Multiple sequence alignment - TraesCS3B01G194400

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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 TraesCS3B01G194400 chr3B 100.000 5285 0 0 1 5285 214564616 214559332 0.000000e+00 9760
1 TraesCS3B01G194400 chr3A 97.801 4366 66 14 7 4354 165421087 165416734 0.000000e+00 7504
2 TraesCS3B01G194400 chr3A 93.630 832 28 11 4456 5284 165416737 165415928 0.000000e+00 1219
3 TraesCS3B01G194400 chr3A 99.074 108 1 0 4353 4460 585500963 585501070 1.500000e-45 195
4 TraesCS3B01G194400 chr3D 98.029 4110 56 14 257 4354 147817129 147821225 0.000000e+00 7118
5 TraesCS3B01G194400 chr3D 95.628 549 16 5 4742 5285 147821590 147822135 0.000000e+00 874
6 TraesCS3B01G194400 chr3D 97.917 288 6 0 4456 4743 147821222 147821509 2.840000e-137 499
7 TraesCS3B01G194400 chr3D 87.281 228 16 5 1 227 147816936 147817151 1.140000e-61 248
8 TraesCS3B01G194400 chr2A 94.836 3815 159 22 554 4351 95991376 95995169 0.000000e+00 5919
9 TraesCS3B01G194400 chr2D 94.849 3786 158 20 583 4351 97219730 97223495 0.000000e+00 5877
10 TraesCS3B01G194400 chr2B 94.450 3838 175 22 536 4353 148237067 148240886 0.000000e+00 5873
11 TraesCS3B01G194400 chr2B 98.261 115 2 0 4345 4459 576089740 576089626 8.970000e-48 202
12 TraesCS3B01G194400 chr2B 96.694 121 3 1 4339 4459 12023428 12023547 3.230000e-47 200
13 TraesCS3B01G194400 chr2B 96.610 118 4 0 4344 4461 5665569 5665452 4.180000e-46 196
14 TraesCS3B01G194400 chr1D 86.724 3367 431 13 942 4298 309078511 309081871 0.000000e+00 3727
15 TraesCS3B01G194400 chr1D 82.638 599 75 15 133 712 108107479 108106891 2.200000e-138 503
16 TraesCS3B01G194400 chr1D 95.652 115 5 0 4346 4460 202554404 202554518 9.040000e-43 185
17 TraesCS3B01G194400 chr1B 86.507 3372 439 14 927 4287 418810313 418813679 0.000000e+00 3692
18 TraesCS3B01G194400 chr1B 86.667 165 15 4 548 712 158539646 158539803 5.440000e-40 176
19 TraesCS3B01G194400 chr1A 86.514 3359 438 14 948 4298 388838782 388842133 0.000000e+00 3679
20 TraesCS3B01G194400 chr1A 82.500 600 75 17 133 712 111129736 111129147 2.840000e-137 499
21 TraesCS3B01G194400 chr1A 95.833 120 3 2 4342 4461 587813021 587813138 5.400000e-45 193
22 TraesCS3B01G194400 chr5D 82.510 3219 519 33 1079 4275 46319141 46322337 0.000000e+00 2785
23 TraesCS3B01G194400 chr5B 81.988 3220 540 30 1082 4281 47579637 47576438 0.000000e+00 2697
24 TraesCS3B01G194400 chr4B 82.197 264 34 8 457 712 329805701 329805443 1.150000e-51 215
25 TraesCS3B01G194400 chr6B 98.246 114 2 0 4352 4465 20752604 20752491 3.230000e-47 200
26 TraesCS3B01G194400 chr6B 94.444 126 6 1 4353 4478 714341457 714341333 5.400000e-45 193
27 TraesCS3B01G194400 chr7B 96.610 118 4 0 4342 4459 191777186 191777303 4.180000e-46 196
28 TraesCS3B01G194400 chr4A 82.843 204 29 4 4935 5135 598715689 598715489 1.510000e-40 178


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 TraesCS3B01G194400 chr3B 214559332 214564616 5284 True 9760.00 9760 100.00000 1 5285 1 chr3B.!!$R1 5284
1 TraesCS3B01G194400 chr3A 165415928 165421087 5159 True 4361.50 7504 95.71550 7 5284 2 chr3A.!!$R1 5277
2 TraesCS3B01G194400 chr3D 147816936 147822135 5199 False 2184.75 7118 94.71375 1 5285 4 chr3D.!!$F1 5284
3 TraesCS3B01G194400 chr2A 95991376 95995169 3793 False 5919.00 5919 94.83600 554 4351 1 chr2A.!!$F1 3797
4 TraesCS3B01G194400 chr2D 97219730 97223495 3765 False 5877.00 5877 94.84900 583 4351 1 chr2D.!!$F1 3768
5 TraesCS3B01G194400 chr2B 148237067 148240886 3819 False 5873.00 5873 94.45000 536 4353 1 chr2B.!!$F2 3817
6 TraesCS3B01G194400 chr1D 309078511 309081871 3360 False 3727.00 3727 86.72400 942 4298 1 chr1D.!!$F2 3356
7 TraesCS3B01G194400 chr1D 108106891 108107479 588 True 503.00 503 82.63800 133 712 1 chr1D.!!$R1 579
8 TraesCS3B01G194400 chr1B 418810313 418813679 3366 False 3692.00 3692 86.50700 927 4287 1 chr1B.!!$F2 3360
9 TraesCS3B01G194400 chr1A 388838782 388842133 3351 False 3679.00 3679 86.51400 948 4298 1 chr1A.!!$F1 3350
10 TraesCS3B01G194400 chr1A 111129147 111129736 589 True 499.00 499 82.50000 133 712 1 chr1A.!!$R1 579
11 TraesCS3B01G194400 chr5D 46319141 46322337 3196 False 2785.00 2785 82.51000 1079 4275 1 chr5D.!!$F1 3196
12 TraesCS3B01G194400 chr5B 47576438 47579637 3199 True 2697.00 2697 81.98800 1082 4281 1 chr5B.!!$R1 3199

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
563 589 0.603707 TTGCCTTGCAGTTCTCTCCG 60.604 55.0 0.0 0.0 40.61 4.63 F
1209 1248 0.541063 TGGGTCACGCCTTCTCACTA 60.541 55.0 0.0 0.0 37.43 2.74 F
2157 2202 1.028330 ATGCACTTCCCATGCTCACG 61.028 55.0 0.0 0.0 43.77 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2228 0.033504 ACTTGGCACACTAGTCACGG 59.966 55.000 0.00 0.0 39.29 4.94 R
2625 2670 3.120060 CCTTCTGCTTCCATTCAGTTTCG 60.120 47.826 0.00 0.0 0.00 3.46 R
4354 4413 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.0 46.06 4.30 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
98 102 1.697082 TTGTGGGGTCGTAGTTGGCA 61.697 55.000 0.00 0.00 0.00 4.92
154 158 1.404391 GTCCTGCAATCCAGCTTCATG 59.596 52.381 0.00 0.00 40.36 3.07
212 219 9.217278 GTCATGAATATCATCTTTCTAGCACAT 57.783 33.333 0.00 0.00 34.28 3.21
250 257 6.213677 GGATTTTTGGTTTCTAACTGGTCAC 58.786 40.000 0.00 0.00 0.00 3.67
308 316 5.883328 TCCTTTCGATTATGTTTCGATCG 57.117 39.130 9.36 9.36 44.32 3.69
319 327 3.679725 TGTTTCGATCGTTGCATATTGC 58.320 40.909 15.94 0.00 45.29 3.56
320 328 3.373748 TGTTTCGATCGTTGCATATTGCT 59.626 39.130 15.94 0.00 45.31 3.91
321 329 3.859745 TTCGATCGTTGCATATTGCTC 57.140 42.857 15.94 0.00 45.31 4.26
322 330 2.135139 TCGATCGTTGCATATTGCTCC 58.865 47.619 15.94 0.00 45.31 4.70
323 331 1.866601 CGATCGTTGCATATTGCTCCA 59.133 47.619 7.03 0.00 45.31 3.86
324 332 2.096565 CGATCGTTGCATATTGCTCCAG 60.097 50.000 7.03 0.00 45.31 3.86
343 355 2.593346 GTCTCCAGACATACTGCAGG 57.407 55.000 19.93 2.38 44.52 4.85
376 388 2.556840 TAGCCAGCATTGTCCAGGGC 62.557 60.000 0.00 0.00 41.65 5.19
385 397 2.359975 GTCCAGGGCGACAAAGGG 60.360 66.667 0.00 0.00 32.74 3.95
386 398 2.852075 TCCAGGGCGACAAAGGGT 60.852 61.111 0.00 0.00 0.00 4.34
431 451 3.809279 AGCAAATTAAAGCCACAAACTGC 59.191 39.130 0.00 0.00 0.00 4.40
462 484 8.485591 GCCGTGACTGTATTATATGTTAACTTC 58.514 37.037 7.22 0.00 0.00 3.01
516 539 8.990163 ATACTTAACAGGAAAGGTCAAAGAAA 57.010 30.769 0.00 0.00 0.00 2.52
530 553 3.631686 TCAAAGAAACATGTCCACTGTGG 59.368 43.478 20.86 20.86 39.43 4.17
533 556 4.431416 AGAAACATGTCCACTGTGGTTA 57.569 40.909 25.15 15.88 39.03 2.85
563 589 0.603707 TTGCCTTGCAGTTCTCTCCG 60.604 55.000 0.00 0.00 40.61 4.63
632 658 5.525745 TGCATCAAATATACCAACCTACACG 59.474 40.000 0.00 0.00 0.00 4.49
725 755 5.044846 ACCTGACCTCCATAATTAGCTTGTT 60.045 40.000 0.00 0.00 0.00 2.83
726 756 6.157994 ACCTGACCTCCATAATTAGCTTGTTA 59.842 38.462 0.00 0.00 0.00 2.41
727 757 7.147302 ACCTGACCTCCATAATTAGCTTGTTAT 60.147 37.037 0.00 0.00 0.00 1.89
728 758 7.721399 CCTGACCTCCATAATTAGCTTGTTATT 59.279 37.037 0.00 0.00 0.00 1.40
782 812 8.236585 TGATGTTTGCTTATGGCTTATTATGT 57.763 30.769 0.00 0.00 42.39 2.29
852 882 6.094742 TGAGTTTGTCAGCTATGTTTGAAACA 59.905 34.615 13.66 13.66 46.94 2.83
878 908 7.441017 AGATATTCAAGGAGATTGCACTACTC 58.559 38.462 0.00 0.00 38.89 2.59
902 933 7.038659 TCAATTCGTCCAAAAACAATGTTTCT 58.961 30.769 12.11 0.00 0.00 2.52
1209 1248 0.541063 TGGGTCACGCCTTCTCACTA 60.541 55.000 0.00 0.00 37.43 2.74
2157 2202 1.028330 ATGCACTTCCCATGCTCACG 61.028 55.000 0.00 0.00 43.77 4.35
2183 2228 4.202245 TGACAGATAAAGGTACTGGCAC 57.798 45.455 0.00 0.00 43.47 5.01
2625 2670 4.114058 TCAGTGGTACATAACTTACGGC 57.886 45.455 0.00 0.00 44.52 5.68
3030 3075 3.977999 ACCCCTTTGATATTCGGGTATCA 59.022 43.478 0.00 6.58 45.37 2.15
3741 3786 5.415701 GCAGGACTCCATTGTTTTAATGAGA 59.584 40.000 0.00 0.00 0.00 3.27
4354 4413 6.438259 TGTCTACTTCTCACTGCATAGTAC 57.562 41.667 0.00 0.00 34.74 2.73
4355 4414 6.181190 TGTCTACTTCTCACTGCATAGTACT 58.819 40.000 0.00 0.00 34.74 2.73
4356 4415 6.316640 TGTCTACTTCTCACTGCATAGTACTC 59.683 42.308 0.00 0.00 34.74 2.59
4357 4416 4.993029 ACTTCTCACTGCATAGTACTCC 57.007 45.455 0.00 0.00 34.74 3.85
4358 4417 3.702045 ACTTCTCACTGCATAGTACTCCC 59.298 47.826 0.00 0.00 34.74 4.30
4359 4418 3.671740 TCTCACTGCATAGTACTCCCT 57.328 47.619 0.00 0.00 34.74 4.20
4360 4419 3.556999 TCTCACTGCATAGTACTCCCTC 58.443 50.000 0.00 0.00 34.74 4.30
4361 4420 2.625790 CTCACTGCATAGTACTCCCTCC 59.374 54.545 0.00 0.00 34.74 4.30
4362 4421 1.338337 CACTGCATAGTACTCCCTCCG 59.662 57.143 0.00 0.00 34.74 4.63
4363 4422 1.063867 ACTGCATAGTACTCCCTCCGT 60.064 52.381 0.00 0.00 34.74 4.69
4364 4423 2.032620 CTGCATAGTACTCCCTCCGTT 58.967 52.381 0.00 0.00 0.00 4.44
4365 4424 2.029623 TGCATAGTACTCCCTCCGTTC 58.970 52.381 0.00 0.00 0.00 3.95
4366 4425 1.001597 GCATAGTACTCCCTCCGTTCG 60.002 57.143 0.00 0.00 0.00 3.95
4367 4426 1.607628 CATAGTACTCCCTCCGTTCGG 59.392 57.143 0.00 4.74 0.00 4.30
4368 4427 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
4369 4428 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
4370 4429 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
4371 4430 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
4372 4431 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
4373 4432 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4374 4433 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4375 4434 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
4376 4435 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
4377 4436 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
4378 4437 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
4379 4438 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
4380 4439 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
4381 4440 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
4382 4441 2.156117 CGTTCGGAATTACTTGTCGCAA 59.844 45.455 0.00 0.00 0.00 4.85
4383 4442 3.363182 CGTTCGGAATTACTTGTCGCAAA 60.363 43.478 0.00 0.00 0.00 3.68
4384 4443 4.529446 GTTCGGAATTACTTGTCGCAAAA 58.471 39.130 0.00 0.00 0.00 2.44
4385 4444 4.815040 TCGGAATTACTTGTCGCAAAAA 57.185 36.364 0.00 0.00 0.00 1.94
4386 4445 5.365403 TCGGAATTACTTGTCGCAAAAAT 57.635 34.783 0.00 0.00 0.00 1.82
4387 4446 5.150683 TCGGAATTACTTGTCGCAAAAATG 58.849 37.500 0.00 0.00 0.00 2.32
4388 4447 4.323336 CGGAATTACTTGTCGCAAAAATGG 59.677 41.667 0.00 0.00 0.00 3.16
4389 4448 5.465935 GGAATTACTTGTCGCAAAAATGGA 58.534 37.500 0.00 0.00 0.00 3.41
4390 4449 6.099341 GGAATTACTTGTCGCAAAAATGGAT 58.901 36.000 0.00 0.00 0.00 3.41
4391 4450 6.034898 GGAATTACTTGTCGCAAAAATGGATG 59.965 38.462 0.00 0.00 0.00 3.51
4392 4451 5.446143 TTACTTGTCGCAAAAATGGATGT 57.554 34.783 0.00 0.00 0.00 3.06
4393 4452 6.561737 TTACTTGTCGCAAAAATGGATGTA 57.438 33.333 0.00 0.00 0.00 2.29
4394 4453 5.643379 ACTTGTCGCAAAAATGGATGTAT 57.357 34.783 0.00 0.00 0.00 2.29
4395 4454 5.640732 ACTTGTCGCAAAAATGGATGTATC 58.359 37.500 0.00 0.00 0.00 2.24
4396 4455 5.415701 ACTTGTCGCAAAAATGGATGTATCT 59.584 36.000 0.00 0.00 0.00 1.98
4397 4456 6.597672 ACTTGTCGCAAAAATGGATGTATCTA 59.402 34.615 0.00 0.00 0.00 1.98
4398 4457 6.603237 TGTCGCAAAAATGGATGTATCTAG 57.397 37.500 0.00 0.00 0.00 2.43
4399 4458 6.345298 TGTCGCAAAAATGGATGTATCTAGA 58.655 36.000 0.00 0.00 0.00 2.43
4400 4459 6.257849 TGTCGCAAAAATGGATGTATCTAGAC 59.742 38.462 0.00 0.00 0.00 2.59
4401 4460 5.462068 TCGCAAAAATGGATGTATCTAGACG 59.538 40.000 0.00 0.00 0.00 4.18
4402 4461 5.234329 CGCAAAAATGGATGTATCTAGACGT 59.766 40.000 0.00 0.00 0.00 4.34
4403 4462 6.419710 CGCAAAAATGGATGTATCTAGACGTA 59.580 38.462 0.00 0.00 0.00 3.57
4404 4463 7.116376 CGCAAAAATGGATGTATCTAGACGTAT 59.884 37.037 0.00 0.00 0.00 3.06
4405 4464 8.774586 GCAAAAATGGATGTATCTAGACGTATT 58.225 33.333 0.00 0.00 0.00 1.89
4430 4489 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
4431 4490 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
4432 4491 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
4433 4492 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
4434 4493 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
4435 4494 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
4436 4495 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
4437 4496 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
4438 4497 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
4439 4498 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
4440 4499 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
4441 4500 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
4442 4501 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
4443 4502 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
4444 4503 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
4445 4504 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
4446 4505 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
4447 4506 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
4448 4507 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
4449 4508 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
4450 4509 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
4451 4510 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
4452 4511 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
4453 4512 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
4454 4513 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
4455 4514 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
4456 4515 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
4457 4516 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
4458 4517 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
4459 4518 1.400737 ATTCCGAACGGAGGGAGTAG 58.599 55.000 15.34 0.00 46.06 2.57
4521 4580 4.003648 ACTGGCTCCTTTTATTCTTCACG 58.996 43.478 0.00 0.00 0.00 4.35
4552 4611 2.691011 GTTGTAGTTTTTGTGCCTGGGA 59.309 45.455 0.00 0.00 0.00 4.37
4805 4947 6.624352 TGCATGTCTTATCTTATTTGAGGC 57.376 37.500 0.00 0.00 0.00 4.70
4928 5072 3.940852 ACGACAAATATTACCCCCGTTTC 59.059 43.478 0.00 0.00 0.00 2.78
5019 5163 0.871163 CAGGTGTTTTGCAAGGCGTG 60.871 55.000 0.00 0.00 0.00 5.34
5036 5180 1.724623 CGTGGTATCGACTGGTTGTTG 59.275 52.381 0.00 0.00 0.00 3.33
5073 5219 0.550914 ATGAGGCGCCTATTGGGAAA 59.449 50.000 32.97 7.98 37.23 3.13
5086 5232 1.937191 TGGGAAAATGGAAAGGAGCC 58.063 50.000 0.00 0.00 0.00 4.70
5123 5269 5.113446 ACTGCAGATGATTGAGAAGGAAT 57.887 39.130 23.35 0.00 0.00 3.01
5145 5291 3.930534 TTTGGTTTCCAAGCTTTTGCCAG 60.931 43.478 0.00 0.00 44.84 4.85
5242 5389 7.417612 ACAGCAATGTCTAGTTTGTTTACTTG 58.582 34.615 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 102 2.232452 AGAGAAGCTACGCATCACTTGT 59.768 45.455 0.00 0.00 0.00 3.16
118 122 0.676151 GGACTTGCAGAGCCAGGAAG 60.676 60.000 0.00 0.00 39.89 3.46
154 158 2.270923 GAAAATTTTGCAGGCCGGATC 58.729 47.619 5.05 0.00 0.00 3.36
212 219 4.314121 CAAAAATCCCTCAAAATTCGCCA 58.686 39.130 0.00 0.00 0.00 5.69
250 257 1.202687 TCAGCAAAGTCCTGACTGTGG 60.203 52.381 17.06 4.07 44.82 4.17
319 327 2.100584 GCAGTATGTCTGGAGACTGGAG 59.899 54.545 8.24 0.00 44.99 3.86
320 328 2.103373 GCAGTATGTCTGGAGACTGGA 58.897 52.381 8.24 0.00 44.99 3.86
321 329 1.827344 TGCAGTATGTCTGGAGACTGG 59.173 52.381 8.24 0.00 44.99 4.00
343 355 3.753272 TGCTGGCTAACTGAATTCACTTC 59.247 43.478 3.38 0.00 0.00 3.01
376 388 4.571919 TGGTACATTTCTACCCTTTGTCG 58.428 43.478 0.00 0.00 36.09 4.35
385 397 7.359181 GCTTTTGTGCATTTGGTACATTTCTAC 60.359 37.037 0.00 0.00 41.91 2.59
386 398 6.644592 GCTTTTGTGCATTTGGTACATTTCTA 59.355 34.615 0.00 0.00 41.91 2.10
431 451 2.665649 TAATACAGTCACGGCACAGG 57.334 50.000 0.00 0.00 0.00 4.00
462 484 5.036737 GCTAAAATTGATTCACGTGGATGG 58.963 41.667 15.75 0.00 0.00 3.51
499 521 5.507985 GGACATGTTTCTTTGACCTTTCCTG 60.508 44.000 0.00 0.00 0.00 3.86
516 539 3.569194 TTGTAACCACAGTGGACATGT 57.431 42.857 27.39 0.00 40.96 3.21
530 553 6.423604 ACTGCAAGGCAATTAACATTTGTAAC 59.576 34.615 0.00 0.00 38.41 2.50
533 556 4.959723 ACTGCAAGGCAATTAACATTTGT 58.040 34.783 0.00 0.00 38.41 2.83
563 589 6.185114 AGATATATGCTAATGGAGATGGCC 57.815 41.667 0.00 0.00 0.00 5.36
726 756 7.765819 GCCATCAAACAAAATTAGCCTTCTAAT 59.234 33.333 0.00 0.00 44.97 1.73
727 757 7.039082 AGCCATCAAACAAAATTAGCCTTCTAA 60.039 33.333 0.00 0.00 38.97 2.10
728 758 6.437162 AGCCATCAAACAAAATTAGCCTTCTA 59.563 34.615 0.00 0.00 0.00 2.10
751 781 3.800506 GCCATAAGCAAACATCATCAAGC 59.199 43.478 0.00 0.00 42.97 4.01
792 822 8.874744 AAGCCATGTGATGAAGCTAATTATAT 57.125 30.769 0.00 0.00 32.39 0.86
793 823 8.696043 AAAGCCATGTGATGAAGCTAATTATA 57.304 30.769 0.00 0.00 32.39 0.98
852 882 7.800092 AGTAGTGCAATCTCCTTGAATATCTT 58.200 34.615 0.00 0.00 36.97 2.40
878 908 7.232945 AGAAACATTGTTTTTGGACGAATTG 57.767 32.000 15.54 0.00 0.00 2.32
1209 1248 1.813513 CACCGAACTCAAGCTTGGAT 58.186 50.000 25.73 11.78 0.00 3.41
2157 2202 5.755861 GCCAGTACCTTTATCTGTCAAGATC 59.244 44.000 0.00 0.00 42.41 2.75
2183 2228 0.033504 ACTTGGCACACTAGTCACGG 59.966 55.000 0.00 0.00 39.29 4.94
2625 2670 3.120060 CCTTCTGCTTCCATTCAGTTTCG 60.120 47.826 0.00 0.00 0.00 3.46
2902 2947 7.716560 CACATATTCCCATACTTCATCTGTCAA 59.283 37.037 0.00 0.00 0.00 3.18
4354 4413 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
4355 4414 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
4356 4415 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
4357 4416 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
4358 4417 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
4359 4418 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
4360 4419 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
4361 4420 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
4362 4421 3.799137 TTGCGACAAGTAATTCCGAAC 57.201 42.857 0.00 0.00 0.00 3.95
4363 4422 4.815040 TTTTGCGACAAGTAATTCCGAA 57.185 36.364 0.00 0.00 0.00 4.30
4364 4423 4.815040 TTTTTGCGACAAGTAATTCCGA 57.185 36.364 0.00 0.00 0.00 4.55
4365 4424 4.323336 CCATTTTTGCGACAAGTAATTCCG 59.677 41.667 0.00 0.00 0.00 4.30
4366 4425 5.465935 TCCATTTTTGCGACAAGTAATTCC 58.534 37.500 0.00 0.00 0.00 3.01
4367 4426 6.586082 ACATCCATTTTTGCGACAAGTAATTC 59.414 34.615 0.00 0.00 0.00 2.17
4368 4427 6.454795 ACATCCATTTTTGCGACAAGTAATT 58.545 32.000 0.00 0.00 0.00 1.40
4369 4428 6.024552 ACATCCATTTTTGCGACAAGTAAT 57.975 33.333 0.00 0.00 0.00 1.89
4370 4429 5.446143 ACATCCATTTTTGCGACAAGTAA 57.554 34.783 0.00 0.00 0.00 2.24
4371 4430 6.597672 AGATACATCCATTTTTGCGACAAGTA 59.402 34.615 0.00 0.00 0.00 2.24
4372 4431 5.415701 AGATACATCCATTTTTGCGACAAGT 59.584 36.000 0.00 0.00 0.00 3.16
4373 4432 5.883661 AGATACATCCATTTTTGCGACAAG 58.116 37.500 0.00 0.00 0.00 3.16
4374 4433 5.895636 AGATACATCCATTTTTGCGACAA 57.104 34.783 0.00 0.00 0.00 3.18
4375 4434 6.257849 GTCTAGATACATCCATTTTTGCGACA 59.742 38.462 0.00 0.00 0.00 4.35
4376 4435 6.562270 CGTCTAGATACATCCATTTTTGCGAC 60.562 42.308 0.00 0.00 0.00 5.19
4377 4436 5.462068 CGTCTAGATACATCCATTTTTGCGA 59.538 40.000 0.00 0.00 0.00 5.10
4378 4437 5.234329 ACGTCTAGATACATCCATTTTTGCG 59.766 40.000 0.00 0.00 0.00 4.85
4379 4438 6.604735 ACGTCTAGATACATCCATTTTTGC 57.395 37.500 0.00 0.00 0.00 3.68
4404 4463 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
4405 4464 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
4406 4465 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
4407 4466 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
4408 4467 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
4409 4468 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
4410 4469 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
4411 4470 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
4412 4471 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
4413 4472 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
4414 4473 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
4415 4474 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
4416 4475 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
4417 4476 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
4418 4477 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
4419 4478 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
4420 4479 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
4421 4480 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
4422 4481 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
4423 4482 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
4424 4483 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
4425 4484 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
4426 4485 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
4427 4486 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
4428 4487 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
4429 4488 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
4430 4489 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
4431 4490 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
4432 4491 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
4433 4492 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
4434 4493 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
4435 4494 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
4436 4495 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
4437 4496 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
4438 4497 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
4439 4498 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
4440 4499 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
4441 4500 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
4442 4501 0.679002 CACTACTCCCTCCGTTCGGA 60.679 60.000 13.34 13.34 0.00 4.55
4443 4502 1.664321 CCACTACTCCCTCCGTTCGG 61.664 65.000 4.74 4.74 0.00 4.30
4444 4503 0.964358 ACCACTACTCCCTCCGTTCG 60.964 60.000 0.00 0.00 0.00 3.95
4445 4504 1.264295 AACCACTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95
4446 4505 1.725803 AAACCACTACTCCCTCCGTT 58.274 50.000 0.00 0.00 0.00 4.44
4447 4506 1.622312 GAAAACCACTACTCCCTCCGT 59.378 52.381 0.00 0.00 0.00 4.69
4448 4507 1.900486 AGAAAACCACTACTCCCTCCG 59.100 52.381 0.00 0.00 0.00 4.63
4449 4508 4.468765 GTAGAAAACCACTACTCCCTCC 57.531 50.000 0.00 0.00 37.71 4.30
4521 4580 7.378728 GGCACAAAAACTACAACAGAATCTAAC 59.621 37.037 0.00 0.00 0.00 2.34
4805 4947 4.052229 GCAGGCAAGCACAGGCAG 62.052 66.667 0.00 0.00 44.61 4.85
4907 5051 3.313249 GGAAACGGGGGTAATATTTGTCG 59.687 47.826 0.00 0.00 0.00 4.35
5019 5163 2.000447 GAGCAACAACCAGTCGATACC 59.000 52.381 0.00 0.00 0.00 2.73
5036 5180 3.801698 TCATGCTAGAATCAACAGGAGC 58.198 45.455 0.00 0.00 0.00 4.70
5086 5232 2.224606 TGCAGTCAAGCTGGAGAAAAG 58.775 47.619 0.00 0.00 45.14 2.27
5123 5269 2.026822 TGGCAAAAGCTTGGAAACCAAA 60.027 40.909 0.00 0.00 43.44 3.28
5145 5291 8.275632 GCATCCACATCTAAAAAGAAACAAAAC 58.724 33.333 0.00 0.00 0.00 2.43
5242 5389 4.380867 CCAGGAATATGTCACAACTTTGGC 60.381 45.833 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.