Multiple sequence alignment - TraesCS5D01G522900

Loading Multiple Alignment...

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 TraesCS5D01G522900 chr5D 100.000 4925 0 0 1 4925 543211581 543216505 0.000000e+00 9095.0
1 TraesCS5D01G522900 chr5D 84.894 1933 223 41 2033 3916 543223498 543225410 0.000000e+00 1888.0
2 TraesCS5D01G522900 chr5D 82.166 2170 328 33 1750 3908 543229375 543231496 0.000000e+00 1808.0
3 TraesCS5D01G522900 chr5D 81.136 2200 327 46 1753 3916 543099645 543101792 0.000000e+00 1683.0
4 TraesCS5D01G522900 chr5D 82.090 1273 184 26 1739 3000 543235440 543236679 0.000000e+00 1048.0
5 TraesCS5D01G522900 chr5D 85.586 888 124 3 2985 3871 543236727 543237611 0.000000e+00 928.0
6 TraesCS5D01G522900 chr5D 93.258 623 28 8 333 945 459572081 459572699 0.000000e+00 905.0
7 TraesCS5D01G522900 chr5D 90.395 354 14 9 1 337 459571206 459571556 9.720000e-122 448.0
8 TraesCS5D01G522900 chr5D 83.043 460 35 21 956 1384 543221615 543222062 1.290000e-100 377.0
9 TraesCS5D01G522900 chr5D 79.869 457 74 9 1739 2190 543067910 543068353 7.960000e-83 318.0
10 TraesCS5D01G522900 chr5D 82.031 128 19 4 4152 4277 543231914 543232039 6.740000e-19 106.0
11 TraesCS5D01G522900 chr5D 81.897 116 13 5 1072 1187 543228394 543228501 1.890000e-14 91.6
12 TraesCS5D01G522900 chr5D 87.179 78 7 2 4634 4709 475563765 475563841 8.780000e-13 86.1
13 TraesCS5D01G522900 chr5D 95.349 43 2 0 4715 4757 478205188 478205146 8.850000e-08 69.4
14 TraesCS5D01G522900 chr5D 100.000 37 0 0 1683 1719 543213174 543213210 8.850000e-08 69.4
15 TraesCS5D01G522900 chr5D 100.000 37 0 0 1594 1630 543213263 543213299 8.850000e-08 69.4
16 TraesCS5D01G522900 chr5B 93.646 2471 102 17 1729 4179 684610493 684612928 0.000000e+00 3642.0
17 TraesCS5D01G522900 chr5B 81.264 2199 326 45 1753 3916 684603971 684606118 0.000000e+00 1700.0
18 TraesCS5D01G522900 chr5B 81.771 1909 306 23 2025 3908 684622168 684624059 0.000000e+00 1559.0
19 TraesCS5D01G522900 chr5B 89.873 632 33 14 946 1574 684609282 684609885 0.000000e+00 784.0
20 TraesCS5D01G522900 chr5B 85.225 467 66 2 3409 3875 684693913 684694376 1.240000e-130 477.0
21 TraesCS5D01G522900 chr5B 82.203 472 36 18 957 1392 684614193 684614652 3.620000e-96 363.0
22 TraesCS5D01G522900 chr5B 78.652 445 79 8 1750 2190 684577976 684578408 1.040000e-71 281.0
23 TraesCS5D01G522900 chr5B 92.500 40 3 0 4715 4754 585805224 585805185 1.910000e-04 58.4
24 TraesCS5D01G522900 chr4A 97.992 2042 40 1 1729 3769 626049670 626047629 0.000000e+00 3542.0
25 TraesCS5D01G522900 chr4A 86.091 1668 195 17 2273 3916 626022080 626020426 0.000000e+00 1760.0
26 TraesCS5D01G522900 chr4A 81.148 2196 334 44 1753 3916 626066008 626063861 0.000000e+00 1688.0
27 TraesCS5D01G522900 chr4A 81.533 2074 323 39 1862 3908 626014306 626012266 0.000000e+00 1653.0
28 TraesCS5D01G522900 chr4A 91.778 973 54 14 3766 4716 626037659 626036691 0.000000e+00 1330.0
29 TraesCS5D01G522900 chr4A 84.526 517 25 18 956 1459 626053589 626053115 1.250000e-125 460.0
30 TraesCS5D01G522900 chr4A 81.951 410 33 13 1006 1392 626023669 626023278 4.790000e-80 309.0
31 TraesCS5D01G522900 chr4A 78.398 412 65 14 1729 2134 626077199 626076806 3.810000e-61 246.0
32 TraesCS5D01G522900 chr4A 87.273 220 10 5 4713 4925 626036662 626036454 8.240000e-58 235.0
33 TraesCS5D01G522900 chr4A 80.242 248 39 9 1729 1973 626022587 626022347 1.410000e-40 178.0
34 TraesCS5D01G522900 chr4A 79.703 202 34 7 1491 1690 626050206 626050010 6.650000e-29 139.0
35 TraesCS5D01G522900 chr2B 92.968 967 39 9 1 945 601140 600181 0.000000e+00 1382.0
36 TraesCS5D01G522900 chr2A 90.491 978 47 16 1 945 19232214 19231250 0.000000e+00 1249.0
37 TraesCS5D01G522900 chr2A 96.386 83 3 0 4634 4716 776460172 776460090 2.390000e-28 137.0
38 TraesCS5D01G522900 chr7B 89.754 976 59 23 1 944 533553866 533554832 0.000000e+00 1210.0
39 TraesCS5D01G522900 chr7B 90.519 770 35 22 1 741 715742406 715743166 0.000000e+00 983.0
40 TraesCS5D01G522900 chr7B 84.369 998 86 31 1 947 131109077 131110055 0.000000e+00 915.0
41 TraesCS5D01G522900 chr7B 81.404 855 97 39 132 945 238534636 238533803 4.160000e-180 641.0
42 TraesCS5D01G522900 chr7B 86.301 146 15 4 4780 4923 745225498 745225640 2.370000e-33 154.0
43 TraesCS5D01G522900 chr7B 81.771 192 22 7 4735 4923 48050481 48050662 1.100000e-31 148.0
44 TraesCS5D01G522900 chr7B 79.535 215 31 10 4715 4923 696593825 696594032 1.850000e-29 141.0
45 TraesCS5D01G522900 chr7B 92.593 81 6 0 4636 4716 151066378 151066298 3.110000e-22 117.0
46 TraesCS5D01G522900 chr7D 86.796 977 63 36 1 946 382280098 382281039 0.000000e+00 1029.0
47 TraesCS5D01G522900 chr7D 80.372 698 61 35 298 954 140809559 140808897 1.250000e-125 460.0
48 TraesCS5D01G522900 chr7D 80.930 215 31 7 4713 4925 112401331 112401537 1.420000e-35 161.0
49 TraesCS5D01G522900 chr3A 90.921 771 31 23 1 741 740757612 740758373 0.000000e+00 1000.0
50 TraesCS5D01G522900 chr3A 87.500 496 47 11 459 945 689365281 689364792 4.310000e-155 558.0
51 TraesCS5D01G522900 chr3A 90.141 71 5 1 4641 4709 71359117 71359187 1.890000e-14 91.6
52 TraesCS5D01G522900 chr1A 90.791 771 31 20 1 741 557506137 557506897 0.000000e+00 994.0
53 TraesCS5D01G522900 chr1A 79.902 204 30 8 4724 4923 30296219 30296023 6.650000e-29 139.0
54 TraesCS5D01G522900 chr1D 85.685 978 87 30 1 945 22561422 22560465 0.000000e+00 981.0
55 TraesCS5D01G522900 chr5A 90.427 773 32 20 1 741 175893786 175893024 0.000000e+00 979.0
56 TraesCS5D01G522900 chr6A 90.867 427 25 8 534 956 537034643 537035059 1.200000e-155 560.0
57 TraesCS5D01G522900 chr6A 95.181 83 4 0 4634 4716 13487064 13486982 1.110000e-26 132.0
58 TraesCS5D01G522900 chr6A 94.340 53 2 1 4715 4766 36272343 36272395 4.090000e-11 80.5
59 TraesCS5D01G522900 chr7A 80.282 213 29 7 4713 4922 735957908 735958110 1.100000e-31 148.0
60 TraesCS5D01G522900 chr6B 83.333 150 13 6 4778 4923 616309651 616309510 1.440000e-25 128.0
61 TraesCS5D01G522900 chr6D 83.007 153 12 9 4775 4923 409833922 409833780 5.180000e-25 126.0
62 TraesCS5D01G522900 chr4D 95.000 80 4 0 4637 4716 52530595 52530516 5.180000e-25 126.0
63 TraesCS5D01G522900 chr1B 94.937 79 4 0 4634 4712 585830474 585830396 1.860000e-24 124.0


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 TraesCS5D01G522900 chr5D 543211581 543216505 4924 False 3077.933333 9095 100.000000 1 4925 3 chr5D.!!$F5 4924
1 TraesCS5D01G522900 chr5D 543099645 543101792 2147 False 1683.000000 1683 81.136000 1753 3916 1 chr5D.!!$F3 2163
2 TraesCS5D01G522900 chr5D 543221615 543237611 15996 False 892.371429 1888 83.101000 956 4277 7 chr5D.!!$F6 3321
3 TraesCS5D01G522900 chr5D 459571206 459572699 1493 False 676.500000 905 91.826500 1 945 2 chr5D.!!$F4 944
4 TraesCS5D01G522900 chr5B 684603971 684614652 10681 False 1622.250000 3642 86.746500 946 4179 4 chr5B.!!$F4 3233
5 TraesCS5D01G522900 chr5B 684622168 684624059 1891 False 1559.000000 1559 81.771000 2025 3908 1 chr5B.!!$F2 1883
6 TraesCS5D01G522900 chr4A 626063861 626066008 2147 True 1688.000000 1688 81.148000 1753 3916 1 chr4A.!!$R2 2163
7 TraesCS5D01G522900 chr4A 626012266 626014306 2040 True 1653.000000 1653 81.533000 1862 3908 1 chr4A.!!$R1 2046
8 TraesCS5D01G522900 chr4A 626047629 626053589 5960 True 1380.333333 3542 87.407000 956 3769 3 chr4A.!!$R6 2813
9 TraesCS5D01G522900 chr4A 626036454 626037659 1205 True 782.500000 1330 89.525500 3766 4925 2 chr4A.!!$R5 1159
10 TraesCS5D01G522900 chr4A 626020426 626023669 3243 True 749.000000 1760 82.761333 1006 3916 3 chr4A.!!$R4 2910
11 TraesCS5D01G522900 chr2B 600181 601140 959 True 1382.000000 1382 92.968000 1 945 1 chr2B.!!$R1 944
12 TraesCS5D01G522900 chr2A 19231250 19232214 964 True 1249.000000 1249 90.491000 1 945 1 chr2A.!!$R1 944
13 TraesCS5D01G522900 chr7B 533553866 533554832 966 False 1210.000000 1210 89.754000 1 944 1 chr7B.!!$F3 943
14 TraesCS5D01G522900 chr7B 715742406 715743166 760 False 983.000000 983 90.519000 1 741 1 chr7B.!!$F5 740
15 TraesCS5D01G522900 chr7B 131109077 131110055 978 False 915.000000 915 84.369000 1 947 1 chr7B.!!$F2 946
16 TraesCS5D01G522900 chr7B 238533803 238534636 833 True 641.000000 641 81.404000 132 945 1 chr7B.!!$R2 813
17 TraesCS5D01G522900 chr7D 382280098 382281039 941 False 1029.000000 1029 86.796000 1 946 1 chr7D.!!$F2 945
18 TraesCS5D01G522900 chr7D 140808897 140809559 662 True 460.000000 460 80.372000 298 954 1 chr7D.!!$R1 656
19 TraesCS5D01G522900 chr3A 740757612 740758373 761 False 1000.000000 1000 90.921000 1 741 1 chr3A.!!$F2 740
20 TraesCS5D01G522900 chr1A 557506137 557506897 760 False 994.000000 994 90.791000 1 741 1 chr1A.!!$F1 740
21 TraesCS5D01G522900 chr1D 22560465 22561422 957 True 981.000000 981 85.685000 1 945 1 chr1D.!!$R1 944
22 TraesCS5D01G522900 chr5A 175893024 175893786 762 True 979.000000 979 90.427000 1 741 1 chr5A.!!$R1 740

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
891 1538 0.373716 GCGCTTCCAAATCGAACGAT 59.626 50.000 0.00 3.8 36.23 3.73 F
1351 5750 0.099082 CCGGCGTGACTAGAACTCTC 59.901 60.000 6.01 0.0 0.00 3.20 F
2116 10389 0.738063 TTGCGCCGGTGTATGTAGTG 60.738 55.000 17.91 0.0 0.00 2.74 F
3341 17801 1.605710 CATTGCGCCCAGAGGAAATAG 59.394 52.381 4.18 0.0 33.47 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 10006 1.080974 GCACACTGCCTGCATTGAC 60.081 57.895 15.27 4.48 37.42 3.18 R
3156 17616 0.811915 ACTCGAAGTGATCAGTCCCG 59.188 55.000 15.24 15.24 0.00 5.14 R
3610 24224 1.516110 ATCTCCTCATCAACCAGGGG 58.484 55.000 0.00 0.00 0.00 4.79 R
4572 25307 1.202290 CGCCACTGAAAACAAGTTGCT 60.202 47.619 1.81 0.00 34.90 3.91 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
120 139 2.112815 GCCGCCCGTAGCTGATTTT 61.113 57.895 0.00 0.00 40.39 1.82
279 309 7.405769 CGAACCATTTTGCTACAATTGTTTTT 58.594 30.769 17.78 0.00 0.00 1.94
395 957 5.279406 CCATACTTTTGATTTGCTGGAACCA 60.279 40.000 0.00 0.00 0.00 3.67
505 1069 1.008995 GCGACGGCTTTTCTTTGCA 60.009 52.632 0.00 0.00 35.83 4.08
592 1159 3.255642 GCATCAGGAGTTTTTGCTACCAA 59.744 43.478 0.00 0.00 0.00 3.67
639 1228 3.509575 CAGCCTAAAAATTGCTACCACCA 59.490 43.478 0.00 0.00 33.16 4.17
891 1538 0.373716 GCGCTTCCAAATCGAACGAT 59.626 50.000 0.00 3.80 36.23 3.73
893 1540 1.393539 CGCTTCCAAATCGAACGATGT 59.606 47.619 10.40 2.16 34.70 3.06
917 1564 2.975799 GACCGGCCGAAACTTGCA 60.976 61.111 30.73 0.00 0.00 4.08
982 5349 0.458260 GTGTTTGGTTTGGTCGGCTT 59.542 50.000 0.00 0.00 0.00 4.35
1081 5450 2.186903 CGCCCGGCATCTGTACTT 59.813 61.111 10.77 0.00 0.00 2.24
1252 5637 2.563050 CTTCTCCAGATGCGGCGTGA 62.563 60.000 9.37 0.00 0.00 4.35
1305 5691 1.843851 ACCAGTTTGGGTTCAGAGTCA 59.156 47.619 0.00 0.00 43.37 3.41
1347 5746 0.248949 GGATCCGGCGTGACTAGAAC 60.249 60.000 6.01 0.00 0.00 3.01
1351 5750 0.099082 CCGGCGTGACTAGAACTCTC 59.901 60.000 6.01 0.00 0.00 3.20
1354 5753 1.062880 GGCGTGACTAGAACTCTCTCG 59.937 57.143 0.00 0.00 32.70 4.04
1360 5759 4.004314 TGACTAGAACTCTCTCGTCAAGG 58.996 47.826 6.95 0.00 46.08 3.61
1361 5760 4.004982 GACTAGAACTCTCTCGTCAAGGT 58.995 47.826 0.00 0.00 41.72 3.50
1368 5767 4.337145 ACTCTCTCGTCAAGGTGTAATCT 58.663 43.478 0.00 0.00 0.00 2.40
1401 5851 2.224066 GCTACAGAGTTCAGGTGTGTGT 60.224 50.000 0.00 0.00 0.00 3.72
1410 5863 1.268625 TCAGGTGTGTGTGCGTAGTAG 59.731 52.381 0.00 0.00 0.00 2.57
1441 5894 2.923655 AGAGATACAAACACACGCGATG 59.076 45.455 15.93 13.76 0.00 3.84
1486 8805 9.947669 ACTGCGTGTCTAGTATAAAAATAGTAG 57.052 33.333 0.00 2.21 33.44 2.57
1564 8898 2.982470 GCAAACAAATTTCGAGCTCTGG 59.018 45.455 12.85 0.00 0.00 3.86
1620 8988 5.914033 TCCAGGGTATTTCTTTATCTGTCG 58.086 41.667 0.00 0.00 0.00 4.35
1621 8989 5.057149 CCAGGGTATTTCTTTATCTGTCGG 58.943 45.833 0.00 0.00 0.00 4.79
1624 8992 3.813724 GGTATTTCTTTATCTGTCGGCCC 59.186 47.826 0.00 0.00 0.00 5.80
1625 8993 3.933861 ATTTCTTTATCTGTCGGCCCT 57.066 42.857 0.00 0.00 0.00 5.19
1627 8995 3.713826 TTCTTTATCTGTCGGCCCTTT 57.286 42.857 0.00 0.00 0.00 3.11
1657 9033 6.017934 GCTACCTTTTCATCATGATTTCGCTA 60.018 38.462 5.16 0.00 0.00 4.26
1670 9047 4.155826 TGATTTCGCTATGTTCTTGGGTTG 59.844 41.667 0.00 0.00 0.00 3.77
1675 9052 3.686016 GCTATGTTCTTGGGTTGAGGAA 58.314 45.455 0.00 0.00 0.00 3.36
1695 9072 5.632034 GAAGTTGTTCCTATCCAGGGTAT 57.368 43.478 0.00 0.00 42.87 2.73
1697 9074 6.402981 AAGTTGTTCCTATCCAGGGTATTT 57.597 37.500 0.00 0.00 42.87 1.40
1700 9077 6.217693 AGTTGTTCCTATCCAGGGTATTTCTT 59.782 38.462 0.00 0.00 42.87 2.52
1701 9078 6.652205 TGTTCCTATCCAGGGTATTTCTTT 57.348 37.500 0.00 0.00 42.87 2.52
1704 9081 8.437575 TGTTCCTATCCAGGGTATTTCTTTATC 58.562 37.037 0.00 0.00 42.87 1.75
1705 9082 8.661345 GTTCCTATCCAGGGTATTTCTTTATCT 58.339 37.037 0.00 0.00 42.87 1.98
1706 9083 8.207350 TCCTATCCAGGGTATTTCTTTATCTG 57.793 38.462 0.00 0.00 42.87 2.90
1708 9085 8.097662 CCTATCCAGGGTATTTCTTTATCTGTC 58.902 40.741 0.00 0.00 38.41 3.51
1710 9087 5.057149 CCAGGGTATTTCTTTATCTGTCGG 58.943 45.833 0.00 0.00 0.00 4.79
1713 9090 3.813724 GGTATTTCTTTATCTGTCGGCCC 59.186 47.826 0.00 0.00 0.00 5.80
1727 9905 4.653868 TGTCGGCCCTTTGTATTTCTTTA 58.346 39.130 0.00 0.00 0.00 1.85
1748 10006 6.817765 TTATCTGCTTGGTTTGGTTCTTAG 57.182 37.500 0.00 0.00 0.00 2.18
1847 10108 1.016653 GTCTGGCACCGCTTCTCTTC 61.017 60.000 0.00 0.00 0.00 2.87
1945 10209 5.334105 CCGACTTTTCTTTCGTCATGTTCAT 60.334 40.000 0.00 0.00 33.23 2.57
1950 10216 7.592533 ACTTTTCTTTCGTCATGTTCATGAATG 59.407 33.333 12.12 7.07 31.60 2.67
2116 10389 0.738063 TTGCGCCGGTGTATGTAGTG 60.738 55.000 17.91 0.00 0.00 2.74
2980 11328 8.439993 TGTATATAAGGCTTATTTTTCACGCA 57.560 30.769 23.72 4.22 0.00 5.24
3156 17616 1.818555 GGATGGGGCAAATGCTGTC 59.181 57.895 5.25 0.00 41.70 3.51
3341 17801 1.605710 CATTGCGCCCAGAGGAAATAG 59.394 52.381 4.18 0.00 33.47 1.73
3596 24210 2.463589 AATGACGGTGATGGTGGCGT 62.464 55.000 0.00 0.00 0.00 5.68
3978 24617 4.340666 TCTTTTCCTGCTATGTTTGTTGCA 59.659 37.500 0.00 0.00 0.00 4.08
3987 24626 2.929531 TGTTTGTTGCACATTCACGT 57.070 40.000 0.00 0.00 0.00 4.49
4018 24657 3.748048 CAGAGCGACATATATGGTTTGGG 59.252 47.826 16.96 1.12 0.00 4.12
4056 24695 6.823678 TTGTTTCGTAAGTCTGAAGAGAAC 57.176 37.500 0.00 0.00 39.48 3.01
4101 24740 0.393077 CCGTGTTCTGTTCTGGGTCT 59.607 55.000 0.00 0.00 0.00 3.85
4234 24966 3.818773 ACCATTAAGTGTTTCCCTCAACG 59.181 43.478 0.00 0.00 0.00 4.10
4256 24988 7.987268 ACGTATCATGTGTGTCAGTATTTAG 57.013 36.000 0.00 0.00 0.00 1.85
4270 25002 8.459635 TGTCAGTATTTAGCTGTAAGTCTGTAG 58.540 37.037 0.00 0.00 35.30 2.74
4333 25065 7.452880 AGATATGAGCTTGTCTCTGATACTC 57.547 40.000 0.00 0.00 42.38 2.59
4356 25088 7.761249 ACTCTGTTTTCTTTCTTTCATTGGTTG 59.239 33.333 0.00 0.00 0.00 3.77
4357 25089 6.534793 TCTGTTTTCTTTCTTTCATTGGTTGC 59.465 34.615 0.00 0.00 0.00 4.17
4360 25092 5.549742 TTCTTTCTTTCATTGGTTGCCAT 57.450 34.783 0.00 0.00 31.53 4.40
4417 25149 9.588096 AAGTCCATATTACTTCCTTGAACTTTT 57.412 29.630 0.00 0.00 31.56 2.27
4419 25151 8.244113 GTCCATATTACTTCCTTGAACTTTTGG 58.756 37.037 0.00 0.00 0.00 3.28
4420 25152 7.947890 TCCATATTACTTCCTTGAACTTTTGGT 59.052 33.333 0.00 0.00 0.00 3.67
4421 25153 8.244113 CCATATTACTTCCTTGAACTTTTGGTC 58.756 37.037 0.00 0.00 36.49 4.02
4425 25157 2.294074 TCCTTGAACTTTTGGTCGTGG 58.706 47.619 0.00 0.00 39.50 4.94
4428 25160 3.119280 CCTTGAACTTTTGGTCGTGGTTT 60.119 43.478 0.00 0.00 39.50 3.27
4431 25163 4.984205 TGAACTTTTGGTCGTGGTTTAAC 58.016 39.130 0.00 0.00 39.50 2.01
4446 25178 3.849708 GGTTTAACCATCGATCAAAACGC 59.150 43.478 9.56 0.00 38.42 4.84
4447 25179 4.468643 GTTTAACCATCGATCAAAACGCA 58.531 39.130 0.00 0.00 0.00 5.24
4452 25184 3.181507 ACCATCGATCAAAACGCATTCAG 60.182 43.478 0.00 0.00 0.00 3.02
4467 25199 3.737266 GCATTCAGAACATGTGTTTGGTG 59.263 43.478 0.00 3.40 38.56 4.17
4468 25200 3.435105 TTCAGAACATGTGTTTGGTGC 57.565 42.857 0.00 0.00 38.56 5.01
4469 25201 1.333308 TCAGAACATGTGTTTGGTGCG 59.667 47.619 0.00 0.00 38.56 5.34
4503 25235 0.731855 CCTCTCGACCGGTTTCGTTC 60.732 60.000 9.42 0.00 40.07 3.95
4531 25263 2.162408 GACTTTGTGCAATAGCCCTGTC 59.838 50.000 0.00 0.00 41.13 3.51
4551 25283 2.166459 TCGACCTGATCATTCTCACCAC 59.834 50.000 0.00 0.00 0.00 4.16
4572 25307 1.741028 TGGGGAGTCCATGACTTTGA 58.259 50.000 12.30 0.00 43.53 2.69
4586 25321 5.384063 TGACTTTGAGCAACTTGTTTTCA 57.616 34.783 0.00 0.00 0.00 2.69
4587 25322 5.401550 TGACTTTGAGCAACTTGTTTTCAG 58.598 37.500 0.00 0.00 0.00 3.02
4626 25363 9.877178 TGAAAGGAAATAGAAGTGAGTCTTATC 57.123 33.333 0.00 0.00 36.40 1.75
4631 25368 9.436957 GGAAATAGAAGTGAGTCTTATCAACAA 57.563 33.333 0.00 0.00 36.40 2.83
4676 25423 7.838193 ACTATATGGTGCCTATAACCCTACTAC 59.162 40.741 0.00 0.00 36.83 2.73
4683 25430 5.221641 TGCCTATAACCCTACTACATGCTTG 60.222 44.000 0.00 0.00 0.00 4.01
4732 25511 1.606480 CCTTCTGAGCTCGAGCACAAA 60.606 52.381 36.87 27.29 45.16 2.83
4734 25513 1.718396 TCTGAGCTCGAGCACAAATG 58.282 50.000 36.87 24.31 45.16 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 128 1.208052 AGAGGAGCGCAAAATCAGCTA 59.792 47.619 11.47 0.00 41.84 3.32
120 139 4.166888 GCCATGGAGAGGAGCGCA 62.167 66.667 18.40 0.00 0.00 6.09
279 309 8.510505 ACAAAACAACGGTAGTAACAAAAACTA 58.489 29.630 0.00 0.00 0.00 2.24
316 347 4.620097 CGATGTCATGGAGATGGATGTAGG 60.620 50.000 0.00 0.00 0.00 3.18
505 1069 2.804911 GCAAAATCCGAGACGGTTGCT 61.805 52.381 21.03 1.80 46.02 3.91
639 1228 2.489971 TCAGCAAAATCGAAAGACGGT 58.510 42.857 0.00 0.00 46.97 4.83
998 5365 4.748409 GAGCTCGCTCCTCCATTC 57.252 61.111 7.68 0.00 37.11 2.67
1252 5637 4.137543 ACTCAGGCTTTGATTCGAAAACT 58.862 39.130 0.00 0.00 34.68 2.66
1341 5740 3.754323 ACACCTTGACGAGAGAGTTCTAG 59.246 47.826 0.00 0.00 32.53 2.43
1347 5746 4.974368 AGATTACACCTTGACGAGAGAG 57.026 45.455 0.00 0.00 0.00 3.20
1351 5750 4.275196 TCGGATAGATTACACCTTGACGAG 59.725 45.833 0.00 0.00 0.00 4.18
1354 5753 5.507650 GGACTCGGATAGATTACACCTTGAC 60.508 48.000 0.00 0.00 0.00 3.18
1401 5851 2.428530 TCTAGTCCGACTCTACTACGCA 59.571 50.000 3.74 0.00 0.00 5.24
1410 5863 5.123502 TGTGTTTGTATCTCTAGTCCGACTC 59.876 44.000 3.74 0.00 0.00 3.36
1486 8805 9.825972 TTTCTTTGTCTCGAATTGTTGATAATC 57.174 29.630 0.00 0.00 0.00 1.75
1488 8807 9.663904 CTTTTCTTTGTCTCGAATTGTTGATAA 57.336 29.630 0.00 0.00 0.00 1.75
1499 8832 2.794910 CGTCTGCTTTTCTTTGTCTCGA 59.205 45.455 0.00 0.00 0.00 4.04
1564 8898 1.450312 CGGCCATGGACTTGTCTCC 60.450 63.158 18.40 2.98 0.00 3.71
1596 8964 6.464465 CCGACAGATAAAGAAATACCCTGGAT 60.464 42.308 0.00 0.00 0.00 3.41
1624 8992 5.437289 TGATGAAAAGGTAGCACACAAAG 57.563 39.130 0.00 0.00 0.00 2.77
1625 8993 5.534278 TCATGATGAAAAGGTAGCACACAAA 59.466 36.000 0.00 0.00 0.00 2.83
1627 8995 4.650734 TCATGATGAAAAGGTAGCACACA 58.349 39.130 0.00 0.00 0.00 3.72
1657 9033 3.884037 ACTTCCTCAACCCAAGAACAT 57.116 42.857 0.00 0.00 0.00 2.71
1685 9062 6.464465 CCGACAGATAAAGAAATACCCTGGAT 60.464 42.308 0.00 0.00 0.00 3.41
1690 9067 3.813724 GGCCGACAGATAAAGAAATACCC 59.186 47.826 0.00 0.00 0.00 3.69
1691 9068 3.813724 GGGCCGACAGATAAAGAAATACC 59.186 47.826 0.00 0.00 0.00 2.73
1693 9070 5.367945 AAGGGCCGACAGATAAAGAAATA 57.632 39.130 0.00 0.00 0.00 1.40
1695 9072 3.713826 AAGGGCCGACAGATAAAGAAA 57.286 42.857 0.00 0.00 0.00 2.52
1697 9074 2.304761 ACAAAGGGCCGACAGATAAAGA 59.695 45.455 0.00 0.00 0.00 2.52
1700 9077 4.497291 AATACAAAGGGCCGACAGATAA 57.503 40.909 0.00 0.00 0.00 1.75
1701 9078 4.163458 AGAAATACAAAGGGCCGACAGATA 59.837 41.667 0.00 0.00 0.00 1.98
1704 9081 2.711542 AGAAATACAAAGGGCCGACAG 58.288 47.619 0.00 0.00 0.00 3.51
1705 9082 2.871096 AGAAATACAAAGGGCCGACA 57.129 45.000 0.00 0.00 0.00 4.35
1706 9083 5.589050 AGATAAAGAAATACAAAGGGCCGAC 59.411 40.000 0.00 0.00 0.00 4.79
1708 9085 5.733373 GCAGATAAAGAAATACAAAGGGCCG 60.733 44.000 0.00 0.00 0.00 6.13
1710 9087 6.456795 AGCAGATAAAGAAATACAAAGGGC 57.543 37.500 0.00 0.00 0.00 5.19
1713 9090 9.696917 AAACCAAGCAGATAAAGAAATACAAAG 57.303 29.630 0.00 0.00 0.00 2.77
1727 9905 4.729868 ACTAAGAACCAAACCAAGCAGAT 58.270 39.130 0.00 0.00 0.00 2.90
1748 10006 1.080974 GCACACTGCCTGCATTGAC 60.081 57.895 15.27 4.48 37.42 3.18
1847 10108 8.207350 TCACTCCTATGAATCCCTTTATTAGG 57.793 38.462 0.00 0.00 44.33 2.69
1909 10173 2.580966 AAAGTCGGCTACCTCGATTC 57.419 50.000 0.00 0.00 38.93 2.52
1945 10209 7.437713 AAATACACATCCTACTCCTCATTCA 57.562 36.000 0.00 0.00 0.00 2.57
1950 10216 9.668497 AAACTAAAAATACACATCCTACTCCTC 57.332 33.333 0.00 0.00 0.00 3.71
2116 10389 1.620822 TTTTCAGCAGGCCTTTCTCC 58.379 50.000 0.00 0.00 0.00 3.71
2980 11328 2.157738 GTCAAAGCCTTGCATCAGAGT 58.842 47.619 0.00 0.00 32.14 3.24
3156 17616 0.811915 ACTCGAAGTGATCAGTCCCG 59.188 55.000 15.24 15.24 0.00 5.14
3610 24224 1.516110 ATCTCCTCATCAACCAGGGG 58.484 55.000 0.00 0.00 0.00 4.79
3978 24617 4.152402 GCTCTGTACATTTCACGTGAATGT 59.848 41.667 30.69 30.69 33.54 2.71
3987 24626 6.868339 CCATATATGTCGCTCTGTACATTTCA 59.132 38.462 11.73 0.00 37.50 2.69
4018 24657 5.165676 ACGAAACAAAGGTCAAAGGAAAAC 58.834 37.500 0.00 0.00 0.00 2.43
4056 24695 2.356386 AAAGTACAAAACACGTCGCG 57.644 45.000 0.00 0.00 0.00 5.87
4137 24791 2.509569 TCTTTGCGCCCAATTCAGTTA 58.490 42.857 4.18 0.00 0.00 2.24
4146 24800 1.742324 TTTGCACATCTTTGCGCCCA 61.742 50.000 4.18 0.00 46.20 5.36
4234 24966 7.492669 ACAGCTAAATACTGACACACATGATAC 59.507 37.037 0.00 0.00 38.55 2.24
4256 24988 9.575783 GATAATAATAGGCTACAGACTTACAGC 57.424 37.037 0.00 0.00 33.72 4.40
4270 25002 7.979444 TTTGTACAGGCAGATAATAATAGGC 57.021 36.000 0.00 0.00 0.00 3.93
4333 25065 6.238184 GGCAACCAATGAAAGAAAGAAAACAG 60.238 38.462 0.00 0.00 0.00 3.16
4405 25137 2.294074 CCACGACCAAAAGTTCAAGGA 58.706 47.619 0.00 0.00 0.00 3.36
4408 25140 5.400703 GTTAAACCACGACCAAAAGTTCAA 58.599 37.500 0.00 0.00 0.00 2.69
4425 25157 4.468643 TGCGTTTTGATCGATGGTTAAAC 58.531 39.130 0.54 6.88 0.00 2.01
4428 25160 4.393371 TGAATGCGTTTTGATCGATGGTTA 59.607 37.500 0.54 0.00 0.00 2.85
4431 25163 3.063861 TCTGAATGCGTTTTGATCGATGG 59.936 43.478 0.54 0.00 0.00 3.51
4446 25178 3.737266 GCACCAAACACATGTTCTGAATG 59.263 43.478 0.00 0.00 37.25 2.67
4447 25179 3.550639 CGCACCAAACACATGTTCTGAAT 60.551 43.478 0.00 0.00 37.25 2.57
4452 25184 1.334960 CCTCGCACCAAACACATGTTC 60.335 52.381 0.00 0.00 37.25 3.18
4467 25199 3.129502 GGCCCGTTAAACCCTCGC 61.130 66.667 0.00 0.00 0.00 5.03
4468 25200 2.437180 GGGCCCGTTAAACCCTCG 60.437 66.667 5.69 0.00 40.75 4.63
4495 25227 3.554731 ACAAAGTCCTTCTCGAACGAAAC 59.445 43.478 0.00 0.00 0.00 2.78
4496 25228 3.554324 CACAAAGTCCTTCTCGAACGAAA 59.446 43.478 0.00 0.00 0.00 3.46
4503 25235 3.181516 GCTATTGCACAAAGTCCTTCTCG 60.182 47.826 0.00 0.00 39.41 4.04
4531 25263 2.544685 GTGGTGAGAATGATCAGGTCG 58.455 52.381 0.09 0.00 0.00 4.79
4559 25291 3.316308 ACAAGTTGCTCAAAGTCATGGAC 59.684 43.478 1.81 0.00 0.00 4.02
4565 25297 5.287035 CACTGAAAACAAGTTGCTCAAAGTC 59.713 40.000 1.81 0.00 0.00 3.01
4571 25306 2.463876 GCCACTGAAAACAAGTTGCTC 58.536 47.619 1.81 0.00 34.39 4.26
4572 25307 1.202290 CGCCACTGAAAACAAGTTGCT 60.202 47.619 1.81 0.00 34.90 3.91
4586 25321 3.088532 TCCTTTCATTTTATGCGCCACT 58.911 40.909 4.18 0.00 0.00 4.00
4587 25322 3.502191 TCCTTTCATTTTATGCGCCAC 57.498 42.857 4.18 0.00 0.00 5.01
4626 25363 9.956720 AGTTATCTTGAATTTCAGAGTTTGTTG 57.043 29.630 0.00 0.00 0.00 3.33
4664 25411 6.126883 TGTTAGCAAGCATGTAGTAGGGTTAT 60.127 38.462 0.00 0.00 0.00 1.89
4676 25423 7.331440 TCAACCAAATATTTGTTAGCAAGCATG 59.669 33.333 23.24 10.94 36.45 4.06
4732 25511 8.363390 TCGATTTTACTATTCATCTGAGCTCAT 58.637 33.333 18.63 3.37 0.00 2.90
4734 25513 8.581057 TTCGATTTTACTATTCATCTGAGCTC 57.419 34.615 6.82 6.82 0.00 4.09
4794 25578 8.255394 ACATTTGTTGAAGTTTTCCTCAAAAG 57.745 30.769 10.22 9.17 36.06 2.27
4798 25582 7.169158 AGAACATTTGTTGAAGTTTTCCTCA 57.831 32.000 0.00 0.00 38.56 3.86
4876 26153 5.982465 TTGGAGCACTAATTTTGTTTTGC 57.018 34.783 0.00 0.00 0.00 3.68
4877 26154 7.376601 GCATTTTGGAGCACTAATTTTGTTTTG 59.623 33.333 0.00 0.00 0.00 2.44
4878 26155 7.282901 AGCATTTTGGAGCACTAATTTTGTTTT 59.717 29.630 0.00 0.00 0.00 2.43
4880 26157 6.290605 AGCATTTTGGAGCACTAATTTTGTT 58.709 32.000 0.00 0.00 0.00 2.83
4881 26158 5.857268 AGCATTTTGGAGCACTAATTTTGT 58.143 33.333 0.00 0.00 0.00 2.83
4883 26160 6.146021 CGAAAGCATTTTGGAGCACTAATTTT 59.854 34.615 0.00 0.00 39.27 1.82
4884 26161 5.634859 CGAAAGCATTTTGGAGCACTAATTT 59.365 36.000 0.00 0.00 39.27 1.82


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

AutoCloner maintained by Alex Coulton.