Multiple sequence alignment - TraesCS4D01G110500

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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 TraesCS4D01G110500 chr4D 100.000 7765 0 0 1 7765 91049741 91057505 0.000000e+00 14340.0
1 TraesCS4D01G110500 chr4D 90.483 662 52 7 4447 5100 319247871 319247213 0.000000e+00 863.0
2 TraesCS4D01G110500 chr4D 90.385 52 4 1 5699 5750 358471754 358471704 5.030000e-07 67.6
3 TraesCS4D01G110500 chr4A 96.215 7002 179 25 158 7123 503212468 503219419 0.000000e+00 11383.0
4 TraesCS4D01G110500 chr4A 90.181 662 54 7 4447 5100 48294020 48293362 0.000000e+00 852.0
5 TraesCS4D01G110500 chr4A 90.596 638 52 7 4468 5100 201602951 201603585 0.000000e+00 839.0
6 TraesCS4D01G110500 chr4A 90.312 609 53 5 7143 7748 699614643 699615248 0.000000e+00 793.0
7 TraesCS4D01G110500 chr4A 89.457 626 56 8 7144 7765 144632348 144631729 0.000000e+00 782.0
8 TraesCS4D01G110500 chr4A 97.222 36 1 0 5712 5747 106909137 106909172 2.340000e-05 62.1
9 TraesCS4D01G110500 chr4B 95.821 4953 130 37 1 4899 127468385 127473314 0.000000e+00 7928.0
10 TraesCS4D01G110500 chr4B 96.436 1936 53 5 4907 6830 127473713 127475644 0.000000e+00 3179.0
11 TraesCS4D01G110500 chr4B 90.714 280 19 5 6848 7123 127475962 127476238 4.430000e-97 366.0
12 TraesCS4D01G110500 chr5B 91.667 624 49 3 7144 7765 223123611 223122989 0.000000e+00 861.0
13 TraesCS4D01G110500 chrUn 90.181 662 53 8 4447 5100 340618188 340618845 0.000000e+00 852.0
14 TraesCS4D01G110500 chrUn 89.540 631 62 4 7137 7765 29316603 29317231 0.000000e+00 797.0
15 TraesCS4D01G110500 chr1B 90.166 661 56 5 4447 5100 216101683 216101025 0.000000e+00 852.0
16 TraesCS4D01G110500 chr1B 89.457 626 61 4 7143 7765 259785031 259785654 0.000000e+00 785.0
17 TraesCS4D01G110500 chr2B 89.954 657 58 7 4447 5100 349916830 349916179 0.000000e+00 841.0
18 TraesCS4D01G110500 chr2D 89.275 662 61 5 4447 5100 608519236 608518577 0.000000e+00 821.0
19 TraesCS4D01G110500 chr7A 89.583 624 59 5 7145 7765 173130576 173131196 0.000000e+00 787.0
20 TraesCS4D01G110500 chr7A 89.365 630 60 6 7140 7765 619191442 619192068 0.000000e+00 785.0
21 TraesCS4D01G110500 chr7A 94.005 367 22 0 2619 2985 579007500 579007866 2.450000e-154 556.0
22 TraesCS4D01G110500 chr2A 89.365 630 60 6 7140 7765 689766939 689767565 0.000000e+00 785.0
23 TraesCS4D01G110500 chr5A 89.206 630 63 5 7137 7763 707992581 707991954 0.000000e+00 782.0
24 TraesCS4D01G110500 chr6A 92.373 354 25 1 2641 2994 531298383 531298032 3.230000e-138 503.0
25 TraesCS4D01G110500 chr6A 100.000 30 0 0 2621 2650 531299316 531299287 1.000000e-03 56.5
26 TraesCS4D01G110500 chr6B 91.667 48 3 1 5701 5748 289179336 289179290 1.810000e-06 65.8
27 TraesCS4D01G110500 chr5D 92.683 41 3 0 5707 5747 255078192 255078232 8.410000e-05 60.2


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 TraesCS4D01G110500 chr4D 91049741 91057505 7764 False 14340.000000 14340 100.000000 1 7765 1 chr4D.!!$F1 7764
1 TraesCS4D01G110500 chr4D 319247213 319247871 658 True 863.000000 863 90.483000 4447 5100 1 chr4D.!!$R1 653
2 TraesCS4D01G110500 chr4A 503212468 503219419 6951 False 11383.000000 11383 96.215000 158 7123 1 chr4A.!!$F3 6965
3 TraesCS4D01G110500 chr4A 48293362 48294020 658 True 852.000000 852 90.181000 4447 5100 1 chr4A.!!$R1 653
4 TraesCS4D01G110500 chr4A 201602951 201603585 634 False 839.000000 839 90.596000 4468 5100 1 chr4A.!!$F2 632
5 TraesCS4D01G110500 chr4A 699614643 699615248 605 False 793.000000 793 90.312000 7143 7748 1 chr4A.!!$F4 605
6 TraesCS4D01G110500 chr4A 144631729 144632348 619 True 782.000000 782 89.457000 7144 7765 1 chr4A.!!$R2 621
7 TraesCS4D01G110500 chr4B 127468385 127476238 7853 False 3824.333333 7928 94.323667 1 7123 3 chr4B.!!$F1 7122
8 TraesCS4D01G110500 chr5B 223122989 223123611 622 True 861.000000 861 91.667000 7144 7765 1 chr5B.!!$R1 621
9 TraesCS4D01G110500 chrUn 340618188 340618845 657 False 852.000000 852 90.181000 4447 5100 1 chrUn.!!$F2 653
10 TraesCS4D01G110500 chrUn 29316603 29317231 628 False 797.000000 797 89.540000 7137 7765 1 chrUn.!!$F1 628
11 TraesCS4D01G110500 chr1B 216101025 216101683 658 True 852.000000 852 90.166000 4447 5100 1 chr1B.!!$R1 653
12 TraesCS4D01G110500 chr1B 259785031 259785654 623 False 785.000000 785 89.457000 7143 7765 1 chr1B.!!$F1 622
13 TraesCS4D01G110500 chr2B 349916179 349916830 651 True 841.000000 841 89.954000 4447 5100 1 chr2B.!!$R1 653
14 TraesCS4D01G110500 chr2D 608518577 608519236 659 True 821.000000 821 89.275000 4447 5100 1 chr2D.!!$R1 653
15 TraesCS4D01G110500 chr7A 173130576 173131196 620 False 787.000000 787 89.583000 7145 7765 1 chr7A.!!$F1 620
16 TraesCS4D01G110500 chr7A 619191442 619192068 626 False 785.000000 785 89.365000 7140 7765 1 chr7A.!!$F3 625
17 TraesCS4D01G110500 chr2A 689766939 689767565 626 False 785.000000 785 89.365000 7140 7765 1 chr2A.!!$F1 625
18 TraesCS4D01G110500 chr5A 707991954 707992581 627 True 782.000000 782 89.206000 7137 7763 1 chr5A.!!$R1 626
19 TraesCS4D01G110500 chr6A 531298032 531299316 1284 True 279.750000 503 96.186500 2621 2994 2 chr6A.!!$R1 373

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
696 710 0.933047 GGTGCGGCGACTTTTTGTTC 60.933 55.0 12.98 0.0 0.00 3.18 F
992 1007 0.969917 TTTGGCATCATCCCCAACCG 60.970 55.0 0.00 0.0 40.60 4.44 F
2711 3639 0.392998 GGTATCACACAGTGGCCCAG 60.393 60.0 5.31 0.0 33.87 4.45 F
3050 3978 0.176680 CAGACCGATGGCAGCTAACT 59.823 55.0 0.00 0.0 0.00 2.24 F
4200 5184 0.551396 CCCCTACCCTTGGACCAATC 59.449 60.0 7.54 0.0 0.00 2.67 F
5306 6702 0.035881 CATGCTGGAGTGTGACTGGT 59.964 55.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1756 0.035458 GGGCTCCCGACATAATCCAG 59.965 60.0 0.00 0.0 0.0 3.86 R
2829 3757 0.954452 GTTTTCAGACCACTGGGCAG 59.046 55.0 2.97 0.0 43.6 4.85 R
3830 4813 0.690762 AAGTAGAAGCCAGGCCGAAA 59.309 50.0 8.22 0.0 0.0 3.46 R
4902 5906 0.610509 ACCCGCAATGTTGTATGGCA 60.611 50.0 0.00 0.0 0.0 4.92 R
5790 7199 0.907704 TACGCTCCACCCCACTGATT 60.908 55.0 0.00 0.0 0.0 2.57 R
6834 8243 0.031414 AGCGACTAAGGTATGGGGGT 60.031 55.0 0.00 0.0 0.0 4.95 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
28 29 8.786826 TCTTCTGAAAACGGATTATACAATGT 57.213 30.769 0.00 0.00 0.00 2.71
29 30 8.879759 TCTTCTGAAAACGGATTATACAATGTC 58.120 33.333 0.00 0.00 0.00 3.06
30 31 8.554835 TTCTGAAAACGGATTATACAATGTCA 57.445 30.769 0.00 0.00 0.00 3.58
32 33 8.611757 TCTGAAAACGGATTATACAATGTCATG 58.388 33.333 0.00 0.00 0.00 3.07
33 34 8.275015 TGAAAACGGATTATACAATGTCATGT 57.725 30.769 0.00 0.00 37.32 3.21
34 35 8.394877 TGAAAACGGATTATACAATGTCATGTC 58.605 33.333 0.00 0.00 34.75 3.06
35 36 8.506168 AAAACGGATTATACAATGTCATGTCT 57.494 30.769 0.00 0.00 34.75 3.41
36 37 7.715265 AACGGATTATACAATGTCATGTCTC 57.285 36.000 0.00 0.00 34.75 3.36
37 38 6.816136 ACGGATTATACAATGTCATGTCTCA 58.184 36.000 0.00 0.00 34.75 3.27
38 39 7.445121 ACGGATTATACAATGTCATGTCTCAT 58.555 34.615 0.00 0.00 34.75 2.90
39 40 7.386025 ACGGATTATACAATGTCATGTCTCATG 59.614 37.037 0.00 3.65 34.75 3.07
44 45 5.618056 ACAATGTCATGTCTCATGTCAAC 57.382 39.130 11.88 4.25 0.00 3.18
51 52 3.961480 TGTCTCATGTCAACCGAGAAT 57.039 42.857 0.00 0.00 37.53 2.40
61 62 6.880822 TGTCAACCGAGAATAAGAAATACG 57.119 37.500 0.00 0.00 0.00 3.06
63 64 7.262772 TGTCAACCGAGAATAAGAAATACGAT 58.737 34.615 0.00 0.00 0.00 3.73
171 183 3.473923 TGATCTGAGAACACTTGCACA 57.526 42.857 0.00 0.00 0.00 4.57
546 559 2.467566 TTTGCTAGGGTTCTTCCGTC 57.532 50.000 0.00 0.00 37.00 4.79
694 708 1.381165 AAGGTGCGGCGACTTTTTGT 61.381 50.000 12.98 0.00 0.00 2.83
695 709 1.065109 GGTGCGGCGACTTTTTGTT 59.935 52.632 12.98 0.00 0.00 2.83
696 710 0.933047 GGTGCGGCGACTTTTTGTTC 60.933 55.000 12.98 0.00 0.00 3.18
832 846 4.744570 TCAAACTCGTAGATCAAATCGCT 58.255 39.130 0.00 0.00 33.89 4.93
992 1007 0.969917 TTTGGCATCATCCCCAACCG 60.970 55.000 0.00 0.00 40.60 4.44
1273 1288 7.228108 CACTGGTTATTGATATTGTGATGCTCT 59.772 37.037 0.00 0.00 0.00 4.09
1300 1315 1.063266 ACAATCCCAACACCACCTGTT 60.063 47.619 0.00 0.00 44.51 3.16
1530 1545 4.193826 TCTCTTCAGGGAGTTGAATTCG 57.806 45.455 0.04 0.00 36.55 3.34
1563 1578 2.289444 CCGTCCACTTAACCTGTCACAT 60.289 50.000 0.00 0.00 0.00 3.21
1741 1756 5.639506 ACACACATGTCAACAGAGCTTATAC 59.360 40.000 0.00 0.00 31.55 1.47
2165 2180 4.010349 CTCCCATCTCAAAACTACAACCC 58.990 47.826 0.00 0.00 0.00 4.11
2701 3629 8.292448 CCTTGCATATAGATTTTGGTATCACAC 58.708 37.037 0.00 0.00 0.00 3.82
2708 3636 1.904287 TTTGGTATCACACAGTGGCC 58.096 50.000 5.31 0.00 33.87 5.36
2711 3639 0.392998 GGTATCACACAGTGGCCCAG 60.393 60.000 5.31 0.00 33.87 4.45
2829 3757 0.457851 AGACGGCTATGTCAGTCAGC 59.542 55.000 0.00 0.00 41.41 4.26
2839 3767 2.359602 CAGTCAGCTGCCCAGTGG 60.360 66.667 9.47 0.63 35.77 4.00
2856 3784 5.701290 CCCAGTGGTCTGAAAACTAAGTTAG 59.299 44.000 8.74 8.41 43.76 2.34
2954 3882 7.933033 AGTTATTCATTTTCAAACTGCATGGTT 59.067 29.630 0.00 0.00 0.00 3.67
2967 3895 5.481105 ACTGCATGGTTTAATGTTTCATGG 58.519 37.500 0.00 0.00 36.62 3.66
3050 3978 0.176680 CAGACCGATGGCAGCTAACT 59.823 55.000 0.00 0.00 0.00 2.24
3270 4247 8.761575 AAGTTGCAAATTATCCAGTTATTGTG 57.238 30.769 10.95 0.00 0.00 3.33
3503 4484 6.544197 TCCTATTATCGAGATAAGCTAGCTGG 59.456 42.308 20.16 9.77 36.79 4.85
3879 4862 6.867662 AGGCGTAGTACGTATATAAGTGTT 57.132 37.500 22.81 2.73 44.73 3.32
3913 4896 8.655970 CACAGAAACATAAAGATTGTCATACGA 58.344 33.333 0.00 0.00 0.00 3.43
4097 5080 9.893305 GACACTGTAAGCAATTGTTACTAATTT 57.107 29.630 21.12 9.85 37.60 1.82
4099 5082 9.891828 CACTGTAAGCAATTGTTACTAATTTGA 57.108 29.630 21.12 7.76 37.60 2.69
4200 5184 0.551396 CCCCTACCCTTGGACCAATC 59.449 60.000 7.54 0.00 0.00 2.67
4291 5279 5.189736 GGGCAGTGTGGAATGAGGATATATA 59.810 44.000 0.00 0.00 0.00 0.86
4385 5373 9.667989 CATTCGAAGTGAAAATATCATGCATAA 57.332 29.630 3.35 0.00 40.97 1.90
4592 5580 3.379372 CCATGGCTAGTTCTTTGGTGATG 59.621 47.826 0.00 0.00 0.00 3.07
4604 5604 2.996249 TGGTGATGCTTCAGATCTCC 57.004 50.000 1.91 1.16 35.09 3.71
4633 5633 1.276421 ACTCCTCCCATGTCAAGTTCG 59.724 52.381 0.00 0.00 0.00 3.95
4634 5634 0.613260 TCCTCCCATGTCAAGTTCGG 59.387 55.000 0.00 0.00 0.00 4.30
4667 5668 4.261952 CGACCTCTCTTGACATATCAGCAT 60.262 45.833 0.00 0.00 35.83 3.79
4709 5712 1.992277 GGAGCTTCTGGAGGCCTGA 60.992 63.158 12.00 0.00 33.44 3.86
4734 5737 4.806892 TGAATATGCCCAAACCATCTCAT 58.193 39.130 0.00 0.00 0.00 2.90
4805 5809 4.341487 TCGTATATCATCATTCCGGACCT 58.659 43.478 1.83 0.00 0.00 3.85
4902 5906 1.045407 TTAGTCGGCCAACACTGAGT 58.955 50.000 2.24 0.00 33.18 3.41
4969 6364 5.299949 CCTTTTAGCTTTTGTGGCATTCTT 58.700 37.500 0.00 0.00 0.00 2.52
4976 6371 4.512571 GCTTTTGTGGCATTCTTTTGTCAT 59.487 37.500 0.00 0.00 33.09 3.06
5302 6698 0.450583 CATGCATGCTGGAGTGTGAC 59.549 55.000 20.33 0.00 0.00 3.67
5305 6701 1.303799 GCATGCTGGAGTGTGACTGG 61.304 60.000 11.37 0.00 0.00 4.00
5306 6702 0.035881 CATGCTGGAGTGTGACTGGT 59.964 55.000 0.00 0.00 0.00 4.00
5406 6802 1.077501 GCATCAGCTGGCCAGGTTA 60.078 57.895 34.41 27.28 36.98 2.85
5504 6900 1.429930 TATCAAGCTTCCCCCGCATA 58.570 50.000 0.00 0.00 0.00 3.14
5725 7134 9.710818 ACTACTACCTCTGATCCAAAATAAGTA 57.289 33.333 0.00 0.00 0.00 2.24
6051 7460 8.078596 GGAATTATTTGTCCAGCATATGAAGTC 58.921 37.037 6.97 0.00 33.79 3.01
6056 7465 3.118629 TGTCCAGCATATGAAGTCACTCC 60.119 47.826 6.97 0.00 0.00 3.85
6163 7572 5.423704 AGAAGGTTCTAGGAAGTAAAGCC 57.576 43.478 0.00 0.00 35.34 4.35
6167 7576 6.734502 AGGTTCTAGGAAGTAAAGCCTATC 57.265 41.667 0.00 0.00 36.26 2.08
6432 7841 0.402121 GGAGGGCCAAGAGACAAACT 59.598 55.000 6.18 0.00 0.00 2.66
6433 7842 1.202940 GGAGGGCCAAGAGACAAACTT 60.203 52.381 6.18 0.00 0.00 2.66
6728 8137 4.275508 CTGCCCCGGGATGATGGG 62.276 72.222 26.32 3.67 45.58 4.00
6760 8169 1.338136 AAACCCGCCGATGGAGATCT 61.338 55.000 0.00 0.00 0.00 2.75
6834 8243 1.568504 AGGTAGCTGACGATTCCCAA 58.431 50.000 0.00 0.00 0.00 4.12
6857 8566 2.296471 CCCCATACCTTAGTCGCTAGTG 59.704 54.545 0.00 0.00 0.00 2.74
6889 8598 4.513692 TGTGCGGCCAAAATCTATATGTAC 59.486 41.667 2.24 0.00 0.00 2.90
6893 8602 5.468746 GCGGCCAAAATCTATATGTACAAGA 59.531 40.000 2.24 0.00 0.00 3.02
6896 8605 8.656849 CGGCCAAAATCTATATGTACAAGATAC 58.343 37.037 2.24 0.00 29.89 2.24
6923 8632 0.695462 TACCCATCCATCCAGCTGCT 60.695 55.000 8.66 0.00 0.00 4.24
6993 8704 4.493350 CGAAATGTTTAGCTGCTTTGATCG 59.507 41.667 7.79 6.02 0.00 3.69
7010 8721 3.187637 TGATCGGATTGTTTTCGGTGAAC 59.812 43.478 0.00 0.00 0.00 3.18
7016 8727 4.907582 GGATTGTTTTCGGTGAACGTTTAG 59.092 41.667 0.46 0.00 44.69 1.85
7024 8736 2.056577 GGTGAACGTTTAGTCTGTCCG 58.943 52.381 0.46 0.00 0.00 4.79
7053 8771 4.460382 AGTTTGATGTTCCATGCTGGTAAG 59.540 41.667 2.68 0.00 39.03 2.34
7081 8800 3.221771 TGTTATCTTTGGTGCTGCAAGT 58.778 40.909 2.77 0.00 35.30 3.16
7083 8802 4.099266 TGTTATCTTTGGTGCTGCAAGTTT 59.901 37.500 2.77 0.00 35.30 2.66
7084 8803 3.825143 ATCTTTGGTGCTGCAAGTTTT 57.175 38.095 2.77 0.00 35.30 2.43
7116 8835 4.202030 GGAGTCGGATGTAGATCGAGTTTT 60.202 45.833 0.00 0.00 36.81 2.43
7123 8842 4.092771 TGTAGATCGAGTTTTCCTGTCG 57.907 45.455 0.00 0.00 34.98 4.35
7124 8843 3.754850 TGTAGATCGAGTTTTCCTGTCGA 59.245 43.478 0.00 0.00 46.03 4.20
7125 8844 3.495670 AGATCGAGTTTTCCTGTCGAG 57.504 47.619 0.00 0.00 45.25 4.04
7126 8845 1.921230 GATCGAGTTTTCCTGTCGAGC 59.079 52.381 0.00 0.00 45.25 5.03
7127 8846 0.959553 TCGAGTTTTCCTGTCGAGCT 59.040 50.000 0.00 0.00 37.79 4.09
7128 8847 1.340248 TCGAGTTTTCCTGTCGAGCTT 59.660 47.619 0.00 0.00 37.79 3.74
7129 8848 1.721926 CGAGTTTTCCTGTCGAGCTTC 59.278 52.381 0.00 0.00 35.70 3.86
7130 8849 2.608261 CGAGTTTTCCTGTCGAGCTTCT 60.608 50.000 0.00 0.00 35.70 2.85
7131 8850 3.394719 GAGTTTTCCTGTCGAGCTTCTT 58.605 45.455 0.00 0.00 0.00 2.52
7132 8851 3.809905 AGTTTTCCTGTCGAGCTTCTTT 58.190 40.909 0.00 0.00 0.00 2.52
7133 8852 4.200092 AGTTTTCCTGTCGAGCTTCTTTT 58.800 39.130 0.00 0.00 0.00 2.27
7134 8853 5.365619 AGTTTTCCTGTCGAGCTTCTTTTA 58.634 37.500 0.00 0.00 0.00 1.52
7135 8854 5.998363 AGTTTTCCTGTCGAGCTTCTTTTAT 59.002 36.000 0.00 0.00 0.00 1.40
7136 8855 6.147985 AGTTTTCCTGTCGAGCTTCTTTTATC 59.852 38.462 0.00 0.00 0.00 1.75
7137 8856 3.770666 TCCTGTCGAGCTTCTTTTATCG 58.229 45.455 0.00 0.00 36.54 2.92
7138 8857 2.282820 CCTGTCGAGCTTCTTTTATCGC 59.717 50.000 0.00 0.00 35.23 4.58
7141 8860 3.367932 TGTCGAGCTTCTTTTATCGCTTG 59.632 43.478 0.00 0.00 35.23 4.01
7183 8902 2.982470 GCAAAAGTTTTGCCTCATCGAG 59.018 45.455 33.57 6.38 39.38 4.04
7192 8911 6.879458 AGTTTTGCCTCATCGAGTAATTAAGT 59.121 34.615 0.00 0.00 0.00 2.24
7219 8938 5.007385 GAGAGTTGCTCGGTTAATTAGGA 57.993 43.478 0.00 0.00 35.36 2.94
7256 8975 8.602472 AAAACCAGATTGCCCAGTTAATTATA 57.398 30.769 0.00 0.00 0.00 0.98
7330 9049 0.107410 ACGCACACCACTCCAAAGAA 60.107 50.000 0.00 0.00 0.00 2.52
7372 9091 0.179137 GGCGTCATCGTCATCACTCA 60.179 55.000 0.00 0.00 41.67 3.41
7409 9128 1.626321 TCGCCATCCCTACACTTTGAA 59.374 47.619 0.00 0.00 0.00 2.69
7538 9259 0.605319 GTGCAACCCCGAATCTGACA 60.605 55.000 0.00 0.00 0.00 3.58
7544 9265 2.472029 ACCCCGAATCTGACAGAGAAT 58.528 47.619 11.52 0.00 33.12 2.40
7546 9267 3.264450 ACCCCGAATCTGACAGAGAATTT 59.736 43.478 11.52 0.00 33.12 1.82
7625 9347 2.764010 AGCCAGTCATCGTATACCACAA 59.236 45.455 0.00 0.00 0.00 3.33
7655 9377 1.446792 CGCAGCTTCGACTCCACAT 60.447 57.895 0.00 0.00 0.00 3.21
7661 9383 1.728971 GCTTCGACTCCACATCAACAG 59.271 52.381 0.00 0.00 0.00 3.16
7749 9473 0.548031 ACATCGCTCCCACCATCATT 59.452 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.397906 ACATGACATTGTATAATCCGTTTTCAG 58.602 33.333 0.00 0.00 0.00 3.02
8 9 8.275015 ACATGACATTGTATAATCCGTTTTCA 57.725 30.769 0.00 0.00 0.00 2.69
23 24 4.436451 CGGTTGACATGAGACATGACATTG 60.436 45.833 16.86 7.31 0.00 2.82
25 26 3.055891 TCGGTTGACATGAGACATGACAT 60.056 43.478 16.86 0.00 0.00 3.06
26 27 2.298729 TCGGTTGACATGAGACATGACA 59.701 45.455 16.86 13.94 0.00 3.58
27 28 2.926200 CTCGGTTGACATGAGACATGAC 59.074 50.000 16.86 11.77 31.31 3.06
28 29 2.825532 TCTCGGTTGACATGAGACATGA 59.174 45.455 16.86 0.00 34.00 3.07
29 30 3.236632 TCTCGGTTGACATGAGACATG 57.763 47.619 0.00 9.72 34.00 3.21
30 31 3.961480 TTCTCGGTTGACATGAGACAT 57.039 42.857 0.00 0.00 38.41 3.06
32 33 5.651530 TCTTATTCTCGGTTGACATGAGAC 58.348 41.667 0.00 0.00 38.41 3.36
33 34 5.914898 TCTTATTCTCGGTTGACATGAGA 57.085 39.130 0.00 2.40 37.00 3.27
34 35 6.968131 TTTCTTATTCTCGGTTGACATGAG 57.032 37.500 0.00 0.00 0.00 2.90
35 36 7.222031 CGTATTTCTTATTCTCGGTTGACATGA 59.778 37.037 0.00 0.00 0.00 3.07
36 37 7.222031 TCGTATTTCTTATTCTCGGTTGACATG 59.778 37.037 0.00 0.00 0.00 3.21
37 38 7.262772 TCGTATTTCTTATTCTCGGTTGACAT 58.737 34.615 0.00 0.00 0.00 3.06
38 39 6.623486 TCGTATTTCTTATTCTCGGTTGACA 58.377 36.000 0.00 0.00 0.00 3.58
39 40 7.434307 TGATCGTATTTCTTATTCTCGGTTGAC 59.566 37.037 0.00 0.00 0.00 3.18
44 45 7.139392 TGACTGATCGTATTTCTTATTCTCGG 58.861 38.462 0.00 0.00 0.00 4.63
51 52 9.764363 AGCATATTTGACTGATCGTATTTCTTA 57.236 29.630 0.00 0.00 0.00 2.10
61 62 5.591877 ACTTTCCCAGCATATTTGACTGATC 59.408 40.000 8.41 0.00 32.24 2.92
63 64 4.922206 ACTTTCCCAGCATATTTGACTGA 58.078 39.130 8.41 0.00 32.24 3.41
141 153 9.033481 CAAGTGTTCTCAGATCATTATCTCTTC 57.967 37.037 0.00 0.00 40.65 2.87
143 155 6.985645 GCAAGTGTTCTCAGATCATTATCTCT 59.014 38.462 0.00 0.00 40.65 3.10
144 156 6.760298 TGCAAGTGTTCTCAGATCATTATCTC 59.240 38.462 0.00 0.00 40.65 2.75
151 163 3.473923 TGTGCAAGTGTTCTCAGATCA 57.526 42.857 0.00 0.00 0.00 2.92
156 168 4.511617 TGTTTTTGTGCAAGTGTTCTCA 57.488 36.364 0.00 0.00 0.00 3.27
241 254 5.780984 TCTCTAAACGACTTTTTCTCCTCC 58.219 41.667 0.00 0.00 0.00 4.30
573 586 4.768145 CAACGCAACGAAACTAAGAATCA 58.232 39.130 0.00 0.00 0.00 2.57
694 708 8.260818 TCAAGAACTGAAGAAGAAGAAGAAGAA 58.739 33.333 0.00 0.00 0.00 2.52
695 709 7.786030 TCAAGAACTGAAGAAGAAGAAGAAGA 58.214 34.615 0.00 0.00 0.00 2.87
696 710 8.497554 CATCAAGAACTGAAGAAGAAGAAGAAG 58.502 37.037 0.00 0.00 37.67 2.85
832 846 5.063204 CACAAATTCTGGTGGTCTAGAACA 58.937 41.667 6.32 6.32 42.32 3.18
894 909 5.580297 TGCCAAAAACTGAGAATTTTGTGAC 59.420 36.000 18.97 12.41 42.28 3.67
992 1007 0.535102 AGTGGCGGCCATAGTTATGC 60.535 55.000 26.68 9.51 35.28 3.14
1273 1288 1.149401 TGTTGGGATTGTCACGCCA 59.851 52.632 0.00 0.00 0.00 5.69
1300 1315 1.588239 ATGATCTTGCCACCCTCAGA 58.412 50.000 0.00 0.00 0.00 3.27
1367 1382 1.202348 GGTTCTTGCTGCCATTACCAC 59.798 52.381 0.00 0.00 0.00 4.16
1530 1545 0.175989 GTGGACGGATTCTCCCAGAC 59.824 60.000 0.00 0.00 31.13 3.51
1563 1578 5.641709 GGCTCGACGAATGATGATATCTTA 58.358 41.667 3.98 0.00 0.00 2.10
1741 1756 0.035458 GGGCTCCCGACATAATCCAG 59.965 60.000 0.00 0.00 0.00 3.86
2055 2070 1.214062 GACCACAGGAGCACTCTCG 59.786 63.158 0.00 0.00 40.26 4.04
2091 2106 1.890894 CAGTCCACTACCTCCACCG 59.109 63.158 0.00 0.00 0.00 4.94
2165 2180 3.831883 CATCAGGCGATGGGGTTG 58.168 61.111 10.25 0.00 44.59 3.77
2433 2448 1.138069 TGCAGTCCGAGTCAACTTCAA 59.862 47.619 0.00 0.00 0.00 2.69
2701 3629 1.001020 TATTGCACCTGGGCCACTG 60.001 57.895 0.00 1.44 0.00 3.66
2733 3661 4.536765 CCCTGTAATTGCCAGATTTAGGT 58.463 43.478 8.16 0.00 31.38 3.08
2829 3757 0.954452 GTTTTCAGACCACTGGGCAG 59.046 55.000 2.97 0.00 43.60 4.85
2839 3767 9.668497 AATATGGGACTAACTTAGTTTTCAGAC 57.332 33.333 1.94 0.00 39.59 3.51
2856 3784 2.565841 GTCCACTGCAGAATATGGGAC 58.434 52.381 23.35 20.20 36.86 4.46
2954 3882 7.757941 TGATGTCAGAACCATGAAACATTAA 57.242 32.000 0.00 0.00 0.00 1.40
2967 3895 7.362662 ACAATTTGTGTACATGATGTCAGAAC 58.637 34.615 0.00 0.00 39.29 3.01
3032 3960 0.176680 CAGTTAGCTGCCATCGGTCT 59.823 55.000 0.00 0.00 35.77 3.85
3479 4460 6.320164 ACCAGCTAGCTTATCTCGATAATAGG 59.680 42.308 16.46 10.38 33.29 2.57
3533 4514 5.658190 ACAGCCCAGATAATTAAAATGCAGT 59.342 36.000 0.00 0.00 0.00 4.40
3714 4695 9.660180 GAAATAATGAGAACCTTGAGAAGTAGT 57.340 33.333 0.00 0.00 0.00 2.73
3830 4813 0.690762 AAGTAGAAGCCAGGCCGAAA 59.309 50.000 8.22 0.00 0.00 3.46
3879 4862 8.980610 CAATCTTTATGTTTCTGTGAATGCAAA 58.019 29.630 0.00 0.00 0.00 3.68
3913 4896 3.441101 TCATGTACACTGGAAGCTACCT 58.559 45.455 0.00 0.00 37.60 3.08
4097 5080 7.628769 TCAGAGCTTGTTTGCAATAATATCA 57.371 32.000 0.00 0.00 33.65 2.15
4099 5082 8.571336 GGTATCAGAGCTTGTTTGCAATAATAT 58.429 33.333 0.00 0.00 33.65 1.28
4102 5085 5.945784 AGGTATCAGAGCTTGTTTGCAATAA 59.054 36.000 0.00 0.00 33.65 1.40
4592 5580 2.431057 TCCGTAAAGGGAGATCTGAAGC 59.569 50.000 0.00 0.00 41.52 3.86
4604 5604 1.139058 CATGGGAGGAGTCCGTAAAGG 59.861 57.143 2.76 0.00 45.05 3.11
4709 5712 2.530460 TGGTTTGGGCATATTCAGCT 57.470 45.000 0.00 0.00 0.00 4.24
4734 5737 3.258372 AGAGAAGCTTGTCCAACATCGTA 59.742 43.478 19.26 0.00 0.00 3.43
4805 5809 1.150536 GCCACACAAGGAAGGACCA 59.849 57.895 0.00 0.00 42.04 4.02
4902 5906 0.610509 ACCCGCAATGTTGTATGGCA 60.611 50.000 0.00 0.00 0.00 4.92
4969 6364 3.953712 TCTGGCGTTCTCTATGACAAA 57.046 42.857 0.00 0.00 27.85 2.83
4998 6393 4.782691 TCAAAGTAGGATGGATGAAGTGGA 59.217 41.667 0.00 0.00 0.00 4.02
5254 6650 9.219603 CACATCCTAAGAACAAGAATTACAAGA 57.780 33.333 0.00 0.00 0.00 3.02
5302 6698 1.486211 CACCCTAGACCCTACACCAG 58.514 60.000 0.00 0.00 0.00 4.00
5305 6701 1.413077 GATGCACCCTAGACCCTACAC 59.587 57.143 0.00 0.00 0.00 2.90
5306 6702 1.691482 GGATGCACCCTAGACCCTACA 60.691 57.143 0.00 0.00 0.00 2.74
5790 7199 0.907704 TACGCTCCACCCCACTGATT 60.908 55.000 0.00 0.00 0.00 2.57
6035 7444 3.133721 AGGAGTGACTTCATATGCTGGAC 59.866 47.826 0.00 0.00 0.00 4.02
6056 7465 4.520492 ACAAAGAGTGGTTTATCCTGCAAG 59.480 41.667 0.00 0.00 37.07 4.01
6163 7572 7.050377 ACATTTAGTCAGTCAATGTGGGATAG 58.950 38.462 0.00 0.00 39.22 2.08
6167 7576 5.707298 AGAACATTTAGTCAGTCAATGTGGG 59.293 40.000 0.00 0.00 39.66 4.61
6529 7938 1.141858 GGGGAGGAGCTTCGATTGATT 59.858 52.381 0.00 0.00 0.00 2.57
6599 8008 1.017701 CAGAGCTTGATGCAGCGTCA 61.018 55.000 13.66 13.66 45.24 4.35
6760 8169 6.034150 CGTCGTCATACTGTATGTTTGCTAAA 59.966 38.462 23.14 3.17 37.45 1.85
6834 8243 0.031414 AGCGACTAAGGTATGGGGGT 60.031 55.000 0.00 0.00 0.00 4.95
6857 8566 2.202892 GGCCGCACACTAGTAGCC 60.203 66.667 12.37 8.55 32.59 3.93
6866 8575 3.550820 ACATATAGATTTTGGCCGCACA 58.449 40.909 0.00 0.00 0.00 4.57
6889 8598 6.298361 TGGATGGGTATTGTCATGTATCTTG 58.702 40.000 0.00 0.00 0.00 3.02
6893 8602 5.312974 TGGATGGATGGGTATTGTCATGTAT 59.687 40.000 0.00 0.00 0.00 2.29
6896 8605 4.077108 CTGGATGGATGGGTATTGTCATG 58.923 47.826 0.00 0.00 0.00 3.07
6923 8632 0.619832 AGCTGGGCCTTCATCTCAGA 60.620 55.000 4.53 0.00 0.00 3.27
6952 8661 9.804758 AACATTTCGGTTTTCAACTTTACATAA 57.195 25.926 0.00 0.00 0.00 1.90
6953 8662 9.804758 AAACATTTCGGTTTTCAACTTTACATA 57.195 25.926 0.00 0.00 37.72 2.29
6954 8663 8.710835 AAACATTTCGGTTTTCAACTTTACAT 57.289 26.923 0.00 0.00 37.72 2.29
6993 8704 3.343380 AACGTTCACCGAAAACAATCC 57.657 42.857 0.00 0.00 40.70 3.01
7010 8721 3.128242 ACTCCATACGGACAGACTAAACG 59.872 47.826 0.00 0.00 35.91 3.60
7016 8727 3.587797 TCAAACTCCATACGGACAGAC 57.412 47.619 0.00 0.00 35.91 3.51
7024 8736 4.641989 AGCATGGAACATCAAACTCCATAC 59.358 41.667 2.62 0.00 46.10 2.39
7053 8771 2.162408 GCACCAAAGATAACAGGTCAGC 59.838 50.000 0.00 0.00 30.44 4.26
7081 8800 4.469945 ACATCCGACTCCAGATCCTTAAAA 59.530 41.667 0.00 0.00 0.00 1.52
7083 8802 3.643237 ACATCCGACTCCAGATCCTTAA 58.357 45.455 0.00 0.00 0.00 1.85
7084 8803 3.314307 ACATCCGACTCCAGATCCTTA 57.686 47.619 0.00 0.00 0.00 2.69
7116 8835 3.770666 CGATAAAAGAAGCTCGACAGGA 58.229 45.455 0.00 0.00 33.07 3.86
7123 8842 6.993175 AAAAACAAGCGATAAAAGAAGCTC 57.007 33.333 0.00 0.00 39.25 4.09
7148 8867 3.780902 ACTTTTGCCTCCGTTTTGAAAG 58.219 40.909 0.00 0.00 0.00 2.62
7183 8902 7.432838 CCGAGCAACTCTCTTCTACTTAATTAC 59.567 40.741 0.00 0.00 39.70 1.89
7192 8911 5.916661 ATTAACCGAGCAACTCTCTTCTA 57.083 39.130 0.00 0.00 39.70 2.10
7219 8938 2.018515 TCTGGTTTTCGCTCGGTTTTT 58.981 42.857 0.00 0.00 0.00 1.94
7256 8975 0.841289 TGGTTTTCACCCGGTTCTCT 59.159 50.000 0.00 0.00 43.49 3.10
7409 9128 0.938168 GCGAAGTCGGAGTCGTTTGT 60.938 55.000 11.36 0.00 39.46 2.83
7546 9267 1.754226 GTGCCTGGTTTTGTCCTTCAA 59.246 47.619 0.00 0.00 0.00 2.69
7655 9377 1.006571 GCCTCGGTTCGTCTGTTGA 60.007 57.895 0.00 0.00 0.00 3.18
7661 9383 1.572941 GGTTTTGCCTCGGTTCGTC 59.427 57.895 0.00 0.00 0.00 4.20
7698 9420 3.675619 ATGGTTGCGGTAGTCGGCC 62.676 63.158 0.00 0.00 38.80 6.13


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

AutoCloner maintained by Alex Coulton.