Multiple sequence alignment - TraesCS4B01G155900

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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 TraesCS4B01G155900 chr4B 100.000 7006 0 0 1 7006 282888874 282881869 0.000000e+00 12938.0
1 TraesCS4B01G155900 chr4B 88.994 318 34 1 2206 2523 107453015 107453331 6.590000e-105 392.0
2 TraesCS4B01G155900 chr4D 96.461 3984 97 13 1156 5128 211389386 211385436 0.000000e+00 6536.0
3 TraesCS4B01G155900 chr4D 92.610 1881 51 22 5127 6943 211385332 211383476 0.000000e+00 2623.0
4 TraesCS4B01G155900 chr4D 98.842 259 3 0 796 1054 211390010 211389752 4.950000e-126 462.0
5 TraesCS4B01G155900 chr4D 88.438 320 37 0 2206 2525 75046292 75046611 3.070000e-103 387.0
6 TraesCS4B01G155900 chr4D 84.076 157 16 6 4424 4578 507718560 507718411 7.330000e-30 143.0
7 TraesCS4B01G155900 chr4D 95.349 86 4 0 1899 1984 270678549 270678634 3.410000e-28 137.0
8 TraesCS4B01G155900 chr4D 95.556 45 1 1 4574 4617 1371517 1371473 3.510000e-08 71.3
9 TraesCS4B01G155900 chr4A 91.838 2193 93 34 4717 6849 204964127 204966293 0.000000e+00 2979.0
10 TraesCS4B01G155900 chr4A 95.808 1813 58 8 2469 4263 204961505 204963317 0.000000e+00 2911.0
11 TraesCS4B01G155900 chr4A 96.587 1084 27 3 796 1870 204956982 204958064 0.000000e+00 1788.0
12 TraesCS4B01G155900 chr4A 91.349 393 9 6 4280 4668 204963466 204963837 1.350000e-141 514.0
13 TraesCS4B01G155900 chr4A 90.852 317 29 0 2209 2525 512543500 512543184 6.500000e-115 425.0
14 TraesCS4B01G155900 chr4A 92.208 77 6 0 1949 2025 204961428 204961504 7.430000e-20 110.0
15 TraesCS4B01G155900 chr4A 94.444 54 3 0 1859 1912 204961381 204961434 4.500000e-12 84.2
16 TraesCS4B01G155900 chr6D 96.044 809 31 1 1 809 318951181 318950374 0.000000e+00 1315.0
17 TraesCS4B01G155900 chr6D 82.545 275 42 6 2185 2458 340843103 340842834 3.270000e-58 237.0
18 TraesCS4B01G155900 chr6D 89.041 146 12 4 2185 2329 340856261 340856119 2.010000e-40 178.0
19 TraesCS4B01G155900 chr5A 95.143 803 38 1 1 803 90614559 90613758 0.000000e+00 1266.0
20 TraesCS4B01G155900 chr5A 85.000 120 11 4 4420 4537 109953097 109953211 1.600000e-21 115.0
21 TraesCS4B01G155900 chr1A 95.037 806 39 1 1 806 442463972 442464776 0.000000e+00 1266.0
22 TraesCS4B01G155900 chr1A 88.679 318 32 3 2208 2525 412467082 412466769 1.100000e-102 385.0
23 TraesCS4B01G155900 chr1A 90.196 102 8 2 1887 1987 584675692 584675592 1.590000e-26 132.0
24 TraesCS4B01G155900 chr6A 94.658 805 38 1 1 805 40615011 40614212 0.000000e+00 1243.0
25 TraesCS4B01G155900 chr6A 86.837 509 66 1 291 799 55035268 55034761 1.020000e-157 568.0
26 TraesCS4B01G155900 chr6A 87.000 200 25 1 603 802 481078821 481078623 2.540000e-54 224.0
27 TraesCS4B01G155900 chr7D 87.980 807 89 6 1 806 234357146 234356347 0.000000e+00 946.0
28 TraesCS4B01G155900 chr7D 86.719 128 13 4 4419 4544 484423865 484423990 9.480000e-29 139.0
29 TraesCS4B01G155900 chr1B 86.692 804 104 3 1 803 393448563 393447762 0.000000e+00 889.0
30 TraesCS4B01G155900 chr1B 88.393 112 12 1 1876 1986 447815472 447815361 4.410000e-27 134.0
31 TraesCS4B01G155900 chr1B 80.000 125 14 8 4445 4559 222306997 222306874 1.620000e-11 82.4
32 TraesCS4B01G155900 chr3D 85.572 804 106 5 3 805 29709440 29708646 0.000000e+00 833.0
33 TraesCS4B01G155900 chr3D 81.988 161 25 3 4418 4578 126947003 126947159 4.410000e-27 134.0
34 TraesCS4B01G155900 chr3D 91.379 58 5 0 4422 4479 126947211 126947268 5.830000e-11 80.5
35 TraesCS4B01G155900 chr7B 86.571 700 93 1 106 805 206346625 206345927 0.000000e+00 771.0
36 TraesCS4B01G155900 chr6B 90.159 315 28 3 2210 2524 26227683 26227994 2.350000e-109 407.0
37 TraesCS4B01G155900 chr6B 89.241 316 33 1 2210 2525 26012970 26012656 1.830000e-105 394.0
38 TraesCS4B01G155900 chr5D 90.323 310 29 1 2210 2519 114976363 114976671 8.460000e-109 405.0
39 TraesCS4B01G155900 chr5D 97.647 85 2 0 1899 1983 318879332 318879416 5.660000e-31 147.0
40 TraesCS4B01G155900 chr3A 88.438 320 29 5 2206 2525 164407965 164407654 5.130000e-101 379.0
41 TraesCS4B01G155900 chr3A 92.857 42 3 0 4438 4479 137577658 137577699 2.110000e-05 62.1
42 TraesCS4B01G155900 chr7A 95.506 89 4 0 1896 1984 608509126 608509214 7.330000e-30 143.0
43 TraesCS4B01G155900 chr5B 95.506 89 4 0 1896 1984 26770502 26770414 7.330000e-30 143.0
44 TraesCS4B01G155900 chr1D 95.455 88 4 0 1898 1985 338394563 338394476 2.630000e-29 141.0
45 TraesCS4B01G155900 chr1D 95.238 42 2 0 4438 4479 158102136 158102177 4.540000e-07 67.6
46 TraesCS4B01G155900 chr2A 93.617 94 5 1 1890 1983 509051635 509051727 9.480000e-29 139.0
47 TraesCS4B01G155900 chr3B 82.716 162 21 4 4418 4578 181286734 181286889 3.410000e-28 137.0
48 TraesCS4B01G155900 chr3B 95.000 60 3 0 4420 4479 181286939 181286998 2.080000e-15 95.3
49 TraesCS4B01G155900 chr3B 88.060 67 8 0 5501 5567 648006615 648006549 5.830000e-11 80.5
50 TraesCS4B01G155900 chr2B 95.161 62 3 0 4418 4479 583158062 583158001 1.610000e-16 99.0


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 TraesCS4B01G155900 chr4B 282881869 282888874 7005 True 12938.0 12938 100.000000 1 7006 1 chr4B.!!$R1 7005
1 TraesCS4B01G155900 chr4D 211383476 211390010 6534 True 3207.0 6536 95.971000 796 6943 3 chr4D.!!$R3 6147
2 TraesCS4B01G155900 chr4A 204956982 204966293 9311 False 1397.7 2979 93.705667 796 6849 6 chr4A.!!$F1 6053
3 TraesCS4B01G155900 chr6D 318950374 318951181 807 True 1315.0 1315 96.044000 1 809 1 chr6D.!!$R1 808
4 TraesCS4B01G155900 chr5A 90613758 90614559 801 True 1266.0 1266 95.143000 1 803 1 chr5A.!!$R1 802
5 TraesCS4B01G155900 chr1A 442463972 442464776 804 False 1266.0 1266 95.037000 1 806 1 chr1A.!!$F1 805
6 TraesCS4B01G155900 chr6A 40614212 40615011 799 True 1243.0 1243 94.658000 1 805 1 chr6A.!!$R1 804
7 TraesCS4B01G155900 chr6A 55034761 55035268 507 True 568.0 568 86.837000 291 799 1 chr6A.!!$R2 508
8 TraesCS4B01G155900 chr7D 234356347 234357146 799 True 946.0 946 87.980000 1 806 1 chr7D.!!$R1 805
9 TraesCS4B01G155900 chr1B 393447762 393448563 801 True 889.0 889 86.692000 1 803 1 chr1B.!!$R2 802
10 TraesCS4B01G155900 chr3D 29708646 29709440 794 True 833.0 833 85.572000 3 805 1 chr3D.!!$R1 802
11 TraesCS4B01G155900 chr7B 206345927 206346625 698 True 771.0 771 86.571000 106 805 1 chr7B.!!$R1 699

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
135 136 1.757699 AGACTCGGTTAGATTCCTGCC 59.242 52.381 0.00 0.0 29.68 4.85 F
1089 1098 2.770048 CCTGCCTTCCCCGATCCT 60.770 66.667 0.00 0.0 0.00 3.24 F
1872 5474 0.105593 ATACGTGCTCTGGCTGGATG 59.894 55.000 0.00 0.0 39.59 3.51 F
2996 6599 0.384309 CCCACATGCATGCACATCTC 59.616 55.000 25.37 0.0 0.00 2.75 F
3141 6744 0.549469 GATACCGGGATTGGGGTTGT 59.451 55.000 6.32 0.0 37.75 3.32 F
4676 8432 0.676782 GGGAGGTGTTGGTCATTCCG 60.677 60.000 0.00 0.0 39.52 4.30 F
5087 9086 2.559840 CTGTGGCTTTGAGCAGCG 59.440 61.111 2.04 0.0 44.75 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2131 0.179037 TATGCATCCAGCCAGAGCAC 60.179 55.000 0.19 0.00 44.83 4.40 R
2719 6321 0.169009 GCTAAGTCGGCCAAAAGCAG 59.831 55.000 2.24 0.00 46.50 4.24 R
3409 7014 1.407299 CCAGATTCGATGCTGGGACAA 60.407 52.381 20.66 0.00 46.24 3.18 R
4547 8303 0.842030 ATCTCCACCCAAGTCAGGCA 60.842 55.000 0.00 0.00 0.00 4.75 R
4861 8859 0.978146 ACCAGCCTCATTAGACCGCT 60.978 55.000 0.00 0.00 0.00 5.52 R
5553 9668 1.063174 CCTAGCTCACAATTGCGCTTC 59.937 52.381 18.62 1.13 41.11 3.86 R
6959 11131 0.171455 AACTAGAAGAGCTCGTGCGG 59.829 55.000 6.97 2.24 45.42 5.69 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
50 51 2.483877 CAGCGTGATTTGGTGCTTCTAA 59.516 45.455 0.00 0.00 34.99 2.10
135 136 1.757699 AGACTCGGTTAGATTCCTGCC 59.242 52.381 0.00 0.00 29.68 4.85
210 211 4.279043 GCCGGTTGTTGCGCCTTT 62.279 61.111 4.18 0.00 0.00 3.11
273 274 3.544684 CAAGCCATGCTGGTATGTCTAA 58.455 45.455 4.45 0.00 39.62 2.10
279 280 5.319453 CCATGCTGGTATGTCTAATTGGAT 58.681 41.667 0.00 0.00 31.35 3.41
618 619 7.431668 GCTTCTTCAAGATAGATCAAACATTGC 59.568 37.037 0.00 0.00 0.00 3.56
628 629 5.841810 AGATCAAACATTGCCTTTCGAAAA 58.158 33.333 12.41 0.00 0.00 2.29
633 634 6.536582 TCAAACATTGCCTTTCGAAAAATTGA 59.463 30.769 12.41 7.84 0.00 2.57
646 647 5.122869 TCGAAAAATTGAGAGAGATGGCAAG 59.877 40.000 0.00 0.00 0.00 4.01
960 969 3.103742 AGTCCAAGCTCCAAAACCAAAA 58.896 40.909 0.00 0.00 0.00 2.44
1089 1098 2.770048 CCTGCCTTCCCCGATCCT 60.770 66.667 0.00 0.00 0.00 3.24
1215 1488 4.077822 CTGTTTTTCTTGGCTCTCAGGAT 58.922 43.478 0.00 0.00 31.33 3.24
1709 1983 8.357402 GTCAACTGAATTTTTAGTATGGGTTGT 58.643 33.333 0.00 0.00 34.11 3.32
1757 2031 4.906618 TCTGCTACTTTAAGACCCTTTGG 58.093 43.478 0.00 0.00 37.80 3.28
1819 2093 6.572898 CGGTGTGTAGGTTAATGTTAGGAAGA 60.573 42.308 0.00 0.00 0.00 2.87
1834 2108 6.269307 TGTTAGGAAGACTATAGGGTAATGCC 59.731 42.308 4.43 0.00 0.00 4.40
1857 2131 6.019801 GCCTGTGATTAGTGAACAGTTATACG 60.020 42.308 0.00 0.00 39.75 3.06
1872 5474 0.105593 ATACGTGCTCTGGCTGGATG 59.894 55.000 0.00 0.00 39.59 3.51
2101 5703 6.664428 AAATTTTAGTTTAGGCAGGCTTGA 57.336 33.333 0.00 0.00 0.00 3.02
2161 5763 1.371467 TATATCCCCCATGCCACAGG 58.629 55.000 0.00 0.00 0.00 4.00
2368 5970 2.894126 ACCATGCACGGGAAAATGTTTA 59.106 40.909 12.94 0.00 0.00 2.01
2369 5971 3.322254 ACCATGCACGGGAAAATGTTTAA 59.678 39.130 12.94 0.00 0.00 1.52
2370 5972 3.677596 CCATGCACGGGAAAATGTTTAAC 59.322 43.478 0.00 0.00 0.00 2.01
2519 6121 1.094785 GCAACATGCGGTGTATCCTT 58.905 50.000 0.00 0.00 41.14 3.36
2705 6307 4.096984 ACTCTTGTGGAAGAAAAGCACTTG 59.903 41.667 0.00 0.00 37.77 3.16
2719 6321 6.885735 AAAGCACTTGAAACACAACAATAC 57.114 33.333 0.00 0.00 34.56 1.89
2808 6411 4.750098 GGATGGATTTATACAGGACACACG 59.250 45.833 0.00 0.00 0.00 4.49
2842 6445 3.777106 TCACTGCTTTCATGAACTCCT 57.223 42.857 7.89 0.00 0.00 3.69
2949 6552 1.068472 CGAGCGACTGTTACACCTCTT 60.068 52.381 0.00 0.00 0.00 2.85
2964 6567 5.491982 ACACCTCTTAGGAAGCTAAATGTG 58.508 41.667 0.00 0.00 37.67 3.21
2996 6599 0.384309 CCCACATGCATGCACATCTC 59.616 55.000 25.37 0.00 0.00 2.75
3141 6744 0.549469 GATACCGGGATTGGGGTTGT 59.451 55.000 6.32 0.00 37.75 3.32
3314 6919 5.935789 GGCTTACAGTAGTAACACCAATGAA 59.064 40.000 0.00 0.00 35.37 2.57
3409 7014 1.566211 CTGGATCAGAGACCTGGTGT 58.434 55.000 2.82 0.00 40.76 4.16
3487 7092 4.020485 GGTCTTGGTAACTGTGGACTATGT 60.020 45.833 0.00 0.00 37.61 2.29
3616 7221 5.235186 TGTTGACCAAAACCATTTATTTGCG 59.765 36.000 0.00 0.00 35.66 4.85
3640 7245 6.811170 CGTATGTTTGCTCCATGGTAAAATTT 59.189 34.615 12.58 5.77 0.00 1.82
3685 7290 8.089625 TCATTGAAACTAGATAACCATCCTGA 57.910 34.615 0.00 0.00 0.00 3.86
3793 7402 7.493971 CAGTCTGATTCTATTGGGTACAAGAAG 59.506 40.741 0.00 0.00 40.49 2.85
3913 7525 6.472016 TCAGGATTGTGTTAATGAGCTGTTA 58.528 36.000 0.00 0.00 0.00 2.41
4055 7674 9.117183 GGGTGTTTGGAAGGTTAGTATAATAAG 57.883 37.037 0.00 0.00 0.00 1.73
4233 7852 2.057137 TTTGTTGCTTCTCAGTGCCT 57.943 45.000 0.00 0.00 0.00 4.75
4519 8275 3.367806 CCTCATCTTCACATCTGACGTGT 60.368 47.826 3.63 0.00 35.79 4.49
4547 8303 1.971149 TGATCAACACCTCCCCTCAT 58.029 50.000 0.00 0.00 0.00 2.90
4562 8318 0.679002 CTCATGCCTGACTTGGGTGG 60.679 60.000 0.00 0.00 0.00 4.61
4563 8319 1.133181 TCATGCCTGACTTGGGTGGA 61.133 55.000 0.00 0.00 0.00 4.02
4564 8320 0.679002 CATGCCTGACTTGGGTGGAG 60.679 60.000 0.00 0.00 0.00 3.86
4565 8321 0.842030 ATGCCTGACTTGGGTGGAGA 60.842 55.000 0.00 0.00 0.00 3.71
4566 8322 0.842030 TGCCTGACTTGGGTGGAGAT 60.842 55.000 0.00 0.00 0.00 2.75
4567 8323 1.204146 GCCTGACTTGGGTGGAGATA 58.796 55.000 0.00 0.00 0.00 1.98
4568 8324 1.559682 GCCTGACTTGGGTGGAGATAA 59.440 52.381 0.00 0.00 0.00 1.75
4569 8325 2.026262 GCCTGACTTGGGTGGAGATAAA 60.026 50.000 0.00 0.00 0.00 1.40
4570 8326 3.372025 GCCTGACTTGGGTGGAGATAAAT 60.372 47.826 0.00 0.00 0.00 1.40
4571 8327 4.202441 CCTGACTTGGGTGGAGATAAATG 58.798 47.826 0.00 0.00 0.00 2.32
4572 8328 4.080356 CCTGACTTGGGTGGAGATAAATGA 60.080 45.833 0.00 0.00 0.00 2.57
4573 8329 5.398353 CCTGACTTGGGTGGAGATAAATGAT 60.398 44.000 0.00 0.00 0.00 2.45
4574 8330 6.078456 TGACTTGGGTGGAGATAAATGATT 57.922 37.500 0.00 0.00 0.00 2.57
4575 8331 5.887598 TGACTTGGGTGGAGATAAATGATTG 59.112 40.000 0.00 0.00 0.00 2.67
4576 8332 5.203528 ACTTGGGTGGAGATAAATGATTGG 58.796 41.667 0.00 0.00 0.00 3.16
4577 8333 4.183223 TGGGTGGAGATAAATGATTGGG 57.817 45.455 0.00 0.00 0.00 4.12
4578 8334 3.790976 TGGGTGGAGATAAATGATTGGGA 59.209 43.478 0.00 0.00 0.00 4.37
4676 8432 0.676782 GGGAGGTGTTGGTCATTCCG 60.677 60.000 0.00 0.00 39.52 4.30
4681 8437 2.838202 AGGTGTTGGTCATTCCGTATCT 59.162 45.455 0.00 0.00 39.52 1.98
4959 8957 8.023706 GGAATTGGTTGAAGAAGATAACAGTTC 58.976 37.037 0.00 0.00 0.00 3.01
5087 9086 2.559840 CTGTGGCTTTGAGCAGCG 59.440 61.111 2.04 0.00 44.75 5.18
5379 9485 3.632604 GCCAGATAGACACTACTACTGCA 59.367 47.826 0.00 0.00 0.00 4.41
5499 9606 4.607293 TGAAGCTGAAGAAGTGCTAGAA 57.393 40.909 0.00 0.00 35.85 2.10
5506 9613 6.816140 AGCTGAAGAAGTGCTAGAAGTTATTC 59.184 38.462 15.99 15.99 35.05 1.75
5599 9735 1.148027 TGCTATGCCTAGAGCCTAGGT 59.852 52.381 22.04 11.19 40.39 3.08
5612 9749 1.681264 GCCTAGGTGCGCCATTTTAAT 59.319 47.619 20.59 0.00 37.19 1.40
5951 10089 6.681777 AGGTTGCTTGAACTGATTGAATTAC 58.318 36.000 0.00 0.00 34.66 1.89
6062 10222 8.193250 TGGTATCTGTACTAAAGCGAAATTTC 57.807 34.615 8.20 8.20 0.00 2.17
6086 10246 5.316327 CCTGCTGAAGGGAGAAATTTTAC 57.684 43.478 0.00 0.00 43.15 2.01
6211 10371 5.016051 TCTTCTGCTTACCATGTCTGATC 57.984 43.478 0.00 0.00 0.00 2.92
6221 10381 7.526860 GCTTACCATGTCTGATCCAATAGAGAT 60.527 40.741 0.00 0.00 0.00 2.75
6333 10496 9.311916 CTGGTTGAAATTGACATTTGAACTTAA 57.688 29.630 9.06 0.00 42.78 1.85
6449 10614 6.094186 GGACCAGTCAACATTCCTAAATTCTC 59.906 42.308 0.00 0.00 0.00 2.87
6512 10678 2.124819 CTGCTGCGGCTCATCCTT 60.125 61.111 20.27 0.00 39.59 3.36
6574 10740 1.985684 GCGGCAATGTTGAAAGCTTAC 59.014 47.619 0.00 0.00 0.00 2.34
6653 10819 7.201652 GGTGCTCTTATATCTGTTTCACCTTTC 60.202 40.741 0.00 0.00 38.61 2.62
6673 10839 4.422073 TCCACGCTTCAATTATCTCCAT 57.578 40.909 0.00 0.00 0.00 3.41
6698 10864 4.101119 CAGTCCGACTCCATAATAACCCTT 59.899 45.833 0.00 0.00 0.00 3.95
6741 10907 4.248402 CGAGACCACGCCGTAAAA 57.752 55.556 0.00 0.00 0.00 1.52
6747 10913 0.179051 ACCACGCCGTAAAACAAGGA 60.179 50.000 0.00 0.00 0.00 3.36
6748 10914 0.515564 CCACGCCGTAAAACAAGGAG 59.484 55.000 0.00 0.00 0.00 3.69
6749 10915 0.515564 CACGCCGTAAAACAAGGAGG 59.484 55.000 0.00 0.00 29.85 4.30
6750 10916 0.393820 ACGCCGTAAAACAAGGAGGA 59.606 50.000 0.00 0.00 29.85 3.71
6751 10917 1.076332 CGCCGTAAAACAAGGAGGAG 58.924 55.000 0.00 0.00 0.00 3.69
6773 10940 2.493030 GGGCTGCATCATGTGTGC 59.507 61.111 15.69 15.69 42.81 4.57
6883 11055 1.067582 GCCCGTCCTCGAAGTATGG 59.932 63.158 0.00 0.00 39.71 2.74
6918 11090 0.606401 CTTATATGTGCCGGCTGGGG 60.606 60.000 29.70 5.75 35.78 4.96
6943 11115 0.820871 GTCCATCTCACGAGCTCCTT 59.179 55.000 8.47 0.00 0.00 3.36
6944 11116 1.205893 GTCCATCTCACGAGCTCCTTT 59.794 52.381 8.47 0.00 0.00 3.11
6945 11117 1.902508 TCCATCTCACGAGCTCCTTTT 59.097 47.619 8.47 0.00 0.00 2.27
6946 11118 2.303022 TCCATCTCACGAGCTCCTTTTT 59.697 45.455 8.47 0.00 0.00 1.94
6970 11142 2.102553 GGAGTACCGCACGAGCTC 59.897 66.667 2.73 2.73 39.10 4.09
6971 11143 2.408241 GGAGTACCGCACGAGCTCT 61.408 63.158 12.85 0.00 39.10 4.09
6972 11144 1.507174 GAGTACCGCACGAGCTCTT 59.493 57.895 12.85 0.00 39.10 2.85
6973 11145 0.523757 GAGTACCGCACGAGCTCTTC 60.524 60.000 12.85 0.00 39.10 2.87
6974 11146 0.961358 AGTACCGCACGAGCTCTTCT 60.961 55.000 12.85 0.00 39.10 2.85
6975 11147 0.731417 GTACCGCACGAGCTCTTCTA 59.269 55.000 12.85 0.00 39.10 2.10
6976 11148 1.015109 TACCGCACGAGCTCTTCTAG 58.985 55.000 12.85 0.00 39.10 2.43
6977 11149 0.961358 ACCGCACGAGCTCTTCTAGT 60.961 55.000 12.85 0.00 39.10 2.57
6978 11150 0.171455 CCGCACGAGCTCTTCTAGTT 59.829 55.000 12.85 0.00 39.10 2.24
6979 11151 1.540407 CGCACGAGCTCTTCTAGTTC 58.460 55.000 12.85 0.00 39.10 3.01
6980 11152 1.795889 CGCACGAGCTCTTCTAGTTCC 60.796 57.143 12.85 0.00 39.10 3.62
6981 11153 1.474879 GCACGAGCTCTTCTAGTTCCT 59.525 52.381 12.85 0.00 37.91 3.36
6982 11154 2.478879 GCACGAGCTCTTCTAGTTCCTC 60.479 54.545 12.85 0.00 37.91 3.71
6983 11155 2.098443 CACGAGCTCTTCTAGTTCCTCC 59.902 54.545 12.85 0.00 32.05 4.30
6984 11156 2.025699 ACGAGCTCTTCTAGTTCCTCCT 60.026 50.000 12.85 0.00 32.05 3.69
6985 11157 2.357637 CGAGCTCTTCTAGTTCCTCCTG 59.642 54.545 12.85 0.00 32.05 3.86
6986 11158 3.361786 GAGCTCTTCTAGTTCCTCCTGT 58.638 50.000 6.43 0.00 29.55 4.00
6987 11159 4.528920 GAGCTCTTCTAGTTCCTCCTGTA 58.471 47.826 6.43 0.00 29.55 2.74
6988 11160 4.274978 AGCTCTTCTAGTTCCTCCTGTAC 58.725 47.826 0.00 0.00 0.00 2.90
6989 11161 4.017867 AGCTCTTCTAGTTCCTCCTGTACT 60.018 45.833 0.00 0.00 0.00 2.73
6990 11162 4.707934 GCTCTTCTAGTTCCTCCTGTACTT 59.292 45.833 0.00 0.00 0.00 2.24
6991 11163 5.186215 GCTCTTCTAGTTCCTCCTGTACTTT 59.814 44.000 0.00 0.00 0.00 2.66
6992 11164 6.626402 GCTCTTCTAGTTCCTCCTGTACTTTC 60.626 46.154 0.00 0.00 0.00 2.62
6993 11165 6.312529 TCTTCTAGTTCCTCCTGTACTTTCA 58.687 40.000 0.00 0.00 0.00 2.69
6994 11166 6.954684 TCTTCTAGTTCCTCCTGTACTTTCAT 59.045 38.462 0.00 0.00 0.00 2.57
6995 11167 6.531503 TCTAGTTCCTCCTGTACTTTCATG 57.468 41.667 0.00 0.00 0.00 3.07
6996 11168 6.253758 TCTAGTTCCTCCTGTACTTTCATGA 58.746 40.000 0.00 0.00 0.00 3.07
6997 11169 6.897966 TCTAGTTCCTCCTGTACTTTCATGAT 59.102 38.462 0.00 0.00 0.00 2.45
6998 11170 6.380079 AGTTCCTCCTGTACTTTCATGATT 57.620 37.500 0.00 0.00 0.00 2.57
6999 11171 6.410540 AGTTCCTCCTGTACTTTCATGATTC 58.589 40.000 0.00 0.00 0.00 2.52
7000 11172 5.011090 TCCTCCTGTACTTTCATGATTCG 57.989 43.478 0.00 0.00 0.00 3.34
7001 11173 3.557595 CCTCCTGTACTTTCATGATTCGC 59.442 47.826 0.00 0.00 0.00 4.70
7002 11174 3.531538 TCCTGTACTTTCATGATTCGCC 58.468 45.455 0.00 0.00 0.00 5.54
7003 11175 2.285220 CCTGTACTTTCATGATTCGCCG 59.715 50.000 0.00 0.00 0.00 6.46
7004 11176 2.930040 CTGTACTTTCATGATTCGCCGT 59.070 45.455 0.00 0.00 0.00 5.68
7005 11177 3.331150 TGTACTTTCATGATTCGCCGTT 58.669 40.909 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.065235 CCTTGGTTTGATTTTTGCAAGGAT 58.935 37.500 0.00 0.00 40.04 3.24
50 51 0.823356 AACCAAGCACGCCAGAACAT 60.823 50.000 0.00 0.00 0.00 2.71
100 101 4.896482 ACCGAGTCTATAATGGAGCTCTTT 59.104 41.667 14.64 10.38 0.00 2.52
135 136 6.127451 ACCCCAAAAAGTAACAGAGAAGTTTG 60.127 38.462 0.00 0.00 33.07 2.93
210 211 5.481824 ACTGACATATGACACTTCTGAGGAA 59.518 40.000 10.38 0.00 0.00 3.36
273 274 2.780010 CCCACAGGAGGTCTAATCCAAT 59.220 50.000 0.00 0.00 39.47 3.16
457 458 3.279504 AAGAGCAGCCTTCAGCCCC 62.280 63.158 0.00 0.00 45.47 5.80
618 619 6.549952 CCATCTCTCTCAATTTTTCGAAAGG 58.450 40.000 10.98 0.00 0.00 3.11
628 629 5.568392 ACTTTCTTGCCATCTCTCTCAATT 58.432 37.500 0.00 0.00 0.00 2.32
633 634 3.080319 GCAACTTTCTTGCCATCTCTCT 58.920 45.455 0.00 0.00 39.38 3.10
646 647 3.753272 TGGCTAACTCATGAGCAACTTTC 59.247 43.478 22.83 7.28 40.64 2.62
702 703 1.408266 CCAGTGGTAGTTGGCCCATAC 60.408 57.143 0.00 0.00 32.32 2.39
1089 1098 1.306141 AGATCTGGTGAAGCCGGGA 60.306 57.895 2.18 0.00 43.94 5.14
1318 1591 7.878621 TCTGGGAGTATCTAATCATTGGATT 57.121 36.000 0.97 0.00 45.50 3.01
1325 1598 6.550108 GGTACAGTTCTGGGAGTATCTAATCA 59.450 42.308 4.82 0.00 33.73 2.57
1709 1983 8.150945 AGTTAGCAATCTCTTCAACTGAACTAA 58.849 33.333 0.00 0.00 0.00 2.24
1819 2093 6.787957 ACTAATCACAGGCATTACCCTATAGT 59.212 38.462 0.00 0.00 40.58 2.12
1834 2108 7.462856 GCACGTATAACTGTTCACTAATCACAG 60.463 40.741 0.00 0.00 43.12 3.66
1857 2131 0.179037 TATGCATCCAGCCAGAGCAC 60.179 55.000 0.19 0.00 44.83 4.40
2039 5641 9.965902 AGAATATTTTCAGATGAGTAAACACCT 57.034 29.630 0.00 0.00 34.08 4.00
2150 5752 1.549203 AGCTAAAACCTGTGGCATGG 58.451 50.000 7.77 7.77 0.00 3.66
2340 5942 0.251121 TCCCGTGCATGGTTGAATGT 60.251 50.000 23.39 0.00 0.00 2.71
2519 6121 3.685756 GCCCAGTGCGTTGTAATAACTAA 59.314 43.478 0.00 0.00 0.00 2.24
2705 6307 5.276820 GCCAAAAGCAGTATTGTTGTGTTTC 60.277 40.000 0.00 0.00 42.97 2.78
2719 6321 0.169009 GCTAAGTCGGCCAAAAGCAG 59.831 55.000 2.24 0.00 46.50 4.24
2808 6411 4.170292 AGCAGTGAATCAAAGATGTTGC 57.830 40.909 0.00 0.00 0.00 4.17
2949 6552 4.383770 GCACCCTACACATTTAGCTTCCTA 60.384 45.833 0.00 0.00 0.00 2.94
2996 6599 4.369182 ACTGTTGGAGTTAACTTGACTCG 58.631 43.478 10.02 7.22 43.47 4.18
3141 6744 4.717877 ACTCAGACCATCATTGACAACAA 58.282 39.130 0.00 0.00 40.42 2.83
3314 6919 6.042093 CCATCACTAACTACCACCACATCTAT 59.958 42.308 0.00 0.00 0.00 1.98
3409 7014 1.407299 CCAGATTCGATGCTGGGACAA 60.407 52.381 20.66 0.00 46.24 3.18
3487 7092 3.503827 ACGACTTGATGTATGAGCGAA 57.496 42.857 0.00 0.00 0.00 4.70
3616 7221 9.646427 TTAAATTTTACCATGGAGCAAACATAC 57.354 29.630 21.47 0.00 0.00 2.39
3713 7318 7.461182 TTGTTCTTTCCACTTTTTGAGAAGA 57.539 32.000 0.00 0.00 0.00 2.87
3806 7415 8.310382 AGCACATCTCTGGAATATGTAATAGAC 58.690 37.037 0.00 0.00 32.70 2.59
3810 7419 9.445878 CATTAGCACATCTCTGGAATATGTAAT 57.554 33.333 0.00 0.00 32.70 1.89
3812 7421 8.193953 TCATTAGCACATCTCTGGAATATGTA 57.806 34.615 0.00 0.00 32.70 2.29
3813 7422 7.071069 TCATTAGCACATCTCTGGAATATGT 57.929 36.000 0.00 0.00 34.22 2.29
4055 7674 1.339438 TGCAGATTCTGGCTCAACCTC 60.339 52.381 15.28 0.00 40.22 3.85
4061 7680 7.074507 CAGAAATATATGCAGATTCTGGCTC 57.925 40.000 15.28 0.00 41.92 4.70
4233 7852 9.515020 GTCACAAGTCAAAAACAATGAGAATAA 57.485 29.630 0.00 0.00 0.00 1.40
4442 8198 1.672881 CAGATCGGTCTTTTGGGATGC 59.327 52.381 0.00 0.00 30.42 3.91
4519 8275 5.014123 GGGGAGGTGTTGATCATTCCATATA 59.986 44.000 0.00 0.00 35.64 0.86
4547 8303 0.842030 ATCTCCACCCAAGTCAGGCA 60.842 55.000 0.00 0.00 0.00 4.75
4567 8323 8.867097 CCAATCATTTATCTCTCCCAATCATTT 58.133 33.333 0.00 0.00 0.00 2.32
4568 8324 7.453752 CCCAATCATTTATCTCTCCCAATCATT 59.546 37.037 0.00 0.00 0.00 2.57
4569 8325 6.952358 CCCAATCATTTATCTCTCCCAATCAT 59.048 38.462 0.00 0.00 0.00 2.45
4570 8326 6.103057 TCCCAATCATTTATCTCTCCCAATCA 59.897 38.462 0.00 0.00 0.00 2.57
4571 8327 6.546484 TCCCAATCATTTATCTCTCCCAATC 58.454 40.000 0.00 0.00 0.00 2.67
4572 8328 6.333702 TCTCCCAATCATTTATCTCTCCCAAT 59.666 38.462 0.00 0.00 0.00 3.16
4573 8329 5.671735 TCTCCCAATCATTTATCTCTCCCAA 59.328 40.000 0.00 0.00 0.00 4.12
4574 8330 5.226803 TCTCCCAATCATTTATCTCTCCCA 58.773 41.667 0.00 0.00 0.00 4.37
4575 8331 5.832539 TCTCCCAATCATTTATCTCTCCC 57.167 43.478 0.00 0.00 0.00 4.30
4576 8332 7.309073 GCATTTCTCCCAATCATTTATCTCTCC 60.309 40.741 0.00 0.00 0.00 3.71
4577 8333 7.572724 CGCATTTCTCCCAATCATTTATCTCTC 60.573 40.741 0.00 0.00 0.00 3.20
4578 8334 6.206243 CGCATTTCTCCCAATCATTTATCTCT 59.794 38.462 0.00 0.00 0.00 3.10
4676 8432 4.261656 CCCCTTCACATCTGACGTAGATAC 60.262 50.000 0.00 0.00 44.34 2.24
4681 8437 1.191535 CCCCCTTCACATCTGACGTA 58.808 55.000 0.00 0.00 0.00 3.57
4722 8719 6.884472 TCTTACCATCTATCCAAAAGACCA 57.116 37.500 0.00 0.00 0.00 4.02
4766 8763 2.672996 CCCAGTTCACAAGCCCCG 60.673 66.667 0.00 0.00 0.00 5.73
4861 8859 0.978146 ACCAGCCTCATTAGACCGCT 60.978 55.000 0.00 0.00 0.00 5.52
4959 8957 1.065709 AGTACACCATACCCAAAGCCG 60.066 52.381 0.00 0.00 0.00 5.52
5087 9086 1.008538 CAAGGAGGCAAACGTGTGC 60.009 57.895 22.88 22.88 44.14 4.57
5173 9277 9.851686 TCAGGTAAGCTTGATGTCAATATAATT 57.148 29.630 9.86 0.00 35.02 1.40
5174 9278 9.851686 TTCAGGTAAGCTTGATGTCAATATAAT 57.148 29.630 9.86 0.00 35.02 1.28
5175 9279 9.851686 ATTCAGGTAAGCTTGATGTCAATATAA 57.148 29.630 9.86 0.00 35.02 0.98
5379 9485 5.558818 TGTGATTAATTTTGCTGGCCAAAT 58.441 33.333 7.01 0.00 42.63 2.32
5478 9585 4.039730 ACTTCTAGCACTTCTTCAGCTTCA 59.960 41.667 0.00 0.00 39.68 3.02
5483 9590 6.809196 ACGAATAACTTCTAGCACTTCTTCAG 59.191 38.462 0.00 0.00 0.00 3.02
5553 9668 1.063174 CCTAGCTCACAATTGCGCTTC 59.937 52.381 18.62 1.13 41.11 3.86
5612 9749 7.125507 ACATTGGAGCATGGATTTTTACCATTA 59.874 33.333 0.00 0.00 44.51 1.90
5750 9888 7.012943 CAGTAAACGCGAGATTTTTCAATACA 58.987 34.615 15.93 0.00 0.00 2.29
5805 9943 8.207545 AGGCAAAAAGGTATTAACAATTTGTGA 58.792 29.630 2.13 0.00 31.73 3.58
5951 10089 2.800250 ACCTCCTGCCATTGAGAAAAG 58.200 47.619 0.00 0.00 0.00 2.27
6007 10145 6.097270 CCAAGCAATTGAAGATCATAAGGGAA 59.903 38.462 10.34 0.00 0.00 3.97
6008 10146 5.595542 CCAAGCAATTGAAGATCATAAGGGA 59.404 40.000 10.34 0.00 0.00 4.20
6186 10346 4.528206 TCAGACATGGTAAGCAGAAGAGAA 59.472 41.667 0.00 0.00 0.00 2.87
6211 10371 5.988561 GGAGAGTTAGCAACATCTCTATTGG 59.011 44.000 17.19 0.00 37.39 3.16
6221 10381 4.365514 TTGAATGGGAGAGTTAGCAACA 57.634 40.909 0.00 0.00 0.00 3.33
6333 10496 3.081061 TCTTGCGTGCAGAATAAACCAT 58.919 40.909 0.00 0.00 0.00 3.55
6424 10587 5.946377 AGAATTTAGGAATGTTGACTGGTCC 59.054 40.000 0.00 0.00 0.00 4.46
6512 10678 5.988561 GGCACATAATTGTTTTTGTCTTGGA 59.011 36.000 0.00 0.00 32.34 3.53
6574 10740 2.475466 GCAGATGGCATGTCACCGG 61.475 63.158 3.81 0.00 43.97 5.28
6653 10819 3.304257 GCATGGAGATAATTGAAGCGTGG 60.304 47.826 0.00 0.00 0.00 4.94
6698 10864 3.073798 TGGTTCACTAGCTGGGATTTTCA 59.926 43.478 0.85 0.00 0.00 2.69
6735 10901 1.076332 CGCCTCCTCCTTGTTTTACG 58.924 55.000 0.00 0.00 0.00 3.18
6797 10967 2.358898 GCTGAGAACTTGGTTTTGCTCA 59.641 45.455 0.00 0.00 0.00 4.26
6802 10973 3.883489 GGTGTAGCTGAGAACTTGGTTTT 59.117 43.478 0.00 0.00 0.00 2.43
6883 11055 7.674937 GCACATATAAGATGAATACGGATGCAC 60.675 40.741 0.00 0.00 0.00 4.57
6918 11090 2.808543 AGCTCGTGAGATGGACAAAAAC 59.191 45.455 0.00 0.00 40.84 2.43
6953 11125 1.935327 AAGAGCTCGTGCGGTACTCC 61.935 60.000 8.37 0.00 45.42 3.85
6954 11126 0.523757 GAAGAGCTCGTGCGGTACTC 60.524 60.000 6.97 0.00 45.42 2.59
6955 11127 0.961358 AGAAGAGCTCGTGCGGTACT 60.961 55.000 6.97 0.00 45.42 2.73
6956 11128 0.731417 TAGAAGAGCTCGTGCGGTAC 59.269 55.000 6.97 0.00 45.42 3.34
6957 11129 1.015109 CTAGAAGAGCTCGTGCGGTA 58.985 55.000 6.97 0.00 45.42 4.02
6958 11130 0.961358 ACTAGAAGAGCTCGTGCGGT 60.961 55.000 6.97 2.90 45.42 5.68
6959 11131 0.171455 AACTAGAAGAGCTCGTGCGG 59.829 55.000 6.97 2.24 45.42 5.69
6960 11132 1.540407 GAACTAGAAGAGCTCGTGCG 58.460 55.000 6.97 0.00 45.42 5.34
6961 11133 1.474879 AGGAACTAGAAGAGCTCGTGC 59.525 52.381 6.97 0.07 36.02 5.34
6962 11134 2.098443 GGAGGAACTAGAAGAGCTCGTG 59.902 54.545 6.97 0.00 41.55 4.35
6963 11135 2.025699 AGGAGGAACTAGAAGAGCTCGT 60.026 50.000 8.37 4.54 41.55 4.18
6964 11136 2.357637 CAGGAGGAACTAGAAGAGCTCG 59.642 54.545 8.37 0.00 41.55 5.03
6965 11137 3.361786 ACAGGAGGAACTAGAAGAGCTC 58.638 50.000 5.27 5.27 41.55 4.09
6966 11138 3.466395 ACAGGAGGAACTAGAAGAGCT 57.534 47.619 0.00 0.00 41.55 4.09
6967 11139 4.274978 AGTACAGGAGGAACTAGAAGAGC 58.725 47.826 0.00 0.00 41.55 4.09
6968 11140 6.434652 TGAAAGTACAGGAGGAACTAGAAGAG 59.565 42.308 0.00 0.00 41.55 2.85
6969 11141 6.312529 TGAAAGTACAGGAGGAACTAGAAGA 58.687 40.000 0.00 0.00 41.55 2.87
6970 11142 6.591750 TGAAAGTACAGGAGGAACTAGAAG 57.408 41.667 0.00 0.00 41.55 2.85
6971 11143 6.724441 TCATGAAAGTACAGGAGGAACTAGAA 59.276 38.462 0.00 0.00 41.55 2.10
6972 11144 6.253758 TCATGAAAGTACAGGAGGAACTAGA 58.746 40.000 0.00 0.00 41.55 2.43
6973 11145 6.531503 TCATGAAAGTACAGGAGGAACTAG 57.468 41.667 0.00 0.00 41.55 2.57
6974 11146 7.496346 AATCATGAAAGTACAGGAGGAACTA 57.504 36.000 0.00 0.00 41.55 2.24
6976 11148 5.292101 CGAATCATGAAAGTACAGGAGGAAC 59.708 44.000 0.00 0.00 34.23 3.62
6977 11149 5.419542 CGAATCATGAAAGTACAGGAGGAA 58.580 41.667 0.00 0.00 34.23 3.36
6978 11150 4.680708 GCGAATCATGAAAGTACAGGAGGA 60.681 45.833 0.00 0.00 34.23 3.71
6979 11151 3.557595 GCGAATCATGAAAGTACAGGAGG 59.442 47.826 0.00 0.00 34.23 4.30
6980 11152 3.557595 GGCGAATCATGAAAGTACAGGAG 59.442 47.826 0.00 0.00 34.23 3.69
6981 11153 3.531538 GGCGAATCATGAAAGTACAGGA 58.468 45.455 0.00 0.00 35.17 3.86
6982 11154 2.285220 CGGCGAATCATGAAAGTACAGG 59.715 50.000 0.00 0.00 0.00 4.00
6983 11155 2.930040 ACGGCGAATCATGAAAGTACAG 59.070 45.455 16.62 0.00 0.00 2.74
6984 11156 2.967362 ACGGCGAATCATGAAAGTACA 58.033 42.857 16.62 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.