Multiple sequence alignment - TraesCS4A01G486500

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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 TraesCS4A01G486500 chr4A 100.000 5750 0 0 1 5750 739604599 739610348 0.000000e+00 10619.0
1 TraesCS4A01G486500 chr4A 95.713 2729 107 5 1206 3930 740150804 740148082 0.000000e+00 4383.0
2 TraesCS4A01G486500 chr4A 85.272 4040 457 91 1459 5422 740494226 740498203 0.000000e+00 4037.0
3 TraesCS4A01G486500 chr4A 85.047 3638 465 54 945 4549 742161143 742157552 0.000000e+00 3631.0
4 TraesCS4A01G486500 chr4A 85.130 2300 276 37 2108 4389 740122925 740120674 0.000000e+00 2292.0
5 TraesCS4A01G486500 chr4A 86.735 2043 233 23 2340 4370 742021130 742023146 0.000000e+00 2237.0
6 TraesCS4A01G486500 chr4A 86.798 1977 236 15 2482 4441 739886473 739888441 0.000000e+00 2182.0
7 TraesCS4A01G486500 chr4A 80.442 2899 448 79 2271 5103 733805926 733808771 0.000000e+00 2102.0
8 TraesCS4A01G486500 chr4A 83.100 2142 315 32 2364 4486 741421972 741424085 0.000000e+00 1906.0
9 TraesCS4A01G486500 chr4A 98.749 879 11 0 3930 4808 740135863 740134985 0.000000e+00 1563.0
10 TraesCS4A01G486500 chr4A 82.193 1842 230 60 522 2300 742019322 742021128 0.000000e+00 1495.0
11 TraesCS4A01G486500 chr4A 86.142 1335 145 18 416 1741 739982850 739981547 0.000000e+00 1404.0
12 TraesCS4A01G486500 chr4A 83.896 1422 181 26 3181 4562 741505836 741504423 0.000000e+00 1314.0
13 TraesCS4A01G486500 chr4A 83.905 1342 189 21 3061 4389 741805100 741806427 0.000000e+00 1256.0
14 TraesCS4A01G486500 chr4A 87.805 984 67 33 4794 5750 740134415 740133458 0.000000e+00 1103.0
15 TraesCS4A01G486500 chr4A 84.395 1115 129 19 951 2024 740124073 740122963 0.000000e+00 1053.0
16 TraesCS4A01G486500 chr4A 91.821 758 51 10 4669 5422 742023261 742024011 0.000000e+00 1046.0
17 TraesCS4A01G486500 chr4A 86.136 779 75 21 4642 5417 733984268 733983520 0.000000e+00 809.0
18 TraesCS4A01G486500 chr4A 85.601 757 79 25 4669 5410 733822151 733822892 0.000000e+00 767.0
19 TraesCS4A01G486500 chr4A 90.959 365 19 3 1 358 739983340 739982983 4.030000e-131 479.0
20 TraesCS4A01G486500 chr4A 91.667 336 19 3 49 384 740493824 740494150 1.890000e-124 457.0
21 TraesCS4A01G486500 chr4A 92.880 309 21 1 5442 5750 740498256 740498563 1.140000e-121 448.0
22 TraesCS4A01G486500 chr4A 90.764 314 27 2 5437 5750 742024070 742024381 8.910000e-113 418.0
23 TraesCS4A01G486500 chr4A 89.490 314 31 2 5437 5750 733809047 733809358 4.180000e-106 396.0
24 TraesCS4A01G486500 chr4A 88.959 317 34 1 5435 5750 740119431 740119115 1.940000e-104 390.0
25 TraesCS4A01G486500 chr4A 87.702 309 35 3 5444 5750 739758433 739758126 1.970000e-94 357.0
26 TraesCS4A01G486500 chr4A 88.327 257 23 2 102 358 741362205 741361956 9.360000e-78 302.0
27 TraesCS4A01G486500 chr4A 94.611 167 9 0 218 384 740492593 740492759 5.720000e-65 259.0
28 TraesCS4A01G486500 chr4A 90.816 196 11 2 25 219 740151983 740151794 7.390000e-64 255.0
29 TraesCS4A01G486500 chr4A 88.194 144 13 3 241 384 742161864 742161725 9.910000e-38 169.0
30 TraesCS4A01G486500 chr4A 74.561 342 71 13 1891 2225 733800036 733800368 1.000000e-27 135.0
31 TraesCS4A01G486500 chr4A 86.139 101 11 2 4590 4690 733821953 733822050 7.880000e-19 106.0
32 TraesCS4A01G486500 chr4A 87.059 85 11 0 687 771 739605221 739605305 4.740000e-16 97.1
33 TraesCS4A01G486500 chr4A 87.059 85 11 0 623 707 739605285 739605369 4.740000e-16 97.1
34 TraesCS4A01G486500 chr4A 86.022 93 6 4 132 224 740490763 740490848 6.130000e-15 93.5
35 TraesCS4A01G486500 chr4A 91.525 59 5 0 113 171 742161945 742161887 1.330000e-11 82.4
36 TraesCS4A01G486500 chr7A 87.175 3657 358 64 959 4550 3844195 3840585 0.000000e+00 4052.0
37 TraesCS4A01G486500 chr7A 84.736 2162 275 34 2306 4444 3154751 3152622 0.000000e+00 2113.0
38 TraesCS4A01G486500 chr7A 84.315 2021 289 18 2390 4392 2800542 2798532 0.000000e+00 1951.0
39 TraesCS4A01G486500 chr7A 93.846 650 39 1 950 1598 3807722 3807073 0.000000e+00 977.0
40 TraesCS4A01G486500 chr7A 82.969 1098 131 34 4647 5713 3802048 3800976 0.000000e+00 941.0
41 TraesCS4A01G486500 chr7A 81.031 1028 170 14 982 1986 2805903 2804878 0.000000e+00 795.0
42 TraesCS4A01G486500 chr7A 86.345 747 67 21 4683 5419 3840309 3839588 0.000000e+00 782.0
43 TraesCS4A01G486500 chr7A 90.997 311 25 3 5442 5750 3839520 3839211 3.200000e-112 416.0
44 TraesCS4A01G486500 chr7A 88.924 316 30 5 5435 5750 2125812 2125502 9.040000e-103 385.0
45 TraesCS4A01G486500 chr7A 81.282 390 52 14 525 909 3808399 3808026 4.360000e-76 296.0
46 TraesCS4A01G486500 chr7D 82.168 3505 521 71 982 4443 3552637 3549194 0.000000e+00 2915.0
47 TraesCS4A01G486500 chr7D 81.691 3512 533 74 980 4444 2904911 2901463 0.000000e+00 2822.0
48 TraesCS4A01G486500 chr7D 86.004 2715 279 55 1891 4562 4009771 4007115 0.000000e+00 2815.0
49 TraesCS4A01G486500 chr7D 87.176 1544 182 12 2356 3887 3423787 3422248 0.000000e+00 1740.0
50 TraesCS4A01G486500 chr7D 92.135 890 67 3 977 1864 4010596 4009708 0.000000e+00 1253.0
51 TraesCS4A01G486500 chr7D 87.995 758 67 15 4669 5419 4006760 4006020 0.000000e+00 874.0
52 TraesCS4A01G486500 chr7D 90.157 508 41 7 4915 5419 2508443 2507942 0.000000e+00 652.0
53 TraesCS4A01G486500 chr7D 85.921 483 53 10 4642 5121 2678646 2678176 8.600000e-138 501.0
54 TraesCS4A01G486500 chr7D 90.615 309 27 1 5442 5750 2676389 2676083 5.360000e-110 409.0
55 TraesCS4A01G486500 chr7D 87.500 312 35 4 5441 5750 3420592 3420283 1.970000e-94 357.0
56 TraesCS4A01G486500 chr3B 77.344 384 62 18 4508 4882 281971565 281971198 2.720000e-48 204.0


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 TraesCS4A01G486500 chr4A 739604599 739610348 5749 False 10619.000000 10619 100.000000 1 5750 1 chr4A.!!$F2 5749
1 TraesCS4A01G486500 chr4A 740148082 740151983 3901 True 2319.000000 4383 93.264500 25 3930 2 chr4A.!!$R8 3905
2 TraesCS4A01G486500 chr4A 739886473 739888441 1968 False 2182.000000 2182 86.798000 2482 4441 1 chr4A.!!$F3 1959
3 TraesCS4A01G486500 chr4A 741421972 741424085 2113 False 1906.000000 1906 83.100000 2364 4486 1 chr4A.!!$F4 2122
4 TraesCS4A01G486500 chr4A 740133458 740135863 2405 True 1333.000000 1563 93.277000 3930 5750 2 chr4A.!!$R7 1820
5 TraesCS4A01G486500 chr4A 741504423 741505836 1413 True 1314.000000 1314 83.896000 3181 4562 1 chr4A.!!$R4 1381
6 TraesCS4A01G486500 chr4A 742019322 742024381 5059 False 1299.000000 2237 87.878250 522 5750 4 chr4A.!!$F10 5228
7 TraesCS4A01G486500 chr4A 742157552 742161945 4393 True 1294.133333 3631 88.255333 113 4549 3 chr4A.!!$R9 4436
8 TraesCS4A01G486500 chr4A 741805100 741806427 1327 False 1256.000000 1256 83.905000 3061 4389 1 chr4A.!!$F5 1328
9 TraesCS4A01G486500 chr4A 733805926 733809358 3432 False 1249.000000 2102 84.966000 2271 5750 2 chr4A.!!$F6 3479
10 TraesCS4A01G486500 chr4A 740119115 740124073 4958 True 1245.000000 2292 86.161333 951 5750 3 chr4A.!!$R6 4799
11 TraesCS4A01G486500 chr4A 740490763 740498563 7800 False 1058.900000 4037 90.090400 49 5750 5 chr4A.!!$F9 5701
12 TraesCS4A01G486500 chr4A 739981547 739983340 1793 True 941.500000 1404 88.550500 1 1741 2 chr4A.!!$R5 1740
13 TraesCS4A01G486500 chr4A 733983520 733984268 748 True 809.000000 809 86.136000 4642 5417 1 chr4A.!!$R1 775
14 TraesCS4A01G486500 chr4A 733821953 733822892 939 False 436.500000 767 85.870000 4590 5410 2 chr4A.!!$F7 820
15 TraesCS4A01G486500 chr7A 3152622 3154751 2129 True 2113.000000 2113 84.736000 2306 4444 1 chr7A.!!$R4 2138
16 TraesCS4A01G486500 chr7A 2798532 2800542 2010 True 1951.000000 1951 84.315000 2390 4392 1 chr7A.!!$R2 2002
17 TraesCS4A01G486500 chr7A 3839211 3844195 4984 True 1750.000000 4052 88.172333 959 5750 3 chr7A.!!$R7 4791
18 TraesCS4A01G486500 chr7A 3800976 3802048 1072 True 941.000000 941 82.969000 4647 5713 1 chr7A.!!$R5 1066
19 TraesCS4A01G486500 chr7A 2804878 2805903 1025 True 795.000000 795 81.031000 982 1986 1 chr7A.!!$R3 1004
20 TraesCS4A01G486500 chr7A 3807073 3808399 1326 True 636.500000 977 87.564000 525 1598 2 chr7A.!!$R6 1073
21 TraesCS4A01G486500 chr7D 3549194 3552637 3443 True 2915.000000 2915 82.168000 982 4443 1 chr7D.!!$R3 3461
22 TraesCS4A01G486500 chr7D 2901463 2904911 3448 True 2822.000000 2822 81.691000 980 4444 1 chr7D.!!$R2 3464
23 TraesCS4A01G486500 chr7D 4006020 4010596 4576 True 1647.333333 2815 88.711333 977 5419 3 chr7D.!!$R6 4442
24 TraesCS4A01G486500 chr7D 3420283 3423787 3504 True 1048.500000 1740 87.338000 2356 5750 2 chr7D.!!$R5 3394
25 TraesCS4A01G486500 chr7D 2507942 2508443 501 True 652.000000 652 90.157000 4915 5419 1 chr7D.!!$R1 504
26 TraesCS4A01G486500 chr7D 2676083 2678646 2563 True 455.000000 501 88.268000 4642 5750 2 chr7D.!!$R4 1108

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
66 74 0.462789 ATGCAGCTAAAAGGGCATGC 59.537 50.0 9.90 9.90 44.64 4.06 F
76 84 0.548510 AAGGGCATGCTTACCTCTCC 59.451 55.0 18.92 7.47 32.29 3.71 F
79 87 0.833287 GGCATGCTTACCTCTCCAGA 59.167 55.0 18.92 0.00 0.00 3.86 F
84 92 0.833287 GCTTACCTCTCCAGATGGCA 59.167 55.0 0.00 0.00 34.44 4.92 F
1008 4474 0.904865 TGAGAGCGACCATGGACCTT 60.905 55.0 21.47 1.26 0.00 3.50 F
2164 5893 0.248539 GGGACTTCCGTCGAATCTCG 60.249 60.0 0.00 0.00 41.16 4.04 F
2337 6070 0.333312 TCTCTCCTGGACTCCTCCAC 59.667 60.0 0.00 0.00 42.15 4.02 F
2800 6554 1.024579 TAGCTAGTTTGCTTGGCGGC 61.025 55.0 0.00 0.00 43.74 6.53 F
3140 6894 1.282817 CATGGAAATGCATGTTGGCG 58.717 50.0 0.00 0.00 36.28 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 4526 1.337260 CGTCTGCAGCTTGTACTCCTT 60.337 52.381 9.47 0.00 0.00 3.36 R
2030 5741 3.736252 GTGATGATAGGACATCGAAACCG 59.264 47.826 0.00 0.00 46.49 4.44 R
2074 5785 3.748568 TCATGCGCAAACAAGTACACATA 59.251 39.130 17.11 0.00 0.00 2.29 R
2104 5819 6.163135 AGAGGGTAGAAAATCTTGATACGG 57.837 41.667 0.00 0.00 0.00 4.02 R
3019 6773 0.042881 GTCCTACCCCTGGTTCCTCT 59.957 60.000 0.00 0.00 37.09 3.69 R
3381 7135 2.548057 TCCAAAGCTAGAACACGCAAAG 59.452 45.455 0.00 0.00 0.00 2.77 R
3694 7451 3.363378 GCTCTGTCACAAAGTTGTCATCG 60.363 47.826 0.00 0.00 39.91 3.84 R
4645 8796 0.999406 GTATCGTGCACGCAGATTGT 59.001 50.000 33.63 14.69 39.60 2.71 R
5103 10096 4.802039 TCTGAGTGAACAACGAAGTAACAC 59.198 41.667 0.00 2.17 45.00 3.32 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
43 51 9.476202 TTTCGTGATATATAGATGAACCTTGTG 57.524 33.333 0.00 0.00 0.00 3.33
47 55 9.764363 GTGATATATAGATGAACCTTGTGTCAA 57.236 33.333 0.00 0.00 0.00 3.18
51 59 3.489355 AGATGAACCTTGTGTCAATGCA 58.511 40.909 0.00 0.00 0.00 3.96
56 64 2.862541 ACCTTGTGTCAATGCAGCTAA 58.137 42.857 0.00 0.00 0.00 3.09
57 65 3.221771 ACCTTGTGTCAATGCAGCTAAA 58.778 40.909 0.00 0.00 0.00 1.85
58 66 3.636300 ACCTTGTGTCAATGCAGCTAAAA 59.364 39.130 0.00 0.00 0.00 1.52
59 67 4.232221 CCTTGTGTCAATGCAGCTAAAAG 58.768 43.478 0.00 0.00 0.00 2.27
61 69 2.557924 TGTGTCAATGCAGCTAAAAGGG 59.442 45.455 0.00 0.00 0.00 3.95
66 74 0.462789 ATGCAGCTAAAAGGGCATGC 59.537 50.000 9.90 9.90 44.64 4.06
67 75 0.612732 TGCAGCTAAAAGGGCATGCT 60.613 50.000 18.92 0.00 36.02 3.79
69 77 1.750778 GCAGCTAAAAGGGCATGCTTA 59.249 47.619 18.92 7.29 34.01 3.09
71 79 2.099756 CAGCTAAAAGGGCATGCTTACC 59.900 50.000 18.92 10.66 0.00 2.85
73 81 2.359214 GCTAAAAGGGCATGCTTACCTC 59.641 50.000 18.92 0.00 32.29 3.85
74 82 2.907458 AAAAGGGCATGCTTACCTCT 57.093 45.000 18.92 0.00 32.29 3.69
75 83 2.426842 AAAGGGCATGCTTACCTCTC 57.573 50.000 18.92 0.00 32.29 3.20
76 84 0.548510 AAGGGCATGCTTACCTCTCC 59.451 55.000 18.92 7.47 32.29 3.71
79 87 0.833287 GGCATGCTTACCTCTCCAGA 59.167 55.000 18.92 0.00 0.00 3.86
80 88 1.419387 GGCATGCTTACCTCTCCAGAT 59.581 52.381 18.92 0.00 0.00 2.90
81 89 2.492012 GCATGCTTACCTCTCCAGATG 58.508 52.381 11.37 0.00 0.00 2.90
82 90 2.809665 GCATGCTTACCTCTCCAGATGG 60.810 54.545 11.37 0.00 0.00 3.51
83 91 0.833287 TGCTTACCTCTCCAGATGGC 59.167 55.000 0.00 0.00 34.44 4.40
84 92 0.833287 GCTTACCTCTCCAGATGGCA 59.167 55.000 0.00 0.00 34.44 4.92
88 96 1.588239 ACCTCTCCAGATGGCATGAA 58.412 50.000 3.81 0.00 34.44 2.57
90 98 2.512896 ACCTCTCCAGATGGCATGAATT 59.487 45.455 3.81 0.00 34.44 2.17
91 99 3.718434 ACCTCTCCAGATGGCATGAATTA 59.282 43.478 3.81 0.00 34.44 1.40
99 107 8.741603 TCCAGATGGCATGAATTACATATATG 57.258 34.615 3.81 11.29 37.07 1.78
101 109 7.776500 CCAGATGGCATGAATTACATATATGGA 59.224 37.037 16.96 5.50 36.62 3.41
102 110 9.181061 CAGATGGCATGAATTACATATATGGAA 57.819 33.333 12.82 12.82 37.46 3.53
103 111 9.182214 AGATGGCATGAATTACATATATGGAAC 57.818 33.333 12.71 2.17 37.46 3.62
104 112 8.882557 ATGGCATGAATTACATATATGGAACA 57.117 30.769 12.71 7.86 39.53 3.18
106 114 8.162746 TGGCATGAATTACATATATGGAACAGA 58.837 33.333 12.71 0.15 38.81 3.41
107 115 8.671921 GGCATGAATTACATATATGGAACAGAG 58.328 37.037 12.71 6.00 38.81 3.35
108 116 9.224267 GCATGAATTACATATATGGAACAGAGT 57.776 33.333 12.71 0.00 38.81 3.24
173 3217 3.077907 CTTCGCTTCCCCTTCCCA 58.922 61.111 0.00 0.00 0.00 4.37
263 3307 2.310309 TGCGTCTCAACTTGCACAG 58.690 52.632 0.00 0.00 31.31 3.66
396 3534 6.237901 TGGTTTATTTGTATGCTGAGTGAGT 58.762 36.000 0.00 0.00 0.00 3.41
397 3535 7.390823 TGGTTTATTTGTATGCTGAGTGAGTA 58.609 34.615 0.00 0.00 0.00 2.59
400 3538 9.098355 GTTTATTTGTATGCTGAGTGAGTATGA 57.902 33.333 0.00 0.00 0.00 2.15
401 3539 8.877808 TTATTTGTATGCTGAGTGAGTATGAG 57.122 34.615 0.00 0.00 0.00 2.90
402 3540 6.530019 TTTGTATGCTGAGTGAGTATGAGA 57.470 37.500 0.00 0.00 0.00 3.27
403 3541 5.764487 TGTATGCTGAGTGAGTATGAGAG 57.236 43.478 0.00 0.00 0.00 3.20
404 3542 5.440610 TGTATGCTGAGTGAGTATGAGAGA 58.559 41.667 0.00 0.00 0.00 3.10
405 3543 6.067350 TGTATGCTGAGTGAGTATGAGAGAT 58.933 40.000 0.00 0.00 0.00 2.75
406 3544 5.710513 ATGCTGAGTGAGTATGAGAGATC 57.289 43.478 0.00 0.00 0.00 2.75
408 3546 4.952335 TGCTGAGTGAGTATGAGAGATCAA 59.048 41.667 0.00 0.00 0.00 2.57
409 3547 5.597594 TGCTGAGTGAGTATGAGAGATCAAT 59.402 40.000 0.00 0.00 0.00 2.57
410 3548 6.774656 TGCTGAGTGAGTATGAGAGATCAATA 59.225 38.462 0.00 0.00 0.00 1.90
411 3549 7.450944 TGCTGAGTGAGTATGAGAGATCAATAT 59.549 37.037 0.00 0.00 0.00 1.28
412 3550 7.756272 GCTGAGTGAGTATGAGAGATCAATATG 59.244 40.741 0.00 0.00 0.00 1.78
413 3551 7.600960 TGAGTGAGTATGAGAGATCAATATGC 58.399 38.462 0.00 0.00 0.00 3.14
414 3552 6.934056 AGTGAGTATGAGAGATCAATATGCC 58.066 40.000 0.00 0.00 0.00 4.40
520 3662 8.511604 AGAAATGTAATGGTAGTTCTTCCATG 57.488 34.615 10.80 0.00 42.73 3.66
545 3690 9.613428 TGCTCAGTATATATAAACATTATGGGC 57.387 33.333 0.00 0.00 0.00 5.36
610 3757 6.759497 AAGACAACCATTAAGCCTTGATAC 57.241 37.500 0.00 0.00 0.00 2.24
724 3874 1.725641 CATTTAGCACGGTCAGAGCA 58.274 50.000 0.00 0.00 38.98 4.26
778 3932 4.332543 CGTTGTACCATGTGCACTTGATAT 59.667 41.667 28.84 17.74 0.00 1.63
860 4051 9.950680 GACAAATTTCTTTGATCTGTAAAGACA 57.049 29.630 6.28 1.89 43.71 3.41
909 4100 2.671351 CGAGCGTGTGAGGACATAACTT 60.671 50.000 0.00 0.00 33.63 2.66
914 4105 3.194968 CGTGTGAGGACATAACTTACCCT 59.805 47.826 0.00 0.00 33.63 4.34
915 4106 4.504858 GTGTGAGGACATAACTTACCCTG 58.495 47.826 0.00 0.00 33.63 4.45
935 4131 4.885270 CCCACCCGCCAACACACA 62.885 66.667 0.00 0.00 0.00 3.72
939 4135 2.826287 CCCGCCAACACACACACA 60.826 61.111 0.00 0.00 0.00 3.72
941 4137 2.402572 CCGCCAACACACACACACA 61.403 57.895 0.00 0.00 0.00 3.72
942 4138 1.062365 CGCCAACACACACACACAG 59.938 57.895 0.00 0.00 0.00 3.66
1008 4474 0.904865 TGAGAGCGACCATGGACCTT 60.905 55.000 21.47 1.26 0.00 3.50
1627 5183 2.038557 GGAGGACTTGGCAAGACAACTA 59.961 50.000 32.50 0.00 0.00 2.24
1681 5237 4.502282 CGCAGTTTGATTGTTGTGCTTTTA 59.498 37.500 0.00 0.00 0.00 1.52
1741 5297 6.664816 TCTCAATGGCATACTCCTTGAAATTT 59.335 34.615 0.00 0.00 0.00 1.82
1752 5308 5.104569 ACTCCTTGAAATTTCTGGGCAAAAA 60.105 36.000 18.64 2.00 0.00 1.94
1915 5500 2.926200 CGAGAACAAGAGGTATGCACTG 59.074 50.000 0.00 0.00 0.00 3.66
1989 5698 5.334414 CGACCCTGAGAAGAAATGAGTTTTG 60.334 44.000 0.00 0.00 0.00 2.44
2072 5783 8.143193 TCATCACTCTTGTGTATTTTGCAAAAT 58.857 29.630 33.26 33.26 44.14 1.82
2073 5784 9.409312 CATCACTCTTGTGTATTTTGCAAAATA 57.591 29.630 31.38 31.38 44.14 1.40
2104 5819 5.331902 ACTTGTTTGCGCATGATAATGTAC 58.668 37.500 12.75 0.00 0.00 2.90
2105 5820 4.285807 TGTTTGCGCATGATAATGTACC 57.714 40.909 12.75 0.00 0.00 3.34
2114 5829 5.861787 CGCATGATAATGTACCGTATCAAGA 59.138 40.000 15.65 0.00 39.52 3.02
2124 5841 6.576185 TGTACCGTATCAAGATTTTCTACCC 58.424 40.000 0.00 0.00 0.00 3.69
2163 5892 0.815734 TGGGACTTCCGTCGAATCTC 59.184 55.000 0.00 0.00 41.16 2.75
2164 5893 0.248539 GGGACTTCCGTCGAATCTCG 60.249 60.000 0.00 0.00 41.16 4.04
2182 5912 7.148869 CGAATCTCGCCGTTGTTTCATATATTA 60.149 37.037 0.00 0.00 31.14 0.98
2300 6032 8.592529 TGGATGATGAAATGGAATTAAACTCA 57.407 30.769 0.00 0.00 33.67 3.41
2330 6062 2.917713 ACATGTCTCTCTCCTGGACT 57.082 50.000 0.00 0.00 0.00 3.85
2337 6070 0.333312 TCTCTCCTGGACTCCTCCAC 59.667 60.000 0.00 0.00 42.15 4.02
2641 6395 6.398918 CAGTGAAGTATACAAGCTACAACCT 58.601 40.000 5.50 0.00 0.00 3.50
2796 6550 5.824904 ATCACAATAGCTAGTTTGCTTGG 57.175 39.130 2.50 0.00 43.74 3.61
2800 6554 1.024579 TAGCTAGTTTGCTTGGCGGC 61.025 55.000 0.00 0.00 43.74 6.53
2857 6611 5.092968 TCAATTGGTTTTGGGGATGAAGAT 58.907 37.500 5.42 0.00 0.00 2.40
3140 6894 1.282817 CATGGAAATGCATGTTGGCG 58.717 50.000 0.00 0.00 36.28 5.69
3188 6942 4.814771 ACATGATGCTGGATATGATATGCG 59.185 41.667 0.00 0.00 0.00 4.73
3228 6982 8.403236 AGAAAAGTTTGTTACTGTATTGGACAC 58.597 33.333 0.00 0.00 37.12 3.67
3281 7035 3.551046 CGATCGTAGGCTAGCTGTTCAAT 60.551 47.826 15.72 1.85 0.00 2.57
3331 7085 5.348997 GTCTACATTACAAGCAAGGTCACTC 59.651 44.000 0.00 0.00 0.00 3.51
3694 7451 3.449377 AGCTAAGCCTAGGAGAAGTTGAC 59.551 47.826 14.75 0.00 0.00 3.18
3841 7607 5.609423 AGCAAGATCCAAGTCATAGACATC 58.391 41.667 0.00 0.00 34.60 3.06
3986 7788 4.104738 TCAATCCCTCACTTCTTCCAAACT 59.895 41.667 0.00 0.00 0.00 2.66
4006 7808 3.886505 ACTTGTCCCATTTAAAACTGCGA 59.113 39.130 0.00 0.00 0.00 5.10
4811 9116 6.515272 TTATCAGGAGGCTTTCATTTGTTC 57.485 37.500 0.00 0.00 0.00 3.18
5103 10096 5.357032 AGTTTGTTTTGAGGGTTGAGTAGTG 59.643 40.000 0.00 0.00 0.00 2.74
5108 10101 5.617528 TTTGAGGGTTGAGTAGTGTGTTA 57.382 39.130 0.00 0.00 0.00 2.41
5188 10181 4.966965 TTATTTGGTGTGTGTCGTTTGT 57.033 36.364 0.00 0.00 0.00 2.83
5189 10182 3.859411 ATTTGGTGTGTGTCGTTTGTT 57.141 38.095 0.00 0.00 0.00 2.83
5224 10217 3.068024 GTCTTGGTTTTGGAGATTGTGCA 59.932 43.478 0.00 0.00 0.00 4.57
5300 10351 3.322541 CGATGTGTATATGGGGGTGTGTA 59.677 47.826 0.00 0.00 0.00 2.90
5452 12196 1.731720 TTGCAACTGGTTTTTGGCAC 58.268 45.000 0.00 0.00 0.00 5.01
5476 12222 5.061721 TCCCTTTTTGCCTCTTAGAGTTT 57.938 39.130 8.55 0.00 0.00 2.66
5532 12280 3.803186 AGCTATATCCTGGCTGCAATT 57.197 42.857 0.50 0.00 40.69 2.32
5607 12357 9.884636 GTATCAGGTATGGCATGTTTATGTATA 57.115 33.333 10.98 0.00 36.65 1.47
5610 12360 8.825774 TCAGGTATGGCATGTTTATGTATAGAT 58.174 33.333 10.98 0.00 36.65 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.082242 TGACACAAGGTTCATCTATATATCACG 58.918 37.037 0.00 0.00 0.00 4.35
43 51 1.545582 TGCCCTTTTAGCTGCATTGAC 59.454 47.619 1.02 0.00 0.00 3.18
47 55 0.462789 GCATGCCCTTTTAGCTGCAT 59.537 50.000 6.36 0.00 44.79 3.96
51 59 2.024941 AGGTAAGCATGCCCTTTTAGCT 60.025 45.455 15.66 17.30 37.08 3.32
56 64 1.064389 GGAGAGGTAAGCATGCCCTTT 60.064 52.381 15.66 9.22 30.28 3.11
57 65 0.548510 GGAGAGGTAAGCATGCCCTT 59.451 55.000 15.66 5.67 30.28 3.95
58 66 0.621571 TGGAGAGGTAAGCATGCCCT 60.622 55.000 15.66 14.25 30.28 5.19
59 67 0.179034 CTGGAGAGGTAAGCATGCCC 60.179 60.000 15.66 8.89 30.28 5.36
61 69 2.492012 CATCTGGAGAGGTAAGCATGC 58.508 52.381 10.51 10.51 0.00 4.06
66 74 2.702478 TCATGCCATCTGGAGAGGTAAG 59.298 50.000 0.00 0.00 37.39 2.34
67 75 2.763039 TCATGCCATCTGGAGAGGTAA 58.237 47.619 0.00 0.00 37.39 2.85
69 77 1.588239 TTCATGCCATCTGGAGAGGT 58.412 50.000 0.00 0.00 37.39 3.85
71 79 4.711399 TGTAATTCATGCCATCTGGAGAG 58.289 43.478 0.00 0.00 37.39 3.20
73 81 8.837389 CATATATGTAATTCATGCCATCTGGAG 58.163 37.037 4.43 0.00 37.91 3.86
74 82 7.776500 CCATATATGTAATTCATGCCATCTGGA 59.224 37.037 11.73 0.00 37.91 3.86
75 83 7.776500 TCCATATATGTAATTCATGCCATCTGG 59.224 37.037 11.73 0.00 37.91 3.86
76 84 8.741603 TCCATATATGTAATTCATGCCATCTG 57.258 34.615 11.73 0.00 37.91 2.90
79 87 8.882557 TGTTCCATATATGTAATTCATGCCAT 57.117 30.769 11.73 0.00 37.91 4.40
80 88 8.162746 TCTGTTCCATATATGTAATTCATGCCA 58.837 33.333 11.73 0.00 37.91 4.92
81 89 8.565896 TCTGTTCCATATATGTAATTCATGCC 57.434 34.615 11.73 0.00 37.91 4.40
82 90 9.224267 ACTCTGTTCCATATATGTAATTCATGC 57.776 33.333 11.73 0.00 37.91 4.06
91 99 9.770097 CTGTTATTCACTCTGTTCCATATATGT 57.230 33.333 11.73 0.00 0.00 2.29
99 107 4.508662 CCTCCTGTTATTCACTCTGTTCC 58.491 47.826 0.00 0.00 0.00 3.62
101 109 3.307762 GCCCTCCTGTTATTCACTCTGTT 60.308 47.826 0.00 0.00 0.00 3.16
102 110 2.237392 GCCCTCCTGTTATTCACTCTGT 59.763 50.000 0.00 0.00 0.00 3.41
103 111 2.237143 TGCCCTCCTGTTATTCACTCTG 59.763 50.000 0.00 0.00 0.00 3.35
104 112 2.503356 CTGCCCTCCTGTTATTCACTCT 59.497 50.000 0.00 0.00 0.00 3.24
106 114 2.026822 CACTGCCCTCCTGTTATTCACT 60.027 50.000 0.00 0.00 0.00 3.41
107 115 2.359900 CACTGCCCTCCTGTTATTCAC 58.640 52.381 0.00 0.00 0.00 3.18
108 116 1.340017 GCACTGCCCTCCTGTTATTCA 60.340 52.381 0.00 0.00 0.00 2.57
109 117 1.383523 GCACTGCCCTCCTGTTATTC 58.616 55.000 0.00 0.00 0.00 1.75
110 118 0.034089 GGCACTGCCCTCCTGTTATT 60.034 55.000 9.13 0.00 44.06 1.40
111 119 1.609783 GGCACTGCCCTCCTGTTAT 59.390 57.895 9.13 0.00 44.06 1.89
112 120 3.077907 GGCACTGCCCTCCTGTTA 58.922 61.111 9.13 0.00 44.06 2.41
173 3217 1.169661 TTCACGGCACCGCTTTGAAT 61.170 50.000 9.43 0.00 44.19 2.57
246 3290 1.082496 GCTGTGCAAGTTGAGACGC 60.082 57.895 7.16 6.76 0.00 5.19
263 3307 6.237306 GCTAATGCGAATTAACAACAGAAAGC 60.237 38.462 0.00 0.00 0.00 3.51
280 3324 7.581011 TGTACATATATTGTGAGCTAATGCG 57.419 36.000 0.00 0.00 40.95 4.73
316 3360 4.021368 TGTTAGTTTTCTCCCTCTCGAAGG 60.021 45.833 6.66 6.66 45.77 3.46
350 3427 6.432783 ACCATTATTGCACTGCTTAACTACAA 59.567 34.615 1.98 0.00 0.00 2.41
392 3530 7.671398 TGTAGGCATATTGATCTCTCATACTCA 59.329 37.037 0.00 0.00 0.00 3.41
393 3531 8.060931 TGTAGGCATATTGATCTCTCATACTC 57.939 38.462 0.00 0.00 0.00 2.59
396 3534 8.835550 ATCTGTAGGCATATTGATCTCTCATA 57.164 34.615 0.00 0.00 0.00 2.15
397 3535 7.736881 ATCTGTAGGCATATTGATCTCTCAT 57.263 36.000 0.00 0.00 0.00 2.90
400 3538 9.282569 GAAAAATCTGTAGGCATATTGATCTCT 57.717 33.333 0.00 0.00 0.00 3.10
401 3539 9.282569 AGAAAAATCTGTAGGCATATTGATCTC 57.717 33.333 0.00 0.00 0.00 2.75
402 3540 9.638176 AAGAAAAATCTGTAGGCATATTGATCT 57.362 29.630 0.00 0.00 0.00 2.75
431 3569 9.929722 GTAGACATATTACAATCGAAATTGCAA 57.070 29.630 0.00 0.00 45.16 4.08
433 3571 9.586150 CTGTAGACATATTACAATCGAAATTGC 57.414 33.333 0.00 0.00 45.16 3.56
474 3612 7.985634 TTCTTTGCAAAATTCTCTTGTGTAC 57.014 32.000 13.84 0.00 0.00 2.90
477 3615 7.912383 ACATTTCTTTGCAAAATTCTCTTGTG 58.088 30.769 13.84 5.55 0.00 3.33
486 3627 9.777297 AACTACCATTACATTTCTTTGCAAAAT 57.223 25.926 13.84 0.87 0.00 1.82
520 3662 9.838339 AGCCCATAATGTTTATATATACTGAGC 57.162 33.333 5.15 0.00 0.00 4.26
610 3757 4.051237 ACTACGTGCATATATGTGCTGTG 58.949 43.478 22.85 15.12 45.27 3.66
720 3870 3.923461 GCTAATCGTGTGGATCTATGCTC 59.077 47.826 0.00 0.00 33.02 4.26
724 3874 5.509840 GGTTCAGCTAATCGTGTGGATCTAT 60.510 44.000 0.00 0.00 33.02 1.98
867 4058 8.853345 CGCTCGTTTTTATAGTGTTTCTAACTA 58.147 33.333 0.00 0.00 34.73 2.24
868 4059 7.383300 ACGCTCGTTTTTATAGTGTTTCTAACT 59.617 33.333 0.00 0.00 30.02 2.24
869 4060 7.473411 CACGCTCGTTTTTATAGTGTTTCTAAC 59.527 37.037 0.00 0.00 31.86 2.34
870 4061 7.169645 ACACGCTCGTTTTTATAGTGTTTCTAA 59.830 33.333 0.00 0.00 38.03 2.10
871 4062 6.642131 ACACGCTCGTTTTTATAGTGTTTCTA 59.358 34.615 0.00 0.00 38.03 2.10
872 4063 5.464389 ACACGCTCGTTTTTATAGTGTTTCT 59.536 36.000 0.00 0.00 38.03 2.52
873 4064 5.558888 CACACGCTCGTTTTTATAGTGTTTC 59.441 40.000 0.00 0.00 39.02 2.78
874 4065 5.234757 TCACACGCTCGTTTTTATAGTGTTT 59.765 36.000 0.00 0.00 39.02 2.83
875 4066 4.746115 TCACACGCTCGTTTTTATAGTGTT 59.254 37.500 0.00 0.00 39.02 3.32
876 4067 4.300803 TCACACGCTCGTTTTTATAGTGT 58.699 39.130 0.00 0.00 41.31 3.55
877 4068 4.201589 CCTCACACGCTCGTTTTTATAGTG 60.202 45.833 0.00 0.00 0.00 2.74
886 4077 0.885879 TATGTCCTCACACGCTCGTT 59.114 50.000 0.00 0.00 34.48 3.85
925 4121 0.098728 GTCTGTGTGTGTGTGTTGGC 59.901 55.000 0.00 0.00 0.00 4.52
928 4124 1.804151 GTGTGTCTGTGTGTGTGTGTT 59.196 47.619 0.00 0.00 0.00 3.32
935 4131 1.819928 TGCTTTGTGTGTCTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
939 4135 5.522456 CACAATAATGCTTTGTGTGTCTGT 58.478 37.500 16.50 1.93 45.60 3.41
1060 4526 1.337260 CGTCTGCAGCTTGTACTCCTT 60.337 52.381 9.47 0.00 0.00 3.36
1741 5297 4.112634 ACTCCAAGTATTTTTGCCCAGA 57.887 40.909 0.00 0.00 0.00 3.86
1752 5308 4.263905 TGCCTTTCATCCAACTCCAAGTAT 60.264 41.667 0.00 0.00 0.00 2.12
1989 5698 5.852827 TCAAACCAAATTTTCCACTCATCC 58.147 37.500 0.00 0.00 0.00 3.51
2030 5741 3.736252 GTGATGATAGGACATCGAAACCG 59.264 47.826 0.00 0.00 46.49 4.44
2072 5783 5.582665 TCATGCGCAAACAAGTACACATATA 59.417 36.000 17.11 0.00 0.00 0.86
2073 5784 4.394610 TCATGCGCAAACAAGTACACATAT 59.605 37.500 17.11 0.00 0.00 1.78
2074 5785 3.748568 TCATGCGCAAACAAGTACACATA 59.251 39.130 17.11 0.00 0.00 2.29
2104 5819 6.163135 AGAGGGTAGAAAATCTTGATACGG 57.837 41.667 0.00 0.00 0.00 4.02
2105 5820 9.032420 GTAAAGAGGGTAGAAAATCTTGATACG 57.968 37.037 0.00 0.00 32.50 3.06
2124 5841 6.486993 GTCCCAGCCCAAATTATAGTAAAGAG 59.513 42.308 0.00 0.00 0.00 2.85
2163 5892 9.350357 AGTACTATAATATATGAAACAACGGCG 57.650 33.333 4.80 4.80 0.00 6.46
2229 5961 9.625009 CAACATTTTCGAATCTAGATACTTTCG 57.375 33.333 16.51 16.51 41.60 3.46
2300 6032 1.753649 AGAGACATGTATGCACGAGCT 59.246 47.619 6.36 0.00 42.74 4.09
2330 6062 1.275291 GTTGAATCAGGACGTGGAGGA 59.725 52.381 0.00 0.00 0.00 3.71
2337 6070 3.058016 AGTTGCATTGTTGAATCAGGACG 60.058 43.478 0.00 0.00 0.00 4.79
2641 6395 9.759473 AAATCCTTGGATAAATCAAGAGAAAGA 57.241 29.630 2.20 0.00 42.94 2.52
2796 6550 4.043200 GCTCCACAGGTTTGCCGC 62.043 66.667 0.00 0.00 40.50 6.53
3019 6773 0.042881 GTCCTACCCCTGGTTCCTCT 59.957 60.000 0.00 0.00 37.09 3.69
3188 6942 8.926715 ACAAACTTTTCTTCCTTTGACAATAC 57.073 30.769 0.00 0.00 0.00 1.89
3228 6982 7.543947 TGTGAAGTTGTATATTGCTCATCAG 57.456 36.000 0.00 0.00 0.00 2.90
3281 7035 4.625805 GCTAGCCAGAGGTCGGACTATATA 60.626 50.000 2.29 0.00 0.00 0.86
3331 7085 7.709947 ACATCTCAATATTACACAAGGCAATG 58.290 34.615 0.00 0.00 0.00 2.82
3381 7135 2.548057 TCCAAAGCTAGAACACGCAAAG 59.452 45.455 0.00 0.00 0.00 2.77
3694 7451 3.363378 GCTCTGTCACAAAGTTGTCATCG 60.363 47.826 0.00 0.00 39.91 3.84
4598 8743 3.090952 TCGGCAATTCCTGTTGTTTTG 57.909 42.857 0.00 0.00 0.00 2.44
4603 8748 4.082787 ACAGTTAATCGGCAATTCCTGTTG 60.083 41.667 8.97 0.00 36.80 3.33
4645 8796 0.999406 GTATCGTGCACGCAGATTGT 59.001 50.000 33.63 14.69 39.60 2.71
4699 8993 7.709947 TCAGTAAATGTATACTTGGAGTACCG 58.290 38.462 4.17 0.00 34.93 4.02
4991 9969 7.266922 TCGTTTTCTTTACTACAAAAGGCAT 57.733 32.000 0.00 0.00 37.13 4.40
5095 10088 5.252969 ACAACGAAGTAACACACTACTCA 57.747 39.130 0.00 0.00 45.00 3.41
5103 10096 4.802039 TCTGAGTGAACAACGAAGTAACAC 59.198 41.667 0.00 2.17 45.00 3.32
5108 10101 5.642063 TCTTTTTCTGAGTGAACAACGAAGT 59.358 36.000 0.00 0.00 36.88 3.01
5188 10181 6.800072 AAACCAAGACCCAAGATACAAAAA 57.200 33.333 0.00 0.00 0.00 1.94
5189 10182 6.407525 CCAAAACCAAGACCCAAGATACAAAA 60.408 38.462 0.00 0.00 0.00 2.44
5224 10217 1.887242 AAGACACACACACGCGCAT 60.887 52.632 5.73 0.00 0.00 4.73
5300 10351 0.903454 CGGAGTTACACCCCCACTCT 60.903 60.000 0.00 0.00 37.64 3.24
5424 12153 4.399004 AAACCAGTTGCAAATGCTACAA 57.601 36.364 21.00 0.00 46.50 2.41
5452 12196 4.657013 ACTCTAAGAGGCAAAAAGGGAAG 58.343 43.478 0.00 0.00 33.35 3.46
5506 12253 0.397941 GCCAGGATATAGCTGCACCA 59.602 55.000 1.02 0.00 0.00 4.17
5532 12280 2.038659 TCATGTACGAGATGGGCATGA 58.961 47.619 0.00 0.00 42.17 3.07
5688 12443 2.770164 GCTCTTTCAGCCAGAGGTTA 57.230 50.000 0.00 0.00 43.17 2.85


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

AutoCloner maintained by Alex Coulton.