Multiple sequence alignment - TraesCS1A01G433900

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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 TraesCS1A01G433900 chr1A 100.000 3614 0 0 1 3614 584810131 584806518 0.000000e+00 6674.0
1 TraesCS1A01G433900 chr1A 91.630 1816 111 20 844 2625 579171795 579173603 0.000000e+00 2473.0
2 TraesCS1A01G433900 chr1A 92.083 240 18 1 3176 3414 579173810 579174049 1.610000e-88 337.0
3 TraesCS1A01G433900 chr1A 85.274 292 17 9 383 655 579171396 579171680 9.880000e-71 278.0
4 TraesCS1A01G433900 chr1D 96.354 1728 53 6 897 2624 427704710 427706427 0.000000e+00 2833.0
5 TraesCS1A01G433900 chr1D 95.169 1801 65 8 844 2630 487224269 487222477 0.000000e+00 2824.0
6 TraesCS1A01G433900 chr1D 93.345 1713 103 4 902 2608 482993627 482991920 0.000000e+00 2521.0
7 TraesCS1A01G433900 chr1D 90.306 588 19 14 3036 3614 487222143 487221585 0.000000e+00 736.0
8 TraesCS1A01G433900 chr1D 86.490 681 48 27 36 692 487225154 487224494 0.000000e+00 708.0
9 TraesCS1A01G433900 chr1D 89.546 507 32 13 168 665 427703764 427704258 1.100000e-174 623.0
10 TraesCS1A01G433900 chr1D 81.766 521 24 25 281 782 482994958 482994490 1.590000e-98 370.0
11 TraesCS1A01G433900 chr1D 92.917 240 16 1 3176 3414 482991703 482991464 7.430000e-92 348.0
12 TraesCS1A01G433900 chr1D 87.405 262 17 8 334 580 482994374 482994114 1.640000e-73 287.0
13 TraesCS1A01G433900 chr1D 84.559 272 21 9 2730 2980 487222418 487222147 2.150000e-62 250.0
14 TraesCS1A01G433900 chr1D 84.577 201 12 8 628 828 482993878 482993697 7.970000e-42 182.0
15 TraesCS1A01G433900 chr1D 94.495 109 5 1 721 828 487224361 487224253 2.230000e-37 167.0
16 TraesCS1A01G433900 chr1D 93.458 107 5 1 724 828 427704385 427704491 1.340000e-34 158.0
17 TraesCS1A01G433900 chr1D 90.090 111 5 3 968 1078 482994475 482994371 4.870000e-29 139.0
18 TraesCS1A01G433900 chr1D 95.890 73 3 0 844 916 482993713 482993641 6.340000e-23 119.0
19 TraesCS1A01G433900 chr1D 93.548 62 4 0 844 905 427704475 427704536 3.840000e-15 93.5
20 TraesCS1A01G433900 chr1B 95.220 1799 71 7 844 2630 678469765 678471560 0.000000e+00 2832.0
21 TraesCS1A01G433900 chr1B 93.546 1658 85 13 957 2608 671258805 671260446 0.000000e+00 2449.0
22 TraesCS1A01G433900 chr1B 86.757 589 50 12 3027 3612 678472300 678472863 6.590000e-177 630.0
23 TraesCS1A01G433900 chr1B 84.615 585 30 25 281 828 671258183 671258744 8.890000e-146 527.0
24 TraesCS1A01G433900 chr1B 88.366 404 22 3 289 692 678469301 678469679 2.540000e-126 462.0
25 TraesCS1A01G433900 chr1B 85.714 273 18 6 2730 2981 678471596 678471868 5.950000e-68 268.0
26 TraesCS1A01G433900 chr1B 93.258 89 6 0 740 828 678469693 678469781 8.140000e-27 132.0
27 TraesCS1A01G433900 chr2D 92.779 1731 84 19 957 2679 94868451 94870148 0.000000e+00 2466.0
28 TraesCS1A01G433900 chr2D 79.567 323 26 12 502 817 94868099 94868388 1.020000e-45 195.0
29 TraesCS1A01G433900 chr2B 91.788 1790 93 18 911 2679 146716119 146717875 0.000000e+00 2442.0
30 TraesCS1A01G433900 chr2B 86.667 195 6 4 502 692 146715766 146715944 7.910000e-47 198.0
31 TraesCS1A01G433900 chr7A 77.417 1510 303 29 1103 2602 517582006 517580525 0.000000e+00 865.0
32 TraesCS1A01G433900 chr7D 78.518 931 172 23 1103 2025 478080283 478081193 1.450000e-163 586.0
33 TraesCS1A01G433900 chr6D 84.286 560 35 17 299 828 56206169 56206705 6.970000e-137 497.0
34 TraesCS1A01G433900 chr6D 85.015 327 22 10 299 615 56194745 56195054 1.260000e-79 307.0


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 TraesCS1A01G433900 chr1A 584806518 584810131 3613 True 6674.000000 6674 100.000000 1 3614 1 chr1A.!!$R1 3613
1 TraesCS1A01G433900 chr1A 579171396 579174049 2653 False 1029.333333 2473 89.662333 383 3414 3 chr1A.!!$F1 3031
2 TraesCS1A01G433900 chr1D 487221585 487225154 3569 True 937.000000 2824 90.203800 36 3614 5 chr1D.!!$R2 3578
3 TraesCS1A01G433900 chr1D 427703764 427706427 2663 False 926.875000 2833 93.226500 168 2624 4 chr1D.!!$F1 2456
4 TraesCS1A01G433900 chr1D 482991464 482994958 3494 True 566.571429 2521 89.427143 281 3414 7 chr1D.!!$R1 3133
5 TraesCS1A01G433900 chr1B 671258183 671260446 2263 False 1488.000000 2449 89.080500 281 2608 2 chr1B.!!$F1 2327
6 TraesCS1A01G433900 chr1B 678469301 678472863 3562 False 864.800000 2832 89.863000 289 3612 5 chr1B.!!$F2 3323
7 TraesCS1A01G433900 chr2D 94868099 94870148 2049 False 1330.500000 2466 86.173000 502 2679 2 chr2D.!!$F1 2177
8 TraesCS1A01G433900 chr2B 146715766 146717875 2109 False 1320.000000 2442 89.227500 502 2679 2 chr2B.!!$F1 2177
9 TraesCS1A01G433900 chr7A 517580525 517582006 1481 True 865.000000 865 77.417000 1103 2602 1 chr7A.!!$R1 1499
10 TraesCS1A01G433900 chr7D 478080283 478081193 910 False 586.000000 586 78.518000 1103 2025 1 chr7D.!!$F1 922
11 TraesCS1A01G433900 chr6D 56206169 56206705 536 False 497.000000 497 84.286000 299 828 1 chr6D.!!$F2 529

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
119 121 0.249741 GCTAGGTCGTGGTGTGTGTT 60.250 55.000 0.0 0.0 0.0 3.32 F
227 241 1.066858 ACGCAGCATACACTAAGCACT 60.067 47.619 0.0 0.0 0.0 4.40 F
977 2226 1.089920 CTCACAGCCATAGTTGCCAC 58.910 55.000 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 3072 0.768622 ATTGGTTCCTTGACCGGACA 59.231 50.000 9.46 5.04 42.83 4.02 R
1946 3225 1.930100 CGATCTTGCATGAGCCGAC 59.070 57.895 16.81 3.65 41.13 4.79 R
2714 4018 0.248825 TGCAACCACATGAAACGTGC 60.249 50.000 0.00 2.97 32.85 5.34 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
20 21 2.586425 AGAATTATTGTGCGATGGGGG 58.414 47.619 0.00 0.00 0.00 5.40
21 22 2.091885 AGAATTATTGTGCGATGGGGGT 60.092 45.455 0.00 0.00 0.00 4.95
22 23 1.691196 ATTATTGTGCGATGGGGGTG 58.309 50.000 0.00 0.00 0.00 4.61
23 24 0.395036 TTATTGTGCGATGGGGGTGG 60.395 55.000 0.00 0.00 0.00 4.61
24 25 1.567208 TATTGTGCGATGGGGGTGGT 61.567 55.000 0.00 0.00 0.00 4.16
25 26 1.567208 ATTGTGCGATGGGGGTGGTA 61.567 55.000 0.00 0.00 0.00 3.25
26 27 1.780107 TTGTGCGATGGGGGTGGTAA 61.780 55.000 0.00 0.00 0.00 2.85
27 28 1.747745 GTGCGATGGGGGTGGTAAC 60.748 63.158 0.00 0.00 0.00 2.50
28 29 2.124445 GCGATGGGGGTGGTAACC 60.124 66.667 0.00 0.00 46.81 2.85
41 42 1.599797 GTAACCGTGGGCTGCAACT 60.600 57.895 0.50 0.00 0.00 3.16
55 56 4.992740 AACTGGCGGGCAATGGCA 62.993 61.111 9.51 0.00 43.71 4.92
88 89 2.715624 GATGTTGAATCGGGCCGC 59.284 61.111 23.83 8.26 0.00 6.53
108 109 4.867599 GAACGCCGGGCTAGGTCG 62.868 72.222 18.34 2.34 37.04 4.79
115 117 2.264794 GGGCTAGGTCGTGGTGTG 59.735 66.667 0.00 0.00 0.00 3.82
119 121 0.249741 GCTAGGTCGTGGTGTGTGTT 60.250 55.000 0.00 0.00 0.00 3.32
121 123 1.864711 CTAGGTCGTGGTGTGTGTTTG 59.135 52.381 0.00 0.00 0.00 2.93
125 127 2.246789 GTCGTGGTGTGTGTTTGTTTG 58.753 47.619 0.00 0.00 0.00 2.93
129 131 3.121194 CGTGGTGTGTGTTTGTTTGTTTG 60.121 43.478 0.00 0.00 0.00 2.93
130 132 3.804873 GTGGTGTGTGTTTGTTTGTTTGT 59.195 39.130 0.00 0.00 0.00 2.83
131 133 4.271291 GTGGTGTGTGTTTGTTTGTTTGTT 59.729 37.500 0.00 0.00 0.00 2.83
132 134 4.876107 TGGTGTGTGTTTGTTTGTTTGTTT 59.124 33.333 0.00 0.00 0.00 2.83
133 135 5.201181 GGTGTGTGTTTGTTTGTTTGTTTG 58.799 37.500 0.00 0.00 0.00 2.93
134 136 5.220681 GGTGTGTGTTTGTTTGTTTGTTTGT 60.221 36.000 0.00 0.00 0.00 2.83
135 137 6.251549 GTGTGTGTTTGTTTGTTTGTTTGTT 58.748 32.000 0.00 0.00 0.00 2.83
142 144 5.679734 TGTTTGTTTGTTTGTTTGCATGT 57.320 30.435 0.00 0.00 0.00 3.21
150 152 2.025767 TTGTTTGCATGTGCCGGCTT 62.026 50.000 29.70 9.86 41.18 4.35
156 158 4.431131 ATGTGCCGGCTTGGGGAG 62.431 66.667 29.70 0.00 38.63 4.30
180 194 1.370172 CGTATCGGCTCGGCTGTAC 60.370 63.158 4.89 0.00 36.18 2.90
218 232 1.206115 CGCATACGACGCAGCATACA 61.206 55.000 0.00 0.00 43.93 2.29
227 241 1.066858 ACGCAGCATACACTAAGCACT 60.067 47.619 0.00 0.00 0.00 4.40
228 242 1.325640 CGCAGCATACACTAAGCACTG 59.674 52.381 0.00 0.00 0.00 3.66
243 257 1.672881 GCACTGTATGACCAGAATGCC 59.327 52.381 0.00 0.00 36.30 4.40
244 258 2.292267 CACTGTATGACCAGAATGCCC 58.708 52.381 0.00 0.00 36.30 5.36
285 299 3.914426 ACCGAAGCAGACCTCAATTAT 57.086 42.857 0.00 0.00 0.00 1.28
463 515 8.940397 AAAAAGAAGATGTCCCTCTAATTTGA 57.060 30.769 0.00 0.00 0.00 2.69
474 526 7.395772 TGTCCCTCTAATTTGAAATATGTTGCA 59.604 33.333 0.00 0.00 0.00 4.08
658 755 1.984026 GCAATGGGGGTGAAGTGGG 60.984 63.158 0.00 0.00 0.00 4.61
692 790 9.823647 AGGTGAGATTAGACACAAAACATATAG 57.176 33.333 0.00 0.00 38.57 1.31
693 791 9.046296 GGTGAGATTAGACACAAAACATATAGG 57.954 37.037 0.00 0.00 38.57 2.57
694 792 9.817809 GTGAGATTAGACACAAAACATATAGGA 57.182 33.333 0.00 0.00 37.05 2.94
818 1823 4.667519 GGAACCACTCCGTCAACTATAT 57.332 45.455 0.00 0.00 33.37 0.86
819 1824 5.779529 GGAACCACTCCGTCAACTATATA 57.220 43.478 0.00 0.00 33.37 0.86
820 1825 6.342338 GGAACCACTCCGTCAACTATATAT 57.658 41.667 0.00 0.00 33.37 0.86
821 1826 6.157211 GGAACCACTCCGTCAACTATATATG 58.843 44.000 0.00 0.00 33.37 1.78
822 1827 6.015688 GGAACCACTCCGTCAACTATATATGA 60.016 42.308 0.00 0.00 33.37 2.15
823 1828 6.971726 ACCACTCCGTCAACTATATATGAA 57.028 37.500 0.00 0.00 0.00 2.57
824 1829 7.356089 ACCACTCCGTCAACTATATATGAAA 57.644 36.000 0.00 0.00 0.00 2.69
825 1830 7.434492 ACCACTCCGTCAACTATATATGAAAG 58.566 38.462 0.00 0.00 0.00 2.62
826 1831 7.287005 ACCACTCCGTCAACTATATATGAAAGA 59.713 37.037 0.00 0.00 0.00 2.52
827 1832 8.307483 CCACTCCGTCAACTATATATGAAAGAT 58.693 37.037 0.00 0.00 0.00 2.40
828 1833 9.347934 CACTCCGTCAACTATATATGAAAGATC 57.652 37.037 0.00 0.00 0.00 2.75
829 1834 8.524487 ACTCCGTCAACTATATATGAAAGATCC 58.476 37.037 0.00 0.00 0.00 3.36
830 1835 7.837863 TCCGTCAACTATATATGAAAGATCCC 58.162 38.462 0.00 0.00 0.00 3.85
831 1836 7.042335 CCGTCAACTATATATGAAAGATCCCC 58.958 42.308 0.00 0.00 0.00 4.81
832 1837 7.042335 CGTCAACTATATATGAAAGATCCCCC 58.958 42.308 0.00 0.00 0.00 5.40
833 1838 7.042335 GTCAACTATATATGAAAGATCCCCCG 58.958 42.308 0.00 0.00 0.00 5.73
834 1839 5.615925 ACTATATATGAAAGATCCCCCGC 57.384 43.478 0.00 0.00 0.00 6.13
835 1840 5.030147 ACTATATATGAAAGATCCCCCGCA 58.970 41.667 0.00 0.00 0.00 5.69
836 1841 4.927267 ATATATGAAAGATCCCCCGCAA 57.073 40.909 0.00 0.00 0.00 4.85
837 1842 3.593442 ATATGAAAGATCCCCCGCAAA 57.407 42.857 0.00 0.00 0.00 3.68
838 1843 2.230130 ATGAAAGATCCCCCGCAAAA 57.770 45.000 0.00 0.00 0.00 2.44
839 1844 2.002505 TGAAAGATCCCCCGCAAAAA 57.997 45.000 0.00 0.00 0.00 1.94
977 2226 1.089920 CTCACAGCCATAGTTGCCAC 58.910 55.000 0.00 0.00 0.00 5.01
1062 2328 2.392662 CTAACCCTCTGCATCCTCTCA 58.607 52.381 0.00 0.00 0.00 3.27
1158 2430 2.765807 CGCCTCATCCAGACCCCT 60.766 66.667 0.00 0.00 0.00 4.79
1614 2892 2.885861 CGCAAGTACGGCCTCTCT 59.114 61.111 0.00 0.00 0.00 3.10
1761 3039 1.895238 GTGGAAGGTGCGGCTAGTA 59.105 57.895 0.00 0.00 0.00 1.82
1794 3072 1.227999 CCGTCACGGTGTTCAGCATT 61.228 55.000 8.54 0.00 42.73 3.56
2034 3313 1.070289 GTCCAGTCCACGGTCTTCTTT 59.930 52.381 0.00 0.00 0.00 2.52
2529 3808 3.575965 AATTTTAAGAGGTTGGCAGCG 57.424 42.857 0.00 0.00 0.00 5.18
2598 3880 4.521062 CCTCCTCTTCCCGCTGCG 62.521 72.222 16.34 16.34 0.00 5.18
2630 3915 5.360591 ACCGTAGATTCCATTTGATCTGAC 58.639 41.667 0.00 0.00 0.00 3.51
2631 3916 5.129485 ACCGTAGATTCCATTTGATCTGACT 59.871 40.000 0.00 0.00 0.00 3.41
2633 3918 6.540189 CCGTAGATTCCATTTGATCTGACTTT 59.460 38.462 0.00 0.00 0.00 2.66
2634 3919 7.254590 CCGTAGATTCCATTTGATCTGACTTTC 60.255 40.741 0.00 0.00 0.00 2.62
2635 3920 7.278646 CGTAGATTCCATTTGATCTGACTTTCA 59.721 37.037 0.00 0.00 0.00 2.69
2676 3980 2.095567 GCTCGTGATTGTCTTTGCATGT 60.096 45.455 0.00 0.00 0.00 3.21
2677 3981 3.740590 CTCGTGATTGTCTTTGCATGTC 58.259 45.455 0.00 0.00 0.00 3.06
2678 3982 3.402110 TCGTGATTGTCTTTGCATGTCT 58.598 40.909 0.00 0.00 0.00 3.41
2679 3983 3.433274 TCGTGATTGTCTTTGCATGTCTC 59.567 43.478 0.00 0.00 0.00 3.36
2680 3984 3.722957 CGTGATTGTCTTTGCATGTCTCG 60.723 47.826 0.00 0.00 0.00 4.04
2681 3985 3.187227 GTGATTGTCTTTGCATGTCTCGT 59.813 43.478 0.00 0.00 0.00 4.18
2682 3986 3.433274 TGATTGTCTTTGCATGTCTCGTC 59.567 43.478 0.00 0.00 0.00 4.20
2683 3987 2.820059 TGTCTTTGCATGTCTCGTCT 57.180 45.000 0.00 0.00 0.00 4.18
2684 3988 3.111853 TGTCTTTGCATGTCTCGTCTT 57.888 42.857 0.00 0.00 0.00 3.01
2685 3989 3.466836 TGTCTTTGCATGTCTCGTCTTT 58.533 40.909 0.00 0.00 0.00 2.52
2686 3990 3.876914 TGTCTTTGCATGTCTCGTCTTTT 59.123 39.130 0.00 0.00 0.00 2.27
2687 3991 4.335315 TGTCTTTGCATGTCTCGTCTTTTT 59.665 37.500 0.00 0.00 0.00 1.94
2713 4017 7.489574 TTTTGAATTGTTTGGATTGCTTACC 57.510 32.000 0.00 0.00 0.00 2.85
2714 4018 4.804108 TGAATTGTTTGGATTGCTTACCG 58.196 39.130 0.00 0.00 0.00 4.02
2715 4019 2.715737 TTGTTTGGATTGCTTACCGC 57.284 45.000 0.00 0.00 39.77 5.68
2723 4027 4.440181 TGCTTACCGCACGTTTCA 57.560 50.000 0.00 0.00 45.47 2.69
2724 4028 2.921374 TGCTTACCGCACGTTTCAT 58.079 47.368 0.00 0.00 45.47 2.57
2725 4029 0.515127 TGCTTACCGCACGTTTCATG 59.485 50.000 0.00 0.00 45.47 3.07
2726 4030 0.515564 GCTTACCGCACGTTTCATGT 59.484 50.000 0.00 0.00 38.92 3.21
2727 4031 1.724654 GCTTACCGCACGTTTCATGTG 60.725 52.381 0.00 0.00 38.13 3.21
2729 4033 3.339731 CCGCACGTTTCATGTGGT 58.660 55.556 0.00 0.00 41.88 4.16
2730 4034 1.652012 CCGCACGTTTCATGTGGTT 59.348 52.632 0.00 0.00 41.88 3.67
2731 4035 0.660005 CCGCACGTTTCATGTGGTTG 60.660 55.000 0.00 0.00 41.88 3.77
2732 4036 1.268113 CGCACGTTTCATGTGGTTGC 61.268 55.000 0.00 0.00 35.71 4.17
2733 4037 0.248825 GCACGTTTCATGTGGTTGCA 60.249 50.000 0.00 0.00 35.71 4.08
2734 4038 1.602668 GCACGTTTCATGTGGTTGCAT 60.603 47.619 0.00 0.00 35.71 3.96
2735 4039 2.052891 CACGTTTCATGTGGTTGCATG 58.947 47.619 0.00 0.00 45.48 4.06
2753 4057 6.552859 TGCATGTTTCGTCTCTTAATTTCA 57.447 33.333 0.00 0.00 0.00 2.69
2777 4086 9.851686 TCATTCTCTATGGCTAAAATATTGTGT 57.148 29.630 0.00 0.00 34.85 3.72
2874 4202 0.823356 TGTCCCTTTGTCCAAGCTGC 60.823 55.000 0.00 0.00 0.00 5.25
2889 4220 2.032528 TGCGACTGGGCTCTTTGG 59.967 61.111 0.00 0.00 0.00 3.28
2921 4264 5.408604 GGTGTGGAAAGACACTACTACAATG 59.591 44.000 0.00 0.00 44.81 2.82
2936 4279 5.809001 ACTACAATGAAAGATGGCTCTTCA 58.191 37.500 0.00 0.00 40.93 3.02
2953 4296 3.005791 TCTTCATTCTCGAACAGAGCACA 59.994 43.478 0.00 0.00 46.44 4.57
2959 4302 0.744281 TCGAACAGAGCACAGACACA 59.256 50.000 0.00 0.00 0.00 3.72
2983 4326 8.331539 CACAATCAAATGTGCACATTACTATC 57.668 34.615 37.92 1.61 45.06 2.08
2984 4327 7.969508 CACAATCAAATGTGCACATTACTATCA 59.030 33.333 37.92 21.18 45.06 2.15
2985 4328 8.522003 ACAATCAAATGTGCACATTACTATCAA 58.478 29.630 37.92 21.01 45.06 2.57
2986 4329 9.356433 CAATCAAATGTGCACATTACTATCAAA 57.644 29.630 37.92 20.14 45.06 2.69
2988 4331 9.926158 ATCAAATGTGCACATTACTATCAAAAA 57.074 25.926 37.92 17.59 45.06 1.94
3021 4364 9.997482 TCATCTCGTTTTATAAATAAAGCAACC 57.003 29.630 0.00 0.00 34.42 3.77
3025 4368 7.022384 TCGTTTTATAAATAAAGCAACCACCG 58.978 34.615 0.00 0.00 34.42 4.94
3029 4758 8.918961 TTTATAAATAAAGCAACCACCGAATG 57.081 30.769 0.00 0.00 0.00 2.67
3034 4763 1.371635 GCAACCACCGAATGTGCAC 60.372 57.895 10.75 10.75 44.01 4.57
3044 4773 4.153296 CACCGAATGTGCACATTACTACAA 59.847 41.667 37.90 7.63 45.72 2.41
3063 4792 7.536855 ACTACAACAAATTAAAAACACCGACA 58.463 30.769 0.00 0.00 0.00 4.35
3118 4847 3.604582 AGCTCCACTTTGTGCTATTCTC 58.395 45.455 0.00 0.00 33.64 2.87
3257 4995 0.963962 TAGGACCGTGTGACTTGTCC 59.036 55.000 9.65 9.65 46.12 4.02
3372 5112 1.066605 GATTCCATGCATGAGTGGCAC 59.933 52.381 28.31 10.29 45.23 5.01
3588 5329 1.592669 CAACGCTAGGCCCTCGATG 60.593 63.158 14.61 9.69 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.091885 ACCCCCATCGCACAATAATTCT 60.092 45.455 0.00 0.00 0.00 2.40
1 2 2.034558 CACCCCCATCGCACAATAATTC 59.965 50.000 0.00 0.00 0.00 2.17
2 3 2.031120 CACCCCCATCGCACAATAATT 58.969 47.619 0.00 0.00 0.00 1.40
4 5 0.395036 CCACCCCCATCGCACAATAA 60.395 55.000 0.00 0.00 0.00 1.40
5 6 1.225983 CCACCCCCATCGCACAATA 59.774 57.895 0.00 0.00 0.00 1.90
6 7 1.567208 TACCACCCCCATCGCACAAT 61.567 55.000 0.00 0.00 0.00 2.71
7 8 1.780107 TTACCACCCCCATCGCACAA 61.780 55.000 0.00 0.00 0.00 3.33
8 9 2.224877 TTACCACCCCCATCGCACA 61.225 57.895 0.00 0.00 0.00 4.57
9 10 1.747745 GTTACCACCCCCATCGCAC 60.748 63.158 0.00 0.00 0.00 5.34
10 11 2.672295 GTTACCACCCCCATCGCA 59.328 61.111 0.00 0.00 0.00 5.10
11 12 2.124445 GGTTACCACCCCCATCGC 60.124 66.667 0.00 0.00 37.03 4.58
12 13 2.188469 CGGTTACCACCCCCATCG 59.812 66.667 1.13 0.00 40.52 3.84
13 14 1.078001 CACGGTTACCACCCCCATC 60.078 63.158 1.13 0.00 40.52 3.51
14 15 2.608550 CCACGGTTACCACCCCCAT 61.609 63.158 1.13 0.00 40.52 4.00
15 16 3.250734 CCACGGTTACCACCCCCA 61.251 66.667 1.13 0.00 40.52 4.96
16 17 4.037760 CCCACGGTTACCACCCCC 62.038 72.222 1.13 0.00 40.52 5.40
17 18 4.728110 GCCCACGGTTACCACCCC 62.728 72.222 1.13 0.00 40.52 4.95
18 19 3.643554 AGCCCACGGTTACCACCC 61.644 66.667 1.13 0.00 40.52 4.61
19 20 2.359478 CAGCCCACGGTTACCACC 60.359 66.667 1.13 0.00 40.16 4.61
20 21 3.053896 GCAGCCCACGGTTACCAC 61.054 66.667 1.13 0.00 0.00 4.16
21 22 3.121406 TTGCAGCCCACGGTTACCA 62.121 57.895 1.13 0.00 0.00 3.25
22 23 2.281900 TTGCAGCCCACGGTTACC 60.282 61.111 0.00 0.00 0.00 2.85
23 24 1.599797 AGTTGCAGCCCACGGTTAC 60.600 57.895 0.00 0.00 0.00 2.50
24 25 1.599518 CAGTTGCAGCCCACGGTTA 60.600 57.895 0.00 0.00 0.00 2.85
25 26 2.906897 CAGTTGCAGCCCACGGTT 60.907 61.111 0.00 0.00 0.00 4.44
26 27 4.954970 CCAGTTGCAGCCCACGGT 62.955 66.667 0.00 0.00 0.00 4.83
34 35 3.376078 ATTGCCCGCCAGTTGCAG 61.376 61.111 0.00 0.00 41.33 4.41
65 66 1.153168 CCGATTCAACATCGCCCCT 60.153 57.895 0.00 0.00 39.95 4.79
75 76 3.885538 TTCACGCGGCCCGATTCAA 62.886 57.895 18.74 0.00 41.02 2.69
96 97 4.143333 CACCACGACCTAGCCCGG 62.143 72.222 0.00 0.00 0.00 5.73
108 109 3.804873 ACAAACAAACAAACACACACCAC 59.195 39.130 0.00 0.00 0.00 4.16
109 110 4.060038 ACAAACAAACAAACACACACCA 57.940 36.364 0.00 0.00 0.00 4.17
115 117 5.739161 TGCAAACAAACAAACAAACAAACAC 59.261 32.000 0.00 0.00 0.00 3.32
119 121 5.911280 CACATGCAAACAAACAAACAAACAA 59.089 32.000 0.00 0.00 0.00 2.83
121 123 4.320427 GCACATGCAAACAAACAAACAAAC 59.680 37.500 0.00 0.00 41.59 2.93
125 127 2.536529 CGGCACATGCAAACAAACAAAC 60.537 45.455 6.15 0.00 44.36 2.93
129 131 1.830368 GCCGGCACATGCAAACAAAC 61.830 55.000 24.80 0.00 44.36 2.93
130 132 1.593750 GCCGGCACATGCAAACAAA 60.594 52.632 24.80 0.00 44.36 2.83
131 133 2.025767 AAGCCGGCACATGCAAACAA 62.026 50.000 31.54 0.00 44.36 2.83
132 134 2.497173 AAGCCGGCACATGCAAACA 61.497 52.632 31.54 0.00 44.36 2.83
133 135 2.023223 CAAGCCGGCACATGCAAAC 61.023 57.895 31.54 0.00 44.36 2.93
134 136 2.339348 CAAGCCGGCACATGCAAA 59.661 55.556 31.54 0.00 44.36 3.68
135 137 3.682885 CCAAGCCGGCACATGCAA 61.683 61.111 31.54 0.00 44.36 4.08
218 232 5.423015 CATTCTGGTCATACAGTGCTTAGT 58.577 41.667 0.00 0.00 39.48 2.24
227 241 5.510690 CGTATAAGGGCATTCTGGTCATACA 60.511 44.000 0.00 0.00 0.00 2.29
228 242 4.929808 CGTATAAGGGCATTCTGGTCATAC 59.070 45.833 0.00 0.00 0.00 2.39
262 276 1.334160 TTGAGGTCTGCTTCGGTACA 58.666 50.000 0.00 0.00 0.00 2.90
265 279 3.914426 ATAATTGAGGTCTGCTTCGGT 57.086 42.857 0.00 0.00 0.00 4.69
266 280 6.293626 CCAATTATAATTGAGGTCTGCTTCGG 60.294 42.308 31.05 12.15 46.72 4.30
267 281 6.293626 CCCAATTATAATTGAGGTCTGCTTCG 60.294 42.308 31.05 14.53 46.72 3.79
268 282 6.015940 CCCCAATTATAATTGAGGTCTGCTTC 60.016 42.308 31.05 0.00 46.72 3.86
269 283 5.835280 CCCCAATTATAATTGAGGTCTGCTT 59.165 40.000 31.05 0.00 46.72 3.91
285 299 3.777522 CAAATTTGTAGGGGCCCCAATTA 59.222 43.478 42.48 23.91 38.92 1.40
326 342 2.092968 TCTAGTAGCATGGGCAAAGTGG 60.093 50.000 0.00 0.00 44.61 4.00
463 515 9.593134 TGAGTAACTTTTGTTTGCAACATATTT 57.407 25.926 0.00 0.00 43.32 1.40
497 549 3.722728 CAAAAGATGCTGCCCCTATTC 57.277 47.619 0.00 0.00 0.00 1.75
587 647 1.885163 CGCCTACCTTCGGTGAACCT 61.885 60.000 0.00 0.00 36.19 3.50
617 688 4.593206 CAGTAAAGCTCCATATCCCCAGTA 59.407 45.833 0.00 0.00 0.00 2.74
817 1822 3.593442 TTTGCGGGGGATCTTTCATAT 57.407 42.857 0.00 0.00 0.00 1.78
818 1823 3.374042 TTTTGCGGGGGATCTTTCATA 57.626 42.857 0.00 0.00 0.00 2.15
819 1824 2.230130 TTTTGCGGGGGATCTTTCAT 57.770 45.000 0.00 0.00 0.00 2.57
820 1825 2.002505 TTTTTGCGGGGGATCTTTCA 57.997 45.000 0.00 0.00 0.00 2.69
848 1853 9.494271 GGTAGTTCAAGCATCATCTTTCATATA 57.506 33.333 0.00 0.00 0.00 0.86
855 1860 2.939103 GCGGTAGTTCAAGCATCATCTT 59.061 45.455 0.00 0.00 0.00 2.40
867 1872 1.299541 CATGTCCCATGCGGTAGTTC 58.700 55.000 0.00 0.00 0.00 3.01
948 2170 0.179111 TGGCTGTGAGCGCTATGTAC 60.179 55.000 11.50 8.31 43.62 2.90
977 2226 4.095334 TGATTGATTGATCCGCAAGTCAAG 59.905 41.667 0.00 0.00 40.42 3.02
1158 2430 2.601067 TAGGACGACGGGGTTGCA 60.601 61.111 0.00 0.00 0.00 4.08
1794 3072 0.768622 ATTGGTTCCTTGACCGGACA 59.231 50.000 9.46 5.04 42.83 4.02
1869 3148 2.989824 AGCACGCGGAGGTACAGT 60.990 61.111 12.47 0.00 0.00 3.55
1946 3225 1.930100 CGATCTTGCATGAGCCGAC 59.070 57.895 16.81 3.65 41.13 4.79
2034 3313 4.415332 GACGTCGCGGAGAAGCCA 62.415 66.667 6.13 0.00 35.94 4.75
2359 3638 2.739932 CGTAAGGCTCCATCTCCTTGTG 60.740 54.545 3.95 0.00 42.29 3.33
2529 3808 1.408822 GGATCCACCATGGTCTTCACC 60.409 57.143 16.53 11.31 39.03 4.02
2598 3880 8.836413 TCAAATGGAATCTACGGTATCATTTTC 58.164 33.333 0.00 0.00 33.00 2.29
2630 3915 4.935702 TGCACACTCCAAAGAAATGAAAG 58.064 39.130 0.00 0.00 0.00 2.62
2631 3916 4.402155 ACTGCACACTCCAAAGAAATGAAA 59.598 37.500 0.00 0.00 0.00 2.69
2633 3918 3.316029 CACTGCACACTCCAAAGAAATGA 59.684 43.478 0.00 0.00 0.00 2.57
2634 3919 3.635331 CACTGCACACTCCAAAGAAATG 58.365 45.455 0.00 0.00 0.00 2.32
2635 3920 2.035066 GCACTGCACACTCCAAAGAAAT 59.965 45.455 0.00 0.00 0.00 2.17
2688 3992 7.254590 CGGTAAGCAATCCAAACAATTCAAAAA 60.255 33.333 0.00 0.00 0.00 1.94
2689 3993 6.201806 CGGTAAGCAATCCAAACAATTCAAAA 59.798 34.615 0.00 0.00 0.00 2.44
2690 3994 5.694006 CGGTAAGCAATCCAAACAATTCAAA 59.306 36.000 0.00 0.00 0.00 2.69
2691 3995 5.226396 CGGTAAGCAATCCAAACAATTCAA 58.774 37.500 0.00 0.00 0.00 2.69
2692 3996 4.804108 CGGTAAGCAATCCAAACAATTCA 58.196 39.130 0.00 0.00 0.00 2.57
2708 4012 1.136085 CCACATGAAACGTGCGGTAAG 60.136 52.381 0.00 0.00 32.85 2.34
2709 4013 0.869068 CCACATGAAACGTGCGGTAA 59.131 50.000 0.00 0.00 32.85 2.85
2710 4014 0.249953 ACCACATGAAACGTGCGGTA 60.250 50.000 0.00 0.00 30.62 4.02
2711 4015 1.098712 AACCACATGAAACGTGCGGT 61.099 50.000 0.00 0.00 33.64 5.68
2712 4016 0.660005 CAACCACATGAAACGTGCGG 60.660 55.000 0.00 0.00 32.85 5.69
2713 4017 1.268113 GCAACCACATGAAACGTGCG 61.268 55.000 0.00 0.00 32.85 5.34
2714 4018 0.248825 TGCAACCACATGAAACGTGC 60.249 50.000 0.00 2.97 32.85 5.34
2715 4019 2.420628 ATGCAACCACATGAAACGTG 57.579 45.000 0.00 0.00 0.00 4.49
2723 4027 2.226437 GAGACGAAACATGCAACCACAT 59.774 45.455 0.00 0.00 0.00 3.21
2724 4028 1.601903 GAGACGAAACATGCAACCACA 59.398 47.619 0.00 0.00 0.00 4.17
2725 4029 1.873591 AGAGACGAAACATGCAACCAC 59.126 47.619 0.00 0.00 0.00 4.16
2726 4030 2.254546 AGAGACGAAACATGCAACCA 57.745 45.000 0.00 0.00 0.00 3.67
2727 4031 4.742438 TTAAGAGACGAAACATGCAACC 57.258 40.909 0.00 0.00 0.00 3.77
2728 4032 6.855914 TGAAATTAAGAGACGAAACATGCAAC 59.144 34.615 0.00 0.00 0.00 4.17
2729 4033 6.964908 TGAAATTAAGAGACGAAACATGCAA 58.035 32.000 0.00 0.00 0.00 4.08
2730 4034 6.552859 TGAAATTAAGAGACGAAACATGCA 57.447 33.333 0.00 0.00 0.00 3.96
2731 4035 7.965107 AGAATGAAATTAAGAGACGAAACATGC 59.035 33.333 0.00 0.00 36.07 4.06
2732 4036 9.483062 GAGAATGAAATTAAGAGACGAAACATG 57.517 33.333 0.00 0.00 36.07 3.21
2733 4037 9.442047 AGAGAATGAAATTAAGAGACGAAACAT 57.558 29.630 0.00 0.00 36.07 2.71
2734 4038 8.833231 AGAGAATGAAATTAAGAGACGAAACA 57.167 30.769 0.00 0.00 36.07 2.83
2753 4057 9.632638 ACACACAATATTTTAGCCATAGAGAAT 57.367 29.630 0.00 0.00 0.00 2.40
2845 4173 6.078456 TGGACAAAGGGACAATATCATTCT 57.922 37.500 0.00 0.00 0.00 2.40
2874 4202 2.328099 GCACCAAAGAGCCCAGTCG 61.328 63.158 0.00 0.00 0.00 4.18
2889 4220 2.000447 GTCTTTCCACACCTATCGCAC 59.000 52.381 0.00 0.00 0.00 5.34
2921 4264 4.437239 TCGAGAATGAAGAGCCATCTTTC 58.563 43.478 0.00 0.00 45.98 2.62
2936 4279 2.297315 TGTCTGTGCTCTGTTCGAGAAT 59.703 45.455 0.00 0.00 42.62 2.40
2953 4296 3.380954 TGTGCACATTTGATTGTGTGTCT 59.619 39.130 17.42 0.00 46.93 3.41
2959 4302 8.054152 TGATAGTAATGTGCACATTTGATTGT 57.946 30.769 41.08 23.53 43.48 2.71
2985 4328 9.974980 TTTATAAAACGAGATGAAAGCCTTTTT 57.025 25.926 0.00 0.00 0.00 1.94
2996 4339 9.781834 TGGTTGCTTTATTTATAAAACGAGATG 57.218 29.630 1.21 0.00 32.39 2.90
2998 4341 8.238631 GGTGGTTGCTTTATTTATAAAACGAGA 58.761 33.333 1.21 0.00 32.39 4.04
2999 4342 7.217447 CGGTGGTTGCTTTATTTATAAAACGAG 59.783 37.037 1.21 1.98 32.39 4.18
3000 4343 7.022384 CGGTGGTTGCTTTATTTATAAAACGA 58.978 34.615 1.21 0.00 32.39 3.85
3001 4344 7.022384 TCGGTGGTTGCTTTATTTATAAAACG 58.978 34.615 1.21 0.00 32.39 3.60
3007 4350 6.329496 CACATTCGGTGGTTGCTTTATTTAT 58.671 36.000 0.00 0.00 44.04 1.40
3025 4368 8.519492 AATTTGTTGTAGTAATGTGCACATTC 57.481 30.769 40.48 30.69 44.67 2.67
3044 4773 6.197364 TCACTGTCGGTGTTTTTAATTTGT 57.803 33.333 11.59 0.00 45.50 2.83
3060 4789 2.489329 CCAATGACCAACCATCACTGTC 59.511 50.000 0.00 0.00 0.00 3.51
3063 4792 3.524095 TTCCAATGACCAACCATCACT 57.476 42.857 0.00 0.00 0.00 3.41
3118 4847 3.780902 TGCACACTATGATACTTGACGG 58.219 45.455 0.00 0.00 0.00 4.79
3326 5066 9.226606 CATGGAACTTTAAGATGGTTTACAGTA 57.773 33.333 0.00 0.00 0.00 2.74
3372 5112 2.084610 TTGATGTCGGTCTTGCAGAG 57.915 50.000 0.00 0.00 0.00 3.35
3485 5225 5.041287 TCGACGTCAATGTTGATCTATTCC 58.959 41.667 17.16 0.00 39.73 3.01


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

AutoCloner maintained by Alex Coulton.