Multiple sequence alignment - TraesCS4D01G294700

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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 TraesCS4D01G294700 chr4D 100.000 3287 0 0 1 3287 465012422 465009136 0.000000e+00 6071.0
1 TraesCS4D01G294700 chr4D 91.081 740 57 5 1 734 13341623 13342359 0.000000e+00 992.0
2 TraesCS4D01G294700 chr4D 90.836 742 60 3 1 737 359114513 359113775 0.000000e+00 987.0
3 TraesCS4D01G294700 chr4D 87.346 648 42 12 2680 3287 1294239 1293592 0.000000e+00 706.0
4 TraesCS4D01G294700 chr4B 92.635 1222 82 4 1337 2558 581323824 581322611 0.000000e+00 1751.0
5 TraesCS4D01G294700 chr4B 92.623 610 38 7 733 1339 581329598 581328993 0.000000e+00 870.0
6 TraesCS4D01G294700 chr2D 92.016 739 50 5 1 734 152877148 152877882 0.000000e+00 1029.0
7 TraesCS4D01G294700 chr1D 91.903 741 51 5 1 734 426866287 426865549 0.000000e+00 1027.0
8 TraesCS4D01G294700 chr1D 85.423 638 62 13 2678 3286 415271256 415270621 4.630000e-178 634.0
9 TraesCS4D01G294700 chr1D 85.135 666 42 15 2671 3287 114787305 114787962 2.150000e-176 628.0
10 TraesCS4D01G294700 chr1D 100.000 28 0 0 2567 2594 132562222 132562249 6.000000e-03 52.8
11 TraesCS4D01G294700 chrUn 91.398 744 56 4 1 737 94262256 94261514 0.000000e+00 1013.0
12 TraesCS4D01G294700 chrUn 91.263 744 57 4 1 737 94298037 94297295 0.000000e+00 1007.0
13 TraesCS4D01G294700 chr7D 91.263 744 57 4 1 739 35068470 35069210 0.000000e+00 1007.0
14 TraesCS4D01G294700 chr7D 84.796 638 64 18 2677 3285 50094568 50093935 7.800000e-171 610.0
15 TraesCS4D01G294700 chr3D 90.995 744 56 6 1 737 527521511 527520772 0.000000e+00 992.0
16 TraesCS4D01G294700 chr3D 85.933 654 52 10 2671 3285 76941093 76941745 0.000000e+00 662.0
17 TraesCS4D01G294700 chr3D 84.219 659 37 13 2678 3287 506060131 506059491 2.200000e-161 579.0
18 TraesCS4D01G294700 chr5D 90.676 740 62 3 1 734 66771655 66772393 0.000000e+00 977.0
19 TraesCS4D01G294700 chr5D 88.226 654 31 8 2671 3287 50860875 50861519 0.000000e+00 739.0
20 TraesCS4D01G294700 chr7B 87.132 645 52 12 2671 3285 440237407 440238050 0.000000e+00 702.0
21 TraesCS4D01G294700 chr5B 89.773 528 54 0 2760 3287 176568181 176567654 0.000000e+00 676.0
22 TraesCS4D01G294700 chr5B 85.460 619 65 14 2687 3287 301194968 301195579 3.600000e-174 621.0
23 TraesCS4D01G294700 chr6D 85.959 641 56 14 2677 3287 364230225 364229589 0.000000e+00 654.0
24 TraesCS4D01G294700 chr6D 85.452 653 48 9 2671 3285 11702119 11702762 1.290000e-178 636.0
25 TraesCS4D01G294700 chr6D 85.193 466 23 13 2671 3090 414035598 414036063 1.400000e-118 436.0
26 TraesCS4D01G294700 chr3A 85.759 646 59 14 2671 3285 588741201 588741844 0.000000e+00 652.0
27 TraesCS4D01G294700 chr2B 84.894 662 62 21 2659 3287 789984845 789984189 4.630000e-178 634.0
28 TraesCS4D01G294700 chr1B 84.711 641 74 13 2671 3287 266934202 266934842 1.300000e-173 619.0
29 TraesCS4D01G294700 chr6A 83.808 667 64 22 2659 3285 601252269 601252931 7.850000e-166 593.0
30 TraesCS4D01G294700 chr6A 81.306 674 71 19 2659 3287 72756039 72755376 2.280000e-136 496.0


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 TraesCS4D01G294700 chr4D 465009136 465012422 3286 True 6071 6071 100.000 1 3287 1 chr4D.!!$R3 3286
1 TraesCS4D01G294700 chr4D 13341623 13342359 736 False 992 992 91.081 1 734 1 chr4D.!!$F1 733
2 TraesCS4D01G294700 chr4D 359113775 359114513 738 True 987 987 90.836 1 737 1 chr4D.!!$R2 736
3 TraesCS4D01G294700 chr4D 1293592 1294239 647 True 706 706 87.346 2680 3287 1 chr4D.!!$R1 607
4 TraesCS4D01G294700 chr4B 581322611 581323824 1213 True 1751 1751 92.635 1337 2558 1 chr4B.!!$R1 1221
5 TraesCS4D01G294700 chr4B 581328993 581329598 605 True 870 870 92.623 733 1339 1 chr4B.!!$R2 606
6 TraesCS4D01G294700 chr2D 152877148 152877882 734 False 1029 1029 92.016 1 734 1 chr2D.!!$F1 733
7 TraesCS4D01G294700 chr1D 426865549 426866287 738 True 1027 1027 91.903 1 734 1 chr1D.!!$R2 733
8 TraesCS4D01G294700 chr1D 415270621 415271256 635 True 634 634 85.423 2678 3286 1 chr1D.!!$R1 608
9 TraesCS4D01G294700 chr1D 114787305 114787962 657 False 628 628 85.135 2671 3287 1 chr1D.!!$F1 616
10 TraesCS4D01G294700 chrUn 94261514 94262256 742 True 1013 1013 91.398 1 737 1 chrUn.!!$R1 736
11 TraesCS4D01G294700 chrUn 94297295 94298037 742 True 1007 1007 91.263 1 737 1 chrUn.!!$R2 736
12 TraesCS4D01G294700 chr7D 35068470 35069210 740 False 1007 1007 91.263 1 739 1 chr7D.!!$F1 738
13 TraesCS4D01G294700 chr7D 50093935 50094568 633 True 610 610 84.796 2677 3285 1 chr7D.!!$R1 608
14 TraesCS4D01G294700 chr3D 527520772 527521511 739 True 992 992 90.995 1 737 1 chr3D.!!$R2 736
15 TraesCS4D01G294700 chr3D 76941093 76941745 652 False 662 662 85.933 2671 3285 1 chr3D.!!$F1 614
16 TraesCS4D01G294700 chr3D 506059491 506060131 640 True 579 579 84.219 2678 3287 1 chr3D.!!$R1 609
17 TraesCS4D01G294700 chr5D 66771655 66772393 738 False 977 977 90.676 1 734 1 chr5D.!!$F2 733
18 TraesCS4D01G294700 chr5D 50860875 50861519 644 False 739 739 88.226 2671 3287 1 chr5D.!!$F1 616
19 TraesCS4D01G294700 chr7B 440237407 440238050 643 False 702 702 87.132 2671 3285 1 chr7B.!!$F1 614
20 TraesCS4D01G294700 chr5B 176567654 176568181 527 True 676 676 89.773 2760 3287 1 chr5B.!!$R1 527
21 TraesCS4D01G294700 chr5B 301194968 301195579 611 False 621 621 85.460 2687 3287 1 chr5B.!!$F1 600
22 TraesCS4D01G294700 chr6D 364229589 364230225 636 True 654 654 85.959 2677 3287 1 chr6D.!!$R1 610
23 TraesCS4D01G294700 chr6D 11702119 11702762 643 False 636 636 85.452 2671 3285 1 chr6D.!!$F1 614
24 TraesCS4D01G294700 chr3A 588741201 588741844 643 False 652 652 85.759 2671 3285 1 chr3A.!!$F1 614
25 TraesCS4D01G294700 chr2B 789984189 789984845 656 True 634 634 84.894 2659 3287 1 chr2B.!!$R1 628
26 TraesCS4D01G294700 chr1B 266934202 266934842 640 False 619 619 84.711 2671 3287 1 chr1B.!!$F1 616
27 TraesCS4D01G294700 chr6A 601252269 601252931 662 False 593 593 83.808 2659 3285 1 chr6A.!!$F1 626
28 TraesCS4D01G294700 chr6A 72755376 72756039 663 True 496 496 81.306 2659 3287 1 chr6A.!!$R1 628

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
606 618 0.324645 GATGGGGCCAAAGGATGTGT 60.325 55.0 4.39 0.0 0.00 3.72 F
1922 1937 0.318191 CTCGACATGGCGACGATGAT 60.318 55.0 22.34 0.0 40.87 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 1953 0.033011 AGCTGTACTCCCCGATGTCT 60.033 55.0 0.00 0.00 0.0 3.41 R
3030 3144 0.469331 TAGTCTTCCGGCCCGATGAT 60.469 55.0 3.71 5.51 0.0 2.45 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
25 27 5.417266 TGGTCAACTTTTGTGAAGACAATCA 59.583 36.000 0.00 0.00 41.77 2.57
119 121 2.079170 TTTGGTGTGCTTCAATCCCA 57.921 45.000 0.00 0.00 0.00 4.37
238 241 0.500178 CGAGCGTGATAACAGCATCG 59.500 55.000 0.00 3.49 0.00 3.84
285 288 4.379652 GTGAAAATGTTGAACCCTTGCAT 58.620 39.130 0.00 0.00 0.00 3.96
295 298 0.400213 ACCCTTGCATCAAGAACCGA 59.600 50.000 8.04 0.00 43.42 4.69
297 300 1.522668 CCTTGCATCAAGAACCGACA 58.477 50.000 8.04 0.00 43.42 4.35
384 387 1.512926 ATGACTTGGTTGAGCACGTC 58.487 50.000 11.45 11.45 0.00 4.34
389 392 0.396435 TTGGTTGAGCACGTCTGGAT 59.604 50.000 0.00 0.00 0.00 3.41
502 507 9.634163 AATTTCGATTGGGTTGTAAAACTATTC 57.366 29.630 0.00 0.00 30.93 1.75
604 616 0.638292 ATGATGGGGCCAAAGGATGT 59.362 50.000 4.39 0.00 0.00 3.06
606 618 0.324645 GATGGGGCCAAAGGATGTGT 60.325 55.000 4.39 0.00 0.00 3.72
645 657 1.296392 CCACCGCATCTCAGGACAA 59.704 57.895 0.00 0.00 0.00 3.18
646 658 1.021390 CCACCGCATCTCAGGACAAC 61.021 60.000 0.00 0.00 0.00 3.32
653 665 0.326618 ATCTCAGGACAACCCCGGAT 60.327 55.000 0.73 0.00 36.73 4.18
743 755 1.001633 GGAGTTGGCCTAACGAACAGA 59.998 52.381 3.32 0.00 44.15 3.41
760 772 2.029828 ACAGACAAGAAGTACGCCTCTG 60.030 50.000 0.00 0.00 0.00 3.35
762 774 0.608640 ACAAGAAGTACGCCTCTGGG 59.391 55.000 3.15 0.00 0.00 4.45
809 821 2.679342 CGCCCAAATCCTCCTCCCA 61.679 63.158 0.00 0.00 0.00 4.37
838 850 3.342377 TCATCGCCAAACATGTCCTTA 57.658 42.857 0.00 0.00 0.00 2.69
839 851 3.884895 TCATCGCCAAACATGTCCTTAT 58.115 40.909 0.00 0.00 0.00 1.73
845 857 5.353123 TCGCCAAACATGTCCTTATCTTTAC 59.647 40.000 0.00 0.00 0.00 2.01
847 859 5.652452 GCCAAACATGTCCTTATCTTTACCT 59.348 40.000 0.00 0.00 0.00 3.08
854 867 7.390718 ACATGTCCTTATCTTTACCTCAACAAC 59.609 37.037 0.00 0.00 0.00 3.32
863 876 7.614124 TCTTTACCTCAACAACTTTTAACGT 57.386 32.000 0.00 0.00 0.00 3.99
948 962 2.915869 TCCAAGGATCACCAGGTACTT 58.084 47.619 0.00 0.00 34.60 2.24
1029 1044 0.857935 CGGAGCGCTTTGATGAGATC 59.142 55.000 13.26 0.00 0.00 2.75
1033 1048 1.431488 GCGCTTTGATGAGATCGCCA 61.431 55.000 0.00 0.00 37.02 5.69
1035 1050 1.372582 GCTTTGATGAGATCGCCACA 58.627 50.000 0.00 0.00 0.00 4.17
1060 1075 4.752594 AGCCACCCCCACCCGTAT 62.753 66.667 0.00 0.00 0.00 3.06
1116 1131 1.139095 GGTGATCACCGACGTCCTC 59.861 63.158 28.52 3.16 42.29 3.71
1128 1143 2.490685 GTCCTCGACCGCCTCTTC 59.509 66.667 0.00 0.00 0.00 2.87
1192 1207 4.459089 GGCGGCGCTTCTTCCTCT 62.459 66.667 32.30 0.00 0.00 3.69
1198 1213 1.975327 CGCTTCTTCCTCTCCACCA 59.025 57.895 0.00 0.00 0.00 4.17
1243 1258 0.610687 GCTCAGAGCCACAAGGTACT 59.389 55.000 11.84 0.00 35.64 2.73
1339 1354 2.103373 TCTCATCCAAACTCCTCTCCG 58.897 52.381 0.00 0.00 0.00 4.63
1362 1377 4.899239 CGCGGCCACCTCATCCTC 62.899 72.222 2.24 0.00 0.00 3.71
1379 1394 2.736670 CTCCTCAAAAGGGGGTATGG 57.263 55.000 0.00 0.00 43.56 2.74
1520 1535 4.920112 CCACACCCGCGACCACAA 62.920 66.667 8.23 0.00 0.00 3.33
1572 1587 4.436998 GACCCTCAGTGGACGCCG 62.437 72.222 0.00 0.00 38.35 6.46
1599 1614 4.410400 CCCCGTGGTGCCTCCTTC 62.410 72.222 0.00 0.00 37.07 3.46
1617 1632 1.095600 TCCTCTCAACCGTGATCGAG 58.904 55.000 0.00 0.00 39.71 4.04
1715 1730 1.227943 ATTCATCCCATGCGGTCCG 60.228 57.895 6.99 6.99 0.00 4.79
1824 1839 2.105930 CGGCTGCTACTCCTGCTC 59.894 66.667 0.00 0.00 0.00 4.26
1897 1912 2.666190 TGCAGAAGGTGAGCGTGC 60.666 61.111 0.71 0.71 34.62 5.34
1899 1914 2.037136 GCAGAAGGTGAGCGTGCAT 61.037 57.895 0.00 0.00 34.18 3.96
1922 1937 0.318191 CTCGACATGGCGACGATGAT 60.318 55.000 22.34 0.00 40.87 2.45
1936 1951 0.534652 GATGATGTGGGAGGAGCTGC 60.535 60.000 0.00 0.00 0.00 5.25
1938 1953 1.300963 GATGTGGGAGGAGCTGCAA 59.699 57.895 8.35 0.00 0.00 4.08
1939 1954 0.747283 GATGTGGGAGGAGCTGCAAG 60.747 60.000 8.35 0.00 0.00 4.01
1983 1998 4.475135 GACTGCCCCGGGAGAAGC 62.475 72.222 26.32 18.15 37.03 3.86
2040 2055 0.606604 TGGCCAACCGAGTCTACTTC 59.393 55.000 0.61 0.00 39.70 3.01
2046 2061 1.736612 ACCGAGTCTACTTCCTCGTC 58.263 55.000 8.08 0.00 46.91 4.20
2048 2063 1.666700 CCGAGTCTACTTCCTCGTCTG 59.333 57.143 8.08 0.00 46.91 3.51
2049 2064 1.062880 CGAGTCTACTTCCTCGTCTGC 59.937 57.143 0.00 0.00 44.14 4.26
2052 2067 1.062880 GTCTACTTCCTCGTCTGCTCG 59.937 57.143 0.00 0.00 0.00 5.03
2054 2069 1.062880 CTACTTCCTCGTCTGCTCGAC 59.937 57.143 0.00 0.00 39.33 4.20
2067 2082 3.027710 CTGCTCGACGTATTACGACTTC 58.972 50.000 22.18 8.91 46.05 3.01
2089 2104 4.329545 GACAGCCGCCCTTCCACA 62.330 66.667 0.00 0.00 0.00 4.17
2090 2105 3.628646 GACAGCCGCCCTTCCACAT 62.629 63.158 0.00 0.00 0.00 3.21
2104 2119 1.600636 CACATGTTCGCACCAGGGT 60.601 57.895 0.00 0.00 0.00 4.34
2133 2148 1.076533 ACAAGTGCTACGATTCGCCG 61.077 55.000 5.86 0.00 0.00 6.46
2163 2178 1.690893 CTCATCTCCCATGACCGTGAT 59.309 52.381 0.00 0.00 0.00 3.06
2214 2229 4.262377 CCGAGCCTCTTCTATCAATCATGT 60.262 45.833 0.00 0.00 0.00 3.21
2246 2261 9.965902 ACTATTTATCAAATCAGATGATACCCC 57.034 33.333 0.00 0.00 38.99 4.95
2255 2270 3.262151 TCAGATGATACCCCAAACGTTGA 59.738 43.478 0.00 0.00 0.00 3.18
2256 2271 4.080582 TCAGATGATACCCCAAACGTTGAT 60.081 41.667 0.00 0.00 0.00 2.57
2453 2468 3.927854 TGTTTCATGCATGTTGAATGGG 58.072 40.909 25.43 0.00 34.10 4.00
2468 2483 1.987807 ATGGGCCTTCGATGAGGTGG 61.988 60.000 4.53 0.00 39.11 4.61
2475 2490 1.026182 TTCGATGAGGTGGCATGTGC 61.026 55.000 0.00 0.00 41.14 4.57
2476 2491 1.746239 CGATGAGGTGGCATGTGCA 60.746 57.895 7.36 0.00 44.36 4.57
2484 2499 2.092267 AGGTGGCATGTGCAATGAGATA 60.092 45.455 7.36 0.00 44.36 1.98
2485 2500 2.292569 GGTGGCATGTGCAATGAGATAG 59.707 50.000 7.36 0.00 44.36 2.08
2486 2501 2.292569 GTGGCATGTGCAATGAGATAGG 59.707 50.000 7.36 0.00 44.36 2.57
2493 2508 4.193865 TGTGCAATGAGATAGGATGTGTG 58.806 43.478 0.00 0.00 0.00 3.82
2504 2519 6.015282 AGATAGGATGTGTGCATGAGATCTA 58.985 40.000 0.00 0.00 35.07 1.98
2511 2526 7.042187 GGATGTGTGCATGAGATCTACTAAAAG 60.042 40.741 0.00 0.00 35.07 2.27
2514 2529 7.118245 TGTGTGCATGAGATCTACTAAAAGTTG 59.882 37.037 0.00 0.00 0.00 3.16
2522 2537 9.208022 TGAGATCTACTAAAAGTTGTTCACATG 57.792 33.333 0.00 0.00 0.00 3.21
2523 2538 9.209175 GAGATCTACTAAAAGTTGTTCACATGT 57.791 33.333 0.00 0.00 0.00 3.21
2524 2539 8.993121 AGATCTACTAAAAGTTGTTCACATGTG 58.007 33.333 20.18 20.18 0.00 3.21
2528 2543 6.208644 ACTAAAAGTTGTTCACATGTGCATC 58.791 36.000 21.38 12.60 0.00 3.91
2544 2559 1.002017 ATCATGGTGGGGCCTTTGG 59.998 57.895 0.84 0.00 38.35 3.28
2552 2567 1.139498 TGGGGCCTTTGGTGAGATGA 61.139 55.000 0.84 0.00 0.00 2.92
2555 2570 1.168714 GGCCTTTGGTGAGATGACAC 58.831 55.000 0.00 0.00 39.70 3.67
2558 2573 2.163010 GCCTTTGGTGAGATGACACATG 59.837 50.000 0.00 0.00 41.88 3.21
2559 2574 3.415212 CCTTTGGTGAGATGACACATGT 58.585 45.455 0.00 0.00 41.88 3.21
2560 2575 3.822735 CCTTTGGTGAGATGACACATGTT 59.177 43.478 0.00 0.00 41.88 2.71
2561 2576 5.003160 CCTTTGGTGAGATGACACATGTTA 58.997 41.667 0.00 0.00 41.88 2.41
2562 2577 5.473162 CCTTTGGTGAGATGACACATGTTAA 59.527 40.000 0.00 0.00 41.88 2.01
2563 2578 6.348786 CCTTTGGTGAGATGACACATGTTAAG 60.349 42.308 0.00 0.00 41.88 1.85
2564 2579 5.482163 TGGTGAGATGACACATGTTAAGA 57.518 39.130 0.00 0.00 41.88 2.10
2565 2580 5.237815 TGGTGAGATGACACATGTTAAGAC 58.762 41.667 0.00 0.00 41.88 3.01
2566 2581 5.221621 TGGTGAGATGACACATGTTAAGACA 60.222 40.000 0.00 0.00 41.88 3.41
2567 2582 5.120830 GGTGAGATGACACATGTTAAGACAC 59.879 44.000 0.00 1.52 41.88 3.67
2568 2583 5.928839 GTGAGATGACACATGTTAAGACACT 59.071 40.000 0.00 0.00 38.91 3.55
2569 2584 6.090088 GTGAGATGACACATGTTAAGACACTC 59.910 42.308 0.00 0.83 38.91 3.51
2570 2585 5.482908 AGATGACACATGTTAAGACACTCC 58.517 41.667 0.00 0.00 38.91 3.85
2571 2586 4.002906 TGACACATGTTAAGACACTCCC 57.997 45.455 0.00 0.00 38.91 4.30
2572 2587 3.646162 TGACACATGTTAAGACACTCCCT 59.354 43.478 0.00 0.00 38.91 4.20
2573 2588 4.246458 GACACATGTTAAGACACTCCCTC 58.754 47.826 0.00 0.00 38.91 4.30
2574 2589 3.008049 ACACATGTTAAGACACTCCCTCC 59.992 47.826 0.00 0.00 38.91 4.30
2575 2590 3.007940 CACATGTTAAGACACTCCCTCCA 59.992 47.826 0.00 0.00 38.91 3.86
2576 2591 3.846588 ACATGTTAAGACACTCCCTCCAT 59.153 43.478 0.00 0.00 38.91 3.41
2577 2592 4.289672 ACATGTTAAGACACTCCCTCCATT 59.710 41.667 0.00 0.00 38.91 3.16
2578 2593 4.993705 TGTTAAGACACTCCCTCCATTT 57.006 40.909 0.00 0.00 0.00 2.32
2579 2594 6.012858 ACATGTTAAGACACTCCCTCCATTTA 60.013 38.462 0.00 0.00 38.91 1.40
2580 2595 5.801380 TGTTAAGACACTCCCTCCATTTAC 58.199 41.667 0.00 0.00 0.00 2.01
2581 2596 5.546499 TGTTAAGACACTCCCTCCATTTACT 59.454 40.000 0.00 0.00 0.00 2.24
2582 2597 6.043938 TGTTAAGACACTCCCTCCATTTACTT 59.956 38.462 0.00 0.00 0.00 2.24
2583 2598 7.236019 TGTTAAGACACTCCCTCCATTTACTTA 59.764 37.037 0.00 0.00 0.00 2.24
2584 2599 6.893020 AAGACACTCCCTCCATTTACTTAT 57.107 37.500 0.00 0.00 0.00 1.73
2585 2600 7.989947 AAGACACTCCCTCCATTTACTTATA 57.010 36.000 0.00 0.00 0.00 0.98
2586 2601 8.568617 AAGACACTCCCTCCATTTACTTATAT 57.431 34.615 0.00 0.00 0.00 0.86
2587 2602 9.670442 AAGACACTCCCTCCATTTACTTATATA 57.330 33.333 0.00 0.00 0.00 0.86
2588 2603 9.091220 AGACACTCCCTCCATTTACTTATATAC 57.909 37.037 0.00 0.00 0.00 1.47
2589 2604 8.792830 ACACTCCCTCCATTTACTTATATACA 57.207 34.615 0.00 0.00 0.00 2.29
2590 2605 9.220906 ACACTCCCTCCATTTACTTATATACAA 57.779 33.333 0.00 0.00 0.00 2.41
2591 2606 9.712305 CACTCCCTCCATTTACTTATATACAAG 57.288 37.037 0.00 0.00 0.00 3.16
2592 2607 8.881262 ACTCCCTCCATTTACTTATATACAAGG 58.119 37.037 0.00 0.00 0.00 3.61
2593 2608 7.686434 TCCCTCCATTTACTTATATACAAGGC 58.314 38.462 0.00 0.00 0.00 4.35
2594 2609 7.516209 TCCCTCCATTTACTTATATACAAGGCT 59.484 37.037 0.00 0.00 0.00 4.58
2595 2610 8.822805 CCCTCCATTTACTTATATACAAGGCTA 58.177 37.037 0.00 0.00 0.00 3.93
2596 2611 9.654663 CCTCCATTTACTTATATACAAGGCTAC 57.345 37.037 0.00 0.00 0.00 3.58
2612 2627 8.924511 ACAAGGCTACTATGCAATATACATTT 57.075 30.769 0.00 0.00 34.04 2.32
2613 2628 9.354673 ACAAGGCTACTATGCAATATACATTTT 57.645 29.630 0.00 0.00 34.04 1.82
2629 2644 7.880160 ATACATTTTACAATTAGAGCCTGCA 57.120 32.000 0.00 0.00 0.00 4.41
2630 2645 6.780457 ACATTTTACAATTAGAGCCTGCAT 57.220 33.333 0.00 0.00 0.00 3.96
2631 2646 7.880160 ACATTTTACAATTAGAGCCTGCATA 57.120 32.000 0.00 0.00 0.00 3.14
2632 2647 7.707104 ACATTTTACAATTAGAGCCTGCATAC 58.293 34.615 0.00 0.00 0.00 2.39
2633 2648 7.557719 ACATTTTACAATTAGAGCCTGCATACT 59.442 33.333 0.00 0.00 0.00 2.12
2634 2649 7.553881 TTTTACAATTAGAGCCTGCATACTC 57.446 36.000 7.82 7.82 0.00 2.59
2635 2650 3.722147 ACAATTAGAGCCTGCATACTCG 58.278 45.455 9.70 0.24 37.99 4.18
2636 2651 2.447244 ATTAGAGCCTGCATACTCGC 57.553 50.000 9.70 0.00 37.99 5.03
2637 2652 0.389391 TTAGAGCCTGCATACTCGCC 59.611 55.000 9.70 0.00 37.99 5.54
2638 2653 1.464376 TAGAGCCTGCATACTCGCCC 61.464 60.000 9.70 0.00 37.99 6.13
2639 2654 4.227134 AGCCTGCATACTCGCCCG 62.227 66.667 0.00 0.00 0.00 6.13
2640 2655 4.221422 GCCTGCATACTCGCCCGA 62.221 66.667 0.00 0.00 0.00 5.14
2641 2656 2.279517 CCTGCATACTCGCCCGAC 60.280 66.667 0.00 0.00 0.00 4.79
2642 2657 2.279517 CTGCATACTCGCCCGACC 60.280 66.667 0.00 0.00 0.00 4.79
2643 2658 3.792053 CTGCATACTCGCCCGACCC 62.792 68.421 0.00 0.00 0.00 4.46
2644 2659 4.603946 GCATACTCGCCCGACCCC 62.604 72.222 0.00 0.00 0.00 4.95
2645 2660 3.925090 CATACTCGCCCGACCCCC 61.925 72.222 0.00 0.00 0.00 5.40
2646 2661 4.468769 ATACTCGCCCGACCCCCA 62.469 66.667 0.00 0.00 0.00 4.96
2647 2662 3.988050 ATACTCGCCCGACCCCCAA 62.988 63.158 0.00 0.00 0.00 4.12
2649 2664 4.109675 CTCGCCCGACCCCCAAAT 62.110 66.667 0.00 0.00 0.00 2.32
2650 2665 3.638592 CTCGCCCGACCCCCAAATT 62.639 63.158 0.00 0.00 0.00 1.82
2651 2666 2.678580 CGCCCGACCCCCAAATTT 60.679 61.111 0.00 0.00 0.00 1.82
2652 2667 2.279810 CGCCCGACCCCCAAATTTT 61.280 57.895 0.00 0.00 0.00 1.82
2653 2668 1.822114 CGCCCGACCCCCAAATTTTT 61.822 55.000 0.00 0.00 0.00 1.94
2987 3083 4.781959 CCGGACGCGTTCGCCTTA 62.782 66.667 33.84 0.00 39.84 2.69
2990 3086 1.735559 GGACGCGTTCGCCTTAGTT 60.736 57.895 15.53 0.00 39.84 2.24
3239 3389 1.170919 AGTACGTCGACCTGTGCAGT 61.171 55.000 10.58 2.50 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 1.415672 TTCTCACCTTGGGGCTTCGT 61.416 55.000 0.00 0.00 35.63 3.85
119 121 1.232119 GTTTCGAACGACACCCCATT 58.768 50.000 0.00 0.00 0.00 3.16
127 129 0.878961 AGTGCAGGGTTTCGAACGAC 60.879 55.000 0.00 0.00 0.00 4.34
238 241 5.371115 TGAAAATCAAATCCTTGGTCGAC 57.629 39.130 7.13 7.13 33.01 4.20
285 288 2.619147 TCAAACGTTGTCGGTTCTTGA 58.381 42.857 0.00 0.00 43.96 3.02
295 298 2.601804 GGCAAACTGTTCAAACGTTGT 58.398 42.857 0.00 0.00 0.00 3.32
297 300 1.546476 TGGGCAAACTGTTCAAACGTT 59.454 42.857 0.00 0.00 0.00 3.99
384 387 1.894466 TGGTTGCCAATGTGAATCCAG 59.106 47.619 0.00 0.00 0.00 3.86
423 427 9.480053 AAATCGAAATTGTCTTGAATGAACATT 57.520 25.926 0.00 0.00 0.00 2.71
578 589 0.409092 TTGGCCCCATCATGTCAGTT 59.591 50.000 0.00 0.00 0.00 3.16
579 590 0.409092 TTTGGCCCCATCATGTCAGT 59.591 50.000 0.00 0.00 0.00 3.41
581 592 0.324552 CCTTTGGCCCCATCATGTCA 60.325 55.000 0.00 0.00 0.00 3.58
637 649 1.324740 CGTATCCGGGGTTGTCCTGA 61.325 60.000 0.00 0.00 44.90 3.86
645 657 0.979187 AATGTGGTCGTATCCGGGGT 60.979 55.000 0.00 0.00 33.95 4.95
646 658 1.042229 TAATGTGGTCGTATCCGGGG 58.958 55.000 0.00 0.00 33.95 5.73
653 665 6.153170 TGTTTGGATAGAGTAATGTGGTCGTA 59.847 38.462 0.00 0.00 0.00 3.43
660 672 7.482169 TCTGTCTGTTTGGATAGAGTAATGT 57.518 36.000 0.00 0.00 31.55 2.71
712 724 2.661537 CAACTCCAGCGCACGACA 60.662 61.111 11.47 0.00 0.00 4.35
743 755 0.608640 CCCAGAGGCGTACTTCTTGT 59.391 55.000 0.00 0.00 0.00 3.16
774 786 3.084579 GCTGGACGAACGCTCATG 58.915 61.111 0.00 0.00 0.00 3.07
788 800 1.821332 GAGGAGGATTTGGGCGCTG 60.821 63.158 7.64 0.00 0.00 5.18
794 806 0.107654 GTCGTGGGAGGAGGATTTGG 60.108 60.000 0.00 0.00 0.00 3.28
838 850 8.217131 ACGTTAAAAGTTGTTGAGGTAAAGAT 57.783 30.769 0.00 0.00 0.00 2.40
839 851 7.333921 TGACGTTAAAAGTTGTTGAGGTAAAGA 59.666 33.333 0.00 0.00 0.00 2.52
845 857 6.750039 ACAAATGACGTTAAAAGTTGTTGAGG 59.250 34.615 0.00 0.00 0.00 3.86
863 876 8.054152 TCGTACAGTATACTACCAACAAATGA 57.946 34.615 4.74 0.00 0.00 2.57
939 953 4.280174 ACGCCACAGTATATAAGTACCTGG 59.720 45.833 0.00 0.00 0.00 4.45
948 962 8.198778 TGACAGAATAAAACGCCACAGTATATA 58.801 33.333 0.00 0.00 0.00 0.86
1020 1035 1.083806 GCGTTGTGGCGATCTCATCA 61.084 55.000 0.00 0.00 0.00 3.07
1022 1037 1.815421 GGCGTTGTGGCGATCTCAT 60.815 57.895 0.00 0.00 0.00 2.90
1023 1038 2.434185 GGCGTTGTGGCGATCTCA 60.434 61.111 0.00 0.00 0.00 3.27
1047 1062 2.761213 GACGATACGGGTGGGGGT 60.761 66.667 0.00 0.00 0.00 4.95
1056 1071 2.722548 CGCAGCTCCGACGATACG 60.723 66.667 0.00 0.00 0.00 3.06
1057 1072 2.353607 CCGCAGCTCCGACGATAC 60.354 66.667 0.00 0.00 0.00 2.24
1058 1073 3.592814 CCCGCAGCTCCGACGATA 61.593 66.667 0.00 0.00 0.00 2.92
1071 1086 3.007323 AGGTTACCCCAGTCCCGC 61.007 66.667 0.00 0.00 34.66 6.13
1110 1125 3.398353 GAAGAGGCGGTCGAGGACG 62.398 68.421 0.00 0.00 41.26 4.79
1116 1131 2.202932 CATGGGAAGAGGCGGTCG 60.203 66.667 0.00 0.00 0.00 4.79
1122 1137 2.507944 CGGAGGCATGGGAAGAGG 59.492 66.667 0.00 0.00 0.00 3.69
1305 1320 2.032681 GAGAAGGCGGGCAGTGTT 59.967 61.111 3.78 0.00 0.00 3.32
1306 1321 2.527951 GATGAGAAGGCGGGCAGTGT 62.528 60.000 3.78 0.00 0.00 3.55
1362 1377 0.751643 CGCCATACCCCCTTTTGAGG 60.752 60.000 0.00 0.00 0.00 3.86
1374 1389 1.371881 GCTACGCTCTCCGCCATAC 60.372 63.158 0.00 0.00 41.76 2.39
1375 1390 1.826487 TGCTACGCTCTCCGCCATA 60.826 57.895 0.00 0.00 41.76 2.74
1376 1391 3.147595 TGCTACGCTCTCCGCCAT 61.148 61.111 0.00 0.00 41.76 4.40
1377 1392 4.129737 GTGCTACGCTCTCCGCCA 62.130 66.667 0.00 0.00 41.76 5.69
1394 1409 2.870161 CGTCGACGACAAGGAGCG 60.870 66.667 33.35 8.02 43.02 5.03
1520 1535 1.404315 GGAAGCGGAGTGAGTCGAATT 60.404 52.381 0.00 0.00 0.00 2.17
1590 1605 1.544825 CGGTTGAGAGGAAGGAGGCA 61.545 60.000 0.00 0.00 0.00 4.75
1599 1614 0.811915 ACTCGATCACGGTTGAGAGG 59.188 55.000 1.42 0.00 40.21 3.69
1675 1690 1.499056 GTGGAGCGTTGACAGCATG 59.501 57.895 0.00 0.00 46.00 4.06
1677 1692 2.661537 CGTGGAGCGTTGACAGCA 60.662 61.111 0.00 0.00 37.01 4.41
1678 1693 4.077188 GCGTGGAGCGTTGACAGC 62.077 66.667 0.00 0.00 43.66 4.40
1806 1821 4.154347 AGCAGGAGTAGCAGCCGC 62.154 66.667 0.00 0.00 38.99 6.53
1815 1830 2.388735 TCCGTCATAATGAGCAGGAGT 58.611 47.619 0.00 0.00 0.00 3.85
1873 1888 0.600557 CTCACCTTCTGCACTCTCGT 59.399 55.000 0.00 0.00 0.00 4.18
1875 1890 0.735632 CGCTCACCTTCTGCACTCTC 60.736 60.000 0.00 0.00 0.00 3.20
1922 1937 1.842920 TCTTGCAGCTCCTCCCACA 60.843 57.895 0.00 0.00 0.00 4.17
1936 1951 1.471676 GCTGTACTCCCCGATGTCTTG 60.472 57.143 0.00 0.00 0.00 3.02
1938 1953 0.033011 AGCTGTACTCCCCGATGTCT 60.033 55.000 0.00 0.00 0.00 3.41
1939 1954 0.824759 AAGCTGTACTCCCCGATGTC 59.175 55.000 0.00 0.00 0.00 3.06
2046 2061 2.733820 AGTCGTAATACGTCGAGCAG 57.266 50.000 12.78 0.00 43.14 4.24
2052 2067 4.025094 GTCTTCCGAAGTCGTAATACGTC 58.975 47.826 12.78 7.32 43.14 4.34
2054 2069 4.007282 TGTCTTCCGAAGTCGTAATACG 57.993 45.455 6.45 6.45 44.19 3.06
2075 2090 3.210012 AACATGTGGAAGGGCGGCT 62.210 57.895 9.56 0.00 0.00 5.52
2089 2104 2.351276 GGACCCTGGTGCGAACAT 59.649 61.111 0.00 0.00 0.00 2.71
2133 2148 1.520342 GGAGATGAGCGCAGACCAC 60.520 63.158 11.47 0.00 0.00 4.16
2163 2178 2.318519 ATATGTGTAGCGGCGGCCAA 62.319 55.000 20.71 0.06 41.24 4.52
2214 2229 9.563748 TCATCTGATTTGATAAATAGTGATGCA 57.436 29.630 0.00 0.00 34.97 3.96
2424 2439 8.484641 TTCAACATGCATGAAACAAGTTTTTA 57.515 26.923 32.75 2.36 34.04 1.52
2431 2446 4.316645 CCCATTCAACATGCATGAAACAA 58.683 39.130 32.75 18.13 39.98 2.83
2432 2447 3.865302 GCCCATTCAACATGCATGAAACA 60.865 43.478 32.75 13.91 39.98 2.83
2453 2468 1.153086 ATGCCACCTCATCGAAGGC 60.153 57.895 2.92 4.54 45.41 4.35
2468 2483 3.819337 ACATCCTATCTCATTGCACATGC 59.181 43.478 0.00 0.00 42.50 4.06
2475 2490 5.061179 TCATGCACACATCCTATCTCATTG 58.939 41.667 0.00 0.00 32.87 2.82
2476 2491 5.071384 TCTCATGCACACATCCTATCTCATT 59.929 40.000 0.00 0.00 32.87 2.57
2484 2499 3.966006 AGTAGATCTCATGCACACATCCT 59.034 43.478 0.00 0.00 32.87 3.24
2485 2500 4.333913 AGTAGATCTCATGCACACATCC 57.666 45.455 0.00 0.00 32.87 3.51
2486 2501 7.493971 ACTTTTAGTAGATCTCATGCACACATC 59.506 37.037 0.00 0.00 32.87 3.06
2493 2508 8.171840 GTGAACAACTTTTAGTAGATCTCATGC 58.828 37.037 0.00 0.00 0.00 4.06
2504 2519 5.574891 TGCACATGTGAACAACTTTTAGT 57.425 34.783 29.80 0.00 0.00 2.24
2522 2537 3.149648 GGCCCCACCATGATGCAC 61.150 66.667 0.00 0.00 38.86 4.57
2523 2538 2.458969 AAAGGCCCCACCATGATGCA 62.459 55.000 0.00 0.00 43.14 3.96
2524 2539 1.686800 AAAGGCCCCACCATGATGC 60.687 57.895 0.00 0.00 43.14 3.91
2528 2543 2.120274 ACCAAAGGCCCCACCATG 59.880 61.111 0.00 0.00 43.14 3.66
2532 2547 0.967380 CATCTCACCAAAGGCCCCAC 60.967 60.000 0.00 0.00 0.00 4.61
2544 2559 5.928839 AGTGTCTTAACATGTGTCATCTCAC 59.071 40.000 0.00 4.15 37.81 3.51
2552 2567 3.008049 GGAGGGAGTGTCTTAACATGTGT 59.992 47.826 0.00 0.00 37.81 3.72
2555 2570 3.981071 TGGAGGGAGTGTCTTAACATG 57.019 47.619 0.00 0.00 37.81 3.21
2558 2573 6.051179 AGTAAATGGAGGGAGTGTCTTAAC 57.949 41.667 0.00 0.00 0.00 2.01
2559 2574 6.697641 AAGTAAATGGAGGGAGTGTCTTAA 57.302 37.500 0.00 0.00 0.00 1.85
2560 2575 7.989947 ATAAGTAAATGGAGGGAGTGTCTTA 57.010 36.000 0.00 0.00 0.00 2.10
2561 2576 6.893020 ATAAGTAAATGGAGGGAGTGTCTT 57.107 37.500 0.00 0.00 0.00 3.01
2562 2577 9.091220 GTATATAAGTAAATGGAGGGAGTGTCT 57.909 37.037 0.00 0.00 0.00 3.41
2563 2578 8.867097 TGTATATAAGTAAATGGAGGGAGTGTC 58.133 37.037 0.00 0.00 0.00 3.67
2564 2579 8.792830 TGTATATAAGTAAATGGAGGGAGTGT 57.207 34.615 0.00 0.00 0.00 3.55
2565 2580 9.712305 CTTGTATATAAGTAAATGGAGGGAGTG 57.288 37.037 1.24 0.00 0.00 3.51
2566 2581 8.881262 CCTTGTATATAAGTAAATGGAGGGAGT 58.119 37.037 8.25 0.00 0.00 3.85
2567 2582 7.824779 GCCTTGTATATAAGTAAATGGAGGGAG 59.175 40.741 8.25 0.00 0.00 4.30
2568 2583 7.516209 AGCCTTGTATATAAGTAAATGGAGGGA 59.484 37.037 8.25 0.00 0.00 4.20
2569 2584 7.690256 AGCCTTGTATATAAGTAAATGGAGGG 58.310 38.462 8.25 0.00 0.00 4.30
2570 2585 9.654663 GTAGCCTTGTATATAAGTAAATGGAGG 57.345 37.037 8.25 0.00 0.00 4.30
2587 2602 8.924511 AAATGTATATTGCATAGTAGCCTTGT 57.075 30.769 0.00 0.00 0.00 3.16
2603 2618 9.573166 TGCAGGCTCTAATTGTAAAATGTATAT 57.427 29.630 0.00 0.00 0.00 0.86
2604 2619 8.972458 TGCAGGCTCTAATTGTAAAATGTATA 57.028 30.769 0.00 0.00 0.00 1.47
2605 2620 7.880160 TGCAGGCTCTAATTGTAAAATGTAT 57.120 32.000 0.00 0.00 0.00 2.29
2606 2621 7.880160 ATGCAGGCTCTAATTGTAAAATGTA 57.120 32.000 0.00 0.00 0.00 2.29
2607 2622 6.780457 ATGCAGGCTCTAATTGTAAAATGT 57.220 33.333 0.00 0.00 0.00 2.71
2608 2623 7.934457 AGTATGCAGGCTCTAATTGTAAAATG 58.066 34.615 0.00 0.00 0.00 2.32
2609 2624 7.041780 CGAGTATGCAGGCTCTAATTGTAAAAT 60.042 37.037 15.42 0.00 0.00 1.82
2610 2625 6.257849 CGAGTATGCAGGCTCTAATTGTAAAA 59.742 38.462 15.42 0.00 0.00 1.52
2611 2626 5.753438 CGAGTATGCAGGCTCTAATTGTAAA 59.247 40.000 15.42 0.00 0.00 2.01
2612 2627 5.289595 CGAGTATGCAGGCTCTAATTGTAA 58.710 41.667 15.42 0.00 0.00 2.41
2613 2628 4.796290 GCGAGTATGCAGGCTCTAATTGTA 60.796 45.833 15.42 0.00 34.15 2.41
2614 2629 3.722147 CGAGTATGCAGGCTCTAATTGT 58.278 45.455 15.42 0.00 0.00 2.71
2615 2630 2.478134 GCGAGTATGCAGGCTCTAATTG 59.522 50.000 15.42 4.17 34.15 2.32
2616 2631 2.548920 GGCGAGTATGCAGGCTCTAATT 60.549 50.000 15.42 0.00 36.28 1.40
2617 2632 1.001406 GGCGAGTATGCAGGCTCTAAT 59.999 52.381 15.42 0.00 36.28 1.73
2618 2633 0.389391 GGCGAGTATGCAGGCTCTAA 59.611 55.000 15.42 0.00 36.28 2.10
2619 2634 1.464376 GGGCGAGTATGCAGGCTCTA 61.464 60.000 15.42 0.00 36.28 2.43
2620 2635 2.801631 GGGCGAGTATGCAGGCTCT 61.802 63.158 15.42 1.53 36.28 4.09
2621 2636 2.280457 GGGCGAGTATGCAGGCTC 60.280 66.667 9.51 9.51 36.28 4.70
2622 2637 4.227134 CGGGCGAGTATGCAGGCT 62.227 66.667 0.00 0.00 36.28 4.58
2623 2638 4.221422 TCGGGCGAGTATGCAGGC 62.221 66.667 0.00 0.00 36.28 4.85
2624 2639 2.279517 GTCGGGCGAGTATGCAGG 60.280 66.667 0.00 0.00 36.28 4.85
2625 2640 2.279517 GGTCGGGCGAGTATGCAG 60.280 66.667 0.00 0.00 36.28 4.41
2626 2641 3.845259 GGGTCGGGCGAGTATGCA 61.845 66.667 0.00 0.00 36.28 3.96
2627 2642 4.603946 GGGGTCGGGCGAGTATGC 62.604 72.222 0.00 0.00 0.00 3.14
2628 2643 3.925090 GGGGGTCGGGCGAGTATG 61.925 72.222 0.00 0.00 0.00 2.39
2629 2644 3.988050 TTGGGGGTCGGGCGAGTAT 62.988 63.158 0.00 0.00 0.00 2.12
2630 2645 4.700448 TTGGGGGTCGGGCGAGTA 62.700 66.667 0.00 0.00 0.00 2.59
2632 2647 3.638592 AATTTGGGGGTCGGGCGAG 62.639 63.158 0.00 0.00 0.00 5.03
2633 2648 2.716833 AAAATTTGGGGGTCGGGCGA 62.717 55.000 0.00 0.00 0.00 5.54
2634 2649 1.822114 AAAAATTTGGGGGTCGGGCG 61.822 55.000 0.00 0.00 0.00 6.13
2635 2650 2.062922 AAAAATTTGGGGGTCGGGC 58.937 52.632 0.00 0.00 0.00 6.13
2987 3083 1.545706 GCTCCTCCTTCACGGGAACT 61.546 60.000 0.00 0.00 34.66 3.01
2990 3086 2.683933 GGCTCCTCCTTCACGGGA 60.684 66.667 0.00 0.00 0.00 5.14
3030 3144 0.469331 TAGTCTTCCGGCCCGATGAT 60.469 55.000 3.71 5.51 0.00 2.45
3239 3389 0.826715 CTCAATCCTCCTCGCCAGAA 59.173 55.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.