Multiple sequence alignment - TraesCS5B01G123900

Loading Multiple Alignment...

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 TraesCS5B01G123900 chr5B 100.000 3927 0 0 1 3927 223250969 223254895 0.000000e+00 7252.0
1 TraesCS5B01G123900 chr5B 96.596 852 29 0 49 900 9773675 9772824 0.000000e+00 1413.0
2 TraesCS5B01G123900 chr5B 96.149 857 33 0 49 905 231320100 231319244 0.000000e+00 1400.0
3 TraesCS5B01G123900 chr5B 92.075 530 39 3 906 1432 223255837 223255308 0.000000e+00 743.0
4 TraesCS5B01G123900 chr5B 90.338 207 19 1 902 1107 615374900 615375106 1.800000e-68 270.0
5 TraesCS5B01G123900 chr5B 86.047 86 7 5 1 84 456020430 456020512 1.940000e-13 87.9
6 TraesCS5B01G123900 chr6D 92.325 2645 127 17 1299 3927 457721321 457723905 0.000000e+00 3690.0
7 TraesCS5B01G123900 chr6D 84.466 309 43 5 906 1211 457720975 457721281 2.290000e-77 300.0
8 TraesCS5B01G123900 chr6B 90.699 2559 146 35 1398 3927 58055927 58053432 0.000000e+00 3323.0
9 TraesCS5B01G123900 chr6B 96.702 849 28 0 49 897 287056397 287057245 0.000000e+00 1413.0
10 TraesCS5B01G123900 chr6B 84.076 314 47 3 904 1215 58056250 58055938 2.290000e-77 300.0
11 TraesCS5B01G123900 chr6B 86.047 86 7 5 1 84 315258967 315259049 1.940000e-13 87.9
12 TraesCS5B01G123900 chr2A 90.996 1255 95 8 1777 3027 459079514 459078274 0.000000e+00 1676.0
13 TraesCS5B01G123900 chr2A 95.050 909 39 5 3023 3927 459076178 459075272 0.000000e+00 1424.0
14 TraesCS5B01G123900 chr2A 85.253 495 49 10 1299 1786 459082436 459081959 4.560000e-134 488.0
15 TraesCS5B01G123900 chr3B 96.816 848 24 1 49 896 728571899 728571055 0.000000e+00 1413.0
16 TraesCS5B01G123900 chr3B 96.584 849 29 0 49 897 443779229 443780077 0.000000e+00 1408.0
17 TraesCS5B01G123900 chr3B 89.231 260 26 2 3648 3905 664120975 664121234 1.360000e-84 324.0
18 TraesCS5B01G123900 chr3B 87.313 268 29 3 3643 3905 664528848 664529115 6.380000e-78 302.0
19 TraesCS5B01G123900 chr3B 86.047 86 7 5 1 84 27010795 27010713 1.940000e-13 87.9
20 TraesCS5B01G123900 chr3B 86.047 86 7 5 1 84 733787217 733787299 1.940000e-13 87.9
21 TraesCS5B01G123900 chr7B 96.383 857 31 0 49 905 457621691 457620835 0.000000e+00 1411.0
22 TraesCS5B01G123900 chr7B 96.149 857 33 0 49 905 457198926 457198070 0.000000e+00 1400.0
23 TraesCS5B01G123900 chr7B 82.736 614 66 20 2508 3099 157809088 157809683 9.730000e-141 510.0
24 TraesCS5B01G123900 chr7B 81.225 506 53 12 1278 1741 157808517 157809022 1.720000e-98 370.0
25 TraesCS5B01G123900 chr7B 88.703 239 25 2 904 1141 1876569 1876332 1.380000e-74 291.0
26 TraesCS5B01G123900 chr7B 87.866 239 26 3 904 1141 1852035 1852271 1.070000e-70 278.0
27 TraesCS5B01G123900 chr7B 85.356 239 29 4 906 1141 665727073 665726838 3.920000e-60 243.0
28 TraesCS5B01G123900 chr7B 84.232 241 32 5 904 1141 553151055 553150818 3.050000e-56 230.0
29 TraesCS5B01G123900 chr1B 96.266 857 31 1 49 905 277586653 277585798 0.000000e+00 1404.0
30 TraesCS5B01G123900 chr3D 96.466 849 30 0 49 897 240446648 240447496 0.000000e+00 1402.0
31 TraesCS5B01G123900 chr3D 89.575 259 25 2 3649 3905 502969992 502970250 1.050000e-85 327.0
32 TraesCS5B01G123900 chr2B 88.877 944 71 8 2512 3442 726685435 726684513 0.000000e+00 1131.0
33 TraesCS5B01G123900 chr2B 86.047 86 7 5 1 84 305147818 305147900 1.940000e-13 87.9
34 TraesCS5B01G123900 chr7D 82.803 628 64 18 2508 3109 194130031 194130640 4.500000e-144 521.0
35 TraesCS5B01G123900 chr7D 83.135 421 52 8 1275 1678 132157185 132157603 2.230000e-97 366.0
36 TraesCS5B01G123900 chr7D 83.141 433 42 15 1274 1678 132830798 132830369 2.230000e-97 366.0
37 TraesCS5B01G123900 chr7D 80.769 494 59 9 1283 1741 194129473 194129965 1.740000e-93 353.0
38 TraesCS5B01G123900 chr7D 83.467 375 44 12 2750 3109 133194577 133194948 2.260000e-87 333.0
39 TraesCS5B01G123900 chr7D 81.775 417 47 12 1288 1678 132741220 132741633 4.900000e-84 322.0
40 TraesCS5B01G123900 chr7D 79.297 512 58 21 1278 1741 132135740 132136251 8.190000e-82 315.0
41 TraesCS5B01G123900 chr7D 81.190 420 51 15 1278 1678 132764460 132764050 2.950000e-81 313.0
42 TraesCS5B01G123900 chr7D 84.298 242 31 5 902 1141 561876924 561876688 3.050000e-56 230.0
43 TraesCS5B01G123900 chr7A 82.736 614 60 16 2508 3099 203697524 203698113 4.530000e-139 505.0
44 TraesCS5B01G123900 chr7A 82.311 424 51 9 1279 1678 130782521 130782944 2.900000e-91 346.0
45 TraesCS5B01G123900 chr7A 82.311 424 51 9 1279 1678 131121414 131120991 2.900000e-91 346.0
46 TraesCS5B01G123900 chr7A 80.415 434 55 11 1338 1741 131109279 131108846 1.770000e-78 303.0
47 TraesCS5B01G123900 chr7A 83.667 300 45 2 1275 1573 203695179 203695475 2.990000e-71 279.0
48 TraesCS5B01G123900 chr7A 87.045 247 24 6 2870 3109 131776925 131777170 5.000000e-69 272.0
49 TraesCS5B01G123900 chr7A 86.047 86 7 5 1 84 102772610 102772528 1.940000e-13 87.9
50 TraesCS5B01G123900 chr4A 89.925 268 22 2 1749 2011 500149195 500149462 1.350000e-89 340.0
51 TraesCS5B01G123900 chr4A 79.339 484 65 20 2059 2510 500149469 500149949 1.370000e-79 307.0
52 TraesCS5B01G123900 chr4D 89.057 265 24 2 1749 2011 87575029 87575290 1.360000e-84 324.0
53 TraesCS5B01G123900 chr4D 88.462 156 15 2 2158 2310 87575432 87575587 6.700000e-43 185.0
54 TraesCS5B01G123900 chr3A 89.231 260 26 2 3648 3905 641866279 641866538 1.360000e-84 324.0
55 TraesCS5B01G123900 chr3A 90.079 252 22 3 3656 3905 743683635 743683385 1.360000e-84 324.0
56 TraesCS5B01G123900 chr3A 87.687 268 28 3 3643 3905 641874942 641875209 1.370000e-79 307.0
57 TraesCS5B01G123900 chr3A 94.915 59 3 0 3620 3678 743687799 743687741 4.180000e-15 93.5
58 TraesCS5B01G123900 chr5A 86.047 86 7 5 1 84 117919297 117919215 1.940000e-13 87.9
59 TraesCS5B01G123900 chr4B 86.047 86 7 5 1 84 363478896 363478814 1.940000e-13 87.9
60 TraesCS5B01G123900 chr2D 86.047 86 7 5 1 84 613963349 613963267 1.940000e-13 87.9


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 TraesCS5B01G123900 chr5B 223250969 223254895 3926 False 7252.0 7252 100.0000 1 3927 1 chr5B.!!$F1 3926
1 TraesCS5B01G123900 chr5B 9772824 9773675 851 True 1413.0 1413 96.5960 49 900 1 chr5B.!!$R1 851
2 TraesCS5B01G123900 chr5B 231319244 231320100 856 True 1400.0 1400 96.1490 49 905 1 chr5B.!!$R3 856
3 TraesCS5B01G123900 chr5B 223255308 223255837 529 True 743.0 743 92.0750 906 1432 1 chr5B.!!$R2 526
4 TraesCS5B01G123900 chr6D 457720975 457723905 2930 False 1995.0 3690 88.3955 906 3927 2 chr6D.!!$F1 3021
5 TraesCS5B01G123900 chr6B 58053432 58056250 2818 True 1811.5 3323 87.3875 904 3927 2 chr6B.!!$R1 3023
6 TraesCS5B01G123900 chr6B 287056397 287057245 848 False 1413.0 1413 96.7020 49 897 1 chr6B.!!$F1 848
7 TraesCS5B01G123900 chr2A 459075272 459082436 7164 True 1196.0 1676 90.4330 1299 3927 3 chr2A.!!$R1 2628
8 TraesCS5B01G123900 chr3B 728571055 728571899 844 True 1413.0 1413 96.8160 49 896 1 chr3B.!!$R2 847
9 TraesCS5B01G123900 chr3B 443779229 443780077 848 False 1408.0 1408 96.5840 49 897 1 chr3B.!!$F1 848
10 TraesCS5B01G123900 chr7B 457620835 457621691 856 True 1411.0 1411 96.3830 49 905 1 chr7B.!!$R3 856
11 TraesCS5B01G123900 chr7B 457198070 457198926 856 True 1400.0 1400 96.1490 49 905 1 chr7B.!!$R2 856
12 TraesCS5B01G123900 chr7B 157808517 157809683 1166 False 440.0 510 81.9805 1278 3099 2 chr7B.!!$F2 1821
13 TraesCS5B01G123900 chr1B 277585798 277586653 855 True 1404.0 1404 96.2660 49 905 1 chr1B.!!$R1 856
14 TraesCS5B01G123900 chr3D 240446648 240447496 848 False 1402.0 1402 96.4660 49 897 1 chr3D.!!$F1 848
15 TraesCS5B01G123900 chr2B 726684513 726685435 922 True 1131.0 1131 88.8770 2512 3442 1 chr2B.!!$R1 930
16 TraesCS5B01G123900 chr7D 194129473 194130640 1167 False 437.0 521 81.7860 1283 3109 2 chr7D.!!$F5 1826
17 TraesCS5B01G123900 chr7D 132135740 132136251 511 False 315.0 315 79.2970 1278 1741 1 chr7D.!!$F1 463
18 TraesCS5B01G123900 chr7A 203695179 203698113 2934 False 392.0 505 83.2015 1275 3099 2 chr7A.!!$F3 1824
19 TraesCS5B01G123900 chr4A 500149195 500149949 754 False 323.5 340 84.6320 1749 2510 2 chr4A.!!$F1 761
20 TraesCS5B01G123900 chr4D 87575029 87575587 558 False 254.5 324 88.7595 1749 2310 2 chr4D.!!$F1 561

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
24 25 0.034960 GAAAGGGAGCTGAGAACCCC 60.035 60.0 10.03 0.64 44.21 4.95 F
35 36 0.534203 GAGAACCCCGTTGCAGACAA 60.534 55.0 0.00 0.00 0.00 3.18 F
1440 1455 0.035176 GCCCGTACAACAACCAGGTA 59.965 55.0 0.00 0.00 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1052 1055 0.034574 TGGCACAAGTTGACCACTGT 60.035 50.0 10.54 0.00 35.12 3.55 R
1532 1555 0.109723 AAACGGTGCACCACAGGTAT 59.890 50.0 34.16 10.73 35.86 2.73 R
3405 9972 0.188587 TCTATCGCTCACCCCTCCAT 59.811 55.0 0.00 0.00 0.00 3.41 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
21 22 4.744795 TGATAGAAAGGGAGCTGAGAAC 57.255 45.455 0.00 0.00 0.00 3.01
22 23 3.452627 TGATAGAAAGGGAGCTGAGAACC 59.547 47.826 0.00 0.00 0.00 3.62
23 24 0.988063 AGAAAGGGAGCTGAGAACCC 59.012 55.000 0.00 0.00 43.55 4.11
24 25 0.034960 GAAAGGGAGCTGAGAACCCC 60.035 60.000 10.03 0.64 44.21 4.95
25 26 1.842381 AAAGGGAGCTGAGAACCCCG 61.842 60.000 10.03 0.00 44.21 5.73
26 27 3.003763 GGGAGCTGAGAACCCCGT 61.004 66.667 0.00 0.00 37.85 5.28
27 28 2.593956 GGGAGCTGAGAACCCCGTT 61.594 63.158 0.00 0.00 37.85 4.44
28 29 1.376037 GGAGCTGAGAACCCCGTTG 60.376 63.158 0.00 0.00 0.00 4.10
29 30 2.032681 AGCTGAGAACCCCGTTGC 59.967 61.111 0.00 0.00 0.00 4.17
30 31 2.281484 GCTGAGAACCCCGTTGCA 60.281 61.111 0.00 0.00 0.00 4.08
31 32 2.328099 GCTGAGAACCCCGTTGCAG 61.328 63.158 0.00 0.00 31.83 4.41
32 33 1.371183 CTGAGAACCCCGTTGCAGA 59.629 57.895 0.00 0.00 30.90 4.26
33 34 0.951040 CTGAGAACCCCGTTGCAGAC 60.951 60.000 0.00 0.00 30.90 3.51
34 35 1.070786 GAGAACCCCGTTGCAGACA 59.929 57.895 0.00 0.00 0.00 3.41
35 36 0.534203 GAGAACCCCGTTGCAGACAA 60.534 55.000 0.00 0.00 0.00 3.18
94 95 3.489785 CGGTCATTAATGCTTCTCGTACC 59.510 47.826 10.76 9.18 0.00 3.34
410 412 6.975772 AGATGCTCGTAAGTTTGTCTTATCTC 59.024 38.462 0.00 0.00 40.23 2.75
426 428 7.765819 TGTCTTATCTCGTGATGAATGTCAAAT 59.234 33.333 10.16 0.00 34.32 2.32
432 434 8.491331 TCTCGTGATGAATGTCAAATAATTGA 57.509 30.769 0.00 0.00 43.18 2.57
471 473 8.686334 ACGTCAAGAAATGCCTATGAATTATTT 58.314 29.630 0.00 0.00 0.00 1.40
472 474 9.173939 CGTCAAGAAATGCCTATGAATTATTTC 57.826 33.333 0.00 0.00 37.78 2.17
544 546 3.450904 TCCTGCCTCTAATGGTTACACT 58.549 45.455 0.00 0.00 0.00 3.55
614 616 5.521906 TCCAACTAGTAGTGCTGATCATC 57.478 43.478 2.90 0.00 0.00 2.92
615 617 5.204292 TCCAACTAGTAGTGCTGATCATCT 58.796 41.667 2.90 0.00 0.00 2.90
626 628 6.282167 AGTGCTGATCATCTCACTTCTATTG 58.718 40.000 15.47 0.00 36.48 1.90
897 899 4.263462 TGCATTATGGGCCTATAGAACTGG 60.263 45.833 8.99 0.00 0.00 4.00
900 902 6.725364 CATTATGGGCCTATAGAACTGGATT 58.275 40.000 8.99 0.00 0.00 3.01
934 936 7.923414 AAATTCACTACAGGTCCATTTACTC 57.077 36.000 0.00 0.00 0.00 2.59
936 938 4.084287 TCACTACAGGTCCATTTACTCGT 58.916 43.478 0.00 0.00 0.00 4.18
948 950 0.883153 TTACTCGTGCTGGCGTTAGA 59.117 50.000 0.00 0.00 0.00 2.10
982 984 7.610305 CCTGTGGTTACAAATACCTGAAATACT 59.390 37.037 0.00 0.00 36.14 2.12
998 1000 5.008613 TGAAATACTGTCACCAAACTTGCTC 59.991 40.000 0.00 0.00 0.00 4.26
1030 1033 7.660208 GTCATCTATGGTCCATTATACGGTTTT 59.340 37.037 10.33 0.00 0.00 2.43
1049 1052 1.835121 TGTGTACGTATGCGCTGATC 58.165 50.000 9.73 0.00 42.83 2.92
1052 1055 1.673920 TGTACGTATGCGCTGATCTGA 59.326 47.619 9.73 0.00 42.83 3.27
1056 1059 1.534805 CGTATGCGCTGATCTGACAGT 60.535 52.381 9.73 0.00 39.73 3.55
1077 1080 3.276091 CAACTTGTGCCACGCGGA 61.276 61.111 12.47 0.00 0.00 5.54
1165 1168 1.076044 ACACAAAACAGCTGGCCCT 60.076 52.632 19.93 0.00 0.00 5.19
1219 1222 4.545706 CCCGCTGCCGCCTTGATA 62.546 66.667 0.00 0.00 0.00 2.15
1221 1224 2.511373 CGCTGCCGCCTTGATACA 60.511 61.111 0.00 0.00 0.00 2.29
1272 1275 2.429058 CCGCCTGCTGCCATCTAT 59.571 61.111 0.00 0.00 36.24 1.98
1291 1299 3.582998 ATGGACAGAGAGAGAGAGAGG 57.417 52.381 0.00 0.00 0.00 3.69
1305 1314 2.370189 GAGAGAGGGAGAGAGAGAGAGG 59.630 59.091 0.00 0.00 0.00 3.69
1402 1417 2.268920 GCGCACTCCATTCTCCCA 59.731 61.111 0.30 0.00 0.00 4.37
1440 1455 0.035176 GCCCGTACAACAACCAGGTA 59.965 55.000 0.00 0.00 0.00 3.08
1442 1457 2.145536 CCCGTACAACAACCAGGTAAC 58.854 52.381 0.00 0.00 0.00 2.50
1444 1459 2.545532 CCGTACAACAACCAGGTAACGA 60.546 50.000 0.00 0.00 46.39 3.85
1461 1479 3.135056 GAAGGTCGGCCGCTACGAT 62.135 63.158 23.51 6.56 42.82 3.73
1512 1530 0.043183 TCATCCCCAGCTTCCTCTCA 59.957 55.000 0.00 0.00 0.00 3.27
1515 1533 0.473694 TCCCCAGCTTCCTCTCACAA 60.474 55.000 0.00 0.00 0.00 3.33
1532 1555 2.557924 CACAAGGTATGCTTTGCTTCCA 59.442 45.455 5.56 0.00 35.40 3.53
1533 1556 3.194116 CACAAGGTATGCTTTGCTTCCAT 59.806 43.478 5.56 0.00 35.40 3.41
1545 1568 0.322456 GCTTCCATACCTGTGGTGCA 60.322 55.000 0.00 0.00 40.27 4.57
1577 1600 5.034554 TGCATTCGTTCTGAAGTCAAATC 57.965 39.130 0.00 0.00 40.65 2.17
1585 1646 5.610552 CGTTCTGAAGTCAAATCGTTCTGAC 60.611 44.000 0.00 5.70 41.90 3.51
1595 3441 2.613026 TCGTTCTGACCAGCTTTTGA 57.387 45.000 0.00 0.00 0.00 2.69
1670 3516 4.459089 GGCCCGTCAGCTGTCTCC 62.459 72.222 14.67 5.88 0.00 3.71
1702 3569 0.329261 CCTCTCCACCATTGCTGGAA 59.671 55.000 2.42 0.00 46.37 3.53
1709 3576 2.324330 CCATTGCTGGAACGTCGCA 61.324 57.895 0.00 0.00 46.37 5.10
1747 3621 2.232298 GAAGGAGGACGACAGGCTGG 62.232 65.000 20.34 4.16 0.00 4.85
1868 6214 3.689347 TGTTCCTGCTGTATCTGCATTT 58.311 40.909 0.00 0.00 37.65 2.32
1885 6231 5.263599 TGCATTTTCCTCATCTTACCATGT 58.736 37.500 0.00 0.00 0.00 3.21
1912 6258 5.871524 GTGACTGATTGATCTTTCAGCTACA 59.128 40.000 19.27 15.22 42.51 2.74
1915 6261 5.072040 TGATTGATCTTTCAGCTACACGA 57.928 39.130 0.00 0.00 32.27 4.35
1927 6273 2.764010 AGCTACACGACCATGGTTGATA 59.236 45.455 34.59 23.82 33.85 2.15
2001 6347 7.201767 GCATGAGAGGTATTCAGCTAAATTTGT 60.202 37.037 0.00 0.00 30.99 2.83
2054 6400 5.584649 TCACTGAAACTGACGTCTTTTTGAT 59.415 36.000 17.92 3.38 0.00 2.57
2127 6478 2.421424 CCTAACATCAGGCTTGCAAGAC 59.579 50.000 30.39 28.05 0.00 3.01
2129 6480 2.211250 ACATCAGGCTTGCAAGACAT 57.789 45.000 33.20 16.87 36.14 3.06
2255 6656 0.033504 ACGACAGCTCCGACAACATT 59.966 50.000 11.50 0.00 0.00 2.71
2267 6668 2.704572 GACAACATTAGAGGCTGCTGT 58.295 47.619 0.00 0.00 0.00 4.40
2277 6678 1.003355 GGCTGCTGTGACAAGGCTA 60.003 57.895 3.85 0.00 0.00 3.93
2293 6694 0.531532 GCTATGCAGATCCTGTGCGT 60.532 55.000 5.57 5.57 44.35 5.24
2310 6711 3.702048 TGCACTACGGGTGGGAGC 61.702 66.667 11.63 0.00 45.44 4.70
2311 6712 3.391382 GCACTACGGGTGGGAGCT 61.391 66.667 11.63 0.00 45.44 4.09
2312 6713 2.579201 CACTACGGGTGGGAGCTG 59.421 66.667 0.00 0.00 41.90 4.24
2313 6714 2.683933 ACTACGGGTGGGAGCTGG 60.684 66.667 0.00 0.00 0.00 4.85
2314 6715 3.470888 CTACGGGTGGGAGCTGGG 61.471 72.222 0.00 0.00 0.00 4.45
2315 6716 3.976490 CTACGGGTGGGAGCTGGGA 62.976 68.421 0.00 0.00 0.00 4.37
2316 6717 3.976490 TACGGGTGGGAGCTGGGAG 62.976 68.421 0.00 0.00 0.00 4.30
2326 6727 0.978146 GAGCTGGGAGGTAAGGCTCA 60.978 60.000 0.00 0.00 45.79 4.26
2365 6766 6.859420 TCTTGTGATCTCAACGAAAAATGA 57.141 33.333 6.11 0.00 0.00 2.57
2413 6838 2.806434 ACATTTTGCTGGATGGCACTA 58.194 42.857 0.00 0.00 42.27 2.74
2420 6845 1.339055 GCTGGATGGCACTACAAGACA 60.339 52.381 0.00 0.00 0.00 3.41
2421 6846 2.875672 GCTGGATGGCACTACAAGACAA 60.876 50.000 0.00 0.00 0.00 3.18
2470 6895 3.338676 GCGGCTGGCATACTACGC 61.339 66.667 1.08 0.00 42.87 4.42
2478 6903 0.249322 GGCATACTACGCGACCATGT 60.249 55.000 15.93 6.29 0.00 3.21
2492 6917 1.740664 CATGTGCGCTGAGTGCTCT 60.741 57.895 19.57 3.21 40.03 4.09
2501 6926 0.391395 CTGAGTGCTCTGCTTCCCTG 60.391 60.000 0.00 0.00 0.00 4.45
2519 6944 1.682344 GGCCACCAAGGAACATCCC 60.682 63.158 0.00 0.00 41.22 3.85
2535 6960 1.121407 TCCCGATGATCAAGGGCGAT 61.121 55.000 26.43 0.00 44.70 4.58
2536 6961 0.608130 CCCGATGATCAAGGGCGATA 59.392 55.000 21.98 0.00 38.51 2.92
2591 7016 3.956314 GGTGCCGGGGTACAACCA 61.956 66.667 2.18 0.00 41.02 3.67
2592 7017 2.353573 GTGCCGGGGTACAACCAT 59.646 61.111 2.18 0.00 41.02 3.55
2646 7071 8.027524 AGATAAACAAGATCAAGGCTGAGATA 57.972 34.615 3.02 0.00 34.23 1.98
2653 7078 7.833183 ACAAGATCAAGGCTGAGATAAAGAATT 59.167 33.333 3.02 0.00 34.23 2.17
2754 7179 3.439476 GCGAGTCAAGTAGTCCTTAGTGA 59.561 47.826 0.00 0.00 0.00 3.41
2811 7248 2.887152 AGAGACACCTTGTTGATTTGGC 59.113 45.455 0.00 0.00 0.00 4.52
2812 7249 1.608590 AGACACCTTGTTGATTTGGCG 59.391 47.619 0.00 0.00 0.00 5.69
2813 7250 1.606668 GACACCTTGTTGATTTGGCGA 59.393 47.619 0.00 0.00 0.00 5.54
2814 7251 2.228822 GACACCTTGTTGATTTGGCGAT 59.771 45.455 0.00 0.00 0.00 4.58
2815 7252 2.030007 ACACCTTGTTGATTTGGCGATG 60.030 45.455 0.00 0.00 0.00 3.84
2816 7253 2.030007 CACCTTGTTGATTTGGCGATGT 60.030 45.455 0.00 0.00 0.00 3.06
2817 7254 2.627699 ACCTTGTTGATTTGGCGATGTT 59.372 40.909 0.00 0.00 0.00 2.71
2818 7255 3.069443 ACCTTGTTGATTTGGCGATGTTT 59.931 39.130 0.00 0.00 0.00 2.83
2819 7256 3.429543 CCTTGTTGATTTGGCGATGTTTG 59.570 43.478 0.00 0.00 0.00 2.93
2820 7257 3.023946 TGTTGATTTGGCGATGTTTGG 57.976 42.857 0.00 0.00 0.00 3.28
2845 7282 6.308041 GTGTCTTTCTTTCTTCGTTTTGCTTT 59.692 34.615 0.00 0.00 0.00 3.51
2853 7290 5.242069 TCTTCGTTTTGCTTTGTTGATCA 57.758 34.783 0.00 0.00 0.00 2.92
2874 7320 1.065199 TCTTGGATCATGGTCTGGTGC 60.065 52.381 5.82 0.00 0.00 5.01
2887 7333 1.064758 TCTGGTGCTGAAGTTGGTTGT 60.065 47.619 0.00 0.00 0.00 3.32
3131 9694 8.421249 TTTAATGGTGAGATTGGTCTTTCAAT 57.579 30.769 0.00 0.00 39.76 2.57
3132 9695 5.909621 ATGGTGAGATTGGTCTTTCAATG 57.090 39.130 0.00 0.00 37.47 2.82
3133 9696 4.728772 TGGTGAGATTGGTCTTTCAATGT 58.271 39.130 0.00 0.00 37.47 2.71
3134 9697 4.761739 TGGTGAGATTGGTCTTTCAATGTC 59.238 41.667 7.49 7.49 43.47 3.06
3168 9732 6.220201 TCAAGTTTGACGTGATGAACTGATA 58.780 36.000 0.00 0.00 31.88 2.15
3216 9780 3.358111 TGTTTGTTCCTCACTGTTCCA 57.642 42.857 0.00 0.00 0.00 3.53
3218 9782 5.042463 TGTTTGTTCCTCACTGTTCCATA 57.958 39.130 0.00 0.00 0.00 2.74
3305 9871 4.502645 GTGTTTTTGTGTGAACAGCCATAC 59.497 41.667 0.00 0.00 36.52 2.39
3306 9872 4.158579 TGTTTTTGTGTGAACAGCCATACA 59.841 37.500 0.00 0.00 36.58 2.29
3314 9880 4.469586 TGTGAACAGCCATACAAGATAGGA 59.530 41.667 0.00 0.00 0.00 2.94
3405 9972 3.805066 TCTGATCCATGTTTGTTCCCA 57.195 42.857 0.00 0.00 0.00 4.37
3506 10073 6.094048 TGAAAATCAATAACTACAGCAGGCTC 59.906 38.462 0.00 0.00 0.00 4.70
3590 10157 1.461075 CCATCCTCCTAGCTGGCCT 60.461 63.158 3.32 0.00 35.26 5.19
3685 10252 1.521010 CAGCCTGCATGGAGTCTCG 60.521 63.158 13.65 0.00 38.35 4.04
3887 10456 2.278206 CGCTCTATCACGCGCAGT 60.278 61.111 5.73 3.19 43.01 4.40
3905 10474 2.813908 GCGGCACCGAAGTCGAAT 60.814 61.111 14.43 0.00 39.34 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.452627 GGTTCTCAGCTCCCTTTCTATCA 59.547 47.826 0.00 0.00 0.00 2.15
3 4 2.188817 GGGTTCTCAGCTCCCTTTCTA 58.811 52.381 0.05 0.00 38.29 2.10
7 8 2.294078 CGGGGTTCTCAGCTCCCTT 61.294 63.158 7.33 0.00 40.88 3.95
8 9 2.685380 CGGGGTTCTCAGCTCCCT 60.685 66.667 7.33 0.00 40.88 4.20
9 10 2.593956 AACGGGGTTCTCAGCTCCC 61.594 63.158 0.00 0.00 40.41 4.30
10 11 1.376037 CAACGGGGTTCTCAGCTCC 60.376 63.158 0.00 0.00 0.00 4.70
11 12 2.035442 GCAACGGGGTTCTCAGCTC 61.035 63.158 0.00 0.00 0.00 4.09
12 13 2.032681 GCAACGGGGTTCTCAGCT 59.967 61.111 0.00 0.00 0.00 4.24
13 14 2.281484 TGCAACGGGGTTCTCAGC 60.281 61.111 0.00 0.00 0.00 4.26
14 15 0.951040 GTCTGCAACGGGGTTCTCAG 60.951 60.000 0.00 0.00 0.00 3.35
15 16 1.070786 GTCTGCAACGGGGTTCTCA 59.929 57.895 0.00 0.00 0.00 3.27
16 17 0.534203 TTGTCTGCAACGGGGTTCTC 60.534 55.000 0.00 0.00 0.00 2.87
17 18 0.818040 GTTGTCTGCAACGGGGTTCT 60.818 55.000 0.00 0.00 44.40 3.01
18 19 1.652563 GTTGTCTGCAACGGGGTTC 59.347 57.895 0.00 0.00 44.40 3.62
19 20 3.836151 GTTGTCTGCAACGGGGTT 58.164 55.556 0.00 0.00 44.40 4.11
26 27 7.119262 GCTATAACCTAGAAAAGTTGTCTGCAA 59.881 37.037 5.77 0.00 0.00 4.08
27 28 6.594159 GCTATAACCTAGAAAAGTTGTCTGCA 59.406 38.462 5.77 0.00 0.00 4.41
28 29 6.819146 AGCTATAACCTAGAAAAGTTGTCTGC 59.181 38.462 5.77 0.00 0.00 4.26
29 30 8.779354 AAGCTATAACCTAGAAAAGTTGTCTG 57.221 34.615 5.77 0.00 0.00 3.51
30 31 9.438228 GAAAGCTATAACCTAGAAAAGTTGTCT 57.562 33.333 0.19 0.19 0.00 3.41
31 32 8.666573 GGAAAGCTATAACCTAGAAAAGTTGTC 58.333 37.037 0.00 0.00 0.00 3.18
32 33 8.383947 AGGAAAGCTATAACCTAGAAAAGTTGT 58.616 33.333 0.00 0.00 0.00 3.32
33 34 8.669243 CAGGAAAGCTATAACCTAGAAAAGTTG 58.331 37.037 0.00 0.00 0.00 3.16
34 35 8.603304 TCAGGAAAGCTATAACCTAGAAAAGTT 58.397 33.333 0.00 0.00 0.00 2.66
35 36 8.147244 TCAGGAAAGCTATAACCTAGAAAAGT 57.853 34.615 0.00 0.00 0.00 2.66
36 37 9.050601 CATCAGGAAAGCTATAACCTAGAAAAG 57.949 37.037 0.00 0.00 0.00 2.27
37 38 8.768397 TCATCAGGAAAGCTATAACCTAGAAAA 58.232 33.333 0.00 0.00 0.00 2.29
38 39 8.319057 TCATCAGGAAAGCTATAACCTAGAAA 57.681 34.615 0.00 0.00 0.00 2.52
39 40 7.914427 TCATCAGGAAAGCTATAACCTAGAA 57.086 36.000 0.00 0.00 0.00 2.10
40 41 7.344612 TGTTCATCAGGAAAGCTATAACCTAGA 59.655 37.037 0.00 0.00 37.23 2.43
41 42 7.500992 TGTTCATCAGGAAAGCTATAACCTAG 58.499 38.462 0.00 0.00 37.23 3.02
42 43 7.432148 TGTTCATCAGGAAAGCTATAACCTA 57.568 36.000 0.00 0.00 37.23 3.08
43 44 6.313519 TGTTCATCAGGAAAGCTATAACCT 57.686 37.500 0.00 0.00 37.23 3.50
44 45 7.573968 ATTGTTCATCAGGAAAGCTATAACC 57.426 36.000 0.00 0.00 37.23 2.85
46 47 8.840321 GCTAATTGTTCATCAGGAAAGCTATAA 58.160 33.333 0.00 0.00 37.23 0.98
47 48 7.171508 CGCTAATTGTTCATCAGGAAAGCTATA 59.828 37.037 0.00 0.00 37.23 1.31
94 95 4.093998 GCATAATCATCATACCAAGGAGCG 59.906 45.833 0.00 0.00 0.00 5.03
225 226 8.138712 GTCTAATAACACCATCTACTCCTTCTG 58.861 40.741 0.00 0.00 0.00 3.02
471 473 7.931578 ATATCAAACGGTTCAATAACAAGGA 57.068 32.000 0.00 0.00 37.34 3.36
472 474 8.859156 CAAATATCAAACGGTTCAATAACAAGG 58.141 33.333 0.00 0.00 37.34 3.61
900 902 9.063615 GGACCTGTAGTGAATTTTTCTCTTTAA 57.936 33.333 0.00 0.00 35.37 1.52
919 921 1.623811 AGCACGAGTAAATGGACCTGT 59.376 47.619 0.00 0.00 0.00 4.00
920 922 2.002586 CAGCACGAGTAAATGGACCTG 58.997 52.381 0.00 0.00 0.00 4.00
934 936 2.268298 ACTAAATCTAACGCCAGCACG 58.732 47.619 0.00 0.00 39.50 5.34
936 938 2.419574 GGGACTAAATCTAACGCCAGCA 60.420 50.000 0.00 0.00 0.00 4.41
948 950 6.888088 GGTATTTGTAACCACAGGGACTAAAT 59.112 38.462 0.00 0.00 34.81 1.40
982 984 2.224523 CCCTAGAGCAAGTTTGGTGACA 60.225 50.000 0.70 0.00 39.30 3.58
998 1000 3.260269 TGGACCATAGATGACCCCTAG 57.740 52.381 0.00 0.00 0.00 3.02
1030 1033 1.404035 AGATCAGCGCATACGTACACA 59.596 47.619 11.47 0.00 42.83 3.72
1052 1055 0.034574 TGGCACAAGTTGACCACTGT 60.035 50.000 10.54 0.00 35.12 3.55
1056 1059 2.477176 GCGTGGCACAAGTTGACCA 61.477 57.895 19.09 13.56 44.16 4.02
1165 1168 1.305549 GGTCCGACTAGGTGGGGAA 60.306 63.158 0.00 0.00 41.99 3.97
1207 1210 1.436195 GCGAATGTATCAAGGCGGCA 61.436 55.000 13.08 0.00 0.00 5.69
1272 1275 1.563879 CCCTCTCTCTCTCTCTGTCCA 59.436 57.143 0.00 0.00 0.00 4.02
1276 1281 3.041211 TCTCTCCCTCTCTCTCTCTCTG 58.959 54.545 0.00 0.00 0.00 3.35
1291 1299 1.143073 GGTCTCCCTCTCTCTCTCTCC 59.857 61.905 0.00 0.00 0.00 3.71
1324 1333 1.173913 GCGGCACCCTTAAAAGTGAT 58.826 50.000 8.37 0.00 36.01 3.06
1327 1336 2.622962 GCGCGGCACCCTTAAAAGT 61.623 57.895 8.83 0.00 0.00 2.66
1433 1448 1.969862 CCGACCTTCGTTACCTGGT 59.030 57.895 4.05 4.05 38.40 4.00
1440 1455 3.376078 TAGCGGCCGACCTTCGTT 61.376 61.111 33.48 5.67 38.40 3.85
1444 1459 3.145551 ATCGTAGCGGCCGACCTT 61.146 61.111 33.48 13.37 37.12 3.50
1461 1479 1.494628 GCTGTAGTCGTCGTCGTCA 59.505 57.895 1.33 0.00 38.33 4.35
1512 1530 2.875296 TGGAAGCAAAGCATACCTTGT 58.125 42.857 0.00 0.00 33.01 3.16
1515 1533 3.555966 GGTATGGAAGCAAAGCATACCT 58.444 45.455 4.32 0.00 42.51 3.08
1532 1555 0.109723 AAACGGTGCACCACAGGTAT 59.890 50.000 34.16 10.73 35.86 2.73
1533 1556 0.533308 GAAACGGTGCACCACAGGTA 60.533 55.000 34.16 0.00 35.86 3.08
1545 1568 2.616842 AGAACGAATGCAAAGAAACGGT 59.383 40.909 0.00 0.00 0.00 4.83
1577 1600 1.070577 CGTCAAAAGCTGGTCAGAACG 60.071 52.381 1.65 0.00 0.00 3.95
1585 1646 1.593196 TCAAGGACGTCAAAAGCTGG 58.407 50.000 18.91 2.21 0.00 4.85
1595 3441 2.744202 GCAGAATCAACATCAAGGACGT 59.256 45.455 0.00 0.00 0.00 4.34
1670 3516 2.835431 AGAGGCCGGTCTCCATCG 60.835 66.667 32.04 0.00 34.46 3.84
1747 3621 4.719369 AAGTGCGTCCTCGACCGC 62.719 66.667 11.28 11.28 39.71 5.68
1844 6186 2.502947 TGCAGATACAGCAGGAACATCT 59.497 45.455 0.00 0.00 37.02 2.90
1868 6214 6.384015 AGTCACATACATGGTAAGATGAGGAA 59.616 38.462 0.00 0.00 0.00 3.36
1885 6231 6.647229 AGCTGAAAGATCAATCAGTCACATA 58.353 36.000 21.70 0.00 43.91 2.29
1912 6258 2.569853 TGGACTTATCAACCATGGTCGT 59.430 45.455 20.07 9.79 0.00 4.34
1915 6261 3.054361 GGTCTGGACTTATCAACCATGGT 60.054 47.826 13.00 13.00 33.08 3.55
1927 6273 0.972883 GAGTGAGCTGGTCTGGACTT 59.027 55.000 8.47 0.00 0.00 3.01
2001 6347 3.268334 ACAATCCAGGTGGTTTATGCCTA 59.732 43.478 0.00 0.00 36.34 3.93
2054 6400 3.295973 GCTGGGGCTACAAATAAATCCA 58.704 45.455 0.00 0.00 35.22 3.41
2127 6478 1.016130 ACGCTCGCTCACCTTTCATG 61.016 55.000 0.00 0.00 0.00 3.07
2129 6480 1.372997 GACGCTCGCTCACCTTTCA 60.373 57.895 0.00 0.00 0.00 2.69
2255 6656 0.610174 CCTTGTCACAGCAGCCTCTA 59.390 55.000 0.00 0.00 0.00 2.43
2267 6668 2.121948 AGGATCTGCATAGCCTTGTCA 58.878 47.619 2.53 0.00 0.00 3.58
2277 6678 2.110967 GCACGCACAGGATCTGCAT 61.111 57.895 6.28 0.00 34.37 3.96
2293 6694 3.702048 GCTCCCACCCGTAGTGCA 61.702 66.667 0.00 0.00 45.83 4.57
2310 6711 3.054065 AGAATTTGAGCCTTACCTCCCAG 60.054 47.826 0.00 0.00 0.00 4.45
2311 6712 2.919602 AGAATTTGAGCCTTACCTCCCA 59.080 45.455 0.00 0.00 0.00 4.37
2312 6713 3.282885 CAGAATTTGAGCCTTACCTCCC 58.717 50.000 0.00 0.00 0.00 4.30
2313 6714 3.956744 ACAGAATTTGAGCCTTACCTCC 58.043 45.455 0.00 0.00 0.00 4.30
2314 6715 5.003804 TCAACAGAATTTGAGCCTTACCTC 58.996 41.667 0.00 0.00 31.68 3.85
2315 6716 4.762251 GTCAACAGAATTTGAGCCTTACCT 59.238 41.667 0.00 0.00 36.15 3.08
2316 6717 4.762251 AGTCAACAGAATTTGAGCCTTACC 59.238 41.667 0.00 0.00 36.15 2.85
2326 6727 6.757897 TCACAAGAACAGTCAACAGAATTT 57.242 33.333 0.00 0.00 0.00 1.82
2365 6766 8.413309 TTGTTTCAGAGAAATGGATCAAATCT 57.587 30.769 0.00 0.00 0.00 2.40
2413 6838 1.497991 CGTCACGTCCATTGTCTTGT 58.502 50.000 0.00 0.00 0.00 3.16
2420 6845 2.358247 GGCACCGTCACGTCCATT 60.358 61.111 0.00 0.00 0.00 3.16
2421 6846 3.311110 AGGCACCGTCACGTCCAT 61.311 61.111 0.00 0.00 0.00 3.41
2462 6887 0.594028 CGCACATGGTCGCGTAGTAT 60.594 55.000 15.64 0.00 46.23 2.12
2463 6888 1.226463 CGCACATGGTCGCGTAGTA 60.226 57.895 15.64 0.00 46.23 1.82
2470 6895 2.433145 ACTCAGCGCACATGGTCG 60.433 61.111 11.47 0.59 0.00 4.79
2481 6906 1.744741 GGGAAGCAGAGCACTCAGC 60.745 63.158 6.92 6.92 46.19 4.26
2483 6908 1.675801 CAGGGAAGCAGAGCACTCA 59.324 57.895 0.00 0.00 0.00 3.41
2492 6917 3.506743 TTGGTGGCCAGGGAAGCA 61.507 61.111 5.11 0.00 33.81 3.91
2501 6926 1.682344 GGGATGTTCCTTGGTGGCC 60.682 63.158 0.00 0.00 36.57 5.36
2519 6944 1.354040 GCTATCGCCCTTGATCATCG 58.646 55.000 0.00 0.00 0.00 3.84
2535 6960 1.109920 CCTAGGGCTGCTTCTCGCTA 61.110 60.000 0.00 0.00 40.11 4.26
2536 6961 2.430610 CCTAGGGCTGCTTCTCGCT 61.431 63.158 0.00 0.00 40.11 4.93
2552 6977 3.264866 GAGTTGTCGTCGCCGTCCT 62.265 63.158 0.00 0.00 35.01 3.85
2573 6998 3.956314 GGTTGTACCCCGGCACCA 61.956 66.667 0.00 0.00 30.04 4.17
2581 7006 2.404083 CCATGCGATGGTTGTACCC 58.596 57.895 6.93 0.00 45.54 3.69
2607 7032 2.921754 GTTTATCTTGTACGCGTCAGCT 59.078 45.455 18.63 4.72 42.32 4.24
2646 7071 1.073923 ACCCAGAGGACGCAATTCTTT 59.926 47.619 0.00 0.00 36.73 2.52
2653 7078 3.311110 GGTCACCCAGAGGACGCA 61.311 66.667 0.00 0.00 36.73 5.24
2720 7145 0.249676 TGACTCGCCTCTCTACTCGT 59.750 55.000 0.00 0.00 0.00 4.18
2754 7179 2.224719 GGCCATCTTCCATGAGCACTAT 60.225 50.000 0.00 0.00 0.00 2.12
2811 7248 5.424121 AGAAAGAAAGACACCAAACATCG 57.576 39.130 0.00 0.00 0.00 3.84
2812 7249 5.909610 CGAAGAAAGAAAGACACCAAACATC 59.090 40.000 0.00 0.00 0.00 3.06
2813 7250 5.357032 ACGAAGAAAGAAAGACACCAAACAT 59.643 36.000 0.00 0.00 0.00 2.71
2814 7251 4.698304 ACGAAGAAAGAAAGACACCAAACA 59.302 37.500 0.00 0.00 0.00 2.83
2815 7252 5.231265 ACGAAGAAAGAAAGACACCAAAC 57.769 39.130 0.00 0.00 0.00 2.93
2816 7253 5.890424 AACGAAGAAAGAAAGACACCAAA 57.110 34.783 0.00 0.00 0.00 3.28
2817 7254 5.890424 AAACGAAGAAAGAAAGACACCAA 57.110 34.783 0.00 0.00 0.00 3.67
2818 7255 5.636837 CAAAACGAAGAAAGAAAGACACCA 58.363 37.500 0.00 0.00 0.00 4.17
2819 7256 4.499399 GCAAAACGAAGAAAGAAAGACACC 59.501 41.667 0.00 0.00 0.00 4.16
2820 7257 5.332707 AGCAAAACGAAGAAAGAAAGACAC 58.667 37.500 0.00 0.00 0.00 3.67
2853 7290 2.422519 GCACCAGACCATGATCCAAGAT 60.423 50.000 0.00 0.00 0.00 2.40
2863 7300 1.546323 CCAACTTCAGCACCAGACCAT 60.546 52.381 0.00 0.00 0.00 3.55
2874 7320 3.941483 ACAGAGTTCACAACCAACTTCAG 59.059 43.478 0.00 0.00 34.10 3.02
2887 7333 8.405531 CAAACTTGAGGAAATTAACAGAGTTCA 58.594 33.333 0.00 0.00 0.00 3.18
3168 9732 1.202582 GAGACTACACACTCGGCACAT 59.797 52.381 0.00 0.00 0.00 3.21
3314 9880 3.960102 TCAACAAAGTGCTCCAGGAAATT 59.040 39.130 0.00 0.00 0.00 1.82
3405 9972 0.188587 TCTATCGCTCACCCCTCCAT 59.811 55.000 0.00 0.00 0.00 3.41
3418 9985 5.818136 TTTTTGGATTGGCTTCTCTATCG 57.182 39.130 0.00 0.00 0.00 2.92
3619 10186 2.445654 GGGCAGGAGGAGGAGGAG 60.446 72.222 0.00 0.00 0.00 3.69
3620 10187 4.465446 CGGGCAGGAGGAGGAGGA 62.465 72.222 0.00 0.00 0.00 3.71
3685 10252 5.452777 GTTCAGATTGTTCAGGTTAAGCAC 58.547 41.667 7.52 0.00 0.00 4.40
3771 10338 0.614697 TCCCTCGCTCCTTGTCATCA 60.615 55.000 0.00 0.00 0.00 3.07
3778 10345 2.756283 CGACCTCCCTCGCTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
3887 10456 3.583276 ATTCGACTTCGGTGCCGCA 62.583 57.895 5.64 0.00 40.29 5.69
3905 10474 0.737367 CTCATGGAGCGCTTCGACAA 60.737 55.000 13.26 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.