Multiple sequence alignment - TraesCS4A01G185800

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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 TraesCS4A01G185800 chr4A 100.000 2444 0 0 1 2444 465224743 465222300 0.000000e+00 4514
1 TraesCS4A01G185800 chr4D 86.681 946 56 25 1297 2206 112099899 112100810 0.000000e+00 985
2 TraesCS4A01G185800 chr4D 93.737 479 24 5 824 1299 112076504 112076979 0.000000e+00 713
3 TraesCS4A01G185800 chr4D 78.704 216 40 4 1740 1950 464851538 464851752 3.280000e-29 139
4 TraesCS4A01G185800 chr4D 93.548 93 3 1 747 839 112076401 112076490 4.240000e-28 135
5 TraesCS4A01G185800 chr2A 94.516 620 28 3 23 642 18543155 18543768 0.000000e+00 952
6 TraesCS4A01G185800 chr2A 86.015 665 84 7 1785 2442 623318736 623319398 0.000000e+00 704
7 TraesCS4A01G185800 chr7A 95.775 568 13 3 1 568 31804453 31803897 0.000000e+00 905
8 TraesCS4A01G185800 chr7A 94.949 99 5 0 546 644 31803895 31803797 3.250000e-34 156
9 TraesCS4A01G185800 chr4B 84.550 822 50 32 848 1627 172753015 172753801 0.000000e+00 743
10 TraesCS4A01G185800 chr4B 86.207 638 79 7 1812 2442 172759686 172760321 0.000000e+00 682
11 TraesCS4A01G185800 chr4B 92.308 117 5 3 747 861 172752879 172752993 1.940000e-36 163
12 TraesCS4A01G185800 chr4B 97.674 43 1 0 709 751 172752821 172752863 9.370000e-10 75
13 TraesCS4A01G185800 chr6B 79.372 669 93 24 1 644 720229968 720230616 1.740000e-116 429
14 TraesCS4A01G185800 chr6B 80.909 220 37 3 1740 1954 482469618 482469399 4.180000e-38 169
15 TraesCS4A01G185800 chr5A 78.875 658 97 27 4 644 336749072 336748440 8.140000e-110 407
16 TraesCS4A01G185800 chr7B 77.410 664 103 25 4 644 190774085 190773446 3.870000e-93 351
17 TraesCS4A01G185800 chr5B 79.412 544 70 17 130 644 691800659 691801189 1.800000e-91 346
18 TraesCS4A01G185800 chr7D 79.487 273 34 13 1 270 472735148 472735401 8.980000e-40 174
19 TraesCS4A01G185800 chr6A 81.373 204 34 3 1757 1956 478311508 478311711 1.940000e-36 163
20 TraesCS4A01G185800 chr6A 80.365 219 39 2 1740 1954 554782053 554782271 1.940000e-36 163
21 TraesCS4A01G185800 chr1D 79.263 217 40 4 1740 1953 221124882 221124668 1.960000e-31 147
22 TraesCS4A01G185800 chr5D 78.704 216 42 2 1740 1951 42067752 42067967 9.110000e-30 141


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 TraesCS4A01G185800 chr4A 465222300 465224743 2443 True 4514.0 4514 100.000000 1 2444 1 chr4A.!!$R1 2443
1 TraesCS4A01G185800 chr4D 112099899 112100810 911 False 985.0 985 86.681000 1297 2206 1 chr4D.!!$F1 909
2 TraesCS4A01G185800 chr4D 112076401 112076979 578 False 424.0 713 93.642500 747 1299 2 chr4D.!!$F3 552
3 TraesCS4A01G185800 chr2A 18543155 18543768 613 False 952.0 952 94.516000 23 642 1 chr2A.!!$F1 619
4 TraesCS4A01G185800 chr2A 623318736 623319398 662 False 704.0 704 86.015000 1785 2442 1 chr2A.!!$F2 657
5 TraesCS4A01G185800 chr7A 31803797 31804453 656 True 530.5 905 95.362000 1 644 2 chr7A.!!$R1 643
6 TraesCS4A01G185800 chr4B 172759686 172760321 635 False 682.0 682 86.207000 1812 2442 1 chr4B.!!$F1 630
7 TraesCS4A01G185800 chr4B 172752821 172753801 980 False 327.0 743 91.510667 709 1627 3 chr4B.!!$F2 918
8 TraesCS4A01G185800 chr6B 720229968 720230616 648 False 429.0 429 79.372000 1 644 1 chr6B.!!$F1 643
9 TraesCS4A01G185800 chr5A 336748440 336749072 632 True 407.0 407 78.875000 4 644 1 chr5A.!!$R1 640
10 TraesCS4A01G185800 chr7B 190773446 190774085 639 True 351.0 351 77.410000 4 644 1 chr7B.!!$R1 640
11 TraesCS4A01G185800 chr5B 691800659 691801189 530 False 346.0 346 79.412000 130 644 1 chr5B.!!$F1 514

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
594 667 0.238289 CCAACGAATGAGCACGCTTT 59.762 50.0 0.00 0.00 0.00 3.51 F
717 790 0.319641 GACGGGTCTGTCTGGACAAC 60.320 60.0 4.94 6.29 41.33 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 1605 0.179000 ATACTACTCGGTCCGGTCGT 59.821 55.0 12.29 12.37 0.00 4.34 R
2250 2473 0.537143 GGTGCCAGGACACAACATCA 60.537 55.0 13.89 0.00 42.55 3.07 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
54 55 4.208686 GGACAGAGGTAGGCGCCG 62.209 72.222 23.20 7.32 0.00 6.46
146 147 2.810852 CAGAAGGAGAAAACTGGCACTC 59.189 50.000 0.00 0.00 0.00 3.51
184 185 1.145377 AAAATCTATCGCCGCCGGT 59.855 52.632 4.45 0.00 34.56 5.28
590 663 1.920574 CTAGTCCAACGAATGAGCACG 59.079 52.381 0.00 0.00 0.00 5.34
594 667 0.238289 CCAACGAATGAGCACGCTTT 59.762 50.000 0.00 0.00 0.00 3.51
644 717 1.093159 CAGTTGGAGATGCAAGGCTC 58.907 55.000 0.00 0.00 0.00 4.70
650 723 2.345124 GAGATGCAAGGCTCCATTCT 57.655 50.000 0.00 0.00 0.00 2.40
651 724 2.652590 GAGATGCAAGGCTCCATTCTT 58.347 47.619 0.00 0.00 0.00 2.52
652 725 2.617774 GAGATGCAAGGCTCCATTCTTC 59.382 50.000 0.00 0.00 0.00 2.87
653 726 1.332997 GATGCAAGGCTCCATTCTTCG 59.667 52.381 0.00 0.00 0.00 3.79
654 727 1.308069 TGCAAGGCTCCATTCTTCGC 61.308 55.000 0.00 0.00 0.00 4.70
655 728 1.717937 CAAGGCTCCATTCTTCGCG 59.282 57.895 0.00 0.00 0.00 5.87
656 729 1.450312 AAGGCTCCATTCTTCGCGG 60.450 57.895 6.13 0.00 0.00 6.46
657 730 3.577313 GGCTCCATTCTTCGCGGC 61.577 66.667 6.13 0.00 0.00 6.53
658 731 3.929948 GCTCCATTCTTCGCGGCG 61.930 66.667 17.70 17.70 0.00 6.46
659 732 3.264897 CTCCATTCTTCGCGGCGG 61.265 66.667 23.46 7.47 0.00 6.13
693 766 4.803426 CGGAGCGGCTCACCTCAC 62.803 72.222 29.33 11.41 31.08 3.51
694 767 4.459089 GGAGCGGCTCACCTCACC 62.459 72.222 29.33 9.03 31.08 4.02
695 768 4.459089 GAGCGGCTCACCTCACCC 62.459 72.222 24.42 0.00 0.00 4.61
701 774 4.778415 CTCACCTCACCCGCGACG 62.778 72.222 8.23 0.00 0.00 5.12
717 790 0.319641 GACGGGTCTGTCTGGACAAC 60.320 60.000 4.94 6.29 41.33 3.32
760 851 4.838152 GAGCTGGCGGGCGATTGA 62.838 66.667 0.00 0.00 37.29 2.57
801 892 0.389948 CGAGTGGTGGGCTTACAGTC 60.390 60.000 0.00 0.00 0.00 3.51
861 1018 1.033574 ATCTCACTCGGAACCGGATC 58.966 55.000 9.46 5.54 40.25 3.36
877 1034 2.286595 CGGATCGCTGGACATCATTTTG 60.287 50.000 0.00 0.00 0.00 2.44
898 1055 1.079503 CTCTACAAAAGCAGCGGGAC 58.920 55.000 0.00 0.00 0.00 4.46
937 1094 1.368850 GCTGTTTCGTTCGTGCACC 60.369 57.895 12.15 0.00 0.00 5.01
938 1095 1.772063 GCTGTTTCGTTCGTGCACCT 61.772 55.000 12.15 0.00 0.00 4.00
1075 1247 2.577059 CGGCCCGCTTAGTCTCAA 59.423 61.111 0.00 0.00 0.00 3.02
1095 1267 1.449956 CTCTCAGCCAGGCAGCTTC 60.450 63.158 15.80 0.00 42.61 3.86
1115 1287 2.826128 TCATCACAGAGTTTCGGCTACT 59.174 45.455 0.00 0.00 0.00 2.57
1140 1312 3.006967 AGCGAGACACTTACTTTCATGGT 59.993 43.478 0.00 0.00 0.00 3.55
1295 1473 2.100031 CGGAGTGCGCTGTATGCAA 61.100 57.895 3.44 0.00 45.23 4.08
1341 1519 2.169789 CAGGAAGATGCCGTGCTCG 61.170 63.158 0.14 0.14 0.00 5.03
1343 1521 3.918220 GAAGATGCCGTGCTCGCG 61.918 66.667 0.00 0.00 35.54 5.87
1498 1699 7.983484 ACTAATTCGGTGGAAACGTAGATTAAT 59.017 33.333 0.00 0.00 35.40 1.40
1515 1716 6.139671 AGATTAATGCCTCCTTAGTCTCAGA 58.860 40.000 0.00 0.00 0.00 3.27
1572 1778 1.859302 AGACTGATGTGGACTCCCTC 58.141 55.000 0.00 0.00 0.00 4.30
1580 1800 2.123589 TGTGGACTCCCTCAAGTTCAA 58.876 47.619 0.00 0.00 36.53 2.69
1581 1801 2.507886 TGTGGACTCCCTCAAGTTCAAA 59.492 45.455 0.00 0.00 36.53 2.69
1582 1802 3.142174 GTGGACTCCCTCAAGTTCAAAG 58.858 50.000 0.00 0.00 36.53 2.77
1583 1803 2.777692 TGGACTCCCTCAAGTTCAAAGT 59.222 45.455 0.00 0.00 31.66 2.66
1584 1804 3.202151 TGGACTCCCTCAAGTTCAAAGTT 59.798 43.478 0.00 0.00 31.66 2.66
1585 1805 3.815962 GGACTCCCTCAAGTTCAAAGTTC 59.184 47.826 0.00 0.00 0.00 3.01
1586 1806 4.451900 GACTCCCTCAAGTTCAAAGTTCA 58.548 43.478 0.00 0.00 0.00 3.18
1643 1863 0.608640 AATCTCGTCTCGCCTTTGGT 59.391 50.000 0.00 0.00 0.00 3.67
1653 1873 3.007506 TCTCGCCTTTGGTTAGACATGAA 59.992 43.478 0.00 0.00 0.00 2.57
1654 1874 3.334691 TCGCCTTTGGTTAGACATGAAG 58.665 45.455 0.00 0.00 0.00 3.02
1655 1875 3.007506 TCGCCTTTGGTTAGACATGAAGA 59.992 43.478 0.00 0.00 0.00 2.87
1656 1876 3.751175 CGCCTTTGGTTAGACATGAAGAA 59.249 43.478 0.00 0.00 0.00 2.52
1657 1877 4.142816 CGCCTTTGGTTAGACATGAAGAAG 60.143 45.833 0.00 0.00 0.00 2.85
1658 1878 4.156739 GCCTTTGGTTAGACATGAAGAAGG 59.843 45.833 0.00 2.80 35.42 3.46
1659 1879 5.316987 CCTTTGGTTAGACATGAAGAAGGT 58.683 41.667 0.00 0.00 0.00 3.50
1660 1880 5.770162 CCTTTGGTTAGACATGAAGAAGGTT 59.230 40.000 0.00 0.00 0.00 3.50
1690 1910 4.017037 TCCCTGCACTATAAATTTTCCCCA 60.017 41.667 0.00 0.00 0.00 4.96
1698 1918 7.062957 CACTATAAATTTTCCCCACCATCTCT 58.937 38.462 0.00 0.00 0.00 3.10
1722 1942 3.937814 CTGCCACACAGGTAAAGTATCA 58.062 45.455 0.00 0.00 43.19 2.15
1723 1943 3.935203 CTGCCACACAGGTAAAGTATCAG 59.065 47.826 0.00 0.00 43.19 2.90
1724 1944 3.580895 TGCCACACAGGTAAAGTATCAGA 59.419 43.478 0.00 0.00 40.61 3.27
1726 1946 4.562757 GCCACACAGGTAAAGTATCAGACA 60.563 45.833 0.00 0.00 40.61 3.41
1727 1947 5.734720 CCACACAGGTAAAGTATCAGACAT 58.265 41.667 0.00 0.00 0.00 3.06
1730 1950 6.873605 CACACAGGTAAAGTATCAGACATTCA 59.126 38.462 0.00 0.00 0.00 2.57
1731 1951 7.387673 CACACAGGTAAAGTATCAGACATTCAA 59.612 37.037 0.00 0.00 0.00 2.69
1733 1953 6.595716 ACAGGTAAAGTATCAGACATTCAAGC 59.404 38.462 0.00 0.00 0.00 4.01
1735 1955 6.595716 AGGTAAAGTATCAGACATTCAAGCAC 59.404 38.462 0.00 0.00 0.00 4.40
1736 1956 6.371548 GGTAAAGTATCAGACATTCAAGCACA 59.628 38.462 0.00 0.00 0.00 4.57
1737 1957 5.869753 AAGTATCAGACATTCAAGCACAC 57.130 39.130 0.00 0.00 0.00 3.82
1738 1958 4.898320 AGTATCAGACATTCAAGCACACA 58.102 39.130 0.00 0.00 0.00 3.72
1739 1959 4.692625 AGTATCAGACATTCAAGCACACAC 59.307 41.667 0.00 0.00 0.00 3.82
1740 1960 3.198409 TCAGACATTCAAGCACACACT 57.802 42.857 0.00 0.00 0.00 3.55
1741 1961 3.544684 TCAGACATTCAAGCACACACTT 58.455 40.909 0.00 0.00 0.00 3.16
1742 1962 4.702831 TCAGACATTCAAGCACACACTTA 58.297 39.130 0.00 0.00 0.00 2.24
1743 1963 5.122519 TCAGACATTCAAGCACACACTTAA 58.877 37.500 0.00 0.00 0.00 1.85
1744 1964 5.237127 TCAGACATTCAAGCACACACTTAAG 59.763 40.000 0.00 0.00 0.00 1.85
1745 1965 4.516698 AGACATTCAAGCACACACTTAAGG 59.483 41.667 7.53 0.00 0.00 2.69
1746 1966 4.460263 ACATTCAAGCACACACTTAAGGA 58.540 39.130 7.53 0.00 0.00 3.36
1747 1967 4.275936 ACATTCAAGCACACACTTAAGGAC 59.724 41.667 7.53 0.00 0.00 3.85
1748 1968 3.552132 TCAAGCACACACTTAAGGACA 57.448 42.857 7.53 0.00 0.00 4.02
1749 1969 4.085357 TCAAGCACACACTTAAGGACAT 57.915 40.909 7.53 0.00 0.00 3.06
1750 1970 3.814842 TCAAGCACACACTTAAGGACATG 59.185 43.478 7.53 0.00 0.00 3.21
1751 1971 3.492102 AGCACACACTTAAGGACATGT 57.508 42.857 7.53 0.00 0.00 3.21
1752 1972 3.141398 AGCACACACTTAAGGACATGTG 58.859 45.455 17.74 17.74 46.32 3.21
1753 1973 3.138304 GCACACACTTAAGGACATGTGA 58.862 45.455 23.37 0.00 44.20 3.58
1754 1974 3.563808 GCACACACTTAAGGACATGTGAA 59.436 43.478 23.37 0.00 44.20 3.18
1755 1975 4.554723 GCACACACTTAAGGACATGTGAAC 60.555 45.833 23.37 14.06 44.20 3.18
1756 1976 3.807622 ACACACTTAAGGACATGTGAACG 59.192 43.478 23.37 4.83 44.20 3.95
1757 1977 4.055360 CACACTTAAGGACATGTGAACGA 58.945 43.478 15.40 0.00 44.20 3.85
1758 1978 4.509970 CACACTTAAGGACATGTGAACGAA 59.490 41.667 15.40 0.00 44.20 3.85
1759 1979 4.750098 ACACTTAAGGACATGTGAACGAAG 59.250 41.667 1.15 2.89 34.81 3.79
1769 1989 4.023450 ACATGTGAACGAAGACTTCTCGTA 60.023 41.667 13.22 0.00 39.30 3.43
1807 2027 2.279073 CTCCGGTAGGGGAGCAGA 59.721 66.667 0.00 0.00 46.53 4.26
1810 2030 1.152440 CCGGTAGGGGAGCAGAGAT 60.152 63.158 0.00 0.00 0.00 2.75
1842 2062 2.351447 CGACGACTCTTTCTGGCTACAA 60.351 50.000 0.00 0.00 0.00 2.41
1853 2073 5.601583 TTCTGGCTACAATATTGGTCGTA 57.398 39.130 19.37 2.29 0.00 3.43
2004 2226 3.784511 ATGCATGAGATTCACCTAGGG 57.215 47.619 14.81 2.03 0.00 3.53
2005 2227 2.481441 TGCATGAGATTCACCTAGGGT 58.519 47.619 14.81 0.00 35.62 4.34
2006 2228 3.653164 TGCATGAGATTCACCTAGGGTA 58.347 45.455 14.81 0.00 32.11 3.69
2008 2230 3.388024 GCATGAGATTCACCTAGGGTACA 59.612 47.826 14.81 3.84 32.11 2.90
2009 2231 4.040952 GCATGAGATTCACCTAGGGTACAT 59.959 45.833 14.81 5.97 32.11 2.29
2010 2232 5.545588 CATGAGATTCACCTAGGGTACATG 58.454 45.833 14.81 13.51 32.11 3.21
2011 2233 3.388024 TGAGATTCACCTAGGGTACATGC 59.612 47.826 14.81 0.00 32.11 4.06
2048 2270 2.688477 GAGATGGGACCCTCTTCTGAT 58.312 52.381 13.00 0.00 0.00 2.90
2051 2273 2.342406 TGGGACCCTCTTCTGATTGA 57.658 50.000 13.00 0.00 0.00 2.57
2121 2344 8.642935 TGTTTTCAATCTACATGGAACCAATA 57.357 30.769 0.00 0.00 0.00 1.90
2122 2345 9.253832 TGTTTTCAATCTACATGGAACCAATAT 57.746 29.630 0.00 0.00 0.00 1.28
2209 2432 1.153349 GAGACCTTAGCTTGGGCCG 60.153 63.158 7.58 0.00 39.73 6.13
2216 2439 1.843462 TTAGCTTGGGCCGCCTTGTA 61.843 55.000 9.86 0.00 39.73 2.41
2233 2456 0.037975 GTAGGCAACCTTTCGGACGA 60.038 55.000 0.00 0.00 34.61 4.20
2234 2457 0.680618 TAGGCAACCTTTCGGACGAA 59.319 50.000 2.62 2.62 34.61 3.85
2279 2502 4.335647 CTGGCACCTGGCTCCGTT 62.336 66.667 0.00 0.00 44.01 4.44
2291 2514 1.134907 GGCTCCGTTCGGATTGTTCTA 60.135 52.381 14.34 0.00 33.34 2.10
2297 2520 4.641541 TCCGTTCGGATTGTTCTATGTAGA 59.358 41.667 10.00 0.00 0.00 2.59
2303 2526 4.036498 CGGATTGTTCTATGTAGACTCGGT 59.964 45.833 0.00 0.00 30.81 4.69
2304 2527 5.282510 GGATTGTTCTATGTAGACTCGGTG 58.717 45.833 0.00 0.00 30.81 4.94
2308 2531 7.400599 TTGTTCTATGTAGACTCGGTGTATT 57.599 36.000 0.00 0.00 30.81 1.89
2309 2532 6.792326 TGTTCTATGTAGACTCGGTGTATTG 58.208 40.000 0.00 0.00 30.81 1.90
2311 2534 7.094075 TGTTCTATGTAGACTCGGTGTATTGTT 60.094 37.037 0.00 0.00 30.81 2.83
2315 2538 2.537143 AGACTCGGTGTATTGTTCCCT 58.463 47.619 0.00 0.00 0.00 4.20
2323 2549 4.117685 GGTGTATTGTTCCCTATGTCGTC 58.882 47.826 0.00 0.00 0.00 4.20
2327 2553 1.259609 TGTTCCCTATGTCGTCCGTT 58.740 50.000 0.00 0.00 0.00 4.44
2335 2561 3.376234 CCTATGTCGTCCGTTGACTCTTA 59.624 47.826 1.48 0.00 39.47 2.10
2342 2568 3.367087 CGTCCGTTGACTCTTACTTGGAT 60.367 47.826 0.00 0.00 39.47 3.41
2350 2576 6.214191 TGACTCTTACTTGGATCACTCATC 57.786 41.667 0.00 0.00 0.00 2.92
2387 2613 5.378180 GCTTTCGTTGAAGATCAAGACTTC 58.622 41.667 0.00 0.00 37.00 3.01
2403 2629 6.038603 TCAAGACTTCCTCATGTCAACTTTTG 59.961 38.462 0.00 0.00 35.81 2.44
2405 2631 3.953612 ACTTCCTCATGTCAACTTTTGCA 59.046 39.130 0.00 0.00 0.00 4.08
2438 2665 0.031616 AGGGGACAAAGGTGGCAAAA 60.032 50.000 0.00 0.00 32.51 2.44
2442 2669 2.103941 GGGACAAAGGTGGCAAAATGAA 59.896 45.455 0.00 0.00 32.51 2.57
2443 2670 3.432890 GGGACAAAGGTGGCAAAATGAAA 60.433 43.478 0.00 0.00 32.51 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 2.050477 GGTTGCAACCTTGTCGATTG 57.950 50.000 36.26 0.00 45.75 2.67
325 351 7.715249 AGATAAGCTAATTGCATCTAAACGGAA 59.285 33.333 0.00 0.00 45.94 4.30
506 555 9.847706 CGCTAGAAACATACTATCATACAAGAT 57.152 33.333 0.00 0.00 0.00 2.40
590 663 4.209495 GCTTTACCGTCAGCTAGATAAAGC 59.791 45.833 14.95 14.95 41.40 3.51
594 667 4.994907 TTGCTTTACCGTCAGCTAGATA 57.005 40.909 0.00 0.00 36.92 1.98
676 749 4.803426 GTGAGGTGAGCCGCTCCG 62.803 72.222 17.81 0.00 40.50 4.63
677 750 4.459089 GGTGAGGTGAGCCGCTCC 62.459 72.222 17.81 8.88 40.11 4.70
678 751 4.459089 GGGTGAGGTGAGCCGCTC 62.459 72.222 13.81 13.81 40.50 5.03
684 757 4.778415 CGTCGCGGGTGAGGTGAG 62.778 72.222 6.13 0.00 0.00 3.51
695 768 4.778415 CCAGACAGACCCGTCGCG 62.778 72.222 0.00 0.00 40.98 5.87
696 769 3.371063 TCCAGACAGACCCGTCGC 61.371 66.667 0.00 0.00 40.98 5.19
697 770 1.802337 TTGTCCAGACAGACCCGTCG 61.802 60.000 0.09 0.00 42.94 5.12
698 771 0.319641 GTTGTCCAGACAGACCCGTC 60.320 60.000 0.09 0.00 42.94 4.79
699 772 1.746517 GTTGTCCAGACAGACCCGT 59.253 57.895 0.09 0.00 42.94 5.28
700 773 1.372997 CGTTGTCCAGACAGACCCG 60.373 63.158 0.09 0.00 42.94 5.28
701 774 1.668151 GCGTTGTCCAGACAGACCC 60.668 63.158 0.09 0.00 42.94 4.46
702 775 0.946221 CTGCGTTGTCCAGACAGACC 60.946 60.000 0.09 0.00 42.94 3.85
703 776 0.249489 ACTGCGTTGTCCAGACAGAC 60.249 55.000 0.09 2.60 42.94 3.51
704 777 0.249447 CACTGCGTTGTCCAGACAGA 60.249 55.000 0.09 0.00 42.94 3.41
705 778 0.530650 ACACTGCGTTGTCCAGACAG 60.531 55.000 0.09 0.00 42.94 3.51
706 779 0.107897 AACACTGCGTTGTCCAGACA 60.108 50.000 0.00 0.00 36.12 3.41
707 780 1.014352 AAACACTGCGTTGTCCAGAC 58.986 50.000 0.00 0.00 38.07 3.51
717 790 0.875474 CAAAAGGCCCAAACACTGCG 60.875 55.000 0.00 0.00 0.00 5.18
760 851 2.695147 GTTGCAAAAGCCTAGCCCATAT 59.305 45.455 0.00 0.00 0.00 1.78
784 875 1.671742 CGACTGTAAGCCCACCACT 59.328 57.895 0.00 0.00 37.60 4.00
861 1018 0.813184 AGCCAAAATGATGTCCAGCG 59.187 50.000 0.00 0.00 0.00 5.18
877 1034 1.648467 CCCGCTGCTTTTGTAGAGCC 61.648 60.000 0.00 0.00 39.38 4.70
937 1094 1.395608 GTGGACGAACGAGAGAGAGAG 59.604 57.143 0.14 0.00 0.00 3.20
938 1095 1.440708 GTGGACGAACGAGAGAGAGA 58.559 55.000 0.14 0.00 0.00 3.10
1012 1169 1.006571 CCGCGTCGTAATATGGGCT 60.007 57.895 4.92 0.00 0.00 5.19
1038 1195 2.280797 GCAGGGCGTGTCTGTTCA 60.281 61.111 9.16 0.00 34.89 3.18
1075 1247 1.273269 AAGCTGCCTGGCTGAGAGAT 61.273 55.000 27.16 9.19 42.24 2.75
1095 1267 2.926200 CAGTAGCCGAAACTCTGTGATG 59.074 50.000 0.00 0.00 0.00 3.07
1115 1287 2.626266 TGAAAGTAAGTGTCTCGCTCCA 59.374 45.455 0.00 0.00 0.00 3.86
1140 1312 1.355796 CGTTACCTCCGCGCATGAAA 61.356 55.000 8.75 0.00 0.00 2.69
1290 1468 0.177604 CCTCGAAGCTCTCCTTGCAT 59.822 55.000 0.00 0.00 32.78 3.96
1295 1473 0.753848 GCCTACCTCGAAGCTCTCCT 60.754 60.000 0.00 0.00 0.00 3.69
1427 1605 0.179000 ATACTACTCGGTCCGGTCGT 59.821 55.000 12.29 12.37 0.00 4.34
1433 1611 1.872313 CGTCCTCATACTACTCGGTCC 59.128 57.143 0.00 0.00 0.00 4.46
1498 1699 5.899547 TGATAATTCTGAGACTAAGGAGGCA 59.100 40.000 0.00 0.00 30.20 4.75
1515 1716 8.846943 TCCATGTATAATCGCTTGTGATAATT 57.153 30.769 0.00 0.00 0.00 1.40
1572 1778 8.071122 TGTTTGAACTTTGAACTTTGAACTTG 57.929 30.769 0.00 0.00 0.00 3.16
1581 1801 9.487790 TCTTTTTCATTGTTTGAACTTTGAACT 57.512 25.926 9.81 0.00 43.99 3.01
1585 1805 9.002080 GCAATCTTTTTCATTGTTTGAACTTTG 57.998 29.630 0.00 0.00 43.99 2.77
1586 1806 8.728833 TGCAATCTTTTTCATTGTTTGAACTTT 58.271 25.926 0.00 0.00 43.99 2.66
1643 1863 9.449719 GGATCTTTTAACCTTCTTCATGTCTAA 57.550 33.333 0.00 0.00 0.00 2.10
1653 1873 4.043435 AGTGCAGGGATCTTTTAACCTTCT 59.957 41.667 0.00 0.00 0.00 2.85
1654 1874 4.336280 AGTGCAGGGATCTTTTAACCTTC 58.664 43.478 0.00 0.00 0.00 3.46
1655 1875 4.388577 AGTGCAGGGATCTTTTAACCTT 57.611 40.909 0.00 0.00 0.00 3.50
1656 1876 5.717119 ATAGTGCAGGGATCTTTTAACCT 57.283 39.130 0.00 0.00 0.00 3.50
1657 1877 7.875327 TTTATAGTGCAGGGATCTTTTAACC 57.125 36.000 0.00 0.00 0.00 2.85
1690 1910 0.901124 GTGTGGCAGAGAGAGATGGT 59.099 55.000 0.00 0.00 0.00 3.55
1716 1936 4.692625 GTGTGTGCTTGAATGTCTGATACT 59.307 41.667 0.00 0.00 0.00 2.12
1717 1937 4.692625 AGTGTGTGCTTGAATGTCTGATAC 59.307 41.667 0.00 0.00 0.00 2.24
1718 1938 4.898320 AGTGTGTGCTTGAATGTCTGATA 58.102 39.130 0.00 0.00 0.00 2.15
1719 1939 3.748083 AGTGTGTGCTTGAATGTCTGAT 58.252 40.909 0.00 0.00 0.00 2.90
1722 1942 4.516698 CCTTAAGTGTGTGCTTGAATGTCT 59.483 41.667 0.97 0.00 0.00 3.41
1723 1943 4.515191 TCCTTAAGTGTGTGCTTGAATGTC 59.485 41.667 0.97 0.00 0.00 3.06
1724 1944 4.275936 GTCCTTAAGTGTGTGCTTGAATGT 59.724 41.667 0.97 0.00 0.00 2.71
1726 1946 4.460263 TGTCCTTAAGTGTGTGCTTGAAT 58.540 39.130 0.97 0.00 0.00 2.57
1727 1947 3.879998 TGTCCTTAAGTGTGTGCTTGAA 58.120 40.909 0.97 0.00 0.00 2.69
1730 1950 3.565482 CACATGTCCTTAAGTGTGTGCTT 59.435 43.478 13.23 0.00 37.70 3.91
1731 1951 3.141398 CACATGTCCTTAAGTGTGTGCT 58.859 45.455 13.23 0.00 37.70 4.40
1733 1953 4.318760 CGTTCACATGTCCTTAAGTGTGTG 60.319 45.833 18.27 16.64 41.88 3.82
1735 1955 4.055360 TCGTTCACATGTCCTTAAGTGTG 58.945 43.478 14.66 14.66 42.40 3.82
1736 1956 4.330944 TCGTTCACATGTCCTTAAGTGT 57.669 40.909 0.00 0.00 33.84 3.55
1737 1957 4.988540 TCTTCGTTCACATGTCCTTAAGTG 59.011 41.667 0.00 0.00 0.00 3.16
1738 1958 4.989168 GTCTTCGTTCACATGTCCTTAAGT 59.011 41.667 0.00 0.00 0.00 2.24
1739 1959 5.230942 AGTCTTCGTTCACATGTCCTTAAG 58.769 41.667 0.00 0.00 0.00 1.85
1740 1960 5.209818 AGTCTTCGTTCACATGTCCTTAA 57.790 39.130 0.00 0.00 0.00 1.85
1741 1961 4.866508 AGTCTTCGTTCACATGTCCTTA 57.133 40.909 0.00 0.00 0.00 2.69
1742 1962 3.753294 AGTCTTCGTTCACATGTCCTT 57.247 42.857 0.00 0.00 0.00 3.36
1743 1963 3.322254 AGAAGTCTTCGTTCACATGTCCT 59.678 43.478 6.94 0.00 34.02 3.85
1744 1964 3.654414 AGAAGTCTTCGTTCACATGTCC 58.346 45.455 6.94 0.00 34.02 4.02
1745 1965 3.362237 CGAGAAGTCTTCGTTCACATGTC 59.638 47.826 6.94 0.00 34.02 3.06
1746 1966 3.243434 ACGAGAAGTCTTCGTTCACATGT 60.243 43.478 6.94 0.00 36.67 3.21
1747 1967 3.309388 ACGAGAAGTCTTCGTTCACATG 58.691 45.455 6.94 0.00 36.67 3.21
1748 1968 3.644884 ACGAGAAGTCTTCGTTCACAT 57.355 42.857 6.94 0.00 36.67 3.21
1749 1969 4.023450 ACATACGAGAAGTCTTCGTTCACA 60.023 41.667 6.94 0.00 40.70 3.58
1750 1970 4.474113 ACATACGAGAAGTCTTCGTTCAC 58.526 43.478 6.94 0.00 40.70 3.18
1751 1971 4.214758 TGACATACGAGAAGTCTTCGTTCA 59.785 41.667 6.94 2.13 40.70 3.18
1752 1972 4.720090 TGACATACGAGAAGTCTTCGTTC 58.280 43.478 6.94 0.00 40.70 3.95
1753 1973 4.761235 TGACATACGAGAAGTCTTCGTT 57.239 40.909 6.94 0.00 40.70 3.85
1754 1974 4.966965 ATGACATACGAGAAGTCTTCGT 57.033 40.909 6.94 5.93 42.92 3.85
1755 1975 5.228220 GTCAATGACATACGAGAAGTCTTCG 59.772 44.000 8.74 0.00 33.56 3.79
1756 1976 6.093404 TGTCAATGACATACGAGAAGTCTTC 58.907 40.000 12.63 4.26 37.67 2.87
1757 1977 6.025749 TGTCAATGACATACGAGAAGTCTT 57.974 37.500 12.63 0.00 37.67 3.01
1758 1978 5.644977 TGTCAATGACATACGAGAAGTCT 57.355 39.130 12.63 0.00 37.67 3.24
1759 1979 6.366332 ACTTTGTCAATGACATACGAGAAGTC 59.634 38.462 17.48 0.00 42.40 3.01
1805 2025 4.315122 CGACGCGCCGCTATCTCT 62.315 66.667 5.73 0.00 0.00 3.10
1807 2027 4.609247 GTCGACGCGCCGCTATCT 62.609 66.667 10.84 0.00 0.00 1.98
1842 2062 3.058432 CGAGACCATCGTACGACCAATAT 60.058 47.826 22.14 5.24 46.62 1.28
1898 2119 5.823570 TCAAAGTTCACCGGAAATACAAAGA 59.176 36.000 9.46 0.00 34.13 2.52
1909 2130 9.062524 TCCAAATATATTATCAAAGTTCACCGG 57.937 33.333 0.00 0.00 0.00 5.28
1970 2192 6.299805 TCTCATGCATACCAACTTAGTTCT 57.700 37.500 0.00 0.00 0.00 3.01
1971 2193 7.280876 TGAATCTCATGCATACCAACTTAGTTC 59.719 37.037 0.00 0.00 0.00 3.01
1982 2204 4.040952 ACCCTAGGTGAATCTCATGCATAC 59.959 45.833 8.29 0.00 32.98 2.39
1986 2208 3.388024 TGTACCCTAGGTGAATCTCATGC 59.612 47.826 8.29 0.00 36.19 4.06
2004 2226 2.821546 TGCTTATGGAGACGCATGTAC 58.178 47.619 0.00 0.00 0.00 2.90
2005 2227 3.535280 TTGCTTATGGAGACGCATGTA 57.465 42.857 0.00 0.00 31.77 2.29
2006 2228 2.401583 TTGCTTATGGAGACGCATGT 57.598 45.000 0.00 0.00 31.77 3.21
2127 2350 1.070134 CTGTGGGAAGTCGAGGAAACA 59.930 52.381 0.00 0.00 0.00 2.83
2220 2443 3.367482 CGACAACTTCGTCCGAAAGGTT 61.367 50.000 3.52 2.89 45.86 3.50
2221 2444 1.866880 CGACAACTTCGTCCGAAAGGT 60.867 52.381 3.52 2.40 45.86 3.50
2233 2456 4.950050 ACATCAGAAGAGTTCGACAACTT 58.050 39.130 0.00 0.00 43.37 2.66
2234 2457 4.592485 ACATCAGAAGAGTTCGACAACT 57.408 40.909 0.00 0.00 46.21 3.16
2242 2465 4.384056 CAGGACACAACATCAGAAGAGTT 58.616 43.478 0.00 0.00 0.00 3.01
2250 2473 0.537143 GGTGCCAGGACACAACATCA 60.537 55.000 13.89 0.00 42.55 3.07
2252 2475 0.538057 CAGGTGCCAGGACACAACAT 60.538 55.000 13.89 0.00 42.55 2.71
2279 2502 4.275196 CCGAGTCTACATAGAACAATCCGA 59.725 45.833 0.00 0.00 33.47 4.55
2291 2514 4.142004 GGGAACAATACACCGAGTCTACAT 60.142 45.833 0.00 0.00 0.00 2.29
2297 2520 3.773119 ACATAGGGAACAATACACCGAGT 59.227 43.478 0.00 0.00 0.00 4.18
2303 2526 3.181484 CGGACGACATAGGGAACAATACA 60.181 47.826 0.00 0.00 0.00 2.29
2304 2527 3.181483 ACGGACGACATAGGGAACAATAC 60.181 47.826 0.00 0.00 0.00 1.89
2308 2531 1.067425 CAACGGACGACATAGGGAACA 60.067 52.381 0.00 0.00 0.00 3.18
2309 2532 1.203052 TCAACGGACGACATAGGGAAC 59.797 52.381 0.00 0.00 0.00 3.62
2311 2534 0.813184 GTCAACGGACGACATAGGGA 59.187 55.000 0.00 0.00 33.68 4.20
2323 2549 3.927142 GTGATCCAAGTAAGAGTCAACGG 59.073 47.826 0.00 0.00 0.00 4.44
2327 2553 5.954752 AGATGAGTGATCCAAGTAAGAGTCA 59.045 40.000 0.00 0.00 0.00 3.41
2335 2561 4.897509 TTCACAGATGAGTGATCCAAGT 57.102 40.909 0.00 0.00 46.90 3.16
2342 2568 3.552890 CGACACCTTTCACAGATGAGTGA 60.553 47.826 0.00 0.00 46.12 3.41
2350 2576 1.070577 CGAAAGCGACACCTTTCACAG 60.071 52.381 13.18 0.00 46.94 3.66
2387 2613 2.886523 TCCTGCAAAAGTTGACATGAGG 59.113 45.455 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.