Multiple sequence alignment - TraesCS3D01G096700

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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 TraesCS3D01G096700 chr3D 100.000 4284 0 0 1 4284 48859540 48863823 0 7912
1 TraesCS3D01G096700 chr3B 94.563 4249 165 37 1 4217 78391142 78395356 0 6506
2 TraesCS3D01G096700 chr3A 93.577 4328 186 36 1 4284 61341361 61345640 0 6368


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 TraesCS3D01G096700 chr3D 48859540 48863823 4283 False 7912 7912 100.000 1 4284 1 chr3D.!!$F1 4283
1 TraesCS3D01G096700 chr3B 78391142 78395356 4214 False 6506 6506 94.563 1 4217 1 chr3B.!!$F1 4216
2 TraesCS3D01G096700 chr3A 61341361 61345640 4279 False 6368 6368 93.577 1 4284 1 chr3A.!!$F1 4283

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
389 391 0.107165 CCTAACAAGGGGCAGGTAGC 60.107 60.0 0.00 0.00 44.65 3.58 F
1914 1916 0.033699 AGGAGGATTTGGAAGCTGCC 60.034 55.0 2.64 2.64 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 1958 1.233919 GCTTAGCTGCTAAGGCCATC 58.766 55.0 36.84 22.91 42.43 3.51 R
3806 3832 0.035630 GCTGTCTCCCTGTTCTGCAT 60.036 55.0 0.00 0.00 0.00 3.96 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
34 35 6.716934 TTACTGAGATCCAAGATAGGTGTC 57.283 41.667 0.00 0.00 0.00 3.67
43 44 3.131933 CCAAGATAGGTGTCTCTGTCCTG 59.868 52.174 0.00 0.00 33.34 3.86
54 55 1.609072 CTCTGTCCTGTCACGACTTGA 59.391 52.381 0.00 2.40 0.00 3.02
164 165 1.202348 GTGTAAGCCAGGCCATGTTTC 59.798 52.381 8.22 0.00 0.00 2.78
182 183 3.961477 TTCGTGGTTGACAGACAAATG 57.039 42.857 0.00 0.00 40.36 2.32
226 227 2.374184 CCGGCCTCAATTATTGGTTGA 58.626 47.619 0.00 0.00 34.63 3.18
271 272 7.984050 TCAACTGCAATTTCAAATTTCACCTTA 59.016 29.630 0.00 0.00 0.00 2.69
363 365 7.410120 TCTGAGTTCACTGAATTATGCTCTA 57.590 36.000 0.00 0.00 0.00 2.43
381 383 3.702045 CTCTACTCTGACCTAACAAGGGG 59.298 52.174 0.00 0.00 0.00 4.79
389 391 0.107165 CCTAACAAGGGGCAGGTAGC 60.107 60.000 0.00 0.00 44.65 3.58
464 466 7.040617 AGCCATGCTTCTATGATGAATTAGTTG 60.041 37.037 0.00 0.00 33.89 3.16
494 496 7.406916 ACTAACATTGGTACCCACAATATTCA 58.593 34.615 10.07 0.00 36.47 2.57
522 524 9.554724 TCAATTTCGCTGTAATAGTTTTTCATC 57.445 29.630 0.00 0.00 0.00 2.92
566 568 9.797642 TGATTTACACATGAATAATGATAGGCT 57.202 29.630 0.00 0.00 38.72 4.58
688 690 0.459899 TCTGTACATAGGCGGTGCAG 59.540 55.000 15.04 15.04 46.30 4.41
861 863 2.223340 CCATAAGCTAACCTTGCAAGCG 60.223 50.000 21.43 15.97 41.19 4.68
1602 1604 3.497332 ACAGAAGGGTAAAAAGGGAAGC 58.503 45.455 0.00 0.00 0.00 3.86
1655 1657 3.515502 TCTGATTCCGAGGTTGATGAAGT 59.484 43.478 0.00 0.00 0.00 3.01
1807 1809 6.601613 TGAAAACCTTGAAGAGAAGTTGCTAA 59.398 34.615 0.00 0.00 0.00 3.09
1914 1916 0.033699 AGGAGGATTTGGAAGCTGCC 60.034 55.000 2.64 2.64 0.00 4.85
1956 1958 6.651225 ACAAGTTCGAGGAATTAAAAGGAGAG 59.349 38.462 0.00 0.00 0.00 3.20
2178 2180 2.359900 CTTGAGGCACAGGTTATGGAC 58.640 52.381 0.00 0.00 0.00 4.02
2235 2237 6.974932 TCTGCTGAAATTAAGAAGCTACAG 57.025 37.500 0.00 0.00 36.60 2.74
2683 2685 5.804692 TCTTAAGACAGAGCTCGAGTTAG 57.195 43.478 15.13 6.97 0.00 2.34
2740 2742 2.634453 TCTGGTTTGCTGAGTGATCTCA 59.366 45.455 0.00 0.00 46.85 3.27
2892 2894 2.028930 GCTCGAGGAAGAGGTTGAGAAA 60.029 50.000 15.58 0.00 38.63 2.52
3003 3005 1.968540 GCAGCTCCGGCAAGTTCTT 60.969 57.895 0.00 0.00 41.70 2.52
3209 3212 3.320673 GTTGCTTCAGCTACTGGTACT 57.679 47.619 6.18 0.00 42.12 2.73
3260 3263 4.405358 TGGACCATTATGGCATTCCTTTTC 59.595 41.667 11.72 0.00 42.67 2.29
3261 3264 4.405358 GGACCATTATGGCATTCCTTTTCA 59.595 41.667 11.72 0.00 42.67 2.69
3262 3265 5.104982 GGACCATTATGGCATTCCTTTTCAA 60.105 40.000 11.72 0.00 42.67 2.69
3275 3278 6.423776 TTCCTTTTCAAAATCAATCTGCCT 57.576 33.333 0.00 0.00 0.00 4.75
3280 3283 3.916761 TCAAAATCAATCTGCCTGTTGC 58.083 40.909 0.00 0.00 41.77 4.17
3284 3287 0.251033 TCAATCTGCCTGTTGCTGCT 60.251 50.000 0.00 0.00 42.00 4.24
3299 3302 2.827921 TGCTGCTGTGAGTCTGAAGATA 59.172 45.455 0.00 0.00 0.00 1.98
3303 3306 5.353678 GCTGCTGTGAGTCTGAAGATAATTT 59.646 40.000 0.00 0.00 0.00 1.82
3313 3316 7.588512 AGTCTGAAGATAATTTCTGTGTTTGC 58.411 34.615 0.00 0.00 33.93 3.68
3318 3321 8.292448 TGAAGATAATTTCTGTGTTTGCTCTTC 58.708 33.333 0.00 0.00 36.84 2.87
3324 3327 4.572985 TCTGTGTTTGCTCTTCCAAATG 57.427 40.909 0.00 0.00 37.09 2.32
3339 3342 5.319140 TCCAAATGCTGATGAACTTGATG 57.681 39.130 0.00 0.00 0.00 3.07
3341 3344 4.081862 CCAAATGCTGATGAACTTGATGGT 60.082 41.667 0.00 0.00 0.00 3.55
3343 3346 6.350361 CCAAATGCTGATGAACTTGATGGTTA 60.350 38.462 0.00 0.00 0.00 2.85
3344 3347 6.839124 AATGCTGATGAACTTGATGGTTAA 57.161 33.333 0.00 0.00 0.00 2.01
3392 3408 7.415318 GCCATTTAATGAGCCTCATATGATCTG 60.415 40.741 14.69 6.33 35.76 2.90
3394 3410 8.666573 CATTTAATGAGCCTCATATGATCTGAC 58.333 37.037 7.81 0.00 35.76 3.51
3395 3411 5.820404 AATGAGCCTCATATGATCTGACA 57.180 39.130 7.81 4.35 35.76 3.58
3403 3419 6.653740 GCCTCATATGATCTGACATGAATTCA 59.346 38.462 11.26 11.26 0.00 2.57
3415 3431 8.579863 TCTGACATGAATTCACATATCTATCGT 58.420 33.333 11.07 0.00 0.00 3.73
3429 3445 7.755822 ACATATCTATCGTCTAATTCGCCTTTC 59.244 37.037 0.00 0.00 0.00 2.62
3430 3446 4.868067 TCTATCGTCTAATTCGCCTTTCC 58.132 43.478 0.00 0.00 0.00 3.13
3431 3447 3.821421 ATCGTCTAATTCGCCTTTCCT 57.179 42.857 0.00 0.00 0.00 3.36
3432 3448 2.888594 TCGTCTAATTCGCCTTTCCTG 58.111 47.619 0.00 0.00 0.00 3.86
3433 3449 2.232941 TCGTCTAATTCGCCTTTCCTGT 59.767 45.455 0.00 0.00 0.00 4.00
3434 3450 3.000727 CGTCTAATTCGCCTTTCCTGTT 58.999 45.455 0.00 0.00 0.00 3.16
3435 3451 3.435671 CGTCTAATTCGCCTTTCCTGTTT 59.564 43.478 0.00 0.00 0.00 2.83
3436 3452 4.628333 CGTCTAATTCGCCTTTCCTGTTTA 59.372 41.667 0.00 0.00 0.00 2.01
3437 3453 5.293569 CGTCTAATTCGCCTTTCCTGTTTAT 59.706 40.000 0.00 0.00 0.00 1.40
3438 3454 6.487103 GTCTAATTCGCCTTTCCTGTTTATG 58.513 40.000 0.00 0.00 0.00 1.90
3472 3488 1.338020 CTGTTGTGAACTTGCCCTTCC 59.662 52.381 0.00 0.00 0.00 3.46
3480 3496 4.522789 GTGAACTTGCCCTTCCATTTCTAA 59.477 41.667 0.00 0.00 0.00 2.10
3481 3497 4.766891 TGAACTTGCCCTTCCATTTCTAAG 59.233 41.667 0.00 0.00 0.00 2.18
3483 3499 4.998051 ACTTGCCCTTCCATTTCTAAGAA 58.002 39.130 0.00 0.00 0.00 2.52
3484 3500 5.012893 ACTTGCCCTTCCATTTCTAAGAAG 58.987 41.667 0.00 0.00 37.37 2.85
3485 3501 4.657814 TGCCCTTCCATTTCTAAGAAGT 57.342 40.909 0.00 0.00 36.16 3.01
3487 3503 4.289672 TGCCCTTCCATTTCTAAGAAGTCT 59.710 41.667 0.00 0.00 36.16 3.24
3489 3505 5.571658 GCCCTTCCATTTCTAAGAAGTCTGA 60.572 44.000 0.00 0.00 36.16 3.27
3492 3508 7.613411 CCCTTCCATTTCTAAGAAGTCTGAAAT 59.387 37.037 0.00 0.00 38.99 2.17
3493 3509 9.672673 CCTTCCATTTCTAAGAAGTCTGAAATA 57.327 33.333 6.39 0.00 37.12 1.40
3507 3523 9.736023 GAAGTCTGAAATACTGAAATTGTGTTT 57.264 29.630 0.00 0.00 32.80 2.83
3514 3530 9.974980 GAAATACTGAAATTGTGTTTAAAGGGA 57.025 29.630 0.00 0.00 30.86 4.20
3516 3532 9.981114 AATACTGAAATTGTGTTTAAAGGGAAG 57.019 29.630 0.00 0.00 0.00 3.46
3517 3533 6.280643 ACTGAAATTGTGTTTAAAGGGAAGC 58.719 36.000 0.00 0.00 0.00 3.86
3518 3534 6.127196 ACTGAAATTGTGTTTAAAGGGAAGCA 60.127 34.615 0.00 0.00 0.00 3.91
3519 3535 6.279882 TGAAATTGTGTTTAAAGGGAAGCAG 58.720 36.000 0.00 0.00 0.00 4.24
3520 3536 4.871933 ATTGTGTTTAAAGGGAAGCAGG 57.128 40.909 0.00 0.00 0.00 4.85
3521 3537 3.586470 TGTGTTTAAAGGGAAGCAGGA 57.414 42.857 0.00 0.00 0.00 3.86
3522 3538 3.219281 TGTGTTTAAAGGGAAGCAGGAC 58.781 45.455 0.00 0.00 0.00 3.85
3523 3539 3.117663 TGTGTTTAAAGGGAAGCAGGACT 60.118 43.478 0.00 0.00 0.00 3.85
3524 3540 4.103469 TGTGTTTAAAGGGAAGCAGGACTA 59.897 41.667 0.00 0.00 0.00 2.59
3526 3542 4.349930 TGTTTAAAGGGAAGCAGGACTAGT 59.650 41.667 0.00 0.00 0.00 2.57
3527 3543 5.544948 TGTTTAAAGGGAAGCAGGACTAGTA 59.455 40.000 0.00 0.00 0.00 1.82
3528 3544 6.214819 TGTTTAAAGGGAAGCAGGACTAGTAT 59.785 38.462 0.00 0.00 0.00 2.12
3529 3545 7.400915 TGTTTAAAGGGAAGCAGGACTAGTATA 59.599 37.037 0.00 0.00 0.00 1.47
3530 3546 7.598759 TTAAAGGGAAGCAGGACTAGTATAG 57.401 40.000 0.00 0.00 46.50 1.31
3531 3547 4.120946 AGGGAAGCAGGACTAGTATAGG 57.879 50.000 0.00 0.00 44.97 2.57
3532 3548 3.727923 AGGGAAGCAGGACTAGTATAGGA 59.272 47.826 0.00 0.00 44.97 2.94
3533 3549 4.083565 GGGAAGCAGGACTAGTATAGGAG 58.916 52.174 0.00 0.00 44.97 3.69
3534 3550 4.083565 GGAAGCAGGACTAGTATAGGAGG 58.916 52.174 0.00 0.00 44.97 4.30
3535 3551 4.202588 GGAAGCAGGACTAGTATAGGAGGA 60.203 50.000 0.00 0.00 44.97 3.71
3536 3552 5.386924 GAAGCAGGACTAGTATAGGAGGAA 58.613 45.833 0.00 0.00 44.97 3.36
3563 3579 3.608316 AGCAAGACCAGTTCAGAGATC 57.392 47.619 0.00 0.00 0.00 2.75
3584 3600 1.004745 ACGGCAGAAATGATGGAGGTT 59.995 47.619 0.00 0.00 0.00 3.50
3620 3643 2.158559 TGTCTGCTGTCTCTGTCTCTC 58.841 52.381 0.00 0.00 0.00 3.20
3645 3668 2.044650 TCCATGCCTTGAGCTGCC 60.045 61.111 0.00 0.00 44.23 4.85
3654 3677 0.247736 CTTGAGCTGCCGACCTTACT 59.752 55.000 0.00 0.00 0.00 2.24
3675 3698 6.749923 ACTTTTCTCCATGATTTGCTCTAC 57.250 37.500 0.00 0.00 0.00 2.59
3694 3717 7.224753 TGCTCTACAAAAGCTTATATAGTGCAC 59.775 37.037 23.14 9.40 40.50 4.57
3695 3718 7.307455 GCTCTACAAAAGCTTATATAGTGCACC 60.307 40.741 14.63 0.00 36.80 5.01
3696 3719 7.792032 TCTACAAAAGCTTATATAGTGCACCT 58.208 34.615 14.63 3.73 0.00 4.00
3727 3752 2.295885 GGAGATGACTGCATTCTTGGG 58.704 52.381 5.59 0.00 34.11 4.12
3740 3765 2.592102 TCTTGGGAGCTGCAAGAAAT 57.408 45.000 7.79 0.00 34.07 2.17
3741 3766 2.440409 TCTTGGGAGCTGCAAGAAATC 58.560 47.619 7.79 0.00 34.07 2.17
3743 3768 2.119801 TGGGAGCTGCAAGAAATCTC 57.880 50.000 7.79 0.00 34.07 2.75
3744 3769 1.352017 TGGGAGCTGCAAGAAATCTCA 59.648 47.619 7.79 0.00 34.07 3.27
3746 3771 3.022406 GGGAGCTGCAAGAAATCTCAAT 58.978 45.455 7.79 0.00 34.07 2.57
3750 3775 5.448904 GGAGCTGCAAGAAATCTCAATTCTC 60.449 44.000 0.00 0.00 36.14 2.87
3754 3779 5.319453 TGCAAGAAATCTCAATTCTCTGGT 58.681 37.500 0.00 0.00 36.14 4.00
3755 3780 6.475504 TGCAAGAAATCTCAATTCTCTGGTA 58.524 36.000 0.00 0.00 36.14 3.25
3756 3781 6.372659 TGCAAGAAATCTCAATTCTCTGGTAC 59.627 38.462 0.00 0.00 36.14 3.34
3757 3782 6.597280 GCAAGAAATCTCAATTCTCTGGTACT 59.403 38.462 0.00 0.00 36.14 2.73
3781 3806 6.363577 AGAAACACGGCATAATTATCACAG 57.636 37.500 0.00 0.00 0.00 3.66
3782 3807 4.552166 AACACGGCATAATTATCACAGC 57.448 40.909 0.00 0.00 0.00 4.40
3788 3814 5.939883 ACGGCATAATTATCACAGCACATAT 59.060 36.000 7.55 0.00 0.00 1.78
3802 3828 8.829612 TCACAGCACATATCATACTGTATTTTG 58.170 33.333 0.00 0.00 39.48 2.44
3803 3829 7.588854 CACAGCACATATCATACTGTATTTTGC 59.411 37.037 0.00 0.00 39.48 3.68
3806 3832 8.685427 AGCACATATCATACTGTATTTTGCAAA 58.315 29.630 8.05 8.05 0.00 3.68
3942 3971 2.884639 ACATGGCTAAGCGTCAGTTTTT 59.115 40.909 0.00 0.00 0.00 1.94
3944 3973 4.700213 ACATGGCTAAGCGTCAGTTTTTAT 59.300 37.500 0.00 0.00 0.00 1.40
3947 3976 3.439129 GGCTAAGCGTCAGTTTTTATGGT 59.561 43.478 0.00 0.00 0.00 3.55
4114 4144 3.838271 TCAGCCGTCCGATCCAGC 61.838 66.667 0.00 0.00 0.00 4.85
4127 4157 0.389391 ATCCAGCGATCCAACGGTAG 59.611 55.000 0.00 0.00 41.95 3.18
4196 4236 2.496899 TCTTTGACTTCTGCATCCCC 57.503 50.000 0.00 0.00 0.00 4.81
4201 4247 1.704628 TGACTTCTGCATCCCCTTCAA 59.295 47.619 0.00 0.00 0.00 2.69
4207 4253 0.541764 TGCATCCCCTTCAAACCCAC 60.542 55.000 0.00 0.00 0.00 4.61
4210 4256 0.251787 ATCCCCTTCAAACCCACTGC 60.252 55.000 0.00 0.00 0.00 4.40
4223 4269 1.668419 CCACTGCTATACAAGGCCAC 58.332 55.000 5.01 0.00 0.00 5.01
4242 4288 4.437239 CCACAAAACATTGCAACTGGTTA 58.563 39.130 0.00 0.00 0.00 2.85
4243 4289 4.507388 CCACAAAACATTGCAACTGGTTAG 59.493 41.667 0.00 6.33 0.00 2.34
4262 4308 7.907389 TGGTTAGTTGATACTTCTCTGTTCAT 58.093 34.615 0.00 0.00 35.78 2.57
4267 4318 7.615403 AGTTGATACTTCTCTGTTCATAAGCA 58.385 34.615 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.609072 TCAAGTCGTGACAGGACAGAG 59.391 52.381 25.55 16.10 35.60 3.35
43 44 7.404139 ACTAGTACATTTTTCAAGTCGTGAC 57.596 36.000 0.00 0.00 35.39 3.67
164 165 3.691049 AACATTTGTCTGTCAACCACG 57.309 42.857 0.00 0.00 35.61 4.94
182 183 9.281075 CGGCCAAGTTTAATAGTACAAAATAAC 57.719 33.333 2.24 0.00 0.00 1.89
271 272 1.644509 GGATCAAAAGGCCAGGGTTT 58.355 50.000 5.01 0.00 0.00 3.27
363 365 0.984995 GCCCCTTGTTAGGTCAGAGT 59.015 55.000 0.00 0.00 40.19 3.24
389 391 0.731514 CAGCGCAAAAGATGTGGCAG 60.732 55.000 11.47 0.00 40.01 4.85
426 428 0.895100 GCATGGCTGGACTTGGTTCA 60.895 55.000 0.00 0.00 0.00 3.18
427 429 0.610232 AGCATGGCTGGACTTGGTTC 60.610 55.000 0.00 0.00 37.57 3.62
494 496 9.906660 TGAAAAACTATTACAGCGAAATTGATT 57.093 25.926 0.00 0.00 0.00 2.57
548 550 6.482524 AGATGCAGCCTATCATTATTCATGT 58.517 36.000 0.00 0.00 34.06 3.21
566 568 6.711277 ACTGATTAACTACCAAGAAGATGCA 58.289 36.000 0.00 0.00 0.00 3.96
688 690 7.173907 CCATGAATGGTATGAAGTATGAAGGTC 59.826 40.741 0.82 0.00 43.05 3.85
1228 1230 7.121759 GGATGAAACATCAGAGAAGGAAATTGA 59.878 37.037 12.66 0.00 0.00 2.57
1602 1604 6.399743 AGAAGAAGATGATGATGATCCATCG 58.600 40.000 7.26 0.00 44.37 3.84
1655 1657 2.827322 CCATTGCCATTCTCTTGGTTCA 59.173 45.455 0.00 0.00 39.11 3.18
1807 1809 5.278660 GGCTGTTGATTTCTGATTGTGAAGT 60.279 40.000 0.00 0.00 0.00 3.01
1812 1814 4.828939 TGAAGGCTGTTGATTTCTGATTGT 59.171 37.500 0.00 0.00 0.00 2.71
1914 1916 4.981794 ACTTGTTCTTGTTTTCCAGAACG 58.018 39.130 7.38 0.00 42.32 3.95
1956 1958 1.233919 GCTTAGCTGCTAAGGCCATC 58.766 55.000 36.84 22.91 42.43 3.51
2133 2135 3.303395 GCAACTTCTCTTCCGACAGTTTG 60.303 47.826 0.00 0.00 0.00 2.93
2178 2180 3.304928 GGCTGTGAGATGTTTGTTCAAGG 60.305 47.826 0.00 0.00 0.00 3.61
2235 2237 4.036144 GCTTGCAGATCCTTGATTACCTTC 59.964 45.833 0.00 0.00 0.00 3.46
2423 2425 0.036732 GACACAGCCCTCCAACATCA 59.963 55.000 0.00 0.00 0.00 3.07
2683 2685 0.871057 GCAGCTTTCTGTGAGGACAC 59.129 55.000 0.00 0.00 46.09 3.67
2740 2742 6.547141 TCCTTCATCTTTTCATCACAAGTTGT 59.453 34.615 1.64 1.64 0.00 3.32
2892 2894 0.392193 CGAAGGCCATGAGCTTCTGT 60.392 55.000 5.01 0.00 43.05 3.41
2937 2939 0.392729 AGAAGCACAGCTGCCTGATC 60.393 55.000 15.27 7.88 45.53 2.92
3184 3187 3.071023 ACCAGTAGCTGAAGCAACTACAA 59.929 43.478 4.90 0.00 45.16 2.41
3275 3278 0.465287 TCAGACTCACAGCAGCAACA 59.535 50.000 0.00 0.00 0.00 3.33
3280 3283 6.817641 AGAAATTATCTTCAGACTCACAGCAG 59.182 38.462 0.00 0.00 33.39 4.24
3284 3287 7.445121 ACACAGAAATTATCTTCAGACTCACA 58.555 34.615 0.00 0.00 35.73 3.58
3299 3302 5.596836 TTGGAAGAGCAAACACAGAAATT 57.403 34.783 0.00 0.00 0.00 1.82
3303 3306 3.243501 GCATTTGGAAGAGCAAACACAGA 60.244 43.478 0.00 0.00 0.00 3.41
3313 3316 5.182570 TCAAGTTCATCAGCATTTGGAAGAG 59.817 40.000 0.00 0.00 0.00 2.85
3318 3321 4.081862 ACCATCAAGTTCATCAGCATTTGG 60.082 41.667 0.00 0.00 0.00 3.28
3324 3327 7.338440 GTTTTTAACCATCAAGTTCATCAGC 57.662 36.000 0.00 0.00 0.00 4.26
3392 3408 8.978564 AGACGATAGATATGTGAATTCATGTC 57.021 34.615 12.12 4.62 36.60 3.06
3403 3419 6.761099 AGGCGAATTAGACGATAGATATGT 57.239 37.500 0.00 0.00 41.38 2.29
3415 3431 5.588648 CCATAAACAGGAAAGGCGAATTAGA 59.411 40.000 0.00 0.00 0.00 2.10
3422 3438 2.122783 TCCCATAAACAGGAAAGGCG 57.877 50.000 0.00 0.00 0.00 5.52
3429 3445 4.202441 CACAAGGAGATCCCATAAACAGG 58.798 47.826 0.00 0.00 37.41 4.00
3430 3446 3.629398 GCACAAGGAGATCCCATAAACAG 59.371 47.826 0.00 0.00 37.41 3.16
3431 3447 3.266772 AGCACAAGGAGATCCCATAAACA 59.733 43.478 0.00 0.00 37.41 2.83
3432 3448 3.629398 CAGCACAAGGAGATCCCATAAAC 59.371 47.826 0.00 0.00 37.41 2.01
3433 3449 3.266772 ACAGCACAAGGAGATCCCATAAA 59.733 43.478 0.00 0.00 37.41 1.40
3434 3450 2.846206 ACAGCACAAGGAGATCCCATAA 59.154 45.455 0.00 0.00 37.41 1.90
3435 3451 2.481441 ACAGCACAAGGAGATCCCATA 58.519 47.619 0.00 0.00 37.41 2.74
3436 3452 1.293062 ACAGCACAAGGAGATCCCAT 58.707 50.000 0.00 0.00 37.41 4.00
3437 3453 1.067295 AACAGCACAAGGAGATCCCA 58.933 50.000 0.00 0.00 37.41 4.37
3438 3454 1.271597 ACAACAGCACAAGGAGATCCC 60.272 52.381 0.00 0.00 36.42 3.85
3480 3496 8.682936 ACACAATTTCAGTATTTCAGACTTCT 57.317 30.769 0.00 0.00 0.00 2.85
3481 3497 9.736023 AAACACAATTTCAGTATTTCAGACTTC 57.264 29.630 0.00 0.00 0.00 3.01
3487 3503 9.757227 CCCTTTAAACACAATTTCAGTATTTCA 57.243 29.630 0.00 0.00 0.00 2.69
3492 3508 7.068839 TGCTTCCCTTTAAACACAATTTCAGTA 59.931 33.333 0.00 0.00 0.00 2.74
3493 3509 6.127196 TGCTTCCCTTTAAACACAATTTCAGT 60.127 34.615 0.00 0.00 0.00 3.41
3504 3520 4.907809 ACTAGTCCTGCTTCCCTTTAAAC 58.092 43.478 0.00 0.00 0.00 2.01
3507 3523 6.075984 CCTATACTAGTCCTGCTTCCCTTTA 58.924 44.000 0.00 0.00 0.00 1.85
3511 3527 4.083565 CTCCTATACTAGTCCTGCTTCCC 58.916 52.174 0.00 0.00 0.00 3.97
3514 3530 5.103430 AGTTCCTCCTATACTAGTCCTGCTT 60.103 44.000 0.00 0.00 0.00 3.91
3516 3532 4.521256 CAGTTCCTCCTATACTAGTCCTGC 59.479 50.000 0.00 0.00 0.00 4.85
3517 3533 5.942961 TCAGTTCCTCCTATACTAGTCCTG 58.057 45.833 0.00 0.00 0.00 3.86
3518 3534 5.912354 TCTCAGTTCCTCCTATACTAGTCCT 59.088 44.000 0.00 0.00 0.00 3.85
3519 3535 6.190346 TCTCAGTTCCTCCTATACTAGTCC 57.810 45.833 0.00 0.00 0.00 3.85
3520 3536 6.206048 GCTTCTCAGTTCCTCCTATACTAGTC 59.794 46.154 0.00 0.00 0.00 2.59
3521 3537 6.066032 GCTTCTCAGTTCCTCCTATACTAGT 58.934 44.000 0.00 0.00 0.00 2.57
3522 3538 6.065374 TGCTTCTCAGTTCCTCCTATACTAG 58.935 44.000 0.00 0.00 0.00 2.57
3523 3539 6.014771 TGCTTCTCAGTTCCTCCTATACTA 57.985 41.667 0.00 0.00 0.00 1.82
3524 3540 4.873010 TGCTTCTCAGTTCCTCCTATACT 58.127 43.478 0.00 0.00 0.00 2.12
3526 3542 5.361285 GTCTTGCTTCTCAGTTCCTCCTATA 59.639 44.000 0.00 0.00 0.00 1.31
3527 3543 4.161377 GTCTTGCTTCTCAGTTCCTCCTAT 59.839 45.833 0.00 0.00 0.00 2.57
3528 3544 3.511934 GTCTTGCTTCTCAGTTCCTCCTA 59.488 47.826 0.00 0.00 0.00 2.94
3529 3545 2.301583 GTCTTGCTTCTCAGTTCCTCCT 59.698 50.000 0.00 0.00 0.00 3.69
3530 3546 2.614229 GGTCTTGCTTCTCAGTTCCTCC 60.614 54.545 0.00 0.00 0.00 4.30
3531 3547 2.037772 TGGTCTTGCTTCTCAGTTCCTC 59.962 50.000 0.00 0.00 0.00 3.71
3532 3548 2.038295 CTGGTCTTGCTTCTCAGTTCCT 59.962 50.000 0.00 0.00 0.00 3.36
3533 3549 2.224402 ACTGGTCTTGCTTCTCAGTTCC 60.224 50.000 0.00 0.00 35.44 3.62
3534 3550 3.118905 ACTGGTCTTGCTTCTCAGTTC 57.881 47.619 0.00 0.00 35.44 3.01
3535 3551 3.567478 AACTGGTCTTGCTTCTCAGTT 57.433 42.857 0.00 0.00 41.89 3.16
3536 3552 2.435805 TGAACTGGTCTTGCTTCTCAGT 59.564 45.455 0.00 0.00 39.97 3.41
3563 3579 1.019673 CCTCCATCATTTCTGCCGTG 58.980 55.000 0.00 0.00 0.00 4.94
3584 3600 2.034532 CAGGTGGTCATGGCTGCA 59.965 61.111 0.50 0.00 0.00 4.41
3620 3643 0.325933 TCAAGGCATGGACTGGTCAG 59.674 55.000 0.00 0.00 0.00 3.51
3645 3668 6.546395 CAAATCATGGAGAAAAGTAAGGTCG 58.454 40.000 0.00 0.00 0.00 4.79
3654 3677 7.523293 TTTGTAGAGCAAATCATGGAGAAAA 57.477 32.000 0.00 0.00 41.68 2.29
3675 3698 7.320443 TCAAGGTGCACTATATAAGCTTTTG 57.680 36.000 17.98 0.00 0.00 2.44
3685 3708 6.065374 TCCAAAACTTTCAAGGTGCACTATA 58.935 36.000 17.98 0.00 0.00 1.31
3694 3717 5.766222 CAGTCATCTCCAAAACTTTCAAGG 58.234 41.667 0.00 0.00 0.00 3.61
3695 3718 5.218139 GCAGTCATCTCCAAAACTTTCAAG 58.782 41.667 0.00 0.00 0.00 3.02
3696 3719 4.644234 TGCAGTCATCTCCAAAACTTTCAA 59.356 37.500 0.00 0.00 0.00 2.69
3727 3752 5.354792 AGAGAATTGAGATTTCTTGCAGCTC 59.645 40.000 0.00 0.00 0.00 4.09
3740 3765 7.575155 CGTGTTTCTAGTACCAGAGAATTGAGA 60.575 40.741 3.95 0.00 31.91 3.27
3741 3766 6.528423 CGTGTTTCTAGTACCAGAGAATTGAG 59.472 42.308 3.95 0.00 31.91 3.02
3743 3768 5.577164 CCGTGTTTCTAGTACCAGAGAATTG 59.423 44.000 3.95 0.00 31.91 2.32
3744 3769 5.721232 CCGTGTTTCTAGTACCAGAGAATT 58.279 41.667 3.95 0.00 31.91 2.17
3746 3771 3.057033 GCCGTGTTTCTAGTACCAGAGAA 60.057 47.826 0.00 0.00 0.00 2.87
3750 3775 2.736144 TGCCGTGTTTCTAGTACCAG 57.264 50.000 0.00 0.00 0.00 4.00
3754 3779 8.198778 TGTGATAATTATGCCGTGTTTCTAGTA 58.801 33.333 1.78 0.00 0.00 1.82
3755 3780 7.045416 TGTGATAATTATGCCGTGTTTCTAGT 58.955 34.615 1.78 0.00 0.00 2.57
3756 3781 7.477144 TGTGATAATTATGCCGTGTTTCTAG 57.523 36.000 1.78 0.00 0.00 2.43
3757 3782 6.018262 GCTGTGATAATTATGCCGTGTTTCTA 60.018 38.462 1.78 0.00 0.00 2.10
3781 3806 8.854979 TTTGCAAAATACAGTATGATATGTGC 57.145 30.769 10.02 0.00 39.69 4.57
3802 3828 1.200948 GTCTCCCTGTTCTGCATTTGC 59.799 52.381 0.00 0.00 42.50 3.68
3803 3829 2.486982 CTGTCTCCCTGTTCTGCATTTG 59.513 50.000 0.00 0.00 0.00 2.32
3806 3832 0.035630 GCTGTCTCCCTGTTCTGCAT 60.036 55.000 0.00 0.00 0.00 3.96
3808 3834 0.952984 GTGCTGTCTCCCTGTTCTGC 60.953 60.000 0.00 0.00 0.00 4.26
3811 3837 0.603975 GGTGTGCTGTCTCCCTGTTC 60.604 60.000 0.00 0.00 0.00 3.18
3812 3838 1.451936 GGTGTGCTGTCTCCCTGTT 59.548 57.895 0.00 0.00 0.00 3.16
3814 3840 2.348998 GGGTGTGCTGTCTCCCTG 59.651 66.667 0.00 0.00 37.92 4.45
3942 3971 3.838317 AGGTGAGTAAAGTGCAGACCATA 59.162 43.478 0.00 0.00 0.00 2.74
3944 3973 2.047061 AGGTGAGTAAAGTGCAGACCA 58.953 47.619 0.00 0.00 0.00 4.02
3947 3976 1.416030 TGCAGGTGAGTAAAGTGCAGA 59.584 47.619 0.00 0.00 39.17 4.26
4114 4144 3.992260 AAGAGATCTACCGTTGGATCG 57.008 47.619 0.00 0.00 42.02 3.69
4127 4157 7.517614 AGGTCAAAGAAAAGGAAAAGAGATC 57.482 36.000 0.00 0.00 0.00 2.75
4187 4227 0.251742 TGGGTTTGAAGGGGATGCAG 60.252 55.000 0.00 0.00 0.00 4.41
4189 4229 0.251787 AGTGGGTTTGAAGGGGATGC 60.252 55.000 0.00 0.00 0.00 3.91
4196 4236 4.396166 CCTTGTATAGCAGTGGGTTTGAAG 59.604 45.833 0.00 0.00 0.00 3.02
4201 4247 1.064685 GGCCTTGTATAGCAGTGGGTT 60.065 52.381 0.00 0.00 0.00 4.11
4207 4253 3.505680 TGTTTTGTGGCCTTGTATAGCAG 59.494 43.478 3.32 0.00 0.00 4.24
4210 4256 4.864247 GCAATGTTTTGTGGCCTTGTATAG 59.136 41.667 3.32 0.00 35.17 1.31
4242 4288 7.615403 TGCTTATGAACAGAGAAGTATCAACT 58.385 34.615 0.00 0.00 37.65 3.16
4243 4289 7.834068 TGCTTATGAACAGAGAAGTATCAAC 57.166 36.000 0.00 0.00 0.00 3.18
4246 4292 9.757227 ATAGTTGCTTATGAACAGAGAAGTATC 57.243 33.333 0.00 0.00 0.00 2.24
4248 4294 9.944376 AAATAGTTGCTTATGAACAGAGAAGTA 57.056 29.630 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.