Multiple sequence alignment - TraesCS6B01G100800

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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 TraesCS6B01G100800 chr6B 100.000 4322 0 0 1 4322 79154235 79149914 0.000000e+00 7982.0
1 TraesCS6B01G100800 chr6B 96.985 1957 57 2 2368 4322 6147393 6145437 0.000000e+00 3286.0
2 TraesCS6B01G100800 chr6B 95.081 1423 56 8 951 2369 6148888 6147476 0.000000e+00 2228.0
3 TraesCS6B01G100800 chr6B 90.556 953 78 8 1 944 536857840 536858789 0.000000e+00 1251.0
4 TraesCS6B01G100800 chr6B 77.518 814 164 17 1 800 696846312 696845504 5.060000e-129 472.0
5 TraesCS6B01G100800 chr6B 87.328 363 36 7 592 945 536852810 536853171 1.450000e-109 407.0
6 TraesCS6B01G100800 chr6B 90.064 312 27 3 4014 4322 620274153 620273843 6.730000e-108 401.0
7 TraesCS6B01G100800 chr6B 79.535 430 86 2 23 451 316455902 316456330 5.430000e-79 305.0
8 TraesCS6B01G100800 chr6B 90.972 144 12 1 3411 3554 627577999 627578141 4.410000e-45 193.0
9 TraesCS6B01G100800 chr6B 95.161 124 2 2 2804 2926 644062767 644062887 4.410000e-45 193.0
10 TraesCS6B01G100800 chr1B 97.778 945 20 1 1 944 321708171 321709115 0.000000e+00 1628.0
11 TraesCS6B01G100800 chr1B 90.356 954 81 7 1 944 157461767 157460815 0.000000e+00 1242.0
12 TraesCS6B01G100800 chr1B 90.959 730 59 2 3593 4322 127992173 127992895 0.000000e+00 976.0
13 TraesCS6B01G100800 chr1B 96.591 352 11 1 595 945 321703152 321703503 2.240000e-162 582.0
14 TraesCS6B01G100800 chr1B 87.580 467 56 1 3593 4059 675991039 675991503 1.370000e-149 540.0
15 TraesCS6B01G100800 chr1B 87.812 361 33 7 595 945 157466797 157466438 3.110000e-111 412.0
16 TraesCS6B01G100800 chr3A 91.096 730 58 2 3593 4322 715535686 715536408 0.000000e+00 981.0
17 TraesCS6B01G100800 chr3A 90.879 307 28 0 4016 4322 528678436 528678130 3.110000e-111 412.0
18 TraesCS6B01G100800 chr3A 88.679 212 15 1 2606 2808 631818878 631819089 2.580000e-62 250.0
19 TraesCS6B01G100800 chr3A 94.355 124 3 2 2804 2926 726475342 726475462 2.050000e-43 187.0
20 TraesCS6B01G100800 chr3A 74.174 333 66 18 595 912 604854902 604854575 2.110000e-23 121.0
21 TraesCS6B01G100800 chr3A 89.855 69 6 1 1704 1771 260681438 260681370 2.140000e-13 87.9
22 TraesCS6B01G100800 chr2D 90.959 730 57 4 3593 4322 564388799 564388079 0.000000e+00 974.0
23 TraesCS6B01G100800 chr2D 73.762 606 139 17 6 601 66847549 66846954 2.020000e-53 220.0
24 TraesCS6B01G100800 chr2D 96.774 124 3 1 2804 2926 3609258 3609381 5.670000e-49 206.0
25 TraesCS6B01G100800 chr7D 90.822 730 60 4 3593 4322 451485229 451484507 0.000000e+00 970.0
26 TraesCS6B01G100800 chr7D 92.950 539 27 5 1173 1710 638188574 638188046 0.000000e+00 774.0
27 TraesCS6B01G100800 chr7B 89.726 730 68 5 3593 4322 504998931 504998209 0.000000e+00 926.0
28 TraesCS6B01G100800 chr7B 85.158 539 54 12 1177 1710 734772195 734772712 2.960000e-146 529.0
29 TraesCS6B01G100800 chr7B 90.079 252 24 1 3346 3596 112653840 112654091 4.170000e-85 326.0
30 TraesCS6B01G100800 chr1A 92.224 643 47 3 1704 2345 45044460 45045100 0.000000e+00 907.0
31 TraesCS6B01G100800 chr1A 90.206 582 54 3 1718 2298 202616992 202616413 0.000000e+00 756.0
32 TraesCS6B01G100800 chr1A 90.418 574 52 3 1726 2298 202568180 202567609 0.000000e+00 752.0
33 TraesCS6B01G100800 chr1A 90.756 476 44 0 3847 4322 3813899 3814374 1.700000e-178 636.0
34 TraesCS6B01G100800 chr1A 86.038 530 73 1 3593 4122 80619321 80618793 6.270000e-158 568.0
35 TraesCS6B01G100800 chr1A 92.784 388 27 1 2421 2808 45045096 45045482 1.050000e-155 560.0
36 TraesCS6B01G100800 chr1A 95.968 124 4 1 2804 2926 346746298 346746421 2.640000e-47 200.0
37 TraesCS6B01G100800 chr1A 84.000 175 17 8 945 1119 45044259 45044422 1.610000e-34 158.0
38 TraesCS6B01G100800 chr7A 89.891 643 46 11 1704 2345 66903739 66904363 0.000000e+00 809.0
39 TraesCS6B01G100800 chr7A 91.280 539 34 6 1184 1714 727897793 727898326 0.000000e+00 723.0
40 TraesCS6B01G100800 chr7A 93.814 388 19 3 2421 2808 66904359 66904741 2.900000e-161 579.0
41 TraesCS6B01G100800 chr7A 88.916 415 40 3 2919 3327 193409778 193410192 1.390000e-139 507.0
42 TraesCS6B01G100800 chr7A 93.467 199 11 2 3399 3596 193437005 193437202 1.180000e-75 294.0
43 TraesCS6B01G100800 chr7A 96.774 124 3 1 2804 2926 369644349 369644472 5.670000e-49 206.0
44 TraesCS6B01G100800 chr7A 91.860 86 7 0 2804 2889 193409694 193409779 2.110000e-23 121.0
45 TraesCS6B01G100800 chr3D 94.331 441 23 2 1704 2143 612660014 612660453 0.000000e+00 675.0
46 TraesCS6B01G100800 chr3D 88.931 533 46 4 2806 3332 116502415 116501890 0.000000e+00 645.0
47 TraesCS6B01G100800 chr3D 79.207 933 159 30 5 915 562387870 562386951 2.210000e-172 616.0
48 TraesCS6B01G100800 chr3D 95.312 320 14 1 2490 2808 612660502 612660821 1.390000e-139 507.0
49 TraesCS6B01G100800 chr3D 90.476 252 23 1 3346 3596 218737101 218737352 8.960000e-87 331.0
50 TraesCS6B01G100800 chr3D 88.208 212 16 1 2606 2808 488269749 488269960 1.200000e-60 244.0
51 TraesCS6B01G100800 chr3D 88.136 177 12 6 945 1121 612659811 612659978 7.330000e-48 202.0
52 TraesCS6B01G100800 chr6D 79.167 936 162 28 1 915 71529590 71528667 6.140000e-173 617.0
53 TraesCS6B01G100800 chr6A 87.476 527 65 1 3593 4119 31919727 31920252 1.330000e-169 606.0
54 TraesCS6B01G100800 chr4D 87.500 520 63 2 3600 4119 244319056 244318539 2.220000e-167 599.0
55 TraesCS6B01G100800 chr4D 90.110 182 17 1 3416 3596 244327233 244327052 7.230000e-58 235.0
56 TraesCS6B01G100800 chr5B 80.843 830 89 37 1796 2609 708841234 708842009 4.810000e-164 588.0
57 TraesCS6B01G100800 chr5B 85.311 531 76 2 3593 4122 170195020 170194491 8.170000e-152 547.0
58 TraesCS6B01G100800 chr5A 93.041 388 26 1 2421 2808 709104351 709103965 2.260000e-157 566.0
59 TraesCS6B01G100800 chr5A 91.617 334 27 1 2015 2348 709122425 709122093 1.100000e-125 460.0
60 TraesCS6B01G100800 chr5A 89.744 312 29 3 1709 2019 709151894 709151585 3.130000e-106 396.0
61 TraesCS6B01G100800 chr5A 83.590 195 19 7 945 1137 709152101 709151918 2.070000e-38 171.0
62 TraesCS6B01G100800 chr4B 84.717 530 80 1 3593 4122 584688441 584688969 2.960000e-146 529.0
63 TraesCS6B01G100800 chr5D 88.916 415 40 3 2919 3327 528155876 528156290 1.390000e-139 507.0
64 TraesCS6B01G100800 chr5D 73.841 604 142 13 6 601 395936223 395935628 4.350000e-55 226.0
65 TraesCS6B01G100800 chr5D 94.186 86 5 0 2804 2889 528155792 528155877 9.750000e-27 132.0
66 TraesCS6B01G100800 chr4A 82.042 529 80 9 3593 4119 324866269 324866784 1.850000e-118 436.0
67 TraesCS6B01G100800 chr1D 83.333 360 43 11 2976 3327 487165033 487165383 2.510000e-82 316.0
68 TraesCS6B01G100800 chr3B 88.571 210 17 2 2606 2808 651276088 651276297 9.280000e-62 248.0


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 TraesCS6B01G100800 chr6B 79149914 79154235 4321 True 7982.000000 7982 100.000000 1 4322 1 chr6B.!!$R1 4321
1 TraesCS6B01G100800 chr6B 6145437 6148888 3451 True 2757.000000 3286 96.033000 951 4322 2 chr6B.!!$R4 3371
2 TraesCS6B01G100800 chr6B 536857840 536858789 949 False 1251.000000 1251 90.556000 1 944 1 chr6B.!!$F3 943
3 TraesCS6B01G100800 chr6B 696845504 696846312 808 True 472.000000 472 77.518000 1 800 1 chr6B.!!$R3 799
4 TraesCS6B01G100800 chr1B 321708171 321709115 944 False 1628.000000 1628 97.778000 1 944 1 chr1B.!!$F3 943
5 TraesCS6B01G100800 chr1B 157460815 157461767 952 True 1242.000000 1242 90.356000 1 944 1 chr1B.!!$R1 943
6 TraesCS6B01G100800 chr1B 127992173 127992895 722 False 976.000000 976 90.959000 3593 4322 1 chr1B.!!$F1 729
7 TraesCS6B01G100800 chr3A 715535686 715536408 722 False 981.000000 981 91.096000 3593 4322 1 chr3A.!!$F2 729
8 TraesCS6B01G100800 chr2D 564388079 564388799 720 True 974.000000 974 90.959000 3593 4322 1 chr2D.!!$R2 729
9 TraesCS6B01G100800 chr2D 66846954 66847549 595 True 220.000000 220 73.762000 6 601 1 chr2D.!!$R1 595
10 TraesCS6B01G100800 chr7D 451484507 451485229 722 True 970.000000 970 90.822000 3593 4322 1 chr7D.!!$R1 729
11 TraesCS6B01G100800 chr7D 638188046 638188574 528 True 774.000000 774 92.950000 1173 1710 1 chr7D.!!$R2 537
12 TraesCS6B01G100800 chr7B 504998209 504998931 722 True 926.000000 926 89.726000 3593 4322 1 chr7B.!!$R1 729
13 TraesCS6B01G100800 chr7B 734772195 734772712 517 False 529.000000 529 85.158000 1177 1710 1 chr7B.!!$F2 533
14 TraesCS6B01G100800 chr1A 202616413 202616992 579 True 756.000000 756 90.206000 1718 2298 1 chr1A.!!$R3 580
15 TraesCS6B01G100800 chr1A 202567609 202568180 571 True 752.000000 752 90.418000 1726 2298 1 chr1A.!!$R2 572
16 TraesCS6B01G100800 chr1A 80618793 80619321 528 True 568.000000 568 86.038000 3593 4122 1 chr1A.!!$R1 529
17 TraesCS6B01G100800 chr1A 45044259 45045482 1223 False 541.666667 907 89.669333 945 2808 3 chr1A.!!$F3 1863
18 TraesCS6B01G100800 chr7A 727897793 727898326 533 False 723.000000 723 91.280000 1184 1714 1 chr7A.!!$F3 530
19 TraesCS6B01G100800 chr7A 66903739 66904741 1002 False 694.000000 809 91.852500 1704 2808 2 chr7A.!!$F4 1104
20 TraesCS6B01G100800 chr3D 116501890 116502415 525 True 645.000000 645 88.931000 2806 3332 1 chr3D.!!$R1 526
21 TraesCS6B01G100800 chr3D 562386951 562387870 919 True 616.000000 616 79.207000 5 915 1 chr3D.!!$R2 910
22 TraesCS6B01G100800 chr3D 612659811 612660821 1010 False 461.333333 675 92.593000 945 2808 3 chr3D.!!$F3 1863
23 TraesCS6B01G100800 chr6D 71528667 71529590 923 True 617.000000 617 79.167000 1 915 1 chr6D.!!$R1 914
24 TraesCS6B01G100800 chr6A 31919727 31920252 525 False 606.000000 606 87.476000 3593 4119 1 chr6A.!!$F1 526
25 TraesCS6B01G100800 chr4D 244318539 244319056 517 True 599.000000 599 87.500000 3600 4119 1 chr4D.!!$R1 519
26 TraesCS6B01G100800 chr5B 708841234 708842009 775 False 588.000000 588 80.843000 1796 2609 1 chr5B.!!$F1 813
27 TraesCS6B01G100800 chr5B 170194491 170195020 529 True 547.000000 547 85.311000 3593 4122 1 chr5B.!!$R1 529
28 TraesCS6B01G100800 chr5A 709151585 709152101 516 True 283.500000 396 86.667000 945 2019 2 chr5A.!!$R3 1074
29 TraesCS6B01G100800 chr4B 584688441 584688969 528 False 529.000000 529 84.717000 3593 4122 1 chr4B.!!$F1 529
30 TraesCS6B01G100800 chr5D 395935628 395936223 595 True 226.000000 226 73.841000 6 601 1 chr5D.!!$R1 595
31 TraesCS6B01G100800 chr4A 324866269 324866784 515 False 436.000000 436 82.042000 3593 4119 1 chr4A.!!$F1 526

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
964 980 1.306226 CCCCTCCCGGTTCTTCTCT 60.306 63.158 0.00 0.0 0.00 3.10 F
1448 1477 0.830444 ACTTGGCTGGACGGACAGTA 60.830 55.000 9.83 0.0 40.59 2.74 F
2030 2061 1.680522 CGCCTCCTCTGGTACTGCAT 61.681 60.000 0.00 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 1859 2.418609 CGATGTCCACTACCTGCATCAA 60.419 50.000 0.00 0.00 36.64 2.57 R
3027 3172 1.209128 GACGCACGATTCAGGTATGG 58.791 55.000 0.00 0.00 0.00 2.74 R
3973 4121 1.372872 CATCTGTGTGACGCGGTCA 60.373 57.895 12.47 9.29 40.50 4.02 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
206 207 4.083377 GCAAAACAAGTTTTATGGCCCATG 60.083 41.667 6.46 0.00 40.45 3.66
291 292 4.510038 ACATCCAGTTTTTCATGTCAGC 57.490 40.909 0.00 0.00 0.00 4.26
382 383 2.107552 ACAGTTAAAACAGGGCCAGCTA 59.892 45.455 6.18 0.00 0.00 3.32
484 485 3.055458 TGAAGATGCAACGTGGGAAGATA 60.055 43.478 0.00 0.00 0.00 1.98
734 747 7.416022 CGTAGATCAAGTCTTACCGTTATTCT 58.584 38.462 0.00 0.00 38.42 2.40
809 823 2.596923 TGGCTGGCAAACGCATCA 60.597 55.556 0.00 0.00 0.00 3.07
890 905 2.434359 GGCGACGTTCTTCCCCAG 60.434 66.667 0.00 0.00 0.00 4.45
917 933 4.585162 TCCTTCTCAAATCCCTAGATCGAC 59.415 45.833 0.00 0.00 0.00 4.20
964 980 1.306226 CCCCTCCCGGTTCTTCTCT 60.306 63.158 0.00 0.00 0.00 3.10
968 984 1.834263 CCTCCCGGTTCTTCTCTGATT 59.166 52.381 0.00 0.00 0.00 2.57
970 986 3.451178 CCTCCCGGTTCTTCTCTGATTTA 59.549 47.826 0.00 0.00 0.00 1.40
975 991 4.740695 CCGGTTCTTCTCTGATTTATCGTC 59.259 45.833 0.00 0.00 0.00 4.20
1039 1056 2.214216 TACACGTCCTGCAGGCCTT 61.214 57.895 28.91 7.60 34.44 4.35
1040 1057 2.167398 TACACGTCCTGCAGGCCTTC 62.167 60.000 28.91 15.91 34.44 3.46
1041 1058 4.379243 ACGTCCTGCAGGCCTTCG 62.379 66.667 28.91 26.77 34.44 3.79
1042 1059 4.379243 CGTCCTGCAGGCCTTCGT 62.379 66.667 28.91 0.00 34.44 3.85
1045 1062 4.379243 CCTGCAGGCCTTCGTCGT 62.379 66.667 22.33 0.00 0.00 4.34
1047 1064 3.865929 CTGCAGGCCTTCGTCGTGT 62.866 63.158 0.00 0.00 0.00 4.49
1048 1065 2.260434 GCAGGCCTTCGTCGTGTA 59.740 61.111 0.00 0.00 0.00 2.90
1049 1066 2.092882 GCAGGCCTTCGTCGTGTAC 61.093 63.158 0.00 0.00 0.00 2.90
1050 1067 1.287815 CAGGCCTTCGTCGTGTACA 59.712 57.895 0.00 0.00 0.00 2.90
1051 1068 1.007336 CAGGCCTTCGTCGTGTACAC 61.007 60.000 16.32 16.32 0.00 2.90
1148 1165 1.666011 GTGACGGCAACTCCTCTCA 59.334 57.895 0.00 0.00 0.00 3.27
1199 1216 1.736645 CCGAGATGTTTGCGACGGT 60.737 57.895 0.00 0.00 36.38 4.83
1200 1217 1.289109 CCGAGATGTTTGCGACGGTT 61.289 55.000 0.00 0.00 36.38 4.44
1221 1238 2.345991 CGGTGGGCGGAGAAGAAA 59.654 61.111 0.00 0.00 0.00 2.52
1257 1274 2.791927 CCGATCGAGCTCACGACA 59.208 61.111 18.66 0.00 44.84 4.35
1258 1275 1.136774 CCGATCGAGCTCACGACAA 59.863 57.895 18.66 0.00 44.84 3.18
1261 1278 1.134530 GATCGAGCTCACGACAACGG 61.135 60.000 15.40 0.00 44.84 4.44
1352 1369 1.885850 ACGTTTGGGAGCACGTCAC 60.886 57.895 0.00 0.00 46.52 3.67
1400 1422 2.166821 GAGATTCATCTCCGCATGCT 57.833 50.000 17.13 0.00 45.88 3.79
1448 1477 0.830444 ACTTGGCTGGACGGACAGTA 60.830 55.000 9.83 0.00 40.59 2.74
1533 1562 3.366052 TTTTCTTCAGGATGTAGGCCC 57.634 47.619 0.00 0.00 33.93 5.80
1621 1650 3.201487 TCAGGCTCATTTCTGACCATGAT 59.799 43.478 0.00 0.00 35.37 2.45
1847 1878 2.305635 TGTTGATGCAGGTAGTGGACAT 59.694 45.455 0.00 0.00 0.00 3.06
2030 2061 1.680522 CGCCTCCTCTGGTACTGCAT 61.681 60.000 0.00 0.00 0.00 3.96
2037 2068 3.776969 TCCTCTGGTACTGCATCATCTTT 59.223 43.478 0.00 0.00 0.00 2.52
2039 2070 3.875727 CTCTGGTACTGCATCATCTTTGG 59.124 47.826 0.00 0.00 0.00 3.28
2099 2131 5.230182 CCTCACTTTGCTCGCATATATACA 58.770 41.667 0.00 0.00 0.00 2.29
2126 2158 5.105269 TCAATTAGTGGTACGTTCATGGCTA 60.105 40.000 0.00 0.00 0.00 3.93
2182 2217 7.001674 TCTTCAGCAGAAAATTGGGTACTTAA 58.998 34.615 0.00 0.00 32.35 1.85
2225 2260 7.996098 ATAAATGTGCCACTTTAGTGTTAGT 57.004 32.000 8.91 0.00 44.21 2.24
2380 2510 5.036117 ACTGTGTTCTATGTGACAACCTT 57.964 39.130 0.00 0.00 0.00 3.50
2468 2605 5.893255 TGGCGAACCCTTAGTAGAGTTATTA 59.107 40.000 0.00 0.00 33.59 0.98
2544 2682 9.559958 GTTGTATGTTGGATCTGTAATTTTCTG 57.440 33.333 0.00 0.00 0.00 3.02
2765 2905 3.521531 TGGTTACCTCATAGAACATGCCA 59.478 43.478 2.07 0.00 0.00 4.92
2783 2923 8.353423 ACATGCCAAAAGTCAAAGTTATAGAT 57.647 30.769 0.00 0.00 0.00 1.98
2923 3063 8.162878 TCTCATGTAGGAGTAATAGGTTAACG 57.837 38.462 0.00 0.00 36.30 3.18
3027 3172 1.544246 GTGGTTTGGCTATTGTGGTCC 59.456 52.381 0.00 0.00 0.00 4.46
3136 3281 3.855689 AAGCACCTGTCAATTACATGC 57.144 42.857 0.00 0.00 42.14 4.06
3194 3339 1.084370 AAGCGTTAGTCTGATGGCGC 61.084 55.000 0.00 0.00 44.36 6.53
3219 3364 4.083484 GGTTTACCATGTGACTGCAGTTAC 60.083 45.833 29.40 29.40 34.21 2.50
3270 3415 9.836864 AGCCTTTTTCAAAATATTTCTCAAAGT 57.163 25.926 0.10 0.00 0.00 2.66
3344 3490 1.546476 GACCTGGTATCGGCATCCTAG 59.454 57.143 0.00 0.00 0.00 3.02
3395 3541 3.641436 CCACTACCACATGCATACCTCTA 59.359 47.826 0.00 0.00 0.00 2.43
3399 3545 4.613925 ACCACATGCATACCTCTATGAG 57.386 45.455 0.00 0.00 32.66 2.90
3488 3634 0.691904 TGATCCTGTGTGCATGGTCA 59.308 50.000 0.00 0.00 29.84 4.02
3504 3650 6.158598 GCATGGTCATGTTATTGTTTCAGTT 58.841 36.000 11.92 0.00 40.80 3.16
3584 3730 0.108615 CACTCTTCTACCTGGCACGG 60.109 60.000 0.00 2.01 0.00 4.94
3674 3820 9.979578 AGAATGTTAACTGTCAAATATTGCAAA 57.020 25.926 1.71 0.00 0.00 3.68
3780 3927 5.626142 TGCATTTAGTAGGTGTCTTTCCAA 58.374 37.500 0.00 0.00 0.00 3.53
3973 4121 0.110486 ACTTTGACATGAAGCCCGGT 59.890 50.000 0.00 0.00 0.00 5.28
4183 4331 8.639761 GGCTTGGTAGATACATTTAGAGAAGTA 58.360 37.037 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 207 1.273327 CCACCTTTTGAATCACCAGGC 59.727 52.381 6.78 0.00 0.00 4.85
484 485 8.658499 GGGAACGTATACTTAATGAAATCAGT 57.342 34.615 0.56 0.00 0.00 3.41
734 747 4.850680 ACAGGGTGAAACAGAACAGTAAA 58.149 39.130 0.00 0.00 39.98 2.01
809 823 6.264744 CCATCTAGGCAAATCACAGAATTCAT 59.735 38.462 8.44 0.00 0.00 2.57
890 905 5.941555 TCTAGGGATTTGAGAAGGAGAAC 57.058 43.478 0.00 0.00 0.00 3.01
917 933 0.104934 ACCCAGCCTGTATCTAGGGG 60.105 60.000 0.00 0.00 40.64 4.79
975 991 2.123640 GGAGAGGGAGAGACGGGG 60.124 72.222 0.00 0.00 0.00 5.73
1045 1062 0.973632 AAGGATGCAGGACGTGTACA 59.026 50.000 0.00 0.00 0.00 2.90
1047 1064 0.535335 GGAAGGATGCAGGACGTGTA 59.465 55.000 0.00 0.00 0.00 2.90
1048 1065 1.194781 AGGAAGGATGCAGGACGTGT 61.195 55.000 0.00 0.00 0.00 4.49
1049 1066 0.460987 GAGGAAGGATGCAGGACGTG 60.461 60.000 0.00 0.00 0.00 4.49
1050 1067 1.617947 GGAGGAAGGATGCAGGACGT 61.618 60.000 0.00 0.00 0.00 4.34
1051 1068 1.144936 GGAGGAAGGATGCAGGACG 59.855 63.158 0.00 0.00 0.00 4.79
1052 1069 0.107459 GTGGAGGAAGGATGCAGGAC 60.107 60.000 0.00 0.00 0.00 3.85
1053 1070 1.274703 GGTGGAGGAAGGATGCAGGA 61.275 60.000 0.00 0.00 0.00 3.86
1054 1071 1.225704 GGTGGAGGAAGGATGCAGG 59.774 63.158 0.00 0.00 0.00 4.85
1055 1072 0.393537 GTGGTGGAGGAAGGATGCAG 60.394 60.000 0.00 0.00 0.00 4.41
1056 1073 1.685224 GTGGTGGAGGAAGGATGCA 59.315 57.895 0.00 0.00 0.00 3.96
1128 1145 1.816863 GAGAGGAGTTGCCGTCACCA 61.817 60.000 0.00 0.00 43.43 4.17
1134 1151 0.820226 TCAGATGAGAGGAGTTGCCG 59.180 55.000 0.00 0.00 43.43 5.69
1148 1165 1.915078 CTCCCCGCACCCTTTCAGAT 61.915 60.000 0.00 0.00 0.00 2.90
1214 1231 2.065799 TCTTGGGCTTCCCTTTCTTCT 58.934 47.619 3.27 0.00 45.70 2.85
1352 1369 0.803768 CAGCAGCAGCAGTAGTACCG 60.804 60.000 3.17 0.00 45.49 4.02
1400 1422 2.642139 GACATTCCGTCGAACAGGTA 57.358 50.000 0.00 0.00 34.19 3.08
1448 1477 3.733337 ACGTTGCAAGAACAGAGAAGAT 58.267 40.909 0.00 0.00 0.00 2.40
1533 1562 0.593128 CTTGCTTGTCAAACCCCTCG 59.407 55.000 0.00 0.00 33.65 4.63
1611 1640 0.465097 GTGAGGCCCATCATGGTCAG 60.465 60.000 2.07 0.00 35.17 3.51
1621 1650 0.899717 GGAATTGCTTGTGAGGCCCA 60.900 55.000 0.00 0.00 0.00 5.36
1784 1814 3.064987 CTCTCCGCCCCTACACGTG 62.065 68.421 15.48 15.48 0.00 4.49
1828 1859 2.418609 CGATGTCCACTACCTGCATCAA 60.419 50.000 0.00 0.00 36.64 2.57
2030 2061 7.015682 GGATCTCATAGTCTTACCCAAAGATGA 59.984 40.741 0.00 0.00 45.84 2.92
2037 2068 7.451877 GTCTAATGGATCTCATAGTCTTACCCA 59.548 40.741 0.00 0.00 34.44 4.51
2039 2070 7.451877 TGGTCTAATGGATCTCATAGTCTTACC 59.548 40.741 0.00 0.00 34.44 2.85
2099 2131 5.642063 CCATGAACGTACCACTAATTGACTT 59.358 40.000 0.00 0.00 0.00 3.01
2273 2315 8.359642 AGTTTGAAGCTTGATAATTTACAGCAA 58.640 29.630 2.10 0.00 0.00 3.91
2380 2510 6.245408 ACTAAATGTGCTCCTCCAATTGTAA 58.755 36.000 4.43 0.00 0.00 2.41
2487 2624 4.406972 AGATACATAGAGCACTGCAAAGGA 59.593 41.667 3.30 0.00 0.00 3.36
2488 2625 4.701765 AGATACATAGAGCACTGCAAAGG 58.298 43.478 3.30 0.00 0.00 3.11
2923 3063 2.639286 CCTGCAGCCGTGTGTTTC 59.361 61.111 8.66 0.00 0.00 2.78
3027 3172 1.209128 GACGCACGATTCAGGTATGG 58.791 55.000 0.00 0.00 0.00 2.74
3238 3383 9.777297 AGAAATATTTTGAAAAAGGCTAGCAAA 57.223 25.926 18.24 6.06 0.00 3.68
3270 3415 3.788227 AGGTCAGGTTGCATCAAGTTA 57.212 42.857 0.00 0.00 0.00 2.24
3327 3473 3.154710 TGTACTAGGATGCCGATACCAG 58.845 50.000 0.00 0.00 0.00 4.00
3344 3490 2.876550 GGTGGACCTTGTCAAACTGTAC 59.123 50.000 0.00 0.00 33.68 2.90
3395 3541 2.164422 TCGATTGACGAGTTCTGCTCAT 59.836 45.455 0.00 0.00 46.45 2.90
3488 3634 6.264292 TGGCACACTAACTGAAACAATAACAT 59.736 34.615 0.00 0.00 0.00 2.71
3638 3784 8.669946 TGACAGTTAACATTCTGTTCAACATA 57.330 30.769 8.61 0.00 43.64 2.29
3836 3983 2.391616 TCGCATTCTTGTGCAGATCT 57.608 45.000 0.00 0.00 45.30 2.75
3973 4121 1.372872 CATCTGTGTGACGCGGTCA 60.373 57.895 12.47 9.29 40.50 4.02
4069 4217 1.779061 ATGGTGGCGTTGAGGTCCTT 61.779 55.000 0.00 0.00 0.00 3.36
4158 4306 9.685828 CTACTTCTCTAAATGTATCTACCAAGC 57.314 37.037 0.00 0.00 0.00 4.01
4183 4331 2.224769 CCACCACCAACCTAACATGACT 60.225 50.000 0.00 0.00 0.00 3.41
4237 4385 7.336427 TCATTTATACATCAGATGCACACAACA 59.664 33.333 10.59 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.