Multiple sequence alignment - TraesCS3B01G527800

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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 TraesCS3B01G527800 chr3B 100.000 5557 0 0 1 5557 769489736 769484180 0.000000e+00 10262.0
1 TraesCS3B01G527800 chr3B 94.096 4590 227 17 655 5210 770404553 770399974 0.000000e+00 6935.0
2 TraesCS3B01G527800 chr3B 93.077 2311 137 12 2798 5100 769376479 769374184 0.000000e+00 3360.0
3 TraesCS3B01G527800 chr3B 91.504 2307 150 12 2798 5100 770086491 770084227 0.000000e+00 3133.0
4 TraesCS3B01G527800 chr3B 91.407 2246 137 24 3346 5557 770355421 770353198 0.000000e+00 3027.0
5 TraesCS3B01G527800 chr3B 91.310 2244 141 22 3348 5557 769307121 769304898 0.000000e+00 3014.0
6 TraesCS3B01G527800 chr3B 91.809 2161 140 15 654 2785 769378723 769376571 0.000000e+00 2976.0
7 TraesCS3B01G527800 chr3B 91.953 2150 131 12 653 2790 769268232 769266113 0.000000e+00 2974.0
8 TraesCS3B01G527800 chr3B 88.703 1797 185 11 855 2640 770313215 770311426 0.000000e+00 2178.0
9 TraesCS3B01G527800 chr3B 86.897 1679 207 7 966 2640 770208706 770207037 0.000000e+00 1869.0
10 TraesCS3B01G527800 chr3B 86.667 1680 208 10 966 2640 769906935 769905267 0.000000e+00 1847.0
11 TraesCS3B01G527800 chr3B 92.143 1311 78 9 4182 5468 769249313 769248004 0.000000e+00 1827.0
12 TraesCS3B01G527800 chr3B 89.416 1455 124 12 653 2087 770097892 770096448 0.000000e+00 1807.0
13 TraesCS3B01G527800 chr3B 91.346 1248 81 12 3984 5210 769419228 769417987 0.000000e+00 1681.0
14 TraesCS3B01G527800 chr3B 86.032 1260 130 29 3340 4578 770311427 770310193 0.000000e+00 1310.0
15 TraesCS3B01G527800 chr3B 80.427 1778 251 51 653 2372 769995473 769993735 0.000000e+00 1266.0
16 TraesCS3B01G527800 chr3B 88.121 1027 89 8 653 1669 770314724 770313721 0.000000e+00 1190.0
17 TraesCS3B01G527800 chr3B 96.933 652 20 0 1 652 447729273 447728622 0.000000e+00 1094.0
18 TraesCS3B01G527800 chr3B 94.274 716 40 1 1421 2135 769456621 769455906 0.000000e+00 1094.0
19 TraesCS3B01G527800 chr3B 91.462 773 53 8 3413 4176 769250123 769249355 0.000000e+00 1050.0
20 TraesCS3B01G527800 chr3B 90.701 785 69 4 2798 3579 769454028 769453245 0.000000e+00 1042.0
21 TraesCS3B01G527800 chr3B 90.301 763 49 11 653 1408 769458637 769457893 0.000000e+00 976.0
22 TraesCS3B01G527800 chr3B 93.023 645 43 2 2087 2730 770089063 770088420 0.000000e+00 941.0
23 TraesCS3B01G527800 chr3B 92.520 615 41 5 2189 2799 769454681 769454068 0.000000e+00 876.0
24 TraesCS3B01G527800 chr3B 84.193 892 98 25 3720 4605 770206662 770205808 0.000000e+00 826.0
25 TraesCS3B01G527800 chr3B 84.157 890 99 23 3720 4605 769904892 769904041 0.000000e+00 824.0
26 TraesCS3B01G527800 chr3B 74.000 1600 323 60 1024 2583 769633119 769631573 1.050000e-156 564.0
27 TraesCS3B01G527800 chr3B 86.742 445 54 2 2849 3289 769265996 769265553 1.800000e-134 490.0
28 TraesCS3B01G527800 chr3B 87.185 437 41 10 670 1099 769330631 769330203 3.010000e-132 483.0
29 TraesCS3B01G527800 chr3B 88.889 396 34 6 1676 2070 770313599 770313213 3.890000e-131 479.0
30 TraesCS3B01G527800 chr3B 90.805 348 28 3 2304 2649 770355764 770355419 3.920000e-126 462.0
31 TraesCS3B01G527800 chr3B 90.169 356 25 4 5205 5557 770310156 770309808 6.560000e-124 455.0
32 TraesCS3B01G527800 chr3B 89.685 349 32 3 2304 2650 769307465 769307119 5.110000e-120 442.0
33 TraesCS3B01G527800 chr3B 91.667 108 9 0 3308 3415 769265564 769265457 3.470000e-32 150.0
34 TraesCS3B01G527800 chr3B 96.552 87 3 0 5471 5557 769232625 769232539 1.610000e-30 145.0
35 TraesCS3B01G527800 chr3B 82.667 150 24 2 3176 3325 770402414 770402561 1.260000e-26 132.0
36 TraesCS3B01G527800 chr3B 74.157 356 63 17 5215 5554 770346536 770346878 2.720000e-23 121.0
37 TraesCS3B01G527800 chr3B 89.831 59 3 3 2728 2784 756683009 756683066 7.720000e-09 73.1
38 TraesCS3B01G527800 chr3B 100.000 34 0 0 5095 5128 769374173 769374140 4.650000e-06 63.9
39 TraesCS3B01G527800 chrUn 91.444 1309 81 11 4182 5466 298659144 298657843 0.000000e+00 1768.0
40 TraesCS3B01G527800 chrUn 91.444 1309 81 11 4182 5466 311034452 311035753 0.000000e+00 1768.0
41 TraesCS3B01G527800 chrUn 91.444 1309 81 11 4182 5466 311053901 311052600 0.000000e+00 1768.0
42 TraesCS3B01G527800 chrUn 91.444 1309 81 11 4182 5466 344523052 344524353 0.000000e+00 1768.0
43 TraesCS3B01G527800 chrUn 91.214 774 53 9 3413 4176 298659962 298659194 0.000000e+00 1038.0
44 TraesCS3B01G527800 chrUn 91.214 774 53 9 3413 4176 341288129 341287361 0.000000e+00 1038.0
45 TraesCS3B01G527800 chr3A 81.165 1975 321 31 653 2601 712655466 712653517 0.000000e+00 1539.0
46 TraesCS3B01G527800 chr2B 97.086 652 19 0 1 652 772106194 772105543 0.000000e+00 1099.0
47 TraesCS3B01G527800 chr2B 96.937 653 20 0 1 653 75937309 75936657 0.000000e+00 1096.0
48 TraesCS3B01G527800 chr2B 96.933 652 20 0 3 654 321718761 321718110 0.000000e+00 1094.0
49 TraesCS3B01G527800 chr2B 92.857 42 3 0 2730 2771 67536629 67536588 1.670000e-05 62.1
50 TraesCS3B01G527800 chr5B 96.804 657 21 0 1 657 510980057 510979401 0.000000e+00 1098.0
51 TraesCS3B01G527800 chr5B 93.333 45 3 0 2727 2771 403109799 403109843 3.590000e-07 67.6
52 TraesCS3B01G527800 chr7B 96.933 652 20 0 1 652 213294314 213294965 0.000000e+00 1094.0
53 TraesCS3B01G527800 chr7B 96.510 659 21 2 1 658 580709292 580708635 0.000000e+00 1088.0
54 TraesCS3B01G527800 chr1B 96.933 652 20 0 1 652 26737678 26737027 0.000000e+00 1094.0
55 TraesCS3B01G527800 chr1B 93.617 47 3 0 2727 2773 82077178 82077132 2.780000e-08 71.3
56 TraesCS3B01G527800 chr4B 96.794 655 20 1 1 655 582026959 582026306 0.000000e+00 1092.0
57 TraesCS3B01G527800 chr2D 86.981 530 66 1 2797 3323 483123858 483124387 1.330000e-165 593.0
58 TraesCS3B01G527800 chr2D 86.466 532 63 3 2798 3326 483080127 483080652 4.830000e-160 575.0
59 TraesCS3B01G527800 chr2D 88.273 469 51 2 2798 3262 483125494 483125962 4.860000e-155 558.0
60 TraesCS3B01G527800 chr2D 87.632 380 39 3 2798 3174 483080896 483081270 8.550000e-118 435.0


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 TraesCS3B01G527800 chr3B 769484180 769489736 5556 True 10262.000000 10262 100.000000 1 5557 1 chr3B.!!$R5 5556
1 TraesCS3B01G527800 chr3B 770399974 770404553 4579 True 6935.000000 6935 94.096000 655 5210 1 chr3B.!!$R9 4555
2 TraesCS3B01G527800 chr3B 769374140 769378723 4583 True 2133.300000 3360 94.962000 654 5128 3 chr3B.!!$R13 4474
3 TraesCS3B01G527800 chr3B 770084227 770089063 4836 True 2037.000000 3133 92.263500 2087 5100 2 chr3B.!!$R16 3013
4 TraesCS3B01G527800 chr3B 770096448 770097892 1444 True 1807.000000 1807 89.416000 653 2087 1 chr3B.!!$R8 1434
5 TraesCS3B01G527800 chr3B 770353198 770355764 2566 True 1744.500000 3027 91.106000 2304 5557 2 chr3B.!!$R19 3253
6 TraesCS3B01G527800 chr3B 769304898 769307465 2567 True 1728.000000 3014 90.497500 2304 5557 2 chr3B.!!$R12 3253
7 TraesCS3B01G527800 chr3B 769417987 769419228 1241 True 1681.000000 1681 91.346000 3984 5210 1 chr3B.!!$R4 1226
8 TraesCS3B01G527800 chr3B 769248004 769250123 2119 True 1438.500000 1827 91.802500 3413 5468 2 chr3B.!!$R10 2055
9 TraesCS3B01G527800 chr3B 770205808 770208706 2898 True 1347.500000 1869 85.545000 966 4605 2 chr3B.!!$R17 3639
10 TraesCS3B01G527800 chr3B 769904041 769906935 2894 True 1335.500000 1847 85.412000 966 4605 2 chr3B.!!$R15 3639
11 TraesCS3B01G527800 chr3B 769993735 769995473 1738 True 1266.000000 1266 80.427000 653 2372 1 chr3B.!!$R7 1719
12 TraesCS3B01G527800 chr3B 769265457 769268232 2775 True 1204.666667 2974 90.120667 653 3415 3 chr3B.!!$R11 2762
13 TraesCS3B01G527800 chr3B 770309808 770314724 4916 True 1122.400000 2178 88.382800 653 5557 5 chr3B.!!$R18 4904
14 TraesCS3B01G527800 chr3B 447728622 447729273 651 True 1094.000000 1094 96.933000 1 652 1 chr3B.!!$R1 651
15 TraesCS3B01G527800 chr3B 769453245 769458637 5392 True 997.000000 1094 91.949000 653 3579 4 chr3B.!!$R14 2926
16 TraesCS3B01G527800 chr3B 769631573 769633119 1546 True 564.000000 564 74.000000 1024 2583 1 chr3B.!!$R6 1559
17 TraesCS3B01G527800 chrUn 311034452 311035753 1301 False 1768.000000 1768 91.444000 4182 5466 1 chrUn.!!$F1 1284
18 TraesCS3B01G527800 chrUn 311052600 311053901 1301 True 1768.000000 1768 91.444000 4182 5466 1 chrUn.!!$R1 1284
19 TraesCS3B01G527800 chrUn 344523052 344524353 1301 False 1768.000000 1768 91.444000 4182 5466 1 chrUn.!!$F2 1284
20 TraesCS3B01G527800 chrUn 298657843 298659962 2119 True 1403.000000 1768 91.329000 3413 5466 2 chrUn.!!$R3 2053
21 TraesCS3B01G527800 chrUn 341287361 341288129 768 True 1038.000000 1038 91.214000 3413 4176 1 chrUn.!!$R2 763
22 TraesCS3B01G527800 chr3A 712653517 712655466 1949 True 1539.000000 1539 81.165000 653 2601 1 chr3A.!!$R1 1948
23 TraesCS3B01G527800 chr2B 772105543 772106194 651 True 1099.000000 1099 97.086000 1 652 1 chr2B.!!$R4 651
24 TraesCS3B01G527800 chr2B 75936657 75937309 652 True 1096.000000 1096 96.937000 1 653 1 chr2B.!!$R2 652
25 TraesCS3B01G527800 chr2B 321718110 321718761 651 True 1094.000000 1094 96.933000 3 654 1 chr2B.!!$R3 651
26 TraesCS3B01G527800 chr5B 510979401 510980057 656 True 1098.000000 1098 96.804000 1 657 1 chr5B.!!$R1 656
27 TraesCS3B01G527800 chr7B 213294314 213294965 651 False 1094.000000 1094 96.933000 1 652 1 chr7B.!!$F1 651
28 TraesCS3B01G527800 chr7B 580708635 580709292 657 True 1088.000000 1088 96.510000 1 658 1 chr7B.!!$R1 657
29 TraesCS3B01G527800 chr1B 26737027 26737678 651 True 1094.000000 1094 96.933000 1 652 1 chr1B.!!$R1 651
30 TraesCS3B01G527800 chr4B 582026306 582026959 653 True 1092.000000 1092 96.794000 1 655 1 chr4B.!!$R1 654
31 TraesCS3B01G527800 chr2D 483123858 483125962 2104 False 575.500000 593 87.627000 2797 3323 2 chr2D.!!$F2 526
32 TraesCS3B01G527800 chr2D 483080127 483081270 1143 False 505.000000 575 87.049000 2798 3326 2 chr2D.!!$F1 528

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
926 940 0.034477 AGGGGAATGTAACAAGGCCG 60.034 55.000 0.0 0.0 0.0 6.13 F
2047 4698 0.467474 TGTCACACCTCACTCTCCGT 60.467 55.000 0.0 0.0 0.0 4.69 F
2801 6667 1.149174 CAGACCCAGTTGCACACCT 59.851 57.895 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2783 6649 1.149174 AGGTGTGCAACTGGGTCTG 59.851 57.895 0.00 0.0 38.04 3.51 R
3415 10152 0.291989 CGTTCTTCGAGCGTGATTCG 59.708 55.000 0.00 0.0 42.86 3.34 R
4796 11617 0.532862 CAGGCTGTTGTCCGTCTGTT 60.533 55.000 6.28 0.0 0.00 3.16 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
169 170 1.671328 GCTTCGTAAGGGGCTGATTTC 59.329 52.381 0.00 0.00 38.47 2.17
174 175 2.224066 CGTAAGGGGCTGATTTCGATCT 60.224 50.000 0.00 0.00 0.00 2.75
258 259 7.801104 TGCAATAGAGGTTAATCATAAGTGGA 58.199 34.615 0.00 0.00 0.00 4.02
319 320 7.233348 GGTCCACCCACATATCAAATTATCAAT 59.767 37.037 0.00 0.00 0.00 2.57
428 429 1.981256 TTGTCCAGGCTTGTCCTTTC 58.019 50.000 0.00 0.00 44.75 2.62
490 491 5.092781 ACTTTTGTTACTTGTTGCTCGTTG 58.907 37.500 0.00 0.00 0.00 4.10
525 526 7.822334 CCTATCACAAAACTATCTGTTACCACA 59.178 37.037 0.00 0.00 38.03 4.17
602 603 1.210967 TCCTTGTTGGGTTCGACACTT 59.789 47.619 0.00 0.00 37.04 3.16
630 631 8.393671 ACTTATCGAAAGGACTACGATAGATT 57.606 34.615 15.42 7.05 45.19 2.40
697 699 8.571336 CATCTCCAAATATATTTTGTCTCACCC 58.429 37.037 8.01 0.00 0.00 4.61
708 710 1.144708 TGTCTCACCCATTTTGCTCCA 59.855 47.619 0.00 0.00 0.00 3.86
761 763 1.138266 GCTAGCGGAGTGGGACAAATA 59.862 52.381 0.00 0.00 44.16 1.40
814 817 2.744202 CAAGCTTAGATGTTTCAGCCGT 59.256 45.455 0.00 0.00 32.25 5.68
815 818 2.622436 AGCTTAGATGTTTCAGCCGTC 58.378 47.619 0.00 0.00 32.25 4.79
816 819 1.324736 GCTTAGATGTTTCAGCCGTCG 59.675 52.381 0.00 0.00 0.00 5.12
859 863 2.621526 TCGATATTTCAGCCGCTCACTA 59.378 45.455 0.00 0.00 0.00 2.74
860 864 2.726760 CGATATTTCAGCCGCTCACTAC 59.273 50.000 0.00 0.00 0.00 2.73
880 893 2.290323 ACGCCAACTAAGCAAGGAGAAT 60.290 45.455 0.00 0.00 0.00 2.40
909 923 7.337942 ACAATAAGAAGCAATAGAACTTGGAGG 59.662 37.037 0.00 0.00 0.00 4.30
910 924 4.227864 AGAAGCAATAGAACTTGGAGGG 57.772 45.455 0.00 0.00 0.00 4.30
912 926 2.562296 AGCAATAGAACTTGGAGGGGA 58.438 47.619 0.00 0.00 0.00 4.81
913 927 2.919602 AGCAATAGAACTTGGAGGGGAA 59.080 45.455 0.00 0.00 0.00 3.97
914 928 3.529319 AGCAATAGAACTTGGAGGGGAAT 59.471 43.478 0.00 0.00 0.00 3.01
917 931 5.631481 GCAATAGAACTTGGAGGGGAATGTA 60.631 44.000 0.00 0.00 0.00 2.29
919 933 4.302559 AGAACTTGGAGGGGAATGTAAC 57.697 45.455 0.00 0.00 0.00 2.50
920 934 3.655777 AGAACTTGGAGGGGAATGTAACA 59.344 43.478 0.00 0.00 0.00 2.41
921 935 4.105697 AGAACTTGGAGGGGAATGTAACAA 59.894 41.667 0.00 0.00 0.00 2.83
922 936 4.034285 ACTTGGAGGGGAATGTAACAAG 57.966 45.455 0.00 0.00 39.60 3.16
923 937 3.245264 ACTTGGAGGGGAATGTAACAAGG 60.245 47.826 0.00 0.00 38.43 3.61
924 938 1.005450 TGGAGGGGAATGTAACAAGGC 59.995 52.381 0.00 0.00 0.00 4.35
925 939 1.685180 GGAGGGGAATGTAACAAGGCC 60.685 57.143 0.00 0.00 0.00 5.19
926 940 0.034477 AGGGGAATGTAACAAGGCCG 60.034 55.000 0.00 0.00 0.00 6.13
944 958 2.910199 CCGATCCATTTCTTGAGCTGA 58.090 47.619 0.00 0.00 0.00 4.26
1014 1044 2.779430 ACAATCCATGGCTGAGATGGTA 59.221 45.455 17.73 0.00 41.19 3.25
1081 1111 2.520458 CCCCCACCAGCAAAGACA 59.480 61.111 0.00 0.00 0.00 3.41
1090 1120 3.096092 ACCAGCAAAGACAAGGACAAAA 58.904 40.909 0.00 0.00 0.00 2.44
1153 2504 0.526096 GATGGCGCGCATCAAAATGT 60.526 50.000 34.42 6.77 35.18 2.71
1182 2533 3.631686 CACTCCAAACATCCAACAAGTGA 59.368 43.478 0.00 0.00 35.95 3.41
1291 2642 3.067833 CAACTTTCTCGGGAAGAAGACC 58.932 50.000 3.73 0.00 44.69 3.85
1460 4078 1.009829 GTGGACGGTGCTGATGAATC 58.990 55.000 0.31 0.00 0.00 2.52
1564 4185 7.148540 GCAAAATGATTGCATATCAGTTGTTGT 60.149 33.333 18.43 6.69 44.34 3.32
1739 4360 4.379082 GGACATAATTGGAACCGTTGTCAC 60.379 45.833 0.00 0.00 35.00 3.67
1740 4361 4.394729 ACATAATTGGAACCGTTGTCACT 58.605 39.130 0.00 0.00 0.00 3.41
2025 4668 2.689983 CCAGTCTGCCAAGTGTTTTTCT 59.310 45.455 0.00 0.00 0.00 2.52
2042 4693 4.585955 TTTCTAGTGTCACACCTCACTC 57.414 45.455 3.66 0.00 42.77 3.51
2047 4698 0.467474 TGTCACACCTCACTCTCCGT 60.467 55.000 0.00 0.00 0.00 4.69
2056 4707 3.323979 ACCTCACTCTCCGTGTACAAAAT 59.676 43.478 0.00 0.00 44.16 1.82
2165 6014 2.881403 GCCTCATGCTTCTTTGGAGGAA 60.881 50.000 10.02 0.00 46.38 3.36
2187 6042 3.181454 ACCTAAGTCTGTTGGTTCCACAG 60.181 47.826 12.05 12.05 0.00 3.66
2275 6130 1.202734 CGAGATGATGATGCCCAAGGT 60.203 52.381 0.00 0.00 0.00 3.50
2312 6167 2.698274 TCTTAATGCCGAGGCTATGTCA 59.302 45.455 15.75 0.00 42.51 3.58
2465 6323 2.913054 TAGTGCAGCAGGATCAGCGC 62.913 60.000 0.00 0.00 37.01 5.92
2494 6355 1.739371 GCTGAATCGGGTAGCTCGTTT 60.739 52.381 0.00 0.00 34.70 3.60
2752 6618 2.512515 GCAGATGGGCCAGACGAC 60.513 66.667 13.78 2.95 0.00 4.34
2753 6619 2.981302 CAGATGGGCCAGACGACA 59.019 61.111 13.78 0.00 0.00 4.35
2754 6620 1.448540 CAGATGGGCCAGACGACAC 60.449 63.158 13.78 0.00 0.00 3.67
2755 6621 2.509336 GATGGGCCAGACGACACG 60.509 66.667 13.78 0.00 0.00 4.49
2760 6626 4.961511 GCCAGACGACACGTGGCA 62.962 66.667 23.63 0.00 44.60 4.92
2761 6627 3.036084 CCAGACGACACGTGGCAC 61.036 66.667 23.63 14.77 41.37 5.01
2764 6630 3.036084 GACGACACGTGGCACCTG 61.036 66.667 23.63 13.48 41.37 4.00
2776 6642 3.434319 CACCTGCCGCCATGTGTC 61.434 66.667 0.00 0.00 34.23 3.67
2777 6643 3.640407 ACCTGCCGCCATGTGTCT 61.640 61.111 0.00 0.00 0.00 3.41
2778 6644 3.129502 CCTGCCGCCATGTGTCTG 61.130 66.667 0.00 0.00 0.00 3.51
2779 6645 3.129502 CTGCCGCCATGTGTCTGG 61.130 66.667 0.00 0.00 39.45 3.86
2785 6651 3.129502 CCATGTGTCTGGCGGCAG 61.130 66.667 31.58 31.58 0.00 4.85
2786 6652 2.046988 CATGTGTCTGGCGGCAGA 60.047 61.111 35.14 35.14 0.00 4.26
2794 6660 4.641645 TGGCGGCAGACCCAGTTG 62.642 66.667 7.97 0.00 0.00 3.16
2797 6663 3.357079 CGGCAGACCCAGTTGCAC 61.357 66.667 0.00 0.00 42.02 4.57
2798 6664 2.203337 GGCAGACCCAGTTGCACA 60.203 61.111 0.00 0.00 42.02 4.57
2800 6666 2.555547 GCAGACCCAGTTGCACACC 61.556 63.158 0.00 0.00 40.02 4.16
2801 6667 1.149174 CAGACCCAGTTGCACACCT 59.851 57.895 0.00 0.00 0.00 4.00
2889 9568 2.005960 GACACGCCGCTACTCCATCT 62.006 60.000 0.00 0.00 0.00 2.90
3279 9969 6.774354 TGACATTTTCGTTTGTAGGTAGTC 57.226 37.500 0.00 0.00 0.00 2.59
3326 10017 7.307337 GCAGATGGTCATTTTTGACGAAAATTT 60.307 33.333 10.21 0.00 43.65 1.82
3338 10029 6.431198 TGACGAAAATTTGTATTCCTAGCC 57.569 37.500 0.00 0.00 0.00 3.93
3395 10132 9.639601 AGGCTTTTTATGACAAAATTTACTAGC 57.360 29.630 0.00 0.00 0.00 3.42
3415 10152 1.134560 CGGTAACAGCTGGTCTAGGTC 59.865 57.143 19.93 0.00 34.17 3.85
3529 10278 0.324830 AGGAAACTCCGAGCCTAGCT 60.325 55.000 0.00 0.00 42.75 3.32
3537 10286 2.808315 GAGCCTAGCTAGCACGCA 59.192 61.111 18.83 0.00 39.88 5.24
4006 10770 0.625849 GTGTCATGGGGAGATGGGTT 59.374 55.000 0.00 0.00 0.00 4.11
4099 10863 4.534500 GGTTAGGGTTGATTTGGGGATTTT 59.466 41.667 0.00 0.00 0.00 1.82
4495 11308 2.165998 GGTGAAAGCAGAATTGGAGCT 58.834 47.619 0.00 0.00 41.03 4.09
4519 11332 6.983906 AAAGAAGTTTCTTGATGGGACAAT 57.016 33.333 7.82 0.00 46.22 2.71
4609 11423 8.336801 TGAGGAGAAGAACCTTAAATAAAAGC 57.663 34.615 0.00 0.00 37.93 3.51
4739 11560 4.927782 GTGGTGGCACGTGCTCCA 62.928 66.667 35.20 35.20 40.38 3.86
4796 11617 8.257306 AGAAGACTAAAGCCAACAAATTTGAAA 58.743 29.630 24.64 0.41 0.00 2.69
4813 11634 1.002792 GAAAACAGACGGACAACAGCC 60.003 52.381 0.00 0.00 0.00 4.85
4856 11677 6.306199 TGGGTACTACGGATATTAGCTACAA 58.694 40.000 0.00 0.00 0.00 2.41
4979 11801 0.239347 CTTGGAAGCAGTTTCGCTGG 59.761 55.000 0.00 0.00 42.89 4.85
5063 11889 0.523072 CTGGTTCCAAATGTGCTCCG 59.477 55.000 0.00 0.00 0.00 4.63
5069 11895 1.361668 CCAAATGTGCTCCGTCTCCG 61.362 60.000 0.00 0.00 0.00 4.63
5128 11971 4.022589 GCAAACCAACTCCCCTTAACTAAC 60.023 45.833 0.00 0.00 0.00 2.34
5129 11972 5.134661 CAAACCAACTCCCCTTAACTAACA 58.865 41.667 0.00 0.00 0.00 2.41
5139 11982 5.105473 TCCCCTTAACTAACAGAATGAGACG 60.105 44.000 0.00 0.00 39.69 4.18
5170 12013 6.489700 TGTGTCTCCATTTCAAGAAATAAGCA 59.510 34.615 7.65 8.15 38.84 3.91
5190 12033 5.923204 AGCAACAGCTAGCATATTTAGAGT 58.077 37.500 18.83 0.00 36.70 3.24
5233 12085 1.076727 GGCCAGGCCTAGGTGTTTT 59.923 57.895 24.99 0.00 46.69 2.43
5263 12115 1.955778 CTTGATTCACCACAGCCAACA 59.044 47.619 0.00 0.00 0.00 3.33
5317 12169 0.993509 TAGAAATGGGGGCCAGAGGG 60.994 60.000 4.39 0.00 36.75 4.30
5399 12253 1.002366 GCTGGCAGTACTCACAATCG 58.998 55.000 17.16 0.00 0.00 3.34
5431 12286 2.295909 TGGTTAGTTCTGCCATTGTTGC 59.704 45.455 0.00 0.00 0.00 4.17
5458 12313 2.352960 CAGTTAGCCGGATCTTTTCTGC 59.647 50.000 5.05 0.00 0.00 4.26
5468 12323 0.534877 TCTTTTCTGCTCTTGCCGCA 60.535 50.000 0.00 0.00 38.71 5.69
5543 12398 1.113517 GGCTGGAGATGGCATGCATT 61.114 55.000 21.36 5.56 0.00 3.56
5546 12401 2.561419 GCTGGAGATGGCATGCATTAAT 59.439 45.455 21.36 7.07 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 170 8.484641 AACCATAGCATGAAACATATAGATCG 57.515 34.615 0.00 0.00 0.00 3.69
174 175 9.860650 AAACCTAACCATAGCATGAAACATATA 57.139 29.630 0.00 0.00 0.00 0.86
258 259 2.171003 GCCCTTACTTGGACAAGCATT 58.829 47.619 11.73 0.00 41.99 3.56
280 281 0.321298 GTGGACCGGTGCTTGTGTAT 60.321 55.000 27.28 0.00 0.00 2.29
284 285 4.265056 GGGTGGACCGGTGCTTGT 62.265 66.667 27.28 0.00 36.71 3.16
319 320 2.847959 TATGATTCGCGTTCGGTACA 57.152 45.000 5.77 0.00 36.13 2.90
428 429 2.233676 GTGGCCCAATCCTTTTTGTAGG 59.766 50.000 0.00 0.00 36.59 3.18
536 537 4.019792 TCAGCAAGGTATTCTCTGCAAA 57.980 40.909 0.00 0.00 34.34 3.68
602 603 9.330063 TCTATCGTAGTCCTTTCGATAAGTAAA 57.670 33.333 7.65 0.00 42.90 2.01
630 631 3.967326 CTGATGACCCACAAGTATAGGGA 59.033 47.826 3.32 0.00 45.80 4.20
697 699 1.213537 CTGCCGGTGGAGCAAAATG 59.786 57.895 1.90 0.00 40.35 2.32
761 763 5.304357 CCTTTTGGGTAAGTGGAGACAAAAT 59.696 40.000 0.00 0.00 37.24 1.82
816 819 1.856802 CCTGTGCTTCCAAAACAAGC 58.143 50.000 0.00 0.00 45.59 4.01
859 863 0.685097 TCTCCTTGCTTAGTTGGCGT 59.315 50.000 0.00 0.00 0.00 5.68
860 864 1.808411 TTCTCCTTGCTTAGTTGGCG 58.192 50.000 0.00 0.00 0.00 5.69
906 920 1.763968 GGCCTTGTTACATTCCCCTC 58.236 55.000 0.00 0.00 0.00 4.30
909 923 1.947456 GATCGGCCTTGTTACATTCCC 59.053 52.381 0.00 0.00 0.00 3.97
910 924 1.947456 GGATCGGCCTTGTTACATTCC 59.053 52.381 0.00 0.00 0.00 3.01
912 926 2.799126 TGGATCGGCCTTGTTACATT 57.201 45.000 0.00 0.00 37.63 2.71
913 927 3.297134 AATGGATCGGCCTTGTTACAT 57.703 42.857 0.00 0.00 37.63 2.29
914 928 2.799126 AATGGATCGGCCTTGTTACA 57.201 45.000 0.00 0.00 37.63 2.41
917 931 2.493278 CAAGAAATGGATCGGCCTTGTT 59.507 45.455 0.00 0.00 37.63 2.83
919 933 2.357009 CTCAAGAAATGGATCGGCCTTG 59.643 50.000 0.00 0.00 37.63 3.61
920 934 2.648059 CTCAAGAAATGGATCGGCCTT 58.352 47.619 0.00 0.00 37.63 4.35
921 935 1.748591 GCTCAAGAAATGGATCGGCCT 60.749 52.381 0.00 0.00 37.63 5.19
922 936 0.665298 GCTCAAGAAATGGATCGGCC 59.335 55.000 0.00 0.00 37.10 6.13
923 937 1.332997 CAGCTCAAGAAATGGATCGGC 59.667 52.381 0.00 0.00 0.00 5.54
924 938 2.910199 TCAGCTCAAGAAATGGATCGG 58.090 47.619 0.00 0.00 0.00 4.18
925 939 3.303857 GCATCAGCTCAAGAAATGGATCG 60.304 47.826 0.00 0.00 37.91 3.69
926 940 3.303857 CGCATCAGCTCAAGAAATGGATC 60.304 47.826 0.00 0.00 39.10 3.36
1014 1044 1.144093 TCCCCAACAATGACCGACTTT 59.856 47.619 0.00 0.00 0.00 2.66
1081 1111 4.889409 TGCTTCTTCATCTGTTTTGTCCTT 59.111 37.500 0.00 0.00 0.00 3.36
1090 1120 3.118334 CCTCCTGATGCTTCTTCATCTGT 60.118 47.826 0.88 0.00 42.44 3.41
1153 2504 0.392461 GATGTTTGGAGTGCGGCCTA 60.392 55.000 0.00 0.00 0.00 3.93
1182 2533 3.056250 GGAGTGATGTGTCAGTGATCTGT 60.056 47.826 0.00 0.00 41.91 3.41
1291 2642 2.859273 CTTACCACCTGCTCCGCCTG 62.859 65.000 0.00 0.00 0.00 4.85
1319 2678 7.531955 GCATGAGCCATCCGTCTAGGAAATA 62.532 48.000 0.00 0.00 43.77 1.40
1442 4060 0.904649 AGATTCATCAGCACCGTCCA 59.095 50.000 0.00 0.00 0.00 4.02
1460 4078 3.319405 ACCGATCTGCACTTACCTGATAG 59.681 47.826 0.00 0.00 0.00 2.08
1470 4088 1.913262 TGTCCCACCGATCTGCACT 60.913 57.895 0.00 0.00 0.00 4.40
1551 4172 4.323792 CCTCCAGGACACAACAACTGATAT 60.324 45.833 0.00 0.00 37.39 1.63
1739 4360 2.159653 GGTGTCATAACTCGCAAGCAAG 60.160 50.000 0.00 0.00 37.18 4.01
1740 4361 1.804151 GGTGTCATAACTCGCAAGCAA 59.196 47.619 0.00 0.00 37.18 3.91
1986 4629 2.874701 CTGGTTCAGGAAATATGCTCGG 59.125 50.000 0.00 0.00 0.00 4.63
2025 4668 2.515854 GGAGAGTGAGGTGTGACACTA 58.484 52.381 16.07 0.00 45.54 2.74
2042 4693 1.737793 GGCAGGATTTTGTACACGGAG 59.262 52.381 0.00 0.00 0.00 4.63
2165 6014 2.775384 TGTGGAACCAACAGACTTAGGT 59.225 45.455 0.00 0.00 34.36 3.08
2187 6042 5.814764 TTCTCTGTATCGACCACTTCTAC 57.185 43.478 0.00 0.00 0.00 2.59
2275 6130 8.246871 CGGCATTAAGATGAAGATAGTCTATCA 58.753 37.037 19.77 3.68 35.11 2.15
2442 6300 2.030371 CTGATCCTGCTGCACTAGAGA 58.970 52.381 0.00 0.00 0.00 3.10
2465 6323 4.319766 GCTACCCGATTCAGCATTTGTATG 60.320 45.833 0.00 0.00 35.35 2.39
2482 6340 6.111382 AGTTTTAGGAATAAACGAGCTACCC 58.889 40.000 0.00 0.00 39.77 3.69
2494 6355 5.130350 GCACAGCCCATAGTTTTAGGAATA 58.870 41.667 0.00 0.00 0.00 1.75
2743 6609 4.961511 TGCCACGTGTCGTCTGGC 62.962 66.667 15.65 9.47 45.16 4.85
2744 6610 3.036084 GTGCCACGTGTCGTCTGG 61.036 66.667 15.65 0.00 38.32 3.86
2745 6611 3.036084 GGTGCCACGTGTCGTCTG 61.036 66.667 15.65 0.00 38.32 3.51
2747 6613 3.036084 CAGGTGCCACGTGTCGTC 61.036 66.667 15.65 0.00 38.32 4.20
2759 6625 3.434319 GACACATGGCGGCAGGTG 61.434 66.667 42.62 42.62 41.92 4.00
2760 6626 3.640407 AGACACATGGCGGCAGGT 61.640 61.111 24.37 24.37 0.00 4.00
2761 6627 3.129502 CAGACACATGGCGGCAGG 61.130 66.667 22.79 22.79 0.00 4.85
2768 6634 3.129502 CTGCCGCCAGACACATGG 61.130 66.667 0.00 0.00 41.77 3.66
2769 6635 2.046988 TCTGCCGCCAGACACATG 60.047 61.111 0.00 0.00 42.98 3.21
2776 6642 4.335647 AACTGGGTCTGCCGCCAG 62.336 66.667 0.00 0.00 40.54 4.85
2777 6643 4.641645 CAACTGGGTCTGCCGCCA 62.642 66.667 0.00 0.00 34.97 5.69
2781 6647 2.203337 TGTGCAACTGGGTCTGCC 60.203 61.111 0.00 0.00 37.79 4.85
2782 6648 2.555547 GGTGTGCAACTGGGTCTGC 61.556 63.158 0.00 0.00 38.04 4.26
2783 6649 1.149174 AGGTGTGCAACTGGGTCTG 59.851 57.895 0.00 0.00 38.04 3.51
2784 6650 1.149174 CAGGTGTGCAACTGGGTCT 59.851 57.895 9.24 0.00 42.28 3.85
2785 6651 3.749981 CAGGTGTGCAACTGGGTC 58.250 61.111 9.24 0.00 42.28 4.46
2795 6661 1.996786 GATGAATGGCGGCAGGTGTG 61.997 60.000 19.29 0.00 0.00 3.82
2796 6662 1.750399 GATGAATGGCGGCAGGTGT 60.750 57.895 19.29 3.41 0.00 4.16
2797 6663 2.484062 GGATGAATGGCGGCAGGTG 61.484 63.158 19.29 0.00 0.00 4.00
2798 6664 2.124151 GGATGAATGGCGGCAGGT 60.124 61.111 19.29 7.86 0.00 4.00
2800 6666 2.191513 CCAGGATGAATGGCGGCAG 61.192 63.158 19.29 0.10 39.69 4.85
2801 6667 2.124193 CCAGGATGAATGGCGGCA 60.124 61.111 16.34 16.34 39.69 5.69
2889 9568 3.482436 ACCGCCTTTGACATCTTTTACA 58.518 40.909 0.00 0.00 0.00 2.41
3174 9864 1.073897 GGTCTGGCTGCAGAACCTT 59.926 57.895 20.43 0.00 32.97 3.50
3326 10017 6.692849 ATTGATGATCTGGCTAGGAATACA 57.307 37.500 0.00 0.00 0.00 2.29
3395 10132 1.134560 GACCTAGACCAGCTGTTACCG 59.865 57.143 13.81 0.00 0.00 4.02
3415 10152 0.291989 CGTTCTTCGAGCGTGATTCG 59.708 55.000 0.00 0.00 42.86 3.34
3529 10278 3.449227 CGGGAGAGGTGCGTGCTA 61.449 66.667 0.00 0.00 0.00 3.49
3669 10427 3.181463 TGGTTATGTGATAACGTAGCCCC 60.181 47.826 11.75 1.69 44.65 5.80
3834 10593 2.589540 CTAATGGCCTCACCCGCA 59.410 61.111 3.32 0.00 37.83 5.69
4006 10770 2.028748 CCGAACCCTTTAGAAGAACCGA 60.029 50.000 0.00 0.00 0.00 4.69
4305 11118 7.404980 ACAAGATTACCCTTAATTCTACCTCCA 59.595 37.037 0.00 0.00 0.00 3.86
4495 11308 8.477419 AATTGTCCCATCAAGAAACTTCTTTA 57.523 30.769 1.87 0.00 44.70 1.85
4558 11371 8.924511 TCCTTCAGCTTATATATCCCTTTTTG 57.075 34.615 0.00 0.00 0.00 2.44
4609 11423 2.476619 CTGCGTTTGAACTAGACACCTG 59.523 50.000 0.00 0.00 0.00 4.00
4739 11560 1.029681 GTCGCTCCCAACTGGTTTTT 58.970 50.000 0.00 0.00 34.77 1.94
4790 11611 3.426963 GCTGTTGTCCGTCTGTTTTCAAA 60.427 43.478 0.00 0.00 0.00 2.69
4796 11617 0.532862 CAGGCTGTTGTCCGTCTGTT 60.533 55.000 6.28 0.00 0.00 3.16
4813 11634 3.119245 CCCAATGTCAATTGCCTCTTCAG 60.119 47.826 0.00 0.00 41.66 3.02
4828 11649 5.778750 AGCTAATATCCGTAGTACCCAATGT 59.221 40.000 0.00 0.00 0.00 2.71
5063 11889 1.320507 GGGACATACTCCTCGGAGAC 58.679 60.000 19.35 5.46 44.53 3.36
5069 11895 8.152023 AGAATATATTTGGGGACATACTCCTC 57.848 38.462 0.00 0.00 40.62 3.71
5128 11971 5.107824 AGACACATGATTCGTCTCATTCTG 58.892 41.667 0.00 2.84 35.02 3.02
5129 11972 5.336150 AGACACATGATTCGTCTCATTCT 57.664 39.130 0.00 0.33 35.02 2.40
5170 12013 8.792830 TGAAAACTCTAAATATGCTAGCTGTT 57.207 30.769 17.23 5.18 0.00 3.16
5233 12085 2.560981 TGGTGAATCAAGTGAGCGACTA 59.439 45.455 0.00 0.00 33.09 2.59
5263 12115 0.037447 GTCCTTGGCTCCTTGCTTCT 59.963 55.000 0.00 0.00 42.39 2.85
5335 12187 4.641989 GGGCTGCTATTCTCAAGAAATGAA 59.358 41.667 0.00 0.00 37.67 2.57
5336 12188 4.202441 GGGCTGCTATTCTCAAGAAATGA 58.798 43.478 0.00 0.00 37.61 2.57
5399 12253 4.125703 CAGAACTAACCATCTCAGCCATC 58.874 47.826 0.00 0.00 0.00 3.51
5431 12286 0.876342 GATCCGGCTAACTGCTTCCG 60.876 60.000 0.00 0.00 42.39 4.30
5468 12323 5.337009 CCATTTATCCTTGACTTTGCTGCTT 60.337 40.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.