Multiple sequence alignment - TraesCS3A01G490900

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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 TraesCS3A01G490900 chr3A 100.000 2377 0 0 1398 3774 718353893 718351517 0.000000e+00 4390.0
1 TraesCS3A01G490900 chr3A 100.000 797 0 0 351 1147 718354940 718354144 0.000000e+00 1472.0
2 TraesCS3A01G490900 chr3A 100.000 142 0 0 1 142 718355290 718355149 2.890000e-66 263.0
3 TraesCS3A01G490900 chr3B 91.726 1813 102 24 1944 3747 786724927 786723154 0.000000e+00 2473.0
4 TraesCS3A01G490900 chr3B 90.348 632 42 5 1456 2078 786725378 786724757 0.000000e+00 811.0
5 TraesCS3A01G490900 chr3B 86.957 552 46 7 602 1147 786726067 786725536 6.980000e-167 597.0
6 TraesCS3A01G490900 chr3B 93.333 60 4 0 1398 1457 786725464 786725405 5.190000e-14 89.8
7 TraesCS3A01G490900 chr2A 84.072 2392 217 71 1470 3773 770013830 770011515 0.000000e+00 2156.0
8 TraesCS3A01G490900 chr2B 85.591 2089 204 40 1715 3773 790751685 790753706 0.000000e+00 2100.0
9 TraesCS3A01G490900 chr2B 90.566 583 44 8 3193 3773 790860526 790861099 0.000000e+00 761.0
10 TraesCS3A01G490900 chr2B 92.398 171 13 0 1908 2078 790751914 790752084 1.050000e-60 244.0
11 TraesCS3A01G490900 chr3D 93.054 1454 72 15 1944 3368 588318796 588317343 0.000000e+00 2098.0
12 TraesCS3A01G490900 chr3D 90.346 694 53 7 1398 2078 588319318 588318626 0.000000e+00 898.0
13 TraesCS3A01G490900 chr3D 88.809 554 40 5 604 1147 588319931 588319390 0.000000e+00 660.0
14 TraesCS3A01G490900 chr3D 91.966 473 31 5 3307 3773 588317345 588316874 0.000000e+00 656.0
15 TraesCS3A01G490900 chr3D 91.367 139 12 0 4 142 588320376 588320238 1.380000e-44 191.0
16 TraesCS3A01G490900 chr2D 85.366 1927 159 62 1908 3773 644722181 644720317 0.000000e+00 1882.0
17 TraesCS3A01G490900 chr2D 84.658 541 65 14 1582 2109 644722551 644722016 1.200000e-144 523.0
18 TraesCS3A01G490900 chr2D 83.777 376 58 1 2094 2469 565982384 565982012 1.670000e-93 353.0
19 TraesCS3A01G490900 chr4B 92.873 449 22 5 3075 3518 76501901 76501458 0.000000e+00 643.0
20 TraesCS3A01G490900 chr1B 92.825 446 22 5 3075 3515 10526202 10526642 4.110000e-179 638.0
21 TraesCS3A01G490900 chr1A 92.650 449 23 5 3075 3518 575302061 575301618 4.110000e-179 638.0
22 TraesCS3A01G490900 chr7B 92.809 445 22 5 3075 3514 571235321 571234882 1.480000e-178 636.0
23 TraesCS3A01G490900 chr5B 92.428 449 24 5 3075 3518 685680830 685680387 1.910000e-177 632.0


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 TraesCS3A01G490900 chr3A 718351517 718355290 3773 True 2041.666667 4390 100.0000 1 3774 3 chr3A.!!$R1 3773
1 TraesCS3A01G490900 chr3B 786723154 786726067 2913 True 992.700000 2473 90.5910 602 3747 4 chr3B.!!$R1 3145
2 TraesCS3A01G490900 chr2A 770011515 770013830 2315 True 2156.000000 2156 84.0720 1470 3773 1 chr2A.!!$R1 2303
3 TraesCS3A01G490900 chr2B 790751685 790753706 2021 False 1172.000000 2100 88.9945 1715 3773 2 chr2B.!!$F2 2058
4 TraesCS3A01G490900 chr2B 790860526 790861099 573 False 761.000000 761 90.5660 3193 3773 1 chr2B.!!$F1 580
5 TraesCS3A01G490900 chr3D 588316874 588320376 3502 True 900.600000 2098 91.1084 4 3773 5 chr3D.!!$R1 3769
6 TraesCS3A01G490900 chr2D 644720317 644722551 2234 True 1202.500000 1882 85.0120 1582 3773 2 chr2D.!!$R2 2191

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
755 791 0.036022 GCTCATGGGCCTGAGGATAC 59.964 60.0 24.77 11.41 42.42 2.24 F
1949 2068 0.255890 CAGGATGGGTGGAAACGGAT 59.744 55.0 0.00 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2557 2748 0.108585 TGGTCTCCACACTTCTTGCC 59.891 55.0 0.0 0.0 0.0 4.52 R
3182 3428 0.178932 AGCCACTCCTGACCACACTA 60.179 55.0 0.0 0.0 0.0 2.74 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
49 50 9.988815 AATACTCCATATAAGTGCTTCTTACAG 57.011 33.333 4.58 0.09 40.80 2.74
51 52 6.098982 ACTCCATATAAGTGCTTCTTACAGCT 59.901 38.462 4.58 0.00 40.80 4.24
59 60 5.719173 AGTGCTTCTTACAGCTAAGAGAAG 58.281 41.667 19.85 19.85 44.89 2.85
60 61 4.867608 GTGCTTCTTACAGCTAAGAGAAGG 59.132 45.833 22.94 11.98 43.23 3.46
76 77 2.168313 AGAAGGTTTTGTTGGCAAGGTG 59.832 45.455 0.00 0.00 35.82 4.00
86 87 0.840617 TGGCAAGGTGGTTCTACACA 59.159 50.000 0.00 0.00 43.08 3.72
88 89 1.523758 GCAAGGTGGTTCTACACAGG 58.476 55.000 0.00 0.00 43.08 4.00
130 131 2.353579 AGGGTTCGCAAATACATAACGC 59.646 45.455 0.00 0.00 34.34 4.84
131 132 2.096174 GGGTTCGCAAATACATAACGCA 59.904 45.455 0.00 0.00 34.31 5.24
421 422 7.272037 TGAAAAGAAGTTACCCTCATTGTTC 57.728 36.000 0.00 0.00 0.00 3.18
424 425 5.825593 AGAAGTTACCCTCATTGTTCAGA 57.174 39.130 0.00 0.00 0.00 3.27
425 426 6.380079 AGAAGTTACCCTCATTGTTCAGAT 57.620 37.500 0.00 0.00 0.00 2.90
426 427 6.784031 AGAAGTTACCCTCATTGTTCAGATT 58.216 36.000 0.00 0.00 0.00 2.40
427 428 7.234355 AGAAGTTACCCTCATTGTTCAGATTT 58.766 34.615 0.00 0.00 0.00 2.17
428 429 6.824305 AGTTACCCTCATTGTTCAGATTTG 57.176 37.500 0.00 0.00 0.00 2.32
429 430 6.542821 AGTTACCCTCATTGTTCAGATTTGA 58.457 36.000 0.00 0.00 0.00 2.69
430 431 6.656693 AGTTACCCTCATTGTTCAGATTTGAG 59.343 38.462 0.00 0.00 34.15 3.02
435 436 3.507233 TCATTGTTCAGATTTGAGCACCC 59.493 43.478 2.09 0.00 43.10 4.61
443 444 3.941483 CAGATTTGAGCACCCGAAGTAAT 59.059 43.478 0.00 0.00 0.00 1.89
462 463 4.937201 AATTTTTCCCATATCTTCCGCC 57.063 40.909 0.00 0.00 0.00 6.13
491 492 0.237498 GCAAATATAACGAGGGGCGC 59.763 55.000 0.00 0.00 46.04 6.53
527 528 2.019984 GTCGGTATAGGGACTCAACGT 58.980 52.381 0.00 0.00 41.75 3.99
529 530 1.003116 CGGTATAGGGACTCAACGTCG 60.003 57.143 0.00 0.00 43.79 5.12
560 561 2.697229 GGCGTAGTAGGTCAAACCCTAT 59.303 50.000 0.00 0.00 39.75 2.57
561 562 3.243670 GGCGTAGTAGGTCAAACCCTATC 60.244 52.174 0.00 0.00 39.75 2.08
562 563 3.382546 GCGTAGTAGGTCAAACCCTATCA 59.617 47.826 0.00 0.00 39.75 2.15
563 564 4.038883 GCGTAGTAGGTCAAACCCTATCAT 59.961 45.833 0.00 0.00 39.75 2.45
615 651 5.924356 TCCGATGGTATGAAGCTGATTTTA 58.076 37.500 0.00 0.00 0.00 1.52
619 655 7.080099 CGATGGTATGAAGCTGATTTTAATGG 58.920 38.462 0.00 0.00 0.00 3.16
624 660 4.260985 TGAAGCTGATTTTAATGGAGCGA 58.739 39.130 0.00 0.00 34.75 4.93
626 662 4.889832 AGCTGATTTTAATGGAGCGAAG 57.110 40.909 0.00 0.00 34.75 3.79
708 744 2.669133 CGGCCTGGAGATGGGTTGA 61.669 63.158 0.00 0.00 0.00 3.18
726 762 1.228154 AGTCGGGCCTTTGTGGTTC 60.228 57.895 0.84 0.00 38.35 3.62
750 786 1.030488 CACTTGCTCATGGGCCTGAG 61.030 60.000 16.70 21.54 44.51 3.35
755 791 0.036022 GCTCATGGGCCTGAGGATAC 59.964 60.000 24.77 11.41 42.42 2.24
783 819 0.320374 CTACACAGCGTTCTCCCCAA 59.680 55.000 0.00 0.00 0.00 4.12
823 862 2.725203 TTCCCGTGCCTTCAACTCCG 62.725 60.000 0.00 0.00 0.00 4.63
825 864 2.027625 CCGTGCCTTCAACTCCGAC 61.028 63.158 0.00 0.00 0.00 4.79
829 868 2.890766 GCCTTCAACTCCGACCCCA 61.891 63.158 0.00 0.00 0.00 4.96
830 869 1.003718 CCTTCAACTCCGACCCCAC 60.004 63.158 0.00 0.00 0.00 4.61
831 870 1.374252 CTTCAACTCCGACCCCACG 60.374 63.158 0.00 0.00 0.00 4.94
924 974 3.114647 CTCCTCGACCGGCTCTTCG 62.115 68.421 0.00 2.96 36.55 3.79
944 994 2.464459 CGCACAATTCCTCCCTCGC 61.464 63.158 0.00 0.00 0.00 5.03
947 997 2.193248 CAATTCCTCCCTCGCCCC 59.807 66.667 0.00 0.00 0.00 5.80
961 1011 3.007973 GCCCCTCTCTGTGTCGACC 62.008 68.421 14.12 5.06 0.00 4.79
1071 1121 3.746949 GATGACAGCGAGGGCCCTG 62.747 68.421 34.59 22.61 41.24 4.45
1466 1516 7.928167 ACAGATAGATAAATTCACAATGCTCGA 59.072 33.333 0.00 0.00 0.00 4.04
1467 1517 8.933807 CAGATAGATAAATTCACAATGCTCGAT 58.066 33.333 0.00 0.00 0.00 3.59
1468 1518 8.933807 AGATAGATAAATTCACAATGCTCGATG 58.066 33.333 0.00 0.00 0.00 3.84
1499 1578 7.304735 TCAACCAGTGATGTAATTTCATTTCG 58.695 34.615 0.00 0.00 0.00 3.46
1534 1613 8.100164 AGAAGAAGATAAGAAGAAAACAGAGGG 58.900 37.037 0.00 0.00 0.00 4.30
1575 1659 7.693952 TCTTTGTTTCTTTGCTACTGTACTTG 58.306 34.615 0.00 0.00 0.00 3.16
1607 1697 2.354821 GCCATTTCCAGCTAACCTAACG 59.645 50.000 0.00 0.00 0.00 3.18
1617 1707 4.866486 CAGCTAACCTAACGAATTAACCGT 59.134 41.667 0.00 0.00 42.61 4.83
1647 1742 1.372872 GTTGGTGACCGCAAATGCC 60.373 57.895 0.00 0.00 37.91 4.40
1652 1747 2.180017 GACCGCAAATGCCTGCTG 59.820 61.111 0.00 0.00 40.33 4.41
1763 1882 2.496470 AGAGTGGTCGGTCTTGTTATCC 59.504 50.000 0.00 0.00 0.00 2.59
1778 1897 4.580868 TGTTATCCGGTGCTTGATACAAA 58.419 39.130 0.00 0.00 0.00 2.83
1879 1998 0.687354 AAGCACGGAACCAGACTGAT 59.313 50.000 3.32 0.00 0.00 2.90
1888 2007 0.321653 ACCAGACTGATGGCGGTTTC 60.322 55.000 3.32 0.00 44.80 2.78
1891 2010 1.201429 AGACTGATGGCGGTTTCCCT 61.201 55.000 0.00 0.00 32.58 4.20
1909 2028 2.613977 CCCTCGTCACTTTGCTGAGAAT 60.614 50.000 0.00 0.00 0.00 2.40
1917 2036 4.456911 TCACTTTGCTGAGAATGGATTCAC 59.543 41.667 2.32 0.00 39.23 3.18
1918 2037 4.216902 CACTTTGCTGAGAATGGATTCACA 59.783 41.667 2.32 1.35 39.23 3.58
1923 2042 2.943690 CTGAGAATGGATTCACAGCTGG 59.056 50.000 19.93 7.28 44.31 4.85
1924 2043 2.306805 TGAGAATGGATTCACAGCTGGT 59.693 45.455 19.93 0.24 39.23 4.00
1925 2044 5.689375 CTGAGAATGGATTCACAGCTGGTG 61.689 50.000 19.93 13.73 44.31 4.17
1932 2051 2.981909 CACAGCTGGTGGTGGCAG 60.982 66.667 19.93 0.00 45.14 4.85
1933 2052 4.275508 ACAGCTGGTGGTGGCAGG 62.276 66.667 19.93 0.00 45.14 4.85
1934 2053 3.957586 CAGCTGGTGGTGGCAGGA 61.958 66.667 5.57 0.00 37.97 3.86
1935 2054 2.937689 AGCTGGTGGTGGCAGGAT 60.938 61.111 0.00 0.00 0.00 3.24
1936 2055 2.753043 GCTGGTGGTGGCAGGATG 60.753 66.667 0.00 0.00 40.87 3.51
1937 2056 2.044650 CTGGTGGTGGCAGGATGG 60.045 66.667 0.00 0.00 35.86 3.51
1938 2057 3.650298 CTGGTGGTGGCAGGATGGG 62.650 68.421 0.00 0.00 35.86 4.00
1939 2058 3.661648 GGTGGTGGCAGGATGGGT 61.662 66.667 0.00 0.00 35.86 4.51
1940 2059 2.361610 GTGGTGGCAGGATGGGTG 60.362 66.667 0.00 0.00 35.86 4.61
1941 2060 3.660571 TGGTGGCAGGATGGGTGG 61.661 66.667 0.00 0.00 35.86 4.61
1942 2061 3.338250 GGTGGCAGGATGGGTGGA 61.338 66.667 0.00 0.00 35.86 4.02
1943 2062 2.763215 GTGGCAGGATGGGTGGAA 59.237 61.111 0.00 0.00 35.86 3.53
1944 2063 1.076549 GTGGCAGGATGGGTGGAAA 59.923 57.895 0.00 0.00 35.86 3.13
1945 2064 1.076549 TGGCAGGATGGGTGGAAAC 59.923 57.895 0.00 0.00 35.86 2.78
1946 2065 2.046285 GGCAGGATGGGTGGAAACG 61.046 63.158 0.00 0.00 35.86 3.60
1947 2066 2.046285 GCAGGATGGGTGGAAACGG 61.046 63.158 0.00 0.00 35.86 4.44
1948 2067 1.682849 CAGGATGGGTGGAAACGGA 59.317 57.895 0.00 0.00 0.00 4.69
1949 2068 0.255890 CAGGATGGGTGGAAACGGAT 59.744 55.000 0.00 0.00 0.00 4.18
1950 2069 0.999712 AGGATGGGTGGAAACGGATT 59.000 50.000 0.00 0.00 0.00 3.01
1951 2070 1.102978 GGATGGGTGGAAACGGATTG 58.897 55.000 0.00 0.00 0.00 2.67
1952 2071 1.340600 GGATGGGTGGAAACGGATTGA 60.341 52.381 0.00 0.00 0.00 2.57
1962 2081 2.264480 CGGATTGACAGCCGGTGA 59.736 61.111 1.90 0.00 43.67 4.02
2085 2276 2.858476 TGGTGGCAGGATGGGTGT 60.858 61.111 0.00 0.00 35.86 4.16
2144 2335 2.121291 TAACATGGAAATGCTGCGGA 57.879 45.000 0.00 0.00 0.00 5.54
2290 2481 3.755628 CGAAAGGGGCGGTCTCGA 61.756 66.667 0.00 0.00 39.00 4.04
2500 2691 4.057428 GACGTGACCCAGCTCGCT 62.057 66.667 0.00 0.00 0.00 4.93
2549 2740 9.945904 AAAAGGTAAGGAAGTAAGACTGATAAG 57.054 33.333 0.00 0.00 0.00 1.73
2551 2742 8.896722 AGGTAAGGAAGTAAGACTGATAAGAA 57.103 34.615 0.00 0.00 0.00 2.52
2552 2743 8.973182 AGGTAAGGAAGTAAGACTGATAAGAAG 58.027 37.037 0.00 0.00 0.00 2.85
2557 2748 2.990066 AAGACTGATAAGAAGCCCCG 57.010 50.000 0.00 0.00 0.00 5.73
2574 2765 0.951040 CCGGCAAGAAGTGTGGAGAC 60.951 60.000 0.00 0.00 0.00 3.36
2647 2842 8.833231 ACTGGTTTCGTAATAATATCATCAGG 57.167 34.615 0.00 0.00 0.00 3.86
2699 2896 5.638234 ACAGTCTTAGATCGGCTTTTGTAAC 59.362 40.000 0.00 0.00 0.00 2.50
2789 2991 2.568623 TGCAGTTCCCTCTCCTTTTC 57.431 50.000 0.00 0.00 0.00 2.29
2793 2995 1.988846 AGTTCCCTCTCCTTTTCTGGG 59.011 52.381 0.00 0.00 39.22 4.45
2799 3001 2.108250 CCTCTCCTTTTCTGGGTTTCCA 59.892 50.000 0.00 0.00 41.58 3.53
2818 3043 2.223805 CCATACGTGCTGAGATGCTACA 60.224 50.000 0.00 0.00 0.00 2.74
2829 3054 6.026513 GCTGAGATGCTACAAATTTCTTGAC 58.973 40.000 0.00 0.00 0.00 3.18
2915 3151 6.065374 TGTTCTGTTTTAATGGTTGGCTCTA 58.935 36.000 0.00 0.00 0.00 2.43
2965 3202 6.358762 GGCGAGAAAATATTCTGAGATTTCG 58.641 40.000 0.00 0.00 45.91 3.46
3042 3285 5.591877 ACTCTTTAGGCCAAAATATGCAGAG 59.408 40.000 5.01 9.82 0.00 3.35
3127 3373 0.038166 GGGGTGAATCTCCTGTGCAA 59.962 55.000 1.11 0.00 32.92 4.08
3210 3463 1.189752 CAGGAGTGGCTTCTCTGCTA 58.810 55.000 9.32 0.00 32.70 3.49
3236 3489 5.452078 TTTTGTCTGCATTAGTTGGAAGG 57.548 39.130 0.00 0.00 0.00 3.46
3519 3857 1.511850 GTGCACACACTACTGCATCA 58.488 50.000 13.17 0.00 44.93 3.07
3528 3866 5.942236 ACACACTACTGCATCAAATCATTCT 59.058 36.000 0.00 0.00 0.00 2.40
3548 3886 3.371898 TCTGCTTGTACATGAATGCTTCG 59.628 43.478 12.65 0.00 0.00 3.79
3553 3891 3.333804 TGTACATGAATGCTTCGCTTCA 58.666 40.909 0.00 0.00 35.95 3.02
3556 3894 2.417933 ACATGAATGCTTCGCTTCAGAC 59.582 45.455 0.00 0.00 35.04 3.51
3605 3943 2.609459 CGATCGATCCTTTTTCCACCAG 59.391 50.000 19.51 0.00 0.00 4.00
3663 4008 0.465097 CTCCAGCCCCAGCATTGTAG 60.465 60.000 0.00 0.00 43.56 2.74
3664 4009 1.207488 TCCAGCCCCAGCATTGTAGT 61.207 55.000 0.00 0.00 43.56 2.73
3665 4010 0.546122 CCAGCCCCAGCATTGTAGTA 59.454 55.000 0.00 0.00 43.56 1.82
3679 4024 5.065218 GCATTGTAGTACTTCACAAGATGGG 59.935 44.000 14.75 5.49 38.01 4.00
3715 4061 2.107204 ACTCCTCACTGCAAGGATTTGT 59.893 45.455 6.08 0.00 42.01 2.83
3747 4093 2.617308 TCCTATTCTGATCGACGTGGTC 59.383 50.000 0.00 0.00 0.00 4.02
3773 4119 1.507140 CCCCTCAATACTACCAGCCA 58.493 55.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.283298 CCATGAATTCTCTGACACGGG 58.717 52.381 7.05 0.00 0.00 5.28
1 2 1.667724 GCCATGAATTCTCTGACACGG 59.332 52.381 7.05 0.00 0.00 4.94
2 3 2.349590 TGCCATGAATTCTCTGACACG 58.650 47.619 7.05 0.00 0.00 4.49
3 4 4.771590 TTTGCCATGAATTCTCTGACAC 57.228 40.909 7.05 0.00 0.00 3.67
4 5 6.182627 AGTATTTGCCATGAATTCTCTGACA 58.817 36.000 7.05 0.57 0.00 3.58
5 6 6.238593 GGAGTATTTGCCATGAATTCTCTGAC 60.239 42.308 7.05 0.00 33.79 3.51
6 7 5.824624 GGAGTATTTGCCATGAATTCTCTGA 59.175 40.000 7.05 0.00 33.79 3.27
49 50 3.317993 TGCCAACAAAACCTTCTCTTAGC 59.682 43.478 0.00 0.00 0.00 3.09
51 52 4.340950 CCTTGCCAACAAAACCTTCTCTTA 59.659 41.667 0.00 0.00 34.74 2.10
59 60 0.539518 ACCACCTTGCCAACAAAACC 59.460 50.000 0.00 0.00 34.74 3.27
60 61 2.093711 AGAACCACCTTGCCAACAAAAC 60.094 45.455 0.00 0.00 34.74 2.43
76 77 2.249139 AGTCAGTCCCTGTGTAGAACC 58.751 52.381 0.00 0.00 32.61 3.62
86 87 2.576615 GTGCTTTGAAAGTCAGTCCCT 58.423 47.619 6.81 0.00 0.00 4.20
88 89 2.210116 TCGTGCTTTGAAAGTCAGTCC 58.790 47.619 6.81 0.00 0.00 3.85
393 394 8.704668 ACAATGAGGGTAACTTCTTTTCAAATT 58.295 29.630 0.00 0.00 44.46 1.82
394 395 8.250143 ACAATGAGGGTAACTTCTTTTCAAAT 57.750 30.769 0.00 0.00 44.46 2.32
395 396 7.654022 ACAATGAGGGTAACTTCTTTTCAAA 57.346 32.000 0.00 0.00 44.46 2.69
403 404 7.174946 TCAAATCTGAACAATGAGGGTAACTTC 59.825 37.037 0.00 0.00 44.40 3.01
421 422 1.813513 ACTTCGGGTGCTCAAATCTG 58.186 50.000 0.00 0.00 0.00 2.90
424 425 5.722021 AAAATTACTTCGGGTGCTCAAAT 57.278 34.783 0.00 0.00 0.00 2.32
425 426 5.508320 GGAAAAATTACTTCGGGTGCTCAAA 60.508 40.000 0.00 0.00 0.00 2.69
426 427 4.022676 GGAAAAATTACTTCGGGTGCTCAA 60.023 41.667 0.00 0.00 0.00 3.02
427 428 3.504520 GGAAAAATTACTTCGGGTGCTCA 59.495 43.478 0.00 0.00 0.00 4.26
428 429 3.119602 GGGAAAAATTACTTCGGGTGCTC 60.120 47.826 0.00 0.00 0.00 4.26
429 430 2.823747 GGGAAAAATTACTTCGGGTGCT 59.176 45.455 0.00 0.00 0.00 4.40
430 431 2.559231 TGGGAAAAATTACTTCGGGTGC 59.441 45.455 0.00 0.00 0.00 5.01
435 436 7.352739 CGGAAGATATGGGAAAAATTACTTCG 58.647 38.462 0.00 0.00 34.17 3.79
443 444 2.661718 GGGCGGAAGATATGGGAAAAA 58.338 47.619 0.00 0.00 0.00 1.94
473 474 0.511221 CGCGCCCCTCGTTATATTTG 59.489 55.000 0.00 0.00 41.07 2.32
474 475 0.601841 CCGCGCCCCTCGTTATATTT 60.602 55.000 0.00 0.00 41.07 1.40
477 478 3.608662 CCCGCGCCCCTCGTTATA 61.609 66.667 0.00 0.00 41.07 0.98
507 508 2.019984 ACGTTGAGTCCCTATACCGAC 58.980 52.381 0.00 0.00 0.00 4.79
536 537 2.355412 GGGTTTGACCTACTACGCCAAT 60.355 50.000 0.00 0.00 38.64 3.16
537 538 1.002315 GGGTTTGACCTACTACGCCAA 59.998 52.381 0.00 0.00 38.64 4.52
543 544 5.839063 CCTCATGATAGGGTTTGACCTACTA 59.161 44.000 0.00 0.00 45.40 1.82
560 561 3.013921 GGCGTGAAATTTACCCTCATGA 58.986 45.455 0.00 0.00 0.00 3.07
561 562 2.752354 TGGCGTGAAATTTACCCTCATG 59.248 45.455 0.00 0.00 0.00 3.07
562 563 2.752903 GTGGCGTGAAATTTACCCTCAT 59.247 45.455 0.00 0.00 0.00 2.90
563 564 2.156098 GTGGCGTGAAATTTACCCTCA 58.844 47.619 0.00 0.00 0.00 3.86
578 580 0.601046 ATCGGATATGCAGTGTGGCG 60.601 55.000 0.00 0.00 36.28 5.69
615 651 0.610174 TGAGACTGCTTCGCTCCATT 59.390 50.000 0.00 0.00 0.00 3.16
619 655 1.502231 TGTTTGAGACTGCTTCGCTC 58.498 50.000 0.00 0.00 0.00 5.03
624 660 1.133668 AGGGCTTGTTTGAGACTGCTT 60.134 47.619 0.00 0.00 0.00 3.91
626 662 2.185004 TAGGGCTTGTTTGAGACTGC 57.815 50.000 0.00 0.00 0.00 4.40
632 668 1.960689 GCTGGTTTAGGGCTTGTTTGA 59.039 47.619 0.00 0.00 0.00 2.69
658 694 1.448985 TAATTGGTTGCCGAGCTGAC 58.551 50.000 0.00 0.00 0.00 3.51
661 697 1.173913 GGTTAATTGGTTGCCGAGCT 58.826 50.000 0.00 0.00 0.00 4.09
708 744 1.228154 GAACCACAAAGGCCCGACT 60.228 57.895 0.00 0.00 43.14 4.18
726 762 1.389609 GCCCATGAGCAAGTGGATGG 61.390 60.000 0.00 0.00 37.72 3.51
750 786 3.553922 GCTGTGTAGCTGATCCAGTATCC 60.554 52.174 0.00 0.00 46.57 2.59
783 819 2.985282 TAACGAGACGTGGGCGGT 60.985 61.111 0.00 0.00 39.99 5.68
839 878 0.393808 GGCGCTGGGAATTGGAGTTA 60.394 55.000 7.64 0.00 0.00 2.24
924 974 2.044946 AGGGAGGAATTGTGCGGC 60.045 61.111 0.00 0.00 0.00 6.53
933 983 3.680920 GAGAGGGGCGAGGGAGGAA 62.681 68.421 0.00 0.00 0.00 3.36
944 994 1.304547 AGGTCGACACAGAGAGGGG 60.305 63.158 18.91 0.00 0.00 4.79
947 997 0.523966 GTCCAGGTCGACACAGAGAG 59.476 60.000 18.91 0.00 32.74 3.20
1007 1057 2.794820 GATCCTCTATGGGCCAGCGC 62.795 65.000 13.78 0.00 36.20 5.92
1011 1061 0.188587 ACGAGATCCTCTATGGGCCA 59.811 55.000 9.61 9.61 36.20 5.36
1121 1171 4.081030 CAGTTGACAGCAGGCGCG 62.081 66.667 0.00 0.00 45.49 6.86
1461 1511 0.810648 TGGTTGAATTGGCATCGAGC 59.189 50.000 0.00 0.00 44.65 5.03
1462 1512 2.086869 ACTGGTTGAATTGGCATCGAG 58.913 47.619 0.00 0.00 0.00 4.04
1463 1513 1.811965 CACTGGTTGAATTGGCATCGA 59.188 47.619 0.00 0.00 0.00 3.59
1464 1514 1.811965 TCACTGGTTGAATTGGCATCG 59.188 47.619 0.00 0.00 0.00 3.84
1466 1516 3.167485 ACATCACTGGTTGAATTGGCAT 58.833 40.909 0.00 0.00 37.92 4.40
1467 1517 2.596346 ACATCACTGGTTGAATTGGCA 58.404 42.857 0.00 0.00 37.92 4.92
1468 1518 4.782019 TTACATCACTGGTTGAATTGGC 57.218 40.909 0.00 0.00 37.92 4.52
1499 1578 8.024145 TCTTCTTATCTTCTTCTAATCCCCAC 57.976 38.462 0.00 0.00 0.00 4.61
1534 1613 9.750125 AGAAACAAAGAAATGATTACAAGAACC 57.250 29.630 0.00 0.00 0.00 3.62
1575 1659 0.247460 GGAAATGGCAAAGGAGGTGC 59.753 55.000 0.00 0.00 41.45 5.01
1617 1707 3.484806 ACCAACAGGCACCGGACA 61.485 61.111 9.46 0.00 0.00 4.02
1652 1747 7.657761 TCAGCTAACAAGATTTAAGGCTATAGC 59.342 37.037 16.78 16.78 41.14 2.97
1763 1882 5.883661 AGATTCAATTTGTATCAAGCACCG 58.116 37.500 15.63 0.00 0.00 4.94
1807 1926 2.356278 GTGAGGCCCTGCAATGGA 59.644 61.111 0.00 0.00 0.00 3.41
1888 2007 0.318441 TCTCAGCAAAGTGACGAGGG 59.682 55.000 0.00 0.00 0.00 4.30
1891 2010 2.037121 TCCATTCTCAGCAAAGTGACGA 59.963 45.455 0.00 0.00 0.00 4.20
1917 2036 3.278072 ATCCTGCCACCACCAGCTG 62.278 63.158 6.78 6.78 0.00 4.24
1918 2037 2.937689 ATCCTGCCACCACCAGCT 60.938 61.111 0.00 0.00 0.00 4.24
1919 2038 2.753043 CATCCTGCCACCACCAGC 60.753 66.667 0.00 0.00 0.00 4.85
1920 2039 2.044650 CCATCCTGCCACCACCAG 60.045 66.667 0.00 0.00 0.00 4.00
1921 2040 3.660571 CCCATCCTGCCACCACCA 61.661 66.667 0.00 0.00 0.00 4.17
1922 2041 3.661648 ACCCATCCTGCCACCACC 61.662 66.667 0.00 0.00 0.00 4.61
1923 2042 2.361610 CACCCATCCTGCCACCAC 60.362 66.667 0.00 0.00 0.00 4.16
1924 2043 3.660571 CCACCCATCCTGCCACCA 61.661 66.667 0.00 0.00 0.00 4.17
1925 2044 2.439553 TTTCCACCCATCCTGCCACC 62.440 60.000 0.00 0.00 0.00 4.61
1926 2045 1.076549 TTTCCACCCATCCTGCCAC 59.923 57.895 0.00 0.00 0.00 5.01
1927 2046 1.076549 GTTTCCACCCATCCTGCCA 59.923 57.895 0.00 0.00 0.00 4.92
1928 2047 2.046285 CGTTTCCACCCATCCTGCC 61.046 63.158 0.00 0.00 0.00 4.85
1929 2048 2.046285 CCGTTTCCACCCATCCTGC 61.046 63.158 0.00 0.00 0.00 4.85
1930 2049 0.255890 ATCCGTTTCCACCCATCCTG 59.744 55.000 0.00 0.00 0.00 3.86
1931 2050 0.999712 AATCCGTTTCCACCCATCCT 59.000 50.000 0.00 0.00 0.00 3.24
1932 2051 1.102978 CAATCCGTTTCCACCCATCC 58.897 55.000 0.00 0.00 0.00 3.51
1933 2052 1.743394 GTCAATCCGTTTCCACCCATC 59.257 52.381 0.00 0.00 0.00 3.51
1934 2053 1.074727 TGTCAATCCGTTTCCACCCAT 59.925 47.619 0.00 0.00 0.00 4.00
1935 2054 0.474614 TGTCAATCCGTTTCCACCCA 59.525 50.000 0.00 0.00 0.00 4.51
1936 2055 1.165270 CTGTCAATCCGTTTCCACCC 58.835 55.000 0.00 0.00 0.00 4.61
1937 2056 0.521735 GCTGTCAATCCGTTTCCACC 59.478 55.000 0.00 0.00 0.00 4.61
1938 2057 0.521735 GGCTGTCAATCCGTTTCCAC 59.478 55.000 0.00 0.00 0.00 4.02
1939 2058 0.953471 CGGCTGTCAATCCGTTTCCA 60.953 55.000 5.31 0.00 40.72 3.53
1940 2059 1.644786 CCGGCTGTCAATCCGTTTCC 61.645 60.000 11.01 0.00 43.87 3.13
1941 2060 0.953960 ACCGGCTGTCAATCCGTTTC 60.954 55.000 0.00 0.00 43.87 2.78
1942 2061 1.072505 ACCGGCTGTCAATCCGTTT 59.927 52.632 0.00 0.00 43.87 3.60
1943 2062 1.671054 CACCGGCTGTCAATCCGTT 60.671 57.895 0.00 0.00 43.87 4.44
1944 2063 1.899437 ATCACCGGCTGTCAATCCGT 61.899 55.000 0.00 0.00 43.87 4.69
1945 2064 1.153369 ATCACCGGCTGTCAATCCG 60.153 57.895 0.00 6.29 44.89 4.18
1946 2065 1.097547 CCATCACCGGCTGTCAATCC 61.098 60.000 0.00 0.00 0.00 3.01
1947 2066 2.397751 CCATCACCGGCTGTCAATC 58.602 57.895 0.00 0.00 0.00 2.67
1948 2067 4.643795 CCATCACCGGCTGTCAAT 57.356 55.556 0.00 0.00 0.00 2.57
1962 2081 0.324645 GTTTCCACCCATCCTGCCAT 60.325 55.000 0.00 0.00 0.00 4.40
2006 2161 0.879090 GTGAATCCGTTTCCACCCAC 59.121 55.000 0.00 0.00 33.04 4.61
2085 2276 4.924019 CGGCTGTGAATCCGGTTA 57.076 55.556 0.00 0.00 41.82 2.85
2110 2301 1.190833 TGTTAAACCGGCCCGACCTA 61.191 55.000 3.71 0.00 35.61 3.08
2290 2481 0.391661 CACCAGCATACCGAGCAAGT 60.392 55.000 0.00 0.00 0.00 3.16
2343 2534 2.094675 CCGATTTGAGGCCAATCTTGT 58.905 47.619 5.01 0.00 31.46 3.16
2359 2550 0.677288 TCACCTTCACAACGACCGAT 59.323 50.000 0.00 0.00 0.00 4.18
2500 2691 0.890542 GCAGCCGGCATCCATTATGA 60.891 55.000 31.54 0.00 43.97 2.15
2549 2740 2.034221 ACTTCTTGCCGGGGCTTC 59.966 61.111 11.55 0.00 42.51 3.86
2551 2742 3.570212 ACACTTCTTGCCGGGGCT 61.570 61.111 11.55 0.00 42.51 5.19
2552 2743 3.365265 CACACTTCTTGCCGGGGC 61.365 66.667 2.18 1.86 42.35 5.80
2557 2748 0.108585 TGGTCTCCACACTTCTTGCC 59.891 55.000 0.00 0.00 0.00 4.52
2789 2991 1.086696 CAGCACGTATGGAAACCCAG 58.913 55.000 0.00 0.00 37.09 4.45
2793 2995 2.030946 GCATCTCAGCACGTATGGAAAC 59.969 50.000 0.00 0.00 0.00 2.78
2799 3001 3.801114 TTGTAGCATCTCAGCACGTAT 57.199 42.857 0.00 0.00 36.85 3.06
2829 3054 7.917505 ACTTCATACTTTTTCACTTCTTGCAAG 59.082 33.333 20.81 20.81 0.00 4.01
2996 3234 6.118852 AGTTGAATTTTGCCCTGCTTAAAAA 58.881 32.000 0.00 0.00 0.00 1.94
3006 3246 4.245660 GCCTAAAGAGTTGAATTTTGCCC 58.754 43.478 0.00 0.00 0.00 5.36
3042 3285 3.244735 GGAAGAGGGAATATGAAGGGAGC 60.245 52.174 0.00 0.00 0.00 4.70
3127 3373 8.004801 CCCACTAATTCCACCCTTCTAATTAAT 58.995 37.037 0.00 0.00 0.00 1.40
3182 3428 0.178932 AGCCACTCCTGACCACACTA 60.179 55.000 0.00 0.00 0.00 2.74
3188 3436 0.248843 CAGAGAAGCCACTCCTGACC 59.751 60.000 4.46 0.00 37.60 4.02
3191 3439 1.189752 TAGCAGAGAAGCCACTCCTG 58.810 55.000 4.46 0.00 37.60 3.86
3210 3463 8.253113 CCTTCCAACTAATGCAGACAAAATAAT 58.747 33.333 0.00 0.00 0.00 1.28
3519 3857 6.755141 GCATTCATGTACAAGCAGAATGATTT 59.245 34.615 28.61 8.30 46.08 2.17
3574 3912 1.614413 AGGATCGATCGGGAGCTTTAC 59.386 52.381 18.81 1.39 0.00 2.01
3605 3943 2.359900 GACGATTGATGGATATGGGCC 58.640 52.381 0.00 0.00 0.00 5.80
3663 4008 2.232941 TCGTCCCCATCTTGTGAAGTAC 59.767 50.000 0.00 0.00 0.00 2.73
3664 4009 2.531771 TCGTCCCCATCTTGTGAAGTA 58.468 47.619 0.00 0.00 0.00 2.24
3665 4010 1.348064 TCGTCCCCATCTTGTGAAGT 58.652 50.000 0.00 0.00 0.00 3.01
3679 4024 3.574396 TGAGGAGTTCCATCATATCGTCC 59.426 47.826 0.28 0.00 38.89 4.79
3715 4061 5.525012 CGATCAGAATAGGATGTTTGCAGAA 59.475 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.