Multiple sequence alignment - TraesCS7D01G437300

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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 TraesCS7D01G437300 chr7D 100.000 2648 0 0 1 2648 556468860 556471507 0.000000e+00 4891.0
1 TraesCS7D01G437300 chr7D 93.002 543 37 1 2102 2644 593264536 593263995 0.000000e+00 791.0
2 TraesCS7D01G437300 chr7D 83.406 229 14 10 2028 2232 589144720 589144492 9.670000e-45 191.0
3 TraesCS7D01G437300 chr7D 90.323 62 5 1 1774 1835 37148843 37148783 2.180000e-11 80.5
4 TraesCS7D01G437300 chr7D 75.287 174 37 6 92 261 39957324 39957153 7.860000e-11 78.7
5 TraesCS7D01G437300 chr7A 91.860 1290 56 13 500 1787 642188353 642189595 0.000000e+00 1755.0
6 TraesCS7D01G437300 chr7A 93.856 472 22 6 3 468 642187885 642188355 0.000000e+00 704.0
7 TraesCS7D01G437300 chr7A 90.991 111 7 3 1992 2099 511549215 511549105 2.120000e-31 147.0
8 TraesCS7D01G437300 chr7B 89.613 1213 62 15 605 1787 603995881 603997059 0.000000e+00 1483.0
9 TraesCS7D01G437300 chr7B 89.948 776 50 10 541 1309 603746116 603746870 0.000000e+00 976.0
10 TraesCS7D01G437300 chr7B 90.735 680 50 7 1112 1787 603746721 603747391 0.000000e+00 894.0
11 TraesCS7D01G437300 chr7B 90.092 545 37 11 19 550 603995206 603995746 0.000000e+00 691.0
12 TraesCS7D01G437300 chr7B 83.636 550 50 8 1256 1787 603835562 603836089 5.130000e-132 481.0
13 TraesCS7D01G437300 chr1A 84.870 846 67 26 1838 2648 593634663 593633844 0.000000e+00 797.0
14 TraesCS7D01G437300 chr1A 89.540 631 49 5 2031 2644 20039174 20039804 0.000000e+00 784.0
15 TraesCS7D01G437300 chr1A 87.914 695 43 13 1988 2645 584748845 584749535 0.000000e+00 780.0
16 TraesCS7D01G437300 chr1A 86.250 80 9 2 155 234 111673896 111673819 4.700000e-13 86.1
17 TraesCS7D01G437300 chr1A 92.982 57 2 2 1780 1835 12261503 12261558 6.070000e-12 82.4
18 TraesCS7D01G437300 chr1A 95.918 49 2 0 1788 1836 586356114 586356066 2.180000e-11 80.5
19 TraesCS7D01G437300 chr1A 92.453 53 3 1 1783 1835 99158599 99158650 1.020000e-09 75.0
20 TraesCS7D01G437300 chr1A 81.176 85 12 3 180 261 21022075 21021992 6.120000e-07 65.8
21 TraesCS7D01G437300 chr5D 90.709 592 48 5 2061 2648 546027959 546027371 0.000000e+00 782.0
22 TraesCS7D01G437300 chr5D 78.824 170 27 8 76 242 389453218 389453055 3.600000e-19 106.0
23 TraesCS7D01G437300 chr5D 95.918 49 2 0 1787 1835 559629645 559629693 2.180000e-11 80.5
24 TraesCS7D01G437300 chr5D 86.486 74 7 3 190 261 353785411 353785483 7.860000e-11 78.7
25 TraesCS7D01G437300 chr5D 100.000 28 0 0 119 146 539977607 539977580 5.000000e-03 52.8
26 TraesCS7D01G437300 chr6A 89.677 620 52 8 2031 2645 38435510 38436122 0.000000e+00 780.0
27 TraesCS7D01G437300 chr6A 76.289 194 32 11 34 219 411145310 411145123 1.010000e-14 91.6
28 TraesCS7D01G437300 chr6A 84.270 89 11 3 180 266 534989939 534989852 1.690000e-12 84.2
29 TraesCS7D01G437300 chr6A 91.379 58 4 1 1779 1835 14500005 14499948 7.860000e-11 78.7
30 TraesCS7D01G437300 chr6A 91.837 49 3 1 181 228 8711335 8711383 1.700000e-07 67.6
31 TraesCS7D01G437300 chr3D 90.492 589 46 7 2064 2648 578552087 578551505 0.000000e+00 769.0
32 TraesCS7D01G437300 chr3D 87.156 654 35 14 2030 2648 19554310 19554949 0.000000e+00 697.0
33 TraesCS7D01G437300 chr3D 93.711 159 10 0 1838 1996 582174225 582174067 3.410000e-59 239.0
34 TraesCS7D01G437300 chr3D 97.959 49 1 0 1787 1835 588019809 588019857 4.700000e-13 86.1
35 TraesCS7D01G437300 chr3D 97.917 48 1 0 1788 1835 353213756 353213803 1.690000e-12 84.2
36 TraesCS7D01G437300 chr3D 96.000 50 2 0 1786 1835 520452833 520452784 6.070000e-12 82.4
37 TraesCS7D01G437300 chr3D 82.558 86 11 3 177 259 20538674 20538758 3.660000e-09 73.1
38 TraesCS7D01G437300 chrUn 90.476 588 47 8 2061 2645 47311143 47311724 0.000000e+00 767.0
39 TraesCS7D01G437300 chrUn 86.936 643 49 16 2030 2648 60982085 60982716 0.000000e+00 689.0
40 TraesCS7D01G437300 chrUn 92.857 56 2 2 180 234 258567156 258567102 2.180000e-11 80.5
41 TraesCS7D01G437300 chrUn 95.833 48 2 0 1788 1835 2653391 2653344 7.860000e-11 78.7
42 TraesCS7D01G437300 chrUn 95.833 48 2 0 1788 1835 214479824 214479777 7.860000e-11 78.7
43 TraesCS7D01G437300 chrUn 95.833 48 2 0 1788 1835 319012186 319012139 7.860000e-11 78.7
44 TraesCS7D01G437300 chrUn 95.833 48 2 0 1788 1835 361040128 361040175 7.860000e-11 78.7
45 TraesCS7D01G437300 chrUn 95.833 48 2 0 1788 1835 389092040 389092087 7.860000e-11 78.7
46 TraesCS7D01G437300 chrUn 93.750 48 3 0 1788 1835 27186196 27186243 3.660000e-09 73.1
47 TraesCS7D01G437300 chrUn 93.750 48 3 0 1788 1835 52720736 52720783 3.660000e-09 73.1
48 TraesCS7D01G437300 chrUn 93.750 48 3 0 1788 1835 68073328 68073281 3.660000e-09 73.1
49 TraesCS7D01G437300 chrUn 92.157 51 4 0 1788 1838 90972352 90972302 3.660000e-09 73.1
50 TraesCS7D01G437300 chr5A 89.796 588 54 5 2061 2645 526435243 526435827 0.000000e+00 749.0
51 TraesCS7D01G437300 chr5A 89.482 599 52 8 2059 2648 586168319 586167723 0.000000e+00 747.0
52 TraesCS7D01G437300 chr6D 94.231 156 8 1 1838 1993 78562431 78562585 1.230000e-58 237.0
53 TraesCS7D01G437300 chr6D 88.083 193 17 5 1838 2026 17445948 17446138 9.540000e-55 224.0
54 TraesCS7D01G437300 chr6D 79.894 189 26 9 80 261 114763967 114764150 7.690000e-26 128.0
55 TraesCS7D01G437300 chr6D 79.200 125 20 6 122 243 388416196 388416075 6.070000e-12 82.4
56 TraesCS7D01G437300 chr6D 95.833 48 2 0 1788 1835 126424085 126424038 7.860000e-11 78.7
57 TraesCS7D01G437300 chr6D 94.000 50 3 0 1787 1836 464390592 464390641 2.830000e-10 76.8
58 TraesCS7D01G437300 chr6D 95.652 46 2 0 1788 1833 446092424 446092379 1.020000e-09 75.0
59 TraesCS7D01G437300 chr5B 94.737 152 7 1 1838 1988 309684978 309684827 4.410000e-58 235.0
60 TraesCS7D01G437300 chr5B 78.241 216 36 8 54 264 401007149 401006940 7.690000e-26 128.0
61 TraesCS7D01G437300 chr5B 94.340 53 3 0 1783 1835 381063189 381063241 6.070000e-12 82.4
62 TraesCS7D01G437300 chr5B 96.000 50 2 0 1787 1836 671863633 671863682 6.070000e-12 82.4
63 TraesCS7D01G437300 chr2B 93.590 156 10 0 1838 1993 106092735 106092890 1.580000e-57 233.0
64 TraesCS7D01G437300 chr2B 92.727 55 4 0 1781 1835 788624450 788624396 2.180000e-11 80.5
65 TraesCS7D01G437300 chr1D 92.949 156 10 1 1838 1993 140516888 140517042 2.650000e-55 226.0
66 TraesCS7D01G437300 chr2A 87.958 191 15 5 1838 2027 142681061 142680878 4.440000e-53 219.0
67 TraesCS7D01G437300 chr2A 96.629 89 3 0 2030 2118 4797167 4797255 5.910000e-32 148.0
68 TraesCS7D01G437300 chr2A 100.000 66 0 0 2030 2095 12735417 12735482 3.580000e-24 122.0
69 TraesCS7D01G437300 chr3A 87.113 194 18 7 1838 2026 9382305 9382496 2.060000e-51 213.0
70 TraesCS7D01G437300 chr1B 78.505 214 32 13 54 261 359206921 359206716 7.690000e-26 128.0
71 TraesCS7D01G437300 chr2D 80.117 171 22 9 80 244 130759855 130759691 1.670000e-22 117.0
72 TraesCS7D01G437300 chr3B 75.248 202 42 7 31 228 721070213 721070410 3.630000e-14 89.8
73 TraesCS7D01G437300 chr3B 96.154 52 2 0 1784 1835 8051401 8051350 4.700000e-13 86.1
74 TraesCS7D01G437300 chr3B 96.078 51 2 0 1786 1836 820147644 820147594 1.690000e-12 84.2
75 TraesCS7D01G437300 chr3B 94.340 53 3 0 1783 1835 638335487 638335435 6.070000e-12 82.4
76 TraesCS7D01G437300 chr4B 75.000 200 41 8 41 234 501765828 501765632 1.690000e-12 84.2
77 TraesCS7D01G437300 chr4D 96.000 50 2 0 1786 1835 16310605 16310556 6.070000e-12 82.4
78 TraesCS7D01G437300 chr4D 96.000 50 2 0 1786 1835 16350882 16350833 6.070000e-12 82.4
79 TraesCS7D01G437300 chr4D 91.071 56 3 2 1788 1842 5226360 5226306 1.020000e-09 75.0
80 TraesCS7D01G437300 chr4A 82.178 101 13 5 53 150 627823804 627823706 6.070000e-12 82.4
81 TraesCS7D01G437300 chr6B 92.857 56 2 2 1780 1835 63690442 63690495 2.180000e-11 80.5
82 TraesCS7D01G437300 chr6B 90.476 63 3 3 1773 1835 522522712 522522771 2.180000e-11 80.5


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 TraesCS7D01G437300 chr7D 556468860 556471507 2647 False 4891.0 4891 100.0000 1 2648 1 chr7D.!!$F1 2647
1 TraesCS7D01G437300 chr7D 593263995 593264536 541 True 791.0 791 93.0020 2102 2644 1 chr7D.!!$R4 542
2 TraesCS7D01G437300 chr7A 642187885 642189595 1710 False 1229.5 1755 92.8580 3 1787 2 chr7A.!!$F1 1784
3 TraesCS7D01G437300 chr7B 603995206 603997059 1853 False 1087.0 1483 89.8525 19 1787 2 chr7B.!!$F3 1768
4 TraesCS7D01G437300 chr7B 603746116 603747391 1275 False 935.0 976 90.3415 541 1787 2 chr7B.!!$F2 1246
5 TraesCS7D01G437300 chr7B 603835562 603836089 527 False 481.0 481 83.6360 1256 1787 1 chr7B.!!$F1 531
6 TraesCS7D01G437300 chr1A 593633844 593634663 819 True 797.0 797 84.8700 1838 2648 1 chr1A.!!$R4 810
7 TraesCS7D01G437300 chr1A 20039174 20039804 630 False 784.0 784 89.5400 2031 2644 1 chr1A.!!$F2 613
8 TraesCS7D01G437300 chr1A 584748845 584749535 690 False 780.0 780 87.9140 1988 2645 1 chr1A.!!$F4 657
9 TraesCS7D01G437300 chr5D 546027371 546027959 588 True 782.0 782 90.7090 2061 2648 1 chr5D.!!$R3 587
10 TraesCS7D01G437300 chr6A 38435510 38436122 612 False 780.0 780 89.6770 2031 2645 1 chr6A.!!$F2 614
11 TraesCS7D01G437300 chr3D 578551505 578552087 582 True 769.0 769 90.4920 2064 2648 1 chr3D.!!$R2 584
12 TraesCS7D01G437300 chr3D 19554310 19554949 639 False 697.0 697 87.1560 2030 2648 1 chr3D.!!$F1 618
13 TraesCS7D01G437300 chrUn 47311143 47311724 581 False 767.0 767 90.4760 2061 2645 1 chrUn.!!$F2 584
14 TraesCS7D01G437300 chrUn 60982085 60982716 631 False 689.0 689 86.9360 2030 2648 1 chrUn.!!$F4 618
15 TraesCS7D01G437300 chr5A 526435243 526435827 584 False 749.0 749 89.7960 2061 2645 1 chr5A.!!$F1 584
16 TraesCS7D01G437300 chr5A 586167723 586168319 596 True 747.0 747 89.4820 2059 2648 1 chr5A.!!$R1 589

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
697 791 1.153549 AATCGAAGAGCCGTGCCTC 60.154 57.895 0.0 0.0 43.63 4.70 F
1173 1286 1.078708 GATACCACCACCACCACCG 60.079 63.158 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1829 0.610232 ACTGGTGCCTGCAATCCTTC 60.610 55.0 0.00 0.0 0.00 3.46 R
2122 2449 1.260538 TGTGCTCAGGCTGGAGTAGG 61.261 60.0 15.73 0.0 39.59 3.18 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
38 39 9.588774 CAATCATACTTTGTGCATTTCTTTTTG 57.411 29.630 0.00 0.00 0.00 2.44
69 70 7.041372 GCATGTTAGGTTTGTCTTAAGTCAAGA 60.041 37.037 13.55 4.84 41.10 3.02
269 273 8.986477 AATATGTGGAGTAAAAACAATGAAGC 57.014 30.769 0.00 0.00 0.00 3.86
271 275 6.214191 TGTGGAGTAAAAACAATGAAGCAA 57.786 33.333 0.00 0.00 0.00 3.91
274 281 7.865385 TGTGGAGTAAAAACAATGAAGCAATAC 59.135 33.333 0.00 0.00 0.00 1.89
282 289 7.759489 AAACAATGAAGCAATACTAAGGTGA 57.241 32.000 0.00 0.00 0.00 4.02
389 399 3.103742 TGAGCCCTTTCCAAAGTTGTTT 58.896 40.909 0.00 0.00 34.20 2.83
399 409 7.762159 CCTTTCCAAAGTTGTTTTTAGTTAGCA 59.238 33.333 0.00 0.00 34.20 3.49
598 664 7.213178 ACTTCTATGGATTTGTCATAGGGTT 57.787 36.000 10.13 0.00 42.44 4.11
629 723 5.670485 AGCACGATTTCAACCATGTCTATA 58.330 37.500 0.00 0.00 0.00 1.31
668 762 3.004944 CCTAGGTAAGATCGAGCTTGTCC 59.995 52.174 25.40 23.86 0.00 4.02
697 791 1.153549 AATCGAAGAGCCGTGCCTC 60.154 57.895 0.00 0.00 43.63 4.70
728 829 9.561069 ACTTGAGTGATTAAGTCAACTTGTAAT 57.439 29.630 5.66 0.00 42.20 1.89
729 830 9.817365 CTTGAGTGATTAAGTCAACTTGTAATG 57.183 33.333 5.66 0.00 42.20 1.90
730 831 8.322906 TGAGTGATTAAGTCAACTTGTAATGG 57.677 34.615 5.66 0.00 38.90 3.16
731 832 7.094805 TGAGTGATTAAGTCAACTTGTAATGGC 60.095 37.037 5.66 0.00 38.90 4.40
732 833 6.021596 GTGATTAAGTCAACTTGTAATGGCG 58.978 40.000 5.66 0.00 38.90 5.69
733 834 5.703592 TGATTAAGTCAACTTGTAATGGCGT 59.296 36.000 5.66 0.00 37.40 5.68
734 835 6.874664 TGATTAAGTCAACTTGTAATGGCGTA 59.125 34.615 5.66 0.00 37.40 4.42
735 836 7.551262 TGATTAAGTCAACTTGTAATGGCGTAT 59.449 33.333 5.66 0.00 37.40 3.06
1104 1217 2.122769 TGTCCGTCCCTTGGTCCA 60.123 61.111 0.00 0.00 0.00 4.02
1117 1230 2.436109 GTCCAGCACCACCACCAT 59.564 61.111 0.00 0.00 0.00 3.55
1120 1233 1.973281 CCAGCACCACCACCATCAC 60.973 63.158 0.00 0.00 0.00 3.06
1122 1235 2.115052 GCACCACCACCATCACCA 59.885 61.111 0.00 0.00 0.00 4.17
1124 1237 1.603455 CACCACCACCATCACCACC 60.603 63.158 0.00 0.00 0.00 4.61
1151 1264 3.702048 GCCGCCACCACCACTAGA 61.702 66.667 0.00 0.00 0.00 2.43
1152 1265 2.579201 CCGCCACCACCACTAGAG 59.421 66.667 0.00 0.00 0.00 2.43
1153 1266 2.579201 CGCCACCACCACTAGAGG 59.421 66.667 4.44 4.44 0.00 3.69
1154 1267 2.269241 GCCACCACCACTAGAGGC 59.731 66.667 6.07 0.00 34.71 4.70
1155 1268 2.579201 CCACCACCACTAGAGGCG 59.421 66.667 6.07 0.00 0.00 5.52
1156 1269 1.982395 CCACCACCACTAGAGGCGA 60.982 63.158 6.07 0.00 0.00 5.54
1157 1270 1.330655 CCACCACCACTAGAGGCGAT 61.331 60.000 6.07 0.00 0.00 4.58
1158 1271 1.399714 CACCACCACTAGAGGCGATA 58.600 55.000 6.07 0.00 0.00 2.92
1173 1286 1.078708 GATACCACCACCACCACCG 60.079 63.158 0.00 0.00 0.00 4.94
1219 1335 2.510691 CGATACCACCACCACCGC 60.511 66.667 0.00 0.00 0.00 5.68
1220 1336 2.124860 GATACCACCACCACCGCC 60.125 66.667 0.00 0.00 0.00 6.13
1221 1337 4.090588 ATACCACCACCACCGCCG 62.091 66.667 0.00 0.00 0.00 6.46
1447 1686 3.633094 GAGAAGAGCCGCTGCGACA 62.633 63.158 25.45 0.00 44.33 4.35
1787 2064 5.647658 TGCAATCAATTTCACTATCGTTCCT 59.352 36.000 0.00 0.00 0.00 3.36
1788 2065 5.967674 GCAATCAATTTCACTATCGTTCCTG 59.032 40.000 0.00 0.00 0.00 3.86
1789 2066 6.403636 GCAATCAATTTCACTATCGTTCCTGT 60.404 38.462 0.00 0.00 0.00 4.00
1790 2067 7.530010 CAATCAATTTCACTATCGTTCCTGTT 58.470 34.615 0.00 0.00 0.00 3.16
1791 2068 8.664798 CAATCAATTTCACTATCGTTCCTGTTA 58.335 33.333 0.00 0.00 0.00 2.41
1792 2069 7.827819 TCAATTTCACTATCGTTCCTGTTAG 57.172 36.000 0.00 0.00 0.00 2.34
1793 2070 7.608153 TCAATTTCACTATCGTTCCTGTTAGA 58.392 34.615 0.00 0.00 0.00 2.10
1794 2071 7.759886 TCAATTTCACTATCGTTCCTGTTAGAG 59.240 37.037 0.00 0.00 0.00 2.43
1795 2072 6.585695 TTTCACTATCGTTCCTGTTAGAGT 57.414 37.500 0.00 0.00 0.00 3.24
1796 2073 6.585695 TTCACTATCGTTCCTGTTAGAGTT 57.414 37.500 0.00 0.00 0.00 3.01
1797 2074 5.950883 TCACTATCGTTCCTGTTAGAGTTG 58.049 41.667 0.00 0.00 0.00 3.16
1798 2075 5.475909 TCACTATCGTTCCTGTTAGAGTTGT 59.524 40.000 0.00 0.00 0.00 3.32
1799 2076 5.573282 CACTATCGTTCCTGTTAGAGTTGTG 59.427 44.000 0.00 0.00 0.00 3.33
1800 2077 4.602340 ATCGTTCCTGTTAGAGTTGTGT 57.398 40.909 0.00 0.00 0.00 3.72
1801 2078 3.973657 TCGTTCCTGTTAGAGTTGTGTC 58.026 45.455 0.00 0.00 0.00 3.67
1802 2079 2.724690 CGTTCCTGTTAGAGTTGTGTCG 59.275 50.000 0.00 0.00 0.00 4.35
1803 2080 3.549423 CGTTCCTGTTAGAGTTGTGTCGA 60.549 47.826 0.00 0.00 0.00 4.20
1804 2081 4.365723 GTTCCTGTTAGAGTTGTGTCGAA 58.634 43.478 0.00 0.00 0.00 3.71
1805 2082 4.866508 TCCTGTTAGAGTTGTGTCGAAT 57.133 40.909 0.00 0.00 0.00 3.34
1806 2083 5.970317 TCCTGTTAGAGTTGTGTCGAATA 57.030 39.130 0.00 0.00 0.00 1.75
1807 2084 6.525578 TCCTGTTAGAGTTGTGTCGAATAT 57.474 37.500 0.00 0.00 0.00 1.28
1808 2085 6.931838 TCCTGTTAGAGTTGTGTCGAATATT 58.068 36.000 0.00 0.00 0.00 1.28
1809 2086 8.058667 TCCTGTTAGAGTTGTGTCGAATATTA 57.941 34.615 0.00 0.00 0.00 0.98
1810 2087 8.692710 TCCTGTTAGAGTTGTGTCGAATATTAT 58.307 33.333 0.00 0.00 0.00 1.28
1811 2088 9.314321 CCTGTTAGAGTTGTGTCGAATATTATT 57.686 33.333 0.00 0.00 0.00 1.40
1813 2090 9.647797 TGTTAGAGTTGTGTCGAATATTATTGT 57.352 29.630 0.00 0.00 0.00 2.71
1817 2094 9.647797 AGAGTTGTGTCGAATATTATTGTACAA 57.352 29.630 11.41 11.41 0.00 2.41
1833 2110 6.557291 TTGTACAATTTAGGTTACGGTTGG 57.443 37.500 3.59 0.00 0.00 3.77
1834 2111 5.862845 TGTACAATTTAGGTTACGGTTGGA 58.137 37.500 0.00 0.00 0.00 3.53
1835 2112 6.474630 TGTACAATTTAGGTTACGGTTGGAT 58.525 36.000 0.00 0.00 0.00 3.41
1836 2113 6.594937 TGTACAATTTAGGTTACGGTTGGATC 59.405 38.462 0.00 0.00 0.00 3.36
1851 2128 4.753107 GGTTGGATCAGTAGAAAAACGACA 59.247 41.667 0.00 0.00 0.00 4.35
1906 2183 0.323629 TCTGGAACCGGCACTAAAGG 59.676 55.000 0.00 0.00 0.00 3.11
1919 2196 3.872630 GCACTAAAGGGTGGGGACTAAAG 60.873 52.174 0.00 0.00 37.65 1.85
2099 2388 5.292834 CCTCATAACTGCTCAAGTGTACATG 59.707 44.000 0.00 0.00 39.81 3.21
2122 2449 2.435693 CCGGTCACCCATCCTCTCC 61.436 68.421 0.00 0.00 0.00 3.71
2566 2911 3.744238 AAATTTGCAAAACGGCCTACT 57.256 38.095 17.19 0.00 0.00 2.57
2567 2912 3.744238 AATTTGCAAAACGGCCTACTT 57.256 38.095 17.19 0.00 0.00 2.24
2576 2921 5.528870 CAAAACGGCCTACTTCTTTCAAAT 58.471 37.500 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.884639 AGACAAACCTAACATGCACACC 59.115 45.455 0.00 0.00 0.00 4.16
264 268 5.692115 TCCATCACCTTAGTATTGCTTCA 57.308 39.130 0.00 0.00 0.00 3.02
267 271 5.957771 TCTTCCATCACCTTAGTATTGCT 57.042 39.130 0.00 0.00 0.00 3.91
312 319 1.528309 ACCACCTTTCACCCGCAAG 60.528 57.895 0.00 0.00 0.00 4.01
389 399 1.631898 GGAGGGGTGGTGCTAACTAAA 59.368 52.381 0.00 0.00 0.00 1.85
399 409 0.336048 CATTTCCATGGAGGGGTGGT 59.664 55.000 15.53 0.00 38.24 4.16
495 507 2.484264 CAGGGGAGTTGTTTTGTCGATC 59.516 50.000 0.00 0.00 0.00 3.69
598 664 6.078202 TGGTTGAAATCGTGCTTTGATTAA 57.922 33.333 0.26 0.00 35.07 1.40
629 723 8.890410 TTACCTAGGAGTATTAGTTTGAGTGT 57.110 34.615 17.98 0.00 0.00 3.55
646 740 3.004944 GGACAAGCTCGATCTTACCTAGG 59.995 52.174 7.41 7.41 0.00 3.02
668 762 2.611292 GCTCTTCGATTGGATTCCACAG 59.389 50.000 4.45 0.00 30.78 3.66
697 791 6.201044 AGTTGACTTAATCACTCAAGTTGACG 59.799 38.462 0.08 1.31 36.92 4.35
728 829 2.435234 GTCCACGCCAATACGCCA 60.435 61.111 0.00 0.00 36.19 5.69
729 830 3.199891 GGTCCACGCCAATACGCC 61.200 66.667 0.00 0.00 36.19 5.68
730 831 3.560278 CGGTCCACGCCAATACGC 61.560 66.667 0.00 0.00 36.19 4.42
1104 1217 2.436109 GGTGATGGTGGTGGTGCT 59.564 61.111 0.00 0.00 0.00 4.40
1134 1247 3.665675 CTCTAGTGGTGGTGGCGGC 62.666 68.421 0.00 0.00 0.00 6.53
1135 1248 2.579201 CTCTAGTGGTGGTGGCGG 59.421 66.667 0.00 0.00 0.00 6.13
1136 1249 2.579201 CCTCTAGTGGTGGTGGCG 59.421 66.667 2.47 0.00 0.00 5.69
1137 1250 2.269241 GCCTCTAGTGGTGGTGGC 59.731 66.667 12.31 0.00 0.00 5.01
1138 1251 1.330655 ATCGCCTCTAGTGGTGGTGG 61.331 60.000 21.14 3.85 38.98 4.61
1139 1252 1.067212 GTATCGCCTCTAGTGGTGGTG 59.933 57.143 21.14 11.32 39.60 4.17
1140 1253 1.400737 GTATCGCCTCTAGTGGTGGT 58.599 55.000 21.14 17.83 38.11 4.16
1141 1254 0.674534 GGTATCGCCTCTAGTGGTGG 59.325 60.000 21.14 10.24 38.11 4.61
1142 1255 1.067212 GTGGTATCGCCTCTAGTGGTG 59.933 57.143 16.65 16.65 38.35 4.17
1143 1256 1.400737 GTGGTATCGCCTCTAGTGGT 58.599 55.000 12.31 0.00 38.35 4.16
1144 1257 0.674534 GGTGGTATCGCCTCTAGTGG 59.325 60.000 6.47 6.47 40.31 4.00
1145 1258 1.067212 GTGGTGGTATCGCCTCTAGTG 59.933 57.143 7.20 0.00 43.72 2.74
1146 1259 1.400737 GTGGTGGTATCGCCTCTAGT 58.599 55.000 7.20 0.00 43.72 2.57
1147 1260 0.674534 GGTGGTGGTATCGCCTCTAG 59.325 60.000 7.20 0.00 43.72 2.43
1148 1261 0.032912 TGGTGGTGGTATCGCCTCTA 60.033 55.000 7.20 0.00 43.72 2.43
1149 1262 1.305802 TGGTGGTGGTATCGCCTCT 60.306 57.895 7.20 0.00 43.72 3.69
1150 1263 1.153429 GTGGTGGTGGTATCGCCTC 60.153 63.158 7.20 2.79 43.72 4.70
1151 1264 2.666098 GGTGGTGGTGGTATCGCCT 61.666 63.158 7.20 0.00 43.72 5.52
1152 1265 2.124860 GGTGGTGGTGGTATCGCC 60.125 66.667 0.00 0.00 43.64 5.54
1153 1266 1.743995 GTGGTGGTGGTGGTATCGC 60.744 63.158 0.00 0.00 0.00 4.58
1154 1267 1.078708 GGTGGTGGTGGTGGTATCG 60.079 63.158 0.00 0.00 0.00 2.92
1155 1268 1.078708 CGGTGGTGGTGGTGGTATC 60.079 63.158 0.00 0.00 0.00 2.24
1156 1269 2.598787 CCGGTGGTGGTGGTGGTAT 61.599 63.158 0.00 0.00 0.00 2.73
1157 1270 3.243053 CCGGTGGTGGTGGTGGTA 61.243 66.667 0.00 0.00 0.00 3.25
1447 1686 0.537188 ATCTTCGGGATCGTGCACTT 59.463 50.000 16.19 1.52 37.69 3.16
1590 1829 0.610232 ACTGGTGCCTGCAATCCTTC 60.610 55.000 0.00 0.00 0.00 3.46
1787 2064 9.647797 ACAATAATATTCGACACAACTCTAACA 57.352 29.630 0.00 0.00 0.00 2.41
1791 2068 9.647797 TTGTACAATAATATTCGACACAACTCT 57.352 29.630 3.59 0.00 0.00 3.24
1807 2084 8.728833 CCAACCGTAACCTAAATTGTACAATAA 58.271 33.333 21.07 11.63 0.00 1.40
1808 2085 8.099537 TCCAACCGTAACCTAAATTGTACAATA 58.900 33.333 21.07 6.22 0.00 1.90
1809 2086 6.941436 TCCAACCGTAACCTAAATTGTACAAT 59.059 34.615 15.47 15.47 0.00 2.71
1810 2087 6.294473 TCCAACCGTAACCTAAATTGTACAA 58.706 36.000 11.41 11.41 0.00 2.41
1811 2088 5.862845 TCCAACCGTAACCTAAATTGTACA 58.137 37.500 0.00 0.00 0.00 2.90
1812 2089 6.594937 TGATCCAACCGTAACCTAAATTGTAC 59.405 38.462 0.00 0.00 0.00 2.90
1813 2090 6.709281 TGATCCAACCGTAACCTAAATTGTA 58.291 36.000 0.00 0.00 0.00 2.41
1814 2091 5.562635 TGATCCAACCGTAACCTAAATTGT 58.437 37.500 0.00 0.00 0.00 2.71
1815 2092 5.646360 ACTGATCCAACCGTAACCTAAATTG 59.354 40.000 0.00 0.00 0.00 2.32
1816 2093 5.812286 ACTGATCCAACCGTAACCTAAATT 58.188 37.500 0.00 0.00 0.00 1.82
1817 2094 5.431179 ACTGATCCAACCGTAACCTAAAT 57.569 39.130 0.00 0.00 0.00 1.40
1818 2095 4.895668 ACTGATCCAACCGTAACCTAAA 57.104 40.909 0.00 0.00 0.00 1.85
1819 2096 5.263599 TCTACTGATCCAACCGTAACCTAA 58.736 41.667 0.00 0.00 0.00 2.69
1820 2097 4.858850 TCTACTGATCCAACCGTAACCTA 58.141 43.478 0.00 0.00 0.00 3.08
1821 2098 3.705051 TCTACTGATCCAACCGTAACCT 58.295 45.455 0.00 0.00 0.00 3.50
1822 2099 4.460948 TTCTACTGATCCAACCGTAACC 57.539 45.455 0.00 0.00 0.00 2.85
1823 2100 6.596703 GTTTTTCTACTGATCCAACCGTAAC 58.403 40.000 0.00 0.00 0.00 2.50
1824 2101 5.406175 CGTTTTTCTACTGATCCAACCGTAA 59.594 40.000 0.00 0.00 0.00 3.18
1825 2102 4.925054 CGTTTTTCTACTGATCCAACCGTA 59.075 41.667 0.00 0.00 0.00 4.02
1826 2103 3.744426 CGTTTTTCTACTGATCCAACCGT 59.256 43.478 0.00 0.00 0.00 4.83
1827 2104 3.991773 TCGTTTTTCTACTGATCCAACCG 59.008 43.478 0.00 0.00 0.00 4.44
1828 2105 4.753107 TGTCGTTTTTCTACTGATCCAACC 59.247 41.667 0.00 0.00 0.00 3.77
1829 2106 5.917541 TGTCGTTTTTCTACTGATCCAAC 57.082 39.130 0.00 0.00 0.00 3.77
1830 2107 7.504924 AAATGTCGTTTTTCTACTGATCCAA 57.495 32.000 0.00 0.00 0.00 3.53
1831 2108 7.876068 ACTAAATGTCGTTTTTCTACTGATCCA 59.124 33.333 0.00 0.00 0.00 3.41
1832 2109 8.252964 ACTAAATGTCGTTTTTCTACTGATCC 57.747 34.615 0.00 0.00 0.00 3.36
1834 2111 9.148104 GGTACTAAATGTCGTTTTTCTACTGAT 57.852 33.333 0.00 0.00 0.00 2.90
1835 2112 7.326789 CGGTACTAAATGTCGTTTTTCTACTGA 59.673 37.037 0.00 0.00 0.00 3.41
1836 2113 7.411157 CCGGTACTAAATGTCGTTTTTCTACTG 60.411 40.741 0.00 0.00 0.00 2.74
1851 2128 4.706962 AGTCCTTACGAACCGGTACTAAAT 59.293 41.667 8.00 0.00 0.00 1.40
1874 2151 3.130280 GTTCCAGAACCGGGACTAAAA 57.870 47.619 6.32 0.00 35.36 1.52
1931 2208 1.824658 TTCGTGTTGAACCCGGACT 59.175 52.632 0.73 0.00 0.00 3.85
2122 2449 1.260538 TGTGCTCAGGCTGGAGTAGG 61.261 60.000 15.73 0.00 39.59 3.18
2451 2792 4.590918 TGGTCAAACTGTGGTCAAACTAA 58.409 39.130 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.