Multiple sequence alignment - TraesCS3A01G274100

Loading Multiple Alignment...

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 TraesCS3A01G274100 chr3A 100.000 3658 0 0 1 3658 502844050 502840393 0.000000e+00 6756.0
1 TraesCS3A01G274100 chr3A 89.429 350 33 3 107 455 502910200 502909854 4.340000e-119 438.0
2 TraesCS3A01G274100 chr3D 90.510 1960 107 32 3 1931 378933481 378931570 0.000000e+00 2516.0
3 TraesCS3A01G274100 chr3D 94.466 759 28 3 1923 2670 378929925 378929170 0.000000e+00 1157.0
4 TraesCS3A01G274100 chr3D 89.149 811 72 11 2855 3658 378929081 378928280 0.000000e+00 996.0
5 TraesCS3A01G274100 chr3D 78.981 314 54 11 151 455 313296502 313296812 1.720000e-48 204.0
6 TraesCS3A01G274100 chr3D 92.453 106 6 2 2758 2862 39333679 39333783 2.280000e-32 150.0
7 TraesCS3A01G274100 chr3B 88.496 1582 68 44 1223 2772 494077296 494075797 0.000000e+00 1808.0
8 TraesCS3A01G274100 chr3B 91.496 682 49 3 2979 3658 494075581 494074907 0.000000e+00 929.0
9 TraesCS3A01G274100 chr3B 86.453 716 52 28 510 1205 494078038 494077348 0.000000e+00 743.0
10 TraesCS3A01G274100 chr3B 93.333 105 5 2 2771 2875 256530599 256530497 1.760000e-33 154.0
11 TraesCS3A01G274100 chr3B 91.304 115 6 2 2861 2975 494075801 494075691 1.760000e-33 154.0
12 TraesCS3A01G274100 chrUn 80.274 365 49 18 107 455 104485812 104486169 1.690000e-63 254.0
13 TraesCS3A01G274100 chrUn 77.035 344 67 10 118 456 302505645 302505309 1.730000e-43 187.0
14 TraesCS3A01G274100 chrUn 77.035 344 67 10 118 456 302523751 302523415 1.730000e-43 187.0
15 TraesCS3A01G274100 chr1B 87.330 221 22 6 238 455 168625640 168625423 7.840000e-62 248.0
16 TraesCS3A01G274100 chr1B 85.714 119 16 1 496 613 3240086 3239968 1.380000e-24 124.0
17 TraesCS3A01G274100 chr1B 84.615 117 15 3 496 610 480419980 480420095 2.990000e-21 113.0
18 TraesCS3A01G274100 chr1B 82.927 123 17 4 496 615 568973231 568973352 1.390000e-19 108.0
19 TraesCS3A01G274100 chr6D 78.611 360 50 19 107 457 227385962 227386303 2.860000e-51 213.0
20 TraesCS3A01G274100 chr7A 78.134 343 62 12 120 455 617033852 617034188 4.790000e-49 206.0
21 TraesCS3A01G274100 chr7A 77.933 358 58 16 107 455 704376592 704376247 1.720000e-48 204.0
22 TraesCS3A01G274100 chr7A 83.051 118 19 1 496 612 653631156 653631273 5.000000e-19 106.0
23 TraesCS3A01G274100 chr5D 96.970 99 3 0 2768 2866 302394851 302394753 2.260000e-37 167.0
24 TraesCS3A01G274100 chr5D 82.787 122 19 2 496 615 473359768 473359889 1.390000e-19 108.0
25 TraesCS3A01G274100 chr5A 98.936 94 0 1 2765 2857 654404372 654404465 2.260000e-37 167.0
26 TraesCS3A01G274100 chr6A 100.000 89 0 0 2770 2858 346347092 346347004 8.130000e-37 165.0
27 TraesCS3A01G274100 chr6A 94.118 102 5 1 2766 2866 1841220 1841119 1.760000e-33 154.0
28 TraesCS3A01G274100 chr2A 96.842 95 3 0 2769 2863 14024413 14024319 3.780000e-35 159.0
29 TraesCS3A01G274100 chr2A 93.578 109 4 3 2765 2872 668087563 668087669 3.780000e-35 159.0
30 TraesCS3A01G274100 chr2A 82.955 88 14 1 3340 3426 118472827 118472740 1.090000e-10 78.7
31 TraesCS3A01G274100 chr7D 94.231 104 5 1 2766 2868 124168221 124168118 1.360000e-34 158.0
32 TraesCS3A01G274100 chr5B 82.787 122 19 2 496 615 402870295 402870174 1.390000e-19 108.0
33 TraesCS3A01G274100 chr7B 74.713 261 55 9 3339 3594 557149269 557149015 5.000000e-19 106.0
34 TraesCS3A01G274100 chr2B 83.051 118 19 1 496 612 794701334 794701451 5.000000e-19 106.0
35 TraesCS3A01G274100 chr4A 81.600 125 21 2 496 619 660676628 660676751 6.460000e-18 102.0


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 TraesCS3A01G274100 chr3A 502840393 502844050 3657 True 6756.000000 6756 100.00000 1 3658 1 chr3A.!!$R1 3657
1 TraesCS3A01G274100 chr3D 378928280 378933481 5201 True 1556.333333 2516 91.37500 3 3658 3 chr3D.!!$R1 3655
2 TraesCS3A01G274100 chr3B 494074907 494078038 3131 True 908.500000 1808 89.43725 510 3658 4 chr3B.!!$R2 3148

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
938 969 0.037303 AAGGATCACACACCCAGCTG 59.963 55.0 6.78 6.78 0.0 4.24 F
1221 1289 0.368907 CGTTCCGTAGCCAATTCGTG 59.631 55.0 0.00 0.00 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 3808 0.397254 ACTGGTCTGGTCGGGATAGG 60.397 60.0 0.0 0.0 0.0 2.57 R
2874 4635 1.029947 GCACAACCTACAATCCCCGG 61.030 60.0 0.0 0.0 0.0 5.73 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
56 57 1.144913 TGGGAGGGGAAAAGTTCTGTG 59.855 52.381 0.00 0.00 0.00 3.66
73 74 5.080969 TCTGTGATTTCTTTACTACCCGG 57.919 43.478 0.00 0.00 0.00 5.73
93 94 4.363999 CGGAACATCTAAGCCTAGAACAG 58.636 47.826 0.00 0.00 37.70 3.16
226 227 0.902984 ATGACGGTGAGTGGGCAGTA 60.903 55.000 0.00 0.00 0.00 2.74
233 234 4.087892 AGTGGGCAGTAGCGGCAG 62.088 66.667 1.45 0.00 43.41 4.85
236 237 4.537433 GGGCAGTAGCGGCAGAGG 62.537 72.222 1.45 0.00 43.41 3.69
248 249 1.255667 GGCAGAGGTTCCCGTCACTA 61.256 60.000 0.00 0.00 0.00 2.74
250 251 1.254026 CAGAGGTTCCCGTCACTACA 58.746 55.000 0.00 0.00 0.00 2.74
279 280 3.703420 CCTAGATCGGTAGGTTTTGTCG 58.297 50.000 0.00 0.00 35.67 4.35
286 287 1.073548 TAGGTTTTGTCGGTGGGGC 59.926 57.895 0.00 0.00 0.00 5.80
288 289 1.073548 GGTTTTGTCGGTGGGGCTA 59.926 57.895 0.00 0.00 0.00 3.93
315 316 1.779683 GCGACAAACCTCGTAGTGC 59.220 57.895 0.00 0.00 35.99 4.40
351 352 2.233922 TCCTCTTTATATAGCCCAGCGC 59.766 50.000 0.00 0.00 37.98 5.92
354 355 2.496070 TCTTTATATAGCCCAGCGCGAT 59.504 45.455 12.10 0.00 44.76 4.58
372 374 1.002087 GATAGGGGCCGTCAACCATAG 59.998 57.143 0.00 0.00 0.00 2.23
386 388 1.691219 CATAGTGGGTTGGGTGCCT 59.309 57.895 0.00 0.00 0.00 4.75
394 396 1.002624 GTTGGGTGCCTCCGATCAA 60.003 57.895 0.00 0.00 37.00 2.57
404 406 1.610102 CCTCCGATCAAGGCATGGATC 60.610 57.143 5.63 5.63 37.22 3.36
457 459 4.392138 CGGGAAGAGATCAACCTAACAAAC 59.608 45.833 0.00 0.00 0.00 2.93
467 469 3.975168 ACCTAACAAACGGTGCTATCT 57.025 42.857 0.00 0.00 30.90 1.98
468 470 3.596214 ACCTAACAAACGGTGCTATCTG 58.404 45.455 0.00 0.00 30.90 2.90
478 480 5.392767 ACGGTGCTATCTGGATAATACTG 57.607 43.478 0.00 9.32 0.00 2.74
479 481 4.177026 CGGTGCTATCTGGATAATACTGC 58.823 47.826 0.00 0.00 0.00 4.40
483 494 5.583854 GTGCTATCTGGATAATACTGCCATG 59.416 44.000 0.00 0.00 0.00 3.66
494 505 4.695993 TGCCATGCGCTCCGAACA 62.696 61.111 9.73 0.00 38.78 3.18
497 508 2.034879 CCATGCGCTCCGAACAACT 61.035 57.895 9.73 0.00 0.00 3.16
502 513 2.437343 CGCTCCGAACAACTCGCTC 61.437 63.158 0.00 0.00 46.71 5.03
503 514 2.437343 GCTCCGAACAACTCGCTCG 61.437 63.158 0.00 0.00 46.71 5.03
507 518 1.081376 CGAACAACTCGCTCGGTCT 60.081 57.895 0.00 0.00 41.49 3.85
515 526 2.877335 ACTCGCTCGGTCTGAAAATAC 58.123 47.619 0.00 0.00 0.00 1.89
518 529 4.157289 ACTCGCTCGGTCTGAAAATACTTA 59.843 41.667 0.00 0.00 0.00 2.24
520 531 5.657474 TCGCTCGGTCTGAAAATACTTATT 58.343 37.500 0.00 0.00 0.00 1.40
522 533 5.518847 CGCTCGGTCTGAAAATACTTATTGA 59.481 40.000 0.00 0.00 0.00 2.57
523 534 6.035650 CGCTCGGTCTGAAAATACTTATTGAA 59.964 38.462 0.00 0.00 0.00 2.69
524 535 7.402640 GCTCGGTCTGAAAATACTTATTGAAG 58.597 38.462 0.00 0.00 38.76 3.02
594 605 5.854010 ATCCATTTCTGCGACTAGTCTTA 57.146 39.130 20.34 8.33 0.00 2.10
617 628 5.365619 ACACACGAAGGAAGTATTTGTCTT 58.634 37.500 0.00 0.00 0.00 3.01
619 630 4.755123 ACACGAAGGAAGTATTTGTCTTGG 59.245 41.667 0.00 0.00 0.00 3.61
620 631 4.994852 CACGAAGGAAGTATTTGTCTTGGA 59.005 41.667 0.00 0.00 0.00 3.53
727 738 3.611674 CCAACCAACAACCCGGCC 61.612 66.667 0.00 0.00 0.00 6.13
728 739 3.611674 CAACCAACAACCCGGCCC 61.612 66.667 0.00 0.00 0.00 5.80
732 743 4.596585 CAACAACCCGGCCCCACT 62.597 66.667 0.00 0.00 0.00 4.00
745 767 1.740285 CCCACTAATCCCGTCTCCG 59.260 63.158 0.00 0.00 0.00 4.63
758 780 1.600013 CGTCTCCGATCGTCTCATCTT 59.400 52.381 15.09 0.00 35.63 2.40
902 924 1.276421 AGAGCACCGTTGAGCTAACAT 59.724 47.619 0.00 0.00 42.04 2.71
930 961 2.369860 AGCACAGAGAAAGGATCACACA 59.630 45.455 0.00 0.00 0.00 3.72
938 969 0.037303 AAGGATCACACACCCAGCTG 59.963 55.000 6.78 6.78 0.00 4.24
979 1010 2.490903 CCAAGAGATCACAAGCCCAAAG 59.509 50.000 0.00 0.00 0.00 2.77
997 1028 3.751479 AAGCACACAGACATACACTCA 57.249 42.857 0.00 0.00 0.00 3.41
998 1029 3.309961 AGCACACAGACATACACTCAG 57.690 47.619 0.00 0.00 0.00 3.35
1083 1114 1.152839 GGAGGGAGAGACGGAGAGG 60.153 68.421 0.00 0.00 0.00 3.69
1207 1241 2.563261 AAGTTTTCCTCCTCCGTTCC 57.437 50.000 0.00 0.00 0.00 3.62
1216 1250 0.974010 TCCTCCGTTCCGTAGCCAAT 60.974 55.000 0.00 0.00 0.00 3.16
1221 1289 0.368907 CGTTCCGTAGCCAATTCGTG 59.631 55.000 0.00 0.00 0.00 4.35
1274 1342 1.849975 ATGTCTGCTTGCAGGAGGCT 61.850 55.000 20.62 0.00 39.18 4.58
1336 1404 3.151022 GGAGGAGGCCGTGGAGAG 61.151 72.222 0.00 0.00 0.00 3.20
1511 1579 2.907042 CCTGGATATCCCCTCAGGTAAC 59.093 54.545 19.34 0.00 41.21 2.50
1551 1619 1.982958 GTGGTTGGGTTCCTCCTAAGA 59.017 52.381 0.00 0.00 37.35 2.10
1592 1666 7.640240 CGTAATTAATTTAGTGAAAGAGCTGGC 59.360 37.037 5.91 0.00 0.00 4.85
1593 1667 7.709149 AATTAATTTAGTGAAAGAGCTGGCT 57.291 32.000 0.00 0.00 0.00 4.75
1594 1668 6.500684 TTAATTTAGTGAAAGAGCTGGCTG 57.499 37.500 0.00 0.00 0.00 4.85
1595 1669 3.492102 TTTAGTGAAAGAGCTGGCTGT 57.508 42.857 0.00 0.00 0.00 4.40
1596 1670 3.492102 TTAGTGAAAGAGCTGGCTGTT 57.508 42.857 0.00 0.00 0.00 3.16
1621 1695 0.389426 CCAGCAGAAAAGTGCATGCC 60.389 55.000 16.68 6.65 46.60 4.40
1684 1768 1.301009 GTGCCGATTCGAGGGATCC 60.301 63.158 7.83 1.92 0.00 3.36
1687 1771 1.007271 CCGATTCGAGGGATCCGTG 60.007 63.158 12.68 4.70 0.00 4.94
1703 1787 4.079980 TCCGTGTTTTGATCCTTCTGAA 57.920 40.909 0.00 0.00 0.00 3.02
1704 1788 4.651778 TCCGTGTTTTGATCCTTCTGAAT 58.348 39.130 0.00 0.00 0.00 2.57
1705 1789 5.070001 TCCGTGTTTTGATCCTTCTGAATT 58.930 37.500 0.00 0.00 0.00 2.17
1706 1790 5.181245 TCCGTGTTTTGATCCTTCTGAATTC 59.819 40.000 0.00 0.00 0.00 2.17
1707 1791 5.182001 CCGTGTTTTGATCCTTCTGAATTCT 59.818 40.000 7.05 0.00 0.00 2.40
1708 1792 6.082338 CGTGTTTTGATCCTTCTGAATTCTG 58.918 40.000 7.05 6.50 0.00 3.02
1709 1793 6.073058 CGTGTTTTGATCCTTCTGAATTCTGA 60.073 38.462 10.68 10.68 0.00 3.27
1732 1816 4.738528 GAAGTGTTCTTCGTTTTGTTGC 57.261 40.909 0.00 0.00 40.24 4.17
1752 1837 3.186409 TGCGCTGTTTAGAGTTGATGAAC 59.814 43.478 9.73 0.00 0.00 3.18
1797 1885 8.436046 ACTAACCATAGTAGTAGAACTTCTCG 57.564 38.462 0.00 0.00 40.62 4.04
1798 1886 8.046107 ACTAACCATAGTAGTAGAACTTCTCGT 58.954 37.037 0.00 0.00 40.62 4.18
1799 1887 7.700022 AACCATAGTAGTAGAACTTCTCGTT 57.300 36.000 0.00 0.00 38.91 3.85
1826 1914 9.557061 AAAGAAGTGGGTAAGAAAAAGTAGTAG 57.443 33.333 0.00 0.00 0.00 2.57
1827 1915 8.260099 AGAAGTGGGTAAGAAAAAGTAGTAGT 57.740 34.615 0.00 0.00 0.00 2.73
1828 1916 9.372189 AGAAGTGGGTAAGAAAAAGTAGTAGTA 57.628 33.333 0.00 0.00 0.00 1.82
1903 1995 6.994421 ATTAAAAGTGTGTGGGAAAAGGAT 57.006 33.333 0.00 0.00 0.00 3.24
1973 3715 2.029307 GACCTGGTCATCCTACGCCC 62.029 65.000 21.70 0.00 32.09 6.13
2002 3744 3.930848 ACGGACGCTTCCAAGTAAATTAG 59.069 43.478 10.24 0.00 43.00 1.73
2038 3780 2.222027 GCCGTCTCCATTATTTCCTGG 58.778 52.381 0.00 0.00 0.00 4.45
2066 3808 2.727798 GTGACATGAACTTGCATTGCAC 59.272 45.455 11.66 0.00 38.71 4.57
2070 3812 3.765511 ACATGAACTTGCATTGCACCTAT 59.234 39.130 11.66 0.00 38.71 2.57
2114 3856 7.118680 ACCAGATGTTATTACACCACGTTTAAG 59.881 37.037 0.00 0.00 37.03 1.85
2141 3894 0.917939 CCAAAACCGCACGACAAAAC 59.082 50.000 0.00 0.00 0.00 2.43
2154 3907 2.116366 GACAAAACGACACATGCCAAC 58.884 47.619 0.00 0.00 0.00 3.77
2171 3924 4.067016 CCCGAAAACCGCACGTCG 62.067 66.667 0.00 0.00 36.84 5.12
2218 3971 1.779569 TCGAAGCTGACGTTTTCCTC 58.220 50.000 12.10 0.00 0.00 3.71
2679 4440 2.046023 TGCATGGCGTCAAGAGGG 60.046 61.111 0.00 0.00 0.00 4.30
2708 4469 1.731709 CCATGGTGTCACGTGTATGTG 59.268 52.381 16.51 8.20 41.28 3.21
2719 4480 3.376859 CACGTGTATGTGCCCATGTTATT 59.623 43.478 7.58 0.00 32.31 1.40
2720 4481 4.572795 CACGTGTATGTGCCCATGTTATTA 59.427 41.667 7.58 0.00 32.31 0.98
2721 4482 5.238432 CACGTGTATGTGCCCATGTTATTAT 59.762 40.000 7.58 0.00 32.31 1.28
2722 4483 6.425417 CACGTGTATGTGCCCATGTTATTATA 59.575 38.462 7.58 0.00 32.31 0.98
2723 4484 6.649141 ACGTGTATGTGCCCATGTTATTATAG 59.351 38.462 0.00 0.00 32.29 1.31
2724 4485 6.871492 CGTGTATGTGCCCATGTTATTATAGA 59.129 38.462 0.00 0.00 32.29 1.98
2725 4486 7.148639 CGTGTATGTGCCCATGTTATTATAGAC 60.149 40.741 0.00 0.00 32.29 2.59
2726 4487 7.119262 GTGTATGTGCCCATGTTATTATAGACC 59.881 40.741 0.00 0.00 32.29 3.85
2757 4518 2.584064 CATGCCGGGCACTGTAGA 59.416 61.111 26.48 0.00 43.04 2.59
2762 4523 2.125106 CGGGCACTGTAGAAGGCC 60.125 66.667 0.00 0.00 43.88 5.19
2764 4525 1.609783 GGGCACTGTAGAAGGCCAT 59.390 57.895 5.01 0.00 46.32 4.40
2767 4528 1.486726 GGCACTGTAGAAGGCCATAGT 59.513 52.381 5.01 0.00 40.26 2.12
2768 4529 2.698797 GGCACTGTAGAAGGCCATAGTA 59.301 50.000 5.01 0.00 40.26 1.82
2769 4530 3.243907 GGCACTGTAGAAGGCCATAGTAG 60.244 52.174 5.01 0.00 40.26 2.57
2770 4531 3.385111 GCACTGTAGAAGGCCATAGTAGT 59.615 47.826 5.01 0.00 0.00 2.73
2771 4532 4.583489 GCACTGTAGAAGGCCATAGTAGTA 59.417 45.833 5.01 0.00 0.00 1.82
2772 4533 5.507650 GCACTGTAGAAGGCCATAGTAGTAC 60.508 48.000 5.01 0.00 0.00 2.73
2773 4534 5.828859 CACTGTAGAAGGCCATAGTAGTACT 59.171 44.000 5.01 8.14 0.00 2.73
2774 4535 6.321690 CACTGTAGAAGGCCATAGTAGTACTT 59.678 42.308 8.40 0.00 0.00 2.24
2775 4536 6.546772 ACTGTAGAAGGCCATAGTAGTACTTC 59.453 42.308 8.40 0.00 35.72 3.01
2776 4537 5.832060 TGTAGAAGGCCATAGTAGTACTTCC 59.168 44.000 8.40 5.45 36.02 3.46
2777 4538 5.145513 AGAAGGCCATAGTAGTACTTCCT 57.854 43.478 8.40 7.56 36.02 3.36
2778 4539 5.141910 AGAAGGCCATAGTAGTACTTCCTC 58.858 45.833 8.40 5.46 36.02 3.71
2779 4540 3.847081 AGGCCATAGTAGTACTTCCTCC 58.153 50.000 8.40 5.79 0.00 4.30
2780 4541 2.557490 GGCCATAGTAGTACTTCCTCCG 59.443 54.545 8.40 0.00 0.00 4.63
2781 4542 3.220940 GCCATAGTAGTACTTCCTCCGT 58.779 50.000 8.40 0.00 0.00 4.69
2782 4543 4.392940 GCCATAGTAGTACTTCCTCCGTA 58.607 47.826 8.40 0.00 0.00 4.02
2783 4544 4.823989 GCCATAGTAGTACTTCCTCCGTAA 59.176 45.833 8.40 0.00 0.00 3.18
2784 4545 5.300286 GCCATAGTAGTACTTCCTCCGTAAA 59.700 44.000 8.40 0.00 0.00 2.01
2785 4546 6.733145 CCATAGTAGTACTTCCTCCGTAAAC 58.267 44.000 8.40 0.00 0.00 2.01
2786 4547 6.545298 CCATAGTAGTACTTCCTCCGTAAACT 59.455 42.308 8.40 0.00 0.00 2.66
2787 4548 7.716998 CCATAGTAGTACTTCCTCCGTAAACTA 59.283 40.741 8.40 0.00 0.00 2.24
2788 4549 9.113838 CATAGTAGTACTTCCTCCGTAAACTAA 57.886 37.037 8.40 0.00 0.00 2.24
2789 4550 9.859152 ATAGTAGTACTTCCTCCGTAAACTAAT 57.141 33.333 8.40 0.00 0.00 1.73
2791 4552 9.859152 AGTAGTACTTCCTCCGTAAACTAATAT 57.141 33.333 0.00 0.00 0.00 1.28
2797 4558 9.418839 ACTTCCTCCGTAAACTAATATAAGAGT 57.581 33.333 0.00 0.00 0.00 3.24
2798 4559 9.680315 CTTCCTCCGTAAACTAATATAAGAGTG 57.320 37.037 0.00 0.00 0.00 3.51
2799 4560 8.757982 TCCTCCGTAAACTAATATAAGAGTGT 57.242 34.615 0.00 0.00 0.00 3.55
2800 4561 9.193806 TCCTCCGTAAACTAATATAAGAGTGTT 57.806 33.333 0.00 0.00 0.00 3.32
2801 4562 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
2849 4610 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2850 4611 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2853 4614 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2874 4635 7.361628 GGGAGTACTTGTTAGTAGAGTGTGTAC 60.362 44.444 0.00 0.00 37.53 2.90
2922 4683 9.525826 AGTCAGGATTTGTAATTTCTTGAATCT 57.474 29.630 0.00 0.00 28.86 2.40
2959 4720 4.701765 AGAGAAATCCGTTGATGGAGATG 58.298 43.478 0.00 0.00 42.45 2.90
3020 4886 8.967918 AGGCTAATTTTCATCCCTTAACTTTAC 58.032 33.333 0.00 0.00 0.00 2.01
3137 5003 7.660169 AGTAGATAGGTTAGGGTTAGGTCTTT 58.340 38.462 0.00 0.00 0.00 2.52
3163 5029 4.451150 GGCACTCGGCGGATGACA 62.451 66.667 7.21 0.00 46.16 3.58
3166 5032 1.439228 CACTCGGCGGATGACAGAT 59.561 57.895 7.21 0.00 0.00 2.90
3200 5068 0.329261 TGGTCTTCCTGCCTCCAATG 59.671 55.000 0.00 0.00 34.23 2.82
3206 5074 1.304713 CCTGCCTCCAATGCACCTT 60.305 57.895 0.00 0.00 34.46 3.50
3275 5143 1.906574 GTCATTACCTCAGGGTGGTCA 59.093 52.381 0.00 0.00 46.75 4.02
3293 5161 4.166531 TGGTCAAGGTTAGGGTTACTTGTT 59.833 41.667 0.00 0.00 40.74 2.83
3300 5168 4.641541 GGTTAGGGTTACTTGTTGTGTGTT 59.358 41.667 0.00 0.00 0.00 3.32
3304 5172 3.367498 GGGTTACTTGTTGTGTGTTTGCA 60.367 43.478 0.00 0.00 0.00 4.08
3305 5173 4.429108 GGTTACTTGTTGTGTGTTTGCAT 58.571 39.130 0.00 0.00 0.00 3.96
3318 5186 2.274437 GTTTGCATGAGCGAGATCTGA 58.726 47.619 0.00 0.00 46.23 3.27
3408 5283 1.618640 GGCACGTGCTCGAAGACTTC 61.619 60.000 36.84 14.82 41.70 3.01
3421 5296 3.605916 CGAAGACTTCTCAGTTGTCATCG 59.394 47.826 13.22 10.91 42.41 3.84
3442 5317 0.465705 CAAGATTAGGCCTGCTCCGA 59.534 55.000 17.99 0.00 0.00 4.55
3501 5376 1.183676 GGTGGTGACGGTAGTGGTCT 61.184 60.000 0.00 0.00 35.45 3.85
3507 5382 1.567649 TGACGGTAGTGGTCTAGGGAT 59.432 52.381 0.00 0.00 35.45 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.095263 CAGGGCAAAGTAAACATCACCG 60.095 50.000 0.00 0.00 0.00 4.94
1 2 2.890945 ACAGGGCAAAGTAAACATCACC 59.109 45.455 0.00 0.00 0.00 4.02
56 57 6.346896 AGATGTTCCGGGTAGTAAAGAAATC 58.653 40.000 0.00 0.00 0.00 2.17
73 74 5.017294 AGCTGTTCTAGGCTTAGATGTTC 57.983 43.478 6.37 0.00 35.88 3.18
93 94 3.550437 ACCTATCAATGGTGTCAGAGC 57.450 47.619 0.00 0.00 36.30 4.09
182 183 4.147587 GCCCTCCACCATGGCCAT 62.148 66.667 14.09 14.09 39.30 4.40
202 203 1.446099 CCACTCACCGTCATCACCG 60.446 63.158 0.00 0.00 0.00 4.94
248 249 1.063114 ACCGATCTAGGTTAGCCCTGT 60.063 52.381 0.00 0.00 45.81 4.00
250 251 4.793890 ACCTACCGATCTAGGTTAGCCCT 61.794 52.174 7.68 0.00 43.58 5.19
297 298 1.779683 GCACTACGAGGTTTGTCGC 59.220 57.895 0.00 0.00 44.06 5.19
324 325 3.246387 GGGCTATATAAAGAGGAGGGGGA 60.246 52.174 0.00 0.00 0.00 4.81
328 329 3.118956 CGCTGGGCTATATAAAGAGGAGG 60.119 52.174 0.00 0.00 0.00 4.30
330 331 2.233922 GCGCTGGGCTATATAAAGAGGA 59.766 50.000 9.69 0.00 39.11 3.71
351 352 2.040009 ATGGTTGACGGCCCCTATCG 62.040 60.000 0.00 0.00 0.00 2.92
354 355 0.325860 ACTATGGTTGACGGCCCCTA 60.326 55.000 0.00 0.00 0.00 3.53
386 388 1.427809 AGATCCATGCCTTGATCGGA 58.572 50.000 4.62 0.00 41.76 4.55
394 396 1.430369 GGGCCCTTAGATCCATGCCT 61.430 60.000 17.04 0.00 38.89 4.75
399 401 2.070039 CACCGGGCCCTTAGATCCA 61.070 63.158 22.43 0.00 0.00 3.41
439 441 4.315803 CACCGTTTGTTAGGTTGATCTCT 58.684 43.478 0.00 0.00 39.00 3.10
457 459 4.177026 GCAGTATTATCCAGATAGCACCG 58.823 47.826 0.00 0.00 0.00 4.94
467 469 1.522668 GCGCATGGCAGTATTATCCA 58.477 50.000 0.30 0.00 42.87 3.41
478 480 3.430862 TTGTTCGGAGCGCATGGC 61.431 61.111 11.47 0.00 44.05 4.40
479 481 1.970917 GAGTTGTTCGGAGCGCATGG 61.971 60.000 11.47 0.00 0.00 3.66
494 505 2.457366 ATTTTCAGACCGAGCGAGTT 57.543 45.000 0.00 0.00 0.00 3.01
497 508 3.587797 AAGTATTTTCAGACCGAGCGA 57.412 42.857 0.00 0.00 0.00 4.93
499 510 6.903883 TCAATAAGTATTTTCAGACCGAGC 57.096 37.500 0.00 0.00 0.00 5.03
564 575 6.757897 AGTCGCAGAAATGGATAAAAATGA 57.242 33.333 0.00 0.00 39.69 2.57
594 605 4.957296 AGACAAATACTTCCTTCGTGTGT 58.043 39.130 0.00 0.00 0.00 3.72
617 628 1.295357 CGTAACGCTTGCCACATCCA 61.295 55.000 0.00 0.00 0.00 3.41
619 630 0.793861 TTCGTAACGCTTGCCACATC 59.206 50.000 0.00 0.00 0.00 3.06
620 631 1.069500 GTTTCGTAACGCTTGCCACAT 60.069 47.619 0.00 0.00 0.00 3.21
745 767 4.297510 CCTGTGATGAAGATGAGACGATC 58.702 47.826 0.00 0.00 0.00 3.69
758 780 3.338250 GGGTGGGGCCTGTGATGA 61.338 66.667 0.84 0.00 37.43 2.92
841 863 1.612462 GGGGTGGCTATAAATACGGGC 60.612 57.143 0.00 0.00 0.00 6.13
845 867 1.003928 CCCCGGGGTGGCTATAAATAC 59.996 57.143 33.25 0.00 35.87 1.89
902 924 2.700371 TCCTTTCTCTGTGCTGTTCAGA 59.300 45.455 3.84 0.00 39.25 3.27
938 969 3.512516 GGCTGCTTGATCGCCACC 61.513 66.667 0.00 0.00 43.25 4.61
979 1010 3.303881 TCTGAGTGTATGTCTGTGTGC 57.696 47.619 0.00 0.00 0.00 4.57
997 1028 1.611673 CGCCTCTTCCACAACCATTCT 60.612 52.381 0.00 0.00 0.00 2.40
998 1029 0.804989 CGCCTCTTCCACAACCATTC 59.195 55.000 0.00 0.00 0.00 2.67
1083 1114 3.966026 CTCGTCGTTCTCCGGCCAC 62.966 68.421 2.24 0.00 38.13 5.01
1104 1135 0.183971 ATCCCTCCTCATCGTCGTCT 59.816 55.000 0.00 0.00 0.00 4.18
1176 1210 2.548480 AGGAAAACTTACGTGAAGCTGC 59.452 45.455 0.00 0.00 38.92 5.25
1207 1241 1.255342 CGATCACACGAATTGGCTACG 59.745 52.381 0.00 0.00 35.09 3.51
1274 1342 2.192861 CGTGCTGGTCTTGCCCAAA 61.193 57.895 0.00 0.00 33.07 3.28
1397 1465 3.709633 ATGCAGCTCCGGCAGTCA 61.710 61.111 0.00 0.00 45.68 3.41
1511 1579 1.528586 CTGTGTCTCGAAAGCAACCAG 59.471 52.381 0.00 0.00 0.00 4.00
1551 1619 8.603242 AATTAATTACGCCGTCTGAAGATTAT 57.397 30.769 0.00 0.00 0.00 1.28
1592 1666 3.629398 ACTTTTCTGCTGGAACTGAACAG 59.371 43.478 0.00 0.00 37.76 3.16
1593 1667 3.378112 CACTTTTCTGCTGGAACTGAACA 59.622 43.478 0.00 0.00 33.13 3.18
1594 1668 3.793465 GCACTTTTCTGCTGGAACTGAAC 60.793 47.826 0.00 0.00 34.06 3.18
1595 1669 2.358898 GCACTTTTCTGCTGGAACTGAA 59.641 45.455 0.00 0.00 34.06 3.02
1596 1670 1.949525 GCACTTTTCTGCTGGAACTGA 59.050 47.619 0.00 0.00 34.06 3.41
1621 1695 3.676216 GGTTTACAGGCCAACCGG 58.324 61.111 5.01 0.00 42.76 5.28
1684 1768 6.073058 TCAGAATTCAGAAGGATCAAAACACG 60.073 38.462 8.44 0.00 0.00 4.49
1687 1771 8.048534 TCATCAGAATTCAGAAGGATCAAAAC 57.951 34.615 8.44 0.00 0.00 2.43
1703 1787 6.867662 AAACGAAGAACACTTCATCAGAAT 57.132 33.333 9.95 0.00 39.71 2.40
1704 1788 6.093495 ACAAAACGAAGAACACTTCATCAGAA 59.907 34.615 9.95 0.00 39.71 3.02
1705 1789 5.584649 ACAAAACGAAGAACACTTCATCAGA 59.415 36.000 9.95 0.00 39.71 3.27
1706 1790 5.810525 ACAAAACGAAGAACACTTCATCAG 58.189 37.500 9.95 0.00 39.71 2.90
1707 1791 5.811399 ACAAAACGAAGAACACTTCATCA 57.189 34.783 9.95 0.00 39.71 3.07
1708 1792 5.052370 GCAACAAAACGAAGAACACTTCATC 60.052 40.000 9.95 0.00 39.71 2.92
1709 1793 4.798387 GCAACAAAACGAAGAACACTTCAT 59.202 37.500 9.95 0.00 39.71 2.57
1732 1816 3.722082 GCGTTCATCAACTCTAAACAGCG 60.722 47.826 0.00 0.00 0.00 5.18
1752 1837 2.551270 GCGAATATGCTTCCGGCG 59.449 61.111 0.00 0.00 45.43 6.46
1798 1886 9.910267 ACTACTTTTTCTTACCCACTTCTTTAA 57.090 29.630 0.00 0.00 0.00 1.52
1826 1914 3.871594 AGGCGAATATGACAAGTTGCTAC 59.128 43.478 1.81 0.00 0.00 3.58
1827 1915 4.137116 AGGCGAATATGACAAGTTGCTA 57.863 40.909 1.81 0.00 0.00 3.49
1828 1916 2.991250 AGGCGAATATGACAAGTTGCT 58.009 42.857 1.81 0.00 0.00 3.91
1927 3669 3.007074 TGAGGCATGCATGTGACATTTTT 59.993 39.130 26.79 3.08 0.00 1.94
1973 3715 3.748021 GGAAGCGTCCGTTTCTTTG 57.252 52.632 14.37 0.00 35.97 2.77
2018 3760 2.222027 CCAGGAAATAATGGAGACGGC 58.778 52.381 0.00 0.00 39.02 5.68
2038 3780 3.799755 GTTCATGTCACGGGCGGC 61.800 66.667 0.00 0.00 0.00 6.53
2066 3808 0.397254 ACTGGTCTGGTCGGGATAGG 60.397 60.000 0.00 0.00 0.00 2.57
2114 3856 1.835121 GTGCGGTTTTGGAAGTGTTC 58.165 50.000 0.00 0.00 0.00 3.18
2141 3894 1.511318 TTTCGGGTTGGCATGTGTCG 61.511 55.000 0.00 0.00 0.00 4.35
2154 3907 4.067016 CGACGTGCGGTTTTCGGG 62.067 66.667 0.00 0.00 39.69 5.14
2171 3924 4.504097 CACCAAACTTTTTGCTTAGCAGAC 59.496 41.667 7.08 0.00 40.61 3.51
2218 3971 1.139734 CGTCACAGATCGACCAGGG 59.860 63.158 0.00 0.00 0.00 4.45
2671 4424 1.891933 TGGCATCATACCCCTCTTGA 58.108 50.000 0.00 0.00 0.00 3.02
2679 4440 1.949525 GTGACACCATGGCATCATACC 59.050 52.381 18.79 5.72 37.93 2.73
2708 4469 5.293569 GCATACGGTCTATAATAACATGGGC 59.706 44.000 0.00 0.00 0.00 5.36
2757 4518 4.224762 GGAGGAAGTACTACTATGGCCTT 58.775 47.826 3.32 0.00 0.00 4.35
2762 4523 7.565323 AGTTTACGGAGGAAGTACTACTATG 57.435 40.000 0.00 0.00 0.00 2.23
2771 4532 9.418839 ACTCTTATATTAGTTTACGGAGGAAGT 57.581 33.333 0.00 0.00 0.00 3.01
2772 4533 9.680315 CACTCTTATATTAGTTTACGGAGGAAG 57.320 37.037 0.00 0.00 0.00 3.46
2773 4534 9.193806 ACACTCTTATATTAGTTTACGGAGGAA 57.806 33.333 0.00 0.00 0.00 3.36
2774 4535 8.757982 ACACTCTTATATTAGTTTACGGAGGA 57.242 34.615 0.00 0.00 0.00 3.71
2775 4536 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
2823 4584 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2824 4585 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2825 4586 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2826 4587 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2827 4588 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2833 4594 9.490083 ACAAGTACTCCCTCTGTAAACTAATAT 57.510 33.333 0.00 0.00 0.00 1.28
2834 4595 8.890410 ACAAGTACTCCCTCTGTAAACTAATA 57.110 34.615 0.00 0.00 0.00 0.98
2835 4596 7.793948 ACAAGTACTCCCTCTGTAAACTAAT 57.206 36.000 0.00 0.00 0.00 1.73
2836 4597 7.607615 AACAAGTACTCCCTCTGTAAACTAA 57.392 36.000 0.00 0.00 0.00 2.24
2837 4598 7.946776 ACTAACAAGTACTCCCTCTGTAAACTA 59.053 37.037 0.00 0.00 0.00 2.24
2838 4599 6.781507 ACTAACAAGTACTCCCTCTGTAAACT 59.218 38.462 0.00 0.00 0.00 2.66
2839 4600 6.990798 ACTAACAAGTACTCCCTCTGTAAAC 58.009 40.000 0.00 0.00 0.00 2.01
2840 4601 8.166061 TCTACTAACAAGTACTCCCTCTGTAAA 58.834 37.037 0.00 0.00 0.00 2.01
2841 4602 7.693132 TCTACTAACAAGTACTCCCTCTGTAA 58.307 38.462 0.00 0.00 0.00 2.41
2842 4603 7.037730 ACTCTACTAACAAGTACTCCCTCTGTA 60.038 40.741 0.00 0.00 0.00 2.74
2843 4604 6.137104 TCTACTAACAAGTACTCCCTCTGT 57.863 41.667 0.00 0.00 0.00 3.41
2844 4605 6.094325 CACTCTACTAACAAGTACTCCCTCTG 59.906 46.154 0.00 0.00 0.00 3.35
2845 4606 6.181908 CACTCTACTAACAAGTACTCCCTCT 58.818 44.000 0.00 0.00 0.00 3.69
2846 4607 5.945191 ACACTCTACTAACAAGTACTCCCTC 59.055 44.000 0.00 0.00 0.00 4.30
2847 4608 5.711036 CACACTCTACTAACAAGTACTCCCT 59.289 44.000 0.00 0.00 0.00 4.20
2848 4609 5.476254 ACACACTCTACTAACAAGTACTCCC 59.524 44.000 0.00 0.00 0.00 4.30
2849 4610 6.572167 ACACACTCTACTAACAAGTACTCC 57.428 41.667 0.00 0.00 0.00 3.85
2850 4611 7.525759 GGTACACACTCTACTAACAAGTACTC 58.474 42.308 0.00 0.00 32.28 2.59
2853 4614 5.412594 CCGGTACACACTCTACTAACAAGTA 59.587 44.000 0.00 0.00 0.00 2.24
2874 4635 1.029947 GCACAACCTACAATCCCCGG 61.030 60.000 0.00 0.00 0.00 5.73
2977 4843 3.626930 AGCCTGTGGTTTGTGAAAACTA 58.373 40.909 1.76 0.00 33.37 2.24
2990 4856 3.635591 AGGGATGAAAATTAGCCTGTGG 58.364 45.455 0.00 0.00 0.00 4.17
3020 4886 2.006169 GTTGCCTGGTTTGTTTGGTTG 58.994 47.619 0.00 0.00 0.00 3.77
3092 4958 3.922640 CTAGAGCTGCCTCCCCGC 61.923 72.222 0.00 0.00 38.96 6.13
3163 5029 5.248640 AGACCATTTTGACAACGATGATCT 58.751 37.500 0.00 6.93 0.00 2.75
3166 5032 4.215399 GGAAGACCATTTTGACAACGATGA 59.785 41.667 0.00 0.00 35.97 2.92
3172 5038 2.627699 GGCAGGAAGACCATTTTGACAA 59.372 45.455 0.00 0.00 38.94 3.18
3200 5068 1.062587 CGATGGACGAATTCAAGGTGC 59.937 52.381 6.22 1.55 45.77 5.01
3275 5143 4.885325 CACACAACAAGTAACCCTAACCTT 59.115 41.667 0.00 0.00 0.00 3.50
3293 5161 0.587768 CTCGCTCATGCAAACACACA 59.412 50.000 0.00 0.00 39.64 3.72
3300 5168 2.159000 ACATCAGATCTCGCTCATGCAA 60.159 45.455 0.00 0.00 39.64 4.08
3304 5172 3.894427 ACCTAACATCAGATCTCGCTCAT 59.106 43.478 0.00 0.00 0.00 2.90
3305 5173 3.291584 ACCTAACATCAGATCTCGCTCA 58.708 45.455 0.00 0.00 0.00 4.26
3318 5186 6.653020 TGAATCAATCTGCAGTACCTAACAT 58.347 36.000 14.67 0.00 0.00 2.71
3370 5245 1.455849 CTTGAGAACAGGCACCCCA 59.544 57.895 0.00 0.00 0.00 4.96
3408 5283 5.518128 CCTAATCTTGTCGATGACAACTGAG 59.482 44.000 8.21 0.00 45.88 3.35
3421 5296 1.808133 CGGAGCAGGCCTAATCTTGTC 60.808 57.143 3.98 0.00 0.00 3.18
3442 5317 4.938080 TGTTGTTTTCGTTGTTGCCATAT 58.062 34.783 0.00 0.00 0.00 1.78
3461 5336 4.080129 ACCAGGATGAGCTAATGACATGTT 60.080 41.667 0.00 0.00 39.69 2.71
3528 5403 6.419791 TCCGAAATACAAATACACCCTCAAT 58.580 36.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.