Multiple sequence alignment - TraesCS3A01G399500

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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 TraesCS3A01G399500 chr3A 100.000 4415 0 0 1 4415 646561107 646556693 0.000000e+00 8154.0
1 TraesCS3A01G399500 chr3A 88.352 2876 212 63 126 2982 646505612 646502841 0.000000e+00 3341.0
2 TraesCS3A01G399500 chr3A 88.958 2744 199 46 260 2982 646530578 646527918 0.000000e+00 3293.0
3 TraesCS3A01G399500 chr3A 88.921 2744 200 46 260 2982 646464646 646461986 0.000000e+00 3288.0
4 TraesCS3A01G399500 chr3A 90.508 1475 80 27 2979 4415 646461953 646460501 0.000000e+00 1893.0
5 TraesCS3A01G399500 chr3A 90.312 1476 80 25 2979 4415 646527885 646526434 0.000000e+00 1875.0
6 TraesCS3A01G399500 chr3A 93.197 1220 49 14 2979 4183 646502808 646501608 0.000000e+00 1762.0
7 TraesCS3A01G399500 chr3A 91.463 820 61 5 2145 2963 646459882 646459071 0.000000e+00 1118.0
8 TraesCS3A01G399500 chr3A 86.270 488 45 11 1790 2264 646507228 646506750 1.100000e-140 510.0
9 TraesCS3A01G399500 chr3A 77.162 902 142 35 3540 4381 646518982 646518085 2.400000e-127 466.0
10 TraesCS3A01G399500 chr3A 74.779 904 161 31 3540 4381 646295803 646294905 1.180000e-90 344.0
11 TraesCS3A01G399500 chr3A 80.672 476 62 13 1790 2264 646466339 646465893 4.230000e-90 342.0
12 TraesCS3A01G399500 chr3A 86.084 309 35 5 2979 3285 646459022 646458720 4.260000e-85 326.0
13 TraesCS3A01G399500 chr3A 78.864 440 71 13 3540 3957 646549218 646548779 1.210000e-70 278.0
14 TraesCS3A01G399500 chr3A 94.578 166 6 3 4252 4415 646501359 646501195 2.040000e-63 254.0
15 TraesCS3A01G399500 chr3A 77.861 402 58 18 3458 3832 646311093 646310696 2.070000e-53 220.0
16 TraesCS3A01G399500 chr3A 87.730 163 18 1 3123 3285 646289833 646289673 5.830000e-44 189.0
17 TraesCS3A01G399500 chr3A 100.000 36 0 0 4380 4415 646518157 646518122 2.850000e-07 67.6
18 TraesCS3A01G399500 chr3A 100.000 36 0 0 4380 4415 646539377 646539342 2.850000e-07 67.6
19 TraesCS3A01G399500 chr3B 90.411 3744 238 65 744 4415 671671048 671667354 0.000000e+00 4813.0
20 TraesCS3A01G399500 chr3B 86.485 2242 195 60 88 2301 671574176 671572015 0.000000e+00 2362.0
21 TraesCS3A01G399500 chr3B 86.660 1027 91 28 2293 3285 671569809 671568795 0.000000e+00 1096.0
22 TraesCS3A01G399500 chr3B 89.435 549 47 2 1 549 671672370 671671833 0.000000e+00 682.0
23 TraesCS3A01G399500 chr3B 85.443 474 48 7 1790 2263 671575748 671575296 1.440000e-129 473.0
24 TraesCS3A01G399500 chr3B 76.644 441 63 23 3472 3878 671568402 671567968 1.610000e-49 207.0
25 TraesCS3A01G399500 chr3B 87.261 157 18 1 3123 3279 671504065 671503911 1.260000e-40 178.0
26 TraesCS3A01G399500 chr3B 87.413 143 15 3 3292 3431 671568619 671568477 1.270000e-35 161.0
27 TraesCS3A01G399500 chr3B 100.000 32 0 0 4383 4414 671521614 671521583 4.770000e-05 60.2
28 TraesCS3A01G399500 chr3B 100.000 32 0 0 4382 4413 671621271 671621240 4.770000e-05 60.2
29 TraesCS3A01G399500 chr3B 97.059 34 1 0 4382 4415 671413210 671413177 1.720000e-04 58.4
30 TraesCS3A01G399500 chr3D 92.115 1598 101 14 1377 2963 508559734 508558151 0.000000e+00 2230.0
31 TraesCS3A01G399500 chr3D 91.935 558 26 5 1 556 508561323 508560783 0.000000e+00 763.0
32 TraesCS3A01G399500 chr3D 89.423 416 36 7 957 1370 508560405 508559996 6.550000e-143 518.0
33 TraesCS3A01G399500 chr3D 87.055 309 32 5 2979 3285 508558102 508557800 4.230000e-90 342.0
34 TraesCS3A01G399500 chr3D 79.957 469 63 10 3540 3979 508550608 508550142 2.560000e-82 316.0
35 TraesCS3A01G399500 chr3D 80.654 367 41 17 558 914 508560749 508560403 1.580000e-64 257.0
36 TraesCS3A01G399500 chr3D 77.594 424 57 22 3472 3861 508557433 508557014 5.750000e-54 222.0
37 TraesCS3A01G399500 chr3D 87.898 157 17 1 3123 3279 508470540 508470386 2.710000e-42 183.0
38 TraesCS3A01G399500 chr3D 87.413 143 15 3 3292 3431 508557650 508557508 1.270000e-35 161.0
39 TraesCS3A01G399500 chr3D 87.395 119 14 1 3294 3412 508470298 508470181 7.700000e-28 135.0


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 TraesCS3A01G399500 chr3A 646556693 646561107 4414 True 8154.000000 8154 100.000000 1 4415 1 chr3A.!!$R6 4414
1 TraesCS3A01G399500 chr3A 646526434 646530578 4144 True 2584.000000 3293 89.635000 260 4415 2 chr3A.!!$R10 4155
2 TraesCS3A01G399500 chr3A 646501195 646507228 6033 True 1466.750000 3341 90.599250 126 4415 4 chr3A.!!$R8 4289
3 TraesCS3A01G399500 chr3A 646458720 646466339 7619 True 1393.400000 3288 87.529600 260 4415 5 chr3A.!!$R7 4155
4 TraesCS3A01G399500 chr3A 646294905 646295803 898 True 344.000000 344 74.779000 3540 4381 1 chr3A.!!$R2 841
5 TraesCS3A01G399500 chr3A 646518085 646518982 897 True 266.800000 466 88.581000 3540 4415 2 chr3A.!!$R9 875
6 TraesCS3A01G399500 chr3B 671667354 671672370 5016 True 2747.500000 4813 89.923000 1 4415 2 chr3B.!!$R6 4414
7 TraesCS3A01G399500 chr3B 671567968 671575748 7780 True 859.800000 2362 84.529000 88 3878 5 chr3B.!!$R5 3790
8 TraesCS3A01G399500 chr3D 508557014 508561323 4309 True 641.857143 2230 86.598429 1 3861 7 chr3D.!!$R3 3860

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
39 40 0.254747 CCTCACCCTCGTCTCTCTCT 59.745 60.000 0.00 0.0 0.00 3.10 F
379 1921 0.877071 ATTTCTCAAGCTGCACACCG 59.123 50.000 1.02 0.0 0.00 4.94 F
1033 3227 0.893270 CAATGTCGCTTTCCCACCCA 60.893 55.000 0.00 0.0 0.00 4.51 F
1099 3295 1.507141 CCTTGAACCGTGTGTGCTCC 61.507 60.000 0.00 0.0 0.00 4.70 F
1828 4294 2.524306 CATTGTTGGGGGAACTGCTAA 58.476 47.619 0.00 0.0 35.37 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 3223 0.680061 GAGAGGACGAAACTGTGGGT 59.320 55.000 0.00 0.00 0.00 4.51 R
1533 3999 1.492176 GATCCTGGGCTTGAAGATCCA 59.508 52.381 0.00 1.86 0.00 3.41 R
2726 7419 0.321830 GCCGCTTAAACCCACCACTA 60.322 55.000 0.00 0.00 0.00 2.74 R
3006 7739 2.100584 GGTTGTGGCACAAAGATGACAA 59.899 45.455 32.60 6.70 40.05 3.18 R
3454 8366 0.669619 CATTCCAGCTGCACACACAA 59.330 50.000 8.66 0.00 0.00 3.33 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
31 32 1.041447 CCGATAACCCTCACCCTCGT 61.041 60.000 0.00 0.00 0.00 4.18
32 33 0.384669 CGATAACCCTCACCCTCGTC 59.615 60.000 0.00 0.00 0.00 4.20
33 34 1.777941 GATAACCCTCACCCTCGTCT 58.222 55.000 0.00 0.00 0.00 4.18
36 37 0.612453 AACCCTCACCCTCGTCTCTC 60.612 60.000 0.00 0.00 0.00 3.20
37 38 1.304952 CCCTCACCCTCGTCTCTCT 59.695 63.158 0.00 0.00 0.00 3.10
38 39 0.750182 CCCTCACCCTCGTCTCTCTC 60.750 65.000 0.00 0.00 0.00 3.20
39 40 0.254747 CCTCACCCTCGTCTCTCTCT 59.745 60.000 0.00 0.00 0.00 3.10
96 97 4.803426 GGTGCGCACTCTCCCTCG 62.803 72.222 36.84 0.00 0.00 4.63
111 112 4.854784 TCGCTGCTCGACATCGGC 62.855 66.667 0.73 4.79 43.16 5.54
283 1818 3.273654 TCCCTCGGTCTCCCCTGT 61.274 66.667 0.00 0.00 0.00 4.00
318 1853 1.673808 GATTGGTACCTCGGCGTCCT 61.674 60.000 14.36 0.00 0.00 3.85
340 1875 2.179517 CGTCTGAGGTCTGCGTCC 59.820 66.667 0.00 0.00 0.00 4.79
379 1921 0.877071 ATTTCTCAAGCTGCACACCG 59.123 50.000 1.02 0.00 0.00 4.94
403 1945 2.917227 TGGAGCTGGCACGTCTGA 60.917 61.111 0.00 0.00 0.00 3.27
509 2052 3.222603 AGGTAGTTTTGTCTGGCTTTGG 58.777 45.455 0.00 0.00 0.00 3.28
542 2085 7.174946 AGTGTCATTGTTAGTTATCAAACTGGG 59.825 37.037 1.11 0.00 45.63 4.45
548 2637 8.644374 TTGTTAGTTATCAAACTGGGCTTATT 57.356 30.769 1.11 0.00 45.63 1.40
550 2639 8.519526 TGTTAGTTATCAAACTGGGCTTATTTG 58.480 33.333 1.11 0.00 45.63 2.32
565 2688 1.382522 ATTTGGCCTGACATAGCACG 58.617 50.000 3.32 0.00 0.00 5.34
611 2745 7.778185 AGAAACCAGAGTACTAAGCTTAAGA 57.222 36.000 6.67 0.00 0.00 2.10
616 2750 8.647256 ACCAGAGTACTAAGCTTAAGACTTTA 57.353 34.615 16.96 0.98 0.00 1.85
638 2772 9.994432 CTTTATTTTGAACTAGCTTCTATGGTG 57.006 33.333 0.00 0.00 0.00 4.17
653 2794 6.392625 TCTATGGTGCTGTAGACAATACTC 57.607 41.667 0.00 0.00 0.00 2.59
680 2821 2.094854 GCTGCCTCCATTTTCAGAAGTG 60.095 50.000 0.00 0.00 0.00 3.16
685 2827 4.392940 CCTCCATTTTCAGAAGTGTCACT 58.607 43.478 0.00 0.00 0.00 3.41
697 2839 7.603651 TCAGAAGTGTCACTAGGAAGTTAATC 58.396 38.462 5.77 0.00 31.97 1.75
701 2843 9.303537 GAAGTGTCACTAGGAAGTTAATCATAC 57.696 37.037 5.77 0.00 31.97 2.39
702 2844 8.362464 AGTGTCACTAGGAAGTTAATCATACA 57.638 34.615 2.87 0.00 31.97 2.29
703 2845 8.812972 AGTGTCACTAGGAAGTTAATCATACAA 58.187 33.333 2.87 0.00 31.97 2.41
733 2917 6.869315 TCTAGGTTTATCATCTCGTCTCTG 57.131 41.667 0.00 0.00 0.00 3.35
739 2923 6.432107 GTTTATCATCTCGTCTCTGTAGGAC 58.568 44.000 0.00 0.00 0.00 3.85
740 2924 3.629142 TCATCTCGTCTCTGTAGGACA 57.371 47.619 0.00 0.00 33.73 4.02
741 2925 4.157849 TCATCTCGTCTCTGTAGGACAT 57.842 45.455 0.00 0.00 33.73 3.06
742 2926 4.527944 TCATCTCGTCTCTGTAGGACATT 58.472 43.478 0.00 0.00 33.73 2.71
743 2927 5.681639 TCATCTCGTCTCTGTAGGACATTA 58.318 41.667 0.00 0.00 33.73 1.90
744 2928 5.760743 TCATCTCGTCTCTGTAGGACATTAG 59.239 44.000 0.00 0.00 33.73 1.73
745 2929 4.452825 TCTCGTCTCTGTAGGACATTAGG 58.547 47.826 0.00 0.00 33.73 2.69
746 2930 4.163649 TCTCGTCTCTGTAGGACATTAGGA 59.836 45.833 0.00 0.00 33.73 2.94
750 2934 5.763698 CGTCTCTGTAGGACATTAGGATGTA 59.236 44.000 0.00 0.00 46.27 2.29
752 2936 7.040340 CGTCTCTGTAGGACATTAGGATGTAAT 60.040 40.741 0.00 0.00 46.27 1.89
780 2964 7.566760 ACAAAACTGTGTTACTTCATCATGA 57.433 32.000 0.00 0.00 0.00 3.07
809 3000 4.892934 ACACCATTGGACTTAAAGCTGAAA 59.107 37.500 10.37 0.00 0.00 2.69
841 3032 2.756760 TGAATTGCAATCTTCCTGCTCC 59.243 45.455 13.38 0.00 40.59 4.70
846 3037 3.548770 TGCAATCTTCCTGCTCCTAATG 58.451 45.455 0.00 0.00 40.59 1.90
850 3041 5.105595 GCAATCTTCCTGCTCCTAATGTTTT 60.106 40.000 0.00 0.00 36.84 2.43
880 3074 4.704057 AGACCATTCTCTTGAATTGAAGCC 59.296 41.667 0.00 0.00 40.61 4.35
899 3093 1.401931 CCGAGGCATTTGCTTCACTTG 60.402 52.381 14.03 2.09 46.03 3.16
900 3094 1.536766 CGAGGCATTTGCTTCACTTGA 59.463 47.619 14.03 0.00 46.03 3.02
907 3101 1.024271 TTGCTTCACTTGACTGCACC 58.976 50.000 5.81 0.00 34.87 5.01
909 3103 1.024271 GCTTCACTTGACTGCACCAA 58.976 50.000 0.00 0.00 0.00 3.67
939 3133 5.395657 CCATCTGACCATACTTCTGCACTTA 60.396 44.000 0.00 0.00 0.00 2.24
963 3157 1.521681 CCCTTCATCCCGTTCGAGC 60.522 63.158 0.00 0.00 0.00 5.03
1029 3223 1.976474 GGCCAATGTCGCTTTCCCA 60.976 57.895 0.00 0.00 0.00 4.37
1033 3227 0.893270 CAATGTCGCTTTCCCACCCA 60.893 55.000 0.00 0.00 0.00 4.51
1035 3229 2.063015 ATGTCGCTTTCCCACCCACA 62.063 55.000 0.00 0.00 0.00 4.17
1036 3230 1.966451 GTCGCTTTCCCACCCACAG 60.966 63.158 0.00 0.00 0.00 3.66
1044 3238 1.599797 CCCACCCACAGTTTCGTCC 60.600 63.158 0.00 0.00 0.00 4.79
1099 3295 1.507141 CCTTGAACCGTGTGTGCTCC 61.507 60.000 0.00 0.00 0.00 4.70
1278 3480 5.324409 TCTGCTTGGACAATTGGTTTATCT 58.676 37.500 10.83 0.00 0.00 1.98
1279 3481 5.183713 TCTGCTTGGACAATTGGTTTATCTG 59.816 40.000 10.83 0.00 0.00 2.90
1351 3553 5.862924 ATGTTGATAGAAGTTGGTGAACG 57.137 39.130 0.00 0.00 37.15 3.95
1356 3558 5.845103 TGATAGAAGTTGGTGAACGTGTTA 58.155 37.500 0.00 0.00 37.15 2.41
1362 3564 2.535012 TGGTGAACGTGTTATCTGCA 57.465 45.000 0.00 0.00 0.00 4.41
1363 3565 2.839975 TGGTGAACGTGTTATCTGCAA 58.160 42.857 0.00 0.00 0.00 4.08
1375 3839 7.010552 ACGTGTTATCTGCAAGTAAGATTCATC 59.989 37.037 0.00 0.00 35.92 2.92
1380 3844 9.617523 TTATCTGCAAGTAAGATTCATCATTCA 57.382 29.630 0.00 0.00 35.92 2.57
1382 3846 8.515695 TCTGCAAGTAAGATTCATCATTCATT 57.484 30.769 0.00 0.00 33.76 2.57
1384 3848 9.661187 CTGCAAGTAAGATTCATCATTCATTAC 57.339 33.333 0.00 0.00 0.00 1.89
1385 3849 9.176460 TGCAAGTAAGATTCATCATTCATTACA 57.824 29.630 0.00 0.00 0.00 2.41
1390 3854 9.941664 GTAAGATTCATCATTCATTACACTTGG 57.058 33.333 0.00 0.00 0.00 3.61
1391 3855 8.812513 AAGATTCATCATTCATTACACTTGGA 57.187 30.769 0.00 0.00 0.00 3.53
1392 3856 8.991783 AGATTCATCATTCATTACACTTGGAT 57.008 30.769 0.00 0.00 0.00 3.41
1393 3857 9.064706 AGATTCATCATTCATTACACTTGGATC 57.935 33.333 0.00 0.00 0.00 3.36
1394 3858 8.991783 ATTCATCATTCATTACACTTGGATCT 57.008 30.769 0.00 0.00 0.00 2.75
1417 3883 4.735369 TGATAGGTTGTTTGGGATGTGTT 58.265 39.130 0.00 0.00 0.00 3.32
1533 3999 9.901172 ACCTTTGTTCCGACTAAATCTTTATAT 57.099 29.630 0.00 0.00 0.00 0.86
1570 4036 4.863689 CAGGATCTTAGCATCTTATCGCAG 59.136 45.833 0.00 0.00 0.00 5.18
1617 4083 8.926710 CAATCGGTATAATCCAATAGTGAAGTC 58.073 37.037 0.00 0.00 0.00 3.01
1704 4170 6.030727 AGTCCTTGCCTATTGGGATTTTAT 57.969 37.500 0.00 0.00 37.23 1.40
1761 4227 6.638096 TGACGTCGATAAGAAATATGGGTA 57.362 37.500 11.62 0.00 0.00 3.69
1784 4250 7.380065 GGTAATTCGATACAAGTTGTTTGCAAA 59.620 33.333 14.90 8.05 40.59 3.68
1828 4294 2.524306 CATTGTTGGGGGAACTGCTAA 58.476 47.619 0.00 0.00 35.37 3.09
1846 4312 8.803397 ACTGCTAATGTCAGATATACCGTATA 57.197 34.615 0.68 0.68 35.61 1.47
1847 4313 8.675504 ACTGCTAATGTCAGATATACCGTATAC 58.324 37.037 0.15 0.00 35.61 1.47
1848 4314 7.993101 TGCTAATGTCAGATATACCGTATACC 58.007 38.462 0.15 0.00 0.00 2.73
1849 4315 7.130917 GCTAATGTCAGATATACCGTATACCG 58.869 42.308 0.15 0.00 0.00 4.02
1850 4316 7.201679 GCTAATGTCAGATATACCGTATACCGT 60.202 40.741 0.15 2.44 33.66 4.83
1851 4317 9.317936 CTAATGTCAGATATACCGTATACCGTA 57.682 37.037 6.55 6.55 33.66 4.02
1852 4318 6.968131 TGTCAGATATACCGTATACCGTAC 57.032 41.667 6.27 0.00 33.66 3.67
1901 4367 5.047660 GGTTTGCCTTTACATTACATGGACA 60.048 40.000 0.00 0.00 33.60 4.02
1996 4462 6.249192 TGAATCAAACTAGTCTCTCTCTCCA 58.751 40.000 0.00 0.00 0.00 3.86
2027 4493 5.519722 AGGTAAGCATGCGTTTTATATTGC 58.480 37.500 12.39 1.46 0.00 3.56
2047 4513 3.253188 TGCAATAGCTGTGTTTCTTGGAC 59.747 43.478 0.00 0.00 42.74 4.02
2058 4524 3.065648 TGTTTCTTGGACGCCTTTTGTAC 59.934 43.478 0.00 0.00 0.00 2.90
2140 4606 5.112129 AGACCACTCTTTTACAGGTTTGT 57.888 39.130 0.00 0.00 41.39 2.83
2152 4618 9.906660 CTTTTACAGGTTTGTATTGAAATGCTA 57.093 29.630 0.00 0.00 39.43 3.49
2164 4630 8.183536 TGTATTGAAATGCTACATGACATGTTC 58.816 33.333 25.34 15.80 41.63 3.18
2363 7044 8.029642 AGAGGTTTGAACATTGAATTACTACG 57.970 34.615 0.00 0.00 0.00 3.51
2417 7102 7.660030 TGAATCCTTATGATCTGTGTGAGTA 57.340 36.000 0.00 0.00 31.61 2.59
2435 7120 6.043411 GTGAGTACTTGAGAAGTTTCACTGT 58.957 40.000 17.69 0.00 43.74 3.55
2634 7327 5.811399 TTGTGGAGTGAACTTGTAGTTTG 57.189 39.130 0.00 0.00 38.80 2.93
2635 7328 5.092554 TGTGGAGTGAACTTGTAGTTTGA 57.907 39.130 0.00 0.00 38.80 2.69
2778 7471 8.770438 TTTGGCAATTCAACTGGTATTATTTC 57.230 30.769 0.00 0.00 0.00 2.17
2779 7472 7.473735 TGGCAATTCAACTGGTATTATTTCA 57.526 32.000 0.00 0.00 0.00 2.69
2967 7664 6.828785 TCTGTAGATTATTTTCTTCCCCTTGC 59.171 38.462 0.00 0.00 0.00 4.01
3025 7758 3.286353 TCTTGTCATCTTTGTGCCACAA 58.714 40.909 6.08 6.08 36.11 3.33
3296 8204 3.350912 CACTGTTGAACACAACGCTTAC 58.649 45.455 0.00 0.00 44.49 2.34
3321 8229 6.320672 CCTGAGGCTGTCAAAATATCTGATTT 59.679 38.462 0.00 0.00 33.60 2.17
3833 8822 1.001641 AGGTGCTAGCAGCCAAAGG 60.002 57.895 36.39 0.00 44.62 3.11
3925 8933 5.916661 AAATGGAAGAAGACGTAGCTAGA 57.083 39.130 0.00 0.00 0.00 2.43
3983 9003 2.549992 GGAAAATTGGCGGAAAAGGCTT 60.550 45.455 0.00 0.00 37.59 4.35
3989 9009 1.482593 TGGCGGAAAAGGCTTGAAAAA 59.517 42.857 0.00 0.00 37.59 1.94
3992 9012 2.483013 GCGGAAAAGGCTTGAAAAAGGT 60.483 45.455 0.00 0.00 0.00 3.50
3993 9013 3.381045 CGGAAAAGGCTTGAAAAAGGTC 58.619 45.455 0.00 0.00 0.00 3.85
3994 9014 3.181480 CGGAAAAGGCTTGAAAAAGGTCA 60.181 43.478 0.00 0.00 0.00 4.02
3996 9016 3.819564 AAAGGCTTGAAAAAGGTCACC 57.180 42.857 0.00 0.00 0.00 4.02
3997 9017 1.318576 AGGCTTGAAAAAGGTCACCG 58.681 50.000 0.00 0.00 0.00 4.94
3999 9019 1.407618 GGCTTGAAAAAGGTCACCGTT 59.592 47.619 0.00 0.00 0.00 4.44
4001 9021 3.517602 GCTTGAAAAAGGTCACCGTTTT 58.482 40.909 19.13 19.13 44.99 2.43
4023 9077 1.433879 CTCCGGCCTCTTACGTCTG 59.566 63.158 0.00 0.00 0.00 3.51
4025 9079 2.711922 CCGGCCTCTTACGTCTGCT 61.712 63.158 0.00 0.00 0.00 4.24
4117 9178 3.944087 ACACAAGGAGTATTGAGCTTCC 58.056 45.455 0.00 0.00 34.20 3.46
4120 9181 3.054802 ACAAGGAGTATTGAGCTTCCCAG 60.055 47.826 0.00 0.00 34.20 4.45
4121 9182 2.839228 AGGAGTATTGAGCTTCCCAGT 58.161 47.619 0.00 0.00 0.00 4.00
4135 9196 1.763770 CCAGTGAGCAACCCCTCTT 59.236 57.895 0.00 0.00 33.02 2.85
4150 9214 2.099098 CCCTCTTTGTGTTGTGTTCACC 59.901 50.000 0.37 0.00 35.25 4.02
4213 9280 6.361433 AGAGTTCGATAAGAGAGATGGAAGA 58.639 40.000 0.00 0.00 0.00 2.87
4277 9525 3.652057 TGCCTCCAAATCTAGGGAAAG 57.348 47.619 0.00 0.00 33.17 2.62
4312 9560 2.663602 GTGAGGATATGCGTATGAAGCG 59.336 50.000 2.36 0.00 37.44 4.68
4346 9594 3.386932 AATGCAAGCTCCCCAAAGATA 57.613 42.857 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.136500 GTGAGGGTTATCGGGACAGAC 59.864 57.143 0.00 0.00 0.00 3.51
31 32 3.994317 TCAGGAGAGAGAGAGAGAGAGA 58.006 50.000 0.00 0.00 0.00 3.10
32 33 4.446371 GTTCAGGAGAGAGAGAGAGAGAG 58.554 52.174 0.00 0.00 0.00 3.20
33 34 3.118775 CGTTCAGGAGAGAGAGAGAGAGA 60.119 52.174 0.00 0.00 0.00 3.10
36 37 2.288666 CCGTTCAGGAGAGAGAGAGAG 58.711 57.143 0.00 0.00 45.00 3.20
37 38 1.680555 GCCGTTCAGGAGAGAGAGAGA 60.681 57.143 0.00 0.00 45.00 3.10
38 39 0.738389 GCCGTTCAGGAGAGAGAGAG 59.262 60.000 0.00 0.00 45.00 3.20
39 40 1.027255 CGCCGTTCAGGAGAGAGAGA 61.027 60.000 0.00 0.00 43.02 3.10
318 1853 1.657751 CGCAGACCTCAGACGGATCA 61.658 60.000 0.00 0.00 0.00 2.92
340 1875 3.560534 TCTCACCAGAGACTCGGAG 57.439 57.895 16.88 2.83 45.73 4.63
384 1926 4.385405 AGACGTGCCAGCTCCAGC 62.385 66.667 0.00 0.00 42.49 4.85
385 1927 2.433838 CAGACGTGCCAGCTCCAG 60.434 66.667 0.00 0.00 0.00 3.86
386 1928 2.917227 TCAGACGTGCCAGCTCCA 60.917 61.111 0.00 0.00 0.00 3.86
387 1929 2.433318 GTCAGACGTGCCAGCTCC 60.433 66.667 0.00 0.00 0.00 4.70
388 1930 2.433318 GGTCAGACGTGCCAGCTC 60.433 66.667 0.00 0.00 0.00 4.09
389 1931 4.363990 CGGTCAGACGTGCCAGCT 62.364 66.667 0.00 0.00 0.00 4.24
410 1952 0.745486 TCCACCGCATCTGCATTGAG 60.745 55.000 2.72 0.00 42.21 3.02
509 2052 5.424121 AACTAACAATGACACTGCAACTC 57.576 39.130 0.00 0.00 0.00 3.01
542 2085 2.951642 TGCTATGTCAGGCCAAATAAGC 59.048 45.455 5.01 7.31 0.00 3.09
548 2637 1.078497 CCGTGCTATGTCAGGCCAA 60.078 57.895 5.01 0.00 0.00 4.52
550 2639 1.078426 AACCGTGCTATGTCAGGCC 60.078 57.895 0.00 0.00 0.00 5.19
611 2745 9.740710 ACCATAGAAGCTAGTTCAAAATAAAGT 57.259 29.630 0.00 0.00 37.67 2.66
616 2750 6.094603 CAGCACCATAGAAGCTAGTTCAAAAT 59.905 38.462 0.00 0.00 37.67 1.82
624 2758 4.339530 TGTCTACAGCACCATAGAAGCTAG 59.660 45.833 0.00 0.00 36.73 3.42
633 2767 5.046304 ACTTGAGTATTGTCTACAGCACCAT 60.046 40.000 0.00 0.00 0.00 3.55
638 2772 4.932200 AGCAACTTGAGTATTGTCTACAGC 59.068 41.667 0.00 0.00 0.00 4.40
653 2794 2.036217 TGAAAATGGAGGCAGCAACTTG 59.964 45.455 0.00 0.00 0.00 3.16
702 2844 9.838339 ACGAGATGATAAACCTAGAATTGATTT 57.162 29.630 0.00 0.00 0.00 2.17
703 2845 9.482627 GACGAGATGATAAACCTAGAATTGATT 57.517 33.333 0.00 0.00 0.00 2.57
709 2851 6.829298 ACAGAGACGAGATGATAAACCTAGAA 59.171 38.462 0.00 0.00 0.00 2.10
715 2897 6.038382 TGTCCTACAGAGACGAGATGATAAAC 59.962 42.308 0.00 0.00 37.04 2.01
766 2950 6.149308 TGGTGTCAATGTCATGATGAAGTAAC 59.851 38.462 0.00 0.00 0.00 2.50
767 2951 6.237154 TGGTGTCAATGTCATGATGAAGTAA 58.763 36.000 0.00 0.00 0.00 2.24
773 2957 4.399934 TCCAATGGTGTCAATGTCATGATG 59.600 41.667 0.00 0.00 0.00 3.07
780 2964 5.278957 GCTTTAAGTCCAATGGTGTCAATGT 60.279 40.000 0.00 0.00 0.00 2.71
809 3000 7.174599 GGAAGATTGCAATTCATCTAGTAGCAT 59.825 37.037 14.33 0.00 0.00 3.79
857 3048 4.704057 GGCTTCAATTCAAGAGAATGGTCT 59.296 41.667 0.00 0.00 43.52 3.85
858 3049 4.437930 CGGCTTCAATTCAAGAGAATGGTC 60.438 45.833 0.00 0.00 43.52 4.02
859 3050 3.441572 CGGCTTCAATTCAAGAGAATGGT 59.558 43.478 0.00 0.00 43.52 3.55
860 3051 3.691118 TCGGCTTCAATTCAAGAGAATGG 59.309 43.478 0.00 0.00 43.52 3.16
880 3074 1.536766 TCAAGTGAAGCAAATGCCTCG 59.463 47.619 0.94 0.00 43.38 4.63
899 3093 1.541588 GATGGGAACTTTGGTGCAGTC 59.458 52.381 0.00 0.00 0.00 3.51
900 3094 1.145738 AGATGGGAACTTTGGTGCAGT 59.854 47.619 0.00 0.00 0.00 4.40
907 3101 4.848357 AGTATGGTCAGATGGGAACTTTG 58.152 43.478 0.00 0.00 0.00 2.77
909 3103 4.785376 AGAAGTATGGTCAGATGGGAACTT 59.215 41.667 0.00 0.00 0.00 2.66
939 3133 0.840722 AACGGGATGAAGGGACTGGT 60.841 55.000 0.00 0.00 40.86 4.00
1009 3203 1.531739 GGGAAAGCGACATTGGCCAA 61.532 55.000 23.00 23.00 0.00 4.52
1029 3223 0.680061 GAGAGGACGAAACTGTGGGT 59.320 55.000 0.00 0.00 0.00 4.51
1033 3227 0.826672 ACCGGAGAGGACGAAACTGT 60.827 55.000 9.46 0.00 45.00 3.55
1035 3229 1.915141 TAACCGGAGAGGACGAAACT 58.085 50.000 9.46 0.00 45.00 2.66
1036 3230 2.229784 TCTTAACCGGAGAGGACGAAAC 59.770 50.000 9.46 0.00 45.00 2.78
1044 3238 3.786635 CCTTGTCATCTTAACCGGAGAG 58.213 50.000 9.46 2.36 0.00 3.20
1127 3323 1.619654 CTGGAAACCATCAAGGCACA 58.380 50.000 0.00 0.00 43.14 4.57
1249 3449 4.202461 ACCAATTGTCCAAGCAGAACTAGA 60.202 41.667 4.43 0.00 0.00 2.43
1259 3459 5.476599 TCCACAGATAAACCAATTGTCCAAG 59.523 40.000 4.43 0.00 29.93 3.61
1278 3480 2.363306 AAATTGCTCCTGTGTCCACA 57.637 45.000 0.00 0.00 39.32 4.17
1279 3481 4.702131 AGATTAAATTGCTCCTGTGTCCAC 59.298 41.667 0.00 0.00 0.00 4.02
1325 3527 7.957484 CGTTCACCAACTTCTATCAACATTAAG 59.043 37.037 0.00 0.00 0.00 1.85
1351 3553 8.201554 TGATGAATCTTACTTGCAGATAACAC 57.798 34.615 0.00 0.00 30.35 3.32
1356 3558 8.693120 ATGAATGATGAATCTTACTTGCAGAT 57.307 30.769 0.00 0.00 31.94 2.90
1375 3839 8.781196 CCTATCAAGATCCAAGTGTAATGAATG 58.219 37.037 0.00 0.00 0.00 2.67
1380 3844 7.633789 ACAACCTATCAAGATCCAAGTGTAAT 58.366 34.615 0.00 0.00 0.00 1.89
1382 3846 6.620877 ACAACCTATCAAGATCCAAGTGTA 57.379 37.500 0.00 0.00 0.00 2.90
1384 3848 6.349611 CCAAACAACCTATCAAGATCCAAGTG 60.350 42.308 0.00 0.00 0.00 3.16
1385 3849 5.711976 CCAAACAACCTATCAAGATCCAAGT 59.288 40.000 0.00 0.00 0.00 3.16
1387 3851 5.016173 CCCAAACAACCTATCAAGATCCAA 58.984 41.667 0.00 0.00 0.00 3.53
1388 3852 4.290985 TCCCAAACAACCTATCAAGATCCA 59.709 41.667 0.00 0.00 0.00 3.41
1389 3853 4.855340 TCCCAAACAACCTATCAAGATCC 58.145 43.478 0.00 0.00 0.00 3.36
1390 3854 5.888161 ACATCCCAAACAACCTATCAAGATC 59.112 40.000 0.00 0.00 0.00 2.75
1391 3855 5.653769 CACATCCCAAACAACCTATCAAGAT 59.346 40.000 0.00 0.00 0.00 2.40
1392 3856 5.009631 CACATCCCAAACAACCTATCAAGA 58.990 41.667 0.00 0.00 0.00 3.02
1393 3857 4.766891 ACACATCCCAAACAACCTATCAAG 59.233 41.667 0.00 0.00 0.00 3.02
1394 3858 4.735369 ACACATCCCAAACAACCTATCAA 58.265 39.130 0.00 0.00 0.00 2.57
1533 3999 1.492176 GATCCTGGGCTTGAAGATCCA 59.508 52.381 0.00 1.86 0.00 3.41
1607 4073 6.773638 ACAACAATTCAGGAGACTTCACTAT 58.226 36.000 0.00 0.00 40.21 2.12
1617 4083 7.382218 GGACATAACAAAACAACAATTCAGGAG 59.618 37.037 0.00 0.00 0.00 3.69
1723 4189 6.548441 TCGACGTCAAAATTTTAATCCAGT 57.452 33.333 17.16 0.00 0.00 4.00
1741 4207 7.539710 TCGAATTACCCATATTTCTTATCGACG 59.460 37.037 0.00 0.00 0.00 5.12
1757 4223 5.798434 GCAAACAACTTGTATCGAATTACCC 59.202 40.000 0.00 0.00 37.36 3.69
1761 4227 7.651304 TGATTTGCAAACAACTTGTATCGAATT 59.349 29.630 15.41 0.00 37.36 2.17
1815 4281 1.559682 TCTGACATTAGCAGTTCCCCC 59.440 52.381 0.00 0.00 34.98 5.40
1849 4315 3.858812 TGCACGGATGTTATACAACGTAC 59.141 43.478 10.90 7.67 41.48 3.67
1850 4316 4.107363 TGCACGGATGTTATACAACGTA 57.893 40.909 10.90 0.00 41.48 3.57
1851 4317 2.962125 TGCACGGATGTTATACAACGT 58.038 42.857 6.97 6.97 43.19 3.99
1852 4318 4.033472 TGATTGCACGGATGTTATACAACG 59.967 41.667 0.00 0.00 37.48 4.10
1996 4462 2.290323 ACGCATGCTTACCTTTTCTCCT 60.290 45.455 17.13 0.00 0.00 3.69
2027 4493 3.667960 GCGTCCAAGAAACACAGCTATTG 60.668 47.826 0.00 0.00 0.00 1.90
2047 4513 1.719780 GTCTCGTCAGTACAAAAGGCG 59.280 52.381 0.00 0.00 0.00 5.52
2058 4524 4.627035 TGCATGAATTAGTTGTCTCGTCAG 59.373 41.667 0.00 0.00 0.00 3.51
2140 4606 8.278729 TGAACATGTCATGTAGCATTTCAATA 57.721 30.769 18.70 0.00 44.07 1.90
2164 4630 6.373774 ACCTTAAGATGAAAGATGCAGAGTTG 59.626 38.462 3.36 0.00 0.00 3.16
2398 7083 6.867550 TCAAGTACTCACACAGATCATAAGG 58.132 40.000 0.00 0.00 0.00 2.69
2488 7181 3.161866 TGGCCATCCAAAAGTAACTTCC 58.838 45.455 0.00 0.00 39.99 3.46
2634 7327 5.471456 AGAAATCAATTGTGTGTGGTCTCTC 59.529 40.000 5.13 0.00 0.00 3.20
2635 7328 5.240183 CAGAAATCAATTGTGTGTGGTCTCT 59.760 40.000 5.13 0.00 0.00 3.10
2726 7419 0.321830 GCCGCTTAAACCCACCACTA 60.322 55.000 0.00 0.00 0.00 2.74
2788 7482 3.604875 AACAGAACGATCAACCCGTAT 57.395 42.857 0.00 0.00 39.57 3.06
3006 7739 2.100584 GGTTGTGGCACAAAGATGACAA 59.899 45.455 32.60 6.70 40.05 3.18
3025 7758 4.475016 ACAATATTCCTAGCAAGTCTGGGT 59.525 41.667 0.00 0.00 43.38 4.51
3118 7852 6.307776 AGCTTTCCAATCTGATGATGATGAT 58.692 36.000 0.00 0.00 32.44 2.45
3119 7853 5.691896 AGCTTTCCAATCTGATGATGATGA 58.308 37.500 0.00 0.00 32.44 2.92
3120 7854 5.334182 CGAGCTTTCCAATCTGATGATGATG 60.334 44.000 0.00 0.00 32.44 3.07
3247 7983 2.752354 ATGGCGCACAGCTATACAAAAA 59.248 40.909 10.83 0.00 45.65 1.94
3296 8204 4.774124 TCAGATATTTTGACAGCCTCAGG 58.226 43.478 0.00 0.00 0.00 3.86
3321 8229 7.095102 GGGTATAGTTCTCTGCAAAACGTTTTA 60.095 37.037 24.79 10.69 0.00 1.52
3454 8366 0.669619 CATTCCAGCTGCACACACAA 59.330 50.000 8.66 0.00 0.00 3.33
3833 8822 3.251972 CACTTTCTCTCCTTGGTGCTTTC 59.748 47.826 0.00 0.00 0.00 2.62
3900 8905 3.437049 AGCTACGTCTTCTTCCATTTTGC 59.563 43.478 0.00 0.00 0.00 3.68
3925 8933 7.823745 ATTCCTAAGACACACATGAAAGTTT 57.176 32.000 0.00 0.00 0.00 2.66
3983 9003 3.839293 CACAAAACGGTGACCTTTTTCA 58.161 40.909 14.95 0.00 41.32 2.69
3989 9009 0.818040 GGAGCACAAAACGGTGACCT 60.818 55.000 0.00 0.00 41.32 3.85
3992 9012 1.890041 CCGGAGCACAAAACGGTGA 60.890 57.895 0.00 0.00 41.32 4.02
3993 9013 2.637025 CCGGAGCACAAAACGGTG 59.363 61.111 0.00 0.00 41.34 4.94
3996 9016 2.966309 GAGGCCGGAGCACAAAACG 61.966 63.158 5.05 0.00 42.56 3.60
3997 9017 1.172812 AAGAGGCCGGAGCACAAAAC 61.173 55.000 5.05 0.00 42.56 2.43
3999 9019 0.321298 GTAAGAGGCCGGAGCACAAA 60.321 55.000 5.05 0.00 42.56 2.83
4001 9021 2.978824 GTAAGAGGCCGGAGCACA 59.021 61.111 5.05 0.00 42.56 4.57
4023 9077 0.460459 GTCGTTGGGCTAGAAGGAGC 60.460 60.000 0.00 0.00 42.05 4.70
4025 9079 1.640917 AAGTCGTTGGGCTAGAAGGA 58.359 50.000 0.00 0.00 0.00 3.36
4117 9178 0.111253 AAAGAGGGGTTGCTCACTGG 59.889 55.000 0.00 0.00 0.00 4.00
4120 9181 0.954452 CACAAAGAGGGGTTGCTCAC 59.046 55.000 0.00 0.00 0.00 3.51
4121 9182 0.550914 ACACAAAGAGGGGTTGCTCA 59.449 50.000 0.00 0.00 0.00 4.26
4135 9196 2.223803 AAGGGGTGAACACAACACAA 57.776 45.000 7.25 0.00 39.65 3.33
4150 9214 4.094887 CCACGAGAATAACACATGAAAGGG 59.905 45.833 0.00 0.00 0.00 3.95
4213 9280 5.249393 CCAACTTCTAGCCATATCCCACTAT 59.751 44.000 0.00 0.00 0.00 2.12
4277 9525 3.695830 TCCTCACCAGTCACCAAATAC 57.304 47.619 0.00 0.00 0.00 1.89
4312 9560 2.780065 TGCATTTCACAAGCACTCAC 57.220 45.000 0.00 0.00 32.55 3.51


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

AutoCloner maintained by Alex Coulton.