Multiple sequence alignment - TraesCS3B01G241500

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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 TraesCS3B01G241500 chr3B 100.000 5410 0 0 1 5410 380885569 380890978 0.000000e+00 9991.0
1 TraesCS3B01G241500 chr3B 85.952 662 73 14 160 806 668894337 668893681 0.000000e+00 689.0
2 TraesCS3B01G241500 chr3B 83.230 483 55 18 215 687 578588705 578589171 2.330000e-113 420.0
3 TraesCS3B01G241500 chr3D 97.219 3632 72 12 872 4488 288102454 288106071 0.000000e+00 6120.0
4 TraesCS3B01G241500 chr3D 86.949 544 38 13 4497 5029 288106122 288106643 1.010000e-161 580.0
5 TraesCS3B01G241500 chr3D 96.835 158 5 0 1 158 265569756 265569599 1.160000e-66 265.0
6 TraesCS3B01G241500 chr3D 95.152 165 8 0 1 165 6270186 6270350 1.490000e-65 261.0
7 TraesCS3B01G241500 chr3D 92.414 145 8 3 5015 5159 288108705 288108846 2.550000e-48 204.0
8 TraesCS3B01G241500 chr3D 95.652 115 3 2 5296 5410 288109087 288109199 3.330000e-42 183.0
9 TraesCS3B01G241500 chr3A 96.627 3558 77 11 959 4488 377793683 377797225 0.000000e+00 5866.0
10 TraesCS3B01G241500 chr3A 90.711 506 29 7 4497 4999 377797289 377797779 0.000000e+00 658.0
11 TraesCS3B01G241500 chr3A 96.091 307 9 1 892 1198 377793382 377793685 1.050000e-136 497.0
12 TraesCS3B01G241500 chr3A 88.587 368 21 9 5060 5410 377798281 377798644 1.390000e-115 427.0
13 TraesCS3B01G241500 chr3A 92.000 50 1 1 5013 5059 377798213 377798262 3.500000e-07 67.6
14 TraesCS3B01G241500 chr5D 89.351 601 40 14 4497 5094 301383609 301383030 0.000000e+00 734.0
15 TraesCS3B01G241500 chr7D 86.033 673 70 13 152 810 560988489 560987827 0.000000e+00 701.0
16 TraesCS3B01G241500 chr2B 85.736 666 83 8 148 808 534643019 534643677 0.000000e+00 693.0
17 TraesCS3B01G241500 chr6B 85.503 676 77 10 151 809 700537317 700536646 0.000000e+00 686.0
18 TraesCS3B01G241500 chr6B 85.169 681 73 13 147 806 125348272 125348945 0.000000e+00 673.0
19 TraesCS3B01G241500 chr6B 85.835 593 76 6 215 806 583465557 583464972 1.650000e-174 623.0
20 TraesCS3B01G241500 chr6B 96.855 159 5 0 1 159 75007252 75007410 3.210000e-67 267.0
21 TraesCS3B01G241500 chr7B 84.727 622 84 9 191 806 138138173 138137557 3.580000e-171 612.0
22 TraesCS3B01G241500 chr7B 84.375 640 69 11 147 777 263664265 263664882 2.790000e-167 599.0
23 TraesCS3B01G241500 chr5B 85.739 568 68 9 249 806 45705152 45705716 6.040000e-164 588.0
24 TraesCS3B01G241500 chr5B 98.052 154 3 0 1 154 473709974 473709821 8.930000e-68 268.0
25 TraesCS3B01G241500 chr5A 98.065 155 3 0 1 155 351658910 351658756 2.480000e-68 270.0
26 TraesCS3B01G241500 chr5A 85.345 232 24 7 1 225 671524951 671524723 1.170000e-56 231.0
27 TraesCS3B01G241500 chr4B 96.835 158 5 0 1 158 60653097 60652940 1.160000e-66 265.0
28 TraesCS3B01G241500 chr4B 96.835 158 5 0 1 158 79140576 79140733 1.160000e-66 265.0
29 TraesCS3B01G241500 chr1B 98.026 152 3 0 1 152 153090377 153090528 1.160000e-66 265.0
30 TraesCS3B01G241500 chr6D 90.909 44 2 2 4497 4540 124252727 124252768 2.100000e-04 58.4
31 TraesCS3B01G241500 chr4D 90.909 44 2 2 4497 4540 128206379 128206420 2.100000e-04 58.4


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 TraesCS3B01G241500 chr3B 380885569 380890978 5409 False 9991.00 9991 100.0000 1 5410 1 chr3B.!!$F1 5409
1 TraesCS3B01G241500 chr3B 668893681 668894337 656 True 689.00 689 85.9520 160 806 1 chr3B.!!$R1 646
2 TraesCS3B01G241500 chr3D 288102454 288109199 6745 False 1771.75 6120 93.0585 872 5410 4 chr3D.!!$F2 4538
3 TraesCS3B01G241500 chr3A 377793382 377798644 5262 False 1503.12 5866 92.8032 892 5410 5 chr3A.!!$F1 4518
4 TraesCS3B01G241500 chr5D 301383030 301383609 579 True 734.00 734 89.3510 4497 5094 1 chr5D.!!$R1 597
5 TraesCS3B01G241500 chr7D 560987827 560988489 662 True 701.00 701 86.0330 152 810 1 chr7D.!!$R1 658
6 TraesCS3B01G241500 chr2B 534643019 534643677 658 False 693.00 693 85.7360 148 808 1 chr2B.!!$F1 660
7 TraesCS3B01G241500 chr6B 700536646 700537317 671 True 686.00 686 85.5030 151 809 1 chr6B.!!$R2 658
8 TraesCS3B01G241500 chr6B 125348272 125348945 673 False 673.00 673 85.1690 147 806 1 chr6B.!!$F2 659
9 TraesCS3B01G241500 chr6B 583464972 583465557 585 True 623.00 623 85.8350 215 806 1 chr6B.!!$R1 591
10 TraesCS3B01G241500 chr7B 138137557 138138173 616 True 612.00 612 84.7270 191 806 1 chr7B.!!$R1 615
11 TraesCS3B01G241500 chr7B 263664265 263664882 617 False 599.00 599 84.3750 147 777 1 chr7B.!!$F1 630
12 TraesCS3B01G241500 chr5B 45705152 45705716 564 False 588.00 588 85.7390 249 806 1 chr5B.!!$F1 557

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
796 858 0.321564 CTTGATGGGCCAACGACTGA 60.322 55.0 11.89 0.0 0.00 3.41 F
867 929 0.676782 GCCGCGGCCATAGGATTAAT 60.677 55.0 39.89 0.0 34.56 1.40 F
1485 1779 1.119574 AGGTATCGATGGTTCCCCCG 61.120 60.0 8.54 0.0 35.15 5.73 F
1833 2130 0.469070 GCATGGCAGAGAGATGGACT 59.531 55.0 0.00 0.0 0.00 3.85 F
3356 3676 1.364626 CGCAGCCTACAGCCTCTTTG 61.365 60.0 0.00 0.0 45.47 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 2111 0.469070 AGTCCATCTCTCTGCCATGC 59.531 55.000 0.00 0.0 0.00 4.06 R
1817 2114 3.229293 CAGATAGTCCATCTCTCTGCCA 58.771 50.000 0.00 0.0 42.40 4.92 R
3482 3802 1.137675 TCAATGATCAGAGCACCTCCG 59.862 52.381 0.09 0.0 0.00 4.63 R
3850 4170 4.129380 GCGGATTGCCTGCATATATATCA 58.871 43.478 0.00 0.0 37.76 2.15 R
4488 4817 0.320697 AGAGCAACCCGACCAAGTAC 59.679 55.000 0.00 0.0 0.00 2.73 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
39 40 7.977789 TGTTTGTCTATGTATTCACACATGT 57.022 32.000 0.00 0.00 39.46 3.21
40 41 9.665719 ATGTTTGTCTATGTATTCACACATGTA 57.334 29.630 0.00 0.00 39.46 2.29
41 42 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
51 52 8.608317 TGTATTCACACATGTATTATGTTTCCG 58.392 33.333 0.00 0.00 0.00 4.30
52 53 6.429791 TTCACACATGTATTATGTTTCCGG 57.570 37.500 0.00 0.00 0.00 5.14
53 54 5.492895 TCACACATGTATTATGTTTCCGGT 58.507 37.500 0.00 0.00 0.00 5.28
54 55 5.941058 TCACACATGTATTATGTTTCCGGTT 59.059 36.000 0.00 0.00 0.00 4.44
55 56 7.104290 TCACACATGTATTATGTTTCCGGTTA 58.896 34.615 0.00 0.00 0.00 2.85
56 57 7.606839 TCACACATGTATTATGTTTCCGGTTAA 59.393 33.333 0.00 0.00 0.00 2.01
57 58 8.402472 CACACATGTATTATGTTTCCGGTTAAT 58.598 33.333 0.00 1.95 0.00 1.40
58 59 9.616156 ACACATGTATTATGTTTCCGGTTAATA 57.384 29.630 0.00 0.00 0.00 0.98
59 60 9.872757 CACATGTATTATGTTTCCGGTTAATAC 57.127 33.333 0.00 12.47 37.73 1.89
60 61 9.616156 ACATGTATTATGTTTCCGGTTAATACA 57.384 29.630 22.83 22.83 44.85 2.29
68 69 7.311364 TGTTTCCGGTTAATACAATTCTAGC 57.689 36.000 0.00 0.00 0.00 3.42
69 70 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
70 71 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
71 72 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
72 73 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
73 74 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
74 75 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
75 76 8.017373 CCGGTTAATACAATTCTAGCATGAATG 58.983 37.037 0.00 3.53 36.84 2.67
76 77 8.773645 CGGTTAATACAATTCTAGCATGAATGA 58.226 33.333 0.00 0.00 36.84 2.57
133 134 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
145 146 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
156 157 1.747444 TTTCCTTCAGCCTCCTCCTT 58.253 50.000 0.00 0.00 0.00 3.36
213 214 4.020378 GCTCGCGGCCGTGAAAAA 62.020 61.111 37.92 19.32 33.98 1.94
268 269 4.176851 GACGGGGAGCTCGACGAC 62.177 72.222 28.05 20.60 0.00 4.34
350 351 0.526524 CGCCCTAGAGCAGTTCGAAG 60.527 60.000 0.00 0.00 0.00 3.79
351 352 0.808060 GCCCTAGAGCAGTTCGAAGC 60.808 60.000 0.00 0.00 0.00 3.86
409 425 3.144300 CGACGATAGCAACGACGAT 57.856 52.632 0.00 0.00 46.85 3.73
550 581 0.756294 TCAACGACTTCTTCAGCCCA 59.244 50.000 0.00 0.00 0.00 5.36
562 596 4.832248 TCTTCAGCCCATAGTTGTAGTTG 58.168 43.478 0.00 0.00 0.00 3.16
626 664 7.994425 ACATGTCGAATATATGCCCAATTTA 57.006 32.000 0.00 0.00 30.12 1.40
629 667 6.299922 TGTCGAATATATGCCCAATTTACCA 58.700 36.000 0.00 0.00 0.00 3.25
650 702 4.453819 CCAAATTTTAGCCGAATTTTGCCA 59.546 37.500 9.67 0.00 35.21 4.92
715 772 2.340443 GGATCGGCGGCTAGGAAG 59.660 66.667 7.21 0.00 0.00 3.46
763 821 4.554036 GGCTCGCCCCAGATGACC 62.554 72.222 0.00 0.00 0.00 4.02
773 831 2.364632 CCCAGATGACCATTTTACGCA 58.635 47.619 0.00 0.00 0.00 5.24
775 833 3.009723 CCAGATGACCATTTTACGCACT 58.990 45.455 0.00 0.00 0.00 4.40
781 843 3.071479 GACCATTTTACGCACTCCTTGA 58.929 45.455 0.00 0.00 0.00 3.02
792 854 1.299648 CTCCTTGATGGGCCAACGA 59.700 57.895 11.89 7.00 36.20 3.85
796 858 0.321564 CTTGATGGGCCAACGACTGA 60.322 55.000 11.89 0.00 0.00 3.41
810 872 4.727507 ACGACTGAAGATGCTCTAATGT 57.272 40.909 0.00 0.00 0.00 2.71
811 873 4.428209 ACGACTGAAGATGCTCTAATGTG 58.572 43.478 0.00 0.00 0.00 3.21
812 874 4.158579 ACGACTGAAGATGCTCTAATGTGA 59.841 41.667 0.00 0.00 0.00 3.58
813 875 4.502282 CGACTGAAGATGCTCTAATGTGAC 59.498 45.833 0.00 0.00 0.00 3.67
814 876 4.428209 ACTGAAGATGCTCTAATGTGACG 58.572 43.478 0.00 0.00 0.00 4.35
815 877 3.785486 TGAAGATGCTCTAATGTGACGG 58.215 45.455 0.00 0.00 0.00 4.79
816 878 2.231215 AGATGCTCTAATGTGACGGC 57.769 50.000 0.00 0.00 0.00 5.68
817 879 0.855349 GATGCTCTAATGTGACGGCG 59.145 55.000 4.80 4.80 0.00 6.46
818 880 1.154205 ATGCTCTAATGTGACGGCGC 61.154 55.000 6.90 0.00 0.00 6.53
819 881 2.860628 GCTCTAATGTGACGGCGCG 61.861 63.158 6.90 0.00 0.00 6.86
820 882 2.202690 TCTAATGTGACGGCGCGG 60.203 61.111 14.03 14.03 0.00 6.46
821 883 2.202690 CTAATGTGACGGCGCGGA 60.203 61.111 22.76 0.00 0.00 5.54
822 884 2.202690 TAATGTGACGGCGCGGAG 60.203 61.111 22.76 8.34 0.00 4.63
823 885 3.709880 TAATGTGACGGCGCGGAGG 62.710 63.158 22.76 3.24 0.00 4.30
863 925 4.320456 CTGCCGCGGCCATAGGAT 62.320 66.667 44.42 0.00 41.09 3.24
864 926 3.832237 CTGCCGCGGCCATAGGATT 62.832 63.158 44.42 0.00 41.09 3.01
865 927 2.345991 GCCGCGGCCATAGGATTA 59.654 61.111 39.89 0.00 34.56 1.75
866 928 1.302192 GCCGCGGCCATAGGATTAA 60.302 57.895 39.89 0.00 34.56 1.40
867 929 0.676782 GCCGCGGCCATAGGATTAAT 60.677 55.000 39.89 0.00 34.56 1.40
868 930 1.369625 CCGCGGCCATAGGATTAATC 58.630 55.000 14.67 6.93 0.00 1.75
869 931 1.338674 CCGCGGCCATAGGATTAATCA 60.339 52.381 14.67 0.00 0.00 2.57
870 932 2.422597 CGCGGCCATAGGATTAATCAA 58.577 47.619 17.07 5.11 0.00 2.57
879 941 9.836864 GGCCATAGGATTAATCAATTTCTTTTT 57.163 29.630 17.07 0.00 0.00 1.94
918 980 2.893682 AAAGTGATAGCCCGGCCAGC 62.894 60.000 5.55 4.79 0.00 4.85
1485 1779 1.119574 AGGTATCGATGGTTCCCCCG 61.120 60.000 8.54 0.00 35.15 5.73
1486 1780 1.301479 GTATCGATGGTTCCCCCGC 60.301 63.158 8.54 0.00 35.15 6.13
1519 1813 5.125097 AGTCTTTAATCTCCATTGCTTGCAG 59.875 40.000 0.00 0.00 0.00 4.41
1814 2111 4.801891 CACACTTGGAAATTCAGTGATGG 58.198 43.478 16.99 5.71 34.86 3.51
1815 2112 3.256631 ACACTTGGAAATTCAGTGATGGC 59.743 43.478 16.99 0.00 34.86 4.40
1816 2113 3.256383 CACTTGGAAATTCAGTGATGGCA 59.744 43.478 7.46 0.00 32.77 4.92
1817 2114 4.081862 CACTTGGAAATTCAGTGATGGCAT 60.082 41.667 0.00 0.00 32.77 4.40
1833 2130 0.469070 GCATGGCAGAGAGATGGACT 59.531 55.000 0.00 0.00 0.00 3.85
1968 2265 8.671384 TGCACCACTATAGTATTATTGGAAAC 57.329 34.615 4.74 0.00 0.00 2.78
2987 3307 8.915654 GCCTTTATGTATCTTCAAGTTTTTGTG 58.084 33.333 0.00 0.00 35.73 3.33
3118 3438 3.295093 TCAATTTCAGGTTGGTGAGCAA 58.705 40.909 0.00 0.00 0.00 3.91
3356 3676 1.364626 CGCAGCCTACAGCCTCTTTG 61.365 60.000 0.00 0.00 45.47 2.77
3378 3698 4.036262 TGATTTTCCTCTCCAAACGTTGTG 59.964 41.667 0.00 2.46 0.00 3.33
3482 3802 2.139118 GACCGAATTAGCTCAGATGGC 58.861 52.381 0.00 0.00 0.00 4.40
3944 4264 2.187707 GCCTATGTTGATTTTGCTGCG 58.812 47.619 0.00 0.00 0.00 5.18
4107 4427 0.743097 GCCAATGACTCAATCCCAGC 59.257 55.000 0.00 0.00 0.00 4.85
4110 4430 1.404391 CAATGACTCAATCCCAGCTGC 59.596 52.381 8.66 0.00 0.00 5.25
4335 4655 3.004315 GCCTGTTCCATTCGAGTGAAAAA 59.996 43.478 9.83 0.00 37.71 1.94
4421 4745 1.425066 ACCCTCTGCAATTCCTGTTGA 59.575 47.619 0.00 0.00 0.00 3.18
4451 4780 8.628280 TGATGATATAGACAGTTGAGTTCAGAG 58.372 37.037 0.00 0.00 0.00 3.35
4467 4796 2.843730 TCAGAGCAGGCTTATTTGGGTA 59.156 45.455 0.00 0.00 0.00 3.69
4476 4805 5.241728 CAGGCTTATTTGGGTAGGCTATTTC 59.758 44.000 0.00 0.00 42.18 2.17
4488 4817 6.166982 GGTAGGCTATTTCCTTGTATGCTAG 58.833 44.000 0.00 0.00 37.66 3.42
4490 4819 6.996180 AGGCTATTTCCTTGTATGCTAGTA 57.004 37.500 0.00 0.00 30.82 1.82
4491 4820 6.760291 AGGCTATTTCCTTGTATGCTAGTAC 58.240 40.000 0.00 0.00 30.82 2.73
4492 4821 6.555360 AGGCTATTTCCTTGTATGCTAGTACT 59.445 38.462 0.00 0.00 30.82 2.73
4493 4822 7.071321 AGGCTATTTCCTTGTATGCTAGTACTT 59.929 37.037 0.00 0.00 30.82 2.24
4495 4824 7.171678 GCTATTTCCTTGTATGCTAGTACTTGG 59.828 40.741 0.00 0.00 0.00 3.61
4527 4923 6.183360 TGCTCTCCTAGTCCTAGTAGAAGTAC 60.183 46.154 0.00 0.00 29.55 2.73
4528 4924 6.403866 TCTCCTAGTCCTAGTAGAAGTACG 57.596 45.833 0.00 0.00 33.97 3.67
4529 4925 5.896678 TCTCCTAGTCCTAGTAGAAGTACGT 59.103 44.000 0.00 0.00 33.97 3.57
4530 4926 7.063593 TCTCCTAGTCCTAGTAGAAGTACGTA 58.936 42.308 0.00 0.00 33.97 3.57
4531 4927 7.013846 TCTCCTAGTCCTAGTAGAAGTACGTAC 59.986 44.444 18.10 18.10 33.97 3.67
4565 4961 3.834447 TTGTCGTCAGCGGGTCGTG 62.834 63.158 0.00 0.00 38.89 4.35
4612 5008 4.180057 TGCATTGTTGGTGAAGTTTTGTC 58.820 39.130 0.00 0.00 0.00 3.18
4693 5094 1.868469 TGCATTTTTGGCAGTCAAGC 58.132 45.000 0.00 0.00 36.11 4.01
4745 5146 5.056480 TCTTGGTGTTTGACATACTGACTG 58.944 41.667 0.00 0.00 0.00 3.51
4806 5207 2.070783 GCATGCATTGTTCCAACTTGG 58.929 47.619 14.21 0.74 39.43 3.61
4862 5267 4.649674 AGTCTCAGAGAAACACACTGGTAA 59.350 41.667 0.20 0.00 37.69 2.85
4863 5268 4.985409 GTCTCAGAGAAACACACTGGTAAG 59.015 45.833 0.20 0.00 37.69 2.34
4864 5269 4.649674 TCTCAGAGAAACACACTGGTAAGT 59.350 41.667 0.00 0.00 37.69 2.24
4948 5353 3.197766 TGGAGAAGTGGAAAGTGCGATAT 59.802 43.478 0.00 0.00 0.00 1.63
4949 5354 3.557595 GGAGAAGTGGAAAGTGCGATATG 59.442 47.826 0.00 0.00 0.00 1.78
4950 5355 4.433615 GAGAAGTGGAAAGTGCGATATGA 58.566 43.478 0.00 0.00 0.00 2.15
4951 5356 5.028549 AGAAGTGGAAAGTGCGATATGAT 57.971 39.130 0.00 0.00 0.00 2.45
4952 5357 6.161855 AGAAGTGGAAAGTGCGATATGATA 57.838 37.500 0.00 0.00 0.00 2.15
5003 5549 7.965045 AGCTTCATTTACTTGATTTAGTCGTC 58.035 34.615 0.00 0.00 0.00 4.20
5014 5560 6.408858 TGATTTAGTCGTCTGAATTTCTGC 57.591 37.500 1.57 0.00 31.50 4.26
5065 7711 4.224678 GTTGAACCAACAACCCATCGGG 62.225 54.545 5.08 0.00 45.00 5.14
5165 7848 2.032377 CGTTGGTGTGGTGATGTGTAAC 60.032 50.000 0.00 0.00 37.35 2.50
5193 7884 7.814264 AGATGGTAGAAAGGCAATTATTGAG 57.186 36.000 9.36 0.00 0.00 3.02
5216 7907 1.006571 GACAGGCAACGAAGACGGA 60.007 57.895 0.00 0.00 44.46 4.69
5240 7931 1.293179 GTGTGCTGAAAATGGCCCC 59.707 57.895 0.00 0.00 0.00 5.80
5244 7935 1.215382 GCTGAAAATGGCCCCGAAC 59.785 57.895 0.00 0.00 0.00 3.95
5246 7937 0.897863 CTGAAAATGGCCCCGAACCA 60.898 55.000 0.00 0.00 42.61 3.67
5275 7966 4.142403 ACAGAAGAGAAAGAGAGCATCGAG 60.142 45.833 0.00 0.00 42.67 4.04
5323 8073 4.744137 CCTATGCTGAATGAAGAGAACTCG 59.256 45.833 0.00 0.00 34.09 4.18
5372 8124 2.663478 CGCGCGCCTAAACAAGACA 61.663 57.895 27.72 0.00 0.00 3.41
5373 8125 1.572447 GCGCGCCTAAACAAGACAA 59.428 52.632 23.24 0.00 0.00 3.18
5374 8126 0.168128 GCGCGCCTAAACAAGACAAT 59.832 50.000 23.24 0.00 0.00 2.71
5376 8128 1.202031 CGCGCCTAAACAAGACAATCC 60.202 52.381 0.00 0.00 0.00 3.01
5377 8129 2.084546 GCGCCTAAACAAGACAATCCT 58.915 47.619 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.665719 ACATGTGTGAATACATAGACAAACATA 57.334 29.630 0.00 0.00 38.58 2.29
14 15 8.565896 ACATGTGTGAATACATAGACAAACAT 57.434 30.769 0.00 0.00 40.42 2.71
15 16 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
25 26 8.608317 CGGAAACATAATACATGTGTGAATACA 58.392 33.333 9.11 0.00 34.63 2.29
26 27 8.067784 CCGGAAACATAATACATGTGTGAATAC 58.932 37.037 9.11 0.00 31.80 1.89
27 28 7.771361 ACCGGAAACATAATACATGTGTGAATA 59.229 33.333 9.46 0.00 31.80 1.75
28 29 6.601613 ACCGGAAACATAATACATGTGTGAAT 59.398 34.615 9.46 0.00 31.80 2.57
29 30 5.941058 ACCGGAAACATAATACATGTGTGAA 59.059 36.000 9.46 0.00 31.80 3.18
30 31 5.492895 ACCGGAAACATAATACATGTGTGA 58.507 37.500 9.46 0.00 31.80 3.58
31 32 5.811399 ACCGGAAACATAATACATGTGTG 57.189 39.130 9.46 4.81 31.80 3.82
32 33 7.925043 TTAACCGGAAACATAATACATGTGT 57.075 32.000 9.46 0.00 31.80 3.72
33 34 9.872757 GTATTAACCGGAAACATAATACATGTG 57.127 33.333 9.46 0.00 39.40 3.21
34 35 9.616156 TGTATTAACCGGAAACATAATACATGT 57.384 29.630 22.31 2.69 42.13 3.21
42 43 9.048446 GCTAGAATTGTATTAACCGGAAACATA 57.952 33.333 9.46 0.00 0.00 2.29
43 44 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
44 45 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
45 46 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
46 47 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
47 48 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
48 49 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
49 50 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
50 51 8.773645 TCATTCATGCTAGAATTGTATTAACCG 58.226 33.333 0.00 0.00 36.13 4.44
124 125 4.805609 GCTGAAGGAAATATGCCCTAGAGG 60.806 50.000 0.00 0.00 39.47 3.69
125 126 4.322567 GCTGAAGGAAATATGCCCTAGAG 58.677 47.826 0.00 0.00 31.36 2.43
126 127 3.073062 GGCTGAAGGAAATATGCCCTAGA 59.927 47.826 0.00 0.00 34.81 2.43
127 128 3.073650 AGGCTGAAGGAAATATGCCCTAG 59.926 47.826 0.00 0.00 41.08 3.02
128 129 3.056080 AGGCTGAAGGAAATATGCCCTA 58.944 45.455 0.00 0.00 41.08 3.53
129 130 1.855599 AGGCTGAAGGAAATATGCCCT 59.144 47.619 0.00 0.00 41.08 5.19
130 131 2.234143 GAGGCTGAAGGAAATATGCCC 58.766 52.381 0.00 0.00 41.08 5.36
131 132 2.158549 AGGAGGCTGAAGGAAATATGCC 60.159 50.000 0.00 0.00 40.54 4.40
132 133 3.145286 GAGGAGGCTGAAGGAAATATGC 58.855 50.000 0.00 0.00 0.00 3.14
133 134 3.393941 AGGAGGAGGCTGAAGGAAATATG 59.606 47.826 0.00 0.00 0.00 1.78
134 135 3.674477 AGGAGGAGGCTGAAGGAAATAT 58.326 45.455 0.00 0.00 0.00 1.28
135 136 3.136641 AGGAGGAGGCTGAAGGAAATA 57.863 47.619 0.00 0.00 0.00 1.40
136 137 1.978361 AGGAGGAGGCTGAAGGAAAT 58.022 50.000 0.00 0.00 0.00 2.17
137 138 1.352352 CAAGGAGGAGGCTGAAGGAAA 59.648 52.381 0.00 0.00 0.00 3.13
138 139 0.987294 CAAGGAGGAGGCTGAAGGAA 59.013 55.000 0.00 0.00 0.00 3.36
139 140 0.911525 CCAAGGAGGAGGCTGAAGGA 60.912 60.000 0.00 0.00 41.22 3.36
140 141 1.606531 CCAAGGAGGAGGCTGAAGG 59.393 63.158 0.00 0.00 41.22 3.46
373 374 3.140225 GAGGACGATGACGCCTCCC 62.140 68.421 16.08 0.00 46.43 4.30
580 618 8.577939 CATGTTCGACATTTTTACATAGCAAAG 58.422 33.333 0.00 0.00 36.53 2.77
626 664 4.454161 GGCAAAATTCGGCTAAAATTTGGT 59.546 37.500 12.21 0.00 36.65 3.67
629 667 6.625873 TTTGGCAAAATTCGGCTAAAATTT 57.374 29.167 10.83 0.00 37.51 1.82
710 767 3.394836 GAGGGCGAGTGGCTTCCT 61.395 66.667 0.00 0.00 40.40 3.36
758 816 3.350219 AGGAGTGCGTAAAATGGTCAT 57.650 42.857 0.00 0.00 0.00 3.06
759 817 2.811431 CAAGGAGTGCGTAAAATGGTCA 59.189 45.455 0.00 0.00 0.00 4.02
763 821 3.181497 CCCATCAAGGAGTGCGTAAAATG 60.181 47.826 0.00 0.00 41.22 2.32
773 831 1.002134 CGTTGGCCCATCAAGGAGT 60.002 57.895 0.00 0.00 41.22 3.85
775 833 1.002624 GTCGTTGGCCCATCAAGGA 60.003 57.895 0.00 0.00 41.22 3.36
781 843 0.620556 ATCTTCAGTCGTTGGCCCAT 59.379 50.000 0.00 0.00 0.00 4.00
846 908 2.449031 TAATCCTATGGCCGCGGCAG 62.449 60.000 46.88 35.43 42.43 4.85
847 909 2.046009 TTAATCCTATGGCCGCGGCA 62.046 55.000 46.88 33.74 44.11 5.69
848 910 0.676782 ATTAATCCTATGGCCGCGGC 60.677 55.000 41.63 41.63 41.06 6.53
849 911 1.338674 TGATTAATCCTATGGCCGCGG 60.339 52.381 24.05 24.05 0.00 6.46
850 912 2.093306 TGATTAATCCTATGGCCGCG 57.907 50.000 12.90 0.00 0.00 6.46
851 913 5.183904 AGAAATTGATTAATCCTATGGCCGC 59.816 40.000 12.90 0.00 0.00 6.53
852 914 6.824305 AGAAATTGATTAATCCTATGGCCG 57.176 37.500 12.90 0.00 0.00 6.13
853 915 9.836864 AAAAAGAAATTGATTAATCCTATGGCC 57.163 29.630 12.90 0.00 0.00 5.36
889 951 4.039973 CGGGCTATCACTTTGATTACCCTA 59.960 45.833 17.58 0.00 43.32 3.53
890 952 3.181454 CGGGCTATCACTTTGATTACCCT 60.181 47.826 17.58 0.00 43.32 4.34
918 980 1.660560 CGCTCCAAAGCCCAATGAGG 61.661 60.000 0.00 0.00 46.34 3.86
932 994 2.808321 GACGACGGGTTTCGCTCC 60.808 66.667 0.00 0.00 43.06 4.70
1198 1491 3.518998 CCTCCGCCTCATCGTCGT 61.519 66.667 0.00 0.00 0.00 4.34
1435 1729 4.137543 CTCTTAAGGTGCTTGACAAGGTT 58.862 43.478 16.80 0.00 0.00 3.50
1485 1779 8.870075 ATGGAGATTAAAGACTAATAATGGGC 57.130 34.615 0.00 0.00 0.00 5.36
1519 1813 3.004315 ACAACCGAATCACATTTCCACAC 59.996 43.478 0.00 0.00 0.00 3.82
1772 2069 6.658816 AGTGTGGCACATTACATGATTCTAAA 59.341 34.615 24.95 0.00 44.52 1.85
1813 2110 0.534652 GTCCATCTCTCTGCCATGCC 60.535 60.000 0.00 0.00 0.00 4.40
1814 2111 0.469070 AGTCCATCTCTCTGCCATGC 59.531 55.000 0.00 0.00 0.00 4.06
1815 2112 3.833650 AGATAGTCCATCTCTCTGCCATG 59.166 47.826 0.00 0.00 40.09 3.66
1816 2113 3.833650 CAGATAGTCCATCTCTCTGCCAT 59.166 47.826 0.00 0.00 42.40 4.40
1817 2114 3.229293 CAGATAGTCCATCTCTCTGCCA 58.771 50.000 0.00 0.00 42.40 4.92
2987 3307 8.445275 AGAAACCCCAAAAATATGTTTGAAAC 57.555 30.769 18.33 0.14 40.29 2.78
3356 3676 4.274950 TCACAACGTTTGGAGAGGAAAATC 59.725 41.667 0.00 0.00 34.12 2.17
3378 3698 1.691434 CTCCTCAGGACTAGCCCATTC 59.309 57.143 0.00 0.00 37.37 2.67
3431 3751 4.458989 TGTTCGCTAATCTCCATTGCTTTT 59.541 37.500 0.00 0.00 0.00 2.27
3482 3802 1.137675 TCAATGATCAGAGCACCTCCG 59.862 52.381 0.09 0.00 0.00 4.63
3850 4170 4.129380 GCGGATTGCCTGCATATATATCA 58.871 43.478 0.00 0.00 37.76 2.15
3944 4264 1.093159 CCTTGGCAGAGTGCTTGATC 58.907 55.000 0.00 0.00 44.28 2.92
4107 4427 2.237143 TGATACCAAGAGAACCCAGCAG 59.763 50.000 0.00 0.00 0.00 4.24
4110 4430 4.559862 AGTTGATACCAAGAGAACCCAG 57.440 45.455 0.00 0.00 32.06 4.45
4335 4655 1.423921 ACAAAGGAAAGGGATCACCGT 59.576 47.619 0.00 0.00 46.96 4.83
4382 4702 9.078990 CAGAGGGTCTCCTTATTTTTAGTTTTT 57.921 33.333 0.00 0.00 45.05 1.94
4383 4703 7.176865 GCAGAGGGTCTCCTTATTTTTAGTTTT 59.823 37.037 0.00 0.00 45.05 2.43
4397 4717 0.915364 AGGAATTGCAGAGGGTCTCC 59.085 55.000 0.00 0.00 0.00 3.71
4421 4745 9.593134 GAACTCAACTGTCTATATCATCAAGTT 57.407 33.333 0.00 0.00 0.00 2.66
4451 4780 1.032794 GCCTACCCAAATAAGCCTGC 58.967 55.000 0.00 0.00 0.00 4.85
4467 4796 5.896073 ACTAGCATACAAGGAAATAGCCT 57.104 39.130 0.00 0.00 40.93 4.58
4476 4805 4.360563 CGACCAAGTACTAGCATACAAGG 58.639 47.826 0.00 0.00 0.00 3.61
4488 4817 0.320697 AGAGCAACCCGACCAAGTAC 59.679 55.000 0.00 0.00 0.00 2.73
4490 4819 1.371558 GAGAGCAACCCGACCAAGT 59.628 57.895 0.00 0.00 0.00 3.16
4491 4820 1.376037 GGAGAGCAACCCGACCAAG 60.376 63.158 0.00 0.00 0.00 3.61
4492 4821 0.543410 TAGGAGAGCAACCCGACCAA 60.543 55.000 0.00 0.00 0.00 3.67
4493 4822 0.970937 CTAGGAGAGCAACCCGACCA 60.971 60.000 0.00 0.00 0.00 4.02
4495 4824 0.456628 GACTAGGAGAGCAACCCGAC 59.543 60.000 0.00 0.00 0.00 4.79
4527 4923 7.854422 ACGACAACACTGTGATTATATAGTACG 59.146 37.037 15.86 6.93 35.30 3.67
4528 4924 9.167239 GACGACAACACTGTGATTATATAGTAC 57.833 37.037 15.86 0.00 35.30 2.73
4529 4925 8.895737 TGACGACAACACTGTGATTATATAGTA 58.104 33.333 15.86 0.00 35.30 1.82
4530 4926 7.768240 TGACGACAACACTGTGATTATATAGT 58.232 34.615 15.86 4.00 35.30 2.12
4531 4927 7.096436 GCTGACGACAACACTGTGATTATATAG 60.096 40.741 15.86 5.08 35.30 1.31
4540 4936 1.559814 CGCTGACGACAACACTGTG 59.440 57.895 6.19 6.19 43.93 3.66
4565 4961 5.503194 GCAAGAGACCGAGAAAAATCATAGC 60.503 44.000 0.00 0.00 0.00 2.97
4612 5008 0.465705 ATACATGGACCAGGCACTCG 59.534 55.000 5.94 0.00 34.60 4.18
4745 5146 2.881074 TGTATCTTCTGCGACTGCTTC 58.119 47.619 0.00 0.00 43.34 3.86
4831 5235 6.142002 GTGTGTTTCTCTGAGACTACGTAAAC 59.858 42.308 6.92 7.89 0.00 2.01
4832 5236 6.039047 AGTGTGTTTCTCTGAGACTACGTAAA 59.961 38.462 6.92 0.00 0.00 2.01
4833 5237 5.530171 AGTGTGTTTCTCTGAGACTACGTAA 59.470 40.000 6.92 0.00 0.00 3.18
4864 5269 2.529136 CCCTCCCTGTGGTCACCA 60.529 66.667 0.00 0.00 0.00 4.17
4865 5270 2.203938 TCCCTCCCTGTGGTCACC 60.204 66.667 0.00 0.00 0.00 4.02
4866 5271 1.128188 AACTCCCTCCCTGTGGTCAC 61.128 60.000 0.00 0.00 0.00 3.67
4867 5272 1.127567 CAACTCCCTCCCTGTGGTCA 61.128 60.000 0.00 0.00 0.00 4.02
4868 5273 0.836400 TCAACTCCCTCCCTGTGGTC 60.836 60.000 0.00 0.00 0.00 4.02
4928 5333 4.433615 TCATATCGCACTTTCCACTTCTC 58.566 43.478 0.00 0.00 0.00 2.87
4948 5353 4.527427 CCTCCATCTCAGCTCTTCATATCA 59.473 45.833 0.00 0.00 0.00 2.15
4949 5354 4.771577 TCCTCCATCTCAGCTCTTCATATC 59.228 45.833 0.00 0.00 0.00 1.63
4950 5355 4.749820 TCCTCCATCTCAGCTCTTCATAT 58.250 43.478 0.00 0.00 0.00 1.78
4951 5356 4.190370 TCCTCCATCTCAGCTCTTCATA 57.810 45.455 0.00 0.00 0.00 2.15
4952 5357 3.043465 TCCTCCATCTCAGCTCTTCAT 57.957 47.619 0.00 0.00 0.00 2.57
5065 7711 2.511637 ACCCTTTCTCCATGGATTCCTC 59.488 50.000 16.63 0.00 0.00 3.71
5165 7848 5.567138 AATTGCCTTTCTACCATCTTTCG 57.433 39.130 0.00 0.00 0.00 3.46
5193 7884 2.062519 GTCTTCGTTGCCTGTCTTCTC 58.937 52.381 0.00 0.00 0.00 2.87
5240 7931 3.664107 TCTCTTCTGTTTCCATGGTTCG 58.336 45.455 12.58 0.00 0.00 3.95
5244 7935 5.555017 TCTCTTTCTCTTCTGTTTCCATGG 58.445 41.667 4.97 4.97 0.00 3.66
5246 7937 5.221803 TGCTCTCTTTCTCTTCTGTTTCCAT 60.222 40.000 0.00 0.00 0.00 3.41
5254 7945 3.381272 CCTCGATGCTCTCTTTCTCTTCT 59.619 47.826 0.00 0.00 0.00 2.85
5275 7966 3.526825 GCATATTCGTGCGGTTTCC 57.473 52.632 0.00 0.00 35.10 3.13
5372 8124 4.218312 GTGAAAGGAATGGCCATAGGATT 58.782 43.478 21.15 12.36 40.02 3.01
5373 8125 3.205056 TGTGAAAGGAATGGCCATAGGAT 59.795 43.478 21.15 2.09 40.02 3.24
5374 8126 2.580322 TGTGAAAGGAATGGCCATAGGA 59.420 45.455 21.15 0.00 40.02 2.94
5376 8128 3.571401 GGATGTGAAAGGAATGGCCATAG 59.429 47.826 21.15 0.00 40.02 2.23
5377 8129 3.565307 GGATGTGAAAGGAATGGCCATA 58.435 45.455 21.15 0.00 40.02 2.74


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

AutoCloner maintained by Alex Coulton.