Multiple sequence alignment - TraesCS3D01G198700

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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 TraesCS3D01G198700 chr3D 100.000 7529 0 0 1 7529 216428813 216421285 0.000000e+00 13904.0
1 TraesCS3D01G198700 chr3D 92.449 437 26 3 6143 6572 216416806 216416370 1.070000e-172 617.0
2 TraesCS3D01G198700 chr3D 88.337 403 35 7 7072 7469 216416364 216415969 2.460000e-129 473.0
3 TraesCS3D01G198700 chr3D 93.930 313 15 3 6575 6883 48940281 48940593 3.180000e-128 470.0
4 TraesCS3D01G198700 chr3D 92.903 310 18 3 6578 6883 289378188 289378497 1.490000e-121 448.0
5 TraesCS3D01G198700 chr3D 91.262 103 9 0 5151 5253 554835965 554836067 2.830000e-29 141.0
6 TraesCS3D01G198700 chr3B 97.014 4153 93 11 1015 5151 311116798 311120935 0.000000e+00 6953.0
7 TraesCS3D01G198700 chr3B 97.494 1277 24 3 5307 6576 311125463 311126738 0.000000e+00 2174.0
8 TraesCS3D01G198700 chr3B 91.494 482 17 6 7071 7529 311126739 311127219 6.370000e-180 641.0
9 TraesCS3D01G198700 chr3B 94.681 188 9 1 5152 5339 311121004 311121190 2.660000e-74 291.0
10 TraesCS3D01G198700 chr3B 88.732 213 23 1 7258 7469 311187959 311188171 7.490000e-65 259.0
11 TraesCS3D01G198700 chr3B 92.063 126 8 2 892 1016 311116636 311116760 7.760000e-40 176.0
12 TraesCS3D01G198700 chr3B 96.875 64 2 0 1178 1241 667460102 667460165 2.870000e-19 108.0
13 TraesCS3D01G198700 chr3A 97.464 2248 37 6 1670 3901 336878291 336880534 0.000000e+00 3818.0
14 TraesCS3D01G198700 chr3A 92.200 1282 65 22 5516 6788 336883799 336885054 0.000000e+00 1781.0
15 TraesCS3D01G198700 chr3A 91.640 1256 67 15 3899 5151 336880847 336882067 0.000000e+00 1703.0
16 TraesCS3D01G198700 chr3A 97.470 672 16 1 1015 1685 336877606 336878277 0.000000e+00 1146.0
17 TraesCS3D01G198700 chr3A 95.796 333 13 1 5151 5483 336882134 336882465 3.090000e-148 536.0
18 TraesCS3D01G198700 chr3A 89.514 391 22 9 1 375 573968292 573968679 1.900000e-130 477.0
19 TraesCS3D01G198700 chr3A 85.861 389 43 7 6578 6961 534994539 534994158 3.270000e-108 403.0
20 TraesCS3D01G198700 chr3A 87.463 335 18 6 7217 7529 336932212 336932544 1.540000e-96 364.0
21 TraesCS3D01G198700 chr3A 85.380 342 46 4 7130 7469 336943446 336943785 1.200000e-92 351.0
22 TraesCS3D01G198700 chr3A 91.379 116 10 0 901 1016 336877453 336877568 7.820000e-35 159.0
23 TraesCS3D01G198700 chr3A 97.619 42 1 0 7030 7071 733965847 733965888 1.050000e-08 73.1
24 TraesCS3D01G198700 chr6D 97.773 898 20 0 1 898 24256599 24255702 0.000000e+00 1548.0
25 TraesCS3D01G198700 chr6D 87.490 1239 134 12 3917 5148 5648586 5649810 0.000000e+00 1410.0
26 TraesCS3D01G198700 chr6D 93.831 308 17 1 6576 6881 285312883 285312576 5.320000e-126 462.0
27 TraesCS3D01G198700 chr6D 92.581 310 19 3 6578 6883 164539001 164539310 6.930000e-120 442.0
28 TraesCS3D01G198700 chr6D 95.135 185 6 3 6846 7027 460832526 460832710 9.560000e-74 289.0
29 TraesCS3D01G198700 chr6D 96.875 64 2 0 1178 1241 422328608 422328671 2.870000e-19 108.0
30 TraesCS3D01G198700 chr4D 93.920 921 33 4 1 898 97480277 97481197 0.000000e+00 1369.0
31 TraesCS3D01G198700 chr4D 75.599 709 142 23 4460 5151 101387790 101387096 9.420000e-84 322.0
32 TraesCS3D01G198700 chr4D 95.098 204 10 0 1 204 496935098 496935301 9.420000e-84 322.0
33 TraesCS3D01G198700 chr5D 92.733 922 44 3 1 899 398262712 398263633 0.000000e+00 1310.0
34 TraesCS3D01G198700 chr5D 86.200 942 76 22 3 899 494244521 494245453 0.000000e+00 970.0
35 TraesCS3D01G198700 chr5D 84.835 910 86 19 12 897 382518965 382518084 0.000000e+00 869.0
36 TraesCS3D01G198700 chr5D 81.907 409 61 10 4751 5151 379407161 379407564 4.350000e-87 333.0
37 TraesCS3D01G198700 chr5D 85.714 154 20 2 7295 7447 207349244 207349092 2.170000e-35 161.0
38 TraesCS3D01G198700 chr5D 94.000 100 6 0 5151 5250 304856896 304856797 1.310000e-32 152.0
39 TraesCS3D01G198700 chr5D 100.000 28 0 0 7042 7069 446271650 446271623 1.400000e-02 52.8
40 TraesCS3D01G198700 chr2D 88.841 932 66 14 1 899 601105761 601106687 0.000000e+00 1110.0
41 TraesCS3D01G198700 chr2D 81.598 413 63 6 4751 5151 646440782 646440371 5.630000e-86 329.0
42 TraesCS3D01G198700 chr2D 90.816 98 9 0 5151 5248 646288897 646288994 1.700000e-26 132.0
43 TraesCS3D01G198700 chr1D 86.818 971 104 12 4194 5151 2760068 2759109 0.000000e+00 1062.0
44 TraesCS3D01G198700 chr1D 90.769 455 36 5 6578 7027 316014761 316014308 3.010000e-168 603.0
45 TraesCS3D01G198700 chr1D 84.746 177 17 8 7296 7466 24886984 24886812 1.300000e-37 169.0
46 TraesCS3D01G198700 chr1D 90.654 107 9 1 5151 5257 440708485 440708590 2.830000e-29 141.0
47 TraesCS3D01G198700 chr4A 86.746 928 89 20 1 902 630837175 630836256 0.000000e+00 1002.0
48 TraesCS3D01G198700 chr4A 82.122 509 74 12 6575 7069 614550120 614550625 3.250000e-113 420.0
49 TraesCS3D01G198700 chr7D 86.484 947 71 27 1 898 545666569 545665631 0.000000e+00 987.0
50 TraesCS3D01G198700 chr7D 85.167 809 61 29 1 781 46571262 46570485 0.000000e+00 774.0
51 TraesCS3D01G198700 chr7D 96.629 178 4 2 6852 7027 537292309 537292486 2.050000e-75 294.0
52 TraesCS3D01G198700 chr7D 95.161 62 3 0 1180 1241 630907826 630907765 1.730000e-16 99.0
53 TraesCS3D01G198700 chr2A 86.567 938 67 25 1 898 769228505 769227587 0.000000e+00 979.0
54 TraesCS3D01G198700 chr2A 85.177 931 84 23 2 898 165245791 165244881 0.000000e+00 905.0
55 TraesCS3D01G198700 chr2A 93.269 312 17 3 6574 6881 71792086 71791775 2.480000e-124 457.0
56 TraesCS3D01G198700 chr2A 95.312 64 3 0 1178 1241 725941338 725941401 1.340000e-17 102.0
57 TraesCS3D01G198700 chr7A 86.472 924 86 23 1 897 563240042 563240953 0.000000e+00 977.0
58 TraesCS3D01G198700 chr7A 86.099 446 55 5 6575 7014 713182300 713182744 2.460000e-129 473.0
59 TraesCS3D01G198700 chr7A 93.417 319 17 3 6574 6888 399853849 399854167 3.180000e-128 470.0
60 TraesCS3D01G198700 chr7A 76.618 680 116 34 4499 5151 68752900 68753563 1.210000e-87 335.0
61 TraesCS3D01G198700 chr7A 76.067 656 137 16 4511 5151 726979206 726978556 2.620000e-84 324.0
62 TraesCS3D01G198700 chr7A 86.047 215 17 7 6849 7061 235482274 235482071 1.270000e-52 219.0
63 TraesCS3D01G198700 chr5A 85.256 936 85 24 3 898 647552047 647551125 0.000000e+00 915.0
64 TraesCS3D01G198700 chr5A 75.527 711 146 17 4443 5133 18724900 18725602 2.620000e-84 324.0
65 TraesCS3D01G198700 chr5A 84.028 288 40 6 6744 7027 650690102 650689817 9.630000e-69 272.0
66 TraesCS3D01G198700 chr5A 82.840 169 27 2 6850 7016 560471692 560471860 4.710000e-32 150.0
67 TraesCS3D01G198700 chr5A 78.808 151 22 3 7298 7447 677900794 677900653 8.040000e-15 93.5
68 TraesCS3D01G198700 chrUn 84.666 913 90 28 3 898 70157714 70158593 0.000000e+00 865.0
69 TraesCS3D01G198700 chrUn 76.067 656 137 16 4511 5151 254810740 254810090 2.620000e-84 324.0
70 TraesCS3D01G198700 chrUn 90.196 102 10 0 5151 5252 353056587 353056688 4.740000e-27 134.0
71 TraesCS3D01G198700 chrUn 89.524 105 11 0 5151 5255 465405790 465405686 4.740000e-27 134.0
72 TraesCS3D01G198700 chr6A 84.177 929 92 32 1 899 536666809 536665906 0.000000e+00 850.0
73 TraesCS3D01G198700 chr6A 82.857 175 25 4 7297 7466 601468960 601468786 1.310000e-32 152.0
74 TraesCS3D01G198700 chr6A 97.674 43 1 0 7028 7070 253443052 253443010 2.910000e-09 75.0
75 TraesCS3D01G198700 chr1B 86.341 615 50 18 1 592 557114530 557113927 2.290000e-179 640.0
76 TraesCS3D01G198700 chr1B 92.473 279 10 3 3 270 529698848 529699126 9.160000e-104 388.0
77 TraesCS3D01G198700 chr1B 80.154 519 78 16 4634 5130 688397673 688398188 1.540000e-96 364.0
78 TraesCS3D01G198700 chr1B 82.353 136 13 7 7298 7430 645009315 645009442 2.870000e-19 108.0
79 TraesCS3D01G198700 chr4B 80.408 245 29 11 7300 7525 39045999 39046243 1.300000e-37 169.0
80 TraesCS3D01G198700 chr6B 92.079 101 8 0 5151 5251 659946912 659947012 7.870000e-30 143.0
81 TraesCS3D01G198700 chr2B 88.525 61 7 0 1179 1239 64559020 64559080 2.910000e-09 75.0


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 TraesCS3D01G198700 chr3D 216421285 216428813 7528 True 13904.000000 13904 100.000000 1 7529 1 chr3D.!!$R1 7528
1 TraesCS3D01G198700 chr3D 216415969 216416806 837 True 545.000000 617 90.393000 6143 7469 2 chr3D.!!$R2 1326
2 TraesCS3D01G198700 chr3B 311116636 311121190 4554 False 2473.333333 6953 94.586000 892 5339 3 chr3B.!!$F3 4447
3 TraesCS3D01G198700 chr3B 311125463 311127219 1756 False 1407.500000 2174 94.494000 5307 7529 2 chr3B.!!$F4 2222
4 TraesCS3D01G198700 chr3A 336877453 336885054 7601 False 1523.833333 3818 94.324833 901 6788 6 chr3A.!!$F5 5887
5 TraesCS3D01G198700 chr6D 24255702 24256599 897 True 1548.000000 1548 97.773000 1 898 1 chr6D.!!$R1 897
6 TraesCS3D01G198700 chr6D 5648586 5649810 1224 False 1410.000000 1410 87.490000 3917 5148 1 chr6D.!!$F1 1231
7 TraesCS3D01G198700 chr4D 97480277 97481197 920 False 1369.000000 1369 93.920000 1 898 1 chr4D.!!$F1 897
8 TraesCS3D01G198700 chr4D 101387096 101387790 694 True 322.000000 322 75.599000 4460 5151 1 chr4D.!!$R1 691
9 TraesCS3D01G198700 chr5D 398262712 398263633 921 False 1310.000000 1310 92.733000 1 899 1 chr5D.!!$F2 898
10 TraesCS3D01G198700 chr5D 494244521 494245453 932 False 970.000000 970 86.200000 3 899 1 chr5D.!!$F3 896
11 TraesCS3D01G198700 chr5D 382518084 382518965 881 True 869.000000 869 84.835000 12 897 1 chr5D.!!$R3 885
12 TraesCS3D01G198700 chr2D 601105761 601106687 926 False 1110.000000 1110 88.841000 1 899 1 chr2D.!!$F1 898
13 TraesCS3D01G198700 chr1D 2759109 2760068 959 True 1062.000000 1062 86.818000 4194 5151 1 chr1D.!!$R1 957
14 TraesCS3D01G198700 chr4A 630836256 630837175 919 True 1002.000000 1002 86.746000 1 902 1 chr4A.!!$R1 901
15 TraesCS3D01G198700 chr4A 614550120 614550625 505 False 420.000000 420 82.122000 6575 7069 1 chr4A.!!$F1 494
16 TraesCS3D01G198700 chr7D 545665631 545666569 938 True 987.000000 987 86.484000 1 898 1 chr7D.!!$R2 897
17 TraesCS3D01G198700 chr7D 46570485 46571262 777 True 774.000000 774 85.167000 1 781 1 chr7D.!!$R1 780
18 TraesCS3D01G198700 chr2A 769227587 769228505 918 True 979.000000 979 86.567000 1 898 1 chr2A.!!$R3 897
19 TraesCS3D01G198700 chr2A 165244881 165245791 910 True 905.000000 905 85.177000 2 898 1 chr2A.!!$R2 896
20 TraesCS3D01G198700 chr7A 563240042 563240953 911 False 977.000000 977 86.472000 1 897 1 chr7A.!!$F3 896
21 TraesCS3D01G198700 chr7A 68752900 68753563 663 False 335.000000 335 76.618000 4499 5151 1 chr7A.!!$F1 652
22 TraesCS3D01G198700 chr7A 726978556 726979206 650 True 324.000000 324 76.067000 4511 5151 1 chr7A.!!$R2 640
23 TraesCS3D01G198700 chr5A 647551125 647552047 922 True 915.000000 915 85.256000 3 898 1 chr5A.!!$R1 895
24 TraesCS3D01G198700 chr5A 18724900 18725602 702 False 324.000000 324 75.527000 4443 5133 1 chr5A.!!$F1 690
25 TraesCS3D01G198700 chrUn 70157714 70158593 879 False 865.000000 865 84.666000 3 898 1 chrUn.!!$F1 895
26 TraesCS3D01G198700 chrUn 254810090 254810740 650 True 324.000000 324 76.067000 4511 5151 1 chrUn.!!$R1 640
27 TraesCS3D01G198700 chr6A 536665906 536666809 903 True 850.000000 850 84.177000 1 899 1 chr6A.!!$R2 898
28 TraesCS3D01G198700 chr1B 557113927 557114530 603 True 640.000000 640 86.341000 1 592 1 chr1B.!!$R1 591
29 TraesCS3D01G198700 chr1B 688397673 688398188 515 False 364.000000 364 80.154000 4634 5130 1 chr1B.!!$F3 496

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
131 132 0.675633 AATGCACTTGGGTTGAGCAC 59.324 50.000 0.00 0.00 38.12 4.40 F
963 1171 0.988832 AGATCAGGCAAAACGGGGTA 59.011 50.000 0.00 0.00 0.00 3.69 F
1513 1760 0.592637 TGTTTCAAGCAGCGGTCATG 59.407 50.000 0.00 0.00 0.00 3.07 F
1762 2039 0.615544 ACATCAAAGCCATGGTGGGG 60.616 55.000 14.67 1.32 38.19 4.96 F
1917 2194 1.874872 CCCTTTTGCTGCCACATTTTG 59.125 47.619 0.00 0.00 0.00 2.44 F
2267 2545 4.298103 AGAGATTCTGACATTGCCAACT 57.702 40.909 0.00 0.00 0.00 3.16 F
2699 2977 5.179452 AGCTGCCAATAAGAGGAAAACTA 57.821 39.130 0.00 0.00 0.00 2.24 F
4286 4901 1.144565 CGACTGATCTGAAGCGGCAG 61.145 60.000 6.60 2.85 37.24 4.85 F
5026 5686 1.271163 CCCTTCTTGAAGGCGTTACCA 60.271 52.381 20.71 0.00 43.14 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1033 1280 1.816863 GAGGAAGCACGGACCTCACA 61.817 60.000 0.00 0.00 46.42 3.58 R
2675 2953 2.315925 TTCCTCTTATTGGCAGCTCG 57.684 50.000 0.00 0.00 0.00 5.03 R
2699 2977 3.370953 GGTCCAGGAGTATGCAGTGAATT 60.371 47.826 0.00 0.00 0.00 2.17 R
2780 3058 3.758755 AGCATCACAGAACACAGAAGA 57.241 42.857 0.00 0.00 0.00 2.87 R
2781 3059 4.309933 TGTAGCATCACAGAACACAGAAG 58.690 43.478 0.00 0.00 0.00 2.85 R
3955 4563 1.383943 ATGGATGGCCTCCCGTGTA 60.384 57.895 15.98 1.01 44.23 2.90 R
4524 5147 2.363018 CCTCACCGGAGAGAGCCA 60.363 66.667 28.09 0.00 44.26 4.75 R
6087 8186 0.912486 ACTTTAGCATCCTCGGGCTT 59.088 50.000 0.00 0.00 41.41 4.35 R
6821 8929 2.838202 CCACAGTGGGAGTAACATAGGT 59.162 50.000 12.40 0.00 32.67 3.08 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
41 42 0.912486 GCATCTAACCTGGACTGGGT 59.088 55.000 0.00 0.00 38.94 4.51
131 132 0.675633 AATGCACTTGGGTTGAGCAC 59.324 50.000 0.00 0.00 38.12 4.40
205 206 4.187694 GCAACCAAAATGACCAACAGAAA 58.812 39.130 0.00 0.00 0.00 2.52
908 1116 9.793252 TTTATACTGTTTACTCCGTCTTACATC 57.207 33.333 0.00 0.00 0.00 3.06
919 1127 2.017049 GTCTTACATCATGGCGGCTTT 58.983 47.619 11.43 0.00 0.00 3.51
927 1135 2.546494 ATGGCGGCTTTATGCGCTC 61.546 57.895 9.73 0.00 44.05 5.03
963 1171 0.988832 AGATCAGGCAAAACGGGGTA 59.011 50.000 0.00 0.00 0.00 3.69
972 1180 2.550639 GCAAAACGGGGTAGTGTCCTTA 60.551 50.000 0.00 0.00 0.00 2.69
1033 1280 1.971357 ACCAGAGACCGAACTCACATT 59.029 47.619 10.42 0.00 39.14 2.71
1188 1435 2.995574 AACCTCCCCGTCGTCCTG 60.996 66.667 0.00 0.00 0.00 3.86
1513 1760 0.592637 TGTTTCAAGCAGCGGTCATG 59.407 50.000 0.00 0.00 0.00 3.07
1643 1890 5.535406 ACCCTCGTTAATGACTGATACCTAG 59.465 44.000 0.00 0.00 0.00 3.02
1762 2039 0.615544 ACATCAAAGCCATGGTGGGG 60.616 55.000 14.67 1.32 38.19 4.96
1917 2194 1.874872 CCCTTTTGCTGCCACATTTTG 59.125 47.619 0.00 0.00 0.00 2.44
1990 2267 9.109393 TGGTAGTTGTTTAGATTAGATTGCATC 57.891 33.333 0.00 0.00 0.00 3.91
2267 2545 4.298103 AGAGATTCTGACATTGCCAACT 57.702 40.909 0.00 0.00 0.00 3.16
2289 2567 9.781834 CAACTACAAAAATGAAGTAAACTGTGA 57.218 29.630 0.00 0.00 0.00 3.58
2675 2953 6.825721 AGAACACATAACCTCCATGAGATTTC 59.174 38.462 0.00 0.00 0.00 2.17
2699 2977 5.179452 AGCTGCCAATAAGAGGAAAACTA 57.821 39.130 0.00 0.00 0.00 2.24
2747 3025 6.946340 TGTTCCTCATTAGCTGATTAACTCA 58.054 36.000 0.00 0.00 33.08 3.41
3665 3958 8.883731 ACTAACTTGCTAACTTGCTATGTTATG 58.116 33.333 0.00 0.00 30.73 1.90
4144 4753 3.376918 GCTGGGTTCCTTGGCTGC 61.377 66.667 0.00 0.00 0.00 5.25
4286 4901 1.144565 CGACTGATCTGAAGCGGCAG 61.145 60.000 6.60 2.85 37.24 4.85
4464 5085 2.697431 GCTTTGCGTGGACAATGTTA 57.303 45.000 0.00 0.00 0.00 2.41
4524 5147 4.791069 ACCGACGGGCCTGGGTAT 62.791 66.667 20.00 0.00 36.48 2.73
4856 5509 3.198582 GCGAACGCCTAGGTCTCT 58.801 61.111 11.31 0.00 33.40 3.10
4932 5587 2.808523 TGCTCAGATAAGCTCGGATG 57.191 50.000 0.00 0.00 42.94 3.51
4968 5624 6.231211 GTGAAAACCTAGATCTGACCTTTGA 58.769 40.000 5.18 0.00 0.00 2.69
5026 5686 1.271163 CCCTTCTTGAAGGCGTTACCA 60.271 52.381 20.71 0.00 43.14 3.25
5244 6042 5.565834 GCAAATAAAATCCACCCTTTGTCGA 60.566 40.000 0.00 0.00 0.00 4.20
5433 6231 7.156876 TCTGTCCCATGTGACATTAAAAATC 57.843 36.000 11.59 0.00 43.86 2.17
5434 6232 6.718912 TCTGTCCCATGTGACATTAAAAATCA 59.281 34.615 11.59 0.00 43.86 2.57
5441 6239 8.374728 CCATGTGACATTAAAAATCATGAAACG 58.625 33.333 0.00 0.00 34.90 3.60
5448 6246 8.567948 ACATTAAAAATCATGAAACGAGTGACT 58.432 29.630 0.00 0.00 0.00 3.41
5670 7769 1.551883 CTTTTGCTCCTCCCCCATTTG 59.448 52.381 0.00 0.00 0.00 2.32
5760 7859 8.393366 GTGAGTAGACGTGTATATGTCAAGTTA 58.607 37.037 13.56 0.00 43.78 2.24
6087 8186 6.491745 TGTAATTGAGCTTTACCATGTCCAAA 59.508 34.615 4.70 0.00 0.00 3.28
6359 8458 9.965824 AGAATTTTGTACAAAGTGAGGTATTTG 57.034 29.630 19.72 0.00 41.22 2.32
6391 8490 2.014128 CTGTTTGTCGGTGACCTGTTT 58.986 47.619 0.00 0.00 0.00 2.83
6399 8498 3.564225 GTCGGTGACCTGTTTGAAATCTT 59.436 43.478 0.00 0.00 0.00 2.40
6537 8640 3.551454 GCGCACTTCCATGCATTTATCAT 60.551 43.478 0.30 0.00 46.47 2.45
6594 8700 4.466726 GGACTTAGACTAGTCACAATGGGT 59.533 45.833 24.44 11.65 45.07 4.51
6601 8707 6.254522 AGACTAGTCACAATGGGTAGTAACT 58.745 40.000 24.44 0.00 0.00 2.24
6604 8710 8.064336 ACTAGTCACAATGGGTAGTAACTTAG 57.936 38.462 0.00 0.00 0.00 2.18
6616 8722 9.182214 TGGGTAGTAACTTAGACTAGTAACATG 57.818 37.037 0.00 0.00 30.08 3.21
6664 8772 6.497259 ACCTCCATAGTGGGTAGTAACATATG 59.503 42.308 0.00 0.00 38.32 1.78
6668 8776 7.346175 TCCATAGTGGGTAGTAACATATGTGTT 59.654 37.037 9.63 12.73 43.67 3.32
6679 8787 5.648178 AACATATGTGTTGTGTCATGCAT 57.352 34.783 9.63 0.00 46.43 3.96
6681 8789 4.701171 ACATATGTGTTGTGTCATGCATCA 59.299 37.500 7.78 0.00 34.01 3.07
6694 8802 8.183536 TGTGTCATGCATCACTTCATTTATTAC 58.816 33.333 16.78 0.00 35.82 1.89
6698 8806 7.909641 TCATGCATCACTTCATTTATTACGTTG 59.090 33.333 0.00 0.00 0.00 4.10
6717 8825 6.513180 ACGTTGTAGACTCATCTTTTCTTGA 58.487 36.000 0.00 0.00 36.29 3.02
6718 8826 7.155328 ACGTTGTAGACTCATCTTTTCTTGAT 58.845 34.615 0.00 0.00 36.29 2.57
6758 8866 4.073293 ACTAGCTATGTTACCACATGCC 57.927 45.455 0.00 0.00 43.92 4.40
6759 8867 3.711704 ACTAGCTATGTTACCACATGCCT 59.288 43.478 0.00 0.00 43.92 4.75
6775 8883 6.320672 CCACATGCCTCTCTTTCTTCATTAAT 59.679 38.462 0.00 0.00 0.00 1.40
6778 8886 8.897752 ACATGCCTCTCTTTCTTCATTAATTAC 58.102 33.333 0.00 0.00 0.00 1.89
6779 8887 8.896744 CATGCCTCTCTTTCTTCATTAATTACA 58.103 33.333 0.00 0.00 0.00 2.41
6788 8896 9.590451 CTTTCTTCATTAATTACATGCCACATT 57.410 29.630 0.00 0.00 0.00 2.71
6802 8910 8.995027 ACATGCCACATTATCTATTTTTCCTA 57.005 30.769 0.00 0.00 0.00 2.94
6804 8912 9.288576 CATGCCACATTATCTATTTTTCCTAGA 57.711 33.333 0.00 0.00 0.00 2.43
6821 8929 9.967451 TTTTCCTAGATAAATGTGATGTTACCA 57.033 29.630 0.00 0.00 0.00 3.25
6836 8944 4.427637 TGTTACCACCTATGTTACTCCCA 58.572 43.478 0.00 0.00 0.00 4.37
6837 8945 4.223477 TGTTACCACCTATGTTACTCCCAC 59.777 45.833 0.00 0.00 0.00 4.61
6839 8947 2.838202 ACCACCTATGTTACTCCCACTG 59.162 50.000 0.00 0.00 0.00 3.66
6840 8948 2.838202 CCACCTATGTTACTCCCACTGT 59.162 50.000 0.00 0.00 0.00 3.55
6841 8949 3.369471 CCACCTATGTTACTCCCACTGTG 60.369 52.174 0.00 0.00 0.00 3.66
6863 8972 5.354792 GTGGGTAGTCTTAGACTAGTCACAG 59.645 48.000 29.24 18.08 44.42 3.66
6876 8985 3.753294 AGTCACAGTGGGAGTAACTTG 57.247 47.619 0.00 0.00 0.00 3.16
6893 9002 7.948357 AGTAACTTGACTAGTAACATCACACA 58.052 34.615 0.00 0.00 35.54 3.72
6897 9006 8.677148 ACTTGACTAGTAACATCACACATTTT 57.323 30.769 0.00 0.00 34.56 1.82
7002 9111 9.725019 ACACATTTCAAGACATAATGAGTCTAA 57.275 29.630 0.00 0.00 45.11 2.10
7041 9159 6.166279 TCTTTCATGAGGCAAGTTACTACTG 58.834 40.000 5.71 0.00 34.01 2.74
7193 9316 6.480320 GCATCTTCAATAGGTGACGTATCTTT 59.520 38.462 0.00 0.00 37.13 2.52
7355 9481 0.035056 GCATTACACCTGGCCTCTGT 60.035 55.000 3.32 4.98 0.00 3.41
7399 9525 7.836842 ACCATAACCAATATCAAGTTCCAAAC 58.163 34.615 0.00 0.00 0.00 2.93
7437 9564 6.933521 GCAGAATACAAGTATCATGTGGAGAT 59.066 38.462 0.00 0.00 32.27 2.75
7490 9634 8.657387 TTCATGTTGGGTAAAAATATCCTTCA 57.343 30.769 0.00 0.00 0.00 3.02
7512 9656 5.071653 TCATTATAGCCTCCAAGCATGTACA 59.928 40.000 0.00 0.00 34.23 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.262405 ACAGGAAGGCGTTTCTATGGTTA 59.738 43.478 0.00 0.00 36.03 2.85
131 132 1.165907 TTCTGTGGCCAACTTGAGCG 61.166 55.000 7.24 0.00 0.00 5.03
205 206 4.397420 TGATTGTGGTATTGAGTGCAGTT 58.603 39.130 0.00 0.00 0.00 3.16
908 1116 2.353839 GCGCATAAAGCCGCCATG 60.354 61.111 0.30 0.00 41.38 3.66
963 1171 0.036306 CCGGCCACTTTAAGGACACT 59.964 55.000 2.24 0.00 31.91 3.55
992 1200 3.177249 GGTACGACGTGCTTCGCC 61.177 66.667 15.69 2.53 43.06 5.54
1001 1209 2.223433 GGTCTCTGGTTATGGTACGACG 60.223 54.545 0.00 0.00 0.00 5.12
1033 1280 1.816863 GAGGAAGCACGGACCTCACA 61.817 60.000 0.00 0.00 46.42 3.58
1188 1435 3.462678 GAGGAGGTGAGGCCCGTC 61.463 72.222 0.00 0.00 38.26 4.79
2267 2545 9.944663 GTCATCACAGTTTACTTCATTTTTGTA 57.055 29.630 0.00 0.00 0.00 2.41
2289 2567 8.731275 TCCAATGTAAACAAATCGATAGTCAT 57.269 30.769 0.00 0.00 37.40 3.06
2356 2634 5.418840 ACAGAATCCCAATTTCGTAAAGCAT 59.581 36.000 0.00 0.00 0.00 3.79
2675 2953 2.315925 TTCCTCTTATTGGCAGCTCG 57.684 50.000 0.00 0.00 0.00 5.03
2699 2977 3.370953 GGTCCAGGAGTATGCAGTGAATT 60.371 47.826 0.00 0.00 0.00 2.17
2747 3025 8.880991 TGGAGTCACTAGTATTTCTAACTTCT 57.119 34.615 0.00 0.00 0.00 2.85
2780 3058 3.758755 AGCATCACAGAACACAGAAGA 57.241 42.857 0.00 0.00 0.00 2.87
2781 3059 4.309933 TGTAGCATCACAGAACACAGAAG 58.690 43.478 0.00 0.00 0.00 2.85
3855 4148 4.563580 GCTTACACTGGATGACTGAAAGGA 60.564 45.833 0.00 0.00 39.30 3.36
3904 4512 5.812642 ACTATTCTCGGACAAATGTGATGAC 59.187 40.000 0.00 0.00 0.00 3.06
3955 4563 1.383943 ATGGATGGCCTCCCGTGTA 60.384 57.895 15.98 1.01 44.23 2.90
4219 4828 3.298619 CATCCACCATGAATTAAGGCCA 58.701 45.455 5.01 0.00 33.80 5.36
4321 4936 5.885912 GGATGTTAGACAAAATTGCTCCCTA 59.114 40.000 0.00 0.00 0.00 3.53
4456 5077 4.675146 GCACGAATGGCAGATTAACATTGT 60.675 41.667 0.00 0.00 35.17 2.71
4464 5085 2.785868 GGAGCACGAATGGCAGATT 58.214 52.632 0.00 0.00 0.00 2.40
4524 5147 2.363018 CCTCACCGGAGAGAGCCA 60.363 66.667 28.09 0.00 44.26 4.75
4825 5475 3.365291 TTCGCCCCGGAACTCGATG 62.365 63.158 0.73 0.00 42.43 3.84
4856 5509 4.350520 TCATTGCCAGGTATATCCATCACA 59.649 41.667 0.00 0.00 39.02 3.58
4932 5587 1.961394 GGTTTTCACCCTGAAGAACCC 59.039 52.381 12.97 0.00 39.20 4.11
4968 5624 1.220749 CGTCACCGGATCCAACCAT 59.779 57.895 9.46 0.00 0.00 3.55
5026 5686 3.868757 TGGACGACGAGATTCTTCAAT 57.131 42.857 0.00 0.00 0.00 2.57
5164 5962 3.941188 CACACACCCGGCCTCTGT 61.941 66.667 0.00 0.00 0.00 3.41
5284 6082 5.730550 ACCACGTCTAAAATAGCAGAATCA 58.269 37.500 0.00 0.00 0.00 2.57
5433 6231 3.555547 TGTCAACAGTCACTCGTTTCATG 59.444 43.478 0.00 0.00 0.00 3.07
5434 6232 3.792401 TGTCAACAGTCACTCGTTTCAT 58.208 40.909 0.00 0.00 0.00 2.57
5441 6239 4.143242 CGTTCATGATGTCAACAGTCACTC 60.143 45.833 0.00 0.00 0.00 3.51
5448 6246 3.118905 TGGTCGTTCATGATGTCAACA 57.881 42.857 0.00 0.00 0.00 3.33
5670 7769 6.775142 TGATAGATATAGTATCCTCCTGCAGC 59.225 42.308 8.66 0.00 0.00 5.25
6087 8186 0.912486 ACTTTAGCATCCTCGGGCTT 59.088 50.000 0.00 0.00 41.41 4.35
6359 8458 3.365364 CCGACAAACAGCCTTTCTGATTC 60.365 47.826 0.00 0.00 45.72 2.52
6439 8538 3.384789 CAGATCCTCAGGTCCACGAATTA 59.615 47.826 0.00 0.00 0.00 1.40
6537 8640 5.476599 CCTGGTTATGAAAATCCAACAGTCA 59.523 40.000 0.00 0.00 0.00 3.41
6616 8722 8.848182 AGGTAGTAACATAGACTAGTAACATGC 58.152 37.037 0.00 0.00 30.08 4.06
6620 8728 8.970859 TGGAGGTAGTAACATAGACTAGTAAC 57.029 38.462 0.00 0.00 30.08 2.50
6623 8731 8.947305 ACTATGGAGGTAGTAACATAGACTAGT 58.053 37.037 15.14 0.00 43.28 2.57
6628 8736 6.125979 ACCCACTATGGAGGTAGTAACATAGA 60.126 42.308 15.14 0.00 43.28 1.98
6643 8751 7.062749 ACACATATGTTACTACCCACTATGG 57.937 40.000 5.37 0.00 34.46 2.74
6664 8772 3.003585 TGAAGTGATGCATGACACAACAC 59.996 43.478 18.76 11.21 39.18 3.32
6668 8776 6.762702 ATAAATGAAGTGATGCATGACACA 57.237 33.333 18.76 16.77 39.18 3.72
6679 8787 9.350357 GAGTCTACAACGTAATAAATGAAGTGA 57.650 33.333 0.00 0.00 0.00 3.41
6681 8789 9.871238 ATGAGTCTACAACGTAATAAATGAAGT 57.129 29.630 0.00 0.00 0.00 3.01
6694 8802 7.588143 ATCAAGAAAAGATGAGTCTACAACG 57.412 36.000 0.00 0.00 33.30 4.10
6698 8806 9.593134 ACACATATCAAGAAAAGATGAGTCTAC 57.407 33.333 0.00 0.00 33.30 2.59
6755 8863 8.896744 CATGTAATTAATGAAGAAAGAGAGGCA 58.103 33.333 0.00 0.00 0.00 4.75
6758 8866 8.896744 TGGCATGTAATTAATGAAGAAAGAGAG 58.103 33.333 10.14 0.00 0.00 3.20
6759 8867 8.677300 GTGGCATGTAATTAATGAAGAAAGAGA 58.323 33.333 0.00 0.00 0.00 3.10
6775 8883 9.420118 AGGAAAAATAGATAATGTGGCATGTAA 57.580 29.630 0.00 0.00 0.00 2.41
6778 8886 9.288576 TCTAGGAAAAATAGATAATGTGGCATG 57.711 33.333 0.00 0.00 0.00 4.06
6795 8903 9.967451 TGGTAACATCACATTTATCTAGGAAAA 57.033 29.630 0.00 0.00 46.17 2.29
6820 8928 3.369471 CCACAGTGGGAGTAACATAGGTG 60.369 52.174 12.40 0.00 32.67 4.00
6821 8929 2.838202 CCACAGTGGGAGTAACATAGGT 59.162 50.000 12.40 0.00 32.67 3.08
6836 8944 5.013913 TGACTAGTCTAAGACTACCCACAGT 59.986 44.000 23.01 0.00 41.51 3.55
6837 8945 5.354792 GTGACTAGTCTAAGACTACCCACAG 59.645 48.000 23.01 0.00 41.51 3.66
6839 8947 5.251764 TGTGACTAGTCTAAGACTACCCAC 58.748 45.833 23.01 9.72 41.51 4.61
6840 8948 5.013913 ACTGTGACTAGTCTAAGACTACCCA 59.986 44.000 23.01 0.00 41.51 4.51
6841 8949 5.354792 CACTGTGACTAGTCTAAGACTACCC 59.645 48.000 23.01 0.00 41.51 3.69
6843 8951 5.354792 CCCACTGTGACTAGTCTAAGACTAC 59.645 48.000 23.01 11.64 41.51 2.73
6844 8952 5.250082 TCCCACTGTGACTAGTCTAAGACTA 59.750 44.000 23.01 0.00 41.51 2.59
6847 8956 4.043059 ACTCCCACTGTGACTAGTCTAAGA 59.957 45.833 23.01 9.51 0.00 2.10
6863 8972 6.336842 TGTTACTAGTCAAGTTACTCCCAC 57.663 41.667 0.00 0.00 38.33 4.61
6897 9006 7.884877 AGCTGCCACATAAGCAATCTTATATTA 59.115 33.333 0.00 0.00 42.10 0.98
6902 9011 3.889815 AGCTGCCACATAAGCAATCTTA 58.110 40.909 0.00 0.00 42.06 2.10
7027 9138 6.755607 GGAGTAACATACAGTAGTAACTTGCC 59.244 42.308 0.00 0.00 31.97 4.52
7028 9139 6.755607 GGGAGTAACATACAGTAGTAACTTGC 59.244 42.308 0.00 0.00 31.97 4.01
7029 9140 7.093640 TGGGGAGTAACATACAGTAGTAACTTG 60.094 40.741 0.00 0.00 31.97 3.16
7030 9141 6.955851 TGGGGAGTAACATACAGTAGTAACTT 59.044 38.462 0.00 0.00 31.97 2.66
7041 9159 3.679083 GCTCACAGTGGGGAGTAACATAC 60.679 52.174 1.60 0.00 33.66 2.39
7069 9187 3.096092 TCCAAAATGGGCTGGTTATGTC 58.904 45.455 0.00 0.00 38.32 3.06
7193 9316 8.178964 GTGATGTAAAACTACTTTTGTGTGACA 58.821 33.333 0.00 0.00 31.74 3.58
7355 9481 8.620416 GTTATGGTTGTGTGCATCTCAATTATA 58.380 33.333 0.00 0.00 33.19 0.98
7399 9525 8.369218 ACTTGTATTCTGCCTTTTTCAATTTG 57.631 30.769 0.00 0.00 0.00 2.32
7490 9634 5.163205 TGTGTACATGCTTGGAGGCTATAAT 60.163 40.000 0.00 0.00 0.00 1.28
7493 9637 2.505407 TGTGTACATGCTTGGAGGCTAT 59.495 45.455 0.00 0.00 0.00 2.97
7501 9645 2.143122 ACGAAGGTGTGTACATGCTTG 58.857 47.619 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.