Multiple sequence alignment - TraesCS4D01G119600

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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 TraesCS4D01G119600 chr4D 100.000 6188 0 0 1 6188 100794460 100800647 0.000000e+00 11428.0
1 TraesCS4D01G119600 chr4D 97.143 175 5 0 4046 4220 482703453 482703627 4.690000e-76 296.0
2 TraesCS4D01G119600 chr4A 98.469 2417 35 2 1808 4224 475422933 475420519 0.000000e+00 4257.0
3 TraesCS4D01G119600 chr4A 94.681 1222 34 15 4269 5468 475419746 475418534 0.000000e+00 1868.0
4 TraesCS4D01G119600 chr4A 92.346 993 28 8 735 1726 475423877 475422932 0.000000e+00 1369.0
5 TraesCS4D01G119600 chr4A 91.600 750 33 8 5454 6186 475414502 475413766 0.000000e+00 1009.0
6 TraesCS4D01G119600 chr4A 96.552 174 6 0 4049 4222 681713083 681712910 7.850000e-74 289.0
7 TraesCS4D01G119600 chr4B 97.447 2507 43 10 1808 4295 143307381 143309885 0.000000e+00 4255.0
8 TraesCS4D01G119600 chr4B 91.607 1823 86 26 4402 6188 143310068 143311859 0.000000e+00 2457.0
9 TraesCS4D01G119600 chr4B 96.538 1011 23 8 718 1726 143306378 143307378 0.000000e+00 1663.0
10 TraesCS4D01G119600 chr4B 94.318 88 5 0 4325 4412 143309879 143309966 1.080000e-27 135.0
11 TraesCS4D01G119600 chr6A 82.409 1586 217 39 2040 3597 592808286 592809837 0.000000e+00 1327.0
12 TraesCS4D01G119600 chr6A 94.118 187 9 2 4046 4232 153373060 153372876 3.650000e-72 283.0
13 TraesCS4D01G119600 chr6A 87.251 251 28 4 3672 3922 592809872 592810118 3.650000e-72 283.0
14 TraesCS4D01G119600 chr6D 84.490 1225 172 11 2040 3261 446129494 446128285 0.000000e+00 1194.0
15 TraesCS4D01G119600 chr6D 86.692 263 29 6 3673 3934 446127913 446127656 2.820000e-73 287.0
16 TraesCS4D01G119600 chr6D 82.043 323 47 9 941 1254 446130874 446130554 1.320000e-66 265.0
17 TraesCS4D01G119600 chr6D 97.403 77 2 0 3438 3514 446128069 446127993 1.400000e-26 132.0
18 TraesCS4D01G119600 chr6D 93.671 79 5 0 1 79 374010679 374010601 1.090000e-22 119.0
19 TraesCS4D01G119600 chr2D 87.231 650 75 6 80 728 188090795 188090153 0.000000e+00 734.0
20 TraesCS4D01G119600 chr2D 87.244 635 78 3 80 713 409635490 409636122 0.000000e+00 721.0
21 TraesCS4D01G119600 chr2D 87.092 643 74 8 80 721 47017967 47018601 0.000000e+00 719.0
22 TraesCS4D01G119600 chr2D 93.750 80 5 0 1 80 322234144 322234065 3.030000e-23 121.0
23 TraesCS4D01G119600 chr2D 84.615 52 8 0 5534 5585 14376924 14376975 1.100000e-02 52.8
24 TraesCS4D01G119600 chr7D 87.092 643 79 4 80 721 441708023 441708662 0.000000e+00 725.0
25 TraesCS4D01G119600 chr2A 86.565 655 85 3 80 734 473191911 473192562 0.000000e+00 719.0
26 TraesCS4D01G119600 chr3D 87.127 637 77 5 80 715 319357352 319357984 0.000000e+00 717.0
27 TraesCS4D01G119600 chr3D 86.503 652 81 7 80 728 290814340 290814987 0.000000e+00 710.0
28 TraesCS4D01G119600 chr3D 97.093 172 5 0 4046 4217 422517622 422517793 2.180000e-74 291.0
29 TraesCS4D01G119600 chr3D 94.565 92 4 1 1725 1815 308274089 308274180 2.330000e-29 141.0
30 TraesCS4D01G119600 chr3D 93.671 79 5 0 1 79 386404525 386404603 1.090000e-22 119.0
31 TraesCS4D01G119600 chr7A 86.656 652 76 10 80 727 175333797 175334441 0.000000e+00 712.0
32 TraesCS4D01G119600 chr7A 97.701 174 4 0 4046 4219 83785006 83784833 3.630000e-77 300.0
33 TraesCS4D01G119600 chr7A 92.553 94 6 1 1716 1809 78824047 78824139 3.890000e-27 134.0
34 TraesCS4D01G119600 chr7A 93.750 80 5 0 1 80 494253917 494253996 3.030000e-23 121.0
35 TraesCS4D01G119600 chr5B 86.308 650 81 8 80 728 244398947 244398305 0.000000e+00 701.0
36 TraesCS4D01G119600 chr5B 92.391 92 7 0 1719 1810 57975957 57975866 1.400000e-26 132.0
37 TraesCS4D01G119600 chr5B 87.500 80 10 0 3448 3527 100177259 100177338 6.600000e-15 93.5
38 TraesCS4D01G119600 chr6B 97.159 176 4 1 4046 4221 720714623 720714449 4.690000e-76 296.0
39 TraesCS4D01G119600 chr6B 91.837 196 15 1 4046 4241 20920570 20920376 7.900000e-69 272.0
40 TraesCS4D01G119600 chr1D 94.505 91 4 1 1720 1810 471923556 471923467 8.360000e-29 139.0
41 TraesCS4D01G119600 chrUn 95.349 86 4 0 1724 1809 17103852 17103767 3.010000e-28 137.0
42 TraesCS4D01G119600 chrUn 95.349 86 4 0 1724 1809 17126196 17126111 3.010000e-28 137.0
43 TraesCS4D01G119600 chrUn 94.937 79 4 0 1 79 115121453 115121375 2.340000e-24 124.0
44 TraesCS4D01G119600 chrUn 87.037 54 6 1 5753 5805 24852948 24853001 6.700000e-05 60.2
45 TraesCS4D01G119600 chr5D 94.318 88 5 0 1725 1812 42242388 42242301 1.080000e-27 135.0
46 TraesCS4D01G119600 chr5D 93.407 91 6 0 1725 1815 249066213 249066123 1.080000e-27 135.0
47 TraesCS4D01G119600 chr5D 96.970 33 1 0 5477 5509 388391892 388391860 8.670000e-04 56.5
48 TraesCS4D01G119600 chr3A 89.320 103 9 2 1725 1825 600920364 600920466 1.810000e-25 128.0
49 TraesCS4D01G119600 chr3A 94.937 79 4 0 1 79 508155611 508155689 2.340000e-24 124.0
50 TraesCS4D01G119600 chr3A 81.699 153 23 4 3448 3597 16217012 16217162 8.420000e-24 122.0
51 TraesCS4D01G119600 chr2B 95.000 80 4 0 1 80 390516191 390516112 6.510000e-25 126.0
52 TraesCS4D01G119600 chr2B 93.750 80 5 0 1 80 57434484 57434405 3.030000e-23 121.0
53 TraesCS4D01G119600 chr1A 93.671 79 5 0 1 79 531322431 531322509 1.090000e-22 119.0
54 TraesCS4D01G119600 chr5A 92.500 80 6 0 3448 3527 607963785 607963864 1.410000e-21 115.0
55 TraesCS4D01G119600 chr5A 91.250 80 7 0 3448 3527 493024035 493024114 6.560000e-20 110.0
56 TraesCS4D01G119600 chr1B 78.947 133 17 7 5676 5805 577668152 577668276 5.140000e-11 80.5


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 TraesCS4D01G119600 chr4D 100794460 100800647 6187 False 11428.0 11428 100.000000 1 6188 1 chr4D.!!$F1 6187
1 TraesCS4D01G119600 chr4A 475418534 475423877 5343 True 2498.0 4257 95.165333 735 5468 3 chr4A.!!$R3 4733
2 TraesCS4D01G119600 chr4A 475413766 475414502 736 True 1009.0 1009 91.600000 5454 6186 1 chr4A.!!$R1 732
3 TraesCS4D01G119600 chr4B 143306378 143311859 5481 False 2127.5 4255 94.977500 718 6188 4 chr4B.!!$F1 5470
4 TraesCS4D01G119600 chr6A 592808286 592810118 1832 False 805.0 1327 84.830000 2040 3922 2 chr6A.!!$F1 1882
5 TraesCS4D01G119600 chr6D 446127656 446130874 3218 True 469.5 1194 87.657000 941 3934 4 chr6D.!!$R2 2993
6 TraesCS4D01G119600 chr2D 188090153 188090795 642 True 734.0 734 87.231000 80 728 1 chr2D.!!$R1 648
7 TraesCS4D01G119600 chr2D 409635490 409636122 632 False 721.0 721 87.244000 80 713 1 chr2D.!!$F3 633
8 TraesCS4D01G119600 chr2D 47017967 47018601 634 False 719.0 719 87.092000 80 721 1 chr2D.!!$F2 641
9 TraesCS4D01G119600 chr7D 441708023 441708662 639 False 725.0 725 87.092000 80 721 1 chr7D.!!$F1 641
10 TraesCS4D01G119600 chr2A 473191911 473192562 651 False 719.0 719 86.565000 80 734 1 chr2A.!!$F1 654
11 TraesCS4D01G119600 chr3D 319357352 319357984 632 False 717.0 717 87.127000 80 715 1 chr3D.!!$F3 635
12 TraesCS4D01G119600 chr3D 290814340 290814987 647 False 710.0 710 86.503000 80 728 1 chr3D.!!$F1 648
13 TraesCS4D01G119600 chr7A 175333797 175334441 644 False 712.0 712 86.656000 80 727 1 chr7A.!!$F2 647
14 TraesCS4D01G119600 chr5B 244398305 244398947 642 True 701.0 701 86.308000 80 728 1 chr5B.!!$R2 648

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
761 765 0.039888 ACGGTTGTATTTGCGCCAAC 60.040 50.000 15.43 15.43 38.15 3.77 F
873 877 1.280710 AGTCGTGGCACCCAAATCATA 59.719 47.619 12.86 0.00 34.18 2.15 F
1740 1757 0.635009 ATCTACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12 F
2730 3140 2.996631 AGCTGGGTCAGATGTTTCATC 58.003 47.619 0.00 1.98 32.44 2.92 F
3710 4174 4.106029 TCTCACTGCGGTATGTCTTTAC 57.894 45.455 0.00 0.00 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1741 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59 R
1791 1808 2.661176 ACTACTCCCTCCATCCCAAA 57.339 50.000 0.00 0.00 0.00 3.28 R
3710 4174 0.038744 AACACCATCTTCCTGCAGGG 59.961 55.000 32.23 17.56 35.41 4.45 R
4089 4553 0.395312 GTTTCCAGGACTCGAACCCA 59.605 55.000 5.66 0.00 0.00 4.51 R
5695 7027 1.073722 CTCAAGTCCAAGCCCAGCA 59.926 57.895 0.00 0.00 0.00 4.41 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
64 65 7.744087 AGTAACAGTAGAAAAACATGATGCA 57.256 32.000 0.00 0.00 0.00 3.96
65 66 8.165239 AGTAACAGTAGAAAAACATGATGCAA 57.835 30.769 0.00 0.00 0.00 4.08
66 67 8.629158 AGTAACAGTAGAAAAACATGATGCAAA 58.371 29.630 0.00 0.00 0.00 3.68
67 68 9.243637 GTAACAGTAGAAAAACATGATGCAAAA 57.756 29.630 0.00 0.00 0.00 2.44
68 69 8.891671 AACAGTAGAAAAACATGATGCAAAAT 57.108 26.923 0.00 0.00 0.00 1.82
69 70 8.301730 ACAGTAGAAAAACATGATGCAAAATG 57.698 30.769 0.00 9.74 0.00 2.32
70 71 8.143193 ACAGTAGAAAAACATGATGCAAAATGA 58.857 29.630 16.47 0.00 0.00 2.57
71 72 8.980610 CAGTAGAAAAACATGATGCAAAATGAA 58.019 29.630 16.47 0.00 0.00 2.57
72 73 8.981647 AGTAGAAAAACATGATGCAAAATGAAC 58.018 29.630 16.47 5.35 0.00 3.18
73 74 6.879962 AGAAAAACATGATGCAAAATGAACG 58.120 32.000 16.47 0.00 0.00 3.95
74 75 6.479660 AGAAAAACATGATGCAAAATGAACGT 59.520 30.769 16.47 0.00 0.00 3.99
75 76 7.651304 AGAAAAACATGATGCAAAATGAACGTA 59.349 29.630 16.47 0.00 0.00 3.57
76 77 7.887996 AAAACATGATGCAAAATGAACGTAT 57.112 28.000 16.47 0.00 0.00 3.06
77 78 7.510428 AAACATGATGCAAAATGAACGTATC 57.490 32.000 16.47 0.00 0.00 2.24
78 79 6.193514 ACATGATGCAAAATGAACGTATCA 57.806 33.333 16.47 0.00 43.67 2.15
202 204 6.772716 ACATCTATGGGATCGTTATTTTGCTT 59.227 34.615 0.00 0.00 31.27 3.91
232 235 4.299586 TGGACAAAGGCACATCATTAGA 57.700 40.909 0.00 0.00 0.00 2.10
240 243 8.970020 ACAAAGGCACATCATTAGAATCAATAA 58.030 29.630 0.00 0.00 0.00 1.40
243 246 8.985315 AGGCACATCATTAGAATCAATAAGAA 57.015 30.769 0.00 0.00 0.00 2.52
244 247 9.584008 AGGCACATCATTAGAATCAATAAGAAT 57.416 29.630 0.00 0.00 0.00 2.40
278 281 5.598417 AGTAACCAATTTCATAAGGGCATCC 59.402 40.000 0.00 0.00 0.00 3.51
350 354 6.963083 ATAGTAGAAGCTCTTTCCGTATGT 57.037 37.500 0.00 0.00 36.40 2.29
355 359 6.222038 AGAAGCTCTTTCCGTATGTCATTA 57.778 37.500 0.00 0.00 36.40 1.90
356 360 6.043411 AGAAGCTCTTTCCGTATGTCATTAC 58.957 40.000 0.00 0.00 36.40 1.89
412 416 6.128138 AGTAGCTTCACCCAAAGTAATCTT 57.872 37.500 0.00 0.00 35.14 2.40
540 544 9.822185 GTAGGGCAATTTCTTATCATCAATTTT 57.178 29.630 0.00 0.00 0.00 1.82
559 563 8.046708 TCAATTTTATCCTTTCTCGAGATTGGA 58.953 33.333 27.85 27.85 32.93 3.53
569 573 4.641396 TCTCGAGATTGGACAACATGTTT 58.359 39.130 12.08 0.41 0.00 2.83
582 586 6.147864 ACAACATGTTTATGCTCAAGTTGT 57.852 33.333 8.77 11.28 45.18 3.32
761 765 0.039888 ACGGTTGTATTTGCGCCAAC 60.040 50.000 15.43 15.43 38.15 3.77
873 877 1.280710 AGTCGTGGCACCCAAATCATA 59.719 47.619 12.86 0.00 34.18 2.15
1041 1052 2.498726 CGGCTCTGCTTCCTCTCC 59.501 66.667 0.00 0.00 0.00 3.71
1360 1372 2.286418 GGACGCAGAAATTAAGCCATCG 60.286 50.000 0.00 0.00 0.00 3.84
1493 1505 9.102453 AGGGTATTTATTCTCCTAGTCATAACC 57.898 37.037 0.00 0.00 0.00 2.85
1548 1560 7.074507 TGTGGAAATGATGCAATTAAAATGC 57.925 32.000 9.10 9.10 44.08 3.56
1640 1653 9.173021 AGAGATATGGATAATCTCTAGAACGTG 57.827 37.037 12.67 0.00 46.49 4.49
1649 1662 2.488545 TCTCTAGAACGTGAACTGCCTC 59.511 50.000 0.00 0.00 0.00 4.70
1707 1720 6.094048 GCAAGTCAGGATTATAAAGCACTTGA 59.906 38.462 19.79 9.74 41.23 3.02
1724 1741 5.788450 CACTTGACAGAGAACAACCTATCT 58.212 41.667 0.00 0.00 0.00 1.98
1725 1742 6.572509 GCACTTGACAGAGAACAACCTATCTA 60.573 42.308 0.00 0.00 0.00 1.98
1726 1743 6.809196 CACTTGACAGAGAACAACCTATCTAC 59.191 42.308 0.00 0.00 0.00 2.59
1727 1744 6.722129 ACTTGACAGAGAACAACCTATCTACT 59.278 38.462 0.00 0.00 0.00 2.57
1728 1745 6.761099 TGACAGAGAACAACCTATCTACTC 57.239 41.667 0.00 0.00 0.00 2.59
1729 1746 5.652891 TGACAGAGAACAACCTATCTACTCC 59.347 44.000 0.00 0.00 0.00 3.85
1730 1747 4.957327 ACAGAGAACAACCTATCTACTCCC 59.043 45.833 0.00 0.00 0.00 4.30
1731 1748 5.205056 CAGAGAACAACCTATCTACTCCCT 58.795 45.833 0.00 0.00 0.00 4.20
1732 1749 5.300792 CAGAGAACAACCTATCTACTCCCTC 59.699 48.000 0.00 0.00 0.00 4.30
1733 1750 4.548669 AGAACAACCTATCTACTCCCTCC 58.451 47.826 0.00 0.00 0.00 4.30
1734 1751 2.946785 ACAACCTATCTACTCCCTCCG 58.053 52.381 0.00 0.00 0.00 4.63
1735 1752 2.244252 ACAACCTATCTACTCCCTCCGT 59.756 50.000 0.00 0.00 0.00 4.69
1736 1753 2.885894 CAACCTATCTACTCCCTCCGTC 59.114 54.545 0.00 0.00 0.00 4.79
1737 1754 1.424684 ACCTATCTACTCCCTCCGTCC 59.575 57.143 0.00 0.00 0.00 4.79
1738 1755 1.272037 CCTATCTACTCCCTCCGTCCC 60.272 61.905 0.00 0.00 0.00 4.46
1739 1756 1.424302 CTATCTACTCCCTCCGTCCCA 59.576 57.143 0.00 0.00 0.00 4.37
1740 1757 0.635009 ATCTACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
1746 1763 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
1752 1769 5.397559 CCCTCCGTCCCAAAATATAAGAACT 60.398 44.000 0.00 0.00 0.00 3.01
1756 1773 8.411991 TCCGTCCCAAAATATAAGAACTTTTT 57.588 30.769 0.00 0.00 0.00 1.94
1924 2161 6.845758 TTCCGAACCTCTTCTATTCTGTAA 57.154 37.500 0.00 0.00 0.00 2.41
2019 2429 8.370940 TGCCTTGTATGAATGTTTTGGAATTAA 58.629 29.630 0.00 0.00 0.00 1.40
2730 3140 2.996631 AGCTGGGTCAGATGTTTCATC 58.003 47.619 0.00 1.98 32.44 2.92
3710 4174 4.106029 TCTCACTGCGGTATGTCTTTAC 57.894 45.455 0.00 0.00 0.00 2.01
4120 4584 3.511362 TGGAAACAGCCTCTTGCAA 57.489 47.368 0.00 0.00 44.83 4.08
4136 4600 4.898861 TCTTGCAAAAATGTAGGGAAAGGT 59.101 37.500 0.00 0.00 0.00 3.50
4140 4604 3.934457 AAAATGTAGGGAAAGGTTGCG 57.066 42.857 0.00 0.00 0.00 4.85
4255 4734 2.543848 TGACACAAGAAATCACTGCGTC 59.456 45.455 0.00 0.00 0.00 5.19
4265 4744 0.738389 TCACTGCGTCGCTGATGATA 59.262 50.000 27.89 0.91 0.00 2.15
4271 5462 2.539688 TGCGTCGCTGATGATACATTTC 59.460 45.455 19.50 0.00 0.00 2.17
4323 5514 9.036980 AGTATTGTACTAGGAGAGTTCAAATGT 57.963 33.333 0.00 0.00 45.27 2.71
4452 5758 8.122472 AGTTCTTTTGGGTATCAATAAACTGG 57.878 34.615 0.00 0.00 33.95 4.00
4508 5814 5.102953 TCTATTTTCTGCCAGCAGTACAT 57.897 39.130 18.61 10.67 43.96 2.29
4663 5969 8.573035 TCACAGAGCGTATGTTGATATAACATA 58.427 33.333 8.06 8.06 40.87 2.29
4763 6069 5.406649 TCAAAAGTTCGTTGCAATGTTTCT 58.593 33.333 17.94 11.59 0.00 2.52
4771 6077 5.448438 TCGTTGCAATGTTTCTTGTATGTC 58.552 37.500 17.94 0.00 0.00 3.06
4822 6129 8.730680 GGTGTTATGATAACTTCTGTGTCAAAT 58.269 33.333 15.57 0.00 0.00 2.32
4914 6221 5.047448 TGCTGGCAATTGCTTGACTATTTTA 60.047 36.000 28.42 2.22 41.34 1.52
4992 6299 4.385748 GCTTACCACAGCTTAAACATTTGC 59.614 41.667 0.00 0.00 36.79 3.68
5006 6313 5.743636 AACATTTGCCTAACCAATGTCAT 57.256 34.783 0.00 0.00 0.00 3.06
5201 6511 9.021863 GTCGAACAGTTAGAGAACTAATATTGG 57.978 37.037 0.00 0.00 44.39 3.16
5424 6756 6.365520 ACATTCCAGCCCCTTTACTTATTAG 58.634 40.000 0.00 0.00 0.00 1.73
5425 6757 6.069029 ACATTCCAGCCCCTTTACTTATTAGT 60.069 38.462 0.00 0.00 38.44 2.24
5426 6758 6.397217 TTCCAGCCCCTTTACTTATTAGTT 57.603 37.500 0.00 0.00 35.78 2.24
5427 6759 7.513560 TTCCAGCCCCTTTACTTATTAGTTA 57.486 36.000 0.00 0.00 35.78 2.24
5428 6760 7.701257 TCCAGCCCCTTTACTTATTAGTTAT 57.299 36.000 0.00 0.00 35.78 1.89
5429 6761 8.109560 TCCAGCCCCTTTACTTATTAGTTATT 57.890 34.615 0.00 0.00 35.78 1.40
5430 6762 9.228077 TCCAGCCCCTTTACTTATTAGTTATTA 57.772 33.333 0.00 0.00 35.78 0.98
5468 6800 4.214971 CGAGAAATGCATCCTTATCCTTGG 59.785 45.833 0.00 0.00 0.00 3.61
5474 6806 2.173569 GCATCCTTATCCTTGGGTCTGT 59.826 50.000 0.00 0.00 0.00 3.41
5475 6807 3.813443 CATCCTTATCCTTGGGTCTGTG 58.187 50.000 0.00 0.00 0.00 3.66
5556 6888 0.817634 TTGTCACTTGAGCCGGGTTG 60.818 55.000 8.00 1.29 0.00 3.77
5597 6929 0.698886 AAGGATATCTGGGCTGGGCA 60.699 55.000 2.05 0.00 0.00 5.36
5695 7027 1.290009 GCTTTGGGCTTGCATTCGT 59.710 52.632 0.00 0.00 38.06 3.85
5707 7039 1.675310 CATTCGTGCTGGGCTTGGA 60.675 57.895 0.00 0.00 0.00 3.53
5956 7288 4.981674 TGTCATGATGCGGTTTTCTTTTTC 59.018 37.500 0.00 0.00 0.00 2.29
6123 7472 1.839994 AGGAGCTACAGCCTGCATTTA 59.160 47.619 0.00 0.00 43.38 1.40
6157 7506 6.398234 AGTCGATAGTGAATGCTATGAACT 57.602 37.500 0.00 0.00 32.32 3.01
6186 7535 0.393944 TATGTGAGGAGTCGGCTCGT 60.394 55.000 12.77 12.77 42.53 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.278978 TGCATCATGTTTTTCTACTGTTACTTA 57.721 29.630 0.00 0.00 0.00 2.24
39 40 8.165239 TGCATCATGTTTTTCTACTGTTACTT 57.835 30.769 0.00 0.00 0.00 2.24
40 41 7.744087 TGCATCATGTTTTTCTACTGTTACT 57.256 32.000 0.00 0.00 0.00 2.24
41 42 8.795786 TTTGCATCATGTTTTTCTACTGTTAC 57.204 30.769 0.00 0.00 0.00 2.50
42 43 9.979578 ATTTTGCATCATGTTTTTCTACTGTTA 57.020 25.926 0.00 0.00 0.00 2.41
43 44 8.767085 CATTTTGCATCATGTTTTTCTACTGTT 58.233 29.630 0.00 0.00 0.00 3.16
44 45 8.143193 TCATTTTGCATCATGTTTTTCTACTGT 58.857 29.630 5.72 0.00 0.00 3.55
45 46 8.523523 TCATTTTGCATCATGTTTTTCTACTG 57.476 30.769 5.72 0.00 0.00 2.74
46 47 8.981647 GTTCATTTTGCATCATGTTTTTCTACT 58.018 29.630 5.72 0.00 0.00 2.57
47 48 7.946237 CGTTCATTTTGCATCATGTTTTTCTAC 59.054 33.333 5.72 0.00 0.00 2.59
48 49 7.651304 ACGTTCATTTTGCATCATGTTTTTCTA 59.349 29.630 5.72 0.00 0.00 2.10
49 50 6.479660 ACGTTCATTTTGCATCATGTTTTTCT 59.520 30.769 5.72 0.00 0.00 2.52
50 51 6.648502 ACGTTCATTTTGCATCATGTTTTTC 58.351 32.000 5.72 0.00 0.00 2.29
51 52 6.601741 ACGTTCATTTTGCATCATGTTTTT 57.398 29.167 5.72 0.00 0.00 1.94
52 53 7.598118 TGATACGTTCATTTTGCATCATGTTTT 59.402 29.630 0.00 0.00 0.00 2.43
53 54 7.089538 TGATACGTTCATTTTGCATCATGTTT 58.910 30.769 0.00 0.00 0.00 2.83
54 55 6.619744 TGATACGTTCATTTTGCATCATGTT 58.380 32.000 0.00 0.00 0.00 2.71
55 56 6.193514 TGATACGTTCATTTTGCATCATGT 57.806 33.333 0.00 0.00 0.00 3.21
56 57 7.509050 TTTGATACGTTCATTTTGCATCATG 57.491 32.000 0.00 0.00 33.34 3.07
57 58 8.597227 CAATTTGATACGTTCATTTTGCATCAT 58.403 29.630 0.00 0.00 33.34 2.45
58 59 7.411696 GCAATTTGATACGTTCATTTTGCATCA 60.412 33.333 23.71 12.27 44.25 3.07
59 60 6.896088 GCAATTTGATACGTTCATTTTGCATC 59.104 34.615 23.71 10.54 44.25 3.91
60 61 6.183360 GGCAATTTGATACGTTCATTTTGCAT 60.183 34.615 26.23 6.13 45.37 3.96
61 62 5.119898 GGCAATTTGATACGTTCATTTTGCA 59.880 36.000 26.23 0.00 45.37 4.08
62 63 5.119898 TGGCAATTTGATACGTTCATTTTGC 59.880 36.000 22.35 22.35 44.18 3.68
63 64 6.702972 TGGCAATTTGATACGTTCATTTTG 57.297 33.333 0.00 6.18 33.34 2.44
64 65 8.994429 TTATGGCAATTTGATACGTTCATTTT 57.006 26.923 0.00 0.00 33.34 1.82
65 66 9.598517 AATTATGGCAATTTGATACGTTCATTT 57.401 25.926 0.00 0.00 33.34 2.32
109 110 9.524496 AGGTAATTTTAATCCTAGGTCGTTTTT 57.476 29.630 9.08 0.00 0.00 1.94
110 111 9.170734 GAGGTAATTTTAATCCTAGGTCGTTTT 57.829 33.333 9.08 0.00 0.00 2.43
202 204 5.798125 TGTGCCTTTGTCCAATTTGATTA 57.202 34.783 0.00 0.00 0.00 1.75
256 259 5.362430 GTGGATGCCCTTATGAAATTGGTTA 59.638 40.000 0.00 0.00 0.00 2.85
272 275 4.702131 ACTTTGAGTGATAAAGTGGATGCC 59.298 41.667 0.00 0.00 44.29 4.40
327 331 6.546403 TGACATACGGAAAGAGCTTCTACTAT 59.454 38.462 0.00 0.00 34.17 2.12
334 338 4.804139 CGTAATGACATACGGAAAGAGCTT 59.196 41.667 0.00 0.00 43.68 3.74
412 416 3.062369 CGTCGCGGGTTGTAATTTTATGA 59.938 43.478 6.13 0.00 0.00 2.15
484 488 8.233868 TGGTTTAAATTTGTGAGTGATCATACG 58.766 33.333 0.00 0.00 0.00 3.06
494 498 7.973944 GCCCTACTTATGGTTTAAATTTGTGAG 59.026 37.037 0.00 0.00 0.00 3.51
495 499 7.451877 TGCCCTACTTATGGTTTAAATTTGTGA 59.548 33.333 0.00 0.00 0.00 3.58
512 516 8.773033 ATTGATGATAAGAAATTGCCCTACTT 57.227 30.769 0.00 0.00 0.00 2.24
540 544 5.186992 TGTTGTCCAATCTCGAGAAAGGATA 59.813 40.000 30.27 26.70 34.86 2.59
549 553 5.163764 GCATAAACATGTTGTCCAATCTCGA 60.164 40.000 12.82 0.00 0.00 4.04
551 555 6.127925 TGAGCATAAACATGTTGTCCAATCTC 60.128 38.462 12.82 12.20 0.00 2.75
609 613 5.554822 TTCCTCCCGTGAAAATTATTTCG 57.445 39.130 0.00 0.00 46.47 3.46
688 692 9.000486 TGCAAAAATTTGATTATCATCTTTGCA 58.000 25.926 25.14 25.14 40.55 4.08
699 703 7.893824 GCATGATACGTGCAAAAATTTGATTA 58.106 30.769 9.96 0.00 42.08 1.75
702 706 5.760193 GCATGATACGTGCAAAAATTTGA 57.240 34.783 9.96 0.00 42.08 2.69
826 830 2.570284 GGTTTTTGGGTCAGCCGGG 61.570 63.158 2.18 0.00 34.97 5.73
873 877 3.118454 CGTTGCGATTCGGTGCCT 61.118 61.111 8.34 0.00 0.00 4.75
1041 1052 1.457455 GAGGAGGAGGAGGAGCAGG 60.457 68.421 0.00 0.00 0.00 4.85
1360 1372 0.960286 GTAGAGTGCCTACGGATCCC 59.040 60.000 6.06 0.00 38.47 3.85
1493 1505 0.814457 AACTGCCTGAGCTAGTCGAG 59.186 55.000 0.00 0.00 40.80 4.04
1640 1653 6.560253 TTTGATCTAAACTTGAGGCAGTTC 57.440 37.500 0.00 0.00 35.87 3.01
1707 1720 4.957327 GGGAGTAGATAGGTTGTTCTCTGT 59.043 45.833 0.00 0.00 0.00 3.41
1724 1741 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1725 1742 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
1726 1743 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
1727 1744 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
1728 1745 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
1729 1746 5.681639 AGTTCTTATATTTTGGGACGGAGG 58.318 41.667 0.00 0.00 0.00 4.30
1730 1747 7.625828 AAAGTTCTTATATTTTGGGACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
1731 1748 8.411991 AAAAAGTTCTTATATTTTGGGACGGA 57.588 30.769 0.00 0.00 0.00 4.69
1773 1790 9.632807 CATCCCAAAATATAAGAACGTTTTTGA 57.367 29.630 13.87 2.81 38.79 2.69
1774 1791 8.868916 CCATCCCAAAATATAAGAACGTTTTTG 58.131 33.333 13.87 12.16 37.14 2.44
1777 1794 7.068226 CCTCCATCCCAAAATATAAGAACGTTT 59.932 37.037 0.46 0.00 0.00 3.60
1779 1796 6.062095 CCTCCATCCCAAAATATAAGAACGT 58.938 40.000 0.00 0.00 0.00 3.99
1780 1797 5.473504 CCCTCCATCCCAAAATATAAGAACG 59.526 44.000 0.00 0.00 0.00 3.95
1782 1799 6.392842 ACTCCCTCCATCCCAAAATATAAGAA 59.607 38.462 0.00 0.00 0.00 2.52
1783 1800 5.917087 ACTCCCTCCATCCCAAAATATAAGA 59.083 40.000 0.00 0.00 0.00 2.10
1784 1801 6.206180 ACTCCCTCCATCCCAAAATATAAG 57.794 41.667 0.00 0.00 0.00 1.73
1785 1802 6.855061 ACTACTCCCTCCATCCCAAAATATAA 59.145 38.462 0.00 0.00 0.00 0.98
1786 1803 6.399013 ACTACTCCCTCCATCCCAAAATATA 58.601 40.000 0.00 0.00 0.00 0.86
1787 1804 5.235534 ACTACTCCCTCCATCCCAAAATAT 58.764 41.667 0.00 0.00 0.00 1.28
1788 1805 4.641868 ACTACTCCCTCCATCCCAAAATA 58.358 43.478 0.00 0.00 0.00 1.40
1791 1808 2.661176 ACTACTCCCTCCATCCCAAA 57.339 50.000 0.00 0.00 0.00 3.28
1792 1809 2.661176 AACTACTCCCTCCATCCCAA 57.339 50.000 0.00 0.00 0.00 4.12
1794 1811 3.655384 AGTTAACTACTCCCTCCATCCC 58.345 50.000 6.26 0.00 28.23 3.85
1795 1812 5.425862 AGAAAGTTAACTACTCCCTCCATCC 59.574 44.000 8.92 0.00 35.54 3.51
1796 1813 6.547930 AGAAAGTTAACTACTCCCTCCATC 57.452 41.667 8.92 0.00 35.54 3.51
1798 1815 6.559429 ACTAGAAAGTTAACTACTCCCTCCA 58.441 40.000 8.92 0.00 35.54 3.86
1924 2161 8.692710 TCTTAGTTCATGACCGTGTAATTATCT 58.307 33.333 0.00 0.00 0.00 1.98
3311 3733 8.506196 TGGCCTAAAGGTCAGAAGTATAATAT 57.494 34.615 3.32 0.00 46.36 1.28
3710 4174 0.038744 AACACCATCTTCCTGCAGGG 59.961 55.000 32.23 17.56 35.41 4.45
4089 4553 0.395312 GTTTCCAGGACTCGAACCCA 59.605 55.000 5.66 0.00 0.00 4.51
4120 4584 3.227614 ACGCAACCTTTCCCTACATTTT 58.772 40.909 0.00 0.00 0.00 1.82
4136 4600 4.382254 CCACTTTGGGTCTATAGTACGCAA 60.382 45.833 20.49 20.49 44.85 4.85
4163 4627 4.281074 AGGGTCCGGGGAAGGGTT 62.281 66.667 0.00 0.00 0.00 4.11
4222 4686 1.603802 CTTGTGTCAGAACAACGCCAT 59.396 47.619 0.00 0.00 37.08 4.40
4225 4689 3.398954 TTTCTTGTGTCAGAACAACGC 57.601 42.857 0.00 0.00 37.08 4.84
4226 4690 4.963953 GTGATTTCTTGTGTCAGAACAACG 59.036 41.667 0.00 0.00 37.08 4.10
4255 4734 2.154462 GGGGGAAATGTATCATCAGCG 58.846 52.381 0.00 0.00 0.00 5.18
4323 5514 4.392921 GGAGTAGCTCATACTGCTTTGA 57.607 45.455 0.00 0.00 46.37 2.69
4452 5758 6.550854 TGAATATCAATCCTTGTTCCAATCCC 59.449 38.462 0.00 0.00 0.00 3.85
4488 5794 7.053498 TGAATATGTACTGCTGGCAGAAAATA 58.947 34.615 26.42 18.66 46.30 1.40
4722 6028 2.876581 TGAGACTGAGACCAGCAACTA 58.123 47.619 0.00 0.00 44.16 2.24
4763 6069 5.412904 TGTTTATGTTCCATGCGACATACAA 59.587 36.000 15.05 11.29 38.18 2.41
4771 6077 8.167985 CCTTAAAAATTGTTTATGTTCCATGCG 58.832 33.333 0.00 0.00 0.00 4.73
4808 6115 5.659440 ACCACAAAATTTGACACAGAAGT 57.341 34.783 13.19 0.00 0.00 3.01
4914 6221 6.098124 TGTGTTGAGGTCAAATTCAAGGAATT 59.902 34.615 0.00 0.00 43.07 2.17
4992 6299 7.390440 TCTGTTACAGAAATGACATTGGTTAGG 59.610 37.037 13.16 0.00 37.57 2.69
5006 6313 7.670140 TGAGACCTCTCTTATCTGTTACAGAAA 59.330 37.037 19.42 12.93 42.38 2.52
5201 6511 5.801947 CCGTGGATTTGATCAAAATTCTCAC 59.198 40.000 23.91 21.41 38.64 3.51
5424 6756 6.810182 TCTCGCCAGTTAAACTCTGTAATAAC 59.190 38.462 0.00 0.00 0.00 1.89
5425 6757 6.927416 TCTCGCCAGTTAAACTCTGTAATAA 58.073 36.000 0.00 0.00 0.00 1.40
5426 6758 6.519679 TCTCGCCAGTTAAACTCTGTAATA 57.480 37.500 0.00 0.00 0.00 0.98
5427 6759 5.401531 TCTCGCCAGTTAAACTCTGTAAT 57.598 39.130 0.00 0.00 0.00 1.89
5428 6760 4.859304 TCTCGCCAGTTAAACTCTGTAA 57.141 40.909 0.00 0.00 0.00 2.41
5429 6761 4.859304 TTCTCGCCAGTTAAACTCTGTA 57.141 40.909 0.00 0.00 0.00 2.74
5430 6762 3.746045 TTCTCGCCAGTTAAACTCTGT 57.254 42.857 0.00 0.00 0.00 3.41
5468 6800 3.334583 TGATCAGGTTTAGCACAGACC 57.665 47.619 0.00 0.00 0.00 3.85
5474 6806 1.284491 TGCCCATGATCAGGTTTAGCA 59.716 47.619 6.62 7.02 0.00 3.49
5475 6807 1.952296 CTGCCCATGATCAGGTTTAGC 59.048 52.381 6.62 4.52 0.00 3.09
5597 6929 4.961438 ATGTTGAAAAATGGAAGCCTGT 57.039 36.364 0.00 0.00 0.00 4.00
5695 7027 1.073722 CTCAAGTCCAAGCCCAGCA 59.926 57.895 0.00 0.00 0.00 4.41
5707 7039 6.400568 CCCAAAAATATGCATGTTCTCAAGT 58.599 36.000 10.16 0.00 0.00 3.16
5791 7123 3.966543 ACCAGGCTGGGTTTCGGG 61.967 66.667 35.34 10.13 43.37 5.14
5900 7232 3.449227 CGTCACCTCGGCAGCCTA 61.449 66.667 10.54 0.00 0.00 3.93
5913 7245 2.309528 AACTCTGAGTTTGTGCGTCA 57.690 45.000 17.00 0.00 34.11 4.35
5939 7271 7.234187 AGAAAAAGAAAAAGAAAACCGCATC 57.766 32.000 0.00 0.00 0.00 3.91
5956 7288 8.663911 TGATGCAACCAAAAGTTAAAGAAAAAG 58.336 29.630 0.00 0.00 36.18 2.27
6105 7454 2.632377 TGTAAATGCAGGCTGTAGCTC 58.368 47.619 17.16 4.84 41.70 4.09
6111 7460 1.066605 GGCTCATGTAAATGCAGGCTG 59.933 52.381 10.94 10.94 0.00 4.85
6123 7472 0.955178 CTATCGACTCGGGCTCATGT 59.045 55.000 0.00 0.00 0.00 3.21
6157 7506 2.773661 ACTCCTCACATATGCATGTCCA 59.226 45.455 10.16 0.00 43.73 4.02


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

AutoCloner maintained by Alex Coulton.