Multiple sequence alignment - TraesCS5D01G139100

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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 TraesCS5D01G139100 chr5D 100.000 5719 0 0 1 5719 221481177 221475459 0.000000e+00 10562.0
1 TraesCS5D01G139100 chr5D 100.000 278 0 0 6159 6436 221475019 221474742 1.240000e-141 514.0
2 TraesCS5D01G139100 chr5D 85.124 121 15 3 6302 6420 114976673 114976554 3.150000e-23 121.0
3 TraesCS5D01G139100 chr5D 93.548 62 4 0 1809 1870 221479142 221479081 6.870000e-15 93.5
4 TraesCS5D01G139100 chr5D 93.548 62 4 0 2036 2097 221479369 221479308 6.870000e-15 93.5
5 TraesCS5D01G139100 chr5A 96.082 3088 100 11 2641 5717 302553950 302557027 0.000000e+00 5012.0
6 TraesCS5D01G139100 chr5A 91.470 2579 103 40 161 2643 302551290 302553847 0.000000e+00 3435.0
7 TraesCS5D01G139100 chr5A 92.553 282 10 3 6159 6429 302557068 302557349 1.680000e-105 394.0
8 TraesCS5D01G139100 chr5A 86.607 112 9 3 1 112 302551185 302551290 1.130000e-22 119.0
9 TraesCS5D01G139100 chr5A 91.045 67 6 0 1804 1870 302553214 302553280 2.470000e-14 91.6
10 TraesCS5D01G139100 chr5A 88.889 72 8 0 2026 2097 302552982 302553053 8.890000e-14 89.8
11 TraesCS5D01G139100 chr5A 100.000 28 0 0 2183 2210 63375598 63375571 1.200000e-02 52.8
12 TraesCS5D01G139100 chr5B 90.605 2629 108 43 251 2812 244011726 244009170 0.000000e+00 3358.0
13 TraesCS5D01G139100 chr5B 94.983 2093 76 11 2809 4879 244008856 244006771 0.000000e+00 3256.0
14 TraesCS5D01G139100 chr5B 95.148 845 33 4 4880 5717 244006687 244005844 0.000000e+00 1327.0
15 TraesCS5D01G139100 chr5B 93.080 289 6 4 6159 6436 244005803 244005518 1.670000e-110 411.0
16 TraesCS5D01G139100 chr5B 90.278 72 7 0 2026 2097 244010163 244010092 1.910000e-15 95.3
17 TraesCS5D01G139100 chr5B 93.548 62 4 0 1809 1870 244009926 244009865 6.870000e-15 93.5
18 TraesCS5D01G139100 chr1D 85.255 1743 193 33 3166 4894 27578453 27576761 0.000000e+00 1736.0
19 TraesCS5D01G139100 chr1D 87.423 978 94 16 3190 4164 27546864 27545913 0.000000e+00 1098.0
20 TraesCS5D01G139100 chr1D 88.694 513 51 6 5015 5522 27576584 27576074 2.550000e-173 619.0
21 TraesCS5D01G139100 chr1D 84.177 632 83 9 4896 5522 27540742 27540123 1.190000e-166 597.0
22 TraesCS5D01G139100 chr1D 81.696 743 97 15 4162 4894 27541492 27540779 3.340000e-162 582.0
23 TraesCS5D01G139100 chr1D 79.123 867 74 50 990 1813 27579472 27578670 3.460000e-137 499.0
24 TraesCS5D01G139100 chr1D 83.969 524 36 22 990 1506 27555965 27555483 5.880000e-125 459.0
25 TraesCS5D01G139100 chr1D 83.251 203 30 3 2403 2601 27578651 27578449 3.960000e-42 183.0
26 TraesCS5D01G139100 chr1D 92.500 40 0 3 2140 2179 8798036 8798000 3.000000e-03 54.7
27 TraesCS5D01G139100 chr1A 86.091 1517 166 31 3312 4799 28363387 28361887 0.000000e+00 1591.0
28 TraesCS5D01G139100 chr1A 83.575 621 85 9 4903 5518 28361760 28361152 3.370000e-157 566.0
29 TraesCS5D01G139100 chr1A 79.239 920 86 47 954 1812 28364604 28363729 1.580000e-150 544.0
30 TraesCS5D01G139100 chr1A 83.048 584 86 7 4896 5477 28379970 28379398 9.570000e-143 518.0
31 TraesCS5D01G139100 chr1A 82.906 585 82 13 4896 5477 28605519 28604950 1.600000e-140 510.0
32 TraesCS5D01G139100 chr1B 85.770 1546 163 38 3366 4883 43045371 43043855 0.000000e+00 1583.0
33 TraesCS5D01G139100 chr1B 88.583 508 51 6 5020 5522 43043705 43043200 1.530000e-170 610.0
34 TraesCS5D01G139100 chr1B 85.660 523 31 22 956 1475 43047679 43047198 1.600000e-140 510.0
35 TraesCS5D01G139100 chr1B 80.171 585 89 17 4896 5477 43215773 43215213 4.640000e-111 412.0
36 TraesCS5D01G139100 chr1B 83.251 203 30 3 2403 2601 43046860 43046658 3.960000e-42 183.0
37 TraesCS5D01G139100 chr1B 86.022 93 11 1 5571 5661 43043198 43043106 1.480000e-16 99.0
38 TraesCS5D01G139100 chr2D 82.009 428 71 6 3554 3977 460728362 460727937 6.140000e-95 359.0
39 TraesCS5D01G139100 chr2D 81.955 133 18 5 6302 6430 350354280 350354150 2.450000e-19 108.0
40 TraesCS5D01G139100 chr2D 91.304 46 3 1 2123 2167 478727515 478727560 1.940000e-05 62.1
41 TraesCS5D01G139100 chr2A 82.057 418 73 2 3554 3970 603549935 603549519 7.940000e-94 355.0
42 TraesCS5D01G139100 chr2A 87.578 161 18 2 1300 1459 603550575 603550416 1.100000e-42 185.0
43 TraesCS5D01G139100 chr2B 81.818 418 66 9 3554 3966 541944963 541944551 6.180000e-90 342.0
44 TraesCS5D01G139100 chr2B 88.136 177 19 2 1300 1475 541945410 541945235 6.540000e-50 209.0
45 TraesCS5D01G139100 chr2B 94.737 38 0 2 2130 2166 468333063 468333027 2.510000e-04 58.4
46 TraesCS5D01G139100 chr2B 100.000 29 0 0 2181 2209 216956212 216956184 3.000000e-03 54.7
47 TraesCS5D01G139100 chr6B 86.207 116 11 5 6319 6430 26227974 26227860 3.150000e-23 121.0
48 TraesCS5D01G139100 chr6B 82.400 125 19 3 6298 6420 26012656 26012779 8.830000e-19 106.0
49 TraesCS5D01G139100 chr6B 90.123 81 7 1 6329 6408 485102806 485102726 3.170000e-18 104.0
50 TraesCS5D01G139100 chr3B 82.609 138 18 5 6297 6430 809343494 809343359 4.080000e-22 117.0
51 TraesCS5D01G139100 chr3B 96.875 32 1 0 2181 2212 505520972 505521003 3.000000e-03 54.7
52 TraesCS5D01G139100 chr6A 82.836 134 16 6 6302 6431 15632209 15632079 5.270000e-21 113.0
53 TraesCS5D01G139100 chr6A 100.000 33 0 0 2134 2166 224613196 224613228 1.940000e-05 62.1
54 TraesCS5D01G139100 chr7D 86.567 67 7 2 2139 2204 230465081 230465016 8.950000e-09 73.1
55 TraesCS5D01G139100 chr3D 97.297 37 1 0 2133 2169 37760810 37760846 5.390000e-06 63.9
56 TraesCS5D01G139100 chr3D 96.875 32 1 0 2181 2212 388518922 388518953 3.000000e-03 54.7
57 TraesCS5D01G139100 chr7B 91.489 47 1 3 2121 2166 328937834 328937878 1.940000e-05 62.1
58 TraesCS5D01G139100 chrUn 96.875 32 1 0 2181 2212 40528198 40528167 3.000000e-03 54.7
59 TraesCS5D01G139100 chrUn 100.000 28 0 0 2183 2210 99106823 99106850 1.200000e-02 52.8


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 TraesCS5D01G139100 chr5D 221474742 221481177 6435 True 2815.750000 10562 96.774000 1 6436 4 chr5D.!!$R2 6435
1 TraesCS5D01G139100 chr5A 302551185 302557349 6164 False 1523.566667 5012 91.107667 1 6429 6 chr5A.!!$F1 6428
2 TraesCS5D01G139100 chr5B 244005518 244011726 6208 True 1423.466667 3358 92.940333 251 6436 6 chr5B.!!$R1 6185
3 TraesCS5D01G139100 chr1D 27545913 27546864 951 True 1098.000000 1098 87.423000 3190 4164 1 chr1D.!!$R2 974
4 TraesCS5D01G139100 chr1D 27576074 27579472 3398 True 759.250000 1736 84.080750 990 5522 4 chr1D.!!$R5 4532
5 TraesCS5D01G139100 chr1D 27540123 27541492 1369 True 589.500000 597 82.936500 4162 5522 2 chr1D.!!$R4 1360
6 TraesCS5D01G139100 chr1A 28361152 28364604 3452 True 900.333333 1591 82.968333 954 5518 3 chr1A.!!$R3 4564
7 TraesCS5D01G139100 chr1A 28379398 28379970 572 True 518.000000 518 83.048000 4896 5477 1 chr1A.!!$R1 581
8 TraesCS5D01G139100 chr1A 28604950 28605519 569 True 510.000000 510 82.906000 4896 5477 1 chr1A.!!$R2 581
9 TraesCS5D01G139100 chr1B 43043106 43047679 4573 True 597.000000 1583 85.857200 956 5661 5 chr1B.!!$R2 4705
10 TraesCS5D01G139100 chr1B 43215213 43215773 560 True 412.000000 412 80.171000 4896 5477 1 chr1B.!!$R1 581
11 TraesCS5D01G139100 chr2A 603549519 603550575 1056 True 270.000000 355 84.817500 1300 3970 2 chr2A.!!$R1 2670
12 TraesCS5D01G139100 chr2B 541944551 541945410 859 True 275.500000 342 84.977000 1300 3966 2 chr2B.!!$R3 2666

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
44 45 0.107066 TGGAGTCGATGTAGGCCGTA 60.107 55.000 0.00 0.00 0.00 4.02 F
1513 1608 0.963225 TGTGCCGTTGCTACTAGTGA 59.037 50.000 5.39 0.00 38.71 3.41 F
2264 2481 0.038251 TTAGGAGTCAGCACTGCACG 60.038 55.000 3.30 0.00 43.38 5.34 F
2269 2486 1.300620 GTCAGCACTGCACGGTACA 60.301 57.895 3.30 0.00 0.00 2.90 F
3062 3723 2.778299 ACACATCGTGCCACTATTTGT 58.222 42.857 0.00 0.00 36.98 2.83 F
4423 6320 0.604073 CACCACAATTGCATCTGCCA 59.396 50.000 5.05 0.00 41.18 4.92 F
5285 7328 0.116342 TCAGCCCTTCAGGACCTGTA 59.884 55.000 21.06 11.05 38.24 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1782 2.675423 ACCAGAGAGCGCCACGTA 60.675 61.111 2.29 0.00 0.00 3.57 R
2324 2541 0.896940 ACCCGAAGACTAACTCGGCA 60.897 55.000 8.32 0.00 43.65 5.69 R
4119 5994 1.607801 ATGCTACTCTGCTGGTGCGA 61.608 55.000 0.00 0.00 43.34 5.10 R
4350 6227 9.766754 AGATATATCTCACATAGATCAGGTTGT 57.233 33.333 9.57 0.00 44.17 3.32 R
5133 7176 1.466856 TGAAGCATGTCAGCCCATTC 58.533 50.000 0.00 0.00 34.23 2.67 R
5345 7388 1.211969 GACGGCGTACAGAAGCTCA 59.788 57.895 14.74 0.00 0.00 4.26 R
6242 8297 1.593196 TCAACTGCTGTAACCACTGC 58.407 50.000 0.00 0.29 46.60 4.40 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
39 40 3.920144 GACGTGGAGTCGATGTAGG 57.080 57.895 0.00 0.00 40.43 3.18
41 42 1.065928 CGTGGAGTCGATGTAGGCC 59.934 63.158 0.00 0.00 0.00 5.19
42 43 1.065928 GTGGAGTCGATGTAGGCCG 59.934 63.158 0.00 0.00 0.00 6.13
43 44 1.379443 TGGAGTCGATGTAGGCCGT 60.379 57.895 0.00 0.00 0.00 5.68
44 45 0.107066 TGGAGTCGATGTAGGCCGTA 60.107 55.000 0.00 0.00 0.00 4.02
46 47 1.268948 GGAGTCGATGTAGGCCGTAAC 60.269 57.143 0.00 0.00 0.00 2.50
47 48 1.674962 GAGTCGATGTAGGCCGTAACT 59.325 52.381 0.00 0.00 0.00 2.24
48 49 2.874701 GAGTCGATGTAGGCCGTAACTA 59.125 50.000 0.00 0.00 0.00 2.24
49 50 3.484407 AGTCGATGTAGGCCGTAACTAT 58.516 45.455 0.00 0.00 0.00 2.12
50 51 3.887716 AGTCGATGTAGGCCGTAACTATT 59.112 43.478 0.00 0.00 0.00 1.73
51 52 5.065914 AGTCGATGTAGGCCGTAACTATTA 58.934 41.667 0.00 0.00 0.00 0.98
52 53 5.049129 AGTCGATGTAGGCCGTAACTATTAC 60.049 44.000 0.00 0.00 0.00 1.89
63 64 8.088981 AGGCCGTAACTATTACTATTGATCTTG 58.911 37.037 0.00 0.00 33.98 3.02
76 77 8.012957 ACTATTGATCTTGAACTCGATACCTT 57.987 34.615 0.00 0.00 0.00 3.50
91 92 4.504461 CGATACCTTCTTGCACTGATACAC 59.496 45.833 0.00 0.00 0.00 2.90
120 121 9.474920 TTGAATTTATGTTTCAGTCAATTGACC 57.525 29.630 30.34 17.44 45.85 4.02
121 122 8.637099 TGAATTTATGTTTCAGTCAATTGACCA 58.363 29.630 30.34 21.83 45.85 4.02
122 123 9.474920 GAATTTATGTTTCAGTCAATTGACCAA 57.525 29.630 30.34 21.65 45.85 3.67
123 124 9.829507 AATTTATGTTTCAGTCAATTGACCAAA 57.170 25.926 30.34 25.24 45.85 3.28
124 125 9.829507 ATTTATGTTTCAGTCAATTGACCAAAA 57.170 25.926 30.34 25.86 45.85 2.44
125 126 9.658799 TTTATGTTTCAGTCAATTGACCAAAAA 57.341 25.926 30.34 23.88 45.85 1.94
126 127 7.775397 ATGTTTCAGTCAATTGACCAAAAAG 57.225 32.000 30.34 15.73 45.85 2.27
127 128 6.696411 TGTTTCAGTCAATTGACCAAAAAGT 58.304 32.000 30.34 11.17 45.85 2.66
128 129 6.589523 TGTTTCAGTCAATTGACCAAAAAGTG 59.410 34.615 30.34 21.00 45.85 3.16
129 130 4.681744 TCAGTCAATTGACCAAAAAGTGC 58.318 39.130 30.34 6.16 45.85 4.40
130 131 3.486841 CAGTCAATTGACCAAAAAGTGCG 59.513 43.478 30.34 6.81 45.85 5.34
131 132 3.380004 AGTCAATTGACCAAAAAGTGCGA 59.620 39.130 30.34 0.00 45.85 5.10
132 133 4.109050 GTCAATTGACCAAAAAGTGCGAA 58.891 39.130 25.26 0.00 39.07 4.70
133 134 4.026886 GTCAATTGACCAAAAAGTGCGAAC 60.027 41.667 25.26 0.00 39.07 3.95
134 135 4.111916 CAATTGACCAAAAAGTGCGAACT 58.888 39.130 0.00 0.00 0.00 3.01
135 136 3.414549 TTGACCAAAAAGTGCGAACTC 57.585 42.857 0.00 0.00 0.00 3.01
136 137 2.360844 TGACCAAAAAGTGCGAACTCA 58.639 42.857 0.00 0.00 0.00 3.41
137 138 2.948979 TGACCAAAAAGTGCGAACTCAT 59.051 40.909 0.00 0.00 0.00 2.90
138 139 3.243035 TGACCAAAAAGTGCGAACTCATG 60.243 43.478 0.00 0.00 0.00 3.07
139 140 2.948979 ACCAAAAAGTGCGAACTCATGA 59.051 40.909 0.00 0.00 0.00 3.07
140 141 3.569701 ACCAAAAAGTGCGAACTCATGAT 59.430 39.130 0.00 0.00 0.00 2.45
141 142 3.916172 CCAAAAAGTGCGAACTCATGATG 59.084 43.478 0.00 0.00 0.00 3.07
142 143 4.320421 CCAAAAAGTGCGAACTCATGATGA 60.320 41.667 0.00 0.00 0.00 2.92
185 186 4.470664 TCAATAATGCCAAGGAGCCATTTT 59.529 37.500 0.00 0.00 0.00 1.82
282 291 7.564128 ACATATAACACATGCTTCGTTAATCG 58.436 34.615 0.00 0.00 41.41 3.34
322 331 3.815401 GCCACACATGCCCTATAAAGTAG 59.185 47.826 0.00 0.00 0.00 2.57
329 338 6.772716 CACATGCCCTATAAAGTAGAAACCAT 59.227 38.462 0.00 0.00 0.00 3.55
419 431 4.990257 GTTGCATGCTGTAACTTGATGAT 58.010 39.130 20.33 0.00 39.40 2.45
446 458 5.030147 TGGAGTACTGGTACTTCCAATCAT 58.970 41.667 19.57 0.00 45.63 2.45
447 459 6.199376 TGGAGTACTGGTACTTCCAATCATA 58.801 40.000 19.57 1.54 45.63 2.15
448 460 6.097839 TGGAGTACTGGTACTTCCAATCATAC 59.902 42.308 19.57 5.56 45.63 2.39
449 461 6.324254 GGAGTACTGGTACTTCCAATCATACT 59.676 42.308 13.64 0.00 45.63 2.12
450 462 7.504911 GGAGTACTGGTACTTCCAATCATACTA 59.495 40.741 13.64 0.00 45.63 1.82
451 463 8.466617 AGTACTGGTACTTCCAATCATACTAG 57.533 38.462 7.51 0.00 46.59 2.57
511 523 6.099269 GGATTACCAACTCATTACTCCTACCA 59.901 42.308 0.00 0.00 35.97 3.25
676 698 2.401583 TGGAACTAGCCGTCGTAGTA 57.598 50.000 0.00 0.00 30.26 1.82
677 699 2.009774 TGGAACTAGCCGTCGTAGTAC 58.990 52.381 0.00 0.00 30.26 2.73
678 700 1.004504 GGAACTAGCCGTCGTAGTACG 60.005 57.143 16.65 16.65 44.19 3.67
679 701 1.661112 GAACTAGCCGTCGTAGTACGT 59.339 52.381 21.38 5.36 43.14 3.57
893 927 1.333931 TGAGTCGTGATTAGCTAGCCG 59.666 52.381 12.13 6.79 0.00 5.52
946 988 1.047801 GAGGAGGAGATCTCTTGCCC 58.952 60.000 20.51 12.56 42.10 5.36
1083 1135 2.687200 ATGGTGGGGCTCGCTGTA 60.687 61.111 0.00 0.00 0.00 2.74
1475 1547 1.553248 CGATCTACCCAGGTTGGTTGA 59.447 52.381 0.00 0.00 42.83 3.18
1512 1607 1.726791 CTTGTGCCGTTGCTACTAGTG 59.273 52.381 5.39 0.00 38.71 2.74
1513 1608 0.963225 TGTGCCGTTGCTACTAGTGA 59.037 50.000 5.39 0.00 38.71 3.41
1515 1610 0.963225 TGCCGTTGCTACTAGTGACA 59.037 50.000 5.39 0.05 38.71 3.58
1516 1611 1.548719 TGCCGTTGCTACTAGTGACAT 59.451 47.619 5.39 0.00 38.71 3.06
1533 1642 5.648092 AGTGACATTTCCCTTTAAGAATCGG 59.352 40.000 0.00 0.00 0.00 4.18
1571 1723 3.020274 TGCCAAGCTTGTTGTGTAAGAA 58.980 40.909 24.35 0.00 0.00 2.52
1702 1877 1.485066 GGTCCTTGGTCACGTGGATAT 59.515 52.381 17.00 0.00 0.00 1.63
1757 1948 5.693555 GGATTTTCCAGCACTTTCAAAAGAG 59.306 40.000 9.39 2.79 36.65 2.85
1932 2128 2.108514 CGAACATGGTGCTGCGGAT 61.109 57.895 0.00 0.00 0.00 4.18
1958 2154 5.057149 CCGATTCACCTTAGGAATTGGTAG 58.943 45.833 4.77 0.00 45.39 3.18
1960 2156 6.183360 CCGATTCACCTTAGGAATTGGTAGTA 60.183 42.308 4.77 0.00 45.39 1.82
2169 2365 3.065371 CCATCCCAAAATAAGTGTCGCTC 59.935 47.826 0.00 0.00 0.00 5.03
2171 2367 3.334691 TCCCAAAATAAGTGTCGCTCAG 58.665 45.455 0.00 0.00 0.00 3.35
2172 2368 2.159517 CCCAAAATAAGTGTCGCTCAGC 60.160 50.000 0.00 0.00 0.00 4.26
2173 2369 2.483877 CCAAAATAAGTGTCGCTCAGCA 59.516 45.455 0.00 0.00 0.00 4.41
2175 2371 3.813529 AAATAAGTGTCGCTCAGCAAC 57.186 42.857 0.00 0.00 0.00 4.17
2176 2372 2.455674 ATAAGTGTCGCTCAGCAACA 57.544 45.000 0.00 0.00 0.00 3.33
2177 2373 1.497991 TAAGTGTCGCTCAGCAACAC 58.502 50.000 13.34 13.34 42.80 3.32
2178 2374 1.443407 AGTGTCGCTCAGCAACACT 59.557 52.632 18.09 18.09 46.55 3.55
2179 2375 2.311294 GTGTCGCTCAGCAACACTT 58.689 52.632 13.94 0.00 40.07 3.16
2181 2377 2.069273 GTGTCGCTCAGCAACACTTAT 58.931 47.619 13.94 0.00 40.07 1.73
2216 2433 5.269991 TGGAGGGAGTATTAGATTATCCGG 58.730 45.833 0.00 0.00 0.00 5.14
2264 2481 0.038251 TTAGGAGTCAGCACTGCACG 60.038 55.000 3.30 0.00 43.38 5.34
2269 2486 1.300620 GTCAGCACTGCACGGTACA 60.301 57.895 3.30 0.00 0.00 2.90
2299 2516 7.175119 GTGAATACCCTTTAACTCTTTGCTCTT 59.825 37.037 0.00 0.00 0.00 2.85
2364 2582 7.661027 TCGGGTAAATAATTAGTTATTTCGGGG 59.339 37.037 16.55 8.04 43.57 5.73
2518 2743 7.501844 AGTCCTCTGGTATTTCTATTGTTAGC 58.498 38.462 0.00 0.00 0.00 3.09
2553 2787 5.109500 TGCACTGTGAAATGTGGGATATA 57.891 39.130 12.86 0.00 34.99 0.86
2598 2833 8.776470 AGTTAAATTTCTTGTTTTCATGCATGG 58.224 29.630 25.97 8.58 0.00 3.66
2632 2867 9.893305 CTTTAATTGAAGTTATTTCGTTGTCCT 57.107 29.630 1.87 0.00 38.71 3.85
2635 2870 5.934935 TGAAGTTATTTCGTTGTCCTTCC 57.065 39.130 0.00 0.00 38.71 3.46
2711 3051 4.633126 ACATAGCTATGCTGGAATATTGCG 59.367 41.667 29.60 5.17 40.10 4.85
2795 3135 6.983890 GCAGATTTCTTTTTCTTTGGGTAACA 59.016 34.615 0.00 0.00 39.74 2.41
2883 3541 7.363793 GGCAATACAAGTCTCACCCAAAATTAT 60.364 37.037 0.00 0.00 0.00 1.28
3048 3709 7.852945 GCATGAGTAGCTAAATAACAACACATC 59.147 37.037 0.00 0.00 0.00 3.06
3062 3723 2.778299 ACACATCGTGCCACTATTTGT 58.222 42.857 0.00 0.00 36.98 2.83
3131 3792 4.203226 TGTTTGCAACATGTAAGAGGACA 58.797 39.130 0.00 0.00 36.25 4.02
3163 3824 9.851686 ATGTGTTGGATCTTATAATGTGTATGT 57.148 29.630 0.00 0.00 0.00 2.29
3423 5257 7.507733 AATAACAGCTGATCATCAATTCCTC 57.492 36.000 23.35 0.00 0.00 3.71
3519 5387 8.353423 TGCTTTTCTCCTCTAAGCATAATTTT 57.647 30.769 4.77 0.00 46.59 1.82
4033 5906 6.573725 CAGTGTTAAATGTTTCTTGTAGACGC 59.426 38.462 0.00 0.00 0.00 5.19
4350 6227 4.955811 ATAGTATGCGATTTCTGGTCCA 57.044 40.909 0.00 0.00 0.00 4.02
4368 6245 4.437239 GTCCACAACCTGATCTATGTGAG 58.563 47.826 16.79 10.22 44.52 3.51
4369 6246 4.160439 GTCCACAACCTGATCTATGTGAGA 59.840 45.833 16.79 11.64 44.52 3.27
4370 6247 8.094547 GGTCCACAACCTGATCTATGTGAGAT 62.095 46.154 16.79 0.00 45.46 2.75
4423 6320 0.604073 CACCACAATTGCATCTGCCA 59.396 50.000 5.05 0.00 41.18 4.92
4637 6534 5.520288 CACTTCAGGTCTGTATAATGAACGG 59.480 44.000 0.00 0.00 0.00 4.44
4647 6548 6.704493 TCTGTATAATGAACGGCTTATCAACC 59.296 38.462 0.00 0.00 0.00 3.77
4726 6627 1.337118 TCAAGGCCCCAAACAATCAC 58.663 50.000 0.00 0.00 0.00 3.06
4855 6757 8.663167 TCAATATATGATCCATCTTTCACCAGT 58.337 33.333 0.00 0.00 31.50 4.00
4887 6873 7.598118 TGCAATTTTACCAAATACATGACAGTG 59.402 33.333 0.00 0.00 31.89 3.66
4906 6922 6.113411 ACAGTGTGGGTTATATAAGCACTTC 58.887 40.000 22.53 15.20 34.04 3.01
4941 6957 9.866655 ATAAATGTTGGCTTCCTGATTTCTATA 57.133 29.630 0.00 0.00 0.00 1.31
4973 6989 7.801547 ACATTGCATTAATTTCTCTTGTTCG 57.198 32.000 0.00 0.00 0.00 3.95
5177 7220 4.463891 CCTGTGCATAATTTTCTTGGGAGT 59.536 41.667 0.00 0.00 0.00 3.85
5279 7322 2.247635 AGTATACCTCAGCCCTTCAGGA 59.752 50.000 0.00 0.00 38.24 3.86
5285 7328 0.116342 TCAGCCCTTCAGGACCTGTA 59.884 55.000 21.06 11.05 38.24 2.74
5380 7423 3.798548 GCCGTCTTCATGAAAAGGCAAAA 60.799 43.478 28.81 1.63 39.87 2.44
5408 7454 3.703556 TGGACCAAAATGTTTCTCTTGCA 59.296 39.130 0.00 0.00 0.00 4.08
5458 7505 2.588925 AAATCCTGGGGTAGGCTACT 57.411 50.000 23.01 0.00 46.87 2.57
5523 7573 1.086067 CCTGCGACGATGATGCTGTT 61.086 55.000 0.00 0.00 0.00 3.16
5529 7579 3.115554 CGACGATGATGCTGTTGATGTA 58.884 45.455 0.00 0.00 0.00 2.29
5541 7591 5.186198 GCTGTTGATGTACTTCCCACTTAT 58.814 41.667 6.32 0.00 0.00 1.73
5661 7716 7.941795 AAGAGCAAAATTGAAGAAAGTCATG 57.058 32.000 0.00 0.00 0.00 3.07
5718 7773 1.584495 GGCAAAAGTGTTAGCCGGG 59.416 57.895 2.18 0.00 37.41 5.73
6249 8304 2.973694 AACGGTATATTCGCAGTGGT 57.026 45.000 0.00 0.00 0.00 4.16
6300 8364 4.442893 CCTTCCCGAGCACTATGATTAACA 60.443 45.833 0.00 0.00 0.00 2.41
6327 8391 0.036164 ACCTTGTGTATTGCTGCGGA 59.964 50.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.472361 TTCAAGATCAATAGTAATAGTTACGGC 57.528 33.333 0.00 0.00 41.01 5.68
48 49 9.915629 GGTATCGAGTTCAAGATCAATAGTAAT 57.084 33.333 0.00 0.00 0.00 1.89
49 50 9.132923 AGGTATCGAGTTCAAGATCAATAGTAA 57.867 33.333 0.00 0.00 0.00 2.24
50 51 8.693120 AGGTATCGAGTTCAAGATCAATAGTA 57.307 34.615 0.00 0.00 0.00 1.82
51 52 7.589958 AGGTATCGAGTTCAAGATCAATAGT 57.410 36.000 0.00 0.00 0.00 2.12
52 53 8.356657 AGAAGGTATCGAGTTCAAGATCAATAG 58.643 37.037 0.00 0.00 0.00 1.73
63 64 3.614616 CAGTGCAAGAAGGTATCGAGTTC 59.385 47.826 0.00 0.00 0.00 3.01
68 69 4.504461 GTGTATCAGTGCAAGAAGGTATCG 59.496 45.833 0.00 0.00 0.00 2.92
71 72 6.791867 ATAGTGTATCAGTGCAAGAAGGTA 57.208 37.500 0.00 0.00 0.00 3.08
76 77 8.565896 AAATTCAATAGTGTATCAGTGCAAGA 57.434 30.769 0.00 0.00 0.00 3.02
112 113 4.111916 AGTTCGCACTTTTTGGTCAATTG 58.888 39.130 0.00 0.00 0.00 2.32
113 114 4.142271 TGAGTTCGCACTTTTTGGTCAATT 60.142 37.500 0.00 0.00 31.22 2.32
114 115 3.380004 TGAGTTCGCACTTTTTGGTCAAT 59.620 39.130 0.00 0.00 31.22 2.57
115 116 2.750166 TGAGTTCGCACTTTTTGGTCAA 59.250 40.909 0.00 0.00 31.22 3.18
116 117 2.360844 TGAGTTCGCACTTTTTGGTCA 58.639 42.857 0.00 0.00 31.22 4.02
117 118 3.003275 TCATGAGTTCGCACTTTTTGGTC 59.997 43.478 0.00 0.00 31.22 4.02
118 119 2.948979 TCATGAGTTCGCACTTTTTGGT 59.051 40.909 0.00 0.00 31.22 3.67
119 120 3.624326 TCATGAGTTCGCACTTTTTGG 57.376 42.857 0.00 0.00 31.22 3.28
120 121 4.786507 TCATCATGAGTTCGCACTTTTTG 58.213 39.130 0.09 0.00 31.22 2.44
121 122 4.756642 TCTCATCATGAGTTCGCACTTTTT 59.243 37.500 14.56 0.00 44.58 1.94
122 123 4.318332 TCTCATCATGAGTTCGCACTTTT 58.682 39.130 14.56 0.00 44.58 2.27
123 124 3.930336 TCTCATCATGAGTTCGCACTTT 58.070 40.909 14.56 0.00 44.58 2.66
124 125 3.599730 TCTCATCATGAGTTCGCACTT 57.400 42.857 14.56 0.00 44.58 3.16
125 126 3.599730 TTCTCATCATGAGTTCGCACT 57.400 42.857 14.56 0.00 44.58 4.40
126 127 4.495349 CCATTTCTCATCATGAGTTCGCAC 60.495 45.833 14.56 0.00 44.58 5.34
127 128 3.624410 CCATTTCTCATCATGAGTTCGCA 59.376 43.478 14.56 0.00 44.58 5.10
128 129 3.003068 CCCATTTCTCATCATGAGTTCGC 59.997 47.826 14.56 0.00 44.58 4.70
129 130 3.003068 GCCCATTTCTCATCATGAGTTCG 59.997 47.826 14.56 2.41 44.58 3.95
130 131 3.949754 TGCCCATTTCTCATCATGAGTTC 59.050 43.478 14.56 0.00 44.58 3.01
131 132 3.972133 TGCCCATTTCTCATCATGAGTT 58.028 40.909 14.56 0.00 44.58 3.01
132 133 3.657398 TGCCCATTTCTCATCATGAGT 57.343 42.857 14.56 0.00 44.58 3.41
133 134 6.835819 ATATTGCCCATTTCTCATCATGAG 57.164 37.500 8.54 8.54 45.59 2.90
147 148 9.264653 TGGCATTATTGAAATATATATTGCCCA 57.735 29.630 20.42 12.15 44.93 5.36
154 155 9.189156 GGCTCCTTGGCATTATTGAAATATATA 57.811 33.333 0.00 0.00 41.37 0.86
155 156 7.675195 TGGCTCCTTGGCATTATTGAAATATAT 59.325 33.333 0.00 0.00 46.76 0.86
156 157 7.009550 TGGCTCCTTGGCATTATTGAAATATA 58.990 34.615 0.00 0.00 46.76 0.86
157 158 5.840149 TGGCTCCTTGGCATTATTGAAATAT 59.160 36.000 0.00 0.00 46.76 1.28
158 159 5.207354 TGGCTCCTTGGCATTATTGAAATA 58.793 37.500 0.00 0.00 46.76 1.40
159 160 4.032310 TGGCTCCTTGGCATTATTGAAAT 58.968 39.130 0.00 0.00 46.76 2.17
160 161 3.439154 TGGCTCCTTGGCATTATTGAAA 58.561 40.909 0.00 0.00 46.76 2.69
161 162 3.098774 TGGCTCCTTGGCATTATTGAA 57.901 42.857 0.00 0.00 46.76 2.69
162 163 2.824689 TGGCTCCTTGGCATTATTGA 57.175 45.000 0.00 0.00 46.76 2.57
185 186 6.353323 TCTTGTGAGGAAAACATGTTAGTCA 58.647 36.000 12.39 9.41 0.00 3.41
511 523 2.499685 GACGTGCCGGCTAGGATT 59.500 61.111 29.70 5.57 45.00 3.01
608 629 3.204526 CCATTACGGCATTACGGGTTAA 58.795 45.455 0.00 0.00 38.39 2.01
676 698 2.420967 GGGGAGTATTTGGCATGTACGT 60.421 50.000 0.00 0.00 0.00 3.57
677 699 2.218603 GGGGAGTATTTGGCATGTACG 58.781 52.381 0.00 0.00 0.00 3.67
678 700 2.949644 GTGGGGAGTATTTGGCATGTAC 59.050 50.000 0.00 0.00 0.00 2.90
679 701 2.578480 TGTGGGGAGTATTTGGCATGTA 59.422 45.455 0.00 0.00 0.00 2.29
918 960 2.447047 AGATCTCCTCCTCCTCTTCCTC 59.553 54.545 0.00 0.00 0.00 3.71
919 961 2.447047 GAGATCTCCTCCTCCTCTTCCT 59.553 54.545 12.00 0.00 35.87 3.36
920 962 2.447047 AGAGATCTCCTCCTCCTCTTCC 59.553 54.545 19.30 0.00 42.97 3.46
921 963 3.884037 AGAGATCTCCTCCTCCTCTTC 57.116 52.381 19.30 0.00 42.97 2.87
922 964 3.914771 CAAGAGATCTCCTCCTCCTCTT 58.085 50.000 19.30 0.73 42.82 2.85
923 965 2.424812 GCAAGAGATCTCCTCCTCCTCT 60.425 54.545 19.30 0.00 42.97 3.69
946 988 1.000283 AGAGAAGAGACCAACAGCACG 60.000 52.381 0.00 0.00 0.00 5.34
1278 1339 4.910585 CCTACCACCATCGCCGCC 62.911 72.222 0.00 0.00 0.00 6.13
1475 1547 4.035675 GCACAAGCAAGAAGTAGTGAAGTT 59.964 41.667 0.00 0.00 41.58 2.66
1512 1607 4.640647 AGCCGATTCTTAAAGGGAAATGTC 59.359 41.667 0.00 0.00 0.00 3.06
1513 1608 4.600062 AGCCGATTCTTAAAGGGAAATGT 58.400 39.130 0.00 0.00 0.00 2.71
1515 1610 5.261216 TCAAGCCGATTCTTAAAGGGAAAT 58.739 37.500 0.00 0.00 0.00 2.17
1516 1611 4.658063 TCAAGCCGATTCTTAAAGGGAAA 58.342 39.130 0.00 0.00 0.00 3.13
1533 1642 4.503741 TGGCAAAACTACAGATTCAAGC 57.496 40.909 0.00 0.00 0.00 4.01
1614 1782 2.675423 ACCAGAGAGCGCCACGTA 60.675 61.111 2.29 0.00 0.00 3.57
1702 1877 5.782893 AACTATAAACTGCAAAGCCAACA 57.217 34.783 0.00 0.00 0.00 3.33
1757 1948 4.455070 AATAAAGCCCATCCTAACCTCC 57.545 45.455 0.00 0.00 0.00 4.30
1932 2128 4.513442 CAATTCCTAAGGTGAATCGGTCA 58.487 43.478 0.00 0.00 31.39 4.02
2169 2365 7.278424 CCATCCCAAAATAAATAAGTGTTGCTG 59.722 37.037 0.00 0.00 0.00 4.41
2171 2367 7.327214 TCCATCCCAAAATAAATAAGTGTTGC 58.673 34.615 0.00 0.00 0.00 4.17
2172 2368 7.981225 CCTCCATCCCAAAATAAATAAGTGTTG 59.019 37.037 0.00 0.00 0.00 3.33
2173 2369 7.125659 CCCTCCATCCCAAAATAAATAAGTGTT 59.874 37.037 0.00 0.00 0.00 3.32
2175 2371 6.838612 TCCCTCCATCCCAAAATAAATAAGTG 59.161 38.462 0.00 0.00 0.00 3.16
2176 2372 6.992235 TCCCTCCATCCCAAAATAAATAAGT 58.008 36.000 0.00 0.00 0.00 2.24
2177 2373 7.069344 ACTCCCTCCATCCCAAAATAAATAAG 58.931 38.462 0.00 0.00 0.00 1.73
2178 2374 6.992235 ACTCCCTCCATCCCAAAATAAATAA 58.008 36.000 0.00 0.00 0.00 1.40
2179 2375 6.606241 ACTCCCTCCATCCCAAAATAAATA 57.394 37.500 0.00 0.00 0.00 1.40
2181 2377 4.965283 ACTCCCTCCATCCCAAAATAAA 57.035 40.909 0.00 0.00 0.00 1.40
2216 2433 3.357079 CACCTGCGGCACCTTGTC 61.357 66.667 0.00 0.00 0.00 3.18
2264 2481 8.344446 AGTTAAAGGGTATTCACAATTGTACC 57.656 34.615 16.75 16.75 36.66 3.34
2269 2486 8.088365 GCAAAGAGTTAAAGGGTATTCACAATT 58.912 33.333 0.00 0.00 0.00 2.32
2324 2541 0.896940 ACCCGAAGACTAACTCGGCA 60.897 55.000 8.32 0.00 43.65 5.69
2327 2544 7.998753 AATTATTTACCCGAAGACTAACTCG 57.001 36.000 0.00 0.00 0.00 4.18
2364 2582 6.575201 GCTAACTCAGCGCATAACATTATTTC 59.425 38.462 11.47 0.00 41.37 2.17
2651 2991 7.041440 CGAGAAAGAATAGCTCTGTGAGATAGA 60.041 40.741 0.00 0.00 34.00 1.98
2711 3051 7.996644 TCCCATCAAATTAACTACCCTAACATC 59.003 37.037 0.00 0.00 0.00 3.06
2795 3135 7.849322 ATTAACTTCACCTAAATTGGGTTGT 57.151 32.000 0.00 0.00 34.44 3.32
2839 3496 6.690194 ATTGCCTACTGAGACATCATTTTC 57.310 37.500 0.00 0.00 34.12 2.29
2995 3656 3.979911 TGATGACCCATGGTAAAGCATT 58.020 40.909 11.73 0.00 35.25 3.56
3062 3723 6.018589 TCATCGACACAAATTAAATGGCAA 57.981 33.333 0.00 0.00 0.00 4.52
3131 3792 2.592102 AAGATCCAACACATGCACCT 57.408 45.000 0.00 0.00 0.00 4.00
3163 3824 3.407424 ACTATTTGCTGCAGTCACAGA 57.593 42.857 16.64 3.73 40.25 3.41
3754 5627 3.181455 ACTCCACAGTGCAATTGTAGTCA 60.181 43.478 7.40 0.00 32.95 3.41
3990 5863 5.300752 ACACTGAGACAGGACAAGTTATTG 58.699 41.667 0.00 0.00 37.87 1.90
4048 5922 3.322541 TGAACACGAAGAAGGTGATGGTA 59.677 43.478 0.00 0.00 38.73 3.25
4119 5994 1.607801 ATGCTACTCTGCTGGTGCGA 61.608 55.000 0.00 0.00 43.34 5.10
4350 6227 9.766754 AGATATATCTCACATAGATCAGGTTGT 57.233 33.333 9.57 0.00 44.17 3.32
4637 6534 3.132467 AGGAAGACGTAGGGTTGATAAGC 59.868 47.826 0.00 0.00 0.00 3.09
4726 6627 2.599578 AAGCCAAGCAGCCTGTGG 60.600 61.111 3.41 3.41 35.39 4.17
4887 6873 6.459710 GCCTTTGAAGTGCTTATATAACCCAC 60.460 42.308 11.14 11.14 0.00 4.61
4899 6915 5.857268 ACATTTATTTGCCTTTGAAGTGCT 58.143 33.333 6.02 0.00 0.00 4.40
4906 6922 5.106594 GGAAGCCAACATTTATTTGCCTTTG 60.107 40.000 0.00 0.00 0.00 2.77
5043 7086 3.138283 TCACCACCTCTGAGGAAAACATT 59.862 43.478 29.71 2.61 37.67 2.71
5133 7176 1.466856 TGAAGCATGTCAGCCCATTC 58.533 50.000 0.00 0.00 34.23 2.67
5177 7220 0.107508 GCAGCTTGGGTCTGATGCTA 60.108 55.000 0.00 0.00 41.65 3.49
5345 7388 1.211969 GACGGCGTACAGAAGCTCA 59.788 57.895 14.74 0.00 0.00 4.26
5380 7423 6.251471 AGAGAAACATTTTGGTCCATCATCT 58.749 36.000 0.00 0.00 0.00 2.90
5408 7454 2.017049 GTGTTCAGTGTTGTTGAGCCT 58.983 47.619 0.00 0.00 0.00 4.58
5458 7505 2.739849 TTTCACCGGGCGAGCATCAA 62.740 55.000 6.32 0.00 33.17 2.57
5523 7573 5.163343 GGCTACATAAGTGGGAAGTACATCA 60.163 44.000 0.00 0.00 0.00 3.07
5529 7579 5.163195 CCATTAGGCTACATAAGTGGGAAGT 60.163 44.000 0.00 0.00 0.00 3.01
5541 7591 3.931907 AATGCTCACCATTAGGCTACA 57.068 42.857 0.00 0.00 42.24 2.74
5661 7716 7.063191 CACAGACTATCACATTCAGCTATATGC 59.937 40.741 7.05 0.00 43.29 3.14
6242 8297 1.593196 TCAACTGCTGTAACCACTGC 58.407 50.000 0.00 0.29 46.60 4.40
6249 8304 2.226330 ACGCCAAATCAACTGCTGTAA 58.774 42.857 0.00 0.00 0.00 2.41
6300 8364 5.431765 CAGCAATACACAAGGTATCCTCTT 58.568 41.667 0.00 0.00 41.87 2.85
6317 8381 1.617850 TCAACCAATTTCCGCAGCAAT 59.382 42.857 0.00 0.00 0.00 3.56
6327 8391 9.352191 TCAATCCAAATTTTCATCAACCAATTT 57.648 25.926 0.00 0.00 30.56 1.82


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

AutoCloner maintained by Alex Coulton.