Multiple sequence alignment - TraesCS4D01G202100

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 TraesCS4D01G202100 chr4D 100.000 2735 0 0 1 2735 349017704 349014970 0.000000e+00 5051.0
1 TraesCS4D01G202100 chr4D 92.453 53 4 0 1941 1993 439770758 439770706 2.920000e-10 76.8
2 TraesCS4D01G202100 chr4D 92.453 53 4 0 1941 1993 466280567 466280515 2.920000e-10 76.8
3 TraesCS4D01G202100 chr4A 95.039 1149 41 8 804 1942 115910284 115911426 0.000000e+00 1792.0
4 TraesCS4D01G202100 chr3B 93.771 1204 55 10 741 1942 581333090 581334275 0.000000e+00 1790.0
5 TraesCS4D01G202100 chr3B 90.439 387 33 3 2103 2488 8496751 8497134 8.740000e-140 507.0
6 TraesCS4D01G202100 chr3B 89.041 73 6 2 553 624 750345600 750345671 3.750000e-14 89.8
7 TraesCS4D01G202100 chr4B 92.794 1138 49 12 810 1942 429099704 429098595 0.000000e+00 1616.0
8 TraesCS4D01G202100 chr4B 86.216 798 58 22 2 777 429100468 429099701 0.000000e+00 817.0
9 TraesCS4D01G202100 chr4B 96.154 52 2 0 1942 1993 187737205 187737154 4.850000e-13 86.1
10 TraesCS4D01G202100 chr4B 87.931 58 5 1 1925 1982 658457159 658457214 1.760000e-07 67.6
11 TraesCS4D01G202100 chr6A 91.032 591 30 13 1 571 466219754 466220341 0.000000e+00 776.0
12 TraesCS4D01G202100 chr6A 91.579 380 27 4 2107 2484 10984299 10984675 1.120000e-143 520.0
13 TraesCS4D01G202100 chr6A 89.091 330 19 5 755 1078 466295044 466295362 7.100000e-106 394.0
14 TraesCS4D01G202100 chr6A 91.753 194 15 1 1750 1942 466322384 466322577 4.490000e-68 268.0
15 TraesCS4D01G202100 chr6A 88.785 107 10 2 1992 2097 158433697 158433802 2.210000e-26 130.0
16 TraesCS4D01G202100 chr6A 84.932 73 10 1 553 624 1245294 1245222 3.780000e-09 73.1
17 TraesCS4D01G202100 chr6A 85.507 69 9 1 1925 1993 543374318 543374385 1.360000e-08 71.3
18 TraesCS4D01G202100 chr2D 93.473 383 21 3 2106 2487 502498009 502498388 1.420000e-157 566.0
19 TraesCS4D01G202100 chr2D 84.146 328 36 6 2 313 551339191 551339518 1.230000e-78 303.0
20 TraesCS4D01G202100 chr2D 88.571 105 11 1 1992 2095 15919515 15919411 2.860000e-25 126.0
21 TraesCS4D01G202100 chr2D 89.333 75 7 1 551 624 646638683 646638757 2.900000e-15 93.5
22 TraesCS4D01G202100 chr2D 90.000 70 6 1 556 624 625475653 625475722 3.750000e-14 89.8
23 TraesCS4D01G202100 chr2D 94.231 52 3 0 1942 1993 328796536 328796485 2.260000e-11 80.5
24 TraesCS4D01G202100 chr2D 83.824 68 10 1 556 622 93278734 93278667 2.270000e-06 63.9
25 TraesCS4D01G202100 chr6D 91.885 382 26 4 2107 2486 418629091 418628713 1.870000e-146 529.0
26 TraesCS4D01G202100 chr6D 91.944 360 28 1 2107 2465 433309323 433309682 1.130000e-138 503.0
27 TraesCS4D01G202100 chr6D 95.730 281 10 2 2456 2735 418628615 418628336 4.150000e-123 451.0
28 TraesCS4D01G202100 chr6D 92.722 316 14 7 2427 2735 433309745 433310058 5.370000e-122 448.0
29 TraesCS4D01G202100 chr6D 92.063 315 18 5 2427 2735 22135320 22135633 1.160000e-118 436.0
30 TraesCS4D01G202100 chr6D 86.301 73 9 1 553 624 400742600 400742672 8.120000e-11 78.7
31 TraesCS4D01G202100 chr6D 86.567 67 7 2 1928 1993 55943809 55943744 3.780000e-09 73.1
32 TraesCS4D01G202100 chr6D 100.000 28 0 0 1941 1968 446531315 446531342 5.000000e-03 52.8
33 TraesCS4D01G202100 chr1D 90.576 382 30 5 2107 2486 29835254 29834877 4.070000e-138 501.0
34 TraesCS4D01G202100 chr1D 92.628 312 16 5 2427 2732 217008997 217009307 2.500000e-120 442.0
35 TraesCS4D01G202100 chr1D 93.478 46 3 0 1940 1985 289963983 289964028 4.890000e-08 69.4
36 TraesCS4D01G202100 chr5A 90.289 381 32 4 2106 2484 7707244 7707621 6.800000e-136 494.0
37 TraesCS4D01G202100 chr5A 86.916 107 13 1 1992 2097 675387997 675388103 4.780000e-23 119.0
38 TraesCS4D01G202100 chr5A 90.541 74 6 1 552 624 573947951 573947878 2.240000e-16 97.1
39 TraesCS4D01G202100 chr5A 82.667 75 8 5 553 624 503545133 503545061 8.180000e-06 62.1
40 TraesCS4D01G202100 chr1A 90.000 380 33 4 2107 2484 460600961 460601337 1.140000e-133 486.0
41 TraesCS4D01G202100 chr7D 89.610 385 34 5 2104 2486 530413291 530412911 4.090000e-133 484.0
42 TraesCS4D01G202100 chr7D 92.675 314 16 6 2427 2735 614073496 614073185 1.930000e-121 446.0
43 TraesCS4D01G202100 chr7D 89.333 75 7 1 551 624 168489602 168489676 2.900000e-15 93.5
44 TraesCS4D01G202100 chr7D 92.453 53 4 0 1941 1993 1021719 1021771 2.920000e-10 76.8
45 TraesCS4D01G202100 chr7D 95.556 45 2 0 1941 1985 606656781 606656825 3.780000e-09 73.1
46 TraesCS4D01G202100 chr5D 92.971 313 16 5 2427 2735 124348947 124348637 4.150000e-123 451.0
47 TraesCS4D01G202100 chr5D 91.772 316 16 8 2427 2735 477485351 477485663 5.410000e-117 431.0
48 TraesCS4D01G202100 chr5D 91.746 315 18 6 2427 2735 535498184 535497872 5.410000e-117 431.0
49 TraesCS4D01G202100 chr5D 87.931 116 13 1 1992 2106 51177884 51177999 4.750000e-28 135.0
50 TraesCS4D01G202100 chr5D 94.444 54 3 0 1940 1993 133319932 133319985 1.750000e-12 84.2
51 TraesCS4D01G202100 chr5D 94.231 52 3 0 1941 1992 84800991 84800940 2.260000e-11 80.5
52 TraesCS4D01G202100 chr5D 83.333 78 12 1 554 630 504998681 504998604 1.360000e-08 71.3
53 TraesCS4D01G202100 chr5D 93.478 46 3 0 1948 1993 272147797 272147752 4.890000e-08 69.4
54 TraesCS4D01G202100 chr5D 94.595 37 0 2 1934 1968 564123625 564123589 3.800000e-04 56.5
55 TraesCS4D01G202100 chr3D 91.693 313 18 6 2427 2733 586940868 586941178 7.000000e-116 427.0
56 TraesCS4D01G202100 chr3A 83.333 348 43 15 2388 2726 595952782 595952441 9.510000e-80 307.0
57 TraesCS4D01G202100 chr3A 82.407 216 20 9 110 307 705114249 705114464 3.620000e-39 172.0
58 TraesCS4D01G202100 chr3A 81.279 219 27 1 110 314 713785459 713785241 6.060000e-37 165.0
59 TraesCS4D01G202100 chr3A 88.793 116 12 1 1992 2106 12613043 12612928 1.020000e-29 141.0
60 TraesCS4D01G202100 chr3A 89.041 73 7 1 553 624 35423442 35423370 3.750000e-14 89.8
61 TraesCS4D01G202100 chr3A 86.842 76 7 3 556 630 39399292 39399219 6.280000e-12 82.4
62 TraesCS4D01G202100 chr7B 90.654 107 9 1 1992 2097 512762966 512763072 1.020000e-29 141.0
63 TraesCS4D01G202100 chr7B 90.541 74 6 1 552 624 637030478 637030405 2.240000e-16 97.1
64 TraesCS4D01G202100 chr7B 85.897 78 10 1 548 624 354388403 354388480 6.280000e-12 82.4
65 TraesCS4D01G202100 chr2A 90.654 107 9 1 1992 2097 532857956 532857850 1.020000e-29 141.0
66 TraesCS4D01G202100 chr2A 92.708 96 5 2 468 563 252086769 252086862 1.320000e-28 137.0
67 TraesCS4D01G202100 chr2A 86.087 115 15 1 1992 2105 113347929 113347815 3.700000e-24 122.0
68 TraesCS4D01G202100 chr6B 87.931 116 13 1 1992 2106 497222195 497222080 4.750000e-28 135.0
69 TraesCS4D01G202100 chr6B 89.189 74 7 1 552 624 91116901 91116828 1.040000e-14 91.6
70 TraesCS4D01G202100 chr5B 89.189 74 4 4 556 627 711460201 711460272 3.750000e-14 89.8
71 TraesCS4D01G202100 chr5B 94.286 35 1 1 591 624 542813893 542813859 5.000000e-03 52.8
72 TraesCS4D01G202100 chr1B 94.340 53 3 0 1941 1993 325989513 325989565 6.280000e-12 82.4
73 TraesCS4D01G202100 chr7A 90.323 62 3 2 1928 1989 26765182 26765124 8.120000e-11 78.7
74 TraesCS4D01G202100 chr7A 89.655 58 4 1 1928 1985 498321249 498321304 3.780000e-09 73.1


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 TraesCS4D01G202100 chr4D 349014970 349017704 2734 True 5051.0 5051 100.0000 1 2735 1 chr4D.!!$R1 2734
1 TraesCS4D01G202100 chr4A 115910284 115911426 1142 False 1792.0 1792 95.0390 804 1942 1 chr4A.!!$F1 1138
2 TraesCS4D01G202100 chr3B 581333090 581334275 1185 False 1790.0 1790 93.7710 741 1942 1 chr3B.!!$F2 1201
3 TraesCS4D01G202100 chr4B 429098595 429100468 1873 True 1216.5 1616 89.5050 2 1942 2 chr4B.!!$R2 1940
4 TraesCS4D01G202100 chr6A 466219754 466220341 587 False 776.0 776 91.0320 1 571 1 chr6A.!!$F3 570
5 TraesCS4D01G202100 chr6D 418628336 418629091 755 True 490.0 529 93.8075 2107 2735 2 chr6D.!!$R2 628
6 TraesCS4D01G202100 chr6D 433309323 433310058 735 False 475.5 503 92.3330 2107 2735 2 chr6D.!!$F4 628

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
726 749 0.301687 CGGCTGTCGTGCATGTTATC 59.698 55.0 5.68 0.0 34.04 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2149 0.103572 GGCAGTTATCGGCGTCCTAA 59.896 55.0 6.85 0.95 35.7 2.69 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
21 22 4.657814 ATAGTGAGGTTGTGGGAATTGT 57.342 40.909 0.00 0.00 0.00 2.71
105 107 5.705905 GTGAAGCACCCTGTAATTCTAAAGT 59.294 40.000 0.00 0.00 0.00 2.66
112 114 7.389607 GCACCCTGTAATTCTAAAGTAAACTCA 59.610 37.037 0.00 0.00 0.00 3.41
175 177 1.133482 GCCCTACCCTGCATTACCATT 60.133 52.381 0.00 0.00 0.00 3.16
195 197 0.698238 AGCACATACCTTGAAGGCCA 59.302 50.000 11.96 0.00 39.63 5.36
404 425 4.803426 GAGGTGCCGCGGACTGAG 62.803 72.222 33.48 0.01 0.00 3.35
420 441 1.136984 GAGGACGGACTACACGCAG 59.863 63.158 0.00 0.00 34.00 5.18
432 453 4.438346 ACGCAGTGGTCTGTTGTC 57.562 55.556 0.00 0.00 42.51 3.18
449 470 1.073125 TGTCGATTGGGCTTTCTTCCA 59.927 47.619 0.00 0.00 0.00 3.53
581 603 3.568007 GTGGTTAGGTTGCATGTCAAGAA 59.432 43.478 3.27 0.00 34.91 2.52
595 617 9.013229 TGCATGTCAAGAAAAATAAGATAGTGT 57.987 29.630 0.00 0.00 0.00 3.55
656 679 2.168313 TGAGGTATTCGAATGCAGAGCA 59.832 45.455 24.64 14.43 44.86 4.26
675 698 4.735132 ACGTGTCCGGGCACATCG 62.735 66.667 36.28 25.81 39.19 3.84
719 742 3.947841 GTTTGCGGCTGTCGTGCA 61.948 61.111 2.76 0.00 41.72 4.57
720 743 2.977456 TTTGCGGCTGTCGTGCAT 60.977 55.556 2.76 0.00 41.72 3.96
721 744 3.252665 TTTGCGGCTGTCGTGCATG 62.253 57.895 2.76 0.00 41.72 4.06
722 745 4.986645 TGCGGCTGTCGTGCATGT 62.987 61.111 5.68 0.00 41.72 3.21
723 746 3.726517 GCGGCTGTCGTGCATGTT 61.727 61.111 5.68 0.00 41.72 2.71
724 747 2.387445 GCGGCTGTCGTGCATGTTA 61.387 57.895 5.68 0.00 41.72 2.41
725 748 1.705337 GCGGCTGTCGTGCATGTTAT 61.705 55.000 5.68 0.00 41.72 1.89
726 749 0.301687 CGGCTGTCGTGCATGTTATC 59.698 55.000 5.68 0.00 34.04 1.75
749 772 4.201980 CCAACACGATCGATACAGTAGGAA 60.202 45.833 24.34 0.00 0.00 3.36
769 792 5.370880 AGGAAATAGTAACATGCAGGGATCT 59.629 40.000 2.31 0.00 0.00 2.75
773 796 3.110705 AGTAACATGCAGGGATCTGACT 58.889 45.455 2.31 0.00 43.49 3.41
797 820 2.161609 GGATCCGTGCAAAATTCGTTCT 59.838 45.455 0.00 0.00 0.00 3.01
808 831 1.956629 ATTCGTTCTGGGCGTCCGAT 61.957 55.000 0.00 0.00 35.24 4.18
874 897 3.387397 GACCAACGCACTACTAACTGTT 58.613 45.455 0.00 0.00 0.00 3.16
959 985 1.461091 TAAGGCGAGCGTATCCAGGG 61.461 60.000 0.00 0.00 0.00 4.45
960 986 4.301027 GGCGAGCGTATCCAGGGG 62.301 72.222 0.00 0.00 0.00 4.79
961 987 3.224324 GCGAGCGTATCCAGGGGA 61.224 66.667 0.00 0.00 35.55 4.81
962 988 2.792947 GCGAGCGTATCCAGGGGAA 61.793 63.158 0.00 0.00 34.34 3.97
1086 1119 2.942879 CGCGAGATCGAGAGGAGG 59.057 66.667 0.00 0.00 41.67 4.30
1212 1245 2.291043 AAAGCGGGAGTGGGTCGAT 61.291 57.895 0.00 0.00 0.00 3.59
1293 1332 2.836306 GAACGATGACGCGCGAGAC 61.836 63.158 39.36 25.45 43.96 3.36
1294 1333 3.604494 AACGATGACGCGCGAGACA 62.604 57.895 39.36 29.86 43.96 3.41
1295 1334 3.308008 CGATGACGCGCGAGACAG 61.308 66.667 39.36 20.02 0.00 3.51
1296 1335 2.100410 GATGACGCGCGAGACAGA 59.900 61.111 39.36 13.04 0.00 3.41
1297 1336 2.202492 ATGACGCGCGAGACAGAC 60.202 61.111 39.36 17.12 0.00 3.51
1298 1337 2.850786 GATGACGCGCGAGACAGACA 62.851 60.000 39.36 21.71 0.00 3.41
1343 1382 0.672342 GAGGAACTATCGGCGGCTTA 59.328 55.000 7.21 0.00 41.55 3.09
1408 1447 3.200887 CTCGAGGAAGATCGGCGGG 62.201 68.421 7.21 0.00 42.93 6.13
1677 1716 2.099062 GCATGCGCAACGAGGAAG 59.901 61.111 17.11 0.00 38.36 3.46
1678 1717 2.390599 GCATGCGCAACGAGGAAGA 61.391 57.895 17.11 0.00 38.36 2.87
1778 1821 4.410743 GCAGCTTTGTCCTGCGGC 62.411 66.667 0.00 0.00 45.20 6.53
1782 1825 2.740714 GCTTTGTCCTGCGGCGTAG 61.741 63.158 18.43 18.43 0.00 3.51
1798 1841 2.316792 CGTAGTCAGAGGTTTCGTGTG 58.683 52.381 0.00 0.00 0.00 3.82
1888 1934 7.610580 TTTGTCTGGATATTTTTCACCCTTT 57.389 32.000 0.00 0.00 0.00 3.11
1901 1947 0.246635 ACCCTTTGTCCTCGATCGTG 59.753 55.000 15.94 12.87 0.00 4.35
1905 1951 4.829518 TGTCCTCGATCGTGCGCG 62.830 66.667 14.79 14.79 39.92 6.86
1954 2000 7.859325 TTATTAGGTCAACTAGAACAATGCC 57.141 36.000 0.00 0.00 35.97 4.40
1955 2001 3.073274 AGGTCAACTAGAACAATGCCC 57.927 47.619 0.00 0.00 35.97 5.36
1956 2002 1.737793 GGTCAACTAGAACAATGCCCG 59.262 52.381 0.00 0.00 32.78 6.13
1957 2003 2.423577 GTCAACTAGAACAATGCCCGT 58.576 47.619 0.00 0.00 0.00 5.28
1958 2004 2.159627 GTCAACTAGAACAATGCCCGTG 59.840 50.000 0.00 0.00 0.00 4.94
1959 2005 1.135689 CAACTAGAACAATGCCCGTGC 60.136 52.381 0.00 0.00 38.26 5.34
1960 2006 1.019278 ACTAGAACAATGCCCGTGCG 61.019 55.000 0.00 0.00 41.78 5.34
1961 2007 1.004320 TAGAACAATGCCCGTGCGT 60.004 52.632 0.00 0.00 41.78 5.24
1966 2012 3.600694 AATGCCCGTGCGTTGCAA 61.601 55.556 0.00 0.00 44.90 4.08
1967 2013 3.839642 AATGCCCGTGCGTTGCAAC 62.840 57.895 19.89 19.89 44.90 4.17
1969 2015 4.560856 GCCCGTGCGTTGCAACAA 62.561 61.111 28.01 13.69 41.47 2.83
1970 2016 2.353376 CCCGTGCGTTGCAACAAG 60.353 61.111 28.01 14.52 41.47 3.16
1971 2017 2.712539 CCGTGCGTTGCAACAAGA 59.287 55.556 28.01 9.09 41.47 3.02
1972 2018 1.282570 CCGTGCGTTGCAACAAGAT 59.717 52.632 28.01 0.00 41.47 2.40
1973 2019 0.515127 CCGTGCGTTGCAACAAGATA 59.485 50.000 28.01 7.20 41.47 1.98
1974 2020 1.130373 CCGTGCGTTGCAACAAGATAT 59.870 47.619 28.01 0.00 41.47 1.63
1975 2021 2.350192 CCGTGCGTTGCAACAAGATATA 59.650 45.455 28.01 4.13 41.47 0.86
1976 2022 3.181515 CCGTGCGTTGCAACAAGATATAA 60.182 43.478 28.01 2.35 41.47 0.98
1977 2023 4.399112 CGTGCGTTGCAACAAGATATAAA 58.601 39.130 28.01 0.84 41.47 1.40
1978 2024 5.027737 CGTGCGTTGCAACAAGATATAAAT 58.972 37.500 28.01 0.00 41.47 1.40
1979 2025 6.188871 CGTGCGTTGCAACAAGATATAAATA 58.811 36.000 28.01 0.00 41.47 1.40
1980 2026 6.850823 CGTGCGTTGCAACAAGATATAAATAT 59.149 34.615 28.01 0.00 41.47 1.28
1981 2027 7.375808 CGTGCGTTGCAACAAGATATAAATATT 59.624 33.333 28.01 0.00 41.47 1.28
1982 2028 8.682016 GTGCGTTGCAACAAGATATAAATATTC 58.318 33.333 28.01 0.00 41.47 1.75
1983 2029 8.620416 TGCGTTGCAACAAGATATAAATATTCT 58.380 29.630 28.01 0.00 34.76 2.40
2083 2129 9.995003 ATTAAAGTGAAATTTGTTCATAAGGCA 57.005 25.926 0.00 0.00 0.00 4.75
2084 2130 9.823647 TTAAAGTGAAATTTGTTCATAAGGCAA 57.176 25.926 0.00 0.00 0.00 4.52
2085 2131 7.951530 AAGTGAAATTTGTTCATAAGGCAAG 57.048 32.000 0.00 0.00 0.00 4.01
2086 2132 7.054491 AGTGAAATTTGTTCATAAGGCAAGT 57.946 32.000 0.00 0.00 0.00 3.16
2087 2133 8.177119 AGTGAAATTTGTTCATAAGGCAAGTA 57.823 30.769 0.00 0.00 0.00 2.24
2088 2134 8.637986 AGTGAAATTTGTTCATAAGGCAAGTAA 58.362 29.630 0.00 0.00 0.00 2.24
2089 2135 9.255304 GTGAAATTTGTTCATAAGGCAAGTAAA 57.745 29.630 0.00 0.00 0.00 2.01
2090 2136 9.995003 TGAAATTTGTTCATAAGGCAAGTAAAT 57.005 25.926 0.00 0.00 0.00 1.40
2095 2141 9.921637 TTTGTTCATAAGGCAAGTAAATTAAGG 57.078 29.630 0.00 0.00 0.00 2.69
2096 2142 8.644374 TGTTCATAAGGCAAGTAAATTAAGGT 57.356 30.769 0.00 0.00 0.00 3.50
2097 2143 9.742144 TGTTCATAAGGCAAGTAAATTAAGGTA 57.258 29.630 0.00 0.00 0.00 3.08
2102 2148 9.930158 ATAAGGCAAGTAAATTAAGGTAATCCA 57.070 29.630 0.00 0.00 35.89 3.41
2103 2149 8.838649 AAGGCAAGTAAATTAAGGTAATCCAT 57.161 30.769 0.00 0.00 35.89 3.41
2104 2150 8.838649 AGGCAAGTAAATTAAGGTAATCCATT 57.161 30.769 0.00 0.00 35.89 3.16
2105 2151 9.930158 AGGCAAGTAAATTAAGGTAATCCATTA 57.070 29.630 0.00 0.00 35.89 1.90
2124 2170 1.227556 GGACGCCGATAACTGCCAT 60.228 57.895 0.00 0.00 0.00 4.40
2269 2315 2.256461 GAACACGTACGGGCGAGT 59.744 61.111 19.40 5.61 37.28 4.18
2299 2345 4.086178 CGCACGACTCGTCTCGGT 62.086 66.667 0.00 0.00 38.32 4.69
2356 2402 1.288127 GTCAGTAACCACGCGTCCT 59.712 57.895 9.86 0.00 0.00 3.85
2422 2468 2.293122 TGAACTACAGTTGCCATGTTGC 59.707 45.455 0.00 0.00 38.56 4.17
2423 2469 2.276732 ACTACAGTTGCCATGTTGCT 57.723 45.000 0.00 0.00 32.02 3.91
2424 2470 3.417069 ACTACAGTTGCCATGTTGCTA 57.583 42.857 0.00 0.00 32.02 3.49
2527 2703 4.571176 GGCAAAAACATGTTTCGGGTAAAA 59.429 37.500 23.47 0.00 31.45 1.52
2528 2704 5.064834 GGCAAAAACATGTTTCGGGTAAAAA 59.935 36.000 23.47 0.00 31.45 1.94
2598 2775 2.496111 CCTGCAAAAACACATGGCAAT 58.504 42.857 0.00 0.00 33.58 3.56
2611 2788 5.047164 ACACATGGCAATTGATAGCTTTTGA 60.047 36.000 10.34 0.00 0.00 2.69
2627 2804 1.279496 TTGATGTGTGGGAGAGGAGG 58.721 55.000 0.00 0.00 0.00 4.30
2696 2873 3.832490 ACACTAGACAGTTGCCATGTAGA 59.168 43.478 0.00 0.00 30.46 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.249393 AGAGTTGGAGAAATAGCAGGAAAGA 59.751 40.000 0.00 0.00 0.00 2.52
105 107 3.581755 CGTTGGATCGACCTTGAGTTTA 58.418 45.455 0.00 0.00 39.86 2.01
112 114 4.598257 CAGCGTTGGATCGACCTT 57.402 55.556 0.00 0.00 39.86 3.50
175 177 1.912731 TGGCCTTCAAGGTATGTGCTA 59.087 47.619 5.03 0.00 37.80 3.49
321 338 2.125106 CCCTGCTGTCCTTACCGC 60.125 66.667 0.00 0.00 36.47 5.68
344 365 2.681778 ACTGCCTCCACTCCTCCG 60.682 66.667 0.00 0.00 0.00 4.63
401 422 1.583495 CTGCGTGTAGTCCGTCCTCA 61.583 60.000 0.00 0.00 0.00 3.86
403 424 1.602888 ACTGCGTGTAGTCCGTCCT 60.603 57.895 0.00 0.00 0.00 3.85
404 425 1.443872 CACTGCGTGTAGTCCGTCC 60.444 63.158 1.24 0.00 0.00 4.79
420 441 1.156736 CCCAATCGACAACAGACCAC 58.843 55.000 0.00 0.00 0.00 4.16
421 442 0.605319 GCCCAATCGACAACAGACCA 60.605 55.000 0.00 0.00 0.00 4.02
423 444 1.523758 AAGCCCAATCGACAACAGAC 58.476 50.000 0.00 0.00 0.00 3.51
431 452 2.290896 ACATGGAAGAAAGCCCAATCGA 60.291 45.455 0.00 0.00 35.85 3.59
432 453 2.094675 ACATGGAAGAAAGCCCAATCG 58.905 47.619 0.00 0.00 35.85 3.34
449 470 3.609175 CGAAGGTGTCAATTCGCAAACAT 60.609 43.478 8.12 0.00 41.43 2.71
623 646 9.698309 CATTCGAATACCTCACAACTATAATCT 57.302 33.333 10.97 0.00 0.00 2.40
624 647 8.436200 GCATTCGAATACCTCACAACTATAATC 58.564 37.037 10.97 0.00 0.00 1.75
625 648 7.931407 TGCATTCGAATACCTCACAACTATAAT 59.069 33.333 10.97 0.00 0.00 1.28
626 649 7.269316 TGCATTCGAATACCTCACAACTATAA 58.731 34.615 10.97 0.00 0.00 0.98
629 652 5.079689 TGCATTCGAATACCTCACAACTA 57.920 39.130 10.97 0.00 0.00 2.24
630 653 3.935203 CTGCATTCGAATACCTCACAACT 59.065 43.478 10.97 0.00 0.00 3.16
631 654 3.932710 TCTGCATTCGAATACCTCACAAC 59.067 43.478 10.97 0.00 0.00 3.32
632 655 4.183865 CTCTGCATTCGAATACCTCACAA 58.816 43.478 10.97 0.00 0.00 3.33
633 656 3.785486 CTCTGCATTCGAATACCTCACA 58.215 45.455 10.97 2.20 0.00 3.58
634 657 2.541762 GCTCTGCATTCGAATACCTCAC 59.458 50.000 10.97 0.00 0.00 3.51
656 679 3.311110 ATGTGCCCGGACACGTCT 61.311 61.111 16.55 0.38 43.74 4.18
679 702 0.524414 AAATCCACGCCCTAAAACGC 59.476 50.000 0.00 0.00 0.00 4.84
681 704 1.890489 ACCAAATCCACGCCCTAAAAC 59.110 47.619 0.00 0.00 0.00 2.43
691 714 0.943835 GCCGCAAACACCAAATCCAC 60.944 55.000 0.00 0.00 0.00 4.02
720 743 5.163591 ACTGTATCGATCGTGTTGGATAACA 60.164 40.000 15.94 4.89 44.17 2.41
721 744 5.279384 ACTGTATCGATCGTGTTGGATAAC 58.721 41.667 15.94 0.59 37.32 1.89
722 745 5.509716 ACTGTATCGATCGTGTTGGATAA 57.490 39.130 15.94 0.00 0.00 1.75
723 746 5.180680 CCTACTGTATCGATCGTGTTGGATA 59.819 44.000 15.94 1.28 0.00 2.59
724 747 4.023107 CCTACTGTATCGATCGTGTTGGAT 60.023 45.833 15.94 2.33 0.00 3.41
725 748 3.314357 CCTACTGTATCGATCGTGTTGGA 59.686 47.826 15.94 0.00 0.00 3.53
726 749 3.314357 TCCTACTGTATCGATCGTGTTGG 59.686 47.826 15.94 15.49 0.00 3.77
741 764 5.760253 CCCTGCATGTTACTATTTCCTACTG 59.240 44.000 0.00 0.00 0.00 2.74
749 772 5.367937 AGTCAGATCCCTGCATGTTACTATT 59.632 40.000 0.00 0.00 40.20 1.73
769 792 2.723586 TTTGCACGGATCCGCAGTCA 62.724 55.000 33.62 22.40 44.19 3.41
773 796 0.170116 GAATTTTGCACGGATCCGCA 59.830 50.000 33.62 21.49 44.19 5.69
775 798 0.446222 ACGAATTTTGCACGGATCCG 59.554 50.000 32.20 32.20 46.03 4.18
797 820 2.246761 ATTTCGGAATCGGACGCCCA 62.247 55.000 0.00 0.00 36.95 5.36
808 831 0.606096 TCTCGCTGGACATTTCGGAA 59.394 50.000 0.00 0.00 0.00 4.30
959 985 2.937149 GGGTGATACGCTCTTTCTTTCC 59.063 50.000 0.00 0.00 0.00 3.13
960 986 2.603560 CGGGTGATACGCTCTTTCTTTC 59.396 50.000 0.00 0.00 0.00 2.62
961 987 2.232941 TCGGGTGATACGCTCTTTCTTT 59.767 45.455 0.00 0.00 0.00 2.52
962 988 1.822990 TCGGGTGATACGCTCTTTCTT 59.177 47.619 0.00 0.00 0.00 2.52
1086 1119 6.197364 TGATCGTACTCTTCCTTTCTCTTC 57.803 41.667 0.00 0.00 0.00 2.87
1212 1245 0.737367 CGATCAGCCGTTTCTGCTCA 60.737 55.000 0.00 0.00 36.81 4.26
1293 1332 1.357258 GCATCCTGCGTCTGTGTCTG 61.357 60.000 0.00 0.00 31.71 3.51
1294 1333 1.079543 GCATCCTGCGTCTGTGTCT 60.080 57.895 0.00 0.00 31.71 3.41
1295 1334 3.479370 GCATCCTGCGTCTGTGTC 58.521 61.111 0.00 0.00 31.71 3.67
1343 1382 2.665603 GGCTCTTCTTGGCCTCGT 59.334 61.111 3.32 0.00 44.48 4.18
1514 1553 4.082523 CGTGCATCTCCACCCGGT 62.083 66.667 0.00 0.00 32.10 5.28
1668 1707 4.381079 CGATCTTCTTCCTTCTTCCTCGTT 60.381 45.833 0.00 0.00 0.00 3.85
1676 1715 5.300792 GGACAGATACGATCTTCTTCCTTCT 59.699 44.000 0.00 0.00 37.58 2.85
1677 1716 5.525199 GGACAGATACGATCTTCTTCCTTC 58.475 45.833 0.00 0.00 37.58 3.46
1678 1717 4.036971 CGGACAGATACGATCTTCTTCCTT 59.963 45.833 0.00 0.00 37.58 3.36
1778 1821 2.316792 CACACGAAACCTCTGACTACG 58.683 52.381 0.00 0.00 0.00 3.51
1782 1825 0.531974 TGGCACACGAAACCTCTGAC 60.532 55.000 0.00 0.00 0.00 3.51
1837 1881 7.062255 GCTAAGATTACCATGCACAAAAGTTTC 59.938 37.037 0.00 0.00 0.00 2.78
1888 1934 4.829518 CGCGCACGATCGAGGACA 62.830 66.667 24.34 0.00 43.93 4.02
1901 1947 2.535934 TTGTGAAAATATCCACGCGC 57.464 45.000 5.73 0.00 36.15 6.86
1932 1978 5.193679 GGGCATTGTTCTAGTTGACCTAAT 58.806 41.667 0.00 0.00 34.24 1.73
1938 1984 2.422597 CACGGGCATTGTTCTAGTTGA 58.577 47.619 0.00 0.00 0.00 3.18
1942 1988 1.019278 ACGCACGGGCATTGTTCTAG 61.019 55.000 11.77 0.00 41.24 2.43
1943 1989 0.604243 AACGCACGGGCATTGTTCTA 60.604 50.000 11.77 0.00 41.24 2.10
1944 1990 1.896660 AACGCACGGGCATTGTTCT 60.897 52.632 11.77 0.00 41.24 3.01
1945 1991 1.729131 CAACGCACGGGCATTGTTC 60.729 57.895 10.90 0.00 38.34 3.18
1946 1992 2.334653 CAACGCACGGGCATTGTT 59.665 55.556 10.90 2.50 38.34 2.83
1947 1993 4.341502 GCAACGCACGGGCATTGT 62.342 61.111 20.63 0.74 44.58 2.71
1948 1994 3.837908 TTGCAACGCACGGGCATTG 62.838 57.895 15.24 15.24 45.48 2.82
1949 1995 3.600694 TTGCAACGCACGGGCATT 61.601 55.556 11.77 0.00 38.71 3.56
1950 1996 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
1952 1998 4.560856 TTGTTGCAACGCACGGGC 62.561 61.111 23.79 0.00 38.71 6.13
1953 1999 2.128853 ATCTTGTTGCAACGCACGGG 62.129 55.000 23.79 10.21 38.71 5.28
1954 2000 0.515127 TATCTTGTTGCAACGCACGG 59.485 50.000 23.79 11.80 38.71 4.94
1955 2001 2.525750 ATATCTTGTTGCAACGCACG 57.474 45.000 23.79 12.05 38.71 5.34
1956 2002 8.560576 AATATTTATATCTTGTTGCAACGCAC 57.439 30.769 23.79 1.83 38.71 5.34
1957 2003 8.620416 AGAATATTTATATCTTGTTGCAACGCA 58.380 29.630 23.79 12.55 36.47 5.24
2057 2103 9.995003 TGCCTTATGAACAAATTTCACTTTAAT 57.005 25.926 0.00 0.00 0.00 1.40
2058 2104 9.823647 TTGCCTTATGAACAAATTTCACTTTAA 57.176 25.926 0.00 0.00 0.00 1.52
2059 2105 9.474920 CTTGCCTTATGAACAAATTTCACTTTA 57.525 29.630 0.00 0.00 0.00 1.85
2060 2106 7.986889 ACTTGCCTTATGAACAAATTTCACTTT 59.013 29.630 0.00 0.00 0.00 2.66
2061 2107 7.500141 ACTTGCCTTATGAACAAATTTCACTT 58.500 30.769 0.00 0.00 0.00 3.16
2062 2108 7.054491 ACTTGCCTTATGAACAAATTTCACT 57.946 32.000 0.00 0.00 0.00 3.41
2063 2109 8.810652 TTACTTGCCTTATGAACAAATTTCAC 57.189 30.769 0.00 0.00 0.00 3.18
2064 2110 9.995003 ATTTACTTGCCTTATGAACAAATTTCA 57.005 25.926 0.00 0.00 0.00 2.69
2069 2115 9.921637 CCTTAATTTACTTGCCTTATGAACAAA 57.078 29.630 0.00 0.00 0.00 2.83
2070 2116 9.084533 ACCTTAATTTACTTGCCTTATGAACAA 57.915 29.630 0.00 0.00 0.00 2.83
2071 2117 8.644374 ACCTTAATTTACTTGCCTTATGAACA 57.356 30.769 0.00 0.00 0.00 3.18
2076 2122 9.930158 TGGATTACCTTAATTTACTTGCCTTAT 57.070 29.630 0.00 0.00 37.04 1.73
2077 2123 9.930158 ATGGATTACCTTAATTTACTTGCCTTA 57.070 29.630 0.00 0.00 37.04 2.69
2078 2124 8.838649 ATGGATTACCTTAATTTACTTGCCTT 57.161 30.769 0.00 0.00 37.04 4.35
2079 2125 8.838649 AATGGATTACCTTAATTTACTTGCCT 57.161 30.769 0.00 0.00 37.04 4.75
2084 2130 9.774413 CGTCCTAATGGATTACCTTAATTTACT 57.226 33.333 0.00 0.00 45.29 2.24
2085 2131 8.501580 GCGTCCTAATGGATTACCTTAATTTAC 58.498 37.037 0.00 0.00 45.29 2.01
2086 2132 7.662669 GGCGTCCTAATGGATTACCTTAATTTA 59.337 37.037 0.00 0.00 45.29 1.40
2087 2133 6.489022 GGCGTCCTAATGGATTACCTTAATTT 59.511 38.462 0.00 0.00 45.29 1.82
2088 2134 6.002082 GGCGTCCTAATGGATTACCTTAATT 58.998 40.000 0.00 0.00 45.29 1.40
2089 2135 5.557866 GGCGTCCTAATGGATTACCTTAAT 58.442 41.667 0.00 0.00 45.29 1.40
2090 2136 4.501915 CGGCGTCCTAATGGATTACCTTAA 60.502 45.833 0.00 0.00 45.29 1.85
2091 2137 3.006110 CGGCGTCCTAATGGATTACCTTA 59.994 47.826 0.00 0.00 45.29 2.69
2092 2138 2.224209 CGGCGTCCTAATGGATTACCTT 60.224 50.000 0.00 0.00 45.29 3.50
2093 2139 1.343465 CGGCGTCCTAATGGATTACCT 59.657 52.381 0.00 0.00 45.29 3.08
2094 2140 1.342174 TCGGCGTCCTAATGGATTACC 59.658 52.381 6.85 0.00 45.29 2.85
2095 2141 2.806608 TCGGCGTCCTAATGGATTAC 57.193 50.000 6.85 0.00 45.29 1.89
2096 2142 4.525487 AGTTATCGGCGTCCTAATGGATTA 59.475 41.667 6.85 0.00 45.29 1.75
2097 2143 3.323979 AGTTATCGGCGTCCTAATGGATT 59.676 43.478 6.85 0.00 45.29 3.01
2098 2144 2.897969 AGTTATCGGCGTCCTAATGGAT 59.102 45.455 6.85 0.00 45.29 3.41
2099 2145 2.035449 CAGTTATCGGCGTCCTAATGGA 59.965 50.000 6.85 0.00 40.69 3.41
2100 2146 2.404215 CAGTTATCGGCGTCCTAATGG 58.596 52.381 6.85 0.00 0.00 3.16
2101 2147 1.792949 GCAGTTATCGGCGTCCTAATG 59.207 52.381 6.85 2.10 0.00 1.90
2102 2148 1.270147 GGCAGTTATCGGCGTCCTAAT 60.270 52.381 6.85 0.00 35.70 1.73
2103 2149 0.103572 GGCAGTTATCGGCGTCCTAA 59.896 55.000 6.85 0.95 35.70 2.69
2104 2150 1.038681 TGGCAGTTATCGGCGTCCTA 61.039 55.000 6.85 0.00 35.70 2.94
2105 2151 1.686325 ATGGCAGTTATCGGCGTCCT 61.686 55.000 6.85 0.00 35.70 3.85
2111 2157 1.858458 CACACGTATGGCAGTTATCGG 59.142 52.381 0.00 0.00 0.00 4.18
2124 2170 0.527113 CACCCGATACACCACACGTA 59.473 55.000 0.00 0.00 0.00 3.57
2254 2300 2.974489 CTCACTCGCCCGTACGTGT 61.974 63.158 15.21 2.18 40.08 4.49
2356 2402 2.046411 ACCATGGCAATCGCGACA 60.046 55.556 12.93 4.98 39.92 4.35
2386 2432 2.862541 AGTTCAGCAACATGGCAACTA 58.137 42.857 0.00 0.00 34.60 2.24
2420 2466 3.750371 ACATGGCAACTGTAGTTTAGCA 58.250 40.909 0.00 0.00 35.83 3.49
2422 2468 3.370978 CCGACATGGCAACTGTAGTTTAG 59.629 47.826 0.00 0.00 35.83 1.85
2423 2469 3.007074 TCCGACATGGCAACTGTAGTTTA 59.993 43.478 0.00 0.00 37.80 2.01
2424 2470 2.151202 CCGACATGGCAACTGTAGTTT 58.849 47.619 0.00 0.00 35.83 2.66
2462 2508 2.808543 GGCAACTGTCCAGTGTTAGAAG 59.191 50.000 0.00 0.00 41.58 2.85
2463 2509 2.171659 TGGCAACTGTCCAGTGTTAGAA 59.828 45.455 0.00 0.00 41.58 2.10
2598 2775 4.661222 TCCCACACATCAAAAGCTATCAA 58.339 39.130 0.00 0.00 0.00 2.57
2611 2788 2.362369 CGCCTCCTCTCCCACACAT 61.362 63.158 0.00 0.00 0.00 3.21
2696 2873 0.105964 TGCCACGTCTGTTTGTAGCT 59.894 50.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.