Multiple sequence alignment - TraesCS3D01G139400

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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 TraesCS3D01G139400 chr3D 100.000 3014 0 0 1 3014 98881933 98884946 0.000000e+00 5566
1 TraesCS3D01G139400 chr3B 93.756 1089 47 10 1158 2240 149463368 149464441 0.000000e+00 1615
2 TraesCS3D01G139400 chr3B 88.470 451 45 3 1 451 149461993 149462436 3.420000e-149 538
3 TraesCS3D01G139400 chr3B 82.111 341 23 16 842 1156 149462782 149463110 1.070000e-64 257
4 TraesCS3D01G139400 chr4D 95.147 783 32 6 2235 3014 10645261 10646040 0.000000e+00 1230
5 TraesCS3D01G139400 chr7D 92.426 779 48 8 2238 3013 197340982 197340212 0.000000e+00 1101
6 TraesCS3D01G139400 chr7D 90.392 791 57 13 2234 3012 164854031 164854814 0.000000e+00 1022
7 TraesCS3D01G139400 chr7D 89.062 128 14 0 1160 1287 629824394 629824521 3.110000e-35 159
8 TraesCS3D01G139400 chr5D 91.720 785 51 8 2236 3011 542531307 542532086 0.000000e+00 1077
9 TraesCS3D01G139400 chr5D 90.470 787 60 9 2237 3012 542605473 542604691 0.000000e+00 1024
10 TraesCS3D01G139400 chr5D 86.782 174 15 6 81 253 542693291 542693457 1.430000e-43 187
11 TraesCS3D01G139400 chr5D 86.207 174 17 4 84 257 150835730 150835564 6.640000e-42 182
12 TraesCS3D01G139400 chr5D 82.587 201 25 8 76 274 53583068 53583260 5.170000e-38 169
13 TraesCS3D01G139400 chr2D 91.248 777 60 6 2236 3011 542194360 542195129 0.000000e+00 1051
14 TraesCS3D01G139400 chr2D 90.689 784 59 10 2234 3013 146729836 146729063 0.000000e+00 1031
15 TraesCS3D01G139400 chr1A 90.757 779 64 5 2237 3014 478365579 478366350 0.000000e+00 1033
16 TraesCS3D01G139400 chr7B 90.488 778 60 11 2238 3010 4387224 4386456 0.000000e+00 1014
17 TraesCS3D01G139400 chr7B 85.311 177 20 3 76 252 490207981 490208151 8.590000e-41 178
18 TraesCS3D01G139400 chr7B 89.062 128 14 0 1160 1287 732644911 732645038 3.110000e-35 159
19 TraesCS3D01G139400 chr3A 92.667 300 15 3 1355 1650 116526297 116526593 2.780000e-115 425
20 TraesCS3D01G139400 chr3A 93.596 203 10 1 1158 1357 116526065 116526267 1.760000e-77 300
21 TraesCS3D01G139400 chr3A 92.486 173 12 1 1787 1959 116526816 116526987 2.320000e-61 246
22 TraesCS3D01G139400 chr3A 77.561 410 51 23 772 1156 116525413 116525806 3.040000e-50 209
23 TraesCS3D01G139400 chr6D 86.905 168 15 5 85 252 431160828 431160668 6.640000e-42 182
24 TraesCS3D01G139400 chr6B 86.905 168 15 5 85 252 650598700 650598540 6.640000e-42 182
25 TraesCS3D01G139400 chr5A 85.632 174 18 5 84 257 206730799 206730633 3.090000e-40 176
26 TraesCS3D01G139400 chr5A 88.793 116 13 0 1172 1287 547720092 547720207 3.130000e-30 143
27 TraesCS3D01G139400 chr2A 85.311 177 18 6 84 260 342647561 342647393 3.090000e-40 176
28 TraesCS3D01G139400 chr7A 88.281 128 15 0 1160 1287 725912790 725912917 1.450000e-33 154


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 TraesCS3D01G139400 chr3D 98881933 98884946 3013 False 5566.000000 5566 100.000000 1 3014 1 chr3D.!!$F1 3013
1 TraesCS3D01G139400 chr3B 149461993 149464441 2448 False 803.333333 1615 88.112333 1 2240 3 chr3B.!!$F1 2239
2 TraesCS3D01G139400 chr4D 10645261 10646040 779 False 1230.000000 1230 95.147000 2235 3014 1 chr4D.!!$F1 779
3 TraesCS3D01G139400 chr7D 197340212 197340982 770 True 1101.000000 1101 92.426000 2238 3013 1 chr7D.!!$R1 775
4 TraesCS3D01G139400 chr7D 164854031 164854814 783 False 1022.000000 1022 90.392000 2234 3012 1 chr7D.!!$F1 778
5 TraesCS3D01G139400 chr5D 542531307 542532086 779 False 1077.000000 1077 91.720000 2236 3011 1 chr5D.!!$F2 775
6 TraesCS3D01G139400 chr5D 542604691 542605473 782 True 1024.000000 1024 90.470000 2237 3012 1 chr5D.!!$R2 775
7 TraesCS3D01G139400 chr2D 542194360 542195129 769 False 1051.000000 1051 91.248000 2236 3011 1 chr2D.!!$F1 775
8 TraesCS3D01G139400 chr2D 146729063 146729836 773 True 1031.000000 1031 90.689000 2234 3013 1 chr2D.!!$R1 779
9 TraesCS3D01G139400 chr1A 478365579 478366350 771 False 1033.000000 1033 90.757000 2237 3014 1 chr1A.!!$F1 777
10 TraesCS3D01G139400 chr7B 4386456 4387224 768 True 1014.000000 1014 90.488000 2238 3010 1 chr7B.!!$R1 772
11 TraesCS3D01G139400 chr3A 116525413 116526987 1574 False 295.000000 425 89.077500 772 1959 4 chr3A.!!$F1 1187

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
534 535 0.321346 TGGATCACACGTGCATGACT 59.679 50.0 17.22 3.43 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 2527 0.187117 TGATTGCCACTGGGGTCAAA 59.813 50.0 9.31 0.0 39.65 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.768275 ACCATCCATTCTGCGGTGATA 59.232 47.619 0.00 0.00 0.00 2.15
35 36 2.745821 CCATCCATTCTGCGGTGATATG 59.254 50.000 0.00 0.00 0.00 1.78
39 40 2.545742 CCATTCTGCGGTGATATGACGA 60.546 50.000 0.00 0.00 0.00 4.20
56 57 1.339097 CGACTAGGGGTCTTATGGGG 58.661 60.000 0.00 0.00 42.44 4.96
60 61 1.768870 CTAGGGGTCTTATGGGGTGTG 59.231 57.143 0.00 0.00 0.00 3.82
93 94 6.911250 TGTGACATCTAAAGTACTCCTTCA 57.089 37.500 0.00 0.00 31.27 3.02
94 95 6.925211 TGTGACATCTAAAGTACTCCTTCAG 58.075 40.000 0.00 0.00 31.27 3.02
98 99 8.088981 TGACATCTAAAGTACTCCTTCAGTTTC 58.911 37.037 0.00 0.00 36.43 2.78
142 143 9.587772 AGATATTTCCATACAGATTACATACGC 57.412 33.333 0.00 0.00 0.00 4.42
143 144 6.706055 ATTTCCATACAGATTACATACGCG 57.294 37.500 3.53 3.53 0.00 6.01
144 145 4.841443 TCCATACAGATTACATACGCGT 57.159 40.909 19.17 19.17 0.00 6.01
145 146 5.945466 TCCATACAGATTACATACGCGTA 57.055 39.130 22.94 22.94 0.00 4.42
146 147 5.692814 TCCATACAGATTACATACGCGTAC 58.307 41.667 23.19 7.71 0.00 3.67
148 149 2.990941 ACAGATTACATACGCGTACGG 58.009 47.619 23.19 18.84 46.04 4.02
149 150 2.355756 ACAGATTACATACGCGTACGGT 59.644 45.455 23.19 23.39 46.04 4.83
193 194 5.615289 AGTGTAGATTCACTCACTTTGCTT 58.385 37.500 0.00 0.00 44.07 3.91
194 195 6.058183 AGTGTAGATTCACTCACTTTGCTTT 58.942 36.000 0.00 0.00 44.07 3.51
195 196 6.017605 AGTGTAGATTCACTCACTTTGCTTTG 60.018 38.462 0.00 0.00 44.07 2.77
202 203 4.023792 TCACTCACTTTGCTTTGTATGCAG 60.024 41.667 0.00 0.00 41.71 4.41
206 207 3.004629 CACTTTGCTTTGTATGCAGTCCA 59.995 43.478 0.00 0.00 41.71 4.02
211 212 7.339212 ACTTTGCTTTGTATGCAGTCCATATTA 59.661 33.333 0.00 0.00 41.71 0.98
218 219 9.851686 TTTGTATGCAGTCCATATTAGAATCTT 57.148 29.630 0.00 0.00 38.60 2.40
254 255 3.684408 ATAGGAACGGAGGGAGTAAGT 57.316 47.619 0.00 0.00 0.00 2.24
324 325 4.782019 TTTGCCCACACATATTGAAGTC 57.218 40.909 0.00 0.00 0.00 3.01
326 327 2.290008 TGCCCACACATATTGAAGTCGT 60.290 45.455 0.00 0.00 0.00 4.34
380 381 9.897744 TTTCTAAATTGCTAACTCACATTTCAG 57.102 29.630 0.00 0.00 0.00 3.02
384 385 8.579682 AAATTGCTAACTCACATTTCAGTTTC 57.420 30.769 0.00 0.00 34.60 2.78
442 443 7.552459 ACACTTTCTCTCTATTTCCTTAGAGC 58.448 38.462 4.05 0.00 43.24 4.09
472 473 5.394562 AGAGCTGCCTATTATTCCCTTTT 57.605 39.130 0.00 0.00 0.00 2.27
495 496 8.893563 TTTTTATGAGACCAGTTATCCCATTT 57.106 30.769 0.00 0.00 0.00 2.32
496 497 8.893563 TTTTATGAGACCAGTTATCCCATTTT 57.106 30.769 0.00 0.00 0.00 1.82
497 498 9.983024 TTTTATGAGACCAGTTATCCCATTTTA 57.017 29.630 0.00 0.00 0.00 1.52
500 501 7.880160 TGAGACCAGTTATCCCATTTTATTG 57.120 36.000 0.00 0.00 0.00 1.90
501 502 7.638444 TGAGACCAGTTATCCCATTTTATTGA 58.362 34.615 0.00 0.00 0.00 2.57
502 503 7.556275 TGAGACCAGTTATCCCATTTTATTGAC 59.444 37.037 0.00 0.00 0.00 3.18
503 504 7.410174 AGACCAGTTATCCCATTTTATTGACA 58.590 34.615 0.00 0.00 0.00 3.58
504 505 7.339466 AGACCAGTTATCCCATTTTATTGACAC 59.661 37.037 0.00 0.00 0.00 3.67
505 506 6.094881 ACCAGTTATCCCATTTTATTGACACG 59.905 38.462 0.00 0.00 0.00 4.49
506 507 6.094881 CCAGTTATCCCATTTTATTGACACGT 59.905 38.462 0.00 0.00 0.00 4.49
507 508 6.966632 CAGTTATCCCATTTTATTGACACGTG 59.033 38.462 15.48 15.48 0.00 4.49
508 509 6.882140 AGTTATCCCATTTTATTGACACGTGA 59.118 34.615 25.01 0.00 0.00 4.35
509 510 7.556275 AGTTATCCCATTTTATTGACACGTGAT 59.444 33.333 25.01 8.10 0.00 3.06
510 511 5.559427 TCCCATTTTATTGACACGTGATG 57.441 39.130 25.01 12.32 0.00 3.07
511 512 4.104776 CCCATTTTATTGACACGTGATGC 58.895 43.478 25.01 11.53 0.00 3.91
512 513 4.380339 CCCATTTTATTGACACGTGATGCA 60.380 41.667 25.01 14.11 0.00 3.96
513 514 4.558470 CCATTTTATTGACACGTGATGCAC 59.442 41.667 25.01 8.35 0.00 4.57
524 525 2.839629 TGATGCACGTGGATCACAC 58.160 52.632 38.71 20.95 45.80 3.82
532 533 2.839629 GTGGATCACACGTGCATGA 58.160 52.632 17.22 13.57 40.85 3.07
533 534 0.443869 GTGGATCACACGTGCATGAC 59.556 55.000 17.22 7.65 40.85 3.06
534 535 0.321346 TGGATCACACGTGCATGACT 59.679 50.000 17.22 3.43 0.00 3.41
535 536 0.723414 GGATCACACGTGCATGACTG 59.277 55.000 17.22 5.26 0.00 3.51
556 557 6.831769 ACTGCTAGTCAACAAATTGTAATCG 58.168 36.000 0.00 0.00 37.11 3.34
557 558 6.128282 ACTGCTAGTCAACAAATTGTAATCGG 60.128 38.462 0.00 0.00 37.11 4.18
558 559 5.703592 TGCTAGTCAACAAATTGTAATCGGT 59.296 36.000 0.00 0.00 37.11 4.69
559 560 6.205853 TGCTAGTCAACAAATTGTAATCGGTT 59.794 34.615 0.00 0.00 37.11 4.44
560 561 6.523201 GCTAGTCAACAAATTGTAATCGGTTG 59.477 38.462 0.00 11.80 37.11 3.77
561 562 6.385649 AGTCAACAAATTGTAATCGGTTGT 57.614 33.333 0.00 5.01 37.11 3.32
562 563 7.499321 AGTCAACAAATTGTAATCGGTTGTA 57.501 32.000 0.00 5.86 37.11 2.41
563 564 8.106247 AGTCAACAAATTGTAATCGGTTGTAT 57.894 30.769 0.00 7.53 37.11 2.29
564 565 9.221933 AGTCAACAAATTGTAATCGGTTGTATA 57.778 29.630 0.00 1.99 37.11 1.47
565 566 9.997482 GTCAACAAATTGTAATCGGTTGTATAT 57.003 29.630 0.00 0.00 37.11 0.86
569 570 9.796120 ACAAATTGTAATCGGTTGTATATTTGG 57.204 29.630 16.94 6.56 35.73 3.28
570 571 9.796120 CAAATTGTAATCGGTTGTATATTTGGT 57.204 29.630 0.00 0.00 30.71 3.67
572 573 8.974060 ATTGTAATCGGTTGTATATTTGGTCT 57.026 30.769 0.00 0.00 0.00 3.85
573 574 8.428186 TTGTAATCGGTTGTATATTTGGTCTC 57.572 34.615 0.00 0.00 0.00 3.36
574 575 6.987992 TGTAATCGGTTGTATATTTGGTCTCC 59.012 38.462 0.00 0.00 0.00 3.71
575 576 5.623956 ATCGGTTGTATATTTGGTCTCCA 57.376 39.130 0.00 0.00 0.00 3.86
576 577 5.423704 TCGGTTGTATATTTGGTCTCCAA 57.576 39.130 0.00 0.00 42.29 3.53
589 590 6.503589 TTGGTCTCCAAAATAAATACCACG 57.496 37.500 0.00 0.00 40.92 4.94
590 591 5.562635 TGGTCTCCAAAATAAATACCACGT 58.437 37.500 0.00 0.00 30.84 4.49
591 592 6.709281 TGGTCTCCAAAATAAATACCACGTA 58.291 36.000 0.00 0.00 30.84 3.57
592 593 7.166851 TGGTCTCCAAAATAAATACCACGTAA 58.833 34.615 0.00 0.00 30.84 3.18
593 594 7.664731 TGGTCTCCAAAATAAATACCACGTAAA 59.335 33.333 0.00 0.00 30.84 2.01
594 595 8.513774 GGTCTCCAAAATAAATACCACGTAAAA 58.486 33.333 0.00 0.00 0.00 1.52
595 596 9.333497 GTCTCCAAAATAAATACCACGTAAAAC 57.667 33.333 0.00 0.00 0.00 2.43
606 607 3.756434 ACCACGTAAAACAATGATCAGGG 59.244 43.478 0.09 0.00 0.00 4.45
615 616 9.191995 GTAAAACAATGATCAGGGTTTTAACAG 57.808 33.333 29.73 4.97 43.32 3.16
621 622 6.817765 TGATCAGGGTTTTAACAGTTGATC 57.182 37.500 17.23 17.23 39.41 2.92
624 625 5.640147 TCAGGGTTTTAACAGTTGATCCAT 58.360 37.500 0.00 0.00 0.00 3.41
628 629 6.434340 AGGGTTTTAACAGTTGATCCATCTTC 59.566 38.462 0.00 0.00 0.00 2.87
648 649 4.337985 TCGTCAGACAATAGTTCGTCTC 57.662 45.455 0.41 0.00 40.50 3.36
650 651 3.119955 CGTCAGACAATAGTTCGTCTCCA 60.120 47.826 0.41 0.00 40.50 3.86
651 652 4.416620 GTCAGACAATAGTTCGTCTCCAG 58.583 47.826 0.00 0.00 40.50 3.86
659 660 3.584406 AGTTCGTCTCCAGTTCATGAG 57.416 47.619 0.00 0.00 0.00 2.90
671 672 2.624838 AGTTCATGAGCAAACCAACAGG 59.375 45.455 12.41 0.00 0.00 4.00
740 770 8.298854 TGAAGATCATAAAACTTTGTGTGGATG 58.701 33.333 0.00 0.00 32.07 3.51
741 771 6.624423 AGATCATAAAACTTTGTGTGGATGC 58.376 36.000 0.00 0.00 32.07 3.91
753 783 8.752187 ACTTTGTGTGGATGCATATAAGAAATT 58.248 29.630 0.00 0.00 0.00 1.82
754 784 8.929827 TTTGTGTGGATGCATATAAGAAATTG 57.070 30.769 0.00 0.00 0.00 2.32
809 839 5.356882 TGAATTCAGTTAGGCGTGAAAAG 57.643 39.130 3.38 0.00 36.31 2.27
831 861 2.316108 TGTGCCAAGACTAGACAGACA 58.684 47.619 0.00 0.00 0.00 3.41
840 870 7.360438 GCCAAGACTAGACAGACACTAATTTTG 60.360 40.741 0.00 0.00 0.00 2.44
846 904 6.808008 AGACAGACACTAATTTTGTCATGG 57.192 37.500 17.58 11.11 45.00 3.66
855 913 4.806640 AATTTTGTCATGGTTAGCCCTG 57.193 40.909 0.00 0.00 0.00 4.45
1013 1088 4.537965 ACGACATCGATGCTATCAAGTAC 58.462 43.478 25.11 3.65 43.02 2.73
1014 1089 4.036380 ACGACATCGATGCTATCAAGTACA 59.964 41.667 25.11 0.00 43.02 2.90
1015 1090 4.614702 CGACATCGATGCTATCAAGTACAG 59.385 45.833 25.11 0.00 43.02 2.74
1016 1091 5.560953 CGACATCGATGCTATCAAGTACAGA 60.561 44.000 25.11 0.00 43.02 3.41
1017 1092 5.767269 ACATCGATGCTATCAAGTACAGAG 58.233 41.667 25.11 0.00 0.00 3.35
1018 1093 4.230314 TCGATGCTATCAAGTACAGAGC 57.770 45.455 0.00 0.00 0.00 4.09
1019 1094 3.004839 TCGATGCTATCAAGTACAGAGCC 59.995 47.826 0.00 0.00 31.98 4.70
1029 1104 0.459489 GTACAGAGCCAGAGCAGGAG 59.541 60.000 0.00 0.00 43.56 3.69
1042 1117 1.691195 GCAGGAGGGAGAAGTAGGGC 61.691 65.000 0.00 0.00 0.00 5.19
1045 1120 1.758906 GAGGGAGAAGTAGGGCGCT 60.759 63.158 7.64 8.86 0.00 5.92
1048 1123 1.740905 GGAGAAGTAGGGCGCTACC 59.259 63.158 30.88 19.61 37.93 3.18
1050 1125 1.077212 AGAAGTAGGGCGCTACCGA 60.077 57.895 30.88 1.91 40.62 4.69
1071 1146 1.927895 CTCAACGGATAGGACAGTGC 58.072 55.000 0.00 0.00 0.00 4.40
1072 1147 1.204704 CTCAACGGATAGGACAGTGCA 59.795 52.381 0.00 0.00 0.00 4.57
1083 1158 1.512926 GACAGTGCACCACTAACCTG 58.487 55.000 14.63 4.99 43.43 4.00
1112 1202 2.830370 GCCATGGAAGAAGGGCGG 60.830 66.667 18.40 0.00 36.58 6.13
1129 1219 3.327404 GGACGGGAAGGAGGCCAA 61.327 66.667 5.01 0.00 0.00 4.52
1138 1228 1.206849 GAAGGAGGCCAAGTCTGAGAG 59.793 57.143 5.01 0.00 0.00 3.20
1156 1246 3.319198 TTCAGAGGACCGGGGCAC 61.319 66.667 6.32 0.00 0.00 5.01
1258 1614 4.812476 TCACCATCGCCTTCGCCG 62.812 66.667 0.00 0.00 35.26 6.46
1336 1695 4.870221 TGAAATGTGATGCGATCAGAAG 57.130 40.909 0.00 0.00 40.53 2.85
1359 1748 7.251704 AGCACTGTAGATTATCCGAAAAATG 57.748 36.000 0.00 0.00 0.00 2.32
1361 1750 7.011482 AGCACTGTAGATTATCCGAAAAATGTC 59.989 37.037 0.00 0.00 0.00 3.06
1408 1797 4.421515 CTGGCTCAGGTGCTGGGG 62.422 72.222 0.00 0.00 31.62 4.96
1578 1967 0.956633 ACGGACGACAGAGCAGTAAA 59.043 50.000 0.00 0.00 0.00 2.01
1663 2101 0.536006 AGCTCTTGCAGGTTGGTGAC 60.536 55.000 0.00 0.00 42.74 3.67
1772 2237 4.838423 TGATCTTACCTCAAACTCCTGACA 59.162 41.667 0.00 0.00 0.00 3.58
1951 2429 2.472029 CCTGGACCTACAACCTCATCT 58.528 52.381 0.00 0.00 0.00 2.90
1960 2438 1.613630 AACCTCATCTGGCTCCCGT 60.614 57.895 0.00 0.00 0.00 5.28
2038 2516 9.958125 AAGGGATTAAAATTAGGAGATGGAAAT 57.042 29.630 0.00 0.00 0.00 2.17
2052 2530 9.223099 AGGAGATGGAAATTTTGCTTTAATTTG 57.777 29.630 2.25 0.00 35.83 2.32
2053 2531 9.218440 GGAGATGGAAATTTTGCTTTAATTTGA 57.782 29.630 2.25 0.00 35.83 2.69
2055 2533 9.002600 AGATGGAAATTTTGCTTTAATTTGACC 57.997 29.630 2.25 5.88 35.83 4.02
2067 2545 1.560505 ATTTGACCCCAGTGGCAATC 58.439 50.000 2.61 0.92 37.83 2.67
2069 2547 0.409092 TTGACCCCAGTGGCAATCAT 59.591 50.000 2.61 0.00 37.83 2.45
2090 2568 8.750515 ATCATATTGTGATGTTACATGGTGAA 57.249 30.769 1.24 0.00 45.76 3.18
2101 2579 9.289303 GATGTTACATGGTGAAAAATGTACATC 57.711 33.333 9.23 14.87 38.62 3.06
2115 2593 1.940613 GTACATCCGCATGGGTCTTTC 59.059 52.381 9.14 0.00 37.00 2.62
2116 2594 0.620556 ACATCCGCATGGGTCTTTCT 59.379 50.000 9.14 0.00 37.00 2.52
2125 2605 4.642429 GCATGGGTCTTTCTACCGATAAT 58.358 43.478 0.00 0.00 40.73 1.28
2137 2617 2.561478 CCGATAATCCCGGTTCCAAT 57.439 50.000 0.00 0.00 41.91 3.16
2138 2618 3.688694 CCGATAATCCCGGTTCCAATA 57.311 47.619 0.00 0.00 41.91 1.90
2141 2621 5.007682 CCGATAATCCCGGTTCCAATAAAT 58.992 41.667 0.00 0.00 41.91 1.40
2156 2639 5.541868 TCCAATAAATGCTCCTTTGTTTCCA 59.458 36.000 0.00 0.00 0.00 3.53
2336 2825 2.430367 GCGAGTTGGTCCCCAGTT 59.570 61.111 0.00 0.00 33.81 3.16
2339 2828 1.966451 GAGTTGGTCCCCAGTTGCG 60.966 63.158 0.00 0.00 33.81 4.85
2431 2926 4.303282 GGCTAAATTTCGGCAAACTTTGA 58.697 39.130 10.88 0.00 0.00 2.69
2557 3064 2.188207 GCGGCCTTCTCCTCCTTC 59.812 66.667 0.00 0.00 0.00 3.46
2558 3065 2.363172 GCGGCCTTCTCCTCCTTCT 61.363 63.158 0.00 0.00 0.00 2.85
2559 3066 1.904990 GCGGCCTTCTCCTCCTTCTT 61.905 60.000 0.00 0.00 0.00 2.52
2737 3253 1.907739 CCTCGCCATCTTCAGGGAA 59.092 57.895 0.00 0.00 0.00 3.97
2812 3329 2.363795 TCTTCACGGCGGGGAGAT 60.364 61.111 17.99 0.00 0.00 2.75
2861 3378 0.966179 GGGTCCGTTTTTGGCTTGAT 59.034 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.823304 GCAGAATGGATGGTTCCTTATCC 59.177 47.826 0.00 0.00 43.07 2.59
8 9 1.683011 CCGCAGAATGGATGGTTCCTT 60.683 52.381 0.00 0.00 43.07 3.36
10 11 0.394352 ACCGCAGAATGGATGGTTCC 60.394 55.000 0.00 0.00 42.94 3.62
16 17 3.668447 GTCATATCACCGCAGAATGGAT 58.332 45.455 0.00 0.00 35.86 3.41
24 25 1.607148 CCTAGTCGTCATATCACCGCA 59.393 52.381 0.00 0.00 0.00 5.69
39 40 1.368558 ACACCCCATAAGACCCCTAGT 59.631 52.381 0.00 0.00 0.00 2.57
56 57 8.942338 TTAGATGTCACATTATTACCTCACAC 57.058 34.615 0.00 0.00 0.00 3.82
119 120 7.372714 ACGCGTATGTAATCTGTATGGAAATA 58.627 34.615 11.67 0.00 0.00 1.40
125 126 4.552276 CCGTACGCGTATGTAATCTGTATG 59.448 45.833 30.66 12.29 36.15 2.39
133 134 2.627863 ACAACCGTACGCGTATGTAA 57.372 45.000 30.66 6.13 34.69 2.41
140 141 4.132529 TGTCTATATACAACCGTACGCG 57.867 45.455 10.49 3.53 37.95 6.01
186 187 3.921119 TGGACTGCATACAAAGCAAAG 57.079 42.857 0.00 0.00 42.17 2.77
190 191 7.496529 TTCTAATATGGACTGCATACAAAGC 57.503 36.000 0.00 0.00 0.00 3.51
191 192 9.499479 AGATTCTAATATGGACTGCATACAAAG 57.501 33.333 0.00 0.00 0.00 2.77
193 194 9.851686 AAAGATTCTAATATGGACTGCATACAA 57.148 29.630 0.00 0.00 0.00 2.41
221 222 7.311109 CCCTCCGTTCCTATATATAAGGCTTTT 60.311 40.741 4.45 0.00 33.84 2.27
234 235 3.684408 ACTTACTCCCTCCGTTCCTAT 57.316 47.619 0.00 0.00 0.00 2.57
352 353 9.899226 GAAATGTGAGTTAGCAATTTAGAAACT 57.101 29.630 0.00 0.00 33.26 2.66
369 370 5.527214 TGTGTGGTAGAAACTGAAATGTGAG 59.473 40.000 0.00 0.00 0.00 3.51
380 381 6.036626 CCAAATTTTGGTTGTGTGGTAGAAAC 59.963 38.462 18.34 0.00 45.93 2.78
475 476 8.281531 TCAATAAAATGGGATAACTGGTCTCAT 58.718 33.333 0.00 0.00 38.41 2.90
476 477 7.556275 GTCAATAAAATGGGATAACTGGTCTCA 59.444 37.037 0.00 0.00 0.00 3.27
477 478 7.556275 TGTCAATAAAATGGGATAACTGGTCTC 59.444 37.037 0.00 0.00 0.00 3.36
478 479 7.339466 GTGTCAATAAAATGGGATAACTGGTCT 59.661 37.037 0.00 0.00 0.00 3.85
479 480 7.480810 GTGTCAATAAAATGGGATAACTGGTC 58.519 38.462 0.00 0.00 0.00 4.02
480 481 6.094881 CGTGTCAATAAAATGGGATAACTGGT 59.905 38.462 0.00 0.00 0.00 4.00
481 482 6.094881 ACGTGTCAATAAAATGGGATAACTGG 59.905 38.462 0.00 0.00 0.00 4.00
482 483 6.966632 CACGTGTCAATAAAATGGGATAACTG 59.033 38.462 7.58 0.00 0.00 3.16
483 484 6.882140 TCACGTGTCAATAAAATGGGATAACT 59.118 34.615 16.51 0.00 0.00 2.24
484 485 7.079182 TCACGTGTCAATAAAATGGGATAAC 57.921 36.000 16.51 0.00 0.00 1.89
487 488 5.450412 GCATCACGTGTCAATAAAATGGGAT 60.450 40.000 16.51 0.00 0.00 3.85
488 489 4.142491 GCATCACGTGTCAATAAAATGGGA 60.142 41.667 16.51 0.00 0.00 4.37
489 490 4.104776 GCATCACGTGTCAATAAAATGGG 58.895 43.478 16.51 0.00 0.00 4.00
490 491 4.558470 GTGCATCACGTGTCAATAAAATGG 59.442 41.667 16.51 0.00 0.00 3.16
491 492 5.669535 GTGCATCACGTGTCAATAAAATG 57.330 39.130 16.51 10.11 0.00 2.32
505 506 0.443869 GTGTGATCCACGTGCATCAC 59.556 55.000 35.26 35.26 46.26 3.06
506 507 2.839629 GTGTGATCCACGTGCATCA 58.160 52.632 18.16 18.16 37.14 3.07
514 515 0.443869 GTCATGCACGTGTGATCCAC 59.556 55.000 18.38 3.26 40.89 4.02
515 516 0.321346 AGTCATGCACGTGTGATCCA 59.679 50.000 18.38 6.33 0.00 3.41
516 517 0.723414 CAGTCATGCACGTGTGATCC 59.277 55.000 18.38 3.27 0.00 3.36
531 532 6.955963 CGATTACAATTTGTTGACTAGCAGTC 59.044 38.462 7.45 8.75 45.26 3.51
532 533 6.128282 CCGATTACAATTTGTTGACTAGCAGT 60.128 38.462 7.45 0.00 0.00 4.40
533 534 6.128282 ACCGATTACAATTTGTTGACTAGCAG 60.128 38.462 7.45 0.00 0.00 4.24
534 535 5.703592 ACCGATTACAATTTGTTGACTAGCA 59.296 36.000 7.45 0.00 0.00 3.49
535 536 6.178239 ACCGATTACAATTTGTTGACTAGC 57.822 37.500 7.45 0.00 0.00 3.42
536 537 7.581476 ACAACCGATTACAATTTGTTGACTAG 58.419 34.615 7.45 0.00 35.52 2.57
537 538 7.499321 ACAACCGATTACAATTTGTTGACTA 57.501 32.000 7.45 0.00 35.52 2.59
538 539 6.385649 ACAACCGATTACAATTTGTTGACT 57.614 33.333 7.45 0.00 35.52 3.41
539 540 9.997482 ATATACAACCGATTACAATTTGTTGAC 57.003 29.630 7.45 0.00 35.52 3.18
543 544 9.796120 CCAAATATACAACCGATTACAATTTGT 57.204 29.630 7.30 7.30 32.55 2.83
544 545 9.796120 ACCAAATATACAACCGATTACAATTTG 57.204 29.630 0.00 0.00 33.64 2.32
546 547 9.403583 AGACCAAATATACAACCGATTACAATT 57.596 29.630 0.00 0.00 0.00 2.32
547 548 8.974060 AGACCAAATATACAACCGATTACAAT 57.026 30.769 0.00 0.00 0.00 2.71
548 549 7.496591 GGAGACCAAATATACAACCGATTACAA 59.503 37.037 0.00 0.00 0.00 2.41
549 550 6.987992 GGAGACCAAATATACAACCGATTACA 59.012 38.462 0.00 0.00 0.00 2.41
550 551 6.987992 TGGAGACCAAATATACAACCGATTAC 59.012 38.462 0.00 0.00 0.00 1.89
551 552 7.127012 TGGAGACCAAATATACAACCGATTA 57.873 36.000 0.00 0.00 0.00 1.75
552 553 5.996644 TGGAGACCAAATATACAACCGATT 58.003 37.500 0.00 0.00 0.00 3.34
553 554 5.623956 TGGAGACCAAATATACAACCGAT 57.376 39.130 0.00 0.00 0.00 4.18
554 555 5.423704 TTGGAGACCAAATATACAACCGA 57.576 39.130 0.43 0.00 40.92 4.69
566 567 6.005198 ACGTGGTATTTATTTTGGAGACCAA 58.995 36.000 0.00 0.00 42.29 3.67
567 568 5.562635 ACGTGGTATTTATTTTGGAGACCA 58.437 37.500 0.00 0.00 33.18 4.02
568 569 7.614124 TTACGTGGTATTTATTTTGGAGACC 57.386 36.000 0.00 0.00 0.00 3.85
569 570 9.333497 GTTTTACGTGGTATTTATTTTGGAGAC 57.667 33.333 0.00 0.00 0.00 3.36
570 571 9.064706 TGTTTTACGTGGTATTTATTTTGGAGA 57.935 29.630 0.00 0.00 0.00 3.71
571 572 9.680315 TTGTTTTACGTGGTATTTATTTTGGAG 57.320 29.630 0.00 0.00 0.00 3.86
579 580 8.670135 CCTGATCATTGTTTTACGTGGTATTTA 58.330 33.333 0.00 0.00 0.00 1.40
580 581 7.362574 CCCTGATCATTGTTTTACGTGGTATTT 60.363 37.037 0.00 0.00 0.00 1.40
581 582 6.094881 CCCTGATCATTGTTTTACGTGGTATT 59.905 38.462 0.00 0.00 0.00 1.89
582 583 5.588648 CCCTGATCATTGTTTTACGTGGTAT 59.411 40.000 0.00 0.00 0.00 2.73
583 584 4.938832 CCCTGATCATTGTTTTACGTGGTA 59.061 41.667 0.00 0.00 0.00 3.25
584 585 3.756434 CCCTGATCATTGTTTTACGTGGT 59.244 43.478 0.00 0.00 0.00 4.16
585 586 3.756434 ACCCTGATCATTGTTTTACGTGG 59.244 43.478 0.00 0.00 0.00 4.94
586 587 5.371115 AACCCTGATCATTGTTTTACGTG 57.629 39.130 0.00 0.00 0.00 4.49
587 588 6.399639 AAAACCCTGATCATTGTTTTACGT 57.600 33.333 23.44 8.88 38.68 3.57
588 589 7.863375 TGTTAAAACCCTGATCATTGTTTTACG 59.137 33.333 26.35 4.63 40.73 3.18
589 590 9.191995 CTGTTAAAACCCTGATCATTGTTTTAC 57.808 33.333 26.35 22.48 40.73 2.01
590 591 8.919145 ACTGTTAAAACCCTGATCATTGTTTTA 58.081 29.630 24.50 24.50 40.35 1.52
591 592 7.791029 ACTGTTAAAACCCTGATCATTGTTTT 58.209 30.769 25.86 25.86 41.99 2.43
592 593 7.360113 ACTGTTAAAACCCTGATCATTGTTT 57.640 32.000 13.93 13.93 32.62 2.83
593 594 6.976934 ACTGTTAAAACCCTGATCATTGTT 57.023 33.333 0.00 0.00 0.00 2.83
594 595 6.549364 TCAACTGTTAAAACCCTGATCATTGT 59.451 34.615 0.00 0.00 0.00 2.71
595 596 6.980593 TCAACTGTTAAAACCCTGATCATTG 58.019 36.000 0.00 0.00 0.00 2.82
606 607 6.899114 ACGAAGATGGATCAACTGTTAAAAC 58.101 36.000 0.00 0.00 0.00 2.43
615 616 3.849911 TGTCTGACGAAGATGGATCAAC 58.150 45.455 2.98 0.00 37.23 3.18
621 622 4.500837 CGAACTATTGTCTGACGAAGATGG 59.499 45.833 1.10 0.00 37.23 3.51
624 625 4.454847 AGACGAACTATTGTCTGACGAAGA 59.545 41.667 1.10 0.00 46.52 2.87
648 649 2.361757 TGTTGGTTTGCTCATGAACTGG 59.638 45.455 0.00 0.00 0.00 4.00
650 651 2.624838 CCTGTTGGTTTGCTCATGAACT 59.375 45.455 0.00 0.00 0.00 3.01
651 652 2.362077 ACCTGTTGGTTTGCTCATGAAC 59.638 45.455 0.00 0.00 46.05 3.18
659 660 1.006086 GTTTGCACCTGTTGGTTTGC 58.994 50.000 0.00 0.00 46.05 3.68
711 714 8.298854 CCACACAAAGTTTTATGATCTTCATGA 58.701 33.333 0.00 0.00 37.70 3.07
716 719 7.092716 GCATCCACACAAAGTTTTATGATCTT 58.907 34.615 4.06 0.00 0.00 2.40
725 755 7.701539 TCTTATATGCATCCACACAAAGTTT 57.298 32.000 0.19 0.00 0.00 2.66
789 819 5.067283 ACAACTTTTCACGCCTAACTGAATT 59.933 36.000 0.00 0.00 0.00 2.17
831 861 5.580022 AGGGCTAACCATGACAAAATTAGT 58.420 37.500 0.00 0.00 43.89 2.24
846 904 0.322546 CTCAACCACCCAGGGCTAAC 60.323 60.000 4.91 0.00 43.89 2.34
855 913 1.232119 CGTAACCAACTCAACCACCC 58.768 55.000 0.00 0.00 0.00 4.61
969 1037 9.217278 GTCGTTCAAGAGTATGTATATCTCCTA 57.783 37.037 0.00 0.00 0.00 2.94
1013 1088 2.733669 CCCTCCTGCTCTGGCTCTG 61.734 68.421 0.00 0.00 39.59 3.35
1014 1089 2.365370 CCCTCCTGCTCTGGCTCT 60.365 66.667 0.00 0.00 39.59 4.09
1015 1090 2.364842 TCCCTCCTGCTCTGGCTC 60.365 66.667 0.00 0.00 39.59 4.70
1016 1091 2.365370 CTCCCTCCTGCTCTGGCT 60.365 66.667 0.00 0.00 39.59 4.75
1017 1092 1.970352 CTTCTCCCTCCTGCTCTGGC 61.970 65.000 0.00 0.00 39.26 4.85
1018 1093 0.617249 ACTTCTCCCTCCTGCTCTGG 60.617 60.000 0.00 0.00 0.00 3.86
1019 1094 2.031120 CTACTTCTCCCTCCTGCTCTG 58.969 57.143 0.00 0.00 0.00 3.35
1029 1104 1.740905 GTAGCGCCCTACTTCTCCC 59.259 63.158 2.29 0.00 40.63 4.30
1045 1120 1.134007 TCCTATCCGTTGAGCTCGGTA 60.134 52.381 9.64 2.50 46.86 4.02
1048 1123 0.738975 TGTCCTATCCGTTGAGCTCG 59.261 55.000 9.64 0.00 0.00 5.03
1050 1125 1.478510 CACTGTCCTATCCGTTGAGCT 59.521 52.381 0.00 0.00 0.00 4.09
1061 1136 1.621814 GGTTAGTGGTGCACTGTCCTA 59.378 52.381 17.98 8.74 45.01 2.94
1071 1146 1.604693 GGTGTCGTCAGGTTAGTGGTG 60.605 57.143 0.00 0.00 0.00 4.17
1072 1147 0.677842 GGTGTCGTCAGGTTAGTGGT 59.322 55.000 0.00 0.00 0.00 4.16
1083 1158 2.509336 CATGGCTCCGGTGTCGTC 60.509 66.667 0.00 0.00 33.95 4.20
1112 1202 3.327404 TTGGCCTCCTTCCCGTCC 61.327 66.667 3.32 0.00 0.00 4.79
1117 1207 0.251634 CTCAGACTTGGCCTCCTTCC 59.748 60.000 3.32 0.00 0.00 3.46
1138 1228 3.319198 TGCCCCGGTCCTCTGAAC 61.319 66.667 0.00 0.00 0.00 3.18
1156 1246 2.880879 CCACACGACGCAGATCCG 60.881 66.667 0.00 0.00 0.00 4.18
1336 1695 7.011482 AGACATTTTTCGGATAATCTACAGTGC 59.989 37.037 0.00 0.00 0.00 4.40
1359 1748 0.877071 CACCTGCAACACATCCAGAC 59.123 55.000 0.00 0.00 0.00 3.51
1361 1750 1.582968 GCACCTGCAACACATCCAG 59.417 57.895 0.00 0.00 41.59 3.86
1500 1889 3.665675 ATGAACTCGAGCGCCACCC 62.666 63.158 13.61 0.00 0.00 4.61
1622 2015 5.118357 GCTATCACATATCAGCAGAAGTTCG 59.882 44.000 0.00 0.00 34.13 3.95
1663 2101 1.302033 AACTGCGAGACCAGCCAAG 60.302 57.895 0.00 0.00 36.29 3.61
1731 2169 4.645136 AGATCAAGACCACGTCTATGCTTA 59.355 41.667 0.00 0.00 42.59 3.09
1772 2237 1.725641 ATGCAACGTCGACATGTCAT 58.274 45.000 24.93 16.21 0.00 3.06
1960 2438 1.971505 CTCCTGGCGATGGGCTTGTA 61.972 60.000 2.36 0.00 42.94 2.41
1998 2476 0.970937 TCCCTTACAGCGGTCTGAGG 60.971 60.000 0.00 0.00 42.95 3.86
2030 2508 8.236586 GGGTCAAATTAAAGCAAAATTTCCATC 58.763 33.333 0.00 0.00 35.00 3.51
2031 2509 7.176515 GGGGTCAAATTAAAGCAAAATTTCCAT 59.823 33.333 0.00 0.00 35.00 3.41
2038 2516 5.363939 CACTGGGGTCAAATTAAAGCAAAA 58.636 37.500 0.00 0.00 0.00 2.44
2049 2527 0.187117 TGATTGCCACTGGGGTCAAA 59.813 50.000 9.31 0.00 39.65 2.69
2050 2528 0.409092 ATGATTGCCACTGGGGTCAA 59.591 50.000 7.98 7.98 39.65 3.18
2051 2529 1.294041 TATGATTGCCACTGGGGTCA 58.706 50.000 0.00 0.00 39.65 4.02
2052 2530 2.624838 CAATATGATTGCCACTGGGGTC 59.375 50.000 0.00 0.00 39.65 4.46
2053 2531 2.024080 ACAATATGATTGCCACTGGGGT 60.024 45.455 0.00 0.00 39.65 4.95
2054 2532 2.363038 CACAATATGATTGCCACTGGGG 59.637 50.000 0.00 0.00 40.85 4.96
2055 2533 3.289836 TCACAATATGATTGCCACTGGG 58.710 45.455 0.00 0.00 29.99 4.45
2067 2545 9.636879 TTTTTCACCATGTAACATCACAATATG 57.363 29.630 0.00 0.00 30.84 1.78
2069 2547 9.636879 CATTTTTCACCATGTAACATCACAATA 57.363 29.630 0.00 0.00 30.84 1.90
2090 2568 2.687935 GACCCATGCGGATGTACATTTT 59.312 45.455 16.17 0.00 34.64 1.82
2101 2579 0.810031 CGGTAGAAAGACCCATGCGG 60.810 60.000 0.00 0.00 35.95 5.69
2125 2605 2.650322 GAGCATTTATTGGAACCGGGA 58.350 47.619 6.32 0.00 0.00 5.14
2130 2610 6.368791 GGAAACAAAGGAGCATTTATTGGAAC 59.631 38.462 0.00 0.00 0.00 3.62
2156 2639 7.687592 GCCAGATACTAATTTCATGGGCAAATT 60.688 37.037 8.23 8.23 37.27 1.82
2214 2698 4.032960 AGTTGTGATAACAAGGCATGGA 57.967 40.909 0.00 0.00 0.00 3.41
2389 2884 2.608546 CCGTGTTTAACCGAACTTCACA 59.391 45.455 7.36 0.00 0.00 3.58
2391 2886 1.598601 GCCGTGTTTAACCGAACTTCA 59.401 47.619 7.36 0.00 0.00 3.02
2431 2926 3.745975 CCGCCGAACATGTCAATATATGT 59.254 43.478 0.00 0.00 38.92 2.29
2485 2989 0.801067 GCGACTACTCGGCGTTCATT 60.801 55.000 6.85 0.00 40.53 2.57
2737 3253 3.211963 GAATGGGCGCGCAAGGAT 61.212 61.111 34.42 17.17 38.28 3.24
2812 3329 3.379445 GGTGAAGACGGAGCCGGA 61.379 66.667 5.05 0.00 44.69 5.14
2844 3361 3.308530 CTTCATCAAGCCAAAAACGGAC 58.691 45.455 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.