Multiple sequence alignment - TraesCS2B01G356800

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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 TraesCS2B01G356800 chr2B 100.000 3154 0 0 1 3154 509576030 509572877 0.000000e+00 5825.0
1 TraesCS2B01G356800 chr2B 94.568 1215 28 10 1961 3154 509996188 509994991 0.000000e+00 1844.0
2 TraesCS2B01G356800 chr2B 85.336 1623 147 32 1083 2662 510062094 510060520 0.000000e+00 1594.0
3 TraesCS2B01G356800 chr2B 92.344 1071 52 9 917 1962 509997415 509996350 0.000000e+00 1496.0
4 TraesCS2B01G356800 chr2B 85.591 1270 123 20 1083 2326 510350278 510349043 0.000000e+00 1277.0
5 TraesCS2B01G356800 chr2B 82.687 1392 116 49 1325 2662 509707444 509706124 0.000000e+00 1120.0
6 TraesCS2B01G356800 chr2B 88.298 470 43 7 29 496 510066328 510065869 1.280000e-153 553.0
7 TraesCS2B01G356800 chr2B 86.150 361 33 10 2808 3154 510348635 510348278 1.070000e-99 374.0
8 TraesCS2B01G356800 chr2B 93.200 250 17 0 1083 1332 509713120 509712871 4.970000e-98 368.0
9 TraesCS2B01G356800 chr2B 90.960 177 9 4 910 1084 510350479 510350308 6.800000e-57 231.0
10 TraesCS2B01G356800 chr2B 80.110 362 28 19 2805 3154 509706129 509705800 2.450000e-56 230.0
11 TraesCS2B01G356800 chr2B 79.558 362 32 16 2805 3154 510060525 510060194 1.470000e-53 220.0
12 TraesCS2B01G356800 chr2B 81.773 203 32 5 498 698 734326570 734326371 7.000000e-37 165.0
13 TraesCS2B01G356800 chr2B 81.633 196 18 8 890 1084 510062304 510062126 2.530000e-31 147.0
14 TraesCS2B01G356800 chr2B 78.531 177 8 9 910 1084 509713298 509713150 4.330000e-14 89.8
15 TraesCS2B01G356800 chr2D 93.682 1662 65 14 910 2544 431385834 431384186 0.000000e+00 2451.0
16 TraesCS2B01G356800 chr2D 94.887 1154 26 7 2016 3154 431004771 431003636 0.000000e+00 1773.0
17 TraesCS2B01G356800 chr2D 92.545 1100 52 10 914 1988 431005860 431004766 0.000000e+00 1550.0
18 TraesCS2B01G356800 chr2D 95.276 635 6 4 2535 3154 431382202 431381577 0.000000e+00 985.0
19 TraesCS2B01G356800 chr2D 88.015 826 64 16 1858 2662 431425972 431425161 0.000000e+00 944.0
20 TraesCS2B01G356800 chr2D 84.908 815 73 14 1083 1871 431428953 431428163 0.000000e+00 778.0
21 TraesCS2B01G356800 chr2D 90.960 177 9 3 910 1084 431429154 431428983 6.800000e-57 231.0
22 TraesCS2B01G356800 chr2D 79.834 362 28 19 2805 3154 431425166 431424838 4.090000e-54 222.0
23 TraesCS2B01G356800 chr2A 86.443 922 83 19 1768 2662 554954160 554955066 0.000000e+00 972.0
24 TraesCS2B01G356800 chr2A 87.671 365 24 12 2805 3154 554955061 554955419 3.790000e-109 405.0
25 TraesCS2B01G356800 chr2A 89.266 177 12 3 910 1084 554953025 554953196 6.850000e-52 215.0
26 TraesCS2B01G356800 chr5B 86.713 715 65 16 1965 2662 100837780 100838481 0.000000e+00 767.0
27 TraesCS2B01G356800 chr5B 86.721 369 22 15 2805 3154 100838476 100838836 4.930000e-103 385.0
28 TraesCS2B01G356800 chr4B 82.920 726 94 16 1 699 40912801 40913523 7.430000e-176 627.0
29 TraesCS2B01G356800 chr1D 82.544 739 79 12 1 699 483354286 483353558 3.480000e-169 604.0
30 TraesCS2B01G356800 chr1D 78.455 738 102 20 1 699 382748490 382749209 2.250000e-116 429.0
31 TraesCS2B01G356800 chr4D 80.159 756 91 29 1 699 358619802 358619049 7.800000e-141 510.0
32 TraesCS2B01G356800 chr4D 77.551 441 47 28 308 699 66651923 66651486 5.300000e-53 219.0
33 TraesCS2B01G356800 chr7D 80.081 738 101 17 1 697 368569057 368569789 1.010000e-139 507.0
34 TraesCS2B01G356800 chr7D 83.333 492 65 9 1 486 12553143 12552663 3.730000e-119 438.0
35 TraesCS2B01G356800 chr7D 82.591 494 78 4 1 486 21032327 21032820 2.250000e-116 429.0
36 TraesCS2B01G356800 chr7D 87.821 156 15 3 2661 2812 83654423 83654268 2.500000e-41 180.0
37 TraesCS2B01G356800 chr5D 85.163 492 63 7 1 486 301586165 301585678 2.190000e-136 496.0
38 TraesCS2B01G356800 chr6D 83.878 490 65 10 6 486 316628891 316629375 3.710000e-124 455.0
39 TraesCS2B01G356800 chr6D 89.109 101 11 0 778 878 42407247 42407347 3.300000e-25 126.0
40 TraesCS2B01G356800 chr1B 82.364 550 65 14 1 527 660942727 660943267 1.730000e-122 449.0
41 TraesCS2B01G356800 chr1B 84.971 173 25 1 707 879 621981473 621981302 1.160000e-39 174.0
42 TraesCS2B01G356800 chr1B 80.117 171 23 2 527 697 156589925 156590084 1.990000e-22 117.0
43 TraesCS2B01G356800 chr1B 80.117 171 23 2 527 697 156590985 156591144 1.990000e-22 117.0
44 TraesCS2B01G356800 chr1B 91.026 78 6 1 498 575 660943260 660943336 1.550000e-18 104.0
45 TraesCS2B01G356800 chr3D 88.816 152 15 1 2660 2809 307237063 307237214 5.370000e-43 185.0
46 TraesCS2B01G356800 chr3D 87.421 159 17 2 2656 2812 120289845 120290002 2.500000e-41 180.0
47 TraesCS2B01G356800 chrUn 87.742 155 13 3 2661 2809 31873106 31873260 3.230000e-40 176.0
48 TraesCS2B01G356800 chr3A 84.091 176 22 5 2651 2822 745072587 745072414 7.000000e-37 165.0
49 TraesCS2B01G356800 chr3A 83.523 176 23 5 2651 2822 744995494 744995321 3.260000e-35 159.0
50 TraesCS2B01G356800 chr6A 82.486 177 27 4 704 878 259778762 259778936 5.450000e-33 152.0
51 TraesCS2B01G356800 chr6A 82.386 176 28 3 704 878 259781339 259781512 1.960000e-32 150.0
52 TraesCS2B01G356800 chr7B 79.730 222 30 11 486 699 6791704 6791490 2.530000e-31 147.0


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 TraesCS2B01G356800 chr2B 509572877 509576030 3153 True 5825.000000 5825 100.000000 1 3154 1 chr2B.!!$R1 3153
1 TraesCS2B01G356800 chr2B 509994991 509997415 2424 True 1670.000000 1844 93.456000 917 3154 2 chr2B.!!$R5 2237
2 TraesCS2B01G356800 chr2B 509705800 509707444 1644 True 675.000000 1120 81.398500 1325 3154 2 chr2B.!!$R3 1829
3 TraesCS2B01G356800 chr2B 510060194 510066328 6134 True 628.500000 1594 83.706250 29 3154 4 chr2B.!!$R6 3125
4 TraesCS2B01G356800 chr2B 510348278 510350479 2201 True 627.333333 1277 87.567000 910 3154 3 chr2B.!!$R7 2244
5 TraesCS2B01G356800 chr2D 431381577 431385834 4257 True 1718.000000 2451 94.479000 910 3154 2 chr2D.!!$R2 2244
6 TraesCS2B01G356800 chr2D 431003636 431005860 2224 True 1661.500000 1773 93.716000 914 3154 2 chr2D.!!$R1 2240
7 TraesCS2B01G356800 chr2D 431424838 431429154 4316 True 543.750000 944 85.929250 910 3154 4 chr2D.!!$R3 2244
8 TraesCS2B01G356800 chr2A 554953025 554955419 2394 False 530.666667 972 87.793333 910 3154 3 chr2A.!!$F1 2244
9 TraesCS2B01G356800 chr5B 100837780 100838836 1056 False 576.000000 767 86.717000 1965 3154 2 chr5B.!!$F1 1189
10 TraesCS2B01G356800 chr4B 40912801 40913523 722 False 627.000000 627 82.920000 1 699 1 chr4B.!!$F1 698
11 TraesCS2B01G356800 chr1D 483353558 483354286 728 True 604.000000 604 82.544000 1 699 1 chr1D.!!$R1 698
12 TraesCS2B01G356800 chr1D 382748490 382749209 719 False 429.000000 429 78.455000 1 699 1 chr1D.!!$F1 698
13 TraesCS2B01G356800 chr4D 358619049 358619802 753 True 510.000000 510 80.159000 1 699 1 chr4D.!!$R2 698
14 TraesCS2B01G356800 chr7D 368569057 368569789 732 False 507.000000 507 80.081000 1 697 1 chr7D.!!$F2 696
15 TraesCS2B01G356800 chr1B 660942727 660943336 609 False 276.500000 449 86.695000 1 575 2 chr1B.!!$F2 574

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
701 1663 0.179163 GCGGCGCTATTTCAAGCTTT 60.179 50.0 26.86 0.0 40.49 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2409 8812 2.200373 ATGTGGGCCTGACTTTGTAC 57.8 50.0 4.53 0.0 0.0 2.9 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
136 141 1.687493 CTTCTCCTCCTCCCGCCTT 60.687 63.158 0.00 0.00 0.00 4.35
193 199 0.372679 GAGCGAGTACGACGACATGA 59.627 55.000 16.85 0.00 42.66 3.07
393 403 2.668632 CAAGGCGACCTAGGGCAA 59.331 61.111 16.92 0.00 31.13 4.52
395 405 1.918800 AAGGCGACCTAGGGCAAGT 60.919 57.895 16.92 0.00 31.13 3.16
397 407 2.820037 GCGACCTAGGGCAAGTGC 60.820 66.667 16.92 5.87 41.14 4.40
438 475 2.600769 AAGGAGCAGGACGACGGT 60.601 61.111 0.00 0.00 0.00 4.83
576 1321 1.025113 TGTGTCGTGTTTGGCCGAAA 61.025 50.000 7.10 1.29 34.47 3.46
582 1327 2.099263 TCGTGTTTGGCCGAAATTTTGA 59.901 40.909 7.10 0.00 0.00 2.69
648 1429 1.527380 GGTTGGGAAACTGACCGCA 60.527 57.895 0.00 0.00 0.00 5.69
653 1434 1.837439 TGGGAAACTGACCGCATCTAT 59.163 47.619 0.00 0.00 0.00 1.98
699 1661 1.026718 AAGCGGCGCTATTTCAAGCT 61.027 50.000 36.59 13.56 38.25 3.74
700 1662 1.026718 AGCGGCGCTATTTCAAGCTT 61.027 50.000 35.68 3.86 40.49 3.74
701 1663 0.179163 GCGGCGCTATTTCAAGCTTT 60.179 50.000 26.86 0.00 40.49 3.51
702 1664 1.063469 GCGGCGCTATTTCAAGCTTTA 59.937 47.619 26.86 0.00 40.49 1.85
703 1665 2.287009 GCGGCGCTATTTCAAGCTTTAT 60.287 45.455 26.86 0.00 40.49 1.40
704 1666 3.059188 GCGGCGCTATTTCAAGCTTTATA 60.059 43.478 26.86 0.00 40.49 0.98
706 1668 5.689819 CGGCGCTATTTCAAGCTTTATAAT 58.310 37.500 7.64 0.00 40.49 1.28
707 1669 5.565259 CGGCGCTATTTCAAGCTTTATAATG 59.435 40.000 7.64 0.00 40.49 1.90
708 1670 5.858581 GGCGCTATTTCAAGCTTTATAATGG 59.141 40.000 7.64 0.28 40.49 3.16
709 1671 6.438763 GCGCTATTTCAAGCTTTATAATGGT 58.561 36.000 0.00 0.00 40.49 3.55
711 1673 8.073768 GCGCTATTTCAAGCTTTATAATGGTTA 58.926 33.333 13.52 2.29 40.49 2.85
712 1674 9.599322 CGCTATTTCAAGCTTTATAATGGTTAG 57.401 33.333 13.52 9.38 40.49 2.34
713 1675 9.399403 GCTATTTCAAGCTTTATAATGGTTAGC 57.601 33.333 13.52 13.90 39.50 3.09
719 1681 9.456147 TCAAGCTTTATAATGGTTAGCTAAACA 57.544 29.630 25.74 25.74 41.05 2.83
720 1682 9.503427 CAAGCTTTATAATGGTTAGCTAAACAC 57.497 33.333 26.04 10.95 41.05 3.32
721 1683 8.221965 AGCTTTATAATGGTTAGCTAAACACC 57.778 34.615 26.04 15.66 40.19 4.16
723 1685 8.129211 GCTTTATAATGGTTAGCTAAACACCTG 58.871 37.037 26.04 12.65 40.08 4.00
726 1688 9.826574 TTATAATGGTTAGCTAAACACCTGTAG 57.173 33.333 26.04 0.00 40.08 2.74
727 1689 6.368779 AATGGTTAGCTAAACACCTGTAGA 57.631 37.500 26.04 1.16 40.08 2.59
728 1690 5.811796 TGGTTAGCTAAACACCTGTAGAA 57.188 39.130 20.33 0.00 40.08 2.10
729 1691 6.177310 TGGTTAGCTAAACACCTGTAGAAA 57.823 37.500 20.33 0.00 40.08 2.52
731 1693 6.183361 TGGTTAGCTAAACACCTGTAGAAAGT 60.183 38.462 20.33 0.00 40.08 2.66
732 1694 6.147328 GGTTAGCTAAACACCTGTAGAAAGTG 59.853 42.308 16.80 0.00 40.08 3.16
734 1696 3.813166 GCTAAACACCTGTAGAAAGTGCA 59.187 43.478 0.00 0.00 34.83 4.57
740 1702 2.440539 CTGTAGAAAGTGCAGGTCGT 57.559 50.000 0.00 0.00 35.33 4.34
741 1703 2.329379 CTGTAGAAAGTGCAGGTCGTC 58.671 52.381 0.00 0.00 35.33 4.20
742 1704 1.684450 TGTAGAAAGTGCAGGTCGTCA 59.316 47.619 0.00 0.00 0.00 4.35
755 1790 1.536149 GTCGTCAGTTCGATTCTCCG 58.464 55.000 0.00 0.00 41.78 4.63
770 1805 0.240945 CTCCGCTGTTCCGCAATTTT 59.759 50.000 0.00 0.00 0.00 1.82
783 1818 7.708752 TGTTCCGCAATTTTCTGAATAGTTTTT 59.291 29.630 0.00 0.00 0.00 1.94
784 1819 7.636259 TCCGCAATTTTCTGAATAGTTTTTG 57.364 32.000 0.00 0.00 0.00 2.44
785 1820 6.145371 TCCGCAATTTTCTGAATAGTTTTTGC 59.855 34.615 6.75 6.75 34.97 3.68
804 1839 5.476752 TTGCGCTTTTTGTTAGCATTTTT 57.523 30.435 9.73 0.00 38.55 1.94
808 1843 3.658988 GCTTTTTGTTAGCATTTTTGCGC 59.341 39.130 0.00 0.00 38.51 6.09
864 1899 2.202570 GAGCGCCGCGTCTCTTAA 60.203 61.111 22.02 0.00 31.32 1.85
865 1900 1.589196 GAGCGCCGCGTCTCTTAAT 60.589 57.895 22.02 0.00 31.32 1.40
866 1901 1.541439 GAGCGCCGCGTCTCTTAATC 61.541 60.000 22.02 2.41 31.32 1.75
868 1903 2.293627 CGCCGCGTCTCTTAATCGG 61.294 63.158 4.92 0.00 42.68 4.18
869 1904 3.614143 CCGCGTCTCTTAATCGGC 58.386 61.111 4.92 0.00 33.36 5.54
870 1905 2.293627 CCGCGTCTCTTAATCGGCG 61.294 63.158 4.92 0.00 33.36 6.46
871 1906 2.917656 CGCGTCTCTTAATCGGCGC 61.918 63.158 0.00 11.64 41.21 6.53
872 1907 2.586773 GCGTCTCTTAATCGGCGCC 61.587 63.158 19.07 19.07 39.11 6.53
873 1908 1.065928 CGTCTCTTAATCGGCGCCT 59.934 57.895 26.68 8.66 0.00 5.52
874 1909 1.209275 CGTCTCTTAATCGGCGCCTG 61.209 60.000 26.68 18.23 0.00 4.85
875 1910 1.227263 TCTCTTAATCGGCGCCTGC 60.227 57.895 26.68 0.00 41.71 4.85
876 1911 1.521457 CTCTTAATCGGCGCCTGCA 60.521 57.895 26.68 8.65 45.35 4.41
877 1912 1.493950 CTCTTAATCGGCGCCTGCAG 61.494 60.000 26.68 6.78 45.35 4.41
878 1913 2.513666 TTAATCGGCGCCTGCAGG 60.514 61.111 29.34 29.34 45.35 4.85
879 1914 2.923426 CTTAATCGGCGCCTGCAGGA 62.923 60.000 37.21 15.82 45.35 3.86
880 1915 2.923426 TTAATCGGCGCCTGCAGGAG 62.923 60.000 37.21 33.52 45.35 3.69
888 4116 3.478274 CCTGCAGGAGCTCCCCTC 61.478 72.222 29.88 18.07 42.74 4.30
902 4130 2.373502 CTCCCCTCTTTTATGCCCTAGG 59.626 54.545 0.06 0.06 0.00 3.02
911 4139 0.399091 TATGCCCTAGGTGCAGCTCT 60.399 55.000 23.94 13.34 42.92 4.09
957 4186 2.237751 AATTCGGGCGCTCGATTCG 61.238 57.895 35.53 14.47 39.03 3.34
958 4187 2.622903 AATTCGGGCGCTCGATTCGA 62.623 55.000 35.53 19.89 39.03 3.71
959 4188 2.421877 ATTCGGGCGCTCGATTCGAT 62.422 55.000 35.53 21.44 39.03 3.59
960 4189 2.622903 TTCGGGCGCTCGATTCGATT 62.623 55.000 35.53 0.00 39.03 3.34
962 4191 2.310966 GGGCGCTCGATTCGATTCC 61.311 63.158 9.54 10.38 34.61 3.01
963 4192 1.300233 GGCGCTCGATTCGATTCCT 60.300 57.895 9.54 0.00 34.61 3.36
964 4193 1.552348 GGCGCTCGATTCGATTCCTG 61.552 60.000 9.54 0.00 34.61 3.86
965 4194 1.552348 GCGCTCGATTCGATTCCTGG 61.552 60.000 9.54 0.00 34.61 4.45
975 4204 3.798954 GATTCCTGGCTCGCCTCGG 62.799 68.421 9.65 9.61 36.94 4.63
1035 4264 3.704231 GACCACATCCATGGGCGCT 62.704 63.158 13.02 0.00 44.81 5.92
1086 4348 9.468532 AAGTAAGAATCAAAACTGAATCTTTGC 57.531 29.630 9.95 5.43 38.53 3.68
1090 4352 4.652421 TCAAAACTGAATCTTTGCTGCA 57.348 36.364 0.00 0.00 33.45 4.41
1105 4367 4.654412 GCATCGAGCCGCCGATCT 62.654 66.667 12.13 0.00 46.26 2.75
1165 4427 3.453679 GAGCGGAGGAGCGGAAGT 61.454 66.667 0.00 0.00 43.00 3.01
1232 4617 6.369059 AGAATCCAATCGATTTGTGTGATC 57.631 37.500 8.21 1.42 41.47 2.92
1377 5243 0.101759 GCGGTGATGAGCATTGCAAT 59.898 50.000 11.91 5.99 31.95 3.56
1397 5263 3.319137 TGGAGAAGTCGTTGGATGAAG 57.681 47.619 0.00 0.00 0.00 3.02
1654 5554 7.279981 TGAATCGATAATTTGTTTCTCGTGGAT 59.720 33.333 0.00 0.00 35.90 3.41
1752 5652 3.815962 TGTAACTTTTGCCGTGCTGATTA 59.184 39.130 0.00 0.00 0.00 1.75
1753 5653 4.457603 TGTAACTTTTGCCGTGCTGATTAT 59.542 37.500 0.00 0.00 0.00 1.28
1754 5654 3.764885 ACTTTTGCCGTGCTGATTATC 57.235 42.857 0.00 0.00 0.00 1.75
1924 8048 3.872182 GACTTTACCCTGCTAAGCTAAGC 59.128 47.826 0.00 0.00 43.08 3.09
2072 8363 7.581213 TTTCTTTCTTGTTGATCCAGCTTAA 57.419 32.000 0.00 0.00 0.00 1.85
2167 8464 7.500227 TCTGAAAATGTGAACAGACAAGATCTT 59.500 33.333 0.88 0.88 34.41 2.40
2190 8495 9.219603 TCTTTAAGATGTGTTTGAATAGGTGAG 57.780 33.333 0.00 0.00 0.00 3.51
2409 8812 1.002366 GCCTCTCATGTGCGTGTTAG 58.998 55.000 0.00 0.00 0.00 2.34
2510 8930 6.331369 TCCAAAAACAGGAGAACATGATTC 57.669 37.500 0.00 0.00 0.00 2.52
2635 11049 7.816945 AATTCAGCTTTTGATTGGATAAACG 57.183 32.000 0.00 0.00 35.27 3.60
2976 11409 5.805486 GCTGATATTGTTCGTTCAGTGTCTA 59.195 40.000 0.00 0.00 38.26 2.59
2979 11412 8.185003 TGATATTGTTCGTTCAGTGTCTATTG 57.815 34.615 0.00 0.00 0.00 1.90
2981 11414 6.861065 ATTGTTCGTTCAGTGTCTATTGTT 57.139 33.333 0.00 0.00 0.00 2.83
2984 11417 7.079182 TGTTCGTTCAGTGTCTATTGTTTTT 57.921 32.000 0.00 0.00 0.00 1.94
2988 11421 7.184106 TCGTTCAGTGTCTATTGTTTTTGTTC 58.816 34.615 0.00 0.00 0.00 3.18
2989 11422 6.964370 CGTTCAGTGTCTATTGTTTTTGTTCA 59.036 34.615 0.00 0.00 0.00 3.18
2992 11425 8.725405 TCAGTGTCTATTGTTTTTGTTCAGTA 57.275 30.769 0.00 0.00 0.00 2.74
2993 11426 9.168451 TCAGTGTCTATTGTTTTTGTTCAGTAA 57.832 29.630 0.00 0.00 0.00 2.24
2994 11427 9.950680 CAGTGTCTATTGTTTTTGTTCAGTAAT 57.049 29.630 0.00 0.00 0.00 1.89
2995 11428 9.950680 AGTGTCTATTGTTTTTGTTCAGTAATG 57.049 29.630 0.00 0.00 0.00 1.90
2996 11429 9.180678 GTGTCTATTGTTTTTGTTCAGTAATGG 57.819 33.333 0.00 0.00 0.00 3.16
2997 11430 7.865385 TGTCTATTGTTTTTGTTCAGTAATGGC 59.135 33.333 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 4.147449 CCCGAGCGGCATCTCACA 62.147 66.667 1.45 0.00 33.41 3.58
120 122 2.364317 CAAGGCGGGAGGAGGAGA 60.364 66.667 0.00 0.00 0.00 3.71
154 159 2.709125 TTCACAGCGACGAACCCCAG 62.709 60.000 0.00 0.00 0.00 4.45
393 403 1.450312 GCCATCCTTACTGCGCACT 60.450 57.895 5.66 0.00 0.00 4.40
395 405 1.450134 CTGCCATCCTTACTGCGCA 60.450 57.895 10.98 10.98 0.00 6.09
397 407 0.391661 ACACTGCCATCCTTACTGCG 60.392 55.000 0.00 0.00 0.00 5.18
582 1327 6.583427 GCCGTTATTTGAAAAATAAACTCGGT 59.417 34.615 21.43 0.00 34.05 4.69
622 1403 4.646877 TTTCCCAACCGCCGTCCC 62.647 66.667 0.00 0.00 0.00 4.46
623 1404 3.359523 GTTTCCCAACCGCCGTCC 61.360 66.667 0.00 0.00 0.00 4.79
624 1405 2.281276 AGTTTCCCAACCGCCGTC 60.281 61.111 0.00 0.00 32.70 4.79
648 1429 5.292834 CGCCGATGAAAATATCAGCATAGAT 59.707 40.000 0.00 0.00 44.81 1.98
653 1434 1.264020 GCGCCGATGAAAATATCAGCA 59.736 47.619 0.00 0.00 44.81 4.41
681 1643 1.026718 AAGCTTGAAATAGCGCCGCT 61.027 50.000 18.67 18.67 45.82 5.52
700 1662 9.826574 CTACAGGTGTTTAGCTAACCATTATAA 57.173 33.333 14.19 0.00 36.37 0.98
701 1663 9.204337 TCTACAGGTGTTTAGCTAACCATTATA 57.796 33.333 14.19 2.72 36.37 0.98
702 1664 8.086143 TCTACAGGTGTTTAGCTAACCATTAT 57.914 34.615 14.19 1.81 36.37 1.28
703 1665 7.484993 TCTACAGGTGTTTAGCTAACCATTA 57.515 36.000 14.19 5.16 36.37 1.90
704 1666 6.368779 TCTACAGGTGTTTAGCTAACCATT 57.631 37.500 14.19 4.38 36.37 3.16
706 1668 5.811796 TTCTACAGGTGTTTAGCTAACCA 57.188 39.130 14.19 7.69 36.37 3.67
707 1669 6.147328 CACTTTCTACAGGTGTTTAGCTAACC 59.853 42.308 5.45 5.25 35.81 2.85
708 1670 6.347483 GCACTTTCTACAGGTGTTTAGCTAAC 60.347 42.308 5.45 2.54 37.26 2.34
709 1671 5.699458 GCACTTTCTACAGGTGTTTAGCTAA 59.301 40.000 0.86 0.86 32.36 3.09
711 1673 4.065789 GCACTTTCTACAGGTGTTTAGCT 58.934 43.478 0.00 0.00 33.96 3.32
712 1674 3.813166 TGCACTTTCTACAGGTGTTTAGC 59.187 43.478 0.00 0.00 33.96 3.09
713 1675 4.452455 CCTGCACTTTCTACAGGTGTTTAG 59.548 45.833 0.00 0.00 44.91 1.85
715 1677 3.214328 CCTGCACTTTCTACAGGTGTTT 58.786 45.455 0.00 0.00 44.91 2.83
716 1678 2.851195 CCTGCACTTTCTACAGGTGTT 58.149 47.619 0.00 0.00 44.91 3.32
717 1679 2.550830 CCTGCACTTTCTACAGGTGT 57.449 50.000 0.00 0.00 44.91 4.16
721 1683 2.288213 TGACGACCTGCACTTTCTACAG 60.288 50.000 0.00 0.00 0.00 2.74
723 1685 2.288273 ACTGACGACCTGCACTTTCTAC 60.288 50.000 0.00 0.00 0.00 2.59
725 1687 0.753262 ACTGACGACCTGCACTTTCT 59.247 50.000 0.00 0.00 0.00 2.52
726 1688 1.527311 GAACTGACGACCTGCACTTTC 59.473 52.381 0.00 0.00 0.00 2.62
727 1689 1.583054 GAACTGACGACCTGCACTTT 58.417 50.000 0.00 0.00 0.00 2.66
728 1690 0.597637 CGAACTGACGACCTGCACTT 60.598 55.000 0.00 0.00 35.09 3.16
729 1691 1.007271 CGAACTGACGACCTGCACT 60.007 57.895 0.00 0.00 35.09 4.40
731 1693 0.317160 AATCGAACTGACGACCTGCA 59.683 50.000 0.00 0.00 44.84 4.41
732 1694 0.992802 GAATCGAACTGACGACCTGC 59.007 55.000 0.00 0.00 44.84 4.85
734 1696 1.473278 GGAGAATCGAACTGACGACCT 59.527 52.381 0.00 0.00 44.84 3.85
736 1698 1.536149 CGGAGAATCGAACTGACGAC 58.464 55.000 0.00 0.00 44.84 4.34
738 1700 0.179161 AGCGGAGAATCGAACTGACG 60.179 55.000 0.00 1.06 34.37 4.35
739 1701 1.272781 CAGCGGAGAATCGAACTGAC 58.727 55.000 0.00 0.00 33.47 3.51
740 1702 0.888619 ACAGCGGAGAATCGAACTGA 59.111 50.000 0.00 0.00 34.73 3.41
741 1703 1.656095 GAACAGCGGAGAATCGAACTG 59.344 52.381 0.00 0.00 36.44 3.16
742 1704 1.404315 GGAACAGCGGAGAATCGAACT 60.404 52.381 0.00 0.00 34.37 3.01
755 1790 2.704725 TCAGAAAATTGCGGAACAGC 57.295 45.000 0.00 0.00 37.71 4.40
770 1805 6.039616 ACAAAAAGCGCAAAAACTATTCAGA 58.960 32.000 11.47 0.00 0.00 3.27
783 1818 4.784710 GCAAAAATGCTAACAAAAAGCGCA 60.785 37.500 11.47 0.00 43.11 6.09
784 1819 3.658988 GCAAAAATGCTAACAAAAAGCGC 59.341 39.130 0.00 0.00 43.11 5.92
785 1820 3.893709 CGCAAAAATGCTAACAAAAAGCG 59.106 39.130 0.00 0.00 43.11 4.68
846 1881 4.531912 TAAGAGACGCGGCGCTCG 62.532 66.667 30.54 17.87 42.76 5.03
847 1882 1.541439 GATTAAGAGACGCGGCGCTC 61.541 60.000 30.54 27.43 33.03 5.03
850 1885 2.293627 CCGATTAAGAGACGCGGCG 61.294 63.158 22.36 22.36 35.17 6.46
851 1886 3.614143 CCGATTAAGAGACGCGGC 58.386 61.111 12.47 7.86 35.17 6.53
852 1887 2.293627 CGCCGATTAAGAGACGCGG 61.294 63.158 12.47 0.00 44.47 6.46
853 1888 2.917656 GCGCCGATTAAGAGACGCG 61.918 63.158 3.53 3.53 36.76 6.01
855 1890 1.065928 AGGCGCCGATTAAGAGACG 59.934 57.895 23.20 0.00 0.00 4.18
857 1892 1.227263 GCAGGCGCCGATTAAGAGA 60.227 57.895 23.20 0.00 0.00 3.10
858 1893 1.493950 CTGCAGGCGCCGATTAAGAG 61.494 60.000 23.20 7.50 37.32 2.85
859 1894 1.521457 CTGCAGGCGCCGATTAAGA 60.521 57.895 23.20 0.73 37.32 2.10
860 1895 2.537560 CCTGCAGGCGCCGATTAAG 61.538 63.158 22.33 15.06 37.32 1.85
861 1896 2.513666 CCTGCAGGCGCCGATTAA 60.514 61.111 22.33 5.44 37.32 1.40
862 1897 3.445518 CTCCTGCAGGCGCCGATTA 62.446 63.158 28.91 7.14 37.32 1.75
871 1906 3.478274 GAGGGGAGCTCCTGCAGG 61.478 72.222 31.36 27.87 42.74 4.85
872 1907 1.560866 AAAGAGGGGAGCTCCTGCAG 61.561 60.000 31.36 6.78 42.74 4.41
873 1908 1.136329 AAAAGAGGGGAGCTCCTGCA 61.136 55.000 31.36 0.00 42.74 4.41
874 1909 0.912486 TAAAAGAGGGGAGCTCCTGC 59.088 55.000 31.36 19.99 37.25 4.85
875 1910 2.747799 GCATAAAAGAGGGGAGCTCCTG 60.748 54.545 31.36 18.96 37.25 3.86
876 1911 1.492599 GCATAAAAGAGGGGAGCTCCT 59.507 52.381 31.36 13.94 40.43 3.69
877 1912 1.477740 GGCATAAAAGAGGGGAGCTCC 60.478 57.143 25.59 25.59 0.00 4.70
878 1913 1.477740 GGGCATAAAAGAGGGGAGCTC 60.478 57.143 4.71 4.71 0.00 4.09
879 1914 0.553333 GGGCATAAAAGAGGGGAGCT 59.447 55.000 0.00 0.00 0.00 4.09
880 1915 0.553333 AGGGCATAAAAGAGGGGAGC 59.447 55.000 0.00 0.00 0.00 4.70
882 1917 2.294263 ACCTAGGGCATAAAAGAGGGGA 60.294 50.000 14.81 0.00 0.00 4.81
883 1918 2.136026 ACCTAGGGCATAAAAGAGGGG 58.864 52.381 14.81 0.00 0.00 4.79
884 1919 2.749800 GCACCTAGGGCATAAAAGAGGG 60.750 54.545 14.81 0.00 0.00 4.30
885 1920 2.092429 TGCACCTAGGGCATAAAAGAGG 60.092 50.000 17.87 0.00 36.11 3.69
888 4116 1.678101 GCTGCACCTAGGGCATAAAAG 59.322 52.381 20.87 12.42 41.06 2.27
902 4130 1.016653 GGAAACGAGGAGAGCTGCAC 61.017 60.000 1.02 0.00 0.00 4.57
911 4139 1.675219 CGGGGAAAGGAAACGAGGA 59.325 57.895 0.00 0.00 0.00 3.71
957 4186 2.279784 CGAGGCGAGCCAGGAATC 60.280 66.667 17.18 3.64 38.92 2.52
958 4187 3.854669 CCGAGGCGAGCCAGGAAT 61.855 66.667 19.28 0.00 38.05 3.01
975 4204 0.321653 AACAACAGGTGAGATCGGCC 60.322 55.000 0.00 0.00 0.00 6.13
1043 4272 2.701163 CTTGCTATCGGCCTCGTCCC 62.701 65.000 0.00 0.00 40.92 4.46
1056 4285 9.507329 AGATTCAGTTTTGATTCTTACTTGCTA 57.493 29.630 0.00 0.00 39.71 3.49
1086 4348 4.957684 ATCGGCGGCTCGATGCAG 62.958 66.667 20.28 6.05 46.52 4.41
1105 4367 5.209818 CTGCGTAGGAATCCAAGGTTATA 57.790 43.478 0.61 0.00 0.00 0.98
1165 4427 1.118965 TTCCTGCACTTGGTCGAGGA 61.119 55.000 0.00 0.00 0.00 3.71
1232 4617 6.279513 TGCACCAAAATTAACCTCTATTGG 57.720 37.500 0.00 0.00 42.29 3.16
1377 5243 2.897326 TCTTCATCCAACGACTTCTCCA 59.103 45.455 0.00 0.00 0.00 3.86
1654 5554 8.082242 GCAGCTTTCCTTTTAATCTGAAAGTTA 58.918 33.333 16.20 0.00 43.43 2.24
1752 5652 6.820152 CCATCCATGTATGTATCATCAACGAT 59.180 38.462 0.00 0.00 0.00 3.73
1753 5653 6.014669 TCCATCCATGTATGTATCATCAACGA 60.015 38.462 0.00 0.00 0.00 3.85
1754 5654 6.165577 TCCATCCATGTATGTATCATCAACG 58.834 40.000 0.00 0.00 0.00 4.10
1850 5761 3.717707 TGTCTCAACCTTCTTGAACTCG 58.282 45.455 0.00 0.00 0.00 4.18
1924 8048 8.205512 AGAGCATTATTATATCTGCAGAGGATG 58.794 37.037 22.96 16.32 37.09 3.51
1925 8049 8.321621 AGAGCATTATTATATCTGCAGAGGAT 57.678 34.615 22.96 18.91 37.09 3.24
1926 8050 7.730672 AGAGCATTATTATATCTGCAGAGGA 57.269 36.000 22.96 12.96 37.09 3.71
1927 8051 8.789825 AAAGAGCATTATTATATCTGCAGAGG 57.210 34.615 22.96 0.00 37.09 3.69
1928 8052 9.433153 TGAAAGAGCATTATTATATCTGCAGAG 57.567 33.333 22.96 6.01 37.09 3.35
1929 8053 9.955102 ATGAAAGAGCATTATTATATCTGCAGA 57.045 29.630 20.79 20.79 37.09 4.26
1931 8055 9.729281 TGATGAAAGAGCATTATTATATCTGCA 57.271 29.630 9.08 0.00 37.09 4.41
1932 8056 9.985318 GTGATGAAAGAGCATTATTATATCTGC 57.015 33.333 0.00 0.73 34.85 4.26
2086 8383 6.301169 ACTTCAGTGTCTATAAGGGAAAGG 57.699 41.667 0.00 0.00 0.00 3.11
2167 8464 8.783093 CAACTCACCTATTCAAACACATCTTAA 58.217 33.333 0.00 0.00 0.00 1.85
2190 8495 7.795272 CACAGATAGCAAAAAGAAAAATGCAAC 59.205 33.333 0.00 0.00 41.18 4.17
2409 8812 2.200373 ATGTGGGCCTGACTTTGTAC 57.800 50.000 4.53 0.00 0.00 2.90
2510 8930 6.200665 GCACTCATTCTACTTCTATTGCTGAG 59.799 42.308 0.00 0.00 35.04 3.35
2976 11409 5.596845 ACGCCATTACTGAACAAAAACAAT 58.403 33.333 0.00 0.00 0.00 2.71
2979 11412 6.399564 GCATTACGCCATTACTGAACAAAAAC 60.400 38.462 0.00 0.00 32.94 2.43
2981 11414 5.048364 AGCATTACGCCATTACTGAACAAAA 60.048 36.000 0.00 0.00 44.04 2.44
2984 11417 3.373748 CAGCATTACGCCATTACTGAACA 59.626 43.478 0.00 0.00 44.04 3.18
2988 11421 4.342772 GTTTCAGCATTACGCCATTACTG 58.657 43.478 0.00 0.00 44.04 2.74
2989 11422 3.063452 CGTTTCAGCATTACGCCATTACT 59.937 43.478 0.00 0.00 44.04 2.24
2992 11425 2.080693 TCGTTTCAGCATTACGCCATT 58.919 42.857 0.00 0.00 44.04 3.16
2993 11426 1.732941 TCGTTTCAGCATTACGCCAT 58.267 45.000 0.00 0.00 44.04 4.40
2994 11427 1.732941 ATCGTTTCAGCATTACGCCA 58.267 45.000 0.00 0.00 44.04 5.69
2995 11428 2.095213 TGAATCGTTTCAGCATTACGCC 59.905 45.455 4.80 0.00 44.04 5.68
2996 11429 3.383546 TGAATCGTTTCAGCATTACGC 57.616 42.857 4.80 0.00 36.94 4.42


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

AutoCloner maintained by Alex Coulton.