Multiple sequence alignment - TraesCS7D01G477100

Loading Multiple Alignment...

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 TraesCS7D01G477100 chr7D 100.000 2799 0 0 1 2799 588161181 588158383 0.000000e+00 5169.0
1 TraesCS7D01G477100 chr7D 96.867 766 20 4 2036 2799 121768938 121769701 0.000000e+00 1279.0
2 TraesCS7D01G477100 chr7D 97.521 726 14 4 2075 2799 546260712 546261434 0.000000e+00 1238.0
3 TraesCS7D01G477100 chr7D 97.245 726 16 4 2075 2799 597579989 597579267 0.000000e+00 1227.0
4 TraesCS7D01G477100 chr7A 92.887 956 48 8 1062 2013 680188960 680188021 0.000000e+00 1371.0
5 TraesCS7D01G477100 chr7A 85.406 603 20 21 455 1016 680189535 680188960 5.230000e-157 564.0
6 TraesCS7D01G477100 chr7A 83.105 438 31 16 1 425 680189940 680189533 2.650000e-95 359.0
7 TraesCS7D01G477100 chr7A 80.531 113 14 6 403 509 680192392 680192282 2.310000e-11 80.5
8 TraesCS7D01G477100 chr7B 92.228 965 45 16 1062 2013 661430633 661429686 0.000000e+00 1339.0
9 TraesCS7D01G477100 chr7B 87.588 709 42 17 1 685 661431707 661431021 0.000000e+00 780.0
10 TraesCS7D01G477100 chr7B 89.368 348 16 14 681 1008 661430979 661430633 4.310000e-113 418.0
11 TraesCS7D01G477100 chr7B 84.043 94 10 5 404 495 661452046 661451956 4.970000e-13 86.1
12 TraesCS7D01G477100 chr2D 97.781 721 13 3 2081 2799 107559127 107558408 0.000000e+00 1240.0
13 TraesCS7D01G477100 chr5D 97.521 726 15 3 2075 2799 277072926 277073649 0.000000e+00 1238.0
14 TraesCS7D01G477100 chr5D 97.379 725 18 1 2075 2799 421451424 421450701 0.000000e+00 1232.0
15 TraesCS7D01G477100 chr5D 97.379 725 17 2 2075 2799 543054716 543053994 0.000000e+00 1232.0
16 TraesCS7D01G477100 chr5D 93.056 72 3 2 2035 2105 330027212 330027282 1.370000e-18 104.0
17 TraesCS7D01G477100 chr5D 90.541 74 3 4 2031 2101 509248714 509248786 8.250000e-16 95.3
18 TraesCS7D01G477100 chr4D 97.649 723 14 3 2079 2799 58930517 58931238 0.000000e+00 1238.0
19 TraesCS7D01G477100 chr4D 97.383 726 15 4 2075 2799 91060863 91061585 0.000000e+00 1232.0
20 TraesCS7D01G477100 chr4D 92.782 665 20 15 2036 2673 49940727 49941390 0.000000e+00 937.0
21 TraesCS7D01G477100 chr4D 94.030 67 2 2 2032 2097 410655296 410655231 1.770000e-17 100.0
22 TraesCS7D01G477100 chr4D 90.541 74 3 4 2031 2101 92080371 92080443 8.250000e-16 95.3
23 TraesCS7D01G477100 chr4D 91.304 69 3 3 2036 2102 214095573 214095506 1.070000e-14 91.6
24 TraesCS7D01G477100 chr3D 94.203 69 4 0 2037 2105 128737828 128737896 3.810000e-19 106.0
25 TraesCS7D01G477100 chr3D 95.312 64 2 1 2034 2097 512517224 512517286 1.770000e-17 100.0
26 TraesCS7D01G477100 chr6D 89.474 76 3 4 2031 2102 134145498 134145572 1.070000e-14 91.6
27 TraesCS7D01G477100 chr1D 91.304 69 3 3 2036 2102 464935284 464935217 1.070000e-14 91.6
28 TraesCS7D01G477100 chr3A 86.364 88 5 6 2020 2101 683293613 683293699 3.840000e-14 89.8


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 TraesCS7D01G477100 chr7D 588158383 588161181 2798 True 5169.000000 5169 100.00000 1 2799 1 chr7D.!!$R1 2798
1 TraesCS7D01G477100 chr7D 121768938 121769701 763 False 1279.000000 1279 96.86700 2036 2799 1 chr7D.!!$F1 763
2 TraesCS7D01G477100 chr7D 546260712 546261434 722 False 1238.000000 1238 97.52100 2075 2799 1 chr7D.!!$F2 724
3 TraesCS7D01G477100 chr7D 597579267 597579989 722 True 1227.000000 1227 97.24500 2075 2799 1 chr7D.!!$R2 724
4 TraesCS7D01G477100 chr7A 680188021 680192392 4371 True 593.625000 1371 85.48225 1 2013 4 chr7A.!!$R1 2012
5 TraesCS7D01G477100 chr7B 661429686 661431707 2021 True 845.666667 1339 89.72800 1 2013 3 chr7B.!!$R2 2012
6 TraesCS7D01G477100 chr2D 107558408 107559127 719 True 1240.000000 1240 97.78100 2081 2799 1 chr2D.!!$R1 718
7 TraesCS7D01G477100 chr5D 277072926 277073649 723 False 1238.000000 1238 97.52100 2075 2799 1 chr5D.!!$F1 724
8 TraesCS7D01G477100 chr5D 421450701 421451424 723 True 1232.000000 1232 97.37900 2075 2799 1 chr5D.!!$R1 724
9 TraesCS7D01G477100 chr5D 543053994 543054716 722 True 1232.000000 1232 97.37900 2075 2799 1 chr5D.!!$R2 724
10 TraesCS7D01G477100 chr4D 58930517 58931238 721 False 1238.000000 1238 97.64900 2079 2799 1 chr4D.!!$F2 720
11 TraesCS7D01G477100 chr4D 91060863 91061585 722 False 1232.000000 1232 97.38300 2075 2799 1 chr4D.!!$F3 724
12 TraesCS7D01G477100 chr4D 49940727 49941390 663 False 937.000000 937 92.78200 2036 2673 1 chr4D.!!$F1 637

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
452 2919 0.037232 GGCGCAAACTAGTCTGGAGT 60.037 55.0 10.83 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 4618 2.880268 TGTTGAGAGACAAACAGCATGG 59.12 45.455 0.0 0.0 40.36 3.66 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
68 2521 1.665442 GAGGGTGCGGTTTTTGCAT 59.335 52.632 0.00 0.00 45.34 3.96
99 2552 1.823169 ATGTGGCCAGCAGCAAAAGG 61.823 55.000 5.11 0.00 46.50 3.11
194 2650 3.941483 CACATTTTCACCTACCTGGCTAG 59.059 47.826 0.00 0.00 40.22 3.42
195 2651 3.587506 ACATTTTCACCTACCTGGCTAGT 59.412 43.478 0.00 0.00 40.22 2.57
196 2652 4.781087 ACATTTTCACCTACCTGGCTAGTA 59.219 41.667 0.00 0.00 40.22 1.82
197 2653 4.813750 TTTTCACCTACCTGGCTAGTAC 57.186 45.455 0.00 0.00 40.22 2.73
198 2654 3.752359 TTCACCTACCTGGCTAGTACT 57.248 47.619 0.00 0.00 40.22 2.73
199 2655 3.294038 TCACCTACCTGGCTAGTACTC 57.706 52.381 0.00 0.00 40.22 2.59
200 2656 2.091994 TCACCTACCTGGCTAGTACTCC 60.092 54.545 0.00 0.00 40.22 3.85
201 2657 2.091775 CACCTACCTGGCTAGTACTCCT 60.092 54.545 0.00 0.00 40.22 3.69
202 2658 3.137913 CACCTACCTGGCTAGTACTCCTA 59.862 52.174 0.00 0.00 40.22 2.94
203 2659 3.138098 ACCTACCTGGCTAGTACTCCTAC 59.862 52.174 0.00 0.00 40.22 3.18
204 2660 3.395273 CCTACCTGGCTAGTACTCCTACT 59.605 52.174 0.00 0.00 37.04 2.57
205 2661 4.141205 CCTACCTGGCTAGTACTCCTACTT 60.141 50.000 0.00 0.00 34.79 2.24
206 2662 3.633418 ACCTGGCTAGTACTCCTACTTG 58.367 50.000 0.00 0.00 34.79 3.16
207 2663 2.362717 CCTGGCTAGTACTCCTACTTGC 59.637 54.545 0.00 5.95 45.65 4.01
210 2666 3.719173 GCTAGTACTCCTACTTGCAGG 57.281 52.381 0.00 0.00 45.67 4.85
228 2684 0.318955 GGTTGCAACATGCTGTCACC 60.319 55.000 29.55 6.52 45.31 4.02
229 2685 0.318955 GTTGCAACATGCTGTCACCC 60.319 55.000 24.52 0.00 45.31 4.61
233 2689 1.600636 AACATGCTGTCACCCACCG 60.601 57.895 0.00 0.00 0.00 4.94
250 2706 1.135286 ACCGGAAAGAACGATACGGAC 60.135 52.381 9.46 0.00 43.69 4.79
251 2707 1.135315 CCGGAAAGAACGATACGGACA 60.135 52.381 0.00 0.00 43.69 4.02
298 2754 0.371645 GAGCCGAGAATTCAACGCAG 59.628 55.000 8.44 3.19 0.00 5.18
315 2778 2.124151 GTAGCACCCCATGGCAGG 60.124 66.667 6.09 5.77 33.59 4.85
384 2851 1.370414 CGACAAAGCAAAGCCACGG 60.370 57.895 0.00 0.00 0.00 4.94
446 2913 3.178539 GCCAGGCGCAAACTAGTC 58.821 61.111 10.83 0.00 37.47 2.59
447 2914 1.376037 GCCAGGCGCAAACTAGTCT 60.376 57.895 10.83 0.00 37.47 3.24
448 2915 1.639298 GCCAGGCGCAAACTAGTCTG 61.639 60.000 10.83 4.21 37.47 3.51
449 2916 1.021390 CCAGGCGCAAACTAGTCTGG 61.021 60.000 10.83 10.36 36.28 3.86
450 2917 0.037326 CAGGCGCAAACTAGTCTGGA 60.037 55.000 10.83 0.00 0.00 3.86
451 2918 0.247736 AGGCGCAAACTAGTCTGGAG 59.752 55.000 10.83 0.00 0.00 3.86
452 2919 0.037232 GGCGCAAACTAGTCTGGAGT 60.037 55.000 10.83 0.00 0.00 3.85
453 2920 1.203994 GGCGCAAACTAGTCTGGAGTA 59.796 52.381 10.83 0.00 0.00 2.59
629 3151 2.029073 CACTTGTGCGGGTCGACT 59.971 61.111 16.46 0.00 0.00 4.18
854 3422 1.339151 GCGGAAAAGATCTCACCACCT 60.339 52.381 0.00 0.00 0.00 4.00
855 3423 2.622436 CGGAAAAGATCTCACCACCTC 58.378 52.381 0.00 0.00 0.00 3.85
856 3424 2.234908 CGGAAAAGATCTCACCACCTCT 59.765 50.000 0.00 0.00 0.00 3.69
858 3426 3.517500 GGAAAAGATCTCACCACCTCTCT 59.482 47.826 0.00 0.00 0.00 3.10
860 3428 2.051334 AGATCTCACCACCTCTCTCG 57.949 55.000 0.00 0.00 0.00 4.04
862 3430 1.040339 ATCTCACCACCTCTCTCGCC 61.040 60.000 0.00 0.00 0.00 5.54
863 3431 3.057547 CTCACCACCTCTCTCGCCG 62.058 68.421 0.00 0.00 0.00 6.46
868 3436 4.779966 ACCTCTCTCGCCGCTCGA 62.780 66.667 0.00 0.00 46.29 4.04
994 3585 3.146828 GCAACCCCACCTCACCCTT 62.147 63.158 0.00 0.00 0.00 3.95
995 3586 1.785353 GCAACCCCACCTCACCCTTA 61.785 60.000 0.00 0.00 0.00 2.69
996 3587 0.037734 CAACCCCACCTCACCCTTAC 59.962 60.000 0.00 0.00 0.00 2.34
997 3588 1.486145 AACCCCACCTCACCCTTACG 61.486 60.000 0.00 0.00 0.00 3.18
998 3589 1.916777 CCCCACCTCACCCTTACGT 60.917 63.158 0.00 0.00 0.00 3.57
999 3590 1.295423 CCCACCTCACCCTTACGTG 59.705 63.158 0.00 0.00 34.93 4.49
1000 3591 1.375523 CCACCTCACCCTTACGTGC 60.376 63.158 0.00 0.00 33.57 5.34
1001 3592 1.736645 CACCTCACCCTTACGTGCG 60.737 63.158 0.00 0.00 33.57 5.34
1002 3593 1.904865 ACCTCACCCTTACGTGCGA 60.905 57.895 0.00 0.00 33.57 5.10
1003 3594 1.153823 CCTCACCCTTACGTGCGAG 60.154 63.158 0.00 0.00 33.57 5.03
1004 3595 1.805945 CTCACCCTTACGTGCGAGC 60.806 63.158 0.00 0.00 33.57 5.03
1005 3596 3.179265 CACCCTTACGTGCGAGCG 61.179 66.667 0.00 0.00 37.94 5.03
1006 3597 3.367743 ACCCTTACGTGCGAGCGA 61.368 61.111 0.00 0.00 35.59 4.93
1007 3598 2.579787 CCCTTACGTGCGAGCGAG 60.580 66.667 0.00 0.00 35.59 5.03
1010 3601 3.994946 CTTACGTGCGAGCGAGCGA 62.995 63.158 0.00 0.00 40.67 4.93
1018 3609 3.568743 GAGCGAGCGAGCGAGAGA 61.569 66.667 1.41 0.00 43.00 3.10
1026 3617 1.934463 CGAGCGAGAGAGAGAGAGC 59.066 63.158 0.00 0.00 0.00 4.09
1027 3618 0.530650 CGAGCGAGAGAGAGAGAGCT 60.531 60.000 0.00 0.00 37.69 4.09
1028 3619 1.269569 CGAGCGAGAGAGAGAGAGCTA 60.270 57.143 0.00 0.00 34.85 3.32
1029 3620 2.408050 GAGCGAGAGAGAGAGAGCTAG 58.592 57.143 0.00 0.00 34.85 3.42
1030 3621 2.035961 GAGCGAGAGAGAGAGAGCTAGA 59.964 54.545 0.00 0.00 34.85 2.43
1031 3622 2.036475 AGCGAGAGAGAGAGAGCTAGAG 59.964 54.545 0.00 0.00 32.73 2.43
1032 3623 2.035961 GCGAGAGAGAGAGAGCTAGAGA 59.964 54.545 0.00 0.00 0.00 3.10
1033 3624 3.858877 GCGAGAGAGAGAGAGCTAGAGAG 60.859 56.522 0.00 0.00 0.00 3.20
1034 3625 3.570125 CGAGAGAGAGAGAGCTAGAGAGA 59.430 52.174 0.00 0.00 0.00 3.10
1035 3626 4.320861 CGAGAGAGAGAGAGCTAGAGAGAG 60.321 54.167 0.00 0.00 0.00 3.20
1036 3627 4.809193 AGAGAGAGAGAGCTAGAGAGAGA 58.191 47.826 0.00 0.00 0.00 3.10
1037 3628 4.832266 AGAGAGAGAGAGCTAGAGAGAGAG 59.168 50.000 0.00 0.00 0.00 3.20
1038 3629 4.809193 AGAGAGAGAGCTAGAGAGAGAGA 58.191 47.826 0.00 0.00 0.00 3.10
1039 3630 4.832266 AGAGAGAGAGCTAGAGAGAGAGAG 59.168 50.000 0.00 0.00 0.00 3.20
1040 3631 4.809193 AGAGAGAGCTAGAGAGAGAGAGA 58.191 47.826 0.00 0.00 0.00 3.10
1041 3632 4.832266 AGAGAGAGCTAGAGAGAGAGAGAG 59.168 50.000 0.00 0.00 0.00 3.20
1042 3633 4.809193 AGAGAGCTAGAGAGAGAGAGAGA 58.191 47.826 0.00 0.00 0.00 3.10
1043 3634 4.832266 AGAGAGCTAGAGAGAGAGAGAGAG 59.168 50.000 0.00 0.00 0.00 3.20
1044 3635 4.809193 AGAGCTAGAGAGAGAGAGAGAGA 58.191 47.826 0.00 0.00 0.00 3.10
1045 3636 4.832266 AGAGCTAGAGAGAGAGAGAGAGAG 59.168 50.000 0.00 0.00 0.00 3.20
1046 3637 4.809193 AGCTAGAGAGAGAGAGAGAGAGA 58.191 47.826 0.00 0.00 0.00 3.10
1047 3638 4.832266 AGCTAGAGAGAGAGAGAGAGAGAG 59.168 50.000 0.00 0.00 0.00 3.20
1048 3639 4.830046 GCTAGAGAGAGAGAGAGAGAGAGA 59.170 50.000 0.00 0.00 0.00 3.10
1049 3640 5.048083 GCTAGAGAGAGAGAGAGAGAGAGAG 60.048 52.000 0.00 0.00 0.00 3.20
1050 3641 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1051 3642 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
1052 3643 5.774690 AGAGAGAGAGAGAGAGAGAGAGATC 59.225 48.000 0.00 0.00 0.00 2.75
1053 3644 5.714863 AGAGAGAGAGAGAGAGAGAGATCT 58.285 45.833 0.00 0.00 0.00 2.75
1054 3645 5.539574 AGAGAGAGAGAGAGAGAGAGATCTG 59.460 48.000 0.00 0.00 0.00 2.90
1055 3646 4.592351 AGAGAGAGAGAGAGAGAGATCTGG 59.408 50.000 0.00 0.00 0.00 3.86
1056 3647 3.072184 AGAGAGAGAGAGAGAGATCTGGC 59.928 52.174 0.00 0.00 0.00 4.85
1057 3648 2.107204 AGAGAGAGAGAGAGATCTGGCC 59.893 54.545 0.00 0.00 0.00 5.36
1058 3649 1.145738 AGAGAGAGAGAGATCTGGCCC 59.854 57.143 0.00 0.00 0.00 5.80
1059 3650 0.178992 AGAGAGAGAGATCTGGCCCG 60.179 60.000 0.00 0.00 0.00 6.13
1060 3651 0.467290 GAGAGAGAGATCTGGCCCGT 60.467 60.000 0.00 0.00 0.00 5.28
1061 3652 0.754957 AGAGAGAGATCTGGCCCGTG 60.755 60.000 0.00 0.00 0.00 4.94
1070 3661 3.832237 CTGGCCCGTGTGCTGAAGT 62.832 63.158 0.00 0.00 0.00 3.01
1204 3795 2.815647 GCCAACTTCCTCGCCTCG 60.816 66.667 0.00 0.00 0.00 4.63
1857 4461 9.818796 GAGTTGAGTAAAAGTTGATCAAATCTC 57.181 33.333 10.35 11.87 40.15 2.75
1944 4548 4.726416 CAGTAAAGTGGATCACATGTTGC 58.274 43.478 0.00 0.00 36.74 4.17
1954 4558 4.806247 GGATCACATGTTGCTCAGTAGTAC 59.194 45.833 0.00 0.00 0.00 2.73
1955 4559 4.188247 TCACATGTTGCTCAGTAGTACC 57.812 45.455 0.00 0.00 0.00 3.34
1957 4561 4.222810 TCACATGTTGCTCAGTAGTACCAT 59.777 41.667 0.00 0.00 0.00 3.55
1958 4562 5.420739 TCACATGTTGCTCAGTAGTACCATA 59.579 40.000 0.00 0.00 0.00 2.74
1959 4563 5.520288 CACATGTTGCTCAGTAGTACCATAC 59.480 44.000 0.00 0.00 0.00 2.39
1960 4564 5.422331 ACATGTTGCTCAGTAGTACCATACT 59.578 40.000 0.00 0.00 42.68 2.12
1962 4566 5.962433 TGTTGCTCAGTAGTACCATACTTC 58.038 41.667 0.00 0.00 40.14 3.01
1963 4567 5.715279 TGTTGCTCAGTAGTACCATACTTCT 59.285 40.000 0.00 0.00 40.14 2.85
1964 4568 6.210784 TGTTGCTCAGTAGTACCATACTTCTT 59.789 38.462 0.00 0.00 40.14 2.52
1965 4569 7.395206 TGTTGCTCAGTAGTACCATACTTCTTA 59.605 37.037 0.00 0.00 40.14 2.10
1966 4570 7.569639 TGCTCAGTAGTACCATACTTCTTAG 57.430 40.000 0.00 0.00 40.14 2.18
1986 4590 8.008513 TCTTAGTAGTAATTTAGCTGGACTGG 57.991 38.462 0.00 0.00 0.00 4.00
2000 4604 3.219281 TGGACTGGTTAGGCTTTTGAAC 58.781 45.455 0.00 0.00 30.42 3.18
2004 4608 4.652822 ACTGGTTAGGCTTTTGAACTAGG 58.347 43.478 13.59 1.90 36.35 3.02
2013 4617 5.191722 AGGCTTTTGAACTAGGTATGGATCA 59.808 40.000 0.00 0.00 0.00 2.92
2014 4618 5.297029 GGCTTTTGAACTAGGTATGGATCAC 59.703 44.000 0.00 0.00 0.00 3.06
2015 4619 5.297029 GCTTTTGAACTAGGTATGGATCACC 59.703 44.000 0.00 0.00 36.22 4.02
2026 4630 2.291209 TGGATCACCATGCTGTTTGT 57.709 45.000 0.00 0.00 41.77 2.83
2027 4631 2.161855 TGGATCACCATGCTGTTTGTC 58.838 47.619 0.00 0.00 41.77 3.18
2028 4632 2.224843 TGGATCACCATGCTGTTTGTCT 60.225 45.455 0.00 0.00 41.77 3.41
2029 4633 2.421424 GGATCACCATGCTGTTTGTCTC 59.579 50.000 0.00 0.00 35.97 3.36
2030 4634 2.936919 TCACCATGCTGTTTGTCTCT 57.063 45.000 0.00 0.00 0.00 3.10
2031 4635 2.771089 TCACCATGCTGTTTGTCTCTC 58.229 47.619 0.00 0.00 0.00 3.20
2032 4636 2.104622 TCACCATGCTGTTTGTCTCTCA 59.895 45.455 0.00 0.00 0.00 3.27
2033 4637 2.880268 CACCATGCTGTTTGTCTCTCAA 59.120 45.455 0.00 0.00 0.00 3.02
2034 4638 2.880890 ACCATGCTGTTTGTCTCTCAAC 59.119 45.455 0.00 0.00 35.61 3.18
2035 4639 2.880268 CCATGCTGTTTGTCTCTCAACA 59.120 45.455 0.00 0.00 35.61 3.33
2036 4640 3.316029 CCATGCTGTTTGTCTCTCAACAA 59.684 43.478 0.00 0.00 37.37 2.83
2037 4641 4.022589 CCATGCTGTTTGTCTCTCAACAAT 60.023 41.667 0.00 0.00 38.83 2.71
2114 4745 4.656112 CCTCACTCCCACCTATGACTTATT 59.344 45.833 0.00 0.00 0.00 1.40
2264 4898 1.264295 GAGGAGTTGGTAGTCCGGTT 58.736 55.000 0.00 0.00 46.76 4.44
2594 5229 7.040409 ACACTTTCCTAATGACAAAAGATCACC 60.040 37.037 0.00 0.00 33.85 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 2511 2.127042 TCGCGCGATGCAAAAACC 60.127 55.556 31.40 0.00 46.97 3.27
68 2521 2.809174 CCACATTCACTCGCGCGA 60.809 61.111 32.60 32.60 0.00 5.87
135 2590 2.202557 CGTCTCACGCCACGCATA 60.203 61.111 0.00 0.00 33.65 3.14
194 2650 2.347731 GCAACCTGCAAGTAGGAGTAC 58.652 52.381 11.30 0.00 44.26 2.73
195 2651 2.762535 GCAACCTGCAAGTAGGAGTA 57.237 50.000 11.30 0.00 44.26 2.59
196 2652 3.633361 GCAACCTGCAAGTAGGAGT 57.367 52.632 11.30 0.00 44.26 3.85
222 2678 0.179040 GTTCTTTCCGGTGGGTGACA 60.179 55.000 0.00 0.00 33.83 3.58
228 2684 1.274596 CGTATCGTTCTTTCCGGTGG 58.725 55.000 0.00 0.00 0.00 4.61
229 2685 1.135315 TCCGTATCGTTCTTTCCGGTG 60.135 52.381 0.00 0.00 36.84 4.94
233 2689 1.925185 GCTGTCCGTATCGTTCTTTCC 59.075 52.381 0.00 0.00 0.00 3.13
271 2727 2.239654 TGAATTCTCGGCTCCTTCCAAT 59.760 45.455 7.05 0.00 0.00 3.16
285 2741 2.076863 GGTGCTACTGCGTTGAATTCT 58.923 47.619 7.05 0.00 43.34 2.40
298 2754 2.124151 CCTGCCATGGGGTGCTAC 60.124 66.667 15.13 0.00 36.17 3.58
315 2778 0.796927 GTCGTACAAGCAAGGAAGCC 59.203 55.000 0.00 0.00 34.23 4.35
429 2896 1.376037 AGACTAGTTTGCGCCTGGC 60.376 57.895 9.11 9.11 43.96 4.85
430 2897 1.021390 CCAGACTAGTTTGCGCCTGG 61.021 60.000 4.18 7.90 35.75 4.45
431 2898 0.037326 TCCAGACTAGTTTGCGCCTG 60.037 55.000 4.18 1.47 0.00 4.85
432 2899 0.247736 CTCCAGACTAGTTTGCGCCT 59.752 55.000 4.18 0.00 0.00 5.52
433 2900 0.037232 ACTCCAGACTAGTTTGCGCC 60.037 55.000 4.18 0.00 0.00 6.53
434 2901 2.260481 GTACTCCAGACTAGTTTGCGC 58.740 52.381 7.89 0.00 0.00 6.09
435 2902 2.095364 ACGTACTCCAGACTAGTTTGCG 60.095 50.000 7.89 8.09 0.00 4.85
436 2903 3.572604 ACGTACTCCAGACTAGTTTGC 57.427 47.619 7.89 0.00 0.00 3.68
437 2904 5.876612 AGTACGTACTCCAGACTAGTTTG 57.123 43.478 22.45 6.43 0.00 2.93
438 2905 5.121454 CGAAGTACGTACTCCAGACTAGTTT 59.879 44.000 27.51 8.21 34.99 2.66
439 2906 4.629200 CGAAGTACGTACTCCAGACTAGTT 59.371 45.833 27.51 8.74 34.99 2.24
440 2907 4.081972 TCGAAGTACGTACTCCAGACTAGT 60.082 45.833 27.51 9.49 43.13 2.57
441 2908 4.428209 TCGAAGTACGTACTCCAGACTAG 58.572 47.826 27.51 11.87 43.13 2.57
442 2909 4.428209 CTCGAAGTACGTACTCCAGACTA 58.572 47.826 27.51 9.13 43.13 2.59
443 2910 3.260740 CTCGAAGTACGTACTCCAGACT 58.739 50.000 27.51 11.74 43.13 3.24
444 2911 2.351111 CCTCGAAGTACGTACTCCAGAC 59.649 54.545 27.51 15.09 43.13 3.51
445 2912 2.625737 CCTCGAAGTACGTACTCCAGA 58.374 52.381 27.51 22.72 43.13 3.86
446 2913 1.669779 CCCTCGAAGTACGTACTCCAG 59.330 57.143 27.51 20.87 43.13 3.86
447 2914 1.679944 CCCCTCGAAGTACGTACTCCA 60.680 57.143 27.51 13.62 43.13 3.86
448 2915 1.020437 CCCCTCGAAGTACGTACTCC 58.980 60.000 27.51 15.62 43.13 3.85
449 2916 1.020437 CCCCCTCGAAGTACGTACTC 58.980 60.000 27.51 18.76 43.13 2.59
450 2917 0.620556 TCCCCCTCGAAGTACGTACT 59.379 55.000 22.45 22.45 43.13 2.73
451 2918 0.735471 GTCCCCCTCGAAGTACGTAC 59.265 60.000 18.10 18.10 43.13 3.67
452 2919 0.744414 CGTCCCCCTCGAAGTACGTA 60.744 60.000 0.00 0.00 43.13 3.57
453 2920 2.042831 CGTCCCCCTCGAAGTACGT 61.043 63.158 0.00 0.00 43.13 3.57
536 3036 4.332543 TTCGAGAGGGGTGGCCCT 62.333 66.667 0.00 0.00 44.66 5.19
537 3037 4.097361 GTTCGAGAGGGGTGGCCC 62.097 72.222 0.00 0.00 44.51 5.80
542 3042 3.441290 CGCGAGTTCGAGAGGGGT 61.441 66.667 0.00 0.00 41.67 4.95
544 3044 4.856607 GCCGCGAGTTCGAGAGGG 62.857 72.222 8.23 1.88 41.67 4.30
545 3045 3.743091 GAGCCGCGAGTTCGAGAGG 62.743 68.421 8.23 6.28 41.67 3.69
551 3051 3.173240 GACGTGAGCCGCGAGTTC 61.173 66.667 8.23 6.05 39.94 3.01
833 3401 1.087501 GTGGTGAGATCTTTTCCGCC 58.912 55.000 0.00 0.25 0.00 6.13
860 3428 0.526954 TTTAAGGACGATCGAGCGGC 60.527 55.000 28.05 25.76 38.96 6.53
862 3430 2.650765 CGTATTTAAGGACGATCGAGCG 59.349 50.000 23.12 23.12 41.60 5.03
863 3431 2.404361 GCGTATTTAAGGACGATCGAGC 59.596 50.000 24.34 13.00 41.60 5.03
868 3436 1.494824 GGCGCGTATTTAAGGACGAT 58.505 50.000 8.43 0.00 41.60 3.73
874 3462 2.888998 GCCGGGGCGCGTATTTAAG 61.889 63.158 22.61 6.49 0.00 1.85
994 3585 4.516135 CTCGCTCGCTCGCACGTA 62.516 66.667 0.00 0.00 0.00 3.57
1000 3591 4.936248 CTCTCGCTCGCTCGCTCG 62.936 72.222 0.00 0.00 0.00 5.03
1001 3592 3.506312 CTCTCTCGCTCGCTCGCTC 62.506 68.421 0.00 0.00 0.00 5.03
1002 3593 3.572539 CTCTCTCGCTCGCTCGCT 61.573 66.667 0.00 0.00 0.00 4.93
1003 3594 3.506312 CTCTCTCTCGCTCGCTCGC 62.506 68.421 0.00 0.00 0.00 5.03
1004 3595 1.821241 CTCTCTCTCTCGCTCGCTCG 61.821 65.000 0.00 0.00 0.00 5.03
1005 3596 0.529773 TCTCTCTCTCTCGCTCGCTC 60.530 60.000 0.00 0.00 0.00 5.03
1006 3597 0.530650 CTCTCTCTCTCTCGCTCGCT 60.531 60.000 0.00 0.00 0.00 4.93
1007 3598 1.934463 CTCTCTCTCTCTCGCTCGC 59.066 63.158 0.00 0.00 0.00 5.03
1010 3601 2.036475 CTCTAGCTCTCTCTCTCTCGCT 59.964 54.545 0.00 0.00 0.00 4.93
1018 3609 4.809193 TCTCTCTCTCTCTAGCTCTCTCT 58.191 47.826 0.00 0.00 0.00 3.10
1026 3617 6.303054 TCTCTCTCTCTCTCTCTCTCTCTAG 58.697 48.000 0.00 0.00 0.00 2.43
1027 3618 6.267492 TCTCTCTCTCTCTCTCTCTCTCTA 57.733 45.833 0.00 0.00 0.00 2.43
1028 3619 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1029 3620 5.774690 AGATCTCTCTCTCTCTCTCTCTCTC 59.225 48.000 0.00 0.00 0.00 3.20
1030 3621 5.539574 CAGATCTCTCTCTCTCTCTCTCTCT 59.460 48.000 0.00 0.00 0.00 3.10
1031 3622 5.279406 CCAGATCTCTCTCTCTCTCTCTCTC 60.279 52.000 0.00 0.00 0.00 3.20
1032 3623 4.592351 CCAGATCTCTCTCTCTCTCTCTCT 59.408 50.000 0.00 0.00 0.00 3.10
1033 3624 4.802248 GCCAGATCTCTCTCTCTCTCTCTC 60.802 54.167 0.00 0.00 0.00 3.20
1034 3625 3.072184 GCCAGATCTCTCTCTCTCTCTCT 59.928 52.174 0.00 0.00 0.00 3.10
1035 3626 3.406764 GCCAGATCTCTCTCTCTCTCTC 58.593 54.545 0.00 0.00 0.00 3.20
1036 3627 2.107204 GGCCAGATCTCTCTCTCTCTCT 59.893 54.545 0.00 0.00 0.00 3.10
1037 3628 2.508526 GGCCAGATCTCTCTCTCTCTC 58.491 57.143 0.00 0.00 0.00 3.20
1038 3629 1.145738 GGGCCAGATCTCTCTCTCTCT 59.854 57.143 4.39 0.00 0.00 3.10
1039 3630 1.620822 GGGCCAGATCTCTCTCTCTC 58.379 60.000 4.39 0.00 0.00 3.20
1040 3631 0.178992 CGGGCCAGATCTCTCTCTCT 60.179 60.000 4.39 0.00 0.00 3.10
1041 3632 0.467290 ACGGGCCAGATCTCTCTCTC 60.467 60.000 10.86 0.00 0.00 3.20
1042 3633 0.754957 CACGGGCCAGATCTCTCTCT 60.755 60.000 10.86 0.00 0.00 3.10
1043 3634 1.040339 ACACGGGCCAGATCTCTCTC 61.040 60.000 10.86 0.00 0.00 3.20
1044 3635 1.000993 ACACGGGCCAGATCTCTCT 59.999 57.895 10.86 0.00 0.00 3.10
1045 3636 1.142748 CACACGGGCCAGATCTCTC 59.857 63.158 10.86 0.00 0.00 3.20
1046 3637 3.023949 GCACACGGGCCAGATCTCT 62.024 63.158 10.86 0.00 0.00 3.10
1047 3638 2.512515 GCACACGGGCCAGATCTC 60.513 66.667 10.86 0.00 0.00 2.75
1048 3639 3.005539 AGCACACGGGCCAGATCT 61.006 61.111 10.86 0.00 0.00 2.75
1049 3640 2.803155 TTCAGCACACGGGCCAGATC 62.803 60.000 10.86 0.00 0.00 2.75
1050 3641 2.809861 CTTCAGCACACGGGCCAGAT 62.810 60.000 10.86 0.00 0.00 2.90
1051 3642 3.535629 CTTCAGCACACGGGCCAGA 62.536 63.158 10.86 0.00 0.00 3.86
1052 3643 3.052082 CTTCAGCACACGGGCCAG 61.052 66.667 4.39 1.85 0.00 4.85
1053 3644 3.414136 AACTTCAGCACACGGGCCA 62.414 57.895 4.39 0.00 0.00 5.36
1054 3645 2.594592 AACTTCAGCACACGGGCC 60.595 61.111 0.00 0.00 0.00 5.80
1055 3646 2.639286 CAACTTCAGCACACGGGC 59.361 61.111 0.00 0.00 0.00 6.13
1056 3647 2.908073 GCCAACTTCAGCACACGGG 61.908 63.158 0.00 0.00 0.00 5.28
1057 3648 2.639286 GCCAACTTCAGCACACGG 59.361 61.111 0.00 0.00 0.00 4.94
1058 3649 2.249309 CGCCAACTTCAGCACACG 59.751 61.111 0.00 0.00 0.00 4.49
1059 3650 1.845809 CTCCGCCAACTTCAGCACAC 61.846 60.000 0.00 0.00 0.00 3.82
1060 3651 1.597854 CTCCGCCAACTTCAGCACA 60.598 57.895 0.00 0.00 0.00 4.57
1061 3652 0.674895 ATCTCCGCCAACTTCAGCAC 60.675 55.000 0.00 0.00 0.00 4.40
1070 3661 2.359850 GCCACACATCTCCGCCAA 60.360 61.111 0.00 0.00 0.00 4.52
1276 3867 4.104417 ACGCAGGAGCTCGACGTC 62.104 66.667 18.07 5.18 39.10 4.34
1355 3949 4.222847 GGGTCTCTTAGCCGCCGG 62.223 72.222 0.00 0.00 35.65 6.13
1360 3954 4.893601 GCGCGGGGTCTCTTAGCC 62.894 72.222 8.83 0.00 45.69 3.93
1944 4548 9.835389 ACTACTAAGAAGTATGGTACTACTGAG 57.165 37.037 0.00 0.00 38.26 3.35
1958 4562 9.257428 AGTCCAGCTAAATTACTACTAAGAAGT 57.743 33.333 0.00 0.00 39.91 3.01
1959 4563 9.522804 CAGTCCAGCTAAATTACTACTAAGAAG 57.477 37.037 0.00 0.00 0.00 2.85
1960 4564 8.475639 CCAGTCCAGCTAAATTACTACTAAGAA 58.524 37.037 0.00 0.00 0.00 2.52
1962 4566 7.783042 ACCAGTCCAGCTAAATTACTACTAAG 58.217 38.462 0.00 0.00 0.00 2.18
1963 4567 7.729124 ACCAGTCCAGCTAAATTACTACTAA 57.271 36.000 0.00 0.00 0.00 2.24
1964 4568 7.729124 AACCAGTCCAGCTAAATTACTACTA 57.271 36.000 0.00 0.00 0.00 1.82
1965 4569 6.622427 AACCAGTCCAGCTAAATTACTACT 57.378 37.500 0.00 0.00 0.00 2.57
1966 4570 6.985059 CCTAACCAGTCCAGCTAAATTACTAC 59.015 42.308 0.00 0.00 0.00 2.73
1986 4590 6.412214 TCCATACCTAGTTCAAAAGCCTAAC 58.588 40.000 0.00 0.00 0.00 2.34
2013 4617 2.880890 GTTGAGAGACAAACAGCATGGT 59.119 45.455 0.00 0.00 38.54 3.55
2014 4618 2.880268 TGTTGAGAGACAAACAGCATGG 59.120 45.455 0.00 0.00 40.36 3.66
2015 4619 4.556942 TTGTTGAGAGACAAACAGCATG 57.443 40.909 0.00 0.00 40.36 4.06
2016 4620 6.883217 AGATATTGTTGAGAGACAAACAGCAT 59.117 34.615 0.00 0.00 42.29 3.79
2017 4621 6.233434 AGATATTGTTGAGAGACAAACAGCA 58.767 36.000 0.00 0.00 42.29 4.41
2018 4622 6.593382 AGAGATATTGTTGAGAGACAAACAGC 59.407 38.462 0.00 0.00 42.29 4.40
2019 4623 9.081997 GTAGAGATATTGTTGAGAGACAAACAG 57.918 37.037 0.00 0.00 42.29 3.16
2020 4624 8.807118 AGTAGAGATATTGTTGAGAGACAAACA 58.193 33.333 0.00 0.00 42.29 2.83
2021 4625 9.296400 GAGTAGAGATATTGTTGAGAGACAAAC 57.704 37.037 0.00 0.00 42.29 2.93
2022 4626 8.470805 GGAGTAGAGATATTGTTGAGAGACAAA 58.529 37.037 0.00 0.00 42.29 2.83
2023 4627 7.836685 AGGAGTAGAGATATTGTTGAGAGACAA 59.163 37.037 0.00 0.00 43.08 3.18
2024 4628 7.350382 AGGAGTAGAGATATTGTTGAGAGACA 58.650 38.462 0.00 0.00 0.00 3.41
2025 4629 7.817418 AGGAGTAGAGATATTGTTGAGAGAC 57.183 40.000 0.00 0.00 0.00 3.36
2028 4632 9.868160 TCATTAGGAGTAGAGATATTGTTGAGA 57.132 33.333 0.00 0.00 0.00 3.27
2031 4635 9.202273 GCTTCATTAGGAGTAGAGATATTGTTG 57.798 37.037 0.00 0.00 0.00 3.33
2032 4636 8.928448 TGCTTCATTAGGAGTAGAGATATTGTT 58.072 33.333 0.00 0.00 0.00 2.83
2033 4637 8.484214 TGCTTCATTAGGAGTAGAGATATTGT 57.516 34.615 0.00 0.00 0.00 2.71
2034 4638 8.984891 CTGCTTCATTAGGAGTAGAGATATTG 57.015 38.462 0.00 0.00 37.53 1.90
2264 4898 6.702716 AGGAAAGTGTTGAAAATAAACCGA 57.297 33.333 0.00 0.00 0.00 4.69
2594 5229 6.982852 TGGCTAAGATAGGAAAGTTAGATCG 58.017 40.000 0.00 0.00 0.00 3.69
2610 5245 5.734720 AGAGATTCGTTGATTTGGCTAAGA 58.265 37.500 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.