Multiple sequence alignment - TraesCS2A01G120800

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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 TraesCS2A01G120800 chr2A 100.000 3510 0 0 235 3744 70868412 70871921 0.000000e+00 6482.0
1 TraesCS2A01G120800 chr2A 90.845 284 26 0 253 536 708668183 708668466 7.590000e-102 381.0
2 TraesCS2A01G120800 chr2A 90.459 283 26 1 253 535 190208462 190208743 4.570000e-99 372.0
3 TraesCS2A01G120800 chr2A 100.000 99 0 0 1 99 70868178 70868276 2.300000e-42 183.0
4 TraesCS2A01G120800 chr2D 94.501 3019 106 23 756 3744 71757850 71760838 0.000000e+00 4601.0
5 TraesCS2A01G120800 chr2D 97.143 35 1 0 738 772 71757808 71757842 4.040000e-05 60.2
6 TraesCS2A01G120800 chr2B 93.968 3034 112 27 740 3744 108229607 108232598 0.000000e+00 4523.0
7 TraesCS2A01G120800 chr1A 93.207 1104 48 11 1183 2261 102167026 102168127 0.000000e+00 1598.0
8 TraesCS2A01G120800 chr1A 89.111 551 18 8 2384 2933 102168138 102168647 0.000000e+00 647.0
9 TraesCS2A01G120800 chr1A 94.718 284 15 0 253 536 488777481 488777764 3.430000e-120 442.0
10 TraesCS2A01G120800 chr1A 89.399 283 30 0 251 533 494699970 494700252 1.280000e-94 357.0
11 TraesCS2A01G120800 chr1A 73.548 310 62 18 1965 2264 381097174 381096875 2.380000e-17 100.0
12 TraesCS2A01G120800 chr5B 93.217 1091 56 11 1186 2261 319887404 319886317 0.000000e+00 1589.0
13 TraesCS2A01G120800 chr5B 88.246 553 23 8 2384 2936 319886306 319885796 1.140000e-174 623.0
14 TraesCS2A01G120800 chr7B 93.025 1104 50 11 1183 2261 747591113 747592214 0.000000e+00 1587.0
15 TraesCS2A01G120800 chr7B 97.087 309 8 1 2384 2692 747592225 747592532 1.540000e-143 520.0
16 TraesCS2A01G120800 chr7A 94.056 286 17 0 251 536 707591560 707591275 5.740000e-118 435.0
17 TraesCS2A01G120800 chr7A 93.750 208 11 2 533 739 707590868 707590662 1.010000e-80 311.0
18 TraesCS2A01G120800 chr6A 91.166 283 24 1 253 535 435782253 435782534 2.110000e-102 383.0
19 TraesCS2A01G120800 chr6A 90.845 284 26 0 253 536 593366058 593366341 7.590000e-102 381.0
20 TraesCS2A01G120800 chr6A 90.071 282 26 2 256 536 319173134 319172854 7.640000e-97 364.0
21 TraesCS2A01G120800 chr4A 89.199 287 29 2 251 536 541425297 541425582 1.280000e-94 357.0
22 TraesCS2A01G120800 chr3D 92.823 209 12 2 534 739 501600297 501600089 2.190000e-77 300.0
23 TraesCS2A01G120800 chr3D 92.344 209 13 2 534 739 147502677 147502885 1.020000e-75 294.0
24 TraesCS2A01G120800 chr1B 92.344 209 13 2 534 739 681861606 681861814 1.020000e-75 294.0
25 TraesCS2A01G120800 chr1B 92.344 209 13 2 534 739 681865584 681865792 1.020000e-75 294.0
26 TraesCS2A01G120800 chr1B 92.344 209 13 2 534 739 681867137 681867345 1.020000e-75 294.0
27 TraesCS2A01G120800 chr5A 92.271 207 15 1 534 739 508535478 508535684 3.660000e-75 292.0
28 TraesCS2A01G120800 chr5A 92.271 207 15 1 534 739 508560366 508560572 3.660000e-75 292.0
29 TraesCS2A01G120800 chr1D 92.271 207 15 1 534 739 391116187 391116393 3.660000e-75 292.0
30 TraesCS2A01G120800 chr1D 100.000 99 0 0 1 99 424502598 424502500 2.300000e-42 183.0
31 TraesCS2A01G120800 chr1D 73.955 311 59 20 1965 2264 303516997 303516698 5.110000e-19 106.0
32 TraesCS2A01G120800 chrUn 98.990 99 1 0 1 99 783915 784013 1.070000e-40 178.0
33 TraesCS2A01G120800 chrUn 98.990 99 1 0 1 99 253490053 253490151 1.070000e-40 178.0
34 TraesCS2A01G120800 chrUn 98.990 99 1 0 1 99 264414264 264414362 1.070000e-40 178.0
35 TraesCS2A01G120800 chr6D 98.990 99 1 0 1 99 90448469 90448371 1.070000e-40 178.0
36 TraesCS2A01G120800 chr6D 98.990 99 1 0 1 99 262573007 262573105 1.070000e-40 178.0
37 TraesCS2A01G120800 chr6D 98.990 99 1 0 1 99 354929388 354929290 1.070000e-40 178.0
38 TraesCS2A01G120800 chr6D 98.990 99 1 0 1 99 360199269 360199171 1.070000e-40 178.0
39 TraesCS2A01G120800 chr6D 98.990 99 1 0 1 99 360311169 360311071 1.070000e-40 178.0


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 TraesCS2A01G120800 chr2A 70868178 70871921 3743 False 3332.5 6482 100.0000 1 3744 2 chr2A.!!$F3 3743
1 TraesCS2A01G120800 chr2D 71757808 71760838 3030 False 2330.6 4601 95.8220 738 3744 2 chr2D.!!$F1 3006
2 TraesCS2A01G120800 chr2B 108229607 108232598 2991 False 4523.0 4523 93.9680 740 3744 1 chr2B.!!$F1 3004
3 TraesCS2A01G120800 chr1A 102167026 102168647 1621 False 1122.5 1598 91.1590 1183 2933 2 chr1A.!!$F3 1750
4 TraesCS2A01G120800 chr5B 319885796 319887404 1608 True 1106.0 1589 90.7315 1186 2936 2 chr5B.!!$R1 1750
5 TraesCS2A01G120800 chr7B 747591113 747592532 1419 False 1053.5 1587 95.0560 1183 2692 2 chr7B.!!$F1 1509
6 TraesCS2A01G120800 chr7A 707590662 707591560 898 True 373.0 435 93.9030 251 739 2 chr7A.!!$R1 488
7 TraesCS2A01G120800 chr1B 681861606 681867345 5739 False 294.0 294 92.3440 534 739 3 chr1B.!!$F1 205

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
20 21 0.531657 TTGCTTGCTTGTGTGCTTGT 59.468 45.0 0.0 0.0 0.00 3.16 F
436 437 0.892358 CACCTCATGCAACAGCCTGT 60.892 55.0 0.0 0.0 0.00 4.00 F
445 446 0.947244 CAACAGCCTGTGAACTCACC 59.053 55.0 0.0 0.0 45.88 4.02 F
2565 6744 0.033504 AAGAGCAACATCGTCACCGT 59.966 50.0 0.0 0.0 35.01 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 5698 0.383590 CTGAGCACCATCGATCGTCT 59.616 55.000 15.94 0.69 0.00 4.18 R
1858 5699 0.596083 CCTGAGCACCATCGATCGTC 60.596 60.000 15.94 3.78 0.00 4.20 R
2705 6884 4.308526 GTCGTAGGTGGAGACGGA 57.691 61.111 0.00 0.00 39.53 4.69 R
3663 7862 1.476891 TGGTCACACTCTTATCCGAGC 59.523 52.381 0.00 0.00 34.35 5.03 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
18 19 3.654178 CTTGCTTGCTTGTGTGCTT 57.346 47.368 0.00 0.00 0.00 3.91
19 20 1.205657 CTTGCTTGCTTGTGTGCTTG 58.794 50.000 0.00 0.00 0.00 4.01
20 21 0.531657 TTGCTTGCTTGTGTGCTTGT 59.468 45.000 0.00 0.00 0.00 3.16
21 22 0.531657 TGCTTGCTTGTGTGCTTGTT 59.468 45.000 0.00 0.00 0.00 2.83
22 23 0.925466 GCTTGCTTGTGTGCTTGTTG 59.075 50.000 0.00 0.00 0.00 3.33
23 24 1.736696 GCTTGCTTGTGTGCTTGTTGT 60.737 47.619 0.00 0.00 0.00 3.32
24 25 2.609350 CTTGCTTGTGTGCTTGTTGTT 58.391 42.857 0.00 0.00 0.00 2.83
25 26 1.993542 TGCTTGTGTGCTTGTTGTTG 58.006 45.000 0.00 0.00 0.00 3.33
26 27 1.271934 TGCTTGTGTGCTTGTTGTTGT 59.728 42.857 0.00 0.00 0.00 3.32
27 28 2.288702 TGCTTGTGTGCTTGTTGTTGTT 60.289 40.909 0.00 0.00 0.00 2.83
28 29 2.092524 GCTTGTGTGCTTGTTGTTGTTG 59.907 45.455 0.00 0.00 0.00 3.33
29 30 1.707632 TGTGTGCTTGTTGTTGTTGC 58.292 45.000 0.00 0.00 0.00 4.17
30 31 1.000171 TGTGTGCTTGTTGTTGTTGCA 60.000 42.857 0.00 0.00 0.00 4.08
31 32 2.270047 GTGTGCTTGTTGTTGTTGCAT 58.730 42.857 0.00 0.00 36.04 3.96
32 33 2.282290 GTGTGCTTGTTGTTGTTGCATC 59.718 45.455 0.00 0.00 36.04 3.91
33 34 2.094338 TGTGCTTGTTGTTGTTGCATCA 60.094 40.909 0.00 0.00 36.04 3.07
34 35 3.125316 GTGCTTGTTGTTGTTGCATCAT 58.875 40.909 0.00 0.00 36.04 2.45
35 36 4.202090 TGTGCTTGTTGTTGTTGCATCATA 60.202 37.500 0.00 0.00 36.04 2.15
36 37 4.925054 GTGCTTGTTGTTGTTGCATCATAT 59.075 37.500 0.00 0.00 36.04 1.78
37 38 6.092092 GTGCTTGTTGTTGTTGCATCATATA 58.908 36.000 0.00 0.00 36.04 0.86
38 39 6.753279 GTGCTTGTTGTTGTTGCATCATATAT 59.247 34.615 0.00 0.00 36.04 0.86
39 40 6.752815 TGCTTGTTGTTGTTGCATCATATATG 59.247 34.615 6.36 6.36 0.00 1.78
40 41 6.753279 GCTTGTTGTTGTTGCATCATATATGT 59.247 34.615 12.42 0.00 0.00 2.29
41 42 7.276218 GCTTGTTGTTGTTGCATCATATATGTT 59.724 33.333 12.42 1.47 0.00 2.71
42 43 8.463456 TTGTTGTTGTTGCATCATATATGTTG 57.537 30.769 16.36 16.36 0.00 3.33
51 52 6.659361 GCATCATATATGTTGCTCACCTAG 57.341 41.667 29.35 5.10 45.38 3.02
52 53 6.169094 GCATCATATATGTTGCTCACCTAGT 58.831 40.000 29.35 0.00 45.38 2.57
53 54 6.652481 GCATCATATATGTTGCTCACCTAGTT 59.348 38.462 29.35 0.00 45.38 2.24
54 55 7.360691 GCATCATATATGTTGCTCACCTAGTTG 60.361 40.741 29.35 3.98 45.38 3.16
55 56 5.991606 TCATATATGTTGCTCACCTAGTTGC 59.008 40.000 12.42 0.00 0.00 4.17
56 57 2.566833 ATGTTGCTCACCTAGTTGCA 57.433 45.000 0.00 0.00 0.00 4.08
57 58 2.566833 TGTTGCTCACCTAGTTGCAT 57.433 45.000 0.00 0.00 35.27 3.96
58 59 3.694043 TGTTGCTCACCTAGTTGCATA 57.306 42.857 0.00 0.00 35.27 3.14
59 60 4.220693 TGTTGCTCACCTAGTTGCATAT 57.779 40.909 0.00 0.00 35.27 1.78
60 61 4.191544 TGTTGCTCACCTAGTTGCATATC 58.808 43.478 0.00 0.00 35.27 1.63
61 62 4.080919 TGTTGCTCACCTAGTTGCATATCT 60.081 41.667 0.00 0.00 35.27 1.98
62 63 5.128663 TGTTGCTCACCTAGTTGCATATCTA 59.871 40.000 0.00 0.00 35.27 1.98
63 64 5.459536 TGCTCACCTAGTTGCATATCTAG 57.540 43.478 11.63 11.63 34.98 2.43
64 65 5.140454 TGCTCACCTAGTTGCATATCTAGA 58.860 41.667 17.11 0.00 36.66 2.43
65 66 5.010112 TGCTCACCTAGTTGCATATCTAGAC 59.990 44.000 17.11 0.00 36.66 2.59
66 67 5.010112 GCTCACCTAGTTGCATATCTAGACA 59.990 44.000 17.11 0.00 36.66 3.41
67 68 6.461648 GCTCACCTAGTTGCATATCTAGACAA 60.462 42.308 17.11 0.00 36.66 3.18
68 69 6.806751 TCACCTAGTTGCATATCTAGACAAC 58.193 40.000 13.43 13.43 42.08 3.32
69 70 5.986135 CACCTAGTTGCATATCTAGACAACC 59.014 44.000 16.29 3.97 42.61 3.77
70 71 5.900123 ACCTAGTTGCATATCTAGACAACCT 59.100 40.000 16.29 9.28 42.61 3.50
71 72 7.014326 CACCTAGTTGCATATCTAGACAACCTA 59.986 40.741 16.29 9.74 42.61 3.08
72 73 7.014422 ACCTAGTTGCATATCTAGACAACCTAC 59.986 40.741 16.29 5.11 42.61 3.18
73 74 7.231722 CCTAGTTGCATATCTAGACAACCTACT 59.768 40.741 16.29 10.57 42.61 2.57
74 75 7.425224 AGTTGCATATCTAGACAACCTACTT 57.575 36.000 16.29 0.58 42.61 2.24
75 76 7.852263 AGTTGCATATCTAGACAACCTACTTT 58.148 34.615 16.29 0.03 42.61 2.66
76 77 7.766278 AGTTGCATATCTAGACAACCTACTTTG 59.234 37.037 16.29 0.00 42.61 2.77
77 78 7.418337 TGCATATCTAGACAACCTACTTTGA 57.582 36.000 0.00 0.00 0.00 2.69
78 79 8.023021 TGCATATCTAGACAACCTACTTTGAT 57.977 34.615 0.00 0.00 0.00 2.57
79 80 7.928167 TGCATATCTAGACAACCTACTTTGATG 59.072 37.037 0.00 0.00 0.00 3.07
80 81 7.095439 GCATATCTAGACAACCTACTTTGATGC 60.095 40.741 0.00 0.00 0.00 3.91
81 82 5.738619 TCTAGACAACCTACTTTGATGCA 57.261 39.130 0.00 0.00 0.00 3.96
82 83 6.109156 TCTAGACAACCTACTTTGATGCAA 57.891 37.500 0.00 0.00 0.00 4.08
83 84 6.530120 TCTAGACAACCTACTTTGATGCAAA 58.470 36.000 0.00 0.00 0.00 3.68
254 255 2.602257 ATCGATCCTTTCATGCGTCA 57.398 45.000 0.00 0.00 0.00 4.35
261 262 1.089920 CTTTCATGCGTCAAGGGAGG 58.910 55.000 0.00 0.00 0.00 4.30
266 267 1.200020 CATGCGTCAAGGGAGGTTTTC 59.800 52.381 0.00 0.00 0.00 2.29
285 286 7.230712 AGGTTTTCATTCAAAAGGTACTACCAG 59.769 37.037 8.01 0.00 41.95 4.00
377 378 2.288666 CATGTCCCAAGTAATGACCCG 58.711 52.381 0.00 0.00 0.00 5.28
383 384 2.089201 CCAAGTAATGACCCGGGTTTC 58.911 52.381 30.89 17.30 0.00 2.78
388 389 3.588396 AGTAATGACCCGGGTTTCCTTAA 59.412 43.478 30.89 7.22 0.00 1.85
391 392 1.706305 TGACCCGGGTTTCCTTAATGT 59.294 47.619 30.89 0.00 0.00 2.71
392 393 2.108601 TGACCCGGGTTTCCTTAATGTT 59.891 45.455 30.89 0.00 0.00 2.71
436 437 0.892358 CACCTCATGCAACAGCCTGT 60.892 55.000 0.00 0.00 0.00 4.00
445 446 0.947244 CAACAGCCTGTGAACTCACC 59.053 55.000 0.00 0.00 45.88 4.02
486 487 5.254115 ACCTTGGCCTATTTTCTTCACTAC 58.746 41.667 3.32 0.00 0.00 2.73
509 510 4.343526 CAGTCCATGTCAGATAGGCTAGTT 59.656 45.833 0.00 0.00 0.00 2.24
694 803 7.088589 ACACCTTATTTATGCAACAGATCAC 57.911 36.000 0.00 0.00 0.00 3.06
695 804 6.095440 ACACCTTATTTATGCAACAGATCACC 59.905 38.462 0.00 0.00 0.00 4.02
781 916 6.241645 CCTTTGAGACTCTTTGGAAGGTAAT 58.758 40.000 3.68 0.00 0.00 1.89
841 976 4.597507 CCCATTGCCCTAGTAGATTTCCTA 59.402 45.833 0.00 0.00 0.00 2.94
1208 2483 2.670934 CGGCAGCAAGAACAGCCT 60.671 61.111 0.00 0.00 44.85 4.58
1240 2519 3.056607 GGTGGTGCTTAATTGCAGAATGT 60.057 43.478 0.00 0.00 44.20 2.71
1807 5642 2.886859 CCATCACGGTGCGTATCTC 58.113 57.895 2.51 0.00 38.32 2.75
1814 5649 1.476891 ACGGTGCGTATCTCAAGATGT 59.523 47.619 2.72 0.00 38.73 3.06
1830 5670 1.105167 ATGTCATGCCAATGCCTCCG 61.105 55.000 0.00 0.00 36.33 4.63
1852 5693 5.425398 CGTTTTGTCATGCATTTTGAACTG 58.575 37.500 0.00 0.00 0.00 3.16
1854 5695 6.455380 CGTTTTGTCATGCATTTTGAACTGTT 60.455 34.615 0.00 0.00 0.00 3.16
1857 5698 8.484641 TTTGTCATGCATTTTGAACTGTTAAA 57.515 26.923 0.00 0.00 0.00 1.52
1858 5699 7.697352 TGTCATGCATTTTGAACTGTTAAAG 57.303 32.000 0.00 0.00 0.00 1.85
2467 6571 0.955428 TGGTGCAGATCAAGAACGCC 60.955 55.000 0.00 0.00 0.00 5.68
2565 6744 0.033504 AAGAGCAACATCGTCACCGT 59.966 50.000 0.00 0.00 35.01 4.83
2747 6926 4.389576 CGCAGCCAGTTTGACGCC 62.390 66.667 0.00 0.00 0.00 5.68
2753 6938 1.067060 AGCCAGTTTGACGCCTTTTTC 59.933 47.619 0.00 0.00 0.00 2.29
2754 6939 1.753956 CCAGTTTGACGCCTTTTTCG 58.246 50.000 0.00 0.00 0.00 3.46
2755 6940 1.064952 CCAGTTTGACGCCTTTTTCGT 59.935 47.619 0.00 0.00 43.49 3.85
2756 6941 2.478879 CCAGTTTGACGCCTTTTTCGTT 60.479 45.455 0.00 0.00 40.59 3.85
2757 6942 3.175929 CAGTTTGACGCCTTTTTCGTTT 58.824 40.909 0.00 0.00 40.59 3.60
2758 6943 3.001168 CAGTTTGACGCCTTTTTCGTTTG 60.001 43.478 0.00 0.00 40.59 2.93
2759 6944 3.119779 AGTTTGACGCCTTTTTCGTTTGA 60.120 39.130 0.00 0.00 40.59 2.69
2760 6945 3.701532 TTGACGCCTTTTTCGTTTGAT 57.298 38.095 0.00 0.00 40.59 2.57
2761 6946 3.701532 TGACGCCTTTTTCGTTTGATT 57.298 38.095 0.00 0.00 40.59 2.57
2762 6947 3.367607 TGACGCCTTTTTCGTTTGATTG 58.632 40.909 0.00 0.00 40.59 2.67
2763 6948 2.724174 GACGCCTTTTTCGTTTGATTGG 59.276 45.455 0.00 0.00 40.59 3.16
2764 6949 2.100087 ACGCCTTTTTCGTTTGATTGGT 59.900 40.909 0.00 0.00 36.72 3.67
2765 6950 3.120041 CGCCTTTTTCGTTTGATTGGTT 58.880 40.909 0.00 0.00 0.00 3.67
2766 6951 3.181575 CGCCTTTTTCGTTTGATTGGTTC 59.818 43.478 0.00 0.00 0.00 3.62
2767 6952 4.116238 GCCTTTTTCGTTTGATTGGTTCA 58.884 39.130 0.00 0.00 0.00 3.18
2768 6953 4.749598 GCCTTTTTCGTTTGATTGGTTCAT 59.250 37.500 0.00 0.00 33.34 2.57
2769 6954 5.333263 GCCTTTTTCGTTTGATTGGTTCATG 60.333 40.000 0.00 0.00 33.34 3.07
2770 6955 5.177327 CCTTTTTCGTTTGATTGGTTCATGG 59.823 40.000 0.00 0.00 33.34 3.66
2771 6956 4.927978 TTTCGTTTGATTGGTTCATGGT 57.072 36.364 0.00 0.00 33.34 3.55
2772 6957 4.927978 TTCGTTTGATTGGTTCATGGTT 57.072 36.364 0.00 0.00 33.34 3.67
2773 6958 6.392625 TTTCGTTTGATTGGTTCATGGTTA 57.607 33.333 0.00 0.00 33.34 2.85
2774 6959 5.365403 TCGTTTGATTGGTTCATGGTTAC 57.635 39.130 0.00 0.00 33.34 2.50
2775 6960 4.216687 TCGTTTGATTGGTTCATGGTTACC 59.783 41.667 0.00 0.00 33.34 2.85
2776 6961 4.217550 CGTTTGATTGGTTCATGGTTACCT 59.782 41.667 2.07 0.00 35.41 3.08
2777 6962 5.278758 CGTTTGATTGGTTCATGGTTACCTT 60.279 40.000 2.07 0.00 35.41 3.50
2778 6963 5.720371 TTGATTGGTTCATGGTTACCTTG 57.280 39.130 10.61 10.61 35.41 3.61
3024 7220 0.451783 GGAATTGTCATGGGTCGTGC 59.548 55.000 0.00 0.00 0.00 5.34
3046 7242 4.082190 GCTAATTCAGTTCCCAGTTTTCCC 60.082 45.833 0.00 0.00 0.00 3.97
3112 7308 1.375396 TGAACCGAACTGCATCCCG 60.375 57.895 0.00 0.00 0.00 5.14
3121 7317 0.179004 ACTGCATCCCGGTTTGACAA 60.179 50.000 0.00 0.00 0.00 3.18
3142 7338 7.500892 TGACAAAATTCTCTAACCTTGCTGTTA 59.499 33.333 0.00 0.00 0.00 2.41
3251 7450 9.035338 CACGAAACACAAAAATAACTTGTTTTG 57.965 29.630 10.00 10.00 45.82 2.44
3321 7520 4.513442 TCCAATACACATACAACTGGAGC 58.487 43.478 0.00 0.00 0.00 4.70
3329 7528 5.359576 ACACATACAACTGGAGCAAAGAAAA 59.640 36.000 0.00 0.00 0.00 2.29
3424 7623 5.755861 GGATATCAAGCTCTACAACAACCTC 59.244 44.000 4.83 0.00 0.00 3.85
3434 7633 0.247736 CAACAACCTCTCCTCCTCCG 59.752 60.000 0.00 0.00 0.00 4.63
3452 7651 1.413382 CGGCTTCTCATATCGAGCAC 58.587 55.000 0.00 0.00 41.98 4.40
3488 7687 1.065126 GCCAGCAACTCCCTTCTACAT 60.065 52.381 0.00 0.00 0.00 2.29
3585 7784 1.003355 ACACAATCTGCAGGTCGGG 60.003 57.895 15.13 0.00 0.00 5.14
3589 7788 1.134401 ACAATCTGCAGGTCGGGTATG 60.134 52.381 15.13 2.90 0.00 2.39
3634 7833 4.697352 TGGATTGAAGCTAACTCTTCTTGC 59.303 41.667 5.30 0.00 42.15 4.01
3663 7862 2.333014 GTCTCCAGAAGTTCGAAGCAG 58.667 52.381 0.00 0.00 0.00 4.24
3674 7873 1.389555 TCGAAGCAGCTCGGATAAGA 58.610 50.000 12.44 0.00 39.35 2.10
3702 7901 4.589908 ACCAACTTCCAGATGTACCATTC 58.410 43.478 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.531657 ACAAGCACACAAGCAAGCAA 59.468 45.000 0.00 0.00 36.85 3.91
3 4 0.925466 CAACAAGCACACAAGCAAGC 59.075 50.000 0.00 0.00 36.85 4.01
4 5 2.282701 ACAACAAGCACACAAGCAAG 57.717 45.000 0.00 0.00 36.85 4.01
5 6 2.288702 ACAACAACAAGCACACAAGCAA 60.289 40.909 0.00 0.00 36.85 3.91
6 7 1.271934 ACAACAACAAGCACACAAGCA 59.728 42.857 0.00 0.00 36.85 3.91
7 8 1.994916 ACAACAACAAGCACACAAGC 58.005 45.000 0.00 0.00 0.00 4.01
9 10 2.064762 GCAACAACAACAAGCACACAA 58.935 42.857 0.00 0.00 0.00 3.33
11 12 1.707632 TGCAACAACAACAAGCACAC 58.292 45.000 0.00 0.00 0.00 3.82
12 13 2.094338 TGATGCAACAACAACAAGCACA 60.094 40.909 0.00 0.00 38.12 4.57
13 14 2.538437 TGATGCAACAACAACAAGCAC 58.462 42.857 0.00 0.00 38.12 4.40
15 16 6.753279 ACATATATGATGCAACAACAACAAGC 59.247 34.615 19.63 0.00 0.00 4.01
16 17 8.588789 CAACATATATGATGCAACAACAACAAG 58.411 33.333 19.63 0.00 0.00 3.16
17 18 8.463456 CAACATATATGATGCAACAACAACAA 57.537 30.769 19.63 0.00 0.00 2.83
29 30 7.360691 GCAACTAGGTGAGCAACATATATGATG 60.361 40.741 19.63 17.89 34.18 3.07
30 31 6.652481 GCAACTAGGTGAGCAACATATATGAT 59.348 38.462 19.63 4.54 0.00 2.45
31 32 5.991606 GCAACTAGGTGAGCAACATATATGA 59.008 40.000 19.63 0.00 0.00 2.15
32 33 5.759763 TGCAACTAGGTGAGCAACATATATG 59.240 40.000 13.29 11.29 33.48 1.78
33 34 5.928976 TGCAACTAGGTGAGCAACATATAT 58.071 37.500 13.29 0.00 33.48 0.86
34 35 5.351948 TGCAACTAGGTGAGCAACATATA 57.648 39.130 13.29 0.00 33.48 0.86
35 36 4.220693 TGCAACTAGGTGAGCAACATAT 57.779 40.909 13.29 0.00 33.48 1.78
36 37 3.694043 TGCAACTAGGTGAGCAACATA 57.306 42.857 13.29 0.00 33.48 2.29
37 38 2.566833 TGCAACTAGGTGAGCAACAT 57.433 45.000 13.29 0.00 33.48 2.71
38 39 2.566833 ATGCAACTAGGTGAGCAACA 57.433 45.000 13.29 0.00 40.76 3.33
39 40 4.446371 AGATATGCAACTAGGTGAGCAAC 58.554 43.478 13.29 0.00 40.76 4.17
40 41 4.760530 AGATATGCAACTAGGTGAGCAA 57.239 40.909 13.29 0.00 40.76 3.91
41 42 5.010112 GTCTAGATATGCAACTAGGTGAGCA 59.990 44.000 13.29 3.07 41.73 4.26
42 43 5.010112 TGTCTAGATATGCAACTAGGTGAGC 59.990 44.000 13.29 0.00 37.34 4.26
43 44 6.641169 TGTCTAGATATGCAACTAGGTGAG 57.359 41.667 13.29 0.00 37.34 3.51
44 45 6.183360 GGTTGTCTAGATATGCAACTAGGTGA 60.183 42.308 13.29 0.00 40.49 4.02
45 46 5.986135 GGTTGTCTAGATATGCAACTAGGTG 59.014 44.000 18.23 2.45 40.49 4.00
46 47 5.900123 AGGTTGTCTAGATATGCAACTAGGT 59.100 40.000 18.23 0.00 40.49 3.08
47 48 6.412362 AGGTTGTCTAGATATGCAACTAGG 57.588 41.667 18.23 7.22 40.49 3.02
48 49 8.172352 AGTAGGTTGTCTAGATATGCAACTAG 57.828 38.462 18.23 15.26 40.49 2.57
49 50 8.534954 AAGTAGGTTGTCTAGATATGCAACTA 57.465 34.615 18.23 9.66 40.49 2.24
50 51 7.425224 AAGTAGGTTGTCTAGATATGCAACT 57.575 36.000 18.23 7.55 40.49 3.16
51 52 7.764443 TCAAAGTAGGTTGTCTAGATATGCAAC 59.236 37.037 13.07 13.07 40.08 4.17
52 53 7.847096 TCAAAGTAGGTTGTCTAGATATGCAA 58.153 34.615 0.00 0.00 0.00 4.08
53 54 7.418337 TCAAAGTAGGTTGTCTAGATATGCA 57.582 36.000 0.00 0.00 0.00 3.96
54 55 7.095439 GCATCAAAGTAGGTTGTCTAGATATGC 60.095 40.741 0.00 0.00 0.00 3.14
55 56 7.928167 TGCATCAAAGTAGGTTGTCTAGATATG 59.072 37.037 0.00 0.00 0.00 1.78
56 57 8.023021 TGCATCAAAGTAGGTTGTCTAGATAT 57.977 34.615 0.00 0.00 0.00 1.63
57 58 7.418337 TGCATCAAAGTAGGTTGTCTAGATA 57.582 36.000 0.00 0.00 0.00 1.98
58 59 6.299805 TGCATCAAAGTAGGTTGTCTAGAT 57.700 37.500 0.00 0.00 0.00 1.98
59 60 5.738619 TGCATCAAAGTAGGTTGTCTAGA 57.261 39.130 0.00 0.00 0.00 2.43
60 61 6.801539 TTTGCATCAAAGTAGGTTGTCTAG 57.198 37.500 0.00 0.00 0.00 2.43
61 62 6.801539 CTTTGCATCAAAGTAGGTTGTCTA 57.198 37.500 10.28 0.00 43.85 2.59
62 63 5.695851 CTTTGCATCAAAGTAGGTTGTCT 57.304 39.130 10.28 0.00 43.85 3.41
234 235 3.726291 TGACGCATGAAAGGATCGATA 57.274 42.857 0.00 0.00 0.00 2.92
235 236 2.602257 TGACGCATGAAAGGATCGAT 57.398 45.000 0.00 0.00 0.00 3.59
236 237 2.270923 CTTGACGCATGAAAGGATCGA 58.729 47.619 0.00 0.00 0.00 3.59
237 238 1.328680 CCTTGACGCATGAAAGGATCG 59.671 52.381 0.00 0.00 42.65 3.69
238 239 1.672881 CCCTTGACGCATGAAAGGATC 59.327 52.381 14.86 0.00 42.65 3.36
239 240 1.281867 TCCCTTGACGCATGAAAGGAT 59.718 47.619 14.86 0.00 42.65 3.24
240 241 0.690192 TCCCTTGACGCATGAAAGGA 59.310 50.000 14.86 0.00 42.65 3.36
241 242 1.089920 CTCCCTTGACGCATGAAAGG 58.910 55.000 0.00 3.45 40.21 3.11
242 243 1.089920 CCTCCCTTGACGCATGAAAG 58.910 55.000 0.00 0.00 0.00 2.62
243 244 0.400213 ACCTCCCTTGACGCATGAAA 59.600 50.000 0.00 0.00 0.00 2.69
244 245 0.400213 AACCTCCCTTGACGCATGAA 59.600 50.000 0.00 0.00 0.00 2.57
245 246 0.400213 AAACCTCCCTTGACGCATGA 59.600 50.000 0.00 0.00 0.00 3.07
246 247 1.200020 GAAAACCTCCCTTGACGCATG 59.800 52.381 0.00 0.00 0.00 4.06
247 248 1.202879 TGAAAACCTCCCTTGACGCAT 60.203 47.619 0.00 0.00 0.00 4.73
248 249 0.181587 TGAAAACCTCCCTTGACGCA 59.818 50.000 0.00 0.00 0.00 5.24
249 250 1.534729 ATGAAAACCTCCCTTGACGC 58.465 50.000 0.00 0.00 0.00 5.19
254 255 4.968719 ACCTTTTGAATGAAAACCTCCCTT 59.031 37.500 0.00 0.00 30.13 3.95
261 262 6.861572 GCTGGTAGTACCTTTTGAATGAAAAC 59.138 38.462 20.07 0.00 39.58 2.43
266 267 7.552687 TGAATAGCTGGTAGTACCTTTTGAATG 59.447 37.037 20.07 2.36 39.58 2.67
304 305 0.528017 CTCACCAGCGAGCTCTTGTA 59.472 55.000 12.85 0.00 0.00 2.41
305 306 1.181741 TCTCACCAGCGAGCTCTTGT 61.182 55.000 12.85 0.27 32.75 3.16
377 378 3.556213 GGGCAACAACATTAAGGAAACCC 60.556 47.826 0.00 0.00 39.74 4.11
383 384 4.057432 CAGTTTGGGCAACAACATTAAGG 58.943 43.478 0.00 0.00 39.19 2.69
436 437 2.737359 GCGTTCATATCCGGTGAGTTCA 60.737 50.000 0.00 0.00 0.00 3.18
445 446 2.814919 AGGTCTAGAGCGTTCATATCCG 59.185 50.000 15.91 0.00 0.00 4.18
486 487 3.894427 ACTAGCCTATCTGACATGGACTG 59.106 47.826 0.00 0.00 0.00 3.51
550 551 9.767228 AATTTTGTTGATCAGATTTGTCATGAA 57.233 25.926 0.00 0.00 0.00 2.57
612 613 8.928448 TGGTGATTATATTTTCTGTCTCTAGCT 58.072 33.333 0.00 0.00 0.00 3.32
613 614 8.983724 GTGGTGATTATATTTTCTGTCTCTAGC 58.016 37.037 0.00 0.00 0.00 3.42
694 803 7.093988 TGGTTAAATGACAAACATGACTATGGG 60.094 37.037 0.00 0.00 39.39 4.00
695 804 7.754924 GTGGTTAAATGACAAACATGACTATGG 59.245 37.037 0.00 0.00 39.39 2.74
786 921 7.444183 GTGCTATTATTAGTGCCACTAATCCAA 59.556 37.037 28.46 20.06 45.49 3.53
795 930 2.158885 TGCCGTGCTATTATTAGTGCCA 60.159 45.455 0.00 0.00 0.00 4.92
841 976 4.976864 ACGTGGGGACTATGTTTAACTTT 58.023 39.130 0.00 0.00 0.00 2.66
961 2010 3.547513 GGGGAACTCGATCGGGGG 61.548 72.222 21.07 10.67 0.00 5.40
1059 2108 2.441164 GCAGCTCCTCCTCCTCGA 60.441 66.667 0.00 0.00 0.00 4.04
1081 2139 2.284405 TCCGAACTCCACCCTCCC 60.284 66.667 0.00 0.00 0.00 4.30
1208 2483 3.936203 GCACCACCACCACCTCGA 61.936 66.667 0.00 0.00 0.00 4.04
1240 2519 2.095213 CGCGCCTTAATTAGTTGAAGCA 59.905 45.455 0.00 0.00 0.00 3.91
1804 5635 2.686405 GCATTGGCATGACATCTTGAGA 59.314 45.455 0.00 0.00 40.72 3.27
1807 5642 1.754803 AGGCATTGGCATGACATCTTG 59.245 47.619 0.00 1.81 41.63 3.02
1814 5649 0.611618 AAACGGAGGCATTGGCATGA 60.612 50.000 13.20 0.00 43.71 3.07
1830 5670 6.348621 ACAGTTCAAAATGCATGACAAAAC 57.651 33.333 0.00 2.13 0.00 2.43
1852 5693 3.187700 AGCACCATCGATCGTCTTTAAC 58.812 45.455 15.94 1.01 0.00 2.01
1854 5695 2.425668 TGAGCACCATCGATCGTCTTTA 59.574 45.455 15.94 0.00 0.00 1.85
1857 5698 0.383590 CTGAGCACCATCGATCGTCT 59.616 55.000 15.94 0.69 0.00 4.18
1858 5699 0.596083 CCTGAGCACCATCGATCGTC 60.596 60.000 15.94 3.78 0.00 4.20
2705 6884 4.308526 GTCGTAGGTGGAGACGGA 57.691 61.111 0.00 0.00 39.53 4.69
2747 6926 5.752955 ACCATGAACCAATCAAACGAAAAAG 59.247 36.000 0.00 0.00 42.54 2.27
2753 6938 4.217550 AGGTAACCATGAACCAATCAAACG 59.782 41.667 12.54 0.00 38.70 3.60
2754 6939 5.722021 AGGTAACCATGAACCAATCAAAC 57.278 39.130 12.54 0.00 38.70 2.93
2755 6940 5.835819 TCAAGGTAACCATGAACCAATCAAA 59.164 36.000 12.54 0.00 38.70 2.69
2756 6941 5.389520 TCAAGGTAACCATGAACCAATCAA 58.610 37.500 12.54 0.00 38.70 2.57
2757 6942 4.991776 TCAAGGTAACCATGAACCAATCA 58.008 39.130 12.54 0.00 38.30 2.57
2758 6943 5.652014 TGATCAAGGTAACCATGAACCAATC 59.348 40.000 12.54 11.66 38.30 2.67
2759 6944 5.579047 TGATCAAGGTAACCATGAACCAAT 58.421 37.500 12.54 5.05 38.30 3.16
2760 6945 4.991776 TGATCAAGGTAACCATGAACCAA 58.008 39.130 12.54 1.32 38.30 3.67
2761 6946 4.649267 TGATCAAGGTAACCATGAACCA 57.351 40.909 12.54 0.00 38.30 3.67
2762 6947 4.580580 GGATGATCAAGGTAACCATGAACC 59.419 45.833 0.00 0.00 36.62 3.62
2763 6948 5.192927 TGGATGATCAAGGTAACCATGAAC 58.807 41.667 0.00 0.00 36.62 3.18
2764 6949 5.449297 TGGATGATCAAGGTAACCATGAA 57.551 39.130 0.00 0.00 36.62 2.57
2765 6950 5.132480 TGATGGATGATCAAGGTAACCATGA 59.868 40.000 16.48 9.75 38.19 3.07
2766 6951 5.379187 TGATGGATGATCAAGGTAACCATG 58.621 41.667 16.48 0.00 38.19 3.66
2767 6952 5.628130 CTGATGGATGATCAAGGTAACCAT 58.372 41.667 0.00 8.32 40.73 3.55
2768 6953 4.686944 GCTGATGGATGATCAAGGTAACCA 60.687 45.833 0.00 3.73 40.73 3.67
2769 6954 3.817647 GCTGATGGATGATCAAGGTAACC 59.182 47.826 0.00 0.00 40.73 2.85
2770 6955 3.817647 GGCTGATGGATGATCAAGGTAAC 59.182 47.826 0.00 0.00 40.73 2.50
2771 6956 3.181440 GGGCTGATGGATGATCAAGGTAA 60.181 47.826 0.00 0.00 40.73 2.85
2772 6957 2.373169 GGGCTGATGGATGATCAAGGTA 59.627 50.000 0.00 0.00 40.73 3.08
2773 6958 1.144503 GGGCTGATGGATGATCAAGGT 59.855 52.381 0.00 0.00 40.73 3.50
2774 6959 1.144298 TGGGCTGATGGATGATCAAGG 59.856 52.381 0.00 0.00 40.73 3.61
2775 6960 2.105993 TCTGGGCTGATGGATGATCAAG 59.894 50.000 0.00 0.00 40.73 3.02
2776 6961 2.129363 TCTGGGCTGATGGATGATCAA 58.871 47.619 0.00 0.00 40.73 2.57
2777 6962 1.810455 TCTGGGCTGATGGATGATCA 58.190 50.000 0.00 0.00 38.87 2.92
2778 6963 2.305052 TCATCTGGGCTGATGGATGATC 59.695 50.000 16.50 0.00 42.82 2.92
3024 7220 4.156008 CGGGAAAACTGGGAACTGAATTAG 59.844 45.833 0.00 0.00 0.00 1.73
3046 7242 6.218019 ACAATTTTGAATGATATGGATGCCG 58.782 36.000 0.00 0.00 0.00 5.69
3103 7299 0.958091 TTTGTCAAACCGGGATGCAG 59.042 50.000 6.32 0.00 0.00 4.41
3112 7308 6.420903 GCAAGGTTAGAGAATTTTGTCAAACC 59.579 38.462 0.00 0.00 0.00 3.27
3151 7347 8.815565 TGTAATGTTTTATGGCTATCTGGAAA 57.184 30.769 0.00 0.00 0.00 3.13
3291 7490 7.556275 CAGTTGTATGTGTATTGGAAATACCCT 59.444 37.037 7.48 0.00 38.00 4.34
3321 7520 9.748708 TGTTCCTGATAAAGTCAATTTTCTTTG 57.251 29.630 12.25 0.00 36.14 2.77
3396 7595 5.907207 TGTTGTAGAGCTTGATATCCTGTC 58.093 41.667 0.00 0.00 0.00 3.51
3488 7687 4.062293 CAGGTGTCGAACAACCAATAGAA 58.938 43.478 13.86 0.00 36.16 2.10
3589 7788 2.480037 GCATTTTTGCTGGGTGTTAAGC 59.520 45.455 0.00 0.00 39.96 3.09
3634 7833 1.889829 ACTTCTGGAGACCTTCAGACG 59.110 52.381 7.50 8.60 39.43 4.18
3663 7862 1.476891 TGGTCACACTCTTATCCGAGC 59.523 52.381 0.00 0.00 34.35 5.03
3674 7873 2.439507 ACATCTGGAAGTTGGTCACACT 59.560 45.455 0.00 0.00 37.97 3.55


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

AutoCloner maintained by Alex Coulton.