Multiple sequence alignment - TraesCS4D01G144400

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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 TraesCS4D01G144400 chr4D 100.000 5589 0 0 1 5589 132773669 132779257 0.000000e+00 10322.0
1 TraesCS4D01G144400 chr4D 100.000 28 0 0 794 821 488192517 488192544 1.000000e-02 52.8
2 TraesCS4D01G144400 chr4B 95.155 4314 121 25 1307 5589 163838587 163834331 0.000000e+00 6728.0
3 TraesCS4D01G144400 chr4B 96.970 165 5 0 1149 1313 163839947 163839783 1.530000e-70 278.0
4 TraesCS4D01G144400 chr4B 84.076 157 24 1 5432 5587 377379342 377379186 3.490000e-32 150.0
5 TraesCS4D01G144400 chr4A 94.971 3977 110 19 1636 5588 429432851 429428941 0.000000e+00 6154.0
6 TraesCS4D01G144400 chr4A 95.866 774 21 6 871 1639 429436025 429435258 0.000000e+00 1242.0
7 TraesCS4D01G144400 chr6B 92.213 732 46 7 1 730 352407758 352407036 0.000000e+00 1026.0
8 TraesCS4D01G144400 chr6B 76.582 158 22 13 5263 5415 142709490 142709637 7.770000e-09 73.1
9 TraesCS4D01G144400 chr2D 98.145 539 7 3 219 755 613124531 613123994 0.000000e+00 937.0
10 TraesCS4D01G144400 chr2D 97.426 544 13 1 204 746 613449629 613450172 0.000000e+00 926.0
11 TraesCS4D01G144400 chr2D 98.495 465 5 2 287 750 486345079 486345542 0.000000e+00 819.0
12 TraesCS4D01G144400 chr2D 95.608 296 8 1 1 291 486338387 486338682 2.360000e-128 470.0
13 TraesCS4D01G144400 chr2D 78.058 556 78 34 190 737 315988008 315988527 1.510000e-80 311.0
14 TraesCS4D01G144400 chr2D 96.196 184 7 0 1 184 613449145 613449328 9.100000e-78 302.0
15 TraesCS4D01G144400 chr2D 95.187 187 7 2 1 185 613124873 613124687 1.520000e-75 294.0
16 TraesCS4D01G144400 chr2D 100.000 30 0 0 794 823 556228665 556228636 7.820000e-04 56.5
17 TraesCS4D01G144400 chr2D 100.000 30 0 0 794 823 556228805 556228776 7.820000e-04 56.5
18 TraesCS4D01G144400 chr5A 92.439 410 28 3 338 746 66000462 66000869 2.900000e-162 582.0
19 TraesCS4D01G144400 chr5A 91.852 405 30 3 340 743 66048535 66048937 3.780000e-156 562.0
20 TraesCS4D01G144400 chr5A 88.259 247 15 7 68 313 66048319 66048552 3.300000e-72 283.0
21 TraesCS4D01G144400 chr5A 87.045 247 19 6 68 313 66000247 66000481 3.320000e-67 267.0
22 TraesCS4D01G144400 chr5A 97.959 49 1 0 1 49 66048274 66048322 9.980000e-13 86.1
23 TraesCS4D01G144400 chr5A 95.918 49 2 0 1 49 66000202 66000250 4.640000e-11 80.5
24 TraesCS4D01G144400 chr3D 85.714 182 25 1 5039 5220 598360330 598360510 2.060000e-44 191.0
25 TraesCS4D01G144400 chr3D 74.679 312 57 16 5270 5562 586418236 586418544 9.840000e-23 119.0
26 TraesCS4D01G144400 chr3D 89.744 78 6 2 5263 5338 85392180 85392257 1.280000e-16 99.0
27 TraesCS4D01G144400 chr1D 77.160 324 59 14 5270 5587 390431756 390431442 2.070000e-39 174.0
28 TraesCS4D01G144400 chrUn 78.092 283 49 11 5285 5558 2703906 2704184 3.460000e-37 167.0
29 TraesCS4D01G144400 chr3A 79.781 183 27 8 5262 5440 545276561 545276737 2.110000e-24 124.0
30 TraesCS4D01G144400 chr3A 100.000 29 0 0 794 822 509418843 509418871 3.000000e-03 54.7
31 TraesCS4D01G144400 chr6A 86.170 94 13 0 1 94 1971363 1971270 9.910000e-18 102.0
32 TraesCS4D01G144400 chr6A 76.970 165 31 6 5263 5424 450092572 450092412 2.770000e-13 87.9
33 TraesCS4D01G144400 chr7B 88.095 84 8 2 5270 5352 242991024 242990942 1.280000e-16 99.0
34 TraesCS4D01G144400 chr7B 76.129 155 27 9 5263 5415 714500971 714501117 7.770000e-09 73.1
35 TraesCS4D01G144400 chr7A 87.356 87 8 3 22 108 138980190 138980273 4.610000e-16 97.1
36 TraesCS4D01G144400 chr7A 100.000 28 0 0 794 821 44354279 44354306 1.000000e-02 52.8
37 TraesCS4D01G144400 chr1A 80.488 123 16 8 5270 5389 372282507 372282390 2.770000e-13 87.9
38 TraesCS4D01G144400 chr7D 76.923 156 29 6 5263 5415 150763435 150763586 1.290000e-11 82.4
39 TraesCS4D01G144400 chr5B 100.000 28 0 0 794 821 509927917 509927890 1.000000e-02 52.8
40 TraesCS4D01G144400 chr5B 100.000 28 0 0 794 821 509928438 509928411 1.000000e-02 52.8


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 TraesCS4D01G144400 chr4D 132773669 132779257 5588 False 10322.000000 10322 100.000000 1 5589 1 chr4D.!!$F1 5588
1 TraesCS4D01G144400 chr4B 163834331 163839947 5616 True 3503.000000 6728 96.062500 1149 5589 2 chr4B.!!$R2 4440
2 TraesCS4D01G144400 chr4A 429428941 429436025 7084 True 3698.000000 6154 95.418500 871 5588 2 chr4A.!!$R1 4717
3 TraesCS4D01G144400 chr6B 352407036 352407758 722 True 1026.000000 1026 92.213000 1 730 1 chr6B.!!$R1 729
4 TraesCS4D01G144400 chr2D 613123994 613124873 879 True 615.500000 937 96.666000 1 755 2 chr2D.!!$R2 754
5 TraesCS4D01G144400 chr2D 613449145 613450172 1027 False 614.000000 926 96.811000 1 746 2 chr2D.!!$F4 745
6 TraesCS4D01G144400 chr2D 315988008 315988527 519 False 311.000000 311 78.058000 190 737 1 chr2D.!!$F1 547
7 TraesCS4D01G144400 chr5A 66048274 66048937 663 False 310.366667 562 92.690000 1 743 3 chr5A.!!$F2 742
8 TraesCS4D01G144400 chr5A 66000202 66000869 667 False 309.833333 582 91.800667 1 746 3 chr5A.!!$F1 745

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
836 1122 0.039617 CGCGACCAATTTCTGCCAAA 60.040 50.000 0.00 0.0 0.00 3.28 F
1658 5561 0.613012 AATGAGCAAAGGTCCTGGCC 60.613 55.000 11.25 0.0 0.00 5.36 F
2445 6348 1.491754 TGAGCCTGCACACATATGGAT 59.508 47.619 7.80 0.0 0.00 3.41 F
3684 7587 1.873591 CACACTACAGCTTGGAACACC 59.126 52.381 0.00 0.0 39.29 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 6405 3.008375 TGCCTATAAGATTAGCAGCAGGG 59.992 47.826 0.00 0.0 0.00 4.45 R
3654 7557 1.071699 GCTGTAGTGTGGGAACAGGAA 59.928 52.381 4.09 0.0 44.46 3.36 R
3908 7811 2.303022 CTCCCTCAAGAACTTGGCAGTA 59.697 50.000 13.46 0.0 40.78 2.74 R
4733 8637 0.683179 GTGCAACATAACCCCCTCCC 60.683 60.000 0.00 0.0 36.32 4.30 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
134 135 1.202348 CGTTGTTCCATTGCAACACCA 60.202 47.619 0.00 0.00 43.52 4.17
166 167 1.985473 ACAAGCTCCAAGCAACATCA 58.015 45.000 1.29 0.00 45.56 3.07
178 179 0.238289 CAACATCACCGGAGTTGCAC 59.762 55.000 9.46 0.00 36.59 4.57
560 844 2.944094 GCGATAGAGAGAGGAGGGATCC 60.944 59.091 1.92 1.92 39.76 3.36
618 904 2.742053 GAGCGAGAAAAATGTGTGGCTA 59.258 45.455 0.00 0.00 0.00 3.93
755 1041 7.441890 AAACAATGGTTTTCCGTTTTTCTTT 57.558 28.000 0.00 0.00 45.98 2.52
756 1042 6.656314 ACAATGGTTTTCCGTTTTTCTTTC 57.344 33.333 0.00 0.00 45.98 2.62
757 1043 6.166982 ACAATGGTTTTCCGTTTTTCTTTCA 58.833 32.000 0.00 0.00 45.98 2.69
758 1044 6.091577 ACAATGGTTTTCCGTTTTTCTTTCAC 59.908 34.615 0.00 0.00 45.98 3.18
759 1045 5.394224 TGGTTTTCCGTTTTTCTTTCACT 57.606 34.783 0.00 0.00 44.36 3.41
760 1046 5.164954 TGGTTTTCCGTTTTTCTTTCACTG 58.835 37.500 0.00 0.00 44.36 3.66
761 1047 4.032445 GGTTTTCCGTTTTTCTTTCACTGC 59.968 41.667 0.00 0.00 0.00 4.40
762 1048 2.748461 TCCGTTTTTCTTTCACTGCG 57.252 45.000 0.00 0.00 0.00 5.18
763 1049 1.120437 CCGTTTTTCTTTCACTGCGC 58.880 50.000 0.00 0.00 0.00 6.09
764 1050 0.764226 CGTTTTTCTTTCACTGCGCG 59.236 50.000 0.00 0.00 0.00 6.86
765 1051 0.498511 GTTTTTCTTTCACTGCGCGC 59.501 50.000 27.26 27.26 0.00 6.86
766 1052 0.927994 TTTTTCTTTCACTGCGCGCG 60.928 50.000 28.44 28.44 0.00 6.86
767 1053 3.855209 TTTCTTTCACTGCGCGCGC 62.855 57.895 45.02 45.02 42.35 6.86
791 1077 4.476752 GGCCGGCCCGACAATGTA 62.477 66.667 36.64 0.00 0.00 2.29
792 1078 2.895372 GCCGGCCCGACAATGTAG 60.895 66.667 18.11 0.00 0.00 2.74
793 1079 2.582436 CCGGCCCGACAATGTAGT 59.418 61.111 3.71 0.00 0.00 2.73
794 1080 1.520787 CCGGCCCGACAATGTAGTC 60.521 63.158 3.71 0.00 35.19 2.59
819 1105 2.921614 GCGAGAAATAGACGCCGC 59.078 61.111 0.00 0.00 45.35 6.53
820 1106 2.917656 GCGAGAAATAGACGCCGCG 61.918 63.158 12.14 12.14 45.35 6.46
821 1107 1.298116 CGAGAAATAGACGCCGCGA 60.298 57.895 21.79 0.00 0.00 5.87
822 1108 1.529883 CGAGAAATAGACGCCGCGAC 61.530 60.000 21.79 14.16 0.00 5.19
823 1109 1.207377 GAGAAATAGACGCCGCGACC 61.207 60.000 21.79 10.70 0.00 4.79
824 1110 1.517694 GAAATAGACGCCGCGACCA 60.518 57.895 21.79 2.07 0.00 4.02
825 1111 1.079681 AAATAGACGCCGCGACCAA 60.080 52.632 21.79 5.02 0.00 3.67
826 1112 0.461339 AAATAGACGCCGCGACCAAT 60.461 50.000 21.79 7.30 0.00 3.16
827 1113 0.461339 AATAGACGCCGCGACCAATT 60.461 50.000 21.79 12.91 0.00 2.32
828 1114 0.461339 ATAGACGCCGCGACCAATTT 60.461 50.000 21.79 0.00 0.00 1.82
829 1115 1.079875 TAGACGCCGCGACCAATTTC 61.080 55.000 21.79 4.35 0.00 2.17
830 1116 2.358247 ACGCCGCGACCAATTTCT 60.358 55.556 21.79 0.00 0.00 2.52
831 1117 2.098298 CGCCGCGACCAATTTCTG 59.902 61.111 8.23 0.00 0.00 3.02
832 1118 2.202479 GCCGCGACCAATTTCTGC 60.202 61.111 8.23 0.00 0.00 4.26
833 1119 2.485122 CCGCGACCAATTTCTGCC 59.515 61.111 8.23 0.00 0.00 4.85
834 1120 2.331893 CCGCGACCAATTTCTGCCA 61.332 57.895 8.23 0.00 0.00 4.92
835 1121 1.578926 CGCGACCAATTTCTGCCAA 59.421 52.632 0.00 0.00 0.00 4.52
836 1122 0.039617 CGCGACCAATTTCTGCCAAA 60.040 50.000 0.00 0.00 0.00 3.28
837 1123 1.601663 CGCGACCAATTTCTGCCAAAA 60.602 47.619 0.00 0.00 0.00 2.44
838 1124 2.478831 GCGACCAATTTCTGCCAAAAA 58.521 42.857 0.00 0.00 0.00 1.94
839 1125 3.066380 GCGACCAATTTCTGCCAAAAAT 58.934 40.909 0.00 0.00 0.00 1.82
840 1126 3.498018 GCGACCAATTTCTGCCAAAAATT 59.502 39.130 0.00 0.00 36.91 1.82
841 1127 4.688413 GCGACCAATTTCTGCCAAAAATTA 59.312 37.500 0.00 0.00 35.20 1.40
842 1128 5.351189 GCGACCAATTTCTGCCAAAAATTAT 59.649 36.000 0.00 0.00 35.20 1.28
843 1129 6.128309 GCGACCAATTTCTGCCAAAAATTATT 60.128 34.615 0.00 0.00 35.20 1.40
844 1130 7.455447 CGACCAATTTCTGCCAAAAATTATTC 58.545 34.615 0.00 0.00 35.20 1.75
845 1131 7.331687 CGACCAATTTCTGCCAAAAATTATTCT 59.668 33.333 0.00 0.00 35.20 2.40
846 1132 8.552083 ACCAATTTCTGCCAAAAATTATTCTC 57.448 30.769 0.00 0.00 35.20 2.87
847 1133 8.156165 ACCAATTTCTGCCAAAAATTATTCTCA 58.844 29.630 0.00 0.00 35.20 3.27
848 1134 9.001542 CCAATTTCTGCCAAAAATTATTCTCAA 57.998 29.630 0.00 0.00 35.20 3.02
883 1169 4.923281 CCAAAAATTAAGCCAAAGGAGACG 59.077 41.667 0.00 0.00 0.00 4.18
925 1211 2.815647 CAGCTCTTTCCCGCGTCC 60.816 66.667 4.92 0.00 0.00 4.79
926 1212 4.083862 AGCTCTTTCCCGCGTCCC 62.084 66.667 4.92 0.00 0.00 4.46
1400 2889 6.857848 TGATAGAGAGAGGACCAGTTATCAT 58.142 40.000 0.00 0.00 0.00 2.45
1441 2930 2.812011 ACCTGTTCTATTGGTTTCGCAC 59.188 45.455 0.00 0.00 0.00 5.34
1581 3073 7.397892 TGTTCTGTTTTGACCATTTTAGTGA 57.602 32.000 0.00 0.00 0.00 3.41
1656 5559 2.503895 AGAATGAGCAAAGGTCCTGG 57.496 50.000 0.00 0.00 0.00 4.45
1658 5561 0.613012 AATGAGCAAAGGTCCTGGCC 60.613 55.000 11.25 0.00 0.00 5.36
1677 5580 3.242870 GGCCTGCATTCGACAGAATAAAG 60.243 47.826 0.00 0.00 44.68 1.85
1830 5733 6.663093 TGATGCTTTTGGATAAACTGTACCAT 59.337 34.615 0.00 0.00 32.31 3.55
1884 5787 4.223556 TCAGTGTAGTTTTGGGTTCACA 57.776 40.909 0.00 0.00 0.00 3.58
2032 5935 5.190528 ACAACTTACTGATGACTGGGATGAT 59.809 40.000 0.00 0.00 0.00 2.45
2356 6259 5.339530 CCTGATTTCTCCCATTACTGGTCTT 60.340 44.000 0.00 0.00 41.37 3.01
2445 6348 1.491754 TGAGCCTGCACACATATGGAT 59.508 47.619 7.80 0.00 0.00 3.41
2502 6405 5.506686 AGAGAGAGTTTTGCTTTTCCAAC 57.493 39.130 0.00 0.00 0.00 3.77
2528 6431 5.624159 TGCTGCTAATCTTATAGGCATTGT 58.376 37.500 0.00 0.00 32.39 2.71
2562 6465 9.026074 GTTTCGAAATTATGTTTTGAAGGTGAA 57.974 29.630 14.69 0.00 34.40 3.18
2633 6536 2.028748 GGACAGCCAAATGCATGTCTTT 60.029 45.455 13.85 0.00 42.62 2.52
2634 6537 3.555586 GGACAGCCAAATGCATGTCTTTT 60.556 43.478 13.85 0.00 42.62 2.27
2821 6724 4.217550 GGCAAAAGCTTGTGTTATCAGGTA 59.782 41.667 17.92 0.00 34.79 3.08
2823 6726 5.629435 GCAAAAGCTTGTGTTATCAGGTAAC 59.371 40.000 17.92 0.00 37.15 2.50
2850 6753 4.019792 TCTGCCTTGTTCAGCATTCTTA 57.980 40.909 0.00 0.00 38.56 2.10
3086 6989 7.103641 TCCAAGAGCTTAGGTAAACACTATTG 58.896 38.462 0.00 0.00 0.00 1.90
3188 7091 8.779354 TGCCATTTGTTTTGTAACTTAAGTTT 57.221 26.923 25.07 10.27 39.31 2.66
3260 7163 3.512724 CACCTGAAAGAATGGCTGGAAAT 59.487 43.478 0.00 0.00 34.07 2.17
3475 7378 7.391554 TCAAACCTTTGTCATATTCTTCCAGAG 59.608 37.037 0.00 0.00 39.18 3.35
3654 7557 3.446516 CGTAAGGTACTAAAGCACTCCCT 59.553 47.826 0.00 0.00 38.49 4.20
3684 7587 1.873591 CACACTACAGCTTGGAACACC 59.126 52.381 0.00 0.00 39.29 4.16
3908 7811 2.868583 CTCGAAGAATGAATGTGCGGAT 59.131 45.455 0.00 0.00 34.09 4.18
4308 8211 2.435410 TGCATGCTGAGGAGTGCG 60.435 61.111 20.33 0.00 40.34 5.34
4311 8214 1.812922 CATGCTGAGGAGTGCGGAC 60.813 63.158 0.00 0.00 0.00 4.79
4367 8270 2.224354 ACCAAGCAAAGAAAATGCAGGG 60.224 45.455 12.46 9.76 46.22 4.45
4392 8295 6.037830 GGTATTGCGAGCTGAAGGTAAATAAA 59.962 38.462 0.00 0.00 0.00 1.40
4466 8369 7.276878 CAGCAATCAATTTATGAACAATGCTCA 59.723 33.333 0.00 0.00 41.61 4.26
4545 8449 5.944007 AGTTCAACAGTCAAAGGTGTAAAGT 59.056 36.000 0.00 0.00 0.00 2.66
4733 8637 0.668535 TACGATGGATGCAGAGGACG 59.331 55.000 0.00 0.00 0.00 4.79
4768 8687 7.678947 ATGTTGCACATATTATAGCTCTTCC 57.321 36.000 0.00 0.00 36.99 3.46
4834 8760 6.198591 CGGTTCCTCGAAGTCTTGTTATAATC 59.801 42.308 0.00 0.00 0.00 1.75
4958 8885 5.186992 GGGTATTTTCTTAAGCCCACACAAT 59.813 40.000 8.31 0.00 36.25 2.71
5000 8927 3.773860 ACATGCAAACAAACGACTGAA 57.226 38.095 0.00 0.00 0.00 3.02
5001 8928 3.694734 ACATGCAAACAAACGACTGAAG 58.305 40.909 0.00 0.00 0.00 3.02
5020 8947 8.193953 ACTGAAGTTTTTGGATGGTCAATATT 57.806 30.769 0.00 0.00 0.00 1.28
5032 8959 3.692101 TGGTCAATATTTGGCGATCGTTT 59.308 39.130 17.81 0.07 35.72 3.60
5052 8979 4.140599 CGCAGCGGGAGAGAGCTT 62.141 66.667 7.00 0.00 42.52 3.74
5073 9000 4.193334 TGCCACCGCTCGATCTCG 62.193 66.667 0.00 0.00 41.45 4.04
5080 9007 0.179134 CCGCTCGATCTCGTTCCTTT 60.179 55.000 0.00 0.00 40.80 3.11
5081 9008 1.630148 CGCTCGATCTCGTTCCTTTT 58.370 50.000 0.00 0.00 40.80 2.27
5117 9044 1.663173 GGAGAGCAGATCCGTAGCC 59.337 63.158 0.00 0.00 0.00 3.93
5118 9045 1.663173 GAGAGCAGATCCGTAGCCC 59.337 63.158 0.00 0.00 0.00 5.19
5119 9046 0.825840 GAGAGCAGATCCGTAGCCCT 60.826 60.000 0.00 0.00 0.00 5.19
5120 9047 0.825840 AGAGCAGATCCGTAGCCCTC 60.826 60.000 0.00 0.00 0.00 4.30
5121 9048 0.825840 GAGCAGATCCGTAGCCCTCT 60.826 60.000 0.00 0.00 0.00 3.69
5122 9049 0.825840 AGCAGATCCGTAGCCCTCTC 60.826 60.000 0.00 0.00 0.00 3.20
5123 9050 1.109920 GCAGATCCGTAGCCCTCTCA 61.110 60.000 0.00 0.00 0.00 3.27
5124 9051 0.671251 CAGATCCGTAGCCCTCTCAC 59.329 60.000 0.00 0.00 0.00 3.51
5125 9052 0.468400 AGATCCGTAGCCCTCTCACC 60.468 60.000 0.00 0.00 0.00 4.02
5137 9064 1.217689 CCTCTCACCATCCTCTCTCCT 59.782 57.143 0.00 0.00 0.00 3.69
5249 9180 2.597510 GCCAGGGGACGTTGCTTT 60.598 61.111 0.00 0.00 0.00 3.51
5250 9181 2.919494 GCCAGGGGACGTTGCTTTG 61.919 63.158 0.00 0.00 0.00 2.77
5251 9182 1.528309 CCAGGGGACGTTGCTTTGT 60.528 57.895 0.00 0.00 0.00 2.83
5252 9183 1.515521 CCAGGGGACGTTGCTTTGTC 61.516 60.000 0.00 0.00 0.00 3.18
5253 9184 0.817634 CAGGGGACGTTGCTTTGTCA 60.818 55.000 0.00 0.00 36.83 3.58
5254 9185 0.818040 AGGGGACGTTGCTTTGTCAC 60.818 55.000 0.00 1.69 37.80 3.67
5255 9186 1.652563 GGGACGTTGCTTTGTCACC 59.347 57.895 0.00 0.00 36.83 4.02
5256 9187 1.278637 GGACGTTGCTTTGTCACCG 59.721 57.895 0.00 0.00 36.83 4.94
5257 9188 1.368850 GACGTTGCTTTGTCACCGC 60.369 57.895 0.00 0.00 35.20 5.68
5258 9189 1.772063 GACGTTGCTTTGTCACCGCT 61.772 55.000 0.00 0.00 35.20 5.52
5259 9190 0.531090 ACGTTGCTTTGTCACCGCTA 60.531 50.000 0.00 0.00 0.00 4.26
5260 9191 0.163788 CGTTGCTTTGTCACCGCTAG 59.836 55.000 0.00 0.00 0.00 3.42
5261 9192 0.517316 GTTGCTTTGTCACCGCTAGG 59.483 55.000 0.00 0.00 45.13 3.02
5262 9193 0.605319 TTGCTTTGTCACCGCTAGGG 60.605 55.000 0.00 0.00 43.47 3.53
5263 9194 1.745489 GCTTTGTCACCGCTAGGGG 60.745 63.158 23.57 23.57 44.22 4.79
5338 9269 2.347490 GCGACATGGGAGTGGTGT 59.653 61.111 0.00 0.00 0.00 4.16
5513 9450 1.690219 GGATCTGATCTGGCCGGTGT 61.690 60.000 12.43 1.09 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.177594 CTGGAGCTCTGCCGGAGTTT 62.178 60.000 14.64 0.00 43.62 2.66
52 53 0.107703 CCGGAGTTGCAATGGAGCTA 60.108 55.000 0.59 0.00 34.99 3.32
134 135 2.193536 GCTTGTTGGGAGCACCGTT 61.194 57.895 0.00 0.00 44.64 4.44
185 187 0.725117 CAAACTCCGGCGATGTTACC 59.275 55.000 9.30 0.00 0.00 2.85
560 844 1.443407 CAGTGCATCCCCTCCTACG 59.557 63.158 0.00 0.00 0.00 3.51
618 904 4.431131 CCACGCAGGGGAAGCCAT 62.431 66.667 0.00 0.00 0.00 4.40
746 1032 0.498511 GCGCGCAGTGAAAGAAAAAC 59.501 50.000 29.10 0.00 43.07 2.43
747 1033 0.927994 CGCGCGCAGTGAAAGAAAAA 60.928 50.000 32.61 0.00 43.07 1.94
748 1034 1.368731 CGCGCGCAGTGAAAGAAAA 60.369 52.632 32.61 0.00 43.07 2.29
749 1035 2.248140 CGCGCGCAGTGAAAGAAA 59.752 55.556 32.61 0.00 43.07 2.52
750 1036 4.368808 GCGCGCGCAGTGAAAGAA 62.369 61.111 46.11 0.00 43.07 2.52
774 1060 4.476752 TACATTGTCGGGCCGGCC 62.477 66.667 38.57 38.57 0.00 6.13
775 1061 2.895372 CTACATTGTCGGGCCGGC 60.895 66.667 26.28 26.28 0.00 6.13
776 1062 1.520787 GACTACATTGTCGGGCCGG 60.521 63.158 27.98 12.18 0.00 6.13
777 1063 4.104143 GACTACATTGTCGGGCCG 57.896 61.111 22.51 22.51 0.00 6.13
803 1089 1.298116 TCGCGGCGTCTATTTCTCG 60.298 57.895 22.90 0.00 0.00 4.04
804 1090 1.207377 GGTCGCGGCGTCTATTTCTC 61.207 60.000 22.90 0.00 0.00 2.87
805 1091 1.226888 GGTCGCGGCGTCTATTTCT 60.227 57.895 22.90 0.00 0.00 2.52
806 1092 1.079875 TTGGTCGCGGCGTCTATTTC 61.080 55.000 22.90 4.17 0.00 2.17
807 1093 0.461339 ATTGGTCGCGGCGTCTATTT 60.461 50.000 22.90 2.90 0.00 1.40
808 1094 0.461339 AATTGGTCGCGGCGTCTATT 60.461 50.000 22.90 18.68 0.00 1.73
809 1095 0.461339 AAATTGGTCGCGGCGTCTAT 60.461 50.000 22.90 14.36 0.00 1.98
810 1096 1.079681 AAATTGGTCGCGGCGTCTA 60.080 52.632 22.90 12.22 0.00 2.59
811 1097 2.358247 AAATTGGTCGCGGCGTCT 60.358 55.556 22.90 0.00 0.00 4.18
812 1098 2.097728 GAAATTGGTCGCGGCGTC 59.902 61.111 22.90 16.88 0.00 5.19
813 1099 2.358247 AGAAATTGGTCGCGGCGT 60.358 55.556 22.90 0.00 0.00 5.68
814 1100 2.098298 CAGAAATTGGTCGCGGCG 59.902 61.111 17.70 17.70 0.00 6.46
815 1101 2.202479 GCAGAAATTGGTCGCGGC 60.202 61.111 6.13 3.04 0.00 6.53
816 1102 1.861542 TTGGCAGAAATTGGTCGCGG 61.862 55.000 6.13 0.00 0.00 6.46
817 1103 0.039617 TTTGGCAGAAATTGGTCGCG 60.040 50.000 0.00 0.00 0.00 5.87
818 1104 2.147436 TTTTGGCAGAAATTGGTCGC 57.853 45.000 0.00 0.00 0.00 5.19
819 1105 6.966435 ATAATTTTTGGCAGAAATTGGTCG 57.034 33.333 28.84 0.00 37.31 4.79
820 1106 8.552083 AGAATAATTTTTGGCAGAAATTGGTC 57.448 30.769 28.84 24.49 37.31 4.02
821 1107 8.156165 TGAGAATAATTTTTGGCAGAAATTGGT 58.844 29.630 28.84 19.79 37.31 3.67
822 1108 8.550710 TGAGAATAATTTTTGGCAGAAATTGG 57.449 30.769 28.84 0.00 37.31 3.16
850 1136 7.579761 TGGCTTAATTTTTGGCAGAATTTTT 57.420 28.000 13.69 2.58 0.00 1.94
851 1137 7.579761 TTGGCTTAATTTTTGGCAGAATTTT 57.420 28.000 13.69 4.59 37.55 1.82
852 1138 7.255555 CCTTTGGCTTAATTTTTGGCAGAATTT 60.256 33.333 13.69 8.97 37.55 1.82
853 1139 6.207221 CCTTTGGCTTAATTTTTGGCAGAATT 59.793 34.615 13.20 13.20 37.55 2.17
854 1140 5.706833 CCTTTGGCTTAATTTTTGGCAGAAT 59.293 36.000 0.00 0.00 37.55 2.40
855 1141 5.062528 CCTTTGGCTTAATTTTTGGCAGAA 58.937 37.500 0.00 0.00 37.55 3.02
856 1142 4.346418 TCCTTTGGCTTAATTTTTGGCAGA 59.654 37.500 0.00 0.00 37.55 4.26
857 1143 4.640364 TCCTTTGGCTTAATTTTTGGCAG 58.360 39.130 0.00 0.00 37.55 4.85
858 1144 4.346418 TCTCCTTTGGCTTAATTTTTGGCA 59.654 37.500 0.00 0.00 34.48 4.92
859 1145 4.690748 GTCTCCTTTGGCTTAATTTTTGGC 59.309 41.667 0.00 0.00 0.00 4.52
860 1146 4.923281 CGTCTCCTTTGGCTTAATTTTTGG 59.077 41.667 0.00 0.00 0.00 3.28
861 1147 4.923281 CCGTCTCCTTTGGCTTAATTTTTG 59.077 41.667 0.00 0.00 0.00 2.44
862 1148 4.560716 GCCGTCTCCTTTGGCTTAATTTTT 60.561 41.667 0.00 0.00 45.40 1.94
863 1149 3.056821 GCCGTCTCCTTTGGCTTAATTTT 60.057 43.478 0.00 0.00 45.40 1.82
864 1150 2.492088 GCCGTCTCCTTTGGCTTAATTT 59.508 45.455 0.00 0.00 45.40 1.82
865 1151 2.092323 GCCGTCTCCTTTGGCTTAATT 58.908 47.619 0.00 0.00 45.40 1.40
866 1152 1.751437 GCCGTCTCCTTTGGCTTAAT 58.249 50.000 0.00 0.00 45.40 1.40
867 1153 0.672401 CGCCGTCTCCTTTGGCTTAA 60.672 55.000 0.60 0.00 46.67 1.85
868 1154 1.079405 CGCCGTCTCCTTTGGCTTA 60.079 57.895 0.60 0.00 46.67 3.09
869 1155 2.358737 CGCCGTCTCCTTTGGCTT 60.359 61.111 0.60 0.00 46.67 4.35
999 1285 1.694133 CCCAGTGAGGCTCCTCCATC 61.694 65.000 12.86 4.55 42.09 3.51
1147 1433 1.153449 CCAATCCGCCGTTAGAGCA 60.153 57.895 0.00 0.00 0.00 4.26
1421 2910 2.159707 CGTGCGAAACCAATAGAACAGG 60.160 50.000 0.00 0.00 0.00 4.00
1441 2930 3.878086 AAATGCAGTACTGTCAACACG 57.122 42.857 23.44 0.00 0.00 4.49
1581 3073 1.567357 AAAACACCCAAACACTGGCT 58.433 45.000 0.00 0.00 44.90 4.75
1607 3099 6.073003 GGAGAAGTACACCAATTTCTTGACAG 60.073 42.308 0.00 0.00 34.04 3.51
1610 3102 6.187727 AGGAGAAGTACACCAATTTCTTGA 57.812 37.500 0.00 0.00 34.04 3.02
1656 5559 3.623060 TCTTTATTCTGTCGAATGCAGGC 59.377 43.478 0.00 0.00 40.04 4.85
1658 5561 8.081208 ACATATCTTTATTCTGTCGAATGCAG 57.919 34.615 0.00 0.00 40.04 4.41
1677 5580 3.118038 TGGGCAGGAGTACCAAACATATC 60.118 47.826 0.00 0.00 38.94 1.63
1830 5733 7.339212 AGCAAAGCATAATGTGTTAACTATGGA 59.661 33.333 7.22 0.00 0.00 3.41
1884 5787 7.164122 CCATACATAGTATCAACCAGCAAGAT 58.836 38.462 0.00 0.00 0.00 2.40
1941 5844 4.403432 CCACAGTAATGAAATCTTGGCCAT 59.597 41.667 6.09 0.00 0.00 4.40
2032 5935 5.105023 AGCTTCAGTCTCTATTGCATTCAGA 60.105 40.000 0.00 0.00 0.00 3.27
2356 6259 5.951148 TGCACAATAGAAATGGAGATGGAAA 59.049 36.000 0.00 0.00 0.00 3.13
2502 6405 3.008375 TGCCTATAAGATTAGCAGCAGGG 59.992 47.826 0.00 0.00 0.00 4.45
2562 6465 7.405292 TGATTCATATCTCTTGGTTCCTTTGT 58.595 34.615 0.00 0.00 0.00 2.83
2634 6537 8.725148 GCTCATAACTCAAAATTTCTCTCTTCA 58.275 33.333 0.00 0.00 0.00 3.02
2821 6724 4.584325 TGCTGAACAAGGCAGAATTTAGTT 59.416 37.500 0.00 0.00 35.39 2.24
2823 6726 4.771590 TGCTGAACAAGGCAGAATTTAG 57.228 40.909 0.00 0.00 35.39 1.85
2850 6753 8.641499 TCTCGCAAAACAAACAAGATTAAAAT 57.359 26.923 0.00 0.00 0.00 1.82
3086 6989 5.098218 ACTAGAGATCGAATGAACTACGC 57.902 43.478 0.00 0.00 0.00 4.42
3138 7041 3.263425 TCATTTCTTACACTGGAGGGGAC 59.737 47.826 0.00 0.00 0.00 4.46
3188 7091 2.162208 GCCATTTCTGCAACGAGATGAA 59.838 45.455 7.75 0.00 29.60 2.57
3260 7163 7.638862 CCTTTGAGGATCTCCATGAAGGAATAA 60.639 40.741 14.48 0.00 41.76 1.40
3654 7557 1.071699 GCTGTAGTGTGGGAACAGGAA 59.928 52.381 4.09 0.00 44.46 3.36
3908 7811 2.303022 CTCCCTCAAGAACTTGGCAGTA 59.697 50.000 13.46 0.00 40.78 2.74
4308 8211 4.200092 AGGTTTCACTCTTGAAGTTGTCC 58.800 43.478 0.00 0.00 42.79 4.02
4311 8214 5.818136 TGAAGGTTTCACTCTTGAAGTTG 57.182 39.130 0.00 0.00 42.79 3.16
4367 8270 2.596904 TACCTTCAGCTCGCAATACC 57.403 50.000 0.00 0.00 0.00 2.73
4392 8295 8.594550 TCTACACTTTTAGTTAGCCAGAGATTT 58.405 33.333 0.00 0.00 0.00 2.17
4466 8369 4.310769 CGACACTCAGTCTGGAAAGAAAT 58.689 43.478 0.00 0.00 45.32 2.17
4733 8637 0.683179 GTGCAACATAACCCCCTCCC 60.683 60.000 0.00 0.00 36.32 4.30
4768 8687 3.306166 GGTTACGCGCTTATATATGCAGG 59.694 47.826 17.84 11.85 0.00 4.85
4958 8885 3.492686 TGGAGACCACAGGATTCCA 57.507 52.632 5.29 8.48 36.79 3.53
5000 8927 6.172630 GCCAAATATTGACCATCCAAAAACT 58.827 36.000 0.00 0.00 0.00 2.66
5001 8928 5.063312 CGCCAAATATTGACCATCCAAAAAC 59.937 40.000 0.00 0.00 0.00 2.43
5073 9000 1.248486 GAGGAGGTGGCAAAAGGAAC 58.752 55.000 0.00 0.00 0.00 3.62
5080 9007 1.150536 GTTGTGGAGGAGGTGGCAA 59.849 57.895 0.00 0.00 0.00 4.52
5081 9008 2.836154 GTTGTGGAGGAGGTGGCA 59.164 61.111 0.00 0.00 0.00 4.92
5117 9044 1.217689 AGGAGAGAGGATGGTGAGAGG 59.782 57.143 0.00 0.00 0.00 3.69
5118 9045 2.754012 AGGAGAGAGGATGGTGAGAG 57.246 55.000 0.00 0.00 0.00 3.20
5119 9046 2.358721 GGAAGGAGAGAGGATGGTGAGA 60.359 54.545 0.00 0.00 0.00 3.27
5120 9047 2.038659 GGAAGGAGAGAGGATGGTGAG 58.961 57.143 0.00 0.00 0.00 3.51
5121 9048 1.343478 GGGAAGGAGAGAGGATGGTGA 60.343 57.143 0.00 0.00 0.00 4.02
5122 9049 1.127343 GGGAAGGAGAGAGGATGGTG 58.873 60.000 0.00 0.00 0.00 4.17
5123 9050 0.719015 TGGGAAGGAGAGAGGATGGT 59.281 55.000 0.00 0.00 0.00 3.55
5124 9051 1.127343 GTGGGAAGGAGAGAGGATGG 58.873 60.000 0.00 0.00 0.00 3.51
5125 9052 1.127343 GGTGGGAAGGAGAGAGGATG 58.873 60.000 0.00 0.00 0.00 3.51
5166 9093 4.323477 CCACCCGAGTTGCCCGAA 62.323 66.667 0.00 0.00 0.00 4.30
5248 9179 2.642254 CGTCCCCTAGCGGTGACAA 61.642 63.158 0.00 0.00 33.61 3.18
5249 9180 3.066190 CGTCCCCTAGCGGTGACA 61.066 66.667 0.00 0.00 33.61 3.58
5250 9181 2.643232 AACGTCCCCTAGCGGTGAC 61.643 63.158 0.00 0.00 0.00 3.67
5251 9182 2.283388 AACGTCCCCTAGCGGTGA 60.283 61.111 0.00 0.00 0.00 4.02
5252 9183 2.125673 CAACGTCCCCTAGCGGTG 60.126 66.667 0.00 0.00 39.46 4.94
5253 9184 4.078516 GCAACGTCCCCTAGCGGT 62.079 66.667 0.00 0.00 0.00 5.68
5254 9185 4.832608 GGCAACGTCCCCTAGCGG 62.833 72.222 0.00 0.00 0.00 5.52
5306 9237 1.749638 TCGCGGGAGAGAGGAAGAC 60.750 63.158 6.13 0.00 33.73 3.01
5331 9262 2.450502 AAGGGGCCTCACACCACT 60.451 61.111 4.79 0.00 45.20 4.00
5534 9471 4.148825 ACCGCCACTGATCTCCGC 62.149 66.667 0.00 0.00 0.00 5.54
5566 9504 1.466950 GCTCGACGATCCTCCATCTAG 59.533 57.143 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.