Multiple sequence alignment - TraesCS4A01G449100

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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 TraesCS4A01G449100 chr4A 100.000 3953 0 0 1 3953 715352689 715356641 0.000000e+00 7300.0
1 TraesCS4A01G449100 chr4A 90.424 2026 171 16 1771 3778 714565190 714567210 0.000000e+00 2645.0
2 TraesCS4A01G449100 chr4A 88.604 2027 216 12 1749 3769 714764540 714766557 0.000000e+00 2449.0
3 TraesCS4A01G449100 chr4A 86.998 1892 229 16 1896 3778 714520828 714522711 0.000000e+00 2115.0
4 TraesCS4A01G449100 chr4A 97.576 495 5 1 1256 1750 714757861 714758348 0.000000e+00 841.0
5 TraesCS4A01G449100 chr4A 86.473 621 63 11 421 1030 714502623 714503233 0.000000e+00 662.0
6 TraesCS4A01G449100 chr4A 93.893 393 15 1 873 1256 714756070 714756462 5.690000e-163 584.0
7 TraesCS4A01G449100 chr4A 87.273 385 26 13 1354 1735 715297384 715297748 6.110000e-113 418.0
8 TraesCS4A01G449100 chr4A 87.879 264 26 5 1241 1501 714520076 714520336 4.960000e-79 305.0
9 TraesCS4A01G449100 chr7D 88.720 1844 205 3 1937 3778 18003705 18001863 0.000000e+00 2250.0
10 TraesCS4A01G449100 chr7D 88.177 406 41 6 2 405 18052477 18052077 9.940000e-131 477.0
11 TraesCS4A01G449100 chr7D 88.837 215 22 1 1042 1256 18044116 18043904 3.030000e-66 263.0
12 TraesCS4A01G449100 chr7D 90.909 132 9 2 421 550 18052092 18051962 1.460000e-39 174.0
13 TraesCS4A01G449100 chr7D 89.720 107 11 0 299 405 425535739 425535633 1.920000e-28 137.0
14 TraesCS4A01G449100 chrUn 88.796 1785 186 11 1749 3527 358633972 358635748 0.000000e+00 2176.0
15 TraesCS4A01G449100 chrUn 88.739 1785 187 11 1749 3527 340741210 340739434 0.000000e+00 2170.0
16 TraesCS4A01G449100 chrUn 97.576 495 5 1 1256 1750 341583973 341584460 0.000000e+00 841.0
17 TraesCS4A01G449100 chrUn 97.783 451 10 0 421 871 271101731 271101281 0.000000e+00 778.0
18 TraesCS4A01G449100 chrUn 95.577 407 16 2 1 407 271102118 271101714 0.000000e+00 651.0
19 TraesCS4A01G449100 chrUn 91.411 163 14 0 1345 1507 50594897 50594735 1.430000e-54 224.0
20 TraesCS4A01G449100 chr7A 86.197 1833 247 6 1949 3778 17425350 17423521 0.000000e+00 1978.0
21 TraesCS4A01G449100 chr7A 85.884 1849 252 9 1940 3783 18036866 18035022 0.000000e+00 1960.0
22 TraesCS4A01G449100 chr7A 84.889 1886 270 14 1905 3784 18316141 18318017 0.000000e+00 1890.0
23 TraesCS4A01G449100 chr7A 88.038 418 39 9 1354 1767 17395059 17394649 5.940000e-133 484.0
24 TraesCS4A01G449100 chr7A 80.645 310 57 2 528 836 711307321 711307014 1.840000e-58 237.0
25 TraesCS4A01G449100 chr7A 80.323 310 58 2 528 836 711310147 711309840 8.540000e-57 231.0
26 TraesCS4A01G449100 chr7A 79.355 310 61 2 528 836 711323675 711323368 8.600000e-52 215.0
27 TraesCS4A01G449100 chr7A 89.764 127 11 2 1363 1489 17867727 17867603 1.140000e-35 161.0
28 TraesCS4A01G449100 chr7A 90.083 121 10 2 1368 1487 17425799 17425680 5.290000e-34 156.0
29 TraesCS4A01G449100 chr7A 86.441 118 13 3 1374 1489 17697950 17697834 4.150000e-25 126.0
30 TraesCS4A01G449100 chr1B 95.513 156 6 1 3777 3931 504521520 504521365 8.480000e-62 248.0
31 TraesCS4A01G449100 chr1B 94.839 155 7 1 3778 3931 1847332 1847486 1.420000e-59 241.0
32 TraesCS4A01G449100 chr2A 94.872 156 8 0 3781 3936 768200847 768200692 1.100000e-60 244.0
33 TraesCS4A01G449100 chr2A 83.333 174 29 0 508 681 434982742 434982915 1.140000e-35 161.0
34 TraesCS4A01G449100 chr2A 94.340 53 2 1 419 470 622146937 622146885 3.270000e-11 80.5
35 TraesCS4A01G449100 chr6B 95.364 151 7 0 3782 3932 140098031 140097881 1.420000e-59 241.0
36 TraesCS4A01G449100 chr6B 95.364 151 6 1 3781 3930 561645359 561645209 5.110000e-59 239.0
37 TraesCS4A01G449100 chr6B 89.730 185 12 7 3764 3944 145338676 145338495 3.070000e-56 230.0
38 TraesCS4A01G449100 chr5D 93.168 161 8 2 3778 3935 216063035 216062875 2.380000e-57 233.0
39 TraesCS4A01G449100 chr4B 93.168 161 8 3 3781 3940 568662298 568662140 2.380000e-57 233.0
40 TraesCS4A01G449100 chr4B 90.909 110 7 3 299 406 394396735 394396843 1.140000e-30 145.0
41 TraesCS4A01G449100 chr2B 92.500 160 12 0 3776 3935 548773762 548773603 3.070000e-56 230.0
42 TraesCS4A01G449100 chr2B 81.675 191 35 0 473 663 397602191 397602381 4.090000e-35 159.0
43 TraesCS4A01G449100 chr2B 88.288 111 13 0 296 406 406121566 406121676 2.480000e-27 134.0
44 TraesCS4A01G449100 chr3A 77.477 333 56 14 706 1028 301324313 301324636 8.730000e-42 182.0
45 TraesCS4A01G449100 chr4D 90.351 114 8 3 295 406 122012768 122012880 3.180000e-31 147.0
46 TraesCS4A01G449100 chr1A 90.000 110 8 3 299 406 242704950 242705058 5.330000e-29 139.0
47 TraesCS4A01G449100 chr1A 89.189 111 11 1 297 406 529240029 529239919 1.920000e-28 137.0
48 TraesCS4A01G449100 chr5A 88.393 112 11 2 297 406 53626542 53626653 2.480000e-27 134.0
49 TraesCS4A01G449100 chr2D 79.394 165 34 0 473 637 328465218 328465382 2.500000e-22 117.0
50 TraesCS4A01G449100 chr7B 85.000 60 7 2 119 177 85301146 85301088 4.270000e-05 60.2


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 TraesCS4A01G449100 chr4A 715352689 715356641 3952 False 7300.0 7300 100.0000 1 3953 1 chr4A.!!$F5 3952
1 TraesCS4A01G449100 chr4A 714565190 714567210 2020 False 2645.0 2645 90.4240 1771 3778 1 chr4A.!!$F2 2007
2 TraesCS4A01G449100 chr4A 714764540 714766557 2017 False 2449.0 2449 88.6040 1749 3769 1 chr4A.!!$F3 2020
3 TraesCS4A01G449100 chr4A 714520076 714522711 2635 False 1210.0 2115 87.4385 1241 3778 2 chr4A.!!$F6 2537
4 TraesCS4A01G449100 chr4A 714756070 714758348 2278 False 712.5 841 95.7345 873 1750 2 chr4A.!!$F7 877
5 TraesCS4A01G449100 chr4A 714502623 714503233 610 False 662.0 662 86.4730 421 1030 1 chr4A.!!$F1 609
6 TraesCS4A01G449100 chr7D 18001863 18003705 1842 True 2250.0 2250 88.7200 1937 3778 1 chr7D.!!$R1 1841
7 TraesCS4A01G449100 chr7D 18051962 18052477 515 True 325.5 477 89.5430 2 550 2 chr7D.!!$R4 548
8 TraesCS4A01G449100 chrUn 358633972 358635748 1776 False 2176.0 2176 88.7960 1749 3527 1 chrUn.!!$F2 1778
9 TraesCS4A01G449100 chrUn 340739434 340741210 1776 True 2170.0 2170 88.7390 1749 3527 1 chrUn.!!$R2 1778
10 TraesCS4A01G449100 chrUn 271101281 271102118 837 True 714.5 778 96.6800 1 871 2 chrUn.!!$R3 870
11 TraesCS4A01G449100 chr7A 18035022 18036866 1844 True 1960.0 1960 85.8840 1940 3783 1 chr7A.!!$R4 1843
12 TraesCS4A01G449100 chr7A 18316141 18318017 1876 False 1890.0 1890 84.8890 1905 3784 1 chr7A.!!$F1 1879
13 TraesCS4A01G449100 chr7A 17423521 17425799 2278 True 1067.0 1978 88.1400 1368 3778 2 chr7A.!!$R6 2410
14 TraesCS4A01G449100 chr7A 711307014 711310147 3133 True 234.0 237 80.4840 528 836 2 chr7A.!!$R7 308

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
494 499 0.394565 GGGAGTGTGACTGTGAGCTT 59.605 55.000 0.0 0.0 0.0 3.74 F
997 1038 1.079127 GCCACACTACGACCATGCT 60.079 57.895 0.0 0.0 0.0 3.79 F
1513 3013 1.133136 ACACCCACACACTCCTACTCT 60.133 52.381 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 3944 0.038166 GGCTCTGGTTTCCCACATGA 59.962 55.0 0.00 0.00 35.17 3.07 R
2240 4087 1.229428 CACGTCAATGTTGCTGGAGT 58.771 50.0 0.00 0.00 0.00 3.85 R
3033 6002 0.394899 TGATCTCGAGCTCTGAGGCA 60.395 55.0 25.15 21.35 34.19 4.75 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
195 196 1.321743 CTTGCGACATGCTCTACGAAC 59.678 52.381 0.00 0.00 46.63 3.95
207 208 2.548904 CTCTACGAACCTAGATCCCACG 59.451 54.545 0.00 0.00 0.00 4.94
222 223 2.415697 CCACGTGGGTTTGTTTGATC 57.584 50.000 27.57 0.00 0.00 2.92
284 287 3.120060 CCTAGCAGTCAATGTGCAAGTTC 60.120 47.826 0.00 0.00 43.82 3.01
331 334 9.865321 TTACTACGCAACTTTATTCTTGTAGAT 57.135 29.630 3.35 0.00 33.91 1.98
344 347 6.959639 TTCTTGTAGATTTTGTTGAGGCTT 57.040 33.333 0.00 0.00 0.00 4.35
407 410 8.877864 TCAAGTGGATGACATAAGGTTTATTT 57.122 30.769 0.00 0.00 0.00 1.40
408 411 9.308000 TCAAGTGGATGACATAAGGTTTATTTT 57.692 29.630 0.00 0.00 0.00 1.82
437 440 7.282901 TGACCATGTGATGACATAAGGTTTATG 59.717 37.037 8.39 7.15 41.12 1.90
494 499 0.394565 GGGAGTGTGACTGTGAGCTT 59.605 55.000 0.00 0.00 0.00 3.74
600 610 7.607250 ACTTTAGACTAAGTGATCACCTTCTG 58.393 38.462 22.21 10.61 37.00 3.02
709 724 3.376859 TCGTGGTTGCAATAGCTATTTGG 59.623 43.478 16.46 7.75 42.74 3.28
838 854 4.344102 TGCTTGAGTAACTTGGAGTGTAGT 59.656 41.667 0.00 0.00 0.00 2.73
906 947 3.257127 GGCTTTTAACATGGCAAGGTACA 59.743 43.478 0.00 0.00 0.00 2.90
984 1025 3.344535 TCCCTATAGAATGGAGCCACA 57.655 47.619 0.00 0.00 0.00 4.17
997 1038 1.079127 GCCACACTACGACCATGCT 60.079 57.895 0.00 0.00 0.00 3.79
1003 1044 1.135112 CACTACGACCATGCTGCTACA 60.135 52.381 0.00 0.00 0.00 2.74
1058 1145 3.436704 ACACATTGGAGCATGTTAGTTCG 59.563 43.478 0.00 0.00 0.00 3.95
1071 1158 5.564213 TGTTAGTTCGTGATGTAACGTTG 57.436 39.130 11.99 0.00 43.96 4.10
1272 2759 5.533482 CGTCCATAGTTATCTCTTCCCTTG 58.467 45.833 0.00 0.00 0.00 3.61
1317 2805 9.899661 ACTCTGCGATCTATCTATAATCTAGTT 57.100 33.333 0.00 0.00 0.00 2.24
1513 3013 1.133136 ACACCCACACACTCCTACTCT 60.133 52.381 0.00 0.00 0.00 3.24
1514 3014 1.971357 CACCCACACACTCCTACTCTT 59.029 52.381 0.00 0.00 0.00 2.85
1515 3015 2.028930 CACCCACACACTCCTACTCTTC 60.029 54.545 0.00 0.00 0.00 2.87
1517 3017 2.494073 CCCACACACTCCTACTCTTCTC 59.506 54.545 0.00 0.00 0.00 2.87
1518 3018 3.426615 CCACACACTCCTACTCTTCTCT 58.573 50.000 0.00 0.00 0.00 3.10
1519 3019 3.192422 CCACACACTCCTACTCTTCTCTG 59.808 52.174 0.00 0.00 0.00 3.35
1832 3653 2.879103 TCTTGCCCTTCCTTTACTGG 57.121 50.000 0.00 0.00 0.00 4.00
1857 3678 9.232473 GGTTTAATAAACAAGAAGAGAGATGGT 57.768 33.333 16.55 0.00 43.15 3.55
1881 3705 2.755655 TCTTACCTGTGCTCTGCTCTAC 59.244 50.000 0.00 0.00 0.00 2.59
1891 3724 2.538437 CTCTGCTCTACTGCATGTGTC 58.462 52.381 0.00 0.00 42.48 3.67
2058 3905 3.625313 GGGCAAAGCAAGTAAGAGATCTC 59.375 47.826 15.29 15.29 0.00 2.75
2073 3920 3.687125 AGATCTCGCCTATGGTATCGAA 58.313 45.455 0.00 0.00 0.00 3.71
2076 3923 2.812591 TCTCGCCTATGGTATCGAAGAC 59.187 50.000 0.00 0.00 42.51 3.01
2097 3944 4.666512 ACTGCCTTGATGAGTTTATGGTT 58.333 39.130 0.00 0.00 0.00 3.67
2108 3955 5.389520 TGAGTTTATGGTTCATGTGGGAAA 58.610 37.500 0.00 0.00 0.00 3.13
2127 3974 2.202544 CAGAGCCAGTCTCGACGC 60.203 66.667 0.00 0.00 46.44 5.19
2130 3977 2.045242 AGCCAGTCTCGACGCCTA 60.045 61.111 0.00 0.00 36.20 3.93
2131 3978 1.654954 GAGCCAGTCTCGACGCCTAA 61.655 60.000 0.00 0.00 36.20 2.69
2240 4087 2.768253 AACTTGATCACCGCTGATGA 57.232 45.000 0.00 0.00 37.24 2.92
2258 4105 1.202639 TGACTCCAGCAACATTGACGT 60.203 47.619 0.00 0.00 0.00 4.34
2268 4115 3.225548 CAACATTGACGTGGTGAATTCG 58.774 45.455 0.00 0.00 39.15 3.34
2299 4146 0.250234 TATTCGCAGCCACTCAGCTT 59.750 50.000 0.00 0.00 42.61 3.74
2340 4187 2.030805 CCTTGTAGGCTTTGTTCAGCAC 60.031 50.000 0.00 0.00 42.10 4.40
2364 4211 9.177608 CACAAAGAGGAATTGATTAAGATGGTA 57.822 33.333 0.00 0.00 0.00 3.25
2376 4223 7.203218 TGATTAAGATGGTAGATGTCAACTCG 58.797 38.462 0.00 0.00 0.00 4.18
2378 4225 4.640789 AGATGGTAGATGTCAACTCGAC 57.359 45.455 0.00 0.00 45.61 4.20
2421 5039 4.740431 GTTGTTGGCATGGGCGGC 62.740 66.667 0.00 0.00 42.47 6.53
2514 5132 0.034756 CATGGGTCACCGTCTCACAA 59.965 55.000 0.00 0.00 40.75 3.33
2541 5159 8.497745 TCCTTTTCCAAGATAGAGATGCTAAAT 58.502 33.333 0.00 0.00 31.66 1.40
2599 5566 6.527372 GCTGAGAAAATGCTTGAAAGATCTTC 59.473 38.462 8.78 3.35 0.00 2.87
2625 5592 4.322123 GGGAAGTCAGTGGAAGTAGAAGAC 60.322 50.000 0.00 0.00 0.00 3.01
2660 5627 6.656632 TCTCACAAAGGAGATAGCGAATAT 57.343 37.500 0.00 0.00 38.95 1.28
2723 5690 4.096833 TGCATGCAAGTGGATCAAAGATAC 59.903 41.667 20.30 0.00 0.00 2.24
2947 5916 8.403236 GGTCAACAAAATAGTAAAGAAGTGTGT 58.597 33.333 0.00 0.00 0.00 3.72
2987 5956 1.615883 ACTCACTATAGGAGGCATGCG 59.384 52.381 12.44 0.00 36.70 4.73
3076 6045 2.356535 CCTAGCCTTGAAGCAATGAGGT 60.357 50.000 0.00 0.00 34.23 3.85
3160 6129 7.177878 TCTAAGCATCTTTCCTGAGGATTTTT 58.822 34.615 0.04 0.00 29.35 1.94
3218 6187 2.025887 CAGAGGGGTTTGTTAGAGCCAT 60.026 50.000 0.00 0.00 36.40 4.40
3304 6273 4.455533 TGATTCAACCATCAAGAAGGAACG 59.544 41.667 0.00 0.00 29.81 3.95
3521 6490 7.445121 TCAGTAACTGTGTTTGATGAGAGATT 58.555 34.615 0.00 0.00 32.61 2.40
3571 6587 2.103094 CCTAACATGAGAATGCTCCGGA 59.897 50.000 2.93 2.93 40.55 5.14
3585 6601 2.667470 CTCCGGACCTTGGATCTAGAA 58.333 52.381 0.00 0.00 34.32 2.10
3599 6615 5.769662 TGGATCTAGAAAATGCACAGTTTGT 59.230 36.000 0.19 0.00 0.00 2.83
3621 6637 7.004555 TGTAGTCACACAAAAGGATATCAGT 57.995 36.000 4.83 0.00 0.00 3.41
3675 6691 4.333926 GTGAATTTTTCTGATCCTCGAGGG 59.666 45.833 30.80 15.09 35.41 4.30
3779 6795 5.627182 ACAGAACTGCCATCTGAGATTAT 57.373 39.130 15.03 0.00 45.74 1.28
3780 6796 6.737720 ACAGAACTGCCATCTGAGATTATA 57.262 37.500 15.03 0.00 45.74 0.98
3804 6820 1.128200 AAAAAGACCAACCCAAGGGC 58.872 50.000 4.70 0.00 39.32 5.19
3807 6823 1.154430 AAGACCAACCCAAGGGCTAA 58.846 50.000 4.70 0.00 46.21 3.09
3808 6824 0.404426 AGACCAACCCAAGGGCTAAC 59.596 55.000 4.70 0.00 44.68 2.34
3809 6825 0.611062 GACCAACCCAAGGGCTAACC 60.611 60.000 4.70 0.00 39.32 2.85
3824 6840 2.779506 CTAACCCTCGTTGGCTTTTCT 58.220 47.619 0.00 0.00 33.17 2.52
3826 6842 2.067365 ACCCTCGTTGGCTTTTCTTT 57.933 45.000 0.00 0.00 0.00 2.52
3827 6843 3.217681 ACCCTCGTTGGCTTTTCTTTA 57.782 42.857 0.00 0.00 0.00 1.85
3828 6844 3.763057 ACCCTCGTTGGCTTTTCTTTAT 58.237 40.909 0.00 0.00 0.00 1.40
3829 6845 4.913784 ACCCTCGTTGGCTTTTCTTTATA 58.086 39.130 0.00 0.00 0.00 0.98
3830 6846 4.941873 ACCCTCGTTGGCTTTTCTTTATAG 59.058 41.667 0.00 0.00 0.00 1.31
3831 6847 4.335594 CCCTCGTTGGCTTTTCTTTATAGG 59.664 45.833 0.00 0.00 0.00 2.57
3834 6850 6.045072 TCGTTGGCTTTTCTTTATAGGAGA 57.955 37.500 0.00 0.00 0.00 3.71
3835 6851 6.469410 TCGTTGGCTTTTCTTTATAGGAGAA 58.531 36.000 0.00 0.00 0.00 2.87
3836 6852 6.938030 TCGTTGGCTTTTCTTTATAGGAGAAA 59.062 34.615 8.49 8.49 40.36 2.52
3837 6853 7.021790 CGTTGGCTTTTCTTTATAGGAGAAAC 58.978 38.462 10.98 4.09 41.42 2.78
3839 6855 7.923414 TGGCTTTTCTTTATAGGAGAAACTC 57.077 36.000 10.98 0.00 41.42 3.01
3847 6863 2.261671 GGAGAAACTCCGCGAGCA 59.738 61.111 8.23 0.00 41.08 4.26
3848 6864 2.095252 GGAGAAACTCCGCGAGCAC 61.095 63.158 8.23 0.00 41.08 4.40
3849 6865 2.048127 AGAAACTCCGCGAGCACC 60.048 61.111 8.23 0.00 32.04 5.01
3850 6866 2.357034 GAAACTCCGCGAGCACCA 60.357 61.111 8.23 0.00 32.04 4.17
3851 6867 2.665185 AAACTCCGCGAGCACCAC 60.665 61.111 8.23 0.00 32.04 4.16
3858 6874 4.961511 GCGAGCACCACGTGTCCA 62.962 66.667 15.65 0.00 35.75 4.02
3859 6875 2.279851 CGAGCACCACGTGTCCAA 60.280 61.111 15.65 0.00 35.75 3.53
3860 6876 2.310233 CGAGCACCACGTGTCCAAG 61.310 63.158 15.65 0.51 35.75 3.61
3861 6877 2.591715 AGCACCACGTGTCCAAGC 60.592 61.111 15.65 10.42 35.75 4.01
3863 6879 3.345808 CACCACGTGTCCAAGCCG 61.346 66.667 15.65 0.00 0.00 5.52
3866 6882 4.308458 CACGTGTCCAAGCCGGGA 62.308 66.667 7.58 0.00 34.36 5.14
3868 6884 2.046314 CGTGTCCAAGCCGGGATT 60.046 61.111 2.18 0.00 39.62 3.01
3869 6885 1.674322 CGTGTCCAAGCCGGGATTT 60.674 57.895 2.18 0.00 39.62 2.17
3870 6886 1.883021 GTGTCCAAGCCGGGATTTG 59.117 57.895 2.18 1.17 39.62 2.32
3871 6887 0.608035 GTGTCCAAGCCGGGATTTGA 60.608 55.000 2.18 4.20 39.62 2.69
3872 6888 0.111446 TGTCCAAGCCGGGATTTGAA 59.889 50.000 2.18 0.00 39.62 2.69
3873 6889 0.526211 GTCCAAGCCGGGATTTGAAC 59.474 55.000 2.18 0.36 39.62 3.18
3875 6891 0.811281 CCAAGCCGGGATTTGAACTC 59.189 55.000 2.18 0.00 0.00 3.01
3876 6892 0.447801 CAAGCCGGGATTTGAACTCG 59.552 55.000 2.18 0.00 0.00 4.18
3878 6894 4.218722 CCGGGATTTGAACTCGGG 57.781 61.111 0.00 0.00 46.21 5.14
3879 6895 1.298667 CCGGGATTTGAACTCGGGT 59.701 57.895 0.00 0.00 46.21 5.28
3880 6896 1.024579 CCGGGATTTGAACTCGGGTG 61.025 60.000 0.00 0.00 46.21 4.61
3881 6897 1.024579 CGGGATTTGAACTCGGGTGG 61.025 60.000 0.00 0.00 0.00 4.61
3882 6898 0.679960 GGGATTTGAACTCGGGTGGG 60.680 60.000 0.00 0.00 0.00 4.61
3883 6899 0.037734 GGATTTGAACTCGGGTGGGT 59.962 55.000 0.00 0.00 0.00 4.51
3884 6900 1.546998 GGATTTGAACTCGGGTGGGTT 60.547 52.381 0.00 0.00 0.00 4.11
3886 6902 0.466555 TTTGAACTCGGGTGGGTTGG 60.467 55.000 0.00 0.00 0.00 3.77
3887 6903 2.671963 GAACTCGGGTGGGTTGGC 60.672 66.667 0.00 0.00 0.00 4.52
3888 6904 3.485346 GAACTCGGGTGGGTTGGCA 62.485 63.158 0.00 0.00 0.00 4.92
3893 6909 3.615709 GGGTGGGTTGGCAGCAAC 61.616 66.667 3.14 0.71 0.00 4.17
3899 6915 2.647297 GTTGGCAGCAACCTCAGC 59.353 61.111 0.00 0.00 0.00 4.26
3900 6916 1.900498 GTTGGCAGCAACCTCAGCT 60.900 57.895 0.00 0.00 44.62 4.24
3905 6921 3.573229 AGCAACCTCAGCTGCCCA 61.573 61.111 9.47 0.00 41.61 5.36
3906 6922 3.060615 GCAACCTCAGCTGCCCAG 61.061 66.667 9.47 0.70 32.18 4.45
3938 6954 4.227134 CCCCGTCCTCGCCATCTG 62.227 72.222 0.00 0.00 35.54 2.90
3939 6955 3.147595 CCCGTCCTCGCCATCTGA 61.148 66.667 0.00 0.00 35.54 3.27
3940 6956 2.415010 CCGTCCTCGCCATCTGAG 59.585 66.667 0.00 0.00 35.54 3.35
3941 6957 2.121538 CCGTCCTCGCCATCTGAGA 61.122 63.158 0.00 0.00 35.43 3.27
3942 6958 1.459455 CCGTCCTCGCCATCTGAGAT 61.459 60.000 0.00 0.00 35.43 2.75
3943 6959 0.387202 CGTCCTCGCCATCTGAGATT 59.613 55.000 0.00 0.00 35.43 2.40
3944 6960 1.609072 CGTCCTCGCCATCTGAGATTA 59.391 52.381 0.00 0.00 35.43 1.75
3945 6961 2.230025 CGTCCTCGCCATCTGAGATTAT 59.770 50.000 0.00 0.00 35.43 1.28
3946 6962 3.305676 CGTCCTCGCCATCTGAGATTATT 60.306 47.826 0.00 0.00 35.43 1.40
3947 6963 4.082733 CGTCCTCGCCATCTGAGATTATTA 60.083 45.833 0.00 0.00 35.43 0.98
3948 6964 5.564848 CGTCCTCGCCATCTGAGATTATTAA 60.565 44.000 0.00 0.00 35.43 1.40
3949 6965 6.223852 GTCCTCGCCATCTGAGATTATTAAA 58.776 40.000 0.00 0.00 35.43 1.52
3950 6966 6.146347 GTCCTCGCCATCTGAGATTATTAAAC 59.854 42.308 0.00 0.00 35.43 2.01
3951 6967 6.042093 TCCTCGCCATCTGAGATTATTAAACT 59.958 38.462 0.00 0.00 35.43 2.66
3952 6968 6.367422 CCTCGCCATCTGAGATTATTAAACTC 59.633 42.308 6.73 6.73 35.43 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
231 234 2.420058 AAGAGGGACTAAATTGCCGG 57.580 50.000 0.00 0.00 41.55 6.13
232 235 3.134081 TCCTAAGAGGGACTAAATTGCCG 59.866 47.826 0.00 0.00 41.55 5.69
284 287 5.896073 AAACATCAATAGGTAGGAGGGAG 57.104 43.478 0.00 0.00 0.00 4.30
331 334 1.535860 GCGCTTGAAGCCTCAACAAAA 60.536 47.619 12.13 0.00 38.18 2.44
344 347 1.668919 CCTACGAAACTCTGCGCTTGA 60.669 52.381 9.73 6.21 0.00 3.02
407 410 6.493115 ACCTTATGTCATCACATGGTCAAAAA 59.507 34.615 0.00 0.00 43.54 1.94
408 411 6.009589 ACCTTATGTCATCACATGGTCAAAA 58.990 36.000 0.00 0.00 43.54 2.44
410 413 5.178096 ACCTTATGTCATCACATGGTCAA 57.822 39.130 0.00 0.00 43.54 3.18
411 414 4.842531 ACCTTATGTCATCACATGGTCA 57.157 40.909 0.00 0.00 43.54 4.02
412 415 7.498900 TCATAAACCTTATGTCATCACATGGTC 59.501 37.037 0.00 0.00 43.54 4.02
413 416 7.345691 TCATAAACCTTATGTCATCACATGGT 58.654 34.615 0.00 0.00 43.54 3.55
414 417 7.806409 TCATAAACCTTATGTCATCACATGG 57.194 36.000 0.00 0.00 43.54 3.66
415 418 9.888878 GATTCATAAACCTTATGTCATCACATG 57.111 33.333 0.00 0.00 43.54 3.21
416 419 9.071276 GGATTCATAAACCTTATGTCATCACAT 57.929 33.333 15.47 0.00 45.73 3.21
417 420 8.052141 TGGATTCATAAACCTTATGTCATCACA 58.948 33.333 15.47 11.28 36.78 3.58
418 421 8.345565 GTGGATTCATAAACCTTATGTCATCAC 58.654 37.037 15.47 11.98 0.00 3.06
419 422 8.052141 TGTGGATTCATAAACCTTATGTCATCA 58.948 33.333 15.47 7.06 0.00 3.07
494 499 5.592104 TCATCTTTAATACCGAGCTCACA 57.408 39.130 15.40 0.00 0.00 3.58
600 610 4.162509 ACAGCTAGACTAAACTCATTCCCC 59.837 45.833 0.00 0.00 0.00 4.81
609 619 3.117046 GGCGATCACAGCTAGACTAAAC 58.883 50.000 0.00 0.00 34.52 2.01
709 724 8.640091 GTGGTACCACTATAAAGCTTAACTAC 57.360 38.462 33.47 4.34 43.12 2.73
791 807 1.000274 GATTGCCCTCACACCAACAAC 60.000 52.381 0.00 0.00 0.00 3.32
838 854 4.463050 AAACCTCATAGAACCACCCAAA 57.537 40.909 0.00 0.00 0.00 3.28
906 947 5.869579 TGACTCTGTCTCCTTAATTGCTTT 58.130 37.500 0.00 0.00 33.15 3.51
997 1038 3.932710 CGGAAGCTTCTACAATTGTAGCA 59.067 43.478 32.12 24.26 45.69 3.49
1058 1145 7.932120 ATAGATCTAAGCAACGTTACATCAC 57.068 36.000 6.52 0.00 0.00 3.06
1142 1230 0.979709 CCCAGGAGATCACTCTGGCA 60.980 60.000 18.07 0.00 42.28 4.92
1272 2759 2.866726 GCTCTGGATCGGAGAGGGC 61.867 68.421 17.66 5.85 43.63 5.19
1317 2805 1.202782 AGGTCGGCTTCGCTATCTAGA 60.203 52.381 0.00 0.00 0.00 2.43
1513 3013 2.289320 GGAAACAGAGCAGAGCAGAGAA 60.289 50.000 0.00 0.00 0.00 2.87
1514 3014 1.274728 GGAAACAGAGCAGAGCAGAGA 59.725 52.381 0.00 0.00 0.00 3.10
1515 3015 1.275856 AGGAAACAGAGCAGAGCAGAG 59.724 52.381 0.00 0.00 0.00 3.35
1517 3017 2.075338 GAAGGAAACAGAGCAGAGCAG 58.925 52.381 0.00 0.00 0.00 4.24
1518 3018 1.606480 CGAAGGAAACAGAGCAGAGCA 60.606 52.381 0.00 0.00 0.00 4.26
1519 3019 1.074752 CGAAGGAAACAGAGCAGAGC 58.925 55.000 0.00 0.00 0.00 4.09
1857 3678 4.026744 AGAGCAGAGCACAGGTAAGATTA 58.973 43.478 0.00 0.00 0.00 1.75
1866 3690 0.245813 TGCAGTAGAGCAGAGCACAG 59.754 55.000 0.00 0.00 40.11 3.66
1881 3705 3.610114 GCAGTTTGTTAGGACACATGCAG 60.610 47.826 0.00 0.00 38.04 4.41
1891 3724 4.516698 AGTGTCATTCTGCAGTTTGTTAGG 59.483 41.667 14.67 0.00 0.00 2.69
2007 3854 6.418819 CCTTCAGTAGCATGTTTTTGTTCTTG 59.581 38.462 0.00 0.00 0.00 3.02
2058 3905 2.922758 GCAGTCTTCGATACCATAGGCG 60.923 54.545 0.00 0.00 0.00 5.52
2073 3920 4.018960 ACCATAAACTCATCAAGGCAGTCT 60.019 41.667 0.00 0.00 0.00 3.24
2076 3923 4.701651 TGAACCATAAACTCATCAAGGCAG 59.298 41.667 0.00 0.00 0.00 4.85
2097 3944 0.038166 GGCTCTGGTTTCCCACATGA 59.962 55.000 0.00 0.00 35.17 3.07
2108 3955 2.336478 CGTCGAGACTGGCTCTGGT 61.336 63.158 9.20 0.00 41.66 4.00
2117 3964 2.688958 AGCTTAATTAGGCGTCGAGACT 59.311 45.455 13.28 0.00 43.68 3.24
2127 3974 4.879545 TGGCGGTCTTTTAGCTTAATTAGG 59.120 41.667 0.00 0.00 0.00 2.69
2130 3977 4.035208 CGATGGCGGTCTTTTAGCTTAATT 59.965 41.667 0.00 0.00 0.00 1.40
2131 3978 3.560068 CGATGGCGGTCTTTTAGCTTAAT 59.440 43.478 0.00 0.00 0.00 1.40
2240 4087 1.229428 CACGTCAATGTTGCTGGAGT 58.771 50.000 0.00 0.00 0.00 3.85
2258 4105 2.296752 TCTTCCGTGTACGAATTCACCA 59.703 45.455 6.22 0.00 43.02 4.17
2268 4115 2.471743 GCTGCGAATATCTTCCGTGTAC 59.528 50.000 0.00 0.00 0.00 2.90
2299 4146 1.814394 GTCTGCCTCATCAATGTTGCA 59.186 47.619 8.24 8.24 35.40 4.08
2340 4187 9.618890 TCTACCATCTTAATCAATTCCTCTTTG 57.381 33.333 0.00 0.00 0.00 2.77
2349 4196 9.553064 GAGTTGACATCTACCATCTTAATCAAT 57.447 33.333 0.00 0.00 0.00 2.57
2514 5132 6.512514 AGCATCTCTATCTTGGAAAAGGAT 57.487 37.500 0.00 0.00 0.00 3.24
2541 5159 4.220382 CCCAAAAGTTGCCTAATCATGTCA 59.780 41.667 0.00 0.00 0.00 3.58
2599 5566 2.938956 ACTTCCACTGACTTCCCTTG 57.061 50.000 0.00 0.00 0.00 3.61
2614 5581 6.831868 AGATACTTGGAGAGGTCTTCTACTTC 59.168 42.308 0.00 0.00 37.67 3.01
2625 5592 4.467795 TCCTTTGTGAGATACTTGGAGAGG 59.532 45.833 0.00 0.00 0.00 3.69
2650 5617 5.961396 ACGAAGTACCTCATATTCGCTAT 57.039 39.130 11.29 0.00 46.29 2.97
2654 5621 6.034591 AGAACAACGAAGTACCTCATATTCG 58.965 40.000 10.15 10.15 45.00 3.34
2656 5623 7.383687 TCAAGAACAACGAAGTACCTCATATT 58.616 34.615 0.00 0.00 45.00 1.28
2660 5627 4.659111 TCAAGAACAACGAAGTACCTCA 57.341 40.909 0.00 0.00 45.00 3.86
2723 5690 6.861065 TGTTGTTTCTACTAGGAAAAGCAG 57.139 37.500 0.00 0.00 37.02 4.24
2947 5916 2.203877 AGCCAACGGTAGACCCCA 60.204 61.111 0.00 0.00 0.00 4.96
3033 6002 0.394899 TGATCTCGAGCTCTGAGGCA 60.395 55.000 25.15 21.35 34.19 4.75
3034 6003 0.743688 TTGATCTCGAGCTCTGAGGC 59.256 55.000 25.15 19.82 34.19 4.70
3076 6045 8.630917 GTGATTGTAGCTTAGAGTAACTATCCA 58.369 37.037 0.00 0.00 0.00 3.41
3106 6075 5.354842 AAGCATGACTTGAGATGAGATGA 57.645 39.130 0.00 0.00 37.17 2.92
3160 6129 7.054751 TCTATCAGACGTCTCCTTTTGATCTA 58.945 38.462 16.96 4.50 0.00 1.98
3218 6187 1.612146 TCAATCCTCACCCGAGCCA 60.612 57.895 0.00 0.00 38.00 4.75
3223 6192 0.833287 ACATCCTCAATCCTCACCCG 59.167 55.000 0.00 0.00 0.00 5.28
3304 6273 5.065346 GGCAGCTCTTAACAATTCCTTCTAC 59.935 44.000 0.00 0.00 0.00 2.59
3521 6490 1.215173 CTGAAGGTGATGGCCCCAATA 59.785 52.381 0.00 0.00 0.00 1.90
3571 6587 4.922206 TGTGCATTTTCTAGATCCAAGGT 58.078 39.130 0.00 0.00 0.00 3.50
3585 6601 4.397730 TGTGTGACTACAAACTGTGCATTT 59.602 37.500 0.00 0.00 38.82 2.32
3599 6615 8.590204 TGTTACTGATATCCTTTTGTGTGACTA 58.410 33.333 0.00 0.00 0.00 2.59
3621 6637 4.839121 AGTGGCGAAACAATCCTATGTTA 58.161 39.130 0.00 0.00 42.49 2.41
3709 6725 2.961741 TGTGCAAGCCTTGTAATTTCCA 59.038 40.909 6.28 0.00 0.00 3.53
3785 6801 1.128200 GCCCTTGGGTTGGTCTTTTT 58.872 50.000 7.61 0.00 0.00 1.94
3786 6802 0.264657 AGCCCTTGGGTTGGTCTTTT 59.735 50.000 7.61 0.00 0.00 2.27
3788 6804 1.154430 TTAGCCCTTGGGTTGGTCTT 58.846 50.000 7.61 0.00 34.28 3.01
3789 6805 0.404426 GTTAGCCCTTGGGTTGGTCT 59.596 55.000 7.61 0.00 34.28 3.85
3790 6806 0.611062 GGTTAGCCCTTGGGTTGGTC 60.611 60.000 7.61 0.00 34.28 4.02
3791 6807 1.463375 GGTTAGCCCTTGGGTTGGT 59.537 57.895 7.61 0.00 34.28 3.67
3792 6808 4.434483 GGTTAGCCCTTGGGTTGG 57.566 61.111 7.61 0.00 34.28 3.77
3808 6824 4.335594 CCTATAAAGAAAAGCCAACGAGGG 59.664 45.833 0.00 0.00 38.09 4.30
3809 6825 5.183228 TCCTATAAAGAAAAGCCAACGAGG 58.817 41.667 0.00 0.00 41.84 4.63
3810 6826 6.106673 TCTCCTATAAAGAAAAGCCAACGAG 58.893 40.000 0.00 0.00 0.00 4.18
3811 6827 6.045072 TCTCCTATAAAGAAAAGCCAACGA 57.955 37.500 0.00 0.00 0.00 3.85
3813 6829 8.112016 AGTTTCTCCTATAAAGAAAAGCCAAC 57.888 34.615 10.15 1.39 42.63 3.77
3815 6831 6.884836 GGAGTTTCTCCTATAAAGAAAAGCCA 59.115 38.462 8.38 0.00 46.41 4.75
3830 6846 2.095252 GTGCTCGCGGAGTTTCTCC 61.095 63.158 6.13 5.79 46.44 3.71
3831 6847 2.095252 GGTGCTCGCGGAGTTTCTC 61.095 63.158 6.13 0.00 31.39 2.87
3834 6850 2.665185 GTGGTGCTCGCGGAGTTT 60.665 61.111 6.13 0.00 31.39 2.66
3842 6858 2.279851 TTGGACACGTGGTGCTCG 60.280 61.111 21.57 0.00 38.87 5.03
3843 6859 2.607892 GCTTGGACACGTGGTGCTC 61.608 63.158 21.57 7.97 38.87 4.26
3844 6860 2.591715 GCTTGGACACGTGGTGCT 60.592 61.111 21.57 0.00 38.87 4.40
3846 6862 3.345808 CGGCTTGGACACGTGGTG 61.346 66.667 21.57 5.88 39.75 4.17
3847 6863 4.619227 CCGGCTTGGACACGTGGT 62.619 66.667 21.57 5.35 42.00 4.16
3849 6865 3.605749 ATCCCGGCTTGGACACGTG 62.606 63.158 15.48 15.48 42.00 4.49
3850 6866 2.406002 AAATCCCGGCTTGGACACGT 62.406 55.000 0.00 0.00 42.00 4.49
3851 6867 1.674322 AAATCCCGGCTTGGACACG 60.674 57.895 0.00 0.00 42.00 4.49
3853 6869 0.111446 TTCAAATCCCGGCTTGGACA 59.889 50.000 0.00 0.00 42.00 4.02
3854 6870 0.526211 GTTCAAATCCCGGCTTGGAC 59.474 55.000 0.00 0.00 42.00 4.02
3856 6872 0.811281 GAGTTCAAATCCCGGCTTGG 59.189 55.000 0.00 0.00 37.55 3.61
3857 6873 0.447801 CGAGTTCAAATCCCGGCTTG 59.552 55.000 0.00 0.00 0.00 4.01
3858 6874 0.676782 CCGAGTTCAAATCCCGGCTT 60.677 55.000 0.00 0.00 33.47 4.35
3859 6875 1.078426 CCGAGTTCAAATCCCGGCT 60.078 57.895 0.00 0.00 33.47 5.52
3860 6876 2.112815 CCCGAGTTCAAATCCCGGC 61.113 63.158 0.00 0.00 38.92 6.13
3861 6877 1.024579 CACCCGAGTTCAAATCCCGG 61.025 60.000 0.00 0.00 39.85 5.73
3863 6879 0.679960 CCCACCCGAGTTCAAATCCC 60.680 60.000 0.00 0.00 0.00 3.85
3865 6881 1.539827 CAACCCACCCGAGTTCAAATC 59.460 52.381 0.00 0.00 0.00 2.17
3866 6882 1.616159 CAACCCACCCGAGTTCAAAT 58.384 50.000 0.00 0.00 0.00 2.32
3868 6884 1.149627 CCAACCCACCCGAGTTCAA 59.850 57.895 0.00 0.00 0.00 2.69
3869 6885 2.833227 CCAACCCACCCGAGTTCA 59.167 61.111 0.00 0.00 0.00 3.18
3870 6886 2.671963 GCCAACCCACCCGAGTTC 60.672 66.667 0.00 0.00 0.00 3.01
3871 6887 3.491598 CTGCCAACCCACCCGAGTT 62.492 63.158 0.00 0.00 0.00 3.01
3872 6888 3.953775 CTGCCAACCCACCCGAGT 61.954 66.667 0.00 0.00 0.00 4.18
3876 6892 3.615709 GTTGCTGCCAACCCACCC 61.616 66.667 0.00 0.00 44.37 4.61
3883 6899 2.517414 AGCTGAGGTTGCTGCCAA 59.483 55.556 0.00 0.00 39.56 4.52
3888 6904 3.564345 CTGGGCAGCTGAGGTTGCT 62.564 63.158 20.43 0.00 46.51 3.91
3921 6937 4.227134 CAGATGGCGAGGACGGGG 62.227 72.222 0.00 0.00 40.15 5.73
3922 6938 3.144120 CTCAGATGGCGAGGACGGG 62.144 68.421 0.00 0.00 40.15 5.28
3923 6939 1.459455 ATCTCAGATGGCGAGGACGG 61.459 60.000 0.00 0.00 40.15 4.79
3924 6940 0.387202 AATCTCAGATGGCGAGGACG 59.613 55.000 0.00 0.00 42.93 4.79
3925 6941 3.951775 ATAATCTCAGATGGCGAGGAC 57.048 47.619 0.00 0.00 0.00 3.85
3926 6942 6.042093 AGTTTAATAATCTCAGATGGCGAGGA 59.958 38.462 0.00 0.00 0.00 3.71
3927 6943 6.226787 AGTTTAATAATCTCAGATGGCGAGG 58.773 40.000 0.00 0.00 0.00 4.63
3928 6944 7.344910 GAGTTTAATAATCTCAGATGGCGAG 57.655 40.000 6.29 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.