Multiple sequence alignment - TraesCS1B01G348100

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 TraesCS1B01G348100 chr1B 100.000 3224 0 0 1 3224 577676949 577673726 0.000000e+00 5954.0
1 TraesCS1B01G348100 chr1B 89.823 904 84 5 923 1826 579571885 579570990 0.000000e+00 1153.0
2 TraesCS1B01G348100 chr1B 89.602 904 86 5 923 1826 579474928 579474033 0.000000e+00 1142.0
3 TraesCS1B01G348100 chr1B 92.699 767 51 4 1 765 301817298 301818061 0.000000e+00 1101.0
4 TraesCS1B01G348100 chr1B 84.843 607 76 13 1820 2422 579460741 579460147 5.950000e-167 597.0
5 TraesCS1B01G348100 chr1B 84.679 607 77 13 1820 2422 579557560 579556966 2.770000e-165 592.0
6 TraesCS1B01G348100 chr1B 77.567 526 102 12 1275 1795 577654127 577653613 1.450000e-78 303.0
7 TraesCS1B01G348100 chr1A 93.333 1080 59 6 876 1946 522472951 522471876 0.000000e+00 1583.0
8 TraesCS1B01G348100 chr1A 94.096 813 48 0 1011 1823 522560867 522560055 0.000000e+00 1236.0
9 TraesCS1B01G348100 chr1A 94.951 515 22 3 1943 2457 522463891 522463381 0.000000e+00 804.0
10 TraesCS1B01G348100 chr1A 85.777 682 35 25 2454 3080 522463128 522462454 0.000000e+00 665.0
11 TraesCS1B01G348100 chr1A 84.437 604 73 12 1820 2422 522555748 522555165 2.790000e-160 575.0
12 TraesCS1B01G348100 chr1A 91.200 125 10 1 3077 3200 522462374 522462250 5.530000e-38 169.0
13 TraesCS1B01G348100 chr1A 96.970 33 0 1 763 794 522473086 522473054 2.000000e-03 54.7
14 TraesCS1B01G348100 chr1D 92.697 890 60 4 934 1823 427486214 427485330 0.000000e+00 1279.0
15 TraesCS1B01G348100 chr1D 86.687 969 67 18 2287 3200 427182852 427181891 0.000000e+00 1018.0
16 TraesCS1B01G348100 chr1D 85.455 605 76 10 1820 2422 427478694 427478100 1.270000e-173 619.0
17 TraesCS1B01G348100 chr1D 94.277 332 13 3 1964 2295 427197523 427197198 1.340000e-138 503.0
18 TraesCS1B01G348100 chr1D 78.137 526 99 12 1275 1795 427158619 427158105 1.440000e-83 320.0
19 TraesCS1B01G348100 chr1D 83.700 227 35 2 1030 1255 427158906 427158681 2.520000e-51 213.0
20 TraesCS1B01G348100 chr6B 92.754 759 53 2 1 758 184630295 184631052 0.000000e+00 1096.0
21 TraesCS1B01G348100 chr5B 92.126 762 58 2 1 761 382571370 382570610 0.000000e+00 1074.0
22 TraesCS1B01G348100 chr7B 91.953 758 60 1 4 761 718942214 718941458 0.000000e+00 1061.0
23 TraesCS1B01G348100 chr7B 91.525 767 59 5 1 765 203858542 203857780 0.000000e+00 1051.0
24 TraesCS1B01G348100 chr7B 91.557 758 62 2 4 761 651416262 651415507 0.000000e+00 1044.0
25 TraesCS1B01G348100 chr4B 91.984 761 54 6 1 758 671846764 671847520 0.000000e+00 1061.0
26 TraesCS1B01G348100 chr3D 91.436 759 62 3 1 758 283323270 283322514 0.000000e+00 1038.0
27 TraesCS1B01G348100 chr3B 91.447 760 59 5 4 761 27181918 27181163 0.000000e+00 1038.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G348100 chr1B 577673726 577676949 3223 True 5954.00 5954 100.000000 1 3224 1 chr1B.!!$R2 3223
1 TraesCS1B01G348100 chr1B 579570990 579571885 895 True 1153.00 1153 89.823000 923 1826 1 chr1B.!!$R6 903
2 TraesCS1B01G348100 chr1B 579474033 579474928 895 True 1142.00 1142 89.602000 923 1826 1 chr1B.!!$R4 903
3 TraesCS1B01G348100 chr1B 301817298 301818061 763 False 1101.00 1101 92.699000 1 765 1 chr1B.!!$F1 764
4 TraesCS1B01G348100 chr1B 579460147 579460741 594 True 597.00 597 84.843000 1820 2422 1 chr1B.!!$R3 602
5 TraesCS1B01G348100 chr1B 579556966 579557560 594 True 592.00 592 84.679000 1820 2422 1 chr1B.!!$R5 602
6 TraesCS1B01G348100 chr1B 577653613 577654127 514 True 303.00 303 77.567000 1275 1795 1 chr1B.!!$R1 520
7 TraesCS1B01G348100 chr1A 522560055 522560867 812 True 1236.00 1236 94.096000 1011 1823 1 chr1A.!!$R2 812
8 TraesCS1B01G348100 chr1A 522471876 522473086 1210 True 818.85 1583 95.151500 763 1946 2 chr1A.!!$R4 1183
9 TraesCS1B01G348100 chr1A 522555165 522555748 583 True 575.00 575 84.437000 1820 2422 1 chr1A.!!$R1 602
10 TraesCS1B01G348100 chr1A 522462250 522463891 1641 True 546.00 804 90.642667 1943 3200 3 chr1A.!!$R3 1257
11 TraesCS1B01G348100 chr1D 427485330 427486214 884 True 1279.00 1279 92.697000 934 1823 1 chr1D.!!$R4 889
12 TraesCS1B01G348100 chr1D 427181891 427182852 961 True 1018.00 1018 86.687000 2287 3200 1 chr1D.!!$R1 913
13 TraesCS1B01G348100 chr1D 427478100 427478694 594 True 619.00 619 85.455000 1820 2422 1 chr1D.!!$R3 602
14 TraesCS1B01G348100 chr1D 427158105 427158906 801 True 266.50 320 80.918500 1030 1795 2 chr1D.!!$R5 765
15 TraesCS1B01G348100 chr6B 184630295 184631052 757 False 1096.00 1096 92.754000 1 758 1 chr6B.!!$F1 757
16 TraesCS1B01G348100 chr5B 382570610 382571370 760 True 1074.00 1074 92.126000 1 761 1 chr5B.!!$R1 760
17 TraesCS1B01G348100 chr7B 718941458 718942214 756 True 1061.00 1061 91.953000 4 761 1 chr7B.!!$R3 757
18 TraesCS1B01G348100 chr7B 203857780 203858542 762 True 1051.00 1051 91.525000 1 765 1 chr7B.!!$R1 764
19 TraesCS1B01G348100 chr7B 651415507 651416262 755 True 1044.00 1044 91.557000 4 761 1 chr7B.!!$R2 757
20 TraesCS1B01G348100 chr4B 671846764 671847520 756 False 1061.00 1061 91.984000 1 758 1 chr4B.!!$F1 757
21 TraesCS1B01G348100 chr3D 283322514 283323270 756 True 1038.00 1038 91.436000 1 758 1 chr3D.!!$R1 757
22 TraesCS1B01G348100 chr3B 27181163 27181918 755 True 1038.00 1038 91.447000 4 761 1 chr3B.!!$R1 757

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
836 863 0.034337 ACCGACGCACCTGTAAATGT 59.966 50.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2506 2865 0.321298 ACTTCATGGCCACACGTACC 60.321 55.0 8.16 0.0 0.0 3.34 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
46 47 2.799562 GCAACAACTGTCCAAAGAAGGC 60.800 50.000 0.00 0.00 0.00 4.35
161 163 7.148052 GGTCTGTGCTCTAGATTTGACTAGTTA 60.148 40.741 0.00 0.00 40.26 2.24
236 239 8.524487 GGGAAGAAGAGTACATCGATATATTGT 58.476 37.037 0.00 0.00 0.00 2.71
335 338 1.067821 GATTAGAGGCTGGACACGAGG 59.932 57.143 0.00 0.00 0.00 4.63
363 366 2.808543 GTGAGGAAGCAACATCGACTTT 59.191 45.455 0.00 0.00 0.00 2.66
415 418 0.324738 TCGAGCCTCCTCCACAGATT 60.325 55.000 0.00 0.00 34.49 2.40
686 690 0.687354 AGAAACTGCCCAGACACGAT 59.313 50.000 1.69 0.00 0.00 3.73
715 719 2.290705 CCCTACCCAAACGGACAGAATT 60.291 50.000 0.00 0.00 34.64 2.17
761 766 2.668550 GTGCGGTGGAGTTGACCC 60.669 66.667 0.00 0.00 0.00 4.46
791 796 1.663643 GCACGAGTTGACAGACACAAA 59.336 47.619 0.00 0.00 0.00 2.83
792 797 2.536928 GCACGAGTTGACAGACACAAAC 60.537 50.000 0.00 0.00 0.00 2.93
793 798 2.670905 CACGAGTTGACAGACACAAACA 59.329 45.455 0.00 0.00 0.00 2.83
794 799 2.671396 ACGAGTTGACAGACACAAACAC 59.329 45.455 0.00 0.00 0.00 3.32
796 801 3.124466 CGAGTTGACAGACACAAACACAA 59.876 43.478 0.00 0.00 0.00 3.33
797 802 4.651994 GAGTTGACAGACACAAACACAAG 58.348 43.478 0.00 0.00 0.00 3.16
800 805 2.161410 TGACAGACACAAACACAAGCAC 59.839 45.455 0.00 0.00 0.00 4.40
802 807 1.472082 CAGACACAAACACAAGCACCA 59.528 47.619 0.00 0.00 0.00 4.17
805 810 3.195396 AGACACAAACACAAGCACCATTT 59.805 39.130 0.00 0.00 0.00 2.32
807 812 2.608546 CACAAACACAAGCACCATTTGG 59.391 45.455 0.00 0.00 42.17 3.28
808 813 2.211806 CAAACACAAGCACCATTTGGG 58.788 47.619 0.96 0.00 44.81 4.12
809 814 1.786937 AACACAAGCACCATTTGGGA 58.213 45.000 0.96 0.00 41.15 4.37
832 859 2.356553 GCACCGACGCACCTGTAA 60.357 61.111 0.00 0.00 0.00 2.41
833 860 1.957186 GCACCGACGCACCTGTAAA 60.957 57.895 0.00 0.00 0.00 2.01
834 861 1.296056 GCACCGACGCACCTGTAAAT 61.296 55.000 0.00 0.00 0.00 1.40
835 862 0.442310 CACCGACGCACCTGTAAATG 59.558 55.000 0.00 0.00 0.00 2.32
836 863 0.034337 ACCGACGCACCTGTAAATGT 59.966 50.000 0.00 0.00 0.00 2.71
837 864 0.719465 CCGACGCACCTGTAAATGTC 59.281 55.000 0.00 0.00 0.00 3.06
838 865 1.424403 CGACGCACCTGTAAATGTCA 58.576 50.000 0.00 0.00 0.00 3.58
839 866 1.126113 CGACGCACCTGTAAATGTCAC 59.874 52.381 0.00 0.00 0.00 3.67
840 867 2.139917 GACGCACCTGTAAATGTCACA 58.860 47.619 0.00 0.00 0.00 3.58
841 868 2.742053 GACGCACCTGTAAATGTCACAT 59.258 45.455 0.00 0.00 0.00 3.21
842 869 2.483877 ACGCACCTGTAAATGTCACATG 59.516 45.455 0.00 0.00 0.00 3.21
843 870 2.728846 CGCACCTGTAAATGTCACATGC 60.729 50.000 0.00 0.00 31.57 4.06
844 871 2.228582 GCACCTGTAAATGTCACATGCA 59.771 45.455 0.00 0.00 33.89 3.96
862 889 1.073964 CACAGGCAACGTGAGATCAG 58.926 55.000 0.00 0.00 41.53 2.90
863 890 0.681733 ACAGGCAACGTGAGATCAGT 59.318 50.000 0.00 0.00 46.39 3.41
864 891 1.073964 CAGGCAACGTGAGATCAGTG 58.926 55.000 0.00 0.00 46.39 3.66
865 892 0.681733 AGGCAACGTGAGATCAGTGT 59.318 50.000 0.00 0.00 46.39 3.55
866 893 0.792640 GGCAACGTGAGATCAGTGTG 59.207 55.000 0.00 0.00 0.00 3.82
867 894 1.502231 GCAACGTGAGATCAGTGTGT 58.498 50.000 0.00 0.00 0.00 3.72
868 895 1.457303 GCAACGTGAGATCAGTGTGTC 59.543 52.381 0.00 0.00 0.00 3.67
869 896 1.716050 CAACGTGAGATCAGTGTGTCG 59.284 52.381 0.00 0.00 0.00 4.35
873 913 3.004002 ACGTGAGATCAGTGTGTCGTTAA 59.996 43.478 0.00 0.00 0.00 2.01
874 914 3.361053 CGTGAGATCAGTGTGTCGTTAAC 59.639 47.826 0.00 0.00 0.00 2.01
970 1014 4.290985 TCTGGTCATTCCACCCATAAAAGA 59.709 41.667 0.00 0.00 41.93 2.52
971 1015 5.004361 TGGTCATTCCACCCATAAAAGAA 57.996 39.130 0.00 0.00 41.93 2.52
972 1016 5.016173 TGGTCATTCCACCCATAAAAGAAG 58.984 41.667 0.00 0.00 41.93 2.85
982 1026 4.019174 CCCATAAAAGAAGCCACATCTGT 58.981 43.478 0.00 0.00 0.00 3.41
983 1027 4.096984 CCCATAAAAGAAGCCACATCTGTC 59.903 45.833 0.00 0.00 0.00 3.51
984 1028 4.701651 CCATAAAAGAAGCCACATCTGTCA 59.298 41.667 0.00 0.00 0.00 3.58
985 1029 5.359009 CCATAAAAGAAGCCACATCTGTCAT 59.641 40.000 0.00 0.00 0.00 3.06
986 1030 6.459298 CCATAAAAGAAGCCACATCTGTCATC 60.459 42.308 0.00 0.00 0.00 2.92
987 1031 3.708403 AAGAAGCCACATCTGTCATCA 57.292 42.857 0.00 0.00 0.00 3.07
989 1033 4.232188 AGAAGCCACATCTGTCATCAAT 57.768 40.909 0.00 0.00 0.00 2.57
990 1034 5.363562 AGAAGCCACATCTGTCATCAATA 57.636 39.130 0.00 0.00 0.00 1.90
992 1036 5.587844 AGAAGCCACATCTGTCATCAATAAC 59.412 40.000 0.00 0.00 0.00 1.89
993 1037 4.847198 AGCCACATCTGTCATCAATAACA 58.153 39.130 0.00 0.00 0.00 2.41
1149 1193 4.467084 GCCATCCACCGCGAAGGA 62.467 66.667 19.34 19.34 45.00 3.36
1242 1286 2.280797 ATGCGTGTGCTCACCGTT 60.281 55.556 13.00 0.00 43.34 4.44
1258 1302 0.942410 CGTTTCAGGCGTCTTCGGAA 60.942 55.000 0.00 0.00 37.56 4.30
1427 1513 1.831652 CTCGGGACTTGGTTCCAGCT 61.832 60.000 0.00 0.00 37.40 4.24
1544 1630 1.375908 GCATGGTCTCCGACAGCAA 60.376 57.895 0.00 0.00 33.68 3.91
1666 1752 2.125673 CGAATGCGTTCCCGGACT 60.126 61.111 13.02 0.00 37.19 3.85
1669 1755 2.253414 GAATGCGTTCCCGGACTTGC 62.253 60.000 0.73 1.76 37.19 4.01
1802 1888 1.071605 CTCAAGGTGCGTCAACTAGC 58.928 55.000 0.00 0.00 27.88 3.42
1826 1912 5.452078 AACACAATGTTGGTACTCCATTG 57.548 39.130 20.82 20.82 45.50 2.82
1869 1960 7.719633 TGTCCATTTTGGGAAAGATATAGCTAC 59.280 37.037 0.00 0.00 39.05 3.58
1903 1994 4.022762 TGTTGTCAATTAACGATTGGGGTG 60.023 41.667 0.00 0.00 44.30 4.61
2073 2164 1.795286 GACCAGAAGCACAAAGAGACG 59.205 52.381 0.00 0.00 0.00 4.18
2129 2220 0.453615 GGTATCGAGCGAGATGAGCG 60.454 60.000 7.13 0.00 40.04 5.03
2157 2248 4.019051 TGGAAGAAGATCATCTTTGAGGCA 60.019 41.667 14.03 0.00 39.70 4.75
2187 2278 2.609350 GACTACAAAATCACGCCCGTA 58.391 47.619 0.00 0.00 0.00 4.02
2252 2343 4.062991 GGTCTTTGATTGGTGAAGTACGT 58.937 43.478 0.00 0.00 0.00 3.57
2253 2344 4.514066 GGTCTTTGATTGGTGAAGTACGTT 59.486 41.667 0.00 0.00 0.00 3.99
2406 2500 5.689383 TGTCTAAATTGTTGCCTTCTCAC 57.311 39.130 0.00 0.00 0.00 3.51
2476 2835 5.003804 AGTATGTGTTTACCTTGAGCTTGG 58.996 41.667 0.00 0.00 0.00 3.61
2477 2836 1.953686 TGTGTTTACCTTGAGCTTGGC 59.046 47.619 0.00 0.00 0.00 4.52
2478 2837 1.269723 GTGTTTACCTTGAGCTTGGCC 59.730 52.381 0.00 0.00 0.00 5.36
2479 2838 0.888619 GTTTACCTTGAGCTTGGCCC 59.111 55.000 0.00 0.00 0.00 5.80
2480 2839 0.480690 TTTACCTTGAGCTTGGCCCA 59.519 50.000 0.00 0.00 0.00 5.36
2481 2840 0.251165 TTACCTTGAGCTTGGCCCAC 60.251 55.000 0.00 0.00 0.00 4.61
2482 2841 2.137177 TACCTTGAGCTTGGCCCACC 62.137 60.000 0.00 0.00 0.00 4.61
2483 2842 2.437897 CTTGAGCTTGGCCCACCT 59.562 61.111 0.00 0.00 36.63 4.00
2484 2843 1.676967 CTTGAGCTTGGCCCACCTC 60.677 63.158 0.00 3.28 36.63 3.85
2485 2844 2.134630 CTTGAGCTTGGCCCACCTCT 62.135 60.000 0.00 0.00 36.63 3.69
2486 2845 1.719063 TTGAGCTTGGCCCACCTCTT 61.719 55.000 0.00 0.00 36.63 2.85
2487 2846 1.676967 GAGCTTGGCCCACCTCTTG 60.677 63.158 0.00 0.00 36.63 3.02
2505 2864 2.574018 GGCCTGCCCAACCAGTTTC 61.574 63.158 0.00 0.00 0.00 2.78
2506 2865 2.919494 GCCTGCCCAACCAGTTTCG 61.919 63.158 0.00 0.00 0.00 3.46
2508 2867 1.528309 CTGCCCAACCAGTTTCGGT 60.528 57.895 0.00 0.00 42.71 4.69
2527 2904 1.463444 GTACGTGTGGCCATGAAGTTC 59.537 52.381 9.72 1.59 0.00 3.01
2575 2960 6.459024 GCAAACTTTGTGTAGTACCATGTGAA 60.459 38.462 3.48 0.00 0.00 3.18
2594 2979 1.734655 ATCGGGCTGATAGTGGGAAT 58.265 50.000 7.13 0.00 34.83 3.01
2691 3076 7.199766 TGTGTTAAAGTGATTGAATGGTCAAC 58.800 34.615 0.00 0.00 46.40 3.18
2731 3116 8.348507 GTTTTTGATAGAGCTTGATGGGATAAG 58.651 37.037 0.00 0.00 0.00 1.73
2773 3158 6.377996 TGAAATCAAGTTGATCCATACCAAGG 59.622 38.462 18.52 0.00 35.76 3.61
2829 3214 6.650807 ACCACAATTGAGAAGTACACTACATG 59.349 38.462 13.59 0.00 0.00 3.21
2903 3289 8.034804 ACTTGCATAACACTTTGTTTCTTTCTT 58.965 29.630 0.00 0.00 41.45 2.52
2906 3292 7.816995 TGCATAACACTTTGTTTCTTTCTTTGT 59.183 29.630 0.00 0.00 41.45 2.83
2955 3351 5.471556 TTCCTAAACACAACGACCAGATA 57.528 39.130 0.00 0.00 0.00 1.98
2957 3353 5.416083 TCCTAAACACAACGACCAGATATG 58.584 41.667 0.00 0.00 0.00 1.78
2958 3354 4.034048 CCTAAACACAACGACCAGATATGC 59.966 45.833 0.00 0.00 0.00 3.14
2961 3357 3.407698 ACACAACGACCAGATATGCAAA 58.592 40.909 0.00 0.00 0.00 3.68
2962 3358 3.436704 ACACAACGACCAGATATGCAAAG 59.563 43.478 0.00 0.00 0.00 2.77
3038 3464 1.028905 CACCAAACAAAGGCTCGGAA 58.971 50.000 0.00 0.00 0.00 4.30
3047 3473 4.119136 ACAAAGGCTCGGAATTTTTGTTG 58.881 39.130 0.00 0.00 38.42 3.33
3071 3497 1.349357 CTTTAGGGCTCTAGATGGGGC 59.651 57.143 0.00 0.00 0.00 5.80
3072 3498 0.267658 TTAGGGCTCTAGATGGGGCA 59.732 55.000 0.00 0.00 0.00 5.36
3074 3500 1.460305 GGGCTCTAGATGGGGCAGA 60.460 63.158 6.40 0.00 0.00 4.26
3081 3591 4.562552 GCTCTAGATGGGGCAGAAAGTATC 60.563 50.000 0.00 0.00 0.00 2.24
3140 3650 8.877864 ATAAACAAGGACAACAAATCCTATCA 57.122 30.769 0.00 0.00 46.36 2.15
3143 3653 5.126061 ACAAGGACAACAAATCCTATCATGC 59.874 40.000 0.00 0.00 46.36 4.06
3156 3666 3.255149 CCTATCATGCCAATGAAAGCTCC 59.745 47.826 0.00 0.00 45.81 4.70
3159 3669 1.098050 ATGCCAATGAAAGCTCCGAC 58.902 50.000 0.00 0.00 0.00 4.79
3160 3670 0.250684 TGCCAATGAAAGCTCCGACA 60.251 50.000 0.00 0.00 0.00 4.35
3168 3678 2.565391 TGAAAGCTCCGACACCAAGATA 59.435 45.455 0.00 0.00 0.00 1.98
3200 3711 5.505780 TGAACCCGATGGATGAGTTAATTT 58.494 37.500 0.00 0.00 34.81 1.82
3201 3712 5.949354 TGAACCCGATGGATGAGTTAATTTT 59.051 36.000 0.00 0.00 34.81 1.82
3202 3713 5.835113 ACCCGATGGATGAGTTAATTTTG 57.165 39.130 0.00 0.00 34.81 2.44
3203 3714 5.261216 ACCCGATGGATGAGTTAATTTTGT 58.739 37.500 0.00 0.00 34.81 2.83
3204 3715 5.714806 ACCCGATGGATGAGTTAATTTTGTT 59.285 36.000 0.00 0.00 34.81 2.83
3205 3716 6.035843 CCCGATGGATGAGTTAATTTTGTTG 58.964 40.000 0.00 0.00 0.00 3.33
3206 3717 6.127758 CCCGATGGATGAGTTAATTTTGTTGA 60.128 38.462 0.00 0.00 0.00 3.18
3207 3718 6.968904 CCGATGGATGAGTTAATTTTGTTGAG 59.031 38.462 0.00 0.00 0.00 3.02
3208 3719 6.968904 CGATGGATGAGTTAATTTTGTTGAGG 59.031 38.462 0.00 0.00 0.00 3.86
3209 3720 7.148255 CGATGGATGAGTTAATTTTGTTGAGGA 60.148 37.037 0.00 0.00 0.00 3.71
3210 3721 7.831691 TGGATGAGTTAATTTTGTTGAGGAA 57.168 32.000 0.00 0.00 0.00 3.36
3211 3722 8.243961 TGGATGAGTTAATTTTGTTGAGGAAA 57.756 30.769 0.00 0.00 0.00 3.13
3212 3723 8.869109 TGGATGAGTTAATTTTGTTGAGGAAAT 58.131 29.630 0.00 0.00 0.00 2.17
3213 3724 9.358872 GGATGAGTTAATTTTGTTGAGGAAATC 57.641 33.333 0.00 0.00 0.00 2.17
3214 3725 8.970691 ATGAGTTAATTTTGTTGAGGAAATCG 57.029 30.769 0.00 0.00 0.00 3.34
3215 3726 7.936584 TGAGTTAATTTTGTTGAGGAAATCGT 58.063 30.769 0.00 0.00 0.00 3.73
3216 3727 8.410141 TGAGTTAATTTTGTTGAGGAAATCGTT 58.590 29.630 0.00 0.00 0.00 3.85
3217 3728 9.887406 GAGTTAATTTTGTTGAGGAAATCGTTA 57.113 29.630 0.00 0.00 0.00 3.18
3221 3732 8.574196 AATTTTGTTGAGGAAATCGTTAACTG 57.426 30.769 3.71 0.00 33.31 3.16
3222 3733 5.682943 TTGTTGAGGAAATCGTTAACTGG 57.317 39.130 3.71 0.00 33.31 4.00
3223 3734 4.710324 TGTTGAGGAAATCGTTAACTGGT 58.290 39.130 3.71 0.00 33.31 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.031870 GGCCTTCTTTGGACAGTTGTT 58.968 47.619 0.00 0.00 34.56 2.83
30 31 0.182775 ACGGCCTTCTTTGGACAGTT 59.817 50.000 0.00 0.00 33.86 3.16
35 36 1.896660 GCACACGGCCTTCTTTGGA 60.897 57.895 0.00 0.00 36.11 3.53
46 47 4.710695 TAGACACGCGGCACACGG 62.711 66.667 12.47 0.00 44.51 4.94
188 191 5.490159 CCAATACCAAAACTTGCATCCATT 58.510 37.500 0.00 0.00 0.00 3.16
236 239 9.431887 ACGAACATCTACTAATTTGCTTTCTAA 57.568 29.630 0.00 0.00 0.00 2.10
241 244 5.411361 TGCACGAACATCTACTAATTTGCTT 59.589 36.000 0.00 0.00 0.00 3.91
242 245 4.935205 TGCACGAACATCTACTAATTTGCT 59.065 37.500 0.00 0.00 0.00 3.91
247 250 7.201530 GCTAAAAGTGCACGAACATCTACTAAT 60.202 37.037 12.01 0.00 0.00 1.73
335 338 1.270839 TGTTGCTTCCTCACACCTAGC 60.271 52.381 0.00 0.00 0.00 3.42
415 418 4.183865 CCTTCTCGATGCACTCATTGTTA 58.816 43.478 0.00 0.00 35.89 2.41
511 514 5.603596 TGACTAGTAAAGCAAGACCGAAAA 58.396 37.500 0.00 0.00 0.00 2.29
515 518 5.917541 TTTTGACTAGTAAAGCAAGACCG 57.082 39.130 0.00 0.00 0.00 4.79
606 610 2.027605 CGCATCCTGTCCGCGTAT 59.972 61.111 4.92 0.00 43.86 3.06
686 690 1.339631 CGTTTGGGTAGGGCAATGAGA 60.340 52.381 0.00 0.00 0.00 3.27
715 719 3.277652 GGACGTCTGTTTTGTCCGA 57.722 52.632 16.46 0.00 42.42 4.55
761 766 0.386352 CAACTCGTGCCACATGCTTG 60.386 55.000 0.00 0.00 42.00 4.01
791 796 1.688197 CTTCCCAAATGGTGCTTGTGT 59.312 47.619 0.00 0.00 34.77 3.72
792 797 1.001181 CCTTCCCAAATGGTGCTTGTG 59.999 52.381 0.00 0.00 34.77 3.33
793 798 1.341080 CCTTCCCAAATGGTGCTTGT 58.659 50.000 0.00 0.00 34.77 3.16
794 799 1.273327 GACCTTCCCAAATGGTGCTTG 59.727 52.381 0.00 0.00 33.74 4.01
796 801 0.609131 CGACCTTCCCAAATGGTGCT 60.609 55.000 0.00 0.00 33.74 4.40
797 802 1.883021 CGACCTTCCCAAATGGTGC 59.117 57.895 0.00 0.00 33.74 5.01
800 805 1.595093 GGTGCGACCTTCCCAAATGG 61.595 60.000 0.00 0.00 34.73 3.16
802 807 1.674322 CGGTGCGACCTTCCCAAAT 60.674 57.895 0.00 0.00 35.66 2.32
832 859 3.039452 TGCCTGTGCATGTGACATT 57.961 47.368 0.00 0.00 44.23 2.71
833 860 4.826248 TGCCTGTGCATGTGACAT 57.174 50.000 0.00 0.00 44.23 3.06
842 869 0.950555 TGATCTCACGTTGCCTGTGC 60.951 55.000 0.00 0.00 37.26 4.57
843 870 1.073964 CTGATCTCACGTTGCCTGTG 58.926 55.000 0.00 0.00 38.70 3.66
844 871 0.681733 ACTGATCTCACGTTGCCTGT 59.318 50.000 0.00 0.00 0.00 4.00
862 889 1.788886 GGACTTCCGTTAACGACACAC 59.211 52.381 28.79 15.62 43.02 3.82
863 890 1.682854 AGGACTTCCGTTAACGACACA 59.317 47.619 28.79 7.16 43.02 3.72
864 891 2.056577 CAGGACTTCCGTTAACGACAC 58.943 52.381 28.79 14.03 43.02 3.67
865 892 1.682854 ACAGGACTTCCGTTAACGACA 59.317 47.619 28.79 12.26 43.02 4.35
866 893 2.056577 CACAGGACTTCCGTTAACGAC 58.943 52.381 28.79 13.40 43.02 4.34
867 894 1.955778 TCACAGGACTTCCGTTAACGA 59.044 47.619 28.79 12.31 43.02 3.85
868 895 2.427232 TCACAGGACTTCCGTTAACG 57.573 50.000 20.99 20.99 42.08 3.18
869 896 3.678548 GTGATCACAGGACTTCCGTTAAC 59.321 47.826 21.07 0.00 42.08 2.01
873 913 1.633774 AGTGATCACAGGACTTCCGT 58.366 50.000 27.02 0.00 42.08 4.69
874 914 2.029020 TCAAGTGATCACAGGACTTCCG 60.029 50.000 27.02 2.74 42.08 4.30
951 992 4.142160 GGCTTCTTTTATGGGTGGAATGAC 60.142 45.833 0.00 0.00 0.00 3.06
970 1014 5.255687 TGTTATTGATGACAGATGTGGCTT 58.744 37.500 0.00 0.00 30.05 4.35
971 1015 4.847198 TGTTATTGATGACAGATGTGGCT 58.153 39.130 0.00 0.00 30.05 4.75
972 1016 4.637534 ACTGTTATTGATGACAGATGTGGC 59.362 41.667 19.04 0.00 44.42 5.01
982 1026 4.273235 CGCCATTGCTACTGTTATTGATGA 59.727 41.667 0.00 0.00 34.43 2.92
983 1027 4.530388 CGCCATTGCTACTGTTATTGATG 58.470 43.478 0.00 0.00 34.43 3.07
984 1028 3.003689 GCGCCATTGCTACTGTTATTGAT 59.996 43.478 0.00 0.00 34.43 2.57
985 1029 2.354510 GCGCCATTGCTACTGTTATTGA 59.645 45.455 0.00 0.00 34.43 2.57
986 1030 2.355756 AGCGCCATTGCTACTGTTATTG 59.644 45.455 2.29 0.00 45.14 1.90
987 1031 2.643551 AGCGCCATTGCTACTGTTATT 58.356 42.857 2.29 0.00 45.14 1.40
989 1033 3.853104 AGCGCCATTGCTACTGTTA 57.147 47.368 2.29 0.00 45.14 2.41
990 1034 4.722193 AGCGCCATTGCTACTGTT 57.278 50.000 2.29 0.00 45.14 3.16
1120 1164 3.204827 GATGGCGTCGGCAATGCT 61.205 61.111 26.08 9.13 42.43 3.79
1242 1286 2.097036 TCTATTCCGAAGACGCCTGAA 58.903 47.619 0.00 0.00 38.29 3.02
1258 1302 1.486211 CCGTCCCTGGAGTGTTCTAT 58.514 55.000 0.00 0.00 0.00 1.98
1666 1752 2.619165 CCATCACGCTGCACTGCAA 61.619 57.895 4.99 0.00 38.41 4.08
1669 1755 2.393768 GGTCCATCACGCTGCACTG 61.394 63.158 0.00 0.00 0.00 3.66
1802 1888 3.135225 TGGAGTACCAACATTGTGTTCG 58.865 45.455 0.00 0.00 43.91 3.95
1826 1912 5.244785 TGGACATTGTGATCGTAGACTAC 57.755 43.478 2.24 2.24 42.51 2.73
1827 1913 6.465439 AATGGACATTGTGATCGTAGACTA 57.535 37.500 0.00 0.00 42.51 2.59
1869 1960 7.589587 TCGTTAATTGACAACATGCTAACTTTG 59.410 33.333 0.95 0.00 0.00 2.77
1903 1994 2.362077 ACTGCAACAATTGAAGGTGGTC 59.638 45.455 13.59 0.00 40.87 4.02
1920 2011 1.108776 AATCATGCATGACCCACTGC 58.891 50.000 30.92 0.00 40.03 4.40
2073 2164 3.003275 TGAAAAGGTCGAACATGACTTGC 59.997 43.478 1.87 0.00 38.91 4.01
2129 2220 4.769345 AAGATGATCTTCTTCCACTCCC 57.231 45.455 16.10 0.00 28.99 4.30
2157 2248 4.631813 GTGATTTTGTAGTCGCTGAATCCT 59.368 41.667 0.00 0.00 0.00 3.24
2187 2278 1.852633 TGATCGATCTCACACCCAGT 58.147 50.000 25.02 0.00 0.00 4.00
2278 2369 7.548075 ACAAATTAATACGGAGACCACACTTAG 59.452 37.037 0.00 0.00 0.00 2.18
2335 2426 5.186198 AGTTTTATTAGCCGAGAAGCACAT 58.814 37.500 0.00 0.00 34.23 3.21
2375 2468 4.923281 GCAACAATTTAGACATCCCACAAC 59.077 41.667 0.00 0.00 0.00 3.32
2432 2526 8.734386 CATACTTTCTGTCTCAAAAGGCTTAAT 58.266 33.333 0.00 0.00 36.91 1.40
2434 2528 7.173218 CACATACTTTCTGTCTCAAAAGGCTTA 59.827 37.037 0.00 0.00 36.91 3.09
2435 2529 6.016777 CACATACTTTCTGTCTCAAAAGGCTT 60.017 38.462 0.00 0.00 36.91 4.35
2479 2838 3.512154 TTGGGCAGGCCAAGAGGTG 62.512 63.158 24.40 0.00 37.98 4.00
2480 2839 3.185203 TTGGGCAGGCCAAGAGGT 61.185 61.111 24.40 0.00 37.98 3.85
2481 2840 2.677875 GTTGGGCAGGCCAAGAGG 60.678 66.667 28.37 0.00 37.98 3.69
2482 2841 2.677875 GGTTGGGCAGGCCAAGAG 60.678 66.667 28.37 0.00 37.98 2.85
2483 2842 3.506743 TGGTTGGGCAGGCCAAGA 61.507 61.111 28.37 15.32 37.98 3.02
2484 2843 2.993264 CTGGTTGGGCAGGCCAAG 60.993 66.667 28.37 13.63 37.98 3.61
2485 2844 2.887738 AAACTGGTTGGGCAGGCCAA 62.888 55.000 24.40 24.40 37.98 4.52
2486 2845 3.387609 AAACTGGTTGGGCAGGCCA 62.388 57.895 12.83 12.83 37.98 5.36
2487 2846 2.524148 AAACTGGTTGGGCAGGCC 60.524 61.111 5.91 5.91 0.00 5.19
2505 2864 1.358725 CTTCATGGCCACACGTACCG 61.359 60.000 8.16 0.00 0.00 4.02
2506 2865 0.321298 ACTTCATGGCCACACGTACC 60.321 55.000 8.16 0.00 0.00 3.34
2508 2867 1.609580 GGAACTTCATGGCCACACGTA 60.610 52.381 8.16 0.00 0.00 3.57
2527 2904 5.657474 CATCAAAAGAATCATGGTGAAGGG 58.343 41.667 0.00 0.00 0.00 3.95
2575 2960 1.349026 CATTCCCACTATCAGCCCGAT 59.651 52.381 0.00 0.00 38.21 4.18
2594 2979 4.821260 GCATGTGATACCATAATGTCACCA 59.179 41.667 0.00 0.00 39.31 4.17
2712 3097 5.279206 CGTGTCTTATCCCATCAAGCTCTAT 60.279 44.000 0.00 0.00 0.00 1.98
2849 3234 9.717942 AGATCCAATAGTTTCAGCTTCATATAC 57.282 33.333 0.00 0.00 0.00 1.47
2921 3308 9.724839 CGTTGTGTTTAGGAATAAAAGAAAAGA 57.275 29.630 0.00 0.00 0.00 2.52
2922 3309 9.724839 TCGTTGTGTTTAGGAATAAAAGAAAAG 57.275 29.630 0.00 0.00 0.00 2.27
2927 3323 6.961576 TGGTCGTTGTGTTTAGGAATAAAAG 58.038 36.000 0.00 0.00 0.00 2.27
3140 3650 1.098050 GTCGGAGCTTTCATTGGCAT 58.902 50.000 0.00 0.00 0.00 4.40
3143 3653 0.804989 GGTGTCGGAGCTTTCATTGG 59.195 55.000 0.00 0.00 0.00 3.16
3156 3666 5.965922 TCATGCCTATATATCTTGGTGTCG 58.034 41.667 0.00 0.00 0.00 4.35
3159 3669 5.882557 GGGTTCATGCCTATATATCTTGGTG 59.117 44.000 0.00 0.00 0.00 4.17
3160 3670 5.338381 CGGGTTCATGCCTATATATCTTGGT 60.338 44.000 0.00 0.00 0.00 3.67
3168 3678 3.181329 TCCATCGGGTTCATGCCTATAT 58.819 45.455 0.00 0.00 34.93 0.86
3200 3711 5.127491 ACCAGTTAACGATTTCCTCAACAA 58.873 37.500 0.00 0.00 0.00 2.83
3201 3712 4.710324 ACCAGTTAACGATTTCCTCAACA 58.290 39.130 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.