Multiple sequence alignment - TraesCS4A01G025200

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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 TraesCS4A01G025200 chr4A 100.000 5844 0 0 1 5844 17268851 17263008 0.000000e+00 10792.0
1 TraesCS4A01G025200 chr4A 95.973 149 5 1 1 149 513314786 513314639 2.100000e-59 241.0
2 TraesCS4A01G025200 chr4D 91.977 4425 186 74 1529 5836 449726003 449730375 0.000000e+00 6048.0
3 TraesCS4A01G025200 chr4D 94.933 967 29 8 544 1501 449724939 449725894 0.000000e+00 1496.0
4 TraesCS4A01G025200 chr4D 95.865 532 18 1 1 528 446988105 446987574 0.000000e+00 857.0
5 TraesCS4A01G025200 chr4B 94.416 3761 133 29 738 4443 562348745 562352483 0.000000e+00 5710.0
6 TraesCS4A01G025200 chr4B 87.853 1416 99 29 4460 5836 562352665 562354046 0.000000e+00 1594.0
7 TraesCS4A01G025200 chr4B 89.202 213 14 4 544 747 562343559 562343771 2.090000e-64 257.0
8 TraesCS4A01G025200 chr2A 97.524 525 13 0 1 525 654734794 654735318 0.000000e+00 898.0
9 TraesCS4A01G025200 chr7A 95.564 541 23 1 1 540 643995736 643995196 0.000000e+00 865.0
10 TraesCS4A01G025200 chr3A 96.381 525 19 0 1 525 157989539 157989015 0.000000e+00 865.0
11 TraesCS4A01G025200 chr3B 95.810 525 20 1 1 525 61097440 61097962 0.000000e+00 846.0
12 TraesCS4A01G025200 chr3B 95.619 525 23 0 1 525 755565012 755564488 0.000000e+00 843.0
13 TraesCS4A01G025200 chr5B 89.150 553 33 10 1 526 532174734 532174182 0.000000e+00 664.0
14 TraesCS4A01G025200 chr5B 91.768 413 31 2 116 527 386025180 386025590 6.570000e-159 571.0
15 TraesCS4A01G025200 chr3D 91.346 416 34 2 111 525 612764481 612764067 8.500000e-158 568.0
16 TraesCS4A01G025200 chr5A 95.973 149 4 2 1 149 653893187 653893333 2.100000e-59 241.0
17 TraesCS4A01G025200 chr6B 100.000 30 0 0 519 548 237280804 237280775 8.180000e-04 56.5


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 TraesCS4A01G025200 chr4A 17263008 17268851 5843 True 10792 10792 100.0000 1 5844 1 chr4A.!!$R1 5843
1 TraesCS4A01G025200 chr4D 449724939 449730375 5436 False 3772 6048 93.4550 544 5836 2 chr4D.!!$F1 5292
2 TraesCS4A01G025200 chr4D 446987574 446988105 531 True 857 857 95.8650 1 528 1 chr4D.!!$R1 527
3 TraesCS4A01G025200 chr4B 562348745 562354046 5301 False 3652 5710 91.1345 738 5836 2 chr4B.!!$F2 5098
4 TraesCS4A01G025200 chr2A 654734794 654735318 524 False 898 898 97.5240 1 525 1 chr2A.!!$F1 524
5 TraesCS4A01G025200 chr7A 643995196 643995736 540 True 865 865 95.5640 1 540 1 chr7A.!!$R1 539
6 TraesCS4A01G025200 chr3A 157989015 157989539 524 True 865 865 96.3810 1 525 1 chr3A.!!$R1 524
7 TraesCS4A01G025200 chr3B 61097440 61097962 522 False 846 846 95.8100 1 525 1 chr3B.!!$F1 524
8 TraesCS4A01G025200 chr3B 755564488 755565012 524 True 843 843 95.6190 1 525 1 chr3B.!!$R1 524
9 TraesCS4A01G025200 chr5B 532174182 532174734 552 True 664 664 89.1500 1 526 1 chr5B.!!$R1 525

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
992 1034 0.256464 GGACCTCGGAGGAAGAGAGA 59.744 60.000 30.13 0.0 37.67 3.10 F
1496 1546 1.128692 GCGCCTAGTGTTGAATGTGTC 59.871 52.381 0.00 0.0 0.00 3.67 F
2691 2861 0.253044 TGGATGGCAAGCTCTACACC 59.747 55.000 0.00 0.0 0.00 4.16 F
3452 3623 0.824109 TGTCCTTGCTAGGTCGATGG 59.176 55.000 14.12 0.0 42.60 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2166 1.280133 CTCTTGATTCCAGTGGAGCCA 59.720 52.381 12.67 11.38 31.21 4.75 R
3452 3623 1.202382 CCACCGAGGTTCGAGAATACC 60.202 57.143 0.00 0.00 43.74 2.73 R
3821 4017 0.621862 GAACTGGGGGATGGAGGACT 60.622 60.000 0.00 0.00 0.00 3.85 R
5086 5458 1.347707 TGCTAACAGCCAGTAAGTGCT 59.652 47.619 0.00 0.00 41.51 4.40 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
56 57 4.672587 AACCATCGCTCACTGTACATAT 57.327 40.909 0.00 0.00 0.00 1.78
237 266 8.231837 GCTCTCTTATGTTCCTACTCGTATAAG 58.768 40.741 0.00 0.00 32.27 1.73
297 326 5.518848 TGACTGCATTGAACTTGATGTTT 57.481 34.783 0.00 0.00 39.30 2.83
469 498 2.488204 TGCGGTTTGATCTTCCATCA 57.512 45.000 0.00 0.00 0.00 3.07
474 503 4.002982 CGGTTTGATCTTCCATCACTTGA 58.997 43.478 0.00 0.00 0.00 3.02
530 563 3.361053 CGCGTTGCCGATCTAGTATTTAG 59.639 47.826 0.00 0.00 35.63 1.85
532 565 4.558095 GCGTTGCCGATCTAGTATTTAGGA 60.558 45.833 0.00 0.00 35.63 2.94
540 573 5.106237 CGATCTAGTATTTAGGAACGGAGGG 60.106 48.000 0.00 0.00 0.00 4.30
541 574 4.477249 TCTAGTATTTAGGAACGGAGGGG 58.523 47.826 0.00 0.00 0.00 4.79
542 575 2.405559 AGTATTTAGGAACGGAGGGGG 58.594 52.381 0.00 0.00 0.00 5.40
598 631 1.374252 GACATCGGCGACCAAGTGT 60.374 57.895 13.76 12.93 0.00 3.55
602 635 1.816863 ATCGGCGACCAAGTGTCAGT 61.817 55.000 13.76 0.00 44.71 3.41
609 642 3.496884 GCGACCAAGTGTCAGTCAAATAA 59.503 43.478 0.00 0.00 44.71 1.40
616 649 6.018262 CCAAGTGTCAGTCAAATAAAAGACGA 60.018 38.462 0.00 0.00 39.67 4.20
705 738 2.193536 GGCCTTCTGTGCCGTTGTT 61.194 57.895 0.00 0.00 39.48 2.83
788 823 4.322953 CCGTTCACTTTAGCTACCCCTTTA 60.323 45.833 0.00 0.00 0.00 1.85
798 833 3.008266 AGCTACCCCTTTACGTAAAAGCA 59.992 43.478 29.35 9.92 42.85 3.91
884 919 9.583765 AGAGGAATCTAAACAAATTCGTACTAC 57.416 33.333 0.00 0.00 33.57 2.73
890 925 7.889469 TCTAAACAAATTCGTACTACTCCACT 58.111 34.615 0.00 0.00 0.00 4.00
990 1032 1.077644 CGGACCTCGGAGGAAGAGA 60.078 63.158 30.13 0.00 37.67 3.10
991 1033 1.098712 CGGACCTCGGAGGAAGAGAG 61.099 65.000 30.13 10.86 37.67 3.20
992 1034 0.256464 GGACCTCGGAGGAAGAGAGA 59.744 60.000 30.13 0.00 37.67 3.10
993 1035 1.675552 GACCTCGGAGGAAGAGAGAG 58.324 60.000 30.13 0.78 37.67 3.20
994 1036 1.210967 GACCTCGGAGGAAGAGAGAGA 59.789 57.143 30.13 0.00 37.67 3.10
995 1037 1.211949 ACCTCGGAGGAAGAGAGAGAG 59.788 57.143 30.13 0.00 37.67 3.20
1386 1434 2.821810 GCCGCTTCTCCTGCTTCC 60.822 66.667 0.00 0.00 0.00 3.46
1407 1455 2.613506 GGTTCGTTTGTCGGCAGGG 61.614 63.158 0.00 0.00 40.32 4.45
1417 1465 3.373565 CGGCAGGGAAGGTTTGGC 61.374 66.667 0.00 0.00 0.00 4.52
1479 1529 1.442769 TCTTCTGGAATGACAAGCGC 58.557 50.000 0.00 0.00 0.00 5.92
1496 1546 1.128692 GCGCCTAGTGTTGAATGTGTC 59.871 52.381 0.00 0.00 0.00 3.67
1540 1685 3.068307 ACTGGTTAGCTAGATTGCTACCG 59.932 47.826 0.00 2.79 44.15 4.02
1552 1697 4.814294 CTACCGCCACCTCACCGC 62.814 72.222 0.00 0.00 0.00 5.68
1592 1737 7.911651 TGAACTGGATTCTTAGAGTGAAGATT 58.088 34.615 0.00 0.00 38.25 2.40
1597 1742 8.789767 TGGATTCTTAGAGTGAAGATTCCTAT 57.210 34.615 19.86 0.00 46.69 2.57
1688 1833 7.106439 TGTTTGTTTCTGGTGATGTTATTGT 57.894 32.000 0.00 0.00 0.00 2.71
1712 1857 7.445096 TGTTGCATGAGTGGTCTTATTATATGG 59.555 37.037 0.00 0.00 0.00 2.74
1717 1862 9.559732 CATGAGTGGTCTTATTATATGGTTTCA 57.440 33.333 0.00 0.00 0.00 2.69
1718 1863 9.784531 ATGAGTGGTCTTATTATATGGTTTCAG 57.215 33.333 0.00 0.00 0.00 3.02
1722 1867 7.282224 GTGGTCTTATTATATGGTTTCAGCACA 59.718 37.037 0.00 0.00 0.00 4.57
1724 1869 8.507249 GGTCTTATTATATGGTTTCAGCACATC 58.493 37.037 0.00 0.00 0.00 3.06
1749 1894 6.936335 CCAGTTATCCTTGCTTTGGAATTTTT 59.064 34.615 0.00 0.00 37.13 1.94
1804 1958 2.872858 AGACAGCTGTCCGAAGTTTTTC 59.127 45.455 37.09 13.69 45.85 2.29
1932 2088 6.655078 ATTTGCTGTTTCCTTGTGTAGAAT 57.345 33.333 0.00 0.00 0.00 2.40
1967 2123 9.373603 TGCGCTTGATAATTCTTAACTTTACTA 57.626 29.630 9.73 0.00 0.00 1.82
2059 2215 3.920446 TGCAGTATGTAGCAAGTTTCGA 58.080 40.909 0.00 0.00 37.90 3.71
2066 2222 4.316205 TGTAGCAAGTTTCGAGAGACAA 57.684 40.909 0.00 0.00 41.84 3.18
2077 2233 1.066914 GAGAGACAAGCAGTTCTGCG 58.933 55.000 17.28 8.30 40.27 5.18
2096 2252 6.086222 TCTGCGTTTATCTTCTTGCATTTTC 58.914 36.000 0.00 0.00 0.00 2.29
2100 2256 6.611381 CGTTTATCTTCTTGCATTTTCCTCA 58.389 36.000 0.00 0.00 0.00 3.86
2168 2324 2.146342 GTGTTCCACAGTCCACATCAG 58.854 52.381 0.00 0.00 34.08 2.90
2557 2727 4.000325 GGTTGGGCAATGTTTGTAAATCC 59.000 43.478 0.00 0.00 0.00 3.01
2691 2861 0.253044 TGGATGGCAAGCTCTACACC 59.747 55.000 0.00 0.00 0.00 4.16
2895 3065 4.418013 TGTTCATGTGTTTATTCGGCAG 57.582 40.909 0.00 0.00 0.00 4.85
2931 3101 1.909302 GGGTTTGATGAGGAGGTGAGA 59.091 52.381 0.00 0.00 0.00 3.27
2983 3153 3.296854 ACGATAGATGAGGTGCCTTGTA 58.703 45.455 0.00 0.00 41.38 2.41
3386 3556 3.418684 AATACGTGGCCTTCAAGTTCT 57.581 42.857 3.32 0.00 38.87 3.01
3452 3623 0.824109 TGTCCTTGCTAGGTCGATGG 59.176 55.000 14.12 0.00 42.60 3.51
3468 3639 2.604855 CGATGGGTATTCTCGAACCTCG 60.605 54.545 4.10 3.20 42.10 4.63
3631 3802 5.560722 TCAACTCACAACCAGGAATCTTA 57.439 39.130 0.00 0.00 0.00 2.10
3643 3814 7.660030 ACCAGGAATCTTAAAAACCATATGG 57.340 36.000 20.68 20.68 42.17 2.74
3826 4022 3.908103 TGGTAGCCTTTCAAGTTAGTCCT 59.092 43.478 0.00 0.00 0.00 3.85
3831 4027 3.942115 GCCTTTCAAGTTAGTCCTCCATC 59.058 47.826 0.00 0.00 0.00 3.51
3884 4080 2.901042 GGTGCCCTCTAACCCTCG 59.099 66.667 0.00 0.00 0.00 4.63
3958 4154 8.428063 AGTTCATTTGGTCAATTTGTTTGGATA 58.572 29.630 0.00 0.00 35.92 2.59
4008 4204 5.776744 ACAATCTCCTGAAACTGAATTTGC 58.223 37.500 0.00 0.00 0.00 3.68
4104 4300 9.582431 CTCTATTGAATGCTTTTTCATTGTGAT 57.418 29.630 0.00 0.00 36.85 3.06
4197 4398 5.035556 AGGAGCAGGTGATAATATATGGCT 58.964 41.667 0.00 0.00 0.00 4.75
4207 4408 7.972277 GGTGATAATATATGGCTTGCATCAAAG 59.028 37.037 0.00 0.00 0.00 2.77
4229 4430 3.971245 TTGTTGCACAAAAAGGAGGTT 57.029 38.095 0.00 0.00 34.76 3.50
4527 4893 4.996758 GGAATTGCAATTGGTGTTAAAGCT 59.003 37.500 28.67 0.00 0.00 3.74
4693 5059 5.705441 CGGATTCCTGCATTTAGCCTATTTA 59.295 40.000 0.30 0.00 44.83 1.40
4903 5269 3.316308 GTGCATTCTTTTGACCTGTCACT 59.684 43.478 0.00 0.00 39.66 3.41
4933 5299 4.859304 TCCTTTCTTCTTAGCACGTACA 57.141 40.909 0.00 0.00 0.00 2.90
4981 5347 6.800408 CGGCATCATTGTATTGATCTTGATTC 59.200 38.462 0.00 0.00 34.09 2.52
5025 5392 3.498777 GCAAACCCTGTCTTTGACTAGTC 59.501 47.826 16.32 16.32 33.15 2.59
5098 5470 6.921857 TCGTATTCTAATTAGCACTTACTGGC 59.078 38.462 7.67 0.00 0.00 4.85
5112 5484 2.191128 ACTGGCTGTTAGCAAGGAAG 57.809 50.000 9.80 0.00 46.63 3.46
5155 5527 6.385176 TCTGTCATCATTCCTCTGGTTCTTAT 59.615 38.462 0.00 0.00 0.00 1.73
5191 5563 1.137872 AGTCATTCTCGAGGATGCCAC 59.862 52.381 26.34 20.13 0.00 5.01
5222 5599 3.005554 CCTGACTGGAAATACACAGCTG 58.994 50.000 13.48 13.48 38.25 4.24
5225 5602 4.713553 TGACTGGAAATACACAGCTGAAA 58.286 39.130 23.35 5.21 38.25 2.69
5226 5603 4.515191 TGACTGGAAATACACAGCTGAAAC 59.485 41.667 23.35 4.17 38.25 2.78
5227 5604 4.460263 ACTGGAAATACACAGCTGAAACA 58.540 39.130 23.35 2.40 38.25 2.83
5228 5605 4.516698 ACTGGAAATACACAGCTGAAACAG 59.483 41.667 23.35 16.93 38.25 3.16
5259 5636 1.630148 CCCGAGAAATCTGTCACGAC 58.370 55.000 0.00 0.00 34.06 4.34
5338 5715 4.053295 CCATTTGCACACTTCTTTCCTTG 58.947 43.478 0.00 0.00 0.00 3.61
5378 5760 2.348591 CGCTGGTCGTTGAGTTTCTTTC 60.349 50.000 0.00 0.00 0.00 2.62
5429 5815 1.108727 ACAATGTGGCTGTGTGGGTG 61.109 55.000 0.00 0.00 0.00 4.61
5430 5816 1.531365 AATGTGGCTGTGTGGGTGG 60.531 57.895 0.00 0.00 0.00 4.61
5431 5817 3.512154 ATGTGGCTGTGTGGGTGGG 62.512 63.158 0.00 0.00 0.00 4.61
5432 5818 4.204028 GTGGCTGTGTGGGTGGGT 62.204 66.667 0.00 0.00 0.00 4.51
5433 5819 2.448736 TGGCTGTGTGGGTGGGTA 60.449 61.111 0.00 0.00 0.00 3.69
5434 5820 1.850289 TGGCTGTGTGGGTGGGTAT 60.850 57.895 0.00 0.00 0.00 2.73
5435 5821 1.077716 GGCTGTGTGGGTGGGTATC 60.078 63.158 0.00 0.00 0.00 2.24
5443 5829 1.065418 GTGGGTGGGTATCTCAACCTG 60.065 57.143 5.28 0.00 42.28 4.00
5453 5839 1.808411 TCTCAACCTGGAAACATCGC 58.192 50.000 0.00 0.00 41.51 4.58
5488 5887 6.406177 CCAGTATAGAGTTTAACTACCCGCAA 60.406 42.308 0.00 0.00 0.00 4.85
5498 5897 1.480954 ACTACCCGCAAATCGATCTGT 59.519 47.619 0.00 0.00 41.67 3.41
5509 5909 5.446473 GCAAATCGATCTGTGACCAGTTAAG 60.446 44.000 0.00 0.00 39.82 1.85
5511 5911 4.174411 TCGATCTGTGACCAGTTAAGTG 57.826 45.455 3.09 3.09 39.82 3.16
5519 5919 0.181824 ACCAGTTAAGTGCCCGTGTT 59.818 50.000 4.65 0.00 0.00 3.32
5525 5925 3.749609 AGTTAAGTGCCCGTGTTTATGTC 59.250 43.478 0.00 0.00 0.00 3.06
5530 5930 3.068560 GTGCCCGTGTTTATGTCTTGTA 58.931 45.455 0.00 0.00 0.00 2.41
5535 5935 5.672819 GCCCGTGTTTATGTCTTGTATGTTC 60.673 44.000 0.00 0.00 0.00 3.18
5536 5936 5.163794 CCCGTGTTTATGTCTTGTATGTTCC 60.164 44.000 0.00 0.00 0.00 3.62
5540 5940 8.073768 CGTGTTTATGTCTTGTATGTTCCTTTT 58.926 33.333 0.00 0.00 0.00 2.27
5542 5942 9.959749 TGTTTATGTCTTGTATGTTCCTTTTTC 57.040 29.630 0.00 0.00 0.00 2.29
5560 5968 5.391312 TTTTCTGAGGGAAAAGCAATAGC 57.609 39.130 0.00 0.00 45.54 2.97
5590 5998 0.759959 TTACACAACGAGGAAGGGCA 59.240 50.000 0.00 0.00 0.00 5.36
5594 6002 1.613437 CACAACGAGGAAGGGCAAATT 59.387 47.619 0.00 0.00 0.00 1.82
5598 6006 0.967380 CGAGGAAGGGCAAATTGGCT 60.967 55.000 18.88 0.00 43.20 4.75
5599 6007 0.533951 GAGGAAGGGCAAATTGGCTG 59.466 55.000 18.88 0.00 43.20 4.85
5600 6008 1.078918 GGAAGGGCAAATTGGCTGC 60.079 57.895 18.88 8.55 43.20 5.25
5607 6015 2.340337 GGCAAATTGGCTGCTACAAAG 58.660 47.619 12.54 0.00 40.14 2.77
5608 6016 3.500404 GGCAAATTGGCTGCTACAAAGC 61.500 50.000 12.54 3.14 40.34 3.51
5609 6017 5.727421 GGCAAATTGGCTGCTACAAAGCT 62.727 47.826 12.54 0.00 41.71 3.74
5633 6041 0.374758 GTACGTGCAGGCACATCATG 59.625 55.000 22.69 9.50 46.47 3.07
5671 6093 2.484264 ACTTGCAGAACACGAAATAGCC 59.516 45.455 0.00 0.00 0.00 3.93
5674 6096 2.028112 TGCAGAACACGAAATAGCCTCT 60.028 45.455 0.00 0.00 0.00 3.69
5679 6101 3.914426 ACACGAAATAGCCTCTCCATT 57.086 42.857 0.00 0.00 0.00 3.16
5681 6103 3.452627 ACACGAAATAGCCTCTCCATTCT 59.547 43.478 0.00 0.00 0.00 2.40
5686 6108 4.232310 GCCTCTCCATTCTGGCAC 57.768 61.111 0.00 0.00 44.34 5.01
5721 6152 5.132816 AGGTTTATTTAGCTCCCTAGTGCAT 59.867 40.000 0.00 0.00 34.89 3.96
5722 6153 5.828328 GGTTTATTTAGCTCCCTAGTGCATT 59.172 40.000 0.00 0.00 34.89 3.56
5735 6166 3.446442 AGTGCATTCAAGAACCTCCAT 57.554 42.857 0.00 0.00 0.00 3.41
5737 6168 2.424956 GTGCATTCAAGAACCTCCATCC 59.575 50.000 0.00 0.00 0.00 3.51
5738 6169 2.041485 TGCATTCAAGAACCTCCATCCA 59.959 45.455 0.00 0.00 0.00 3.41
5739 6170 3.294214 GCATTCAAGAACCTCCATCCAT 58.706 45.455 0.00 0.00 0.00 3.41
5740 6171 3.703052 GCATTCAAGAACCTCCATCCATT 59.297 43.478 0.00 0.00 0.00 3.16
5741 6172 4.202090 GCATTCAAGAACCTCCATCCATTC 60.202 45.833 0.00 0.00 0.00 2.67
5742 6173 3.652057 TCAAGAACCTCCATCCATTCC 57.348 47.619 0.00 0.00 0.00 3.01
5745 6176 4.017222 TCAAGAACCTCCATCCATTCCATT 60.017 41.667 0.00 0.00 0.00 3.16
5769 6200 3.134458 GGAGAAATTAGTGCGGAGATGG 58.866 50.000 0.00 0.00 0.00 3.51
5770 6201 3.181465 GGAGAAATTAGTGCGGAGATGGA 60.181 47.826 0.00 0.00 0.00 3.41
5771 6202 4.442706 GAGAAATTAGTGCGGAGATGGAA 58.557 43.478 0.00 0.00 0.00 3.53
5772 6203 4.192317 AGAAATTAGTGCGGAGATGGAAC 58.808 43.478 0.00 0.00 0.00 3.62
5773 6204 3.914426 AATTAGTGCGGAGATGGAACT 57.086 42.857 0.00 0.00 0.00 3.01
5774 6205 2.961526 TTAGTGCGGAGATGGAACTC 57.038 50.000 0.00 0.00 36.31 3.01
5800 6231 4.790962 CCATCGCTGCAGCCAGGT 62.791 66.667 32.07 13.56 39.54 4.00
5836 6267 0.873054 GAGCTCAGCGCATGCATTAT 59.127 50.000 19.57 0.00 46.23 1.28
5837 6268 1.266175 GAGCTCAGCGCATGCATTATT 59.734 47.619 19.57 0.00 46.23 1.40
5838 6269 2.481568 GAGCTCAGCGCATGCATTATTA 59.518 45.455 19.57 0.00 46.23 0.98
5839 6270 2.225019 AGCTCAGCGCATGCATTATTAC 59.775 45.455 19.57 0.79 46.23 1.89
5840 6271 2.225019 GCTCAGCGCATGCATTATTACT 59.775 45.455 19.57 0.00 46.23 2.24
5841 6272 3.666374 GCTCAGCGCATGCATTATTACTC 60.666 47.826 19.57 0.00 46.23 2.59
5842 6273 2.807967 TCAGCGCATGCATTATTACTCC 59.192 45.455 19.57 0.00 46.23 3.85
5843 6274 2.549329 CAGCGCATGCATTATTACTCCA 59.451 45.455 19.57 0.00 46.23 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 5.009610 GCACTTGTGATTTCCCTCTAAAACA 59.990 40.000 4.79 0.00 0.00 2.83
123 152 1.351076 TCAACTGCCTCCATGAGTGA 58.649 50.000 0.00 0.00 0.00 3.41
297 326 1.668826 ATCCACCCCAGAAGTAGCAA 58.331 50.000 0.00 0.00 0.00 3.91
379 408 5.602145 ACTGATTTTCTGGTTCATGGGAAAA 59.398 36.000 0.00 0.00 40.38 2.29
469 498 3.369471 CCAGTCCAACCGATATGTCAAGT 60.369 47.826 0.00 0.00 0.00 3.16
474 503 0.908910 TGCCAGTCCAACCGATATGT 59.091 50.000 0.00 0.00 0.00 2.29
530 563 0.826715 GTTAGTACCCCCTCCGTTCC 59.173 60.000 0.00 0.00 0.00 3.62
532 565 0.116940 TGGTTAGTACCCCCTCCGTT 59.883 55.000 0.00 0.00 44.35 4.44
540 573 1.406477 CCTCGGCTTTGGTTAGTACCC 60.406 57.143 0.00 0.00 44.35 3.69
541 574 2.010544 GCCTCGGCTTTGGTTAGTACC 61.011 57.143 0.00 0.00 40.49 3.34
542 575 1.338389 TGCCTCGGCTTTGGTTAGTAC 60.338 52.381 9.65 0.00 42.51 2.73
551 584 1.673168 GATCTCAATGCCTCGGCTTT 58.327 50.000 9.65 6.37 42.51 3.51
609 642 4.113354 GGCGAGTCTATGAATTCGTCTTT 58.887 43.478 2.72 0.00 35.04 2.52
616 649 2.032620 ACCTCGGCGAGTCTATGAATT 58.967 47.619 32.41 5.02 0.00 2.17
699 732 2.753989 TCATGTGACAGCAAACAACG 57.246 45.000 0.00 0.00 0.00 4.10
705 738 0.534877 ACGCCTTCATGTGACAGCAA 60.535 50.000 0.00 0.00 0.00 3.91
765 798 1.553704 AGGGGTAGCTAAAGTGAACGG 59.446 52.381 0.00 0.00 0.00 4.44
769 802 3.834231 ACGTAAAGGGGTAGCTAAAGTGA 59.166 43.478 0.00 0.00 0.00 3.41
883 918 0.179100 CGATTGGCGATGAGTGGAGT 60.179 55.000 0.00 0.00 44.57 3.85
884 919 0.179100 ACGATTGGCGATGAGTGGAG 60.179 55.000 0.00 0.00 44.57 3.86
890 925 1.588932 GCGAGACGATTGGCGATGA 60.589 57.895 0.00 0.00 44.57 2.92
990 1032 2.430610 GGTCGCCATGGCTCTCTCT 61.431 63.158 33.07 0.00 39.32 3.10
991 1033 2.107953 GGTCGCCATGGCTCTCTC 59.892 66.667 33.07 17.59 39.32 3.20
992 1034 2.685017 TGGTCGCCATGGCTCTCT 60.685 61.111 33.07 0.00 39.32 3.10
993 1035 2.512515 GTGGTCGCCATGGCTCTC 60.513 66.667 33.07 21.54 35.28 3.20
994 1036 4.101448 GGTGGTCGCCATGGCTCT 62.101 66.667 33.07 0.00 35.28 4.09
1042 1084 3.391382 CCGGGTCAGGGTCTGGAC 61.391 72.222 0.00 0.00 31.51 4.02
1210 1258 1.135746 GGTGAAGAGGTCGTAGTCGTG 60.136 57.143 0.00 0.00 38.33 4.35
1356 1404 1.019278 AAGCGGCATCCACTTACGTG 61.019 55.000 1.45 0.00 40.89 4.49
1368 1416 2.046892 GAAGCAGGAGAAGCGGCA 60.047 61.111 1.45 0.00 37.01 5.69
1369 1417 2.821810 GGAAGCAGGAGAAGCGGC 60.822 66.667 0.00 0.00 37.01 6.53
1370 1418 2.510238 CGGAAGCAGGAGAAGCGG 60.510 66.667 0.00 0.00 37.01 5.52
1386 1434 2.247267 GCCGACAAACGAACCACG 59.753 61.111 0.00 0.00 45.77 4.94
1479 1529 1.390123 CGCGACACATTCAACACTAGG 59.610 52.381 0.00 0.00 0.00 3.02
1511 1561 3.876274 TCTAGCTAACCAGTGCAGAAG 57.124 47.619 0.00 0.00 0.00 2.85
1592 1737 6.499106 TGAGAACTGAATGGCATAATAGGA 57.501 37.500 0.00 0.00 0.00 2.94
1597 1742 5.499313 TGTGATGAGAACTGAATGGCATAA 58.501 37.500 0.00 0.00 0.00 1.90
1688 1833 7.517320 ACCATATAATAAGACCACTCATGCAA 58.483 34.615 0.00 0.00 0.00 4.08
1712 1857 4.265073 AGGATAACTGGATGTGCTGAAAC 58.735 43.478 0.00 0.00 0.00 2.78
1717 1862 2.240667 AGCAAGGATAACTGGATGTGCT 59.759 45.455 0.00 0.00 36.31 4.40
1718 1863 2.648059 AGCAAGGATAACTGGATGTGC 58.352 47.619 0.00 0.00 0.00 4.57
1722 1867 4.591321 TCCAAAGCAAGGATAACTGGAT 57.409 40.909 0.00 0.00 0.00 3.41
1724 1869 5.665916 AATTCCAAAGCAAGGATAACTGG 57.334 39.130 0.00 0.00 34.56 4.00
1921 2077 4.672542 CGCATGGGTTCAATTCTACACAAG 60.673 45.833 0.68 0.00 30.33 3.16
1922 2078 3.190327 CGCATGGGTTCAATTCTACACAA 59.810 43.478 0.68 0.00 30.33 3.33
1925 2081 1.742831 GCGCATGGGTTCAATTCTACA 59.257 47.619 11.82 0.00 0.00 2.74
1932 2088 2.121291 TATCAAGCGCATGGGTTCAA 57.879 45.000 13.33 0.00 33.12 2.69
2009 2165 1.918262 TCTTGATTCCAGTGGAGCCAT 59.082 47.619 12.67 2.91 31.21 4.40
2010 2166 1.280133 CTCTTGATTCCAGTGGAGCCA 59.720 52.381 12.67 11.38 31.21 4.75
2012 2168 1.280421 ACCTCTTGATTCCAGTGGAGC 59.720 52.381 12.67 9.43 31.21 4.70
2013 2169 2.938756 GCACCTCTTGATTCCAGTGGAG 60.939 54.545 12.67 0.00 31.21 3.86
2056 2212 2.713895 CAGAACTGCTTGTCTCTCGA 57.286 50.000 0.00 0.00 0.00 4.04
2077 2233 7.370383 TGTGAGGAAAATGCAAGAAGATAAAC 58.630 34.615 0.00 0.00 0.00 2.01
2096 2252 6.573664 TTGACAAACCAAGATATTGTGAGG 57.426 37.500 0.00 0.00 37.41 3.86
2133 2289 4.728772 TGGAACACAGAAAGATTGGACAT 58.271 39.130 0.00 0.00 0.00 3.06
2168 2324 5.232414 GTGCTAAACAGTCCTCAATCGATAC 59.768 44.000 0.00 0.00 0.00 2.24
2557 2727 6.924060 CAGTCTATCTATCCCAACTTTAACCG 59.076 42.308 0.00 0.00 0.00 4.44
2691 2861 7.096023 CCAACAGCTATAAGTATGTTCTTAGCG 60.096 40.741 0.00 0.00 35.46 4.26
2736 2906 4.161189 ACATGCTCTATTCCTGGGATATCG 59.839 45.833 0.00 0.00 0.00 2.92
2874 3044 3.365868 GCTGCCGAATAAACACATGAACA 60.366 43.478 0.00 0.00 0.00 3.18
2895 3065 4.037089 TCAAACCCTCTTAAAACTTTCGGC 59.963 41.667 0.00 0.00 0.00 5.54
3119 3289 8.527810 ACCAATAGTTTCTTTGTTTGTCTTCAA 58.472 29.630 0.00 0.00 0.00 2.69
3386 3556 5.048083 GTCATGGTGACAATAAAAGCCAGAA 60.048 40.000 5.28 0.00 46.22 3.02
3452 3623 1.202382 CCACCGAGGTTCGAGAATACC 60.202 57.143 0.00 0.00 43.74 2.73
3468 3639 1.901833 ACAGCCCAAATTGAATCCACC 59.098 47.619 0.00 0.00 0.00 4.61
3649 3820 0.673437 AACAACCATTGCCTCAACGG 59.327 50.000 0.00 0.00 32.53 4.44
3650 3821 1.608590 AGAACAACCATTGCCTCAACG 59.391 47.619 0.00 0.00 0.00 4.10
3685 3856 4.641396 CCACTCATGGTCAACTAACAAGA 58.359 43.478 0.00 0.00 41.64 3.02
3821 4017 0.621862 GAACTGGGGGATGGAGGACT 60.622 60.000 0.00 0.00 0.00 3.85
3826 4022 1.296832 TCCATAGAACTGGGGGATGGA 59.703 52.381 0.00 0.00 42.94 3.41
3831 4027 1.146263 GCGTCCATAGAACTGGGGG 59.854 63.158 0.00 0.00 36.89 5.40
3884 4080 7.945033 TCAAATTTTAGTTCATTTGGCTGAC 57.055 32.000 5.11 0.00 39.76 3.51
3958 4154 5.482006 GCTGGGTGAAGCAGAAAAATATTT 58.518 37.500 0.00 0.00 43.01 1.40
4184 4385 9.918630 AAACTTTGATGCAAGCCATATATTATC 57.081 29.630 0.00 0.00 33.29 1.75
4219 4420 3.700538 TGCATATGAGCAACCTCCTTTT 58.299 40.909 6.97 0.00 42.46 2.27
4527 4893 4.580995 TCAAAATCTTGCTTCGTTAACCCA 59.419 37.500 0.00 0.00 32.14 4.51
4745 5111 9.905171 CACATCGTATATATAGATAATGCAGCT 57.095 33.333 0.00 0.00 0.00 4.24
4762 5128 8.573035 ACAAAGTGTAAATTTTCCACATCGTAT 58.427 29.630 17.73 0.25 27.89 3.06
4903 5269 5.130975 TGCTAAGAAGAAAGGATGGCATAGA 59.869 40.000 0.00 0.00 0.00 1.98
5011 5377 6.145338 AGAAAACTCGACTAGTCAAAGACA 57.855 37.500 22.37 0.00 37.50 3.41
5012 5378 8.745464 ATAAGAAAACTCGACTAGTCAAAGAC 57.255 34.615 22.37 12.04 37.50 3.01
5075 5447 7.711339 ACAGCCAGTAAGTGCTAATTAGAATAC 59.289 37.037 16.85 10.91 35.69 1.89
5086 5458 1.347707 TGCTAACAGCCAGTAAGTGCT 59.652 47.619 0.00 0.00 41.51 4.40
5098 5470 3.686726 CCAAGCTACTTCCTTGCTAACAG 59.313 47.826 0.00 0.00 38.63 3.16
5112 5484 1.379044 ACATGCCTGGCCAAGCTAC 60.379 57.895 26.24 5.59 0.00 3.58
5155 5527 4.916983 ATGACTGCAGCAACAAACTAAA 57.083 36.364 15.27 0.00 0.00 1.85
5191 5563 2.742372 CAGTCAGGTTTCGGCCGG 60.742 66.667 27.83 8.07 0.00 6.13
5259 5636 2.422479 TCGTACATCTTCAGAGGGTTCG 59.578 50.000 0.00 0.00 32.03 3.95
5313 5690 3.259123 GGAAAGAAGTGTGCAAATGGGAT 59.741 43.478 0.00 0.00 0.00 3.85
5338 5715 2.197643 GTGCTCAAGCCTCAAGCAGC 62.198 60.000 1.55 0.00 45.99 5.25
5378 5760 2.158564 ACACATGAATAGCAGATGGGGG 60.159 50.000 0.00 0.00 0.00 5.40
5429 5815 3.713826 TGTTTCCAGGTTGAGATACCC 57.286 47.619 0.00 0.00 39.08 3.69
5430 5816 3.871594 CGATGTTTCCAGGTTGAGATACC 59.128 47.826 0.00 0.00 38.53 2.73
5431 5817 3.309954 GCGATGTTTCCAGGTTGAGATAC 59.690 47.826 0.00 0.00 0.00 2.24
5432 5818 3.197766 AGCGATGTTTCCAGGTTGAGATA 59.802 43.478 0.00 0.00 0.00 1.98
5433 5819 2.026822 AGCGATGTTTCCAGGTTGAGAT 60.027 45.455 0.00 0.00 0.00 2.75
5434 5820 1.347707 AGCGATGTTTCCAGGTTGAGA 59.652 47.619 0.00 0.00 0.00 3.27
5435 5821 1.734465 GAGCGATGTTTCCAGGTTGAG 59.266 52.381 0.00 0.00 0.00 3.02
5443 5829 1.865340 GTATTCGGGAGCGATGTTTCC 59.135 52.381 0.00 0.00 0.00 3.13
5453 5839 6.651975 AAACTCTATACTGGTATTCGGGAG 57.348 41.667 0.00 5.37 0.00 4.30
5498 5897 0.250124 CACGGGCACTTAACTGGTCA 60.250 55.000 0.00 0.00 0.00 4.02
5509 5909 1.877443 ACAAGACATAAACACGGGCAC 59.123 47.619 0.00 0.00 0.00 5.01
5511 5911 3.687698 ACATACAAGACATAAACACGGGC 59.312 43.478 0.00 0.00 0.00 6.13
5519 5919 9.567776 TCAGAAAAAGGAACATACAAGACATAA 57.432 29.630 0.00 0.00 0.00 1.90
5525 5925 6.003950 TCCCTCAGAAAAAGGAACATACAAG 58.996 40.000 0.00 0.00 35.83 3.16
5562 5970 9.550406 CCCTTCCTCGTTGTGTAATAATAATAA 57.450 33.333 0.00 0.00 0.00 1.40
5563 5971 7.658575 GCCCTTCCTCGTTGTGTAATAATAATA 59.341 37.037 0.00 0.00 0.00 0.98
5564 5972 6.485648 GCCCTTCCTCGTTGTGTAATAATAAT 59.514 38.462 0.00 0.00 0.00 1.28
5565 5973 5.818857 GCCCTTCCTCGTTGTGTAATAATAA 59.181 40.000 0.00 0.00 0.00 1.40
5566 5974 5.104859 TGCCCTTCCTCGTTGTGTAATAATA 60.105 40.000 0.00 0.00 0.00 0.98
5567 5975 4.196971 GCCCTTCCTCGTTGTGTAATAAT 58.803 43.478 0.00 0.00 0.00 1.28
5570 5978 1.349688 TGCCCTTCCTCGTTGTGTAAT 59.650 47.619 0.00 0.00 0.00 1.89
5575 5983 1.613437 CAATTTGCCCTTCCTCGTTGT 59.387 47.619 0.00 0.00 0.00 3.32
5581 5989 1.547472 GCAGCCAATTTGCCCTTCCT 61.547 55.000 0.00 0.00 35.54 3.36
5586 5994 0.607620 TTGTAGCAGCCAATTTGCCC 59.392 50.000 0.00 0.00 42.48 5.36
5599 6007 5.052828 GCACGTACTGCTAGCTTTGTAGC 62.053 52.174 17.23 11.64 44.38 3.58
5600 6008 2.599082 GCACGTACTGCTAGCTTTGTAG 59.401 50.000 17.23 6.88 43.33 2.74
5644 6052 1.070134 TCGTGTTCTGCAAGTAGCCTT 59.930 47.619 0.00 0.00 44.83 4.35
5645 6053 0.679505 TCGTGTTCTGCAAGTAGCCT 59.320 50.000 0.00 0.00 44.83 4.58
5646 6054 1.508632 TTCGTGTTCTGCAAGTAGCC 58.491 50.000 0.00 0.00 44.83 3.93
5648 6056 4.201724 GGCTATTTCGTGTTCTGCAAGTAG 60.202 45.833 0.00 0.00 33.76 2.57
5649 6057 3.682858 GGCTATTTCGTGTTCTGCAAGTA 59.317 43.478 0.00 0.00 33.76 2.24
5650 6058 2.484264 GGCTATTTCGTGTTCTGCAAGT 59.516 45.455 0.00 0.00 33.76 3.16
5655 6077 3.190874 GGAGAGGCTATTTCGTGTTCTG 58.809 50.000 0.00 0.00 0.00 3.02
5658 6080 3.914426 ATGGAGAGGCTATTTCGTGTT 57.086 42.857 0.00 0.00 0.00 3.32
5679 6101 0.671472 CTGCTCATCAACGTGCCAGA 60.671 55.000 0.00 0.00 0.00 3.86
5681 6103 1.672030 CCTGCTCATCAACGTGCCA 60.672 57.895 0.00 0.00 0.00 4.92
5686 6108 5.065218 AGCTAAATAAACCTGCTCATCAACG 59.935 40.000 0.00 0.00 0.00 4.10
5721 6152 3.333381 TGGAATGGATGGAGGTTCTTGAA 59.667 43.478 0.00 0.00 0.00 2.69
5722 6153 2.918934 TGGAATGGATGGAGGTTCTTGA 59.081 45.455 0.00 0.00 0.00 3.02
5740 6171 4.157656 CCGCACTAATTTCTCCAAAATGGA 59.842 41.667 0.00 0.00 45.98 3.41
5741 6172 4.157656 TCCGCACTAATTTCTCCAAAATGG 59.842 41.667 0.00 0.00 39.43 3.16
5742 6173 5.123820 TCTCCGCACTAATTTCTCCAAAATG 59.876 40.000 0.00 0.00 0.00 2.32
5745 6176 4.280436 TCTCCGCACTAATTTCTCCAAA 57.720 40.909 0.00 0.00 0.00 3.28
5751 6182 4.192317 AGTTCCATCTCCGCACTAATTTC 58.808 43.478 0.00 0.00 0.00 2.17
5769 6200 1.335506 GCGATGGAGGATCTCGAGTTC 60.336 57.143 13.13 13.63 34.41 3.01
5770 6201 0.671251 GCGATGGAGGATCTCGAGTT 59.329 55.000 13.13 3.51 34.41 3.01
5771 6202 0.179004 AGCGATGGAGGATCTCGAGT 60.179 55.000 13.13 0.00 34.41 4.18
5772 6203 0.240678 CAGCGATGGAGGATCTCGAG 59.759 60.000 5.93 5.93 34.41 4.04
5773 6204 1.800283 GCAGCGATGGAGGATCTCGA 61.800 60.000 1.46 0.00 34.41 4.04
5774 6205 1.372748 GCAGCGATGGAGGATCTCG 60.373 63.158 1.46 0.00 33.73 4.04
5800 6231 3.949754 GAGCTCCATGGTGATGATTCAAA 59.050 43.478 17.98 0.00 32.48 2.69


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

AutoCloner maintained by Alex Coulton.