Multiple sequence alignment - TraesCS3D01G359000

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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 TraesCS3D01G359000 chr3D 100.000 7957 0 0 1 7957 472447208 472439252 0.000000e+00 14694.0
1 TraesCS3D01G359000 chr3D 82.643 1400 190 34 2343 3716 472444589 472443217 0.000000e+00 1190.0
2 TraesCS3D01G359000 chr3D 82.643 1400 190 34 2620 3992 472444866 472443493 0.000000e+00 1190.0
3 TraesCS3D01G359000 chr3D 82.386 1232 180 25 2343 3556 472444450 472443238 0.000000e+00 1038.0
4 TraesCS3D01G359000 chr3D 82.386 1232 180 25 2759 3971 472444866 472443653 0.000000e+00 1038.0
5 TraesCS3D01G359000 chr3D 77.835 1552 275 50 2341 3859 472444730 472443215 0.000000e+00 896.0
6 TraesCS3D01G359000 chr3D 77.835 1552 275 50 2479 3994 472444868 472443350 0.000000e+00 896.0
7 TraesCS3D01G359000 chr3D 83.758 942 125 18 2343 3272 472444178 472443253 0.000000e+00 867.0
8 TraesCS3D01G359000 chr3D 83.758 942 125 18 3031 3956 472444866 472443937 0.000000e+00 867.0
9 TraesCS3D01G359000 chr3D 78.376 1133 193 38 2336 3441 472444322 472443215 0.000000e+00 688.0
10 TraesCS3D01G359000 chr3D 78.376 1133 193 38 2887 3994 472444873 472443768 0.000000e+00 688.0
11 TraesCS3D01G359000 chr3D 83.038 678 94 14 2367 3033 472443882 472443215 5.320000e-166 595.0
12 TraesCS3D01G359000 chr3D 83.038 678 94 14 3327 3994 472444842 472444176 5.320000e-166 595.0
13 TraesCS3D01G359000 chr3D 85.361 485 51 10 195 669 472449400 472448926 1.200000e-132 484.0
14 TraesCS3D01G359000 chr3D 95.113 266 13 0 1651 1916 472445495 472445230 3.430000e-113 420.0
15 TraesCS3D01G359000 chr3D 95.113 266 13 0 1714 1979 472445558 472445293 3.430000e-113 420.0
16 TraesCS3D01G359000 chr3D 95.074 203 10 0 1651 1853 472445432 472445230 3.580000e-83 320.0
17 TraesCS3D01G359000 chr3D 95.074 203 10 0 1777 1979 472445558 472445356 3.580000e-83 320.0
18 TraesCS3D01G359000 chr3D 98.795 166 2 0 4198 4363 2350725 2350560 6.040000e-76 296.0
19 TraesCS3D01G359000 chr3D 97.076 171 5 0 4196 4366 250054187 250054017 1.010000e-73 289.0
20 TraesCS3D01G359000 chr3D 89.655 203 20 1 664 866 472448895 472448694 2.850000e-64 257.0
21 TraesCS3D01G359000 chr3D 93.571 140 9 0 1651 1790 472445369 472445230 8.090000e-50 209.0
22 TraesCS3D01G359000 chr3D 93.571 140 9 0 1840 1979 472445558 472445419 8.090000e-50 209.0
23 TraesCS3D01G359000 chr3D 100.000 29 0 0 6512 6540 472440640 472440612 4.000000e-03 54.7
24 TraesCS3D01G359000 chr3D 100.000 29 0 0 6569 6597 472440697 472440669 4.000000e-03 54.7
25 TraesCS3D01G359000 chr3A 95.784 2680 89 12 4360 7025 614799745 614797076 0.000000e+00 4301.0
26 TraesCS3D01G359000 chr3A 94.963 1747 83 3 1651 3394 614801938 614800194 0.000000e+00 2734.0
27 TraesCS3D01G359000 chr3A 92.373 1403 63 16 600 1979 614803180 614801799 0.000000e+00 1958.0
28 TraesCS3D01G359000 chr3A 83.691 1073 129 30 2620 3668 614801244 614800194 0.000000e+00 970.0
29 TraesCS3D01G359000 chr3A 82.817 1065 155 21 2759 3809 614801244 614800194 0.000000e+00 928.0
30 TraesCS3D01G359000 chr3A 84.607 942 116 18 3031 3956 614801244 614800316 0.000000e+00 909.0
31 TraesCS3D01G359000 chr3A 91.734 617 50 1 1 616 614803808 614803192 0.000000e+00 856.0
32 TraesCS3D01G359000 chr3A 93.886 458 21 3 3745 4200 614800194 614799742 0.000000e+00 684.0
33 TraesCS3D01G359000 chr3A 85.449 646 80 11 2343 2984 614800829 614800194 0.000000e+00 660.0
34 TraesCS3D01G359000 chr3A 78.571 938 157 33 2343 3261 614801105 614800193 5.350000e-161 579.0
35 TraesCS3D01G359000 chr3A 93.051 331 21 1 1651 1979 614802066 614801736 4.320000e-132 483.0
36 TraesCS3D01G359000 chr3A 92.401 329 25 0 1651 1979 614802001 614801673 3.360000e-128 470.0
37 TraesCS3D01G359000 chr3A 93.233 266 18 0 1651 1916 614801875 614801610 7.490000e-105 392.0
38 TraesCS3D01G359000 chr3A 93.750 224 12 1 1758 1979 614802085 614801862 1.280000e-87 335.0
39 TraesCS3D01G359000 chr3A 94.581 203 11 0 1651 1853 614801812 614801610 1.670000e-81 315.0
40 TraesCS3D01G359000 chr3A 100.000 29 0 0 6569 6597 614797589 614797561 4.000000e-03 54.7
41 TraesCS3D01G359000 chr3B 94.422 1721 75 10 5318 7025 627920955 627919243 0.000000e+00 2627.0
42 TraesCS3D01G359000 chr3B 91.281 1835 102 31 1 1790 627926440 627924619 0.000000e+00 2449.0
43 TraesCS3D01G359000 chr3B 84.786 2123 229 50 1906 3994 627924692 627922630 0.000000e+00 2045.0
44 TraesCS3D01G359000 chr3B 87.798 1680 155 28 2343 4012 627923976 627922337 0.000000e+00 1921.0
45 TraesCS3D01G359000 chr3B 88.262 869 102 0 7089 7957 439862072 439862940 0.000000e+00 1040.0
46 TraesCS3D01G359000 chr3B 88.018 868 101 2 7090 7957 666929849 666928985 0.000000e+00 1024.0
47 TraesCS3D01G359000 chr3B 87.903 868 102 2 7090 7957 668819539 668818675 0.000000e+00 1018.0
48 TraesCS3D01G359000 chr3B 91.586 725 35 7 4360 5083 627922197 627921498 0.000000e+00 977.0
49 TraesCS3D01G359000 chr3B 81.500 1227 193 26 2479 3683 627924254 627923040 0.000000e+00 977.0
50 TraesCS3D01G359000 chr3B 84.275 903 120 12 3088 3978 627924195 627923303 0.000000e+00 861.0
51 TraesCS3D01G359000 chr3B 83.136 676 100 10 3327 3994 627924228 627923559 8.830000e-169 604.0
52 TraesCS3D01G359000 chr3B 98.193 166 3 0 4199 4364 666692237 666692402 2.810000e-74 291.0
53 TraesCS3D01G359000 chr3B 94.558 147 8 0 5066 5212 627921324 627921178 2.230000e-55 228.0
54 TraesCS3D01G359000 chr3B 89.091 165 9 3 4037 4200 627922350 627922194 6.300000e-46 196.0
55 TraesCS3D01G359000 chr3B 100.000 39 0 0 5287 5325 627921179 627921141 1.110000e-08 73.1
56 TraesCS3D01G359000 chr3B 100.000 29 0 0 6512 6540 627919698 627919670 4.000000e-03 54.7
57 TraesCS3D01G359000 chr3B 100.000 29 0 0 6569 6597 627919755 627919727 4.000000e-03 54.7
58 TraesCS3D01G359000 chr4D 88.364 868 98 2 7090 7957 51915806 51916670 0.000000e+00 1040.0
59 TraesCS3D01G359000 chr4D 97.110 173 4 1 4196 4367 475146216 475146388 2.810000e-74 291.0
60 TraesCS3D01G359000 chr4B 88.262 869 101 1 7089 7957 527980586 527981453 0.000000e+00 1038.0
61 TraesCS3D01G359000 chr5B 88.134 868 100 2 7090 7957 659592227 659593091 0.000000e+00 1029.0
62 TraesCS3D01G359000 chr7A 88.018 868 101 2 7090 7957 122033169 122032305 0.000000e+00 1024.0
63 TraesCS3D01G359000 chr7B 87.903 868 102 2 7090 7957 32465622 32464758 0.000000e+00 1018.0
64 TraesCS3D01G359000 chr6D 87.788 868 102 2 7090 7957 458726241 458725378 0.000000e+00 1013.0
65 TraesCS3D01G359000 chr6D 98.204 167 3 0 4198 4364 119803538 119803704 7.810000e-75 292.0
66 TraesCS3D01G359000 chr6D 94.972 179 9 0 4185 4363 445676079 445676257 1.690000e-71 281.0
67 TraesCS3D01G359000 chr5D 95.580 181 8 0 4184 4364 547239890 547239710 2.810000e-74 291.0
68 TraesCS3D01G359000 chr1D 96.552 174 4 2 4198 4369 403044477 403044304 3.630000e-73 287.0
69 TraesCS3D01G359000 chr2D 97.006 167 5 0 4198 4364 142056950 142056784 1.690000e-71 281.0


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 TraesCS3D01G359000 chr3D 472439252 472447208 7956 True 14694.000000 14694 100.000000 1 7957 1 chr3D.!!$R3 7956
1 TraesCS3D01G359000 chr3D 472440612 472449400 8788 True 604.381818 1190 87.209273 195 6597 22 chr3D.!!$R4 6402
2 TraesCS3D01G359000 chr3A 614797076 614803808 6732 True 1039.293750 4301 90.680688 1 7025 16 chr3A.!!$R1 7024
3 TraesCS3D01G359000 chr3B 439862072 439862940 868 False 1040.000000 1040 88.262000 7089 7957 1 chr3B.!!$F1 868
4 TraesCS3D01G359000 chr3B 666928985 666929849 864 True 1024.000000 1024 88.018000 7090 7957 1 chr3B.!!$R1 867
5 TraesCS3D01G359000 chr3B 668818675 668819539 864 True 1018.000000 1018 87.903000 7090 7957 1 chr3B.!!$R2 867
6 TraesCS3D01G359000 chr3B 627919243 627926440 7197 True 1005.192308 2627 90.956385 1 7025 13 chr3B.!!$R3 7024
7 TraesCS3D01G359000 chr4D 51915806 51916670 864 False 1040.000000 1040 88.364000 7090 7957 1 chr4D.!!$F1 867
8 TraesCS3D01G359000 chr4B 527980586 527981453 867 False 1038.000000 1038 88.262000 7089 7957 1 chr4B.!!$F1 868
9 TraesCS3D01G359000 chr5B 659592227 659593091 864 False 1029.000000 1029 88.134000 7090 7957 1 chr5B.!!$F1 867
10 TraesCS3D01G359000 chr7A 122032305 122033169 864 True 1024.000000 1024 88.018000 7090 7957 1 chr7A.!!$R1 867
11 TraesCS3D01G359000 chr7B 32464758 32465622 864 True 1018.000000 1018 87.903000 7090 7957 1 chr7B.!!$R1 867
12 TraesCS3D01G359000 chr6D 458725378 458726241 863 True 1013.000000 1013 87.788000 7090 7957 1 chr6D.!!$R1 867

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
148 149 0.604511 CCAACCCGGCCGTATATTCC 60.605 60.000 26.12 0.0 0.0 3.01 F
1811 4440 1.238439 CCTGCGGTGAAGTGATGTTT 58.762 50.000 0.00 0.0 0.0 2.83 F
1876 4505 3.009723 CCTGCGGTGAAGTGATGTTTAT 58.990 45.455 0.00 0.0 0.0 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 4517 3.153919 TGCATTTCCTACAACTCCAACC 58.846 45.455 0.00 0.0 0.00 3.77 R
6891 10348 3.779759 TGCAGTTTTCACAACAACCATC 58.220 40.909 0.00 0.0 0.00 3.51 R
7009 10466 9.283768 TGTAAACATGAATTCAAAGAGAAGCTA 57.716 29.630 13.09 0.0 40.15 3.32 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
18 19 2.597903 GAGGGATGGTTGGGAGGC 59.402 66.667 0.00 0.00 0.00 4.70
19 20 2.003548 GAGGGATGGTTGGGAGGCT 61.004 63.158 0.00 0.00 0.00 4.58
86 87 4.161333 GGACGAGAATTGCATCACAAAAG 58.839 43.478 0.00 0.00 42.86 2.27
133 134 3.061848 CACGGGCATGGTCCCAAC 61.062 66.667 8.89 0.00 46.92 3.77
148 149 0.604511 CCAACCCGGCCGTATATTCC 60.605 60.000 26.12 0.00 0.00 3.01
180 181 2.834574 ACTCTATGTGAACTCGAGCG 57.165 50.000 13.61 0.00 0.00 5.03
1759 4325 7.852454 CGGTGAAGTGATGTTTATTCATATGTG 59.148 37.037 1.90 0.00 34.45 3.21
1811 4440 1.238439 CCTGCGGTGAAGTGATGTTT 58.762 50.000 0.00 0.00 0.00 2.83
1822 4451 7.852454 CGGTGAAGTGATGTTTATTCATATGTG 59.148 37.037 1.90 0.00 34.45 3.21
1835 4464 9.778741 TTTATTCATATGTGATAGTTGGAGTCC 57.221 33.333 0.73 0.73 33.56 3.85
1858 4487 6.013379 TCCTAGGAAATGCATAATCCTACCTG 60.013 42.308 26.14 19.60 43.28 4.00
1876 4505 3.009723 CCTGCGGTGAAGTGATGTTTAT 58.990 45.455 0.00 0.00 0.00 1.40
1897 4526 8.686334 GTTTATTCATATGTGATGGTTGGAGTT 58.314 33.333 1.90 0.00 33.56 3.01
1898 4527 6.704289 ATTCATATGTGATGGTTGGAGTTG 57.296 37.500 1.90 0.00 33.56 3.16
1902 4531 3.417069 TGTGATGGTTGGAGTTGTAGG 57.583 47.619 0.00 0.00 0.00 3.18
1948 4577 9.040939 CGGTGAAGTGATGTTTATTCATATGTA 57.959 33.333 1.90 0.00 34.45 2.29
1975 4604 4.853468 TGGTGTCCTAGGAAATGCATAA 57.147 40.909 14.65 0.00 0.00 1.90
6891 10348 7.035004 TGGATTTTGAACTTTGTCTTCTGTTG 58.965 34.615 0.00 0.00 0.00 3.33
6904 10361 4.335315 GTCTTCTGTTGATGGTTGTTGTGA 59.665 41.667 0.00 0.00 0.00 3.58
7027 10484 9.725019 TTACAGATTAGCTTCTCTTTGAATTCA 57.275 29.630 3.38 3.38 33.71 2.57
7028 10485 8.804912 ACAGATTAGCTTCTCTTTGAATTCAT 57.195 30.769 9.40 0.00 33.71 2.57
7029 10486 8.675504 ACAGATTAGCTTCTCTTTGAATTCATG 58.324 33.333 9.40 5.84 33.71 3.07
7030 10487 8.675504 CAGATTAGCTTCTCTTTGAATTCATGT 58.324 33.333 9.40 0.00 33.71 3.21
7031 10488 9.240734 AGATTAGCTTCTCTTTGAATTCATGTT 57.759 29.630 9.40 0.00 33.71 2.71
7032 10489 9.852091 GATTAGCTTCTCTTTGAATTCATGTTT 57.148 29.630 9.40 0.00 33.71 2.83
7035 10492 8.169977 AGCTTCTCTTTGAATTCATGTTTACA 57.830 30.769 9.40 0.00 33.71 2.41
7036 10493 8.295288 AGCTTCTCTTTGAATTCATGTTTACAG 58.705 33.333 9.40 2.27 33.71 2.74
7037 10494 8.292448 GCTTCTCTTTGAATTCATGTTTACAGA 58.708 33.333 9.40 1.92 33.71 3.41
7046 10503 9.453572 TGAATTCATGTTTACAGATTAGCTTCT 57.546 29.630 3.38 0.00 0.00 2.85
7047 10504 9.928236 GAATTCATGTTTACAGATTAGCTTCTC 57.072 33.333 0.00 0.00 0.00 2.87
7048 10505 9.678260 AATTCATGTTTACAGATTAGCTTCTCT 57.322 29.630 0.00 0.00 0.00 3.10
7049 10506 8.709386 TTCATGTTTACAGATTAGCTTCTCTC 57.291 34.615 0.00 0.00 0.00 3.20
7050 10507 6.975197 TCATGTTTACAGATTAGCTTCTCTCG 59.025 38.462 0.00 0.00 0.00 4.04
7051 10508 6.510879 TGTTTACAGATTAGCTTCTCTCGA 57.489 37.500 0.00 0.00 0.00 4.04
7052 10509 6.556212 TGTTTACAGATTAGCTTCTCTCGAG 58.444 40.000 5.93 5.93 0.00 4.04
7053 10510 5.759506 TTACAGATTAGCTTCTCTCGAGG 57.240 43.478 13.56 3.44 0.00 4.63
7054 10511 2.360801 ACAGATTAGCTTCTCTCGAGGC 59.639 50.000 13.56 7.99 42.11 4.70
7055 10512 2.360483 CAGATTAGCTTCTCTCGAGGCA 59.640 50.000 13.56 0.00 44.03 4.75
7056 10513 2.622942 AGATTAGCTTCTCTCGAGGCAG 59.377 50.000 13.56 3.43 44.03 4.85
7057 10514 1.840737 TTAGCTTCTCTCGAGGCAGT 58.159 50.000 13.56 0.00 44.03 4.40
7058 10515 1.098869 TAGCTTCTCTCGAGGCAGTG 58.901 55.000 13.56 3.07 44.03 3.66
7059 10516 1.809209 GCTTCTCTCGAGGCAGTGC 60.809 63.158 13.56 6.55 41.49 4.40
7071 10528 2.301577 GGCAGTGCCTACTACTTCAG 57.698 55.000 27.48 0.00 46.69 3.02
7072 10529 1.646189 GCAGTGCCTACTACTTCAGC 58.354 55.000 2.85 0.00 34.74 4.26
7073 10530 1.205893 GCAGTGCCTACTACTTCAGCT 59.794 52.381 2.85 0.00 34.74 4.24
7074 10531 2.737039 GCAGTGCCTACTACTTCAGCTC 60.737 54.545 2.85 0.00 34.74 4.09
7075 10532 2.104170 AGTGCCTACTACTTCAGCTCC 58.896 52.381 0.00 0.00 34.74 4.70
7076 10533 1.825474 GTGCCTACTACTTCAGCTCCA 59.175 52.381 0.00 0.00 0.00 3.86
7077 10534 1.825474 TGCCTACTACTTCAGCTCCAC 59.175 52.381 0.00 0.00 0.00 4.02
7078 10535 1.825474 GCCTACTACTTCAGCTCCACA 59.175 52.381 0.00 0.00 0.00 4.17
7079 10536 2.432510 GCCTACTACTTCAGCTCCACAT 59.567 50.000 0.00 0.00 0.00 3.21
7080 10537 3.739519 GCCTACTACTTCAGCTCCACATG 60.740 52.174 0.00 0.00 0.00 3.21
7081 10538 3.181471 CCTACTACTTCAGCTCCACATGG 60.181 52.174 0.00 0.00 0.00 3.66
7082 10539 1.065854 ACTACTTCAGCTCCACATGGC 60.066 52.381 0.00 0.00 34.44 4.40
7083 10540 0.108186 TACTTCAGCTCCACATGGCG 60.108 55.000 0.00 0.00 34.44 5.69
7084 10541 2.747460 TTCAGCTCCACATGGCGC 60.747 61.111 4.66 4.66 45.80 6.53
7134 10591 2.158900 AGATTGGCGAGGATGTTTCGAT 60.159 45.455 0.00 0.00 40.36 3.59
7136 10593 0.534873 TGGCGAGGATGTTTCGATCA 59.465 50.000 0.00 0.00 40.36 2.92
7143 10600 1.678728 GGATGTTTCGATCAGGTGGCA 60.679 52.381 0.00 0.00 0.00 4.92
7238 10695 1.667830 CTCCCGCTGCTTTTCGTCA 60.668 57.895 0.00 0.00 0.00 4.35
7246 10703 0.884704 TGCTTTTCGTCACCCTGCTC 60.885 55.000 0.00 0.00 0.00 4.26
7264 10721 0.317160 TCTCAATGTGCGACGTCCTT 59.683 50.000 10.58 0.00 0.00 3.36
7297 10754 3.190874 CTGAGAGATAGGTGTTTTCGGC 58.809 50.000 0.00 0.00 0.00 5.54
7350 10807 1.212688 AGGGATCCAATTCGATGCACA 59.787 47.619 15.23 0.00 32.58 4.57
7400 10857 2.287608 GCTTTTGCCGTGTTAAGAAGCT 60.288 45.455 0.00 0.00 40.15 3.74
7406 10863 2.289547 GCCGTGTTAAGAAGCTTGTTCA 59.710 45.455 12.76 2.82 0.00 3.18
7418 10875 0.947244 CTTGTTCACCAAGCTTCGCT 59.053 50.000 0.00 0.00 43.84 4.93
7425 10882 2.396955 CCAAGCTTCGCTGCTCCAG 61.397 63.158 0.00 0.00 43.24 3.86
7436 10893 1.846007 CTGCTCCAGTGTCCTACTCT 58.154 55.000 0.00 0.00 37.60 3.24
7444 10901 4.725304 TCCAGTGTCCTACTCTATCACCTA 59.275 45.833 0.00 0.00 37.60 3.08
7467 10924 0.179073 CCACCGGTGACATCTCCATC 60.179 60.000 36.07 0.00 0.00 3.51
7491 10948 6.071391 TCACAGATGTGCAGTTTCAGTCTATA 60.071 38.462 8.11 0.00 45.25 1.31
7566 11023 1.146041 TGACTGCCTTGTGCGAGTT 59.854 52.632 0.00 0.00 45.60 3.01
7629 11086 1.375523 GGTGGTGTCGGATGTGTCC 60.376 63.158 0.00 0.00 41.40 4.02
7637 11094 2.581354 GGATGTGTCCTCGCTGCT 59.419 61.111 0.00 0.00 41.60 4.24
7650 11107 0.651551 CGCTGCTTGAGCTTCAGATC 59.348 55.000 4.44 0.00 46.64 2.75
7675 11132 1.376466 GTGCCTGATGTGTCCCTGT 59.624 57.895 0.00 0.00 0.00 4.00
7719 11176 0.249447 CCGACGAGGAAGCATGCATA 60.249 55.000 21.98 0.00 45.00 3.14
7742 11199 3.811031 GAGATCTCTCCCCTCGTGA 57.189 57.895 15.80 0.00 37.02 4.35
7749 11206 1.537638 CTCTCCCCTCGTGATACATCG 59.462 57.143 0.00 0.00 0.00 3.84
7766 11223 2.518312 CGTGTCGGTTGTCGTTGCA 61.518 57.895 0.00 0.00 40.32 4.08
7774 11231 0.303493 GTTGTCGTTGCATGTCGTGT 59.697 50.000 0.00 0.00 0.00 4.49
7777 11234 2.019408 TCGTTGCATGTCGTGTCGG 61.019 57.895 0.00 0.00 0.00 4.79
7787 11244 0.596600 GTCGTGTCGGTTGCTTCTGA 60.597 55.000 0.00 0.00 0.00 3.27
7802 11259 3.303659 GCTTCTGAGAGTGAAGTTGTTGC 60.304 47.826 0.00 0.00 41.94 4.17
7878 11336 2.102588 GGAGCCTACTTCGCCTATTTCA 59.897 50.000 0.00 0.00 0.00 2.69
7901 11359 2.119495 GGTGCTTCCTAAGGAGATGGA 58.881 52.381 0.00 0.00 31.21 3.41
7905 11363 3.034635 GCTTCCTAAGGAGATGGAGTCA 58.965 50.000 0.00 0.00 31.21 3.41
7917 11375 4.884961 AGATGGAGTCACTTGTAGGGTAT 58.115 43.478 0.00 0.00 0.00 2.73
7938 11396 2.125912 GTGATGCCGACTGCGACT 60.126 61.111 0.00 0.00 45.60 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.190578 CCGAGCCTCCCAACCATC 59.809 66.667 0.00 0.00 0.00 3.51
18 19 1.677637 GAGGAACCCTAGCCACCGAG 61.678 65.000 0.00 0.00 31.76 4.63
19 20 1.684734 GAGGAACCCTAGCCACCGA 60.685 63.158 0.00 0.00 31.76 4.69
61 62 1.398390 GTGATGCAATTCTCGTCCACC 59.602 52.381 0.00 0.00 0.00 4.61
63 64 2.470983 TGTGATGCAATTCTCGTCCA 57.529 45.000 0.00 0.00 0.00 4.02
66 67 3.820467 TCCTTTTGTGATGCAATTCTCGT 59.180 39.130 0.00 0.00 36.89 4.18
86 87 2.579207 TGAACGATCGAGGACAATCC 57.421 50.000 24.34 0.40 36.58 3.01
133 134 0.320421 CACAGGAATATACGGCCGGG 60.320 60.000 31.76 2.28 0.00 5.73
148 149 5.102313 TCACATAGAGTATGCGTTTCACAG 58.898 41.667 0.00 0.00 39.79 3.66
1759 4325 5.163301 TGCATTTCCTAGGACTCCAACTATC 60.163 44.000 12.22 0.00 0.00 2.08
1811 4440 8.727100 AGGACTCCAACTATCACATATGAATA 57.273 34.615 10.38 6.12 38.69 1.75
1822 4451 5.163301 TGCATTTCCTAGGACTCCAACTATC 60.163 44.000 12.22 0.00 0.00 2.08
1835 4464 5.645497 GCAGGTAGGATTATGCATTTCCTAG 59.355 44.000 26.58 19.64 41.58 3.02
1858 4487 4.678509 TGAATAAACATCACTTCACCGC 57.321 40.909 0.00 0.00 0.00 5.68
1876 4505 5.569355 ACAACTCCAACCATCACATATGAA 58.431 37.500 10.38 0.00 38.69 2.57
1888 4517 3.153919 TGCATTTCCTACAACTCCAACC 58.846 45.455 0.00 0.00 0.00 3.77
1902 4531 4.410492 CGCAGGTAGGATTATGCATTTC 57.590 45.455 3.54 2.35 38.60 2.17
1948 4577 5.193679 GCATTTCCTAGGACACCAACTATT 58.806 41.667 12.22 0.00 0.00 1.73
1957 4586 5.645056 TGGATTATGCATTTCCTAGGACA 57.355 39.130 22.11 5.26 0.00 4.02
1975 4604 4.771577 TGTGCCAATAAGAACACAATGGAT 59.228 37.500 0.00 0.00 39.91 3.41
6891 10348 3.779759 TGCAGTTTTCACAACAACCATC 58.220 40.909 0.00 0.00 0.00 3.51
7009 10466 9.283768 TGTAAACATGAATTCAAAGAGAAGCTA 57.716 29.630 13.09 0.00 40.15 3.32
7025 10482 6.975197 CGAGAGAAGCTAATCTGTAAACATGA 59.025 38.462 0.00 0.00 0.00 3.07
7026 10483 6.975197 TCGAGAGAAGCTAATCTGTAAACATG 59.025 38.462 5.38 0.00 37.03 3.21
7027 10484 7.101652 TCGAGAGAAGCTAATCTGTAAACAT 57.898 36.000 5.38 0.00 37.03 2.71
7028 10485 6.404844 CCTCGAGAGAAGCTAATCTGTAAACA 60.405 42.308 15.71 0.00 41.32 2.83
7029 10486 5.974751 CCTCGAGAGAAGCTAATCTGTAAAC 59.025 44.000 15.71 0.00 41.32 2.01
7030 10487 5.450688 GCCTCGAGAGAAGCTAATCTGTAAA 60.451 44.000 15.71 0.00 44.06 2.01
7031 10488 4.036971 GCCTCGAGAGAAGCTAATCTGTAA 59.963 45.833 15.71 0.00 44.06 2.41
7032 10489 3.566322 GCCTCGAGAGAAGCTAATCTGTA 59.434 47.826 15.71 0.00 44.06 2.74
7033 10490 2.360801 GCCTCGAGAGAAGCTAATCTGT 59.639 50.000 15.71 0.00 44.06 3.41
7034 10491 3.011949 GCCTCGAGAGAAGCTAATCTG 57.988 52.381 15.71 0.00 44.06 2.90
7042 10499 1.153667 GGCACTGCCTCGAGAGAAG 60.154 63.158 15.71 10.58 46.69 2.85
7043 10500 2.973899 GGCACTGCCTCGAGAGAA 59.026 61.111 15.71 0.00 46.69 2.87
7053 10510 1.205893 AGCTGAAGTAGTAGGCACTGC 59.794 52.381 0.00 0.00 41.52 4.40
7054 10511 2.159170 GGAGCTGAAGTAGTAGGCACTG 60.159 54.545 0.00 0.00 41.52 3.66
7055 10512 2.104170 GGAGCTGAAGTAGTAGGCACT 58.896 52.381 0.00 0.00 46.37 4.40
7056 10513 1.825474 TGGAGCTGAAGTAGTAGGCAC 59.175 52.381 0.00 0.00 0.00 5.01
7057 10514 1.825474 GTGGAGCTGAAGTAGTAGGCA 59.175 52.381 0.00 0.00 0.00 4.75
7058 10515 1.825474 TGTGGAGCTGAAGTAGTAGGC 59.175 52.381 0.00 0.00 0.00 3.93
7059 10516 3.181471 CCATGTGGAGCTGAAGTAGTAGG 60.181 52.174 0.00 0.00 37.39 3.18
7060 10517 3.739519 GCCATGTGGAGCTGAAGTAGTAG 60.740 52.174 2.55 0.00 37.39 2.57
7061 10518 2.168521 GCCATGTGGAGCTGAAGTAGTA 59.831 50.000 2.55 0.00 37.39 1.82
7062 10519 1.065854 GCCATGTGGAGCTGAAGTAGT 60.066 52.381 2.55 0.00 37.39 2.73
7063 10520 1.661341 GCCATGTGGAGCTGAAGTAG 58.339 55.000 2.55 0.00 37.39 2.57
7064 10521 0.108186 CGCCATGTGGAGCTGAAGTA 60.108 55.000 2.55 0.00 37.39 2.24
7065 10522 1.376424 CGCCATGTGGAGCTGAAGT 60.376 57.895 2.55 0.00 37.39 3.01
7066 10523 3.494378 CGCCATGTGGAGCTGAAG 58.506 61.111 2.55 0.00 37.39 3.02
7072 10529 2.872557 CAACAGCGCCATGTGGAG 59.127 61.111 2.29 0.03 37.39 3.86
7073 10530 3.364441 GCAACAGCGCCATGTGGA 61.364 61.111 2.29 0.00 37.39 4.02
7100 10557 1.299648 CAATCTCCCCAGCACGGAA 59.700 57.895 0.00 0.00 36.56 4.30
7105 10562 3.008517 TCGCCAATCTCCCCAGCA 61.009 61.111 0.00 0.00 0.00 4.41
7134 10591 4.357947 GTCGACGCTGCCACCTGA 62.358 66.667 0.00 0.00 0.00 3.86
7136 10593 4.363990 CTGTCGACGCTGCCACCT 62.364 66.667 11.62 0.00 0.00 4.00
7238 10695 1.376424 CGCACATTGAGAGCAGGGT 60.376 57.895 0.00 0.00 32.95 4.34
7246 10703 0.716108 GAAGGACGTCGCACATTGAG 59.284 55.000 9.92 0.00 0.00 3.02
7350 10807 0.105039 GGCCGGATCGAAGACAATCT 59.895 55.000 5.05 0.00 42.51 2.40
7383 10840 2.294074 ACAAGCTTCTTAACACGGCAA 58.706 42.857 0.00 0.00 0.00 4.52
7418 10875 3.053619 TGATAGAGTAGGACACTGGAGCA 60.054 47.826 0.00 0.00 37.72 4.26
7425 10882 5.474189 GGATGTAGGTGATAGAGTAGGACAC 59.526 48.000 0.00 0.00 0.00 3.67
7436 10893 2.464796 ACCGGTGGATGTAGGTGATA 57.535 50.000 6.12 0.00 35.36 2.15
7444 10901 0.537188 GAGATGTCACCGGTGGATGT 59.463 55.000 33.40 22.87 0.00 3.06
7566 11023 1.725169 CCCTCCCCAAAACACTCCCA 61.725 60.000 0.00 0.00 0.00 4.37
7601 11058 1.616865 CCGACACCACCTCTAGTTTGA 59.383 52.381 0.00 0.00 0.00 2.69
7637 11094 0.984230 AACCCCGATCTGAAGCTCAA 59.016 50.000 0.00 0.00 0.00 3.02
7650 11107 2.034066 ACATCAGGCACAACCCCG 59.966 61.111 0.00 0.00 40.58 5.73
7675 11132 1.299648 CAACCTGGATCTCGGGCAA 59.700 57.895 0.00 0.00 46.01 4.52
7704 11161 3.865446 TCCATATATGCATGCTTCCTCG 58.135 45.455 20.33 3.55 0.00 4.63
7706 11163 5.429109 AGATCTCCATATATGCATGCTTCCT 59.571 40.000 20.33 6.54 0.00 3.36
7742 11199 1.200716 ACGACAACCGACACGATGTAT 59.799 47.619 0.00 0.00 41.76 2.29
7749 11206 0.384230 CATGCAACGACAACCGACAC 60.384 55.000 0.00 0.00 41.76 3.67
7766 11223 0.033504 AGAAGCAACCGACACGACAT 59.966 50.000 0.00 0.00 0.00 3.06
7774 11231 1.328279 TCACTCTCAGAAGCAACCGA 58.672 50.000 0.00 0.00 0.00 4.69
7777 11234 3.873952 ACAACTTCACTCTCAGAAGCAAC 59.126 43.478 0.00 0.00 44.87 4.17
7787 11244 1.541233 CCTCGGCAACAACTTCACTCT 60.541 52.381 0.00 0.00 0.00 3.24
7802 11259 2.742372 CCGAAGCCACAACCTCGG 60.742 66.667 0.00 0.00 0.00 4.63
7835 11292 2.555325 CCACAAATCTTCTGCAGCTCAA 59.445 45.455 9.47 0.00 0.00 3.02
7878 11336 3.117738 CCATCTCCTTAGGAAGCACCATT 60.118 47.826 1.41 0.00 42.04 3.16
7901 11359 4.595781 TCACCAAATACCCTACAAGTGACT 59.404 41.667 0.00 0.00 0.00 3.41
7905 11363 4.270008 GCATCACCAAATACCCTACAAGT 58.730 43.478 0.00 0.00 0.00 3.16
7917 11375 2.324330 CGCAGTCGGCATCACCAAA 61.324 57.895 0.00 0.00 45.17 3.28
7938 11396 3.507597 CTCCAACGACGATGGTGAA 57.492 52.632 21.78 4.16 39.09 3.18


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

AutoCloner maintained by Alex Coulton.