Multiple sequence alignment - TraesCS7D01G138500

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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 TraesCS7D01G138500 chr7D 100.000 2386 0 0 1 2386 88647973 88650358 0.000000e+00 4407
1 TraesCS7D01G138500 chr7D 95.046 323 13 2 1637 1956 231605019 231605341 2.740000e-139 505
2 TraesCS7D01G138500 chr7D 94.753 324 14 2 1637 1957 231543909 231543586 3.540000e-138 501
3 TraesCS7D01G138500 chr7D 96.759 216 7 0 1944 2159 231555082 231555297 6.270000e-96 361
4 TraesCS7D01G138500 chr7D 93.416 243 15 1 1944 2185 88622074 88622316 2.260000e-95 359
5 TraesCS7D01G138500 chr7D 97.354 189 5 0 2197 2385 77248184 77248372 2.960000e-84 322
6 TraesCS7D01G138500 chr7D 97.354 189 5 0 2197 2385 231606529 231606341 2.960000e-84 322
7 TraesCS7D01G138500 chr7D 97.354 189 5 0 2197 2385 231607567 231607379 2.960000e-84 322
8 TraesCS7D01G138500 chr5D 95.917 1543 60 2 105 1644 503266652 503265110 0.000000e+00 2497
9 TraesCS7D01G138500 chr5D 95.858 1545 59 2 105 1644 503243923 503245467 0.000000e+00 2494
10 TraesCS7D01G138500 chr5D 94.753 324 13 3 1637 1957 503248170 503247848 3.540000e-138 501
11 TraesCS7D01G138500 chr5D 94.753 324 13 3 1637 1957 503261878 503262200 3.540000e-138 501
12 TraesCS7D01G138500 chr5D 96.296 216 8 0 1944 2159 503244615 503244400 2.920000e-94 355
13 TraesCS7D01G138500 chr5D 97.354 189 5 0 2197 2385 503247205 503247393 2.960000e-84 322
14 TraesCS7D01G138500 chr5D 97.354 189 5 0 2197 2385 503262843 503262655 2.960000e-84 322
15 TraesCS7D01G138500 chr5D 95.775 71 3 0 1 71 432403077 432403007 5.390000e-22 115
16 TraesCS7D01G138500 chr6D 95.858 1545 59 2 105 1644 389247171 389245627 0.000000e+00 2494
17 TraesCS7D01G138500 chr6D 96.296 216 8 0 1944 2159 389246479 389246694 2.920000e-94 355
18 TraesCS7D01G138500 chr6D 95.775 71 3 0 1 71 168255346 168255416 5.390000e-22 115
19 TraesCS7D01G138500 chr2A 95.858 1545 59 2 105 1644 726907804 726906260 0.000000e+00 2494
20 TraesCS7D01G138500 chr2A 95.062 324 13 2 1637 1957 726903556 726903879 7.610000e-140 507
21 TraesCS7D01G138500 chr7B 95.728 1545 61 2 105 1644 663100774 663099230 0.000000e+00 2483
22 TraesCS7D01G138500 chr7B 95.405 1545 66 2 105 1644 662725055 662726599 0.000000e+00 2455
23 TraesCS7D01G138500 chr3D 95.723 1543 62 3 105 1644 589264872 589263331 0.000000e+00 2481
24 TraesCS7D01G138500 chr3D 96.296 216 8 0 1944 2159 589264181 589264396 2.920000e-94 355
25 TraesCS7D01G138500 chr3A 95.661 1544 63 2 105 1644 66006481 66004938 0.000000e+00 2477
26 TraesCS7D01G138500 chr3A 95.062 324 13 2 1637 1957 66002234 66002557 7.610000e-140 507
27 TraesCS7D01G138500 chr3A 96.296 216 8 0 1944 2159 66005789 66006004 2.920000e-94 355
28 TraesCS7D01G138500 chr1D 95.402 1544 67 2 105 1644 254383370 254381827 0.000000e+00 2455
29 TraesCS7D01G138500 chr1D 96.296 216 8 0 1944 2159 254382678 254382893 2.920000e-94 355
30 TraesCS7D01G138500 chrUn 95.370 324 12 2 1637 1957 433991088 433990765 1.640000e-141 512
31 TraesCS7D01G138500 chrUn 95.062 324 13 2 1637 1957 428083993 428084316 7.610000e-140 507
32 TraesCS7D01G138500 chrUn 95.062 324 13 2 1637 1957 461210745 461211068 7.610000e-140 507
33 TraesCS7D01G138500 chrUn 95.833 216 9 0 1944 2159 216506775 216506990 1.360000e-92 350
34 TraesCS7D01G138500 chrUn 97.354 189 5 0 2197 2385 365941029 365941217 2.960000e-84 322
35 TraesCS7D01G138500 chrUn 97.354 189 5 0 2197 2385 428084959 428084771 2.960000e-84 322
36 TraesCS7D01G138500 chrUn 97.354 189 5 0 2197 2385 433990122 433990310 2.960000e-84 322
37 TraesCS7D01G138500 chrUn 95.775 71 3 0 1 71 93409211 93409141 5.390000e-22 115
38 TraesCS7D01G138500 chrUn 95.775 71 3 0 1 71 372771233 372771163 5.390000e-22 115
39 TraesCS7D01G138500 chrUn 95.775 71 3 0 1 71 389445456 389445526 5.390000e-22 115
40 TraesCS7D01G138500 chr2D 96.296 216 8 0 1944 2159 591983952 591983737 2.920000e-94 355
41 TraesCS7D01G138500 chr2D 97.354 189 5 0 2197 2385 591986542 591986730 2.960000e-84 322
42 TraesCS7D01G138500 chr4D 95.775 71 3 0 1 71 19928994 19929064 5.390000e-22 115
43 TraesCS7D01G138500 chr4D 95.775 71 3 0 1 71 386828494 386828564 5.390000e-22 115
44 TraesCS7D01G138500 chr4B 95.775 71 3 0 1 71 70585069 70584999 5.390000e-22 115
45 TraesCS7D01G138500 chr1A 95.775 71 3 0 1 71 554512668 554512738 5.390000e-22 115


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 TraesCS7D01G138500 chr7D 88647973 88650358 2385 False 4407.0 4407 100.0000 1 2386 1 chr7D.!!$F3 2385
1 TraesCS7D01G138500 chr7D 231606341 231607567 1226 True 322.0 322 97.3540 2197 2385 2 chr7D.!!$R2 188
2 TraesCS7D01G138500 chr5D 503262655 503266652 3997 True 1409.5 2497 96.6355 105 2385 2 chr5D.!!$R3 2280
3 TraesCS7D01G138500 chr5D 503243923 503247393 3470 False 1408.0 2494 96.6060 105 2385 2 chr5D.!!$F2 2280
4 TraesCS7D01G138500 chr5D 503244400 503248170 3770 True 428.0 501 95.5245 1637 2159 2 chr5D.!!$R2 522
5 TraesCS7D01G138500 chr6D 389245627 389247171 1544 True 2494.0 2494 95.8580 105 1644 1 chr6D.!!$R1 1539
6 TraesCS7D01G138500 chr2A 726906260 726907804 1544 True 2494.0 2494 95.8580 105 1644 1 chr2A.!!$R1 1539
7 TraesCS7D01G138500 chr7B 663099230 663100774 1544 True 2483.0 2483 95.7280 105 1644 1 chr7B.!!$R1 1539
8 TraesCS7D01G138500 chr7B 662725055 662726599 1544 False 2455.0 2455 95.4050 105 1644 1 chr7B.!!$F1 1539
9 TraesCS7D01G138500 chr3D 589263331 589264872 1541 True 2481.0 2481 95.7230 105 1644 1 chr3D.!!$R1 1539
10 TraesCS7D01G138500 chr3A 66004938 66006481 1543 True 2477.0 2477 95.6610 105 1644 1 chr3A.!!$R1 1539
11 TraesCS7D01G138500 chr3A 66002234 66006004 3770 False 431.0 507 95.6790 1637 2159 2 chr3A.!!$F1 522
12 TraesCS7D01G138500 chr1D 254381827 254383370 1543 True 2455.0 2455 95.4020 105 1644 1 chr1D.!!$R1 1539

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
321 322 0.250234 CCTCAGTTCGGATTGCAGGA 59.75 55.0 0.25 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1503 0.10576 TGGCCAGAAAAAGGAAGGCA 60.106 50.0 0.0 0.0 46.96 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
27 28 9.763465 TTTGATTCCGTCGAAAATCTATTTTAC 57.237 29.630 16.30 0.00 39.86 2.01
28 29 7.614908 TGATTCCGTCGAAAATCTATTTTACG 58.385 34.615 16.30 13.00 39.86 3.18
30 31 5.707411 CCGTCGAAAATCTATTTTACGGT 57.293 39.130 22.67 0.00 46.43 4.83
32 33 7.398834 CCGTCGAAAATCTATTTTACGGTAT 57.601 36.000 22.67 0.00 46.43 2.73
34 35 8.633408 CCGTCGAAAATCTATTTTACGGTATAG 58.367 37.037 22.67 7.66 46.43 1.31
35 36 8.633408 CGTCGAAAATCTATTTTACGGTATAGG 58.367 37.037 12.45 2.78 39.86 2.57
36 37 8.430828 GTCGAAAATCTATTTTACGGTATAGGC 58.569 37.037 14.28 0.00 39.86 3.93
37 38 7.326789 TCGAAAATCTATTTTACGGTATAGGCG 59.673 37.037 14.28 0.00 39.86 5.52
38 39 6.716898 AAATCTATTTTACGGTATAGGCGC 57.283 37.500 0.00 0.00 0.00 6.53
39 40 5.656213 ATCTATTTTACGGTATAGGCGCT 57.344 39.130 7.64 0.00 0.00 5.92
40 41 5.458041 TCTATTTTACGGTATAGGCGCTT 57.542 39.130 7.64 0.52 0.00 4.68
41 42 6.573664 TCTATTTTACGGTATAGGCGCTTA 57.426 37.500 7.64 3.82 0.00 3.09
42 43 7.161773 TCTATTTTACGGTATAGGCGCTTAT 57.838 36.000 16.77 16.77 0.00 1.73
43 44 7.031372 TCTATTTTACGGTATAGGCGCTTATG 58.969 38.462 21.14 7.92 0.00 1.90
44 45 4.852134 TTTACGGTATAGGCGCTTATGA 57.148 40.909 21.14 3.80 0.00 2.15
45 46 2.719426 ACGGTATAGGCGCTTATGAC 57.281 50.000 21.14 14.17 0.00 3.06
48 49 2.029290 CGGTATAGGCGCTTATGACCTT 60.029 50.000 21.14 0.00 34.92 3.50
49 50 3.586892 GGTATAGGCGCTTATGACCTTC 58.413 50.000 21.14 5.51 34.92 3.46
50 51 2.841442 ATAGGCGCTTATGACCTTCC 57.159 50.000 11.70 0.00 34.92 3.46
51 52 0.756903 TAGGCGCTTATGACCTTCCC 59.243 55.000 7.64 0.00 34.92 3.97
52 53 1.526225 GGCGCTTATGACCTTCCCC 60.526 63.158 7.64 0.00 0.00 4.81
55 56 1.527370 GCTTATGACCTTCCCCGCT 59.473 57.895 0.00 0.00 0.00 5.52
56 57 0.756903 GCTTATGACCTTCCCCGCTA 59.243 55.000 0.00 0.00 0.00 4.26
59 60 0.685097 TATGACCTTCCCCGCTATGC 59.315 55.000 0.00 0.00 0.00 3.14
64 65 2.124320 TTCCCCGCTATGCCTTGC 60.124 61.111 0.00 0.00 0.00 4.01
66 67 2.891941 TTCCCCGCTATGCCTTGCTG 62.892 60.000 0.00 0.00 0.00 4.41
67 68 2.124570 CCCGCTATGCCTTGCTGT 60.125 61.111 0.00 0.00 0.00 4.40
69 70 0.463654 CCCGCTATGCCTTGCTGTAA 60.464 55.000 0.00 0.00 0.00 2.41
70 71 1.597742 CCGCTATGCCTTGCTGTAAT 58.402 50.000 0.00 0.00 0.00 1.89
71 72 2.549992 CCCGCTATGCCTTGCTGTAATA 60.550 50.000 0.00 0.00 0.00 0.98
72 73 2.480419 CCGCTATGCCTTGCTGTAATAC 59.520 50.000 0.00 0.00 0.00 1.89
73 74 3.393800 CGCTATGCCTTGCTGTAATACT 58.606 45.455 0.00 0.00 0.00 2.12
74 75 4.556233 CGCTATGCCTTGCTGTAATACTA 58.444 43.478 0.00 0.00 0.00 1.82
75 76 4.988540 CGCTATGCCTTGCTGTAATACTAA 59.011 41.667 0.00 0.00 0.00 2.24
76 77 5.639506 CGCTATGCCTTGCTGTAATACTAAT 59.360 40.000 0.00 0.00 0.00 1.73
77 78 6.401474 CGCTATGCCTTGCTGTAATACTAATG 60.401 42.308 0.00 0.00 0.00 1.90
78 79 6.428159 GCTATGCCTTGCTGTAATACTAATGT 59.572 38.462 0.00 0.00 0.00 2.71
80 81 5.989477 TGCCTTGCTGTAATACTAATGTCT 58.011 37.500 0.00 0.00 0.00 3.41
81 82 5.817296 TGCCTTGCTGTAATACTAATGTCTG 59.183 40.000 0.00 0.00 0.00 3.51
82 83 5.817816 GCCTTGCTGTAATACTAATGTCTGT 59.182 40.000 0.00 0.00 0.00 3.41
83 84 6.316390 GCCTTGCTGTAATACTAATGTCTGTT 59.684 38.462 0.00 0.00 0.00 3.16
84 85 7.494625 GCCTTGCTGTAATACTAATGTCTGTTA 59.505 37.037 0.00 0.00 0.00 2.41
87 88 6.984474 TGCTGTAATACTAATGTCTGTTAGGC 59.016 38.462 0.00 0.00 36.27 3.93
88 89 7.147724 TGCTGTAATACTAATGTCTGTTAGGCT 60.148 37.037 0.00 0.00 36.27 4.58
89 90 8.358148 GCTGTAATACTAATGTCTGTTAGGCTA 58.642 37.037 0.00 0.00 36.27 3.93
91 92 9.417561 TGTAATACTAATGTCTGTTAGGCTACT 57.582 33.333 0.00 0.00 36.27 2.57
92 93 9.680315 GTAATACTAATGTCTGTTAGGCTACTG 57.320 37.037 0.00 0.00 36.27 2.74
93 94 7.899648 ATACTAATGTCTGTTAGGCTACTGT 57.100 36.000 0.00 0.00 36.27 3.55
94 95 6.607004 ACTAATGTCTGTTAGGCTACTGTT 57.393 37.500 0.00 0.00 36.27 3.16
96 97 5.746990 AATGTCTGTTAGGCTACTGTTCT 57.253 39.130 0.00 0.00 0.00 3.01
97 98 4.785511 TGTCTGTTAGGCTACTGTTCTC 57.214 45.455 0.00 0.00 0.00 2.87
98 99 3.510360 TGTCTGTTAGGCTACTGTTCTCC 59.490 47.826 0.00 0.00 0.00 3.71
99 100 3.764972 GTCTGTTAGGCTACTGTTCTCCT 59.235 47.826 0.00 0.00 0.00 3.69
100 101 4.948621 GTCTGTTAGGCTACTGTTCTCCTA 59.051 45.833 0.00 0.00 0.00 2.94
101 102 5.595133 GTCTGTTAGGCTACTGTTCTCCTAT 59.405 44.000 0.00 0.00 31.86 2.57
102 103 6.097129 GTCTGTTAGGCTACTGTTCTCCTATT 59.903 42.308 0.00 0.00 31.86 1.73
103 104 6.321690 TCTGTTAGGCTACTGTTCTCCTATTC 59.678 42.308 0.00 0.00 31.86 1.75
104 105 6.195700 TGTTAGGCTACTGTTCTCCTATTCT 58.804 40.000 0.00 0.00 31.86 2.40
105 106 6.321690 TGTTAGGCTACTGTTCTCCTATTCTC 59.678 42.308 0.00 0.00 31.86 2.87
106 107 5.137412 AGGCTACTGTTCTCCTATTCTCT 57.863 43.478 0.00 0.00 0.00 3.10
146 147 5.142061 TCGTCTTTAGTTGCCACTATGAA 57.858 39.130 0.00 0.00 35.32 2.57
206 207 1.148048 GGAGAGGATGAGGCCAAGC 59.852 63.158 5.01 0.00 0.00 4.01
321 322 0.250234 CCTCAGTTCGGATTGCAGGA 59.750 55.000 0.25 0.00 0.00 3.86
409 410 1.761174 CCAGGCCTTGTACACACCT 59.239 57.895 0.00 0.00 0.00 4.00
412 413 0.473886 AGGCCTTGTACACACCTCCT 60.474 55.000 0.00 0.00 0.00 3.69
535 536 2.967397 CCGTACTGGAAGGTGCGA 59.033 61.111 6.67 0.00 45.39 5.10
596 597 8.602472 ATGCTTATAGGGTATTTTGGTTTGAA 57.398 30.769 0.00 0.00 0.00 2.69
613 614 1.673920 TGAAACTTCTTCACGCCCAAC 59.326 47.619 0.00 0.00 0.00 3.77
627 628 1.957113 GCCCAACAAGAAGGCAGCTAT 60.957 52.381 0.00 0.00 46.34 2.97
663 664 7.020827 ACTTGGATATGGAAGTCTTCTTTCA 57.979 36.000 12.31 2.81 42.55 2.69
960 961 4.514441 GGATAGTTCAATGTGCTCATCAGG 59.486 45.833 1.01 0.00 32.56 3.86
1016 1017 0.851469 AGGATGGCGTACTCCTCCTA 59.149 55.000 16.65 0.00 37.30 2.94
1054 1055 4.095782 TGAAACCAAACAAACTTCTCCTCG 59.904 41.667 0.00 0.00 0.00 4.63
1070 1071 0.115349 CTCGGGAGGATAGATGGGGT 59.885 60.000 0.00 0.00 0.00 4.95
1305 1310 1.075374 CCCTTTCATTCTGGGGTGACA 59.925 52.381 0.00 0.00 37.37 3.58
1401 1407 3.394645 TCCTAATCCTCCCTTCCTTTCC 58.605 50.000 0.00 0.00 0.00 3.13
1413 1419 0.034337 TCCTTTCCGGAAGAACGTGG 59.966 55.000 17.97 13.14 39.40 4.94
1436 1442 7.602644 GTGGAATTCTTTTTCCTTAAATGGGAC 59.397 37.037 5.23 0.00 44.63 4.46
1442 1448 5.592587 TTTTCCTTAAATGGGACCAGAGA 57.407 39.130 0.00 0.00 31.94 3.10
1449 1455 6.457159 TTAAATGGGACCAGAGAAGGTTTA 57.543 37.500 0.00 0.00 43.38 2.01
1497 1503 1.512735 GGCCAGGAGGGTCTCTTAAT 58.487 55.000 0.00 0.00 38.65 1.40
1513 1519 5.711976 TCTCTTAATGCCTTCCTTTTTCTGG 59.288 40.000 0.00 0.00 0.00 3.86
1528 2063 4.764050 TTTCTGGCCATCGGAGTTATTA 57.236 40.909 5.51 0.00 31.44 0.98
1530 2065 2.035449 TCTGGCCATCGGAGTTATTACG 59.965 50.000 5.51 0.00 0.00 3.18
1583 2118 3.471680 GGAAGAAGCACACTTGAAGAGT 58.528 45.455 0.00 0.00 39.89 3.24
1707 2242 4.779733 GCCTCCTCCGTCCCTCCA 62.780 72.222 0.00 0.00 0.00 3.86
1764 2299 1.135199 GTCCATCGACTACGCCTTTCA 60.135 52.381 0.00 0.00 39.58 2.69
1794 2329 2.607750 GCCCTGACTCACCCTCCA 60.608 66.667 0.00 0.00 0.00 3.86
1800 2335 0.117140 TGACTCACCCTCCATGGACT 59.883 55.000 11.44 0.00 38.35 3.85
1810 2345 0.981183 TCCATGGACTAACCTTGCGT 59.019 50.000 11.44 0.00 40.94 5.24
1839 2374 1.378378 GGGTTTTTGGGGCATTGGG 59.622 57.895 0.00 0.00 0.00 4.12
1846 2381 0.251742 TTGGGGCATTGGGTTCTCAG 60.252 55.000 0.00 0.00 0.00 3.35
1906 2441 2.739132 GTCGACCCCCACTTTCGT 59.261 61.111 3.51 0.00 34.35 3.85
1965 5749 4.854924 TGACATCCCCATGCCGCG 62.855 66.667 0.00 0.00 32.57 6.46
1993 6061 3.728373 GGGGACATGGGGACGCTT 61.728 66.667 0.00 0.00 0.00 4.68
2025 6093 9.660180 GGGATCCTATCACTATCAACTAATTTC 57.340 37.037 12.58 0.00 0.00 2.17
2071 6139 2.972713 TGAGCTTGGTCTTACTTCACCT 59.027 45.455 0.00 0.00 33.36 4.00
2090 6158 6.579865 TCACCTTAAACGAAAGAAGACTTCT 58.420 36.000 12.12 12.12 43.15 2.85
2159 6227 6.378564 TGAAGAAGTGTCAAACCAAAATACCA 59.621 34.615 0.00 0.00 0.00 3.25
2160 6228 6.783708 AGAAGTGTCAAACCAAAATACCAA 57.216 33.333 0.00 0.00 0.00 3.67
2161 6229 6.805713 AGAAGTGTCAAACCAAAATACCAAG 58.194 36.000 0.00 0.00 0.00 3.61
2162 6230 4.944048 AGTGTCAAACCAAAATACCAAGC 58.056 39.130 0.00 0.00 0.00 4.01
2163 6231 4.649218 AGTGTCAAACCAAAATACCAAGCT 59.351 37.500 0.00 0.00 0.00 3.74
2166 6234 3.886505 TCAAACCAAAATACCAAGCTCGT 59.113 39.130 0.00 0.00 0.00 4.18
2169 6570 3.219281 ACCAAAATACCAAGCTCGTGTT 58.781 40.909 0.00 0.00 0.00 3.32
2179 6580 5.302360 ACCAAGCTCGTGTTAAATAGAACA 58.698 37.500 0.00 0.00 36.98 3.18
2180 6581 5.408604 ACCAAGCTCGTGTTAAATAGAACAG 59.591 40.000 0.00 0.00 39.93 3.16
2181 6582 5.637810 CCAAGCTCGTGTTAAATAGAACAGA 59.362 40.000 0.00 0.00 39.93 3.41
2183 6584 6.952935 AGCTCGTGTTAAATAGAACAGAAG 57.047 37.500 0.00 0.00 39.93 2.85
2184 6585 5.869888 AGCTCGTGTTAAATAGAACAGAAGG 59.130 40.000 0.00 0.00 39.93 3.46
2185 6586 5.638234 GCTCGTGTTAAATAGAACAGAAGGT 59.362 40.000 0.00 0.00 39.93 3.50
2186 6587 6.147328 GCTCGTGTTAAATAGAACAGAAGGTT 59.853 38.462 0.00 0.00 39.93 3.50
2213 6631 5.709164 CCAATTTGGAAAGTGATCTCTGACT 59.291 40.000 10.03 0.00 40.96 3.41
2222 6640 0.741326 GATCTCTGACTGCGTGCCTA 59.259 55.000 0.00 0.00 0.00 3.93
2259 6677 1.409064 CGACTCATAGGCAGTGGCTTA 59.591 52.381 25.69 11.07 39.70 3.09
2327 6745 0.674895 AGGGCGATTGTCACTGCTTC 60.675 55.000 0.00 0.00 0.00 3.86
2356 6774 3.832490 CGAACCTGGGTGATCTATCCATA 59.168 47.826 0.00 0.00 0.00 2.74
2385 6803 5.882557 GGATGAAGCTTGGATGAAACTAAGA 59.117 40.000 2.10 0.00 31.56 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.763465 GTAAAATAGATTTTCGACGGAATCAAA 57.237 29.630 19.68 11.79 40.24 2.69
3 4 7.614908 CGTAAAATAGATTTTCGACGGAATCA 58.385 34.615 19.68 10.81 40.24 2.57
9 10 8.633408 CCTATACCGTAAAATAGATTTTCGACG 58.367 37.037 12.76 12.76 39.52 5.12
10 11 8.430828 GCCTATACCGTAAAATAGATTTTCGAC 58.569 37.037 15.12 6.11 40.24 4.20
13 14 7.117379 AGCGCCTATACCGTAAAATAGATTTTC 59.883 37.037 2.29 0.00 40.24 2.29
14 15 6.932960 AGCGCCTATACCGTAAAATAGATTTT 59.067 34.615 2.29 5.61 42.21 1.82
16 17 6.034161 AGCGCCTATACCGTAAAATAGATT 57.966 37.500 2.29 0.00 0.00 2.40
17 18 5.656213 AGCGCCTATACCGTAAAATAGAT 57.344 39.130 2.29 0.00 0.00 1.98
18 19 5.458041 AAGCGCCTATACCGTAAAATAGA 57.542 39.130 2.29 0.00 0.00 1.98
20 21 6.808212 GTCATAAGCGCCTATACCGTAAAATA 59.192 38.462 2.29 0.00 0.00 1.40
21 22 5.636543 GTCATAAGCGCCTATACCGTAAAAT 59.363 40.000 2.29 0.00 0.00 1.82
22 23 4.984161 GTCATAAGCGCCTATACCGTAAAA 59.016 41.667 2.29 0.00 0.00 1.52
23 24 4.549458 GTCATAAGCGCCTATACCGTAAA 58.451 43.478 2.29 0.00 0.00 2.01
24 25 3.057315 GGTCATAAGCGCCTATACCGTAA 60.057 47.826 2.29 0.00 0.00 3.18
26 27 1.271656 GGTCATAAGCGCCTATACCGT 59.728 52.381 2.29 0.00 0.00 4.83
27 28 1.544691 AGGTCATAAGCGCCTATACCG 59.455 52.381 2.29 0.00 0.00 4.02
28 29 3.586892 GAAGGTCATAAGCGCCTATACC 58.413 50.000 2.29 9.77 31.43 2.73
30 31 2.565834 GGGAAGGTCATAAGCGCCTATA 59.434 50.000 2.29 0.00 31.43 1.31
32 33 0.756903 GGGAAGGTCATAAGCGCCTA 59.243 55.000 2.29 0.00 31.43 3.93
34 35 1.526225 GGGGAAGGTCATAAGCGCC 60.526 63.158 2.29 0.00 0.00 6.53
35 36 1.887707 CGGGGAAGGTCATAAGCGC 60.888 63.158 0.00 0.00 0.00 5.92
36 37 1.887707 GCGGGGAAGGTCATAAGCG 60.888 63.158 0.00 0.00 0.00 4.68
37 38 0.756903 TAGCGGGGAAGGTCATAAGC 59.243 55.000 0.00 0.00 0.00 3.09
38 39 2.872038 GCATAGCGGGGAAGGTCATAAG 60.872 54.545 0.00 0.00 0.00 1.73
39 40 1.071699 GCATAGCGGGGAAGGTCATAA 59.928 52.381 0.00 0.00 0.00 1.90
40 41 0.685097 GCATAGCGGGGAAGGTCATA 59.315 55.000 0.00 0.00 0.00 2.15
41 42 1.451936 GCATAGCGGGGAAGGTCAT 59.548 57.895 0.00 0.00 0.00 3.06
42 43 2.742116 GGCATAGCGGGGAAGGTCA 61.742 63.158 0.00 0.00 0.00 4.02
43 44 1.984288 AAGGCATAGCGGGGAAGGTC 61.984 60.000 0.00 0.00 0.00 3.85
44 45 2.001269 AAGGCATAGCGGGGAAGGT 61.001 57.895 0.00 0.00 0.00 3.50
45 46 1.526917 CAAGGCATAGCGGGGAAGG 60.527 63.158 0.00 0.00 0.00 3.46
48 49 3.089874 AGCAAGGCATAGCGGGGA 61.090 61.111 0.00 0.00 35.48 4.81
49 50 2.324014 TACAGCAAGGCATAGCGGGG 62.324 60.000 0.00 0.00 35.48 5.73
50 51 0.463654 TTACAGCAAGGCATAGCGGG 60.464 55.000 0.00 0.00 35.48 6.13
51 52 1.597742 ATTACAGCAAGGCATAGCGG 58.402 50.000 0.00 0.00 35.48 5.52
52 53 3.393800 AGTATTACAGCAAGGCATAGCG 58.606 45.455 0.00 0.00 35.48 4.26
55 56 7.657354 CAGACATTAGTATTACAGCAAGGCATA 59.343 37.037 0.00 0.00 0.00 3.14
56 57 6.484643 CAGACATTAGTATTACAGCAAGGCAT 59.515 38.462 0.00 0.00 0.00 4.40
59 60 7.849804 AACAGACATTAGTATTACAGCAAGG 57.150 36.000 0.00 0.00 0.00 3.61
64 65 9.680315 GTAGCCTAACAGACATTAGTATTACAG 57.320 37.037 0.00 0.00 31.29 2.74
66 67 9.680315 CAGTAGCCTAACAGACATTAGTATTAC 57.320 37.037 0.00 0.00 31.29 1.89
67 68 9.417561 ACAGTAGCCTAACAGACATTAGTATTA 57.582 33.333 0.00 0.00 31.29 0.98
69 70 7.899648 ACAGTAGCCTAACAGACATTAGTAT 57.100 36.000 0.00 0.00 31.29 2.12
70 71 7.614583 AGAACAGTAGCCTAACAGACATTAGTA 59.385 37.037 0.00 0.00 31.29 1.82
71 72 6.437793 AGAACAGTAGCCTAACAGACATTAGT 59.562 38.462 0.00 0.00 31.29 2.24
72 73 6.868622 AGAACAGTAGCCTAACAGACATTAG 58.131 40.000 0.00 0.00 32.78 1.73
73 74 6.127423 GGAGAACAGTAGCCTAACAGACATTA 60.127 42.308 0.00 0.00 0.00 1.90
74 75 5.337652 GGAGAACAGTAGCCTAACAGACATT 60.338 44.000 0.00 0.00 0.00 2.71
75 76 4.160626 GGAGAACAGTAGCCTAACAGACAT 59.839 45.833 0.00 0.00 0.00 3.06
76 77 3.510360 GGAGAACAGTAGCCTAACAGACA 59.490 47.826 0.00 0.00 0.00 3.41
77 78 3.764972 AGGAGAACAGTAGCCTAACAGAC 59.235 47.826 0.00 0.00 0.00 3.51
78 79 4.048970 AGGAGAACAGTAGCCTAACAGA 57.951 45.455 0.00 0.00 0.00 3.41
80 81 6.195700 AGAATAGGAGAACAGTAGCCTAACA 58.804 40.000 0.00 0.00 36.65 2.41
81 82 6.548251 AGAGAATAGGAGAACAGTAGCCTAAC 59.452 42.308 0.00 0.00 36.65 2.34
82 83 6.674573 AGAGAATAGGAGAACAGTAGCCTAA 58.325 40.000 0.00 0.00 36.65 2.69
83 84 6.268855 AGAGAATAGGAGAACAGTAGCCTA 57.731 41.667 0.00 0.00 37.40 3.93
84 85 5.137412 AGAGAATAGGAGAACAGTAGCCT 57.863 43.478 0.00 0.00 34.56 4.58
87 88 6.214191 TGCAAGAGAATAGGAGAACAGTAG 57.786 41.667 0.00 0.00 0.00 2.57
88 89 6.014584 TGTTGCAAGAGAATAGGAGAACAGTA 60.015 38.462 0.00 0.00 0.00 2.74
89 90 5.221722 TGTTGCAAGAGAATAGGAGAACAGT 60.222 40.000 0.00 0.00 0.00 3.55
91 92 5.227569 TGTTGCAAGAGAATAGGAGAACA 57.772 39.130 0.00 0.00 0.00 3.18
92 93 5.391416 GCTTGTTGCAAGAGAATAGGAGAAC 60.391 44.000 12.45 0.00 42.31 3.01
93 94 4.697352 GCTTGTTGCAAGAGAATAGGAGAA 59.303 41.667 12.45 0.00 42.31 2.87
94 95 4.256920 GCTTGTTGCAAGAGAATAGGAGA 58.743 43.478 12.45 0.00 42.31 3.71
96 97 3.002791 CGCTTGTTGCAAGAGAATAGGA 58.997 45.455 12.45 0.00 43.06 2.94
97 98 2.476854 GCGCTTGTTGCAAGAGAATAGG 60.477 50.000 14.89 0.00 43.06 2.57
98 99 2.160219 TGCGCTTGTTGCAAGAGAATAG 59.840 45.455 9.73 1.82 43.06 1.73
99 100 2.150390 TGCGCTTGTTGCAAGAGAATA 58.850 42.857 9.73 0.39 43.06 1.75
100 101 0.953727 TGCGCTTGTTGCAAGAGAAT 59.046 45.000 9.73 0.00 43.06 2.40
101 102 0.737804 TTGCGCTTGTTGCAAGAGAA 59.262 45.000 9.73 3.32 46.62 2.87
102 103 2.403024 TTGCGCTTGTTGCAAGAGA 58.597 47.368 9.73 0.00 46.62 3.10
146 147 2.814097 CGGTCTGTTCAGGGTTCCAAAT 60.814 50.000 0.00 0.00 0.00 2.32
186 187 0.758123 CTTGGCCTCATCCTCTCCTC 59.242 60.000 3.32 0.00 0.00 3.71
206 207 0.901580 GGGCATAAGGGGCATGATGG 60.902 60.000 0.00 0.00 34.52 3.51
242 243 1.184970 CCTTTGTCCCGCCCATTGTT 61.185 55.000 0.00 0.00 0.00 2.83
298 299 1.554617 TGCAATCCGAACTGAGGATGA 59.445 47.619 0.00 0.00 46.99 2.92
347 348 1.402968 TGACCGGCGATTACTAGTGAC 59.597 52.381 9.30 0.00 0.00 3.67
350 351 0.384669 GCTGACCGGCGATTACTAGT 59.615 55.000 9.30 0.00 0.00 2.57
409 410 3.291584 CAGCTCCTATAGTGTGACAGGA 58.708 50.000 0.00 0.00 35.85 3.86
412 413 1.757118 GCCAGCTCCTATAGTGTGACA 59.243 52.381 0.00 0.00 0.00 3.58
579 580 7.125053 TGAAGAAGTTTCAAACCAAAATACCCT 59.875 33.333 0.00 0.00 0.00 4.34
596 597 1.676006 CTTGTTGGGCGTGAAGAAGTT 59.324 47.619 0.00 0.00 0.00 2.66
613 614 3.196463 CTCAGACATAGCTGCCTTCTTG 58.804 50.000 0.00 0.00 35.86 3.02
627 628 5.425217 TCCATATCCAAGTTTAGCTCAGACA 59.575 40.000 0.00 0.00 0.00 3.41
663 664 4.323257 CCTTGGTCGTACTTCACCCTAAAT 60.323 45.833 3.73 0.00 0.00 1.40
883 884 1.663643 CGACACAATTATCACGGGTGG 59.336 52.381 0.00 0.00 33.91 4.61
885 886 2.739913 CAACGACACAATTATCACGGGT 59.260 45.455 0.00 0.00 0.00 5.28
889 890 3.188460 AGGCACAACGACACAATTATCAC 59.812 43.478 0.00 0.00 0.00 3.06
960 961 1.450312 CACATCTTCGGGTCAGGCC 60.450 63.158 0.00 0.00 0.00 5.19
1016 1017 5.782893 TGGTTTCAAACTCCGATTCAAAT 57.217 34.783 0.00 0.00 0.00 2.32
1054 1055 2.350863 ATCACCCCATCTATCCTCCC 57.649 55.000 0.00 0.00 0.00 4.30
1070 1071 3.117745 ACATGGGATCTCACCTGAATCA 58.882 45.455 0.00 0.00 0.00 2.57
1305 1310 2.231529 CTCGAATGGTACGATCCCTCT 58.768 52.381 0.00 0.00 39.02 3.69
1401 1407 4.483476 AAAAGAATTCCACGTTCTTCCG 57.517 40.909 0.65 0.00 43.19 4.30
1413 1419 7.676004 TGGTCCCATTTAAGGAAAAAGAATTC 58.324 34.615 0.00 0.00 34.43 2.17
1497 1503 0.105760 TGGCCAGAAAAAGGAAGGCA 60.106 50.000 0.00 0.00 46.96 4.75
1513 1519 1.860676 TGCGTAATAACTCCGATGGC 58.139 50.000 0.00 0.00 0.00 4.40
1583 2118 0.250124 CAACTCCCCGTTGTACTGCA 60.250 55.000 0.00 0.00 46.23 4.41
1649 2184 5.941647 TGGTTATAGGTTTAAGGACACAAGC 59.058 40.000 0.00 0.00 0.00 4.01
1707 2242 3.778629 CCTGTACTACCCCTTGTTGGTAT 59.221 47.826 0.00 0.00 37.70 2.73
1794 2329 2.463752 TCCTACGCAAGGTTAGTCCAT 58.536 47.619 4.46 0.00 46.62 3.41
1800 2335 3.404899 CAAGGTTTCCTACGCAAGGTTA 58.595 45.455 4.46 0.00 46.62 2.85
1828 2363 1.383799 CTGAGAACCCAATGCCCCA 59.616 57.895 0.00 0.00 0.00 4.96
1839 2374 5.748592 AGTAACGAAAACATTGCTGAGAAC 58.251 37.500 0.00 0.00 0.00 3.01
1846 2381 3.668656 GGCTTGAGTAACGAAAACATTGC 59.331 43.478 0.00 0.00 0.00 3.56
1906 2441 0.328258 GCCTTAGAGGGAAGCAACCA 59.672 55.000 0.00 0.00 35.37 3.67
1993 6061 9.225682 AGTTGATAGTGATAGGATCCCTTTTTA 57.774 33.333 8.55 0.00 34.61 1.52
2090 6158 6.710597 ACGTCTGAGCTAAACTTGGATATA 57.289 37.500 0.00 0.00 0.00 0.86
2159 6227 6.369065 CCTTCTGTTCTATTTAACACGAGCTT 59.631 38.462 0.00 0.00 35.56 3.74
2160 6228 5.869888 CCTTCTGTTCTATTTAACACGAGCT 59.130 40.000 0.00 0.00 35.56 4.09
2161 6229 5.638234 ACCTTCTGTTCTATTTAACACGAGC 59.362 40.000 0.00 0.00 35.56 5.03
2162 6230 7.653767 AACCTTCTGTTCTATTTAACACGAG 57.346 36.000 0.00 0.00 35.56 4.18
2189 6590 5.709164 AGTCAGAGATCACTTTCCAAATTGG 59.291 40.000 5.48 5.48 39.43 3.16
2191 6592 5.182760 GCAGTCAGAGATCACTTTCCAAATT 59.817 40.000 0.00 0.00 0.00 1.82
2192 6593 4.699257 GCAGTCAGAGATCACTTTCCAAAT 59.301 41.667 0.00 0.00 0.00 2.32
2193 6594 4.067896 GCAGTCAGAGATCACTTTCCAAA 58.932 43.478 0.00 0.00 0.00 3.28
2194 6595 3.668447 GCAGTCAGAGATCACTTTCCAA 58.332 45.455 0.00 0.00 0.00 3.53
2195 6596 2.353109 CGCAGTCAGAGATCACTTTCCA 60.353 50.000 0.00 0.00 0.00 3.53
2213 6631 2.938451 CTCATTCTTCAATAGGCACGCA 59.062 45.455 0.00 0.00 0.00 5.24
2222 6640 0.107703 TCGCCGGCTCATTCTTCAAT 60.108 50.000 26.68 0.00 0.00 2.57
2259 6677 1.072806 GTGGGTTCCGTTCCCTTAACT 59.927 52.381 8.00 0.00 44.84 2.24
2356 6774 2.309755 TCATCCAAGCTTCATCCTGGTT 59.690 45.455 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.