Multiple sequence alignment - TraesCS5D01G406300

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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 TraesCS5D01G406300 chr5D 100.000 6900 0 0 1 6900 472226268 472233167 0.000000e+00 12743.0
1 TraesCS5D01G406300 chr5D 88.158 76 6 2 5687 5761 476041534 476041607 3.430000e-13 87.9
2 TraesCS5D01G406300 chr5D 88.571 70 6 2 5689 5758 446570688 446570621 4.430000e-12 84.2
3 TraesCS5D01G406300 chr5B 95.581 5929 146 40 981 6851 578529941 578535811 0.000000e+00 9391.0
4 TraesCS5D01G406300 chr5A 94.219 2041 77 11 2648 4663 591434994 591437018 0.000000e+00 3077.0
5 TraesCS5D01G406300 chr5A 97.377 1182 23 3 4794 5975 591391587 591392760 0.000000e+00 2004.0
6 TraesCS5D01G406300 chr5A 94.903 1138 53 4 981 2117 591433131 591434264 0.000000e+00 1775.0
7 TraesCS5D01G406300 chr5A 92.440 992 54 7 1 972 562821066 562822056 0.000000e+00 1397.0
8 TraesCS5D01G406300 chr5A 92.370 983 59 4 1 968 562846979 562847960 0.000000e+00 1386.0
9 TraesCS5D01G406300 chr5A 91.889 900 51 11 4805 5690 591437405 591438296 0.000000e+00 1238.0
10 TraesCS5D01G406300 chr5A 89.004 773 59 15 6063 6813 591438631 591439399 0.000000e+00 933.0
11 TraesCS5D01G406300 chr5A 91.594 571 24 14 2104 2650 591434321 591434891 0.000000e+00 767.0
12 TraesCS5D01G406300 chr5A 92.661 218 13 2 5757 5974 591438301 591438515 1.870000e-80 311.0
13 TraesCS5D01G406300 chr5A 92.763 152 9 2 4656 4806 591437153 591437303 1.170000e-52 219.0
14 TraesCS5D01G406300 chr7D 93.044 992 50 8 1 980 47598827 47597843 0.000000e+00 1432.0
15 TraesCS5D01G406300 chr7D 93.243 74 4 1 5689 5762 18437347 18437275 2.630000e-19 108.0
16 TraesCS5D01G406300 chr7D 91.781 73 2 1 5688 5760 515468080 515468148 1.580000e-16 99.0
17 TraesCS5D01G406300 chr1A 92.814 1002 44 4 1 975 274787982 274786982 0.000000e+00 1426.0
18 TraesCS5D01G406300 chr1A 81.887 265 28 10 6581 6831 551506568 551506826 9.070000e-49 206.0
19 TraesCS5D01G406300 chr1A 90.000 80 2 2 5689 5762 11617140 11617219 1.580000e-16 99.0
20 TraesCS5D01G406300 chr1A 96.296 54 2 0 5685 5738 557480154 557480101 9.530000e-14 89.8
21 TraesCS5D01G406300 chr2A 92.462 995 50 12 1 972 319008422 319009414 0.000000e+00 1399.0
22 TraesCS5D01G406300 chr2A 89.610 77 6 1 5688 5762 754467810 754467886 5.700000e-16 97.1
23 TraesCS5D01G406300 chr6B 92.457 981 58 8 1 977 703000849 703001817 0.000000e+00 1387.0
24 TraesCS5D01G406300 chr6B 91.768 984 52 11 1 977 703049536 703050497 0.000000e+00 1341.0
25 TraesCS5D01G406300 chr6B 89.855 69 5 1 5689 5757 706122030 706121964 3.430000e-13 87.9
26 TraesCS5D01G406300 chr4A 91.916 1002 49 16 1 975 489098329 489097333 0.000000e+00 1373.0
27 TraesCS5D01G406300 chr2B 90.429 1003 70 11 1 980 229962918 229961919 0.000000e+00 1297.0
28 TraesCS5D01G406300 chr2B 90.130 1003 74 9 1 980 229977438 229976438 0.000000e+00 1280.0
29 TraesCS5D01G406300 chr2B 90.116 951 59 11 36 973 229991336 229990408 0.000000e+00 1203.0
30 TraesCS5D01G406300 chr1B 91.309 955 63 7 37 980 398834784 398833839 0.000000e+00 1286.0
31 TraesCS5D01G406300 chr1B 82.329 249 33 7 6584 6831 533759059 533758821 9.070000e-49 206.0
32 TraesCS5D01G406300 chr1B 81.928 249 34 7 6584 6831 640478827 640478589 4.220000e-47 200.0
33 TraesCS5D01G406300 chr3D 91.304 69 5 1 5689 5757 224894413 224894346 7.370000e-15 93.5
34 TraesCS5D01G406300 chr6D 90.141 71 5 2 5688 5757 95358 95427 2.650000e-14 91.6
35 TraesCS5D01G406300 chr6D 94.828 58 2 1 5678 5735 218263284 218263228 9.530000e-14 89.8
36 TraesCS5D01G406300 chr6D 89.189 74 5 3 5689 5759 420732481 420732408 9.530000e-14 89.8
37 TraesCS5D01G406300 chr6D 89.855 69 6 1 5689 5757 18118451 18118518 3.430000e-13 87.9
38 TraesCS5D01G406300 chr6D 88.889 72 5 2 5689 5757 29889977 29889906 1.230000e-12 86.1
39 TraesCS5D01G406300 chr6D 96.154 52 1 1 5689 5740 261280424 261280474 4.430000e-12 84.2
40 TraesCS5D01G406300 chr6D 96.154 52 1 1 5685 5735 462014551 462014500 4.430000e-12 84.2
41 TraesCS5D01G406300 chr6D 94.340 53 3 0 5686 5738 72012738 72012790 1.600000e-11 82.4
42 TraesCS5D01G406300 chr6A 89.333 75 2 1 5689 5757 32658709 32658783 9.530000e-14 89.8
43 TraesCS5D01G406300 chr4D 98.000 50 1 0 5686 5735 5081573 5081622 3.430000e-13 87.9
44 TraesCS5D01G406300 chr1D 98.000 50 1 0 5689 5738 23299589 23299638 3.430000e-13 87.9
45 TraesCS5D01G406300 chr1D 87.324 71 9 0 5687 5757 474820676 474820746 1.600000e-11 82.4
46 TraesCS5D01G406300 chrUn 97.917 48 1 0 5688 5735 100699370 100699417 4.430000e-12 84.2
47 TraesCS5D01G406300 chrUn 97.917 48 1 0 5688 5735 311997020 311997067 4.430000e-12 84.2
48 TraesCS5D01G406300 chrUn 97.917 48 1 0 5688 5735 379298535 379298488 4.430000e-12 84.2
49 TraesCS5D01G406300 chrUn 97.872 47 1 0 5689 5735 75836645 75836599 1.600000e-11 82.4
50 TraesCS5D01G406300 chrUn 97.872 47 1 0 5689 5735 104546003 104546049 1.600000e-11 82.4
51 TraesCS5D01G406300 chrUn 97.872 47 1 0 5689 5735 110488151 110488197 1.600000e-11 82.4
52 TraesCS5D01G406300 chrUn 97.872 47 1 0 5689 5735 116768212 116768166 1.600000e-11 82.4
53 TraesCS5D01G406300 chrUn 97.872 47 1 0 5689 5735 322507512 322507558 1.600000e-11 82.4
54 TraesCS5D01G406300 chrUn 97.826 46 1 0 5689 5734 101377987 101378032 5.740000e-11 80.5
55 TraesCS5D01G406300 chrUn 96.000 50 1 1 5689 5738 267226691 267226739 5.740000e-11 80.5
56 TraesCS5D01G406300 chrUn 96.000 50 1 1 5689 5738 346385121 346385169 5.740000e-11 80.5
57 TraesCS5D01G406300 chrUn 86.486 74 5 3 5689 5757 47494622 47494549 7.420000e-10 76.8
58 TraesCS5D01G406300 chr7B 86.250 80 5 4 5689 5762 748396224 748396145 1.600000e-11 82.4
59 TraesCS5D01G406300 chr4B 87.671 73 5 3 5689 5757 604958883 604958955 1.600000e-11 82.4
60 TraesCS5D01G406300 chr4B 85.897 78 5 4 5689 5760 397908528 397908451 2.060000e-10 78.7


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 TraesCS5D01G406300 chr5D 472226268 472233167 6899 False 12743.000000 12743 100.000000 1 6900 1 chr5D.!!$F1 6899
1 TraesCS5D01G406300 chr5B 578529941 578535811 5870 False 9391.000000 9391 95.581000 981 6851 1 chr5B.!!$F1 5870
2 TraesCS5D01G406300 chr5A 591391587 591392760 1173 False 2004.000000 2004 97.377000 4794 5975 1 chr5A.!!$F3 1181
3 TraesCS5D01G406300 chr5A 562821066 562822056 990 False 1397.000000 1397 92.440000 1 972 1 chr5A.!!$F1 971
4 TraesCS5D01G406300 chr5A 562846979 562847960 981 False 1386.000000 1386 92.370000 1 968 1 chr5A.!!$F2 967
5 TraesCS5D01G406300 chr5A 591433131 591439399 6268 False 1188.571429 3077 92.433286 981 6813 7 chr5A.!!$F4 5832
6 TraesCS5D01G406300 chr7D 47597843 47598827 984 True 1432.000000 1432 93.044000 1 980 1 chr7D.!!$R2 979
7 TraesCS5D01G406300 chr1A 274786982 274787982 1000 True 1426.000000 1426 92.814000 1 975 1 chr1A.!!$R1 974
8 TraesCS5D01G406300 chr2A 319008422 319009414 992 False 1399.000000 1399 92.462000 1 972 1 chr2A.!!$F1 971
9 TraesCS5D01G406300 chr6B 703000849 703001817 968 False 1387.000000 1387 92.457000 1 977 1 chr6B.!!$F1 976
10 TraesCS5D01G406300 chr6B 703049536 703050497 961 False 1341.000000 1341 91.768000 1 977 1 chr6B.!!$F2 976
11 TraesCS5D01G406300 chr4A 489097333 489098329 996 True 1373.000000 1373 91.916000 1 975 1 chr4A.!!$R1 974
12 TraesCS5D01G406300 chr2B 229961919 229962918 999 True 1297.000000 1297 90.429000 1 980 1 chr2B.!!$R1 979
13 TraesCS5D01G406300 chr2B 229976438 229977438 1000 True 1280.000000 1280 90.130000 1 980 1 chr2B.!!$R2 979
14 TraesCS5D01G406300 chr2B 229990408 229991336 928 True 1203.000000 1203 90.116000 36 973 1 chr2B.!!$R3 937
15 TraesCS5D01G406300 chr1B 398833839 398834784 945 True 1286.000000 1286 91.309000 37 980 1 chr1B.!!$R1 943

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
404 450 0.544697 ACAGACTTGGACGTGGGTTT 59.455 50.000 0.0 0.0 0.00 3.27 F
1174 1254 0.790814 GCACGCTTCTACTTGTGGTC 59.209 55.000 0.0 0.0 33.04 4.02 F
1475 1555 0.037326 GGATGAGTCTGTGGCGTTCA 60.037 55.000 0.0 0.0 0.00 3.18 F
3109 3392 5.059833 GGAGTGATGGTTTAGCTTCATAGG 58.940 45.833 0.0 0.0 0.00 2.57 F
4461 4765 2.810852 GCTGCTTGAGGTAATATCTGGC 59.189 50.000 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 1555 0.179000 GATCCATCTGAACCGCCTGT 59.821 55.000 0.00 0.0 0.00 4.00 R
2816 3099 7.054124 TGAATTCAAGTCATACCTGGGAATAC 58.946 38.462 5.45 0.0 0.00 1.89 R
3448 3732 3.951680 GGGGAATCTTTTGCCTTAATCGA 59.048 43.478 0.00 0.0 42.66 3.59 R
4563 4868 1.151413 AGGAGGACCTTGGGTAAGACA 59.849 52.381 0.00 0.0 45.36 3.41 R
6230 6887 0.039527 GCCAAAGCGGATTTTCGTGT 60.040 50.000 0.00 0.0 36.56 4.49 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
17 18 3.688032 AAGGACAAAGTGGGCCCT 58.312 55.556 25.70 0.00 0.00 5.19
107 108 1.694696 CTCTAAGGGCCCATGTAGGTC 59.305 57.143 27.56 0.00 34.66 3.85
298 340 4.537433 GCGGGATTGAGCCGAGCT 62.537 66.667 0.00 0.00 43.88 4.09
347 393 2.558795 TCAGGAACGGAGAGTCTTTGAG 59.441 50.000 0.00 0.00 0.00 3.02
387 433 1.409064 GACGTCAGATCATGGGCTACA 59.591 52.381 11.55 0.00 0.00 2.74
404 450 0.544697 ACAGACTTGGACGTGGGTTT 59.455 50.000 0.00 0.00 0.00 3.27
500 554 3.842923 CATCTCCGCCTCCACGCT 61.843 66.667 0.00 0.00 0.00 5.07
575 633 2.342279 CGGTTGACGGGAGAGCAA 59.658 61.111 0.00 0.00 39.42 3.91
699 758 2.038426 TCACCTTCGTCATCACCATGTT 59.962 45.455 0.00 0.00 0.00 2.71
806 883 4.673968 TGGAGGGTATACATCGCTTATCT 58.326 43.478 5.01 0.00 0.00 1.98
824 901 7.918033 CGCTTATCTCTCTCATGTTTCTTTCTA 59.082 37.037 0.00 0.00 0.00 2.10
977 1057 6.636562 TTGAAAAACGGCCTATTTACTCAA 57.363 33.333 15.63 15.63 0.00 3.02
1174 1254 0.790814 GCACGCTTCTACTTGTGGTC 59.209 55.000 0.00 0.00 33.04 4.02
1475 1555 0.037326 GGATGAGTCTGTGGCGTTCA 60.037 55.000 0.00 0.00 0.00 3.18
2030 2111 5.813513 ATTGGGCAGAAGAAAGTTGAAAT 57.186 34.783 0.00 0.00 0.00 2.17
2204 2356 5.618056 TTCAGAACATGAAGCAATCACTC 57.382 39.130 0.00 0.00 43.09 3.51
2816 3099 6.642540 TGCATTAGTATTTACGCTGATGAGAG 59.357 38.462 0.00 0.00 32.55 3.20
3109 3392 5.059833 GGAGTGATGGTTTAGCTTCATAGG 58.940 45.833 0.00 0.00 0.00 2.57
3226 3510 6.953101 TGTATTTACTTCTACCATTGGAGCA 58.047 36.000 10.37 0.00 0.00 4.26
3291 3575 5.298989 TGGTAACTTCTAGCCTTGACAAA 57.701 39.130 0.00 0.00 37.61 2.83
3447 3731 6.543831 GGTATGACATGAGGAATTTAACAGCT 59.456 38.462 0.00 0.00 0.00 4.24
3448 3732 7.067494 GGTATGACATGAGGAATTTAACAGCTT 59.933 37.037 0.00 0.00 0.00 3.74
4064 4366 3.572584 CTCATTTGCTTCAGTTTCCTGC 58.427 45.455 0.00 0.00 38.66 4.85
4126 4428 9.353999 GAACATAGTTGGCATTTTTAAAGTAGG 57.646 33.333 0.00 0.00 0.00 3.18
4461 4765 2.810852 GCTGCTTGAGGTAATATCTGGC 59.189 50.000 0.00 0.00 0.00 4.85
4481 4785 8.723942 TCTGGCTCTTCTAAAAATTACATCTC 57.276 34.615 0.00 0.00 0.00 2.75
4697 5147 7.272037 TCTGAGAAACCATTGTAAAAAGACC 57.728 36.000 0.00 0.00 0.00 3.85
5417 5975 0.394352 CATGTTGACTGGGCCCTACC 60.394 60.000 25.70 12.10 37.93 3.18
5697 6268 3.764972 CTCTTTTCGGTTCTACTCCCTCT 59.235 47.826 0.00 0.00 0.00 3.69
5964 6557 4.876107 ACTTGTACAATTAATCGAGCCCTG 59.124 41.667 9.13 0.00 0.00 4.45
5967 6560 0.588252 CAATTAATCGAGCCCTGCCG 59.412 55.000 0.00 0.00 0.00 5.69
6013 6640 7.753309 TGTATGTATGTTTAGGCTTTGTTGT 57.247 32.000 0.00 0.00 0.00 3.32
6014 6641 8.172352 TGTATGTATGTTTAGGCTTTGTTGTT 57.828 30.769 0.00 0.00 0.00 2.83
6015 6642 8.079203 TGTATGTATGTTTAGGCTTTGTTGTTG 58.921 33.333 0.00 0.00 0.00 3.33
6043 6670 2.017049 ACATAGGCGACCATCTTTTGC 58.983 47.619 0.00 0.00 0.00 3.68
6044 6671 1.334869 CATAGGCGACCATCTTTTGCC 59.665 52.381 0.00 0.00 43.22 4.52
6051 6678 2.684881 CGACCATCTTTTGCCTGCTATT 59.315 45.455 0.00 0.00 0.00 1.73
6055 6682 4.340381 ACCATCTTTTGCCTGCTATTCATC 59.660 41.667 0.00 0.00 0.00 2.92
6056 6683 4.583489 CCATCTTTTGCCTGCTATTCATCT 59.417 41.667 0.00 0.00 0.00 2.90
6201 6845 6.456181 CGCTGTATTTTCCTTTTCTGCTAGAG 60.456 42.308 0.00 0.00 0.00 2.43
6202 6846 6.183360 GCTGTATTTTCCTTTTCTGCTAGAGG 60.183 42.308 0.00 0.00 0.00 3.69
6218 6875 4.688413 GCTAGAGGCTGCATATGTTAGAAC 59.312 45.833 4.29 1.42 38.06 3.01
6220 6877 5.365021 AGAGGCTGCATATGTTAGAACTT 57.635 39.130 4.29 0.00 0.00 2.66
6221 6878 6.485830 AGAGGCTGCATATGTTAGAACTTA 57.514 37.500 4.29 0.00 0.00 2.24
6225 6882 6.989169 AGGCTGCATATGTTAGAACTTAGAAG 59.011 38.462 4.29 0.00 0.00 2.85
6226 6883 6.763610 GGCTGCATATGTTAGAACTTAGAAGT 59.236 38.462 4.29 0.00 42.04 3.01
6227 6884 7.926555 GGCTGCATATGTTAGAACTTAGAAGTA 59.073 37.037 4.29 0.00 38.57 2.24
6228 6885 8.973378 GCTGCATATGTTAGAACTTAGAAGTAG 58.027 37.037 4.29 0.00 38.57 2.57
6229 6886 9.469807 CTGCATATGTTAGAACTTAGAAGTAGG 57.530 37.037 4.29 0.00 38.57 3.18
6230 6887 9.197306 TGCATATGTTAGAACTTAGAAGTAGGA 57.803 33.333 4.29 0.00 38.57 2.94
6231 6888 9.465985 GCATATGTTAGAACTTAGAAGTAGGAC 57.534 37.037 4.29 0.00 38.57 3.85
6239 6896 7.668492 AGAACTTAGAAGTAGGACACGAAAAT 58.332 34.615 0.00 0.00 38.57 1.82
6240 6897 7.813627 AGAACTTAGAAGTAGGACACGAAAATC 59.186 37.037 0.00 0.00 38.57 2.17
6248 6905 1.401018 GGACACGAAAATCCGCTTTGG 60.401 52.381 0.00 0.00 40.09 3.28
6264 6921 1.577468 TTGGCATGGCGAATACGTAG 58.423 50.000 15.27 0.00 41.98 3.51
6321 6978 5.285651 GTCAGAATCGATAAGGTTCAGAGG 58.714 45.833 0.00 0.00 42.37 3.69
6653 7315 3.228017 GCCCTCCGCCTCCTACTC 61.228 72.222 0.00 0.00 0.00 2.59
6657 7319 1.227664 CTCCGCCTCCTACTCTCCA 59.772 63.158 0.00 0.00 0.00 3.86
6658 7320 0.395862 CTCCGCCTCCTACTCTCCAA 60.396 60.000 0.00 0.00 0.00 3.53
6659 7321 0.683504 TCCGCCTCCTACTCTCCAAC 60.684 60.000 0.00 0.00 0.00 3.77
6660 7322 1.677637 CCGCCTCCTACTCTCCAACC 61.678 65.000 0.00 0.00 0.00 3.77
6661 7323 0.684805 CGCCTCCTACTCTCCAACCT 60.685 60.000 0.00 0.00 0.00 3.50
6662 7324 1.574263 GCCTCCTACTCTCCAACCTT 58.426 55.000 0.00 0.00 0.00 3.50
6669 7333 1.821088 ACTCTCCAACCTTTCCCTGT 58.179 50.000 0.00 0.00 0.00 4.00
6702 7371 6.073440 TCCGTACTTTGCTTAAACATTGTCTC 60.073 38.462 0.00 0.00 0.00 3.36
6818 7487 1.941812 CAATCGTAATGCTCCCGGC 59.058 57.895 0.00 0.00 42.22 6.13
6819 7488 1.227853 AATCGTAATGCTCCCGGCC 60.228 57.895 0.00 0.00 40.92 6.13
6821 7490 1.768684 ATCGTAATGCTCCCGGCCAT 61.769 55.000 2.24 0.00 40.92 4.40
6828 7497 0.471022 TGCTCCCGGCCATACTGATA 60.471 55.000 2.24 0.00 40.92 2.15
6832 7501 1.003118 TCCCGGCCATACTGATATTGC 59.997 52.381 2.24 0.00 0.00 3.56
6837 7506 4.333649 CCGGCCATACTGATATTGCTATTG 59.666 45.833 2.24 0.00 31.53 1.90
6838 7507 5.178061 CGGCCATACTGATATTGCTATTGA 58.822 41.667 2.24 0.00 31.53 2.57
6841 7510 7.658982 CGGCCATACTGATATTGCTATTGATAT 59.341 37.037 2.24 0.00 31.53 1.63
6842 7511 9.347240 GGCCATACTGATATTGCTATTGATATT 57.653 33.333 0.00 0.00 31.53 1.28
6848 7517 7.831193 ACTGATATTGCTATTGATATTCACCCC 59.169 37.037 0.00 0.00 0.00 4.95
6849 7518 7.118723 TGATATTGCTATTGATATTCACCCCC 58.881 38.462 0.00 0.00 0.00 5.40
6850 7519 4.805140 TTGCTATTGATATTCACCCCCA 57.195 40.909 0.00 0.00 0.00 4.96
6851 7520 4.805140 TGCTATTGATATTCACCCCCAA 57.195 40.909 0.00 0.00 0.00 4.12
6852 7521 5.337956 TGCTATTGATATTCACCCCCAAT 57.662 39.130 0.00 0.00 0.00 3.16
6853 7522 5.078949 TGCTATTGATATTCACCCCCAATG 58.921 41.667 0.00 0.00 0.00 2.82
6854 7523 5.079643 GCTATTGATATTCACCCCCAATGT 58.920 41.667 0.00 0.00 0.00 2.71
6855 7524 5.183904 GCTATTGATATTCACCCCCAATGTC 59.816 44.000 0.00 0.00 0.00 3.06
6856 7525 3.207265 TGATATTCACCCCCAATGTCG 57.793 47.619 0.00 0.00 0.00 4.35
6857 7526 2.774809 TGATATTCACCCCCAATGTCGA 59.225 45.455 0.00 0.00 0.00 4.20
6858 7527 3.201045 TGATATTCACCCCCAATGTCGAA 59.799 43.478 0.00 0.00 0.00 3.71
6859 7528 2.826674 ATTCACCCCCAATGTCGAAT 57.173 45.000 0.00 0.00 0.00 3.34
6860 7529 2.122783 TTCACCCCCAATGTCGAATC 57.877 50.000 0.00 0.00 0.00 2.52
6861 7530 0.254747 TCACCCCCAATGTCGAATCC 59.745 55.000 0.00 0.00 0.00 3.01
6862 7531 0.255890 CACCCCCAATGTCGAATCCT 59.744 55.000 0.00 0.00 0.00 3.24
6863 7532 0.255890 ACCCCCAATGTCGAATCCTG 59.744 55.000 0.00 0.00 0.00 3.86
6864 7533 1.103398 CCCCCAATGTCGAATCCTGC 61.103 60.000 0.00 0.00 0.00 4.85
6865 7534 0.107017 CCCCAATGTCGAATCCTGCT 60.107 55.000 0.00 0.00 0.00 4.24
6866 7535 1.303309 CCCAATGTCGAATCCTGCTC 58.697 55.000 0.00 0.00 0.00 4.26
6867 7536 1.134280 CCCAATGTCGAATCCTGCTCT 60.134 52.381 0.00 0.00 0.00 4.09
6868 7537 1.938577 CCAATGTCGAATCCTGCTCTG 59.061 52.381 0.00 0.00 0.00 3.35
6869 7538 1.329906 CAATGTCGAATCCTGCTCTGC 59.670 52.381 0.00 0.00 0.00 4.26
6870 7539 0.829333 ATGTCGAATCCTGCTCTGCT 59.171 50.000 0.00 0.00 0.00 4.24
6871 7540 0.610174 TGTCGAATCCTGCTCTGCTT 59.390 50.000 0.00 0.00 0.00 3.91
6872 7541 1.002430 TGTCGAATCCTGCTCTGCTTT 59.998 47.619 0.00 0.00 0.00 3.51
6873 7542 2.233676 TGTCGAATCCTGCTCTGCTTTA 59.766 45.455 0.00 0.00 0.00 1.85
6874 7543 2.863137 GTCGAATCCTGCTCTGCTTTAG 59.137 50.000 0.00 0.00 0.00 1.85
6875 7544 2.497675 TCGAATCCTGCTCTGCTTTAGT 59.502 45.455 0.00 0.00 0.00 2.24
6876 7545 3.055819 TCGAATCCTGCTCTGCTTTAGTT 60.056 43.478 0.00 0.00 0.00 2.24
6877 7546 3.308323 CGAATCCTGCTCTGCTTTAGTTC 59.692 47.826 0.00 0.00 0.00 3.01
6878 7547 2.770164 TCCTGCTCTGCTTTAGTTCC 57.230 50.000 0.00 0.00 0.00 3.62
6879 7548 1.279271 TCCTGCTCTGCTTTAGTTCCC 59.721 52.381 0.00 0.00 0.00 3.97
6880 7549 1.003580 CCTGCTCTGCTTTAGTTCCCA 59.996 52.381 0.00 0.00 0.00 4.37
6881 7550 2.356535 CCTGCTCTGCTTTAGTTCCCAT 60.357 50.000 0.00 0.00 0.00 4.00
6882 7551 3.350833 CTGCTCTGCTTTAGTTCCCATT 58.649 45.455 0.00 0.00 0.00 3.16
6883 7552 3.347216 TGCTCTGCTTTAGTTCCCATTC 58.653 45.455 0.00 0.00 0.00 2.67
6884 7553 3.009473 TGCTCTGCTTTAGTTCCCATTCT 59.991 43.478 0.00 0.00 0.00 2.40
6885 7554 4.013050 GCTCTGCTTTAGTTCCCATTCTT 58.987 43.478 0.00 0.00 0.00 2.52
6886 7555 4.460731 GCTCTGCTTTAGTTCCCATTCTTT 59.539 41.667 0.00 0.00 0.00 2.52
6887 7556 5.047731 GCTCTGCTTTAGTTCCCATTCTTTT 60.048 40.000 0.00 0.00 0.00 2.27
6888 7557 6.575162 TCTGCTTTAGTTCCCATTCTTTTC 57.425 37.500 0.00 0.00 0.00 2.29
6889 7558 6.068010 TCTGCTTTAGTTCCCATTCTTTTCA 58.932 36.000 0.00 0.00 0.00 2.69
6890 7559 6.207417 TCTGCTTTAGTTCCCATTCTTTTCAG 59.793 38.462 0.00 0.00 0.00 3.02
6891 7560 5.833131 TGCTTTAGTTCCCATTCTTTTCAGT 59.167 36.000 0.00 0.00 0.00 3.41
6892 7561 6.323739 TGCTTTAGTTCCCATTCTTTTCAGTT 59.676 34.615 0.00 0.00 0.00 3.16
6893 7562 7.504238 TGCTTTAGTTCCCATTCTTTTCAGTTA 59.496 33.333 0.00 0.00 0.00 2.24
6894 7563 7.808381 GCTTTAGTTCCCATTCTTTTCAGTTAC 59.192 37.037 0.00 0.00 0.00 2.50
6895 7564 8.754991 TTTAGTTCCCATTCTTTTCAGTTACA 57.245 30.769 0.00 0.00 0.00 2.41
6896 7565 8.934023 TTAGTTCCCATTCTTTTCAGTTACAT 57.066 30.769 0.00 0.00 0.00 2.29
6897 7566 7.839680 AGTTCCCATTCTTTTCAGTTACATT 57.160 32.000 0.00 0.00 0.00 2.71
6898 7567 7.661040 AGTTCCCATTCTTTTCAGTTACATTG 58.339 34.615 0.00 0.00 0.00 2.82
6899 7568 7.287696 AGTTCCCATTCTTTTCAGTTACATTGT 59.712 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.565759 CAATCCCCCACCAGATCTCAA 59.434 52.381 0.00 0.00 0.00 3.02
107 108 2.334946 CCCACCACCTTGTCATGCG 61.335 63.158 0.00 0.00 0.00 4.73
347 393 1.622811 CTCAGATCATGGCCCTACCTC 59.377 57.143 0.00 0.00 40.22 3.85
387 433 1.270678 GCTAAACCCACGTCCAAGTCT 60.271 52.381 0.00 0.00 0.00 3.24
404 450 2.044555 CGTGGAGAGACGTGGGCTA 61.045 63.158 0.00 0.00 34.56 3.93
431 477 3.431626 GCAGCGCCCCACATATATATGTA 60.432 47.826 24.50 0.00 44.57 2.29
500 554 0.390340 GCAGCAGAGGAATGACGTGA 60.390 55.000 0.00 0.00 0.00 4.35
507 561 1.749638 GCAGCAGCAGCAGAGGAAT 60.750 57.895 4.63 0.00 45.49 3.01
723 782 3.854669 CCTCGGCGGCCTTCTCAT 61.855 66.667 18.34 0.00 0.00 2.90
806 883 8.314021 TGCTACAATAGAAAGAAACATGAGAGA 58.686 33.333 0.00 0.00 0.00 3.10
824 901 5.403246 GCATATCGCTAGTACTGCTACAAT 58.597 41.667 5.39 2.28 37.77 2.71
963 1043 7.064728 CAGAAAGTAGTGTTGAGTAAATAGGCC 59.935 40.741 0.00 0.00 0.00 5.19
977 1057 1.068472 CGCGGTCTCAGAAAGTAGTGT 60.068 52.381 0.00 0.00 0.00 3.55
1174 1254 0.807667 CCGCCCTCGAATCTGAACAG 60.808 60.000 0.00 0.00 38.10 3.16
1475 1555 0.179000 GATCCATCTGAACCGCCTGT 59.821 55.000 0.00 0.00 0.00 4.00
1585 1665 5.506708 GACAGTACCCCTACATTTGGAAAT 58.493 41.667 0.00 0.00 0.00 2.17
2204 2356 8.700051 CACAAATAGATATACTGGAGATAGGGG 58.300 40.741 0.00 0.00 0.00 4.79
2816 3099 7.054124 TGAATTCAAGTCATACCTGGGAATAC 58.946 38.462 5.45 0.00 0.00 1.89
3291 3575 7.012989 GTGTGTGTATCCCAGAAAAGTAACTTT 59.987 37.037 0.00 0.00 34.94 2.66
3447 3731 4.401202 GGGGAATCTTTTGCCTTAATCGAA 59.599 41.667 0.00 0.00 42.66 3.71
3448 3732 3.951680 GGGGAATCTTTTGCCTTAATCGA 59.048 43.478 0.00 0.00 42.66 3.59
3476 3760 4.024893 CACAAAGACACCGTATATGATGCC 60.025 45.833 0.00 0.00 0.00 4.40
3955 4255 7.489113 ACTCATGTTGATTTCGATTTTATTGCC 59.511 33.333 0.00 0.00 0.00 4.52
4064 4366 6.372659 CCTTCGGTGAATGAATATAAGATGGG 59.627 42.308 0.00 0.00 0.00 4.00
4126 4428 4.900054 TGTTCTAGGCTTAGATTAGTCCCC 59.100 45.833 6.37 0.00 35.88 4.81
4481 4785 8.420374 TTTTTAGGTCAAGCAGTCTATAATCG 57.580 34.615 0.00 0.00 0.00 3.34
4563 4868 1.151413 AGGAGGACCTTGGGTAAGACA 59.849 52.381 0.00 0.00 45.36 3.41
4673 5123 6.831353 TGGTCTTTTTACAATGGTTTCTCAGA 59.169 34.615 0.00 0.00 0.00 3.27
4697 5147 7.750458 GTCCAATGTGTATGTAAATGTGAAGTG 59.250 37.037 0.00 0.00 0.00 3.16
4774 5225 2.158726 ACAGCCCACTTCTTTCGGTTTA 60.159 45.455 0.00 0.00 0.00 2.01
5697 6268 3.061322 CCACGACGAGTAATTTGGAACA 58.939 45.455 0.00 0.00 0.00 3.18
5964 6557 1.722011 ACACAACATACTACAGCGGC 58.278 50.000 0.00 0.00 0.00 6.53
5967 6560 6.262601 ACAACAAAACACAACATACTACAGC 58.737 36.000 0.00 0.00 0.00 4.40
6013 6640 3.055747 TGGTCGCCTATGTAATGTGACAA 60.056 43.478 0.00 0.00 40.39 3.18
6014 6641 2.498078 TGGTCGCCTATGTAATGTGACA 59.502 45.455 0.00 0.00 40.39 3.58
6015 6642 3.173668 TGGTCGCCTATGTAATGTGAC 57.826 47.619 0.00 0.00 38.47 3.67
6043 6670 3.307550 CCAGGATCCAGATGAATAGCAGG 60.308 52.174 15.82 0.00 0.00 4.85
6044 6671 3.327172 ACCAGGATCCAGATGAATAGCAG 59.673 47.826 15.82 0.00 0.00 4.24
6051 6678 0.543277 GCACACCAGGATCCAGATGA 59.457 55.000 15.82 0.00 0.00 2.92
6055 6682 0.679002 CAAGGCACACCAGGATCCAG 60.679 60.000 15.82 5.70 39.06 3.86
6056 6683 1.379916 CAAGGCACACCAGGATCCA 59.620 57.895 15.82 0.00 39.06 3.41
6141 6780 2.838736 TCAAGCTCAACTCCACACTTC 58.161 47.619 0.00 0.00 0.00 3.01
6148 6787 1.339438 TGCAGGATCAAGCTCAACTCC 60.339 52.381 9.60 0.00 0.00 3.85
6201 6845 6.763610 ACTTCTAAGTTCTAACATATGCAGCC 59.236 38.462 1.58 0.00 35.21 4.85
6202 6846 7.778470 ACTTCTAAGTTCTAACATATGCAGC 57.222 36.000 1.58 0.00 35.21 5.25
6218 6875 5.515626 CGGATTTTCGTGTCCTACTTCTAAG 59.484 44.000 0.00 0.00 32.19 2.18
6220 6877 4.676196 GCGGATTTTCGTGTCCTACTTCTA 60.676 45.833 0.00 0.00 32.19 2.10
6221 6878 3.846360 CGGATTTTCGTGTCCTACTTCT 58.154 45.455 0.00 0.00 32.19 2.85
6225 6882 2.005971 AGCGGATTTTCGTGTCCTAC 57.994 50.000 0.00 0.00 32.19 3.18
6226 6883 2.739913 CAAAGCGGATTTTCGTGTCCTA 59.260 45.455 0.00 0.00 32.19 2.94
6227 6884 1.535462 CAAAGCGGATTTTCGTGTCCT 59.465 47.619 0.00 0.00 32.19 3.85
6228 6885 1.401018 CCAAAGCGGATTTTCGTGTCC 60.401 52.381 0.00 0.00 36.56 4.02
6229 6886 1.963747 CCAAAGCGGATTTTCGTGTC 58.036 50.000 0.00 0.00 36.56 3.67
6230 6887 0.039527 GCCAAAGCGGATTTTCGTGT 60.040 50.000 0.00 0.00 36.56 4.49
6231 6888 0.039617 TGCCAAAGCGGATTTTCGTG 60.040 50.000 0.00 0.00 44.31 4.35
6232 6889 0.887933 ATGCCAAAGCGGATTTTCGT 59.112 45.000 0.00 0.00 44.31 3.85
6233 6890 1.270971 CATGCCAAAGCGGATTTTCG 58.729 50.000 0.00 0.00 44.31 3.46
6248 6905 2.034001 GTCAACTACGTATTCGCCATGC 60.034 50.000 0.00 0.00 41.18 4.06
6270 6927 1.463444 GTTGGTGGAGACGTATTGCAC 59.537 52.381 13.55 13.55 36.31 4.57
6646 7308 2.113777 AGGGAAAGGTTGGAGAGTAGGA 59.886 50.000 0.00 0.00 0.00 2.94
6647 7309 2.237392 CAGGGAAAGGTTGGAGAGTAGG 59.763 54.545 0.00 0.00 0.00 3.18
6648 7310 2.907042 ACAGGGAAAGGTTGGAGAGTAG 59.093 50.000 0.00 0.00 0.00 2.57
6651 7313 2.959465 AACAGGGAAAGGTTGGAGAG 57.041 50.000 0.00 0.00 0.00 3.20
6652 7314 2.158519 GGAAACAGGGAAAGGTTGGAGA 60.159 50.000 0.00 0.00 0.00 3.71
6653 7315 2.239400 GGAAACAGGGAAAGGTTGGAG 58.761 52.381 0.00 0.00 0.00 3.86
6657 7319 3.432262 CCGGAAACAGGGAAAGGTT 57.568 52.632 0.00 0.00 0.00 3.50
6669 7333 0.603439 GCAAAGTACGGACCCGGAAA 60.603 55.000 13.43 0.00 44.69 3.13
6702 7371 0.860203 CGCATCGAATTGCTGCACAG 60.860 55.000 0.00 0.00 39.69 3.66
6821 7490 9.890629 GGGTGAATATCAATAGCAATATCAGTA 57.109 33.333 0.00 0.00 0.00 2.74
6828 7497 5.337956 TGGGGGTGAATATCAATAGCAAT 57.662 39.130 0.00 0.00 0.00 3.56
6832 7501 5.412594 CGACATTGGGGGTGAATATCAATAG 59.587 44.000 0.00 0.00 0.00 1.73
6837 7506 3.485463 TCGACATTGGGGGTGAATATC 57.515 47.619 0.00 0.00 0.00 1.63
6838 7507 3.943671 TTCGACATTGGGGGTGAATAT 57.056 42.857 0.00 0.00 0.00 1.28
6841 7510 1.340600 GGATTCGACATTGGGGGTGAA 60.341 52.381 0.00 0.00 0.00 3.18
6842 7511 0.254747 GGATTCGACATTGGGGGTGA 59.745 55.000 0.00 0.00 0.00 4.02
6844 7513 0.255890 CAGGATTCGACATTGGGGGT 59.744 55.000 0.00 0.00 0.00 4.95
6848 7517 1.938577 CAGAGCAGGATTCGACATTGG 59.061 52.381 0.00 0.00 0.00 3.16
6849 7518 1.329906 GCAGAGCAGGATTCGACATTG 59.670 52.381 0.00 0.00 0.00 2.82
6850 7519 1.209019 AGCAGAGCAGGATTCGACATT 59.791 47.619 0.00 0.00 0.00 2.71
6851 7520 0.829333 AGCAGAGCAGGATTCGACAT 59.171 50.000 0.00 0.00 0.00 3.06
6852 7521 0.610174 AAGCAGAGCAGGATTCGACA 59.390 50.000 0.00 0.00 0.00 4.35
6853 7522 1.731720 AAAGCAGAGCAGGATTCGAC 58.268 50.000 0.00 0.00 0.00 4.20
6854 7523 2.497675 ACTAAAGCAGAGCAGGATTCGA 59.502 45.455 0.00 0.00 0.00 3.71
6855 7524 2.898705 ACTAAAGCAGAGCAGGATTCG 58.101 47.619 0.00 0.00 0.00 3.34
6856 7525 3.625313 GGAACTAAAGCAGAGCAGGATTC 59.375 47.826 0.00 0.00 0.00 2.52
6857 7526 3.615155 GGAACTAAAGCAGAGCAGGATT 58.385 45.455 0.00 0.00 0.00 3.01
6858 7527 2.092699 GGGAACTAAAGCAGAGCAGGAT 60.093 50.000 0.00 0.00 0.00 3.24
6859 7528 1.279271 GGGAACTAAAGCAGAGCAGGA 59.721 52.381 0.00 0.00 0.00 3.86
6860 7529 1.003580 TGGGAACTAAAGCAGAGCAGG 59.996 52.381 0.00 0.00 0.00 4.85
6861 7530 2.479566 TGGGAACTAAAGCAGAGCAG 57.520 50.000 0.00 0.00 0.00 4.24
6862 7531 3.009473 AGAATGGGAACTAAAGCAGAGCA 59.991 43.478 0.00 0.00 0.00 4.26
6863 7532 3.615155 AGAATGGGAACTAAAGCAGAGC 58.385 45.455 0.00 0.00 0.00 4.09
6864 7533 6.207417 TGAAAAGAATGGGAACTAAAGCAGAG 59.793 38.462 0.00 0.00 0.00 3.35
6865 7534 6.068010 TGAAAAGAATGGGAACTAAAGCAGA 58.932 36.000 0.00 0.00 0.00 4.26
6866 7535 6.015940 ACTGAAAAGAATGGGAACTAAAGCAG 60.016 38.462 0.00 0.00 0.00 4.24
6867 7536 5.833131 ACTGAAAAGAATGGGAACTAAAGCA 59.167 36.000 0.00 0.00 0.00 3.91
6868 7537 6.332735 ACTGAAAAGAATGGGAACTAAAGC 57.667 37.500 0.00 0.00 0.00 3.51
6869 7538 8.846211 TGTAACTGAAAAGAATGGGAACTAAAG 58.154 33.333 0.00 0.00 0.00 1.85
6870 7539 8.754991 TGTAACTGAAAAGAATGGGAACTAAA 57.245 30.769 0.00 0.00 0.00 1.85
6871 7540 8.934023 ATGTAACTGAAAAGAATGGGAACTAA 57.066 30.769 0.00 0.00 0.00 2.24
6872 7541 8.792633 CAATGTAACTGAAAAGAATGGGAACTA 58.207 33.333 0.00 0.00 0.00 2.24
6873 7542 7.287696 ACAATGTAACTGAAAAGAATGGGAACT 59.712 33.333 0.00 0.00 0.00 3.01
6874 7543 7.433680 ACAATGTAACTGAAAAGAATGGGAAC 58.566 34.615 0.00 0.00 0.00 3.62
6875 7544 7.595819 ACAATGTAACTGAAAAGAATGGGAA 57.404 32.000 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.