Multiple sequence alignment - TraesCS6B01G167700

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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 TraesCS6B01G167700 chr6B 100.000 5131 0 0 1 5131 176284885 176279755 0.000000e+00 9439.0
1 TraesCS6B01G167700 chr6B 99.796 982 2 0 1 982 197236906 197235925 0.000000e+00 1803.0
2 TraesCS6B01G167700 chr6B 88.235 187 22 0 796 982 176285963 176286149 1.860000e-54 224.0
3 TraesCS6B01G167700 chr6B 88.235 187 22 0 796 982 197237984 197238170 1.860000e-54 224.0
4 TraesCS6B01G167700 chr6A 94.395 3176 116 30 1007 4171 111566727 111563603 0.000000e+00 4822.0
5 TraesCS6B01G167700 chr6A 95.192 208 4 3 4930 5131 111559277 111559070 1.780000e-84 324.0
6 TraesCS6B01G167700 chr6A 93.750 192 8 2 4605 4794 111559679 111559490 8.410000e-73 285.0
7 TraesCS6B01G167700 chr6A 92.908 141 6 2 4156 4296 111559966 111559830 8.710000e-48 202.0
8 TraesCS6B01G167700 chr6A 94.444 126 6 1 4376 4501 111559833 111559709 5.240000e-45 193.0
9 TraesCS6B01G167700 chr6D 94.856 1983 66 10 993 2962 91849196 91847237 0.000000e+00 3064.0
10 TraesCS6B01G167700 chr6D 93.772 1397 69 13 2906 4296 91847231 91845847 0.000000e+00 2082.0
11 TraesCS6B01G167700 chr6D 93.214 501 18 8 4644 5131 91845398 91844901 0.000000e+00 723.0
12 TraesCS6B01G167700 chr6D 93.522 247 15 1 4376 4622 91845850 91845605 2.920000e-97 366.0
13 TraesCS6B01G167700 chr6D 97.059 34 1 0 4832 4865 368780360 368780393 2.000000e-04 58.4
14 TraesCS6B01G167700 chr3A 99.695 982 3 0 1 982 610758880 610759861 0.000000e+00 1797.0
15 TraesCS6B01G167700 chr3A 99.497 596 1 1 387 982 487852246 487852839 0.000000e+00 1083.0
16 TraesCS6B01G167700 chr3A 97.208 394 2 1 1 385 487851685 487852078 0.000000e+00 660.0
17 TraesCS6B01G167700 chr3A 88.235 187 22 0 796 982 487850607 487850421 1.860000e-54 224.0
18 TraesCS6B01G167700 chr3A 87.283 173 21 1 796 967 610757802 610757630 4.050000e-46 196.0
19 TraesCS6B01G167700 chr3A 100.000 86 0 0 4294 4379 402135969 402136054 5.320000e-35 159.0
20 TraesCS6B01G167700 chr3A 96.842 95 3 0 4286 4380 443203579 443203673 5.320000e-35 159.0
21 TraesCS6B01G167700 chr3A 88.298 94 10 1 890 982 303529543 303529636 1.510000e-20 111.0
22 TraesCS6B01G167700 chr2A 99.491 982 5 0 1 982 463995929 463994948 0.000000e+00 1786.0
23 TraesCS6B01G167700 chr2A 82.452 416 60 12 3344 3753 593299595 593299187 8.170000e-93 351.0
24 TraesCS6B01G167700 chr2A 88.235 187 22 0 796 982 463997007 463997193 1.860000e-54 224.0
25 TraesCS6B01G167700 chr1A 82.275 1213 167 26 2055 3247 532597048 532598232 0.000000e+00 1005.0
26 TraesCS6B01G167700 chr1A 81.781 730 92 22 2276 2993 532669016 532669716 1.600000e-159 573.0
27 TraesCS6B01G167700 chr1A 81.818 385 45 11 3754 4132 532670387 532670752 3.000000e-77 300.0
28 TraesCS6B01G167700 chr1A 94.000 100 4 1 4280 4379 69995982 69995885 3.200000e-32 150.0
29 TraesCS6B01G167700 chr1A 92.523 107 4 3 4292 4395 575557358 575557253 3.200000e-32 150.0
30 TraesCS6B01G167700 chr1A 95.556 90 4 0 4292 4381 518044814 518044903 1.490000e-30 145.0
31 TraesCS6B01G167700 chr1D 80.323 1240 179 33 2029 3247 435045731 435046926 0.000000e+00 878.0
32 TraesCS6B01G167700 chr1D 82.367 414 58 15 3348 3755 442791822 442791418 3.800000e-91 346.0
33 TraesCS6B01G167700 chrUn 84.439 392 46 14 3354 3735 61736290 61736676 6.270000e-99 372.0
34 TraesCS6B01G167700 chr3D 83.095 420 50 19 3344 3753 454744553 454744145 3.780000e-96 363.0
35 TraesCS6B01G167700 chr4D 83.290 389 52 10 3340 3724 323597567 323597188 3.800000e-91 346.0
36 TraesCS6B01G167700 chr4D 82.382 403 54 15 3357 3753 101440144 101440535 8.230000e-88 335.0
37 TraesCS6B01G167700 chr4D 75.881 369 44 23 342 674 12038615 12038256 4.140000e-31 147.0
38 TraesCS6B01G167700 chr4D 97.059 34 1 0 4832 4865 101653251 101653218 2.000000e-04 58.4
39 TraesCS6B01G167700 chr2D 82.734 417 42 20 3344 3751 99740793 99740398 1.370000e-90 344.0
40 TraesCS6B01G167700 chr2D 97.059 34 1 0 4832 4865 54674288 54674321 2.000000e-04 58.4
41 TraesCS6B01G167700 chr1B 83.228 316 53 0 2932 3247 588424955 588425270 1.810000e-74 291.0
42 TraesCS6B01G167700 chr1B 93.204 103 4 2 4277 4379 22881980 22881881 1.150000e-31 148.0
43 TraesCS6B01G167700 chr1B 87.037 54 3 4 4832 4883 194349360 194349411 2.000000e-04 58.4
44 TraesCS6B01G167700 chr7B 85.561 187 27 0 796 982 284268723 284268909 4.050000e-46 196.0
45 TraesCS6B01G167700 chr7B 97.059 34 1 0 4832 4865 744296 744329 2.000000e-04 58.4
46 TraesCS6B01G167700 chr5A 95.745 94 4 0 4295 4388 428189353 428189446 8.900000e-33 152.0
47 TraesCS6B01G167700 chr5A 90.265 113 6 5 4270 4379 324692542 324692652 5.360000e-30 143.0
48 TraesCS6B01G167700 chr4B 91.667 108 5 4 4273 4379 454519234 454519338 4.140000e-31 147.0
49 TraesCS6B01G167700 chr7D 93.023 43 1 2 4832 4873 608735104 608735063 1.540000e-05 62.1
50 TraesCS6B01G167700 chr2B 89.796 49 2 3 4832 4878 85321944 85321991 5.550000e-05 60.2
51 TraesCS6B01G167700 chr2B 90.909 44 2 2 4832 4874 576653159 576653117 2.000000e-04 58.4


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 TraesCS6B01G167700 chr6B 176279755 176284885 5130 True 9439.00 9439 100.0000 1 5131 1 chr6B.!!$R1 5130
1 TraesCS6B01G167700 chr6B 197235925 197236906 981 True 1803.00 1803 99.7960 1 982 1 chr6B.!!$R2 981
2 TraesCS6B01G167700 chr6A 111559070 111566727 7657 True 1165.20 4822 94.1378 1007 5131 5 chr6A.!!$R1 4124
3 TraesCS6B01G167700 chr6D 91844901 91849196 4295 True 1558.75 3064 93.8410 993 5131 4 chr6D.!!$R1 4138
4 TraesCS6B01G167700 chr3A 610758880 610759861 981 False 1797.00 1797 99.6950 1 982 1 chr3A.!!$F4 981
5 TraesCS6B01G167700 chr3A 487851685 487852839 1154 False 871.50 1083 98.3525 1 982 2 chr3A.!!$F5 981
6 TraesCS6B01G167700 chr2A 463994948 463995929 981 True 1786.00 1786 99.4910 1 982 1 chr2A.!!$R1 981
7 TraesCS6B01G167700 chr1A 532597048 532598232 1184 False 1005.00 1005 82.2750 2055 3247 1 chr1A.!!$F2 1192
8 TraesCS6B01G167700 chr1A 532669016 532670752 1736 False 436.50 573 81.7995 2276 4132 2 chr1A.!!$F3 1856
9 TraesCS6B01G167700 chr1D 435045731 435046926 1195 False 878.00 878 80.3230 2029 3247 1 chr1D.!!$F1 1218

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
198 208 2.456119 CGTCTTGATGCCCAGCGAC 61.456 63.158 0.00 0.00 0.00 5.19 F
1543 1725 0.108585 AACCCTGTGCTTCGTGTCAT 59.891 50.000 0.00 0.00 0.00 3.06 F
1669 1851 0.323725 GCAGGGGCAGAAGGATTGAA 60.324 55.000 0.00 0.00 40.72 2.69 F
1685 1867 0.895530 TGAAGAGCCAGGTCCGTAAG 59.104 55.000 0.00 0.00 0.00 2.34 F
2159 2347 1.009078 GACGATGCATGCTGCTAACA 58.991 50.000 20.33 0.00 45.31 2.41 F
3771 4451 3.055747 TCCCGTTGCATGTATGACTTACA 60.056 43.478 3.87 3.87 44.71 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1888 0.764271 TCTCATCCACACACTTGCCA 59.236 50.000 0.00 0.0 0.00 4.92 R
3330 4001 1.967066 CCCTACCACATGCAACCAAAA 59.033 47.619 0.00 0.0 0.00 2.44 R
3582 4258 0.886490 AGCGTTGACTTCAGGGCAAG 60.886 55.000 6.42 0.0 44.60 4.01 R
3583 4259 1.148273 AGCGTTGACTTCAGGGCAA 59.852 52.632 6.42 0.0 41.27 4.52 R
4087 4770 0.543277 GTCCCAGATCATCTGCACCA 59.457 55.000 9.41 0.0 42.98 4.17 R
4928 9567 0.034863 AACCAACGGTGTCCTGTGTT 60.035 50.000 0.00 0.0 35.34 3.32 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
198 208 2.456119 CGTCTTGATGCCCAGCGAC 61.456 63.158 0.00 0.00 0.00 5.19
1155 1331 3.691118 CGTCCAACAACAAGATCATCCAT 59.309 43.478 0.00 0.00 0.00 3.41
1156 1332 4.875536 CGTCCAACAACAAGATCATCCATA 59.124 41.667 0.00 0.00 0.00 2.74
1326 1502 1.469335 AAAACTCCTCCGACTCCGCA 61.469 55.000 0.00 0.00 0.00 5.69
1368 1544 0.970937 TCGAGAGGTTCTTGCCGGAT 60.971 55.000 5.05 0.00 0.00 4.18
1467 1649 2.524148 GCAAGGGTGGGCAAGGTT 60.524 61.111 0.00 0.00 0.00 3.50
1505 1687 5.014858 AGTCTTCTCCTACATTTGTCCGTA 58.985 41.667 0.00 0.00 0.00 4.02
1515 1697 2.932855 TTTGTCCGTACCACCATTCA 57.067 45.000 0.00 0.00 0.00 2.57
1543 1725 0.108585 AACCCTGTGCTTCGTGTCAT 59.891 50.000 0.00 0.00 0.00 3.06
1552 1734 4.694982 TGTGCTTCGTGTCATATCACATTT 59.305 37.500 0.00 0.00 38.12 2.32
1634 1816 0.900647 CCGTCTCCCTGGACTCTGTT 60.901 60.000 0.00 0.00 34.38 3.16
1666 1848 0.411058 AAAGCAGGGGCAGAAGGATT 59.589 50.000 0.00 0.00 44.61 3.01
1669 1851 0.323725 GCAGGGGCAGAAGGATTGAA 60.324 55.000 0.00 0.00 40.72 2.69
1685 1867 0.895530 TGAAGAGCCAGGTCCGTAAG 59.104 55.000 0.00 0.00 0.00 2.34
1751 1933 4.327680 GGATGTATATTGGGAAGCTGACC 58.672 47.826 0.00 0.00 0.00 4.02
1815 1997 4.463515 GTTTGGACGTCCTAACAGTTTC 57.536 45.455 39.35 21.99 46.31 2.78
1852 2034 7.648142 TGGTTATTTTTCAGATGAGTGTGAAC 58.352 34.615 0.00 0.00 37.35 3.18
1876 2058 2.291996 ACTTTGGGGCCTGTAAATACCC 60.292 50.000 0.84 0.00 42.01 3.69
1968 2150 3.631453 TGTGATCCACAAGGTCTGC 57.369 52.632 0.00 0.00 41.69 4.26
2052 2239 7.011950 CGCTAACACAGTATGAAATATTGGGAA 59.988 37.037 0.00 0.00 41.97 3.97
2053 2240 8.850156 GCTAACACAGTATGAAATATTGGGAAT 58.150 33.333 0.00 0.00 41.97 3.01
2147 2335 4.572389 AGTTGGTATTCATTGAGACGATGC 59.428 41.667 0.00 0.00 0.00 3.91
2159 2347 1.009078 GACGATGCATGCTGCTAACA 58.991 50.000 20.33 0.00 45.31 2.41
2199 2388 5.302568 TCATGCTTGTCTTTGTTCAAAGGAT 59.697 36.000 20.41 4.49 0.00 3.24
2374 2566 6.829298 TGTTTGTGGTCTATAACTTGGACAAA 59.171 34.615 0.00 0.00 31.47 2.83
2570 2766 8.721478 TGTTTCTTTTCATTCTACTGCTGATAC 58.279 33.333 0.00 0.00 0.00 2.24
2665 2861 6.539826 GCCAGTTGGTTAGGTTATAATACGTT 59.460 38.462 0.00 0.00 37.57 3.99
2845 3058 7.670364 CCTGTCCAAAGATTTTGATTTAAGGT 58.330 34.615 3.24 0.00 0.00 3.50
2922 3135 5.763876 ACTACCTTGAGCCTTTCTGTTAT 57.236 39.130 0.00 0.00 0.00 1.89
2933 3146 7.930325 TGAGCCTTTCTGTTATGATCTTATCTG 59.070 37.037 0.00 0.00 0.00 2.90
2940 3153 5.303165 TGTTATGATCTTATCTGCTGCAGG 58.697 41.667 27.79 12.95 31.51 4.85
3330 4001 5.069516 ACTTGTGATGTTCCTGAGCAAATTT 59.930 36.000 0.00 0.00 0.00 1.82
3652 4329 4.737054 AGTGCAAAAGAGTGTCAAGTTTG 58.263 39.130 0.00 0.00 33.35 2.93
3771 4451 3.055747 TCCCGTTGCATGTATGACTTACA 60.056 43.478 3.87 3.87 44.71 2.41
3837 4517 8.954950 ACAATCCTCTTGTGTCTATTTCATAG 57.045 34.615 0.00 0.00 0.00 2.23
3848 4528 6.594744 TGTCTATTTCATAGGCATGTGATGT 58.405 36.000 0.00 0.00 42.15 3.06
3884 4564 3.983344 CCTGTTTTAGTGCTGACATTTGC 59.017 43.478 0.00 0.00 0.00 3.68
3908 4588 8.147704 TGCGTACTCTCAATTGGAATTATCATA 58.852 33.333 5.42 0.00 0.00 2.15
4087 4770 0.548682 AAGGGGATGCTGGAGTCTGT 60.549 55.000 0.00 0.00 0.00 3.41
4108 4791 1.142465 GGTGCAGATGATCTGGGACAT 59.858 52.381 22.69 0.00 44.43 3.06
4228 8563 3.326588 TGCTTTGGTCTTCCTTGCTAGTA 59.673 43.478 0.00 0.00 34.23 1.82
4229 8564 3.935828 GCTTTGGTCTTCCTTGCTAGTAG 59.064 47.826 0.00 0.00 34.23 2.57
4230 8565 4.563786 GCTTTGGTCTTCCTTGCTAGTAGT 60.564 45.833 0.00 0.00 34.23 2.73
4268 8603 2.639286 GTTTGCAGACCCGCTGTG 59.361 61.111 0.00 0.00 46.62 3.66
4277 8612 3.612004 GCAGACCCGCTGTGTATATAGAC 60.612 52.174 3.09 3.09 46.62 2.59
4300 8635 9.625747 AGACTTGTAGTAGTATTTAGTACTCCC 57.374 37.037 0.00 3.09 42.63 4.30
4301 8636 9.625747 GACTTGTAGTAGTATTTAGTACTCCCT 57.374 37.037 0.00 0.00 42.63 4.20
4302 8637 9.625747 ACTTGTAGTAGTATTTAGTACTCCCTC 57.374 37.037 0.00 0.00 42.63 4.30
4303 8638 9.624373 CTTGTAGTAGTATTTAGTACTCCCTCA 57.376 37.037 0.00 3.42 42.63 3.86
4304 8639 9.624373 TTGTAGTAGTATTTAGTACTCCCTCAG 57.376 37.037 0.00 0.00 42.63 3.35
4305 8640 8.776119 TGTAGTAGTATTTAGTACTCCCTCAGT 58.224 37.037 0.00 0.00 42.63 3.41
4321 8656 8.862085 ACTCCCTCAGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 31.37 4.09
4322 8657 7.883217 TCCCTCAGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
4323 8658 7.504911 TCCCTCAGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
4324 8659 8.142551 CCCTCAGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
4325 8660 9.530633 CCTCAGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
4342 8677 8.859517 AGAGCGTTTAGATCACTAAAATAGTC 57.140 34.615 0.00 0.00 45.97 2.59
4343 8678 8.467598 AGAGCGTTTAGATCACTAAAATAGTCA 58.532 33.333 0.00 0.00 45.97 3.41
4344 8679 9.250624 GAGCGTTTAGATCACTAAAATAGTCAT 57.749 33.333 0.00 0.00 45.97 3.06
4345 8680 9.250624 AGCGTTTAGATCACTAAAATAGTCATC 57.749 33.333 0.00 0.00 45.97 2.92
4346 8681 9.250624 GCGTTTAGATCACTAAAATAGTCATCT 57.749 33.333 8.62 8.62 46.42 2.90
4373 8708 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
4374 8709 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
4375 8710 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
4376 8711 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
4377 8712 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
4378 8713 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
4411 8746 1.993956 TTGCCATGCTGGTTAACTGT 58.006 45.000 5.42 0.00 40.46 3.55
4422 8757 2.105134 TGGTTAACTGTCACGGGAATGT 59.895 45.455 5.42 0.00 0.00 2.71
4436 8771 1.544537 GGAATGTGGTGTGTGCTACCA 60.545 52.381 0.00 0.00 45.52 3.25
4448 8783 2.536718 GTGCTACCAGCTGAGTTGCAG 61.537 57.143 29.47 16.56 44.50 4.41
4482 8817 2.031508 TCGCATTTCAGTTTTCGTTCCC 60.032 45.455 0.00 0.00 0.00 3.97
4512 8847 4.330250 CCTTGGCAACCTAGATGGATATG 58.670 47.826 0.00 0.00 39.71 1.78
4513 8848 3.423539 TGGCAACCTAGATGGATATGC 57.576 47.619 0.00 0.00 40.19 3.14
4546 8881 7.987458 ACGAATGAACTAGATGGATATGTTTGT 59.013 33.333 0.00 0.00 0.00 2.83
4551 8886 5.930135 ACTAGATGGATATGTTTGTCCCAC 58.070 41.667 0.00 0.00 32.32 4.61
4602 8937 3.181465 ACAACATATAGTCTCCCCTTGCG 60.181 47.826 0.00 0.00 0.00 4.85
4603 8938 2.958818 ACATATAGTCTCCCCTTGCGA 58.041 47.619 0.00 0.00 0.00 5.10
4604 8939 3.305720 ACATATAGTCTCCCCTTGCGAA 58.694 45.455 0.00 0.00 0.00 4.70
4605 8940 3.709653 ACATATAGTCTCCCCTTGCGAAA 59.290 43.478 0.00 0.00 0.00 3.46
4606 8941 2.693267 ATAGTCTCCCCTTGCGAAAC 57.307 50.000 0.00 0.00 0.00 2.78
4607 8942 1.344065 TAGTCTCCCCTTGCGAAACA 58.656 50.000 0.00 0.00 0.00 2.83
4608 8943 0.472471 AGTCTCCCCTTGCGAAACAA 59.528 50.000 0.00 0.00 36.62 2.83
4609 8944 0.591659 GTCTCCCCTTGCGAAACAAC 59.408 55.000 0.00 0.00 33.68 3.32
4610 8945 0.181587 TCTCCCCTTGCGAAACAACA 59.818 50.000 0.00 0.00 33.68 3.33
4611 8946 1.202879 TCTCCCCTTGCGAAACAACAT 60.203 47.619 0.00 0.00 33.68 2.71
4612 8947 2.039216 TCTCCCCTTGCGAAACAACATA 59.961 45.455 0.00 0.00 33.68 2.29
4679 9222 9.827411 CTGTTTAAACAAATTAAGGAGAGCTAC 57.173 33.333 20.89 0.00 38.66 3.58
4829 9372 6.238759 GGAATACAGTGACTAATTTGATGGGC 60.239 42.308 0.00 0.00 0.00 5.36
4834 9384 5.647658 CAGTGACTAATTTGATGGGCTTGTA 59.352 40.000 0.00 0.00 0.00 2.41
4865 9499 1.724545 TGTATTATGGGACGGAGGGG 58.275 55.000 0.00 0.00 0.00 4.79
4888 9527 6.183360 GGGTCATAAAGGTAAGCTGATTTCAC 60.183 42.308 0.00 0.00 0.00 3.18
4891 9530 9.109393 GTCATAAAGGTAAGCTGATTTCACATA 57.891 33.333 0.00 0.00 0.00 2.29
4924 9563 7.697710 ACATATACACATGATTTTCGCAACAAG 59.302 33.333 0.00 0.00 0.00 3.16
5084 9724 9.459640 CACCATGATGAAATAAAAGATCATGTC 57.540 33.333 15.90 0.00 45.69 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1004 1180 4.791069 GGTGGGGCGGGAGGTAGA 62.791 72.222 0.00 0.00 0.00 2.59
1467 1649 1.410004 AGACTCACGGTTGGAACAGA 58.590 50.000 0.00 0.00 42.39 3.41
1505 1687 4.040339 GGGTTCAAGAAATTGAATGGTGGT 59.960 41.667 6.69 0.00 42.20 4.16
1526 1708 2.205074 GATATGACACGAAGCACAGGG 58.795 52.381 0.00 0.00 0.00 4.45
1543 1725 7.972832 TCTTTGCGCATTAATCAAAATGTGATA 59.027 29.630 12.75 0.00 46.80 2.15
1634 1816 4.368808 GCTTTTGCTGCGTCGCGA 62.369 61.111 13.38 3.71 43.35 5.87
1666 1848 0.895530 CTTACGGACCTGGCTCTTCA 59.104 55.000 0.00 0.00 0.00 3.02
1669 1851 1.313812 CGACTTACGGACCTGGCTCT 61.314 60.000 0.00 0.00 38.46 4.09
1706 1888 0.764271 TCTCATCCACACACTTGCCA 59.236 50.000 0.00 0.00 0.00 4.92
1751 1933 5.956171 TTGATGAATCGAACTTCAGATCG 57.044 39.130 7.47 0.27 38.47 3.69
1815 1997 9.383519 TCTGAAAAATAACCAGCTATAACTCTG 57.616 33.333 0.00 0.00 0.00 3.35
1852 2034 2.286365 TTTACAGGCCCCAAAGTCAG 57.714 50.000 0.00 0.00 0.00 3.51
1876 2058 2.159653 GCTGCTTGTCAAACACCTATCG 60.160 50.000 0.00 0.00 0.00 2.92
1968 2150 7.661040 ACCAAAAGAAAGGACAGAAATGTATG 58.339 34.615 0.00 0.00 0.00 2.39
2053 2240 9.388346 CGTAAAAGAACAAAACTATGCACAATA 57.612 29.630 0.00 0.00 0.00 1.90
2147 2335 4.037089 TGATGGCTAAATGTTAGCAGCATG 59.963 41.667 18.84 0.00 42.06 4.06
2159 2347 7.959175 ACAAGCATGATAATTGATGGCTAAAT 58.041 30.769 0.00 0.00 0.00 1.40
2570 2766 3.515104 AGGGAAAATGTTATGCCCAACAG 59.485 43.478 0.00 0.00 41.48 3.16
2638 2834 5.727243 ATTATAACCTAACCAACTGGCCT 57.273 39.130 3.32 0.00 39.32 5.19
2845 3058 4.902443 TCCTTTTTGTACGCAACATCAA 57.098 36.364 0.00 0.00 38.10 2.57
2922 3135 2.251409 GCCTGCAGCAGATAAGATCA 57.749 50.000 24.90 0.00 42.97 2.92
2933 3146 2.289506 TGATATCAGATGAGCCTGCAGC 60.290 50.000 8.66 3.91 44.25 5.25
2940 3153 3.186817 GCTGCAAGTGATATCAGATGAGC 59.813 47.826 17.67 17.20 35.30 4.26
3306 3976 2.936919 TGCTCAGGAACATCACAAGT 57.063 45.000 0.00 0.00 0.00 3.16
3307 3977 4.778534 ATTTGCTCAGGAACATCACAAG 57.221 40.909 0.00 0.00 0.00 3.16
3330 4001 1.967066 CCCTACCACATGCAACCAAAA 59.033 47.619 0.00 0.00 0.00 2.44
3489 4161 9.594478 TGAAAAGAAGTCAAAAGGTTTTTATCC 57.406 29.630 0.00 0.00 0.00 2.59
3577 4253 3.706698 GTTGACTTCAGGGCAAGAAAAC 58.293 45.455 0.00 0.00 44.60 2.43
3582 4258 0.886490 AGCGTTGACTTCAGGGCAAG 60.886 55.000 6.42 0.00 44.60 4.01
3583 4259 1.148273 AGCGTTGACTTCAGGGCAA 59.852 52.632 6.42 0.00 41.27 4.52
3584 4260 1.597854 CAGCGTTGACTTCAGGGCA 60.598 57.895 0.00 0.00 0.00 5.36
3762 4442 7.503566 AGCCAGTATAAAATGCATGTAAGTCAT 59.496 33.333 0.00 0.00 37.22 3.06
3771 4451 5.603170 AGCAAAGCCAGTATAAAATGCAT 57.397 34.783 0.00 0.00 35.11 3.96
3848 4528 6.597672 CACTAAAACAGGATATTAGGTGTGCA 59.402 38.462 0.00 0.00 32.25 4.57
3908 4588 6.359804 ACAGAATATTAGGTGTGCACATGAT 58.640 36.000 24.69 12.60 0.00 2.45
4087 4770 0.543277 GTCCCAGATCATCTGCACCA 59.457 55.000 9.41 0.00 42.98 4.17
4108 4791 5.643777 GGCTAGATCTTGTAGCTCAAAACAA 59.356 40.000 14.17 0.00 42.27 2.83
4162 4845 6.610456 CACACAATGACAATGCAATGTACTA 58.390 36.000 7.55 0.00 31.12 1.82
4277 8612 9.624373 TGAGGGAGTACTAAATACTACTACAAG 57.376 37.037 0.00 0.00 44.64 3.16
4296 8631 8.024285 CGCTCTTATATTAGTTTACTGAGGGAG 58.976 40.741 0.00 0.00 35.10 4.30
4297 8632 7.504911 ACGCTCTTATATTAGTTTACTGAGGGA 59.495 37.037 0.00 0.00 36.36 4.20
4298 8633 7.659186 ACGCTCTTATATTAGTTTACTGAGGG 58.341 38.462 0.00 0.00 37.76 4.30
4299 8634 9.530633 AAACGCTCTTATATTAGTTTACTGAGG 57.469 33.333 0.00 0.00 31.14 3.86
4316 8651 9.303537 GACTATTTTAGTGATCTAAACGCTCTT 57.696 33.333 0.00 0.00 43.20 2.85
4317 8652 8.467598 TGACTATTTTAGTGATCTAAACGCTCT 58.532 33.333 0.00 0.00 43.20 4.09
4318 8653 8.630278 TGACTATTTTAGTGATCTAAACGCTC 57.370 34.615 0.00 0.00 43.20 5.03
4319 8654 9.250624 GATGACTATTTTAGTGATCTAAACGCT 57.749 33.333 6.81 0.00 43.33 5.07
4347 8682 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
4348 8683 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
4349 8684 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
4350 8685 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
4351 8686 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
4352 8687 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4353 8688 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
4354 8689 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
4355 8690 9.071276 CACTACTCCCTCCGTAAACTAATATAA 57.929 37.037 0.00 0.00 0.00 0.98
4356 8691 8.439971 TCACTACTCCCTCCGTAAACTAATATA 58.560 37.037 0.00 0.00 0.00 0.86
4357 8692 7.293073 TCACTACTCCCTCCGTAAACTAATAT 58.707 38.462 0.00 0.00 0.00 1.28
4358 8693 6.662755 TCACTACTCCCTCCGTAAACTAATA 58.337 40.000 0.00 0.00 0.00 0.98
4359 8694 5.513233 TCACTACTCCCTCCGTAAACTAAT 58.487 41.667 0.00 0.00 0.00 1.73
4360 8695 4.922206 TCACTACTCCCTCCGTAAACTAA 58.078 43.478 0.00 0.00 0.00 2.24
4361 8696 4.574674 TCACTACTCCCTCCGTAAACTA 57.425 45.455 0.00 0.00 0.00 2.24
4362 8697 3.446442 TCACTACTCCCTCCGTAAACT 57.554 47.619 0.00 0.00 0.00 2.66
4363 8698 4.732672 ATTCACTACTCCCTCCGTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
4364 8699 5.954150 AGTAATTCACTACTCCCTCCGTAAA 59.046 40.000 0.00 0.00 34.98 2.01
4365 8700 5.359009 CAGTAATTCACTACTCCCTCCGTAA 59.641 44.000 0.00 0.00 34.98 3.18
4366 8701 4.885907 CAGTAATTCACTACTCCCTCCGTA 59.114 45.833 0.00 0.00 34.98 4.02
4367 8702 3.700038 CAGTAATTCACTACTCCCTCCGT 59.300 47.826 0.00 0.00 34.98 4.69
4368 8703 3.952323 TCAGTAATTCACTACTCCCTCCG 59.048 47.826 0.00 0.00 34.98 4.63
4369 8704 5.934402 TTCAGTAATTCACTACTCCCTCC 57.066 43.478 0.00 0.00 34.98 4.30
4370 8705 6.258947 GCAATTCAGTAATTCACTACTCCCTC 59.741 42.308 0.00 0.00 34.98 4.30
4371 8706 6.116126 GCAATTCAGTAATTCACTACTCCCT 58.884 40.000 0.00 0.00 34.98 4.20
4372 8707 5.297029 GGCAATTCAGTAATTCACTACTCCC 59.703 44.000 0.00 0.00 34.98 4.30
4373 8708 5.880332 TGGCAATTCAGTAATTCACTACTCC 59.120 40.000 0.00 0.00 34.98 3.85
4374 8709 6.985188 TGGCAATTCAGTAATTCACTACTC 57.015 37.500 0.00 0.00 34.98 2.59
4375 8710 6.183360 GCATGGCAATTCAGTAATTCACTACT 60.183 38.462 0.00 0.00 34.98 2.57
4376 8711 5.973565 GCATGGCAATTCAGTAATTCACTAC 59.026 40.000 0.00 0.00 34.98 2.73
4377 8712 5.887598 AGCATGGCAATTCAGTAATTCACTA 59.112 36.000 0.00 0.00 34.98 2.74
4378 8713 4.708421 AGCATGGCAATTCAGTAATTCACT 59.292 37.500 0.00 0.00 38.32 3.41
4411 8746 0.533978 CACACACCACATTCCCGTGA 60.534 55.000 0.00 0.00 39.34 4.35
4422 8757 1.071299 CAGCTGGTAGCACACACCA 59.929 57.895 5.57 0.00 45.56 4.17
4436 8771 2.923121 TCTGAAAACTGCAACTCAGCT 58.077 42.857 8.43 0.00 46.76 4.24
4448 8783 5.687285 ACTGAAATGCGAACAATCTGAAAAC 59.313 36.000 0.00 0.00 0.00 2.43
4482 8817 1.908299 GGTTGCCAAGGGAAGGTGG 60.908 63.158 0.00 0.00 38.00 4.61
4512 8847 1.324736 CTAGTTCATTCGTGAAGGCGC 59.675 52.381 0.00 0.00 0.00 6.53
4513 8848 2.876091 TCTAGTTCATTCGTGAAGGCG 58.124 47.619 0.00 0.00 0.00 5.52
4546 8881 1.065199 CAGCAATCTAAGGCAGTGGGA 60.065 52.381 0.00 0.00 0.00 4.37
4592 8927 1.247567 ATGTTGTTTCGCAAGGGGAG 58.752 50.000 0.00 0.00 37.83 4.30
4594 8929 2.159382 ACTATGTTGTTTCGCAAGGGG 58.841 47.619 0.00 0.00 37.83 4.79
4602 8937 3.440522 GCAAGGGGAGACTATGTTGTTTC 59.559 47.826 0.00 0.00 0.00 2.78
4603 8938 3.421844 GCAAGGGGAGACTATGTTGTTT 58.578 45.455 0.00 0.00 0.00 2.83
4604 8939 2.615493 CGCAAGGGGAGACTATGTTGTT 60.615 50.000 0.00 0.00 0.00 2.83
4605 8940 1.066143 CGCAAGGGGAGACTATGTTGT 60.066 52.381 0.00 0.00 0.00 3.32
4606 8941 1.207089 TCGCAAGGGGAGACTATGTTG 59.793 52.381 0.00 0.00 38.47 3.33
4607 8942 1.568504 TCGCAAGGGGAGACTATGTT 58.431 50.000 0.00 0.00 38.47 2.71
4608 8943 1.568504 TTCGCAAGGGGAGACTATGT 58.431 50.000 0.00 0.00 38.47 2.29
4609 8944 2.280628 GTTTCGCAAGGGGAGACTATG 58.719 52.381 0.00 0.00 38.47 2.23
4610 8945 1.906574 TGTTTCGCAAGGGGAGACTAT 59.093 47.619 5.75 0.00 32.41 2.12
4611 8946 1.344065 TGTTTCGCAAGGGGAGACTA 58.656 50.000 5.75 0.00 32.41 2.59
4612 8947 0.472471 TTGTTTCGCAAGGGGAGACT 59.528 50.000 5.75 0.00 32.41 3.24
4679 9222 2.231964 ACAACCTAATGTGCCATGCTTG 59.768 45.455 0.00 0.00 30.82 4.01
4707 9250 5.308825 AGATGCTATGTTGCCTGTAATACC 58.691 41.667 0.00 0.00 0.00 2.73
4789 9332 9.295825 TCACTGTATTCCATTGATTTGTAAGTT 57.704 29.630 0.00 0.00 28.66 2.66
4841 9391 3.555168 CCTCCGTCCCATAATACAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
4847 9397 1.622312 GACCCCTCCGTCCCATAATAC 59.378 57.143 0.00 0.00 0.00 1.89
4865 9499 7.377766 TGTGAAATCAGCTTACCTTTATGAC 57.622 36.000 0.00 0.00 0.00 3.06
4891 9530 9.773328 CGAAAATCATGTGTATATGTTGAACTT 57.227 29.630 0.00 0.00 0.00 2.66
4912 9551 4.387256 CCTGTGTTTTTCTTGTTGCGAAAA 59.613 37.500 0.00 0.00 38.26 2.29
4924 9563 2.478879 CCAACGGTGTCCTGTGTTTTTC 60.479 50.000 0.00 0.00 0.00 2.29
4928 9567 0.034863 AACCAACGGTGTCCTGTGTT 60.035 50.000 0.00 0.00 35.34 3.32
5084 9724 8.642020 GTTTAGTGTTTACATACCAGAACGTAG 58.358 37.037 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.