Multiple sequence alignment - TraesCS7D01G029500

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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 TraesCS7D01G029500 chr7D 100.000 3374 0 0 1 3374 14822493 14819120 0.000000e+00 6231.0
1 TraesCS7D01G029500 chr7D 72.450 951 216 35 1363 2293 166886918 166885994 2.580000e-66 263.0
2 TraesCS7D01G029500 chr7A 96.689 2507 64 8 883 3374 14042542 14040040 0.000000e+00 4152.0
3 TraesCS7D01G029500 chr7A 89.457 313 30 2 87 399 14050961 14050652 3.160000e-105 392.0
4 TraesCS7D01G029500 chr7A 85.494 324 28 6 455 760 14050639 14050317 1.510000e-83 320.0
5 TraesCS7D01G029500 chr7A 82.086 374 41 10 3002 3374 14039189 14038841 2.550000e-76 296.0
6 TraesCS7D01G029500 chr7A 72.029 951 220 35 1363 2293 167986879 167985955 1.210000e-59 241.0
7 TraesCS7D01G029500 chr7A 91.772 158 13 0 756 913 14042738 14042581 1.580000e-53 220.0
8 TraesCS7D01G029500 chr7A 96.667 90 3 0 1 90 14051085 14050996 2.100000e-32 150.0
9 TraesCS7D01G029500 chr4A 93.816 1520 82 8 833 2347 721826021 721827533 0.000000e+00 2276.0
10 TraesCS7D01G029500 chr4A 92.392 999 54 7 2382 3373 721827535 721828518 0.000000e+00 1404.0
11 TraesCS7D01G029500 chr4A 80.685 321 54 7 242 559 340318393 340318078 3.360000e-60 243.0
12 TraesCS7D01G029500 chr4A 79.456 331 61 5 235 562 447471927 447471601 9.420000e-56 228.0
13 TraesCS7D01G029500 chrUn 77.285 1105 216 31 1264 2346 237783033 237784124 4.780000e-173 617.0
14 TraesCS7D01G029500 chrUn 100.000 28 0 0 752 779 222055285 222055258 6.000000e-03 52.8
15 TraesCS7D01G029500 chrUn 100.000 28 0 0 752 779 243186288 243186315 6.000000e-03 52.8
16 TraesCS7D01G029500 chrUn 100.000 28 0 0 752 779 268963610 268963637 6.000000e-03 52.8
17 TraesCS7D01G029500 chr6B 77.285 1105 216 31 1264 2346 19922473 19923564 4.780000e-173 617.0
18 TraesCS7D01G029500 chr6B 79.253 241 45 4 235 473 650970647 650970410 2.690000e-36 163.0
19 TraesCS7D01G029500 chr6B 75.074 337 76 6 235 568 650976096 650975765 2.100000e-32 150.0
20 TraesCS7D01G029500 chr6D 76.784 1107 224 28 1265 2346 10640964 10642062 1.040000e-164 590.0
21 TraesCS7D01G029500 chr6D 77.091 275 63 0 2019 2293 11181643 11181369 3.480000e-35 159.0
22 TraesCS7D01G029500 chr6D 93.333 90 6 0 1 90 130457215 130457126 2.110000e-27 134.0
23 TraesCS7D01G029500 chr6D 84.615 78 10 2 707 783 80604827 80604903 3.610000e-10 76.8
24 TraesCS7D01G029500 chr4D 76.730 838 174 17 1146 1971 3923473 3924301 6.640000e-122 448.0
25 TraesCS7D01G029500 chr5B 89.139 267 27 1 90 356 397396226 397395962 6.980000e-87 331.0
26 TraesCS7D01G029500 chr5B 88.519 270 29 1 87 356 397391834 397391567 3.250000e-85 326.0
27 TraesCS7D01G029500 chr5B 88.636 264 28 1 87 350 585501177 585501438 1.510000e-83 320.0
28 TraesCS7D01G029500 chr5B 76.696 339 73 5 232 568 95469844 95470178 2.070000e-42 183.0
29 TraesCS7D01G029500 chr5B 76.331 338 74 5 232 567 338922734 338923067 3.460000e-40 176.0
30 TraesCS7D01G029500 chr5B 86.441 59 8 0 724 782 511348056 511347998 7.810000e-07 65.8
31 TraesCS7D01G029500 chr3B 88.889 270 28 1 87 356 159517417 159517150 6.980000e-87 331.0
32 TraesCS7D01G029500 chr3B 88.519 270 29 1 87 356 159511729 159511462 3.250000e-85 326.0
33 TraesCS7D01G029500 chr3B 88.679 265 26 3 87 350 438337787 438338048 1.510000e-83 320.0
34 TraesCS7D01G029500 chr3B 94.444 90 5 0 1 90 565364137 565364226 4.540000e-29 139.0
35 TraesCS7D01G029500 chr3B 94.444 90 5 0 1 90 565372670 565372759 4.540000e-29 139.0
36 TraesCS7D01G029500 chr7B 89.015 264 27 1 87 350 402801439 402801700 3.250000e-85 326.0
37 TraesCS7D01G029500 chr7B 71.639 952 222 37 1363 2293 130897904 130896980 5.670000e-53 219.0
38 TraesCS7D01G029500 chr7B 93.333 90 6 0 1 90 438831021 438830932 2.110000e-27 134.0
39 TraesCS7D01G029500 chr4B 88.679 265 26 3 87 350 644348402 644348663 1.510000e-83 320.0
40 TraesCS7D01G029500 chr1A 72.737 950 213 39 1363 2292 22535135 22536058 9.220000e-71 278.0
41 TraesCS7D01G029500 chr1A 71.732 941 226 32 1369 2292 20919075 20918158 9.420000e-56 228.0
42 TraesCS7D01G029500 chr2A 80.588 340 64 2 2008 2346 5787984 5787646 9.290000e-66 261.0
43 TraesCS7D01G029500 chr2A 97.561 82 2 0 9 90 411619212 411619131 1.260000e-29 141.0
44 TraesCS7D01G029500 chr2A 94.444 90 5 0 1 90 411627729 411627640 4.540000e-29 139.0
45 TraesCS7D01G029500 chr1D 73.109 595 138 17 1707 2293 18994668 18994088 3.440000e-45 193.0
46 TraesCS7D01G029500 chr2B 76.401 339 74 5 232 568 528875839 528876173 9.620000e-41 178.0
47 TraesCS7D01G029500 chr2B 93.333 90 6 0 1 90 71959449 71959360 2.110000e-27 134.0
48 TraesCS7D01G029500 chr2D 76.036 338 77 3 232 568 633402920 633403254 4.480000e-39 172.0
49 TraesCS7D01G029500 chr2D 88.889 54 6 0 781 834 82882773 82882826 2.170000e-07 67.6
50 TraesCS7D01G029500 chr1B 72.250 591 146 14 1711 2292 28162455 28161874 2.080000e-37 167.0
51 TraesCS7D01G029500 chr5D 76.254 299 69 2 271 568 475761617 475761320 1.250000e-34 158.0
52 TraesCS7D01G029500 chr5D 83.562 73 11 1 707 779 461878738 461878667 2.170000e-07 67.6
53 TraesCS7D01G029500 chr5A 94.444 90 5 0 1 90 405058440 405058351 4.540000e-29 139.0
54 TraesCS7D01G029500 chr5A 83.333 90 12 3 690 777 524922271 524922359 2.790000e-11 80.5
55 TraesCS7D01G029500 chr3D 77.419 124 19 8 3234 3354 394144950 394144833 7.810000e-07 65.8


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 TraesCS7D01G029500 chr7D 14819120 14822493 3373 True 6231.000000 6231 100.000000 1 3374 1 chr7D.!!$R1 3373
1 TraesCS7D01G029500 chr7D 166885994 166886918 924 True 263.000000 263 72.450000 1363 2293 1 chr7D.!!$R2 930
2 TraesCS7D01G029500 chr7A 14038841 14042738 3897 True 1556.000000 4152 90.182333 756 3374 3 chr7A.!!$R2 2618
3 TraesCS7D01G029500 chr7A 14050317 14051085 768 True 287.333333 392 90.539333 1 760 3 chr7A.!!$R3 759
4 TraesCS7D01G029500 chr7A 167985955 167986879 924 True 241.000000 241 72.029000 1363 2293 1 chr7A.!!$R1 930
5 TraesCS7D01G029500 chr4A 721826021 721828518 2497 False 1840.000000 2276 93.104000 833 3373 2 chr4A.!!$F1 2540
6 TraesCS7D01G029500 chrUn 237783033 237784124 1091 False 617.000000 617 77.285000 1264 2346 1 chrUn.!!$F1 1082
7 TraesCS7D01G029500 chr6B 19922473 19923564 1091 False 617.000000 617 77.285000 1264 2346 1 chr6B.!!$F1 1082
8 TraesCS7D01G029500 chr6D 10640964 10642062 1098 False 590.000000 590 76.784000 1265 2346 1 chr6D.!!$F1 1081
9 TraesCS7D01G029500 chr4D 3923473 3924301 828 False 448.000000 448 76.730000 1146 1971 1 chr4D.!!$F1 825
10 TraesCS7D01G029500 chr7B 130896980 130897904 924 True 219.000000 219 71.639000 1363 2293 1 chr7B.!!$R1 930
11 TraesCS7D01G029500 chr1A 22535135 22536058 923 False 278.000000 278 72.737000 1363 2292 1 chr1A.!!$F1 929
12 TraesCS7D01G029500 chr1A 20918158 20919075 917 True 228.000000 228 71.732000 1369 2292 1 chr1A.!!$R1 923

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
305 344 0.316204 AACCGTTTCGACGAGATGGT 59.684 50.0 22.85 22.85 32.71 3.55 F
975 1114 0.452585 GACCTAGACGCACAGACTCC 59.547 60.0 0.00 0.00 0.00 3.85 F
1925 2079 0.529378 GCCCTGAAAGCCAACATCAG 59.471 55.0 0.00 0.00 40.17 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1390 0.390340 TCATGAAGGAGACGCTGTGC 60.390 55.000 0.0 0.00 0.0 4.57 R
2214 2383 1.289109 CCGTGTCGTTCTTCCGCATT 61.289 55.000 0.0 0.00 0.0 3.56 R
2779 2953 2.693762 GGGGCGGCGACCTTTTAAC 61.694 63.158 33.6 10.18 0.0 2.01 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
60 61 8.094798 AGATGAAAAAGTTGTAGATGCGTTTA 57.905 30.769 0.00 0.00 0.00 2.01
97 136 1.717194 TCAATCGGCCGTACAAGAAC 58.283 50.000 27.15 0.00 0.00 3.01
105 144 1.798813 GCCGTACAAGAACAGGACTTG 59.201 52.381 0.00 0.00 46.69 3.16
144 183 9.880157 AATCATCAAAATCTAACCAAATTCAGG 57.120 29.630 0.00 0.00 0.00 3.86
161 200 2.182030 GCTTCTCACGACCTCCGG 59.818 66.667 0.00 0.00 43.93 5.14
193 232 1.893919 GCTCTAGGCCCGGATGATCC 61.894 65.000 0.73 0.08 34.27 3.36
240 279 3.436704 AGCACATTGATCAGGTTGTAACG 59.563 43.478 0.00 0.00 0.00 3.18
245 284 3.889196 TGATCAGGTTGTAACGTTTGC 57.111 42.857 5.91 0.30 0.00 3.68
246 285 3.206964 TGATCAGGTTGTAACGTTTGCA 58.793 40.909 5.91 3.38 0.00 4.08
256 295 3.544682 TGTAACGTTTGCATACGATCTCG 59.455 43.478 31.66 8.65 43.99 4.04
259 298 2.223735 ACGTTTGCATACGATCTCGGAT 60.224 45.455 31.66 7.89 45.12 4.18
262 301 4.443063 CGTTTGCATACGATCTCGGATTAA 59.557 41.667 22.93 0.00 40.60 1.40
263 302 5.051307 CGTTTGCATACGATCTCGGATTAAA 60.051 40.000 22.93 2.87 40.60 1.52
296 335 9.332301 GTTTTATATCAAAATCAACCGTTTCGA 57.668 29.630 0.00 0.00 0.00 3.71
297 336 8.883789 TTTATATCAAAATCAACCGTTTCGAC 57.116 30.769 0.00 0.00 0.00 4.20
298 337 3.241783 TCAAAATCAACCGTTTCGACG 57.758 42.857 0.00 0.00 0.00 5.12
304 343 0.713883 CAACCGTTTCGACGAGATGG 59.286 55.000 21.63 21.63 34.64 3.51
305 344 0.316204 AACCGTTTCGACGAGATGGT 59.684 50.000 22.85 22.85 32.71 3.55
350 389 4.916041 TGATTTGAGGTCATCTTGAGGT 57.084 40.909 0.00 0.00 0.00 3.85
355 394 2.711009 TGAGGTCATCTTGAGGTGGTTT 59.289 45.455 0.00 0.00 0.00 3.27
357 396 2.711009 AGGTCATCTTGAGGTGGTTTGA 59.289 45.455 0.00 0.00 0.00 2.69
358 397 3.331889 AGGTCATCTTGAGGTGGTTTGAT 59.668 43.478 0.00 0.00 0.00 2.57
365 404 4.523943 TCTTGAGGTGGTTTGATCCATTTG 59.476 41.667 0.00 0.00 39.81 2.32
373 412 6.038356 GTGGTTTGATCCATTTGCTAATCTG 58.962 40.000 0.00 0.00 39.81 2.90
381 420 6.441093 TCCATTTGCTAATCTGATGTCAAC 57.559 37.500 0.00 0.00 0.00 3.18
386 425 4.256110 TGCTAATCTGATGTCAACACAGG 58.744 43.478 10.65 0.00 35.41 4.00
399 438 4.935808 GTCAACACAGGTATCTCCGAAATT 59.064 41.667 0.00 0.00 41.99 1.82
400 439 5.063564 GTCAACACAGGTATCTCCGAAATTC 59.936 44.000 0.00 0.00 41.99 2.17
401 440 5.046591 TCAACACAGGTATCTCCGAAATTCT 60.047 40.000 0.00 0.00 41.99 2.40
402 441 4.759782 ACACAGGTATCTCCGAAATTCTG 58.240 43.478 0.00 0.00 41.99 3.02
404 443 5.129485 ACACAGGTATCTCCGAAATTCTGAT 59.871 40.000 0.00 0.00 41.99 2.90
411 450 8.664211 GTATCTCCGAAATTCTGATACCTTTT 57.336 34.615 14.03 0.00 35.67 2.27
412 451 6.985188 TCTCCGAAATTCTGATACCTTTTG 57.015 37.500 0.00 0.00 0.00 2.44
413 452 5.354234 TCTCCGAAATTCTGATACCTTTTGC 59.646 40.000 0.00 0.00 0.00 3.68
414 453 5.007034 TCCGAAATTCTGATACCTTTTGCA 58.993 37.500 0.00 0.00 0.00 4.08
415 454 5.652014 TCCGAAATTCTGATACCTTTTGCAT 59.348 36.000 0.00 0.00 0.00 3.96
416 455 5.973565 CCGAAATTCTGATACCTTTTGCATC 59.026 40.000 0.00 0.00 0.00 3.91
417 456 6.183360 CCGAAATTCTGATACCTTTTGCATCT 60.183 38.462 0.00 0.00 0.00 2.90
418 457 6.909357 CGAAATTCTGATACCTTTTGCATCTC 59.091 38.462 0.00 0.00 0.00 2.75
419 458 7.414429 CGAAATTCTGATACCTTTTGCATCTCA 60.414 37.037 0.00 0.00 0.00 3.27
420 459 6.939132 ATTCTGATACCTTTTGCATCTCAG 57.061 37.500 0.00 0.00 0.00 3.35
421 460 4.194640 TCTGATACCTTTTGCATCTCAGC 58.805 43.478 0.00 0.00 31.08 4.26
422 461 4.080695 TCTGATACCTTTTGCATCTCAGCT 60.081 41.667 0.00 0.00 34.99 4.24
423 462 4.194640 TGATACCTTTTGCATCTCAGCTC 58.805 43.478 0.00 0.00 34.99 4.09
424 463 1.831580 ACCTTTTGCATCTCAGCTCC 58.168 50.000 0.00 0.00 34.99 4.70
425 464 0.731417 CCTTTTGCATCTCAGCTCCG 59.269 55.000 0.00 0.00 34.99 4.63
426 465 1.446907 CTTTTGCATCTCAGCTCCGT 58.553 50.000 0.00 0.00 34.99 4.69
427 466 2.621338 CTTTTGCATCTCAGCTCCGTA 58.379 47.619 0.00 0.00 34.99 4.02
428 467 2.988010 TTTGCATCTCAGCTCCGTAT 57.012 45.000 0.00 0.00 34.99 3.06
429 468 2.988010 TTGCATCTCAGCTCCGTATT 57.012 45.000 0.00 0.00 34.99 1.89
430 469 2.229675 TGCATCTCAGCTCCGTATTG 57.770 50.000 0.00 0.00 34.99 1.90
431 470 1.202568 TGCATCTCAGCTCCGTATTGG 60.203 52.381 0.00 0.00 40.09 3.16
433 472 2.748605 CATCTCAGCTCCGTATTGGAC 58.251 52.381 0.00 0.00 43.74 4.02
434 473 1.112113 TCTCAGCTCCGTATTGGACC 58.888 55.000 0.00 0.00 43.74 4.46
435 474 0.824109 CTCAGCTCCGTATTGGACCA 59.176 55.000 0.00 0.00 43.74 4.02
436 475 1.414181 CTCAGCTCCGTATTGGACCAT 59.586 52.381 0.00 0.00 43.74 3.55
437 476 1.412710 TCAGCTCCGTATTGGACCATC 59.587 52.381 0.00 0.00 43.74 3.51
438 477 1.414181 CAGCTCCGTATTGGACCATCT 59.586 52.381 0.00 0.00 43.74 2.90
439 478 2.119495 AGCTCCGTATTGGACCATCTT 58.881 47.619 0.00 0.00 43.74 2.40
440 479 2.103263 AGCTCCGTATTGGACCATCTTC 59.897 50.000 0.00 0.00 43.74 2.87
441 480 2.743938 CTCCGTATTGGACCATCTTCG 58.256 52.381 0.00 0.00 43.74 3.79
442 481 2.100916 CTCCGTATTGGACCATCTTCGT 59.899 50.000 0.00 0.00 43.74 3.85
443 482 3.289836 TCCGTATTGGACCATCTTCGTA 58.710 45.455 0.00 0.00 43.74 3.43
444 483 3.893200 TCCGTATTGGACCATCTTCGTAT 59.107 43.478 0.00 0.00 43.74 3.06
445 484 4.022589 TCCGTATTGGACCATCTTCGTATC 60.023 45.833 0.00 0.00 43.74 2.24
446 485 4.022242 CCGTATTGGACCATCTTCGTATCT 60.022 45.833 0.00 0.00 42.00 1.98
447 486 5.182570 CCGTATTGGACCATCTTCGTATCTA 59.817 44.000 0.00 0.00 42.00 1.98
448 487 6.127703 CCGTATTGGACCATCTTCGTATCTAT 60.128 42.308 0.00 0.00 42.00 1.98
449 488 7.313646 CGTATTGGACCATCTTCGTATCTATT 58.686 38.462 0.00 0.00 0.00 1.73
450 489 7.273598 CGTATTGGACCATCTTCGTATCTATTG 59.726 40.741 0.00 0.00 0.00 1.90
451 490 5.468540 TGGACCATCTTCGTATCTATTGG 57.531 43.478 0.00 0.00 0.00 3.16
452 491 4.283467 TGGACCATCTTCGTATCTATTGGG 59.717 45.833 0.00 0.00 0.00 4.12
453 492 4.283722 GGACCATCTTCGTATCTATTGGGT 59.716 45.833 0.00 0.00 0.00 4.51
468 507 7.443302 TCTATTGGGTTCATCTTGAAGAGAT 57.557 36.000 0.00 0.00 46.12 2.75
469 508 7.504403 TCTATTGGGTTCATCTTGAAGAGATC 58.496 38.462 0.00 0.00 43.32 2.75
473 512 5.044624 TGGGTTCATCTTGAAGAGATCCATT 60.045 40.000 16.42 0.00 43.32 3.16
478 517 9.334947 GTTCATCTTGAAGAGATCCATTGAATA 57.665 33.333 0.00 0.00 43.32 1.75
523 562 6.506538 AACCTCATCTTGTTATAGCCTCAT 57.493 37.500 0.00 0.00 0.00 2.90
527 566 6.463472 CCTCATCTTGTTATAGCCTCATGTCA 60.463 42.308 0.00 0.00 0.00 3.58
530 569 5.664457 TCTTGTTATAGCCTCATGTCACTG 58.336 41.667 0.00 0.00 0.00 3.66
535 574 2.645838 AGCCTCATGTCACTGTTTGT 57.354 45.000 0.00 0.00 0.00 2.83
564 603 1.169661 ATTTTCGAGCGCCAACACCA 61.170 50.000 2.29 0.00 0.00 4.17
572 611 1.081242 CGCCAACACCATGCTTCAC 60.081 57.895 0.00 0.00 0.00 3.18
576 615 0.518636 CAACACCATGCTTCACGGAG 59.481 55.000 0.00 0.00 0.00 4.63
601 640 2.512515 CTACTCTTGCCCTGCCGC 60.513 66.667 0.00 0.00 0.00 6.53
621 660 2.868044 GCTGAAGCATATACGTCTGGGG 60.868 54.545 0.00 0.00 41.59 4.96
630 669 1.337384 TACGTCTGGGGCTCATGCAT 61.337 55.000 0.00 0.00 41.91 3.96
634 673 1.826921 CTGGGGCTCATGCATGTCC 60.827 63.158 25.43 24.26 41.91 4.02
640 679 0.866427 GCTCATGCATGTCCGATGAG 59.134 55.000 25.43 15.69 44.01 2.90
641 680 0.866427 CTCATGCATGTCCGATGAGC 59.134 55.000 25.43 0.00 37.40 4.26
663 702 1.004679 GGTGCCGAACGTAGGGAAA 60.005 57.895 8.87 0.00 0.00 3.13
685 724 3.198635 ACCATCGTGTGAGAATGGAGATT 59.801 43.478 7.57 0.00 36.33 2.40
687 726 4.436332 CATCGTGTGAGAATGGAGATTCA 58.564 43.478 0.00 0.00 40.59 2.57
696 753 5.046735 TGAGAATGGAGATTCATAGCCTAGC 60.047 44.000 0.00 0.00 40.59 3.42
771 828 2.368655 ATGAAAATCAGCCGGTTTGC 57.631 45.000 1.90 0.00 0.00 3.68
777 834 1.477553 ATCAGCCGGTTTGCATGAAT 58.522 45.000 1.90 0.00 0.00 2.57
969 1108 3.128764 CAGAACATAGACCTAGACGCACA 59.871 47.826 0.00 0.00 0.00 4.57
970 1109 3.378742 AGAACATAGACCTAGACGCACAG 59.621 47.826 0.00 0.00 0.00 3.66
975 1114 0.452585 GACCTAGACGCACAGACTCC 59.547 60.000 0.00 0.00 0.00 3.85
1005 1144 2.351418 TCAGCGATTCAAAGTTATGGCG 59.649 45.455 0.00 0.00 31.74 5.69
1017 1156 3.793559 AGTTATGGCGTTGATACCTCAC 58.206 45.455 0.00 0.00 0.00 3.51
1104 1243 2.043248 GTCCTGGCCGGTCTCCTA 60.043 66.667 7.97 0.00 0.00 2.94
1159 1298 1.205064 CGCCGTACCGTATACCTCG 59.795 63.158 0.00 0.00 0.00 4.63
1205 1344 1.717937 GCAGCTGTCGTATGCCAAG 59.282 57.895 16.64 0.00 33.81 3.61
1251 1390 2.679837 CCTCAACCCATTGTTCGATGAG 59.320 50.000 1.95 0.89 37.11 2.90
1318 1457 2.681778 AGGAGACCAGACTGCCCG 60.682 66.667 0.00 0.00 0.00 6.13
1791 1945 4.838486 CTCTCGCACCTCGTCCGC 62.838 72.222 0.00 0.00 39.67 5.54
1925 2079 0.529378 GCCCTGAAAGCCAACATCAG 59.471 55.000 0.00 0.00 40.17 2.90
2231 2400 0.093026 CGAATGCGGAAGAACGACAC 59.907 55.000 0.00 0.00 35.47 3.67
2779 2953 0.389391 ATAGGTGACTCGGGCAATCG 59.611 55.000 0.00 0.00 43.67 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.127907 GTTTTGTCTCTCCCTCGTTCTTT 58.872 43.478 0.00 0.00 0.00 2.52
19 20 4.451629 TCATCTACGTTTTGTCTCTCCC 57.548 45.455 0.00 0.00 0.00 4.30
60 61 4.427096 TTGAACAACAACACACAATCGT 57.573 36.364 0.00 0.00 33.18 3.73
97 136 2.281761 ACGGCAAGGCAAGTCCTG 60.282 61.111 0.00 0.00 46.94 3.86
105 144 0.101219 GATGATTTGGACGGCAAGGC 59.899 55.000 0.00 0.00 0.00 4.35
142 181 2.344203 CGGAGGTCGTGAGAAGCCT 61.344 63.158 0.00 0.00 45.01 4.58
205 244 3.570975 TCAATGTGCTGCTGTCAGAAATT 59.429 39.130 3.32 0.00 42.95 1.82
240 279 5.900339 TTAATCCGAGATCGTATGCAAAC 57.100 39.130 0.00 0.00 37.74 2.93
290 329 2.673833 AGTTGACCATCTCGTCGAAAC 58.326 47.619 0.00 0.00 35.40 2.78
296 335 4.008074 ACATGAAAGTTGACCATCTCGT 57.992 40.909 0.00 0.00 0.00 4.18
324 363 7.234166 ACCTCAAGATGACCTCAAATCAAAAAT 59.766 33.333 0.00 0.00 0.00 1.82
342 381 4.387026 AATGGATCAAACCACCTCAAGA 57.613 40.909 0.00 0.00 43.03 3.02
350 389 5.951148 TCAGATTAGCAAATGGATCAAACCA 59.049 36.000 0.00 0.00 44.41 3.67
355 394 6.358991 TGACATCAGATTAGCAAATGGATCA 58.641 36.000 0.00 0.00 0.00 2.92
357 396 6.604396 TGTTGACATCAGATTAGCAAATGGAT 59.396 34.615 0.00 0.00 0.00 3.41
358 397 5.945191 TGTTGACATCAGATTAGCAAATGGA 59.055 36.000 0.00 0.00 0.00 3.41
365 404 4.256920 ACCTGTGTTGACATCAGATTAGC 58.743 43.478 12.28 0.00 31.35 3.09
373 412 3.130516 TCGGAGATACCTGTGTTGACATC 59.869 47.826 0.00 0.00 36.31 3.06
381 420 5.011090 TCAGAATTTCGGAGATACCTGTG 57.989 43.478 0.00 0.00 35.04 3.66
386 425 8.552034 CAAAAGGTATCAGAATTTCGGAGATAC 58.448 37.037 19.89 19.89 39.98 2.24
399 438 4.080695 AGCTGAGATGCAAAAGGTATCAGA 60.081 41.667 11.97 0.00 40.69 3.27
400 439 4.197750 AGCTGAGATGCAAAAGGTATCAG 58.802 43.478 4.83 4.83 40.69 2.90
401 440 4.194640 GAGCTGAGATGCAAAAGGTATCA 58.805 43.478 0.00 0.00 40.69 2.15
402 441 3.563390 GGAGCTGAGATGCAAAAGGTATC 59.437 47.826 0.00 0.00 38.74 2.24
404 443 2.677902 CGGAGCTGAGATGCAAAAGGTA 60.678 50.000 0.00 0.00 34.99 3.08
407 446 1.446907 ACGGAGCTGAGATGCAAAAG 58.553 50.000 0.00 0.00 34.99 2.27
408 447 2.760634 TACGGAGCTGAGATGCAAAA 57.239 45.000 0.00 0.00 34.99 2.44
410 449 2.554142 CAATACGGAGCTGAGATGCAA 58.446 47.619 0.00 0.00 34.99 4.08
411 450 1.202568 CCAATACGGAGCTGAGATGCA 60.203 52.381 0.00 0.00 36.56 3.96
412 451 1.069204 TCCAATACGGAGCTGAGATGC 59.931 52.381 0.00 0.00 39.64 3.91
422 461 2.104967 ACGAAGATGGTCCAATACGGA 58.895 47.619 0.00 0.00 43.61 4.69
423 462 2.596904 ACGAAGATGGTCCAATACGG 57.403 50.000 0.00 0.00 0.00 4.02
424 463 5.122512 AGATACGAAGATGGTCCAATACG 57.877 43.478 0.00 2.69 0.00 3.06
425 464 7.545965 CCAATAGATACGAAGATGGTCCAATAC 59.454 40.741 0.00 0.00 0.00 1.89
426 465 7.310423 CCCAATAGATACGAAGATGGTCCAATA 60.310 40.741 0.00 0.00 0.00 1.90
427 466 6.467677 CCAATAGATACGAAGATGGTCCAAT 58.532 40.000 0.00 0.00 0.00 3.16
428 467 5.221641 CCCAATAGATACGAAGATGGTCCAA 60.222 44.000 0.00 0.00 0.00 3.53
429 468 4.283467 CCCAATAGATACGAAGATGGTCCA 59.717 45.833 0.00 0.00 0.00 4.02
430 469 4.283722 ACCCAATAGATACGAAGATGGTCC 59.716 45.833 0.00 0.00 0.00 4.46
431 470 5.470047 ACCCAATAGATACGAAGATGGTC 57.530 43.478 0.00 0.00 0.00 4.02
432 471 5.365605 TGAACCCAATAGATACGAAGATGGT 59.634 40.000 0.00 0.00 0.00 3.55
433 472 5.853936 TGAACCCAATAGATACGAAGATGG 58.146 41.667 0.00 0.00 0.00 3.51
434 473 7.382110 AGATGAACCCAATAGATACGAAGATG 58.618 38.462 0.00 0.00 0.00 2.90
435 474 7.546250 AGATGAACCCAATAGATACGAAGAT 57.454 36.000 0.00 0.00 0.00 2.40
436 475 6.978674 AGATGAACCCAATAGATACGAAGA 57.021 37.500 0.00 0.00 0.00 2.87
437 476 7.210174 TCAAGATGAACCCAATAGATACGAAG 58.790 38.462 0.00 0.00 0.00 3.79
438 477 7.119709 TCAAGATGAACCCAATAGATACGAA 57.880 36.000 0.00 0.00 0.00 3.85
439 478 6.724893 TCAAGATGAACCCAATAGATACGA 57.275 37.500 0.00 0.00 0.00 3.43
440 479 7.210174 TCTTCAAGATGAACCCAATAGATACG 58.790 38.462 0.00 0.00 32.21 3.06
441 480 8.424918 TCTCTTCAAGATGAACCCAATAGATAC 58.575 37.037 0.00 0.00 32.21 2.24
442 481 8.553085 TCTCTTCAAGATGAACCCAATAGATA 57.447 34.615 0.00 0.00 32.21 1.98
443 482 7.443302 TCTCTTCAAGATGAACCCAATAGAT 57.557 36.000 0.00 0.00 32.21 1.98
444 483 6.874278 TCTCTTCAAGATGAACCCAATAGA 57.126 37.500 0.00 0.00 32.21 1.98
445 484 6.709846 GGATCTCTTCAAGATGAACCCAATAG 59.290 42.308 0.00 0.00 45.06 1.73
446 485 6.158520 TGGATCTCTTCAAGATGAACCCAATA 59.841 38.462 9.29 0.00 45.06 1.90
447 486 5.044624 TGGATCTCTTCAAGATGAACCCAAT 60.045 40.000 9.29 0.00 45.06 3.16
448 487 4.289410 TGGATCTCTTCAAGATGAACCCAA 59.711 41.667 9.29 0.00 45.06 4.12
449 488 3.845992 TGGATCTCTTCAAGATGAACCCA 59.154 43.478 9.29 8.08 45.06 4.51
450 489 4.494091 TGGATCTCTTCAAGATGAACCC 57.506 45.455 9.29 6.36 45.06 4.11
451 490 6.118170 TCAATGGATCTCTTCAAGATGAACC 58.882 40.000 0.00 0.00 45.06 3.62
452 491 7.621428 TTCAATGGATCTCTTCAAGATGAAC 57.379 36.000 0.00 0.00 45.06 3.18
453 492 9.557061 CTATTCAATGGATCTCTTCAAGATGAA 57.443 33.333 0.91 0.91 45.06 2.57
468 507 6.710278 TGAGTTCATGTCACTATTCAATGGA 58.290 36.000 0.00 0.00 0.00 3.41
469 508 6.990341 TGAGTTCATGTCACTATTCAATGG 57.010 37.500 0.00 0.00 0.00 3.16
497 536 8.034313 TGAGGCTATAACAAGATGAGGTTAAT 57.966 34.615 0.00 0.00 33.60 1.40
502 541 5.862845 ACATGAGGCTATAACAAGATGAGG 58.137 41.667 0.00 0.00 0.00 3.86
510 549 5.420725 AACAGTGACATGAGGCTATAACA 57.579 39.130 0.00 0.00 0.00 2.41
527 566 4.877378 AAATGGCATGATCACAAACAGT 57.123 36.364 0.00 0.00 0.00 3.55
530 569 4.484236 TCGAAAATGGCATGATCACAAAC 58.516 39.130 0.00 0.00 0.00 2.93
535 574 1.331447 CGCTCGAAAATGGCATGATCA 59.669 47.619 0.00 0.00 0.00 2.92
564 603 3.376935 CTCCGCCTCCGTGAAGCAT 62.377 63.158 0.00 0.00 0.00 3.79
572 611 3.597728 GAGTAGCCTCCGCCTCCG 61.598 72.222 0.00 0.00 34.57 4.63
576 615 2.202946 GCAAGAGTAGCCTCCGCC 60.203 66.667 0.00 0.00 38.58 6.13
597 636 0.784778 GACGTATATGCTTCAGCGGC 59.215 55.000 0.00 0.00 45.83 6.53
601 640 2.868044 GCCCCAGACGTATATGCTTCAG 60.868 54.545 0.00 0.00 0.00 3.02
621 660 0.866427 CTCATCGGACATGCATGAGC 59.134 55.000 32.75 21.89 37.73 4.26
654 693 1.067425 TCACACGATGGTTTCCCTACG 60.067 52.381 0.00 0.00 36.56 3.51
660 699 3.334691 TCCATTCTCACACGATGGTTTC 58.665 45.455 0.00 0.00 34.23 2.78
663 702 2.179427 TCTCCATTCTCACACGATGGT 58.821 47.619 0.00 0.00 34.23 3.55
669 708 4.754114 GGCTATGAATCTCCATTCTCACAC 59.246 45.833 0.00 0.00 39.49 3.82
723 780 7.011828 ACCAGACGGAATTTATTACATTTCG 57.988 36.000 2.42 2.42 38.41 3.46
739 796 5.621197 TGATTTTCATACAAACCAGACGG 57.379 39.130 0.00 0.00 38.77 4.79
740 797 5.088739 GCTGATTTTCATACAAACCAGACG 58.911 41.667 0.00 0.00 0.00 4.18
771 828 1.192312 CATCCGTCCGCGTAATTCATG 59.808 52.381 4.92 0.00 36.15 3.07
787 844 1.014352 ACAAATTCGCTACCGCATCC 58.986 50.000 0.00 0.00 35.30 3.51
795 852 2.851263 ACTGACCCACAAATTCGCTA 57.149 45.000 0.00 0.00 0.00 4.26
890 951 3.797039 CGGTGCTCTCATTTATGGAGAA 58.203 45.455 10.49 0.74 40.64 2.87
969 1108 1.539065 CGCTGAAACTGTGTGGAGTCT 60.539 52.381 0.00 0.00 0.00 3.24
970 1109 0.861837 CGCTGAAACTGTGTGGAGTC 59.138 55.000 0.00 0.00 0.00 3.36
975 1114 3.607422 TTGAATCGCTGAAACTGTGTG 57.393 42.857 0.00 0.00 0.00 3.82
1017 1156 3.508840 GCCACGAAATGCCTCGGG 61.509 66.667 0.00 0.70 43.22 5.14
1072 1211 1.221021 GGACGAGGTGGATGGGTTC 59.779 63.158 0.00 0.00 0.00 3.62
1114 1253 1.836999 ATCAGCTGTACGGTGGCCAA 61.837 55.000 7.24 0.00 41.41 4.52
1159 1298 1.929836 CTGGAAGCAAGCATAGTCGAC 59.070 52.381 7.70 7.70 0.00 4.20
1205 1344 0.807667 ATGCTCGATGAACGTGGCTC 60.808 55.000 0.00 0.00 43.13 4.70
1251 1390 0.390340 TCATGAAGGAGACGCTGTGC 60.390 55.000 0.00 0.00 0.00 4.57
1318 1457 2.027625 GCATATACAGGTCGCCGGC 61.028 63.158 19.07 19.07 0.00 6.13
1908 2062 1.471684 GCTCTGATGTTGGCTTTCAGG 59.528 52.381 0.00 0.00 37.93 3.86
2040 2209 1.291877 GCACGCAGAAGTGGTCGAAT 61.292 55.000 0.00 0.00 42.09 3.34
2214 2383 1.289109 CCGTGTCGTTCTTCCGCATT 61.289 55.000 0.00 0.00 0.00 3.56
2231 2400 2.286950 CCAAACGCAATCATCCATACCG 60.287 50.000 0.00 0.00 0.00 4.02
2715 2886 8.519799 AGAAAAGAACTGAACAAAATGGTCTA 57.480 30.769 0.00 0.00 34.53 2.59
2779 2953 2.693762 GGGGCGGCGACCTTTTAAC 61.694 63.158 33.60 10.18 0.00 2.01
2931 3105 5.188751 ACTTTTAGAGTATTGAGAGGCTGCT 59.811 40.000 0.00 0.00 36.65 4.24
3286 3462 7.683222 GAGTTTGCACTATGAGTAGCTGATACT 60.683 40.741 5.10 5.10 39.52 2.12


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

AutoCloner maintained by Alex Coulton.