Multiple sequence alignment - TraesCS3A01G485800

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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 TraesCS3A01G485800 chr3A 100.000 2690 0 0 1 2690 714595097 714597786 0.000000e+00 4968.0
1 TraesCS3A01G485800 chr3A 72.468 1264 242 79 581 1800 702421607 702420406 2.600000e-80 309.0
2 TraesCS3A01G485800 chr3A 88.106 227 22 5 510 732 699533357 699533582 5.710000e-67 265.0
3 TraesCS3A01G485800 chr3A 90.625 64 6 0 726 789 700441703 700441640 4.770000e-13 86.1
4 TraesCS3A01G485800 chr3D 91.064 1354 90 4 466 1799 579582863 579581521 0.000000e+00 1801.0
5 TraesCS3A01G485800 chr3D 92.554 1249 76 3 565 1799 579398533 579399778 0.000000e+00 1775.0
6 TraesCS3A01G485800 chr3D 85.112 759 64 19 1935 2682 579581304 579580584 0.000000e+00 730.0
7 TraesCS3A01G485800 chr3D 87.645 518 43 12 1935 2447 579399996 579400497 1.390000e-162 582.0
8 TraesCS3A01G485800 chr3D 92.344 209 14 2 2475 2682 579400493 579400700 2.020000e-76 296.0
9 TraesCS3A01G485800 chr3D 81.299 385 46 16 525 886 565641909 565642290 3.390000e-74 289.0
10 TraesCS3A01G485800 chr3D 74.290 634 133 25 1088 1702 568235447 568236069 9.620000e-60 241.0
11 TraesCS3A01G485800 chr3D 82.593 270 47 0 525 794 565830738 565831007 3.460000e-59 239.0
12 TraesCS3A01G485800 chr3D 74.843 477 78 29 2222 2673 569396125 569395666 7.650000e-41 178.0
13 TraesCS3A01G485800 chr3D 92.857 98 6 1 1783 1880 579399808 579399904 1.000000e-29 141.0
14 TraesCS3A01G485800 chr3D 77.477 222 38 6 1073 1291 567687178 567686966 3.640000e-24 122.0
15 TraesCS3A01G485800 chr3D 85.567 97 14 0 693 789 568136871 568136967 4.740000e-18 102.0
16 TraesCS3A01G485800 chr3D 75.385 195 30 12 136 317 579583233 579583044 7.980000e-11 78.7
17 TraesCS3A01G485800 chr3B 89.978 1357 101 9 466 1799 773746986 773748330 0.000000e+00 1720.0
18 TraesCS3A01G485800 chr3B 86.082 582 49 11 507 1077 773882827 773882267 4.960000e-167 597.0
19 TraesCS3A01G485800 chr3B 91.826 367 29 1 1433 1799 773882268 773881903 6.640000e-141 510.0
20 TraesCS3A01G485800 chr3B 93.438 320 18 2 1933 2249 773881696 773881377 3.130000e-129 472.0
21 TraesCS3A01G485800 chr3B 86.293 321 24 9 2246 2561 773881056 773880751 5.550000e-87 331.0
22 TraesCS3A01G485800 chr3B 72.703 1110 225 57 586 1664 756440294 756439232 1.570000e-77 300.0
23 TraesCS3A01G485800 chr3B 88.584 219 25 0 526 744 752973257 752973039 1.590000e-67 267.0
24 TraesCS3A01G485800 chr3B 83.513 279 38 6 523 800 684514005 684513734 1.240000e-63 254.0
25 TraesCS3A01G485800 chr3B 87.831 189 7 9 139 311 773883146 773882958 9.760000e-50 207.0
26 TraesCS3A01G485800 chr3B 74.833 449 98 11 1224 1663 754331007 754331449 3.540000e-44 189.0
27 TraesCS3A01G485800 chr3B 87.857 140 6 4 66 200 37739787 37739920 1.290000e-33 154.0
28 TraesCS3A01G485800 chr3B 97.368 76 2 0 326 401 773746862 773746937 2.170000e-26 130.0
29 TraesCS3A01G485800 chr3B 97.674 43 0 1 419 460 773746923 773746965 3.710000e-09 73.1
30 TraesCS3A01G485800 chr7A 74.857 525 107 22 1190 1702 41048137 41047626 5.830000e-52 215.0
31 TraesCS3A01G485800 chr7D 74.181 519 107 22 1190 1694 41601215 41600710 9.830000e-45 191.0
32 TraesCS3A01G485800 chr1B 89.209 139 5 5 66 200 670761337 670761205 5.960000e-37 165.0
33 TraesCS3A01G485800 chr4A 72.901 524 116 23 1190 1701 648794677 648794168 9.970000e-35 158.0
34 TraesCS3A01G485800 chr4A 77.778 270 24 19 65 321 714667310 714667064 1.680000e-27 134.0
35 TraesCS3A01G485800 chr4B 87.143 140 7 4 66 200 622342377 622342510 6.000000e-32 148.0
36 TraesCS3A01G485800 chr4B 84.800 125 6 6 65 177 430672208 430672085 2.190000e-21 113.0
37 TraesCS3A01G485800 chr2B 80.583 206 26 7 2382 2585 68197378 68197571 2.160000e-31 147.0
38 TraesCS3A01G485800 chr2B 79.630 162 24 6 1535 1690 773351349 773351507 1.020000e-19 108.0
39 TraesCS3A01G485800 chrUn 77.778 270 24 19 65 321 230759870 230759624 1.680000e-27 134.0
40 TraesCS3A01G485800 chr2D 89.888 89 6 2 2499 2584 43291232 43291320 7.870000e-21 111.0
41 TraesCS3A01G485800 chr1D 88.372 86 9 1 2483 2567 38282296 38282211 4.740000e-18 102.0
42 TraesCS3A01G485800 chr7B 85.567 97 13 1 2468 2563 750344698 750344794 1.700000e-17 100.0


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 TraesCS3A01G485800 chr3A 714595097 714597786 2689 False 4968.000000 4968 100.000000 1 2690 1 chr3A.!!$F2 2689
1 TraesCS3A01G485800 chr3A 702420406 702421607 1201 True 309.000000 309 72.468000 581 1800 1 chr3A.!!$R2 1219
2 TraesCS3A01G485800 chr3D 579580584 579583233 2649 True 869.900000 1801 83.853667 136 2682 3 chr3D.!!$R3 2546
3 TraesCS3A01G485800 chr3D 579398533 579400700 2167 False 698.500000 1775 91.350000 565 2682 4 chr3D.!!$F5 2117
4 TraesCS3A01G485800 chr3D 568235447 568236069 622 False 241.000000 241 74.290000 1088 1702 1 chr3D.!!$F4 614
5 TraesCS3A01G485800 chr3B 773746862 773748330 1468 False 641.033333 1720 95.006667 326 1799 3 chr3B.!!$F3 1473
6 TraesCS3A01G485800 chr3B 773880751 773883146 2395 True 423.400000 597 89.094000 139 2561 5 chr3B.!!$R4 2422
7 TraesCS3A01G485800 chr3B 756439232 756440294 1062 True 300.000000 300 72.703000 586 1664 1 chr3B.!!$R3 1078
8 TraesCS3A01G485800 chr7A 41047626 41048137 511 True 215.000000 215 74.857000 1190 1702 1 chr7A.!!$R1 512

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
296 325 0.457851 CGGTAGGGTTCAGAGCTGAG 59.542 60.0 0.00 0.0 41.13 3.35 F
1053 1193 0.037697 TGTTGATGTTCCGGGACTCG 60.038 55.0 15.59 0.0 38.88 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1295 1.078848 GAATGTCAGCACCTCCGCT 60.079 57.895 0.0 0.0 45.21 5.52 R
2378 3016 1.337703 TGCAACCATGAAACAGTCAGC 59.662 47.619 0.0 0.0 40.43 4.26 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
22 23 4.668576 ACAGTACAACATTGAATCAGCG 57.331 40.909 0.00 0.00 0.00 5.18
23 24 3.120199 ACAGTACAACATTGAATCAGCGC 60.120 43.478 0.00 0.00 0.00 5.92
24 25 3.073678 AGTACAACATTGAATCAGCGCA 58.926 40.909 11.47 0.00 0.00 6.09
25 26 3.691118 AGTACAACATTGAATCAGCGCAT 59.309 39.130 11.47 0.00 0.00 4.73
26 27 4.875536 AGTACAACATTGAATCAGCGCATA 59.124 37.500 11.47 0.00 0.00 3.14
27 28 4.019919 ACAACATTGAATCAGCGCATAC 57.980 40.909 11.47 0.00 0.00 2.39
28 29 3.439825 ACAACATTGAATCAGCGCATACA 59.560 39.130 11.47 0.00 0.00 2.29
29 30 3.680642 ACATTGAATCAGCGCATACAC 57.319 42.857 11.47 0.00 0.00 2.90
30 31 3.273434 ACATTGAATCAGCGCATACACT 58.727 40.909 11.47 0.00 0.00 3.55
31 32 3.691118 ACATTGAATCAGCGCATACACTT 59.309 39.130 11.47 0.00 0.00 3.16
32 33 4.875536 ACATTGAATCAGCGCATACACTTA 59.124 37.500 11.47 0.00 0.00 2.24
33 34 5.353956 ACATTGAATCAGCGCATACACTTAA 59.646 36.000 11.47 0.00 0.00 1.85
34 35 4.857871 TGAATCAGCGCATACACTTAAC 57.142 40.909 11.47 0.00 0.00 2.01
35 36 4.249661 TGAATCAGCGCATACACTTAACA 58.750 39.130 11.47 0.00 0.00 2.41
36 37 4.875536 TGAATCAGCGCATACACTTAACAT 59.124 37.500 11.47 0.00 0.00 2.71
37 38 5.006649 TGAATCAGCGCATACACTTAACATC 59.993 40.000 11.47 0.00 0.00 3.06
38 39 4.123497 TCAGCGCATACACTTAACATCT 57.877 40.909 11.47 0.00 0.00 2.90
39 40 4.112634 TCAGCGCATACACTTAACATCTC 58.887 43.478 11.47 0.00 0.00 2.75
40 41 4.115516 CAGCGCATACACTTAACATCTCT 58.884 43.478 11.47 0.00 0.00 3.10
41 42 4.208047 CAGCGCATACACTTAACATCTCTC 59.792 45.833 11.47 0.00 0.00 3.20
42 43 3.491267 GCGCATACACTTAACATCTCTCC 59.509 47.826 0.30 0.00 0.00 3.71
43 44 3.731216 CGCATACACTTAACATCTCTCCG 59.269 47.826 0.00 0.00 0.00 4.63
44 45 4.497507 CGCATACACTTAACATCTCTCCGA 60.498 45.833 0.00 0.00 0.00 4.55
45 46 4.740695 GCATACACTTAACATCTCTCCGAC 59.259 45.833 0.00 0.00 0.00 4.79
46 47 5.678871 GCATACACTTAACATCTCTCCGACA 60.679 44.000 0.00 0.00 0.00 4.35
47 48 4.866508 ACACTTAACATCTCTCCGACAA 57.133 40.909 0.00 0.00 0.00 3.18
48 49 4.810790 ACACTTAACATCTCTCCGACAAG 58.189 43.478 0.00 0.00 0.00 3.16
49 50 3.614616 CACTTAACATCTCTCCGACAAGC 59.385 47.826 0.00 0.00 0.00 4.01
50 51 3.258372 ACTTAACATCTCTCCGACAAGCA 59.742 43.478 0.00 0.00 0.00 3.91
51 52 4.081420 ACTTAACATCTCTCCGACAAGCAT 60.081 41.667 0.00 0.00 0.00 3.79
52 53 5.127194 ACTTAACATCTCTCCGACAAGCATA 59.873 40.000 0.00 0.00 0.00 3.14
53 54 3.724508 ACATCTCTCCGACAAGCATAG 57.275 47.619 0.00 0.00 0.00 2.23
54 55 3.291584 ACATCTCTCCGACAAGCATAGA 58.708 45.455 0.00 0.00 0.00 1.98
55 56 3.894427 ACATCTCTCCGACAAGCATAGAT 59.106 43.478 0.00 0.00 0.00 1.98
56 57 4.343526 ACATCTCTCCGACAAGCATAGATT 59.656 41.667 0.00 0.00 0.00 2.40
57 58 5.163364 ACATCTCTCCGACAAGCATAGATTT 60.163 40.000 0.00 0.00 0.00 2.17
58 59 4.938080 TCTCTCCGACAAGCATAGATTTC 58.062 43.478 0.00 0.00 0.00 2.17
59 60 4.402474 TCTCTCCGACAAGCATAGATTTCA 59.598 41.667 0.00 0.00 0.00 2.69
60 61 4.686972 TCTCCGACAAGCATAGATTTCAG 58.313 43.478 0.00 0.00 0.00 3.02
61 62 4.402474 TCTCCGACAAGCATAGATTTCAGA 59.598 41.667 0.00 0.00 0.00 3.27
62 63 5.084818 TCCGACAAGCATAGATTTCAGAA 57.915 39.130 0.00 0.00 0.00 3.02
63 64 5.111989 TCCGACAAGCATAGATTTCAGAAG 58.888 41.667 0.00 0.00 0.00 2.85
64 65 5.105351 TCCGACAAGCATAGATTTCAGAAGA 60.105 40.000 0.00 0.00 0.00 2.87
65 66 5.006165 CCGACAAGCATAGATTTCAGAAGAC 59.994 44.000 0.00 0.00 0.00 3.01
66 67 5.809562 CGACAAGCATAGATTTCAGAAGACT 59.190 40.000 0.00 0.00 0.00 3.24
67 68 6.237781 CGACAAGCATAGATTTCAGAAGACTG 60.238 42.308 0.00 0.00 44.66 3.51
90 91 8.873830 ACTGAATCAATGTATAAACTCAAGACG 58.126 33.333 0.00 0.00 0.00 4.18
91 92 7.684670 TGAATCAATGTATAAACTCAAGACGC 58.315 34.615 0.00 0.00 0.00 5.19
92 93 7.333174 TGAATCAATGTATAAACTCAAGACGCA 59.667 33.333 0.00 0.00 0.00 5.24
93 94 6.403333 TCAATGTATAAACTCAAGACGCAC 57.597 37.500 0.00 0.00 0.00 5.34
94 95 6.163476 TCAATGTATAAACTCAAGACGCACT 58.837 36.000 0.00 0.00 0.00 4.40
95 96 6.649141 TCAATGTATAAACTCAAGACGCACTT 59.351 34.615 0.00 0.00 39.70 3.16
106 107 4.900635 AAGACGCACTTGTTCTTCAATT 57.099 36.364 0.00 0.00 37.45 2.32
107 108 4.900635 AGACGCACTTGTTCTTCAATTT 57.099 36.364 0.00 0.00 35.35 1.82
108 109 5.248870 AGACGCACTTGTTCTTCAATTTT 57.751 34.783 0.00 0.00 35.35 1.82
109 110 5.650543 AGACGCACTTGTTCTTCAATTTTT 58.349 33.333 0.00 0.00 35.35 1.94
110 111 6.791303 AGACGCACTTGTTCTTCAATTTTTA 58.209 32.000 0.00 0.00 35.35 1.52
111 112 6.691388 AGACGCACTTGTTCTTCAATTTTTAC 59.309 34.615 0.00 0.00 35.35 2.01
112 113 6.326375 ACGCACTTGTTCTTCAATTTTTACA 58.674 32.000 0.00 0.00 35.35 2.41
113 114 6.472163 ACGCACTTGTTCTTCAATTTTTACAG 59.528 34.615 0.00 0.00 35.35 2.74
114 115 6.472163 CGCACTTGTTCTTCAATTTTTACAGT 59.528 34.615 0.00 0.00 35.35 3.55
115 116 7.513505 CGCACTTGTTCTTCAATTTTTACAGTG 60.514 37.037 0.00 0.00 35.35 3.66
116 117 7.254084 GCACTTGTTCTTCAATTTTTACAGTGG 60.254 37.037 0.00 0.00 35.35 4.00
117 118 7.973388 CACTTGTTCTTCAATTTTTACAGTGGA 59.027 33.333 0.00 0.00 35.35 4.02
118 119 7.973944 ACTTGTTCTTCAATTTTTACAGTGGAC 59.026 33.333 0.00 0.00 35.35 4.02
119 120 7.397892 TGTTCTTCAATTTTTACAGTGGACA 57.602 32.000 0.00 0.00 0.00 4.02
120 121 7.831753 TGTTCTTCAATTTTTACAGTGGACAA 58.168 30.769 0.00 0.00 0.00 3.18
121 122 8.307483 TGTTCTTCAATTTTTACAGTGGACAAA 58.693 29.630 0.00 0.00 0.00 2.83
122 123 9.145865 GTTCTTCAATTTTTACAGTGGACAAAA 57.854 29.630 0.00 0.00 0.00 2.44
123 124 9.712305 TTCTTCAATTTTTACAGTGGACAAAAA 57.288 25.926 12.01 12.01 36.06 1.94
200 214 5.741962 TTCAATTGATGCCCTTCAATGAA 57.258 34.783 9.40 0.00 43.73 2.57
228 246 1.153997 GAGGACGACTGAACGAGCC 60.154 63.158 0.00 0.00 37.03 4.70
296 325 0.457851 CGGTAGGGTTCAGAGCTGAG 59.542 60.000 0.00 0.00 41.13 3.35
345 405 2.047844 CGAGTGTCTGGGCCTGTG 60.048 66.667 4.53 0.00 0.00 3.66
401 482 2.618045 CCGTTTAGGCCCAGTTCAATCT 60.618 50.000 0.00 0.00 0.00 2.40
402 483 3.081804 CGTTTAGGCCCAGTTCAATCTT 58.918 45.455 0.00 0.00 0.00 2.40
403 484 3.506067 CGTTTAGGCCCAGTTCAATCTTT 59.494 43.478 0.00 0.00 0.00 2.52
404 485 4.022329 CGTTTAGGCCCAGTTCAATCTTTT 60.022 41.667 0.00 0.00 0.00 2.27
405 486 5.508994 CGTTTAGGCCCAGTTCAATCTTTTT 60.509 40.000 0.00 0.00 0.00 1.94
432 513 2.873797 GGTGAGGCCCAGTTCAATC 58.126 57.895 0.00 0.00 0.00 2.67
448 529 0.965866 AATCCACGAGACGAGAGGCA 60.966 55.000 0.00 0.00 46.78 4.75
452 533 0.784778 CACGAGACGAGAGGCAAAAC 59.215 55.000 0.00 0.00 46.78 2.43
553 651 2.045926 GGTGGATGCCGCAAGAGT 60.046 61.111 0.00 0.00 43.02 3.24
554 652 2.401766 GGTGGATGCCGCAAGAGTG 61.402 63.158 0.00 0.00 43.02 3.51
698 805 4.772231 ACCCGCCGCTTCCTCCTA 62.772 66.667 0.00 0.00 0.00 2.94
705 812 2.359169 CGCTTCCTCCTAGCCCACA 61.359 63.158 0.00 0.00 35.18 4.17
1043 1183 2.925306 GCGACTACCGACTGTTGATGTT 60.925 50.000 0.00 0.00 41.76 2.71
1053 1193 0.037697 TGTTGATGTTCCGGGACTCG 60.038 55.000 15.59 0.00 38.88 4.18
1069 1209 3.175152 GACTCGGTATCGATGCATCATC 58.825 50.000 25.70 12.06 45.04 2.92
1155 1295 0.539986 GGCACATAGGGTTCCTCGAA 59.460 55.000 0.00 0.00 34.61 3.71
1172 1312 0.674895 GAAGCGGAGGTGCTGACATT 60.675 55.000 0.00 0.00 46.60 2.71
1182 1322 1.270550 GTGCTGACATTCACCTTTGGG 59.729 52.381 0.00 0.00 38.88 4.12
1489 1646 0.923358 AAGTTCTTGGGTGGTGGTCA 59.077 50.000 0.00 0.00 0.00 4.02
1496 1653 1.678970 GGGTGGTGGTCATGCCTTC 60.679 63.158 7.54 2.10 38.35 3.46
1510 1670 0.392998 GCCTTCGGATGGTGATGTGT 60.393 55.000 11.16 0.00 0.00 3.72
1611 1780 0.320374 TCGGTCCTGCAAATCTTCGT 59.680 50.000 0.00 0.00 0.00 3.85
1649 1818 7.505585 TCTTGTTCAACATACCTTCTTTCCAAT 59.494 33.333 0.00 0.00 0.00 3.16
1757 1937 1.534163 CCTCATGAGTTGCAGTGTGTG 59.466 52.381 21.11 0.00 0.00 3.82
1792 1977 4.510711 CACTATGAGCCAGCTAGTTTCATG 59.489 45.833 10.06 0.00 31.49 3.07
1804 2034 9.507280 CCAGCTAGTTTCATGTTTATGTTTATG 57.493 33.333 0.00 0.00 35.73 1.90
1850 2080 1.185618 AGTGGCTGCCGTGAGTCTTA 61.186 55.000 14.98 0.00 0.00 2.10
1878 2108 7.013274 TGCTAAAATTGCAAGTCTCTGTTTACT 59.987 33.333 4.94 0.00 37.51 2.24
1879 2109 7.862873 GCTAAAATTGCAAGTCTCTGTTTACTT 59.137 33.333 4.94 0.00 36.38 2.24
1880 2110 9.736023 CTAAAATTGCAAGTCTCTGTTTACTTT 57.264 29.630 4.94 0.00 33.72 2.66
1996 2295 7.322664 TGAAATGAGGCAAATTATCCTGTTTC 58.677 34.615 16.56 16.56 35.92 2.78
2003 2305 7.267857 AGGCAAATTATCCTGTTTCAATTAGC 58.732 34.615 0.00 0.00 0.00 3.09
2026 2328 7.725251 AGCCAATTTTTCAGTGAAATGTTCTA 58.275 30.769 18.69 0.23 31.34 2.10
2031 2333 7.621832 TTTTTCAGTGAAATGTTCTATTGCG 57.378 32.000 18.69 0.00 31.34 4.85
2053 2356 7.318893 TGCGGTTCATTTTTATTCATGATTCA 58.681 30.769 0.00 0.00 29.45 2.57
2055 2358 8.110002 GCGGTTCATTTTTATTCATGATTCAAC 58.890 33.333 0.00 0.00 29.45 3.18
2072 2376 7.367285 TGATTCAACTGCATTTGGTTAAGTAC 58.633 34.615 15.87 0.00 0.00 2.73
2178 2482 7.205297 AGCCATTTTAAGGAATCAATGATTCG 58.795 34.615 24.46 11.87 46.47 3.34
2348 2986 2.098934 GCAATGCGTATGAATTGGGTCA 59.901 45.455 16.07 0.00 40.91 4.02
2378 3016 4.156008 AGCCGGCTAGTTTCTTTTTATGTG 59.844 41.667 31.86 0.00 0.00 3.21
2401 3039 2.288334 TGACTGTTTCATGGTTGCATGC 60.288 45.455 11.82 11.82 32.87 4.06
2409 3047 6.128254 TGTTTCATGGTTGCATGCAATTTATG 60.128 34.615 33.94 31.05 38.28 1.90
2429 3067 5.971895 ATGCTTGTGTGAAAATTGTGAAC 57.028 34.783 0.00 0.00 0.00 3.18
2478 3116 9.582431 AGCATGTTGATTCTAAAAATCATGAAG 57.418 29.630 0.00 0.00 36.63 3.02
2605 3250 7.993183 TCTTTCACTGTTTCTTAAAGGTCATCT 59.007 33.333 0.00 0.00 0.00 2.90
2617 3262 8.041323 TCTTAAAGGTCATCTAGTGGTTTCATC 58.959 37.037 0.00 0.00 0.00 2.92
2625 3271 9.871238 GTCATCTAGTGGTTTCATCTACTAAAA 57.129 33.333 0.00 0.00 32.62 1.52
2673 3319 4.355437 TGTTTCCATGTTTTGTTGTAGCG 58.645 39.130 0.00 0.00 0.00 4.26
2674 3320 4.096532 TGTTTCCATGTTTTGTTGTAGCGA 59.903 37.500 0.00 0.00 0.00 4.93
2682 3328 5.688823 TGTTTTGTTGTAGCGAATGATCAG 58.311 37.500 0.09 0.00 0.00 2.90
2683 3329 4.340894 TTTGTTGTAGCGAATGATCAGC 57.659 40.909 0.09 0.00 0.00 4.26
2684 3330 3.251479 TGTTGTAGCGAATGATCAGCT 57.749 42.857 12.09 12.09 44.24 4.24
2685 3331 2.931969 TGTTGTAGCGAATGATCAGCTG 59.068 45.455 16.05 7.63 41.80 4.24
2686 3332 1.575244 TGTAGCGAATGATCAGCTGC 58.425 50.000 16.05 15.05 41.80 5.25
2687 3333 1.137675 TGTAGCGAATGATCAGCTGCT 59.862 47.619 19.31 18.95 42.65 4.24
2688 3334 2.362077 TGTAGCGAATGATCAGCTGCTA 59.638 45.455 19.31 18.15 42.65 3.49
2689 3335 2.835580 AGCGAATGATCAGCTGCTAT 57.164 45.000 9.47 0.00 40.07 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.613622 GCGCTGATTCAATGTTGTACTGTT 60.614 41.667 0.00 0.00 0.00 3.16
1 2 3.120199 GCGCTGATTCAATGTTGTACTGT 60.120 43.478 0.00 0.00 0.00 3.55
2 3 3.120234 TGCGCTGATTCAATGTTGTACTG 60.120 43.478 9.73 0.00 0.00 2.74
3 4 3.073678 TGCGCTGATTCAATGTTGTACT 58.926 40.909 9.73 0.00 0.00 2.73
4 5 3.469899 TGCGCTGATTCAATGTTGTAC 57.530 42.857 9.73 0.00 0.00 2.90
5 6 4.633565 TGTATGCGCTGATTCAATGTTGTA 59.366 37.500 9.73 0.00 0.00 2.41
6 7 3.439825 TGTATGCGCTGATTCAATGTTGT 59.560 39.130 9.73 0.00 0.00 3.32
7 8 3.787634 GTGTATGCGCTGATTCAATGTTG 59.212 43.478 9.73 0.00 0.00 3.33
8 9 3.691118 AGTGTATGCGCTGATTCAATGTT 59.309 39.130 9.73 0.00 33.62 2.71
9 10 3.273434 AGTGTATGCGCTGATTCAATGT 58.727 40.909 9.73 0.00 33.62 2.71
10 11 3.957671 AGTGTATGCGCTGATTCAATG 57.042 42.857 9.73 0.00 33.62 2.82
11 12 5.353956 TGTTAAGTGTATGCGCTGATTCAAT 59.646 36.000 9.73 0.00 35.34 2.57
12 13 4.693095 TGTTAAGTGTATGCGCTGATTCAA 59.307 37.500 9.73 0.00 35.34 2.69
13 14 4.249661 TGTTAAGTGTATGCGCTGATTCA 58.750 39.130 9.73 0.00 35.34 2.57
14 15 4.857871 TGTTAAGTGTATGCGCTGATTC 57.142 40.909 9.73 0.00 35.34 2.52
15 16 5.118990 AGATGTTAAGTGTATGCGCTGATT 58.881 37.500 9.73 0.00 35.34 2.57
16 17 4.697514 AGATGTTAAGTGTATGCGCTGAT 58.302 39.130 9.73 0.00 35.34 2.90
17 18 4.112634 GAGATGTTAAGTGTATGCGCTGA 58.887 43.478 9.73 0.00 35.34 4.26
18 19 4.115516 AGAGATGTTAAGTGTATGCGCTG 58.884 43.478 9.73 0.00 35.34 5.18
19 20 4.363999 GAGAGATGTTAAGTGTATGCGCT 58.636 43.478 9.73 0.00 36.97 5.92
20 21 3.491267 GGAGAGATGTTAAGTGTATGCGC 59.509 47.826 0.00 0.00 0.00 6.09
21 22 3.731216 CGGAGAGATGTTAAGTGTATGCG 59.269 47.826 0.00 0.00 0.00 4.73
22 23 4.740695 GTCGGAGAGATGTTAAGTGTATGC 59.259 45.833 0.00 0.00 36.95 3.14
23 24 5.891451 TGTCGGAGAGATGTTAAGTGTATG 58.109 41.667 0.00 0.00 36.95 2.39
24 25 6.525578 TTGTCGGAGAGATGTTAAGTGTAT 57.474 37.500 0.00 0.00 36.95 2.29
25 26 5.621555 GCTTGTCGGAGAGATGTTAAGTGTA 60.622 44.000 0.00 0.00 36.95 2.90
26 27 4.810790 CTTGTCGGAGAGATGTTAAGTGT 58.189 43.478 0.00 0.00 36.95 3.55
27 28 3.614616 GCTTGTCGGAGAGATGTTAAGTG 59.385 47.826 0.00 0.00 36.95 3.16
28 29 3.258372 TGCTTGTCGGAGAGATGTTAAGT 59.742 43.478 0.00 0.00 36.95 2.24
29 30 3.849911 TGCTTGTCGGAGAGATGTTAAG 58.150 45.455 0.00 0.00 36.95 1.85
30 31 3.953712 TGCTTGTCGGAGAGATGTTAA 57.046 42.857 0.00 0.00 36.95 2.01
31 32 4.887655 TCTATGCTTGTCGGAGAGATGTTA 59.112 41.667 0.00 0.00 36.95 2.41
32 33 3.701542 TCTATGCTTGTCGGAGAGATGTT 59.298 43.478 0.00 0.00 36.95 2.71
33 34 3.291584 TCTATGCTTGTCGGAGAGATGT 58.708 45.455 0.00 0.00 36.95 3.06
34 35 3.998099 TCTATGCTTGTCGGAGAGATG 57.002 47.619 0.00 0.00 36.95 2.90
35 36 5.069648 TGAAATCTATGCTTGTCGGAGAGAT 59.930 40.000 0.00 0.00 42.80 2.75
36 37 4.402474 TGAAATCTATGCTTGTCGGAGAGA 59.598 41.667 0.00 0.00 36.95 3.10
37 38 4.686972 TGAAATCTATGCTTGTCGGAGAG 58.313 43.478 0.00 0.00 36.95 3.20
38 39 4.402474 TCTGAAATCTATGCTTGTCGGAGA 59.598 41.667 0.00 0.00 0.00 3.71
39 40 4.686972 TCTGAAATCTATGCTTGTCGGAG 58.313 43.478 0.00 0.00 0.00 4.63
40 41 4.736126 TCTGAAATCTATGCTTGTCGGA 57.264 40.909 0.00 0.00 0.00 4.55
41 42 5.006165 GTCTTCTGAAATCTATGCTTGTCGG 59.994 44.000 0.00 0.00 0.00 4.79
42 43 5.809562 AGTCTTCTGAAATCTATGCTTGTCG 59.190 40.000 0.00 0.00 0.00 4.35
43 44 6.815641 TCAGTCTTCTGAAATCTATGCTTGTC 59.184 38.462 0.00 0.00 46.17 3.18
44 45 6.705302 TCAGTCTTCTGAAATCTATGCTTGT 58.295 36.000 0.00 0.00 46.17 3.16
64 65 8.873830 CGTCTTGAGTTTATACATTGATTCAGT 58.126 33.333 0.00 0.00 0.00 3.41
65 66 7.848051 GCGTCTTGAGTTTATACATTGATTCAG 59.152 37.037 0.00 0.00 0.00 3.02
66 67 7.333174 TGCGTCTTGAGTTTATACATTGATTCA 59.667 33.333 0.00 0.00 0.00 2.57
67 68 7.636359 GTGCGTCTTGAGTTTATACATTGATTC 59.364 37.037 0.00 0.00 0.00 2.52
68 69 7.334421 AGTGCGTCTTGAGTTTATACATTGATT 59.666 33.333 0.00 0.00 0.00 2.57
69 70 6.818644 AGTGCGTCTTGAGTTTATACATTGAT 59.181 34.615 0.00 0.00 0.00 2.57
70 71 6.163476 AGTGCGTCTTGAGTTTATACATTGA 58.837 36.000 0.00 0.00 0.00 2.57
71 72 6.408858 AGTGCGTCTTGAGTTTATACATTG 57.591 37.500 0.00 0.00 0.00 2.82
85 86 4.900635 AATTGAAGAACAAGTGCGTCTT 57.099 36.364 0.00 0.00 42.02 3.01
86 87 4.900635 AAATTGAAGAACAAGTGCGTCT 57.099 36.364 0.00 0.00 42.02 4.18
87 88 5.949233 AAAAATTGAAGAACAAGTGCGTC 57.051 34.783 0.00 0.00 42.02 5.19
88 89 6.326375 TGTAAAAATTGAAGAACAAGTGCGT 58.674 32.000 0.00 0.00 42.02 5.24
89 90 6.472163 ACTGTAAAAATTGAAGAACAAGTGCG 59.528 34.615 0.00 0.00 42.02 5.34
90 91 7.254084 CCACTGTAAAAATTGAAGAACAAGTGC 60.254 37.037 0.00 0.00 42.02 4.40
91 92 7.973388 TCCACTGTAAAAATTGAAGAACAAGTG 59.027 33.333 0.00 0.00 42.02 3.16
92 93 7.973944 GTCCACTGTAAAAATTGAAGAACAAGT 59.026 33.333 0.00 0.00 42.02 3.16
93 94 7.973388 TGTCCACTGTAAAAATTGAAGAACAAG 59.027 33.333 0.00 0.00 42.02 3.16
94 95 7.831753 TGTCCACTGTAAAAATTGAAGAACAA 58.168 30.769 0.00 0.00 42.95 2.83
95 96 7.397892 TGTCCACTGTAAAAATTGAAGAACA 57.602 32.000 0.00 0.00 0.00 3.18
96 97 8.696410 TTTGTCCACTGTAAAAATTGAAGAAC 57.304 30.769 0.00 0.00 0.00 3.01
97 98 9.712305 TTTTTGTCCACTGTAAAAATTGAAGAA 57.288 25.926 0.00 0.00 30.79 2.52
122 123 5.351233 TCGAATTCGTGTACTGCATTTTT 57.649 34.783 25.93 0.00 40.80 1.94
123 124 5.351233 TTCGAATTCGTGTACTGCATTTT 57.649 34.783 25.93 0.00 40.80 1.82
124 125 5.121611 TCATTCGAATTCGTGTACTGCATTT 59.878 36.000 25.93 0.00 40.80 2.32
125 126 4.629634 TCATTCGAATTCGTGTACTGCATT 59.370 37.500 25.93 0.00 40.80 3.56
126 127 4.180817 TCATTCGAATTCGTGTACTGCAT 58.819 39.130 25.93 5.50 40.80 3.96
127 128 3.580731 TCATTCGAATTCGTGTACTGCA 58.419 40.909 25.93 2.59 40.80 4.41
128 129 4.577687 TTCATTCGAATTCGTGTACTGC 57.422 40.909 25.93 0.00 40.80 4.40
129 130 7.671827 TGTTATTCATTCGAATTCGTGTACTG 58.328 34.615 25.93 16.40 42.06 2.74
130 131 7.821595 TGTTATTCATTCGAATTCGTGTACT 57.178 32.000 25.93 11.18 42.06 2.73
200 214 4.458829 TCGTCCTCGGGCATCCCT 62.459 66.667 0.00 0.00 42.67 4.20
228 246 2.202440 CGCCACTAGACACGGTCG 60.202 66.667 0.00 0.00 37.67 4.79
317 347 0.330604 AGACACTCGGCCCAGTAGTA 59.669 55.000 1.43 0.00 0.00 1.82
319 349 1.513158 CAGACACTCGGCCCAGTAG 59.487 63.158 1.43 0.47 0.00 2.57
321 351 3.314331 CCAGACACTCGGCCCAGT 61.314 66.667 0.00 0.00 0.00 4.00
322 352 4.087892 CCCAGACACTCGGCCCAG 62.088 72.222 0.00 0.00 0.00 4.45
414 495 0.681243 GGATTGAACTGGGCCTCACC 60.681 60.000 4.53 0.00 37.93 4.02
415 496 0.038166 TGGATTGAACTGGGCCTCAC 59.962 55.000 4.53 0.00 0.00 3.51
416 497 0.038166 GTGGATTGAACTGGGCCTCA 59.962 55.000 4.53 0.00 0.00 3.86
417 498 1.026718 CGTGGATTGAACTGGGCCTC 61.027 60.000 4.53 0.00 0.00 4.70
418 499 1.002134 CGTGGATTGAACTGGGCCT 60.002 57.895 4.53 0.00 0.00 5.19
419 500 1.002624 TCGTGGATTGAACTGGGCC 60.003 57.895 0.00 0.00 0.00 5.80
420 501 0.036388 TCTCGTGGATTGAACTGGGC 60.036 55.000 0.00 0.00 0.00 5.36
421 502 1.726853 GTCTCGTGGATTGAACTGGG 58.273 55.000 0.00 0.00 0.00 4.45
422 503 1.067846 TCGTCTCGTGGATTGAACTGG 60.068 52.381 0.00 0.00 0.00 4.00
423 504 2.095212 TCTCGTCTCGTGGATTGAACTG 60.095 50.000 0.00 0.00 0.00 3.16
424 505 2.160205 TCTCGTCTCGTGGATTGAACT 58.840 47.619 0.00 0.00 0.00 3.01
425 506 2.520979 CTCTCGTCTCGTGGATTGAAC 58.479 52.381 0.00 0.00 0.00 3.18
426 507 1.472878 CCTCTCGTCTCGTGGATTGAA 59.527 52.381 0.00 0.00 0.00 2.69
427 508 1.095600 CCTCTCGTCTCGTGGATTGA 58.904 55.000 0.00 0.00 0.00 2.57
428 509 0.526524 GCCTCTCGTCTCGTGGATTG 60.527 60.000 0.00 0.00 0.00 2.67
429 510 0.965866 TGCCTCTCGTCTCGTGGATT 60.966 55.000 0.00 0.00 0.00 3.01
430 511 0.965866 TTGCCTCTCGTCTCGTGGAT 60.966 55.000 0.00 0.00 0.00 3.41
431 512 1.176619 TTTGCCTCTCGTCTCGTGGA 61.177 55.000 0.00 0.00 0.00 4.02
432 513 0.319555 TTTTGCCTCTCGTCTCGTGG 60.320 55.000 0.00 0.00 0.00 4.94
448 529 1.232621 GCGGCGTTGAGGTAGGTTTT 61.233 55.000 9.37 0.00 0.00 2.43
538 636 1.375908 GTCACTCTTGCGGCATCCA 60.376 57.895 2.28 0.00 0.00 3.41
827 964 1.009389 GTGGAAGTCGGAGTCTTGCG 61.009 60.000 0.00 0.00 45.32 4.85
1053 1193 3.434641 CCAGTTGATGATGCATCGATACC 59.565 47.826 21.34 9.40 43.14 2.73
1058 1198 2.545526 GGTACCAGTTGATGATGCATCG 59.454 50.000 21.34 7.26 43.14 3.84
1069 1209 1.736645 CGGCGTCAGGTACCAGTTG 60.737 63.158 15.94 3.74 0.00 3.16
1155 1295 1.078848 GAATGTCAGCACCTCCGCT 60.079 57.895 0.00 0.00 45.21 5.52
1182 1322 2.671632 GCTACCACGAAACAGGAGAGAC 60.672 54.545 0.00 0.00 0.00 3.36
1283 1429 1.751927 GCATGGCCAGGAGGAACAG 60.752 63.158 24.18 0.00 36.89 3.16
1338 1493 1.401552 GTCGCTGCATCATTAAAGCCA 59.598 47.619 0.00 0.00 31.84 4.75
1496 1653 2.168521 AGTAGGAACACATCACCATCCG 59.831 50.000 0.00 0.00 35.31 4.18
1510 1670 5.055265 TCACCAAAATTGACCAGTAGGAA 57.945 39.130 0.00 0.00 38.69 3.36
1546 1712 2.546373 CCAACTTGCCACCAATGTCAAG 60.546 50.000 0.00 0.00 41.07 3.02
1611 1780 4.699735 TGTTGAACAAGAGTTTGCTTGAGA 59.300 37.500 10.71 0.00 46.31 3.27
1757 1937 2.213499 CTCATAGTGGGCCGAATTCAC 58.787 52.381 6.22 0.00 0.00 3.18
1804 2034 6.038050 CAGCCCAGAAGAATATTCAGAGAAAC 59.962 42.308 17.56 2.61 0.00 2.78
1850 2080 6.336842 ACAGAGACTTGCAATTTTAGCATT 57.663 33.333 0.00 0.00 42.33 3.56
1948 2247 9.809096 TTCATTGTCAGCTAAAACAAAACATAA 57.191 25.926 11.21 2.24 38.74 1.90
1996 2295 8.776470 ACATTTCACTGAAAAATTGGCTAATTG 58.224 29.630 8.97 0.00 36.65 2.32
2026 2328 8.721019 AATCATGAATAAAAATGAACCGCAAT 57.279 26.923 0.00 0.00 36.44 3.56
2053 2356 6.296026 TCTCAGTACTTAACCAAATGCAGTT 58.704 36.000 0.00 0.00 0.00 3.16
2055 2358 6.992063 ATCTCAGTACTTAACCAAATGCAG 57.008 37.500 0.00 0.00 0.00 4.41
2072 2376 9.553064 AGGCAGAATTAAAACAGTATATCTCAG 57.447 33.333 0.00 0.00 0.00 3.35
2154 2458 6.980397 ACGAATCATTGATTCCTTAAAATGGC 59.020 34.615 26.13 5.38 43.70 4.40
2348 2986 2.766828 AGAAACTAGCCGGCTCATAGTT 59.233 45.455 36.73 32.15 40.55 2.24
2378 3016 1.337703 TGCAACCATGAAACAGTCAGC 59.662 47.619 0.00 0.00 40.43 4.26
2401 3039 8.549548 TCACAATTTTCACACAAGCATAAATTG 58.450 29.630 13.50 13.50 43.39 2.32
2409 3047 5.050837 GGATGTTCACAATTTTCACACAAGC 60.051 40.000 0.00 0.00 0.00 4.01
2422 3060 2.676748 AGCCCAAAAGGATGTTCACAA 58.323 42.857 0.00 0.00 38.24 3.33
2504 3142 1.462283 CACGAGACAGAACAATGGCAG 59.538 52.381 0.00 0.00 0.00 4.85
2513 3151 4.360563 GAAAACAGAGACACGAGACAGAA 58.639 43.478 0.00 0.00 0.00 3.02
2586 3229 7.162082 ACCACTAGATGACCTTTAAGAAACAG 58.838 38.462 0.00 0.00 0.00 3.16
2588 3231 7.981102 AACCACTAGATGACCTTTAAGAAAC 57.019 36.000 0.00 0.00 0.00 2.78
2625 3271 9.255029 AGGAAACAAGTGTATATTGGCTAAATT 57.745 29.630 0.00 0.00 31.76 1.82


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

AutoCloner maintained by Alex Coulton.