Multiple sequence alignment - TraesCS5D01G348400

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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 TraesCS5D01G348400 chr5D 100.000 2426 0 0 1 2426 434322155 434324580 0.000000e+00 4481.0
1 TraesCS5D01G348400 chr5D 89.755 1308 80 10 439 1718 434403429 434402148 0.000000e+00 1624.0
2 TraesCS5D01G348400 chr5D 80.256 1408 193 46 439 1803 434394232 434392867 0.000000e+00 981.0
3 TraesCS5D01G348400 chr5D 85.792 915 82 23 736 1608 435237353 435238261 0.000000e+00 926.0
4 TraesCS5D01G348400 chr5D 82.267 547 54 17 439 969 434329499 434330018 1.330000e-117 433.0
5 TraesCS5D01G348400 chr5D 86.173 405 37 8 1717 2108 434402075 434401677 1.040000e-113 420.0
6 TraesCS5D01G348400 chr5D 84.281 299 34 9 2134 2426 434401678 434401387 1.840000e-71 279.0
7 TraesCS5D01G348400 chr5D 88.085 235 23 5 1675 1904 435238277 435238511 8.550000e-70 274.0
8 TraesCS5D01G348400 chr5D 82.848 309 27 13 742 1028 434392090 434391786 1.110000e-63 254.0
9 TraesCS5D01G348400 chr5D 92.771 83 3 2 240 322 434403517 434403438 1.520000e-22 117.0
10 TraesCS5D01G348400 chr5D 97.959 49 1 0 317 365 434322424 434322472 4.300000e-13 86.1
11 TraesCS5D01G348400 chr5D 97.959 49 1 0 270 318 434322471 434322519 4.300000e-13 86.1
12 TraesCS5D01G348400 chr5D 97.727 44 1 0 320 363 434403487 434403444 2.590000e-10 76.8
13 TraesCS5D01G348400 chr5B 89.718 992 43 7 484 1475 527065211 527064279 0.000000e+00 1212.0
14 TraesCS5D01G348400 chr5B 92.070 681 44 7 1753 2426 527064283 527063606 0.000000e+00 950.0
15 TraesCS5D01G348400 chr5B 82.752 1119 131 27 439 1522 527050289 527049198 0.000000e+00 941.0
16 TraesCS5D01G348400 chr5B 82.348 1099 131 33 671 1729 528524387 528525462 0.000000e+00 896.0
17 TraesCS5D01G348400 chr5B 82.575 1033 118 34 736 1729 527061081 527060072 0.000000e+00 854.0
18 TraesCS5D01G348400 chr5B 81.589 1070 130 37 575 1611 527059357 527058322 0.000000e+00 822.0
19 TraesCS5D01G348400 chr5B 82.609 552 85 7 1044 1586 526587394 526586845 6.070000e-131 477.0
20 TraesCS5D01G348400 chr5B 90.076 262 23 3 1349 1608 528537969 528538229 1.070000e-88 337.0
21 TraesCS5D01G348400 chr5A 90.470 829 53 9 1603 2426 548239246 548238439 0.000000e+00 1070.0
22 TraesCS5D01G348400 chr5A 92.550 698 37 10 827 1513 548240494 548239801 0.000000e+00 987.0
23 TraesCS5D01G348400 chr5A 80.155 1416 187 55 439 1803 548231316 548229944 0.000000e+00 972.0
24 TraesCS5D01G348400 chr5A 81.509 1087 132 27 670 1725 549153488 549154536 0.000000e+00 830.0
25 TraesCS5D01G348400 chr5A 91.420 338 13 7 439 775 548240817 548240495 1.320000e-122 449.0
26 TraesCS5D01G348400 chr5A 96.457 254 8 1 1 254 548241196 548240944 3.730000e-113 418.0
27 TraesCS5D01G348400 chr5A 81.366 322 32 16 731 1028 548229088 548228771 1.120000e-58 237.0


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 TraesCS5D01G348400 chr5D 434322155 434324580 2425 False 1551.066667 4481 98.639333 1 2426 3 chr5D.!!$F2 2425
1 TraesCS5D01G348400 chr5D 434391786 434394232 2446 True 617.500000 981 81.552000 439 1803 2 chr5D.!!$R1 1364
2 TraesCS5D01G348400 chr5D 435237353 435238511 1158 False 600.000000 926 86.938500 736 1904 2 chr5D.!!$F3 1168
3 TraesCS5D01G348400 chr5D 434401387 434403517 2130 True 503.360000 1624 90.141400 240 2426 5 chr5D.!!$R2 2186
4 TraesCS5D01G348400 chr5D 434329499 434330018 519 False 433.000000 433 82.267000 439 969 1 chr5D.!!$F1 530
5 TraesCS5D01G348400 chr5B 527058322 527065211 6889 True 959.500000 1212 86.488000 484 2426 4 chr5B.!!$R3 1942
6 TraesCS5D01G348400 chr5B 527049198 527050289 1091 True 941.000000 941 82.752000 439 1522 1 chr5B.!!$R2 1083
7 TraesCS5D01G348400 chr5B 528524387 528525462 1075 False 896.000000 896 82.348000 671 1729 1 chr5B.!!$F1 1058
8 TraesCS5D01G348400 chr5B 526586845 526587394 549 True 477.000000 477 82.609000 1044 1586 1 chr5B.!!$R1 542
9 TraesCS5D01G348400 chr5A 549153488 549154536 1048 False 830.000000 830 81.509000 670 1725 1 chr5A.!!$F1 1055
10 TraesCS5D01G348400 chr5A 548238439 548241196 2757 True 731.000000 1070 92.724250 1 2426 4 chr5A.!!$R2 2425
11 TraesCS5D01G348400 chr5A 548228771 548231316 2545 True 604.500000 972 80.760500 439 1803 2 chr5A.!!$R1 1364

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
73 74 0.248743 ACGTCACGCATACATACGGG 60.249 55.0 0.0 0.0 37.86 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 6238 0.46487 CTCTGTGGAGCAGGATGGAG 59.535 60.0 0.0 0.0 45.08 3.86 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 33 6.575162 ATTTGTGTCTGAAACCCAACTATC 57.425 37.500 0.00 0.00 0.00 2.08
44 45 5.772393 ACCCAACTATCACAGGAAACATA 57.228 39.130 0.00 0.00 0.00 2.29
73 74 0.248743 ACGTCACGCATACATACGGG 60.249 55.000 0.00 0.00 37.86 5.28
111 112 1.369692 CCAACACACGGTAGAGGCA 59.630 57.895 0.00 0.00 0.00 4.75
113 114 1.359848 CAACACACGGTAGAGGCATC 58.640 55.000 0.00 0.00 0.00 3.91
205 206 3.003480 GGTCTTGTTCTAGTCATGTGCC 58.997 50.000 0.00 0.00 0.00 5.01
263 315 5.801380 TGAACAAATACTCCCTCTGTAACC 58.199 41.667 0.00 0.00 0.00 2.85
316 368 1.614996 TGTGACATGCCGGAAATTGT 58.385 45.000 5.05 0.00 0.00 2.71
317 369 1.959985 TGTGACATGCCGGAAATTGTT 59.040 42.857 5.05 0.00 0.00 2.83
322 374 2.363680 ACATGCCGGAAATTGTTCACAA 59.636 40.909 5.05 0.00 40.51 3.33
323 375 2.791383 TGCCGGAAATTGTTCACAAG 57.209 45.000 5.05 0.00 39.47 3.16
324 376 1.339610 TGCCGGAAATTGTTCACAAGG 59.660 47.619 5.05 0.00 39.47 3.61
325 377 1.934849 GCCGGAAATTGTTCACAAGGC 60.935 52.381 5.05 4.63 39.47 4.35
327 379 2.223923 CCGGAAATTGTTCACAAGGCAA 60.224 45.455 0.00 0.00 39.47 4.52
328 380 3.052036 CGGAAATTGTTCACAAGGCAAG 58.948 45.455 0.00 0.00 39.47 4.01
329 381 3.243367 CGGAAATTGTTCACAAGGCAAGA 60.243 43.478 0.00 0.00 39.47 3.02
330 382 4.692228 GGAAATTGTTCACAAGGCAAGAA 58.308 39.130 0.00 0.00 39.47 2.52
331 383 5.299949 GGAAATTGTTCACAAGGCAAGAAT 58.700 37.500 0.00 0.00 39.47 2.40
332 384 5.178067 GGAAATTGTTCACAAGGCAAGAATG 59.822 40.000 0.00 0.00 39.47 2.67
333 385 3.731652 TTGTTCACAAGGCAAGAATGG 57.268 42.857 0.00 0.00 0.00 3.16
334 386 1.962807 TGTTCACAAGGCAAGAATGGG 59.037 47.619 0.00 0.00 0.00 4.00
335 387 0.968405 TTCACAAGGCAAGAATGGGC 59.032 50.000 0.00 0.00 32.54 5.36
342 394 2.654749 GGCAAGAATGGGCTGTAAAC 57.345 50.000 0.00 0.00 0.00 2.01
343 395 1.892474 GGCAAGAATGGGCTGTAAACA 59.108 47.619 0.00 0.00 0.00 2.83
344 396 2.497273 GGCAAGAATGGGCTGTAAACAT 59.503 45.455 0.00 0.00 0.00 2.71
345 397 3.514645 GCAAGAATGGGCTGTAAACATG 58.485 45.455 0.00 0.00 0.00 3.21
346 398 3.056607 GCAAGAATGGGCTGTAAACATGT 60.057 43.478 0.00 0.00 0.00 3.21
347 399 4.487948 CAAGAATGGGCTGTAAACATGTG 58.512 43.478 0.00 0.00 0.00 3.21
348 400 4.032960 AGAATGGGCTGTAAACATGTGA 57.967 40.909 0.00 0.00 0.00 3.58
349 401 3.758554 AGAATGGGCTGTAAACATGTGAC 59.241 43.478 0.00 1.15 0.00 3.67
350 402 2.647683 TGGGCTGTAAACATGTGACA 57.352 45.000 12.06 12.06 0.00 3.58
351 403 3.153369 TGGGCTGTAAACATGTGACAT 57.847 42.857 12.82 0.00 0.00 3.06
352 404 2.819019 TGGGCTGTAAACATGTGACATG 59.181 45.455 22.97 22.97 0.00 3.21
353 405 2.415893 GGGCTGTAAACATGTGACATGC 60.416 50.000 24.32 9.18 0.00 4.06
354 406 2.415893 GGCTGTAAACATGTGACATGCC 60.416 50.000 24.32 23.38 33.42 4.40
355 407 2.489329 GCTGTAAACATGTGACATGCCT 59.511 45.455 24.32 14.23 0.00 4.75
356 408 3.671433 GCTGTAAACATGTGACATGCCTG 60.671 47.826 24.32 14.14 0.00 4.85
357 409 3.749226 TGTAAACATGTGACATGCCTGA 58.251 40.909 24.32 3.44 0.00 3.86
358 410 4.140536 TGTAAACATGTGACATGCCTGAA 58.859 39.130 24.32 6.15 0.00 3.02
359 411 4.582240 TGTAAACATGTGACATGCCTGAAA 59.418 37.500 24.32 4.60 0.00 2.69
360 412 4.877378 AAACATGTGACATGCCTGAAAT 57.123 36.364 24.32 1.05 0.00 2.17
361 413 4.877378 AACATGTGACATGCCTGAAATT 57.123 36.364 24.32 7.42 0.00 1.82
362 414 4.182693 ACATGTGACATGCCTGAAATTG 57.817 40.909 24.32 0.00 0.00 2.32
363 415 3.575256 ACATGTGACATGCCTGAAATTGT 59.425 39.130 24.32 0.23 0.00 2.71
364 416 4.039488 ACATGTGACATGCCTGAAATTGTT 59.961 37.500 24.32 0.00 0.00 2.83
365 417 5.243507 ACATGTGACATGCCTGAAATTGTTA 59.756 36.000 24.32 0.00 0.00 2.41
366 418 5.781210 TGTGACATGCCTGAAATTGTTAA 57.219 34.783 0.00 0.00 0.00 2.01
367 419 6.343716 TGTGACATGCCTGAAATTGTTAAT 57.656 33.333 0.00 0.00 0.00 1.40
368 420 7.459795 TGTGACATGCCTGAAATTGTTAATA 57.540 32.000 0.00 0.00 0.00 0.98
369 421 8.065473 TGTGACATGCCTGAAATTGTTAATAT 57.935 30.769 0.00 0.00 0.00 1.28
370 422 7.975058 TGTGACATGCCTGAAATTGTTAATATG 59.025 33.333 0.00 0.00 0.00 1.78
371 423 7.975616 GTGACATGCCTGAAATTGTTAATATGT 59.024 33.333 0.00 0.00 0.00 2.29
372 424 8.530311 TGACATGCCTGAAATTGTTAATATGTT 58.470 29.630 0.00 0.00 0.00 2.71
373 425 8.931385 ACATGCCTGAAATTGTTAATATGTTC 57.069 30.769 0.00 0.00 0.00 3.18
374 426 8.752187 ACATGCCTGAAATTGTTAATATGTTCT 58.248 29.630 0.00 0.00 0.00 3.01
375 427 9.027129 CATGCCTGAAATTGTTAATATGTTCTG 57.973 33.333 0.00 0.00 0.00 3.02
376 428 8.347004 TGCCTGAAATTGTTAATATGTTCTGA 57.653 30.769 0.00 0.00 0.00 3.27
377 429 8.801299 TGCCTGAAATTGTTAATATGTTCTGAA 58.199 29.630 0.00 0.00 0.00 3.02
378 430 9.294030 GCCTGAAATTGTTAATATGTTCTGAAG 57.706 33.333 0.00 0.00 0.00 3.02
379 431 9.294030 CCTGAAATTGTTAATATGTTCTGAAGC 57.706 33.333 0.00 0.00 0.00 3.86
380 432 9.294030 CTGAAATTGTTAATATGTTCTGAAGCC 57.706 33.333 0.00 0.00 0.00 4.35
381 433 7.967854 TGAAATTGTTAATATGTTCTGAAGCCG 59.032 33.333 0.00 0.00 0.00 5.52
382 434 4.875544 TGTTAATATGTTCTGAAGCCGC 57.124 40.909 0.00 0.00 0.00 6.53
383 435 3.625764 TGTTAATATGTTCTGAAGCCGCC 59.374 43.478 0.00 0.00 0.00 6.13
384 436 2.717639 AATATGTTCTGAAGCCGCCT 57.282 45.000 0.00 0.00 0.00 5.52
385 437 2.717639 ATATGTTCTGAAGCCGCCTT 57.282 45.000 0.00 0.00 0.00 4.35
386 438 3.838244 ATATGTTCTGAAGCCGCCTTA 57.162 42.857 0.00 0.00 0.00 2.69
387 439 2.489938 ATGTTCTGAAGCCGCCTTAA 57.510 45.000 0.00 0.00 0.00 1.85
388 440 2.489938 TGTTCTGAAGCCGCCTTAAT 57.510 45.000 0.00 0.00 0.00 1.40
389 441 2.790433 TGTTCTGAAGCCGCCTTAATT 58.210 42.857 0.00 0.00 0.00 1.40
390 442 2.747446 TGTTCTGAAGCCGCCTTAATTC 59.253 45.455 0.00 0.00 0.00 2.17
391 443 3.010420 GTTCTGAAGCCGCCTTAATTCT 58.990 45.455 0.00 0.00 0.00 2.40
392 444 3.350219 TCTGAAGCCGCCTTAATTCTT 57.650 42.857 0.00 0.00 0.00 2.52
393 445 3.009723 TCTGAAGCCGCCTTAATTCTTG 58.990 45.455 0.00 0.00 0.00 3.02
394 446 2.749621 CTGAAGCCGCCTTAATTCTTGT 59.250 45.455 0.00 0.00 0.00 3.16
395 447 3.938963 CTGAAGCCGCCTTAATTCTTGTA 59.061 43.478 0.00 0.00 0.00 2.41
396 448 4.523083 TGAAGCCGCCTTAATTCTTGTAT 58.477 39.130 0.00 0.00 0.00 2.29
397 449 5.676552 TGAAGCCGCCTTAATTCTTGTATA 58.323 37.500 0.00 0.00 0.00 1.47
398 450 5.526111 TGAAGCCGCCTTAATTCTTGTATAC 59.474 40.000 0.00 0.00 0.00 1.47
399 451 4.386711 AGCCGCCTTAATTCTTGTATACC 58.613 43.478 0.00 0.00 0.00 2.73
400 452 3.185797 GCCGCCTTAATTCTTGTATACCG 59.814 47.826 0.00 0.00 0.00 4.02
401 453 4.624015 CCGCCTTAATTCTTGTATACCGA 58.376 43.478 0.00 0.00 0.00 4.69
402 454 4.684703 CCGCCTTAATTCTTGTATACCGAG 59.315 45.833 0.00 0.00 0.00 4.63
403 455 4.684703 CGCCTTAATTCTTGTATACCGAGG 59.315 45.833 0.00 0.00 0.00 4.63
404 456 4.995487 GCCTTAATTCTTGTATACCGAGGG 59.005 45.833 0.00 0.00 0.00 4.30
405 457 5.221581 GCCTTAATTCTTGTATACCGAGGGA 60.222 44.000 0.00 0.00 0.00 4.20
406 458 6.687139 GCCTTAATTCTTGTATACCGAGGGAA 60.687 42.308 0.00 0.00 0.00 3.97
407 459 7.450903 CCTTAATTCTTGTATACCGAGGGAAT 58.549 38.462 0.00 1.22 0.00 3.01
408 460 8.591072 CCTTAATTCTTGTATACCGAGGGAATA 58.409 37.037 0.00 0.00 0.00 1.75
409 461 9.420551 CTTAATTCTTGTATACCGAGGGAATAC 57.579 37.037 0.00 8.89 0.00 1.89
410 462 5.796424 TTCTTGTATACCGAGGGAATACC 57.204 43.478 0.00 0.00 40.67 2.73
411 463 4.806892 TCTTGTATACCGAGGGAATACCA 58.193 43.478 0.00 3.81 43.89 3.25
412 464 5.399991 TCTTGTATACCGAGGGAATACCAT 58.600 41.667 0.00 0.00 43.89 3.55
413 465 5.245301 TCTTGTATACCGAGGGAATACCATG 59.755 44.000 0.00 0.00 43.89 3.66
414 466 4.743124 TGTATACCGAGGGAATACCATGA 58.257 43.478 0.00 0.00 43.89 3.07
415 467 5.338632 TGTATACCGAGGGAATACCATGAT 58.661 41.667 0.00 0.00 43.89 2.45
416 468 4.826274 ATACCGAGGGAATACCATGATG 57.174 45.455 0.00 0.00 43.89 3.07
417 469 1.699634 ACCGAGGGAATACCATGATGG 59.300 52.381 10.53 10.53 45.02 3.51
418 470 1.003580 CCGAGGGAATACCATGATGGG 59.996 57.143 17.04 0.00 43.37 4.00
419 471 1.611673 CGAGGGAATACCATGATGGGC 60.612 57.143 17.04 2.03 43.37 5.36
420 472 1.707427 GAGGGAATACCATGATGGGCT 59.293 52.381 17.04 0.00 43.37 5.19
421 473 1.426598 AGGGAATACCATGATGGGCTG 59.573 52.381 17.04 0.00 43.37 4.85
422 474 1.145738 GGGAATACCATGATGGGCTGT 59.854 52.381 17.04 0.00 43.37 4.40
423 475 2.375174 GGGAATACCATGATGGGCTGTA 59.625 50.000 17.04 0.00 43.37 2.74
424 476 3.181434 GGGAATACCATGATGGGCTGTAA 60.181 47.826 17.04 0.00 43.37 2.41
425 477 4.469657 GGAATACCATGATGGGCTGTAAA 58.530 43.478 17.04 0.00 43.37 2.01
426 478 4.278419 GGAATACCATGATGGGCTGTAAAC 59.722 45.833 17.04 0.00 43.37 2.01
427 479 2.897271 ACCATGATGGGCTGTAAACA 57.103 45.000 17.04 0.00 43.37 2.83
428 480 3.168035 ACCATGATGGGCTGTAAACAA 57.832 42.857 17.04 0.00 43.37 2.83
429 481 3.505386 ACCATGATGGGCTGTAAACAAA 58.495 40.909 17.04 0.00 43.37 2.83
430 482 4.095946 ACCATGATGGGCTGTAAACAAAT 58.904 39.130 17.04 0.00 43.37 2.32
431 483 5.268387 ACCATGATGGGCTGTAAACAAATA 58.732 37.500 17.04 0.00 43.37 1.40
432 484 5.127031 ACCATGATGGGCTGTAAACAAATAC 59.873 40.000 17.04 0.00 43.37 1.89
433 485 5.360714 CCATGATGGGCTGTAAACAAATACT 59.639 40.000 2.79 0.00 32.67 2.12
434 486 6.460123 CCATGATGGGCTGTAAACAAATACTC 60.460 42.308 2.79 0.00 32.67 2.59
435 487 4.947388 TGATGGGCTGTAAACAAATACTCC 59.053 41.667 0.00 0.00 0.00 3.85
436 488 3.692690 TGGGCTGTAAACAAATACTCCC 58.307 45.455 0.00 0.00 38.56 4.30
437 489 3.332485 TGGGCTGTAAACAAATACTCCCT 59.668 43.478 12.86 0.00 38.72 4.20
477 529 5.456822 GCTTTTCAACTGAATGTTCACAGAC 59.543 40.000 0.00 0.00 36.63 3.51
482 534 7.189693 TCAACTGAATGTTCACAGACAATAC 57.810 36.000 0.00 0.00 36.63 1.89
654 709 1.336755 GCCATGTTTTCGACACACCTT 59.663 47.619 0.00 0.00 42.04 3.50
655 710 2.858260 GCCATGTTTTCGACACACCTTG 60.858 50.000 0.00 0.00 42.04 3.61
656 711 2.616376 CCATGTTTTCGACACACCTTGA 59.384 45.455 0.00 0.00 42.04 3.02
657 712 3.066064 CCATGTTTTCGACACACCTTGAA 59.934 43.478 0.00 0.00 42.04 2.69
658 713 4.261572 CCATGTTTTCGACACACCTTGAAT 60.262 41.667 0.00 0.00 42.04 2.57
659 714 4.545823 TGTTTTCGACACACCTTGAATC 57.454 40.909 0.00 0.00 32.00 2.52
660 715 4.196193 TGTTTTCGACACACCTTGAATCT 58.804 39.130 0.00 0.00 32.00 2.40
661 716 4.035091 TGTTTTCGACACACCTTGAATCTG 59.965 41.667 0.00 0.00 32.00 2.90
662 717 2.455674 TCGACACACCTTGAATCTGG 57.544 50.000 0.00 0.00 0.00 3.86
663 718 1.967779 TCGACACACCTTGAATCTGGA 59.032 47.619 0.48 0.00 0.00 3.86
664 719 2.367241 TCGACACACCTTGAATCTGGAA 59.633 45.455 0.48 0.00 0.00 3.53
665 720 2.480419 CGACACACCTTGAATCTGGAAC 59.520 50.000 0.48 0.00 0.00 3.62
666 721 2.814336 GACACACCTTGAATCTGGAACC 59.186 50.000 0.48 0.00 0.00 3.62
667 722 2.162681 CACACCTTGAATCTGGAACCC 58.837 52.381 0.48 0.00 0.00 4.11
682 737 0.251165 AACCCATTGTTGGCTACGCT 60.251 50.000 0.00 0.00 42.15 5.07
1060 1172 0.324943 GCAGAGGGTGGAAGCACTTA 59.675 55.000 0.00 0.00 34.77 2.24
1099 1211 3.569701 GGTGTCAGCCAAAGAAGATCAAA 59.430 43.478 0.00 0.00 0.00 2.69
1101 1213 5.218139 GTGTCAGCCAAAGAAGATCAAAAG 58.782 41.667 0.00 0.00 0.00 2.27
1476 5560 6.063640 TGATGATGTCTTCTGTTTTGTGTG 57.936 37.500 0.00 0.00 0.00 3.82
1483 5567 3.193267 TCTTCTGTTTTGTGTGCTTTGCT 59.807 39.130 0.00 0.00 0.00 3.91
1612 6178 6.748333 TGCATTCTTCTCTTACATTTCAGG 57.252 37.500 0.00 0.00 0.00 3.86
1670 6238 8.589335 TGAGATTATTTTTAGACATCGGTAGC 57.411 34.615 0.00 0.00 0.00 3.58
1739 6383 7.164122 TCTATCATCTAAGCCAAGGCATTAAG 58.836 38.462 14.40 4.93 44.88 1.85
1748 6393 6.705863 AGCCAAGGCATTAAGAAGATTAAG 57.294 37.500 14.40 0.00 44.88 1.85
1836 6482 8.657074 AAAATATTGCAATGACATCAATCCAG 57.343 30.769 22.27 0.00 33.13 3.86
1993 6654 4.232221 CTGTTTGCAGCTCCTAATGTTTG 58.768 43.478 0.00 0.00 35.77 2.93
2003 6675 5.470098 AGCTCCTAATGTTTGTGTGTTAGTG 59.530 40.000 0.00 0.00 0.00 2.74
2015 6687 8.395633 GTTTGTGTGTTAGTGAAGTAGTTTGAT 58.604 33.333 0.00 0.00 0.00 2.57
2057 6729 7.174253 ACGGAAATTGTGCTTCTCTTAATGTTA 59.826 33.333 0.00 0.00 0.00 2.41
2085 6757 0.819582 ATTGCCATTCTTCCCGCTTG 59.180 50.000 0.00 0.00 0.00 4.01
2104 6776 4.797349 GCTTGCACTTGAGAAATTGCTATC 59.203 41.667 0.00 0.00 35.91 2.08
2305 8010 7.332678 TCATGTTATAGCACAGTATGATCATGC 59.667 37.037 18.72 16.94 39.69 4.06
2351 8063 6.526674 GGTAATGCCTACAAAACAAAAGATCG 59.473 38.462 0.00 0.00 31.45 3.69
2358 8070 6.695278 CCTACAAAACAAAAGATCGAAAGCAA 59.305 34.615 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.566545 TTGCAGTGTTATGTTTCCTGTG 57.433 40.909 0.00 0.00 0.00 3.66
44 45 1.061887 GCGTGACGTTTGCAGTGTT 59.938 52.632 6.91 0.00 0.00 3.32
73 74 3.325716 TGGGTTGACTACTTACTGGGTTC 59.674 47.826 0.00 0.00 0.00 3.62
82 83 2.557317 CGTGTGTTGGGTTGACTACTT 58.443 47.619 0.00 0.00 0.00 2.24
111 112 1.958579 TGTTTGCAAGCTGAAGCAGAT 59.041 42.857 14.67 0.00 45.16 2.90
113 114 2.058798 CATGTTTGCAAGCTGAAGCAG 58.941 47.619 14.67 0.00 45.16 4.24
121 122 1.535462 AGGTACGTCATGTTTGCAAGC 59.465 47.619 6.31 6.31 0.00 4.01
205 206 5.768164 GGGAGTATTTGTTATGGGTACATGG 59.232 44.000 0.00 0.00 37.97 3.66
316 368 0.968405 GCCCATTCTTGCCTTGTGAA 59.032 50.000 0.00 0.00 0.00 3.18
317 369 0.112995 AGCCCATTCTTGCCTTGTGA 59.887 50.000 0.00 0.00 0.00 3.58
322 374 2.171003 GTTTACAGCCCATTCTTGCCT 58.829 47.619 0.00 0.00 0.00 4.75
323 375 1.892474 TGTTTACAGCCCATTCTTGCC 59.108 47.619 0.00 0.00 0.00 4.52
324 376 3.056607 ACATGTTTACAGCCCATTCTTGC 60.057 43.478 0.00 0.00 0.00 4.01
325 377 4.218200 TCACATGTTTACAGCCCATTCTTG 59.782 41.667 0.00 0.00 0.00 3.02
327 379 3.758554 GTCACATGTTTACAGCCCATTCT 59.241 43.478 0.00 0.00 0.00 2.40
328 380 3.505680 TGTCACATGTTTACAGCCCATTC 59.494 43.478 0.00 0.00 0.00 2.67
329 381 3.495331 TGTCACATGTTTACAGCCCATT 58.505 40.909 0.00 0.00 0.00 3.16
330 382 3.153369 TGTCACATGTTTACAGCCCAT 57.847 42.857 0.00 0.00 0.00 4.00
331 383 2.647683 TGTCACATGTTTACAGCCCA 57.352 45.000 0.00 0.00 0.00 5.36
332 384 2.415893 GCATGTCACATGTTTACAGCCC 60.416 50.000 19.13 0.00 0.00 5.19
333 385 2.415893 GGCATGTCACATGTTTACAGCC 60.416 50.000 19.13 22.00 33.49 4.85
334 386 2.489329 AGGCATGTCACATGTTTACAGC 59.511 45.455 19.13 15.40 0.00 4.40
335 387 3.752747 TCAGGCATGTCACATGTTTACAG 59.247 43.478 19.13 5.10 0.00 2.74
336 388 3.749226 TCAGGCATGTCACATGTTTACA 58.251 40.909 19.13 12.03 0.00 2.41
337 389 4.764679 TTCAGGCATGTCACATGTTTAC 57.235 40.909 19.13 7.57 0.00 2.01
338 390 5.981088 ATTTCAGGCATGTCACATGTTTA 57.019 34.783 19.13 0.29 0.00 2.01
339 391 4.877378 ATTTCAGGCATGTCACATGTTT 57.123 36.364 19.13 5.08 0.00 2.83
340 392 4.039488 ACAATTTCAGGCATGTCACATGTT 59.961 37.500 19.13 5.44 0.00 2.71
341 393 3.575256 ACAATTTCAGGCATGTCACATGT 59.425 39.130 19.13 0.00 0.00 3.21
342 394 4.182693 ACAATTTCAGGCATGTCACATG 57.817 40.909 13.93 13.93 0.00 3.21
343 395 4.877378 AACAATTTCAGGCATGTCACAT 57.123 36.364 0.00 0.00 0.00 3.21
344 396 5.781210 TTAACAATTTCAGGCATGTCACA 57.219 34.783 0.00 0.00 0.00 3.58
345 397 7.975616 ACATATTAACAATTTCAGGCATGTCAC 59.024 33.333 0.00 0.00 0.00 3.67
346 398 8.065473 ACATATTAACAATTTCAGGCATGTCA 57.935 30.769 0.00 0.00 0.00 3.58
347 399 8.931385 AACATATTAACAATTTCAGGCATGTC 57.069 30.769 0.00 0.00 0.00 3.06
348 400 8.752187 AGAACATATTAACAATTTCAGGCATGT 58.248 29.630 0.00 0.00 0.00 3.21
349 401 9.027129 CAGAACATATTAACAATTTCAGGCATG 57.973 33.333 0.00 0.00 0.00 4.06
350 402 8.970020 TCAGAACATATTAACAATTTCAGGCAT 58.030 29.630 0.00 0.00 0.00 4.40
351 403 8.347004 TCAGAACATATTAACAATTTCAGGCA 57.653 30.769 0.00 0.00 0.00 4.75
352 404 9.294030 CTTCAGAACATATTAACAATTTCAGGC 57.706 33.333 0.00 0.00 0.00 4.85
353 405 9.294030 GCTTCAGAACATATTAACAATTTCAGG 57.706 33.333 0.00 0.00 0.00 3.86
354 406 9.294030 GGCTTCAGAACATATTAACAATTTCAG 57.706 33.333 0.00 0.00 0.00 3.02
355 407 7.967854 CGGCTTCAGAACATATTAACAATTTCA 59.032 33.333 0.00 0.00 0.00 2.69
356 408 7.044052 GCGGCTTCAGAACATATTAACAATTTC 60.044 37.037 0.00 0.00 0.00 2.17
357 409 6.751888 GCGGCTTCAGAACATATTAACAATTT 59.248 34.615 0.00 0.00 0.00 1.82
358 410 6.265577 GCGGCTTCAGAACATATTAACAATT 58.734 36.000 0.00 0.00 0.00 2.32
359 411 5.221048 GGCGGCTTCAGAACATATTAACAAT 60.221 40.000 0.00 0.00 0.00 2.71
360 412 4.095782 GGCGGCTTCAGAACATATTAACAA 59.904 41.667 0.00 0.00 0.00 2.83
361 413 3.625764 GGCGGCTTCAGAACATATTAACA 59.374 43.478 0.00 0.00 0.00 2.41
362 414 3.877508 AGGCGGCTTCAGAACATATTAAC 59.122 43.478 5.25 0.00 0.00 2.01
363 415 4.150897 AGGCGGCTTCAGAACATATTAA 57.849 40.909 5.25 0.00 0.00 1.40
364 416 3.838244 AGGCGGCTTCAGAACATATTA 57.162 42.857 5.25 0.00 0.00 0.98
365 417 2.717639 AGGCGGCTTCAGAACATATT 57.282 45.000 5.25 0.00 0.00 1.28
366 418 2.717639 AAGGCGGCTTCAGAACATAT 57.282 45.000 19.90 0.00 0.00 1.78
367 419 3.620427 TTAAGGCGGCTTCAGAACATA 57.380 42.857 29.05 4.81 0.00 2.29
368 420 2.489938 TTAAGGCGGCTTCAGAACAT 57.510 45.000 29.05 3.85 0.00 2.71
369 421 2.489938 ATTAAGGCGGCTTCAGAACA 57.510 45.000 29.05 6.50 0.00 3.18
370 422 3.010420 AGAATTAAGGCGGCTTCAGAAC 58.990 45.455 29.05 15.96 0.00 3.01
371 423 3.350219 AGAATTAAGGCGGCTTCAGAA 57.650 42.857 29.05 17.41 0.00 3.02
372 424 3.009723 CAAGAATTAAGGCGGCTTCAGA 58.990 45.455 29.05 15.54 0.00 3.27
373 425 2.749621 ACAAGAATTAAGGCGGCTTCAG 59.250 45.455 29.05 12.57 0.00 3.02
374 426 2.790433 ACAAGAATTAAGGCGGCTTCA 58.210 42.857 29.05 18.51 0.00 3.02
375 427 5.049612 GGTATACAAGAATTAAGGCGGCTTC 60.050 44.000 29.05 14.13 0.00 3.86
376 428 4.820173 GGTATACAAGAATTAAGGCGGCTT 59.180 41.667 28.23 28.23 0.00 4.35
377 429 4.386711 GGTATACAAGAATTAAGGCGGCT 58.613 43.478 5.25 5.25 0.00 5.52
378 430 3.185797 CGGTATACAAGAATTAAGGCGGC 59.814 47.826 0.00 0.00 0.00 6.53
379 431 4.624015 TCGGTATACAAGAATTAAGGCGG 58.376 43.478 5.01 0.00 0.00 6.13
380 432 4.684703 CCTCGGTATACAAGAATTAAGGCG 59.315 45.833 5.01 0.00 0.00 5.52
381 433 4.995487 CCCTCGGTATACAAGAATTAAGGC 59.005 45.833 5.01 0.00 0.00 4.35
382 434 6.415206 TCCCTCGGTATACAAGAATTAAGG 57.585 41.667 5.01 1.44 0.00 2.69
383 435 9.420551 GTATTCCCTCGGTATACAAGAATTAAG 57.579 37.037 5.01 0.00 36.43 1.85
384 436 8.370182 GGTATTCCCTCGGTATACAAGAATTAA 58.630 37.037 5.01 0.00 37.58 1.40
385 437 7.510001 TGGTATTCCCTCGGTATACAAGAATTA 59.490 37.037 5.01 0.00 37.58 1.40
386 438 6.328148 TGGTATTCCCTCGGTATACAAGAATT 59.672 38.462 5.01 0.00 37.58 2.17
387 439 5.842328 TGGTATTCCCTCGGTATACAAGAAT 59.158 40.000 5.01 7.53 37.58 2.40
388 440 5.210430 TGGTATTCCCTCGGTATACAAGAA 58.790 41.667 5.01 0.60 37.58 2.52
389 441 4.806892 TGGTATTCCCTCGGTATACAAGA 58.193 43.478 5.01 2.83 37.58 3.02
390 442 5.245301 TCATGGTATTCCCTCGGTATACAAG 59.755 44.000 5.01 1.52 37.58 3.16
391 443 5.149239 TCATGGTATTCCCTCGGTATACAA 58.851 41.667 5.01 0.00 37.58 2.41
392 444 4.743124 TCATGGTATTCCCTCGGTATACA 58.257 43.478 5.01 0.00 37.58 2.29
393 445 5.395324 CCATCATGGTATTCCCTCGGTATAC 60.395 48.000 0.00 0.00 35.92 1.47
394 446 4.714802 CCATCATGGTATTCCCTCGGTATA 59.285 45.833 0.00 0.00 31.35 1.47
395 447 3.519510 CCATCATGGTATTCCCTCGGTAT 59.480 47.826 0.00 0.00 31.35 2.73
396 448 2.903784 CCATCATGGTATTCCCTCGGTA 59.096 50.000 0.00 0.00 31.35 4.02
397 449 1.699634 CCATCATGGTATTCCCTCGGT 59.300 52.381 0.00 0.00 31.35 4.69
398 450 1.003580 CCCATCATGGTATTCCCTCGG 59.996 57.143 2.07 0.00 35.17 4.63
399 451 1.611673 GCCCATCATGGTATTCCCTCG 60.612 57.143 2.07 0.00 35.17 4.63
400 452 1.707427 AGCCCATCATGGTATTCCCTC 59.293 52.381 2.07 0.00 35.17 4.30
401 453 1.426598 CAGCCCATCATGGTATTCCCT 59.573 52.381 2.07 0.00 35.17 4.20
402 454 1.145738 ACAGCCCATCATGGTATTCCC 59.854 52.381 2.07 0.00 35.17 3.97
403 455 2.664402 ACAGCCCATCATGGTATTCC 57.336 50.000 2.07 0.00 35.17 3.01
404 456 4.887071 TGTTTACAGCCCATCATGGTATTC 59.113 41.667 2.07 0.00 35.17 1.75
405 457 4.865905 TGTTTACAGCCCATCATGGTATT 58.134 39.130 2.07 0.00 35.17 1.89
406 458 4.518278 TGTTTACAGCCCATCATGGTAT 57.482 40.909 2.07 0.00 35.17 2.73
407 459 4.308526 TTGTTTACAGCCCATCATGGTA 57.691 40.909 2.07 0.00 35.17 3.25
408 460 2.897271 TGTTTACAGCCCATCATGGT 57.103 45.000 2.07 0.00 35.17 3.55
409 461 4.741321 ATTTGTTTACAGCCCATCATGG 57.259 40.909 0.00 0.00 37.25 3.66
410 462 6.455360 AGTATTTGTTTACAGCCCATCATG 57.545 37.500 0.00 0.00 0.00 3.07
411 463 5.594317 GGAGTATTTGTTTACAGCCCATCAT 59.406 40.000 0.00 0.00 0.00 2.45
412 464 4.947388 GGAGTATTTGTTTACAGCCCATCA 59.053 41.667 0.00 0.00 0.00 3.07
413 465 4.338400 GGGAGTATTTGTTTACAGCCCATC 59.662 45.833 0.00 0.00 38.16 3.51
414 466 4.017499 AGGGAGTATTTGTTTACAGCCCAT 60.017 41.667 0.00 0.00 39.53 4.00
415 467 3.332485 AGGGAGTATTTGTTTACAGCCCA 59.668 43.478 0.00 0.00 39.53 5.36
416 468 3.945921 GAGGGAGTATTTGTTTACAGCCC 59.054 47.826 0.00 0.00 38.36 5.19
417 469 4.844884 AGAGGGAGTATTTGTTTACAGCC 58.155 43.478 0.00 0.00 0.00 4.85
418 470 6.757478 GTCTAGAGGGAGTATTTGTTTACAGC 59.243 42.308 0.00 0.00 0.00 4.40
419 471 7.266400 GGTCTAGAGGGAGTATTTGTTTACAG 58.734 42.308 0.00 0.00 0.00 2.74
420 472 6.127535 CGGTCTAGAGGGAGTATTTGTTTACA 60.128 42.308 0.00 0.00 0.00 2.41
421 473 6.096001 TCGGTCTAGAGGGAGTATTTGTTTAC 59.904 42.308 0.00 0.00 0.00 2.01
422 474 6.189859 TCGGTCTAGAGGGAGTATTTGTTTA 58.810 40.000 0.00 0.00 0.00 2.01
423 475 5.021458 TCGGTCTAGAGGGAGTATTTGTTT 58.979 41.667 0.00 0.00 0.00 2.83
424 476 4.607239 TCGGTCTAGAGGGAGTATTTGTT 58.393 43.478 0.00 0.00 0.00 2.83
425 477 4.208746 CTCGGTCTAGAGGGAGTATTTGT 58.791 47.826 10.50 0.00 34.74 2.83
426 478 3.004944 GCTCGGTCTAGAGGGAGTATTTG 59.995 52.174 17.06 0.00 38.63 2.32
427 479 3.224269 GCTCGGTCTAGAGGGAGTATTT 58.776 50.000 17.06 0.00 38.63 1.40
428 480 2.175069 TGCTCGGTCTAGAGGGAGTATT 59.825 50.000 17.06 0.00 38.63 1.89
429 481 1.775459 TGCTCGGTCTAGAGGGAGTAT 59.225 52.381 17.06 0.00 38.63 2.12
430 482 1.134159 GTGCTCGGTCTAGAGGGAGTA 60.134 57.143 17.06 12.17 38.63 2.59
431 483 0.394625 GTGCTCGGTCTAGAGGGAGT 60.395 60.000 17.06 0.00 38.63 3.85
432 484 1.440938 CGTGCTCGGTCTAGAGGGAG 61.441 65.000 13.30 13.30 38.63 4.30
433 485 1.451567 CGTGCTCGGTCTAGAGGGA 60.452 63.158 0.00 0.00 38.63 4.20
434 486 1.440938 CTCGTGCTCGGTCTAGAGGG 61.441 65.000 8.49 0.00 38.63 4.30
435 487 2.018544 CTCGTGCTCGGTCTAGAGG 58.981 63.158 8.49 0.00 38.63 3.69
436 488 1.353804 GCTCGTGCTCGGTCTAGAG 59.646 63.158 8.49 0.00 41.03 2.43
437 489 3.499050 GCTCGTGCTCGGTCTAGA 58.501 61.111 8.49 0.00 37.69 2.43
477 529 5.761165 TCATGCACCTGATCAATGTATTG 57.239 39.130 7.29 0.00 39.10 1.90
482 534 4.443913 TTGTTCATGCACCTGATCAATG 57.556 40.909 8.92 0.00 32.58 2.82
654 709 3.164268 CCAACAATGGGTTCCAGATTCA 58.836 45.455 0.00 0.00 43.51 2.57
655 710 3.874392 CCAACAATGGGTTCCAGATTC 57.126 47.619 0.00 0.00 43.51 2.52
1060 1172 1.684049 CCGTGAGCCTCTTCCTCCT 60.684 63.158 0.00 0.00 0.00 3.69
1246 1358 0.745845 GGCAGTGTGATCTCGCCATT 60.746 55.000 4.76 0.00 42.50 3.16
1330 5388 0.727970 GAGCTCAGCAATGCACTCTG 59.272 55.000 9.40 0.00 0.00 3.35
1476 5560 6.763610 ACTATCTTACACTATCCAAGCAAAGC 59.236 38.462 0.00 0.00 0.00 3.51
1483 5567 8.630917 GCTGTCTAACTATCTTACACTATCCAA 58.369 37.037 0.00 0.00 0.00 3.53
1572 5686 1.731433 GCATACTGCTGGTGGCCATG 61.731 60.000 9.72 3.54 40.96 3.66
1647 6213 7.873505 GGAGCTACCGATGTCTAAAAATAATCT 59.126 37.037 0.00 0.00 0.00 2.40
1670 6238 0.464870 CTCTGTGGAGCAGGATGGAG 59.535 60.000 0.00 0.00 45.08 3.86
1739 6383 8.993121 TCACTGATTCACAACTTCTTAATCTTC 58.007 33.333 0.00 0.00 0.00 2.87
1748 6393 6.145535 GGTCATTTCACTGATTCACAACTTC 58.854 40.000 0.00 0.00 0.00 3.01
1873 6522 2.160205 GTGGAGTAAACCCTGCTTTCC 58.840 52.381 0.00 0.00 0.00 3.13
1931 6592 5.851177 CAGTTAACCATCACTTGCTTTTACG 59.149 40.000 0.88 0.00 0.00 3.18
2015 6687 8.711170 ACAATTTCCGTTTCCCTTCTATCTATA 58.289 33.333 0.00 0.00 0.00 1.31
2032 6704 5.942872 ACATTAAGAGAAGCACAATTTCCG 58.057 37.500 0.00 0.00 0.00 4.30
2057 6729 5.677567 GGGAAGAATGGCAATGATTTCATT 58.322 37.500 0.00 0.00 46.62 2.57
2070 6742 0.962356 AGTGCAAGCGGGAAGAATGG 60.962 55.000 0.00 0.00 0.00 3.16
2104 6776 5.636543 CCTTGCAAGATTGAAAAGGCTTTAG 59.363 40.000 28.05 2.11 37.01 1.85
2132 6804 5.108385 ACAGGTTTCTGCTTAATTCGTTG 57.892 39.130 0.00 0.00 44.59 4.10
2140 6812 4.394729 CTGGGTTAACAGGTTTCTGCTTA 58.605 43.478 8.10 0.00 44.59 3.09
2141 6813 3.222603 CTGGGTTAACAGGTTTCTGCTT 58.777 45.455 8.10 0.00 44.59 3.91
2247 7465 8.270137 TGGCATATAAAAGAGGGTATCTGTTA 57.730 34.615 0.00 0.00 41.13 2.41
2305 8010 5.321927 ACCCCAAAAGTAGATAAACACCAG 58.678 41.667 0.00 0.00 0.00 4.00
2307 8012 7.629866 GCATTACCCCAAAAGTAGATAAACACC 60.630 40.741 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.