Multiple sequence alignment - TraesCS5D01G335700

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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 TraesCS5D01G335700 chr5D 100.000 3349 0 0 1 3349 425078628 425075280 0.000000e+00 6185.0
1 TraesCS5D01G335700 chr5D 87.861 346 23 7 3010 3349 425040469 425040137 4.050000e-104 388.0
2 TraesCS5D01G335700 chr5D 84.426 122 17 2 1533 1653 200501539 200501659 5.870000e-23 119.0
3 TraesCS5D01G335700 chr5A 88.163 3075 142 90 107 3112 539094517 539091596 0.000000e+00 3458.0
4 TraesCS5D01G335700 chr5A 84.000 200 6 5 3135 3330 539091340 539091163 5.750000e-38 169.0
5 TraesCS5D01G335700 chr5A 84.426 122 17 2 1533 1653 214166890 214167010 5.870000e-23 119.0
6 TraesCS5D01G335700 chr5A 100.000 34 0 0 76 109 539094591 539094558 2.790000e-06 63.9
7 TraesCS5D01G335700 chr5B 91.174 2300 83 38 107 2334 514280688 514278437 0.000000e+00 3013.0
8 TraesCS5D01G335700 chr5B 81.417 1087 76 47 2332 3321 514278163 514277106 0.000000e+00 773.0
9 TraesCS5D01G335700 chr5B 82.958 311 22 17 3052 3349 514077118 514076826 5.550000e-63 252.0
10 TraesCS5D01G335700 chr5B 84.426 122 17 2 1533 1653 211146510 211146630 5.870000e-23 119.0
11 TraesCS5D01G335700 chr3A 93.609 266 17 0 1144 1409 633922101 633922366 6.730000e-107 398.0
12 TraesCS5D01G335700 chr3B 92.857 266 19 0 1144 1409 653152051 653152316 1.460000e-103 387.0
13 TraesCS5D01G335700 chr3D 92.481 266 20 0 1144 1409 492131424 492131689 6.780000e-102 381.0
14 TraesCS5D01G335700 chr1A 91.729 266 22 0 1144 1409 463461697 463461432 1.470000e-98 370.0
15 TraesCS5D01G335700 chr1B 90.741 270 25 0 1144 1413 487951482 487951213 8.830000e-96 361.0
16 TraesCS5D01G335700 chr1D 90.406 271 24 2 1144 1413 364625272 364625003 4.110000e-94 355.0
17 TraesCS5D01G335700 chr7D 89.434 265 28 0 1144 1408 262698956 262698692 5.350000e-88 335.0
18 TraesCS5D01G335700 chr7D 91.579 95 8 0 1559 1653 262698671 262698577 7.540000e-27 132.0
19 TraesCS5D01G335700 chr4B 75.493 355 61 21 1273 1620 100576660 100576995 2.080000e-32 150.0
20 TraesCS5D01G335700 chr7A 91.011 89 8 0 1565 1653 285576317 285576229 1.630000e-23 121.0
21 TraesCS5D01G335700 chr7B 84.483 116 18 0 1538 1653 241107945 241108060 7.590000e-22 115.0


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 TraesCS5D01G335700 chr5D 425075280 425078628 3348 True 6185.0 6185 100.0000 1 3349 1 chr5D.!!$R2 3348
1 TraesCS5D01G335700 chr5A 539091163 539094591 3428 True 1230.3 3458 90.7210 76 3330 3 chr5A.!!$R1 3254
2 TraesCS5D01G335700 chr5B 514277106 514280688 3582 True 1893.0 3013 86.2955 107 3321 2 chr5B.!!$R2 3214

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
282 342 0.541863 AAATGGCTCGGGGAGTAGTG 59.458 55.0 0.0 0.0 31.39 2.74 F
1424 1553 0.661552 AGTACGTCCATCCATCGTCG 59.338 55.0 0.0 0.0 38.69 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1601 0.542467 ACAAGGCCATGCATGTGGAA 60.542 50.0 24.58 0.00 42.02 3.53 R
2729 3183 0.179215 GTTTGACGGCATGCTCTTCG 60.179 55.0 18.92 14.89 0.00 3.79 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
23 24 5.565509 TGTTAATACCTCATCCAGTTTGCA 58.434 37.500 0.00 0.00 0.00 4.08
24 25 5.414454 TGTTAATACCTCATCCAGTTTGCAC 59.586 40.000 0.00 0.00 0.00 4.57
25 26 4.307032 AATACCTCATCCAGTTTGCACT 57.693 40.909 0.00 0.00 0.00 4.40
26 27 5.435686 AATACCTCATCCAGTTTGCACTA 57.564 39.130 0.00 0.00 0.00 2.74
27 28 5.636903 ATACCTCATCCAGTTTGCACTAT 57.363 39.130 0.00 0.00 0.00 2.12
28 29 3.614092 ACCTCATCCAGTTTGCACTATG 58.386 45.455 0.00 0.00 0.00 2.23
29 30 2.947652 CCTCATCCAGTTTGCACTATGG 59.052 50.000 4.24 4.24 0.00 2.74
30 31 3.370846 CCTCATCCAGTTTGCACTATGGA 60.371 47.826 13.69 13.69 45.48 3.41
31 32 3.609853 TCATCCAGTTTGCACTATGGAC 58.390 45.455 13.62 0.00 44.28 4.02
32 33 3.008923 TCATCCAGTTTGCACTATGGACA 59.991 43.478 13.62 3.27 44.28 4.02
33 34 3.719268 TCCAGTTTGCACTATGGACAT 57.281 42.857 8.52 0.00 36.92 3.06
34 35 4.032960 TCCAGTTTGCACTATGGACATT 57.967 40.909 8.52 0.00 36.92 2.71
35 36 3.758023 TCCAGTTTGCACTATGGACATTG 59.242 43.478 8.52 0.00 36.92 2.82
36 37 3.119388 CCAGTTTGCACTATGGACATTGG 60.119 47.826 4.57 0.00 34.60 3.16
37 38 2.493278 AGTTTGCACTATGGACATTGGC 59.507 45.455 0.00 0.00 0.00 4.52
38 39 2.493278 GTTTGCACTATGGACATTGGCT 59.507 45.455 0.00 0.00 0.00 4.75
39 40 2.512692 TGCACTATGGACATTGGCTT 57.487 45.000 0.00 0.00 0.00 4.35
40 41 2.093890 TGCACTATGGACATTGGCTTG 58.906 47.619 0.00 0.00 0.00 4.01
41 42 2.094675 GCACTATGGACATTGGCTTGT 58.905 47.619 0.00 0.00 0.00 3.16
42 43 3.278574 GCACTATGGACATTGGCTTGTA 58.721 45.455 0.00 0.00 0.00 2.41
43 44 3.885297 GCACTATGGACATTGGCTTGTAT 59.115 43.478 0.00 0.00 0.00 2.29
44 45 4.261322 GCACTATGGACATTGGCTTGTATG 60.261 45.833 0.00 0.00 0.00 2.39
45 46 4.276678 CACTATGGACATTGGCTTGTATGG 59.723 45.833 0.00 0.00 0.00 2.74
46 47 2.142356 TGGACATTGGCTTGTATGGG 57.858 50.000 0.00 0.00 0.00 4.00
47 48 1.357420 TGGACATTGGCTTGTATGGGT 59.643 47.619 0.00 0.00 0.00 4.51
48 49 1.750778 GGACATTGGCTTGTATGGGTG 59.249 52.381 0.00 0.00 0.00 4.61
49 50 1.134946 GACATTGGCTTGTATGGGTGC 59.865 52.381 0.00 0.00 0.00 5.01
50 51 1.184431 CATTGGCTTGTATGGGTGCA 58.816 50.000 0.00 0.00 0.00 4.57
51 52 1.135024 CATTGGCTTGTATGGGTGCAC 60.135 52.381 8.80 8.80 0.00 4.57
52 53 0.897863 TTGGCTTGTATGGGTGCACC 60.898 55.000 28.57 28.57 40.81 5.01
60 61 2.845784 TGGGTGCACCAGAGCATT 59.154 55.556 35.78 0.00 46.80 3.56
61 62 2.074099 TGGGTGCACCAGAGCATTA 58.926 52.632 35.78 9.38 46.80 1.90
62 63 0.625316 TGGGTGCACCAGAGCATTAT 59.375 50.000 35.78 0.00 46.80 1.28
63 64 1.005805 TGGGTGCACCAGAGCATTATT 59.994 47.619 35.78 0.00 46.80 1.40
64 65 2.557229 TGGGTGCACCAGAGCATTATTT 60.557 45.455 35.78 0.00 46.80 1.40
65 66 4.436006 TGGGTGCACCAGAGCATTATTTC 61.436 47.826 35.78 14.85 46.80 2.17
67 68 3.370840 TGCACCAGAGCATTATTTCCT 57.629 42.857 0.00 0.00 40.11 3.36
68 69 3.700538 TGCACCAGAGCATTATTTCCTT 58.299 40.909 0.00 0.00 40.11 3.36
69 70 3.444742 TGCACCAGAGCATTATTTCCTTG 59.555 43.478 0.00 0.00 40.11 3.61
70 71 3.445096 GCACCAGAGCATTATTTCCTTGT 59.555 43.478 0.00 0.00 0.00 3.16
71 72 4.082026 GCACCAGAGCATTATTTCCTTGTT 60.082 41.667 0.00 0.00 0.00 2.83
72 73 5.125417 GCACCAGAGCATTATTTCCTTGTTA 59.875 40.000 0.00 0.00 0.00 2.41
73 74 6.350110 GCACCAGAGCATTATTTCCTTGTTAA 60.350 38.462 0.00 0.00 0.00 2.01
74 75 7.601856 CACCAGAGCATTATTTCCTTGTTAAA 58.398 34.615 0.00 0.00 0.00 1.52
127 171 6.404513 GGCTCGTCTACAACTAATACTCTGTT 60.405 42.308 0.00 0.00 0.00 3.16
128 172 6.687958 GCTCGTCTACAACTAATACTCTGTTC 59.312 42.308 0.00 0.00 0.00 3.18
129 173 7.414319 GCTCGTCTACAACTAATACTCTGTTCT 60.414 40.741 0.00 0.00 0.00 3.01
130 174 9.096160 CTCGTCTACAACTAATACTCTGTTCTA 57.904 37.037 0.00 0.00 0.00 2.10
179 223 3.006859 TGTCGACATGATTGAGTTGGAGT 59.993 43.478 15.76 0.00 0.00 3.85
277 337 1.202698 CCTAGAAAATGGCTCGGGGAG 60.203 57.143 0.00 0.00 0.00 4.30
282 342 0.541863 AAATGGCTCGGGGAGTAGTG 59.458 55.000 0.00 0.00 31.39 2.74
290 350 1.079336 GGGGAGTAGTGTCCAACGC 60.079 63.158 0.00 0.00 38.52 4.84
351 412 8.849168 AGACAAATTATCATTGAGTTTGTGTCA 58.151 29.630 21.92 0.00 41.50 3.58
368 429 5.389520 TGTGTCATACAAAAAGATTGGGGA 58.610 37.500 0.00 0.00 36.06 4.81
517 578 1.742268 GCAGCATCAAGGGAAAGAGAC 59.258 52.381 0.00 0.00 0.00 3.36
523 588 1.978580 TCAAGGGAAAGAGACTGGGAC 59.021 52.381 0.00 0.00 0.00 4.46
589 654 3.399181 GGAGGCATCACGGGTGGA 61.399 66.667 0.00 0.00 0.00 4.02
590 655 2.746375 GGAGGCATCACGGGTGGAT 61.746 63.158 0.00 0.00 0.00 3.41
613 678 4.996062 TGCGGTTAGTTAGCTGTTAAAC 57.004 40.909 0.00 0.00 0.00 2.01
615 680 3.181527 GCGGTTAGTTAGCTGTTAAACCG 60.182 47.826 27.21 27.21 39.66 4.44
616 681 4.236935 CGGTTAGTTAGCTGTTAAACCGA 58.763 43.478 27.40 3.23 39.09 4.69
617 682 4.685628 CGGTTAGTTAGCTGTTAAACCGAA 59.314 41.667 27.40 8.12 39.09 4.30
652 717 4.109656 AGGGTAGGCAGGGGGAGG 62.110 72.222 0.00 0.00 0.00 4.30
677 742 4.246458 GAGCTTACCTCACTTTACACCTG 58.754 47.826 0.00 0.00 40.45 4.00
717 782 0.897621 GGCAAGTAGGCAGGCAAATT 59.102 50.000 0.00 0.00 43.51 1.82
840 916 1.625315 TGAGTTGAGGTGAGGTCATGG 59.375 52.381 0.00 0.00 0.00 3.66
845 921 2.262774 GAGGTGAGGTCATGGCCTGG 62.263 65.000 27.08 0.00 39.34 4.45
853 951 2.693864 CATGGCCTGGGGGAGAGT 60.694 66.667 3.32 0.00 33.58 3.24
854 952 2.367512 ATGGCCTGGGGGAGAGTC 60.368 66.667 3.32 0.00 33.58 3.36
855 953 4.741239 TGGCCTGGGGGAGAGTCC 62.741 72.222 3.32 0.00 35.23 3.85
859 957 4.075793 CTGGGGGAGAGTCCGGGA 62.076 72.222 0.00 0.00 37.43 5.14
860 958 4.075793 TGGGGGAGAGTCCGGGAG 62.076 72.222 0.00 0.00 37.43 4.30
889 987 1.945071 AGGGGGAGGCCTACCAGTA 60.945 63.158 35.75 0.00 39.06 2.74
890 988 1.459730 GGGGGAGGCCTACCAGTAG 60.460 68.421 35.75 0.00 39.06 2.57
986 1094 1.347707 CCGCCTATAAAGATCCAGCCA 59.652 52.381 0.00 0.00 0.00 4.75
987 1095 2.224523 CCGCCTATAAAGATCCAGCCAA 60.225 50.000 0.00 0.00 0.00 4.52
988 1096 3.476552 CGCCTATAAAGATCCAGCCAAA 58.523 45.455 0.00 0.00 0.00 3.28
1096 1215 1.403679 CACCACCGAGCACAAGAAAAA 59.596 47.619 0.00 0.00 0.00 1.94
1103 1232 2.096019 CGAGCACAAGAAAAAGGAGAGC 60.096 50.000 0.00 0.00 0.00 4.09
1417 1546 1.084289 GGCAACAAGTACGTCCATCC 58.916 55.000 0.00 0.00 0.00 3.51
1418 1547 1.609580 GGCAACAAGTACGTCCATCCA 60.610 52.381 0.00 0.00 0.00 3.41
1419 1548 2.356135 GCAACAAGTACGTCCATCCAT 58.644 47.619 0.00 0.00 0.00 3.41
1420 1549 2.351726 GCAACAAGTACGTCCATCCATC 59.648 50.000 0.00 0.00 0.00 3.51
1421 1550 2.579207 ACAAGTACGTCCATCCATCG 57.421 50.000 0.00 0.00 0.00 3.84
1422 1551 1.822990 ACAAGTACGTCCATCCATCGT 59.177 47.619 0.00 0.00 40.78 3.73
1423 1552 2.159282 ACAAGTACGTCCATCCATCGTC 60.159 50.000 0.00 0.00 38.69 4.20
1424 1553 0.661552 AGTACGTCCATCCATCGTCG 59.338 55.000 0.00 0.00 38.69 5.12
1444 1573 6.708949 TCGTCGTATCCATAGCATATATAGCA 59.291 38.462 9.01 0.00 0.00 3.49
1447 1576 6.072673 TCGTATCCATAGCATATATAGCACCG 60.073 42.308 9.01 0.00 0.00 4.94
1451 1580 5.011023 TCCATAGCATATATAGCACCGATGG 59.989 44.000 15.06 15.06 34.41 3.51
1458 1587 2.550830 ATAGCACCGATGGATGAACC 57.449 50.000 0.00 0.00 39.54 3.62
1472 1601 4.213564 GATGAACCATCCTCTGTTCTGT 57.786 45.455 0.00 0.00 41.10 3.41
1475 1604 3.244561 TGAACCATCCTCTGTTCTGTTCC 60.245 47.826 0.00 0.00 41.10 3.62
1620 1749 1.088340 CGCACATCAGGAGGAAGCTG 61.088 60.000 0.00 0.00 0.00 4.24
1923 2058 2.668550 GTGGACACCAAGCCCGTC 60.669 66.667 0.00 0.00 34.18 4.79
2100 2252 3.952799 GAGCACCCCCTCCCTCCTT 62.953 68.421 0.00 0.00 0.00 3.36
2204 2365 1.879380 TGATCTTGTGTTTCGCCAAGG 59.121 47.619 0.00 0.00 38.83 3.61
2211 2372 1.880027 GTGTTTCGCCAAGGTCATCTT 59.120 47.619 0.00 0.00 35.79 2.40
2322 2486 0.618680 ATACTCTGGTGCTGGCTGGA 60.619 55.000 0.00 0.00 0.00 3.86
2422 2864 0.690411 AGGAGAGCAGACCAGATGGG 60.690 60.000 3.48 0.00 44.81 4.00
2596 3039 1.959985 TGCTTTTCTTTTCGATGCCCA 59.040 42.857 0.00 0.00 0.00 5.36
2597 3040 2.363680 TGCTTTTCTTTTCGATGCCCAA 59.636 40.909 0.00 0.00 0.00 4.12
2598 3041 3.181471 TGCTTTTCTTTTCGATGCCCAAA 60.181 39.130 0.00 0.00 0.00 3.28
2599 3042 3.184379 GCTTTTCTTTTCGATGCCCAAAC 59.816 43.478 0.00 0.00 0.00 2.93
2600 3043 4.620982 CTTTTCTTTTCGATGCCCAAACT 58.379 39.130 0.00 0.00 0.00 2.66
2601 3044 4.664150 TTTCTTTTCGATGCCCAAACTT 57.336 36.364 0.00 0.00 0.00 2.66
2602 3045 4.664150 TTCTTTTCGATGCCCAAACTTT 57.336 36.364 0.00 0.00 0.00 2.66
2603 3046 3.976169 TCTTTTCGATGCCCAAACTTTG 58.024 40.909 0.00 0.00 0.00 2.77
2619 3069 2.290705 ACTTTGGGGTGGCTACATACAC 60.291 50.000 1.52 0.00 36.89 2.90
2632 3082 5.296035 GGCTACATACACACATAACCCTTTC 59.704 44.000 0.00 0.00 0.00 2.62
2637 3087 7.882179 ACATACACACATAACCCTTTCTTTTC 58.118 34.615 0.00 0.00 0.00 2.29
2640 3090 5.238650 ACACACATAACCCTTTCTTTTCTCG 59.761 40.000 0.00 0.00 0.00 4.04
2641 3091 4.215613 ACACATAACCCTTTCTTTTCTCGC 59.784 41.667 0.00 0.00 0.00 5.03
2642 3092 3.435671 ACATAACCCTTTCTTTTCTCGCG 59.564 43.478 0.00 0.00 0.00 5.87
2643 3093 2.249844 AACCCTTTCTTTTCTCGCGA 57.750 45.000 9.26 9.26 0.00 5.87
2647 3097 3.568430 ACCCTTTCTTTTCTCGCGAAAAT 59.432 39.130 11.33 0.00 45.27 1.82
2689 3142 7.908082 GTCCATGTGAATATTTTTCGAATCGAA 59.092 33.333 14.59 14.59 44.28 3.71
2697 3150 3.204505 TTCGAATCGAAACCGCAGT 57.795 47.368 16.25 0.00 43.00 4.40
2698 3151 1.065358 TTCGAATCGAAACCGCAGTC 58.935 50.000 16.25 0.00 43.00 3.51
2699 3152 0.242825 TCGAATCGAAACCGCAGTCT 59.757 50.000 1.57 0.00 31.06 3.24
2730 3184 8.442605 AATTTTACATCCGTTGTTAAACATCG 57.557 30.769 0.00 0.00 39.04 3.84
2731 3185 6.782298 TTTACATCCGTTGTTAAACATCGA 57.218 33.333 0.00 0.00 42.15 3.59
2735 3189 5.120208 ACATCCGTTGTTAAACATCGAAGAG 59.880 40.000 0.00 0.00 42.15 2.85
2736 3190 3.430895 TCCGTTGTTAAACATCGAAGAGC 59.569 43.478 0.00 0.00 42.15 4.09
2740 3194 4.340894 TGTTAAACATCGAAGAGCATGC 57.659 40.909 10.51 10.51 43.63 4.06
2900 3403 4.213482 GTGTATCTGAAACCAGGTGTGTTC 59.787 45.833 0.00 0.00 32.62 3.18
2901 3404 1.948104 TCTGAAACCAGGTGTGTTCG 58.052 50.000 0.00 0.00 32.62 3.95
2921 3424 2.236395 CGTTCAGGGAGAAGGTGGTAAT 59.764 50.000 0.00 0.00 36.78 1.89
2931 3434 4.526970 AGAAGGTGGTAATGGCATTAGTG 58.473 43.478 19.79 0.00 0.00 2.74
2933 3436 4.316025 AGGTGGTAATGGCATTAGTGTT 57.684 40.909 19.79 3.25 0.00 3.32
2939 3442 4.576463 GGTAATGGCATTAGTGTTGGAGAG 59.424 45.833 19.79 0.00 0.00 3.20
2981 3484 4.752879 GAGCGGCTAACCACGGCA 62.753 66.667 0.60 0.00 35.96 5.69
2983 3486 4.097863 GCGGCTAACCACGGCAAC 62.098 66.667 0.00 0.00 34.57 4.17
2990 3493 2.223618 GCTAACCACGGCAACAAAGAAA 60.224 45.455 0.00 0.00 0.00 2.52
2991 3494 3.735514 GCTAACCACGGCAACAAAGAAAA 60.736 43.478 0.00 0.00 0.00 2.29
2992 3495 2.577449 ACCACGGCAACAAAGAAAAG 57.423 45.000 0.00 0.00 0.00 2.27
2997 3507 3.020984 ACGGCAACAAAGAAAAGAGGAA 58.979 40.909 0.00 0.00 0.00 3.36
2998 3508 3.066760 ACGGCAACAAAGAAAAGAGGAAG 59.933 43.478 0.00 0.00 0.00 3.46
2999 3509 3.550842 CGGCAACAAAGAAAAGAGGAAGG 60.551 47.826 0.00 0.00 0.00 3.46
3000 3510 3.384789 GGCAACAAAGAAAAGAGGAAGGT 59.615 43.478 0.00 0.00 0.00 3.50
3001 3511 4.583073 GGCAACAAAGAAAAGAGGAAGGTA 59.417 41.667 0.00 0.00 0.00 3.08
3002 3512 5.507482 GGCAACAAAGAAAAGAGGAAGGTAC 60.507 44.000 0.00 0.00 0.00 3.34
3003 3513 5.507482 GCAACAAAGAAAAGAGGAAGGTACC 60.507 44.000 2.73 2.73 0.00 3.34
3004 3514 5.382664 ACAAAGAAAAGAGGAAGGTACCA 57.617 39.130 15.94 0.00 0.00 3.25
3005 3515 5.377478 ACAAAGAAAAGAGGAAGGTACCAG 58.623 41.667 15.94 0.00 0.00 4.00
3006 3516 4.642466 AAGAAAAGAGGAAGGTACCAGG 57.358 45.455 15.94 0.00 0.00 4.45
3007 3517 3.870559 AGAAAAGAGGAAGGTACCAGGA 58.129 45.455 15.94 0.00 0.00 3.86
3008 3518 3.583526 AGAAAAGAGGAAGGTACCAGGAC 59.416 47.826 15.94 1.00 0.00 3.85
3039 3549 1.954382 GTGACAAAGGGACAAGGGAAC 59.046 52.381 0.00 0.00 0.00 3.62
3092 3602 2.204059 AGCCCAGCCACCTCTTCT 60.204 61.111 0.00 0.00 0.00 2.85
3093 3603 2.270527 GCCCAGCCACCTCTTCTC 59.729 66.667 0.00 0.00 0.00 2.87
3094 3604 2.297129 GCCCAGCCACCTCTTCTCT 61.297 63.158 0.00 0.00 0.00 3.10
3188 3936 1.534959 TCCAGTCAGCAGCACCTCT 60.535 57.895 0.00 0.00 0.00 3.69
3284 4047 2.228103 GGGTTTTGGACGGATTCACTTC 59.772 50.000 0.00 0.00 0.00 3.01
3348 4118 3.864686 GCGTGCGGCGTCATGAAT 61.865 61.111 21.72 0.00 43.66 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.414454 GTGCAAACTGGATGAGGTATTAACA 59.586 40.000 0.00 0.00 0.00 2.41
1 2 5.648092 AGTGCAAACTGGATGAGGTATTAAC 59.352 40.000 0.00 0.00 0.00 2.01
2 3 5.815581 AGTGCAAACTGGATGAGGTATTAA 58.184 37.500 0.00 0.00 0.00 1.40
3 4 5.435686 AGTGCAAACTGGATGAGGTATTA 57.564 39.130 0.00 0.00 0.00 0.98
4 5 4.307032 AGTGCAAACTGGATGAGGTATT 57.693 40.909 0.00 0.00 0.00 1.89
5 6 5.371526 CATAGTGCAAACTGGATGAGGTAT 58.628 41.667 0.00 0.00 0.00 2.73
6 7 4.384098 CCATAGTGCAAACTGGATGAGGTA 60.384 45.833 4.10 0.00 0.00 3.08
7 8 3.614092 CATAGTGCAAACTGGATGAGGT 58.386 45.455 0.00 0.00 0.00 3.85
8 9 2.947652 CCATAGTGCAAACTGGATGAGG 59.052 50.000 4.10 0.00 0.00 3.86
9 10 3.624861 GTCCATAGTGCAAACTGGATGAG 59.375 47.826 13.65 0.00 39.81 2.90
10 11 3.008923 TGTCCATAGTGCAAACTGGATGA 59.991 43.478 13.65 3.91 39.81 2.92
11 12 3.346315 TGTCCATAGTGCAAACTGGATG 58.654 45.455 13.65 0.00 39.81 3.51
12 13 3.719268 TGTCCATAGTGCAAACTGGAT 57.281 42.857 13.65 0.00 39.81 3.41
13 14 3.719268 ATGTCCATAGTGCAAACTGGA 57.281 42.857 8.00 8.00 35.46 3.86
14 15 3.119388 CCAATGTCCATAGTGCAAACTGG 60.119 47.826 0.00 0.00 0.00 4.00
15 16 3.674138 GCCAATGTCCATAGTGCAAACTG 60.674 47.826 0.00 0.00 0.00 3.16
16 17 2.493278 GCCAATGTCCATAGTGCAAACT 59.507 45.455 0.00 0.00 0.00 2.66
17 18 2.493278 AGCCAATGTCCATAGTGCAAAC 59.507 45.455 0.00 0.00 0.00 2.93
18 19 2.806434 AGCCAATGTCCATAGTGCAAA 58.194 42.857 0.00 0.00 0.00 3.68
19 20 2.492881 CAAGCCAATGTCCATAGTGCAA 59.507 45.455 0.00 0.00 0.00 4.08
20 21 2.093890 CAAGCCAATGTCCATAGTGCA 58.906 47.619 0.00 0.00 0.00 4.57
21 22 2.094675 ACAAGCCAATGTCCATAGTGC 58.905 47.619 0.00 0.00 0.00 4.40
22 23 4.276678 CCATACAAGCCAATGTCCATAGTG 59.723 45.833 0.00 0.00 34.75 2.74
23 24 4.464008 CCATACAAGCCAATGTCCATAGT 58.536 43.478 0.00 0.00 34.75 2.12
24 25 3.822735 CCCATACAAGCCAATGTCCATAG 59.177 47.826 0.00 0.00 34.75 2.23
25 26 3.204158 ACCCATACAAGCCAATGTCCATA 59.796 43.478 0.00 0.00 34.75 2.74
26 27 2.024080 ACCCATACAAGCCAATGTCCAT 60.024 45.455 0.00 0.00 34.75 3.41
27 28 1.357420 ACCCATACAAGCCAATGTCCA 59.643 47.619 0.00 0.00 34.75 4.02
28 29 1.750778 CACCCATACAAGCCAATGTCC 59.249 52.381 0.00 0.00 34.75 4.02
29 30 1.134946 GCACCCATACAAGCCAATGTC 59.865 52.381 0.00 0.00 34.75 3.06
30 31 1.185315 GCACCCATACAAGCCAATGT 58.815 50.000 0.00 0.00 37.32 2.71
31 32 1.135024 GTGCACCCATACAAGCCAATG 60.135 52.381 5.22 0.00 0.00 2.82
32 33 1.185315 GTGCACCCATACAAGCCAAT 58.815 50.000 5.22 0.00 0.00 3.16
33 34 0.897863 GGTGCACCCATACAAGCCAA 60.898 55.000 26.31 0.00 0.00 4.52
34 35 1.304052 GGTGCACCCATACAAGCCA 60.304 57.895 26.31 0.00 0.00 4.75
35 36 1.304052 TGGTGCACCCATACAAGCC 60.304 57.895 32.62 4.42 38.72 4.35
36 37 0.322456 TCTGGTGCACCCATACAAGC 60.322 55.000 32.62 5.17 44.15 4.01
37 38 1.742761 CTCTGGTGCACCCATACAAG 58.257 55.000 32.62 21.38 44.15 3.16
38 39 0.322456 GCTCTGGTGCACCCATACAA 60.322 55.000 32.62 12.36 44.15 2.41
39 40 1.299648 GCTCTGGTGCACCCATACA 59.700 57.895 32.62 13.14 44.15 2.29
40 41 0.107017 ATGCTCTGGTGCACCCATAC 60.107 55.000 32.62 19.56 46.33 2.39
41 42 0.625316 AATGCTCTGGTGCACCCATA 59.375 50.000 32.62 16.68 46.33 2.74
42 43 0.625316 TAATGCTCTGGTGCACCCAT 59.375 50.000 32.62 23.94 46.33 4.00
43 44 0.625316 ATAATGCTCTGGTGCACCCA 59.375 50.000 32.62 22.77 46.33 4.51
44 45 1.767759 AATAATGCTCTGGTGCACCC 58.232 50.000 32.62 17.66 46.33 4.61
45 46 2.099756 GGAAATAATGCTCTGGTGCACC 59.900 50.000 29.67 29.67 46.33 5.01
46 47 3.019564 AGGAAATAATGCTCTGGTGCAC 58.980 45.455 8.80 8.80 46.33 4.57
48 49 3.445096 ACAAGGAAATAATGCTCTGGTGC 59.555 43.478 0.00 0.00 0.00 5.01
49 50 5.649782 AACAAGGAAATAATGCTCTGGTG 57.350 39.130 0.00 0.00 0.00 4.17
50 51 7.775053 TTTAACAAGGAAATAATGCTCTGGT 57.225 32.000 0.00 0.00 0.00 4.00
64 65 9.320295 ACCATTTCTCCATTTATTTAACAAGGA 57.680 29.630 0.00 0.00 0.00 3.36
171 215 3.421844 GGGCTGTTTTGATACTCCAACT 58.578 45.455 0.00 0.00 0.00 3.16
196 240 6.018589 ACATGATGTCGTCTATGGACTATG 57.981 41.667 7.68 5.19 40.10 2.23
277 337 2.356553 TGCCGCGTTGGACACTAC 60.357 61.111 4.92 0.00 42.00 2.73
282 342 0.027586 GAATATGTGCCGCGTTGGAC 59.972 55.000 4.92 2.19 42.00 4.02
388 449 5.227908 AGTAAATTATCCGCATCGACGATT 58.772 37.500 7.83 0.00 34.06 3.34
431 492 4.066139 AATCCAGGGCCAGGGTGC 62.066 66.667 15.80 0.00 0.00 5.01
517 578 0.965363 CACCCAATTTCCCGTCCCAG 60.965 60.000 0.00 0.00 0.00 4.45
523 588 2.500392 TAGGTTCACCCAATTTCCCG 57.500 50.000 0.00 0.00 36.42 5.14
589 654 6.259387 GGTTTAACAGCTAACTAACCGCATAT 59.741 38.462 0.00 0.00 0.00 1.78
590 655 5.581874 GGTTTAACAGCTAACTAACCGCATA 59.418 40.000 0.00 0.00 0.00 3.14
613 678 4.748083 GCGCGTTCGTTCGTTCGG 62.748 66.667 8.43 5.58 38.14 4.30
615 680 3.213009 TTGGCGCGTTCGTTCGTTC 62.213 57.895 8.43 0.00 38.14 3.95
616 681 3.218209 CTTGGCGCGTTCGTTCGTT 62.218 57.895 8.43 0.00 38.14 3.85
617 682 3.698463 CTTGGCGCGTTCGTTCGT 61.698 61.111 8.43 0.00 38.14 3.85
652 717 2.570302 TGTAAAGTGAGGTAAGCTCCCC 59.430 50.000 0.00 0.00 0.00 4.81
653 718 3.597255 GTGTAAAGTGAGGTAAGCTCCC 58.403 50.000 0.00 0.00 0.00 4.30
717 782 1.227943 GCACAGGACAACAGGCTCA 60.228 57.895 0.00 0.00 0.00 4.26
845 921 4.862823 CCCTCCCGGACTCTCCCC 62.863 77.778 0.73 0.00 31.13 4.81
867 965 4.902258 GTAGGCCTCCCCCTCCCC 62.902 77.778 9.68 0.00 36.41 4.81
868 966 4.902258 GGTAGGCCTCCCCCTCCC 62.902 77.778 9.68 0.00 36.41 4.30
986 1094 2.452491 AGGGGTGGGTGAGCCTTT 60.452 61.111 1.06 0.00 42.49 3.11
987 1095 2.936032 GAGGGGTGGGTGAGCCTT 60.936 66.667 1.06 0.00 42.49 4.35
1125 1254 6.071984 TCCCCATCTCACTATCTCTTTAGAC 58.928 44.000 0.00 0.00 33.57 2.59
1126 1255 6.281190 TCCCCATCTCACTATCTCTTTAGA 57.719 41.667 0.00 0.00 35.80 2.10
1127 1256 5.480073 CCTCCCCATCTCACTATCTCTTTAG 59.520 48.000 0.00 0.00 0.00 1.85
1417 1546 7.694367 GCTATATATGCTATGGATACGACGATG 59.306 40.741 0.00 0.00 42.51 3.84
1418 1547 7.390718 TGCTATATATGCTATGGATACGACGAT 59.609 37.037 0.00 0.00 42.51 3.73
1419 1548 6.708949 TGCTATATATGCTATGGATACGACGA 59.291 38.462 0.00 0.00 42.51 4.20
1420 1549 6.797513 GTGCTATATATGCTATGGATACGACG 59.202 42.308 0.00 0.00 42.51 5.12
1421 1550 7.085116 GGTGCTATATATGCTATGGATACGAC 58.915 42.308 0.00 0.00 42.51 4.34
1422 1551 6.072673 CGGTGCTATATATGCTATGGATACGA 60.073 42.308 0.00 0.00 42.51 3.43
1423 1552 6.072673 TCGGTGCTATATATGCTATGGATACG 60.073 42.308 0.00 0.00 42.51 3.06
1424 1553 7.215719 TCGGTGCTATATATGCTATGGATAC 57.784 40.000 0.00 0.00 0.00 2.24
1451 1580 4.213564 ACAGAACAGAGGATGGTTCATC 57.786 45.455 7.20 0.00 44.46 2.92
1458 1587 3.407424 TGTGGAACAGAACAGAGGATG 57.593 47.619 0.00 0.00 45.67 3.51
1472 1601 0.542467 ACAAGGCCATGCATGTGGAA 60.542 50.000 24.58 0.00 42.02 3.53
1475 1604 0.604073 TTCACAAGGCCATGCATGTG 59.396 50.000 24.58 17.95 43.90 3.21
1551 1680 4.787280 CTCCCCGGCAGTCTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
1923 2058 4.148825 CCGGCCTCCCTCTTCACG 62.149 72.222 0.00 0.00 0.00 4.35
2100 2252 5.104776 CCAATATCCAAGAGTCACAGGAGAA 60.105 44.000 0.00 0.00 32.91 2.87
2204 2365 2.698274 GGGAGGAGAAGAGGAAGATGAC 59.302 54.545 0.00 0.00 0.00 3.06
2275 2437 4.270325 GCTCATGATTAGTCAAACGGTACC 59.730 45.833 0.16 0.16 38.01 3.34
2276 2438 4.868171 TGCTCATGATTAGTCAAACGGTAC 59.132 41.667 0.00 0.00 38.01 3.34
2422 2864 1.672356 ACGGGCACACTGAATCTGC 60.672 57.895 0.00 0.00 0.00 4.26
2448 2891 2.851071 GCCCCGGTCTCGAGATCAG 61.851 68.421 24.78 14.09 39.00 2.90
2582 3025 3.976169 CAAAGTTTGGGCATCGAAAAGA 58.024 40.909 7.78 0.00 0.00 2.52
2596 3039 2.694616 ATGTAGCCACCCCAAAGTTT 57.305 45.000 0.00 0.00 0.00 2.66
2597 3040 2.377193 TGTATGTAGCCACCCCAAAGTT 59.623 45.455 0.00 0.00 0.00 2.66
2598 3041 1.989586 TGTATGTAGCCACCCCAAAGT 59.010 47.619 0.00 0.00 0.00 2.66
2599 3042 2.290641 TGTGTATGTAGCCACCCCAAAG 60.291 50.000 0.00 0.00 0.00 2.77
2600 3043 1.705745 TGTGTATGTAGCCACCCCAAA 59.294 47.619 0.00 0.00 0.00 3.28
2601 3044 1.003812 GTGTGTATGTAGCCACCCCAA 59.996 52.381 0.00 0.00 0.00 4.12
2602 3045 0.616371 GTGTGTATGTAGCCACCCCA 59.384 55.000 0.00 0.00 0.00 4.96
2603 3046 0.616371 TGTGTGTATGTAGCCACCCC 59.384 55.000 0.00 0.00 0.00 4.95
2606 3049 3.875134 GGGTTATGTGTGTATGTAGCCAC 59.125 47.826 0.00 0.00 0.00 5.01
2607 3050 3.778075 AGGGTTATGTGTGTATGTAGCCA 59.222 43.478 0.00 0.00 0.00 4.75
2608 3051 4.417426 AGGGTTATGTGTGTATGTAGCC 57.583 45.455 0.00 0.00 0.00 3.93
2609 3052 6.113411 AGAAAGGGTTATGTGTGTATGTAGC 58.887 40.000 0.00 0.00 0.00 3.58
2610 3053 8.561738 AAAGAAAGGGTTATGTGTGTATGTAG 57.438 34.615 0.00 0.00 0.00 2.74
2619 3069 4.669197 CGCGAGAAAAGAAAGGGTTATGTG 60.669 45.833 0.00 0.00 0.00 3.21
2637 3087 4.732285 ATAGGTTATGCATTTTCGCGAG 57.268 40.909 9.59 0.00 33.35 5.03
2640 3090 7.378728 GGACTAAAATAGGTTATGCATTTTCGC 59.621 37.037 3.54 0.00 34.57 4.70
2641 3091 8.402472 TGGACTAAAATAGGTTATGCATTTTCG 58.598 33.333 3.54 0.00 34.57 3.46
2647 3097 7.342581 TCACATGGACTAAAATAGGTTATGCA 58.657 34.615 0.00 0.00 0.00 3.96
2689 3142 7.733402 TGTAAAATTACTTAAGACTGCGGTT 57.267 32.000 10.09 0.00 34.77 4.44
2690 3143 7.065443 GGATGTAAAATTACTTAAGACTGCGGT 59.935 37.037 10.09 0.00 34.77 5.68
2691 3144 7.407337 GGATGTAAAATTACTTAAGACTGCGG 58.593 38.462 10.09 0.00 34.77 5.69
2692 3145 7.117454 CGGATGTAAAATTACTTAAGACTGCG 58.883 38.462 10.09 0.00 34.77 5.18
2693 3146 7.971455 ACGGATGTAAAATTACTTAAGACTGC 58.029 34.615 10.09 0.00 34.77 4.40
2694 3147 9.755064 CAACGGATGTAAAATTACTTAAGACTG 57.245 33.333 10.09 0.00 34.77 3.51
2695 3148 9.498176 ACAACGGATGTAAAATTACTTAAGACT 57.502 29.630 10.09 0.00 41.63 3.24
2728 3182 0.320334 TTTGACGGCATGCTCTTCGA 60.320 50.000 18.92 8.47 0.00 3.71
2729 3183 0.179215 GTTTGACGGCATGCTCTTCG 60.179 55.000 18.92 14.89 0.00 3.79
2730 3184 1.160137 AGTTTGACGGCATGCTCTTC 58.840 50.000 18.92 11.75 0.00 2.87
2731 3185 1.267806 CAAGTTTGACGGCATGCTCTT 59.732 47.619 18.92 1.33 0.00 2.85
2735 3189 0.593128 AGACAAGTTTGACGGCATGC 59.407 50.000 9.90 9.90 0.00 4.06
2736 3190 3.364964 GGTTAGACAAGTTTGACGGCATG 60.365 47.826 0.00 0.00 0.00 4.06
2740 3194 5.494632 AAAAGGTTAGACAAGTTTGACGG 57.505 39.130 0.00 0.00 0.00 4.79
2840 3318 0.378257 CACTTGCGTGTGGATATGCC 59.622 55.000 1.49 0.00 36.39 4.40
2861 3339 6.034591 CAGATACACACGGTCTTACCTTTAG 58.965 44.000 0.00 0.00 35.66 1.85
2900 3403 1.263356 TACCACCTTCTCCCTGAACG 58.737 55.000 0.00 0.00 0.00 3.95
2901 3404 3.610911 CATTACCACCTTCTCCCTGAAC 58.389 50.000 0.00 0.00 0.00 3.18
2921 3424 2.637382 TGACTCTCCAACACTAATGCCA 59.363 45.455 0.00 0.00 0.00 4.92
2931 3434 3.003480 GCAGTAACCATGACTCTCCAAC 58.997 50.000 0.00 0.00 0.00 3.77
2933 3436 1.555075 GGCAGTAACCATGACTCTCCA 59.445 52.381 0.00 0.00 0.00 3.86
2939 3442 3.064820 CCATTAACGGCAGTAACCATGAC 59.935 47.826 0.00 0.00 0.00 3.06
2981 3484 5.762279 TGGTACCTTCCTCTTTTCTTTGTT 58.238 37.500 14.36 0.00 0.00 2.83
2983 3486 4.762251 CCTGGTACCTTCCTCTTTTCTTTG 59.238 45.833 14.36 0.00 0.00 2.77
2990 3493 1.558233 CGTCCTGGTACCTTCCTCTT 58.442 55.000 14.36 0.00 0.00 2.85
2991 3494 0.324460 CCGTCCTGGTACCTTCCTCT 60.324 60.000 14.36 0.00 0.00 3.69
2992 3495 0.324091 TCCGTCCTGGTACCTTCCTC 60.324 60.000 14.36 0.00 39.52 3.71
2997 3507 1.305046 CCTGTCCGTCCTGGTACCT 60.305 63.158 14.36 0.00 39.52 3.08
2998 3508 0.901580 TTCCTGTCCGTCCTGGTACC 60.902 60.000 4.43 4.43 39.52 3.34
2999 3509 0.531200 CTTCCTGTCCGTCCTGGTAC 59.469 60.000 0.00 0.00 39.52 3.34
3000 3510 0.613853 CCTTCCTGTCCGTCCTGGTA 60.614 60.000 0.00 0.00 39.52 3.25
3001 3511 1.913762 CCTTCCTGTCCGTCCTGGT 60.914 63.158 0.00 0.00 39.52 4.00
3002 3512 1.913762 ACCTTCCTGTCCGTCCTGG 60.914 63.158 0.00 0.00 40.09 4.45
3003 3513 1.185618 TCACCTTCCTGTCCGTCCTG 61.186 60.000 0.00 0.00 0.00 3.86
3004 3514 1.155390 TCACCTTCCTGTCCGTCCT 59.845 57.895 0.00 0.00 0.00 3.85
3005 3515 1.292541 GTCACCTTCCTGTCCGTCC 59.707 63.158 0.00 0.00 0.00 4.79
3006 3516 0.391597 TTGTCACCTTCCTGTCCGTC 59.608 55.000 0.00 0.00 0.00 4.79
3007 3517 0.834612 TTTGTCACCTTCCTGTCCGT 59.165 50.000 0.00 0.00 0.00 4.69
3008 3518 1.512926 CTTTGTCACCTTCCTGTCCG 58.487 55.000 0.00 0.00 0.00 4.79
3039 3549 2.073056 GCAAGCCCCGTTTTAAAATGG 58.927 47.619 26.18 26.18 43.28 3.16
3048 3558 1.303317 CTAACCAGCAAGCCCCGTT 60.303 57.895 0.00 0.00 0.00 4.44
3050 3560 1.906105 TACCTAACCAGCAAGCCCCG 61.906 60.000 0.00 0.00 0.00 5.73
3114 3624 9.355215 CGATGCCGAGTACTAGAAAATAATATT 57.645 33.333 4.34 0.00 38.22 1.28
3115 3625 7.974501 CCGATGCCGAGTACTAGAAAATAATAT 59.025 37.037 4.34 0.00 38.22 1.28
3116 3626 7.310664 CCGATGCCGAGTACTAGAAAATAATA 58.689 38.462 4.34 0.00 38.22 0.98
3117 3627 6.157211 CCGATGCCGAGTACTAGAAAATAAT 58.843 40.000 4.34 0.00 38.22 1.28
3121 3631 2.100252 CCCGATGCCGAGTACTAGAAAA 59.900 50.000 4.34 0.00 38.22 2.29
3123 3633 1.315690 CCCGATGCCGAGTACTAGAA 58.684 55.000 4.34 0.00 38.22 2.10
3125 3635 1.286260 GCCCGATGCCGAGTACTAG 59.714 63.158 0.00 0.00 38.22 2.57
3127 3637 2.758327 TGCCCGATGCCGAGTACT 60.758 61.111 0.00 0.00 40.16 2.73
3128 3638 2.279517 CTGCCCGATGCCGAGTAC 60.280 66.667 0.00 0.00 40.16 2.73
3145 3893 0.861837 CGAGTGAGTGAGTTGTTGGC 59.138 55.000 0.00 0.00 0.00 4.52
3188 3936 0.597377 CGACCGCGGATGATGATGAA 60.597 55.000 35.90 0.00 0.00 2.57
3250 4013 2.700371 CCAAAACCCTCTGCCTTTCTTT 59.300 45.455 0.00 0.00 0.00 2.52
3251 4014 2.091333 TCCAAAACCCTCTGCCTTTCTT 60.091 45.455 0.00 0.00 0.00 2.52
3284 4047 3.451056 AAGTTGCCCACCCACCCAG 62.451 63.158 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.