Multiple sequence alignment - TraesCS6D01G207400

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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 TraesCS6D01G207400 chr6D 100.000 3455 0 0 1 3455 292781342 292784796 0.000000e+00 6381.0
1 TraesCS6D01G207400 chr6D 95.789 950 36 4 2509 3455 432917705 432916757 0.000000e+00 1530.0
2 TraesCS6D01G207400 chr6B 97.592 1744 29 5 762 2500 457309498 457311233 0.000000e+00 2976.0
3 TraesCS6D01G207400 chr6B 95.597 954 37 5 2505 3455 717855874 717854923 0.000000e+00 1524.0
4 TraesCS6D01G207400 chr6B 85.152 330 41 7 1 328 457265225 457265548 7.150000e-87 331.0
5 TraesCS6D01G207400 chr6B 88.710 186 19 2 485 670 176254344 176254527 3.470000e-55 226.0
6 TraesCS6D01G207400 chr6B 92.424 66 5 0 421 486 457304760 457304825 1.020000e-15 95.3
7 TraesCS6D01G207400 chr6A 96.743 1750 36 9 771 2503 428303515 428301770 0.000000e+00 2896.0
8 TraesCS6D01G207400 chr6A 96.004 951 35 1 2508 3455 459078000 459078950 0.000000e+00 1543.0
9 TraesCS6D01G207400 chr6A 81.197 468 58 9 21 486 428304399 428303960 1.970000e-92 350.0
10 TraesCS6D01G207400 chr6A 87.037 54 2 4 141 190 576893515 576893463 4.820000e-04 56.5
11 TraesCS6D01G207400 chr2D 96.845 951 25 3 2508 3455 638413585 638412637 0.000000e+00 1585.0
12 TraesCS6D01G207400 chr2D 87.164 483 58 4 1954 2434 466810476 466810956 2.340000e-151 545.0
13 TraesCS6D01G207400 chr2D 76.641 792 154 22 1084 1864 466809613 466810384 3.210000e-110 409.0
14 TraesCS6D01G207400 chr1D 96.316 950 32 1 2509 3455 345893780 345894729 0.000000e+00 1557.0
15 TraesCS6D01G207400 chr1D 95.789 950 37 3 2509 3455 59878525 59877576 0.000000e+00 1530.0
16 TraesCS6D01G207400 chr1D 93.548 62 4 0 199 260 25947209 25947148 3.670000e-15 93.5
17 TraesCS6D01G207400 chr4D 96.218 952 32 4 2508 3455 505233261 505234212 0.000000e+00 1555.0
18 TraesCS6D01G207400 chr4D 90.374 187 17 1 484 670 35722300 35722485 9.580000e-61 244.0
19 TraesCS6D01G207400 chr4D 91.061 179 15 1 487 665 163743307 163743130 1.240000e-59 241.0
20 TraesCS6D01G207400 chr5D 95.820 957 34 4 2502 3455 352169484 352170437 0.000000e+00 1541.0
21 TraesCS6D01G207400 chr5D 91.954 174 13 1 485 658 536316692 536316520 3.450000e-60 243.0
22 TraesCS6D01G207400 chr2B 95.507 957 39 4 2502 3455 528830258 528831213 0.000000e+00 1526.0
23 TraesCS6D01G207400 chr2B 87.164 483 58 4 1954 2434 545433529 545434009 2.340000e-151 545.0
24 TraesCS6D01G207400 chr2B 81.087 460 77 7 1407 1864 545432965 545433416 3.280000e-95 359.0
25 TraesCS6D01G207400 chr2B 91.209 182 15 1 487 668 771215317 771215137 2.660000e-61 246.0
26 TraesCS6D01G207400 chr2A 87.785 483 55 4 1954 2434 607875826 607875346 2.330000e-156 562.0
27 TraesCS6D01G207400 chr2A 75.727 791 163 20 1084 1864 607876686 607875915 1.510000e-98 370.0
28 TraesCS6D01G207400 chr5A 90.659 182 17 0 484 665 7700911 7701092 3.450000e-60 243.0
29 TraesCS6D01G207400 chr3D 90.270 185 18 0 485 669 506177129 506177313 3.450000e-60 243.0
30 TraesCS6D01G207400 chr3D 90.503 179 17 0 487 665 104098849 104099027 1.600000e-58 237.0
31 TraesCS6D01G207400 chr5B 89.730 185 18 1 485 669 445146629 445146812 5.760000e-58 235.0
32 TraesCS6D01G207400 chr4B 76.471 187 25 15 74 247 636110186 636110366 2.210000e-12 84.2
33 TraesCS6D01G207400 chr3B 96.970 33 0 1 145 177 72093434 72093403 2.000000e-03 54.7


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 TraesCS6D01G207400 chr6D 292781342 292784796 3454 False 6381 6381 100.0000 1 3455 1 chr6D.!!$F1 3454
1 TraesCS6D01G207400 chr6D 432916757 432917705 948 True 1530 1530 95.7890 2509 3455 1 chr6D.!!$R1 946
2 TraesCS6D01G207400 chr6B 457309498 457311233 1735 False 2976 2976 97.5920 762 2500 1 chr6B.!!$F4 1738
3 TraesCS6D01G207400 chr6B 717854923 717855874 951 True 1524 1524 95.5970 2505 3455 1 chr6B.!!$R1 950
4 TraesCS6D01G207400 chr6A 428301770 428304399 2629 True 1623 2896 88.9700 21 2503 2 chr6A.!!$R2 2482
5 TraesCS6D01G207400 chr6A 459078000 459078950 950 False 1543 1543 96.0040 2508 3455 1 chr6A.!!$F1 947
6 TraesCS6D01G207400 chr2D 638412637 638413585 948 True 1585 1585 96.8450 2508 3455 1 chr2D.!!$R1 947
7 TraesCS6D01G207400 chr2D 466809613 466810956 1343 False 477 545 81.9025 1084 2434 2 chr2D.!!$F1 1350
8 TraesCS6D01G207400 chr1D 345893780 345894729 949 False 1557 1557 96.3160 2509 3455 1 chr1D.!!$F1 946
9 TraesCS6D01G207400 chr1D 59877576 59878525 949 True 1530 1530 95.7890 2509 3455 1 chr1D.!!$R2 946
10 TraesCS6D01G207400 chr4D 505233261 505234212 951 False 1555 1555 96.2180 2508 3455 1 chr4D.!!$F2 947
11 TraesCS6D01G207400 chr5D 352169484 352170437 953 False 1541 1541 95.8200 2502 3455 1 chr5D.!!$F1 953
12 TraesCS6D01G207400 chr2B 528830258 528831213 955 False 1526 1526 95.5070 2502 3455 1 chr2B.!!$F1 953
13 TraesCS6D01G207400 chr2B 545432965 545434009 1044 False 452 545 84.1255 1407 2434 2 chr2B.!!$F2 1027
14 TraesCS6D01G207400 chr2A 607875346 607876686 1340 True 466 562 81.7560 1084 2434 2 chr2A.!!$R1 1350

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
713 976 0.034896 GGGCTCTCGAGTTTTGTCCA 59.965 55.0 13.13 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2698 2996 1.137086 CGGTCCACCATCTCTTTCGAT 59.863 52.381 0.0 0.0 35.14 3.59 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 26 6.734502 TTGTTTAGGGTTTAGGGGAAAAAG 57.265 37.500 0.00 0.00 0.00 2.27
28 29 6.324512 TGTTTAGGGTTTAGGGGAAAAAGAAC 59.675 38.462 0.00 0.00 0.00 3.01
38 40 4.017130 AGGGGAAAAAGAACTATGCTCCAT 60.017 41.667 0.00 0.00 0.00 3.41
41 43 5.067023 GGGAAAAAGAACTATGCTCCATGAG 59.933 44.000 0.00 0.00 0.00 2.90
49 51 5.758790 ACTATGCTCCATGAGAAGCATAT 57.241 39.130 24.84 17.11 45.42 1.78
53 55 8.327271 ACTATGCTCCATGAGAAGCATATATTT 58.673 33.333 24.84 14.17 45.42 1.40
68 70 6.647067 AGCATATATTTACTTCTCGTTGAGGC 59.353 38.462 0.00 0.00 0.00 4.70
72 74 2.724977 TACTTCTCGTTGAGGCACTG 57.275 50.000 0.00 0.00 41.55 3.66
100 102 2.718452 TTCGCGAGAAGCACAACTGTG 61.718 52.381 9.59 5.45 46.92 3.66
109 111 2.996444 CACAACTGTGCTCTGCAGA 58.004 52.632 17.19 17.19 40.08 4.26
110 112 1.302366 CACAACTGTGCTCTGCAGAA 58.698 50.000 18.85 0.00 40.08 3.02
111 113 1.672363 CACAACTGTGCTCTGCAGAAA 59.328 47.619 18.85 6.25 40.08 2.52
113 115 2.216046 CAACTGTGCTCTGCAGAAAGA 58.784 47.619 18.85 6.80 40.08 2.52
114 116 2.615447 CAACTGTGCTCTGCAGAAAGAA 59.385 45.455 18.85 0.00 40.08 2.52
137 139 1.698506 AAAAACCATGCCTCCACGAA 58.301 45.000 0.00 0.00 0.00 3.85
140 142 1.698506 AACCATGCCTCCACGAAAAA 58.301 45.000 0.00 0.00 0.00 1.94
144 146 1.336440 CATGCCTCCACGAAAAACACA 59.664 47.619 0.00 0.00 0.00 3.72
151 153 5.768317 CCTCCACGAAAAACACATATTTGT 58.232 37.500 0.00 0.00 36.15 2.83
156 158 7.646130 TCCACGAAAAACACATATTTGTTTCTC 59.354 33.333 17.87 13.66 46.68 2.87
160 162 8.555166 GAAAAACACATATTTGTTTCTCGTGA 57.445 30.769 17.87 0.00 46.68 4.35
163 165 6.241207 ACACATATTTGTTTCTCGTGAAGG 57.759 37.500 0.00 0.00 32.34 3.46
166 168 3.626028 ATTTGTTTCTCGTGAAGGCAC 57.374 42.857 0.00 0.00 41.67 5.01
177 179 3.126858 TCGTGAAGGCACATATTTGCTTC 59.873 43.478 13.29 13.81 45.41 3.86
179 181 4.332543 CGTGAAGGCACATATTTGCTTCTA 59.667 41.667 13.29 0.00 45.41 2.10
193 195 6.481954 TTTGCTTCTACGAGGAAAATCTTC 57.518 37.500 0.00 0.00 34.61 2.87
254 256 1.872952 TCTCGTGGAAGCACATGTTTG 59.127 47.619 0.00 0.00 0.00 2.93
299 301 4.014569 TGGATTTCCACGAGAATCACAA 57.985 40.909 0.00 0.00 42.01 3.33
301 303 5.009631 TGGATTTCCACGAGAATCACAAAT 58.990 37.500 0.00 0.00 42.01 2.32
305 307 4.159377 TCCACGAGAATCACAAATTTGC 57.841 40.909 18.12 1.44 33.17 3.68
314 316 5.244402 AGAATCACAAATTTGCTGTCATGGA 59.756 36.000 18.12 3.98 0.00 3.41
317 319 2.028748 ACAAATTTGCTGTCATGGAGGC 60.029 45.455 18.12 0.00 0.00 4.70
326 328 0.248215 GTCATGGAGGCGCGAATTTG 60.248 55.000 12.10 0.00 0.00 2.32
399 401 5.539048 TGTTTCCGGTTTTTCTTTTGTTCA 58.461 33.333 0.00 0.00 0.00 3.18
435 437 6.697641 TTTGGAAACCTACTAGGATCTTGT 57.302 37.500 9.28 0.00 37.67 3.16
472 474 6.426937 ACGCTTGTGAACAGACATATTTTACT 59.573 34.615 0.00 0.00 0.00 2.24
492 494 2.658548 GGAAAGCCCAAAGGGTCTG 58.341 57.895 3.68 0.00 45.47 3.51
494 496 1.704641 GAAAGCCCAAAGGGTCTGTT 58.295 50.000 3.68 0.47 45.47 3.16
495 497 2.039418 GAAAGCCCAAAGGGTCTGTTT 58.961 47.619 3.68 0.00 45.47 2.83
496 498 3.227614 GAAAGCCCAAAGGGTCTGTTTA 58.772 45.455 3.68 0.00 45.47 2.01
497 499 2.586648 AGCCCAAAGGGTCTGTTTAG 57.413 50.000 3.68 0.00 46.51 1.85
498 500 1.075536 AGCCCAAAGGGTCTGTTTAGG 59.924 52.381 3.68 0.00 46.51 2.69
500 502 2.791655 CCCAAAGGGTCTGTTTAGGAC 58.208 52.381 0.00 0.00 38.25 3.85
501 503 2.107552 CCCAAAGGGTCTGTTTAGGACA 59.892 50.000 0.00 0.00 38.25 4.02
502 504 3.146847 CCAAAGGGTCTGTTTAGGACAC 58.853 50.000 0.00 0.00 37.38 3.67
503 505 3.434453 CCAAAGGGTCTGTTTAGGACACA 60.434 47.826 0.00 0.00 39.36 3.72
504 506 4.398319 CAAAGGGTCTGTTTAGGACACAT 58.602 43.478 0.00 0.00 39.36 3.21
505 507 3.983044 AGGGTCTGTTTAGGACACATC 57.017 47.619 0.00 0.00 39.36 3.06
506 508 3.521727 AGGGTCTGTTTAGGACACATCT 58.478 45.455 0.00 0.00 39.36 2.90
508 510 4.712337 AGGGTCTGTTTAGGACACATCTAG 59.288 45.833 0.00 0.00 39.36 2.43
509 511 4.710375 GGGTCTGTTTAGGACACATCTAGA 59.290 45.833 0.00 0.00 37.11 2.43
511 513 6.276847 GGTCTGTTTAGGACACATCTAGATG 58.723 44.000 27.63 27.63 44.15 2.90
544 546 9.113838 AGTTATGTCACATTTAATCTGATGTCC 57.886 33.333 0.00 0.00 34.42 4.02
545 547 8.892723 GTTATGTCACATTTAATCTGATGTCCA 58.107 33.333 0.00 0.00 34.42 4.02
546 548 6.741992 TGTCACATTTAATCTGATGTCCAC 57.258 37.500 0.00 0.00 34.42 4.02
547 549 6.475504 TGTCACATTTAATCTGATGTCCACT 58.524 36.000 0.00 0.00 34.42 4.00
548 550 6.595326 TGTCACATTTAATCTGATGTCCACTC 59.405 38.462 0.00 0.00 34.42 3.51
549 551 6.820656 GTCACATTTAATCTGATGTCCACTCT 59.179 38.462 0.00 0.00 34.42 3.24
550 552 6.820152 TCACATTTAATCTGATGTCCACTCTG 59.180 38.462 0.00 0.00 34.42 3.35
551 553 6.596888 CACATTTAATCTGATGTCCACTCTGT 59.403 38.462 0.00 0.00 34.42 3.41
552 554 7.120285 CACATTTAATCTGATGTCCACTCTGTT 59.880 37.037 0.00 0.00 34.42 3.16
553 555 7.667219 ACATTTAATCTGATGTCCACTCTGTTT 59.333 33.333 0.00 0.00 31.07 2.83
554 556 7.439157 TTTAATCTGATGTCCACTCTGTTTG 57.561 36.000 0.00 0.00 0.00 2.93
555 557 4.630644 ATCTGATGTCCACTCTGTTTGT 57.369 40.909 0.00 0.00 0.00 2.83
556 558 3.732212 TCTGATGTCCACTCTGTTTGTG 58.268 45.455 0.00 0.00 35.39 3.33
557 559 3.387699 TCTGATGTCCACTCTGTTTGTGA 59.612 43.478 0.00 0.00 37.60 3.58
558 560 4.040829 TCTGATGTCCACTCTGTTTGTGAT 59.959 41.667 0.00 0.00 37.60 3.06
559 561 4.318332 TGATGTCCACTCTGTTTGTGATC 58.682 43.478 0.00 0.00 37.60 2.92
560 562 4.040829 TGATGTCCACTCTGTTTGTGATCT 59.959 41.667 0.00 0.00 37.60 2.75
561 563 4.422073 TGTCCACTCTGTTTGTGATCTT 57.578 40.909 0.00 0.00 37.60 2.40
562 564 4.780815 TGTCCACTCTGTTTGTGATCTTT 58.219 39.130 0.00 0.00 37.60 2.52
563 565 5.192927 TGTCCACTCTGTTTGTGATCTTTT 58.807 37.500 0.00 0.00 37.60 2.27
564 566 5.652014 TGTCCACTCTGTTTGTGATCTTTTT 59.348 36.000 0.00 0.00 37.60 1.94
616 618 8.298729 TGTTGTTGCATTATATATTTGTGGGA 57.701 30.769 0.00 0.00 0.00 4.37
617 619 8.412456 TGTTGTTGCATTATATATTTGTGGGAG 58.588 33.333 0.00 0.00 0.00 4.30
618 620 6.980593 TGTTGCATTATATATTTGTGGGAGC 58.019 36.000 0.00 0.00 0.00 4.70
619 621 6.777091 TGTTGCATTATATATTTGTGGGAGCT 59.223 34.615 0.00 0.00 0.00 4.09
620 622 7.287466 TGTTGCATTATATATTTGTGGGAGCTT 59.713 33.333 0.00 0.00 0.00 3.74
621 623 8.792633 GTTGCATTATATATTTGTGGGAGCTTA 58.207 33.333 0.00 0.00 0.00 3.09
629 786 3.334583 TTGTGGGAGCTTAGATGTGAC 57.665 47.619 0.00 0.00 0.00 3.67
630 787 2.256306 TGTGGGAGCTTAGATGTGACA 58.744 47.619 0.00 0.00 0.00 3.58
631 788 2.840038 TGTGGGAGCTTAGATGTGACAT 59.160 45.455 0.00 0.00 0.00 3.06
632 789 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
635 792 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
636 793 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
640 797 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
674 831 9.515020 GATATTAATTGAACAAATTGAAGCCGA 57.485 29.630 0.00 0.00 38.93 5.54
675 832 9.868277 ATATTAATTGAACAAATTGAAGCCGAA 57.132 25.926 0.00 0.00 38.93 4.30
677 834 6.917217 AATTGAACAAATTGAAGCCGAAAA 57.083 29.167 0.00 0.00 37.09 2.29
678 835 7.495135 AATTGAACAAATTGAAGCCGAAAAT 57.505 28.000 0.00 0.00 37.09 1.82
679 836 8.600449 AATTGAACAAATTGAAGCCGAAAATA 57.400 26.923 0.00 0.00 37.09 1.40
682 839 6.644592 TGAACAAATTGAAGCCGAAAATAAGG 59.355 34.615 0.00 0.00 0.00 2.69
695 958 1.392589 AATAAGGCCAGCATGAACGG 58.607 50.000 5.01 0.00 39.69 4.44
701 964 1.817099 CCAGCATGAACGGGCTCTC 60.817 63.158 0.00 0.00 39.69 3.20
702 965 2.169789 CAGCATGAACGGGCTCTCG 61.170 63.158 0.00 0.00 39.69 4.04
703 966 2.184322 GCATGAACGGGCTCTCGA 59.816 61.111 0.00 0.00 0.00 4.04
704 967 1.880340 GCATGAACGGGCTCTCGAG 60.880 63.158 5.93 5.93 0.00 4.04
705 968 1.513158 CATGAACGGGCTCTCGAGT 59.487 57.895 13.13 0.00 0.00 4.18
706 969 0.108615 CATGAACGGGCTCTCGAGTT 60.109 55.000 13.13 0.00 0.00 3.01
707 970 0.608640 ATGAACGGGCTCTCGAGTTT 59.391 50.000 13.13 0.00 0.00 2.66
708 971 0.391597 TGAACGGGCTCTCGAGTTTT 59.608 50.000 13.13 0.00 0.00 2.43
709 972 0.790814 GAACGGGCTCTCGAGTTTTG 59.209 55.000 13.13 2.79 0.00 2.44
710 973 0.106149 AACGGGCTCTCGAGTTTTGT 59.894 50.000 13.13 3.43 0.00 2.83
711 974 0.319641 ACGGGCTCTCGAGTTTTGTC 60.320 55.000 13.13 3.15 0.00 3.18
712 975 1.014564 CGGGCTCTCGAGTTTTGTCC 61.015 60.000 13.13 11.01 0.00 4.02
713 976 0.034896 GGGCTCTCGAGTTTTGTCCA 59.965 55.000 13.13 0.00 0.00 4.02
714 977 1.542547 GGGCTCTCGAGTTTTGTCCAA 60.543 52.381 13.13 0.00 0.00 3.53
715 978 2.218603 GGCTCTCGAGTTTTGTCCAAA 58.781 47.619 13.13 0.00 0.00 3.28
716 979 2.224314 GGCTCTCGAGTTTTGTCCAAAG 59.776 50.000 13.13 0.00 0.00 2.77
717 980 3.131396 GCTCTCGAGTTTTGTCCAAAGA 58.869 45.455 13.13 0.00 0.00 2.52
745 1008 1.265454 ACTCCAGAGGCCCTTTACCG 61.265 60.000 0.00 0.00 0.00 4.02
746 1009 1.229400 TCCAGAGGCCCTTTACCGT 60.229 57.895 0.00 0.00 0.00 4.83
747 1010 0.041535 TCCAGAGGCCCTTTACCGTA 59.958 55.000 0.00 0.00 0.00 4.02
748 1011 1.129058 CCAGAGGCCCTTTACCGTAT 58.871 55.000 0.00 0.00 0.00 3.06
749 1012 1.489230 CCAGAGGCCCTTTACCGTATT 59.511 52.381 0.00 0.00 0.00 1.89
750 1013 2.561569 CAGAGGCCCTTTACCGTATTG 58.438 52.381 0.00 0.00 0.00 1.90
751 1014 1.134189 AGAGGCCCTTTACCGTATTGC 60.134 52.381 0.00 0.00 0.00 3.56
752 1015 0.106868 AGGCCCTTTACCGTATTGCC 60.107 55.000 0.00 0.00 37.68 4.52
753 1016 1.441732 GGCCCTTTACCGTATTGCCG 61.442 60.000 0.00 0.00 0.00 5.69
754 1017 0.745486 GCCCTTTACCGTATTGCCGT 60.745 55.000 0.00 0.00 0.00 5.68
755 1018 1.011333 CCCTTTACCGTATTGCCGTG 58.989 55.000 0.00 0.00 0.00 4.94
756 1019 1.405797 CCCTTTACCGTATTGCCGTGA 60.406 52.381 0.00 0.00 0.00 4.35
757 1020 1.931172 CCTTTACCGTATTGCCGTGAG 59.069 52.381 0.00 0.00 0.00 3.51
758 1021 2.613691 CTTTACCGTATTGCCGTGAGT 58.386 47.619 0.00 0.00 0.00 3.41
759 1022 1.999048 TTACCGTATTGCCGTGAGTG 58.001 50.000 0.00 0.00 0.00 3.51
760 1023 0.458889 TACCGTATTGCCGTGAGTGC 60.459 55.000 0.00 0.00 0.00 4.40
783 1046 1.112315 ACATTGCCAAAACGGGAGCA 61.112 50.000 0.00 0.00 35.90 4.26
787 1050 1.172180 TGCCAAAACGGGAGCAGAAG 61.172 55.000 0.00 0.00 34.06 2.85
788 1051 1.581447 CCAAAACGGGAGCAGAAGC 59.419 57.895 0.00 0.00 42.56 3.86
864 1127 2.202932 ACGCCATGGTCATCGAGC 60.203 61.111 14.67 0.00 0.00 5.03
966 1229 5.925969 CCGAATTGGAAAAGTAAAATGCAGT 59.074 36.000 0.00 0.00 42.00 4.40
973 1236 8.121167 TGGAAAAGTAAAATGCAGTAAAAACG 57.879 30.769 0.00 0.00 0.00 3.60
1444 1710 2.049802 AGTACGCGGTGGTGTTCG 60.050 61.111 12.47 0.00 38.08 3.95
2364 2656 4.680567 GTCTTCGTCTTCTACAACTTCCAC 59.319 45.833 0.00 0.00 0.00 4.02
2500 2798 1.757574 CATGCACGTTTCCAAGTGTG 58.242 50.000 0.00 0.00 40.26 3.82
2501 2799 1.065401 CATGCACGTTTCCAAGTGTGT 59.935 47.619 0.00 0.00 40.26 3.72
2502 2800 2.025589 TGCACGTTTCCAAGTGTGTA 57.974 45.000 0.00 0.00 40.26 2.90
2503 2801 2.566913 TGCACGTTTCCAAGTGTGTAT 58.433 42.857 0.00 0.00 40.26 2.29
2504 2802 3.729966 TGCACGTTTCCAAGTGTGTATA 58.270 40.909 0.00 0.00 40.26 1.47
2505 2803 3.495377 TGCACGTTTCCAAGTGTGTATAC 59.505 43.478 0.00 0.00 40.26 1.47
2506 2804 3.495377 GCACGTTTCCAAGTGTGTATACA 59.505 43.478 0.08 0.08 40.26 2.29
2507 2805 4.377022 GCACGTTTCCAAGTGTGTATACAG 60.377 45.833 5.62 0.00 40.26 2.74
2605 2903 2.826128 CGGCCTCTGCATAACTAGGATA 59.174 50.000 0.00 0.00 40.13 2.59
2698 2996 4.948004 CCATAGACCGACACTATGCCTATA 59.052 45.833 13.79 0.00 43.10 1.31
2830 3128 1.743958 ACTCTGCTCGTTGTAGCGTAT 59.256 47.619 0.00 0.00 45.85 3.06
2943 3241 4.891992 AAGCGACCATAGTAAGGCATAT 57.108 40.909 0.00 0.00 0.00 1.78
2988 3286 6.751514 TTGTATGCATTTGAAATACCGTCT 57.248 33.333 3.54 0.00 0.00 4.18
2989 3287 6.117911 TGTATGCATTTGAAATACCGTCTG 57.882 37.500 3.54 0.00 0.00 3.51
3037 3335 4.156922 CACTTGTGGGCGGATACAAATTTA 59.843 41.667 0.00 0.00 36.47 1.40
3053 3351 6.930731 ACAAATTTAACGCTATTTGGATGGT 58.069 32.000 12.62 0.00 42.96 3.55
3338 3639 3.418684 AGTAAGGTTCCAGCGAAACAT 57.581 42.857 0.00 0.00 38.24 2.71
3369 3670 5.104941 ACCTTGTGTCAGGATAATCGAATCA 60.105 40.000 0.00 0.00 37.39 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.552350 AGTTCTTTTTCCCCTAAACCCTAAAC 59.448 38.462 0.00 0.00 0.00 2.01
6 7 6.283948 AGTTCTTTTTCCCCTAAACCCTAA 57.716 37.500 0.00 0.00 0.00 2.69
7 8 5.935668 AGTTCTTTTTCCCCTAAACCCTA 57.064 39.130 0.00 0.00 0.00 3.53
8 9 4.827036 AGTTCTTTTTCCCCTAAACCCT 57.173 40.909 0.00 0.00 0.00 4.34
9 10 5.105473 GCATAGTTCTTTTTCCCCTAAACCC 60.105 44.000 0.00 0.00 0.00 4.11
10 11 5.715279 AGCATAGTTCTTTTTCCCCTAAACC 59.285 40.000 0.00 0.00 0.00 3.27
11 12 6.127703 GGAGCATAGTTCTTTTTCCCCTAAAC 60.128 42.308 0.00 0.00 0.00 2.01
12 13 5.949952 GGAGCATAGTTCTTTTTCCCCTAAA 59.050 40.000 0.00 0.00 0.00 1.85
13 14 5.014755 TGGAGCATAGTTCTTTTTCCCCTAA 59.985 40.000 0.00 0.00 0.00 2.69
14 15 4.538490 TGGAGCATAGTTCTTTTTCCCCTA 59.462 41.667 0.00 0.00 0.00 3.53
15 16 3.333680 TGGAGCATAGTTCTTTTTCCCCT 59.666 43.478 0.00 0.00 0.00 4.79
16 17 3.697166 TGGAGCATAGTTCTTTTTCCCC 58.303 45.455 0.00 0.00 0.00 4.81
17 18 4.949856 TCATGGAGCATAGTTCTTTTTCCC 59.050 41.667 0.00 0.00 0.00 3.97
18 19 5.882557 TCTCATGGAGCATAGTTCTTTTTCC 59.117 40.000 0.00 0.00 0.00 3.13
19 20 6.992063 TCTCATGGAGCATAGTTCTTTTTC 57.008 37.500 0.00 0.00 0.00 2.29
25 26 3.801698 TGCTTCTCATGGAGCATAGTTC 58.198 45.455 13.06 0.00 31.84 3.01
41 43 8.704234 CCTCAACGAGAAGTAAATATATGCTTC 58.296 37.037 13.03 13.03 38.01 3.86
47 49 6.978659 CAGTGCCTCAACGAGAAGTAAATATA 59.021 38.462 0.00 0.00 0.00 0.86
49 51 5.047590 TCAGTGCCTCAACGAGAAGTAAATA 60.048 40.000 0.00 0.00 0.00 1.40
53 55 2.235891 TCAGTGCCTCAACGAGAAGTA 58.764 47.619 0.00 0.00 0.00 2.24
60 62 3.389741 GCAAATCAGTGCCTCAACG 57.610 52.632 0.00 0.00 38.66 4.10
68 70 0.095935 CTCGCGAAGGCAAATCAGTG 59.904 55.000 11.33 0.00 39.92 3.66
71 73 1.078709 CTTCTCGCGAAGGCAAATCA 58.921 50.000 11.33 0.00 42.35 2.57
72 74 0.247854 GCTTCTCGCGAAGGCAAATC 60.248 55.000 16.39 0.00 45.41 2.17
81 83 1.067416 ACAGTTGTGCTTCTCGCGA 59.933 52.632 9.26 9.26 43.27 5.87
82 84 1.202568 CACAGTTGTGCTTCTCGCG 59.797 57.895 0.00 0.00 43.27 5.87
96 98 3.976793 TTTTCTTTCTGCAGAGCACAG 57.023 42.857 17.43 11.56 33.79 3.66
120 122 1.698506 TTTTCGTGGAGGCATGGTTT 58.301 45.000 0.00 0.00 0.00 3.27
128 130 5.768317 ACAAATATGTGTTTTTCGTGGAGG 58.232 37.500 0.00 0.00 38.69 4.30
140 142 5.334879 GCCTTCACGAGAAACAAATATGTGT 60.335 40.000 0.00 0.00 40.46 3.72
144 146 4.759693 TGTGCCTTCACGAGAAACAAATAT 59.240 37.500 0.00 0.00 46.01 1.28
151 153 4.379394 GCAAATATGTGCCTTCACGAGAAA 60.379 41.667 6.61 0.00 46.01 2.52
156 158 3.127548 AGAAGCAAATATGTGCCTTCACG 59.872 43.478 21.80 0.00 46.14 4.35
157 159 4.708726 AGAAGCAAATATGTGCCTTCAC 57.291 40.909 21.80 9.54 46.14 3.18
160 162 4.513442 TCGTAGAAGCAAATATGTGCCTT 58.487 39.130 14.50 8.09 46.14 4.35
163 165 4.119862 TCCTCGTAGAAGCAAATATGTGC 58.880 43.478 10.09 10.09 45.28 4.57
166 168 8.147642 AGATTTTCCTCGTAGAAGCAAATATG 57.852 34.615 0.00 0.00 34.09 1.78
177 179 7.891183 TTTTCAGAGAAGATTTTCCTCGTAG 57.109 36.000 0.00 0.00 33.64 3.51
210 212 4.808558 GCAAATGTGTGCTTCTTATGGAA 58.191 39.130 0.00 0.00 41.51 3.53
211 213 4.439305 GCAAATGTGTGCTTCTTATGGA 57.561 40.909 0.00 0.00 41.51 3.41
221 223 1.664016 CCACGAGAAGCAAATGTGTGC 60.664 52.381 0.00 0.00 45.28 4.57
282 284 4.981674 GCAAATTTGTGATTCTCGTGGAAA 59.018 37.500 19.03 0.00 37.49 3.13
286 288 4.539870 ACAGCAAATTTGTGATTCTCGTG 58.460 39.130 19.03 6.20 0.00 4.35
299 301 0.813184 CGCCTCCATGACAGCAAATT 59.187 50.000 0.00 0.00 0.00 1.82
301 303 2.334946 GCGCCTCCATGACAGCAAA 61.335 57.895 0.00 0.00 0.00 3.68
305 307 1.091771 AATTCGCGCCTCCATGACAG 61.092 55.000 0.00 0.00 0.00 3.51
314 316 1.154225 CGAAAGCAAATTCGCGCCT 60.154 52.632 0.00 0.00 44.69 5.52
372 374 7.260558 ACAAAAGAAAAACCGGAAACAAAAA 57.739 28.000 9.46 0.00 0.00 1.94
373 375 6.862711 ACAAAAGAAAAACCGGAAACAAAA 57.137 29.167 9.46 0.00 0.00 2.44
374 376 6.482308 TGAACAAAAGAAAAACCGGAAACAAA 59.518 30.769 9.46 0.00 0.00 2.83
375 377 5.989777 TGAACAAAAGAAAAACCGGAAACAA 59.010 32.000 9.46 0.00 0.00 2.83
376 378 5.539048 TGAACAAAAGAAAAACCGGAAACA 58.461 33.333 9.46 0.00 0.00 2.83
416 418 7.598189 GTGAAACAAGATCCTAGTAGGTTTC 57.402 40.000 16.02 15.87 41.60 2.78
435 437 4.251543 TCACAAGCGTAGATCTGTGAAA 57.748 40.909 5.18 0.00 39.48 2.69
486 488 3.983044 AGATGTGTCCTAAACAGACCC 57.017 47.619 0.00 0.00 38.97 4.46
487 489 5.916661 TCTAGATGTGTCCTAAACAGACC 57.083 43.478 0.00 0.00 38.97 3.85
518 520 9.113838 GGACATCAGATTAAATGTGACATAACT 57.886 33.333 0.00 0.00 36.28 2.24
519 521 8.892723 TGGACATCAGATTAAATGTGACATAAC 58.107 33.333 0.00 0.00 36.28 1.89
520 522 8.892723 GTGGACATCAGATTAAATGTGACATAA 58.107 33.333 0.00 0.00 36.28 1.90
521 523 8.267183 AGTGGACATCAGATTAAATGTGACATA 58.733 33.333 0.00 0.00 36.28 2.29
522 524 7.114754 AGTGGACATCAGATTAAATGTGACAT 58.885 34.615 0.00 0.00 36.28 3.06
523 525 6.475504 AGTGGACATCAGATTAAATGTGACA 58.524 36.000 0.00 0.00 36.28 3.58
524 526 6.820656 AGAGTGGACATCAGATTAAATGTGAC 59.179 38.462 0.00 0.00 36.28 3.67
525 527 6.820152 CAGAGTGGACATCAGATTAAATGTGA 59.180 38.462 0.00 0.00 36.28 3.58
526 528 6.596888 ACAGAGTGGACATCAGATTAAATGTG 59.403 38.462 0.00 0.00 36.28 3.21
527 529 6.715280 ACAGAGTGGACATCAGATTAAATGT 58.285 36.000 0.00 0.00 38.78 2.71
528 530 7.621428 AACAGAGTGGACATCAGATTAAATG 57.379 36.000 0.00 0.00 0.00 2.32
529 531 7.667219 ACAAACAGAGTGGACATCAGATTAAAT 59.333 33.333 0.00 0.00 0.00 1.40
530 532 6.998074 ACAAACAGAGTGGACATCAGATTAAA 59.002 34.615 0.00 0.00 0.00 1.52
531 533 6.427853 CACAAACAGAGTGGACATCAGATTAA 59.572 38.462 0.00 0.00 33.43 1.40
532 534 5.934043 CACAAACAGAGTGGACATCAGATTA 59.066 40.000 0.00 0.00 33.43 1.75
533 535 4.758674 CACAAACAGAGTGGACATCAGATT 59.241 41.667 0.00 0.00 33.43 2.40
534 536 4.040829 TCACAAACAGAGTGGACATCAGAT 59.959 41.667 0.00 0.00 37.58 2.90
535 537 3.387699 TCACAAACAGAGTGGACATCAGA 59.612 43.478 0.00 0.00 37.58 3.27
536 538 3.732212 TCACAAACAGAGTGGACATCAG 58.268 45.455 0.00 0.00 37.58 2.90
537 539 3.836365 TCACAAACAGAGTGGACATCA 57.164 42.857 0.00 0.00 37.58 3.07
538 540 4.573900 AGATCACAAACAGAGTGGACATC 58.426 43.478 0.00 0.00 37.58 3.06
539 541 4.630644 AGATCACAAACAGAGTGGACAT 57.369 40.909 0.00 0.00 37.58 3.06
540 542 4.422073 AAGATCACAAACAGAGTGGACA 57.578 40.909 0.00 0.00 37.58 4.02
541 543 5.757850 AAAAGATCACAAACAGAGTGGAC 57.242 39.130 0.00 0.00 37.58 4.02
590 592 8.753133 TCCCACAAATATATAATGCAACAACAA 58.247 29.630 0.00 0.00 0.00 2.83
592 594 7.382218 GCTCCCACAAATATATAATGCAACAAC 59.618 37.037 0.00 0.00 0.00 3.32
593 595 7.287466 AGCTCCCACAAATATATAATGCAACAA 59.713 33.333 0.00 0.00 0.00 2.83
594 596 6.777091 AGCTCCCACAAATATATAATGCAACA 59.223 34.615 0.00 0.00 0.00 3.33
595 597 7.219484 AGCTCCCACAAATATATAATGCAAC 57.781 36.000 0.00 0.00 0.00 4.17
602 604 9.100197 TCACATCTAAGCTCCCACAAATATATA 57.900 33.333 0.00 0.00 0.00 0.86
603 605 7.880195 GTCACATCTAAGCTCCCACAAATATAT 59.120 37.037 0.00 0.00 0.00 0.86
604 606 7.147567 TGTCACATCTAAGCTCCCACAAATATA 60.148 37.037 0.00 0.00 0.00 0.86
606 608 5.045942 TGTCACATCTAAGCTCCCACAAATA 60.046 40.000 0.00 0.00 0.00 1.40
607 609 4.263462 TGTCACATCTAAGCTCCCACAAAT 60.263 41.667 0.00 0.00 0.00 2.32
609 611 2.637382 TGTCACATCTAAGCTCCCACAA 59.363 45.455 0.00 0.00 0.00 3.33
611 613 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
612 614 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
614 616 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
649 806 9.868277 TTCGGCTTCAATTTGTTCAATTAATAT 57.132 25.926 0.00 0.00 32.90 1.28
650 807 9.698309 TTTCGGCTTCAATTTGTTCAATTAATA 57.302 25.926 0.00 0.00 32.90 0.98
655 812 8.600449 TTATTTTCGGCTTCAATTTGTTCAAT 57.400 26.923 0.00 0.00 0.00 2.57
658 815 6.401047 GCCTTATTTTCGGCTTCAATTTGTTC 60.401 38.462 0.00 0.00 42.98 3.18
659 816 5.408299 GCCTTATTTTCGGCTTCAATTTGTT 59.592 36.000 0.00 0.00 42.98 2.83
660 817 4.929211 GCCTTATTTTCGGCTTCAATTTGT 59.071 37.500 0.00 0.00 42.98 2.83
661 818 4.329801 GGCCTTATTTTCGGCTTCAATTTG 59.670 41.667 0.00 0.00 45.57 2.32
663 820 3.513515 TGGCCTTATTTTCGGCTTCAATT 59.486 39.130 3.32 0.00 45.57 2.32
664 821 3.096092 TGGCCTTATTTTCGGCTTCAAT 58.904 40.909 3.32 0.00 45.57 2.57
666 823 2.091541 CTGGCCTTATTTTCGGCTTCA 58.908 47.619 3.32 0.00 45.57 3.02
667 824 1.202302 GCTGGCCTTATTTTCGGCTTC 60.202 52.381 3.32 0.00 45.57 3.86
668 825 0.817654 GCTGGCCTTATTTTCGGCTT 59.182 50.000 3.32 0.00 45.57 4.35
669 826 0.323360 TGCTGGCCTTATTTTCGGCT 60.323 50.000 3.32 0.00 45.57 5.52
670 827 0.746659 ATGCTGGCCTTATTTTCGGC 59.253 50.000 3.32 0.00 45.55 5.54
672 829 3.438360 GTTCATGCTGGCCTTATTTTCG 58.562 45.455 3.32 0.00 0.00 3.46
674 831 2.166254 CCGTTCATGCTGGCCTTATTTT 59.834 45.455 3.32 0.00 0.00 1.82
675 832 1.750778 CCGTTCATGCTGGCCTTATTT 59.249 47.619 3.32 0.00 0.00 1.40
677 834 0.466189 CCCGTTCATGCTGGCCTTAT 60.466 55.000 3.32 0.00 0.00 1.73
678 835 1.077787 CCCGTTCATGCTGGCCTTA 60.078 57.895 3.32 0.00 0.00 2.69
679 836 2.361610 CCCGTTCATGCTGGCCTT 60.362 61.111 3.32 0.00 0.00 4.35
682 839 3.512516 GAGCCCGTTCATGCTGGC 61.513 66.667 6.53 6.53 44.35 4.85
683 840 1.817099 GAGAGCCCGTTCATGCTGG 60.817 63.158 0.00 0.00 38.11 4.85
684 841 2.169789 CGAGAGCCCGTTCATGCTG 61.170 63.158 0.00 0.00 38.11 4.41
687 844 0.108615 AACTCGAGAGCCCGTTCATG 60.109 55.000 21.68 0.00 0.00 3.07
695 958 1.878953 TTGGACAAAACTCGAGAGCC 58.121 50.000 21.68 10.69 0.00 4.70
730 993 2.561569 CAATACGGTAAAGGGCCTCTG 58.438 52.381 6.46 1.47 0.00 3.35
749 1012 0.534877 AATGTCTTGCACTCACGGCA 60.535 50.000 0.00 0.00 40.00 5.69
750 1013 0.110056 CAATGTCTTGCACTCACGGC 60.110 55.000 0.00 0.00 0.00 5.68
760 1023 1.339610 TCCCGTTTTGGCAATGTCTTG 59.660 47.619 0.00 0.00 35.87 3.02
783 1046 3.115554 GCGACATTGTTTGTTTGCTTCT 58.884 40.909 0.00 0.00 39.18 2.85
787 1050 1.851658 AGGCGACATTGTTTGTTTGC 58.148 45.000 0.00 0.00 39.18 3.68
788 1051 3.705604 AGAAGGCGACATTGTTTGTTTG 58.294 40.909 0.00 0.00 39.18 2.93
864 1127 2.180017 GCAATGGACAAGCGGCAG 59.820 61.111 1.45 0.00 0.00 4.85
966 1229 5.444877 CGCTGTGGATTAATCGTCGTTTTTA 60.445 40.000 9.32 0.00 0.00 1.52
971 1234 1.135199 ACGCTGTGGATTAATCGTCGT 60.135 47.619 9.32 10.26 0.00 4.34
972 1235 1.556564 ACGCTGTGGATTAATCGTCG 58.443 50.000 9.32 9.72 0.00 5.12
973 1236 2.536928 GCAACGCTGTGGATTAATCGTC 60.537 50.000 9.32 5.63 0.00 4.20
1010 1273 4.181010 CCGAGGTGCCCATGGAGG 62.181 72.222 15.22 0.00 37.03 4.30
2007 2299 1.455587 CACCACCAGCACCAGGTTT 60.456 57.895 0.00 0.00 37.23 3.27
2364 2656 2.669240 GGGTTCTTCTCCACCGGG 59.331 66.667 6.32 0.00 33.34 5.73
2445 2737 7.851387 AGTATGAACTAAAGCTTAGAAAGCC 57.149 36.000 0.00 0.00 44.61 4.35
2515 2813 7.333423 TGAGATAATAAAATCGCCCTTTATCGG 59.667 37.037 0.00 0.00 33.43 4.18
2605 2903 2.656947 ACTGGTATTTGGCTGTGTGT 57.343 45.000 0.00 0.00 0.00 3.72
2698 2996 1.137086 CGGTCCACCATCTCTTTCGAT 59.863 52.381 0.00 0.00 35.14 3.59
2830 3128 0.166597 CACTCGCTTCGTACGTGGTA 59.833 55.000 16.05 0.00 0.00 3.25
2943 3241 0.468226 CGCTAATAAGGGTGGGAGCA 59.532 55.000 0.00 0.00 0.00 4.26
2988 3286 4.841422 CCAATATTTTTGGTCATTGGCCA 58.159 39.130 5.72 5.72 40.58 5.36
3037 3335 2.752903 GGTCAACCATCCAAATAGCGTT 59.247 45.455 0.00 0.00 35.64 4.84
3053 3351 0.102663 TGTGCGTTCTACGTGGTCAA 59.897 50.000 0.00 0.00 44.73 3.18
3291 3592 2.897969 GGGGTCTTTCACAGTAGACTCA 59.102 50.000 4.53 0.00 42.46 3.41
3369 3670 6.494666 TGGAATAATCTATTGTCCCGTCTT 57.505 37.500 5.34 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.