Multiple sequence alignment - TraesCS5A01G120300

Loading Multiple Alignment...

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 TraesCS5A01G120300 chr5A 100.000 3575 0 0 1 3575 257489414 257492988 0.000000e+00 6602
1 TraesCS5A01G120300 chr3A 98.008 3413 58 9 5 3410 286012549 286015958 0.000000e+00 5917
2 TraesCS5A01G120300 chr3A 97.865 3420 56 13 1 3410 320855402 320858814 0.000000e+00 5895
3 TraesCS5A01G120300 chrUn 97.926 3424 54 12 1 3410 145662336 145665756 0.000000e+00 5914
4 TraesCS5A01G120300 chrUn 97.925 3421 53 13 1 3410 118651556 118654969 0.000000e+00 5908
5 TraesCS5A01G120300 chrUn 97.867 3423 56 11 1 3411 13616664 13620081 0.000000e+00 5901
6 TraesCS5A01G120300 chr6A 97.867 3423 56 12 1 3410 282820741 282824159 0.000000e+00 5901
7 TraesCS5A01G120300 chr6A 97.836 3420 60 9 1 3410 286515271 286511856 0.000000e+00 5893
8 TraesCS5A01G120300 chr4A 97.866 3421 58 11 1 3410 271085006 271081590 0.000000e+00 5899
9 TraesCS5A01G120300 chr1B 97.838 3423 56 13 1 3411 239486131 239489547 0.000000e+00 5895
10 TraesCS5A01G120300 chr1B 95.758 165 7 0 3411 3575 192302292 192302456 2.120000e-67 267
11 TraesCS5A01G120300 chr6B 96.364 165 6 0 3411 3575 500946644 500946480 4.550000e-69 272
12 TraesCS5A01G120300 chr7B 95.758 165 7 0 3411 3575 97042719 97042883 2.120000e-67 267
13 TraesCS5A01G120300 chr5D 95.758 165 7 0 3411 3575 69072849 69072685 2.120000e-67 267
14 TraesCS5A01G120300 chr5D 95.758 165 7 0 3411 3575 258677226 258677062 2.120000e-67 267
15 TraesCS5A01G120300 chr5D 95.152 165 8 0 3411 3575 355250246 355250082 9.840000e-66 261
16 TraesCS5A01G120300 chr4D 95.758 165 7 0 3411 3575 422492132 422492296 2.120000e-67 267
17 TraesCS5A01G120300 chr3D 95.758 165 7 0 3411 3575 299160595 299160431 2.120000e-67 267
18 TraesCS5A01G120300 chr1D 95.758 165 7 0 3411 3575 316839123 316839287 2.120000e-67 267


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 TraesCS5A01G120300 chr5A 257489414 257492988 3574 False 6602 6602 100.000 1 3575 1 chr5A.!!$F1 3574
1 TraesCS5A01G120300 chr3A 286012549 286015958 3409 False 5917 5917 98.008 5 3410 1 chr3A.!!$F1 3405
2 TraesCS5A01G120300 chr3A 320855402 320858814 3412 False 5895 5895 97.865 1 3410 1 chr3A.!!$F2 3409
3 TraesCS5A01G120300 chrUn 145662336 145665756 3420 False 5914 5914 97.926 1 3410 1 chrUn.!!$F3 3409
4 TraesCS5A01G120300 chrUn 118651556 118654969 3413 False 5908 5908 97.925 1 3410 1 chrUn.!!$F2 3409
5 TraesCS5A01G120300 chrUn 13616664 13620081 3417 False 5901 5901 97.867 1 3411 1 chrUn.!!$F1 3410
6 TraesCS5A01G120300 chr6A 282820741 282824159 3418 False 5901 5901 97.867 1 3410 1 chr6A.!!$F1 3409
7 TraesCS5A01G120300 chr6A 286511856 286515271 3415 True 5893 5893 97.836 1 3410 1 chr6A.!!$R1 3409
8 TraesCS5A01G120300 chr4A 271081590 271085006 3416 True 5899 5899 97.866 1 3410 1 chr4A.!!$R1 3409
9 TraesCS5A01G120300 chr1B 239486131 239489547 3416 False 5895 5895 97.838 1 3411 1 chr1B.!!$F2 3410

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
703 737 1.219393 GCCTAGGACCAGCACAGTC 59.781 63.158 14.75 0.0 0.00 3.51 F
863 897 3.879912 CGGAGTTACTTGACACCGT 57.120 52.632 5.86 0.0 45.01 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1642 1676 1.237285 ACTCTTGGAATGTGCACCGC 61.237 55.0 15.69 3.11 0.0 5.68 R
2635 2673 5.594926 AGAGAACTTTTTGGACAGCAAATG 58.405 37.5 0.00 0.00 0.0 2.32 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
90 112 9.898152 AAGAGAGAGAAGAAAAAGAGAAAAAGA 57.102 29.630 0.00 0.00 0.00 2.52
91 113 9.898152 AGAGAGAGAAGAAAAAGAGAAAAAGAA 57.102 29.630 0.00 0.00 0.00 2.52
202 236 5.467399 TGTTCGGTAAAACAGGTGTATCTTG 59.533 40.000 0.00 0.00 34.31 3.02
297 331 7.686438 TGCAGAAGCTAGTTCAATATTTGAA 57.314 32.000 0.00 0.00 43.59 2.69
703 737 1.219393 GCCTAGGACCAGCACAGTC 59.781 63.158 14.75 0.00 0.00 3.51
863 897 3.879912 CGGAGTTACTTGACACCGT 57.120 52.632 5.86 0.00 45.01 4.83
931 965 8.340618 ACATTGATATTTGCTTTACTGTGAGT 57.659 30.769 0.00 0.00 0.00 3.41
1399 1433 6.017523 TCGTGACATGATTAAGAAGTTGCAAA 60.018 34.615 0.00 0.00 0.00 3.68
1642 1676 2.430921 ACGAGGAGAACAAGCGCG 60.431 61.111 0.00 0.00 0.00 6.86
2063 2097 4.082625 TGGTGATGATTCTGTGTTGAATGC 60.083 41.667 0.00 0.00 36.86 3.56
2238 2272 7.122501 TGCAATATTTTCATGCCTTCTACTTCA 59.877 33.333 0.00 0.00 39.31 3.02
2635 2673 9.612066 ATGAAGATAAGGAAGAAAGAGATGTTC 57.388 33.333 0.00 0.00 0.00 3.18
2950 2988 1.852157 ATCACCTCCACTTGGGCCA 60.852 57.895 0.00 0.00 36.21 5.36
3173 3212 8.108999 TCCCCACCATTATCAATACTTCATATG 58.891 37.037 0.00 0.00 0.00 1.78
3213 3252 8.565416 CAGATTGCTTTATCATATTCTTGCTCA 58.435 33.333 0.00 0.00 0.00 4.26
3294 3333 3.193691 CGTCAGTAACCTCAGGAGATTGT 59.806 47.826 0.00 0.00 0.00 2.71
3411 3452 1.343069 GGACCCTCGCCTCTATCATT 58.657 55.000 0.00 0.00 0.00 2.57
3412 3453 1.694696 GGACCCTCGCCTCTATCATTT 59.305 52.381 0.00 0.00 0.00 2.32
3413 3454 2.548920 GGACCCTCGCCTCTATCATTTG 60.549 54.545 0.00 0.00 0.00 2.32
3414 3455 2.103263 GACCCTCGCCTCTATCATTTGT 59.897 50.000 0.00 0.00 0.00 2.83
3415 3456 2.158900 ACCCTCGCCTCTATCATTTGTG 60.159 50.000 0.00 0.00 0.00 3.33
3416 3457 2.103094 CCCTCGCCTCTATCATTTGTGA 59.897 50.000 0.00 0.00 0.00 3.58
3417 3458 3.244353 CCCTCGCCTCTATCATTTGTGAT 60.244 47.826 0.00 0.00 0.00 3.06
3418 3459 3.744942 CCTCGCCTCTATCATTTGTGATG 59.255 47.826 1.37 0.00 0.00 3.07
3419 3460 3.732212 TCGCCTCTATCATTTGTGATGG 58.268 45.455 1.37 0.00 0.00 3.51
3420 3461 2.810274 CGCCTCTATCATTTGTGATGGG 59.190 50.000 1.37 2.94 0.00 4.00
3421 3462 3.745480 CGCCTCTATCATTTGTGATGGGT 60.745 47.826 1.37 0.00 0.00 4.51
3422 3463 4.210331 GCCTCTATCATTTGTGATGGGTT 58.790 43.478 1.37 0.00 0.00 4.11
3423 3464 4.276926 GCCTCTATCATTTGTGATGGGTTC 59.723 45.833 1.37 0.00 0.00 3.62
3424 3465 4.512944 CCTCTATCATTTGTGATGGGTTCG 59.487 45.833 1.37 0.00 0.00 3.95
3425 3466 5.351948 TCTATCATTTGTGATGGGTTCGA 57.648 39.130 1.37 0.00 0.00 3.71
3426 3467 5.928976 TCTATCATTTGTGATGGGTTCGAT 58.071 37.500 1.37 0.00 0.00 3.59
3427 3468 5.991606 TCTATCATTTGTGATGGGTTCGATC 59.008 40.000 1.37 0.00 0.00 3.69
3428 3469 4.220693 TCATTTGTGATGGGTTCGATCT 57.779 40.909 0.00 0.00 0.00 2.75
3429 3470 4.588899 TCATTTGTGATGGGTTCGATCTT 58.411 39.130 0.00 0.00 0.00 2.40
3430 3471 5.739959 TCATTTGTGATGGGTTCGATCTTA 58.260 37.500 0.00 0.00 0.00 2.10
3431 3472 6.356556 TCATTTGTGATGGGTTCGATCTTAT 58.643 36.000 0.00 0.00 0.00 1.73
3432 3473 6.260714 TCATTTGTGATGGGTTCGATCTTATG 59.739 38.462 0.00 0.00 0.00 1.90
3433 3474 4.071961 TGTGATGGGTTCGATCTTATGG 57.928 45.455 0.00 0.00 0.00 2.74
3434 3475 3.454447 TGTGATGGGTTCGATCTTATGGT 59.546 43.478 0.00 0.00 0.00 3.55
3435 3476 3.809832 GTGATGGGTTCGATCTTATGGTG 59.190 47.826 0.00 0.00 0.00 4.17
3436 3477 2.325583 TGGGTTCGATCTTATGGTGC 57.674 50.000 0.00 0.00 0.00 5.01
3437 3478 1.837439 TGGGTTCGATCTTATGGTGCT 59.163 47.619 0.00 0.00 0.00 4.40
3438 3479 2.158957 TGGGTTCGATCTTATGGTGCTC 60.159 50.000 0.00 0.00 0.00 4.26
3439 3480 2.128035 GGTTCGATCTTATGGTGCTCG 58.872 52.381 0.00 0.00 0.00 5.03
3440 3481 2.223735 GGTTCGATCTTATGGTGCTCGA 60.224 50.000 0.00 0.00 36.65 4.04
3441 3482 3.553096 GGTTCGATCTTATGGTGCTCGAT 60.553 47.826 0.00 0.00 38.07 3.59
3442 3483 3.560902 TCGATCTTATGGTGCTCGATC 57.439 47.619 0.00 0.00 33.80 3.69
3443 3484 2.229062 TCGATCTTATGGTGCTCGATCC 59.771 50.000 0.00 0.00 33.80 3.36
3444 3485 2.230025 CGATCTTATGGTGCTCGATCCT 59.770 50.000 0.00 0.00 0.00 3.24
3445 3486 3.440522 CGATCTTATGGTGCTCGATCCTA 59.559 47.826 0.00 0.00 0.00 2.94
3446 3487 4.438065 CGATCTTATGGTGCTCGATCCTAG 60.438 50.000 0.00 0.00 0.00 3.02
3447 3488 3.833732 TCTTATGGTGCTCGATCCTAGT 58.166 45.455 0.00 0.00 0.00 2.57
3448 3489 3.570125 TCTTATGGTGCTCGATCCTAGTG 59.430 47.826 0.00 0.00 0.00 2.74
3449 3490 2.073252 ATGGTGCTCGATCCTAGTGA 57.927 50.000 0.00 0.00 0.00 3.41
3450 3491 1.103803 TGGTGCTCGATCCTAGTGAC 58.896 55.000 0.00 0.00 0.00 3.67
3451 3492 1.103803 GGTGCTCGATCCTAGTGACA 58.896 55.000 0.00 0.00 0.00 3.58
3452 3493 1.066303 GGTGCTCGATCCTAGTGACAG 59.934 57.143 0.00 0.00 0.00 3.51
3453 3494 2.017782 GTGCTCGATCCTAGTGACAGA 58.982 52.381 0.00 0.00 0.00 3.41
3454 3495 2.423892 GTGCTCGATCCTAGTGACAGAA 59.576 50.000 0.00 0.00 0.00 3.02
3455 3496 2.685388 TGCTCGATCCTAGTGACAGAAG 59.315 50.000 0.00 0.00 0.00 2.85
3456 3497 2.034053 GCTCGATCCTAGTGACAGAAGG 59.966 54.545 0.00 0.00 0.00 3.46
3457 3498 2.621055 CTCGATCCTAGTGACAGAAGGG 59.379 54.545 3.70 0.00 0.00 3.95
3458 3499 1.683917 CGATCCTAGTGACAGAAGGGG 59.316 57.143 3.70 0.00 0.00 4.79
3459 3500 2.687014 CGATCCTAGTGACAGAAGGGGA 60.687 54.545 3.70 0.00 0.00 4.81
3460 3501 3.375699 GATCCTAGTGACAGAAGGGGAA 58.624 50.000 3.70 0.00 0.00 3.97
3461 3502 2.537143 TCCTAGTGACAGAAGGGGAAC 58.463 52.381 3.70 0.00 0.00 3.62
3475 3516 2.877043 GGGAACCGACACGTATGTAT 57.123 50.000 0.00 0.00 40.86 2.29
3476 3517 3.169355 GGGAACCGACACGTATGTATT 57.831 47.619 0.00 0.00 40.86 1.89
3477 3518 2.861935 GGGAACCGACACGTATGTATTG 59.138 50.000 0.00 0.00 40.86 1.90
3478 3519 3.514645 GGAACCGACACGTATGTATTGT 58.485 45.455 0.00 0.00 39.95 2.71
3479 3520 3.928375 GGAACCGACACGTATGTATTGTT 59.072 43.478 0.00 0.00 39.95 2.83
3480 3521 4.389687 GGAACCGACACGTATGTATTGTTT 59.610 41.667 0.00 0.00 39.95 2.83
3481 3522 5.445010 GGAACCGACACGTATGTATTGTTTC 60.445 44.000 0.00 0.00 39.95 2.78
3482 3523 4.813027 ACCGACACGTATGTATTGTTTCT 58.187 39.130 0.00 0.00 39.95 2.52
3483 3524 5.953183 ACCGACACGTATGTATTGTTTCTA 58.047 37.500 0.00 0.00 39.95 2.10
3484 3525 6.567050 ACCGACACGTATGTATTGTTTCTAT 58.433 36.000 0.00 0.00 39.95 1.98
3485 3526 7.037438 ACCGACACGTATGTATTGTTTCTATT 58.963 34.615 0.00 0.00 39.95 1.73
3486 3527 8.190122 ACCGACACGTATGTATTGTTTCTATTA 58.810 33.333 0.00 0.00 39.95 0.98
3487 3528 9.022915 CCGACACGTATGTATTGTTTCTATTAA 57.977 33.333 0.00 0.00 39.95 1.40
3506 3547 9.629649 TCTATTAAGGATAACAATATGGGGTCT 57.370 33.333 0.00 0.00 0.00 3.85
3512 3553 8.525729 AGGATAACAATATGGGGTCTATTTCT 57.474 34.615 0.00 0.00 0.00 2.52
3513 3554 9.629649 AGGATAACAATATGGGGTCTATTTCTA 57.370 33.333 0.00 0.00 0.00 2.10
3514 3555 9.668497 GGATAACAATATGGGGTCTATTTCTAC 57.332 37.037 0.00 0.00 0.00 2.59
3543 3584 9.671279 AAATACATCTTGTCTACATCATGTCAA 57.329 29.630 0.00 0.00 33.31 3.18
3544 3585 6.974932 ACATCTTGTCTACATCATGTCAAC 57.025 37.500 0.00 0.00 0.00 3.18
3545 3586 5.578336 ACATCTTGTCTACATCATGTCAACG 59.422 40.000 0.00 0.00 0.00 4.10
3546 3587 5.134202 TCTTGTCTACATCATGTCAACGT 57.866 39.130 0.00 0.00 0.00 3.99
3547 3588 5.538118 TCTTGTCTACATCATGTCAACGTT 58.462 37.500 0.00 0.00 0.00 3.99
3548 3589 5.633601 TCTTGTCTACATCATGTCAACGTTC 59.366 40.000 0.00 0.00 0.00 3.95
3549 3590 5.134202 TGTCTACATCATGTCAACGTTCT 57.866 39.130 0.00 0.00 0.00 3.01
3550 3591 5.538118 TGTCTACATCATGTCAACGTTCTT 58.462 37.500 0.00 0.00 0.00 2.52
3551 3592 6.683715 TGTCTACATCATGTCAACGTTCTTA 58.316 36.000 0.00 0.00 0.00 2.10
3552 3593 7.320399 TGTCTACATCATGTCAACGTTCTTAT 58.680 34.615 0.00 0.00 0.00 1.73
3553 3594 7.817478 TGTCTACATCATGTCAACGTTCTTATT 59.183 33.333 0.00 0.00 0.00 1.40
3554 3595 8.110612 GTCTACATCATGTCAACGTTCTTATTG 58.889 37.037 0.00 0.00 0.00 1.90
3555 3596 5.631026 ACATCATGTCAACGTTCTTATTGC 58.369 37.500 0.00 0.00 0.00 3.56
3556 3597 5.181056 ACATCATGTCAACGTTCTTATTGCA 59.819 36.000 0.00 0.00 0.00 4.08
3557 3598 5.878332 TCATGTCAACGTTCTTATTGCAT 57.122 34.783 0.00 0.00 0.00 3.96
3558 3599 6.252967 TCATGTCAACGTTCTTATTGCATT 57.747 33.333 0.00 0.00 0.00 3.56
3559 3600 7.371126 TCATGTCAACGTTCTTATTGCATTA 57.629 32.000 0.00 0.00 0.00 1.90
3560 3601 7.240674 TCATGTCAACGTTCTTATTGCATTAC 58.759 34.615 0.00 0.00 0.00 1.89
3561 3602 6.795098 TGTCAACGTTCTTATTGCATTACT 57.205 33.333 0.00 0.00 0.00 2.24
3562 3603 6.827641 TGTCAACGTTCTTATTGCATTACTC 58.172 36.000 0.00 0.00 0.00 2.59
3563 3604 6.128391 TGTCAACGTTCTTATTGCATTACTCC 60.128 38.462 0.00 0.00 0.00 3.85
3564 3605 5.062934 TCAACGTTCTTATTGCATTACTCCG 59.937 40.000 0.00 0.00 0.00 4.63
3565 3606 4.501071 ACGTTCTTATTGCATTACTCCGT 58.499 39.130 0.00 0.00 0.00 4.69
3566 3607 4.933400 ACGTTCTTATTGCATTACTCCGTT 59.067 37.500 0.00 0.00 0.00 4.44
3567 3608 5.410439 ACGTTCTTATTGCATTACTCCGTTT 59.590 36.000 0.00 0.00 0.00 3.60
3568 3609 5.957796 CGTTCTTATTGCATTACTCCGTTTC 59.042 40.000 0.00 0.00 0.00 2.78
3569 3610 6.183360 CGTTCTTATTGCATTACTCCGTTTCT 60.183 38.462 0.00 0.00 0.00 2.52
3570 3611 6.903883 TCTTATTGCATTACTCCGTTTCTC 57.096 37.500 0.00 0.00 0.00 2.87
3571 3612 5.815740 TCTTATTGCATTACTCCGTTTCTCC 59.184 40.000 0.00 0.00 0.00 3.71
3572 3613 3.410631 TTGCATTACTCCGTTTCTCCA 57.589 42.857 0.00 0.00 0.00 3.86
3573 3614 3.627395 TGCATTACTCCGTTTCTCCAT 57.373 42.857 0.00 0.00 0.00 3.41
3574 3615 3.270027 TGCATTACTCCGTTTCTCCATG 58.730 45.455 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 236 3.424962 GCCAAAACTGACTTCGTATGAGC 60.425 47.826 0.00 0.00 0.00 4.26
297 331 7.162082 CCTATTTAGAAGCCGATTATGAGGTT 58.838 38.462 0.00 0.00 0.00 3.50
483 517 5.895928 ACTTTCCTCTTGAAAAGTTTGAGC 58.104 37.500 0.00 0.00 46.34 4.26
773 807 1.496444 TATGTGGAGCTGGGTTGGCA 61.496 55.000 0.00 0.00 0.00 4.92
863 897 3.053291 GCGGTGATCGGCAACCAA 61.053 61.111 1.31 0.00 39.26 3.67
931 965 4.986054 ACTAGGATGTGGTGGTAAAACA 57.014 40.909 0.00 0.00 0.00 2.83
1003 1037 3.272574 TGAATTGACTCTGGATCCTGC 57.727 47.619 14.23 0.53 0.00 4.85
1399 1433 8.344446 ACAGTTTCACTACCTTGTTTTAAGTT 57.656 30.769 0.00 0.00 0.00 2.66
1642 1676 1.237285 ACTCTTGGAATGTGCACCGC 61.237 55.000 15.69 3.11 0.00 5.68
2635 2673 5.594926 AGAGAACTTTTTGGACAGCAAATG 58.405 37.500 0.00 0.00 0.00 2.32
2950 2988 2.835764 TCTAGGTCGTACAAGGCCAATT 59.164 45.455 5.01 0.00 0.00 2.32
3213 3252 2.715046 TCCTGCAAGCAATCGAAGAAT 58.285 42.857 0.00 0.00 43.58 2.40
3411 3452 4.080582 ACCATAAGATCGAACCCATCACAA 60.081 41.667 0.00 0.00 0.00 3.33
3412 3453 3.454447 ACCATAAGATCGAACCCATCACA 59.546 43.478 0.00 0.00 0.00 3.58
3413 3454 3.809832 CACCATAAGATCGAACCCATCAC 59.190 47.826 0.00 0.00 0.00 3.06
3414 3455 3.744214 GCACCATAAGATCGAACCCATCA 60.744 47.826 0.00 0.00 0.00 3.07
3415 3456 2.808543 GCACCATAAGATCGAACCCATC 59.191 50.000 0.00 0.00 0.00 3.51
3416 3457 2.439507 AGCACCATAAGATCGAACCCAT 59.560 45.455 0.00 0.00 0.00 4.00
3417 3458 1.837439 AGCACCATAAGATCGAACCCA 59.163 47.619 0.00 0.00 0.00 4.51
3418 3459 2.484889 GAGCACCATAAGATCGAACCC 58.515 52.381 0.00 0.00 0.00 4.11
3419 3460 2.128035 CGAGCACCATAAGATCGAACC 58.872 52.381 0.00 0.00 35.47 3.62
3420 3461 3.079960 TCGAGCACCATAAGATCGAAC 57.920 47.619 0.79 0.00 39.26 3.95
3421 3462 3.305403 GGATCGAGCACCATAAGATCGAA 60.305 47.826 7.61 0.00 44.55 3.71
3422 3463 2.229062 GGATCGAGCACCATAAGATCGA 59.771 50.000 1.84 6.00 45.34 3.59
3423 3464 2.230025 AGGATCGAGCACCATAAGATCG 59.770 50.000 1.84 0.00 38.75 3.69
3424 3465 3.951775 AGGATCGAGCACCATAAGATC 57.048 47.619 1.84 0.00 37.55 2.75
3425 3466 4.219507 CACTAGGATCGAGCACCATAAGAT 59.780 45.833 1.84 0.00 0.00 2.40
3426 3467 3.570125 CACTAGGATCGAGCACCATAAGA 59.430 47.826 1.84 0.00 0.00 2.10
3427 3468 3.570125 TCACTAGGATCGAGCACCATAAG 59.430 47.826 1.84 2.96 0.00 1.73
3428 3469 3.318275 GTCACTAGGATCGAGCACCATAA 59.682 47.826 1.84 0.00 0.00 1.90
3429 3470 2.885266 GTCACTAGGATCGAGCACCATA 59.115 50.000 1.84 0.00 0.00 2.74
3430 3471 1.683917 GTCACTAGGATCGAGCACCAT 59.316 52.381 1.84 0.00 0.00 3.55
3431 3472 1.103803 GTCACTAGGATCGAGCACCA 58.896 55.000 1.84 0.00 0.00 4.17
3432 3473 1.066303 CTGTCACTAGGATCGAGCACC 59.934 57.143 1.84 0.04 0.00 5.01
3433 3474 2.017782 TCTGTCACTAGGATCGAGCAC 58.982 52.381 1.84 0.00 0.00 4.40
3434 3475 2.420058 TCTGTCACTAGGATCGAGCA 57.580 50.000 1.84 0.00 0.00 4.26
3435 3476 2.034053 CCTTCTGTCACTAGGATCGAGC 59.966 54.545 0.00 0.00 0.00 5.03
3436 3477 2.621055 CCCTTCTGTCACTAGGATCGAG 59.379 54.545 0.00 0.00 0.00 4.04
3437 3478 2.656002 CCCTTCTGTCACTAGGATCGA 58.344 52.381 0.00 0.00 0.00 3.59
3438 3479 1.683917 CCCCTTCTGTCACTAGGATCG 59.316 57.143 0.00 0.00 0.00 3.69
3439 3480 3.033659 TCCCCTTCTGTCACTAGGATC 57.966 52.381 0.00 0.00 0.00 3.36
3440 3481 3.108376 GTTCCCCTTCTGTCACTAGGAT 58.892 50.000 0.00 0.00 0.00 3.24
3441 3482 2.537143 GTTCCCCTTCTGTCACTAGGA 58.463 52.381 0.00 0.00 0.00 2.94
3442 3483 1.555533 GGTTCCCCTTCTGTCACTAGG 59.444 57.143 0.00 0.00 0.00 3.02
3443 3484 1.204941 CGGTTCCCCTTCTGTCACTAG 59.795 57.143 0.00 0.00 0.00 2.57
3444 3485 1.203087 TCGGTTCCCCTTCTGTCACTA 60.203 52.381 0.00 0.00 0.00 2.74
3445 3486 0.471211 TCGGTTCCCCTTCTGTCACT 60.471 55.000 0.00 0.00 0.00 3.41
3446 3487 0.320508 GTCGGTTCCCCTTCTGTCAC 60.321 60.000 0.00 0.00 0.00 3.67
3447 3488 0.761323 TGTCGGTTCCCCTTCTGTCA 60.761 55.000 0.00 0.00 0.00 3.58
3448 3489 0.320508 GTGTCGGTTCCCCTTCTGTC 60.321 60.000 0.00 0.00 0.00 3.51
3449 3490 1.752833 GTGTCGGTTCCCCTTCTGT 59.247 57.895 0.00 0.00 0.00 3.41
3450 3491 1.374252 CGTGTCGGTTCCCCTTCTG 60.374 63.158 0.00 0.00 0.00 3.02
3451 3492 0.540365 TACGTGTCGGTTCCCCTTCT 60.540 55.000 0.00 0.00 0.00 2.85
3452 3493 0.533951 ATACGTGTCGGTTCCCCTTC 59.466 55.000 0.00 0.00 0.00 3.46
3453 3494 0.248289 CATACGTGTCGGTTCCCCTT 59.752 55.000 0.00 0.00 0.00 3.95
3454 3495 0.901580 ACATACGTGTCGGTTCCCCT 60.902 55.000 0.00 0.00 31.41 4.79
3455 3496 0.817013 TACATACGTGTCGGTTCCCC 59.183 55.000 0.00 0.00 39.77 4.81
3456 3497 2.861935 CAATACATACGTGTCGGTTCCC 59.138 50.000 0.00 0.00 39.77 3.97
3457 3498 3.514645 ACAATACATACGTGTCGGTTCC 58.485 45.455 0.00 0.00 39.77 3.62
3458 3499 5.346822 AGAAACAATACATACGTGTCGGTTC 59.653 40.000 0.00 0.00 39.77 3.62
3459 3500 5.232463 AGAAACAATACATACGTGTCGGTT 58.768 37.500 0.00 0.00 39.77 4.44
3460 3501 4.813027 AGAAACAATACATACGTGTCGGT 58.187 39.130 0.00 0.00 39.77 4.69
3461 3502 7.459394 AATAGAAACAATACATACGTGTCGG 57.541 36.000 0.00 0.00 39.77 4.79
3480 3521 9.629649 AGACCCCATATTGTTATCCTTAATAGA 57.370 33.333 0.00 0.00 0.00 1.98
3486 3527 8.960064 AGAAATAGACCCCATATTGTTATCCTT 58.040 33.333 0.00 0.00 0.00 3.36
3487 3528 8.525729 AGAAATAGACCCCATATTGTTATCCT 57.474 34.615 0.00 0.00 0.00 3.24
3488 3529 9.668497 GTAGAAATAGACCCCATATTGTTATCC 57.332 37.037 0.00 0.00 0.00 2.59
3517 3558 9.671279 TTGACATGATGTAGACAAGATGTATTT 57.329 29.630 0.00 0.00 34.13 1.40
3518 3559 9.102757 GTTGACATGATGTAGACAAGATGTATT 57.897 33.333 0.00 0.00 34.13 1.89
3519 3560 7.436376 CGTTGACATGATGTAGACAAGATGTAT 59.564 37.037 0.00 0.00 34.13 2.29
3520 3561 6.751888 CGTTGACATGATGTAGACAAGATGTA 59.248 38.462 0.00 0.00 34.13 2.29
3521 3562 5.578336 CGTTGACATGATGTAGACAAGATGT 59.422 40.000 0.00 8.79 35.64 3.06
3522 3563 5.578336 ACGTTGACATGATGTAGACAAGATG 59.422 40.000 0.00 3.79 0.00 2.90
3523 3564 5.724328 ACGTTGACATGATGTAGACAAGAT 58.276 37.500 0.00 0.00 0.00 2.40
3524 3565 5.134202 ACGTTGACATGATGTAGACAAGA 57.866 39.130 0.00 0.00 0.00 3.02
3525 3566 5.635280 AGAACGTTGACATGATGTAGACAAG 59.365 40.000 5.00 0.00 0.00 3.16
3526 3567 5.538118 AGAACGTTGACATGATGTAGACAA 58.462 37.500 5.00 0.00 0.00 3.18
3527 3568 5.134202 AGAACGTTGACATGATGTAGACA 57.866 39.130 5.00 0.00 0.00 3.41
3528 3569 7.757097 ATAAGAACGTTGACATGATGTAGAC 57.243 36.000 5.00 0.00 0.00 2.59
3529 3570 7.201522 GCAATAAGAACGTTGACATGATGTAGA 60.202 37.037 5.00 0.00 0.00 2.59
3530 3571 6.901887 GCAATAAGAACGTTGACATGATGTAG 59.098 38.462 5.00 0.00 0.00 2.74
3531 3572 6.370166 TGCAATAAGAACGTTGACATGATGTA 59.630 34.615 5.00 0.00 0.00 2.29
3532 3573 5.181056 TGCAATAAGAACGTTGACATGATGT 59.819 36.000 5.00 0.00 0.00 3.06
3533 3574 5.630061 TGCAATAAGAACGTTGACATGATG 58.370 37.500 5.00 0.00 0.00 3.07
3534 3575 5.878332 TGCAATAAGAACGTTGACATGAT 57.122 34.783 5.00 0.00 0.00 2.45
3535 3576 5.878332 ATGCAATAAGAACGTTGACATGA 57.122 34.783 5.00 0.00 0.00 3.07
3536 3577 7.243487 AGTAATGCAATAAGAACGTTGACATG 58.757 34.615 5.00 0.00 0.00 3.21
3537 3578 7.377766 AGTAATGCAATAAGAACGTTGACAT 57.622 32.000 5.00 0.00 0.00 3.06
3538 3579 6.128391 GGAGTAATGCAATAAGAACGTTGACA 60.128 38.462 5.00 0.00 0.00 3.58
3539 3580 6.248631 GGAGTAATGCAATAAGAACGTTGAC 58.751 40.000 5.00 0.00 0.00 3.18
3540 3581 5.062934 CGGAGTAATGCAATAAGAACGTTGA 59.937 40.000 5.00 0.00 0.00 3.18
3541 3582 5.163893 ACGGAGTAATGCAATAAGAACGTTG 60.164 40.000 5.00 0.00 41.94 4.10
3542 3583 4.933400 ACGGAGTAATGCAATAAGAACGTT 59.067 37.500 0.00 0.00 41.94 3.99
3543 3584 4.501071 ACGGAGTAATGCAATAAGAACGT 58.499 39.130 0.00 0.00 41.94 3.99
3544 3585 5.464965 AACGGAGTAATGCAATAAGAACG 57.535 39.130 0.00 0.00 45.00 3.95
3545 3586 7.073342 AGAAACGGAGTAATGCAATAAGAAC 57.927 36.000 0.00 0.00 45.00 3.01
3546 3587 6.315393 GGAGAAACGGAGTAATGCAATAAGAA 59.685 38.462 0.00 0.00 45.00 2.52
3547 3588 5.815740 GGAGAAACGGAGTAATGCAATAAGA 59.184 40.000 0.00 0.00 45.00 2.10
3548 3589 5.584649 TGGAGAAACGGAGTAATGCAATAAG 59.415 40.000 0.00 0.00 45.00 1.73
3549 3590 5.492895 TGGAGAAACGGAGTAATGCAATAA 58.507 37.500 0.00 0.00 45.00 1.40
3550 3591 5.092554 TGGAGAAACGGAGTAATGCAATA 57.907 39.130 0.00 0.00 45.00 1.90
3551 3592 3.950397 TGGAGAAACGGAGTAATGCAAT 58.050 40.909 0.00 0.00 45.00 3.56
3552 3593 3.410631 TGGAGAAACGGAGTAATGCAA 57.589 42.857 0.00 0.00 45.00 4.08
3553 3594 3.270027 CATGGAGAAACGGAGTAATGCA 58.730 45.455 0.00 0.00 45.00 3.96
3554 3595 3.951979 CATGGAGAAACGGAGTAATGC 57.048 47.619 0.00 0.00 45.00 3.56


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

AutoCloner maintained by Alex Coulton.