Multiple sequence alignment - TraesCS2B01G461600

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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 TraesCS2B01G461600 chr2B 100.000 2665 0 0 1 2665 655211702 655214366 0.000000e+00 4922.0
1 TraesCS2B01G461600 chr2B 86.139 101 14 0 974 1074 655228773 655228873 2.800000e-20 110.0
2 TraesCS2B01G461600 chr2D 91.197 1454 76 15 926 2355 548255204 548256629 0.000000e+00 1929.0
3 TraesCS2B01G461600 chr2D 85.911 582 37 17 1918 2491 548256633 548257177 1.780000e-161 579.0
4 TraesCS2B01G461600 chr2D 82.322 577 90 4 1166 1741 549984054 549983489 8.570000e-135 490.0
5 TraesCS2B01G461600 chr2D 81.282 577 87 7 1166 1741 549510024 549509468 5.230000e-122 448.0
6 TraesCS2B01G461600 chr2D 76.546 857 150 33 1166 2003 548265551 548266375 3.170000e-114 422.0
7 TraesCS2B01G461600 chr2D 93.220 118 6 2 996 1112 548265350 548265466 3.530000e-39 172.0
8 TraesCS2B01G461600 chr6B 93.696 920 50 6 1 914 409625079 409625996 0.000000e+00 1371.0
9 TraesCS2B01G461600 chr6B 98.318 535 7 2 1 534 502009650 502010183 0.000000e+00 937.0
10 TraesCS2B01G461600 chr6B 90.032 632 47 7 310 927 409624553 409623924 0.000000e+00 804.0
11 TraesCS2B01G461600 chr6A 92.086 935 61 9 1 925 500294875 500293944 0.000000e+00 1304.0
12 TraesCS2B01G461600 chr6A 89.987 769 50 20 1697 2454 146500172 146499420 0.000000e+00 968.0
13 TraesCS2B01G461600 chr6A 92.857 42 2 1 2514 2555 481046994 481047034 2.860000e-05 60.2
14 TraesCS2B01G461600 chr4B 94.262 854 41 6 1 848 64816868 64816017 0.000000e+00 1299.0
15 TraesCS2B01G461600 chr7B 96.296 729 20 7 1 724 244391655 244392381 0.000000e+00 1190.0
16 TraesCS2B01G461600 chr7B 95.270 740 27 7 1 733 71270764 71271502 0.000000e+00 1166.0
17 TraesCS2B01G461600 chr7B 90.000 640 43 12 303 925 71270244 71269609 0.000000e+00 808.0
18 TraesCS2B01G461600 chr7B 100.000 36 0 0 2519 2554 707519370 707519335 1.710000e-07 67.6
19 TraesCS2B01G461600 chr4D 86.518 942 100 17 3 925 152600547 152601480 0.000000e+00 1011.0
20 TraesCS2B01G461600 chr4D 97.222 36 1 0 2519 2554 98910513 98910478 7.970000e-06 62.1
21 TraesCS2B01G461600 chrUn 91.346 728 41 11 931 1647 307426874 307427590 0.000000e+00 976.0
22 TraesCS2B01G461600 chrUn 82.388 829 75 36 1695 2480 307427598 307428398 0.000000e+00 656.0
23 TraesCS2B01G461600 chrUn 89.796 49 2 3 2512 2557 196943350 196943398 2.860000e-05 60.2
24 TraesCS2B01G461600 chr2A 91.346 728 41 11 931 1647 690913762 690913046 0.000000e+00 976.0
25 TraesCS2B01G461600 chr2A 82.388 829 75 36 1695 2480 690913038 690912238 0.000000e+00 656.0
26 TraesCS2B01G461600 chr1B 84.567 946 116 20 1 926 25885036 25885971 0.000000e+00 911.0
27 TraesCS2B01G461600 chr5A 92.611 609 33 5 1 600 649502018 649502623 0.000000e+00 865.0
28 TraesCS2B01G461600 chr4A 97.297 37 1 0 2516 2552 658953546 658953510 2.210000e-06 63.9
29 TraesCS2B01G461600 chr7D 94.872 39 2 0 2516 2554 235581266 235581304 7.970000e-06 62.1
30 TraesCS2B01G461600 chr5D 97.222 36 1 0 2519 2554 135719430 135719395 7.970000e-06 62.1
31 TraesCS2B01G461600 chr5D 94.872 39 2 0 2516 2554 408763836 408763874 7.970000e-06 62.1
32 TraesCS2B01G461600 chr3D 94.872 39 2 0 2516 2554 428545779 428545817 7.970000e-06 62.1


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 TraesCS2B01G461600 chr2B 655211702 655214366 2664 False 4922 4922 100.000 1 2665 1 chr2B.!!$F1 2664
1 TraesCS2B01G461600 chr2D 548255204 548257177 1973 False 1254 1929 88.554 926 2491 2 chr2D.!!$F1 1565
2 TraesCS2B01G461600 chr2D 549983489 549984054 565 True 490 490 82.322 1166 1741 1 chr2D.!!$R2 575
3 TraesCS2B01G461600 chr2D 549509468 549510024 556 True 448 448 81.282 1166 1741 1 chr2D.!!$R1 575
4 TraesCS2B01G461600 chr2D 548265350 548266375 1025 False 297 422 84.883 996 2003 2 chr2D.!!$F2 1007
5 TraesCS2B01G461600 chr6B 409625079 409625996 917 False 1371 1371 93.696 1 914 1 chr6B.!!$F1 913
6 TraesCS2B01G461600 chr6B 502009650 502010183 533 False 937 937 98.318 1 534 1 chr6B.!!$F2 533
7 TraesCS2B01G461600 chr6B 409623924 409624553 629 True 804 804 90.032 310 927 1 chr6B.!!$R1 617
8 TraesCS2B01G461600 chr6A 500293944 500294875 931 True 1304 1304 92.086 1 925 1 chr6A.!!$R2 924
9 TraesCS2B01G461600 chr6A 146499420 146500172 752 True 968 968 89.987 1697 2454 1 chr6A.!!$R1 757
10 TraesCS2B01G461600 chr4B 64816017 64816868 851 True 1299 1299 94.262 1 848 1 chr4B.!!$R1 847
11 TraesCS2B01G461600 chr7B 244391655 244392381 726 False 1190 1190 96.296 1 724 1 chr7B.!!$F2 723
12 TraesCS2B01G461600 chr7B 71270764 71271502 738 False 1166 1166 95.270 1 733 1 chr7B.!!$F1 732
13 TraesCS2B01G461600 chr7B 71269609 71270244 635 True 808 808 90.000 303 925 1 chr7B.!!$R1 622
14 TraesCS2B01G461600 chr4D 152600547 152601480 933 False 1011 1011 86.518 3 925 1 chr4D.!!$F1 922
15 TraesCS2B01G461600 chrUn 307426874 307428398 1524 False 816 976 86.867 931 2480 2 chrUn.!!$F2 1549
16 TraesCS2B01G461600 chr2A 690912238 690913762 1524 True 816 976 86.867 931 2480 2 chr2A.!!$R1 1549
17 TraesCS2B01G461600 chr1B 25885036 25885971 935 False 911 911 84.567 1 926 1 chr1B.!!$F1 925
18 TraesCS2B01G461600 chr5A 649502018 649502623 605 False 865 865 92.611 1 600 1 chr5A.!!$F1 599

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
898 925 0.813184 ACCAATCTGCTTCCAATGCG 59.187 50.0 0.0 0.0 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 3151 0.52847 GAGCGTTCACAGACTAGGCT 59.472 55.0 0.0 0.0 35.89 4.58 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
343 348 2.999507 AAAATGTTCACCGCGCATTA 57.000 40.000 8.75 0.00 33.13 1.90
474 489 4.811557 AGCGCTTCAGAATGGTATAAGAAC 59.188 41.667 2.64 0.00 36.16 3.01
564 580 1.814169 GTCGCAGGTTCGATTCCCC 60.814 63.158 3.93 0.00 40.84 4.81
592 609 8.330466 TCGCCTGATTTTCTGTTTCTTTTATA 57.670 30.769 0.00 0.00 0.00 0.98
762 789 1.008875 CATGACACGTCGACACCTGG 61.009 60.000 17.16 0.66 0.00 4.45
898 925 0.813184 ACCAATCTGCTTCCAATGCG 59.187 50.000 0.00 0.00 0.00 4.73
905 932 1.134753 CTGCTTCCAATGCGCCAATTA 59.865 47.619 4.18 0.00 0.00 1.40
908 935 2.223782 GCTTCCAATGCGCCAATTATGA 60.224 45.455 4.18 0.00 0.00 2.15
971 1004 1.795170 ATCGCCGCAACTGCAAAACT 61.795 50.000 2.12 0.00 42.21 2.66
972 1005 1.588667 CGCCGCAACTGCAAAACTT 60.589 52.632 2.12 0.00 42.21 2.66
1016 1054 3.443045 CATGGCCACCTTCACCGC 61.443 66.667 8.16 0.00 0.00 5.68
1017 1055 3.650950 ATGGCCACCTTCACCGCT 61.651 61.111 8.16 0.00 0.00 5.52
1164 1238 1.719529 TTCTTTCACCGTCCCTACCA 58.280 50.000 0.00 0.00 0.00 3.25
1174 1248 3.118371 ACCGTCCCTACCATCTTTGATTC 60.118 47.826 0.00 0.00 0.00 2.52
1259 1333 0.902984 TCAACCGCCTGAAGGAGCTA 60.903 55.000 0.00 0.00 37.39 3.32
1301 1375 0.103755 TGCACGAGCTGATGGAGATC 59.896 55.000 6.36 0.00 42.74 2.75
1325 1399 2.105128 GAGCTGCGCGACTACCAT 59.895 61.111 12.10 0.00 0.00 3.55
1418 1504 0.739462 CCGCCTACGTCAAGCATCAA 60.739 55.000 0.00 0.00 37.70 2.57
1567 1653 2.571202 TCATGGATGAGTACAGCAACCA 59.429 45.455 16.30 16.30 33.73 3.67
1568 1654 3.008923 TCATGGATGAGTACAGCAACCAA 59.991 43.478 17.39 4.38 33.73 3.67
1601 1687 3.134127 GGGATGCTGGCGTTGGTC 61.134 66.667 0.00 0.00 0.00 4.02
1672 1812 4.079787 CCCCCAAGATCAGTAGGAATTGAA 60.080 45.833 0.00 0.00 31.36 2.69
1674 1814 6.131961 CCCCAAGATCAGTAGGAATTGAATT 58.868 40.000 0.00 0.00 31.36 2.17
1686 1826 5.683681 AGGAATTGAATTTGTTTGCTTGGT 58.316 33.333 0.00 0.00 0.00 3.67
1687 1827 5.528320 AGGAATTGAATTTGTTTGCTTGGTG 59.472 36.000 0.00 0.00 0.00 4.17
1688 1828 5.296531 GGAATTGAATTTGTTTGCTTGGTGT 59.703 36.000 0.00 0.00 0.00 4.16
1689 1829 5.738118 ATTGAATTTGTTTGCTTGGTGTG 57.262 34.783 0.00 0.00 0.00 3.82
1690 1830 3.529533 TGAATTTGTTTGCTTGGTGTGG 58.470 40.909 0.00 0.00 0.00 4.17
1691 1831 3.196469 TGAATTTGTTTGCTTGGTGTGGA 59.804 39.130 0.00 0.00 0.00 4.02
1692 1832 3.902881 ATTTGTTTGCTTGGTGTGGAA 57.097 38.095 0.00 0.00 0.00 3.53
1693 1833 2.663826 TTGTTTGCTTGGTGTGGAAC 57.336 45.000 0.00 0.00 37.35 3.62
1741 1886 5.688823 TGAGAACGAAATGTTGCTATGTTG 58.311 37.500 0.00 0.00 42.09 3.33
1748 1893 5.108292 CGAAATGTTGCTATGTTGTGTTGTG 60.108 40.000 0.00 0.00 0.00 3.33
1749 1894 4.916983 ATGTTGCTATGTTGTGTTGTGT 57.083 36.364 0.00 0.00 0.00 3.72
1851 1997 7.962964 TCATGTGGACTAGTCTTTTAGTTTG 57.037 36.000 21.88 9.50 34.13 2.93
1855 2003 8.795842 TGTGGACTAGTCTTTTAGTTTGAAAA 57.204 30.769 21.88 0.00 34.13 2.29
1891 2056 7.834068 TGCTATGTTCTGAACTTCTGATTAC 57.166 36.000 20.18 3.42 0.00 1.89
2006 2179 3.637273 GGCACGGAAGGAGGGTGT 61.637 66.667 0.00 0.00 34.25 4.16
2094 2267 1.067142 CAAAGCTACGACCTGCCTACA 60.067 52.381 0.00 0.00 0.00 2.74
2117 2290 2.105993 GGTTTGGTCTTGGACAGTAGGT 59.894 50.000 0.14 0.00 33.68 3.08
2118 2291 3.325716 GGTTTGGTCTTGGACAGTAGGTA 59.674 47.826 0.14 0.00 33.68 3.08
2119 2292 4.019591 GGTTTGGTCTTGGACAGTAGGTAT 60.020 45.833 0.14 0.00 33.68 2.73
2120 2293 5.188359 GGTTTGGTCTTGGACAGTAGGTATA 59.812 44.000 0.14 0.00 33.68 1.47
2170 2343 7.114953 GCAGAAAGAAAAACTAATTCGGGAAAG 59.885 37.037 0.00 0.00 32.04 2.62
2176 2349 2.711542 ACTAATTCGGGAAAGCAGTGG 58.288 47.619 0.00 0.00 0.00 4.00
2177 2350 2.304761 ACTAATTCGGGAAAGCAGTGGA 59.695 45.455 0.00 0.00 0.00 4.02
2185 2358 1.517242 GAAAGCAGTGGAGTCTGTGG 58.483 55.000 0.00 0.00 37.70 4.17
2199 2372 6.262273 TGGAGTCTGTGGAAAATGAAGTAAAC 59.738 38.462 0.00 0.00 0.00 2.01
2293 2940 4.097286 TGGCTTCAGAAACTGTGTTAAACC 59.903 41.667 0.00 0.00 32.61 3.27
2294 2941 4.097286 GGCTTCAGAAACTGTGTTAAACCA 59.903 41.667 0.00 0.00 32.61 3.67
2367 3015 6.769822 TTTCAAAAGCATAATGCCTTTGGAAA 59.230 30.769 17.47 17.47 44.67 3.13
2377 3025 6.670695 AATGCCTTTGGAAACTAGTGAATT 57.329 33.333 0.00 0.00 0.00 2.17
2428 3076 7.926018 GTGTCTTATGTGTTTCCCTTGATTTTT 59.074 33.333 0.00 0.00 0.00 1.94
2430 3078 8.141268 GTCTTATGTGTTTCCCTTGATTTTTCA 58.859 33.333 0.00 0.00 0.00 2.69
2431 3079 8.869109 TCTTATGTGTTTCCCTTGATTTTTCAT 58.131 29.630 0.00 0.00 0.00 2.57
2432 3080 9.492973 CTTATGTGTTTCCCTTGATTTTTCATT 57.507 29.630 0.00 0.00 0.00 2.57
2434 3082 8.831715 ATGTGTTTCCCTTGATTTTTCATTAC 57.168 30.769 0.00 0.00 0.00 1.89
2456 3104 3.550820 TGAGCCTAAACACAAGAGCAAA 58.449 40.909 0.00 0.00 0.00 3.68
2457 3105 3.951037 TGAGCCTAAACACAAGAGCAAAA 59.049 39.130 0.00 0.00 0.00 2.44
2458 3106 4.584325 TGAGCCTAAACACAAGAGCAAAAT 59.416 37.500 0.00 0.00 0.00 1.82
2459 3107 4.874970 AGCCTAAACACAAGAGCAAAATG 58.125 39.130 0.00 0.00 0.00 2.32
2460 3108 3.429881 GCCTAAACACAAGAGCAAAATGC 59.570 43.478 0.00 0.00 45.46 3.56
2491 3140 3.256383 TGCATTTGGAATCTCTGTGGTTG 59.744 43.478 0.00 0.00 0.00 3.77
2492 3141 3.841643 CATTTGGAATCTCTGTGGTTGC 58.158 45.455 0.00 0.00 0.00 4.17
2493 3142 2.957402 TTGGAATCTCTGTGGTTGCT 57.043 45.000 0.00 0.00 0.00 3.91
2494 3143 4.365514 TTTGGAATCTCTGTGGTTGCTA 57.634 40.909 0.00 0.00 0.00 3.49
2495 3144 3.334583 TGGAATCTCTGTGGTTGCTAC 57.665 47.619 0.00 0.00 0.00 3.58
2496 3145 2.906389 TGGAATCTCTGTGGTTGCTACT 59.094 45.455 0.00 0.00 0.00 2.57
2497 3146 3.327757 TGGAATCTCTGTGGTTGCTACTT 59.672 43.478 0.00 0.00 0.00 2.24
2498 3147 3.686726 GGAATCTCTGTGGTTGCTACTTG 59.313 47.826 0.00 0.00 0.00 3.16
2499 3148 4.563580 GGAATCTCTGTGGTTGCTACTTGA 60.564 45.833 0.00 0.00 0.00 3.02
2500 3149 3.667497 TCTCTGTGGTTGCTACTTGAG 57.333 47.619 0.00 2.05 0.00 3.02
2501 3150 3.230976 TCTCTGTGGTTGCTACTTGAGA 58.769 45.455 0.00 4.16 0.00 3.27
2502 3151 3.641436 TCTCTGTGGTTGCTACTTGAGAA 59.359 43.478 0.00 0.00 31.16 2.87
2503 3152 3.993081 CTCTGTGGTTGCTACTTGAGAAG 59.007 47.826 0.00 0.00 0.00 2.85
2504 3153 2.481952 CTGTGGTTGCTACTTGAGAAGC 59.518 50.000 0.00 0.00 39.25 3.86
2505 3154 1.807142 GTGGTTGCTACTTGAGAAGCC 59.193 52.381 0.00 0.00 37.97 4.35
2506 3155 1.699634 TGGTTGCTACTTGAGAAGCCT 59.300 47.619 0.00 0.00 37.97 4.58
2507 3156 2.903784 TGGTTGCTACTTGAGAAGCCTA 59.096 45.455 0.00 0.00 37.97 3.93
2508 3157 3.055819 TGGTTGCTACTTGAGAAGCCTAG 60.056 47.826 0.00 0.00 37.97 3.02
2509 3158 3.055747 GGTTGCTACTTGAGAAGCCTAGT 60.056 47.826 0.00 0.00 37.97 2.57
2510 3159 4.177783 GTTGCTACTTGAGAAGCCTAGTC 58.822 47.826 0.00 0.00 37.97 2.59
2511 3160 3.702792 TGCTACTTGAGAAGCCTAGTCT 58.297 45.455 0.00 0.00 37.97 3.24
2512 3161 3.445450 TGCTACTTGAGAAGCCTAGTCTG 59.555 47.826 0.00 0.00 37.97 3.51
2513 3162 3.445805 GCTACTTGAGAAGCCTAGTCTGT 59.554 47.826 0.00 0.00 32.40 3.41
2514 3163 3.951775 ACTTGAGAAGCCTAGTCTGTG 57.048 47.619 0.00 0.00 0.00 3.66
2515 3164 3.501349 ACTTGAGAAGCCTAGTCTGTGA 58.499 45.455 0.00 0.00 0.00 3.58
2516 3165 3.898123 ACTTGAGAAGCCTAGTCTGTGAA 59.102 43.478 0.00 0.00 0.00 3.18
2517 3166 3.944055 TGAGAAGCCTAGTCTGTGAAC 57.056 47.619 0.00 0.00 0.00 3.18
2518 3167 2.229062 TGAGAAGCCTAGTCTGTGAACG 59.771 50.000 0.00 0.00 0.00 3.95
2519 3168 1.067495 AGAAGCCTAGTCTGTGAACGC 60.067 52.381 0.00 0.00 0.00 4.84
2520 3169 0.969894 AAGCCTAGTCTGTGAACGCT 59.030 50.000 0.00 0.00 0.00 5.07
2521 3170 0.528470 AGCCTAGTCTGTGAACGCTC 59.472 55.000 0.00 0.00 0.00 5.03
2522 3171 0.528470 GCCTAGTCTGTGAACGCTCT 59.472 55.000 0.00 0.00 0.00 4.09
2523 3172 1.067495 GCCTAGTCTGTGAACGCTCTT 60.067 52.381 0.00 0.00 0.00 2.85
2524 3173 2.163815 GCCTAGTCTGTGAACGCTCTTA 59.836 50.000 0.00 0.00 0.00 2.10
2525 3174 3.181485 GCCTAGTCTGTGAACGCTCTTAT 60.181 47.826 0.00 0.00 0.00 1.73
2526 3175 4.036498 GCCTAGTCTGTGAACGCTCTTATA 59.964 45.833 0.00 0.00 0.00 0.98
2527 3176 5.278561 GCCTAGTCTGTGAACGCTCTTATAT 60.279 44.000 0.00 0.00 0.00 0.86
2528 3177 6.736243 GCCTAGTCTGTGAACGCTCTTATATT 60.736 42.308 0.00 0.00 0.00 1.28
2529 3178 7.203910 CCTAGTCTGTGAACGCTCTTATATTT 58.796 38.462 0.00 0.00 0.00 1.40
2530 3179 7.380065 CCTAGTCTGTGAACGCTCTTATATTTC 59.620 40.741 0.00 0.00 0.00 2.17
2531 3180 6.868622 AGTCTGTGAACGCTCTTATATTTCT 58.131 36.000 0.00 0.00 0.00 2.52
2532 3181 7.324178 AGTCTGTGAACGCTCTTATATTTCTT 58.676 34.615 0.00 0.00 0.00 2.52
2533 3182 7.819900 AGTCTGTGAACGCTCTTATATTTCTTT 59.180 33.333 0.00 0.00 0.00 2.52
2534 3183 9.084164 GTCTGTGAACGCTCTTATATTTCTTTA 57.916 33.333 0.00 0.00 0.00 1.85
2535 3184 9.084164 TCTGTGAACGCTCTTATATTTCTTTAC 57.916 33.333 0.00 0.00 0.00 2.01
2536 3185 8.766000 TGTGAACGCTCTTATATTTCTTTACA 57.234 30.769 0.00 0.00 0.00 2.41
2537 3186 8.869897 TGTGAACGCTCTTATATTTCTTTACAG 58.130 33.333 0.00 0.00 0.00 2.74
2538 3187 9.084164 GTGAACGCTCTTATATTTCTTTACAGA 57.916 33.333 0.00 0.00 0.00 3.41
2539 3188 9.302345 TGAACGCTCTTATATTTCTTTACAGAG 57.698 33.333 0.00 0.00 0.00 3.35
2540 3189 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
2541 3190 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
2542 3191 6.647067 CGCTCTTATATTTCTTTACAGAGGGG 59.353 42.308 0.00 0.00 36.63 4.79
2543 3192 6.937465 GCTCTTATATTTCTTTACAGAGGGGG 59.063 42.308 0.00 0.00 0.00 5.40
2544 3193 7.420330 GCTCTTATATTTCTTTACAGAGGGGGT 60.420 40.741 0.00 0.00 0.00 4.95
2545 3194 9.155785 CTCTTATATTTCTTTACAGAGGGGGTA 57.844 37.037 0.00 0.00 0.00 3.69
2546 3195 9.684702 TCTTATATTTCTTTACAGAGGGGGTAT 57.315 33.333 0.00 0.00 0.00 2.73
2547 3196 9.726438 CTTATATTTCTTTACAGAGGGGGTATG 57.274 37.037 0.00 0.00 0.00 2.39
2548 3197 7.707467 ATATTTCTTTACAGAGGGGGTATGT 57.293 36.000 0.00 0.00 34.14 2.29
2549 3198 5.853572 TTTCTTTACAGAGGGGGTATGTT 57.146 39.130 0.00 0.00 31.40 2.71
2550 3199 5.853572 TTCTTTACAGAGGGGGTATGTTT 57.146 39.130 0.00 0.00 31.40 2.83
2551 3200 5.853572 TCTTTACAGAGGGGGTATGTTTT 57.146 39.130 0.00 0.00 31.40 2.43
2552 3201 6.208840 TCTTTACAGAGGGGGTATGTTTTT 57.791 37.500 0.00 0.00 31.40 1.94
2553 3202 7.332433 TCTTTACAGAGGGGGTATGTTTTTA 57.668 36.000 0.00 0.00 31.40 1.52
2554 3203 7.935405 TCTTTACAGAGGGGGTATGTTTTTAT 58.065 34.615 0.00 0.00 31.40 1.40
2555 3204 8.395605 TCTTTACAGAGGGGGTATGTTTTTATT 58.604 33.333 0.00 0.00 31.40 1.40
2556 3205 8.959676 TTTACAGAGGGGGTATGTTTTTATTT 57.040 30.769 0.00 0.00 31.40 1.40
2557 3206 6.850752 ACAGAGGGGGTATGTTTTTATTTG 57.149 37.500 0.00 0.00 0.00 2.32
2558 3207 6.319715 ACAGAGGGGGTATGTTTTTATTTGT 58.680 36.000 0.00 0.00 0.00 2.83
2559 3208 6.436218 ACAGAGGGGGTATGTTTTTATTTGTC 59.564 38.462 0.00 0.00 0.00 3.18
2560 3209 5.955959 AGAGGGGGTATGTTTTTATTTGTCC 59.044 40.000 0.00 0.00 0.00 4.02
2561 3210 5.910931 AGGGGGTATGTTTTTATTTGTCCT 58.089 37.500 0.00 0.00 0.00 3.85
2562 3211 6.327781 AGGGGGTATGTTTTTATTTGTCCTT 58.672 36.000 0.00 0.00 0.00 3.36
2563 3212 6.790461 AGGGGGTATGTTTTTATTTGTCCTTT 59.210 34.615 0.00 0.00 0.00 3.11
2564 3213 7.293771 AGGGGGTATGTTTTTATTTGTCCTTTT 59.706 33.333 0.00 0.00 0.00 2.27
2565 3214 7.940137 GGGGGTATGTTTTTATTTGTCCTTTTT 59.060 33.333 0.00 0.00 0.00 1.94
2611 3260 9.819267 AGTATAGTCTAGTAGTTTCCATTTTGC 57.181 33.333 0.00 0.00 0.00 3.68
2612 3261 9.819267 GTATAGTCTAGTAGTTTCCATTTTGCT 57.181 33.333 0.00 0.00 0.00 3.91
2614 3263 9.740710 ATAGTCTAGTAGTTTCCATTTTGCTTT 57.259 29.630 0.00 0.00 0.00 3.51
2615 3264 8.100508 AGTCTAGTAGTTTCCATTTTGCTTTC 57.899 34.615 0.00 0.00 0.00 2.62
2616 3265 7.719633 AGTCTAGTAGTTTCCATTTTGCTTTCA 59.280 33.333 0.00 0.00 0.00 2.69
2617 3266 8.349983 GTCTAGTAGTTTCCATTTTGCTTTCAA 58.650 33.333 0.00 0.00 0.00 2.69
2618 3267 8.908903 TCTAGTAGTTTCCATTTTGCTTTCAAA 58.091 29.630 0.00 0.00 40.17 2.69
2635 3284 9.875675 TGCTTTCAAAACAATGCAATAATAAAC 57.124 25.926 0.00 0.00 34.46 2.01
2636 3285 9.875675 GCTTTCAAAACAATGCAATAATAAACA 57.124 25.926 0.00 0.00 0.00 2.83
2658 3307 8.669394 AACAAAAACAAAACAAAACAAAACGA 57.331 23.077 0.00 0.00 0.00 3.85
2659 3308 8.316777 ACAAAAACAAAACAAAACAAAACGAG 57.683 26.923 0.00 0.00 0.00 4.18
2660 3309 7.429630 ACAAAAACAAAACAAAACAAAACGAGG 59.570 29.630 0.00 0.00 0.00 4.63
2661 3310 6.606234 AAACAAAACAAAACAAAACGAGGT 57.394 29.167 0.00 0.00 0.00 3.85
2662 3311 5.832568 ACAAAACAAAACAAAACGAGGTC 57.167 34.783 0.00 0.00 0.00 3.85
2663 3312 5.534407 ACAAAACAAAACAAAACGAGGTCT 58.466 33.333 0.00 0.00 0.00 3.85
2664 3313 6.679843 ACAAAACAAAACAAAACGAGGTCTA 58.320 32.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
474 489 0.378962 TTTGAACACAGGCGTTTCCG 59.621 50.000 0.00 0.00 40.77 4.30
564 580 1.826385 AACAGAAAATCAGGCGAGGG 58.174 50.000 0.00 0.00 0.00 4.30
592 609 5.461032 TTTTCCGCCACTTGAACAAATAT 57.539 34.783 0.00 0.00 0.00 1.28
747 774 4.640855 CGCCAGGTGTCGACGTGT 62.641 66.667 11.62 0.00 36.42 4.49
800 827 9.696917 CAAATCAGACTAAAAGTGCCTTTTATT 57.303 29.630 15.85 12.32 42.53 1.40
807 834 4.503741 TGCAAATCAGACTAAAAGTGCC 57.496 40.909 0.00 0.00 0.00 5.01
868 895 2.846206 AGCAGATTGGTACCAGGATTGA 59.154 45.455 15.65 0.00 0.00 2.57
874 901 2.787473 TGGAAGCAGATTGGTACCAG 57.213 50.000 15.65 4.48 0.00 4.00
898 925 9.185192 GAGTTAATTGCAAGTATCATAATTGGC 57.815 33.333 15.19 0.66 34.59 4.52
905 932 8.481314 TCAGAGAGAGTTAATTGCAAGTATCAT 58.519 33.333 15.19 5.43 0.00 2.45
908 935 7.651304 CGATCAGAGAGAGTTAATTGCAAGTAT 59.349 37.037 7.53 0.00 0.00 2.12
971 1004 1.914764 AGGGGTAACGGCGAGGAAA 60.915 57.895 16.62 0.00 37.60 3.13
972 1005 2.284112 AGGGGTAACGGCGAGGAA 60.284 61.111 16.62 0.00 37.60 3.36
1164 1238 3.254060 CGACGACACCAGAATCAAAGAT 58.746 45.455 0.00 0.00 0.00 2.40
1174 1248 3.220999 TTCCCTGCGACGACACCAG 62.221 63.158 0.00 0.00 0.00 4.00
1224 1298 4.292178 GATCCTCCGCCGCTCCTG 62.292 72.222 0.00 0.00 0.00 3.86
1233 1307 2.202932 CAGGCGGTTGATCCTCCG 60.203 66.667 17.57 17.57 45.20 4.63
1259 1333 2.994995 TCCATCCCTGACGCGTGT 60.995 61.111 20.70 0.00 0.00 4.49
1325 1399 1.289066 CCGGAACAGAAGCTCGTCA 59.711 57.895 0.00 0.00 0.00 4.35
1543 1629 2.910199 TGCTGTACTCATCCATGAAGC 58.090 47.619 0.00 4.61 37.42 3.86
1567 1653 0.259356 CCCTCTCCGGTACTCCTCTT 59.741 60.000 0.00 0.00 0.00 2.85
1568 1654 0.623911 TCCCTCTCCGGTACTCCTCT 60.624 60.000 0.00 0.00 0.00 3.69
1616 1702 2.107141 GGGGCTCCGTTCTCATCG 59.893 66.667 0.00 0.00 0.00 3.84
1658 1797 7.288810 AGCAAACAAATTCAATTCCTACTGA 57.711 32.000 0.00 0.00 0.00 3.41
1659 1798 7.095523 CCAAGCAAACAAATTCAATTCCTACTG 60.096 37.037 0.00 0.00 0.00 2.74
1662 1801 6.705381 CACCAAGCAAACAAATTCAATTCCTA 59.295 34.615 0.00 0.00 0.00 2.94
1664 1803 5.296531 ACACCAAGCAAACAAATTCAATTCC 59.703 36.000 0.00 0.00 0.00 3.01
1665 1804 6.193761 CACACCAAGCAAACAAATTCAATTC 58.806 36.000 0.00 0.00 0.00 2.17
1666 1805 5.066246 CCACACCAAGCAAACAAATTCAATT 59.934 36.000 0.00 0.00 0.00 2.32
1669 1809 3.196469 TCCACACCAAGCAAACAAATTCA 59.804 39.130 0.00 0.00 0.00 2.57
1672 1812 3.197549 AGTTCCACACCAAGCAAACAAAT 59.802 39.130 0.00 0.00 0.00 2.32
1674 1814 2.094286 CAGTTCCACACCAAGCAAACAA 60.094 45.455 0.00 0.00 0.00 2.83
1686 1826 1.543208 GCACTCATCCACAGTTCCACA 60.543 52.381 0.00 0.00 0.00 4.17
1687 1827 1.160137 GCACTCATCCACAGTTCCAC 58.840 55.000 0.00 0.00 0.00 4.02
1688 1828 1.059098 AGCACTCATCCACAGTTCCA 58.941 50.000 0.00 0.00 0.00 3.53
1689 1829 1.808945 CAAGCACTCATCCACAGTTCC 59.191 52.381 0.00 0.00 0.00 3.62
1690 1830 2.498167 ACAAGCACTCATCCACAGTTC 58.502 47.619 0.00 0.00 0.00 3.01
1691 1831 2.645838 ACAAGCACTCATCCACAGTT 57.354 45.000 0.00 0.00 0.00 3.16
1692 1832 2.645838 AACAAGCACTCATCCACAGT 57.354 45.000 0.00 0.00 0.00 3.55
1693 1833 5.392380 GGATTAAACAAGCACTCATCCACAG 60.392 44.000 0.00 0.00 30.81 3.66
1741 1886 2.639065 TCCTGAACCTGAACACAACAC 58.361 47.619 0.00 0.00 0.00 3.32
1748 1893 4.810191 AGTAGTCATCCTGAACCTGAAC 57.190 45.455 0.00 0.00 0.00 3.18
1749 1894 4.593206 ACAAGTAGTCATCCTGAACCTGAA 59.407 41.667 0.00 0.00 0.00 3.02
1855 2003 8.834465 GTTCAGAACATAGCAATATGACTCAAT 58.166 33.333 8.54 0.00 0.00 2.57
1858 2006 8.430801 AAGTTCAGAACATAGCAATATGACTC 57.569 34.615 15.85 0.00 0.00 3.36
2094 2267 3.181443 CCTACTGTCCAAGACCAAACCTT 60.181 47.826 0.00 0.00 0.00 3.50
2117 2290 6.158520 ACAATAGCCATCCTGCCACATATATA 59.841 38.462 0.00 0.00 0.00 0.86
2118 2291 5.044624 ACAATAGCCATCCTGCCACATATAT 60.045 40.000 0.00 0.00 0.00 0.86
2119 2292 4.289410 ACAATAGCCATCCTGCCACATATA 59.711 41.667 0.00 0.00 0.00 0.86
2120 2293 3.074985 ACAATAGCCATCCTGCCACATAT 59.925 43.478 0.00 0.00 0.00 1.78
2147 2320 6.921307 TGCTTTCCCGAATTAGTTTTTCTTTC 59.079 34.615 0.00 0.00 0.00 2.62
2156 2329 2.304761 TCCACTGCTTTCCCGAATTAGT 59.695 45.455 0.00 0.00 0.00 2.24
2170 2343 1.967319 TTTTCCACAGACTCCACTGC 58.033 50.000 0.00 0.00 41.06 4.40
2176 2349 6.486993 AGGTTTACTTCATTTTCCACAGACTC 59.513 38.462 0.00 0.00 0.00 3.36
2177 2350 6.365520 AGGTTTACTTCATTTTCCACAGACT 58.634 36.000 0.00 0.00 0.00 3.24
2377 3025 7.347222 ACATAAGGTGGAGGTCAACATATCTAA 59.653 37.037 0.00 0.00 34.94 2.10
2428 3076 6.109156 TCTTGTGTTTAGGCTCAGTAATGA 57.891 37.500 0.00 0.00 0.00 2.57
2430 3078 4.938226 GCTCTTGTGTTTAGGCTCAGTAAT 59.062 41.667 0.00 0.00 0.00 1.89
2431 3079 4.202315 TGCTCTTGTGTTTAGGCTCAGTAA 60.202 41.667 0.00 0.00 0.00 2.24
2432 3080 3.323691 TGCTCTTGTGTTTAGGCTCAGTA 59.676 43.478 0.00 0.00 0.00 2.74
2434 3082 2.771089 TGCTCTTGTGTTTAGGCTCAG 58.229 47.619 0.00 0.00 0.00 3.35
2460 3108 7.386848 ACAGAGATTCCAAATGCAATTTCTTTG 59.613 33.333 0.00 0.00 44.81 2.77
2470 3119 3.841643 CAACCACAGAGATTCCAAATGC 58.158 45.455 0.00 0.00 0.00 3.56
2491 3140 3.445805 ACAGACTAGGCTTCTCAAGTAGC 59.554 47.826 0.00 0.40 37.67 3.58
2492 3141 4.702612 TCACAGACTAGGCTTCTCAAGTAG 59.297 45.833 0.00 0.00 0.00 2.57
2493 3142 4.663334 TCACAGACTAGGCTTCTCAAGTA 58.337 43.478 0.00 0.00 0.00 2.24
2494 3143 3.501349 TCACAGACTAGGCTTCTCAAGT 58.499 45.455 0.00 0.00 0.00 3.16
2495 3144 4.241681 GTTCACAGACTAGGCTTCTCAAG 58.758 47.826 0.00 0.00 0.00 3.02
2496 3145 3.305403 CGTTCACAGACTAGGCTTCTCAA 60.305 47.826 0.00 0.00 0.00 3.02
2497 3146 2.229062 CGTTCACAGACTAGGCTTCTCA 59.771 50.000 0.00 0.00 0.00 3.27
2498 3147 2.869897 CGTTCACAGACTAGGCTTCTC 58.130 52.381 0.00 0.00 0.00 2.87
2499 3148 1.067495 GCGTTCACAGACTAGGCTTCT 60.067 52.381 0.00 0.00 0.00 2.85
2500 3149 1.067495 AGCGTTCACAGACTAGGCTTC 60.067 52.381 0.00 0.00 29.54 3.86
2501 3150 0.969894 AGCGTTCACAGACTAGGCTT 59.030 50.000 0.00 0.00 29.54 4.35
2502 3151 0.528470 GAGCGTTCACAGACTAGGCT 59.472 55.000 0.00 0.00 35.89 4.58
2503 3152 0.528470 AGAGCGTTCACAGACTAGGC 59.472 55.000 1.01 0.00 0.00 3.93
2504 3153 4.640789 ATAAGAGCGTTCACAGACTAGG 57.359 45.455 1.01 0.00 0.00 3.02
2505 3154 8.132362 AGAAATATAAGAGCGTTCACAGACTAG 58.868 37.037 1.01 0.00 0.00 2.57
2506 3155 7.997482 AGAAATATAAGAGCGTTCACAGACTA 58.003 34.615 1.01 0.00 0.00 2.59
2507 3156 6.868622 AGAAATATAAGAGCGTTCACAGACT 58.131 36.000 1.01 0.00 0.00 3.24
2508 3157 7.527084 AAGAAATATAAGAGCGTTCACAGAC 57.473 36.000 1.01 0.00 0.00 3.51
2509 3158 9.084164 GTAAAGAAATATAAGAGCGTTCACAGA 57.916 33.333 1.01 0.00 0.00 3.41
2510 3159 8.869897 TGTAAAGAAATATAAGAGCGTTCACAG 58.130 33.333 1.01 0.00 0.00 3.66
2511 3160 8.766000 TGTAAAGAAATATAAGAGCGTTCACA 57.234 30.769 1.01 0.00 0.00 3.58
2512 3161 9.084164 TCTGTAAAGAAATATAAGAGCGTTCAC 57.916 33.333 1.01 0.00 0.00 3.18
2513 3162 9.302345 CTCTGTAAAGAAATATAAGAGCGTTCA 57.698 33.333 1.01 0.00 0.00 3.18
2514 3163 8.756864 CCTCTGTAAAGAAATATAAGAGCGTTC 58.243 37.037 0.00 0.00 0.00 3.95
2515 3164 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
2516 3165 7.210873 CCCTCTGTAAAGAAATATAAGAGCGT 58.789 38.462 0.00 0.00 0.00 5.07
2517 3166 6.647067 CCCCTCTGTAAAGAAATATAAGAGCG 59.353 42.308 0.00 0.00 0.00 5.03
2518 3167 6.937465 CCCCCTCTGTAAAGAAATATAAGAGC 59.063 42.308 0.00 0.00 0.00 4.09
2519 3168 8.035448 ACCCCCTCTGTAAAGAAATATAAGAG 57.965 38.462 0.00 0.00 0.00 2.85
2520 3169 9.684702 ATACCCCCTCTGTAAAGAAATATAAGA 57.315 33.333 0.00 0.00 0.00 2.10
2521 3170 9.726438 CATACCCCCTCTGTAAAGAAATATAAG 57.274 37.037 0.00 0.00 0.00 1.73
2522 3171 9.232882 ACATACCCCCTCTGTAAAGAAATATAA 57.767 33.333 0.00 0.00 0.00 0.98
2523 3172 8.808240 ACATACCCCCTCTGTAAAGAAATATA 57.192 34.615 0.00 0.00 0.00 0.86
2524 3173 7.707467 ACATACCCCCTCTGTAAAGAAATAT 57.293 36.000 0.00 0.00 0.00 1.28
2525 3174 7.519347 AACATACCCCCTCTGTAAAGAAATA 57.481 36.000 0.00 0.00 0.00 1.40
2526 3175 6.402981 AACATACCCCCTCTGTAAAGAAAT 57.597 37.500 0.00 0.00 0.00 2.17
2527 3176 5.853572 AACATACCCCCTCTGTAAAGAAA 57.146 39.130 0.00 0.00 0.00 2.52
2528 3177 5.853572 AAACATACCCCCTCTGTAAAGAA 57.146 39.130 0.00 0.00 0.00 2.52
2529 3178 5.853572 AAAACATACCCCCTCTGTAAAGA 57.146 39.130 0.00 0.00 0.00 2.52
2530 3179 8.589701 AATAAAAACATACCCCCTCTGTAAAG 57.410 34.615 0.00 0.00 0.00 1.85
2531 3180 8.808092 CAAATAAAAACATACCCCCTCTGTAAA 58.192 33.333 0.00 0.00 0.00 2.01
2532 3181 7.951245 ACAAATAAAAACATACCCCCTCTGTAA 59.049 33.333 0.00 0.00 0.00 2.41
2533 3182 7.471890 ACAAATAAAAACATACCCCCTCTGTA 58.528 34.615 0.00 0.00 0.00 2.74
2534 3183 6.319715 ACAAATAAAAACATACCCCCTCTGT 58.680 36.000 0.00 0.00 0.00 3.41
2535 3184 6.127451 GGACAAATAAAAACATACCCCCTCTG 60.127 42.308 0.00 0.00 0.00 3.35
2536 3185 5.955959 GGACAAATAAAAACATACCCCCTCT 59.044 40.000 0.00 0.00 0.00 3.69
2537 3186 5.955959 AGGACAAATAAAAACATACCCCCTC 59.044 40.000 0.00 0.00 0.00 4.30
2538 3187 5.910931 AGGACAAATAAAAACATACCCCCT 58.089 37.500 0.00 0.00 0.00 4.79
2539 3188 6.614694 AAGGACAAATAAAAACATACCCCC 57.385 37.500 0.00 0.00 0.00 5.40
2540 3189 8.911918 AAAAAGGACAAATAAAAACATACCCC 57.088 30.769 0.00 0.00 0.00 4.95
2585 3234 9.819267 GCAAAATGGAAACTACTAGACTATACT 57.181 33.333 0.00 0.00 0.00 2.12
2586 3235 9.819267 AGCAAAATGGAAACTACTAGACTATAC 57.181 33.333 0.00 0.00 0.00 1.47
2588 3237 9.740710 AAAGCAAAATGGAAACTACTAGACTAT 57.259 29.630 0.00 0.00 0.00 2.12
2589 3238 9.216117 GAAAGCAAAATGGAAACTACTAGACTA 57.784 33.333 0.00 0.00 0.00 2.59
2590 3239 7.719633 TGAAAGCAAAATGGAAACTACTAGACT 59.280 33.333 0.00 0.00 0.00 3.24
2591 3240 7.871853 TGAAAGCAAAATGGAAACTACTAGAC 58.128 34.615 0.00 0.00 0.00 2.59
2592 3241 8.458573 TTGAAAGCAAAATGGAAACTACTAGA 57.541 30.769 0.00 0.00 0.00 2.43
2593 3242 9.528018 TTTTGAAAGCAAAATGGAAACTACTAG 57.472 29.630 0.00 0.00 46.09 2.57
2609 3258 9.875675 GTTTATTATTGCATTGTTTTGAAAGCA 57.124 25.926 0.00 0.00 0.00 3.91
2610 3259 9.875675 TGTTTATTATTGCATTGTTTTGAAAGC 57.124 25.926 0.00 0.00 0.00 3.51
2632 3281 9.124807 TCGTTTTGTTTTGTTTTGTTTTTGTTT 57.875 22.222 0.00 0.00 0.00 2.83
2633 3282 8.669394 TCGTTTTGTTTTGTTTTGTTTTTGTT 57.331 23.077 0.00 0.00 0.00 2.83
2634 3283 7.429630 CCTCGTTTTGTTTTGTTTTGTTTTTGT 59.570 29.630 0.00 0.00 0.00 2.83
2635 3284 7.429630 ACCTCGTTTTGTTTTGTTTTGTTTTTG 59.570 29.630 0.00 0.00 0.00 2.44
2636 3285 7.473366 ACCTCGTTTTGTTTTGTTTTGTTTTT 58.527 26.923 0.00 0.00 0.00 1.94
2637 3286 7.011576 AGACCTCGTTTTGTTTTGTTTTGTTTT 59.988 29.630 0.00 0.00 0.00 2.43
2638 3287 6.480651 AGACCTCGTTTTGTTTTGTTTTGTTT 59.519 30.769 0.00 0.00 0.00 2.83
2639 3288 5.986741 AGACCTCGTTTTGTTTTGTTTTGTT 59.013 32.000 0.00 0.00 0.00 2.83
2640 3289 5.534407 AGACCTCGTTTTGTTTTGTTTTGT 58.466 33.333 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.