Multiple sequence alignment - TraesCS3D01G448400

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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 TraesCS3D01G448400 chr3D 100.000 3797 0 0 1 3797 556853968 556857764 0.000000e+00 7012.0
1 TraesCS3D01G448400 chr3D 80.965 1907 300 39 954 2806 556626033 556627930 0.000000e+00 1452.0
2 TraesCS3D01G448400 chr3D 76.144 721 133 28 2064 2760 556958331 556957626 3.630000e-90 342.0
3 TraesCS3D01G448400 chr3D 77.684 354 59 13 974 1318 557482280 557481938 8.320000e-47 198.0
4 TraesCS3D01G448400 chr3D 83.784 111 18 0 1891 2001 556033850 556033740 5.190000e-19 106.0
5 TraesCS3D01G448400 chr3D 97.059 34 1 0 2971 3004 26289495 26289528 1.470000e-04 58.4
6 TraesCS3D01G448400 chr3B 91.969 2926 209 11 1 2913 739326440 739329352 0.000000e+00 4078.0
7 TraesCS3D01G448400 chr3B 89.474 798 67 12 3010 3797 739329926 739330716 0.000000e+00 992.0
8 TraesCS3D01G448400 chr3B 75.533 703 142 21 2064 2742 739542007 739541311 6.120000e-83 318.0
9 TraesCS3D01G448400 chr3B 80.970 268 47 4 2495 2760 739650303 739650038 3.840000e-50 209.0
10 TraesCS3D01G448400 chr3B 84.615 182 28 0 981 1162 739543154 739542973 8.380000e-42 182.0
11 TraesCS3D01G448400 chr3B 75.281 356 69 13 974 1318 739517848 739517501 6.570000e-33 152.0
12 TraesCS3D01G448400 chr3B 78.641 206 41 2 2130 2332 739710567 739710362 2.380000e-27 134.0
13 TraesCS3D01G448400 chr6D 100.000 37 0 0 2968 3004 450360323 450360287 6.810000e-08 69.4
14 TraesCS3D01G448400 chr1D 97.297 37 1 0 2968 3004 208240333 208240369 3.170000e-06 63.9
15 TraesCS3D01G448400 chr1D 94.872 39 2 0 2966 3004 19254257 19254219 1.140000e-05 62.1
16 TraesCS3D01G448400 chr4A 97.222 36 1 0 2969 3004 516580722 516580687 1.140000e-05 62.1
17 TraesCS3D01G448400 chr6A 94.595 37 2 0 2969 3005 608296793 608296757 1.470000e-04 58.4
18 TraesCS3D01G448400 chr5A 97.059 34 1 0 2971 3004 18904169 18904136 1.470000e-04 58.4
19 TraesCS3D01G448400 chr1B 92.308 39 3 0 2966 3004 646055242 646055204 5.300000e-04 56.5
20 TraesCS3D01G448400 chr1A 92.308 39 2 1 2966 3003 30281992 30281954 2.000000e-03 54.7


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 TraesCS3D01G448400 chr3D 556853968 556857764 3796 False 7012 7012 100.0000 1 3797 1 chr3D.!!$F3 3796
1 TraesCS3D01G448400 chr3D 556626033 556627930 1897 False 1452 1452 80.9650 954 2806 1 chr3D.!!$F2 1852
2 TraesCS3D01G448400 chr3D 556957626 556958331 705 True 342 342 76.1440 2064 2760 1 chr3D.!!$R2 696
3 TraesCS3D01G448400 chr3B 739326440 739330716 4276 False 2535 4078 90.7215 1 3797 2 chr3B.!!$F1 3796
4 TraesCS3D01G448400 chr3B 739541311 739543154 1843 True 250 318 80.0740 981 2742 2 chr3B.!!$R4 1761

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
143 144 0.525455 CATCGTCGCCATCTTCGTCA 60.525 55.0 0.0 0.0 0.0 4.35 F
1473 1523 0.028637 GCCGCTACGACACCTACTAC 59.971 60.0 0.0 0.0 0.0 2.73 F
1797 1894 0.120377 ATACTTCTCCCCCACCACCA 59.880 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1774 0.676466 GCCCAATGGTGATGACGACA 60.676 55.0 0.00 0.0 0.00 4.35 R
2313 2482 0.390603 CCGTGGTAAGGTTGATGCGA 60.391 55.0 0.00 0.0 0.00 5.10 R
3701 4408 0.407528 TGTAGGCCAATTGCTCCCAA 59.592 50.0 5.01 0.0 40.92 4.12 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
113 114 7.781763 GTATCCACGAAAATTTTCTTCACAG 57.218 36.000 24.53 12.80 35.07 3.66
131 132 2.456119 GCTGGAGCCAACATCGTCG 61.456 63.158 0.00 0.00 34.31 5.12
137 138 1.815421 GCCAACATCGTCGCCATCT 60.815 57.895 0.00 0.00 0.00 2.90
143 144 0.525455 CATCGTCGCCATCTTCGTCA 60.525 55.000 0.00 0.00 0.00 4.35
150 151 1.203928 GCCATCTTCGTCATCTGTCG 58.796 55.000 0.00 0.00 0.00 4.35
153 154 2.467838 CATCTTCGTCATCTGTCGCAT 58.532 47.619 0.00 0.00 0.00 4.73
176 177 2.024868 TGAATGGTCGTCGGCGTTG 61.025 57.895 10.18 0.00 39.49 4.10
212 213 1.336517 CGGCTGACGTCTTTAACCTCA 60.337 52.381 17.92 0.00 37.93 3.86
216 217 4.745620 GGCTGACGTCTTTAACCTCATATC 59.254 45.833 17.92 0.00 0.00 1.63
251 252 3.283684 CGTTCGGGGTGCTTGCAA 61.284 61.111 0.00 0.00 0.00 4.08
317 318 0.729116 CATGCTTCAGGGCGTAAGTG 59.271 55.000 0.00 0.00 41.68 3.16
349 350 1.070105 CCGTGGTCTTTTGGTCGGA 59.930 57.895 0.00 0.00 40.29 4.55
352 353 1.463444 CGTGGTCTTTTGGTCGGAATC 59.537 52.381 0.00 0.00 0.00 2.52
353 354 2.500229 GTGGTCTTTTGGTCGGAATCA 58.500 47.619 0.00 0.00 0.00 2.57
466 467 3.773370 GGTGACGACTGAGGACCA 58.227 61.111 0.00 0.00 0.00 4.02
468 469 1.461091 GGTGACGACTGAGGACCACA 61.461 60.000 0.00 0.00 0.00 4.17
503 504 6.423001 GGTGATTTATGTACTCGGTGGAATAC 59.577 42.308 0.00 0.00 0.00 1.89
506 507 8.862085 TGATTTATGTACTCGGTGGAATACATA 58.138 33.333 2.37 2.37 42.13 2.29
507 508 9.871238 GATTTATGTACTCGGTGGAATACATAT 57.129 33.333 6.33 0.00 43.44 1.78
512 513 5.624344 ACTCGGTGGAATACATATAGTCG 57.376 43.478 0.00 0.00 0.00 4.18
518 519 5.388944 GTGGAATACATATAGTCGTCGTCC 58.611 45.833 0.00 0.00 0.00 4.79
522 523 2.928334 ACATATAGTCGTCGTCCACCT 58.072 47.619 0.00 0.00 0.00 4.00
590 591 2.662596 GTGTGGACGATGGCCAGA 59.337 61.111 13.05 0.00 35.77 3.86
679 680 4.166011 GCCAAGCACGACATCGCC 62.166 66.667 0.14 0.00 44.43 5.54
689 690 1.587613 GACATCGCCGAGACTGCTC 60.588 63.158 0.00 0.00 37.81 4.26
731 738 2.158959 CCGTTCGACGATCTGGTGC 61.159 63.158 0.00 0.00 46.05 5.01
764 773 3.255379 GCGCTCCCGTTCGACATC 61.255 66.667 0.00 0.00 36.67 3.06
792 801 2.569354 GGCGGCGATCTCAGGATCT 61.569 63.158 12.98 0.00 44.42 2.75
793 802 1.080839 GCGGCGATCTCAGGATCTC 60.081 63.158 12.98 0.00 44.42 2.75
794 803 1.208870 CGGCGATCTCAGGATCTCG 59.791 63.158 0.00 0.00 44.42 4.04
795 804 1.231296 CGGCGATCTCAGGATCTCGA 61.231 60.000 0.00 0.00 44.42 4.04
817 826 1.690219 GGAGATGCCGTGTGGAGGAT 61.690 60.000 0.00 0.00 37.49 3.24
830 839 4.030913 TGTGGAGGATTAGAGATCGGTTT 58.969 43.478 0.00 0.00 0.00 3.27
857 867 3.649986 GTTGCGTCGTTGCCTGCT 61.650 61.111 0.00 0.00 0.00 4.24
946 957 3.651423 CGATCCCTAAACCCTAATTCCCT 59.349 47.826 0.00 0.00 0.00 4.20
947 958 4.842380 CGATCCCTAAACCCTAATTCCCTA 59.158 45.833 0.00 0.00 0.00 3.53
948 959 5.487845 CGATCCCTAAACCCTAATTCCCTAT 59.512 44.000 0.00 0.00 0.00 2.57
949 960 6.351966 CGATCCCTAAACCCTAATTCCCTATC 60.352 46.154 0.00 0.00 0.00 2.08
950 961 5.167921 TCCCTAAACCCTAATTCCCTATCC 58.832 45.833 0.00 0.00 0.00 2.59
983 994 0.588980 CGAGAACGTGATCGCATCGA 60.589 55.000 7.12 0.00 39.83 3.59
1179 1190 2.248487 GTCGAACGCATAGAACGACTT 58.752 47.619 0.00 0.00 42.76 3.01
1228 1242 1.738099 CTGGAGGCCACGTTCTTCG 60.738 63.158 5.01 0.00 46.00 3.79
1393 1431 0.321564 CCAGGACCAAAGCGTGATCA 60.322 55.000 0.00 0.00 0.00 2.92
1473 1523 0.028637 GCCGCTACGACACCTACTAC 59.971 60.000 0.00 0.00 0.00 2.73
1479 1529 0.321919 ACGACACCTACTACGAGCCA 60.322 55.000 0.00 0.00 0.00 4.75
1480 1530 0.806868 CGACACCTACTACGAGCCAA 59.193 55.000 0.00 0.00 0.00 4.52
1495 1545 0.392998 GCCAAAGAAGGAGATCGCCA 60.393 55.000 18.44 0.00 0.00 5.69
1577 1627 1.143305 CTCGAACTCACCAACTGCAG 58.857 55.000 13.48 13.48 0.00 4.41
1674 1732 2.509916 GATGCCCTCCAGAGCCTG 59.490 66.667 0.00 0.00 0.00 4.85
1675 1733 2.285969 ATGCCCTCCAGAGCCTGT 60.286 61.111 2.18 0.00 0.00 4.00
1680 1738 1.333636 CCCTCCAGAGCCTGTTCGAT 61.334 60.000 0.00 0.00 0.00 3.59
1716 1774 0.898320 CCATCGTCCACCTTGAGTCT 59.102 55.000 0.00 0.00 0.00 3.24
1739 1800 0.819582 GTCATCACCATTGGGCCAAG 59.180 55.000 25.16 14.35 37.90 3.61
1742 1803 0.685458 ATCACCATTGGGCCAAGAGC 60.685 55.000 25.16 0.00 42.60 4.09
1797 1894 0.120377 ATACTTCTCCCCCACCACCA 59.880 55.000 0.00 0.00 0.00 4.17
1824 1930 1.549243 TAGTGCTCCAATGTCCGGCA 61.549 55.000 0.00 0.00 0.00 5.69
1829 1935 3.136123 CCAATGTCCGGCAGCCAG 61.136 66.667 13.30 0.00 0.00 4.85
1830 1936 2.046023 CAATGTCCGGCAGCCAGA 60.046 61.111 13.30 1.67 0.00 3.86
1868 2010 1.823041 GCAGCTGGAGAGGGAATGC 60.823 63.158 17.12 0.00 0.00 3.56
1874 2016 1.144936 GGAGAGGGAATGCTGACGG 59.855 63.158 0.00 0.00 0.00 4.79
1937 2079 4.130281 GCGGCGCTTCGTGTACAC 62.130 66.667 26.86 16.32 0.00 2.90
2014 2156 1.662044 CTGCACCTTTTCTGGCCAC 59.338 57.895 0.00 0.00 0.00 5.01
2018 2160 2.978010 CCTTTTCTGGCCACGCGT 60.978 61.111 5.58 5.58 0.00 6.01
2027 2169 2.170273 GCCACGCGTCGAGAAAAC 59.830 61.111 9.86 0.00 0.00 2.43
2071 2240 2.583593 GCAGCGACGAGGATCCAC 60.584 66.667 15.82 6.85 0.00 4.02
2078 2247 2.240162 GACGAGGATCCACACCCCAC 62.240 65.000 15.82 0.00 0.00 4.61
2120 2289 1.608717 CTCCAGGACCTAAGCAGCGT 61.609 60.000 0.00 0.00 0.00 5.07
2163 2332 1.811266 CAACCTCGAGGACATGGCG 60.811 63.158 37.69 12.87 38.94 5.69
2170 2339 4.101448 AGGACATGGCGGTGCTCC 62.101 66.667 0.00 0.00 33.95 4.70
2211 2380 2.034066 CTGCCCGCCTTCTCCAAA 59.966 61.111 0.00 0.00 0.00 3.28
2340 2509 2.038269 CCTTACCACGGCGCAACAT 61.038 57.895 10.83 0.00 0.00 2.71
2350 2519 1.735360 GCGCAACATGGTGCCATAT 59.265 52.632 29.32 0.00 41.73 1.78
2359 2528 7.308288 CGCAACATGGTGCCATATTAAAGTATA 60.308 37.037 29.32 0.00 41.73 1.47
2430 2611 7.556844 ACAAGTCAATAGATCTTATCAACCGT 58.443 34.615 0.00 0.00 0.00 4.83
2443 2624 3.865929 AACCGTGCAGAGCCGACAG 62.866 63.158 0.00 0.00 0.00 3.51
2444 2625 4.363990 CCGTGCAGAGCCGACAGT 62.364 66.667 0.00 0.00 0.00 3.55
2480 2667 2.355197 TGATGGCGATGTTAACAGTGG 58.645 47.619 14.65 6.69 0.00 4.00
2565 2752 4.043200 GTGGGCTTGCAGTTCCGC 62.043 66.667 0.00 0.00 0.00 5.54
2689 2876 2.159531 TGCGAGCATATGAACAACAAGC 60.160 45.455 6.97 0.69 0.00 4.01
2697 2884 7.661040 AGCATATGAACAACAAGCTTAAAACT 58.339 30.769 6.97 0.00 33.67 2.66
2732 2922 5.567037 TCATCCAAAAGGAGAAAGTCAGA 57.433 39.130 0.00 0.00 0.00 3.27
2840 3030 8.141909 TCAAGTATTCATCGTTAATACAGGGAG 58.858 37.037 14.87 5.16 40.65 4.30
2843 3033 4.931661 TCATCGTTAATACAGGGAGGAC 57.068 45.455 0.00 0.00 0.00 3.85
2899 3089 3.132824 GGCCACTGATAAAATTTCTGGGG 59.867 47.826 0.00 0.00 38.33 4.96
2900 3090 3.132824 GCCACTGATAAAATTTCTGGGGG 59.867 47.826 6.08 1.31 36.43 5.40
2902 3092 4.402474 CCACTGATAAAATTTCTGGGGGAC 59.598 45.833 0.00 0.00 33.31 4.46
2928 3411 9.817809 CATGTAATAGGTTAGTTTTGCTCTCTA 57.182 33.333 0.00 0.00 0.00 2.43
2936 3419 6.430000 GGTTAGTTTTGCTCTCTAATGTTCCA 59.570 38.462 0.00 0.00 0.00 3.53
2937 3420 7.040686 GGTTAGTTTTGCTCTCTAATGTTCCAA 60.041 37.037 0.00 0.00 0.00 3.53
2938 3421 6.566197 AGTTTTGCTCTCTAATGTTCCAAG 57.434 37.500 0.00 0.00 0.00 3.61
2976 3673 9.134055 ACTATGTATAGTCTCAAAACTACTCCC 57.866 37.037 0.00 0.00 39.27 4.30
2977 3674 9.357161 CTATGTATAGTCTCAAAACTACTCCCT 57.643 37.037 0.00 0.00 34.68 4.20
2978 3675 7.642082 TGTATAGTCTCAAAACTACTCCCTC 57.358 40.000 0.00 0.00 34.68 4.30
2979 3676 6.606395 TGTATAGTCTCAAAACTACTCCCTCC 59.394 42.308 0.00 0.00 34.68 4.30
2980 3677 2.826725 AGTCTCAAAACTACTCCCTCCG 59.173 50.000 0.00 0.00 0.00 4.63
2981 3678 2.561858 GTCTCAAAACTACTCCCTCCGT 59.438 50.000 0.00 0.00 0.00 4.69
2982 3679 2.824341 TCTCAAAACTACTCCCTCCGTC 59.176 50.000 0.00 0.00 0.00 4.79
2983 3680 1.897802 TCAAAACTACTCCCTCCGTCC 59.102 52.381 0.00 0.00 0.00 4.79
2984 3681 1.900486 CAAAACTACTCCCTCCGTCCT 59.100 52.381 0.00 0.00 0.00 3.85
2985 3682 3.094572 CAAAACTACTCCCTCCGTCCTA 58.905 50.000 0.00 0.00 0.00 2.94
2986 3683 3.684408 AAACTACTCCCTCCGTCCTAT 57.316 47.619 0.00 0.00 0.00 2.57
2987 3684 4.803329 AAACTACTCCCTCCGTCCTATA 57.197 45.455 0.00 0.00 0.00 1.31
2988 3685 4.803329 AACTACTCCCTCCGTCCTATAA 57.197 45.455 0.00 0.00 0.00 0.98
2989 3686 5.336491 AACTACTCCCTCCGTCCTATAAT 57.664 43.478 0.00 0.00 0.00 1.28
2990 3687 6.460103 AACTACTCCCTCCGTCCTATAATA 57.540 41.667 0.00 0.00 0.00 0.98
2991 3688 6.655376 ACTACTCCCTCCGTCCTATAATAT 57.345 41.667 0.00 0.00 0.00 1.28
2992 3689 7.761981 ACTACTCCCTCCGTCCTATAATATA 57.238 40.000 0.00 0.00 0.00 0.86
2993 3690 8.167691 ACTACTCCCTCCGTCCTATAATATAA 57.832 38.462 0.00 0.00 0.00 0.98
2994 3691 8.618385 ACTACTCCCTCCGTCCTATAATATAAA 58.382 37.037 0.00 0.00 0.00 1.40
2995 3692 9.471702 CTACTCCCTCCGTCCTATAATATAAAA 57.528 37.037 0.00 0.00 0.00 1.52
2996 3693 8.363761 ACTCCCTCCGTCCTATAATATAAAAG 57.636 38.462 0.00 0.00 0.00 2.27
2997 3694 7.093421 ACTCCCTCCGTCCTATAATATAAAAGC 60.093 40.741 0.00 0.00 0.00 3.51
2998 3695 6.727231 TCCCTCCGTCCTATAATATAAAAGCA 59.273 38.462 0.00 0.00 0.00 3.91
2999 3696 7.402071 TCCCTCCGTCCTATAATATAAAAGCAT 59.598 37.037 0.00 0.00 0.00 3.79
3000 3697 8.047310 CCCTCCGTCCTATAATATAAAAGCATT 58.953 37.037 0.00 0.00 0.00 3.56
3001 3698 9.449719 CCTCCGTCCTATAATATAAAAGCATTT 57.550 33.333 0.00 0.00 42.41 2.32
3026 3723 9.643735 TTTTAAGGTAATTAAGTCCAAGGTTCA 57.356 29.630 0.00 0.00 34.86 3.18
3050 3748 6.107901 ACTATATGCAGAAAGTCCCATCTC 57.892 41.667 0.00 0.00 0.00 2.75
3066 3764 1.482954 TCTCTGGATGGTGCTCTCTG 58.517 55.000 0.00 0.00 0.00 3.35
3067 3765 0.179078 CTCTGGATGGTGCTCTCTGC 60.179 60.000 0.00 0.00 43.25 4.26
3084 3782 5.198965 TCTCTGCCGGACTACTTAACTATT 58.801 41.667 5.05 0.00 0.00 1.73
3246 3944 8.587952 AACATGTACAAGTTTATTTCTTTGCC 57.412 30.769 10.57 0.00 0.00 4.52
3262 3960 6.638096 TCTTTGCCAATGTGGTCATATATG 57.362 37.500 6.36 6.36 40.46 1.78
3267 3965 3.500108 CCAATGTGGTCATATATGGGCCA 60.500 47.826 9.61 9.61 33.49 5.36
3288 3986 7.173390 GGGCCATCTTTATTTCATACTGTCTAC 59.827 40.741 4.39 0.00 0.00 2.59
3291 3989 8.755941 CCATCTTTATTTCATACTGTCTACGTG 58.244 37.037 0.00 0.00 0.00 4.49
3295 3993 9.953825 CTTTATTTCATACTGTCTACGTGTTTC 57.046 33.333 0.00 0.00 0.00 2.78
3296 3994 9.701098 TTTATTTCATACTGTCTACGTGTTTCT 57.299 29.630 0.00 0.00 0.00 2.52
3304 4002 7.404139 ACTGTCTACGTGTTTCTAAAATGTC 57.596 36.000 0.00 0.00 0.00 3.06
3305 4003 6.982141 ACTGTCTACGTGTTTCTAAAATGTCA 59.018 34.615 0.00 0.00 0.00 3.58
3333 4031 6.538945 TTGCCACATGAGTACTATAGTTCA 57.461 37.500 11.40 10.12 0.00 3.18
3418 4120 4.771127 ACGAAGCACACGTGGATT 57.229 50.000 21.57 13.58 42.37 3.01
3419 4121 3.898380 ACGAAGCACACGTGGATTA 57.102 47.368 21.57 0.00 42.37 1.75
3423 4125 2.159841 CGAAGCACACGTGGATTAAGTG 60.160 50.000 21.57 8.12 43.31 3.16
3428 4130 3.308866 GCACACGTGGATTAAGTGGATAC 59.691 47.826 21.57 0.00 42.18 2.24
3457 4159 8.487970 ACGATAGAGCAAATAATAACATTCGTG 58.512 33.333 0.00 0.00 41.38 4.35
3482 4184 5.083533 TGAATTTTGGCAGTGTTGTTTCT 57.916 34.783 0.00 0.00 0.00 2.52
3488 4190 3.879998 TGGCAGTGTTGTTTCTGTCTAA 58.120 40.909 0.00 0.00 37.23 2.10
3495 4197 7.642669 CAGTGTTGTTTCTGTCTAATTCATGT 58.357 34.615 0.00 0.00 0.00 3.21
3537 4240 8.015658 ACAGAATGCTAAAATTCTTACGTTGTC 58.984 33.333 0.00 0.00 42.92 3.18
3553 4257 5.565695 ACGTTGTCAATGTTGTTTGTAGTC 58.434 37.500 4.51 0.00 0.00 2.59
3557 4261 5.518812 TGTCAATGTTGTTTGTAGTCATGC 58.481 37.500 0.00 0.00 0.00 4.06
3563 4267 4.819088 TGTTGTTTGTAGTCATGCTTAGCA 59.181 37.500 10.09 10.09 44.86 3.49
3582 4286 5.420725 AGCATAGGTGTCAGATGTTGTTA 57.579 39.130 0.00 0.00 0.00 2.41
3589 4293 7.149569 AGGTGTCAGATGTTGTTATGAATTG 57.850 36.000 0.00 0.00 0.00 2.32
3665 4369 5.528690 TCATCTAATGTGCATAGTCCTTTGC 59.471 40.000 0.00 3.18 37.90 3.68
3674 4378 3.316308 GCATAGTCCTTTGCCTTATGGTG 59.684 47.826 0.00 0.00 32.54 4.17
3679 4383 3.826729 GTCCTTTGCCTTATGGTGTTTCT 59.173 43.478 0.00 0.00 35.27 2.52
3685 4389 4.535781 TGCCTTATGGTGTTTCTATGCAT 58.464 39.130 3.79 3.79 35.27 3.96
3695 4402 6.700960 TGGTGTTTCTATGCATTTCAACAAAG 59.299 34.615 3.54 0.00 0.00 2.77
3712 4419 5.869649 ACAAAGTAAACTTGGGAGCAATT 57.130 34.783 2.43 0.00 36.12 2.32
3717 4424 0.178924 AACTTGGGAGCAATTGGCCT 60.179 50.000 3.32 0.00 46.50 5.19
3722 4429 1.203112 TGGGAGCAATTGGCCTACAAA 60.203 47.619 3.32 0.00 46.50 2.83
3752 4459 1.681264 ACCCAAAACAAAAGGAGAGCG 59.319 47.619 0.00 0.00 0.00 5.03
3759 4466 1.668151 AAAAGGAGAGCGGCGTGAC 60.668 57.895 9.37 0.00 0.00 3.67
3760 4467 2.377628 AAAAGGAGAGCGGCGTGACA 62.378 55.000 9.37 0.00 0.00 3.58
3773 4480 2.668457 GGCGTGACAGAAACATGTAGAG 59.332 50.000 0.00 0.00 32.25 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 1.801332 CGGAGAGTACACCGTCCTG 59.199 63.158 14.81 0.00 43.28 3.86
72 73 4.315588 CGGAGAGTACACCGTCCT 57.684 61.111 14.81 0.00 43.28 3.85
111 112 1.364626 GACGATGTTGGCTCCAGCTG 61.365 60.000 6.78 6.78 41.70 4.24
113 114 2.456119 CGACGATGTTGGCTCCAGC 61.456 63.158 0.00 0.00 41.14 4.85
131 132 1.203928 CGACAGATGACGAAGATGGC 58.796 55.000 0.00 0.00 35.37 4.40
137 138 0.460109 CCCATGCGACAGATGACGAA 60.460 55.000 8.80 0.00 35.37 3.85
143 144 0.548031 ATTCACCCCATGCGACAGAT 59.452 50.000 0.00 0.00 0.00 2.90
150 151 1.376609 GACGACCATTCACCCCATGC 61.377 60.000 0.00 0.00 0.00 4.06
153 154 2.660206 CGACGACCATTCACCCCA 59.340 61.111 0.00 0.00 0.00 4.96
193 194 2.450609 TGAGGTTAAAGACGTCAGCC 57.549 50.000 19.50 8.75 45.40 4.85
197 198 3.734735 GGCGATATGAGGTTAAAGACGTC 59.265 47.826 7.70 7.70 42.17 4.34
201 202 5.135508 GCTAGGCGATATGAGGTTAAAGA 57.864 43.478 0.00 0.00 0.00 2.52
236 237 1.664873 CATTTGCAAGCACCCCGAA 59.335 52.632 0.00 0.00 0.00 4.30
251 252 3.470888 CTCGGCCGAGACCCCATT 61.471 66.667 45.28 0.00 44.53 3.16
349 350 4.915809 TGGGAGTGAGATTGGGATATGATT 59.084 41.667 0.00 0.00 0.00 2.57
352 353 3.008813 CCTGGGAGTGAGATTGGGATATG 59.991 52.174 0.00 0.00 0.00 1.78
353 354 3.254960 CCTGGGAGTGAGATTGGGATAT 58.745 50.000 0.00 0.00 0.00 1.63
503 504 2.096367 CGAGGTGGACGACGACTATATG 60.096 54.545 0.00 0.00 0.00 1.78
506 507 0.392193 ACGAGGTGGACGACGACTAT 60.392 55.000 0.00 0.00 34.70 2.12
507 508 1.004560 ACGAGGTGGACGACGACTA 60.005 57.895 0.00 0.00 34.70 2.59
512 513 1.016130 TCTACGACGAGGTGGACGAC 61.016 60.000 0.00 0.00 34.70 4.34
518 519 1.001268 CCCATCATCTACGACGAGGTG 60.001 57.143 0.00 1.39 0.00 4.00
522 523 0.668535 CAGCCCATCATCTACGACGA 59.331 55.000 0.00 0.00 0.00 4.20
540 541 2.435938 GGATGAGCGGCCGAAACA 60.436 61.111 33.48 24.24 0.00 2.83
549 550 1.227764 CCCTGGACATGGATGAGCG 60.228 63.158 0.00 0.00 0.00 5.03
650 651 0.394192 TGCTTGGCCATATCCTCTCG 59.606 55.000 6.09 0.00 0.00 4.04
679 680 1.135731 GACCGTCTGAGCAGTCTCG 59.864 63.158 0.00 2.37 42.26 4.04
714 721 2.497092 CGCACCAGATCGTCGAACG 61.497 63.158 0.00 0.00 44.19 3.95
811 820 7.321908 GGTTATAAACCGATCTCTAATCCTCC 58.678 42.308 0.00 0.00 42.62 4.30
843 853 2.187599 ATTTGAGCAGGCAACGACGC 62.188 55.000 0.00 0.00 46.39 5.19
946 957 1.080329 TCGATGGGATGGGATGGGATA 59.920 52.381 0.00 0.00 0.00 2.59
947 958 0.178864 TCGATGGGATGGGATGGGAT 60.179 55.000 0.00 0.00 0.00 3.85
948 959 0.837691 CTCGATGGGATGGGATGGGA 60.838 60.000 0.00 0.00 0.00 4.37
949 960 0.837691 TCTCGATGGGATGGGATGGG 60.838 60.000 0.00 0.00 0.00 4.00
950 961 1.059098 TTCTCGATGGGATGGGATGG 58.941 55.000 0.00 0.00 0.00 3.51
1146 1157 2.312436 TTCGACGTGCGTCTCGAGA 61.312 57.895 12.08 12.08 42.54 4.04
1164 1175 3.581024 TGGTAAAGTCGTTCTATGCGT 57.419 42.857 0.00 0.00 0.00 5.24
1179 1190 0.991920 CCTCTCCCCAGCTTTGGTAA 59.008 55.000 0.00 0.00 0.00 2.85
1393 1431 2.584391 GGTGGGAGAGAAGCGTGGT 61.584 63.158 0.00 0.00 0.00 4.16
1449 1490 2.508663 GTGTCGTAGCGGCCTTCC 60.509 66.667 0.00 0.00 0.00 3.46
1456 1497 1.257415 CTCGTAGTAGGTGTCGTAGCG 59.743 57.143 0.00 0.00 0.00 4.26
1459 1500 1.066215 TGGCTCGTAGTAGGTGTCGTA 60.066 52.381 0.00 0.00 0.00 3.43
1473 1523 1.565305 CGATCTCCTTCTTTGGCTCG 58.435 55.000 0.00 0.00 0.00 5.03
1479 1529 1.573108 TCCTGGCGATCTCCTTCTTT 58.427 50.000 2.88 0.00 0.00 2.52
1480 1530 1.573108 TTCCTGGCGATCTCCTTCTT 58.427 50.000 2.88 0.00 0.00 2.52
1495 1545 1.823610 GTACTCGCCTACCACTTTCCT 59.176 52.381 0.00 0.00 0.00 3.36
1577 1627 2.825836 CCGGTGGAAGGATGCTGC 60.826 66.667 0.00 0.00 0.00 5.25
1700 1758 0.959553 GACAGACTCAAGGTGGACGA 59.040 55.000 0.00 0.00 0.00 4.20
1716 1774 0.676466 GCCCAATGGTGATGACGACA 60.676 55.000 0.00 0.00 0.00 4.35
1765 1826 1.735376 GAAGTATCGCCCGAGGAGCA 61.735 60.000 0.00 0.00 0.00 4.26
1768 1862 0.822532 GGAGAAGTATCGCCCGAGGA 60.823 60.000 0.00 0.00 39.43 3.71
1775 1869 1.335132 TGGTGGGGGAGAAGTATCGC 61.335 60.000 0.00 0.00 0.00 4.58
1797 1894 4.319177 GACATTGGAGCACTACTTCTGTT 58.681 43.478 0.00 0.00 0.00 3.16
1868 2010 4.760047 CGGGGGTCTTGCCGTCAG 62.760 72.222 0.00 0.00 38.44 3.51
1874 2016 2.511600 CGATGACGGGGGTCTTGC 60.512 66.667 0.00 0.00 35.72 4.01
2002 2144 2.556287 GACGCGTGGCCAGAAAAG 59.444 61.111 20.70 0.00 0.00 2.27
2008 2150 3.793775 TTTTCTCGACGCGTGGCCA 62.794 57.895 20.70 0.00 0.00 5.36
2014 2156 1.323136 ACGTACGTTTTCTCGACGCG 61.323 55.000 16.72 3.53 43.92 6.01
2018 2160 3.188254 TGGATACACGTACGTTTTCTCGA 59.812 43.478 20.23 7.69 46.17 4.04
2044 2192 3.482783 GTCGCTGCGGTGCTTCTC 61.483 66.667 23.03 0.00 0.00 2.87
2054 2202 2.583593 GTGGATCCTCGTCGCTGC 60.584 66.667 14.23 0.00 0.00 5.25
2055 2203 1.517257 GTGTGGATCCTCGTCGCTG 60.517 63.158 14.23 0.00 0.00 5.18
2071 2240 4.016706 GGTCACGAGGGTGGGGTG 62.017 72.222 0.00 0.00 44.50 4.61
2078 2247 2.266055 GCCAGAAGGTCACGAGGG 59.734 66.667 0.00 0.00 37.19 4.30
2120 2289 0.979665 CCTCAGCTTCAACTCCCTGA 59.020 55.000 0.00 0.00 33.65 3.86
2313 2482 0.390603 CCGTGGTAAGGTTGATGCGA 60.391 55.000 0.00 0.00 0.00 5.10
2316 2485 1.977594 GCGCCGTGGTAAGGTTGATG 61.978 60.000 0.00 0.00 0.00 3.07
2340 2509 5.470777 GCGGTTATACTTTAATATGGCACCA 59.529 40.000 0.00 0.00 0.00 4.17
2350 2519 7.128234 ACCCTTCTATGCGGTTATACTTTAA 57.872 36.000 0.00 0.00 0.00 1.52
2359 2528 1.134907 CACGTACCCTTCTATGCGGTT 60.135 52.381 0.00 0.00 0.00 4.44
2430 2611 2.324014 AAACCACTGTCGGCTCTGCA 62.324 55.000 0.00 0.00 0.00 4.41
2443 2624 3.944015 CCATCATCTTCCAGAGAAACCAC 59.056 47.826 0.00 0.00 38.06 4.16
2444 2625 3.623203 GCCATCATCTTCCAGAGAAACCA 60.623 47.826 0.00 0.00 38.06 3.67
2480 2667 4.390264 GCCAGGGATATCTAAAACCTCAC 58.610 47.826 2.05 0.00 0.00 3.51
2580 2767 2.136298 TCAGCTTGACACCCAAACAA 57.864 45.000 0.00 0.00 33.76 2.83
2689 2876 6.539649 TGAACTGACGATCCAAGTTTTAAG 57.460 37.500 0.00 0.00 0.00 1.85
2840 3030 1.881324 GCTAGATACCTCAGGACGTCC 59.119 57.143 27.67 27.67 0.00 4.79
2843 3033 3.482436 AGAAGCTAGATACCTCAGGACG 58.518 50.000 0.00 0.00 0.00 4.79
2848 3038 4.507691 GCTAGGGAGAAGCTAGATACCTCA 60.508 50.000 11.03 0.00 37.01 3.86
2899 3089 7.553044 AGAGCAAAACTAACCTATTACATGTCC 59.447 37.037 0.00 0.00 0.00 4.02
2900 3090 8.494016 AGAGCAAAACTAACCTATTACATGTC 57.506 34.615 0.00 0.00 0.00 3.06
2902 3092 8.723942 AGAGAGCAAAACTAACCTATTACATG 57.276 34.615 0.00 0.00 0.00 3.21
2928 3411 9.975218 ATAGTTTCCTGTATTACTTGGAACATT 57.025 29.630 16.08 10.24 39.30 2.71
2973 3670 6.727231 TGCTTTTATATTATAGGACGGAGGGA 59.273 38.462 0.00 0.00 0.00 4.20
2974 3671 6.942976 TGCTTTTATATTATAGGACGGAGGG 58.057 40.000 0.00 0.00 0.00 4.30
2975 3672 9.449719 AAATGCTTTTATATTATAGGACGGAGG 57.550 33.333 0.00 0.00 0.00 4.30
2996 3693 9.366216 CCTTGGACTTAATTACCTTAAAAATGC 57.634 33.333 0.00 0.00 0.00 3.56
3000 3697 9.643735 TGAACCTTGGACTTAATTACCTTAAAA 57.356 29.630 0.00 0.00 0.00 1.52
3001 3698 9.643735 TTGAACCTTGGACTTAATTACCTTAAA 57.356 29.630 0.00 0.00 0.00 1.52
3002 3699 9.070179 GTTGAACCTTGGACTTAATTACCTTAA 57.930 33.333 0.00 0.00 0.00 1.85
3003 3700 8.442374 AGTTGAACCTTGGACTTAATTACCTTA 58.558 33.333 0.00 0.00 0.00 2.69
3004 3701 7.295340 AGTTGAACCTTGGACTTAATTACCTT 58.705 34.615 0.00 0.00 0.00 3.50
3005 3702 6.849151 AGTTGAACCTTGGACTTAATTACCT 58.151 36.000 0.00 0.00 0.00 3.08
3006 3703 8.803397 ATAGTTGAACCTTGGACTTAATTACC 57.197 34.615 0.00 0.00 0.00 2.85
3026 3723 6.328672 AGAGATGGGACTTTCTGCATATAGTT 59.671 38.462 0.00 0.00 0.00 2.24
3050 3748 4.536316 GCAGAGAGCACCATCCAG 57.464 61.111 0.00 0.00 44.79 3.86
3066 3764 7.413767 CCAAAAAGAATAGTTAAGTAGTCCGGC 60.414 40.741 12.88 0.00 0.00 6.13
3067 3765 7.820872 TCCAAAAAGAATAGTTAAGTAGTCCGG 59.179 37.037 12.88 0.00 0.00 5.14
3084 3782 8.055181 ACTCAGCCAATATAATCTCCAAAAAGA 58.945 33.333 0.00 0.00 0.00 2.52
3107 3805 8.709386 TTGTGCTCTTTATATCTGAGAAACTC 57.291 34.615 0.00 0.00 0.00 3.01
3242 3940 4.151121 CCCATATATGACCACATTGGCAA 58.849 43.478 14.54 0.68 42.67 4.52
3245 3943 3.091545 GGCCCATATATGACCACATTGG 58.908 50.000 14.54 5.29 45.02 3.16
3246 3944 3.765381 TGGCCCATATATGACCACATTG 58.235 45.455 18.38 0.33 37.87 2.82
3262 3960 6.064717 AGACAGTATGAAATAAAGATGGCCC 58.935 40.000 0.00 0.00 39.69 5.80
3267 3965 9.871238 AACACGTAGACAGTATGAAATAAAGAT 57.129 29.630 0.00 0.00 39.69 2.40
3281 3979 7.402811 TGACATTTTAGAAACACGTAGACAG 57.597 36.000 0.00 0.00 0.00 3.51
3318 4016 7.934665 GTCATCTCTCCTGAACTATAGTACTCA 59.065 40.741 5.65 6.46 0.00 3.41
3319 4017 7.934665 TGTCATCTCTCCTGAACTATAGTACTC 59.065 40.741 5.65 1.56 0.00 2.59
3326 4024 6.865834 AAGTTGTCATCTCTCCTGAACTAT 57.134 37.500 0.00 0.00 0.00 2.12
3391 4089 1.375908 GTGCTTCGTGGCATCTCCA 60.376 57.895 8.09 0.00 44.34 3.86
3408 4110 4.464951 TCTGTATCCACTTAATCCACGTGT 59.535 41.667 15.65 0.00 0.00 4.49
3412 4114 5.258456 TCGTCTGTATCCACTTAATCCAC 57.742 43.478 0.00 0.00 0.00 4.02
3416 4118 6.490381 TGCTCTATCGTCTGTATCCACTTAAT 59.510 38.462 0.00 0.00 0.00 1.40
3417 4119 5.826208 TGCTCTATCGTCTGTATCCACTTAA 59.174 40.000 0.00 0.00 0.00 1.85
3418 4120 5.374071 TGCTCTATCGTCTGTATCCACTTA 58.626 41.667 0.00 0.00 0.00 2.24
3419 4121 4.207955 TGCTCTATCGTCTGTATCCACTT 58.792 43.478 0.00 0.00 0.00 3.16
3423 4125 9.856488 TTATTATTTGCTCTATCGTCTGTATCC 57.144 33.333 0.00 0.00 0.00 2.59
3457 4159 3.993920 ACAACACTGCCAAAATTCATCC 58.006 40.909 0.00 0.00 0.00 3.51
3482 4184 6.656270 AGATTTGCTCACACATGAATTAGACA 59.344 34.615 0.00 0.00 33.30 3.41
3488 4190 6.207221 TGTGTAAGATTTGCTCACACATGAAT 59.793 34.615 0.00 0.00 43.22 2.57
3495 4197 5.335113 GCATTCTGTGTAAGATTTGCTCACA 60.335 40.000 0.00 0.00 39.55 3.58
3529 4232 6.313164 TGACTACAAACAACATTGACAACGTA 59.687 34.615 0.00 0.00 34.38 3.57
3531 4234 5.564768 TGACTACAAACAACATTGACAACG 58.435 37.500 0.00 0.00 34.38 4.10
3537 4240 6.306356 GCTAAGCATGACTACAAACAACATTG 59.694 38.462 0.00 0.00 36.37 2.82
3557 4261 5.423015 ACAACATCTGACACCTATGCTAAG 58.577 41.667 0.00 0.00 0.00 2.18
3563 4267 8.896744 CAATTCATAACAACATCTGACACCTAT 58.103 33.333 0.00 0.00 0.00 2.57
3582 4286 8.388103 GCAGTAAGACAACGTTATACAATTCAT 58.612 33.333 0.00 0.00 0.00 2.57
3595 4299 7.959733 TGAGTTTATTATGCAGTAAGACAACG 58.040 34.615 0.00 0.00 0.00 4.10
3641 4345 5.528690 GCAAAGGACTATGCACATTAGATGA 59.471 40.000 0.00 0.00 42.12 2.92
3665 4369 7.099266 TGAAATGCATAGAAACACCATAAGG 57.901 36.000 0.00 0.00 42.21 2.69
3679 4383 7.655328 CCCAAGTTTACTTTGTTGAAATGCATA 59.345 33.333 0.00 0.00 33.11 3.14
3685 4389 5.186021 TGCTCCCAAGTTTACTTTGTTGAAA 59.814 36.000 0.00 0.00 33.11 2.69
3695 4402 2.353704 GGCCAATTGCTCCCAAGTTTAC 60.354 50.000 0.00 0.00 40.92 2.01
3701 4408 0.407528 TGTAGGCCAATTGCTCCCAA 59.592 50.000 5.01 0.00 40.92 4.12
3712 4419 2.691011 GTTTTGTCTGGTTTGTAGGCCA 59.309 45.455 5.01 0.00 0.00 5.36
3717 4424 5.011738 TGTTTTGGGTTTTGTCTGGTTTGTA 59.988 36.000 0.00 0.00 0.00 2.41
3722 4429 4.625607 TTTGTTTTGGGTTTTGTCTGGT 57.374 36.364 0.00 0.00 0.00 4.00
3752 4459 2.668457 CTCTACATGTTTCTGTCACGCC 59.332 50.000 2.30 0.00 0.00 5.68
3759 4466 7.130917 GCAATTAGATGCTCTACATGTTTCTG 58.869 38.462 2.30 0.00 43.06 3.02
3760 4467 7.256756 GCAATTAGATGCTCTACATGTTTCT 57.743 36.000 2.30 0.42 43.06 2.52


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

AutoCloner maintained by Alex Coulton.