Multiple sequence alignment - TraesCS3B01G259500

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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 TraesCS3B01G259500 chr3B 100.000 3772 0 0 1 3772 417373534 417377305 0.000000e+00 6966.0
1 TraesCS3B01G259500 chr3B 78.386 347 71 4 2410 2754 267412 267756 4.900000e-54 222.0
2 TraesCS3B01G259500 chr3D 93.781 2991 90 42 765 3714 304030573 304027638 0.000000e+00 4405.0
3 TraesCS3B01G259500 chr3D 95.918 49 2 0 3724 3772 304026251 304026203 3.120000e-11 80.5
4 TraesCS3B01G259500 chr3A 95.535 2195 70 18 1583 3772 430526502 430528673 0.000000e+00 3485.0
5 TraesCS3B01G259500 chr3A 91.638 873 37 14 744 1587 430525563 430526428 0.000000e+00 1175.0
6 TraesCS3B01G259500 chr3A 93.023 86 5 1 652 737 430525399 430525483 1.420000e-24 124.0
7 TraesCS3B01G259500 chr4D 90.506 632 58 2 17 646 52750033 52750664 0.000000e+00 833.0
8 TraesCS3B01G259500 chr4D 89.825 629 57 7 17 643 80086690 80086067 0.000000e+00 800.0
9 TraesCS3B01G259500 chr4D 86.747 83 6 2 2907 2985 484149209 484149290 1.870000e-13 87.9
10 TraesCS3B01G259500 chr7A 90.545 624 55 4 21 642 219167135 219166514 0.000000e+00 822.0
11 TraesCS3B01G259500 chr7A 90.000 630 59 4 17 644 689538122 689538749 0.000000e+00 811.0
12 TraesCS3B01G259500 chr6B 89.905 634 61 3 17 649 560790546 560789915 0.000000e+00 813.0
13 TraesCS3B01G259500 chr2B 89.825 629 61 3 21 646 571240009 571239381 0.000000e+00 804.0
14 TraesCS3B01G259500 chr2B 89.415 633 63 4 17 646 799580372 799581003 0.000000e+00 795.0
15 TraesCS3B01G259500 chr2B 89.694 621 63 1 17 636 626105559 626106179 0.000000e+00 791.0
16 TraesCS3B01G259500 chr7B 89.507 629 63 3 17 643 110879401 110880028 0.000000e+00 793.0
17 TraesCS3B01G259500 chr7B 95.161 62 2 1 2907 2968 457244584 457244644 3.100000e-16 97.1
18 TraesCS3B01G259500 chr1B 95.238 63 2 1 2906 2968 67023344 67023405 8.620000e-17 99.0
19 TraesCS3B01G259500 chr6D 93.846 65 2 2 2904 2968 139369338 139369276 3.100000e-16 97.1
20 TraesCS3B01G259500 chr6D 88.462 78 1 3 2909 2986 87332496 87332565 1.870000e-13 87.9
21 TraesCS3B01G259500 chr5B 89.744 78 2 2 2909 2986 324964799 324964728 1.120000e-15 95.3
22 TraesCS3B01G259500 chr5B 87.059 85 2 3 2911 2986 542235632 542235548 1.870000e-13 87.9
23 TraesCS3B01G259500 chr5A 87.342 79 4 5 2908 2985 698351717 698351790 6.710000e-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 TraesCS3B01G259500 chr3B 417373534 417377305 3771 False 6966.000000 6966 100.000000 1 3772 1 chr3B.!!$F2 3771
1 TraesCS3B01G259500 chr3D 304026203 304030573 4370 True 2242.750000 4405 94.849500 765 3772 2 chr3D.!!$R1 3007
2 TraesCS3B01G259500 chr3A 430525399 430528673 3274 False 1594.666667 3485 93.398667 652 3772 3 chr3A.!!$F1 3120
3 TraesCS3B01G259500 chr4D 52750033 52750664 631 False 833.000000 833 90.506000 17 646 1 chr4D.!!$F1 629
4 TraesCS3B01G259500 chr4D 80086067 80086690 623 True 800.000000 800 89.825000 17 643 1 chr4D.!!$R1 626
5 TraesCS3B01G259500 chr7A 219166514 219167135 621 True 822.000000 822 90.545000 21 642 1 chr7A.!!$R1 621
6 TraesCS3B01G259500 chr7A 689538122 689538749 627 False 811.000000 811 90.000000 17 644 1 chr7A.!!$F1 627
7 TraesCS3B01G259500 chr6B 560789915 560790546 631 True 813.000000 813 89.905000 17 649 1 chr6B.!!$R1 632
8 TraesCS3B01G259500 chr2B 571239381 571240009 628 True 804.000000 804 89.825000 21 646 1 chr2B.!!$R1 625
9 TraesCS3B01G259500 chr2B 799580372 799581003 631 False 795.000000 795 89.415000 17 646 1 chr2B.!!$F2 629
10 TraesCS3B01G259500 chr2B 626105559 626106179 620 False 791.000000 791 89.694000 17 636 1 chr2B.!!$F1 619
11 TraesCS3B01G259500 chr7B 110879401 110880028 627 False 793.000000 793 89.507000 17 643 1 chr7B.!!$F1 626

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
374 376 0.107703 GTTCGATGGCATGTCTGGGA 60.108 55.000 3.81 0.00 0.00 4.37 F
663 669 0.249398 AGGCACTAAGGTTACGCTGG 59.751 55.000 0.00 0.00 36.02 4.85 F
665 671 0.391263 GCACTAAGGTTACGCTGGCT 60.391 55.000 0.00 0.00 0.00 4.75 F
2183 2377 1.078708 GATCTTCACGCCCGGGAAA 60.079 57.895 29.31 11.32 37.06 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 2008 0.117340 AGGGCAGGTAGAAGAGGTGT 59.883 55.000 0.00 0.00 0.00 4.16 R
2501 2695 0.532573 AGTTGTCGGCGATGATCACT 59.467 50.000 14.79 8.17 0.00 3.41 R
2564 2758 3.901797 CTTCTCCGCCACCACCACC 62.902 68.421 0.00 0.00 0.00 4.61 R
3330 3545 0.904865 TGTCGAGGTTCAGCCAGGAT 60.905 55.000 0.00 0.00 40.61 3.24 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 2.015243 ATGGGGGTGCTCATCATGGG 62.015 60.000 0.00 0.00 0.00 4.00
53 54 1.511305 GGCGTCTCGGAGTTGATGA 59.489 57.895 4.69 0.00 0.00 2.92
97 98 3.319441 ATCGGCGGCGTTAGGGTTT 62.319 57.895 31.06 4.35 0.00 3.27
163 164 1.076187 TCTCTCCTTCTGCTCTGTCCA 59.924 52.381 0.00 0.00 0.00 4.02
183 184 2.373540 TGTTGCTACGGCGTTATCTT 57.626 45.000 21.24 0.00 42.25 2.40
197 198 3.729762 CGTTATCTTCGACGTCATGGTGA 60.730 47.826 17.16 6.30 34.75 4.02
212 213 1.777878 TGGTGAAGCAGGGAGGTTTTA 59.222 47.619 0.00 0.00 38.24 1.52
218 219 2.188817 AGCAGGGAGGTTTTATCGTCT 58.811 47.619 0.00 0.00 0.00 4.18
288 289 2.481104 CGCATCTTGTGTTGGGTTTGTT 60.481 45.455 0.00 0.00 0.00 2.83
296 297 3.322254 TGTGTTGGGTTTGTTGTTGAAGT 59.678 39.130 0.00 0.00 0.00 3.01
301 302 4.277476 TGGGTTTGTTGTTGAAGTCTGAT 58.723 39.130 0.00 0.00 0.00 2.90
305 306 6.293462 GGGTTTGTTGTTGAAGTCTGATAGTC 60.293 42.308 0.00 0.00 0.00 2.59
370 372 3.291584 TCTAGAGTTCGATGGCATGTCT 58.708 45.455 3.81 1.56 0.00 3.41
374 376 0.107703 GTTCGATGGCATGTCTGGGA 60.108 55.000 3.81 0.00 0.00 4.37
384 388 2.978156 ATGTCTGGGAACATGTTGGT 57.022 45.000 17.58 0.00 41.51 3.67
422 426 1.139163 CGGCAATGGTTTTGCTTCAC 58.861 50.000 9.86 0.00 44.36 3.18
441 445 4.854399 TCACGCAAACTATTTTTGAGGTG 58.146 39.130 11.84 11.84 37.04 4.00
512 517 5.749462 AGGTGATATGTCTCCTTTTCCTTG 58.251 41.667 7.22 0.00 43.96 3.61
528 533 0.987294 CTTGGTGGAGAGGGACATGT 59.013 55.000 0.00 0.00 0.00 3.21
663 669 0.249398 AGGCACTAAGGTTACGCTGG 59.751 55.000 0.00 0.00 36.02 4.85
665 671 0.391263 GCACTAAGGTTACGCTGGCT 60.391 55.000 0.00 0.00 0.00 4.75
677 683 1.525535 GCTGGCTATGGCTGTCCTG 60.526 63.158 0.00 0.00 38.73 3.86
683 689 1.198713 CTATGGCTGTCCTGGTCAGT 58.801 55.000 19.60 5.52 35.60 3.41
688 694 1.451504 CTGTCCTGGTCAGTGCCAA 59.548 57.895 12.08 0.00 38.18 4.52
777 856 4.150454 CGCCCCTCTCTCCCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
778 857 2.123033 GCCCCTCTCTCCCCTCTC 60.123 72.222 0.00 0.00 0.00 3.20
856 946 6.748333 AAAGGTTTACGCTAATTAACTCCC 57.252 37.500 0.00 0.00 0.00 4.30
864 954 2.210116 CTAATTAACTCCCATGCGCGT 58.790 47.619 8.43 0.00 0.00 6.01
880 974 1.910819 CGCGTGTTTGTAATTGGCATC 59.089 47.619 0.00 0.00 0.00 3.91
931 1025 4.457466 TCGCCCCTATAAGATTTGTTTCC 58.543 43.478 0.00 0.00 0.00 3.13
1251 1351 1.153784 GCCGCCACATCCAACATTG 60.154 57.895 0.00 0.00 0.00 2.82
1275 1375 4.699522 GTGTCACCTCCACCGCCC 62.700 72.222 0.00 0.00 0.00 6.13
1289 1401 2.046314 GCCCGCAGAACCAGCTAA 60.046 61.111 0.00 0.00 0.00 3.09
1329 1442 1.512926 AACGAGAGGTACGTACGTGT 58.487 50.000 30.25 20.51 43.16 4.49
1361 1474 1.828979 TGGGGATTGAAAGTAACGGC 58.171 50.000 0.00 0.00 0.00 5.68
1455 1568 4.409247 AGGTACGCCAAGAAGGAGATAATT 59.591 41.667 0.00 0.00 40.01 1.40
1461 1574 3.209410 CAAGAAGGAGATAATTGCCGCT 58.791 45.455 0.00 0.00 0.00 5.52
1538 1651 4.342359 GTCTCCCAGTTCAAGAGGTACTA 58.658 47.826 0.00 0.00 41.55 1.82
1539 1652 4.399934 GTCTCCCAGTTCAAGAGGTACTAG 59.600 50.000 0.00 0.00 41.55 2.57
1572 1686 8.604640 AGACATGCTCAACATTATAATCTCTG 57.395 34.615 0.00 0.00 36.64 3.35
1580 1694 9.674824 CTCAACATTATAATCTCTGCATTTTCC 57.325 33.333 0.00 0.00 0.00 3.13
1633 1825 7.165647 CGCATCATCAATTTAATTGTAGCGAAA 59.834 33.333 24.05 7.08 39.91 3.46
1729 1921 1.207488 CCATCTTCCACACCCCTCCA 61.207 60.000 0.00 0.00 0.00 3.86
1788 1980 2.186384 CCTCAAGGAGAGCAGGCG 59.814 66.667 0.00 0.00 43.31 5.52
1897 2089 2.203209 CATAACCTGCGCCCCCTC 60.203 66.667 4.18 0.00 0.00 4.30
1898 2090 2.366972 ATAACCTGCGCCCCCTCT 60.367 61.111 4.18 0.00 0.00 3.69
2036 2229 8.464404 CATCTGGATGACTCAACATTTTTGTAT 58.536 33.333 4.72 0.00 41.20 2.29
2037 2230 8.044060 TCTGGATGACTCAACATTTTTGTATC 57.956 34.615 0.00 0.00 0.00 2.24
2038 2231 6.841119 TGGATGACTCAACATTTTTGTATCG 58.159 36.000 0.00 0.00 0.00 2.92
2039 2232 5.739161 GGATGACTCAACATTTTTGTATCGC 59.261 40.000 0.00 0.00 0.00 4.58
2040 2233 5.681337 TGACTCAACATTTTTGTATCGCA 57.319 34.783 0.00 0.00 0.00 5.10
2041 2234 5.688823 TGACTCAACATTTTTGTATCGCAG 58.311 37.500 0.00 0.00 0.00 5.18
2183 2377 1.078708 GATCTTCACGCCCGGGAAA 60.079 57.895 29.31 11.32 37.06 3.13
2282 2476 4.208632 CGCATCCTCGCCTTCTTT 57.791 55.556 0.00 0.00 0.00 2.52
2465 2659 1.669440 GTACGAGGTGAACAGCCCA 59.331 57.895 0.00 0.00 0.00 5.36
2564 2758 2.202676 GACTGGAGCGCCTTCTCG 60.203 66.667 8.34 0.00 33.98 4.04
2663 2857 2.661566 CGACTGTGTCAAGCGGCTG 61.662 63.158 1.81 0.00 32.09 4.85
2744 2938 0.323178 ACTCCATTTGGCTCAGCAGG 60.323 55.000 0.00 0.00 34.44 4.85
2966 3162 9.509956 AGATCACTACGCTCTTATATTAGTCTT 57.490 33.333 0.00 0.00 0.00 3.01
2969 3165 9.775854 TCACTACGCTCTTATATTAGTCTTAGT 57.224 33.333 0.00 0.00 0.00 2.24
3031 3227 7.279536 AGCACAATGACTATTCTACTTGACATG 59.720 37.037 0.00 0.00 0.00 3.21
3098 3295 1.244697 TGACGAGTCAGAGGTCAGGC 61.245 60.000 1.24 0.00 35.89 4.85
3109 3306 1.201429 AGGTCAGGCCCGAGAACAAT 61.201 55.000 0.00 0.00 38.26 2.71
3144 3341 3.802139 TCGATCGTATGATTTCTGGCAAC 59.198 43.478 15.94 0.00 34.09 4.17
3218 3431 4.502777 GGGAAAGGGATGAACCGTATCTAC 60.503 50.000 0.00 0.00 40.11 2.59
3582 3797 0.462581 GATCTCACCCAGCGATTGCA 60.463 55.000 7.90 0.00 46.23 4.08
3596 3811 2.279741 GATTGCACGATTGAGTAGGCA 58.720 47.619 0.00 0.00 0.00 4.75
3647 3862 2.159156 CCTGACATGTCATGCAATTGGG 60.159 50.000 28.00 18.60 39.13 4.12
3648 3863 2.756207 CTGACATGTCATGCAATTGGGA 59.244 45.455 28.00 1.51 39.13 4.37
3649 3864 3.163467 TGACATGTCATGCAATTGGGAA 58.837 40.909 24.56 0.00 34.14 3.97
3650 3865 3.193903 TGACATGTCATGCAATTGGGAAG 59.806 43.478 24.56 0.00 34.14 3.46
3651 3866 3.433343 ACATGTCATGCAATTGGGAAGA 58.567 40.909 12.91 0.00 0.00 2.87
3652 3867 3.833650 ACATGTCATGCAATTGGGAAGAA 59.166 39.130 12.91 0.00 0.00 2.52
3653 3868 3.940209 TGTCATGCAATTGGGAAGAAC 57.060 42.857 7.72 0.00 0.00 3.01
3654 3869 3.229293 TGTCATGCAATTGGGAAGAACA 58.771 40.909 7.72 0.00 0.00 3.18
3662 3877 4.706962 GCAATTGGGAAGAACAGAGGTTAT 59.293 41.667 7.72 0.00 37.36 1.89
3722 3944 4.616181 CTTCCAAAAGCCAGTATAACGG 57.384 45.455 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.829096 CCATGGATGGGCGAATGCA 60.829 57.895 5.56 0.00 44.31 3.96
1 2 3.045142 CCATGGATGGGCGAATGC 58.955 61.111 5.56 0.00 44.31 3.56
10 11 0.538977 GATGAGCACCCCCATGGATG 60.539 60.000 15.22 9.78 38.00 3.51
11 12 0.995132 TGATGAGCACCCCCATGGAT 60.995 55.000 15.22 0.00 38.00 3.41
12 13 0.995132 ATGATGAGCACCCCCATGGA 60.995 55.000 15.22 0.00 38.00 3.41
13 14 0.826256 CATGATGAGCACCCCCATGG 60.826 60.000 4.14 4.14 41.37 3.66
14 15 0.826256 CCATGATGAGCACCCCCATG 60.826 60.000 0.00 0.00 35.61 3.66
15 16 1.540166 CCATGATGAGCACCCCCAT 59.460 57.895 0.00 0.00 0.00 4.00
34 35 1.519455 CATCAACTCCGAGACGCCC 60.519 63.158 1.33 0.00 0.00 6.13
53 54 0.796312 GATCGGCAAACACACGATGT 59.204 50.000 3.36 0.00 46.12 3.06
97 98 1.739667 CTCGCCGACACCATCCATA 59.260 57.895 0.00 0.00 0.00 2.74
125 126 2.499289 GAGACACACCTGATGGAGTCAT 59.501 50.000 0.00 0.00 34.94 3.06
163 164 2.596904 AGATAACGCCGTAGCAACAT 57.403 45.000 0.00 0.00 39.83 2.71
183 184 0.388520 CTGCTTCACCATGACGTCGA 60.389 55.000 11.62 0.00 0.00 4.20
197 198 2.572104 AGACGATAAAACCTCCCTGCTT 59.428 45.455 0.00 0.00 0.00 3.91
212 213 0.812811 TGCGCGTACTCCTAGACGAT 60.813 55.000 8.43 0.00 41.60 3.73
218 219 1.153978 CCGTTTGCGCGTACTCCTA 60.154 57.895 8.43 0.00 36.67 2.94
267 268 1.066908 ACAAACCCAACACAAGATGCG 59.933 47.619 0.00 0.00 0.00 4.73
288 289 4.160329 ACCAGGACTATCAGACTTCAACA 58.840 43.478 0.00 0.00 0.00 3.33
296 297 3.012959 AGGAGGAAACCAGGACTATCAGA 59.987 47.826 0.00 0.00 0.00 3.27
301 302 1.618888 CGGAGGAGGAAACCAGGACTA 60.619 57.143 0.00 0.00 0.00 2.59
305 306 1.597461 GTCGGAGGAGGAAACCAGG 59.403 63.158 0.00 0.00 0.00 4.45
370 372 0.695924 ATCGGACCAACATGTTCCCA 59.304 50.000 8.48 0.00 0.00 4.37
374 376 3.634397 ATCAGATCGGACCAACATGTT 57.366 42.857 4.92 4.92 0.00 2.71
383 387 3.307242 CCGTTGAAAGAATCAGATCGGAC 59.693 47.826 0.00 0.00 44.04 4.79
384 388 3.521560 CCGTTGAAAGAATCAGATCGGA 58.478 45.455 0.00 0.00 44.04 4.55
388 392 4.142315 CCATTGCCGTTGAAAGAATCAGAT 60.142 41.667 0.00 0.00 39.77 2.90
422 426 2.656422 CGCACCTCAAAAATAGTTTGCG 59.344 45.455 3.45 3.45 35.82 4.85
431 435 2.542824 GCAGCTTTACGCACCTCAAAAA 60.543 45.455 0.00 0.00 42.61 1.94
512 517 1.078143 GCACATGTCCCTCTCCACC 60.078 63.158 0.00 0.00 0.00 4.61
528 533 5.068987 GGATAATCCTATGCAAAAACCAGCA 59.931 40.000 0.00 0.00 38.20 4.41
579 585 7.944729 AGATTCAGTTACAAGCCACATAAAT 57.055 32.000 0.00 0.00 0.00 1.40
647 653 2.953466 TAGCCAGCGTAACCTTAGTG 57.047 50.000 0.00 0.00 0.00 2.74
648 654 2.102588 CCATAGCCAGCGTAACCTTAGT 59.897 50.000 0.00 0.00 0.00 2.24
649 655 2.755650 CCATAGCCAGCGTAACCTTAG 58.244 52.381 0.00 0.00 0.00 2.18
650 656 1.202604 GCCATAGCCAGCGTAACCTTA 60.203 52.381 0.00 0.00 0.00 2.69
663 669 0.179062 CTGACCAGGACAGCCATAGC 60.179 60.000 5.96 0.00 40.32 2.97
665 671 0.904649 CACTGACCAGGACAGCCATA 59.095 55.000 17.84 0.00 38.74 2.74
698 704 4.320861 CGCATGGAAGTTCATAACCAAACA 60.321 41.667 5.01 0.00 36.00 2.83
777 856 2.799126 AATTTACATGTGCTCCCCGA 57.201 45.000 9.11 0.00 0.00 5.14
778 857 3.510719 CAAAATTTACATGTGCTCCCCG 58.489 45.455 9.11 0.00 0.00 5.73
856 946 1.648191 CCAATTACAAACACGCGCATG 59.352 47.619 5.73 4.48 0.00 4.06
864 954 5.999205 AATCTGGATGCCAATTACAAACA 57.001 34.783 0.00 0.00 30.80 2.83
880 974 5.499139 TCTAATTTAGCCGCAAAATCTGG 57.501 39.130 0.00 0.00 0.00 3.86
931 1025 1.755783 GCAGGAAATGGGAGGCAGG 60.756 63.158 0.00 0.00 0.00 4.85
1146 1240 0.173708 GCGAGAAGGTGAGGAACGAT 59.826 55.000 0.00 0.00 0.00 3.73
1147 1241 0.894184 AGCGAGAAGGTGAGGAACGA 60.894 55.000 0.00 0.00 0.00 3.85
1251 1351 2.280552 TGGAGGTGACACCGTAGCC 61.281 63.158 18.93 17.72 44.90 3.93
1275 1375 1.078759 CGGACTTAGCTGGTTCTGCG 61.079 60.000 0.00 0.00 33.59 5.18
1329 1442 4.738998 CCCCAACCTGCATGCGGA 62.739 66.667 28.32 2.26 0.00 5.54
1361 1474 5.324739 ACACAGAACGAAAATAGACAACG 57.675 39.130 0.00 0.00 0.00 4.10
1587 1701 5.720202 TGCGTTTAGTCACTCACTGAATAT 58.280 37.500 0.00 0.00 33.42 1.28
1633 1825 3.394940 AGCTCCTGGATGATGATCACATT 59.605 43.478 0.00 0.00 36.82 2.71
1674 1866 7.360361 GTCCTGGTAAATGTAAACTTTGAGTG 58.640 38.462 0.00 0.00 0.00 3.51
1816 2008 0.117340 AGGGCAGGTAGAAGAGGTGT 59.883 55.000 0.00 0.00 0.00 4.16
1897 2089 3.002862 CGAAATCTCTGAGGTAGACGGAG 59.997 52.174 4.59 0.00 40.78 4.63
1898 2090 2.943690 CGAAATCTCTGAGGTAGACGGA 59.056 50.000 4.59 0.00 0.00 4.69
2032 2225 2.599473 TCGTACTGCGACTGCGATACA 61.599 52.381 0.00 0.00 45.68 2.29
2040 2233 9.174799 TTACTCCAGTAAAATCGTACTGCGACT 62.175 40.741 6.81 0.00 46.47 4.18
2041 2234 7.111865 TTACTCCAGTAAAATCGTACTGCGAC 61.112 42.308 6.81 0.00 46.47 5.19
2117 2311 1.747709 CCTTGATGCTGTTCCTGGAG 58.252 55.000 0.00 0.00 0.00 3.86
2183 2377 1.377463 CTCCGGGAGAGACACGTCT 60.377 63.158 19.57 0.00 46.50 4.18
2266 2460 1.431036 GCAAAGAAGGCGAGGATGC 59.569 57.895 0.00 0.00 0.00 3.91
2465 2659 2.041265 AGGGCCTCCACGATCCTT 59.959 61.111 0.00 0.00 34.83 3.36
2501 2695 0.532573 AGTTGTCGGCGATGATCACT 59.467 50.000 14.79 8.17 0.00 3.41
2564 2758 3.901797 CTTCTCCGCCACCACCACC 62.902 68.421 0.00 0.00 0.00 4.61
2687 2881 1.061033 AGATCATACCTGAGGGGCCTT 60.061 52.381 2.38 0.00 39.10 4.35
2744 2938 3.380004 TGTCAAGTTGAACATGGTTCACC 59.620 43.478 7.25 5.03 0.00 4.02
2795 2989 8.800370 TTACATGTAAAATCTCAGTGCCATAA 57.200 30.769 15.92 0.00 0.00 1.90
2964 3160 5.051816 CGAGTACTCCCTCTGTAGACTAAG 58.948 50.000 17.23 0.00 0.00 2.18
2965 3161 4.713814 TCGAGTACTCCCTCTGTAGACTAA 59.286 45.833 17.23 0.00 0.00 2.24
2966 3162 4.285020 TCGAGTACTCCCTCTGTAGACTA 58.715 47.826 17.23 0.00 0.00 2.59
2967 3163 3.106054 TCGAGTACTCCCTCTGTAGACT 58.894 50.000 17.23 0.00 0.00 3.24
2968 3164 3.118665 ACTCGAGTACTCCCTCTGTAGAC 60.119 52.174 18.46 0.00 0.00 2.59
2969 3165 3.106054 ACTCGAGTACTCCCTCTGTAGA 58.894 50.000 18.46 5.14 0.00 2.59
2970 3166 3.547054 ACTCGAGTACTCCCTCTGTAG 57.453 52.381 18.46 6.09 0.00 2.74
3098 3295 2.945447 TACCGTACATTGTTCTCGGG 57.055 50.000 22.05 7.93 44.54 5.14
3109 3306 2.554142 ACGATCGACTGATACCGTACA 58.446 47.619 24.34 0.00 34.09 2.90
3218 3431 9.421806 CTAATCTCTTCAGCATGGTCTAATTAG 57.578 37.037 6.11 6.11 36.16 1.73
3330 3545 0.904865 TGTCGAGGTTCAGCCAGGAT 60.905 55.000 0.00 0.00 40.61 3.24
3582 3797 1.135373 CGTCTGTGCCTACTCAATCGT 60.135 52.381 0.00 0.00 0.00 3.73
3635 3850 3.760151 CTCTGTTCTTCCCAATTGCATGA 59.240 43.478 0.00 0.00 0.00 3.07
3662 3877 6.372931 TCTTTCATCTTCTTGGGAGGAAAAA 58.627 36.000 0.00 0.00 40.97 1.94
3704 3926 4.638421 TGAATCCGTTATACTGGCTTTTGG 59.362 41.667 0.00 0.00 0.00 3.28
3715 3937 4.100498 GTCCCTGAACCTGAATCCGTTATA 59.900 45.833 0.00 0.00 0.00 0.98
3720 3942 0.905357 AGTCCCTGAACCTGAATCCG 59.095 55.000 0.00 0.00 0.00 4.18
3722 3944 1.743996 GCAGTCCCTGAACCTGAATC 58.256 55.000 0.00 0.00 32.44 2.52


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

AutoCloner maintained by Alex Coulton.