Multiple sequence alignment - TraesCS5A01G128300

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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 TraesCS5A01G128300 chr5A 100.000 7003 0 0 1 7003 285996728 286003730 0.000000e+00 12933.0
1 TraesCS5A01G128300 chr5A 85.263 475 33 12 6558 7001 482617719 482617251 8.280000e-124 455.0
2 TraesCS5A01G128300 chr5A 90.000 130 12 1 2 131 275667966 275667838 4.340000e-37 167.0
3 TraesCS5A01G128300 chr5A 87.786 131 14 2 1 131 275664449 275664321 1.220000e-32 152.0
4 TraesCS5A01G128300 chr5D 95.564 5884 183 40 202 6054 216382716 216388552 0.000000e+00 9348.0
5 TraesCS5A01G128300 chr5D 94.988 419 17 3 6039 6456 216388570 216388985 0.000000e+00 654.0
6 TraesCS5A01G128300 chr5D 82.989 435 64 8 6570 7003 526686350 526685925 1.100000e-102 385.0
7 TraesCS5A01G128300 chr5D 86.139 202 24 2 2 203 216382458 216382655 1.530000e-51 215.0
8 TraesCS5A01G128300 chr5D 90.000 130 12 1 2 131 212457378 212457250 4.340000e-37 167.0
9 TraesCS5A01G128300 chr5D 89.922 129 7 5 10 135 27254446 27254321 2.020000e-35 161.0
10 TraesCS5A01G128300 chr5D 88.462 130 14 1 2 131 212458485 212458357 9.410000e-34 156.0
11 TraesCS5A01G128300 chr5B 95.787 4201 133 26 648 4830 232556127 232560301 0.000000e+00 6737.0
12 TraesCS5A01G128300 chr5B 96.545 1621 49 7 4840 6456 232560432 232562049 0.000000e+00 2676.0
13 TraesCS5A01G128300 chr5B 86.747 415 40 9 202 612 232555419 232555822 1.390000e-121 448.0
14 TraesCS5A01G128300 chr5B 80.978 552 65 12 6490 7003 670022883 670022334 1.090000e-107 401.0
15 TraesCS5A01G128300 chr5B 86.634 202 22 3 2 203 232554985 232555181 1.180000e-52 219.0
16 TraesCS5A01G128300 chr6D 84.045 539 48 20 6491 7003 355867267 355867793 1.060000e-132 484.0
17 TraesCS5A01G128300 chr6D 78.070 570 74 37 6456 7003 285243675 285244215 5.270000e-81 313.0
18 TraesCS5A01G128300 chr6D 100.000 31 0 0 5097 5127 10448541 10448571 2.730000e-04 58.4
19 TraesCS5A01G128300 chr6D 100.000 28 0 0 5099 5126 399221449 399221422 1.300000e-02 52.8
20 TraesCS5A01G128300 chr1D 87.016 439 43 8 6570 7003 432033039 432033468 3.800000e-132 483.0
21 TraesCS5A01G128300 chr1D 80.247 567 53 17 6491 7003 63881542 63882103 8.580000e-99 372.0
22 TraesCS5A01G128300 chr1D 79.964 549 67 18 6491 7003 288544643 288544102 1.440000e-96 364.0
23 TraesCS5A01G128300 chr1D 76.891 714 84 39 1034 1719 407296214 407296874 5.240000e-86 329.0
24 TraesCS5A01G128300 chr1D 96.774 31 1 0 5099 5129 8319030 8319060 1.300000e-02 52.8
25 TraesCS5A01G128300 chr1D 100.000 28 0 0 5102 5129 48211110 48211137 1.300000e-02 52.8
26 TraesCS5A01G128300 chr1D 96.774 31 1 0 5096 5126 98834884 98834914 1.300000e-02 52.8
27 TraesCS5A01G128300 chr1D 100.000 28 0 0 5102 5129 229357848 229357821 1.300000e-02 52.8
28 TraesCS5A01G128300 chr1D 92.105 38 1 2 5095 5130 411170598 411170561 1.300000e-02 52.8
29 TraesCS5A01G128300 chr4A 82.640 553 53 17 6491 7003 713361722 713362271 3.850000e-122 449.0
30 TraesCS5A01G128300 chr4A 87.681 138 14 3 2 137 590615802 590615666 2.610000e-34 158.0
31 TraesCS5A01G128300 chr7D 82.420 529 61 18 6491 7003 427904103 427903591 3.880000e-117 433.0
32 TraesCS5A01G128300 chr7D 94.737 38 0 2 5091 5127 465577023 465576987 2.730000e-04 58.4
33 TraesCS5A01G128300 chr3D 81.919 542 60 14 6494 7003 609902992 609902457 2.340000e-114 424.0
34 TraesCS5A01G128300 chr7A 81.901 547 53 18 6494 7003 649980339 649979802 3.020000e-113 420.0
35 TraesCS5A01G128300 chr7A 89.552 67 1 3 6456 6520 575339095 575339033 5.820000e-11 80.5
36 TraesCS5A01G128300 chr1B 78.225 721 86 40 1023 1724 547701648 547702316 5.090000e-106 396.0
37 TraesCS5A01G128300 chr1B 82.000 100 12 3 6456 6553 664336501 664336406 5.820000e-11 80.5
38 TraesCS5A01G128300 chr3A 80.446 583 56 25 1149 1707 692347255 692347803 6.590000e-105 392.0
39 TraesCS5A01G128300 chr3A 94.444 36 2 0 5100 5135 632608538 632608573 1.000000e-03 56.5
40 TraesCS5A01G128300 chr4D 81.025 527 68 17 6491 7003 488727948 488727440 2.370000e-104 390.0
41 TraesCS5A01G128300 chr4D 100.000 31 0 0 5097 5127 32941723 32941753 2.730000e-04 58.4
42 TraesCS5A01G128300 chr4D 100.000 31 0 0 5099 5129 116152450 116152480 2.730000e-04 58.4
43 TraesCS5A01G128300 chr4D 100.000 29 0 0 5098 5126 301747402 301747430 4.000000e-03 54.7
44 TraesCS5A01G128300 chr2D 89.216 306 33 0 6698 7003 630677446 630677751 3.960000e-102 383.0
45 TraesCS5A01G128300 chr2D 88.673 309 32 3 6698 7003 4377905 4377597 2.390000e-99 374.0
46 TraesCS5A01G128300 chr2D 88.350 309 33 3 6698 7003 4321182 4320874 1.110000e-97 368.0
47 TraesCS5A01G128300 chr2D 89.552 67 1 3 6456 6520 460841573 460841511 5.820000e-11 80.5
48 TraesCS5A01G128300 chr2D 84.337 83 6 4 6440 6520 633086445 633086368 2.710000e-09 75.0
49 TraesCS5A01G128300 chr2D 96.875 32 1 0 5100 5131 619265862 619265893 4.000000e-03 54.7
50 TraesCS5A01G128300 chr2B 80.108 553 67 14 6491 7003 410193318 410192769 8.580000e-99 372.0
51 TraesCS5A01G128300 chr3B 77.883 529 59 26 1220 1724 658558488 658557994 6.920000e-70 276.0
52 TraesCS5A01G128300 chr6B 75.313 559 67 35 6456 6968 80141071 80141604 1.190000e-47 202.0
53 TraesCS5A01G128300 chrUn 86.154 130 17 1 2 130 233314930 233314801 9.470000e-29 139.0
54 TraesCS5A01G128300 chr4B 86.154 130 17 1 2 130 630651533 630651662 9.470000e-29 139.0
55 TraesCS5A01G128300 chr4B 86.154 130 17 1 2 130 630656574 630656703 9.470000e-29 139.0
56 TraesCS5A01G128300 chr4B 86.154 130 17 1 2 130 630664221 630664350 9.470000e-29 139.0
57 TraesCS5A01G128300 chr4B 80.000 95 14 3 6456 6545 461732943 461732849 1.630000e-06 65.8
58 TraesCS5A01G128300 chr4B 100.000 31 0 0 5102 5132 576197130 576197160 2.730000e-04 58.4
59 TraesCS5A01G128300 chr1A 88.571 70 2 3 6453 6520 373258444 373258509 5.820000e-11 80.5
60 TraesCS5A01G128300 chr1A 85.897 78 4 4 6446 6520 396263412 396263485 7.530000e-10 76.8


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 TraesCS5A01G128300 chr5A 285996728 286003730 7002 False 12933.000000 12933 100.000000 1 7003 1 chr5A.!!$F1 7002
1 TraesCS5A01G128300 chr5D 216382458 216388985 6527 False 3405.666667 9348 92.230333 2 6456 3 chr5D.!!$F1 6454
2 TraesCS5A01G128300 chr5B 232554985 232562049 7064 False 2520.000000 6737 91.428250 2 6456 4 chr5B.!!$F1 6454
3 TraesCS5A01G128300 chr5B 670022334 670022883 549 True 401.000000 401 80.978000 6490 7003 1 chr5B.!!$R1 513
4 TraesCS5A01G128300 chr6D 355867267 355867793 526 False 484.000000 484 84.045000 6491 7003 1 chr6D.!!$F3 512
5 TraesCS5A01G128300 chr6D 285243675 285244215 540 False 313.000000 313 78.070000 6456 7003 1 chr6D.!!$F2 547
6 TraesCS5A01G128300 chr1D 63881542 63882103 561 False 372.000000 372 80.247000 6491 7003 1 chr1D.!!$F3 512
7 TraesCS5A01G128300 chr1D 288544102 288544643 541 True 364.000000 364 79.964000 6491 7003 1 chr1D.!!$R2 512
8 TraesCS5A01G128300 chr1D 407296214 407296874 660 False 329.000000 329 76.891000 1034 1719 1 chr1D.!!$F5 685
9 TraesCS5A01G128300 chr4A 713361722 713362271 549 False 449.000000 449 82.640000 6491 7003 1 chr4A.!!$F1 512
10 TraesCS5A01G128300 chr7D 427903591 427904103 512 True 433.000000 433 82.420000 6491 7003 1 chr7D.!!$R1 512
11 TraesCS5A01G128300 chr3D 609902457 609902992 535 True 424.000000 424 81.919000 6494 7003 1 chr3D.!!$R1 509
12 TraesCS5A01G128300 chr7A 649979802 649980339 537 True 420.000000 420 81.901000 6494 7003 1 chr7A.!!$R2 509
13 TraesCS5A01G128300 chr1B 547701648 547702316 668 False 396.000000 396 78.225000 1023 1724 1 chr1B.!!$F1 701
14 TraesCS5A01G128300 chr3A 692347255 692347803 548 False 392.000000 392 80.446000 1149 1707 1 chr3A.!!$F2 558
15 TraesCS5A01G128300 chr4D 488727440 488727948 508 True 390.000000 390 81.025000 6491 7003 1 chr4D.!!$R1 512
16 TraesCS5A01G128300 chr2B 410192769 410193318 549 True 372.000000 372 80.108000 6491 7003 1 chr2B.!!$R1 512
17 TraesCS5A01G128300 chr6B 80141071 80141604 533 False 202.000000 202 75.313000 6456 6968 1 chr6B.!!$F1 512

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
432 673 0.240678 CATGTTTGCCGCTACTTGCA 59.759 50.000 0.00 0.00 43.06 4.08 F
434 675 0.310543 TGTTTGCCGCTACTTGCAAG 59.689 50.000 24.84 24.84 46.99 4.01 F
996 1518 0.591170 CTACCAACACCAAACCGCAG 59.409 55.000 0.00 0.00 0.00 5.18 F
1234 1767 1.041437 CGATCCCTGTTCCTCCTACC 58.959 60.000 0.00 0.00 0.00 3.18 F
2146 2732 1.137086 GGACGTGGTGCATCTACAGAT 59.863 52.381 0.00 0.00 34.56 2.90 F
3230 3821 0.963355 GTGCTGGGGATGGCGTTTTA 60.963 55.000 0.00 0.00 0.00 1.52 F
4083 4678 2.634940 CCCTGAGAAGAAGGTGAGTTCA 59.365 50.000 0.00 0.00 32.45 3.18 F
4660 5255 0.953727 TGCTACTGCTGCCAAAACTG 59.046 50.000 0.00 0.00 40.48 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1865 0.392336 GGCTCCGCTCTCATTCAGAT 59.608 55.000 0.00 0.00 0.00 2.90 R
1510 2084 0.537188 TTTCCCCGAGCTGAGCTAAG 59.463 55.000 7.08 4.49 39.88 2.18 R
2381 2968 0.820871 AAAAACACGGCAGGCAGAAA 59.179 45.000 0.00 0.00 0.00 2.52 R
3223 3814 1.173913 AGGCCAGACCAATAAAACGC 58.826 50.000 5.01 0.00 43.14 4.84 R
4056 4651 1.074566 ACCTTCTTCTCAGGGGCTTTG 59.925 52.381 0.00 0.00 35.46 2.77 R
4637 5232 0.108396 TTTGGCAGCAGTAGCAGACA 59.892 50.000 0.00 0.00 44.30 3.41 R
5876 6598 0.636101 ATGGGATGGGGCTGCTAAAA 59.364 50.000 0.00 0.00 0.00 1.52 R
6322 7077 0.467290 TGAGCAAACCAGGTTGGGTC 60.467 55.000 26.53 26.53 35.52 4.46 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
33 34 6.494952 TGTAGTTCCTCTAGGAGAAGATGTT 58.505 40.000 0.00 0.00 46.36 2.71
37 38 7.164803 AGTTCCTCTAGGAGAAGATGTTTTTG 58.835 38.462 0.00 0.00 46.36 2.44
77 79 5.192927 TCCTTCCTTATGGCTTGTGTAATG 58.807 41.667 0.00 0.00 0.00 1.90
297 538 2.356432 CCAGAATCATCACCCAGCTCAA 60.356 50.000 0.00 0.00 0.00 3.02
305 546 1.613630 ACCCAGCTCAATCCGTCCT 60.614 57.895 0.00 0.00 0.00 3.85
356 597 2.520536 GCCTACATGATCCGCCCCT 61.521 63.158 0.00 0.00 0.00 4.79
359 600 1.909302 CCTACATGATCCGCCCCTAAT 59.091 52.381 0.00 0.00 0.00 1.73
369 610 3.057337 CCCCTAATACGGCCCTCG 58.943 66.667 0.00 0.00 45.88 4.63
376 617 3.700038 CCTAATACGGCCCTCGATTAGAT 59.300 47.826 16.55 0.00 42.43 1.98
390 631 7.324178 CCTCGATTAGATATAAAACCAGGAGG 58.676 42.308 0.00 0.00 42.21 4.30
423 664 1.072116 CACGCAATCCATGTTTGCCG 61.072 55.000 19.27 16.72 45.19 5.69
424 665 2.160221 CGCAATCCATGTTTGCCGC 61.160 57.895 19.27 2.94 45.19 6.53
425 666 1.216178 GCAATCCATGTTTGCCGCT 59.784 52.632 16.02 0.00 42.84 5.52
426 667 0.455410 GCAATCCATGTTTGCCGCTA 59.545 50.000 16.02 0.00 42.84 4.26
427 668 1.798813 GCAATCCATGTTTGCCGCTAC 60.799 52.381 16.02 0.00 42.84 3.58
428 669 1.745087 CAATCCATGTTTGCCGCTACT 59.255 47.619 0.00 0.00 0.00 2.57
429 670 2.128771 ATCCATGTTTGCCGCTACTT 57.871 45.000 0.00 0.00 0.00 2.24
432 673 0.240678 CATGTTTGCCGCTACTTGCA 59.759 50.000 0.00 0.00 43.06 4.08
434 675 0.310543 TGTTTGCCGCTACTTGCAAG 59.689 50.000 24.84 24.84 46.99 4.01
452 693 1.092921 AGTTGCAACACCGAAGCGAA 61.093 50.000 30.11 0.00 0.00 4.70
454 695 1.781025 TTGCAACACCGAAGCGAAGG 61.781 55.000 0.00 0.00 0.00 3.46
455 696 2.556287 CAACACCGAAGCGAAGGC 59.444 61.111 0.00 0.00 40.37 4.35
479 721 5.186942 TCATTTGGCATTACGGCTACTTTA 58.813 37.500 0.00 0.00 41.89 1.85
480 722 5.648526 TCATTTGGCATTACGGCTACTTTAA 59.351 36.000 0.00 0.00 41.89 1.52
481 723 5.961396 TTTGGCATTACGGCTACTTTAAA 57.039 34.783 0.00 0.00 41.89 1.52
529 772 7.552459 TCAGAGAATAATCGTACCAATTGACA 58.448 34.615 7.12 0.00 0.00 3.58
681 1198 0.937304 CCGTGTGGTGTGTCAGAAAG 59.063 55.000 0.00 0.00 0.00 2.62
954 1472 1.675007 CTCCCTCCCTTTTTCTCCCT 58.325 55.000 0.00 0.00 0.00 4.20
995 1517 0.820074 CCTACCAACACCAAACCGCA 60.820 55.000 0.00 0.00 0.00 5.69
996 1518 0.591170 CTACCAACACCAAACCGCAG 59.409 55.000 0.00 0.00 0.00 5.18
1234 1767 1.041437 CGATCCCTGTTCCTCCTACC 58.959 60.000 0.00 0.00 0.00 3.18
1310 1865 2.188469 GATCGGGGTGGCGCTTTA 59.812 61.111 7.64 0.00 0.00 1.85
1406 1970 1.373748 GTCGCTGCGGTTCCACTTA 60.374 57.895 23.03 0.00 0.00 2.24
1497 2071 3.367498 GGTTCTGCGAACTAGTCATCTGT 60.367 47.826 16.93 0.00 0.00 3.41
1505 2079 5.814764 GAACTAGTCATCTGTTCGGTAGA 57.185 43.478 0.00 0.00 32.25 2.59
1510 2084 5.189659 AGTCATCTGTTCGGTAGATTAGC 57.810 43.478 0.00 0.00 32.75 3.09
1535 2109 1.342819 CTCAGCTCGGGGAAATCCTAG 59.657 57.143 0.00 0.00 35.95 3.02
1853 2439 7.402862 AGTAACCATTTTGTTAGGAGCAGTAT 58.597 34.615 0.00 0.00 31.66 2.12
1858 2444 7.285401 ACCATTTTGTTAGGAGCAGTATAATGG 59.715 37.037 0.00 0.00 42.33 3.16
1879 2465 5.708948 TGGACGCAATTAAGAAGGAAATTG 58.291 37.500 3.93 3.93 43.05 2.32
1912 2498 6.379133 AGAATAGAATTGCAGCTTTTCATCCA 59.621 34.615 14.17 0.00 0.00 3.41
1914 2500 4.563061 AGAATTGCAGCTTTTCATCCAAC 58.437 39.130 9.63 0.00 0.00 3.77
2009 2595 2.102252 GGACCAATTTTCCTGCACAACA 59.898 45.455 0.00 0.00 0.00 3.33
2086 2672 1.164411 CGATGTGCAAAGCCCAGTTA 58.836 50.000 0.00 0.00 0.00 2.24
2093 2679 1.892474 GCAAAGCCCAGTTATGTTCCA 59.108 47.619 0.00 0.00 0.00 3.53
2103 2689 8.004215 AGCCCAGTTATGTTCCATTCATATTTA 58.996 33.333 0.00 0.00 0.00 1.40
2146 2732 1.137086 GGACGTGGTGCATCTACAGAT 59.863 52.381 0.00 0.00 34.56 2.90
2286 2872 7.384660 GCACCATTGAAAACACATGAATTCTAA 59.615 33.333 7.05 0.00 0.00 2.10
2381 2968 2.748209 AAAGGGTAGTGGCACAAGTT 57.252 45.000 21.41 0.74 44.16 2.66
2702 3289 4.330620 CAGCCTTGCAAATTCGCATAAAAT 59.669 37.500 0.00 0.00 42.62 1.82
2703 3290 4.330620 AGCCTTGCAAATTCGCATAAAATG 59.669 37.500 0.00 0.00 42.62 2.32
2704 3291 4.093261 GCCTTGCAAATTCGCATAAAATGT 59.907 37.500 0.00 0.00 42.62 2.71
2705 3292 5.552807 CCTTGCAAATTCGCATAAAATGTG 58.447 37.500 0.00 0.00 42.62 3.21
2706 3293 5.120519 CCTTGCAAATTCGCATAAAATGTGT 59.879 36.000 0.00 0.00 42.62 3.72
2780 3371 9.875675 CTTTCAGTTTTAGAAAATCTCAGTCTG 57.124 33.333 0.00 0.00 34.84 3.51
2823 3414 4.713792 ATTTATTCTTCTGAGGGCCGAT 57.286 40.909 0.00 0.00 0.00 4.18
2874 3465 7.766278 CAGGTGTCAAAGTAGTTCTGCTTATAT 59.234 37.037 3.84 0.00 0.00 0.86
2927 3518 5.628797 TGTATGGATAGAGATGCCAACAA 57.371 39.130 0.00 0.00 34.95 2.83
2929 3520 6.604171 TGTATGGATAGAGATGCCAACAATT 58.396 36.000 0.00 0.00 34.95 2.32
3215 3806 4.981806 ACGGTATGCATTTTATTGTGCT 57.018 36.364 3.54 0.00 41.78 4.40
3223 3814 3.742013 GCATTTTATTGTGCTGGGGATGG 60.742 47.826 0.00 0.00 38.30 3.51
3230 3821 0.963355 GTGCTGGGGATGGCGTTTTA 60.963 55.000 0.00 0.00 0.00 1.52
3309 3900 7.726079 TGTATCTATAAATTATTGCGTCGTGC 58.274 34.615 0.00 0.00 46.70 5.34
3507 4098 6.223351 CTTCGAGAAGTAAAGGAGGGTATT 57.777 41.667 4.76 0.00 33.87 1.89
3664 4259 6.425114 TGCATTCAAGTACTGTTTCTCTCTTC 59.575 38.462 0.00 0.00 0.00 2.87
3966 4561 7.389607 TGGTGTTTGGTAGCTTTAGATTAGTTC 59.610 37.037 0.00 0.00 0.00 3.01
4083 4678 2.634940 CCCTGAGAAGAAGGTGAGTTCA 59.365 50.000 0.00 0.00 32.45 3.18
4166 4761 5.456548 TTTTCGTTTTAGGGATGGGTTTC 57.543 39.130 0.00 0.00 0.00 2.78
4219 4814 4.655963 ACAGACATCCAAGTGTTATGCTT 58.344 39.130 0.00 0.00 31.16 3.91
4290 4885 4.164796 TCTCTATGGCAGGTTGATGTTGAT 59.835 41.667 0.00 0.00 0.00 2.57
4604 5199 9.899661 TCTTGTATATGTACCAAAGCACTATTT 57.100 29.630 0.00 0.00 0.00 1.40
4646 5241 8.573035 ACTAAATCTCTAGCTATTGTCTGCTAC 58.427 37.037 0.00 0.00 40.35 3.58
4660 5255 0.953727 TGCTACTGCTGCCAAAACTG 59.046 50.000 0.00 0.00 40.48 3.16
4663 5258 2.229784 GCTACTGCTGCCAAAACTGATT 59.770 45.455 0.00 0.00 36.03 2.57
4676 5271 3.455619 AACTGATTTTCACGTGATCGC 57.544 42.857 20.80 9.90 41.18 4.58
4705 5300 7.817962 CCTAGTATCATAATGGAGGGTTTTACG 59.182 40.741 0.00 0.00 0.00 3.18
4724 5319 1.464608 CGTGGGCAGTGACTACATTTG 59.535 52.381 13.50 0.00 0.00 2.32
4841 5561 9.192642 TGCATTTGACTAGTAGTAAGGTATGTA 57.807 33.333 1.88 0.90 0.00 2.29
4985 5705 8.435982 ACACCTTTAAAATGAAAAATGGGATGA 58.564 29.630 6.21 0.00 0.00 2.92
5013 5733 5.837438 GGTATAGAAAGGACAGGCTAGGTAA 59.163 44.000 0.00 0.00 0.00 2.85
5014 5734 6.497606 GGTATAGAAAGGACAGGCTAGGTAAT 59.502 42.308 0.00 0.00 0.00 1.89
5075 5795 1.069022 CATGCTGACGGAACTTGTTGG 60.069 52.381 0.00 0.00 0.00 3.77
5257 5977 9.965824 GATCTGTTTCTCATTTTTCTTGGTTTA 57.034 29.630 0.00 0.00 0.00 2.01
5534 6254 4.899502 AGTTTCATGTGAGTTACAGAGGG 58.100 43.478 0.00 0.00 43.80 4.30
5560 6280 6.128526 GCAAAACTTAACAGCTCGTTATCTCT 60.129 38.462 8.82 0.00 39.81 3.10
5840 6562 4.783621 TGGGCCGTCTGATGCAGC 62.784 66.667 0.00 0.00 0.00 5.25
5876 6598 2.943265 ATGTGGCCCTTGGGAGCT 60.943 61.111 10.36 0.00 0.00 4.09
5934 6656 0.040514 CGTTGGAAAGCATTCACGCA 60.041 50.000 3.82 0.00 37.29 5.24
6098 6853 1.270550 GTGTCATTGGTTTGAGGCTGG 59.729 52.381 0.00 0.00 0.00 4.85
6115 6870 1.478510 CTGGCTGGTCTCGACACTATT 59.521 52.381 0.00 0.00 0.00 1.73
6124 6879 4.425520 GTCTCGACACTATTTTCCTCCTG 58.574 47.826 0.00 0.00 0.00 3.86
6143 6898 0.949105 GTGGACACGGGCTACTGTTG 60.949 60.000 0.00 0.00 32.69 3.33
6322 7077 4.578105 GCCATCCTCTAAACCTGAATCTTG 59.422 45.833 0.00 0.00 0.00 3.02
6323 7078 5.630069 GCCATCCTCTAAACCTGAATCTTGA 60.630 44.000 0.00 0.00 0.00 3.02
6324 7079 5.819901 CCATCCTCTAAACCTGAATCTTGAC 59.180 44.000 0.00 0.00 0.00 3.18
6325 7080 5.422214 TCCTCTAAACCTGAATCTTGACC 57.578 43.478 0.00 0.00 0.00 4.02
6362 7119 2.158755 ACCAACCAGGACAAGACTTCTG 60.159 50.000 0.00 0.00 41.22 3.02
6371 7128 3.471680 GACAAGACTTCTGAGGTGCTTT 58.528 45.455 0.00 0.00 0.00 3.51
6510 7272 1.153249 CGCTAAAATCGGCCTGGGA 60.153 57.895 0.00 0.00 0.00 4.37
6522 7284 2.657237 CTGGGAGCGAGTCGGTTT 59.343 61.111 19.53 0.00 37.83 3.27
6554 7318 2.284331 TAGGGCCGCCTCAAGACA 60.284 61.111 9.86 0.00 0.00 3.41
6658 7487 8.138365 TCGGACATTACATAGCAAAGTTATTC 57.862 34.615 0.00 0.00 0.00 1.75
6659 7488 7.042992 TCGGACATTACATAGCAAAGTTATTCG 60.043 37.037 0.00 0.00 0.00 3.34
6684 7513 6.724893 AAAAGGCCACAACTACAACTATTT 57.275 33.333 5.01 0.00 0.00 1.40
6685 7514 6.724893 AAAGGCCACAACTACAACTATTTT 57.275 33.333 5.01 0.00 0.00 1.82
6755 7614 0.915364 GGCCTTCTCCTCCTTGATGT 59.085 55.000 0.00 0.00 0.00 3.06
6759 7618 1.280133 CTTCTCCTCCTTGATGTGGCA 59.720 52.381 0.00 0.00 0.00 4.92
6921 7798 3.062466 CTCCAGCTCCGTCCGTGA 61.062 66.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.894364 TCTCCTAGAGGAACTACAATGTTTAGT 59.106 37.037 0.00 0.00 44.91 2.24
21 22 9.981460 ATAGTTTATCCAAAAACATCTTCTCCT 57.019 29.630 2.68 0.00 40.97 3.69
150 152 6.492007 TTTCTCTACGATTCTAACGTCAGT 57.508 37.500 0.00 0.00 43.62 3.41
194 196 6.819397 TGCTGCTGTAGGTACTAGTATATG 57.181 41.667 5.75 0.00 44.14 1.78
208 449 1.167851 GAAACTGGCATGCTGCTGTA 58.832 50.000 18.92 0.00 44.28 2.74
297 538 1.137872 GAGCAATCACAGAGGACGGAT 59.862 52.381 0.00 0.00 0.00 4.18
305 546 5.824624 ACTTTTTCTCTTGAGCAATCACAGA 59.175 36.000 0.00 0.00 0.00 3.41
356 597 8.523915 TTTATATCTAATCGAGGGCCGTATTA 57.476 34.615 0.00 0.00 39.75 0.98
359 600 6.350445 GGTTTTATATCTAATCGAGGGCCGTA 60.350 42.308 0.00 0.00 39.75 4.02
363 604 5.875359 CCTGGTTTTATATCTAATCGAGGGC 59.125 44.000 0.00 0.00 0.00 5.19
369 610 7.094592 GCTTGCCTCCTGGTTTTATATCTAATC 60.095 40.741 0.00 0.00 35.27 1.75
376 617 4.473559 ACTAGCTTGCCTCCTGGTTTTATA 59.526 41.667 0.00 0.00 35.27 0.98
432 673 1.092921 TCGCTTCGGTGTTGCAACTT 61.093 50.000 28.61 0.00 0.00 2.66
434 675 0.657368 CTTCGCTTCGGTGTTGCAAC 60.657 55.000 22.83 22.83 0.00 4.17
452 693 1.392589 CCGTAATGCCAAATGAGCCT 58.607 50.000 0.00 0.00 0.00 4.58
454 695 0.740737 AGCCGTAATGCCAAATGAGC 59.259 50.000 0.00 0.00 0.00 4.26
455 696 3.206150 AGTAGCCGTAATGCCAAATGAG 58.794 45.455 0.00 0.00 0.00 2.90
456 697 3.275617 AGTAGCCGTAATGCCAAATGA 57.724 42.857 0.00 0.00 0.00 2.57
457 698 4.370364 AAAGTAGCCGTAATGCCAAATG 57.630 40.909 0.00 0.00 0.00 2.32
458 699 6.518208 TTTAAAGTAGCCGTAATGCCAAAT 57.482 33.333 0.00 0.00 0.00 2.32
459 700 5.961396 TTTAAAGTAGCCGTAATGCCAAA 57.039 34.783 0.00 0.00 0.00 3.28
514 757 4.517285 AGCTTCATGTCAATTGGTACGAT 58.483 39.130 5.42 0.00 0.00 3.73
515 758 3.932710 GAGCTTCATGTCAATTGGTACGA 59.067 43.478 5.42 0.00 0.00 3.43
527 770 2.740981 CAGCGAAAGAAGAGCTTCATGT 59.259 45.455 12.32 0.00 41.84 3.21
529 772 2.354259 CCAGCGAAAGAAGAGCTTCAT 58.646 47.619 12.32 0.00 41.84 2.57
1265 1798 1.871039 ACTCGAACCAATCCAACAACG 59.129 47.619 0.00 0.00 0.00 4.10
1309 1864 1.615883 GGCTCCGCTCTCATTCAGATA 59.384 52.381 0.00 0.00 0.00 1.98
1310 1865 0.392336 GGCTCCGCTCTCATTCAGAT 59.608 55.000 0.00 0.00 0.00 2.90
1406 1970 4.478317 TCCCATTATTCAACCCAGTGAGAT 59.522 41.667 0.00 0.00 0.00 2.75
1497 2071 4.261656 GCTGAGCTAAGCTAATCTACCGAA 60.262 45.833 16.54 0.00 39.88 4.30
1510 2084 0.537188 TTTCCCCGAGCTGAGCTAAG 59.463 55.000 7.08 4.49 39.88 2.18
1535 2109 1.550976 CGGTAGCATCTATTCCTCCCC 59.449 57.143 0.00 0.00 0.00 4.81
1853 2439 7.639113 ATTTCCTTCTTAATTGCGTCCATTA 57.361 32.000 0.00 0.00 0.00 1.90
1858 2444 7.044052 GCATACAATTTCCTTCTTAATTGCGTC 60.044 37.037 0.00 0.00 42.62 5.19
1879 2465 7.375106 AGCTGCAATTCTATTCTATGCATAC 57.625 36.000 1.16 0.00 45.03 2.39
1912 2498 2.550830 ACTTTGTGCTGATCCGAGTT 57.449 45.000 0.00 0.00 0.00 3.01
1914 2500 5.356882 TTTTTACTTTGTGCTGATCCGAG 57.643 39.130 0.00 0.00 0.00 4.63
2009 2595 5.163281 ACAGACAGAGCAATCTGAAATCT 57.837 39.130 12.00 2.24 44.32 2.40
2016 2602 5.221601 TGAGAGAAAACAGACAGAGCAATCT 60.222 40.000 0.00 0.00 0.00 2.40
2086 2672 8.481492 TTCCAGCATAAATATGAATGGAACAT 57.519 30.769 23.14 0.00 45.65 2.71
2093 2679 7.255730 GGCACTTCTTCCAGCATAAATATGAAT 60.256 37.037 4.63 0.00 35.75 2.57
2103 2689 1.615392 GTTTGGCACTTCTTCCAGCAT 59.385 47.619 0.00 0.00 33.32 3.79
2381 2968 0.820871 AAAAACACGGCAGGCAGAAA 59.179 45.000 0.00 0.00 0.00 2.52
2444 3031 2.553602 CAGCACAGCCAATACAGACAAA 59.446 45.455 0.00 0.00 0.00 2.83
2702 3289 4.956075 TGCTCAGGAATATGAGTCTACACA 59.044 41.667 5.69 0.00 46.93 3.72
2703 3290 5.521906 TGCTCAGGAATATGAGTCTACAC 57.478 43.478 5.69 0.00 46.93 2.90
2704 3291 6.324770 TCATTGCTCAGGAATATGAGTCTACA 59.675 38.462 5.69 0.00 46.93 2.74
2705 3292 6.753180 TCATTGCTCAGGAATATGAGTCTAC 58.247 40.000 5.69 0.00 46.93 2.59
2706 3293 6.983906 TCATTGCTCAGGAATATGAGTCTA 57.016 37.500 5.69 0.00 46.93 2.59
2780 3371 8.438676 AAATTGTACAGTGAGACATAATAGGC 57.561 34.615 0.00 0.00 0.00 3.93
2788 3379 9.208022 CAGAAGAATAAATTGTACAGTGAGACA 57.792 33.333 0.00 0.00 0.00 3.41
2823 3414 4.469586 TGTCTAGGACCATATTGCTTCACA 59.530 41.667 0.00 0.00 0.00 3.58
2874 3465 7.977789 TGTTGAAATATGTAGCAACTCTTGA 57.022 32.000 0.00 0.00 40.78 3.02
3215 3806 1.272760 ACCAATAAAACGCCATCCCCA 60.273 47.619 0.00 0.00 0.00 4.96
3223 3814 1.173913 AGGCCAGACCAATAAAACGC 58.826 50.000 5.01 0.00 43.14 4.84
3230 3821 1.635487 TCTAAGCAAGGCCAGACCAAT 59.365 47.619 5.01 0.00 43.14 3.16
3309 3900 4.534168 CTTCATCTGCAAACAGTGAACAG 58.466 43.478 0.00 0.00 44.77 3.16
3507 4098 7.039853 TCCAAAAGTGATGAATCAAGCATACAA 60.040 33.333 0.00 0.00 38.75 2.41
3935 4530 8.644374 ATCTAAAGCTACCAAACACCAAAATA 57.356 30.769 0.00 0.00 0.00 1.40
3999 4594 6.402550 CGCTTGATTCCTATACACATATTGCC 60.403 42.308 0.00 0.00 0.00 4.52
4056 4651 1.074566 ACCTTCTTCTCAGGGGCTTTG 59.925 52.381 0.00 0.00 35.46 2.77
4187 4782 9.744468 AACACTTGGATGTCTGTTTTAAAATAC 57.256 29.630 3.52 4.33 30.55 1.89
4604 5199 9.337396 AGAGATTTAGTTTGTCAAATGTGTACA 57.663 29.630 0.40 0.00 0.00 2.90
4637 5232 0.108396 TTTGGCAGCAGTAGCAGACA 59.892 50.000 0.00 0.00 44.30 3.41
4646 5241 3.492011 GTGAAAATCAGTTTTGGCAGCAG 59.508 43.478 0.00 0.00 37.65 4.24
4660 5255 3.187700 AGGTAGCGATCACGTGAAAATC 58.812 45.455 24.13 14.76 41.98 2.17
4663 5258 2.751259 ACTAGGTAGCGATCACGTGAAA 59.249 45.455 24.13 0.00 41.98 2.69
4676 5271 8.437274 AAACCCTCCATTATGATACTAGGTAG 57.563 38.462 0.00 0.00 0.00 3.18
4705 5300 1.200020 GCAAATGTAGTCACTGCCCAC 59.800 52.381 0.00 0.00 32.74 4.61
4724 5319 5.586243 TCAACAAGATAAGTATGCCTCAAGC 59.414 40.000 0.00 0.00 44.14 4.01
4841 5561 3.056213 CCAAACTTGGGAGGCACAT 57.944 52.632 0.09 0.00 44.70 3.21
4842 5562 4.597032 CCAAACTTGGGAGGCACA 57.403 55.556 0.09 0.00 44.70 4.57
4985 5705 5.717119 AGCCTGTCCTTTCTATACCAAAT 57.283 39.130 0.00 0.00 0.00 2.32
5013 5733 4.287067 ACCAAATCCAGCAGTCCGATATAT 59.713 41.667 0.00 0.00 0.00 0.86
5014 5734 3.646162 ACCAAATCCAGCAGTCCGATATA 59.354 43.478 0.00 0.00 0.00 0.86
5257 5977 6.384015 TGGTGAGGAAGTAGATGATGTACATT 59.616 38.462 10.30 0.00 39.56 2.71
5376 6096 3.008266 TCTCAGCTGATTCCACATCAACA 59.992 43.478 18.63 0.00 0.00 3.33
5534 6254 3.349488 AACGAGCTGTTAAGTTTTGCC 57.651 42.857 0.00 0.00 39.61 4.52
5807 6528 3.616076 CGGCCCAGTTTTAATGCATTTCA 60.616 43.478 18.75 1.73 0.00 2.69
5840 6562 4.984785 CACATGTCCGACCATAGAACATAG 59.015 45.833 0.00 0.00 0.00 2.23
5876 6598 0.636101 ATGGGATGGGGCTGCTAAAA 59.364 50.000 0.00 0.00 0.00 1.52
5916 6638 1.987770 CATGCGTGAATGCTTTCCAAC 59.012 47.619 0.00 2.01 35.36 3.77
5934 6656 2.891580 ACTTACAGACCACACTCGACAT 59.108 45.455 0.00 0.00 0.00 3.06
6098 6853 2.930682 GGAAAATAGTGTCGAGACCAGC 59.069 50.000 9.40 0.00 0.00 4.85
6115 6870 1.752198 CCGTGTCCACAGGAGGAAA 59.248 57.895 0.91 0.00 39.92 3.13
6124 6879 0.949105 CAACAGTAGCCCGTGTCCAC 60.949 60.000 0.00 0.00 0.00 4.02
6143 6898 4.872691 CACCACACTTGATGGAGAAGATAC 59.127 45.833 0.00 0.00 39.87 2.24
6312 7067 2.440409 CAGGTTGGGTCAAGATTCAGG 58.560 52.381 0.00 0.00 0.00 3.86
6322 7077 0.467290 TGAGCAAACCAGGTTGGGTC 60.467 55.000 26.53 26.53 35.52 4.46
6323 7078 0.755327 GTGAGCAAACCAGGTTGGGT 60.755 55.000 11.53 11.53 40.89 4.51
6324 7079 1.463553 GGTGAGCAAACCAGGTTGGG 61.464 60.000 5.30 2.54 43.37 4.12
6325 7080 0.754957 TGGTGAGCAAACCAGGTTGG 60.755 55.000 5.30 3.38 45.43 3.77
6362 7119 0.744414 TAGCATCGCCAAAGCACCTC 60.744 55.000 0.00 0.00 39.83 3.85
6371 7128 1.305219 GCAAACCACTAGCATCGCCA 61.305 55.000 0.00 0.00 0.00 5.69
6505 7267 1.446272 GAAACCGACTCGCTCCCAG 60.446 63.158 0.00 0.00 0.00 4.45
6510 7272 2.048127 GCTGGAAACCGACTCGCT 60.048 61.111 0.00 0.00 0.00 4.93
6658 7487 3.066203 AGTTGTAGTTGTGGCCTTTTTCG 59.934 43.478 3.32 0.00 0.00 3.46
6659 7488 4.649088 AGTTGTAGTTGTGGCCTTTTTC 57.351 40.909 3.32 0.00 0.00 2.29
6684 7513 2.088950 CGACTTCTTCGCCCCTTAAA 57.911 50.000 0.00 0.00 41.87 1.52
6685 7514 3.826637 CGACTTCTTCGCCCCTTAA 57.173 52.632 0.00 0.00 41.87 1.85
6811 7670 0.313987 ACGACAGCAACGATGACTCA 59.686 50.000 0.00 0.00 34.70 3.41
6813 7684 0.729478 CGACGACAGCAACGATGACT 60.729 55.000 0.00 0.00 34.70 3.41


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

AutoCloner maintained by Alex Coulton.