Multiple sequence alignment - TraesCS6B01G098500

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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 TraesCS6B01G098500 chr6B 100.000 3203 0 0 1 3203 75991636 75988434 0.000000e+00 5915.0
1 TraesCS6B01G098500 chr6B 99.069 537 5 0 2667 3203 606303262 606302726 0.000000e+00 965.0
2 TraesCS6B01G098500 chr6B 78.108 1311 216 46 1030 2297 76177389 76176107 0.000000e+00 765.0
3 TraesCS6B01G098500 chr6B 78.078 593 104 14 1022 1592 75510357 75509769 5.080000e-93 351.0
4 TraesCS6B01G098500 chr6B 71.928 1286 284 56 1007 2243 82004624 82005881 1.440000e-78 303.0
5 TraesCS6B01G098500 chr6B 72.429 1128 243 50 1049 2129 82156729 82157835 6.720000e-77 298.0
6 TraesCS6B01G098500 chr6A 93.851 1236 63 8 1443 2669 40529293 40528062 0.000000e+00 1849.0
7 TraesCS6B01G098500 chr6A 95.434 876 24 5 1 876 40533213 40532354 0.000000e+00 1382.0
8 TraesCS6B01G098500 chr6A 97.834 554 8 4 2651 3203 573859078 573858528 0.000000e+00 953.0
9 TraesCS6B01G098500 chr6A 78.839 1309 223 34 1031 2297 40543272 40541976 0.000000e+00 833.0
10 TraesCS6B01G098500 chr6A 90.617 373 19 11 1007 1379 40531027 40530671 6.210000e-132 481.0
11 TraesCS6B01G098500 chr6A 74.378 804 174 22 1526 2307 40623003 40622210 6.670000e-82 315.0
12 TraesCS6B01G098500 chr6A 76.361 643 103 31 1007 1612 39878003 39877373 1.870000e-77 300.0
13 TraesCS6B01G098500 chr6A 72.213 1166 258 46 1007 2129 47488142 47487000 6.720000e-77 298.0
14 TraesCS6B01G098500 chr6A 86.145 166 20 3 796 961 550066550 550066388 3.280000e-40 176.0
15 TraesCS6B01G098500 chr6A 77.253 233 50 3 1832 2062 33016481 33016250 2.000000e-27 134.0
16 TraesCS6B01G098500 chr6A 75.836 269 55 8 1789 2052 30652563 30652826 9.330000e-26 128.0
17 TraesCS6B01G098500 chr6A 81.618 136 23 2 1075 1209 45863480 45863614 9.390000e-21 111.0
18 TraesCS6B01G098500 chr6A 91.379 58 3 1 1445 1500 33216075 33216018 9.530000e-11 78.7
19 TraesCS6B01G098500 chr5B 99.069 537 5 0 2667 3203 48316277 48315741 0.000000e+00 965.0
20 TraesCS6B01G098500 chr5A 99.069 537 5 0 2667 3203 174601592 174601056 0.000000e+00 965.0
21 TraesCS6B01G098500 chr4B 99.069 537 5 0 2667 3203 5372861 5373397 0.000000e+00 965.0
22 TraesCS6B01G098500 chr3B 98.891 541 5 1 2663 3203 389957590 389958129 0.000000e+00 965.0
23 TraesCS6B01G098500 chr2A 99.069 537 5 0 2667 3203 518944213 518943677 0.000000e+00 965.0
24 TraesCS6B01G098500 chr2A 99.069 537 5 0 2667 3203 676079643 676079107 0.000000e+00 965.0
25 TraesCS6B01G098500 chr1B 98.713 544 6 1 2661 3203 56892336 56891793 0.000000e+00 965.0
26 TraesCS6B01G098500 chr6D 76.366 1299 240 49 1045 2296 36323919 36325197 1.250000e-178 636.0
27 TraesCS6B01G098500 chr6D 77.561 615 97 29 1032 1612 36106084 36105477 1.840000e-87 333.0
28 TraesCS6B01G098500 chr6D 76.861 618 122 14 1006 1611 35667513 35666905 2.380000e-86 329.0
29 TraesCS6B01G098500 chr1D 77.240 558 114 8 1046 1592 37880051 37880606 6.670000e-82 315.0
30 TraesCS6B01G098500 chrUn 75.645 349 70 10 1791 2129 27073888 27074231 3.310000e-35 159.0
31 TraesCS6B01G098500 chr1A 81.757 148 23 3 1447 1592 36789282 36789427 1.560000e-23 121.0


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 TraesCS6B01G098500 chr6B 75988434 75991636 3202 True 5915.000000 5915 100.000000 1 3203 1 chr6B.!!$R2 3202
1 TraesCS6B01G098500 chr6B 606302726 606303262 536 True 965.000000 965 99.069000 2667 3203 1 chr6B.!!$R4 536
2 TraesCS6B01G098500 chr6B 76176107 76177389 1282 True 765.000000 765 78.108000 1030 2297 1 chr6B.!!$R3 1267
3 TraesCS6B01G098500 chr6B 75509769 75510357 588 True 351.000000 351 78.078000 1022 1592 1 chr6B.!!$R1 570
4 TraesCS6B01G098500 chr6B 82004624 82005881 1257 False 303.000000 303 71.928000 1007 2243 1 chr6B.!!$F1 1236
5 TraesCS6B01G098500 chr6B 82156729 82157835 1106 False 298.000000 298 72.429000 1049 2129 1 chr6B.!!$F2 1080
6 TraesCS6B01G098500 chr6A 40528062 40533213 5151 True 1237.333333 1849 93.300667 1 2669 3 chr6A.!!$R9 2668
7 TraesCS6B01G098500 chr6A 573858528 573859078 550 True 953.000000 953 97.834000 2651 3203 1 chr6A.!!$R8 552
8 TraesCS6B01G098500 chr6A 40541976 40543272 1296 True 833.000000 833 78.839000 1031 2297 1 chr6A.!!$R4 1266
9 TraesCS6B01G098500 chr6A 40622210 40623003 793 True 315.000000 315 74.378000 1526 2307 1 chr6A.!!$R5 781
10 TraesCS6B01G098500 chr6A 39877373 39878003 630 True 300.000000 300 76.361000 1007 1612 1 chr6A.!!$R3 605
11 TraesCS6B01G098500 chr6A 47487000 47488142 1142 True 298.000000 298 72.213000 1007 2129 1 chr6A.!!$R6 1122
12 TraesCS6B01G098500 chr5B 48315741 48316277 536 True 965.000000 965 99.069000 2667 3203 1 chr5B.!!$R1 536
13 TraesCS6B01G098500 chr5A 174601056 174601592 536 True 965.000000 965 99.069000 2667 3203 1 chr5A.!!$R1 536
14 TraesCS6B01G098500 chr4B 5372861 5373397 536 False 965.000000 965 99.069000 2667 3203 1 chr4B.!!$F1 536
15 TraesCS6B01G098500 chr3B 389957590 389958129 539 False 965.000000 965 98.891000 2663 3203 1 chr3B.!!$F1 540
16 TraesCS6B01G098500 chr2A 518943677 518944213 536 True 965.000000 965 99.069000 2667 3203 1 chr2A.!!$R1 536
17 TraesCS6B01G098500 chr2A 676079107 676079643 536 True 965.000000 965 99.069000 2667 3203 1 chr2A.!!$R2 536
18 TraesCS6B01G098500 chr1B 56891793 56892336 543 True 965.000000 965 98.713000 2661 3203 1 chr1B.!!$R1 542
19 TraesCS6B01G098500 chr6D 36323919 36325197 1278 False 636.000000 636 76.366000 1045 2296 1 chr6D.!!$F1 1251
20 TraesCS6B01G098500 chr6D 36105477 36106084 607 True 333.000000 333 77.561000 1032 1612 1 chr6D.!!$R2 580
21 TraesCS6B01G098500 chr6D 35666905 35667513 608 True 329.000000 329 76.861000 1006 1611 1 chr6D.!!$R1 605
22 TraesCS6B01G098500 chr1D 37880051 37880606 555 False 315.000000 315 77.240000 1046 1592 1 chr1D.!!$F1 546

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
979 980 0.472471 GACTCCACCACACTTTCCCA 59.528 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 5118 0.60813 CCACCACGGTCTCATCTTGA 59.392 55.0 0.0 0.0 0.0 3.02 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
54 55 6.332901 AGGGTGAGATAATAGTTGCCCTTAAT 59.667 38.462 0.00 0.00 42.09 1.40
106 107 7.520451 AGATTCAAATACCATGGTGATGATG 57.480 36.000 28.17 17.43 0.00 3.07
167 168 3.521126 ACATACTGCTCATCCAAGTCCTT 59.479 43.478 0.00 0.00 0.00 3.36
302 303 3.256879 TCACAGTGGAGTCAGAAGATGTC 59.743 47.826 0.00 0.00 0.00 3.06
305 306 1.067565 GTGGAGTCAGAAGATGTCGCA 60.068 52.381 0.00 0.00 0.00 5.10
342 343 5.049405 CGGTGATAGATTGCACTTATTTCCC 60.049 44.000 0.00 0.00 35.43 3.97
344 345 6.205658 GGTGATAGATTGCACTTATTTCCCTC 59.794 42.308 0.00 0.00 35.43 4.30
345 346 5.991606 TGATAGATTGCACTTATTTCCCTCG 59.008 40.000 0.00 0.00 0.00 4.63
346 347 4.487714 AGATTGCACTTATTTCCCTCGA 57.512 40.909 0.00 0.00 0.00 4.04
347 348 5.041191 AGATTGCACTTATTTCCCTCGAT 57.959 39.130 0.00 0.00 0.00 3.59
348 349 4.818546 AGATTGCACTTATTTCCCTCGATG 59.181 41.667 0.00 0.00 0.00 3.84
349 350 2.288666 TGCACTTATTTCCCTCGATGC 58.711 47.619 0.00 0.00 0.00 3.91
350 351 1.604278 GCACTTATTTCCCTCGATGCC 59.396 52.381 0.00 0.00 0.00 4.40
351 352 2.222027 CACTTATTTCCCTCGATGCCC 58.778 52.381 0.00 0.00 0.00 5.36
352 353 1.202651 ACTTATTTCCCTCGATGCCCG 60.203 52.381 0.00 0.00 40.25 6.13
353 354 0.834612 TTATTTCCCTCGATGCCCGT 59.165 50.000 0.00 0.00 39.75 5.28
354 355 0.834612 TATTTCCCTCGATGCCCGTT 59.165 50.000 0.00 0.00 39.75 4.44
355 356 0.748005 ATTTCCCTCGATGCCCGTTG 60.748 55.000 0.00 0.00 39.75 4.10
356 357 2.119484 TTTCCCTCGATGCCCGTTGT 62.119 55.000 0.00 0.00 39.75 3.32
357 358 2.511600 CCCTCGATGCCCGTTGTC 60.512 66.667 0.00 0.00 39.75 3.18
373 374 3.900116 CGTTGTCGCAGAATTGTAGTTTG 59.100 43.478 0.00 0.00 39.69 2.93
378 379 3.994392 TCGCAGAATTGTAGTTTGGTCTC 59.006 43.478 0.00 0.00 0.00 3.36
379 380 3.997021 CGCAGAATTGTAGTTTGGTCTCT 59.003 43.478 0.00 0.00 0.00 3.10
380 381 4.143030 CGCAGAATTGTAGTTTGGTCTCTG 60.143 45.833 0.00 0.00 33.72 3.35
381 382 4.757149 GCAGAATTGTAGTTTGGTCTCTGT 59.243 41.667 0.00 0.00 33.25 3.41
526 527 2.071540 GGAGCGGTAACTTTGTACACC 58.928 52.381 0.00 0.00 0.00 4.16
541 542 6.450845 TTGTACACCTTTTACGTGTATTCG 57.549 37.500 0.00 0.00 45.67 3.34
560 561 9.577110 TGTATTCGGTACAGTAGTTCTTTTATG 57.423 33.333 0.00 0.00 38.37 1.90
602 603 7.868775 TGATACATTTGAATCTGCATAGCTTC 58.131 34.615 0.00 0.00 31.35 3.86
612 613 7.656542 TGAATCTGCATAGCTTCAGAGAATAAG 59.343 37.037 15.16 0.00 41.95 1.73
677 678 6.165700 TCCTTTTACTCTAGTTTTCGTGGT 57.834 37.500 0.00 0.00 0.00 4.16
732 733 1.539560 ATCTCACTGCCAGCGTGACT 61.540 55.000 11.44 2.85 36.54 3.41
876 877 3.074857 TCAAGGAGGTTATGGGGCTAT 57.925 47.619 0.00 0.00 0.00 2.97
878 879 4.572978 TCAAGGAGGTTATGGGGCTATTA 58.427 43.478 0.00 0.00 0.00 0.98
879 880 5.170198 TCAAGGAGGTTATGGGGCTATTAT 58.830 41.667 0.00 0.00 0.00 1.28
880 881 5.615261 TCAAGGAGGTTATGGGGCTATTATT 59.385 40.000 0.00 0.00 0.00 1.40
882 883 6.893020 AGGAGGTTATGGGGCTATTATTAG 57.107 41.667 0.00 0.00 0.00 1.73
884 885 6.215636 AGGAGGTTATGGGGCTATTATTAGTG 59.784 42.308 0.00 0.00 0.00 2.74
885 886 6.214819 GGAGGTTATGGGGCTATTATTAGTGA 59.785 42.308 0.00 0.00 0.00 3.41
886 887 7.259088 AGGTTATGGGGCTATTATTAGTGAG 57.741 40.000 0.00 0.00 0.00 3.51
887 888 7.023120 AGGTTATGGGGCTATTATTAGTGAGA 58.977 38.462 0.00 0.00 0.00 3.27
888 889 7.684619 AGGTTATGGGGCTATTATTAGTGAGAT 59.315 37.037 0.00 0.00 0.00 2.75
892 893 8.917414 ATGGGGCTATTATTAGTGAGATTAGA 57.083 34.615 0.00 0.00 0.00 2.10
893 894 8.736097 TGGGGCTATTATTAGTGAGATTAGAA 57.264 34.615 0.00 0.00 0.00 2.10
894 895 9.166222 TGGGGCTATTATTAGTGAGATTAGAAA 57.834 33.333 0.00 0.00 0.00 2.52
895 896 9.660180 GGGGCTATTATTAGTGAGATTAGAAAG 57.340 37.037 0.00 0.00 0.00 2.62
907 908 9.479549 AGTGAGATTAGAAAGAGATCTTCTTCT 57.520 33.333 18.81 18.81 45.41 2.85
936 937 8.742554 AATTGTACTTTTATTTTCGAAGGCAG 57.257 30.769 0.00 0.00 0.00 4.85
937 938 7.499321 TTGTACTTTTATTTTCGAAGGCAGA 57.501 32.000 0.00 0.00 0.00 4.26
938 939 7.129109 TGTACTTTTATTTTCGAAGGCAGAG 57.871 36.000 0.00 0.00 0.00 3.35
939 940 5.048153 ACTTTTATTTTCGAAGGCAGAGC 57.952 39.130 0.00 0.00 0.00 4.09
961 962 2.964740 GCTAATGGCGATGCTGATAGA 58.035 47.619 0.00 0.00 0.00 1.98
962 963 2.670414 GCTAATGGCGATGCTGATAGAC 59.330 50.000 0.00 0.00 0.00 2.59
963 964 3.616076 GCTAATGGCGATGCTGATAGACT 60.616 47.826 0.00 0.00 0.00 3.24
964 965 2.739885 ATGGCGATGCTGATAGACTC 57.260 50.000 0.00 0.00 0.00 3.36
965 966 0.676184 TGGCGATGCTGATAGACTCC 59.324 55.000 0.00 0.00 0.00 3.85
966 967 0.676184 GGCGATGCTGATAGACTCCA 59.324 55.000 0.00 0.00 0.00 3.86
967 968 1.604185 GGCGATGCTGATAGACTCCAC 60.604 57.143 0.00 0.00 0.00 4.02
968 969 1.604185 GCGATGCTGATAGACTCCACC 60.604 57.143 0.00 0.00 0.00 4.61
970 971 2.544694 CGATGCTGATAGACTCCACCAC 60.545 54.545 0.00 0.00 0.00 4.16
971 972 1.937191 TGCTGATAGACTCCACCACA 58.063 50.000 0.00 0.00 0.00 4.17
972 973 1.550524 TGCTGATAGACTCCACCACAC 59.449 52.381 0.00 0.00 0.00 3.82
973 974 1.827969 GCTGATAGACTCCACCACACT 59.172 52.381 0.00 0.00 0.00 3.55
975 976 3.307059 GCTGATAGACTCCACCACACTTT 60.307 47.826 0.00 0.00 0.00 2.66
976 977 4.499183 CTGATAGACTCCACCACACTTTC 58.501 47.826 0.00 0.00 0.00 2.62
978 979 0.765510 AGACTCCACCACACTTTCCC 59.234 55.000 0.00 0.00 0.00 3.97
979 980 0.472471 GACTCCACCACACTTTCCCA 59.528 55.000 0.00 0.00 0.00 4.37
980 981 1.073923 GACTCCACCACACTTTCCCAT 59.926 52.381 0.00 0.00 0.00 4.00
981 982 1.202927 ACTCCACCACACTTTCCCATG 60.203 52.381 0.00 0.00 0.00 3.66
983 984 1.073763 TCCACCACACTTTCCCATGAG 59.926 52.381 0.00 0.00 0.00 2.90
986 987 2.294233 CACCACACTTTCCCATGAGTTG 59.706 50.000 0.00 0.00 0.00 3.16
987 988 2.091885 ACCACACTTTCCCATGAGTTGT 60.092 45.455 0.00 0.00 0.00 3.32
990 991 3.003689 CACACTTTCCCATGAGTTGTGAC 59.996 47.826 0.00 0.00 32.05 3.67
991 992 2.224079 CACTTTCCCATGAGTTGTGACG 59.776 50.000 0.00 0.00 0.00 4.35
993 994 2.455674 TTCCCATGAGTTGTGACGAG 57.544 50.000 0.00 0.00 0.00 4.18
994 995 0.608130 TCCCATGAGTTGTGACGAGG 59.392 55.000 0.00 0.00 0.00 4.63
996 997 1.673033 CCCATGAGTTGTGACGAGGAC 60.673 57.143 0.00 0.00 0.00 3.85
997 998 1.000843 CCATGAGTTGTGACGAGGACA 59.999 52.381 0.00 0.00 0.00 4.02
998 999 2.547855 CCATGAGTTGTGACGAGGACAA 60.548 50.000 0.00 0.00 0.00 3.18
999 1000 2.509052 TGAGTTGTGACGAGGACAAG 57.491 50.000 0.00 0.00 34.02 3.16
1000 1001 2.028876 TGAGTTGTGACGAGGACAAGA 58.971 47.619 0.00 0.00 34.02 3.02
1001 1002 2.628178 TGAGTTGTGACGAGGACAAGAT 59.372 45.455 0.00 0.00 34.02 2.40
1002 1003 2.989840 GAGTTGTGACGAGGACAAGATG 59.010 50.000 0.00 0.00 34.02 2.90
1003 1004 2.628178 AGTTGTGACGAGGACAAGATGA 59.372 45.455 0.00 0.00 34.02 2.92
1004 1005 2.989840 GTTGTGACGAGGACAAGATGAG 59.010 50.000 0.00 0.00 34.02 2.90
1073 2270 1.258676 GAGGACGACAACCTCCTCTT 58.741 55.000 9.62 0.00 46.48 2.85
1138 2335 2.637383 GCCTCCGTCGTCTCCAAGT 61.637 63.158 0.00 0.00 0.00 3.16
1356 2599 1.280133 CTCATCTTCCAGTTGAGGCCA 59.720 52.381 5.01 0.00 38.03 5.36
1380 2623 3.570212 GTGCTGGTGTGGGACCCT 61.570 66.667 13.00 0.00 45.45 4.34
1893 4483 1.895131 GATGGTGTTGCTTCATGGGTT 59.105 47.619 0.00 0.00 0.00 4.11
2053 4646 6.395426 TTGAGTCATTGCAGTTCAAGAAAT 57.605 33.333 0.00 0.00 38.22 2.17
2096 4689 4.676018 GTCTCGCTATTATCCACTCGAAAC 59.324 45.833 0.00 0.00 0.00 2.78
2124 4717 1.242076 CTGCAGGTAATAGCATGCCC 58.758 55.000 15.66 8.05 40.42 5.36
2132 4725 4.065789 GGTAATAGCATGCCCTTACACTC 58.934 47.826 27.71 15.27 0.00 3.51
2195 4789 4.089065 GTCGCAATGCTGTTCAAATCTTTC 59.911 41.667 2.94 0.00 0.00 2.62
2281 4884 4.782019 TCAACACAGAGCAAAGTTGTTT 57.218 36.364 0.00 0.00 41.43 2.83
2288 4891 6.373216 ACACAGAGCAAAGTTGTTTTGTAGTA 59.627 34.615 4.20 0.00 46.35 1.82
2331 4934 3.945346 TGGTGGCGTTCTGTGTAATTAT 58.055 40.909 0.00 0.00 0.00 1.28
2332 4935 3.687212 TGGTGGCGTTCTGTGTAATTATG 59.313 43.478 0.00 0.00 0.00 1.90
2334 4937 4.155280 GGTGGCGTTCTGTGTAATTATGTT 59.845 41.667 0.00 0.00 0.00 2.71
2335 4938 5.086058 GTGGCGTTCTGTGTAATTATGTTG 58.914 41.667 0.00 0.00 0.00 3.33
2338 4941 5.793457 GGCGTTCTGTGTAATTATGTTGTTC 59.207 40.000 0.00 0.00 0.00 3.18
2339 4942 5.503376 GCGTTCTGTGTAATTATGTTGTTCG 59.497 40.000 0.00 0.00 0.00 3.95
2340 4943 6.616893 GCGTTCTGTGTAATTATGTTGTTCGA 60.617 38.462 0.00 0.00 0.00 3.71
2341 4944 7.285069 CGTTCTGTGTAATTATGTTGTTCGAA 58.715 34.615 0.00 0.00 0.00 3.71
2363 4974 3.445008 TGAGAGGTGGCAAACTCTATCT 58.555 45.455 9.20 0.00 43.71 1.98
2366 4977 2.237392 GAGGTGGCAAACTCTATCTGGT 59.763 50.000 0.00 0.00 0.00 4.00
2380 4991 7.331791 ACTCTATCTGGTACAAAGATTGGAAC 58.668 38.462 13.67 0.00 38.70 3.62
2394 5005 2.472695 TGGAACGTGAGGAAGATTGG 57.527 50.000 0.00 0.00 0.00 3.16
2400 5011 2.749621 ACGTGAGGAAGATTGGCATTTC 59.250 45.455 0.00 0.00 0.00 2.17
2504 5115 7.320443 CATTACTGCATAGTTATGGTGTTGT 57.680 36.000 0.00 0.00 39.23 3.32
2505 5116 7.761409 CATTACTGCATAGTTATGGTGTTGTT 58.239 34.615 0.00 0.00 39.23 2.83
2506 5117 5.880054 ACTGCATAGTTATGGTGTTGTTC 57.120 39.130 0.00 0.00 31.66 3.18
2507 5118 5.560724 ACTGCATAGTTATGGTGTTGTTCT 58.439 37.500 0.00 0.00 31.66 3.01
2543 5154 3.383185 TGGTGGTTGGAAAATGAAGTCAC 59.617 43.478 0.00 0.00 0.00 3.67
2544 5155 3.636764 GGTGGTTGGAAAATGAAGTCACT 59.363 43.478 0.00 0.00 0.00 3.41
2551 5162 6.573664 TGGAAAATGAAGTCACTTACATGG 57.426 37.500 0.00 0.00 0.00 3.66
2577 5188 4.871933 AAACTAGCTTGAACCAAATGGG 57.128 40.909 1.04 0.00 44.81 4.00
2712 5328 4.468153 ACAAAGCCTTTAGTCCCAAACAAA 59.532 37.500 0.00 0.00 0.00 2.83
2762 5378 2.234661 AGATCTCGCAACCAACTCATGA 59.765 45.455 0.00 0.00 0.00 3.07
2919 5535 2.740826 GCACGCTTTAGCCGTCCA 60.741 61.111 0.00 0.00 37.91 4.02
3104 5720 1.754803 CATCTCCGCCACACCTAACTA 59.245 52.381 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.900112 ACTATTATCTCACCCTAGGTTCTTTAT 57.100 33.333 8.29 0.00 31.02 1.40
34 35 8.718734 CGGTTTATTAAGGGCAACTATTATCTC 58.281 37.037 0.00 0.00 0.00 2.75
54 55 1.810151 GGATCTGTGCTTTGCGGTTTA 59.190 47.619 0.00 0.00 0.00 2.01
106 107 2.086054 AATGACTTCCTGTGTCGAGC 57.914 50.000 0.00 0.00 37.26 5.03
265 266 4.037923 CCACTGTGACCAACATAGCTTTTT 59.962 41.667 9.86 0.00 40.60 1.94
342 343 3.554692 GCGACAACGGGCATCGAG 61.555 66.667 5.71 1.08 42.43 4.04
344 345 3.853330 CTGCGACAACGGGCATCG 61.853 66.667 0.00 0.00 45.88 3.84
345 346 1.369091 ATTCTGCGACAACGGGCATC 61.369 55.000 0.00 0.00 38.69 3.91
346 347 0.960364 AATTCTGCGACAACGGGCAT 60.960 50.000 0.00 0.00 38.69 4.40
347 348 1.599518 AATTCTGCGACAACGGGCA 60.600 52.632 0.00 0.00 40.15 5.36
348 349 1.154225 CAATTCTGCGACAACGGGC 60.154 57.895 0.00 0.00 40.15 6.13
349 350 1.393539 CTACAATTCTGCGACAACGGG 59.606 52.381 0.00 0.00 40.15 5.28
350 351 2.066262 ACTACAATTCTGCGACAACGG 58.934 47.619 0.00 0.00 40.15 4.44
351 352 3.788434 AACTACAATTCTGCGACAACG 57.212 42.857 0.00 0.00 42.93 4.10
352 353 4.219033 CCAAACTACAATTCTGCGACAAC 58.781 43.478 0.00 0.00 0.00 3.32
353 354 3.880490 ACCAAACTACAATTCTGCGACAA 59.120 39.130 0.00 0.00 0.00 3.18
354 355 3.472652 ACCAAACTACAATTCTGCGACA 58.527 40.909 0.00 0.00 0.00 4.35
355 356 3.746492 AGACCAAACTACAATTCTGCGAC 59.254 43.478 0.00 0.00 0.00 5.19
356 357 3.994392 GAGACCAAACTACAATTCTGCGA 59.006 43.478 0.00 0.00 0.00 5.10
357 358 3.997021 AGAGACCAAACTACAATTCTGCG 59.003 43.478 0.00 0.00 0.00 5.18
373 374 0.673956 GGGAAAAGCGGACAGAGACC 60.674 60.000 0.00 0.00 0.00 3.85
434 435 2.283298 CCCCATTCATTCGTGTCTCAG 58.717 52.381 0.00 0.00 0.00 3.35
485 486 4.036971 TCCCCTCAAAATGTACACAAAACG 59.963 41.667 0.00 0.00 0.00 3.60
526 527 7.023575 ACTACTGTACCGAATACACGTAAAAG 58.976 38.462 0.00 0.00 38.95 2.27
541 542 7.224167 CGGAATCCATAAAAGAACTACTGTACC 59.776 40.741 0.00 0.00 0.00 3.34
560 561 6.140303 TGTATCAACTACTGTACGGAATCC 57.860 41.667 9.17 0.00 0.00 3.01
612 613 8.785329 ACAGGACATAGAGATTTTTCTTCTTC 57.215 34.615 0.00 0.00 0.00 2.87
627 628 4.333649 CCACAGCACATAAACAGGACATAG 59.666 45.833 0.00 0.00 0.00 2.23
628 629 4.260985 CCACAGCACATAAACAGGACATA 58.739 43.478 0.00 0.00 0.00 2.29
677 678 2.320681 TCCCTTCTTTTCGGGAGAGA 57.679 50.000 0.00 0.00 44.42 3.10
732 733 3.712733 AGTAGTGTACCAACCAAAGTGGA 59.287 43.478 0.18 0.00 40.96 4.02
767 768 2.612972 CCTCAGCCACGATGTGTAGTTT 60.613 50.000 0.00 0.00 0.00 2.66
768 769 1.066858 CCTCAGCCACGATGTGTAGTT 60.067 52.381 0.00 0.00 0.00 2.24
769 770 0.532573 CCTCAGCCACGATGTGTAGT 59.467 55.000 0.00 0.00 0.00 2.73
910 911 9.191995 CTGCCTTCGAAAATAAAAGTACAATTT 57.808 29.630 0.00 0.00 0.00 1.82
913 914 7.499321 TCTGCCTTCGAAAATAAAAGTACAA 57.501 32.000 0.00 0.00 0.00 2.41
916 917 5.123344 GGCTCTGCCTTCGAAAATAAAAGTA 59.877 40.000 0.00 0.00 46.69 2.24
917 918 4.082733 GGCTCTGCCTTCGAAAATAAAAGT 60.083 41.667 0.00 0.00 46.69 2.66
918 919 4.415735 GGCTCTGCCTTCGAAAATAAAAG 58.584 43.478 0.00 0.00 46.69 2.27
941 942 2.670414 GTCTATCAGCATCGCCATTAGC 59.330 50.000 0.00 0.00 38.52 3.09
942 943 4.172505 GAGTCTATCAGCATCGCCATTAG 58.827 47.826 0.00 0.00 0.00 1.73
943 944 3.056536 GGAGTCTATCAGCATCGCCATTA 60.057 47.826 0.00 0.00 0.00 1.90
944 945 2.289320 GGAGTCTATCAGCATCGCCATT 60.289 50.000 0.00 0.00 0.00 3.16
946 947 0.676184 GGAGTCTATCAGCATCGCCA 59.324 55.000 0.00 0.00 0.00 5.69
947 948 0.676184 TGGAGTCTATCAGCATCGCC 59.324 55.000 0.00 0.00 0.00 5.54
948 949 1.604185 GGTGGAGTCTATCAGCATCGC 60.604 57.143 0.00 0.00 0.00 4.58
949 950 1.683385 TGGTGGAGTCTATCAGCATCG 59.317 52.381 4.13 0.00 36.61 3.84
950 951 2.432146 TGTGGTGGAGTCTATCAGCATC 59.568 50.000 9.75 6.00 42.22 3.91
951 952 2.169352 GTGTGGTGGAGTCTATCAGCAT 59.831 50.000 9.75 0.00 42.22 3.79
953 954 1.827969 AGTGTGGTGGAGTCTATCAGC 59.172 52.381 0.00 0.00 0.00 4.26
955 956 3.260884 GGAAAGTGTGGTGGAGTCTATCA 59.739 47.826 0.00 0.00 0.00 2.15
956 957 3.369576 GGGAAAGTGTGGTGGAGTCTATC 60.370 52.174 0.00 0.00 0.00 2.08
957 958 2.572104 GGGAAAGTGTGGTGGAGTCTAT 59.428 50.000 0.00 0.00 0.00 1.98
958 959 1.975680 GGGAAAGTGTGGTGGAGTCTA 59.024 52.381 0.00 0.00 0.00 2.59
960 961 0.472471 TGGGAAAGTGTGGTGGAGTC 59.528 55.000 0.00 0.00 0.00 3.36
961 962 1.149101 ATGGGAAAGTGTGGTGGAGT 58.851 50.000 0.00 0.00 0.00 3.85
962 963 1.073763 TCATGGGAAAGTGTGGTGGAG 59.926 52.381 0.00 0.00 0.00 3.86
963 964 1.073763 CTCATGGGAAAGTGTGGTGGA 59.926 52.381 0.00 0.00 0.00 4.02
964 965 1.202927 ACTCATGGGAAAGTGTGGTGG 60.203 52.381 0.00 0.00 0.00 4.61
965 966 2.276732 ACTCATGGGAAAGTGTGGTG 57.723 50.000 0.00 0.00 0.00 4.17
966 967 2.091885 ACAACTCATGGGAAAGTGTGGT 60.092 45.455 0.00 0.00 0.00 4.16
967 968 2.294233 CACAACTCATGGGAAAGTGTGG 59.706 50.000 0.00 0.00 32.54 4.17
968 969 3.003689 GTCACAACTCATGGGAAAGTGTG 59.996 47.826 0.00 8.25 44.92 3.82
970 971 2.224079 CGTCACAACTCATGGGAAAGTG 59.776 50.000 0.00 5.00 44.92 3.16
971 972 2.104111 TCGTCACAACTCATGGGAAAGT 59.896 45.455 0.00 0.00 44.92 2.66
972 973 2.738846 CTCGTCACAACTCATGGGAAAG 59.261 50.000 0.00 0.00 44.92 2.62
973 974 2.549992 CCTCGTCACAACTCATGGGAAA 60.550 50.000 0.00 0.00 44.92 3.13
975 976 0.608130 CCTCGTCACAACTCATGGGA 59.392 55.000 0.00 0.00 39.84 4.37
976 977 0.608130 TCCTCGTCACAACTCATGGG 59.392 55.000 0.00 0.00 0.00 4.00
978 979 2.438868 TGTCCTCGTCACAACTCATG 57.561 50.000 0.00 0.00 0.00 3.07
979 980 2.628178 TCTTGTCCTCGTCACAACTCAT 59.372 45.455 0.00 0.00 30.49 2.90
980 981 2.028876 TCTTGTCCTCGTCACAACTCA 58.971 47.619 0.00 0.00 30.49 3.41
981 982 2.795175 TCTTGTCCTCGTCACAACTC 57.205 50.000 0.00 0.00 30.49 3.01
983 984 2.989840 CTCATCTTGTCCTCGTCACAAC 59.010 50.000 0.00 0.00 30.49 3.32
986 987 3.732471 GCTACTCATCTTGTCCTCGTCAC 60.732 52.174 0.00 0.00 0.00 3.67
987 988 2.423892 GCTACTCATCTTGTCCTCGTCA 59.576 50.000 0.00 0.00 0.00 4.35
990 991 1.268794 CGGCTACTCATCTTGTCCTCG 60.269 57.143 0.00 0.00 0.00 4.63
991 992 1.537135 GCGGCTACTCATCTTGTCCTC 60.537 57.143 0.00 0.00 0.00 3.71
993 994 0.530870 GGCGGCTACTCATCTTGTCC 60.531 60.000 0.00 0.00 0.00 4.02
994 995 0.461961 AGGCGGCTACTCATCTTGTC 59.538 55.000 11.03 0.00 0.00 3.18
996 997 0.249657 GGAGGCGGCTACTCATCTTG 60.250 60.000 15.23 0.00 36.70 3.02
997 998 0.397816 AGGAGGCGGCTACTCATCTT 60.398 55.000 19.89 0.00 36.70 2.40
998 999 0.825840 GAGGAGGCGGCTACTCATCT 60.826 60.000 38.60 13.11 41.23 2.90
999 1000 1.663173 GAGGAGGCGGCTACTCATC 59.337 63.158 38.60 18.61 38.39 2.92
1000 1001 1.834822 GGAGGAGGCGGCTACTCAT 60.835 63.158 41.79 17.11 36.70 2.90
1001 1002 2.442272 GGAGGAGGCGGCTACTCA 60.442 66.667 41.79 0.00 36.70 3.41
1002 1003 3.228017 GGGAGGAGGCGGCTACTC 61.228 72.222 36.80 36.80 0.00 2.59
1003 1004 4.075793 TGGGAGGAGGCGGCTACT 62.076 66.667 26.09 26.09 0.00 2.57
1004 1005 3.851128 GTGGGAGGAGGCGGCTAC 61.851 72.222 14.62 14.62 0.00 3.58
1073 2270 2.203365 GGCGGAGGAGGATCTCGA 60.203 66.667 0.00 0.00 34.74 4.04
1138 2335 1.915489 AGATATGAGGTGGTGCCAACA 59.085 47.619 9.13 3.18 40.61 3.33
1145 2342 1.414158 CGGGTCAGATATGAGGTGGT 58.586 55.000 0.00 0.00 0.00 4.16
1148 2345 1.122019 GCCCGGGTCAGATATGAGGT 61.122 60.000 24.63 0.00 0.00 3.85
1356 2599 1.149174 CCACACCAGCACCTTGAGT 59.851 57.895 0.00 0.00 0.00 3.41
1380 2623 1.887242 GTGCAGTTCGCCAGTGACA 60.887 57.895 0.00 0.00 41.33 3.58
1428 2842 2.605257 CCATTAGTCGGGGTCTCCATA 58.395 52.381 0.00 0.00 34.36 2.74
1893 4483 5.768164 GTCCAGTTCAATAGTTTTTCCCAGA 59.232 40.000 0.00 0.00 0.00 3.86
1968 4561 5.018809 ACCACATTATTGTCCTCAGCAAAT 58.981 37.500 0.00 0.00 32.34 2.32
2096 4689 3.064545 GCTATTACCTGCAGCAAAGACAG 59.935 47.826 8.66 4.91 35.35 3.51
2124 4717 6.092259 GTGCTTTGTTATACCCAGAGTGTAAG 59.908 42.308 0.00 0.00 33.26 2.34
2132 4725 9.507329 AAGATATATGTGCTTTGTTATACCCAG 57.493 33.333 0.00 0.00 0.00 4.45
2174 4768 4.089493 CAGAAAGATTTGAACAGCATTGCG 59.911 41.667 2.38 1.04 0.00 4.85
2288 4891 9.048446 CACCAAAAATCAATCAGAAAAGAACAT 57.952 29.630 0.00 0.00 0.00 2.71
2309 4912 2.264005 ATTACACAGAACGCCACCAA 57.736 45.000 0.00 0.00 0.00 3.67
2331 4934 2.766313 CCACCTCTCATTCGAACAACA 58.234 47.619 0.00 0.00 0.00 3.33
2332 4935 1.464997 GCCACCTCTCATTCGAACAAC 59.535 52.381 0.00 0.00 0.00 3.32
2334 4937 0.684535 TGCCACCTCTCATTCGAACA 59.315 50.000 0.00 0.00 0.00 3.18
2335 4938 1.808411 TTGCCACCTCTCATTCGAAC 58.192 50.000 0.00 0.00 0.00 3.95
2338 4941 1.734465 GAGTTTGCCACCTCTCATTCG 59.266 52.381 0.00 0.00 0.00 3.34
2339 4942 3.064900 AGAGTTTGCCACCTCTCATTC 57.935 47.619 0.00 0.00 32.65 2.67
2340 4943 4.472833 AGATAGAGTTTGCCACCTCTCATT 59.527 41.667 0.00 0.00 38.86 2.57
2341 4944 4.036518 AGATAGAGTTTGCCACCTCTCAT 58.963 43.478 0.00 0.00 38.86 2.90
2363 4974 4.062293 CTCACGTTCCAATCTTTGTACCA 58.938 43.478 0.00 0.00 0.00 3.25
2366 4977 4.610605 TCCTCACGTTCCAATCTTTGTA 57.389 40.909 0.00 0.00 0.00 2.41
2380 4991 3.012518 AGAAATGCCAATCTTCCTCACG 58.987 45.455 0.00 0.00 0.00 4.35
2430 5041 4.216902 TGAATATGTCAATAGGCATGCAGC 59.783 41.667 21.36 2.42 36.31 5.25
2431 5042 5.952526 TGAATATGTCAATAGGCATGCAG 57.047 39.130 21.36 3.52 31.51 4.41
2485 5096 5.643348 TGAGAACAACACCATAACTATGCAG 59.357 40.000 0.00 0.00 32.40 4.41
2487 5098 6.371548 TCTTGAGAACAACACCATAACTATGC 59.628 38.462 0.00 0.00 31.12 3.14
2506 5117 1.404717 CCACCACGGTCTCATCTTGAG 60.405 57.143 0.00 0.00 45.59 3.02
2507 5118 0.608130 CCACCACGGTCTCATCTTGA 59.392 55.000 0.00 0.00 0.00 3.02
2520 5131 3.383185 TGACTTCATTTTCCAACCACCAC 59.617 43.478 0.00 0.00 0.00 4.16
2521 5132 3.383185 GTGACTTCATTTTCCAACCACCA 59.617 43.478 0.00 0.00 0.00 4.17
2522 5133 3.636764 AGTGACTTCATTTTCCAACCACC 59.363 43.478 0.00 0.00 0.00 4.61
2543 5154 7.672983 TCAAGCTAGTTTTTCTCCATGTAAG 57.327 36.000 0.00 0.00 0.00 2.34
2544 5155 7.040686 GGTTCAAGCTAGTTTTTCTCCATGTAA 60.041 37.037 0.00 0.00 0.00 2.41
2551 5162 6.642540 CCATTTGGTTCAAGCTAGTTTTTCTC 59.357 38.462 0.00 0.00 0.00 2.87
2577 5188 6.512415 GCCAACTGAGCTACATATTTGACATC 60.512 42.308 0.00 0.00 0.00 3.06
2646 5257 9.417284 GTTGTTGGTAAATATCGAACTAAATCG 57.583 33.333 0.00 0.00 44.04 3.34
2652 5263 7.499321 TGTTGTTGTTGGTAAATATCGAACT 57.501 32.000 0.00 0.00 0.00 3.01
2712 5328 1.294068 TCACCTCTAGCCTACCCCAAT 59.706 52.381 0.00 0.00 0.00 3.16
2762 5378 1.206878 TGCTATCCATGTGCCAGAGT 58.793 50.000 0.00 0.00 0.00 3.24
2919 5535 2.507058 TCCAGAAGCTCCAATGCATAGT 59.493 45.455 0.00 0.00 34.99 2.12
3104 5720 5.296813 GACTAAAAGGCGACATGTTCAAT 57.703 39.130 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.