Multiple sequence alignment - TraesCS5D01G107200

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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 TraesCS5D01G107200 chr5D 100.000 2312 0 0 1 2312 120889687 120887376 0.000000e+00 4270
1 TraesCS5D01G107200 chr5B 89.399 2264 121 43 75 2312 134025814 134023644 0.000000e+00 2741
2 TraesCS5D01G107200 chr5A 91.592 1903 100 34 6 1900 131787204 131785354 0.000000e+00 2573
3 TraesCS5D01G107200 chr5A 88.201 339 23 9 1963 2294 131785069 131784741 2.790000e-104 388


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 TraesCS5D01G107200 chr5D 120887376 120889687 2311 True 4270.0 4270 100.0000 1 2312 1 chr5D.!!$R1 2311
1 TraesCS5D01G107200 chr5B 134023644 134025814 2170 True 2741.0 2741 89.3990 75 2312 1 chr5B.!!$R1 2237
2 TraesCS5D01G107200 chr5A 131784741 131787204 2463 True 1480.5 2573 89.8965 6 2294 2 chr5A.!!$R1 2288

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
863 866 0.036732 GAACCCAGTGACTCCATGCA 59.963 55.0 0.0 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2298 0.10576 GGCATGGGAGAGAGAGGAGA 60.106 60.0 0.0 0.0 0.0 3.71 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
22 23 1.251251 AGGCACTTCAGGCATCAAAC 58.749 50.000 0.00 0.00 27.25 2.93
32 33 3.689161 TCAGGCATCAAACGGATACAAAG 59.311 43.478 0.00 0.00 33.95 2.77
41 42 7.384439 TCAAACGGATACAAAGCATAATGAA 57.616 32.000 0.00 0.00 0.00 2.57
48 49 7.376866 CGGATACAAAGCATAATGAACAACATC 59.623 37.037 0.00 0.00 38.38 3.06
52 53 6.127647 ACAAAGCATAATGAACAACATCCGAT 60.128 34.615 0.00 0.00 38.38 4.18
53 54 7.066887 ACAAAGCATAATGAACAACATCCGATA 59.933 33.333 0.00 0.00 38.38 2.92
56 57 7.164122 AGCATAATGAACAACATCCGATATCT 58.836 34.615 0.34 0.00 38.38 1.98
58 59 7.095060 GCATAATGAACAACATCCGATATCTGT 60.095 37.037 0.34 0.00 38.38 3.41
110 112 9.376075 ACAAACAGTCTGACATGAGATAAATAG 57.624 33.333 10.88 0.00 0.00 1.73
148 150 7.324178 AGATTCATATAGGACCGAAACTATGC 58.676 38.462 0.00 0.00 32.51 3.14
149 151 6.665992 TTCATATAGGACCGAAACTATGCT 57.334 37.500 0.00 0.00 32.51 3.79
151 153 6.455647 TCATATAGGACCGAAACTATGCTTG 58.544 40.000 0.00 0.00 32.51 4.01
152 154 6.266786 TCATATAGGACCGAAACTATGCTTGA 59.733 38.462 0.00 0.00 32.51 3.02
153 155 3.914426 AGGACCGAAACTATGCTTGAT 57.086 42.857 0.00 0.00 0.00 2.57
154 156 3.535561 AGGACCGAAACTATGCTTGATG 58.464 45.455 0.00 0.00 0.00 3.07
155 157 3.055094 AGGACCGAAACTATGCTTGATGT 60.055 43.478 0.00 0.00 0.00 3.06
156 158 3.309954 GGACCGAAACTATGCTTGATGTC 59.690 47.826 0.00 0.00 0.00 3.06
223 225 5.535030 AGCCTTCTTTGTTCGTATTTTCCTT 59.465 36.000 0.00 0.00 0.00 3.36
426 428 3.071479 GGCAACTTGAACCGATTCTGTA 58.929 45.455 0.00 0.00 35.69 2.74
446 448 5.525484 TGTACCTACAGATAAGTGATGGGT 58.475 41.667 0.00 0.00 0.00 4.51
451 453 3.454858 ACAGATAAGTGATGGGTGGAGT 58.545 45.455 0.00 0.00 0.00 3.85
452 454 4.620723 ACAGATAAGTGATGGGTGGAGTA 58.379 43.478 0.00 0.00 0.00 2.59
513 515 1.103987 TGCGCACTTGGCTGGTTTTA 61.104 50.000 5.66 0.00 41.67 1.52
626 629 3.384668 ACTGATCTCGTCAATATTGCCG 58.615 45.455 12.46 12.46 36.14 5.69
628 631 2.135139 GATCTCGTCAATATTGCCGCA 58.865 47.619 13.75 3.70 28.49 5.69
630 633 1.006086 CTCGTCAATATTGCCGCACA 58.994 50.000 13.75 0.00 28.49 4.57
631 634 1.599071 CTCGTCAATATTGCCGCACAT 59.401 47.619 13.75 0.00 28.49 3.21
632 635 1.330213 TCGTCAATATTGCCGCACATG 59.670 47.619 13.75 0.32 28.49 3.21
633 636 1.597690 CGTCAATATTGCCGCACATGG 60.598 52.381 10.76 0.00 0.00 3.66
634 637 1.405105 GTCAATATTGCCGCACATGGT 59.595 47.619 10.76 0.00 0.00 3.55
635 638 1.675483 TCAATATTGCCGCACATGGTC 59.325 47.619 10.76 0.00 0.00 4.02
636 639 1.677576 CAATATTGCCGCACATGGTCT 59.322 47.619 1.74 0.00 0.00 3.85
637 640 2.877786 CAATATTGCCGCACATGGTCTA 59.122 45.455 1.74 0.00 0.00 2.59
638 641 2.700722 TATTGCCGCACATGGTCTAA 57.299 45.000 0.00 0.00 0.00 2.10
639 642 1.094785 ATTGCCGCACATGGTCTAAC 58.905 50.000 0.00 0.00 0.00 2.34
640 643 0.958382 TTGCCGCACATGGTCTAACC 60.958 55.000 0.00 0.00 39.22 2.85
676 679 3.944015 CAGAAAAGTAGATGGCCCTTGAG 59.056 47.826 0.00 0.00 0.00 3.02
718 721 4.912586 TCTGAGATTCCTCTATAGGTCGG 58.087 47.826 0.00 0.00 44.09 4.79
734 737 3.134804 AGGTCGGCACAAGCTAATATTCT 59.865 43.478 0.00 0.00 41.70 2.40
748 751 5.048434 GCTAATATTCTGAAGTCCATTGGCC 60.048 44.000 0.00 0.00 0.00 5.36
755 758 2.314549 TGAAGTCCATTGGCCCCTAATT 59.685 45.455 0.00 0.00 0.00 1.40
758 761 4.832560 AGTCCATTGGCCCCTAATTAAT 57.167 40.909 0.00 0.00 0.00 1.40
759 762 4.482990 AGTCCATTGGCCCCTAATTAATG 58.517 43.478 0.00 1.01 0.00 1.90
760 763 4.169856 AGTCCATTGGCCCCTAATTAATGA 59.830 41.667 10.45 0.00 32.05 2.57
761 764 4.898861 GTCCATTGGCCCCTAATTAATGAA 59.101 41.667 10.45 0.00 32.05 2.57
762 765 5.365314 GTCCATTGGCCCCTAATTAATGAAA 59.635 40.000 10.45 0.00 32.05 2.69
766 769 7.365473 CCATTGGCCCCTAATTAATGAAAAAGA 60.365 37.037 10.45 0.00 32.05 2.52
778 781 3.997319 TGAAAAAGACTGATCGATGCG 57.003 42.857 0.54 0.00 0.00 4.73
787 790 1.200948 CTGATCGATGCGCTATCCAGA 59.799 52.381 9.73 4.64 31.82 3.86
796 799 2.257894 GCGCTATCCAGATTGATCTCG 58.742 52.381 0.00 0.00 34.22 4.04
801 804 4.683781 GCTATCCAGATTGATCTCGTGAAC 59.316 45.833 0.00 0.00 34.22 3.18
825 828 3.551082 CGTACGTACTGTTTCAACCAACA 59.449 43.478 22.55 0.00 35.33 3.33
826 829 4.548726 CGTACGTACTGTTTCAACCAACAC 60.549 45.833 22.55 0.00 33.04 3.32
851 854 2.614057 CAGCGCTATAAAAGGAACCCAG 59.386 50.000 10.99 0.00 0.00 4.45
863 866 0.036732 GAACCCAGTGACTCCATGCA 59.963 55.000 0.00 0.00 0.00 3.96
920 924 2.286833 GCACAAACTACTCGCAAGTTCA 59.713 45.455 0.00 0.00 36.17 3.18
1357 1366 3.838903 AGTCGGAGGGATGGATATTTACC 59.161 47.826 0.00 0.00 0.00 2.85
1396 1405 4.638865 ACCACTCGGCAAAATAAATAGTCC 59.361 41.667 0.00 0.00 34.57 3.85
1419 1428 5.335127 CAAGAGTGTGGAAGACAAGTTTTG 58.665 41.667 0.00 0.00 35.91 2.44
1425 1434 7.231467 AGTGTGGAAGACAAGTTTTGGTATAT 58.769 34.615 0.00 0.00 35.91 0.86
1426 1435 8.380099 AGTGTGGAAGACAAGTTTTGGTATATA 58.620 33.333 0.00 0.00 35.91 0.86
1454 1463 8.228905 AGAATAACCTCAGAGCCTAAGTAGTAT 58.771 37.037 0.00 0.00 0.00 2.12
1467 1476 7.038445 AGCCTAAGTAGTATGTCGAGATAGGTA 60.038 40.741 1.90 0.00 32.00 3.08
1481 1490 8.578151 GTCGAGATAGGTATTTTCAAGTCCTAT 58.422 37.037 0.00 0.00 42.08 2.57
1505 1514 5.841810 TCTGACAACAAATTTTGGATCACC 58.158 37.500 13.42 0.00 34.12 4.02
1507 1516 6.041865 TCTGACAACAAATTTTGGATCACCAT 59.958 34.615 13.42 0.00 46.34 3.55
1508 1517 7.232330 TCTGACAACAAATTTTGGATCACCATA 59.768 33.333 13.42 0.00 46.34 2.74
1509 1518 7.905265 TGACAACAAATTTTGGATCACCATAT 58.095 30.769 13.42 0.00 46.34 1.78
1510 1519 7.818446 TGACAACAAATTTTGGATCACCATATG 59.182 33.333 13.42 0.00 46.34 1.78
1511 1520 7.678837 ACAACAAATTTTGGATCACCATATGT 58.321 30.769 13.42 1.15 46.34 2.29
1512 1521 7.603404 ACAACAAATTTTGGATCACCATATGTG 59.397 33.333 13.42 0.77 46.34 3.21
1513 1522 6.642430 ACAAATTTTGGATCACCATATGTGG 58.358 36.000 13.42 6.99 46.34 4.17
1515 1524 7.398618 ACAAATTTTGGATCACCATATGTGGTA 59.601 33.333 14.48 3.74 45.72 3.25
1751 1791 5.762711 TCAAATGGAAGAAAGAATGACACGA 59.237 36.000 0.00 0.00 0.00 4.35
1788 1828 0.995132 TGCATGGGATGGGAGGTCAT 60.995 55.000 0.00 0.00 0.00 3.06
1789 1829 1.067295 GCATGGGATGGGAGGTCATA 58.933 55.000 0.00 0.00 0.00 2.15
1790 1830 1.425066 GCATGGGATGGGAGGTCATAA 59.575 52.381 0.00 0.00 0.00 1.90
1791 1831 2.042162 GCATGGGATGGGAGGTCATAAT 59.958 50.000 0.00 0.00 0.00 1.28
1822 1862 3.755112 TTGATAGTGTCGGTTTGGTCA 57.245 42.857 0.00 0.00 0.00 4.02
1863 1903 4.062991 ACGTTTAGGTCTCATTTGTGGAC 58.937 43.478 0.00 0.00 0.00 4.02
1901 1941 2.066393 CCTTCTCCCCCGAGCATCA 61.066 63.158 0.00 0.00 35.94 3.07
1926 1966 0.098200 CCTGCTCGCATGACACATTG 59.902 55.000 0.00 0.00 0.00 2.82
1928 1968 1.465777 CTGCTCGCATGACACATTGAA 59.534 47.619 0.00 0.00 0.00 2.69
1929 1969 1.465777 TGCTCGCATGACACATTGAAG 59.534 47.619 0.00 0.00 0.00 3.02
1932 1972 0.452987 CGCATGACACATTGAAGGGG 59.547 55.000 0.00 0.00 0.00 4.79
1969 2230 3.406682 GCTCCAAGCGGTTGATTTG 57.593 52.632 27.92 11.61 35.46 2.32
1971 2232 1.810151 GCTCCAAGCGGTTGATTTGTA 59.190 47.619 27.92 5.76 35.46 2.41
2031 2294 4.753186 TCCATTCCCTAGGTTATCTCTCC 58.247 47.826 8.29 0.00 0.00 3.71
2032 2295 3.841255 CCATTCCCTAGGTTATCTCTCCC 59.159 52.174 8.29 0.00 0.00 4.30
2033 2296 2.973983 TCCCTAGGTTATCTCTCCCG 57.026 55.000 8.29 0.00 0.00 5.14
2034 2297 1.428139 TCCCTAGGTTATCTCTCCCGG 59.572 57.143 8.29 0.00 0.00 5.73
2035 2298 1.147399 CCCTAGGTTATCTCTCCCGGT 59.853 57.143 8.29 0.00 0.00 5.28
2036 2299 2.516906 CCTAGGTTATCTCTCCCGGTC 58.483 57.143 0.00 0.00 0.00 4.79
2037 2300 2.108601 CCTAGGTTATCTCTCCCGGTCT 59.891 54.545 0.00 0.00 0.00 3.85
2038 2301 2.368311 AGGTTATCTCTCCCGGTCTC 57.632 55.000 0.00 0.00 0.00 3.36
2047 2310 0.179029 CTCCCGGTCTCCTCTCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
2080 2343 3.490348 TCCGGTAACACTACTATAGGGC 58.510 50.000 0.00 0.00 30.38 5.19
2081 2344 2.227388 CCGGTAACACTACTATAGGGCG 59.773 54.545 4.43 0.00 30.38 6.13
2082 2345 2.227388 CGGTAACACTACTATAGGGCGG 59.773 54.545 4.43 0.00 30.38 6.13
2083 2346 2.029560 GGTAACACTACTATAGGGCGGC 60.030 54.545 0.00 0.00 30.38 6.53
2084 2347 1.784358 AACACTACTATAGGGCGGCA 58.216 50.000 12.47 0.00 30.38 5.69
2107 2373 2.290641 ACTGACCGGCCAAAACATATCA 60.291 45.455 0.00 0.00 0.00 2.15
2142 2408 0.404040 GGACCCATGAACAGTTCCCA 59.596 55.000 10.93 0.00 0.00 4.37
2151 2417 1.002087 GAACAGTTCCCAGTCGGTGAT 59.998 52.381 1.29 0.00 0.00 3.06
2203 2469 8.348285 TGACCGATTAGTGATGACATATATCA 57.652 34.615 0.00 0.00 32.44 2.15
2218 2484 5.126222 ACATATATCAGTGATGGCCTAGTCG 59.874 44.000 16.15 0.00 0.00 4.18
2288 2556 5.607939 ATCATCCTTACACACGTTCCATA 57.392 39.130 0.00 0.00 0.00 2.74
2289 2557 5.607939 TCATCCTTACACACGTTCCATAT 57.392 39.130 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.983467 TGATGCCTGAAGTGCCTACA 59.017 50.000 0.00 0.00 0.00 2.74
1 2 2.113860 TTGATGCCTGAAGTGCCTAC 57.886 50.000 0.00 0.00 0.00 3.18
2 3 2.436417 GTTTGATGCCTGAAGTGCCTA 58.564 47.619 0.00 0.00 0.00 3.93
3 4 1.251251 GTTTGATGCCTGAAGTGCCT 58.749 50.000 0.00 0.00 0.00 4.75
4 5 0.109597 CGTTTGATGCCTGAAGTGCC 60.110 55.000 0.00 0.00 0.00 5.01
5 6 0.109597 CCGTTTGATGCCTGAAGTGC 60.110 55.000 0.00 0.00 0.00 4.40
6 7 1.522668 TCCGTTTGATGCCTGAAGTG 58.477 50.000 0.00 0.00 0.00 3.16
7 8 2.496899 ATCCGTTTGATGCCTGAAGT 57.503 45.000 0.00 0.00 30.54 3.01
8 9 3.270027 TGTATCCGTTTGATGCCTGAAG 58.730 45.455 0.00 0.00 35.40 3.02
12 13 2.423538 GCTTTGTATCCGTTTGATGCCT 59.576 45.455 0.00 0.00 35.40 4.75
22 23 6.550843 TGTTGTTCATTATGCTTTGTATCCG 58.449 36.000 0.00 0.00 0.00 4.18
32 33 7.095060 ACAGATATCGGATGTTGTTCATTATGC 60.095 37.037 10.01 0.00 36.83 3.14
48 49 8.190784 TGTGCATGATAGTTATACAGATATCGG 58.809 37.037 0.00 0.88 0.00 4.18
52 53 8.860088 ACTGTGTGCATGATAGTTATACAGATA 58.140 33.333 0.00 0.00 37.16 1.98
53 54 7.730084 ACTGTGTGCATGATAGTTATACAGAT 58.270 34.615 0.00 0.00 37.16 2.90
56 57 6.872920 TGACTGTGTGCATGATAGTTATACA 58.127 36.000 0.00 0.00 0.00 2.29
58 59 7.821846 TGTTTGACTGTGTGCATGATAGTTATA 59.178 33.333 0.00 0.00 0.00 0.98
66 67 2.363683 TGTGTTTGACTGTGTGCATGA 58.636 42.857 0.00 0.00 0.00 3.07
143 145 4.938080 ACCTACTTCGACATCAAGCATAG 58.062 43.478 0.00 0.00 0.00 2.23
145 147 3.895232 ACCTACTTCGACATCAAGCAT 57.105 42.857 0.00 0.00 0.00 3.79
146 148 3.678056 AACCTACTTCGACATCAAGCA 57.322 42.857 0.00 0.00 0.00 3.91
147 149 4.451096 TCAAAACCTACTTCGACATCAAGC 59.549 41.667 0.00 0.00 0.00 4.01
148 150 5.465390 TGTCAAAACCTACTTCGACATCAAG 59.535 40.000 0.00 0.00 0.00 3.02
149 151 5.361427 TGTCAAAACCTACTTCGACATCAA 58.639 37.500 0.00 0.00 0.00 2.57
151 153 5.917541 TTGTCAAAACCTACTTCGACATC 57.082 39.130 0.00 0.00 33.72 3.06
152 154 6.540914 TCTTTTGTCAAAACCTACTTCGACAT 59.459 34.615 6.65 0.00 33.72 3.06
153 155 5.875910 TCTTTTGTCAAAACCTACTTCGACA 59.124 36.000 6.65 0.00 0.00 4.35
154 156 6.354039 TCTTTTGTCAAAACCTACTTCGAC 57.646 37.500 6.65 0.00 0.00 4.20
155 157 8.665643 TTATCTTTTGTCAAAACCTACTTCGA 57.334 30.769 6.65 1.40 0.00 3.71
156 158 9.893305 ATTTATCTTTTGTCAAAACCTACTTCG 57.107 29.630 6.65 0.00 0.00 3.79
426 428 3.711704 CCACCCATCACTTATCTGTAGGT 59.288 47.826 0.00 0.00 0.00 3.08
445 447 7.500992 TCAGAATAACATCCAGATTACTCCAC 58.499 38.462 0.00 0.00 0.00 4.02
446 448 7.675161 TCAGAATAACATCCAGATTACTCCA 57.325 36.000 0.00 0.00 0.00 3.86
451 453 9.605275 CTCAGTTTCAGAATAACATCCAGATTA 57.395 33.333 0.00 0.00 0.00 1.75
452 454 7.555554 CCTCAGTTTCAGAATAACATCCAGATT 59.444 37.037 0.00 0.00 0.00 2.40
497 499 1.605457 GCCTTAAAACCAGCCAAGTGC 60.605 52.381 0.00 0.00 41.71 4.40
498 500 1.686052 TGCCTTAAAACCAGCCAAGTG 59.314 47.619 0.00 0.00 0.00 3.16
632 635 2.507407 TGGATTTGGCTGGTTAGACC 57.493 50.000 0.00 0.00 39.22 3.85
633 636 2.099756 GCATGGATTTGGCTGGTTAGAC 59.900 50.000 0.00 0.00 0.00 2.59
634 637 2.291475 TGCATGGATTTGGCTGGTTAGA 60.291 45.455 0.00 0.00 0.00 2.10
635 638 2.100252 CTGCATGGATTTGGCTGGTTAG 59.900 50.000 0.00 0.00 0.00 2.34
636 639 2.101783 CTGCATGGATTTGGCTGGTTA 58.898 47.619 0.00 0.00 0.00 2.85
637 640 0.899720 CTGCATGGATTTGGCTGGTT 59.100 50.000 0.00 0.00 0.00 3.67
638 641 0.040058 TCTGCATGGATTTGGCTGGT 59.960 50.000 0.00 0.00 0.00 4.00
639 642 1.187974 TTCTGCATGGATTTGGCTGG 58.812 50.000 0.00 0.00 0.00 4.85
640 643 3.259064 CTTTTCTGCATGGATTTGGCTG 58.741 45.455 0.00 0.00 0.00 4.85
641 644 2.901839 ACTTTTCTGCATGGATTTGGCT 59.098 40.909 0.00 0.00 0.00 4.75
676 679 5.527951 CAGATATATCTGCCTATCGGAAGC 58.472 45.833 25.81 0.00 46.63 3.86
718 721 5.586243 TGGACTTCAGAATATTAGCTTGTGC 59.414 40.000 0.00 0.00 40.05 4.57
734 737 1.377690 TTAGGGGCCAATGGACTTCA 58.622 50.000 4.56 0.00 0.00 3.02
748 751 9.109393 TCGATCAGTCTTTTTCATTAATTAGGG 57.891 33.333 0.00 0.00 0.00 3.53
755 758 5.502382 GCGCATCGATCAGTCTTTTTCATTA 60.502 40.000 0.30 0.00 0.00 1.90
758 761 2.094258 GCGCATCGATCAGTCTTTTTCA 59.906 45.455 0.30 0.00 0.00 2.69
759 762 2.349886 AGCGCATCGATCAGTCTTTTTC 59.650 45.455 11.47 0.00 0.00 2.29
760 763 2.350522 AGCGCATCGATCAGTCTTTTT 58.649 42.857 11.47 0.00 0.00 1.94
761 764 2.015736 AGCGCATCGATCAGTCTTTT 57.984 45.000 11.47 0.00 0.00 2.27
762 765 2.871182 TAGCGCATCGATCAGTCTTT 57.129 45.000 11.47 0.00 0.00 2.52
766 769 0.961753 TGGATAGCGCATCGATCAGT 59.038 50.000 11.47 0.00 34.12 3.41
778 781 4.511617 TCACGAGATCAATCTGGATAGC 57.488 45.455 8.75 0.00 37.25 2.97
787 790 3.168963 CGTACGTGTTCACGAGATCAAT 58.831 45.455 27.77 9.40 40.56 2.57
796 799 3.790820 TGAAACAGTACGTACGTGTTCAC 59.209 43.478 30.25 24.74 33.25 3.18
801 804 3.114809 TGGTTGAAACAGTACGTACGTG 58.885 45.455 30.25 16.42 0.00 4.49
809 812 1.328069 CGCGTGTTGGTTGAAACAGTA 59.672 47.619 0.00 0.00 40.60 2.74
813 816 1.199852 CTGCGCGTGTTGGTTGAAAC 61.200 55.000 8.43 0.00 0.00 2.78
851 854 1.000274 GGTTTGGTTGCATGGAGTCAC 60.000 52.381 0.00 0.00 0.00 3.67
863 866 2.364002 CGAAACTTGGGATGGTTTGGTT 59.636 45.455 0.00 0.00 36.04 3.67
940 944 2.350522 CTGGTATCAACGAGCTTGCTT 58.649 47.619 0.00 0.00 0.00 3.91
1357 1366 1.033746 TGGTACCGGAGTTAGGCTCG 61.034 60.000 9.46 0.00 45.03 5.03
1396 1405 5.335127 CAAAACTTGTCTTCCACACTCTTG 58.665 41.667 0.00 0.00 33.41 3.02
1419 1428 9.649316 AGGCTCTGAGGTTATTCTATATATACC 57.351 37.037 6.83 0.00 0.00 2.73
1425 1434 9.742144 CTACTTAGGCTCTGAGGTTATTCTATA 57.258 37.037 6.83 0.00 0.00 1.31
1426 1435 8.228905 ACTACTTAGGCTCTGAGGTTATTCTAT 58.771 37.037 6.83 0.00 0.00 1.98
1438 1447 5.057819 TCTCGACATACTACTTAGGCTCTG 58.942 45.833 0.00 0.00 0.00 3.35
1454 1463 6.380274 AGGACTTGAAAATACCTATCTCGACA 59.620 38.462 0.00 0.00 31.32 4.35
1467 1476 8.463930 TTGTTGTCAGAATAGGACTTGAAAAT 57.536 30.769 0.00 0.00 36.26 1.82
1481 1490 6.127225 TGGTGATCCAAAATTTGTTGTCAGAA 60.127 34.615 4.92 0.00 41.25 3.02
1513 1522 7.063934 ACTACATAGATTGGGGTAAGCTTAC 57.936 40.000 25.52 25.52 36.26 2.34
1514 1523 8.786710 TTACTACATAGATTGGGGTAAGCTTA 57.213 34.615 0.86 0.86 36.26 3.09
1515 1524 7.685849 TTACTACATAGATTGGGGTAAGCTT 57.314 36.000 3.48 3.48 36.26 3.74
1516 1525 7.304497 CTTACTACATAGATTGGGGTAAGCT 57.696 40.000 0.00 0.00 37.51 3.74
1518 1527 7.304497 AGCTTACTACATAGATTGGGGTAAG 57.696 40.000 0.00 0.00 41.76 2.34
1519 1528 8.812972 CATAGCTTACTACATAGATTGGGGTAA 58.187 37.037 0.00 0.00 0.00 2.85
1520 1529 7.954056 ACATAGCTTACTACATAGATTGGGGTA 59.046 37.037 0.00 0.00 0.00 3.69
1521 1530 6.787957 ACATAGCTTACTACATAGATTGGGGT 59.212 38.462 0.00 0.00 0.00 4.95
1522 1531 7.099764 CACATAGCTTACTACATAGATTGGGG 58.900 42.308 0.00 0.00 0.00 4.96
1523 1532 7.671302 ACACATAGCTTACTACATAGATTGGG 58.329 38.462 0.00 0.00 0.00 4.12
1524 1533 9.847706 CTACACATAGCTTACTACATAGATTGG 57.152 37.037 0.00 0.00 0.00 3.16
1525 1534 9.847706 CCTACACATAGCTTACTACATAGATTG 57.152 37.037 0.00 0.00 0.00 2.67
1526 1535 9.589461 ACCTACACATAGCTTACTACATAGATT 57.411 33.333 0.00 0.00 0.00 2.40
1527 1536 9.589461 AACCTACACATAGCTTACTACATAGAT 57.411 33.333 0.00 0.00 0.00 1.98
1528 1537 8.847196 CAACCTACACATAGCTTACTACATAGA 58.153 37.037 0.00 0.00 0.00 1.98
1529 1538 7.595502 GCAACCTACACATAGCTTACTACATAG 59.404 40.741 0.00 0.00 0.00 2.23
1568 1596 7.316393 TGGATACATAGATTGGGGTAAGAAG 57.684 40.000 0.00 0.00 46.17 2.85
1683 1722 1.202582 CTCTTGACGAGGTTCCGTGAT 59.797 52.381 0.00 0.00 43.49 3.06
1684 1723 0.596577 CTCTTGACGAGGTTCCGTGA 59.403 55.000 0.00 0.00 43.49 4.35
1685 1724 1.009389 GCTCTTGACGAGGTTCCGTG 61.009 60.000 0.00 0.00 43.49 4.94
1686 1725 1.289380 GCTCTTGACGAGGTTCCGT 59.711 57.895 0.00 0.00 46.43 4.69
1687 1726 0.108615 ATGCTCTTGACGAGGTTCCG 60.109 55.000 0.00 0.00 40.25 4.30
1775 1815 9.588096 AAAAGTATTAATTATGACCTCCCATCC 57.412 33.333 0.00 0.00 0.00 3.51
1863 1903 3.573967 AGGAACAATGTTGGGCAACTTAG 59.426 43.478 2.20 0.00 41.67 2.18
1901 1941 0.179089 GTCATGCGAGCAGGTCAGAT 60.179 55.000 9.57 0.00 0.00 2.90
1932 1972 2.675423 GGAAAACTCCCACGGCCC 60.675 66.667 0.00 0.00 0.00 5.80
2031 2294 1.152839 GGGAGAGAGAGGAGACCGG 60.153 68.421 0.00 0.00 0.00 5.28
2032 2295 0.184933 ATGGGAGAGAGAGGAGACCG 59.815 60.000 0.00 0.00 0.00 4.79
2033 2296 1.703411 CATGGGAGAGAGAGGAGACC 58.297 60.000 0.00 0.00 0.00 3.85
2034 2297 1.039856 GCATGGGAGAGAGAGGAGAC 58.960 60.000 0.00 0.00 0.00 3.36
2035 2298 0.105760 GGCATGGGAGAGAGAGGAGA 60.106 60.000 0.00 0.00 0.00 3.71
2036 2299 1.120795 GGGCATGGGAGAGAGAGGAG 61.121 65.000 0.00 0.00 0.00 3.69
2037 2300 1.074926 GGGCATGGGAGAGAGAGGA 60.075 63.158 0.00 0.00 0.00 3.71
2038 2301 0.189574 TAGGGCATGGGAGAGAGAGG 59.810 60.000 0.00 0.00 0.00 3.69
2047 2310 1.052124 TTACCGGAGTAGGGCATGGG 61.052 60.000 9.46 0.00 35.02 4.00
2081 2344 4.947147 TTGGCCGGTCAGTGTGCC 62.947 66.667 9.61 0.00 44.27 5.01
2082 2345 2.485795 TTTTGGCCGGTCAGTGTGC 61.486 57.895 9.61 0.00 0.00 4.57
2083 2346 1.358759 GTTTTGGCCGGTCAGTGTG 59.641 57.895 9.61 0.00 0.00 3.82
2084 2347 0.467290 ATGTTTTGGCCGGTCAGTGT 60.467 50.000 9.61 0.00 0.00 3.55
2186 2452 7.364144 GGCCATCACTGATATATGTCATCACTA 60.364 40.741 2.30 0.00 0.00 2.74
2191 2457 6.671340 ACTAGGCCATCACTGATATATGTCAT 59.329 38.462 5.01 0.00 0.00 3.06
2203 2469 1.276622 AAACCGACTAGGCCATCACT 58.723 50.000 5.01 0.00 46.52 3.41
2288 2556 4.520179 ACCATATGCATGCGTGATGATAT 58.480 39.130 22.77 10.97 33.31 1.63
2289 2557 3.941573 ACCATATGCATGCGTGATGATA 58.058 40.909 22.77 9.04 33.31 2.15


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

AutoCloner maintained by Alex Coulton.