Multiple sequence alignment - TraesCS6D01G060800

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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 TraesCS6D01G060800 chr6D 100.000 4516 0 0 1 4516 28417041 28412526 0.000000e+00 8340.0
1 TraesCS6D01G060800 chr6D 82.996 494 71 8 1036 1526 27711117 27711600 6.940000e-118 435.0
2 TraesCS6D01G060800 chr6D 80.000 455 79 11 1048 1493 28334402 28333951 4.360000e-85 326.0
3 TraesCS6D01G060800 chr6D 78.214 459 70 22 993 1436 29094619 29094176 2.680000e-67 267.0
4 TraesCS6D01G060800 chr6D 77.124 459 84 18 989 1436 29152883 29152435 3.490000e-61 246.0
5 TraesCS6D01G060800 chr6D 91.124 169 14 1 3101 3269 57999639 57999806 1.260000e-55 228.0
6 TraesCS6D01G060800 chr6D 78.529 340 53 14 3463 3787 27862249 27862583 5.920000e-49 206.0
7 TraesCS6D01G060800 chr6D 88.652 141 14 2 2277 2415 27988842 27988982 2.160000e-38 171.0
8 TraesCS6D01G060800 chr6D 70.566 1077 248 52 1095 2141 27553761 27552724 7.770000e-38 169.0
9 TraesCS6D01G060800 chr6D 76.970 330 55 16 3801 4120 27974032 27974350 7.770000e-38 169.0
10 TraesCS6D01G060800 chr6D 75.714 280 52 11 1559 1830 28328581 28328310 4.740000e-25 126.0
11 TraesCS6D01G060800 chr6D 81.132 159 23 6 3277 3430 27862111 27862267 2.210000e-23 121.0
12 TraesCS6D01G060800 chrUn 96.304 1380 35 4 2137 3515 80233792 80232428 0.000000e+00 2252.0
13 TraesCS6D01G060800 chrUn 93.498 1215 73 6 960 2170 80235031 80233819 0.000000e+00 1801.0
14 TraesCS6D01G060800 chrUn 93.498 1215 73 6 960 2170 327160332 327161544 0.000000e+00 1801.0
15 TraesCS6D01G060800 chrUn 94.406 1019 38 5 3514 4516 80232298 80231283 0.000000e+00 1548.0
16 TraesCS6D01G060800 chrUn 86.599 791 59 17 1 782 252430255 252429503 0.000000e+00 830.0
17 TraesCS6D01G060800 chrUn 86.599 791 59 17 1 782 396605687 396604935 0.000000e+00 830.0
18 TraesCS6D01G060800 chrUn 86.730 211 9 7 781 974 252429449 252429241 2.740000e-52 217.0
19 TraesCS6D01G060800 chrUn 86.730 211 9 7 781 974 396604881 396604673 2.740000e-52 217.0
20 TraesCS6D01G060800 chr6A 93.457 1238 78 3 1017 2253 29471840 29473075 0.000000e+00 1834.0
21 TraesCS6D01G060800 chr6A 94.754 629 31 1 2778 3406 29491537 29492163 0.000000e+00 977.0
22 TraesCS6D01G060800 chr6A 92.105 532 24 10 2250 2780 29490373 29490887 0.000000e+00 734.0
23 TraesCS6D01G060800 chr6A 87.762 621 44 18 3439 4043 29492162 29492766 0.000000e+00 697.0
24 TraesCS6D01G060800 chr6A 81.930 487 76 10 1048 1528 30422648 30423128 7.040000e-108 401.0
25 TraesCS6D01G060800 chr6A 83.411 428 65 6 1102 1526 30283377 30282953 4.240000e-105 392.0
26 TraesCS6D01G060800 chr6A 83.110 373 34 12 4071 4415 29494478 29494849 3.390000e-81 313.0
27 TraesCS6D01G060800 chr6A 82.670 352 44 12 1661 2011 30282839 30282504 3.420000e-76 296.0
28 TraesCS6D01G060800 chr6A 79.439 428 70 14 1655 2080 30423233 30423644 2.060000e-73 287.0
29 TraesCS6D01G060800 chr6A 83.333 306 40 5 1660 1964 30263357 30263062 5.760000e-69 272.0
30 TraesCS6D01G060800 chr6A 91.176 68 6 0 831 898 29471737 29471804 4.810000e-15 93.5
31 TraesCS6D01G060800 chr6B 77.648 1114 199 29 1036 2127 51559018 51560103 2.290000e-177 632.0
32 TraesCS6D01G060800 chr6B 75.975 1128 228 31 1037 2138 51732113 51733223 3.970000e-150 542.0
33 TraesCS6D01G060800 chr6B 81.062 565 94 9 1036 1591 51537991 51538551 5.360000e-119 438.0
34 TraesCS6D01G060800 chr6B 91.124 169 13 2 3101 3269 130075218 130075384 1.260000e-55 228.0
35 TraesCS6D01G060800 chr6B 79.331 329 58 9 3266 3589 51564023 51564346 5.880000e-54 222.0
36 TraesCS6D01G060800 chr6B 75.604 414 83 12 1389 1790 52370652 52370245 5.960000e-44 189.0
37 TraesCS6D01G060800 chr6B 87.368 95 12 0 1986 2080 51553678 51553772 4.780000e-20 110.0
38 TraesCS6D01G060800 chr7A 81.040 327 43 10 426 751 216341459 216341767 4.510000e-60 243.0
39 TraesCS6D01G060800 chr3B 94.839 155 7 1 3119 3272 552226557 552226403 1.620000e-59 241.0
40 TraesCS6D01G060800 chr3B 82.353 187 24 9 459 642 25285922 25286102 2.180000e-33 154.0
41 TraesCS6D01G060800 chr4B 92.308 169 12 1 3108 3275 182666353 182666185 5.840000e-59 239.0
42 TraesCS6D01G060800 chr3A 92.593 162 11 1 3108 3269 726768968 726769128 9.770000e-57 231.0
43 TraesCS6D01G060800 chr5A 91.071 168 15 0 3103 3270 573811663 573811496 1.260000e-55 228.0
44 TraesCS6D01G060800 chr4A 87.701 187 16 5 3088 3269 101750497 101750313 1.270000e-50 211.0
45 TraesCS6D01G060800 chr4A 79.032 186 31 7 517 697 739069193 739069011 2.210000e-23 121.0
46 TraesCS6D01G060800 chr2A 78.114 297 53 9 448 738 612840567 612840857 1.290000e-40 178.0
47 TraesCS6D01G060800 chr7B 85.606 132 17 2 518 648 384027257 384027387 2.190000e-28 137.0
48 TraesCS6D01G060800 chr7B 93.023 43 2 1 666 707 82702723 82702681 1.360000e-05 62.1
49 TraesCS6D01G060800 chr1A 74.359 273 65 5 1809 2080 536810640 536810372 1.330000e-20 111.0
50 TraesCS6D01G060800 chr1D 80.137 146 21 6 556 698 10388593 10388453 7.990000e-18 102.0
51 TraesCS6D01G060800 chr2D 85.227 88 11 2 584 670 471060773 471060859 6.220000e-14 89.8
52 TraesCS6D01G060800 chr5D 74.312 218 30 17 999 1212 482318993 482318798 8.110000e-08 69.4


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 TraesCS6D01G060800 chr6D 28412526 28417041 4515 True 8340.00 8340 100.00000 1 4516 1 chr6D.!!$R4 4515
1 TraesCS6D01G060800 chrUn 80231283 80235031 3748 True 1867.00 2252 94.73600 960 4516 3 chrUn.!!$R1 3556
2 TraesCS6D01G060800 chrUn 327160332 327161544 1212 False 1801.00 1801 93.49800 960 2170 1 chrUn.!!$F1 1210
3 TraesCS6D01G060800 chrUn 252429241 252430255 1014 True 523.50 830 86.66450 1 974 2 chrUn.!!$R2 973
4 TraesCS6D01G060800 chrUn 396604673 396605687 1014 True 523.50 830 86.66450 1 974 2 chrUn.!!$R3 973
5 TraesCS6D01G060800 chr6A 29471737 29473075 1338 False 963.75 1834 92.31650 831 2253 2 chr6A.!!$F1 1422
6 TraesCS6D01G060800 chr6A 29490373 29494849 4476 False 680.25 977 89.43275 2250 4415 4 chr6A.!!$F2 2165
7 TraesCS6D01G060800 chr6A 30282504 30283377 873 True 344.00 392 83.04050 1102 2011 2 chr6A.!!$R2 909
8 TraesCS6D01G060800 chr6A 30422648 30423644 996 False 344.00 401 80.68450 1048 2080 2 chr6A.!!$F3 1032
9 TraesCS6D01G060800 chr6B 51732113 51733223 1110 False 542.00 542 75.97500 1037 2138 1 chr6B.!!$F3 1101
10 TraesCS6D01G060800 chr6B 51537991 51538551 560 False 438.00 438 81.06200 1036 1591 1 chr6B.!!$F1 555
11 TraesCS6D01G060800 chr6B 51559018 51564346 5328 False 427.00 632 78.48950 1036 3589 2 chr6B.!!$F5 2553

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
291 295 0.106918 AACGGAAACCACAAGCAGGA 60.107 50.000 0.0 0.0 0.0 3.86 F
292 296 0.110486 ACGGAAACCACAAGCAGGAT 59.890 50.000 0.0 0.0 0.0 3.24 F
1319 1403 0.035317 TTGCAGCTCGACCACAGATT 59.965 50.000 0.0 0.0 0.0 2.40 F
1322 1406 0.390866 CAGCTCGACCACAGATTGCT 60.391 55.000 0.0 0.0 0.0 3.91 F
1537 1638 1.546923 TGTTAGAGGCCGACGATCAAA 59.453 47.619 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1401 0.175302 CGAGGACAGAGCAGAGCAAT 59.825 55.000 0.00 0.00 0.00 3.56 R
1446 1532 1.173043 GGATCGGGTTTGCAATCACA 58.827 50.000 10.27 0.00 0.00 3.58 R
3046 6376 0.690762 TAGAGGCCAACAGACCAACC 59.309 55.000 5.01 0.00 0.00 3.77 R
3201 6531 6.477669 ACAGACTACGTACGGATGTATATG 57.522 41.667 21.06 14.72 32.11 1.78 R
3515 6848 2.164219 CGCAGCAACCAGAATACCATTT 59.836 45.455 0.00 0.00 0.00 2.32 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
32 34 9.710900 AAAATCTTAGGAATTGTTTCATTCACC 57.289 29.630 0.00 0.00 33.23 4.02
43 45 9.703892 AATTGTTTCATTCACCGATCAAAATAA 57.296 25.926 0.00 0.00 0.00 1.40
64 66 3.060479 ACACTCCCATAGATTAGGCCA 57.940 47.619 5.01 0.00 0.00 5.36
76 78 1.279025 TTAGGCCATCACTGACCCCC 61.279 60.000 5.01 0.00 0.00 5.40
117 119 6.422400 GTGGTTTTGAAGAAAATTGCCGATAA 59.578 34.615 0.00 0.00 33.63 1.75
128 130 3.644966 TTGCCGATAAAAGTCCTCCAT 57.355 42.857 0.00 0.00 0.00 3.41
139 141 3.136641 AGTCCTCCATGGTCCATTACT 57.863 47.619 12.58 5.49 37.07 2.24
156 158 8.686334 GTCCATTACTGATAACATTTCACCATT 58.314 33.333 0.00 0.00 0.00 3.16
158 160 9.304731 CCATTACTGATAACATTTCACCATTTG 57.695 33.333 0.00 0.00 0.00 2.32
169 171 1.271934 TCACCATTTGCAAACCATCGG 59.728 47.619 15.41 12.19 0.00 4.18
179 181 0.671251 AAACCATCGGCGAGCAAAAA 59.329 45.000 17.22 0.00 0.00 1.94
223 227 1.590238 CTGATTTGATCCACGTCGAGC 59.410 52.381 0.00 0.00 0.00 5.03
226 230 0.172578 TTTGATCCACGTCGAGCGAT 59.827 50.000 13.06 0.00 44.77 4.58
252 256 2.264480 CCGAGGATGGCAACGACA 59.736 61.111 0.00 0.00 42.51 4.35
258 262 0.447801 GGATGGCAACGACATGTGTC 59.552 55.000 1.15 3.07 41.47 3.67
286 290 1.666700 TCGACAAACGGAAACCACAAG 59.333 47.619 0.00 0.00 42.82 3.16
289 293 1.134175 ACAAACGGAAACCACAAGCAG 59.866 47.619 0.00 0.00 0.00 4.24
290 294 0.744281 AAACGGAAACCACAAGCAGG 59.256 50.000 0.00 0.00 0.00 4.85
291 295 0.106918 AACGGAAACCACAAGCAGGA 60.107 50.000 0.00 0.00 0.00 3.86
292 296 0.110486 ACGGAAACCACAAGCAGGAT 59.890 50.000 0.00 0.00 0.00 3.24
293 297 0.523072 CGGAAACCACAAGCAGGATG 59.477 55.000 0.00 0.00 40.87 3.51
294 298 1.881925 CGGAAACCACAAGCAGGATGA 60.882 52.381 0.00 0.00 39.69 2.92
295 299 1.541588 GGAAACCACAAGCAGGATGAC 59.458 52.381 0.00 0.00 39.69 3.06
296 300 1.541588 GAAACCACAAGCAGGATGACC 59.458 52.381 0.00 0.00 39.69 4.02
298 302 0.773644 ACCACAAGCAGGATGACCTT 59.226 50.000 0.00 0.00 45.36 3.50
299 303 1.271597 ACCACAAGCAGGATGACCTTC 60.272 52.381 0.00 0.00 45.36 3.46
300 304 1.457346 CACAAGCAGGATGACCTTCC 58.543 55.000 0.00 0.00 45.36 3.46
301 305 0.329596 ACAAGCAGGATGACCTTCCC 59.670 55.000 0.00 0.00 45.36 3.97
302 306 0.329261 CAAGCAGGATGACCTTCCCA 59.671 55.000 0.00 0.00 45.36 4.37
303 307 1.075601 AAGCAGGATGACCTTCCCAA 58.924 50.000 0.00 0.00 45.36 4.12
304 308 0.329596 AGCAGGATGACCTTCCCAAC 59.670 55.000 0.00 0.00 45.36 3.77
305 309 0.329596 GCAGGATGACCTTCCCAACT 59.670 55.000 0.00 0.00 45.36 3.16
313 317 1.052124 ACCTTCCCAACTGTCGTGGA 61.052 55.000 0.02 0.00 0.00 4.02
353 358 4.100498 TCCTTGTCGTTACTCCCATTATCC 59.900 45.833 0.00 0.00 0.00 2.59
358 363 3.069586 TCGTTACTCCCATTATCCTGCTG 59.930 47.826 0.00 0.00 0.00 4.41
398 405 6.652205 ATACAACCCTAAGGATTTTCCAGA 57.348 37.500 0.00 0.00 39.61 3.86
408 415 8.660435 CCTAAGGATTTTCCAGAATACATAGGA 58.340 37.037 5.58 0.00 41.00 2.94
425 432 7.361457 ACATAGGAATTCCAAGTTATCTCGA 57.639 36.000 26.22 0.00 38.89 4.04
426 433 7.437748 ACATAGGAATTCCAAGTTATCTCGAG 58.562 38.462 26.22 5.93 38.89 4.04
427 434 5.941555 AGGAATTCCAAGTTATCTCGAGT 57.058 39.130 26.22 2.46 38.89 4.18
428 435 5.665459 AGGAATTCCAAGTTATCTCGAGTG 58.335 41.667 26.22 1.65 38.89 3.51
429 436 4.271291 GGAATTCCAAGTTATCTCGAGTGC 59.729 45.833 20.04 1.49 35.64 4.40
430 437 2.561733 TCCAAGTTATCTCGAGTGCG 57.438 50.000 13.13 0.00 39.35 5.34
431 438 2.089201 TCCAAGTTATCTCGAGTGCGA 58.911 47.619 13.13 0.00 45.71 5.10
432 439 2.159421 TCCAAGTTATCTCGAGTGCGAC 60.159 50.000 13.13 7.50 42.51 5.19
433 440 2.159366 CCAAGTTATCTCGAGTGCGACT 60.159 50.000 13.13 9.60 42.51 4.18
434 441 3.064958 CCAAGTTATCTCGAGTGCGACTA 59.935 47.826 13.13 0.00 42.51 2.59
435 442 4.261238 CCAAGTTATCTCGAGTGCGACTAT 60.261 45.833 13.13 0.00 42.51 2.12
436 443 5.274718 CAAGTTATCTCGAGTGCGACTATT 58.725 41.667 13.13 0.00 42.51 1.73
437 444 5.098218 AGTTATCTCGAGTGCGACTATTC 57.902 43.478 13.13 0.00 42.51 1.75
445 452 1.979262 TGCGACTATTCTGCACCCA 59.021 52.632 0.00 0.00 32.86 4.51
449 456 0.464554 GACTATTCTGCACCCAGGCC 60.465 60.000 0.00 0.00 39.61 5.19
460 467 1.997311 CCCAGGCCCAGATGAGTCA 60.997 63.158 0.00 0.00 0.00 3.41
480 487 3.142951 CAGGGTGTGAACGGTAAAATCA 58.857 45.455 0.00 0.00 0.00 2.57
496 503 9.245284 CGGTAAAATCATTTTAAATCGCAAAAC 57.755 29.630 4.06 0.00 36.91 2.43
511 519 9.824534 AAATCGCAAAACAATTTAAAATCATCC 57.175 25.926 0.00 0.00 0.00 3.51
515 523 8.167985 CGCAAAACAATTTAAAATCATCCGATT 58.832 29.630 0.00 0.00 43.94 3.34
547 555 2.037136 GCCAGATGCTCAAGTGCGT 61.037 57.895 0.00 0.00 36.87 5.24
569 578 1.126488 TGCCTGTGCAAAATTTGGGA 58.874 45.000 7.89 0.00 46.66 4.37
575 584 4.639755 CCTGTGCAAAATTTGGGAAGTTTT 59.360 37.500 7.89 0.00 31.30 2.43
576 585 5.819901 CCTGTGCAAAATTTGGGAAGTTTTA 59.180 36.000 7.89 0.00 31.30 1.52
588 597 7.429636 TTGGGAAGTTTTAACATACGAAGAG 57.570 36.000 0.00 0.00 0.00 2.85
592 601 6.367969 GGAAGTTTTAACATACGAAGAGCTCA 59.632 38.462 17.77 0.00 0.00 4.26
621 631 3.708563 AAGACAAATTTCGGGTGTGTG 57.291 42.857 0.00 0.00 0.00 3.82
651 661 7.962917 ACTTTTGAAAACAACACTATTTGCAG 58.037 30.769 0.00 0.00 0.00 4.41
664 674 6.430925 ACACTATTTGCAGCTGATTTTGTCTA 59.569 34.615 20.43 0.00 0.00 2.59
691 701 0.379669 CCATGAGCGCCTCAAATGTC 59.620 55.000 2.29 0.00 44.04 3.06
707 717 7.353414 TCAAATGTCCAAACACCTTGAAATA 57.647 32.000 3.64 0.00 37.51 1.40
714 724 6.007076 TCCAAACACCTTGAAATACTGCATA 58.993 36.000 0.00 0.00 37.17 3.14
716 726 7.014711 TCCAAACACCTTGAAATACTGCATAAA 59.985 33.333 0.00 0.00 37.17 1.40
742 752 3.650281 TGCCTTTGAGCATCTTGGATA 57.350 42.857 0.00 0.00 38.00 2.59
798 863 6.147864 TCTGCTATTTTATTGTCCATTGGC 57.852 37.500 0.00 0.00 0.00 4.52
799 864 5.655974 TCTGCTATTTTATTGTCCATTGGCA 59.344 36.000 0.00 0.00 0.00 4.92
943 1020 1.506493 CTGCTTCACTCCAGTGTCAC 58.494 55.000 6.61 0.00 45.76 3.67
960 1039 1.003355 ACCATCCCGCAGTTCACTG 60.003 57.895 2.31 2.31 46.40 3.66
962 1041 2.045926 ATCCCGCAGTTCACTGGC 60.046 61.111 9.01 0.96 43.94 4.85
963 1042 3.628646 ATCCCGCAGTTCACTGGCC 62.629 63.158 9.01 0.00 43.94 5.36
964 1043 4.335647 CCCGCAGTTCACTGGCCT 62.336 66.667 3.32 0.00 43.94 5.19
965 1044 3.052082 CCGCAGTTCACTGGCCTG 61.052 66.667 8.29 8.29 43.94 4.85
966 1045 2.031012 CGCAGTTCACTGGCCTGA 59.969 61.111 17.64 3.14 43.94 3.86
967 1046 2.031516 CGCAGTTCACTGGCCTGAG 61.032 63.158 17.64 8.84 43.94 3.35
970 1049 1.462238 AGTTCACTGGCCTGAGGGT 60.462 57.895 17.64 0.00 34.45 4.34
972 1051 0.606673 GTTCACTGGCCTGAGGGTTC 60.607 60.000 17.64 0.00 34.45 3.62
986 1067 0.883370 GGGTTCGAGTCCACCACAAC 60.883 60.000 6.36 0.00 34.36 3.32
989 1070 1.052124 TTCGAGTCCACCACAACCCT 61.052 55.000 0.00 0.00 0.00 4.34
990 1071 0.178955 TCGAGTCCACCACAACCCTA 60.179 55.000 0.00 0.00 0.00 3.53
991 1072 0.246635 CGAGTCCACCACAACCCTAG 59.753 60.000 0.00 0.00 0.00 3.02
992 1073 1.640917 GAGTCCACCACAACCCTAGA 58.359 55.000 0.00 0.00 0.00 2.43
994 1075 0.613777 GTCCACCACAACCCTAGAGG 59.386 60.000 0.00 0.00 43.78 3.69
995 1076 1.198759 TCCACCACAACCCTAGAGGC 61.199 60.000 0.00 0.00 40.58 4.70
1258 1342 1.366319 AGGCATCTCCTTCACACCTT 58.634 50.000 0.00 0.00 44.75 3.50
1317 1401 1.005748 CTTGCAGCTCGACCACAGA 60.006 57.895 0.00 0.00 0.00 3.41
1319 1403 0.035317 TTGCAGCTCGACCACAGATT 59.965 50.000 0.00 0.00 0.00 2.40
1320 1404 0.671472 TGCAGCTCGACCACAGATTG 60.671 55.000 0.00 0.00 0.00 2.67
1322 1406 0.390866 CAGCTCGACCACAGATTGCT 60.391 55.000 0.00 0.00 0.00 3.91
1446 1532 1.839354 GCCATTCCCCATTGGTTCAAT 59.161 47.619 1.20 0.00 35.34 2.57
1537 1638 1.546923 TGTTAGAGGCCGACGATCAAA 59.453 47.619 0.00 0.00 0.00 2.69
1710 1829 1.873591 CTTTACTGGCGTCTTGCTGTT 59.126 47.619 0.00 0.00 45.43 3.16
1776 1895 2.903784 AGGTGTGATACAAGTGCCTGTA 59.096 45.455 0.00 0.00 36.27 2.74
2247 2731 4.335315 CACTTCAACATATACCAATGGCGT 59.665 41.667 0.00 0.00 0.00 5.68
2277 2761 2.698274 GTTCTTTCCCCATGTTGGTGTT 59.302 45.455 0.00 0.00 35.17 3.32
2516 3658 9.712305 GATAGATATATAACAGTTGCAACCTGT 57.288 33.333 25.62 23.14 0.00 4.00
3046 6376 6.210287 AGGAGGTATCTAAAGTTCTGAACG 57.790 41.667 14.35 1.26 36.23 3.95
3112 6442 7.268586 ACTGGAGAATGTGCTAATAGTACTTG 58.731 38.462 0.00 0.00 31.77 3.16
3121 6451 5.524281 GTGCTAATAGTACTTGCTCCTTTCC 59.476 44.000 0.00 0.00 0.00 3.13
3187 6517 5.295292 CGGAGCAAAATGAGTGAATCTACAT 59.705 40.000 0.00 0.00 0.00 2.29
3244 6574 7.403231 AGTCTGTATTGAAATCTCTAAAGGGGA 59.597 37.037 0.00 0.00 0.00 4.81
3515 6848 6.069673 ACATTGATTGATCCACAGGTACCTAA 60.070 38.462 15.80 3.53 0.00 2.69
3535 6999 3.874392 AAATGGTATTCTGGTTGCTGC 57.126 42.857 0.00 0.00 0.00 5.25
3567 7032 1.719600 AGCTTCTGCGATGTGTCTTC 58.280 50.000 0.00 0.00 45.42 2.87
3646 7111 2.640826 TGGGAAGTGGAAAATCGTAGGT 59.359 45.455 0.00 0.00 0.00 3.08
3754 7223 9.915629 TGGTTTATTTTGTATTTGTGGTACATC 57.084 29.630 0.00 0.00 44.52 3.06
3802 7274 0.829990 TGCCTGCCTGACGATCATTA 59.170 50.000 0.00 0.00 0.00 1.90
3829 7301 5.013079 TGTTGTATCTGGTCAGGAGATTTGT 59.987 40.000 0.00 0.00 32.32 2.83
4038 9200 7.668525 ACTGACCGAAAACTATAAAGGAAAG 57.331 36.000 0.00 0.00 0.00 2.62
4044 9206 7.991460 ACCGAAAACTATAAAGGAAAGATAGGG 59.009 37.037 0.00 0.00 0.00 3.53
4063 9225 0.391130 GCACTCCGGCACAAGTATGA 60.391 55.000 0.00 0.00 0.00 2.15
4202 9384 8.004344 GTCATTATCATGTCGATAAACTTTCGG 58.996 37.037 0.00 0.00 46.99 4.30
4224 9406 8.253867 TCGGTATGGGTTACAGTATAAGAAAT 57.746 34.615 0.00 0.00 31.99 2.17
4262 9445 3.141398 ACTTGCACACACTGTAGATTGG 58.859 45.455 0.00 0.00 0.00 3.16
4341 9541 4.655963 TGCCTTTGCTTCTCTTCATTACT 58.344 39.130 0.00 0.00 38.71 2.24
4376 9576 5.287674 TCTCTCCATCAATGATCTTCCAC 57.712 43.478 0.00 0.00 0.00 4.02
4407 9607 3.141272 AGTTCCTTTTACCACATCCCCAA 59.859 43.478 0.00 0.00 0.00 4.12
4418 9618 3.026694 CACATCCCCAAAAATCCTCCTC 58.973 50.000 0.00 0.00 0.00 3.71
4419 9619 2.654385 ACATCCCCAAAAATCCTCCTCA 59.346 45.455 0.00 0.00 0.00 3.86
4434 9634 3.107601 CTCCTCAGGTCAGGGTATTTCA 58.892 50.000 0.00 0.00 33.81 2.69
4437 9637 2.503356 CTCAGGTCAGGGTATTTCAGCT 59.497 50.000 0.00 0.00 0.00 4.24
4438 9638 2.501723 TCAGGTCAGGGTATTTCAGCTC 59.498 50.000 0.00 0.00 0.00 4.09
4457 9657 3.254892 CTCTTTCAGCTCGGGTAGTTTC 58.745 50.000 0.00 0.00 0.00 2.78
4459 9659 0.963962 TTCAGCTCGGGTAGTTTCGT 59.036 50.000 0.00 0.00 0.00 3.85
4481 9681 9.849166 TTCGTTTTCCAAAATTTCATATACTCC 57.151 29.630 0.00 0.00 0.00 3.85
4497 9697 9.749340 TCATATACTCCTAAAATATCGAGACCA 57.251 33.333 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 7.786178 TCTATGGGAGTGTTTATTTTGATCG 57.214 36.000 0.00 0.00 0.00 3.69
43 45 3.393687 TGGCCTAATCTATGGGAGTGTT 58.606 45.455 3.32 0.00 0.00 3.32
76 78 3.217231 ACGAGTGGCGGGATTAGG 58.783 61.111 0.00 0.00 46.49 2.69
100 102 6.621613 AGGACTTTTATCGGCAATTTTCTTC 58.378 36.000 0.00 0.00 0.00 2.87
117 119 3.852578 AGTAATGGACCATGGAGGACTTT 59.147 43.478 21.47 11.41 41.22 2.66
128 130 6.601613 GGTGAAATGTTATCAGTAATGGACCA 59.398 38.462 0.00 0.00 0.00 4.02
139 141 6.426328 GGTTTGCAAATGGTGAAATGTTATCA 59.574 34.615 16.21 0.00 0.00 2.15
156 158 2.976840 GCTCGCCGATGGTTTGCAA 61.977 57.895 0.00 0.00 0.00 4.08
158 160 2.470801 TTTGCTCGCCGATGGTTTGC 62.471 55.000 0.00 0.00 0.00 3.68
179 181 7.930325 CAGACATGAGATGTTATCACTGGTATT 59.070 37.037 0.00 0.00 45.03 1.89
180 182 7.288621 TCAGACATGAGATGTTATCACTGGTAT 59.711 37.037 0.00 0.00 45.03 2.73
181 183 6.607198 TCAGACATGAGATGTTATCACTGGTA 59.393 38.462 0.00 0.00 45.03 3.25
185 189 8.262933 TCAAATCAGACATGAGATGTTATCACT 58.737 33.333 0.00 0.00 45.03 3.41
200 204 2.230266 TCGACGTGGATCAAATCAGACA 59.770 45.455 0.00 0.00 0.00 3.41
223 227 0.962489 ATCCTCGGCTCCAGTTATCG 59.038 55.000 0.00 0.00 0.00 2.92
226 230 2.516448 CCATCCTCGGCTCCAGTTA 58.484 57.895 0.00 0.00 0.00 2.24
249 253 1.073216 CGACAGCCTCGACACATGTC 61.073 60.000 0.00 1.70 46.14 3.06
250 254 1.080501 CGACAGCCTCGACACATGT 60.081 57.895 0.00 0.00 46.14 3.21
251 255 1.212751 TCGACAGCCTCGACACATG 59.787 57.895 0.03 0.00 46.75 3.21
252 256 3.681473 TCGACAGCCTCGACACAT 58.319 55.556 0.03 0.00 46.75 3.21
258 262 2.372690 CCGTTTGTCGACAGCCTCG 61.373 63.158 19.11 19.07 44.44 4.63
263 267 1.004292 GTGGTTTCCGTTTGTCGACAG 60.004 52.381 19.11 7.29 42.86 3.51
268 272 1.133407 TGCTTGTGGTTTCCGTTTGTC 59.867 47.619 0.00 0.00 0.00 3.18
271 275 0.744281 CCTGCTTGTGGTTTCCGTTT 59.256 50.000 0.00 0.00 0.00 3.60
286 290 0.329596 AGTTGGGAAGGTCATCCTGC 59.670 55.000 0.00 0.00 44.35 4.85
289 293 1.676014 CGACAGTTGGGAAGGTCATCC 60.676 57.143 0.00 0.00 38.86 3.51
290 294 1.002087 ACGACAGTTGGGAAGGTCATC 59.998 52.381 0.00 0.00 0.00 2.92
291 295 1.056660 ACGACAGTTGGGAAGGTCAT 58.943 50.000 0.00 0.00 0.00 3.06
292 296 0.105964 CACGACAGTTGGGAAGGTCA 59.894 55.000 0.00 0.00 0.00 4.02
293 297 0.602905 CCACGACAGTTGGGAAGGTC 60.603 60.000 0.00 0.00 0.00 3.85
294 298 1.052124 TCCACGACAGTTGGGAAGGT 61.052 55.000 0.00 0.00 0.00 3.50
295 299 0.107831 TTCCACGACAGTTGGGAAGG 59.892 55.000 6.64 0.00 34.63 3.46
296 300 1.873591 CTTTCCACGACAGTTGGGAAG 59.126 52.381 0.00 0.00 40.27 3.46
297 301 1.476110 CCTTTCCACGACAGTTGGGAA 60.476 52.381 6.64 6.64 37.63 3.97
298 302 0.107831 CCTTTCCACGACAGTTGGGA 59.892 55.000 0.00 0.00 0.00 4.37
299 303 0.179029 ACCTTTCCACGACAGTTGGG 60.179 55.000 0.00 0.00 0.00 4.12
300 304 1.226746 GACCTTTCCACGACAGTTGG 58.773 55.000 0.00 0.00 0.00 3.77
301 305 1.226746 GGACCTTTCCACGACAGTTG 58.773 55.000 0.00 0.00 42.30 3.16
302 306 3.700198 GGACCTTTCCACGACAGTT 57.300 52.632 0.00 0.00 42.30 3.16
313 317 3.261818 AGGAGACTAGTGTGGACCTTT 57.738 47.619 0.00 0.00 40.61 3.11
385 392 9.942526 AATTCCTATGTATTCTGGAAAATCCTT 57.057 29.630 0.00 0.00 41.22 3.36
394 401 9.799106 ATAACTTGGAATTCCTATGTATTCTGG 57.201 33.333 24.73 5.42 36.82 3.86
398 405 9.712305 CGAGATAACTTGGAATTCCTATGTATT 57.288 33.333 24.73 12.52 36.82 1.89
408 415 3.865745 CGCACTCGAGATAACTTGGAATT 59.134 43.478 21.68 0.00 38.10 2.17
425 432 0.108138 GGGTGCAGAATAGTCGCACT 60.108 55.000 26.55 0.00 45.44 4.40
426 433 0.391130 TGGGTGCAGAATAGTCGCAC 60.391 55.000 22.71 22.71 45.42 5.34
427 434 0.108186 CTGGGTGCAGAATAGTCGCA 60.108 55.000 5.77 5.77 33.09 5.10
428 435 0.811616 CCTGGGTGCAGAATAGTCGC 60.812 60.000 0.00 1.07 0.00 5.19
429 436 0.811616 GCCTGGGTGCAGAATAGTCG 60.812 60.000 0.00 0.00 0.00 4.18
430 437 0.464554 GGCCTGGGTGCAGAATAGTC 60.465 60.000 0.00 0.00 0.00 2.59
431 438 1.609783 GGCCTGGGTGCAGAATAGT 59.390 57.895 0.00 0.00 0.00 2.12
432 439 1.152881 GGGCCTGGGTGCAGAATAG 60.153 63.158 0.84 0.00 0.00 1.73
433 440 1.925285 CTGGGCCTGGGTGCAGAATA 61.925 60.000 4.53 0.00 0.00 1.75
434 441 3.267233 TGGGCCTGGGTGCAGAAT 61.267 61.111 4.53 0.00 0.00 2.40
435 442 3.970410 CTGGGCCTGGGTGCAGAA 61.970 66.667 4.53 0.00 0.00 3.02
436 443 4.980592 TCTGGGCCTGGGTGCAGA 62.981 66.667 10.79 2.34 0.00 4.26
437 444 3.736224 ATCTGGGCCTGGGTGCAG 61.736 66.667 10.79 0.00 0.00 4.41
445 452 4.063335 CCTGACTCATCTGGGCCT 57.937 61.111 4.53 0.00 39.67 5.19
449 456 1.269958 TCACACCCTGACTCATCTGG 58.730 55.000 0.00 0.00 42.30 3.86
460 467 3.495434 TGATTTTACCGTTCACACCCT 57.505 42.857 0.00 0.00 0.00 4.34
530 538 1.642037 CCACGCACTTGAGCATCTGG 61.642 60.000 0.00 0.00 34.92 3.86
569 578 7.148407 CCATGAGCTCTTCGTATGTTAAAACTT 60.148 37.037 16.19 0.00 0.00 2.66
575 584 3.132111 TGCCATGAGCTCTTCGTATGTTA 59.868 43.478 16.19 0.00 44.23 2.41
576 585 2.093500 TGCCATGAGCTCTTCGTATGTT 60.093 45.455 16.19 0.00 44.23 2.71
614 624 5.923684 TGTTTTCAAAAGTTTCTCACACACC 59.076 36.000 0.00 0.00 0.00 4.16
670 680 1.097232 CATTTGAGGCGCTCATGGAA 58.903 50.000 7.64 1.38 40.39 3.53
673 683 0.379669 GGACATTTGAGGCGCTCATG 59.620 55.000 7.64 7.98 40.39 3.07
674 684 0.035152 TGGACATTTGAGGCGCTCAT 60.035 50.000 7.64 0.00 40.39 2.90
680 690 1.963515 AGGTGTTTGGACATTTGAGGC 59.036 47.619 0.00 0.00 38.23 4.70
691 701 4.582701 TGCAGTATTTCAAGGTGTTTGG 57.417 40.909 0.00 0.00 37.39 3.28
812 877 3.165875 CCGGCTCATCTAGAATCCCTAA 58.834 50.000 0.00 0.00 0.00 2.69
813 878 2.557676 CCCGGCTCATCTAGAATCCCTA 60.558 54.545 0.00 0.00 0.00 3.53
814 879 1.638529 CCGGCTCATCTAGAATCCCT 58.361 55.000 0.00 0.00 0.00 4.20
816 881 0.036858 GCCCGGCTCATCTAGAATCC 60.037 60.000 0.71 0.00 0.00 3.01
817 882 0.972883 AGCCCGGCTCATCTAGAATC 59.027 55.000 5.94 0.00 30.62 2.52
818 883 3.155897 AGCCCGGCTCATCTAGAAT 57.844 52.632 5.94 0.00 30.62 2.40
819 884 4.707584 AGCCCGGCTCATCTAGAA 57.292 55.556 5.94 0.00 30.62 2.10
943 1020 1.746615 CCAGTGAACTGCGGGATGG 60.747 63.158 4.87 0.00 42.47 3.51
960 1039 2.579738 GACTCGAACCCTCAGGCC 59.420 66.667 0.00 0.00 36.11 5.19
962 1041 1.592223 GTGGACTCGAACCCTCAGG 59.408 63.158 5.96 0.00 40.04 3.86
963 1042 1.185618 TGGTGGACTCGAACCCTCAG 61.186 60.000 1.62 0.00 35.44 3.35
964 1043 1.152419 TGGTGGACTCGAACCCTCA 60.152 57.895 1.62 0.45 35.44 3.86
965 1044 1.292541 GTGGTGGACTCGAACCCTC 59.707 63.158 1.62 0.00 35.44 4.30
966 1045 1.052124 TTGTGGTGGACTCGAACCCT 61.052 55.000 1.62 0.00 35.44 4.34
967 1046 0.883370 GTTGTGGTGGACTCGAACCC 60.883 60.000 1.62 0.00 35.44 4.11
970 1049 1.052124 AGGGTTGTGGTGGACTCGAA 61.052 55.000 0.00 0.00 0.00 3.71
972 1051 0.246635 CTAGGGTTGTGGTGGACTCG 59.753 60.000 0.00 0.00 0.00 4.18
986 1067 1.519751 CGTCATCTCGGCCTCTAGGG 61.520 65.000 0.00 0.00 35.18 3.53
989 1070 4.159266 CCGTCATCTCGGCCTCTA 57.841 61.111 0.00 0.00 43.96 2.43
1258 1342 1.480212 CGATCGGGGGAATCCATGGA 61.480 60.000 18.88 18.88 37.22 3.41
1290 1374 1.375268 GAGCTGCAAGGAGAAGCGT 60.375 57.895 1.02 0.00 41.88 5.07
1317 1401 0.175302 CGAGGACAGAGCAGAGCAAT 59.825 55.000 0.00 0.00 0.00 3.56
1319 1403 2.346541 CCGAGGACAGAGCAGAGCA 61.347 63.158 0.00 0.00 0.00 4.26
1320 1404 2.493973 CCGAGGACAGAGCAGAGC 59.506 66.667 0.00 0.00 0.00 4.09
1322 1406 2.036414 AGCCGAGGACAGAGCAGA 59.964 61.111 0.00 0.00 0.00 4.26
1382 1466 1.743772 CGGGATCCCACACAATGACTC 60.744 57.143 30.42 0.00 35.37 3.36
1446 1532 1.173043 GGATCGGGTTTGCAATCACA 58.827 50.000 10.27 0.00 0.00 3.58
1537 1638 2.009774 GCAGACAATGGCTCGTGTATT 58.990 47.619 0.00 0.00 0.00 1.89
1710 1829 7.558807 TCAAACTCGAGAATAGTATAGGAACCA 59.441 37.037 21.68 0.00 0.00 3.67
1757 1876 4.188247 TCTACAGGCACTTGTATCACAC 57.812 45.455 0.00 0.00 34.60 3.82
1776 1895 8.121305 AGTCAATCTTCGCTTCAGATATATCT 57.879 34.615 9.57 9.57 37.72 1.98
2247 2731 5.701224 ACATGGGGAAAGAACACTAAAGAA 58.299 37.500 0.00 0.00 0.00 2.52
2318 2803 4.699925 AACTAAGCTAAACCAGACACCA 57.300 40.909 0.00 0.00 0.00 4.17
2516 3658 8.621532 ACAGCTAAATCTCATTGTTCAACTTA 57.378 30.769 0.00 0.00 0.00 2.24
2598 3746 7.147742 TGCTCATGTGTTCAGTATGGAGTATTA 60.148 37.037 0.00 0.00 36.16 0.98
2605 3753 3.314357 CCATGCTCATGTGTTCAGTATGG 59.686 47.826 12.10 12.10 37.11 2.74
3046 6376 0.690762 TAGAGGCCAACAGACCAACC 59.309 55.000 5.01 0.00 0.00 3.77
3112 6442 8.982091 AAAGGTCTTATATTTAGGAAAGGAGC 57.018 34.615 0.00 0.00 0.00 4.70
3201 6531 6.477669 ACAGACTACGTACGGATGTATATG 57.522 41.667 21.06 14.72 32.11 1.78
3244 6574 9.597681 TCTACTCCCTCCGTTTCTAAATATAAT 57.402 33.333 0.00 0.00 0.00 1.28
3382 6714 7.277981 CAGTAAACATTAGCTTCGTCATAAGGT 59.722 37.037 0.00 0.00 40.20 3.50
3515 6848 2.164219 CGCAGCAACCAGAATACCATTT 59.836 45.455 0.00 0.00 0.00 2.32
3535 6999 3.921969 CAGAAGCTAGTTTCTGCATCG 57.078 47.619 29.07 11.59 45.21 3.84
3567 7032 5.391950 CCCGTGTGAAGGATACAAAATGAAG 60.392 44.000 0.00 0.00 41.41 3.02
3646 7111 4.933400 GGAAGTTAGCACTGGACGATTAAA 59.067 41.667 0.00 0.00 31.60 1.52
3802 7274 4.096681 TCTCCTGACCAGATACAACACAT 58.903 43.478 0.00 0.00 0.00 3.21
3829 7301 3.057386 TGGACATAAGCAAAGTACGACGA 60.057 43.478 0.00 0.00 0.00 4.20
4038 9200 2.109181 GTGCCGGAGTGCCCTATC 59.891 66.667 5.05 0.00 0.00 2.08
4044 9206 0.391130 TCATACTTGTGCCGGAGTGC 60.391 55.000 5.05 0.00 0.00 4.40
4224 9406 3.751175 GCAAGTAGTGGTGACTTTGCATA 59.249 43.478 0.00 0.00 34.90 3.14
4262 9445 8.856490 TTCTTTTCTCTTCTAACAAACAATGC 57.144 30.769 0.00 0.00 0.00 3.56
4300 9500 1.135575 CAAGCCTCTTGGATTTCGTGC 60.136 52.381 0.00 0.00 40.42 5.34
4341 9541 5.132502 TGATGGAGAGAACTGCAAGAAAAA 58.867 37.500 0.00 0.00 46.58 1.94
4376 9576 2.614734 GGTAAAAGGAACTCCGACTGGG 60.615 54.545 0.00 0.00 38.49 4.45
4407 9607 1.918957 CCCTGACCTGAGGAGGATTTT 59.081 52.381 4.99 0.00 42.93 1.82
4418 9618 2.503356 AGAGCTGAAATACCCTGACCTG 59.497 50.000 0.00 0.00 0.00 4.00
4419 9619 2.839228 AGAGCTGAAATACCCTGACCT 58.161 47.619 0.00 0.00 0.00 3.85
4437 9637 2.352421 CGAAACTACCCGAGCTGAAAGA 60.352 50.000 0.00 0.00 34.07 2.52
4438 9638 1.993370 CGAAACTACCCGAGCTGAAAG 59.007 52.381 0.00 0.00 0.00 2.62
4445 9645 2.758009 TGGAAAACGAAACTACCCGAG 58.242 47.619 0.00 0.00 0.00 4.63
4448 9648 6.757478 TGAAATTTTGGAAAACGAAACTACCC 59.243 34.615 0.00 0.00 35.34 3.69
4477 9677 7.621796 ACTTTTGGTCTCGATATTTTAGGAGT 58.378 34.615 0.00 0.00 0.00 3.85
4478 9678 9.595823 TTACTTTTGGTCTCGATATTTTAGGAG 57.404 33.333 0.00 0.00 0.00 3.69
4487 9687 6.103997 GGACACATTACTTTTGGTCTCGATA 58.896 40.000 0.00 0.00 0.00 2.92
4491 9691 6.385649 TTTGGACACATTACTTTTGGTCTC 57.614 37.500 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.