Multiple sequence alignment - TraesCS5A01G316300

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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 TraesCS5A01G316300 chr5A 100.000 3822 0 0 1 3822 526582767 526586588 0 7059
1 TraesCS5A01G316300 chr5D 92.227 3898 202 48 1 3822 414068114 414071986 0 5426
2 TraesCS5A01G316300 chr5B 91.726 3904 225 47 1 3822 499121766 499125653 0 5330


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 TraesCS5A01G316300 chr5A 526582767 526586588 3821 False 7059 7059 100.000 1 3822 1 chr5A.!!$F1 3821
1 TraesCS5A01G316300 chr5D 414068114 414071986 3872 False 5426 5426 92.227 1 3822 1 chr5D.!!$F1 3821
2 TraesCS5A01G316300 chr5B 499121766 499125653 3887 False 5330 5330 91.726 1 3822 1 chr5B.!!$F1 3821

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
242 243 0.321741 TAGTCGGAAAAATGCCCGCA 60.322 50.0 0.0 0.0 44.96 5.69 F
593 595 0.332972 GGACCTCCCCTGCAAATTCT 59.667 55.0 0.0 0.0 0.00 2.40 F
886 920 0.616111 CCTAGGGGCACTCTGTCTGT 60.616 60.0 0.0 0.0 0.00 3.41 F
1582 1636 0.172803 GGTGGTACTGCTGTCTACCG 59.827 60.0 0.0 0.0 35.44 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1625 0.038599 TAGGGACACGGTAGACAGCA 59.961 55.0 0.0 0.0 0.0 4.41 R
1582 1636 0.529378 ACCGAACATCGTAGGGACAC 59.471 55.0 0.0 0.0 38.4 3.67 R
2664 2729 0.387878 AGTGCTCAGCTCGAAAGTCG 60.388 55.0 0.0 0.0 42.1 4.18 R
3516 3612 0.328258 GCAGTAACATGTCCCCCAGT 59.672 55.0 0.0 0.0 0.0 4.00 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
102 103 6.648192 AGGTTAGTCAGAAATCAGAATCCAG 58.352 40.000 0.00 0.00 0.00 3.86
182 183 6.151312 ACTTATTCGAGCTACTTTGACTGAGA 59.849 38.462 0.00 0.00 0.00 3.27
183 184 5.590530 ATTCGAGCTACTTTGACTGAGAT 57.409 39.130 0.00 0.00 0.00 2.75
184 185 4.362932 TCGAGCTACTTTGACTGAGATG 57.637 45.455 0.00 0.00 0.00 2.90
185 186 3.129462 TCGAGCTACTTTGACTGAGATGG 59.871 47.826 0.00 0.00 0.00 3.51
188 189 3.584848 AGCTACTTTGACTGAGATGGGTT 59.415 43.478 0.00 0.00 0.00 4.11
230 231 6.040504 ACATATGTTATGTCTGCTTAGTCGGA 59.959 38.462 1.41 0.00 0.00 4.55
241 242 0.806241 TTAGTCGGAAAAATGCCCGC 59.194 50.000 0.00 0.00 44.96 6.13
242 243 0.321741 TAGTCGGAAAAATGCCCGCA 60.322 50.000 0.00 0.00 44.96 5.69
289 290 1.304879 GCTGGGTGGGGTGCAAATA 60.305 57.895 0.00 0.00 0.00 1.40
308 309 6.728200 CAAATAGACTGAAACTTGTTCTGCA 58.272 36.000 0.00 0.00 0.00 4.41
351 352 4.832248 ACCTCTCTGCATCGTTTGATTTA 58.168 39.130 0.00 0.00 30.49 1.40
454 455 1.843851 TCCCGGATGCTGATAAACCTT 59.156 47.619 0.73 0.00 0.00 3.50
471 472 2.912956 ACCTTGGCCATCTTCTCAGTTA 59.087 45.455 6.09 0.00 0.00 2.24
473 474 4.018050 ACCTTGGCCATCTTCTCAGTTATT 60.018 41.667 6.09 0.00 0.00 1.40
580 582 0.685097 TGGTAACACAGCTGGACCTC 59.315 55.000 19.93 5.35 46.17 3.85
593 595 0.332972 GGACCTCCCCTGCAAATTCT 59.667 55.000 0.00 0.00 0.00 2.40
654 659 5.637810 TGTCAAAGTTTCTTATGCTACGAGG 59.362 40.000 0.00 0.00 0.00 4.63
671 676 6.237861 GCTACGAGGACATGTATGTTTTTCTC 60.238 42.308 0.00 4.44 41.95 2.87
714 719 4.788521 GCCGTTTCTGTCGAAATTTCAACT 60.789 41.667 17.99 0.00 40.91 3.16
886 920 0.616111 CCTAGGGGCACTCTGTCTGT 60.616 60.000 0.00 0.00 0.00 3.41
965 1004 1.966493 CTCGTCCAATCCAAACCGCG 61.966 60.000 0.00 0.00 0.00 6.46
1386 1436 1.897398 GCTGCACGTAACCTGTTCGG 61.897 60.000 0.00 0.00 39.35 4.30
1531 1585 1.656818 GCCGCTGCTTATTTCTGGCA 61.657 55.000 6.13 0.00 40.66 4.92
1566 1620 5.233083 ACTGTGGATATGGACATATGGTG 57.767 43.478 9.40 0.00 34.36 4.17
1571 1625 5.248477 GTGGATATGGACATATGGTGGTACT 59.752 44.000 9.40 0.00 34.36 2.73
1576 1630 2.170607 GGACATATGGTGGTACTGCTGT 59.829 50.000 7.80 0.66 0.00 4.40
1582 1636 0.172803 GGTGGTACTGCTGTCTACCG 59.827 60.000 0.00 0.00 35.44 4.02
1587 1641 1.135460 GTACTGCTGTCTACCGTGTCC 60.135 57.143 0.00 0.00 0.00 4.02
1592 1646 0.731417 CTGTCTACCGTGTCCCTACG 59.269 60.000 0.00 0.00 43.35 3.51
1598 1652 0.529378 ACCGTGTCCCTACGATGTTC 59.471 55.000 0.00 0.00 46.46 3.18
1623 1677 1.205064 CGCCGCTCTTGTGTTTGAG 59.795 57.895 0.00 0.00 0.00 3.02
1648 1702 4.072088 GGCGCCGACGAACTTGTG 62.072 66.667 12.58 0.00 43.93 3.33
1650 1704 2.355363 CGCCGACGAACTTGTGGA 60.355 61.111 0.00 0.00 43.93 4.02
1652 1706 1.289109 CGCCGACGAACTTGTGGAAT 61.289 55.000 0.00 0.00 43.93 3.01
1661 1715 5.003160 ACGAACTTGTGGAATGATGAATGA 58.997 37.500 0.00 0.00 0.00 2.57
1693 1747 5.741388 ATTAGCCAAACAATAGAAGCTCG 57.259 39.130 0.00 0.00 0.00 5.03
1713 1767 0.673333 CAGTAGGCGCATGTGGTTCA 60.673 55.000 10.83 0.00 0.00 3.18
1758 1812 1.663379 CGGTGGGACTGCGATAGACA 61.663 60.000 0.00 0.00 39.76 3.41
1774 1828 2.665165 AGACAGACTAGATGCAGGGAG 58.335 52.381 0.00 0.00 0.00 4.30
1780 1834 2.497675 GACTAGATGCAGGGAGTGTGAA 59.502 50.000 0.00 0.00 0.00 3.18
1785 1839 4.922206 AGATGCAGGGAGTGTGAAATTTA 58.078 39.130 0.00 0.00 0.00 1.40
1959 2018 4.880759 ACTGAGATAATGAGATGCTTCCG 58.119 43.478 0.00 0.00 0.00 4.30
1968 2027 3.329386 TGAGATGCTTCCGTTTCTTCTG 58.671 45.455 0.00 0.00 0.00 3.02
1970 2029 1.806542 GATGCTTCCGTTTCTTCTGCA 59.193 47.619 0.00 0.00 0.00 4.41
2288 2353 5.104259 AGGATCGAAGCTTTTGGAATACT 57.896 39.130 0.00 0.00 0.00 2.12
2304 2369 5.104776 TGGAATACTTCAGGTGGAGAAGATG 60.105 44.000 9.65 0.00 44.00 2.90
2324 2389 8.684386 AAGATGTCGATAAAGATAGTGAGAGA 57.316 34.615 0.00 0.00 0.00 3.10
2335 2400 7.716799 AAGATAGTGAGAGACTTGAATCTGT 57.283 36.000 0.00 0.00 35.96 3.41
2444 2509 2.933495 TTCGATCATCGGTCGTTCTT 57.067 45.000 7.33 0.00 40.88 2.52
2586 2651 5.243507 TGATGCCATTGCTAAAAACTTCTCA 59.756 36.000 0.00 0.00 38.71 3.27
2664 2729 0.729690 GCTTTGCTCGAATCTGGGAC 59.270 55.000 0.00 0.00 0.00 4.46
2666 2731 0.606096 TTTGCTCGAATCTGGGACGA 59.394 50.000 0.00 0.00 34.90 4.20
2668 2733 0.965866 TGCTCGAATCTGGGACGACT 60.966 55.000 0.00 0.00 32.72 4.18
2671 2736 2.531206 CTCGAATCTGGGACGACTTTC 58.469 52.381 0.00 0.00 32.72 2.62
2675 2740 0.173708 ATCTGGGACGACTTTCGAGC 59.826 55.000 1.94 0.00 43.74 5.03
2725 2790 3.402110 TCTTGATGGTGCAGTTAGTGTG 58.598 45.455 0.00 0.00 0.00 3.82
2829 2894 7.615582 CTGCAAGGAAACAATAGATTCTGTA 57.384 36.000 0.00 0.00 0.00 2.74
2831 2896 7.816640 TGCAAGGAAACAATAGATTCTGTAAC 58.183 34.615 0.00 0.00 0.00 2.50
2859 2925 9.866655 AATCTGGAATACAACACATATATTGGT 57.133 29.630 0.00 0.00 0.00 3.67
2870 2936 9.089601 CAACACATATATTGGTTACTACGTTGA 57.910 33.333 3.44 0.00 31.52 3.18
2871 2937 9.826574 AACACATATATTGGTTACTACGTTGAT 57.173 29.630 3.44 0.00 0.00 2.57
2872 2938 9.472361 ACACATATATTGGTTACTACGTTGATC 57.528 33.333 3.44 0.00 0.00 2.92
2909 2975 8.985315 TGCTGATTTCTTAGATTCATAATGGT 57.015 30.769 0.00 0.00 0.00 3.55
2932 2998 4.551702 AATATTTTTCCCTGTGCAACCC 57.448 40.909 0.00 0.00 34.36 4.11
2960 3026 9.840427 CGTTTCCTCAAGTTTATCAAATAATGT 57.160 29.630 0.00 0.00 0.00 2.71
3002 3068 5.673337 TCTTGTCTTGTTTCCTCAAATCG 57.327 39.130 0.00 0.00 0.00 3.34
3007 3073 8.786826 TTGTCTTGTTTCCTCAAATCGTATAT 57.213 30.769 0.00 0.00 0.00 0.86
3008 3074 8.196802 TGTCTTGTTTCCTCAAATCGTATATG 57.803 34.615 0.00 0.00 0.00 1.78
3009 3075 8.038351 TGTCTTGTTTCCTCAAATCGTATATGA 58.962 33.333 0.00 0.00 0.00 2.15
3010 3076 8.879759 GTCTTGTTTCCTCAAATCGTATATGAA 58.120 33.333 0.00 0.00 0.00 2.57
3011 3077 9.443323 TCTTGTTTCCTCAAATCGTATATGAAA 57.557 29.630 0.00 0.00 0.00 2.69
3062 3153 5.936956 TGAATTTTGCTTCCTTTGTGTGTTT 59.063 32.000 0.00 0.00 0.00 2.83
3072 3163 4.819630 TCCTTTGTGTGTTTGTCCTGTATC 59.180 41.667 0.00 0.00 0.00 2.24
3077 3168 4.518590 TGTGTGTTTGTCCTGTATCATTGG 59.481 41.667 0.00 0.00 0.00 3.16
3080 3171 4.218417 GTGTTTGTCCTGTATCATTGGCTT 59.782 41.667 0.00 0.00 0.00 4.35
3085 3176 1.685803 CCTGTATCATTGGCTTGCCCA 60.686 52.381 9.35 0.00 43.51 5.36
3112 3203 8.907222 AATGCAATTATTTGTTTCTGTTCCTT 57.093 26.923 0.00 0.00 32.46 3.36
3130 3221 7.576403 TGTTCCTTCCATATCATTGATCTTCA 58.424 34.615 1.55 0.00 0.00 3.02
3131 3222 7.500227 TGTTCCTTCCATATCATTGATCTTCAC 59.500 37.037 1.55 0.00 0.00 3.18
3174 3265 9.643693 GATTTTCTCTTGAATTAAATGCTTCCA 57.356 29.630 0.00 0.00 31.56 3.53
3188 3279 9.859427 TTAAATGCTTCCAATATCTGTTTCAAG 57.141 29.630 0.00 0.00 0.00 3.02
3189 3280 7.472334 AATGCTTCCAATATCTGTTTCAAGT 57.528 32.000 0.00 0.00 0.00 3.16
3195 3286 7.815840 TCCAATATCTGTTTCAAGTGTTTCA 57.184 32.000 0.00 0.00 0.00 2.69
3198 3289 7.592533 CCAATATCTGTTTCAAGTGTTTCACAG 59.407 37.037 2.80 0.00 36.74 3.66
3201 3292 4.398988 TCTGTTTCAAGTGTTTCACAGCAT 59.601 37.500 2.80 0.00 36.74 3.79
3227 3318 3.162202 TGTGAAATGTTGCACAACCTG 57.838 42.857 10.82 0.00 41.61 4.00
3232 3323 4.343526 TGAAATGTTGCACAACCTGGTATT 59.656 37.500 10.82 1.37 40.46 1.89
3234 3325 2.235016 TGTTGCACAACCTGGTATTCC 58.765 47.619 10.82 0.00 40.46 3.01
3235 3326 2.235016 GTTGCACAACCTGGTATTCCA 58.765 47.619 0.00 0.00 42.08 3.53
3236 3327 2.825532 GTTGCACAACCTGGTATTCCAT 59.174 45.455 0.00 0.00 43.43 3.41
3293 3384 6.349115 GCATGTCCATGTATCAATCTTCATCC 60.349 42.308 8.91 0.00 40.80 3.51
3334 3430 6.761242 CCTACTCATGATCGTCCAATGTTTTA 59.239 38.462 0.00 0.00 0.00 1.52
3342 3438 8.741101 TGATCGTCCAATGTTTTAAAATTCTG 57.259 30.769 3.52 2.12 0.00 3.02
3367 3463 6.822667 TGAAGAAGCAACATTGTGTGATAT 57.177 33.333 0.00 0.00 0.00 1.63
3463 3559 1.895798 ACTAGCTGCTGAACTGTGCTA 59.104 47.619 13.43 0.00 35.47 3.49
3478 3574 9.278978 TGAACTGTGCTAAAATTTGATACAGTA 57.721 29.630 21.08 11.02 44.39 2.74
3516 3612 2.751436 GCGCCAAGCCAGATGGAA 60.751 61.111 2.18 0.00 40.56 3.53
3518 3614 1.377725 CGCCAAGCCAGATGGAACT 60.378 57.895 2.18 0.00 40.56 3.01
3519 3615 1.651240 CGCCAAGCCAGATGGAACTG 61.651 60.000 2.18 0.00 40.56 3.16
3532 3628 1.353022 TGGAACTGGGGGACATGTTAC 59.647 52.381 0.00 0.00 0.00 2.50
3556 3652 1.956297 TTACAAATATGGGTCCGCGG 58.044 50.000 22.12 22.12 0.00 6.46
3564 3660 4.324991 GGGTCCGCGGGAAGTTGT 62.325 66.667 27.83 0.00 31.38 3.32
3565 3661 2.741211 GGTCCGCGGGAAGTTGTC 60.741 66.667 27.83 5.71 31.38 3.18
3574 3670 2.673833 CGGGAAGTTGTCACTGTAGAC 58.326 52.381 4.21 4.21 38.99 2.59
3590 3686 5.952347 ACTGTAGACAGATGGATGTAGAACA 59.048 40.000 16.44 0.00 46.59 3.18
3614 3710 4.660105 GCATTTCTGCTCTTGTGAGATTC 58.340 43.478 0.00 0.00 45.32 2.52
3618 3714 0.737367 TGCTCTTGTGAGATTCGGCG 60.737 55.000 0.00 0.00 42.73 6.46
3619 3715 1.424493 GCTCTTGTGAGATTCGGCGG 61.424 60.000 7.21 0.00 42.73 6.13
3620 3716 0.108615 CTCTTGTGAGATTCGGCGGT 60.109 55.000 7.21 0.00 42.73 5.68
3651 3748 2.486907 GGGCTCTCTTCATCCATCAAGG 60.487 54.545 0.00 0.00 39.47 3.61
3674 3780 1.148273 TGGACGCAGCCTGAAAGTT 59.852 52.632 0.00 0.00 0.00 2.66
3678 3784 0.465460 ACGCAGCCTGAAAGTTGGAA 60.465 50.000 0.00 0.00 0.00 3.53
3693 3799 1.444895 GGAACTTGCTGGCATTGCG 60.445 57.895 1.91 0.00 0.00 4.85
3696 3802 0.388659 AACTTGCTGGCATTGCGAAA 59.611 45.000 1.91 0.00 0.00 3.46
3701 3807 1.273048 TGCTGGCATTGCGAAAAAGAT 59.727 42.857 1.91 0.00 0.00 2.40
3705 3811 4.675510 CTGGCATTGCGAAAAAGATATGT 58.324 39.130 1.91 0.00 0.00 2.29
3707 3813 5.820131 TGGCATTGCGAAAAAGATATGTAG 58.180 37.500 1.91 0.00 0.00 2.74
3714 3820 6.403049 TGCGAAAAAGATATGTAGGTCTCAA 58.597 36.000 0.00 0.00 0.00 3.02
3715 3821 7.047891 TGCGAAAAAGATATGTAGGTCTCAAT 58.952 34.615 0.00 0.00 0.00 2.57
3762 3868 1.153958 GATTGTGCAGGGAAAGCGC 60.154 57.895 0.00 0.00 42.56 5.92
3765 3871 3.435186 GTGCAGGGAAAGCGCCTC 61.435 66.667 2.29 0.00 36.54 4.70
3777 3883 2.456119 GCGCCTCATGAACCGTCAG 61.456 63.158 13.95 0.00 37.14 3.51
3793 3899 3.870633 GTCAGACGGACAAGGTTATCT 57.129 47.619 0.42 0.00 46.19 1.98
3795 3901 4.566987 GTCAGACGGACAAGGTTATCTTT 58.433 43.478 0.42 0.00 46.19 2.52
3796 3902 5.717119 GTCAGACGGACAAGGTTATCTTTA 58.283 41.667 0.42 0.00 46.19 1.85
3798 3904 5.244402 TCAGACGGACAAGGTTATCTTTACA 59.756 40.000 0.00 0.00 32.41 2.41
3799 3905 5.347907 CAGACGGACAAGGTTATCTTTACAC 59.652 44.000 0.00 0.00 32.41 2.90
3800 3906 5.011329 AGACGGACAAGGTTATCTTTACACA 59.989 40.000 0.00 0.00 32.41 3.72
3806 3912 7.065923 GGACAAGGTTATCTTTACACATTCTCC 59.934 40.741 0.00 0.00 32.41 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 2.159085 AGGGAGCATAGTTGAAGCGTAC 60.159 50.000 0.00 0.00 0.00 3.67
174 175 7.148086 GCAAATACAAATAACCCATCTCAGTCA 60.148 37.037 0.00 0.00 0.00 3.41
182 183 7.220030 TGTTGTTGCAAATACAAATAACCCAT 58.780 30.769 0.00 0.00 37.26 4.00
183 184 6.582636 TGTTGTTGCAAATACAAATAACCCA 58.417 32.000 0.00 0.00 37.26 4.51
184 185 7.665561 ATGTTGTTGCAAATACAAATAACCC 57.334 32.000 16.12 0.45 37.26 4.11
230 231 2.837532 ATTGTTCTGCGGGCATTTTT 57.162 40.000 0.00 0.00 0.00 1.94
241 242 9.751542 CTACTTGGTAGGAGTATAATTGTTCTG 57.248 37.037 0.00 0.00 32.98 3.02
242 243 8.422566 GCTACTTGGTAGGAGTATAATTGTTCT 58.577 37.037 6.81 0.00 36.71 3.01
289 290 3.496130 CGATGCAGAACAAGTTTCAGTCT 59.504 43.478 0.00 0.00 0.00 3.24
308 309 8.258708 AGAGGTTTAGCTTACAGAATTTACGAT 58.741 33.333 0.00 0.00 0.00 3.73
351 352 0.252197 GGTTAGGATCAACGGCCTGT 59.748 55.000 0.00 0.00 35.73 4.00
454 455 3.266772 ACCAATAACTGAGAAGATGGCCA 59.733 43.478 8.56 8.56 0.00 5.36
471 472 4.962362 AGGAAACACAAAGGAAAGACCAAT 59.038 37.500 0.00 0.00 42.04 3.16
473 474 3.976015 AGGAAACACAAAGGAAAGACCA 58.024 40.909 0.00 0.00 42.04 4.02
580 582 1.962807 TGTCACAAGAATTTGCAGGGG 59.037 47.619 0.00 0.00 37.85 4.79
654 659 9.121517 CACAAGAATGAGAAAAACATACATGTC 57.878 33.333 0.00 0.00 40.80 3.06
671 676 3.428045 GGCTCGAAATTCCCACAAGAATG 60.428 47.826 0.00 0.00 36.59 2.67
714 719 0.403655 TATGCAGCCCTGTTTGGACA 59.596 50.000 0.00 0.00 38.35 4.02
830 847 9.587772 TGGAAGAACGTTTTATTTCAAAATCAA 57.412 25.926 0.46 0.00 0.00 2.57
921 955 1.524863 CGAGGAGTTCCACTCACCGT 61.525 60.000 6.25 0.00 46.79 4.83
944 983 1.024579 CGGTTTGGATTGGACGAGGG 61.025 60.000 0.00 0.00 0.00 4.30
975 1014 3.642778 TTCTCGGCTACTGCGTGCC 62.643 63.158 0.00 0.00 45.25 5.01
982 1021 1.093159 ATCGTCGTTTCTCGGCTACT 58.907 50.000 0.00 0.00 42.47 2.57
1257 1307 4.393155 ATGTCCGCGAGCTTGGCA 62.393 61.111 8.23 0.00 0.00 4.92
1454 1504 3.414700 CACTGGCCGCTCACGAAC 61.415 66.667 0.00 0.00 43.93 3.95
1531 1585 2.362736 TCCACAGTAGCGTAGAATCGT 58.637 47.619 0.00 0.00 0.00 3.73
1566 1620 0.886563 ACACGGTAGACAGCAGTACC 59.113 55.000 0.00 0.00 36.15 3.34
1571 1625 0.038599 TAGGGACACGGTAGACAGCA 59.961 55.000 0.00 0.00 0.00 4.41
1576 1630 1.065199 ACATCGTAGGGACACGGTAGA 60.065 52.381 0.00 0.00 42.19 2.59
1582 1636 0.529378 ACCGAACATCGTAGGGACAC 59.471 55.000 0.00 0.00 38.40 3.67
1587 1641 3.340727 GGTCACCGAACATCGTAGG 57.659 57.895 0.00 0.00 38.40 3.18
1647 1701 7.885009 TTAAAGAGCATCATTCATCATTCCA 57.115 32.000 0.00 0.00 37.82 3.53
1650 1704 9.909644 GCTAATTAAAGAGCATCATTCATCATT 57.090 29.630 7.01 0.00 38.62 2.57
1652 1706 7.503230 TGGCTAATTAAAGAGCATCATTCATCA 59.497 33.333 12.51 0.00 40.64 3.07
1661 1715 9.189156 TCTATTGTTTGGCTAATTAAAGAGCAT 57.811 29.630 12.51 1.63 40.64 3.79
1674 1728 1.740025 GCGAGCTTCTATTGTTTGGCT 59.260 47.619 0.00 0.00 0.00 4.75
1693 1747 1.982073 GAACCACATGCGCCTACTGC 61.982 60.000 4.18 0.00 0.00 4.40
1758 1812 2.106566 CACACTCCCTGCATCTAGTCT 58.893 52.381 0.00 0.00 0.00 3.24
1785 1839 6.511767 CGTCTGTGAGCAAATAAAACTCAAGT 60.512 38.462 0.00 0.00 41.80 3.16
1959 2018 9.813080 CTAGTACTTTATGTTTGCAGAAGAAAC 57.187 33.333 0.00 0.00 34.48 2.78
1968 2027 5.873179 TGCCACTAGTACTTTATGTTTGC 57.127 39.130 0.00 2.33 0.00 3.68
1970 2029 6.128007 GCACATGCCACTAGTACTTTATGTTT 60.128 38.462 0.00 0.00 34.31 2.83
2000 2062 1.203237 TCATCACGGGACCACATGAT 58.797 50.000 0.00 0.00 31.93 2.45
2183 2248 2.610433 CGCTGTGACTCTGCAATCTTA 58.390 47.619 7.10 0.00 40.30 2.10
2288 2353 2.525368 TCGACATCTTCTCCACCTGAA 58.475 47.619 0.00 0.00 0.00 3.02
2304 2369 7.921787 TCAAGTCTCTCACTATCTTTATCGAC 58.078 38.462 0.00 0.00 32.30 4.20
2324 2389 4.320788 GCTGCAGCTTTTACAGATTCAAGT 60.321 41.667 31.33 0.00 38.21 3.16
2335 2400 3.828451 AGAGGAAATTGCTGCAGCTTTTA 59.172 39.130 36.61 20.53 42.66 1.52
2438 2503 7.148983 CCAAACAATGCACAACTTATAAGAACG 60.149 37.037 19.38 8.86 0.00 3.95
2444 2509 6.488344 TGACTCCAAACAATGCACAACTTATA 59.512 34.615 0.00 0.00 0.00 0.98
2604 2669 7.873719 TCAGTTTCAGTGAAGAAAATAACCA 57.126 32.000 5.56 0.00 39.05 3.67
2651 2716 2.531206 GAAAGTCGTCCCAGATTCGAG 58.469 52.381 0.00 0.00 34.33 4.04
2653 2718 1.135489 TCGAAAGTCGTCCCAGATTCG 60.135 52.381 0.00 0.00 41.35 3.34
2664 2729 0.387878 AGTGCTCAGCTCGAAAGTCG 60.388 55.000 0.00 0.00 42.10 4.18
2666 2731 0.676184 TCAGTGCTCAGCTCGAAAGT 59.324 50.000 0.00 0.00 0.00 2.66
2668 2733 1.718396 CATCAGTGCTCAGCTCGAAA 58.282 50.000 0.00 0.00 0.00 3.46
2725 2790 7.555965 ACAGAAATATAAAAATGCTCCCAACC 58.444 34.615 0.00 0.00 0.00 3.77
2797 2862 1.146774 TGTTTCCTTGCAGGGAATGGA 59.853 47.619 28.78 13.31 43.82 3.41
2843 2908 8.875803 CAACGTAGTAACCAATATATGTGTTGT 58.124 33.333 9.34 2.09 45.00 3.32
2864 2930 8.831715 TCAGCAATATTACATATGATCAACGT 57.168 30.769 10.38 0.00 0.00 3.99
2909 2975 5.046231 GGGGTTGCACAGGGAAAAATATTTA 60.046 40.000 0.01 0.00 0.00 1.40
2915 2981 1.051556 GGGGGTTGCACAGGGAAAAA 61.052 55.000 0.00 0.00 0.00 1.94
2916 2982 1.458588 GGGGGTTGCACAGGGAAAA 60.459 57.895 0.00 0.00 0.00 2.29
2932 2998 5.699097 TTTGATAAACTTGAGGAAACGGG 57.301 39.130 0.00 0.00 0.00 5.28
2966 3032 8.934023 AACAAGACAAGATCCACCTAATAAAA 57.066 30.769 0.00 0.00 0.00 1.52
2975 3041 4.389374 TGAGGAAACAAGACAAGATCCAC 58.611 43.478 0.00 0.00 0.00 4.02
2978 3044 6.073003 ACGATTTGAGGAAACAAGACAAGATC 60.073 38.462 0.00 0.00 0.00 2.75
3007 3073 7.011389 CACAACGGAGCTGAATTATCTATTTCA 59.989 37.037 0.00 0.00 0.00 2.69
3008 3074 7.011482 ACACAACGGAGCTGAATTATCTATTTC 59.989 37.037 0.00 0.00 0.00 2.17
3009 3075 6.823689 ACACAACGGAGCTGAATTATCTATTT 59.176 34.615 0.00 0.00 0.00 1.40
3010 3076 6.349300 ACACAACGGAGCTGAATTATCTATT 58.651 36.000 0.00 0.00 0.00 1.73
3011 3077 5.918608 ACACAACGGAGCTGAATTATCTAT 58.081 37.500 0.00 0.00 0.00 1.98
3013 3079 4.207891 ACACAACGGAGCTGAATTATCT 57.792 40.909 0.00 0.00 0.00 1.98
3014 3080 5.109903 AGTACACAACGGAGCTGAATTATC 58.890 41.667 0.00 0.00 0.00 1.75
3015 3081 5.086104 AGTACACAACGGAGCTGAATTAT 57.914 39.130 0.00 0.00 0.00 1.28
3017 3083 3.402628 AGTACACAACGGAGCTGAATT 57.597 42.857 0.00 0.00 0.00 2.17
3018 3084 3.067106 CAAGTACACAACGGAGCTGAAT 58.933 45.455 0.00 0.00 0.00 2.57
3019 3085 2.101750 TCAAGTACACAACGGAGCTGAA 59.898 45.455 0.00 0.00 0.00 3.02
3020 3086 1.684450 TCAAGTACACAACGGAGCTGA 59.316 47.619 0.00 0.00 0.00 4.26
3021 3087 2.148916 TCAAGTACACAACGGAGCTG 57.851 50.000 0.00 0.00 0.00 4.24
3023 3089 4.483476 AAATTCAAGTACACAACGGAGC 57.517 40.909 0.00 0.00 0.00 4.70
3024 3090 4.675114 GCAAAATTCAAGTACACAACGGAG 59.325 41.667 0.00 0.00 0.00 4.63
3025 3091 4.336993 AGCAAAATTCAAGTACACAACGGA 59.663 37.500 0.00 0.00 0.00 4.69
3026 3092 4.606961 AGCAAAATTCAAGTACACAACGG 58.393 39.130 0.00 0.00 0.00 4.44
3027 3093 5.173131 GGAAGCAAAATTCAAGTACACAACG 59.827 40.000 0.00 0.00 0.00 4.10
3062 3153 2.368439 GCAAGCCAATGATACAGGACA 58.632 47.619 0.00 0.00 0.00 4.02
3072 3163 0.461339 GCATTCTGGGCAAGCCAATG 60.461 55.000 13.87 14.41 37.98 2.82
3080 3171 4.822685 ACAAATAATTGCATTCTGGGCA 57.177 36.364 0.00 0.00 40.34 5.36
3085 3176 8.370182 AGGAACAGAAACAAATAATTGCATTCT 58.630 29.630 6.42 6.42 42.28 2.40
3112 3203 4.043310 GGGGGTGAAGATCAATGATATGGA 59.957 45.833 0.00 0.00 0.00 3.41
3136 3227 9.793252 ATTCAAGAGAAAATCAAATATTCCACG 57.207 29.630 0.00 0.00 37.29 4.94
3172 3263 7.424803 TGTGAAACACTTGAAACAGATATTGG 58.575 34.615 0.00 0.00 45.67 3.16
3174 3265 7.141363 GCTGTGAAACACTTGAAACAGATATT 58.859 34.615 4.87 0.00 45.67 1.28
3187 3278 3.701040 ACAAAAGGATGCTGTGAAACACT 59.299 39.130 5.33 0.00 45.67 3.55
3188 3279 3.798337 CACAAAAGGATGCTGTGAAACAC 59.202 43.478 5.33 0.00 45.67 3.32
3195 3286 4.942761 ACATTTCACAAAAGGATGCTGT 57.057 36.364 0.00 0.00 30.85 4.40
3198 3289 4.394099 GCAACATTTCACAAAAGGATGC 57.606 40.909 2.87 2.87 44.00 3.91
3201 3292 4.462508 TGTGCAACATTTCACAAAAGGA 57.537 36.364 0.00 0.00 45.67 3.36
3334 3430 7.929785 ACAATGTTGCTTCTTCATCAGAATTTT 59.070 29.630 0.00 0.00 40.95 1.82
3342 3438 5.112220 TCACACAATGTTGCTTCTTCATC 57.888 39.130 0.00 0.00 0.00 2.92
3367 3463 9.809096 CTGTACAGAGAGCATTAATAAGAAAGA 57.191 33.333 18.45 0.00 0.00 2.52
3478 3574 7.230510 TGGCGCTTTATGAAATACCAGAATATT 59.769 33.333 7.64 0.00 0.00 1.28
3479 3575 6.714810 TGGCGCTTTATGAAATACCAGAATAT 59.285 34.615 7.64 0.00 0.00 1.28
3508 3604 0.921896 ATGTCCCCCAGTTCCATCTG 59.078 55.000 0.00 0.00 35.45 2.90
3509 3605 0.921896 CATGTCCCCCAGTTCCATCT 59.078 55.000 0.00 0.00 0.00 2.90
3516 3612 0.328258 GCAGTAACATGTCCCCCAGT 59.672 55.000 0.00 0.00 0.00 4.00
3518 3614 0.998928 ATGCAGTAACATGTCCCCCA 59.001 50.000 0.00 0.00 0.00 4.96
3519 3615 2.143876 AATGCAGTAACATGTCCCCC 57.856 50.000 0.00 0.00 0.00 5.40
3532 3628 3.304659 GCGGACCCATATTTGTAATGCAG 60.305 47.826 0.00 0.00 0.00 4.41
3556 3652 4.585955 TCTGTCTACAGTGACAACTTCC 57.414 45.455 9.81 0.00 44.98 3.46
3564 3660 5.755849 TCTACATCCATCTGTCTACAGTGA 58.244 41.667 9.81 6.21 44.12 3.41
3565 3661 6.127619 TGTTCTACATCCATCTGTCTACAGTG 60.128 42.308 9.81 7.60 44.12 3.66
3574 3670 3.548745 TGCCTGTTCTACATCCATCTG 57.451 47.619 0.00 0.00 0.00 2.90
3590 3686 2.039480 TCTCACAAGAGCAGAAATGCCT 59.961 45.455 0.00 0.00 41.81 4.75
3618 3714 1.049402 GAGAGCCCCAGGTACATACC 58.951 60.000 0.00 0.00 46.82 2.73
3619 3715 2.089600 AGAGAGCCCCAGGTACATAC 57.910 55.000 0.00 0.00 0.00 2.39
3620 3716 2.023404 TGAAGAGAGCCCCAGGTACATA 60.023 50.000 0.00 0.00 0.00 2.29
3651 3748 0.955428 TTCAGGCTGCGTCCACAATC 60.955 55.000 10.34 0.00 0.00 2.67
3674 3780 1.667151 GCAATGCCAGCAAGTTCCA 59.333 52.632 0.00 0.00 0.00 3.53
3678 3784 0.388659 TTTTCGCAATGCCAGCAAGT 59.611 45.000 0.00 0.00 0.00 3.16
3693 3799 9.396022 TGGAATTGAGACCTACATATCTTTTTC 57.604 33.333 0.00 0.00 0.00 2.29
3696 3802 7.446625 GCATGGAATTGAGACCTACATATCTTT 59.553 37.037 0.00 0.00 0.00 2.52
3701 3807 5.366477 TCAGCATGGAATTGAGACCTACATA 59.634 40.000 0.00 0.00 36.16 2.29
3705 3811 4.842531 TTCAGCATGGAATTGAGACCTA 57.157 40.909 0.00 0.00 36.16 3.08
3707 3813 4.303086 CATTCAGCATGGAATTGAGACC 57.697 45.455 0.00 0.00 35.37 3.85
3731 3837 2.360191 CAATCCCCCACCACCAGG 59.640 66.667 0.00 0.00 42.21 4.45
3732 3838 1.304381 CACAATCCCCCACCACCAG 60.304 63.158 0.00 0.00 0.00 4.00
3762 3868 3.036026 CGTCTGACGGTTCATGAGG 57.964 57.895 21.78 0.00 38.08 3.86
3777 3883 5.232463 TGTGTAAAGATAACCTTGTCCGTC 58.768 41.667 0.00 0.00 34.79 4.79
3786 3892 9.614792 AATACAGGAGAATGTGTAAAGATAACC 57.385 33.333 0.00 0.00 32.98 2.85


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

AutoCloner maintained by Alex Coulton.