Multiple sequence alignment - TraesCS6A01G163700

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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 TraesCS6A01G163700 chr6A 100.000 4626 0 0 837 5462 158947571 158942946 0.000000e+00 8543.0
1 TraesCS6A01G163700 chr6A 100.000 471 0 0 1 471 158948407 158947937 0.000000e+00 870.0
2 TraesCS6A01G163700 chr6A 84.569 499 45 9 3300 3772 286423439 286423931 2.980000e-127 466.0
3 TraesCS6A01G163700 chr6A 82.389 494 57 16 2659 3127 35181565 35182053 2.370000e-108 403.0
4 TraesCS6A01G163700 chr6A 84.241 349 37 7 3787 4126 286424089 286424428 1.900000e-84 324.0
5 TraesCS6A01G163700 chr6A 77.007 548 69 29 3336 3839 35146113 35146647 1.510000e-65 261.0
6 TraesCS6A01G163700 chr6A 80.995 221 28 12 3458 3674 27040180 27040390 4.380000e-36 163.0
7 TraesCS6A01G163700 chr6A 87.342 79 7 2 3221 3296 35146017 35146095 2.710000e-13 87.9
8 TraesCS6A01G163700 chr6D 94.730 3264 109 25 1060 4293 120674538 120671308 0.000000e+00 5016.0
9 TraesCS6A01G163700 chr6D 88.283 734 39 21 4338 5036 120671298 120670577 0.000000e+00 835.0
10 TraesCS6A01G163700 chr6B 94.762 1852 58 11 1696 3547 212414353 212416165 0.000000e+00 2846.0
11 TraesCS6A01G163700 chr6B 90.724 1423 55 33 3539 4909 212416347 212417744 0.000000e+00 1825.0
12 TraesCS6A01G163700 chr6B 90.411 657 33 7 1031 1684 212413461 212414090 0.000000e+00 837.0
13 TraesCS6A01G163700 chr6B 87.712 472 45 8 5000 5459 212417858 212418328 6.230000e-149 538.0
14 TraesCS6A01G163700 chr6B 84.190 253 34 4 2880 3127 64326100 64326351 1.970000e-59 241.0
15 TraesCS6A01G163700 chr6B 100.000 38 0 0 4946 4983 212417820 212417857 2.730000e-08 71.3
16 TraesCS6A01G163700 chr7A 96.588 469 16 0 1 469 603506380 603505912 0.000000e+00 778.0
17 TraesCS6A01G163700 chr7A 96.178 471 18 0 1 471 714027979 714028449 0.000000e+00 771.0
18 TraesCS6A01G163700 chr7A 93.846 195 11 1 837 1031 714028458 714028651 5.350000e-75 292.0
19 TraesCS6A01G163700 chr7A 92.821 195 12 2 837 1031 603505901 603505709 1.160000e-71 281.0
20 TraesCS6A01G163700 chr1A 95.541 471 21 0 1 471 52481231 52481701 0.000000e+00 754.0
21 TraesCS6A01G163700 chr1A 95.127 472 21 2 1 471 434698379 434697909 0.000000e+00 743.0
22 TraesCS6A01G163700 chr1A 95.455 198 7 2 837 1033 582558810 582559006 1.140000e-81 315.0
23 TraesCS6A01G163700 chr1A 93.401 197 11 2 837 1032 434697900 434697705 1.920000e-74 291.0
24 TraesCS6A01G163700 chr2A 94.904 471 24 0 1 471 726336760 726337230 0.000000e+00 737.0
25 TraesCS6A01G163700 chr2A 96.568 437 15 0 1 437 102100018 102100454 0.000000e+00 725.0
26 TraesCS6A01G163700 chr2A 93.333 195 11 2 837 1031 102100477 102100669 2.490000e-73 287.0
27 TraesCS6A01G163700 chr2A 93.651 189 10 1 843 1031 17875409 17875223 1.160000e-71 281.0
28 TraesCS6A01G163700 chr4B 94.268 471 24 2 1 471 87428916 87429383 0.000000e+00 717.0
29 TraesCS6A01G163700 chr5B 93.376 468 28 2 4 471 685295222 685294758 0.000000e+00 689.0
30 TraesCS6A01G163700 chr5B 92.308 195 14 1 837 1031 685294749 685294556 5.390000e-70 276.0
31 TraesCS6A01G163700 chr5B 92.268 194 14 1 837 1030 685304180 685304372 1.940000e-69 274.0
32 TraesCS6A01G163700 chr3A 92.600 473 31 4 1 471 184666020 184665550 0.000000e+00 676.0
33 TraesCS6A01G163700 chr3A 95.000 200 9 1 837 1035 184665542 184665343 4.110000e-81 313.0
34 TraesCS6A01G163700 chr3D 86.373 499 33 18 3300 3772 420472561 420472072 3.770000e-141 512.0
35 TraesCS6A01G163700 chr3D 86.784 454 45 7 1611 2059 513861099 513861542 4.920000e-135 492.0
36 TraesCS6A01G163700 chr3D 86.818 440 47 5 1621 2059 420473070 420472641 1.060000e-131 481.0
37 TraesCS6A01G163700 chr3D 89.118 340 28 5 3300 3636 513861622 513861955 1.090000e-111 414.0
38 TraesCS6A01G163700 chr3D 90.244 82 5 2 3653 3734 513874358 513874436 2.690000e-18 104.0
39 TraesCS6A01G163700 chr7B 85.030 501 41 16 3300 3772 616810129 616810623 3.830000e-131 479.0
40 TraesCS6A01G163700 chr7B 82.796 372 37 14 3770 4126 616810757 616811116 1.910000e-79 307.0
41 TraesCS6A01G163700 chrUn 83.992 481 45 16 2658 3130 103113370 103113826 3.020000e-117 433.0
42 TraesCS6A01G163700 chrUn 80.620 387 47 14 2662 3025 103129715 103130096 1.940000e-69 274.0
43 TraesCS6A01G163700 chrUn 84.577 201 14 8 3286 3481 103113871 103114059 3.360000e-42 183.0
44 TraesCS6A01G163700 chrUn 75.443 395 67 15 3732 4124 103132879 103133245 1.220000e-36 165.0
45 TraesCS6A01G163700 chrUn 100.000 29 0 0 3224 3252 103113829 103113857 3.000000e-03 54.7


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 TraesCS6A01G163700 chr6A 158942946 158948407 5461 True 4706.500000 8543 100.0000 1 5462 2 chr6A.!!$R1 5461
1 TraesCS6A01G163700 chr6A 286423439 286424428 989 False 395.000000 466 84.4050 3300 4126 2 chr6A.!!$F4 826
2 TraesCS6A01G163700 chr6D 120670577 120674538 3961 True 2925.500000 5016 91.5065 1060 5036 2 chr6D.!!$R1 3976
3 TraesCS6A01G163700 chr6B 212413461 212418328 4867 False 1223.460000 2846 92.7218 1031 5459 5 chr6B.!!$F2 4428
4 TraesCS6A01G163700 chr7A 714027979 714028651 672 False 531.500000 771 95.0120 1 1031 2 chr7A.!!$F1 1030
5 TraesCS6A01G163700 chr7A 603505709 603506380 671 True 529.500000 778 94.7045 1 1031 2 chr7A.!!$R1 1030
6 TraesCS6A01G163700 chr1A 434697705 434698379 674 True 517.000000 743 94.2640 1 1032 2 chr1A.!!$R1 1031
7 TraesCS6A01G163700 chr2A 102100018 102100669 651 False 506.000000 725 94.9505 1 1031 2 chr2A.!!$F2 1030
8 TraesCS6A01G163700 chr5B 685294556 685295222 666 True 482.500000 689 92.8420 4 1031 2 chr5B.!!$R1 1027
9 TraesCS6A01G163700 chr3A 184665343 184666020 677 True 494.500000 676 93.8000 1 1035 2 chr3A.!!$R1 1034
10 TraesCS6A01G163700 chr3D 420472072 420473070 998 True 496.500000 512 86.5955 1621 3772 2 chr3D.!!$R1 2151
11 TraesCS6A01G163700 chr3D 513861099 513861955 856 False 453.000000 492 87.9510 1611 3636 2 chr3D.!!$F2 2025
12 TraesCS6A01G163700 chr7B 616810129 616811116 987 False 393.000000 479 83.9130 3300 4126 2 chr7B.!!$F1 826
13 TraesCS6A01G163700 chrUn 103113370 103114059 689 False 223.566667 433 89.5230 2658 3481 3 chrUn.!!$F1 823
14 TraesCS6A01G163700 chrUn 103129715 103133245 3530 False 219.500000 274 78.0315 2662 4124 2 chrUn.!!$F2 1462

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
963 965 3.903530 AATGAGGGGGTCTCTTTTGTT 57.096 42.857 0.00 0.0 42.86 2.83 F
1736 2003 0.178903 AGAGGGGCTGTGGTACTTGA 60.179 55.000 0.00 0.0 0.00 3.02 F
1737 2004 0.250513 GAGGGGCTGTGGTACTTGAG 59.749 60.000 0.00 0.0 0.00 3.02 F
1738 2005 0.473886 AGGGGCTGTGGTACTTGAGT 60.474 55.000 0.00 0.0 0.00 3.41 F
1786 2054 1.066587 CTCGCATCCTCCTCGTTCC 59.933 63.158 0.00 0.0 0.00 3.62 F
1788 2056 1.227089 CGCATCCTCCTCGTTCCAG 60.227 63.158 0.00 0.0 0.00 3.86 F
1977 2248 2.182284 CCGGTGTATGAACGCGGA 59.818 61.111 12.47 0.0 38.36 5.54 F
2348 2619 2.354704 GCTGTGCACTCACTATGGGTTA 60.355 50.000 19.41 0.0 43.49 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2232 2.162754 GGTCCGCGTTCATACACCG 61.163 63.158 4.92 0.0 0.00 4.94 R
3555 4203 1.339151 GCCAGTCCCACTTTCTACCAG 60.339 57.143 0.00 0.0 0.00 4.00 R
3861 6695 7.446001 AAGAGTTGCATAGAGAAGGAAAAAG 57.554 36.000 0.00 0.0 0.00 2.27 R
3966 6804 1.809619 CATGCGTGTCACTACCCCG 60.810 63.158 0.65 0.0 0.00 5.73 R
4195 7041 4.631813 GCATCGTCTAATGTGGACTCTTTT 59.368 41.667 0.00 0.0 0.00 2.27 R
4217 7063 3.445008 TGGAGATCCCCTAGTATGATGC 58.555 50.000 0.00 0.0 34.29 3.91 R
4346 7194 7.408756 TCCAAAAGCTGCAATTGAGTAATAT 57.591 32.000 10.34 0.0 0.00 1.28 R
4758 7640 0.655733 CACCAAGTTCCACGACACAC 59.344 55.000 0.00 0.0 0.00 3.82 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
963 965 3.903530 AATGAGGGGGTCTCTTTTGTT 57.096 42.857 0.00 0.00 42.86 2.83
1007 1010 3.009103 TGGCAATTCCAATGGGCAT 57.991 47.368 0.00 0.00 43.21 4.40
1058 1061 0.536460 GCGGGAGGAAAACAACAGGA 60.536 55.000 0.00 0.00 0.00 3.86
1062 1065 1.613925 GGAGGAAAACAACAGGAAGGC 59.386 52.381 0.00 0.00 0.00 4.35
1111 1114 2.389715 CACGGTATCTTCTCCCTTCCT 58.610 52.381 0.00 0.00 0.00 3.36
1112 1115 2.362717 CACGGTATCTTCTCCCTTCCTC 59.637 54.545 0.00 0.00 0.00 3.71
1113 1116 1.964933 CGGTATCTTCTCCCTTCCTCC 59.035 57.143 0.00 0.00 0.00 4.30
1114 1117 2.425102 CGGTATCTTCTCCCTTCCTCCT 60.425 54.545 0.00 0.00 0.00 3.69
1216 1219 3.918220 CCAAGCACGCGCGATCTC 61.918 66.667 39.36 20.64 45.49 2.75
1321 1324 3.706563 GAGCTGCTCGGCGTCATCA 62.707 63.158 14.68 0.00 37.29 3.07
1382 1385 3.488090 CCTTTTCTCGTCGGCGCC 61.488 66.667 19.07 19.07 38.14 6.53
1437 1440 3.571119 CAGGTTCTGCGGCTTCTG 58.429 61.111 0.00 0.00 0.00 3.02
1438 1441 2.359230 AGGTTCTGCGGCTTCTGC 60.359 61.111 0.00 0.00 38.76 4.26
1451 1454 0.527817 CTTCTGCCCGTGGTACGATC 60.528 60.000 2.52 0.00 46.05 3.69
1568 1577 1.154035 GCCGTGCTGGTTAATGTGC 60.154 57.895 0.00 0.00 41.21 4.57
1629 1645 6.801539 TTGACAAATAGTTCTGCTAACCAG 57.198 37.500 0.00 0.00 43.17 4.00
1654 1670 7.846823 AGGAGAGGATAAACATATGGGGTATAG 59.153 40.741 7.80 0.00 0.00 1.31
1660 1676 3.955650 ACATATGGGGTATAGCACGAC 57.044 47.619 7.80 0.00 0.00 4.34
1679 1695 3.691498 GACGCTTTATGGGTTGCATAAC 58.309 45.455 0.00 0.00 42.14 1.89
1687 1703 3.431673 TGGGTTGCATAACTCATCACA 57.568 42.857 0.00 0.00 42.22 3.58
1691 1707 5.104374 GGGTTGCATAACTCATCACATTTG 58.896 41.667 0.00 0.00 37.24 2.32
1735 2002 0.693049 AAGAGGGGCTGTGGTACTTG 59.307 55.000 0.00 0.00 0.00 3.16
1736 2003 0.178903 AGAGGGGCTGTGGTACTTGA 60.179 55.000 0.00 0.00 0.00 3.02
1737 2004 0.250513 GAGGGGCTGTGGTACTTGAG 59.749 60.000 0.00 0.00 0.00 3.02
1738 2005 0.473886 AGGGGCTGTGGTACTTGAGT 60.474 55.000 0.00 0.00 0.00 3.41
1739 2006 1.203262 AGGGGCTGTGGTACTTGAGTA 60.203 52.381 0.00 0.00 0.00 2.59
1786 2054 1.066587 CTCGCATCCTCCTCGTTCC 59.933 63.158 0.00 0.00 0.00 3.62
1788 2056 1.227089 CGCATCCTCCTCGTTCCAG 60.227 63.158 0.00 0.00 0.00 3.86
1845 2114 4.069304 TCTTCCATCCGTTTTAGGTTGTG 58.931 43.478 0.00 0.00 30.89 3.33
1961 2232 4.374843 TGCATATGCTGTTGATTTCACC 57.625 40.909 27.13 0.00 42.66 4.02
1963 2234 3.793129 GCATATGCTGTTGATTTCACCGG 60.793 47.826 20.64 0.00 38.21 5.28
1977 2248 2.182284 CCGGTGTATGAACGCGGA 59.818 61.111 12.47 0.00 38.36 5.54
1991 2262 3.685836 ACGCGGACCTTAAATTTATGC 57.314 42.857 12.47 0.00 0.00 3.14
2085 2356 4.336889 TCTTGAAGTCGTCACCAAGAAT 57.663 40.909 11.81 0.00 41.13 2.40
2187 2458 7.034967 TCCTTTAGGTTTGGCTCCTTTATTA 57.965 36.000 0.00 0.00 36.60 0.98
2188 2459 7.471890 TCCTTTAGGTTTGGCTCCTTTATTAA 58.528 34.615 0.00 0.00 36.60 1.40
2323 2594 5.475220 TGAGGATTGCTTTATTTTTCGGACA 59.525 36.000 0.00 0.00 0.00 4.02
2348 2619 2.354704 GCTGTGCACTCACTATGGGTTA 60.355 50.000 19.41 0.00 43.49 2.85
2383 2654 6.431234 ACTGATTTGGAAGGTGACAATTCTAC 59.569 38.462 0.00 0.00 31.67 2.59
2419 2690 7.211966 AGCAATAGAATGATTTATGACTGGC 57.788 36.000 0.00 0.00 0.00 4.85
2469 2740 7.568349 TGAGCCATTTTGACTAGAGAATATGT 58.432 34.615 0.00 0.00 0.00 2.29
2672 2943 4.880886 TGCATGTATCATTCTTGAACCG 57.119 40.909 0.00 0.00 34.96 4.44
3140 3547 6.530181 CGTGCAGCAGATACGGATTTATAATA 59.470 38.462 0.00 0.00 34.43 0.98
3350 3808 3.756434 CCGCCCACTTTTCTTCTTTATGA 59.244 43.478 0.00 0.00 0.00 2.15
3555 4203 8.654230 TCAGAGTTGCTAAATAATCATCAGTC 57.346 34.615 0.00 0.00 0.00 3.51
3651 6318 8.251026 TCTCATGTTTACGTCTGTATTCTCATT 58.749 33.333 0.00 0.00 0.00 2.57
3724 6392 5.702670 TGAGCAGTTCTGAACTAATCTTTGG 59.297 40.000 21.65 8.93 40.46 3.28
3861 6695 3.147629 CTCATTGATCCTGGATGGCTTC 58.852 50.000 15.25 0.01 35.26 3.86
3888 6722 8.918202 TTTTCCTTCTCTATGCAACTCTTTAA 57.082 30.769 0.00 0.00 0.00 1.52
3966 6804 3.604582 ACAGATAGTTGAAGAAGCTGGC 58.395 45.455 0.00 0.00 0.00 4.85
4188 7034 2.978156 AGGCAAAGGGTCAATCTGAA 57.022 45.000 0.00 0.00 0.00 3.02
4195 7041 6.462347 GGCAAAGGGTCAATCTGAAAAACTTA 60.462 38.462 0.00 0.00 0.00 2.24
4217 7063 7.545965 ACTTAAAAGAGTCCACATTAGACGATG 59.454 37.037 0.00 0.00 39.31 3.84
4329 7175 8.474025 TGTGTTGTTTCTTGGAGAAATTGTATT 58.526 29.630 6.42 0.00 44.94 1.89
4424 7272 7.700022 AGAAGAAAGGAATTGATTTCTCCAG 57.300 36.000 12.55 0.00 43.25 3.86
4431 7279 4.158579 GGAATTGATTTCTCCAGGTGGTTC 59.841 45.833 0.00 0.00 34.56 3.62
4507 7380 0.390340 TCTCTGTCAAGCGACCATGC 60.390 55.000 0.00 0.00 41.85 4.06
4581 7454 4.937201 AAAGCCAAACTTTACTGAAGGG 57.063 40.909 0.00 0.00 46.95 3.95
4620 7493 3.157087 TCCTCACTGGATTCCTTTTTGC 58.843 45.455 3.95 0.00 40.56 3.68
4623 7496 4.039609 CCTCACTGGATTCCTTTTTGCTTT 59.960 41.667 3.95 0.00 38.35 3.51
4624 7497 4.947645 TCACTGGATTCCTTTTTGCTTTG 58.052 39.130 3.95 0.00 0.00 2.77
4625 7498 4.648762 TCACTGGATTCCTTTTTGCTTTGA 59.351 37.500 3.95 0.00 0.00 2.69
4673 7555 4.119862 AGTGTTGTATCGTATGCATGGTC 58.880 43.478 10.16 0.00 0.00 4.02
4680 7562 1.217585 CGTATGCATGGTCTCTGCCG 61.218 60.000 10.16 0.00 38.89 5.69
4696 7578 0.879090 GCCGGTTGTACTTGGGAAAG 59.121 55.000 1.90 0.00 0.00 2.62
4705 7587 7.551617 CGGTTGTACTTGGGAAAGATATAACTT 59.448 37.037 0.00 0.00 0.00 2.66
4758 7640 4.380867 GGCTTCCAACAAGACATACAATGG 60.381 45.833 0.00 0.00 33.60 3.16
4800 7682 4.475944 CTTTTGCCGTTTCTCCATGTAAG 58.524 43.478 0.00 0.00 0.00 2.34
4802 7684 0.733150 GCCGTTTCTCCATGTAAGCC 59.267 55.000 0.00 0.00 0.00 4.35
4838 7721 5.248640 AGAAATGTGATGTCATCGTCCTTT 58.751 37.500 8.29 8.85 0.00 3.11
4840 7723 3.961480 TGTGATGTCATCGTCCTTTCT 57.039 42.857 8.29 0.00 0.00 2.52
4875 7758 2.561419 CACGACTGGTTTCTTCCTCCTA 59.439 50.000 0.00 0.00 0.00 2.94
4877 7760 3.447944 ACGACTGGTTTCTTCCTCCTATC 59.552 47.826 0.00 0.00 0.00 2.08
4878 7761 3.181474 CGACTGGTTTCTTCCTCCTATCC 60.181 52.174 0.00 0.00 0.00 2.59
4911 7794 2.853235 AACTAAGCTGGTGGGTACAC 57.147 50.000 0.00 0.00 46.97 2.90
4927 7810 0.109458 ACACATGAGCTGCAAATGCG 60.109 50.000 12.70 7.50 45.83 4.73
5021 7943 2.288666 TCAGAAACGCAGCAGAAAAGT 58.711 42.857 0.00 0.00 0.00 2.66
5026 7948 4.844267 GAAACGCAGCAGAAAAGTTTCTA 58.156 39.130 5.99 0.00 45.23 2.10
5047 7969 3.555966 ACAGATATTTGGTTAGCCCAGC 58.444 45.455 0.00 0.00 46.31 4.85
5051 7973 2.008242 ATTTGGTTAGCCCAGCAACA 57.992 45.000 0.00 0.00 46.31 3.33
5057 7979 0.606401 TTAGCCCAGCAACAGAGCAC 60.606 55.000 0.00 0.00 36.85 4.40
5062 7984 2.667536 AGCAACAGAGCACTGCCG 60.668 61.111 11.37 3.64 46.95 5.69
5116 8038 6.379988 GGGTTTTATTTGCCTTCTGGATAAGA 59.620 38.462 0.00 0.00 34.57 2.10
5119 8041 7.630242 TTTATTTGCCTTCTGGATAAGACAG 57.370 36.000 0.00 0.00 33.46 3.51
5121 8043 1.908619 TGCCTTCTGGATAAGACAGCA 59.091 47.619 0.00 0.00 39.65 4.41
5122 8044 2.284190 GCCTTCTGGATAAGACAGCAC 58.716 52.381 0.00 0.00 34.60 4.40
5123 8045 2.544685 CCTTCTGGATAAGACAGCACG 58.455 52.381 0.00 0.00 33.46 5.34
5125 8047 1.847328 TCTGGATAAGACAGCACGGA 58.153 50.000 0.00 0.00 35.94 4.69
5126 8048 2.388735 TCTGGATAAGACAGCACGGAT 58.611 47.619 0.00 0.00 35.94 4.18
5127 8049 2.101415 TCTGGATAAGACAGCACGGATG 59.899 50.000 0.00 0.00 35.94 3.51
5129 8051 1.412710 GGATAAGACAGCACGGATGGA 59.587 52.381 0.00 0.00 0.00 3.41
5130 8052 2.037772 GGATAAGACAGCACGGATGGAT 59.962 50.000 0.00 0.00 0.00 3.41
5131 8053 2.602257 TAAGACAGCACGGATGGATG 57.398 50.000 0.00 0.00 0.00 3.51
5132 8054 0.904649 AAGACAGCACGGATGGATGA 59.095 50.000 0.00 0.00 0.00 2.92
5133 8055 1.126488 AGACAGCACGGATGGATGAT 58.874 50.000 0.00 0.00 0.00 2.45
5134 8056 2.319844 AGACAGCACGGATGGATGATA 58.680 47.619 0.00 0.00 0.00 2.15
5135 8057 2.298446 AGACAGCACGGATGGATGATAG 59.702 50.000 0.00 0.00 0.00 2.08
5153 8076 6.183810 TGATAGATCATGTGAGGCTCAAAT 57.816 37.500 20.62 17.43 0.00 2.32
5177 8100 5.949952 TGGCACACTAGAACTAGATAGAACA 59.050 40.000 14.64 4.92 36.97 3.18
5179 8102 6.752815 GGCACACTAGAACTAGATAGAACAAC 59.247 42.308 14.64 0.00 36.97 3.32
5180 8103 6.752815 GCACACTAGAACTAGATAGAACAACC 59.247 42.308 14.64 0.00 36.97 3.77
5181 8104 7.259161 CACACTAGAACTAGATAGAACAACCC 58.741 42.308 14.64 0.00 36.97 4.11
5182 8105 6.952358 ACACTAGAACTAGATAGAACAACCCA 59.048 38.462 14.64 0.00 36.97 4.51
5206 8139 4.273318 AGGGAAATATCTTGTGTTCCAGC 58.727 43.478 3.87 0.00 41.17 4.85
5207 8140 4.016444 GGGAAATATCTTGTGTTCCAGCA 58.984 43.478 3.87 0.00 41.17 4.41
5212 8145 7.603784 GGAAATATCTTGTGTTCCAGCATTTTT 59.396 33.333 0.00 0.00 39.51 1.94
5221 8154 1.541147 TCCAGCATTTTTCCTCTTGCG 59.459 47.619 0.00 0.00 40.00 4.85
5245 8178 2.514824 GCCCATGCTCCTCGTTCC 60.515 66.667 0.00 0.00 33.53 3.62
5260 8193 3.427573 TCGTTCCTCCACAACTATCAGA 58.572 45.455 0.00 0.00 0.00 3.27
5262 8195 4.282449 TCGTTCCTCCACAACTATCAGAAA 59.718 41.667 0.00 0.00 0.00 2.52
5274 8207 2.839486 ATCAGAAACAGAAGCGACCA 57.161 45.000 0.00 0.00 0.00 4.02
5306 8239 3.243907 CGATATCTGTCCCTTGGGAGAAC 60.244 52.174 8.93 0.00 0.00 3.01
5311 8244 0.110486 GTCCCTTGGGAGAACTGCAA 59.890 55.000 8.93 0.00 0.00 4.08
5338 8271 1.974236 CTCTGAAGACCTTCACCCTGT 59.026 52.381 8.27 0.00 43.90 4.00
5344 8277 0.326264 GACCTTCACCCTGTGCTCAT 59.674 55.000 0.00 0.00 32.98 2.90
5354 8287 3.201290 CCCTGTGCTCATCATGTAAGTC 58.799 50.000 0.00 0.00 0.00 3.01
5370 8303 5.850614 TGTAAGTCACACTTTCTACCTTCC 58.149 41.667 0.00 0.00 39.51 3.46
5372 8305 6.779049 TGTAAGTCACACTTTCTACCTTCCTA 59.221 38.462 0.00 0.00 39.51 2.94
5377 8310 7.878644 AGTCACACTTTCTACCTTCCTAAATTC 59.121 37.037 0.00 0.00 0.00 2.17
5381 8314 8.661345 ACACTTTCTACCTTCCTAAATTCTTCT 58.339 33.333 0.00 0.00 0.00 2.85
5382 8315 8.940952 CACTTTCTACCTTCCTAAATTCTTCTG 58.059 37.037 0.00 0.00 0.00 3.02
5383 8316 8.881262 ACTTTCTACCTTCCTAAATTCTTCTGA 58.119 33.333 0.00 0.00 0.00 3.27
5384 8317 9.157104 CTTTCTACCTTCCTAAATTCTTCTGAC 57.843 37.037 0.00 0.00 0.00 3.51
5385 8318 7.184067 TCTACCTTCCTAAATTCTTCTGACC 57.816 40.000 0.00 0.00 0.00 4.02
5386 8319 6.960542 TCTACCTTCCTAAATTCTTCTGACCT 59.039 38.462 0.00 0.00 0.00 3.85
5400 8333 5.418840 TCTTCTGACCTTTTTATTCCCATGC 59.581 40.000 0.00 0.00 0.00 4.06
5404 8337 4.462483 TGACCTTTTTATTCCCATGCTCAC 59.538 41.667 0.00 0.00 0.00 3.51
5405 8338 3.769300 ACCTTTTTATTCCCATGCTCACC 59.231 43.478 0.00 0.00 0.00 4.02
5413 8346 0.604578 CCCATGCTCACCCAGTTTTG 59.395 55.000 0.00 0.00 0.00 2.44
5459 8392 0.178995 TTGGCCTGTGTTCTGCATGA 60.179 50.000 3.32 0.00 0.00 3.07
5460 8393 0.890542 TGGCCTGTGTTCTGCATGAC 60.891 55.000 3.32 0.00 0.00 3.06
5461 8394 0.890542 GGCCTGTGTTCTGCATGACA 60.891 55.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
932 934 1.149174 CCCTCATTAGTGGCGGCAT 59.851 57.895 17.19 7.05 0.00 4.40
944 946 5.536497 ATTAACAAAAGAGACCCCCTCAT 57.464 39.130 0.00 0.00 44.40 2.90
963 965 1.222387 CCCCCTGCGGACGAAATTA 59.778 57.895 0.00 0.00 0.00 1.40
1000 1003 1.417890 CGAAAGAGACCCTATGCCCAT 59.582 52.381 0.00 0.00 0.00 4.00
1058 1061 3.181429 TGAGAGAAAGGGTTTGATGCCTT 60.181 43.478 0.00 0.00 0.00 4.35
1062 1065 3.190118 GTGCTGAGAGAAAGGGTTTGATG 59.810 47.826 0.00 0.00 0.00 3.07
1212 1215 2.507944 GCCACCGCCATGAGAGAT 59.492 61.111 0.00 0.00 0.00 2.75
1213 1216 4.147449 CGCCACCGCCATGAGAGA 62.147 66.667 0.00 0.00 0.00 3.10
1388 1391 1.228154 GAGTCAACCCCACCACACC 60.228 63.158 0.00 0.00 0.00 4.16
1392 1395 3.948719 GCGGAGTCAACCCCACCA 61.949 66.667 0.00 0.00 0.00 4.17
1431 1434 2.573609 ATCGTACCACGGGCAGAAGC 62.574 60.000 0.00 0.00 42.81 3.86
1432 1435 0.527817 GATCGTACCACGGGCAGAAG 60.528 60.000 0.00 0.00 42.81 2.85
1433 1436 1.514087 GATCGTACCACGGGCAGAA 59.486 57.895 0.00 0.00 42.81 3.02
1434 1437 2.420568 GGATCGTACCACGGGCAGA 61.421 63.158 0.00 0.00 42.81 4.26
1435 1438 2.106332 GGATCGTACCACGGGCAG 59.894 66.667 0.00 0.00 42.81 4.85
1436 1439 3.829044 CGGATCGTACCACGGGCA 61.829 66.667 0.00 0.00 42.81 5.36
1437 1440 2.398128 CTACGGATCGTACCACGGGC 62.398 65.000 0.00 0.00 42.81 6.13
1438 1441 0.815213 TCTACGGATCGTACCACGGG 60.815 60.000 0.00 0.00 42.81 5.28
1451 1454 3.242870 GGAGCAAGCAATTCAATCTACGG 60.243 47.826 0.00 0.00 0.00 4.02
1493 1502 6.377327 TCTTTCTTTGAAACTAAGTGGCAG 57.623 37.500 0.00 0.00 0.00 4.85
1589 1598 4.408276 TGTCAAATTTATCCCCGGAAACA 58.592 39.130 0.73 0.00 0.00 2.83
1629 1645 6.893020 ATACCCCATATGTTTATCCTCTCC 57.107 41.667 1.24 0.00 0.00 3.71
1654 1670 0.179200 CAACCCATAAAGCGTCGTGC 60.179 55.000 0.00 0.00 46.98 5.34
1660 1676 3.376859 TGAGTTATGCAACCCATAAAGCG 59.623 43.478 0.00 0.00 45.36 4.68
1679 1695 2.821378 TGGGCACTTCAAATGTGATGAG 59.179 45.455 5.80 0.00 37.60 2.90
1684 1700 2.288395 GGAACTGGGCACTTCAAATGTG 60.288 50.000 0.00 0.00 38.36 3.21
1687 1703 2.158475 TGAGGAACTGGGCACTTCAAAT 60.158 45.455 0.00 0.00 41.55 2.32
1691 1707 2.206576 AATGAGGAACTGGGCACTTC 57.793 50.000 0.00 0.00 41.55 3.01
1735 2002 2.173569 AGGGCATGGAATGGAAGTACTC 59.826 50.000 0.00 0.00 46.86 2.59
1736 2003 2.208872 AGGGCATGGAATGGAAGTACT 58.791 47.619 0.00 0.00 46.86 2.73
1737 2004 2.689983 CAAGGGCATGGAATGGAAGTAC 59.310 50.000 0.00 0.00 46.86 2.73
1738 2005 2.311542 ACAAGGGCATGGAATGGAAGTA 59.688 45.455 0.00 0.00 46.86 2.24
1739 2006 1.077663 ACAAGGGCATGGAATGGAAGT 59.922 47.619 0.00 0.00 46.86 3.01
1740 2007 1.479323 CACAAGGGCATGGAATGGAAG 59.521 52.381 0.00 0.00 46.86 3.46
1741 2008 1.559368 CACAAGGGCATGGAATGGAA 58.441 50.000 0.00 0.00 46.86 3.53
1742 2009 0.971959 GCACAAGGGCATGGAATGGA 60.972 55.000 0.00 0.00 46.86 3.41
1786 2054 8.030692 TGGCTGAGAATTTATTCATCAAAACTG 58.969 33.333 5.36 0.00 39.23 3.16
1788 2056 8.031277 ACTGGCTGAGAATTTATTCATCAAAAC 58.969 33.333 5.36 1.72 39.23 2.43
1845 2114 3.304057 GCGGCTTATTAACAGCTTCCATC 60.304 47.826 8.10 0.00 37.43 3.51
1961 2232 2.162754 GGTCCGCGTTCATACACCG 61.163 63.158 4.92 0.00 0.00 4.94
1963 2234 2.282701 TAAGGTCCGCGTTCATACAC 57.717 50.000 4.92 0.00 0.00 2.90
1977 2248 8.028938 GTGAGAACACATGCATAAATTTAAGGT 58.971 33.333 0.00 0.00 45.32 3.50
2085 2356 5.070001 CCAAGTATGAGGTGGTCTTTGAAA 58.930 41.667 0.00 0.00 0.00 2.69
2348 2619 4.823989 CCTTCCAAATCAGTGAAACAGACT 59.176 41.667 0.00 0.00 41.43 3.24
2419 2690 4.946157 AGAATGCCTCAGTGAAATTAGGTG 59.054 41.667 0.00 0.00 0.00 4.00
2541 2812 6.633500 TTGTTGTTCCATCTAAACAAGAGG 57.367 37.500 1.92 0.00 44.73 3.69
2542 2813 7.707104 AGTTTGTTGTTCCATCTAAACAAGAG 58.293 34.615 1.92 0.00 44.73 2.85
2672 2943 9.725019 TGTGTCTCCAATATTCCATAATCATAC 57.275 33.333 0.00 0.00 0.00 2.39
3555 4203 1.339151 GCCAGTCCCACTTTCTACCAG 60.339 57.143 0.00 0.00 0.00 4.00
3861 6695 7.446001 AAGAGTTGCATAGAGAAGGAAAAAG 57.554 36.000 0.00 0.00 0.00 2.27
3966 6804 1.809619 CATGCGTGTCACTACCCCG 60.810 63.158 0.65 0.00 0.00 5.73
4188 7034 8.557029 CGTCTAATGTGGACTCTTTTAAGTTTT 58.443 33.333 0.00 0.00 0.00 2.43
4195 7041 4.631813 GCATCGTCTAATGTGGACTCTTTT 59.368 41.667 0.00 0.00 0.00 2.27
4217 7063 3.445008 TGGAGATCCCCTAGTATGATGC 58.555 50.000 0.00 0.00 34.29 3.91
4346 7194 7.408756 TCCAAAAGCTGCAATTGAGTAATAT 57.591 32.000 10.34 0.00 0.00 1.28
4424 7272 1.620822 ATTGTCAGGCTTGAACCACC 58.379 50.000 0.00 0.00 34.49 4.61
4431 7279 3.941483 CAGTAGGGTAATTGTCAGGCTTG 59.059 47.826 0.00 0.00 0.00 4.01
4507 7380 8.017373 CCTTGAAATGTATTGTCAGTGTAAGTG 58.983 37.037 0.00 0.00 39.10 3.16
4581 7454 3.153919 AGGATCTCATTCGAGCTCTACC 58.846 50.000 12.85 0.00 39.30 3.18
4618 7491 9.617523 TTTCTGATACATTCTATCATCAAAGCA 57.382 29.630 0.00 0.00 33.93 3.91
4649 7522 4.141937 ACCATGCATACGATACAACACTCT 60.142 41.667 0.00 0.00 0.00 3.24
4651 7524 4.119862 GACCATGCATACGATACAACACT 58.880 43.478 0.00 0.00 0.00 3.55
4673 7555 0.673644 CCCAAGTACAACCGGCAGAG 60.674 60.000 0.00 0.00 0.00 3.35
4680 7562 8.803397 AAGTTATATCTTTCCCAAGTACAACC 57.197 34.615 0.00 0.00 0.00 3.77
4736 7618 4.218417 ACCATTGTATGTCTTGTTGGAAGC 59.782 41.667 0.00 0.00 0.00 3.86
4758 7640 0.655733 CACCAAGTTCCACGACACAC 59.344 55.000 0.00 0.00 0.00 3.82
4763 7645 1.403679 CAAAAGCACCAAGTTCCACGA 59.596 47.619 0.00 0.00 0.00 4.35
4802 7684 1.288932 ACATTTCTCCCCCAGGATTGG 59.711 52.381 0.00 0.00 42.93 3.16
4875 7758 9.988815 CAGCTTAGTTTCATACAACTATAGGAT 57.011 33.333 4.43 0.00 38.71 3.24
4877 7760 8.204836 ACCAGCTTAGTTTCATACAACTATAGG 58.795 37.037 4.43 0.00 38.71 2.57
4878 7761 9.035607 CACCAGCTTAGTTTCATACAACTATAG 57.964 37.037 0.00 0.00 38.71 1.31
4911 7794 2.221552 CGCGCATTTGCAGCTCATG 61.222 57.895 8.75 0.00 42.21 3.07
4918 7801 0.376852 GGTTATCTCGCGCATTTGCA 59.623 50.000 8.75 0.00 42.21 4.08
4927 7810 2.798847 GGTAAATCCACGGTTATCTCGC 59.201 50.000 0.00 0.00 35.97 5.03
4989 7911 5.530519 TGCGTTTCTGAATTCTGATACAC 57.469 39.130 24.68 19.20 0.00 2.90
5042 7964 2.623915 GCAGTGCTCTGTTGCTGGG 61.624 63.158 16.59 0.00 43.05 4.45
5047 7969 2.667536 AGCGGCAGTGCTCTGTTG 60.668 61.111 16.11 10.52 42.95 3.33
5116 8038 2.319844 TCTATCATCCATCCGTGCTGT 58.680 47.619 0.00 0.00 0.00 4.40
5119 8041 3.599730 TGATCTATCATCCATCCGTGC 57.400 47.619 0.00 0.00 0.00 5.34
5121 8043 4.774200 TCACATGATCTATCATCCATCCGT 59.226 41.667 0.00 0.00 45.23 4.69
5122 8044 5.334724 TCACATGATCTATCATCCATCCG 57.665 43.478 0.00 0.00 45.23 4.18
5123 8045 5.672503 CCTCACATGATCTATCATCCATCC 58.327 45.833 0.00 0.00 45.23 3.51
5125 8047 4.783763 AGCCTCACATGATCTATCATCCAT 59.216 41.667 0.00 0.00 45.23 3.41
5126 8048 4.165760 AGCCTCACATGATCTATCATCCA 58.834 43.478 0.00 0.00 45.23 3.41
5127 8049 4.222366 TGAGCCTCACATGATCTATCATCC 59.778 45.833 0.00 0.00 45.23 3.51
5130 8052 5.619132 TTTGAGCCTCACATGATCTATCA 57.381 39.130 0.00 0.00 41.70 2.15
5131 8053 5.411977 CCATTTGAGCCTCACATGATCTATC 59.588 44.000 19.85 0.00 36.85 2.08
5132 8054 5.314529 CCATTTGAGCCTCACATGATCTAT 58.685 41.667 19.85 0.00 36.85 1.98
5133 8055 4.711399 CCATTTGAGCCTCACATGATCTA 58.289 43.478 19.85 0.00 36.85 1.98
5134 8056 3.552875 CCATTTGAGCCTCACATGATCT 58.447 45.455 19.85 0.00 36.85 2.75
5135 8057 2.034305 GCCATTTGAGCCTCACATGATC 59.966 50.000 19.85 9.13 36.85 2.92
5153 8076 5.949952 TGTTCTATCTAGTTCTAGTGTGCCA 59.050 40.000 6.73 0.00 0.00 4.92
5177 8100 5.402630 ACACAAGATATTTCCCTTTGGGTT 58.597 37.500 2.25 0.00 44.74 4.11
5179 8102 5.105351 GGAACACAAGATATTTCCCTTTGGG 60.105 44.000 0.00 0.00 46.11 4.12
5180 8103 5.480073 TGGAACACAAGATATTTCCCTTTGG 59.520 40.000 0.00 0.00 37.33 3.28
5181 8104 6.588719 TGGAACACAAGATATTTCCCTTTG 57.411 37.500 0.00 0.00 37.33 2.77
5182 8105 5.185828 GCTGGAACACAAGATATTTCCCTTT 59.814 40.000 0.00 0.00 37.33 3.11
5197 8125 4.301628 CAAGAGGAAAAATGCTGGAACAC 58.698 43.478 0.00 0.00 0.00 3.32
5198 8126 3.243839 GCAAGAGGAAAAATGCTGGAACA 60.244 43.478 0.00 0.00 35.93 3.18
5199 8127 3.320626 GCAAGAGGAAAAATGCTGGAAC 58.679 45.455 0.00 0.00 35.93 3.62
5232 8165 0.904865 TGTGGAGGAACGAGGAGCAT 60.905 55.000 0.00 0.00 0.00 3.79
5236 8169 2.297698 TAGTTGTGGAGGAACGAGGA 57.702 50.000 0.00 0.00 0.00 3.71
5245 8178 5.121454 GCTTCTGTTTCTGATAGTTGTGGAG 59.879 44.000 0.00 0.00 0.00 3.86
5260 8193 0.663153 GCTTGTGGTCGCTTCTGTTT 59.337 50.000 0.00 0.00 0.00 2.83
5262 8195 0.601311 GAGCTTGTGGTCGCTTCTGT 60.601 55.000 0.00 0.00 36.45 3.41
5274 8207 2.033550 GGACAGATATCGTCGAGCTTGT 59.966 50.000 16.24 2.80 34.04 3.16
5311 8244 2.439507 TGAAGGTCTTCAGAGGCAAACT 59.560 45.455 9.13 0.00 43.90 2.66
5338 8271 4.541973 AGTGTGACTTACATGATGAGCA 57.458 40.909 0.00 0.00 42.24 4.26
5344 8277 6.665992 AGGTAGAAAGTGTGACTTACATGA 57.334 37.500 0.00 0.00 42.24 3.07
5354 8287 8.622948 AAGAATTTAGGAAGGTAGAAAGTGTG 57.377 34.615 0.00 0.00 0.00 3.82
5372 8305 8.491045 TGGGAATAAAAAGGTCAGAAGAATTT 57.509 30.769 0.00 0.00 0.00 1.82
5377 8310 5.420104 AGCATGGGAATAAAAAGGTCAGAAG 59.580 40.000 0.00 0.00 0.00 2.85
5381 8314 4.462483 GTGAGCATGGGAATAAAAAGGTCA 59.538 41.667 0.00 0.00 0.00 4.02
5382 8315 4.142160 GGTGAGCATGGGAATAAAAAGGTC 60.142 45.833 0.00 0.00 0.00 3.85
5383 8316 3.769300 GGTGAGCATGGGAATAAAAAGGT 59.231 43.478 0.00 0.00 0.00 3.50
5384 8317 3.132824 GGGTGAGCATGGGAATAAAAAGG 59.867 47.826 0.00 0.00 0.00 3.11
5385 8318 3.768757 TGGGTGAGCATGGGAATAAAAAG 59.231 43.478 0.00 0.00 0.00 2.27
5386 8319 3.768757 CTGGGTGAGCATGGGAATAAAAA 59.231 43.478 0.00 0.00 0.00 1.94
5393 8326 0.482446 AAAACTGGGTGAGCATGGGA 59.518 50.000 0.00 0.00 0.00 4.37
5400 8333 0.609131 ATCGGGCAAAACTGGGTGAG 60.609 55.000 0.00 0.00 0.00 3.51
5404 8337 0.527565 CTGAATCGGGCAAAACTGGG 59.472 55.000 0.00 0.00 0.00 4.45
5405 8338 0.527565 CCTGAATCGGGCAAAACTGG 59.472 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.