Multiple sequence alignment - TraesCS2D01G163400

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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 TraesCS2D01G163400 chr2D 100.000 3540 0 0 1 3540 107716865 107720404 0.000000e+00 6538.0
1 TraesCS2D01G163400 chr2D 94.726 493 23 3 3047 3539 638925246 638925735 0.000000e+00 763.0
2 TraesCS2D01G163400 chr2D 94.523 493 25 2 3047 3539 476462775 476463265 0.000000e+00 760.0
3 TraesCS2D01G163400 chr2D 100.000 47 0 0 859 905 598724957 598724911 1.750000e-13 87.9
4 TraesCS2D01G163400 chr2B 95.667 1708 48 9 1048 2748 157756863 157758551 0.000000e+00 2721.0
5 TraesCS2D01G163400 chr2B 92.248 387 14 7 475 860 157756243 157756614 5.200000e-148 534.0
6 TraesCS2D01G163400 chr2B 90.650 246 10 6 205 449 157755704 157755937 7.380000e-82 315.0
7 TraesCS2D01G163400 chr2B 93.750 208 7 1 1 202 157755464 157755671 1.230000e-79 307.0
8 TraesCS2D01G163400 chr2B 97.973 148 3 0 902 1049 157756612 157756759 1.260000e-64 257.0
9 TraesCS2D01G163400 chr2B 96.053 152 5 1 2832 2982 157758610 157758761 2.730000e-61 246.0
10 TraesCS2D01G163400 chr2A 95.327 1070 28 7 1674 2738 104119363 104120415 0.000000e+00 1679.0
11 TraesCS2D01G163400 chr2A 96.839 696 22 0 902 1597 104118512 104119207 0.000000e+00 1164.0
12 TraesCS2D01G163400 chr2A 96.188 341 13 0 519 859 104118173 104118513 3.090000e-155 558.0
13 TraesCS2D01G163400 chr2A 94.059 303 14 2 205 504 104117570 104117871 1.160000e-124 457.0
14 TraesCS2D01G163400 chr2A 93.365 211 5 3 1 202 104117313 104117523 1.600000e-78 303.0
15 TraesCS2D01G163400 chr2A 93.085 188 10 1 2858 3045 104120422 104120606 4.500000e-69 272.0
16 TraesCS2D01G163400 chr2A 93.023 129 7 2 2730 2856 182151639 182151767 1.680000e-43 187.0
17 TraesCS2D01G163400 chr3D 94.980 498 24 1 3042 3539 516852356 516851860 0.000000e+00 780.0
18 TraesCS2D01G163400 chr3D 93.333 60 4 0 860 919 471939269 471939210 4.870000e-14 89.8
19 TraesCS2D01G163400 chr6D 94.726 493 24 2 3047 3539 226717129 226716639 0.000000e+00 765.0
20 TraesCS2D01G163400 chr6D 94.320 493 27 1 3047 3539 413807064 413806573 0.000000e+00 754.0
21 TraesCS2D01G163400 chr6D 100.000 46 0 0 860 905 61144176 61144221 6.300000e-13 86.1
22 TraesCS2D01G163400 chr6D 100.000 45 0 0 860 904 83173546 83173502 2.260000e-12 84.2
23 TraesCS2D01G163400 chr6D 100.000 45 0 0 860 904 375737592 375737636 2.260000e-12 84.2
24 TraesCS2D01G163400 chr6D 97.917 48 1 0 863 910 450889948 450889901 2.260000e-12 84.2
25 TraesCS2D01G163400 chr6D 97.872 47 1 0 859 905 367864159 367864113 8.140000e-12 82.4
26 TraesCS2D01G163400 chr6D 95.918 49 2 0 860 908 54235900 54235852 2.930000e-11 80.5
27 TraesCS2D01G163400 chr1D 94.523 493 26 1 3047 3539 455897625 455898116 0.000000e+00 760.0
28 TraesCS2D01G163400 chr1D 93.625 502 30 2 3039 3539 460579375 460578875 0.000000e+00 749.0
29 TraesCS2D01G163400 chr1D 96.078 51 1 1 855 905 491552769 491552720 8.140000e-12 82.4
30 TraesCS2D01G163400 chr7D 94.320 493 27 1 3047 3539 292317949 292318440 0.000000e+00 754.0
31 TraesCS2D01G163400 chr7D 96.364 55 1 1 860 913 136985046 136984992 4.870000e-14 89.8
32 TraesCS2D01G163400 chr7D 98.039 51 0 1 855 905 185574964 185575013 1.750000e-13 87.9
33 TraesCS2D01G163400 chr7D 90.625 64 5 1 860 923 592857560 592857498 2.260000e-12 84.2
34 TraesCS2D01G163400 chr7D 87.838 74 6 3 856 927 597660554 597660626 2.260000e-12 84.2
35 TraesCS2D01G163400 chr5A 93.164 512 31 4 3025 3534 310715790 310716299 0.000000e+00 749.0
36 TraesCS2D01G163400 chr5A 98.214 112 2 0 2737 2848 528581386 528581275 2.790000e-46 196.0
37 TraesCS2D01G163400 chr5A 95.868 121 4 1 2730 2849 69844780 69844900 1.000000e-45 195.0
38 TraesCS2D01G163400 chr5A 100.000 47 0 0 859 905 673005844 673005798 1.750000e-13 87.9
39 TraesCS2D01G163400 chr5A 88.889 63 6 1 860 921 563835489 563835551 3.790000e-10 76.8
40 TraesCS2D01G163400 chr7B 99.091 110 1 0 2736 2845 667088651 667088760 7.750000e-47 198.0
41 TraesCS2D01G163400 chr5D 96.552 116 4 0 2729 2844 134808388 134808273 3.610000e-45 193.0
42 TraesCS2D01G163400 chr5D 100.000 46 0 0 860 905 418431100 418431145 6.300000e-13 86.1
43 TraesCS2D01G163400 chr5D 96.000 50 2 0 860 909 518923062 518923111 8.140000e-12 82.4
44 TraesCS2D01G163400 chr1A 96.581 117 3 1 2737 2852 376145949 376145833 3.610000e-45 193.0
45 TraesCS2D01G163400 chr1A 95.763 118 5 0 2726 2843 577843325 577843442 1.300000e-44 191.0
46 TraesCS2D01G163400 chr1A 100.000 47 0 0 863 909 575361705 575361659 1.750000e-13 87.9
47 TraesCS2D01G163400 chr1A 94.545 55 2 1 860 914 547903053 547903106 2.260000e-12 84.2
48 TraesCS2D01G163400 chr7A 93.600 125 7 1 2719 2843 133053212 133053335 6.030000e-43 185.0
49 TraesCS2D01G163400 chr4A 90.780 141 5 6 2737 2871 278329260 278329122 7.810000e-42 182.0
50 TraesCS2D01G163400 chr4D 100.000 46 0 0 860 905 475120322 475120367 6.300000e-13 86.1
51 TraesCS2D01G163400 chr4D 100.000 45 0 0 860 904 116821958 116821914 2.260000e-12 84.2
52 TraesCS2D01G163400 chr4D 96.078 51 1 1 855 905 38750012 38749963 8.140000e-12 82.4
53 TraesCS2D01G163400 chr4D 96.078 51 1 1 855 905 89281489 89281538 8.140000e-12 82.4
54 TraesCS2D01G163400 chr4D 96.078 51 1 1 855 905 344669953 344670002 8.140000e-12 82.4
55 TraesCS2D01G163400 chr4D 96.000 50 2 0 859 908 396431077 396431028 8.140000e-12 82.4
56 TraesCS2D01G163400 chr4D 94.231 52 3 0 863 914 71301643 71301694 2.930000e-11 80.5
57 TraesCS2D01G163400 chr4B 97.959 49 1 0 860 908 464223303 464223351 6.300000e-13 86.1
58 TraesCS2D01G163400 chrUn 97.917 48 1 0 860 907 94636299 94636346 2.260000e-12 84.2
59 TraesCS2D01G163400 chrUn 97.872 47 1 0 859 905 324448660 324448706 8.140000e-12 82.4
60 TraesCS2D01G163400 chrUn 97.826 46 1 0 860 905 56557282 56557237 2.930000e-11 80.5
61 TraesCS2D01G163400 chrUn 97.826 46 1 0 860 905 117245739 117245694 2.930000e-11 80.5
62 TraesCS2D01G163400 chrUn 97.826 46 0 1 859 904 6054438 6054482 1.050000e-10 78.7
63 TraesCS2D01G163400 chrUn 97.778 45 1 0 860 904 21367795 21367751 1.050000e-10 78.7
64 TraesCS2D01G163400 chrUn 97.778 45 1 0 860 904 50785676 50785720 1.050000e-10 78.7
65 TraesCS2D01G163400 chrUn 97.778 45 1 0 860 904 79676552 79676596 1.050000e-10 78.7
66 TraesCS2D01G163400 chrUn 97.778 45 1 0 861 905 88217904 88217860 1.050000e-10 78.7
67 TraesCS2D01G163400 chr3B 97.674 43 1 0 863 905 13813745 13813787 1.360000e-09 75.0


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 TraesCS2D01G163400 chr2D 107716865 107720404 3539 False 6538.000000 6538 100.000000 1 3540 1 chr2D.!!$F1 3539
1 TraesCS2D01G163400 chr2B 157755464 157758761 3297 False 730.000000 2721 94.390167 1 2982 6 chr2B.!!$F1 2981
2 TraesCS2D01G163400 chr2A 104117313 104120606 3293 False 738.833333 1679 94.810500 1 3045 6 chr2A.!!$F2 3044
3 TraesCS2D01G163400 chr1D 460578875 460579375 500 True 749.000000 749 93.625000 3039 3539 1 chr1D.!!$R1 500
4 TraesCS2D01G163400 chr5A 310715790 310716299 509 False 749.000000 749 93.164000 3025 3534 1 chr5A.!!$F2 509

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
387 446 0.040067 CCTGCGCAACAAGAAGGAAC 60.040 55.0 13.05 0.0 0.0 3.62 F
1113 1856 0.322546 GTTGCGGTCTCCATTCCCTT 60.323 55.0 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 2036 0.462937 TGTTGCAGTTGCGTACCAGT 60.463 50.0 0.00 0.0 45.83 4.00 R
3045 3880 0.179121 CGCACGGGCATTGTACTAGA 60.179 55.0 11.77 0.0 41.24 2.43 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
154 164 3.416382 GCGGCGGCGACTTGTTAA 61.416 61.111 36.87 0.00 0.00 2.01
162 172 3.680789 CGGCGACTTGTTAATTGATTCC 58.319 45.455 0.00 0.00 0.00 3.01
202 212 1.469767 GCCGGCCAGCTCTTTATTTTG 60.470 52.381 18.11 0.00 0.00 2.44
263 317 2.007608 TCGATCTCGATCTGTTGTCGT 58.992 47.619 0.00 0.00 44.22 4.34
280 335 7.299586 TGTTGTCGTGCTAATTTTAATACCAC 58.700 34.615 0.00 0.00 0.00 4.16
313 368 6.540438 TTCGTCAGAATAGGATGGTTTAGT 57.460 37.500 0.00 0.00 0.00 2.24
314 369 7.649533 TTCGTCAGAATAGGATGGTTTAGTA 57.350 36.000 0.00 0.00 0.00 1.82
315 370 7.649533 TCGTCAGAATAGGATGGTTTAGTAA 57.350 36.000 0.00 0.00 0.00 2.24
316 371 7.486647 TCGTCAGAATAGGATGGTTTAGTAAC 58.513 38.462 0.00 0.00 0.00 2.50
333 392 8.702438 GTTTAGTAACTAATCTGCGTTTGTGTA 58.298 33.333 0.00 0.00 0.00 2.90
386 445 1.795170 GCCTGCGCAACAAGAAGGAA 61.795 55.000 13.05 0.00 34.03 3.36
387 446 0.040067 CCTGCGCAACAAGAAGGAAC 60.040 55.000 13.05 0.00 0.00 3.62
388 447 0.384725 CTGCGCAACAAGAAGGAACG 60.385 55.000 13.05 0.00 0.00 3.95
454 542 2.704725 TCGCAGTTCAAAGGCAAATC 57.295 45.000 0.00 0.00 0.00 2.17
535 1173 6.125029 ACATATAATGCAGGATATCCTTGGC 58.875 40.000 22.29 21.97 46.09 4.52
552 1190 1.076332 GGCCACATACACTCGTTGAC 58.924 55.000 0.00 0.00 0.00 3.18
577 1215 2.588314 CGAGATGCTGCTCAGGCC 60.588 66.667 0.00 0.00 37.74 5.19
635 1273 1.412710 CCTATGCCAGGCTCGACTTTA 59.587 52.381 14.15 0.00 37.70 1.85
662 1300 6.710597 TGTACACACTAGGATTACTGGATC 57.289 41.667 0.00 0.00 0.00 3.36
663 1301 5.597182 TGTACACACTAGGATTACTGGATCC 59.403 44.000 4.20 4.20 44.91 3.36
698 1336 1.006832 GTCGATTGGTCCCATTGACG 58.993 55.000 7.42 0.00 45.46 4.35
857 1495 2.227388 GGTGTTCAGACATTCAGGCTTG 59.773 50.000 0.00 0.00 38.23 4.01
858 1496 2.880890 GTGTTCAGACATTCAGGCTTGT 59.119 45.455 0.00 0.00 38.23 3.16
859 1497 4.065088 GTGTTCAGACATTCAGGCTTGTA 58.935 43.478 0.00 0.00 38.23 2.41
860 1498 4.515191 GTGTTCAGACATTCAGGCTTGTAA 59.485 41.667 0.00 0.00 38.23 2.41
861 1499 4.756642 TGTTCAGACATTCAGGCTTGTAAG 59.243 41.667 0.00 0.00 27.44 2.34
862 1500 4.623932 TCAGACATTCAGGCTTGTAAGT 57.376 40.909 0.00 0.00 27.44 2.24
863 1501 4.973168 TCAGACATTCAGGCTTGTAAGTT 58.027 39.130 0.00 0.00 27.44 2.66
864 1502 6.109156 TCAGACATTCAGGCTTGTAAGTTA 57.891 37.500 0.00 0.00 27.44 2.24
865 1503 6.166279 TCAGACATTCAGGCTTGTAAGTTAG 58.834 40.000 0.00 0.00 27.44 2.34
866 1504 5.934625 CAGACATTCAGGCTTGTAAGTTAGT 59.065 40.000 0.00 0.00 27.44 2.24
867 1505 7.039293 TCAGACATTCAGGCTTGTAAGTTAGTA 60.039 37.037 0.00 0.00 27.44 1.82
868 1506 7.063544 CAGACATTCAGGCTTGTAAGTTAGTAC 59.936 40.741 0.00 0.00 27.44 2.73
869 1507 6.765403 ACATTCAGGCTTGTAAGTTAGTACA 58.235 36.000 0.00 0.00 32.11 2.90
870 1508 7.221450 ACATTCAGGCTTGTAAGTTAGTACAA 58.779 34.615 0.00 0.00 40.75 2.41
871 1509 7.717875 ACATTCAGGCTTGTAAGTTAGTACAAA 59.282 33.333 0.00 0.00 42.03 2.83
872 1510 7.724305 TTCAGGCTTGTAAGTTAGTACAAAG 57.276 36.000 0.00 0.00 42.03 2.77
873 1511 6.823497 TCAGGCTTGTAAGTTAGTACAAAGT 58.177 36.000 0.00 0.00 42.03 2.66
874 1512 7.277396 TCAGGCTTGTAAGTTAGTACAAAGTT 58.723 34.615 0.00 0.00 42.03 2.66
875 1513 7.225931 TCAGGCTTGTAAGTTAGTACAAAGTTG 59.774 37.037 0.00 0.00 42.03 3.16
876 1514 6.485648 AGGCTTGTAAGTTAGTACAAAGTTGG 59.514 38.462 0.00 0.00 42.03 3.77
877 1515 6.293790 GGCTTGTAAGTTAGTACAAAGTTGGG 60.294 42.308 0.00 0.00 42.03 4.12
878 1516 6.261603 GCTTGTAAGTTAGTACAAAGTTGGGT 59.738 38.462 0.00 0.00 42.03 4.51
879 1517 7.519488 GCTTGTAAGTTAGTACAAAGTTGGGTC 60.519 40.741 0.00 0.00 42.03 4.46
880 1518 6.887013 TGTAAGTTAGTACAAAGTTGGGTCA 58.113 36.000 0.00 0.00 31.03 4.02
881 1519 7.511268 TGTAAGTTAGTACAAAGTTGGGTCAT 58.489 34.615 0.00 0.00 31.03 3.06
882 1520 7.658575 TGTAAGTTAGTACAAAGTTGGGTCATC 59.341 37.037 0.00 0.00 31.03 2.92
883 1521 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
884 1522 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
885 1523 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
886 1524 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
887 1525 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
888 1526 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
889 1527 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
890 1528 7.942341 AGTACAAAGTTGGGTCATCTATTTTGA 59.058 33.333 0.00 0.00 0.00 2.69
891 1529 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
892 1530 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
893 1531 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
894 1532 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
895 1533 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
896 1534 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
897 1535 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
898 1536 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
899 1537 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
900 1538 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
1063 1806 0.543749 ATCTAGCAGCAACAGGGGAC 59.456 55.000 0.00 0.00 0.00 4.46
1071 1814 2.915659 AACAGGGGACGCTCGACA 60.916 61.111 0.00 0.00 0.00 4.35
1083 1826 4.802039 GGACGCTCGACAATTACATCTTTA 59.198 41.667 0.00 0.00 0.00 1.85
1113 1856 0.322546 GTTGCGGTCTCCATTCCCTT 60.323 55.000 0.00 0.00 0.00 3.95
1205 1948 5.971763 ACTTATCTGCTTCCTGTCTACTTG 58.028 41.667 0.00 0.00 0.00 3.16
1210 1953 3.764434 CTGCTTCCTGTCTACTTGTCCTA 59.236 47.826 0.00 0.00 0.00 2.94
1219 1962 4.246458 GTCTACTTGTCCTAGTTTGCAGG 58.754 47.826 0.00 0.00 34.20 4.85
1221 1964 4.777896 TCTACTTGTCCTAGTTTGCAGGAT 59.222 41.667 0.00 0.00 43.96 3.24
1293 2036 0.672091 TGTCGCGGCTCAAATTGCTA 60.672 50.000 13.81 0.00 0.00 3.49
1344 2087 0.322366 TTGGATGCGATGCTCCACAA 60.322 50.000 8.74 0.00 41.20 3.33
1494 2237 1.618837 ACTAAGCTTCCTTCAGTCGCA 59.381 47.619 0.00 0.00 32.47 5.10
1516 2259 4.572389 CACCAAATATTAGCTCGCTTGTCT 59.428 41.667 0.00 0.00 0.00 3.41
1659 2457 3.074390 TCATCCCACCAAAGACATTGACT 59.926 43.478 0.00 0.00 41.85 3.41
1731 2553 5.898174 AGTTTTAGTGGGCTTTGTTACAAC 58.102 37.500 0.00 0.00 0.00 3.32
1812 2637 5.595885 TGCTAATAGTTGAGCATCTCTGTC 58.404 41.667 0.00 0.00 43.64 3.51
1828 2653 2.731451 TCTGTCGTTTCTTCAGATTGCG 59.269 45.455 0.00 0.00 34.00 4.85
1989 2815 7.428282 TCATCTTGCGTGTAAGTCAAATTTA 57.572 32.000 0.00 0.00 0.00 1.40
2198 3032 1.072159 GCCATTCCGGGAGATCCTG 59.928 63.158 0.00 0.26 42.13 3.86
2433 3267 1.719063 AAGGCCCTCTTGGAAGCACA 61.719 55.000 0.00 0.00 35.39 4.57
2496 3330 5.316987 AGTCCCCTCAAGTGTTAAATTCAG 58.683 41.667 0.00 0.00 0.00 3.02
2595 3429 9.657121 GTTGCATAAGAGCTAGTTCAAATAATC 57.343 33.333 9.43 0.00 34.99 1.75
2667 3501 3.452264 AGAGATAGCCTTATGCACACACA 59.548 43.478 0.00 0.00 44.83 3.72
2675 3509 5.653769 AGCCTTATGCACACACATTAAGATT 59.346 36.000 0.00 0.00 44.83 2.40
2676 3510 6.828273 AGCCTTATGCACACACATTAAGATTA 59.172 34.615 0.00 0.00 44.83 1.75
2677 3511 7.503566 AGCCTTATGCACACACATTAAGATTAT 59.496 33.333 0.00 0.00 44.83 1.28
2678 3512 8.783093 GCCTTATGCACACACATTAAGATTATA 58.217 33.333 0.00 0.00 40.77 0.98
2748 3582 3.773119 TGCTAAAAGATACTCCCTCCGTT 59.227 43.478 0.00 0.00 0.00 4.44
2750 3584 3.908643 AAAAGATACTCCCTCCGTTCC 57.091 47.619 0.00 0.00 0.00 3.62
2751 3585 1.400737 AAGATACTCCCTCCGTTCCG 58.599 55.000 0.00 0.00 0.00 4.30
2752 3586 0.549950 AGATACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
2754 3588 1.962100 GATACTCCCTCCGTTCCGAAT 59.038 52.381 0.00 0.00 0.00 3.34
2756 3590 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2757 3591 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2758 3592 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2759 3593 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2761 3595 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2762 3596 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2764 3598 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
2765 3599 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
2766 3600 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
2767 3601 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
2768 3602 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
2769 3603 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
2770 3604 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
2771 3605 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
2772 3606 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
2774 3608 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
2775 3609 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
2776 3610 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
2777 3611 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
2778 3612 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
2784 3618 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
2785 3619 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
2786 3620 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
2788 3622 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
2789 3623 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
2819 3653 9.705471 GTTCTAGATATATCCATTTCTACGACG 57.295 37.037 9.18 0.00 0.00 5.12
2820 3654 9.662947 TTCTAGATATATCCATTTCTACGACGA 57.337 33.333 9.18 0.00 0.00 4.20
2821 3655 9.315525 TCTAGATATATCCATTTCTACGACGAG 57.684 37.037 9.18 0.00 0.00 4.18
2822 3656 7.925043 AGATATATCCATTTCTACGACGAGT 57.075 36.000 9.18 0.00 0.00 4.18
2824 3658 9.445878 AGATATATCCATTTCTACGACGAGTAA 57.554 33.333 9.18 0.00 34.45 2.24
2828 3662 6.880822 TCCATTTCTACGACGAGTAATTTG 57.119 37.500 0.00 0.00 34.45 2.32
2829 3663 5.808540 TCCATTTCTACGACGAGTAATTTGG 59.191 40.000 0.00 0.59 34.45 3.28
2830 3664 5.808540 CCATTTCTACGACGAGTAATTTGGA 59.191 40.000 0.00 0.00 34.45 3.53
2854 3688 6.749036 ACGGAGGGAGTAGATCATTTAAAT 57.251 37.500 0.00 0.00 0.00 1.40
2917 3752 3.181412 ACCATTGGAGGAGGCCTTAAAAA 60.181 43.478 6.77 0.00 31.76 1.94
2918 3753 3.195610 CCATTGGAGGAGGCCTTAAAAAC 59.804 47.826 6.77 0.00 31.76 2.43
2982 3817 4.406003 CCTCCTAGCCAGCTTTTCTACTTA 59.594 45.833 0.00 0.00 0.00 2.24
2983 3818 5.104900 CCTCCTAGCCAGCTTTTCTACTTAA 60.105 44.000 0.00 0.00 0.00 1.85
2986 3821 5.813157 CCTAGCCAGCTTTTCTACTTAACTC 59.187 44.000 0.00 0.00 0.00 3.01
2996 3831 8.479689 GCTTTTCTACTTAACTCTAATCCTCCT 58.520 37.037 0.00 0.00 0.00 3.69
3067 3902 0.037139 AGTACAATGCCCGTGCGTTA 60.037 50.000 0.00 0.00 44.83 3.18
3087 3922 3.277142 ACCACGGGCTCTTAAAATAGG 57.723 47.619 0.00 0.00 0.00 2.57
3090 3925 3.377172 CCACGGGCTCTTAAAATAGGTTG 59.623 47.826 0.00 0.00 0.00 3.77
3136 3971 6.240665 CACACGTACAAACAATATAGCACAG 58.759 40.000 0.00 0.00 0.00 3.66
3303 4138 9.076596 GCGCTTAAGAAATTCTTTCACAATATT 57.923 29.630 13.89 0.00 42.10 1.28
3510 4346 4.201851 CGTTCCACCAGAGCATAAAATGAG 60.202 45.833 0.00 0.00 0.00 2.90
3539 4375 0.322277 AGCCAGACACATTCCTGCAG 60.322 55.000 6.78 6.78 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 58 7.543520 CGGTTCCGATATGATGATATATGATGG 59.456 40.741 5.19 0.00 0.00 3.51
154 164 1.001406 GGAGCCGATCGAGGAATCAAT 59.999 52.381 18.66 0.00 0.00 2.57
162 172 2.265182 GGAGAGGGAGCCGATCGAG 61.265 68.421 18.66 8.00 0.00 4.04
280 335 8.663025 CATCCTATTCTGACGAATGATTTATGG 58.337 37.037 0.00 0.00 40.04 2.74
313 368 6.146510 CCACTTACACAAACGCAGATTAGTTA 59.853 38.462 0.00 0.00 0.00 2.24
314 369 5.049680 CCACTTACACAAACGCAGATTAGTT 60.050 40.000 0.00 0.00 0.00 2.24
315 370 4.451096 CCACTTACACAAACGCAGATTAGT 59.549 41.667 0.00 0.00 0.00 2.24
316 371 4.688879 TCCACTTACACAAACGCAGATTAG 59.311 41.667 0.00 0.00 0.00 1.73
321 380 3.554524 CAATCCACTTACACAAACGCAG 58.445 45.455 0.00 0.00 0.00 5.18
333 392 1.203994 GAGCTGCAATGCAATCCACTT 59.796 47.619 9.92 0.00 38.41 3.16
386 445 4.064491 GACCGTCGTCGTCGTCGT 62.064 66.667 17.80 8.23 44.09 4.34
387 446 3.954218 CTGACCGTCGTCGTCGTCG 62.954 68.421 13.54 13.54 44.85 5.12
388 447 2.202146 CTGACCGTCGTCGTCGTC 60.202 66.667 10.76 8.72 42.37 4.20
535 1173 0.713883 GCGTCAACGAGTGTATGTGG 59.286 55.000 6.75 0.00 43.02 4.17
577 1215 3.349006 GCATGGGATACGCAGGCG 61.349 66.667 12.71 12.71 43.15 5.52
635 1273 6.439375 TCCAGTAATCCTAGTGTGTACATGTT 59.561 38.462 2.30 0.00 0.00 2.71
678 1316 1.006832 GTCAATGGGACCAATCGACG 58.993 55.000 0.00 0.00 40.83 5.12
683 1321 3.433306 TTCTTCGTCAATGGGACCAAT 57.567 42.857 0.00 0.00 43.95 3.16
776 1414 7.443575 TCTGGCAGAGAATTCTTTTATGATAGC 59.556 37.037 14.43 1.78 0.00 2.97
857 1495 7.876582 AGATGACCCAACTTTGTACTAACTTAC 59.123 37.037 0.00 0.00 0.00 2.34
858 1496 7.970102 AGATGACCCAACTTTGTACTAACTTA 58.030 34.615 0.00 0.00 0.00 2.24
859 1497 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
860 1498 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
861 1499 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
862 1500 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
863 1501 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
864 1502 7.942341 TCAAAATAGATGACCCAACTTTGTACT 59.058 33.333 0.00 0.00 0.00 2.73
865 1503 8.106247 TCAAAATAGATGACCCAACTTTGTAC 57.894 34.615 0.00 0.00 0.00 2.90
866 1504 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
867 1505 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
868 1506 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
869 1507 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
870 1508 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
871 1509 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
872 1510 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
873 1511 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
874 1512 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
875 1513 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
876 1514 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
877 1515 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
878 1516 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
879 1517 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
880 1518 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
881 1519 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
882 1520 4.874396 GGTACTCCCTCCGTTTCAAAATAG 59.126 45.833 0.00 0.00 0.00 1.73
883 1521 4.533311 AGGTACTCCCTCCGTTTCAAAATA 59.467 41.667 0.00 0.00 40.71 1.40
884 1522 3.329814 AGGTACTCCCTCCGTTTCAAAAT 59.670 43.478 0.00 0.00 40.71 1.82
885 1523 2.707257 AGGTACTCCCTCCGTTTCAAAA 59.293 45.455 0.00 0.00 40.71 2.44
886 1524 2.332117 AGGTACTCCCTCCGTTTCAAA 58.668 47.619 0.00 0.00 40.71 2.69
887 1525 2.019807 AGGTACTCCCTCCGTTTCAA 57.980 50.000 0.00 0.00 40.71 2.69
888 1526 3.780307 AGGTACTCCCTCCGTTTCA 57.220 52.632 0.00 0.00 40.71 2.69
1063 1806 5.462068 TGGATAAAGATGTAATTGTCGAGCG 59.538 40.000 0.00 0.00 0.00 5.03
1071 1814 7.902920 ACCAGCAATGGATAAAGATGTAATT 57.097 32.000 0.31 0.00 0.00 1.40
1083 1826 1.304381 ACCGCAACCAGCAATGGAT 60.304 52.632 0.31 0.00 46.13 3.41
1113 1856 1.529010 CAAGCAGCCAACCCTGTCA 60.529 57.895 0.00 0.00 35.28 3.58
1219 1962 3.338249 TGCAGTAGGAAAGTTGCAGATC 58.662 45.455 0.00 0.00 41.23 2.75
1221 1964 2.928801 TGCAGTAGGAAAGTTGCAGA 57.071 45.000 0.00 0.00 41.23 4.26
1293 2036 0.462937 TGTTGCAGTTGCGTACCAGT 60.463 50.000 0.00 0.00 45.83 4.00
1344 2087 5.374921 CCATCATATCCAAAGCTCTTGAGT 58.625 41.667 9.37 2.42 0.00 3.41
1494 2237 4.770795 AGACAAGCGAGCTAATATTTGGT 58.229 39.130 1.14 1.14 0.00 3.67
1516 2259 5.587443 CACTGACCTCAAAGCATGATGATAA 59.413 40.000 0.00 0.00 37.44 1.75
1659 2457 5.726980 AATGTTGATAGCCAAAGAAAGCA 57.273 34.783 0.00 0.00 36.36 3.91
1812 2637 2.092838 GGAGTCGCAATCTGAAGAAACG 59.907 50.000 0.00 0.00 0.00 3.60
1828 2653 8.593492 ATTTGTTAAGCTTTTTCATTGGAGTC 57.407 30.769 3.20 0.00 0.00 3.36
1989 2815 5.776358 TGAATTTAGGCTTTCATATGGGGT 58.224 37.500 2.13 0.00 0.00 4.95
2214 3048 2.223249 CCCCTCATATGCGTTTTTCGTG 60.223 50.000 0.00 0.00 42.13 4.35
2433 3267 6.105333 GTCTTGATGACATCTACAGCTTTCT 58.895 40.000 16.25 0.00 44.73 2.52
2549 3383 3.978610 ACTATTGGAGGAGGTCTAACGT 58.021 45.455 0.00 0.00 0.00 3.99
2550 3384 4.683832 CAACTATTGGAGGAGGTCTAACG 58.316 47.826 0.00 0.00 0.00 3.18
2551 3385 4.081087 TGCAACTATTGGAGGAGGTCTAAC 60.081 45.833 0.00 0.00 0.00 2.34
2675 3509 8.466798 CACCCACACGTCATCTTCATATATATA 58.533 37.037 0.00 0.00 0.00 0.86
2676 3510 7.323420 CACCCACACGTCATCTTCATATATAT 58.677 38.462 0.00 0.00 0.00 0.86
2677 3511 6.295067 CCACCCACACGTCATCTTCATATATA 60.295 42.308 0.00 0.00 0.00 0.86
2678 3512 5.511373 CCACCCACACGTCATCTTCATATAT 60.511 44.000 0.00 0.00 0.00 0.86
2748 3582 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
2750 3584 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
2751 3585 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
2752 3586 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
2754 3588 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
2756 3590 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
2757 3591 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
2758 3592 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
2759 3593 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
2761 3595 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
2762 3596 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
2793 3627 9.705471 CGTCGTAGAAATGGATATATCTAGAAC 57.295 37.037 12.42 2.68 39.69 3.01
2802 3636 9.193133 CAAATTACTCGTCGTAGAAATGGATAT 57.807 33.333 0.00 0.00 39.69 1.63
2803 3637 7.650504 CCAAATTACTCGTCGTAGAAATGGATA 59.349 37.037 0.00 0.00 39.69 2.59
2805 3639 5.808540 CCAAATTACTCGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
2806 3640 5.808540 TCCAAATTACTCGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
2807 3641 6.880822 TCCAAATTACTCGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
2808 3642 6.034256 CGTTCCAAATTACTCGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
2809 3643 5.343058 CGTTCCAAATTACTCGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
2810 3644 4.853196 CGTTCCAAATTACTCGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
2811 3645 4.406069 CGTTCCAAATTACTCGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
2812 3646 3.545078 CCGTTCCAAATTACTCGTCGTAG 59.455 47.826 0.00 0.00 0.00 3.51
2813 3647 3.190327 TCCGTTCCAAATTACTCGTCGTA 59.810 43.478 0.00 0.00 0.00 3.43
2814 3648 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2815 3649 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2816 3650 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2817 3651 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2818 3652 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2819 3653 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2820 3654 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2821 3655 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2822 3656 4.355549 TCTACTCCCTCCGTTCCAAATTA 58.644 43.478 0.00 0.00 0.00 1.40
2823 3657 3.178865 TCTACTCCCTCCGTTCCAAATT 58.821 45.455 0.00 0.00 0.00 1.82
2824 3658 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
2825 3659 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
2826 3660 2.291996 TGATCTACTCCCTCCGTTCCAA 60.292 50.000 0.00 0.00 0.00 3.53
2827 3661 1.286849 TGATCTACTCCCTCCGTTCCA 59.713 52.381 0.00 0.00 0.00 3.53
2828 3662 2.068834 TGATCTACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
2829 3663 4.674281 AAATGATCTACTCCCTCCGTTC 57.326 45.455 0.00 0.00 0.00 3.95
2830 3664 6.555463 TTTAAATGATCTACTCCCTCCGTT 57.445 37.500 0.00 0.00 0.00 4.44
2854 3688 9.555727 AGCTCTAAACAGTCTAAAACACAATTA 57.444 29.630 0.00 0.00 0.00 1.40
2982 3817 7.778853 TCGACTTACATAAGGAGGATTAGAGTT 59.221 37.037 3.79 0.00 37.62 3.01
2983 3818 7.288560 TCGACTTACATAAGGAGGATTAGAGT 58.711 38.462 3.79 0.00 37.62 3.24
2986 3821 7.513371 ACTCGACTTACATAAGGAGGATTAG 57.487 40.000 3.79 0.00 37.62 1.73
3045 3880 0.179121 CGCACGGGCATTGTACTAGA 60.179 55.000 11.77 0.00 41.24 2.43
3052 3887 2.328856 TGGTAACGCACGGGCATTG 61.329 57.895 11.77 0.00 41.24 2.82
3067 3902 2.574824 ACCTATTTTAAGAGCCCGTGGT 59.425 45.455 0.00 0.00 0.00 4.16
3090 3925 9.503427 GTGTGGAATTTAATATGTAACTCTTGC 57.497 33.333 0.00 0.00 0.00 4.01
3186 4021 9.834628 GGACATGTCGTTAATTTTTCTTTATGA 57.165 29.630 19.33 0.00 0.00 2.15
3370 4206 2.684881 GTTTGTGCAGGATGGGTATGAG 59.315 50.000 0.00 0.00 35.86 2.90
3510 4346 5.863935 GGAATGTGTCTGGCTATTTTGTTTC 59.136 40.000 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.