Multiple sequence alignment - TraesCS5D01G248700

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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 TraesCS5D01G248700 chr5D 100.000 3038 0 0 1 3038 355675887 355678924 0.000000e+00 5611.0
1 TraesCS5D01G248700 chr5D 79.112 608 92 25 1098 1682 479194578 479195173 1.320000e-103 387.0
2 TraesCS5D01G248700 chr5D 81.771 384 53 13 1293 1666 356189272 356189648 3.810000e-79 305.0
3 TraesCS5D01G248700 chr5B 91.750 2097 78 37 1 2054 420385148 420387192 0.000000e+00 2826.0
4 TraesCS5D01G248700 chr5B 84.875 681 60 21 2351 3016 420387837 420388489 0.000000e+00 647.0
5 TraesCS5D01G248700 chr5B 80.729 384 57 14 1293 1666 420856666 420856290 1.780000e-72 283.0
6 TraesCS5D01G248700 chr5B 82.748 313 20 11 2056 2356 420387228 420387518 6.500000e-62 248.0
7 TraesCS5D01G248700 chr5A 87.612 2446 154 62 623 3023 457540433 457538092 0.000000e+00 2700.0
8 TraesCS5D01G248700 chr5A 80.000 590 90 21 1098 1672 597941094 597941670 7.840000e-111 411.0
9 TraesCS5D01G248700 chr5A 81.212 495 30 20 17 485 457540952 457540495 1.040000e-89 340.0
10 TraesCS5D01G248700 chr5A 80.570 386 60 10 1293 1666 457881064 457881446 1.780000e-72 283.0
11 TraesCS5D01G248700 chr5A 97.222 36 1 0 530 565 457540467 457540432 9.090000e-06 62.1
12 TraesCS5D01G248700 chr2A 88.265 196 17 2 1800 1989 756837438 756837633 2.360000e-56 230.0


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 TraesCS5D01G248700 chr5D 355675887 355678924 3037 False 5611.000000 5611 100.000000 1 3038 1 chr5D.!!$F1 3037
1 TraesCS5D01G248700 chr5D 479194578 479195173 595 False 387.000000 387 79.112000 1098 1682 1 chr5D.!!$F3 584
2 TraesCS5D01G248700 chr5B 420385148 420388489 3341 False 1240.333333 2826 86.457667 1 3016 3 chr5B.!!$F1 3015
3 TraesCS5D01G248700 chr5A 457538092 457540952 2860 True 1034.033333 2700 88.682000 17 3023 3 chr5A.!!$R1 3006
4 TraesCS5D01G248700 chr5A 597941094 597941670 576 False 411.000000 411 80.000000 1098 1672 1 chr5A.!!$F2 574

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
108 109 0.033991 TCTCTCCTCTTCCTCCCGTG 60.034 60.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2186 0.738762 CAGAGCACTCATGTCGGGTG 60.739 60.0 0.0 0.0 0.0 4.61 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
78 79 1.841663 GCACAAGCGTCCGTGAACAT 61.842 55.000 4.71 0.00 35.02 2.71
94 95 4.629200 GTGAACATCACACCATCTTCTCTC 59.371 45.833 5.65 0.00 46.22 3.20
98 99 3.464720 TCACACCATCTTCTCTCCTCT 57.535 47.619 0.00 0.00 0.00 3.69
99 100 3.784178 TCACACCATCTTCTCTCCTCTT 58.216 45.455 0.00 0.00 0.00 2.85
100 101 3.766591 TCACACCATCTTCTCTCCTCTTC 59.233 47.826 0.00 0.00 0.00 2.87
101 102 3.103742 ACACCATCTTCTCTCCTCTTCC 58.896 50.000 0.00 0.00 0.00 3.46
102 103 3.245948 ACACCATCTTCTCTCCTCTTCCT 60.246 47.826 0.00 0.00 0.00 3.36
103 104 3.384467 CACCATCTTCTCTCCTCTTCCTC 59.616 52.174 0.00 0.00 0.00 3.71
104 105 2.965147 CCATCTTCTCTCCTCTTCCTCC 59.035 54.545 0.00 0.00 0.00 4.30
105 106 2.838637 TCTTCTCTCCTCTTCCTCCC 57.161 55.000 0.00 0.00 0.00 4.30
106 107 1.064314 TCTTCTCTCCTCTTCCTCCCG 60.064 57.143 0.00 0.00 0.00 5.14
107 108 0.705253 TTCTCTCCTCTTCCTCCCGT 59.295 55.000 0.00 0.00 0.00 5.28
108 109 0.033991 TCTCTCCTCTTCCTCCCGTG 60.034 60.000 0.00 0.00 0.00 4.94
109 110 0.033991 CTCTCCTCTTCCTCCCGTGA 60.034 60.000 0.00 0.00 0.00 4.35
110 111 0.631753 TCTCCTCTTCCTCCCGTGAT 59.368 55.000 0.00 0.00 0.00 3.06
111 112 0.749649 CTCCTCTTCCTCCCGTGATG 59.250 60.000 0.00 0.00 0.00 3.07
112 113 1.144936 CCTCTTCCTCCCGTGATGC 59.855 63.158 0.00 0.00 0.00 3.91
113 114 1.227089 CTCTTCCTCCCGTGATGCG 60.227 63.158 0.00 0.00 40.95 4.73
114 115 1.949847 CTCTTCCTCCCGTGATGCGT 61.950 60.000 0.00 0.00 39.32 5.24
115 116 1.811266 CTTCCTCCCGTGATGCGTG 60.811 63.158 0.00 0.00 39.32 5.34
116 117 2.225791 CTTCCTCCCGTGATGCGTGA 62.226 60.000 0.00 0.00 39.32 4.35
117 118 2.202797 CCTCCCGTGATGCGTGAG 60.203 66.667 0.00 0.00 43.19 3.51
138 140 2.480555 GTGACCGCAATTCCGCAG 59.519 61.111 0.00 0.00 0.00 5.18
169 175 2.671177 CGGCTCCACGAAAGCTGTG 61.671 63.158 8.46 0.00 40.54 3.66
200 206 4.007644 TCCAGGGTGTGCAGCGAG 62.008 66.667 0.00 0.00 0.00 5.03
279 285 4.598257 TGGCGACAAAGCTAGCTC 57.402 55.556 19.65 4.50 37.44 4.09
370 401 1.151679 GGGGAGCCCTTGATTAGCC 59.848 63.158 5.38 0.00 41.34 3.93
488 524 2.883730 GCATTGTCGCGCTACGGA 60.884 61.111 5.56 0.00 43.89 4.69
489 525 2.860628 GCATTGTCGCGCTACGGAG 61.861 63.158 5.56 0.00 43.89 4.63
501 537 1.816863 CTACGGAGCAGTGTGGTGGT 61.817 60.000 0.00 0.00 0.00 4.16
503 539 2.510906 GGAGCAGTGTGGTGGTGT 59.489 61.111 0.00 0.00 0.00 4.16
504 540 1.893808 GGAGCAGTGTGGTGGTGTG 60.894 63.158 0.00 0.00 0.00 3.82
512 548 0.254462 TGTGGTGGTGTGTGTGTGAT 59.746 50.000 0.00 0.00 0.00 3.06
513 549 0.662619 GTGGTGGTGTGTGTGTGATG 59.337 55.000 0.00 0.00 0.00 3.07
514 550 0.254462 TGGTGGTGTGTGTGTGATGT 59.746 50.000 0.00 0.00 0.00 3.06
515 551 0.662619 GGTGGTGTGTGTGTGATGTG 59.337 55.000 0.00 0.00 0.00 3.21
516 552 1.662517 GTGGTGTGTGTGTGATGTGA 58.337 50.000 0.00 0.00 0.00 3.58
517 553 2.013400 GTGGTGTGTGTGTGATGTGAA 58.987 47.619 0.00 0.00 0.00 3.18
518 554 2.013400 TGGTGTGTGTGTGATGTGAAC 58.987 47.619 0.00 0.00 0.00 3.18
519 555 1.333619 GGTGTGTGTGTGATGTGAACC 59.666 52.381 0.00 0.00 0.00 3.62
520 556 1.003972 GTGTGTGTGTGATGTGAACCG 60.004 52.381 0.00 0.00 0.00 4.44
521 557 1.295792 GTGTGTGTGATGTGAACCGT 58.704 50.000 0.00 0.00 0.00 4.83
522 558 1.003972 GTGTGTGTGATGTGAACCGTG 60.004 52.381 0.00 0.00 0.00 4.94
523 559 0.586319 GTGTGTGATGTGAACCGTGG 59.414 55.000 0.00 0.00 0.00 4.94
524 560 0.179234 TGTGTGATGTGAACCGTGGT 59.821 50.000 0.00 0.00 0.00 4.16
525 561 1.305201 GTGTGATGTGAACCGTGGTT 58.695 50.000 3.43 3.43 41.54 3.67
526 562 1.673920 GTGTGATGTGAACCGTGGTTT 59.326 47.619 5.63 0.00 38.60 3.27
527 563 2.098443 GTGTGATGTGAACCGTGGTTTT 59.902 45.455 5.63 0.00 38.60 2.43
528 564 2.356382 TGTGATGTGAACCGTGGTTTTC 59.644 45.455 5.63 3.36 38.60 2.29
589 625 5.036117 TGAAACCTGCTGTCTTTTCTACT 57.964 39.130 9.46 0.00 0.00 2.57
619 656 8.647796 TCTCTATTTCTGTTGTGAAAGGAGTAA 58.352 33.333 15.20 0.00 39.01 2.24
635 672 9.798994 GAAAGGAGTAATATGTAAAGACGAGAA 57.201 33.333 0.00 0.00 0.00 2.87
713 758 3.508840 GTGAATGAAGCGGGCGGG 61.509 66.667 0.00 0.00 0.00 6.13
904 950 1.170919 AACCTCAAGCAGCACAGCAG 61.171 55.000 0.00 0.00 36.85 4.24
954 1000 0.104855 GCTCACAGTCACACTCCACA 59.895 55.000 0.00 0.00 0.00 4.17
974 1020 4.729918 CTGCCTGCCACTCCCCAC 62.730 72.222 0.00 0.00 0.00 4.61
2076 2200 2.436646 GCCCACCCGACATGAGTG 60.437 66.667 0.00 1.30 0.00 3.51
2090 2214 0.735471 TGAGTGCTCTGCTACGCTAG 59.265 55.000 0.00 0.00 0.00 3.42
2119 2246 1.273887 CGTACGTACGTAGCGAGGG 59.726 63.158 33.95 14.41 44.13 4.30
2126 2253 4.222847 CGTAGCGAGGGGGAAGGC 62.223 72.222 0.00 0.00 0.00 4.35
2131 2258 2.044946 CGAGGGGGAAGGCCTTTG 60.045 66.667 21.54 0.00 0.00 2.77
2132 2259 2.360585 GAGGGGGAAGGCCTTTGG 59.639 66.667 21.54 0.00 0.00 3.28
2135 2262 1.152118 GGGGGAAGGCCTTTGGTTT 60.152 57.895 21.54 0.00 0.00 3.27
2137 2264 0.471022 GGGGAAGGCCTTTGGTTTGA 60.471 55.000 21.54 0.00 0.00 2.69
2154 2292 4.446234 GTTTGAGTCGATTTCTTGTGTCG 58.554 43.478 0.00 0.00 36.75 4.35
2261 2413 1.264749 ACCGACCCATCTGCAGCTAA 61.265 55.000 9.47 0.00 0.00 3.09
2262 2414 0.531532 CCGACCCATCTGCAGCTAAG 60.532 60.000 9.47 0.12 0.00 2.18
2263 2415 1.156645 CGACCCATCTGCAGCTAAGC 61.157 60.000 9.47 0.00 0.00 3.09
2264 2416 0.107508 GACCCATCTGCAGCTAAGCA 60.108 55.000 9.47 0.00 43.35 3.91
2265 2417 0.329261 ACCCATCTGCAGCTAAGCAA 59.671 50.000 9.47 0.00 45.13 3.91
2266 2418 1.022735 CCCATCTGCAGCTAAGCAAG 58.977 55.000 9.47 0.00 45.13 4.01
2292 2444 1.070443 GTAGCTTGCAACGTTAACGCA 60.070 47.619 27.07 14.66 44.43 5.24
2293 2445 0.041312 AGCTTGCAACGTTAACGCAG 60.041 50.000 27.07 19.86 44.43 5.18
2315 2467 3.589495 AGTAGTAGTTGGCCGTTTCTC 57.411 47.619 0.00 0.00 0.00 2.87
2325 2477 2.733218 CGTTTCTCGCAGTCGCCA 60.733 61.111 0.00 0.00 35.26 5.69
2326 2478 2.720758 CGTTTCTCGCAGTCGCCAG 61.721 63.158 0.00 0.00 35.26 4.85
2327 2479 1.664965 GTTTCTCGCAGTCGCCAGT 60.665 57.895 0.00 0.00 35.26 4.00
2356 2508 4.873746 ACTACCGAGCCGTATACTACTA 57.126 45.455 0.56 0.00 0.00 1.82
2402 2878 0.108186 CCTAGCGATTGCAGTGTCCA 60.108 55.000 7.90 0.00 46.23 4.02
2450 2926 1.098712 GTGAACTGGCCGTGTGGAAA 61.099 55.000 0.00 0.00 37.49 3.13
2489 2965 4.284178 AGTATTACCCGAGCTGGTTTCTA 58.716 43.478 0.33 0.00 39.91 2.10
2496 2972 1.383523 GAGCTGGTTTCTATGTGGCC 58.616 55.000 0.00 0.00 0.00 5.36
2508 2984 2.240493 ATGTGGCCGCATCTAGTTAC 57.760 50.000 26.27 0.19 0.00 2.50
2558 3034 1.354337 CGGCGGAGAATGTGTGTCTG 61.354 60.000 0.00 0.00 0.00 3.51
2573 3049 3.513515 TGTGTCTGGCCTTTGTTTTCTTT 59.486 39.130 3.32 0.00 0.00 2.52
2578 3054 1.858458 GGCCTTTGTTTTCTTTGACGC 59.142 47.619 0.00 0.00 0.00 5.19
2582 3058 3.428862 CCTTTGTTTTCTTTGACGCTGGT 60.429 43.478 0.00 0.00 0.00 4.00
2583 3059 2.842208 TGTTTTCTTTGACGCTGGTG 57.158 45.000 0.00 0.00 0.00 4.17
2599 3075 4.961511 TGCGTGCGGGTCTGTGTC 62.962 66.667 0.00 0.00 0.00 3.67
2600 3076 4.961511 GCGTGCGGGTCTGTGTCA 62.962 66.667 0.00 0.00 0.00 3.58
2619 3096 2.158957 TCAGTCAGTCAGTGTGTTTCCC 60.159 50.000 0.00 0.00 0.00 3.97
2641 3118 1.553248 CATTCAGGGGACTCGGTTGTA 59.447 52.381 0.00 0.00 40.21 2.41
2642 3119 1.263356 TTCAGGGGACTCGGTTGTAG 58.737 55.000 0.00 0.00 40.21 2.74
2643 3120 0.113776 TCAGGGGACTCGGTTGTAGT 59.886 55.000 0.00 0.00 40.21 2.73
2644 3121 1.355381 TCAGGGGACTCGGTTGTAGTA 59.645 52.381 0.00 0.00 40.21 1.82
2645 3122 1.749634 CAGGGGACTCGGTTGTAGTAG 59.250 57.143 0.00 0.00 40.21 2.57
2646 3123 1.357079 AGGGGACTCGGTTGTAGTAGT 59.643 52.381 0.00 0.00 32.90 2.73
2647 3124 2.578021 AGGGGACTCGGTTGTAGTAGTA 59.422 50.000 0.00 0.00 32.90 1.82
2648 3125 2.685388 GGGGACTCGGTTGTAGTAGTAC 59.315 54.545 0.37 0.37 0.00 2.73
2649 3126 2.352960 GGGACTCGGTTGTAGTAGTACG 59.647 54.545 3.32 0.00 30.95 3.67
2661 3138 3.001395 AGTAGTACGAAGCATCATCGC 57.999 47.619 0.00 0.00 43.88 4.58
2662 3139 2.619177 AGTAGTACGAAGCATCATCGCT 59.381 45.455 0.00 0.00 46.67 4.93
2688 3165 4.025401 CACCGCGCCCTGTTGTTC 62.025 66.667 0.00 0.00 0.00 3.18
2695 3185 2.424302 CCCTGTTGTTCGGACGGT 59.576 61.111 0.00 0.00 0.00 4.83
2696 3186 1.959226 CCCTGTTGTTCGGACGGTG 60.959 63.158 0.00 0.00 0.00 4.94
2794 3289 2.182181 CATGGCGTGCGATCATGGT 61.182 57.895 15.26 0.00 35.82 3.55
2931 3432 1.663161 GGTACTTTTGAGCTTGCACGC 60.663 52.381 7.16 7.16 0.00 5.34
2953 3471 2.287457 TATTCCACTTCCCGTCGCCG 62.287 60.000 0.00 0.00 0.00 6.46
2972 3490 4.201679 TATCTGCGACCCCGTGCG 62.202 66.667 0.00 0.00 38.24 5.34
3027 3545 4.084888 CGGTGGCCTCGCGTTTTC 62.085 66.667 5.77 0.00 0.00 2.29
3028 3546 3.733960 GGTGGCCTCGCGTTTTCC 61.734 66.667 5.77 4.21 0.00 3.13
3029 3547 4.084888 GTGGCCTCGCGTTTTCCG 62.085 66.667 5.77 0.00 40.40 4.30
3030 3548 4.612412 TGGCCTCGCGTTTTCCGT 62.612 61.111 5.77 0.00 39.32 4.69
3031 3549 3.351416 GGCCTCGCGTTTTCCGTT 61.351 61.111 5.77 0.00 39.32 4.44
3032 3550 2.028733 GGCCTCGCGTTTTCCGTTA 61.029 57.895 5.77 0.00 39.32 3.18
3033 3551 1.418755 GCCTCGCGTTTTCCGTTAG 59.581 57.895 5.77 0.00 39.32 2.34
3034 3552 1.418755 CCTCGCGTTTTCCGTTAGC 59.581 57.895 5.77 0.00 39.32 3.09
3035 3553 1.418755 CTCGCGTTTTCCGTTAGCC 59.581 57.895 5.77 0.00 39.32 3.93
3036 3554 2.095096 CGCGTTTTCCGTTAGCCG 59.905 61.111 0.00 0.00 39.32 5.52
3037 3555 2.202260 GCGTTTTCCGTTAGCCGC 60.202 61.111 0.00 0.00 39.32 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.533266 TGTTCTTCCTGTGAGCAGTC 57.467 50.000 0.00 0.00 41.02 3.51
12 13 3.281727 TTTGTTCTTCCTGTGAGCAGT 57.718 42.857 0.00 0.00 41.02 4.40
13 14 3.378112 TGTTTTGTTCTTCCTGTGAGCAG 59.622 43.478 0.00 0.00 42.22 4.24
14 15 3.351740 TGTTTTGTTCTTCCTGTGAGCA 58.648 40.909 0.00 0.00 0.00 4.26
15 16 4.354587 CTTGTTTTGTTCTTCCTGTGAGC 58.645 43.478 0.00 0.00 0.00 4.26
25 26 1.000274 GATGGCGCCTTGTTTTGTTCT 60.000 47.619 29.70 0.00 0.00 3.01
78 79 3.464720 AGAGGAGAGAAGATGGTGTGA 57.535 47.619 0.00 0.00 0.00 3.58
82 83 3.629796 GGAGGAAGAGGAGAGAAGATGGT 60.630 52.174 0.00 0.00 0.00 3.55
94 95 1.144936 GCATCACGGGAGGAAGAGG 59.855 63.158 2.08 0.00 0.00 3.69
106 107 3.490759 CACGGGCTCACGCATCAC 61.491 66.667 0.00 0.00 38.10 3.06
107 108 3.690280 TCACGGGCTCACGCATCA 61.690 61.111 0.00 0.00 38.10 3.07
108 109 3.188786 GTCACGGGCTCACGCATC 61.189 66.667 0.00 0.00 38.10 3.91
109 110 4.760047 GGTCACGGGCTCACGCAT 62.760 66.667 0.00 0.00 38.10 4.73
113 114 4.980805 TTGCGGTCACGGGCTCAC 62.981 66.667 0.00 0.00 41.36 3.51
114 115 3.545124 AATTGCGGTCACGGGCTCA 62.545 57.895 0.00 0.00 41.36 4.26
115 116 2.746277 AATTGCGGTCACGGGCTC 60.746 61.111 0.00 0.00 41.36 4.70
116 117 2.746277 GAATTGCGGTCACGGGCT 60.746 61.111 0.00 0.00 41.36 5.19
117 118 3.810896 GGAATTGCGGTCACGGGC 61.811 66.667 0.00 0.00 41.36 6.13
138 140 1.014564 GGAGCCGCGCCATAGAATAC 61.015 60.000 8.47 0.00 0.00 1.89
198 204 4.479993 ACGCATGGAGCCTGCCTC 62.480 66.667 0.00 0.00 41.38 4.70
279 285 2.745884 TCCAGCGCCATCGGTTTG 60.746 61.111 2.29 0.00 44.90 2.93
301 314 2.125552 CGCTCCGGCAATCAGTGA 60.126 61.111 0.00 0.00 38.60 3.41
370 401 3.000819 TGGTCTGGCTGGTACCCG 61.001 66.667 10.07 3.73 31.97 5.28
485 521 2.666190 CACCACCACACTGCTCCG 60.666 66.667 0.00 0.00 0.00 4.63
486 522 1.893808 CACACCACCACACTGCTCC 60.894 63.158 0.00 0.00 0.00 4.70
488 524 1.451927 CACACACCACCACACTGCT 60.452 57.895 0.00 0.00 0.00 4.24
489 525 1.748879 ACACACACCACCACACTGC 60.749 57.895 0.00 0.00 0.00 4.40
491 527 0.676466 CACACACACACCACCACACT 60.676 55.000 0.00 0.00 0.00 3.55
492 528 0.675208 TCACACACACACCACCACAC 60.675 55.000 0.00 0.00 0.00 3.82
493 529 0.254462 ATCACACACACACCACCACA 59.746 50.000 0.00 0.00 0.00 4.17
494 530 0.662619 CATCACACACACACCACCAC 59.337 55.000 0.00 0.00 0.00 4.16
495 531 0.254462 ACATCACACACACACCACCA 59.746 50.000 0.00 0.00 0.00 4.17
498 534 2.013400 GTTCACATCACACACACACCA 58.987 47.619 0.00 0.00 0.00 4.17
501 537 1.294857 CGGTTCACATCACACACACA 58.705 50.000 0.00 0.00 0.00 3.72
503 539 1.294857 CACGGTTCACATCACACACA 58.705 50.000 0.00 0.00 0.00 3.72
504 540 0.586319 CCACGGTTCACATCACACAC 59.414 55.000 0.00 0.00 0.00 3.82
512 548 1.340211 ACCAGAAAACCACGGTTCACA 60.340 47.619 1.05 0.00 37.35 3.58
513 549 1.064952 CACCAGAAAACCACGGTTCAC 59.935 52.381 1.05 0.00 37.35 3.18
514 550 1.065345 TCACCAGAAAACCACGGTTCA 60.065 47.619 1.05 0.00 37.35 3.18
515 551 1.670791 TCACCAGAAAACCACGGTTC 58.329 50.000 1.05 0.00 37.35 3.62
516 552 2.131776 TTCACCAGAAAACCACGGTT 57.868 45.000 0.00 0.00 40.45 4.44
517 553 1.746787 GTTTCACCAGAAAACCACGGT 59.253 47.619 0.00 0.00 44.75 4.83
518 554 1.066454 GGTTTCACCAGAAAACCACGG 59.934 52.381 11.80 0.00 44.01 4.94
519 555 2.485266 GGTTTCACCAGAAAACCACG 57.515 50.000 11.80 0.00 44.01 4.94
523 559 5.774498 AGATTCAGGTTTCACCAGAAAAC 57.226 39.130 5.01 0.00 45.05 2.43
524 560 6.406849 CCAAAGATTCAGGTTTCACCAGAAAA 60.407 38.462 5.01 0.00 45.05 2.29
525 561 5.068987 CCAAAGATTCAGGTTTCACCAGAAA 59.931 40.000 5.01 0.00 45.05 2.52
526 562 4.584325 CCAAAGATTCAGGTTTCACCAGAA 59.416 41.667 3.50 3.50 45.78 3.02
527 563 4.144297 CCAAAGATTCAGGTTTCACCAGA 58.856 43.478 0.00 0.00 41.95 3.86
528 564 3.256631 CCCAAAGATTCAGGTTTCACCAG 59.743 47.826 0.00 0.00 41.95 4.00
589 625 8.156820 TCCTTTCACAACAGAAATAGAGAATCA 58.843 33.333 0.00 0.00 36.94 2.57
619 656 5.220416 GCGCAAACTTCTCGTCTTTACATAT 60.220 40.000 0.30 0.00 0.00 1.78
621 658 3.120649 GCGCAAACTTCTCGTCTTTACAT 60.121 43.478 0.30 0.00 0.00 2.29
635 672 2.629656 GCCTGTGATGGCGCAAACT 61.630 57.895 10.83 0.00 43.74 2.66
755 800 4.715523 CTCCCTTTCCCGCCGCAA 62.716 66.667 0.00 0.00 0.00 4.85
887 932 3.264947 CTGCTGTGCTGCTTGAGG 58.735 61.111 0.00 0.00 0.00 3.86
2062 2186 0.738762 CAGAGCACTCATGTCGGGTG 60.739 60.000 0.00 0.00 0.00 4.61
2063 2187 1.593787 CAGAGCACTCATGTCGGGT 59.406 57.895 0.00 0.00 0.00 5.28
2119 2246 0.969149 CTCAAACCAAAGGCCTTCCC 59.031 55.000 20.79 0.00 0.00 3.97
2126 2253 5.215160 CAAGAAATCGACTCAAACCAAAGG 58.785 41.667 0.00 0.00 0.00 3.11
2131 2258 4.608445 CGACACAAGAAATCGACTCAAACC 60.608 45.833 0.00 0.00 38.10 3.27
2132 2259 4.446234 CGACACAAGAAATCGACTCAAAC 58.554 43.478 0.00 0.00 38.10 2.93
2135 2262 2.058798 GCGACACAAGAAATCGACTCA 58.941 47.619 0.00 0.00 38.10 3.41
2137 2264 1.270094 TGGCGACACAAGAAATCGACT 60.270 47.619 0.00 0.00 44.40 4.18
2154 2292 2.809601 CGCACTCTACACCGTGGC 60.810 66.667 3.03 0.00 0.00 5.01
2239 2378 4.408821 TGCAGATGGGTCGGTGGC 62.409 66.667 0.00 0.00 0.00 5.01
2249 2388 3.920144 GCTTGCTTAGCTGCAGATG 57.080 52.632 20.43 0.36 46.77 2.90
2267 2419 1.512926 AACGTTGCAAGCTACTCCAG 58.487 50.000 0.00 0.00 0.00 3.86
2268 2420 2.803956 GTTAACGTTGCAAGCTACTCCA 59.196 45.455 11.99 0.00 0.00 3.86
2269 2421 2.159881 CGTTAACGTTGCAAGCTACTCC 60.160 50.000 19.75 0.00 34.11 3.85
2270 2422 2.720891 GCGTTAACGTTGCAAGCTACTC 60.721 50.000 27.28 3.96 42.22 2.59
2271 2423 1.193874 GCGTTAACGTTGCAAGCTACT 59.806 47.619 27.28 0.00 42.22 2.57
2272 2424 1.070443 TGCGTTAACGTTGCAAGCTAC 60.070 47.619 27.28 8.66 42.22 3.58
2273 2425 1.193650 CTGCGTTAACGTTGCAAGCTA 59.806 47.619 27.28 4.43 42.22 3.32
2274 2426 0.041312 CTGCGTTAACGTTGCAAGCT 60.041 50.000 27.28 0.00 42.22 3.74
2292 2444 4.085009 AGAAACGGCCAACTACTACTACT 58.915 43.478 2.24 0.00 0.00 2.57
2293 2445 4.419280 GAGAAACGGCCAACTACTACTAC 58.581 47.826 2.24 0.00 0.00 2.73
2294 2446 3.127548 CGAGAAACGGCCAACTACTACTA 59.872 47.826 2.24 0.00 38.46 1.82
2315 2467 1.012086 TACTACTACTGGCGACTGCG 58.988 55.000 0.00 0.00 44.10 5.18
2327 2479 3.543680 ACGGCTCGGTAGTTACTACTA 57.456 47.619 20.15 9.51 37.16 1.82
2402 2878 5.448632 GCAGCAGTACAAAAAGTTACACACT 60.449 40.000 0.00 0.00 37.30 3.55
2450 2926 7.724061 GGGTAATACTAAATCACACCATTCCAT 59.276 37.037 0.00 0.00 0.00 3.41
2474 2950 1.656652 CACATAGAAACCAGCTCGGG 58.343 55.000 7.06 0.00 40.22 5.14
2489 2965 1.202651 GGTAACTAGATGCGGCCACAT 60.203 52.381 5.79 5.79 0.00 3.21
2496 2972 2.560504 TGCCAATGGTAACTAGATGCG 58.439 47.619 0.00 0.00 37.61 4.73
2508 2984 0.526739 CACGTGCATGATGCCAATGG 60.527 55.000 15.70 0.00 44.23 3.16
2558 3034 1.858458 GCGTCAAAGAAAACAAAGGCC 59.142 47.619 0.00 0.00 0.00 5.19
2582 3058 4.961511 GACACAGACCCGCACGCA 62.962 66.667 0.00 0.00 0.00 5.24
2583 3059 4.961511 TGACACAGACCCGCACGC 62.962 66.667 0.00 0.00 0.00 5.34
2590 3066 1.683917 ACTGACTGACTGACACAGACC 59.316 52.381 5.76 0.00 38.55 3.85
2592 3068 2.099756 CACACTGACTGACTGACACAGA 59.900 50.000 5.76 0.00 38.55 3.41
2593 3069 2.159184 ACACACTGACTGACTGACACAG 60.159 50.000 0.00 0.00 40.68 3.66
2596 3072 3.521560 GAAACACACTGACTGACTGACA 58.478 45.455 0.00 0.00 0.00 3.58
2598 3074 2.158957 GGGAAACACACTGACTGACTGA 60.159 50.000 0.00 0.00 0.00 3.41
2599 3075 2.213499 GGGAAACACACTGACTGACTG 58.787 52.381 0.00 0.00 0.00 3.51
2600 3076 1.202533 CGGGAAACACACTGACTGACT 60.203 52.381 0.00 0.00 0.00 3.41
2619 3096 2.202932 CCGAGTCCCCTGAATGCG 60.203 66.667 0.00 0.00 0.00 4.73
2635 3112 4.990257 TGATGCTTCGTACTACTACAACC 58.010 43.478 0.00 0.00 0.00 3.77
2641 3118 2.619177 AGCGATGATGCTTCGTACTACT 59.381 45.455 0.00 0.00 44.46 2.57
2642 3119 2.721603 CAGCGATGATGCTTCGTACTAC 59.278 50.000 0.00 0.00 44.46 2.73
2643 3120 2.858646 GCAGCGATGATGCTTCGTACTA 60.859 50.000 4.02 0.00 44.46 1.82
2644 3121 1.845266 CAGCGATGATGCTTCGTACT 58.155 50.000 0.00 0.00 44.46 2.73
2645 3122 0.230769 GCAGCGATGATGCTTCGTAC 59.769 55.000 4.02 0.00 44.46 3.67
2646 3123 1.208642 CGCAGCGATGATGCTTCGTA 61.209 55.000 9.98 0.00 44.65 3.43
2647 3124 2.520039 CGCAGCGATGATGCTTCGT 61.520 57.895 9.98 0.00 44.65 3.85
2648 3125 2.244669 CGCAGCGATGATGCTTCG 59.755 61.111 9.98 0.00 44.46 3.79
2675 3152 3.723348 GTCCGAACAACAGGGCGC 61.723 66.667 0.00 0.00 0.00 6.53
2678 3155 1.959226 CACCGTCCGAACAACAGGG 60.959 63.158 0.00 0.00 0.00 4.45
2679 3156 2.604174 GCACCGTCCGAACAACAGG 61.604 63.158 0.00 0.00 0.00 4.00
2680 3157 2.935955 GCACCGTCCGAACAACAG 59.064 61.111 0.00 0.00 0.00 3.16
2681 3158 2.962786 CGCACCGTCCGAACAACA 60.963 61.111 0.00 0.00 0.00 3.33
2879 3374 9.124807 GTACAGTTGATTAAAGCATTAAACACC 57.875 33.333 4.17 0.00 34.66 4.16
2931 3432 1.597663 GCGACGGGAAGTGGAATAATG 59.402 52.381 0.00 0.00 0.00 1.90
2953 3471 2.106332 CACGGGGTCGCAGATACC 59.894 66.667 0.00 0.00 40.67 2.73
2954 3472 2.585247 GCACGGGGTCGCAGATAC 60.585 66.667 0.00 0.00 40.67 2.24
2972 3490 0.036590 TACCGGGGTAAAAGTGGCAC 59.963 55.000 10.29 10.29 0.00 5.01
2973 3491 0.769873 TTACCGGGGTAAAAGTGGCA 59.230 50.000 6.32 0.00 37.61 4.92
2974 3492 2.019249 GATTACCGGGGTAAAAGTGGC 58.981 52.381 13.86 0.00 42.82 5.01


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

AutoCloner maintained by Alex Coulton.