAACCGCTTCACGCTCTGTA 60.666 55.000 0.00 0.00 41.76 2.74
2361 5264 0.388649 AACCGCTTCACGCTCTGTAG 60.389 55.000 0.00 0.00 41.76 2.74
2362 5265 1.213013 CCGCTTCACGCTCTGTAGT 59.787 57.895 0.00 0.00 41.76 2.73
2368 5272 4.039032 GCTTCACGCTCTGTAGTCTTATC 58.961 47.826 0.00 0.00 35.14 1.75
2382 5286 4.232091 AGTCTTATCGGGTCCATGGTATT 58.768 43.478 12.58 0.00 0.00 1.89
2383 5287 5.399991 AGTCTTATCGGGTCCATGGTATTA 58.600 41.667 12.58 0.00 0.00 0.98
2384 5288 6.023603 AGTCTTATCGGGTCCATGGTATTAT 58.976 40.000 12.58 3.36 0.00 1.28
2385 5289 6.500751 AGTCTTATCGGGTCCATGGTATTATT 59.499 38.462 12.58 0.00 0.00 1.40
2386 5290 7.017254 AGTCTTATCGGGTCCATGGTATTATTT 59.983 37.037 12.58 0.00 0.00 1.40
2522 5430 2.054799 TGTTCTTTGCCAGGGACTAGT 58.945 47.619 0.00 0.00 36.02 2.57
2533 5441 2.744202 CAGGGACTAGTGTTTGACATGC 59.256 50.000 0.00 0.00 36.02 4.06
2554 5462 7.546667 ACATGCTGATTGTTTTGTGAATTATCC 59.453 33.333 0.00 0.00 0.00 2.59
2573 5484 9.533831 AATTATCCACAGATAAAAGGAACAGTT 57.466 29.630 0.02 0.00 45.71 3.16
2614 5525 3.701664 CCAAGAACCAATTAGAAGGCCT 58.298 45.455 0.00 0.00 0.00 5.19
2686 5597 0.454600 AATCTGCAGCAAGGCAATCG 59.545 50.000 9.47 0.00 44.40 3.34
2699 5610 3.053291 AATCGCGGCCGCAAGAAA 61.053 55.556 45.26 26.52 42.06 2.52
2911 5822 8.962679 TGTGGTTGTTTTATTCATACTAATCCC 58.037 33.333 0.00 0.00 0.00 3.85
2984 5895 3.194062 GCTTCGAGCAAAGCTAGATCTT 58.806 45.455 0.00 0.00 46.51 2.40
3020 5931 4.905412 GTTAGAACTGGCAACTAACTCG 57.095 45.455 20.98 0.00 41.20 4.18
3119 6034 7.604657 ATTTTGGGTTTGTTATTACCTGTGA 57.395 32.000 0.00 0.00 34.75 3.58
3121 6036 4.066490 TGGGTTTGTTATTACCTGTGACG 58.934 43.478 0.00 0.00 34.75 4.35
3122 6037 3.437741 GGGTTTGTTATTACCTGTGACGG 59.562 47.826 0.00 0.00 34.75 4.79
3451 6367 2.351726 GGAATTGGTCGTCGAAATGAGG 59.648 50.000 0.00 0.00 0.00 3.86
3452 6368 1.369625 ATTGGTCGTCGAAATGAGGC 58.630 50.000 0.00 0.00 32.48 4.70
3469 6385 1.035139 GGCGCCAATTCCATTCATCT 58.965 50.000 24.80 0.00 0.00 2.90
3604 6526 2.124903 CGTACTTGCGAAACTGTGTCT 58.875 47.619 0.00 0.00 0.00 3.41
3607 6529 2.627945 ACTTGCGAAACTGTGTCTTGA 58.372 42.857 0.00 0.00 0.00 3.02
3682 6610 5.470047 AACCTGTAAAGATGAGACGAGTT 57.530 39.130 0.00 0.00 0.00 3.01
3789 6717 2.180131 CTCTGCTTGCCTTGTCGCAC 62.180 60.000 0.00 0.00 38.83 5.34
3791 6719 2.253452 GCTTGCCTTGTCGCACTG 59.747 61.111 0.00 0.00 38.83 3.66
3792 6720 2.253452 CTTGCCTTGTCGCACTGC 59.747 61.111 0.00 0.00 38.83 4.40
3793 6721 2.515757 TTGCCTTGTCGCACTGCA 60.516 55.556 1.11 0.00 38.83 4.41
3795 6723 2.974698 GCCTTGTCGCACTGCAGT 60.975 61.111 15.25 15.25 0.00 4.40
3798 6726 3.245948 CTTGTCGCACTGCAGTGGC 62.246 63.158 39.92 30.94 45.72 5.01
3854 6782 2.431057 GGGTGCAGTACTAGTATGTGCT 59.569 50.000 27.42 11.63 35.11 4.40
3904 6843 4.017808 TCCCTACTGAAGCTGAGTAGTTC 58.982 47.826 22.68 3.07 40.90 3.01
3911 6850 3.508012 TGAAGCTGAGTAGTTCCACTCTC 59.492 47.826 5.00 0.00 44.41 3.20
3931 6870 2.344535 GCAAGACTGCCACCACAAT 58.655 52.632 0.00 0.00 43.26 2.71
3999 6941 9.495572 TTTTTACCAACACAATTTTCACTTTCT 57.504 25.926 0.00 0.00 0.00 2.52
4169 8949 1.144503 GGATCATTCCATGCCTGGTCT 59.855 52.381 7.98 0.00 43.61 3.85
4174 8954 0.038166 TTCCATGCCTGGTCTGGAAC 59.962 55.000 21.04 0.00 42.60 3.62
4179 8959 1.079750 GCCTGGTCTGGAACGAGAC 60.080 63.158 8.14 8.14 41.55 3.36
4234 9018 2.770130 GGGTGGATTCCCAAGCCA 59.230 61.111 0.00 0.00 46.37 4.75
4269 9055 2.223618 GCTTTGTGTGAACGCCCTAAAA 60.224 45.455 0.00 0.00 0.00 1.52
4270 9056 3.735514 GCTTTGTGTGAACGCCCTAAAAA 60.736 43.478 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.593134 TGTTTAGTTTGTTTAATGCACAAGATT 57.407 25.926 0.00 0.00 35.57 2.40
1 2 9.030301 GTGTTTAGTTTGTTTAATGCACAAGAT 57.970 29.630 0.00 0.00 35.57 2.40
95 1401 6.205270 GGTGCAAACTTGAATTCAAATCCATT 59.795 34.615 20.82 9.31 35.15 3.16
97 1403 5.055812 GGTGCAAACTTGAATTCAAATCCA 58.944 37.500 20.82 11.16 35.15 3.41
99 1405 5.332506 CGTGGTGCAAACTTGAATTCAAATC 60.333 40.000 20.82 6.93 35.15 2.17
100 1406 4.507388 CGTGGTGCAAACTTGAATTCAAAT 59.493 37.500 20.82 9.42 35.15 2.32
101 1407 3.862267 CGTGGTGCAAACTTGAATTCAAA 59.138 39.130 20.82 3.25 35.15 2.69
143 2658 6.927294 TTTGTGTTTCTCTTCTCTCTTTCC 57.073 37.500 0.00 0.00 0.00 3.13
179 2695 1.173043 GGAAATGGCATGAACCGTGA 58.827 50.000 0.00 0.00 0.00 4.35
273 2789 0.884704 GTGTTTCGGCAAGGCTCAGA 60.885 55.000 0.00 0.00 0.00 3.27
320 2836 1.012302 AGGAGAGGGGTAGGACTAGGA 59.988 57.143 0.00 0.00 0.00 2.94
322 2838 1.854280 ACAGGAGAGGGGTAGGACTAG 59.146 57.143 0.00 0.00 0.00 2.57
323 2839 1.851653 GACAGGAGAGGGGTAGGACTA 59.148 57.143 0.00 0.00 0.00 2.59
324 2840 0.632294 GACAGGAGAGGGGTAGGACT 59.368 60.000 0.00 0.00 0.00 3.85
325 2841 0.397394 GGACAGGAGAGGGGTAGGAC 60.397 65.000 0.00 0.00 0.00 3.85
326 2842 1.591280 GGGACAGGAGAGGGGTAGGA 61.591 65.000 0.00 0.00 0.00 2.94
327 2843 1.075151 GGGACAGGAGAGGGGTAGG 60.075 68.421 0.00 0.00 0.00 3.18
427 2962 2.267642 CGATTTCCGCCAGGTCCA 59.732 61.111 0.00 0.00 39.05 4.02
436 2971 2.705826 GCTGCTCAGCGATTTCCG 59.294 61.111 6.08 0.00 45.29 4.30
619 3480 2.845317 GGGTTTTTGCCCCGGGTT 60.845 61.111 21.85 0.00 42.89 4.11
646 3507 3.445987 AGGAAGAACGAAAGGGAGAGAT 58.554 45.455 0.00 0.00 0.00 2.75
686 3547 3.450115 GAGGACGGGACCGGTGAG 61.450 72.222 14.63 5.23 44.69 3.51
738 3605 5.960811 TCCACCAGAATCTATCTATCCATCC 59.039 44.000 0.00 0.00 36.32 3.51
739 3606 7.418827 CCATCCACCAGAATCTATCTATCCATC 60.419 44.444 0.00 0.00 36.32 3.51
740 3607 6.386342 CCATCCACCAGAATCTATCTATCCAT 59.614 42.308 0.00 0.00 36.32 3.41
741 3608 5.723405 CCATCCACCAGAATCTATCTATCCA 59.277 44.000 0.00 0.00 36.32 3.41
784 3651 0.532862 ACACCCAGACGCAAGAACTG 60.533 55.000 0.00 0.00 41.73 3.16
857 3725 4.280174 TCCGTTACAGGGCAAGATAGATAC 59.720 45.833 0.00 0.00 0.00 2.24
869 3745 3.396260 TTCAGTTCTTCCGTTACAGGG 57.604 47.619 0.00 0.00 0.00 4.45
872 3748 3.256383 TCCGATTCAGTTCTTCCGTTACA 59.744 43.478 0.00 0.00 0.00 2.41
933 3809 2.284699 CCCACTCCTTCCTCCCGT 60.285 66.667 0.00 0.00 0.00 5.28
934 3810 1.489560 AAACCCACTCCTTCCTCCCG 61.490 60.000 0.00 0.00 0.00 5.14
1463 4365 0.184933 TTACCAGCCAACAACCAGCT 59.815 50.000 0.00 0.00 37.32 4.24
1604 4506 1.103803 GAGCTCCTGTGGATGTCGTA 58.896 55.000 0.87 0.00 0.00 3.43
1689 4592 1.412710 TCCCAATCGCAGTGACCTATC 59.587 52.381 0.00 0.00 0.00 2.08
1886 4789 0.039256 CACACGAAACATGCCAAGGG 60.039 55.000 0.00 0.00 0.00 3.95
2033 4936 1.203087 TGGAACGGAGGGAGTACAAGA 60.203 52.381 0.00 0.00 0.00 3.02
2040 4943 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2041 4944 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2043 4946 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2044 4947 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2045 4948 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2046 4949 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2047 4950 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2084 4987 9.739276 TCCAAAATAGATGAGTCAACTTTGTAT 57.261 29.630 8.34 0.00 0.00 2.29
2085 4988 9.567776 TTCCAAAATAGATGAGTCAACTTTGTA 57.432 29.630 8.34 0.00 0.00 2.41
2086 4989 8.352942 GTTCCAAAATAGATGAGTCAACTTTGT 58.647 33.333 8.34 0.00 0.00 2.83
2087 4990 7.535258 CGTTCCAAAATAGATGAGTCAACTTTG 59.465 37.037 8.34 7.19 0.00 2.77
2088 4991 7.308589 CCGTTCCAAAATAGATGAGTCAACTTT 60.309 37.037 8.34 0.00 0.00 2.66
2089 4992 6.149474 CCGTTCCAAAATAGATGAGTCAACTT 59.851 38.462 8.34 0.00 0.00 2.66
2090 4993 5.643777 CCGTTCCAAAATAGATGAGTCAACT 59.356 40.000 8.12 8.12 0.00 3.16
2091 4994 5.642063 TCCGTTCCAAAATAGATGAGTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2092 4995 5.800296 TCCGTTCCAAAATAGATGAGTCAA 58.200 37.500 0.00 0.00 0.00 3.18
2093 4996 5.414789 TCCGTTCCAAAATAGATGAGTCA 57.585 39.130 0.00 0.00 0.00 3.41
2094 4997 4.811557 CCTCCGTTCCAAAATAGATGAGTC 59.188 45.833 0.00 0.00 0.00 3.36
2095 4998 4.384208 CCCTCCGTTCCAAAATAGATGAGT 60.384 45.833 0.00 0.00 0.00 3.41
2096 4999 4.130118 CCCTCCGTTCCAAAATAGATGAG 58.870 47.826 0.00 0.00 0.00 2.90
2097 5000 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2098 5001 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2099 5002 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2100 5003 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2101 5004 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2102 5005 6.687139 GCTTATACTCCCTCCGTTCCAAAATA 60.687 42.308 0.00 0.00 0.00 1.40
2103 5006 5.681639 CTTATACTCCCTCCGTTCCAAAAT 58.318 41.667 0.00 0.00 0.00 1.82
2104 5007 4.624604 GCTTATACTCCCTCCGTTCCAAAA 60.625 45.833 0.00 0.00 0.00 2.44
2105 5008 3.118519 GCTTATACTCCCTCCGTTCCAAA 60.119 47.826 0.00 0.00 0.00 3.28
2106 5009 2.433239 GCTTATACTCCCTCCGTTCCAA 59.567 50.000 0.00 0.00 0.00 3.53
2107 5010 2.037144 GCTTATACTCCCTCCGTTCCA 58.963 52.381 0.00 0.00 0.00 3.53
2108 5011 2.317973 AGCTTATACTCCCTCCGTTCC 58.682 52.381 0.00 0.00 0.00 3.62
2109 5012 4.143543 AGTAGCTTATACTCCCTCCGTTC 58.856 47.826 0.00 0.00 0.00 3.95
2110 5013 4.181799 AGTAGCTTATACTCCCTCCGTT 57.818 45.455 0.00 0.00 0.00 4.44
2111 5014 3.880168 AGTAGCTTATACTCCCTCCGT 57.120 47.619 0.00 0.00 0.00 4.69
2112 5015 4.909001 ACTAGTAGCTTATACTCCCTCCG 58.091 47.826 0.00 0.00 0.00 4.63
2113 5016 7.019656 ACTACTAGTAGCTTATACTCCCTCC 57.980 44.000 26.54 0.00 36.66 4.30
2115 5018 9.962809 CATAACTACTAGTAGCTTATACTCCCT 57.037 37.037 26.54 2.98 36.66 4.20
2116 5019 9.737844 ACATAACTACTAGTAGCTTATACTCCC 57.262 37.037 26.54 0.00 36.66 4.30
2119 5022 9.796180 AGCACATAACTACTAGTAGCTTATACT 57.204 33.333 26.54 19.95 36.66 2.12
2122 5025 8.719648 CGTAGCACATAACTACTAGTAGCTTAT 58.280 37.037 26.54 22.85 38.27 1.73
2123 5026 7.928167 TCGTAGCACATAACTACTAGTAGCTTA 59.072 37.037 26.54 21.92 38.27 3.09
2124 5027 6.765036 TCGTAGCACATAACTACTAGTAGCTT 59.235 38.462 26.54 20.78 38.27 3.74
2125 5028 6.202570 GTCGTAGCACATAACTACTAGTAGCT 59.797 42.308 26.54 18.67 38.27 3.32
2126 5029 6.202570 AGTCGTAGCACATAACTACTAGTAGC 59.797 42.308 26.54 13.66 38.27 3.58
2127 5030 7.712264 AGTCGTAGCACATAACTACTAGTAG 57.288 40.000 25.30 25.30 38.27 2.57
2128 5031 8.417106 AGTAGTCGTAGCACATAACTACTAGTA 58.583 37.037 10.81 1.89 46.55 1.82
2129 5032 7.271511 AGTAGTCGTAGCACATAACTACTAGT 58.728 38.462 10.81 0.00 46.55 2.57
2130 5033 7.712264 AGTAGTCGTAGCACATAACTACTAG 57.288 40.000 10.81 0.00 46.55 2.57
2133 5036 6.779117 TGAAGTAGTCGTAGCACATAACTAC 58.221 40.000 0.00 0.00 41.55 2.73
2146 5049 9.035607 CAATTAATCAGCTAATGAAGTAGTCGT 57.964 33.333 0.00 0.00 42.53 4.34
2147 5050 9.035607 ACAATTAATCAGCTAATGAAGTAGTCG 57.964 33.333 0.00 0.00 42.53 4.18
2175 5078 3.706802 TGCGAATTGTTTGCAGAAGAA 57.293 38.095 0.60 0.00 44.84 2.52
2297 5200 0.179089 CTGAGAGCCGGATGGAAGTG 60.179 60.000 5.05 0.00 37.49 3.16
2333 5236 2.159572 GCGTGAAGCGGTTGATTTATGT 60.160 45.455 3.70 0.00 41.69 2.29
2334 5237 2.440501 GCGTGAAGCGGTTGATTTATG 58.559 47.619 3.70 0.00 41.69 1.90
2349 5252 2.612672 CCGATAAGACTACAGAGCGTGA 59.387 50.000 0.00 0.00 0.00 4.35
2350 5253 2.287069 CCCGATAAGACTACAGAGCGTG 60.287 54.545 0.00 0.00 0.00 5.34
2351 5254 1.948145 CCCGATAAGACTACAGAGCGT 59.052 52.381 0.00 0.00 0.00 5.07
2353 5256 2.293955 GGACCCGATAAGACTACAGAGC 59.706 54.545 0.00 0.00 0.00 4.09
2354 5257 3.552875 TGGACCCGATAAGACTACAGAG 58.447 50.000 0.00 0.00 0.00 3.35
2355 5258 3.657398 TGGACCCGATAAGACTACAGA 57.343 47.619 0.00 0.00 0.00 3.41
2356 5259 3.005897 CCATGGACCCGATAAGACTACAG 59.994 52.174 5.56 0.00 0.00 2.74
2357 5260 2.963101 CCATGGACCCGATAAGACTACA 59.037 50.000 5.56 0.00 0.00 2.74
2358 5261 2.963782 ACCATGGACCCGATAAGACTAC 59.036 50.000 21.47 0.00 0.00 2.73
2359 5262 3.323774 ACCATGGACCCGATAAGACTA 57.676 47.619 21.47 0.00 0.00 2.59
2360 5263 2.176247 ACCATGGACCCGATAAGACT 57.824 50.000 21.47 0.00 0.00 3.24
2361 5264 4.618920 AATACCATGGACCCGATAAGAC 57.381 45.455 21.47 0.00 0.00 3.01
2362 5265 6.945636 AATAATACCATGGACCCGATAAGA 57.054 37.500 21.47 0.00 0.00 2.10
2368 5272 5.412594 CAGATCAAATAATACCATGGACCCG 59.587 44.000 21.47 0.00 0.00 5.28
2384 5288 9.904198 TTCCAGATATAATTGTGTCAGATCAAA 57.096 29.630 1.99 0.00 0.00 2.69
2401 5305 8.280258 TGGTTATCCTGAGAAATTCCAGATAT 57.720 34.615 11.35 7.99 32.37 1.63
2402 5306 7.202130 CCTGGTTATCCTGAGAAATTCCAGATA 60.202 40.741 11.35 1.94 41.37 1.98
2522 5430 5.291371 CACAAAACAATCAGCATGTCAAACA 59.709 36.000 0.00 0.00 37.40 2.83
2533 5441 8.298854 TCTGTGGATAATTCACAAAACAATCAG 58.701 33.333 1.15 0.00 43.45 2.90
2554 5462 7.078228 GCTGTAAACTGTTCCTTTTATCTGTG 58.922 38.462 0.00 0.00 0.00 3.66
2562 5473 1.607148 GCCGCTGTAAACTGTTCCTTT 59.393 47.619 0.00 0.00 0.00 3.11
2573 5484 4.169696 CCCCGGATGCCGCTGTAA 62.170 66.667 0.73 0.00 46.86 2.41
2911 5822 0.245539 CAGGGCAGGCACAGAATTTG 59.754 55.000 0.00 0.00 0.00 2.32
3002 5913 3.654414 CTTCGAGTTAGTTGCCAGTTCT 58.346 45.455 0.00 0.00 0.00 3.01
3020 5931 3.775202 TCGCTTTGTCATCTCTAGCTTC 58.225 45.455 0.00 0.00 0.00 3.86
3056 5967 7.223193 CACATACCGTTATCGAATTCTTGGTAA 59.777 37.037 3.52 0.00 39.71 2.85
3119 6034 0.736636 CAGCAATGATGTGATGCCGT 59.263 50.000 0.00 0.00 40.93 5.68
3121 6036 0.249322 GCCAGCAATGATGTGATGCC 60.249 55.000 0.00 0.00 40.93 4.40
3122 6037 0.744874 AGCCAGCAATGATGTGATGC 59.255 50.000 0.00 0.00 40.34 3.91
3206 6121 3.840890 TGGCAAAATTAGCACGGTTAG 57.159 42.857 5.33 0.00 0.00 2.34
3210 6125 3.181397 CTCATTGGCAAAATTAGCACGG 58.819 45.455 3.01 0.00 0.00 4.94
3255 6170 9.920133 TCATTACTCAAATCACATATAGAGCTC 57.080 33.333 5.27 5.27 0.00 4.09
3288 6203 5.816258 TCTTTGCTGCAATCACAATCAAAAA 59.184 32.000 16.77 0.00 0.00 1.94
3299 6215 2.415625 CCTCTGCTTCTTTGCTGCAATC 60.416 50.000 16.77 4.34 36.22 2.67
3451 6367 2.030805 GGTAGATGAATGGAATTGGCGC 60.031 50.000 0.00 0.00 36.07 6.53
3452 6368 3.213506 TGGTAGATGAATGGAATTGGCG 58.786 45.455 0.00 0.00 36.07 5.69
3552 6474 6.595682 AGCCTTATTGCTGATGTTATGTACT 58.404 36.000 0.00 0.00 40.90 2.73
3587 6509 2.351726 GTCAAGACACAGTTTCGCAAGT 59.648 45.455 0.00 0.00 39.48 3.16
3682 6610 4.932799 CACCATCGATTAGTACCACAACAA 59.067 41.667 0.00 0.00 0.00 2.83
3820 6748 2.278330 GCACCCCAAAAGGCCTCTG 61.278 63.158 5.23 6.79 0.00 3.35
3854 6782 4.214119 CCACTCTGAATTCAGCGAAAAGAA 59.786 41.667 27.70 10.10 43.46 2.52
3999 6941 4.226394 TCTGCCCTAATGGTAGCACTTTTA 59.774 41.667 0.00 0.00 45.82 1.52
4003 6945 1.879575 TCTGCCCTAATGGTAGCACT 58.120 50.000 0.00 0.00 45.82 4.40
4055 7011 5.491323 TGGGGGCAAACCTTAAAATAAAG 57.509 39.130 0.00 0.00 40.03 1.85
4093 8865 2.115266 AAGAAAGCCCGGTGGGTG 59.885 61.111 0.00 0.00 46.51 4.61
4094 8866 2.115266 CAAGAAAGCCCGGTGGGT 59.885 61.111 0.00 0.00 46.51 4.51
4125 8897 1.668628 CGCCCATTTGAAAAAGGACGG 60.669 52.381 0.00 0.00 0.00 4.79
4126 8898 1.268352 TCGCCCATTTGAAAAAGGACG 59.732 47.619 0.15 0.15 0.00 4.79
4169 8949 0.536687 AGGTCACTCGTCTCGTTCCA 60.537 55.000 0.00 0.00 0.00 3.53
4174 8954 1.805345 ACTTGTAGGTCACTCGTCTCG 59.195 52.381 0.00 0.00 0.00 4.04
4179 8959 3.364889 TCAACACTTGTAGGTCACTCG 57.635 47.619 0.00 0.00 0.00 4.18
4346 9184 3.006859 TGATCATCGACCTGTTTGTCAGT 59.993 43.478 0.00 0.00 42.19 3.41
4348 9186 3.676291 TGATCATCGACCTGTTTGTCA 57.324 42.857 0.00 0.00 34.88 3.58
4349 9187 4.631377 TGAATGATCATCGACCTGTTTGTC 59.369 41.667 9.06 0.00 0.00 3.18
4359 9197 1.485895 TGGGCAGTGAATGATCATCGA 59.514 47.619 9.06 0.00 38.01 3.59


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

AutoCloner maintained by Alex Coulton.