Multiple sequence alignment - TraesCS1D01G001300

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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 TraesCS1D01G001300 chr1D 100.000 3125 0 0 1 3125 341882 338758 0.000000e+00 5771.0
1 TraesCS1D01G001300 chr1D 87.835 411 49 1 823 1233 328297 327888 6.060000e-132 481.0
2 TraesCS1D01G001300 chr1D 85.808 458 40 3 1351 1808 327550 327118 2.200000e-126 462.0
3 TraesCS1D01G001300 chr1B 88.344 2282 190 27 92 2367 5005773 5003562 0.000000e+00 2671.0
4 TraesCS1D01G001300 chr1A 91.418 1037 81 6 224 1254 3775487 3776521 0.000000e+00 1415.0
5 TraesCS1D01G001300 chr1A 86.928 1224 111 11 1282 2494 3776501 3777686 0.000000e+00 1328.0
6 TraesCS1D01G001300 chr1A 86.031 766 83 9 1459 2204 3795341 3796102 0.000000e+00 800.0
7 TraesCS1D01G001300 chr1A 86.190 420 57 1 823 1242 3794808 3795226 1.320000e-123 453.0
8 TraesCS1D01G001300 chr2D 89.946 557 45 8 2571 3125 560560557 560560010 0.000000e+00 708.0
9 TraesCS1D01G001300 chr2D 86.772 635 64 17 2507 3125 537993094 537993724 0.000000e+00 689.0
10 TraesCS1D01G001300 chr6D 88.776 588 50 10 2541 3125 60241571 60242145 0.000000e+00 706.0
11 TraesCS1D01G001300 chr6D 88.889 72 6 2 199 270 352721969 352721900 1.540000e-13 87.9
12 TraesCS1D01G001300 chr4D 91.569 510 41 2 2617 3125 360911119 360910611 0.000000e+00 702.0
13 TraesCS1D01G001300 chr4A 87.560 627 52 23 2517 3125 163924211 163924829 0.000000e+00 702.0
14 TraesCS1D01G001300 chr4A 87.692 65 7 1 196 260 616242065 616242128 1.200000e-09 75.0
15 TraesCS1D01G001300 chr3A 88.000 600 55 10 2542 3125 6799180 6799778 0.000000e+00 693.0
16 TraesCS1D01G001300 chr3A 87.833 600 56 10 2542 3125 6870787 6871385 0.000000e+00 688.0
17 TraesCS1D01G001300 chr3A 87.333 600 59 10 2542 3125 6822637 6823235 0.000000e+00 671.0
18 TraesCS1D01G001300 chr3A 88.235 68 6 2 194 260 597230048 597230114 2.580000e-11 80.5
19 TraesCS1D01G001300 chr3A 87.324 71 8 1 196 266 624836030 624836099 2.580000e-11 80.5
20 TraesCS1D01G001300 chr6A 87.034 617 59 19 2524 3125 141292054 141291444 0.000000e+00 676.0
21 TraesCS1D01G001300 chr6A 85.366 82 11 1 186 267 20335373 20335293 2.000000e-12 84.2
22 TraesCS1D01G001300 chr3D 90.323 62 5 1 199 260 443602074 443602014 2.580000e-11 80.5
23 TraesCS1D01G001300 chr6B 86.301 73 9 1 196 268 20419557 20419628 9.290000e-11 78.7


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 TraesCS1D01G001300 chr1D 338758 341882 3124 True 5771.0 5771 100.0000 1 3125 1 chr1D.!!$R1 3124
1 TraesCS1D01G001300 chr1D 327118 328297 1179 True 471.5 481 86.8215 823 1808 2 chr1D.!!$R2 985
2 TraesCS1D01G001300 chr1B 5003562 5005773 2211 True 2671.0 2671 88.3440 92 2367 1 chr1B.!!$R1 2275
3 TraesCS1D01G001300 chr1A 3775487 3777686 2199 False 1371.5 1415 89.1730 224 2494 2 chr1A.!!$F1 2270
4 TraesCS1D01G001300 chr1A 3794808 3796102 1294 False 626.5 800 86.1105 823 2204 2 chr1A.!!$F2 1381
5 TraesCS1D01G001300 chr2D 560560010 560560557 547 True 708.0 708 89.9460 2571 3125 1 chr2D.!!$R1 554
6 TraesCS1D01G001300 chr2D 537993094 537993724 630 False 689.0 689 86.7720 2507 3125 1 chr2D.!!$F1 618
7 TraesCS1D01G001300 chr6D 60241571 60242145 574 False 706.0 706 88.7760 2541 3125 1 chr6D.!!$F1 584
8 TraesCS1D01G001300 chr4D 360910611 360911119 508 True 702.0 702 91.5690 2617 3125 1 chr4D.!!$R1 508
9 TraesCS1D01G001300 chr4A 163924211 163924829 618 False 702.0 702 87.5600 2517 3125 1 chr4A.!!$F1 608
10 TraesCS1D01G001300 chr3A 6799180 6799778 598 False 693.0 693 88.0000 2542 3125 1 chr3A.!!$F1 583
11 TraesCS1D01G001300 chr3A 6870787 6871385 598 False 688.0 688 87.8330 2542 3125 1 chr3A.!!$F3 583
12 TraesCS1D01G001300 chr3A 6822637 6823235 598 False 671.0 671 87.3330 2542 3125 1 chr3A.!!$F2 583
13 TraesCS1D01G001300 chr6A 141291444 141292054 610 True 676.0 676 87.0340 2524 3125 1 chr6A.!!$R2 601

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
215 216 0.100861 GCGACCCAAACGGACAAAAA 59.899 50.0 0.0 0.0 34.64 1.94 F
220 221 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.0 0.0 0.0 0.00 5.54 F
250 251 0.865111 TGTCCGTTTGAGTCATTGCG 59.135 50.0 0.0 0.0 0.00 4.85 F
1445 1703 0.888619 TCCCGCAACAACAACAACAA 59.111 45.0 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1209 0.322098 CGGGTATGGTTGTTGCTGGA 60.322 55.0 0.00 0.0 0.0 3.86 R
1464 1722 0.387202 TGCGGGAATTGTGGTTGTTG 59.613 50.0 0.00 0.0 0.0 3.33 R
1465 1723 1.115467 TTGCGGGAATTGTGGTTGTT 58.885 45.0 0.00 0.0 0.0 2.83 R
2907 3239 0.036388 GAAGAACCACCGGATGAGCA 60.036 55.0 9.46 0.0 0.0 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
39 40 4.735132 GTGCTGCTGCGGGTCGTA 62.735 66.667 10.99 0.00 43.34 3.43
40 41 4.435436 TGCTGCTGCGGGTCGTAG 62.435 66.667 10.99 1.25 42.13 3.51
41 42 4.436998 GCTGCTGCGGGTCGTAGT 62.437 66.667 10.99 0.00 41.34 2.73
42 43 3.060020 GCTGCTGCGGGTCGTAGTA 62.060 63.158 10.99 2.19 41.34 1.82
43 44 1.064296 CTGCTGCGGGTCGTAGTAG 59.936 63.158 8.65 8.65 43.56 2.57
44 45 2.337749 CTGCTGCGGGTCGTAGTAGG 62.338 65.000 13.42 0.00 44.71 3.18
45 46 2.117156 GCTGCGGGTCGTAGTAGGA 61.117 63.158 7.19 0.00 41.34 2.94
46 47 2.023318 CTGCGGGTCGTAGTAGGAG 58.977 63.158 0.00 0.00 35.06 3.69
47 48 2.061182 CTGCGGGTCGTAGTAGGAGC 62.061 65.000 12.51 12.51 35.06 4.70
48 49 2.843352 GCGGGTCGTAGTAGGAGCC 61.843 68.421 24.67 24.67 44.56 4.70
49 50 4.672251 GGGTCGTAGTAGGAGCCA 57.328 61.111 27.90 0.00 46.52 4.75
50 51 2.892025 GGGTCGTAGTAGGAGCCAA 58.108 57.895 27.90 0.00 46.52 4.52
51 52 0.745468 GGGTCGTAGTAGGAGCCAAG 59.255 60.000 27.90 0.00 46.52 3.61
52 53 0.745468 GGTCGTAGTAGGAGCCAAGG 59.255 60.000 10.28 0.00 0.00 3.61
53 54 0.102663 GTCGTAGTAGGAGCCAAGGC 59.897 60.000 2.02 2.02 42.33 4.35
80 81 3.712907 GGGTGGCTCGGGCTGTTA 61.713 66.667 7.48 0.00 38.73 2.41
81 82 2.590092 GGTGGCTCGGGCTGTTAT 59.410 61.111 7.48 0.00 38.73 1.89
82 83 1.819632 GGTGGCTCGGGCTGTTATG 60.820 63.158 7.48 0.00 38.73 1.90
83 84 2.124736 TGGCTCGGGCTGTTATGC 60.125 61.111 7.48 0.00 38.73 3.14
84 85 3.272334 GGCTCGGGCTGTTATGCG 61.272 66.667 7.48 0.00 38.73 4.73
85 86 3.272334 GCTCGGGCTGTTATGCGG 61.272 66.667 0.00 0.00 35.22 5.69
86 87 2.588877 CTCGGGCTGTTATGCGGG 60.589 66.667 0.00 0.00 0.00 6.13
116 117 0.755327 ACACCAAGCCCTCAACAACC 60.755 55.000 0.00 0.00 0.00 3.77
123 124 1.959226 CCCTCAACAACCGTGTCCG 60.959 63.158 0.00 0.00 36.80 4.79
137 138 0.834612 TGTCCGTTTCAGTTGGGTCT 59.165 50.000 0.00 0.00 0.00 3.85
138 139 1.210967 TGTCCGTTTCAGTTGGGTCTT 59.789 47.619 0.00 0.00 0.00 3.01
139 140 1.871676 GTCCGTTTCAGTTGGGTCTTC 59.128 52.381 0.00 0.00 0.00 2.87
140 141 1.202722 TCCGTTTCAGTTGGGTCTTCC 60.203 52.381 0.00 0.00 0.00 3.46
141 142 1.476110 CCGTTTCAGTTGGGTCTTCCA 60.476 52.381 0.00 0.00 45.43 3.53
147 148 1.888512 CAGTTGGGTCTTCCATGTTGG 59.111 52.381 0.00 0.00 46.52 3.77
153 154 2.433436 GGTCTTCCATGTTGGGTACAC 58.567 52.381 0.00 0.00 40.19 2.90
154 155 2.039879 GGTCTTCCATGTTGGGTACACT 59.960 50.000 0.00 0.00 40.19 3.55
169 170 3.626924 ACTGGTGGTGTCCGGCTC 61.627 66.667 0.00 0.00 37.37 4.70
171 172 3.302347 CTGGTGGTGTCCGGCTCTC 62.302 68.421 0.00 0.00 0.00 3.20
183 184 3.749064 GCTCTCCGTCTGCGTCCA 61.749 66.667 0.00 0.00 36.15 4.02
190 191 2.444624 CGTCTGCGTCCATTGTCCG 61.445 63.158 0.00 0.00 0.00 4.79
198 199 0.386731 GTCCATTGTCCGTTTTGGCG 60.387 55.000 0.00 0.00 37.80 5.69
214 215 1.726533 GGCGACCCAAACGGACAAAA 61.727 55.000 0.00 0.00 34.64 2.44
215 216 0.100861 GCGACCCAAACGGACAAAAA 59.899 50.000 0.00 0.00 34.64 1.94
216 217 1.862411 GCGACCCAAACGGACAAAAAG 60.862 52.381 0.00 0.00 34.64 2.27
217 218 1.847818 GACCCAAACGGACAAAAAGC 58.152 50.000 0.00 0.00 34.64 3.51
219 220 0.596341 CCCAAACGGACAAAAAGCGG 60.596 55.000 0.00 0.00 0.00 5.52
220 221 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.000 0.00 0.00 0.00 5.54
221 222 1.472990 CAAACGGACAAAAAGCGGAC 58.527 50.000 0.00 0.00 0.00 4.79
222 223 1.096416 AAACGGACAAAAAGCGGACA 58.904 45.000 0.00 0.00 0.00 4.02
228 229 3.553917 CGGACAAAAAGCGGACAAAAATT 59.446 39.130 0.00 0.00 0.00 1.82
241 242 4.344448 GACAAAAATTCGTGTCCGTTTGA 58.656 39.130 9.35 0.00 38.57 2.69
246 247 2.519377 TTCGTGTCCGTTTGAGTCAT 57.481 45.000 0.00 0.00 35.01 3.06
250 251 0.865111 TGTCCGTTTGAGTCATTGCG 59.135 50.000 0.00 0.00 0.00 4.85
305 308 4.997395 ACTCAACGCACTCTAATTCACATT 59.003 37.500 0.00 0.00 0.00 2.71
353 356 5.888691 TTTGATACACCGTGTGCAATATT 57.111 34.783 14.66 0.00 36.98 1.28
423 428 8.749354 GTTCCTCAAAGGGTTTAATATCATGTT 58.251 33.333 0.00 0.00 35.59 2.71
497 503 8.328146 CAACTCATACGACATTACTAACATTGG 58.672 37.037 0.00 0.00 0.00 3.16
583 590 8.937634 AACTACGAAGTTAGTTCAGAAAGAAA 57.062 30.769 0.53 0.00 44.26 2.52
584 591 9.543783 AACTACGAAGTTAGTTCAGAAAGAAAT 57.456 29.630 0.53 0.00 44.26 2.17
645 652 2.185004 ACAACGCCAAGCAAGACTAT 57.815 45.000 0.00 0.00 0.00 2.12
659 666 6.338937 AGCAAGACTATAAACTTAGTTCCCG 58.661 40.000 0.00 0.00 32.59 5.14
677 684 1.134521 CCGACAAGCTATGCCAACCTA 60.135 52.381 0.00 0.00 0.00 3.08
696 703 3.375299 CCTAGATGTGCCTAACAACTTGC 59.625 47.826 0.00 0.00 43.61 4.01
797 805 6.483307 TCATTACGATTATCAAGCTTTCCTGG 59.517 38.462 0.00 0.00 0.00 4.45
817 825 1.092348 CACTCCATGGATGTGTGCTG 58.908 55.000 24.75 12.16 0.00 4.41
844 852 2.440409 AGCAACTTTGGCGATCAATCT 58.560 42.857 0.00 0.00 34.98 2.40
845 853 2.163010 AGCAACTTTGGCGATCAATCTG 59.837 45.455 0.00 0.00 34.98 2.90
1015 1023 3.498121 CCCTTCCATCATCCATCCTTCAG 60.498 52.174 0.00 0.00 0.00 3.02
1017 1025 4.141321 CCTTCCATCATCCATCCTTCAGAA 60.141 45.833 0.00 0.00 0.00 3.02
1038 1046 1.927487 TTTGGAGCACAAGCATCCAT 58.073 45.000 8.66 0.00 43.07 3.41
1040 1048 2.804986 TGGAGCACAAGCATCCATAA 57.195 45.000 0.00 0.00 45.49 1.90
1146 1154 4.803426 CCGCACAGCTCGACCCTC 62.803 72.222 0.00 0.00 0.00 4.30
1201 1209 2.862541 TCTGCAACAGCAACCACTTAT 58.137 42.857 0.00 0.00 37.91 1.73
1216 1224 4.263727 ACCACTTATCCAGCAACAACCATA 60.264 41.667 0.00 0.00 0.00 2.74
1223 1231 1.677633 GCAACAACCATACCCGCCT 60.678 57.895 0.00 0.00 0.00 5.52
1286 1294 1.870055 AACCATTTCCGCTGCAGCAG 61.870 55.000 36.03 26.87 42.21 4.24
1322 1330 3.280295 ACAACAACCGTATCCACAACAA 58.720 40.909 0.00 0.00 0.00 2.83
1330 1338 2.482721 CGTATCCACAACAACCACTTCC 59.517 50.000 0.00 0.00 0.00 3.46
1335 1343 1.408702 CACAACAACCACTTCCCCAAG 59.591 52.381 0.00 0.00 35.50 3.61
1445 1703 0.888619 TCCCGCAACAACAACAACAA 59.111 45.000 0.00 0.00 0.00 2.83
1446 1704 0.995728 CCCGCAACAACAACAACAAC 59.004 50.000 0.00 0.00 0.00 3.32
1447 1705 1.670087 CCCGCAACAACAACAACAACA 60.670 47.619 0.00 0.00 0.00 3.33
1448 1706 2.061773 CCGCAACAACAACAACAACAA 58.938 42.857 0.00 0.00 0.00 2.83
1449 1707 2.091899 CCGCAACAACAACAACAACAAG 59.908 45.455 0.00 0.00 0.00 3.16
1450 1708 2.983136 CGCAACAACAACAACAACAAGA 59.017 40.909 0.00 0.00 0.00 3.02
1451 1709 3.426859 CGCAACAACAACAACAACAAGAA 59.573 39.130 0.00 0.00 0.00 2.52
1452 1710 4.662891 CGCAACAACAACAACAACAAGAAC 60.663 41.667 0.00 0.00 0.00 3.01
1453 1711 4.210120 GCAACAACAACAACAACAAGAACA 59.790 37.500 0.00 0.00 0.00 3.18
1454 1712 5.277058 GCAACAACAACAACAACAAGAACAA 60.277 36.000 0.00 0.00 0.00 2.83
1455 1713 5.898630 ACAACAACAACAACAAGAACAAC 57.101 34.783 0.00 0.00 0.00 3.32
1456 1714 5.596845 ACAACAACAACAACAAGAACAACT 58.403 33.333 0.00 0.00 0.00 3.16
1457 1715 5.689961 ACAACAACAACAACAAGAACAACTC 59.310 36.000 0.00 0.00 0.00 3.01
1458 1716 4.805219 ACAACAACAACAAGAACAACTCC 58.195 39.130 0.00 0.00 0.00 3.85
1459 1717 4.173256 CAACAACAACAAGAACAACTCCC 58.827 43.478 0.00 0.00 0.00 4.30
1460 1718 3.426615 ACAACAACAAGAACAACTCCCA 58.573 40.909 0.00 0.00 0.00 4.37
1461 1719 3.192633 ACAACAACAAGAACAACTCCCAC 59.807 43.478 0.00 0.00 0.00 4.61
1462 1720 3.080300 ACAACAAGAACAACTCCCACA 57.920 42.857 0.00 0.00 0.00 4.17
1463 1721 3.426615 ACAACAAGAACAACTCCCACAA 58.573 40.909 0.00 0.00 0.00 3.33
1464 1722 3.192633 ACAACAAGAACAACTCCCACAAC 59.807 43.478 0.00 0.00 0.00 3.32
1465 1723 3.080300 ACAAGAACAACTCCCACAACA 57.920 42.857 0.00 0.00 0.00 3.33
1533 1791 6.322712 ACAACCATTAACACAACAACCATACT 59.677 34.615 0.00 0.00 0.00 2.12
1622 1880 1.072159 GTTCCTCCTGCAGCAGTGT 59.928 57.895 21.26 0.00 0.00 3.55
1628 1886 1.073025 CCTGCAGCAGTGTAACCCA 59.927 57.895 21.26 0.00 37.80 4.51
1855 2132 1.152777 CACAACAGTTGGGCCAGGA 60.153 57.895 17.76 0.00 34.12 3.86
1890 2167 0.896923 TCAACATCAATTGGGCCAGC 59.103 50.000 6.23 0.00 0.00 4.85
1891 2168 0.609151 CAACATCAATTGGGCCAGCA 59.391 50.000 6.23 0.00 0.00 4.41
1894 2171 0.458669 CATCAATTGGGCCAGCACTC 59.541 55.000 6.23 0.00 0.00 3.51
1921 2198 2.616524 ACCTCAACAACTAGCCCAGTA 58.383 47.619 0.00 0.00 36.04 2.74
1923 2200 2.354805 CCTCAACAACTAGCCCAGTACC 60.355 54.545 0.00 0.00 36.04 3.34
1955 2232 4.351111 AGGTTACTTGTGATTCAGACCCTT 59.649 41.667 0.00 0.00 0.00 3.95
2054 2331 6.167685 CAATGGTGGACAATGAAATCACAAT 58.832 36.000 0.00 0.00 31.41 2.71
2121 2398 4.449068 GGACGATCGATGTAGCAATGAAAT 59.551 41.667 24.34 0.00 0.00 2.17
2204 2482 8.785329 TGGGAATAAAGGCAAACAAAATATTC 57.215 30.769 0.00 0.00 0.00 1.75
2215 2493 5.384063 AACAAAATATTCCACGTCATGCA 57.616 34.783 0.00 0.00 0.00 3.96
2222 2500 2.293677 TCCACGTCATGCACATCTAC 57.706 50.000 0.00 0.00 0.00 2.59
2225 2503 3.002791 CCACGTCATGCACATCTACTTT 58.997 45.455 0.00 0.00 0.00 2.66
2250 2528 4.422073 AGGAACTGCAATCCATCGATTA 57.578 40.909 17.87 0.00 39.55 1.75
2252 2530 4.758674 AGGAACTGCAATCCATCGATTATG 59.241 41.667 17.87 0.00 39.55 1.90
2258 2536 7.108194 ACTGCAATCCATCGATTATGTATCAT 58.892 34.615 0.00 0.00 36.54 2.45
2286 2564 6.681729 TTCATAGGTATATCAACCCAGTCC 57.318 41.667 0.00 0.00 40.71 3.85
2289 2567 3.046374 AGGTATATCAACCCAGTCCCAC 58.954 50.000 0.00 0.00 40.71 4.61
2291 2569 1.979809 ATATCAACCCAGTCCCACCA 58.020 50.000 0.00 0.00 0.00 4.17
2294 2572 1.065410 TCAACCCAGTCCCACCATGT 61.065 55.000 0.00 0.00 0.00 3.21
2295 2573 0.895100 CAACCCAGTCCCACCATGTG 60.895 60.000 0.00 0.00 0.00 3.21
2300 2578 1.679944 CCAGTCCCACCATGTGATGTC 60.680 57.143 0.00 0.00 35.23 3.06
2345 2623 5.880332 CGGAAAATTTAGTTCAGGGATCTCA 59.120 40.000 0.00 0.00 0.00 3.27
2357 2635 3.625649 GGGATCTCATGCCTCTAATCC 57.374 52.381 0.00 0.00 37.84 3.01
2376 2655 2.505982 CCCAGCCACCATAGTCCG 59.494 66.667 0.00 0.00 0.00 4.79
2378 2657 1.602237 CCAGCCACCATAGTCCGTT 59.398 57.895 0.00 0.00 0.00 4.44
2383 2662 0.528924 CCACCATAGTCCGTTGACGA 59.471 55.000 4.91 0.00 46.51 4.20
2405 2684 1.112113 GCGTGGAGGTAGGATCTCAA 58.888 55.000 0.00 0.00 33.18 3.02
2406 2685 1.689273 GCGTGGAGGTAGGATCTCAAT 59.311 52.381 0.00 0.00 33.18 2.57
2416 2695 3.853355 AGGATCTCAATGTCATGTCCC 57.147 47.619 0.00 0.00 0.00 4.46
2421 2701 0.251916 TCAATGTCATGTCCCGGTCC 59.748 55.000 0.00 0.00 0.00 4.46
2426 2706 1.904771 TCATGTCCCGGTCCATGAC 59.095 57.895 22.56 13.37 41.77 3.06
2456 2739 2.223479 GCATGTGTCGTGTGACCTTTTT 60.223 45.455 0.00 0.00 44.86 1.94
2457 2740 3.362295 CATGTGTCGTGTGACCTTTTTG 58.638 45.455 0.00 0.00 44.86 2.44
2458 2741 1.740585 TGTGTCGTGTGACCTTTTTGG 59.259 47.619 0.00 0.00 44.86 3.28
2459 2742 2.011222 GTGTCGTGTGACCTTTTTGGA 58.989 47.619 0.00 0.00 44.86 3.53
2484 2767 4.647424 AAATGTGTTCGTGTGTGGATTT 57.353 36.364 0.00 0.00 0.00 2.17
2485 2768 3.624326 ATGTGTTCGTGTGTGGATTTG 57.376 42.857 0.00 0.00 0.00 2.32
2486 2769 1.673400 TGTGTTCGTGTGTGGATTTGG 59.327 47.619 0.00 0.00 0.00 3.28
2494 2777 4.020928 TCGTGTGTGGATTTGGTGTATAGT 60.021 41.667 0.00 0.00 0.00 2.12
2495 2778 4.092821 CGTGTGTGGATTTGGTGTATAGTG 59.907 45.833 0.00 0.00 0.00 2.74
2496 2779 5.001232 GTGTGTGGATTTGGTGTATAGTGT 58.999 41.667 0.00 0.00 0.00 3.55
2497 2780 5.472137 GTGTGTGGATTTGGTGTATAGTGTT 59.528 40.000 0.00 0.00 0.00 3.32
2498 2781 5.471797 TGTGTGGATTTGGTGTATAGTGTTG 59.528 40.000 0.00 0.00 0.00 3.33
2499 2782 5.703592 GTGTGGATTTGGTGTATAGTGTTGA 59.296 40.000 0.00 0.00 0.00 3.18
2500 2783 5.703592 TGTGGATTTGGTGTATAGTGTTGAC 59.296 40.000 0.00 0.00 0.00 3.18
2501 2784 5.123344 GTGGATTTGGTGTATAGTGTTGACC 59.877 44.000 0.00 0.00 0.00 4.02
2502 2785 5.221945 TGGATTTGGTGTATAGTGTTGACCA 60.222 40.000 0.00 0.00 34.85 4.02
2503 2786 5.885912 GGATTTGGTGTATAGTGTTGACCAT 59.114 40.000 0.00 0.00 36.59 3.55
2504 2787 6.038271 GGATTTGGTGTATAGTGTTGACCATC 59.962 42.308 0.00 0.00 36.59 3.51
2505 2788 5.755409 TTGGTGTATAGTGTTGACCATCT 57.245 39.130 0.00 0.00 36.59 2.90
2508 2791 4.503910 GTGTATAGTGTTGACCATCTGCA 58.496 43.478 0.00 0.00 0.00 4.41
2681 3012 1.598130 GCTATGTCATCCACCGCCC 60.598 63.158 0.00 0.00 0.00 6.13
2705 3036 1.229400 TACTCCAACCCCTTCGCCT 60.229 57.895 0.00 0.00 0.00 5.52
2714 3045 4.020617 CCTTCGCCTGGCTGGACA 62.021 66.667 17.92 0.00 38.35 4.02
2728 3059 2.261671 GACACCGCTGACATCCGT 59.738 61.111 0.00 0.00 0.00 4.69
2785 3116 1.537814 ATGCCACCGACTCCACGTAA 61.538 55.000 0.00 0.00 0.00 3.18
2800 3131 1.336148 ACGTAATTCGCGTGGAAGACA 60.336 47.619 5.77 0.00 44.19 3.41
2867 3199 3.434319 GCACCGTCGACTCCCGTA 61.434 66.667 14.70 0.00 39.75 4.02
3033 3365 1.166531 ACCGACAACAAGCTTCAGCC 61.167 55.000 0.00 0.00 43.38 4.85
3034 3366 0.886490 CCGACAACAAGCTTCAGCCT 60.886 55.000 0.00 0.00 43.38 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.527583 CTGCCGCCTCCTGCTCTC 62.528 72.222 0.00 0.00 38.05 3.20
22 23 4.735132 TACGACCCGCAGCAGCAC 62.735 66.667 0.82 0.00 42.27 4.40
23 24 4.435436 CTACGACCCGCAGCAGCA 62.435 66.667 0.82 0.00 42.27 4.41
24 25 2.938539 CTACTACGACCCGCAGCAGC 62.939 65.000 0.00 0.00 37.42 5.25
25 26 1.064296 CTACTACGACCCGCAGCAG 59.936 63.158 0.00 0.00 0.00 4.24
26 27 2.412323 CCTACTACGACCCGCAGCA 61.412 63.158 0.00 0.00 0.00 4.41
27 28 2.061182 CTCCTACTACGACCCGCAGC 62.061 65.000 0.00 0.00 0.00 5.25
28 29 2.023318 CTCCTACTACGACCCGCAG 58.977 63.158 0.00 0.00 0.00 5.18
29 30 2.117156 GCTCCTACTACGACCCGCA 61.117 63.158 0.00 0.00 0.00 5.69
30 31 2.720605 GCTCCTACTACGACCCGC 59.279 66.667 0.00 0.00 0.00 6.13
31 32 1.033746 TTGGCTCCTACTACGACCCG 61.034 60.000 0.00 0.00 0.00 5.28
32 33 0.745468 CTTGGCTCCTACTACGACCC 59.255 60.000 0.00 0.00 0.00 4.46
33 34 0.745468 CCTTGGCTCCTACTACGACC 59.255 60.000 0.00 0.00 0.00 4.79
34 35 0.102663 GCCTTGGCTCCTACTACGAC 59.897 60.000 4.11 0.00 0.00 4.34
35 36 1.381928 CGCCTTGGCTCCTACTACGA 61.382 60.000 10.12 0.00 0.00 3.43
36 37 1.065928 CGCCTTGGCTCCTACTACG 59.934 63.158 10.12 0.00 0.00 3.51
37 38 1.442148 CCGCCTTGGCTCCTACTAC 59.558 63.158 10.12 0.00 0.00 2.73
38 39 3.950232 CCGCCTTGGCTCCTACTA 58.050 61.111 10.12 0.00 0.00 1.82
63 64 3.043999 ATAACAGCCCGAGCCACCC 62.044 63.158 0.00 0.00 41.25 4.61
64 65 1.819632 CATAACAGCCCGAGCCACC 60.820 63.158 0.00 0.00 41.25 4.61
65 66 2.472909 GCATAACAGCCCGAGCCAC 61.473 63.158 0.00 0.00 41.25 5.01
66 67 2.124736 GCATAACAGCCCGAGCCA 60.125 61.111 0.00 0.00 41.25 4.75
67 68 3.272334 CGCATAACAGCCCGAGCC 61.272 66.667 0.00 0.00 41.25 4.70
68 69 3.272334 CCGCATAACAGCCCGAGC 61.272 66.667 0.00 0.00 40.32 5.03
69 70 2.588877 CCCGCATAACAGCCCGAG 60.589 66.667 0.00 0.00 0.00 4.63
70 71 4.849310 GCCCGCATAACAGCCCGA 62.849 66.667 0.00 0.00 0.00 5.14
91 92 4.379243 AGGGCTTGGTGTCGCTCG 62.379 66.667 0.00 0.00 0.00 5.03
92 93 2.435059 GAGGGCTTGGTGTCGCTC 60.435 66.667 0.00 0.00 35.61 5.03
93 94 2.818169 TTGAGGGCTTGGTGTCGCT 61.818 57.895 0.00 0.00 0.00 4.93
94 95 2.281484 TTGAGGGCTTGGTGTCGC 60.281 61.111 0.00 0.00 0.00 5.19
95 96 0.817634 TTGTTGAGGGCTTGGTGTCG 60.818 55.000 0.00 0.00 0.00 4.35
102 103 0.818040 GACACGGTTGTTGAGGGCTT 60.818 55.000 0.00 0.00 35.47 4.35
107 108 2.685364 AACGGACACGGTTGTTGAG 58.315 52.632 0.00 0.00 46.48 3.02
137 138 1.777878 ACCAGTGTACCCAACATGGAA 59.222 47.619 0.00 0.00 40.96 3.53
138 139 1.073125 CACCAGTGTACCCAACATGGA 59.927 52.381 0.00 0.00 40.96 3.41
139 140 1.533625 CACCAGTGTACCCAACATGG 58.466 55.000 0.00 0.00 41.10 3.66
140 141 1.202879 ACCACCAGTGTACCCAACATG 60.203 52.381 0.00 0.00 41.10 3.21
141 142 1.145571 ACCACCAGTGTACCCAACAT 58.854 50.000 0.00 0.00 41.10 2.71
153 154 3.302347 GAGAGCCGGACACCACCAG 62.302 68.421 5.05 0.00 0.00 4.00
154 155 3.311110 GAGAGCCGGACACCACCA 61.311 66.667 5.05 0.00 0.00 4.17
169 170 1.078759 GACAATGGACGCAGACGGAG 61.079 60.000 0.00 0.00 46.04 4.63
171 172 2.100631 GGACAATGGACGCAGACGG 61.101 63.158 0.00 0.00 46.04 4.79
183 184 1.520600 GGGTCGCCAAAACGGACAAT 61.521 55.000 0.00 0.00 36.56 2.71
190 191 1.299544 CCGTTTGGGTCGCCAAAAC 60.300 57.895 15.09 15.09 40.66 2.43
198 199 1.847818 GCTTTTTGTCCGTTTGGGTC 58.152 50.000 0.00 0.00 37.00 4.46
206 207 2.196295 TTTTGTCCGCTTTTTGTCCG 57.804 45.000 0.00 0.00 0.00 4.79
210 211 4.032331 ACACGAATTTTTGTCCGCTTTTTG 59.968 37.500 0.00 0.00 0.00 2.44
214 215 2.994849 GACACGAATTTTTGTCCGCTT 58.005 42.857 8.52 0.00 36.85 4.68
215 216 2.681152 GACACGAATTTTTGTCCGCT 57.319 45.000 8.52 0.00 36.85 5.52
219 220 4.344448 TCAAACGGACACGAATTTTTGTC 58.656 39.130 10.50 10.50 44.60 3.18
220 221 4.142556 ACTCAAACGGACACGAATTTTTGT 60.143 37.500 0.00 0.00 44.60 2.83
221 222 4.347813 ACTCAAACGGACACGAATTTTTG 58.652 39.130 0.00 0.00 44.60 2.44
222 223 4.095185 TGACTCAAACGGACACGAATTTTT 59.905 37.500 0.00 0.00 44.60 1.94
228 229 2.131972 CAATGACTCAAACGGACACGA 58.868 47.619 0.00 0.00 44.60 4.35
235 236 2.661504 TCAACGCAATGACTCAAACG 57.338 45.000 0.00 0.00 0.00 3.60
241 242 1.001378 GCCAACTTCAACGCAATGACT 60.001 47.619 0.00 0.00 0.00 3.41
246 247 1.681538 TAAGGCCAACTTCAACGCAA 58.318 45.000 5.01 0.00 40.64 4.85
250 251 5.450550 GGAATAGCATAAGGCCAACTTCAAC 60.451 44.000 5.01 0.00 46.50 3.18
321 324 5.062934 ACACGGTGTATCAAATACAATGACG 59.937 40.000 12.96 7.10 46.36 4.35
400 404 8.292444 TGAACATGATATTAAACCCTTTGAGG 57.708 34.615 0.00 0.00 34.30 3.86
423 428 2.398840 TTTCCGCGGGAACACCATGA 62.399 55.000 27.83 0.00 41.87 3.07
645 652 4.612264 AGCTTGTCGGGAACTAAGTTTA 57.388 40.909 0.00 0.00 0.00 2.01
659 666 3.543680 TCTAGGTTGGCATAGCTTGTC 57.456 47.619 0.00 0.00 0.00 3.18
677 684 2.816087 CTGCAAGTTGTTAGGCACATCT 59.184 45.455 4.48 0.00 37.07 2.90
734 742 9.935682 CATTTTACATGCGAAACACTTATCTAT 57.064 29.630 0.00 0.00 0.00 1.98
817 825 0.854705 CGCCAAAGTTGCTTTCTTGC 59.145 50.000 0.00 0.00 30.60 4.01
844 852 6.347888 GGCGCTACTTACAAGTGTAATTTTCA 60.348 38.462 7.64 0.00 39.49 2.69
845 853 6.019762 GGCGCTACTTACAAGTGTAATTTTC 58.980 40.000 7.64 0.00 39.49 2.29
1015 1023 3.256558 GGATGCTTGTGCTCCAAATTTC 58.743 45.455 0.00 0.00 40.48 2.17
1017 1025 2.250031 TGGATGCTTGTGCTCCAAATT 58.750 42.857 0.00 0.00 40.70 1.82
1083 1091 1.201429 ACGAGGAGGGCAAAGACCAT 61.201 55.000 0.00 0.00 29.21 3.55
1133 1141 3.069980 GATGCGAGGGTCGAGCTGT 62.070 63.158 15.18 1.84 43.74 4.40
1146 1154 1.402968 CCTTTCTTGGTCATGGATGCG 59.597 52.381 0.00 0.00 0.00 4.73
1201 1209 0.322098 CGGGTATGGTTGTTGCTGGA 60.322 55.000 0.00 0.00 0.00 3.86
1216 1224 4.021925 GTGGCTCTTGAGGCGGGT 62.022 66.667 17.27 0.00 37.15 5.28
1223 1231 1.064758 AGTGGTTGTTGTGGCTCTTGA 60.065 47.619 0.00 0.00 0.00 3.02
1286 1294 1.339610 TGTTGTTGCTGGTATTGTGGC 59.660 47.619 0.00 0.00 0.00 5.01
1293 1301 2.616634 TACGGTTGTTGTTGCTGGTA 57.383 45.000 0.00 0.00 0.00 3.25
1322 1330 1.569072 AGTTGTTCTTGGGGAAGTGGT 59.431 47.619 0.00 0.00 34.23 4.16
1330 1338 1.620822 CTGGGGAAGTTGTTCTTGGG 58.379 55.000 0.00 0.00 36.40 4.12
1335 1343 1.398692 TGTTGCTGGGGAAGTTGTTC 58.601 50.000 0.00 0.00 0.00 3.18
1445 1703 3.080300 TGTTGTGGGAGTTGTTCTTGT 57.920 42.857 0.00 0.00 0.00 3.16
1446 1704 3.192422 TGTTGTTGTGGGAGTTGTTCTTG 59.808 43.478 0.00 0.00 0.00 3.02
1447 1705 3.426615 TGTTGTTGTGGGAGTTGTTCTT 58.573 40.909 0.00 0.00 0.00 2.52
1448 1706 3.080300 TGTTGTTGTGGGAGTTGTTCT 57.920 42.857 0.00 0.00 0.00 3.01
1449 1707 3.507786 GTTGTTGTTGTGGGAGTTGTTC 58.492 45.455 0.00 0.00 0.00 3.18
1450 1708 2.232696 GGTTGTTGTTGTGGGAGTTGTT 59.767 45.455 0.00 0.00 0.00 2.83
1451 1709 1.822371 GGTTGTTGTTGTGGGAGTTGT 59.178 47.619 0.00 0.00 0.00 3.32
1452 1710 1.821753 TGGTTGTTGTTGTGGGAGTTG 59.178 47.619 0.00 0.00 0.00 3.16
1453 1711 1.822371 GTGGTTGTTGTTGTGGGAGTT 59.178 47.619 0.00 0.00 0.00 3.01
1454 1712 1.272203 TGTGGTTGTTGTTGTGGGAGT 60.272 47.619 0.00 0.00 0.00 3.85
1455 1713 1.468985 TGTGGTTGTTGTTGTGGGAG 58.531 50.000 0.00 0.00 0.00 4.30
1456 1714 1.924731 TTGTGGTTGTTGTTGTGGGA 58.075 45.000 0.00 0.00 0.00 4.37
1457 1715 2.977772 ATTGTGGTTGTTGTTGTGGG 57.022 45.000 0.00 0.00 0.00 4.61
1458 1716 3.194062 GGAATTGTGGTTGTTGTTGTGG 58.806 45.455 0.00 0.00 0.00 4.17
1459 1717 3.194062 GGGAATTGTGGTTGTTGTTGTG 58.806 45.455 0.00 0.00 0.00 3.33
1460 1718 2.159170 CGGGAATTGTGGTTGTTGTTGT 60.159 45.455 0.00 0.00 0.00 3.32
1461 1719 2.468831 CGGGAATTGTGGTTGTTGTTG 58.531 47.619 0.00 0.00 0.00 3.33
1462 1720 1.202475 GCGGGAATTGTGGTTGTTGTT 60.202 47.619 0.00 0.00 0.00 2.83
1463 1721 0.387565 GCGGGAATTGTGGTTGTTGT 59.612 50.000 0.00 0.00 0.00 3.32
1464 1722 0.387202 TGCGGGAATTGTGGTTGTTG 59.613 50.000 0.00 0.00 0.00 3.33
1465 1723 1.115467 TTGCGGGAATTGTGGTTGTT 58.885 45.000 0.00 0.00 0.00 2.83
1622 1880 2.561419 CGACAGTTTCTCCTCTGGGTTA 59.439 50.000 0.00 0.00 36.17 2.85
1628 1886 4.769859 GAGTAACGACAGTTTCTCCTCT 57.230 45.455 6.72 0.00 44.14 3.69
1890 2167 5.923733 AGTTGTTGAGGTAGGATAGAGTG 57.076 43.478 0.00 0.00 0.00 3.51
1891 2168 5.595133 GCTAGTTGTTGAGGTAGGATAGAGT 59.405 44.000 0.00 0.00 0.00 3.24
1894 2171 4.039366 GGGCTAGTTGTTGAGGTAGGATAG 59.961 50.000 0.00 0.00 0.00 2.08
1923 2200 6.485313 TGAATCACAAGTAACCTAACCAACTG 59.515 38.462 0.00 0.00 0.00 3.16
2033 2310 6.009589 ACTATTGTGATTTCATTGTCCACCA 58.990 36.000 0.00 0.00 0.00 4.17
2054 2331 9.168553 AGGTCCATCTATCTAGTAGTACAACTA 57.831 37.037 2.52 0.00 0.00 2.24
2121 2398 4.521130 TGGTGCACGGCATTTTATTTTA 57.479 36.364 11.45 0.00 41.91 1.52
2133 2411 1.159713 ACGCATATGATGGTGCACGG 61.160 55.000 11.45 0.00 41.32 4.94
2204 2482 2.299993 AGTAGATGTGCATGACGTGG 57.700 50.000 0.00 0.00 0.00 4.94
2215 2493 6.299805 TGCAGTTCCTATCAAAGTAGATGT 57.700 37.500 0.00 0.00 0.00 3.06
2222 2500 5.277683 CGATGGATTGCAGTTCCTATCAAAG 60.278 44.000 16.22 5.12 34.17 2.77
2225 2503 3.387699 TCGATGGATTGCAGTTCCTATCA 59.612 43.478 16.22 0.10 34.17 2.15
2264 2542 5.091552 GGGACTGGGTTGATATACCTATGA 58.908 45.833 0.00 0.00 38.30 2.15
2265 2543 4.844085 TGGGACTGGGTTGATATACCTATG 59.156 45.833 0.00 0.00 38.30 2.23
2266 2544 4.844655 GTGGGACTGGGTTGATATACCTAT 59.155 45.833 0.00 0.00 38.30 2.57
2267 2545 4.228824 GTGGGACTGGGTTGATATACCTA 58.771 47.826 0.00 0.00 38.30 3.08
2269 2547 2.105993 GGTGGGACTGGGTTGATATACC 59.894 54.545 0.00 0.00 37.47 2.73
2280 2558 0.329261 ACATCACATGGTGGGACTGG 59.671 55.000 0.00 0.00 29.32 4.00
2284 2562 2.967745 TTTGACATCACATGGTGGGA 57.032 45.000 0.00 0.00 32.34 4.37
2317 2595 6.316280 TCCCTGAACTAAATTTTCCGGATA 57.684 37.500 4.15 0.00 30.87 2.59
2357 2635 2.757124 GGACTATGGTGGCTGGGGG 61.757 68.421 0.00 0.00 0.00 5.40
2383 2662 2.043248 ATCCTACCTCCACGCCGT 60.043 61.111 0.00 0.00 0.00 5.68
2385 2664 0.755698 TGAGATCCTACCTCCACGCC 60.756 60.000 0.00 0.00 0.00 5.68
2388 2667 3.706594 TGACATTGAGATCCTACCTCCAC 59.293 47.826 0.00 0.00 0.00 4.02
2389 2668 3.994317 TGACATTGAGATCCTACCTCCA 58.006 45.455 0.00 0.00 0.00 3.86
2397 2676 2.487934 CGGGACATGACATTGAGATCC 58.512 52.381 0.00 0.00 0.00 3.36
2405 2684 0.181114 CATGGACCGGGACATGACAT 59.819 55.000 27.11 9.56 45.55 3.06
2406 2685 0.907230 TCATGGACCGGGACATGACA 60.907 55.000 28.70 15.20 46.05 3.58
2421 2701 3.076621 ACACATGCTGGTACAAGTCATG 58.923 45.455 22.65 22.65 38.70 3.07
2426 2706 1.460743 CACGACACATGCTGGTACAAG 59.539 52.381 0.00 0.00 38.70 3.16
2471 2754 2.912690 TACACCAAATCCACACACGA 57.087 45.000 0.00 0.00 0.00 4.35
2481 2764 6.599244 CAGATGGTCAACACTATACACCAAAT 59.401 38.462 0.00 0.00 40.51 2.32
2484 2767 4.622933 GCAGATGGTCAACACTATACACCA 60.623 45.833 0.00 0.00 41.36 4.17
2485 2768 3.871594 GCAGATGGTCAACACTATACACC 59.128 47.826 0.00 0.00 0.00 4.16
2486 2769 4.503910 TGCAGATGGTCAACACTATACAC 58.496 43.478 0.00 0.00 0.00 2.90
2494 2777 1.672030 CGGCTGCAGATGGTCAACA 60.672 57.895 20.43 0.00 0.00 3.33
2495 2778 3.044059 GCGGCTGCAGATGGTCAAC 62.044 63.158 20.43 0.00 42.15 3.18
2496 2779 2.747460 GCGGCTGCAGATGGTCAA 60.747 61.111 20.43 0.00 42.15 3.18
2497 2780 4.783621 GGCGGCTGCAGATGGTCA 62.784 66.667 20.43 0.00 45.35 4.02
2609 2934 1.541620 GGTTTGGGGAGGAGGAGGT 60.542 63.158 0.00 0.00 0.00 3.85
2665 2996 2.448582 GGGGGCGGTGGATGACATA 61.449 63.158 0.00 0.00 0.00 2.29
2681 3012 0.845102 AAGGGGTTGGAGTAGGTGGG 60.845 60.000 0.00 0.00 0.00 4.61
2705 3036 4.314440 GTCAGCGGTGTCCAGCCA 62.314 66.667 15.22 0.00 0.00 4.75
2714 3045 1.888436 ATGTCACGGATGTCAGCGGT 61.888 55.000 0.00 0.00 0.00 5.68
2728 3059 2.096466 GCGTTCGTGAATGTTGATGTCA 60.096 45.455 3.94 0.00 0.00 3.58
2785 3116 2.961526 AGTATGTCTTCCACGCGAAT 57.038 45.000 15.93 0.00 0.00 3.34
2800 3131 1.066303 CGGAAGAGCAGCGAGAAGTAT 59.934 52.381 0.00 0.00 0.00 2.12
2866 3198 1.105167 CGGAGTCGCCCACCATAGTA 61.105 60.000 0.00 0.00 0.00 1.82
2867 3199 2.423898 CGGAGTCGCCCACCATAGT 61.424 63.158 0.00 0.00 0.00 2.12
2907 3239 0.036388 GAAGAACCACCGGATGAGCA 60.036 55.000 9.46 0.00 0.00 4.26
2986 3318 1.507141 CGTTGAGCTTGACCCACACC 61.507 60.000 0.00 0.00 0.00 4.16
3033 3365 0.723790 CTGCTGCAGAAAAACGCGAG 60.724 55.000 24.88 0.00 32.44 5.03
3034 3366 1.279539 CTGCTGCAGAAAAACGCGA 59.720 52.632 24.88 0.00 32.44 5.87


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

AutoCloner maintained by Alex Coulton.