Multiple sequence alignment - TraesCS3D01G137300

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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 TraesCS3D01G137300 chr3D 100.000 2780 0 0 1 2780 95958470 95955691 0.000000e+00 5134.0
1 TraesCS3D01G137300 chr3D 95.329 942 40 4 3 941 81834137 81835077 0.000000e+00 1493.0
2 TraesCS3D01G137300 chr3D 94.628 968 43 4 3 968 562584402 562583442 0.000000e+00 1491.0
3 TraesCS3D01G137300 chr3D 94.416 967 45 5 3 967 6288380 6289339 0.000000e+00 1478.0
4 TraesCS3D01G137300 chr3D 94.112 968 47 3 4 969 93188806 93189765 0.000000e+00 1463.0
5 TraesCS3D01G137300 chr3D 90.798 739 46 12 1058 1785 96124905 96124178 0.000000e+00 968.0
6 TraesCS3D01G137300 chr3A 91.667 1380 73 20 1037 2376 114048122 114046745 0.000000e+00 1873.0
7 TraesCS3D01G137300 chr3A 90.204 735 54 7 1058 1783 114238859 114238134 0.000000e+00 942.0
8 TraesCS3D01G137300 chr3A 86.711 301 16 5 673 972 598684792 598684515 2.080000e-81 313.0
9 TraesCS3D01G137300 chr3A 94.030 201 9 3 2579 2778 101612766 101612568 4.500000e-78 302.0
10 TraesCS3D01G137300 chr3A 86.014 143 11 2 2388 2530 101613143 101613010 8.020000e-31 145.0
11 TraesCS3D01G137300 chr7D 95.072 974 32 5 3 974 561524430 561523471 0.000000e+00 1519.0
12 TraesCS3D01G137300 chr7D 95.026 965 40 2 4 967 174132764 174133721 0.000000e+00 1509.0
13 TraesCS3D01G137300 chr7D 94.835 968 41 7 3 968 433076691 433077651 0.000000e+00 1502.0
14 TraesCS3D01G137300 chr7D 94.742 970 40 5 3 968 188555375 188554413 0.000000e+00 1498.0
15 TraesCS3D01G137300 chr7D 89.256 726 43 11 249 967 626191547 626192244 0.000000e+00 876.0
16 TraesCS3D01G137300 chr7D 87.418 612 36 12 365 969 554904939 554905516 0.000000e+00 665.0
17 TraesCS3D01G137300 chr4D 95.052 970 39 3 3 971 15239672 15238711 0.000000e+00 1517.0
18 TraesCS3D01G137300 chr6D 94.634 969 43 5 3 969 275680683 275679722 0.000000e+00 1493.0
19 TraesCS3D01G137300 chr3B 88.209 1111 66 31 1033 2097 146891475 146890384 0.000000e+00 1266.0
20 TraesCS3D01G137300 chr3B 89.145 737 55 9 1063 1785 147184231 147183506 0.000000e+00 894.0
21 TraesCS3D01G137300 chr5A 90.819 403 19 10 2390 2780 405023467 405023071 8.820000e-145 523.0
22 TraesCS3D01G137300 chr7A 90.716 377 16 9 2417 2780 563407446 563407816 4.160000e-133 484.0
23 TraesCS3D01G137300 chr7A 77.389 429 54 24 2381 2772 210578709 210579131 6.030000e-52 215.0
24 TraesCS3D01G137300 chr6B 84.750 400 34 10 575 972 88575714 88575340 2.610000e-100 375.0
25 TraesCS3D01G137300 chr6B 81.250 128 15 5 844 970 72402786 72402667 8.200000e-16 95.3
26 TraesCS3D01G137300 chr2B 77.861 402 52 23 2389 2770 15313267 15313651 6.030000e-52 215.0
27 TraesCS3D01G137300 chrUn 78.571 224 32 12 2389 2602 358853655 358853438 1.740000e-27 134.0
28 TraesCS3D01G137300 chr2A 87.850 107 8 5 2395 2498 247004269 247004373 1.350000e-23 121.0
29 TraesCS3D01G137300 chr5D 78.010 191 28 9 2385 2570 418928589 418928770 1.050000e-19 108.0
30 TraesCS3D01G137300 chr1D 88.636 88 9 1 2391 2478 418757480 418757394 3.790000e-19 106.0


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 TraesCS3D01G137300 chr3D 95955691 95958470 2779 True 5134.0 5134 100.000 1 2780 1 chr3D.!!$R1 2779
1 TraesCS3D01G137300 chr3D 81834137 81835077 940 False 1493.0 1493 95.329 3 941 1 chr3D.!!$F2 938
2 TraesCS3D01G137300 chr3D 562583442 562584402 960 True 1491.0 1491 94.628 3 968 1 chr3D.!!$R3 965
3 TraesCS3D01G137300 chr3D 6288380 6289339 959 False 1478.0 1478 94.416 3 967 1 chr3D.!!$F1 964
4 TraesCS3D01G137300 chr3D 93188806 93189765 959 False 1463.0 1463 94.112 4 969 1 chr3D.!!$F3 965
5 TraesCS3D01G137300 chr3D 96124178 96124905 727 True 968.0 968 90.798 1058 1785 1 chr3D.!!$R2 727
6 TraesCS3D01G137300 chr3A 114046745 114048122 1377 True 1873.0 1873 91.667 1037 2376 1 chr3A.!!$R1 1339
7 TraesCS3D01G137300 chr3A 114238134 114238859 725 True 942.0 942 90.204 1058 1783 1 chr3A.!!$R2 725
8 TraesCS3D01G137300 chr3A 101612568 101613143 575 True 223.5 302 90.022 2388 2778 2 chr3A.!!$R4 390
9 TraesCS3D01G137300 chr7D 561523471 561524430 959 True 1519.0 1519 95.072 3 974 1 chr7D.!!$R2 971
10 TraesCS3D01G137300 chr7D 174132764 174133721 957 False 1509.0 1509 95.026 4 967 1 chr7D.!!$F1 963
11 TraesCS3D01G137300 chr7D 433076691 433077651 960 False 1502.0 1502 94.835 3 968 1 chr7D.!!$F2 965
12 TraesCS3D01G137300 chr7D 188554413 188555375 962 True 1498.0 1498 94.742 3 968 1 chr7D.!!$R1 965
13 TraesCS3D01G137300 chr7D 626191547 626192244 697 False 876.0 876 89.256 249 967 1 chr7D.!!$F4 718
14 TraesCS3D01G137300 chr7D 554904939 554905516 577 False 665.0 665 87.418 365 969 1 chr7D.!!$F3 604
15 TraesCS3D01G137300 chr4D 15238711 15239672 961 True 1517.0 1517 95.052 3 971 1 chr4D.!!$R1 968
16 TraesCS3D01G137300 chr6D 275679722 275680683 961 True 1493.0 1493 94.634 3 969 1 chr6D.!!$R1 966
17 TraesCS3D01G137300 chr3B 146890384 146891475 1091 True 1266.0 1266 88.209 1033 2097 1 chr3B.!!$R1 1064
18 TraesCS3D01G137300 chr3B 147183506 147184231 725 True 894.0 894 89.145 1063 1785 1 chr3B.!!$R2 722

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
976 990 0.108329 AAACACGCCCTATGAGACGG 60.108 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2218 0.106918 AAAACAGTCCGGGTTCAGCA 60.107 50.0 0.0 0.0 0.0 4.41 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
92 93 3.470888 CCCACCGCCGAGGAAGAT 61.471 66.667 3.89 0.00 45.00 2.40
105 106 0.175989 GGAAGATCCGAAGACGCCTT 59.824 55.000 0.00 0.00 38.29 4.35
113 114 1.885163 CGAAGACGCCTTAGGGTGGT 61.885 60.000 9.51 0.00 46.67 4.16
560 568 6.432107 CCTAAGTACTATCGAGTCTGCTTTC 58.568 44.000 0.00 0.00 37.10 2.62
606 615 5.294356 TGCGTAGAACTGTTATGAAGTGTT 58.706 37.500 0.00 0.00 0.00 3.32
666 678 5.265191 TCCTCTGTTTATACTCTGCTCTGT 58.735 41.667 0.00 0.00 0.00 3.41
864 877 2.034878 TGCAGGCAACCAAACAACATA 58.965 42.857 0.00 0.00 37.17 2.29
906 920 2.170166 CATTTGCTTAGCCAGGTTGGA 58.830 47.619 0.29 0.00 40.96 3.53
936 950 2.168728 TGTATGCAATGCGGGTACTGTA 59.831 45.455 13.50 0.00 36.83 2.74
974 988 1.338769 ACCAAACACGCCCTATGAGAC 60.339 52.381 0.00 0.00 0.00 3.36
975 989 0.999406 CAAACACGCCCTATGAGACG 59.001 55.000 0.00 0.00 0.00 4.18
976 990 0.108329 AAACACGCCCTATGAGACGG 60.108 55.000 0.00 0.00 0.00 4.79
977 991 0.968901 AACACGCCCTATGAGACGGA 60.969 55.000 0.00 0.00 0.00 4.69
978 992 1.360551 CACGCCCTATGAGACGGAG 59.639 63.158 0.00 0.00 0.00 4.63
979 993 1.828660 ACGCCCTATGAGACGGAGG 60.829 63.158 0.00 0.00 0.00 4.30
983 997 3.831651 CCTATGAGACGGAGGGAGT 57.168 57.895 0.00 0.00 0.00 3.85
984 998 2.953284 CCTATGAGACGGAGGGAGTA 57.047 55.000 0.00 0.00 0.00 2.59
985 999 2.506444 CCTATGAGACGGAGGGAGTAC 58.494 57.143 0.00 0.00 0.00 2.73
986 1000 2.106857 CCTATGAGACGGAGGGAGTACT 59.893 54.545 0.00 0.00 0.00 2.73
987 1001 2.060050 ATGAGACGGAGGGAGTACTG 57.940 55.000 0.00 0.00 0.00 2.74
988 1002 0.697079 TGAGACGGAGGGAGTACTGT 59.303 55.000 0.00 0.00 0.00 3.55
989 1003 1.096416 GAGACGGAGGGAGTACTGTG 58.904 60.000 0.00 0.00 0.00 3.66
990 1004 0.404812 AGACGGAGGGAGTACTGTGT 59.595 55.000 0.00 0.00 0.00 3.72
991 1005 1.632409 AGACGGAGGGAGTACTGTGTA 59.368 52.381 0.00 0.00 0.00 2.90
992 1006 2.241685 AGACGGAGGGAGTACTGTGTAT 59.758 50.000 0.00 0.00 0.00 2.29
993 1007 3.457380 AGACGGAGGGAGTACTGTGTATA 59.543 47.826 0.00 0.00 0.00 1.47
994 1008 3.549794 ACGGAGGGAGTACTGTGTATAC 58.450 50.000 0.00 0.00 0.00 1.47
995 1009 3.054139 ACGGAGGGAGTACTGTGTATACA 60.054 47.826 0.00 0.08 35.08 2.29
996 1010 3.314635 CGGAGGGAGTACTGTGTATACAC 59.685 52.174 25.99 25.99 46.59 2.90
997 1011 3.635836 GGAGGGAGTACTGTGTATACACC 59.364 52.174 28.67 15.71 45.88 4.16
998 1012 3.285484 AGGGAGTACTGTGTATACACCG 58.715 50.000 28.67 25.07 45.88 4.94
999 1013 2.360165 GGGAGTACTGTGTATACACCGG 59.640 54.545 28.67 23.01 45.88 5.28
1000 1014 3.282021 GGAGTACTGTGTATACACCGGA 58.718 50.000 28.67 19.19 45.88 5.14
1001 1015 3.887716 GGAGTACTGTGTATACACCGGAT 59.112 47.826 28.67 14.87 45.88 4.18
1002 1016 4.261489 GGAGTACTGTGTATACACCGGATG 60.261 50.000 28.67 16.99 45.88 3.51
1003 1017 4.529897 AGTACTGTGTATACACCGGATGA 58.470 43.478 28.67 11.54 45.88 2.92
1004 1018 5.138276 AGTACTGTGTATACACCGGATGAT 58.862 41.667 28.67 11.82 45.88 2.45
1005 1019 4.322080 ACTGTGTATACACCGGATGATG 57.678 45.455 28.67 13.05 45.88 3.07
1006 1020 3.069586 ACTGTGTATACACCGGATGATGG 59.930 47.826 28.67 12.18 45.88 3.51
1007 1021 2.224185 TGTGTATACACCGGATGATGGC 60.224 50.000 28.67 4.43 45.88 4.40
1008 1022 1.346395 TGTATACACCGGATGATGGCC 59.654 52.381 9.46 0.00 0.00 5.36
1015 1029 3.070076 CGGATGATGGCCGGATATG 57.930 57.895 5.05 0.00 44.87 1.78
1016 1030 0.462581 CGGATGATGGCCGGATATGG 60.463 60.000 5.05 0.00 44.87 2.74
1017 1031 0.107017 GGATGATGGCCGGATATGGG 60.107 60.000 5.05 0.00 0.00 4.00
1018 1032 0.620556 GATGATGGCCGGATATGGGT 59.379 55.000 5.05 0.00 0.00 4.51
1019 1033 0.329261 ATGATGGCCGGATATGGGTG 59.671 55.000 5.05 0.00 0.00 4.61
1020 1034 1.059584 TGATGGCCGGATATGGGTGT 61.060 55.000 5.05 0.00 0.00 4.16
1021 1035 0.321653 GATGGCCGGATATGGGTGTC 60.322 60.000 5.05 0.00 0.00 3.67
1022 1036 0.768221 ATGGCCGGATATGGGTGTCT 60.768 55.000 5.05 0.00 0.00 3.41
1023 1037 0.986019 TGGCCGGATATGGGTGTCTT 60.986 55.000 5.05 0.00 0.00 3.01
1024 1038 1.053424 GGCCGGATATGGGTGTCTTA 58.947 55.000 5.05 0.00 0.00 2.10
1025 1039 1.418637 GGCCGGATATGGGTGTCTTAA 59.581 52.381 5.05 0.00 0.00 1.85
1026 1040 2.039879 GGCCGGATATGGGTGTCTTAAT 59.960 50.000 5.05 0.00 0.00 1.40
1027 1041 3.262405 GGCCGGATATGGGTGTCTTAATA 59.738 47.826 5.05 0.00 0.00 0.98
1028 1042 4.504858 GCCGGATATGGGTGTCTTAATAG 58.495 47.826 5.05 0.00 0.00 1.73
1029 1043 4.222145 GCCGGATATGGGTGTCTTAATAGA 59.778 45.833 5.05 0.00 0.00 1.98
1030 1044 5.279809 GCCGGATATGGGTGTCTTAATAGAA 60.280 44.000 5.05 0.00 30.65 2.10
1031 1045 6.743208 GCCGGATATGGGTGTCTTAATAGAAA 60.743 42.308 5.05 0.00 30.65 2.52
1035 1049 7.599245 GGATATGGGTGTCTTAATAGAAACTCG 59.401 40.741 0.00 0.00 41.39 4.18
1076 1092 1.644786 CCCCGAATGGACAAGCGAAC 61.645 60.000 0.00 0.00 37.49 3.95
1851 1900 0.898320 ACAGCAAGCCGTAGATCTGT 59.102 50.000 5.18 0.00 0.00 3.41
1960 2027 2.297701 GGTTTTCCTTGTGCTCTGACA 58.702 47.619 0.00 0.00 36.94 3.58
1963 2030 3.558931 TTTCCTTGTGCTCTGACAGAA 57.441 42.857 6.61 0.00 0.00 3.02
1982 2049 6.634805 ACAGAAGCTCTTTGATCTTCGATTA 58.365 36.000 0.00 0.00 39.06 1.75
1991 2058 5.773239 TTGATCTTCGATTACGGTTTCAC 57.227 39.130 0.00 0.00 40.21 3.18
1995 2062 2.442212 TCGATTACGGTTTCACTGCA 57.558 45.000 0.00 0.00 40.21 4.41
2048 2118 5.559799 GCTCTTTGCTGTTAGACTGAACTTG 60.560 44.000 0.00 0.00 38.95 3.16
2076 2153 2.076100 TGACTGCATGAACGATGAACC 58.924 47.619 0.00 0.00 33.31 3.62
2139 2216 4.399618 CAGATCTGGTAGAAAGTCCGAGAA 59.600 45.833 15.38 0.00 0.00 2.87
2140 2217 4.642885 AGATCTGGTAGAAAGTCCGAGAAG 59.357 45.833 0.00 0.00 0.00 2.85
2141 2218 3.764218 TCTGGTAGAAAGTCCGAGAAGT 58.236 45.455 0.00 0.00 0.00 3.01
2142 2219 3.506455 TCTGGTAGAAAGTCCGAGAAGTG 59.494 47.826 0.00 0.00 0.00 3.16
2153 2231 1.671742 GAGAAGTGCTGAACCCGGA 59.328 57.895 0.73 0.00 0.00 5.14
2155 2233 1.122019 AGAAGTGCTGAACCCGGACT 61.122 55.000 0.73 0.00 0.00 3.85
2177 2255 5.591877 ACTGTTTTCTTGATGAAAGTGAGCT 59.408 36.000 0.00 0.00 44.40 4.09
2178 2256 6.096001 ACTGTTTTCTTGATGAAAGTGAGCTT 59.904 34.615 0.00 0.00 44.40 3.74
2247 2331 6.529125 CGGACATAATACACTAAAACGTGTCT 59.471 38.462 0.00 0.00 44.32 3.41
2253 2337 9.865321 ATAATACACTAAAACGTGTCTGTGTAT 57.135 29.630 21.29 21.29 44.32 2.29
2303 2391 7.056635 ACATCTTATATTTGTGAGTGAAGGGG 58.943 38.462 0.00 0.00 0.00 4.79
2305 2393 5.729229 TCTTATATTTGTGAGTGAAGGGGGA 59.271 40.000 0.00 0.00 0.00 4.81
2311 2399 2.225017 TGTGAGTGAAGGGGGAATTTCC 60.225 50.000 6.91 6.91 35.23 3.13
2315 2403 4.355588 TGAGTGAAGGGGGAATTTCCTAAA 59.644 41.667 14.95 0.00 36.57 1.85
2316 2404 5.016245 TGAGTGAAGGGGGAATTTCCTAAAT 59.984 40.000 14.95 0.36 36.57 1.40
2329 2431 9.799106 GGAATTTCCTAAATCTATCATTCTCCA 57.201 33.333 8.25 0.00 32.53 3.86
2337 2439 3.743521 TCTATCATTCTCCAAATGCCGG 58.256 45.455 0.00 0.00 0.00 6.13
2338 2440 1.696063 ATCATTCTCCAAATGCCGGG 58.304 50.000 2.18 0.00 0.00 5.73
2356 2458 3.129638 CCGGGAACACTTCTTTTGTTTCA 59.870 43.478 0.00 0.00 37.31 2.69
2359 2461 5.474825 GGGAACACTTCTTTTGTTTCAACA 58.525 37.500 0.00 0.00 37.31 3.33
2376 2478 5.982465 TCAACAAAAGGCATAAGTTTTGC 57.018 34.783 9.55 9.55 44.18 3.68
2393 2495 7.410120 AGTTTTGCCTCATTTATTAAGGGAG 57.590 36.000 0.00 0.00 31.71 4.30
2395 2497 7.122799 AGTTTTGCCTCATTTATTAAGGGAGAC 59.877 37.037 7.58 0.00 31.71 3.36
2409 2511 0.388263 GGAGACGTTTCCAGACGGAC 60.388 60.000 19.71 0.00 46.77 4.79
2454 2556 4.785512 CCTCGCTCGCTCGCTTGT 62.786 66.667 0.00 0.00 0.00 3.16
2456 2558 4.342987 TCGCTCGCTCGCTTGTGT 62.343 61.111 0.00 0.00 0.00 3.72
2457 2559 2.504026 CGCTCGCTCGCTTGTGTA 60.504 61.111 0.00 0.00 0.00 2.90
2458 2560 2.778997 CGCTCGCTCGCTTGTGTAC 61.779 63.158 0.00 0.00 0.00 2.90
2459 2561 2.778997 GCTCGCTCGCTTGTGTACG 61.779 63.158 0.00 0.00 0.00 3.67
2460 2562 2.778997 CTCGCTCGCTTGTGTACGC 61.779 63.158 0.00 0.00 0.00 4.42
2491 2593 0.605319 GGGCCACACGAGTTTGATGA 60.605 55.000 4.39 0.00 0.00 2.92
2500 2602 3.438087 CACGAGTTTGATGAGCCTTCAAT 59.562 43.478 0.00 0.00 36.78 2.57
2501 2603 4.074970 ACGAGTTTGATGAGCCTTCAATT 58.925 39.130 0.00 0.00 36.78 2.32
2502 2604 4.154918 ACGAGTTTGATGAGCCTTCAATTC 59.845 41.667 0.00 5.66 36.78 2.17
2503 2605 4.154737 CGAGTTTGATGAGCCTTCAATTCA 59.845 41.667 4.97 0.00 36.78 2.57
2504 2606 5.335113 CGAGTTTGATGAGCCTTCAATTCAA 60.335 40.000 4.97 0.00 36.78 2.69
2515 2617 3.937706 CCTTCAATTCAAGCGAGATGTCT 59.062 43.478 0.00 0.00 0.00 3.41
2521 2623 5.793026 ATTCAAGCGAGATGTCTCTTTTC 57.207 39.130 8.28 0.00 40.75 2.29
2526 2628 6.533012 TCAAGCGAGATGTCTCTTTTCTTATG 59.467 38.462 8.28 0.00 40.75 1.90
2530 2632 6.533367 GCGAGATGTCTCTTTTCTTATGTCTT 59.467 38.462 8.28 0.00 40.75 3.01
2531 2633 7.064016 GCGAGATGTCTCTTTTCTTATGTCTTT 59.936 37.037 8.28 0.00 40.75 2.52
2532 2634 8.591312 CGAGATGTCTCTTTTCTTATGTCTTTC 58.409 37.037 8.28 0.00 40.75 2.62
2533 2635 8.472683 AGATGTCTCTTTTCTTATGTCTTTCG 57.527 34.615 0.00 0.00 0.00 3.46
2534 2636 6.467723 TGTCTCTTTTCTTATGTCTTTCGC 57.532 37.500 0.00 0.00 0.00 4.70
2535 2637 5.118664 TGTCTCTTTTCTTATGTCTTTCGCG 59.881 40.000 0.00 0.00 0.00 5.87
2536 2638 5.118817 GTCTCTTTTCTTATGTCTTTCGCGT 59.881 40.000 5.77 0.00 0.00 6.01
2537 2639 6.307318 GTCTCTTTTCTTATGTCTTTCGCGTA 59.693 38.462 5.77 0.00 0.00 4.42
2538 2640 6.864685 TCTCTTTTCTTATGTCTTTCGCGTAA 59.135 34.615 5.77 0.76 0.00 3.18
2539 2641 7.544566 TCTCTTTTCTTATGTCTTTCGCGTAAT 59.455 33.333 5.77 0.00 0.00 1.89
2540 2642 8.025243 TCTTTTCTTATGTCTTTCGCGTAATT 57.975 30.769 5.77 0.00 0.00 1.40
2541 2643 8.500773 TCTTTTCTTATGTCTTTCGCGTAATTT 58.499 29.630 5.77 0.00 0.00 1.82
2542 2644 9.113876 CTTTTCTTATGTCTTTCGCGTAATTTT 57.886 29.630 5.77 0.00 0.00 1.82
2543 2645 9.453325 TTTTCTTATGTCTTTCGCGTAATTTTT 57.547 25.926 5.77 0.00 0.00 1.94
2565 2667 6.625873 TTTTTCTCTGCTTTCTTCTTCCTC 57.374 37.500 0.00 0.00 0.00 3.71
2566 2668 5.559148 TTTCTCTGCTTTCTTCTTCCTCT 57.441 39.130 0.00 0.00 0.00 3.69
2567 2669 5.559148 TTCTCTGCTTTCTTCTTCCTCTT 57.441 39.130 0.00 0.00 0.00 2.85
2568 2670 4.892433 TCTCTGCTTTCTTCTTCCTCTTG 58.108 43.478 0.00 0.00 0.00 3.02
2569 2671 3.406764 TCTGCTTTCTTCTTCCTCTTGC 58.593 45.455 0.00 0.00 0.00 4.01
2570 2672 3.072184 TCTGCTTTCTTCTTCCTCTTGCT 59.928 43.478 0.00 0.00 0.00 3.91
2571 2673 3.819902 CTGCTTTCTTCTTCCTCTTGCTT 59.180 43.478 0.00 0.00 0.00 3.91
2572 2674 3.817647 TGCTTTCTTCTTCCTCTTGCTTC 59.182 43.478 0.00 0.00 0.00 3.86
2573 2675 4.071423 GCTTTCTTCTTCCTCTTGCTTCT 58.929 43.478 0.00 0.00 0.00 2.85
2574 2676 4.154015 GCTTTCTTCTTCCTCTTGCTTCTC 59.846 45.833 0.00 0.00 0.00 2.87
2575 2677 5.550290 CTTTCTTCTTCCTCTTGCTTCTCT 58.450 41.667 0.00 0.00 0.00 3.10
2576 2678 4.799564 TCTTCTTCCTCTTGCTTCTCTC 57.200 45.455 0.00 0.00 0.00 3.20
2577 2679 3.513515 TCTTCTTCCTCTTGCTTCTCTCC 59.486 47.826 0.00 0.00 0.00 3.71
2594 2891 4.520874 TCTCTCCTCTCTTGTTACACACAG 59.479 45.833 0.00 0.00 36.48 3.66
2609 2906 1.063806 CACAGTAAGCTCGTCAGTGC 58.936 55.000 0.00 0.00 37.15 4.40
2610 2907 0.038159 ACAGTAAGCTCGTCAGTGCC 60.038 55.000 0.00 0.00 37.57 5.01
2649 2946 1.298014 CTTCTGTGAGCACCCCCTC 59.702 63.158 0.00 0.00 0.00 4.30
2720 3018 2.223829 CGATGCTACAACCGGAGAGATT 60.224 50.000 9.46 0.00 0.00 2.40
2742 3040 4.360951 TTTTCCTAGAACCGGTGACAAT 57.639 40.909 8.52 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 1.304713 ACCCTAAGGCGTCTTCGGA 60.305 57.895 21.03 0.00 37.87 4.55
105 106 1.676635 CCTCGTCGTCACCACCCTA 60.677 63.158 0.00 0.00 0.00 3.53
113 114 2.678580 TCCATGCCCTCGTCGTCA 60.679 61.111 0.00 0.00 0.00 4.35
152 153 0.523072 GGTAGTGGTCGTAGTTGCGA 59.477 55.000 0.00 0.00 38.68 5.10
242 245 1.604278 GAAGTGCTTGGTGAAGTCCAC 59.396 52.381 0.00 0.00 44.95 4.02
322 325 0.035317 TGCCGTTCATCAGCTTCACT 59.965 50.000 0.00 0.00 0.00 3.41
560 568 8.582930 CGCATAAACCATAAACATAAACAGTTG 58.417 33.333 0.00 0.00 0.00 3.16
606 615 7.730084 AGAGCATATTTCAGATAAGCAGTACA 58.270 34.615 0.00 0.00 0.00 2.90
666 678 5.181056 CACAACCAGTAGCACACATCATAAA 59.819 40.000 0.00 0.00 0.00 1.40
721 734 2.506231 TGGTGTGTGGTAACCTCTTTGA 59.494 45.455 0.00 0.00 37.36 2.69
864 877 2.688446 CAGCCTCAAATGCATCATCTGT 59.312 45.455 0.00 0.00 0.00 3.41
906 920 3.005050 CCGCATTGCATACATTTCTCCAT 59.995 43.478 9.69 0.00 0.00 3.41
974 988 3.314635 GTGTATACACAGTACTCCCTCCG 59.685 52.174 27.37 0.00 45.75 4.63
975 989 4.915158 GTGTATACACAGTACTCCCTCC 57.085 50.000 27.37 0.00 45.75 4.30
987 1001 2.413837 GCCATCATCCGGTGTATACAC 58.586 52.381 25.00 25.00 45.72 2.90
988 1002 1.346395 GGCCATCATCCGGTGTATACA 59.654 52.381 0.08 0.08 0.00 2.29
989 1003 1.671850 CGGCCATCATCCGGTGTATAC 60.672 57.143 2.24 0.00 42.99 1.47
990 1004 0.606096 CGGCCATCATCCGGTGTATA 59.394 55.000 2.24 0.00 42.99 1.47
991 1005 1.371183 CGGCCATCATCCGGTGTAT 59.629 57.895 2.24 0.00 42.99 2.29
992 1006 2.818841 CGGCCATCATCCGGTGTA 59.181 61.111 2.24 0.00 42.99 2.90
997 1011 0.462581 CCATATCCGGCCATCATCCG 60.463 60.000 2.24 0.00 46.05 4.18
998 1012 0.107017 CCCATATCCGGCCATCATCC 60.107 60.000 2.24 0.00 0.00 3.51
999 1013 0.620556 ACCCATATCCGGCCATCATC 59.379 55.000 2.24 0.00 0.00 2.92
1000 1014 0.329261 CACCCATATCCGGCCATCAT 59.671 55.000 2.24 0.00 0.00 2.45
1001 1015 1.059584 ACACCCATATCCGGCCATCA 61.060 55.000 2.24 0.00 0.00 3.07
1002 1016 0.321653 GACACCCATATCCGGCCATC 60.322 60.000 2.24 0.00 0.00 3.51
1003 1017 0.768221 AGACACCCATATCCGGCCAT 60.768 55.000 2.24 0.00 0.00 4.40
1004 1018 0.986019 AAGACACCCATATCCGGCCA 60.986 55.000 2.24 0.00 0.00 5.36
1005 1019 1.053424 TAAGACACCCATATCCGGCC 58.947 55.000 0.00 0.00 0.00 6.13
1006 1020 2.922740 TTAAGACACCCATATCCGGC 57.077 50.000 0.00 0.00 0.00 6.13
1007 1021 5.995565 TCTATTAAGACACCCATATCCGG 57.004 43.478 0.00 0.00 0.00 5.14
1008 1022 7.442656 AGTTTCTATTAAGACACCCATATCCG 58.557 38.462 0.00 0.00 33.64 4.18
1009 1023 7.599245 CGAGTTTCTATTAAGACACCCATATCC 59.401 40.741 0.00 0.00 33.64 2.59
1010 1024 8.358148 TCGAGTTTCTATTAAGACACCCATATC 58.642 37.037 0.00 0.00 33.64 1.63
1011 1025 8.246430 TCGAGTTTCTATTAAGACACCCATAT 57.754 34.615 0.00 0.00 33.64 1.78
1012 1026 7.649533 TCGAGTTTCTATTAAGACACCCATA 57.350 36.000 0.00 0.00 33.64 2.74
1013 1027 6.540438 TCGAGTTTCTATTAAGACACCCAT 57.460 37.500 0.00 0.00 33.64 4.00
1014 1028 5.988310 TCGAGTTTCTATTAAGACACCCA 57.012 39.130 0.00 0.00 33.64 4.51
1015 1029 6.476053 GTGATCGAGTTTCTATTAAGACACCC 59.524 42.308 0.00 0.00 33.64 4.61
1016 1030 6.476053 GGTGATCGAGTTTCTATTAAGACACC 59.524 42.308 0.00 0.00 33.64 4.16
1017 1031 7.259161 AGGTGATCGAGTTTCTATTAAGACAC 58.741 38.462 0.00 0.00 33.39 3.67
1018 1032 7.406031 AGGTGATCGAGTTTCTATTAAGACA 57.594 36.000 0.00 0.00 0.00 3.41
1019 1033 7.917720 GAGGTGATCGAGTTTCTATTAAGAC 57.082 40.000 0.00 0.00 0.00 3.01
1035 1049 2.028125 TTGGGGATCGCGAGGTGATC 62.028 60.000 16.66 6.53 45.50 2.92
1076 1092 1.162698 CTTCTCCACTGTGCACATGG 58.837 55.000 28.34 28.34 34.58 3.66
1230 1246 1.276622 TGGAGAAGTACTTGCCCTCC 58.723 55.000 24.93 24.93 42.72 4.30
1811 1860 7.117199 CTGTGGATTCAGAGCCAATTCTTGG 62.117 48.000 1.43 1.43 44.25 3.61
1812 1861 3.760151 TGTGGATTCAGAGCCAATTCTTG 59.240 43.478 0.00 0.00 44.25 3.02
1851 1900 1.768275 TCTGTTCCCAGCTGAAGTTCA 59.232 47.619 17.39 5.25 38.66 3.18
1936 2003 0.310854 GAGCACAAGGAAAACCACCG 59.689 55.000 0.00 0.00 0.00 4.94
1963 2030 4.142138 ACCGTAATCGAAGATCAAAGAGCT 60.142 41.667 0.00 0.00 45.12 4.09
1995 2062 0.677731 AGCAACAGCATACGCCACAT 60.678 50.000 0.00 0.00 39.83 3.21
2035 2102 5.466728 GTCATGCTTCACAAGTTCAGTCTAA 59.533 40.000 0.00 0.00 0.00 2.10
2139 2216 1.696097 AACAGTCCGGGTTCAGCACT 61.696 55.000 0.00 0.00 0.00 4.40
2140 2217 0.818040 AAACAGTCCGGGTTCAGCAC 60.818 55.000 0.00 0.00 0.00 4.40
2141 2218 0.106918 AAAACAGTCCGGGTTCAGCA 60.107 50.000 0.00 0.00 0.00 4.41
2142 2219 0.591659 GAAAACAGTCCGGGTTCAGC 59.408 55.000 0.00 0.00 0.00 4.26
2153 2231 5.591877 AGCTCACTTTCATCAAGAAAACAGT 59.408 36.000 0.00 0.00 45.11 3.55
2155 2233 6.319658 AGAAGCTCACTTTCATCAAGAAAACA 59.680 34.615 0.00 0.00 45.11 2.83
2177 2255 5.372343 TGCAAAGCATCTTATAGGGAGAA 57.628 39.130 0.00 0.00 31.71 2.87
2201 2283 9.826574 TGTCCGTATATAGCCCATATTAAAATC 57.173 33.333 0.00 0.00 31.96 2.17
2296 2384 5.813965 AGATTTAGGAAATTCCCCCTTCA 57.186 39.130 8.66 0.00 37.19 3.02
2298 2386 7.480222 TGATAGATTTAGGAAATTCCCCCTT 57.520 36.000 8.66 0.00 37.19 3.95
2299 2387 7.669677 ATGATAGATTTAGGAAATTCCCCCT 57.330 36.000 8.66 1.95 37.19 4.79
2303 2391 9.799106 TGGAGAATGATAGATTTAGGAAATTCC 57.201 33.333 3.29 3.29 36.58 3.01
2311 2399 7.361542 CCGGCATTTGGAGAATGATAGATTTAG 60.362 40.741 3.12 0.00 0.00 1.85
2315 2403 4.330250 CCGGCATTTGGAGAATGATAGAT 58.670 43.478 3.12 0.00 0.00 1.98
2316 2404 3.496692 CCCGGCATTTGGAGAATGATAGA 60.497 47.826 0.00 0.00 0.00 1.98
2329 2431 1.995376 AAGAAGTGTTCCCGGCATTT 58.005 45.000 0.00 0.00 0.00 2.32
2330 2432 1.995376 AAAGAAGTGTTCCCGGCATT 58.005 45.000 0.00 0.00 0.00 3.56
2376 2478 6.260271 GGAAACGTCTCCCTTAATAAATGAGG 59.740 42.308 0.00 0.00 0.00 3.86
2377 2479 6.821665 TGGAAACGTCTCCCTTAATAAATGAG 59.178 38.462 5.23 0.00 34.22 2.90
2378 2480 6.713276 TGGAAACGTCTCCCTTAATAAATGA 58.287 36.000 5.23 0.00 34.22 2.57
2379 2481 6.821665 TCTGGAAACGTCTCCCTTAATAAATG 59.178 38.462 5.23 0.00 34.22 2.32
2380 2482 6.822170 GTCTGGAAACGTCTCCCTTAATAAAT 59.178 38.462 5.23 0.00 34.22 1.40
2381 2483 6.168389 GTCTGGAAACGTCTCCCTTAATAAA 58.832 40.000 5.23 0.00 34.22 1.40
2382 2484 5.622914 CGTCTGGAAACGTCTCCCTTAATAA 60.623 44.000 5.23 0.00 37.86 1.40
2383 2485 4.142315 CGTCTGGAAACGTCTCCCTTAATA 60.142 45.833 5.23 0.00 37.86 0.98
2384 2486 3.368116 CGTCTGGAAACGTCTCCCTTAAT 60.368 47.826 5.23 0.00 37.86 1.40
2385 2487 2.029649 CGTCTGGAAACGTCTCCCTTAA 60.030 50.000 5.23 0.00 37.86 1.85
2386 2488 1.542915 CGTCTGGAAACGTCTCCCTTA 59.457 52.381 5.23 0.00 37.86 2.69
2491 2593 2.479566 TCTCGCTTGAATTGAAGGCT 57.520 45.000 6.79 0.00 0.00 4.58
2515 2617 7.591006 ATTACGCGAAAGACATAAGAAAAGA 57.409 32.000 15.93 0.00 0.00 2.52
2542 2644 6.360618 AGAGGAAGAAGAAAGCAGAGAAAAA 58.639 36.000 0.00 0.00 0.00 1.94
2543 2645 5.934781 AGAGGAAGAAGAAAGCAGAGAAAA 58.065 37.500 0.00 0.00 0.00 2.29
2544 2646 5.559148 AGAGGAAGAAGAAAGCAGAGAAA 57.441 39.130 0.00 0.00 0.00 2.52
2545 2647 5.303971 CAAGAGGAAGAAGAAAGCAGAGAA 58.696 41.667 0.00 0.00 0.00 2.87
2546 2648 4.802248 GCAAGAGGAAGAAGAAAGCAGAGA 60.802 45.833 0.00 0.00 0.00 3.10
2547 2649 3.436359 GCAAGAGGAAGAAGAAAGCAGAG 59.564 47.826 0.00 0.00 0.00 3.35
2548 2650 3.072184 AGCAAGAGGAAGAAGAAAGCAGA 59.928 43.478 0.00 0.00 0.00 4.26
2549 2651 3.410508 AGCAAGAGGAAGAAGAAAGCAG 58.589 45.455 0.00 0.00 0.00 4.24
2550 2652 3.498774 AGCAAGAGGAAGAAGAAAGCA 57.501 42.857 0.00 0.00 0.00 3.91
2551 2653 4.071423 AGAAGCAAGAGGAAGAAGAAAGC 58.929 43.478 0.00 0.00 0.00 3.51
2552 2654 5.550290 AGAGAAGCAAGAGGAAGAAGAAAG 58.450 41.667 0.00 0.00 0.00 2.62
2553 2655 5.512232 GGAGAGAAGCAAGAGGAAGAAGAAA 60.512 44.000 0.00 0.00 0.00 2.52
2554 2656 4.020662 GGAGAGAAGCAAGAGGAAGAAGAA 60.021 45.833 0.00 0.00 0.00 2.52
2555 2657 3.513515 GGAGAGAAGCAAGAGGAAGAAGA 59.486 47.826 0.00 0.00 0.00 2.87
2556 2658 3.515104 AGGAGAGAAGCAAGAGGAAGAAG 59.485 47.826 0.00 0.00 0.00 2.85
2557 2659 3.513515 GAGGAGAGAAGCAAGAGGAAGAA 59.486 47.826 0.00 0.00 0.00 2.52
2558 2660 3.096092 GAGGAGAGAAGCAAGAGGAAGA 58.904 50.000 0.00 0.00 0.00 2.87
2559 2661 3.099141 AGAGGAGAGAAGCAAGAGGAAG 58.901 50.000 0.00 0.00 0.00 3.46
2560 2662 3.096092 GAGAGGAGAGAAGCAAGAGGAA 58.904 50.000 0.00 0.00 0.00 3.36
2561 2663 2.311542 AGAGAGGAGAGAAGCAAGAGGA 59.688 50.000 0.00 0.00 0.00 3.71
2562 2664 2.738743 AGAGAGGAGAGAAGCAAGAGG 58.261 52.381 0.00 0.00 0.00 3.69
2563 2665 3.511146 ACAAGAGAGGAGAGAAGCAAGAG 59.489 47.826 0.00 0.00 0.00 2.85
2564 2666 3.505386 ACAAGAGAGGAGAGAAGCAAGA 58.495 45.455 0.00 0.00 0.00 3.02
2565 2667 3.959535 ACAAGAGAGGAGAGAAGCAAG 57.040 47.619 0.00 0.00 0.00 4.01
2566 2668 4.588951 TGTAACAAGAGAGGAGAGAAGCAA 59.411 41.667 0.00 0.00 0.00 3.91
2567 2669 4.021894 GTGTAACAAGAGAGGAGAGAAGCA 60.022 45.833 0.00 0.00 36.32 3.91
2568 2670 4.490743 GTGTAACAAGAGAGGAGAGAAGC 58.509 47.826 0.00 0.00 36.32 3.86
2594 2891 1.071567 GTCGGCACTGACGAGCTTAC 61.072 60.000 7.39 0.00 46.55 2.34
2609 2906 2.030562 AGGAAGTTGTGCCGTCGG 59.969 61.111 6.99 6.99 0.00 4.79
2610 2907 2.954753 GCAGGAAGTTGTGCCGTCG 61.955 63.158 0.00 0.00 33.29 5.12
2720 3018 3.842007 TGTCACCGGTTCTAGGAAAAA 57.158 42.857 2.97 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.