Multiple sequence alignment - TraesCS4A01G494600

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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 TraesCS4A01G494600 chr4A 100.000 4355 0 0 1 4355 742318703 742323057 0.000000e+00 8043.0
1 TraesCS4A01G494600 chr4A 87.838 3034 260 51 845 3831 742314830 742311859 0.000000e+00 3458.0
2 TraesCS4A01G494600 chr4A 85.607 535 41 16 3828 4355 742311670 742311165 2.980000e-146 529.0
3 TraesCS4A01G494600 chr4A 81.616 631 40 26 263 860 742315433 742314846 1.850000e-123 453.0
4 TraesCS4A01G494600 chr4A 88.000 50 2 4 68 117 383898235 383898190 6.080000e-04 56.5
5 TraesCS4A01G494600 chr7D 90.447 3580 230 50 115 3636 2336566 2333041 0.000000e+00 4614.0
6 TraesCS4A01G494600 chr7D 88.493 730 64 9 3637 4355 2333007 2332287 0.000000e+00 865.0
7 TraesCS4A01G494600 chr7D 97.059 34 1 0 1 34 2336597 2336564 1.690000e-04 58.4
8 TraesCS4A01G494600 chr7A 92.793 777 41 2 2868 3629 1981557 1980781 0.000000e+00 1110.0
9 TraesCS4A01G494600 chr7A 90.229 829 50 4 3476 4303 1976333 1975535 0.000000e+00 1053.0
10 TraesCS4A01G494600 chr7A 91.525 59 5 0 31 89 134420135 134420193 1.000000e-11 82.4
11 TraesCS4A01G494600 chr6A 93.750 64 2 2 28 89 616974702 616974765 1.290000e-15 95.3
12 TraesCS4A01G494600 chr6A 94.737 38 0 2 81 118 26364402 26364367 1.690000e-04 58.4
13 TraesCS4A01G494600 chr2B 91.045 67 6 0 32 98 265432009 265432075 1.670000e-14 91.6
14 TraesCS4A01G494600 chrUn 86.047 86 7 5 31 116 1598766 1598686 2.160000e-13 87.9
15 TraesCS4A01G494600 chr3D 88.571 70 8 0 29 98 593088472 593088541 7.760000e-13 86.1
16 TraesCS4A01G494600 chr5A 88.406 69 8 0 23 91 633991701 633991769 2.790000e-12 84.2
17 TraesCS4A01G494600 chr3B 91.379 58 5 0 31 88 796508623 796508680 3.610000e-11 80.5
18 TraesCS4A01G494600 chr3B 94.595 37 0 2 81 117 212114389 212114423 6.080000e-04 56.5
19 TraesCS4A01G494600 chr1B 87.143 70 8 1 23 91 10063911 10063842 1.300000e-10 78.7
20 TraesCS4A01G494600 chr1B 85.915 71 9 1 21 91 293775206 293775137 1.680000e-09 75.0
21 TraesCS4A01G494600 chr1B 92.683 41 1 2 81 121 436984604 436984566 1.690000e-04 58.4
22 TraesCS4A01G494600 chr7B 95.000 40 0 2 81 120 131081580 131081543 1.310000e-05 62.1
23 TraesCS4A01G494600 chr6B 94.737 38 0 2 81 118 112745649 112745684 1.690000e-04 58.4
24 TraesCS4A01G494600 chr5B 92.500 40 1 2 81 120 317304235 317304198 6.080000e-04 56.5
25 TraesCS4A01G494600 chr5B 89.362 47 2 2 74 117 585009763 585009717 6.080000e-04 56.5


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 TraesCS4A01G494600 chr4A 742318703 742323057 4354 False 8043.0 8043 100.000000 1 4355 1 chr4A.!!$F1 4354
1 TraesCS4A01G494600 chr4A 742311165 742315433 4268 True 1480.0 3458 85.020333 263 4355 3 chr4A.!!$R2 4092
2 TraesCS4A01G494600 chr7D 2332287 2336597 4310 True 1845.8 4614 91.999667 1 4355 3 chr7D.!!$R1 4354
3 TraesCS4A01G494600 chr7A 1980781 1981557 776 True 1110.0 1110 92.793000 2868 3629 1 chr7A.!!$R2 761
4 TraesCS4A01G494600 chr7A 1975535 1976333 798 True 1053.0 1053 90.229000 3476 4303 1 chr7A.!!$R1 827

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
955 1025 0.471780 TGAGGCAGACCCAAGAGTCA 60.472 55.0 0.0 0.0 39.34 3.41 F
1668 1768 0.036105 TGGTGGCTGACTACATGCAG 60.036 55.0 0.0 0.0 35.28 4.41 F
2263 2369 0.036010 CTCCTCCAGTCATGCGGTTT 60.036 55.0 0.0 0.0 0.00 3.27 F
2566 2672 0.037882 CTCGCTTCTCAACTCCTGCA 60.038 55.0 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 2298 0.179056 CGCGGGGACATTGGAGTAAT 60.179 55.000 0.00 0.00 0.00 1.89 R
2892 2998 0.322906 TGGACAGTGTGGTTGCAACA 60.323 50.000 29.55 13.95 0.00 3.33 R
3094 3209 0.520404 GACATGTCTTGCTGCACTGG 59.480 55.000 18.83 0.00 0.00 4.00 R
4015 4411 1.141858 GGTCTAAGGAGCAAGATGGGG 59.858 57.143 0.00 0.00 39.51 4.96 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
46 47 9.461734 ACCTTAAATAATACTCCCTATGTTCCT 57.538 33.333 0.00 0.00 0.00 3.36
58 59 9.900112 ACTCCCTATGTTCCTAAATATAAGTCT 57.100 33.333 0.00 0.00 0.00 3.24
108 109 8.365647 ACATACAGACTTATATTTAGGAACGGG 58.634 37.037 0.00 0.00 0.00 5.28
109 110 6.170846 ACAGACTTATATTTAGGAACGGGG 57.829 41.667 0.00 0.00 0.00 5.73
110 111 5.071384 ACAGACTTATATTTAGGAACGGGGG 59.929 44.000 0.00 0.00 0.00 5.40
145 146 6.341316 TGAAGAGACAAATCAGTACTATGCC 58.659 40.000 0.00 0.00 0.00 4.40
184 185 2.303175 GGCCCGATATTGGTTGCTTTA 58.697 47.619 8.26 0.00 0.00 1.85
186 187 3.490249 GGCCCGATATTGGTTGCTTTAAC 60.490 47.826 8.26 0.00 38.60 2.01
187 188 3.790789 GCCCGATATTGGTTGCTTTAACG 60.791 47.826 8.26 0.00 40.28 3.18
201 202 3.390135 CTTTAACGTCCTGAGCTTGTCA 58.610 45.455 0.00 0.00 0.00 3.58
255 256 7.398618 TGAGTTCTACTTCTCCTTCAATGATCT 59.601 37.037 0.00 0.00 0.00 2.75
265 266 9.610705 TTCTCCTTCAATGATCTCTATTTTCTG 57.389 33.333 0.00 0.00 0.00 3.02
355 356 5.645624 TGTTGTTGCAATATAATTGGTCCG 58.354 37.500 0.59 0.00 0.00 4.79
370 371 6.790232 ATTGGTCCGGAAATATTGTCATTT 57.210 33.333 5.23 0.00 0.00 2.32
374 375 7.767261 TGGTCCGGAAATATTGTCATTTAAAG 58.233 34.615 5.23 0.00 0.00 1.85
418 419 5.011635 GGATACATGGTTCCCAAGTTTTGTT 59.988 40.000 0.00 0.00 36.76 2.83
420 421 5.941555 ACATGGTTCCCAAGTTTTGTTAA 57.058 34.783 0.00 0.00 36.95 2.01
478 480 5.297776 ACGAGCAAATGAAAATGATAGAGGG 59.702 40.000 0.00 0.00 0.00 4.30
482 484 7.529555 AGCAAATGAAAATGATAGAGGGGATA 58.470 34.615 0.00 0.00 0.00 2.59
490 492 7.951347 AAATGATAGAGGGGATAATGAATGC 57.049 36.000 0.00 0.00 0.00 3.56
586 588 6.375945 ACAAAATTGGAACATGCTTTTTCC 57.624 33.333 9.94 9.94 41.62 3.13
660 668 3.737559 AATGGTTCACATGGCTCCTTA 57.262 42.857 0.00 0.00 40.44 2.69
663 671 4.150897 TGGTTCACATGGCTCCTTATAC 57.849 45.455 0.00 0.00 0.00 1.47
670 678 0.670162 TGGCTCCTTATACGCGTACC 59.330 55.000 23.19 16.43 0.00 3.34
676 684 3.485394 TCCTTATACGCGTACCACCATA 58.515 45.455 23.19 7.11 0.00 2.74
735 760 7.926555 AGGTTTGTAAGTCTACATCAATATCCG 59.073 37.037 0.00 0.00 37.86 4.18
736 761 7.170998 GGTTTGTAAGTCTACATCAATATCCGG 59.829 40.741 0.00 0.00 37.86 5.14
772 797 3.772572 AGGAGAGGAAGAAAGCTTACCTC 59.227 47.826 22.79 22.79 42.49 3.85
776 801 2.639839 AGGAAGAAAGCTTACCTCTGCA 59.360 45.455 0.00 0.00 35.42 4.41
823 861 2.922740 TACCTTGGTTCTCACACACC 57.077 50.000 0.00 0.00 0.00 4.16
840 878 0.620556 ACCCCATCTCTTGTGCGATT 59.379 50.000 0.00 0.00 0.00 3.34
841 879 1.837439 ACCCCATCTCTTGTGCGATTA 59.163 47.619 0.00 0.00 0.00 1.75
842 880 2.158900 ACCCCATCTCTTGTGCGATTAG 60.159 50.000 0.00 0.00 0.00 1.73
884 954 6.067217 ACCACCTTTCATAAGACTAAGCAT 57.933 37.500 0.00 0.00 32.92 3.79
885 955 6.116126 ACCACCTTTCATAAGACTAAGCATC 58.884 40.000 0.00 0.00 32.92 3.91
886 956 5.529060 CCACCTTTCATAAGACTAAGCATCC 59.471 44.000 0.00 0.00 32.92 3.51
897 967 2.832129 ACTAAGCATCCTCCTCGTCAAA 59.168 45.455 0.00 0.00 0.00 2.69
923 993 6.068670 TCTGTCTAGCTATATAGTTGGCACA 58.931 40.000 11.38 11.41 0.00 4.57
927 997 6.642950 GTCTAGCTATATAGTTGGCACACTTG 59.357 42.308 11.38 0.00 39.29 3.16
955 1025 0.471780 TGAGGCAGACCCAAGAGTCA 60.472 55.000 0.00 0.00 39.34 3.41
1013 1083 9.186323 CTAGATTGAGAAAATGTACTCGGTATG 57.814 37.037 0.00 0.00 36.11 2.39
1016 1089 4.468510 TGAGAAAATGTACTCGGTATGGGT 59.531 41.667 0.00 0.00 36.11 4.51
1018 1091 2.614829 AATGTACTCGGTATGGGTGC 57.385 50.000 0.00 0.00 0.00 5.01
1027 1100 0.764890 GGTATGGGTGCTGCTATGGA 59.235 55.000 0.00 0.00 0.00 3.41
1028 1101 1.352352 GGTATGGGTGCTGCTATGGAT 59.648 52.381 0.00 0.00 0.00 3.41
1037 1110 5.415221 GGTGCTGCTATGGATCTTATACTC 58.585 45.833 0.00 0.00 0.00 2.59
1038 1111 5.186797 GGTGCTGCTATGGATCTTATACTCT 59.813 44.000 0.00 0.00 0.00 3.24
1040 1113 7.416213 GGTGCTGCTATGGATCTTATACTCTAG 60.416 44.444 0.00 0.00 0.00 2.43
1064 1146 1.452110 CACATCAGCATGTTTCCCGA 58.548 50.000 0.00 0.00 40.66 5.14
1066 1148 2.424601 CACATCAGCATGTTTCCCGAAT 59.575 45.455 0.00 0.00 40.66 3.34
1067 1149 3.091545 ACATCAGCATGTTTCCCGAATT 58.908 40.909 0.00 0.00 40.66 2.17
1071 1153 4.191544 TCAGCATGTTTCCCGAATTAGAG 58.808 43.478 0.00 0.00 37.40 2.43
1093 1178 1.001815 GAGATCTGTCGCTAGGTCTGC 60.002 57.143 0.00 0.00 38.25 4.26
1121 1221 2.879813 GATACCCCGGCGCCAGAAAA 62.880 60.000 28.98 8.91 0.00 2.29
1324 1424 2.731571 GGCTACACCATCGGCCTCA 61.732 63.158 0.00 0.00 41.20 3.86
1356 1456 0.185901 AGGAGCCCAAACAGCTTGAA 59.814 50.000 0.00 0.00 41.75 2.69
1393 1493 1.823295 GTCGGGCTATTGCTCCTCA 59.177 57.895 0.00 0.00 35.98 3.86
1585 1685 3.388024 GGTGTATAGCATCTTGAGGGTCA 59.612 47.826 0.00 0.00 0.00 4.02
1668 1768 0.036105 TGGTGGCTGACTACATGCAG 60.036 55.000 0.00 0.00 35.28 4.41
1695 1795 3.072476 GCCTCTGGCTCTGGTGAA 58.928 61.111 0.73 0.00 46.69 3.18
1700 1800 1.349026 CTCTGGCTCTGGTGAAAGGAA 59.651 52.381 0.00 0.00 0.00 3.36
1706 1806 4.166725 TGGCTCTGGTGAAAGGAATCATAT 59.833 41.667 0.00 0.00 0.00 1.78
1714 1814 4.768968 GTGAAAGGAATCATATCCCCATGG 59.231 45.833 4.14 4.14 40.59 3.66
1716 1816 4.664688 AAGGAATCATATCCCCATGGAC 57.335 45.455 15.22 0.00 45.58 4.02
1740 1840 4.848357 ACATGGCTAAGTGCAAGTATCTT 58.152 39.130 0.00 0.00 45.15 2.40
1781 1881 4.722700 CAGCCCACCGTCCAAGGG 62.723 72.222 0.00 0.00 45.68 3.95
1839 1939 2.604914 GCTCATCACGTTCGACATGATT 59.395 45.455 0.00 0.00 30.58 2.57
1905 2005 1.078567 CCAGAAGCCTGTGCCTCTC 60.079 63.158 0.00 0.00 36.10 3.20
1914 2014 2.544685 CCTGTGCCTCTCAAAGATACG 58.455 52.381 0.00 0.00 31.35 3.06
1987 2087 2.520982 CCATCGCCGAGGAGGGTA 60.521 66.667 0.00 0.00 41.48 3.69
2097 2197 4.388499 ACCAAGTACCCGGCGCTG 62.388 66.667 9.96 9.96 0.00 5.18
2146 2246 0.239347 TCTCCGTTTCGTCGTCCTTC 59.761 55.000 0.00 0.00 0.00 3.46
2170 2270 1.151668 CTTGTTCAAGGTGCTCCTCG 58.848 55.000 7.99 0.00 44.35 4.63
2179 2279 1.906574 AGGTGCTCCTCGTGGATTTTA 59.093 47.619 6.68 0.00 40.58 1.52
2187 2287 5.276726 GCTCCTCGTGGATTTTATTTACGAC 60.277 44.000 6.68 0.00 42.29 4.34
2195 2295 5.202640 GGATTTTATTTACGACGGCATCAC 58.797 41.667 0.00 0.00 0.00 3.06
2198 2298 6.905544 TTTTATTTACGACGGCATCACATA 57.094 33.333 0.00 0.00 0.00 2.29
2199 2299 7.485418 TTTTATTTACGACGGCATCACATAT 57.515 32.000 0.00 0.00 0.00 1.78
2209 2309 4.756642 ACGGCATCACATATTACTCCAATG 59.243 41.667 0.00 0.00 0.00 2.82
2256 2362 0.397254 CGGGGTACTCCTCCAGTCAT 60.397 60.000 10.83 0.00 36.43 3.06
2263 2369 0.036010 CTCCTCCAGTCATGCGGTTT 60.036 55.000 0.00 0.00 0.00 3.27
2270 2376 2.350772 CCAGTCATGCGGTTTTCTTCAC 60.351 50.000 0.00 0.00 0.00 3.18
2406 2512 1.251527 TGAGAAGGAGGACAGACGGC 61.252 60.000 0.00 0.00 0.00 5.68
2511 2617 4.700365 GCACGCCGGGCAAAGAAC 62.700 66.667 20.71 0.00 0.00 3.01
2553 2659 2.885861 CTCGGCCAGTACTCGCTT 59.114 61.111 12.38 0.00 0.00 4.68
2566 2672 0.037882 CTCGCTTCTCAACTCCTGCA 60.038 55.000 0.00 0.00 0.00 4.41
2658 2764 1.298859 GGAAGCGCGACAAGGATGTT 61.299 55.000 12.10 0.00 40.74 2.71
2659 2765 0.179215 GAAGCGCGACAAGGATGTTG 60.179 55.000 12.10 0.00 40.74 3.33
2665 2771 0.321564 CGACAAGGATGTTGCCCTGA 60.322 55.000 0.00 0.00 40.74 3.86
2682 2788 2.263077 CTGACGGACGAAATCAAGGAG 58.737 52.381 0.00 0.00 0.00 3.69
2691 2797 3.328050 ACGAAATCAAGGAGGAGGTTCTT 59.672 43.478 0.00 0.00 0.00 2.52
2758 2864 1.338200 GCGATCTGAGGAACAAGGTGT 60.338 52.381 0.00 0.00 0.00 4.16
2778 2884 2.359602 CAGCTGGACTGGGTGCTG 60.360 66.667 5.57 0.00 45.15 4.41
2799 2905 2.965783 GACCTCTCGAGCAGCACA 59.034 61.111 7.81 0.00 0.00 4.57
2801 2907 2.147315 GACCTCTCGAGCAGCACACA 62.147 60.000 7.81 0.00 0.00 3.72
2849 2955 1.152984 CCATATGCGCCAACCAGGA 60.153 57.895 4.18 0.00 41.22 3.86
2850 2956 0.751277 CCATATGCGCCAACCAGGAA 60.751 55.000 4.18 0.00 41.22 3.36
2851 2957 0.381801 CATATGCGCCAACCAGGAAC 59.618 55.000 4.18 0.00 41.22 3.62
2919 3025 0.681733 CCACACTGTCCAGCTACTGT 59.318 55.000 0.00 0.00 32.43 3.55
2950 3056 1.375523 GCTTTCGTCCCGGACATGT 60.376 57.895 17.87 0.00 32.09 3.21
3049 3158 1.167851 AACATTGTCGGGCAGATGTG 58.832 50.000 9.88 0.00 32.91 3.21
3086 3201 2.670934 AAAGCCGGACAGCAGCAG 60.671 61.111 5.05 0.00 34.23 4.24
3094 3209 0.449388 GGACAGCAGCAGCAACATAC 59.551 55.000 3.17 0.00 45.49 2.39
3163 3278 2.154854 CAAGCTCTTGTCGGAGAACA 57.845 50.000 1.61 0.00 39.69 3.18
3262 3377 2.365635 ATGCCGACCACCTAGCCT 60.366 61.111 0.00 0.00 0.00 4.58
3335 3450 0.391263 GTTCACCGTCCAGACATCCC 60.391 60.000 0.00 0.00 0.00 3.85
3346 3461 0.622136 AGACATCCCTGCTGCATCAA 59.378 50.000 1.31 0.00 0.00 2.57
3347 3462 1.214673 AGACATCCCTGCTGCATCAAT 59.785 47.619 1.31 0.00 0.00 2.57
3349 3464 2.029623 ACATCCCTGCTGCATCAATTC 58.970 47.619 1.31 0.00 0.00 2.17
3377 3492 1.370778 CCGACGTGTCAAGCGTACA 60.371 57.895 0.00 0.00 43.04 2.90
3384 3499 2.029970 CGTGTCAAGCGTACAACACTTT 59.970 45.455 10.14 0.00 39.82 2.66
3540 3698 5.606348 ATTGGACTTGTTTTGTAAAGCCA 57.394 34.783 0.00 0.00 31.86 4.75
3624 3787 3.055819 AGCCGATATTATGGGTGCTACTG 60.056 47.826 6.59 0.00 34.00 2.74
3691 3887 4.003648 CCTAGTGCGAAATTCCAGAAAGT 58.996 43.478 0.00 0.00 0.00 2.66
3692 3888 4.455877 CCTAGTGCGAAATTCCAGAAAGTT 59.544 41.667 0.00 0.00 0.00 2.66
3744 3942 9.638176 AAATCTAATTGGAAAGCAGATATGTCT 57.362 29.630 0.00 0.00 31.38 3.41
3788 3986 8.017418 TCCTATCTTTTGTTTGTTGGAAATGT 57.983 30.769 0.00 0.00 0.00 2.71
3799 3997 7.175641 TGTTTGTTGGAAATGTGTTGGAAAATT 59.824 29.630 0.00 0.00 0.00 1.82
3826 4216 2.668001 GCACGCACAAATATGCAAGACA 60.668 45.455 0.00 0.00 46.47 3.41
3853 4244 5.652014 CAGCAATACTCATCCCTAAACCAAA 59.348 40.000 0.00 0.00 0.00 3.28
3857 4248 8.860088 GCAATACTCATCCCTAAACCAAATATT 58.140 33.333 0.00 0.00 0.00 1.28
4059 4455 1.011595 TCTCTGCCTCCTTAGACCCT 58.988 55.000 0.00 0.00 0.00 4.34
4060 4456 1.063567 TCTCTGCCTCCTTAGACCCTC 60.064 57.143 0.00 0.00 0.00 4.30
4063 4459 0.032017 TGCCTCCTTAGACCCTCCTC 60.032 60.000 0.00 0.00 0.00 3.71
4064 4460 0.761323 GCCTCCTTAGACCCTCCTCC 60.761 65.000 0.00 0.00 0.00 4.30
4065 4461 0.637195 CCTCCTTAGACCCTCCTCCA 59.363 60.000 0.00 0.00 0.00 3.86
4066 4462 1.221781 CCTCCTTAGACCCTCCTCCAT 59.778 57.143 0.00 0.00 0.00 3.41
4067 4463 2.324541 CTCCTTAGACCCTCCTCCATG 58.675 57.143 0.00 0.00 0.00 3.66
4068 4464 0.761802 CCTTAGACCCTCCTCCATGC 59.238 60.000 0.00 0.00 0.00 4.06
4070 4466 0.343372 TTAGACCCTCCTCCATGCCT 59.657 55.000 0.00 0.00 0.00 4.75
4071 4467 0.105453 TAGACCCTCCTCCATGCCTC 60.105 60.000 0.00 0.00 0.00 4.70
4072 4468 1.383803 GACCCTCCTCCATGCCTCT 60.384 63.158 0.00 0.00 0.00 3.69
4073 4469 1.692042 ACCCTCCTCCATGCCTCTG 60.692 63.158 0.00 0.00 0.00 3.35
4074 4470 2.509916 CCTCCTCCATGCCTCTGC 59.490 66.667 0.00 0.00 38.26 4.26
4253 4654 4.381612 CCAGACGAGCAAGAGTAACCAATA 60.382 45.833 0.00 0.00 0.00 1.90
4311 4712 6.527057 TTTATGTTGCATGTGGAATGATCA 57.473 33.333 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.900112 AGACTTATATTTAGGAACATAGGGAGT 57.100 33.333 0.00 0.00 0.00 3.85
82 83 8.365647 CCCGTTCCTAAATATAAGTCTGTATGT 58.634 37.037 0.00 0.00 0.00 2.29
83 84 7.817962 CCCCGTTCCTAAATATAAGTCTGTATG 59.182 40.741 0.00 0.00 0.00 2.39
84 85 7.038516 CCCCCGTTCCTAAATATAAGTCTGTAT 60.039 40.741 0.00 0.00 0.00 2.29
85 86 6.268387 CCCCCGTTCCTAAATATAAGTCTGTA 59.732 42.308 0.00 0.00 0.00 2.74
86 87 5.071384 CCCCCGTTCCTAAATATAAGTCTGT 59.929 44.000 0.00 0.00 0.00 3.41
87 88 5.548406 CCCCCGTTCCTAAATATAAGTCTG 58.452 45.833 0.00 0.00 0.00 3.51
88 89 5.820404 CCCCCGTTCCTAAATATAAGTCT 57.180 43.478 0.00 0.00 0.00 3.24
107 108 2.904434 TCTCTTCAACTTGTACTCCCCC 59.096 50.000 0.00 0.00 0.00 5.40
108 109 3.323979 TGTCTCTTCAACTTGTACTCCCC 59.676 47.826 0.00 0.00 0.00 4.81
109 110 4.602340 TGTCTCTTCAACTTGTACTCCC 57.398 45.455 0.00 0.00 0.00 4.30
110 111 6.706270 TGATTTGTCTCTTCAACTTGTACTCC 59.294 38.462 0.00 0.00 0.00 3.85
111 112 7.439655 ACTGATTTGTCTCTTCAACTTGTACTC 59.560 37.037 0.00 0.00 0.00 2.59
112 113 7.275920 ACTGATTTGTCTCTTCAACTTGTACT 58.724 34.615 0.00 0.00 0.00 2.73
113 114 7.484035 ACTGATTTGTCTCTTCAACTTGTAC 57.516 36.000 0.00 0.00 0.00 2.90
145 146 5.059833 GGGCCAGATATTTGTCTCTTGTAG 58.940 45.833 4.39 0.00 0.00 2.74
184 185 1.139058 AGTTGACAAGCTCAGGACGTT 59.861 47.619 0.00 0.00 0.00 3.99
186 187 1.871080 AAGTTGACAAGCTCAGGACG 58.129 50.000 0.00 0.00 0.00 4.79
187 188 2.945668 ACAAAGTTGACAAGCTCAGGAC 59.054 45.455 0.00 0.00 0.00 3.85
201 202 1.610522 GATGCTGGTGCTCACAAAGTT 59.389 47.619 2.21 0.00 40.48 2.66
312 313 8.174733 ACAACATGTCTTGAGAAGATGAAAAT 57.825 30.769 0.00 0.00 40.18 1.82
325 326 8.597227 CCAATTATATTGCAACAACATGTCTTG 58.403 33.333 0.00 5.33 0.00 3.02
370 371 7.507956 TCCAACATCCGGTTATAGATCTCTTTA 59.492 37.037 0.00 0.00 37.72 1.85
374 375 5.723672 TCCAACATCCGGTTATAGATCTC 57.276 43.478 0.00 0.00 37.72 2.75
478 480 6.317088 CACATTATGTCCGCATTCATTATCC 58.683 40.000 0.00 0.00 36.58 2.59
482 484 3.380954 TGCACATTATGTCCGCATTCATT 59.619 39.130 6.30 0.00 36.58 2.57
490 492 4.891627 TTGGTTATGCACATTATGTCCG 57.108 40.909 0.00 0.00 0.00 4.79
552 554 9.319143 CATGTTCCAATTTTGTTGGTAAACTTA 57.681 29.630 6.70 0.00 40.40 2.24
602 604 0.482446 AACTGTTTGGGCCATCAGGA 59.518 50.000 29.47 7.38 36.89 3.86
660 668 3.845178 CATGATATGGTGGTACGCGTAT 58.155 45.455 23.56 8.81 41.51 3.06
663 671 0.790207 GCATGATATGGTGGTACGCG 59.210 55.000 3.53 3.53 41.51 6.01
670 678 7.041984 GCTGATATAGACATGCATGATATGGTG 60.042 40.741 32.75 18.55 0.00 4.17
676 684 5.642491 GTGTGCTGATATAGACATGCATGAT 59.358 40.000 32.75 21.47 32.98 2.45
735 760 9.907229 TCTTCCTCTCCTCTTATTTTTAAATCC 57.093 33.333 0.00 0.00 0.00 3.01
772 797 1.238439 AGTTCCCACACGATTTGCAG 58.762 50.000 0.00 0.00 0.00 4.41
773 798 2.422597 CTAGTTCCCACACGATTTGCA 58.577 47.619 0.00 0.00 0.00 4.08
776 801 1.001633 ACGCTAGTTCCCACACGATTT 59.998 47.619 0.00 0.00 0.00 2.17
823 861 3.185246 ACTAATCGCACAAGAGATGGG 57.815 47.619 0.00 0.00 34.34 4.00
884 954 1.887198 GACAGAGTTTGACGAGGAGGA 59.113 52.381 0.00 0.00 0.00 3.71
885 955 1.889829 AGACAGAGTTTGACGAGGAGG 59.110 52.381 0.00 0.00 0.00 4.30
886 956 3.426963 GCTAGACAGAGTTTGACGAGGAG 60.427 52.174 0.00 0.00 0.00 3.69
897 967 6.207810 GTGCCAACTATATAGCTAGACAGAGT 59.792 42.308 9.78 0.00 0.00 3.24
923 993 0.761187 TGCCTCAGCTCTGAACAAGT 59.239 50.000 0.93 0.00 39.39 3.16
927 997 0.390998 GGTCTGCCTCAGCTCTGAAC 60.391 60.000 0.93 0.00 39.39 3.18
955 1025 3.578716 TGCTCTTAGCTCTAGGTGTGTTT 59.421 43.478 0.00 0.00 42.97 2.83
981 1051 7.213678 AGTACATTTTCTCAATCTAGCTAGCC 58.786 38.462 16.35 0.00 0.00 3.93
1013 1083 3.710209 ATAAGATCCATAGCAGCACCC 57.290 47.619 0.00 0.00 0.00 4.61
1016 1089 7.178573 ACTAGAGTATAAGATCCATAGCAGCA 58.821 38.462 0.00 0.00 0.00 4.41
1018 1091 8.892723 CAGACTAGAGTATAAGATCCATAGCAG 58.107 40.741 0.00 0.00 0.00 4.24
1064 1146 3.571590 AGCGACAGATCTCCCTCTAATT 58.428 45.455 0.00 0.00 0.00 1.40
1066 1148 2.738587 AGCGACAGATCTCCCTCTAA 57.261 50.000 0.00 0.00 0.00 2.10
1067 1149 2.039216 CCTAGCGACAGATCTCCCTCTA 59.961 54.545 0.00 0.00 0.00 2.43
1071 1153 0.955905 GACCTAGCGACAGATCTCCC 59.044 60.000 0.00 0.00 0.00 4.30
1121 1221 0.176680 CAACATGTCGCTAGGGCTCT 59.823 55.000 0.00 0.00 36.09 4.09
1177 1277 0.533755 GCACTAAGCATGGCGAGGAT 60.534 55.000 0.00 0.00 44.79 3.24
1307 1407 0.601311 GATGAGGCCGATGGTGTAGC 60.601 60.000 0.00 0.00 0.00 3.58
1356 1456 2.914097 GCCCACAACAGCTGGCTT 60.914 61.111 19.93 0.37 40.77 4.35
1383 1483 0.032678 CGCTACCGATGAGGAGCAAT 59.967 55.000 0.00 0.00 45.00 3.56
1384 1484 1.320344 ACGCTACCGATGAGGAGCAA 61.320 55.000 0.00 0.00 45.00 3.91
1393 1493 4.203076 GCCGTCCACGCTACCGAT 62.203 66.667 0.00 0.00 38.18 4.18
1513 1613 4.016706 CCCGCCCTTGGAGACGTT 62.017 66.667 0.00 0.00 0.00 3.99
1522 1622 3.966543 CAAGACCACCCCGCCCTT 61.967 66.667 0.00 0.00 0.00 3.95
1534 1634 2.418060 GGAGGAAGTAGAGCAGCAAGAC 60.418 54.545 0.00 0.00 0.00 3.01
1542 1642 1.408702 CAGCAGAGGAGGAAGTAGAGC 59.591 57.143 0.00 0.00 0.00 4.09
1585 1685 1.078143 GCGCCTTCATCTTCTGGGT 60.078 57.895 0.00 0.00 0.00 4.51
1689 1789 3.790976 TGGGGATATGATTCCTTTCACCA 59.209 43.478 0.38 0.38 35.97 4.17
1714 1814 1.394917 CTTGCACTTAGCCATGTCGTC 59.605 52.381 0.00 0.00 44.83 4.20
1715 1815 1.270839 ACTTGCACTTAGCCATGTCGT 60.271 47.619 0.00 0.00 44.83 4.34
1716 1816 1.442769 ACTTGCACTTAGCCATGTCG 58.557 50.000 0.00 0.00 44.83 4.35
1758 1858 2.997897 GACGGTGGGCTGGAGTCT 60.998 66.667 0.00 0.00 0.00 3.24
1781 1881 1.381872 TCTGAGAGGTAGCAGGGCC 60.382 63.158 0.00 0.00 33.05 5.80
1839 1939 1.032014 GCTTGTCCTTGCTGTTCCAA 58.968 50.000 0.00 0.00 0.00 3.53
1877 1977 1.215647 GGCTTCTGGTCGTCGTCAT 59.784 57.895 0.00 0.00 0.00 3.06
1884 1984 2.743928 GGCACAGGCTTCTGGTCG 60.744 66.667 0.00 0.00 42.60 4.79
1905 2005 4.434330 GCGAAGGAAAGACACGTATCTTTG 60.434 45.833 25.51 12.12 46.57 2.77
1914 2014 1.594331 ACAAGGCGAAGGAAAGACAC 58.406 50.000 0.00 0.00 0.00 3.67
1987 2087 0.251341 AATTTCAGCGCCTCCAGGTT 60.251 50.000 2.29 0.00 37.57 3.50
1991 2091 1.003839 ACGAATTTCAGCGCCTCCA 60.004 52.632 2.29 0.00 0.00 3.86
2021 2121 1.760192 GAGATGGAAGGCATGCTTGT 58.240 50.000 18.92 2.52 0.00 3.16
2127 2227 0.239347 GAAGGACGACGAAACGGAGA 59.761 55.000 0.00 0.00 37.61 3.71
2146 2246 1.000938 GAGCACCTTGAACAAGCCAAG 60.001 52.381 8.81 0.00 40.37 3.61
2170 2270 4.603231 TGCCGTCGTAAATAAAATCCAC 57.397 40.909 0.00 0.00 0.00 4.02
2179 2279 6.220930 AGTAATATGTGATGCCGTCGTAAAT 58.779 36.000 0.00 0.00 0.00 1.40
2187 2287 4.756642 ACATTGGAGTAATATGTGATGCCG 59.243 41.667 0.00 0.00 31.66 5.69
2195 2295 3.074412 GCGGGGACATTGGAGTAATATG 58.926 50.000 0.00 0.00 0.00 1.78
2198 2298 0.179056 CGCGGGGACATTGGAGTAAT 60.179 55.000 0.00 0.00 0.00 1.89
2199 2299 1.219664 CGCGGGGACATTGGAGTAA 59.780 57.895 0.00 0.00 0.00 2.24
2220 2326 2.420022 CCCCGTGTTATTCTCAAGCAAG 59.580 50.000 0.00 0.00 0.00 4.01
2256 2362 0.472471 AGAGGGTGAAGAAAACCGCA 59.528 50.000 0.00 0.00 38.70 5.69
2263 2369 3.202906 CGTTGTTGAAGAGGGTGAAGAA 58.797 45.455 0.00 0.00 0.00 2.52
2270 2376 1.792949 CGAGAACGTTGTTGAAGAGGG 59.207 52.381 5.00 0.00 34.56 4.30
2406 2512 3.726517 CAACCCTTGCTGCCGTCG 61.727 66.667 0.00 0.00 0.00 5.12
2421 2527 1.838112 GCTTCACCATCATCCACCAA 58.162 50.000 0.00 0.00 0.00 3.67
2473 2579 1.682854 CGCCACCCATTTAATGAGCAT 59.317 47.619 6.50 0.00 0.00 3.79
2515 2621 0.687920 TTGTTATCCCACCAGTGCGA 59.312 50.000 0.00 0.00 0.00 5.10
2553 2659 1.273606 GTGTAGCTGCAGGAGTTGAGA 59.726 52.381 17.12 0.00 0.00 3.27
2566 2672 2.738521 CTTGTGCGCGGTGTAGCT 60.739 61.111 8.83 0.00 34.40 3.32
2648 2754 0.606401 CGTCAGGGCAACATCCTTGT 60.606 55.000 0.00 0.00 37.82 3.16
2658 2764 1.079405 GATTTCGTCCGTCAGGGCA 60.079 57.895 0.00 0.00 43.99 5.36
2659 2765 0.672401 TTGATTTCGTCCGTCAGGGC 60.672 55.000 0.00 0.00 39.22 5.19
2665 2771 1.204941 CTCCTCCTTGATTTCGTCCGT 59.795 52.381 0.00 0.00 0.00 4.69
2691 2797 1.909302 CCACTTTTCCTGAGGGAGCTA 59.091 52.381 0.00 0.00 43.29 3.32
2702 2808 3.680786 GCCGGCCACCACTTTTCC 61.681 66.667 18.11 0.00 0.00 3.13
2735 2841 1.757118 CCTTGTTCCTCAGATCGCCTA 59.243 52.381 0.00 0.00 0.00 3.93
2758 2864 2.113774 CACCCAGTCCAGCTGCAA 59.886 61.111 8.66 0.00 43.71 4.08
2793 2899 1.293963 CGAGGACCATGTGTGTGCTG 61.294 60.000 0.00 0.00 34.28 4.41
2801 2907 2.347490 GCCACACGAGGACCATGT 59.653 61.111 0.00 0.00 0.00 3.21
2849 2955 1.152756 GTGCCCTGGTCCTGTTGTT 60.153 57.895 0.00 0.00 0.00 2.83
2850 2956 2.515901 GTGCCCTGGTCCTGTTGT 59.484 61.111 0.00 0.00 0.00 3.32
2851 2957 2.282462 GGTGCCCTGGTCCTGTTG 60.282 66.667 0.00 0.00 0.00 3.33
2878 2984 4.388499 AACACGGCGGCTACTGGG 62.388 66.667 13.24 0.00 0.00 4.45
2879 2985 3.118454 CAACACGGCGGCTACTGG 61.118 66.667 13.24 0.00 0.00 4.00
2892 2998 0.322906 TGGACAGTGTGGTTGCAACA 60.323 50.000 29.55 13.95 0.00 3.33
2919 3025 0.955428 CGAAAGCAAGCAGGTAGGCA 60.955 55.000 0.00 0.00 35.83 4.75
2950 3056 2.345991 GTAGCTGTGGTCGGGCAA 59.654 61.111 0.00 0.00 0.00 4.52
3026 3132 1.974265 TCTGCCCGACAATGTTTTGA 58.026 45.000 0.00 0.00 36.64 2.69
3049 3158 6.368791 GGCTTTCCCAATTGTAACATCTTTTC 59.631 38.462 4.43 0.00 0.00 2.29
3086 3201 0.597568 TTGCTGCACTGGTATGTTGC 59.402 50.000 0.00 0.00 0.00 4.17
3094 3209 0.520404 GACATGTCTTGCTGCACTGG 59.480 55.000 18.83 0.00 0.00 4.00
3262 3377 4.812476 CATGAACTCGCCGCCGGA 62.812 66.667 7.68 0.00 34.56 5.14
3335 3450 2.479730 GCTCAAGGAATTGATGCAGCAG 60.480 50.000 4.20 0.00 0.00 4.24
3346 3461 1.448540 CGTCGGCAGCTCAAGGAAT 60.449 57.895 0.00 0.00 0.00 3.01
3347 3462 2.048222 CGTCGGCAGCTCAAGGAA 60.048 61.111 0.00 0.00 0.00 3.36
3349 3464 3.114616 CACGTCGGCAGCTCAAGG 61.115 66.667 0.00 0.00 0.00 3.61
3377 3492 4.788679 ACAAAGGCAGTAGGTAAAGTGTT 58.211 39.130 0.00 0.00 0.00 3.32
3384 3499 4.951094 ACAAAACAACAAAGGCAGTAGGTA 59.049 37.500 0.00 0.00 0.00 3.08
3744 3942 9.354673 AGATAGGAAAACTCAAAAACAAGATCA 57.645 29.630 0.00 0.00 0.00 2.92
3788 3986 3.862642 GCGTGCCCATTAATTTTCCAACA 60.863 43.478 0.00 0.00 0.00 3.33
3799 3997 2.223688 GCATATTTGTGCGTGCCCATTA 60.224 45.455 0.00 0.00 35.10 1.90
3826 4216 6.101150 TGGTTTAGGGATGAGTATTGCTGTAT 59.899 38.462 0.00 0.00 0.00 2.29
3857 4248 6.127366 GCCTGAAAATAGATGTTGGATGGAAA 60.127 38.462 0.00 0.00 0.00 3.13
3925 4321 8.492673 ACGAACTTTAGCATGAAGAATAATCA 57.507 30.769 0.00 0.00 0.00 2.57
4015 4411 1.141858 GGTCTAAGGAGCAAGATGGGG 59.858 57.143 0.00 0.00 39.51 4.96
4067 4463 2.713770 CGATGTGCATGCAGAGGC 59.286 61.111 23.41 15.05 41.68 4.70
4068 4464 2.831366 GCCGATGTGCATGCAGAGG 61.831 63.158 23.41 19.16 0.00 3.69
4070 4466 2.825387 GGCCGATGTGCATGCAGA 60.825 61.111 23.41 22.08 0.00 4.26
4071 4467 3.896133 GGGCCGATGTGCATGCAG 61.896 66.667 23.41 10.32 0.00 4.41
4072 4468 4.429522 AGGGCCGATGTGCATGCA 62.430 61.111 18.46 18.46 0.00 3.96
4073 4469 3.589881 GAGGGCCGATGTGCATGC 61.590 66.667 11.82 11.82 0.00 4.06
4074 4470 2.898920 AAGGAGGGCCGATGTGCATG 62.899 60.000 0.00 0.00 39.96 4.06
4075 4471 2.615227 GAAGGAGGGCCGATGTGCAT 62.615 60.000 0.00 0.00 39.96 3.96
4253 4654 5.296780 CACCGGCATACTCATCTTAAAACAT 59.703 40.000 0.00 0.00 0.00 2.71
4311 4712 4.721132 TCGGAAAACAAAAGTAGGTCCAT 58.279 39.130 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.