Multiple sequence alignment - TraesCS6D01G231800

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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 TraesCS6D01G231800 chr6D 100.000 3500 0 0 1 3500 325404551 325401052 0.000000e+00 6464.0
1 TraesCS6D01G231800 chr6D 91.724 145 12 0 3294 3438 246062304 246062160 5.920000e-48 202.0
2 TraesCS6D01G231800 chr6B 95.297 2594 89 17 722 3298 497881122 497883699 0.000000e+00 4084.0
3 TraesCS6D01G231800 chr6B 87.208 727 69 9 15 737 497880403 497881109 0.000000e+00 806.0
4 TraesCS6D01G231800 chr6B 85.567 194 23 5 1588 1781 125173026 125173214 7.660000e-47 198.0
5 TraesCS6D01G231800 chr6A 94.106 2596 94 22 724 3298 463540800 463538243 0.000000e+00 3892.0
6 TraesCS6D01G231800 chr6A 89.959 727 53 12 15 737 463541551 463540841 0.000000e+00 920.0
7 TraesCS6D01G231800 chr6A 100.000 33 0 0 3452 3484 459529159 459529127 1.050000e-05 62.1
8 TraesCS6D01G231800 chr6A 94.737 38 1 1 3452 3489 599041409 599041373 1.360000e-04 58.4
9 TraesCS6D01G231800 chr4D 86.379 301 35 2 1032 1332 397686403 397686109 1.210000e-84 324.0
10 TraesCS6D01G231800 chr4D 90.132 152 15 0 3287 3438 175798152 175798001 7.660000e-47 198.0
11 TraesCS6D01G231800 chr5B 93.662 142 9 0 3294 3435 603648024 603648165 2.740000e-51 213.0
12 TraesCS6D01G231800 chr5B 92.254 142 11 0 3293 3434 577516049 577516190 5.920000e-48 202.0
13 TraesCS6D01G231800 chr4B 92.958 142 10 0 3293 3434 515161120 515160979 1.270000e-49 207.0
14 TraesCS6D01G231800 chr2B 91.892 148 12 0 3287 3434 559957419 559957272 1.270000e-49 207.0
15 TraesCS6D01G231800 chr7A 92.308 143 11 0 3292 3434 309920772 309920914 1.650000e-48 204.0
16 TraesCS6D01G231800 chrUn 92.308 143 10 1 3292 3434 252478072 252477931 5.920000e-48 202.0
17 TraesCS6D01G231800 chr2D 91.156 147 13 0 3288 3434 475088508 475088362 2.130000e-47 200.0
18 TraesCS6D01G231800 chr2D 100.000 33 0 0 3452 3484 190934344 190934376 1.050000e-05 62.1
19 TraesCS6D01G231800 chr2D 100.000 33 0 0 3452 3484 197811762 197811794 1.050000e-05 62.1
20 TraesCS6D01G231800 chr1D 97.297 37 1 0 3452 3488 86519594 86519558 2.920000e-06 63.9
21 TraesCS6D01G231800 chr1B 97.297 37 1 0 3452 3488 1716435 1716399 2.920000e-06 63.9
22 TraesCS6D01G231800 chr7D 100.000 33 0 0 3452 3484 248097114 248097146 1.050000e-05 62.1
23 TraesCS6D01G231800 chr7D 100.000 33 0 0 3452 3484 550376592 550376624 1.050000e-05 62.1
24 TraesCS6D01G231800 chr5D 97.059 34 1 0 3455 3488 308623358 308623391 1.360000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G231800 chr6D 325401052 325404551 3499 True 6464 6464 100.0000 1 3500 1 chr6D.!!$R2 3499
1 TraesCS6D01G231800 chr6B 497880403 497883699 3296 False 2445 4084 91.2525 15 3298 2 chr6B.!!$F2 3283
2 TraesCS6D01G231800 chr6A 463538243 463541551 3308 True 2406 3892 92.0325 15 3298 2 chr6A.!!$R3 3283

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
399 402 1.040646 CGCTATAGAGCCCAAGGACA 58.959 55.000 3.21 0.0 46.86 4.02 F
757 817 1.130561 CGTTCCGCTTCCAATCCTTTC 59.869 52.381 0.00 0.0 0.00 2.62 F
1435 1497 0.531974 CCGCCCGTGCATACTTGTAT 60.532 55.000 0.00 0.0 37.32 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1498 1.135517 GGCGCGCAAGATTAAAGGAAA 60.136 47.619 34.42 0.00 43.02 3.13 R
1789 1851 1.291877 CCGTGGAACAGCACTAGCAC 61.292 60.000 0.00 0.00 45.49 4.40 R
2867 2944 0.110238 CCAACAGAACCGCGATTGTG 60.110 55.000 9.12 9.12 0.00 3.33 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
189 190 2.224159 ACCGCCCAACATGTCTCCT 61.224 57.895 0.00 0.00 0.00 3.69
274 276 9.862371 GAGTCTTCAAAGTAGATCATCAACTTA 57.138 33.333 0.00 0.00 33.24 2.24
280 282 9.770097 TCAAAGTAGATCATCAACTTATCCATC 57.230 33.333 0.00 0.00 33.24 3.51
283 285 5.815233 AGATCATCAACTTATCCATCGGT 57.185 39.130 0.00 0.00 0.00 4.69
285 287 6.595682 AGATCATCAACTTATCCATCGGTTT 58.404 36.000 0.00 0.00 0.00 3.27
286 288 6.708054 AGATCATCAACTTATCCATCGGTTTC 59.292 38.462 0.00 0.00 0.00 2.78
287 289 4.808895 TCATCAACTTATCCATCGGTTTCG 59.191 41.667 0.00 0.00 37.82 3.46
288 290 3.527533 TCAACTTATCCATCGGTTTCGG 58.472 45.455 0.00 0.00 36.95 4.30
289 291 3.196039 TCAACTTATCCATCGGTTTCGGA 59.804 43.478 0.00 0.00 36.95 4.55
295 297 1.072648 TCCATCGGTTTCGGAGGTTTT 59.927 47.619 0.00 0.00 36.95 2.43
333 335 1.736645 CGTTTCCGCCGTCATCACT 60.737 57.895 0.00 0.00 0.00 3.41
375 378 1.667236 TGTGAAGGATTAGGCATGCG 58.333 50.000 12.44 0.00 0.00 4.73
399 402 1.040646 CGCTATAGAGCCCAAGGACA 58.959 55.000 3.21 0.00 46.86 4.02
500 505 3.500201 ACCCTAGGTTTTACGGGGT 57.500 52.632 8.29 0.00 44.66 4.95
526 531 4.228824 TCTTCTGTACAACCCTTACACCT 58.771 43.478 0.00 0.00 0.00 4.00
564 569 4.302455 CTCTCGATGATGGTTGGTATGTC 58.698 47.826 0.00 0.00 0.00 3.06
565 570 3.052745 CTCGATGATGGTTGGTATGTCG 58.947 50.000 0.00 0.00 0.00 4.35
568 573 3.001228 CGATGATGGTTGGTATGTCGTTG 59.999 47.826 0.00 0.00 0.00 4.10
572 577 4.580995 TGATGGTTGGTATGTCGTTGTTTT 59.419 37.500 0.00 0.00 0.00 2.43
573 578 4.985538 TGGTTGGTATGTCGTTGTTTTT 57.014 36.364 0.00 0.00 0.00 1.94
574 579 4.922719 TGGTTGGTATGTCGTTGTTTTTC 58.077 39.130 0.00 0.00 0.00 2.29
665 670 4.099824 GTTTTGACACCGAACACGAAATT 58.900 39.130 0.00 0.00 0.00 1.82
679 684 6.963017 ACACGAAATTGTCAAAATAACGTC 57.037 33.333 0.00 0.00 0.00 4.34
689 694 6.312487 TGTCAAAATAACGTCGACACAAAAA 58.688 32.000 17.16 0.00 31.92 1.94
719 724 6.500041 TCTGTTTTCATTCTTTTGTAACCGG 58.500 36.000 0.00 0.00 0.00 5.28
757 817 1.130561 CGTTCCGCTTCCAATCCTTTC 59.869 52.381 0.00 0.00 0.00 2.62
829 889 2.743183 GCCGAACAGGATCAGCTATTGT 60.743 50.000 0.00 0.00 45.00 2.71
830 890 3.535561 CCGAACAGGATCAGCTATTGTT 58.464 45.455 0.00 0.00 45.00 2.83
831 891 3.310774 CCGAACAGGATCAGCTATTGTTG 59.689 47.826 0.00 0.00 45.00 3.33
832 892 3.310774 CGAACAGGATCAGCTATTGTTGG 59.689 47.826 0.00 2.11 32.58 3.77
833 893 3.287867 ACAGGATCAGCTATTGTTGGG 57.712 47.619 0.00 0.00 0.00 4.12
834 894 2.578021 ACAGGATCAGCTATTGTTGGGT 59.422 45.455 0.00 0.00 0.00 4.51
835 895 3.209410 CAGGATCAGCTATTGTTGGGTC 58.791 50.000 0.00 0.00 0.00 4.46
841 901 1.710809 AGCTATTGTTGGGTCTTGGGT 59.289 47.619 0.00 0.00 0.00 4.51
859 919 1.152984 TGTGCGGCCCAATATGGAG 60.153 57.895 0.00 0.00 40.96 3.86
891 951 2.852075 TTCCTTCCCAGCCCGTGT 60.852 61.111 0.00 0.00 0.00 4.49
1134 1196 1.886886 TCTCCAGGTAAACAAACGGC 58.113 50.000 0.00 0.00 0.00 5.68
1435 1497 0.531974 CCGCCCGTGCATACTTGTAT 60.532 55.000 0.00 0.00 37.32 2.29
1436 1498 1.295792 CGCCCGTGCATACTTGTATT 58.704 50.000 0.00 0.00 37.32 1.89
1554 1616 5.400066 TTCCTGTCGATGATTCTGTGTAA 57.600 39.130 0.00 0.00 0.00 2.41
1638 1700 5.923204 TCCATTTGGTGTTTGTTTGCTATT 58.077 33.333 0.00 0.00 36.34 1.73
1699 1761 7.174107 AGATGGTTTGACTAATGAAAATGGG 57.826 36.000 0.00 0.00 0.00 4.00
1717 1779 4.982241 TGGGGAATTAGAGATGTCCATC 57.018 45.455 0.00 0.00 38.09 3.51
1789 1851 3.450578 ACACCGTATTGGCGTAATAGTG 58.549 45.455 9.93 9.93 43.94 2.74
1871 1933 6.001460 TCTGTTTATGTTTGGGTAGGAACAG 58.999 40.000 0.00 0.00 42.30 3.16
1897 1959 7.201350 GCAAATCACTTTAATTCTTAGGTTGCG 60.201 37.037 0.00 0.00 0.00 4.85
1931 1993 1.484240 CCTTTGGGTCTCTCTAGCTGG 59.516 57.143 0.00 0.00 0.00 4.85
1981 2043 3.759618 CCTACACTCCGAGAGAGAAAACT 59.240 47.826 1.33 0.00 46.50 2.66
2202 2266 6.426937 TGTCAAATTTGTACCTGAAGACTAGC 59.573 38.462 17.47 0.00 0.00 3.42
2249 2314 2.494059 CCGCCTTTCTTGAAGAACAGA 58.506 47.619 7.21 0.00 37.57 3.41
2285 2350 4.976224 ACGCCATTTCCCTATGTTTTAC 57.024 40.909 0.00 0.00 0.00 2.01
2290 2355 4.351192 CATTTCCCTATGTTTTACGCAGC 58.649 43.478 0.00 0.00 0.00 5.25
2310 2375 1.463056 CGGTCGTGATTTTGCTAAGCA 59.537 47.619 0.00 0.00 36.47 3.91
2689 2757 9.430623 TGCTTAAATTTAAAGAATAAAGGTGCC 57.569 29.630 11.62 0.00 0.00 5.01
2690 2758 9.430623 GCTTAAATTTAAAGAATAAAGGTGCCA 57.569 29.630 11.62 0.00 0.00 4.92
2867 2944 5.453648 TGTGGTAATTTATTTGTGACACGC 58.546 37.500 0.22 0.00 0.00 5.34
3050 3127 3.249559 GCAGTATTGCCTGTCTGCTATTC 59.750 47.826 0.00 0.00 46.35 1.75
3062 3139 6.127758 CCTGTCTGCTATTCGATATTCTAGCT 60.128 42.308 0.00 0.00 37.92 3.32
3083 3160 5.039333 GCTGCATTCATACAAGTCATTTCC 58.961 41.667 0.00 0.00 0.00 3.13
3088 3165 6.403636 GCATTCATACAAGTCATTTCCGAACT 60.404 38.462 0.00 0.00 0.00 3.01
3122 3199 3.933886 ACATCCCACCAGATAGTCTCAT 58.066 45.455 0.00 0.00 0.00 2.90
3124 3201 4.723789 ACATCCCACCAGATAGTCTCATTT 59.276 41.667 0.00 0.00 0.00 2.32
3145 3222 3.614092 TCTTCATTTCCATGGTCTCTGC 58.386 45.455 12.58 0.00 0.00 4.26
3146 3223 3.009363 TCTTCATTTCCATGGTCTCTGCA 59.991 43.478 12.58 0.00 0.00 4.41
3203 3281 5.642686 TCCAGGTTTTGTCACGTTTTAAAG 58.357 37.500 0.00 0.00 0.00 1.85
3204 3282 5.183522 TCCAGGTTTTGTCACGTTTTAAAGT 59.816 36.000 0.00 0.00 0.00 2.66
3212 3290 5.812652 TGTCACGTTTTAAAGTGTGGAATC 58.187 37.500 16.96 9.34 39.07 2.52
3228 3306 2.128853 AATCGTTGTGGTTGCTGGCG 62.129 55.000 0.00 0.00 0.00 5.69
3298 3384 7.923414 AATGAAAACCTGTGTATTCTACTCC 57.077 36.000 0.00 0.00 0.00 3.85
3299 3385 5.801380 TGAAAACCTGTGTATTCTACTCCC 58.199 41.667 0.00 0.00 0.00 4.30
3300 3386 5.546499 TGAAAACCTGTGTATTCTACTCCCT 59.454 40.000 0.00 0.00 0.00 4.20
3301 3387 5.678955 AAACCTGTGTATTCTACTCCCTC 57.321 43.478 0.00 0.00 0.00 4.30
3302 3388 4.611564 ACCTGTGTATTCTACTCCCTCT 57.388 45.455 0.00 0.00 0.00 3.69
3303 3389 4.282496 ACCTGTGTATTCTACTCCCTCTG 58.718 47.826 0.00 0.00 0.00 3.35
3304 3390 3.068873 CCTGTGTATTCTACTCCCTCTGC 59.931 52.174 0.00 0.00 0.00 4.26
3305 3391 3.957497 CTGTGTATTCTACTCCCTCTGCT 59.043 47.826 0.00 0.00 0.00 4.24
3306 3392 3.954904 TGTGTATTCTACTCCCTCTGCTC 59.045 47.826 0.00 0.00 0.00 4.26
3307 3393 3.319689 GTGTATTCTACTCCCTCTGCTCC 59.680 52.174 0.00 0.00 0.00 4.70
3308 3394 3.205507 TGTATTCTACTCCCTCTGCTCCT 59.794 47.826 0.00 0.00 0.00 3.69
3309 3395 4.415846 TGTATTCTACTCCCTCTGCTCCTA 59.584 45.833 0.00 0.00 0.00 2.94
3310 3396 4.544564 ATTCTACTCCCTCTGCTCCTAA 57.455 45.455 0.00 0.00 0.00 2.69
3311 3397 4.332683 TTCTACTCCCTCTGCTCCTAAA 57.667 45.455 0.00 0.00 0.00 1.85
3312 3398 4.544564 TCTACTCCCTCTGCTCCTAAAT 57.455 45.455 0.00 0.00 0.00 1.40
3313 3399 5.664815 TCTACTCCCTCTGCTCCTAAATA 57.335 43.478 0.00 0.00 0.00 1.40
3314 3400 6.220881 TCTACTCCCTCTGCTCCTAAATAT 57.779 41.667 0.00 0.00 0.00 1.28
3315 3401 6.625267 TCTACTCCCTCTGCTCCTAAATATT 58.375 40.000 0.00 0.00 0.00 1.28
3316 3402 7.076446 TCTACTCCCTCTGCTCCTAAATATTT 58.924 38.462 5.89 5.89 0.00 1.40
3317 3403 5.934781 ACTCCCTCTGCTCCTAAATATTTG 58.065 41.667 11.05 1.40 0.00 2.32
3318 3404 5.430089 ACTCCCTCTGCTCCTAAATATTTGT 59.570 40.000 11.05 0.00 0.00 2.83
3319 3405 5.930135 TCCCTCTGCTCCTAAATATTTGTC 58.070 41.667 11.05 0.00 0.00 3.18
3320 3406 5.667626 TCCCTCTGCTCCTAAATATTTGTCT 59.332 40.000 11.05 0.00 0.00 3.41
3321 3407 6.158695 TCCCTCTGCTCCTAAATATTTGTCTT 59.841 38.462 11.05 0.00 0.00 3.01
3322 3408 6.830838 CCCTCTGCTCCTAAATATTTGTCTTT 59.169 38.462 11.05 0.00 0.00 2.52
3323 3409 7.012799 CCCTCTGCTCCTAAATATTTGTCTTTC 59.987 40.741 11.05 0.00 0.00 2.62
3324 3410 7.772757 CCTCTGCTCCTAAATATTTGTCTTTCT 59.227 37.037 11.05 0.00 0.00 2.52
3325 3411 9.823647 CTCTGCTCCTAAATATTTGTCTTTCTA 57.176 33.333 11.05 0.00 0.00 2.10
3326 3412 9.823647 TCTGCTCCTAAATATTTGTCTTTCTAG 57.176 33.333 11.05 0.00 0.00 2.43
3327 3413 9.823647 CTGCTCCTAAATATTTGTCTTTCTAGA 57.176 33.333 11.05 0.00 0.00 2.43
3355 3441 8.597662 TTTTAATAGGTGAATACATACGGAGC 57.402 34.615 0.00 0.00 0.00 4.70
3356 3442 5.801531 AATAGGTGAATACATACGGAGCA 57.198 39.130 0.00 0.00 0.00 4.26
3357 3443 5.801531 ATAGGTGAATACATACGGAGCAA 57.198 39.130 0.00 0.00 0.00 3.91
3358 3444 4.481368 AGGTGAATACATACGGAGCAAA 57.519 40.909 0.00 0.00 0.00 3.68
3359 3445 4.839121 AGGTGAATACATACGGAGCAAAA 58.161 39.130 0.00 0.00 0.00 2.44
3360 3446 5.437060 AGGTGAATACATACGGAGCAAAAT 58.563 37.500 0.00 0.00 0.00 1.82
3361 3447 5.296780 AGGTGAATACATACGGAGCAAAATG 59.703 40.000 0.00 0.00 0.00 2.32
3362 3448 5.295787 GGTGAATACATACGGAGCAAAATGA 59.704 40.000 0.00 0.00 0.00 2.57
3363 3449 6.422223 GTGAATACATACGGAGCAAAATGAG 58.578 40.000 0.00 0.00 0.00 2.90
3364 3450 6.037172 GTGAATACATACGGAGCAAAATGAGT 59.963 38.462 0.00 0.00 0.00 3.41
3365 3451 5.991328 ATACATACGGAGCAAAATGAGTG 57.009 39.130 0.00 0.00 0.00 3.51
3366 3452 3.009723 ACATACGGAGCAAAATGAGTGG 58.990 45.455 0.00 0.00 0.00 4.00
3367 3453 3.270027 CATACGGAGCAAAATGAGTGGA 58.730 45.455 0.00 0.00 0.00 4.02
3368 3454 2.496899 ACGGAGCAAAATGAGTGGAT 57.503 45.000 0.00 0.00 0.00 3.41
3369 3455 2.359900 ACGGAGCAAAATGAGTGGATC 58.640 47.619 0.00 0.00 0.00 3.36
3370 3456 2.026822 ACGGAGCAAAATGAGTGGATCT 60.027 45.455 0.00 0.00 0.00 2.75
3371 3457 3.197766 ACGGAGCAAAATGAGTGGATCTA 59.802 43.478 0.00 0.00 0.00 1.98
3372 3458 3.557595 CGGAGCAAAATGAGTGGATCTAC 59.442 47.826 0.00 0.00 0.00 2.59
3373 3459 4.517285 GGAGCAAAATGAGTGGATCTACA 58.483 43.478 12.16 0.00 0.00 2.74
3374 3460 4.333926 GGAGCAAAATGAGTGGATCTACAC 59.666 45.833 12.16 5.82 41.63 2.90
3471 3557 8.792830 TCTGTATCTAAGACAAGAATTTTGGG 57.207 34.615 5.68 0.00 0.00 4.12
3472 3558 8.602424 TCTGTATCTAAGACAAGAATTTTGGGA 58.398 33.333 5.68 0.00 0.00 4.37
3473 3559 8.792830 TGTATCTAAGACAAGAATTTTGGGAG 57.207 34.615 5.68 0.00 0.00 4.30
3474 3560 7.829211 TGTATCTAAGACAAGAATTTTGGGAGG 59.171 37.037 5.68 0.00 0.00 4.30
3475 3561 5.570320 TCTAAGACAAGAATTTTGGGAGGG 58.430 41.667 5.68 0.00 0.00 4.30
3476 3562 4.469469 AAGACAAGAATTTTGGGAGGGA 57.531 40.909 5.68 0.00 0.00 4.20
3477 3563 4.039603 AGACAAGAATTTTGGGAGGGAG 57.960 45.455 5.68 0.00 0.00 4.30
3478 3564 3.092301 GACAAGAATTTTGGGAGGGAGG 58.908 50.000 5.68 0.00 0.00 4.30
3479 3565 2.225369 ACAAGAATTTTGGGAGGGAGGG 60.225 50.000 5.68 0.00 0.00 4.30
3480 3566 2.042979 CAAGAATTTTGGGAGGGAGGGA 59.957 50.000 0.00 0.00 0.00 4.20
3481 3567 1.925959 AGAATTTTGGGAGGGAGGGAG 59.074 52.381 0.00 0.00 0.00 4.30
3482 3568 1.641192 GAATTTTGGGAGGGAGGGAGT 59.359 52.381 0.00 0.00 0.00 3.85
3483 3569 2.680439 ATTTTGGGAGGGAGGGAGTA 57.320 50.000 0.00 0.00 0.00 2.59
3484 3570 1.966845 TTTTGGGAGGGAGGGAGTAG 58.033 55.000 0.00 0.00 0.00 2.57
3485 3571 0.797579 TTTGGGAGGGAGGGAGTAGT 59.202 55.000 0.00 0.00 0.00 2.73
3486 3572 1.702699 TTGGGAGGGAGGGAGTAGTA 58.297 55.000 0.00 0.00 0.00 1.82
3487 3573 1.937098 TGGGAGGGAGGGAGTAGTAT 58.063 55.000 0.00 0.00 0.00 2.12
3488 3574 2.233178 TGGGAGGGAGGGAGTAGTATT 58.767 52.381 0.00 0.00 0.00 1.89
3489 3575 2.179424 TGGGAGGGAGGGAGTAGTATTC 59.821 54.545 0.00 0.00 0.00 1.75
3490 3576 2.451659 GGGAGGGAGGGAGTAGTATTCT 59.548 54.545 0.00 0.00 0.00 2.40
3491 3577 3.661654 GGGAGGGAGGGAGTAGTATTCTA 59.338 52.174 0.00 0.00 0.00 2.10
3492 3578 4.508943 GGGAGGGAGGGAGTAGTATTCTAC 60.509 54.167 1.43 1.43 44.79 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.034066 AACACGACAGGCCCATGG 59.966 61.111 4.14 4.14 0.00 3.66
6 7 2.040544 GGAACACGACAGGCCCATG 61.041 63.158 0.00 0.00 0.00 3.66
7 8 2.351276 GGAACACGACAGGCCCAT 59.649 61.111 0.00 0.00 0.00 4.00
8 9 3.164977 TGGAACACGACAGGCCCA 61.165 61.111 0.00 0.00 0.00 5.36
9 10 2.358737 CTGGAACACGACAGGCCC 60.359 66.667 0.00 0.00 0.00 5.80
10 11 1.668151 GACTGGAACACGACAGGCC 60.668 63.158 0.00 0.00 36.74 5.19
11 12 0.667792 GAGACTGGAACACGACAGGC 60.668 60.000 0.00 0.00 43.15 4.85
12 13 0.038159 GGAGACTGGAACACGACAGG 60.038 60.000 0.00 0.00 39.00 4.00
13 14 0.673985 TGGAGACTGGAACACGACAG 59.326 55.000 0.00 0.00 40.48 3.51
207 208 3.006752 TGATGTTGTTGATCTTTTGGGCC 59.993 43.478 0.00 0.00 0.00 5.80
274 276 0.909623 AACCTCCGAAACCGATGGAT 59.090 50.000 0.00 0.00 0.00 3.41
280 282 1.467342 GATCCAAAACCTCCGAAACCG 59.533 52.381 0.00 0.00 0.00 4.44
283 285 2.961531 TGGATCCAAAACCTCCGAAA 57.038 45.000 13.46 0.00 31.36 3.46
285 287 1.211949 GGATGGATCCAAAACCTCCGA 59.788 52.381 20.67 0.00 46.38 4.55
286 288 1.680338 GGATGGATCCAAAACCTCCG 58.320 55.000 20.67 0.00 46.38 4.63
333 335 2.024273 CCTGGAGGAGGAAGTAGTGGTA 60.024 54.545 0.00 0.00 46.33 3.25
383 386 3.394606 GGGAAATGTCCTTGGGCTCTATA 59.605 47.826 0.82 0.00 44.28 1.31
399 402 1.553248 TCCTCGTTGACATCGGGAAAT 59.447 47.619 7.37 0.00 0.00 2.17
430 435 3.693085 ACTCATCTTTTACCGACGCTCTA 59.307 43.478 0.00 0.00 0.00 2.43
434 439 2.347755 GGAACTCATCTTTTACCGACGC 59.652 50.000 0.00 0.00 0.00 5.19
495 500 3.937079 GGTTGTACAGAAGATTTACCCCG 59.063 47.826 0.00 0.00 0.00 5.73
500 505 7.016858 AGGTGTAAGGGTTGTACAGAAGATTTA 59.983 37.037 0.00 0.00 32.23 1.40
526 531 3.056179 TCGAGAGGTGCATGATACAACAA 60.056 43.478 0.00 0.00 0.00 2.83
564 569 3.991773 TCTATCACCTCGGAAAAACAACG 59.008 43.478 0.00 0.00 0.00 4.10
565 570 4.143179 CGTCTATCACCTCGGAAAAACAAC 60.143 45.833 0.00 0.00 0.00 3.32
568 573 3.582780 ACGTCTATCACCTCGGAAAAAC 58.417 45.455 0.00 0.00 0.00 2.43
572 577 2.439409 TCAACGTCTATCACCTCGGAA 58.561 47.619 0.00 0.00 0.00 4.30
573 578 2.118313 TCAACGTCTATCACCTCGGA 57.882 50.000 0.00 0.00 0.00 4.55
574 579 2.933495 TTCAACGTCTATCACCTCGG 57.067 50.000 0.00 0.00 0.00 4.63
665 670 5.466432 TTTGTGTCGACGTTATTTTGACA 57.534 34.783 11.62 3.22 37.24 3.58
689 694 9.796120 TTACAAAAGAATGAAAACAGAATCGTT 57.204 25.926 0.00 0.00 0.00 3.85
696 701 6.416750 GTCCGGTTACAAAAGAATGAAAACAG 59.583 38.462 0.00 0.00 0.00 3.16
698 703 5.397240 CGTCCGGTTACAAAAGAATGAAAAC 59.603 40.000 0.00 0.00 0.00 2.43
703 708 4.212636 AGTTCGTCCGGTTACAAAAGAATG 59.787 41.667 0.00 0.00 0.00 2.67
704 709 4.383173 AGTTCGTCCGGTTACAAAAGAAT 58.617 39.130 0.00 0.00 0.00 2.40
705 710 3.795877 AGTTCGTCCGGTTACAAAAGAA 58.204 40.909 0.00 0.00 0.00 2.52
706 711 3.457610 AGTTCGTCCGGTTACAAAAGA 57.542 42.857 0.00 0.00 0.00 2.52
707 712 5.636543 AGAATAGTTCGTCCGGTTACAAAAG 59.363 40.000 0.00 0.00 34.02 2.27
821 881 1.710809 ACCCAAGACCCAACAATAGCT 59.289 47.619 0.00 0.00 0.00 3.32
829 889 2.203280 CGCACACCCAAGACCCAA 60.203 61.111 0.00 0.00 0.00 4.12
830 890 4.263572 CCGCACACCCAAGACCCA 62.264 66.667 0.00 0.00 0.00 4.51
841 901 1.152984 CTCCATATTGGGCCGCACA 60.153 57.895 0.00 0.00 38.32 4.57
853 913 2.846206 AGGACACATTTCCAGCTCCATA 59.154 45.455 0.00 0.00 38.25 2.74
859 919 2.206576 AGGAAGGACACATTTCCAGC 57.793 50.000 6.09 0.00 44.26 4.85
950 1012 4.491409 GGAAAGGGAGAGGCGGGC 62.491 72.222 0.00 0.00 0.00 6.13
1134 1196 2.203800 TAAGGCTATCAACTGCGTCG 57.796 50.000 0.00 0.00 0.00 5.12
1435 1497 2.591133 GCGCGCAAGATTAAAGGAAAA 58.409 42.857 29.10 0.00 43.02 2.29
1436 1498 1.135517 GGCGCGCAAGATTAAAGGAAA 60.136 47.619 34.42 0.00 43.02 3.13
1554 1616 5.096443 ACCACACACATTTGGACAAAAAT 57.904 34.783 1.17 0.00 36.28 1.82
1659 1721 5.269505 ACCATCTACAGTGAGCTGAATAC 57.730 43.478 0.00 0.00 45.28 1.89
1699 1761 4.965814 TGCAGATGGACATCTCTAATTCC 58.034 43.478 11.68 0.00 45.78 3.01
1775 1837 4.119862 CACTAGCACACTATTACGCCAAT 58.880 43.478 0.00 0.00 0.00 3.16
1789 1851 1.291877 CCGTGGAACAGCACTAGCAC 61.292 60.000 0.00 0.00 45.49 4.40
1848 1910 5.335661 GCTGTTCCTACCCAAACATAAACAG 60.336 44.000 7.38 7.38 43.12 3.16
1871 1933 7.201350 CGCAACCTAAGAATTAAAGTGATTTGC 60.201 37.037 0.00 0.00 0.00 3.68
1897 1959 1.470098 CCAAAGGTAGCACTGACATGC 59.530 52.381 0.00 2.70 46.50 4.06
1931 1993 4.218852 GGAGGTATAGTATGGAGTGCTGAC 59.781 50.000 0.00 0.00 0.00 3.51
2149 2213 4.851843 AGGCACTCATTCTTGATGATTGA 58.148 39.130 9.62 0.00 44.11 2.57
2249 2314 7.378181 GGAAATGGCGTATTTTATCCATCAAT 58.622 34.615 0.00 0.00 39.06 2.57
2285 2350 1.509787 CAAAATCACGACCGCTGCG 60.510 57.895 16.34 16.34 0.00 5.18
2290 2355 1.463056 TGCTTAGCAAAATCACGACCG 59.537 47.619 3.67 0.00 34.76 4.79
2310 2375 9.723601 ATTGCATATATTTTTCACAAACAGGTT 57.276 25.926 0.00 0.00 0.00 3.50
2344 2410 8.270744 AGAGAGAACAATATAGGAAAGTTGCAT 58.729 33.333 0.00 0.00 0.00 3.96
2361 2427 5.234329 CGTCTTACAAAGCAAAGAGAGAACA 59.766 40.000 0.00 0.00 32.56 3.18
2633 2699 1.299541 CAGCGTTGAAGTGTTCCTGT 58.700 50.000 0.00 0.00 0.00 4.00
2689 2757 3.624410 TCAGGAGATTGAACATCGCAATG 59.376 43.478 0.00 0.00 36.19 2.82
2690 2758 3.877559 TCAGGAGATTGAACATCGCAAT 58.122 40.909 0.00 0.00 38.58 3.56
2788 2856 1.068434 TCAGACTGATTGCACGACACA 59.932 47.619 0.00 0.00 0.00 3.72
2867 2944 0.110238 CCAACAGAACCGCGATTGTG 60.110 55.000 9.12 9.12 0.00 3.33
2875 2952 1.524008 GGAAAGGCCCAACAGAACCG 61.524 60.000 0.00 0.00 0.00 4.44
2951 3028 4.991153 TGTTAACAAACACAGCCATCAA 57.009 36.364 5.64 0.00 0.00 2.57
3050 3127 7.330454 ACTTGTATGAATGCAGCTAGAATATCG 59.670 37.037 0.00 0.00 0.00 2.92
3062 3139 4.940654 TCGGAAATGACTTGTATGAATGCA 59.059 37.500 0.00 0.00 0.00 3.96
3083 3160 4.034510 GGATGTAAGCTGATTCCAAGTTCG 59.965 45.833 0.00 0.00 0.00 3.95
3088 3165 3.620488 GTGGGATGTAAGCTGATTCCAA 58.380 45.455 2.80 0.00 0.00 3.53
3122 3199 4.460382 GCAGAGACCATGGAAATGAAGAAA 59.540 41.667 21.47 0.00 0.00 2.52
3124 3201 3.009363 TGCAGAGACCATGGAAATGAAGA 59.991 43.478 21.47 0.00 0.00 2.87
3203 3281 1.599419 GCAACCACAACGATTCCACAC 60.599 52.381 0.00 0.00 0.00 3.82
3204 3282 0.665835 GCAACCACAACGATTCCACA 59.334 50.000 0.00 0.00 0.00 4.17
3212 3290 3.582120 ACGCCAGCAACCACAACG 61.582 61.111 0.00 0.00 0.00 4.10
3228 3306 1.610522 ACAGCCATTTCTTCACAGCAC 59.389 47.619 0.00 0.00 0.00 4.40
3298 3384 7.772757 AGAAAGACAAATATTTAGGAGCAGAGG 59.227 37.037 0.00 0.00 0.00 3.69
3299 3385 8.729805 AGAAAGACAAATATTTAGGAGCAGAG 57.270 34.615 0.00 0.00 0.00 3.35
3300 3386 9.823647 CTAGAAAGACAAATATTTAGGAGCAGA 57.176 33.333 0.00 0.00 0.00 4.26
3301 3387 9.823647 TCTAGAAAGACAAATATTTAGGAGCAG 57.176 33.333 0.00 0.00 0.00 4.24
3329 3415 9.216117 GCTCCGTATGTATTCACCTATTAAAAT 57.784 33.333 0.00 0.00 0.00 1.82
3330 3416 8.205512 TGCTCCGTATGTATTCACCTATTAAAA 58.794 33.333 0.00 0.00 0.00 1.52
3331 3417 7.728148 TGCTCCGTATGTATTCACCTATTAAA 58.272 34.615 0.00 0.00 0.00 1.52
3332 3418 7.292713 TGCTCCGTATGTATTCACCTATTAA 57.707 36.000 0.00 0.00 0.00 1.40
3333 3419 6.904463 TGCTCCGTATGTATTCACCTATTA 57.096 37.500 0.00 0.00 0.00 0.98
3334 3420 5.801531 TGCTCCGTATGTATTCACCTATT 57.198 39.130 0.00 0.00 0.00 1.73
3335 3421 5.801531 TTGCTCCGTATGTATTCACCTAT 57.198 39.130 0.00 0.00 0.00 2.57
3336 3422 5.601583 TTTGCTCCGTATGTATTCACCTA 57.398 39.130 0.00 0.00 0.00 3.08
3337 3423 4.481368 TTTGCTCCGTATGTATTCACCT 57.519 40.909 0.00 0.00 0.00 4.00
3338 3424 5.295787 TCATTTTGCTCCGTATGTATTCACC 59.704 40.000 0.00 0.00 0.00 4.02
3339 3425 6.037172 ACTCATTTTGCTCCGTATGTATTCAC 59.963 38.462 0.00 0.00 0.00 3.18
3340 3426 6.037062 CACTCATTTTGCTCCGTATGTATTCA 59.963 38.462 0.00 0.00 0.00 2.57
3341 3427 6.422223 CACTCATTTTGCTCCGTATGTATTC 58.578 40.000 0.00 0.00 0.00 1.75
3342 3428 5.296780 CCACTCATTTTGCTCCGTATGTATT 59.703 40.000 0.00 0.00 0.00 1.89
3343 3429 4.816385 CCACTCATTTTGCTCCGTATGTAT 59.184 41.667 0.00 0.00 0.00 2.29
3344 3430 4.081365 TCCACTCATTTTGCTCCGTATGTA 60.081 41.667 0.00 0.00 0.00 2.29
3345 3431 3.009723 CCACTCATTTTGCTCCGTATGT 58.990 45.455 0.00 0.00 0.00 2.29
3346 3432 3.270027 TCCACTCATTTTGCTCCGTATG 58.730 45.455 0.00 0.00 0.00 2.39
3347 3433 3.627395 TCCACTCATTTTGCTCCGTAT 57.373 42.857 0.00 0.00 0.00 3.06
3348 3434 3.197766 AGATCCACTCATTTTGCTCCGTA 59.802 43.478 0.00 0.00 0.00 4.02
3349 3435 2.026822 AGATCCACTCATTTTGCTCCGT 60.027 45.455 0.00 0.00 0.00 4.69
3350 3436 2.636830 AGATCCACTCATTTTGCTCCG 58.363 47.619 0.00 0.00 0.00 4.63
3351 3437 4.333926 GTGTAGATCCACTCATTTTGCTCC 59.666 45.833 0.00 0.00 32.50 4.70
3352 3438 5.181748 AGTGTAGATCCACTCATTTTGCTC 58.818 41.667 0.00 0.00 41.84 4.26
3353 3439 5.171339 AGTGTAGATCCACTCATTTTGCT 57.829 39.130 0.00 0.00 41.84 3.91
3445 3531 9.401058 CCCAAAATTCTTGTCTTAGATACAGAT 57.599 33.333 0.00 0.00 0.00 2.90
3446 3532 8.602424 TCCCAAAATTCTTGTCTTAGATACAGA 58.398 33.333 0.00 0.00 0.00 3.41
3447 3533 8.792830 TCCCAAAATTCTTGTCTTAGATACAG 57.207 34.615 0.00 0.00 0.00 2.74
3448 3534 7.829211 CCTCCCAAAATTCTTGTCTTAGATACA 59.171 37.037 0.00 0.00 0.00 2.29
3449 3535 7.283354 CCCTCCCAAAATTCTTGTCTTAGATAC 59.717 40.741 0.00 0.00 0.00 2.24
3450 3536 7.183839 TCCCTCCCAAAATTCTTGTCTTAGATA 59.816 37.037 0.00 0.00 0.00 1.98
3451 3537 6.011628 TCCCTCCCAAAATTCTTGTCTTAGAT 60.012 38.462 0.00 0.00 0.00 1.98
3452 3538 5.312178 TCCCTCCCAAAATTCTTGTCTTAGA 59.688 40.000 0.00 0.00 0.00 2.10
3453 3539 5.570320 TCCCTCCCAAAATTCTTGTCTTAG 58.430 41.667 0.00 0.00 0.00 2.18
3454 3540 5.516591 CCTCCCTCCCAAAATTCTTGTCTTA 60.517 44.000 0.00 0.00 0.00 2.10
3455 3541 4.411013 CTCCCTCCCAAAATTCTTGTCTT 58.589 43.478 0.00 0.00 0.00 3.01
3456 3542 3.245407 CCTCCCTCCCAAAATTCTTGTCT 60.245 47.826 0.00 0.00 0.00 3.41
3457 3543 3.092301 CCTCCCTCCCAAAATTCTTGTC 58.908 50.000 0.00 0.00 0.00 3.18
3458 3544 2.225369 CCCTCCCTCCCAAAATTCTTGT 60.225 50.000 0.00 0.00 0.00 3.16
3459 3545 2.042979 TCCCTCCCTCCCAAAATTCTTG 59.957 50.000 0.00 0.00 0.00 3.02
3460 3546 2.313041 CTCCCTCCCTCCCAAAATTCTT 59.687 50.000 0.00 0.00 0.00 2.52
3461 3547 1.925959 CTCCCTCCCTCCCAAAATTCT 59.074 52.381 0.00 0.00 0.00 2.40
3462 3548 1.641192 ACTCCCTCCCTCCCAAAATTC 59.359 52.381 0.00 0.00 0.00 2.17
3463 3549 1.773541 ACTCCCTCCCTCCCAAAATT 58.226 50.000 0.00 0.00 0.00 1.82
3464 3550 2.226170 ACTACTCCCTCCCTCCCAAAAT 60.226 50.000 0.00 0.00 0.00 1.82
3465 3551 1.153565 ACTACTCCCTCCCTCCCAAAA 59.846 52.381 0.00 0.00 0.00 2.44
3466 3552 0.797579 ACTACTCCCTCCCTCCCAAA 59.202 55.000 0.00 0.00 0.00 3.28
3467 3553 1.702699 TACTACTCCCTCCCTCCCAA 58.297 55.000 0.00 0.00 0.00 4.12
3468 3554 1.937098 ATACTACTCCCTCCCTCCCA 58.063 55.000 0.00 0.00 0.00 4.37
3469 3555 2.451659 AGAATACTACTCCCTCCCTCCC 59.548 54.545 0.00 0.00 0.00 4.30
3470 3556 3.907459 AGAATACTACTCCCTCCCTCC 57.093 52.381 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.