Multiple sequence alignment - TraesCS6D01G138600

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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 TraesCS6D01G138600 chr6D 100.000 6021 0 0 1 6021 107392881 107386861 0.000000e+00 11119.0
1 TraesCS6D01G138600 chr6D 86.979 768 85 7 5259 6019 106703284 106704043 0.000000e+00 850.0
2 TraesCS6D01G138600 chr6D 95.652 276 10 2 1 275 52060139 52059865 5.540000e-120 442.0
3 TraesCS6D01G138600 chr6D 95.652 276 10 2 1 275 52062769 52062495 5.540000e-120 442.0
4 TraesCS6D01G138600 chr6D 95.620 274 9 2 3 275 52061451 52061180 2.580000e-118 436.0
5 TraesCS6D01G138600 chr6D 94.969 159 8 0 265 423 107525493 107525335 3.600000e-62 250.0
6 TraesCS6D01G138600 chr6B 96.186 2412 68 11 3616 6019 194863362 194860967 0.000000e+00 3923.0
7 TraesCS6D01G138600 chr6B 96.330 654 12 6 627 1276 194866741 194866096 0.000000e+00 1064.0
8 TraesCS6D01G138600 chr6B 89.624 771 42 14 2833 3577 194864116 194863358 0.000000e+00 946.0
9 TraesCS6D01G138600 chr6B 87.435 764 81 7 5263 6019 194424173 194424928 0.000000e+00 865.0
10 TraesCS6D01G138600 chr6B 89.929 566 19 12 1353 1915 194865697 194865167 0.000000e+00 695.0
11 TraesCS6D01G138600 chr6B 90.680 515 14 6 1896 2403 194865151 194864664 0.000000e+00 654.0
12 TraesCS6D01G138600 chr6B 95.165 393 17 1 2420 2810 194864571 194864179 2.380000e-173 619.0
13 TraesCS6D01G138600 chr6B 90.759 303 10 3 292 578 194868164 194867864 7.320000e-104 388.0
14 TraesCS6D01G138600 chr6B 97.727 44 1 0 586 629 194866831 194866788 6.470000e-10 76.8
15 TraesCS6D01G138600 chr6A 93.588 2012 79 21 4021 6019 131231841 131229867 0.000000e+00 2955.0
16 TraesCS6D01G138600 chr6A 89.374 2268 104 52 631 2817 131235378 131233167 0.000000e+00 2726.0
17 TraesCS6D01G138600 chr6A 91.674 1093 59 11 2970 4044 131232928 131231850 0.000000e+00 1485.0
18 TraesCS6D01G138600 chr6A 87.435 764 81 7 5263 6019 129938258 129939013 0.000000e+00 865.0
19 TraesCS6D01G138600 chr6A 82.967 182 13 7 421 584 131240290 131240109 1.350000e-31 148.0
20 TraesCS6D01G138600 chr6A 87.500 104 8 3 2833 2936 131233112 131233014 1.370000e-21 115.0
21 TraesCS6D01G138600 chr6A 94.340 53 1 2 586 636 131239347 131239295 5.000000e-11 80.5
22 TraesCS6D01G138600 chr6A 82.609 69 4 6 515 576 131239914 131239847 3.000000e-03 54.7
23 TraesCS6D01G138600 chr7D 78.737 776 130 26 5260 6021 600450360 600449606 2.520000e-133 486.0
24 TraesCS6D01G138600 chr7D 81.313 594 103 8 4392 4981 599721970 599722559 5.460000e-130 475.0
25 TraesCS6D01G138600 chr7D 78.475 669 127 14 5260 5917 599808423 599809085 7.220000e-114 422.0
26 TraesCS6D01G138600 chr7D 79.417 583 103 13 5349 5920 599797146 599797722 4.370000e-106 396.0
27 TraesCS6D01G138600 chr7D 77.363 402 77 13 5530 5924 509630733 509631127 6.070000e-55 226.0
28 TraesCS6D01G138600 chr7D 85.430 151 20 2 1144 1293 599720977 599721126 8.080000e-34 156.0
29 TraesCS6D01G138600 chr7D 78.395 162 15 8 438 581 88708309 88708468 2.990000e-13 87.9
30 TraesCS6D01G138600 chr7D 89.041 73 3 5 515 584 153121499 153121429 1.080000e-12 86.1
31 TraesCS6D01G138600 chr7A 95.172 290 12 2 1 289 130100130 130099842 1.980000e-124 457.0
32 TraesCS6D01G138600 chr7A 85.034 147 20 2 1144 1289 692018665 692018810 1.350000e-31 148.0
33 TraesCS6D01G138600 chr7A 93.056 72 3 2 515 584 107911586 107911657 2.970000e-18 104.0
34 TraesCS6D01G138600 chr5D 96.981 265 7 1 1 264 125592229 125591965 1.540000e-120 444.0
35 TraesCS6D01G138600 chr5D 95.000 160 7 1 265 423 74885700 74885541 3.600000e-62 250.0
36 TraesCS6D01G138600 chr5D 72.849 674 134 33 5279 5913 406417543 406416880 1.030000e-42 185.0
37 TraesCS6D01G138600 chr5D 91.549 71 3 3 517 584 419762690 419762620 1.790000e-15 95.3
38 TraesCS6D01G138600 chr5D 87.500 72 4 5 517 584 454288419 454288489 1.800000e-10 78.7
39 TraesCS6D01G138600 chr5D 87.324 71 4 2 515 584 454212993 454213059 6.470000e-10 76.8
40 TraesCS6D01G138600 chr5D 86.765 68 6 3 520 584 374319463 374319530 8.370000e-09 73.1
41 TraesCS6D01G138600 chr2D 96.970 264 7 1 1 264 96279501 96279763 5.540000e-120 442.0
42 TraesCS6D01G138600 chr2D 90.667 150 14 0 274 423 107386588 107386737 3.680000e-47 200.0
43 TraesCS6D01G138600 chr2D 89.375 160 16 1 265 423 452430702 452430861 3.680000e-47 200.0
44 TraesCS6D01G138600 chr2D 91.304 69 4 2 515 582 324285708 324285641 6.430000e-15 93.5
45 TraesCS6D01G138600 chr2D 88.462 78 7 2 515 591 386816259 386816335 6.430000e-15 93.5
46 TraesCS6D01G138600 chr2D 89.189 74 4 4 515 584 178489932 178490005 8.310000e-14 89.8
47 TraesCS6D01G138600 chr2D 89.041 73 4 4 515 583 178621256 178621328 2.990000e-13 87.9
48 TraesCS6D01G138600 chr3D 95.324 278 12 1 1 278 363486824 363486548 1.990000e-119 440.0
49 TraesCS6D01G138600 chr3D 95.636 275 10 2 1 274 421696470 421696197 1.990000e-119 440.0
50 TraesCS6D01G138600 chr4D 95.896 268 11 0 1 268 477281764 477282031 9.270000e-118 435.0
51 TraesCS6D01G138600 chr4D 79.630 108 15 5 481 584 490397065 490396961 3.010000e-08 71.3
52 TraesCS6D01G138600 chr7B 78.593 668 124 16 5262 5917 679671460 679672120 2.010000e-114 424.0
53 TraesCS6D01G138600 chr7B 79.245 583 104 13 5349 5920 679633666 679634242 2.030000e-104 390.0
54 TraesCS6D01G138600 chr7B 78.697 568 102 15 5263 5818 679793713 679793153 1.600000e-95 361.0
55 TraesCS6D01G138600 chr7B 81.622 185 22 9 410 584 61610150 61610332 6.290000e-30 143.0
56 TraesCS6D01G138600 chr7B 83.444 151 23 2 1144 1293 679629618 679629767 8.140000e-29 139.0
57 TraesCS6D01G138600 chr7B 91.429 70 4 2 517 584 463413900 463413831 1.790000e-15 95.3
58 TraesCS6D01G138600 chr5B 93.243 148 10 0 276 423 709948120 709947973 1.020000e-52 219.0
59 TraesCS6D01G138600 chr5B 96.364 55 2 0 515 569 496984527 496984581 2.310000e-14 91.6
60 TraesCS6D01G138600 chr5B 88.732 71 2 6 515 582 66287260 66287193 1.390000e-11 82.4
61 TraesCS6D01G138600 chr2B 91.195 159 14 0 265 423 440240472 440240314 3.650000e-52 217.0
62 TraesCS6D01G138600 chr3B 90.566 159 14 1 265 423 760545736 760545893 6.110000e-50 209.0
63 TraesCS6D01G138600 chr5A 88.679 159 17 1 265 422 411611436 411611594 6.160000e-45 193.0
64 TraesCS6D01G138600 chr2A 93.056 72 2 3 515 584 762852859 762852929 1.070000e-17 102.0
65 TraesCS6D01G138600 chr1A 90.278 72 5 2 515 584 551229142 551229071 6.430000e-15 93.5
66 TraesCS6D01G138600 chr1A 87.037 54 3 1 515 564 42900373 42900426 2.340000e-04 58.4
67 TraesCS6D01G138600 chr1D 98.077 52 1 0 518 569 435747085 435747034 2.310000e-14 91.6
68 TraesCS6D01G138600 chr1D 97.143 35 0 1 535 569 435747365 435747332 2.340000e-04 58.4


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 TraesCS6D01G138600 chr6D 107386861 107392881 6020 True 11119.000 11119 100.000000 1 6021 1 chr6D.!!$R1 6020
1 TraesCS6D01G138600 chr6D 106703284 106704043 759 False 850.000 850 86.979000 5259 6019 1 chr6D.!!$F1 760
2 TraesCS6D01G138600 chr6D 52059865 52062769 2904 True 440.000 442 95.641333 1 275 3 chr6D.!!$R3 274
3 TraesCS6D01G138600 chr6B 194860967 194868164 7197 True 1045.725 3923 93.300000 292 6019 8 chr6B.!!$R1 5727
4 TraesCS6D01G138600 chr6B 194424173 194424928 755 False 865.000 865 87.435000 5263 6019 1 chr6B.!!$F1 756
5 TraesCS6D01G138600 chr6A 131229867 131240290 10423 True 1080.600 2955 88.864571 421 6019 7 chr6A.!!$R1 5598
6 TraesCS6D01G138600 chr6A 129938258 129939013 755 False 865.000 865 87.435000 5263 6019 1 chr6A.!!$F1 756
7 TraesCS6D01G138600 chr7D 600449606 600450360 754 True 486.000 486 78.737000 5260 6021 1 chr7D.!!$R2 761
8 TraesCS6D01G138600 chr7D 599808423 599809085 662 False 422.000 422 78.475000 5260 5917 1 chr7D.!!$F4 657
9 TraesCS6D01G138600 chr7D 599797146 599797722 576 False 396.000 396 79.417000 5349 5920 1 chr7D.!!$F3 571
10 TraesCS6D01G138600 chr7D 599720977 599722559 1582 False 315.500 475 83.371500 1144 4981 2 chr7D.!!$F5 3837
11 TraesCS6D01G138600 chr7B 679671460 679672120 660 False 424.000 424 78.593000 5262 5917 1 chr7B.!!$F2 655
12 TraesCS6D01G138600 chr7B 679793153 679793713 560 True 361.000 361 78.697000 5263 5818 1 chr7B.!!$R2 555
13 TraesCS6D01G138600 chr7B 679629618 679634242 4624 False 264.500 390 81.344500 1144 5920 2 chr7B.!!$F3 4776

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
677 8315 0.172578 TGACGGTCATTAGGCGAGTG 59.827 55.0 6.76 0.0 0.00 3.51 F
976 8644 0.393673 CACAGAGCCGGAGAGAGAGA 60.394 60.0 5.05 0.0 0.00 3.10 F
2614 10756 0.317479 AACTGCACCGAGTGAGTACC 59.683 55.0 8.04 0.0 35.23 3.34 F
3528 11788 0.387239 GAAGTGTGTGCCGCCATTTC 60.387 55.0 0.00 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 9714 0.040425 GTTTCCCACATGTGACGTGC 60.040 55.000 27.46 10.22 32.85 5.34 R
2680 10822 0.393402 TGATCATGTGGGCAGCTCAC 60.393 55.000 19.44 19.44 35.82 3.51 R
3803 12069 0.905357 ACAGGGATCAGGAAAGGACG 59.095 55.000 0.00 0.00 0.00 4.79 R
5502 15973 1.064208 CGTGGGAGACAGACTACGATG 59.936 57.143 0.00 0.00 33.78 3.84 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
26 27 0.850100 TCAACTTTGCCCCTCTTCCA 59.150 50.000 0.00 0.00 0.00 3.53
43 44 3.678056 TCCATTAGGTGCGCTTATAGG 57.322 47.619 9.73 2.08 35.89 2.57
102 1419 6.095021 GGCCTTTGACCGTTAGATTTTTCTAT 59.905 38.462 0.00 0.00 0.00 1.98
148 1465 4.083484 CCTTTGACTGGACGGAAAATGTAC 60.083 45.833 0.00 0.00 0.00 2.90
230 1547 4.748277 TTTAGGGGTAAAGATGAGGTCG 57.252 45.455 0.00 0.00 0.00 4.79
238 1555 3.721087 AAAGATGAGGTCGGGACAAAT 57.279 42.857 0.75 0.00 0.00 2.32
363 2993 3.673338 TCTCGTAACAACAAGCATCTTCG 59.327 43.478 0.00 0.00 0.00 3.79
365 2995 2.157668 CGTAACAACAAGCATCTTCGCT 59.842 45.455 0.00 0.00 46.67 4.93
406 3036 8.256605 TCAAACTCTTTTGACCATTTCATCAAA 58.743 29.630 0.00 0.00 45.08 2.69
417 3047 7.656948 TGACCATTTCATCAAAACAAAGATTCC 59.343 33.333 0.00 0.00 0.00 3.01
629 4341 1.065782 ACACGCACAGGTGGCATATAA 60.066 47.619 1.10 0.00 42.23 0.98
637 8272 5.807721 GCACAGGTGGCATATAAATATCCCT 60.808 44.000 1.10 0.00 0.00 4.20
644 8279 8.523658 GGTGGCATATAAATATCCCTTTTCTTC 58.476 37.037 0.00 0.00 0.00 2.87
677 8315 0.172578 TGACGGTCATTAGGCGAGTG 59.827 55.000 6.76 0.00 0.00 3.51
709 8347 2.599757 GCCCCCGGTAACCTCTGTT 61.600 63.158 0.00 0.00 38.52 3.16
976 8644 0.393673 CACAGAGCCGGAGAGAGAGA 60.394 60.000 5.05 0.00 0.00 3.10
1064 8736 2.759795 GGGCAGCAGGAAGAAGGT 59.240 61.111 0.00 0.00 0.00 3.50
1317 8992 2.473365 CCCCCTCCAATCCATCCCC 61.473 68.421 0.00 0.00 0.00 4.81
1334 9009 1.174712 CCCCCGATTCATCCACATGC 61.175 60.000 0.00 0.00 0.00 4.06
1340 9015 1.162181 ATTCATCCACATGCTCCGCG 61.162 55.000 0.00 0.00 0.00 6.46
1345 9020 4.505217 CACATGCTCCGCGCGAAC 62.505 66.667 34.63 20.24 43.27 3.95
1347 9022 4.214383 CATGCTCCGCGCGAACTG 62.214 66.667 34.63 15.21 43.27 3.16
1348 9023 4.435436 ATGCTCCGCGCGAACTGA 62.435 61.111 34.63 19.05 43.27 3.41
1351 9026 2.202610 CTCCGCGCGAACTGATCA 60.203 61.111 34.63 0.00 0.00 2.92
1385 9382 4.383226 CCAATCCATTGATTTGACATGGCA 60.383 41.667 0.00 0.00 39.20 4.92
1501 9504 2.595238 GGGGATCATGAGGTACGTACT 58.405 52.381 24.07 11.06 0.00 2.73
1549 9552 4.656112 TGACTTTCCTTTTCTCTCTGTCCT 59.344 41.667 0.00 0.00 0.00 3.85
1573 9576 8.682710 CCTCCGGAATAAGAAAATGATTGTTTA 58.317 33.333 5.23 0.00 0.00 2.01
1613 9619 8.473358 TCAATAATGATTTGATTGCCTCTGAT 57.527 30.769 0.00 0.00 31.86 2.90
1678 9684 2.993937 ACTTGAAACGGTCTTCCAACA 58.006 42.857 0.00 0.00 0.00 3.33
1708 9714 2.486636 TAACTCACCACCGCAGCTCG 62.487 60.000 0.00 0.00 38.08 5.03
1718 9724 3.114616 GCAGCTCGCACGTCACAT 61.115 61.111 3.64 0.00 41.79 3.21
1720 9726 2.023771 CAGCTCGCACGTCACATGT 61.024 57.895 0.00 0.00 0.00 3.21
1722 9728 3.015293 GCTCGCACGTCACATGTGG 62.015 63.158 25.16 12.86 35.71 4.17
1723 9729 2.356913 TCGCACGTCACATGTGGG 60.357 61.111 25.16 18.90 45.86 4.61
1889 9896 1.129998 CGACTCTTTCTGCATTGCCAG 59.870 52.381 6.12 4.13 0.00 4.85
1899 9906 3.072038 TCTGCATTGCCAGCTACTGATAT 59.928 43.478 6.12 0.00 32.44 1.63
1980 10020 1.107538 ATGCTGCCCATGTGAGATGC 61.108 55.000 0.00 0.00 31.48 3.91
1996 10036 0.588252 ATGCGACAAGAACACACTGC 59.412 50.000 0.00 0.00 0.00 4.40
2053 10093 3.277742 GAACGAGGTTCGCGCACAC 62.278 63.158 11.73 2.16 45.12 3.82
2059 10099 3.411351 GTTCGCGCACACGGACAT 61.411 61.111 8.75 0.00 41.36 3.06
2172 10214 5.378292 TGGCGCAAATTACAGATTTGTTA 57.622 34.783 10.83 0.00 40.19 2.41
2300 10348 9.209175 ACTGCTACTACTTTGTTTATGAAAGAG 57.791 33.333 0.00 0.00 34.94 2.85
2301 10349 9.424319 CTGCTACTACTTTGTTTATGAAAGAGA 57.576 33.333 0.00 0.00 34.94 3.10
2308 10356 6.551227 ACTTTGTTTATGAAAGAGAAAGGCCT 59.449 34.615 0.00 0.00 34.94 5.19
2310 10358 6.976934 TGTTTATGAAAGAGAAAGGCCTTT 57.023 33.333 30.83 30.83 35.52 3.11
2331 10379 4.650545 TTAGTTACGTGCCGTTCATTTC 57.349 40.909 0.00 0.00 41.54 2.17
2403 10457 5.518847 TCAATCGGTAAGAAACGCATCTAAG 59.481 40.000 0.00 0.00 0.00 2.18
2404 10458 4.707030 TCGGTAAGAAACGCATCTAAGA 57.293 40.909 0.00 0.00 0.00 2.10
2405 10459 4.669318 TCGGTAAGAAACGCATCTAAGAG 58.331 43.478 0.00 0.00 0.00 2.85
2406 10460 4.397103 TCGGTAAGAAACGCATCTAAGAGA 59.603 41.667 0.00 0.00 0.00 3.10
2446 10577 3.127895 TGTTTCCGGATAATTTTCCAGCG 59.872 43.478 4.15 1.81 35.34 5.18
2614 10756 0.317479 AACTGCACCGAGTGAGTACC 59.683 55.000 8.04 0.00 35.23 3.34
2680 10822 1.741528 TGCATGGACAGCTGTGTATG 58.258 50.000 27.27 25.81 36.88 2.39
2747 10889 9.809395 ACTATAGTATAGAGGATGCACTACAAA 57.191 33.333 21.59 0.00 33.29 2.83
2801 10943 7.037586 ACAATAGGTCAAATCAGTTCCCTCTAA 60.038 37.037 0.00 0.00 0.00 2.10
2811 10953 7.979786 ATCAGTTCCCTCTAAATAACTCTGA 57.020 36.000 0.00 0.00 29.93 3.27
2813 10955 8.380742 TCAGTTCCCTCTAAATAACTCTGAAT 57.619 34.615 0.00 0.00 29.93 2.57
2816 10958 8.997734 AGTTCCCTCTAAATAACTCTGAATCAT 58.002 33.333 0.00 0.00 0.00 2.45
2817 10959 9.050601 GTTCCCTCTAAATAACTCTGAATCATG 57.949 37.037 0.00 0.00 0.00 3.07
2818 10960 8.324191 TCCCTCTAAATAACTCTGAATCATGT 57.676 34.615 0.00 0.00 0.00 3.21
2819 10961 8.772250 TCCCTCTAAATAACTCTGAATCATGTT 58.228 33.333 6.90 6.90 0.00 2.71
2826 10968 8.853077 AATAACTCTGAATCATGTTTGTCTGA 57.147 30.769 6.99 0.00 0.00 3.27
2828 10970 7.756395 AACTCTGAATCATGTTTGTCTGAAT 57.244 32.000 0.00 0.00 0.00 2.57
2829 10971 8.853077 AACTCTGAATCATGTTTGTCTGAATA 57.147 30.769 0.00 0.00 0.00 1.75
2831 11013 7.879677 ACTCTGAATCATGTTTGTCTGAATACA 59.120 33.333 0.00 0.00 0.00 2.29
2838 11020 5.651172 TGTTTGTCTGAATACAAGACGTG 57.349 39.130 0.00 0.00 40.29 4.49
2847 11029 5.120399 TGAATACAAGACGTGTTTTGACCT 58.880 37.500 9.90 0.00 41.98 3.85
2849 11031 2.980568 ACAAGACGTGTTTTGACCTGA 58.019 42.857 9.90 0.00 37.01 3.86
2850 11032 3.541632 ACAAGACGTGTTTTGACCTGAT 58.458 40.909 9.90 0.00 37.01 2.90
2868 11050 4.586841 CCTGATGGGTTTCTTTGGTTTACA 59.413 41.667 0.00 0.00 0.00 2.41
3023 11272 3.991367 TGCATCACATGAAAAATGCACA 58.009 36.364 18.18 4.62 46.91 4.57
3233 11484 3.820467 TGAAGTAAAATGGCCTCACACTG 59.180 43.478 3.32 0.00 0.00 3.66
3249 11500 6.604795 CCTCACACTGAAAATTCATTAGGGAT 59.395 38.462 0.00 0.00 36.46 3.85
3255 11506 7.869429 CACTGAAAATTCATTAGGGATAATGGC 59.131 37.037 7.85 0.00 37.86 4.40
3261 11512 4.901868 TCATTAGGGATAATGGCCGTAAC 58.098 43.478 0.00 0.00 38.23 2.50
3298 11549 3.525862 AGGGTTGACTTGAGATCCTCTT 58.474 45.455 0.00 0.00 0.00 2.85
3336 11587 2.531522 TATGATCACTGTCGCATGGG 57.468 50.000 0.00 2.76 0.00 4.00
3337 11588 0.543277 ATGATCACTGTCGCATGGGT 59.457 50.000 9.86 0.00 0.00 4.51
3493 11753 4.019174 ACCCTGAATCATGAAATGTGGAC 58.981 43.478 0.00 0.00 46.80 4.02
3528 11788 0.387239 GAAGTGTGTGCCGCCATTTC 60.387 55.000 0.00 0.00 0.00 2.17
3596 11856 7.315890 GTTGAGGAATTTACCAGAGGAAATTG 58.684 38.462 0.81 0.00 35.82 2.32
3607 11867 5.106157 ACCAGAGGAAATTGACTAAATTGCG 60.106 40.000 0.00 0.00 38.52 4.85
3650 11910 8.039603 TGAAATAGCACTGACGAATAATTTGT 57.960 30.769 0.00 0.00 0.00 2.83
3651 11911 9.157104 TGAAATAGCACTGACGAATAATTTGTA 57.843 29.630 0.00 0.00 0.00 2.41
3803 12069 1.222115 GGACAACTCGTGAGTGGTGC 61.222 60.000 14.60 13.46 45.19 5.01
3854 12120 0.464735 CAACCTGACCAACCGACCAA 60.465 55.000 0.00 0.00 0.00 3.67
3875 12141 0.035056 ACCAAGGAGCCATGTGTAGC 60.035 55.000 0.00 0.00 0.00 3.58
3959 12225 0.235926 GAACAAACACGCTGCCTCTC 59.764 55.000 0.00 0.00 0.00 3.20
4046 12348 5.809562 ACGATTCTTTTGCAACATTTTCACA 59.190 32.000 0.00 0.00 0.00 3.58
4060 12362 1.985473 TTCACATTTGCTCACCTGCT 58.015 45.000 0.00 0.00 0.00 4.24
4100 12402 3.186613 CAGCTACTTCTTCGGTTTGAACC 59.813 47.826 2.75 2.75 45.76 3.62
4147 12449 3.321968 AGACCAAGTGGCAAAATCTTTCC 59.678 43.478 0.00 0.00 39.32 3.13
4237 12542 3.001395 ACTCGAAATATTCTCTCGCCG 57.999 47.619 3.63 1.17 32.66 6.46
4239 12544 3.230355 CTCGAAATATTCTCTCGCCGAG 58.770 50.000 8.05 8.05 41.30 4.63
4274 12590 7.712264 TTTACATGCCAAACAGAGATTTTTG 57.288 32.000 0.00 0.00 33.30 2.44
4303 12619 6.007936 TGTTATGTTTGCAGTTATCGCTTT 57.992 33.333 0.00 0.00 0.00 3.51
4357 12674 2.671619 GTTTGCGTGCAGGGCCTA 60.672 61.111 5.28 0.00 0.00 3.93
5164 14089 4.671964 CGTGTGAACTTGTGATTTGACATG 59.328 41.667 0.00 0.00 0.00 3.21
5165 14090 4.442073 GTGTGAACTTGTGATTTGACATGC 59.558 41.667 0.00 0.00 0.00 4.06
5166 14091 4.097589 TGTGAACTTGTGATTTGACATGCA 59.902 37.500 0.00 0.00 0.00 3.96
5167 14092 4.678287 GTGAACTTGTGATTTGACATGCAG 59.322 41.667 0.00 0.00 0.00 4.41
5168 14093 4.338964 TGAACTTGTGATTTGACATGCAGT 59.661 37.500 0.00 0.00 0.00 4.40
5305 15662 3.702529 TACTCCGGGCCGACGATGA 62.703 63.158 30.79 14.87 35.47 2.92
5502 15973 1.673329 GCTTCCGAGAACTTCCTCACC 60.673 57.143 0.00 0.00 32.86 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.003648 GCATTCCTATAAGCGCACCTAAT 58.996 43.478 11.47 0.00 0.00 1.73
43 44 3.181490 GGAAAATGTACGGAAGGGCATTC 60.181 47.826 2.72 2.72 38.14 2.67
102 1419 0.318529 TTGACCGTTAAGTGCGCGTA 60.319 50.000 8.43 0.00 0.00 4.42
148 1465 3.678548 GCGCTTATAGAAATACCCTTCCG 59.321 47.826 0.00 0.00 0.00 4.30
273 2903 8.763356 GCTTGACACATTGTTGATTTGAAATAA 58.237 29.630 0.00 0.00 0.00 1.40
275 2905 6.762187 TGCTTGACACATTGTTGATTTGAAAT 59.238 30.769 0.00 0.00 0.00 2.17
276 2906 6.104665 TGCTTGACACATTGTTGATTTGAAA 58.895 32.000 0.00 0.00 0.00 2.69
277 2907 5.658468 TGCTTGACACATTGTTGATTTGAA 58.342 33.333 0.00 0.00 0.00 2.69
278 2908 5.259832 TGCTTGACACATTGTTGATTTGA 57.740 34.783 0.00 0.00 0.00 2.69
331 2961 6.381481 TTGTTGTTACGAGAGAGTAAGTGA 57.619 37.500 0.00 0.00 37.28 3.41
340 2970 4.201532 CGAAGATGCTTGTTGTTACGAGAG 60.202 45.833 0.00 0.00 37.92 3.20
344 2974 2.157668 AGCGAAGATGCTTGTTGTTACG 59.842 45.455 0.00 0.00 44.46 3.18
578 3224 2.283316 GGGCCCTGGCGGTTTTTA 60.283 61.111 17.04 0.00 43.06 1.52
629 4341 6.423358 AAAGGGGAGAAGAAAAGGGATATT 57.577 37.500 0.00 0.00 0.00 1.28
637 8272 6.430000 CGTCAGATTTAAAGGGGAGAAGAAAA 59.570 38.462 0.00 0.00 0.00 2.29
644 8279 3.055385 TGACCGTCAGATTTAAAGGGGAG 60.055 47.826 0.00 0.00 0.00 4.30
958 8624 0.107214 CTCTCTCTCTCCGGCTCTGT 60.107 60.000 0.00 0.00 0.00 3.41
961 8627 0.468226 TCTCTCTCTCTCTCCGGCTC 59.532 60.000 0.00 0.00 0.00 4.70
967 8635 2.565841 GTGCCTCTCTCTCTCTCTCTC 58.434 57.143 0.00 0.00 0.00 3.20
1317 8992 1.233019 GAGCATGTGGATGAATCGGG 58.767 55.000 0.00 0.00 0.00 5.14
1334 9009 1.351430 TTTGATCAGTTCGCGCGGAG 61.351 55.000 31.69 16.96 0.00 4.63
1347 9022 8.962500 CAATGGATTGGCCGATCGATTTGATC 62.962 46.154 30.66 14.98 40.72 2.92
1348 9023 2.154462 GGATTGGCCGATCGATTTGAT 58.846 47.619 24.09 3.69 41.06 2.57
1351 9026 2.276732 ATGGATTGGCCGATCGATTT 57.723 45.000 24.09 6.12 40.66 2.17
1385 9382 1.671054 CCTGCGGAAATCACACGGT 60.671 57.895 0.00 0.00 0.00 4.83
1501 9504 4.214119 GTCGTGTGTTCTGTAGTGTAGGTA 59.786 45.833 0.00 0.00 0.00 3.08
1511 9514 2.961526 AGTCAAGTCGTGTGTTCTGT 57.038 45.000 0.00 0.00 0.00 3.41
1549 9552 8.178964 CGTAAACAATCATTTTCTTATTCCGGA 58.821 33.333 0.00 0.00 0.00 5.14
1573 9576 9.528018 AATCATTATTGAAGTTTGAACAAACGT 57.472 25.926 19.83 17.90 43.14 3.99
1613 9619 1.841556 ACGCAGAAGGGAGTGGGAA 60.842 57.895 0.00 0.00 0.00 3.97
1678 9684 4.614993 CGGTGGTGAGTTAATTCGCATTTT 60.615 41.667 12.82 0.00 0.00 1.82
1708 9714 0.040425 GTTTCCCACATGTGACGTGC 60.040 55.000 27.46 10.22 32.85 5.34
1718 9724 2.938838 ACAAATTCGAGGTTTCCCACA 58.061 42.857 0.00 0.00 0.00 4.17
1720 9726 4.577834 GAAACAAATTCGAGGTTTCCCA 57.422 40.909 16.59 0.00 42.69 4.37
1889 9896 6.754193 AGACTTGGAGCTTAATATCAGTAGC 58.246 40.000 0.00 0.00 0.00 3.58
1899 9906 3.244561 CCAGTTGGAGACTTGGAGCTTAA 60.245 47.826 0.00 0.00 36.10 1.85
1980 10020 0.532862 AGGGCAGTGTGTTCTTGTCG 60.533 55.000 0.00 0.00 0.00 4.35
2070 10112 1.069765 CGGATAATGCACGGAGGCT 59.930 57.895 0.00 0.00 34.04 4.58
2172 10214 1.202770 CGTTTCAGACTTGGAACCCCT 60.203 52.381 0.00 0.00 39.27 4.79
2300 10348 3.365666 GGCACGTAACTAAAAGGCCTTTC 60.366 47.826 30.49 15.81 37.00 2.62
2301 10349 2.555325 GGCACGTAACTAAAAGGCCTTT 59.445 45.455 25.47 25.47 37.00 3.11
2331 10379 1.734477 CACCACGAACCTGCGAGAG 60.734 63.158 0.00 0.00 34.83 3.20
2405 10459 9.327529 CGGAAACAAGATAAGATACTACGTATC 57.672 37.037 0.00 6.00 43.52 2.24
2406 10460 8.295288 CCGGAAACAAGATAAGATACTACGTAT 58.705 37.037 0.00 0.00 0.00 3.06
2416 10546 8.899771 GGAAAATTATCCGGAAACAAGATAAGA 58.100 33.333 9.01 0.00 38.13 2.10
2525 10656 4.705337 AGTCACCTTGATAGAACTCGTC 57.295 45.455 0.00 0.00 0.00 4.20
2680 10822 0.393402 TGATCATGTGGGCAGCTCAC 60.393 55.000 19.44 19.44 35.82 3.51
2779 10921 6.945636 TTTAGAGGGAACTGATTTGACCTA 57.054 37.500 0.00 0.00 44.43 3.08
2801 10943 8.853077 TCAGACAAACATGATTCAGAGTTATT 57.147 30.769 0.00 0.06 0.00 1.40
2811 10953 7.173218 ACGTCTTGTATTCAGACAAACATGATT 59.827 33.333 0.00 0.00 38.80 2.57
2813 10955 5.989168 ACGTCTTGTATTCAGACAAACATGA 59.011 36.000 0.00 0.00 38.80 3.07
2816 10958 5.113383 ACACGTCTTGTATTCAGACAAACA 58.887 37.500 1.29 0.00 38.80 2.83
2817 10959 5.652744 ACACGTCTTGTATTCAGACAAAC 57.347 39.130 1.29 0.00 38.80 2.93
2818 10960 6.671614 AAACACGTCTTGTATTCAGACAAA 57.328 33.333 1.29 0.00 38.80 2.83
2819 10961 6.314152 TCAAAACACGTCTTGTATTCAGACAA 59.686 34.615 1.29 0.00 37.51 3.18
2821 10963 6.127403 GTCAAAACACGTCTTGTATTCAGAC 58.873 40.000 0.00 0.00 37.51 3.51
2822 10964 5.235616 GGTCAAAACACGTCTTGTATTCAGA 59.764 40.000 0.00 0.00 37.51 3.27
2823 10965 5.236478 AGGTCAAAACACGTCTTGTATTCAG 59.764 40.000 0.00 0.00 37.51 3.02
2826 10968 5.120399 TCAGGTCAAAACACGTCTTGTATT 58.880 37.500 0.00 0.00 37.51 1.89
2828 10970 4.126208 TCAGGTCAAAACACGTCTTGTA 57.874 40.909 0.00 0.00 37.51 2.41
2829 10971 2.980568 TCAGGTCAAAACACGTCTTGT 58.019 42.857 0.00 0.00 41.74 3.16
2831 11013 2.878406 CCATCAGGTCAAAACACGTCTT 59.122 45.455 0.00 0.00 0.00 3.01
2847 11029 6.778069 TGTATGTAAACCAAAGAAACCCATCA 59.222 34.615 0.00 0.00 0.00 3.07
2849 11031 7.507616 TCTTGTATGTAAACCAAAGAAACCCAT 59.492 33.333 0.00 0.00 0.00 4.00
2850 11032 6.834451 TCTTGTATGTAAACCAAAGAAACCCA 59.166 34.615 0.00 0.00 0.00 4.51
2865 11047 8.951787 ACCACGCTTTTATAATCTTGTATGTA 57.048 30.769 0.00 0.00 0.00 2.29
2901 11083 3.994392 TGGCATCTCAAGTCTACGTTTTC 59.006 43.478 0.00 0.00 0.00 2.29
2983 11232 5.365403 TGCAACCGGATAACTTTTACAAG 57.635 39.130 9.46 0.00 35.92 3.16
2985 11234 5.004448 TGATGCAACCGGATAACTTTTACA 58.996 37.500 9.46 0.00 0.00 2.41
3233 11484 6.015434 ACGGCCATTATCCCTAATGAATTTTC 60.015 38.462 2.24 0.00 44.70 2.29
3255 11506 0.526954 CGGATGGAAGGACGTTACGG 60.527 60.000 10.20 0.00 0.00 4.02
3261 11512 0.603569 CCCTATCGGATGGAAGGACG 59.396 60.000 6.83 0.00 0.00 4.79
3284 11535 7.419057 TTGTTGTTACAGAAGAGGATCTCAAGT 60.419 37.037 0.00 0.00 39.38 3.16
3285 11536 6.931281 TTGTTGTTACAGAAGAGGATCTCAAG 59.069 38.462 0.00 0.00 39.38 3.02
3298 11549 7.390162 TGATCATAACAGCATTGTTGTTACAGA 59.610 33.333 23.01 22.11 46.63 3.41
3493 11753 7.134815 CACACACTTCTTTGGTTCTGATTAAG 58.865 38.462 0.00 0.00 0.00 1.85
3528 11788 9.295825 ACTCTCTATACTATGATTGGTCAAGAG 57.704 37.037 0.00 0.00 38.01 2.85
3596 11856 6.251376 CACTTAAATGGAAGCGCAATTTAGTC 59.749 38.462 11.47 0.00 29.93 2.59
3607 11867 7.486232 GCTATTTCAGAACACTTAAATGGAAGC 59.514 37.037 0.00 0.00 0.00 3.86
3657 11917 8.152898 TCTCTCCTTATTTGTATCATCCACATG 58.847 37.037 0.00 0.00 0.00 3.21
3694 11954 9.956720 CCTCCTACATTCATATTTTTCAATGTC 57.043 33.333 0.00 0.00 39.58 3.06
3695 11955 9.479549 ACCTCCTACATTCATATTTTTCAATGT 57.520 29.630 0.00 0.00 41.33 2.71
3700 11960 9.495572 CCTCTACCTCCTACATTCATATTTTTC 57.504 37.037 0.00 0.00 0.00 2.29
3803 12069 0.905357 ACAGGGATCAGGAAAGGACG 59.095 55.000 0.00 0.00 0.00 4.79
3854 12120 2.795329 CTACACATGGCTCCTTGGTTT 58.205 47.619 0.00 0.00 0.00 3.27
3875 12141 4.237724 TGAACTAGATTCGAAGTGCACAG 58.762 43.478 21.04 10.11 40.56 3.66
4046 12348 2.363683 GCTTCTAGCAGGTGAGCAAAT 58.636 47.619 0.00 0.00 41.89 2.32
4100 12402 3.731652 TGCTCAACAGAACCAATTTGG 57.268 42.857 14.02 14.02 45.02 3.28
4147 12449 6.417327 GCAGAAATCAACGATAAGATGACTG 58.583 40.000 0.00 0.00 34.40 3.51
4237 12542 4.511454 TGGCATGTAAAACTATCGCATCTC 59.489 41.667 0.00 0.00 0.00 2.75
4239 12544 4.811555 TGGCATGTAAAACTATCGCATC 57.188 40.909 0.00 0.00 0.00 3.91
4274 12590 6.519761 CGATAACTGCAAACATAACAGTGAAC 59.480 38.462 0.00 0.00 43.63 3.18
4303 12619 1.153597 CGCGCTCTAATCATGTGCCA 61.154 55.000 5.56 0.00 34.16 4.92
4828 13151 2.992689 TAGAACCAGGCGCCGACA 60.993 61.111 23.20 0.00 0.00 4.35
4969 13292 2.035155 TTCTCCCGCCAGTCGAGA 59.965 61.111 0.00 0.00 41.67 4.04
5021 13344 3.294493 TTCCAACAAGCCGCCTGC 61.294 61.111 0.00 0.00 41.71 4.85
5022 13345 1.455383 AAGTTCCAACAAGCCGCCTG 61.455 55.000 0.00 0.00 0.00 4.85
5023 13346 1.152756 AAGTTCCAACAAGCCGCCT 60.153 52.632 0.00 0.00 0.00 5.52
5060 13383 3.940852 CCAATGATTCTCGAATGACACCA 59.059 43.478 0.00 0.00 0.00 4.17
5180 14105 4.692625 GGCGCAATCTCATCAACTGTATAT 59.307 41.667 10.83 0.00 0.00 0.86
5181 14106 4.058124 GGCGCAATCTCATCAACTGTATA 58.942 43.478 10.83 0.00 0.00 1.47
5502 15973 1.064208 CGTGGGAGACAGACTACGATG 59.936 57.143 0.00 0.00 33.78 3.84
5856 16332 2.195567 GGCAAGCTCACCAACTGCA 61.196 57.895 6.63 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.