Multiple sequence alignment - TraesCS6B01G128400

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 TraesCS6B01G128400 chr6B 100.000 4069 0 0 1 4069 123909941 123914009 0.000000e+00 7515.0
1 TraesCS6B01G128400 chr6B 77.403 1217 233 35 1269 2470 71496559 71495370 0.000000e+00 686.0
2 TraesCS6B01G128400 chr6B 76.588 850 171 20 1642 2486 71352346 71351520 3.730000e-120 442.0
3 TraesCS6B01G128400 chr6B 76.680 506 80 25 153 637 90963123 90962635 3.140000e-61 246.0
4 TraesCS6B01G128400 chr6B 74.513 616 127 20 29 633 223568086 223568682 1.460000e-59 241.0
5 TraesCS6B01G128400 chr6B 79.114 316 44 15 332 631 625792267 625792576 8.920000e-47 198.0
6 TraesCS6B01G128400 chr6B 73.664 524 113 19 1953 2468 124084950 124085456 3.230000e-41 180.0
7 TraesCS6B01G128400 chr6B 77.899 276 41 12 332 590 615603447 615603175 1.960000e-33 154.0
8 TraesCS6B01G128400 chr6B 94.118 51 3 0 3603 3653 35414403 35414453 1.210000e-10 78.7
9 TraesCS6B01G128400 chr6B 80.000 90 18 0 3018 3107 31259779 31259690 2.620000e-07 67.6
10 TraesCS6B01G128400 chr6B 78.889 90 19 0 3018 3107 30555916 30555827 1.220000e-05 62.1
11 TraesCS6B01G128400 chr6D 91.158 4162 214 48 6 4069 47639641 47635536 0.000000e+00 5505.0
12 TraesCS6B01G128400 chr6D 77.265 1214 239 32 1269 2470 34588541 34587353 0.000000e+00 678.0
13 TraesCS6B01G128400 chr6D 77.289 841 163 19 1651 2486 34583878 34583061 1.710000e-128 470.0
14 TraesCS6B01G128400 chr6D 79.447 253 39 9 150 400 26355920 26356161 2.520000e-37 167.0
15 TraesCS6B01G128400 chr6D 80.667 150 24 5 3857 4001 2699782 2699633 1.200000e-20 111.0
16 TraesCS6B01G128400 chr6D 92.157 51 4 0 3603 3653 20552690 20552740 5.640000e-09 73.1
17 TraesCS6B01G128400 chr6D 95.455 44 2 0 3404 3447 3822293 3822250 2.030000e-08 71.3
18 TraesCS6B01G128400 chr6D 78.788 99 20 1 3018 3115 17468651 17468553 9.440000e-07 65.8
19 TraesCS6B01G128400 chr6A 92.024 3686 179 51 1 3616 67640684 67644324 0.000000e+00 5072.0
20 TraesCS6B01G128400 chr6A 89.637 386 19 1 3705 4069 67644372 67644757 4.760000e-129 472.0
21 TraesCS6B01G128400 chr6A 78.157 293 45 11 332 611 560039489 560039775 6.990000e-38 169.0
22 TraesCS6B01G128400 chr6A 93.617 47 3 0 3401 3447 3686474 3686520 2.030000e-08 71.3
23 TraesCS6B01G128400 chr6A 80.000 90 18 0 3018 3107 18354149 18354060 2.620000e-07 67.6
24 TraesCS6B01G128400 chr1A 81.833 1222 216 5 1267 2486 560181258 560180041 0.000000e+00 1022.0
25 TraesCS6B01G128400 chr1A 76.323 359 51 13 145 499 545419318 545419646 1.170000e-35 161.0
26 TraesCS6B01G128400 chr1D 81.015 1222 214 9 1268 2486 467801323 467802529 0.000000e+00 955.0
27 TraesCS6B01G128400 chr1D 77.666 1294 237 39 1175 2451 47649064 47650322 0.000000e+00 741.0
28 TraesCS6B01G128400 chr1B 80.154 1300 234 16 1192 2486 645707388 645708668 0.000000e+00 950.0
29 TraesCS6B01G128400 chr5A 77.303 608 107 21 44 637 573815257 573814667 3.030000e-86 329.0
30 TraesCS6B01G128400 chr5A 85.246 183 23 3 1267 1447 655072313 655072133 6.950000e-43 185.0
31 TraesCS6B01G128400 chr5A 72.121 660 119 47 10 642 570471910 570471289 5.480000e-29 139.0
32 TraesCS6B01G128400 chr2A 77.649 519 93 15 124 635 539397115 539397617 1.110000e-75 294.0
33 TraesCS6B01G128400 chr2A 75.932 644 112 31 5 632 572070363 572070979 1.430000e-74 291.0
34 TraesCS6B01G128400 chr2A 80.000 90 17 1 3706 3794 29814567 29814656 9.440000e-07 65.8
35 TraesCS6B01G128400 chr4A 75.207 605 121 17 44 635 691156951 691156363 4.030000e-65 259.0
36 TraesCS6B01G128400 chr4A 76.846 298 56 12 29 317 722444334 722444627 5.450000e-34 156.0
37 TraesCS6B01G128400 chr4A 75.325 231 38 14 2898 3121 602373946 602374164 4.330000e-15 93.5
38 TraesCS6B01G128400 chr4A 75.897 195 36 10 2909 3096 602381472 602381662 5.600000e-14 89.8
39 TraesCS6B01G128400 chr2D 74.961 647 119 32 4 632 418042904 418042283 1.450000e-64 257.0
40 TraesCS6B01G128400 chr2D 74.254 536 79 31 124 637 402310491 402310989 1.940000e-38 171.0
41 TraesCS6B01G128400 chr7D 75.086 582 100 29 42 601 459077313 459077871 3.160000e-56 230.0
42 TraesCS6B01G128400 chr3B 74.109 645 127 23 4 622 55113138 55113768 3.160000e-56 230.0
43 TraesCS6B01G128400 chr4D 75.787 413 70 14 216 612 408802849 408803247 8.980000e-42 182.0
44 TraesCS6B01G128400 chr4D 77.003 287 46 15 342 611 13604444 13604727 3.280000e-31 147.0
45 TraesCS6B01G128400 chr4D 75.399 313 52 16 329 623 445482625 445482930 1.190000e-25 128.0
46 TraesCS6B01G128400 chr4D 74.026 231 41 14 2898 3121 3227304 3227086 4.360000e-10 76.8
47 TraesCS6B01G128400 chr4B 75.366 410 74 16 215 611 532724880 532725275 5.410000e-39 172.0
48 TraesCS6B01G128400 chr5B 82.540 189 33 0 1267 1455 536910840 536910652 2.520000e-37 167.0
49 TraesCS6B01G128400 chr5B 81.148 122 16 5 509 623 502472620 502472499 1.560000e-14 91.6
50 TraesCS6B01G128400 chr5D 82.011 189 34 0 1267 1455 441239151 441238963 1.170000e-35 161.0
51 TraesCS6B01G128400 chr5D 73.504 468 95 22 176 623 487270275 487270733 2.530000e-32 150.0
52 TraesCS6B01G128400 chr7B 75.649 308 58 11 330 622 323835880 323836185 1.970000e-28 137.0
53 TraesCS6B01G128400 chr7B 84.884 86 11 2 324 408 28507353 28507437 7.250000e-13 86.1
54 TraesCS6B01G128400 chrUn 76.316 152 25 8 2901 3045 412749023 412748876 2.030000e-08 71.3


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 TraesCS6B01G128400 chr6B 123909941 123914009 4068 False 7515 7515 100.0000 1 4069 1 chr6B.!!$F2 4068
1 TraesCS6B01G128400 chr6B 71495370 71496559 1189 True 686 686 77.4030 1269 2470 1 chr6B.!!$R4 1201
2 TraesCS6B01G128400 chr6B 71351520 71352346 826 True 442 442 76.5880 1642 2486 1 chr6B.!!$R3 844
3 TraesCS6B01G128400 chr6B 223568086 223568682 596 False 241 241 74.5130 29 633 1 chr6B.!!$F4 604
4 TraesCS6B01G128400 chr6D 47635536 47639641 4105 True 5505 5505 91.1580 6 4069 1 chr6D.!!$R4 4063
5 TraesCS6B01G128400 chr6D 34583061 34588541 5480 True 574 678 77.2770 1269 2486 2 chr6D.!!$R5 1217
6 TraesCS6B01G128400 chr6A 67640684 67644757 4073 False 2772 5072 90.8305 1 4069 2 chr6A.!!$F3 4068
7 TraesCS6B01G128400 chr1A 560180041 560181258 1217 True 1022 1022 81.8330 1267 2486 1 chr1A.!!$R1 1219
8 TraesCS6B01G128400 chr1D 467801323 467802529 1206 False 955 955 81.0150 1268 2486 1 chr1D.!!$F2 1218
9 TraesCS6B01G128400 chr1D 47649064 47650322 1258 False 741 741 77.6660 1175 2451 1 chr1D.!!$F1 1276
10 TraesCS6B01G128400 chr1B 645707388 645708668 1280 False 950 950 80.1540 1192 2486 1 chr1B.!!$F1 1294
11 TraesCS6B01G128400 chr5A 573814667 573815257 590 True 329 329 77.3030 44 637 1 chr5A.!!$R2 593
12 TraesCS6B01G128400 chr2A 539397115 539397617 502 False 294 294 77.6490 124 635 1 chr2A.!!$F2 511
13 TraesCS6B01G128400 chr2A 572070363 572070979 616 False 291 291 75.9320 5 632 1 chr2A.!!$F3 627
14 TraesCS6B01G128400 chr4A 691156363 691156951 588 True 259 259 75.2070 44 635 1 chr4A.!!$R1 591
15 TraesCS6B01G128400 chr2D 418042283 418042904 621 True 257 257 74.9610 4 632 1 chr2D.!!$R1 628
16 TraesCS6B01G128400 chr7D 459077313 459077871 558 False 230 230 75.0860 42 601 1 chr7D.!!$F1 559
17 TraesCS6B01G128400 chr3B 55113138 55113768 630 False 230 230 74.1090 4 622 1 chr3B.!!$F1 618

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
114 119 0.458025 CCCTCTGCCTACGTTTCGAC 60.458 60.0 0.00 0.00 0.0 4.20 F
705 757 0.681243 GGGAATTCACCTGACCCAGC 60.681 60.0 7.93 0.00 40.2 4.85 F
1259 1347 0.749454 GACATCCATGGGCCAGTGTC 60.749 60.0 20.73 20.73 0.0 3.67 F
1318 1406 1.025041 TCGAGATCCTCATCCGTGTG 58.975 55.0 0.00 0.00 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1018 1093 0.036306 ATGTCTCACCGTTGGGGAAC 59.964 55.000 0.00 0.0 33.19 3.62 R
2187 6563 0.171455 GTCCTCGAGCGTGTGATCTT 59.829 55.000 6.99 0.0 0.00 2.40 R
2500 6881 2.256117 ATGAAGGTATTACCCGCAGC 57.744 50.000 9.31 0.0 39.75 5.25 R
3249 7643 3.118629 AGCAGACACATCCGACATGTAAT 60.119 43.478 0.00 0.0 0.00 1.89 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
38 40 2.901839 TCGTTTCCTTGCTAACCCTAGT 59.098 45.455 0.00 0.00 0.00 2.57
73 76 5.230323 ACTTTTCTCTCCAGACTTTACCC 57.770 43.478 0.00 0.00 0.00 3.69
80 83 1.080093 CAGACTTTACCCGCGAGCA 60.080 57.895 8.23 0.00 0.00 4.26
107 112 3.541713 GCCTCCCCTCTGCCTACG 61.542 72.222 0.00 0.00 0.00 3.51
108 113 2.042843 CCTCCCCTCTGCCTACGT 60.043 66.667 0.00 0.00 0.00 3.57
112 117 1.153628 CCCCTCTGCCTACGTTTCG 60.154 63.158 0.00 0.00 0.00 3.46
114 119 0.458025 CCCTCTGCCTACGTTTCGAC 60.458 60.000 0.00 0.00 0.00 4.20
115 120 0.797249 CCTCTGCCTACGTTTCGACG 60.797 60.000 0.00 0.00 39.31 5.12
212 223 1.145759 GCGCTCGAACGGATGATGAA 61.146 55.000 10.60 0.00 0.00 2.57
300 312 0.830023 GGAGCTCCGGCCTAGATTCT 60.830 60.000 19.06 0.00 39.73 2.40
317 329 1.192146 TCTTGTCGTCTCCTTGGGGG 61.192 60.000 0.00 0.00 0.00 5.40
318 330 1.460689 TTGTCGTCTCCTTGGGGGT 60.461 57.895 0.00 0.00 36.25 4.95
319 331 1.057851 TTGTCGTCTCCTTGGGGGTT 61.058 55.000 0.00 0.00 36.25 4.11
324 336 3.672503 CTCCTTGGGGGTTGGGGG 61.673 72.222 0.00 0.00 36.25 5.40
381 404 6.536582 CGAGATTTGATGTCAGGTACTTCAAT 59.463 38.462 7.13 0.49 46.04 2.57
441 467 3.205419 GACATTGGTCCTTAAGGGCACC 61.205 54.545 26.91 23.47 42.93 5.01
465 491 1.048601 TGAAGACTTCCTCGGCTGTT 58.951 50.000 12.66 0.00 0.00 3.16
476 502 2.607187 CTCGGCTGTTATCGACAAAGT 58.393 47.619 0.00 0.00 37.93 2.66
531 573 2.509336 CGTTCTGGCGGCAGTAGG 60.509 66.667 34.57 27.18 0.00 3.18
537 580 4.509737 GGCGGCAGTAGGGTCGTC 62.510 72.222 3.07 0.00 38.35 4.20
548 591 1.606889 GGGTCGTCCAGTGGTCTCT 60.607 63.158 9.54 0.00 35.00 3.10
562 605 5.473162 CAGTGGTCTCTGAGTCTGGATATAG 59.527 48.000 4.32 0.00 37.61 1.31
705 757 0.681243 GGGAATTCACCTGACCCAGC 60.681 60.000 7.93 0.00 40.20 4.85
710 762 1.194781 TTCACCTGACCCAGCTCTCC 61.195 60.000 0.00 0.00 0.00 3.71
711 763 2.681778 ACCTGACCCAGCTCTCCG 60.682 66.667 0.00 0.00 0.00 4.63
731 791 1.228657 GCCTCCGTGACTCCACAAAC 61.229 60.000 0.00 0.00 43.34 2.93
737 797 2.286184 CCGTGACTCCACAAACGAAAAG 60.286 50.000 0.00 0.00 43.34 2.27
743 803 5.047943 TGACTCCACAAACGAAAAGGAAAAA 60.048 36.000 0.00 0.00 0.00 1.94
866 935 6.941857 AGTTCTTCTTCTTCCTGTAATCTCC 58.058 40.000 0.00 0.00 0.00 3.71
870 939 3.452627 TCTTCTTCCTGTAATCTCCCAGC 59.547 47.826 0.00 0.00 0.00 4.85
874 943 3.121929 TCCTGTAATCTCCCAGCTTCT 57.878 47.619 0.00 0.00 0.00 2.85
879 948 5.105997 CCTGTAATCTCCCAGCTTCTTTTTG 60.106 44.000 0.00 0.00 0.00 2.44
892 967 5.009510 AGCTTCTTTTTGCTTTCTCTTCTCC 59.990 40.000 0.00 0.00 35.86 3.71
1036 1111 1.448497 GTTCCCCAACGGTGAGACA 59.552 57.895 0.00 0.00 0.00 3.41
1045 1120 1.573108 ACGGTGAGACATCCAATCCT 58.427 50.000 0.00 0.00 0.00 3.24
1050 1135 4.195416 GGTGAGACATCCAATCCTTTCTC 58.805 47.826 0.00 0.00 0.00 2.87
1057 1142 4.787534 ACATCCAATCCTTTCTCTTCTCCT 59.212 41.667 0.00 0.00 0.00 3.69
1063 1148 5.832539 ATCCTTTCTCTTCTCCTCAACAA 57.167 39.130 0.00 0.00 0.00 2.83
1097 1182 2.480555 CGTTCCGCTGGATGTTGC 59.519 61.111 0.00 0.00 0.00 4.17
1229 1314 0.970640 TGGCAATCAACAGCAGCATT 59.029 45.000 0.00 0.00 0.00 3.56
1230 1315 1.067425 TGGCAATCAACAGCAGCATTC 60.067 47.619 0.00 0.00 0.00 2.67
1231 1316 1.636988 GCAATCAACAGCAGCATTCC 58.363 50.000 0.00 0.00 0.00 3.01
1232 1317 1.738030 GCAATCAACAGCAGCATTCCC 60.738 52.381 0.00 0.00 0.00 3.97
1233 1318 1.546923 CAATCAACAGCAGCATTCCCA 59.453 47.619 0.00 0.00 0.00 4.37
1234 1319 1.927487 ATCAACAGCAGCATTCCCAA 58.073 45.000 0.00 0.00 0.00 4.12
1258 1346 1.210204 AGACATCCATGGGCCAGTGT 61.210 55.000 13.78 13.97 0.00 3.55
1259 1347 0.749454 GACATCCATGGGCCAGTGTC 60.749 60.000 20.73 20.73 0.00 3.67
1260 1348 1.303948 CATCCATGGGCCAGTGTCA 59.696 57.895 13.78 0.00 0.00 3.58
1261 1349 1.033746 CATCCATGGGCCAGTGTCAC 61.034 60.000 13.78 0.00 0.00 3.67
1262 1350 1.499913 ATCCATGGGCCAGTGTCACA 61.500 55.000 13.78 0.00 0.00 3.58
1318 1406 1.025041 TCGAGATCCTCATCCGTGTG 58.975 55.000 0.00 0.00 0.00 3.82
1399 1487 3.692406 GACCGCGGGTTCCTCTGT 61.692 66.667 31.76 3.99 35.25 3.41
1687 1775 4.161942 CCTGAGAGAGACATGGACTTCATT 59.838 45.833 0.00 0.00 32.92 2.57
1906 1997 2.558286 GCTGCCTGCACTGAAAGCA 61.558 57.895 0.00 0.00 42.31 3.91
2187 6563 2.291475 TGTGGGCTAATTTGAGGATGCA 60.291 45.455 0.00 0.00 0.00 3.96
2486 6867 3.042887 GTTGAGGCTAGTTTGTTTTGCG 58.957 45.455 0.00 0.00 0.00 4.85
2500 6881 6.450845 TTGTTTTGCGCAGAAATTTCTATG 57.549 33.333 20.07 15.62 35.34 2.23
2597 6978 7.995463 TGTGGAAGTTTAAAGTTTGTTATGC 57.005 32.000 9.60 0.00 0.00 3.14
2781 7162 1.126488 TTTGTTTGGCCCATTGAGCA 58.874 45.000 0.00 0.00 0.00 4.26
2851 7232 5.698832 TCTGTGAACAGTCAAACAGTTTTG 58.301 37.500 10.14 0.00 44.12 2.44
3115 7505 6.258947 GGTTGAGCAGGTGAAGTAAATCTATC 59.741 42.308 0.00 0.00 0.00 2.08
3280 7674 3.066760 CGGATGTGTCTGCTATGTACTCA 59.933 47.826 0.00 0.00 0.00 3.41
3319 7713 4.352600 CAGCTAATTGTTCTTCTGCTGG 57.647 45.455 0.00 0.00 41.59 4.85
3320 7714 2.751806 AGCTAATTGTTCTTCTGCTGGC 59.248 45.455 0.00 0.00 0.00 4.85
3325 7719 0.250467 TGTTCTTCTGCTGGCTGGAC 60.250 55.000 0.00 0.00 0.00 4.02
3338 7732 1.401539 GGCTGGACGATGCTTGTTTTC 60.402 52.381 0.00 0.00 0.00 2.29
3347 7741 5.488341 ACGATGCTTGTTTTCTGTAGGTAT 58.512 37.500 0.00 0.00 0.00 2.73
3360 7754 8.665643 TTTCTGTAGGTATGTTTCTTTTTCGA 57.334 30.769 0.00 0.00 0.00 3.71
3374 7768 5.569413 TCTTTTTCGAGAAACAGCTTCAAC 58.431 37.500 6.81 0.00 36.40 3.18
3486 7880 4.068599 GGGCAATCAAGGATAGCTAAGAC 58.931 47.826 0.00 0.00 0.00 3.01
3505 7899 0.983378 CAACCTAGAGGGACAGGGGG 60.983 65.000 0.00 0.00 40.27 5.40
3506 7900 1.461706 AACCTAGAGGGACAGGGGGT 61.462 60.000 0.00 0.00 40.27 4.95
3507 7901 1.396594 CCTAGAGGGACAGGGGGTT 59.603 63.158 0.00 0.00 37.23 4.11
3508 7902 0.640495 CCTAGAGGGACAGGGGGTTA 59.360 60.000 0.00 0.00 37.23 2.85
3514 7908 1.218844 GGGACAGGGGGTTATTAGCA 58.781 55.000 0.00 0.00 0.00 3.49
3546 7940 5.829391 TGTGGTCGTCAAGCTAATATACCTA 59.171 40.000 8.43 0.00 0.00 3.08
3589 7983 9.953697 GTATGTTTGGAGTTTTGTTGTATAACA 57.046 29.630 0.24 0.24 44.66 2.41
3608 8002 4.462508 ACAGAATCGATGTGTCATGTCT 57.537 40.909 0.00 0.00 0.00 3.41
3609 8003 4.179298 ACAGAATCGATGTGTCATGTCTG 58.821 43.478 14.79 14.79 37.77 3.51
3610 8004 4.179298 CAGAATCGATGTGTCATGTCTGT 58.821 43.478 0.00 0.00 0.00 3.41
3611 8005 5.105756 ACAGAATCGATGTGTCATGTCTGTA 60.106 40.000 18.71 0.00 41.88 2.74
3612 8006 5.981915 CAGAATCGATGTGTCATGTCTGTAT 59.018 40.000 0.00 0.00 0.00 2.29
3613 8007 5.981915 AGAATCGATGTGTCATGTCTGTATG 59.018 40.000 0.00 0.00 0.00 2.39
3614 8008 3.447742 TCGATGTGTCATGTCTGTATGC 58.552 45.455 0.00 0.00 0.00 3.14
3615 8009 3.131046 TCGATGTGTCATGTCTGTATGCT 59.869 43.478 0.00 0.00 0.00 3.79
3616 8010 3.244579 CGATGTGTCATGTCTGTATGCTG 59.755 47.826 0.00 0.00 0.00 4.41
3617 8011 3.959535 TGTGTCATGTCTGTATGCTGA 57.040 42.857 0.00 0.00 0.00 4.26
3618 8012 4.270245 TGTGTCATGTCTGTATGCTGAA 57.730 40.909 0.00 0.00 0.00 3.02
3619 8013 4.248058 TGTGTCATGTCTGTATGCTGAAG 58.752 43.478 0.00 0.00 0.00 3.02
3620 8014 3.063180 GTGTCATGTCTGTATGCTGAAGC 59.937 47.826 0.00 0.00 42.50 3.86
3631 8025 3.156157 GCTGAAGCATGCTGTCTCT 57.844 52.632 23.48 4.36 41.59 3.10
3632 8026 1.008329 GCTGAAGCATGCTGTCTCTC 58.992 55.000 23.48 15.17 41.59 3.20
3633 8027 1.675116 GCTGAAGCATGCTGTCTCTCA 60.675 52.381 23.48 19.08 41.59 3.27
3634 8028 2.001159 CTGAAGCATGCTGTCTCTCAC 58.999 52.381 23.48 6.26 0.00 3.51
3635 8029 1.345415 TGAAGCATGCTGTCTCTCACA 59.655 47.619 23.48 8.69 0.00 3.58
3636 8030 2.027469 TGAAGCATGCTGTCTCTCACAT 60.027 45.455 23.48 0.00 33.23 3.21
3637 8031 2.025589 AGCATGCTGTCTCTCACATG 57.974 50.000 21.98 0.00 37.95 3.21
3638 8032 1.015109 GCATGCTGTCTCTCACATGG 58.985 55.000 11.37 0.00 36.75 3.66
3639 8033 1.406477 GCATGCTGTCTCTCACATGGA 60.406 52.381 11.37 0.00 36.75 3.41
3640 8034 2.745482 GCATGCTGTCTCTCACATGGAT 60.745 50.000 11.37 0.00 36.75 3.41
3641 8035 3.542648 CATGCTGTCTCTCACATGGATT 58.457 45.455 0.00 0.00 34.80 3.01
3642 8036 3.708403 TGCTGTCTCTCACATGGATTT 57.292 42.857 0.00 0.00 33.23 2.17
3643 8037 3.603532 TGCTGTCTCTCACATGGATTTC 58.396 45.455 0.00 0.00 33.23 2.17
3644 8038 3.008266 TGCTGTCTCTCACATGGATTTCA 59.992 43.478 0.00 0.00 33.23 2.69
3645 8039 4.005650 GCTGTCTCTCACATGGATTTCAA 58.994 43.478 0.00 0.00 33.23 2.69
3646 8040 4.639310 GCTGTCTCTCACATGGATTTCAAT 59.361 41.667 0.00 0.00 33.23 2.57
3647 8041 5.125097 GCTGTCTCTCACATGGATTTCAATT 59.875 40.000 0.00 0.00 33.23 2.32
3648 8042 6.317140 GCTGTCTCTCACATGGATTTCAATTA 59.683 38.462 0.00 0.00 33.23 1.40
3649 8043 7.013083 GCTGTCTCTCACATGGATTTCAATTAT 59.987 37.037 0.00 0.00 33.23 1.28
3650 8044 8.217131 TGTCTCTCACATGGATTTCAATTATG 57.783 34.615 0.00 0.00 0.00 1.90
3651 8045 8.048514 TGTCTCTCACATGGATTTCAATTATGA 58.951 33.333 0.00 0.00 0.00 2.15
3652 8046 8.896744 GTCTCTCACATGGATTTCAATTATGAA 58.103 33.333 0.00 0.00 43.70 2.57
3653 8047 8.896744 TCTCTCACATGGATTTCAATTATGAAC 58.103 33.333 0.00 0.00 45.01 3.18
3654 8048 7.999679 TCTCACATGGATTTCAATTATGAACC 58.000 34.615 0.00 0.00 45.01 3.62
3655 8049 6.794374 TCACATGGATTTCAATTATGAACCG 58.206 36.000 0.00 0.00 45.01 4.44
3656 8050 6.376864 TCACATGGATTTCAATTATGAACCGT 59.623 34.615 0.00 0.00 45.01 4.83
3657 8051 7.554476 TCACATGGATTTCAATTATGAACCGTA 59.446 33.333 0.00 0.00 45.01 4.02
3658 8052 8.352201 CACATGGATTTCAATTATGAACCGTAT 58.648 33.333 0.00 0.00 45.01 3.06
3659 8053 8.352201 ACATGGATTTCAATTATGAACCGTATG 58.648 33.333 0.00 0.00 45.01 2.39
3660 8054 6.734137 TGGATTTCAATTATGAACCGTATGC 58.266 36.000 0.00 0.00 45.01 3.14
3661 8055 6.545666 TGGATTTCAATTATGAACCGTATGCT 59.454 34.615 0.00 0.00 45.01 3.79
3662 8056 7.078228 GGATTTCAATTATGAACCGTATGCTC 58.922 38.462 0.00 0.00 45.01 4.26
3663 8057 6.993786 TTTCAATTATGAACCGTATGCTCA 57.006 33.333 0.00 0.00 45.01 4.26
3664 8058 7.566760 TTTCAATTATGAACCGTATGCTCAT 57.433 32.000 3.93 3.93 45.01 2.90
3665 8059 6.544038 TCAATTATGAACCGTATGCTCATG 57.456 37.500 7.63 0.00 32.22 3.07
3666 8060 5.469760 TCAATTATGAACCGTATGCTCATGG 59.530 40.000 0.00 0.00 32.22 3.66
3667 8061 4.415881 TTATGAACCGTATGCTCATGGT 57.584 40.909 0.00 0.00 39.60 3.55
3669 8063 3.897141 TGAACCGTATGCTCATGGTTA 57.103 42.857 12.86 2.70 45.77 2.85
3696 8152 8.344831 TGTATGCTTTCTGTTTCATATATGTGC 58.655 33.333 12.42 5.11 0.00 4.57
3703 8159 8.467963 TTCTGTTTCATATATGTGCCAATGAT 57.532 30.769 12.42 0.00 0.00 2.45
3755 8232 7.983166 AGTATAGTATCTGGGTGTGGTTTTA 57.017 36.000 0.00 0.00 0.00 1.52
3758 8235 3.914435 AGTATCTGGGTGTGGTTTTACCT 59.086 43.478 0.00 0.00 39.58 3.08
3764 8241 4.658063 TGGGTGTGGTTTTACCTTCTATG 58.342 43.478 0.00 0.00 39.58 2.23
3787 8264 1.305930 CGCTTGTAGTTTGGGAGGGC 61.306 60.000 0.00 0.00 0.00 5.19
3799 8276 1.749033 GGAGGGCTATCAAGGGTCG 59.251 63.158 0.00 0.00 0.00 4.79
3876 8353 4.104102 AGTTGGACCTCCATTTGTAGAACA 59.896 41.667 0.00 0.00 46.97 3.18
3978 8455 4.438744 CGCCATGTGAAGAAAAAGGGATAC 60.439 45.833 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 40 6.499350 TGGAGAGAAAAGTTTACCCTAGCTAA 59.501 38.462 0.00 0.00 0.00 3.09
58 60 0.609957 TCGCGGGTAAAGTCTGGAGA 60.610 55.000 6.13 0.00 0.00 3.71
73 76 2.780643 CAAGTCCACATGCTCGCG 59.219 61.111 0.00 0.00 0.00 5.87
80 83 1.542375 AGGGGAGGCAAGTCCACAT 60.542 57.895 4.24 0.00 43.31 3.21
107 112 3.708734 CACCACCGCCGTCGAAAC 61.709 66.667 0.00 0.00 38.10 2.78
108 113 4.973055 CCACCACCGCCGTCGAAA 62.973 66.667 0.00 0.00 38.10 3.46
115 120 3.316573 CTTCTCTCCCACCACCGCC 62.317 68.421 0.00 0.00 0.00 6.13
129 137 3.003763 GGAGGTGGCGGGACTTCT 61.004 66.667 0.00 0.00 0.00 2.85
212 223 4.372656 CAGACAAACTCGGAGAAGAAACT 58.627 43.478 12.86 1.34 34.09 2.66
300 312 1.057851 AACCCCCAAGGAGACGACAA 61.058 55.000 0.00 0.00 39.89 3.18
324 336 5.360429 ACGAGAAACTCTAATCTTACCCTCC 59.640 44.000 0.00 0.00 0.00 4.30
326 340 5.950549 TGACGAGAAACTCTAATCTTACCCT 59.049 40.000 0.00 0.00 0.00 4.34
331 354 6.102663 CCACATGACGAGAAACTCTAATCTT 58.897 40.000 0.00 0.00 0.00 2.40
381 404 6.347644 CGTCATTGTTGAACTCTTGCATAGAA 60.348 38.462 3.74 0.00 32.48 2.10
441 467 1.801913 CGAGGAAGTCTTCACGCGG 60.802 63.158 12.47 0.00 0.00 6.46
442 468 1.801913 CCGAGGAAGTCTTCACGCG 60.802 63.158 14.49 3.53 32.61 6.01
445 471 0.318762 ACAGCCGAGGAAGTCTTCAC 59.681 55.000 14.49 6.89 0.00 3.18
446 472 1.048601 AACAGCCGAGGAAGTCTTCA 58.951 50.000 14.49 0.00 0.00 3.02
465 491 2.343101 CCGGCTTGAACTTTGTCGATA 58.657 47.619 0.00 0.00 0.00 2.92
531 573 0.894184 TCAGAGACCACTGGACGACC 60.894 60.000 0.71 0.00 38.31 4.79
537 580 0.894141 CCAGACTCAGAGACCACTGG 59.106 60.000 3.79 12.57 38.77 4.00
688 740 1.280421 AGAGCTGGGTCAGGTGAATTC 59.720 52.381 4.26 0.00 42.53 2.17
711 763 2.391724 TTTGTGGAGTCACGGAGGCC 62.392 60.000 0.00 0.00 46.42 5.19
715 767 0.460722 TTCGTTTGTGGAGTCACGGA 59.539 50.000 0.76 0.00 46.42 4.69
815 881 2.020100 ATCGAATCGGGAGAGGGGGA 62.020 60.000 1.76 0.00 45.48 4.81
817 883 1.968310 GATCGAATCGGGAGAGGGG 59.032 63.158 1.76 0.00 45.48 4.79
866 935 4.581077 AGAGAAAGCAAAAAGAAGCTGG 57.419 40.909 0.00 0.00 41.70 4.85
870 939 6.486320 AGAGGAGAAGAGAAAGCAAAAAGAAG 59.514 38.462 0.00 0.00 0.00 2.85
874 943 4.752101 CGAGAGGAGAAGAGAAAGCAAAAA 59.248 41.667 0.00 0.00 0.00 1.94
879 948 1.797348 CGCGAGAGGAGAAGAGAAAGC 60.797 57.143 0.00 0.00 0.00 3.51
892 967 1.589196 GGGTTCGATTCCGCGAGAG 60.589 63.158 8.23 0.00 41.79 3.20
985 1060 2.174685 TCCATCGATCTTCCTTCCCA 57.825 50.000 0.00 0.00 0.00 4.37
1018 1093 0.036306 ATGTCTCACCGTTGGGGAAC 59.964 55.000 0.00 0.00 33.19 3.62
1036 1111 5.035556 TGAGGAGAAGAGAAAGGATTGGAT 58.964 41.667 0.00 0.00 0.00 3.41
1045 1120 8.525290 AAAGAAATTGTTGAGGAGAAGAGAAA 57.475 30.769 0.00 0.00 0.00 2.52
1050 1135 6.890979 AGGAAAGAAATTGTTGAGGAGAAG 57.109 37.500 0.00 0.00 0.00 2.85
1057 1142 6.544564 ACGGACTAAAGGAAAGAAATTGTTGA 59.455 34.615 0.00 0.00 0.00 3.18
1097 1182 0.319469 GGGGCAAAACATCCAACACG 60.319 55.000 0.00 0.00 0.00 4.49
1229 1314 1.496001 CATGGATGTCTGGGATTGGGA 59.504 52.381 0.00 0.00 0.00 4.37
1230 1315 1.479942 CCATGGATGTCTGGGATTGGG 60.480 57.143 5.56 0.00 0.00 4.12
1231 1316 1.991121 CCATGGATGTCTGGGATTGG 58.009 55.000 5.56 0.00 0.00 3.16
1258 1346 0.384309 GCACCTCGGATATCGTGTGA 59.616 55.000 13.45 2.45 41.49 3.58
1259 1347 0.385751 AGCACCTCGGATATCGTGTG 59.614 55.000 9.35 8.50 41.70 3.82
1260 1348 1.112113 AAGCACCTCGGATATCGTGT 58.888 50.000 9.35 0.00 40.32 4.49
1261 1349 3.050619 GTTAAGCACCTCGGATATCGTG 58.949 50.000 0.00 0.58 40.32 4.35
1262 1350 2.287427 CGTTAAGCACCTCGGATATCGT 60.287 50.000 0.00 0.00 40.32 3.73
1318 1406 2.286197 AGGGTGGTAGGGAAGCCC 60.286 66.667 0.00 0.00 45.90 5.19
1600 1688 2.035961 GCGGTATCTGGTGAAGATGCTA 59.964 50.000 3.92 0.00 45.64 3.49
1687 1775 3.948719 GCGGTTGGGAGTGGTGGA 61.949 66.667 0.00 0.00 0.00 4.02
2187 6563 0.171455 GTCCTCGAGCGTGTGATCTT 59.829 55.000 6.99 0.00 0.00 2.40
2486 6867 2.542411 CCCGCAGCATAGAAATTTCTGC 60.542 50.000 27.37 23.15 44.68 4.26
2500 6881 2.256117 ATGAAGGTATTACCCGCAGC 57.744 50.000 9.31 0.00 39.75 5.25
2564 6945 7.639113 ACTTTAAACTTCCACAAGTGATTCA 57.361 32.000 0.94 0.00 42.45 2.57
2781 7162 4.036971 GTCGAGAGAGCTTGTACCATGTAT 59.963 45.833 0.00 0.00 43.49 2.29
2851 7232 6.855836 TCATAATCTTTTGCCAAGACATGTC 58.144 36.000 18.47 18.47 0.00 3.06
3128 7518 8.964150 CGTCACCTTTTAAATTGGTAAGAAAAG 58.036 33.333 11.52 0.00 37.03 2.27
3153 7546 7.757526 TGGAATCCTAAAACAATGTATCAACG 58.242 34.615 0.00 0.00 0.00 4.10
3244 7638 6.037500 CAGACACATCCGACATGTAATTCAAT 59.962 38.462 0.00 0.00 0.00 2.57
3249 7643 3.118629 AGCAGACACATCCGACATGTAAT 60.119 43.478 0.00 0.00 0.00 1.89
3280 7674 5.068215 AGCTGTACTATCATACCTCCACT 57.932 43.478 0.00 0.00 0.00 4.00
3319 7713 1.537202 AGAAAACAAGCATCGTCCAGC 59.463 47.619 0.00 0.00 0.00 4.85
3320 7714 2.549754 ACAGAAAACAAGCATCGTCCAG 59.450 45.455 0.00 0.00 0.00 3.86
3325 7719 5.351465 ACATACCTACAGAAAACAAGCATCG 59.649 40.000 0.00 0.00 0.00 3.84
3338 7732 7.884816 TCTCGAAAAAGAAACATACCTACAG 57.115 36.000 0.00 0.00 0.00 2.74
3402 7796 5.189145 ACACCCCTATTACGAATGTTTCTCT 59.811 40.000 0.00 0.00 0.00 3.10
3486 7880 0.983378 CCCCCTGTCCCTCTAGGTTG 60.983 65.000 0.00 0.00 36.75 3.77
3505 7899 6.479001 ACGACCACAGTTCATATGCTAATAAC 59.521 38.462 0.00 0.00 0.00 1.89
3506 7900 6.578944 ACGACCACAGTTCATATGCTAATAA 58.421 36.000 0.00 0.00 0.00 1.40
3507 7901 6.156748 ACGACCACAGTTCATATGCTAATA 57.843 37.500 0.00 0.00 0.00 0.98
3508 7902 5.023533 ACGACCACAGTTCATATGCTAAT 57.976 39.130 0.00 0.00 0.00 1.73
3514 7908 3.055819 AGCTTGACGACCACAGTTCATAT 60.056 43.478 0.00 0.00 0.00 1.78
3546 7940 8.960591 CCAAACATACAAAGGATTGATACTCTT 58.039 33.333 0.00 0.00 38.94 2.85
3570 7964 7.658167 TCGATTCTGTTATACAACAAAACTCCA 59.342 33.333 0.00 0.00 43.92 3.86
3589 7983 4.462508 ACAGACATGACACATCGATTCT 57.537 40.909 0.00 0.00 0.00 2.40
3613 8007 1.008329 GAGAGACAGCATGCTTCAGC 58.992 55.000 19.98 14.05 42.53 4.26
3614 8008 2.001159 GTGAGAGACAGCATGCTTCAG 58.999 52.381 19.98 9.98 42.53 3.02
3615 8009 1.345415 TGTGAGAGACAGCATGCTTCA 59.655 47.619 19.98 16.27 42.53 3.02
3616 8010 2.090400 TGTGAGAGACAGCATGCTTC 57.910 50.000 19.98 18.16 42.53 3.86
3617 8011 2.357075 CATGTGAGAGACAGCATGCTT 58.643 47.619 19.98 9.90 42.53 3.91
3618 8012 1.407025 CCATGTGAGAGACAGCATGCT 60.407 52.381 16.30 16.30 42.53 3.79
3619 8013 1.015109 CCATGTGAGAGACAGCATGC 58.985 55.000 10.51 10.51 42.53 4.06
3620 8014 2.685850 TCCATGTGAGAGACAGCATG 57.314 50.000 0.00 0.00 46.00 4.06
3621 8015 3.928005 AATCCATGTGAGAGACAGCAT 57.072 42.857 0.00 0.00 38.23 3.79
3622 8016 3.008266 TGAAATCCATGTGAGAGACAGCA 59.992 43.478 0.00 0.00 38.23 4.41
3623 8017 3.603532 TGAAATCCATGTGAGAGACAGC 58.396 45.455 0.00 0.00 38.23 4.40
3624 8018 6.754702 AATTGAAATCCATGTGAGAGACAG 57.245 37.500 0.00 0.00 38.23 3.51
3625 8019 8.048514 TCATAATTGAAATCCATGTGAGAGACA 58.951 33.333 0.00 0.00 39.53 3.41
3626 8020 8.442632 TCATAATTGAAATCCATGTGAGAGAC 57.557 34.615 0.00 0.00 0.00 3.36
3627 8021 8.896744 GTTCATAATTGAAATCCATGTGAGAGA 58.103 33.333 0.00 0.00 43.29 3.10
3628 8022 8.133627 GGTTCATAATTGAAATCCATGTGAGAG 58.866 37.037 0.00 0.00 43.29 3.20
3629 8023 7.201723 CGGTTCATAATTGAAATCCATGTGAGA 60.202 37.037 0.00 0.00 43.29 3.27
3630 8024 6.914215 CGGTTCATAATTGAAATCCATGTGAG 59.086 38.462 0.00 0.00 43.29 3.51
3631 8025 6.376864 ACGGTTCATAATTGAAATCCATGTGA 59.623 34.615 0.00 0.00 43.29 3.58
3632 8026 6.563422 ACGGTTCATAATTGAAATCCATGTG 58.437 36.000 0.00 0.00 43.29 3.21
3633 8027 6.773976 ACGGTTCATAATTGAAATCCATGT 57.226 33.333 0.00 0.00 43.29 3.21
3634 8028 7.326789 GCATACGGTTCATAATTGAAATCCATG 59.673 37.037 0.00 0.00 43.29 3.66
3635 8029 7.231317 AGCATACGGTTCATAATTGAAATCCAT 59.769 33.333 0.00 0.00 43.29 3.41
3636 8030 6.545666 AGCATACGGTTCATAATTGAAATCCA 59.454 34.615 0.00 0.00 43.29 3.41
3637 8031 6.970484 AGCATACGGTTCATAATTGAAATCC 58.030 36.000 0.00 0.00 43.29 3.01
3638 8032 7.639039 TGAGCATACGGTTCATAATTGAAATC 58.361 34.615 0.00 0.00 43.29 2.17
3639 8033 7.566760 TGAGCATACGGTTCATAATTGAAAT 57.433 32.000 0.00 0.00 43.29 2.17
3640 8034 6.993786 TGAGCATACGGTTCATAATTGAAA 57.006 33.333 0.00 0.00 43.29 2.69
3641 8035 6.017192 CCATGAGCATACGGTTCATAATTGAA 60.017 38.462 0.00 0.00 44.51 2.69
3642 8036 5.469760 CCATGAGCATACGGTTCATAATTGA 59.530 40.000 0.00 0.00 44.51 2.57
3643 8037 5.239306 ACCATGAGCATACGGTTCATAATTG 59.761 40.000 0.00 0.00 44.51 2.32
3644 8038 5.376625 ACCATGAGCATACGGTTCATAATT 58.623 37.500 0.00 0.00 44.51 1.40
3645 8039 4.973168 ACCATGAGCATACGGTTCATAAT 58.027 39.130 0.00 0.00 44.51 1.28
3646 8040 4.415881 ACCATGAGCATACGGTTCATAA 57.584 40.909 0.00 0.00 44.51 1.90
3647 8041 4.415881 AACCATGAGCATACGGTTCATA 57.584 40.909 0.00 0.00 44.51 2.15
3648 8042 3.281727 AACCATGAGCATACGGTTCAT 57.718 42.857 0.00 0.00 46.90 2.57
3649 8043 2.779755 AACCATGAGCATACGGTTCA 57.220 45.000 0.00 0.00 37.12 3.18
3650 8044 4.127171 ACATAACCATGAGCATACGGTTC 58.873 43.478 8.09 0.00 40.84 3.62
3651 8045 4.150897 ACATAACCATGAGCATACGGTT 57.849 40.909 9.35 9.35 43.92 4.44
3652 8046 3.838244 ACATAACCATGAGCATACGGT 57.162 42.857 0.00 0.00 35.96 4.83
3653 8047 4.093408 GCATACATAACCATGAGCATACGG 59.907 45.833 0.00 0.00 35.96 4.02
3654 8048 4.931601 AGCATACATAACCATGAGCATACG 59.068 41.667 0.00 0.00 35.96 3.06
3655 8049 6.808008 AAGCATACATAACCATGAGCATAC 57.192 37.500 0.00 0.00 35.96 2.39
3656 8050 7.173735 CAGAAAGCATACATAACCATGAGCATA 59.826 37.037 0.00 0.00 35.96 3.14
3657 8051 6.016527 CAGAAAGCATACATAACCATGAGCAT 60.017 38.462 0.00 0.00 35.96 3.79
3658 8052 5.297527 CAGAAAGCATACATAACCATGAGCA 59.702 40.000 0.00 0.00 35.96 4.26
3659 8053 5.297776 ACAGAAAGCATACATAACCATGAGC 59.702 40.000 0.00 0.00 35.96 4.26
3660 8054 6.932356 ACAGAAAGCATACATAACCATGAG 57.068 37.500 0.00 0.00 35.96 2.90
3661 8055 7.392953 TGAAACAGAAAGCATACATAACCATGA 59.607 33.333 0.00 0.00 35.96 3.07
3662 8056 7.537715 TGAAACAGAAAGCATACATAACCATG 58.462 34.615 0.00 0.00 38.21 3.66
3663 8057 7.701539 TGAAACAGAAAGCATACATAACCAT 57.298 32.000 0.00 0.00 0.00 3.55
3664 8058 7.701539 ATGAAACAGAAAGCATACATAACCA 57.298 32.000 0.00 0.00 0.00 3.67
3729 8206 5.871396 ACCACACCCAGATACTATACTTG 57.129 43.478 0.00 0.00 0.00 3.16
3736 8213 3.914435 AGGTAAAACCACACCCAGATACT 59.086 43.478 0.00 0.00 41.95 2.12
3740 8217 2.781174 AGAAGGTAAAACCACACCCAGA 59.219 45.455 0.00 0.00 41.95 3.86
3755 8232 1.276622 ACAAGCGGGTCATAGAAGGT 58.723 50.000 0.00 0.00 0.00 3.50
3758 8235 4.250464 CAAACTACAAGCGGGTCATAGAA 58.750 43.478 5.10 0.00 0.00 2.10
3764 8241 0.035739 TCCCAAACTACAAGCGGGTC 59.964 55.000 0.00 0.00 38.15 4.46
3787 8264 0.474184 AATGCCCCGACCCTTGATAG 59.526 55.000 0.00 0.00 0.00 2.08
3799 8276 8.409358 AGAACTGTTCATATAATAAATGCCCC 57.591 34.615 21.50 0.00 0.00 5.80
3833 8310 6.653320 CCAACTCTATGCAGTACCAAAAAGTA 59.347 38.462 0.00 0.00 0.00 2.24
3840 8317 2.500098 GGTCCAACTCTATGCAGTACCA 59.500 50.000 0.00 0.00 0.00 3.25
3876 8353 4.424842 AGGATCTGGAGAACTGAGAAGTT 58.575 43.478 0.00 0.00 34.29 2.66
3978 8455 2.500098 TGTGATCTAAAGACCTTCCGGG 59.500 50.000 0.00 0.00 41.89 5.73


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

AutoCloner maintained by Alex Coulton.