Multiple sequence alignment - TraesCS3D01G107300

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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 TraesCS3D01G107300 chr3D 100.000 3695 0 0 1 3695 59857705 59854011 0.000000e+00 6824.0
1 TraesCS3D01G107300 chr3D 91.935 62 3 2 3274 3334 583290770 583290830 6.570000e-13 86.1
2 TraesCS3D01G107300 chr3B 92.209 3183 104 38 43 3159 95462882 95459778 0.000000e+00 4372.0
3 TraesCS3D01G107300 chr3A 93.725 1992 65 16 914 2864 68869757 68867785 0.000000e+00 2931.0
4 TraesCS3D01G107300 chr3A 90.397 958 38 28 1 926 68870722 68869787 0.000000e+00 1210.0
5 TraesCS3D01G107300 chr3A 92.079 202 13 2 3343 3543 68867096 68866897 7.810000e-72 281.0
6 TraesCS3D01G107300 chr3A 88.318 214 14 4 3454 3667 68866486 68866284 2.850000e-61 246.0
7 TraesCS3D01G107300 chr3A 89.437 142 12 3 3082 3220 68867333 68867192 3.790000e-40 176.0
8 TraesCS3D01G107300 chr3A 93.333 90 4 1 3343 3432 68866812 68866725 8.330000e-27 132.0
9 TraesCS3D01G107300 chr3A 93.443 61 4 0 3222 3282 68867163 68867103 1.410000e-14 91.6
10 TraesCS3D01G107300 chr2A 89.826 403 41 0 1263 1665 657813642 657813240 5.470000e-143 518.0
11 TraesCS3D01G107300 chr4A 89.975 399 37 1 1263 1661 34787856 34787461 2.540000e-141 512.0
12 TraesCS3D01G107300 chr4A 96.000 50 1 1 3285 3334 594011410 594011362 3.060000e-11 80.5
13 TraesCS3D01G107300 chr2D 89.578 403 42 0 1263 1665 513765035 513764633 2.540000e-141 512.0
14 TraesCS3D01G107300 chr4D 89.724 399 38 1 1263 1661 433393651 433393256 1.180000e-139 507.0
15 TraesCS3D01G107300 chr6D 88.998 409 43 2 1263 1670 332499023 332499430 4.260000e-139 505.0
16 TraesCS3D01G107300 chr6D 96.364 55 0 2 3279 3333 408737536 408737588 5.080000e-14 89.8
17 TraesCS3D01G107300 chr6B 88.998 409 43 2 1263 1670 487835471 487835064 4.260000e-139 505.0
18 TraesCS3D01G107300 chr6B 94.737 57 3 0 3278 3334 102081432 102081488 5.080000e-14 89.8
19 TraesCS3D01G107300 chr6B 88.406 69 6 2 3285 3352 393583211 393583144 8.500000e-12 82.4
20 TraesCS3D01G107300 chr4B 88.808 411 43 1 1263 1673 531580983 531580576 5.510000e-138 501.0
21 TraesCS3D01G107300 chr5D 96.364 55 2 0 3280 3334 526884229 526884283 1.410000e-14 91.6
22 TraesCS3D01G107300 chr5A 94.643 56 3 0 3279 3334 569715316 569715261 1.830000e-13 87.9
23 TraesCS3D01G107300 chr1D 94.737 57 2 1 3279 3334 441002260 441002316 1.830000e-13 87.9
24 TraesCS3D01G107300 chr5B 91.803 61 5 0 3273 3333 230783530 230783590 6.570000e-13 86.1


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 TraesCS3D01G107300 chr3D 59854011 59857705 3694 True 6824.000000 6824 100.000000 1 3695 1 chr3D.!!$R1 3694
1 TraesCS3D01G107300 chr3B 95459778 95462882 3104 True 4372.000000 4372 92.209000 43 3159 1 chr3B.!!$R1 3116
2 TraesCS3D01G107300 chr3A 68866284 68870722 4438 True 723.942857 2931 91.533143 1 3667 7 chr3A.!!$R1 3666

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
697 735 0.179134 CCTACCTCGGTTCTTGCTCG 60.179 60.000 0.0 0.0 0.00 5.03 F
1268 1365 1.134729 TCGTTTTGCGGTATAGACCCC 60.135 52.381 0.0 0.0 43.64 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2608 0.244178 GTCTCTGGTCCACTCCGAAC 59.756 60.0 0.0 0.0 0.0 3.95 R
3241 3706 0.039437 AGTCTCACGCCGTACAACAG 60.039 55.0 0.0 0.0 0.0 3.16 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
31 32 1.098869 TTTCGGTGCAAAACAGAGCA 58.901 45.000 0.00 0.00 34.30 4.26
38 39 0.317020 GCAAAACAGAGCACGTCCAC 60.317 55.000 0.00 0.00 0.00 4.02
207 214 6.736794 GCAAGATCACCACCATTCATTATTCC 60.737 42.308 0.00 0.00 0.00 3.01
323 331 3.197766 AGTCACACGAGAGAGAGAGAGAT 59.802 47.826 0.00 0.00 0.00 2.75
326 334 4.647399 TCACACGAGAGAGAGAGAGATAGA 59.353 45.833 0.00 0.00 0.00 1.98
337 345 4.074970 GAGAGAGATAGAGAGAGGCCAAG 58.925 52.174 5.01 0.00 0.00 3.61
416 438 7.390440 TGTTTTTAGAGAGAGAGAGAGAGAGTG 59.610 40.741 0.00 0.00 0.00 3.51
444 466 1.739929 TACAGTGTGATTGCGGGCG 60.740 57.895 5.88 0.00 0.00 6.13
445 467 3.803082 CAGTGTGATTGCGGGCGG 61.803 66.667 0.00 0.00 0.00 6.13
492 514 4.711949 CACTTGCGCCTGCCTCCT 62.712 66.667 4.18 0.00 41.78 3.69
493 515 3.003173 ACTTGCGCCTGCCTCCTA 61.003 61.111 4.18 0.00 41.78 2.94
494 516 2.512515 CTTGCGCCTGCCTCCTAC 60.513 66.667 4.18 0.00 41.78 3.18
495 517 4.096003 TTGCGCCTGCCTCCTACC 62.096 66.667 4.18 0.00 41.78 3.18
599 621 4.461198 ACCTGGTTGGCATAGCTTATTAC 58.539 43.478 0.00 0.00 40.22 1.89
697 735 0.179134 CCTACCTCGGTTCTTGCTCG 60.179 60.000 0.00 0.00 0.00 5.03
759 803 4.319037 AGTTGCTGTACTACTAGTCCCT 57.681 45.455 0.00 0.00 32.22 4.20
872 916 2.125753 GCTGCCGTCAGGTCTCAG 60.126 66.667 0.00 0.00 40.65 3.35
952 1038 2.042259 CAGGAATTCGGCAGCAGCA 61.042 57.895 2.65 0.00 44.61 4.41
953 1039 1.748122 AGGAATTCGGCAGCAGCAG 60.748 57.895 2.65 0.00 44.61 4.24
954 1040 2.101770 GAATTCGGCAGCAGCAGC 59.898 61.111 2.65 0.00 44.61 5.25
982 1069 1.367840 GGTTGATCGATCGAGGGGG 59.632 63.158 23.84 0.00 0.00 5.40
1214 1310 9.868277 TTATTTATGCTGTTCTTGGTTATTTGG 57.132 29.630 0.00 0.00 0.00 3.28
1223 1319 7.657336 TGTTCTTGGTTATTTGGTTCTTGATC 58.343 34.615 0.00 0.00 0.00 2.92
1224 1320 6.834168 TCTTGGTTATTTGGTTCTTGATCC 57.166 37.500 0.00 0.00 0.00 3.36
1225 1321 5.714806 TCTTGGTTATTTGGTTCTTGATCCC 59.285 40.000 0.00 0.00 0.00 3.85
1226 1322 5.004361 TGGTTATTTGGTTCTTGATCCCA 57.996 39.130 0.00 0.00 0.00 4.37
1238 1335 2.936919 TGATCCCAAGGATTCATCGG 57.063 50.000 0.00 0.00 43.27 4.18
1268 1365 1.134729 TCGTTTTGCGGTATAGACCCC 60.135 52.381 0.00 0.00 43.64 4.95
1784 1893 2.796617 GTGCGTGCATGCGTTGAC 60.797 61.111 25.05 14.22 37.81 3.18
1857 1966 3.844090 GAGGAGAGTGCGAGGGCC 61.844 72.222 0.00 0.00 38.85 5.80
1909 2024 1.299468 GGGATGCTCTACTCGCACG 60.299 63.158 0.00 0.00 40.65 5.34
1910 2025 1.299468 GGATGCTCTACTCGCACGG 60.299 63.158 0.00 0.00 40.65 4.94
1911 2026 1.946650 GATGCTCTACTCGCACGGC 60.947 63.158 0.00 0.00 40.65 5.68
2265 2416 4.399395 CTGCTCCAGAAGGCGGCA 62.399 66.667 13.08 0.00 39.66 5.69
2448 2608 4.116328 TTCGAGTCGCCGGCTCAG 62.116 66.667 26.68 11.49 33.45 3.35
2483 2643 0.249398 AGACCCAGTGCCAATCGTAC 59.751 55.000 0.00 0.00 0.00 3.67
2667 2827 2.925706 TACGACCAGCAAGGGCCA 60.926 61.111 6.18 0.00 45.73 5.36
2706 2866 3.433598 GGCATGGCTAGTAATCAACCTCA 60.434 47.826 12.86 0.00 0.00 3.86
2747 2907 2.754552 ACCATTGATGAACCGAACCATG 59.245 45.455 0.00 0.00 0.00 3.66
2752 2912 2.009774 GATGAACCGAACCATGTCCAG 58.990 52.381 0.00 0.00 0.00 3.86
2827 2989 6.458342 CGGCATTGCTCGATCATATACTACTA 60.458 42.308 8.82 0.00 0.00 1.82
2869 3031 4.041567 TCAGTAAGTTGGATTCAGCCTTCA 59.958 41.667 0.00 0.00 0.00 3.02
2872 3034 1.707427 AGTTGGATTCAGCCTTCAGGT 59.293 47.619 0.00 0.00 37.57 4.00
2897 3059 9.607285 GTCGATAAAGCAAAATCAAGTTCTTTA 57.393 29.630 0.00 0.00 32.69 1.85
2909 3071 8.667076 AATCAAGTTCTTTAATTTTGCTTGCT 57.333 26.923 0.00 0.00 33.88 3.91
2915 3077 8.413229 AGTTCTTTAATTTTGCTTGCTACTCAA 58.587 29.630 0.00 0.00 0.00 3.02
2924 3086 9.933723 ATTTTGCTTGCTACTCAATTTATCTTT 57.066 25.926 0.00 0.00 33.57 2.52
2978 3406 9.935241 CAGTTCACTTGCTATATATATGGAACT 57.065 33.333 10.09 6.54 41.12 3.01
3052 3487 7.862873 GCTGTTGTAATAAAGATGATTTAGCCC 59.137 37.037 0.00 0.00 0.00 5.19
3067 3502 6.772716 TGATTTAGCCCTTCTTTCCATACATC 59.227 38.462 0.00 0.00 0.00 3.06
3096 3531 5.637810 ACTACCAGTGTTCATGTCGTTTATG 59.362 40.000 0.00 0.00 0.00 1.90
3166 3604 7.883391 TCTGTTTACTAGAGAATACTCCCTG 57.117 40.000 0.00 0.00 43.53 4.45
3167 3605 7.411808 TCTGTTTACTAGAGAATACTCCCTGT 58.588 38.462 0.00 0.00 43.53 4.00
3169 3607 6.952358 TGTTTACTAGAGAATACTCCCTGTGT 59.048 38.462 0.00 0.00 43.53 3.72
3170 3608 7.122353 TGTTTACTAGAGAATACTCCCTGTGTC 59.878 40.741 0.00 0.00 43.53 3.67
3174 3612 2.168728 GAGAATACTCCCTGTGTCCCAC 59.831 54.545 0.00 0.00 37.19 4.61
3186 3624 3.280295 TGTGTCCCACAACATAAAACGT 58.720 40.909 0.00 0.00 41.69 3.99
3191 3629 5.577164 TGTCCCACAACATAAAACGTTTTTG 59.423 36.000 29.42 25.37 0.00 2.44
3204 3642 5.448926 AACGTTTTTGCAAGCTAAAACAG 57.551 34.783 29.55 25.11 45.11 3.16
3220 3658 7.385668 CTAAAACAGCTTGTGAAAACATCTG 57.614 36.000 0.00 6.93 0.00 2.90
3224 3689 5.526115 ACAGCTTGTGAAAACATCTGAATG 58.474 37.500 12.56 0.00 38.93 2.67
3227 3692 4.384846 GCTTGTGAAAACATCTGAATGCTG 59.615 41.667 0.00 0.00 36.26 4.41
3241 3706 5.936372 TCTGAATGCTGAATGCTGATATACC 59.064 40.000 0.00 0.00 43.37 2.73
3244 3709 4.694760 TGCTGAATGCTGATATACCTGT 57.305 40.909 0.00 0.00 43.37 4.00
3304 3769 7.905144 AATAATTATTACTCCCTCCATCCCA 57.095 36.000 8.99 0.00 0.00 4.37
3305 3770 7.905144 ATAATTATTACTCCCTCCATCCCAA 57.095 36.000 0.00 0.00 0.00 4.12
3306 3771 6.606241 AATTATTACTCCCTCCATCCCAAA 57.394 37.500 0.00 0.00 0.00 3.28
3307 3772 6.606241 ATTATTACTCCCTCCATCCCAAAA 57.394 37.500 0.00 0.00 0.00 2.44
3308 3773 6.606241 TTATTACTCCCTCCATCCCAAAAT 57.394 37.500 0.00 0.00 0.00 1.82
3309 3774 4.965283 TTACTCCCTCCATCCCAAAATT 57.035 40.909 0.00 0.00 0.00 1.82
3310 3775 3.388552 ACTCCCTCCATCCCAAAATTC 57.611 47.619 0.00 0.00 0.00 2.17
3311 3776 2.929043 ACTCCCTCCATCCCAAAATTCT 59.071 45.455 0.00 0.00 0.00 2.40
3312 3777 3.337909 ACTCCCTCCATCCCAAAATTCTT 59.662 43.478 0.00 0.00 0.00 2.52
3313 3778 3.703052 CTCCCTCCATCCCAAAATTCTTG 59.297 47.826 0.00 0.00 0.00 3.02
3314 3779 3.077391 TCCCTCCATCCCAAAATTCTTGT 59.923 43.478 0.00 0.00 0.00 3.16
3315 3780 3.448660 CCCTCCATCCCAAAATTCTTGTC 59.551 47.826 0.00 0.00 0.00 3.18
3316 3781 4.347607 CCTCCATCCCAAAATTCTTGTCT 58.652 43.478 0.00 0.00 0.00 3.41
3317 3782 4.774200 CCTCCATCCCAAAATTCTTGTCTT 59.226 41.667 0.00 0.00 0.00 3.01
3318 3783 5.951747 CCTCCATCCCAAAATTCTTGTCTTA 59.048 40.000 0.00 0.00 0.00 2.10
3319 3784 6.096001 CCTCCATCCCAAAATTCTTGTCTTAG 59.904 42.308 0.00 0.00 0.00 2.18
3320 3785 6.789268 TCCATCCCAAAATTCTTGTCTTAGA 58.211 36.000 0.00 0.00 0.00 2.10
3321 3786 7.413446 TCCATCCCAAAATTCTTGTCTTAGAT 58.587 34.615 0.00 0.00 0.00 1.98
3322 3787 7.895429 TCCATCCCAAAATTCTTGTCTTAGATT 59.105 33.333 0.00 0.00 0.00 2.40
3323 3788 8.534496 CCATCCCAAAATTCTTGTCTTAGATTT 58.466 33.333 0.00 0.00 0.00 2.17
3324 3789 9.362539 CATCCCAAAATTCTTGTCTTAGATTTG 57.637 33.333 0.00 0.00 29.84 2.32
3325 3790 8.477419 TCCCAAAATTCTTGTCTTAGATTTGT 57.523 30.769 0.00 0.00 28.79 2.83
3326 3791 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3327 3792 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3335 3800 9.702253 TCTTGTCTTAGATTTGTCTAGATACCT 57.298 33.333 0.00 0.00 0.00 3.08
3338 3803 9.575868 TGTCTTAGATTTGTCTAGATACCTAGG 57.424 37.037 7.41 7.41 42.06 3.02
3339 3804 9.016438 GTCTTAGATTTGTCTAGATACCTAGGG 57.984 40.741 14.81 0.00 42.06 3.53
3340 3805 8.956860 TCTTAGATTTGTCTAGATACCTAGGGA 58.043 37.037 14.81 4.35 42.06 4.20
3341 3806 9.238368 CTTAGATTTGTCTAGATACCTAGGGAG 57.762 40.741 14.81 2.29 42.06 4.30
3359 3824 8.711170 CCTAGGGAGTATATTTCAAACACCTTA 58.289 37.037 0.00 0.00 0.00 2.69
3387 3852 7.838079 AGTATATTGCATTTGGGAGCATTTA 57.162 32.000 0.00 0.00 40.94 1.40
3404 3869 9.609346 GGAGCATTTATTAACCAAGTACTCTAA 57.391 33.333 0.00 0.00 0.00 2.10
3528 3994 7.652909 TGAACAGTTGCATTCCTATTTTTCAAG 59.347 33.333 0.00 0.00 0.00 3.02
3533 3999 8.031277 AGTTGCATTCCTATTTTTCAAGTGATC 58.969 33.333 0.00 0.00 0.00 2.92
3537 4003 7.699812 GCATTCCTATTTTTCAAGTGATCAGAC 59.300 37.037 0.00 0.00 0.00 3.51
3548 4508 6.005823 TCAAGTGATCAGACCATTTTGACAT 58.994 36.000 0.00 0.00 0.00 3.06
3551 4511 7.294017 AGTGATCAGACCATTTTGACATTTT 57.706 32.000 0.00 0.00 0.00 1.82
3563 4523 9.814899 CCATTTTGACATTTTTGGTAGCATATA 57.185 29.630 0.00 0.00 0.00 0.86
3566 4526 9.853555 TTTTGACATTTTTGGTAGCATATACTG 57.146 29.630 0.00 0.00 0.00 2.74
3567 4527 8.574251 TTGACATTTTTGGTAGCATATACTGT 57.426 30.769 0.00 0.00 0.00 3.55
3648 4608 9.443283 GCTGAAATATAACACTTTAGCAGATTG 57.557 33.333 0.00 0.00 0.00 2.67
3654 4614 7.921786 ATAACACTTTAGCAGATTGTAAGCA 57.078 32.000 0.00 0.00 0.00 3.91
3656 4616 5.063204 ACACTTTAGCAGATTGTAAGCACA 58.937 37.500 0.00 0.00 0.00 4.57
3671 4631 6.548171 TGTAAGCACAACCGAAAAATATAGC 58.452 36.000 0.00 0.00 0.00 2.97
3672 4632 5.897377 AAGCACAACCGAAAAATATAGCT 57.103 34.783 0.00 0.00 0.00 3.32
3673 4633 5.897377 AGCACAACCGAAAAATATAGCTT 57.103 34.783 0.00 0.00 0.00 3.74
3674 4634 6.267496 AGCACAACCGAAAAATATAGCTTT 57.733 33.333 0.00 0.00 0.00 3.51
3675 4635 6.322491 AGCACAACCGAAAAATATAGCTTTC 58.678 36.000 0.00 0.00 0.00 2.62
3676 4636 5.515270 GCACAACCGAAAAATATAGCTTTCC 59.485 40.000 0.00 0.00 0.00 3.13
3677 4637 6.625081 GCACAACCGAAAAATATAGCTTTCCT 60.625 38.462 0.00 0.00 0.00 3.36
3678 4638 6.967199 CACAACCGAAAAATATAGCTTTCCTC 59.033 38.462 0.00 0.00 0.00 3.71
3679 4639 5.986004 ACCGAAAAATATAGCTTTCCTCG 57.014 39.130 0.00 0.00 0.00 4.63
3680 4640 5.667466 ACCGAAAAATATAGCTTTCCTCGA 58.333 37.500 0.00 0.00 30.72 4.04
3681 4641 5.522824 ACCGAAAAATATAGCTTTCCTCGAC 59.477 40.000 0.00 0.00 30.72 4.20
3682 4642 5.522460 CCGAAAAATATAGCTTTCCTCGACA 59.478 40.000 0.00 0.00 30.72 4.35
3683 4643 6.036735 CCGAAAAATATAGCTTTCCTCGACAA 59.963 38.462 0.00 0.00 30.72 3.18
3684 4644 7.254795 CCGAAAAATATAGCTTTCCTCGACAAT 60.255 37.037 0.00 0.00 30.72 2.71
3685 4645 7.794349 CGAAAAATATAGCTTTCCTCGACAATC 59.206 37.037 0.00 0.00 30.72 2.67
3686 4646 7.497925 AAAATATAGCTTTCCTCGACAATCC 57.502 36.000 0.00 0.00 0.00 3.01
3687 4647 2.981859 TAGCTTTCCTCGACAATCCC 57.018 50.000 0.00 0.00 0.00 3.85
3688 4648 1.280457 AGCTTTCCTCGACAATCCCT 58.720 50.000 0.00 0.00 0.00 4.20
3689 4649 2.467880 AGCTTTCCTCGACAATCCCTA 58.532 47.619 0.00 0.00 0.00 3.53
3690 4650 3.041946 AGCTTTCCTCGACAATCCCTAT 58.958 45.455 0.00 0.00 0.00 2.57
3691 4651 4.223953 AGCTTTCCTCGACAATCCCTATA 58.776 43.478 0.00 0.00 0.00 1.31
3692 4652 4.039366 AGCTTTCCTCGACAATCCCTATAC 59.961 45.833 0.00 0.00 0.00 1.47
3693 4653 4.039366 GCTTTCCTCGACAATCCCTATACT 59.961 45.833 0.00 0.00 0.00 2.12
3694 4654 5.243283 GCTTTCCTCGACAATCCCTATACTA 59.757 44.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.549793 TGCTCTGTTTTGCACCGA 57.450 50.000 0.00 0.00 33.94 4.69
41 42 2.029666 AGAGGAGCGTGTGTGTGC 59.970 61.111 0.00 0.00 0.00 4.57
228 235 4.067896 CTCACTAATCCCATTCCCATTCG 58.932 47.826 0.00 0.00 0.00 3.34
323 331 2.642171 TTTCCCTTGGCCTCTCTCTA 57.358 50.000 3.32 0.00 0.00 2.43
326 334 1.352687 GTCTTTTCCCTTGGCCTCTCT 59.647 52.381 3.32 0.00 0.00 3.10
337 345 3.062466 GGGCCGCTGTCTTTTCCC 61.062 66.667 0.00 0.00 0.00 3.97
416 438 1.045407 TCACACTGTACTCCCACACC 58.955 55.000 0.00 0.00 0.00 4.16
444 466 0.398948 ACCCATTCCATTCCATGCCC 60.399 55.000 0.00 0.00 0.00 5.36
445 467 0.754472 CACCCATTCCATTCCATGCC 59.246 55.000 0.00 0.00 0.00 4.40
446 468 0.754472 CCACCCATTCCATTCCATGC 59.246 55.000 0.00 0.00 0.00 4.06
447 469 2.457813 TCCACCCATTCCATTCCATG 57.542 50.000 0.00 0.00 0.00 3.66
448 470 2.426708 CCATCCACCCATTCCATTCCAT 60.427 50.000 0.00 0.00 0.00 3.41
449 471 1.063038 CCATCCACCCATTCCATTCCA 60.063 52.381 0.00 0.00 0.00 3.53
450 472 1.708341 CCATCCACCCATTCCATTCC 58.292 55.000 0.00 0.00 0.00 3.01
451 473 1.043022 GCCATCCACCCATTCCATTC 58.957 55.000 0.00 0.00 0.00 2.67
452 474 0.398948 GGCCATCCACCCATTCCATT 60.399 55.000 0.00 0.00 0.00 3.16
492 514 0.976641 GATGCGGATGGATGAGGGTA 59.023 55.000 0.00 0.00 0.00 3.69
493 515 0.765903 AGATGCGGATGGATGAGGGT 60.766 55.000 0.00 0.00 0.00 4.34
494 516 0.036577 GAGATGCGGATGGATGAGGG 60.037 60.000 0.00 0.00 0.00 4.30
495 517 0.975135 AGAGATGCGGATGGATGAGG 59.025 55.000 0.00 0.00 0.00 3.86
521 543 2.705658 TGCTAGGGAGAGAGAGAGAGAG 59.294 54.545 0.00 0.00 0.00 3.20
534 556 3.039011 GACTAGGGTTGATTGCTAGGGA 58.961 50.000 0.00 0.00 0.00 4.20
599 621 0.467804 GGGCTGAAGGAAGAGGCTAG 59.532 60.000 0.00 0.00 35.18 3.42
697 735 2.263741 CCATGGAGGCGGCTATTGC 61.264 63.158 13.24 0.00 38.76 3.56
750 788 4.796408 CTGAGGCCAGGGACTAGT 57.204 61.111 5.01 0.00 36.02 2.57
759 803 0.914644 CTCCTTGAATCCTGAGGCCA 59.085 55.000 5.01 0.00 0.00 5.36
869 913 0.687427 TCCGATCATGTGAGCCCTGA 60.687 55.000 0.00 0.00 0.00 3.86
870 914 0.395686 ATCCGATCATGTGAGCCCTG 59.604 55.000 0.00 0.00 0.00 4.45
871 915 0.683973 GATCCGATCATGTGAGCCCT 59.316 55.000 3.33 0.00 0.00 5.19
872 916 0.668706 CGATCCGATCATGTGAGCCC 60.669 60.000 9.07 0.00 0.00 5.19
952 1038 0.179936 GATCAACCAGCCAGCTAGCT 59.820 55.000 12.68 12.68 46.45 3.32
953 1039 1.156645 CGATCAACCAGCCAGCTAGC 61.157 60.000 6.62 6.62 0.00 3.42
954 1040 0.461548 TCGATCAACCAGCCAGCTAG 59.538 55.000 0.00 0.00 0.00 3.42
955 1041 1.069204 GATCGATCAACCAGCCAGCTA 59.931 52.381 20.52 0.00 0.00 3.32
956 1042 0.179062 GATCGATCAACCAGCCAGCT 60.179 55.000 20.52 0.00 0.00 4.24
958 1044 0.103026 TCGATCGATCAACCAGCCAG 59.897 55.000 24.40 5.61 0.00 4.85
982 1069 3.750371 TCATCTCGATCCTCTCTTCTCC 58.250 50.000 0.00 0.00 0.00 3.71
1223 1319 0.464036 TCGACCGATGAATCCTTGGG 59.536 55.000 0.00 0.00 0.00 4.12
1224 1320 2.224042 TGATCGACCGATGAATCCTTGG 60.224 50.000 9.83 0.00 34.60 3.61
1225 1321 3.097877 TGATCGACCGATGAATCCTTG 57.902 47.619 9.83 0.00 34.60 3.61
1226 1322 3.819564 TTGATCGACCGATGAATCCTT 57.180 42.857 9.83 0.00 34.60 3.36
1304 1401 1.875364 GTACCGGTTCGTCGCCATC 60.875 63.158 15.04 0.00 0.00 3.51
1784 1893 1.718757 GCTGTCCCGCCTGCAATTAG 61.719 60.000 0.00 0.00 0.00 1.73
1864 1979 4.767255 CTGCTCCTCCACGGCCAC 62.767 72.222 2.24 0.00 0.00 5.01
1926 2041 4.424711 GCCGGCATCTGGAACCCA 62.425 66.667 24.80 0.00 0.00 4.51
2226 2377 1.741770 GGTGGCCGACATGTGAGAC 60.742 63.158 1.15 0.00 0.00 3.36
2265 2416 1.968017 CAGCGTTGCACCCATCTGT 60.968 57.895 0.00 0.00 0.00 3.41
2336 2496 1.666553 GTGACGTTGGTGATGGCGA 60.667 57.895 0.00 0.00 0.00 5.54
2448 2608 0.244178 GTCTCTGGTCCACTCCGAAC 59.756 60.000 0.00 0.00 0.00 3.95
2655 2815 2.360852 CTCTGTGGCCCTTGCTGG 60.361 66.667 0.00 0.00 37.74 4.85
2667 2827 1.303888 CCATGGGTTGCTGCTCTGT 60.304 57.895 2.85 0.00 0.00 3.41
2747 2907 3.488047 CGCATCAAATCATCAACCTGGAC 60.488 47.826 0.00 0.00 0.00 4.02
2752 2912 1.134753 TGCCGCATCAAATCATCAACC 59.865 47.619 0.00 0.00 0.00 3.77
2827 2989 5.869579 ACTGATCAGTGTGATTAACCTTGT 58.130 37.500 27.37 0.00 40.75 3.16
2869 3031 6.431234 AGAACTTGATTTTGCTTTATCGACCT 59.569 34.615 0.00 0.00 0.00 3.85
2897 3059 9.933723 AAGATAAATTGAGTAGCAAGCAAAATT 57.066 25.926 0.00 0.00 40.42 1.82
2929 3091 0.253347 AGCCCATTCCTCCTCCAAGA 60.253 55.000 0.00 0.00 0.00 3.02
2930 3092 0.182299 GAGCCCATTCCTCCTCCAAG 59.818 60.000 0.00 0.00 0.00 3.61
2931 3093 0.253347 AGAGCCCATTCCTCCTCCAA 60.253 55.000 0.00 0.00 0.00 3.53
2932 3094 0.253347 AAGAGCCCATTCCTCCTCCA 60.253 55.000 0.00 0.00 0.00 3.86
2933 3095 0.472044 GAAGAGCCCATTCCTCCTCC 59.528 60.000 0.00 0.00 0.00 4.30
2934 3096 1.140652 CTGAAGAGCCCATTCCTCCTC 59.859 57.143 0.00 0.00 0.00 3.71
2935 3097 1.211456 CTGAAGAGCCCATTCCTCCT 58.789 55.000 0.00 0.00 0.00 3.69
2945 3107 1.889545 AGCAAGTGAACTGAAGAGCC 58.110 50.000 0.00 0.00 0.00 4.70
2978 3406 7.966246 AGCATGAACAAGAATTTATTTGCAA 57.034 28.000 0.00 0.00 0.00 4.08
3025 3453 7.862873 GGCTAAATCATCTTTATTACAACAGCC 59.137 37.037 0.00 0.00 0.00 4.85
3052 3487 8.258007 TGGTAGTAACAGATGTATGGAAAGAAG 58.742 37.037 0.00 0.00 0.00 2.85
3059 3494 6.222038 ACACTGGTAGTAACAGATGTATGG 57.778 41.667 22.14 4.71 39.24 2.74
3067 3502 4.621460 CGACATGAACACTGGTAGTAACAG 59.379 45.833 13.87 13.87 41.64 3.16
3096 3531 6.817184 TCTCATAAACTGCTTATCTACCCAC 58.183 40.000 0.00 0.00 0.00 4.61
3167 3605 4.985538 AAACGTTTTATGTTGTGGGACA 57.014 36.364 7.96 0.00 0.00 4.02
3169 3607 4.567159 GCAAAAACGTTTTATGTTGTGGGA 59.433 37.500 25.44 0.00 0.00 4.37
3170 3608 4.330074 TGCAAAAACGTTTTATGTTGTGGG 59.670 37.500 25.44 8.70 0.00 4.61
3174 3612 5.794720 AGCTTGCAAAAACGTTTTATGTTG 58.205 33.333 25.44 19.89 0.00 3.33
3204 3642 4.384846 CAGCATTCAGATGTTTTCACAAGC 59.615 41.667 0.00 0.00 36.16 4.01
3224 3689 4.818546 ACAACAGGTATATCAGCATTCAGC 59.181 41.667 0.00 0.00 46.19 4.26
3227 3692 5.405571 CCGTACAACAGGTATATCAGCATTC 59.594 44.000 0.00 0.00 33.76 2.67
3241 3706 0.039437 AGTCTCACGCCGTACAACAG 60.039 55.000 0.00 0.00 0.00 3.16
3244 3709 2.034432 TGTTAAGTCTCACGCCGTACAA 59.966 45.455 0.00 0.00 0.00 2.41
3282 3747 7.715267 TTTGGGATGGAGGGAGTAATAATTA 57.285 36.000 0.00 0.00 0.00 1.40
3284 3749 6.606241 TTTTGGGATGGAGGGAGTAATAAT 57.394 37.500 0.00 0.00 0.00 1.28
3287 3752 5.196574 AGAATTTTGGGATGGAGGGAGTAAT 59.803 40.000 0.00 0.00 0.00 1.89
3288 3753 4.544152 AGAATTTTGGGATGGAGGGAGTAA 59.456 41.667 0.00 0.00 0.00 2.24
3289 3754 4.119155 AGAATTTTGGGATGGAGGGAGTA 58.881 43.478 0.00 0.00 0.00 2.59
3290 3755 2.929043 AGAATTTTGGGATGGAGGGAGT 59.071 45.455 0.00 0.00 0.00 3.85
3291 3756 3.677156 AGAATTTTGGGATGGAGGGAG 57.323 47.619 0.00 0.00 0.00 4.30
3292 3757 3.077391 ACAAGAATTTTGGGATGGAGGGA 59.923 43.478 5.68 0.00 0.00 4.20
3293 3758 3.444029 ACAAGAATTTTGGGATGGAGGG 58.556 45.455 5.68 0.00 0.00 4.30
3294 3759 4.347607 AGACAAGAATTTTGGGATGGAGG 58.652 43.478 5.68 0.00 0.00 4.30
3295 3760 5.990120 AAGACAAGAATTTTGGGATGGAG 57.010 39.130 5.68 0.00 0.00 3.86
3296 3761 6.789268 TCTAAGACAAGAATTTTGGGATGGA 58.211 36.000 5.68 0.00 0.00 3.41
3297 3762 7.651027 ATCTAAGACAAGAATTTTGGGATGG 57.349 36.000 5.68 0.00 0.00 3.51
3298 3763 9.362539 CAAATCTAAGACAAGAATTTTGGGATG 57.637 33.333 5.68 0.00 28.49 3.51
3299 3764 9.093458 ACAAATCTAAGACAAGAATTTTGGGAT 57.907 29.630 0.00 0.00 33.04 3.85
3300 3765 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3301 3766 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3309 3774 9.702253 AGGTATCTAGACAAATCTAAGACAAGA 57.298 33.333 0.00 0.00 36.98 3.02
3312 3777 9.575868 CCTAGGTATCTAGACAAATCTAAGACA 57.424 37.037 11.86 0.00 44.35 3.41
3313 3778 9.016438 CCCTAGGTATCTAGACAAATCTAAGAC 57.984 40.741 11.86 0.00 44.35 3.01
3314 3779 8.956860 TCCCTAGGTATCTAGACAAATCTAAGA 58.043 37.037 11.86 0.00 44.35 2.10
3315 3780 9.238368 CTCCCTAGGTATCTAGACAAATCTAAG 57.762 40.741 11.86 0.00 44.35 2.18
3316 3781 8.734763 ACTCCCTAGGTATCTAGACAAATCTAA 58.265 37.037 11.86 0.00 44.35 2.10
3317 3782 8.290463 ACTCCCTAGGTATCTAGACAAATCTA 57.710 38.462 11.86 0.00 44.35 1.98
3318 3783 7.169287 ACTCCCTAGGTATCTAGACAAATCT 57.831 40.000 11.86 0.00 44.35 2.40
3328 3793 9.670442 TGTTTGAAATATACTCCCTAGGTATCT 57.330 33.333 8.29 0.00 32.85 1.98
3329 3794 9.708092 GTGTTTGAAATATACTCCCTAGGTATC 57.292 37.037 8.29 0.00 32.85 2.24
3330 3795 8.657712 GGTGTTTGAAATATACTCCCTAGGTAT 58.342 37.037 8.29 1.78 34.69 2.73
3331 3796 7.847848 AGGTGTTTGAAATATACTCCCTAGGTA 59.152 37.037 8.29 0.00 0.00 3.08
3332 3797 6.677076 AGGTGTTTGAAATATACTCCCTAGGT 59.323 38.462 8.29 0.00 0.00 3.08
3333 3798 7.138054 AGGTGTTTGAAATATACTCCCTAGG 57.862 40.000 0.06 0.06 0.00 3.02
3336 3801 8.557450 ACATAAGGTGTTTGAAATATACTCCCT 58.443 33.333 0.00 0.00 38.01 4.20
3337 3802 8.747538 ACATAAGGTGTTTGAAATATACTCCC 57.252 34.615 0.00 0.00 38.01 4.30
3359 3824 6.306199 TGCTCCCAAATGCAATATACTACAT 58.694 36.000 0.00 0.00 36.15 2.29
3366 3831 9.492973 GTTAATAAATGCTCCCAAATGCAATAT 57.507 29.630 0.00 0.00 42.74 1.28
3510 3976 7.394077 TCTGATCACTTGAAAAATAGGAATGCA 59.606 33.333 0.00 0.00 0.00 3.96
3528 3994 7.095523 CCAAAAATGTCAAAATGGTCTGATCAC 60.096 37.037 0.00 0.00 0.00 3.06
3533 3999 6.146021 GCTACCAAAAATGTCAAAATGGTCTG 59.854 38.462 0.00 0.00 41.22 3.51
3537 4003 8.721019 ATATGCTACCAAAAATGTCAAAATGG 57.279 30.769 0.00 0.00 0.00 3.16
3563 4523 6.573664 TCAGCTGCAATTAAACAATACAGT 57.426 33.333 9.47 0.00 0.00 3.55
3564 4524 9.740239 ATAATCAGCTGCAATTAAACAATACAG 57.260 29.630 9.47 0.00 0.00 2.74
3574 4534 8.105197 AGATGTGGATATAATCAGCTGCAATTA 58.895 33.333 9.47 9.53 0.00 1.40
3628 4588 9.613428 TGCTTACAATCTGCTAAAGTGTTATAT 57.387 29.630 0.00 0.00 0.00 0.86
3648 4608 6.782150 AGCTATATTTTTCGGTTGTGCTTAC 58.218 36.000 0.00 0.00 0.00 2.34
3649 4609 6.995511 AGCTATATTTTTCGGTTGTGCTTA 57.004 33.333 0.00 0.00 0.00 3.09
3654 4614 6.183360 CGAGGAAAGCTATATTTTTCGGTTGT 60.183 38.462 0.00 0.00 34.83 3.32
3656 4616 6.036844 GTCGAGGAAAGCTATATTTTTCGGTT 59.963 38.462 0.00 0.00 34.83 4.44
3660 4620 8.070769 GGATTGTCGAGGAAAGCTATATTTTTC 58.929 37.037 0.00 0.00 33.58 2.29
3667 4627 3.041946 AGGGATTGTCGAGGAAAGCTAT 58.958 45.455 0.00 0.00 0.00 2.97
3668 4628 2.467880 AGGGATTGTCGAGGAAAGCTA 58.532 47.619 0.00 0.00 0.00 3.32
3669 4629 1.280457 AGGGATTGTCGAGGAAAGCT 58.720 50.000 0.00 0.00 0.00 3.74
3670 4630 2.981859 TAGGGATTGTCGAGGAAAGC 57.018 50.000 0.00 0.00 0.00 3.51
3671 4631 5.793030 AGTATAGGGATTGTCGAGGAAAG 57.207 43.478 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.