Multiple sequence alignment - TraesCS1D01G340500

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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 TraesCS1D01G340500 chr1D 100.000 6147 0 0 1 6147 430421737 430415591 0.000000e+00 11352.0
1 TraesCS1D01G340500 chr1D 86.579 760 82 8 1481 2235 355665104 355664360 0.000000e+00 821.0
2 TraesCS1D01G340500 chr1D 90.361 581 52 3 60 639 288909862 288909285 0.000000e+00 760.0
3 TraesCS1D01G340500 chr1D 90.017 581 36 11 1 560 342118808 342119387 0.000000e+00 732.0
4 TraesCS1D01G340500 chr1D 89.619 578 51 5 1 570 435464175 435464751 0.000000e+00 726.0
5 TraesCS1D01G340500 chr1D 100.000 28 0 0 757 784 486307081 486307108 1.100000e-02 52.8
6 TraesCS1D01G340500 chr1A 93.140 4198 152 45 792 4905 527963327 527959182 0.000000e+00 6032.0
7 TraesCS1D01G340500 chr1A 93.822 696 30 7 5460 6147 527956274 527955584 0.000000e+00 1035.0
8 TraesCS1D01G340500 chr1A 88.182 550 59 4 2 546 403427758 403428306 0.000000e+00 651.0
9 TraesCS1D01G340500 chr1A 92.068 353 23 4 4895 5247 527957173 527956826 5.540000e-135 492.0
10 TraesCS1D01G340500 chr1B 87.658 1345 73 37 1674 2986 581210661 581209378 0.000000e+00 1478.0
11 TraesCS1D01G340500 chr1B 91.289 838 37 17 910 1713 581211522 581210687 0.000000e+00 1110.0
12 TraesCS1D01G340500 chr1B 88.816 608 35 12 5023 5605 581207278 581206679 0.000000e+00 715.0
13 TraesCS1D01G340500 chr1B 86.003 643 68 15 1 636 670876455 670875828 0.000000e+00 669.0
14 TraesCS1D01G340500 chr1B 87.785 483 34 13 5651 6112 581206064 581205586 5.420000e-150 542.0
15 TraesCS1D01G340500 chr1B 81.672 682 63 37 3027 3650 581209251 581208574 1.530000e-140 510.0
16 TraesCS1D01G340500 chr1B 87.805 410 34 11 4580 4979 581207686 581207283 3.360000e-127 466.0
17 TraesCS1D01G340500 chr1B 98.077 52 1 0 1611 1662 581210697 581210646 2.360000e-14 91.6
18 TraesCS1D01G340500 chr3D 87.406 802 64 16 1 786 560652331 560653111 0.000000e+00 887.0
19 TraesCS1D01G340500 chr3B 89.530 659 55 10 1 650 819946977 819947630 0.000000e+00 822.0
20 TraesCS1D01G340500 chr3A 88.156 667 64 10 1 657 742783515 742784176 0.000000e+00 780.0
21 TraesCS1D01G340500 chr7D 92.402 487 36 1 1 487 430935455 430935940 0.000000e+00 693.0
22 TraesCS1D01G340500 chr6A 85.023 434 45 11 233 650 57890780 57891209 2.050000e-114 424.0
23 TraesCS1D01G340500 chr6A 85.417 144 20 1 641 784 449700686 449700828 1.380000e-31 148.0
24 TraesCS1D01G340500 chr6A 79.348 92 16 3 698 787 30772178 30772268 1.850000e-05 62.1
25 TraesCS1D01G340500 chr2A 80.400 500 64 22 166 639 5111249 5110758 3.530000e-92 350.0
26 TraesCS1D01G340500 chr2A 84.286 140 13 4 1247 1379 776209122 776209259 1.800000e-25 128.0
27 TraesCS1D01G340500 chr2D 87.143 70 9 0 717 786 170814327 170814258 5.110000e-11 80.5
28 TraesCS1D01G340500 chr4B 85.965 57 8 0 731 787 147497127 147497183 1.850000e-05 62.1
29 TraesCS1D01G340500 chr5D 94.286 35 2 0 752 786 34809993 34810027 3.000000e-03 54.7
30 TraesCS1D01G340500 chr4D 100.000 28 0 0 5932 5959 109242465 109242438 1.100000e-02 52.8
31 TraesCS1D01G340500 chr4A 100.000 28 0 0 5932 5959 467264670 467264697 1.100000e-02 52.8


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 TraesCS1D01G340500 chr1D 430415591 430421737 6146 True 11352.000000 11352 100.000000 1 6147 1 chr1D.!!$R3 6146
1 TraesCS1D01G340500 chr1D 355664360 355665104 744 True 821.000000 821 86.579000 1481 2235 1 chr1D.!!$R2 754
2 TraesCS1D01G340500 chr1D 288909285 288909862 577 True 760.000000 760 90.361000 60 639 1 chr1D.!!$R1 579
3 TraesCS1D01G340500 chr1D 342118808 342119387 579 False 732.000000 732 90.017000 1 560 1 chr1D.!!$F1 559
4 TraesCS1D01G340500 chr1D 435464175 435464751 576 False 726.000000 726 89.619000 1 570 1 chr1D.!!$F2 569
5 TraesCS1D01G340500 chr1A 527955584 527963327 7743 True 2519.666667 6032 93.010000 792 6147 3 chr1A.!!$R1 5355
6 TraesCS1D01G340500 chr1A 403427758 403428306 548 False 651.000000 651 88.182000 2 546 1 chr1A.!!$F1 544
7 TraesCS1D01G340500 chr1B 581205586 581211522 5936 True 701.800000 1478 89.014571 910 6112 7 chr1B.!!$R2 5202
8 TraesCS1D01G340500 chr1B 670875828 670876455 627 True 669.000000 669 86.003000 1 636 1 chr1B.!!$R1 635
9 TraesCS1D01G340500 chr3D 560652331 560653111 780 False 887.000000 887 87.406000 1 786 1 chr3D.!!$F1 785
10 TraesCS1D01G340500 chr3B 819946977 819947630 653 False 822.000000 822 89.530000 1 650 1 chr3B.!!$F1 649
11 TraesCS1D01G340500 chr3A 742783515 742784176 661 False 780.000000 780 88.156000 1 657 1 chr3A.!!$F1 656

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
890 923 0.530650 CGCGAACCACATGCTCCTAT 60.531 55.000 0.0 0.0 0.00 2.57 F
1375 1428 1.456705 CTCCCTCTCTCCCCCTTCG 60.457 68.421 0.0 0.0 0.00 3.79 F
1802 1972 1.685224 CCCCCTGCTTGCTCAGTAA 59.315 57.895 0.0 0.0 32.32 2.24 F
1826 1996 2.141517 CTGCATCTTATCTCTTGGGCG 58.858 52.381 0.0 0.0 0.00 6.13 F
3717 4144 3.689161 CCGTTGAAGCACAGAAATATCCA 59.311 43.478 0.0 0.0 0.00 3.41 F
4334 4771 0.033228 TGCCCGGTTGCATTTCAAAG 59.967 50.000 0.0 0.0 36.04 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2798 2987 0.796312 CGGGACAAGAAACATGGTCG 59.204 55.000 0.00 0.0 0.00 4.79 R
2900 3092 0.898320 ATGAAGCTGGCGTAGACTGT 59.102 50.000 0.00 0.0 36.60 3.55 R
3717 4144 1.242076 GCCACTGAGTGCAAGTGATT 58.758 50.000 16.84 0.0 35.75 2.57 R
3789 4216 5.079689 TGCGAACAGATTAGTGGAATACA 57.920 39.130 0.00 0.0 0.00 2.29 R
4863 5309 1.133790 GTAAGAGAAGAACCGCGGCTA 59.866 52.381 28.58 0.0 0.00 3.93 R
6048 9451 0.307760 CGAAAGGACAACTGGTGCAC 59.692 55.000 8.80 8.8 40.89 4.57 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 2.411504 GCTCCGACTCGCTCTCCTT 61.412 63.158 0.00 0.00 0.00 3.36
528 551 2.828868 GGCATGTAGATGGCGGGA 59.171 61.111 10.76 0.00 44.46 5.14
560 585 1.519455 GCAGTGGCTAGGCGTAGTG 60.519 63.158 14.52 9.23 36.96 2.74
577 603 0.813184 GTGTGGCGTAGTAGTAGGCA 59.187 55.000 20.62 10.66 41.06 4.75
580 606 3.067180 GTGTGGCGTAGTAGTAGGCATAA 59.933 47.826 20.62 6.14 41.06 1.90
639 667 2.811431 TGAAATTTCGCCGAGTTCATGT 59.189 40.909 13.34 0.00 0.00 3.21
650 680 1.523095 GAGTTCATGTTATCGCCGAGC 59.477 52.381 0.00 0.00 0.00 5.03
651 681 0.582005 GTTCATGTTATCGCCGAGCC 59.418 55.000 0.00 0.00 0.00 4.70
661 691 4.996434 GCCGAGCCTGCGCCATAT 62.996 66.667 4.18 0.00 34.57 1.78
662 692 2.281070 CCGAGCCTGCGCCATATT 60.281 61.111 4.18 0.00 34.57 1.28
663 693 2.610694 CCGAGCCTGCGCCATATTG 61.611 63.158 4.18 0.00 34.57 1.90
664 694 2.610694 CGAGCCTGCGCCATATTGG 61.611 63.158 4.18 0.00 41.55 3.16
675 705 1.523711 CATATTGGCGGCGACCTGT 60.524 57.895 11.74 6.78 0.00 4.00
677 707 1.966901 ATATTGGCGGCGACCTGTGA 61.967 55.000 11.74 0.00 0.00 3.58
684 714 4.357947 GCGACCTGTGAGCCGACA 62.358 66.667 0.00 0.00 0.00 4.35
688 718 0.946221 GACCTGTGAGCCGACAACTG 60.946 60.000 0.00 0.00 0.00 3.16
689 719 1.367471 CCTGTGAGCCGACAACTGA 59.633 57.895 0.00 0.00 0.00 3.41
700 730 1.687628 GACAACTGAGAACGGAGTCG 58.312 55.000 0.00 0.00 45.00 4.18
721 751 1.153647 CCCACGCGTCAATCTAGCA 60.154 57.895 9.86 0.00 0.00 3.49
728 758 1.722011 CGTCAATCTAGCACCGGTTT 58.278 50.000 2.97 0.00 0.00 3.27
737 767 4.278513 CACCGGTTTGCCCCCAGA 62.279 66.667 2.97 0.00 0.00 3.86
741 771 4.280019 GGTTTGCCCCCAGACGGT 62.280 66.667 0.00 0.00 0.00 4.83
743 773 1.830847 GTTTGCCCCCAGACGGTTT 60.831 57.895 0.00 0.00 0.00 3.27
744 774 1.830408 TTTGCCCCCAGACGGTTTG 60.830 57.895 0.00 0.00 0.00 2.93
753 783 0.661020 CAGACGGTTTGTTTTCGGCT 59.339 50.000 0.00 0.00 43.74 5.52
786 817 3.548415 CGAACGGCTGGAGATACTCTTAC 60.548 52.174 0.00 0.00 0.00 2.34
787 818 1.948145 ACGGCTGGAGATACTCTTACG 59.052 52.381 0.00 0.00 0.00 3.18
788 819 1.335142 CGGCTGGAGATACTCTTACGC 60.335 57.143 0.00 0.00 0.00 4.42
789 820 1.335142 GGCTGGAGATACTCTTACGCG 60.335 57.143 3.53 3.53 0.00 6.01
790 821 1.602851 GCTGGAGATACTCTTACGCGA 59.397 52.381 15.93 0.00 0.00 5.87
791 822 2.033049 GCTGGAGATACTCTTACGCGAA 59.967 50.000 15.93 1.35 0.00 4.70
792 823 3.850374 GCTGGAGATACTCTTACGCGAAG 60.850 52.174 15.93 12.57 36.38 3.79
814 845 5.278604 AGCAGTTGTTATTTTCGGAAACAC 58.721 37.500 1.96 1.66 33.10 3.32
815 846 4.145756 GCAGTTGTTATTTTCGGAAACACG 59.854 41.667 1.96 0.00 33.10 4.49
819 850 4.835344 TGTTATTTTCGGAAACACGTGAC 58.165 39.130 25.01 12.63 34.94 3.67
867 900 4.204799 CAGCAGATCCATTTTCCAGATCA 58.795 43.478 0.00 0.00 39.10 2.92
881 914 4.673298 ATCACCGCGCGAACCACA 62.673 61.111 34.63 8.92 0.00 4.17
882 915 3.950794 ATCACCGCGCGAACCACAT 62.951 57.895 34.63 11.01 0.00 3.21
883 916 4.444024 CACCGCGCGAACCACATG 62.444 66.667 34.63 14.59 0.00 3.21
886 919 4.505217 CGCGCGAACCACATGCTC 62.505 66.667 28.94 0.00 0.00 4.26
887 920 4.166011 GCGCGAACCACATGCTCC 62.166 66.667 12.10 0.00 0.00 4.70
888 921 2.434884 CGCGAACCACATGCTCCT 60.435 61.111 0.00 0.00 0.00 3.69
889 922 1.153647 CGCGAACCACATGCTCCTA 60.154 57.895 0.00 0.00 0.00 2.94
890 923 0.530650 CGCGAACCACATGCTCCTAT 60.531 55.000 0.00 0.00 0.00 2.57
891 924 1.668419 GCGAACCACATGCTCCTATT 58.332 50.000 0.00 0.00 0.00 1.73
892 925 2.017049 GCGAACCACATGCTCCTATTT 58.983 47.619 0.00 0.00 0.00 1.40
893 926 3.202906 GCGAACCACATGCTCCTATTTA 58.797 45.455 0.00 0.00 0.00 1.40
894 927 3.815401 GCGAACCACATGCTCCTATTTAT 59.185 43.478 0.00 0.00 0.00 1.40
895 928 4.275936 GCGAACCACATGCTCCTATTTATT 59.724 41.667 0.00 0.00 0.00 1.40
896 929 5.221048 GCGAACCACATGCTCCTATTTATTT 60.221 40.000 0.00 0.00 0.00 1.40
897 930 6.017440 GCGAACCACATGCTCCTATTTATTTA 60.017 38.462 0.00 0.00 0.00 1.40
898 931 7.468084 GCGAACCACATGCTCCTATTTATTTAA 60.468 37.037 0.00 0.00 0.00 1.52
899 932 8.567948 CGAACCACATGCTCCTATTTATTTAAT 58.432 33.333 0.00 0.00 0.00 1.40
990 1031 3.016474 GCGACCTGCTTGAAGCGAC 62.016 63.158 13.05 3.02 46.26 5.19
993 1034 2.348998 CCTGCTTGAAGCGACCCT 59.651 61.111 13.05 0.00 46.26 4.34
1346 1398 3.827898 CTCCTCGAGGTCCGTGCC 61.828 72.222 30.17 0.00 39.75 5.01
1354 1406 2.060980 AGGTCCGTGCCTCCAGATC 61.061 63.158 0.00 0.00 32.39 2.75
1364 1417 1.673928 CCTCCAGATCCCCTCCCTCT 61.674 65.000 0.00 0.00 0.00 3.69
1375 1428 1.456705 CTCCCTCTCTCCCCCTTCG 60.457 68.421 0.00 0.00 0.00 3.79
1376 1429 2.231540 CTCCCTCTCTCCCCCTTCGT 62.232 65.000 0.00 0.00 0.00 3.85
1390 1463 2.159517 CCCTTCGTCTGCTTAAATGTGC 60.160 50.000 0.00 0.00 0.00 4.57
1412 1485 4.794246 GCGTGTAGTTCTATCTGACAACTC 59.206 45.833 2.66 0.00 32.56 3.01
1504 1579 5.747565 TCATTTTCTAACAGTGCAGAAACG 58.252 37.500 16.25 12.08 39.76 3.60
1588 1679 5.521372 GGAATGACAAATCAAATAGCAAGGC 59.479 40.000 0.00 0.00 38.69 4.35
1802 1972 1.685224 CCCCCTGCTTGCTCAGTAA 59.315 57.895 0.00 0.00 32.32 2.24
1822 1992 8.363390 TCAGTAATACCTGCATCTTATCTCTTG 58.637 37.037 0.00 0.00 32.32 3.02
1825 1995 2.158696 ACCTGCATCTTATCTCTTGGGC 60.159 50.000 0.00 0.00 0.00 5.36
1826 1996 2.141517 CTGCATCTTATCTCTTGGGCG 58.858 52.381 0.00 0.00 0.00 6.13
2416 2588 6.588719 AAAAGTATACATTTGCTCTTGCCA 57.411 33.333 5.50 0.00 38.71 4.92
2716 2905 4.422840 TGCATGGTCATCTTTTATTTGCG 58.577 39.130 0.00 0.00 0.00 4.85
2877 3069 9.049523 CATTACAGAGAAGATGCAATTAAGCTA 57.950 33.333 0.00 0.00 34.99 3.32
2900 3092 7.816031 GCTAACAGTTTACAGTACACTCCATTA 59.184 37.037 0.00 0.00 0.00 1.90
2903 3095 7.152645 ACAGTTTACAGTACACTCCATTACAG 58.847 38.462 0.00 0.00 0.00 2.74
2904 3096 7.152645 CAGTTTACAGTACACTCCATTACAGT 58.847 38.462 0.00 0.00 0.00 3.55
2905 3097 7.328737 CAGTTTACAGTACACTCCATTACAGTC 59.671 40.741 0.00 0.00 0.00 3.51
2906 3098 7.232941 AGTTTACAGTACACTCCATTACAGTCT 59.767 37.037 0.00 0.00 0.00 3.24
3290 3599 8.932791 TGTCGTTTTGTATTAGAAGAAGAATCC 58.067 33.333 0.00 0.00 0.00 3.01
3505 3840 4.033817 CCAAAGAGATTGCGAGAGAATGAC 59.966 45.833 0.00 0.00 37.73 3.06
3593 3938 9.924650 GTCATCTTTTTCCTAGTACTTAACTGA 57.075 33.333 0.00 0.00 39.39 3.41
3639 3987 6.711277 TCAGAGGTAGTGCTAAATCAATGTT 58.289 36.000 0.00 0.00 0.00 2.71
3717 4144 3.689161 CCGTTGAAGCACAGAAATATCCA 59.311 43.478 0.00 0.00 0.00 3.41
3789 4216 7.821846 TGCTGGTTGTTTTTGAAATTAAAGTCT 59.178 29.630 0.00 0.00 0.00 3.24
3931 4363 4.380531 TCAGGCCGTGATATTTCTTCATC 58.619 43.478 0.00 0.00 0.00 2.92
3934 4366 4.101585 AGGCCGTGATATTTCTTCATCTGA 59.898 41.667 0.00 0.00 0.00 3.27
4147 4584 6.615264 ACACATCATCTGCTTATTCACATC 57.385 37.500 0.00 0.00 0.00 3.06
4188 4625 7.381766 TCATTCTGTGATGAAAACCATACTG 57.618 36.000 0.00 0.00 35.17 2.74
4230 4667 6.650390 ACCTGTTCAAAATCATTTTATGGTGC 59.350 34.615 0.00 0.00 0.00 5.01
4312 4749 4.681483 GCAACTTGTTTGTGAATAAGGCTC 59.319 41.667 0.00 0.00 38.04 4.70
4334 4771 0.033228 TGCCCGGTTGCATTTCAAAG 59.967 50.000 0.00 0.00 36.04 2.77
4335 4772 0.316841 GCCCGGTTGCATTTCAAAGA 59.683 50.000 0.00 0.00 36.26 2.52
4336 4773 1.270041 GCCCGGTTGCATTTCAAAGAA 60.270 47.619 0.00 0.00 36.26 2.52
4337 4774 2.804933 GCCCGGTTGCATTTCAAAGAAA 60.805 45.455 0.00 0.00 36.26 2.52
4338 4775 3.663025 CCCGGTTGCATTTCAAAGAAAT 58.337 40.909 0.00 0.00 36.26 2.17
4339 4776 3.432933 CCCGGTTGCATTTCAAAGAAATG 59.567 43.478 21.88 21.88 39.84 2.32
4340 4777 4.305769 CCGGTTGCATTTCAAAGAAATGA 58.694 39.130 27.47 14.66 39.36 2.57
4341 4778 4.749099 CCGGTTGCATTTCAAAGAAATGAA 59.251 37.500 27.47 19.00 39.36 2.57
4342 4779 5.107375 CCGGTTGCATTTCAAAGAAATGAAG 60.107 40.000 27.47 15.79 40.21 3.02
4343 4780 5.613142 CGGTTGCATTTCAAAGAAATGAAGC 60.613 40.000 27.47 21.28 40.21 3.86
4344 4781 5.368374 GTTGCATTTCAAAGAAATGAAGCG 58.632 37.500 27.47 8.78 40.21 4.68
4345 4782 4.869215 TGCATTTCAAAGAAATGAAGCGA 58.131 34.783 27.47 9.29 40.21 4.93
4346 4783 4.919168 TGCATTTCAAAGAAATGAAGCGAG 59.081 37.500 27.47 7.64 40.21 5.03
4347 4784 4.919754 GCATTTCAAAGAAATGAAGCGAGT 59.080 37.500 27.47 0.00 40.21 4.18
4348 4785 5.403466 GCATTTCAAAGAAATGAAGCGAGTT 59.597 36.000 27.47 0.00 40.21 3.01
4349 4786 6.399354 GCATTTCAAAGAAATGAAGCGAGTTC 60.399 38.462 27.47 9.64 40.21 3.01
4374 4811 2.137523 CTTTGTGCCCAGTTGCATTTC 58.862 47.619 0.00 0.00 44.30 2.17
4378 4815 2.104451 TGTGCCCAGTTGCATTTCAAAT 59.896 40.909 0.00 0.00 44.30 2.32
4473 4910 1.565156 CTCAAAACGCACGCAGCCTA 61.565 55.000 0.00 0.00 41.38 3.93
4507 4944 1.464608 CTGGTATCTTGCACCGTTGTG 59.535 52.381 0.00 0.00 45.65 3.33
4552 4989 2.290641 ACTTTCCTACTGCAAAGCAACG 59.709 45.455 0.00 0.00 38.41 4.10
4735 5172 0.912486 ACCTCTGTTGGCCCTGTATC 59.088 55.000 0.00 0.00 0.00 2.24
4745 5182 1.202651 GGCCCTGTATCGTAACTGCAT 60.203 52.381 0.00 0.00 0.00 3.96
4775 5219 4.641541 TGCACCATATGTTTCTCCATTCAG 59.358 41.667 1.24 0.00 0.00 3.02
4800 5244 3.629398 GCTAAGTAAATGAGCATGTGCCT 59.371 43.478 0.57 0.00 43.38 4.75
4892 5338 5.154932 CGGTTCTTCTCTTACTGTACTGTG 58.845 45.833 15.01 0.19 0.00 3.66
5008 7472 1.153667 GAGTTCAGGAGGAGCAGCG 60.154 63.158 0.00 0.00 0.00 5.18
5058 7522 4.102367 GGAGTGAATAAGAGCATCCTCCTT 59.898 45.833 0.00 0.00 38.96 3.36
5080 7544 4.556233 TCGAGGTGTTGTTCATCTTGTAG 58.444 43.478 0.00 0.00 37.67 2.74
5084 7548 6.590292 CGAGGTGTTGTTCATCTTGTAGTATT 59.410 38.462 0.00 0.00 37.67 1.89
5146 7610 6.813649 TCAGTTCAGTAGTACAGATCATTTGC 59.186 38.462 2.52 0.00 0.00 3.68
5254 7850 7.609532 TCCTCTTCCTAACTGTTACAGTACTAC 59.390 40.741 18.93 0.00 44.62 2.73
5256 7852 8.558973 TCTTCCTAACTGTTACAGTACTACTC 57.441 38.462 18.93 0.00 44.62 2.59
5257 7853 7.609532 TCTTCCTAACTGTTACAGTACTACTCC 59.390 40.741 18.93 0.00 44.62 3.85
5338 7954 7.671827 TCGTGATGAATAATCAGTAAAACACG 58.328 34.615 0.00 0.00 46.09 4.49
5397 8015 7.624549 GGAGACCTTATTATTATCATCAGCCA 58.375 38.462 0.00 0.00 0.00 4.75
5407 8025 8.853077 TTATTATCATCAGCCATAAGAGTTGG 57.147 34.615 0.00 0.00 37.31 3.77
5430 8048 6.821665 TGGGGTAAGCTAATGATAATAATCGC 59.178 38.462 0.00 0.00 34.60 4.58
5434 8052 3.551890 AGCTAATGATAATAATCGCGCCG 59.448 43.478 0.00 0.00 34.60 6.46
5451 8069 3.642705 CGCCGAGTTCTAATGATGATGA 58.357 45.455 0.00 0.00 0.00 2.92
5452 8070 3.426859 CGCCGAGTTCTAATGATGATGAC 59.573 47.826 0.00 0.00 0.00 3.06
5453 8071 3.426859 GCCGAGTTCTAATGATGATGACG 59.573 47.826 0.00 0.00 0.00 4.35
5502 8314 4.567558 TGTGCTGCACTTGAAAATGAAAAG 59.432 37.500 30.43 0.00 35.11 2.27
5571 8384 4.760204 AGCAAAAACTAATACCAAGCGAGT 59.240 37.500 0.00 0.00 0.00 4.18
5646 9029 4.389374 AGTCAATCGGTGTCTCAATTTGT 58.611 39.130 0.00 0.00 0.00 2.83
5679 9062 0.112995 AATGGGCCTGAGTTTCAGCA 59.887 50.000 4.53 0.00 42.98 4.41
5780 9172 0.376852 GCGACGAAATTGGCATAGCA 59.623 50.000 0.00 0.00 0.00 3.49
5964 9367 8.488668 TCATTTGAATCTCATCCTTGATAGTCA 58.511 33.333 0.00 0.00 33.11 3.41
6048 9451 1.813513 AATCAAGCCGACAGACAAGG 58.186 50.000 0.00 0.00 0.00 3.61
6053 9456 2.607892 GCCGACAGACAAGGTGCAC 61.608 63.158 8.80 8.80 0.00 4.57
6067 9470 0.307760 GTGCACCAGTTGTCCTTTCG 59.692 55.000 5.22 0.00 0.00 3.46
6080 9484 2.876550 GTCCTTTCGCAGGTTTAACACT 59.123 45.455 0.00 0.00 44.37 3.55
6125 9529 3.009916 ACAGAAGAGAAACATGGGAGCAT 59.990 43.478 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
262 264 2.509964 AGTCCTCCTTCGCCCATTTTAT 59.490 45.455 0.00 0.00 0.00 1.40
359 361 4.175489 CGAGGACGATGACGCCGT 62.175 66.667 0.00 0.00 43.96 5.68
493 516 1.066787 GCCGAGAAGCCTGTAGAAACT 60.067 52.381 0.00 0.00 0.00 2.66
560 585 3.996150 TTATGCCTACTACTACGCCAC 57.004 47.619 0.00 0.00 0.00 5.01
610 638 4.634004 ACTCGGCGAAATTTCATTGACATA 59.366 37.500 17.99 0.00 0.00 2.29
613 641 3.471495 ACTCGGCGAAATTTCATTGAC 57.529 42.857 17.99 3.36 0.00 3.18
657 687 1.523711 ACAGGTCGCCGCCAATATG 60.524 57.895 0.70 0.00 0.00 1.78
658 688 1.523711 CACAGGTCGCCGCCAATAT 60.524 57.895 0.70 0.00 0.00 1.28
659 689 2.125310 CACAGGTCGCCGCCAATA 60.125 61.111 0.70 0.00 0.00 1.90
660 690 3.958147 CTCACAGGTCGCCGCCAAT 62.958 63.158 0.70 0.00 0.00 3.16
661 691 4.680237 CTCACAGGTCGCCGCCAA 62.680 66.667 0.70 0.00 0.00 4.52
675 705 0.318699 CGTTCTCAGTTGTCGGCTCA 60.319 55.000 0.00 0.00 0.00 4.26
677 707 1.006102 CCGTTCTCAGTTGTCGGCT 60.006 57.895 0.00 0.00 35.01 5.52
679 709 0.314302 ACTCCGTTCTCAGTTGTCGG 59.686 55.000 0.00 0.00 42.12 4.79
683 713 1.009389 GGCGACTCCGTTCTCAGTTG 61.009 60.000 0.00 0.00 38.24 3.16
684 714 1.289380 GGCGACTCCGTTCTCAGTT 59.711 57.895 0.00 0.00 38.24 3.16
688 718 4.144703 GGGGGCGACTCCGTTCTC 62.145 72.222 0.00 0.00 44.84 2.87
700 730 3.379865 TAGATTGACGCGTGGGGGC 62.380 63.158 20.70 1.01 0.00 5.80
710 740 1.130561 GCAAACCGGTGCTAGATTGAC 59.869 52.381 8.52 0.54 41.51 3.18
711 741 1.448985 GCAAACCGGTGCTAGATTGA 58.551 50.000 8.52 0.00 41.51 2.57
715 745 2.349755 GGGCAAACCGGTGCTAGA 59.650 61.111 8.52 0.00 44.31 2.43
721 751 4.280019 GTCTGGGGGCAAACCGGT 62.280 66.667 0.00 0.00 41.60 5.28
728 758 2.575455 AAACAAACCGTCTGGGGGCA 62.575 55.000 0.00 0.00 41.60 5.36
737 767 0.464916 AGGAGCCGAAAACAAACCGT 60.465 50.000 0.00 0.00 0.00 4.83
741 771 1.036707 CCCAAGGAGCCGAAAACAAA 58.963 50.000 0.00 0.00 0.00 2.83
743 773 1.228429 CCCCAAGGAGCCGAAAACA 60.228 57.895 0.00 0.00 33.47 2.83
744 774 1.977009 CCCCCAAGGAGCCGAAAAC 60.977 63.158 0.00 0.00 38.24 2.43
779 810 1.269621 ACAACTGCTTCGCGTAAGAGT 60.270 47.619 18.36 15.07 37.38 3.24
786 817 2.583801 CGAAAATAACAACTGCTTCGCG 59.416 45.455 0.00 0.00 30.63 5.87
787 818 2.908626 CCGAAAATAACAACTGCTTCGC 59.091 45.455 0.00 0.00 35.52 4.70
788 819 4.398549 TCCGAAAATAACAACTGCTTCG 57.601 40.909 0.00 0.00 36.36 3.79
789 820 5.974751 TGTTTCCGAAAATAACAACTGCTTC 59.025 36.000 0.00 0.00 0.00 3.86
790 821 5.746721 GTGTTTCCGAAAATAACAACTGCTT 59.253 36.000 0.00 0.00 33.96 3.91
791 822 5.278604 GTGTTTCCGAAAATAACAACTGCT 58.721 37.500 0.00 0.00 33.96 4.24
792 823 4.145756 CGTGTTTCCGAAAATAACAACTGC 59.854 41.667 0.00 0.00 33.96 4.40
793 824 5.170625 CACGTGTTTCCGAAAATAACAACTG 59.829 40.000 7.58 0.00 33.96 3.16
794 825 5.064962 TCACGTGTTTCCGAAAATAACAACT 59.935 36.000 16.51 0.00 33.96 3.16
808 839 1.176838 GTGCAAACGTCACGTGTTTC 58.823 50.000 16.51 6.75 39.99 2.78
815 846 4.582452 GGAACGTGCAAACGTCAC 57.418 55.556 4.18 0.00 46.41 3.67
835 866 1.694133 GGATCTGCTGGGAGGAGGTG 61.694 65.000 0.00 0.00 34.13 4.00
993 1034 3.390521 CTGTGCCGGCTGGGAGTA 61.391 66.667 29.70 1.01 35.57 2.59
1341 1393 2.765807 AGGGGATCTGGAGGCACG 60.766 66.667 0.00 0.00 0.00 5.34
1343 1395 2.040464 GGAGGGGATCTGGAGGCA 60.040 66.667 0.00 0.00 0.00 4.75
1346 1398 0.178935 GAGAGGGAGGGGATCTGGAG 60.179 65.000 0.00 0.00 0.00 3.86
1354 1406 4.179599 GGGGGAGAGAGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
1364 1417 0.040646 TAAGCAGACGAAGGGGGAGA 59.959 55.000 0.00 0.00 0.00 3.71
1375 1428 2.969443 ACACGCACATTTAAGCAGAC 57.031 45.000 0.00 0.00 0.00 3.51
1376 1429 3.659786 ACTACACGCACATTTAAGCAGA 58.340 40.909 0.00 0.00 0.00 4.26
1390 1463 5.333513 GGAGTTGTCAGATAGAACTACACG 58.666 45.833 0.00 0.00 41.53 4.49
1412 1485 3.068165 GGTTTGACTTCCAAAGAACTGGG 59.932 47.826 0.00 0.00 44.64 4.45
1545 1621 9.988350 GTCATTCCTATGTAAACATGTACTTTG 57.012 33.333 0.00 0.00 37.15 2.77
1679 1835 7.770897 AGACATGATAGGTTAACTGTTTCATCC 59.229 37.037 5.42 4.86 0.00 3.51
1802 1972 4.263243 GCCCAAGAGATAAGATGCAGGTAT 60.263 45.833 0.00 0.00 0.00 2.73
1822 1992 5.578776 CAAAACTATCAGAAATTACCGCCC 58.421 41.667 0.00 0.00 0.00 6.13
1825 1995 6.128007 ACAGGCAAAACTATCAGAAATTACCG 60.128 38.462 0.00 0.00 0.00 4.02
1826 1996 7.029563 CACAGGCAAAACTATCAGAAATTACC 58.970 38.462 0.00 0.00 0.00 2.85
2260 2432 8.355806 GTTGACGTCGATAATTTTTGTTCATTC 58.644 33.333 9.14 0.00 0.00 2.67
2277 2449 4.463209 ACTAAATTTGCATGTTGACGTCG 58.537 39.130 11.62 0.00 0.00 5.12
2334 2506 7.141758 TCTCAATTTGAGGCTGTCCTAATAT 57.858 36.000 22.86 0.00 44.39 1.28
2416 2588 2.816087 GGTTCTTCACTGCATCACATGT 59.184 45.455 0.00 0.00 0.00 3.21
2716 2905 6.524101 TTAGTGCCAATACAATTTTCTCCC 57.476 37.500 0.00 0.00 0.00 4.30
2798 2987 0.796312 CGGGACAAGAAACATGGTCG 59.204 55.000 0.00 0.00 0.00 4.79
2863 3055 8.237267 ACTGTAAACTGTTAGCTTAATTGCATC 58.763 33.333 0.00 0.00 34.99 3.91
2877 3069 7.502696 TGTAATGGAGTGTACTGTAAACTGTT 58.497 34.615 15.19 9.48 0.00 3.16
2900 3092 0.898320 ATGAAGCTGGCGTAGACTGT 59.102 50.000 0.00 0.00 36.60 3.55
2903 3095 2.010145 TTGATGAAGCTGGCGTAGAC 57.990 50.000 0.00 0.00 0.00 2.59
2904 3096 2.028112 AGTTTGATGAAGCTGGCGTAGA 60.028 45.455 0.00 0.00 0.00 2.59
2905 3097 2.350522 AGTTTGATGAAGCTGGCGTAG 58.649 47.619 0.00 0.00 0.00 3.51
2906 3098 2.472695 AGTTTGATGAAGCTGGCGTA 57.527 45.000 0.00 0.00 0.00 4.42
3227 3532 1.774254 TCAAGGAGAAAAGGAGCACCA 59.226 47.619 2.07 0.00 38.94 4.17
3290 3599 8.400947 CAAAGATAAAATGTGATGAGTACCCAG 58.599 37.037 0.00 0.00 0.00 4.45
3505 3840 5.264060 TCTTGAAGAAACTTGATAACGCG 57.736 39.130 3.53 3.53 0.00 6.01
3593 3938 3.806949 TTAGGCTGGTTGAGTCCAAAT 57.193 42.857 0.00 0.00 37.01 2.32
3717 4144 1.242076 GCCACTGAGTGCAAGTGATT 58.758 50.000 16.84 0.00 35.75 2.57
3789 4216 5.079689 TGCGAACAGATTAGTGGAATACA 57.920 39.130 0.00 0.00 0.00 2.29
3829 4256 4.405358 GCCAAACAAGGATAAATGGGATGA 59.595 41.667 0.00 0.00 0.00 2.92
3863 4290 7.646548 TGATAGCAGCCTAGTAATATGTAGG 57.353 40.000 0.00 2.82 39.18 3.18
3867 4294 9.224267 ACATTTTGATAGCAGCCTAGTAATATG 57.776 33.333 0.00 0.00 0.00 1.78
3931 4363 3.616956 TTGCCTAAGTGATCTGGTCAG 57.383 47.619 0.00 0.00 37.56 3.51
3934 4366 2.038557 ACGTTTGCCTAAGTGATCTGGT 59.961 45.455 0.00 0.00 0.00 4.00
4147 4584 2.034066 AGGGCATGGTCAACACGG 59.966 61.111 0.00 0.00 0.00 4.94
4188 4625 1.647084 GTAATCCGCCATTCCGTGC 59.353 57.895 0.00 0.00 0.00 5.34
4230 4667 3.388350 CCTGCTTAGTAGGGAAACTAGGG 59.612 52.174 8.56 0.00 33.62 3.53
4320 4757 5.613142 CGCTTCATTTCTTTGAAATGCAACC 60.613 40.000 21.41 12.06 37.50 3.77
4334 4771 2.481952 AGCTGTGAACTCGCTTCATTTC 59.518 45.455 0.00 0.00 41.10 2.17
4335 4772 2.498167 AGCTGTGAACTCGCTTCATTT 58.502 42.857 0.00 0.00 41.10 2.32
4336 4773 2.175878 AGCTGTGAACTCGCTTCATT 57.824 45.000 0.00 0.00 41.10 2.57
4337 4774 2.175878 AAGCTGTGAACTCGCTTCAT 57.824 45.000 0.00 0.00 41.10 2.57
4338 4775 1.599071 CAAAGCTGTGAACTCGCTTCA 59.401 47.619 0.00 0.00 42.65 3.02
4339 4776 1.599542 ACAAAGCTGTGAACTCGCTTC 59.400 47.619 11.93 0.00 42.65 3.86
4340 4777 1.668419 ACAAAGCTGTGAACTCGCTT 58.332 45.000 11.93 5.21 45.13 4.68
4341 4778 3.386543 ACAAAGCTGTGAACTCGCT 57.613 47.368 11.93 0.00 33.30 4.93
4374 4811 5.284660 GCTGTGAACTCGCTTCATTTATTTG 59.715 40.000 0.00 0.00 41.10 2.32
4378 4815 3.664107 AGCTGTGAACTCGCTTCATTTA 58.336 40.909 0.00 0.00 41.10 1.40
4398 4835 0.318120 GGGTTGTGATGGGCAACAAG 59.682 55.000 9.83 0.00 45.64 3.16
4473 4910 6.239317 GCAAGATACCAGTTTTCTTTTCCCTT 60.239 38.462 0.00 0.00 0.00 3.95
4507 4944 3.448301 TGGAATTCATGCATTGGAGGAAC 59.552 43.478 7.42 0.00 0.00 3.62
4727 5164 4.585955 AGTATGCAGTTACGATACAGGG 57.414 45.455 0.00 0.00 0.00 4.45
4745 5182 6.070481 TGGAGAAACATATGGTGCAGTAAGTA 60.070 38.462 7.80 0.00 0.00 2.24
4775 5219 2.614057 ACATGCTCATTTACTTAGCGGC 59.386 45.455 0.00 0.00 39.14 6.53
4863 5309 1.133790 GTAAGAGAAGAACCGCGGCTA 59.866 52.381 28.58 0.00 0.00 3.93
4892 5338 3.135225 TGGTACACAACACTGTACATGC 58.865 45.455 10.73 0.00 45.76 4.06
5008 7472 3.243336 CCGAAACACTACAGCTACTGAC 58.757 50.000 0.78 0.00 35.18 3.51
5020 7484 1.937899 CACTCCGAAAACCGAAACACT 59.062 47.619 0.00 0.00 41.76 3.55
5021 7485 1.935199 TCACTCCGAAAACCGAAACAC 59.065 47.619 0.00 0.00 41.76 3.32
5058 7522 3.469008 ACAAGATGAACAACACCTCGA 57.531 42.857 0.00 0.00 0.00 4.04
5080 7544 7.527516 CGAACGTACGGACTACTGTTATAATAC 59.472 40.741 21.06 0.00 36.89 1.89
5084 7548 4.260212 GCGAACGTACGGACTACTGTTATA 60.260 45.833 21.06 0.00 36.89 0.98
5097 7561 2.398036 GCCAATGGCGAACGTACG 59.602 61.111 15.01 15.01 39.62 3.67
5146 7610 4.611355 CGCTGATACTGACAACCAAGTTTG 60.611 45.833 0.00 0.00 0.00 2.93
5254 7850 5.976458 ACTCTGCTAGAAAGATTCAAGGAG 58.024 41.667 0.00 0.00 0.00 3.69
5256 7852 5.752955 GCTACTCTGCTAGAAAGATTCAAGG 59.247 44.000 0.00 0.00 0.00 3.61
5257 7853 6.255453 GTGCTACTCTGCTAGAAAGATTCAAG 59.745 42.308 0.00 0.00 0.00 3.02
5293 7909 5.751028 CACGAGTCTGGGAAAGAATAGATTC 59.249 44.000 0.00 0.00 36.40 2.52
5382 8000 7.884877 CCCAACTCTTATGGCTGATGATAATAA 59.115 37.037 0.00 0.00 36.58 1.40
5383 8001 7.397221 CCCAACTCTTATGGCTGATGATAATA 58.603 38.462 0.00 0.00 36.58 0.98
5384 8002 6.243900 CCCAACTCTTATGGCTGATGATAAT 58.756 40.000 0.00 0.00 36.58 1.28
5397 8015 6.824958 TCATTAGCTTACCCCAACTCTTAT 57.175 37.500 0.00 0.00 0.00 1.73
5407 8025 6.509677 GCGCGATTATTATCATTAGCTTACCC 60.510 42.308 12.10 0.00 0.00 3.69
5430 8048 3.426859 GTCATCATCATTAGAACTCGGCG 59.573 47.826 0.00 0.00 0.00 6.46
5434 8052 7.539712 TTTTCCGTCATCATCATTAGAACTC 57.460 36.000 0.00 0.00 0.00 3.01
5451 8069 7.282450 GGAGATTGACATAAACCTATTTTCCGT 59.718 37.037 0.00 0.00 0.00 4.69
5452 8070 7.255139 GGGAGATTGACATAAACCTATTTTCCG 60.255 40.741 0.00 0.00 0.00 4.30
5453 8071 7.780271 AGGGAGATTGACATAAACCTATTTTCC 59.220 37.037 0.00 0.00 0.00 3.13
5502 8314 1.986575 GCACAGCGCAGGGAGATTTC 61.987 60.000 11.47 0.00 41.79 2.17
5524 8337 2.368655 AATGTTTTGCCCGAATGAGC 57.631 45.000 0.00 0.00 0.00 4.26
5564 8377 4.428209 CTGATGATACTTGACACTCGCTT 58.572 43.478 0.00 0.00 0.00 4.68
5571 8384 6.544928 TTTCCTAGCTGATGATACTTGACA 57.455 37.500 0.00 0.00 0.00 3.58
5646 9029 2.630580 GGCCCATTTGTTTTCCACAGTA 59.369 45.455 0.00 0.00 36.48 2.74
5679 9062 7.201418 GCTTTTAACGTCGCTATTTCTTAGACT 60.201 37.037 0.00 0.00 0.00 3.24
5747 9131 2.173669 GTCGCCATGTCCATGTCCG 61.174 63.158 6.53 8.39 37.11 4.79
5765 9156 3.251729 ACTGCTATGCTATGCCAATTTCG 59.748 43.478 0.00 0.00 0.00 3.46
5823 9226 9.148879 AGTAGTTAGTATTGCTGATTATCACCT 57.851 33.333 0.00 0.00 0.00 4.00
5842 9245 9.325198 CATAATGCCATGAACTTACAGTAGTTA 57.675 33.333 0.00 0.00 38.43 2.24
5880 9283 9.555727 CTGGCTATATTTTACCTTAGTTTGCTA 57.444 33.333 0.00 0.00 0.00 3.49
5898 9301 5.090845 TGTGCACCCTTATATCTGGCTATA 58.909 41.667 15.69 0.00 0.00 1.31
5964 9367 1.535462 GTAATGTTGCGCAGGTGTCTT 59.465 47.619 11.31 2.70 0.00 3.01
6048 9451 0.307760 CGAAAGGACAACTGGTGCAC 59.692 55.000 8.80 8.80 40.89 4.57
6067 9470 7.859325 TGGAGAATATTAGTGTTAAACCTGC 57.141 36.000 0.00 0.00 0.00 4.85
6098 9502 4.594920 TCCCATGTTTCTCTTCTGTTCTCT 59.405 41.667 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.