Multiple sequence alignment - TraesCS3D01G212200

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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 TraesCS3D01G212200 chr3D 100.000 4405 0 0 1 4405 284815152 284819556 0.000000e+00 8135.0
1 TraesCS3D01G212200 chr3D 88.610 597 37 14 314 884 321520361 321520952 0.000000e+00 697.0
2 TraesCS3D01G212200 chr3D 87.671 146 8 4 3881 4016 389080963 389080818 1.270000e-35 161.0
3 TraesCS3D01G212200 chr3D 92.929 99 7 0 3173 3271 477910649 477910551 1.280000e-30 145.0
4 TraesCS3D01G212200 chr3D 85.034 147 10 7 3881 4016 67533517 67533372 5.940000e-29 139.0
5 TraesCS3D01G212200 chr3D 91.837 98 8 0 3167 3264 190256581 190256484 2.140000e-28 137.0
6 TraesCS3D01G212200 chr3D 84.058 138 16 4 3884 4016 394196944 394197080 1.290000e-25 128.0
7 TraesCS3D01G212200 chr3D 100.000 28 0 0 875 902 496434195 496434168 8.000000e-03 52.8
8 TraesCS3D01G212200 chr3B 97.820 2844 38 6 901 3733 378462040 378459210 0.000000e+00 4887.0
9 TraesCS3D01G212200 chr3B 91.080 426 6 14 3989 4405 378457422 378457020 8.330000e-152 547.0
10 TraesCS3D01G212200 chr3B 87.714 350 28 4 567 902 407664013 407663665 1.150000e-105 394.0
11 TraesCS3D01G212200 chr3B 96.774 217 6 1 1 216 378462453 378462237 1.160000e-95 361.0
12 TraesCS3D01G212200 chr3B 94.578 166 6 1 3832 3997 378458387 378458225 2.030000e-63 254.0
13 TraesCS3D01G212200 chr3B 90.196 153 14 1 736 887 592328985 592328833 9.660000e-47 198.0
14 TraesCS3D01G212200 chr3B 89.313 131 7 4 3892 4016 813919596 813919725 1.640000e-34 158.0
15 TraesCS3D01G212200 chr3B 87.050 139 13 3 3883 4016 671410103 671410241 7.630000e-33 152.0
16 TraesCS3D01G212200 chr3B 85.211 142 13 5 3881 4016 553049445 553049584 5.940000e-29 139.0
17 TraesCS3D01G212200 chr3B 85.294 136 14 4 3886 4016 360083295 360083161 7.680000e-28 135.0
18 TraesCS3D01G212200 chr3A 95.813 1648 49 11 2097 3733 372195140 372196778 0.000000e+00 2643.0
19 TraesCS3D01G212200 chr3A 95.385 1170 34 12 901 2065 372193986 372195140 0.000000e+00 1844.0
20 TraesCS3D01G212200 chr3A 89.167 600 34 12 314 884 528985883 528986480 0.000000e+00 719.0
21 TraesCS3D01G212200 chr3A 93.519 216 9 1 1 216 372193552 372193762 2.560000e-82 316.0
22 TraesCS3D01G212200 chr7D 91.525 590 28 8 314 884 381841600 381842186 0.000000e+00 793.0
23 TraesCS3D01G212200 chr7D 87.667 600 44 12 314 884 456517564 456518162 0.000000e+00 671.0
24 TraesCS3D01G212200 chr7D 89.926 407 24 10 4015 4405 561620287 561619882 3.930000e-140 508.0
25 TraesCS3D01G212200 chr7D 86.333 300 24 7 620 903 588376877 588376579 1.190000e-80 311.0
26 TraesCS3D01G212200 chr7D 88.235 136 15 1 748 882 551448255 551448120 1.270000e-35 161.0
27 TraesCS3D01G212200 chr7D 86.179 123 12 4 3143 3264 267124047 267124165 1.290000e-25 128.0
28 TraesCS3D01G212200 chr7D 100.000 28 0 0 875 902 178715733 178715760 8.000000e-03 52.8
29 TraesCS3D01G212200 chr6D 91.017 590 32 10 314 884 253840258 253839671 0.000000e+00 776.0
30 TraesCS3D01G212200 chr6D 93.750 96 3 3 3923 4016 9020918 9021012 1.650000e-29 141.0
31 TraesCS3D01G212200 chr6D 77.113 284 38 11 3755 4016 350908722 350909000 5.940000e-29 139.0
32 TraesCS3D01G212200 chr6D 90.217 92 9 0 3173 3264 467788048 467787957 2.150000e-23 121.0
33 TraesCS3D01G212200 chr6D 88.776 98 9 2 3174 3270 317078875 317078779 7.740000e-23 119.0
34 TraesCS3D01G212200 chr6D 88.776 98 10 1 3174 3270 391925896 391925993 7.740000e-23 119.0
35 TraesCS3D01G212200 chr4D 90.847 590 34 7 314 884 416253528 416252940 0.000000e+00 773.0
36 TraesCS3D01G212200 chr4D 88.182 110 10 3 3157 3263 509105454 509105345 1.290000e-25 128.0
37 TraesCS3D01G212200 chr4D 92.593 81 6 0 3183 3263 476868310 476868390 2.780000e-22 117.0
38 TraesCS3D01G212200 chr4D 86.111 108 14 1 3163 3270 23909763 23909657 1.000000e-21 115.0
39 TraesCS3D01G212200 chr4D 87.755 98 12 0 3174 3271 261560028 261560125 1.000000e-21 115.0
40 TraesCS3D01G212200 chr4D 89.041 73 4 1 3944 4016 504060607 504060539 2.180000e-13 87.9
41 TraesCS3D01G212200 chr7B 89.216 612 47 11 314 906 245206673 245207284 0.000000e+00 747.0
42 TraesCS3D01G212200 chr7B 89.344 122 11 2 759 879 475249863 475249983 7.630000e-33 152.0
43 TraesCS3D01G212200 chr7B 91.071 112 9 1 3155 3265 216938224 216938335 2.740000e-32 150.0
44 TraesCS3D01G212200 chr6A 86.957 598 40 15 315 875 482715288 482715884 4.800000e-179 638.0
45 TraesCS3D01G212200 chr6A 87.469 407 33 13 4015 4405 268194954 268195358 1.870000e-123 453.0
46 TraesCS3D01G212200 chr6A 89.908 109 11 0 3156 3264 465228920 465229028 1.650000e-29 141.0
47 TraesCS3D01G212200 chr6A 91.753 97 7 1 3920 4016 593004996 593005091 2.760000e-27 134.0
48 TraesCS3D01G212200 chr4A 87.346 569 38 12 314 852 346595246 346594682 4.840000e-174 621.0
49 TraesCS3D01G212200 chr1A 91.061 358 17 5 4048 4405 485230112 485229770 1.850000e-128 470.0
50 TraesCS3D01G212200 chr1A 91.818 110 9 0 3154 3263 352174090 352174199 2.120000e-33 154.0
51 TraesCS3D01G212200 chr1A 88.793 116 12 1 3156 3271 306866086 306865972 1.650000e-29 141.0
52 TraesCS3D01G212200 chr1A 90.196 102 9 1 3163 3263 188149094 188148993 9.940000e-27 132.0
53 TraesCS3D01G212200 chr1A 92.391 92 7 0 3173 3264 188150937 188150846 9.940000e-27 132.0
54 TraesCS3D01G212200 chr1A 92.391 92 7 0 3935 4026 366363846 366363755 9.940000e-27 132.0
55 TraesCS3D01G212200 chrUn 87.775 409 32 13 4014 4405 43174431 43174838 3.100000e-126 462.0
56 TraesCS3D01G212200 chrUn 87.775 409 32 13 4014 4405 178597497 178597904 3.100000e-126 462.0
57 TraesCS3D01G212200 chrUn 87.531 409 33 13 4014 4405 43022000 43021593 1.440000e-124 457.0
58 TraesCS3D01G212200 chrUn 88.776 98 10 1 3173 3269 52409762 52409859 7.740000e-23 119.0
59 TraesCS3D01G212200 chrUn 91.463 82 7 0 3182 3263 126941322 126941241 3.600000e-21 113.0
60 TraesCS3D01G212200 chrUn 88.172 93 11 0 3174 3266 3061967 3061875 1.300000e-20 111.0
61 TraesCS3D01G212200 chrUn 87.778 90 11 0 3174 3263 19227907 19227818 6.030000e-19 106.0
62 TraesCS3D01G212200 chrUn 86.022 93 13 0 3174 3266 3062182 3062090 2.800000e-17 100.0
63 TraesCS3D01G212200 chrUn 89.706 68 7 0 3179 3246 77900042 77899975 2.180000e-13 87.9
64 TraesCS3D01G212200 chrUn 82.653 98 16 1 3167 3264 5249480 5249384 7.850000e-13 86.1
65 TraesCS3D01G212200 chrUn 86.301 73 10 0 3174 3246 31028380 31028452 3.650000e-11 80.5
66 TraesCS3D01G212200 chr1D 90.566 265 12 7 4152 4405 200759961 200759699 5.460000e-89 339.0
67 TraesCS3D01G212200 chr1D 91.626 203 14 2 4013 4213 385131222 385131021 1.210000e-70 278.0
68 TraesCS3D01G212200 chr1D 88.268 179 14 2 4234 4405 385130666 385130488 1.610000e-49 207.0
69 TraesCS3D01G212200 chr1D 92.079 101 8 0 3163 3263 379139997 379139897 4.590000e-30 143.0
70 TraesCS3D01G212200 chr1D 88.618 123 5 4 3902 4016 469122535 469122656 1.650000e-29 141.0
71 TraesCS3D01G212200 chr1D 91.304 92 8 0 3173 3264 128530406 128530315 4.630000e-25 126.0
72 TraesCS3D01G212200 chr1D 91.209 91 8 0 3174 3264 100459074 100458984 1.660000e-24 124.0
73 TraesCS3D01G212200 chr1D 92.857 42 3 0 3973 4014 47930410 47930369 1.320000e-05 62.1
74 TraesCS3D01G212200 chr6B 86.486 148 18 2 739 885 135849779 135849633 1.270000e-35 161.0
75 TraesCS3D01G212200 chr6B 96.667 90 3 0 3926 4015 674556585 674556496 2.740000e-32 150.0
76 TraesCS3D01G212200 chr6B 90.588 85 3 3 4321 4405 481018578 481018499 1.680000e-19 108.0
77 TraesCS3D01G212200 chr6B 100.000 28 0 0 875 902 628983382 628983409 8.000000e-03 52.8
78 TraesCS3D01G212200 chr7A 85.161 155 20 2 733 884 33733728 33733882 5.900000e-34 156.0
79 TraesCS3D01G212200 chr7A 83.929 168 15 5 3861 4016 7564044 7563877 2.740000e-32 150.0
80 TraesCS3D01G212200 chr2A 95.876 97 3 1 3920 4016 558594899 558594804 5.900000e-34 156.0
81 TraesCS3D01G212200 chr2A 90.588 85 3 3 4321 4405 404930681 404930760 1.680000e-19 108.0
82 TraesCS3D01G212200 chr2D 87.500 136 13 3 3884 4016 560950366 560950500 2.120000e-33 154.0
83 TraesCS3D01G212200 chr2D 86.400 125 11 3 3897 4016 317874368 317874245 9.940000e-27 132.0
84 TraesCS3D01G212200 chr1B 92.523 107 8 0 3157 3263 301273396 301273502 2.120000e-33 154.0
85 TraesCS3D01G212200 chr1B 86.607 112 15 0 3905 4016 282083951 282083840 1.660000e-24 124.0
86 TraesCS3D01G212200 chr1B 86.607 112 15 0 3905 4016 282108450 282108339 1.660000e-24 124.0
87 TraesCS3D01G212200 chr5D 95.604 91 3 1 3927 4016 529055102 529055012 1.280000e-30 145.0
88 TraesCS3D01G212200 chr5B 85.915 142 12 3 3883 4016 603414171 603414312 1.280000e-30 145.0
89 TraesCS3D01G212200 chr5B 94.505 91 4 1 3927 4016 666648152 666648062 5.940000e-29 139.0
90 TraesCS3D01G212200 chr5B 91.089 101 9 0 3155 3255 501956952 501957052 2.140000e-28 137.0
91 TraesCS3D01G212200 chr2B 83.439 157 21 5 733 884 511768147 511767991 1.650000e-29 141.0
92 TraesCS3D01G212200 chr2B 80.203 197 28 11 712 902 100983305 100983114 2.140000e-28 137.0
93 TraesCS3D01G212200 chr4B 86.822 129 12 2 3892 4015 658162808 658162936 5.940000e-29 139.0
94 TraesCS3D01G212200 chr4B 93.333 90 6 0 3174 3263 518879479 518879390 2.760000e-27 134.0
95 TraesCS3D01G212200 chr4B 90.816 98 8 1 3174 3271 479155527 479155623 3.580000e-26 130.0
96 TraesCS3D01G212200 chr4B 89.691 97 10 0 3168 3264 14768116 14768212 1.660000e-24 124.0
97 TraesCS3D01G212200 chr4B 88.235 102 12 0 3163 3264 105626742 105626641 5.980000e-24 122.0
98 TraesCS3D01G212200 chr4B 89.412 85 4 3 4321 4405 654112256 654112177 7.790000e-18 102.0
99 TraesCS3D01G212200 chr5A 90.588 85 3 3 4321 4405 2102045 2101966 1.680000e-19 108.0


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 TraesCS3D01G212200 chr3D 284815152 284819556 4404 False 8135.00 8135 100.000000 1 4405 1 chr3D.!!$F1 4404
1 TraesCS3D01G212200 chr3D 321520361 321520952 591 False 697.00 697 88.610000 314 884 1 chr3D.!!$F2 570
2 TraesCS3D01G212200 chr3B 378457020 378462453 5433 True 1512.25 4887 95.063000 1 4405 4 chr3B.!!$R4 4404
3 TraesCS3D01G212200 chr3A 372193552 372196778 3226 False 1601.00 2643 94.905667 1 3733 3 chr3A.!!$F2 3732
4 TraesCS3D01G212200 chr3A 528985883 528986480 597 False 719.00 719 89.167000 314 884 1 chr3A.!!$F1 570
5 TraesCS3D01G212200 chr7D 381841600 381842186 586 False 793.00 793 91.525000 314 884 1 chr7D.!!$F3 570
6 TraesCS3D01G212200 chr7D 456517564 456518162 598 False 671.00 671 87.667000 314 884 1 chr7D.!!$F4 570
7 TraesCS3D01G212200 chr6D 253839671 253840258 587 True 776.00 776 91.017000 314 884 1 chr6D.!!$R1 570
8 TraesCS3D01G212200 chr4D 416252940 416253528 588 True 773.00 773 90.847000 314 884 1 chr4D.!!$R2 570
9 TraesCS3D01G212200 chr7B 245206673 245207284 611 False 747.00 747 89.216000 314 906 1 chr7B.!!$F2 592
10 TraesCS3D01G212200 chr6A 482715288 482715884 596 False 638.00 638 86.957000 315 875 1 chr6A.!!$F3 560
11 TraesCS3D01G212200 chr4A 346594682 346595246 564 True 621.00 621 87.346000 314 852 1 chr4A.!!$R1 538
12 TraesCS3D01G212200 chr1D 385130488 385131222 734 True 242.50 278 89.947000 4013 4405 2 chr1D.!!$R6 392

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
100 101 0.032678 CTAGCATCGACATCGGCCTT 59.967 55.000 0.00 0.0 40.29 4.35 F
1003 1226 0.106719 TCCCCCGGAAGAATGAATGC 60.107 55.000 0.73 0.0 0.00 3.56 F
1008 1231 1.672881 CCGGAAGAATGAATGCTCCAC 59.327 52.381 0.00 0.0 0.00 4.02 F
1591 1815 2.016393 GCCTTTGGGGGCGATTAAGC 62.016 60.000 0.00 0.0 42.82 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1035 1258 1.743252 GAAGAGGTGAAGGGCGCAG 60.743 63.158 10.83 0.0 0.0 5.18 R
2763 2990 4.172505 CTCTCCAGTCTTCAAGTTCGATG 58.827 47.826 0.00 0.0 0.0 3.84 R
3294 3521 3.436704 ACGAAACAGTACCATTGCATCAG 59.563 43.478 0.00 0.0 0.0 2.90 R
3793 4803 0.248702 GCAAACCGCGTTTTCCTCAA 60.249 50.000 4.92 0.0 33.1 3.02 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
100 101 0.032678 CTAGCATCGACATCGGCCTT 59.967 55.000 0.00 0.00 40.29 4.35
137 138 2.959465 AGAAGAAACCTGGGGAGTTG 57.041 50.000 0.00 0.00 0.00 3.16
555 737 6.264970 AGCATTAATTGGGTGTTTTTGCAAAT 59.735 30.769 13.65 0.00 0.00 2.32
583 765 6.933514 AAAAATATTCCACCACTCACCATT 57.066 33.333 0.00 0.00 0.00 3.16
661 843 6.996282 GGGGTAACATAAGTAGTAACATGCAT 59.004 38.462 0.00 0.00 39.74 3.96
671 853 4.032960 AGTAACATGCATTTGGGACTCA 57.967 40.909 0.00 0.00 0.00 3.41
902 1125 1.569653 AACCGGAAAGGAGGGAGTAG 58.430 55.000 9.46 0.00 45.00 2.57
903 1126 0.976590 ACCGGAAAGGAGGGAGTAGC 60.977 60.000 9.46 0.00 45.00 3.58
904 1127 0.688087 CCGGAAAGGAGGGAGTAGCT 60.688 60.000 0.00 0.00 45.00 3.32
905 1128 1.411216 CCGGAAAGGAGGGAGTAGCTA 60.411 57.143 0.00 0.00 45.00 3.32
906 1129 1.957877 CGGAAAGGAGGGAGTAGCTAG 59.042 57.143 0.00 0.00 0.00 3.42
907 1130 2.687314 CGGAAAGGAGGGAGTAGCTAGT 60.687 54.545 0.00 0.00 0.00 2.57
908 1131 2.696187 GGAAAGGAGGGAGTAGCTAGTG 59.304 54.545 5.62 0.00 0.00 2.74
1003 1226 0.106719 TCCCCCGGAAGAATGAATGC 60.107 55.000 0.73 0.00 0.00 3.56
1008 1231 1.672881 CCGGAAGAATGAATGCTCCAC 59.327 52.381 0.00 0.00 0.00 4.02
1248 1471 3.909258 CTACAAGGTGACGCGCCGT 62.909 63.158 5.73 2.55 45.10 5.68
1591 1815 2.016393 GCCTTTGGGGGCGATTAAGC 62.016 60.000 0.00 0.00 42.82 3.09
2763 2990 7.959109 GCCAGATAATGCAAAAAGACAAAATTC 59.041 33.333 0.00 0.00 0.00 2.17
3294 3521 3.006967 TCCTAGTTTGGACTCTTGCTCAC 59.993 47.826 0.00 0.00 37.33 3.51
3428 3656 9.066892 TGACATTTTCTTGTGCTCTATTTAAGT 57.933 29.630 0.00 0.00 0.00 2.24
3753 4763 2.032799 TCAAAACGCGATTTGCTGAACT 59.967 40.909 30.07 0.00 43.27 3.01
3757 4767 2.683968 ACGCGATTTGCTGAACTCTTA 58.316 42.857 15.93 0.00 43.27 2.10
3776 4786 6.946583 ACTCTTATATCGCTGACCCTTATACA 59.053 38.462 0.00 0.00 0.00 2.29
3785 4795 4.982916 GCTGACCCTTATACACGATTACAG 59.017 45.833 0.00 0.00 0.00 2.74
3786 4796 5.451520 GCTGACCCTTATACACGATTACAGT 60.452 44.000 0.00 0.00 0.00 3.55
3787 4797 6.534475 TGACCCTTATACACGATTACAGTT 57.466 37.500 0.00 0.00 0.00 3.16
3788 4798 7.643569 TGACCCTTATACACGATTACAGTTA 57.356 36.000 0.00 0.00 0.00 2.24
3789 4799 7.483307 TGACCCTTATACACGATTACAGTTAC 58.517 38.462 0.00 0.00 0.00 2.50
3790 4800 7.122501 TGACCCTTATACACGATTACAGTTACA 59.877 37.037 0.00 0.00 0.00 2.41
3791 4801 7.486647 ACCCTTATACACGATTACAGTTACAG 58.513 38.462 0.00 0.00 0.00 2.74
3792 4802 7.123247 ACCCTTATACACGATTACAGTTACAGT 59.877 37.037 0.00 0.00 0.00 3.55
3793 4803 7.977853 CCCTTATACACGATTACAGTTACAGTT 59.022 37.037 0.00 0.00 0.00 3.16
3794 4804 9.362539 CCTTATACACGATTACAGTTACAGTTT 57.637 33.333 0.00 0.00 0.00 2.66
3796 4806 9.911138 TTATACACGATTACAGTTACAGTTTGA 57.089 29.630 0.00 0.00 0.00 2.69
3797 4807 6.764877 ACACGATTACAGTTACAGTTTGAG 57.235 37.500 0.00 0.00 0.00 3.02
3798 4808 5.694910 ACACGATTACAGTTACAGTTTGAGG 59.305 40.000 0.00 0.00 0.00 3.86
3799 4809 5.924254 CACGATTACAGTTACAGTTTGAGGA 59.076 40.000 0.00 0.00 0.00 3.71
3800 4810 6.422701 CACGATTACAGTTACAGTTTGAGGAA 59.577 38.462 0.00 0.00 0.00 3.36
3801 4811 6.987992 ACGATTACAGTTACAGTTTGAGGAAA 59.012 34.615 0.00 0.00 0.00 3.13
3802 4812 7.496591 ACGATTACAGTTACAGTTTGAGGAAAA 59.503 33.333 0.00 0.00 0.00 2.29
3809 4819 3.930400 GTTTGAGGAAAACGCGGTT 57.070 47.368 12.47 7.61 38.92 4.44
3810 4820 2.197792 GTTTGAGGAAAACGCGGTTT 57.802 45.000 24.31 24.31 38.92 3.27
3811 4821 1.849829 GTTTGAGGAAAACGCGGTTTG 59.150 47.619 29.34 0.00 38.92 2.93
3812 4822 0.248702 TTGAGGAAAACGCGGTTTGC 60.249 50.000 30.65 30.65 35.80 3.68
3813 4823 1.098712 TGAGGAAAACGCGGTTTGCT 61.099 50.000 38.48 38.48 41.31 3.91
3814 4824 0.660300 GAGGAAAACGCGGTTTGCTG 60.660 55.000 41.91 0.00 39.04 4.41
3815 4825 1.660264 GGAAAACGCGGTTTGCTGG 60.660 57.895 30.51 0.00 43.27 4.85
3816 4826 2.279186 AAAACGCGGTTTGCTGGC 60.279 55.556 23.39 0.00 43.27 4.85
3817 4827 2.677573 GAAAACGCGGTTTGCTGGCT 62.678 55.000 29.34 0.00 43.27 4.75
3818 4828 2.291457 AAAACGCGGTTTGCTGGCTT 62.291 50.000 23.39 0.00 43.27 4.35
3819 4829 2.952291 AAACGCGGTTTGCTGGCTTG 62.952 55.000 12.47 0.00 43.27 4.01
3820 4830 3.964875 CGCGGTTTGCTGGCTTGT 61.965 61.111 0.00 0.00 43.27 3.16
3821 4831 2.355009 GCGGTTTGCTGGCTTGTG 60.355 61.111 0.00 0.00 41.73 3.33
3822 4832 2.355009 CGGTTTGCTGGCTTGTGC 60.355 61.111 0.00 0.00 38.76 4.57
3823 4833 2.355009 GGTTTGCTGGCTTGTGCG 60.355 61.111 0.00 0.00 40.82 5.34
3824 4834 2.355009 GTTTGCTGGCTTGTGCGG 60.355 61.111 0.00 0.00 40.82 5.69
3825 4835 3.604667 TTTGCTGGCTTGTGCGGG 61.605 61.111 0.00 0.00 40.82 6.13
3860 4870 3.460144 GCACGTAGCGGAACAGAC 58.540 61.111 0.00 0.00 0.00 3.51
3861 4871 1.080705 GCACGTAGCGGAACAGACT 60.081 57.895 0.00 0.00 0.00 3.24
3862 4872 0.169672 GCACGTAGCGGAACAGACTA 59.830 55.000 0.00 0.00 0.00 2.59
4061 5884 6.148948 TGTCTCTGGTAATTTTGCGAAAATG 58.851 36.000 2.54 0.00 40.05 2.32
4165 5988 4.828925 GCACTCTGCTCGGCTCCC 62.829 72.222 0.00 0.00 40.96 4.30
4166 5989 4.154347 CACTCTGCTCGGCTCCCC 62.154 72.222 0.00 0.00 0.00 4.81
4167 5990 4.704103 ACTCTGCTCGGCTCCCCA 62.704 66.667 0.00 0.00 0.00 4.96
4168 5991 3.393970 CTCTGCTCGGCTCCCCAA 61.394 66.667 0.00 0.00 0.00 4.12
4169 5992 3.382803 CTCTGCTCGGCTCCCCAAG 62.383 68.421 0.00 0.00 0.00 3.61
4170 5993 3.393970 CTGCTCGGCTCCCCAAGA 61.394 66.667 0.00 0.00 0.00 3.02
4171 5994 2.927856 TGCTCGGCTCCCCAAGAA 60.928 61.111 0.00 0.00 0.00 2.52
4172 5995 2.124942 GCTCGGCTCCCCAAGAAG 60.125 66.667 0.00 0.00 0.00 2.85
4173 5996 2.124942 CTCGGCTCCCCAAGAAGC 60.125 66.667 0.00 0.00 0.00 3.86
4174 5997 2.607750 TCGGCTCCCCAAGAAGCT 60.608 61.111 0.00 0.00 0.00 3.74
4175 5998 2.190488 CTCGGCTCCCCAAGAAGCTT 62.190 60.000 0.00 0.00 0.00 3.74
4176 5999 1.746991 CGGCTCCCCAAGAAGCTTC 60.747 63.158 19.11 19.11 0.00 3.86
4177 6000 1.688211 GGCTCCCCAAGAAGCTTCT 59.312 57.895 23.49 23.49 39.74 2.85
4178 6001 0.679321 GGCTCCCCAAGAAGCTTCTG 60.679 60.000 29.09 20.90 37.65 3.02
4179 6002 1.311651 GCTCCCCAAGAAGCTTCTGC 61.312 60.000 29.09 21.67 37.65 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 8.626526 GTTTCTTCTTAAGTGGTTGTTTGGATA 58.373 33.333 1.63 0.00 0.00 2.59
137 138 2.426842 AGCTCCAAAGGCCTATTCAC 57.573 50.000 5.16 0.00 0.00 3.18
186 187 7.867909 GTCTCAAAATCCCTCGAAAAAGAAAAT 59.132 33.333 0.00 0.00 0.00 1.82
197 198 8.438676 AAAATACTATGTCTCAAAATCCCTCG 57.561 34.615 0.00 0.00 0.00 4.63
299 467 6.500751 AGGAGGGAGTATGTCTTAAAACTTGA 59.499 38.462 0.00 0.00 0.00 3.02
308 476 2.766828 CGGAAAGGAGGGAGTATGTCTT 59.233 50.000 0.00 0.00 0.00 3.01
363 531 8.592809 ACAACCAAATTGAGCCTTATAAAATGA 58.407 29.630 0.00 0.00 41.23 2.57
564 746 5.193728 AGGTAAATGGTGAGTGGTGGAATAT 59.806 40.000 0.00 0.00 0.00 1.28
583 765 5.894393 TCAAAAATCTCACCAACCAAGGTAA 59.106 36.000 0.00 0.00 40.77 2.85
661 843 2.665165 AGCATGTTTGTGAGTCCCAAA 58.335 42.857 0.00 0.00 0.00 3.28
671 853 2.231964 CCTGCCACATAAGCATGTTTGT 59.768 45.455 4.89 0.00 42.98 2.83
865 1087 2.504175 GGTTTAGGCTGGTCATAGTGGA 59.496 50.000 0.00 0.00 0.00 4.02
908 1131 9.690434 CGAGCTAGTCAAGTTTATTTATCAAAC 57.310 33.333 0.00 0.00 36.37 2.93
962 1185 2.510906 CCCAAGGGCCCATCTACG 59.489 66.667 27.56 4.76 0.00 3.51
1035 1258 1.743252 GAAGAGGTGAAGGGCGCAG 60.743 63.158 10.83 0.00 0.00 5.18
1248 1471 2.039418 CGGGAGAGAGAGAGAGAGAGA 58.961 57.143 0.00 0.00 0.00 3.10
1249 1472 1.762957 ACGGGAGAGAGAGAGAGAGAG 59.237 57.143 0.00 0.00 0.00 3.20
1250 1473 1.760613 GACGGGAGAGAGAGAGAGAGA 59.239 57.143 0.00 0.00 0.00 3.10
1251 1474 1.762957 AGACGGGAGAGAGAGAGAGAG 59.237 57.143 0.00 0.00 0.00 3.20
1624 1848 8.419435 CGACACAACAATTCACATTAAGAAATG 58.581 33.333 0.00 0.00 46.66 2.32
1625 1849 7.594758 CCGACACAACAATTCACATTAAGAAAT 59.405 33.333 0.00 0.00 0.00 2.17
2763 2990 4.172505 CTCTCCAGTCTTCAAGTTCGATG 58.827 47.826 0.00 0.00 0.00 3.84
3294 3521 3.436704 ACGAAACAGTACCATTGCATCAG 59.563 43.478 0.00 0.00 0.00 2.90
3753 4763 6.128090 CGTGTATAAGGGTCAGCGATATAAGA 60.128 42.308 0.00 0.00 0.00 2.10
3757 4767 4.077108 TCGTGTATAAGGGTCAGCGATAT 58.923 43.478 0.00 0.00 0.00 1.63
3776 4786 6.092955 TCCTCAAACTGTAACTGTAATCGT 57.907 37.500 0.00 0.00 0.00 3.73
3785 4795 3.285745 CGCGTTTTCCTCAAACTGTAAC 58.714 45.455 0.00 0.00 42.51 2.50
3786 4796 2.288458 CCGCGTTTTCCTCAAACTGTAA 59.712 45.455 4.92 0.00 42.51 2.41
3787 4797 1.868498 CCGCGTTTTCCTCAAACTGTA 59.132 47.619 4.92 0.00 42.51 2.74
3788 4798 0.661020 CCGCGTTTTCCTCAAACTGT 59.339 50.000 4.92 0.00 42.51 3.55
3789 4799 0.661020 ACCGCGTTTTCCTCAAACTG 59.339 50.000 4.92 0.00 42.51 3.16
3790 4800 1.385528 AACCGCGTTTTCCTCAAACT 58.614 45.000 4.92 0.00 42.51 2.66
3791 4801 1.849829 CAAACCGCGTTTTCCTCAAAC 59.150 47.619 4.92 0.00 41.42 2.93
3792 4802 1.799548 GCAAACCGCGTTTTCCTCAAA 60.800 47.619 4.92 0.00 33.10 2.69
3793 4803 0.248702 GCAAACCGCGTTTTCCTCAA 60.249 50.000 4.92 0.00 33.10 3.02
3794 4804 1.357334 GCAAACCGCGTTTTCCTCA 59.643 52.632 4.92 0.00 33.10 3.86
3795 4805 4.221873 GCAAACCGCGTTTTCCTC 57.778 55.556 4.92 0.00 33.10 3.71
3804 4814 2.355009 CACAAGCCAGCAAACCGC 60.355 61.111 0.00 0.00 42.91 5.68
3805 4815 2.355009 GCACAAGCCAGCAAACCG 60.355 61.111 0.00 0.00 33.58 4.44
3806 4816 2.355009 CGCACAAGCCAGCAAACC 60.355 61.111 0.00 0.00 37.52 3.27
3807 4817 2.355009 CCGCACAAGCCAGCAAAC 60.355 61.111 0.00 0.00 37.52 2.93
3808 4818 3.604667 CCCGCACAAGCCAGCAAA 61.605 61.111 0.00 0.00 37.52 3.68
3826 4836 3.114616 CAGTCTGTTCGGCCGCAG 61.115 66.667 23.51 22.86 0.00 5.18
3830 4840 2.758770 TACGTGCAGTCTGTTCGGCC 62.759 60.000 17.83 0.00 0.00 6.13
3845 4855 1.202268 GCATAGTCTGTTCCGCTACGT 60.202 52.381 0.00 0.00 0.00 3.57
3860 4870 1.988834 GCCGAACAAACCCCGCATAG 61.989 60.000 0.00 0.00 0.00 2.23
3861 4871 2.041686 GCCGAACAAACCCCGCATA 61.042 57.895 0.00 0.00 0.00 3.14
3862 4872 3.370231 GCCGAACAAACCCCGCAT 61.370 61.111 0.00 0.00 0.00 4.73
3907 4917 7.750458 ACTGTGTAAATTATGCGTCAAATTCAG 59.250 33.333 0.00 0.00 0.00 3.02
4061 5884 0.179081 GTCGGGAATACAGTGAGGGC 60.179 60.000 0.00 0.00 0.00 5.19
4150 5973 4.704103 TGGGGAGCCGAGCAGAGT 62.704 66.667 0.00 0.00 0.00 3.24
4160 5983 1.311651 GCAGAAGCTTCTTGGGGAGC 61.312 60.000 26.44 20.40 34.74 4.70
4161 5984 2.865492 GCAGAAGCTTCTTGGGGAG 58.135 57.895 26.44 14.78 34.74 4.30


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

AutoCloner maintained by Alex Coulton.