Multiple sequence alignment - TraesCS1B01G077900

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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 TraesCS1B01G077900 chr1B 100.000 3674 0 0 1 3674 60966434 60962761 0.000000e+00 6785.0
1 TraesCS1B01G077900 chr1B 81.294 1144 161 31 1000 2130 60725800 60724697 0.000000e+00 878.0
2 TraesCS1B01G077900 chr1B 76.154 780 134 35 2314 3086 60724558 60723824 2.700000e-96 363.0
3 TraesCS1B01G077900 chr1B 90.000 280 21 5 456 730 61020230 61019953 4.510000e-94 355.0
4 TraesCS1B01G077900 chr1B 87.770 278 18 11 454 722 61041403 61041133 9.910000e-81 311.0
5 TraesCS1B01G077900 chr1B 82.768 383 31 14 81 454 61022446 61022090 3.560000e-80 309.0
6 TraesCS1B01G077900 chr1B 79.587 387 36 16 497 876 61013374 61013024 1.710000e-58 237.0
7 TraesCS1B01G077900 chr1B 88.824 170 10 7 94 254 61016072 61015903 2.240000e-47 200.0
8 TraesCS1B01G077900 chr1B 90.441 136 7 2 582 717 61412115 61412244 1.360000e-39 174.0
9 TraesCS1B01G077900 chr1B 90.441 136 7 2 582 717 61433915 61434044 1.360000e-39 174.0
10 TraesCS1B01G077900 chr1B 86.131 137 6 8 81 210 61041769 61041639 6.400000e-28 135.0
11 TraesCS1B01G077900 chr1B 86.250 80 6 5 81 157 61016959 61016882 8.460000e-12 82.4
12 TraesCS1B01G077900 chr1A 89.122 2004 121 32 81 2056 40915026 40913092 0.000000e+00 2403.0
13 TraesCS1B01G077900 chr1A 88.683 1131 52 19 2073 3165 40913102 40912010 0.000000e+00 1310.0
14 TraesCS1B01G077900 chr1A 80.944 1165 166 31 1000 2151 40901097 40899976 0.000000e+00 870.0
15 TraesCS1B01G077900 chr1A 91.065 291 14 3 81 359 40919160 40918870 2.070000e-102 383.0
16 TraesCS1B01G077900 chr1A 90.000 280 11 7 81 343 41540898 41540619 2.720000e-91 346.0
17 TraesCS1B01G077900 chr1A 89.453 256 27 0 3418 3673 40911094 40910839 1.270000e-84 324.0
18 TraesCS1B01G077900 chr1A 83.578 341 36 9 383 717 41708398 41708072 5.960000e-78 302.0
19 TraesCS1B01G077900 chr1A 84.982 273 28 8 497 767 40917582 40917321 7.820000e-67 265.0
20 TraesCS1B01G077900 chr1D 91.890 1381 70 13 686 2056 41302602 41301254 0.000000e+00 1892.0
21 TraesCS1B01G077900 chr1D 88.023 1052 56 21 2073 3078 41301264 41300237 0.000000e+00 1181.0
22 TraesCS1B01G077900 chr1D 89.770 870 56 15 2417 3267 41296713 41295858 0.000000e+00 1083.0
23 TraesCS1B01G077900 chr1D 81.202 1165 160 26 1000 2151 41158169 41157051 0.000000e+00 883.0
24 TraesCS1B01G077900 chr1D 86.092 870 64 20 2094 2923 41196160 41195308 0.000000e+00 883.0
25 TraesCS1B01G077900 chr1D 89.980 489 36 9 2688 3165 41291550 41291064 1.450000e-173 619.0
26 TraesCS1B01G077900 chr1D 85.714 364 38 8 2917 3267 41186178 41185816 4.480000e-99 372.0
27 TraesCS1B01G077900 chr1D 89.844 256 26 0 3418 3673 41290420 41290165 2.740000e-86 329.0
28 TraesCS1B01G077900 chr1D 87.402 254 27 5 3421 3673 41176711 41176462 1.670000e-73 287.0
29 TraesCS1B01G077900 chr1D 84.281 299 30 10 81 367 41303128 41302835 3.610000e-70 276.0
30 TraesCS1B01G077900 chr1D 84.711 242 25 9 497 729 41303816 41303578 7.930000e-57 231.0
31 TraesCS1B01G077900 chr1D 87.037 162 15 4 203 359 41305190 41305030 1.050000e-40 178.0
32 TraesCS1B01G077900 chr1D 83.871 124 15 3 3149 3267 41300053 41299930 3.000000e-21 113.0


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 TraesCS1B01G077900 chr1B 60962761 60966434 3673 True 6785.000000 6785 100.000000 1 3674 1 chr1B.!!$R1 3673
1 TraesCS1B01G077900 chr1B 60723824 60725800 1976 True 620.500000 878 78.724000 1000 3086 2 chr1B.!!$R2 2086
2 TraesCS1B01G077900 chr1B 61013024 61022446 9422 True 236.680000 355 85.485800 81 876 5 chr1B.!!$R3 795
3 TraesCS1B01G077900 chr1B 61041133 61041769 636 True 223.000000 311 86.950500 81 722 2 chr1B.!!$R4 641
4 TraesCS1B01G077900 chr1A 40910839 40919160 8321 True 937.000000 2403 88.661000 81 3673 5 chr1A.!!$R4 3592
5 TraesCS1B01G077900 chr1A 40899976 40901097 1121 True 870.000000 870 80.944000 1000 2151 1 chr1A.!!$R1 1151
6 TraesCS1B01G077900 chr1D 41157051 41158169 1118 True 883.000000 883 81.202000 1000 2151 1 chr1D.!!$R1 1151
7 TraesCS1B01G077900 chr1D 41195308 41196160 852 True 883.000000 883 86.092000 2094 2923 1 chr1D.!!$R4 829
8 TraesCS1B01G077900 chr1D 41295858 41305190 9332 True 707.714286 1892 87.083286 81 3267 7 chr1D.!!$R6 3186
9 TraesCS1B01G077900 chr1D 41290165 41291550 1385 True 474.000000 619 89.912000 2688 3673 2 chr1D.!!$R5 985

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
33 34 0.033366 GCTGCCATTTTTCCACCGTT 59.967 50.0 0.0 0.0 0.00 4.44 F
982 15852 0.248990 TTCTTGCCGCTGCTTGTTTG 60.249 50.0 0.7 0.0 38.71 2.93 F
1409 16291 0.896940 AACTTCTGGGAGCGGACGTA 60.897 55.0 0.0 0.0 0.00 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 16911 0.325296 TCGTAGTTCCCCAGCTCCAT 60.325 55.0 0.00 0.00 0.00 3.41 R
2029 16917 0.391263 GTTGGCTCGTAGTTCCCCAG 60.391 60.0 0.00 0.00 0.00 4.45 R
3393 18887 0.396001 TCATCCACACATGCCCATGG 60.396 55.0 4.14 4.14 42.91 3.66 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
18 19 1.153823 CTCATTGCTGGCTTGCTGC 60.154 57.895 0.00 0.00 41.94 5.25
28 29 3.610637 GCTTGCTGCCATTTTTCCA 57.389 47.368 0.00 0.00 35.15 3.53
29 30 1.150827 GCTTGCTGCCATTTTTCCAC 58.849 50.000 0.00 0.00 35.15 4.02
30 31 1.799544 CTTGCTGCCATTTTTCCACC 58.200 50.000 0.00 0.00 0.00 4.61
32 33 1.112315 TGCTGCCATTTTTCCACCGT 61.112 50.000 0.00 0.00 0.00 4.83
33 34 0.033366 GCTGCCATTTTTCCACCGTT 59.967 50.000 0.00 0.00 0.00 4.44
36 37 1.757118 TGCCATTTTTCCACCGTTTCA 59.243 42.857 0.00 0.00 0.00 2.69
37 38 2.366916 TGCCATTTTTCCACCGTTTCAT 59.633 40.909 0.00 0.00 0.00 2.57
38 39 3.574396 TGCCATTTTTCCACCGTTTCATA 59.426 39.130 0.00 0.00 0.00 2.15
39 40 4.039245 TGCCATTTTTCCACCGTTTCATAA 59.961 37.500 0.00 0.00 0.00 1.90
40 41 4.991687 GCCATTTTTCCACCGTTTCATAAA 59.008 37.500 0.00 0.00 0.00 1.40
41 42 5.467063 GCCATTTTTCCACCGTTTCATAAAA 59.533 36.000 0.00 0.00 0.00 1.52
42 43 6.148645 GCCATTTTTCCACCGTTTCATAAAAT 59.851 34.615 0.00 0.00 0.00 1.82
44 45 8.868916 CCATTTTTCCACCGTTTCATAAAATAG 58.131 33.333 0.00 0.00 0.00 1.73
45 46 9.418045 CATTTTTCCACCGTTTCATAAAATAGT 57.582 29.630 0.00 0.00 0.00 2.12
48 49 8.851541 TTTCCACCGTTTCATAAAATAGTAGT 57.148 30.769 0.00 0.00 0.00 2.73
49 50 9.941325 TTTCCACCGTTTCATAAAATAGTAGTA 57.059 29.630 0.00 0.00 0.00 1.82
51 52 8.752187 TCCACCGTTTCATAAAATAGTAGTACT 58.248 33.333 8.14 8.14 0.00 2.73
52 53 9.028185 CCACCGTTTCATAAAATAGTAGTACTC 57.972 37.037 5.96 0.00 0.00 2.59
54 55 7.917505 ACCGTTTCATAAAATAGTAGTACTCCG 59.082 37.037 5.96 0.00 0.00 4.63
55 56 7.096312 CCGTTTCATAAAATAGTAGTACTCCGC 60.096 40.741 5.96 0.00 0.00 5.54
56 57 7.646922 CGTTTCATAAAATAGTAGTACTCCGCT 59.353 37.037 5.96 0.00 0.00 5.52
64 65 4.915158 AGTAGTACTCCGCTATTTCACC 57.085 45.455 0.00 0.00 0.00 4.02
66 67 1.202382 AGTACTCCGCTATTTCACCGC 60.202 52.381 0.00 0.00 0.00 5.68
70 71 2.709475 CGCTATTTCACCGCTGGC 59.291 61.111 0.00 0.00 0.00 4.85
71 72 2.709475 GCTATTTCACCGCTGGCG 59.291 61.111 8.08 8.08 39.44 5.69
72 73 2.709475 CTATTTCACCGCTGGCGC 59.291 61.111 9.63 0.00 38.24 6.53
75 76 1.643868 TATTTCACCGCTGGCGCTTG 61.644 55.000 7.64 8.68 38.24 4.01
93 2076 3.670637 GAGATGACCGGCTGCTGCA 62.671 63.158 17.89 0.88 41.91 4.41
138 2124 0.320771 AGCTGTGGCAGTTTCTACCG 60.321 55.000 0.00 0.00 41.70 4.02
241 2248 4.711949 AGCCCAGTTGCCTCTGCG 62.712 66.667 0.48 0.00 41.78 5.18
340 6473 5.382303 CACGCAACAACGATATCTTTCTTT 58.618 37.500 0.34 0.00 36.70 2.52
341 6474 5.851177 CACGCAACAACGATATCTTTCTTTT 59.149 36.000 0.34 0.00 36.70 2.27
342 6475 7.012943 CACGCAACAACGATATCTTTCTTTTA 58.987 34.615 0.34 0.00 36.70 1.52
343 6476 7.006210 CACGCAACAACGATATCTTTCTTTTAC 59.994 37.037 0.34 0.00 36.70 2.01
380 6524 4.018506 AGGAATGTGATTGACATGGGTGTA 60.019 41.667 0.00 0.00 45.12 2.90
390 6534 6.662865 TTGACATGGGTGTACATTTTGATT 57.337 33.333 0.00 0.00 39.09 2.57
398 6542 6.721668 TGGGTGTACATTTTGATTGTGGATTA 59.278 34.615 0.00 0.00 0.00 1.75
471 8480 8.955388 TGTAAGCTATAAATGATTTGACTGCAA 58.045 29.630 0.00 0.00 0.00 4.08
492 8501 6.321181 TGCAAATTCTGGATTATAACCTGGTC 59.679 38.462 0.00 0.00 0.00 4.02
505 8517 1.278127 ACCTGGTCGGGTAACATGAAG 59.722 52.381 0.00 0.00 37.90 3.02
508 8520 2.496070 CTGGTCGGGTAACATGAAGAGA 59.504 50.000 0.00 0.00 39.74 3.10
515 8527 5.479375 TCGGGTAACATGAAGAGAAGTACTT 59.521 40.000 8.13 8.13 39.74 2.24
516 8528 5.577164 CGGGTAACATGAAGAGAAGTACTTG 59.423 44.000 14.14 0.00 39.74 3.16
517 8529 6.571731 CGGGTAACATGAAGAGAAGTACTTGA 60.572 42.308 14.14 0.00 39.74 3.02
557 8578 4.981806 TCTGTTTCCAAACTCAAAGTGG 57.018 40.909 3.92 0.00 39.59 4.00
565 8586 3.007182 CCAAACTCAAAGTGGATGGCATT 59.993 43.478 0.00 0.00 34.05 3.56
598 8625 1.737199 TAGTACAAGGCCCCAACTGT 58.263 50.000 0.00 0.00 0.00 3.55
648 8675 2.752354 TGCATGGCATTGTACTACCAAC 59.248 45.455 0.00 0.00 35.41 3.77
681 8710 8.664211 AGAAACTCGAAATAGACAAGAAACTT 57.336 30.769 0.00 0.00 0.00 2.66
718 15555 4.159506 TCTGGAAAAGAAAACAACCACCTG 59.840 41.667 0.00 0.00 29.54 4.00
735 15572 0.798776 CTGCCTTTTGCTCACGTAGG 59.201 55.000 0.00 0.00 42.00 3.18
807 15655 2.202932 CTTCCCATCGCCTCACCG 60.203 66.667 0.00 0.00 0.00 4.94
929 15791 2.675371 CCCCTTCCCCCTTTCGAC 59.325 66.667 0.00 0.00 0.00 4.20
976 15846 1.639298 GATCGTTTCTTGCCGCTGCT 61.639 55.000 0.70 0.00 38.71 4.24
977 15847 1.237285 ATCGTTTCTTGCCGCTGCTT 61.237 50.000 0.70 0.00 38.71 3.91
978 15848 1.727022 CGTTTCTTGCCGCTGCTTG 60.727 57.895 0.70 0.00 38.71 4.01
979 15849 1.360192 GTTTCTTGCCGCTGCTTGT 59.640 52.632 0.70 0.00 38.71 3.16
980 15850 0.249031 GTTTCTTGCCGCTGCTTGTT 60.249 50.000 0.70 0.00 38.71 2.83
981 15851 0.459489 TTTCTTGCCGCTGCTTGTTT 59.541 45.000 0.70 0.00 38.71 2.83
982 15852 0.248990 TTCTTGCCGCTGCTTGTTTG 60.249 50.000 0.70 0.00 38.71 2.93
983 15853 2.279385 TTGCCGCTGCTTGTTTGC 60.279 55.556 0.70 0.00 38.71 3.68
984 15854 2.957484 CTTGCCGCTGCTTGTTTGCA 62.957 55.000 0.70 0.00 41.05 4.08
1044 15914 3.119096 GAAGGAGCGGTCGCCAAC 61.119 66.667 11.95 2.82 43.17 3.77
1145 16018 4.308458 CCAGCGAACCCGTGACCA 62.308 66.667 0.00 0.00 38.24 4.02
1244 16117 3.586961 CGAGCGCGAGGAGGATGA 61.587 66.667 12.10 0.00 40.82 2.92
1245 16118 2.913765 CGAGCGCGAGGAGGATGAT 61.914 63.158 12.10 0.00 40.82 2.45
1409 16291 0.896940 AACTTCTGGGAGCGGACGTA 60.897 55.000 0.00 0.00 0.00 3.57
2029 16917 2.109126 GTGGAAGACGCCATGGAGC 61.109 63.158 18.40 8.91 40.68 4.70
2033 16921 3.335356 AAGACGCCATGGAGCTGGG 62.335 63.158 18.40 0.00 36.75 4.45
2045 16966 2.187163 GCTGGGGAACTACGAGCC 59.813 66.667 0.00 0.00 0.00 4.70
2046 16967 2.656069 GCTGGGGAACTACGAGCCA 61.656 63.158 0.00 0.00 0.00 4.75
2047 16968 1.980052 CTGGGGAACTACGAGCCAA 59.020 57.895 0.00 0.00 0.00 4.52
2048 16969 0.391263 CTGGGGAACTACGAGCCAAC 60.391 60.000 0.00 0.00 0.00 3.77
2049 16970 1.078637 GGGGAACTACGAGCCAACC 60.079 63.158 0.00 0.00 0.00 3.77
2050 16971 1.078637 GGGAACTACGAGCCAACCC 60.079 63.158 0.00 0.00 0.00 4.11
2051 16972 1.078637 GGAACTACGAGCCAACCCC 60.079 63.158 0.00 0.00 0.00 4.95
2052 16973 1.675219 GAACTACGAGCCAACCCCA 59.325 57.895 0.00 0.00 0.00 4.96
2053 16974 0.672711 GAACTACGAGCCAACCCCAC 60.673 60.000 0.00 0.00 0.00 4.61
2054 16975 1.412453 AACTACGAGCCAACCCCACA 61.412 55.000 0.00 0.00 0.00 4.17
2055 16976 1.079127 CTACGAGCCAACCCCACAG 60.079 63.158 0.00 0.00 0.00 3.66
2056 16977 3.248446 TACGAGCCAACCCCACAGC 62.248 63.158 0.00 0.00 0.00 4.40
2061 16982 4.684134 CCAACCCCACAGCCCCTG 62.684 72.222 0.00 0.00 37.52 4.45
2062 16983 3.902112 CAACCCCACAGCCCCTGT 61.902 66.667 0.00 0.00 46.51 4.00
2063 16984 3.580319 AACCCCACAGCCCCTGTC 61.580 66.667 0.00 0.00 43.43 3.51
2068 16989 4.624364 CACAGCCCCTGTCGCACA 62.624 66.667 0.00 0.00 43.43 4.57
2069 16990 3.872603 ACAGCCCCTGTCGCACAA 61.873 61.111 0.00 0.00 41.21 3.33
2070 16991 3.052082 CAGCCCCTGTCGCACAAG 61.052 66.667 0.00 0.00 0.00 3.16
2071 16992 4.335647 AGCCCCTGTCGCACAAGG 62.336 66.667 0.00 0.00 29.44 3.61
2346 17282 2.359975 CTGAACTTCACCGGCCCC 60.360 66.667 0.00 0.00 0.00 5.80
2640 17576 1.072015 GAGGCTGAGGGAATGGATCTG 59.928 57.143 0.00 0.00 0.00 2.90
2681 17617 0.527385 GCTCTTCACTAGCTGGCTCG 60.527 60.000 0.00 0.00 37.01 5.03
2802 17770 3.057315 TGCTGTTTATCTCTTTTGCAGGC 60.057 43.478 0.00 0.00 0.00 4.85
2938 17910 0.967662 TTGTGTTGCATCCATGTGGG 59.032 50.000 0.00 0.00 35.41 4.61
2969 17941 4.864806 CGTAGTAGCATCACACATCAGTTT 59.135 41.667 0.00 0.00 0.00 2.66
3015 17987 6.768078 ACTACAAACTGTTGTTTCACTTACG 58.232 36.000 0.00 0.00 46.01 3.18
3016 17988 4.976987 ACAAACTGTTGTTTCACTTACGG 58.023 39.130 0.00 0.00 46.01 4.02
3021 17993 2.946329 TGTTGTTTCACTTACGGCATGT 59.054 40.909 0.00 0.00 0.00 3.21
3068 18132 5.477510 AGACATCTAAGCCGATGATGATTC 58.522 41.667 13.29 2.84 42.63 2.52
3131 18203 4.153117 GCATTATAAGCTGGGTCATTCGAG 59.847 45.833 0.00 0.00 0.00 4.04
3138 18210 2.096013 GCTGGGTCATTCGAGCTAAAAC 59.904 50.000 0.00 0.00 39.68 2.43
3151 18223 5.405571 TCGAGCTAAAACTTGTAGCAGAAAG 59.594 40.000 12.65 0.99 45.33 2.62
3182 18288 6.756074 TCCATGTTGTGTTCAATTTTTGTCTC 59.244 34.615 0.00 0.00 35.92 3.36
3184 18290 7.254185 CCATGTTGTGTTCAATTTTTGTCTCAG 60.254 37.037 0.00 0.00 35.92 3.35
3189 18295 7.944061 TGTGTTCAATTTTTGTCTCAGATGAT 58.056 30.769 0.00 0.00 0.00 2.45
3191 18297 9.897744 GTGTTCAATTTTTGTCTCAGATGATTA 57.102 29.630 0.00 0.00 0.00 1.75
3192 18298 9.897744 TGTTCAATTTTTGTCTCAGATGATTAC 57.102 29.630 0.00 0.00 0.00 1.89
3193 18299 9.897744 GTTCAATTTTTGTCTCAGATGATTACA 57.102 29.630 0.00 0.00 0.00 2.41
3195 18301 8.239314 TCAATTTTTGTCTCAGATGATTACAGC 58.761 33.333 0.00 0.00 0.00 4.40
3196 18302 7.692460 ATTTTTGTCTCAGATGATTACAGCA 57.308 32.000 0.00 0.00 34.60 4.41
3200 18310 5.363101 TGTCTCAGATGATTACAGCAATCC 58.637 41.667 0.00 0.00 42.17 3.01
3202 18312 5.996513 GTCTCAGATGATTACAGCAATCCAT 59.003 40.000 0.00 0.00 42.17 3.41
3214 18324 3.485947 GCAATCCATGCGTTTAGACAA 57.514 42.857 0.00 0.00 46.87 3.18
3215 18325 3.832276 GCAATCCATGCGTTTAGACAAA 58.168 40.909 0.00 0.00 46.87 2.83
3255 18366 3.884895 CCTTGGTATTGGTGTATCAGCA 58.115 45.455 0.00 0.00 40.20 4.41
3267 18378 4.100189 GGTGTATCAGCAGTAATCCAGAGT 59.900 45.833 0.00 0.00 0.00 3.24
3269 18380 6.015010 GGTGTATCAGCAGTAATCCAGAGTAT 60.015 42.308 0.00 0.00 0.00 2.12
3273 18478 4.716784 TCAGCAGTAATCCAGAGTATTGGT 59.283 41.667 0.00 0.00 39.35 3.67
3278 18483 6.106673 CAGTAATCCAGAGTATTGGTCGTTT 58.893 40.000 0.00 0.00 39.35 3.60
3309 18514 0.467384 CCATGAGCTCCTCGGATGTT 59.533 55.000 12.15 0.00 32.35 2.71
3318 18523 3.681594 GCTCCTCGGATGTTATTTGACCA 60.682 47.826 0.00 0.00 0.00 4.02
3329 18534 9.434420 GGATGTTATTTGACCATGAAAATTTGA 57.566 29.630 0.00 0.00 0.00 2.69
3340 18545 5.121142 CCATGAAAATTTGAATGCACCTGAC 59.879 40.000 0.00 0.00 0.00 3.51
3341 18546 4.297510 TGAAAATTTGAATGCACCTGACG 58.702 39.130 0.00 0.00 0.00 4.35
3358 18850 2.901192 TGACGGTCTTGGATTCCAGTTA 59.099 45.455 9.88 0.00 33.81 2.24
3399 18893 4.870123 TTTTGAATTCACTGTCCATGGG 57.130 40.909 13.02 0.00 0.00 4.00
3414 18908 0.754217 ATGGGCATGTGTGGATGAGC 60.754 55.000 0.00 0.00 0.00 4.26
3503 19294 7.340122 TCAACAATTTTGGAGTCACACATTA 57.660 32.000 0.00 0.00 0.00 1.90
3571 19362 3.778629 AGTATTGGGGTCGTCAAGGTATT 59.221 43.478 0.00 0.00 0.00 1.89
3583 19374 6.363357 GTCGTCAAGGTATTACGTTACAAACT 59.637 38.462 0.00 0.00 37.83 2.66
3643 19434 1.580845 GCATGTGCTCACAGACACCC 61.581 60.000 8.74 0.00 45.48 4.61
3645 19436 2.357517 GTGCTCACAGACACCCGG 60.358 66.667 0.00 0.00 0.00 5.73
3648 19439 2.276116 GCTCACAGACACCCGGAGA 61.276 63.158 0.73 0.00 0.00 3.71
3673 19464 2.180086 TCATCCCACTAGTCTAGGGCAT 59.820 50.000 11.23 4.51 42.52 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.967397 GCAGCAAGCCAGCAATGA 59.033 55.556 0.55 0.00 37.23 2.57
10 11 1.150827 GTGGAAAAATGGCAGCAAGC 58.849 50.000 0.00 0.00 44.65 4.01
11 12 1.799544 GGTGGAAAAATGGCAGCAAG 58.200 50.000 0.00 0.00 0.00 4.01
12 13 0.033228 CGGTGGAAAAATGGCAGCAA 59.967 50.000 0.00 0.00 0.00 3.91
13 14 1.112315 ACGGTGGAAAAATGGCAGCA 61.112 50.000 0.00 0.00 0.00 4.41
14 15 0.033366 AACGGTGGAAAAATGGCAGC 59.967 50.000 0.00 0.00 0.00 5.25
15 16 2.223923 TGAAACGGTGGAAAAATGGCAG 60.224 45.455 0.00 0.00 0.00 4.85
16 17 1.757118 TGAAACGGTGGAAAAATGGCA 59.243 42.857 0.00 0.00 0.00 4.92
17 18 2.517650 TGAAACGGTGGAAAAATGGC 57.482 45.000 0.00 0.00 0.00 4.40
18 19 7.665561 ATTTTATGAAACGGTGGAAAAATGG 57.334 32.000 0.00 0.00 0.00 3.16
19 20 9.418045 ACTATTTTATGAAACGGTGGAAAAATG 57.582 29.630 0.00 0.00 0.00 2.32
22 23 9.287373 ACTACTATTTTATGAAACGGTGGAAAA 57.713 29.630 7.22 0.00 0.00 2.29
23 24 8.851541 ACTACTATTTTATGAAACGGTGGAAA 57.148 30.769 7.22 0.00 0.00 3.13
24 25 9.369904 GTACTACTATTTTATGAAACGGTGGAA 57.630 33.333 7.22 0.00 0.00 3.53
25 26 8.752187 AGTACTACTATTTTATGAAACGGTGGA 58.248 33.333 0.00 0.00 0.00 4.02
27 28 9.028185 GGAGTACTACTATTTTATGAAACGGTG 57.972 37.037 0.00 0.00 0.00 4.94
28 29 7.917505 CGGAGTACTACTATTTTATGAAACGGT 59.082 37.037 2.99 0.00 0.00 4.83
29 30 7.096312 GCGGAGTACTACTATTTTATGAAACGG 60.096 40.741 2.99 0.00 0.00 4.44
30 31 7.646922 AGCGGAGTACTACTATTTTATGAAACG 59.353 37.037 2.99 0.00 0.00 3.60
37 38 9.956720 GTGAAATAGCGGAGTACTACTATTTTA 57.043 33.333 24.57 20.93 42.45 1.52
38 39 7.924947 GGTGAAATAGCGGAGTACTACTATTTT 59.075 37.037 24.57 12.50 42.45 1.82
39 40 7.432059 GGTGAAATAGCGGAGTACTACTATTT 58.568 38.462 24.29 24.29 44.12 1.40
40 41 6.293845 CGGTGAAATAGCGGAGTACTACTATT 60.294 42.308 14.89 14.89 45.98 1.73
41 42 5.180868 CGGTGAAATAGCGGAGTACTACTAT 59.819 44.000 2.99 5.27 45.98 2.12
42 43 4.512944 CGGTGAAATAGCGGAGTACTACTA 59.487 45.833 2.99 3.05 45.98 1.82
44 45 3.625938 CGGTGAAATAGCGGAGTACTAC 58.374 50.000 0.00 0.00 45.98 2.73
45 46 3.976793 CGGTGAAATAGCGGAGTACTA 57.023 47.619 0.00 0.00 45.98 1.82
46 47 2.865343 CGGTGAAATAGCGGAGTACT 57.135 50.000 0.00 0.00 45.98 2.73
54 55 2.709475 CGCCAGCGGTGAAATAGC 59.291 61.111 17.83 9.49 34.74 2.97
55 56 2.709475 GCGCCAGCGGTGAAATAG 59.291 61.111 17.83 0.00 40.19 1.73
66 67 2.169789 CGGTCATCTCAAGCGCCAG 61.170 63.158 2.29 0.00 0.00 4.85
70 71 2.169789 CAGCCGGTCATCTCAAGCG 61.170 63.158 1.90 0.00 37.37 4.68
71 72 2.467826 GCAGCCGGTCATCTCAAGC 61.468 63.158 1.90 0.00 0.00 4.01
72 73 1.088340 CAGCAGCCGGTCATCTCAAG 61.088 60.000 1.90 0.00 0.00 3.02
75 76 2.894387 GCAGCAGCCGGTCATCTC 60.894 66.667 1.90 0.00 33.58 2.75
77 78 3.200593 CTGCAGCAGCCGGTCATC 61.201 66.667 10.14 0.00 41.13 2.92
138 2124 3.709987 TCAGAAAGCAAAAGCAAAGCTC 58.290 40.909 0.00 0.00 38.25 4.09
241 2248 1.293924 CTGTTGCGGATCAGATCACC 58.706 55.000 12.66 3.01 34.02 4.02
264 2271 4.658063 ACACGAAGTAAAATTCCATGGGA 58.342 39.130 13.02 2.34 41.61 4.37
266 2273 5.621197 TGACACGAAGTAAAATTCCATGG 57.379 39.130 4.97 4.97 41.61 3.66
271 2278 5.182380 TGGGGATTGACACGAAGTAAAATTC 59.818 40.000 0.00 0.00 41.61 2.17
340 6473 6.017770 CACATTCCTACTGTTTTTCACCGTAA 60.018 38.462 0.00 0.00 0.00 3.18
341 6474 5.467399 CACATTCCTACTGTTTTTCACCGTA 59.533 40.000 0.00 0.00 0.00 4.02
342 6475 4.274950 CACATTCCTACTGTTTTTCACCGT 59.725 41.667 0.00 0.00 0.00 4.83
343 6476 4.513692 TCACATTCCTACTGTTTTTCACCG 59.486 41.667 0.00 0.00 0.00 4.94
380 6524 7.174946 AGTCGACTTAATCCACAATCAAAATGT 59.825 33.333 13.58 0.00 0.00 2.71
390 6534 4.707934 TGATACCAGTCGACTTAATCCACA 59.292 41.667 17.26 7.82 0.00 4.17
471 8480 5.456186 CCCGACCAGGTTATAATCCAGAATT 60.456 44.000 0.00 0.00 38.74 2.17
486 8495 1.553248 TCTTCATGTTACCCGACCAGG 59.447 52.381 0.00 0.00 40.63 4.45
492 8501 5.326200 AGTACTTCTCTTCATGTTACCCG 57.674 43.478 0.00 0.00 0.00 5.28
505 8517 7.065085 TGCTTGCTTTATCATCAAGTACTTCTC 59.935 37.037 4.77 0.00 39.36 2.87
508 8520 7.452880 TTGCTTGCTTTATCATCAAGTACTT 57.547 32.000 1.12 1.12 39.36 2.24
515 8527 6.376299 ACAGAAGATTGCTTGCTTTATCATCA 59.624 34.615 0.00 0.00 33.61 3.07
516 8528 6.793349 ACAGAAGATTGCTTGCTTTATCATC 58.207 36.000 0.00 0.00 33.61 2.92
517 8529 6.770746 ACAGAAGATTGCTTGCTTTATCAT 57.229 33.333 0.00 0.00 33.61 2.45
524 8536 3.225104 TGGAAACAGAAGATTGCTTGCT 58.775 40.909 0.00 0.00 31.52 3.91
557 8578 5.762825 ATGATGAACAGTACAATGCCATC 57.237 39.130 0.00 3.86 35.67 3.51
565 8586 6.338146 GCCTTGTACTATGATGAACAGTACA 58.662 40.000 9.18 9.18 42.08 2.90
598 8625 5.707298 CCTCTTTTACTGCCTCTGATTTTGA 59.293 40.000 0.00 0.00 0.00 2.69
656 8684 8.664211 AAGTTTCTTGTCTATTTCGAGTTTCT 57.336 30.769 0.00 0.00 0.00 2.52
668 8696 7.551617 ACGAAAGAGGAAAAAGTTTCTTGTCTA 59.448 33.333 0.00 0.00 30.77 2.59
718 15555 1.502190 GCCTACGTGAGCAAAAGGC 59.498 57.895 7.47 7.47 45.37 4.35
735 15572 2.579738 GTGAGACGGAGGGAAGGC 59.420 66.667 0.00 0.00 0.00 4.35
807 15655 0.682852 GGGTTTGGTTGGGGTTTAGC 59.317 55.000 0.00 0.00 0.00 3.09
929 15791 1.444553 GTCCTCGCCTCGTCTGTTG 60.445 63.158 0.00 0.00 0.00 3.33
976 15846 1.760086 CCACCCACCCTGCAAACAA 60.760 57.895 0.00 0.00 0.00 2.83
977 15847 2.123511 CCACCCACCCTGCAAACA 60.124 61.111 0.00 0.00 0.00 2.83
978 15848 2.123468 ACCACCCACCCTGCAAAC 60.123 61.111 0.00 0.00 0.00 2.93
979 15849 2.123511 CACCACCCACCCTGCAAA 60.124 61.111 0.00 0.00 0.00 3.68
980 15850 3.099841 TCACCACCCACCCTGCAA 61.100 61.111 0.00 0.00 0.00 4.08
981 15851 3.884774 GTCACCACCCACCCTGCA 61.885 66.667 0.00 0.00 0.00 4.41
982 15852 4.660938 GGTCACCACCCACCCTGC 62.661 72.222 0.00 0.00 36.54 4.85
983 15853 2.538141 ATGGTCACCACCCACCCTG 61.538 63.158 0.00 0.00 42.99 4.45
984 15854 2.121506 ATGGTCACCACCCACCCT 60.122 61.111 0.00 0.00 42.99 4.34
985 15855 2.035626 CATGGTCACCACCCACCC 59.964 66.667 0.00 0.00 42.99 4.61
986 15856 2.035626 CCATGGTCACCACCCACC 59.964 66.667 0.00 0.00 42.99 4.61
987 15857 2.676471 GCCATGGTCACCACCCAC 60.676 66.667 14.67 0.00 42.99 4.61
988 15858 4.343323 CGCCATGGTCACCACCCA 62.343 66.667 14.67 0.00 42.99 4.51
1145 16018 2.960688 GCCTTCTTCCTGGTCCGCT 61.961 63.158 0.00 0.00 0.00 5.52
1237 16110 2.746359 CCCCGCCTCATCATCCTC 59.254 66.667 0.00 0.00 0.00 3.71
1238 16111 3.564218 GCCCCGCCTCATCATCCT 61.564 66.667 0.00 0.00 0.00 3.24
1511 16393 2.978824 CGAACGGGGACATGGTCT 59.021 61.111 0.00 0.00 32.47 3.85
1837 16719 1.717194 CCGTAGCAAACCGTGTACAT 58.283 50.000 0.00 0.00 0.00 2.29
1919 16801 4.410400 GTCCCCTCTTGGCGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
2023 16911 0.325296 TCGTAGTTCCCCAGCTCCAT 60.325 55.000 0.00 0.00 0.00 3.41
2029 16917 0.391263 GTTGGCTCGTAGTTCCCCAG 60.391 60.000 0.00 0.00 0.00 4.45
2033 16921 1.078637 GGGGTTGGCTCGTAGTTCC 60.079 63.158 0.00 0.00 0.00 3.62
2045 16966 3.868200 GACAGGGGCTGTGGGGTTG 62.868 68.421 0.00 0.00 45.44 3.77
2046 16967 3.580319 GACAGGGGCTGTGGGGTT 61.580 66.667 0.00 0.00 45.44 4.11
2051 16972 4.624364 TGTGCGACAGGGGCTGTG 62.624 66.667 0.00 0.00 45.44 3.66
2053 16974 3.052082 CTTGTGCGACAGGGGCTG 61.052 66.667 0.00 0.00 37.52 4.85
2054 16975 4.335647 CCTTGTGCGACAGGGGCT 62.336 66.667 8.83 0.00 41.21 5.19
2064 16985 1.008538 CTTTGTGGTCGCCTTGTGC 60.009 57.895 0.00 0.00 0.00 4.57
2065 16986 1.069022 CATCTTTGTGGTCGCCTTGTG 60.069 52.381 0.00 0.00 0.00 3.33
2066 16987 1.238439 CATCTTTGTGGTCGCCTTGT 58.762 50.000 0.00 0.00 0.00 3.16
2067 16988 0.523072 CCATCTTTGTGGTCGCCTTG 59.477 55.000 0.00 0.00 34.46 3.61
2068 16989 0.609131 CCCATCTTTGTGGTCGCCTT 60.609 55.000 0.00 0.00 37.57 4.35
2069 16990 1.002134 CCCATCTTTGTGGTCGCCT 60.002 57.895 0.00 0.00 37.57 5.52
2070 16991 2.046285 CCCCATCTTTGTGGTCGCC 61.046 63.158 0.00 0.00 37.57 5.54
2071 16992 0.608035 TTCCCCATCTTTGTGGTCGC 60.608 55.000 0.00 0.00 37.57 5.19
2180 17101 2.525124 ATCCCCACACCAGCGTTCA 61.525 57.895 0.00 0.00 0.00 3.18
2640 17576 3.322318 GACTGCCAGGAGGTCCAGC 62.322 68.421 0.00 1.52 38.89 4.85
2681 17617 0.604780 TGAGCAGCAGAAACCTGAGC 60.605 55.000 0.00 0.00 35.70 4.26
2802 17770 7.449395 TCCATTGCCTTCTCATATCCAAAATAG 59.551 37.037 0.00 0.00 0.00 1.73
2898 17868 6.587990 CACAACTGACTACTTCCTGAACTATG 59.412 42.308 0.00 0.00 0.00 2.23
2938 17910 1.475280 TGATGCTACTACGTCACCACC 59.525 52.381 0.00 0.00 30.65 4.61
2969 17941 4.104383 AGAAGACAGGCCAAAAAGATGA 57.896 40.909 5.01 0.00 0.00 2.92
3015 17987 5.065218 CCACAGATAACTCACTAAACATGCC 59.935 44.000 0.00 0.00 0.00 4.40
3016 17988 5.643777 ACCACAGATAACTCACTAAACATGC 59.356 40.000 0.00 0.00 0.00 4.06
3021 17993 5.222079 TGCACCACAGATAACTCACTAAA 57.778 39.130 0.00 0.00 0.00 1.85
3091 18155 1.093972 TGCAGGCAATACATCAACGG 58.906 50.000 0.00 0.00 0.00 4.44
3092 18156 3.425577 AATGCAGGCAATACATCAACG 57.574 42.857 0.00 0.00 0.00 4.10
3097 18168 5.184479 CCAGCTTATAATGCAGGCAATACAT 59.816 40.000 0.00 0.00 30.71 2.29
3131 18203 6.495706 ACAACTTTCTGCTACAAGTTTTAGC 58.504 36.000 13.11 13.11 40.52 3.09
3138 18210 5.499139 TGGAAACAACTTTCTGCTACAAG 57.501 39.130 0.00 0.00 36.71 3.16
3195 18301 5.401550 ACATTTGTCTAAACGCATGGATTG 58.598 37.500 0.00 0.00 0.00 2.67
3196 18302 5.643379 ACATTTGTCTAAACGCATGGATT 57.357 34.783 0.00 0.00 0.00 3.01
3200 18310 6.550843 TGGATAACATTTGTCTAAACGCATG 58.449 36.000 0.00 0.00 0.00 4.06
3202 18312 6.751514 ATGGATAACATTTGTCTAAACGCA 57.248 33.333 0.00 0.00 35.97 5.24
3212 18322 9.467258 CAAGGCTTGTAATATGGATAACATTTG 57.533 33.333 19.07 0.00 41.03 2.32
3214 18324 7.784550 ACCAAGGCTTGTAATATGGATAACATT 59.215 33.333 24.57 0.00 41.03 2.71
3215 18325 7.297614 ACCAAGGCTTGTAATATGGATAACAT 58.702 34.615 24.57 0.00 43.68 2.71
3230 18340 4.269183 TGATACACCAATACCAAGGCTTG 58.731 43.478 20.31 20.31 0.00 4.01
3233 18343 2.618709 GCTGATACACCAATACCAAGGC 59.381 50.000 0.00 0.00 0.00 4.35
3255 18366 5.934402 AACGACCAATACTCTGGATTACT 57.066 39.130 0.00 0.00 38.96 2.24
3293 18498 3.450817 TCAAATAACATCCGAGGAGCTCA 59.549 43.478 17.19 0.00 0.00 4.26
3309 18514 8.719648 GTGCATTCAAATTTTCATGGTCAAATA 58.280 29.630 0.00 0.00 0.00 1.40
3318 18523 4.925054 CGTCAGGTGCATTCAAATTTTCAT 59.075 37.500 0.00 0.00 0.00 2.57
3340 18545 5.183140 ACAAAATAACTGGAATCCAAGACCG 59.817 40.000 2.61 0.00 30.80 4.79
3341 18546 6.590234 ACAAAATAACTGGAATCCAAGACC 57.410 37.500 2.61 0.00 30.80 3.85
3369 18861 8.474025 TGGACAGTGAATTCAAAAACAATAGTT 58.526 29.630 10.35 0.00 40.40 2.24
3376 18870 4.990426 CCCATGGACAGTGAATTCAAAAAC 59.010 41.667 15.22 0.00 0.00 2.43
3387 18881 0.609957 ACACATGCCCATGGACAGTG 60.610 55.000 20.79 20.79 42.91 3.66
3393 18887 0.396001 TCATCCACACATGCCCATGG 60.396 55.000 4.14 4.14 42.91 3.66
3399 18893 1.434622 CGAGGCTCATCCACACATGC 61.435 60.000 15.95 0.00 37.29 4.06
3414 18908 2.483876 ACATGATACGAATTGCCGAGG 58.516 47.619 0.00 0.00 0.00 4.63
3474 19265 7.148000 TGTGTGACTCCAAAATTGTTGATGTTA 60.148 33.333 0.00 0.00 0.00 2.41
3485 19276 8.805175 TGAAATGATAATGTGTGACTCCAAAAT 58.195 29.630 0.00 0.00 0.00 1.82
3486 19277 8.175925 TGAAATGATAATGTGTGACTCCAAAA 57.824 30.769 0.00 0.00 0.00 2.44
3489 19280 7.943079 ATTGAAATGATAATGTGTGACTCCA 57.057 32.000 0.00 0.00 0.00 3.86
3540 19331 4.485875 ACGACCCCAATACTATGGATGTA 58.514 43.478 0.00 0.00 43.54 2.29
3545 19336 3.494398 CCTTGACGACCCCAATACTATGG 60.494 52.174 0.00 0.00 40.35 2.74
3547 19338 3.381335 ACCTTGACGACCCCAATACTAT 58.619 45.455 0.00 0.00 0.00 2.12
3552 19343 3.431207 CGTAATACCTTGACGACCCCAAT 60.431 47.826 0.00 0.00 38.88 3.16
3571 19362 3.641648 CGGTCAAGGAGTTTGTAACGTA 58.358 45.455 0.00 0.00 38.01 3.57
3583 19374 1.591703 CTACTGCAGCGGTCAAGGA 59.408 57.895 15.27 0.00 0.00 3.36
3643 19434 3.754323 GACTAGTGGGATGAGTATCTCCG 59.246 52.174 0.00 0.00 34.52 4.63
3645 19436 6.177610 CCTAGACTAGTGGGATGAGTATCTC 58.822 48.000 0.00 0.00 34.92 2.75
3648 19439 4.509482 GCCCTAGACTAGTGGGATGAGTAT 60.509 50.000 18.75 0.00 43.47 2.12


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

AutoCloner maintained by Alex Coulton.