Multiple sequence alignment - TraesCS5D01G095900

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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 TraesCS5D01G095900 chr5D 100.000 2771 0 0 1 2771 105351389 105348619 0.000000e+00 5118.0
1 TraesCS5D01G095900 chr5D 88.205 585 64 5 1 584 312055045 312055625 0.000000e+00 693.0
2 TraesCS5D01G095900 chr5A 93.534 1160 60 7 602 1749 109344922 109343766 0.000000e+00 1712.0
3 TraesCS5D01G095900 chr5A 96.269 670 24 1 2103 2771 109343435 109342766 0.000000e+00 1098.0
4 TraesCS5D01G095900 chr5A 89.691 291 21 5 1829 2118 109343734 109343452 2.030000e-96 363.0
5 TraesCS5D01G095900 chr5A 97.368 38 1 0 1755 1792 109343773 109343736 6.410000e-07 65.8
6 TraesCS5D01G095900 chr5B 89.503 886 53 13 1240 2118 115319586 115318734 0.000000e+00 1085.0
7 TraesCS5D01G095900 chr5B 90.060 835 45 15 602 1405 115320296 115319469 0.000000e+00 1048.0
8 TraesCS5D01G095900 chr5B 94.627 670 20 7 2103 2771 115318715 115318061 0.000000e+00 1024.0
9 TraesCS5D01G095900 chr6B 90.409 563 48 6 18 577 172728260 172727701 0.000000e+00 736.0
10 TraesCS5D01G095900 chr6D 92.184 499 36 2 1 499 90122420 90122915 0.000000e+00 702.0
11 TraesCS5D01G095900 chr4A 88.850 574 60 4 1 573 5249920 5250490 0.000000e+00 702.0
12 TraesCS5D01G095900 chr7D 87.847 576 67 3 1 575 358727318 358727891 0.000000e+00 673.0
13 TraesCS5D01G095900 chr7A 87.586 580 63 4 1 578 730868038 730868610 0.000000e+00 664.0
14 TraesCS5D01G095900 chr3B 87.609 573 67 4 1 572 750336675 750336106 0.000000e+00 662.0
15 TraesCS5D01G095900 chr1B 87.478 575 69 3 1 573 288173863 288174436 0.000000e+00 660.0
16 TraesCS5D01G095900 chr2D 87.153 576 66 8 1 573 384745648 384746218 0.000000e+00 647.0


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 TraesCS5D01G095900 chr5D 105348619 105351389 2770 True 5118.000000 5118 100.000000 1 2771 1 chr5D.!!$R1 2770
1 TraesCS5D01G095900 chr5D 312055045 312055625 580 False 693.000000 693 88.205000 1 584 1 chr5D.!!$F1 583
2 TraesCS5D01G095900 chr5A 109342766 109344922 2156 True 809.700000 1712 94.215500 602 2771 4 chr5A.!!$R1 2169
3 TraesCS5D01G095900 chr5B 115318061 115320296 2235 True 1052.333333 1085 91.396667 602 2771 3 chr5B.!!$R1 2169
4 TraesCS5D01G095900 chr6B 172727701 172728260 559 True 736.000000 736 90.409000 18 577 1 chr6B.!!$R1 559
5 TraesCS5D01G095900 chr4A 5249920 5250490 570 False 702.000000 702 88.850000 1 573 1 chr4A.!!$F1 572
6 TraesCS5D01G095900 chr7D 358727318 358727891 573 False 673.000000 673 87.847000 1 575 1 chr7D.!!$F1 574
7 TraesCS5D01G095900 chr7A 730868038 730868610 572 False 664.000000 664 87.586000 1 578 1 chr7A.!!$F1 577
8 TraesCS5D01G095900 chr3B 750336106 750336675 569 True 662.000000 662 87.609000 1 572 1 chr3B.!!$R1 571
9 TraesCS5D01G095900 chr1B 288173863 288174436 573 False 660.000000 660 87.478000 1 573 1 chr1B.!!$F1 572
10 TraesCS5D01G095900 chr2D 384745648 384746218 570 False 647.000000 647 87.153000 1 573 1 chr2D.!!$F1 572

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
716 731 0.102300 GTGCCACTTGTTTGTGTCCC 59.898 55.0 0.0 0.0 36.3 4.46 F
1744 1835 0.103208 GCCTCAGTGTATCTCCCGTG 59.897 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
1748 1839 0.676736 TGGTACATCACACGCACTGA 59.323 50.0 0.0 0.0 0.0 3.41 R
2621 2751 2.606308 GCAATGCTTATCTTGATGGCCG 60.606 50.0 0.0 0.0 0.0 6.13 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
25 26 1.540363 GCACGAAGAAGTTGTGGGAGA 60.540 52.381 0.00 0.00 34.24 3.71
178 179 8.578448 TGAACAGTTCATCCAATTTCATCATA 57.422 30.769 12.24 0.00 34.08 2.15
423 426 2.181975 CCATTGAAAATGGAGGCCAGT 58.818 47.619 12.75 0.00 41.64 4.00
445 448 2.778299 GGCCACGCTGATAAATATGGA 58.222 47.619 0.00 0.00 0.00 3.41
456 459 2.157834 AAATATGGATCGGCGCGTTA 57.842 45.000 8.43 0.00 0.00 3.18
459 462 1.457823 TATGGATCGGCGCGTTAGGT 61.458 55.000 8.43 0.00 0.00 3.08
461 464 2.202703 GATCGGCGCGTTAGGTGT 60.203 61.111 8.43 0.00 0.00 4.16
473 476 1.597797 TTAGGTGTACTGCCGACCCG 61.598 60.000 0.00 0.00 0.00 5.28
476 479 1.586028 GTGTACTGCCGACCCGTAA 59.414 57.895 0.00 0.00 0.00 3.18
477 480 0.733909 GTGTACTGCCGACCCGTAAC 60.734 60.000 0.00 0.00 0.00 2.50
512 516 2.423898 ATCGAATGGGCGGTCGTCT 61.424 57.895 0.00 0.00 38.41 4.18
516 520 1.805120 CGAATGGGCGGTCGTCTAAAT 60.805 52.381 0.00 0.00 32.61 1.40
543 548 5.580297 ACAAAAAGCGAACAAATGTGTCATT 59.420 32.000 0.00 0.00 36.80 2.57
551 556 3.380142 ACAAATGTGTCATTCGTTTGGC 58.620 40.909 12.85 0.00 42.52 4.52
562 567 2.311701 CGTTTGGCTCGGCGTGTTA 61.312 57.895 6.85 0.00 0.00 2.41
591 596 5.112220 CTCTAAGAGCATTGCACAAAACA 57.888 39.130 11.91 0.00 0.00 2.83
592 597 5.112220 TCTAAGAGCATTGCACAAAACAG 57.888 39.130 11.91 0.00 0.00 3.16
593 598 2.144482 AGAGCATTGCACAAAACAGC 57.856 45.000 11.91 0.00 0.00 4.40
594 599 1.684983 AGAGCATTGCACAAAACAGCT 59.315 42.857 11.91 0.00 0.00 4.24
595 600 2.886523 AGAGCATTGCACAAAACAGCTA 59.113 40.909 11.91 0.00 0.00 3.32
596 601 2.982470 GAGCATTGCACAAAACAGCTAC 59.018 45.455 11.91 0.00 0.00 3.58
597 602 2.061028 GCATTGCACAAAACAGCTACC 58.939 47.619 3.15 0.00 0.00 3.18
598 603 2.676076 CATTGCACAAAACAGCTACCC 58.324 47.619 0.00 0.00 0.00 3.69
599 604 2.065899 TTGCACAAAACAGCTACCCT 57.934 45.000 0.00 0.00 0.00 4.34
600 605 2.065899 TGCACAAAACAGCTACCCTT 57.934 45.000 0.00 0.00 0.00 3.95
601 606 2.383855 TGCACAAAACAGCTACCCTTT 58.616 42.857 0.00 0.00 0.00 3.11
602 607 2.360801 TGCACAAAACAGCTACCCTTTC 59.639 45.455 0.00 0.00 0.00 2.62
603 608 2.623416 GCACAAAACAGCTACCCTTTCT 59.377 45.455 0.00 0.00 0.00 2.52
604 609 3.304726 GCACAAAACAGCTACCCTTTCTC 60.305 47.826 0.00 0.00 0.00 2.87
605 610 4.137543 CACAAAACAGCTACCCTTTCTCT 58.862 43.478 0.00 0.00 0.00 3.10
606 611 4.023707 CACAAAACAGCTACCCTTTCTCTG 60.024 45.833 0.00 0.00 0.00 3.35
607 612 3.425162 AAACAGCTACCCTTTCTCTGG 57.575 47.619 0.00 0.00 0.00 3.86
709 724 1.090625 TGCGTACGTGCCACTTGTTT 61.091 50.000 17.90 0.00 0.00 2.83
716 731 0.102300 GTGCCACTTGTTTGTGTCCC 59.898 55.000 0.00 0.00 36.30 4.46
717 732 1.040339 TGCCACTTGTTTGTGTCCCC 61.040 55.000 0.00 0.00 36.30 4.81
733 748 2.116772 CCGGCGGGGTCCTAGATA 59.883 66.667 20.56 0.00 0.00 1.98
858 875 3.304928 GGTGACATGAACAAAAGCTGAGG 60.305 47.826 0.00 0.00 0.00 3.86
960 977 3.447944 CCGGGCCTATAAATCCTCTACTC 59.552 52.174 0.84 0.00 0.00 2.59
961 978 4.345854 CGGGCCTATAAATCCTCTACTCT 58.654 47.826 0.84 0.00 0.00 3.24
1233 1255 2.884207 CCCTAAACTCGCGCCGAC 60.884 66.667 0.00 0.00 0.00 4.79
1273 1307 4.038080 GCGCCAAAACCTGACCCG 62.038 66.667 0.00 0.00 0.00 5.28
1278 1312 0.671796 CCAAAACCTGACCCGAAACC 59.328 55.000 0.00 0.00 0.00 3.27
1279 1313 1.394618 CAAAACCTGACCCGAAACCA 58.605 50.000 0.00 0.00 0.00 3.67
1280 1314 1.336755 CAAAACCTGACCCGAAACCAG 59.663 52.381 0.00 0.00 0.00 4.00
1281 1315 0.841289 AAACCTGACCCGAAACCAGA 59.159 50.000 0.00 0.00 0.00 3.86
1282 1316 0.108019 AACCTGACCCGAAACCAGAC 59.892 55.000 0.00 0.00 0.00 3.51
1283 1317 1.003718 CCTGACCCGAAACCAGACC 60.004 63.158 0.00 0.00 0.00 3.85
1284 1318 1.003718 CTGACCCGAAACCAGACCC 60.004 63.158 0.00 0.00 0.00 4.46
1285 1319 2.047560 GACCCGAAACCAGACCCG 60.048 66.667 0.00 0.00 0.00 5.28
1286 1320 4.324991 ACCCGAAACCAGACCCGC 62.325 66.667 0.00 0.00 0.00 6.13
1287 1321 4.323477 CCCGAAACCAGACCCGCA 62.323 66.667 0.00 0.00 0.00 5.69
1288 1322 2.742372 CCGAAACCAGACCCGCAG 60.742 66.667 0.00 0.00 0.00 5.18
1289 1323 3.423154 CGAAACCAGACCCGCAGC 61.423 66.667 0.00 0.00 0.00 5.25
1351 1439 4.397832 GACCCTAAACCGGCGCCA 62.398 66.667 28.98 4.99 0.00 5.69
1363 1451 4.038080 GCGCCAAAACCTGACCCG 62.038 66.667 0.00 0.00 0.00 5.28
1364 1452 2.281208 CGCCAAAACCTGACCCGA 60.281 61.111 0.00 0.00 0.00 5.14
1366 1454 2.613506 GCCAAAACCTGACCCGACG 61.614 63.158 0.00 0.00 0.00 5.12
1599 1687 0.733150 GCCGCTTGGTAATGGAGAAC 59.267 55.000 0.00 0.00 34.16 3.01
1656 1744 2.754946 TTGTCTCCGGTGATGGTTAC 57.245 50.000 9.83 0.00 0.00 2.50
1675 1765 7.534282 TGGTTACTAATGTATTGCATGTGTTG 58.466 34.615 0.00 0.00 37.96 3.33
1704 1794 2.552743 CTCTGTACGTGTTGTCTCCAGA 59.447 50.000 0.00 0.00 32.38 3.86
1727 1818 0.955428 TTCGTGTGAGCCATCTTGCC 60.955 55.000 0.00 0.00 0.00 4.52
1741 1832 2.111384 TCTTGCCTCAGTGTATCTCCC 58.889 52.381 0.00 0.00 0.00 4.30
1742 1833 0.824109 TTGCCTCAGTGTATCTCCCG 59.176 55.000 0.00 0.00 0.00 5.14
1743 1834 0.324368 TGCCTCAGTGTATCTCCCGT 60.324 55.000 0.00 0.00 0.00 5.28
1744 1835 0.103208 GCCTCAGTGTATCTCCCGTG 59.897 60.000 0.00 0.00 0.00 4.94
1745 1836 1.475403 CCTCAGTGTATCTCCCGTGT 58.525 55.000 0.00 0.00 0.00 4.49
1746 1837 1.135139 CCTCAGTGTATCTCCCGTGTG 59.865 57.143 0.00 0.00 0.00 3.82
1747 1838 2.092323 CTCAGTGTATCTCCCGTGTGA 58.908 52.381 0.00 0.00 0.00 3.58
1748 1839 2.690497 CTCAGTGTATCTCCCGTGTGAT 59.310 50.000 0.00 0.00 0.00 3.06
1749 1840 2.688446 TCAGTGTATCTCCCGTGTGATC 59.312 50.000 0.00 0.00 0.00 2.92
1750 1841 2.427095 CAGTGTATCTCCCGTGTGATCA 59.573 50.000 0.00 0.00 0.00 2.92
1751 1842 2.690497 AGTGTATCTCCCGTGTGATCAG 59.310 50.000 0.00 0.00 0.00 2.90
1752 1843 2.427453 GTGTATCTCCCGTGTGATCAGT 59.573 50.000 0.00 0.00 0.00 3.41
1753 1844 2.427095 TGTATCTCCCGTGTGATCAGTG 59.573 50.000 0.00 0.00 0.00 3.66
1788 1879 5.126061 ACCATGAATAAACAGAGGAACATGC 59.874 40.000 0.00 0.00 34.51 4.06
1792 1883 5.065090 TGAATAAACAGAGGAACATGCATCG 59.935 40.000 0.00 0.00 0.00 3.84
1817 1908 4.963953 GCATGTATCTGAACGTACATTTGC 59.036 41.667 0.00 0.00 38.98 3.68
1860 1951 3.582647 TCTGGTTGTTGCTCTCATTCCTA 59.417 43.478 0.00 0.00 0.00 2.94
1861 1952 4.041567 TCTGGTTGTTGCTCTCATTCCTAA 59.958 41.667 0.00 0.00 0.00 2.69
1866 1957 6.823689 GGTTGTTGCTCTCATTCCTAATCTAA 59.176 38.462 0.00 0.00 0.00 2.10
1867 1958 7.201652 GGTTGTTGCTCTCATTCCTAATCTAAC 60.202 40.741 0.00 0.00 0.00 2.34
1880 1971 7.419711 TCCTAATCTAACACCACTCCTTTAG 57.580 40.000 0.00 0.00 0.00 1.85
1889 1980 5.308825 ACACCACTCCTTTAGTTTCATCTG 58.691 41.667 0.00 0.00 35.76 2.90
1905 1996 8.575589 AGTTTCATCTGTGTTGCAATGTTATTA 58.424 29.630 0.59 0.00 0.00 0.98
1953 2044 7.148154 TGTGTAGTGTTCCATAATATTTGTGGC 60.148 37.037 12.44 3.71 41.26 5.01
1954 2045 7.067008 GTGTAGTGTTCCATAATATTTGTGGCT 59.933 37.037 12.44 7.97 41.26 4.75
1955 2046 8.268605 TGTAGTGTTCCATAATATTTGTGGCTA 58.731 33.333 12.44 7.27 41.26 3.93
1956 2047 7.568199 AGTGTTCCATAATATTTGTGGCTAC 57.432 36.000 12.44 12.49 41.26 3.58
1957 2048 7.346471 AGTGTTCCATAATATTTGTGGCTACT 58.654 34.615 12.44 12.31 41.26 2.57
1958 2049 7.283127 AGTGTTCCATAATATTTGTGGCTACTG 59.717 37.037 12.44 0.00 41.26 2.74
1959 2050 6.039270 TGTTCCATAATATTTGTGGCTACTGC 59.961 38.462 12.44 0.00 41.26 4.40
1983 2074 0.783206 TGGGAAATGGAAAGGCAGGA 59.217 50.000 0.00 0.00 0.00 3.86
2028 2120 5.236478 TCAGAACTTCATTCCTCAAACGAAC 59.764 40.000 0.00 0.00 38.16 3.95
2078 2173 4.103469 TCAGTTAGAACTTGGGCCTGTTTA 59.897 41.667 14.62 8.12 37.08 2.01
2123 2252 4.576053 TGAGATTATTTTGCAGGTGGATCG 59.424 41.667 0.00 0.00 0.00 3.69
2135 2264 1.691976 GGTGGATCGTGACCCATATGA 59.308 52.381 3.65 0.00 34.58 2.15
2163 2292 5.471257 GCAGAGAAAGATATAGGTTACCCG 58.529 45.833 0.00 0.00 35.12 5.28
2244 2374 9.730705 ATTATAATGGAGTATGTGATTCCTGTG 57.269 33.333 0.00 0.00 34.96 3.66
2372 2502 1.068055 CCTCCAGCAAACAATGTCTGC 60.068 52.381 3.04 3.04 34.10 4.26
2454 2584 7.487822 TCTTCCTTCTCAGTTTCATATCACT 57.512 36.000 0.00 0.00 0.00 3.41
2465 2595 8.100164 TCAGTTTCATATCACTGGTCAATACAA 58.900 33.333 6.44 0.00 40.81 2.41
2492 2622 1.196808 GGTTGTACATGCTGTTGGTCG 59.803 52.381 0.00 0.00 0.00 4.79
2517 2647 0.318699 CATGTGGTGACGACGACACT 60.319 55.000 25.15 7.17 42.78 3.55
2609 2739 1.882623 CAGGAACAAGCCAAAGGAGAC 59.117 52.381 0.00 0.00 0.00 3.36
2621 2751 2.185103 AAGGAGACGACGAGTGACGC 62.185 60.000 0.00 0.00 46.94 5.19
2682 2812 3.332919 GCTCAAGAAGAAGATGACTGCA 58.667 45.455 0.00 0.00 0.00 4.41
2759 2889 7.195646 TGTCATTTTTCAAGACAAGCTTAGTG 58.804 34.615 0.00 0.00 39.15 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.946606 TGATCACACAAGCAGTCATCAT 58.053 40.909 0.00 0.00 0.00 2.45
91 92 3.897505 CCCTGAAACTGAAACCCTTGATT 59.102 43.478 0.00 0.00 0.00 2.57
178 179 4.744631 GTGAGTTTTCCAATCACGCATTTT 59.255 37.500 0.00 0.00 34.55 1.82
242 243 5.948758 TGATACATCTATTGGTTGCCAACAA 59.051 36.000 10.18 0.00 46.95 2.83
394 396 5.221501 CCTCCATTTTCAATGGACACTTTGT 60.222 40.000 13.25 0.00 42.81 2.83
403 406 2.167075 GACTGGCCTCCATTTTCAATGG 59.833 50.000 3.32 8.96 40.48 3.16
423 426 2.412870 CATATTTATCAGCGTGGCCGA 58.587 47.619 0.00 0.00 35.63 5.54
445 448 1.226773 GTACACCTAACGCGCCGAT 60.227 57.895 5.73 0.00 0.00 4.18
456 459 2.769652 TACGGGTCGGCAGTACACCT 62.770 60.000 0.00 0.00 0.00 4.00
459 462 1.177895 TGTTACGGGTCGGCAGTACA 61.178 55.000 0.00 0.00 0.00 2.90
461 464 0.678395 TTTGTTACGGGTCGGCAGTA 59.322 50.000 0.00 0.00 0.00 2.74
499 502 2.035576 GTCTATTTAGACGACCGCCCAT 59.964 50.000 2.18 0.00 42.72 4.00
512 516 8.963130 CACATTTGTTCGCTTTTTGTCTATTTA 58.037 29.630 0.00 0.00 0.00 1.40
516 520 5.885881 ACACATTTGTTCGCTTTTTGTCTA 58.114 33.333 0.00 0.00 28.43 2.59
543 548 2.696409 TAACACGCCGAGCCAAACGA 62.696 55.000 0.00 0.00 0.00 3.85
551 556 0.388649 AGCAACTCTAACACGCCGAG 60.389 55.000 0.00 0.00 0.00 4.63
577 582 2.061028 GGTAGCTGTTTTGTGCAATGC 58.939 47.619 0.00 0.00 0.00 3.56
578 583 2.297033 AGGGTAGCTGTTTTGTGCAATG 59.703 45.455 0.00 0.00 0.00 2.82
579 584 2.597455 AGGGTAGCTGTTTTGTGCAAT 58.403 42.857 0.00 0.00 0.00 3.56
581 586 2.065899 AAGGGTAGCTGTTTTGTGCA 57.934 45.000 0.00 0.00 0.00 4.57
582 587 2.623416 AGAAAGGGTAGCTGTTTTGTGC 59.377 45.455 0.00 0.00 0.00 4.57
583 588 4.023707 CAGAGAAAGGGTAGCTGTTTTGTG 60.024 45.833 0.00 0.00 0.00 3.33
584 589 4.137543 CAGAGAAAGGGTAGCTGTTTTGT 58.862 43.478 0.00 0.00 0.00 2.83
585 590 3.503748 CCAGAGAAAGGGTAGCTGTTTTG 59.496 47.826 0.00 0.00 0.00 2.44
586 591 3.498661 CCCAGAGAAAGGGTAGCTGTTTT 60.499 47.826 0.00 0.00 41.61 2.43
587 592 2.040412 CCCAGAGAAAGGGTAGCTGTTT 59.960 50.000 0.00 0.00 41.61 2.83
588 593 1.630878 CCCAGAGAAAGGGTAGCTGTT 59.369 52.381 0.00 0.00 41.61 3.16
589 594 1.203313 TCCCAGAGAAAGGGTAGCTGT 60.203 52.381 0.00 0.00 46.82 4.40
590 595 1.573108 TCCCAGAGAAAGGGTAGCTG 58.427 55.000 0.00 0.00 46.82 4.24
591 596 2.122768 CATCCCAGAGAAAGGGTAGCT 58.877 52.381 0.00 0.00 46.82 3.32
592 597 1.141858 CCATCCCAGAGAAAGGGTAGC 59.858 57.143 0.00 0.00 46.82 3.58
593 598 2.764269 TCCATCCCAGAGAAAGGGTAG 58.236 52.381 0.00 0.00 46.82 3.18
594 599 2.961536 TCCATCCCAGAGAAAGGGTA 57.038 50.000 0.00 0.00 46.82 3.69
595 600 2.131023 GATCCATCCCAGAGAAAGGGT 58.869 52.381 0.00 0.00 46.82 4.34
597 602 2.036992 CTCGATCCATCCCAGAGAAAGG 59.963 54.545 0.00 0.00 0.00 3.11
598 603 2.697751 ACTCGATCCATCCCAGAGAAAG 59.302 50.000 0.00 0.00 33.53 2.62
599 604 2.752030 ACTCGATCCATCCCAGAGAAA 58.248 47.619 0.00 0.00 33.53 2.52
600 605 2.461300 ACTCGATCCATCCCAGAGAA 57.539 50.000 0.00 0.00 33.53 2.87
601 606 2.443632 ACTACTCGATCCATCCCAGAGA 59.556 50.000 0.00 0.00 33.53 3.10
602 607 2.817258 GACTACTCGATCCATCCCAGAG 59.183 54.545 0.00 0.00 35.28 3.35
603 608 2.810767 CGACTACTCGATCCATCCCAGA 60.811 54.545 0.00 0.00 43.06 3.86
604 609 1.537638 CGACTACTCGATCCATCCCAG 59.462 57.143 0.00 0.00 43.06 4.45
605 610 1.142262 TCGACTACTCGATCCATCCCA 59.858 52.381 0.00 0.00 44.14 4.37
606 611 1.893544 TCGACTACTCGATCCATCCC 58.106 55.000 0.00 0.00 44.14 3.85
626 631 1.461897 GCTTTTGCTACGCGTTCCTTA 59.538 47.619 20.78 0.00 43.35 2.69
716 731 1.305046 ATATCTAGGACCCCGCCGG 60.305 63.158 0.00 0.00 37.81 6.13
717 732 1.654954 CGATATCTAGGACCCCGCCG 61.655 65.000 0.34 0.00 0.00 6.46
858 875 1.550524 TGACCAGCTACAGTGACATCC 59.449 52.381 0.00 0.00 0.00 3.51
900 917 3.263941 GCGTGTCCATCGCCTTTT 58.736 55.556 0.00 0.00 46.61 2.27
960 977 0.940126 GTGTGAGTGTGTGGCAGAAG 59.060 55.000 0.00 0.00 0.00 2.85
961 978 0.251634 TGTGTGAGTGTGTGGCAGAA 59.748 50.000 0.00 0.00 0.00 3.02
993 1011 4.670221 GCTCACTTGCTTTGTAGTATGTGC 60.670 45.833 0.00 0.00 39.98 4.57
1062 1084 2.678934 ACAGCGAGAAGGCGGGTA 60.679 61.111 0.00 0.00 38.18 3.69
1233 1255 0.906775 TTTAGGGTCGGGCTTAGGTG 59.093 55.000 0.00 0.00 0.00 4.00
1273 1307 3.056328 GGCTGCGGGTCTGGTTTC 61.056 66.667 0.00 0.00 0.00 2.78
1278 1312 4.767255 GGTCTGGCTGCGGGTCTG 62.767 72.222 0.00 0.00 0.00 3.51
1282 1316 4.659172 TTTGGGTCTGGCTGCGGG 62.659 66.667 0.00 0.00 0.00 6.13
1283 1317 2.597217 TTTTGGGTCTGGCTGCGG 60.597 61.111 0.00 0.00 0.00 5.69
1284 1318 2.644992 GTTTTGGGTCTGGCTGCG 59.355 61.111 0.00 0.00 0.00 5.18
1285 1319 2.919494 CGGTTTTGGGTCTGGCTGC 61.919 63.158 0.00 0.00 0.00 5.25
1286 1320 2.268076 CCGGTTTTGGGTCTGGCTG 61.268 63.158 0.00 0.00 0.00 4.85
1287 1321 2.115266 CCGGTTTTGGGTCTGGCT 59.885 61.111 0.00 0.00 0.00 4.75
1288 1322 3.680786 GCCGGTTTTGGGTCTGGC 61.681 66.667 1.90 0.00 46.60 4.85
1289 1323 3.361977 CGCCGGTTTTGGGTCTGG 61.362 66.667 1.90 0.00 0.00 3.86
1309 1397 0.336737 TGGGTGTTGGGTCAGGTTTT 59.663 50.000 0.00 0.00 0.00 2.43
1351 1439 2.281276 GGCGTCGGGTCAGGTTTT 60.281 61.111 0.00 0.00 0.00 2.43
1599 1687 1.436336 GCAAATGCAGGCAGGCTAG 59.564 57.895 0.00 0.00 41.59 3.42
1704 1794 2.479566 AGATGGCTCACACGAACAAT 57.520 45.000 0.00 0.00 0.00 2.71
1727 1818 2.092323 TCACACGGGAGATACACTGAG 58.908 52.381 0.00 0.00 0.00 3.35
1741 1832 0.939106 TCACACGCACTGATCACACG 60.939 55.000 0.00 0.00 0.00 4.49
1742 1833 1.127397 CATCACACGCACTGATCACAC 59.873 52.381 0.00 0.00 0.00 3.82
1743 1834 1.270252 ACATCACACGCACTGATCACA 60.270 47.619 0.00 0.00 0.00 3.58
1744 1835 1.432514 ACATCACACGCACTGATCAC 58.567 50.000 0.00 0.00 0.00 3.06
1745 1836 2.606108 GTACATCACACGCACTGATCA 58.394 47.619 0.00 0.00 0.00 2.92
1746 1837 1.927174 GGTACATCACACGCACTGATC 59.073 52.381 0.00 0.00 0.00 2.92
1747 1838 1.275010 TGGTACATCACACGCACTGAT 59.725 47.619 0.00 0.00 0.00 2.90
1748 1839 0.676736 TGGTACATCACACGCACTGA 59.323 50.000 0.00 0.00 0.00 3.41
1749 1840 3.209266 TGGTACATCACACGCACTG 57.791 52.632 0.00 0.00 0.00 3.66
1788 1879 2.860136 ACGTTCAGATACATGCACGATG 59.140 45.455 5.94 0.00 41.42 3.84
1792 1883 5.718649 AATGTACGTTCAGATACATGCAC 57.281 39.130 0.00 0.00 40.36 4.57
1804 1895 5.840940 AGTACTGAAGCAAATGTACGTTC 57.159 39.130 0.00 0.00 39.87 3.95
1817 1908 7.227512 ACCAGAAAATCAAGTGAAGTACTGAAG 59.772 37.037 0.00 0.00 40.26 3.02
1860 1951 7.514721 TGAAACTAAAGGAGTGGTGTTAGATT 58.485 34.615 0.00 0.00 38.87 2.40
1861 1952 7.074653 TGAAACTAAAGGAGTGGTGTTAGAT 57.925 36.000 0.00 0.00 38.87 1.98
1866 1957 5.163195 ACAGATGAAACTAAAGGAGTGGTGT 60.163 40.000 0.00 0.00 38.87 4.16
1867 1958 5.180117 CACAGATGAAACTAAAGGAGTGGTG 59.820 44.000 0.00 0.00 38.87 4.17
1880 1971 7.642071 AATAACATTGCAACACAGATGAAAC 57.358 32.000 0.00 0.00 0.00 2.78
1889 1980 7.812191 TGAAGGAACATAATAACATTGCAACAC 59.188 33.333 0.00 0.00 0.00 3.32
1905 1996 5.880332 ACAATACGCATAGTTGAAGGAACAT 59.120 36.000 0.00 0.00 36.98 2.71
1953 2044 2.771943 TCCATTTCCCAGTAGGCAGTAG 59.228 50.000 0.00 0.00 34.51 2.57
1954 2045 2.840511 TCCATTTCCCAGTAGGCAGTA 58.159 47.619 0.00 0.00 34.51 2.74
1955 2046 1.668826 TCCATTTCCCAGTAGGCAGT 58.331 50.000 0.00 0.00 34.51 4.40
1956 2047 2.806945 TTCCATTTCCCAGTAGGCAG 57.193 50.000 0.00 0.00 34.51 4.85
1957 2048 2.291540 CCTTTCCATTTCCCAGTAGGCA 60.292 50.000 0.00 0.00 34.51 4.75
1958 2049 2.379005 CCTTTCCATTTCCCAGTAGGC 58.621 52.381 0.00 0.00 34.51 3.93
1959 2050 2.291540 TGCCTTTCCATTTCCCAGTAGG 60.292 50.000 0.00 0.00 0.00 3.18
2048 2141 3.882888 CCCAAGTTCTAACTGAAACTGCA 59.117 43.478 0.00 0.00 39.66 4.41
2049 2142 3.304726 GCCCAAGTTCTAACTGAAACTGC 60.305 47.826 0.00 0.00 39.66 4.40
2101 2196 4.576463 ACGATCCACCTGCAAAATAATCTC 59.424 41.667 0.00 0.00 0.00 2.75
2123 2252 3.620488 TCTGCCTTTTCATATGGGTCAC 58.380 45.455 2.13 0.00 0.00 3.67
2135 2264 7.993758 GGTAACCTATATCTTTCTCTGCCTTTT 59.006 37.037 0.00 0.00 0.00 2.27
2163 2292 9.462174 TCAAACAAGTGATGATATTTTGTGTTC 57.538 29.630 0.00 0.00 32.75 3.18
2244 2374 3.319137 TGCCTATGACTGTGTCTTGTC 57.681 47.619 0.00 0.00 33.15 3.18
2260 2390 6.012745 ACTTTTCAATCTCCTGTTATTGCCT 58.987 36.000 0.00 0.00 33.91 4.75
2454 2584 3.569194 ACCACACTGTTGTATTGACCA 57.431 42.857 0.00 0.00 33.30 4.02
2465 2595 2.221169 CAGCATGTACAACCACACTGT 58.779 47.619 0.00 0.00 0.00 3.55
2517 2647 1.621317 TCCTATTTCGGTGTGCAGACA 59.379 47.619 16.68 0.00 0.00 3.41
2621 2751 2.606308 GCAATGCTTATCTTGATGGCCG 60.606 50.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.