Multiple sequence alignment - TraesCS4D01G310900

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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 TraesCS4D01G310900 chr4D 100.000 4657 0 0 1 4657 477862833 477867489 0.000000e+00 8600
1 TraesCS4D01G310900 chr4B 95.587 3807 117 27 893 4657 604000802 604004599 0.000000e+00 6052
2 TraesCS4D01G310900 chr4B 85.526 836 34 20 66 853 603999789 604000585 0.000000e+00 793
3 TraesCS4D01G310900 chr1B 79.215 1121 186 26 1012 2091 1712984 1711870 0.000000e+00 736
4 TraesCS4D01G310900 chr1B 77.435 1232 222 40 999 2205 1953306 1954506 0.000000e+00 684
5 TraesCS4D01G310900 chr1B 75.080 943 189 35 3741 4657 1971382 1972304 9.390000e-107 398
6 TraesCS4D01G310900 chr1B 74.973 943 190 36 3741 4657 2303446 2302524 4.370000e-105 392
7 TraesCS4D01G310900 chr1B 73.403 955 187 44 3741 4657 2101884 2100959 1.270000e-75 294
8 TraesCS4D01G310900 chr1B 82.680 306 43 7 3093 3390 1710950 1710647 3.570000e-66 263
9 TraesCS4D01G310900 chr3A 84.588 571 75 8 948 1507 737796961 737797529 5.260000e-154 555
10 TraesCS4D01G310900 chr3A 75.873 945 178 37 3741 4657 737799756 737800678 1.990000e-118 436
11 TraesCS4D01G310900 chr3B 84.722 504 71 4 1015 1512 815476533 815477036 2.500000e-137 499
12 TraesCS4D01G310900 chr3B 75.636 944 185 37 3741 4657 815478549 815479474 1.200000e-115 427
13 TraesCS4D01G310900 chr3B 81.433 307 48 6 1601 1900 815477227 815477531 4.660000e-60 243
14 TraesCS4D01G310900 chr2B 76.497 885 157 29 1270 2131 1395585 1394729 7.160000e-118 435
15 TraesCS4D01G310900 chr5D 72.515 855 172 44 1031 1853 449040702 449039879 7.850000e-53 219
16 TraesCS4D01G310900 chr7D 71.734 934 206 42 3750 4657 18918496 18917595 4.720000e-50 209
17 TraesCS4D01G310900 chr5A 71.831 852 175 47 1031 1853 567926100 567925285 2.860000e-42 183
18 TraesCS4D01G310900 chrUn 77.344 256 54 3 1237 1490 252520813 252520560 1.040000e-31 148


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 TraesCS4D01G310900 chr4D 477862833 477867489 4656 False 8600.000000 8600 100.0000 1 4657 1 chr4D.!!$F1 4656
1 TraesCS4D01G310900 chr4B 603999789 604004599 4810 False 3422.500000 6052 90.5565 66 4657 2 chr4B.!!$F1 4591
2 TraesCS4D01G310900 chr1B 1953306 1954506 1200 False 684.000000 684 77.4350 999 2205 1 chr1B.!!$F1 1206
3 TraesCS4D01G310900 chr1B 1710647 1712984 2337 True 499.500000 736 80.9475 1012 3390 2 chr1B.!!$R3 2378
4 TraesCS4D01G310900 chr1B 1971382 1972304 922 False 398.000000 398 75.0800 3741 4657 1 chr1B.!!$F2 916
5 TraesCS4D01G310900 chr1B 2302524 2303446 922 True 392.000000 392 74.9730 3741 4657 1 chr1B.!!$R2 916
6 TraesCS4D01G310900 chr1B 2100959 2101884 925 True 294.000000 294 73.4030 3741 4657 1 chr1B.!!$R1 916
7 TraesCS4D01G310900 chr3A 737796961 737800678 3717 False 495.500000 555 80.2305 948 4657 2 chr3A.!!$F1 3709
8 TraesCS4D01G310900 chr3B 815476533 815479474 2941 False 389.666667 499 80.5970 1015 4657 3 chr3B.!!$F1 3642
9 TraesCS4D01G310900 chr2B 1394729 1395585 856 True 435.000000 435 76.4970 1270 2131 1 chr2B.!!$R1 861
10 TraesCS4D01G310900 chr5D 449039879 449040702 823 True 219.000000 219 72.5150 1031 1853 1 chr5D.!!$R1 822
11 TraesCS4D01G310900 chr7D 18917595 18918496 901 True 209.000000 209 71.7340 3750 4657 1 chr7D.!!$R1 907

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
879 1084 0.035458 ACTGTACCAAGTCAGCCAGC 59.965 55.0 0.0 0.0 35.37 4.85 F
2295 2793 0.035458 CTGGTCGGTCAAAGGCTTCT 59.965 55.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2854 3414 1.134220 TGGGTAATGAGAATGGACGCC 60.134 52.381 0.0 0.0 0.0 5.68 R
4031 4736 0.118346 TCCCAGCCACCTCCTCTAAA 59.882 55.000 0.0 0.0 0.0 1.85 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
35 36 4.150994 TTTTTCTTGCGCGGGTCT 57.849 50.000 8.83 0.00 0.00 3.85
36 37 1.652012 TTTTTCTTGCGCGGGTCTG 59.348 52.632 8.83 0.00 0.00 3.51
37 38 1.791103 TTTTTCTTGCGCGGGTCTGG 61.791 55.000 8.83 0.00 0.00 3.86
38 39 2.951475 TTTTCTTGCGCGGGTCTGGT 62.951 55.000 8.83 0.00 0.00 4.00
39 40 2.951475 TTTCTTGCGCGGGTCTGGTT 62.951 55.000 8.83 0.00 0.00 3.67
40 41 3.726517 CTTGCGCGGGTCTGGTTG 61.727 66.667 8.83 0.00 0.00 3.77
41 42 4.243008 TTGCGCGGGTCTGGTTGA 62.243 61.111 8.83 0.00 0.00 3.18
42 43 3.758973 TTGCGCGGGTCTGGTTGAA 62.759 57.895 8.83 0.00 0.00 2.69
43 44 3.723348 GCGCGGGTCTGGTTGAAC 61.723 66.667 8.83 0.00 0.00 3.18
56 57 3.399440 GGTTGAACCAAATCCATGCAA 57.601 42.857 9.98 0.00 38.42 4.08
57 58 3.066380 GGTTGAACCAAATCCATGCAAC 58.934 45.455 9.98 0.00 38.42 4.17
58 59 3.244181 GGTTGAACCAAATCCATGCAACT 60.244 43.478 9.98 0.00 38.42 3.16
59 60 4.021544 GGTTGAACCAAATCCATGCAACTA 60.022 41.667 9.98 0.00 38.42 2.24
60 61 5.510520 GGTTGAACCAAATCCATGCAACTAA 60.511 40.000 9.98 0.00 38.42 2.24
61 62 5.798125 TGAACCAAATCCATGCAACTAAA 57.202 34.783 0.00 0.00 0.00 1.85
62 63 6.166984 TGAACCAAATCCATGCAACTAAAA 57.833 33.333 0.00 0.00 0.00 1.52
63 64 6.222389 TGAACCAAATCCATGCAACTAAAAG 58.778 36.000 0.00 0.00 0.00 2.27
64 65 4.568956 ACCAAATCCATGCAACTAAAAGC 58.431 39.130 0.00 0.00 0.00 3.51
151 152 7.018769 TCCATGAGTAGATAATGGAGAATGGA 58.981 38.462 0.00 0.00 43.85 3.41
170 181 2.405172 GAGAAACTGGACACGGTTCTC 58.595 52.381 11.16 11.16 45.24 2.87
205 216 4.406972 TGACAGGTTGAAGATATCCTCCTG 59.593 45.833 18.81 18.81 45.41 3.86
225 236 4.022068 CCTGACCTCTCATATCTCAAGCTC 60.022 50.000 0.00 0.00 0.00 4.09
237 248 1.134175 CTCAAGCTCGAGTCTCCTTCC 59.866 57.143 15.13 0.00 0.00 3.46
239 250 0.251832 AAGCTCGAGTCTCCTTCCCA 60.252 55.000 15.13 0.00 0.00 4.37
290 301 2.651701 AGCTCGCGTCGACTTATATTG 58.348 47.619 14.70 0.00 0.00 1.90
388 422 3.684788 CCGGATCCAGTTTGTTCTAGTTG 59.315 47.826 13.41 0.00 0.00 3.16
389 423 3.125316 CGGATCCAGTTTGTTCTAGTTGC 59.875 47.826 13.41 0.00 0.00 4.17
390 424 4.327680 GGATCCAGTTTGTTCTAGTTGCT 58.672 43.478 6.95 0.00 0.00 3.91
392 426 5.938125 GGATCCAGTTTGTTCTAGTTGCTTA 59.062 40.000 6.95 0.00 0.00 3.09
394 428 4.748102 TCCAGTTTGTTCTAGTTGCTTACG 59.252 41.667 0.00 0.00 0.00 3.18
396 430 3.497262 AGTTTGTTCTAGTTGCTTACGGC 59.503 43.478 0.00 0.00 42.22 5.68
398 432 2.683968 TGTTCTAGTTGCTTACGGCTG 58.316 47.619 0.00 0.00 42.39 4.85
399 433 2.036733 TGTTCTAGTTGCTTACGGCTGT 59.963 45.455 2.42 2.42 42.39 4.40
400 434 2.363788 TCTAGTTGCTTACGGCTGTG 57.636 50.000 8.92 0.00 42.39 3.66
401 435 1.067142 TCTAGTTGCTTACGGCTGTGG 60.067 52.381 8.92 2.08 42.39 4.17
413 459 1.160137 GGCTGTGGTCACTGAATCAC 58.840 55.000 11.31 6.77 32.81 3.06
414 460 1.271054 GGCTGTGGTCACTGAATCACT 60.271 52.381 11.31 0.00 32.81 3.41
417 463 2.221169 TGTGGTCACTGAATCACTTGC 58.779 47.619 12.35 0.00 0.00 4.01
418 464 2.221169 GTGGTCACTGAATCACTTGCA 58.779 47.619 6.55 0.00 0.00 4.08
419 465 2.816087 GTGGTCACTGAATCACTTGCAT 59.184 45.455 0.00 0.00 0.00 3.96
420 466 4.002982 GTGGTCACTGAATCACTTGCATA 58.997 43.478 0.00 0.00 0.00 3.14
456 502 6.072508 GGTGATTTGTGTGATTCTTCTGCTAA 60.073 38.462 0.00 0.00 0.00 3.09
457 503 7.362401 GGTGATTTGTGTGATTCTTCTGCTAAT 60.362 37.037 0.00 0.00 0.00 1.73
458 504 8.668353 GTGATTTGTGTGATTCTTCTGCTAATA 58.332 33.333 0.00 0.00 0.00 0.98
459 505 8.886719 TGATTTGTGTGATTCTTCTGCTAATAG 58.113 33.333 0.00 0.00 0.00 1.73
460 506 9.102757 GATTTGTGTGATTCTTCTGCTAATAGA 57.897 33.333 0.00 0.00 0.00 1.98
461 507 8.846943 TTTGTGTGATTCTTCTGCTAATAGAA 57.153 30.769 0.00 0.00 35.51 2.10
462 508 8.846943 TTGTGTGATTCTTCTGCTAATAGAAA 57.153 30.769 0.00 0.00 36.34 2.52
463 509 8.256611 TGTGTGATTCTTCTGCTAATAGAAAC 57.743 34.615 0.00 0.00 36.34 2.78
464 510 8.097038 TGTGTGATTCTTCTGCTAATAGAAACT 58.903 33.333 0.00 0.00 36.34 2.66
465 511 8.386606 GTGTGATTCTTCTGCTAATAGAAACTG 58.613 37.037 0.00 0.00 36.34 3.16
466 512 7.065085 TGTGATTCTTCTGCTAATAGAAACTGC 59.935 37.037 0.00 0.00 36.34 4.40
467 513 7.065085 GTGATTCTTCTGCTAATAGAAACTGCA 59.935 37.037 0.00 0.00 36.34 4.41
468 514 7.607607 TGATTCTTCTGCTAATAGAAACTGCAA 59.392 33.333 0.00 0.00 36.34 4.08
469 515 6.727824 TCTTCTGCTAATAGAAACTGCAAC 57.272 37.500 0.00 0.00 36.34 4.17
470 516 5.643777 TCTTCTGCTAATAGAAACTGCAACC 59.356 40.000 0.00 0.00 36.34 3.77
471 517 4.905429 TCTGCTAATAGAAACTGCAACCA 58.095 39.130 0.00 0.00 33.07 3.67
472 518 4.937620 TCTGCTAATAGAAACTGCAACCAG 59.062 41.667 0.00 0.00 44.80 4.00
473 519 4.905429 TGCTAATAGAAACTGCAACCAGA 58.095 39.130 0.00 0.00 41.77 3.86
474 520 4.937620 TGCTAATAGAAACTGCAACCAGAG 59.062 41.667 0.00 0.00 41.77 3.35
475 521 4.201861 GCTAATAGAAACTGCAACCAGAGC 60.202 45.833 0.00 0.00 41.77 4.09
476 522 3.710209 ATAGAAACTGCAACCAGAGCT 57.290 42.857 0.00 0.00 41.77 4.09
506 552 2.391389 GCAGTGCTTCGCCAGGTAC 61.391 63.158 8.18 0.00 0.00 3.34
514 560 2.354403 GCTTCGCCAGGTACTTTCCTTA 60.354 50.000 0.00 0.00 34.60 2.69
515 561 3.522553 CTTCGCCAGGTACTTTCCTTAG 58.477 50.000 0.00 0.00 34.60 2.18
516 562 2.811410 TCGCCAGGTACTTTCCTTAGA 58.189 47.619 0.00 0.00 34.60 2.10
517 563 2.494870 TCGCCAGGTACTTTCCTTAGAC 59.505 50.000 0.00 0.00 34.60 2.59
519 565 2.418334 GCCAGGTACTTTCCTTAGACCG 60.418 54.545 0.00 0.00 34.60 4.79
520 566 2.167900 CCAGGTACTTTCCTTAGACCGG 59.832 54.545 0.00 0.00 34.60 5.28
543 590 5.244851 GGCTTCTCCAGATTCTTTCCTTTTT 59.755 40.000 0.00 0.00 34.01 1.94
562 609 5.622770 TTTTTAACGCAGGATCTTTCTCC 57.377 39.130 0.00 0.00 35.37 3.71
606 653 4.141642 TGCATATAGGTGATCTGTGTGCTT 60.142 41.667 11.92 0.00 46.42 3.91
681 728 2.291800 ACATTTTGGGATGGAGGGAGTG 60.292 50.000 0.00 0.00 0.00 3.51
684 731 3.083997 GGGATGGAGGGAGTGCGT 61.084 66.667 0.00 0.00 0.00 5.24
685 732 1.760875 GGGATGGAGGGAGTGCGTA 60.761 63.158 0.00 0.00 0.00 4.42
686 733 1.122019 GGGATGGAGGGAGTGCGTAT 61.122 60.000 0.00 0.00 0.00 3.06
687 734 0.759346 GGATGGAGGGAGTGCGTATT 59.241 55.000 0.00 0.00 0.00 1.89
688 735 1.141053 GGATGGAGGGAGTGCGTATTT 59.859 52.381 0.00 0.00 0.00 1.40
689 736 2.367567 GGATGGAGGGAGTGCGTATTTA 59.632 50.000 0.00 0.00 0.00 1.40
690 737 3.181458 GGATGGAGGGAGTGCGTATTTAA 60.181 47.826 0.00 0.00 0.00 1.52
691 738 3.536956 TGGAGGGAGTGCGTATTTAAG 57.463 47.619 0.00 0.00 0.00 1.85
692 739 2.169769 TGGAGGGAGTGCGTATTTAAGG 59.830 50.000 0.00 0.00 0.00 2.69
693 740 2.169978 GGAGGGAGTGCGTATTTAAGGT 59.830 50.000 0.00 0.00 0.00 3.50
694 741 3.370209 GGAGGGAGTGCGTATTTAAGGTT 60.370 47.826 0.00 0.00 0.00 3.50
695 742 3.869832 GAGGGAGTGCGTATTTAAGGTTC 59.130 47.826 0.00 0.00 0.00 3.62
696 743 3.262405 AGGGAGTGCGTATTTAAGGTTCA 59.738 43.478 0.00 0.00 0.00 3.18
697 744 4.004982 GGGAGTGCGTATTTAAGGTTCAA 58.995 43.478 0.00 0.00 0.00 2.69
698 745 4.456566 GGGAGTGCGTATTTAAGGTTCAAA 59.543 41.667 0.00 0.00 0.00 2.69
699 746 5.124936 GGGAGTGCGTATTTAAGGTTCAAAT 59.875 40.000 0.00 0.00 0.00 2.32
718 765 1.191535 TTCCCTGATCGTCCGAATGT 58.808 50.000 0.00 0.00 0.00 2.71
719 766 0.459899 TCCCTGATCGTCCGAATGTG 59.540 55.000 0.00 0.00 0.00 3.21
727 774 1.360931 CGTCCGAATGTGCTGCATCA 61.361 55.000 5.27 6.49 36.67 3.07
743 792 3.243367 TGCATCAGCTTTTTGGTACACAC 60.243 43.478 0.00 0.00 39.43 3.82
758 807 3.350219 ACACACAGTCCAAACAAGACT 57.650 42.857 0.00 0.00 45.45 3.24
762 811 1.202651 ACAGTCCAAACAAGACTCGGG 60.203 52.381 0.00 0.00 42.69 5.14
838 887 4.456911 TCTTATCGTTGTGTACTTCCTCGT 59.543 41.667 0.00 0.00 0.00 4.18
861 1066 3.071747 TCCCAAAATAAGGGGTGCAAAAC 59.928 43.478 0.00 0.00 46.77 2.43
876 1081 2.287608 GCAAAACTGTACCAAGTCAGCC 60.288 50.000 0.00 0.00 35.37 4.85
877 1082 2.948979 CAAAACTGTACCAAGTCAGCCA 59.051 45.455 0.00 0.00 35.37 4.75
878 1083 2.550830 AACTGTACCAAGTCAGCCAG 57.449 50.000 0.00 0.00 35.37 4.85
879 1084 0.035458 ACTGTACCAAGTCAGCCAGC 59.965 55.000 0.00 0.00 35.37 4.85
887 1092 0.882042 AAGTCAGCCAGCGACACTTG 60.882 55.000 14.04 0.00 35.77 3.16
936 1166 2.753055 TCGTAATTGGTGTAGCTGCA 57.247 45.000 0.00 0.00 0.00 4.41
958 1188 5.453339 GCACCTAGTAGCCTCACAAATGATA 60.453 44.000 0.00 0.00 33.22 2.15
1097 1330 1.004504 GCCGCTATCGCTTCTGAAAAG 60.005 52.381 0.00 0.00 0.00 2.27
1194 1427 5.066913 TCTCAGCTATCCCAGTCTTGATA 57.933 43.478 0.00 0.00 0.00 2.15
1199 1432 5.762218 CAGCTATCCCAGTCTTGATAAAAGG 59.238 44.000 0.00 0.00 0.00 3.11
1203 1436 5.165961 TCCCAGTCTTGATAAAAGGTCAG 57.834 43.478 0.00 0.00 0.00 3.51
1346 1592 3.851458 TGTCTCATGATAGCCAAGCAT 57.149 42.857 0.00 0.00 0.00 3.79
1550 1828 7.223584 TCAGTTCTAAAGACCATGTGATTCAA 58.776 34.615 0.00 0.00 0.00 2.69
1616 1984 4.380531 ACACACACTTGGAGTATGTCAAG 58.619 43.478 0.00 0.00 32.80 3.02
1668 2039 5.923114 CCATAGATATGTCTTGTGGACTTCG 59.077 44.000 14.58 0.00 44.74 3.79
1859 2233 9.456147 TGCAAAGCCAAGTTATTACTAAGATAA 57.544 29.630 0.00 0.00 33.17 1.75
1883 2257 2.223845 GGAACGCCGTAAGTTTGCTAAA 59.776 45.455 0.00 0.00 31.14 1.85
2295 2793 0.035458 CTGGTCGGTCAAAGGCTTCT 59.965 55.000 0.00 0.00 0.00 2.85
2300 2798 1.291877 CGGTCAAAGGCTTCTGTCCG 61.292 60.000 22.09 22.09 0.00 4.79
2328 2826 2.091333 ACCACATTTGAACAAGAGGGGT 60.091 45.455 8.63 8.63 30.90 4.95
2408 2912 4.393680 TGTTTCGCCGATATTTAGCACTTT 59.606 37.500 0.00 0.00 0.00 2.66
2409 2913 4.530094 TTCGCCGATATTTAGCACTTTG 57.470 40.909 0.00 0.00 0.00 2.77
2672 3227 2.555757 AGAACAAAACTGAGCATGCTCC 59.444 45.455 37.92 23.40 42.09 4.70
2689 3244 1.895798 CTCCTTACAGAGACACCAGCA 59.104 52.381 0.00 0.00 35.82 4.41
2764 3324 9.712305 TTGGATGAGTACTTTTCAAAACAAAAA 57.288 25.926 0.00 0.00 0.00 1.94
2765 3325 9.145865 TGGATGAGTACTTTTCAAAACAAAAAC 57.854 29.630 0.00 0.00 0.00 2.43
2839 3399 7.765695 AAATTTACATGGCCCTATATGTGAG 57.234 36.000 14.97 0.00 37.98 3.51
2954 3514 4.848357 ACATGGTTTCTTCTGGTATCTGG 58.152 43.478 0.00 0.00 0.00 3.86
2962 3522 6.448369 TTCTTCTGGTATCTGGGAAGAAAA 57.552 37.500 12.56 0.00 45.61 2.29
2972 3532 0.377203 GGGAAGAAAATAGGCGTGCG 59.623 55.000 0.00 0.00 0.00 5.34
2993 3554 7.643764 CGTGCGTTCTCATTTATTTTTATGGAT 59.356 33.333 0.00 0.00 0.00 3.41
3091 3684 9.476202 GCTAGTTTCACATTTTAAAAGATGGTT 57.524 29.630 6.79 0.00 0.00 3.67
3701 4361 9.480053 ACAAATATGACAGTTTTTGGAGAAATG 57.520 29.630 10.49 0.00 34.23 2.32
3796 4498 3.117888 GCAGTATTTTCCCCAGAGGATCA 60.118 47.826 0.00 0.00 46.94 2.92
3886 4588 4.187694 CAGAAGACATGGAAGAAGTAGCC 58.812 47.826 0.00 0.00 0.00 3.93
4029 4734 5.668471 AGATTGCTTCAGAATCGAGAATGA 58.332 37.500 0.00 0.00 35.36 2.57
4031 4736 4.462508 TGCTTCAGAATCGAGAATGACT 57.537 40.909 0.00 0.00 0.00 3.41
4032 4737 4.825422 TGCTTCAGAATCGAGAATGACTT 58.175 39.130 0.00 0.00 0.00 3.01
4041 4752 5.782893 ATCGAGAATGACTTTAGAGGAGG 57.217 43.478 0.00 0.00 0.00 4.30
4092 4803 8.562892 AGATATCCAGCATCTTTTAATTCGTTG 58.437 33.333 0.00 0.00 28.01 4.10
4129 4840 3.388024 TGATTACCGAGAAGATCCTTGGG 59.612 47.826 9.39 0.51 41.18 4.12
4164 4875 7.615582 TGCTCACTCTCATTGTTTATAAAGG 57.384 36.000 0.00 0.00 0.00 3.11
4166 4877 7.334421 TGCTCACTCTCATTGTTTATAAAGGTC 59.666 37.037 0.00 0.00 0.00 3.85
4179 4893 3.832237 AAGGTCACGCAGCACCAGG 62.832 63.158 3.34 0.00 34.80 4.45
4334 5060 1.067821 AGCACCTACGCTATCTTGCTC 59.932 52.381 0.00 0.00 41.55 4.26
4350 5076 4.774726 TCTTGCTCTCAGGACAAATAGAGT 59.225 41.667 0.00 0.00 38.18 3.24
4362 5097 8.338259 CAGGACAAATAGAGTATGCATGTTAAC 58.662 37.037 10.16 0.00 0.00 2.01
4387 5125 8.545472 ACCATACCAAGAGCACTAAATAAACTA 58.455 33.333 0.00 0.00 0.00 2.24
4389 5127 8.827677 CATACCAAGAGCACTAAATAAACTACC 58.172 37.037 0.00 0.00 0.00 3.18
4390 5128 6.775708 ACCAAGAGCACTAAATAAACTACCA 58.224 36.000 0.00 0.00 0.00 3.25
4391 5129 7.228590 ACCAAGAGCACTAAATAAACTACCAA 58.771 34.615 0.00 0.00 0.00 3.67
4393 5131 7.606456 CCAAGAGCACTAAATAAACTACCAAGA 59.394 37.037 0.00 0.00 0.00 3.02
4394 5132 8.660373 CAAGAGCACTAAATAAACTACCAAGAG 58.340 37.037 0.00 0.00 0.00 2.85
4395 5133 7.908453 AGAGCACTAAATAAACTACCAAGAGT 58.092 34.615 0.00 0.00 0.00 3.24
4436 5183 2.101917 GGTGATGGCAAATTGGATGAGG 59.898 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.652012 CAGACCCGCGCAAGAAAAA 59.348 52.632 8.75 0.00 43.02 1.94
19 20 2.258013 CCAGACCCGCGCAAGAAAA 61.258 57.895 8.75 0.00 43.02 2.29
20 21 2.668212 CCAGACCCGCGCAAGAAA 60.668 61.111 8.75 0.00 43.02 2.52
21 22 3.469863 AACCAGACCCGCGCAAGAA 62.470 57.895 8.75 0.00 43.02 2.52
22 23 3.936203 AACCAGACCCGCGCAAGA 61.936 61.111 8.75 0.00 43.02 3.02
23 24 3.726517 CAACCAGACCCGCGCAAG 61.727 66.667 8.75 0.00 43.44 4.01
24 25 3.758973 TTCAACCAGACCCGCGCAA 62.759 57.895 8.75 0.00 0.00 4.85
25 26 4.243008 TTCAACCAGACCCGCGCA 62.243 61.111 8.75 0.00 0.00 6.09
26 27 3.723348 GTTCAACCAGACCCGCGC 61.723 66.667 0.00 0.00 0.00 6.86
27 28 3.047877 GGTTCAACCAGACCCGCG 61.048 66.667 0.01 0.00 38.42 6.46
28 29 2.112297 TGGTTCAACCAGACCCGC 59.888 61.111 4.67 0.00 44.79 6.13
36 37 3.066380 GTTGCATGGATTTGGTTCAACC 58.934 45.455 0.00 0.00 39.22 3.77
37 38 3.993920 AGTTGCATGGATTTGGTTCAAC 58.006 40.909 0.00 0.00 34.31 3.18
38 39 5.798125 TTAGTTGCATGGATTTGGTTCAA 57.202 34.783 0.00 0.00 0.00 2.69
39 40 5.798125 TTTAGTTGCATGGATTTGGTTCA 57.202 34.783 0.00 0.00 0.00 3.18
40 41 5.120674 GCTTTTAGTTGCATGGATTTGGTTC 59.879 40.000 0.00 0.00 0.00 3.62
41 42 4.996758 GCTTTTAGTTGCATGGATTTGGTT 59.003 37.500 0.00 0.00 0.00 3.67
42 43 4.563374 GGCTTTTAGTTGCATGGATTTGGT 60.563 41.667 0.00 0.00 0.00 3.67
43 44 3.934579 GGCTTTTAGTTGCATGGATTTGG 59.065 43.478 0.00 0.00 0.00 3.28
44 45 4.567971 TGGCTTTTAGTTGCATGGATTTG 58.432 39.130 0.00 0.00 0.00 2.32
45 46 4.888326 TGGCTTTTAGTTGCATGGATTT 57.112 36.364 0.00 0.00 0.00 2.17
46 47 4.888326 TTGGCTTTTAGTTGCATGGATT 57.112 36.364 0.00 0.00 0.00 3.01
47 48 4.322953 CCTTTGGCTTTTAGTTGCATGGAT 60.323 41.667 0.00 0.00 0.00 3.41
48 49 3.006752 CCTTTGGCTTTTAGTTGCATGGA 59.993 43.478 0.00 0.00 0.00 3.41
49 50 3.328505 CCTTTGGCTTTTAGTTGCATGG 58.671 45.455 0.00 0.00 0.00 3.66
50 51 3.328505 CCCTTTGGCTTTTAGTTGCATG 58.671 45.455 0.00 0.00 0.00 4.06
51 52 3.683365 CCCTTTGGCTTTTAGTTGCAT 57.317 42.857 0.00 0.00 0.00 3.96
136 137 6.484977 GTCCAGTTTCTCCATTCTCCATTATC 59.515 42.308 0.00 0.00 0.00 1.75
151 152 2.040178 AGAGAACCGTGTCCAGTTTCT 58.960 47.619 0.00 0.00 0.00 2.52
205 216 3.818210 TCGAGCTTGAGATATGAGAGGTC 59.182 47.826 0.00 0.00 0.00 3.85
225 236 0.961358 ACGACTGGGAAGGAGACTCG 60.961 60.000 0.00 0.00 42.68 4.18
237 248 3.889538 TCAGGTATAATCTGGACGACTGG 59.110 47.826 0.00 0.00 33.36 4.00
239 250 5.202004 AGTTCAGGTATAATCTGGACGACT 58.798 41.667 9.05 4.96 43.60 4.18
368 382 4.327680 AGCAACTAGAACAAACTGGATCC 58.672 43.478 4.20 4.20 0.00 3.36
388 422 1.004918 AGTGACCACAGCCGTAAGC 60.005 57.895 2.78 0.00 44.25 3.09
389 423 0.317160 TCAGTGACCACAGCCGTAAG 59.683 55.000 2.78 0.00 0.00 2.34
390 424 0.753867 TTCAGTGACCACAGCCGTAA 59.246 50.000 0.00 0.00 0.00 3.18
392 426 0.320771 GATTCAGTGACCACAGCCGT 60.321 55.000 0.00 0.00 0.00 5.68
394 428 1.160137 GTGATTCAGTGACCACAGCC 58.840 55.000 16.03 0.00 0.00 4.85
396 430 2.225019 GCAAGTGATTCAGTGACCACAG 59.775 50.000 20.59 15.20 32.35 3.66
398 432 2.221169 TGCAAGTGATTCAGTGACCAC 58.779 47.619 14.04 14.04 0.00 4.16
399 433 2.636647 TGCAAGTGATTCAGTGACCA 57.363 45.000 0.00 0.00 0.00 4.02
400 434 4.002982 TGTATGCAAGTGATTCAGTGACC 58.997 43.478 0.00 0.00 0.00 4.02
401 435 5.808042 ATGTATGCAAGTGATTCAGTGAC 57.192 39.130 0.00 0.00 0.00 3.67
413 459 3.134623 TCACCTCCCTGTATGTATGCAAG 59.865 47.826 0.00 0.00 0.00 4.01
414 460 3.111484 TCACCTCCCTGTATGTATGCAA 58.889 45.455 0.00 0.00 0.00 4.08
417 463 5.528690 CACAAATCACCTCCCTGTATGTATG 59.471 44.000 0.00 0.00 0.00 2.39
418 464 5.191722 ACACAAATCACCTCCCTGTATGTAT 59.808 40.000 0.00 0.00 0.00 2.29
419 465 4.534500 ACACAAATCACCTCCCTGTATGTA 59.466 41.667 0.00 0.00 0.00 2.29
420 466 3.330701 ACACAAATCACCTCCCTGTATGT 59.669 43.478 0.00 0.00 0.00 2.29
456 502 3.710209 AGCTCTGGTTGCAGTTTCTAT 57.290 42.857 0.00 0.00 0.00 1.98
457 503 3.306780 GGTAGCTCTGGTTGCAGTTTCTA 60.307 47.826 0.00 0.00 0.00 2.10
458 504 2.551071 GGTAGCTCTGGTTGCAGTTTCT 60.551 50.000 0.00 0.00 0.00 2.52
459 505 1.807142 GGTAGCTCTGGTTGCAGTTTC 59.193 52.381 0.00 0.00 0.00 2.78
460 506 1.878102 CGGTAGCTCTGGTTGCAGTTT 60.878 52.381 0.00 0.00 0.00 2.66
461 507 0.320771 CGGTAGCTCTGGTTGCAGTT 60.321 55.000 0.00 0.00 0.00 3.16
462 508 1.293498 CGGTAGCTCTGGTTGCAGT 59.707 57.895 0.00 0.00 0.00 4.40
463 509 0.530744 TACGGTAGCTCTGGTTGCAG 59.469 55.000 0.00 0.00 0.00 4.41
464 510 1.191535 ATACGGTAGCTCTGGTTGCA 58.808 50.000 0.00 0.00 0.00 4.08
465 511 2.311124 AATACGGTAGCTCTGGTTGC 57.689 50.000 0.00 0.00 0.00 4.17
466 512 4.360563 CTGTAATACGGTAGCTCTGGTTG 58.639 47.826 0.00 0.00 0.00 3.77
467 513 3.181478 GCTGTAATACGGTAGCTCTGGTT 60.181 47.826 0.00 0.00 33.53 3.67
468 514 2.361438 GCTGTAATACGGTAGCTCTGGT 59.639 50.000 0.00 0.00 33.53 4.00
469 515 2.361119 TGCTGTAATACGGTAGCTCTGG 59.639 50.000 0.00 0.00 37.10 3.86
470 516 3.066900 ACTGCTGTAATACGGTAGCTCTG 59.933 47.826 15.67 3.62 40.30 3.35
471 517 3.066900 CACTGCTGTAATACGGTAGCTCT 59.933 47.826 15.67 0.00 40.30 4.09
472 518 3.372954 CACTGCTGTAATACGGTAGCTC 58.627 50.000 15.67 0.00 40.30 4.09
473 519 2.481449 GCACTGCTGTAATACGGTAGCT 60.481 50.000 15.67 0.00 40.30 3.32
474 520 1.859080 GCACTGCTGTAATACGGTAGC 59.141 52.381 15.67 5.86 40.30 3.58
475 521 3.438297 AGCACTGCTGTAATACGGTAG 57.562 47.619 14.44 14.44 42.03 3.18
476 522 3.732774 CGAAGCACTGCTGTAATACGGTA 60.733 47.826 3.73 0.00 39.62 4.02
506 552 2.418884 GGAGAAGCCGGTCTAAGGAAAG 60.419 54.545 1.90 0.00 0.00 2.62
514 560 0.827368 GAATCTGGAGAAGCCGGTCT 59.173 55.000 1.90 0.00 44.00 3.85
515 561 0.827368 AGAATCTGGAGAAGCCGGTC 59.173 55.000 1.90 0.00 44.00 4.79
516 562 1.280457 AAGAATCTGGAGAAGCCGGT 58.720 50.000 1.90 0.00 44.00 5.28
517 563 2.284190 GAAAGAATCTGGAGAAGCCGG 58.716 52.381 0.00 0.00 45.07 6.13
519 565 3.643199 AGGAAAGAATCTGGAGAAGCC 57.357 47.619 0.00 0.00 37.10 4.35
520 566 5.973899 AAAAGGAAAGAATCTGGAGAAGC 57.026 39.130 0.00 0.00 0.00 3.86
543 590 2.418197 CCGGAGAAAGATCCTGCGTTAA 60.418 50.000 0.00 0.00 42.63 2.01
550 597 0.042731 TGGGTCCGGAGAAAGATCCT 59.957 55.000 3.06 0.00 37.20 3.24
627 674 3.664107 TGACACTTGCTCTGTTGTATCC 58.336 45.455 0.00 0.00 0.00 2.59
681 728 6.033966 CAGGGAATTTGAACCTTAAATACGC 58.966 40.000 0.00 0.00 30.66 4.42
684 731 7.832187 ACGATCAGGGAATTTGAACCTTAAATA 59.168 33.333 0.00 0.00 30.66 1.40
685 732 6.663523 ACGATCAGGGAATTTGAACCTTAAAT 59.336 34.615 0.00 0.00 30.66 1.40
686 733 6.007703 ACGATCAGGGAATTTGAACCTTAAA 58.992 36.000 0.00 0.00 30.66 1.52
687 734 5.566469 ACGATCAGGGAATTTGAACCTTAA 58.434 37.500 0.00 0.00 30.66 1.85
688 735 5.174037 ACGATCAGGGAATTTGAACCTTA 57.826 39.130 0.00 0.00 30.66 2.69
689 736 4.010349 GACGATCAGGGAATTTGAACCTT 58.990 43.478 0.00 0.00 30.66 3.50
690 737 3.610911 GACGATCAGGGAATTTGAACCT 58.389 45.455 0.00 0.00 34.19 3.50
691 738 2.683362 GGACGATCAGGGAATTTGAACC 59.317 50.000 0.00 0.00 0.00 3.62
692 739 2.351726 CGGACGATCAGGGAATTTGAAC 59.648 50.000 0.00 0.00 0.00 3.18
693 740 2.235155 TCGGACGATCAGGGAATTTGAA 59.765 45.455 0.00 0.00 0.00 2.69
694 741 1.828595 TCGGACGATCAGGGAATTTGA 59.171 47.619 0.00 0.00 0.00 2.69
695 742 2.309528 TCGGACGATCAGGGAATTTG 57.690 50.000 0.00 0.00 0.00 2.32
696 743 3.206150 CATTCGGACGATCAGGGAATTT 58.794 45.455 0.00 0.00 0.00 1.82
697 744 2.170607 ACATTCGGACGATCAGGGAATT 59.829 45.455 0.00 0.00 0.00 2.17
698 745 1.762957 ACATTCGGACGATCAGGGAAT 59.237 47.619 0.00 0.00 0.00 3.01
699 746 1.134818 CACATTCGGACGATCAGGGAA 60.135 52.381 0.00 0.00 0.00 3.97
727 774 2.949644 GGACTGTGTGTACCAAAAAGCT 59.050 45.455 0.00 0.00 0.00 3.74
735 782 3.311596 GTCTTGTTTGGACTGTGTGTACC 59.688 47.826 0.00 0.00 0.00 3.34
743 792 1.070134 TCCCGAGTCTTGTTTGGACTG 59.930 52.381 0.93 0.00 43.13 3.51
861 1066 1.016130 CGCTGGCTGACTTGGTACAG 61.016 60.000 0.00 0.00 42.39 2.74
876 1081 4.014847 TGAAAGAAAACAAGTGTCGCTG 57.985 40.909 0.00 0.00 0.00 5.18
877 1082 4.335315 TCATGAAAGAAAACAAGTGTCGCT 59.665 37.500 0.00 0.00 0.00 4.93
878 1083 4.597079 TCATGAAAGAAAACAAGTGTCGC 58.403 39.130 0.00 0.00 0.00 5.19
879 1084 8.955061 ATAATCATGAAAGAAAACAAGTGTCG 57.045 30.769 0.00 0.00 0.00 4.35
907 1137 5.934935 ACACCAATTACGAAAGTTACTGG 57.065 39.130 0.00 0.00 46.40 4.00
936 1166 5.661312 TGTATCATTTGTGAGGCTACTAGGT 59.339 40.000 0.00 0.00 0.00 3.08
958 1188 6.649557 CGGTAACCTGAAAATAGAAGAAGTGT 59.350 38.462 0.00 0.00 0.00 3.55
1097 1330 7.631822 CTCATCAGAGAAATCATGTGTGATTC 58.368 38.462 4.32 0.14 45.99 2.52
1194 1427 3.281727 TCAGTTGTCAGCTGACCTTTT 57.718 42.857 37.23 20.79 44.15 2.27
1199 1432 1.869767 CCACTTCAGTTGTCAGCTGAC 59.130 52.381 35.04 35.04 42.00 3.51
1203 1436 1.268743 GCAACCACTTCAGTTGTCAGC 60.269 52.381 5.62 0.00 45.14 4.26
1550 1828 5.232347 AGGTGGGTACTAAATGTGGGATAT 58.768 41.667 0.00 0.00 0.00 1.63
1668 2039 0.671251 CTGATAGCGGTCTCTCCACC 59.329 60.000 0.00 0.00 35.57 4.61
1859 2233 1.223187 CAAACTTACGGCGTTCCAGT 58.777 50.000 21.24 15.44 0.00 4.00
1883 2257 5.866207 AGAATACTGAACTTTCGAAAGGGT 58.134 37.500 34.49 27.17 40.31 4.34
1916 2292 7.448777 TGAGCAAGGTAACAAAATATTGGTGTA 59.551 33.333 5.67 0.00 41.01 2.90
2212 2625 7.244886 TCTCTAAATCTTTCAGTCATGGTGA 57.755 36.000 0.00 0.00 0.00 4.02
2251 2749 6.677913 AGGTTCAAATCCAAACTTTCATACG 58.322 36.000 0.00 0.00 0.00 3.06
2295 2793 2.264005 AATGTGGTTAGTTGCGGACA 57.736 45.000 0.00 0.00 0.00 4.02
2300 2798 5.587289 TCTTGTTCAAATGTGGTTAGTTGC 58.413 37.500 0.00 0.00 0.00 4.17
2408 2912 3.499338 ACTGCTGATTTGTGGGATTTCA 58.501 40.909 0.00 0.00 0.00 2.69
2409 2913 4.525912 AACTGCTGATTTGTGGGATTTC 57.474 40.909 0.00 0.00 0.00 2.17
2492 3012 4.558178 TCACATGTTGAATTGAACCATGC 58.442 39.130 14.93 0.00 0.00 4.06
2672 3227 3.367498 GGTACTGCTGGTGTCTCTGTAAG 60.367 52.174 0.00 0.00 0.00 2.34
2839 3399 3.434299 TGGACGCCTATTTTCTTTCGTTC 59.566 43.478 0.00 0.00 0.00 3.95
2854 3414 1.134220 TGGGTAATGAGAATGGACGCC 60.134 52.381 0.00 0.00 0.00 5.68
2954 3514 1.084289 ACGCACGCCTATTTTCTTCC 58.916 50.000 0.00 0.00 0.00 3.46
2962 3522 2.024176 AAATGAGAACGCACGCCTAT 57.976 45.000 0.00 0.00 0.00 2.57
3064 3641 8.860088 ACCATCTTTTAAAATGTGAAACTAGCT 58.140 29.630 0.09 0.00 38.04 3.32
3392 4003 6.415702 CAACAAAAATGCAAGTGAAGATGTG 58.584 36.000 0.00 0.00 0.00 3.21
3596 4237 5.187186 AGTGGGTACGATCTTTTAGACACAT 59.813 40.000 0.00 0.00 0.00 3.21
3600 4241 5.717119 TCAAGTGGGTACGATCTTTTAGAC 58.283 41.667 0.00 0.00 0.00 2.59
3604 4245 6.894339 AATTTCAAGTGGGTACGATCTTTT 57.106 33.333 0.00 0.00 0.00 2.27
3607 4248 7.166167 AGTAAAATTTCAAGTGGGTACGATCT 58.834 34.615 0.00 0.00 0.00 2.75
3611 4252 5.704053 AGGAGTAAAATTTCAAGTGGGTACG 59.296 40.000 0.00 0.00 0.00 3.67
3616 4276 5.841810 TGCAAGGAGTAAAATTTCAAGTGG 58.158 37.500 0.00 0.00 0.00 4.00
3701 4361 2.100584 TGAACATGTCAAGGTTTGCCAC 59.899 45.455 0.00 0.00 37.19 5.01
3796 4498 5.855045 ACTAACTCGACCATTCTCAACTTT 58.145 37.500 0.00 0.00 0.00 2.66
3886 4588 3.320673 AACTCTTGAAAGTAGCCCTCG 57.679 47.619 0.00 0.00 0.00 4.63
4029 4734 1.280457 CCAGCCACCTCCTCTAAAGT 58.720 55.000 0.00 0.00 0.00 2.66
4031 4736 0.118346 TCCCAGCCACCTCCTCTAAA 59.882 55.000 0.00 0.00 0.00 1.85
4032 4737 0.118346 TTCCCAGCCACCTCCTCTAA 59.882 55.000 0.00 0.00 0.00 2.10
4041 4752 1.349357 GGATATCTCCTTCCCAGCCAC 59.651 57.143 2.05 0.00 38.65 5.01
4092 4803 6.734137 TCGGTAATCAATTTGCCATCATAAC 58.266 36.000 0.00 0.00 39.90 1.89
4129 4840 5.186996 TGAGAGTGAGCAAATTTTCCAAC 57.813 39.130 0.00 0.00 0.00 3.77
4164 4875 3.349006 CACCTGGTGCTGCGTGAC 61.349 66.667 14.87 0.00 0.00 3.67
4166 4877 3.046087 CTCACCTGGTGCTGCGTG 61.046 66.667 22.02 4.06 32.98 5.34
4179 4893 5.146010 ACTCTCAATCACTCTTTCCTCAC 57.854 43.478 0.00 0.00 0.00 3.51
4334 5060 6.286758 ACATGCATACTCTATTTGTCCTGAG 58.713 40.000 0.00 0.00 0.00 3.35
4350 5076 5.530915 GCTCTTGGTATGGTTAACATGCATA 59.469 40.000 8.10 3.66 43.15 3.14
4362 5097 7.865706 AGTTTATTTAGTGCTCTTGGTATGG 57.134 36.000 0.00 0.00 0.00 2.74
4387 5125 2.269940 AGCACCTGGATAACTCTTGGT 58.730 47.619 0.00 0.00 0.00 3.67
4389 5127 5.543507 ATCTAGCACCTGGATAACTCTTG 57.456 43.478 0.00 0.00 30.02 3.02
4390 5128 6.567602 AAATCTAGCACCTGGATAACTCTT 57.432 37.500 0.00 0.00 30.53 2.85
4391 5129 6.352516 CAAAATCTAGCACCTGGATAACTCT 58.647 40.000 0.00 0.00 30.53 3.24
4393 5131 5.044846 ACCAAAATCTAGCACCTGGATAACT 60.045 40.000 0.00 0.00 30.53 2.24
4394 5132 5.066505 CACCAAAATCTAGCACCTGGATAAC 59.933 44.000 0.00 0.00 30.53 1.89
4395 5133 5.045213 TCACCAAAATCTAGCACCTGGATAA 60.045 40.000 0.00 0.00 30.53 1.75


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

AutoCloner maintained by Alex Coulton.