Multiple sequence alignment - TraesCS5B01G242500

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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 TraesCS5B01G242500 chr5B 100.000 4449 0 0 1 4449 421862840 421858392 0.000000e+00 8216.0
1 TraesCS5B01G242500 chr5B 80.918 1263 188 41 1003 2243 421838199 421836968 0.000000e+00 948.0
2 TraesCS5B01G242500 chr5B 82.737 643 93 11 2708 3339 421836649 421836014 1.400000e-154 556.0
3 TraesCS5B01G242500 chr5B 81.089 661 98 20 1214 1865 421998529 421997887 1.850000e-138 503.0
4 TraesCS5B01G242500 chr5B 79.518 664 106 22 1214 1865 422040744 422040099 3.160000e-121 446.0
5 TraesCS5B01G242500 chr5B 78.586 481 87 4 4 468 374367571 374367091 2.010000e-78 303.0
6 TraesCS5B01G242500 chr5B 81.667 120 20 2 2014 2132 422039983 422039865 1.020000e-16 99.0
7 TraesCS5B01G242500 chr5B 92.308 39 3 0 495 533 635575977 635575939 6.220000e-04 56.5
8 TraesCS5B01G242500 chr5A 90.261 2608 160 34 997 3562 458331503 458328948 0.000000e+00 3323.0
9 TraesCS5B01G242500 chr5A 86.454 1004 107 16 4 984 458332551 458331554 0.000000e+00 1074.0
10 TraesCS5B01G242500 chr5A 81.092 1264 190 37 1001 2243 458320565 458319330 0.000000e+00 965.0
11 TraesCS5B01G242500 chr5A 81.740 816 111 24 746 1551 458493921 458493134 0.000000e+00 647.0
12 TraesCS5B01G242500 chr5A 82.660 594 80 11 2756 3339 458318969 458318389 5.140000e-139 505.0
13 TraesCS5B01G242500 chr5A 80.988 668 95 24 1208 1864 458525195 458524549 6.640000e-138 501.0
14 TraesCS5B01G242500 chr5A 80.960 667 93 23 1214 1865 458562229 458561582 8.590000e-137 497.0
15 TraesCS5B01G242500 chr5A 82.692 208 27 6 2643 2844 458341466 458341262 4.570000e-40 176.0
16 TraesCS5B01G242500 chr5A 95.238 63 3 0 632 694 669894695 669894757 2.830000e-17 100.0
17 TraesCS5B01G242500 chr5A 96.154 52 1 1 3590 3641 458325418 458325368 2.850000e-12 84.2
18 TraesCS5B01G242500 chr5A 84.722 72 11 0 395 466 662396132 662396203 6.170000e-09 73.1
19 TraesCS5B01G242500 chr5D 91.792 1401 84 16 997 2376 357080695 357079305 0.000000e+00 1921.0
20 TraesCS5B01G242500 chr5D 92.381 1155 61 13 2391 3531 357079320 357078179 0.000000e+00 1620.0
21 TraesCS5B01G242500 chr5D 88.742 986 88 7 16 984 357081725 357080746 0.000000e+00 1184.0
22 TraesCS5B01G242500 chr5D 82.833 1165 160 31 1001 2155 357065637 357064503 0.000000e+00 1007.0
23 TraesCS5B01G242500 chr5D 80.995 663 98 20 1214 1865 357396705 357396060 6.640000e-138 501.0
24 TraesCS5B01G242500 chr5D 84.553 246 29 5 3099 3339 357063684 357063443 7.440000e-58 235.0
25 TraesCS5B01G242500 chr5D 81.667 120 20 2 2014 2132 357395944 357395826 1.020000e-16 99.0
26 TraesCS5B01G242500 chr5D 92.157 51 4 0 2064 2114 357370985 357370935 6.170000e-09 73.1
27 TraesCS5B01G242500 chr2B 92.910 804 53 2 3646 4449 731475404 731474605 0.000000e+00 1166.0
28 TraesCS5B01G242500 chr7B 90.988 810 69 2 3641 4449 99740132 99740938 0.000000e+00 1088.0
29 TraesCS5B01G242500 chr7B 82.445 319 53 3 14 330 388163661 388163344 4.380000e-70 276.0
30 TraesCS5B01G242500 chr4B 89.877 810 75 4 3641 4449 420092212 420091409 0.000000e+00 1035.0
31 TraesCS5B01G242500 chr4B 87.719 57 6 1 2052 2108 9695555 9695610 1.030000e-06 65.8
32 TraesCS5B01G242500 chr6B 89.039 812 80 5 3641 4449 8104175 8103370 0.000000e+00 998.0
33 TraesCS5B01G242500 chr4D 88.656 811 82 7 3641 4449 101626909 101627711 0.000000e+00 979.0
34 TraesCS5B01G242500 chr4D 83.562 73 10 2 2043 2114 5580139 5580210 2.870000e-07 67.6
35 TraesCS5B01G242500 chr4D 87.719 57 6 1 2052 2108 5573126 5573181 1.030000e-06 65.8
36 TraesCS5B01G242500 chr3D 92.208 693 47 4 3641 4332 168848993 168848307 0.000000e+00 974.0
37 TraesCS5B01G242500 chr3D 77.515 507 93 17 4 493 85217185 85216683 7.280000e-73 285.0
38 TraesCS5B01G242500 chr3D 79.245 424 73 11 1 413 170077675 170078094 9.420000e-72 281.0
39 TraesCS5B01G242500 chr6D 88.010 809 92 3 3641 4449 25466770 25465967 0.000000e+00 952.0
40 TraesCS5B01G242500 chr6A 86.453 812 101 7 3640 4449 17036674 17037478 0.000000e+00 881.0
41 TraesCS5B01G242500 chr4A 86.436 811 102 6 3641 4449 717905403 717906207 0.000000e+00 881.0
42 TraesCS5B01G242500 chr4A 88.462 52 6 0 2063 2114 597944913 597944862 3.720000e-06 63.9
43 TraesCS5B01G242500 chr3B 80.271 664 100 21 1226 1865 148500145 148499489 5.210000e-129 472.0
44 TraesCS5B01G242500 chr3B 89.091 55 6 0 1636 1690 605016971 605016917 7.990000e-08 69.4
45 TraesCS5B01G242500 chr3A 79.310 464 70 16 4 449 426868182 426867727 7.230000e-78 302.0
46 TraesCS5B01G242500 chr3A 85.345 116 17 0 2920 3035 115848045 115847930 2.170000e-23 121.0
47 TraesCS5B01G242500 chr3A 75.000 228 46 10 1346 1566 600319771 600319548 1.320000e-15 95.3
48 TraesCS5B01G242500 chr2D 77.932 503 92 9 1 485 606408062 606408563 3.360000e-76 296.0
49 TraesCS5B01G242500 chr2D 77.778 504 88 16 1 485 337853161 337853659 5.630000e-74 289.0
50 TraesCS5B01G242500 chr7D 84.946 93 13 1 368 460 3104802 3104711 4.740000e-15 93.5
51 TraesCS5B01G242500 chr7D 90.000 60 5 1 373 432 3158971 3159029 4.770000e-10 76.8


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 TraesCS5B01G242500 chr5B 421858392 421862840 4448 True 8216.000000 8216 100.000000 1 4449 1 chr5B.!!$R2 4448
1 TraesCS5B01G242500 chr5B 421836014 421838199 2185 True 752.000000 948 81.827500 1003 3339 2 chr5B.!!$R5 2336
2 TraesCS5B01G242500 chr5B 421997887 421998529 642 True 503.000000 503 81.089000 1214 1865 1 chr5B.!!$R3 651
3 TraesCS5B01G242500 chr5B 422039865 422040744 879 True 272.500000 446 80.592500 1214 2132 2 chr5B.!!$R6 918
4 TraesCS5B01G242500 chr5A 458325368 458332551 7183 True 1493.733333 3323 90.956333 4 3641 3 chr5A.!!$R6 3637
5 TraesCS5B01G242500 chr5A 458318389 458320565 2176 True 735.000000 965 81.876000 1001 3339 2 chr5A.!!$R5 2338
6 TraesCS5B01G242500 chr5A 458493134 458493921 787 True 647.000000 647 81.740000 746 1551 1 chr5A.!!$R2 805
7 TraesCS5B01G242500 chr5A 458524549 458525195 646 True 501.000000 501 80.988000 1208 1864 1 chr5A.!!$R3 656
8 TraesCS5B01G242500 chr5A 458561582 458562229 647 True 497.000000 497 80.960000 1214 1865 1 chr5A.!!$R4 651
9 TraesCS5B01G242500 chr5D 357078179 357081725 3546 True 1575.000000 1921 90.971667 16 3531 3 chr5D.!!$R3 3515
10 TraesCS5B01G242500 chr5D 357063443 357065637 2194 True 621.000000 1007 83.693000 1001 3339 2 chr5D.!!$R2 2338
11 TraesCS5B01G242500 chr5D 357395826 357396705 879 True 300.000000 501 81.331000 1214 2132 2 chr5D.!!$R4 918
12 TraesCS5B01G242500 chr2B 731474605 731475404 799 True 1166.000000 1166 92.910000 3646 4449 1 chr2B.!!$R1 803
13 TraesCS5B01G242500 chr7B 99740132 99740938 806 False 1088.000000 1088 90.988000 3641 4449 1 chr7B.!!$F1 808
14 TraesCS5B01G242500 chr4B 420091409 420092212 803 True 1035.000000 1035 89.877000 3641 4449 1 chr4B.!!$R1 808
15 TraesCS5B01G242500 chr6B 8103370 8104175 805 True 998.000000 998 89.039000 3641 4449 1 chr6B.!!$R1 808
16 TraesCS5B01G242500 chr4D 101626909 101627711 802 False 979.000000 979 88.656000 3641 4449 1 chr4D.!!$F3 808
17 TraesCS5B01G242500 chr3D 168848307 168848993 686 True 974.000000 974 92.208000 3641 4332 1 chr3D.!!$R2 691
18 TraesCS5B01G242500 chr3D 85216683 85217185 502 True 285.000000 285 77.515000 4 493 1 chr3D.!!$R1 489
19 TraesCS5B01G242500 chr6D 25465967 25466770 803 True 952.000000 952 88.010000 3641 4449 1 chr6D.!!$R1 808
20 TraesCS5B01G242500 chr6A 17036674 17037478 804 False 881.000000 881 86.453000 3640 4449 1 chr6A.!!$F1 809
21 TraesCS5B01G242500 chr4A 717905403 717906207 804 False 881.000000 881 86.436000 3641 4449 1 chr4A.!!$F1 808
22 TraesCS5B01G242500 chr3B 148499489 148500145 656 True 472.000000 472 80.271000 1226 1865 1 chr3B.!!$R1 639
23 TraesCS5B01G242500 chr2D 606408062 606408563 501 False 296.000000 296 77.932000 1 485 1 chr2D.!!$F2 484

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
852 884 0.106569 TCCTTCCGCCCGATGTACTA 60.107 55.0 0.0 0.0 0.0 1.82 F
1926 2056 0.177141 GCGGCATCTTGGTAGGTACA 59.823 55.0 0.0 0.0 0.0 2.90 F
2514 2654 0.172803 GCATCGACCACTACGTCCTT 59.827 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2079 0.591659 GCGGGACAAAAAGAGGTGAC 59.408 55.0 0.0 0.0 0.00 3.67 R
3141 3392 0.176680 ACTGCTGAACATAGCCTCCG 59.823 55.0 0.0 0.0 43.02 4.63 R
4205 7979 0.106217 ACCTTGTGTGGGGAACTTGG 60.106 55.0 0.0 0.0 0.00 3.61 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
157 164 2.874086 CGTCATCAGCATTGAATAGGCA 59.126 45.455 0.00 0.00 36.78 4.75
265 272 1.568612 CCGTCTTCAATGTGCAGCGT 61.569 55.000 0.00 0.00 0.00 5.07
357 373 0.322456 CAGGATGGTCAAAAGCGGGA 60.322 55.000 0.00 0.00 0.00 5.14
362 378 1.228154 GGTCAAAAGCGGGAGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
424 445 2.243602 TTTACGGGAGAAAGTGCGTT 57.756 45.000 0.00 0.00 0.00 4.84
468 489 2.332654 GCCCGCGTTGGATGACTTT 61.333 57.895 4.92 0.00 42.00 2.66
477 498 1.052617 TGGATGACTTTCACGGTCCA 58.947 50.000 0.00 0.00 33.63 4.02
533 554 1.079405 TCGACGTGAAAGATGCCCC 60.079 57.895 0.00 0.00 0.00 5.80
550 571 2.627699 GCCCCAAACATTTGAGAGTTCA 59.372 45.455 5.91 0.00 40.55 3.18
584 605 4.074970 TGAACTCCTCATTTTGCTCTTCC 58.925 43.478 0.00 0.00 0.00 3.46
588 609 4.895297 ACTCCTCATTTTGCTCTTCCAAAA 59.105 37.500 2.98 2.98 45.50 2.44
690 717 4.687018 ACGTAATCAAGTGCGTTTACATCA 59.313 37.500 0.00 0.00 33.54 3.07
694 721 3.937814 TCAAGTGCGTTTACATCAGGAT 58.062 40.909 0.00 0.00 0.00 3.24
752 779 5.422012 ACATTTACCATTTCCATCTTGGTCC 59.578 40.000 0.00 0.00 42.65 4.46
766 793 6.821665 CCATCTTGGTCCTAATCGAAGTAAAA 59.178 38.462 0.00 0.00 31.35 1.52
793 820 7.930513 GCAGTAAGCCCATTATGTTAAAATC 57.069 36.000 0.00 0.00 37.23 2.17
820 851 1.988834 GCCGGCATTCTTAACCCACG 61.989 60.000 24.80 0.00 0.00 4.94
841 873 0.175989 CTAGAGTTGGGTCCTTCCGC 59.824 60.000 0.00 0.00 37.00 5.54
842 874 1.262640 TAGAGTTGGGTCCTTCCGCC 61.263 60.000 0.00 0.00 37.00 6.13
843 875 3.623703 GAGTTGGGTCCTTCCGCCC 62.624 68.421 0.00 0.00 45.04 6.13
852 884 0.106569 TCCTTCCGCCCGATGTACTA 60.107 55.000 0.00 0.00 0.00 1.82
853 885 0.966920 CCTTCCGCCCGATGTACTAT 59.033 55.000 0.00 0.00 0.00 2.12
855 887 2.094854 CCTTCCGCCCGATGTACTATAC 60.095 54.545 0.00 0.00 0.00 1.47
874 906 3.627732 ACGGTTAGCTATCATCGTCTG 57.372 47.619 0.00 0.00 0.00 3.51
876 908 3.821600 ACGGTTAGCTATCATCGTCTGAT 59.178 43.478 0.00 8.03 46.49 2.90
984 1020 2.941064 GCTGCATGCTTCTATTCAGACA 59.059 45.455 20.33 0.00 38.95 3.41
986 1022 4.439968 CTGCATGCTTCTATTCAGACAGA 58.560 43.478 20.33 0.00 0.00 3.41
987 1023 4.186926 TGCATGCTTCTATTCAGACAGAC 58.813 43.478 20.33 0.00 0.00 3.51
988 1024 4.081254 TGCATGCTTCTATTCAGACAGACT 60.081 41.667 20.33 0.00 0.00 3.24
989 1025 4.270566 GCATGCTTCTATTCAGACAGACTG 59.729 45.833 11.37 0.00 46.97 3.51
1015 1089 8.721133 ACTGATTACACCATATATACACCTCA 57.279 34.615 0.00 0.00 0.00 3.86
1048 1122 5.527214 ACTGATCTTTCACACGATCACAAAA 59.473 36.000 0.00 0.00 40.62 2.44
1064 1139 3.059166 ACAAAATCACAAGCGAAATGGC 58.941 40.909 0.00 0.00 0.00 4.40
1163 1238 4.645535 CTCAGGAAGTTCATCTTGTCCAA 58.354 43.478 5.01 0.00 36.40 3.53
1204 1280 2.336478 CGGGCCCGTAATGCAAACA 61.336 57.895 36.64 0.00 34.35 2.83
1205 1281 1.214325 GGGCCCGTAATGCAAACAC 59.786 57.895 5.69 0.00 0.00 3.32
1218 1294 0.474184 CAAACACACCTGAGGGACCT 59.526 55.000 2.38 0.00 36.25 3.85
1222 1301 0.833834 CACACCTGAGGGACCTGACT 60.834 60.000 2.38 0.00 36.25 3.41
1543 1625 4.379243 ACGGCAAGACCCTGAGCG 62.379 66.667 0.00 0.00 33.26 5.03
1578 1660 3.463944 CTGGAACAACCGTAAGTGTCTT 58.536 45.455 0.00 0.00 42.61 3.01
1589 1692 4.344448 CGTAAGTGTCTTAGCAGAGTAGC 58.656 47.826 0.00 0.00 0.00 3.58
1600 1727 2.616376 AGCAGAGTAGCTACACTGATCG 59.384 50.000 39.07 22.34 44.30 3.69
1611 1741 3.251479 ACACTGATCGCTGATGCTTAA 57.749 42.857 0.00 0.00 36.97 1.85
1620 1750 3.618594 TCGCTGATGCTTAATGAACTGAC 59.381 43.478 0.00 0.00 36.97 3.51
1628 1758 8.668353 TGATGCTTAATGAACTGACAAGATTAC 58.332 33.333 0.00 0.00 0.00 1.89
1629 1759 7.977789 TGCTTAATGAACTGACAAGATTACA 57.022 32.000 0.00 0.00 0.00 2.41
1644 1774 0.953471 TTACACGATGTGCAGTGGCC 60.953 55.000 8.49 0.00 42.25 5.36
1851 1981 2.180769 CACTACGTGCCGCAGCTA 59.819 61.111 0.00 0.00 40.80 3.32
1921 2051 1.592669 CTCCGCGGCATCTTGGTAG 60.593 63.158 23.51 5.10 0.00 3.18
1926 2056 0.177141 GCGGCATCTTGGTAGGTACA 59.823 55.000 0.00 0.00 0.00 2.90
1947 2077 4.870426 ACAAGTACCTAGTTTGATCGCATG 59.130 41.667 0.00 0.00 0.00 4.06
1949 2079 4.433615 AGTACCTAGTTTGATCGCATGTG 58.566 43.478 0.00 0.00 0.00 3.21
1971 2101 1.407258 CACCTCTTTTTGTCCCGCAAA 59.593 47.619 0.00 0.00 44.52 3.68
1997 2130 3.141398 CCACCCATATCCATTTCTCGTG 58.859 50.000 0.00 0.00 0.00 4.35
1998 2131 3.141398 CACCCATATCCATTTCTCGTGG 58.859 50.000 0.00 0.00 38.11 4.94
2007 2140 4.055360 TCCATTTCTCGTGGCGTTATATG 58.945 43.478 0.00 0.00 36.66 1.78
2230 2369 1.123928 CCCCGATCTGCCTTAAGTCT 58.876 55.000 0.97 0.00 0.00 3.24
2231 2370 2.317040 CCCCGATCTGCCTTAAGTCTA 58.683 52.381 0.97 0.00 0.00 2.59
2514 2654 0.172803 GCATCGACCACTACGTCCTT 59.827 55.000 0.00 0.00 0.00 3.36
2703 2846 3.758973 TTTGAGCGCAACACCCGGA 62.759 57.895 11.47 0.00 32.79 5.14
2708 2851 1.883084 GCGCAACACCCGGATCTAG 60.883 63.158 0.73 0.00 0.00 2.43
2725 2868 3.113322 TCTAGCTAATTTGCACTACGCG 58.887 45.455 14.27 3.53 46.97 6.01
2743 2902 2.158449 CGCGACTTCATTTCTTTCAGCT 59.842 45.455 0.00 0.00 0.00 4.24
2745 2904 3.910767 GCGACTTCATTTCTTTCAGCTTG 59.089 43.478 0.00 0.00 0.00 4.01
2783 2942 1.607467 GCCCAGTTTCCATGGTGCT 60.607 57.895 12.58 5.66 35.96 4.40
2805 2964 5.293079 GCTAACCATCAGAAAGCTAGTCAAG 59.707 44.000 0.00 0.00 0.00 3.02
2858 3094 7.748691 ACTATATATGCATGCACACAATGAA 57.251 32.000 25.37 3.14 0.00 2.57
2881 3117 6.674694 ACATTGAGCAGAATAAAGTAGCTG 57.325 37.500 0.00 0.00 35.36 4.24
3069 3305 6.364568 TCAGAAATGGACATCAGAAAGAGA 57.635 37.500 0.00 0.00 0.00 3.10
3122 3373 4.320546 TCCTGTGATGAAATTGATGGGT 57.679 40.909 0.00 0.00 0.00 4.51
3130 3381 5.777223 TGATGAAATTGATGGGTTTGTGGTA 59.223 36.000 0.00 0.00 0.00 3.25
3132 3383 5.144100 TGAAATTGATGGGTTTGTGGTAGT 58.856 37.500 0.00 0.00 0.00 2.73
3136 3387 6.584185 ATTGATGGGTTTGTGGTAGTTTAC 57.416 37.500 0.00 0.00 0.00 2.01
3141 3392 3.817084 GGGTTTGTGGTAGTTTACAGGTC 59.183 47.826 0.00 0.00 0.00 3.85
3366 3622 2.575921 ATTGACTCCCTCTCCATCCA 57.424 50.000 0.00 0.00 0.00 3.41
3396 3653 5.607119 ATCATCGGTTACACACAAACTTC 57.393 39.130 0.00 0.00 0.00 3.01
3452 3721 5.606348 AACCCTTGTGTGCTTATGAAAAA 57.394 34.783 0.00 0.00 0.00 1.94
3509 3778 1.953559 TCTGCCGGATAAGCATGTTC 58.046 50.000 5.05 0.00 40.04 3.18
3522 3791 9.387123 GGATAAGCATGTTCGAATTTTAATCTC 57.613 33.333 0.00 0.00 0.00 2.75
3523 3792 8.993852 ATAAGCATGTTCGAATTTTAATCTCG 57.006 30.769 0.00 0.00 0.00 4.04
3532 3801 6.642917 TCGAATTTTAATCTCGGCGTATTTC 58.357 36.000 6.85 2.17 33.44 2.17
3533 3802 5.844396 CGAATTTTAATCTCGGCGTATTTCC 59.156 40.000 6.85 0.00 0.00 3.13
3534 3803 6.510478 CGAATTTTAATCTCGGCGTATTTCCA 60.510 38.462 6.85 0.00 0.00 3.53
3550 3822 6.632834 CGTATTTCCACTTGTTAAGCATATGC 59.367 38.462 20.36 20.36 42.49 3.14
3586 7313 7.783090 ATAGGATATTCATGATCATTGTCGC 57.217 36.000 5.16 0.00 0.00 5.19
3587 7314 5.554070 AGGATATTCATGATCATTGTCGCA 58.446 37.500 5.16 0.00 0.00 5.10
3590 7317 7.494952 AGGATATTCATGATCATTGTCGCATAG 59.505 37.037 5.16 0.00 0.00 2.23
3622 7395 4.025979 CGTTGTAGAATACCAATCGGCTTC 60.026 45.833 0.00 0.00 42.12 3.86
3648 7421 8.371699 CCCCTTACCACATTTTCATTTTTAGAA 58.628 33.333 0.00 0.00 0.00 2.10
3716 7489 2.741228 GCACAACCAACATCCAAGCAAA 60.741 45.455 0.00 0.00 0.00 3.68
3743 7517 6.657541 ACAGTAACAGGACAGACAAAGAAAAA 59.342 34.615 0.00 0.00 0.00 1.94
3760 7534 5.941788 AGAAAAAGAGTTCAGGTACATGGT 58.058 37.500 7.81 0.00 0.00 3.55
3799 7573 0.652592 CGCAGGCCAGAAATAAGACG 59.347 55.000 5.01 0.00 0.00 4.18
3889 7663 0.829990 TCTTGGACGCCATAGCATCA 59.170 50.000 0.00 0.00 39.83 3.07
3899 7673 1.202687 CCATAGCATCAAAGGCCTCGA 60.203 52.381 5.23 6.49 0.00 4.04
3900 7674 2.564771 CATAGCATCAAAGGCCTCGAA 58.435 47.619 5.23 0.00 0.00 3.71
3903 7677 2.450476 AGCATCAAAGGCCTCGAAATT 58.550 42.857 5.23 0.00 0.00 1.82
4003 7777 7.152645 GGAAGATATGCTCGATGGTAAACTTA 58.847 38.462 0.00 0.00 0.00 2.24
4013 7787 7.705325 GCTCGATGGTAAACTTATTTCTAGTGA 59.295 37.037 0.00 0.00 0.00 3.41
4205 7979 3.626028 AGAAAATGTGCTCCGTGTTTC 57.374 42.857 0.00 0.00 0.00 2.78
4224 7999 0.106217 CCAAGTTCCCCACACAAGGT 60.106 55.000 0.00 0.00 0.00 3.50
4239 8014 3.684305 CACAAGGTGCATCTATTCGAACA 59.316 43.478 0.00 0.00 0.00 3.18
4240 8015 3.935203 ACAAGGTGCATCTATTCGAACAG 59.065 43.478 0.00 0.00 0.00 3.16
4244 8019 2.115427 TGCATCTATTCGAACAGGGGA 58.885 47.619 3.15 0.00 0.00 4.81
4365 8141 4.743955 GCACTTGAACTTGGAAGTAGGAGT 60.744 45.833 0.00 0.00 38.57 3.85
4370 8146 0.984230 CTTGGAAGTAGGAGTGCCCA 59.016 55.000 0.00 0.00 37.41 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.171828 ATTGACACACCCGGACGCA 62.172 57.895 0.73 0.00 0.00 5.24
157 164 3.667282 CACGTCTCCGGTGTCCGT 61.667 66.667 14.86 14.86 46.80 4.69
192 199 4.555709 TGAAGTGGTGCGCCGGTT 62.556 61.111 12.58 7.27 37.67 4.44
204 211 0.687354 ACTGCCTCCGTCATTGAAGT 59.313 50.000 0.00 0.00 0.00 3.01
265 272 3.925362 ATGCCGTTGTACAGCGCGA 62.925 57.895 24.61 13.94 33.61 5.87
330 337 1.264749 TTGACCATCCTGACCCCTCG 61.265 60.000 0.00 0.00 0.00 4.63
338 345 0.322456 TCCCGCTTTTGACCATCCTG 60.322 55.000 0.00 0.00 0.00 3.86
339 346 0.035056 CTCCCGCTTTTGACCATCCT 60.035 55.000 0.00 0.00 0.00 3.24
342 349 0.609131 CCACTCCCGCTTTTGACCAT 60.609 55.000 0.00 0.00 0.00 3.55
357 373 0.390735 GCGTCCGGACAATAACCACT 60.391 55.000 32.80 0.00 0.00 4.00
384 403 1.052124 TGGAGACAAACGTGGGGAGT 61.052 55.000 0.00 0.00 37.44 3.85
468 489 2.910479 ACGCTGTCTGGACCGTGA 60.910 61.111 11.46 0.00 30.29 4.35
477 498 2.581354 GCCTGGATCACGCTGTCT 59.419 61.111 0.00 0.00 0.00 3.41
533 554 5.471456 ACCTAGCTGAACTCTCAAATGTTTG 59.529 40.000 0.00 0.00 39.48 2.93
550 571 0.977395 GGAGTTCACCACACCTAGCT 59.023 55.000 0.00 0.00 33.41 3.32
588 609 9.325198 GCATTTTTAATCGATCCCCTAAATTTT 57.675 29.630 0.00 0.00 0.00 1.82
590 611 8.250143 AGCATTTTTAATCGATCCCCTAAATT 57.750 30.769 0.00 0.00 0.00 1.82
690 717 6.856757 AGATGTTTTATATTCCAGGCATCCT 58.143 36.000 0.00 0.00 33.93 3.24
752 779 7.126398 GCTTACTGCCATTTTACTTCGATTAG 58.874 38.462 0.00 0.00 35.15 1.73
820 851 0.542333 GGAAGGACCCAACTCTAGCC 59.458 60.000 0.00 0.00 0.00 3.93
841 873 3.755378 AGCTAACCGTATAGTACATCGGG 59.245 47.826 17.33 5.93 46.06 5.14
842 874 6.314648 TGATAGCTAACCGTATAGTACATCGG 59.685 42.308 0.00 13.51 46.98 4.18
843 875 7.299787 TGATAGCTAACCGTATAGTACATCG 57.700 40.000 0.00 0.00 0.00 3.84
844 876 8.063038 CGATGATAGCTAACCGTATAGTACATC 58.937 40.741 0.00 0.00 0.00 3.06
852 884 5.001874 TCAGACGATGATAGCTAACCGTAT 58.998 41.667 0.00 0.00 31.12 3.06
853 885 4.383173 TCAGACGATGATAGCTAACCGTA 58.617 43.478 0.00 0.00 31.12 4.02
855 887 3.898517 TCAGACGATGATAGCTAACCG 57.101 47.619 0.00 1.78 31.12 4.44
874 906 3.255379 GGCGCGAACGGTCAGATC 61.255 66.667 12.10 0.00 40.57 2.75
876 908 4.063967 ATGGCGCGAACGGTCAGA 62.064 61.111 12.10 0.00 40.57 3.27
984 1020 9.588096 TGTATATATGGTGTAATCAGTCAGTCT 57.412 33.333 0.00 0.00 0.00 3.24
986 1022 8.585881 GGTGTATATATGGTGTAATCAGTCAGT 58.414 37.037 0.00 0.00 0.00 3.41
987 1023 8.807118 AGGTGTATATATGGTGTAATCAGTCAG 58.193 37.037 0.00 0.00 0.00 3.51
988 1024 8.721133 AGGTGTATATATGGTGTAATCAGTCA 57.279 34.615 0.00 0.00 0.00 3.41
989 1025 8.803235 TGAGGTGTATATATGGTGTAATCAGTC 58.197 37.037 0.00 0.00 0.00 3.51
990 1026 8.721133 TGAGGTGTATATATGGTGTAATCAGT 57.279 34.615 0.00 0.00 0.00 3.41
991 1027 9.424319 GTTGAGGTGTATATATGGTGTAATCAG 57.576 37.037 0.00 0.00 0.00 2.90
992 1028 8.929487 TGTTGAGGTGTATATATGGTGTAATCA 58.071 33.333 0.00 0.00 0.00 2.57
993 1029 9.424319 CTGTTGAGGTGTATATATGGTGTAATC 57.576 37.037 0.00 0.00 0.00 1.75
994 1030 9.154632 TCTGTTGAGGTGTATATATGGTGTAAT 57.845 33.333 0.00 0.00 0.00 1.89
995 1031 8.418662 GTCTGTTGAGGTGTATATATGGTGTAA 58.581 37.037 0.00 0.00 0.00 2.41
999 1073 6.839134 TCTGTCTGTTGAGGTGTATATATGGT 59.161 38.462 0.00 0.00 0.00 3.55
1015 1089 5.053145 GTGTGAAAGATCAGTCTGTCTGTT 58.947 41.667 0.00 0.00 43.97 3.16
1048 1122 0.813184 CCAGCCATTTCGCTTGTGAT 59.187 50.000 0.00 0.00 36.82 3.06
1064 1139 0.321653 GAAGGTAGTGGTGTGCCCAG 60.322 60.000 0.00 0.00 46.45 4.45
1163 1238 0.257616 AGCTAGCCTCTTCTCGGACT 59.742 55.000 12.13 0.00 0.00 3.85
1204 1280 0.543174 GAGTCAGGTCCCTCAGGTGT 60.543 60.000 0.00 0.00 0.00 4.16
1205 1281 0.542938 TGAGTCAGGTCCCTCAGGTG 60.543 60.000 0.00 0.00 32.93 4.00
1218 1294 4.451150 GCGTCGGCCCATGAGTCA 62.451 66.667 0.00 0.00 0.00 3.41
1543 1625 0.899717 TTCCAGGCATGCTTGTTCCC 60.900 55.000 25.99 4.43 0.00 3.97
1578 1660 3.810386 CGATCAGTGTAGCTACTCTGCTA 59.190 47.826 35.20 25.65 43.65 3.49
1600 1727 4.952262 TGTCAGTTCATTAAGCATCAGC 57.048 40.909 0.00 0.00 42.56 4.26
1611 1741 6.091305 CACATCGTGTAATCTTGTCAGTTCAT 59.909 38.462 0.00 0.00 0.00 2.57
1620 1750 3.181517 CCACTGCACATCGTGTAATCTTG 60.182 47.826 3.47 0.00 35.75 3.02
1628 1758 2.260154 TTGGCCACTGCACATCGTG 61.260 57.895 3.88 0.00 40.13 4.35
1629 1759 2.112928 TTGGCCACTGCACATCGT 59.887 55.556 3.88 0.00 40.13 3.73
1644 1774 2.663602 CGACTCCAAGAAGATCACGTTG 59.336 50.000 0.00 0.00 0.00 4.10
1687 1817 4.368808 CGGGTTGTTGCTCGCGTG 62.369 66.667 5.77 4.44 35.78 5.34
1851 1981 0.821517 TGTATTCGATCACGGTGGCT 59.178 50.000 8.50 0.00 40.21 4.75
1921 2051 4.802563 GCGATCAAACTAGGTACTTGTACC 59.197 45.833 19.22 19.22 44.86 3.34
1926 2056 4.870426 CACATGCGATCAAACTAGGTACTT 59.130 41.667 0.00 0.00 41.75 2.24
1947 2077 1.602377 CGGGACAAAAAGAGGTGACAC 59.398 52.381 0.00 0.00 0.00 3.67
1949 2079 0.591659 GCGGGACAAAAAGAGGTGAC 59.408 55.000 0.00 0.00 0.00 3.67
1971 2101 4.315993 AGAAATGGATATGGGTGGGTACT 58.684 43.478 0.00 0.00 0.00 2.73
1997 2130 4.418392 CCGACCTACATACATATAACGCC 58.582 47.826 0.00 0.00 0.00 5.68
1998 2131 3.855950 GCCGACCTACATACATATAACGC 59.144 47.826 0.00 0.00 0.00 4.84
2007 2140 2.902705 TGGATTGCCGACCTACATAC 57.097 50.000 0.00 0.00 36.79 2.39
2181 2317 1.293924 GTGGAGATCGATGTTGCCTG 58.706 55.000 0.54 0.00 0.00 4.85
2421 2561 8.688747 TGTGAATGGCCAAAGATTTTTATTTT 57.311 26.923 10.96 0.00 0.00 1.82
2425 2565 6.418057 ACTGTGAATGGCCAAAGATTTTTA 57.582 33.333 10.96 0.00 0.00 1.52
2514 2654 1.164411 CGCCATTGTTGAGGTAAGCA 58.836 50.000 0.00 0.00 0.00 3.91
2623 2766 6.896021 AGCAGGTATCGTGTGTAATATACT 57.104 37.500 0.00 0.00 0.00 2.12
2677 2820 2.020720 TGTTGCGCTCAAAGGAAAAGA 58.979 42.857 9.73 0.00 33.37 2.52
2703 2846 3.736252 CGCGTAGTGCAAATTAGCTAGAT 59.264 43.478 0.00 0.00 46.97 1.98
2708 2851 1.659098 AGTCGCGTAGTGCAAATTAGC 59.341 47.619 5.77 0.00 46.97 3.09
2725 2868 5.240403 AGTCCAAGCTGAAAGAAATGAAGTC 59.760 40.000 0.00 0.00 34.07 3.01
2743 2902 3.119388 CCGTCGTTATAGTCCAAGTCCAA 60.119 47.826 0.00 0.00 0.00 3.53
2745 2904 2.797439 GCCGTCGTTATAGTCCAAGTCC 60.797 54.545 0.00 0.00 0.00 3.85
2783 2942 5.178797 GCTTGACTAGCTTTCTGATGGTTA 58.821 41.667 0.00 0.00 46.77 2.85
2805 2964 0.730840 GCCATACACTTAACCCACGC 59.269 55.000 0.00 0.00 0.00 5.34
2858 3094 5.065731 GCAGCTACTTTATTCTGCTCAATGT 59.934 40.000 5.89 0.00 46.00 2.71
2881 3117 3.846360 TCTAGTTAGAAACCTGAAGCGC 58.154 45.455 0.00 0.00 0.00 5.92
3122 3373 3.387374 TCCGACCTGTAAACTACCACAAA 59.613 43.478 0.00 0.00 0.00 2.83
3130 3381 2.226962 TAGCCTCCGACCTGTAAACT 57.773 50.000 0.00 0.00 0.00 2.66
3132 3383 2.463752 ACATAGCCTCCGACCTGTAAA 58.536 47.619 0.00 0.00 0.00 2.01
3136 3387 0.824109 TGAACATAGCCTCCGACCTG 59.176 55.000 0.00 0.00 0.00 4.00
3141 3392 0.176680 ACTGCTGAACATAGCCTCCG 59.823 55.000 0.00 0.00 43.02 4.63
3346 3602 3.309296 GTGGATGGAGAGGGAGTCAATA 58.691 50.000 0.00 0.00 0.00 1.90
3366 3622 6.403049 TGTGTGTAACCGATGATTATTCTGT 58.597 36.000 0.00 0.00 34.36 3.41
3491 3760 0.583438 CGAACATGCTTATCCGGCAG 59.417 55.000 0.00 0.00 43.15 4.85
3509 3778 5.844396 GGAAATACGCCGAGATTAAAATTCG 59.156 40.000 0.00 1.10 0.00 3.34
3522 3791 3.726782 GCTTAACAAGTGGAAATACGCCG 60.727 47.826 0.00 0.00 0.00 6.46
3523 3792 3.189702 TGCTTAACAAGTGGAAATACGCC 59.810 43.478 0.00 0.00 0.00 5.68
3566 7293 8.416485 TCTATGCGACAATGATCATGAATATC 57.584 34.615 9.46 2.33 0.00 1.63
3567 7294 8.959705 ATCTATGCGACAATGATCATGAATAT 57.040 30.769 9.46 2.79 0.00 1.28
3573 7300 7.554211 ACATCTATCTATGCGACAATGATCAT 58.446 34.615 1.18 1.18 0.00 2.45
3586 7313 9.776158 GGTATTCTACAACGACATCTATCTATG 57.224 37.037 0.00 0.00 0.00 2.23
3587 7314 9.516546 TGGTATTCTACAACGACATCTATCTAT 57.483 33.333 0.00 0.00 0.00 1.98
3590 7317 9.130312 GATTGGTATTCTACAACGACATCTATC 57.870 37.037 0.00 0.00 0.00 2.08
3622 7395 7.902087 TCTAAAAATGAAAATGTGGTAAGGGG 58.098 34.615 0.00 0.00 0.00 4.79
3648 7421 3.339253 AAGTCGGGCGTATACCTTTTT 57.661 42.857 0.00 0.00 0.00 1.94
3655 7428 7.331687 GGCTTTATTTATAAAGTCGGGCGTATA 59.668 37.037 18.51 0.00 46.78 1.47
3683 7456 0.321671 GGTTGTGCTACTCTGCCTGA 59.678 55.000 0.00 0.00 0.00 3.86
3716 7489 4.161565 TCTTTGTCTGTCCTGTTACTGTGT 59.838 41.667 0.00 0.00 0.00 3.72
3743 7517 5.030147 TGGATAACCATGTACCTGAACTCT 58.970 41.667 0.00 0.00 41.77 3.24
3799 7573 7.610305 TCTTAAACCATGGTGTCTCCTTTAATC 59.390 37.037 20.60 0.00 37.07 1.75
3889 7663 2.952310 GGATGCTAATTTCGAGGCCTTT 59.048 45.455 6.77 0.00 0.00 3.11
3899 7673 7.753630 AGATCATTGACTAGGGATGCTAATTT 58.246 34.615 0.00 0.00 0.00 1.82
3900 7674 7.327064 AGATCATTGACTAGGGATGCTAATT 57.673 36.000 0.00 0.00 0.00 1.40
3903 7677 4.774726 GGAGATCATTGACTAGGGATGCTA 59.225 45.833 0.00 0.00 0.00 3.49
4003 7777 4.020573 TGGTCGTTGTGGATCACTAGAAAT 60.021 41.667 0.00 0.00 35.11 2.17
4013 7787 2.699954 GATCTGTTGGTCGTTGTGGAT 58.300 47.619 0.00 0.00 0.00 3.41
4064 7838 9.508642 GGTCAATGGTTTATTTGGGAATTAAAA 57.491 29.630 0.00 0.00 0.00 1.52
4065 7839 8.660435 TGGTCAATGGTTTATTTGGGAATTAAA 58.340 29.630 0.00 0.00 0.00 1.52
4066 7840 8.207350 TGGTCAATGGTTTATTTGGGAATTAA 57.793 30.769 0.00 0.00 0.00 1.40
4067 7841 7.798710 TGGTCAATGGTTTATTTGGGAATTA 57.201 32.000 0.00 0.00 0.00 1.40
4205 7979 0.106217 ACCTTGTGTGGGGAACTTGG 60.106 55.000 0.00 0.00 0.00 3.61
4224 7999 2.115427 TCCCCTGTTCGAATAGATGCA 58.885 47.619 22.00 3.70 0.00 3.96
4239 8014 0.331616 CCGGAAAAGGAACATCCCCT 59.668 55.000 0.00 0.00 37.19 4.79
4240 8015 0.330267 TCCGGAAAAGGAACATCCCC 59.670 55.000 0.00 0.00 37.19 4.81
4244 8019 3.506398 ACCAAATCCGGAAAAGGAACAT 58.494 40.909 21.88 1.45 44.50 2.71
4365 8141 2.235016 ACGCTAAACTGATTTTGGGCA 58.765 42.857 0.00 0.00 37.11 5.36
4370 8146 7.448748 AATCCTTGTACGCTAAACTGATTTT 57.551 32.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.