Multiple sequence alignment - TraesCS3A01G463800

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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 TraesCS3A01G463800 chr3A 100.000 2738 0 0 1 2738 698032093 698029356 0.000000e+00 5057.0
1 TraesCS3A01G463800 chr3A 83.099 142 19 3 2235 2376 698167455 698167319 1.030000e-24 124.0
2 TraesCS3A01G463800 chr3D 89.093 1091 71 29 1131 2187 563435251 563434175 0.000000e+00 1312.0
3 TraesCS3A01G463800 chr3D 88.576 569 35 10 2184 2738 563432882 563432330 0.000000e+00 664.0
4 TraesCS3A01G463800 chr3D 94.783 345 15 2 9 350 563435590 563435246 4.010000e-148 534.0
5 TraesCS3A01G463800 chr3D 92.241 232 14 2 2181 2412 563433909 563433682 2.630000e-85 326.0
6 TraesCS3A01G463800 chr3D 86.572 283 32 6 1905 2184 133227452 133227173 9.520000e-80 307.0
7 TraesCS3A01G463800 chr3D 86.614 127 13 3 2062 2187 563433410 563433287 1.320000e-28 137.0
8 TraesCS3A01G463800 chr3D 83.099 142 19 3 2235 2376 563594949 563594813 1.030000e-24 124.0
9 TraesCS3A01G463800 chr3B 94.759 706 30 4 1134 1838 750901240 750900541 0.000000e+00 1092.0
10 TraesCS3A01G463800 chr3B 93.043 345 21 2 9 350 750902804 750902460 4.070000e-138 501.0
11 TraesCS3A01G463800 chr3B 96.316 190 7 0 348 537 737561834 737562023 2.050000e-81 313.0
12 TraesCS3A01G463800 chr3B 99.275 138 1 0 347 484 30905751 30905888 1.630000e-62 250.0
13 TraesCS3A01G463800 chr3B 100.000 135 0 0 350 484 30907053 30907187 1.630000e-62 250.0
14 TraesCS3A01G463800 chr3B 98.519 135 2 0 350 484 792725086 792725220 3.520000e-59 239.0
15 TraesCS3A01G463800 chr3B 98.507 134 2 0 350 483 792723762 792723895 1.270000e-58 237.0
16 TraesCS3A01G463800 chr3B 79.032 372 47 17 1830 2187 751013776 751013422 2.740000e-55 226.0
17 TraesCS3A01G463800 chr3B 83.803 142 18 3 2235 2376 751013777 751013641 2.210000e-26 130.0
18 TraesCS3A01G463800 chr3B 100.000 37 0 0 2702 2738 750899833 750899797 4.890000e-08 69.4
19 TraesCS3A01G463800 chr1A 87.240 768 49 36 401 1130 22076706 22075950 0.000000e+00 830.0
20 TraesCS3A01G463800 chr1A 87.063 773 51 36 401 1135 22075270 22074509 0.000000e+00 828.0
21 TraesCS3A01G463800 chr6B 86.883 770 50 36 401 1130 712758 713516 0.000000e+00 815.0
22 TraesCS3A01G463800 chr6B 91.111 540 42 5 388 925 640352594 640352059 0.000000e+00 726.0
23 TraesCS3A01G463800 chr6B 79.927 274 21 21 869 1130 422311576 422311827 1.300000e-38 171.0
24 TraesCS3A01G463800 chr6B 79.273 275 21 21 869 1128 422310264 422310517 2.820000e-35 159.0
25 TraesCS3A01G463800 chr5B 86.152 751 75 20 388 1130 688051222 688051951 0.000000e+00 784.0
26 TraesCS3A01G463800 chr5B 91.949 236 15 3 898 1130 672118465 672118699 7.310000e-86 327.0
27 TraesCS3A01G463800 chr5B 80.000 275 22 23 870 1130 534667816 534667561 3.620000e-39 172.0
28 TraesCS3A01G463800 chr2B 84.807 803 75 32 349 1130 114555867 114556643 0.000000e+00 763.0
29 TraesCS3A01G463800 chr4A 80.506 790 107 33 359 1132 603279070 603278312 1.840000e-156 562.0
30 TraesCS3A01G463800 chr5A 81.602 674 81 33 359 1014 567748468 567749116 4.040000e-143 518.0
31 TraesCS3A01G463800 chr2D 84.874 357 41 4 456 810 612736408 612736063 5.610000e-92 348.0
32 TraesCS3A01G463800 chr4B 96.237 186 7 0 352 537 1794173 1793988 3.430000e-79 305.0
33 TraesCS3A01G463800 chr4B 84.722 144 7 6 995 1130 196389320 196389184 2.210000e-26 130.0
34 TraesCS3A01G463800 chr4B 83.333 144 9 7 995 1130 196390650 196390514 4.790000e-23 119.0
35 TraesCS3A01G463800 chr1B 78.976 371 47 21 796 1140 19341635 19342000 9.870000e-55 224.0
36 TraesCS3A01G463800 chr1B 78.976 371 47 21 796 1140 19440372 19440737 9.870000e-55 224.0
37 TraesCS3A01G463800 chr1D 83.884 242 21 11 897 1130 19569269 19569038 5.940000e-52 215.0
38 TraesCS3A01G463800 chr7B 93.233 133 4 2 1005 1137 13262690 13262817 1.000000e-44 191.0
39 TraesCS3A01G463800 chr7B 94.444 126 2 2 1005 1130 13261364 13261484 3.600000e-44 189.0
40 TraesCS3A01G463800 chr4D 79.401 267 32 6 1905 2171 344344254 344344497 1.690000e-37 167.0


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 TraesCS3A01G463800 chr3A 698029356 698032093 2737 True 5057.000000 5057 100.0000 1 2738 1 chr3A.!!$R1 2737
1 TraesCS3A01G463800 chr3D 563432330 563435590 3260 True 594.600000 1312 90.2614 9 2738 5 chr3D.!!$R3 2729
2 TraesCS3A01G463800 chr3B 750899797 750902804 3007 True 554.133333 1092 95.9340 9 2738 3 chr3B.!!$R1 2729
3 TraesCS3A01G463800 chr3B 30905751 30907187 1436 False 250.000000 250 99.6375 347 484 2 chr3B.!!$F2 137
4 TraesCS3A01G463800 chr3B 792723762 792725220 1458 False 238.000000 239 98.5130 350 484 2 chr3B.!!$F3 134
5 TraesCS3A01G463800 chr1A 22074509 22076706 2197 True 829.000000 830 87.1515 401 1135 2 chr1A.!!$R1 734
6 TraesCS3A01G463800 chr6B 712758 713516 758 False 815.000000 815 86.8830 401 1130 1 chr6B.!!$F1 729
7 TraesCS3A01G463800 chr6B 640352059 640352594 535 True 726.000000 726 91.1110 388 925 1 chr6B.!!$R1 537
8 TraesCS3A01G463800 chr5B 688051222 688051951 729 False 784.000000 784 86.1520 388 1130 1 chr5B.!!$F2 742
9 TraesCS3A01G463800 chr2B 114555867 114556643 776 False 763.000000 763 84.8070 349 1130 1 chr2B.!!$F1 781
10 TraesCS3A01G463800 chr4A 603278312 603279070 758 True 562.000000 562 80.5060 359 1132 1 chr4A.!!$R1 773
11 TraesCS3A01G463800 chr5A 567748468 567749116 648 False 518.000000 518 81.6020 359 1014 1 chr5A.!!$F1 655

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
937 1069 0.323178 AGGGCTGAGCACCAAAGATG 60.323 55.0 1.49 0.0 28.43 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 3992 0.23359 CGCGACAAATGTTCAACGGA 59.766 50.0 0.0 0.0 0.0 4.69 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
148 152 3.760035 GCCTCTTCGTCCTGGCGA 61.760 66.667 8.74 8.74 39.28 5.54
339 343 1.224592 GGCTGGTCCCGACAATGAT 59.775 57.895 0.00 0.00 0.00 2.45
344 348 3.873910 CTGGTCCCGACAATGATAGTTT 58.126 45.455 0.00 0.00 0.00 2.66
345 349 3.869065 TGGTCCCGACAATGATAGTTTC 58.131 45.455 0.00 0.00 0.00 2.78
466 487 2.894387 GAGGCATGCGGAGACTGC 60.894 66.667 12.44 0.00 36.05 4.40
467 488 4.827087 AGGCATGCGGAGACTGCG 62.827 66.667 12.54 12.54 37.34 5.18
468 489 4.819761 GGCATGCGGAGACTGCGA 62.820 66.667 21.39 5.78 37.34 5.10
469 490 3.260483 GCATGCGGAGACTGCGAG 61.260 66.667 21.39 9.79 30.86 5.03
470 491 2.491621 CATGCGGAGACTGCGAGA 59.508 61.111 21.39 5.75 30.86 4.04
471 492 1.067084 CATGCGGAGACTGCGAGAT 59.933 57.895 21.39 7.98 30.86 2.75
472 493 1.067084 ATGCGGAGACTGCGAGATG 59.933 57.895 21.39 0.00 30.86 2.90
473 494 2.959071 GCGGAGACTGCGAGATGC 60.959 66.667 21.39 0.00 46.70 3.91
474 495 2.279120 CGGAGACTGCGAGATGCC 60.279 66.667 11.36 0.00 45.60 4.40
475 496 2.279120 GGAGACTGCGAGATGCCG 60.279 66.667 0.00 0.00 45.60 5.69
476 497 2.279120 GAGACTGCGAGATGCCGG 60.279 66.667 0.00 0.00 45.60 6.13
477 498 3.781770 GAGACTGCGAGATGCCGGG 62.782 68.421 2.18 0.00 45.60 5.73
490 511 4.155733 CCGGGCTGCCGTGTGATA 62.156 66.667 13.40 0.00 0.00 2.15
491 512 2.890474 CGGGCTGCCGTGTGATAC 60.890 66.667 13.40 0.00 0.00 2.24
768 881 8.093307 GTGATGCATATCCTGAAGAGATTCTAA 58.907 37.037 0.00 0.00 32.09 2.10
934 1066 1.073722 TGAGGGCTGAGCACCAAAG 59.926 57.895 1.49 0.00 28.43 2.77
935 1067 1.376466 GAGGGCTGAGCACCAAAGA 59.624 57.895 1.49 0.00 28.43 2.52
937 1069 0.323178 AGGGCTGAGCACCAAAGATG 60.323 55.000 1.49 0.00 28.43 2.90
938 1070 0.610232 GGGCTGAGCACCAAAGATGT 60.610 55.000 6.82 0.00 0.00 3.06
939 1071 1.340017 GGGCTGAGCACCAAAGATGTA 60.340 52.381 6.82 0.00 0.00 2.29
944 1076 2.012673 GAGCACCAAAGATGTAGCCAG 58.987 52.381 0.00 0.00 0.00 4.85
948 1082 3.868369 GCACCAAAGATGTAGCCAGTGTA 60.868 47.826 0.00 0.00 0.00 2.90
966 1101 4.047822 GTGTATTCATCAAGGAGAGAGCG 58.952 47.826 0.00 0.00 0.00 5.03
967 1102 2.237393 ATTCATCAAGGAGAGAGCGC 57.763 50.000 0.00 0.00 0.00 5.92
996 1134 3.482156 AGCTCTTGTGCTTCTTCTTGA 57.518 42.857 0.00 0.00 40.93 3.02
1025 1169 3.262420 GTGTGTGTGTGTTGAGTCTTCT 58.738 45.455 0.00 0.00 0.00 2.85
1026 1170 3.684788 GTGTGTGTGTGTTGAGTCTTCTT 59.315 43.478 0.00 0.00 0.00 2.52
1027 1171 4.154195 GTGTGTGTGTGTTGAGTCTTCTTT 59.846 41.667 0.00 0.00 0.00 2.52
1032 1176 4.200092 GTGTGTTGAGTCTTCTTTCCCTT 58.800 43.478 0.00 0.00 0.00 3.95
1054 1216 4.686972 TGTGTGTGTTCTTGAGAAGAGAG 58.313 43.478 0.00 0.00 39.03 3.20
1060 1226 5.812642 TGTGTTCTTGAGAAGAGAGAAACAC 59.187 40.000 7.82 7.82 39.03 3.32
1082 1256 2.042464 AGTGAGAGTTGTGAGAGGCAA 58.958 47.619 0.00 0.00 0.00 4.52
1097 1271 2.682155 GGCAACTCGAGGAAGAAGAT 57.318 50.000 18.41 0.00 0.00 2.40
1104 1278 3.186119 CTCGAGGAAGAAGATGAAGTGC 58.814 50.000 3.91 0.00 0.00 4.40
1108 1282 0.371645 GAAGAAGATGAAGTGCGGCG 59.628 55.000 0.51 0.51 0.00 6.46
1109 1283 1.639298 AAGAAGATGAAGTGCGGCGC 61.639 55.000 27.44 27.44 0.00 6.53
1110 1284 2.046892 AAGATGAAGTGCGGCGCT 60.047 55.556 33.26 13.47 0.00 5.92
1112 1286 4.527157 GATGAAGTGCGGCGCTGC 62.527 66.667 34.00 34.00 0.00 5.25
1140 1315 0.739813 GCGCCAACATCTTCTACGGT 60.740 55.000 0.00 0.00 0.00 4.83
1217 3009 0.731855 GGTCTCTACACCAACGACGC 60.732 60.000 0.00 0.00 36.32 5.19
1237 3029 1.135315 CCACAACGGGATTCATTGCAG 60.135 52.381 0.00 0.00 0.00 4.41
1318 3110 0.534203 TGTCTGGCGTTTCCTGGTTC 60.534 55.000 0.00 0.00 34.80 3.62
1437 3229 2.537560 GCATGCCATCTTCGTCGGG 61.538 63.158 6.36 0.00 0.00 5.14
1537 3329 1.236616 TTTGTCAGCCCACATCTGCG 61.237 55.000 0.00 0.00 0.00 5.18
1695 3487 2.739996 CCGGGATTCTCAGCTGCCT 61.740 63.158 9.47 0.00 0.00 4.75
1710 3502 1.876156 CTGCCTTTGAAAGAAGACGCT 59.124 47.619 6.49 0.00 0.00 5.07
1712 3504 1.068954 GCCTTTGAAAGAAGACGCTGG 60.069 52.381 6.49 0.00 0.00 4.85
1717 3509 0.110644 GAAAGAAGACGCTGGCAACG 60.111 55.000 9.01 9.01 42.51 4.10
1755 3547 9.204570 TGGTTTTAATTTTCTCTCTAGTCTTCG 57.795 33.333 0.00 0.00 0.00 3.79
1773 3585 6.708949 AGTCTTCGTTCTGTTAATTTTGGCTA 59.291 34.615 0.00 0.00 0.00 3.93
1776 3588 7.442969 TCTTCGTTCTGTTAATTTTGGCTAAGA 59.557 33.333 0.00 0.00 0.00 2.10
1777 3589 7.499321 TCGTTCTGTTAATTTTGGCTAAGAA 57.501 32.000 0.00 0.00 0.00 2.52
1778 3590 7.357303 TCGTTCTGTTAATTTTGGCTAAGAAC 58.643 34.615 0.00 0.00 39.11 3.01
1779 3591 7.227910 TCGTTCTGTTAATTTTGGCTAAGAACT 59.772 33.333 9.69 0.00 39.90 3.01
1780 3592 7.860872 CGTTCTGTTAATTTTGGCTAAGAACTT 59.139 33.333 9.69 0.00 39.90 2.66
1781 3593 9.181805 GTTCTGTTAATTTTGGCTAAGAACTTC 57.818 33.333 0.00 0.00 39.29 3.01
1782 3594 8.458573 TCTGTTAATTTTGGCTAAGAACTTCA 57.541 30.769 0.00 0.00 0.00 3.02
1783 3595 8.567948 TCTGTTAATTTTGGCTAAGAACTTCAG 58.432 33.333 0.00 0.00 0.00 3.02
1784 3596 8.458573 TGTTAATTTTGGCTAAGAACTTCAGA 57.541 30.769 0.00 0.00 0.00 3.27
1785 3597 8.908903 TGTTAATTTTGGCTAAGAACTTCAGAA 58.091 29.630 0.00 0.00 0.00 3.02
1786 3598 9.399403 GTTAATTTTGGCTAAGAACTTCAGAAG 57.601 33.333 8.77 8.77 0.00 2.85
1787 3599 7.823745 AATTTTGGCTAAGAACTTCAGAAGA 57.176 32.000 17.56 0.00 0.00 2.87
1788 3600 6.867662 TTTTGGCTAAGAACTTCAGAAGAG 57.132 37.500 17.56 4.41 0.00 2.85
1789 3601 4.543590 TGGCTAAGAACTTCAGAAGAGG 57.456 45.455 17.56 1.74 0.00 3.69
1790 3602 3.266636 GGCTAAGAACTTCAGAAGAGGC 58.733 50.000 17.56 11.32 0.00 4.70
1791 3603 3.055458 GGCTAAGAACTTCAGAAGAGGCT 60.055 47.826 17.56 7.63 0.00 4.58
1792 3604 3.932089 GCTAAGAACTTCAGAAGAGGCTG 59.068 47.826 17.56 3.81 37.24 4.85
1793 3605 4.322349 GCTAAGAACTTCAGAAGAGGCTGA 60.322 45.833 17.56 3.40 42.81 4.26
1794 3606 3.676291 AGAACTTCAGAAGAGGCTGAC 57.324 47.619 17.56 0.69 44.08 3.51
1795 3607 3.238597 AGAACTTCAGAAGAGGCTGACT 58.761 45.455 17.56 0.00 44.08 3.41
1796 3608 3.258123 AGAACTTCAGAAGAGGCTGACTC 59.742 47.826 17.56 1.11 44.08 3.36
1838 3650 2.571653 TGGTGGATGGAAGGAAGTACTG 59.428 50.000 0.00 0.00 0.00 2.74
1839 3651 2.572104 GGTGGATGGAAGGAAGTACTGT 59.428 50.000 0.00 0.00 0.00 3.55
1842 3654 4.455877 GTGGATGGAAGGAAGTACTGTTTG 59.544 45.833 0.00 0.00 0.00 2.93
1845 3657 3.815809 TGGAAGGAAGTACTGTTTGTGG 58.184 45.455 0.00 0.00 0.00 4.17
1846 3658 2.552743 GGAAGGAAGTACTGTTTGTGGC 59.447 50.000 0.00 0.00 0.00 5.01
1847 3659 2.271944 AGGAAGTACTGTTTGTGGCC 57.728 50.000 0.00 0.00 0.00 5.36
1848 3660 1.774856 AGGAAGTACTGTTTGTGGCCT 59.225 47.619 3.32 0.00 0.00 5.19
1849 3661 2.174854 AGGAAGTACTGTTTGTGGCCTT 59.825 45.455 3.32 0.00 0.00 4.35
1850 3662 3.393278 AGGAAGTACTGTTTGTGGCCTTA 59.607 43.478 3.32 0.00 0.00 2.69
1852 3664 4.023450 GGAAGTACTGTTTGTGGCCTTAAC 60.023 45.833 3.32 6.28 0.00 2.01
1889 3755 4.736611 ATGAACCCAATGCTCCATCTAT 57.263 40.909 0.00 0.00 0.00 1.98
1893 3759 6.430864 TGAACCCAATGCTCCATCTATTTTA 58.569 36.000 0.00 0.00 0.00 1.52
1925 3791 6.378280 TGCTATCTCTCATCTCTGTTTGTGTA 59.622 38.462 0.00 0.00 0.00 2.90
1939 3805 4.396790 TGTTTGTGTACACTTGTTCTTCCC 59.603 41.667 25.60 0.00 0.00 3.97
1948 3814 4.399303 ACACTTGTTCTTCCCTTGTTTCAG 59.601 41.667 0.00 0.00 0.00 3.02
1975 3841 0.325933 TGCAGTCTGGTGCTAGCAAT 59.674 50.000 21.29 0.00 44.32 3.56
1979 3845 3.866651 CAGTCTGGTGCTAGCAATAGTT 58.133 45.455 21.29 10.42 0.00 2.24
1985 3851 3.244735 TGGTGCTAGCAATAGTTGGTTCA 60.245 43.478 21.29 2.69 42.20 3.18
1989 3855 4.020218 TGCTAGCAATAGTTGGTTCAGACT 60.020 41.667 16.84 0.00 42.20 3.24
2014 3880 4.519540 TTGCTGTTTCTGAATTTAGCCC 57.480 40.909 14.37 0.00 0.00 5.19
2060 3926 2.666619 CGGTTCTCTGCAGCATTTGTTC 60.667 50.000 9.47 0.00 0.00 3.18
2079 3945 6.768029 TGTTCATTTTTCAGTAGCAAATGC 57.232 33.333 0.00 0.00 37.67 3.56
2093 3960 2.477754 GCAAATGCAGGCTCTGTTTTTC 59.522 45.455 0.00 0.00 41.59 2.29
2108 3976 5.299279 TCTGTTTTTCGCTCCTTTCTGAATT 59.701 36.000 0.00 0.00 0.00 2.17
2114 3982 3.888930 TCGCTCCTTTCTGAATTTGGTTT 59.111 39.130 0.00 0.00 0.00 3.27
2124 3992 4.278170 TCTGAATTTGGTTTCGCAGTTGAT 59.722 37.500 0.00 0.00 0.00 2.57
2160 4028 3.906660 CGTAGCTGGTTGTTCTCCA 57.093 52.632 0.00 0.00 0.00 3.86
2205 4346 2.996621 CTCTGGTCTTGCTAAGAAACCG 59.003 50.000 0.96 0.00 39.67 4.44
2218 4359 3.553828 AGAAACCGGTTTGACTCTTGA 57.446 42.857 36.17 0.00 32.11 3.02
2233 4442 7.482169 TGACTCTTGATTAGATTACCTGTGT 57.518 36.000 0.00 0.00 30.92 3.72
2252 4461 0.250124 TTGGCACTACTGTTCGTGGG 60.250 55.000 10.54 0.00 0.00 4.61
2263 4472 4.007659 ACTGTTCGTGGGCTTAATTAAGG 58.992 43.478 23.37 9.15 33.95 2.69
2295 4504 3.242011 ACCCAATGCTCCATCTGTTTTT 58.758 40.909 0.00 0.00 0.00 1.94
2300 4509 3.507162 TGCTCCATCTGTTTTTCCTGA 57.493 42.857 0.00 0.00 0.00 3.86
2334 4543 6.230472 TGTGTATATGTGCACTTGTTCTTCT 58.770 36.000 19.41 0.00 41.01 2.85
2346 4555 8.097038 TGCACTTGTTCTTCTCTTATATCACTT 58.903 33.333 0.00 0.00 0.00 3.16
2347 4556 9.587772 GCACTTGTTCTTCTCTTATATCACTTA 57.412 33.333 0.00 0.00 0.00 2.24
2376 4585 8.647796 ACTAATGTAGTATGGTGCTAGCAAATA 58.352 33.333 21.29 17.08 37.23 1.40
2388 4597 6.694411 GGTGCTAGCAAATAAGTCATTGAATG 59.306 38.462 21.29 0.00 0.00 2.67
2401 5643 3.555547 TCATTGAATGTATGCGGTTCTCG 59.444 43.478 4.93 0.00 42.76 4.04
2409 5651 2.510768 ATGCGGTTCTCGGTAAGATC 57.489 50.000 0.00 0.00 39.69 2.75
2420 5662 8.727910 GGTTCTCGGTAAGATCAGTTTATTTTT 58.272 33.333 0.00 0.00 32.82 1.94
2475 5722 4.099266 TCACCTTTCTGAATTTGGTTGTGG 59.901 41.667 7.28 0.00 0.00 4.17
2498 5745 5.447818 GGAGTTGAATGGTCGAGCATTTTAG 60.448 44.000 35.51 0.00 0.00 1.85
2500 5747 4.944962 TGAATGGTCGAGCATTTTAGTG 57.055 40.909 35.51 0.00 0.00 2.74
2528 5775 2.452600 AGGCTTTGTTCCTTGTTGGA 57.547 45.000 0.00 0.00 44.51 3.53
2532 5779 3.118775 GGCTTTGTTCCTTGTTGGACTTT 60.119 43.478 0.00 0.00 46.14 2.66
2547 5794 9.527157 TTGTTGGACTTTTCATATCCTGATAAA 57.473 29.630 0.00 0.00 32.72 1.40
2556 5803 8.613060 TTTCATATCCTGATAAACTGATGCTC 57.387 34.615 0.00 0.00 32.72 4.26
2609 5856 6.055231 TGTCCAAATTTCTGACAGTTTACG 57.945 37.500 13.48 0.00 34.28 3.18
2621 5868 5.297547 TGACAGTTTACGATTTCTGCTTCT 58.702 37.500 0.00 0.00 0.00 2.85
2622 5869 6.452242 TGACAGTTTACGATTTCTGCTTCTA 58.548 36.000 0.00 0.00 0.00 2.10
2623 5870 6.586463 TGACAGTTTACGATTTCTGCTTCTAG 59.414 38.462 0.00 0.00 0.00 2.43
2624 5871 6.688578 ACAGTTTACGATTTCTGCTTCTAGA 58.311 36.000 0.00 0.00 0.00 2.43
2625 5872 6.809196 ACAGTTTACGATTTCTGCTTCTAGAG 59.191 38.462 0.00 0.00 0.00 2.43
2626 5873 6.254589 CAGTTTACGATTTCTGCTTCTAGAGG 59.745 42.308 0.00 0.00 0.00 3.69
2627 5874 3.810310 ACGATTTCTGCTTCTAGAGGG 57.190 47.619 3.79 0.00 0.00 4.30
2628 5875 2.432510 ACGATTTCTGCTTCTAGAGGGG 59.567 50.000 3.79 0.00 0.00 4.79
2629 5876 2.432510 CGATTTCTGCTTCTAGAGGGGT 59.567 50.000 3.79 0.00 0.00 4.95
2630 5877 3.118592 CGATTTCTGCTTCTAGAGGGGTT 60.119 47.826 3.79 0.00 0.00 4.11
2631 5878 4.624125 CGATTTCTGCTTCTAGAGGGGTTT 60.624 45.833 3.79 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 152 2.526046 CGTGGGGAGGGTTCCTGTT 61.526 63.158 0.00 0.00 43.49 3.16
483 504 2.217112 GCATCTCGCCGTATCACAC 58.783 57.895 0.00 0.00 32.94 3.82
484 505 4.730081 GCATCTCGCCGTATCACA 57.270 55.556 0.00 0.00 32.94 3.58
768 881 1.414181 CGGCATAACACCATCTCCTCT 59.586 52.381 0.00 0.00 0.00 3.69
929 1058 5.185454 TGAATACACTGGCTACATCTTTGG 58.815 41.667 0.00 0.00 0.00 3.28
930 1061 6.539826 TGATGAATACACTGGCTACATCTTTG 59.460 38.462 0.00 0.00 35.30 2.77
934 1066 5.468072 CCTTGATGAATACACTGGCTACATC 59.532 44.000 0.00 0.00 34.98 3.06
935 1067 5.130975 TCCTTGATGAATACACTGGCTACAT 59.869 40.000 0.00 0.00 0.00 2.29
937 1069 5.023533 TCCTTGATGAATACACTGGCTAC 57.976 43.478 0.00 0.00 0.00 3.58
938 1070 4.962362 TCTCCTTGATGAATACACTGGCTA 59.038 41.667 0.00 0.00 0.00 3.93
939 1071 3.776969 TCTCCTTGATGAATACACTGGCT 59.223 43.478 0.00 0.00 0.00 4.75
944 1076 4.047822 CGCTCTCTCCTTGATGAATACAC 58.952 47.826 0.00 0.00 0.00 2.90
948 1082 1.202627 GGCGCTCTCTCCTTGATGAAT 60.203 52.381 7.64 0.00 0.00 2.57
966 1101 1.968540 ACAAGAGCTTTGCCGAGGC 60.969 57.895 7.26 7.26 42.35 4.70
967 1102 1.871772 CACAAGAGCTTTGCCGAGG 59.128 57.895 8.09 0.00 0.00 4.63
979 1115 5.122869 GCATACATCAAGAAGAAGCACAAGA 59.877 40.000 0.00 0.00 0.00 3.02
980 1116 5.330295 GCATACATCAAGAAGAAGCACAAG 58.670 41.667 0.00 0.00 0.00 3.16
996 1134 1.877637 ACACACACACACGCATACAT 58.122 45.000 0.00 0.00 0.00 2.29
1025 1169 3.691575 TCAAGAACACACACAAGGGAAA 58.308 40.909 0.00 0.00 0.00 3.13
1026 1170 3.054728 TCTCAAGAACACACACAAGGGAA 60.055 43.478 0.00 0.00 0.00 3.97
1027 1171 2.503765 TCTCAAGAACACACACAAGGGA 59.496 45.455 0.00 0.00 0.00 4.20
1032 1176 4.402474 TCTCTCTTCTCAAGAACACACACA 59.598 41.667 0.00 0.00 37.02 3.72
1054 1216 4.870426 TCTCACAACTCTCACTTGTGTTTC 59.130 41.667 10.27 0.00 45.84 2.78
1060 1226 2.224137 TGCCTCTCACAACTCTCACTTG 60.224 50.000 0.00 0.00 0.00 3.16
1082 1256 3.367910 GCACTTCATCTTCTTCCTCGAGT 60.368 47.826 12.31 0.00 0.00 4.18
1140 1315 0.770557 ACTCCTTGGCCTTGTACCCA 60.771 55.000 3.32 0.00 0.00 4.51
1217 3009 0.887247 TGCAATGAATCCCGTTGTGG 59.113 50.000 0.00 0.00 42.38 4.17
1318 3110 0.466189 AGCACCTGTCCACCAAGTTG 60.466 55.000 0.00 0.00 0.00 3.16
1495 3287 3.304525 CCCCGTCGATCAATGTAGTAGAC 60.305 52.174 0.00 0.00 0.00 2.59
1537 3329 1.215647 CGTCCCTGAGGCTGTACAC 59.784 63.158 0.00 0.00 0.00 2.90
1695 3487 1.674359 TGCCAGCGTCTTCTTTCAAA 58.326 45.000 0.00 0.00 0.00 2.69
1755 3547 9.181805 GAAGTTCTTAGCCAAAATTAACAGAAC 57.818 33.333 0.00 0.00 34.10 3.01
1773 3585 3.645687 AGTCAGCCTCTTCTGAAGTTCTT 59.354 43.478 16.43 0.32 43.89 2.52
1776 3588 3.676291 GAGTCAGCCTCTTCTGAAGTT 57.324 47.619 16.43 0.00 43.89 2.66
1786 3598 6.963083 TCTAATTAACCTAGAGTCAGCCTC 57.037 41.667 0.00 0.00 40.80 4.70
1787 3599 7.014808 GTGATCTAATTAACCTAGAGTCAGCCT 59.985 40.741 0.00 0.00 0.00 4.58
1788 3600 7.149307 GTGATCTAATTAACCTAGAGTCAGCC 58.851 42.308 0.00 0.00 0.00 4.85
1789 3601 7.014808 AGGTGATCTAATTAACCTAGAGTCAGC 59.985 40.741 4.99 17.32 41.28 4.26
1790 3602 8.356657 CAGGTGATCTAATTAACCTAGAGTCAG 58.643 40.741 6.31 0.00 41.14 3.51
1791 3603 7.839705 ACAGGTGATCTAATTAACCTAGAGTCA 59.160 37.037 6.31 4.53 41.14 3.41
1792 3604 8.138712 CACAGGTGATCTAATTAACCTAGAGTC 58.861 40.741 6.31 0.00 41.14 3.36
1793 3605 7.070074 CCACAGGTGATCTAATTAACCTAGAGT 59.930 40.741 6.31 0.00 41.14 3.24
1794 3606 7.070074 ACCACAGGTGATCTAATTAACCTAGAG 59.930 40.741 6.31 2.15 41.14 2.43
1795 3607 6.901300 ACCACAGGTGATCTAATTAACCTAGA 59.099 38.462 6.31 0.00 41.14 2.43
1796 3608 7.125792 ACCACAGGTGATCTAATTAACCTAG 57.874 40.000 6.31 4.82 41.14 3.02
1838 3650 6.127814 GGTCCTAATTAGTTAAGGCCACAAAC 60.128 42.308 5.01 6.11 28.40 2.93
1839 3651 5.947566 GGTCCTAATTAGTTAAGGCCACAAA 59.052 40.000 5.01 0.00 28.40 2.83
1842 3654 5.104652 TCAGGTCCTAATTAGTTAAGGCCAC 60.105 44.000 5.01 0.00 29.95 5.01
1845 3657 8.594550 TCATATCAGGTCCTAATTAGTTAAGGC 58.405 37.037 11.50 0.00 0.00 4.35
1849 3661 8.877195 GGGTTCATATCAGGTCCTAATTAGTTA 58.123 37.037 11.50 0.00 0.00 2.24
1850 3662 7.349859 TGGGTTCATATCAGGTCCTAATTAGTT 59.650 37.037 11.50 0.00 0.00 2.24
1852 3664 7.316393 TGGGTTCATATCAGGTCCTAATTAG 57.684 40.000 5.43 5.43 0.00 1.73
1905 3771 5.536538 AGTGTACACAAACAGAGATGAGAGA 59.463 40.000 27.06 0.00 0.00 3.10
1906 3772 5.777802 AGTGTACACAAACAGAGATGAGAG 58.222 41.667 27.06 0.00 0.00 3.20
1907 3773 5.791336 AGTGTACACAAACAGAGATGAGA 57.209 39.130 27.06 0.00 0.00 3.27
1908 3774 5.755375 ACAAGTGTACACAAACAGAGATGAG 59.245 40.000 27.06 3.60 0.00 2.90
1909 3775 5.670485 ACAAGTGTACACAAACAGAGATGA 58.330 37.500 27.06 0.00 0.00 2.92
1910 3776 5.991328 ACAAGTGTACACAAACAGAGATG 57.009 39.130 27.06 12.95 0.00 2.90
1911 3777 6.349300 AGAACAAGTGTACACAAACAGAGAT 58.651 36.000 27.06 0.61 0.00 2.75
1925 3791 4.340617 TGAAACAAGGGAAGAACAAGTGT 58.659 39.130 0.00 0.00 0.00 3.55
1939 3805 3.866910 ACTGCATTGCAAACTGAAACAAG 59.133 39.130 13.18 0.00 38.41 3.16
1948 3814 1.774639 CACCAGACTGCATTGCAAAC 58.225 50.000 13.18 9.38 38.41 2.93
1995 3861 3.674410 GCAGGGCTAAATTCAGAAACAGC 60.674 47.826 5.74 5.74 0.00 4.40
2052 3918 9.588774 CATTTGCTACTGAAAAATGAACAAATG 57.411 29.630 9.41 9.41 41.64 2.32
2060 3926 4.092383 GCCTGCATTTGCTACTGAAAAATG 59.908 41.667 3.94 0.00 41.88 2.32
2079 3945 0.519077 GGAGCGAAAAACAGAGCCTG 59.481 55.000 0.00 1.16 37.52 4.85
2093 3960 3.923017 AACCAAATTCAGAAAGGAGCG 57.077 42.857 6.65 0.00 0.00 5.03
2108 3976 0.871722 CGGATCAACTGCGAAACCAA 59.128 50.000 0.00 0.00 41.93 3.67
2114 3982 1.144969 GTTCAACGGATCAACTGCGA 58.855 50.000 0.00 0.00 41.93 5.10
2124 3992 0.233590 CGCGACAAATGTTCAACGGA 59.766 50.000 0.00 0.00 0.00 4.69
2160 4028 6.654582 AGAATGCAACAAGAAACAAAACCTTT 59.345 30.769 0.00 0.00 0.00 3.11
2205 4346 7.824779 ACAGGTAATCTAATCAAGAGTCAAACC 59.175 37.037 0.00 0.00 37.74 3.27
2233 4442 0.250124 CCCACGAACAGTAGTGCCAA 60.250 55.000 0.00 0.00 37.07 4.52
2252 4461 7.039784 TGGGTTCATATCATGCCTTAATTAAGC 60.040 37.037 18.18 14.00 32.02 3.09
2263 4472 3.057033 GGAGCATTGGGTTCATATCATGC 60.057 47.826 0.00 0.00 0.00 4.06
2295 4504 7.820872 CACATATACACATGATAGCATTCAGGA 59.179 37.037 0.00 0.00 32.03 3.86
2300 4509 6.938596 AGTGCACATATACACATGATAGCATT 59.061 34.615 21.04 0.00 39.30 3.56
2360 4569 7.053498 TCAATGACTTATTTGCTAGCACCATA 58.947 34.615 19.17 13.88 0.00 2.74
2376 4585 4.943705 AGAACCGCATACATTCAATGACTT 59.056 37.500 3.79 0.00 0.00 3.01
2388 4597 2.857592 TCTTACCGAGAACCGCATAC 57.142 50.000 0.00 0.00 36.84 2.39
2420 5662 7.892609 TCTGAGACTACATTTGCAACTAGTAA 58.107 34.615 0.00 0.00 0.00 2.24
2423 5665 7.840342 AATCTGAGACTACATTTGCAACTAG 57.160 36.000 0.00 0.93 0.00 2.57
2451 5698 5.395103 CCACAACCAAATTCAGAAAGGTGAA 60.395 40.000 6.17 0.00 40.68 3.18
2452 5699 4.099266 CCACAACCAAATTCAGAAAGGTGA 59.901 41.667 6.17 0.00 31.86 4.02
2475 5722 4.425577 AAAATGCTCGACCATTCAACTC 57.574 40.909 6.42 0.00 34.50 3.01
2528 5775 8.844244 GCATCAGTTTATCAGGATATGAAAAGT 58.156 33.333 0.00 0.00 42.53 2.66
2532 5779 6.870439 CGAGCATCAGTTTATCAGGATATGAA 59.130 38.462 0.00 0.00 36.80 2.57
2553 5800 3.989698 TTCTGCAGTAGCGCCGAGC 62.990 63.158 14.67 3.98 46.23 5.03
2556 5803 2.528743 CCATTCTGCAGTAGCGCCG 61.529 63.158 14.67 0.00 46.23 6.46
2609 5856 4.495690 AACCCCTCTAGAAGCAGAAATC 57.504 45.455 0.00 0.00 0.00 2.17
2621 5868 5.006896 TCTGAGTCTACAAAACCCCTCTA 57.993 43.478 0.00 0.00 0.00 2.43
2622 5869 3.858135 TCTGAGTCTACAAAACCCCTCT 58.142 45.455 0.00 0.00 0.00 3.69
2623 5870 4.020128 ACATCTGAGTCTACAAAACCCCTC 60.020 45.833 0.00 0.00 0.00 4.30
2624 5871 3.910627 ACATCTGAGTCTACAAAACCCCT 59.089 43.478 0.00 0.00 0.00 4.79
2625 5872 4.287766 ACATCTGAGTCTACAAAACCCC 57.712 45.455 0.00 0.00 0.00 4.95
2626 5873 6.635030 AAAACATCTGAGTCTACAAAACCC 57.365 37.500 0.00 0.00 0.00 4.11
2627 5874 8.149973 TGTAAAACATCTGAGTCTACAAAACC 57.850 34.615 0.00 0.00 0.00 3.27
2673 5920 2.903798 TCAATCAGTGCGCATGTATCA 58.096 42.857 15.91 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.