Multiple sequence alignment - TraesCS1A01G124100

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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 TraesCS1A01G124100 chr1A 100.000 2812 0 0 1 2812 145987761 145990572 0.000000e+00 5193.0
1 TraesCS1A01G124100 chr1A 88.276 290 32 2 1 289 395477400 395477688 2.070000e-91 346.0
2 TraesCS1A01G124100 chr1A 81.910 398 50 11 32 425 567632099 567632478 1.630000e-82 316.0
3 TraesCS1A01G124100 chr1A 84.295 312 27 13 457 768 440151703 440151992 4.580000e-73 285.0
4 TraesCS1A01G124100 chr1A 77.886 511 64 20 285 769 567632964 567633451 3.570000e-69 272.0
5 TraesCS1A01G124100 chr1B 95.676 1110 28 4 815 1918 193004687 193003592 0.000000e+00 1766.0
6 TraesCS1A01G124100 chr1B 90.461 912 53 10 1921 2810 193003485 193002586 0.000000e+00 1171.0
7 TraesCS1A01G124100 chr1B 100.000 44 0 0 767 810 193004768 193004725 6.460000e-12 82.4
8 TraesCS1A01G124100 chr1D 95.112 982 15 7 766 1743 143439483 143438531 0.000000e+00 1517.0
9 TraesCS1A01G124100 chr1D 84.022 726 71 29 2097 2801 143438186 143437485 0.000000e+00 656.0
10 TraesCS1A01G124100 chr1D 94.190 327 14 2 1786 2109 143438533 143438209 7.000000e-136 494.0
11 TraesCS1A01G124100 chr5A 92.562 484 35 1 284 767 7492476 7491994 0.000000e+00 693.0
12 TraesCS1A01G124100 chr5A 89.376 433 42 2 342 774 465283624 465283196 2.460000e-150 542.0
13 TraesCS1A01G124100 chr5A 81.961 571 51 30 1 549 5292125 5292665 1.200000e-118 436.0
14 TraesCS1A01G124100 chr5A 91.279 172 15 0 285 456 5292319 5292490 4.680000e-58 235.0
15 TraesCS1A01G124100 chr5A 86.634 202 24 2 199 400 465283712 465283514 1.310000e-53 220.0
16 TraesCS1A01G124100 chr5A 85.354 198 20 1 572 769 5292618 5292806 2.210000e-46 196.0
17 TraesCS1A01G124100 chr4A 90.714 420 39 0 350 769 679265508 679265089 6.800000e-156 560.0
18 TraesCS1A01G124100 chr4A 81.436 571 54 30 1 549 616209007 616209547 1.200000e-113 420.0
19 TraesCS1A01G124100 chr4A 89.965 289 29 0 1 289 586443825 586443537 9.510000e-100 374.0
20 TraesCS1A01G124100 chr4A 77.167 600 82 30 195 769 616209147 616209716 5.890000e-77 298.0
21 TraesCS1A01G124100 chr4A 83.636 330 28 9 457 769 606787715 606787395 1.270000e-73 287.0
22 TraesCS1A01G124100 chr4A 90.643 171 16 0 285 455 134204202 134204032 7.840000e-56 228.0
23 TraesCS1A01G124100 chr4A 90.173 173 17 0 285 457 616209201 616209373 2.820000e-55 226.0
24 TraesCS1A01G124100 chr7A 81.436 571 54 31 1 549 603528209 603528749 1.200000e-113 420.0
25 TraesCS1A01G124100 chr7A 90.311 289 28 0 1 289 520058914 520058626 2.040000e-101 379.0
26 TraesCS1A01G124100 chr7A 76.373 601 86 25 195 769 603528349 603528919 3.570000e-69 272.0
27 TraesCS1A01G124100 chr7A 80.645 310 51 7 2399 2702 197291464 197291770 6.060000e-57 231.0
28 TraesCS1A01G124100 chr7A 89.595 173 18 0 285 457 603528403 603528575 1.310000e-53 220.0
29 TraesCS1A01G124100 chr5D 90.064 312 30 1 457 767 359001640 359001951 1.210000e-108 403.0
30 TraesCS1A01G124100 chr5D 81.429 350 31 13 10 354 358998986 358999306 3.590000e-64 255.0
31 TraesCS1A01G124100 chr2A 90.647 278 26 0 3 280 645309171 645308894 1.230000e-98 370.0
32 TraesCS1A01G124100 chr2A 79.814 322 45 15 2389 2704 680540201 680540508 1.700000e-52 217.0
33 TraesCS1A01G124100 chr3A 89.384 292 29 2 1 292 175810763 175811052 1.590000e-97 366.0
34 TraesCS1A01G124100 chr3A 87.586 290 34 2 1 289 27657853 27658141 4.490000e-88 335.0
35 TraesCS1A01G124100 chr3A 86.387 191 17 1 579 769 175811636 175811817 1.710000e-47 200.0
36 TraesCS1A01G124100 chr3A 90.588 85 5 2 2573 2657 666227275 666227356 2.960000e-20 110.0
37 TraesCS1A01G124100 chr7D 79.565 460 72 14 2250 2704 461647354 461647796 2.720000e-80 309.0
38 TraesCS1A01G124100 chr5B 82.422 256 29 12 2458 2704 14279007 14279255 2.840000e-50 209.0
39 TraesCS1A01G124100 chr2D 78.641 309 56 6 2400 2704 538316203 538316505 2.210000e-46 196.0
40 TraesCS1A01G124100 chr2B 78.387 310 53 11 2400 2704 641186189 641186489 3.700000e-44 189.0
41 TraesCS1A01G124100 chr2B 74.627 201 41 7 2255 2451 462208016 462207822 2.320000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G124100 chr1A 145987761 145990572 2811 False 5193.000000 5193 100.000000 1 2812 1 chr1A.!!$F1 2811
1 TraesCS1A01G124100 chr1A 567632099 567633451 1352 False 294.000000 316 79.898000 32 769 2 chr1A.!!$F4 737
2 TraesCS1A01G124100 chr1B 193002586 193004768 2182 True 1006.466667 1766 95.379000 767 2810 3 chr1B.!!$R1 2043
3 TraesCS1A01G124100 chr1D 143437485 143439483 1998 True 889.000000 1517 91.108000 766 2801 3 chr1D.!!$R1 2035
4 TraesCS1A01G124100 chr5A 465283196 465283712 516 True 381.000000 542 88.005000 199 774 2 chr5A.!!$R2 575
5 TraesCS1A01G124100 chr5A 5292125 5292806 681 False 289.000000 436 86.198000 1 769 3 chr5A.!!$F1 768
6 TraesCS1A01G124100 chr4A 616209007 616209716 709 False 314.666667 420 82.925333 1 769 3 chr4A.!!$F1 768
7 TraesCS1A01G124100 chr7A 603528209 603528919 710 False 304.000000 420 82.468000 1 769 3 chr7A.!!$F2 768
8 TraesCS1A01G124100 chr5D 358998986 359001951 2965 False 329.000000 403 85.746500 10 767 2 chr5D.!!$F1 757
9 TraesCS1A01G124100 chr3A 175810763 175811817 1054 False 283.000000 366 87.885500 1 769 2 chr3A.!!$F3 768

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
567 3818 0.103208 GCGTGAGGGTGATAGGACAG 59.897 60.0 0.0 0.0 0.0 3.51 F
1021 4321 0.242017 ACGTTTTCCTCCTACCGTCG 59.758 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 5055 0.109643 TCATGAACAAGTGCGCATGC 60.110 50.0 15.91 7.91 38.34 4.06 R
2312 5833 0.391661 TTCTGCACCATCTTCGCTCC 60.392 55.0 0.00 0.00 0.00 4.70 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
20 21 3.948719 GCCTGTTGTCCGTCCCCA 61.949 66.667 0.00 0.00 0.00 4.96
26 27 3.122727 TTGTCCGTCCCCAACCCAC 62.123 63.158 0.00 0.00 0.00 4.61
28 29 2.773053 TCCGTCCCCAACCCACAA 60.773 61.111 0.00 0.00 0.00 3.33
40 41 1.703411 ACCCACAACTGACCCAAATG 58.297 50.000 0.00 0.00 0.00 2.32
95 96 4.379243 CTCTCGCCCACCGCTGTT 62.379 66.667 0.00 0.00 36.73 3.16
171 172 2.509336 CCATCGGTGCTGGTCGTC 60.509 66.667 0.00 0.00 0.00 4.20
172 173 2.261361 CATCGGTGCTGGTCGTCA 59.739 61.111 0.00 0.00 0.00 4.35
174 175 3.296709 ATCGGTGCTGGTCGTCACC 62.297 63.158 1.54 1.54 46.95 4.02
225 226 4.760047 GCCATCGGTGCTGGTCGT 62.760 66.667 0.00 0.00 36.10 4.34
228 229 1.807165 CATCGGTGCTGGTCGTCAG 60.807 63.158 4.59 4.59 46.03 3.51
497 3280 0.107848 GAAAAATCTCGCGGGGGAGA 60.108 55.000 16.38 16.38 46.37 3.71
541 3792 3.141488 GGCGCGAGGGAGAGAGAA 61.141 66.667 12.10 0.00 0.00 2.87
542 3793 2.411290 GCGCGAGGGAGAGAGAAG 59.589 66.667 12.10 0.00 0.00 2.85
543 3794 3.115556 CGCGAGGGAGAGAGAAGG 58.884 66.667 0.00 0.00 0.00 3.46
544 3795 2.485795 CGCGAGGGAGAGAGAAGGG 61.486 68.421 0.00 0.00 0.00 3.95
545 3796 2.131067 GCGAGGGAGAGAGAAGGGG 61.131 68.421 0.00 0.00 0.00 4.79
546 3797 2.131067 CGAGGGAGAGAGAAGGGGC 61.131 68.421 0.00 0.00 0.00 5.80
547 3798 2.042435 AGGGAGAGAGAAGGGGCG 60.042 66.667 0.00 0.00 0.00 6.13
548 3799 3.157949 GGGAGAGAGAAGGGGCGG 61.158 72.222 0.00 0.00 0.00 6.13
549 3800 3.855853 GGAGAGAGAAGGGGCGGC 61.856 72.222 0.00 0.00 0.00 6.53
550 3801 4.214327 GAGAGAGAAGGGGCGGCG 62.214 72.222 0.51 0.51 0.00 6.46
552 3803 4.821589 GAGAGAAGGGGCGGCGTG 62.822 72.222 9.37 0.00 0.00 5.34
554 3805 4.821589 GAGAAGGGGCGGCGTGAG 62.822 72.222 9.37 0.00 0.00 3.51
561 3812 3.845259 GGCGGCGTGAGGGTGATA 61.845 66.667 9.37 0.00 0.00 2.15
562 3813 2.279517 GCGGCGTGAGGGTGATAG 60.280 66.667 9.37 0.00 0.00 2.08
563 3814 2.417516 CGGCGTGAGGGTGATAGG 59.582 66.667 0.00 0.00 0.00 2.57
564 3815 2.125326 CGGCGTGAGGGTGATAGGA 61.125 63.158 0.00 0.00 0.00 2.94
565 3816 1.442148 GGCGTGAGGGTGATAGGAC 59.558 63.158 0.00 0.00 0.00 3.85
566 3817 1.327690 GGCGTGAGGGTGATAGGACA 61.328 60.000 0.00 0.00 0.00 4.02
567 3818 0.103208 GCGTGAGGGTGATAGGACAG 59.897 60.000 0.00 0.00 0.00 3.51
568 3819 0.747255 CGTGAGGGTGATAGGACAGG 59.253 60.000 0.00 0.00 0.00 4.00
569 3820 0.466124 GTGAGGGTGATAGGACAGGC 59.534 60.000 0.00 0.00 0.00 4.85
570 3821 1.043116 TGAGGGTGATAGGACAGGCG 61.043 60.000 0.00 0.00 0.00 5.52
571 3822 2.109181 GGGTGATAGGACAGGCGC 59.891 66.667 0.00 0.00 0.00 6.53
572 3823 2.109181 GGTGATAGGACAGGCGCC 59.891 66.667 21.89 21.89 0.00 6.53
573 3824 2.279517 GTGATAGGACAGGCGCCG 60.280 66.667 23.20 18.60 0.00 6.46
574 3825 4.221422 TGATAGGACAGGCGCCGC 62.221 66.667 23.20 14.72 0.00 6.53
617 3868 2.614013 GGGAGAAAGGAGGGGGCA 60.614 66.667 0.00 0.00 0.00 5.36
618 3869 2.009302 GGGAGAAAGGAGGGGGCAT 61.009 63.158 0.00 0.00 0.00 4.40
619 3870 0.697854 GGGAGAAAGGAGGGGGCATA 60.698 60.000 0.00 0.00 0.00 3.14
622 3873 0.326238 AGAAAGGAGGGGGCATACGA 60.326 55.000 0.00 0.00 0.00 3.43
677 3929 3.855159 GGATACAAGCCTTGTCCGT 57.145 52.632 14.46 1.42 44.12 4.69
685 3937 1.303317 GCCTTGTCCGTCCCATGTT 60.303 57.895 0.00 0.00 0.00 2.71
704 3956 3.221222 GCTAGGCGGACAGGTGAT 58.779 61.111 0.00 0.00 0.00 3.06
810 4063 5.091910 TGTACACGATGCTACTATTCTCG 57.908 43.478 0.00 0.00 35.56 4.04
811 4064 4.812626 TGTACACGATGCTACTATTCTCGA 59.187 41.667 0.00 0.00 33.74 4.04
812 4065 4.895224 ACACGATGCTACTATTCTCGAA 57.105 40.909 0.00 0.00 33.74 3.71
818 4104 5.232202 CGATGCTACTATTCTCGAAAAAGCA 59.768 40.000 0.00 0.00 42.34 3.91
846 4132 2.151502 ACTGAGTCCACGATCCAGAT 57.848 50.000 0.00 0.00 0.00 2.90
847 4133 2.028130 ACTGAGTCCACGATCCAGATC 58.972 52.381 0.00 0.00 34.56 2.75
855 4141 2.419198 GATCCAGATCGTGCCGCT 59.581 61.111 0.00 0.00 0.00 5.52
994 4294 4.796231 CGAGTTCAGTCCGCCCCG 62.796 72.222 0.00 0.00 0.00 5.73
1021 4321 0.242017 ACGTTTTCCTCCTACCGTCG 59.758 55.000 0.00 0.00 0.00 5.12
1022 4322 1.074872 CGTTTTCCTCCTACCGTCGC 61.075 60.000 0.00 0.00 0.00 5.19
1023 4323 0.738762 GTTTTCCTCCTACCGTCGCC 60.739 60.000 0.00 0.00 0.00 5.54
1024 4324 2.216750 TTTTCCTCCTACCGTCGCCG 62.217 60.000 0.00 0.00 0.00 6.46
1289 4592 1.600957 CTCGCGCATTTCTCCATGAAT 59.399 47.619 8.75 0.00 34.24 2.57
1622 4925 0.319083 GGTACACATCCGTCACACCA 59.681 55.000 0.00 0.00 0.00 4.17
1705 5008 3.218453 TGTGAATTGTGTTCCGTGGATT 58.782 40.909 0.00 0.00 0.00 3.01
1744 5047 9.620660 AATTATTTTGTTGAGTTGTATCCGTTC 57.379 29.630 0.00 0.00 0.00 3.95
1745 5048 6.877611 ATTTTGTTGAGTTGTATCCGTTCT 57.122 33.333 0.00 0.00 0.00 3.01
1746 5049 6.687081 TTTTGTTGAGTTGTATCCGTTCTT 57.313 33.333 0.00 0.00 0.00 2.52
1747 5050 7.789273 TTTTGTTGAGTTGTATCCGTTCTTA 57.211 32.000 0.00 0.00 0.00 2.10
1748 5051 7.789273 TTTGTTGAGTTGTATCCGTTCTTAA 57.211 32.000 0.00 0.00 0.00 1.85
1749 5052 7.972832 TTGTTGAGTTGTATCCGTTCTTAAT 57.027 32.000 0.00 0.00 0.00 1.40
1750 5053 7.591006 TGTTGAGTTGTATCCGTTCTTAATC 57.409 36.000 0.00 0.00 0.00 1.75
1751 5054 6.592607 TGTTGAGTTGTATCCGTTCTTAATCC 59.407 38.462 0.00 0.00 0.00 3.01
1752 5055 5.345702 TGAGTTGTATCCGTTCTTAATCCG 58.654 41.667 0.00 0.00 0.00 4.18
1753 5056 4.117685 AGTTGTATCCGTTCTTAATCCGC 58.882 43.478 0.00 0.00 0.00 5.54
1754 5057 3.804786 TGTATCCGTTCTTAATCCGCA 57.195 42.857 0.00 0.00 0.00 5.69
1755 5058 4.330944 TGTATCCGTTCTTAATCCGCAT 57.669 40.909 0.00 0.00 0.00 4.73
1756 5059 4.055360 TGTATCCGTTCTTAATCCGCATG 58.945 43.478 0.00 0.00 0.00 4.06
1757 5060 1.295792 TCCGTTCTTAATCCGCATGC 58.704 50.000 7.91 7.91 0.00 4.06
1758 5061 0.042188 CCGTTCTTAATCCGCATGCG 60.042 55.000 32.60 32.60 39.44 4.73
1759 5062 0.654472 CGTTCTTAATCCGCATGCGC 60.654 55.000 34.00 15.83 38.24 6.09
1760 5063 0.376852 GTTCTTAATCCGCATGCGCA 59.623 50.000 34.00 22.51 38.40 6.09
1761 5064 0.376852 TTCTTAATCCGCATGCGCAC 59.623 50.000 34.00 0.00 38.40 5.34
1762 5065 0.461870 TCTTAATCCGCATGCGCACT 60.462 50.000 34.00 20.83 38.40 4.40
1763 5066 0.378257 CTTAATCCGCATGCGCACTT 59.622 50.000 34.00 25.22 38.40 3.16
1764 5067 0.098552 TTAATCCGCATGCGCACTTG 59.901 50.000 34.00 19.95 38.40 3.16
1765 5068 1.024046 TAATCCGCATGCGCACTTGT 61.024 50.000 34.00 16.68 38.40 3.16
1766 5069 1.865788 AATCCGCATGCGCACTTGTT 61.866 50.000 34.00 17.15 38.40 2.83
1767 5070 2.257286 ATCCGCATGCGCACTTGTTC 62.257 55.000 34.00 0.00 38.40 3.18
1768 5071 2.251963 CGCATGCGCACTTGTTCA 59.748 55.556 29.09 0.00 38.40 3.18
1769 5072 1.154169 CGCATGCGCACTTGTTCAT 60.154 52.632 29.09 0.00 38.40 2.57
1770 5073 1.400246 CGCATGCGCACTTGTTCATG 61.400 55.000 29.09 5.44 39.29 3.07
1771 5074 0.109643 GCATGCGCACTTGTTCATGA 60.110 50.000 14.90 0.00 38.77 3.07
1772 5075 1.666599 GCATGCGCACTTGTTCATGAA 60.667 47.619 14.90 3.38 38.77 2.57
1773 5076 2.871133 CATGCGCACTTGTTCATGAAT 58.129 42.857 14.90 0.00 38.77 2.57
1774 5077 3.731565 GCATGCGCACTTGTTCATGAATA 60.732 43.478 14.90 6.04 38.77 1.75
1775 5078 4.413969 CATGCGCACTTGTTCATGAATAA 58.586 39.130 14.90 14.21 38.77 1.40
1776 5079 4.700268 TGCGCACTTGTTCATGAATAAT 57.300 36.364 16.75 6.17 0.00 1.28
1777 5080 5.809719 TGCGCACTTGTTCATGAATAATA 57.190 34.783 16.75 0.00 0.00 0.98
1778 5081 5.568482 TGCGCACTTGTTCATGAATAATAC 58.432 37.500 16.75 9.21 0.00 1.89
1779 5082 5.353956 TGCGCACTTGTTCATGAATAATACT 59.646 36.000 16.75 1.98 0.00 2.12
1780 5083 5.904080 GCGCACTTGTTCATGAATAATACTC 59.096 40.000 16.75 7.14 0.00 2.59
1781 5084 6.422223 CGCACTTGTTCATGAATAATACTCC 58.578 40.000 16.75 0.27 0.00 3.85
1782 5085 6.422223 GCACTTGTTCATGAATAATACTCCG 58.578 40.000 16.75 7.80 0.00 4.63
1783 5086 6.037172 GCACTTGTTCATGAATAATACTCCGT 59.963 38.462 16.75 8.36 0.00 4.69
1784 5087 7.223971 GCACTTGTTCATGAATAATACTCCGTA 59.776 37.037 16.75 0.00 0.00 4.02
1803 5144 3.480825 CGTACGTGCGAAATAAGTGTTCC 60.481 47.826 21.98 0.00 0.00 3.62
1822 5163 8.143835 AGTGTTCCTGTTCCATTTTTATCTTTG 58.856 33.333 0.00 0.00 0.00 2.77
1949 5394 0.444260 GCTTAGCTCACAAGGCGTTC 59.556 55.000 0.00 0.00 34.52 3.95
1999 5444 2.115910 TTGCCTTGTGCTCCAGGG 59.884 61.111 7.90 4.64 43.13 4.45
2045 5490 3.417069 TTGAGATTGGGACGTTGATGT 57.583 42.857 0.00 0.00 0.00 3.06
2212 5715 1.004277 TGCTAGGGATGAAAACGGCTT 59.996 47.619 0.00 0.00 0.00 4.35
2217 5720 2.962421 AGGGATGAAAACGGCTTGAAAA 59.038 40.909 0.00 0.00 0.00 2.29
2220 5723 3.491792 GGATGAAAACGGCTTGAAAACCA 60.492 43.478 0.00 0.00 0.00 3.67
2222 5725 3.254892 TGAAAACGGCTTGAAAACCAAC 58.745 40.909 0.00 0.00 0.00 3.77
2227 5730 2.116366 CGGCTTGAAAACCAACGAAAG 58.884 47.619 0.00 0.00 0.00 2.62
2266 5786 8.767085 CATTTGTGAAAGCAGAAACAAATACAT 58.233 29.630 15.64 0.00 46.28 2.29
2312 5833 5.675778 ACATACTATCGAAAACGAACACG 57.324 39.130 0.00 0.00 0.00 4.49
2378 5899 5.903010 ACCAGAACTTAAAAACCCCTTGAAT 59.097 36.000 0.00 0.00 0.00 2.57
2538 6062 5.473504 GTGGTAATTAGACATAAGGGCCATG 59.526 44.000 6.18 3.97 0.00 3.66
2554 6078 4.647399 GGGCCATGTATAAGCAAAACCTAA 59.353 41.667 4.39 0.00 0.00 2.69
2571 6095 8.960591 CAAAACCTAATGTATCAGGTCATCTTT 58.039 33.333 0.00 0.00 44.55 2.52
2661 6185 6.183360 CCATTATGGTTACAATCAGGGCAAAT 60.183 38.462 2.48 0.00 31.35 2.32
2696 6220 1.423541 ACAGAAGTTGGGCCACACATA 59.576 47.619 5.23 0.00 0.00 2.29
2728 6252 4.304537 TGTGTGATGTTTGATGGTTGTG 57.695 40.909 0.00 0.00 0.00 3.33
2748 6279 2.486203 TGTTGCTAACGGCTTAACATGG 59.514 45.455 0.00 0.00 42.39 3.66
2783 6315 9.554395 CCAACAACCTAACAAAAGGAAAATAAT 57.446 29.630 0.00 0.00 39.15 1.28
2802 6334 7.759489 AATAATGTTAAGAGAAAGGCACACA 57.241 32.000 0.00 0.00 0.00 3.72
2807 6339 0.546122 AGAGAAAGGCACACACACCA 59.454 50.000 0.00 0.00 0.00 4.17
2810 6342 0.248458 GAAAGGCACACACACCAACG 60.248 55.000 0.00 0.00 0.00 4.10
2811 6343 0.963355 AAAGGCACACACACCAACGT 60.963 50.000 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.773053 TGGGTTGGGGACGGACAA 60.773 61.111 0.00 0.00 0.00 3.18
20 21 2.038659 CATTTGGGTCAGTTGTGGGTT 58.961 47.619 0.00 0.00 0.00 4.11
40 41 3.119137 GCTTCATACCCATTTGTTCCCAC 60.119 47.826 0.00 0.00 0.00 4.61
157 158 3.986006 GGTGACGACCAGCACCGA 61.986 66.667 0.00 0.00 44.39 4.69
196 197 3.818787 GATGGCCTTGCTGCGGTG 61.819 66.667 3.32 0.00 0.00 4.94
497 3280 0.184933 CTCTCCTCCTCACGGATCCT 59.815 60.000 10.75 0.00 39.01 3.24
505 3288 3.015332 GCCCCTCCTCTCCTCCTCA 62.015 68.421 0.00 0.00 0.00 3.86
544 3795 3.792053 CTATCACCCTCACGCCGCC 62.792 68.421 0.00 0.00 0.00 6.13
545 3796 2.279517 CTATCACCCTCACGCCGC 60.280 66.667 0.00 0.00 0.00 6.53
546 3797 2.125326 TCCTATCACCCTCACGCCG 61.125 63.158 0.00 0.00 0.00 6.46
547 3798 1.327690 TGTCCTATCACCCTCACGCC 61.328 60.000 0.00 0.00 0.00 5.68
548 3799 0.103208 CTGTCCTATCACCCTCACGC 59.897 60.000 0.00 0.00 0.00 5.34
549 3800 0.747255 CCTGTCCTATCACCCTCACG 59.253 60.000 0.00 0.00 0.00 4.35
550 3801 0.466124 GCCTGTCCTATCACCCTCAC 59.534 60.000 0.00 0.00 0.00 3.51
551 3802 1.043116 CGCCTGTCCTATCACCCTCA 61.043 60.000 0.00 0.00 0.00 3.86
552 3803 1.742768 CGCCTGTCCTATCACCCTC 59.257 63.158 0.00 0.00 0.00 4.30
553 3804 2.435693 GCGCCTGTCCTATCACCCT 61.436 63.158 0.00 0.00 0.00 4.34
554 3805 2.109181 GCGCCTGTCCTATCACCC 59.891 66.667 0.00 0.00 0.00 4.61
555 3806 2.109181 GGCGCCTGTCCTATCACC 59.891 66.667 22.15 0.00 0.00 4.02
556 3807 2.279517 CGGCGCCTGTCCTATCAC 60.280 66.667 26.68 0.00 0.00 3.06
557 3808 4.221422 GCGGCGCCTGTCCTATCA 62.221 66.667 26.68 0.00 0.00 2.15
571 3822 4.493747 GTCCCCTTCTCGTCGCGG 62.494 72.222 6.13 0.00 0.00 6.46
572 3823 4.831307 CGTCCCCTTCTCGTCGCG 62.831 72.222 0.00 0.00 0.00 5.87
573 3824 4.493747 CCGTCCCCTTCTCGTCGC 62.494 72.222 0.00 0.00 0.00 5.19
574 3825 3.823330 CCCGTCCCCTTCTCGTCG 61.823 72.222 0.00 0.00 0.00 5.12
575 3826 4.144703 GCCCGTCCCCTTCTCGTC 62.145 72.222 0.00 0.00 0.00 4.20
606 3857 2.432300 CGTCGTATGCCCCCTCCTT 61.432 63.158 0.00 0.00 0.00 3.36
617 3868 0.179145 CCAAACTCTCCGCGTCGTAT 60.179 55.000 4.92 0.00 0.00 3.06
618 3869 1.210931 CCAAACTCTCCGCGTCGTA 59.789 57.895 4.92 0.00 0.00 3.43
619 3870 2.049433 CCAAACTCTCCGCGTCGT 60.049 61.111 4.92 0.00 0.00 4.34
622 3873 2.207924 AGACCCAAACTCTCCGCGT 61.208 57.895 4.92 0.00 0.00 6.01
668 3920 1.019278 CGAACATGGGACGGACAAGG 61.019 60.000 0.00 0.00 0.00 3.61
704 3956 0.651551 CCGTTTCGTGTTCGTTTGGA 59.348 50.000 0.00 0.00 38.33 3.53
810 4063 6.261158 GGACTCAGTTATCCCTATGCTTTTTC 59.739 42.308 0.00 0.00 0.00 2.29
811 4064 6.122964 GGACTCAGTTATCCCTATGCTTTTT 58.877 40.000 0.00 0.00 0.00 1.94
812 4065 5.191722 TGGACTCAGTTATCCCTATGCTTTT 59.808 40.000 0.00 0.00 33.69 2.27
818 4104 4.180377 TCGTGGACTCAGTTATCCCTAT 57.820 45.455 0.00 0.00 33.69 2.57
848 4134 1.019805 GGACTTGTAGGAAGCGGCAC 61.020 60.000 1.45 0.00 0.00 5.01
849 4135 1.295423 GGACTTGTAGGAAGCGGCA 59.705 57.895 1.45 0.00 0.00 5.69
850 4136 1.019805 GTGGACTTGTAGGAAGCGGC 61.020 60.000 0.00 0.00 0.00 6.53
851 4137 0.391263 GGTGGACTTGTAGGAAGCGG 60.391 60.000 0.00 0.00 0.00 5.52
852 4138 0.608640 AGGTGGACTTGTAGGAAGCG 59.391 55.000 0.00 0.00 0.00 4.68
853 4139 2.168728 CCTAGGTGGACTTGTAGGAAGC 59.831 54.545 0.00 0.00 34.99 3.86
854 4140 2.168728 GCCTAGGTGGACTTGTAGGAAG 59.831 54.545 11.31 0.00 34.99 3.46
855 4141 2.185387 GCCTAGGTGGACTTGTAGGAA 58.815 52.381 11.31 0.00 34.99 3.36
994 4294 1.658114 GAGGAAAACGTGTTGGGGC 59.342 57.895 0.00 0.00 0.00 5.80
1409 4712 1.153549 GTGGCCGAAGAGAGCGAAT 60.154 57.895 0.00 0.00 0.00 3.34
1410 4713 2.261671 GTGGCCGAAGAGAGCGAA 59.738 61.111 0.00 0.00 0.00 4.70
1499 4802 0.907704 AGGTGAGGATGTTGCCGGTA 60.908 55.000 1.90 0.00 0.00 4.02
1611 4914 4.293648 CTGCGGTGGTGTGACGGA 62.294 66.667 0.00 0.00 0.00 4.69
1622 4925 0.964358 AAGACTAGTACGGCTGCGGT 60.964 55.000 17.06 17.06 0.00 5.68
1705 5008 6.007936 ACAAAATAATTAACGAGTGCTGCA 57.992 33.333 0.00 0.00 0.00 4.41
1740 5043 0.654472 GCGCATGCGGATTAAGAACG 60.654 55.000 38.22 9.27 40.19 3.95
1741 5044 3.148823 GCGCATGCGGATTAAGAAC 57.851 52.632 38.22 16.72 40.19 3.01
1752 5055 0.109643 TCATGAACAAGTGCGCATGC 60.110 50.000 15.91 7.91 38.34 4.06
1753 5056 2.334971 TTCATGAACAAGTGCGCATG 57.665 45.000 15.91 12.12 39.47 4.06
1754 5057 4.700268 TTATTCATGAACAAGTGCGCAT 57.300 36.364 15.91 0.00 0.00 4.73
1755 5058 4.700268 ATTATTCATGAACAAGTGCGCA 57.300 36.364 11.07 5.66 0.00 6.09
1756 5059 5.810525 AGTATTATTCATGAACAAGTGCGC 58.189 37.500 11.07 0.00 0.00 6.09
1757 5060 6.422223 GGAGTATTATTCATGAACAAGTGCG 58.578 40.000 11.07 0.00 0.00 5.34
1758 5061 6.037172 ACGGAGTATTATTCATGAACAAGTGC 59.963 38.462 11.07 2.96 41.94 4.40
1759 5062 7.539712 ACGGAGTATTATTCATGAACAAGTG 57.460 36.000 11.07 0.00 41.94 3.16
1776 5079 3.126858 ACTTATTTCGCACGTACGGAGTA 59.873 43.478 21.06 0.00 45.11 2.59
1778 5081 2.278094 CACTTATTTCGCACGTACGGAG 59.722 50.000 21.06 12.76 0.00 4.63
1779 5082 2.252747 CACTTATTTCGCACGTACGGA 58.747 47.619 21.06 4.26 0.00 4.69
1780 5083 1.987770 ACACTTATTTCGCACGTACGG 59.012 47.619 21.06 9.73 0.00 4.02
1781 5084 3.480825 GGAACACTTATTTCGCACGTACG 60.481 47.826 15.01 15.01 0.00 3.67
1782 5085 3.676646 AGGAACACTTATTTCGCACGTAC 59.323 43.478 0.00 0.00 0.00 3.67
1783 5086 3.676172 CAGGAACACTTATTTCGCACGTA 59.324 43.478 0.00 0.00 0.00 3.57
1784 5087 2.478894 CAGGAACACTTATTTCGCACGT 59.521 45.455 0.00 0.00 0.00 4.49
1822 5163 5.349817 AGTTCATCGTCTCATCAATGTTCAC 59.650 40.000 0.00 0.00 0.00 3.18
1928 5373 0.671781 ACGCCTTGTGAGCTAAGCAG 60.672 55.000 0.00 0.00 0.00 4.24
1949 5394 3.056107 TGACCATGTACTTCCTTCTTCCG 60.056 47.826 0.00 0.00 0.00 4.30
1999 5444 2.604174 CGTCGGTTTCTGGCCACAC 61.604 63.158 0.00 0.00 0.00 3.82
2045 5490 4.281435 TGGTTCAACTAGTTCATACGGTCA 59.719 41.667 4.77 0.00 0.00 4.02
2132 5612 2.674357 TCCTTTCGTGCCGTAAAATAGC 59.326 45.455 0.00 0.00 0.00 2.97
2193 5696 1.401905 CAAGCCGTTTTCATCCCTAGC 59.598 52.381 0.00 0.00 0.00 3.42
2212 5715 4.819630 AGCATCTACTTTCGTTGGTTTTCA 59.180 37.500 0.00 0.00 0.00 2.69
2217 5720 5.109903 GTGATAGCATCTACTTTCGTTGGT 58.890 41.667 0.00 0.00 0.00 3.67
2220 5723 7.334421 ACAAATGTGATAGCATCTACTTTCGTT 59.666 33.333 0.00 0.00 0.00 3.85
2222 5725 7.239166 ACAAATGTGATAGCATCTACTTTCG 57.761 36.000 0.00 0.00 0.00 3.46
2312 5833 0.391661 TTCTGCACCATCTTCGCTCC 60.392 55.000 0.00 0.00 0.00 4.70
2490 6011 5.789643 AAATGTCTGTATTGCCACAGTTT 57.210 34.783 9.29 2.39 45.11 2.66
2532 6056 5.845391 TTAGGTTTTGCTTATACATGGCC 57.155 39.130 0.00 0.00 0.00 5.36
2538 6062 9.338622 ACCTGATACATTAGGTTTTGCTTATAC 57.661 33.333 0.00 0.00 43.45 1.47
2661 6185 4.469657 ACTTCTGTTACCATGCAAGGAAA 58.530 39.130 16.33 0.00 0.00 3.13
2696 6220 5.245751 TCAAACATCACACAATTAATGGCCT 59.754 36.000 3.32 0.00 0.00 5.19
2748 6279 5.132897 TGTTAGGTTGTTGGATCAATTGC 57.867 39.130 0.00 0.00 0.00 3.56
2783 6315 3.625764 GTGTGTGTGCCTTTCTCTTAACA 59.374 43.478 0.00 0.00 0.00 2.41
2793 6325 1.377987 ACGTTGGTGTGTGTGCCTT 60.378 52.632 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.