Multiple sequence alignment - TraesCS7D01G117000

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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 TraesCS7D01G117000 chr7D 100.000 5894 0 0 1 5894 72169415 72175308 0.000000e+00 10885.0
1 TraesCS7D01G117000 chr7D 85.980 2204 231 35 1 2148 71548575 71546394 0.000000e+00 2287.0
2 TraesCS7D01G117000 chr7D 84.087 2212 266 48 1 2149 71318818 71316630 0.000000e+00 2056.0
3 TraesCS7D01G117000 chr7D 87.846 1374 138 14 1 1351 71345146 71346513 0.000000e+00 1585.0
4 TraesCS7D01G117000 chr7D 86.277 1370 156 16 2 1351 71216001 71214644 0.000000e+00 1459.0
5 TraesCS7D01G117000 chr7D 82.952 962 132 16 2434 3368 71316513 71315557 0.000000e+00 839.0
6 TraesCS7D01G117000 chr7D 81.835 1057 137 25 1066 2100 71361796 71362819 0.000000e+00 837.0
7 TraesCS7D01G117000 chr7D 82.472 987 128 28 2433 3383 70751620 70752597 0.000000e+00 822.0
8 TraesCS7D01G117000 chr7D 87.260 730 77 7 2564 3277 71546055 71545326 0.000000e+00 819.0
9 TraesCS7D01G117000 chr7D 81.560 987 137 25 2433 3383 69938855 69937878 0.000000e+00 773.0
10 TraesCS7D01G117000 chr7D 83.666 851 105 16 2508 3325 71213702 71212853 0.000000e+00 771.0
11 TraesCS7D01G117000 chr7D 86.061 660 76 11 4309 4962 71349014 71349663 0.000000e+00 695.0
12 TraesCS7D01G117000 chr7D 86.589 604 67 9 4305 4905 71544800 71544208 0.000000e+00 654.0
13 TraesCS7D01G117000 chr7D 98.333 180 3 0 2277 2456 72171512 72171691 3.430000e-82 316.0
14 TraesCS7D01G117000 chr7D 98.333 180 3 0 2098 2277 72171691 72171870 3.430000e-82 316.0
15 TraesCS7D01G117000 chr7D 85.859 198 23 4 4739 4932 71313760 71313564 7.740000e-49 206.0
16 TraesCS7D01G117000 chr7B 95.830 3645 116 10 2277 5894 14998459 15002094 0.000000e+00 5856.0
17 TraesCS7D01G117000 chr7B 95.161 2294 89 6 1 2274 14996344 14998635 0.000000e+00 3602.0
18 TraesCS7D01G117000 chr7B 87.666 1427 146 13 1 1400 13116942 13115519 0.000000e+00 1633.0
19 TraesCS7D01G117000 chr7B 88.137 1374 135 13 1 1351 13879471 13878103 0.000000e+00 1609.0
20 TraesCS7D01G117000 chr7B 84.372 979 117 22 2432 3383 14065964 14064995 0.000000e+00 928.0
21 TraesCS7D01G117000 chr7B 81.818 979 130 29 2444 3383 12534414 12533445 0.000000e+00 778.0
22 TraesCS7D01G117000 chr7B 86.495 659 76 8 4309 4962 13873466 13872816 0.000000e+00 712.0
23 TraesCS7D01G117000 chr7B 85.822 663 77 12 4305 4964 14064372 14063724 0.000000e+00 688.0
24 TraesCS7D01G117000 chr7B 88.889 540 49 7 1386 1920 13115472 13114939 0.000000e+00 654.0
25 TraesCS7D01G117000 chr7B 77.645 501 75 21 4738 5213 13812926 13812438 2.710000e-68 270.0
26 TraesCS7D01G117000 chr7A 94.579 2066 88 9 1 2047 77159505 77161565 0.000000e+00 3173.0
27 TraesCS7D01G117000 chr7A 95.080 1809 55 10 3562 5343 77163053 77164854 0.000000e+00 2817.0
28 TraesCS7D01G117000 chr7A 96.546 1274 37 5 2303 3573 77161764 77163033 0.000000e+00 2102.0
29 TraesCS7D01G117000 chr7A 97.302 556 15 0 5339 5894 77166681 77167236 0.000000e+00 944.0
30 TraesCS7D01G117000 chr7A 83.784 962 105 27 2414 3339 76982539 76981593 0.000000e+00 865.0
31 TraesCS7D01G117000 chr7A 83.228 793 106 15 2525 3292 77024698 77023908 0.000000e+00 702.0
32 TraesCS7D01G117000 chr7A 95.455 154 4 1 2124 2277 77161764 77161914 5.900000e-60 243.0
33 TraesCS7D01G117000 chrUn 87.245 1866 173 22 4 1839 82528521 82526691 0.000000e+00 2067.0
34 TraesCS7D01G117000 chrUn 86.180 1932 224 24 1 1897 84435770 84437693 0.000000e+00 2049.0
35 TraesCS7D01G117000 chrUn 86.578 1870 184 23 1 1839 84248976 84247143 0.000000e+00 2001.0
36 TraesCS7D01G117000 chrUn 84.407 1956 243 29 1 1919 84238109 84236179 0.000000e+00 1866.0
37 TraesCS7D01G117000 chrUn 85.193 1371 154 19 2 1351 84286450 84285108 0.000000e+00 1362.0
38 TraesCS7D01G117000 chrUn 85.193 1371 154 19 2 1351 226939775 226938433 0.000000e+00 1362.0
39 TraesCS7D01G117000 chrUn 85.747 884 100 15 2414 3277 82526399 82525522 0.000000e+00 911.0
40 TraesCS7D01G117000 chrUn 85.248 888 103 15 2414 3277 84246851 84245968 0.000000e+00 889.0
41 TraesCS7D01G117000 chrUn 83.101 1006 128 23 2411 3378 82516097 82515096 0.000000e+00 878.0
42 TraesCS7D01G117000 chrUn 84.361 876 103 15 2482 3325 84284286 84283413 0.000000e+00 828.0
43 TraesCS7D01G117000 chrUn 84.361 876 103 15 2482 3325 226937611 226936738 0.000000e+00 828.0
44 TraesCS7D01G117000 chrUn 85.113 665 80 7 4308 4964 84245440 84244787 0.000000e+00 662.0
45 TraesCS7D01G117000 chrUn 85.327 627 63 20 4302 4924 82514516 82513915 6.490000e-174 621.0
46 TraesCS7D01G117000 chrUn 83.308 647 61 26 4304 4942 329448565 329449172 2.400000e-153 553.0
47 TraesCS7D01G117000 chrUn 88.416 423 44 3 4305 4725 82524997 82524578 6.820000e-139 505.0
48 TraesCS7D01G117000 chrUn 86.404 228 29 2 4738 4964 82524540 82524314 1.270000e-61 248.0
49 TraesCS7D01G117000 chr2B 88.145 1375 133 15 1 1351 723403399 723402031 0.000000e+00 1609.0
50 TraesCS7D01G117000 chr2B 83.089 1774 221 42 400 2137 723394705 723392975 0.000000e+00 1541.0
51 TraesCS7D01G117000 chr2B 86.441 649 78 7 4309 4954 723399400 723398759 0.000000e+00 702.0
52 TraesCS7D01G117000 chr2B 87.097 62 5 3 3417 3476 838178 838118 3.810000e-07 67.6
53 TraesCS7D01G117000 chr5B 81.143 175 23 6 3393 3563 166540405 166540573 1.330000e-26 132.0
54 TraesCS7D01G117000 chr6B 88.406 69 7 1 3416 3483 579212897 579212965 1.360000e-11 82.4
55 TraesCS7D01G117000 chr3D 89.394 66 4 2 3419 3481 604604725 604604660 4.900000e-11 80.5
56 TraesCS7D01G117000 chr2D 85.294 68 7 2 3422 3486 35638206 35638139 3.810000e-07 67.6
57 TraesCS7D01G117000 chr3B 91.667 48 3 1 3416 3462 716574277 716574324 1.370000e-06 65.8
58 TraesCS7D01G117000 chr3B 84.615 65 9 1 3439 3502 20096726 20096790 4.930000e-06 63.9
59 TraesCS7D01G117000 chr1A 96.774 31 1 0 5261 5291 394593071 394593101 1.100000e-02 52.8


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 TraesCS7D01G117000 chr7D 72169415 72175308 5893 False 3839.000000 10885 98.888667 1 5894 3 chr7D.!!$F4 5893
1 TraesCS7D01G117000 chr7D 71544208 71548575 4367 True 1253.333333 2287 86.609667 1 4905 3 chr7D.!!$R4 4904
2 TraesCS7D01G117000 chr7D 71345146 71349663 4517 False 1140.000000 1585 86.953500 1 4962 2 chr7D.!!$F3 4961
3 TraesCS7D01G117000 chr7D 71212853 71216001 3148 True 1115.000000 1459 84.971500 2 3325 2 chr7D.!!$R2 3323
4 TraesCS7D01G117000 chr7D 71313564 71318818 5254 True 1033.666667 2056 84.299333 1 4932 3 chr7D.!!$R3 4931
5 TraesCS7D01G117000 chr7D 71361796 71362819 1023 False 837.000000 837 81.835000 1066 2100 1 chr7D.!!$F2 1034
6 TraesCS7D01G117000 chr7D 70751620 70752597 977 False 822.000000 822 82.472000 2433 3383 1 chr7D.!!$F1 950
7 TraesCS7D01G117000 chr7D 69937878 69938855 977 True 773.000000 773 81.560000 2433 3383 1 chr7D.!!$R1 950
8 TraesCS7D01G117000 chr7B 14996344 15002094 5750 False 4729.000000 5856 95.495500 1 5894 2 chr7B.!!$F1 5893
9 TraesCS7D01G117000 chr7B 13878103 13879471 1368 True 1609.000000 1609 88.137000 1 1351 1 chr7B.!!$R4 1350
10 TraesCS7D01G117000 chr7B 13114939 13116942 2003 True 1143.500000 1633 88.277500 1 1920 2 chr7B.!!$R5 1919
11 TraesCS7D01G117000 chr7B 14063724 14065964 2240 True 808.000000 928 85.097000 2432 4964 2 chr7B.!!$R6 2532
12 TraesCS7D01G117000 chr7B 12533445 12534414 969 True 778.000000 778 81.818000 2444 3383 1 chr7B.!!$R1 939
13 TraesCS7D01G117000 chr7B 13872816 13873466 650 True 712.000000 712 86.495000 4309 4962 1 chr7B.!!$R3 653
14 TraesCS7D01G117000 chr7A 77159505 77167236 7731 False 1855.800000 3173 95.792400 1 5894 5 chr7A.!!$F1 5893
15 TraesCS7D01G117000 chr7A 76981593 76982539 946 True 865.000000 865 83.784000 2414 3339 1 chr7A.!!$R1 925
16 TraesCS7D01G117000 chr7A 77023908 77024698 790 True 702.000000 702 83.228000 2525 3292 1 chr7A.!!$R2 767
17 TraesCS7D01G117000 chrUn 84435770 84437693 1923 False 2049.000000 2049 86.180000 1 1897 1 chrUn.!!$F1 1896
18 TraesCS7D01G117000 chrUn 84236179 84238109 1930 True 1866.000000 1866 84.407000 1 1919 1 chrUn.!!$R1 1918
19 TraesCS7D01G117000 chrUn 84244787 84248976 4189 True 1184.000000 2001 85.646333 1 4964 3 chrUn.!!$R4 4963
20 TraesCS7D01G117000 chrUn 84283413 84286450 3037 True 1095.000000 1362 84.777000 2 3325 2 chrUn.!!$R5 3323
21 TraesCS7D01G117000 chrUn 226936738 226939775 3037 True 1095.000000 1362 84.777000 2 3325 2 chrUn.!!$R6 3323
22 TraesCS7D01G117000 chrUn 82524314 82528521 4207 True 932.750000 2067 86.953000 4 4964 4 chrUn.!!$R3 4960
23 TraesCS7D01G117000 chrUn 82513915 82516097 2182 True 749.500000 878 84.214000 2411 4924 2 chrUn.!!$R2 2513
24 TraesCS7D01G117000 chrUn 329448565 329449172 607 False 553.000000 553 83.308000 4304 4942 1 chrUn.!!$F2 638
25 TraesCS7D01G117000 chr2B 723392975 723394705 1730 True 1541.000000 1541 83.089000 400 2137 1 chr2B.!!$R2 1737
26 TraesCS7D01G117000 chr2B 723398759 723403399 4640 True 1155.500000 1609 87.293000 1 4954 2 chr2B.!!$R3 4953

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
161 162 0.659427 CTGTTGATGCCCATACAGCG 59.341 55.000 0.00 0.0 31.94 5.18 F
966 1000 1.076332 GTCGTTGTTCTTGGGATCCG 58.924 55.000 5.45 0.0 0.00 4.18 F
2247 3380 0.824109 TCTCCAGGCAGAATACGGTG 59.176 55.000 0.00 0.0 0.00 4.94 F
2427 3610 0.462047 GTCCAGGCAGAATACGGTGG 60.462 60.000 0.00 0.0 0.00 4.61 F
3686 5088 2.444766 AGCCAATTAGGGGAATCTCAGG 59.555 50.000 0.00 0.0 38.09 3.86 F
4642 7039 5.899299 TCTCTTACCGGCAACTTATTAGAC 58.101 41.667 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2793 4.281182 CGTGGAGGGAGTATAAGTATGCTT 59.719 45.833 0.56 0.56 38.66 3.91 R
2273 3406 0.617413 ATGCACAGGTAAGCTCAGCT 59.383 50.000 0.00 0.00 42.56 4.24 R
3740 5249 0.469144 AACCCAACTTTCGGTGCCAT 60.469 50.000 0.00 0.00 30.96 4.40 R
4746 7175 5.408604 GCATACATCATTAGTACGGGAAAGG 59.591 44.000 0.00 0.00 0.00 3.11 R
4806 7244 0.986527 TCTCCATGAGCTTTGCAGGA 59.013 50.000 0.00 0.00 0.00 3.86 R
5503 9781 4.712829 TCGATTCCTTGTAGGTTATCCACA 59.287 41.667 0.00 0.00 36.53 4.17 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
161 162 0.659427 CTGTTGATGCCCATACAGCG 59.341 55.000 0.00 0.00 31.94 5.18
177 178 3.321497 ACAGCGACAAGTCTCTTCAATC 58.679 45.455 0.00 0.00 0.00 2.67
198 199 8.654094 TCAATCTAAGGATCATATTCAGCAGAA 58.346 33.333 0.00 0.00 38.31 3.02
202 203 5.045012 AGGATCATATTCAGCAGAAGCAA 57.955 39.130 0.00 0.00 45.49 3.91
300 302 4.065321 CAAGACTGTTCTCTTGGTGACT 57.935 45.455 1.63 0.00 42.40 3.41
343 345 5.105228 CCTGCATTTGACTCCATTTTGGTAT 60.105 40.000 0.00 0.00 39.03 2.73
691 725 2.035961 GCTATCACCGGCAGATCAACTA 59.964 50.000 12.78 0.00 0.00 2.24
723 757 2.989571 AGGAAAGAGAAACAGGGGATGT 59.010 45.455 0.00 0.00 46.97 3.06
739 773 4.449131 GGGATGTAGGTGTTAAGCCTTAC 58.551 47.826 4.08 0.00 37.54 2.34
866 900 5.512060 GCTGCTAATGTCCAGAATCCTCATA 60.512 44.000 0.00 0.00 0.00 2.15
876 910 5.773176 TCCAGAATCCTCATATTAGTACGCA 59.227 40.000 0.00 0.00 0.00 5.24
966 1000 1.076332 GTCGTTGTTCTTGGGATCCG 58.924 55.000 5.45 0.00 0.00 4.18
1051 1104 1.767088 GGGTTCTTAGCCGGGTAAGAT 59.233 52.381 41.48 4.26 38.53 2.40
1064 1117 6.072119 AGCCGGGTAAGATTTCTTAAACAAAG 60.072 38.462 3.10 0.00 39.84 2.77
1104 1157 5.048846 ACAGTTCTGTTTTACACCCAGAT 57.951 39.130 0.00 0.00 35.32 2.90
1357 2086 9.774742 CTTTGTTACTTTATGGCTAATTCTCAC 57.225 33.333 0.00 0.00 0.00 3.51
1677 2486 7.631377 GCCAGTCCATATTTCTGTAATTTTGCT 60.631 37.037 0.00 0.00 0.00 3.91
2224 3357 6.422701 TGTCTTGTGTTTACGAATTGAGGTAG 59.577 38.462 0.00 0.00 0.00 3.18
2226 3359 7.596248 GTCTTGTGTTTACGAATTGAGGTAGTA 59.404 37.037 0.00 0.00 0.00 1.82
2229 3362 8.470040 TGTGTTTACGAATTGAGGTAGTAATC 57.530 34.615 0.00 0.00 0.00 1.75
2231 3364 8.805688 GTGTTTACGAATTGAGGTAGTAATCTC 58.194 37.037 0.00 0.00 0.00 2.75
2232 3365 7.977853 TGTTTACGAATTGAGGTAGTAATCTCC 59.022 37.037 0.00 0.00 0.00 3.71
2233 3366 7.649533 TTACGAATTGAGGTAGTAATCTCCA 57.350 36.000 0.00 0.00 0.00 3.86
2234 3367 6.150396 ACGAATTGAGGTAGTAATCTCCAG 57.850 41.667 0.00 0.00 0.00 3.86
2235 3368 5.069251 ACGAATTGAGGTAGTAATCTCCAGG 59.931 44.000 0.00 0.00 0.00 4.45
2236 3369 4.965200 ATTGAGGTAGTAATCTCCAGGC 57.035 45.455 0.00 0.00 0.00 4.85
2237 3370 3.398318 TGAGGTAGTAATCTCCAGGCA 57.602 47.619 0.00 0.00 0.00 4.75
2238 3371 3.300388 TGAGGTAGTAATCTCCAGGCAG 58.700 50.000 0.00 0.00 0.00 4.85
2239 3372 3.052869 TGAGGTAGTAATCTCCAGGCAGA 60.053 47.826 0.00 0.00 0.00 4.26
2240 3373 3.961408 GAGGTAGTAATCTCCAGGCAGAA 59.039 47.826 0.00 0.00 0.00 3.02
2241 3374 4.561752 AGGTAGTAATCTCCAGGCAGAAT 58.438 43.478 0.00 0.00 0.00 2.40
2242 3375 5.716979 AGGTAGTAATCTCCAGGCAGAATA 58.283 41.667 0.00 0.00 0.00 1.75
2243 3376 5.540719 AGGTAGTAATCTCCAGGCAGAATAC 59.459 44.000 6.22 6.22 31.33 1.89
2244 3377 4.592485 AGTAATCTCCAGGCAGAATACG 57.408 45.455 7.78 0.00 34.96 3.06
2245 3378 2.918712 AATCTCCAGGCAGAATACGG 57.081 50.000 0.00 0.00 0.00 4.02
2246 3379 1.794714 ATCTCCAGGCAGAATACGGT 58.205 50.000 0.00 0.00 0.00 4.83
2247 3380 0.824109 TCTCCAGGCAGAATACGGTG 59.176 55.000 0.00 0.00 0.00 4.94
2248 3381 0.824109 CTCCAGGCAGAATACGGTGA 59.176 55.000 0.00 0.00 0.00 4.02
2249 3382 1.207089 CTCCAGGCAGAATACGGTGAA 59.793 52.381 0.00 0.00 0.00 3.18
2250 3383 1.837439 TCCAGGCAGAATACGGTGAAT 59.163 47.619 0.00 0.00 0.00 2.57
2251 3384 3.035363 TCCAGGCAGAATACGGTGAATA 58.965 45.455 0.00 0.00 0.00 1.75
2252 3385 3.452990 TCCAGGCAGAATACGGTGAATAA 59.547 43.478 0.00 0.00 0.00 1.40
2253 3386 4.080807 TCCAGGCAGAATACGGTGAATAAA 60.081 41.667 0.00 0.00 0.00 1.40
2254 3387 4.638421 CCAGGCAGAATACGGTGAATAAAA 59.362 41.667 0.00 0.00 0.00 1.52
2255 3388 5.124776 CCAGGCAGAATACGGTGAATAAAAA 59.875 40.000 0.00 0.00 0.00 1.94
2275 3408 3.308438 AACACCATGCATTTCTCAAGC 57.692 42.857 0.00 0.00 0.00 4.01
2276 3409 2.522185 ACACCATGCATTTCTCAAGCT 58.478 42.857 0.00 0.00 0.00 3.74
2277 3410 2.230508 ACACCATGCATTTCTCAAGCTG 59.769 45.455 0.00 0.00 0.00 4.24
2278 3411 2.490509 CACCATGCATTTCTCAAGCTGA 59.509 45.455 0.00 0.00 0.00 4.26
2279 3412 2.753452 ACCATGCATTTCTCAAGCTGAG 59.247 45.455 0.00 6.79 45.59 3.35
2280 3413 2.479730 CCATGCATTTCTCAAGCTGAGC 60.480 50.000 0.00 0.00 43.95 4.26
2281 3414 2.195741 TGCATTTCTCAAGCTGAGCT 57.804 45.000 0.00 0.00 43.95 4.09
2291 3424 2.061220 AGCTGAGCTTACCTGTGCA 58.939 52.632 0.00 0.00 33.89 4.57
2292 3425 0.617413 AGCTGAGCTTACCTGTGCAT 59.383 50.000 0.00 0.00 33.89 3.96
2293 3426 1.833630 AGCTGAGCTTACCTGTGCATA 59.166 47.619 0.00 0.00 33.89 3.14
2294 3427 1.936547 GCTGAGCTTACCTGTGCATAC 59.063 52.381 0.00 0.00 0.00 2.39
2295 3428 2.677902 GCTGAGCTTACCTGTGCATACA 60.678 50.000 0.00 0.00 35.08 2.29
2296 3429 6.946173 AGCTGAGCTTACCTGTGCATACAC 62.946 50.000 0.00 0.00 41.12 2.90
2312 3445 7.792925 GTGCATACACGTTTCATATAATAGCA 58.207 34.615 0.00 0.00 36.98 3.49
2313 3446 7.740346 GTGCATACACGTTTCATATAATAGCAC 59.260 37.037 0.00 0.00 36.98 4.40
2314 3447 7.655732 TGCATACACGTTTCATATAATAGCACT 59.344 33.333 0.00 0.00 0.00 4.40
2315 3448 8.162880 GCATACACGTTTCATATAATAGCACTC 58.837 37.037 0.00 0.00 0.00 3.51
2316 3449 9.191995 CATACACGTTTCATATAATAGCACTCA 57.808 33.333 0.00 0.00 0.00 3.41
2317 3450 9.758651 ATACACGTTTCATATAATAGCACTCAA 57.241 29.630 0.00 0.00 0.00 3.02
2318 3451 8.487313 ACACGTTTCATATAATAGCACTCAAA 57.513 30.769 0.00 0.00 0.00 2.69
2319 3452 8.604035 ACACGTTTCATATAATAGCACTCAAAG 58.396 33.333 0.00 0.00 0.00 2.77
2320 3453 8.604035 CACGTTTCATATAATAGCACTCAAAGT 58.396 33.333 0.00 0.00 0.00 2.66
2321 3454 9.162764 ACGTTTCATATAATAGCACTCAAAGTT 57.837 29.630 0.00 0.00 0.00 2.66
2330 3463 7.751768 AATAGCACTCAAAGTTAGAAAAGCT 57.248 32.000 0.00 0.00 0.00 3.74
2331 3464 7.751768 ATAGCACTCAAAGTTAGAAAAGCTT 57.248 32.000 0.00 0.00 0.00 3.74
2332 3465 6.456795 AGCACTCAAAGTTAGAAAAGCTTT 57.543 33.333 5.69 5.69 33.28 3.51
2333 3466 7.568199 AGCACTCAAAGTTAGAAAAGCTTTA 57.432 32.000 13.10 0.00 32.01 1.85
2334 3467 7.418408 AGCACTCAAAGTTAGAAAAGCTTTAC 58.582 34.615 13.10 6.93 32.01 2.01
2335 3468 7.283354 AGCACTCAAAGTTAGAAAAGCTTTACT 59.717 33.333 13.10 9.32 32.01 2.24
2336 3469 7.915923 GCACTCAAAGTTAGAAAAGCTTTACTT 59.084 33.333 13.10 14.89 41.70 2.24
2337 3470 9.226345 CACTCAAAGTTAGAAAAGCTTTACTTG 57.774 33.333 20.41 15.46 39.09 3.16
2338 3471 7.915923 ACTCAAAGTTAGAAAAGCTTTACTTGC 59.084 33.333 20.41 9.43 39.09 4.01
2339 3472 7.996385 TCAAAGTTAGAAAAGCTTTACTTGCT 58.004 30.769 20.41 11.16 43.32 3.91
2340 3473 9.116067 TCAAAGTTAGAAAAGCTTTACTTGCTA 57.884 29.630 20.41 11.56 40.22 3.49
2341 3474 9.387123 CAAAGTTAGAAAAGCTTTACTTGCTAG 57.613 33.333 20.41 10.77 40.22 3.42
2342 3475 8.678593 AAGTTAGAAAAGCTTTACTTGCTAGT 57.321 30.769 19.46 6.00 40.22 2.57
2343 3476 8.089115 AGTTAGAAAAGCTTTACTTGCTAGTG 57.911 34.615 13.10 0.00 40.22 2.74
2344 3477 7.931948 AGTTAGAAAAGCTTTACTTGCTAGTGA 59.068 33.333 13.10 0.00 40.22 3.41
2345 3478 8.557029 GTTAGAAAAGCTTTACTTGCTAGTGAA 58.443 33.333 13.10 8.14 40.22 3.18
2346 3479 7.195839 AGAAAAGCTTTACTTGCTAGTGAAG 57.804 36.000 22.49 22.49 45.76 3.02
2347 3480 6.768381 AGAAAAGCTTTACTTGCTAGTGAAGT 59.232 34.615 25.50 14.49 45.15 3.01
2348 3481 6.944234 AAAGCTTTACTTGCTAGTGAAGTT 57.056 33.333 25.50 20.18 45.15 2.66
2349 3482 8.446599 AAAAGCTTTACTTGCTAGTGAAGTTA 57.553 30.769 25.50 2.34 45.15 2.24
2350 3483 7.659652 AAGCTTTACTTGCTAGTGAAGTTAG 57.340 36.000 25.50 9.11 45.15 2.34
2351 3484 6.994221 AGCTTTACTTGCTAGTGAAGTTAGA 58.006 36.000 25.50 0.00 45.15 2.10
2352 3485 7.442656 AGCTTTACTTGCTAGTGAAGTTAGAA 58.557 34.615 25.50 3.83 45.15 2.10
2353 3486 7.931948 AGCTTTACTTGCTAGTGAAGTTAGAAA 59.068 33.333 25.50 10.23 45.15 2.52
2354 3487 8.722394 GCTTTACTTGCTAGTGAAGTTAGAAAT 58.278 33.333 25.50 0.00 45.15 2.17
2356 3489 9.555727 TTTACTTGCTAGTGAAGTTAGAAATGT 57.444 29.630 11.27 0.00 35.30 2.71
2357 3490 9.555727 TTACTTGCTAGTGAAGTTAGAAATGTT 57.444 29.630 11.27 0.00 35.30 2.71
2358 3491 8.451908 ACTTGCTAGTGAAGTTAGAAATGTTT 57.548 30.769 0.00 0.00 31.99 2.83
2359 3492 9.555727 ACTTGCTAGTGAAGTTAGAAATGTTTA 57.444 29.630 0.00 0.00 31.99 2.01
2427 3610 0.462047 GTCCAGGCAGAATACGGTGG 60.462 60.000 0.00 0.00 0.00 4.61
2991 4333 4.080356 TCCAAGGTGGAGATAAGATTGGTG 60.080 45.833 0.00 0.00 42.67 4.17
3361 4725 5.700832 CAGTCATCTTTAGTACTGTGGCAAA 59.299 40.000 5.39 0.00 35.66 3.68
3415 4783 8.673275 CGAAAATATAGTGCACATTCGAATTTC 58.327 33.333 21.04 17.02 40.22 2.17
3521 4890 8.619146 TCATCACGAAATTTATTTTCATCTGC 57.381 30.769 0.00 0.00 43.32 4.26
3618 5018 2.991866 GCGGAGTGAGTACCTAACAAAC 59.008 50.000 0.00 0.00 0.00 2.93
3686 5088 2.444766 AGCCAATTAGGGGAATCTCAGG 59.555 50.000 0.00 0.00 38.09 3.86
3740 5249 8.187480 TGACAACTTTTCATTCATCGAAGAAAA 58.813 29.630 7.22 9.30 43.58 2.29
4018 6374 8.800370 TGCACTTCATCTATAATTGGTTTACA 57.200 30.769 0.00 0.00 0.00 2.41
4642 7039 5.899299 TCTCTTACCGGCAACTTATTAGAC 58.101 41.667 0.00 0.00 0.00 2.59
4688 7086 6.891361 TCAACCCATCATCTTATTGACAACAT 59.109 34.615 0.00 0.00 0.00 2.71
4806 7244 4.586841 GGGAGAGTAGCAGAGTATGACAAT 59.413 45.833 0.00 0.00 0.00 2.71
4990 7431 3.674997 TGCTTTCCAAAAGAGATACGCT 58.325 40.909 3.68 0.00 0.00 5.07
5055 7497 6.817140 CCTAGGAAAAACAGTACCATCTGTAC 59.183 42.308 1.05 0.00 46.25 2.90
5299 7746 6.197096 GCAACCATCTTTTATTATGAAGCGTG 59.803 38.462 0.00 0.00 0.00 5.34
5503 9781 3.005472 CCACGTACGGATCCAATAGTCAT 59.995 47.826 21.06 0.00 0.00 3.06
5526 9804 4.712829 TGTGGATAACCTACAAGGAATCGA 59.287 41.667 0.00 0.00 37.67 3.59
5571 9849 4.068599 TGTCAACGATTAATGAACAGCCA 58.931 39.130 0.00 0.00 0.00 4.75
5702 9980 4.080687 GGATGAGTAATAGCCCTACGTCT 58.919 47.826 0.00 0.00 0.00 4.18
5756 10034 5.385198 ACAATGGTCATGAACTTGTAGGTT 58.615 37.500 20.21 3.31 0.00 3.50
5788 10073 5.550232 TCAGACACACAATATGCATGAAC 57.450 39.130 10.16 0.00 0.00 3.18
5789 10074 5.002516 TCAGACACACAATATGCATGAACA 58.997 37.500 10.16 0.00 0.00 3.18
5790 10075 5.648960 TCAGACACACAATATGCATGAACAT 59.351 36.000 10.16 0.00 0.00 2.71
5791 10076 6.151480 TCAGACACACAATATGCATGAACATT 59.849 34.615 10.16 0.00 0.00 2.71
5792 10077 6.252655 CAGACACACAATATGCATGAACATTG 59.747 38.462 10.16 13.39 35.10 2.82
5793 10078 6.151480 AGACACACAATATGCATGAACATTGA 59.849 34.615 21.28 0.00 33.56 2.57
5794 10079 6.689554 ACACACAATATGCATGAACATTGAA 58.310 32.000 21.28 0.00 33.56 2.69
5859 10144 6.593268 ATGACCAATTGAACATGTCATCAA 57.407 33.333 16.77 13.84 41.48 2.57
5879 10164 9.406113 TCATCAATTCACACAATTGACCATATA 57.594 29.630 13.59 0.00 45.86 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 7.551585 TGATCCTTAGATTGAAGAGACTTGTC 58.448 38.462 0.00 0.00 30.90 3.18
177 178 6.228995 TGCTTCTGCTGAATATGATCCTTAG 58.771 40.000 6.48 0.00 40.48 2.18
198 199 9.638239 CACAACCAAATAGTAATACAATTTGCT 57.362 29.630 0.00 0.00 32.60 3.91
300 302 4.651778 CAGGTAGAAAATCCACTTGGTGA 58.348 43.478 0.00 0.00 35.23 4.02
343 345 4.347876 TGACATTTTCCAAGTGGAGAGAGA 59.652 41.667 0.00 0.00 46.36 3.10
375 377 9.770097 ATATAAATCATAGAGGCACCAATATCG 57.230 33.333 0.00 0.00 0.00 2.92
382 384 9.678260 AAGATCAATATAAATCATAGAGGCACC 57.322 33.333 0.00 0.00 0.00 5.01
441 463 6.449635 ACTGCCAAAAATCATCGCTAATTA 57.550 33.333 0.00 0.00 0.00 1.40
667 701 1.486310 TGATCTGCCGGTGATAGCTTT 59.514 47.619 1.90 0.00 0.00 3.51
691 725 7.230309 CCTGTTTCTCTTTCCTCTTTCTTGATT 59.770 37.037 0.00 0.00 0.00 2.57
739 773 1.302366 TCTGGCGCAGATAAAGCATG 58.698 50.000 10.83 0.00 35.39 4.06
966 1000 6.129179 TGGGAAAATAAGGATCTTGATGTCC 58.871 40.000 0.00 0.00 34.64 4.02
1051 1104 8.041323 TGTTGTATTTGCCCTTTGTTTAAGAAA 58.959 29.630 0.00 0.00 35.80 2.52
1064 1117 5.447624 ACTGTAGTTTGTTGTATTTGCCC 57.552 39.130 0.00 0.00 0.00 5.36
1933 2793 4.281182 CGTGGAGGGAGTATAAGTATGCTT 59.719 45.833 0.56 0.56 38.66 3.91
2224 3357 3.069729 ACCGTATTCTGCCTGGAGATTAC 59.930 47.826 0.00 7.74 0.00 1.89
2226 3359 2.119495 ACCGTATTCTGCCTGGAGATT 58.881 47.619 0.00 0.00 0.00 2.40
2229 3362 0.824109 TCACCGTATTCTGCCTGGAG 59.176 55.000 0.00 0.00 0.00 3.86
2231 3364 2.332063 ATTCACCGTATTCTGCCTGG 57.668 50.000 0.00 0.00 0.00 4.45
2232 3365 5.811399 TTTTATTCACCGTATTCTGCCTG 57.189 39.130 0.00 0.00 0.00 4.85
2252 3385 4.512571 GCTTGAGAAATGCATGGTGTTTTT 59.487 37.500 0.00 0.00 0.00 1.94
2253 3386 4.060205 GCTTGAGAAATGCATGGTGTTTT 58.940 39.130 0.00 0.00 0.00 2.43
2254 3387 3.322828 AGCTTGAGAAATGCATGGTGTTT 59.677 39.130 0.00 0.00 0.00 2.83
2255 3388 2.895404 AGCTTGAGAAATGCATGGTGTT 59.105 40.909 0.00 0.00 0.00 3.32
2256 3389 2.230508 CAGCTTGAGAAATGCATGGTGT 59.769 45.455 0.00 0.00 35.49 4.16
2257 3390 2.490509 TCAGCTTGAGAAATGCATGGTG 59.509 45.455 0.00 1.55 39.08 4.17
2258 3391 2.799017 TCAGCTTGAGAAATGCATGGT 58.201 42.857 0.00 0.00 0.00 3.55
2273 3406 0.617413 ATGCACAGGTAAGCTCAGCT 59.383 50.000 0.00 0.00 42.56 4.24
2274 3407 1.936547 GTATGCACAGGTAAGCTCAGC 59.063 52.381 0.00 0.00 0.00 4.26
2275 3408 2.932614 GTGTATGCACAGGTAAGCTCAG 59.067 50.000 9.26 0.00 44.64 3.35
2276 3409 2.673893 CGTGTATGCACAGGTAAGCTCA 60.674 50.000 14.55 0.00 45.50 4.26
2277 3410 1.927174 CGTGTATGCACAGGTAAGCTC 59.073 52.381 14.55 0.00 45.50 4.09
2278 3411 2.010145 CGTGTATGCACAGGTAAGCT 57.990 50.000 14.55 0.00 45.50 3.74
2284 3417 6.597262 TTATATGAAACGTGTATGCACAGG 57.403 37.500 14.55 0.80 45.50 4.00
2285 3418 7.952101 GCTATTATATGAAACGTGTATGCACAG 59.048 37.037 14.55 9.11 45.50 3.66
2286 3419 7.439655 TGCTATTATATGAAACGTGTATGCACA 59.560 33.333 14.55 0.00 45.50 4.57
2287 3420 7.740346 GTGCTATTATATGAAACGTGTATGCAC 59.260 37.037 3.51 3.51 41.97 4.57
2288 3421 7.655732 AGTGCTATTATATGAAACGTGTATGCA 59.344 33.333 0.00 0.00 0.00 3.96
2289 3422 8.018677 AGTGCTATTATATGAAACGTGTATGC 57.981 34.615 0.00 0.00 0.00 3.14
2290 3423 9.191995 TGAGTGCTATTATATGAAACGTGTATG 57.808 33.333 0.00 0.00 0.00 2.39
2291 3424 9.758651 TTGAGTGCTATTATATGAAACGTGTAT 57.241 29.630 0.00 0.00 0.00 2.29
2292 3425 9.589111 TTTGAGTGCTATTATATGAAACGTGTA 57.411 29.630 0.00 0.00 0.00 2.90
2293 3426 8.487313 TTTGAGTGCTATTATATGAAACGTGT 57.513 30.769 0.00 0.00 0.00 4.49
2294 3427 8.604035 ACTTTGAGTGCTATTATATGAAACGTG 58.396 33.333 0.00 0.00 0.00 4.49
2295 3428 8.718102 ACTTTGAGTGCTATTATATGAAACGT 57.282 30.769 0.00 0.00 0.00 3.99
2304 3437 9.454859 AGCTTTTCTAACTTTGAGTGCTATTAT 57.545 29.630 0.00 0.00 0.00 1.28
2305 3438 8.848474 AGCTTTTCTAACTTTGAGTGCTATTA 57.152 30.769 0.00 0.00 0.00 0.98
2306 3439 7.751768 AGCTTTTCTAACTTTGAGTGCTATT 57.248 32.000 0.00 0.00 0.00 1.73
2307 3440 7.751768 AAGCTTTTCTAACTTTGAGTGCTAT 57.248 32.000 0.00 0.00 0.00 2.97
2308 3441 7.568199 AAAGCTTTTCTAACTTTGAGTGCTA 57.432 32.000 5.69 0.00 32.58 3.49
2309 3442 6.456795 AAAGCTTTTCTAACTTTGAGTGCT 57.543 33.333 5.69 0.00 32.58 4.40
2310 3443 7.418408 AGTAAAGCTTTTCTAACTTTGAGTGC 58.582 34.615 18.47 0.00 35.38 4.40
2311 3444 9.226345 CAAGTAAAGCTTTTCTAACTTTGAGTG 57.774 33.333 18.47 5.67 34.69 3.51
2312 3445 7.915923 GCAAGTAAAGCTTTTCTAACTTTGAGT 59.084 33.333 18.47 0.00 34.69 3.41
2313 3446 8.131731 AGCAAGTAAAGCTTTTCTAACTTTGAG 58.868 33.333 18.47 9.83 39.87 3.02
2314 3447 7.996385 AGCAAGTAAAGCTTTTCTAACTTTGA 58.004 30.769 18.47 0.00 39.87 2.69
2315 3448 9.387123 CTAGCAAGTAAAGCTTTTCTAACTTTG 57.613 33.333 18.47 12.64 43.25 2.77
2316 3449 9.121658 ACTAGCAAGTAAAGCTTTTCTAACTTT 57.878 29.630 18.47 9.07 43.25 2.66
2317 3450 8.560374 CACTAGCAAGTAAAGCTTTTCTAACTT 58.440 33.333 18.47 16.98 43.25 2.66
2318 3451 7.931948 TCACTAGCAAGTAAAGCTTTTCTAACT 59.068 33.333 18.47 18.35 43.25 2.24
2319 3452 8.084590 TCACTAGCAAGTAAAGCTTTTCTAAC 57.915 34.615 18.47 12.54 43.25 2.34
2320 3453 8.671384 TTCACTAGCAAGTAAAGCTTTTCTAA 57.329 30.769 18.47 3.38 43.25 2.10
2321 3454 7.931948 ACTTCACTAGCAAGTAAAGCTTTTCTA 59.068 33.333 18.47 9.98 43.25 2.10
2322 3455 6.768381 ACTTCACTAGCAAGTAAAGCTTTTCT 59.232 34.615 18.47 14.99 43.25 2.52
2323 3456 6.960468 ACTTCACTAGCAAGTAAAGCTTTTC 58.040 36.000 18.47 12.64 43.25 2.29
2324 3457 6.944234 ACTTCACTAGCAAGTAAAGCTTTT 57.056 33.333 18.47 0.00 43.25 2.27
2325 3458 6.944234 AACTTCACTAGCAAGTAAAGCTTT 57.056 33.333 17.30 17.30 43.25 3.51
2326 3459 7.442656 TCTAACTTCACTAGCAAGTAAAGCTT 58.557 34.615 7.86 0.00 43.25 3.74
2327 3460 6.994221 TCTAACTTCACTAGCAAGTAAAGCT 58.006 36.000 7.86 0.00 45.77 3.74
2328 3461 7.653767 TTCTAACTTCACTAGCAAGTAAAGC 57.346 36.000 7.86 0.00 34.69 3.51
2330 3463 9.555727 ACATTTCTAACTTCACTAGCAAGTAAA 57.444 29.630 7.86 6.23 32.71 2.01
2331 3464 9.555727 AACATTTCTAACTTCACTAGCAAGTAA 57.444 29.630 7.86 0.94 32.71 2.24
2332 3465 9.555727 AAACATTTCTAACTTCACTAGCAAGTA 57.444 29.630 7.86 0.00 32.71 2.24
2333 3466 8.451908 AAACATTTCTAACTTCACTAGCAAGT 57.548 30.769 2.44 2.44 35.51 3.16
2360 3493 9.520204 CACAAGACATTCTAAAAAGTGTTCATT 57.480 29.630 0.00 0.00 0.00 2.57
2361 3494 8.686334 ACACAAGACATTCTAAAAAGTGTTCAT 58.314 29.630 0.00 0.00 34.38 2.57
2362 3495 8.050778 ACACAAGACATTCTAAAAAGTGTTCA 57.949 30.769 0.00 0.00 34.38 3.18
2363 3496 8.911247 AACACAAGACATTCTAAAAAGTGTTC 57.089 30.769 0.00 0.00 42.05 3.18
2365 3498 9.783256 GTAAACACAAGACATTCTAAAAAGTGT 57.217 29.630 0.00 0.00 39.13 3.55
2366 3499 8.943925 CGTAAACACAAGACATTCTAAAAAGTG 58.056 33.333 0.00 0.00 0.00 3.16
2367 3500 8.885722 TCGTAAACACAAGACATTCTAAAAAGT 58.114 29.630 0.00 0.00 0.00 2.66
2368 3501 9.710979 TTCGTAAACACAAGACATTCTAAAAAG 57.289 29.630 0.00 0.00 0.00 2.27
2371 3504 9.658475 CAATTCGTAAACACAAGACATTCTAAA 57.342 29.630 0.00 0.00 0.00 1.85
2372 3505 9.047371 TCAATTCGTAAACACAAGACATTCTAA 57.953 29.630 0.00 0.00 0.00 2.10
2373 3506 8.596271 TCAATTCGTAAACACAAGACATTCTA 57.404 30.769 0.00 0.00 0.00 2.10
2374 3507 7.307989 CCTCAATTCGTAAACACAAGACATTCT 60.308 37.037 0.00 0.00 0.00 2.40
2375 3508 6.797033 CCTCAATTCGTAAACACAAGACATTC 59.203 38.462 0.00 0.00 0.00 2.67
2376 3509 6.262273 ACCTCAATTCGTAAACACAAGACATT 59.738 34.615 0.00 0.00 0.00 2.71
2377 3510 5.763204 ACCTCAATTCGTAAACACAAGACAT 59.237 36.000 0.00 0.00 0.00 3.06
2991 4333 1.617357 ACTTCCTGTCCGACCAACTAC 59.383 52.381 0.00 0.00 0.00 2.73
3187 4529 7.724490 TCTAGATCTGAGAATTGTCCAAGAA 57.276 36.000 5.18 0.00 0.00 2.52
3322 4677 6.992063 AGATGACTGTCACATGATTAAACC 57.008 37.500 13.50 0.00 0.00 3.27
3361 4725 8.686334 ACAAAATGTCAAAGTAACTGAGTTGAT 58.314 29.630 8.33 0.00 32.93 2.57
3618 5018 6.732531 TGATAATGTGCTGAACTTTCTGAG 57.267 37.500 0.39 0.00 0.00 3.35
3686 5088 4.737855 TCCTAGGCAATCTAGTTGTCAC 57.262 45.455 2.96 2.47 44.94 3.67
3740 5249 0.469144 AACCCAACTTTCGGTGCCAT 60.469 50.000 0.00 0.00 30.96 4.40
4746 7175 5.408604 GCATACATCATTAGTACGGGAAAGG 59.591 44.000 0.00 0.00 0.00 3.11
4806 7244 0.986527 TCTCCATGAGCTTTGCAGGA 59.013 50.000 0.00 0.00 0.00 3.86
4969 7410 3.674997 AGCGTATCTCTTTTGGAAAGCA 58.325 40.909 0.00 0.00 0.00 3.91
4990 7431 4.480115 TCCTCCGAGGAATATAGCTTCAA 58.520 43.478 15.21 0.00 42.51 2.69
5109 7552 4.111198 CAGCTAACTATGACAGCTCACAG 58.889 47.826 0.00 0.00 43.66 3.66
5128 7571 7.201600 GGATTTACTCTCTTCAACTTCATCAGC 60.202 40.741 0.00 0.00 0.00 4.26
5351 9629 2.102588 AGTGCGTCATGTTATCCCTACC 59.897 50.000 0.00 0.00 0.00 3.18
5503 9781 4.712829 TCGATTCCTTGTAGGTTATCCACA 59.287 41.667 0.00 0.00 36.53 4.17
5571 9849 7.875041 CCTCGACTCCATGTAGATCATAAAATT 59.125 37.037 0.00 0.00 34.67 1.82
5756 10034 7.657354 GCATATTGTGTGTCTGATATGGAGTTA 59.343 37.037 0.00 0.00 34.56 2.24
5824 10109 8.482128 TGTTCAATTGGTCATTTAATTATCCCC 58.518 33.333 5.42 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.