Multiple sequence alignment - TraesCS5A01G519200

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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 TraesCS5A01G519200 chr5A 100.000 3798 0 0 431 4228 680832106 680835903 0.000000e+00 7014.0
1 TraesCS5A01G519200 chr5A 87.455 558 49 13 1977 2522 675447680 675448228 1.290000e-174 623.0
2 TraesCS5A01G519200 chr5A 100.000 304 0 0 1 304 680831676 680831979 2.850000e-156 562.0
3 TraesCS5A01G519200 chr5A 91.525 59 4 1 1924 1981 675447589 675447647 3.500000e-11 80.5
4 TraesCS5A01G519200 chr4D 94.486 2267 88 7 1975 4228 500014607 500016849 0.000000e+00 3459.0
5 TraesCS5A01G519200 chr4D 89.834 1505 85 28 510 1981 500013106 500014575 0.000000e+00 1869.0
6 TraesCS5A01G519200 chr4D 81.933 238 26 12 75 304 500012769 500012997 7.220000e-43 185.0
7 TraesCS5A01G519200 chr4B 95.130 965 38 4 1976 2940 643282982 643283937 0.000000e+00 1513.0
8 TraesCS5A01G519200 chr4B 88.889 1170 88 24 832 1981 643281803 643282950 0.000000e+00 1402.0
9 TraesCS5A01G519200 chr4B 95.390 629 29 0 2939 3567 643283998 643284626 0.000000e+00 1002.0
10 TraesCS5A01G519200 chr4B 91.148 305 12 4 3936 4228 643284754 643285055 2.370000e-107 399.0
11 TraesCS5A01G519200 chr4B 81.395 215 19 14 75 277 643281240 643281445 5.660000e-34 156.0
12 TraesCS5A01G519200 chr1B 87.545 554 47 13 1982 2522 593781002 593781546 4.640000e-174 621.0
13 TraesCS5A01G519200 chr1B 91.525 59 4 1 1924 1981 593780906 593780964 3.500000e-11 80.5
14 TraesCS5A01G519200 chr5B 87.276 558 50 13 1977 2522 691741181 691741729 6.010000e-173 617.0
15 TraesCS5A01G519200 chr5B 91.525 59 4 1 1924 1981 691741090 691741148 3.500000e-11 80.5
16 TraesCS5A01G519200 chr1A 87.646 429 19 8 3820 4228 564614996 564614582 6.400000e-128 468.0
17 TraesCS5A01G519200 chr1A 86.636 434 24 9 3815 4228 252835366 252835785 2.320000e-122 449.0
18 TraesCS5A01G519200 chr1A 93.878 98 6 0 2108 2205 252835274 252835371 9.470000e-32 148.0


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 TraesCS5A01G519200 chr5A 680831676 680835903 4227 False 3788.000000 7014 100.0000 1 4228 2 chr5A.!!$F2 4227
1 TraesCS5A01G519200 chr5A 675447589 675448228 639 False 351.750000 623 89.4900 1924 2522 2 chr5A.!!$F1 598
2 TraesCS5A01G519200 chr4D 500012769 500016849 4080 False 1837.666667 3459 88.7510 75 4228 3 chr4D.!!$F1 4153
3 TraesCS5A01G519200 chr4B 643281240 643285055 3815 False 894.400000 1513 90.3904 75 4228 5 chr4B.!!$F1 4153
4 TraesCS5A01G519200 chr1B 593780906 593781546 640 False 350.750000 621 89.5350 1924 2522 2 chr1B.!!$F1 598
5 TraesCS5A01G519200 chr5B 691741090 691741729 639 False 348.750000 617 89.4005 1924 2522 2 chr5B.!!$F1 598
6 TraesCS5A01G519200 chr1A 252835274 252835785 511 False 298.500000 449 90.2570 2108 4228 2 chr1A.!!$F1 2120

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
697 729 0.037232 GAGGAACCTTGGAGTCGTGG 60.037 60.0 0.00 0.0 0.00 4.94 F
842 885 0.603975 GCCACAGGAGTTGGTCTCAC 60.604 60.0 0.00 0.0 44.40 3.51 F
1095 1143 0.840288 TTCTTGCTCCCCTGCCAGTA 60.840 55.0 0.00 0.0 0.00 2.74 F
1135 1185 0.869880 CGACTCGAATGCATGCCGTA 60.870 55.0 16.68 0.0 0.00 4.02 F
1397 1455 0.947244 CATAGGTCATTGCCGCCTTC 59.053 55.0 0.00 0.0 34.07 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 2280 0.462581 TTGGAGCATGATCAGCGGTC 60.463 55.0 13.85 15.37 37.01 4.79 R
2238 2352 0.616371 TAACCACTCCATTGACCCGG 59.384 55.0 0.00 0.00 0.00 5.73 R
3036 3223 2.675348 GGAACGAGAAAAGAGCCATCTG 59.325 50.0 0.00 0.00 35.37 2.90 R
3178 3365 5.335976 GGGTCTGCAAAGTTCCTGAAAATAG 60.336 44.0 0.00 0.00 0.00 1.73 R
3353 3540 2.681848 GTCAACAAGATCCTCATGCCTG 59.318 50.0 0.00 0.00 0.00 4.85 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
18 19 2.738147 ACGTCTTGACGCTATGTGC 58.262 52.632 21.01 0.00 36.44 4.57
33 34 6.337853 GCTATGTGCGTCATATAGGATTTC 57.662 41.667 18.09 5.04 36.51 2.17
34 35 6.102663 GCTATGTGCGTCATATAGGATTTCT 58.897 40.000 18.09 0.00 36.51 2.52
35 36 6.254589 GCTATGTGCGTCATATAGGATTTCTC 59.745 42.308 18.09 4.10 36.51 2.87
36 37 4.883083 TGTGCGTCATATAGGATTTCTCC 58.117 43.478 0.00 0.00 42.43 3.71
37 38 4.343814 TGTGCGTCATATAGGATTTCTCCA 59.656 41.667 0.00 0.00 44.79 3.86
38 39 5.163353 TGTGCGTCATATAGGATTTCTCCAA 60.163 40.000 0.00 0.00 44.79 3.53
39 40 5.934625 GTGCGTCATATAGGATTTCTCCAAT 59.065 40.000 0.00 0.00 44.79 3.16
40 41 6.091441 GTGCGTCATATAGGATTTCTCCAATC 59.909 42.308 0.00 0.00 44.79 2.67
46 47 2.720659 GATTTCTCCAATCCCGGGC 58.279 57.895 18.49 0.00 36.02 6.13
47 48 0.183731 GATTTCTCCAATCCCGGGCT 59.816 55.000 18.49 1.75 36.02 5.19
48 49 0.106519 ATTTCTCCAATCCCGGGCTG 60.107 55.000 18.49 15.72 0.00 4.85
49 50 2.837031 TTTCTCCAATCCCGGGCTGC 62.837 60.000 18.49 0.00 0.00 5.25
50 51 4.113815 CTCCAATCCCGGGCTGCA 62.114 66.667 18.49 0.00 0.00 4.41
51 52 4.113815 TCCAATCCCGGGCTGCAG 62.114 66.667 18.49 10.11 0.00 4.41
62 63 2.260434 GCTGCAGCCCAACACATG 59.740 61.111 28.76 0.00 34.31 3.21
63 64 2.260434 CTGCAGCCCAACACATGC 59.740 61.111 0.00 0.00 39.14 4.06
64 65 3.620300 CTGCAGCCCAACACATGCG 62.620 63.158 0.00 0.00 41.58 4.73
65 66 3.364441 GCAGCCCAACACATGCGA 61.364 61.111 0.00 0.00 0.00 5.10
66 67 2.918345 GCAGCCCAACACATGCGAA 61.918 57.895 0.00 0.00 0.00 4.70
67 68 1.210931 CAGCCCAACACATGCGAAG 59.789 57.895 0.00 0.00 0.00 3.79
68 69 1.073025 AGCCCAACACATGCGAAGA 59.927 52.632 0.00 0.00 0.00 2.87
69 70 0.537143 AGCCCAACACATGCGAAGAA 60.537 50.000 0.00 0.00 0.00 2.52
70 71 0.313672 GCCCAACACATGCGAAGAAA 59.686 50.000 0.00 0.00 0.00 2.52
71 72 1.269517 GCCCAACACATGCGAAGAAAA 60.270 47.619 0.00 0.00 0.00 2.29
72 73 2.664916 CCCAACACATGCGAAGAAAAG 58.335 47.619 0.00 0.00 0.00 2.27
73 74 2.053627 CCAACACATGCGAAGAAAAGC 58.946 47.619 0.00 0.00 0.00 3.51
169 184 1.144276 TCACTCCAAAACCGTCGCA 59.856 52.632 0.00 0.00 0.00 5.10
170 185 0.878523 TCACTCCAAAACCGTCGCAG 60.879 55.000 0.00 0.00 0.00 5.18
172 187 0.878961 ACTCCAAAACCGTCGCAGTC 60.879 55.000 0.00 0.00 0.00 3.51
173 188 1.566018 CTCCAAAACCGTCGCAGTCC 61.566 60.000 0.00 0.00 0.00 3.85
174 189 1.597027 CCAAAACCGTCGCAGTCCT 60.597 57.895 0.00 0.00 0.00 3.85
175 190 1.566018 CCAAAACCGTCGCAGTCCTC 61.566 60.000 0.00 0.00 0.00 3.71
176 191 1.301479 AAAACCGTCGCAGTCCTCC 60.301 57.895 0.00 0.00 0.00 4.30
235 267 3.182263 CCACCACCCAGACCCCAA 61.182 66.667 0.00 0.00 0.00 4.12
448 480 4.217159 CGACCGACCGATTCCCCC 62.217 72.222 0.00 0.00 0.00 5.40
449 481 4.217159 GACCGACCGATTCCCCCG 62.217 72.222 0.00 0.00 0.00 5.73
452 484 4.157120 CGACCGATTCCCCCGCTT 62.157 66.667 0.00 0.00 0.00 4.68
453 485 2.203029 GACCGATTCCCCCGCTTC 60.203 66.667 0.00 0.00 0.00 3.86
454 486 3.752088 GACCGATTCCCCCGCTTCC 62.752 68.421 0.00 0.00 0.00 3.46
455 487 3.792736 CCGATTCCCCCGCTTCCA 61.793 66.667 0.00 0.00 0.00 3.53
495 527 1.819632 GGCCAGTCCAATCGCGATT 60.820 57.895 27.94 27.94 34.01 3.34
496 528 1.376609 GGCCAGTCCAATCGCGATTT 61.377 55.000 30.71 14.61 34.01 2.17
497 529 0.248215 GCCAGTCCAATCGCGATTTG 60.248 55.000 30.71 26.57 0.00 2.32
498 530 0.248215 CCAGTCCAATCGCGATTTGC 60.248 55.000 30.71 21.68 41.47 3.68
548 580 4.180946 CGGTCTCCTCGGTCAGCG 62.181 72.222 0.00 0.00 0.00 5.18
580 612 3.725459 TCTTCGCGCGTGGTCGTA 61.725 61.111 30.98 5.11 39.49 3.43
581 613 3.530104 CTTCGCGCGTGGTCGTAC 61.530 66.667 30.98 0.00 39.49 3.67
582 614 3.940975 CTTCGCGCGTGGTCGTACT 62.941 63.158 30.98 0.00 39.49 2.73
583 615 3.933900 TTCGCGCGTGGTCGTACTC 62.934 63.158 30.98 0.00 39.49 2.59
632 664 2.651361 CGGTAGCTAGGGCATCGG 59.349 66.667 0.00 0.00 41.70 4.18
665 697 2.096713 GCTAGCTAATGGTCGCGATTTG 60.097 50.000 14.06 4.96 0.00 2.32
692 724 2.657237 CGCGAGGAACCTTGGAGT 59.343 61.111 0.00 0.00 0.00 3.85
693 725 1.446272 CGCGAGGAACCTTGGAGTC 60.446 63.158 0.00 0.00 0.00 3.36
695 727 1.965219 CGAGGAACCTTGGAGTCGT 59.035 57.895 0.34 0.00 0.00 4.34
697 729 0.037232 GAGGAACCTTGGAGTCGTGG 60.037 60.000 0.00 0.00 0.00 4.94
698 730 1.003718 GGAACCTTGGAGTCGTGGG 60.004 63.158 0.00 0.00 0.00 4.61
699 731 1.671379 GAACCTTGGAGTCGTGGGC 60.671 63.158 0.00 0.00 0.00 5.36
705 748 4.131088 GGAGTCGTGGGCGGACTC 62.131 72.222 18.18 18.18 40.77 3.36
739 782 5.294552 GGGTGATGATTAGAGAAAAAGACCG 59.705 44.000 0.00 0.00 0.00 4.79
740 783 6.106673 GGTGATGATTAGAGAAAAAGACCGA 58.893 40.000 0.00 0.00 0.00 4.69
741 784 6.594159 GGTGATGATTAGAGAAAAAGACCGAA 59.406 38.462 0.00 0.00 0.00 4.30
742 785 7.119262 GGTGATGATTAGAGAAAAAGACCGAAA 59.881 37.037 0.00 0.00 0.00 3.46
743 786 8.504005 GTGATGATTAGAGAAAAAGACCGAAAA 58.496 33.333 0.00 0.00 0.00 2.29
744 787 9.062524 TGATGATTAGAGAAAAAGACCGAAAAA 57.937 29.630 0.00 0.00 0.00 1.94
745 788 9.548208 GATGATTAGAGAAAAAGACCGAAAAAG 57.452 33.333 0.00 0.00 0.00 2.27
746 789 8.671384 TGATTAGAGAAAAAGACCGAAAAAGA 57.329 30.769 0.00 0.00 0.00 2.52
747 790 8.557029 TGATTAGAGAAAAAGACCGAAAAAGAC 58.443 33.333 0.00 0.00 0.00 3.01
748 791 5.405331 AGAGAAAAAGACCGAAAAAGACG 57.595 39.130 0.00 0.00 0.00 4.18
796 839 4.176752 GGTCCCGGCCACTCCATC 62.177 72.222 2.24 0.00 34.01 3.51
797 840 4.176752 GTCCCGGCCACTCCATCC 62.177 72.222 2.24 0.00 34.01 3.51
798 841 4.731853 TCCCGGCCACTCCATCCA 62.732 66.667 2.24 0.00 34.01 3.41
823 866 1.621301 CCTTTCGACTCAGCTGTGCG 61.621 60.000 14.67 17.74 0.00 5.34
842 885 0.603975 GCCACAGGAGTTGGTCTCAC 60.604 60.000 0.00 0.00 44.40 3.51
884 927 9.678941 TCTGTTTCTATATAACTTCGCACTATG 57.321 33.333 0.00 0.00 0.00 2.23
897 945 4.496360 TCGCACTATGTTCCGATTGTTTA 58.504 39.130 0.00 0.00 0.00 2.01
902 950 6.715464 CACTATGTTCCGATTGTTTATCACC 58.285 40.000 0.00 0.00 32.45 4.02
944 992 9.477484 TTTGCTTATTCTCGGAGTAAATCTATC 57.523 33.333 4.69 0.00 0.00 2.08
1083 1131 5.234466 AGTGTATTCACCTCTTTCTTGCT 57.766 39.130 0.00 0.00 44.83 3.91
1093 1141 0.964358 CTTTCTTGCTCCCCTGCCAG 60.964 60.000 0.00 0.00 0.00 4.85
1094 1142 1.719063 TTTCTTGCTCCCCTGCCAGT 61.719 55.000 0.00 0.00 0.00 4.00
1095 1143 0.840288 TTCTTGCTCCCCTGCCAGTA 60.840 55.000 0.00 0.00 0.00 2.74
1096 1144 1.078143 CTTGCTCCCCTGCCAGTAC 60.078 63.158 0.00 0.00 0.00 2.73
1097 1145 2.543067 CTTGCTCCCCTGCCAGTACC 62.543 65.000 0.00 0.00 0.00 3.34
1098 1146 2.689034 GCTCCCCTGCCAGTACCT 60.689 66.667 0.00 0.00 0.00 3.08
1099 1147 2.301738 GCTCCCCTGCCAGTACCTT 61.302 63.158 0.00 0.00 0.00 3.50
1100 1148 0.981277 GCTCCCCTGCCAGTACCTTA 60.981 60.000 0.00 0.00 0.00 2.69
1135 1185 0.869880 CGACTCGAATGCATGCCGTA 60.870 55.000 16.68 0.00 0.00 4.02
1141 1191 4.234574 CTCGAATGCATGCCGTACTATTA 58.765 43.478 16.68 0.00 0.00 0.98
1142 1192 4.816392 TCGAATGCATGCCGTACTATTAT 58.184 39.130 16.68 0.00 0.00 1.28
1145 1195 5.790003 CGAATGCATGCCGTACTATTATTTG 59.210 40.000 16.68 4.94 0.00 2.32
1146 1196 6.565811 CGAATGCATGCCGTACTATTATTTGT 60.566 38.462 16.68 0.00 0.00 2.83
1147 1197 5.666969 TGCATGCCGTACTATTATTTGTC 57.333 39.130 16.68 0.00 0.00 3.18
1149 1199 5.236263 TGCATGCCGTACTATTATTTGTCAG 59.764 40.000 16.68 0.00 0.00 3.51
1150 1200 5.334105 GCATGCCGTACTATTATTTGTCAGG 60.334 44.000 6.36 0.00 0.00 3.86
1151 1201 4.699637 TGCCGTACTATTATTTGTCAGGG 58.300 43.478 0.00 0.00 0.00 4.45
1178 1232 1.197721 GTTGGATCCAGTGCTGTTTCG 59.802 52.381 15.53 0.00 0.00 3.46
1189 1243 3.376859 AGTGCTGTTTCGACAAATTGACA 59.623 39.130 0.00 0.00 0.00 3.58
1192 1246 3.300009 CTGTTTCGACAAATTGACAGGC 58.700 45.455 0.00 0.00 32.88 4.85
1206 1260 1.541588 GACAGGCATGGTTTGGTTCTC 59.458 52.381 2.31 0.00 0.00 2.87
1207 1261 1.145738 ACAGGCATGGTTTGGTTCTCT 59.854 47.619 2.31 0.00 0.00 3.10
1294 1348 6.522054 TGAAATCGTAACCATCCTAATCTCC 58.478 40.000 0.00 0.00 0.00 3.71
1307 1361 5.357257 TCCTAATCTCCGATGCTTGTTTAC 58.643 41.667 0.00 0.00 0.00 2.01
1316 1370 4.201851 CCGATGCTTGTTTACCATCTTCAG 60.202 45.833 0.00 0.00 34.63 3.02
1318 1372 5.106555 CGATGCTTGTTTACCATCTTCAGTT 60.107 40.000 0.00 0.00 34.63 3.16
1319 1373 5.689383 TGCTTGTTTACCATCTTCAGTTC 57.311 39.130 0.00 0.00 0.00 3.01
1320 1374 4.518970 TGCTTGTTTACCATCTTCAGTTCC 59.481 41.667 0.00 0.00 0.00 3.62
1321 1375 4.518970 GCTTGTTTACCATCTTCAGTTCCA 59.481 41.667 0.00 0.00 0.00 3.53
1322 1376 5.009610 GCTTGTTTACCATCTTCAGTTCCAA 59.990 40.000 0.00 0.00 0.00 3.53
1323 1377 6.294731 GCTTGTTTACCATCTTCAGTTCCAAT 60.295 38.462 0.00 0.00 0.00 3.16
1324 1378 7.094377 GCTTGTTTACCATCTTCAGTTCCAATA 60.094 37.037 0.00 0.00 0.00 1.90
1326 1383 8.877864 TGTTTACCATCTTCAGTTCCAATAAT 57.122 30.769 0.00 0.00 0.00 1.28
1360 1417 9.846248 GAAATTTATGAGTTACTTGCAAGTGAT 57.154 29.630 36.50 23.58 40.07 3.06
1367 1424 7.330262 TGAGTTACTTGCAAGTGATGATGATA 58.670 34.615 36.50 14.80 40.07 2.15
1397 1455 0.947244 CATAGGTCATTGCCGCCTTC 59.053 55.000 0.00 0.00 34.07 3.46
1454 1512 3.197092 TCGCTGCATGCATCACGG 61.197 61.111 27.14 16.11 43.06 4.94
1467 1525 1.647545 ATCACGGCAGGTCAAATGCG 61.648 55.000 0.00 0.00 44.80 4.73
1476 1534 2.086869 AGGTCAAATGCGGATGTCTTG 58.913 47.619 0.00 0.00 0.00 3.02
1500 1569 3.067106 TGTTTCTCTGGCGTGATTCTTC 58.933 45.455 0.00 0.00 0.00 2.87
1501 1570 3.067106 GTTTCTCTGGCGTGATTCTTCA 58.933 45.455 0.00 0.00 0.00 3.02
1536 1605 1.203440 ACCCTGTACCTTCCCTGTGAT 60.203 52.381 0.00 0.00 0.00 3.06
1642 1711 4.397730 ACTGACAAAACATGCACAGTAACA 59.602 37.500 0.00 0.00 43.34 2.41
1707 1776 1.598882 TTACTTGTGATGGTTGCGCA 58.401 45.000 5.66 5.66 0.00 6.09
1715 1784 2.285220 GTGATGGTTGCGCATAGTACTG 59.715 50.000 12.75 0.00 0.00 2.74
2021 2135 4.565166 GCACGCTATACTGTTGTATTGACA 59.435 41.667 0.00 0.00 39.77 3.58
2032 2146 6.321181 ACTGTTGTATTGACAATTGTCCTGTT 59.679 34.615 30.66 17.10 46.98 3.16
2081 2195 5.083533 ACCAATTGTTGCTTGTCTTTTCA 57.916 34.783 4.43 0.00 0.00 2.69
2145 2259 2.227149 GAGTGCTGCACATTTGACATCA 59.773 45.455 31.90 0.00 36.74 3.07
2166 2280 1.808945 GATTGTGTGCCTGAAGGTGAG 59.191 52.381 0.00 0.00 37.57 3.51
2238 2352 6.699895 TTGTTCAACGACACATATACAGTC 57.300 37.500 0.00 0.00 0.00 3.51
2250 2364 1.874129 ATACAGTCCGGGTCAATGGA 58.126 50.000 0.00 0.00 0.00 3.41
2337 2454 7.939588 GGCAAGAATATCTATCCCAGTAACTTT 59.060 37.037 0.00 0.00 0.00 2.66
2393 2510 1.134367 TGAGAGCATACCAGTACGTGC 59.866 52.381 0.00 0.00 37.84 5.34
2484 2606 8.915871 ACACTTACAATCATTTTATGCACATC 57.084 30.769 0.00 0.00 0.00 3.06
2728 2855 1.064166 ACTGCATCTTGGATTGGAGGG 60.064 52.381 0.00 0.00 35.81 4.30
2746 2873 4.058124 GAGGGAAAAACAACTTCATTGGC 58.942 43.478 0.00 0.00 43.20 4.52
2749 2876 4.213906 GGGAAAAACAACTTCATTGGCATG 59.786 41.667 0.00 0.00 43.20 4.06
2821 2948 7.318141 TCTTAGTTCTCTACATGGTTAAACGG 58.682 38.462 0.00 0.00 0.00 4.44
2881 3008 7.673641 ACTGGACATCTCATTTCTCTATCTT 57.326 36.000 0.00 0.00 0.00 2.40
2882 3009 8.774546 ACTGGACATCTCATTTCTCTATCTTA 57.225 34.615 0.00 0.00 0.00 2.10
2922 3049 9.182214 AGCATTCATATCACACTTACTTTTCAT 57.818 29.630 0.00 0.00 0.00 2.57
2949 3136 9.322773 GAACCCTCTTGTTATTAGTATGTTACC 57.677 37.037 0.00 0.00 0.00 2.85
3021 3208 8.786898 TCTGTCAATTTGAGTGAAATTAGGAAG 58.213 33.333 0.00 0.00 41.50 3.46
3028 3215 9.638176 ATTTGAGTGAAATTAGGAAGATGCTAT 57.362 29.630 0.00 0.00 29.22 2.97
3036 3223 8.572855 AAATTAGGAAGATGCTATAATGAGCC 57.427 34.615 0.00 0.00 42.11 4.70
3178 3365 4.037690 GCGCCAAGATAATCACATTTGAC 58.962 43.478 0.00 0.00 33.38 3.18
3287 3474 8.689061 TGAGAATAAAAGATCATTCAATGGGTG 58.311 33.333 0.00 0.00 34.28 4.61
3353 3540 1.303561 TGGGCTTGTCATGGCTCAC 60.304 57.895 11.41 0.00 33.66 3.51
3384 3571 1.981256 TCTTGTTGACTTTGGAGCCC 58.019 50.000 0.00 0.00 0.00 5.19
3594 3781 8.642935 TTTGATCACATAAAAGGTATCACCAA 57.357 30.769 0.00 0.00 41.95 3.67
3667 3854 4.098914 TGTCTGGCAATGTCCTAAACTT 57.901 40.909 0.00 0.00 0.00 2.66
3731 3918 2.959465 AGCCAACTTTCTACCTTGCT 57.041 45.000 0.00 0.00 0.00 3.91
3767 3954 5.221422 TGCCAAATTTAGTCCTCAAACCAAG 60.221 40.000 0.00 0.00 0.00 3.61
3793 3980 8.719648 GCATGTCCTTAATATTGAAGATCTGAG 58.280 37.037 0.00 0.00 0.00 3.35
4020 4217 6.183360 TGTGATCACTTTATCAAAACGATCGG 60.183 38.462 25.55 0.89 37.61 4.18
4030 4227 3.621268 TCAAAACGATCGGCAGATAAAGG 59.379 43.478 20.98 0.00 37.19 3.11
4087 4285 5.114785 ACGACTGATGAGTATAGTGATGC 57.885 43.478 0.00 0.00 30.16 3.91
4112 4310 3.011119 ACACTTAACAAAACACTGCCGA 58.989 40.909 0.00 0.00 0.00 5.54
4163 4371 8.644374 AAATTAAACACTCCCACTAATAAGCA 57.356 30.769 0.00 0.00 0.00 3.91
4182 4390 2.425773 GCACTGTTTGCGAGCACG 60.426 61.111 0.00 0.00 42.79 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.102663 AGAAATCCTATATGACGCACATAGC 58.897 40.000 8.45 0.00 43.48 2.97
11 12 6.754209 GGAGAAATCCTATATGACGCACATAG 59.246 42.308 8.45 4.31 43.48 2.23
12 13 6.210584 TGGAGAAATCCTATATGACGCACATA 59.789 38.462 5.59 5.59 44.21 2.29
13 14 5.012046 TGGAGAAATCCTATATGACGCACAT 59.988 40.000 0.00 1.60 42.39 3.21
14 15 4.343814 TGGAGAAATCCTATATGACGCACA 59.656 41.667 0.00 0.00 0.00 4.57
15 16 4.883083 TGGAGAAATCCTATATGACGCAC 58.117 43.478 0.00 0.00 0.00 5.34
16 17 5.545063 TTGGAGAAATCCTATATGACGCA 57.455 39.130 0.00 0.00 0.00 5.24
17 18 6.654793 GATTGGAGAAATCCTATATGACGC 57.345 41.667 0.00 0.00 39.08 5.19
28 29 0.183731 AGCCCGGGATTGGAGAAATC 59.816 55.000 29.31 0.36 43.52 2.17
29 30 0.106519 CAGCCCGGGATTGGAGAAAT 60.107 55.000 29.31 0.00 0.00 2.17
30 31 1.302949 CAGCCCGGGATTGGAGAAA 59.697 57.895 29.31 0.00 0.00 2.52
31 32 2.998097 CAGCCCGGGATTGGAGAA 59.002 61.111 29.31 0.00 0.00 2.87
32 33 3.797353 GCAGCCCGGGATTGGAGA 61.797 66.667 29.31 0.00 0.00 3.71
33 34 4.113815 TGCAGCCCGGGATTGGAG 62.114 66.667 29.31 7.16 0.00 3.86
34 35 4.113815 CTGCAGCCCGGGATTGGA 62.114 66.667 29.31 21.56 0.00 3.53
45 46 2.260434 CATGTGTTGGGCTGCAGC 59.740 61.111 30.88 30.88 41.14 5.25
46 47 2.260434 GCATGTGTTGGGCTGCAG 59.740 61.111 10.11 10.11 34.77 4.41
47 48 3.672447 CGCATGTGTTGGGCTGCA 61.672 61.111 0.50 0.00 34.29 4.41
48 49 2.807631 CTTCGCATGTGTTGGGCTGC 62.808 60.000 6.09 0.00 38.14 5.25
49 50 1.210931 CTTCGCATGTGTTGGGCTG 59.789 57.895 6.09 0.00 38.14 4.85
50 51 0.537143 TTCTTCGCATGTGTTGGGCT 60.537 50.000 6.09 0.00 38.14 5.19
51 52 0.313672 TTTCTTCGCATGTGTTGGGC 59.686 50.000 6.09 0.00 38.14 5.36
52 53 2.664916 CTTTTCTTCGCATGTGTTGGG 58.335 47.619 6.09 0.00 39.56 4.12
53 54 2.053627 GCTTTTCTTCGCATGTGTTGG 58.946 47.619 6.09 0.00 0.00 3.77
54 55 2.053627 GGCTTTTCTTCGCATGTGTTG 58.946 47.619 6.09 0.74 0.00 3.33
55 56 1.000274 GGGCTTTTCTTCGCATGTGTT 60.000 47.619 6.09 0.00 0.00 3.32
56 57 0.598065 GGGCTTTTCTTCGCATGTGT 59.402 50.000 6.09 0.00 0.00 3.72
57 58 0.454957 CGGGCTTTTCTTCGCATGTG 60.455 55.000 0.00 0.00 0.00 3.21
58 59 0.889186 ACGGGCTTTTCTTCGCATGT 60.889 50.000 0.00 0.00 0.00 3.21
59 60 0.454957 CACGGGCTTTTCTTCGCATG 60.455 55.000 0.00 0.00 0.00 4.06
60 61 0.889186 ACACGGGCTTTTCTTCGCAT 60.889 50.000 0.00 0.00 0.00 4.73
61 62 1.525077 ACACGGGCTTTTCTTCGCA 60.525 52.632 0.00 0.00 0.00 5.10
62 63 1.082104 CACACGGGCTTTTCTTCGC 60.082 57.895 0.00 0.00 0.00 4.70
63 64 1.574428 CCACACGGGCTTTTCTTCG 59.426 57.895 0.00 0.00 0.00 3.79
145 160 1.841663 CGGTTTTGGAGTGACAGCGG 61.842 60.000 0.00 0.00 0.00 5.52
169 184 2.778899 CCACAAGGAAGGGAGGACT 58.221 57.895 0.00 0.00 36.89 3.85
176 191 1.304464 GGGAAGCCCACAAGGAAGG 60.304 63.158 0.00 0.00 44.65 3.46
430 462 4.217159 GGGGAATCGGTCGGTCGG 62.217 72.222 0.00 0.00 0.00 4.79
431 463 4.217159 GGGGGAATCGGTCGGTCG 62.217 72.222 0.00 0.00 0.00 4.79
432 464 4.217159 CGGGGGAATCGGTCGGTC 62.217 72.222 0.00 0.00 0.00 4.79
439 471 2.513897 GTGGAAGCGGGGGAATCG 60.514 66.667 0.00 0.00 0.00 3.34
473 505 2.264480 CGATTGGACTGGCCGACA 59.736 61.111 0.00 0.00 40.66 4.35
569 601 2.572647 GACGAGTACGACCACGCG 60.573 66.667 3.53 3.53 45.59 6.01
570 602 1.225963 GAGACGAGTACGACCACGC 60.226 63.158 0.00 0.00 43.96 5.34
571 603 1.423056 GGAGACGAGTACGACCACG 59.577 63.158 0.00 0.00 42.66 4.94
607 639 2.722487 CTAGCTACCGGGCGACTG 59.278 66.667 6.32 0.00 37.29 3.51
608 640 2.518825 CCTAGCTACCGGGCGACT 60.519 66.667 6.32 0.00 37.29 4.18
609 641 3.603671 CCCTAGCTACCGGGCGAC 61.604 72.222 6.32 0.00 37.29 5.19
615 647 2.651361 CCGATGCCCTAGCTACCG 59.349 66.667 0.00 0.00 40.80 4.02
619 651 1.486997 ATGATGCCGATGCCCTAGCT 61.487 55.000 0.00 0.00 40.80 3.32
665 697 2.341101 TTCCTCGCGGTCTCTGTCC 61.341 63.158 6.13 0.00 0.00 4.02
697 729 1.067582 CTAATGACCCGAGTCCGCC 59.932 63.158 0.00 0.00 42.81 6.13
698 730 1.067582 CCTAATGACCCGAGTCCGC 59.932 63.158 0.00 0.00 42.81 5.54
699 731 1.041447 ACCCTAATGACCCGAGTCCG 61.041 60.000 0.00 0.00 42.81 4.79
705 748 3.492102 AATCATCACCCTAATGACCCG 57.508 47.619 0.00 0.00 36.04 5.28
744 787 5.437191 AATGATAGAAAAAGACCCCGTCT 57.563 39.130 0.00 0.00 45.64 4.18
745 788 5.880887 AGAAATGATAGAAAAAGACCCCGTC 59.119 40.000 0.00 0.00 0.00 4.79
746 789 5.816682 AGAAATGATAGAAAAAGACCCCGT 58.183 37.500 0.00 0.00 0.00 5.28
747 790 6.183360 GGAAGAAATGATAGAAAAAGACCCCG 60.183 42.308 0.00 0.00 0.00 5.73
748 791 6.892456 AGGAAGAAATGATAGAAAAAGACCCC 59.108 38.462 0.00 0.00 0.00 4.95
749 792 7.394641 ACAGGAAGAAATGATAGAAAAAGACCC 59.605 37.037 0.00 0.00 0.00 4.46
750 793 8.239998 CACAGGAAGAAATGATAGAAAAAGACC 58.760 37.037 0.00 0.00 0.00 3.85
751 794 8.239998 CCACAGGAAGAAATGATAGAAAAAGAC 58.760 37.037 0.00 0.00 0.00 3.01
752 795 7.394359 CCCACAGGAAGAAATGATAGAAAAAGA 59.606 37.037 0.00 0.00 33.47 2.52
753 796 7.363268 CCCCACAGGAAGAAATGATAGAAAAAG 60.363 40.741 0.00 0.00 38.24 2.27
754 797 6.437162 CCCCACAGGAAGAAATGATAGAAAAA 59.563 38.462 0.00 0.00 38.24 1.94
755 798 5.951747 CCCCACAGGAAGAAATGATAGAAAA 59.048 40.000 0.00 0.00 38.24 2.29
756 799 5.509498 CCCCACAGGAAGAAATGATAGAAA 58.491 41.667 0.00 0.00 38.24 2.52
757 800 4.079787 CCCCCACAGGAAGAAATGATAGAA 60.080 45.833 0.00 0.00 38.24 2.10
758 801 3.459598 CCCCCACAGGAAGAAATGATAGA 59.540 47.826 0.00 0.00 38.24 1.98
759 802 3.203040 ACCCCCACAGGAAGAAATGATAG 59.797 47.826 0.00 0.00 38.24 2.08
760 803 3.197983 ACCCCCACAGGAAGAAATGATA 58.802 45.455 0.00 0.00 38.24 2.15
786 829 0.756815 GGGGATTTGGATGGAGTGGC 60.757 60.000 0.00 0.00 0.00 5.01
795 838 1.982226 TGAGTCGAAAGGGGATTTGGA 59.018 47.619 0.00 0.00 33.73 3.53
796 839 2.359900 CTGAGTCGAAAGGGGATTTGG 58.640 52.381 0.00 0.00 0.00 3.28
797 840 1.740025 GCTGAGTCGAAAGGGGATTTG 59.260 52.381 0.00 0.00 0.00 2.32
798 841 1.630878 AGCTGAGTCGAAAGGGGATTT 59.369 47.619 0.00 0.00 0.00 2.17
823 866 0.603975 GTGAGACCAACTCCTGTGGC 60.604 60.000 0.00 0.00 44.34 5.01
842 885 3.399440 ACAGAGAAGAGTCAAAGCCAG 57.601 47.619 0.00 0.00 0.00 4.85
877 920 6.192360 GTGATAAACAATCGGAACATAGTGC 58.808 40.000 0.00 0.00 37.42 4.40
884 927 7.787725 ATTAGAGGTGATAAACAATCGGAAC 57.212 36.000 0.00 0.00 37.42 3.62
897 945 6.149474 GCAAACGGCATATAATTAGAGGTGAT 59.851 38.462 0.00 0.00 43.97 3.06
914 962 1.327764 CTCCGAGAATAAGCAAACGGC 59.672 52.381 0.00 0.00 45.30 5.68
1083 1131 2.280308 AATAAGGTACTGGCAGGGGA 57.720 50.000 20.34 0.14 40.86 4.81
1135 1185 8.576442 CAACAAAAGACCCTGACAAATAATAGT 58.424 33.333 0.00 0.00 0.00 2.12
1141 1191 4.285863 TCCAACAAAAGACCCTGACAAAT 58.714 39.130 0.00 0.00 0.00 2.32
1142 1192 3.702792 TCCAACAAAAGACCCTGACAAA 58.297 40.909 0.00 0.00 0.00 2.83
1145 1195 2.820197 GGATCCAACAAAAGACCCTGAC 59.180 50.000 6.95 0.00 0.00 3.51
1146 1196 2.445145 TGGATCCAACAAAAGACCCTGA 59.555 45.455 13.46 0.00 0.00 3.86
1147 1197 2.821969 CTGGATCCAACAAAAGACCCTG 59.178 50.000 17.00 0.00 0.00 4.45
1149 1199 2.558359 CACTGGATCCAACAAAAGACCC 59.442 50.000 17.00 0.00 0.00 4.46
1150 1200 2.029918 GCACTGGATCCAACAAAAGACC 60.030 50.000 17.00 0.00 0.00 3.85
1151 1201 2.887152 AGCACTGGATCCAACAAAAGAC 59.113 45.455 17.00 1.52 0.00 3.01
1178 1232 3.665745 AACCATGCCTGTCAATTTGTC 57.334 42.857 0.00 0.00 0.00 3.18
1189 1243 1.707427 AGAGAGAACCAAACCATGCCT 59.293 47.619 0.00 0.00 0.00 4.75
1192 1246 3.750130 CAGACAGAGAGAACCAAACCATG 59.250 47.826 0.00 0.00 0.00 3.66
1335 1392 9.630098 CATCACTTGCAAGTAACTCATAAATTT 57.370 29.630 30.67 0.97 37.08 1.82
1342 1399 5.550290 TCATCATCACTTGCAAGTAACTCA 58.450 37.500 30.67 14.58 37.08 3.41
1343 1400 6.674694 ATCATCATCACTTGCAAGTAACTC 57.325 37.500 30.67 0.00 37.08 3.01
1348 1405 5.763698 CCAGATATCATCATCACTTGCAAGT 59.236 40.000 26.36 26.36 40.60 3.16
1352 1409 5.303165 TGTCCAGATATCATCATCACTTGC 58.697 41.667 5.32 0.00 0.00 4.01
1353 1410 6.128254 GCATGTCCAGATATCATCATCACTTG 60.128 42.308 5.32 3.05 0.00 3.16
1360 1417 5.486419 ACCTATGCATGTCCAGATATCATCA 59.514 40.000 10.16 0.00 0.00 3.07
1367 1424 4.395625 CAATGACCTATGCATGTCCAGAT 58.604 43.478 10.16 0.00 0.00 2.90
1454 1512 0.099436 GACATCCGCATTTGACCTGC 59.901 55.000 0.00 0.00 36.26 4.85
1467 1525 3.944015 CCAGAGAAACATCCAAGACATCC 59.056 47.826 0.00 0.00 0.00 3.51
1476 1534 2.029838 ATCACGCCAGAGAAACATCC 57.970 50.000 0.00 0.00 0.00 3.51
1500 1569 3.006752 ACAGGGTAAACAAATGCACCATG 59.993 43.478 10.62 10.62 45.78 3.66
1501 1570 3.238597 ACAGGGTAAACAAATGCACCAT 58.761 40.909 0.00 0.00 32.42 3.55
1536 1605 0.813610 CACCAGTTCGACAACCTGCA 60.814 55.000 0.00 0.00 32.22 4.41
1642 1711 6.757897 TTTCACTTGAAACTCACAGTCATT 57.242 33.333 0.07 0.00 38.94 2.57
1707 1776 7.340743 AGACTATCTCAACAACAGCAGTACTAT 59.659 37.037 0.00 0.00 0.00 2.12
1715 1784 6.147821 TGCTTAAAGACTATCTCAACAACAGC 59.852 38.462 0.00 0.00 0.00 4.40
1764 1833 4.404073 TGAAAGGCATACAACAACCAGTTT 59.596 37.500 0.00 0.00 38.74 2.66
1894 1969 3.117512 ACCAACCAGGGAAGCAATATAGG 60.118 47.826 0.00 0.00 43.89 2.57
2021 2135 7.734942 ACATAATTTGTTCCAACAGGACAATT 58.265 30.769 5.56 5.56 40.50 2.32
2032 2146 7.100409 TGAGTATGTCGACATAATTTGTTCCA 58.900 34.615 33.71 23.40 40.18 3.53
2081 2195 5.886474 TCACTTCGACTTCTCACATACCTAT 59.114 40.000 0.00 0.00 0.00 2.57
2145 2259 1.421268 TCACCTTCAGGCACACAATCT 59.579 47.619 0.00 0.00 39.32 2.40
2166 2280 0.462581 TTGGAGCATGATCAGCGGTC 60.463 55.000 13.85 15.37 37.01 4.79
2238 2352 0.616371 TAACCACTCCATTGACCCGG 59.384 55.000 0.00 0.00 0.00 5.73
2250 2364 7.996644 TCCTTTTTATTCACTTGAGTAACCACT 59.003 33.333 0.00 0.00 37.87 4.00
2337 2454 3.711704 CACCTATAAGCCTTCCCTTCTGA 59.288 47.826 0.00 0.00 0.00 3.27
2393 2510 5.393787 GCATATGCAGGGTGATGGAAATATG 60.394 44.000 22.84 0.00 41.59 1.78
2419 2536 6.202954 CGCAGATCCCTTAATACCAAAAGTAG 59.797 42.308 0.00 0.00 33.42 2.57
2728 2855 4.319694 GCCATGCCAATGAAGTTGTTTTTC 60.320 41.667 0.00 0.00 35.67 2.29
2746 2873 4.698780 CCACCAATAGTCAGATATGCCATG 59.301 45.833 0.00 0.00 0.00 3.66
2749 2876 4.357918 ACCACCAATAGTCAGATATGCC 57.642 45.455 0.00 0.00 0.00 4.40
2821 2948 6.204882 AGTCAGCAAACTGTTAAACATACCTC 59.795 38.462 0.00 0.00 44.77 3.85
2836 2963 6.253746 CAGTATGAAATAGCAGTCAGCAAAC 58.746 40.000 0.00 0.00 43.34 2.93
2843 2970 6.520272 AGATGTCCAGTATGAAATAGCAGTC 58.480 40.000 0.00 0.00 39.69 3.51
2881 3008 9.585099 GATATGAATGCTCCAAAACATGTTTTA 57.415 29.630 30.65 18.38 40.45 1.52
2882 3009 8.095792 TGATATGAATGCTCCAAAACATGTTTT 58.904 29.630 27.01 27.01 42.91 2.43
2895 3022 8.668353 TGAAAAGTAAGTGTGATATGAATGCTC 58.332 33.333 0.00 0.00 0.00 4.26
2922 3049 9.880157 GTAACATACTAATAACAAGAGGGTTCA 57.120 33.333 0.00 0.00 32.29 3.18
2942 3129 7.215789 TCAAACAAAATGCATTCAGGTAACAT 58.784 30.769 13.38 0.00 41.41 2.71
2977 3164 8.458573 TTGACAGAACCAATAACTACATTGTT 57.541 30.769 0.00 0.00 34.67 2.83
2978 3165 8.635765 ATTGACAGAACCAATAACTACATTGT 57.364 30.769 0.00 0.00 34.67 2.71
2981 3168 9.295825 TCAAATTGACAGAACCAATAACTACAT 57.704 29.630 0.00 0.00 33.51 2.29
3036 3223 2.675348 GGAACGAGAAAAGAGCCATCTG 59.325 50.000 0.00 0.00 35.37 2.90
3178 3365 5.335976 GGGTCTGCAAAGTTCCTGAAAATAG 60.336 44.000 0.00 0.00 0.00 1.73
3353 3540 2.681848 GTCAACAAGATCCTCATGCCTG 59.318 50.000 0.00 0.00 0.00 4.85
3425 3612 7.317722 AGGTCAGATAAGGTTTAAGTCAACT 57.682 36.000 0.00 0.00 0.00 3.16
3437 3624 6.678568 ATGGTCAGATAAGGTCAGATAAGG 57.321 41.667 0.00 0.00 0.00 2.69
3594 3781 2.158900 AGCATGCCGTAAGATTAGCACT 60.159 45.455 15.66 0.00 38.21 4.40
3731 3918 7.978975 GGACTAAATTTGGCATGCTAATGTTTA 59.021 33.333 17.82 20.60 36.08 2.01
3767 3954 8.613060 TCAGATCTTCAATATTAAGGACATGC 57.387 34.615 0.00 0.00 0.00 4.06
3793 3980 1.133668 AGAATCCCAGCACATTAGCCC 60.134 52.381 0.00 0.00 34.23 5.19
4020 4217 3.181506 GCAGCAGTTGTACCTTTATCTGC 60.182 47.826 6.83 6.83 45.48 4.26
4030 4227 2.169832 TCCAAGAGCAGCAGTTGTAC 57.830 50.000 0.00 0.00 0.00 2.90
4087 4285 4.326009 GGCAGTGTTTTGTTAAGTGTGTTG 59.674 41.667 0.00 0.00 0.00 3.33
4182 4390 6.312918 TGAACATTAAGACGATTCAAGCTACC 59.687 38.462 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.