Multiple sequence alignment - TraesCS7D01G128200

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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 TraesCS7D01G128200 chr7D 100.000 2513 0 0 1 2513 80463561 80461049 0.000000e+00 4641.0
1 TraesCS7D01G128200 chr7D 90.216 879 66 10 1099 1961 80417341 80416467 0.000000e+00 1129.0
2 TraesCS7D01G128200 chr7D 84.383 1127 97 40 514 1622 80199104 80198039 0.000000e+00 1033.0
3 TraesCS7D01G128200 chr7D 85.950 726 53 25 909 1622 80298631 80297943 0.000000e+00 730.0
4 TraesCS7D01G128200 chr7D 87.255 408 32 7 2067 2462 80323884 80323485 4.930000e-122 448.0
5 TraesCS7D01G128200 chr7D 89.076 357 28 9 101 454 80384751 80384403 1.380000e-117 433.0
6 TraesCS7D01G128200 chr7D 86.719 384 32 11 130 509 80302005 80301637 2.330000e-110 409.0
7 TraesCS7D01G128200 chr7D 86.047 387 34 9 128 509 80200806 80200435 5.040000e-107 398.0
8 TraesCS7D01G128200 chr7D 85.399 363 40 8 1605 1963 80325032 80324679 5.110000e-97 364.0
9 TraesCS7D01G128200 chr7D 84.848 363 42 8 1605 1963 80469751 80469398 1.110000e-93 353.0
10 TraesCS7D01G128200 chr7D 75.789 665 99 36 1279 1921 80383075 80382451 1.900000e-71 279.0
11 TraesCS7D01G128200 chr7D 93.293 164 10 1 2062 2225 80416387 80416225 8.980000e-60 241.0
12 TraesCS7D01G128200 chr7D 90.374 187 12 3 812 992 112411442 112411628 8.980000e-60 241.0
13 TraesCS7D01G128200 chr7D 89.634 164 15 2 2300 2462 80468380 80468218 9.110000e-50 207.0
14 TraesCS7D01G128200 chr7D 86.667 195 15 6 2265 2458 80391345 80391161 3.280000e-49 206.0
15 TraesCS7D01G128200 chr7D 92.929 99 6 1 2067 2165 80468478 80468381 2.610000e-30 143.0
16 TraesCS7D01G128200 chr7D 92.771 83 6 0 1 83 80266883 80266801 1.220000e-23 121.0
17 TraesCS7D01G128200 chr7D 96.774 62 2 0 130 191 80266695 80266634 1.230000e-18 104.0
18 TraesCS7D01G128200 chr7D 80.263 76 12 3 2124 2199 80195754 80195682 1.000000e-03 54.7
19 TraesCS7D01G128200 chr7A 87.500 1160 94 18 812 1958 83142422 83141301 0.000000e+00 1291.0
20 TraesCS7D01G128200 chr7A 82.765 1526 120 58 135 1622 83107366 83105946 0.000000e+00 1229.0
21 TraesCS7D01G128200 chr7A 83.580 676 87 18 1300 1961 83225112 83224447 1.650000e-171 612.0
22 TraesCS7D01G128200 chr7A 92.965 398 25 3 2062 2458 83138694 83138299 6.030000e-161 577.0
23 TraesCS7D01G128200 chr7A 78.114 859 129 36 1092 1927 83157748 83156926 8.080000e-135 490.0
24 TraesCS7D01G128200 chr7A 92.905 296 19 2 2164 2458 83224238 83223944 1.790000e-116 429.0
25 TraesCS7D01G128200 chr7A 80.866 554 50 24 514 1051 83170200 83169687 3.920000e-103 385.0
26 TraesCS7D01G128200 chr7A 87.347 245 14 9 118 361 83148301 83148073 5.330000e-67 265.0
27 TraesCS7D01G128200 chr7A 88.690 168 5 2 395 562 83148076 83147923 2.550000e-45 193.0
28 TraesCS7D01G128200 chr7A 92.793 111 6 2 2062 2171 83224367 83224258 2.590000e-35 159.0
29 TraesCS7D01G128200 chr7A 97.436 39 0 1 84 121 83150472 83150434 5.800000e-07 65.8
30 TraesCS7D01G128200 chr7B 84.391 1166 116 39 514 1666 27487300 27486188 0.000000e+00 1085.0
31 TraesCS7D01G128200 chr7B 82.243 642 92 15 1300 1932 27594697 27594069 3.680000e-148 534.0
32 TraesCS7D01G128200 chr7B 84.916 358 27 10 2125 2462 27495133 27494783 1.110000e-88 337.0
33 TraesCS7D01G128200 chr7B 89.474 247 16 4 1066 1302 27594992 27594746 1.130000e-78 303.0


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 TraesCS7D01G128200 chr7D 80461049 80463561 2512 True 4641.000000 4641 100.000000 1 2513 1 chr7D.!!$R2 2512
1 TraesCS7D01G128200 chr7D 80416225 80417341 1116 True 685.000000 1129 91.754500 1099 2225 2 chr7D.!!$R8 1126
2 TraesCS7D01G128200 chr7D 80297943 80302005 4062 True 569.500000 730 86.334500 130 1622 2 chr7D.!!$R5 1492
3 TraesCS7D01G128200 chr7D 80195682 80200806 5124 True 495.233333 1033 83.564333 128 2199 3 chr7D.!!$R3 2071
4 TraesCS7D01G128200 chr7D 80323485 80325032 1547 True 406.000000 448 86.327000 1605 2462 2 chr7D.!!$R6 857
5 TraesCS7D01G128200 chr7D 80382451 80384751 2300 True 356.000000 433 82.432500 101 1921 2 chr7D.!!$R7 1820
6 TraesCS7D01G128200 chr7D 80468218 80469751 1533 True 234.333333 353 89.137000 1605 2462 3 chr7D.!!$R9 857
7 TraesCS7D01G128200 chr7A 83105946 83107366 1420 True 1229.000000 1229 82.765000 135 1622 1 chr7A.!!$R1 1487
8 TraesCS7D01G128200 chr7A 83138299 83142422 4123 True 934.000000 1291 90.232500 812 2458 2 chr7A.!!$R4 1646
9 TraesCS7D01G128200 chr7A 83156926 83157748 822 True 490.000000 490 78.114000 1092 1927 1 chr7A.!!$R2 835
10 TraesCS7D01G128200 chr7A 83223944 83225112 1168 True 400.000000 612 89.759333 1300 2458 3 chr7A.!!$R6 1158
11 TraesCS7D01G128200 chr7A 83169687 83170200 513 True 385.000000 385 80.866000 514 1051 1 chr7A.!!$R3 537
12 TraesCS7D01G128200 chr7B 27486188 27487300 1112 True 1085.000000 1085 84.391000 514 1666 1 chr7B.!!$R1 1152
13 TraesCS7D01G128200 chr7B 27594069 27594992 923 True 418.500000 534 85.858500 1066 1932 2 chr7B.!!$R3 866

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
624 3362 0.110678 TCGACCTCCACTGTCAGTCT 59.889 55.0 1.37 0.0 32.91 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2458 9764 0.612229 CTGGAGAGAAGAGCAAGGCA 59.388 55.0 0.0 0.0 0.0 4.75 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
26 27 7.325660 ACATTCATATCAGACACATTTCACC 57.674 36.000 0.00 0.00 0.00 4.02
27 28 7.114754 ACATTCATATCAGACACATTTCACCT 58.885 34.615 0.00 0.00 0.00 4.00
28 29 7.613022 ACATTCATATCAGACACATTTCACCTT 59.387 33.333 0.00 0.00 0.00 3.50
29 30 8.464404 CATTCATATCAGACACATTTCACCTTT 58.536 33.333 0.00 0.00 0.00 3.11
30 31 8.408043 TTCATATCAGACACATTTCACCTTTT 57.592 30.769 0.00 0.00 0.00 2.27
31 32 8.408043 TCATATCAGACACATTTCACCTTTTT 57.592 30.769 0.00 0.00 0.00 1.94
52 53 7.492352 TTTTTCTTAGCTAGTGGAAACTGAC 57.508 36.000 14.07 0.00 0.00 3.51
53 54 4.436242 TCTTAGCTAGTGGAAACTGACG 57.564 45.455 0.00 0.00 0.00 4.35
54 55 3.825014 TCTTAGCTAGTGGAAACTGACGT 59.175 43.478 0.00 0.00 0.00 4.34
55 56 5.005740 TCTTAGCTAGTGGAAACTGACGTA 58.994 41.667 0.00 0.00 0.00 3.57
56 57 3.851976 AGCTAGTGGAAACTGACGTAG 57.148 47.619 0.00 0.00 0.00 3.51
69 70 2.508439 CGTAGTGCACGCCCGAAT 60.508 61.111 12.01 0.00 45.03 3.34
70 71 2.098233 CGTAGTGCACGCCCGAATT 61.098 57.895 12.01 0.00 45.03 2.17
71 72 0.802994 CGTAGTGCACGCCCGAATTA 60.803 55.000 12.01 0.00 45.03 1.40
72 73 0.648958 GTAGTGCACGCCCGAATTAC 59.351 55.000 12.01 1.94 0.00 1.89
73 74 0.533491 TAGTGCACGCCCGAATTACT 59.467 50.000 12.01 0.00 0.00 2.24
74 75 0.321298 AGTGCACGCCCGAATTACTT 60.321 50.000 12.01 0.00 0.00 2.24
75 76 0.519961 GTGCACGCCCGAATTACTTT 59.480 50.000 0.00 0.00 0.00 2.66
76 77 1.068816 GTGCACGCCCGAATTACTTTT 60.069 47.619 0.00 0.00 0.00 2.27
77 78 1.068885 TGCACGCCCGAATTACTTTTG 60.069 47.619 0.00 0.00 0.00 2.44
78 79 1.198178 GCACGCCCGAATTACTTTTGA 59.802 47.619 0.00 0.00 0.00 2.69
79 80 2.846693 CACGCCCGAATTACTTTTGAC 58.153 47.619 0.00 0.00 0.00 3.18
80 81 2.224549 CACGCCCGAATTACTTTTGACA 59.775 45.455 0.00 0.00 0.00 3.58
81 82 2.879646 ACGCCCGAATTACTTTTGACAA 59.120 40.909 0.00 0.00 0.00 3.18
82 83 3.315749 ACGCCCGAATTACTTTTGACAAA 59.684 39.130 0.00 0.00 0.00 2.83
83 84 3.666797 CGCCCGAATTACTTTTGACAAAC 59.333 43.478 0.00 0.00 0.00 2.93
84 85 4.555906 CGCCCGAATTACTTTTGACAAACT 60.556 41.667 0.00 0.00 0.00 2.66
85 86 4.679654 GCCCGAATTACTTTTGACAAACTG 59.320 41.667 0.00 0.00 0.00 3.16
86 87 4.679654 CCCGAATTACTTTTGACAAACTGC 59.320 41.667 0.00 0.00 0.00 4.40
87 88 5.277825 CCGAATTACTTTTGACAAACTGCA 58.722 37.500 0.00 0.00 0.00 4.41
88 89 5.173131 CCGAATTACTTTTGACAAACTGCAC 59.827 40.000 0.00 0.00 0.00 4.57
89 90 5.741510 CGAATTACTTTTGACAAACTGCACA 59.258 36.000 0.00 0.00 0.00 4.57
90 91 6.291060 CGAATTACTTTTGACAAACTGCACAC 60.291 38.462 0.00 0.00 0.00 3.82
91 92 2.862512 ACTTTTGACAAACTGCACACG 58.137 42.857 0.00 0.00 0.00 4.49
92 93 1.583404 CTTTTGACAAACTGCACACGC 59.417 47.619 0.00 0.00 39.24 5.34
203 209 2.436469 TGCATGCGCATCGAAGGT 60.436 55.556 22.51 0.00 45.36 3.50
270 277 0.607489 GCATGGAGTTGGAGCAGTGT 60.607 55.000 0.00 0.00 0.00 3.55
271 278 1.162698 CATGGAGTTGGAGCAGTGTG 58.837 55.000 0.00 0.00 0.00 3.82
284 291 0.664761 CAGTGTGGCTGGTTTGTCTG 59.335 55.000 0.00 0.00 41.42 3.51
294 301 2.023673 TGGTTTGTCTGCCTTGACTTG 58.976 47.619 0.00 0.00 37.79 3.16
324 336 3.405592 CTGCGGCATGTCCATGTGC 62.406 63.158 1.75 15.25 40.80 4.57
327 339 4.324471 GGCATGTCCATGTGCTGA 57.676 55.556 8.91 0.00 41.04 4.26
328 340 2.104267 GGCATGTCCATGTGCTGAG 58.896 57.895 8.91 0.00 41.04 3.35
331 343 2.110967 ATGTCCATGTGCTGAGCGC 61.111 57.895 11.70 11.70 39.75 5.92
430 447 1.764054 CCCCCTCGATCTGGCTCTT 60.764 63.158 0.00 0.00 0.00 2.85
456 473 3.047280 TGACACCATTGACGCCGC 61.047 61.111 0.00 0.00 0.00 6.53
457 474 4.147322 GACACCATTGACGCCGCG 62.147 66.667 12.14 12.14 0.00 6.46
466 483 1.947597 TTGACGCCGCGGTACCTATT 61.948 55.000 28.70 2.79 0.00 1.73
468 485 2.340453 GACGCCGCGGTACCTATTCA 62.340 60.000 28.70 0.00 0.00 2.57
477 494 3.808174 GCGGTACCTATTCAATCCTGAAC 59.192 47.826 10.90 0.00 44.28 3.18
597 3333 1.276145 GCACACGACGAGTTCACTCC 61.276 60.000 0.00 0.00 39.79 3.85
621 3359 1.133982 CAGATCGACCTCCACTGTCAG 59.866 57.143 0.00 0.00 32.91 3.51
622 3360 1.178276 GATCGACCTCCACTGTCAGT 58.822 55.000 0.00 0.00 32.91 3.41
623 3361 1.133407 GATCGACCTCCACTGTCAGTC 59.867 57.143 1.37 0.00 32.91 3.51
624 3362 0.110678 TCGACCTCCACTGTCAGTCT 59.889 55.000 1.37 0.00 32.91 3.24
625 3363 0.242286 CGACCTCCACTGTCAGTCTG 59.758 60.000 1.37 0.00 32.91 3.51
626 3364 1.333177 GACCTCCACTGTCAGTCTGT 58.667 55.000 1.37 0.00 32.91 3.41
627 3365 1.271102 GACCTCCACTGTCAGTCTGTC 59.729 57.143 1.37 4.02 32.91 3.51
628 3366 1.332195 CCTCCACTGTCAGTCTGTCA 58.668 55.000 1.37 0.00 0.00 3.58
629 3367 1.000283 CCTCCACTGTCAGTCTGTCAC 60.000 57.143 1.37 0.00 0.00 3.67
630 3368 1.000283 CTCCACTGTCAGTCTGTCACC 60.000 57.143 1.37 0.00 0.00 4.02
631 3369 0.752658 CCACTGTCAGTCTGTCACCA 59.247 55.000 1.37 0.00 0.00 4.17
632 3370 1.345741 CCACTGTCAGTCTGTCACCAT 59.654 52.381 1.37 0.00 0.00 3.55
633 3371 2.410939 CACTGTCAGTCTGTCACCATG 58.589 52.381 1.37 0.00 0.00 3.66
634 3372 1.270518 ACTGTCAGTCTGTCACCATGC 60.271 52.381 0.00 0.00 0.00 4.06
635 3373 0.758123 TGTCAGTCTGTCACCATGCA 59.242 50.000 0.00 0.00 0.00 3.96
636 3374 1.348696 TGTCAGTCTGTCACCATGCAT 59.651 47.619 0.00 0.00 0.00 3.96
716 3530 4.988598 CCTCACTGCGTTGCCGGT 62.989 66.667 1.90 0.00 33.68 5.28
717 3531 3.414700 CTCACTGCGTTGCCGGTC 61.415 66.667 1.90 0.00 33.68 4.79
731 3561 1.649815 CGGTCGGAGTAGCTAGCTG 59.350 63.158 27.68 10.14 0.00 4.24
800 3638 0.387565 CGAAGGGAAGGAGAGCTAGC 59.612 60.000 6.62 6.62 0.00 3.42
1047 3933 1.062258 GGTGTTCAATGCAATGCACG 58.938 50.000 11.23 4.94 43.04 5.34
1048 3934 1.602668 GGTGTTCAATGCAATGCACGT 60.603 47.619 11.23 0.00 43.04 4.49
1049 3935 2.351253 GGTGTTCAATGCAATGCACGTA 60.351 45.455 11.23 0.00 43.04 3.57
1050 3936 2.910482 GTGTTCAATGCAATGCACGTAG 59.090 45.455 11.23 0.52 43.04 3.51
1051 3937 2.095314 TGTTCAATGCAATGCACGTAGG 60.095 45.455 11.23 0.00 43.04 3.18
1052 3938 1.819928 TCAATGCAATGCACGTAGGT 58.180 45.000 11.23 0.00 43.04 3.08
1053 3939 1.737236 TCAATGCAATGCACGTAGGTC 59.263 47.619 11.23 0.00 43.04 3.85
1054 3940 0.726827 AATGCAATGCACGTAGGTCG 59.273 50.000 11.23 0.00 43.04 4.79
1103 3992 3.050275 GACCTGGCCGAGTGCAAC 61.050 66.667 1.54 0.00 43.89 4.17
1340 4960 2.361610 GTCGACGGGGACTGGGTA 60.362 66.667 0.00 0.00 40.47 3.69
1349 4969 2.413142 GGACTGGGTACTCGTCGGG 61.413 68.421 10.29 0.00 0.00 5.14
1458 5108 0.179100 AGTGAGGTGCCGAATCGATG 60.179 55.000 3.36 0.00 0.00 3.84
1519 5175 4.569966 AGATACTACTCGTGTAACCGACTG 59.430 45.833 0.00 0.00 32.57 3.51
1649 5353 2.094854 ACGTCGACAAGTATGGGACTTC 60.095 50.000 17.16 0.00 45.81 3.01
1654 5358 3.133003 CGACAAGTATGGGACTTCCTGAT 59.867 47.826 0.00 0.00 45.81 2.90
1655 5359 4.698575 GACAAGTATGGGACTTCCTGATC 58.301 47.826 0.00 0.00 45.81 2.92
1656 5360 3.133003 ACAAGTATGGGACTTCCTGATCG 59.867 47.826 0.00 0.00 45.81 3.69
1657 5361 3.314307 AGTATGGGACTTCCTGATCGA 57.686 47.619 0.00 0.00 33.13 3.59
1666 5370 5.047188 GGACTTCCTGATCGATTTTCTCTC 58.953 45.833 0.00 0.00 0.00 3.20
1667 5371 5.394663 GGACTTCCTGATCGATTTTCTCTCA 60.395 44.000 0.00 0.00 0.00 3.27
1668 5372 5.415221 ACTTCCTGATCGATTTTCTCTCAC 58.585 41.667 0.00 0.00 0.00 3.51
1669 5373 4.392921 TCCTGATCGATTTTCTCTCACC 57.607 45.455 0.00 0.00 0.00 4.02
1670 5374 3.133003 TCCTGATCGATTTTCTCTCACCC 59.867 47.826 0.00 0.00 0.00 4.61
1689 5393 4.519730 CACCCGTCCAAGGTTTAATGTTTA 59.480 41.667 0.00 0.00 34.56 2.01
1695 5399 6.517605 GTCCAAGGTTTAATGTTTAGGCAAA 58.482 36.000 0.00 0.00 0.00 3.68
1708 5412 8.729805 ATGTTTAGGCAAAAGAACAAATTCAA 57.270 26.923 0.00 0.00 37.29 2.69
1716 5420 7.439056 GGCAAAAGAACAAATTCAATCTTCAGA 59.561 33.333 0.00 0.00 37.29 3.27
1788 5493 7.899178 ATTTTAATGGGTTTTGACCGAATTC 57.101 32.000 0.00 0.00 0.00 2.17
1857 5563 4.609691 AATATTTTGGTACACGCGGAAG 57.390 40.909 12.47 1.86 39.29 3.46
2024 9024 5.049405 GGCATTACGGAACCATCATAAAGAG 60.049 44.000 0.00 0.00 0.00 2.85
2038 9040 7.555554 CCATCATAAAGAGTCCAGAGACATTTT 59.444 37.037 0.00 0.00 46.15 1.82
2152 9418 5.923684 ACAACAAAAGTACAACCAAACTGTG 59.076 36.000 0.00 0.00 0.00 3.66
2162 9428 1.021202 CCAAACTGTGCGTTGGAGAA 58.979 50.000 4.10 0.00 35.61 2.87
2399 9705 0.250234 CACCCTCTTCGCCAATCTCA 59.750 55.000 0.00 0.00 0.00 3.27
2403 9709 2.158842 CCCTCTTCGCCAATCTCAGAAT 60.159 50.000 0.00 0.00 0.00 2.40
2458 9764 2.434359 GCGGGCAAACGAGCTAGT 60.434 61.111 0.00 0.00 35.47 2.57
2462 9768 4.285851 GCAAACGAGCTAGTGCCT 57.714 55.556 0.00 0.00 40.80 4.75
2463 9769 2.544726 GCAAACGAGCTAGTGCCTT 58.455 52.632 0.00 0.00 40.80 4.35
2464 9770 0.166814 GCAAACGAGCTAGTGCCTTG 59.833 55.000 0.00 2.92 40.80 3.61
2465 9771 0.166814 CAAACGAGCTAGTGCCTTGC 59.833 55.000 0.00 1.54 40.80 4.01
2466 9772 0.035458 AAACGAGCTAGTGCCTTGCT 59.965 50.000 0.00 9.99 44.27 3.91
2470 9776 3.851051 AGCTAGTGCCTTGCTCTTC 57.149 52.632 5.57 0.00 38.02 2.87
2471 9777 1.274712 AGCTAGTGCCTTGCTCTTCT 58.725 50.000 5.57 0.00 38.02 2.85
2472 9778 1.206849 AGCTAGTGCCTTGCTCTTCTC 59.793 52.381 5.57 0.00 38.02 2.87
2473 9779 1.206849 GCTAGTGCCTTGCTCTTCTCT 59.793 52.381 0.00 0.00 34.22 3.10
2474 9780 2.738321 GCTAGTGCCTTGCTCTTCTCTC 60.738 54.545 0.00 0.00 34.22 3.20
2475 9781 0.612744 AGTGCCTTGCTCTTCTCTCC 59.387 55.000 0.00 0.00 0.00 3.71
2476 9782 0.322975 GTGCCTTGCTCTTCTCTCCA 59.677 55.000 0.00 0.00 0.00 3.86
2477 9783 0.612229 TGCCTTGCTCTTCTCTCCAG 59.388 55.000 0.00 0.00 0.00 3.86
2478 9784 0.901124 GCCTTGCTCTTCTCTCCAGA 59.099 55.000 0.00 0.00 0.00 3.86
2479 9785 1.134729 GCCTTGCTCTTCTCTCCAGAG 60.135 57.143 0.00 0.00 43.36 3.35
2492 9798 3.994317 TCTCCAGAGAGAGAGAGAGAGA 58.006 50.000 0.00 0.00 44.42 3.10
2493 9799 3.963374 TCTCCAGAGAGAGAGAGAGAGAG 59.037 52.174 0.00 0.00 44.42 3.20
2494 9800 3.963374 CTCCAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 43.39 3.10
2495 9801 3.963374 TCCAGAGAGAGAGAGAGAGAGAG 59.037 52.174 0.00 0.00 0.00 3.20
2496 9802 3.963374 CCAGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
2497 9803 4.039004 CCAGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
2498 9804 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
2499 9805 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
2500 9806 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2501 9807 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2502 9808 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2503 9809 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2504 9810 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2505 9811 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2506 9812 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2507 9813 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2508 9814 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2509 9815 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2510 9816 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2511 9817 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2512 9818 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.246180 GGTGAAATGTGTCTGATATGAATGTTT 58.754 33.333 0.00 0.00 0.00 2.83
1 2 7.613022 AGGTGAAATGTGTCTGATATGAATGTT 59.387 33.333 0.00 0.00 0.00 2.71
2 3 7.114754 AGGTGAAATGTGTCTGATATGAATGT 58.885 34.615 0.00 0.00 0.00 2.71
3 4 7.563888 AGGTGAAATGTGTCTGATATGAATG 57.436 36.000 0.00 0.00 0.00 2.67
4 5 8.585471 AAAGGTGAAATGTGTCTGATATGAAT 57.415 30.769 0.00 0.00 0.00 2.57
5 6 8.408043 AAAAGGTGAAATGTGTCTGATATGAA 57.592 30.769 0.00 0.00 0.00 2.57
6 7 8.408043 AAAAAGGTGAAATGTGTCTGATATGA 57.592 30.769 0.00 0.00 0.00 2.15
28 29 6.202188 CGTCAGTTTCCACTAGCTAAGAAAAA 59.798 38.462 12.41 2.25 30.55 1.94
29 30 5.694910 CGTCAGTTTCCACTAGCTAAGAAAA 59.305 40.000 12.41 1.96 30.55 2.29
30 31 5.221382 ACGTCAGTTTCCACTAGCTAAGAAA 60.221 40.000 8.46 8.46 0.00 2.52
31 32 4.280174 ACGTCAGTTTCCACTAGCTAAGAA 59.720 41.667 0.00 0.00 0.00 2.52
32 33 3.825014 ACGTCAGTTTCCACTAGCTAAGA 59.175 43.478 0.00 0.00 0.00 2.10
33 34 4.175787 ACGTCAGTTTCCACTAGCTAAG 57.824 45.455 0.00 0.00 0.00 2.18
34 35 4.763793 ACTACGTCAGTTTCCACTAGCTAA 59.236 41.667 0.00 0.00 31.59 3.09
35 36 4.155462 CACTACGTCAGTTTCCACTAGCTA 59.845 45.833 0.00 0.00 34.26 3.32
36 37 3.057456 CACTACGTCAGTTTCCACTAGCT 60.057 47.826 0.00 0.00 34.26 3.32
37 38 3.243336 CACTACGTCAGTTTCCACTAGC 58.757 50.000 0.00 0.00 34.26 3.42
38 39 3.243336 GCACTACGTCAGTTTCCACTAG 58.757 50.000 0.00 0.00 34.26 2.57
39 40 2.624364 TGCACTACGTCAGTTTCCACTA 59.376 45.455 0.00 0.00 34.26 2.74
40 41 1.411246 TGCACTACGTCAGTTTCCACT 59.589 47.619 0.00 0.00 34.26 4.00
41 42 1.525619 GTGCACTACGTCAGTTTCCAC 59.474 52.381 10.32 0.00 34.26 4.02
42 43 1.860676 GTGCACTACGTCAGTTTCCA 58.139 50.000 10.32 0.00 34.26 3.53
53 54 0.648958 GTAATTCGGGCGTGCACTAC 59.351 55.000 16.19 6.74 0.00 2.73
54 55 0.533491 AGTAATTCGGGCGTGCACTA 59.467 50.000 16.19 0.00 0.00 2.74
55 56 0.321298 AAGTAATTCGGGCGTGCACT 60.321 50.000 16.19 0.00 0.00 4.40
56 57 0.519961 AAAGTAATTCGGGCGTGCAC 59.480 50.000 6.82 6.82 0.00 4.57
57 58 1.068885 CAAAAGTAATTCGGGCGTGCA 60.069 47.619 0.00 0.00 0.00 4.57
58 59 1.198178 TCAAAAGTAATTCGGGCGTGC 59.802 47.619 0.00 0.00 0.00 5.34
59 60 2.224549 TGTCAAAAGTAATTCGGGCGTG 59.775 45.455 0.00 0.00 0.00 5.34
60 61 2.496111 TGTCAAAAGTAATTCGGGCGT 58.504 42.857 0.00 0.00 0.00 5.68
61 62 3.546002 TTGTCAAAAGTAATTCGGGCG 57.454 42.857 0.00 0.00 0.00 6.13
62 63 4.679654 CAGTTTGTCAAAAGTAATTCGGGC 59.320 41.667 0.00 0.00 0.00 6.13
63 64 4.679654 GCAGTTTGTCAAAAGTAATTCGGG 59.320 41.667 0.00 0.00 0.00 5.14
64 65 5.173131 GTGCAGTTTGTCAAAAGTAATTCGG 59.827 40.000 0.00 0.00 0.00 4.30
65 66 5.741510 TGTGCAGTTTGTCAAAAGTAATTCG 59.258 36.000 0.00 0.00 0.00 3.34
66 67 6.291060 CGTGTGCAGTTTGTCAAAAGTAATTC 60.291 38.462 0.00 0.00 0.00 2.17
67 68 5.514914 CGTGTGCAGTTTGTCAAAAGTAATT 59.485 36.000 0.00 0.00 0.00 1.40
68 69 5.034152 CGTGTGCAGTTTGTCAAAAGTAAT 58.966 37.500 0.00 0.00 0.00 1.89
69 70 4.407818 CGTGTGCAGTTTGTCAAAAGTAA 58.592 39.130 0.00 0.00 0.00 2.24
70 71 3.729462 GCGTGTGCAGTTTGTCAAAAGTA 60.729 43.478 0.00 0.00 42.15 2.24
71 72 2.862512 CGTGTGCAGTTTGTCAAAAGT 58.137 42.857 0.00 0.00 0.00 2.66
72 73 1.583404 GCGTGTGCAGTTTGTCAAAAG 59.417 47.619 0.00 0.00 42.15 2.27
73 74 1.623359 GCGTGTGCAGTTTGTCAAAA 58.377 45.000 0.00 0.00 42.15 2.44
74 75 3.320884 GCGTGTGCAGTTTGTCAAA 57.679 47.368 0.00 0.00 42.15 2.69
171 172 4.324471 GCATGGAGCATGGACACA 57.676 55.556 0.00 0.00 41.64 3.72
190 196 2.520465 ATCCACACCTTCGATGCGCA 62.520 55.000 14.96 14.96 0.00 6.09
191 197 1.766143 GATCCACACCTTCGATGCGC 61.766 60.000 0.00 0.00 0.00 6.09
192 198 0.460109 TGATCCACACCTTCGATGCG 60.460 55.000 0.00 0.00 0.00 4.73
193 199 1.293924 CTGATCCACACCTTCGATGC 58.706 55.000 0.00 0.00 0.00 3.91
194 200 1.945387 CCTGATCCACACCTTCGATG 58.055 55.000 0.00 0.00 0.00 3.84
203 209 0.035317 GACAGTGTGCCTGATCCACA 59.965 55.000 0.00 0.00 44.49 4.17
260 267 2.283143 AAACCAGCCACACTGCTCCA 62.283 55.000 0.00 0.00 45.78 3.86
339 351 4.477975 CTCCTCGTCGTCCGCACC 62.478 72.222 0.00 0.00 36.19 5.01
456 473 4.049186 CGTTCAGGATTGAATAGGTACCG 58.951 47.826 6.18 0.00 44.62 4.02
457 474 4.809426 CACGTTCAGGATTGAATAGGTACC 59.191 45.833 2.73 2.73 44.62 3.34
466 483 2.826128 AGCTAGACACGTTCAGGATTGA 59.174 45.455 0.00 0.00 0.00 2.57
468 485 3.258372 TCAAGCTAGACACGTTCAGGATT 59.742 43.478 0.00 0.00 0.00 3.01
477 494 1.002366 GCATGGTCAAGCTAGACACG 58.998 55.000 0.00 0.00 40.29 4.49
597 3333 0.396417 AGTGGAGGTCGATCTGGAGG 60.396 60.000 0.91 0.00 0.00 4.30
633 3371 1.004292 GGTTACGTTCGGTGCATATGC 60.004 52.381 21.09 21.09 42.50 3.14
634 3372 2.272678 TGGTTACGTTCGGTGCATATG 58.727 47.619 0.00 0.00 0.00 1.78
635 3373 2.676632 TGGTTACGTTCGGTGCATAT 57.323 45.000 0.00 0.00 0.00 1.78
636 3374 2.542597 GATGGTTACGTTCGGTGCATA 58.457 47.619 0.00 0.00 0.00 3.14
642 3380 1.265568 CAGTCGATGGTTACGTTCGG 58.734 55.000 6.74 0.00 0.00 4.30
716 3530 1.134189 TGCTACAGCTAGCTACTCCGA 60.134 52.381 18.86 0.00 45.20 4.55
717 3531 1.002251 GTGCTACAGCTAGCTACTCCG 60.002 57.143 18.86 7.23 45.20 4.63
996 3873 1.003580 ACTCACTTGTTGCCCATCGAT 59.996 47.619 0.00 0.00 0.00 3.59
997 3874 0.396435 ACTCACTTGTTGCCCATCGA 59.604 50.000 0.00 0.00 0.00 3.59
998 3875 0.518636 CACTCACTTGTTGCCCATCG 59.481 55.000 0.00 0.00 0.00 3.84
999 3876 1.609208 ACACTCACTTGTTGCCCATC 58.391 50.000 0.00 0.00 0.00 3.51
1047 3933 2.103736 GCGCACCTACCGACCTAC 59.896 66.667 0.30 0.00 0.00 3.18
1048 3934 3.511595 CGCGCACCTACCGACCTA 61.512 66.667 8.75 0.00 0.00 3.08
1103 3992 1.515020 CCTCTTCCTCCTGCACGAG 59.485 63.158 5.79 5.79 0.00 4.18
1324 4944 2.361610 GTACCCAGTCCCCGTCGA 60.362 66.667 0.00 0.00 0.00 4.20
1391 5014 2.257409 AATGAGAGGGGAATGCGCGT 62.257 55.000 8.43 0.00 0.00 6.01
1458 5108 1.876156 CTGACAAAGTCCCTGCAAGAC 59.124 52.381 8.21 8.21 34.07 3.01
1649 5353 3.462021 GGGTGAGAGAAAATCGATCAGG 58.538 50.000 0.00 0.00 0.00 3.86
1654 5358 1.203994 GGACGGGTGAGAGAAAATCGA 59.796 52.381 0.00 0.00 0.00 3.59
1655 5359 1.067142 TGGACGGGTGAGAGAAAATCG 60.067 52.381 0.00 0.00 0.00 3.34
1656 5360 2.762535 TGGACGGGTGAGAGAAAATC 57.237 50.000 0.00 0.00 0.00 2.17
1657 5361 2.290323 CCTTGGACGGGTGAGAGAAAAT 60.290 50.000 0.00 0.00 0.00 1.82
1666 5370 2.510613 ACATTAAACCTTGGACGGGTG 58.489 47.619 0.00 0.00 37.13 4.61
1667 5371 2.963599 ACATTAAACCTTGGACGGGT 57.036 45.000 0.00 0.00 38.94 5.28
1668 5372 4.157105 CCTAAACATTAAACCTTGGACGGG 59.843 45.833 0.00 0.00 0.00 5.28
1669 5373 4.380128 GCCTAAACATTAAACCTTGGACGG 60.380 45.833 0.00 0.00 0.00 4.79
1670 5374 4.216687 TGCCTAAACATTAAACCTTGGACG 59.783 41.667 0.00 0.00 0.00 4.79
1689 5393 7.274447 TGAAGATTGAATTTGTTCTTTTGCCT 58.726 30.769 0.00 0.00 0.00 4.75
1695 5399 8.081025 GCTTCTCTGAAGATTGAATTTGTTCTT 58.919 33.333 11.03 0.00 0.00 2.52
1708 5412 1.464734 TCCGACGCTTCTCTGAAGAT 58.535 50.000 11.03 0.00 0.00 2.40
1716 5420 5.642063 TCTGAAATAATTTTCCGACGCTTCT 59.358 36.000 0.00 0.00 40.49 2.85
1874 5580 6.419413 GCATGGTTCAAAAACTCAACGAATTA 59.581 34.615 0.00 0.00 35.61 1.40
1978 8958 8.472683 TGCCACTAAACATGCATTATTTTTAC 57.527 30.769 10.23 0.28 0.00 2.01
1990 8971 4.438200 GGTTCCGTAATGCCACTAAACATG 60.438 45.833 0.00 0.00 0.00 3.21
2050 9052 4.630069 CGGTGAAAGGTCTTAGGTTGTATG 59.370 45.833 0.00 0.00 0.00 2.39
2052 9054 3.896888 TCGGTGAAAGGTCTTAGGTTGTA 59.103 43.478 0.00 0.00 0.00 2.41
2056 9058 3.170717 TCATCGGTGAAAGGTCTTAGGT 58.829 45.455 0.00 0.00 0.00 3.08
2057 9059 3.887621 TCATCGGTGAAAGGTCTTAGG 57.112 47.619 0.00 0.00 0.00 2.69
2058 9060 4.822026 AGTTCATCGGTGAAAGGTCTTAG 58.178 43.478 13.77 0.00 45.38 2.18
2059 9061 4.884668 AGTTCATCGGTGAAAGGTCTTA 57.115 40.909 13.77 0.00 45.38 2.10
2060 9062 3.771577 AGTTCATCGGTGAAAGGTCTT 57.228 42.857 13.77 0.00 45.38 3.01
2065 9331 3.187227 CAGTCCAAGTTCATCGGTGAAAG 59.813 47.826 13.77 6.25 45.38 2.62
2162 9428 1.873698 AAGCACCATTACAACGACGT 58.126 45.000 0.00 0.00 0.00 4.34
2173 9467 4.218417 GTCCAGAACATACAAAAGCACCAT 59.782 41.667 0.00 0.00 0.00 3.55
2255 9559 9.708092 TTCATTTTCATGCATGATTTTAGTTCA 57.292 25.926 29.13 8.97 36.56 3.18
2306 9611 2.103153 TCAACCTCTCCACCTTCTGT 57.897 50.000 0.00 0.00 0.00 3.41
2350 9656 5.556382 CGTTATCGATGGCAATGAACTACAC 60.556 44.000 8.54 0.00 39.71 2.90
2399 9705 7.173907 CCGATATGATAACCAAGCTTCAATTCT 59.826 37.037 0.00 0.00 0.00 2.40
2403 9709 5.063204 CCCGATATGATAACCAAGCTTCAA 58.937 41.667 0.00 0.00 0.00 2.69
2439 9745 4.770874 TAGCTCGTTTGCCCGCCC 62.771 66.667 0.00 0.00 0.00 6.13
2442 9748 2.740714 GCACTAGCTCGTTTGCCCG 61.741 63.158 0.00 0.00 37.91 6.13
2458 9764 0.612229 CTGGAGAGAAGAGCAAGGCA 59.388 55.000 0.00 0.00 0.00 4.75
2471 9777 3.963374 CTCTCTCTCTCTCTCTCTGGAGA 59.037 52.174 0.20 0.20 45.30 3.71
2472 9778 3.963374 TCTCTCTCTCTCTCTCTCTGGAG 59.037 52.174 0.00 0.00 40.73 3.86
2473 9779 3.963374 CTCTCTCTCTCTCTCTCTCTGGA 59.037 52.174 0.00 0.00 0.00 3.86
2474 9780 3.963374 TCTCTCTCTCTCTCTCTCTCTGG 59.037 52.174 0.00 0.00 0.00 3.86
2475 9781 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
2476 9782 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2477 9783 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2478 9784 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2479 9785 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2480 9786 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2481 9787 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2482 9788 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2483 9789 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2484 9790 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2485 9791 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2486 9792 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2487 9793 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2488 9794 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2489 9795 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2490 9796 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.