Multiple sequence alignment - TraesCS5A01G247000

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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 TraesCS5A01G247000 chr5A 100.000 3352 0 0 845 4196 461232003 461228652 0.000000e+00 6191.0
1 TraesCS5A01G247000 chr5A 90.941 861 33 13 845 1690 461007439 461008269 0.000000e+00 1116.0
2 TraesCS5A01G247000 chr5A 100.000 536 0 0 1 536 461232847 461232312 0.000000e+00 990.0
3 TraesCS5A01G247000 chr5A 92.664 518 26 4 2816 3327 461008891 461009402 0.000000e+00 736.0
4 TraesCS5A01G247000 chr5A 88.806 536 26 16 1690 2209 461008355 461008872 9.900000e-176 627.0
5 TraesCS5A01G247000 chr5A 84.008 519 46 19 44 536 461006896 461007403 8.220000e-127 464.0
6 TraesCS5A01G247000 chr5D 88.335 883 53 27 845 1690 360048537 360049406 0.000000e+00 1014.0
7 TraesCS5A01G247000 chr5D 88.642 810 35 21 3340 4139 360368719 360367957 0.000000e+00 933.0
8 TraesCS5A01G247000 chr5D 87.949 780 42 18 946 1690 360370739 360369977 0.000000e+00 872.0
9 TraesCS5A01G247000 chr5D 90.592 574 27 11 1690 2250 360369869 360369310 0.000000e+00 736.0
10 TraesCS5A01G247000 chr5D 90.485 515 31 8 2821 3329 360369303 360368801 0.000000e+00 664.0
11 TraesCS5A01G247000 chr5D 89.655 522 28 13 2813 3330 360050042 360050541 3.540000e-180 641.0
12 TraesCS5A01G247000 chr5D 88.538 506 34 14 1690 2183 360049518 360050011 3.610000e-165 592.0
13 TraesCS5A01G247000 chr5D 84.386 570 41 21 11 536 360047935 360048500 2.240000e-142 516.0
14 TraesCS5A01G247000 chr5D 83.214 560 48 30 14 536 360371438 360370888 4.910000e-129 472.0
15 TraesCS5A01G247000 chr5D 93.878 49 3 0 3340 3388 360050622 360050670 1.620000e-09 75.0
16 TraesCS5A01G247000 chr5D 97.297 37 1 0 4153 4189 360367960 360367924 3.500000e-06 63.9
17 TraesCS5A01G247000 chr5B 88.558 874 46 38 845 1690 425380098 425380945 0.000000e+00 1011.0
18 TraesCS5A01G247000 chr5B 86.981 891 61 30 845 1690 425612264 425611384 0.000000e+00 952.0
19 TraesCS5A01G247000 chr5B 89.272 522 35 8 2813 3327 425381954 425382461 5.920000e-178 634.0
20 TraesCS5A01G247000 chr5B 88.722 532 40 13 1690 2220 425611307 425610795 2.130000e-177 632.0
21 TraesCS5A01G247000 chr5B 88.676 521 38 11 2813 3327 425610615 425610110 2.140000e-172 616.0
22 TraesCS5A01G247000 chr5B 90.084 474 16 16 1690 2144 425381022 425381483 1.680000e-163 586.0
23 TraesCS5A01G247000 chr5B 81.865 579 50 26 10 536 425379486 425380061 1.790000e-118 436.0
24 TraesCS5A01G247000 chr5B 89.238 223 17 5 320 536 425612522 425612301 5.350000e-69 272.0
25 TraesCS5A01G247000 chr5B 82.934 334 23 14 11 314 425613930 425613601 1.920000e-68 270.0
26 TraesCS5A01G247000 chr5B 94.068 118 6 1 2141 2258 425381848 425381964 1.200000e-40 178.0
27 TraesCS5A01G247000 chr5B 91.304 46 4 0 3341 3386 425382546 425382591 3.500000e-06 63.9
28 TraesCS5A01G247000 chr7A 97.326 561 15 0 2254 2814 561805193 561804633 0.000000e+00 953.0
29 TraesCS5A01G247000 chr7A 94.964 556 28 0 2259 2814 504850857 504851412 0.000000e+00 872.0
30 TraesCS5A01G247000 chr2A 95.332 557 25 1 2259 2815 332040380 332039825 0.000000e+00 883.0
31 TraesCS5A01G247000 chr2A 94.464 560 31 0 2255 2814 475815055 475815614 0.000000e+00 863.0
32 TraesCS5A01G247000 chr3A 94.794 557 29 0 2258 2814 686126800 686127356 0.000000e+00 869.0
33 TraesCS5A01G247000 chr1A 94.604 556 30 0 2259 2814 291976429 291976984 0.000000e+00 861.0
34 TraesCS5A01G247000 chr1A 77.931 145 28 4 3552 3694 570188317 570188459 2.080000e-13 87.9
35 TraesCS5A01G247000 chr1D 94.255 557 32 0 2259 2815 250740831 250741387 0.000000e+00 852.0
36 TraesCS5A01G247000 chr1D 94.245 556 32 0 2259 2814 19874681 19875236 0.000000e+00 850.0
37 TraesCS5A01G247000 chr4A 93.929 560 34 0 2258 2817 190185118 190185677 0.000000e+00 846.0
38 TraesCS5A01G247000 chrUn 99.522 209 1 0 1690 1898 478540157 478539949 8.510000e-102 381.0
39 TraesCS5A01G247000 chrUn 99.145 117 1 0 1574 1690 478540350 478540234 1.180000e-50 211.0
40 TraesCS5A01G247000 chr3B 79.167 168 19 9 3532 3696 482490925 482490771 7.420000e-18 102.0
41 TraesCS5A01G247000 chr3B 83.529 85 8 6 3669 3750 458188134 458188215 1.620000e-09 75.0
42 TraesCS5A01G247000 chr6D 87.500 48 6 0 3668 3715 306428676 306428629 5.860000e-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 TraesCS5A01G247000 chr5A 461228652 461232847 4195 True 3590.500000 6191 100.000000 1 4196 2 chr5A.!!$R1 4195
1 TraesCS5A01G247000 chr5A 461006896 461009402 2506 False 735.750000 1116 89.104750 44 3327 4 chr5A.!!$F1 3283
2 TraesCS5A01G247000 chr5D 360367924 360371438 3514 True 623.483333 933 89.696500 14 4189 6 chr5D.!!$R1 4175
3 TraesCS5A01G247000 chr5D 360047935 360050670 2735 False 567.600000 1014 88.958400 11 3388 5 chr5D.!!$F1 3377
4 TraesCS5A01G247000 chr5B 425610110 425613930 3820 True 548.400000 952 87.310200 11 3327 5 chr5B.!!$R1 3316
5 TraesCS5A01G247000 chr5B 425379486 425382591 3105 False 484.816667 1011 89.191833 10 3386 6 chr5B.!!$F1 3376
6 TraesCS5A01G247000 chr7A 561804633 561805193 560 True 953.000000 953 97.326000 2254 2814 1 chr7A.!!$R1 560
7 TraesCS5A01G247000 chr7A 504850857 504851412 555 False 872.000000 872 94.964000 2259 2814 1 chr7A.!!$F1 555
8 TraesCS5A01G247000 chr2A 332039825 332040380 555 True 883.000000 883 95.332000 2259 2815 1 chr2A.!!$R1 556
9 TraesCS5A01G247000 chr2A 475815055 475815614 559 False 863.000000 863 94.464000 2255 2814 1 chr2A.!!$F1 559
10 TraesCS5A01G247000 chr3A 686126800 686127356 556 False 869.000000 869 94.794000 2258 2814 1 chr3A.!!$F1 556
11 TraesCS5A01G247000 chr1A 291976429 291976984 555 False 861.000000 861 94.604000 2259 2814 1 chr1A.!!$F1 555
12 TraesCS5A01G247000 chr1D 250740831 250741387 556 False 852.000000 852 94.255000 2259 2815 1 chr1D.!!$F2 556
13 TraesCS5A01G247000 chr1D 19874681 19875236 555 False 850.000000 850 94.245000 2259 2814 1 chr1D.!!$F1 555
14 TraesCS5A01G247000 chr4A 190185118 190185677 559 False 846.000000 846 93.929000 2258 2817 1 chr4A.!!$F1 559

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
238 274 0.464036 TATCTCATTTCACGCCGGCT 59.536 50.0 26.68 8.92 0.0 5.52 F
456 1617 0.670239 CCGTGGAAAATTTGGCTGCC 60.670 55.0 12.87 12.87 0.0 4.85 F
1997 3425 1.089920 AAATCTCACGCTGTGGCATC 58.910 50.0 8.46 0.00 38.6 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 3347 1.203928 GACAGATCGATGGTTCTGCG 58.796 55.000 12.56 0.0 41.61 5.18 R
2080 3508 1.451927 CAGCAAGCCGCCTTATGGA 60.452 57.895 0.00 0.0 44.04 3.41 R
3333 5305 0.321387 CCTTGCTCTCTTGCTGCTGA 60.321 55.000 0.00 0.0 0.00 4.26 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
82 83 1.544724 TTTGCTGAAAATCCCCTCCG 58.455 50.000 0.00 0.00 0.00 4.63
135 143 2.771943 TCATCCCCTTGCTTAACTCGAT 59.228 45.455 0.00 0.00 0.00 3.59
138 146 4.402056 TCCCCTTGCTTAACTCGATAAG 57.598 45.455 2.06 2.06 36.24 1.73
190 207 4.989044 TGTGTCCGTTTCTTTCCTTTTTC 58.011 39.130 0.00 0.00 0.00 2.29
192 209 5.184287 TGTGTCCGTTTCTTTCCTTTTTCTT 59.816 36.000 0.00 0.00 0.00 2.52
193 210 6.097356 GTGTCCGTTTCTTTCCTTTTTCTTT 58.903 36.000 0.00 0.00 0.00 2.52
238 274 0.464036 TATCTCATTTCACGCCGGCT 59.536 50.000 26.68 8.92 0.00 5.52
345 1492 2.768253 ATGCAGGAATTCACTCACGA 57.232 45.000 7.93 0.00 0.00 4.35
456 1617 0.670239 CCGTGGAAAATTTGGCTGCC 60.670 55.000 12.87 12.87 0.00 4.85
503 1664 2.282180 TTGCCCGTCTTTGCCTCC 60.282 61.111 0.00 0.00 0.00 4.30
869 2037 1.550374 TCCCCTCCTCTCCCTCCTT 60.550 63.158 0.00 0.00 0.00 3.36
1228 2457 2.124403 GGGAGGACTACGCGGAGA 60.124 66.667 28.55 0.41 0.00 3.71
1319 2569 2.523015 TCTTTCCTTAATCGACGCGAC 58.477 47.619 15.93 5.54 39.18 5.19
1327 2581 2.579241 AATCGACGCGACCTGTCTCG 62.579 60.000 15.93 10.29 42.77 4.04
1334 2588 2.176140 CGACCTGTCTCGCTCTCTT 58.824 57.895 0.00 0.00 0.00 2.85
1335 2589 1.370609 CGACCTGTCTCGCTCTCTTA 58.629 55.000 0.00 0.00 0.00 2.10
1423 2690 2.796651 CGTACTACGGCTTCGGCT 59.203 61.111 0.26 0.00 38.08 5.52
1426 2693 1.303309 GTACTACGGCTTCGGCTCTA 58.697 55.000 0.00 0.00 41.44 2.43
1431 2698 1.320344 ACGGCTTCGGCTCTATCACA 61.320 55.000 0.00 0.00 41.44 3.58
1997 3425 1.089920 AAATCTCACGCTGTGGCATC 58.910 50.000 8.46 0.00 38.60 3.91
2084 3512 1.375523 GGAAGAACACGCCGTCCAT 60.376 57.895 0.00 0.00 33.32 3.41
2124 3552 2.096980 CACGTAGATAAGGTGAGACGCA 59.903 50.000 0.00 0.00 44.95 5.24
2276 4225 9.949174 GTTCTTGTGGCAAATTTGATAAATTTT 57.051 25.926 22.31 0.00 46.01 1.82
2418 4367 2.671619 GCTACACGCCTGGCCAAA 60.672 61.111 14.12 0.00 0.00 3.28
2635 4584 6.293407 GCTGCACACTGACTTAGTAATTTTCA 60.293 38.462 0.00 0.00 37.60 2.69
2713 4662 1.007336 GTGTAGTGTGACGCCTTCGG 61.007 60.000 0.00 0.00 40.69 4.30
2817 4766 6.183360 GGTCAAATTTGTCAATTTTGCCTGTT 60.183 34.615 20.61 0.00 40.09 3.16
2818 4767 6.906678 GTCAAATTTGTCAATTTTGCCTGTTC 59.093 34.615 20.61 8.70 40.09 3.18
2819 4768 6.822676 TCAAATTTGTCAATTTTGCCTGTTCT 59.177 30.769 20.61 0.00 40.09 3.01
2848 4798 0.108756 GCGTACTTCTCCAGACACCC 60.109 60.000 0.00 0.00 0.00 4.61
2884 4839 4.690748 GTGAGCTGCATTTACACTCTGTAA 59.309 41.667 1.02 0.00 40.70 2.41
2885 4840 5.352569 GTGAGCTGCATTTACACTCTGTAAT 59.647 40.000 1.02 0.00 41.83 1.89
2886 4841 5.352293 TGAGCTGCATTTACACTCTGTAATG 59.648 40.000 1.02 0.00 41.83 1.90
2887 4842 5.248640 AGCTGCATTTACACTCTGTAATGT 58.751 37.500 1.02 0.00 41.83 2.71
2888 4843 6.406370 AGCTGCATTTACACTCTGTAATGTA 58.594 36.000 1.02 0.00 41.83 2.29
2991 4946 0.536460 CCGTGCCACCACCTAAAACT 60.536 55.000 0.00 0.00 38.79 2.66
3171 5135 4.704103 AGCTCCCCGGTCAGCAGA 62.704 66.667 20.80 0.00 38.18 4.26
3229 5194 2.146342 GATGATATGCTCCACAACCCG 58.854 52.381 0.00 0.00 0.00 5.28
3287 5255 0.106708 AAAGGTCTCTTCTGTGCGCA 59.893 50.000 5.66 5.66 31.82 6.09
3313 5285 0.395862 ATCGTCATCTCTCGGTGGGT 60.396 55.000 0.00 0.00 0.00 4.51
3330 5302 2.225167 TGGGTAAGTCAAATGGTTCCCC 60.225 50.000 0.00 0.00 33.40 4.81
3331 5303 2.089201 GGTAAGTCAAATGGTTCCCCG 58.911 52.381 0.00 0.00 0.00 5.73
3332 5304 2.089201 GTAAGTCAAATGGTTCCCCGG 58.911 52.381 0.00 0.00 0.00 5.73
3333 5305 0.481128 AAGTCAAATGGTTCCCCGGT 59.519 50.000 0.00 0.00 0.00 5.28
3334 5306 0.037734 AGTCAAATGGTTCCCCGGTC 59.962 55.000 0.00 0.00 0.00 4.79
3335 5307 0.250989 GTCAAATGGTTCCCCGGTCA 60.251 55.000 0.00 0.00 0.00 4.02
3336 5308 0.037590 TCAAATGGTTCCCCGGTCAG 59.962 55.000 0.00 0.00 0.00 3.51
3337 5309 1.304134 AAATGGTTCCCCGGTCAGC 60.304 57.895 0.00 0.00 0.00 4.26
3338 5310 2.075355 AAATGGTTCCCCGGTCAGCA 62.075 55.000 0.00 0.00 0.00 4.41
3355 5398 1.015868 GCAGCAAGAGAGCAAGGATC 58.984 55.000 0.00 0.00 36.85 3.36
3399 5442 3.578456 CCAGACAATGGTGGTCGC 58.422 61.111 0.00 0.00 44.91 5.19
3429 5473 1.120437 CAAAGGTTTTGCGCGAAGAC 58.880 50.000 12.10 11.34 0.00 3.01
3430 5474 0.736053 AAAGGTTTTGCGCGAAGACA 59.264 45.000 12.10 0.00 0.00 3.41
3431 5475 0.736053 AAGGTTTTGCGCGAAGACAA 59.264 45.000 12.10 0.34 0.00 3.18
3432 5476 0.736053 AGGTTTTGCGCGAAGACAAA 59.264 45.000 12.10 8.04 34.11 2.83
3433 5477 1.120437 GGTTTTGCGCGAAGACAAAG 58.880 50.000 12.10 0.00 37.11 2.77
3434 5478 0.498511 GTTTTGCGCGAAGACAAAGC 59.501 50.000 12.10 9.19 37.11 3.51
3435 5479 0.380378 TTTTGCGCGAAGACAAAGCT 59.620 45.000 12.10 0.00 37.11 3.74
3436 5480 0.316937 TTTGCGCGAAGACAAAGCTG 60.317 50.000 12.10 0.00 32.28 4.24
3437 5481 1.436195 TTGCGCGAAGACAAAGCTGT 61.436 50.000 12.10 0.00 38.98 4.40
3438 5482 1.439365 GCGCGAAGACAAAGCTGTG 60.439 57.895 12.10 1.09 35.30 3.66
3445 5489 1.154150 GACAAAGCTGTGGATGCGC 60.154 57.895 9.18 0.00 35.30 6.09
3496 5540 0.533755 CGGCCCAATTCCAGAGCTAG 60.534 60.000 0.00 0.00 0.00 3.42
3514 5558 4.314440 TGGCAGGCACCGACTGTC 62.314 66.667 0.00 0.00 44.68 3.51
3517 5561 2.743718 CAGGCACCGACTGTCCTT 59.256 61.111 1.55 0.00 33.29 3.36
3665 5709 7.678947 AAAGTAGGCATCACAGCATATATTC 57.321 36.000 0.00 0.00 33.02 1.75
3955 6003 4.508124 GCCACTTGTAGACGATTCCTAATG 59.492 45.833 0.00 0.00 0.00 1.90
3984 6034 2.352821 CGACCGTATGGGGGACACA 61.353 63.158 5.82 0.00 41.60 3.72
3985 6035 1.682451 CGACCGTATGGGGGACACAT 61.682 60.000 5.82 0.00 41.60 3.21
3986 6036 1.416243 GACCGTATGGGGGACACATA 58.584 55.000 5.82 0.00 41.60 2.29
3987 6037 1.343465 GACCGTATGGGGGACACATAG 59.657 57.143 5.82 0.00 41.60 2.23
3988 6038 0.034896 CCGTATGGGGGACACATAGC 59.965 60.000 0.00 0.00 31.92 2.97
3989 6039 1.048601 CGTATGGGGGACACATAGCT 58.951 55.000 0.00 0.00 31.92 3.32
3990 6040 1.000955 CGTATGGGGGACACATAGCTC 59.999 57.143 0.00 0.00 31.92 4.09
3991 6041 2.330216 GTATGGGGGACACATAGCTCT 58.670 52.381 0.00 0.00 31.92 4.09
3992 6042 1.428869 ATGGGGGACACATAGCTCTC 58.571 55.000 0.00 0.00 0.00 3.20
3993 6043 1.043116 TGGGGGACACATAGCTCTCG 61.043 60.000 0.00 0.00 0.00 4.04
3994 6044 1.068250 GGGGACACATAGCTCTCGC 59.932 63.158 0.00 0.00 0.00 5.03
3995 6045 1.068250 GGGACACATAGCTCTCGCC 59.932 63.158 0.00 0.00 36.60 5.54
3996 6046 1.299468 GGACACATAGCTCTCGCCG 60.299 63.158 0.00 0.00 36.60 6.46
3997 6047 1.299468 GACACATAGCTCTCGCCGG 60.299 63.158 0.00 0.00 36.60 6.13
3998 6048 2.005960 GACACATAGCTCTCGCCGGT 62.006 60.000 1.90 0.00 36.60 5.28
4042 6094 2.084121 TTTAAGGATCCCCTGGGGTT 57.916 50.000 30.69 23.35 43.48 4.11
4046 6098 4.106725 GATCCCCTGGGGTTCCAT 57.893 61.111 30.69 17.28 44.74 3.41
4047 6099 1.846973 GATCCCCTGGGGTTCCATC 59.153 63.158 30.69 21.44 44.74 3.51
4048 6100 2.056906 GATCCCCTGGGGTTCCATCG 62.057 65.000 30.69 3.18 44.74 3.84
4049 6101 2.561378 ATCCCCTGGGGTTCCATCGA 62.561 60.000 30.69 9.93 44.74 3.59
4050 6102 2.746375 CCCCTGGGGTTCCATCGAG 61.746 68.421 24.54 0.00 43.11 4.04
4051 6103 2.190578 CCTGGGGTTCCATCGAGC 59.809 66.667 0.00 0.00 43.11 5.03
4052 6104 2.202932 CTGGGGTTCCATCGAGCG 60.203 66.667 0.00 0.00 43.11 5.03
4053 6105 2.682136 TGGGGTTCCATCGAGCGA 60.682 61.111 0.00 0.00 38.32 4.93
4054 6106 2.238847 CTGGGGTTCCATCGAGCGAA 62.239 60.000 0.00 0.00 43.11 4.70
4055 6107 1.814169 GGGGTTCCATCGAGCGAAC 60.814 63.158 15.60 15.60 38.10 3.95
4056 6108 1.079405 GGGTTCCATCGAGCGAACA 60.079 57.895 22.01 0.00 40.13 3.18
4057 6109 0.672401 GGGTTCCATCGAGCGAACAA 60.672 55.000 22.01 0.00 40.13 2.83
4058 6110 1.153353 GGTTCCATCGAGCGAACAAA 58.847 50.000 22.01 0.00 40.13 2.83
4059 6111 1.533731 GGTTCCATCGAGCGAACAAAA 59.466 47.619 22.01 0.00 40.13 2.44
4060 6112 2.161609 GGTTCCATCGAGCGAACAAAAT 59.838 45.455 22.01 0.00 40.13 1.82
4061 6113 3.417185 GTTCCATCGAGCGAACAAAATC 58.583 45.455 17.90 0.00 38.58 2.17
4062 6114 1.658596 TCCATCGAGCGAACAAAATCG 59.341 47.619 0.00 0.00 45.41 3.34
4063 6115 1.393539 CCATCGAGCGAACAAAATCGT 59.606 47.619 0.00 0.00 44.49 3.73
4064 6116 2.421523 CATCGAGCGAACAAAATCGTG 58.578 47.619 0.00 0.00 44.49 4.35
4065 6117 1.493772 TCGAGCGAACAAAATCGTGT 58.506 45.000 0.00 0.00 44.49 4.49
4066 6118 1.454276 TCGAGCGAACAAAATCGTGTC 59.546 47.619 0.00 0.00 44.49 3.67
4067 6119 1.461888 CGAGCGAACAAAATCGTGTCC 60.462 52.381 0.00 0.00 44.49 4.02
4068 6120 1.798813 GAGCGAACAAAATCGTGTCCT 59.201 47.619 0.00 0.00 44.49 3.85
4069 6121 2.218603 AGCGAACAAAATCGTGTCCTT 58.781 42.857 0.00 0.00 44.49 3.36
4070 6122 3.395639 AGCGAACAAAATCGTGTCCTTA 58.604 40.909 0.00 0.00 44.49 2.69
4096 6148 2.658285 CCAGTGTGTGTGTACGAGTAC 58.342 52.381 6.46 6.46 36.63 2.73
4115 6168 2.159819 CTCGAGTATGCATCCCGGGG 62.160 65.000 23.50 6.77 0.00 5.73
4131 6184 2.358737 GGTCGTCACCCTTGCAGG 60.359 66.667 0.00 0.00 36.54 4.85
4145 6198 2.505006 CAGGGCTGCCAGCTAGAG 59.495 66.667 22.05 0.63 41.99 2.43
4146 6199 2.062777 CAGGGCTGCCAGCTAGAGA 61.063 63.158 22.05 0.00 41.99 3.10
4147 6200 1.074623 AGGGCTGCCAGCTAGAGAT 60.075 57.895 22.05 0.00 41.99 2.75
4148 6201 0.693767 AGGGCTGCCAGCTAGAGATT 60.694 55.000 22.05 0.00 41.99 2.40
4149 6202 0.182299 GGGCTGCCAGCTAGAGATTT 59.818 55.000 22.05 0.00 41.99 2.17
4150 6203 1.417890 GGGCTGCCAGCTAGAGATTTA 59.582 52.381 22.05 0.00 41.99 1.40
4151 6204 2.488952 GGCTGCCAGCTAGAGATTTAC 58.511 52.381 17.55 0.00 41.99 2.01
4152 6205 2.131183 GCTGCCAGCTAGAGATTTACG 58.869 52.381 10.04 0.00 38.45 3.18
4153 6206 2.131183 CTGCCAGCTAGAGATTTACGC 58.869 52.381 0.00 0.00 0.00 4.42
4154 6207 1.202533 TGCCAGCTAGAGATTTACGCC 60.203 52.381 0.00 0.00 0.00 5.68
4155 6208 1.202533 GCCAGCTAGAGATTTACGCCA 60.203 52.381 0.00 0.00 0.00 5.69
4156 6209 2.474816 CCAGCTAGAGATTTACGCCAC 58.525 52.381 0.00 0.00 0.00 5.01
4157 6210 2.474816 CAGCTAGAGATTTACGCCACC 58.525 52.381 0.00 0.00 0.00 4.61
4158 6211 2.108168 AGCTAGAGATTTACGCCACCA 58.892 47.619 0.00 0.00 0.00 4.17
4192 6245 2.430244 CCGTCTTGTCGGTCGGTG 60.430 66.667 0.00 0.00 44.77 4.94
4193 6246 3.103911 CGTCTTGTCGGTCGGTGC 61.104 66.667 0.00 0.00 0.00 5.01
4194 6247 3.103911 GTCTTGTCGGTCGGTGCG 61.104 66.667 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.616371 TTGGACCCCAATACACGGAG 59.384 55.000 0.00 0.00 38.75 4.63
5 6 1.912417 TTTTGGACCCCAATACACGG 58.088 50.000 0.00 0.00 43.55 4.94
6 7 5.646577 TTATTTTTGGACCCCAATACACG 57.353 39.130 0.00 0.00 43.55 4.49
7 8 6.999950 AGTTTATTTTTGGACCCCAATACAC 58.000 36.000 0.00 0.00 43.55 2.90
8 9 8.722622 TTAGTTTATTTTTGGACCCCAATACA 57.277 30.769 0.00 0.00 43.55 2.29
11 12 9.777008 TCTATTAGTTTATTTTTGGACCCCAAT 57.223 29.630 0.00 0.00 43.55 3.16
12 13 9.603189 TTCTATTAGTTTATTTTTGGACCCCAA 57.397 29.630 0.00 0.00 42.29 4.12
82 83 6.430308 ACATATGATCATGATGGTTCTTCTGC 59.570 38.462 18.72 0.00 0.00 4.26
135 143 2.790433 GACAATGACACCTTGGCCTTA 58.210 47.619 3.32 0.00 0.00 2.69
138 146 1.875963 CGACAATGACACCTTGGCC 59.124 57.895 0.00 0.00 0.00 5.36
190 207 3.264947 TGCAGAAGATGATGACGGAAAG 58.735 45.455 0.00 0.00 0.00 2.62
192 209 3.333029 TTGCAGAAGATGATGACGGAA 57.667 42.857 0.00 0.00 0.00 4.30
193 210 3.118665 TGATTGCAGAAGATGATGACGGA 60.119 43.478 0.00 0.00 0.00 4.69
238 274 4.151689 GCGTAAAAAGAGATGCTGTGTACA 59.848 41.667 0.00 0.00 0.00 2.90
503 1664 1.908299 GGAGGGGTGTTTTGGGCAG 60.908 63.158 0.00 0.00 0.00 4.85
862 2030 1.376037 GTGTGGAAGCGAAGGAGGG 60.376 63.158 0.00 0.00 0.00 4.30
869 2037 2.741092 GGTGAGGTGTGGAAGCGA 59.259 61.111 0.00 0.00 0.00 4.93
1319 2569 1.673920 GAGGTAAGAGAGCGAGACAGG 59.326 57.143 0.00 0.00 0.00 4.00
1327 2581 4.356289 GAACGAATCAGAGGTAAGAGAGC 58.644 47.826 0.00 0.00 0.00 4.09
1553 2829 2.020131 GGCTCACATGAATCAGCCG 58.980 57.895 0.00 0.00 42.10 5.52
1930 3347 1.203928 GACAGATCGATGGTTCTGCG 58.796 55.000 12.56 0.00 41.61 5.18
1936 3353 2.035704 GCATCTCTGACAGATCGATGGT 59.964 50.000 24.94 0.00 40.20 3.55
1938 3355 3.366440 TGCATCTCTGACAGATCGATG 57.634 47.619 21.88 21.88 40.20 3.84
2080 3508 1.451927 CAGCAAGCCGCCTTATGGA 60.452 57.895 0.00 0.00 44.04 3.41
2084 3512 3.055719 GTGCAGCAAGCCGCCTTA 61.056 61.111 0.00 0.00 44.83 2.69
2236 4184 3.050275 GAACAGGGGCGACTGCAC 61.050 66.667 7.62 0.00 46.66 4.57
2276 4225 4.152759 GTGATTTGATTTCGTTCACGGGTA 59.847 41.667 0.00 0.00 40.29 3.69
2418 4367 2.664402 AGACAGTTTGGGATGCAACT 57.336 45.000 0.00 0.00 33.29 3.16
2713 4662 1.064952 CTTTTTGTGTGACACCCGACC 59.935 52.381 13.85 0.00 32.73 4.79
2720 4669 1.748493 GGCTGACCTTTTTGTGTGACA 59.252 47.619 0.00 0.00 0.00 3.58
2817 4766 2.202518 GTACGCGCGGCTACAAGA 60.203 61.111 35.22 5.29 0.00 3.02
2818 4767 1.740043 GAAGTACGCGCGGCTACAAG 61.740 60.000 35.22 3.55 0.00 3.16
2819 4768 1.802715 GAAGTACGCGCGGCTACAA 60.803 57.895 35.22 8.95 0.00 2.41
2848 4798 3.114616 CTCACGCGTTCCCTGCAG 61.115 66.667 10.22 6.78 0.00 4.41
2867 4817 7.971183 TGTTACATTACAGAGTGTAAATGCA 57.029 32.000 3.74 0.00 44.84 3.96
2884 4839 3.315191 GCCATTAAGTCGCCATGTTACAT 59.685 43.478 0.00 0.00 0.00 2.29
2885 4840 2.680841 GCCATTAAGTCGCCATGTTACA 59.319 45.455 0.00 0.00 0.00 2.41
2886 4841 2.943033 AGCCATTAAGTCGCCATGTTAC 59.057 45.455 0.00 0.00 0.00 2.50
2887 4842 3.275617 AGCCATTAAGTCGCCATGTTA 57.724 42.857 0.00 0.00 0.00 2.41
2888 4843 2.128771 AGCCATTAAGTCGCCATGTT 57.871 45.000 0.00 0.00 0.00 2.71
2979 4934 0.539669 GGCCTGCAGTTTTAGGTGGT 60.540 55.000 13.81 0.00 36.44 4.16
3006 4964 4.815973 ATGGCGGGGGAGTAGGCA 62.816 66.667 0.00 0.00 44.36 4.75
3110 5068 2.511373 GCGACGATGCCATGGTGA 60.511 61.111 14.67 0.10 0.00 4.02
3132 5090 4.537433 AATCCAGAGCTCGCGGGC 62.537 66.667 26.87 26.87 0.00 6.13
3133 5091 2.279784 GAATCCAGAGCTCGCGGG 60.280 66.667 21.00 17.50 0.00 6.13
3147 5111 2.683933 ACCGGGGAGCTGTCGAAT 60.684 61.111 6.32 0.00 0.00 3.34
3171 5135 3.448934 TCTGCTGATCTTCCTCCTCTTT 58.551 45.455 0.00 0.00 0.00 2.52
3264 5232 3.181516 GCGCACAGAAGAGACCTTTAATG 60.182 47.826 0.30 0.00 31.62 1.90
3287 5255 1.611006 CGAGAGATGACGATGATGGGT 59.389 52.381 0.00 0.00 0.00 4.51
3330 5302 2.099431 GCTCTCTTGCTGCTGACCG 61.099 63.158 0.00 0.00 0.00 4.79
3331 5303 0.604780 TTGCTCTCTTGCTGCTGACC 60.605 55.000 0.00 0.00 0.00 4.02
3332 5304 0.797542 CTTGCTCTCTTGCTGCTGAC 59.202 55.000 0.00 0.00 0.00 3.51
3333 5305 0.321387 CCTTGCTCTCTTGCTGCTGA 60.321 55.000 0.00 0.00 0.00 4.26
3334 5306 0.321387 TCCTTGCTCTCTTGCTGCTG 60.321 55.000 0.00 0.00 0.00 4.41
3335 5307 0.619505 ATCCTTGCTCTCTTGCTGCT 59.380 50.000 0.00 0.00 0.00 4.24
3336 5308 1.015868 GATCCTTGCTCTCTTGCTGC 58.984 55.000 0.00 0.00 0.00 5.25
3337 5309 2.553086 GAGATCCTTGCTCTCTTGCTG 58.447 52.381 0.00 0.00 36.91 4.41
3338 5310 1.485895 GGAGATCCTTGCTCTCTTGCT 59.514 52.381 0.55 0.00 39.30 3.91
3399 5442 3.557185 GCAAAACCTTTGCTCTTTTGGAG 59.443 43.478 15.16 0.00 44.49 3.86
3429 5473 1.154093 CAGCGCATCCACAGCTTTG 60.154 57.895 11.47 0.00 39.48 2.77
3430 5474 1.302752 TCAGCGCATCCACAGCTTT 60.303 52.632 11.47 0.00 39.48 3.51
3431 5475 1.744368 CTCAGCGCATCCACAGCTT 60.744 57.895 11.47 0.00 39.48 3.74
3432 5476 1.969200 ATCTCAGCGCATCCACAGCT 61.969 55.000 11.47 0.00 42.64 4.24
3433 5477 1.523258 ATCTCAGCGCATCCACAGC 60.523 57.895 11.47 0.00 0.00 4.40
3434 5478 1.158484 CCATCTCAGCGCATCCACAG 61.158 60.000 11.47 0.00 0.00 3.66
3435 5479 1.153309 CCATCTCAGCGCATCCACA 60.153 57.895 11.47 0.00 0.00 4.17
3436 5480 1.890979 CCCATCTCAGCGCATCCAC 60.891 63.158 11.47 0.00 0.00 4.02
3437 5481 2.065789 TCCCATCTCAGCGCATCCA 61.066 57.895 11.47 0.00 0.00 3.41
3438 5482 1.596477 GTCCCATCTCAGCGCATCC 60.596 63.158 11.47 0.00 0.00 3.51
3496 5540 4.626081 ACAGTCGGTGCCTGCCAC 62.626 66.667 0.00 0.00 43.90 5.01
3514 5558 4.358851 TGAACAAACAAAATCGAGCAAGG 58.641 39.130 0.00 0.00 0.00 3.61
3517 5561 5.635280 TGTTTTGAACAAACAAAATCGAGCA 59.365 32.000 0.00 0.00 46.44 4.26
3709 5753 8.158169 TCTCATATACATCAGGAACATTTTGC 57.842 34.615 0.00 0.00 0.00 3.68
3791 5835 9.495572 TTTGGTTTTCACTAATTTTCTTTGTGT 57.504 25.926 0.00 0.00 0.00 3.72
3792 5836 9.971744 CTTTGGTTTTCACTAATTTTCTTTGTG 57.028 29.630 0.00 0.00 0.00 3.33
3793 5837 9.936759 TCTTTGGTTTTCACTAATTTTCTTTGT 57.063 25.926 0.00 0.00 0.00 2.83
3855 5901 0.653636 TCTGTCGTGCGGTTTTTCAC 59.346 50.000 0.00 0.00 0.00 3.18
3897 5945 7.052142 ACCCAATACTGTAGCAGAGTATTAC 57.948 40.000 14.08 0.00 42.27 1.89
3971 6021 2.300437 GAGAGCTATGTGTCCCCCATAC 59.700 54.545 0.00 0.00 0.00 2.39
3974 6024 1.043116 CGAGAGCTATGTGTCCCCCA 61.043 60.000 0.00 0.00 0.00 4.96
3988 6038 4.760047 CAACCCCACCGGCGAGAG 62.760 72.222 9.30 0.00 33.26 3.20
4040 6092 2.961522 TTTTGTTCGCTCGATGGAAC 57.038 45.000 17.24 17.24 42.17 3.62
4042 6094 1.658596 CGATTTTGTTCGCTCGATGGA 59.341 47.619 0.00 0.00 33.07 3.41
4044 6096 2.159841 ACACGATTTTGTTCGCTCGATG 60.160 45.455 0.00 0.00 42.82 3.84
4045 6097 2.066262 ACACGATTTTGTTCGCTCGAT 58.934 42.857 0.00 0.00 42.82 3.59
4046 6098 1.454276 GACACGATTTTGTTCGCTCGA 59.546 47.619 0.00 0.00 42.82 4.04
4047 6099 1.461888 GGACACGATTTTGTTCGCTCG 60.462 52.381 0.00 0.00 42.82 5.03
4048 6100 1.798813 AGGACACGATTTTGTTCGCTC 59.201 47.619 0.00 0.00 42.82 5.03
4049 6101 1.878953 AGGACACGATTTTGTTCGCT 58.121 45.000 0.00 0.00 42.82 4.93
4050 6102 2.681152 AAGGACACGATTTTGTTCGC 57.319 45.000 0.00 0.00 42.82 4.70
4051 6103 5.013236 CGAATAAGGACACGATTTTGTTCG 58.987 41.667 0.00 0.00 44.56 3.95
4052 6104 5.321516 CCGAATAAGGACACGATTTTGTTC 58.678 41.667 0.00 0.00 0.00 3.18
4053 6105 4.379082 GCCGAATAAGGACACGATTTTGTT 60.379 41.667 0.00 0.00 0.00 2.83
4054 6106 3.126343 GCCGAATAAGGACACGATTTTGT 59.874 43.478 0.00 0.00 0.00 2.83
4055 6107 3.486875 GGCCGAATAAGGACACGATTTTG 60.487 47.826 0.00 0.00 39.73 2.44
4056 6108 2.681344 GGCCGAATAAGGACACGATTTT 59.319 45.455 0.00 0.00 39.73 1.82
4057 6109 2.285977 GGCCGAATAAGGACACGATTT 58.714 47.619 0.00 0.00 39.73 2.17
4058 6110 1.208535 TGGCCGAATAAGGACACGATT 59.791 47.619 0.00 0.00 46.16 3.34
4059 6111 0.828022 TGGCCGAATAAGGACACGAT 59.172 50.000 0.00 0.00 46.16 3.73
4060 6112 0.174845 CTGGCCGAATAAGGACACGA 59.825 55.000 0.00 0.00 46.16 4.35
4061 6113 0.108329 ACTGGCCGAATAAGGACACG 60.108 55.000 0.00 0.00 46.16 4.49
4062 6114 1.338769 ACACTGGCCGAATAAGGACAC 60.339 52.381 0.00 0.00 46.16 3.67
4064 6116 1.338769 ACACACTGGCCGAATAAGGAC 60.339 52.381 0.00 0.00 40.61 3.85
4065 6117 0.981183 ACACACTGGCCGAATAAGGA 59.019 50.000 0.00 0.00 0.00 3.36
4066 6118 1.086696 CACACACTGGCCGAATAAGG 58.913 55.000 0.00 0.00 0.00 2.69
4067 6119 1.464608 CACACACACTGGCCGAATAAG 59.535 52.381 0.00 0.00 0.00 1.73
4068 6120 1.202710 ACACACACACTGGCCGAATAA 60.203 47.619 0.00 0.00 0.00 1.40
4069 6121 0.394938 ACACACACACTGGCCGAATA 59.605 50.000 0.00 0.00 0.00 1.75
4070 6122 0.394938 TACACACACACTGGCCGAAT 59.605 50.000 0.00 0.00 0.00 3.34
4096 6148 1.290324 CCCGGGATGCATACTCGAG 59.710 63.158 18.48 11.84 0.00 4.04
4131 6184 2.488952 GTAAATCTCTAGCTGGCAGCC 58.511 52.381 34.33 17.49 43.77 4.85
4139 6192 2.474816 CTGGTGGCGTAAATCTCTAGC 58.525 52.381 0.00 0.00 0.00 3.42
4141 6194 2.596904 GCTGGTGGCGTAAATCTCTA 57.403 50.000 0.00 0.00 0.00 2.43
4142 6195 3.460648 GCTGGTGGCGTAAATCTCT 57.539 52.632 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.