Multiple sequence alignment - TraesCS1D01G453200

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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 TraesCS1D01G453200 chr1D 100.000 2486 0 0 1 2486 494168119 494170604 0.000000e+00 4591.0
1 TraesCS1D01G453200 chr1D 88.979 617 43 6 930 1545 494328036 494328628 0.000000e+00 739.0
2 TraesCS1D01G453200 chr1D 87.702 618 67 6 932 1545 494424138 494424750 0.000000e+00 712.0
3 TraesCS1D01G453200 chr1D 84.520 562 71 6 936 1485 494306795 494307352 2.170000e-150 542.0
4 TraesCS1D01G453200 chr1D 82.456 342 40 11 20 345 494423139 494423476 5.230000e-72 281.0
5 TraesCS1D01G453200 chr1D 95.294 170 8 0 347 516 180851574 180851743 1.130000e-68 270.0
6 TraesCS1D01G453200 chr1D 89.806 206 11 7 151 348 494327251 494327454 3.170000e-64 255.0
7 TraesCS1D01G453200 chr1D 78.571 308 34 18 510 811 494327453 494327734 9.140000e-40 174.0
8 TraesCS1D01G453200 chr1D 90.123 81 6 2 1598 1676 493781965 493781885 1.220000e-18 104.0
9 TraesCS1D01G453200 chr1D 92.453 53 4 0 572 624 494423588 494423640 2.650000e-10 76.8
10 TraesCS1D01G453200 chr1A 93.726 1036 41 12 932 1963 592852015 592853030 0.000000e+00 1531.0
11 TraesCS1D01G453200 chr1A 88.942 624 55 12 928 1545 593214735 593215350 0.000000e+00 758.0
12 TraesCS1D01G453200 chr1A 88.817 617 45 9 930 1545 592977954 592978547 0.000000e+00 736.0
13 TraesCS1D01G453200 chr1A 86.859 624 64 12 928 1545 593217834 593218445 0.000000e+00 682.0
14 TraesCS1D01G453200 chr1A 90.526 380 16 1 2107 2486 592853030 592853389 3.720000e-133 484.0
15 TraesCS1D01G453200 chr1A 94.643 280 14 1 655 934 592851610 592851888 1.370000e-117 433.0
16 TraesCS1D01G453200 chr1A 85.948 306 29 10 47 348 592977047 592977342 5.160000e-82 315.0
17 TraesCS1D01G453200 chr1A 88.760 258 14 8 32 276 592851287 592851542 4.020000e-78 302.0
18 TraesCS1D01G453200 chr1A 82.544 338 46 10 20 348 593213771 593214104 4.050000e-73 285.0
19 TraesCS1D01G453200 chr1A 79.573 328 28 14 510 811 592977341 592977655 5.420000e-47 198.0
20 TraesCS1D01G453200 chr1A 85.714 133 18 1 2354 2486 387371951 387372082 3.330000e-29 139.0
21 TraesCS1D01G453200 chr1A 80.741 135 9 6 507 624 593214100 593214234 3.410000e-14 89.8
22 TraesCS1D01G453200 chr1B 91.603 917 47 9 932 1845 687423104 687423993 0.000000e+00 1240.0
23 TraesCS1D01G453200 chr1B 87.097 620 62 13 932 1545 687650957 687651564 0.000000e+00 686.0
24 TraesCS1D01G453200 chr1B 86.645 614 33 13 1876 2482 687423994 687424565 3.490000e-178 634.0
25 TraesCS1D01G453200 chr1B 89.943 348 18 12 9 348 687422146 687422484 1.370000e-117 433.0
26 TraesCS1D01G453200 chr1B 90.164 244 16 4 557 797 687422571 687422809 6.680000e-81 311.0
27 TraesCS1D01G453200 chr1B 81.471 340 47 12 20 348 687649997 687650331 5.270000e-67 265.0
28 TraesCS1D01G453200 chr1B 91.411 163 11 2 774 934 687422815 687422976 1.160000e-53 220.0
29 TraesCS1D01G453200 chr1B 87.218 133 16 1 2354 2486 417282375 417282506 1.540000e-32 150.0
30 TraesCS1D01G453200 chr1B 100.000 46 0 0 510 555 687422483 687422528 4.410000e-13 86.1
31 TraesCS1D01G453200 chr1B 92.727 55 4 0 1491 1545 687517610 687517664 2.050000e-11 80.5
32 TraesCS1D01G453200 chrUn 89.286 560 37 4 930 1489 358967912 358967376 0.000000e+00 680.0
33 TraesCS1D01G453200 chrUn 84.164 562 73 5 936 1485 290638880 290638323 4.710000e-147 531.0
34 TraesCS1D01G453200 chrUn 84.164 562 73 5 936 1485 290644605 290644048 4.710000e-147 531.0
35 TraesCS1D01G453200 chrUn 86.557 305 29 5 54 348 358968829 358968527 2.380000e-85 326.0
36 TraesCS1D01G453200 chrUn 96.364 165 6 0 347 511 108810833 108810997 3.150000e-69 272.0
37 TraesCS1D01G453200 chrUn 81.685 273 29 10 549 814 358968470 358968212 9.010000e-50 207.0
38 TraesCS1D01G453200 chr7D 97.576 165 4 0 347 511 404245330 404245494 1.460000e-72 283.0
39 TraesCS1D01G453200 chr7D 94.886 176 9 0 345 520 479128258 479128433 2.440000e-70 276.0
40 TraesCS1D01G453200 chr2D 96.407 167 6 0 345 511 582102117 582101951 2.440000e-70 276.0
41 TraesCS1D01G453200 chr2D 86.047 129 15 3 2359 2486 391464800 391464674 4.310000e-28 135.0
42 TraesCS1D01G453200 chr7B 94.350 177 9 1 341 516 595442065 595441889 1.130000e-68 270.0
43 TraesCS1D01G453200 chr7B 94.152 171 10 0 345 515 393400696 393400866 6.820000e-66 261.0
44 TraesCS1D01G453200 chr3D 95.783 166 7 0 347 512 90138476 90138311 4.080000e-68 268.0
45 TraesCS1D01G453200 chr3D 76.952 269 52 7 2226 2486 157174318 157174584 7.170000e-31 145.0
46 TraesCS1D01G453200 chr2B 86.636 217 23 6 321 535 651353969 651354181 4.130000e-58 235.0
47 TraesCS1D01G453200 chr2B 85.075 134 18 2 2353 2486 463213409 463213278 4.310000e-28 135.0
48 TraesCS1D01G453200 chr2B 92.308 52 4 0 2430 2481 166404422 166404473 9.540000e-10 75.0
49 TraesCS1D01G453200 chr5D 84.324 185 26 3 2303 2486 210992858 210993040 7.070000e-41 178.0
50 TraesCS1D01G453200 chr5D 86.154 65 4 4 2233 2294 402182687 402182749 5.740000e-07 65.8
51 TraesCS1D01G453200 chr2A 81.203 133 24 1 2354 2486 117299797 117299928 3.380000e-19 106.0
52 TraesCS1D01G453200 chr5A 78.169 142 19 11 2179 2312 507962183 507962320 2.050000e-11 80.5
53 TraesCS1D01G453200 chr5A 77.519 129 19 10 2190 2316 640631575 640631455 4.440000e-08 69.4
54 TraesCS1D01G453200 chr5B 79.487 117 18 6 2192 2305 643294294 643294181 7.370000e-11 78.7
55 TraesCS1D01G453200 chr6B 92.453 53 2 2 2243 2293 618946094 618946146 9.540000e-10 75.0
56 TraesCS1D01G453200 chr4B 93.182 44 2 1 2252 2294 522499436 522499479 2.060000e-06 63.9


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 TraesCS1D01G453200 chr1D 494168119 494170604 2485 False 4591.000000 4591 100.000000 1 2486 1 chr1D.!!$F2 2485
1 TraesCS1D01G453200 chr1D 494306795 494307352 557 False 542.000000 542 84.520000 936 1485 1 chr1D.!!$F3 549
2 TraesCS1D01G453200 chr1D 494327251 494328628 1377 False 389.333333 739 85.785333 151 1545 3 chr1D.!!$F4 1394
3 TraesCS1D01G453200 chr1D 494423139 494424750 1611 False 356.600000 712 87.537000 20 1545 3 chr1D.!!$F5 1525
4 TraesCS1D01G453200 chr1A 592851287 592853389 2102 False 687.500000 1531 91.913750 32 2486 4 chr1A.!!$F2 2454
5 TraesCS1D01G453200 chr1A 593213771 593218445 4674 False 453.700000 758 84.771500 20 1545 4 chr1A.!!$F4 1525
6 TraesCS1D01G453200 chr1A 592977047 592978547 1500 False 416.333333 736 84.779333 47 1545 3 chr1A.!!$F3 1498
7 TraesCS1D01G453200 chr1B 687422146 687424565 2419 False 487.350000 1240 91.627667 9 2482 6 chr1B.!!$F3 2473
8 TraesCS1D01G453200 chr1B 687649997 687651564 1567 False 475.500000 686 84.284000 20 1545 2 chr1B.!!$F4 1525
9 TraesCS1D01G453200 chrUn 290638323 290638880 557 True 531.000000 531 84.164000 936 1485 1 chrUn.!!$R1 549
10 TraesCS1D01G453200 chrUn 290644048 290644605 557 True 531.000000 531 84.164000 936 1485 1 chrUn.!!$R2 549
11 TraesCS1D01G453200 chrUn 358967376 358968829 1453 True 404.333333 680 85.842667 54 1489 3 chrUn.!!$R3 1435

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
360 406 0.324091 TCCACTACTCCCTCCGTTCC 60.324 60.0 0.0 0.0 0.00 3.62 F
1279 1755 0.541392 TTGGATGGTCACCTCATCGG 59.459 55.0 0.0 0.0 41.24 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 1870 1.376424 AGCACCGGCACTCATGAAG 60.376 57.895 0.0 0.0 44.61 3.02 R
2381 3549 0.251297 CACCATGCCAAAGAGGGACA 60.251 55.000 0.0 0.0 42.31 4.02 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
111 115 6.974622 CGAAATATTTGATTTTCCTGGTGGAG 59.025 38.462 5.17 0.00 44.24 3.86
136 144 1.094785 AAGCGGTGCAACATGGATAC 58.905 50.000 0.98 0.00 39.98 2.24
201 216 0.476771 ACCGGCCACCCCTATAAATG 59.523 55.000 0.00 0.00 0.00 2.32
234 262 1.228003 CCGGGTACAAGCCACACAA 60.228 57.895 0.00 0.00 34.89 3.33
269 300 4.240049 GCAGCAAGCAAGAGCAAC 57.760 55.556 0.00 0.00 45.49 4.17
306 352 6.818644 TCAGTCATAAGCTCAAAGGTTCATAC 59.181 38.462 0.00 0.00 37.16 2.39
347 393 2.560981 TCTTGTCGTGCATCTTCCACTA 59.439 45.455 0.00 0.00 0.00 2.74
348 394 2.363788 TGTCGTGCATCTTCCACTAC 57.636 50.000 0.00 0.00 31.71 2.73
349 395 1.893137 TGTCGTGCATCTTCCACTACT 59.107 47.619 0.00 0.00 32.16 2.57
350 396 2.094700 TGTCGTGCATCTTCCACTACTC 60.095 50.000 0.00 0.00 32.16 2.59
351 397 1.476891 TCGTGCATCTTCCACTACTCC 59.523 52.381 0.00 0.00 0.00 3.85
352 398 1.471676 CGTGCATCTTCCACTACTCCC 60.472 57.143 0.00 0.00 0.00 4.30
353 399 1.834263 GTGCATCTTCCACTACTCCCT 59.166 52.381 0.00 0.00 0.00 4.20
354 400 2.111384 TGCATCTTCCACTACTCCCTC 58.889 52.381 0.00 0.00 0.00 4.30
355 401 1.414550 GCATCTTCCACTACTCCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
356 402 1.683917 CATCTTCCACTACTCCCTCCG 59.316 57.143 0.00 0.00 0.00 4.63
357 403 0.702902 TCTTCCACTACTCCCTCCGT 59.297 55.000 0.00 0.00 0.00 4.69
358 404 1.076677 TCTTCCACTACTCCCTCCGTT 59.923 52.381 0.00 0.00 0.00 4.44
359 405 1.477295 CTTCCACTACTCCCTCCGTTC 59.523 57.143 0.00 0.00 0.00 3.95
360 406 0.324091 TCCACTACTCCCTCCGTTCC 60.324 60.000 0.00 0.00 0.00 3.62
361 407 0.613853 CCACTACTCCCTCCGTTCCA 60.614 60.000 0.00 0.00 0.00 3.53
362 408 1.263356 CACTACTCCCTCCGTTCCAA 58.737 55.000 0.00 0.00 0.00 3.53
363 409 1.621814 CACTACTCCCTCCGTTCCAAA 59.378 52.381 0.00 0.00 0.00 3.28
364 410 2.038033 CACTACTCCCTCCGTTCCAAAA 59.962 50.000 0.00 0.00 0.00 2.44
365 411 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
366 412 4.081309 CACTACTCCCTCCGTTCCAAAATA 60.081 45.833 0.00 0.00 0.00 1.40
367 413 4.720273 ACTACTCCCTCCGTTCCAAAATAT 59.280 41.667 0.00 0.00 0.00 1.28
368 414 5.901276 ACTACTCCCTCCGTTCCAAAATATA 59.099 40.000 0.00 0.00 0.00 0.86
369 415 5.703730 ACTCCCTCCGTTCCAAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
370 416 5.681639 ACTCCCTCCGTTCCAAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
371 417 5.191124 ACTCCCTCCGTTCCAAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
372 418 5.677567 TCCCTCCGTTCCAAAATATAAGTC 58.322 41.667 0.00 0.00 0.00 3.01
373 419 5.427481 TCCCTCCGTTCCAAAATATAAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
374 420 6.069847 TCCCTCCGTTCCAAAATATAAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
375 421 6.602009 CCCTCCGTTCCAAAATATAAGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
376 422 7.771826 CCCTCCGTTCCAAAATATAAGTCTTTA 59.228 37.037 0.00 0.00 0.00 1.85
377 423 9.338622 CCTCCGTTCCAAAATATAAGTCTTTAT 57.661 33.333 0.00 0.00 34.04 1.40
405 451 9.855361 GAGATTTCAAATGAACTATCACATACG 57.145 33.333 9.37 0.00 38.69 3.06
406 452 8.830580 AGATTTCAAATGAACTATCACATACGG 58.169 33.333 9.37 0.00 38.69 4.02
407 453 8.731275 ATTTCAAATGAACTATCACATACGGA 57.269 30.769 0.00 0.00 38.69 4.69
408 454 8.731275 TTTCAAATGAACTATCACATACGGAT 57.269 30.769 0.00 0.00 38.69 4.18
409 455 7.713764 TCAAATGAACTATCACATACGGATG 57.286 36.000 5.94 5.94 38.69 3.51
411 457 8.417884 TCAAATGAACTATCACATACGGATGTA 58.582 33.333 14.23 2.61 44.82 2.29
412 458 9.208022 CAAATGAACTATCACATACGGATGTAT 57.792 33.333 14.23 10.02 44.82 2.29
419 465 9.901172 ACTATCACATACGGATGTATATAGACA 57.099 33.333 30.73 11.02 44.82 3.41
452 498 6.681777 AGTGTAAATTCACTCATTTTGCTCC 58.318 36.000 0.00 0.00 44.07 4.70
453 499 5.569059 GTGTAAATTCACTCATTTTGCTCCG 59.431 40.000 0.00 0.00 35.68 4.63
454 500 4.853924 AAATTCACTCATTTTGCTCCGT 57.146 36.364 0.00 0.00 0.00 4.69
455 501 5.957842 AAATTCACTCATTTTGCTCCGTA 57.042 34.783 0.00 0.00 0.00 4.02
456 502 6.515272 AAATTCACTCATTTTGCTCCGTAT 57.485 33.333 0.00 0.00 0.00 3.06
457 503 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
458 504 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
459 505 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
460 506 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
461 507 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
462 508 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
463 509 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
464 510 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
465 511 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
466 512 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
467 513 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
468 514 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
469 515 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
470 516 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
471 517 4.868171 GCTCCGTATGTAGTCATTTGTTGA 59.132 41.667 0.00 0.00 35.70 3.18
472 518 5.350365 GCTCCGTATGTAGTCATTTGTTGAA 59.650 40.000 0.00 0.00 35.70 2.69
473 519 6.128391 GCTCCGTATGTAGTCATTTGTTGAAA 60.128 38.462 0.00 0.00 35.70 2.69
474 520 7.414098 GCTCCGTATGTAGTCATTTGTTGAAAT 60.414 37.037 0.00 0.00 35.70 2.17
475 521 7.970384 TCCGTATGTAGTCATTTGTTGAAATC 58.030 34.615 0.00 0.00 35.70 2.17
476 522 7.822334 TCCGTATGTAGTCATTTGTTGAAATCT 59.178 33.333 0.00 0.00 35.70 2.40
477 523 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
478 524 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
482 528 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
485 531 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
486 532 9.818796 GTCATTTGTTGAAATCTCTAGAAAGAC 57.181 33.333 0.00 0.00 35.70 3.01
487 533 9.003658 TCATTTGTTGAAATCTCTAGAAAGACC 57.996 33.333 0.00 0.00 28.65 3.85
488 534 9.007901 CATTTGTTGAAATCTCTAGAAAGACCT 57.992 33.333 0.00 0.00 28.65 3.85
842 1094 3.806625 AATTTGGCTCCATGCATACAC 57.193 42.857 0.00 0.00 45.15 2.90
862 1114 4.707448 ACACAGATCGAGATTGTTAGAGGT 59.293 41.667 0.00 0.00 0.00 3.85
890 1148 4.099881 CCTAAACCATGCACTGCCAATATT 59.900 41.667 0.00 0.00 0.00 1.28
933 1397 3.935203 CCTATGAAACGTGTGCTGATCTT 59.065 43.478 0.00 0.00 0.00 2.40
1118 1586 4.324563 CCTGGCTAAGAATGGGAAAGAAGA 60.325 45.833 0.00 0.00 0.00 2.87
1188 1656 3.959495 AAGGACATGCCCATAATGACT 57.041 42.857 0.00 0.00 37.37 3.41
1279 1755 0.541392 TTGGATGGTCACCTCATCGG 59.459 55.000 0.00 0.00 41.24 4.18
1313 1797 7.517320 ACATGTTACTCCATATAGGCAATCAA 58.483 34.615 0.00 0.00 37.29 2.57
1471 1955 3.251479 TGATTCAGGAGGTCATCAACG 57.749 47.619 0.00 0.00 0.00 4.10
1472 1956 2.567169 TGATTCAGGAGGTCATCAACGT 59.433 45.455 0.00 0.00 0.00 3.99
1501 1985 1.909376 TTAGTGACGCTTGCTCGATC 58.091 50.000 0.00 0.00 0.00 3.69
1584 2069 7.234782 AGGGATATACCGTGAATGTTTGATAGA 59.765 37.037 0.00 0.00 40.11 1.98
1649 2134 8.528044 TTTAGTTTCAAGGTCATGTTAAAGGT 57.472 30.769 0.00 0.00 0.00 3.50
1730 2216 9.521841 TGGAATCAATGTAATGTGTAACCTTTA 57.478 29.630 0.00 0.00 34.36 1.85
1773 2259 2.558359 GCTAATTTGTGCTTCAGGGTGT 59.442 45.455 0.00 0.00 0.00 4.16
1774 2260 3.612479 GCTAATTTGTGCTTCAGGGTGTG 60.612 47.826 0.00 0.00 0.00 3.82
1997 2486 8.725405 TCATTTAATCACTAAAGATACGCCAA 57.275 30.769 0.00 0.00 32.98 4.52
2013 2502 8.257306 AGATACGCCAACCAATATTTGATTTTT 58.743 29.630 0.00 0.00 0.00 1.94
2037 2526 5.640732 TCTTGATGAAATTAGAAAAGCGGC 58.359 37.500 0.00 0.00 0.00 6.53
2038 2527 5.182950 TCTTGATGAAATTAGAAAAGCGGCA 59.817 36.000 1.45 0.00 0.00 5.69
2081 3240 6.203338 ACTTTTTGAATGAAATCAAATGCGCT 59.797 30.769 9.73 0.00 45.77 5.92
2117 3276 0.735471 TCTCGAGCTCAACTGATCCG 59.265 55.000 15.40 0.00 0.00 4.18
2167 3326 0.318441 GCATACGCCTCATGCTCCTA 59.682 55.000 4.93 0.00 44.35 2.94
2189 3348 7.347222 TCCTACAAGTCTATCTTCTCTCTCTCT 59.653 40.741 0.00 0.00 33.63 3.10
2190 3349 7.657761 CCTACAAGTCTATCTTCTCTCTCTCTC 59.342 44.444 0.00 0.00 33.63 3.20
2191 3350 7.200434 ACAAGTCTATCTTCTCTCTCTCTCT 57.800 40.000 0.00 0.00 33.63 3.10
2192 3351 7.275920 ACAAGTCTATCTTCTCTCTCTCTCTC 58.724 42.308 0.00 0.00 33.63 3.20
2193 3352 7.126421 ACAAGTCTATCTTCTCTCTCTCTCTCT 59.874 40.741 0.00 0.00 33.63 3.10
2194 3353 7.296628 AGTCTATCTTCTCTCTCTCTCTCTC 57.703 44.000 0.00 0.00 0.00 3.20
2195 3354 7.072562 AGTCTATCTTCTCTCTCTCTCTCTCT 58.927 42.308 0.00 0.00 0.00 3.10
2196 3355 7.232534 AGTCTATCTTCTCTCTCTCTCTCTCTC 59.767 44.444 0.00 0.00 0.00 3.20
2197 3356 7.232534 GTCTATCTTCTCTCTCTCTCTCTCTCT 59.767 44.444 0.00 0.00 0.00 3.10
2198 3357 5.860941 TCTTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
2199 3358 5.523588 TCTTCTCTCTCTCTCTCTCTCTCT 58.476 45.833 0.00 0.00 0.00 3.10
2200 3359 5.596361 TCTTCTCTCTCTCTCTCTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
2201 3360 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2202 3361 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2203 3362 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2204 3363 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2205 3364 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2206 3365 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2207 3366 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2208 3367 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2300 3467 2.655407 TGTACCTCTCCTCCTCCTTCTT 59.345 50.000 0.00 0.00 0.00 2.52
2381 3549 3.384467 CACTTGTTTCCCATCACTTGGTT 59.616 43.478 0.00 0.00 44.83 3.67
2396 3564 0.482446 TGGTTGTCCCTCTTTGGCAT 59.518 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.575256 TCCGGAAAGAACTTACTACAGCA 59.425 43.478 0.00 0.00 0.00 4.41
5 6 4.184079 TCCGGAAAGAACTTACTACAGC 57.816 45.455 0.00 0.00 0.00 4.40
6 7 5.987347 TGTTTCCGGAAAGAACTTACTACAG 59.013 40.000 29.63 0.00 0.00 2.74
7 8 5.916318 TGTTTCCGGAAAGAACTTACTACA 58.084 37.500 29.63 17.28 0.00 2.74
8 9 6.647895 TCATGTTTCCGGAAAGAACTTACTAC 59.352 38.462 29.63 14.86 0.00 2.73
9 10 6.761312 TCATGTTTCCGGAAAGAACTTACTA 58.239 36.000 29.63 8.37 0.00 1.82
10 11 5.617252 TCATGTTTCCGGAAAGAACTTACT 58.383 37.500 29.63 9.76 0.00 2.24
11 12 5.934935 TCATGTTTCCGGAAAGAACTTAC 57.065 39.130 29.63 17.04 0.00 2.34
12 13 6.945938 TTTCATGTTTCCGGAAAGAACTTA 57.054 33.333 29.63 12.97 0.00 2.24
13 14 5.845391 TTTCATGTTTCCGGAAAGAACTT 57.155 34.783 29.63 14.18 0.00 2.66
14 15 5.845391 TTTTCATGTTTCCGGAAAGAACT 57.155 34.783 29.63 12.05 32.68 3.01
111 115 2.584791 CATGTTGCACCGCTTTCTAAC 58.415 47.619 0.00 0.00 0.00 2.34
136 144 1.603678 GGGTTGCTTCACACATGCAAG 60.604 52.381 0.00 0.00 43.78 4.01
164 179 4.570663 CGATCTCGGCCGTCCACC 62.571 72.222 27.15 10.85 35.37 4.61
165 180 3.515286 TCGATCTCGGCCGTCCAC 61.515 66.667 27.15 14.30 40.29 4.02
201 216 4.796495 CGGCCAAGGTACAGGGGC 62.796 72.222 2.24 11.28 45.67 5.80
234 262 1.457455 CTTGGGGCTTTGGTGGTGT 60.457 57.895 0.00 0.00 0.00 4.16
263 294 2.322161 TGAAACTACTACGCGTTGCTC 58.678 47.619 20.78 8.56 0.00 4.26
266 297 3.302555 TGACTGAAACTACTACGCGTTG 58.697 45.455 20.78 19.75 0.00 4.10
267 298 3.631145 TGACTGAAACTACTACGCGTT 57.369 42.857 20.78 1.73 0.00 4.84
268 299 3.844577 ATGACTGAAACTACTACGCGT 57.155 42.857 19.17 19.17 0.00 6.01
269 300 4.204573 GCTTATGACTGAAACTACTACGCG 59.795 45.833 3.53 3.53 0.00 6.01
306 352 0.829333 CAGAGATGGAGGACAGTGGG 59.171 60.000 0.00 0.00 0.00 4.61
347 393 5.191124 ACTTATATTTTGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
348 394 5.681639 ACTTATATTTTGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
349 395 5.427481 AGACTTATATTTTGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
350 396 5.681639 AGACTTATATTTTGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
351 397 7.625828 AAAGACTTATATTTTGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
379 425 9.855361 CGTATGTGATAGTTCATTTGAAATCTC 57.145 33.333 0.00 0.00 35.58 2.75
380 426 8.830580 CCGTATGTGATAGTTCATTTGAAATCT 58.169 33.333 0.00 0.00 35.58 2.40
381 427 8.826710 TCCGTATGTGATAGTTCATTTGAAATC 58.173 33.333 0.00 0.00 35.58 2.17
382 428 8.731275 TCCGTATGTGATAGTTCATTTGAAAT 57.269 30.769 0.00 0.00 35.58 2.17
383 429 8.611757 CATCCGTATGTGATAGTTCATTTGAAA 58.388 33.333 0.00 0.00 35.58 2.69
384 430 7.768582 ACATCCGTATGTGATAGTTCATTTGAA 59.231 33.333 0.00 0.00 44.79 2.69
385 431 7.272244 ACATCCGTATGTGATAGTTCATTTGA 58.728 34.615 0.00 0.00 44.79 2.69
386 432 7.482654 ACATCCGTATGTGATAGTTCATTTG 57.517 36.000 0.00 0.00 44.79 2.32
393 439 9.901172 TGTCTATATACATCCGTATGTGATAGT 57.099 33.333 17.08 3.55 45.99 2.12
429 475 5.569059 CGGAGCAAAATGAGTGAATTTACAC 59.431 40.000 2.93 0.00 40.60 2.90
430 476 5.240623 ACGGAGCAAAATGAGTGAATTTACA 59.759 36.000 2.93 0.00 0.00 2.41
431 477 5.699839 ACGGAGCAAAATGAGTGAATTTAC 58.300 37.500 0.00 0.00 0.00 2.01
432 478 5.957842 ACGGAGCAAAATGAGTGAATTTA 57.042 34.783 0.00 0.00 0.00 1.40
433 479 4.853924 ACGGAGCAAAATGAGTGAATTT 57.146 36.364 0.00 0.00 0.00 1.82
434 480 5.415701 ACATACGGAGCAAAATGAGTGAATT 59.584 36.000 0.00 0.00 0.00 2.17
435 481 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
436 482 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
437 483 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
438 484 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
439 485 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
440 486 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
441 487 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
442 488 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
443 489 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
444 490 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
445 491 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
446 492 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
447 493 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
448 494 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
449 495 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
450 496 7.822334 AGATTTCAACAAATGACTACATACGGA 59.178 33.333 0.00 0.00 37.92 4.69
451 497 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
452 498 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
456 502 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
459 505 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
460 506 9.818796 GTCTTTCTAGAGATTTCAACAAATGAC 57.181 33.333 0.00 0.00 37.92 3.06
461 507 9.003658 GGTCTTTCTAGAGATTTCAACAAATGA 57.996 33.333 0.00 0.00 31.94 2.57
462 508 9.007901 AGGTCTTTCTAGAGATTTCAACAAATG 57.992 33.333 0.00 0.00 31.94 2.32
487 533 8.350852 ACTACTCCATCCGTTCCTAAATATAG 57.649 38.462 0.00 0.00 0.00 1.31
488 534 8.716674 AACTACTCCATCCGTTCCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
489 535 7.613551 AACTACTCCATCCGTTCCTAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
490 536 7.427989 AAACTACTCCATCCGTTCCTAAATA 57.572 36.000 0.00 0.00 0.00 1.40
491 537 5.952347 AACTACTCCATCCGTTCCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
492 538 5.750352 AAACTACTCCATCCGTTCCTAAA 57.250 39.130 0.00 0.00 0.00 1.85
493 539 5.482878 AGAAAACTACTCCATCCGTTCCTAA 59.517 40.000 0.00 0.00 0.00 2.69
494 540 5.021458 AGAAAACTACTCCATCCGTTCCTA 58.979 41.667 0.00 0.00 0.00 2.94
495 541 3.838903 AGAAAACTACTCCATCCGTTCCT 59.161 43.478 0.00 0.00 0.00 3.36
496 542 4.081586 AGAGAAAACTACTCCATCCGTTCC 60.082 45.833 0.00 0.00 35.27 3.62
497 543 4.865365 CAGAGAAAACTACTCCATCCGTTC 59.135 45.833 0.00 0.00 35.27 3.95
498 544 4.822026 CAGAGAAAACTACTCCATCCGTT 58.178 43.478 0.00 0.00 35.27 4.44
499 545 3.368531 GCAGAGAAAACTACTCCATCCGT 60.369 47.826 0.00 0.00 35.27 4.69
500 546 3.190874 GCAGAGAAAACTACTCCATCCG 58.809 50.000 0.00 0.00 35.27 4.18
501 547 4.207891 TGCAGAGAAAACTACTCCATCC 57.792 45.455 0.00 0.00 35.27 3.51
502 548 4.034975 GCATGCAGAGAAAACTACTCCATC 59.965 45.833 14.21 0.00 35.27 3.51
503 549 3.944015 GCATGCAGAGAAAACTACTCCAT 59.056 43.478 14.21 0.00 35.27 3.41
504 550 3.244526 TGCATGCAGAGAAAACTACTCCA 60.245 43.478 18.46 0.00 35.27 3.86
505 551 3.338249 TGCATGCAGAGAAAACTACTCC 58.662 45.455 18.46 0.00 35.27 3.85
506 552 4.906423 CATGCATGCAGAGAAAACTACTC 58.094 43.478 26.69 0.00 34.95 2.59
507 553 4.959596 CATGCATGCAGAGAAAACTACT 57.040 40.909 26.69 0.84 0.00 2.57
668 783 9.859427 CTTTATGAAATGCTTCACCAGAAATAA 57.141 29.630 0.00 0.00 44.28 1.40
674 790 4.142093 CCCCTTTATGAAATGCTTCACCAG 60.142 45.833 0.00 0.00 44.28 4.00
842 1094 4.098654 ACCACCTCTAACAATCTCGATCTG 59.901 45.833 0.00 0.00 0.00 2.90
890 1148 0.894141 AACAACAGCCAGTGCAACAA 59.106 45.000 0.00 0.00 41.43 2.83
978 1446 7.661968 CCATGATCAGCTAGCTAAAGTAACTA 58.338 38.462 18.86 0.00 0.00 2.24
1050 1518 4.681781 CGTAGCATGAAGGAGAGAACCATT 60.682 45.833 0.00 0.00 0.00 3.16
1118 1586 5.456921 ACCCTCAAGGAACATATCAACAT 57.543 39.130 0.00 0.00 39.89 2.71
1188 1656 4.023980 CTCAAGTACATACCTCAGGACCA 58.976 47.826 0.00 0.00 0.00 4.02
1279 1755 9.464714 CTATATGGAGTAACATGTACAAGTGTC 57.535 37.037 4.21 2.69 32.39 3.67
1313 1797 1.967066 CTCCCATAGCACGGATCTTCT 59.033 52.381 0.00 0.00 0.00 2.85
1386 1870 1.376424 AGCACCGGCACTCATGAAG 60.376 57.895 0.00 0.00 44.61 3.02
1471 1955 5.960105 GCAAGCGTCACTAATTATTCTTCAC 59.040 40.000 0.00 0.00 0.00 3.18
1472 1956 5.874810 AGCAAGCGTCACTAATTATTCTTCA 59.125 36.000 0.00 0.00 0.00 3.02
1501 1985 6.014840 AGCTTAATTTATTCATCCATGGCTGG 60.015 38.462 15.42 3.40 44.64 4.85
1594 2079 7.649705 ACAACACGACAACAATATAATGCAAAA 59.350 29.630 0.00 0.00 0.00 2.44
1608 2093 6.743627 TGAAACTAAAATGACAACACGACAAC 59.256 34.615 0.00 0.00 0.00 3.32
1649 2134 1.524848 TTTTTGCTTATCACGCCCGA 58.475 45.000 0.00 0.00 0.00 5.14
1738 2224 7.764443 AGCACAAATTAGCGAGAAGTAATAGAA 59.236 33.333 0.00 0.00 35.48 2.10
1963 2452 9.851686 TCTTTAGTGATTAAATGAGCCATGTAT 57.148 29.630 0.00 0.00 31.12 2.29
1964 2453 9.851686 ATCTTTAGTGATTAAATGAGCCATGTA 57.148 29.630 0.00 0.00 31.12 2.29
1965 2454 8.757982 ATCTTTAGTGATTAAATGAGCCATGT 57.242 30.769 0.00 0.00 31.12 3.21
1967 2456 8.993121 CGTATCTTTAGTGATTAAATGAGCCAT 58.007 33.333 0.00 0.00 31.12 4.40
2013 2502 6.092748 GCCGCTTTTCTAATTTCATCAAGAA 58.907 36.000 0.00 0.00 0.00 2.52
2016 2505 5.160641 GTGCCGCTTTTCTAATTTCATCAA 58.839 37.500 0.00 0.00 0.00 2.57
2081 3240 4.586884 TCGAGAAAGAGAGGTTGTAGCTA 58.413 43.478 0.00 0.00 0.00 3.32
2117 3276 2.158645 GCTCGAGAAGGCAAAGACTTTC 59.841 50.000 18.75 0.00 26.99 2.62
2167 3326 7.126421 AGAGAGAGAGAGAGAAGATAGACTTGT 59.874 40.741 0.00 0.00 39.13 3.16
2189 3348 5.026121 ACTTGAGAGAGAGAGAGAGAGAGA 58.974 45.833 0.00 0.00 0.00 3.10
2190 3349 5.350504 ACTTGAGAGAGAGAGAGAGAGAG 57.649 47.826 0.00 0.00 0.00 3.20
2191 3350 5.013079 ACAACTTGAGAGAGAGAGAGAGAGA 59.987 44.000 0.00 0.00 0.00 3.10
2192 3351 5.248640 ACAACTTGAGAGAGAGAGAGAGAG 58.751 45.833 0.00 0.00 0.00 3.20
2193 3352 5.241403 ACAACTTGAGAGAGAGAGAGAGA 57.759 43.478 0.00 0.00 0.00 3.10
2194 3353 6.655003 AGTTACAACTTGAGAGAGAGAGAGAG 59.345 42.308 0.00 0.00 35.21 3.20
2195 3354 6.539173 AGTTACAACTTGAGAGAGAGAGAGA 58.461 40.000 0.00 0.00 35.21 3.10
2196 3355 6.817765 AGTTACAACTTGAGAGAGAGAGAG 57.182 41.667 0.00 0.00 35.21 3.20
2229 3388 1.382695 GATTGGGACCGGGAGAGGA 60.383 63.158 6.32 0.00 34.73 3.71
2300 3467 1.576577 AGTGTCTGCCATCATGGAGA 58.423 50.000 8.30 4.76 40.96 3.71
2381 3549 0.251297 CACCATGCCAAAGAGGGACA 60.251 55.000 0.00 0.00 42.31 4.02
2396 3564 2.121963 AGGAGGGACAAGCCACCA 60.122 61.111 0.00 0.00 38.95 4.17


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

AutoCloner maintained by Alex Coulton.