Multiple sequence alignment - TraesCS4B01G108900

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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 TraesCS4B01G108900 chr4B 100.000 4361 0 0 1 4361 119825900 119821540 0.000000e+00 8054
1 TraesCS4B01G108900 chr4A 93.813 3669 154 31 723 4359 497442822 497439195 0.000000e+00 5450
2 TraesCS4B01G108900 chr4A 90.688 494 21 7 152 625 497443354 497442866 6.150000e-178 634
3 TraesCS4B01G108900 chr4D 93.546 3672 133 51 723 4337 84547995 84544371 0.000000e+00 5373
4 TraesCS4B01G108900 chr4D 89.474 551 26 10 147 686 84548523 84547994 0.000000e+00 667
5 TraesCS4B01G108900 chr5D 86.005 393 55 0 2492 2884 5817277 5816885 5.210000e-114 422
6 TraesCS4B01G108900 chr5D 86.275 102 7 5 2915 3012 11950048 11949950 2.150000e-18 104
7 TraesCS4B01G108900 chr2A 76.695 811 131 47 2481 3271 530380563 530381335 8.790000e-107 398
8 TraesCS4B01G108900 chr2D 75.985 812 144 40 2476 3271 392525893 392526669 5.330000e-99 372
9 TraesCS4B01G108900 chr2B 76.184 781 132 40 2476 3237 464466512 464467257 3.210000e-96 363
10 TraesCS4B01G108900 chr7D 74.256 672 107 47 2368 3021 407072271 407071648 5.680000e-54 222
11 TraesCS4B01G108900 chr7A 74.030 670 112 47 2368 3021 464573277 464572654 2.640000e-52 217
12 TraesCS4B01G108900 chr7B 73.958 672 109 47 2368 3021 418049671 418049048 1.230000e-50 211


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 TraesCS4B01G108900 chr4B 119821540 119825900 4360 True 8054 8054 100.0000 1 4361 1 chr4B.!!$R1 4360
1 TraesCS4B01G108900 chr4A 497439195 497443354 4159 True 3042 5450 92.2505 152 4359 2 chr4A.!!$R1 4207
2 TraesCS4B01G108900 chr4D 84544371 84548523 4152 True 3020 5373 91.5100 147 4337 2 chr4D.!!$R1 4190
3 TraesCS4B01G108900 chr2A 530380563 530381335 772 False 398 398 76.6950 2481 3271 1 chr2A.!!$F1 790
4 TraesCS4B01G108900 chr2D 392525893 392526669 776 False 372 372 75.9850 2476 3271 1 chr2D.!!$F1 795
5 TraesCS4B01G108900 chr2B 464466512 464467257 745 False 363 363 76.1840 2476 3237 1 chr2B.!!$F1 761
6 TraesCS4B01G108900 chr7D 407071648 407072271 623 True 222 222 74.2560 2368 3021 1 chr7D.!!$R1 653
7 TraesCS4B01G108900 chr7A 464572654 464573277 623 True 217 217 74.0300 2368 3021 1 chr7A.!!$R1 653
8 TraesCS4B01G108900 chr7B 418049048 418049671 623 True 211 211 73.9580 2368 3021 1 chr7B.!!$R1 653

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
804 826 0.534412 CAGACACTCTAGGCCAGTGG 59.466 60.000 21.96 4.2 44.86 4.00 F
966 1000 0.617413 TTCCGTCCGTCTCCTACTCT 59.383 55.000 0.00 0.0 0.00 3.24 F
1845 1891 0.680280 AGTACATCGACGTCCAGGCT 60.680 55.000 10.58 0.0 0.00 4.58 F
2328 2374 2.498167 GAGCATTTCACACTGGACACT 58.502 47.619 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 1868 0.599060 TGGACGTCGATGTACTGCAA 59.401 50.000 20.49 0.0 0.00 4.08 R
2940 3010 0.820871 GCTGCAGCCTGTAGTACTCT 59.179 55.000 28.76 0.0 32.42 3.24 R
3057 3127 1.599797 GTCCACCACGTTCTTGGGG 60.600 63.158 6.94 0.0 41.49 4.96 R
4076 4191 0.104304 ACTCTCGTTTTGCCGTGTCT 59.896 50.000 0.00 0.0 0.00 3.41 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
21 22 3.414549 TTGTCTCGGTCAACTTTTTGC 57.585 42.857 0.00 0.00 32.17 3.68
22 23 2.639065 TGTCTCGGTCAACTTTTTGCT 58.361 42.857 0.00 0.00 32.17 3.91
23 24 3.799366 TGTCTCGGTCAACTTTTTGCTA 58.201 40.909 0.00 0.00 32.17 3.49
24 25 3.807622 TGTCTCGGTCAACTTTTTGCTAG 59.192 43.478 0.00 0.00 32.17 3.42
25 26 4.056050 GTCTCGGTCAACTTTTTGCTAGA 58.944 43.478 0.00 0.00 32.17 2.43
26 27 4.510340 GTCTCGGTCAACTTTTTGCTAGAA 59.490 41.667 0.00 0.00 32.17 2.10
27 28 5.007332 GTCTCGGTCAACTTTTTGCTAGAAA 59.993 40.000 0.00 0.00 32.17 2.52
28 29 5.763204 TCTCGGTCAACTTTTTGCTAGAAAT 59.237 36.000 0.00 0.00 32.17 2.17
29 30 6.262273 TCTCGGTCAACTTTTTGCTAGAAATT 59.738 34.615 0.00 0.00 32.17 1.82
30 31 6.801575 TCGGTCAACTTTTTGCTAGAAATTT 58.198 32.000 0.00 0.00 32.17 1.82
31 32 6.915843 TCGGTCAACTTTTTGCTAGAAATTTC 59.084 34.615 10.33 10.33 32.17 2.17
32 33 6.143919 CGGTCAACTTTTTGCTAGAAATTTCC 59.856 38.462 14.61 0.43 32.17 3.13
33 34 6.423905 GGTCAACTTTTTGCTAGAAATTTCCC 59.576 38.462 14.61 4.58 32.17 3.97
34 35 7.210174 GTCAACTTTTTGCTAGAAATTTCCCT 58.790 34.615 14.61 0.00 32.17 4.20
35 36 8.357402 GTCAACTTTTTGCTAGAAATTTCCCTA 58.643 33.333 14.61 1.07 32.17 3.53
36 37 8.357402 TCAACTTTTTGCTAGAAATTTCCCTAC 58.643 33.333 14.61 3.22 32.17 3.18
37 38 8.360390 CAACTTTTTGCTAGAAATTTCCCTACT 58.640 33.333 14.61 0.00 0.00 2.57
38 39 8.478775 ACTTTTTGCTAGAAATTTCCCTACTT 57.521 30.769 14.61 0.00 0.00 2.24
39 40 8.360390 ACTTTTTGCTAGAAATTTCCCTACTTG 58.640 33.333 14.61 0.00 0.00 3.16
40 41 5.897377 TTGCTAGAAATTTCCCTACTTGC 57.103 39.130 14.61 8.81 0.00 4.01
41 42 4.917385 TGCTAGAAATTTCCCTACTTGCA 58.083 39.130 14.61 11.12 37.11 4.08
42 43 5.321102 TGCTAGAAATTTCCCTACTTGCAA 58.679 37.500 14.61 0.00 36.71 4.08
43 44 5.772672 TGCTAGAAATTTCCCTACTTGCAAA 59.227 36.000 14.61 0.00 36.71 3.68
44 45 6.093404 GCTAGAAATTTCCCTACTTGCAAAC 58.907 40.000 14.61 0.00 31.93 2.93
45 46 6.071896 GCTAGAAATTTCCCTACTTGCAAACT 60.072 38.462 14.61 0.00 31.93 2.66
46 47 7.120726 GCTAGAAATTTCCCTACTTGCAAACTA 59.879 37.037 14.61 0.00 31.93 2.24
47 48 7.833285 AGAAATTTCCCTACTTGCAAACTAA 57.167 32.000 14.61 0.00 0.00 2.24
48 49 8.245195 AGAAATTTCCCTACTTGCAAACTAAA 57.755 30.769 14.61 0.00 0.00 1.85
49 50 8.870116 AGAAATTTCCCTACTTGCAAACTAAAT 58.130 29.630 14.61 0.00 0.00 1.40
50 51 9.489084 GAAATTTCCCTACTTGCAAACTAAATT 57.511 29.630 6.95 4.98 0.00 1.82
51 52 9.845740 AAATTTCCCTACTTGCAAACTAAATTT 57.154 25.926 0.00 10.08 32.24 1.82
63 64 6.939551 CAAACTAAATTTGCCACTCTCATG 57.060 37.500 0.00 0.00 41.30 3.07
64 65 4.708726 ACTAAATTTGCCACTCTCATGC 57.291 40.909 0.00 0.00 0.00 4.06
65 66 3.445096 ACTAAATTTGCCACTCTCATGCC 59.555 43.478 0.00 0.00 0.00 4.40
66 67 1.927487 AATTTGCCACTCTCATGCCA 58.073 45.000 0.00 0.00 0.00 4.92
67 68 1.927487 ATTTGCCACTCTCATGCCAA 58.073 45.000 0.00 0.00 0.00 4.52
68 69 1.927487 TTTGCCACTCTCATGCCAAT 58.073 45.000 0.00 0.00 0.00 3.16
69 70 2.804986 TTGCCACTCTCATGCCAATA 57.195 45.000 0.00 0.00 0.00 1.90
70 71 3.301794 TTGCCACTCTCATGCCAATAT 57.698 42.857 0.00 0.00 0.00 1.28
71 72 4.436113 TTGCCACTCTCATGCCAATATA 57.564 40.909 0.00 0.00 0.00 0.86
72 73 4.436113 TGCCACTCTCATGCCAATATAA 57.564 40.909 0.00 0.00 0.00 0.98
73 74 4.790937 TGCCACTCTCATGCCAATATAAA 58.209 39.130 0.00 0.00 0.00 1.40
74 75 5.387788 TGCCACTCTCATGCCAATATAAAT 58.612 37.500 0.00 0.00 0.00 1.40
75 76 5.834742 TGCCACTCTCATGCCAATATAAATT 59.165 36.000 0.00 0.00 0.00 1.82
76 77 6.154445 GCCACTCTCATGCCAATATAAATTG 58.846 40.000 0.00 0.00 41.90 2.32
77 78 6.154445 CCACTCTCATGCCAATATAAATTGC 58.846 40.000 0.00 0.00 41.06 3.56
78 79 6.154445 CACTCTCATGCCAATATAAATTGCC 58.846 40.000 0.00 0.00 41.06 4.52
79 80 5.834742 ACTCTCATGCCAATATAAATTGCCA 59.165 36.000 0.00 0.00 41.06 4.92
80 81 6.495872 ACTCTCATGCCAATATAAATTGCCAT 59.504 34.615 0.00 0.00 40.74 4.40
81 82 7.670979 ACTCTCATGCCAATATAAATTGCCATA 59.329 33.333 0.00 0.00 38.69 2.74
82 83 8.058667 TCTCATGCCAATATAAATTGCCATAG 57.941 34.615 0.00 0.00 38.69 2.23
83 84 7.889600 TCTCATGCCAATATAAATTGCCATAGA 59.110 33.333 0.00 0.00 38.69 1.98
84 85 8.419922 TCATGCCAATATAAATTGCCATAGAA 57.580 30.769 0.00 0.00 38.69 2.10
85 86 8.868103 TCATGCCAATATAAATTGCCATAGAAA 58.132 29.630 0.00 0.00 38.69 2.52
86 87 9.491675 CATGCCAATATAAATTGCCATAGAAAA 57.508 29.630 0.00 0.00 38.69 2.29
98 99 6.740411 TGCCATAGAAAAATTCAATTTGGC 57.260 33.333 12.56 12.56 40.12 4.52
99 100 6.474630 TGCCATAGAAAAATTCAATTTGGCT 58.525 32.000 18.01 11.15 40.24 4.75
100 101 6.941436 TGCCATAGAAAAATTCAATTTGGCTT 59.059 30.769 18.01 1.30 40.24 4.35
101 102 7.094720 TGCCATAGAAAAATTCAATTTGGCTTG 60.095 33.333 18.01 9.68 40.24 4.01
102 103 7.245604 CCATAGAAAAATTCAATTTGGCTTGC 58.754 34.615 0.00 0.00 31.77 4.01
103 104 5.694231 AGAAAAATTCAATTTGGCTTGCC 57.306 34.783 4.43 4.43 31.77 4.52
104 105 5.379187 AGAAAAATTCAATTTGGCTTGCCT 58.621 33.333 13.18 0.00 31.77 4.75
105 106 6.532826 AGAAAAATTCAATTTGGCTTGCCTA 58.467 32.000 13.18 2.12 31.77 3.93
106 107 6.427853 AGAAAAATTCAATTTGGCTTGCCTAC 59.572 34.615 13.18 0.00 31.77 3.18
107 108 4.888326 AATTCAATTTGGCTTGCCTACA 57.112 36.364 13.18 0.00 0.00 2.74
108 109 4.888326 ATTCAATTTGGCTTGCCTACAA 57.112 36.364 13.18 3.89 0.00 2.41
109 110 6.205270 AAAATTCAATTTGGCTTGCCTACAAG 59.795 34.615 13.18 1.44 43.14 3.16
110 111 8.120995 AAAATTCAATTTGGCTTGCCTACAAGT 61.121 33.333 13.18 0.25 42.71 3.16
119 120 3.930336 CTTGCCTACAAGTCTGACATCA 58.070 45.455 10.88 0.00 46.84 3.07
120 121 3.599730 TGCCTACAAGTCTGACATCAG 57.400 47.619 10.88 2.24 45.08 2.90
121 122 4.322273 CTTGCCTACAAGTCTGACATCAGA 60.322 45.833 10.88 7.52 46.84 3.27
135 136 6.471976 TGACATCAGATTATTAGCATTCGC 57.528 37.500 0.00 0.00 38.99 4.70
136 137 5.990996 TGACATCAGATTATTAGCATTCGCA 59.009 36.000 0.00 0.00 42.27 5.10
137 138 6.482973 TGACATCAGATTATTAGCATTCGCAA 59.517 34.615 0.00 0.00 42.27 4.85
138 139 7.012232 TGACATCAGATTATTAGCATTCGCAAA 59.988 33.333 0.00 0.00 42.27 3.68
139 140 7.706159 ACATCAGATTATTAGCATTCGCAAAA 58.294 30.769 0.00 0.00 42.27 2.44
140 141 8.190122 ACATCAGATTATTAGCATTCGCAAAAA 58.810 29.630 0.00 0.00 42.27 1.94
170 171 5.702670 ACATCAGATTATTAGCATTCCCGTG 59.297 40.000 0.00 0.00 0.00 4.94
237 239 1.074889 GACCAGGCTAAAAAGGACCCA 59.925 52.381 0.00 0.00 0.00 4.51
273 275 1.382522 ATTAACCACGCAGCATCCTG 58.617 50.000 0.00 0.00 42.13 3.86
382 388 3.495100 CGTTAGCAAAGGCCTATCCTGAT 60.495 47.826 5.16 2.56 46.94 2.90
484 498 0.663153 GGCACTATCATTTGTCCGGC 59.337 55.000 0.00 0.00 0.00 6.13
566 582 2.260247 CAGTGGGCAGTGGAACATG 58.740 57.895 0.00 0.00 44.52 3.21
586 602 1.893808 CAAACCGACCTGCTGCTGT 60.894 57.895 0.00 0.00 0.00 4.40
618 640 2.994355 TGGTGGTAGGTAGTTTTCCCT 58.006 47.619 0.00 0.00 34.74 4.20
632 654 1.971149 TTCCCTGGATGACACATCCT 58.029 50.000 24.73 0.00 38.95 3.24
653 675 1.150536 AGGAAGCAAACAAGCCGGA 59.849 52.632 5.05 0.00 34.23 5.14
654 676 0.890996 AGGAAGCAAACAAGCCGGAG 60.891 55.000 5.05 0.00 34.23 4.63
657 679 0.890996 AAGCAAACAAGCCGGAGAGG 60.891 55.000 5.05 0.00 44.97 3.69
684 706 1.079681 CACAATGCCCACATGCACC 60.080 57.895 0.00 0.00 45.48 5.01
685 707 1.533513 ACAATGCCCACATGCACCA 60.534 52.632 0.00 0.00 45.48 4.17
686 708 1.216977 CAATGCCCACATGCACCAG 59.783 57.895 0.00 0.00 45.48 4.00
687 709 2.652095 AATGCCCACATGCACCAGC 61.652 57.895 0.00 0.00 45.48 4.85
715 737 4.514577 CTCCGCGCAATCCCGTCT 62.515 66.667 8.75 0.00 0.00 4.18
716 738 4.508128 TCCGCGCAATCCCGTCTC 62.508 66.667 8.75 0.00 0.00 3.36
721 743 4.508128 GCAATCCCGTCTCGGCGA 62.508 66.667 10.14 10.14 46.86 5.54
781 803 2.978278 AGCCATTATCTTCTCCAGGAGG 59.022 50.000 17.10 1.24 0.00 4.30
782 804 2.039613 GCCATTATCTTCTCCAGGAGGG 59.960 54.545 17.10 9.97 34.83 4.30
797 819 1.002274 AGGGGGCAGACACTCTAGG 59.998 63.158 0.00 0.00 0.00 3.02
798 820 2.736826 GGGGGCAGACACTCTAGGC 61.737 68.421 0.00 0.00 0.00 3.93
799 821 2.736826 GGGGCAGACACTCTAGGCC 61.737 68.421 0.00 0.00 43.86 5.19
800 822 1.990060 GGGCAGACACTCTAGGCCA 60.990 63.158 5.01 0.00 46.37 5.36
801 823 1.519719 GGCAGACACTCTAGGCCAG 59.480 63.158 5.01 0.00 44.01 4.85
802 824 1.261238 GGCAGACACTCTAGGCCAGT 61.261 60.000 5.01 0.00 44.01 4.00
804 826 0.534412 CAGACACTCTAGGCCAGTGG 59.466 60.000 21.96 4.20 44.86 4.00
835 869 1.475930 GGGAATAGTTGGCAGAGCTCC 60.476 57.143 10.93 0.00 0.00 4.70
849 883 4.191544 CAGAGCTCCGGTGAAATGAAATA 58.808 43.478 10.93 0.00 0.00 1.40
851 885 4.080863 AGAGCTCCGGTGAAATGAAATACT 60.081 41.667 10.93 0.00 0.00 2.12
852 886 5.128827 AGAGCTCCGGTGAAATGAAATACTA 59.871 40.000 10.93 0.00 0.00 1.82
853 887 5.360591 AGCTCCGGTGAAATGAAATACTAG 58.639 41.667 7.92 0.00 0.00 2.57
946 980 1.133976 GGCTGCTCTACCATGTCCATT 60.134 52.381 0.00 0.00 0.00 3.16
947 981 2.648059 GCTGCTCTACCATGTCCATTT 58.352 47.619 0.00 0.00 0.00 2.32
956 990 1.448985 CATGTCCATTTTCCGTCCGT 58.551 50.000 0.00 0.00 0.00 4.69
966 1000 0.617413 TTCCGTCCGTCTCCTACTCT 59.383 55.000 0.00 0.00 0.00 3.24
981 1015 1.754621 CTCTGCTCCACCGCTCCTA 60.755 63.158 0.00 0.00 0.00 2.94
983 1017 2.037367 TGCTCCACCGCTCCTACT 59.963 61.111 0.00 0.00 0.00 2.57
986 1020 1.076632 CTCCACCGCTCCTACTCCT 60.077 63.158 0.00 0.00 0.00 3.69
987 1021 1.076923 TCCACCGCTCCTACTCCTC 60.077 63.158 0.00 0.00 0.00 3.71
988 1022 2.128507 CCACCGCTCCTACTCCTCC 61.129 68.421 0.00 0.00 0.00 4.30
1033 1067 1.518133 CTCTTCCTCGCCTTGCTCG 60.518 63.158 0.00 0.00 0.00 5.03
1034 1068 2.219325 CTCTTCCTCGCCTTGCTCGT 62.219 60.000 0.00 0.00 0.00 4.18
1035 1069 2.048222 TTCCTCGCCTTGCTCGTG 60.048 61.111 0.00 0.00 0.00 4.35
1327 1373 1.006571 GACCTGTCCAAGAACGCGA 60.007 57.895 15.93 0.00 0.00 5.87
1339 1385 2.765250 GAACGCGAGCAGGTCCAAGA 62.765 60.000 15.93 0.00 0.00 3.02
1491 1537 2.360726 GTTGCCGTGGGTAAGGGG 60.361 66.667 0.00 0.00 34.15 4.79
1674 1720 1.379977 CCTCTCGTGCTGGGGTAGA 60.380 63.158 0.00 0.00 0.00 2.59
1710 1756 4.681978 GGTGAGAACGCCACCGCT 62.682 66.667 0.00 0.00 43.80 5.52
1845 1891 0.680280 AGTACATCGACGTCCAGGCT 60.680 55.000 10.58 0.00 0.00 4.58
1902 1948 4.590553 TCCCTGGTGTGCTGGGGA 62.591 66.667 0.00 0.00 44.76 4.81
2205 2251 4.609018 CTCCTATGGTGCCGCCGG 62.609 72.222 0.00 0.00 41.21 6.13
2328 2374 2.498167 GAGCATTTCACACTGGACACT 58.502 47.619 0.00 0.00 0.00 3.55
3390 3460 4.101790 CCATTGACCGCCACGCAC 62.102 66.667 0.00 0.00 0.00 5.34
3391 3461 4.444024 CATTGACCGCCACGCACG 62.444 66.667 0.00 0.00 0.00 5.34
3436 3506 0.882042 GCGATGTCTGGATCCGCATT 60.882 55.000 7.39 0.00 44.55 3.56
3605 3684 3.262936 CCAATTTCGTGGCGAGCA 58.737 55.556 0.00 0.00 37.14 4.26
3703 3783 4.712425 ACCGGTTTCCGCTCGTCG 62.712 66.667 0.00 0.00 46.86 5.12
3768 3848 0.673437 ACACGGCACCATGGAAAAAG 59.327 50.000 21.47 8.05 0.00 2.27
3779 3859 3.364549 CATGGAAAAAGGGAGGCATACA 58.635 45.455 0.00 0.00 0.00 2.29
3783 3863 4.222588 TGGAAAAAGGGAGGCATACATTTG 59.777 41.667 0.00 0.00 0.00 2.32
3854 3962 6.515035 CGCCTCCATTTGTTCTTTACTCTTTT 60.515 38.462 0.00 0.00 0.00 2.27
3875 3983 0.468214 TTGTTTCATTGGGCGTGGGA 60.468 50.000 0.00 0.00 0.00 4.37
3936 4045 3.841845 TCCGGGGGATAATTGTGTATAGG 59.158 47.826 0.00 0.00 0.00 2.57
3973 4082 8.519526 TCAAAAGATTATTACAAAGCGTGGATT 58.480 29.630 0.00 0.00 0.00 3.01
3999 4112 7.841915 TTTTTCTTTTTGTTCATGGTTCTCC 57.158 32.000 0.00 0.00 0.00 3.71
4007 4120 7.654022 TTTGTTCATGGTTCTCCTTTACTTT 57.346 32.000 0.00 0.00 34.23 2.66
4008 4121 6.877611 TGTTCATGGTTCTCCTTTACTTTC 57.122 37.500 0.00 0.00 34.23 2.62
4009 4122 5.468746 TGTTCATGGTTCTCCTTTACTTTCG 59.531 40.000 0.00 0.00 34.23 3.46
4011 4124 5.235516 TCATGGTTCTCCTTTACTTTCGTC 58.764 41.667 0.00 0.00 34.23 4.20
4014 4127 3.427863 GGTTCTCCTTTACTTTCGTCACG 59.572 47.826 0.00 0.00 0.00 4.35
4022 4135 4.650545 TTACTTTCGTCACGTAATTGCC 57.349 40.909 0.00 0.00 0.00 4.52
4035 4148 2.596046 TTGCCCGTCCGTTGCAAT 60.596 55.556 0.59 0.00 39.86 3.56
4037 4150 3.053291 GCCCGTCCGTTGCAATGA 61.053 61.111 20.36 8.83 0.00 2.57
4041 4154 0.374758 CCGTCCGTTGCAATGAGATG 59.625 55.000 20.36 17.91 0.00 2.90
4052 4165 7.379529 CCGTTGCAATGAGATGTAAATATTTCC 59.620 37.037 20.36 0.00 0.00 3.13
4053 4166 8.131100 CGTTGCAATGAGATGTAAATATTTCCT 58.869 33.333 13.63 0.00 0.00 3.36
4086 4201 4.966965 TTTGAAGTTTTAGACACGGCAA 57.033 36.364 0.00 0.00 0.00 4.52
4110 4225 2.704572 GAGAGTTGGGAACATGTCTGG 58.295 52.381 0.00 0.00 42.32 3.86
4178 4293 3.636153 ACATCCTTGAAAGGTCTAGCC 57.364 47.619 8.91 0.00 46.54 3.93
4206 4321 8.305046 TGATTTTTATATGGTCAAAAGGGAGG 57.695 34.615 0.00 0.00 0.00 4.30
4253 4368 5.751243 TTCTTTTTCTTGGTAGTGCTCAC 57.249 39.130 0.00 0.00 0.00 3.51
4275 4390 1.136147 CGCATGCTGCTCACTTTCC 59.864 57.895 17.13 0.00 42.25 3.13
4293 4408 4.934797 TTCCAGTGATTCTCCCTTTCAT 57.065 40.909 0.00 0.00 0.00 2.57
4312 4427 3.711190 TCATAGATCACTTTGCCTGCCTA 59.289 43.478 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.442273 AGCAAAAAGTTGACCGAGACAAA 59.558 39.130 0.00 0.00 36.83 2.83
1 2 3.013921 AGCAAAAAGTTGACCGAGACAA 58.986 40.909 0.00 0.00 36.83 3.18
2 3 2.639065 AGCAAAAAGTTGACCGAGACA 58.361 42.857 0.00 0.00 36.83 3.41
4 5 4.330944 TCTAGCAAAAAGTTGACCGAGA 57.669 40.909 0.00 0.00 36.83 4.04
5 6 5.418310 TTTCTAGCAAAAAGTTGACCGAG 57.582 39.130 0.00 0.00 36.83 4.63
6 7 6.385649 AATTTCTAGCAAAAAGTTGACCGA 57.614 33.333 0.00 0.00 36.83 4.69
7 8 6.143919 GGAAATTTCTAGCAAAAAGTTGACCG 59.856 38.462 17.42 0.00 36.83 4.79
8 9 6.423905 GGGAAATTTCTAGCAAAAAGTTGACC 59.576 38.462 17.42 1.28 36.83 4.02
9 10 7.210174 AGGGAAATTTCTAGCAAAAAGTTGAC 58.790 34.615 17.42 0.00 36.83 3.18
10 11 7.360113 AGGGAAATTTCTAGCAAAAAGTTGA 57.640 32.000 17.42 0.00 36.83 3.18
11 12 8.360390 AGTAGGGAAATTTCTAGCAAAAAGTTG 58.640 33.333 17.42 0.00 37.83 3.16
12 13 8.478775 AGTAGGGAAATTTCTAGCAAAAAGTT 57.521 30.769 17.42 0.00 0.00 2.66
13 14 8.360390 CAAGTAGGGAAATTTCTAGCAAAAAGT 58.640 33.333 17.42 0.00 0.00 2.66
14 15 7.329471 GCAAGTAGGGAAATTTCTAGCAAAAAG 59.671 37.037 17.42 2.99 0.00 2.27
15 16 7.151976 GCAAGTAGGGAAATTTCTAGCAAAAA 58.848 34.615 17.42 0.00 0.00 1.94
16 17 6.266558 TGCAAGTAGGGAAATTTCTAGCAAAA 59.733 34.615 17.42 0.00 0.00 2.44
17 18 5.772672 TGCAAGTAGGGAAATTTCTAGCAAA 59.227 36.000 17.42 0.00 0.00 3.68
18 19 5.321102 TGCAAGTAGGGAAATTTCTAGCAA 58.679 37.500 17.42 0.00 0.00 3.91
19 20 4.917385 TGCAAGTAGGGAAATTTCTAGCA 58.083 39.130 17.42 13.11 0.00 3.49
20 21 5.897377 TTGCAAGTAGGGAAATTTCTAGC 57.103 39.130 17.42 11.09 0.00 3.42
21 22 7.454260 AGTTTGCAAGTAGGGAAATTTCTAG 57.546 36.000 17.42 2.38 30.73 2.43
22 23 8.927675 TTAGTTTGCAAGTAGGGAAATTTCTA 57.072 30.769 17.42 0.80 30.73 2.10
23 24 7.833285 TTAGTTTGCAAGTAGGGAAATTTCT 57.167 32.000 17.42 1.79 30.73 2.52
24 25 9.489084 AATTTAGTTTGCAAGTAGGGAAATTTC 57.511 29.630 9.83 9.83 30.73 2.17
25 26 9.845740 AAATTTAGTTTGCAAGTAGGGAAATTT 57.154 25.926 15.73 15.73 30.73 1.82
26 27 9.271828 CAAATTTAGTTTGCAAGTAGGGAAATT 57.728 29.630 0.00 5.25 40.62 1.82
27 28 8.831715 CAAATTTAGTTTGCAAGTAGGGAAAT 57.168 30.769 0.00 0.00 40.62 2.17
41 42 5.473039 GCATGAGAGTGGCAAATTTAGTTT 58.527 37.500 0.00 0.00 0.00 2.66
42 43 4.082026 GGCATGAGAGTGGCAAATTTAGTT 60.082 41.667 0.00 0.00 43.52 2.24
43 44 3.445096 GGCATGAGAGTGGCAAATTTAGT 59.555 43.478 0.00 0.00 43.52 2.24
44 45 4.037858 GGCATGAGAGTGGCAAATTTAG 57.962 45.455 0.00 0.00 43.52 1.85
52 53 5.972107 ATTTATATTGGCATGAGAGTGGC 57.028 39.130 0.00 0.00 44.24 5.01
53 54 6.154445 GCAATTTATATTGGCATGAGAGTGG 58.846 40.000 0.00 0.00 41.21 4.00
72 73 8.245491 GCCAAATTGAATTTTTCTATGGCAATT 58.755 29.630 18.93 0.00 35.54 2.32
73 74 7.612633 AGCCAAATTGAATTTTTCTATGGCAAT 59.387 29.630 23.31 7.90 36.85 3.56
74 75 6.941436 AGCCAAATTGAATTTTTCTATGGCAA 59.059 30.769 23.31 0.00 36.85 4.52
75 76 6.474630 AGCCAAATTGAATTTTTCTATGGCA 58.525 32.000 23.31 0.00 36.85 4.92
76 77 6.990341 AGCCAAATTGAATTTTTCTATGGC 57.010 33.333 17.07 17.07 35.62 4.40
77 78 7.245604 GCAAGCCAAATTGAATTTTTCTATGG 58.754 34.615 0.00 0.22 31.55 2.74
78 79 7.120138 AGGCAAGCCAAATTGAATTTTTCTATG 59.880 33.333 14.40 0.00 38.92 2.23
79 80 7.170277 AGGCAAGCCAAATTGAATTTTTCTAT 58.830 30.769 14.40 0.00 38.92 1.98
80 81 6.532826 AGGCAAGCCAAATTGAATTTTTCTA 58.467 32.000 14.40 0.00 38.92 2.10
81 82 5.379187 AGGCAAGCCAAATTGAATTTTTCT 58.621 33.333 14.40 0.00 38.92 2.52
82 83 5.694231 AGGCAAGCCAAATTGAATTTTTC 57.306 34.783 14.40 0.00 38.92 2.29
83 84 6.060788 TGTAGGCAAGCCAAATTGAATTTTT 58.939 32.000 14.40 0.00 38.92 1.94
84 85 5.619220 TGTAGGCAAGCCAAATTGAATTTT 58.381 33.333 14.40 0.00 38.92 1.82
85 86 5.226194 TGTAGGCAAGCCAAATTGAATTT 57.774 34.783 14.40 0.00 38.92 1.82
86 87 4.888326 TGTAGGCAAGCCAAATTGAATT 57.112 36.364 14.40 0.00 38.92 2.17
87 88 4.824289 CTTGTAGGCAAGCCAAATTGAAT 58.176 39.130 14.40 0.00 44.54 2.57
88 89 4.255833 CTTGTAGGCAAGCCAAATTGAA 57.744 40.909 14.40 0.00 44.54 2.69
89 90 3.940209 CTTGTAGGCAAGCCAAATTGA 57.060 42.857 14.40 0.00 44.54 2.57
97 98 5.678964 CTGATGTCAGACTTGTAGGCAAGC 61.679 50.000 3.96 1.62 46.59 4.01
98 99 3.931468 CTGATGTCAGACTTGTAGGCAAG 59.069 47.826 3.96 5.87 46.59 4.01
99 100 3.930336 CTGATGTCAGACTTGTAGGCAA 58.070 45.455 3.96 0.00 46.59 4.52
100 101 3.599730 CTGATGTCAGACTTGTAGGCA 57.400 47.619 3.96 0.00 46.59 4.75
109 110 7.621013 GCGAATGCTAATAATCTGATGTCAGAC 60.621 40.741 14.46 0.00 46.07 3.51
110 111 6.367149 GCGAATGCTAATAATCTGATGTCAGA 59.633 38.462 14.52 14.52 46.70 3.27
111 112 6.146673 TGCGAATGCTAATAATCTGATGTCAG 59.853 38.462 3.61 3.61 42.88 3.51
112 113 5.990996 TGCGAATGCTAATAATCTGATGTCA 59.009 36.000 0.00 0.00 43.34 3.58
113 114 6.471976 TGCGAATGCTAATAATCTGATGTC 57.528 37.500 0.00 0.00 43.34 3.06
114 115 6.866010 TTGCGAATGCTAATAATCTGATGT 57.134 33.333 0.00 0.00 43.34 3.06
115 116 8.564648 TTTTTGCGAATGCTAATAATCTGATG 57.435 30.769 0.00 0.00 43.34 3.07
141 142 8.854117 GGGAATGCTAATAATCTGATGTCTTTT 58.146 33.333 0.00 0.00 0.00 2.27
142 143 7.173907 CGGGAATGCTAATAATCTGATGTCTTT 59.826 37.037 0.00 0.00 0.00 2.52
143 144 6.652481 CGGGAATGCTAATAATCTGATGTCTT 59.348 38.462 0.00 0.00 0.00 3.01
144 145 6.169094 CGGGAATGCTAATAATCTGATGTCT 58.831 40.000 0.00 0.00 0.00 3.41
145 146 5.934625 ACGGGAATGCTAATAATCTGATGTC 59.065 40.000 0.00 0.00 0.00 3.06
207 209 3.741245 TTAGCCTGGTCTCTACTCACT 57.259 47.619 0.00 0.00 0.00 3.41
208 210 4.803098 TTTTAGCCTGGTCTCTACTCAC 57.197 45.455 0.00 0.00 0.00 3.51
209 211 4.223032 CCTTTTTAGCCTGGTCTCTACTCA 59.777 45.833 0.00 0.00 0.00 3.41
210 212 4.466726 TCCTTTTTAGCCTGGTCTCTACTC 59.533 45.833 0.00 0.00 0.00 2.59
211 213 4.223255 GTCCTTTTTAGCCTGGTCTCTACT 59.777 45.833 0.00 0.00 0.00 2.57
212 214 4.505808 GTCCTTTTTAGCCTGGTCTCTAC 58.494 47.826 0.00 0.00 0.00 2.59
213 215 3.518303 GGTCCTTTTTAGCCTGGTCTCTA 59.482 47.826 0.00 0.00 0.00 2.43
214 216 2.306219 GGTCCTTTTTAGCCTGGTCTCT 59.694 50.000 0.00 0.00 0.00 3.10
237 239 8.028938 CGTGGTTAATTCTTCTTTGAATGGAAT 58.971 33.333 0.00 0.00 36.84 3.01
273 275 1.112113 TTCAGGTGTAGGCTCGATCC 58.888 55.000 0.00 0.00 0.00 3.36
484 498 1.179152 TGGAGATGGCTGCAACAATG 58.821 50.000 0.50 0.00 39.70 2.82
500 516 0.108804 GTTTCGTCTCTCCGCATGGA 60.109 55.000 0.00 0.00 43.88 3.41
586 602 6.955851 ACTACCTACCACCATCTACTTAACAA 59.044 38.462 0.00 0.00 0.00 2.83
618 640 3.114643 TCCTGTAGGATGTGTCATCCA 57.885 47.619 24.56 12.01 39.78 3.41
632 654 1.234821 CGGCTTGTTTGCTTCCTGTA 58.765 50.000 0.00 0.00 0.00 2.74
653 675 1.915141 CATTGTGGGTTGCTTCCTCT 58.085 50.000 0.00 0.00 0.00 3.69
654 676 0.244721 GCATTGTGGGTTGCTTCCTC 59.755 55.000 0.00 0.00 35.95 3.71
657 679 1.293179 GGGCATTGTGGGTTGCTTC 59.707 57.895 0.00 0.00 38.88 3.86
713 735 0.744281 TGCTTATCATGTCGCCGAGA 59.256 50.000 0.00 0.00 0.00 4.04
714 736 1.258982 GTTGCTTATCATGTCGCCGAG 59.741 52.381 0.00 0.00 0.00 4.63
715 737 1.134818 AGTTGCTTATCATGTCGCCGA 60.135 47.619 0.00 0.00 0.00 5.54
716 738 1.258982 GAGTTGCTTATCATGTCGCCG 59.741 52.381 0.00 0.00 0.00 6.46
717 739 1.258982 CGAGTTGCTTATCATGTCGCC 59.741 52.381 0.00 0.00 0.00 5.54
718 740 1.927174 ACGAGTTGCTTATCATGTCGC 59.073 47.619 0.00 0.00 35.08 5.19
719 741 3.439293 AGACGAGTTGCTTATCATGTCG 58.561 45.455 0.00 0.00 36.73 4.35
720 742 3.799420 GGAGACGAGTTGCTTATCATGTC 59.201 47.826 0.00 0.00 0.00 3.06
721 743 3.430929 GGGAGACGAGTTGCTTATCATGT 60.431 47.826 0.00 0.00 0.00 3.21
781 803 2.736826 GGCCTAGAGTGTCTGCCCC 61.737 68.421 0.00 0.00 31.44 5.80
782 804 1.965754 CTGGCCTAGAGTGTCTGCCC 61.966 65.000 3.32 0.00 35.39 5.36
799 821 2.567497 CCCACCAGCTTTGCCACTG 61.567 63.158 0.00 0.00 0.00 3.66
800 822 2.203538 CCCACCAGCTTTGCCACT 60.204 61.111 0.00 0.00 0.00 4.00
801 823 1.187567 ATTCCCACCAGCTTTGCCAC 61.188 55.000 0.00 0.00 0.00 5.01
802 824 0.407528 TATTCCCACCAGCTTTGCCA 59.592 50.000 0.00 0.00 0.00 4.92
804 826 1.839424 ACTATTCCCACCAGCTTTGC 58.161 50.000 0.00 0.00 0.00 3.68
835 869 7.495934 ACTTCATCCTAGTATTTCATTTCACCG 59.504 37.037 0.00 0.00 0.00 4.94
849 883 1.041437 GCCGCCTACTTCATCCTAGT 58.959 55.000 0.00 0.00 0.00 2.57
851 885 2.670019 TAGCCGCCTACTTCATCCTA 57.330 50.000 0.00 0.00 0.00 2.94
852 886 1.689273 CTTAGCCGCCTACTTCATCCT 59.311 52.381 0.00 0.00 0.00 3.24
853 887 1.874320 GCTTAGCCGCCTACTTCATCC 60.874 57.143 0.00 0.00 0.00 3.51
929 963 3.620488 GGAAAATGGACATGGTAGAGCA 58.380 45.455 0.00 0.00 0.00 4.26
946 980 1.004044 AGAGTAGGAGACGGACGGAAA 59.996 52.381 0.00 0.00 0.00 3.13
947 981 0.617413 AGAGTAGGAGACGGACGGAA 59.383 55.000 0.00 0.00 0.00 4.30
956 990 0.394488 CGGTGGAGCAGAGTAGGAGA 60.394 60.000 0.00 0.00 0.00 3.71
966 1000 2.037367 AGTAGGAGCGGTGGAGCA 59.963 61.111 0.00 0.00 40.15 4.26
1013 1047 2.237534 GAGCAAGGCGAGGAAGAGCT 62.238 60.000 0.00 0.00 0.00 4.09
1099 1145 1.204941 GCACACTATGGTCGTCTCCTT 59.795 52.381 0.00 0.00 0.00 3.36
1327 1373 0.413832 TAGACCCTCTTGGACCTGCT 59.586 55.000 0.00 0.00 38.00 4.24
1476 1522 2.855014 AACCCCTTACCCACGGCA 60.855 61.111 0.00 0.00 0.00 5.69
1482 1528 1.673337 GCACACGAACCCCTTACCC 60.673 63.158 0.00 0.00 0.00 3.69
1485 1531 2.344500 CCGCACACGAACCCCTTA 59.656 61.111 0.00 0.00 43.93 2.69
1491 1537 3.348967 GACGATGCCGCACACGAAC 62.349 63.158 22.57 14.25 43.93 3.95
1537 1583 0.310854 GTCTTGTTCCCAAAGCACCG 59.689 55.000 0.00 0.00 0.00 4.94
1545 1591 2.241281 TATCCTCCGTCTTGTTCCCA 57.759 50.000 0.00 0.00 0.00 4.37
1689 1735 3.103911 GTGGCGTTCTCACCGTCG 61.104 66.667 0.00 0.00 31.27 5.12
1821 1867 1.269166 GGACGTCGATGTACTGCAAG 58.731 55.000 13.00 0.00 42.29 4.01
1822 1868 0.599060 TGGACGTCGATGTACTGCAA 59.401 50.000 20.49 0.00 0.00 4.08
1902 1948 2.665185 GCGTTGAACTCGTGGCCT 60.665 61.111 3.32 0.00 0.00 5.19
2028 2074 2.327343 GCAGTCCACGCAGATGCAA 61.327 57.895 5.55 0.00 42.21 4.08
2108 2154 6.067350 GCCCAAATAATGATCTTTCTCCTCT 58.933 40.000 0.00 0.00 0.00 3.69
2151 2197 1.674764 CCACCACCAGCACAAGCAAA 61.675 55.000 0.00 0.00 45.49 3.68
2364 2410 3.917760 CTCCCTGACCCGATCCGC 61.918 72.222 0.00 0.00 0.00 5.54
2376 2422 4.698625 ACCGACCCGAAGCTCCCT 62.699 66.667 0.00 0.00 0.00 4.20
2940 3010 0.820871 GCTGCAGCCTGTAGTACTCT 59.179 55.000 28.76 0.00 32.42 3.24
3057 3127 1.599797 GTCCACCACGTTCTTGGGG 60.600 63.158 6.94 0.00 41.49 4.96
3768 3848 2.961062 AGAATGCAAATGTATGCCTCCC 59.039 45.455 0.00 0.00 45.83 4.30
3834 3915 8.702163 ACAACAAAAGAGTAAAGAACAAATGG 57.298 30.769 0.00 0.00 0.00 3.16
3854 3962 0.387202 CCACGCCCAATGAAACAACA 59.613 50.000 0.00 0.00 0.00 3.33
4007 4120 0.733566 GACGGGCAATTACGTGACGA 60.734 55.000 13.70 0.00 44.24 4.20
4008 4121 1.689352 GGACGGGCAATTACGTGACG 61.689 60.000 2.24 2.24 44.24 4.35
4009 4122 1.689352 CGGACGGGCAATTACGTGAC 61.689 60.000 0.00 0.00 44.24 3.67
4011 4124 1.293267 AACGGACGGGCAATTACGTG 61.293 55.000 0.00 0.00 44.24 4.49
4014 4127 1.135939 GCAACGGACGGGCAATTAC 59.864 57.895 5.89 0.00 0.00 1.89
4022 4135 0.374758 CATCTCATTGCAACGGACGG 59.625 55.000 0.00 0.00 0.00 4.79
4056 4169 9.128107 CGTGTCTAAAACTTCAAATATTGCATT 57.872 29.630 0.00 0.00 0.00 3.56
4057 4170 7.754924 CCGTGTCTAAAACTTCAAATATTGCAT 59.245 33.333 0.00 0.00 0.00 3.96
4063 4178 6.621316 TTGCCGTGTCTAAAACTTCAAATA 57.379 33.333 0.00 0.00 0.00 1.40
4064 4179 5.508200 TTGCCGTGTCTAAAACTTCAAAT 57.492 34.783 0.00 0.00 0.00 2.32
4075 4190 1.338973 ACTCTCGTTTTGCCGTGTCTA 59.661 47.619 0.00 0.00 0.00 2.59
4076 4191 0.104304 ACTCTCGTTTTGCCGTGTCT 59.896 50.000 0.00 0.00 0.00 3.41
4077 4192 0.935196 AACTCTCGTTTTGCCGTGTC 59.065 50.000 0.00 0.00 0.00 3.67
4086 4201 3.139077 GACATGTTCCCAACTCTCGTTT 58.861 45.455 0.00 0.00 0.00 3.60
4131 4246 8.079203 ACTCAATTGTTTCGCATTATGTTTGTA 58.921 29.630 5.13 0.00 0.00 2.41
4132 4247 6.922957 ACTCAATTGTTTCGCATTATGTTTGT 59.077 30.769 5.13 0.00 0.00 2.83
4178 4293 6.697019 CCCTTTTGACCATATAAAAATCAGCG 59.303 38.462 0.00 0.00 0.00 5.18
4206 4321 5.186256 AGGGATTTCCTCTTCTTTCCTTC 57.814 43.478 0.00 0.00 44.06 3.46
4293 4408 3.107601 AGTAGGCAGGCAAAGTGATCTA 58.892 45.455 0.00 0.00 0.00 1.98
4312 4427 2.305095 CTCCCCTTGCATCTGGAGT 58.695 57.895 14.61 0.00 39.64 3.85


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

AutoCloner maintained by Alex Coulton.