Multiple sequence alignment - TraesCS1B01G170400

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 TraesCS1B01G170400 chr1B 100.000 4109 0 0 1 4109 302506575 302510683 0.000000e+00 7589.0
1 TraesCS1B01G170400 chr1B 95.706 326 6 1 828 1153 10976720 10976403 6.090000e-143 518.0
2 TraesCS1B01G170400 chr1B 90.099 101 7 3 3439 3537 436383761 436383662 1.200000e-25 128.0
3 TraesCS1B01G170400 chr1B 95.385 65 1 2 413 477 10976910 10976848 7.270000e-18 102.0
4 TraesCS1B01G170400 chr1D 97.715 3239 55 7 226 3452 212724561 212721330 0.000000e+00 5553.0
5 TraesCS1B01G170400 chr1D 93.836 584 17 4 3532 4109 212721331 212720761 0.000000e+00 861.0
6 TraesCS1B01G170400 chr1A 95.522 3216 100 13 226 3433 269582858 269579679 0.000000e+00 5101.0
7 TraesCS1B01G170400 chr1A 94.081 321 16 2 3530 3847 269579673 269579353 6.180000e-133 484.0
8 TraesCS1B01G170400 chr1A 94.118 238 10 3 3874 4109 269575958 269575723 3.910000e-95 359.0
9 TraesCS1B01G170400 chr1A 86.667 210 21 5 1 209 269583180 269582977 4.130000e-55 226.0
10 TraesCS1B01G170400 chr1A 90.816 98 4 5 3442 3537 561611236 561611330 4.310000e-25 126.0
11 TraesCS1B01G170400 chr1A 91.379 58 1 3 3732 3787 268937201 268937146 4.400000e-10 76.8
12 TraesCS1B01G170400 chr1A 100.000 35 0 0 3839 3873 269575980 269575946 9.530000e-07 65.8
13 TraesCS1B01G170400 chr5B 97.124 591 15 1 565 1153 94271909 94271319 0.000000e+00 996.0
14 TraesCS1B01G170400 chr5B 95.385 65 1 2 413 477 94271959 94271897 7.270000e-18 102.0
15 TraesCS1B01G170400 chr5B 100.000 34 0 0 176 209 498719415 498719448 3.430000e-06 63.9
16 TraesCS1B01G170400 chrUn 100.000 394 0 0 1503 1896 479446559 479446166 0.000000e+00 728.0
17 TraesCS1B01G170400 chr2D 89.720 107 7 4 3451 3554 325754100 325753995 2.580000e-27 134.0
18 TraesCS1B01G170400 chr2D 88.679 106 9 3 3432 3534 603651232 603651337 4.310000e-25 126.0
19 TraesCS1B01G170400 chr2D 100.000 33 0 0 177 209 569192698 569192666 1.230000e-05 62.1
20 TraesCS1B01G170400 chr4B 93.407 91 3 3 3451 3538 131980664 131980574 9.270000e-27 132.0
21 TraesCS1B01G170400 chr3B 93.407 91 3 3 3451 3538 107157958 107158048 9.270000e-27 132.0
22 TraesCS1B01G170400 chr7D 92.391 92 5 2 3444 3533 45570132 45570041 3.330000e-26 130.0
23 TraesCS1B01G170400 chr6B 92.391 92 5 2 3449 3538 374144306 374144397 3.330000e-26 130.0
24 TraesCS1B01G170400 chr5A 89.796 98 8 2 3443 3538 112221125 112221028 1.550000e-24 124.0
25 TraesCS1B01G170400 chr5A 100.000 34 0 0 176 209 526378011 526378044 3.430000e-06 63.9
26 TraesCS1B01G170400 chr4D 97.297 37 0 1 178 214 506714229 506714194 1.230000e-05 62.1


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 TraesCS1B01G170400 chr1B 302506575 302510683 4108 False 7589.00 7589 100.0000 1 4109 1 chr1B.!!$F1 4108
1 TraesCS1B01G170400 chr1B 10976403 10976910 507 True 310.00 518 95.5455 413 1153 2 chr1B.!!$R2 740
2 TraesCS1B01G170400 chr1D 212720761 212724561 3800 True 3207.00 5553 95.7755 226 4109 2 chr1D.!!$R1 3883
3 TraesCS1B01G170400 chr1A 269575723 269583180 7457 True 1247.16 5101 94.0776 1 4109 5 chr1A.!!$R2 4108
4 TraesCS1B01G170400 chr5B 94271319 94271959 640 True 549.00 996 96.2545 413 1153 2 chr5B.!!$R1 740

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
52 53 0.324738 AGACTTCGGGAGAGCCATGA 60.325 55.000 0.00 0.00 41.75 3.07 F
259 363 1.075601 TCAGCCCAGAAGGTCCAAAT 58.924 50.000 0.00 0.00 38.26 2.32 F
1299 1405 3.403038 AGAGTTTGCTTATGCGACAAGT 58.597 40.909 8.82 0.34 43.34 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1405 1.673993 ATCAATGGCGGCGAACACA 60.674 52.632 12.98 3.44 0.00 3.72 R
1501 1607 3.827876 ACATTCATCATGCCTGACAACAA 59.172 39.130 0.00 0.00 36.14 2.83 R
3206 3323 0.106167 GGGAGGGGTTAAAGATGCCC 60.106 60.000 0.00 0.00 41.62 5.36 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
30 31 9.449719 AATATCAAAGGTATCGAATACAATCCC 57.550 33.333 0.00 0.00 37.48 3.85
31 32 6.241882 TCAAAGGTATCGAATACAATCCCA 57.758 37.500 0.00 0.00 37.48 4.37
32 33 6.837312 TCAAAGGTATCGAATACAATCCCAT 58.163 36.000 0.00 0.00 37.48 4.00
33 34 7.969004 TCAAAGGTATCGAATACAATCCCATA 58.031 34.615 0.00 0.00 37.48 2.74
34 35 8.094548 TCAAAGGTATCGAATACAATCCCATAG 58.905 37.037 0.00 0.00 37.48 2.23
35 36 7.792364 AAGGTATCGAATACAATCCCATAGA 57.208 36.000 0.00 0.00 37.48 1.98
36 37 7.171630 AGGTATCGAATACAATCCCATAGAC 57.828 40.000 0.00 0.00 37.48 2.59
48 49 0.676736 CCATAGACTTCGGGAGAGCC 59.323 60.000 0.00 0.00 41.75 4.70
52 53 0.324738 AGACTTCGGGAGAGCCATGA 60.325 55.000 0.00 0.00 41.75 3.07
88 90 2.935849 CACCGCATTGCTTGTGTCTATA 59.064 45.455 15.88 0.00 33.82 1.31
94 96 5.200454 GCATTGCTTGTGTCTATATCGTTG 58.800 41.667 0.16 0.00 0.00 4.10
115 117 5.389859 TGATGCTGAATGGTAAACTTTGG 57.610 39.130 0.00 0.00 0.00 3.28
120 122 6.825610 TGCTGAATGGTAAACTTTGGAAATT 58.174 32.000 0.00 0.00 0.00 1.82
126 128 6.576662 TGGTAAACTTTGGAAATTATGCGA 57.423 33.333 0.00 0.00 0.00 5.10
176 178 8.012957 TGTTCTAAACATAAAAACACCACCAT 57.987 30.769 0.00 0.00 36.25 3.55
209 211 1.684450 TCAGTTGGTTAGAGCGTGTGA 59.316 47.619 0.00 0.00 0.00 3.58
224 328 3.187700 CGTGTGAGCCCAGTAATACTTC 58.812 50.000 0.00 0.00 0.00 3.01
259 363 1.075601 TCAGCCCAGAAGGTCCAAAT 58.924 50.000 0.00 0.00 38.26 2.32
299 403 4.017037 ACAGATTCTCTCTCCTCCTTACCA 60.017 45.833 0.00 0.00 29.16 3.25
300 404 5.147032 CAGATTCTCTCTCCTCCTTACCAT 58.853 45.833 0.00 0.00 29.16 3.55
301 405 5.602145 CAGATTCTCTCTCCTCCTTACCATT 59.398 44.000 0.00 0.00 29.16 3.16
302 406 6.780031 CAGATTCTCTCTCCTCCTTACCATTA 59.220 42.308 0.00 0.00 29.16 1.90
303 407 6.780522 AGATTCTCTCTCCTCCTTACCATTAC 59.219 42.308 0.00 0.00 0.00 1.89
304 408 4.805744 TCTCTCTCCTCCTTACCATTACC 58.194 47.826 0.00 0.00 0.00 2.85
305 409 4.232122 TCTCTCTCCTCCTTACCATTACCA 59.768 45.833 0.00 0.00 0.00 3.25
306 410 4.547671 TCTCTCCTCCTTACCATTACCAG 58.452 47.826 0.00 0.00 0.00 4.00
1299 1405 3.403038 AGAGTTTGCTTATGCGACAAGT 58.597 40.909 8.82 0.34 43.34 3.16
1501 1607 6.944862 AGGTCAGAAAGAACTAGCAAATGAAT 59.055 34.615 0.00 0.00 44.30 2.57
2055 2161 1.073897 GGCATCAGGGTATGGGAGC 59.926 63.158 0.00 0.00 0.00 4.70
2265 2371 8.635765 TGCCTAGAGATGTTAAAAGATTGTTT 57.364 30.769 0.00 0.00 0.00 2.83
2738 2844 3.390967 TGTAGCTGGCTATATCTTGGCAA 59.609 43.478 5.58 0.00 38.26 4.52
2778 2884 1.064463 GCTGGAGATTTGTCCCATCCA 60.064 52.381 0.00 0.00 37.71 3.41
2952 3058 1.314534 TTTCCATGCGTGCCCATGAG 61.315 55.000 0.00 0.00 44.12 2.90
3175 3292 8.945481 TGGAAAATTAAAGCAATATGTGATGG 57.055 30.769 0.00 0.00 0.00 3.51
3198 3315 1.340889 GCAACCAATGAAACTGCCAGA 59.659 47.619 0.00 0.00 0.00 3.86
3205 3322 4.060205 CAATGAAACTGCCAGAAAAAGGG 58.940 43.478 0.00 0.00 0.00 3.95
3206 3323 2.038659 TGAAACTGCCAGAAAAAGGGG 58.961 47.619 0.00 0.00 0.00 4.79
3269 3386 1.778383 AGGGGAGGTTGAAAGCCCA 60.778 57.895 0.00 0.00 42.52 5.36
3366 3486 3.601443 AGTATTCTGCGGATATCCAGC 57.399 47.619 21.70 22.69 36.54 4.85
3413 3540 3.719268 TCATACTGCTGATGGGTTGTT 57.281 42.857 0.00 0.00 0.00 2.83
3414 3541 3.346315 TCATACTGCTGATGGGTTGTTG 58.654 45.455 0.00 0.00 0.00 3.33
3415 3542 2.198827 TACTGCTGATGGGTTGTTGG 57.801 50.000 0.00 0.00 0.00 3.77
3450 3580 9.394767 TCTGTTATGTAAGCATTTGTATGACAT 57.605 29.630 0.00 0.00 36.58 3.06
3455 3585 7.786178 TGTAAGCATTTGTATGACATACTCC 57.214 36.000 22.85 9.27 36.70 3.85
3456 3586 6.765989 TGTAAGCATTTGTATGACATACTCCC 59.234 38.462 22.85 9.56 36.70 4.30
3457 3587 5.636903 AGCATTTGTATGACATACTCCCT 57.363 39.130 22.85 11.23 36.70 4.20
3458 3588 5.615289 AGCATTTGTATGACATACTCCCTC 58.385 41.667 22.85 11.51 36.70 4.30
3459 3589 4.757149 GCATTTGTATGACATACTCCCTCC 59.243 45.833 22.85 6.95 36.70 4.30
3460 3590 5.687441 GCATTTGTATGACATACTCCCTCCA 60.687 44.000 22.85 2.01 36.70 3.86
3461 3591 6.537355 CATTTGTATGACATACTCCCTCCAT 58.463 40.000 22.85 5.44 36.70 3.41
3462 3592 5.808366 TTGTATGACATACTCCCTCCATC 57.192 43.478 22.85 0.00 36.70 3.51
3463 3593 4.160329 TGTATGACATACTCCCTCCATCC 58.840 47.826 22.85 0.00 36.70 3.51
3464 3594 2.103153 TGACATACTCCCTCCATCCC 57.897 55.000 0.00 0.00 0.00 3.85
3465 3595 1.293763 TGACATACTCCCTCCATCCCA 59.706 52.381 0.00 0.00 0.00 4.37
3466 3596 2.089982 TGACATACTCCCTCCATCCCAT 60.090 50.000 0.00 0.00 0.00 4.00
3467 3597 3.143933 TGACATACTCCCTCCATCCCATA 59.856 47.826 0.00 0.00 0.00 2.74
3468 3598 4.168101 GACATACTCCCTCCATCCCATAA 58.832 47.826 0.00 0.00 0.00 1.90
3469 3599 4.779386 ACATACTCCCTCCATCCCATAAT 58.221 43.478 0.00 0.00 0.00 1.28
3470 3600 4.537688 ACATACTCCCTCCATCCCATAATG 59.462 45.833 0.00 0.00 0.00 1.90
3471 3601 3.080660 ACTCCCTCCATCCCATAATGT 57.919 47.619 0.00 0.00 0.00 2.71
3472 3602 4.228237 ACTCCCTCCATCCCATAATGTA 57.772 45.455 0.00 0.00 0.00 2.29
3473 3603 4.577096 ACTCCCTCCATCCCATAATGTAA 58.423 43.478 0.00 0.00 0.00 2.41
3474 3604 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
3475 3605 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
3476 3606 5.231552 TCCCTCCATCCCATAATGTAAGAA 58.768 41.667 0.00 0.00 0.00 2.52
3477 3607 5.073144 TCCCTCCATCCCATAATGTAAGAAC 59.927 44.000 0.00 0.00 0.00 3.01
3478 3608 4.997395 CCTCCATCCCATAATGTAAGAACG 59.003 45.833 0.00 0.00 0.00 3.95
3479 3609 5.454755 CCTCCATCCCATAATGTAAGAACGT 60.455 44.000 0.00 0.00 0.00 3.99
3480 3610 5.996644 TCCATCCCATAATGTAAGAACGTT 58.003 37.500 0.00 0.00 38.41 3.99
3481 3611 6.419791 TCCATCCCATAATGTAAGAACGTTT 58.580 36.000 0.46 0.00 36.28 3.60
3482 3612 6.887545 TCCATCCCATAATGTAAGAACGTTTT 59.112 34.615 0.46 0.00 36.28 2.43
3483 3613 6.972328 CCATCCCATAATGTAAGAACGTTTTG 59.028 38.462 0.46 0.00 36.28 2.44
3484 3614 7.148154 CCATCCCATAATGTAAGAACGTTTTGA 60.148 37.037 0.46 0.00 36.31 2.69
3485 3615 7.136289 TCCCATAATGTAAGAACGTTTTGAC 57.864 36.000 0.46 0.00 36.31 3.18
3486 3616 6.938030 TCCCATAATGTAAGAACGTTTTGACT 59.062 34.615 0.46 0.00 36.31 3.41
3487 3617 7.446013 TCCCATAATGTAAGAACGTTTTGACTT 59.554 33.333 0.46 3.60 36.31 3.01
3488 3618 8.723311 CCCATAATGTAAGAACGTTTTGACTTA 58.277 33.333 0.46 2.53 36.31 2.24
3489 3619 9.755064 CCATAATGTAAGAACGTTTTGACTTAG 57.245 33.333 0.46 0.00 36.31 2.18
3492 3622 7.781548 ATGTAAGAACGTTTTGACTTAGTGT 57.218 32.000 0.46 0.00 0.00 3.55
3493 3623 8.876275 ATGTAAGAACGTTTTGACTTAGTGTA 57.124 30.769 0.46 0.00 0.00 2.90
3494 3624 8.343974 TGTAAGAACGTTTTGACTTAGTGTAG 57.656 34.615 0.46 0.00 0.00 2.74
3495 3625 7.975616 TGTAAGAACGTTTTGACTTAGTGTAGT 59.024 33.333 0.46 0.00 0.00 2.73
3496 3626 6.823678 AGAACGTTTTGACTTAGTGTAGTG 57.176 37.500 0.46 0.00 0.00 2.74
3497 3627 6.335777 AGAACGTTTTGACTTAGTGTAGTGT 58.664 36.000 0.46 0.00 0.00 3.55
3498 3628 6.474751 AGAACGTTTTGACTTAGTGTAGTGTC 59.525 38.462 0.46 0.00 0.00 3.67
3499 3629 5.653507 ACGTTTTGACTTAGTGTAGTGTCA 58.346 37.500 0.00 0.00 37.62 3.58
3500 3630 6.101332 ACGTTTTGACTTAGTGTAGTGTCAA 58.899 36.000 0.00 0.00 44.41 3.18
3505 3635 6.578020 TGACTTAGTGTAGTGTCAAAAACG 57.422 37.500 0.00 0.00 36.64 3.60
3506 3636 6.101332 TGACTTAGTGTAGTGTCAAAAACGT 58.899 36.000 0.00 0.00 36.64 3.99
3507 3637 6.591062 TGACTTAGTGTAGTGTCAAAAACGTT 59.409 34.615 0.00 0.00 36.64 3.99
3508 3638 6.997222 ACTTAGTGTAGTGTCAAAAACGTTC 58.003 36.000 0.00 0.00 0.00 3.95
3509 3639 6.815142 ACTTAGTGTAGTGTCAAAAACGTTCT 59.185 34.615 0.00 0.00 0.00 3.01
3510 3640 7.332678 ACTTAGTGTAGTGTCAAAAACGTTCTT 59.667 33.333 0.00 0.00 0.00 2.52
3511 3641 8.700722 TTAGTGTAGTGTCAAAAACGTTCTTA 57.299 30.769 0.00 0.00 0.00 2.10
3512 3642 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
3513 3643 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
3514 3644 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
3520 3650 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3521 3651 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3528 3658 8.307582 ACGTTCTTATATTATGGGATAGAGGG 57.692 38.462 0.00 0.00 0.00 4.30
3667 3800 1.004440 GTCAGAGCTGTGGGGTGTC 60.004 63.158 11.47 0.00 0.00 3.67
3739 3872 6.777091 TGATATGGTGAATAATGGTTTCCTGG 59.223 38.462 0.00 0.00 0.00 4.45
3873 7387 2.151202 TCTGAAACACCATTCTTCGGC 58.849 47.619 0.00 0.00 0.00 5.54
3874 7388 1.879380 CTGAAACACCATTCTTCGGCA 59.121 47.619 0.00 0.00 0.00 5.69
3875 7389 1.606668 TGAAACACCATTCTTCGGCAC 59.393 47.619 0.00 0.00 0.00 5.01
3876 7390 0.958822 AAACACCATTCTTCGGCACC 59.041 50.000 0.00 0.00 0.00 5.01
3877 7391 0.179004 AACACCATTCTTCGGCACCA 60.179 50.000 0.00 0.00 0.00 4.17
3878 7392 0.038166 ACACCATTCTTCGGCACCAT 59.962 50.000 0.00 0.00 0.00 3.55
3879 7393 1.176527 CACCATTCTTCGGCACCATT 58.823 50.000 0.00 0.00 0.00 3.16
3880 7394 1.545582 CACCATTCTTCGGCACCATTT 59.454 47.619 0.00 0.00 0.00 2.32
3881 7395 2.029110 CACCATTCTTCGGCACCATTTT 60.029 45.455 0.00 0.00 0.00 1.82
3882 7396 2.632512 ACCATTCTTCGGCACCATTTTT 59.367 40.909 0.00 0.00 0.00 1.94
3883 7397 3.253230 CCATTCTTCGGCACCATTTTTC 58.747 45.455 0.00 0.00 0.00 2.29
3884 7398 2.697431 TTCTTCGGCACCATTTTTCG 57.303 45.000 0.00 0.00 0.00 3.46
3885 7399 0.878416 TCTTCGGCACCATTTTTCGG 59.122 50.000 0.00 0.00 0.00 4.30
3894 7408 3.283751 CACCATTTTTCGGGCAGGTATA 58.716 45.455 0.00 0.00 0.00 1.47
3910 7424 6.260271 GGCAGGTATACATTCTTTAGTGGTTC 59.740 42.308 5.01 0.00 0.00 3.62
3991 7507 9.733556 TTTCTCTTACAATAAGCACCAAATCTA 57.266 29.630 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.449719 GGGATTGTATTCGATACCTTTGATATT 57.550 33.333 0.00 0.00 35.90 1.28
15 16 7.362660 CCGAAGTCTATGGGATTGTATTCGATA 60.363 40.741 5.19 0.00 39.33 2.92
28 29 0.676736 GCTCTCCCGAAGTCTATGGG 59.323 60.000 3.34 3.34 44.75 4.00
29 30 0.676736 GGCTCTCCCGAAGTCTATGG 59.323 60.000 0.00 0.00 0.00 2.74
30 31 1.403814 TGGCTCTCCCGAAGTCTATG 58.596 55.000 0.00 0.00 35.87 2.23
31 32 1.967066 CATGGCTCTCCCGAAGTCTAT 59.033 52.381 0.00 0.00 35.87 1.98
32 33 1.063942 TCATGGCTCTCCCGAAGTCTA 60.064 52.381 0.00 0.00 35.87 2.59
33 34 0.324738 TCATGGCTCTCCCGAAGTCT 60.325 55.000 0.00 0.00 35.87 3.24
34 35 0.537188 TTCATGGCTCTCCCGAAGTC 59.463 55.000 0.00 0.00 35.87 3.01
35 36 0.250513 GTTCATGGCTCTCCCGAAGT 59.749 55.000 0.00 0.00 35.87 3.01
36 37 0.539051 AGTTCATGGCTCTCCCGAAG 59.461 55.000 0.00 0.00 35.87 3.79
88 90 4.943705 AGTTTACCATTCAGCATCAACGAT 59.056 37.500 0.00 0.00 0.00 3.73
94 96 5.643379 TCCAAAGTTTACCATTCAGCATC 57.357 39.130 0.00 0.00 0.00 3.91
151 153 7.406031 TGGTGGTGTTTTTATGTTTAGAACA 57.594 32.000 0.00 0.00 46.94 3.18
155 157 7.754924 CAGCTATGGTGGTGTTTTTATGTTTAG 59.245 37.037 0.00 0.00 0.00 1.85
188 190 2.061773 CACACGCTCTAACCAACTGAG 58.938 52.381 0.00 0.00 0.00 3.35
197 199 1.185618 ACTGGGCTCACACGCTCTAA 61.186 55.000 0.00 0.00 0.00 2.10
204 206 4.473477 AGAAGTATTACTGGGCTCACAC 57.527 45.455 0.00 0.00 0.00 3.82
209 211 5.763876 ACTCAAAGAAGTATTACTGGGCT 57.236 39.130 0.00 0.00 0.00 5.19
259 363 1.074775 GTGCTTGTGGACCATGGGA 59.925 57.895 18.09 0.00 0.00 4.37
299 403 2.099405 CCGGCATTTCCAACTGGTAAT 58.901 47.619 0.00 0.00 35.88 1.89
300 404 1.074084 TCCGGCATTTCCAACTGGTAA 59.926 47.619 0.00 0.00 36.34 2.85
301 405 0.693622 TCCGGCATTTCCAACTGGTA 59.306 50.000 0.00 0.00 36.34 3.25
302 406 0.893727 GTCCGGCATTTCCAACTGGT 60.894 55.000 0.00 0.00 36.34 4.00
303 407 1.595093 GGTCCGGCATTTCCAACTGG 61.595 60.000 0.00 0.00 34.01 4.00
304 408 1.883021 GGTCCGGCATTTCCAACTG 59.117 57.895 0.00 0.00 34.01 3.16
305 409 1.674322 CGGTCCGGCATTTCCAACT 60.674 57.895 2.34 0.00 34.01 3.16
306 410 1.673009 TCGGTCCGGCATTTCCAAC 60.673 57.895 12.29 0.00 34.01 3.77
1299 1405 1.673993 ATCAATGGCGGCGAACACA 60.674 52.632 12.98 3.44 0.00 3.72
1501 1607 3.827876 ACATTCATCATGCCTGACAACAA 59.172 39.130 0.00 0.00 36.14 2.83
2055 2161 4.007282 CTGTATGAAACCATGCAGTTCG 57.993 45.455 13.05 0.00 44.47 3.95
2265 2371 9.140286 CGAGTTCTAGATTGTTCAAGTATTTCA 57.860 33.333 0.00 0.00 0.00 2.69
2738 2844 2.293399 GCCTCAAACGAATCCACACTTT 59.707 45.455 0.00 0.00 0.00 2.66
2778 2884 8.627403 CATGTACTCAAAATATCCTCAAATGCT 58.373 33.333 0.00 0.00 0.00 3.79
2952 3058 1.008767 CTTCGAGACCCGTATCGGC 60.009 63.158 11.52 0.00 46.86 5.54
3160 3268 1.063038 TGCCCCCATCACATATTGCTT 60.063 47.619 0.00 0.00 0.00 3.91
3175 3292 0.320683 GCAGTTTCATTGGTTGCCCC 60.321 55.000 0.00 0.00 0.00 5.80
3206 3323 0.106167 GGGAGGGGTTAAAGATGCCC 60.106 60.000 0.00 0.00 41.62 5.36
3208 3325 0.927029 AGGGGAGGGGTTAAAGATGC 59.073 55.000 0.00 0.00 0.00 3.91
3345 3462 3.324846 TGCTGGATATCCGCAGAATACTT 59.675 43.478 26.80 0.00 39.37 2.24
3352 3472 1.224075 CACTTGCTGGATATCCGCAG 58.776 55.000 27.95 24.37 42.83 5.18
3413 3540 3.052455 ACATAACAGACGCAATCACCA 57.948 42.857 0.00 0.00 0.00 4.17
3414 3541 4.494199 GCTTACATAACAGACGCAATCACC 60.494 45.833 0.00 0.00 0.00 4.02
3415 3542 4.092821 TGCTTACATAACAGACGCAATCAC 59.907 41.667 0.00 0.00 0.00 3.06
3450 3580 4.228237 ACATTATGGGATGGAGGGAGTA 57.772 45.455 0.00 0.00 0.00 2.59
3451 3581 3.080660 ACATTATGGGATGGAGGGAGT 57.919 47.619 0.00 0.00 0.00 3.85
3452 3582 4.846367 TCTTACATTATGGGATGGAGGGAG 59.154 45.833 0.00 0.00 0.00 4.30
3453 3583 4.838403 TCTTACATTATGGGATGGAGGGA 58.162 43.478 0.00 0.00 0.00 4.20
3454 3584 5.316987 GTTCTTACATTATGGGATGGAGGG 58.683 45.833 0.00 0.00 0.00 4.30
3455 3585 4.997395 CGTTCTTACATTATGGGATGGAGG 59.003 45.833 0.00 0.00 0.00 4.30
3456 3586 5.611374 ACGTTCTTACATTATGGGATGGAG 58.389 41.667 0.00 0.00 0.00 3.86
3457 3587 5.623956 ACGTTCTTACATTATGGGATGGA 57.376 39.130 0.00 0.00 0.00 3.41
3458 3588 6.693315 AAACGTTCTTACATTATGGGATGG 57.307 37.500 0.00 0.00 0.00 3.51
3459 3589 7.696453 GTCAAAACGTTCTTACATTATGGGATG 59.304 37.037 0.00 0.00 0.00 3.51
3460 3590 7.610305 AGTCAAAACGTTCTTACATTATGGGAT 59.390 33.333 0.00 0.00 0.00 3.85
3461 3591 6.938030 AGTCAAAACGTTCTTACATTATGGGA 59.062 34.615 0.00 0.00 0.00 4.37
3462 3592 7.141100 AGTCAAAACGTTCTTACATTATGGG 57.859 36.000 0.00 0.00 0.00 4.00
3463 3593 9.755064 CTAAGTCAAAACGTTCTTACATTATGG 57.245 33.333 0.00 0.00 0.00 2.74
3466 3596 9.316730 ACACTAAGTCAAAACGTTCTTACATTA 57.683 29.630 0.00 0.00 0.00 1.90
3467 3597 8.205131 ACACTAAGTCAAAACGTTCTTACATT 57.795 30.769 0.00 0.00 0.00 2.71
3468 3598 7.781548 ACACTAAGTCAAAACGTTCTTACAT 57.218 32.000 0.00 0.00 0.00 2.29
3469 3599 7.975616 ACTACACTAAGTCAAAACGTTCTTACA 59.024 33.333 0.00 0.00 0.00 2.41
3470 3600 8.264632 CACTACACTAAGTCAAAACGTTCTTAC 58.735 37.037 0.00 0.00 0.00 2.34
3471 3601 7.975616 ACACTACACTAAGTCAAAACGTTCTTA 59.024 33.333 0.00 4.16 0.00 2.10
3472 3602 6.815142 ACACTACACTAAGTCAAAACGTTCTT 59.185 34.615 0.00 3.04 0.00 2.52
3473 3603 6.335777 ACACTACACTAAGTCAAAACGTTCT 58.664 36.000 0.00 0.00 0.00 3.01
3474 3604 6.254157 TGACACTACACTAAGTCAAAACGTTC 59.746 38.462 0.00 0.00 37.99 3.95
3475 3605 6.101332 TGACACTACACTAAGTCAAAACGTT 58.899 36.000 0.00 0.00 37.99 3.99
3476 3606 5.653507 TGACACTACACTAAGTCAAAACGT 58.346 37.500 0.00 0.00 37.99 3.99
3477 3607 6.578020 TTGACACTACACTAAGTCAAAACG 57.422 37.500 4.55 0.00 45.01 3.60
3481 3611 6.591062 ACGTTTTTGACACTACACTAAGTCAA 59.409 34.615 0.00 0.00 45.94 3.18
3482 3612 6.101332 ACGTTTTTGACACTACACTAAGTCA 58.899 36.000 0.00 0.00 39.06 3.41
3483 3613 6.579491 ACGTTTTTGACACTACACTAAGTC 57.421 37.500 0.00 0.00 0.00 3.01
3484 3614 6.815142 AGAACGTTTTTGACACTACACTAAGT 59.185 34.615 0.46 0.00 0.00 2.24
3485 3615 7.230466 AGAACGTTTTTGACACTACACTAAG 57.770 36.000 0.46 0.00 0.00 2.18
3486 3616 7.599630 AAGAACGTTTTTGACACTACACTAA 57.400 32.000 0.46 0.00 0.00 2.24
3487 3617 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
3488 3618 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
3494 3624 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3495 3625 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3502 3632 8.759782 CCCTCTATCCCATAATATAAGAACGTT 58.240 37.037 0.00 0.00 0.00 3.99
3503 3633 8.120538 TCCCTCTATCCCATAATATAAGAACGT 58.879 37.037 0.00 0.00 0.00 3.99
3504 3634 8.534954 TCCCTCTATCCCATAATATAAGAACG 57.465 38.462 0.00 0.00 0.00 3.95
3505 3635 9.495382 ACTCCCTCTATCCCATAATATAAGAAC 57.505 37.037 0.00 0.00 0.00 3.01
3512 3642 9.494055 CAAATCTACTCCCTCTATCCCATAATA 57.506 37.037 0.00 0.00 0.00 0.98
3513 3643 7.964293 ACAAATCTACTCCCTCTATCCCATAAT 59.036 37.037 0.00 0.00 0.00 1.28
3514 3644 7.313731 ACAAATCTACTCCCTCTATCCCATAA 58.686 38.462 0.00 0.00 0.00 1.90
3515 3645 6.875469 ACAAATCTACTCCCTCTATCCCATA 58.125 40.000 0.00 0.00 0.00 2.74
3516 3646 5.731924 ACAAATCTACTCCCTCTATCCCAT 58.268 41.667 0.00 0.00 0.00 4.00
3517 3647 5.157770 ACAAATCTACTCCCTCTATCCCA 57.842 43.478 0.00 0.00 0.00 4.37
3518 3648 6.316513 ACTACAAATCTACTCCCTCTATCCC 58.683 44.000 0.00 0.00 0.00 3.85
3519 3649 7.506261 TGAACTACAAATCTACTCCCTCTATCC 59.494 40.741 0.00 0.00 0.00 2.59
3520 3650 8.466617 TGAACTACAAATCTACTCCCTCTATC 57.533 38.462 0.00 0.00 0.00 2.08
3521 3651 8.840200 TTGAACTACAAATCTACTCCCTCTAT 57.160 34.615 0.00 0.00 35.39 1.98
3522 3652 7.342284 CCTTGAACTACAAATCTACTCCCTCTA 59.658 40.741 0.00 0.00 38.08 2.43
3523 3653 6.155393 CCTTGAACTACAAATCTACTCCCTCT 59.845 42.308 0.00 0.00 38.08 3.69
3524 3654 6.154706 TCCTTGAACTACAAATCTACTCCCTC 59.845 42.308 0.00 0.00 38.08 4.30
3525 3655 6.023603 TCCTTGAACTACAAATCTACTCCCT 58.976 40.000 0.00 0.00 38.08 4.20
3526 3656 6.295719 TCCTTGAACTACAAATCTACTCCC 57.704 41.667 0.00 0.00 38.08 4.30
3527 3657 7.824779 ACAATCCTTGAACTACAAATCTACTCC 59.175 37.037 0.00 0.00 38.08 3.85
3528 3658 8.779354 ACAATCCTTGAACTACAAATCTACTC 57.221 34.615 0.00 0.00 38.08 2.59
3739 3872 8.751335 CGCTGAAGAGAGAATAAGATAGAAAAC 58.249 37.037 0.00 0.00 0.00 2.43
3819 3952 1.671845 CTCTCTCCGTCTCTTAACCGG 59.328 57.143 0.00 0.00 43.03 5.28
3873 7387 1.540267 TACCTGCCCGAAAAATGGTG 58.460 50.000 0.00 0.00 0.00 4.17
3874 7388 2.525105 ATACCTGCCCGAAAAATGGT 57.475 45.000 0.00 0.00 0.00 3.55
3875 7389 3.283751 TGTATACCTGCCCGAAAAATGG 58.716 45.455 0.00 0.00 0.00 3.16
3876 7390 5.299279 AGAATGTATACCTGCCCGAAAAATG 59.701 40.000 0.00 0.00 0.00 2.32
3877 7391 5.445964 AGAATGTATACCTGCCCGAAAAAT 58.554 37.500 0.00 0.00 0.00 1.82
3878 7392 4.850680 AGAATGTATACCTGCCCGAAAAA 58.149 39.130 0.00 0.00 0.00 1.94
3879 7393 4.497291 AGAATGTATACCTGCCCGAAAA 57.503 40.909 0.00 0.00 0.00 2.29
3880 7394 4.497291 AAGAATGTATACCTGCCCGAAA 57.503 40.909 0.00 0.00 0.00 3.46
3881 7395 4.497291 AAAGAATGTATACCTGCCCGAA 57.503 40.909 0.00 0.00 0.00 4.30
3882 7396 4.652421 ACTAAAGAATGTATACCTGCCCGA 59.348 41.667 0.00 0.00 0.00 5.14
3883 7397 4.750098 CACTAAAGAATGTATACCTGCCCG 59.250 45.833 0.00 0.00 0.00 6.13
3884 7398 5.063880 CCACTAAAGAATGTATACCTGCCC 58.936 45.833 0.00 0.00 0.00 5.36
3885 7399 5.681639 ACCACTAAAGAATGTATACCTGCC 58.318 41.667 0.00 0.00 0.00 4.85
3894 7408 3.335579 GCCTCGAACCACTAAAGAATGT 58.664 45.455 0.00 0.00 0.00 2.71
3910 7424 3.142393 CCAGGGATAGTGGCCTCG 58.858 66.667 3.32 0.00 0.00 4.63
4013 7533 7.659390 CCTTCTCTAGCATGGTTAGGAAATAAG 59.341 40.741 1.12 1.40 0.00 1.73


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

AutoCloner maintained by Alex Coulton.