Multiple sequence alignment - TraesCS4D01G107300

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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 TraesCS4D01G107300 chr4D 100.000 2177 0 0 553 2729 85587752 85589928 0.000000e+00 4021.0
1 TraesCS4D01G107300 chr4D 100.000 150 0 0 1 150 85587200 85587349 7.440000e-71 278.0
2 TraesCS4D01G107300 chr4A 94.614 1374 68 2 554 1926 499351304 499352672 0.000000e+00 2122.0
3 TraesCS4D01G107300 chr4A 89.645 338 27 5 2185 2515 499352959 499353295 9.030000e-115 424.0
4 TraesCS4D01G107300 chr4A 98.000 150 3 0 1 150 499351002 499351151 7.500000e-66 261.0
5 TraesCS4D01G107300 chr4A 95.402 87 4 0 2643 2729 499353298 499353384 3.660000e-29 139.0
6 TraesCS4D01G107300 chr4B 94.625 1172 60 1 553 1721 122558427 122559598 0.000000e+00 1812.0
7 TraesCS4D01G107300 chr4B 88.088 319 33 2 1729 2047 122559665 122559978 9.230000e-100 374.0
8 TraesCS4D01G107300 chr4B 97.333 150 4 0 1 150 122557930 122558079 3.490000e-64 255.0
9 TraesCS4D01G107300 chr4B 96.226 53 2 0 2463 2515 122561845 122561897 1.350000e-13 87.9
10 TraesCS4D01G107300 chr3D 97.080 137 2 1 2516 2650 455618049 455618185 2.110000e-56 230.0
11 TraesCS4D01G107300 chr5D 97.638 127 3 0 2516 2642 361358708 361358582 4.580000e-53 219.0
12 TraesCS4D01G107300 chr6D 96.241 133 4 1 2511 2643 327308921 327309052 1.650000e-52 217.0
13 TraesCS4D01G107300 chr6D 96.212 132 5 0 2516 2647 363593555 363593424 1.650000e-52 217.0
14 TraesCS4D01G107300 chr1B 94.964 139 6 1 2516 2654 653080749 653080612 1.650000e-52 217.0
15 TraesCS4D01G107300 chr7D 96.183 131 5 0 2512 2642 548483688 548483818 5.920000e-52 215.0
16 TraesCS4D01G107300 chr3A 95.522 134 5 1 2513 2645 59486884 59487017 2.130000e-51 213.0
17 TraesCS4D01G107300 chr5A 90.909 154 13 1 2505 2657 9840818 9840971 3.560000e-49 206.0
18 TraesCS4D01G107300 chrUn 92.701 137 8 2 2512 2647 23715008 23715143 2.140000e-46 196.0


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 TraesCS4D01G107300 chr4D 85587200 85589928 2728 False 2149.500 4021 100.00000 1 2729 2 chr4D.!!$F1 2728
1 TraesCS4D01G107300 chr4A 499351002 499353384 2382 False 736.500 2122 94.41525 1 2729 4 chr4A.!!$F1 2728
2 TraesCS4D01G107300 chr4B 122557930 122561897 3967 False 632.225 1812 94.06800 1 2515 4 chr4B.!!$F1 2514

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
719 720 0.531753 GAGCATTCCTCCTTCCTCGC 60.532 60.0 0.0 0.0 34.35 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2515 4041 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 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
109 110 2.043450 CACCCTCTCCTCTCCGCT 60.043 66.667 0.00 0.00 0.00 5.52
719 720 0.531753 GAGCATTCCTCCTTCCTCGC 60.532 60.000 0.00 0.00 34.35 5.03
876 877 0.612174 AGTGCGGAGAGAAGCTGGTA 60.612 55.000 0.00 0.00 0.00 3.25
985 986 2.285368 TGCCGGAGTTCCAGGGAT 60.285 61.111 5.05 0.00 35.14 3.85
1002 1003 5.337009 CCAGGGATTTTGGAAAGACTTGATG 60.337 44.000 0.00 0.00 37.96 3.07
1011 1012 3.512516 GACTTGATGCTGGCCCGC 61.513 66.667 12.95 12.95 0.00 6.13
1015 1016 4.657408 TGATGCTGGCCCGCAACA 62.657 61.111 26.35 25.49 44.06 3.33
1016 1017 4.120331 GATGCTGGCCCGCAACAC 62.120 66.667 26.35 15.80 44.06 3.32
1096 1097 0.880278 GGAGACGCAACTGCTGTTCA 60.880 55.000 5.94 0.00 39.32 3.18
1103 1104 2.475685 CGCAACTGCTGTTCATGATGAG 60.476 50.000 5.94 0.00 39.32 2.90
1120 1121 1.271543 TGAGCAATGTGAAGTGGGGAG 60.272 52.381 0.00 0.00 0.00 4.30
1305 1306 0.036732 TGACTAGTTGCAGCAAGGGG 59.963 55.000 8.49 3.91 0.00 4.79
1341 1342 0.438830 CGAAGTTGGCGCTGTTCTAC 59.561 55.000 7.64 0.00 0.00 2.59
1514 1515 2.202987 GGAGGCCATCGAGCAGTG 60.203 66.667 5.01 0.00 0.00 3.66
1532 1533 3.503363 CAGTGTGTGAGGTGTGCATTTAT 59.497 43.478 0.00 0.00 0.00 1.40
1579 1580 3.192001 CCCATCATTGGAGTTGTTGACAG 59.808 47.826 0.00 0.00 46.92 3.51
1602 1603 3.345737 CGAGAAGCTGTCGCCATTA 57.654 52.632 5.86 0.00 36.60 1.90
1739 1802 2.668457 GCTCCAACTAGATGTCACAACG 59.332 50.000 0.00 0.00 0.00 4.10
1740 1803 3.254060 CTCCAACTAGATGTCACAACGG 58.746 50.000 0.00 0.00 0.00 4.44
1742 1805 3.827876 TCCAACTAGATGTCACAACGGTA 59.172 43.478 0.00 0.00 0.00 4.02
1784 1847 2.423538 GTCAGCACCAATCCACCAATAC 59.576 50.000 0.00 0.00 0.00 1.89
1788 1851 3.088532 GCACCAATCCACCAATACTTCA 58.911 45.455 0.00 0.00 0.00 3.02
1792 1855 4.085733 CCAATCCACCAATACTTCAACCA 58.914 43.478 0.00 0.00 0.00 3.67
1814 1877 4.498894 TGTGAATGATCTGAGAAGGCAT 57.501 40.909 0.00 0.00 0.00 4.40
1818 1881 5.819379 GTGAATGATCTGAGAAGGCATACAA 59.181 40.000 0.00 0.00 0.00 2.41
1826 1889 5.190528 TCTGAGAAGGCATACAAAGAGGAAT 59.809 40.000 0.00 0.00 0.00 3.01
1836 1899 6.456988 GCATACAAAGAGGAATTACAAGACCG 60.457 42.308 0.00 0.00 0.00 4.79
1848 1911 1.883926 ACAAGACCGCACCAATTTACC 59.116 47.619 0.00 0.00 0.00 2.85
1865 1928 2.957402 ACCAGCAATTCAGGTGAAGA 57.043 45.000 0.00 0.00 39.26 2.87
1885 1949 4.077822 AGACATCCCTTGAGCAAGAAAAG 58.922 43.478 11.61 2.38 40.79 2.27
1886 1950 4.074970 GACATCCCTTGAGCAAGAAAAGA 58.925 43.478 11.61 3.85 40.79 2.52
1887 1951 4.473444 ACATCCCTTGAGCAAGAAAAGAA 58.527 39.130 11.61 0.00 40.79 2.52
1888 1952 4.895297 ACATCCCTTGAGCAAGAAAAGAAA 59.105 37.500 11.61 0.00 40.79 2.52
1889 1953 5.363580 ACATCCCTTGAGCAAGAAAAGAAAA 59.636 36.000 11.61 0.00 40.79 2.29
1895 1959 6.256539 CCTTGAGCAAGAAAAGAAAAAGGAAC 59.743 38.462 11.61 0.00 40.79 3.62
1896 1960 5.660460 TGAGCAAGAAAAGAAAAAGGAACC 58.340 37.500 0.00 0.00 0.00 3.62
1903 1967 5.958380 AGAAAAGAAAAAGGAACCTGGAGTT 59.042 36.000 0.00 0.00 43.07 3.01
1917 1981 1.303309 GGAGTTTGGGCTCATCATCG 58.697 55.000 0.00 0.00 37.24 3.84
1970 2034 6.263842 CCTCACCAATATGCACAGAATATGTT 59.736 38.462 0.00 0.00 41.41 2.71
1971 2035 7.445096 CCTCACCAATATGCACAGAATATGTTA 59.555 37.037 0.00 0.00 41.41 2.41
2028 2094 6.246420 AGAAGTCAATTCAATTCCGTTCAG 57.754 37.500 0.00 0.00 40.67 3.02
2064 2173 7.982761 AATGCCAATTTTTAATTTCTGCTGA 57.017 28.000 0.00 0.00 0.00 4.26
2083 2192 6.671190 TGCTGATTGAAAACTATGACAAGTG 58.329 36.000 0.00 0.00 0.00 3.16
2096 2206 7.151308 ACTATGACAAGTGAAGAGTTTCTCAG 58.849 38.462 0.00 0.00 34.31 3.35
2099 2209 2.447244 AGTGAAGAGTTTCTCAGCCG 57.553 50.000 0.00 0.00 34.31 5.52
2103 2213 1.663135 GAAGAGTTTCTCAGCCGATGC 59.337 52.381 0.00 0.00 32.06 3.91
2107 2217 7.858402 TGAAGAGTTTCTCAGCCGATGCTATA 61.858 42.308 0.00 0.00 38.88 1.31
2121 2231 7.205992 GCCGATGCTATATCTGATTAATCTGA 58.794 38.462 22.56 22.56 35.59 3.27
2124 2234 8.754096 CGATGCTATATCTGATTAATCTGAAGC 58.246 37.037 25.58 25.58 38.09 3.86
2127 2237 9.379791 TGCTATATCTGATTAATCTGAAGCATG 57.620 33.333 28.40 18.93 39.25 4.06
2128 2238 9.597170 GCTATATCTGATTAATCTGAAGCATGA 57.403 33.333 26.48 13.17 36.73 3.07
2172 2303 5.431765 AGACCGCTTCTTGTGATTCATTAT 58.568 37.500 0.00 0.00 0.00 1.28
2173 2304 5.525378 AGACCGCTTCTTGTGATTCATTATC 59.475 40.000 0.00 0.00 0.00 1.75
2178 2309 7.166970 CCGCTTCTTGTGATTCATTATCATTTG 59.833 37.037 0.00 0.00 44.75 2.32
2179 2310 7.911727 CGCTTCTTGTGATTCATTATCATTTGA 59.088 33.333 0.00 0.00 44.75 2.69
2180 2311 9.577110 GCTTCTTGTGATTCATTATCATTTGAA 57.423 29.630 0.00 0.00 44.75 2.69
2182 2313 9.577110 TTCTTGTGATTCATTATCATTTGAAGC 57.423 29.630 0.00 0.00 44.75 3.86
2183 2314 8.963725 TCTTGTGATTCATTATCATTTGAAGCT 58.036 29.630 3.08 0.00 44.75 3.74
2223 2364 1.303309 AGCAACAACTCTCTGCACAC 58.697 50.000 0.00 0.00 38.58 3.82
2275 2426 1.273327 CCTCATGGCCCTTTTGACAAC 59.727 52.381 0.00 0.00 0.00 3.32
2276 2427 1.962807 CTCATGGCCCTTTTGACAACA 59.037 47.619 0.00 0.00 0.00 3.33
2278 2429 1.047801 ATGGCCCTTTTGACAACACC 58.952 50.000 0.00 0.00 0.00 4.16
2279 2430 0.324738 TGGCCCTTTTGACAACACCA 60.325 50.000 0.00 0.00 0.00 4.17
2293 2444 7.433708 TGACAACACCAAGATAAATACACAG 57.566 36.000 0.00 0.00 0.00 3.66
2297 2448 8.946085 ACAACACCAAGATAAATACACAGTATG 58.054 33.333 0.00 0.00 46.00 2.39
2323 2474 6.541278 TGGATTGAATGATGTGATCAGACTTC 59.459 38.462 0.00 0.31 43.53 3.01
2345 2496 3.755628 CCTGGTGGCATGTGCAGC 61.756 66.667 7.36 3.92 44.36 5.25
2408 2568 3.278574 TGTTCAGGCATGCTAATACACC 58.721 45.455 18.92 0.00 0.00 4.16
2410 2570 3.475566 TCAGGCATGCTAATACACCTC 57.524 47.619 18.92 0.00 0.00 3.85
2437 2597 4.202264 GGAGAAGTCACATACACCATAGGG 60.202 50.000 0.00 0.00 41.29 3.53
2447 2607 6.495181 CACATACACCATAGGGAGTCTCTATT 59.505 42.308 10.01 0.00 38.95 1.73
2459 2619 7.961351 AGGGAGTCTCTATTGATGTATTTCTG 58.039 38.462 0.00 0.00 0.00 3.02
2461 3987 6.364706 GGAGTCTCTATTGATGTATTTCTGCG 59.635 42.308 0.00 0.00 0.00 5.18
2515 4041 5.708697 GGCCAACCTTATGTACTTGTAAACT 59.291 40.000 0.00 0.00 0.00 2.66
2516 4042 6.880529 GGCCAACCTTATGTACTTGTAAACTA 59.119 38.462 0.00 0.00 0.00 2.24
2517 4043 7.148356 GGCCAACCTTATGTACTTGTAAACTAC 60.148 40.741 0.00 0.00 0.00 2.73
2518 4044 7.605309 GCCAACCTTATGTACTTGTAAACTACT 59.395 37.037 0.00 0.00 0.00 2.57
2519 4045 9.148104 CCAACCTTATGTACTTGTAAACTACTC 57.852 37.037 0.00 0.00 0.00 2.59
2520 4046 9.148104 CAACCTTATGTACTTGTAAACTACTCC 57.852 37.037 0.00 0.00 0.00 3.85
2521 4047 7.845037 ACCTTATGTACTTGTAAACTACTCCC 58.155 38.462 0.00 0.00 0.00 4.30
2522 4048 7.677319 ACCTTATGTACTTGTAAACTACTCCCT 59.323 37.037 0.00 0.00 0.00 4.20
2523 4049 8.196103 CCTTATGTACTTGTAAACTACTCCCTC 58.804 40.741 0.00 0.00 0.00 4.30
2524 4050 5.990120 TGTACTTGTAAACTACTCCCTCC 57.010 43.478 0.00 0.00 0.00 4.30
2525 4051 4.460382 TGTACTTGTAAACTACTCCCTCCG 59.540 45.833 0.00 0.00 0.00 4.63
2526 4052 3.504375 ACTTGTAAACTACTCCCTCCGT 58.496 45.455 0.00 0.00 0.00 4.69
2527 4053 3.509184 ACTTGTAAACTACTCCCTCCGTC 59.491 47.826 0.00 0.00 0.00 4.79
2528 4054 2.450476 TGTAAACTACTCCCTCCGTCC 58.550 52.381 0.00 0.00 0.00 4.79
2529 4055 1.403323 GTAAACTACTCCCTCCGTCCG 59.597 57.143 0.00 0.00 0.00 4.79
2530 4056 0.969409 AAACTACTCCCTCCGTCCGG 60.969 60.000 0.00 0.00 0.00 5.14
2531 4057 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
2532 4058 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
2533 4059 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
2534 4060 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2535 4061 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2536 4062 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2537 4063 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2538 4064 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2539 4065 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2540 4066 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2541 4067 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2542 4068 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2543 4069 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2544 4070 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2545 4071 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2546 4072 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2547 4073 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2548 4074 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2549 4075 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2550 4076 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2551 4077 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
2552 4078 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
2553 4079 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
2561 4087 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
2562 4088 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
2563 4089 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
2564 4090 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
2565 4091 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
2566 4092 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
2569 4095 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
2575 4101 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
2583 4109 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
2597 4123 9.708092 GATGTATTTTAGTTCTAGATACACCCC 57.292 37.037 14.34 8.08 36.40 4.95
2598 4124 8.849543 TGTATTTTAGTTCTAGATACACCCCT 57.150 34.615 0.00 0.00 30.60 4.79
2599 4125 9.275572 TGTATTTTAGTTCTAGATACACCCCTT 57.724 33.333 0.00 0.00 30.60 3.95
2603 4129 8.857694 TTTAGTTCTAGATACACCCCTTTTTG 57.142 34.615 0.00 0.00 0.00 2.44
2604 4130 6.449830 AGTTCTAGATACACCCCTTTTTGT 57.550 37.500 0.00 0.00 0.00 2.83
2605 4131 6.473758 AGTTCTAGATACACCCCTTTTTGTC 58.526 40.000 0.00 0.00 0.00 3.18
2606 4132 6.272558 AGTTCTAGATACACCCCTTTTTGTCT 59.727 38.462 0.00 0.00 0.00 3.41
2607 4133 7.456902 AGTTCTAGATACACCCCTTTTTGTCTA 59.543 37.037 0.00 0.00 0.00 2.59
2608 4134 7.989947 TCTAGATACACCCCTTTTTGTCTAT 57.010 36.000 0.00 0.00 0.00 1.98
2609 4135 8.388656 TCTAGATACACCCCTTTTTGTCTATT 57.611 34.615 0.00 0.00 0.00 1.73
2610 4136 8.832735 TCTAGATACACCCCTTTTTGTCTATTT 58.167 33.333 0.00 0.00 0.00 1.40
2611 4137 7.703058 AGATACACCCCTTTTTGTCTATTTG 57.297 36.000 0.00 0.00 0.00 2.32
2612 4138 7.466804 AGATACACCCCTTTTTGTCTATTTGA 58.533 34.615 0.00 0.00 0.00 2.69
2613 4139 7.947890 AGATACACCCCTTTTTGTCTATTTGAA 59.052 33.333 0.00 0.00 0.00 2.69
2614 4140 6.994421 ACACCCCTTTTTGTCTATTTGAAT 57.006 33.333 0.00 0.00 0.00 2.57
2615 4141 6.758254 ACACCCCTTTTTGTCTATTTGAATG 58.242 36.000 0.00 0.00 0.00 2.67
2616 4142 6.553100 ACACCCCTTTTTGTCTATTTGAATGA 59.447 34.615 0.00 0.00 0.00 2.57
2617 4143 6.868339 CACCCCTTTTTGTCTATTTGAATGAC 59.132 38.462 0.00 0.00 0.00 3.06
2618 4144 6.553100 ACCCCTTTTTGTCTATTTGAATGACA 59.447 34.615 0.00 0.00 38.71 3.58
2619 4145 7.070571 ACCCCTTTTTGTCTATTTGAATGACAA 59.929 33.333 13.04 13.04 45.31 3.18
2620 4146 7.599998 CCCCTTTTTGTCTATTTGAATGACAAG 59.400 37.037 14.93 8.82 46.72 3.16
2621 4147 8.143835 CCCTTTTTGTCTATTTGAATGACAAGT 58.856 33.333 14.93 0.00 46.72 3.16
2622 4148 9.533253 CCTTTTTGTCTATTTGAATGACAAGTT 57.467 29.630 14.93 0.00 46.72 2.66
2653 4179 6.183360 GGACGGAGGGAGTATTTGTAATTACT 60.183 42.308 16.33 0.00 0.00 2.24
2674 4200 9.953565 ATTACTGGCTTTTGTTATTCAGTAGTA 57.046 29.630 0.00 0.00 38.44 1.82
2710 4236 6.295039 TCGTATTTTGTGTCTTGTCCTTTC 57.705 37.500 0.00 0.00 0.00 2.62
2711 4237 5.050634 TCGTATTTTGTGTCTTGTCCTTTCG 60.051 40.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 2.944954 TCGGGGAGGAGGAGGTGA 60.945 66.667 0.00 0.00 0.00 4.02
639 640 4.824515 CGGCGGAGGAGGGAGAGT 62.825 72.222 0.00 0.00 0.00 3.24
686 687 4.933064 GCTCGCGGATGAGGTCGG 62.933 72.222 6.13 0.00 36.47 4.79
759 760 4.214327 GCGAGGAGGCGGAGGAAG 62.214 72.222 0.00 0.00 0.00 3.46
876 877 1.513158 CACCGAGACGCAGAAGGAT 59.487 57.895 0.00 0.00 0.00 3.24
903 904 2.253758 CGTGCACACCTGGAAGTGG 61.254 63.158 18.64 5.67 42.28 4.00
985 986 3.243839 GCCAGCATCAAGTCTTTCCAAAA 60.244 43.478 0.00 0.00 0.00 2.44
1011 1012 1.300971 CCCGGCAGATGTCAGTGTTG 61.301 60.000 0.00 0.00 0.00 3.33
1015 1016 1.003355 CAACCCGGCAGATGTCAGT 60.003 57.895 0.00 0.00 0.00 3.41
1016 1017 1.003355 ACAACCCGGCAGATGTCAG 60.003 57.895 0.00 0.00 0.00 3.51
1096 1097 3.021695 CCCACTTCACATTGCTCATCAT 58.978 45.455 0.00 0.00 0.00 2.45
1103 1104 1.598701 GCCTCCCCACTTCACATTGC 61.599 60.000 0.00 0.00 0.00 3.56
1120 1121 1.222113 GCTGGTACCTCTTCTGGCC 59.778 63.158 14.36 0.00 0.00 5.36
1203 1204 1.226746 GGTACCCGCAGCATATGAAC 58.773 55.000 6.97 0.00 0.00 3.18
1305 1306 3.306166 ACTTCGCATTCGCTACAATGTAC 59.694 43.478 0.00 0.00 36.32 2.90
1444 1445 8.439286 CAGAAGAAATAAGAACTCAAGTAGCAC 58.561 37.037 0.00 0.00 0.00 4.40
1514 1515 4.437390 GCACTATAAATGCACACCTCACAC 60.437 45.833 0.00 0.00 42.88 3.82
1532 1533 2.972713 ACTCCTTTCTTCACCAGCACTA 59.027 45.455 0.00 0.00 0.00 2.74
1560 1561 2.821969 GCCTGTCAACAACTCCAATGAT 59.178 45.455 0.00 0.00 0.00 2.45
1579 1580 3.184683 CGACAGCTTCTCGCAGCC 61.185 66.667 0.00 0.00 41.12 4.85
1600 1601 3.674997 CCACAAGCTTCTGCCTAAGTAA 58.325 45.455 0.00 0.00 40.80 2.24
1602 1603 1.884067 GCCACAAGCTTCTGCCTAAGT 60.884 52.381 0.00 0.00 40.80 2.24
1739 1802 4.455533 TGCAGTTCATTCTTGACACATACC 59.544 41.667 0.00 0.00 0.00 2.73
1740 1803 5.180117 ACTGCAGTTCATTCTTGACACATAC 59.820 40.000 15.25 0.00 0.00 2.39
1742 1805 4.139786 ACTGCAGTTCATTCTTGACACAT 58.860 39.130 15.25 0.00 0.00 3.21
1746 1809 3.364764 GCTGACTGCAGTTCATTCTTGAC 60.365 47.826 22.65 4.28 44.17 3.18
1784 1847 5.878669 TCTCAGATCATTCACATGGTTGAAG 59.121 40.000 0.00 0.00 38.87 3.02
1788 1851 5.191426 CCTTCTCAGATCATTCACATGGTT 58.809 41.667 0.00 0.00 0.00 3.67
1792 1855 4.498894 TGCCTTCTCAGATCATTCACAT 57.501 40.909 0.00 0.00 0.00 3.21
1814 1877 4.933400 GCGGTCTTGTAATTCCTCTTTGTA 59.067 41.667 0.00 0.00 0.00 2.41
1818 1881 3.335579 GTGCGGTCTTGTAATTCCTCTT 58.664 45.455 0.00 0.00 0.00 2.85
1826 1889 3.502979 GGTAAATTGGTGCGGTCTTGTAA 59.497 43.478 0.00 0.00 0.00 2.41
1836 1899 3.924144 TGAATTGCTGGTAAATTGGTGC 58.076 40.909 0.00 0.00 0.00 5.01
1848 1911 3.128242 GGATGTCTTCACCTGAATTGCTG 59.872 47.826 0.00 0.00 33.01 4.41
1865 1928 4.104383 TCTTTTCTTGCTCAAGGGATGT 57.896 40.909 9.48 0.00 38.88 3.06
1885 1949 3.069586 CCCAAACTCCAGGTTCCTTTTTC 59.930 47.826 0.00 0.00 37.12 2.29
1886 1950 3.038280 CCCAAACTCCAGGTTCCTTTTT 58.962 45.455 0.00 0.00 37.12 1.94
1887 1951 2.677914 CCCAAACTCCAGGTTCCTTTT 58.322 47.619 0.00 0.00 37.12 2.27
1888 1952 1.757764 GCCCAAACTCCAGGTTCCTTT 60.758 52.381 0.00 0.00 37.12 3.11
1889 1953 0.178961 GCCCAAACTCCAGGTTCCTT 60.179 55.000 0.00 0.00 37.12 3.36
1895 1959 0.329261 TGATGAGCCCAAACTCCAGG 59.671 55.000 0.00 0.00 35.72 4.45
1896 1960 2.295885 GATGATGAGCCCAAACTCCAG 58.704 52.381 0.00 0.00 35.72 3.86
1903 1967 0.749091 CAAGCCGATGATGAGCCCAA 60.749 55.000 0.00 0.00 0.00 4.12
1917 1981 1.378646 GTAGGTCCAAGGGCAAGCC 60.379 63.158 1.52 1.52 0.00 4.35
1957 2021 8.693542 AGCTTTTGATTTAACATATTCTGTGC 57.306 30.769 0.00 0.00 38.39 4.57
1970 2034 6.148645 TGAATCGCACAGTAGCTTTTGATTTA 59.851 34.615 0.00 0.00 0.00 1.40
1971 2035 5.048782 TGAATCGCACAGTAGCTTTTGATTT 60.049 36.000 0.00 0.00 0.00 2.17
1979 2044 3.045601 AGTTTGAATCGCACAGTAGCT 57.954 42.857 0.00 0.00 0.00 3.32
1986 2051 7.061752 ACTTCTAATGTAGTTTGAATCGCAC 57.938 36.000 0.00 0.00 32.50 5.34
2064 2173 8.682936 ACTCTTCACTTGTCATAGTTTTCAAT 57.317 30.769 0.00 0.00 0.00 2.57
2083 2192 1.663135 GCATCGGCTGAGAAACTCTTC 59.337 52.381 0.00 0.00 36.96 2.87
2096 2206 7.205992 TCAGATTAATCAGATATAGCATCGGC 58.794 38.462 17.56 0.00 41.61 5.54
2099 2209 9.597170 TGCTTCAGATTAATCAGATATAGCATC 57.403 33.333 22.09 3.18 32.44 3.91
2107 2217 9.350951 TCATTTCATGCTTCAGATTAATCAGAT 57.649 29.630 17.56 0.00 0.00 2.90
2121 2231 9.169592 CCCTTCAATTAAATTCATTTCATGCTT 57.830 29.630 0.00 0.00 0.00 3.91
2127 2237 9.803315 GGTCTACCCTTCAATTAAATTCATTTC 57.197 33.333 0.00 0.00 0.00 2.17
2128 2238 8.466798 CGGTCTACCCTTCAATTAAATTCATTT 58.533 33.333 0.00 0.00 0.00 2.32
2140 2271 1.640917 AGAAGCGGTCTACCCTTCAA 58.359 50.000 21.94 0.00 41.59 2.69
2145 2276 0.606604 TCACAAGAAGCGGTCTACCC 59.393 55.000 0.00 0.00 34.56 3.69
2172 2303 6.384224 CAGCACTTCAATTAGCTTCAAATGA 58.616 36.000 0.00 0.00 34.61 2.57
2173 2304 5.575606 CCAGCACTTCAATTAGCTTCAAATG 59.424 40.000 0.00 0.00 34.61 2.32
2178 2309 2.489329 TGCCAGCACTTCAATTAGCTTC 59.511 45.455 0.00 0.00 34.61 3.86
2179 2310 2.490903 CTGCCAGCACTTCAATTAGCTT 59.509 45.455 0.00 0.00 34.61 3.74
2180 2311 2.089980 CTGCCAGCACTTCAATTAGCT 58.910 47.619 0.00 0.00 37.95 3.32
2181 2312 1.468736 GCTGCCAGCACTTCAATTAGC 60.469 52.381 12.82 0.00 41.89 3.09
2182 2313 2.556534 GCTGCCAGCACTTCAATTAG 57.443 50.000 12.82 0.00 41.89 1.73
2206 2347 2.283298 AGTGTGTGCAGAGAGTTGTTG 58.717 47.619 0.00 0.00 0.00 3.33
2223 2364 4.251268 TCAGTTCAAGCAGATGATGAGTG 58.749 43.478 0.00 0.00 0.00 3.51
2275 2426 7.768582 TCCACATACTGTGTATTTATCTTGGTG 59.231 37.037 6.53 0.00 46.45 4.17
2276 2427 7.857456 TCCACATACTGTGTATTTATCTTGGT 58.143 34.615 6.53 0.00 46.45 3.67
2293 2444 7.443272 TCTGATCACATCATTCAATCCACATAC 59.557 37.037 0.00 0.00 38.85 2.39
2297 2448 5.821470 AGTCTGATCACATCATTCAATCCAC 59.179 40.000 0.00 0.00 38.85 4.02
2323 2474 1.870055 GCACATGCCACCAGGTCTTG 61.870 60.000 0.00 0.00 32.95 3.02
2345 2496 3.702330 CTTAATGTGCATGATGCCTGTG 58.298 45.455 15.70 0.00 44.23 3.66
2350 2508 3.550275 CACAAGCTTAATGTGCATGATGC 59.450 43.478 11.12 11.12 45.29 3.91
2363 2521 3.868757 ACACTCGCTATCACAAGCTTA 57.131 42.857 0.00 0.00 40.49 3.09
2408 2568 4.437239 GTGTATGTGACTTCTCCCATGAG 58.563 47.826 0.00 0.00 40.17 2.90
2410 2570 3.055167 TGGTGTATGTGACTTCTCCCATG 60.055 47.826 0.00 0.00 0.00 3.66
2437 2597 6.364706 CCGCAGAAATACATCAATAGAGACTC 59.635 42.308 0.00 0.00 0.00 3.36
2447 2607 6.266786 TCCTATAACTCCGCAGAAATACATCA 59.733 38.462 0.00 0.00 0.00 3.07
2459 2619 2.553172 AGACGATGTCCTATAACTCCGC 59.447 50.000 0.00 0.00 32.18 5.54
2461 3987 5.708230 AGATCAGACGATGTCCTATAACTCC 59.292 44.000 0.00 0.00 32.18 3.85
2501 4027 5.126707 CGGAGGGAGTAGTTTACAAGTACAT 59.873 44.000 0.00 0.00 39.30 2.29
2515 4041 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2516 4042 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2517 4043 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2518 4044 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2519 4045 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2520 4046 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2521 4047 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2522 4048 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2523 4049 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2524 4050 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2525 4051 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2526 4052 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
2527 4053 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
2528 4054 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
2535 4061 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
2536 4062 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
2537 4063 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
2538 4064 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
2539 4065 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
2540 4066 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
2543 4069 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
2549 4075 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
2557 4083 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
2571 4097 9.708092 GGGGTGTATCTAGAACTAAAATACATC 57.292 37.037 0.00 13.73 35.81 3.06
2572 4098 9.448587 AGGGGTGTATCTAGAACTAAAATACAT 57.551 33.333 0.00 3.35 35.81 2.29
2573 4099 8.849543 AGGGGTGTATCTAGAACTAAAATACA 57.150 34.615 0.00 0.00 32.07 2.29
2577 4103 9.292195 CAAAAAGGGGTGTATCTAGAACTAAAA 57.708 33.333 0.00 0.00 0.00 1.52
2578 4104 8.442374 ACAAAAAGGGGTGTATCTAGAACTAAA 58.558 33.333 0.00 0.00 0.00 1.85
2579 4105 7.981142 ACAAAAAGGGGTGTATCTAGAACTAA 58.019 34.615 0.00 0.00 0.00 2.24
2580 4106 7.456902 AGACAAAAAGGGGTGTATCTAGAACTA 59.543 37.037 0.00 0.00 0.00 2.24
2581 4107 6.272558 AGACAAAAAGGGGTGTATCTAGAACT 59.727 38.462 0.00 0.00 0.00 3.01
2582 4108 6.473758 AGACAAAAAGGGGTGTATCTAGAAC 58.526 40.000 0.00 0.00 0.00 3.01
2583 4109 6.697641 AGACAAAAAGGGGTGTATCTAGAA 57.302 37.500 0.00 0.00 0.00 2.10
2584 4110 7.989947 ATAGACAAAAAGGGGTGTATCTAGA 57.010 36.000 0.00 0.00 0.00 2.43
2585 4111 8.893727 CAAATAGACAAAAAGGGGTGTATCTAG 58.106 37.037 0.00 0.00 0.00 2.43
2586 4112 8.607713 TCAAATAGACAAAAAGGGGTGTATCTA 58.392 33.333 0.00 0.00 0.00 1.98
2587 4113 7.466804 TCAAATAGACAAAAAGGGGTGTATCT 58.533 34.615 0.00 0.00 0.00 1.98
2588 4114 7.696992 TCAAATAGACAAAAAGGGGTGTATC 57.303 36.000 0.00 0.00 0.00 2.24
2589 4115 8.531146 CATTCAAATAGACAAAAAGGGGTGTAT 58.469 33.333 0.00 0.00 0.00 2.29
2590 4116 7.726291 TCATTCAAATAGACAAAAAGGGGTGTA 59.274 33.333 0.00 0.00 0.00 2.90
2591 4117 6.553100 TCATTCAAATAGACAAAAAGGGGTGT 59.447 34.615 0.00 0.00 0.00 4.16
2592 4118 6.868339 GTCATTCAAATAGACAAAAAGGGGTG 59.132 38.462 0.00 0.00 32.68 4.61
2593 4119 6.553100 TGTCATTCAAATAGACAAAAAGGGGT 59.447 34.615 0.00 0.00 39.15 4.95
2594 4120 6.991938 TGTCATTCAAATAGACAAAAAGGGG 58.008 36.000 0.00 0.00 39.15 4.79
2623 4149 4.076394 CAAATACTCCCTCCGTCCAAAAA 58.924 43.478 0.00 0.00 0.00 1.94
2624 4150 3.073356 ACAAATACTCCCTCCGTCCAAAA 59.927 43.478 0.00 0.00 0.00 2.44
2625 4151 2.640826 ACAAATACTCCCTCCGTCCAAA 59.359 45.455 0.00 0.00 0.00 3.28
2626 4152 2.262637 ACAAATACTCCCTCCGTCCAA 58.737 47.619 0.00 0.00 0.00 3.53
2627 4153 1.946984 ACAAATACTCCCTCCGTCCA 58.053 50.000 0.00 0.00 0.00 4.02
2628 4154 4.684484 ATTACAAATACTCCCTCCGTCC 57.316 45.455 0.00 0.00 0.00 4.79
2629 4155 6.700520 CAGTAATTACAAATACTCCCTCCGTC 59.299 42.308 17.65 0.00 30.09 4.79
2630 4156 6.407752 CCAGTAATTACAAATACTCCCTCCGT 60.408 42.308 17.65 0.00 30.09 4.69
2631 4157 5.989777 CCAGTAATTACAAATACTCCCTCCG 59.010 44.000 17.65 0.00 30.09 4.63
2632 4158 5.763698 GCCAGTAATTACAAATACTCCCTCC 59.236 44.000 17.65 0.00 30.09 4.30
2633 4159 6.592870 AGCCAGTAATTACAAATACTCCCTC 58.407 40.000 17.65 0.00 30.09 4.30
2634 4160 6.576778 AGCCAGTAATTACAAATACTCCCT 57.423 37.500 17.65 0.00 30.09 4.20
2635 4161 7.640597 AAAGCCAGTAATTACAAATACTCCC 57.359 36.000 17.65 0.00 30.09 4.30
2636 4162 8.520351 ACAAAAGCCAGTAATTACAAATACTCC 58.480 33.333 17.65 0.00 30.09 3.85
2637 4163 9.908152 AACAAAAGCCAGTAATTACAAATACTC 57.092 29.630 17.65 0.31 30.09 2.59
2674 4200 7.666623 ACACAAAATACGATGAAAGGGATTTT 58.333 30.769 0.00 0.00 0.00 1.82
2710 4236 4.598257 CACCTAGTGCCCTCAACG 57.402 61.111 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.